H5hut/src
0
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Compare commits

base: H5hut/src:1.2
Branches Tags
H5hut/src:master H5hut/src:int8 H5hut/src:1.99.x H5hut/src:1.99 H5hut/src:1.6 H5hut/src:1.4 H5hut/src:1.2 H5hut/src:1.0
H5hut/src:H5hut-2.0.0rc7 H5hut/src:H5hut-2.0.0rc6 H5hut/src:H5hut-2.0.0rc5 H5hut/src:H5hut-2.0.0rc4 H5hut/src:H5hut-2.0.0rc1 H5hut/src:H5hut-2.0.0rc3 H5hut/src:H5hut-2.0.0rc2 H5hut/src:1.99.13 H5hut/src:1.99.12 H5hut/src:1.99.11 H5hut/src:1.99.10 H5hut/src:1.99.9 H5hut/src:1.99.8 H5hut/src:1.99.7 H5hut/src:H5Part-1.6.5 H5hut/src:1.99.6 H5hut/src:H5Part-1.6.4 H5hut/src:1.99.5 H5hut/src:H5Part-1.6.3 H5hut/src:1.99.4 H5hut/src:1.99.3 H5hut/src:1.99.2 H5hut/src:H5hut-1.99.1 H5hut/src:1.99.0 H5hut/src:H5Part-1.6.2 H5hut/src:H5Part-1.6.1 H5hut/src:H5Part-1.6.0 H5hut/src:H5Part-1.4 H5hut/src:H5Part-1.3.3 H5hut/src:H5Part-1.3.2 H5hut/src:H5Part-1.3.1
..
compare: H5hut/src:H5hut-2.0.0rc2
Branches Tags
H5hut/src:master H5hut/src:int8 H5hut/src:1.99.x H5hut/src:1.99 H5hut/src:1.6 H5hut/src:1.4 H5hut/src:1.2 H5hut/src:1.0
H5hut/src:H5hut-2.0.0rc7 H5hut/src:H5hut-2.0.0rc6 H5hut/src:H5hut-2.0.0rc5 H5hut/src:H5hut-2.0.0rc4 H5hut/src:H5hut-2.0.0rc1 H5hut/src:H5hut-2.0.0rc3 H5hut/src:H5hut-2.0.0rc2 H5hut/src:1.99.13 H5hut/src:1.99.12 H5hut/src:1.99.11 H5hut/src:1.99.10 H5hut/src:1.99.9 H5hut/src:1.99.8 H5hut/src:1.99.7 H5hut/src:H5Part-1.6.5 H5hut/src:1.99.6 H5hut/src:H5Part-1.6.4 H5hut/src:1.99.5 H5hut/src:H5Part-1.6.3 H5hut/src:1.99.4 H5hut/src:1.99.3 H5hut/src:1.99.2 H5hut/src:H5hut-1.99.1 H5hut/src:1.99.0 H5hut/src:H5Part-1.6.2 H5hut/src:H5Part-1.6.1 H5hut/src:H5Part-1.6.0 H5hut/src:H5Part-1.4 H5hut/src:H5Part-1.3.3 H5hut/src:H5Part-1.3.2 H5hut/src:H5Part-1.3.1

278 Commits
1.2 .. H5hut-2.0.0rc2

Author SHA1 Message Date
gsell ad52833022 configure.ac 
- set version to 2.0.0rc2
 2016-09-23 13:05:59 +02:00
gsell 3425a30068 src/include/h5core/Makefile.am 
- we have to use 'otherinclude_HEADER' instead of 'include_HEADERS'
 2016-09-23 13:05:37 +02:00
gsell 9f3a677ea6 src/h5core/Makefile.am 
- private/h5_const.h added to EXTRA_HEADERS
 2016-09-23 13:04:16 +02:00
gsell 23807ff972 examples/H5/write_file_attribs.py 
- added
 2016-07-28 17:34:56 +02:00
gsell 93d4f60116 src/Python 
- wrappers for reading/writing attributes
 2016-07-28 17:34:22 +02:00
gsell 20cd5aae98 src/h5core/h5t_io.c 
- adapted to changed 'h5priv_write_attrib()'
 2016-07-28 17:32:13 +02:00
gsell cae3b00855 implement proper handling of append-only file mode for attributes 2016-07-28 17:31:06 +02:00
gsell 2a462733ca src/h5core/private/h5_file.h 
- is_writable() is now static inline not a macro
- macro CHECK_READABLE_MODE() added
 2016-07-28 17:29:13 +02:00
gsell 6fb8b77baa src/h5core/h5_attachements.c 
- h5_add_attachment(): check file mode, return error if read-only
- adapted to new function 'h5priv_create_group()'
 2016-07-28 17:27:05 +02:00
gsell c26d6a84e3 adapted to new/changed function: 
h5priv_open_group(): open existing group
h5priv_create_group(): create or open existing group
h5priv_open_group_with_intermediates(): open existing group
h5priv_create_group_with_intermediates(): create or open existing group
 2016-07-28 17:24:34 +02:00
gsell 54ccc3b576 src/inlcude/H5_step_attribs() 
- H5GetStepAttribName() added
- use const types where applicable
 2016-07-28 17:17:18 +02:00
gsell 8ffe944519 test/Makefile.am 
- link static if debug is enabled
 2016-07-28 17:15:39 +02:00
gsell 2bb3d688ae test/h5{b,u}_{read,write}.c 
- fixes for serial version
- h5u_test_write4(): bugfix: we have to write new attributes since we are in append-only mode
 2016-07-28 16:05:36 +02:00
gsell 647af5847e src/include/H5_file_attrib.h 
- H5ReadFileAttribString(): bugdix in format of H5_API_ENTER(), print pointer value not string
 2016-07-28 16:01:11 +02:00
gsell aa4f40ee3d src/h5core/private/h5_model.h 
- h5priv_normalize_type(): bugfix: wrong type in H5_PRIV_API_ENTER() set
 2016-07-28 15:59:35 +02:00
gsell f1daa56cb8 src/h5core/private/h5_model.c 
- h5u_set_num_points(): set step to '0' if not already set
- h5u_set_chunk(): CHECK_TIMEGROUP(f) removed. The step must not be set before setting a chunk size
 2016-07-28 15:57:34 +02:00
gsell 2ea8245bba src/h5core/h5b_io.c 
- write_data():
  - bugfix: convert passed type is from H5hut to HDF5 type
  - parameter 'field_name' removed
- read_data():
  - bugfix: convert passed type is from H5hut to HDF5 type
  - compare type passed as parameter and type of dataset
- remove prefixing underscore from static functions
- adaptions to coding style
 2016-07-28 15:54:52 +02:00
gsell 04fe7fdd9e configure.ac: 
- do not ignore CC an CXX
 2016-07-28 12:18:25 +02:00
gsell 075b2f39da src/Python/H5hut.i 
- towards a more usable wrapper
 2016-07-15 17:46:02 +02:00
gsell 7b05c32ad9 src/h5core/private/h5_attrib.h 
- get_attrib_info(): wrong length was return for string attributes
 2016-07-15 17:43:59 +02:00
gsell 825ee8ac5f examples/H5/Makefile.am 
- build static executables if debug is enabled
 2016-07-15 17:40:37 +02:00
gsell 9d70c07476 src/Python/H5hut.i 
- some issues with inquiring file-attributes and datasets fixed
 2016-07-08 17:13:18 +02:00
gsell 03986b00ac src/include/g5core/h5_{file.types}.h 
- enum used for file modes instead of macros
 2016-07-08 17:11:28 +02:00
gsell ad83c3841b C-API: 
- declare more args as const
- H5GetFileAttribName() added
 2016-07-08 17:09:16 +02:00
gsell 73fabd043b src/h5core/h5b_modules.c 
- check file-handle and opened step
- h5b_3d_has_view(): debug output added
 2016-07-08 17:07:18 +02:00
gsell 0aa44727c6 src/h5core/h5_file.c 
- check file-handle and opened step
- h5_open_file2(): bugfix: move setting of step name format to the end of the function
- h5_flush_step(): bugfix: flush step data only, if a step is open
 2016-07-08 17:06:07 +02:00
gsell babd19ddd4 core API: 
- add checks for file-handle and opened step
 2016-07-08 17:03:18 +02:00
gsell c80f6f5679 use new macro H5_RETURN_ERROR where possible 2016-07-01 17:59:12 +02:00
gsell 7b1079ae5f example/H5Fed/Makefile.am 
- compile static if ENABLE_DEBUG is set. This makes life simpler if we build shared libs
 2016-07-01 16:29:10 +02:00
gsell ecd2723419 examples/H5Fed/tetmesh_{adjacencies,read_tags}.c 
- cleanup
 2016-07-01 16:18:17 +02:00
gsell c9044d8e1b src/h5core/private/h5_init.{c,h} 
- initialize MPI if not yet done
 2016-07-01 16:10:37 +02:00
gsell 5b57bedade examples/H5Fed/dump_field_attributes.c: 
- bugfix in printing string attributes
 2016-07-01 16:07:02 +02:00
gsell 222789a1cf examples/H5Block: 
- inline function changed to static inline (otherwise gcc >= 5.3 complains)
 2016-07-01 15:36:30 +02:00
gsell 21dd57c9c6 Fortran-API: 
- use enumeration for data-types
 2016-07-01 15:34:31 +02:00
gsell fc29f7b6f0 src/h5core/private/h5_hdf5.h 
- cleanup and minor changes
- more wrapper functions added
 2016-07-01 15:33:53 +02:00
gsell e56872ce92 src/include/H5_err.h: 
- remove debug output from H5AbortOnError()
 2016-07-01 15:32:54 +02:00
gsell 85ecf4c387 core API/C-API: use enumeration for data-types 2016-07-01 15:31:55 +02:00
gsell 6979a358ae .gitignore: 
- exclude all files matching *.h5
 2016-06-24 16:40:43 +02:00
gsell 9fc3b233bc examples/H5Part: 
- include of stdlib.h added
 2016-06-24 16:37:59 +02:00
gsell f5eb26d2ec examples/H5Part/query.c: 
- added examples to query dataset in steps
 2016-06-24 16:36:54 +02:00
gsell 6af129b338 examples/H5Block/read_write_scalar_field.c: 
- include stdlib.h added
 2016-06-24 16:35:43 +02:00
gsell 215d1a7d79 examples/H5/read_step_attribs: 
- include required stdlib.h
 2016-06-24 15:55:20 +02:00
gsell 8bb22e4400 exampkes/H5/read_file_attribs.c 
- use macros to define verbosity and debug mask
 2016-06-24 15:54:40 +02:00
gsell caad81996a examples/H5/attache_file.c: 
- use macros for verbosity level and debug mask
- open file rw in second part
 2016-06-24 15:53:36 +02:00
gsell f97e3c8f2d core API: 
- debugging macros simplified
- cleanup
- h5_delete_attachment(): check of file mode added
 2016-06-24 15:51:39 +02:00
gsell fba78db1c0 test/h5u_read.c: 
- h5u_test_read3(): bugfix
 2016-06-24 15:45:26 +02:00
gsell 291328b997 src/h5core/private/h5_init.h 
- cosmetic change
 2016-06-22 16:15:03 +02:00
gsell 2c1bca01aa src/include/H5Block_model.h 
- break down some longer lines
 2016-06-22 16:14:18 +02:00
gsell a633b362a6 src/include/H5Part_model.h: 
- break down some long lines
- H5PartGetDatasetName(): pass pointer to dataset name as const pointer
 2016-06-22 16:13:16 +02:00
gsell a12908ed90 src/include/h5core/h5_err.h: 
- declaration of h5_error() moved to this file
 2016-06-22 16:10:20 +02:00
gsell b83d9cc8a7 src/include/h5core/h5_log.h 
- hh5_{warn,info,debug} are not static inline any more
 2016-06-22 16:08:46 +02:00
gsell 6ad9ae50e0 src/include/h5core/h5_types.h 
- H5T_COMPOUND removed from enum h5_types_t
src/h5core/private/h5_init.c
- use H5T_COMPOUND in creation of compound types
 2016-06-22 16:05:21 +02:00
gsell 9ac7e09423 src/include/h5core/h5_file_attribs.h 
src/include/h5core/h5_step_attribs.h
src/include/h5core/h5b_attribs.h:
- use new H5hut enum type for attribute data-types
 2016-06-22 16:01:46 +02:00
gsell 66452a274b src/include/h5core/h5b_io.h 
src/include/h5core/h5u_io.h:
- pass data-type as H5hut enum
 2016-06-22 15:40:32 +02:00
gsell d947f51c2d src/h5core/...: 
- introduce/implement new H5hut types
 2016-06-22 15:38:24 +02:00
gsell f5729f6f07 src/h5core/h5_model.c 
src/h5core/h5b_attribs.c:
- cleanup/review header file we have to include
 2016-06-22 15:24:05 +02:00
gsell a64f2ce03a src/h5core/h5_err.c 
src/h5core/h5_log.c:
- define args as const where possible
- h5_verror() is now in h5_err.c
- h5priv_vprintf() is now in h5_log.c
 2016-06-22 15:19:23 +02:00
gsell b880bd397f C-API: 
- use new H5hut type enumeration, not HDF5 types
 2016-06-22 14:52:02 +02:00
gsell cd2c9031b9 src/h5core/h5_attribs.c: 
- define args as const where possible
 2016-06-22 14:48:19 +02:00
gsell fb5e55990f src/h5core/h5file 
src/h5core/h5b_io.h:
- define args as const where possible
 2016-06-22 14:38:09 +02:00
gsell 25dff9257c src/h5core/Makefile.am 
- h5_init.h is now in 'private'
 2016-06-22 14:34:44 +02:00
gsell ac37d5fc2f Fortran API: 
- use new enumeration of types for I/O. HDF5 types are not used any more in the high level API
 2016-06-22 14:33:48 +02:00
gsell 983496104b src/h5core/h5_log.c 
src/h5core/h5_init.h
src/h5core/h5_log.h:
- cleanup, minor changes
 2016-06-22 14:24:54 +02:00
gsell aaeca8b6b7 examples/H5/read_file_attribs.c: 
- call MPI_Init() before any H5hut functions
 2016-06-22 13:47:53 +02:00
gsell 0182d60835 src/h5core/h5_init.c: 
- moved to src/h5core/private
 2016-06-22 13:46:40 +02:00
gsell f75ef09cf9 consolidation of log/debug message interface 2016-06-17 13:50:07 +02:00
gsell c831a90a2e src/h5core/h5_errorhandling.c: 
- renamed to h5_err.c
 2016-06-17 13:49:35 +02:00
gsell bdcc8f2089 this commits includes several changes which should have been done in 
multiple steps:
- the functions for inquiring datasets and attributes do not return
  an HDF5 type any more but an enum of type h5_types_t. This change
  was required for the Python module.
- bugfix in reading attributes: See https://git.psi.ch/H5hut/src/issues/4
- several consts and macros have been moved from the public C-API to
  the core API
- more consitent file naming
- several 'private' function have been moved to their 'private' header
  files as 'static inline'.
- minor formatting changes
 2016-06-17 10:44:25 +02:00
gsell bbbaa6a21b src/h5core/h5t_octree.c: 
- definition of 'h5_oct_dta_types' moved from header file to this file
 2016-06-03 17:25:48 +02:00
gsell 4c5b16169d src/Fortran/Makefile.am: 
- bugfix: H5Block_attribs.f90 were listed twice
 2016-06-03 17:24:36 +02:00
gsell cc46b433e1 .gitignore: some files added 2016-06-03 17:23:43 +02:00
gsell a8e209a7d3 src/Python: 
- file and step attributes added
- all attribute i/o function have exactly 3 arguments now
- string attributes are handled the same way as attributes of other type
 2016-06-03 17:23:15 +02:00
gsell 80cf35e807 src/Python: ignore file added 2016-06-03 17:18:00 +02:00
gsell d53c5b3171 tools/vtk2h5grid/Makefile.am: use AM_LDFLAGS not LDFLAGS 2016-05-20 18:12:00 +02:00
gsell 8edb48aff8 src/Python/Makefile.am: use same name for serial and parallel version 2016-05-20 18:10:30 +02:00
gsell 24af2ae2a3 src/Makefile.am: Python sub-dir added 2016-05-20 18:09:28 +02:00
gsell 7fbd5c5de1 configure.ac: set version to 2.0.0rc1; correct indentation 2016-05-20 18:08:44 +02:00
gsell 18611991a5 Python support added 2016-05-12 13:19:51 +02:00
gsell 603366bcd6 src/h5t_io.c 
- format errors fixed
- bugfixes
 2016-04-29 18:10:25 +02:00
gsell 17317bb261 ignore file changed 2016-04-29 16:34:33 +02:00
gsell 52d44e3b3c - re-organize file hierarchy 
- years in copyright changed
 2016-04-29 16:34:07 +02:00
gsell 3d6230629c some missing query function implemented, see issue#1 in Gitlab 2016-04-22 18:06:58 +02:00
gsell 44ffea4fd5 examples/H5Block/write_field.c: H5hut file renamed to example_field.h5 2016-04-15 19:02:15 +02:00
gsell 97516866c7 examples/H5Block: attach_field_attribs and dump_field_attribs added 2016-04-15 19:01:00 +02:00
gsell 1dfcd9f876 fixes for hdf5 1.10.x 2016-04-15 18:58:10 +02:00
gsell 2dd2c625b7 .gitignore: has_field added 2016-04-08 19:07:52 +02:00
gsell 3137063d22 example/H5Block: 
- has_field.c added
 2016-04-08 19:06:42 +02:00
gsell 9a16fa090a example/H5Block/write_field.c: 
- slice in Z direction
 2016-04-08 19:06:15 +02:00
gsell df0750df4c examples/H5Block/read_write_scalar_field.c: 
- cleanup
 2016-04-07 11:11:00 +02:00
gsell b69aa9b92d example/H5Block 
- write_field added
 2016-04-07 11:10:22 +02:00
gsell 99699d4bf7 documentation updated 2016-04-01 19:12:34 +02:00
gsell 9df1a57778 src/h5core/h5b_model.c: 
- h5b_has_field() added
 2016-04-01 19:12:15 +02:00
gsell 1ed4f3985b src/include/H5Block_attribs.h: documentation updated 2016-03-30 18:05:15 +02:00
gsell 2c850612ab functions added to query existence of file-, step-. field-attributes amd to get information by name 2016-03-29 17:49:32 +02:00
gsell bc528f27e6 more cleanup on header files 2016-03-29 15:30:30 +02:00
gsell 5444b0e0ef .gitignore: vtk2h5grid added 2016-03-29 14:57:09 +02:00
gsell ae9e4cee01 C header files: 
- cleanup
 2016-03-29 14:55:35 +02:00
gsell 7490eed535 tools/vtk2h5grid/Makefile.am: 
- libH5hut library path changed
 2016-03-29 14:49:09 +02:00
gsell 84fa4a0b0a Merge branch 'master' of git.psi.ch:H5hut/src 2016-03-29 10:47:23 +02:00
gsell 718ef785f8 doc/H5.dox: re-structured 2016-03-29 10:46:35 +02:00
gsell 7002b73e82 src/{Fortran,h5core}/Makefile.am: 
- do not install the libs in src/lib
 2016-03-23 22:01:55 +01:00
gsell 2a8a43af39 src/include/H5_debug.f90: 
- h5_set_debug_mask(): bugfix
 2016-03-23 21:51:00 +01:00
gsell f0c2f29091 src/include/H5hut.f90: 
- bugfix in included files
 2016-03-23 21:50:10 +01:00
gsell 5362498a95 src/include/H5_const.f90: 
- bugfix in definition of H5_FAILED
 2016-03-23 21:49:34 +01:00
gsell 851905361d src/Fortran/H5.c: 
- h5_setprop_file_corevfd(): bugfix
 2016-03-23 21:47:40 +01:00
gsell 3c8b11f9eb src/{C,Fortran}/Makefile.am: 
- include_HEADERS fixed
 2016-03-23 21:46:37 +01:00
gsell 4dde2b61d2 COPYING: 
- year in copyright changed to 2016
 2016-03-23 21:45:25 +01:00
gsell d980f4d2b9 header files and documentation reorganized and reviewed 2016-03-18 17:58:30 +01:00
gsell 3f7c84dbf5 header files and documentation reorganized 2016-03-18 16:37:13 +01:00
gsell c5a05a1261 year in copyright changed 2016-03-18 14:25:30 +01:00
gsell 230f9a7b90 year in copyright changed 2016-03-18 14:23:49 +01:00
gsell 2cd718b7a1 src/include/h5core/h5.h: 
- h5_open_file1() return type is 'h5_file_p' not 'h5_file_t'
 2016-03-18 11:29:36 +01:00
gsell c73d10ffb7 src/include/H5Fed_model.h: 
- syntax errors fixed
 2016-03-18 11:28:40 +01:00
gsell 6209bc6cf9 src/include/H5.h: 
- bugfixes in H5OpenFile1() and H5GetVerbosityLevel1()
 2016-03-18 11:27:29 +01:00
gsell a013d43075 src/h5core/h5_openclose.c: 
- h5_open_file1(): fix return type
 2016-03-18 11:26:21 +01:00
gsell f151a24796 examples/H5Part/{read,write}_core_vfd.c: 
- missing 'incr' argument added to H5SetPropFileCoreVFD() call
 2016-03-18 11:25:25 +01:00
gsell 9d37783868 examples/H5Block/fields.c: 
- include H5hut.h
- write dims in right order
 2016-03-18 11:24:08 +01:00
gsell a8444e041b examples/H5/read_file_attribs(): 
- type cast fixed
 2016-03-18 11:22:38 +01:00
gsell dc9723dfe2 examples/H5/openclose.c 
- H5SetPropFileMPIO() renamed to H5SetFileMPIOCollective()
 2016-03-18 11:21:53 +01:00
gsell 91e7ed8c5b test/*: 
- H5SetPropFileMPIO() renamed to H5SetPropFileMPIOCollective()
 2016-03-18 11:04:11 +01:00
gsell b284ad9776 src/h5core/h5_attach.c: 
- in h5_get_attachment(): redundant check of file mode removed
 2016-03-17 17:55:41 +01:00
gsell f965ed4f18 src/h5core/*: 
- all *_has_* functions: return TRUE, FALSE or H5_FAILURE
 2016-03-17 17:53:32 +01:00
gsell 91316f314d src/include/*: 
- update/review documentation
- re-introduce old API functions
 2016-03-17 17:50:42 +01:00
gsell 538c9cdd76 src/h5core/h5u_model.c: 
- h5u_has_view() now returns H5_SUCCESS or H5_NOK
 2016-03-11 17:54:54 +01:00
gsell 28fc118118 src/h5core/h5b_model.c: 
- h5b_3d_has_view() now returns H5_SUCCESS or H5_NOK
 2016-03-11 17:53:30 +01:00
gsell 59fd8ea6c6 increment can now be specified for the core vfd driver 2016-03-11 17:51:17 +01:00
gsell 1273baf99e src/include/*: 
- doxgen documentation reviewed
 2016-03-11 17:49:09 +01:00
gsell befaccddaf doc/H5.dox: 
- document structure reviewed
 2016-03-11 17:48:37 +01:00
gsell 5204cb532b sdoc/Doxyfile 
- reviewed
 2016-03-11 17:47:59 +01:00
gsell 9917f12d96 .gitignore: 
- ignore doxygen output
 2016-03-11 17:46:54 +01:00
gsell 4b1d719d6c src/include/H5.h,H5Block_attribs.h: 
- add/review documentation
 2016-02-12 17:39:46 +01:00
gsell 43bc72b7d0 src/h5core/h5_openclose.c: 
- typo fixed
 2016-02-12 17:31:47 +01:00
gsell 64b4a3be09 doc/H5.dox: 
- update author list
- minor changes in overall structure
 2016-02-12 17:31:19 +01:00
gsell f4e7defffa doc/DoxygenLayout.xml: 
- deleted
 2016-02-12 17:30:38 +01:00
gsell 320fd77398 doc/Doxyfile: 
- changes required by new Doxygen version
- parse only files in src/include
- enable static function
 2016-02-12 17:29:32 +01:00
gsell 5714c390ec examples/*: 
- type cast malloc() result
 2016-02-09 10:10:57 +01:00
gsell a07d4101a2 examples/H5Block/read_write_scalar_field.c: 
- type cast malloc(2) return value to make C++ happy
 2016-02-09 09:55:17 +01:00
gsell 56787866fb test wheter I can commit again 2016-01-18 13:22:28 +01:00
gsell fb3b876f78 ignore zipped tar-balls 2016-01-18 13:18:55 +01:00
gsell e4ebb0f453 Makefiles.am's: 
- missing head-files added
 2015-10-16 18:39:35 +02:00
gsell 51f2210ff1 test/h5b_test.c: 
- run  tests 'write2' and 'read2' only in parallel case
 2015-10-16 18:16:27 +02:00
gsell 511fbb89de src/h5core/h5b_model.c: 
- h5b_3d_set_view(): bugfix in serial code
 2015-10-16 18:14:27 +02:00
gsell 87fcc4930b h5core: 
- H5_VER_STRING defined from PACKAGE_VERSION as const char*
 2015-10-16 18:13:18 +02:00
gsell 49460b62c3 examples: 
- compile Fortran examples only if parallel is enabled
 2015-10-16 18:11:56 +02:00
gsell 8ae12f7ee9 configure.ac 
- copyright notice added
- set version to 1.99.15rc1
 2015-10-16 18:10:46 +02:00
gsell ca7dd3b99c examples/H5Part/read_strided{.c,f.f90} 
- compute and set a canonical view
 2015-10-16 16:02:17 +02:00
gsell 6efdfce033 examples/H5Part/read_setnparticles{.c,f.f90} 
- changes in comment lines
 2015-10-16 16:01:32 +02:00
gsell 55cc6bb7d0 src/h5core/h5u_model.c 
- h5u_set_num_points(): print start index of view if debug enabled
 2015-10-16 15:59:24 +02:00
gsell 4fcc1ed3b3 .gitignore 
- *.dSYM added
 2015-10-16 15:58:12 +02:00
gsell 23bb1ced99 examples/H5Part/read_strided.c 
- bugfix in printing data
 2015-10-16 13:57:20 +02:00
gsell 1f629ee7f8 examples: 
- output format warnings fixed
 2015-10-15 17:29:18 +02:00
gsell 3c825fc71d src/Fortran/h5_private.h 
- we do not have Underscore.h any more
 2015-10-15 17:28:31 +02:00
gsell 089dc3e1ba src/Fortran: 
- debug output warnings fixed
 2015-10-15 17:27:51 +02:00
gsell 158fc17a2b src/h5core/h5t_octree_private.h 
- include 'mpi.h' if PARALLEL_IO is set
 2015-10-08 17:51:03 +02:00
gsell 149c144eee examples 
- several simple fixes
 2015-10-08 16:58:05 +02:00
gsell 4e42972ebb src/include/h5core/h5.h 
- typedef MPI_Comm to int if we compile serial code
- suppress warning about unused variables in definition of MPI_Comm_size() and MPI_Comm_rank()
 2015-10-08 16:57:12 +02:00
gsell 73c07240c2 .gitignore 
- more to ignore
 2015-10-08 16:28:47 +02:00
gsell e637522073 example/H5Fed 
- fixes
- adapted to new API
 2015-10-08 16:28:23 +02:00
gsell ec9626a0e5 src/h5core/h5t_xyz 
- get serial mesh working again
 2015-10-08 16:26:35 +02:00
gsell 86755932d9 src/h5core/h5_maps_private.h 
- indentation fixes
 2015-10-08 16:24:48 +02:00
gsell 95e21118e4 src/h5core/h5t_map_private.h 
- bugfix: we have to use a signed type for 'low', 'mid' and ' high'
 2015-10-08 16:23:46 +02:00
gsell 3fe0cc74be src/h5core/h5u_readwrite.c 
- include 'h5core/h5.h' added
 2015-10-08 16:19:23 +02:00
gsell 40c2c7d498 src/include/H5Fed_retrieve.h 
- bugfix in allocating iterators
 2015-10-08 16:17:48 +02:00
gsell cf067f7c56 src/include/h5core/h5.h 
- definition of UNUSED_ARGUMENTS() moved to 'src/h5core/h5_private.h'
 2015-10-08 16:14:09 +02:00
gsell 33129a4793 src/h5core/Makefile.am 
- bugfix: we have to compile grid stuff in any case
 2015-10-08 16:12:36 +02:00
gsell 41f2e87fc7 src/h5core/h5_module_private-h: 
- bugfix in serial version of h5priv_end_throttle()
 2015-10-08 16:11:01 +02:00
gsell 347a447302 configure.ac 
- fix problem with AC_PROG_CC/CXX
- define 'WITH_PARALLEL_H5GRID' on '--enable-experimental'
 2015-10-08 16:09:00 +02:00
gsell 03531ab4af src/h5core 
- h5priv_start_throttle() and h5priv_end_throttle() are now inline
  functions, whereby the serial version is just a dummy
 2015-09-11 14:41:52 +02:00
gsell 3d8ce28609 src/h5core/h5t_* 
- cleanup
 2015-09-11 14:12:01 +02:00
gsell cc719d116c src/h5core/h5u_models.c 
- correct error message in h5u_set_num_points()
 2015-09-11 14:11:23 +02:00
gsell 748eb1b3ab src/h5core/h5t_module.c: 
- compile error fixed in h5t_close_mesh()
 2015-09-11 14:10:25 +02:00
gsell f430c71d06 configure.ac and related Makefile.am's: 
- conditionally compile examples
 2015-09-11 14:09:05 +02:00
gsell 4a1d4d2d10 test/Makefile.am: 
- unused h5_attach_test stuff removed
 2015-09-11 14:04:53 +02:00
gsell 937d3f9c0e examples/H5Part/* 
- cleanup and fixes
 2015-09-11 14:04:12 +02:00
gsell 4d9d3dc879 examples/H5Part/... 
- bugfixes
 2015-09-09 18:25:27 +02:00
gsell 106be817d9 examples/H5Part 
- reviewed
 2015-09-08 20:53:07 +02:00
gsell ec3a29d7e4 src/Fortran/H5Part_model.c 
- adapted to refactored h5u_get_num_points()
 2015-09-08 20:52:19 +02:00
gsell c5ce2f06ac src/include/H5.f90: 
- typo fixed in function name h5_setprop_file_corevfd()
 2015-09-08 20:50:44 +02:00
gsell 992e8cf58e src/include/H5_const.f90 
- H5_DEBUG_* masks added
 2015-09-08 20:49:29 +02:00
gsell a618acf686 src/h5core/h5_errorhandling.c 
src/include/h5core/h5_errorhandling.h
- h5_error(), h5_warn(), h5_info(): print message if debug-level > 3
 2015-09-08 20:48:26 +02:00
gsell 47bee153ba src/h5core/h5_hdf5_private.h 
- minor changes in debug output
 2015-09-08 20:46:21 +02:00
gsell 390a4296b4 src/h5core/h5_hdf5.c 
- hdf5_get_name_of_dataset_by_idx(): bugfix, return H5_NOK, if dataset are in step
 2015-09-08 20:45:27 +02:00
gsell 4f7c666b1f src/h5core/h5u_module.c 
- refactore "*num_particles*" to "*num_points*"
- h5u_set_view() can now be used for writing, there are still some limitations
 2015-09-08 20:43:38 +02:00
gsell a620715ccc src/include/H5Part_io.h: 
- documentation update
 2015-09-08 17:50:06 +02:00
gsell 37bf9b35a6 src/h5core/h5_mpi_private.h: 
- all mpi wrappers are now inline
 2015-09-08 17:47:39 +02:00
gsell 2a7628c1e2 examples/H5Block/read_write_scalar_field.c: 
- write of 32-bit values added
 2015-09-03 17:27:47 +02:00
gsell 5a588415d0 Fortran H5Part examples: 
- read_canonicalviewf.f90 read_setnparticlesf.f90, read_setviewf.f90, read_stridedf.f90 implemented
 2015-09-03 17:26:54 +02:00
gsell d5fce5b2a0 examples/H5Part/write_{setviewf,stridedf}.f90: 
- bugfixes: take Fortran indexing into account
 2015-09-03 17:24:37 +02:00
gsell 7bf3985219 examples/H5Block/read_write_scalar_fieldf-f90: 
- bugfix: open file read-only
 2015-09-03 17:23:09 +02:00
gsell d939354990 example/H5/write_step_attribsf.f90: 
- bugfix
 2015-09-03 17:22:10 +02:00
gsell 8fb9834d3b C examples: 
- fix some comments
 2015-09-03 17:21:12 +02:00
gsell 2fd5d52125 src/Fortran/H5_modeul.c: 
- h5_hasstep(), h5_setstep(): decrement step number by 1
 2015-09-03 17:20:08 +02:00
gsell a1226feafd copyright notice fixed in examples 2015-09-03 13:31:29 +02:00
gsell cc7c558065 src/Fortran/H5.c: 
- conditionally compile h5_setprop_file_mpio_posix()
 2015-07-27 10:20:25 +02:00
gsell 51f90df374 Testprogramms for Fortran symbol name mangling removed 2015-07-24 18:38:58 +02:00
gsell 62c2d53324 Fortran symbol mangling simplified 2015-07-24 18:36:31 +02:00
gsell 8e9e0d84f3 change year in copyright 2015-07-23 14:59:43 +02:00
gsell d9daf9f0c7 src/h5core/h5u_module.c: 
- bugfix in h5u_set_canonical_view()
 2015-07-23 14:54:23 +02:00
gsell 559f2d8d9c test/*: 
- fix some warning if compiled serial
 2015-07-17 17:14:31 +02:00
gsell 403e535a50 ignore file edited. 2015-07-17 16:53:45 +02:00
gsell 14aa4fbd15 test/testframe.h: 
- set VERBO_HI to 65535
 2015-07-03 17:48:47 +02:00
gsell 319d7b4324 test/h5u_test.c: 
- cleanup
 2015-07-03 17:48:16 +02:00
gsell 4511fde9d1 bugfix: throttle only if VFD is MPIO independent or POSIX 2015-07-03 17:47:37 +02:00
gsell 707cafb2d8 src/h5core/h5u_model.c: 
- bugfix with h5u_set_view (0, -1)
 2015-07-03 17:45:49 +02:00
gsell 877b611758 test/testframe.c 
- initialize 'ret_value' in 'TestPrintf()' and 'TestErrPrintf()'
 2015-07-02 15:57:05 +02:00
gsell 9fb11ca838 no MPIO_POSIX in hdf5 > 1.8.12 2015-07-02 15:55:57 +02:00
gsell 7c2a315760 src/h5core/h5b_readwrite.c: fix early return in _select_hyperslab_for_writing() 2015-06-18 14:58:17 +02:00
gsell cc0135b4fc src/h5core/h5b_readwrite.c: 
- fix early return in  _select_hyperslab_for_writing()

# Conflicts:
#	src/h5core/h5b_readwrite.c
 2015-06-18 14:17:10 +02:00
gsell f47fbbf075 tools/vtk2h5grid/Makefile.am: fixes 2015-06-18 14:10:17 +02:00
gsell fd8c1e37b1 src/h5core/h5b_model.c: 
- bugfix in serial code of h5b_3d_set_view()

# Conflicts:
#	src/h5core/h5b_model.c
 2015-06-18 14:09:32 +02:00
Gsell Achim 4d770f8c84 option to shift mesh added 2015-06-18 13:51:40 +02:00
gsell 1f79b924df work on H5Block examples 2014-01-31 15:38:13 +01:00
gsell b1f143a5d7 src/examples/H5Block: ignore file added 2014-01-31 15:36:59 +01:00
gsell d6718bb866 examples/H5Part/read_canonicalviewf.f90: some fixes, but still broken 2014-01-31 15:34:20 +01:00
gsell 9deeacff51 copyright notice changed 2014-01-31 15:32:55 +01:00
gsell 5dbe8fb161 src/include/H5Block_attribs.f90: bugfix in declaration of h5bl_writefieldattrib_string() 2014-01-31 15:31:31 +01:00
gsell c3add7dde4 src/include/H5.f90: empty line removed 2014-01-31 15:30:46 +01:00
gsell 9d49361c43 some H5Block examples renamed 2014-01-31 15:29:10 +01:00
gsell 1a1878402c fixes in H5Part Fortran examples 2014-01-29 10:07:14 +01:00
gsell 069f9b64fc ignore file added to examples/H5Part 2014-01-29 10:05:15 +01:00
gsell ca6b4cc52d names of Fortran API header files fixed 2014-01-29 08:57:37 +01:00
gsell 60df95b10a most missing functions added to Fortran API 2014-01-28 17:31:22 +01:00
gsell d508f9e591 include/H5_attribs.h: reorder declarations 2014-01-28 17:30:00 +01:00
gsell 36702c6207 macros defining the names of internal attributes moved to public core file 2014-01-28 17:28:08 +01:00
gsell fa091cc2ab Fortran API files for H5Part data model renamed 2014-01-28 14:44:57 +01:00
gsell 1121a22956 Fortran API files for H5Block model renamed 2014-01-28 14:06:09 +01:00
gsell d5b8a4c0c8 ignore file edited 2013-11-15 16:50:32 +01:00
gsell 1cc3614c74 Fortran stubs added 2013-11-15 16:49:10 +01:00
gsell ca5f4abc7c comment for zero-sized selections reviewed 2013-11-15 16:46:36 +01:00
gsell 9d3c006409 MPI rank variable renamed to comm_rank 2013-11-15 16:45:06 +01:00
gsell d79d0ddf1a basic read_strided example implemented 2013-11-15 16:44:07 +01:00
gsell a1ad62bc74 'use_core_vfd.c' renamed to 'write_core_vfd.c' 2013-10-31 15:32:32 +01:00
gsell 950bcef057 explicit set of verbosity level to default; refactor variables for MPI communicator size and rank to 'comm_size' and 'comm_rank' 2013-10-31 15:30:43 +01:00
gsell 468a5d6871 H5Part examples reviewed 2013-10-31 13:44:06 +01:00
gsell cf09862f4b ignore file updated 2013-10-31 13:42:07 +01:00
gsell 6b6f290ebb MPI initialization added to vtk2h5grid.cc 2013-10-31 13:41:09 +01:00
gsell c8eecb51ae typo in filename 'examples/H5Part/use_core_vfd.c' fixed 2013-10-31 13:39:40 +01:00
gsell 23c2bdd189 typo in filename 'examples/H5Part/use_core_vfd.c' fixed 2013-10-31 13:38:27 +01:00
gsell 3e69059afc macro H5_VERBOSE_DEFAULT defined 2013-10-28 18:28:19 +01:00
gsell a6f81be2cd h5u_set_view() supports zero particle selections now, h5u_set_view_start_length() renamed to h5u_set_view_length() 2013-10-28 18:26:59 +01:00
gsell 89b91d6b46 --with-vtk added to configure.ac 2013-10-28 18:23:09 +01:00
gsell 4975de7a74 ignore list edited 2013-10-10 17:10:23 +02:00
gsell 3fe4c39e5e fix renamed macros in tests 2013-10-10 17:10:05 +02:00
gsell 89bb9ef48c missing set file property functions implemented, bugfixes 2013-10-10 17:08:32 +02:00
gsell d15993ecdc missing file property functions added 2013-10-10 17:03:13 +02:00
gsell da723dda5e missing file property functions added 2013-10-10 17:02:39 +02:00
gsell 0dcc666e5e more work on examples 2013-10-10 17:00:44 +02:00
gsell 61d17a352f same examples renamed 2013-10-10 16:56:25 +02:00
gsell 006e1cda4a examples Bench.c, H5test.c and H5testF.f90 removed 2013-09-26 16:47:51 +02:00
gsell 11e399b6c7 C and Fortran examples reviewed, new examples added 2013-09-26 15:59:09 +02:00
gsell e839226f2b unit tests adapted to new API 2013-09-26 15:54:47 +02:00
gsell 2702f846cb old file open API removed 2013-09-26 15:53:54 +02:00
gsell ee23c8cc4b Fortran API review 2013-09-26 15:51:49 +02:00
gsell c3a74c8ed4 functions added to query attributes by name 2013-09-26 15:47:43 +02:00
gsell 969acd3642 definition of H5_MAX_NAME_LEN moved to public API 2013-09-26 15:38:54 +02:00
gsell ee07f01abd C header files specified with full path 2013-09-26 15:23:54 +02:00
gsell 06f0a8b4e7 compile with -O3 if debug is disabled, compile with -Wall in always 2013-09-26 15:20:45 +02:00
gsell 205a1a5c37 .gitignore added 2013-09-02 11:20:16 +02:00
gsell 7174b36a20 fixes to Fortran API 2013-09-02 09:31:14 +02:00
gsell 273b1831d9 fixes to autotool files 2013-09-02 09:30:23 +02:00
gsell 83c5a66814 handle MPI compiler on NERSC system 2013-07-11 12:18:53 +00:00
gsell db81cb3d33 attachment test moved to examples 2013-07-11 07:50:57 +00:00
gsell 4a8eedd31e autotool fixes 2013-07-10 14:05:21 +00:00
gsell 11a1cc7c1e reformated 2013-07-10 14:04:53 +00:00
gsell a509000711 warnings popped up on Linux fixed 2013-07-05 14:45:47 +00:00
gsell a65ee3bbb7 bugfixes 2013-07-04 14:58:18 +00:00
gsell f69ee003f6 ignore list edited 2013-06-27 16:27:46 +00:00
gsell 0b18373f8c bugfixes 2013-06-27 16:25:09 +00:00
gsell 311cdad1c8 bugfix 2013-06-27 16:24:02 +00:00
gsell 6f84edd791 autotool cleanup and fixes 2013-06-27 16:21:18 +00:00
gsell 1614f9519b autotool cleanup and fixes 2013-06-27 16:20:43 +00:00
gsell 65757c1974 bug fixes, some private functions renamed, formating changes 2013-06-27 16:18:08 +00:00
gsell 80523c6df7 examples fixed 2013-06-27 16:14:22 +00:00
gsell f17f1d028c fixes for building outside source tree 2013-05-02 14:14:26 +00:00
gsell 78078c322e definitions for H5_VERBOSE_{NONE,ERROR,WARN,INFO} added 2013-05-02 14:12:43 +00:00
gsell 1284d545e1 ported to new API 2013-05-02 14:11:06 +00:00
gsell 96af35450a added something to NEWS (still work in progress) 2013-05-02 14:09:22 +00:00
gsell 5abb40125b new trunk merged from old trunk, Roman's master thesis and my changes in the sandbox 2013-04-12 12:32:58 +00:00
733 changed files with 243064 additions and 55511 deletions
Expand all files Collapse all files
.gitattributes
+564 -111
View File
@@ -1,130 +1,583 @@
* text=auto !eol
/AUTHORS -text
/COPYRIGHT -text
/COPYING -text
/ChangeLog -text
/GNUmakefile.orig -text
H5Fed/applications/gmsh2h5fed.cc -text
H5Fed/applications/gmsh2h5fed.hh -text
H5Fed/applications/makefile.am -text
H5Fed/autogen.sh -text
H5Fed/configure.ac -text
H5Fed/grids/cube0.geo -text
H5Fed/grids/cube0.msh -text
H5Fed/grids/cubeincube.geo -text
H5Fed/grids/cubeincube.msh -text
H5Fed/grids/sphere.geo -text
H5Fed/grids/sphere.msh -text
H5Fed/libsrc/gmsh/gmsh.cc -text
H5Fed/libsrc/gmsh/gmsh.hh -text
H5Fed/libsrc/gmsh/gmshconst.hh -text
H5Fed/libsrc/gmsh/gmshgrammar.hh -text
H5Fed/libsrc/gmsh/gmshsemanticaction.hh -text
H5Fed/libsrc/gmsh/makefile.am -text
H5Fed/libsrc/h5fed/h5fed.cc -text
H5Fed/libsrc/h5fed/h5fed.hh -text
H5Fed/libsrc/h5fed/h5fedconst.hh -text
H5Fed/libsrc/h5fed/makefile.am -text
H5Fed/libsrc/makefile.am -text
H5Fed/libsrc/stdincl/nonsciconst.h -text
H5Fed/libsrc/stdincl/physicomath.h -text
H5Fed/makefile.am -text
/Makefile.am -text
/Makefile.orig -text
/NEWS -text
/README -text
/autogen.sh -text
/config.guess -text
/config.h.in -text
/config.sub -text
/configure.ac -text
/depcomp -text
doc/2006-Berkeley-Visit/BethelSAP_1page-4.doc -text
doc/2006-Berkeley-Visit/H5Part.ppt -text
doc/2006-Berkeley-Visit/H5xxx.ppt -text
doc/2006-Berkeley-Visit/H5xxxVisIt.fig -text
doc/2006-Berkeley-Visit/SAP-Combined-v6.doc -text
doc/2006-Berkeley-Visit/aqpsi2006mar22.pdf -text
doc/2006-Berkeley-Visit/hdf.ps -text
doc/Building.html -text
doc/BuildingHDF5.html -text
doc/Downloading.html -text
doc/Doxyfile -text
doc/H5PartExpress.html -text
doc/H5PartIDL.html -text
doc/H5PartParaview.html -text
doc/H5PartTools.html -text
doc/H5PartVisIt.html -text
doc/H5PartVisIt/cloud_visit.png -text
doc/H5PartVisIt/cloud_visit.s.png -text
doc/H5PartVisIt/cloud_visit_2D.png -text
doc/H5PartVisIt/cloud_visit_2D.s.png -text
doc/H5PartVisIt/visit_query1.png -text
doc/H5PartVisIt/visit_query1.s.png -text
doc/H5tools/H5tools.htm -text
doc/H5tools/H5tools_files/snapshot1.jpg -text
doc/H5xxx/H5xxx.tex -text
doc/H5xxx/JAC2003.cls -text
doc/H5xxx/makefile -text
doc/InternalLayout.html -text
doc/ReferencePages/H5PartF_8c.html -text
doc/ReferencePages/H5Part_8c.html -text
doc/ReferencePages/H5Part_8h-source.html -text
doc/ReferencePages/H5Part_8h.html -text
doc/ReferencePages/annotated.html -text
doc/ReferencePages/doxygen.css -text
doc/ReferencePages/doxygen.png -text
doc/ReferencePages/files.html -text
doc/ReferencePages/functions.html -text
doc/ReferencePages/functions_vars.html -text
doc/ReferencePages/globals.html -text
doc/ReferencePages/globals_defs.html -text
doc/ReferencePages/globals_func.html -text
doc/ReferencePages/globals_type.html -text
doc/ReferencePages/index.html -text
doc/ReferencePages/structH5IO__getname__t-members.html -text
doc/ReferencePages/structH5IO__getname__t.html -text
doc/ReferencePages/structH5PartFile-members.html -text
doc/ReferencePages/structH5PartFile.html -text
doc/UsingC.html -text
doc/UsingF.html -text
doc/collision_6.png -text
doc/collision_6.s.png -text
doc/h5part.html -text
doc/hdf5.pdf -text
doc/layout.png -text
/install-sh -text
doc/DoxygenLayout.xml -text
doc/Examples/meshexample.dxf -text
doc/Examples/meshexample.txt -text
doc/Examples/simple_tet.vtk -text
doc/Examples/simple_tet_level0.vtk -text
doc/Examples/simple_tet_level1.vtk -text
doc/Examples/simple_tet_level2.vtk -text
doc/Examples/trimesh_dgraph_level0.metis -text
doc/Examples/trimesh_dgraph_level0.metis.part.2 -text
doc/Examples/trimesh_dgraph_level0.metis.part.3 -text
doc/Examples/trimesh_dnode_level1.metis -text
doc/Examples/trimesh_dnode_level1.metis.part.2 -text
doc/Examples/trimesh_level0.metis -text
doc/Examples/trimesh_level0.metis.epart.2 -text
doc/Examples/trimesh_level0.metis.ngraph -text
doc/Examples/trimesh_level0.metis.npart.2 -text
doc/Examples/trimesh_level1.metis -text
doc/Examples/trimesh_level1.metis.part.2 -text
doc/H5.dox -text
doc/H5X_File_Format.txt -text
doc/Makefile.am -text
doc/TracFooter.html -text
doc/TracHeader.html -text
doc/doxyfooter -text
doc/doxyheader -text
doc/html2twiki -text
doc/meshexample.dxf -text
doc/postprocess.py -text
doc/tetrahedron_refinements/1-edge/edge_01_refined/01.png -text
doc/tetrahedron_refinements/1-edge/edge_01_refined/01.pvsm -text
doc/tetrahedron_refinements/1-edge/edge_01_refined/01.txt -text
doc/tetrahedron_refinements/1-edge/edge_01_refined/01.vtk -text
doc/tetrahedron_refinements/1-edge/edge_01_refined/01_smal.png -text
doc/tetrahedron_refinements/1-edge/edge_01_refined/01_small.png -text
doc/tetrahedron_refinements/1-edge/edge_12_refined/12.png -text
doc/tetrahedron_refinements/1-edge/edge_12_refined/12.pvsm -text
doc/tetrahedron_refinements/1-edge/edge_12_refined/12.txt -text
doc/tetrahedron_refinements/1-edge/edge_12_refined/12.vtk -text
doc/tetrahedron_refinements/1-edge/edge_12_refined/12_small.png -text
doc/tetrahedron_refinements/1-edge/edge_20_refined/20.png -text
doc/tetrahedron_refinements/1-edge/edge_20_refined/20.pvsm -text
doc/tetrahedron_refinements/1-edge/edge_20_refined/20.txt -text
doc/tetrahedron_refinements/1-edge/edge_20_refined/20.vtk -text
doc/tetrahedron_refinements/1-edge/edge_20_refined/20_small.png -text
doc/tetrahedron_refinements/1-edge/edge_23_refined/23.png -text
doc/tetrahedron_refinements/1-edge/edge_23_refined/23.pvsm -text
doc/tetrahedron_refinements/1-edge/edge_23_refined/23.txt -text
doc/tetrahedron_refinements/1-edge/edge_23_refined/23.vtk -text
doc/tetrahedron_refinements/1-edge/edge_23_refined/23_small.png -text
doc/tetrahedron_refinements/1-edge/edge_30_refined/30.png -text
doc/tetrahedron_refinements/1-edge/edge_30_refined/30.pvsm -text
doc/tetrahedron_refinements/1-edge/edge_30_refined/30.txt -text
doc/tetrahedron_refinements/1-edge/edge_30_refined/30.vtk -text
doc/tetrahedron_refinements/1-edge/edge_30_refined/30_small.png -text
doc/tetrahedron_refinements/1-edge/edge_31_refined/31.png -text
doc/tetrahedron_refinements/1-edge/edge_31_refined/31.pvsm -text
doc/tetrahedron_refinements/1-edge/edge_31_refined/31.txt -text
doc/tetrahedron_refinements/1-edge/edge_31_refined/31.vtk -text
doc/tetrahedron_refinements/1-edge/edge_31_refined/31_small.png -text
doc/tetrahedron_refinements/2-edges/edge_01-12_refined/01-12.png -text
doc/tetrahedron_refinements/2-edges/edge_01-12_refined/01-12.pvsm -text
doc/tetrahedron_refinements/2-edges/edge_01-12_refined/01-12.txt -text
doc/tetrahedron_refinements/2-edges/edge_01-12_refined/01-12.vtk -text
doc/tetrahedron_refinements/2-edges/edge_01-12_refined/01-12_smal.png -text
doc/tetrahedron_refinements/2-edges/edge_01-12_refined/01-12_small.png -text
doc/tetrahedron_refinements/2-edges/edge_01-20_refined/01-20.png -text
doc/tetrahedron_refinements/2-edges/edge_01-20_refined/01-20.pvsm -text
doc/tetrahedron_refinements/2-edges/edge_01-20_refined/01-20.txt -text
doc/tetrahedron_refinements/2-edges/edge_01-20_refined/01-20.vtk -text
doc/tetrahedron_refinements/2-edges/edge_01-20_refined/01-20_small.png -text
doc/tetrahedron_refinements/2-edges/edge_01-23_refined/01-23.png -text
doc/tetrahedron_refinements/2-edges/edge_01-23_refined/01-23.pvsm -text
doc/tetrahedron_refinements/2-edges/edge_01-23_refined/01-23.txt -text
doc/tetrahedron_refinements/2-edges/edge_01-23_refined/01-23.vtk -text
doc/tetrahedron_refinements/2-edges/edge_01-23_refined/01-23_smal.png -text
doc/tetrahedron_refinements/2-edges/edge_01-23_refined/01-23_small.png -text
doc/tetrahedron_refinements/2-edges/edge_01-30_refined/01-30.png -text
doc/tetrahedron_refinements/2-edges/edge_01-30_refined/01-30.pvsm -text
doc/tetrahedron_refinements/2-edges/edge_01-30_refined/01-30.txt -text
doc/tetrahedron_refinements/2-edges/edge_01-30_refined/01-30.vtk -text
doc/tetrahedron_refinements/2-edges/edge_01-30_refined/01-30_small.png -text
doc/tetrahedron_refinements/2-edges/edge_01-31_refined/01-31.png -text
doc/tetrahedron_refinements/2-edges/edge_01-31_refined/01-31.pvsm -text
doc/tetrahedron_refinements/2-edges/edge_01-31_refined/01-31.txt -text
doc/tetrahedron_refinements/2-edges/edge_01-31_refined/01-31.vtk -text
doc/tetrahedron_refinements/2-edges/edge_01-31_refined/01-31_small.png -text
doc/tetrahedron_refinements/2-edges/edge_12-20_refined/12-20.png -text
doc/tetrahedron_refinements/2-edges/edge_12-20_refined/12-20.pvsm -text
doc/tetrahedron_refinements/2-edges/edge_12-20_refined/12-20.txt -text
doc/tetrahedron_refinements/2-edges/edge_12-20_refined/12-20.vtk -text
doc/tetrahedron_refinements/2-edges/edge_12-20_refined/12-20_small.png -text
doc/tetrahedron_refinements/2-edges/edge_12-23_refined/12-23.png -text
doc/tetrahedron_refinements/2-edges/edge_12-23_refined/12-23.pvsm -text
doc/tetrahedron_refinements/2-edges/edge_12-23_refined/12-23.txt -text
doc/tetrahedron_refinements/2-edges/edge_12-23_refined/12-23.vtk -text
doc/tetrahedron_refinements/2-edges/edge_12-23_refined/12-23_small.png -text
doc/tetrahedron_refinements/2-edges/edge_12-30_refined/12-30.png -text
doc/tetrahedron_refinements/2-edges/edge_12-30_refined/12-30.pvsm -text
doc/tetrahedron_refinements/2-edges/edge_12-30_refined/12-30.txt -text
doc/tetrahedron_refinements/2-edges/edge_12-30_refined/12-30.vtk -text
doc/tetrahedron_refinements/2-edges/edge_12-30_refined/12-30_small.png -text
doc/tetrahedron_refinements/2-edges/edge_12-31_refined/12-31.png -text
doc/tetrahedron_refinements/2-edges/edge_12-31_refined/12-31.pvsm -text
doc/tetrahedron_refinements/2-edges/edge_12-31_refined/12-31.txt -text
doc/tetrahedron_refinements/2-edges/edge_12-31_refined/12-31.vtk -text
doc/tetrahedron_refinements/2-edges/edge_12-31_refined/12-31_small.png -text
doc/tetrahedron_refinements/2-edges/edge_20-23_refined/20-23.png -text
doc/tetrahedron_refinements/2-edges/edge_20-23_refined/20-23.pvsm -text
doc/tetrahedron_refinements/2-edges/edge_20-23_refined/20-23.txt -text
doc/tetrahedron_refinements/2-edges/edge_20-23_refined/20-23.vtk -text
doc/tetrahedron_refinements/2-edges/edge_20-23_refined/20-23_small.png -text
doc/tetrahedron_refinements/2-edges/edge_20-30_refined/20-30.png -text
doc/tetrahedron_refinements/2-edges/edge_20-30_refined/20-30.pvsm -text
doc/tetrahedron_refinements/2-edges/edge_20-30_refined/20-30.txt -text
doc/tetrahedron_refinements/2-edges/edge_20-30_refined/20-30.vtk -text
doc/tetrahedron_refinements/2-edges/edge_20-30_refined/20-30_small.png -text
doc/tetrahedron_refinements/2-edges/edge_20-31_refined/20-31.png -text
doc/tetrahedron_refinements/2-edges/edge_20-31_refined/20-31.pvsm -text
doc/tetrahedron_refinements/2-edges/edge_20-31_refined/20-31.txt -text
doc/tetrahedron_refinements/2-edges/edge_20-31_refined/20-31.vtk -text
doc/tetrahedron_refinements/2-edges/edge_20-31_refined/20-31_small.png -text
doc/tetrahedron_refinements/2-edges/edge_23-30_refined/23-30.png -text
doc/tetrahedron_refinements/2-edges/edge_23-30_refined/23-30.pvsm -text
doc/tetrahedron_refinements/2-edges/edge_23-30_refined/23-30.txt -text
doc/tetrahedron_refinements/2-edges/edge_23-30_refined/23-30.vtk -text
doc/tetrahedron_refinements/2-edges/edge_23-30_refined/23-30_small.png -text
doc/tetrahedron_refinements/2-edges/edge_23-31_refined/23-31.png -text
doc/tetrahedron_refinements/2-edges/edge_23-31_refined/23-31.pvsm -text
doc/tetrahedron_refinements/2-edges/edge_23-31_refined/23-31.txt -text
doc/tetrahedron_refinements/2-edges/edge_23-31_refined/23-31.vtk -text
doc/tetrahedron_refinements/2-edges/edge_23-31_refined/23-31_small.png -text
doc/tetrahedron_refinements/2-edges/edge_30-31_refined/30-31.png -text
doc/tetrahedron_refinements/2-edges/edge_30-31_refined/30-31.pvsm -text
doc/tetrahedron_refinements/2-edges/edge_30-31_refined/30-31.txt -text
doc/tetrahedron_refinements/2-edges/edge_30-31_refined/30-31.vtk -text
doc/tetrahedron_refinements/2-edges/edge_30-31_refined/30-31_small.png -text
doc/tetrahedron_refinements/3-edges/edge_01-12-20_refined/01-12-20.png -text
doc/tetrahedron_refinements/3-edges/edge_01-12-20_refined/01-12-20.pvsm -text
doc/tetrahedron_refinements/3-edges/edge_01-12-20_refined/01-12-20.txt -text
doc/tetrahedron_refinements/3-edges/edge_01-12-20_refined/01-12-20.vtk -text
doc/tetrahedron_refinements/3-edges/edge_01-12-20_refined/01-12-20_small.png -text
doc/tetrahedron_refinements/3-edges/edge_01-12-23_refined/01-12-23.png -text
doc/tetrahedron_refinements/3-edges/edge_01-12-23_refined/01-12-23.pvsm -text
doc/tetrahedron_refinements/3-edges/edge_01-12-23_refined/01-12-23.txt -text
doc/tetrahedron_refinements/3-edges/edge_01-12-23_refined/01-12-23.vtk -text
doc/tetrahedron_refinements/3-edges/edge_01-12-23_refined/01-12-23_small.png -text
doc/tetrahedron_refinements/3-edges/edge_01-12-30_refined/01-12-30.png -text
doc/tetrahedron_refinements/3-edges/edge_01-12-30_refined/01-12-30.pvsm -text
doc/tetrahedron_refinements/3-edges/edge_01-12-30_refined/01-12-30.txt -text
doc/tetrahedron_refinements/3-edges/edge_01-12-30_refined/01-12-30.vtk -text
doc/tetrahedron_refinements/3-edges/edge_01-12-30_refined/01-12-30_small.png -text
doc/tetrahedron_refinements/3-edges/edge_01-12-31_refined/01-12-31.png -text
doc/tetrahedron_refinements/3-edges/edge_01-12-31_refined/01-12-31.pvsm -text
doc/tetrahedron_refinements/3-edges/edge_01-12-31_refined/01-12-31.txt -text
doc/tetrahedron_refinements/3-edges/edge_01-12-31_refined/01-12-31.vtk -text
doc/tetrahedron_refinements/3-edges/edge_01-12-31_refined/01-12-31_small.png -text
doc/tetrahedron_refinements/3-edges/edge_01-20-23_refined/01-20-23.png -text
doc/tetrahedron_refinements/3-edges/edge_01-20-23_refined/01-20-23.pvsm -text
doc/tetrahedron_refinements/3-edges/edge_01-20-23_refined/01-20-23.txt -text
doc/tetrahedron_refinements/3-edges/edge_01-20-23_refined/01-20-23.vtk -text
doc/tetrahedron_refinements/3-edges/edge_01-20-23_refined/01-20-23_small.png -text
doc/tetrahedron_refinements/3-edges/edge_01-20-30_refined/01-20-30.png -text
doc/tetrahedron_refinements/3-edges/edge_01-20-30_refined/01-20-30.pvsm -text
doc/tetrahedron_refinements/3-edges/edge_01-20-30_refined/01-20-30.txt -text
doc/tetrahedron_refinements/3-edges/edge_01-20-30_refined/01-20-30.vtk -text
doc/tetrahedron_refinements/3-edges/edge_01-20-30_refined/01-20-30_small.png -text
doc/tetrahedron_refinements/3-edges/edge_01-20-31_refined/01-20-31.png -text
doc/tetrahedron_refinements/3-edges/edge_01-20-31_refined/01-20-31.pvsm -text
doc/tetrahedron_refinements/3-edges/edge_01-20-31_refined/01-20-31.txt -text
doc/tetrahedron_refinements/3-edges/edge_01-20-31_refined/01-20-31.vtk -text
doc/tetrahedron_refinements/3-edges/edge_01-20-31_refined/01-20-31_small.png -text
doc/tetrahedron_refinements/3-edges/edge_01-23-30_refined/01-23-30.png -text
doc/tetrahedron_refinements/3-edges/edge_01-23-30_refined/01-23-30.pvsm -text
doc/tetrahedron_refinements/3-edges/edge_01-23-30_refined/01-23-30.txt -text
doc/tetrahedron_refinements/3-edges/edge_01-23-30_refined/01-23-30.vtk -text
doc/tetrahedron_refinements/3-edges/edge_01-23-30_refined/01-23-30_small.png -text
doc/tetrahedron_refinements/3-edges/edge_01-23-31_refined/01-23-31.png -text
doc/tetrahedron_refinements/3-edges/edge_01-23-31_refined/01-23-31.pvsm -text
doc/tetrahedron_refinements/3-edges/edge_01-23-31_refined/01-23-31.txt -text
doc/tetrahedron_refinements/3-edges/edge_01-23-31_refined/01-23-31.vtk -text
doc/tetrahedron_refinements/3-edges/edge_01-23-31_refined/01-23-31_small.png -text
doc/tetrahedron_refinements/3-edges/edge_01-30-31_refined/01-30-31.png -text
doc/tetrahedron_refinements/3-edges/edge_01-30-31_refined/01-30-31.pvsm -text
doc/tetrahedron_refinements/3-edges/edge_01-30-31_refined/01-30-31.txt -text
doc/tetrahedron_refinements/3-edges/edge_01-30-31_refined/01-30-31.vtk -text
doc/tetrahedron_refinements/3-edges/edge_01-30-31_refined/01-30-31_small.png -text
doc/tetrahedron_refinements/3-edges/edge_12-20-23_refined/12-20-23.png -text
doc/tetrahedron_refinements/3-edges/edge_12-20-23_refined/12-20-23.pvsm -text
doc/tetrahedron_refinements/3-edges/edge_12-20-23_refined/12-20-23.txt -text
doc/tetrahedron_refinements/3-edges/edge_12-20-23_refined/12-20-23.vtk -text
doc/tetrahedron_refinements/3-edges/edge_12-20-23_refined/12-20-23_small.png -text
doc/tetrahedron_refinements/3-edges/edge_12-20-30_refined/12-20-30.png -text
doc/tetrahedron_refinements/3-edges/edge_12-20-30_refined/12-20-30.pvsm -text
doc/tetrahedron_refinements/3-edges/edge_12-20-30_refined/12-20-30.txt -text
doc/tetrahedron_refinements/3-edges/edge_12-20-30_refined/12-20-30.vtk -text
doc/tetrahedron_refinements/3-edges/edge_12-20-30_refined/12-20-30_small.png -text
doc/tetrahedron_refinements/3-edges/edge_12-20-31_refined/12-20-31.png -text
doc/tetrahedron_refinements/3-edges/edge_12-20-31_refined/12-20-31.pvsm -text
doc/tetrahedron_refinements/3-edges/edge_12-20-31_refined/12-20-31.txt -text
doc/tetrahedron_refinements/3-edges/edge_12-20-31_refined/12-20-31.vtk -text
doc/tetrahedron_refinements/3-edges/edge_12-20-31_refined/12-20-31_small.png -text
doc/tetrahedron_refinements/3-edges/edge_12-23-30_refined/12-23-30.png -text
doc/tetrahedron_refinements/3-edges/edge_12-23-30_refined/12-23-30.pvsm -text
doc/tetrahedron_refinements/3-edges/edge_12-23-30_refined/12-23-30.txt -text
doc/tetrahedron_refinements/3-edges/edge_12-23-30_refined/12-23-30.vtk -text
doc/tetrahedron_refinements/3-edges/edge_12-23-30_refined/12-23-30_small.png -text
doc/tetrahedron_refinements/3-edges/edge_12-23-31_refined/12-23-31.png -text
doc/tetrahedron_refinements/3-edges/edge_12-23-31_refined/12-23-31.pvsm -text
doc/tetrahedron_refinements/3-edges/edge_12-23-31_refined/12-23-31.txt -text
doc/tetrahedron_refinements/3-edges/edge_12-23-31_refined/12-23-31.vtk -text
doc/tetrahedron_refinements/3-edges/edge_12-23-31_refined/12-23-31_small.png -text
doc/tetrahedron_refinements/3-edges/edge_12-30-31_refined/12-30-31.png -text
doc/tetrahedron_refinements/3-edges/edge_12-30-31_refined/12-30-31.pvsm -text
doc/tetrahedron_refinements/3-edges/edge_12-30-31_refined/12-30-31.txt -text
doc/tetrahedron_refinements/3-edges/edge_12-30-31_refined/12-30-31.vtk -text
doc/tetrahedron_refinements/3-edges/edge_12-30-31_refined/12-30-31_small.png -text
doc/tetrahedron_refinements/3-edges/edge_20-23-30_refined/20-23-30.png -text
doc/tetrahedron_refinements/3-edges/edge_20-23-30_refined/20-23-30.pvsm -text
doc/tetrahedron_refinements/3-edges/edge_20-23-30_refined/20-23-30.txt -text
doc/tetrahedron_refinements/3-edges/edge_20-23-30_refined/20-23-30.vtk -text
doc/tetrahedron_refinements/3-edges/edge_20-23-30_refined/20-23-30_small.png -text
doc/tetrahedron_refinements/3-edges/edge_20-23-31_refined/20-23-31.png -text
doc/tetrahedron_refinements/3-edges/edge_20-23-31_refined/20-23-31.pvsm -text
doc/tetrahedron_refinements/3-edges/edge_20-23-31_refined/20-23-31.txt -text
doc/tetrahedron_refinements/3-edges/edge_20-23-31_refined/20-23-31.vtk -text
doc/tetrahedron_refinements/3-edges/edge_20-23-31_refined/20-23-31_small.png -text
doc/tetrahedron_refinements/3-edges/edge_20-30-31_refined/20-30-31.png -text
doc/tetrahedron_refinements/3-edges/edge_20-30-31_refined/20-30-31.pvsm -text
doc/tetrahedron_refinements/3-edges/edge_20-30-31_refined/20-30-31.txt -text
doc/tetrahedron_refinements/3-edges/edge_20-30-31_refined/20-30-31.vtk -text
doc/tetrahedron_refinements/3-edges/edge_20-30-31_refined/20-30-31_small.png -text
doc/tetrahedron_refinements/3-edges/edge_23-30-31_refined/23-30-31.png -text
doc/tetrahedron_refinements/3-edges/edge_23-30-31_refined/23-30-31.pvsm -text
doc/tetrahedron_refinements/3-edges/edge_23-30-31_refined/23-30-31.txt -text
doc/tetrahedron_refinements/3-edges/edge_23-30-31_refined/23-30-31.vtk -text
doc/tetrahedron_refinements/3-edges/edge_23-30-31_refined/23-30-31_small.png -text
doc/tetrahedron_refinements/4-edges/edge_01-12-20-23_refined/01-12-20-23.png -text
doc/tetrahedron_refinements/4-edges/edge_01-12-20-23_refined/01-12-20-23.pvsm -text
doc/tetrahedron_refinements/4-edges/edge_01-12-20-23_refined/01-12-20-23.txt -text
doc/tetrahedron_refinements/4-edges/edge_01-12-20-23_refined/01-12-20-23.vtk -text
doc/tetrahedron_refinements/4-edges/edge_01-12-20-23_refined/01-12-20-23_small.png -text
doc/tetrahedron_refinements/4-edges/edge_01-12-20-30_refined/01-12-20-30.png -text
doc/tetrahedron_refinements/4-edges/edge_01-12-20-30_refined/01-12-20-30.pvsm -text
doc/tetrahedron_refinements/4-edges/edge_01-12-20-30_refined/01-12-20-30.txt -text
doc/tetrahedron_refinements/4-edges/edge_01-12-20-30_refined/01-12-20-30.vtk -text
doc/tetrahedron_refinements/4-edges/edge_01-12-20-30_refined/01-12-20-30_small.png -text
doc/tetrahedron_refinements/4-edges/edge_01-12-20-31_refined/01-12-20-31.png -text
doc/tetrahedron_refinements/4-edges/edge_01-12-20-31_refined/01-12-20-31.pvsm -text
doc/tetrahedron_refinements/4-edges/edge_01-12-20-31_refined/01-12-20-31.txt -text
doc/tetrahedron_refinements/4-edges/edge_01-12-20-31_refined/01-12-20-31.vtk -text
doc/tetrahedron_refinements/4-edges/edge_01-12-20-31_refined/01-12-20-31_small.png -text
doc/tetrahedron_refinements/4-edges/edge_01-12-23-30_refined/01-12-23-30.png -text
doc/tetrahedron_refinements/4-edges/edge_01-12-23-30_refined/01-12-23-30.pvsm -text
doc/tetrahedron_refinements/4-edges/edge_01-12-23-30_refined/01-12-23-30.txt -text
doc/tetrahedron_refinements/4-edges/edge_01-12-23-30_refined/01-12-23-30.vtk -text
doc/tetrahedron_refinements/4-edges/edge_01-12-23-30_refined/01-12-23-30_small.png -text
doc/tetrahedron_refinements/4-edges/edge_01-12-23-31_refined/01-12-23-31.png -text
doc/tetrahedron_refinements/4-edges/edge_01-12-23-31_refined/01-12-23-31.pvsm -text
doc/tetrahedron_refinements/4-edges/edge_01-12-23-31_refined/01-12-23-31.txt -text
doc/tetrahedron_refinements/4-edges/edge_01-12-23-31_refined/01-12-23-31.vtk -text
doc/tetrahedron_refinements/4-edges/edge_01-12-23-31_refined/01-12-23-31_small.png -text
doc/tetrahedron_refinements/4-edges/edge_01-12-30-31_refined/01-12-30-31.png -text
doc/tetrahedron_refinements/4-edges/edge_01-12-30-31_refined/01-12-30-31.pvsm -text
doc/tetrahedron_refinements/4-edges/edge_01-12-30-31_refined/01-12-30-31.txt -text
doc/tetrahedron_refinements/4-edges/edge_01-12-30-31_refined/01-12-30-31.vtk -text
doc/tetrahedron_refinements/4-edges/edge_01-12-30-31_refined/01-12-30-31_small.png -text
doc/tetrahedron_refinements/4-edges/edge_01-20-23-30_refined/01-20-23-30.png -text
doc/tetrahedron_refinements/4-edges/edge_01-20-23-30_refined/01-20-23-30.pvsm -text
doc/tetrahedron_refinements/4-edges/edge_01-20-23-30_refined/01-20-23-30.txt -text
doc/tetrahedron_refinements/4-edges/edge_01-20-23-30_refined/01-20-23-30.vtk -text
doc/tetrahedron_refinements/4-edges/edge_01-20-23-30_refined/01-20-23-30_small.png -text
doc/tetrahedron_refinements/4-edges/edge_01-20-23-31_refined/01-20-23-31.png -text
doc/tetrahedron_refinements/4-edges/edge_01-20-23-31_refined/01-20-23-31.pvsm -text
doc/tetrahedron_refinements/4-edges/edge_01-20-23-31_refined/01-20-23-31.txt -text
doc/tetrahedron_refinements/4-edges/edge_01-20-23-31_refined/01-20-23-31.vtk -text
doc/tetrahedron_refinements/4-edges/edge_01-20-23-31_refined/01-20-23-31_small.png -text
doc/tetrahedron_refinements/4-edges/edge_01-20-30-31_refined/01-20-30-31.png -text
doc/tetrahedron_refinements/4-edges/edge_01-20-30-31_refined/01-20-30-31.pvsm -text
doc/tetrahedron_refinements/4-edges/edge_01-20-30-31_refined/01-20-30-31.txt -text
doc/tetrahedron_refinements/4-edges/edge_01-20-30-31_refined/01-20-30-31.vtk -text
doc/tetrahedron_refinements/4-edges/edge_01-20-30-31_refined/01-20-30-31_small.png -text
doc/tetrahedron_refinements/4-edges/edge_01-23-30-31_refined/01-23-30-31.png -text
doc/tetrahedron_refinements/4-edges/edge_01-23-30-31_refined/01-23-30-31.pvsm -text
doc/tetrahedron_refinements/4-edges/edge_01-23-30-31_refined/01-23-30-31.txt -text
doc/tetrahedron_refinements/4-edges/edge_01-23-30-31_refined/01-23-30-31.vtk -text
doc/tetrahedron_refinements/4-edges/edge_01-23-30-31_refined/01-23-30-31_small.png -text
doc/tetrahedron_refinements/4-edges/edge_12-20-23-30_refined/12-20-23-30.png -text
doc/tetrahedron_refinements/4-edges/edge_12-20-23-30_refined/12-20-23-30.pvsm -text
doc/tetrahedron_refinements/4-edges/edge_12-20-23-30_refined/12-20-23-30.txt -text
doc/tetrahedron_refinements/4-edges/edge_12-20-23-30_refined/12-20-23-30.vtk -text
doc/tetrahedron_refinements/4-edges/edge_12-20-23-30_refined/12-20-23-30_small.png -text
doc/tetrahedron_refinements/4-edges/edge_12-20-23-31_refined/12-20-23-31.png -text
doc/tetrahedron_refinements/4-edges/edge_12-20-23-31_refined/12-20-23-31.pvsm -text
doc/tetrahedron_refinements/4-edges/edge_12-20-23-31_refined/12-20-23-31.txt -text
doc/tetrahedron_refinements/4-edges/edge_12-20-23-31_refined/12-20-23-31.vtk -text
doc/tetrahedron_refinements/4-edges/edge_12-20-23-31_refined/12-20-23-31_small.png -text
doc/tetrahedron_refinements/4-edges/edge_12-20-30-31_refined/12-20-30-31.png -text
doc/tetrahedron_refinements/4-edges/edge_12-20-30-31_refined/12-20-30-31.pvsm -text
doc/tetrahedron_refinements/4-edges/edge_12-20-30-31_refined/12-20-30-31.txt -text
doc/tetrahedron_refinements/4-edges/edge_12-20-30-31_refined/12-20-30-31.vtk -text
doc/tetrahedron_refinements/4-edges/edge_12-20-30-31_refined/12-20-30-31_small.png -text
doc/tetrahedron_refinements/4-edges/edge_12-23-30-31_refined/12-23-30-31.png -text
doc/tetrahedron_refinements/4-edges/edge_12-23-30-31_refined/12-23-30-31.pvsm -text
doc/tetrahedron_refinements/4-edges/edge_12-23-30-31_refined/12-23-30-31.txt -text
doc/tetrahedron_refinements/4-edges/edge_12-23-30-31_refined/12-23-30-31.vtk -text
doc/tetrahedron_refinements/4-edges/edge_12-23-30-31_refined/12-23-30-31_small.png -text
doc/tetrahedron_refinements/4-edges/edge_20-23-30-31_refined/20-23-30-31.png -text
doc/tetrahedron_refinements/4-edges/edge_20-23-30-31_refined/20-23-30-31.pvsm -text
doc/tetrahedron_refinements/4-edges/edge_20-23-30-31_refined/20-23-30-31.txt -text
doc/tetrahedron_refinements/4-edges/edge_20-23-30-31_refined/20-23-30-31.vtk -text
doc/tetrahedron_refinements/4-edges/edge_20-23-30-31_refined/20-23-30-31_small.png -text
doc/tetrahedron_refinements/5-edges/edge_01-12-20-23-30_refined/01-12-20-23-30.png -text
doc/tetrahedron_refinements/5-edges/edge_01-12-20-23-30_refined/01-12-20-23-30.pvsm -text
doc/tetrahedron_refinements/5-edges/edge_01-12-20-23-30_refined/01-12-20-23-30.txt -text
doc/tetrahedron_refinements/5-edges/edge_01-12-20-23-30_refined/01-12-20-23-30.vtk -text
doc/tetrahedron_refinements/5-edges/edge_01-12-20-23-30_refined/01-12-20-23-30_small.png -text
doc/tetrahedron_refinements/5-edges/edge_01-12-20-23-31_refined/01-12-20-23-31.png -text
doc/tetrahedron_refinements/5-edges/edge_01-12-20-23-31_refined/01-12-20-23-31.pvsm -text
doc/tetrahedron_refinements/5-edges/edge_01-12-20-23-31_refined/01-12-20-23-31.txt -text
doc/tetrahedron_refinements/5-edges/edge_01-12-20-23-31_refined/01-12-20-23-31.vtk -text
doc/tetrahedron_refinements/5-edges/edge_01-12-20-23-31_refined/01-12-20-23-31_small.png -text
doc/tetrahedron_refinements/5-edges/edge_01-12-20-30-31_refined/01-12-20-30-31.png -text
doc/tetrahedron_refinements/5-edges/edge_01-12-20-30-31_refined/01-12-20-30-31.pvsm -text
doc/tetrahedron_refinements/5-edges/edge_01-12-20-30-31_refined/01-12-20-30-31.txt -text
doc/tetrahedron_refinements/5-edges/edge_01-12-20-30-31_refined/01-12-20-30-31.vtk -text
doc/tetrahedron_refinements/5-edges/edge_01-12-20-30-31_refined/01-12-20-30-31_small.png -text
doc/tetrahedron_refinements/5-edges/edge_01-12-23-30-31_refined/01-12-23-30-31.png -text
doc/tetrahedron_refinements/5-edges/edge_01-12-23-30-31_refined/01-12-23-30-31.pvsm -text
doc/tetrahedron_refinements/5-edges/edge_01-12-23-30-31_refined/01-12-23-30-31.txt -text
doc/tetrahedron_refinements/5-edges/edge_01-12-23-30-31_refined/01-12-23-30-31.vtk -text
doc/tetrahedron_refinements/5-edges/edge_01-12-23-30-31_refined/01-12-23-30-31_small.png -text
doc/tetrahedron_refinements/5-edges/edge_01-20-23-30-31_refined/01-20-23-30-31.png -text
doc/tetrahedron_refinements/5-edges/edge_01-20-23-30-31_refined/01-20-23-30-31.pvsm -text
doc/tetrahedron_refinements/5-edges/edge_01-20-23-30-31_refined/01-20-23-30-31.txt -text
doc/tetrahedron_refinements/5-edges/edge_01-20-23-30-31_refined/01-20-23-30-31.vtk -text
doc/tetrahedron_refinements/5-edges/edge_01-20-23-30-31_refined/01-20-23-30-31_small.png -text
doc/tetrahedron_refinements/5-edges/edge_12-20-23-30-31_refined/12-20-23-30-31.png -text
doc/tetrahedron_refinements/5-edges/edge_12-20-23-30-31_refined/12-20-23-30-31.pvsm -text
doc/tetrahedron_refinements/5-edges/edge_12-20-23-30-31_refined/12-20-23-30-31.txt -text
doc/tetrahedron_refinements/5-edges/edge_12-20-23-30-31_refined/12-20-23-30-31.vtk -text
doc/tetrahedron_refinements/5-edges/edge_12-20-23-30-31_refined/12-20-23-30-31_small.png -text
doc/tetrahedron_refinements/6-edges/edge_01-12-20-23-30-31_refined/01-12-20-23-30-31.aux -text
doc/tetrahedron_refinements/6-edges/edge_01-12-20-23-30-31_refined/01-12-20-23-30-31.log -text
doc/tetrahedron_refinements/6-edges/edge_01-12-20-23-30-31_refined/01-12-20-23-30-31.pdf -text
doc/tetrahedron_refinements/6-edges/edge_01-12-20-23-30-31_refined/01-12-20-23-30-31.png -text
doc/tetrahedron_refinements/6-edges/edge_01-12-20-23-30-31_refined/01-12-20-23-30-31.pvsm -text
doc/tetrahedron_refinements/6-edges/edge_01-12-20-23-30-31_refined/01-12-20-23-30-31.tex -text
doc/tetrahedron_refinements/6-edges/edge_01-12-20-23-30-31_refined/01-12-20-23-30-31.tex.orig -text
doc/tetrahedron_refinements/6-edges/edge_01-12-20-23-30-31_refined/01-12-20-23-30-31.txt -text
doc/tetrahedron_refinements/6-edges/edge_01-12-20-23-30-31_refined/01-12-20-23-30-31.vtk -text
doc/tetrahedron_refinements/6-edges/edge_01-12-20-23-30-31_refined/01-12-20-23-30-31_small.png -text
doc/tetrahedron_refinements/6-edges/edge_01-12-20-23-30-31_refined/buildlatex.bash -text
doc/tetrahedron_refinements/6-edges/edge_01-12-20-23-30-31_refined/output_file.jpg -text
doc/tetrahedron_refinements/README -text
doc/tetrahedron_refinements/text2vtk.py -text
examples/H5/Makefile.am -text
examples/H5/attach_file.c -text
examples/H5/file_attribs.c -text
examples/H5/openclose.c -text
examples/H5Block/H5BlockExample.pbs -text
examples/H5Block/H5BlockExampleF.f90 -text
examples/H5Block/Makefile.am -text
examples/H5Block/README -text
examples/H5Block/fields.c -text
examples/H5Block/read_write.c -text
examples/H5Fed/Makefile.am -text
examples/H5Fed/map_tet2globalid.c -text
examples/H5Fed/map_triangle2globalid.c -text
examples/H5Fed/tetmesh_adjacencies.c -text
examples/H5Fed/tetmesh_read.c -text
examples/H5Fed/tetmesh_read_tags.c -text
examples/H5Fed/tetmesh_write.c -text
examples/H5Fed/tetmesh_write1.c -text
examples/H5Fed/tetmesh_write2.c -text
examples/H5Fed/tetmesh_write_tags.c -text
examples/H5Fed/trimesh_2gnuplot.c -text
examples/H5Fed/trimesh_adjacencies.c -text
examples/H5Fed/trimesh_read.c -text
examples/H5Fed/trimesh_write.c -text
examples/H5Fed/trimesh_write_dunetest.c -text
examples/H5Fed/write_boundary.c -text
examples/H5Part/Bench.c -text
examples/H5Part/H5test.c -text
examples/H5Part/H5testF.f90 -text
examples/H5Part/Makefile.am -text
examples/H5Part/core_vfd.c -text
examples/H5Part/particles.c -text
examples/H5Part/read_canonicalview.c -text
examples/H5Part/simplef.f90 -text
examples/H5Part/stridedf.f90 -text
examples/H5Part/write_setnumparticles.c -text
examples/H5Part/write_setview.c -text
/license.txt -text
/missing -text
/rules.make -text
src/H5Part++.cc -text
src/H5Part++.hh -text
src/H5Part.c -text
src/H5Part.cc -text
src/H5Part.h -text
src/H5Part.hh -text
src/H5Part.inc -text
src/H5PartF.c -text
src/H5PartPrivate.h -text
src/H5PartTypes.h -text
src/C/Makefile.am -text
src/Fortran/H5.c -text
src/Fortran/H5Block.c -text
src/Fortran/H5BlockF.f90 -text
src/Fortran/H5Block_F.c -text
src/Fortran/H5Block_attribs.c -text
src/Fortran/H5Block_attribsF.f90 -text
src/Fortran/H5Block_io.c -text
src/Fortran/H5Block_ioF.f90 -text
src/Fortran/H5Block_readwrite_F.c -text
src/Fortran/H5F.f90 -text
src/Fortran/H5Part.c -text
src/Fortran/H5PartF.f90 -text
src/Fortran/H5Part_F.c -text
src/Fortran/H5Part_io.c -text
src/Fortran/H5Part_ioF.f90 -text
src/Fortran/H5_F.c -text
src/Fortran/H5_attribs.c -text
src/Fortran/H5_attribsF.f90 -text
src/Fortran/H5_attribs_F.c -text
src/Fortran/H5_constF.f90 -text
src/Fortran/Makefile.am -text
src/Fortran/TestUnderscore.f -text
src/Fortran/TestUnderscoreC.c -text
src/Fortran/h5_private.h -text
src/Makefile.am -text
src/TestUnderscore.f -text
src/TestUnderscoreC.c -text
src/addToDoxygenMainPage.h -text
test/Bench.c -text
test/H5ParallelTest.cc -text
test/H5PartAndreasTest.cc -text
test/H5PartTest.cc -text
test/H5PartTestParallel.cc -text
test/H5ecloudExample.cc -text
test/H5test.cc -text
test/H5testF.f -text
test/H5testFpar.f -text
src/h5core/Makefile.am -text
src/h5core/h5_attach.c -text
src/h5core/h5_attribs.c -text
src/h5core/h5_attribs_private.h -text
src/h5core/h5_debug_private.h -text
src/h5core/h5_errorhandling.c -text
src/h5core/h5_errorhandling_private.h -text
src/h5core/h5_fcmp.c -text
src/h5core/h5_fcmp_private.h -text
src/h5core/h5_hdf5.c -text
src/h5core/h5_hdf5_private.h -text
src/h5core/h5_hsearch.c -text
src/h5core/h5_hsearch_private.h -text
src/h5core/h5_init.c -text
src/h5core/h5_init_private.h -text
src/h5core/h5_lustre.c -text
src/h5core/h5_lustre_private.h -text
src/h5core/h5_maps.c -text
src/h5core/h5_maps_private.h -text
src/h5core/h5_model.c -text
src/h5core/h5_model_private.h -text
src/h5core/h5_mpi.c -text
src/h5core/h5_mpi_private.h -text
src/h5core/h5_openclose.c -text
src/h5core/h5_private.h -text
src/h5core/h5_qsort.c -text
src/h5core/h5_qsort_private.h -text
src/h5core/h5_qsort_r.c -text
src/h5core/h5_readwrite.c -text
src/h5core/h5_readwrite_private.h -text
src/h5core/h5_syscall.c -text
src/h5core/h5_syscall_private.h -text
src/h5core/h5_types_private.h -text
src/h5core/h5_va_macros.h -text
src/h5core/h5b_attribs.c -text
src/h5core/h5b_model.c -text
src/h5core/h5b_model_private.h -text
src/h5core/h5b_readwrite.c -text
src/h5core/h5b_readwrite_private.h -text
src/h5core/h5b_types_private.h -text
src/h5core/h5t_access_private.h -text
src/h5core/h5t_access_tetm.c -text
src/h5core/h5t_access_trim.c -text
src/h5core/h5t_adjacencies.c -text
src/h5core/h5t_adjacencies_private.h -text
src/h5core/h5t_adjacencies_tetm.c -text
src/h5core/h5t_adjacencies_trim.c -text
src/h5core/h5t_core.c -text
src/h5core/h5t_core_private.h -text
src/h5core/h5t_core_tetm.c -text
src/h5core/h5t_core_trim.c -text
src/h5core/h5t_errorhandling_private.h -text
src/h5core/h5t_map.c -text
src/h5core/h5t_map_private.h -text
src/h5core/h5t_model.c -text
src/h5core/h5t_model_private.h -text
src/h5core/h5t_model_tetm.c -text
src/h5core/h5t_model_trim.c -text
src/h5core/h5t_octree.c -text
src/h5core/h5t_octree_private.h -text
src/h5core/h5t_readwrite.c -text
src/h5core/h5t_readwrite_private.h -text
src/h5core/h5t_readwrite_tetm.c -text
src/h5core/h5t_readwrite_trim.c -text
src/h5core/h5t_ref_elements.c -text
src/h5core/h5t_ref_elements_private.h -text
src/h5core/h5t_retrieve.c -text
src/h5core/h5t_retrieve_private.h -text
src/h5core/h5t_retrieve_tetm.c -text
src/h5core/h5t_retrieve_trim.c -text
src/h5core/h5t_store.c -text
src/h5core/h5t_store_private.h -text
src/h5core/h5t_store_tetm.c -text
src/h5core/h5t_store_trim.c -text
src/h5core/h5t_tags.c -text
src/h5core/h5t_tags_private.h -text
src/h5core/h5t_types_private.h -text
src/h5core/h5u_errorhandling_private.h -text
src/h5core/h5u_model.c -text
src/h5core/h5u_readwrite.c -text
src/h5core/h5u_readwrite_private.h -text
src/h5core/h5u_types_private.h -text
src/include/H5.h -text
src/include/H5Block.h -text
src/include/H5Block_attribs.h -text
src/include/H5Block_io.h -text
src/include/H5Block_model.h -text
src/include/H5Fed.h -text
src/include/H5Fed_adjacency.h -text
src/include/H5Fed_model.h -text
src/include/H5Fed_retrieve.h -text
src/include/H5Fed_store.h -text
src/include/H5Fed_tags.h -text
src/include/H5Part.h -text
src/include/H5Part_io.h -text
src/include/H5Part_model.h -text
src/include/H5_attribs.h -text
src/include/H5_model.h -text
src/include/H5hut.h -text
src/include/Makefile.am -text
src/include/h5core/Makefile.am -text
src/include/h5core/h5.h -text
src/include/h5core/h5_attribs.h -text
src/include/h5core/h5_debug.h -text
src/include/h5core/h5_errorhandling.h -text
src/include/h5core/h5_model.h -text
src/include/h5core/h5_syscall.h -text
src/include/h5core/h5_types.h -text
src/include/h5core/h5b_attribs.h -text
src/include/h5core/h5b_io.h -text
src/include/h5core/h5b_model.h -text
src/include/h5core/h5t_adjacencies.h -text
src/include/h5core/h5t_map.h -text
src/include/h5core/h5t_model.h -text
src/include/h5core/h5t_octree.h -text
src/include/h5core/h5t_retrieve.h -text
src/include/h5core/h5t_store.h -text
src/include/h5core/h5t_tags.h -text
src/include/h5core/h5u_io.h -text
src/include/h5core/h5u_model.h -text
test/Makefile.am -text
test/h5b_read.c -text
test/h5b_test.c -text
test/h5b_write.c -text
test/h5u_read.c -text
test/h5u_test.c -text
test/h5u_write.c -text
test/params.h -text
test/testframe.c -text
test/testframe.h -text
tools/H5PartMerge/AUTHORS -text
tools/H5PartMerge/COPYING -text
tools/H5PartMerge/ChangeLog -text
tools/H5PartMerge/INSTALL -text
tools/H5PartMerge/NEWS -text
tools/H5PartMerge/README -text
tools/H5PartMerge/autogen.sh -text
tools/H5PartMerge/configure.ac -text
tools/H5PartMerge/makefile.am -text
tools/H5PartMerge/src/H5merge.cpp -text
tools/H5PartMerge/src/optparse.cpp -text
tools/H5PartMerge/src/optparse.hh -text
tools/Makefile.am -text
tools/README -text
tools/h5PartDcToVtk.cc -text
tools/h5PartSurfaceToVtk.cc -text
tools/h5hutcc.in -text
tools/h5pAttrib.cc -text
tools/h5pToGNUplot.cc -text
tools/h5pToGNUplot.py -text
tools/vtk2h5grid/Makefile.am -text
tools/vtk2h5grid/vtk2h5grid.cc -text
visit_plugins/databases/H5Part/.depend -text
visit_plugins/databases/H5Part/Makefile -text
visit_plugins/databases/H5Part/README.txt -text
.gitignore
+94
View File
@@ -0,0 +1,94 @@
*.tar.gz
*.[oa]
*.la
*.lo
*.so
*.dSYM
*~
*.h5
.deps
.dirstamp
.libs
INSTALL
Makefile
Makefile.in
aclocal.m4
attach_field_attributes
dump_field_attributes
autom4te.cache/
compile
config.guess
config.h
config.h.in
config.log
config.status
config.sub
configure
depcomp
py-compile
examples/H5/attach_file
examples/H5/examples.h
examples/H5/h5hut.mod
examples/H5/openclose
examples/H5/openclosef
examples/H5/query
examples/H5/queryf
examples/H5/read_file_attribs
examples/H5/read_file_attribsf
examples/H5/read_step_attribs
examples/H5/read_step_attribsf
examples/H5/write_file_attribs
examples/H5/write_file_attribsf
examples/H5/write_step_attribs
examples/H5/write_step_attribsf
examples/H5Block/H5BlockExampleF
examples/H5Block/fields
examples/H5Block/read_write
examples/H5Part/Bench
examples/H5Part/H5test
examples/H5Part/H5testF
examples/H5Part/core_vfd
examples/H5Part/examples.h
examples/H5Part/h5hut.mod
examples/H5Part/particles
examples/H5Part/read_canonicalview
examples/H5Part/read_setnparticles
examples/H5Part/read_setview
examples/H5Part/read_strided
examples/H5Part/write_core_vfd
examples/H5Part/write_setnparticles
examples/H5Part/write_setnumparticles
examples/H5Part/write_setview
examples/H5Part/write_setviewf
examples/H5Part/write_strided
has_field
install-sh
libtool
ltmain.sh
m4/
missing
src/Fortran/TestUnderscore
src/Fortran/Underscore.h
src/include/H5hut.f
src/include/H5hutF.h
stamp-h1
test/h5b_test
test/h5u_test
test/h5_attach_test
tools/h5hutcc
tetmesh_adjacencies
tetmesh_read
tetmesh_read_tags
tetmesh_write
tetmesh_write1
examples/H5Fed/tetmesh_write2
examples/H5Fed/trimesh_2gnuplot
examples/H5Fed/trimesh_adjacencies
examples/H5Fed/trimesh_read
examples/H5Fed/trimesh_write
examples/H5Fed/trimesh_write_dunetest
tetmesh_write_tags
write_field
*.gch
ReferencePages
vtk2h5grid
AUTHORS
+1 -1
View File
@@ -7,4 +7,4 @@ Wes Bethel (NERSC/LBNL)
John Shalf (NERSC/LBNL)
Cristina Siegerist (NERSC/LBNL)
Please use h5part@lists.psi.ch for communicaion.
Please use h5part@lists.psi.ch for communication.
COPYING
+71
View File
@@ -0,0 +1,71 @@
*** Copyright Notice ***
H5hut Copyright (c) 2006-2016, The Regents of the University of California,
through Lawrence Berkeley National Laboratory (subject to receipt of any
required approvals from the U.S. Dept. of Energy) and the Paul Scherrer
Institut (Switzerland). All rights reserved.
If you have questions about your rights to use or distribute this
software, please contact Berkeley Lab's Technology Transfer Department
at TTD@lbl.gov referring to "H5Part (LBNL Ref CR-2255)"
NOTICE. This software was developed under partial funding from the U.S.
Department of Energy. As such, the U.S. Government has been granted for
itself and others acting on its behalf a paid-up, nonexclusive,
irrevocable, worldwide license in the Software to reproduce, prepare
derivative works, and perform publicly and display publicly. Beginning
five (5) years after the date permission to assert copyright is obtained
from the U.S. Department of Energy, and subject to any subsequent five
(5) year renewals, the U.S. Government is granted for itself and others
acting on its behalf a paid-up, nonexclusive, irrevocable, worldwide
license in the Software to reproduce, prepare derivative works,
distribute copies to the public, perform publicly and display publicly,
and to permit others to do so.
*** License agreement ***
H5hut Copyright (c) 2006-2016, The Regents of the University of California,
through Lawrence Berkeley National Laboratory (subject to receipt of any
required approvals from the U.S. Dept. of Energy) and the Paul Scherrer
Institut (Switzerland). All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
(1) Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
(2) Redistributions in binary form must reproduce the above copyright
notice, this list of conditions and the following disclaimer in the
documentation and/or other materials provided with the distribution.
(3) Neither the name of the University of California, Lawrence Berkeley
National Laboratory, U.S. Dept. of Energy, Paul Scherrer Institut
(Switzerland) nor the names of its contributors may be used to endorse
or promote products derived from this software without specific prior
written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS
IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER
OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
You are under no obligation whatsoever to provide any bug fixes,
patches, or upgrades to the features, functionality or performance of
the source code ("Enhancements") to anyone; however, if you choose to
make your Enhancements available either publicly, or directly to
Lawrence Berkeley National Laboratory, without imposing a separate
written license agreement for such Enhancements, then you hereby grant
the following license: a non-exclusive, royalty-free perpetual license
to install, use, modify, prepare derivative works, incorporate into
other computer software, distribute, and sublicense such enhancements or
derivative works thereof, in binary and source code form.
COPYRIGHT
-7
View File
@@ -1,7 +0,0 @@
*** Copyright Notice ***
H5Part Copyright (c) 2006, The Regents of the University of California, through Lawrence Berkeley National Laboratory (subject to receipt of any required approvals from the U.S. Dept. of Energy) and the Paul Scherrer Institut (Switzerland). All rights reserved.
If you have questions about your rights to use or distribute this software, please contact Berkeley Lab's Technology Transfer Department at TTD@lbl.gov referring to "H5Part (LBNL Ref CR-2255)"
NOTICE. This software was developed under partial funding from the U.S. Department of Energy. As such, the U.S. Government has been granted for itself and others acting on its behalf a paid-up, nonexclusive, irrevocable, worldwide license in the Software to reproduce, prepare derivative works, and perform publicly and display publicly. Beginning five (5) years after the date permission to assert copyright is obtained from the U.S. Department of Energy, and subject to any subsequent five (5) year renewals, the U.S. Government is granted for itself and others acting on its behalf a paid-up, nonexclusive, irrevocable, worldwide license in the Software to reproduce, prepare derivative works, distribute copies to the public, perform publicly and display publicly, and to permit others to do so.
GNUmakefile.orig
-133
View File
@@ -1,133 +0,0 @@
UNAME := $(shell uname | perl -pe 's/(sn\d\d\d\d|jsimpson)/UNICOS\/mk/')
# for host specific options
HOST := $(shell hostname)
# for processor-specific options
ifeq ($(UNAME), Linux)
PROC := $(shell uname -p)
endif
CXX = c++
CC = cc
H5HOME = /usr/local/hdf5
CFLAGS = -g -I$(H5HOME)/include
LDFLAGS = -L$(H5HOME)/lib -lhdf5 -lz -lm
# MacOS-X Serial
ifeq ($(UNAME), Darwin)
ifeq ($(PARALLEL), yes)
CXX = g++
CC = mpicc
H5HOME = /usr/local
CFLAGS = -O -g -I$(H5HOME)/include -DPARALLEL_IO
LDFLAGS = -L$(H5HOME)/lib -lmpich -lpmpich -lhdf5 -lz -lm
else
CXX = c++
CC = cc
F90 = xlf
H5HOME = /usr/local
CFLAGS = -O -g -I$(H5HOME)/include
LDFLAGS = -L$(H5HOME)/lib -lhdf5 -lz -lm
endif
endif
# SGI MIPS/Irix
ifeq ($(UNAME), IRIX64)
CXX = CC
CC = cc
F90 = f90
ifeq ($(PARALLEL), yes)
H5HOME = $(HDF5_DIR)
CFLAGS = -64 -O3 -I$(H5HOME)/include -DPARALLEL_IO
LDFLAGS = -64 -O3 -L$(H5HOME)/lib -lhdf5 -lz -lmpi -lm
else
H5HOME = /usr/local
CFLAGS = -O3 -I$(H5HOME)/include
LDFLAGS = -L$(H5HOME)/lib -lhdf5 -lz -lm
endif
endif
# AIX/SP-2 Parallel/serial : Seaborg
ifeq ($(UNAME), AIX)
ifeq ($(PARALLEL), yes) # parallel
CXX = mpCC_r
CC = mpxlc_r
# H5HOME = /usr/common/usg/hdf5_64/1.4.5-post2/parallel
H5HOME = /usr/common/usg/hdf5_64/1.6.1/parallel
# /usr/common/usg/hdf5/1.4.4/parallel
H4HOME = /usr/common/usg/hdf/default
OPT = -qarch=auto -qtune=auto-qcache=auto -O3 -qhot
CFLAGS = -q64 -I$(H5HOME)/include
LDFLAGS = -L$(H5HOME)/lib -lhdf5 -L$(H4HOME)/lib -lz -lsz -lm
else # serial
CXX = xlC
CC = xlc
H5HOME = /usr/common/usg/hdf5/1.4.4/serial
H4HOME = /usr/common/usg/hdf/default
OPT = -qarch=auto -qtune=auto-qcache=auto -O3 -qhot
CFLAGS = -g -bmaxdata:800000000 -bmaxstack:256000000 -I$(H5HOME)/include
LDFLAGS = -L$(H5HOME)/lib -lhdf5 -L$(H4HOME)/lib -lz -lm
endif
endif
# Linux
ifeq ($(UNAME), Linux)
# if this machine is NERSC/Davinci Altix system
ifeq ($(PROC), ia64)
CC = icc
CXX = icc
ifeq ($(PARALLEL), yes)
# IA64 Linux Parallel
ifeq ($(HOST), davinci)
H5HOME = $(HDF5_PAR)
MPILIB = -lmpi
else
H5HOME = /usr/local
HDF5_PAR_LIB = -L$(H5HOME)/lib -lhdf5 -lz -lm
HDF5_PAR_INCLUDE = -I$(H5HOME)/include
MPIHOME = /usr/local
MPILIB = -lmpich
endif # HOST
CFLAGS = -O3 -DPARALLEL_IO -DH5_HAVE_PARALLEL $(HDF5_PAR_INCLUDE)
LDFLAGS = $(HDF5_PAR_LIB) $(MPILIB)
else # IA64 Linux Serial
CFLAGS = -O3 $(HDF5_INCLUDE)
LDFLAGS = $(HDF5_LIB) -lm
endif # PARALLEL
# else this is standard IA32 linux
else
ifeq ($(PARALLEL), yes)
# Linux Parallel
CC = gcc
CXX = g++
H5HOME = /usr/local
MPIHOME = /usr/local
CFLAGS = -O -g -DPARALLEL_IO -DH5_HAVE_PARALLEL -I$(H5HOME)/include
LDFLAGS = -L$(H5HOME)/lib -lhdf5 -lmpich -lrt -lz -lm
else # Linux Serial
CXX = g++
CC = gcc
CFLAGS = -O -g -I$(H5HOME)/include
LDFLAGS = -L$(H5HOME)/lib -lhdf5 -lz -lm
endif # !PARALLEL
endif # PROC!ia64
endif # !Linux
ifeq ($(PARALLEL), yes) #parallel
ifdef F90
all: H5PartTest H5PartTest.o H5Part.o H5PartTestParallel H5PartAndreasTest H5PartF.o
else
all: H5PartTest H5PartTest.o H5Part.o H5PartTestParallel H5PartAndreasTest
endif
else
ifdef F90
all: H5PartTest H5PartTest.o H5Part.o H5PartF.o
else
all: H5PartTest H5PartTest.o H5Part.o
endif
endif
include rules.make
H5Fed/applications/gmsh2h5fed.cc
-427
View File
@@ -1,427 +0,0 @@
// rights - 2006-, copyright patrick leidenberger and benedikt oswald,
// all rights reserved
// project - gmsh2h5fed
// file name - gmsh2h5fed.cc
// file type - c++ implementaton file
// objective - main file for the gmsh to hdf5fed converter
// modified - 2006 jun 26, creation, patrick leidenberger
// modified - 2006 aug 25, extend, patrick leidenberger
// modified - 2006 aug 26, pl, integrate automatic index mapping.
//
// feature - Implements the a mesh preprocessor.
// feature - It will read gmsh's mesh files of version 2.0 and write the mesh
// feature - into an HDF5/FiniteElementData file.
// required software - rlog library, boost library
#include <gmsh2h5fed.hh>
using namespace rlog;
int main(int argc, char **argv)
{
//=================//
// Initialize RLog //
//=================//
// Make a instance of the class for RLog.
StdioNode stdLog;
/** Subscchar* inFile_;ribe output channels.
* Compile with -DRLOG_DEBUG to get the debug output.
**/
#ifdef USE_RLOG_DEBUG_CHANNEL
stdLog.subscribeTo(GetGlobalChannel("debug"));
#endif //USE_RLOG_DEBUG_CHANNEL
#ifdef USE_RLOG_ERROR_CHANNEL
stdLog.subscribeTo(GetGlobalChannel("error"));
#endif //USE_RLOG_ERROR_CHANNEL
#ifdef USE_RLOG_INFO_CHANNEL
stdLog.subscribeTo(GetGlobalChannel("info"));
#endif //USE_RLOG_INFO_CHANNEL
#ifdef USE_RLOG_WARNING_CHANNEL
stdLog.subscribeTo(GetGlobalChannel("warning"));
#endif //USE_RLOG_WARNING_CHANNEL
// Define variables that hold the command line parameters.
string gmshInputFile;
string hdf5fedOutputFile;
bool writeFileForce = false;
//==================================================//
// Parse the comand line options //
// with the program_options from the boost library. //
//==================================================//
try
{
// Define and instance of the program_options class and name it.
boost::program_options::options_description
desc("Allowed program options");
// Define the command line options parsing rules.
desc.add_options()
("help", "produce this help")
("input-file", boost::program_options::value<string>(),
"gmsh v2.0 input file")
("output-file", boost::program_options::value<string>(),
"hdf5fed output file")
("force", "if output file already exists, overwrite");
// Parse the command line.
boost::program_options::variables_map varMap;
boost::program_options::store
(boost::program_options::parse_command_line(argc, argv, desc),
varMap);
boost::program_options::notify(varMap);
// Action in relation to the command line options.
if (varMap.count("help"))
{
cout << desc << "\n";
return ERRORCODE;
}
else if ((varMap.count("input-file"))
&& (varMap.count("output-file")))
{
gmshInputFile = varMap["input-file"].as<string>();
hdf5fedOutputFile = varMap["output-file"].as<string>();
rInfo("Input filename: %s",
gmshInputFile.c_str());
rInfo("Output filename: %s",
hdf5fedOutputFile.c_str());
// Check it --force is set.
// --force writes the output file, if the file already exists.
if (varMap.count("force"))
writeFileForce = true;
else
writeFileForce = false;
}
else
{
rError("You have insert wrong options.");
rError("For details use: --help.");
return ERRORCODE;
}
}
catch(exception& error)
{
rError("Error: %d",error.what());
return ERRORCODE;
}
//==========================//
// Start with the main work //
//==========================//
//---------------------------------------//
// Variables for the data form gmsh file //
//---------------------------------------//
// Variable for the gmsh nodes.
std::vector<vector<double> > gmshNodes;
gmshNodes.clear();
// Vector for the gmshs nodes index.
std::vector<unsigned int> gmshNodesIndex;
gmshNodesIndex.clear();
// Vector for the gmshs tetrahedrons.
std::vector<std::vector<unsigned int> > gmshTetrahedron;
gmshTetrahedron.clear();
// Vector for the gmshs tetrahedrons.
std::vector<std::vector<unsigned int> > gmshTetrahedronTag;
gmshTetrahedronTag.clear();
// Make an instance of the vtk class.
gmsh gmshInFile;
// Set the file name of the input file
gmshInFile.gmshFileName(gmshInputFile);
// Open the gmsh mesh file, write the content to a string and close the
// file.
gmshInFile.gmshOpen();
// Parse the gmsh mesh file.
gmshInFile.gmshParseFile(&gmshInFile);
// Get a vector with all node coordinates from the gmsh file.
gmshNodes = gmshInFile.gmshNode();
// Put all H5Fed funktions in here.
#ifdef HAVE_HDF5
// Create H5Fed class instance.
H5Fed::H5Fed h5fedFile;
// Open H5Fed file for writing. Filename and file write access comes
// from command line parameters.
if (writeFileForce == false)
h5fedFile.open(hdf5fedOutputFile,FILE_CREATE);
else
h5fedFile.open(hdf5fedOutputFile,FILE_CREATE_FORCE);
// Create the group hierarchie in the hdf5fed file.
h5fedFile.createGroupHierarchie();
// Get the gmsh node index vector
gmshNodesIndex = gmshInFile.gmshNodeNumber();
// The gmsh node index has gaps and is not consecutive.
// So we activate the automatic index mapping from the h5fed api.
h5fedFile.beginIndexMapping(&gmshNodesIndex);
// Get a vector with all node coordinates from the gmsh file.
gmshNodes = gmshInFile.gmshNode();
// Write the nodes to the h5fed file.
h5fedFile.coord3d(&gmshNodes);
// Every node in h5fed file, so we can save memory.
gmshNodes.clear();
//Get a vector with all tetrahedrons from gmsh file.
gmshTetrahedron = gmshInFile.gmshTetrahedron();
for(int varI = 0; varI<gmshTetrahedron.size(); varI++)
{
// rDebug("Elem: %d Nodes: %d; %d; %d; %d", varI, gmshTetrahedron[varI][0], gmshTetrahedron[varI][1], gmshTetrahedron[varI][2], gmshTetrahedron[varI][3]);
}
// Write the tetrahedrons to the h5fed file on the respective level.
h5fedFile.tetrahedron(0,&gmshTetrahedron);
// Every terahedron in h5fed file, so we can save memory.
gmshTetrahedron.clear();
//Get a vector with all tetrahedrons from gmsh file.
gmshTetrahedronTag = gmshInFile.gmshTetrahedronTag();
for(int varI = 0; varI<gmshTetrahedronTag.size(); varI++)
{
// rDebug("Elem: %d Nodes: %d; %d", varI, gmshTetrahedronTag[varI][0], gmshTetrahedronTag[varI][1]);
}
// End with the automatic index mapping because we have no further actcion
// with an gmsh file index.
h5fedFile.endIndexMapping();
// Close H5Fed file.
h5fedFile.close();
#endif // HAVE_HDF5
/*
// Write all vtkPoints_ to the screen.
for (int i = 0; i<(gmshInFile.getVtkVecSize()); i++)
{
rDebug("%d vtkPoint x, y, z: %e %e %e",
i, gmshInFile.getVtkVec(i,0),gmshInFile.getVtkVec(i,1),gmshInFile.getVtkVec(i,2));
}
*/
/*
//Write all vktCells_ with cell types and cell points on the screen.
for (int i = 0;
(i<(gmshInFile.getVtkCellTypesN())) && (i<(gmshInFile.getVtkCellsN()));
i++)
{
rDebug("vtkCellType: %d", gmshInFile.getVtkCellType(i));
for (int j = 0; j<(gmshInFile.getVtkCellPointN(i)); j++)
{
rDebug(" vtkPoint: %d", gmshInFile.getVtkCellPoint(i,j));
}
}
// Write all vtk point datas on the screen.
//rDebug("size: %d", gmshInFile.vtkVectorSize("vtkPointData_"));
for (int i = 0;
i<(gmshInFile.vtkVectorSize("vtkPointData_"));
i++)
{
for (int j = 0; j<(gmshInFile.vtkVectorSize("vtkPointData_",i)); j++)
{
for(int k = 0; k<(gmshInFile.vtkVectorSize("vtkPointData_",i,j)); k++)
rDebug("vtk point vector element i, j, k, value: %d %d %d %e",
i,j,k,gmshInFile.vtkVector("vtkPointData_",i,j,k));
}
}
// Write all vtkPointsType_ to the screen.
rDebug("size of vtkPointDataType_: %d", gmshInFile.vtkVectorSize("vtkPointDataType_"));
for (int i = 0; i<(gmshInFile.vtkVectorSize("vtkPointDataType_")); i++)
{
rDebug("vtkPointDataType_ %s", gmshInFile.vtkVector("vtkPointDataType_",i).c_str());
}
// Write all vtkPointsName_ to the screen.
rDebug("size of vtkPointDataName_: %d", gmshInFile.vtkVectorSize("vtkPointDataName_"));
for (int i = 0; i<(gmshInFile.vtkVectorSize("vtkPointDataName_")); i++)
{
rDebug("vtkPointName_ %s", gmshInFile.vtkVector("vtkPointDataName_",i).c_str());
}
// Write all vtkPointsFormat_ to the screen.
rDebug("size of vtkPointDataFormat_: %d", gmshInFile.vtkVectorSize("vtkPointDataFormat_"));
for (int i = 0; i<(gmshInFile.vtkVectorSize("vtkPointDataFormat_")); i++)
{
rDebug("vtkPointFormat_ %s", (gmshInFile.vtkVector("vtkPointDataFormat_",i)).c_str());
}
// Write all vtk point datas on the screen.
//rDebug("size: %d", gmshInFile.vtkVectorSize("vtkCellData_"));
for (int i = 0;
i<(gmshInFile.vtkVectorSize("vtkCellData_"));
i++)
{
for (int j = 0; j<(gmshInFile.vtkVectorSize("vtkCellData_",i)); j++)
{
for(int k = 0; k<(gmshInFile.vtkVectorSize("vtkCellData_",i,j)); k++)
rDebug("vtk cell vector element i, j, k, value: %d %d %d %e",
i,j,k,gmshInFile.vtkVector("vtkCellData_",i,j,k));
}
}
// Write all vtkCellsType_ to the screen.
rDebug("size of vtkCellDataType_: %d", gmshInFile.vtkVectorSize("vtkCellDataType_"));
for (int i = 0; i<(gmshInFile.vtkVectorSize("vtkCellDataType_")); i++)
{
rDebug("vtkCellDataType_ %s", (gmshInFile.vtkVector("vtkCellDataType_",i)).c_str());
}
// Write all vtkCellsName_ to the screen.
rDebug("size of vtkCellDataName_: %d", gmshInFile.vtkVectorSize("vtkCellDataName_"));
for (int i = 0; i<(gmshInFile.vtkVectorSize("vtkCellDataName_")); i++)
{
rDebug("vtkCellDataName_ %s", (gmshInFile.vtkVector("vtkCellDataName_",i)).c_str());
}
// Write all vtkCellsFormat_ to the screen.
rDebug("size of vtkCellDataFormat_: %d", gmshInFile.vtkVectorSize("vtkCellDataFormat_"));
for (int i = 0; i<(gmshInFile.vtkVectorSize("vtkCellDataFormat_")); i++)
{
rDebug("vtkCellDataFormat_ %s", (gmshInFile.vtkVector("vtkCellDataFormat_",i)).c_str());
}
*/
// cout <<"\n\n" <<gmshInFile.getUg PointsN()<< "\n\n";
// int i = gmshInFile.openVtk();
//vtk* vtkPt;
//vtkPt = &gmshInFile;
//vtkPt->vtkVersion();
//gmshInFile.vtkVersion();
// This vector is used in loops to transport datas from vtk to ristream.
vector<double> dataVector1;
/*
// Scaling factor for the vtk input data.
double scale = 15.0;
ristream rib;
// Set the filname of the .rib file.
rib.RibsFile(ribOutputFile);
rib.openRibs();
rib.RibsFormat(1024,768);
rib.RibsLightSource("distantlight");
rib.RibsProjection("perspective");
//rib.RibsProjection("orthographic");
// Give the center or the rotation.
double rotCenterX = 0.0;
double rotCenterY = 0.0;
double rotRadius = 1.6;
double cameraPosX = sqrt(3.92); // Only the camera postion if nLoop = 1;
double cameraPosY = 0;
cameraPosX = 1; // Only the camera postion if nLoop = 1;
cameraPosY = -1;
char filename[20];
const int nLoop = 1;
for(int i = 0; i<nLoop; i++)
{
if (nLoop > 1)
{
cameraPosX = -rotRadius*cos(2*PI*i/(double)nLoop) + rotCenterX;
cameraPosY = -rotRadius*sin(2*PI*i/(double)nLoop) + rotCenterY;
}
rib.RibsFrameBegin();
// Set the file name for the renderer output image.
string tempstring = "";
tempstring = "tests/movie_data/Hallo";
//tempstring.append("%d.tiff",i);
//tempstring.append((string)i);
tempstring.append(".tiff");
//sprintf ( tempchar ,"tests/movie_data/Hallo%d.tiff",i );
// rib.RibsFrameFilename("");
rib.RibsDisplay(frameName);
rDebug(tempstring.c_str());
// Camera Position and orientation:
// The default camera postion is the world coordinate origin and it
// looks in the -z-direction.
// The function RibsPlaceCamera set the position of the camera in world
// coordinates and the point, where to look at in world coordinates.
// To get a skew view, you can roll the camera.
// This function must be called befor RibsWorldBegin!
rib.RibsPlaceCamera(1.5*cameraPosX, 1.5*cameraPosY, 2.0, // position
0.0, 0.0, 1.2, // look-at point
0.0) ; // roll angle (in degree)
rib.RibsWorldBegin();
rib.RibsSurface("plastic");
rib.RibsCoordinateSystem();
//Write all vktCells_ with cell types and cell points on the screen.
//rDebug("getVtkCellTypesN(): %d", gmshInFile.getVtkCellTypesN());
for (int i = 0; i<(gmshInFile.getVtkCellTypesN()); i++)
{
// Look if there is a thetrahedron.
if (gmshInFile.getVtkCellType(i) == 10)
{
// Clear the data structur to save the point cooridnates temporal.
dataVector1.clear();
// Read the points of a tetrahedron.
//rDebug("getVtkCellPointN(%d): %d", i, gmshInFile.getVtkCellPointN(i));
for (int j = 0; j<(gmshInFile.getVtkCellPointN(i)); j++)
{
int tempInt = gmshInFile.getVtkCellPoint(i,j);
dataVector1.push_back(gmshInFile.getVtkVec(tempInt, 0));
dataVector1.push_back(gmshInFile.getVtkVec(tempInt, 1));
dataVector1.push_back(gmshInFile.getVtkVec(tempInt, 2));
//rDebug("vtkPoint: %d, %f %f %f", tempInt,
// gmshInFile.getVtkVec(tempInt, 0),
// gmshInFile.getVtkVec(tempInt, 1),
// gmshInFile.getVtkVec(tempInt, 2));
}
rib.RibsColor(0.0,0,1.0,1.0);
rib.RibsTetrahedron(scale*dataVector1[0], scale*dataVector1[1], scale*dataVector1[2],
scale*dataVector1[3], scale*dataVector1[4], scale*dataVector1[5],
scale*dataVector1[6], scale*dataVector1[7], scale*dataVector1[8],
scale*dataVector1[9], scale*dataVector1[10],scale*dataVector1[11],
0.8);
}
}
*/
/*
rib.RibsColor(1.0,0,0,0.6);
rib.RibsTetrahedron(0.3, 0.3, 0.0,
2.0, 0.3, 0.0,
0.3, 2.0, 0.0,
0.3, 0.3, 0.5,
1.0);
rib.RibsColor(0,1.0,0,0.7);
rib.RibsTetrahedron(0.3, 0.3, 0.0,
2.0, 0.3, 0.0,
0.3, 2.0, 0.0,
0.3, 0.3, 0.5,
0.6);
rib.RibsColor(0.0,0,1.0,1.0);
rib.RibsTetrahedron(0.3, 0.3, 0.0,
2.0, 0.3, 0.0,
0.3, 2.0, 0.0,
0.3, 0.3, 0.5,
0.3);
*/
// rib,RibsAxes();
// rib.RibsVector(0,0,0,0.5);
/*
rib.RibsWorldEnd();
rib.RibsFrameEnd();
}
rib.closeRibs();
*/
// return(0);
}
H5Fed/applications/gmsh2h5fed.hh
-69
View File
@@ -1,69 +0,0 @@
// rights - 2006-, copyright benedikt oswald and patrick leidenberger, all rights reserved
// project - phidias3d
// file name - phidias3d.h
// file type - c++ header file
// objective - header file for the phidias3d visualization postprocessor
// modified - 2006 jun 26, creation, benedikt oswald
// modified - 2006 jun 28,
// modified - 2006 jul 30, Add include for command line argument parser
// with boost::program_options, pl.
// inheritance -
// feature - implements the phidias3d visualization postprocessor; the features
// feature - will be (1) read VTK legacy formatted files (2) read HDF5/ELECTROMAGNETIC
// feature - structures files (3) export VTK legacy formatted files (4) export
// feature - data, both meshes and fields, throught the Renderman Interface
// feature - routines.
// required software -
/* include standard header files */
#include <cmath>
#include <complex>
#include <string>
#include <vector>
#include <iostream>
#include <iterator>
#include <math.h>
/* Include the files for rlog. */
#include <rlog/rlog.h>
#include <rlog/rloglocation.h>
#include <rlog/Error.h>
#include <rlog/RLogChannel.h>
#include <rlog/StdioNode.h>
// Include this if you want to log the time.
#include <rlog/RLogTime.h>
// Include the boost program program_options to parse the comand line
// options.
#include <boost/program_options.hpp>
/* include standard proprietary header files */
#include <nonsciconst.h>
#include <physicomath.h>
//#include <ristream.h>
#include <gmsh.hh>
// Include the Hdf5FiniteElementData API.
#ifdef HAVE_HDF5
// Include the Hdf5FiniteElementData API.
#include <h5fed.hh>
// Include h5fed specific constants.
#include <h5fedconst.hh>
#else
#warning No hdf5 lib found!!
#endif
#ifndef PHIDIAS3D_H_
#define PHIDIAS3D_H_
using namespace physicomath;
using namespace nonsciconst;
using namespace gmshtohdf5fed;
#endif /*PHIDIAS3D_H_*/
H5Fed/applications/makefile.am
-26
View File
@@ -1,26 +0,0 @@
## Makefile.am -- process this file with automake to produce Makefile.in
##
## authors - benedikt oswald and patrick leidenberger
## modified - 2006 aug 21, patrick leidenberger, creation
## modified - 2006 aug 23, pl, adaped to changed directory structure.
## modified - 2006 aug 25, pl, adaped to changed directory structure.
#
## objective - automake input file for the gmsh directory
## project - gmsh2h5fed
noinst_PROGRAMS = gmsh2h5fed
gmsh2h5fed_SOURCES = gmsh2h5fed.cc
gmsh2h5fed_DEPENDENCIES = ../libsrc/stdincl/nonsciconst.h \
../libsrc/stdincl/physicomath.h \
../libsrc/gmsh/gmsh.hh \
../libsrc/gmsh/gmsh.cc \
../libsrc/gmsh/gmshconst.hh \
../libsrc/gmsh/gmshgrammar.hh \
../libsrc/gmsh/gmshsemanticaction.hh \
../libsrc/h5fed/h5fed.hh \
../libsrc/h5fed/h5fed.cc
gmsh2h5fed_LDADD = @GMSH2H5FED_LIBS@
#AM_CPPFLAGS = @AM_CPPFLAGS@
H5Fed/autogen.sh
-10
View File
@@ -1,10 +0,0 @@
libtoolize -f && \
aclocal && \
autoconf && \
autoheader && \
automake --add-missing && \
CC='mpicc' F9X='mpif90' CXX='mpiCC' ./configure --with-rlog=$HOME/extlib/rlog-1.3.7 --with-boost='' --with-hdf5=$HOME/extlib/hdf5-1.6.5 &&\
make clean && \
make all
H5Fed/configure.ac
-106
View File
@@ -1,106 +0,0 @@
## Process this file with autoconf to produce a configure script
##
## author - benedikt oswald and patrick leidenberger
## modified - 2006 aug 21, pl, creation.
## modified - 2006 aug 24, pl, add h5fed path.
##
## to do : The rlog lib needs a -DRLOG_COMPONENT="some name", I don't know
## how tho do this so that the quotation marks are in the output
## stream as well, pl, 2006 jul 04.
##
## objective - develop input file for GNU autotools/configure
## project - H5Fed
##
AC_PREREQ(2.59)
AC_COPYRIGHT([This configure script is copyright by Benedikt Oswald and Patrick Leidenberger, 2006])
AC_INIT([gmshtohdf5fed], [1.0], [in case of problems mail to: benedikt.oswald@psi.ch or patrick.leidenberger@psi.ch])
# library creation
AC_PROG_LIBTOOL
# standard macros
AC_CONFIG_AUX_DIR(./)
AM_INIT_AUTOMAKE
AC_CONFIG_HEADER([./config.h:./config.in])
# set cppflags to zero
CPPFLAGS=""
CFFLAGS=""
CXXFLAGS=""
# provide include directories
AC_SUBST([AM_CPPFLAGS], '-I$(top_srcdir)/libsrc/stdincl -I$(top_srcdir)/libsrc/gmsh -I$(top_srcdir)/libsrc/h5fed')
AC_SUBST([GMSH2H5FED_LIBS],'$(top_srcdir)/libsrc/gmsh/libgmsh.la $(top_srcdir)/libsrc/h5fed/libh5fed.la')
# Make available external libraries
AC_ARG_WITH(boost,
AC_HELP_STRING([--with-boost=PREFIX],
[prefix where the Boost libraries and include files are to be found]),
[BOOST_PREFIX=$withval
LDFLAGS="-lz -lboost_program_options "])
AC_ARG_WITH(rlog,
AC_HELP_STRING([--with-rlog=PREFIX],
[prefix where the rlog libraries and include files are to be found]),
[RLOG_PREFIX=$withval
CPPFLAGS="-I"$RLOG_PREFIX"/include "${CPPFLAGS}
LDFLAGS=$RLOG_PREFIX"/lib/librlog.la "${LDFLAGS}])
AC_ARG_ENABLE(rlog-debug,
AC_HELP_STRING([--disable-rlog-debug],
[disable the debug output channel of rlog]),
[],
[CFFLAGS="-DUSE_RLOG_DEBUG_CHANNEL "${CFFLAGS}
CXXFLAGS="-DUSE_RLOG_DEBUG_CHANNEL "${CXXFLAGS}])
AC_ARG_ENABLE(rlog-error,
AC_HELP_STRING([--disable-rlog-error],
[disable the error output channel of rlog]),
[],
[CFFLAGS="-DUSE_RLOG_ERROR_CHANNEL "${CFFLAGS}
CXXFLAGS="-DUSE_RLOG_ERROR_CHANNEL "${CXXFLAGS}])
AC_ARG_ENABLE(rlog-info,
AC_HELP_STRING([--disable-rlog-info],
[disable the info output channel of rlog]),
[],
[CFFLAGS="-DUSE_RLOG_INFO_CHANNEL "${CFFLAGS}
CXXFLAGS="-DUSE_RLOG_INFO_CHANNEL "${CXXFLAGS}])
AC_ARG_ENABLE(rlog-warning,
AC_HELP_STRING([--disable-rlog-warning],
[disable the warning output channel of rlog]),
[],
[CFFLAGS="-DUSE_RLOG_WARNING_CHANNEL "${CFFLAGS}
CXXFLAGS="-DUSE_RLOG_WARNING_CHANNEL "${CXXFLAGS}])
AC_ARG_WITH(hdf5,
AC_HELP_STRING([--with-hdf5=PREFIX],
[prefix to hdf5 libraries and include files]),
[HDF5_PREFIX=$withval
CPPFLAGS="-DHAVE_HDF5 -I"$HDF5_PREFIX"/include "${CPPFLAGS}
LDFLAGS="-L"$HDF5_PREFIX"/lib -lhdf5 "${LDFLAGS}])
# LDFLAGS=$HDF5_PREFIX"/lib/libhdf5.la "${LDFLAGS}])
# Set C/C++ compiler flags.
CPPFLAGS=${CPPFLAGS}
CFFLAGS="-g3 "${CFFLAGS}
CXXFLAGS="-g3 "${CXXFLAGS}
AM_INIT_AUTOMAKE([1.9 foreign])
AC_PROG_CC
AC_PROG_MAKE_SET
AC_PROG_INSTALL([install])
AC_CONFIG_FILES([makefile
applications/makefile
libsrc/makefile
libsrc/gmsh/makefile
libsrc/h5fed/makefile])
AC_OUTPUT
H5Fed/grids/cube0.geo
-114
View File
@@ -1,114 +0,0 @@
// rights - 2002-2005, benedikt oswald,
// project - aq
// file name - cube0.geo
// file type - GMSH script file
// objective - model cube fundamental cube
// modified - 2005 jan 25, benedikt oswald, creation
// modified - 2005 jan 25, benedikt oswald, added background hexahedron, subsurface hexahedron
// modified - 2005 feb 01, benedikt oswald, adapted to the simple.geo problem
// modified - 2005 mar 08, benedikt oswald, adapted to the cube in cube geometry
// modified - 2005 mar 22, benedikt oswald, adapted to model fundamental cube
// inheritance -
// feature - models fundamental cube, used for benchmark calculations of a Hertzian dipole
// feature - radiating into free space; the model uses standard physical domain tags;
// 1 modeling constants
lcl1=0.50; // characteristic length in fractions of lambda@1 GHz for air domain
lcl2=0.50; // characteristic length in fractions of lambda@1 GHz for air domain
lambda=0.30; // wavelength of electromagntic wave at a frequency of 1 GHz
lx=2.0; // x dim of computational domain
ly=2.0; // y dim of computational domain
lz=2.0; // z dim of computational domain
cx=0.5*lx; // calculate center of computational domain
cy=0.5*ly; // calculate center of computational domain
cz=0.5*lz; // calculate center of computational domain
// 1.2 Define physical material domains
vacuum=609; // physical entity vacuum
air=709; // physical entity air
subsurface=809; // physical entity subsurface
pml=1301; // physical entity pml material
icelens=4001; // physical entity icelens
vacuum_background_bnd=12701; // boundary to background, i.e. vacuum
interelement_bnd=12702; // interior boundary, separating different material domains
// 2 Define cubes
// 2.1.1 Define points of cube
p0=newp; Point(p0) = {0.0, 0.0, 0.0, lambda * lcl1};
p1=newp; Point(p1) = { lx, 0.0, 0.0, lambda * lcl1};
p2=newp; Point(p2) = { lx, ly, 0.0, lambda * lcl1};
p3=newp; Point(p3) = {0.0, ly, 0.0, lambda * lcl1};
p4=newp; Point(p4) = {0.0, 0.0, lz, lambda * lcl1};
p5=newp; Point(p5) = { lx, 0.0, lz, lambda * lcl1};
p6=newp; Point(p6) = { lx, ly, lz, lambda * lcl1};
p7=newp; Point(p7) = {0.0, ly, lz, lambda * lcl1};
// 2.1.3 Define lines of cube
// lower xy plane
li0=newl; Line(li0) = {p0,p1};
li1=newl; Line(li1) = {p1,p2};
li2=newl; Line(li2) = {p2,p3};
li3=newl; Line(li3) = {p3,p0};
// upper xy plane
li4=newl; Line(li4) = {p4,p5};
li5=newl; Line(li5) = {p5,p6};
li6=newl; Line(li6) = {p6,p7};
li7=newl; Line(li7) = {p7,p4};
// vertical lines
li8=newl; Line(li8) = {p0,p4};
li9=newl; Line(li9) = {p1,p5};
li10=newl; Line(li10) = {p2,p6};
li11=newl; Line(li11) = {p3,p7};
// 2.1.5 Define line 6 line loops for the 6 faces of the cube
lloop0= newreg; Line Loop(lloop0) = { li0, li1, li2, li3};
lloop1= newreg; Line Loop(lloop1) = { li4, li5, li6, li7};
lloop2= newreg; Line Loop(lloop2) = { li0, li9, -li4, -li8 };
lloop3= newreg; Line Loop(lloop3) = { li1, li10, -li5, -li9};
lloop4= newreg; Line Loop(lloop4) = { li2, li11, -li6, -li10};
lloop5= newreg; Line Loop(lloop5) = { li3, li8, -li7, -li11};
// 2.1.7 define plane surfaces for the cube
s0=news; Plane Surface(s0) = {lloop0};
s1=news; Plane Surface(s1) = {lloop1};
s2=news; Plane Surface(s2) = {lloop2};
s3=news; Plane Surface(s3) = {lloop3};
s4=news; Plane Surface(s4) = {lloop4};
s5=news; Plane Surface(s5) = {lloop5};
// 2.1.9 Define surface loops required for volume definition of the cube
sloop0=newreg; Surface Loop(sloop0) ={s0,s1,s2,s3,s4,s5};
// 2.1.10 Define volume of the cube
v0=newv; Volume(v0) = {sloop0};
// 3.0 define physical entitites
Physical Point(vacuum_background_bnd) = {p0:p7};
Physical Line(vacuum_background_bnd) = {li0:li11};
Physical Surface(vacuum_background_bnd) = {s0:s5};
Physical Volume(air) = {v0};
H5Fed/grids/cube0.msh
-21463
View File
File diff suppressed because it is too large Load Diff
H5Fed/grids/cubeincube.geo
-206
View File
@@ -1,206 +0,0 @@
// rights - 2002-2005, benedikt oswald,
// project - aq
// file name - cubeincube.geo
// file type - GMSH script file
// objective - model cube in a cube mesh, useful for PML booundary conditions
// modified - 2005 jan 25, benedikt oswald, creation
// modified - 2005 jan 25, benedikt oswald, added background hexahedron, subsurface hexahedron
// modified - 2005 feb 01, benedikt oswald, adapted to the simple.geo problem
// modified - 2005 mar 08, benedikt oswald, adapted to the cube in cube geometry
// inheritance -
// feature - models a cube in a cube mesh, useful for PML booundary conditions;
// feature - the PML boundary model is based on a 3D region with special electromagnetic
// feature - material properties which guarantee, in theory, perfect absorption of incident
// feature - electromagnetic waves independent of the angle between the wave vector
// feature - and the boundary; in order to model the PML material domain a separate mesh
// feature - region is created so that there is a clean boundary between the PML and
// feature - and the air region.
// 1 modeling constants
lcair=0.90; // characteristic length in fractions of lambda@1 GHz for air domain
lcpml=0.70; // characteristic length in fractions of lambda@1 GHz for PML region
lambda=0.30; // wavelength of electromagntic wave at a frequency of 1 GHz
lx=1.0; // x dim of computational domain
ly=1.0; // y dim of computational domain
lz=1.0; // z dim of computational domain
cx=0.5*lx; // calculate center of computational domain
cy=0.5*ly; // calculate center of computational domain
cz=0.5*lz; // calculate center of computational domain
lpmlxl=0.1; // thickness of PML region
lpmlxh=0.1; // thickness of PML region
lpmlyl=0.1; // thickness of PML region
lpmlyh=0.1; // thickness of PML region
lpmlzl=0.1; // thickness of PML region
lpmlzh=0.1; // thickness of PML region
xminic=lpmlxl; // x min of inner cube
xmaxic=lx-lpmlxh; // x max of inner cube
yminic=lpmlyl; // y min of inner cube
ymaxic=ly-lpmlyh; // y max of inner cube
zminic=lpmlzl; // z min of inner cube
zmaxic=lz-lpmlzh; // z max of inner cube
// 1.2 Define physical material domains
vacuum=609; // physical entity vacuum
air=709; // physical entity air
pml=1301; // physical entity pml material
icelens=4001; // physical entity icelens
vacuum_background_bnd=12701; // boundary to background, i.e. vacuum
interelement_bnd=12702; // interior boundary, separating different material domains
// 2 Define cubes
// 2.1.1 Define points of outer cube
p0=newp; Point(p0) = {0.0, 0.0, 0.0, lambda * lcpml};
p1=newp; Point(p1) = { lx, 0.0, 0.0, lambda * lcpml};
p2=newp; Point(p2) = { lx, ly, 0.0, lambda * lcpml};
p3=newp; Point(p3) = {0.0, ly, 0.0, lambda * lcpml};
p4=newp; Point(p4) = {0.0, 0.0, lz, lambda * lcpml};
p5=newp; Point(p5) = { lx, 0.0, lz, lambda * lcpml};
p6=newp; Point(p6) = { lx, ly, lz, lambda * lcpml};
p7=newp; Point(p7) = {0.0, ly, lz, lambda * lcpml};
// 2.1.2 Define points of inner cube
p100=newp; Point(p100) = {xminic, yminic, zminic, lambda * lcair};
p101=newp; Point(p101) = {xmaxic, yminic, zminic, lambda * lcair};
p102=newp; Point(p102) = {xmaxic, ymaxic, zminic, lambda * lcair};
p103=newp; Point(p103) = {xminic, ymaxic, zminic, lambda * lcair};
p104=newp; Point(p104) = {xminic, yminic, zmaxic, lambda * lcair};
p105=newp; Point(p105) = {xmaxic, yminic, zmaxic, lambda * lcair};
p106=newp; Point(p106) = {xmaxic, ymaxic, zmaxic, lambda * lcair};
p107=newp; Point(p107) = {xminic, ymaxic, zmaxic, lambda * lcair};
// 2.1.3 Define lines of outer cube
// lower xy plane
li0=newl; Line(li0) = {p0,p1};
li1=newl; Line(li1) = {p1,p2};
li2=newl; Line(li2) = {p2,p3};
li3=newl; Line(li3) = {p3,p0};
// upper xy plane
li4=newl; Line(li4) = {p4,p5};
li5=newl; Line(li5) = {p5,p6};
li6=newl; Line(li6) = {p6,p7};
li7=newl; Line(li7) = {p7,p4};
// vertical lines
li8=newl; Line(li8) = {p0,p4};
li9=newl; Line(li9) = {p1,p5};
li10=newl; Line(li10) = {p2,p6};
li11=newl; Line(li11) = {p3,p7};
// 2.1.4 Define lines of outer cube
// lower xy plane
li100=newl; Line(li100) = {p100,p101};
li101=newl; Line(li101) = {p101,p102};
li102=newl; Line(li102) = {p102,p103};
li103=newl; Line(li103) = {p103,p100};
// upper xy plane
li104=newl; Line(li104) = {p104,p105};
li105=newl; Line(li105) = {p105,p106};
li106=newl; Line(li106) = {p106,p107};
li107=newl; Line(li107) = {p107,p104};
// vertical lines
li108=newl; Line(li108) = {p100,p104};
li109=newl; Line(li109) = {p101,p105};
li110=newl; Line(li110) = {p102,p106};
li111=newl; Line(li111) = {p103,p107};
// 2.1.5 Define line 6 line loops for the 6 faces of outer cube
lloop0= newreg; Line Loop(lloop0) = { li0, li1, li2, li3};
lloop1= newreg; Line Loop(lloop1) = { li4, li5, li6, li7};
lloop2= newreg; Line Loop(lloop2) = { li0, li9, -li4, -li8 };
lloop3= newreg; Line Loop(lloop3) = { li1, li10, -li5, -li9};
lloop4= newreg; Line Loop(lloop4) = { li2, li11, -li6, -li10};
lloop5= newreg; Line Loop(lloop5) = { li3, li8, -li7, -li11};
// 2.1.6 Define line 6 line loops for the 6 faces of inner cube
lloop100= newreg; Line Loop(lloop100) = { li100, li101, li102, li103};
lloop101= newreg; Line Loop(lloop101) = { li104, li105, li106, li107};
lloop102= newreg; Line Loop(lloop102) = { li100, li109, -li104, -li108 };
lloop103= newreg; Line Loop(lloop103) = { li101, li110, -li105, -li109};
lloop104= newreg; Line Loop(lloop104) = { li102, li111, -li106, -li110};
lloop105= newreg; Line Loop(lloop105) = { li103, li108, -li107, -li111};
// 2.1.7 define plane surfaces for outer cube
s0=news; Plane Surface(s0) = {lloop0};
s1=news; Plane Surface(s1) = {lloop1};
s2=news; Plane Surface(s2) = {lloop2};
s3=news; Plane Surface(s3) = {lloop3};
s4=news; Plane Surface(s4) = {lloop4};
s5=news; Plane Surface(s5) = {lloop5};
// 2.1.8 define plane surfaces for inner cube
s100=news; Plane Surface(s100) = {lloop100};
s101=news; Plane Surface(s101) = {lloop101};
s102=news; Plane Surface(s102) = {lloop102};
s103=news; Plane Surface(s103) = {lloop103};
s104=news; Plane Surface(s104) = {lloop104};
s105=news; Plane Surface(s105) = {lloop105};
// 2.1.9 Define surface loops required for volume definition of outer cube
sloop0=newreg; Surface Loop(sloop0) ={s0,s1,s2,s3,s4,s5};
// 2.1.9 Define surface loops required for volume definition of inner cube
sloop100=newreg; Surface Loop(sloop100) ={s100,s101,s102,s103,s104,s105};
// 2.1.10 Define volume of outer cube
v0=newv; Volume(v0) = {sloop0,sloop100};
// 2.1.11 Define volume of inner cube
v100=newv; Volume(v100) = {sloop100};
// 3.0 define physical entitites
Physical Point(vacuum_background_bnd) = {p0,p1,p2,p3,p4,p5,p6,p7};
Physical Line(vacuum_background_bnd) = {li0,li1,li2,li3,li4,li5,li6,li7,li8,li9,li10,li11};
//Physical Line Loop(vacuum_background_bnd) = {lloop0,lloop1,lloop2,lloop3,lloop4,lloop5};
Physical Surface(vacuum_background_bnd) = {s0,s1,s2,s3,s4,s5};
//Physical Surface Loop(vacuum_background_bnd) = {sloop0};
Physical Volume(pml) = {v0};
Physical Point(interelement_bnd) = {p100,p101,p102,p103,p104,p105,p106,p107};
Physical Line(interelement_bnd) = {li100,li101,li102,li103,li104,li105,li106,li107,li108,li109,li110,li111};
//Physical Line Loop(interelement_bnd) = {lloop100,lloop101,lloop102,lloop103,lloop104,lloop105};
Physical Surface(interelement_bnd) = {s100,s101,s102,s103,s104,s105};
//Physical Surface Loop(interelement_bnd) = {sloop100};
Physical Volume(air) = {v100};
H5Fed/grids/cubeincube.msh
-2368
View File
File diff suppressed because it is too large Load Diff
H5Fed/grids/sphere.geo
-135
View File
@@ -1,135 +0,0 @@
// rights - 2002-2005, benedikt oswald,
// project - aq
// file name - sphere.geo
// file type - GMSH script file
// objective - model cube in a cube, 2 spherical objects mesh to investigate sub lambda resolution capability
// modified - 2005 jan 25, benedikt oswald, creation
// modified - 2005 jan 25, benedikt oswald, added background hexahedron, subsurface hexahedron
// modified - 2005 feb 01, benedikt oswald, adapted to the simple.geo problem
// modified - 2005 mar 08, benedikt oswald, adapted to the cube in cube geometry
// modified - 2005 mar 09, benedikt oswald, adapted to cube in cube and spherical particle configuration
// modified - 2005 mar 11, benedikt oswald, adapted to investigation of sub-lambda resolution capability
// modified - 2005 mar 22, benedikt oswald, adapted to be based on reference background medium subLambda310.geo
// modified - 2005 mar 23, benedikt oswald, adapted to model a microresonator geometry
// modified - 2005 mar 29, benedikt oswald, adapted to model a high quality sphere for a Hertzian dipole benchmark
// modified - 2005
// inheritance -
// feature - models a microresonator geometry; a dielectric sphere within an air sphere; the dielectric
// feature - sphere will be excited by a Hertzian dipole in the vicinity of the sphere;
// feature -
// 1 modeling constants
lcair=1.20; // characteristic length in fractions of lambda@1 GHz for air domain
lcsubsurface=1.20; // characteristic length in fractions of lambda@1 GHz for subsurface domain
lcil1=0.80; // characteristic length in fractions of lambda@1 GHz for icelens region
lcil2=0.40; // characteristic length in fractions of lambda@1 GHz for icelens 2 region
lambda=3.0e-1; // wavelength of electromagntic wave at a frequency of 1 GHz
lx=3.0; // x dim of computational domain
ly=3.0; // y dim of computational domain
lz=2.0; // z dim of computational domain
cx=0.5*lx; // calculate center of computational domain
cy=0.5*ly; // calculate center of computational domain
cz=0.5*lz; // calculate center of computational domain
dxl=0.3; // thickness of PML region
dxh=0.3; // thickness of PML region
dyl=0.3; // thickness of PML region
dyh=0.3; // thickness of PML region
dzl=0.30; // thickness of PML region
dzh=0.60; // thickness of PML region
xminic=dxl; // x min of inner cube
xmaxic=lx-dxh; // x max of inner cube
yminic=dyl; // y min of inner cube
ymaxic=ly-dyh; // y max of inner cube
zminic=dzl; // z min of inner cube
zmaxic=lz-dzh; // z max of inner cube
dsx=0.10; // x distance separating the two spherical scatterers
dsy=0.00; // y distance separating the two spherical scatterers
dsz=0.00; // z distance separating the two spherical scatterers
r1=1.0; // radius of air sphere
ilcx=0.0; // x center of air sphere
ilcy=0.0; // y center of
ilcz=0.0; // z center of
r2=2.0e-6; // radius of dielectric sphere
il2cx=0.0; // x center of dielectric sphere
il2cy=0.0; // y center of dielectric sphere
il2cz=0.0; // z center of dielectric sphere
// 1.2 Define physical material domains
vacuum=609; // physical entity vacuum
air=709; // physical entity air
subsurface=809; // physical entity subsurface
pml=1301; // physical entity pml material
icelens1=4001; // physical entity icelens
icelens2=4003; // physical entity icelens 2
dielsphere=4005; // physical entity dielectric sphere
vacuum_background_bnd=12701; // boundary to background, i.e. vacuum
air_soil_bnd=12702; // interior boundary, separating air and subsurface material
soil_icelens1_bnd=12703; // interior boundary, separating background subsurface from icelens particle
soil_icelens2_bnd=12705; // interior boundary, separating background subsurface from icelens 2 particle
dielectric_sphere_bnd=12707; // interior boundary, separting air background from dielectric sphere
// 2.2.1 Define air sphere 1
ilp1 = newp; Point(ilp1) = {ilcx, ilcy, ilcz, lcil1 * lambda} ;
ilp2 = newp; Point(ilp2) = {ilcx+r1, ilcy, ilcz, lcil1 * lambda} ;
ilp3 = newp; Point(ilp3) = {ilcx, ilcy+r1, ilcz, lcil1 * lambda} ;
ilp4 = newp; Point(ilp4) = {ilcx, ilcy, ilcz+r1, lcil1 * lambda} ;
ilp5 = newp; Point(ilp5) = {ilcx-r1, ilcy, ilcz, lcil1 * lambda} ;
ilp6 = newp; Point(ilp6) = {ilcx, ilcy-r1, ilcz, lcil1 * lambda} ;
ilp7 = newp; Point(ilp7) = {ilcx, ilcy, ilcz-r1, lcil1 * lambda} ;
ilc1 = newreg; Circle(ilc1) = {ilp2,ilp1,ilp7};
ilc2 = newreg; Circle(ilc2) = {ilp7,ilp1,ilp5};
ilc3 = newreg; Circle(ilc3) = {ilp5,ilp1,ilp4};
ilc4 = newreg; Circle(ilc4) = {ilp4,ilp1,ilp2};
ilc5 = newreg; Circle(ilc5) = {ilp2,ilp1,ilp3};
ilc6 = newreg; Circle(ilc6) = {ilp3,ilp1,ilp5};
ilc7 = newreg; Circle(ilc7) = {ilp5,ilp1,ilp6};
ilc8 = newreg; Circle(ilc8) = {ilp6,ilp1,ilp2};
ilc9 = newreg; Circle(ilc9) = {ilp7,ilp1,ilp3};
ilc10 = newreg; Circle(ilc10) = {ilp3,ilp1,ilp4};
ilc11 = newreg; Circle(ilc11) = {ilp4,ilp1,ilp6};
ilc12 = newreg; Circle(ilc12) = {ilp6,ilp1,ilp7};
// We need non-plane surfaces to define the spherical icelens:
// here we use ruled surfaces, which can have 3 or 4
// sides:
ill1 = newreg; Line Loop(ill1) = {ilc5,ilc10,ilc4}; ilruls1=newreg; Ruled Surface(ilruls1) = {ill1};
ill2 = newreg; Line Loop(ill2) = {ilc9,-ilc5,ilc1}; ilruls2=newreg; Ruled Surface(ilruls2) = {ill2};
ill3 = newreg; Line Loop(ill3) = {ilc12,-ilc8,-ilc1}; ilruls3=newreg; Ruled Surface(ilruls3) = {ill3};
ill4 = newreg; Line Loop(ill4) = {ilc8,-ilc4,ilc11}; ilruls4=newreg; Ruled Surface(ilruls4) = {ill4};
ill5 = newreg; Line Loop(ill5) = {-ilc10,ilc6,ilc3}; ilruls5=newreg; Ruled Surface(ilruls5) = {ill5};
ill6 = newreg; Line Loop(ill6) = {-ilc11,-ilc3,ilc7}; ilruls6=newreg; Ruled Surface(ilruls6) = {ill6};
ill7 = newreg; Line Loop(ill7) = {-ilc2,-ilc7,-ilc12};ilruls7=newreg; Ruled Surface(ilruls7) = {ill7};
ill8 = newreg; Line Loop(ill8) = {-ilc6,-ilc9,ilc2}; ilruls8=newreg; Ruled Surface(ilruls8) = {ill8};
ilsloop0 = newreg;
Surface Loop(ilsloop0) = {ill8+1,ill5+1,ill1+1,ill2+1,ill3+1,ill7+1,ill6+1,ill4+1};
// 2.3.3 Define volume of air sphere
vil1=newv; Volume(vil1) = {ilsloop0};
// 3.0 define physical entitites
Physical Point(vacuum_background_bnd) = {ilp1,ilp2,ilp3,ilp4,ilp5,ilp6,ilp7};
Physical Surface(vacuum_background_bnd) = {ilruls1,ilruls2,ilruls3,ilruls4,ilruls5,ilruls6,ilruls7,ilruls8};
Physical Volume(air) = {vil1};
H5Fed/grids/sphere.msh
-2887
View File
File diff suppressed because it is too large Load Diff
H5Fed/libsrc/gmsh/gmsh.cc
-375
View File
@@ -1,375 +0,0 @@
// rights - 2006-, copyright patrick leidenberger and benedikt oswald,
// all rights reserved
// project - gmsh2h5fed
// file name - gmsh.cc
// file type - c++ implementation file
// objective - implement class for readind gmsh data files
// modified - 2006 aug 24, creation, patrick leidenberger
// modified - 2006 aug 26, pl, Access to private members.
#include "gmsh.hh"
using namespace boost::spirit;
using namespace gmshtohdf5fed;
using namespace rlog;
using namespace std;
#include <boost/spirit/core.hpp>
#include <boost/spirit/iterator/file_iterator.hpp>
#include <iostream>
#include <sstream>
#include <fstream>
#include <string>
#include <vector>
#include "gmshgrammar.hh"
#include "gmshsemanticaction.hh"
gmsh::gmsh()
{
//rDebug("Enter vtk constructor.");
// Clean the gmsh data structure.
gmshNodes_.clear();
gmshNodesNumber_.clear();
gmshLine_.clear();
gmshLineTag_.clear();
gmshTriangle_.clear();
gmshTriangleTag_.clear();
gmshQuadrangle_.clear();
gmshQuadrangleTag_.clear();
gmshTetrahedron_.clear();
gmshTetrahedronTag_.clear();
gmshHexahedron_.clear();
gmshHexahedronTag_.clear();
gmshPrism_.clear();
gmshPrismTag_.clear();
gmshPyramid_.clear();
gmshPyramidTag_.clear();
gmsh2ndLineTag_.clear();
gmsh2ndTriangle_.clear();
gmsh2ndTriangleTag_.clear();
gmsh2ndQuadrangle_.clear();
gmsh2ndQuadrangleTag_.clear();
gmsh2ndTetrahedron_.clear();
gmsh2ndTetrahedronTag_.clear();
gmsh2ndHexahedron_.clear();
gmsh2ndHexahedronTag_.clear();
gmsh2ndPrism_.clear();
gmsh2ndPrismTag_.clear();
gmsh2ndPyramid_.clear();
gmsh2ndPyramidTag_.clear();
gmshPoint_.clear();
gmshPointTag_.clear();
//rDebug("Leafe vtk constructor.");
}
gmsh::~gmsh()
{
//rDebug("Enter vtk destructor.");
//rDebug("Leafe vtk destructor.");
}
int gmsh::gmshFileName(char* fileName)
{
//rDebug("Enter fileName.");
// Erase the fileName_.
fileName_.erase();
// Copy fileName in private string fileName_.
gmshCpString(fileName, &fileName_);
// rDebug("fileName_= %s",fileName_.c_str());
//rDebug("Leafe fileName");
return OKCODE;
}
int gmsh::gmshFileName(string fileName)
{
//rDebug("Enter fileName.");
// Erase the fileName_.
fileName_.erase();
// Copy fileName in private string fileName_.
fileName_ = fileName;
// rDebug("fileName_= %s",fileName_.c_str());
//rDebug("Leafe fileName");
}
int gmsh::gmshOpen(void)
{
//rDebug("Enter openVtk.");
// Open a stream to read the gmsh file in a string.
ifstream inFile (fileName_.c_str());
// Check if file was opened corretly.
if (! inFile)
{
rError("Cannot open file %s.", fileName_.c_str());
return ERRORCODE;
}
else
{
rInfo("Open file %s", fileName_.c_str());
// Read file content into a string
fileContent.erase();
char chr;
while (inFile.get(chr))
{
fileContent.append(1,chr);
}
rInfo(" File has been read.");
//rDebug("Input file:\n%s",fileContent.c_str());
// Close input file.
inFile.close();
rInfo(" File Closed.");
return OKCODE;
}
//rDebug("Leave openVtk.");
}
int gmsh::gmshParseFile(gmsh* gmshSelf)
{
//rDebug("Enter parseFile.");
// Provide an instance of the grammar describing the gmsh file format.
stack<long> gmshStack;
// Our vtk parser.
// Give the parser a pointer to the instance of the gmsh class. So we can
// call member functions as semantic action.
gmsh_g gmsh_p(gmshSelf);
// Call the parser.
parse_info <iterator_t> info = parse(fileContent.c_str(),gmsh_p,space_p);
// Feedback to user on parsing outcome.
if (info.full)
{
rInfo("-------------------------");
rInfo("parsing succeeded :-)");
rInfo("-------------------------");
return OKCODE;
}
else
{
ostringstream temp;
temp << info.stop ;
rError("-------------------------");
rError("parsing failed :-(");
rError("stopped at line: %s", temp.str().c_str());
rError("-------------------------");
return ERRORCODE;
}
//rDebug("Leave parseFile.");
}
int gmsh::gmshPushNode(vector<double>* nodeCoords)
{
//rDebug("gmshPushNode(vector<double>* nodeCoords).");
gmshNodes_.push_back(*nodeCoords);
return OKCODE;
}
int gmsh::gmshPushNodeNumber(unsigned int* nodeNumber)
{
gmshNodesNumber_.push_back(*nodeNumber);
return OKCODE;
}
int gmsh::gmshPushElem(unsigned short int elemType,
vector<unsigned int>* nodeVector)
{
//rDebug("Inside gmshPushElem.");
if (elemType == GMSH_LINE)
gmshLine_.push_back(*nodeVector);
else if (elemType == GMSH_TRIANGLE)
gmshTriangle_.push_back(*nodeVector);
else if (elemType == GMSH_QUADRANGLE)
gmshQuadrangle_.push_back(*nodeVector);
else if (elemType == GMSH_TETRAHEDRON)
gmshTetrahedron_.push_back(*nodeVector);
else if (elemType == GMSH_HEXAHEDRON)
gmshHexahedron_.push_back(*nodeVector);
else if (elemType == GMSH_PRISM)
gmshPrism_.push_back(*nodeVector);
else if (elemType == GMSH_PYRAMID)
gmshPyramid_.push_back(*nodeVector);
else if (elemType == GMSH_2ND_LINE)
gmsh2ndLine_.push_back(*nodeVector);
else if (elemType == GMSH_2ND_TRIANGLE)
gmsh2ndTriangle_.push_back(*nodeVector);
else if (elemType == GMSH_2ND_QUADRANGLE)
gmsh2ndQuadrangle_.push_back(*nodeVector);
else if (elemType == GMSH_2ND_TETRAHEDRON)
gmsh2ndTetrahedron_.push_back(*nodeVector);
else if (elemType == GMSH_2ND_HEXAHEDRON)
gmsh2ndHexahedron_.push_back(*nodeVector);
else if (elemType == GMSH_2ND_PRISM)
gmsh2ndPrism_.push_back(*nodeVector);
else if (elemType == GMSH_2ND_PYRAMID)
gmsh2ndPyramid_.push_back(*nodeVector);
else if (elemType == GMSH_POINT)
gmshPoint_.push_back(*nodeVector);
else
{
rError("A unknown element type found!");
rError("Element type: %d", elemType);
}
return OKCODE;
}
int gmsh::gmshPushTag(unsigned short int elemType,
vector<unsigned int>* tagVector)
{
//rDebug("Inside gmshPushElem.");
if (elemType == GMSH_LINE)
{
//rDebug(" Line pushedback");
}
else if (elemType == GMSH_TRIANGLE)
{
//rDebug(" Triangle pushedback");
}
else if (elemType == GMSH_QUADRANGLE)
{
//rDebug(" Quadrangle pushedback");
}
else if (elemType == GMSH_TETRAHEDRON)
{
//rDebug(" Tetrahedron pushedback");
gmshTetrahedronTag_.push_back(*tagVector);
}
else
{
}
return OKCODE;
}
int gmsh::gmshShowElemResult()
{
rInfo("Elements found in gmsh file:");
rInfo(" lines: %d",gmshLine_.size());
rInfo(" triangles: %d",gmshTriangle_.size());
rInfo(" quadrangles: %d",gmshQuadrangle_.size());
rInfo(" tetrahedrons: %d",gmshTetrahedron_.size());
rInfo(" hexahedrons: %d",gmshHexahedron_.size());
rInfo(" prisms: %d",gmshPrism_.size());
rInfo(" pyramids: %d",gmshPyramid_.size());
rInfo(" 2nd order lines: %d",gmsh2ndLine_.size());
rInfo(" 2nd order Triangles: %d",gmsh2ndTriangle_.size());
rInfo(" 2nd order Quadrangles: %d",gmsh2ndQuadrangle_.size());
rInfo(" 2nd order Tetrahedrons: %d",gmsh2ndTetrahedron_.size());
rInfo(" 2nd order Hexahedrons: %d",gmsh2ndHexahedron_.size());
rInfo(" 2nd order Prisms: %d",gmsh2ndPrism_.size());
rInfo(" 2nd order Pyramids: %d",gmsh2ndPyramid_.size());
rInfo(" Points : %d",gmshPoint_.size());
return OKCODE;
}
void gmsh::cpString(char const* first,
char const* last,
string* str)
{
//rDebug("Enter cpString.");
// Erase the str content.
str->erase();
// Copy version in str.
for(unsigned int i = 0; i<strlen(first)-strlen(last); i++)
{
str->append(1,first[i]);
}
//rDebug("*str= %s",str->c_str());
//rDebug("Leafe cpString.");
}
string gmsh::cpString(char const* first,
char const* last)
{
//rDebug("Enter cpString.");
// Create and erase a tempral string;
string tempString;
tempString.erase();
// Copy version in str.
for(unsigned int i = 0; i<strlen(first)-strlen(last); i++)
{
tempString.append(1,first[i]);
}
//rDebug("tempString= %s",tempString.c_str());
//rDebug("Leafe cpString.");
return tempString;
}
int gmsh::gmshCpString(char const* first,
string*str)
{
// Create and erase a tempral string;
std::string tempString;
tempString.erase();
// Copy the character sign for sign into the string.
for(unsigned int i = 0; i<strlen(first); i++)
{
tempString.append(1,first[i]);
}
//rDebug("tempString= %s",tempString.c_str());
//rDebug("Leafe cpString.");
return OKCODE;
}
int gmsh::gmshCheckVersion(int* version)
{
if ((int)(*version) == 2)
{
rInfo("Gmsh file has format 2.");
return OKCODE;
}
else
{
rError("Gmsh file has format: %d.", (int)(*version));
rError("But this program can only read format 2.");
rError("Exit");
exit(ERRORCODE);
}
}
int gmsh::gmshCheckFileType(int* fileType)
{
if ((int)(*fileType) == 0)
{
rInfo("Gmsh file has ascii format.");
return OKCODE;
}
else
{
rError("Gmsh file has format: %d.", (int)(*fileType));
rError("But this program can only read format 0 (ascii).");
rError("Exit");
exit(ERRORCODE);
}
}
std::vector< std::vector <double> > gmsh::gmshNode()
{
return gmshNodes_;
}
std::vector<unsigned int> gmsh::gmshNodeNumber()
{
return gmshNodesNumber_;
}
std::vector< std::vector<unsigned int> > gmsh::gmshTetrahedron()
{
return gmshTetrahedron_;
}
std::vector< std::vector<unsigned int> > gmsh::gmshTetrahedronTag()
{
return gmshTetrahedronTag_;
}
H5Fed/libsrc/gmsh/gmsh.hh
-142
View File
@@ -1,142 +0,0 @@
// rights - 2006-, copyright patrick leidenberger and benedikt oswald,
// all rights reserved
// project - gmsh2h5fed
// file name - gmsh.hh
// file type - c++ header file
// objective - declare class for readind gmsh mesh files v2.0
//
// modified - 2006 aug 21, creation, Patrick Leidenberger
// modified - 2006 aug 22, pl.
// modified - 2006 aug 23, pl.
// modified - 2006 aug 24, pl, delete old things.
// modified - 2006 aug 26, pl, Access to private members.
#ifndef GMSH_HH_
#define GMSH_HH_
#include <iostream>
#include <string>
#include <vector>
#include <boost/spirit/core.hpp>
#include <boost/spirit/iterator/file_iterator.hpp>
#include <boost/spirit/core.hpp>
/* Include the files for rlog. */
#include <rlog/rlog.h>
#include <rlog/rloglocation.h>
#include <rlog/Error.h>
#include <rlog/RLogChannel.h>
#include <rlog/StdioNode.h>
#include <rlog/RLogTime.h>
#include <nonsciconst.h>
// Include gmsh specific constants.
#include "gmshconst.hh"
using namespace std;
using namespace nonsciconst;
namespace gmshtohdf5fed
{
class gmsh
{
public:
// Constructor: Here we clear all private data vectors.
gmsh();
// Destructor.
~gmsh();
int gmshFileName(char* fileName);
int gmshFileName(string fileName);
int gmshOpen(void);
int gmshParseFile(gmsh* vtkSelf);
void cpString(char const* first,
char const* last,
string* str);
string cpString(char const* first,
char const* last);
int gmshCpString(char const* first,
string*str);
// Check if gmsh file is of version 2.
int gmshCheckVersion(int* version);
// Check if the gmsh file is in ascii format.
int gmshCheckFileType(int* fileType);
// Pushes the three coordinates of a node in the gmshNodes_ vector.
int gmshPushNode(vector<double>* nodeCoords);
// Pushes the number of a node in the gmshNodesNumber_ vector.
int gmshPushNodeNumber(unsigned int * nodeNumber);
// Push the node vector nodeVector to the appropriate data structure
// denoted by the string.
int gmshPushElem(unsigned short int elemType,
vector<unsigned int>* nodeVector);
// Push the tag vector tagVector to the appropriate data structure
// denoted by the string.
int gmshPushTag(unsigned short int elemType,
vector<unsigned int>* tagVector);
// Show the size of the element vectors.
int gmshShowElemResult();
//-------------------------------------//
// Access to private stored gmsh data. //
//-------------------------------------//
std::vector< std::vector <double> > gmshNode();
std::vector<unsigned int> gmshNodeNumber();
std::vector< std::vector<unsigned int> > gmshTetrahedron();
std::vector< std::vector<unsigned int> > gmshTetrahedronTag();
private:
string fileName_;
string fileContent;
// Data structure for node coordinates from gmsh file.
vector<vector<double> > gmshNodes_;
// Data structure for gmsh node number.
// A number belongs to the respective node coordinate in the gmshNodes_
// vector.
vector<unsigned int> gmshNodesNumber_;
// Data structure for the topological entities and their tags stored in
// the gmsh file. The 'gmsh2nd..' denote second order Elements.
vector<vector<unsigned int> > gmshLine_;
vector<vector<unsigned int> > gmshLineTag_;
vector<vector<unsigned int> > gmshTriangle_;
vector<vector<unsigned int> > gmshTriangleTag_;
vector<vector<unsigned int> > gmshQuadrangle_;
vector<vector<unsigned int> > gmshQuadrangleTag_;
vector<vector<unsigned int> > gmshTetrahedron_;
vector<vector<unsigned int> > gmshTetrahedronTag_;
vector<vector<unsigned int> > gmshHexahedron_;
vector<vector<unsigned int> > gmshHexahedronTag_;
vector<vector<unsigned int> > gmshPrism_;
vector<vector<unsigned int> > gmshPrismTag_;
vector<vector<unsigned int> > gmshPyramid_;
vector<vector<unsigned int> > gmshPyramidTag_;
vector<vector<unsigned int> > gmsh2ndLine_;
vector<vector<unsigned int> > gmsh2ndLineTag_;
vector<vector<unsigned int> > gmsh2ndTriangle_;
vector<vector<unsigned int> > gmsh2ndTriangleTag_;
vector<vector<unsigned int> > gmsh2ndQuadrangle_;
vector<vector<unsigned int> > gmsh2ndQuadrangleTag_;
vector<vector<unsigned int> > gmsh2ndTetrahedron_;
vector<vector<unsigned int> > gmsh2ndTetrahedronTag_;
vector<vector<unsigned int> > gmsh2ndHexahedron_;
vector<vector<unsigned int> > gmsh2ndHexahedronTag_;
vector<vector<unsigned int> > gmsh2ndPrism_;
vector<vector<unsigned int> > gmsh2ndPrismTag_;
vector<vector<unsigned int> > gmsh2ndPyramid_;
vector<vector<unsigned int> > gmsh2ndPyramidTag_;
vector<vector<unsigned int> > gmshPoint_;
vector<vector<unsigned int> > gmshPointTag_;
};
}
#endif //GMSH_HH_
H5Fed/libsrc/gmsh/gmshconst.hh
-28
View File
@@ -1,28 +0,0 @@
#ifndef GMSHCONST_HH_
#define GMSHCONST_HH_
// Contants of gmsh element types.
// See Gmsh Reference Manual (14 May 2006) page 147-148.
const unsigned short int GMSH_LINE = 1;
const unsigned short int GMSH_TRIANGLE = 2;
const unsigned short int GMSH_QUADRANGLE = 3;
const unsigned short int GMSH_TETRAHEDRON = 4;
const unsigned short int GMSH_HEXAHEDRON = 5;
const unsigned short int GMSH_PRISM = 6;
const unsigned short int GMSH_PYRAMID = 7;
const unsigned short int GMSH_2ND_LINE = 8;
const unsigned short int GMSH_2ND_TRIANGLE = 9;
const unsigned short int GMSH_2ND_QUADRANGLE = 10;
const unsigned short int GMSH_2ND_TETRAHEDRON = 11;
const unsigned short int GMSH_2ND_HEXAHEDRON = 12;
const unsigned short int GMSH_2ND_PRISM = 13;
const unsigned short int GMSH_2ND_PYRAMID = 14;
const unsigned short int GMSH_POINT = 15;
// Every element has an spesific number of tags.
// This is the list of the number. There is a leading zero, because there is
// no element with the index 0.
const unsigned short int GMSH_ELEM_N_NODES[] = { 0, 2, 3, 4, 4, 8, 6, 5, 3,
6, 9, 10, 27, 18, 14, 1 };
#endif //GMSHCONST_HH_
H5Fed/libsrc/gmsh/gmshgrammar.hh
-242
View File
@@ -1,242 +0,0 @@
/** \brief Definition of gmsh file format v2.0 parser data types and variables
*
* rights - patrick leidenberger and benedikt oswald
* file name - gmshgrammar.hh
* file type - include file
* objective - define grammar of gmsh file format v2.0
* author - patrick leidenberger and benedikt oswald
* modified - 2006 jun 29, pl, creation
* features - defines grammar of gmsh files v2.0
*/
/* include standard header files */
#include <boost/spirit/core.hpp>
#include <boost/spirit/iterator/file_iterator.hpp>
#include <boost/spirit/actor/assign_actor.hpp>
#include <boost/spirit/utility/functor_parser.hpp>
#include <boost/spirit/utility/escape_char.hpp>
#include <boost/spirit/utility/loops.hpp>
#include <boost/spirit/dynamic/if.hpp>
#include <iostream>
#include <functional>
#include <map>
#include <stack>
#include <string>
#include <boost/bind.hpp>
#include <boost/ref.hpp>
/* include proprietary header files */
#include "gmshsemanticaction.hh"
#include "gmsh.hh"
// Include gmsh specific constants.
#include "gmshconst.hh"
#ifndef GMSHGRAMMAR_HH_
#define GMSHGRAMMAR_HH_
/* activate namespaces */
using namespace std;
using namespace boost::spirit;
using namespace gmshtohdf5fed;
/* type definitions */
//typedef char char_t;
//typedef file_iterator<char_t> iterator_t;
//typedef scanner<iterator_t> scanner_t;
//typedef rule<scanner_t> rule_t;
////////////////////////////////////////////////////////////////////////////
//
// Our calculator grammar
//
////////////////////////////////////////////////////////////////////////////
struct gmsh_g : public grammar<gmsh_g>
{
// vtk_g(/*stack<long>& eval_*/)
// /*: eval(eval_)*/ {}
gmsh_g(gmsh* gmshSelf)
: gmshSelf_(gmshSelf)
{
}
template <typename ScannerT>
struct definition
{
definition(gmsh_g const& self)
{
gmsh_import_r = gmsh_mesh_format_r
>> gmsh_nodes_r
>> gmsh_elements_r;
//////////////////////////////////////////////////////////////////////////
// GENERAL NOTE: All tranport of numbers to gmshsemanticaction.hh must //
// be done by reference, not by value. Transport by //
// value fails! You have to debug long for it! //
/////////////////////////////////////////////////////////////////////////
// Rules for the MeshFormat section.
gmsh_mesh_format_r = str_p("$MeshFormat")
>> int_p[assign_a(tempInt1_)]
[gmsh_version_a(self.gmshSelf_, &tempInt1_)]
>> int_p[assign_a(tempInt1_)]
[gmsh_file_type_a(self.gmshSelf_, &tempInt1_)]
>> int_p[assign_a(tempInt1_)]
>> str_p("$EndMeshFormat");
// Rules for the Nodes section.
gmsh_nodes_r = str_p("$Nodes")
>> eps_p[gmsh_clear_map_a<unsigned int,
vector<double> >(&tempCoordMap_)]
>> int_p[assign_a(tempUnInt1_)]
>> eps_p[gmsh_info_msg_a("Nodes in gmsh file: ",
&tempUnInt1_)]
>> repeat_p(boost::ref(tempUnInt1_))
[
eps_p[gmsh_clear_vec_a<double>(&tempVecDouble1_)]
>> int_p[assign_a(tempUnInt2_)]
>> repeat_p(3)
[real_p[assign_a(tempDouble1_)]
[gmsh_push_vec_a<double>(&tempVecDouble1_,
&tempDouble1_)]
]
[gmsh_insert_map_a<unsigned int,
vector<double> >
(&tempCoordMap_, &tempUnInt2_,
&tempVecDouble1_)
]
]
>> str_p("$EndNodes")
>> eps_p[gmsh_transport_nodes_a(self.gmshSelf_,
&tempCoordMap_)];
// Rules for the Elements section.
gmsh_elements_r = str_p("$Elements")
>> int_p[assign_a(tempUnInt1_)]
>> eps_p[gmsh_info_msg_a("Elements in gmsh file: ",
&tempUnInt1_)]
>> gmsh_element_r
>> str_p("$EndElements");
gmsh_element_r = repeat_p(boost::ref(tempUnInt1_))
[ // Parse one element
// Clear the vectors for nodes and tags of an elem.
eps_p[gmsh_clear_vec_a<unsigned int>
(&tempElemNode_)]
>> eps_p[gmsh_clear_vec_a<unsigned int>
(&tempElemTag_)]
// Parse the element number. We don't need it.
>> int_p[assign_a(tempUnInt2_)]
// Parse the element type.
>> int_p[assign_a(tempUnShortInt1_)]
// Parse the number of tags.
>> int_p[assign_a(tempUnInt3_)]
// Parse the tags.
>> repeat_p(boost::ref(tempUnInt3_))
[
// Parse a single tag.
int_p[assign_a(tempUnInt4_)]
// Copy to vector.
>> eps_p[gmsh_push_vec_a<unsigned int>
(&tempElemTag_, &tempUnInt4_)]
][gmsh_nothing_a()]
// Copy the number of nodes of the actual element
// type (in tempUnShortInt1_) from the
// GMSH_ELEM_N_NODES array in gmshconst.hh in
// tempUnShortInt2_.
// Do this, because I don't get the direct array
// access not work.
>> eps_p[gmsh_array_access_a<unsigned short int>
(&tempUnShortInt2_, &tempUnShortInt1_)]
// Parse the respective number of nodes.
>> repeat_p(boost::ref(tempUnShortInt2_))
[
// Parse a sigle node.
int_p[assign_a(tempUnInt4_)]
// Copy to vector.
>> eps_p[gmsh_push_vec_a<unsigned int>
(&tempElemNode_, &tempUnInt4_)]
]
[
// Transport the parsed element nodes in the
// respective gmsh.hh data structure.
gmsh_transport_elem_a(self.gmshSelf_,
&tempUnShortInt1_, &tempElemNode_)
]
[
// Transport the parsed element tags in the
// respective gmsh.hh data structure.
gmsh_transport_tag_a(self.gmshSelf_,
&tempUnShortInt1_, &tempElemTag_)
]
// This short section demonstrates, like con-
// ditional parsing can be used instead:
//
//>> if_p(gmsh_compare_a<unsigned short int>
// (&tempUnShortInt1_,&(elemType_[0])))
// [
// // Element type 1 == line.
// repeat_p(2)
// [
// int_p[assign_a(tempUnInt4_)]
// ][gmsh_nothing_a()]
// ]
//
]
[
// All elements are parsed.
// Show what we have paresd.
gmsh_show_elem_result_a(self.gmshSelf_)
];
}
rule<ScannerT> expression, term, factor, integer;
rule<ScannerT> vtk_import_r;
rule<ScannerT> gmsh_import_r;
rule<ScannerT> gmsh_mesh_format_r;
rule<ScannerT> gmsh_nodes_r;
rule<ScannerT> gmsh_elements_r;
rule<ScannerT> gmsh_element_r;
rule<ScannerT> const&
start() const { return gmsh_import_r; }
// These are temporal variables used during the parsing process.
// These variables are used at different places for different things,
// they are only valid in small ranges.
int tempInt1_;
unsigned int tempUnInt1_;
unsigned int tempUnInt2_;
unsigned int tempUnInt3_;
unsigned int tempUnInt4_;
unsigned short int tempUnShortInt1_;
unsigned short int tempUnShortInt2_;
double tempDouble1_;
vector<int> tempIntVec1_;
vector<double> tempDoubleVec1_;
vector<vector<double> > tempDoubleVec2_;
vector<double> tempVecDouble1_;
// Data structure for node coordinates.
// The gmsh node coordinates are not stored and numbered consecutive. So we
// have to sort and map them to a consecutive index set using this map.
map<unsigned int, vector<double> > tempCoordMap_;
// Data structure to store the nodes of an element.
vector<unsigned int> tempElemNode_;
// Data structure to store an elements tags.
vector<unsigned int> tempElemTag_;
};
gmsh* gmshSelf_;
};
#endif // GMSHGRAMMAR_HH_
H5Fed/libsrc/gmsh/gmshsemanticaction.hh
-344
View File
@@ -1,344 +0,0 @@
// rights - 2006-, copyright benedikt oswald and patrick leidenberger,
// all rights reserved
/** \brief Definition of VTK ASCII file format parser
* project - phidias3d
* file name - vtksemanticaction.h
* file type - c++ include file
* objective - declare semantic action for the vtk file parser
* modified - 2006 jul 03, creation, pl
* modified - 2006 jul 05, insert fuctionality of calling member functions
* of the vtk class, pl
* modified - 2006 jul 06, Add actions for vtk file header and file format.
* modified - 2006 jul 11, Add a lot of action to store the unstructured
* grid dataset. This section is complete.
* modified - 2006 jul 13, Make the action work well: it is not a good idea
* to transport pointers or strings! Use pointers of
* characters.
* modified - 2006 aug 27, Correct error in pushNode function, pl.
**/
/* include standard header files */
#include <boost/spirit/core.hpp>
#include <boost/spirit/iterator/file_iterator.hpp>
#include <iostream>
//#include <iterator>
#include <string>
#include <vector>
#include <map>
#include <functional>
#include <stack>
#include "gmsh.hh"
/* include proprietary header files */
//#include "ansyscnx.h"
/* activate namespaces */
using namespace std;
using namespace boost;
using namespace boost::spirit;
//using namespace phidias3d;
using namespace gmshtohdf5fed;
/* type definitions */
typedef char char_t;
typedef file_iterator<char_t> iterator_t;
typedef scanner<iterator_t> scanner_t;
typedef rule<scanner_t> rule_t;
#ifndef GMSHSEMANTICACTION_HH_
#define GMSHSEMANTICACTION_HH_
/* semantic actions */
// Call version-check of gmsh file.
struct gmsh_version_a
{
gmsh_version_a(gmsh* gmshSelf, int* tempInt)
: gmshSelf_(gmshSelf), tempInt_(tempInt) {}
void operator()(int value) const
{
//rDebug("Inside gmsh_version_a.");
gmshSelf_->gmshCheckVersion(tempInt_);
};
gmsh* gmshSelf_;
int* tempInt_;
};
struct gmsh_file_type_a
{
gmsh_file_type_a(gmsh* gmshSelf, int* tempInt)
: gmshSelf_(gmshSelf), tempInt_(tempInt) {}
void operator()(int value) const
{
//rDebug("Inside gmsh_version_a.");
gmshSelf_->gmshCheckFileType(tempInt_);
};
gmsh* gmshSelf_;
int* tempInt_;
};
template<typename Type>
struct gmsh_clear_vec_a
{
gmsh_clear_vec_a(vector<Type>* vect)
: vect_(vect) {}
void operator()(char const* first, char const* last)
const
{
//rDebug("Clear temporal vector.");
(*vect_).clear();
};
vector<Type>* vect_;
};
template<typename type>
struct gmsh_resize_vec_a
{
gmsh_resize_vec_a(vector<type>* vec, unsigned int size)
: vec_(vec), size_(size) {}
void operator() (char const* first,char const* last)
const
{
//rDebug("Inside gmsh_resize_vec_a.");
(*vec_).resize(size_);
};
void operator() (const int tempInt)
const
{
//rDebug("Inside gmsh_resize_vec_a.");
(*vec_).resize(size_);
};
unsigned int size_;
vector<type> * vec_;
};
template<typename type>
struct gmsh_insert_vec_a
{
gmsh_insert_vec_a(vector<type>* vec, unsigned int const position,
type* value)
: vec_(vec), position_(position), value_(value) {}
void operator() (char const* first,char const* last)
const
{
(*vec_)[position_]=*value_;
}
vector<type> * vec_;
unsigned int position_;
type* value_;
};
template<typename type>
struct gmsh_push_vec_a
{
gmsh_push_vec_a(vector<type>* vec, type* value)
: vec_(vec), value_(value){}
void operator() (char const* first,char const* last)
const
{
//rDebug(" Push value to vector.");
(*vec_).push_back(*value_);
};
void operator() (const double tempDouble)
const
{
//rDebug(" Push value to vector.");
(*vec_).push_back(*value_);
};
type* value_;
vector<type> * vec_;
};
template<typename type1, typename type2>
struct gmsh_insert_map_a
{
gmsh_insert_map_a(map<type1, type2>* tempMap, type1* key,
type2* value)
: map_(tempMap), key_(key), value_(value) {}
void operator() (char const* first,char const* last)
const
{
(*map_)[(*key_)]=*value_;
};
map<type1, type2> * map_;
type1* key_;
type2* value_;
};
template<typename type1, typename type2>
struct gmsh_clear_map_a
{
gmsh_clear_map_a(map<type1, type2>* tempMap)
: map_(tempMap) {}
void operator() (char const* first,char const* last)
const
{
(*map_).clear();
};
map<type1, type2> * map_;
};
struct gmsh_transport_nodes_a
{
gmsh_transport_nodes_a(gmsh* gmshSelf,
map<unsigned int, vector<double> >* tempMap)
: gmshSelf_(gmshSelf), map_(tempMap) {}
void operator() (char const* first,char const* last)
const
{
//rDebug("Copy nodes in data structure.");
for (map<unsigned int, vector<double> >::iterator
iter = (*map_).begin(); iter != (*map_).end(); iter++)
{
vector<double>* temp;
unsigned int tempNumber;
temp = &((*iter).second);
tempNumber = ((*iter).first);
gmshSelf_->gmshPushNode(temp);
gmshSelf_->gmshPushNodeNumber(&tempNumber);
//rDebug("%f %f %f", (*temp)[0], (*temp)[1], (*temp)[2]);
}
};
map<unsigned int, vector<double> >* map_;
gmsh* gmshSelf_;
};
struct gmsh_transport_elem_a
{
gmsh_transport_elem_a(gmsh* gmshSelf, unsigned short int* elemType,
vector <unsigned int>* tempElemNode)
: gmshSelf_(gmshSelf), elemType_(elemType), tempElemNode_(tempElemNode) {}
void operator() (char const* first,char const* last)
const
{
//rDebug("Copy element type %d in data structure.", *elemType_);
gmshSelf_->gmshPushElem(*elemType_, tempElemNode_);
};
gmsh* gmshSelf_;
unsigned short int* elemType_;
vector <unsigned int>* tempElemNode_;
};
struct gmsh_transport_tag_a
{
gmsh_transport_tag_a(gmsh* gmshSelf, unsigned short int* elemType,
vector <unsigned int>* tempElemTag)
: gmshSelf_(gmshSelf), elemType_(elemType), tempElemTag_(tempElemTag) {}
void operator() (char const* first,char const* last)
const
{
//rDebug("Copy element tag list in data structure.");
gmshSelf_->gmshPushTag(*elemType_, tempElemTag_);
};
gmsh* gmshSelf_;
unsigned short int* elemType_;
vector <unsigned int>* tempElemTag_;
};
// Print actions.
struct gmshEMsg_a
{
gmshEMsg_a(string gmshEMsg, unsigned int* tempUnLongInt)
: gmshEMsg_(gmshEMsg), tempUnLongInt_(tempUnLongInt) {}
void operator()(char const* first, char const* last)
const
{
rError("%s %d",gmshEMsg_.c_str(),(*tempUnLongInt_));
};
string gmshEMsg_;
unsigned int* tempUnLongInt_;
};
struct gmsh_info_msg_a
{
gmsh_info_msg_a(string gmsh_info_msg)
: gmsh_info_msg_(gmsh_info_msg), tempUnLongInt_(NULL), tempUnShortInt_(NULL) {}
gmsh_info_msg_a(string gmsh_info_msg, unsigned int* tempUnLongInt)
: gmsh_info_msg_(gmsh_info_msg), tempUnLongInt_(tempUnLongInt), tempUnShortInt_(NULL) {}
gmsh_info_msg_a(string gmsh_info_msg, unsigned short int* tempUnShortInt)
: gmsh_info_msg_(gmsh_info_msg), tempUnLongInt_(NULL), tempUnShortInt_(tempUnShortInt) {}
void operator()(char const* first, char const* last)
const
{
if ((tempUnLongInt_ == NULL) && (tempUnShortInt_ == NULL))
rInfo("%s",gmsh_info_msg_.c_str());
else if ((tempUnLongInt_ != NULL) && (tempUnShortInt_ == NULL))
rInfo("%s%d",gmsh_info_msg_.c_str(),(*tempUnLongInt_));
else if ((tempUnLongInt_ == NULL) && (tempUnShortInt_ != NULL))
rInfo("%s%d",gmsh_info_msg_.c_str(),(*tempUnShortInt_));
};
string gmsh_info_msg_;
unsigned int* tempUnLongInt_;
unsigned short int* tempUnShortInt_;
};
struct gmsh_nothing_a
{
gmsh_nothing_a()
{}
void operator()(char const* first, char const* last)
const
{
};
};
template<typename type>
struct gmsh_compare_a
{
gmsh_compare_a(type* a, type* b)
: a_(a), b_(b) {}
bool operator () () const
{
if (*a_ == *b_)
{
//rDebug("Return TRUE! a = %d b = %d", *a_, *b_);
return true;
}
else
{
//rDebug("Return FALSE! a = %d b = %d", *a_, *b_);
return false;
}
};
type* a_;
type* b_;
};
template<typename type>
struct gmsh_array_access_a
{
gmsh_array_access_a(type* a, type* b)
: a_(a), b_(b) {}
void operator()(char const* first, char const* last) const
{
*a_ = GMSH_ELEM_N_NODES[*b_];
};
type* a_;
type* b_;
};
struct gmsh_show_elem_result_a
{
gmsh_show_elem_result_a(gmsh* gmshSelf)
: gmshSelf_(gmshSelf) {}
void operator()(char const* first, char const* last)
const
{
gmshSelf_->gmshShowElemResult();
};
gmsh* gmshSelf_;
};
#endif // GMSHSEMANTICACTION_HH_
H5Fed/libsrc/gmsh/makefile.am
-18
View File
@@ -1,18 +0,0 @@
## Makefile.am -- process this file with automake to produce Makefile.in
##
## authors - benedikt oswald and patrick leidenberger
## modified - 2006 aug 21, patrick leidenberger, creation
## modified - 2006 aug 23, pl, adaped to new directory structure.
#
## objective - automake input file for the gmsh directory
## project - gmshtohdf5fed
noinst_LTLIBRARIES = libgmsh.la
gmshdir = $(topleveldir)/libsrc/gmsh
gmsh_HEADERS = gmsh.hh
libgmsh_la_SOURCES = gmsh.cc \
gmsh.hh \
gmshconst.hh \
gmshgrammer.hh \
gmshsemanticaction.hh
AM_CPPFLAGS = @AM_CPPFLAGS@
H5Fed/libsrc/h5fed/h5fed.cc
-37
View File
@@ -1,37 +0,0 @@
// rights - 2006-, copyright benedikt, all rights reserved
// project - phidias3d
// file name - hdf5em.h
// file type - c++ implementation file
// objective - implement class for HDF5/ELECTROMAGNETIC file format access
// modified - 2006 jun 26, creation, benedikt oswald
// modified - 2006
// inheritance -
// feature - implements the base class for HDF5/ELECTROMAGNETIC file format access.
// feature -
// required software -
/* include standard header files */
//#include <h5.h>
/* include proprietary files */
#include "h5fed.hh"
#ifdef HAVE_HDF5
namespace hdf5em
{
//
// hdf5em::hdf5em()
// {
// ;
// }
//
// hdf5em::~hdf5em()
// {
// ;
// }
//
}
#endif // HAVE_HDF5
H5Fed/libsrc/h5fed/h5fed.hh
-658
View File
@@ -1,658 +0,0 @@
// rights - 2006-, copyright benedikt, all rights reserved
// project - phidias3d
// file name - hdf5em.h
// file type - c++ header file
// objective - declare class for HDF5/ELECTROMAGNETIC file format access
// modified - 2006 jun 26, creation, benedikt oswald
// modified - 2006 aug 26, pl, integrate automatic index mapping.
// inheritance -
// feature - declares the base class for HDF5/ELECTROMAGNETIC file format access;
// feature - this class is completely self contained, i.e. it does not need anything
// feature - external, except the STL and the HDF5 header files and the corresponding
// feature - library.
// required software -
#ifndef H5FED_HH_
#define H5FED_HH_
#ifdef HAVE_HDF5
/* include standard header files */
#include <cmath>
#include <iostream>
#include <complex>
#include <string>
#include <vector>
// Include the files for rlog.
#include <rlog/rlog.h>
#include <rlog/rloglocation.h>
#include <rlog/Error.h>
#include <rlog/RLogChannel.h>
#include <rlog/StdioNode.h>
#include <rlog/RLogTime.h>
// Include HDF5 headers.
#include <hdf5.h>
// Include h5fed specific constants.
#include "h5fedconst.hh"
/* include standard proprietary header files */
#include "nonsciconst.h"
#include "physicomath.h"
using namespace std;
using namespace physicomath;
using namespace nonsciconst;
namespace H5Fed
{
class H5Fed {
public:
/** \brief constructor and destructor */
H5Fed()
{
doIndexMapping_ = false;
indexMap_.clear();
positionMap_.clear();
// Deactivate the HDF5 error output.
H5Eset_auto (0, NULL );
};
// The Destructor.
~H5Fed(){};
//! Open an hdf5 finite element data file with appropriate access.
int open(string fileName, string fileAccess)
{
// Store filename and file access in private variable.
fileName_ = fileName;
fileAccess_ = fileAccess;
// Open file with respective rights via HDF5 API.
if (!fileAccess_.compare(FILE_READ))
{
hdf5FileIdent_ = H5Fopen(fileName_.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT);
return OKCODE;
}
else if (!fileAccess_.compare(FILE_READ_WRITE))
{
hdf5FileIdent_ = H5Fopen(fileName_.c_str(), H5F_ACC_RDWR, H5P_DEFAULT);
return OKCODE;
}
else if (!fileAccess_.compare(FILE_CREATE))
{
hdf5FileIdent_ = H5Fcreate(fileName_.c_str(), H5F_ACC_EXCL,
H5P_DEFAULT, H5P_DEFAULT);
if (hdf5FileIdent_ < 0)
{
rError("The file %s already exist.",fileName_.c_str());
rError("To overwrite use the --force option.");
exit(ERRORCODE);
}
else
return OKCODE;
}
else if (!fileAccess_.compare(FILE_CREATE_FORCE))
{
hdf5FileIdent_ = H5Fcreate(fileName_.c_str(), H5F_ACC_TRUNC,
H5P_DEFAULT, H5P_DEFAULT);
return OKCODE;
}
else
{
rError("Unknown file-open-attribute for hdf5 file.");
exit(ERRORCODE);
}
};
// Close an open hdf5 file.
int close(void)
{
if (hdf5FileIdent_ >= 0)
{
hdf5Status_ = H5Fclose(hdf5FileIdent_);
return OKCODE;
}
else
{
rError("You cannot close a file that is not opened.");
return ERRORCODE;
}
};
// Create the empty HDF5 Finite Element Stardart group hierarchy.
int createGroupHierarchie()
{
// Hdf5 group identifier for group access, localy valid (this method).
hid_t hdf5GroupIdent_;
// Create the groups. All group-name strings are defined in h5fedconst.hh.
hdf5GroupIdent_ = H5Gcreate(hdf5FileIdent_,
H5FED_G_ROOT.c_str(),H5P_DEFAULT);
hdf5GroupIdent_ = H5Gcreate(hdf5FileIdent_,
H5FED_G_COORD.c_str(),H5P_DEFAULT);
hdf5GroupIdent_ = H5Gcreate(hdf5FileIdent_,
H5FED_G_VOLUME_MESH.c_str(),H5P_DEFAULT);
hdf5GroupIdent_ = H5Gcreate(hdf5FileIdent_,
H5FED_G_BOUNDARY_MESH.c_str(),H5P_DEFAULT);
hdf5GroupIdent_ = H5Gcreate(hdf5FileIdent_,
H5FED_G_MATERIAL.c_str(),H5P_DEFAULT);
hdf5GroupIdent_ = H5Gcreate(hdf5FileIdent_,
H5FED_G_ELECTROMAGNETIC.c_str(),H5P_DEFAULT);
hdf5GroupIdent_ = H5Gcreate(hdf5FileIdent_,
H5FED_G_DISCRETE.c_str(),H5P_DEFAULT);
hdf5GroupIdent_ = H5Gcreate(hdf5FileIdent_,
H5FED_G_PHYSICAL.c_str(),H5P_DEFAULT);
hdf5GroupIdent_ = H5Gcreate(hdf5FileIdent_,
H5FED_G_DEBYE.c_str(),H5P_DEFAULT);
hdf5GroupIdent_ = H5Gcreate(hdf5FileIdent_,
H5FED_G_LORENTZ.c_str(),H5P_DEFAULT);
hdf5GroupIdent_ = H5Gcreate(hdf5FileIdent_,
H5FED_G_DRUDE.c_str(),H5P_DEFAULT);
hdf5GroupIdent_ = H5Gcreate(hdf5FileIdent_,
H5FED_G_DOF.c_str(),H5P_DEFAULT);
hdf5GroupIdent_ = H5Gcreate(hdf5FileIdent_,
H5FED_G_FIELD.c_str(),H5P_DEFAULT);
return OKCODE;
};
// This function activate the automatic index mapping to create a gapfree
// and consecutive index set for the hdf5fed file.
// The indexVec holdes the numbers of the nodes in the same way, as the
// nodes are in the node vector.
int beginIndexMapping(std::vector<unsigned int>* indexVec)
{
rDebug("Begin automatic index mapping.");
doIndexMapping_ = true;
indexMap_.clear();
positionMap_.clear();
// Copy the old index to the map as map-key.
for(unsigned int varI = 0; varI < indexVec->size(); varI++)
{
indexMap_.insert(make_pair((*indexVec)[varI],0));
}
// Number all elements in the map consecutive, starting with zero, that
// is the new index set.
unsigned int tempUnInt = 0;
for(std::map<unsigned int, unsigned int>::iterator
iter = indexMap_.begin();
iter != indexMap_.end(); iter ++)
{
iter->second = tempUnInt;
tempUnInt++;
}
// The first column contains the new index, the second the old position
// of the coordinate in the vector.
for(unsigned int varI = 0; varI < indexVec->size(); varI++)
{
positionMap_.insert(make_pair(
(indexMap_.find((*indexVec)[varI]))->second,varI));
}
return OKCODE;
};
// This function deactivate the automatic index mapping.
// The uses index sets must be consecutive and gapfree.
int endIndexMapping()
{
rDebug("End automatic index mapping.");
doIndexMapping_ = false;
indexMap_.clear();
return OKCODE;
};
// Write 3dim coordinates to h5fed file.
int coord3d (std::vector<std::vector<double> >* coord)
{
// All these operations are only allowed, if there is a valid file
// identifier.
if (hdf5FileIdent_ >= 0)
{
// Define the rank of the different dataspaces.
const int rank = 2;
// Hdf5 error handling variable for Hdf5 actions.
herr_t hdf5Status;
// Hdf5 dataspace identifier.
hid_t hdf5DataspaceId;
// Hdf5 dataset identifier.
hid_t hdf5DatasetId;
// Define the dimension of the data array.
// Number of rows: as much as coordinates.
// Number of colums: 3, one for each dimension.
hsize_t dim[2];
dim[0] = coord->size();
dim[1] = 3;
// We copy the coordinates from coord in an standart array, so that
// hdf5 can handle it.
// We do this in portions, so we save memory.
// Subdimension of hyperslab in memory: 1 line, 3 columns.
hsize_t dim_sub_mem[2];
dim_sub_mem[0] = 1;
dim_sub_mem[1] = 3;
// Subdimension of hyperslab in file: 1 line, 3 columns.
hsize_t dim_sub_file[2];
dim_sub_file[0] = 1;
dim_sub_file[1] = 3;
// Define the offset for reading from the memory.
// Always fixed.
hsize_t offset_mem[2];
offset_mem[0] = 0;
offset_mem[1] = 0;
// Define the offset for writing into the file.
hsize_t offset_file[2];
offset_file[0] = 0; // Row only at the beginning. We iterate over it.
offset_file[1] = 0; // We have no offset respective to the column.
// Array for x, y and z component of one coordinate.
double coordinate[3];
// Dimesion and datatype of the file dataset, read out form file.
// This is not the fastest, but the most robust way.
hsize_t dim_out[2];
hid_t dataType;
// Create dataspace of full size.
hdf5DataspaceId = H5Screate_simple(rank, dim, H5P_DEFAULT);
// Create dataset of full size.
hdf5DatasetId = H5Dcreate(hdf5FileIdent_, H5FED_D_COORD3D.c_str(),
H5T_IEEE_F64LE, hdf5DataspaceId, H5P_DEFAULT);
// Loop over all rows of the dataset (file) and copy the coord vector
// element wise.
hdf5Status = H5Sget_simple_extent_dims(hdf5DataspaceId, dim_out, H5P_DEFAULT);
dataType = H5Dget_type(hdf5DatasetId);
// If we use automatic mapping we need an interator to the map.
std::map<unsigned int, unsigned int>::iterator
iter = positionMap_.begin();
for (unsigned int varI = 0; varI < dim_out[0]; varI++)
{
// Iterate over the rows in file dataspace.
offset_file[0] = varI;
// Copy every element of a coordinate.
for (unsigned int varJ = 0; varJ < dim_out[1]; varJ++)
{
// Here is the only special case for automated mapping:
// Do not copy the next in the input vector, copy the coord
// with the next following number.
if (doIndexMapping_ == true)
coordinate[varJ] = (*coord)[iter->second][varJ];
else
coordinate[varJ] = (*coord)[varI][varJ];
}
// Select hyperslab ('region') in file dataspace.
hdf5Status = H5Sselect_hyperslab(hdf5DataspaceId, H5S_SELECT_SET,
offset_file, H5P_DEFAULT,
dim_sub_file, H5P_DEFAULT);
// Define memory Dataspace.
hid_t hdf5MemspaceId;
hdf5MemspaceId = H5Screate_simple(rank, dim_sub_mem, H5P_DEFAULT);
// Select hyperslab ('region') in memory.
hdf5Status = H5Sselect_hyperslab(hdf5MemspaceId, H5S_SELECT_SET,
offset_mem, H5P_DEFAULT,
dim_sub_mem, H5P_DEFAULT);
// Copy dataset to dataset from memory to file.
hdf5Status = H5Dwrite(hdf5DatasetId, H5T_NATIVE_DOUBLE,
hdf5MemspaceId, hdf5DataspaceId,
H5P_DEFAULT, coordinate);
H5Sclose(hdf5MemspaceId);
// Increment the map iterator if we make automatic mapping.
if (doIndexMapping_)
iter++;
}
// Close hdf5 identifier.
hdf5Status = H5Dclose(hdf5DatasetId);
hdf5Status = H5Sclose(hdf5DataspaceId);
return OKCODE;
}
else
{
rError("You cannot operate to dataset COORD3D.");
rError("There is no valid file identifier.");
return ERRORCODE;
}
};
// Read and return tetrahedron on of the given level.
std::vector<std::vector<unsigned int> > tetrahedron(unsigned int level)
{
rError("The function: tetrahedron(unsigned int level) is not implemented.");
};
// Copy the tetrahedon elements to the h5fed file.
int tetrahedron(unsigned int level,
std::vector< std::vector<unsigned int> >* elem)
{
// Set dimension of an elements vector.
unsigned int elemDim = H5FED_TET_N_NODE;
// Set the name of the dataset, we want to operate.
string datasetName = H5FED_D_TETMESH + stringify(level);
// This function does the real work for all elements.
element_(level, elem, datasetName, elemDim);
return OKCODE;
}
int element_(unsigned int level,
std::vector< std::vector<unsigned int> >* elem,
std::string datasetName,
unsigned int elemDim )
{
// All these operations are only allowed, if there is a valid file
// identifier.
if (hdf5FileIdent_ >= 0)
{
rDebug("Insert a check, if the selected level exits,");
rDebug("and if it is consecutive.");
// Define the rank of the different dataspaces.
const int rank = 2;
// Hdf5 error handling variable for Hdf5 actions.
herr_t hdf5Status;
// Hdf5 dataspace identifier.
hid_t hdf5DataspaceId;
// Hdf5 dataset identifier.
hid_t hdf5DatasetId;
// Define the dimension of the data array.
hsize_t dim[2];
// Number of rows: as much as elements.
dim[0] = elem->size();
// Number of colums: dimenstion of an elements vector.
dim[1] = elemDim;
// We copy the element nodes from a element in an standart array,
// so that hdf5 can handle it.
// We do this for every element separate, so we save memory.
// Subdimension of hyperslab in memory: 1 line, elemDim columns.
hsize_t dim_sub_mem[2];
dim_sub_mem[0] = 1;
dim_sub_mem[1] = elemDim;
// Subdimension of hyperslab in file: 1 line, elemDim columns.
hsize_t dim_sub_file[2];
dim_sub_file[0] = 1;
dim_sub_file[1] = elemDim;
// Define the offset for reading from the memory.
// Always fixed, because memory has exactly the same size.
hsize_t offset_mem[2];
offset_mem[0] = 0;
offset_mem[1] = 0;
// Define the offset for writing into the file.
hsize_t offset_file[2];
offset_file[0] = 0; // Row ofsett zero only at the beginning.
offset_file[1] = 0; // We have no offset respective to the column.
// Array for single elements of an element vector.
unsigned int element[elemDim];
// Dimesion and datatype of the file dataset, read out form file.
// This is not the fastest, but the most robust way.
hsize_t dim_out[2];
hid_t dataType;
// Create dataspace of full size.
hdf5DataspaceId = H5Screate_simple(rank, dim, H5P_DEFAULT);
// Create dataset of full size.
hdf5DatasetId = H5Dcreate(hdf5FileIdent_, datasetName.c_str(),
H5T_STD_U32LE, hdf5DataspaceId, H5P_DEFAULT);
// Loop over all rows of the dataset (file) and copy the elem vector
// row wise.
hdf5Status = H5Sget_simple_extent_dims(hdf5DataspaceId, dim_out,
H5P_DEFAULT);
// Get the datatype of the datas we want to write.
dataType = H5Dget_type(hdf5DatasetId);
for (unsigned int varI = 0; varI < dim_out[0]; varI++)
{
// Iterate over the rows in file dataspace.
offset_file[0] = varI;
// Copy every element of a coordinate.
for (unsigned int varJ = 0; varJ < dim_out[1]; varJ++)
{
// Here is the only special case for automated mapping:
// Do not copy the next in the input vector, copy the coord
// with the next following number.
if (doIndexMapping_ == true)
{
std::map<unsigned int, unsigned int>::iterator iter;
iter = indexMap_.find((*elem)[varI][varJ]);
element[varJ] = iter->second;
}
else
element[varJ] = (*elem)[varI][varJ];
}
// Select hyperslab ('region') in file dataspace.
hdf5Status = H5Sselect_hyperslab(hdf5DataspaceId, H5S_SELECT_SET,
offset_file, H5P_DEFAULT,
dim_sub_file, H5P_DEFAULT);
// Define memory Dataspace.
hid_t hdf5MemspaceId;
hdf5MemspaceId = H5Screate_simple(rank, dim_sub_mem, H5P_DEFAULT);
// Select hyperslab ('region') in memory.
hdf5Status = H5Sselect_hyperslab(hdf5MemspaceId, H5S_SELECT_SET,
offset_mem, H5P_DEFAULT,
dim_sub_mem, H5P_DEFAULT);
// Copy dataset to dataset from memory to file.
hdf5Status = H5Dwrite(hdf5DatasetId, dataType,
hdf5MemspaceId, hdf5DataspaceId,
H5P_DEFAULT, element);
// Close the memory space identifier.
H5Sclose(hdf5MemspaceId);
}
// Close hdf5 identifier.
hdf5Status = H5Dclose(hdf5DatasetId);
hdf5Status = H5Sclose(hdf5DataspaceId);
return OKCODE;
}
else
{
rError("You cannot operate to a dataset.");
rError("There is no valid file identifier.");
exit(ERRORCODE);
}
};
/** \brief Inquire existence of HDF5 groups */
// existsVolumeMesh()
// existsCoord()
// virtual bool existsMesh(){ return(false); }
// virtual bool existsVertices(){ return(false); }
// virtual bool existsEdges(){ return(false); }
// virtual bool existsTriangles(){ return(false); }
// virtual bool existsBoundaryTriangles(){ return(false); }
// /** \brief Data access both reading and writing */
// virtual unsigned int nDim(){ return(ndim_); } /* retrieve number of mesh dimension */
// virtual unsigned int nLevel(){ return(nlevel_); } /* retrieve number of mesh levels */
// virtual unsigned int nCoord(){ return(nvertex_); } /* retrieve total number of all vertices */
// virtual unsigned int nCoord(unsigned int level){ return(nvertex_); } /* retrieve total number of vertices used for defining the mesh */
// Überladen greifen auf nelem zu
// virtual std::vector<unsigned int> nTet(){ return(ntet_); } /* retrieve vector containing number of tetrahedra present in levels of the mesh */
// virtual std::vector<unsigned int> nBoundary(){ return(nboundary_); } /* retrieve vector containing number of boundary meshes present on a level of the mesh */
// Pism, ...
// nBoundaryTriangle
// Quad..
// Edge
/** \brief HDF5EM data access routines */
/** \brief Electromagnetic boundary conditions */
//_______________________________
// virtual int triangleBC(unsigned int level, unsigned int triangle, unsigned int bc){} /* set electromagnetic boundary condition for triangle on level */
// virtual unsigned int triangleBC(unsigned int level, unsigned int triangle){} /* retrieve electromagnetic boundary condition type */
//
// virtual int rhoSurfaceImpedance(unsigned int level, unsigned int triangle, double rho){} /* store resistance of surface impedance for triangle on level */
// virtual double rhoSurfaceImpedance(unsigned int level, unsigned int triangle){} /* retrieve resistance of surface impedance boundary condition */
//
// /** \brief Mesh */
// stl vectoren
// virtual unsigned int** tetrahedron(unsigned int level){} /* read tetrahedra on level l stored in hdf5 file and return them in simple form */
// virtual int tetrahedron(unsigned int level, unsigned int ntetrahedron, unsigned int** tetrahedron){}
// virtual unsigned int* vertexId(){} /* read identification tag of vertices */
//
// virtual double** vertex(unsigned int level){} /* read vertices */
// virtual int vertex(unsigned int nvertex, double** vertex){} /* write vertices */
//
// virtual unsigned int** boundary(unsigned int level, unsigned int wboundary){} /* read boundary meshes stored in the hdf5 file on level and return number of them */
// virtual int boundary(unsigned int level, unsigned int** boundary, unsigned int wboundary){} /* write whichboundary boundary mesh into file */
//
// virtual unsigned int** edge(unsigned int level, aqmedge* &edge){} /* read edges on level and return number of them */
// virtual int edge(unsigned int level, unsigned int* edge){} /* write edges on level and return number of them */
//
// virtual unsigned int** triangle(unsigned int level){} /* read Triangular faces on level */
// virtual int triangle(unsigned int level, unsigned int** triangle){} /* write Triangular faces on level */
//
// /** \brief Materials */
// bool existsMaterials() /* find out if there are materials parameters at discrete frequencies, energies or wavelength */
//
// vector<double> frequency(){} /* read a vector of discrete frequencies stored in the file */
// int frequency(vector<double> f){} /* store a vector of discrete frequencies into the file */
//
// vector<double> energy(){} /* read a vector of discrete energies stored in the file */
// int energy(vector<double> e){} /* store a vector of discrete wavelengths into the file */
//
// vector<double> wavelength(){} /* read a vector of discrete wavelengths stored in the file */
// int wavelength(vector<double> lambda){} /* store a vector of discrete wavelengths into the file */
//
// vector< complex<double> > permittivity(){} /* read a vector of complex valued relative permittivities from the file */
// int permittivity( vector< complex<double> > epsilonr){} /* store a vector of complex valued relative permittivities into the file */
//
// vector< complex<double> > permeability(){} /* read a vector of complex valued relative permittivities from the file */
// int permeability( vector< complex<double> > mur){} /* store a vector of complex valued relative permittivities into the file */
//
// vector< complex<double> > conductivity(){} /* read a vector of complex valued relative permittivities from the file */
// int conductivity( vector< complex<double> sigma>){} /* store a vector of complex valued relative permittivities into the file */
//
// /** \brief Materials */
// bool existsDebyeMaterial(){} /* are the Debye material model paramters */
// bool existsLorentz(){} /* are there Lorentz material model parameters */
// bool existsDrudeMaterial(){} /* are there Drude material model parameters */
//
// /* Debye dielectric material model parameters, cf. Taflove et al. pp. 354 */
// std<double> weightsDebye(){} /* retrieve vector of Debye material model weights */
// int weightsDebye(vector<double> weightsdebye){} /* store vector of Debye material model weights */
//
// std<double> relaxationFrequencyDebye(){} /* retrieve vector of Debye material model relaxation frequencies */
// int relaxationFrequencyDebye(vector<double> relaxfreq){} /* retrieve vector of Debye material model relaxation frequencies */
//
// double epsilonStaticDebye(){} /* retrieve static limit of relative permittivitiye */
// int epsilonStaticDebye(double epsilonstaticr){} /* store static limit of relative permittivitiye */
//
// double epsilonInfinityDebye(){} /* retrieve infinite limit of relative permittivity */
// int epsilonInfinityDebye(double epsiloninftyr){} /* store infinite limit of relative permittivity */
//
// /* Lorentz dielectric material model parameters, cf. Taflove et al. pp. 354 */
// std<double> weightsLorentz(){} /* retrieve vector of Debye material model weights */
// int weightsLorentz(vector<double> weightsdebye){} /* store vector of Debye material model weights */
//
// std<double> poleFrequencyLorentz(){} /* retrieve vector of Lorentz material model relaxation frequencies */
// int poleFrequencyDebye(vector<double> polefreq){} /* retrieve vector of Lorentz material model relaxation frequencies */
//
// std<double> dampingCoefficientLorentz(){} /* retrieve vector of Lorentz material model damping coefficients */
// int dampingCoefficientLorentz(vector<double> dampingcoeff){} /* retrieve vector of Lorentz material model damping coefficients */
//
// double epsilonStaticLorentz(){} /* retrieve static limit of relative permittivitiye */
// int epsilonStaticLorentz(double epsilonstaticr){} /* store static limit of relative permittivitiye */
//
// double epsilonInfinityLorentz(){} /* retrieve infinite limit of relative permittivity */
// int epsilonInfinityLorentz(double epsiloninftyr){} /* store infinite limit of relative permittivity */
//
// /* Drude dielectric material model parameters, cf. Taflove et al. pp. 354 */
// std<double> weightsDrude(){} /* retrieve vector of Drude material model weights */
// int weightsDrude(vector<double> weightsdebye){} /* store vector of Drude material model weights */
//
// std<double> poleFrequencyDrude(){} /* retrieve vector of Drude material model pole frequencies */
// int poleFrequencyDrude(vector<double> relaxfreq){} /* retrieve vector of Drude material model pole frequencies */
//
// std<double> inversePoleRelaxationTimeDrude(){} /* retrieve vector of Lorentz material model inverse pole relaxation time */
// int inversePoleRelaxationTimeDrude(vector<double> inversepolerelaxtime){} /* retrieve vector of Lorentz material model inverse pole relaxation time */
//
// double epsilonStaticDrude(){} /* retrieve static limit of relative permittivitiye */
// int epsilonStaticDrude(double epsilonstaticr){} /* store static limit of relative permittivitiye */
//
// double epsilonInfinityDrude(){} /* retrieve infinite limit of relative permittivity */
// int epsilonInfinityDRude(double epsiloninftyr){} /* store infinite limit of relative permittivity */
//________________________________________________________________
// protected:
//
private:
//-----------------------------------------------------------------------//
// Private data structure. //
//-----------------------------------------------------------------------//
// Store the filename of the H5Fed here.
string fileName_;
// Store the file access rights of the H5Fed here.
string fileAccess_;
// Hdf5 error variable stores the success of an Hdf5 action.
herr_t hdf5Status_;
// Hdf5 file identifier for file access. If a file access fails, the
// identifyer is negetive.
hid_t hdf5FileIdent_;
// If the elements we want to write to the h5fed file are not consecutive
// and with gaps numbered, this API shoud be able to map this to an gapfree
// and consecutive index set.
// To activate this function we have the following variable.
bool doIndexMapping_;
// The first entry in indexMap_ is the old index of a coordinate, the
// second is the new index usend in the h5fed file.
std::map<unsigned int, unsigned int> indexMap_;
// The first entry in positionMap_ is the new index usend in the h5fed
// file, the second is the old postion in the coordinate vector.
std::map<unsigned int, unsigned int> positionMap_;
//-----------------------------------------------------------------------//
// Private helper functions. //
//-----------------------------------------------------------------------//
// This function converts a number to a string.
template<typename type>
inline std::string stringify(type value)
{
std::ostringstream oStream;
try
{
oStream << value;
}
catch(exception& error)
{
rError("Cannot convert this variable to a string.");
rError("Error: %d",error.what());
exit(ERRORCODE);
}
return oStream.str();
}
};
} // End of namespace H5Fed
#endif // HAVE_HDF5
#endif //H5FED_HH_
H5Fed/libsrc/h5fed/h5fedconst.hh
-50
View File
@@ -1,50 +0,0 @@
#ifndef H5FEDCONST_HH_
#define H5FEDCONST_HH_
#include<string>
using namespace std;
//! Hdf5 specific file access:
// "r" for read only access.
// "w" for read and write access.
// "c" create a new a new file with if it does not exist already.
// "cf" create a new file, overwrite it if it exists already.
const string FILE_READ("r");
const string FILE_READ_WRITE("w");
const string FILE_CREATE("c");
const string FILE_CREATE_FORCE("cf");
// Define the group names of the H5Fed starndard groups.
const string H5FED_G_ROOT ("/HDF5_FINITE_ELEMENT_DATA");
const string H5FED_G_COORD (H5FED_G_ROOT+"/COORD");
const string H5FED_G_VOLUME_MESH (H5FED_G_ROOT+"/VOLUME_MESH");
const string H5FED_G_BOUNDARY_MESH (H5FED_G_ROOT+"/BOUNDARY_MESH");
const string H5FED_G_MATERIAL (H5FED_G_ROOT+"/MATERIAL");
const string H5FED_G_ELECTROMAGNETIC (H5FED_G_MATERIAL+"/ELECTROMAGNETIC");
const string H5FED_G_DISCRETE (H5FED_G_ELECTROMAGNETIC+"/DISCRETE");
const string H5FED_G_PHYSICAL (H5FED_G_ELECTROMAGNETIC+"/PHYSICAL");
const string H5FED_G_DEBYE (H5FED_G_PHYSICAL+"/DEBYE");
const string H5FED_G_LORENTZ (H5FED_G_PHYSICAL+"/LORENTZ");
const string H5FED_G_DRUDE (H5FED_G_PHYSICAL+"/DRUDE");
const string H5FED_G_DOF (H5FED_G_ROOT+"/DOF");
const string H5FED_G_FIELD (H5FED_G_ROOT+"/FIELD");
// Define the dataset names of the H5Fed standard datasets.
const string H5FED_D_COORD3D (H5FED_G_COORD+"/COORD3D");
const string H5FED_D_TETMESH (H5FED_G_VOLUME_MESH+"/TETMESH_L");
const string H5FED_D_HEXMESH (H5FED_G_VOLUME_MESH+"/HEXMESH_L");
const string H5FED_D_PRISMATICMESH (H5FED_G_VOLUME_MESH+"/PRISMATICMESH_L");
const string H5FED_D_PYRAMIDMESH (H5FED_G_VOLUME_MESH+"/PYRAMIDMESH_L");
const string H5FED_D_TRIANGLEMESH (H5FED_G_VOLUME_MESH+"/TRIANGLEMESH_L");
const string H5FED_D_QUADRANGLEMESH (H5FED_G_VOLUME_MESH+"/QUADRANGLEMESH_L");
// How much nodes have a geometric figure.
const unsigned short int H5FED_TET_N_NODE = 4;
const unsigned short int H5FED_HEX_N_NODE = 8;
const unsigned short int H5FED_PRISMATIC_N_NODE = 6;
const unsigned short int H5FED_PYRAMID_N_NODE = 5;
const unsigned short int H5FED_TRIANGLE_N_NODE = 3;
const unsigned short int H5FED_QUADRANGLE_N_NODE = 4;
#endif /*H5FEDCONST_HH_*/
H5Fed/libsrc/h5fed/makefile.am
-14
View File
@@ -1,14 +0,0 @@
## Makefile.am -- process this file with automake to produce Makefile.in
##
## authors - benedikt oswald and patrick leidenberger
## modified - 2006 aug 24, patrick leidenberger, creation
#
## objective - automake input file for the h5fed directory
## project - gmsh2h5fed
noinst_LTLIBRARIES = libh5fed.la
h5feddir = $(topleveldir)/libsrc/h5fed
h5fed_HEADERS = h5fed.hh
libh5fed_la_SOURCES = h5fed.cc \
h5fed.hh
AM_CPPFLAGS = @AM_CPPFLAGS@
H5Fed/libsrc/makefile.am
-11
View File
@@ -1,11 +0,0 @@
## Makefile.am -- process this file with automake to produce Makefile.in
##
## authors - benedikt oswald and patrick leidenberger
## modified - 2006 aug 21, patrick leidenberger, creation
## modified - 2006 aug 24, pl, add h5fed path.
#
## objective - automake input file for the libsrc directory
## project - gmsh2h5fed
SUBDIRS = gmsh h5fed
AM_CPPFLAGS = @AM_CPPFLAGS@
H5Fed/libsrc/stdincl/nonsciconst.h
-143
View File
@@ -1,143 +0,0 @@
// rights - copyright by benedikt oswald, 2002-2006, all rights reserved
// project - phidias3d
// file name - nonsciconst.h
// file type - c++ include file
// author - benedikt oswald
// modified - 2004 may 21, creation, benedikt oswald
// modified - 2004 jun 11, added font definitions, benedikt oswald
// modified - 2006 jun 26, transferred to project phidias3d, benedikt oswald
// modified - 2006 jun 28, correction of RIGHTANGLE_DEG from int to double,
// patrick leidenberger
// modified - 2006 jul 11, add vtk cell type constants,
// patrick leidenberger
// objective - define technical, non-scientific constants, e.g. plot paper
// dimensions etc.
/* include standard libraries */
#include <cmath>
#include <complex>
#include <string>
#include <vector>
#ifndef _NONSCICONST_
#define _NONSCICONST_
using namespace std;
namespace nonsciconst
{
const double A4WIDTH = 210.0;
const double A4HEIGHT = 297.0;
const double A5WIDHT = 105.0;
const double A5HEIGHT = 148.5;
const unsigned int FRAMED = 1;
const unsigned int NOTFRAMED = 0;
const unsigned int BELOW = 1;
const unsigned int ABOVE = 0;
const unsigned int ATLEFT = 1;
const unsigned int ATRIGHT = 0;
const unsigned int FILLED = 1;
const unsigned int NOTFILLED = 0;
const unsigned int OUTERFACES = 1;
const unsigned int INNERFACES = 0;
const double RIGHTANGLE_DEG = 90.0;
const unsigned int DRAW_GRID_NODES_FLAG = 1;
const unsigned int DRAW_GRID_LINES_FLAG = 1;
const double MAXHUE = 0.7;
const double MAXSAT = 1.0;
const double MAXBRG = 1.0;
const unsigned int GRAY_COLORSPACE = 0;
const unsigned int RGB_COLORSPACE = 2;
const unsigned int HSB_COLORSPACE = 4;
const unsigned int CMYK_COLORSPACE = 8;
const double HSB_H_BLUE = 0.7;
const double HSB_H_RED = 1.0;
const double HSB_H_BLACK = 0.1;
const unsigned int LEGEND_HORIZONTAL = 1;
const unsigned int LEGEND_VERTICAL = 0;
const unsigned int NUMCHARPLTFLNM = 256;
const unsigned int NUMCHARSTRINGPLOTPROD = 256;
const unsigned int DSPLYSTRLE = 512;
const unsigned int MAXFILENAMSTRLEN = 512;
const unsigned int DSPSTRLEN = 256;
const double MINIMUM_DB_VAL = -60.0;
const string HELVETICA_OBLIQUE_FNT("Helvetica-Oblique");
const string HELVETICA_FNT("Helvetica");
const string TIMES_FNT("Times-Roman");
const string ARIAL_FNT("Arial");
const string SYMBOL_FNT("Symbol");
const double INCHINPT = 72.0; /* define an inch in points, a typographic unit */
const double INCHINMM = 25.4; /* define an inch in millimeter */
const string ELECTRIC_FIELD_UNIT_STRING("[V/m]");
const string ELECTRIC_FIELD_UNIT_STRING_DB("[norm. dB]");
const double TEXT_DOWN_DIR_DEG = 270.0;
const double TEXT_RIGHT_DIR_DEG = 0.0;
const unsigned int COLRSPCDIM = 3;
const double PSGRAF3_SYMBOL_RADIUS_PCOORD=0.3;
const int PSGRAF3_SYMBOL_CIRCLE = 0;
const int PSGRAF3_SYMBOL_SQUARE = 1;
const int PSGRAF3_SYMBOL_RHOMBUS = 2;
const int PSGRAF3_SYMBOL_TRIANGLE_TIPUP = 3;
const int PSGRAF3_SYMBOL_TRIANGLE_TIPDOWN = 4;
const int OKCODE = 0;
const int ERRORCODE = 1;
const int ERROR_SINGULAR_MATRIX = 2;
const int ERROR_PSGRAF3_NOT_AVAILABLE = 3;
const int ERROR_NNZ_IS_ZERO = 100;
const string VTK_LFF_EXTENSION(".vtk");
const string HDF5_EXTENSION(".h5");
const string TAB_STRING("\t");
const string SINGLE_SPACE(" ");
const int DEFAULT_FLOAT_PRECISION=6;
// Define constants for vtk cell types.
const unsigned int VTK_VERTEX = 1;
const unsigned int VTK_POLY_VERTEX = 2;
const unsigned int VTK_LINE = 3;
const unsigned int VTK_POLY_LINE = 4;
const unsigned int VTK_TRIANGLE = 5;
const unsigned int VTK_TRIANGEL_STRIP = 6;
const unsigned int VTK_POLYGON = 7;
const unsigned int VTK_PIXEL = 8;
const unsigned int VTK_QUAD = 9;
const unsigned int VTK_TETRA = 10;
const unsigned int VTK_VOXEL = 11;
const unsigned int VTK_HEXAHEDRON = 12;
const unsigned int VTK_WEDGE = 13;
const unsigned int VTK_PYRAMID = 14;
const unsigned int VTK_QUADRATIC_EDGE = 21;
const unsigned int VTK_QUADRATIC_TRIANGLE = 22;
const unsigned int VTK_QUADRATIC_QUAD = 23;
const unsigned int VTK_QUADRATIC_TETRA = 24;
const unsigned int VTK_QUATRATIC_HEXAHEDRON = 25;
}
#endif
H5Fed/libsrc/stdincl/physicomath.h
-72
View File
@@ -1,72 +0,0 @@
// rights - copyright by benedikt oswald, 2002-2006, all rights reserved
// project - phidias3d
// file name - physicomath.h
// file type - c++ include file
// author - benedikt oswald
// modified - 2003 jan 30, creation -
// modified - 2006 jun 26, transferred to project phidias3d, benedikt oswald
// objective - physical and mathematical quantities, constansts etc.
#include <cmath>
#include <complex>
#ifndef _PHYSICO_MATH_
#define _PHYSICO_MATH_
using namespace std;
namespace physicomath
{
const double ZERO = 0;
const int INT_ZERO = 0;
const unsigned int UNSIGNED_INT_ZERO = 0;
const double DOUBLE_ZERO = 0.0;
const int INT_ONE = 1;
const unsigned int UNSIGNED_INT_ONE = 1;
const int INT_TWO = 2;
const double DOUBLE_ONE = 1.0;
const double DOUBLE_TWO = 2.0;
#ifndef IMAGINARY_UNIT_
#define IMAGINARY_UNIT_
const complex<double> IU(0.0,1.0);
#endif
const double PI = 3.1415926535;
const double EPSILON_ZERO = 8.85418782e-12;
const double MU_ZERO = 4.0 * PI * 1.0e-7;
const double SPEED_OF_LIGHT = (1.0/(sqrt(EPSILON_ZERO*MU_ZERO)));
const double Z0 = sqrt(MU_ZERO/EPSILON_ZERO);
const double TERAHERTZ = 1.0e12;
const double GIGAHERTZ = 1.0e9;
const double MEGAHERTZ = 1.0e6;
const double KILOHERTZ = 1.0e3;
const double SECOND = 1.0e0;
const double MILLISECOND = 1.0e-3;
const double MICROSECOND = 1.0e-6;
const double NANOSECOND = 1.0e-9;
const double PICOSECOND = 1.0e-12;
const double FEMTOSECOND = 1.0e-15;
const double L_BAND_CENTER_FREQUENCY=1.414e9;
const double DOUBLE_REL_ZERO_LIMIT=1.0e-100;
const double METER = 1.0; /* define a meter, the standard */
const double DECIMETER = 0.1; /* define a tenth of a meter */
const double CENTIMETER = 1.0e-2; /* define a centimeter */
const double MICROMETER = 1.0e-6; /* define a micrometer */
const double NANOMETER = 1.0e-9; /* define a nanomenter */
const double ANGSTROM = 1.0e-10; /* define an angstrom */
}
#endif
H5Fed/makefile.am
-10
View File
@@ -1,10 +0,0 @@
## Makefile.am -- process this file with automake to produce Makefile.in
##
## authors - patrick leidenberger
## modified - 2006 aug 21, patrick leidenberger, creation
## objective - top level automake file for H5Fed
## project - H5Fed
SUBDIRS = libsrc applications
AM_CPPFLAGS = @AM_CPPFLAGS@
Makefile.am
+16 -11
View File
@@ -1,14 +1,19 @@
# Trial by Antino Kim
# Top level Makefile.am
ACLOCAL_AMFLAGS = -I m4
EXTRA_DIST = autogen.sh
SUBDIRS = \
src \
test \
tools
SUBDIRS = \
src \
test \
tools \
doc \
examples/H5 \
examples/H5Part \
examples/H5Block \
examples/H5Fed
MAINTAINERCLEANFILES = \
config.h \
config.log \
config.status \
stamp-h.in \
MAINTAINERCLEANFILES = \
config.h \
config.log \
config.status \
stamp-h.in \
stamp-h1
Makefile.orig
-59
View File
@@ -1,59 +0,0 @@
# This is a very rudimentary multiarchitecture makefile
# You need to uncomment the default block of make variables you need
# Some key things to watch for are the following defines
# -DREGRESSIONTEST : enables a main(){} inside of
# the H5Part.cc file that does simple regression testing.
# -DPARALLEL_IO : If you want to use parallel HDF5, you have to
# enable this. Otherwise, you get only the serial
# implementation of the library.
# MacOS-X Serial
#CXX = c++
#CC = cc
#F90 = xlf
#H5HOME = /usr/local
#CFLAGS = -O -g -I$(H5HOME)/include
#LDFLAGS = -L$(H5HOME)/lib -lhdf5 -lz -lm
# AIX/SP-2 Parallel : Seaborg
#CXX = mpCC_r
#CC = mpcc_r
#F90 = mpxlf
#H5HOME = /usr/common/usg/hdf5/1.4.4/parallel
#H4HOME = /usr/common/usg/hdf/default
#OPT = -qarch=auto -qtune=auto-qcache=auto -O3 -qhot
#CFLAGS = -g -bmaxdata:800000000 -bmaxstack:256000000 -I$(H5HOME)/include
#LDFLAGS = -L$(H5HOME)/lib -lhdf5 -L$(H4HOME)/lib -lz -lm
# Linux Serial
#CXX = g++
#CC = gcc
#F90 = g77 # or could be pgif90
#CFLAGS = -O -g -I$(H5HOME)/include
#LDFLAGS = -L$(H5HOME)/lib -lhdf5 -lz -lm
# Linux Jacquard
CC = mpicc
CXX = mpicxx
F90 = mpif90
H5HOME = /usr/common/usg/hdf5/1.6.3/parallel
CFLAGS = -O2 -DPARALLEL_IO -DH5_HAVE_PARALLEL -I$(H5HOME)/include
LDFLAGS = -L$(H5HOME)/lib -lhdf5 -lz -lm
# Linux Parallel
#CC = gcc
#CXX = g++
#F90 = g77
#H5HOME = /usr/local
# /usr/common/usg/hdf5/1.6.3/parallel
#MPIHOME = /usr/local
#CFLAGS = -O -g -DPARALLEL_IO -DH5_HAVE_PARALLEL -I$(H5HOME)/include
#LDFLAGS = -L$(H5HOME)/lib -lhdf5 -lmpich -lrt -lz -lm
all: H5PartTest H5PartTest.o H5Part.o
parallel: H5PartTest H5PartTest.o H5Part.o H5PartTestParallel H5PartAndreasTest # parallel regression tests
fortran: H5PartF.o # fortran bindings
include rules.make
NEWS
+254
View File
@@ -1,3 +1,257 @@
#### H5PART trunk ############################################################
* h5_file_t is now uintptr_t
* experimental version of parallel H5Fed
* new API function for file open using properties (similiar to hdf5 properties)
#### H5PART 1.99.10 ############################################################
* C99 compiler required
* C API with inline functions
#### H5PART 1.99.0 ############################################################
rudimental implementation of a grid manager
Important changes from version 1.6 to 1.99.0
Renamed type:
H5PartFile -> h5_file_t
h5part_int64_t -> h5_int64_t
h5part_float64_t -> h5_float_t
Renamed functions:
All function not related to a specific data model have been renamed from
H5PartFunction() to H5Function().
Example:
H5PartOpenFile() -> H5OpenFile()
Removed functions:
To simplify the API, there is just one function to open a file. It's the
same function for serial and parallel code.
#### H5PART 1.6.6 ############################################################
Fixed typo (Write instead of Read) in the h5bl_3d_read_scalar_field* Fortran
interface.
Added missing type normalization for int32 type.
Rewrite of h5pAttrib tool.
#### H5PART 1.6.5 ############################################################
Fixed several build errors reported by Iuri Prilepov on Ubuntu 11.04.
#### H5PART 1.6.4 ############################################################
Fixed bug where H5PartSetViewIndices was not setting an empty view when the
number of elements is 0.
Set a threshold on the HDF5 alignment parameter so that small metadata writes
are not aligned, which causes large gaps in the file.
#### H5PART 1.6.3 ############################################################
New build system uses libtool and can build shared libraries.
Fixed a bug that incorrectly identifies the number of selected points in a view
when using H5PartSetViewIndices.
Fixed bug in Fortran test reported by several people, as well as several
incorrect views set in the C test that were causing segfaults.
Fixed name mismatches in the Fortran interface, and an off-by-one indexing
problem.
#### H5PART 1.6.2 ############################################################
Removed H5PartSetViewEmpty
--------------------------
An empty view can now be selected with:
H5PartSetNumParticles(file, 0);
Bug Fixes to Attribute Calls in Fortran API
-------------------------------------------
Fixed a problem where attribute values were reverting to zero.
#### H5PART 1.6.1 ############################################################
Chunking in the H5Part API
--------------------------
There is now an H5Part equivalent H5PartSetChunkSize to the existing
H5BlockDefine3DChunkDims call. Both of these calls enable the chunking
mechanism in the underlying HDF5 layer. Chunking is used in combination
with the aligned open calls to pad datasets to alignment multiples
on disk.
All Steps Available on Write
----------------------------
Previously, existing steps in a file were only accessible in read-only mode.
Now, all steps are available in all modes, including write-truncate and
write-append. Thus, it is now possible to overwrite existing data in write
mode. To help alert the user to this possibility, a warning is issued every
time an existing dataset is written to. Warnings can be printed by setting
the verbosity to H5PART_VERB_WARN or higher.
New Throttling Routine
----------------------
Previously, a throttle factor of N meant that for P processors, the total
number of P writes were divided into N batches of P/N writes.
To better accommodate round-robin lustre striping, the new policy is to
execute P/N batches of N writes. Thus, matching N to the number of stripes
results in the desirable 1-1 matching of writers to stripes.
Other Fixes
-----------
* The configure script should correctly detect PGI compilers now.
* There was a small memory leak in the Fortran file open calls.
* There was a compile error with HDF5 1.6.x due to a missing assignment.
#### H5PART 1.6 ##############################################################
Updated Documentation
---------------------
The Fortran API has been added to the doxygen documentation. Most entries have
a reference to their respective C API call.
Regression Test Suite
---------------------
The test subdirectory has been reorganized to include a systematic series
of regression tests of common use cases for the API. The goal is to have both
complete coverage of the API (every call is exercised) and testing of some
unlikely or unsuspected values and cases.
Currently, the C test covers the entire H5Part API and the Fortran test is
still in development.
Benchmark Utilities
-------------------
Two benchmarking utilities, H5PartBench and H5BlockBench, have been added to
the tools collection. Both require the parallel library and have functionality
and syntax similar to the IOR benchmark:
http://sourceforge.net/projects/ior-sio/
File Mode Flags
---------------
Previously, the only flags used were H5PART_READ, H5PART_WRITE, and
H5PART_APPEND, and these were mutually exclusive. Additional flags have been
added to select the underlying virtual file driver (VFD) that HDF5 uses in
parallel mode and to accommodate the lustre filesystem:
H5PART_VFD_MPIPOSIX (use the MPI-POSIX driver, which bypasses MPI-IO)
H5PART_VFD_MPIIO_IND (use MPI-IO in independent mode)
H5PART_FS_LUSTRE (activate H5P tunings for the lustre stripe size)
These flags can be specified using the typical bitwise OR method, e.g.
char flag = H5PART_WRITE | H5PART_VFD_MPIPOSIX | H5PART_FS_LUSTRE;
will select write mode with these two additional options.
The parallel library now defaults to using the MPI-IO collective mode driver
(previously it used independent mode). The collective buffering algorithm in
the Cray XT4/5 environment has been substantially improved in the last year,
and defaulting to collective mode allows us to take advantage of these
improvements automatically.
There are also new open calls H5PartOpenAlign and H5PartOpenParallelAlign that
take an additional 'alignment' value. This value is passed to HDF5 and used to
pad out objects so that they align to filesystem boundaries. For instance, it
would make sense to use the stripe size as the alignment value when writing to
a lustre filesystem.
Unified 'View' Model
--------------------
Views are now supported in both read and write mode (previously only supported
in read mode). It is possible to specify non-sensical views: you could for
instance specify a read view that is larger than the dataset on disk. Or you
could create a write view that is larger than the data in memory. In those
cases, you will encounter an error when you try to perform a read or write
operation on a dataset.
There are two new methods for selecting views. H5PartSetNumParticlesStrided
selects a view with $n$ particles per processor, but such that the data in
memory is expected to have a 'stride' factor. For instance, if you have
particle data with fields $x$ and $y$ and a single array with entries
$x1,y1,x2,y2...$, then the stride factor is 2. Striding works for both reads
and writes and only affects the view of memory: individual fields are still
stored as individual arrays on disk.
The second new method is H5PartSetViewIndices, which allows for point
selections of datasets. You can pass a list of indices for the points you
want to select. This is useful, for instance, when interfacing with FastBit
to perform queries that select a small subset of non-contiguous particles.
Because views are now supported on write, it is possible to write a dataset
using multiple 'passes' or to leave some values unwritten.
Also, all views are now *inclusive*, so that a view of (0,9) corresponds
to the 10 items 0, 1, 2, ... 9.
Internal Handling of Dataspaces
-------------------------------
H5PartSetNumParticles and H5PartSetNumParticlesStrided now share the same
HDF5 dataspace state in the H5PartFile struct with the calls that modify
the view (H5PartSetView etc.). Previously, the memory and disk dataspaces
were regenerated from the view on every read access, which was unnecessary.
Autogeneration of API Calls
---------------------------
Python scripts have been added to automatically generate read/write call
variants for different data types.
Renamed Fortran Include
-----------------------
The automake system no longer greps the *F90.inc files to generate an include
called 'H5Part.inc'. Instead, the *F90.inc files have been renamed to *.f90,
and awk is used to generate an 'H5PartF.h' file (the same naming convention
as in MPI's 'mpif.h').
The change to *.f90 was necessary to facilitate integration of the Fortran
API into doxygen. Note that the *.f90 files will not compile, nor can they
be included directly. Simply use
include 'H5PartF.h'
in your Fortran code to include all the definitions for Fortran H5Part/H5Block
calls.
64 Char Limit on Dataset Names
------------------------------
Previously, a user could overrun internal buffers for dataset names. Now, a
fixed limit of 64 chars is imposed. Dataset names that are longer than this are
truncated and a warning is printed. We expect that most users are using
short canonical names like x, px, id, etc.
Changes to Existing API
-----------------------
The H5BlockGetFieldInfo and H5BlockGetFieldInfoByName calls now both include
a parameter for the 'type' of the field.
#### H5PART 1.4 ##############################################################
Error Handling
--------------
Now all functions, in which an error could occure, are returning a
README
-393
View File
@@ -1,393 +0,0 @@
==============================================================================
README file for H5Part configure
==============================================================================
+ 0. HDF5 library
-----------------
Make sure you have a working version of the HDF5 library in your computer. If you plan
to use parallel I/O you need to use a parallel HDF5 version. If you don't have the
library download the sources from http://hdf.ncsa.uiuc.edu/HDF5/
+ 1. Quick start (If you feel lucky...)
----------------------------------------
For many platforms, where compilers are installed in the "default" location
and all the environment variables are set correctly, it should be sufficient
to type:
./configure [OPTIONS] && make [install]
to have the libraries and test program compiled.
==============================================================================
+ 2. configure line options
----------------------------
(1) Enable options
--enable-fortran
--enable-parallel
--enable-tools
--enable-python
--enable-64 (only for AIX and Irix)
(2) Setting compilers related variables manually
To assign environment variables (e.g., CC, CFLAGS...), specify them as
VAR=VALUE. See below for descriptions of some of the useful variables.
Compiler environment variables:
CC C compiler command
CXX C++ compiler command
FC Fortran compiler command
(3) Setting prefix for installation manually
--prefix=PREFIX install files in PREFIX
For more information, type:
./configure --help
==============================================================================
+ 3. Platform specific settings for compiling libraries & test programs
------------------------------------------------------------------------
Building
make : builds the libraries and test programs
make install: builds and installs
make clean : removes extraneous object files
make distclean : returns configuration to unconfigured state
As tested on hosts:
(1) Davinci <davinci.nersc.gov> (Linux"SUSE"-ia64)
---------------------------------------------------
FIRST THING FIRST!! Type:
module load intel
to have the proper compilers set up for use.
module load hdf5_par
[NOTE: module load hdf5 does not work at this moment.
Possible installation error of HDF5 on Davinci.]
Brief profile:
CC = icc
CXX = icc
FC = ifort
MPICC = icc
MPICXX = icc
MPIFC = ifort
If default doesn't work, try:
For C shell:
env CC=icc CXX=icc FC=ifort MPICC=icc MPICXX=icc MPIFC=ifort ./configure && make install
For Korn or Bourne shell:
CC=icc CXX=icc FC=ifort MPICC=icc MPICXX=icc MPIFC=ifort ./configure && make install
And, of course, you should add configure options, such as --enable-fortran --enable-parallel.
On this host, executing:
For C shell:
env CC=icc CXX=icc FC=ifort MPICC=icc MPICXX=icc MPIFC=ifort ./configure --enable-fortran --enable-parallel && make install
For Korn or Bourne shell:
CC=icc CXX=icc FC=ifort MPICC=icc MPICXX=icc MPIFC=ifort ./configure --enable-fortran --enable-parallel && make install
has functioned correctly.
To run test program, go to test directory:
(i) Serial test
run:
./H5testF
./H5PartTest
(ii) Parallel test
run:
mpirun 2 H5testFpar
mpirun 2 H5PartTestP
NOTE: Number 2 above is a arbitrary number that indicates the number of processes.
(2) Jacquard <jacquard.nersc.gov> (Linux"SUSE"-x86_64)
-------------------------------------------------------
Brief profile:
CC = pathcc
CXX = pathCC
FC = pathf90
MPICC = mpicc
MPICXX = mpicxx
MPIFC = mpif90
If default doesn't work, try:
For C shell:
env CC=pathcc CXX=pathCC FC=pathf90 MPICC=mpicc MPICXX=mpicxx MPIFC=mpif90 ./configure && make install
For Korn or Bourne shell:
CC=pathcc CXX=pathCC FC=pathf90 MPICC=mpicc MPICXX=mpicxx MPIFC=mpif90 ./configure && make install
And, of course, you should add configure options, such as --enable-fortran --enable-parallel.
On this host, executing:
For C shell:
env CC=pathcc CXX=pathCC FC=pathf90 MPICC=mpicc MPICXX=mpicxx MPIFC=mpif90 ./configure --enable-fortran --enable-parallel && make install
For Korn or Bourne shell:
CC=pathcc CXX=pathCC FC=pathf90 MPICC=mpicc MPICXX=mpicxx MPIFC=mpif90 ./configure --enable-fortran --enable-parallel && make install
has functioned correctly.
To run test program, go to test directory:
(i) Serial test
run:
./H5testF
./H5PartTest
(ii) Parallel test
In Jacquard, we need a script to run parallel programs, since Jacquard does not support interactive parallel processing. Instead, we need to submit the task to a queue. A sample script (run_H5testFpar.scr) may look like below:
+++++++++++++++++++++++++++++++++++++++
#!/bin/csh
#PBS -l nodes=1:ppn=2,walltime=00:05:00
#PBS -N H5testFpar
#PBS -o H5testFpar.out
#PBS -e H5testFpar.err
#PBS -q debug
#PBS -A mpccc
#PBS -V
setenv PBS_OWORKDIR /home/H5Part/test
cd $PBS_O_WORKDIR
mpirun -np 2 ./H5testFpar
+++++++++++++++++++++++++++++++++++++++
Then, we need to submit the task to a queue by running:
qsub run_H5testFpar.scr
After processed, the result will appear in H5testFpar.out, and error messages will appear in H5testFpar.err.
(3) Bassi <bassi.nersc.ogv> (AIX5.3.0.0-Power 3)
-------------------------------------------------
FIRST THING FIRST!! Type:
module load gcc
to have the proper compilers set up for use.
Brief profile:
CC = cc_r
CXX = cc_r
FC = xlf_r
MPICC = mpcc_r
MPICXX = mpcc_r
MPIFC = mpxlf_r
If default doesn't work, try:
For C shell:
env CC=cc_r CXX=cc_r FC=xlf_r MPICC=mpcc_r MPICXX=mpcc_r MPIFC=mpxlf_r ./configure && make install
For Korn or Bourne shell:
CC=cc_r CXX=cc_r FC=xlf_r MPICC=mpcc_r MPICXX=mpcc_r MPIFC=mpxlf_r ./configure && make install
And, of course, you should add configure options, such as --enable-fortran --enable-parallel.
On this host, executing:
For C shell:
env CC=cc_r CXX=cc_r FC=xlf_r MPICC=mpcc_r MPICXX=mpcc_r MPIFC=mpxlf_r ./configure --enable-fortran --enable-parallel && make install
For Korn or Bourne shell:
CC=cc_r CXX=cc_r FC=xlf_r MPICC=mpcc_r MPICXX=mpcc_r MPIFC=mpxlf_r ./configure --enable-fortran --enable-parallel && make install
has functioned correctly.
To run test program, go to test directory:
(i) Serial test
run:
./H5testF
./H5PartTest
(ii) Parallel test
run:
unsetenv MP_SINGLE_THREAD
poe ./H5PartTestP -procs 2 -nodes 1
poe ./H5testFpar -procs 2 -nodes 1
For more details on how to run parallel programs on Bassi, go to:
http://www.nersc.gov/nusers/resources/bassi/running_jobs/
(4) Starsky <starsky.lbl.gov> (Darwin8.5.0-PowerPC)
----------------------------------------------------
FIRST THING FIRST!! Set environment variables: (in tcsh)
setenv LD_LIBRARY_PATH /usr/local/g95/lib/gcc-lib/powerpc-apple-darwin8.5.0/4.0.3/
setenv PATH ${PATH}:/usr/local/g95/bin
NOTE: This environment variable setting is specifit to Starsky. It is to make configure find the fortran compiler.
Brief profile:
CC = gcc
CXX = g++
FC = g95
If default doesn't work, try:
For C shell:
env CC=gcc CXX=g++ FC=g95 ./configure && make install
For Korn or Bourne shell:
CC=gcc CXX=g++ FC=g95 ./configure && make install
And, of course, you should add configure options, such as --enable-fortran --enable-parallel.
On this host, executing:
For C shell:
env CC=gcc CXX=g++ FC=g95 ./configure --enable-fortran && make install
For Korn or Bourne shell:
CC=gcc CXX=g++ FC=g95 ./configure --enable-fortran && make install
has functioned correctly.
To run test program, go to test directory:
(i) Serial test
run:
./H5testF
./H5PartTest
(5) Linux AMD64 Visualization group workstations (Linux"SUSE"-x86_64)
---------------------------------------------------------
Brief profile:
CC = gcc
CXX = g++
FC = g95
If default doesn't work, try:
For C shell:
env CC=gcc CXX=g++ FC=g95 ./configure && make install
For Korn or Bourne shell:
CC=gcc CXX=g++ FC=g95 ./configure && make install
And, of course, you should add configure options, such as --enable-fortran --enable-parallel.
On this host, executing:
For C shell:
env CC=gcc CXX=g++ FC=g95 ./configure --enable-fortran && make install
For Korn or Bourne shell:
CC=gcc CXX=g++ FC=g95 ./configure --enable-fortran && make install
has functioned correctly.
To run test program, go to test directory:
(i) Serial test
run:
./H5testF
./H5PartTest
==============================================================================
+ 4. Trouble shooting (Things to check for...)
--------------------------------------------
(0) Have you set the LD_LIBRARY_PATH?
---Some systems require the user to manually set the environment variable, LD_LIBRARY_PATH. To do so:
set the environment variable HDF5ROOT or PHDF5ROOT to point to your installation of HDF5 (serial and/or parallel respectively).
For Korn or Bourne shell:
LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${HDF5ROOT}/lib;export LD_LIBRARY_PATH
LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:{PHDF5ROOT}/lib;export LD_LIBRARY_PATH
For C shell:
setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:${HDF5ROOT}/lib
setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:${PHDF5ROOT}/lib
Note that the values of HDF5ROOT & PHDF5ROOT will be in the "summary" section when you run configure.
Not properly set LD_LIBRARY_PATH value may result in a runtime error:
./H5PartTest: error while loading shared libraries: libhdf5.so.0: cannot open shared object file: No such file or directory
(1) Are the compilers set correctly?
---Check with: which COMPILER
(2) Have you installed HDF5?
---You can get it at: http://vis.lbl.gov/Research/AcceleratorSAPP/index.html
(3) Have you loaded the proper modules?
---It is necessary in Davinci & Bassi, and configure && make install may not work without it.
autogen.sh
+26 -24
View File
@@ -1,46 +1,48 @@
#!/bin/sh
# Run this to generate all the initial makefiles, etc.
ACLOCAL_FLAGS="-I m4 -I . $ACLOCAL_FLAGS"
LIBTOOLIZE_FLAGS="--force $LIBTOOLIZE_FLAGS"
AUTOMAKE_FLAGS="--add-missing --copy --foreign $AUTOMAKE_FLAGS"
LIBTOOLIZE=`which libtoolize`
if [ "$LIBTOOLIZE" = "" ]; then
LIBTOOLIZE=`which glibtoolize`
fi
if [ "$LIBTOOLIZE" = "" ]; then
echo "libtoolize not found" 1>&2
exit 1
fi
echo "+ making misc files ..."
touch NEWS README AUTHORS ChangeLog
echo
echo
$LIBTOOLIZE $LIBTOOLIZE_FLAGS || {
echo "libtoolize failed"
exit 1
}
echo
echo "+ running aclocal ..."
aclocal $ACLOCAL_FLAGS || {
echo
echo "aclocal failed - check that all needed development files are present on system"
exit 1
echo "aclocal failed - check that all needed development files are present on system"
exit 1
}
echo
echo
echo
echo
echo "+ running autoheader ... "
autoheader || {
echo
echo "autoheader failed"
exit 1
echo "autoheader failed"
exit 1
}
echo
echo
echo
echo "+ running autoconf ... "
autoconf || {
echo
echo "autoconf failed"
exit 1
echo "autoconf failed"
exit 1
}
echo
echo
echo
echo "+ running automake ... "
automake -a -c --foreign || {
echo
echo "automake failed"
exit 1
automake $AUTOMAKE_FLAGS || {
echo "automake failed"
exit 1
}
echo
echo
echo
ax_pkg_swig.m4
+135
View File
@@ -0,0 +1,135 @@
# ===========================================================================
# http://www.gnu.org/software/autoconf-archive/ax_pkg_swig.html
# ===========================================================================
#
# SYNOPSIS
#
# AX_PKG_SWIG([major.minor.micro], [action-if-found], [action-if-not-found])
#
# DESCRIPTION
#
# This macro searches for a SWIG installation on your system. If found,
# then SWIG is AC_SUBST'd; if not found, then $SWIG is empty. If SWIG is
# found, then SWIG_LIB is set to the SWIG library path, and AC_SUBST'd.
#
# You can use the optional first argument to check if the version of the
# available SWIG is greater than or equal to the value of the argument. It
# should have the format: N[.N[.N]] (N is a number between 0 and 999. Only
# the first N is mandatory.) If the version argument is given (e.g.
# 1.3.17), AX_PKG_SWIG checks that the swig package is this version number
# or higher.
#
# As usual, action-if-found is executed if SWIG is found, otherwise
# action-if-not-found is executed.
#
# In configure.in, use as:
#
# AX_PKG_SWIG(1.3.17, [], [ AC_MSG_ERROR([SWIG is required to build..]) ])
# AX_SWIG_ENABLE_CXX
# AX_SWIG_MULTI_MODULE_SUPPORT
# AX_SWIG_PYTHON
#
# LICENSE
#
# Copyright (c) 2008 Sebastian Huber <sebastian-huber@web.de>
# Copyright (c) 2008 Alan W. Irwin
# Copyright (c) 2008 Rafael Laboissiere <rafael@laboissiere.net>
# Copyright (c) 2008 Andrew Collier
# Copyright (c) 2011 Murray Cumming <murrayc@openismus.com>
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the
# Free Software Foundation; either version 2 of the License, or (at your
# option) any later version.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
# Public License for more details.
#
# You should have received a copy of the GNU General Public License along
# with this program. If not, see <http://www.gnu.org/licenses/>.
#
# As a special exception, the respective Autoconf Macro's copyright owner
# gives unlimited permission to copy, distribute and modify the configure
# scripts that are the output of Autoconf when processing the Macro. You
# need not follow the terms of the GNU General Public License when using
# or distributing such scripts, even though portions of the text of the
# Macro appear in them. The GNU General Public License (GPL) does govern
# all other use of the material that constitutes the Autoconf Macro.
#
# This special exception to the GPL applies to versions of the Autoconf
# Macro released by the Autoconf Archive. When you make and distribute a
# modified version of the Autoconf Macro, you may extend this special
# exception to the GPL to apply to your modified version as well.
#serial 11
AC_DEFUN([AX_PKG_SWIG],[
# Ubuntu has swig 2.0 as /usr/bin/swig2.0
AC_PATH_PROGS([SWIG],[swig swig2.0])
if test -z "$SWIG" ; then
m4_ifval([$3],[$3],[:])
elif test -n "$1" ; then
AC_MSG_CHECKING([SWIG version])
[swig_version=`$SWIG -version 2>&1 | grep 'SWIG Version' | sed 's/.*\([0-9][0-9]*\.[0-9][0-9]*\.[0-9][0-9]*\).*/\1/g'`]
AC_MSG_RESULT([$swig_version])
if test -n "$swig_version" ; then
# Calculate the required version number components
[required=$1]
[required_major=`echo $required | sed 's/[^0-9].*//'`]
if test -z "$required_major" ; then
[required_major=0]
fi
[required=`echo $required | sed 's/[0-9]*[^0-9]//'`]
[required_minor=`echo $required | sed 's/[^0-9].*//'`]
if test -z "$required_minor" ; then
[required_minor=0]
fi
[required=`echo $required | sed 's/[0-9]*[^0-9]//'`]
[required_patch=`echo $required | sed 's/[^0-9].*//'`]
if test -z "$required_patch" ; then
[required_patch=0]
fi
# Calculate the available version number components
[available=$swig_version]
[available_major=`echo $available | sed 's/[^0-9].*//'`]
if test -z "$available_major" ; then
[available_major=0]
fi
[available=`echo $available | sed 's/[0-9]*[^0-9]//'`]
[available_minor=`echo $available | sed 's/[^0-9].*//'`]
if test -z "$available_minor" ; then
[available_minor=0]
fi
[available=`echo $available | sed 's/[0-9]*[^0-9]//'`]
[available_patch=`echo $available | sed 's/[^0-9].*//'`]
if test -z "$available_patch" ; then
[available_patch=0]
fi
# Convert the version tuple into a single number for easier comparison.
# Using base 100 should be safe since SWIG internally uses BCD values
# to encode its version number.
required_swig_vernum=`expr $required_major \* 10000 \
\+ $required_minor \* 100 \+ $required_patch`
available_swig_vernum=`expr $available_major \* 10000 \
\+ $available_minor \* 100 \+ $available_patch`
if test $available_swig_vernum -lt $required_swig_vernum; then
AC_MSG_WARN([SWIG version >= $1 is required. You have $swig_version.])
SWIG=''
m4_ifval([$3],[$3],[])
else
AC_MSG_CHECKING([for SWIG library])
SWIG_LIB=`$SWIG -swiglib`
AC_MSG_RESULT([$SWIG_LIB])
m4_ifval([$2],[$2],[])
fi
else
AC_MSG_WARN([cannot determine SWIG version])
SWIG=''
m4_ifval([$3],[$3],[])
fi
fi
AC_SUBST([SWIG_LIB])
])
config.guess
Vendored
-1469
View File
File diff suppressed because it is too large Load Diff
config.h.in
-44
View File
@@ -1,44 +0,0 @@
/* config.h.in. Generated from configure.ac by autoheader. */
/* "" */
#undef MY_BUILD_CPU
/* "" */
#undef MY_BUILD_OS
/* "" */
#undef MY_BUILD_VENDOR
/* "" */
#undef MY_GNUNAME
/* "" */
#undef MY_UNAME
/* Name of package */
#undef PACKAGE
/* Define to the address where bug reports for this package should be sent. */
#undef PACKAGE_BUGREPORT
/* Define to the full name of this package. */
#undef PACKAGE_NAME
/* Define to the full name and version of this package. */
#undef PACKAGE_STRING
/* Define to the one symbol short name of this package. */
#undef PACKAGE_TARNAME
/* Define to the version of this package. */
#undef PACKAGE_VERSION
/* Version number of package */
#undef VERSION
/* Define to 1 if on AIX 3.
System headers sometimes define this.
We just want to avoid a redefinition error message. */
#ifndef _ALL_SOURCE
# undef _ALL_SOURCE
#endif
config.sub
Vendored
-1563
View File
File diff suppressed because it is too large Load Diff
configure.ac
+453 -566
View File
File diff suppressed because it is too large Load Diff
depcomp
-529
View File
@@ -1,529 +0,0 @@
#! /bin/sh
# depcomp - compile a program generating dependencies as side-effects
scriptversion=2005-02-09.22
# Copyright (C) 1999, 2000, 2003, 2004, 2005 Free Software Foundation, Inc.
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2, or (at your option)
# any later version.
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA
# 02111-1307, USA.
# As a special exception to the GNU General Public License, if you
# distribute this file as part of a program that contains a
# configuration script generated by Autoconf, you may include it under
# the same distribution terms that you use for the rest of that program.
# Originally written by Alexandre Oliva <oliva@dcc.unicamp.br>.
case $1 in
'')
echo "$0: No command. Try \`$0 --help' for more information." 1>&2
exit 1;
;;
-h | --h*)
cat <<\EOF
Usage: depcomp [--help] [--version] PROGRAM [ARGS]
Run PROGRAMS ARGS to compile a file, generating dependencies
as side-effects.
Environment variables:
depmode Dependency tracking mode.
source Source file read by `PROGRAMS ARGS'.
object Object file output by `PROGRAMS ARGS'.
DEPDIR directory where to store dependencies.
depfile Dependency file to output.
tmpdepfile Temporary file to use when outputing dependencies.
libtool Whether libtool is used (yes/no).
Report bugs to <bug-automake@gnu.org>.
EOF
exit $?
;;
-v | --v*)
echo "depcomp $scriptversion"
exit $?
;;
esac
if test -z "$depmode" || test -z "$source" || test -z "$object"; then
echo "depcomp: Variables source, object and depmode must be set" 1>&2
exit 1
fi
# Dependencies for sub/bar.o or sub/bar.obj go into sub/.deps/bar.Po.
depfile=${depfile-`echo "$object" |
sed 's|[^\\/]*$|'${DEPDIR-.deps}'/&|;s|\.\([^.]*\)$|.P\1|;s|Pobj$|Po|'`}
tmpdepfile=${tmpdepfile-`echo "$depfile" | sed 's/\.\([^.]*\)$/.T\1/'`}
rm -f "$tmpdepfile"
# Some modes work just like other modes, but use different flags. We
# parameterize here, but still list the modes in the big case below,
# to make depend.m4 easier to write. Note that we *cannot* use a case
# here, because this file can only contain one case statement.
if test "$depmode" = hp; then
# HP compiler uses -M and no extra arg.
gccflag=-M
depmode=gcc
fi
if test "$depmode" = dashXmstdout; then
# This is just like dashmstdout with a different argument.
dashmflag=-xM
depmode=dashmstdout
fi
case "$depmode" in
gcc3)
## gcc 3 implements dependency tracking that does exactly what
## we want. Yay! Note: for some reason libtool 1.4 doesn't like
## it if -MD -MP comes after the -MF stuff. Hmm.
"$@" -MT "$object" -MD -MP -MF "$tmpdepfile"
stat=$?
if test $stat -eq 0; then :
else
rm -f "$tmpdepfile"
exit $stat
fi
mv "$tmpdepfile" "$depfile"
;;
gcc)
## There are various ways to get dependency output from gcc. Here's
## why we pick this rather obscure method:
## - Don't want to use -MD because we'd like the dependencies to end
## up in a subdir. Having to rename by hand is ugly.
## (We might end up doing this anyway to support other compilers.)
## - The DEPENDENCIES_OUTPUT environment variable makes gcc act like
## -MM, not -M (despite what the docs say).
## - Using -M directly means running the compiler twice (even worse
## than renaming).
if test -z "$gccflag"; then
gccflag=-MD,
fi
"$@" -Wp,"$gccflag$tmpdepfile"
stat=$?
if test $stat -eq 0; then :
else
rm -f "$tmpdepfile"
exit $stat
fi
rm -f "$depfile"
echo "$object : \\" > "$depfile"
alpha=ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz
## The second -e expression handles DOS-style file names with drive letters.
sed -e 's/^[^:]*: / /' \
-e 's/^['$alpha']:\/[^:]*: / /' < "$tmpdepfile" >> "$depfile"
## This next piece of magic avoids the `deleted header file' problem.
## The problem is that when a header file which appears in a .P file
## is deleted, the dependency causes make to die (because there is
## typically no way to rebuild the header). We avoid this by adding
## dummy dependencies for each header file. Too bad gcc doesn't do
## this for us directly.
tr ' ' '
' < "$tmpdepfile" |
## Some versions of gcc put a space before the `:'. On the theory
## that the space means something, we add a space to the output as
## well.
## Some versions of the HPUX 10.20 sed can't process this invocation
## correctly. Breaking it into two sed invocations is a workaround.
sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile"
rm -f "$tmpdepfile"
;;
hp)
# This case exists only to let depend.m4 do its work. It works by
# looking at the text of this script. This case will never be run,
# since it is checked for above.
exit 1
;;
sgi)
if test "$libtool" = yes; then
"$@" "-Wp,-MDupdate,$tmpdepfile"
else
"$@" -MDupdate "$tmpdepfile"
fi
stat=$?
if test $stat -eq 0; then :
else
rm -f "$tmpdepfile"
exit $stat
fi
rm -f "$depfile"
if test -f "$tmpdepfile"; then # yes, the sourcefile depend on other files
echo "$object : \\" > "$depfile"
# Clip off the initial element (the dependent). Don't try to be
# clever and replace this with sed code, as IRIX sed won't handle
# lines with more than a fixed number of characters (4096 in
# IRIX 6.2 sed, 8192 in IRIX 6.5). We also remove comment lines;
# the IRIX cc adds comments like `#:fec' to the end of the
# dependency line.
tr ' ' '
' < "$tmpdepfile" \
| sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' | \
tr '
' ' ' >> $depfile
echo >> $depfile
# The second pass generates a dummy entry for each header file.
tr ' ' '
' < "$tmpdepfile" \
| sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' -e 's/$/:/' \
>> $depfile
else
# The sourcefile does not contain any dependencies, so just
# store a dummy comment line, to avoid errors with the Makefile
# "include basename.Plo" scheme.
echo "#dummy" > "$depfile"
fi
rm -f "$tmpdepfile"
;;
aix)
# The C for AIX Compiler uses -M and outputs the dependencies
# in a .u file. In older versions, this file always lives in the
# current directory. Also, the AIX compiler puts `$object:' at the
# start of each line; $object doesn't have directory information.
# Version 6 uses the directory in both cases.
stripped=`echo "$object" | sed 's/\(.*\)\..*$/\1/'`
tmpdepfile="$stripped.u"
if test "$libtool" = yes; then
"$@" -Wc,-M
else
"$@" -M
fi
stat=$?
if test -f "$tmpdepfile"; then :
else
stripped=`echo "$stripped" | sed 's,^.*/,,'`
tmpdepfile="$stripped.u"
fi
if test $stat -eq 0; then :
else
rm -f "$tmpdepfile"
exit $stat
fi
if test -f "$tmpdepfile"; then
outname="$stripped.o"
# Each line is of the form `foo.o: dependent.h'.
# Do two passes, one to just change these to
# `$object: dependent.h' and one to simply `dependent.h:'.
sed -e "s,^$outname:,$object :," < "$tmpdepfile" > "$depfile"
sed -e "s,^$outname: \(.*\)$,\1:," < "$tmpdepfile" >> "$depfile"
else
# The sourcefile does not contain any dependencies, so just
# store a dummy comment line, to avoid errors with the Makefile
# "include basename.Plo" scheme.
echo "#dummy" > "$depfile"
fi
rm -f "$tmpdepfile"
;;
icc)
# Intel's C compiler understands `-MD -MF file'. However on
# icc -MD -MF foo.d -c -o sub/foo.o sub/foo.c
# ICC 7.0 will fill foo.d with something like
# foo.o: sub/foo.c
# foo.o: sub/foo.h
# which is wrong. We want:
# sub/foo.o: sub/foo.c
# sub/foo.o: sub/foo.h
# sub/foo.c:
# sub/foo.h:
# ICC 7.1 will output
# foo.o: sub/foo.c sub/foo.h
# and will wrap long lines using \ :
# foo.o: sub/foo.c ... \
# sub/foo.h ... \
# ...
"$@" -MD -MF "$tmpdepfile"
stat=$?
if test $stat -eq 0; then :
else
rm -f "$tmpdepfile"
exit $stat
fi
rm -f "$depfile"
# Each line is of the form `foo.o: dependent.h',
# or `foo.o: dep1.h dep2.h \', or ` dep3.h dep4.h \'.
# Do two passes, one to just change these to
# `$object: dependent.h' and one to simply `dependent.h:'.
sed "s,^[^:]*:,$object :," < "$tmpdepfile" > "$depfile"
# Some versions of the HPUX 10.20 sed can't process this invocation
# correctly. Breaking it into two sed invocations is a workaround.
sed 's,^[^:]*: \(.*\)$,\1,;s/^\\$//;/^$/d;/:$/d' < "$tmpdepfile" |
sed -e 's/$/ :/' >> "$depfile"
rm -f "$tmpdepfile"
;;
tru64)
# The Tru64 compiler uses -MD to generate dependencies as a side
# effect. `cc -MD -o foo.o ...' puts the dependencies into `foo.o.d'.
# At least on Alpha/Redhat 6.1, Compaq CCC V6.2-504 seems to put
# dependencies in `foo.d' instead, so we check for that too.
# Subdirectories are respected.
dir=`echo "$object" | sed -e 's|/[^/]*$|/|'`
test "x$dir" = "x$object" && dir=
base=`echo "$object" | sed -e 's|^.*/||' -e 's/\.o$//' -e 's/\.lo$//'`
if test "$libtool" = yes; then
# With Tru64 cc, shared objects can also be used to make a
# static library. This mecanism is used in libtool 1.4 series to
# handle both shared and static libraries in a single compilation.
# With libtool 1.4, dependencies were output in $dir.libs/$base.lo.d.
#
# With libtool 1.5 this exception was removed, and libtool now
# generates 2 separate objects for the 2 libraries. These two
# compilations output dependencies in in $dir.libs/$base.o.d and
# in $dir$base.o.d. We have to check for both files, because
# one of the two compilations can be disabled. We should prefer
# $dir$base.o.d over $dir.libs/$base.o.d because the latter is
# automatically cleaned when .libs/ is deleted, while ignoring
# the former would cause a distcleancheck panic.
tmpdepfile1=$dir.libs/$base.lo.d # libtool 1.4
tmpdepfile2=$dir$base.o.d # libtool 1.5
tmpdepfile3=$dir.libs/$base.o.d # libtool 1.5
tmpdepfile4=$dir.libs/$base.d # Compaq CCC V6.2-504
"$@" -Wc,-MD
else
tmpdepfile1=$dir$base.o.d
tmpdepfile2=$dir$base.d
tmpdepfile3=$dir$base.d
tmpdepfile4=$dir$base.d
"$@" -MD
fi
stat=$?
if test $stat -eq 0; then :
else
rm -f "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3" "$tmpdepfile4"
exit $stat
fi
for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3" "$tmpdepfile4"
do
test -f "$tmpdepfile" && break
done
if test -f "$tmpdepfile"; then
sed -e "s,^.*\.[a-z]*:,$object:," < "$tmpdepfile" > "$depfile"
# That's a tab and a space in the [].
sed -e 's,^.*\.[a-z]*:[ ]*,,' -e 's,$,:,' < "$tmpdepfile" >> "$depfile"
else
echo "#dummy" > "$depfile"
fi
rm -f "$tmpdepfile"
;;
#nosideeffect)
# This comment above is used by automake to tell side-effect
# dependency tracking mechanisms from slower ones.
dashmstdout)
# Important note: in order to support this mode, a compiler *must*
# always write the preprocessed file to stdout, regardless of -o.
"$@" || exit $?
# Remove the call to Libtool.
if test "$libtool" = yes; then
while test $1 != '--mode=compile'; do
shift
done
shift
fi
# Remove `-o $object'.
IFS=" "
for arg
do
case $arg in
-o)
shift
;;
$object)
shift
;;
*)
set fnord "$@" "$arg"
shift # fnord
shift # $arg
;;
esac
done
test -z "$dashmflag" && dashmflag=-M
# Require at least two characters before searching for `:'
# in the target name. This is to cope with DOS-style filenames:
# a dependency such as `c:/foo/bar' could be seen as target `c' otherwise.
"$@" $dashmflag |
sed 's:^[ ]*[^: ][^:][^:]*\:[ ]*:'"$object"'\: :' > "$tmpdepfile"
rm -f "$depfile"
cat < "$tmpdepfile" > "$depfile"
tr ' ' '
' < "$tmpdepfile" | \
## Some versions of the HPUX 10.20 sed can't process this invocation
## correctly. Breaking it into two sed invocations is a workaround.
sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile"
rm -f "$tmpdepfile"
;;
dashXmstdout)
# This case only exists to satisfy depend.m4. It is never actually
# run, as this mode is specially recognized in the preamble.
exit 1
;;
makedepend)
"$@" || exit $?
# Remove any Libtool call
if test "$libtool" = yes; then
while test $1 != '--mode=compile'; do
shift
done
shift
fi
# X makedepend
shift
cleared=no
for arg in "$@"; do
case $cleared in
no)
set ""; shift
cleared=yes ;;
esac
case "$arg" in
-D*|-I*)
set fnord "$@" "$arg"; shift ;;
# Strip any option that makedepend may not understand. Remove
# the object too, otherwise makedepend will parse it as a source file.
-*|$object)
;;
*)
set fnord "$@" "$arg"; shift ;;
esac
done
obj_suffix="`echo $object | sed 's/^.*\././'`"
touch "$tmpdepfile"
${MAKEDEPEND-makedepend} -o"$obj_suffix" -f"$tmpdepfile" "$@"
rm -f "$depfile"
cat < "$tmpdepfile" > "$depfile"
sed '1,2d' "$tmpdepfile" | tr ' ' '
' | \
## Some versions of the HPUX 10.20 sed can't process this invocation
## correctly. Breaking it into two sed invocations is a workaround.
sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile"
rm -f "$tmpdepfile" "$tmpdepfile".bak
;;
cpp)
# Important note: in order to support this mode, a compiler *must*
# always write the preprocessed file to stdout.
"$@" || exit $?
# Remove the call to Libtool.
if test "$libtool" = yes; then
while test $1 != '--mode=compile'; do
shift
done
shift
fi
# Remove `-o $object'.
IFS=" "
for arg
do
case $arg in
-o)
shift
;;
$object)
shift
;;
*)
set fnord "$@" "$arg"
shift # fnord
shift # $arg
;;
esac
done
"$@" -E |
sed -n '/^# [0-9][0-9]* "\([^"]*\)".*/ s:: \1 \\:p' |
sed '$ s: \\$::' > "$tmpdepfile"
rm -f "$depfile"
echo "$object : \\" > "$depfile"
cat < "$tmpdepfile" >> "$depfile"
sed < "$tmpdepfile" '/^$/d;s/^ //;s/ \\$//;s/$/ :/' >> "$depfile"
rm -f "$tmpdepfile"
;;
msvisualcpp)
# Important note: in order to support this mode, a compiler *must*
# always write the preprocessed file to stdout, regardless of -o,
# because we must use -o when running libtool.
"$@" || exit $?
IFS=" "
for arg
do
case "$arg" in
"-Gm"|"/Gm"|"-Gi"|"/Gi"|"-ZI"|"/ZI")
set fnord "$@"
shift
shift
;;
*)
set fnord "$@" "$arg"
shift
shift
;;
esac
done
"$@" -E |
sed -n '/^#line [0-9][0-9]* "\([^"]*\)"/ s::echo "`cygpath -u \\"\1\\"`":p' | sort | uniq > "$tmpdepfile"
rm -f "$depfile"
echo "$object : \\" > "$depfile"
. "$tmpdepfile" | sed 's% %\\ %g' | sed -n '/^\(.*\)$/ s:: \1 \\:p' >> "$depfile"
echo " " >> "$depfile"
. "$tmpdepfile" | sed 's% %\\ %g' | sed -n '/^\(.*\)$/ s::\1\::p' >> "$depfile"
rm -f "$tmpdepfile"
;;
none)
exec "$@"
;;
*)
echo "Unknown depmode $depmode" 1>&2
exit 1
;;
esac
exit 0
# Local Variables:
# mode: shell-script
# sh-indentation: 2
# eval: (add-hook 'write-file-hooks 'time-stamp)
# time-stamp-start: "scriptversion="
# time-stamp-format: "%:y-%02m-%02d.%02H"
# time-stamp-end: "$"
# End:
doc/2006-Berkeley-Visit/BethelSAP_1page-4.doc
BIN
View File
Binary file not shown.
doc/2006-Berkeley-Visit/H5Part.ppt
BIN
View File
Binary file not shown.
doc/2006-Berkeley-Visit/H5xxx.ppt
BIN
View File
Binary file not shown.
doc/2006-Berkeley-Visit/H5xxxVisIt.fig
-294
View File
@@ -1,294 +0,0 @@
#FIG 3.2
Landscape
Center
Inches
Letter
100.00
Single
-2
1200 2
0 32 #c6b797
0 33 #eff8ff
0 34 #dccba6
0 35 #404040
0 36 #808080
0 37 #c0c0c0
0 38 #e0e0e0
0 39 #8e8f8e
0 40 #aaaaaa
0 41 #555555
0 42 #bebebe
0 43 #515151
0 44 #e7e3e7
0 45 #000049
0 46 #797979
0 47 #303430
0 48 #414141
0 49 #c7b696
0 50 #8e8e8e
0 51 #414541
0 52 #8e8e8e
0 53 #000079
0 54 #ff8200
0 55 #007d00
0 56 #0000be
# Desktop computer
6 375 2400 2025 4050
6 1575 3825 2025 4050
2 3 0 1 -1 7 2 0 20 0.000 0 0 -1 0 0 8
1615 3916 1719 3874 1908 3874 1950 3853 1972 3853 1846 3937
1615 3937 1615 3916
2 3 0 1 -1 7 2 0 20 0.000 0 0 -1 0 0 6
1888 3853 1846 3874 1908 3874 1950 3853 1908 3853 1888 3853
2 3 0 1 -1 7 2 0 20 0.000 0 0 -1 0 0 5
1846 3874 1888 3853 1846 3853 1803 3874 1846 3874
2 3 0 1 -1 7 2 0 20 0.000 0 0 -1 0 0 5
1803 3874 1740 3874 1803 3853 1824 3853 1803 3874
2 3 0 1 -1 7 2 0 20 0.000 0 0 -1 0 0 6
1846 3958 1866 3916 1972 3853 1992 3895 1846 3979 1846 3958
2 3 0 1 -1 7 2 0 20 0.000 0 0 -1 0 0 5
1615 3937 1866 3937 1846 3958 1615 3958 1615 3937
2 3 0 1 -1 7 2 0 20 0.000 0 0 -1 0 0 9
1615 3958 1594 4000 1719 4000 1846 4000 1866 4000 1992 3916
1992 3895 1846 3958 1615 3958
-6
6 600 2400 1950 3675
2 3 0 1 -1 7 2 0 15 0.000 0 0 -1 0 0 6
669 2530 648 3307 1594 3307 1615 2468 1594 2468 669 2530
2 3 0 1 -1 7 0 0 10 0.000 0 0 -1 0 0 5
1615 2468 1594 3307 1719 3307 1719 2509 1615 2468
2 3 0 1 -1 7 0 0 15 0.000 0 0 -1 0 0 5
1762 2677 1908 2719 1908 3139 1762 3203 1762 2677
2 3 0 1 -1 7 2 0 15 0.000 0 0 -1 0 0 6
732 3349 732 3412 1594 3454 1594 3371 753 3349 732 3349
2 3 0 1 -1 7 1 0 15 0.000 0 0 -1 0 0 5
1594 3371 1846 3280 1846 3348 1594 3454 1594 3371
2 3 0 1 -1 7 2 0 15 0.000 0 0 -1 0 0 5
732 3433 732 3559 1594 3601 1594 3454 732 3433
2 3 0 1 -1 0 2 0 20 0.000 0 0 -1 0 0 5
1594 3454 732 3412 753 3433 1572 3454 1594 3454
2 3 0 1 -1 7 2 0 8 0.000 0 0 -1 0 0 5
1594 3454 1594 3601 1635 3580 1635 3433 1594 3454
2 3 0 1 -1 7 2 0 8 0.000 0 0 -1 0 0 5
1719 3538 1846 3475 1846 3349 1719 3391 1719 3538
2 3 0 1 -1 7 2 0 10 0.000 0 0 -1 0 0 5
1635 3496 1719 3454 1719 3391 1635 3433 1635 3496
2 3 0 1 -1 7 2 0 10 0.000 0 0 -1 0 0 5
1635 3580 1719 3538 1719 3475 1635 3517 1635 3580
2 1 0 2 -1 7 2 0 8 0.000 0 0 -1 0 0 2
1635 3496 1719 3454
2 1 0 2 -1 7 2 0 8 0.000 0 0 -1 0 0 2
1635 3517 1719 3475
2 3 0 1 -1 7 3 0 10 0.000 0 0 -1 0 0 7
732 3559 732 3601 816 3601 963 3559 963 3538 816 3559
732 3559
2 3 0 1 -1 7 3 0 10 0.000 1 0 -1 0 0 5
1490 3596 1490 3641 1594 3643 1594 3601 1490 3596
2 3 0 1 -1 7 3 0 10 0.000 1 0 -1 0 0 5
1594 3643 1635 3601 1635 3580 1594 3601 1594 3643
2 3 0 1 -1 7 3 0 10 0.000 0 0 -1 0 0 5
1846 3475 1846 3496 1803 3517 1803 3496 1846 3475
2 3 0 1 -1 7 3 0 10 0.000 0 0 -1 0 0 4
1803 3517 1740 3517 1803 3496 1803 3517
2 3 0 1 -1 7 4 0 15 0.000 1 0 -1 0 0 6
879 3307 732 3349 1594 3371 1846 3279 1762 3265 879 3307
2 3 0 1 -1 7 0 0 10 0.000 1 0 -1 0 0 5
1719 2509 1719 3307 1762 3265 1762 2552 1719 2509
3 1 0 1 -1 7 1 0 20 0.000 0 0 0 11
774 2656 816 2614 1488 2572 1510 2593 1530 2636 1530 3139
1510 3181 1467 3203 837 3203 795 3181 774 3160
1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000
1.000 1.000 1.000
-6
6 375 3675 1650 4050
2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 8
1207 3935 1205 3897 1229 3888 1265 3890 1264 3922 1244 3937
1212 3937 1207 3935
2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 8
1264 3939 1261 3900 1285 3892 1320 3893 1319 3925 1300 3940
1268 3940 1264 3939
2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 8
1318 3950 1315 3912 1339 3904 1374 3905 1374 3937 1355 3953
1322 3953 1318 3950
2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 8
1151 3935 1150 3897 1173 3888 1209 3890 1207 3922 1188 3937
1157 3937 1151 3935
2 3 0 1 -1 7 1 0 20 0.000 0 0 -1 0 0 8
1169 3900 1166 3861 1190 3853 1226 3854 1224 3886 1205 3901
1173 3901 1169 3900
2 3 0 1 -1 7 1 0 20 0.000 0 0 -1 0 0 8
1225 3904 1223 3865 1247 3857 1282 3858 1281 3891 1262 3906
1230 3906 1225 3904
2 3 0 1 -1 7 1 0 20 0.000 0 0 -1 0 0 8
1281 3908 1279 3869 1303 3860 1338 3862 1337 3893 1318 3909
1286 3909 1281 3908
2 3 0 1 -1 7 1 0 20 0.000 0 0 -1 0 0 8
1344 3909 1342 3870 1366 3862 1401 3863 1399 3895 1381 3911
1349 3911 1344 3909
2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
1214 3854 1214 3835 1233 3822 1272 3825 1272 3831 1260 3839
1258 3856 1211 3854 1214 3854
2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
1258 3855 1258 3836 1277 3823 1315 3826 1315 3831 1304 3839
1302 3857 1255 3855 1258 3855
2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
1300 3862 1300 3843 1319 3830 1359 3833 1359 3838 1346 3846
1344 3863 1297 3862 1300 3862
2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
1344 3863 1344 3845 1363 3831 1402 3835 1402 3839 1390 3848
1389 3865 1341 3863 1344 3863
2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
1387 3869 1387 3850 1406 3836 1444 3839 1444 3845 1436 3871
1417 3882 1383 3869 1387 3869
2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
708 3798 708 3779 727 3766 766 3769 766 3774 755 3783
752 3800 705 3798 708 3798
2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
747 3803 747 3784 766 3771 805 3775 805 3780 793 3788
791 3805 744 3803 747 3803
2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
794 3805 794 3787 813 3773 852 3777 852 3781 840 3790
839 3807 791 3805 794 3805
2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
832 3810 832 3792 850 3778 889 3781 889 3787 878 3795
876 3812 828 3810 832 3810
2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
876 3812 876 3793 894 3780 934 3784 934 3788 921 3797
919 3814 872 3812 876 3812
2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
919 3816 919 3797 938 3784 977 3787 977 3792 965 3800
964 3817 916 3816 919 3816
2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
962 3816 962 3797 981 3784 1019 3787 1019 3792 1008 3800
1006 3817 959 3816 962 3816
2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
1001 3819 1001 3800 1019 3787 1058 3790 1058 3795 1047 3803
1045 3820 997 3819 1001 3819
2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
1049 3819 1049 3800 1067 3787 1106 3790 1106 3795 1094 3803
1092 3820 1045 3819 1049 3819
2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
661 3822 661 3803 679 3790 718 3793 718 3799 706 3807
704 3824 658 3822 661 3822
2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
704 3831 704 3812 724 3799 762 3802 762 3807 750 3816
748 3832 702 3831 704 3831
2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
748 3834 748 3816 768 3802 806 3805 806 3810 794 3819
793 3835 746 3834 748 3834
2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
789 3838 789 3819 808 3805 847 3808 847 3814 835 3822
833 3839 786 3838 789 3838
2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
832 3840 832 3822 850 3808 889 3812 889 3817 878 3825
876 3842 828 3840 832 3840
2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
874 3842 874 3824 893 3810 932 3814 932 3819 919 3827
918 3844 871 3842 874 3842
2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
916 3846 916 3827 934 3814 974 3817 974 3822 962 3831
960 3847 913 3846 916 3846
2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
961 3846 961 3828 980 3814 1018 3817 1018 3823 1007 3831
1005 3847 957 3846 961 3846
2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
1005 3849 1005 3831 1023 3817 1062 3821 1062 3826 1050 3834
1049 3851 1002 3849 1005 3849
2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
1049 3851 1049 3832 1067 3819 1107 3823 1107 3828 1095 3836
1093 3853 1045 3851 1049 3851
2 3 0 1 -1 7 1 0 20 0.000 0 0 -1 0 0 8
656 3866 655 3827 678 3819 714 3820 713 3853 693 3868
662 3868 656 3866
2 3 0 1 -1 7 1 0 20 0.000 0 0 -1 0 0 8
700 3869 698 3831 722 3822 757 3824 755 3856 737 3871
704 3871 700 3869
2 3 0 1 -1 7 1 0 20 0.000 0 0 -1 0 0 8
744 3876 741 3838 766 3829 801 3831 799 3862 781 3878
748 3878 744 3876
2 3 0 1 -1 7 1 0 20 0.000 0 0 -1 0 0 8
792 3882 790 3842 814 3834 849 3835 848 3868 829 3883
797 3883 792 3882
2 3 0 1 -1 7 1 0 20 0.000 0 0 -1 0 0 8
832 3884 830 3846 854 3837 889 3839 887 3870 869 3886
836 3886 832 3884
2 3 0 1 -1 7 1 0 20 0.000 0 0 -1 0 0 8
880 3890 879 3851 902 3842 938 3844 936 3876 918 3892
886 3892 880 3890
2 3 0 1 -1 7 1 0 20 0.000 0 0 -1 0 0 8
932 3893 930 3854 954 3846 989 3847 988 3879 969 3895
936 3895 932 3893
2 3 0 1 -1 7 1 0 20 0.000 0 0 -1 0 0 8
982 3895 981 3856 1004 3847 1040 3849 1038 3882 1019 3897
988 3897 982 3895
2 3 0 1 -1 7 1 0 20 0.000 0 0 -1 0 0 8
1025 3898 1023 3860 1047 3851 1082 3853 1080 3885 1062 3900
1029 3900 1025 3898
2 3 0 1 -1 7 1 0 20 0.000 0 0 -1 0 0 8
618 3861 616 3822 640 3814 675 3816 674 3847 655 3862
623 3862 618 3861
2 3 0 1 -1 7 1 0 20 0.000 0 0 -1 0 0 8
572 3888 571 3849 594 3840 630 3842 629 3875 609 3890
578 3890 572 3888
2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
609 3888 609 3869 629 3856 667 3860 667 3864 655 3873
654 3890 607 3888 609 3888
2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 7
654 3893 984 3934 988 3898 664 3866 652 3882 652 3888
654 3893
2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
986 3931 986 3913 1004 3900 1043 3902 1043 3908 1032 3916
1029 3933 982 3931 986 3931
2 3 0 1 -1 7 5 0 15 0.000 0 0 -1 0 0 9
429 3871 683 3743 1551 3816 1576 3831 1573 3840 1426 3990
427 3883 427 3869 429 3871
2 1 0 1 -1 7 0 0 -1 0.000 0 0 -1 0 0 3
423 3910 1434 4014 1575 3875
2 3 0 0 -1 7 5 0 10 0.000 0 0 -1 0 0 8
429 3885 429 3928 1430 4050 1580 3895 1576 3831 1423 3990
425 3882 429 3885
-6
-6
6 4050 3000 7500 3750
2 1 0 1 0 0 0 0 -1 0.000 0 0 -1 0 0 4
7500 3000 5430 3000 6120 3690 4050 3690
-6
# TB Data
6 8025 6000 9000 7425
5 1 0 1 -1 -1 0 0 -1 0.000 0 1 0 0 8490.000 5700.000 8040 6300 8490 6450 8940 6300
5 1 0 1 -1 -1 0 0 -1 0.000 0 1 0 0 8490.000 6600.000 8040 7200 8490 7350 8940 7200
1 2 0 1 -1 -1 0 0 -1 0.000 1 0.0000 8490 6150 450 150 8040 6000 8940 6300
2 1 0 1 -1 -1 0 0 -1 0.000 0 0 0 0 0 2
8940 6225 8940 7200
2 1 0 1 -1 -1 0 0 -1 0.000 0 0 0 0 0 2
8040 6225 8040 7200
4 1 -1 0 0 2 12 0.0000 6 135 270 8490 6675 TB\001
4 1 -1 0 0 2 12 0.0000 6 135 405 8490 7275 Data\001
-6
2 1 0 1 0 7 50 0 -1 0.000 0 0 -1 1 1 2
0 0 1.00 60.00 120.00
0 0 1.00 60.00 120.00
2025 3075 2475 3075
2 4 0 1 0 7 50 0 -1 0.000 0 0 7 0 0 5
3750 4650 3750 2100 2550 2100 2550 4650 3750 4650
2 4 0 1 0 7 50 0 -1 0.000 0 0 7 0 0 5
9075 4650 9075 2100 7875 2100 7875 4650 9075 4650
2 1 0 1 0 7 50 0 -1 0.000 0 0 -1 0 1 2
0 0 3.00 60.00 120.00
8400 4800 8400 6000
2 1 0 1 0 7 50 0 -1 0.000 0 0 -1 0 1 2
0 0 3.00 60.00 120.00
8250 4800 8250 6000
2 1 0 1 0 7 50 0 -1 0.000 0 0 -1 0 1 2
0 0 3.00 60.00 120.00
8100 4800 8100 6000
2 1 0 1 0 7 50 0 -1 0.000 0 0 -1 0 1 2
0 0 3.00 60.00 120.00
8850 4800 8850 6000
2 4 0 1 0 7 50 -1 -1 0.000 0 0 7 0 0 5
12000 4500 12000 3975 8175 3975 8175 4500 12000 4500
4 0 0 50 0 2 15 0.0000 4 30 360 8475 5550 ......\001
4 0 0 50 0 0 20 0.0000 4 195 570 2625 3375 VisIt\001
4 0 0 50 0 0 20 0.0000 4 195 570 7950 3375 VisIt\001
4 0 0 50 -1 2 16 0.0000 4 225 1410 9375 4275 H5xxx plugin\001
4 0 0 50 0 0 20 0.0000 4 255 1650 6450 5550 n-way parallel\001
doc/2006-Berkeley-Visit/SAP-Combined-v6.doc
BIN
View File
Binary file not shown.
doc/2006-Berkeley-Visit/aqpsi2006mar22.pdf
BIN
View File
Binary file not shown.
doc/2006-Berkeley-Visit/hdf.ps
-1994
View File
File diff suppressed because one or more lines are too long
doc/Building.html
-262
View File
@@ -1,262 +0,0 @@
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<title>Put your title here!!</title>
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
<meta name="keywords" content="scientific visualization">
<meta name="sitemap" content="put a brief descriptive phrase here that will show up in the site map:foo">
<div id="maincenter">
<head>
<title>Building H5Part</title>
</head>
<body bgcolor="#F0F0F0">
<font face="arial,helvetica" size="+2" color="#555588"><h2>Building H5Part</h2></font>
<UL>
<LI><a href="#Quickstart">Quickstart guide for the impatient.</a>
<LI><a href="#Details">Details of the Configuration Script</a>
<!-- <LI><a href="UsingC++.html">Using the C++ interface</a> -->
<LI><a href="#ConfigOptions">Important Configure Options</a>
<LI><a href="#EnvVariables">Important Environment Variables</a>
</UL>
<hr>
<a name="Quickstart">
<h2>Quickstart <i>for the impatient</i></h2>
</a>
<OL>
<LI><b>Configure</b>:<br>
For the serial implementation
<pre>
./configure
</pre>
For the parallel implementation configure with
<pre>
./configure --enable-parallel
</pre>
If you also want to build fortran bindings, add the
<code>--enable-fortran</code> flag to the configure line.
</LI><p>
<LI><b>Make the Library</b>:<br>
Type <code>make</code> to build the library. The libraries are
named accordingly.
<UL>
<LI>libH5Part.a: Serial C/C++ Library.</LI>
<LI>libpH5Part.a: Parallel C/C++ library.</LI>
<LI>libH5PartF.a: Serial F77/F90 library.</LI>
<LI>libpH5PartF.a: Parallel F77/F90 library.</LI>
</UL>
</LI><p>
<LI><b>Make Regression Tests and Examples</b>:<br>
Just type <code>make tests</code> to build regression tests
and/or example programs for H5Part. These tests are
<UL>
<LI>H5PartF: Fortran example (only build if --enable-fortran
is specified).</LI>
<LI>H5PartFpar: Parallel Fortran example (only built if both
--enable-fortran and --enable-parallel are specified).</LI>
<LI>H5PartTest: Serial C example. This test writes a sample
datafile and then reopens it for reading. It demonstrates
the most basic reading/writing capabilities.</LI>
<LI>H5PartTestP: Parallel C example (only built if
--enable-parallel is specified). This program only works
as an MPI/parallel program.</LI>
<LI>Bench: This program will only be built if
--enable-parallel is specified. It compares the
performance of raw binary
I/O (one file per processor), raw binary MPI-IO based
parallel I/O to a single file, and the parallel H5Part/HDF5 to
a single file. Generally, H5Part should be very close to the
MPI-IO implementation in terms of performance, but slower
than one-file-per-processor. If HDF5 is slower the
MPI-IO, it would indicate that some performance tuning
will be required for your platform (contact us, and we will
see what we can do!).</LI>
</UL>
</LI><p>
<LI><b>Building Your Own Programs</b>:<br>
There are many different subtleties to linking on various
computer platforms, but typically one does the following.
<UL>
<LI>C/C++ Serial:
<br><code>#include
&lt H5Part.h &gt </code> into your
source file.
<br><code>$CC -I<i>path_to_H5Part.h</i>
-I<i>path_to_hdf5.h</i> -o outfile
MyFile.cc -L<i>path_to_libH5Part.a</i> -lH5Part
-L<i>path_to_libhdf5</i> -lhdf5 -lz <i>-lsz</i></code>
</LI>
<LI>C/C++ Parallel:
<br><code>#include
&lt H5Part.h &gt </code> into your
source file.
<br><code>$MPICC -I<i>path_to_H5Part.h</i>
-I<i>path_to_hdf5.h</i> -DPARALLEL_IO
-DH5_HAVE_PARALLEL -o outfile
MyFile.cc -L<i>path_to_libH5Part.a</i> -lH5Part
-L<i>path_to_libhdf5</i> -lhdf5 -lz <i>-lsz</i></code>
</LI>
<LI>Fortran Serial:
<br><code>include
'H5Part.inc'</code> into your
source file.
<br><code>$FC -I<i>path_to_H5Part.h</i>
-I<i>path_to_hdf5.h</i> -o outfile
MyFile.cc -L<i>path_to_libH5PartF.a</i> -lH5PartF
-L<i>path_to_libhdf5</i> -lhdf5 -lz <i>-lsz</i> -lc</code>
</LI>
<LI>Fortran Parallel:
<br><code>include
'H5Part.inc'</code> into your
source file.
<br><code>$MPIF90 -I<i>path_to_H5Part.h</i>
-o outfile
MyFile.cc -L<i>path_to_libpH5PartF.a</i> -lpH5PartF
-L<i>path_to_libhdf5</i> -lhdf5 -lz <i>-lsz</i> -lc</code>
</LI><p>
</UL>
</OL>
<hr>
<a name="Details">
<h1>Details for H5Part Configure and Build</h1>
</a>
<a name="ConfigOptions">
<h2>Configure Options</h2>
</a>
H5Part uses GNU Autoconf to generate a Makefile from the makefile
template called <code>Makefile.in</code>.
The configure script pays attention to the following
configure options;<p>
<UL>
<LI><b>--prefix=PREFIX</b> Install files in PREFIX</LI>
<LI><b>--enable-fortran</b> By default H5part will make no attempt to
build Fortran bindings. If you add the
<code>--enable-fortran</code> flag to the ./configure line, it
will create a small test program to determine how to generate
the fortran bindings and then create a library that includes
those bindings. You may need to set the fortran compiler by
setting the <code>FC</code> environment variable in your shell.</LI>
<LI><b>--enable-parallel</b> The version of HDF5 that you build for
Parallel I/O differs from the library you would build for
serial I/O. Consequently, the H5Part libraries must be built
specifically for the kind of I/O you have in mind (parallel or
serial). The configure script will attempt to find an
<code>mpicc</code> if it is available. If no
<code>mpicc</code> is available it will use the regular
C-compiler and will try to locate the location of the MPI
include files and libraries. You can assist the configure
program in its search by setting the <code>MPIROOT</code>
environment variable.</LI>
<LI><b>--enable-tools</b> Builds the currently available tools
<br>
<b>h5pAttrib</b>, an inspection tool that prints the number of timesteps in a file
the file attributes, the step attributes, the dataset names and their values.
<br>
<b>h5pToGNUplot</b>, a converter to two column ASCII format to load in GNUplot.
</LI>
<LI><b>--enable-python</b><font color=red> Under construction</font> Option to build python bindings. It has not been tested.
</LI>
<LI><b>--help</b> Prints configure options.
</LI>
</UL>
<p>
<a name="MakeOptions">
<h2>Make Options</h2>
</a>
<UL>
<LI>make</LI>builds the libraries and test programs
<LI>make install</LI>builds and installs
<LI>make clean</LI>removes extraneous object files
<LI>make distclean</LI>returns configuration to unconfigured state
</UL>
<a name="EnvVariables">
<h2>Environment Variables for Configure</h2>
</a>
The
configuration script is of limited intelligence. Sometimes, you
have to define the following environment variables in order to
help it on its way. You will often only need to tell it where to
find the HDF5 libraries (<code>H5ROOT</code> for serial or
<code>PHDF5ROOT</code> for parallel builds). All of these
environment variables can also be overidden in the Makefile that
is generated by the autoconfigure script.
The configure script pays attention to the following
environment variables;
<p>
<UL>
<LI><b>CC</b>: Use the <code>CC</code> environment variable to tell the
configure script where to find the C compiler. You can
also directly modify this variable in the
<code>Makefile</code> that is generated by the autoconfigure</LI>
<LI><b>CXX</b>: Use the <code>CXX</code> environment variable to tell the
configure script where to find the C++ compiler. You can
also directly modify this variable in the
<code>Makefile</code> that is generated by the autoconfigure</LI>
<LI><b>FC</b>: Use the <code>FC</code> environment variable to tell the
configure script where to find the fortran compiler. You can
also directly modify this variable in the
<code>Makefile</code> that is generated by the autoconfigure</LI>
<LI><b>MPICC</b>: If you are building for parallel C I/O, then it is
useful to tell the configure script where to find the
<code>mpicc</code> script. Normally, <code>mpicc</code> is
merely a wrapper script for a build using a regular C-compiler.
If no <code>mpicc</code> is available, then the
<code>configure</code> script will attempt to locate the mpi
header files and libraries. In that case, it may be useful to
define the <code>MPI_HOME</code> environment variable.</LI>
<LI><b>MPICXX</b>If you are building for parallel C++</LI>
<LI><b>MPIFC</b>: If you are building for parallel Fortran I/O, then it is
useful to tell the configure script where to find the parallel fortran compiler.
<LI><b>MPIROOT</b>: Set this environment variable to help the
configure script to locate the MPI libraries that should be
used to build the parallel version of the libraries. This
variable will be ignored if configured only to build the
serial implementation of the library.</LI>
<LI><b>HDF5ROOT</b>: Find the path to your serial HDF5 installation. If you
are building the serial version of H5part, then you should set
the <code>PHDF5ROOT</code> environment variable.</LI>
</UL><p>
<h3>Common compiler environemt variables for NERSC platforms</h3>
<UL>
<LI><b>DaVinci</b>: Linux ia64 </LI>
CC=icc CXX=icc F90=ifort MPICC=icc MPIFC=ifort MPILIB=-L/usr/lib/ -lmpi MPIINC=-I/usr/include
<LI><b>Bassi</b>: AIX</LI>
CC=cc_r CXX=cc_r FC=xlf_r MPICC=mpcc_r MPICXX=mpcc_r MPIFC=mpxlf_r
<LI><b>Jacquard</b>: Linux x86_64</LI>
CC=pathcc CXX=pathCC FC=pathf90 MPICC=mpicc MPICXX=mpicxx MPIFC=mpif90
<LI><b>Starsky.lbl.gov:</b> (Darwin) PowerPC</LI>
CC=gcc CXX=g++ FC=g95
</UL>
<br>
NOTE: You might need to set the MPI library path (MPILIB) and MPI includes (MPIIINC) if they are in non standard places. For example: <br>
MPILIB=-L/usr/lpp/ppe.poe/lib -lmpi_r MPIINC=-I/usr/lpp/ppe.poe/include/thread
<h3>How to set the variables for configure:</h3>
It is very simple just call env with the variables together with configure. Notice the quotes in MPILIB.
<pre>
% env CC=icc CXX=icc F90=ifort MPICC=icc MPILIB=-L/usr/lib/ -lmpi MPIINC=-I/usr/include ./configure (configure options follow here)
</pre>
In the worst case, you can edit the <code>src/Makefile.am</code> and <code>test/Makefile.am</code> as
needed to perform the proper build.
</div>
doc/BuildingHDF5.html
-68
View File
@@ -1,68 +0,0 @@
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<title>Put your title here!!</title>
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
<meta name="keywords" content="scientific visualization">
<meta name="sitemap" content="put a brief descriptive phrase here that will show up in the site map:foo">
<!--#include virtual="/include/topIncludes.html"-->
<div id="maincenter">
<head>
<title>Building HDF5</title>
</head>
<body bgcolor="#F0F0F0">
<font face="arial,helvetica" size="+2" color="#555588"><h2>Building H5Part</h2></font>
<UL>
<LI><a href="#ConfigOptions">Configure Options</a>
<LI><a href="#EnvVariables">Important Environment Variables</a>
</UL>
<hr>
<a name="ConfigOptions">
<h2>Configure options</h2></a>
</a>
To set the installation path configure with
<pre>
./configure --prefix=your hdf5 installation full path, e.g.--prefix=/usr/local/hdf5
</pre>
For the serial implementation configure with
<pre>
./configure
</pre>
For the parallel implementation configure with
<pre>
./configure --enable-parallel
</pre>
To enable shared objects configure with
<pre>
./configure --enable-shared
</pre>
<a name="EnvVariables">
<h2>Environment Variables</h2></a>
</a>
To add HDF5 to your PATH and LD_LIBRARY_PATH edit your
.tcshr, or .cshrc depending on the shell you are using and add
<pre>
setenv HDF5 "your hdf5 installation full path"
setenv PATH ${PATH}:${HDF5}/bin
setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:${HDF5}/lib
</pre>
if you are using bash, add to your .bashrc
<pre>
export HDF5="your hdf5 installation full path"
export PATH=$PATH:${HDF5}/bin
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:${HDF5}/lib
</pre>
Open a new terminal or do a
source .tcshr (.cshrc, .bashrc) in the one that you are using.
You can <a href="http://vis.lbl.gov/Research/AcceleratorSAPP/Downloading.html">continue <a/>downloading and installing H5Part.
</div>
<!--#include virtual="/include/dateFooter.html"-->
doc/Downloading.html
-48
View File
@@ -1,48 +0,0 @@
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<title>Put your title here!!</title>
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
<meta name="keywords" content="scientific visualization">
<meta name="sitemap" content="put a brief descriptive phrase here that will show up in the site map:foo">
<!--#include virtual="/include/topIncludes.html"-->
<div id="maincenter">
<head>
<title>Downloading H5Part</title>
</head>
<body bgcolor="#F0F0F0">
<font face="arial,helvetica" size="+2" color="#555588"><h2>Downloading H5Part</h2></font>
<UL>
<LI><a href="#svnano">Subversion access.</a>
</UL>
<hr>
<a name="svnano">
<h2>Subversion access</h2>
</a>
<LI><b>Anonymous via. Savannah</b>:<br>
Use svn from <a href="http://subversion.tigris.org"> tigris </a>
<pre>
svn checkout svn+ssh://svn@savannah.psi.ch/afs/psi.ch/project/amas/svn/root/amas/H5Part/ .
</pre>
Password is svn.
<LI><b>Using AFS</b>:<br>
You need AFS (openAFS) and must have an AFS-Account at PSI which in consequence gives you
the needed access right.
</LI><p>
<pre>
svn checkout file:///afs/psi.ch/project/amas/svn/root/amas/H5Part/ .
</pre>
In case of trouble please contact the person mentioned at the bottom of this page.
<hr>
<address><a href="mailto:andreas.adelmann@psi.ch">Andreas Adelmann</a></address>
<!-- Created: March 7 12:52:52 PST 2005 -->
<!-- hhmts start -->
Last modified: Mon Jan 9 22:18:55 CET 2006
<!-- hhmts end -->
</div>
<!--#include virtual="/include/dateFooter.html"-->
doc/Doxyfile
+2311 -165
View File
File diff suppressed because it is too large Load Diff
doc/Examples/meshexample.dxf
+47962
View File
File diff suppressed because it is too large Load Diff
doc/Examples/meshexample.txt
+77
View File
@@ -0,0 +1,77 @@
NumLevels: 2
NumVerticesOnLevel: 11 20 29
Vertices:
1 0.0 0.0
2 60.0 -70.0
3 90.0 -10.0
4 140.0 -70.0
5 180.0 -10.0
6 240.0 -60.0
7 220.0 60.0
8 140.0 90.0
9 200.0 120.0
10 130.0 150.0
11 50.0 80.0
12 115.0 40.0
13 95.0 85.0
14 70.0 35.0
15 160.0 -40.0
16 135.0 -10.0
17 115.0 -40.0
18 200.0 25.0
19 180.0 75.0
20 160.0 40.0
21 125.0 15.0
22 112.5 -10.0
23 102.5 15.0
24 147.5 15.0
25 137.5 40.0
26 150.0 65.0
27 127.5 65.0
28 117.5 87.5
29 105.0 62.5
NumElemsOnLevel: 12 24 36
NumElems: 12 28 44
Elements:
ID PID CID VertexIDs Adj Translation Tbl (dim num lvls - 1)
1 -1 -1 1 2 3 2 11 -1 1
2 -1 -1 2 3 4 3 -1 1 2
3 -1 12 3 4 5 4 12 2 -1
4 -1 -1 4 5 6 5 -1 3 3
5 -1 -1 5 7 6 -1 4 6 4
6 -1 17 8 5 7 5 7 12 -1
7 -1 -1 8 9 7 -1 6 8 5
8 -1 -1 10 8 9 7 -1 9 6
9 -1 -1 11 10 8 8 10 -1 7
10 -1 25 11 3 8 12 9 11 -1
11 -1 -1 1 11 3 10 1 -1 8
12 -1 21 3 8 5 6 3 10 -1
13 3 -1 3 14 13 16 21 2 9
14 3 -1 14 4 12 4 16 2 10
15 3 -1 13 12 5 4 23 16 11
16 3 -1 14 13 12 15 14 13 12
17 6 -1 8 17 16 20 5 22 13
18 6 -1 17 5 15 5 20 23 14
19 6 -1 16 15 7 5 7 20 15
20 6 -1 17 16 15 19 18 17 16
21 12 -1 3 18 13 24 13 26 17
22 12 -1 18 8 17 17 24 27 18
23 12 -1 13 17 5 18 15 24 19
24 12 -1 18 13 17 23 22 21 20
25 10 -1 11 20 19 28 9 11 21
26 10 -1 20 3 18 21 28 11 22
27 10 -1 19 18 8 22 9 28 23
28 10 -1 20 3 18 27 26 25 24
3,0 3,1 4,2 2,3 16,4
1 2 -1 3 4
1 2 3
1 3 6
2 11 1 13 14
doc/Examples/simple_tet.vtk
+107
View File
@@ -0,0 +1,107 @@
# vtk DataFile Version 2.0
VTK LEGACY FILE FORMAT ASCII - tetrahedral sample file for H5FED test
ASCII
DATASET UNSTRUCTURED_GRID
POINTS 17 DOUBLE
-1 0 0
1 0 0
0 1 0
0 0 1
0 -1 0
-0.5 0 0.5
-0.5 0.5 0
0 0 0
0 0.5 0.5
0.5 0 0.5
0.5 0.5 0
-0.75 0 0.25
-0.75 0.25 0
-0.5 0 0
-0.5 0.25 0.25
-0.25 0 0.25
-0.25 0.25 0
CELLS 18 90
4 0 3 2 1
4 0 4 3 1
4 0 5 6 7
4 5 3 8 9
4 6 8 2 10
4 7 9 10 1
4 5 6 7 9
4 5 6 8 9
4 6 7 9 10
4 6 8 9 10
4 0 11 12 13
4 11 5 14 15
4 12 14 6 16
4 13 15 16 7
4 11 12 13 15
4 11 12 14 15
4 12 13 15 16
4 12 14 15 16
CELL_TYPES 18
10
10
10
10
10
10
10
10
10
10
10
10
10
10
10
10
10
10
POINT_DATA 17
SCALARS vertex_id int 1
LOOKUP_TABLE default
0
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
CELL_DATA 18
SCALARS cell_attribute_data int 1
LOOKUP_TABLE default
0
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
doc/Examples/simple_tet_level0.vtk
+59
View File
@@ -0,0 +1,59 @@
# vtk DataFile Version 2.0
VTK LEGACY FILE FORMAT ASCII - tetrahedral sample file for H5FED test
ASCII
DATASET UNSTRUCTURED_GRID
POINTS 17 DOUBLE
-1 0 0
1 0 0
0 1 0
0 0 1
0 -1 0
-0.5 0 0.5
-0.5 0.5 0
0 0 0
0 0.5 0.5
0.5 0 0.5
0.5 0.5 0
-0.75 0 0.25
-0.75 0.25 0
-0.5 0 0
-0.5 0.25 0.25
-0.25 0 0.25
-0.25 0.25 0
CELLS 2 10
4 0 3 2 1
4 0 4 3 1
CELL_TYPES 2
10
10
POINT_DATA 17
SCALARS vertex_id int 1
LOOKUP_TABLE default
0
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
CELL_DATA 2
SCALARS cell_attribute_data int 1
LOOKUP_TABLE default
0
1
doc/Examples/simple_tet_level1.vtk
+80
View File
@@ -0,0 +1,80 @@
# vtk DataFile Version 2.0
VTK LEGACY FILE FORMAT ASCII - tetrahedral sample file for H5FED test
ASCII
DATASET UNSTRUCTURED_GRID
POINTS 17 DOUBLE
-1 0 0
1 0 0
0 1 0
0 0 1
0 -1 0
-0.5 0 0.5
-0.5 0.5 0
0 0 0
0 0.5 0.5
0.5 0 0.5
0.5 0.5 0
-0.75 0 0.25
-0.75 0.25 0
-0.5 0 0
-0.5 0.25 0.25
-0.25 0 0.25
-0.25 0.25 0
CELLS 9 45
4 0 4 3 1
4 0 5 6 7
4 5 3 8 9
4 6 8 2 10
4 7 9 10 1
4 5 6 7 9
4 5 6 8 9
4 6 7 9 10
4 6 8 9 10
CELL_TYPES 9
10
10
10
10
10
10
10
10
10
POINT_DATA 17
SCALARS vertex_id int 1
LOOKUP_TABLE default
0
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
CELL_DATA 9
SCALARS cell_attribute_data int 1
LOOKUP_TABLE default
0
1
2
3
4
5
6
7
8
doc/Examples/simple_tet_level2.vtk
+101
View File
@@ -0,0 +1,101 @@
# vtk DataFile Version 2.0
VTK LEGACY FILE FORMAT ASCII - tetrahedral sample file for H5FED test
ASCII
DATASET UNSTRUCTURED_GRID
POINTS 17 DOUBLE
-1 0 0
1 0 0
0 1 0
0 0 1
0 -1 0
-0.5 0 0.5
-0.5 0.5 0
0 0 0
0 0.5 0.5
0.5 0 0.5
0.5 0.5 0
-0.75 0 0.25
-0.75 0.25 0
-0.5 0 0
-0.5 0.25 0.25
-0.25 0 0.25
-0.25 0.25 0
CELLS 16 80
4 0 4 3 1
4 5 3 8 9
4 6 8 2 10
4 7 9 10 1
4 5 6 7 9
4 5 6 8 9
4 6 7 9 10
4 6 8 9 10
4 0 11 12 13
4 11 5 14 15
4 12 14 6 16
4 13 15 16 7
4 11 12 13 15
4 11 12 14 15
4 12 13 15 16
4 12 14 15 16
CELL_TYPES 16
10
10
10
10
10
10
10
10
10
10
10
10
10
10
10
10
POINT_DATA 17
SCALARS vertex_id int 1
LOOKUP_TABLE default
0
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
CELL_DATA 16
SCALARS cell_attribute_data int 1
LOOKUP_TABLE default
1
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
doc/Examples/trimesh_dgraph_level0.metis
+13
View File
@@ -0,0 +1,13 @@
12 14
2 11
1 3
2 4 12
3 5
4 6
5 7 12
6 8
7 9
8 10
9 11 12
1 10
3 6 10
doc/Examples/trimesh_dgraph_level0.metis.part.2
+12
View File
@@ -0,0 +1,12 @@
0
1
1
1
1
1
0
0
0
0
0
1
doc/Examples/trimesh_dgraph_level0.metis.part.3
+12
View File
@@ -0,0 +1,12 @@
1
1
2
2
2
0
0
0
0
1
1
2
doc/Examples/trimesh_dnode_level1.metis
+49
View File
@@ -0,0 +1,49 @@
24 35
%1
2 8
%2
1 9 10
%3
4 10 11
%4
3 14 15
%5
6 13 15
%6
5 7
%7
6 21 23
%8
1 21 22
%9
2 12 17
%10
2 3 12
%11
3 12 19
%12
9 10 11
%13
5 16 18
%14
4 16 19
%15
4 5 16
%16
13 14 15
%17
9 20 22
%18
13 20 23
%19
11 14 20
%20
17 18 19
%21
7 8 24
%22
8 17 24
%23
7 18 24
%24
21 22 23
doc/Examples/trimesh_dnode_level1.metis.part.2
+24
View File
@@ -0,0 +1,24 @@
1
1
0
0
0
0
1
1
1
1
0
1
0
0
0
0
1
0
0
0
1
1
1
1
doc/Examples/trimesh_level0.metis
+13
View File
@@ -0,0 +1,13 @@
12 1
1 2 3
2 3 4
3 4 6
4 5 6
5 6 7
6 7 8
7 8 11
8 10 11
8 9 10
3 8 9
1 3 9
3 6 8
doc/Examples/trimesh_level0.metis.epart.2
+12
View File
@@ -0,0 +1,12 @@
1
1
1
1
0
0
0
0
0
0
1
1
doc/Examples/trimesh_level0.metis.ngraph
+12
View File
@@ -0,0 +1,12 @@
11 22
2 3 9
1 3 4
1 2 4 6 8 9
2 3 6 5
4 6 7
3 4 5 7 8
5 6 8 11
6 7 11 10 9 3
8 10 3 1
8 11 9
7 8 10
doc/Examples/trimesh_level0.metis.npart.2
+11
View File
@@ -0,0 +1,11 @@
1
1
1
1
1
0
0
0
0
0
0
doc/Examples/trimesh_level1.metis
+41
View File
@@ -0,0 +1,41 @@
20 43
%1
2 3 11
%2
1 3 4
%3
1 2 14 13 18 20
%4
2 14 12 6
%5
12 6 15 17 13
%6
4 5 7
%7
6 15 16 9
%8
9 10 19 18 17 16
%9
7 8 10
%10
8 9 11
%11
1 20 19 10
%12
4 14 13 5
%13
3 14 12 5 17 18
%14
3 13 12 4
%15
5 17 17 7
%16
7 8 17 15
%17
5 15 16 8 18 13
%18
3 13 17 8 19 20
%19
8 11 20 18
%20
3 18 19 11
doc/Examples/trimesh_level1.metis.part.2
+20
View File
@@ -0,0 +1,20 @@
1
1
1
0
0
0
0
1
1
1
1
0
0
0
0
0
0
1
1
1
doc/H5.dox
+171
View File
@@ -0,0 +1,171 @@
/*!
\mainpage H5hut: A High-Performance I/O Library for Particle-based Simulations
Particle-based simulations running on large high-performance computing systems
over many time steps can generate an enormous amount of particle- and
field-based data for post-processing and analysis. Achieving high-performance
I/O for this data, effectively managing it on disk, and interfacing it with
analysis and visualization tools can be challenging, especially for domain
scientists who do not have I/O and data management expertise. We present the
H5hut library, an implementation of several data models for particle-based
simulations that encapsulates the complexity of HDF5 and is simple to use, yet
does not compromise performance.
Developers:
<UL>
<LI> Andreas Adelmann (PSI) </LI>
<LI> Achim Gsell (PSI) </LI>
<LI> Mark Howison (NERSC/LBNL) </LI>
<LI> Prabhat (NERSC/LBNL) </LI>
<LI> Wes Bethel (NERSC/LBNL) </LI>
</UL>
Previous developers:
<UL>
<LI> Benedikt Oswald (PSI) </LI>
<LI> Cristina Siegerist (NERSC/LBNL)</LI>
<LI> John Shalf (NERSC/LBNL)</LI>
</UL>
For more information, please contact the
<a href="mailto:h5part@lists.psi.ch">h5part</a> mailing list.
\defgroup c_api C API
@{
\note The C API is implemented with '\c static \c inline' functions to minimize overhead.
\defgroup h5_c_api H5
@{
\defgroup h5_file File interface
In this section we document the interface for accessing H5hut files.
\defgroup h5_model Setting up the data model
The fundamental data model of H5hut is pretty simple. There
are (time-)steps to group data, that's it. In this section we
document the interface to these (time-)steps.
\defgroup h5_file_attribs File attributes interface
File attributes are small datasets that can be used to
describe specific properties of a file. The H5hut API provides
functions to attach (write), read and inquire file attributes.
\defgroup h5_step_attribs Step attributes interface
Step attributes are similar to file attributes but are
attached to (time-)steps. They can be used to describe
specific properties of a specific step. The H5hut API provides
functions to attach (write), read and inquire step attributes.
\defgroup h5_attach Attaching files
Sometimes it is required (or at least useful) to attach
additional information to H5hut files. H5hut provides
functions to attach other files to H5hut files. The attached
files can be of any type.
\defgroup h5_log Controlling verbosity level
Controlling the verbosity level of H5hut. By default only
error messages are printed. For debugging it might be helpful
to increase the verbosity level.
\defgroup h5_debug Controlling debug output
Debug output mainly intended for developers.
\defgroup h5_error Error handling interface
H5hut comes with two error handler. The default error handler
prints an error message (which can be suppressed by setting
the verbosity level to \c 0), sets an internal error number
and returns to the calling program with the value \c
H5_FAILURE. It is up to the programmer to handle the error
properly. In certain use-cases it make sense just to abort the
program, so no additional error handling is needed. H5hut
provides an abort error-handler for this use-cases-
@}
\defgroup h5part_c_api H5Part
@{
\defgroup h5part_model Setting up the data model
The H5Part data model interface provides functions to set and
inquire (per core) views on datasets.
\defgroup h5part_io Dataset interface
The dataset interface provides functions to read and write
datasets. The following data types are supported:
- 64-bit floating point numbers (\c h5_float64_t)
- 32-bit floating point numbers (\c h5_float32_t)
- 64-bit integers (\c h5_int64_t)
- 32-bit integers (\c h5_int32_t)
\note Before you can write or read a dataset, you have to
define a "view" on the dataset for each core.
@}
\defgroup h5block_c_api H5Block
@{
\defgroup h5block_model Setting up the data model
The H5Block data model interface provides functions to set and
inquire (per core) views on fields.
\defgroup h5block_io Interface to block structured data
H5Block provides functions to store and retrieve
- 3-dimensional fields with scalar values
- 3-dimensional fields with 3-dimensional vectors as values
The following datatypes are supported:
- 64-bit floating point numbers (\c h5_float64_t)
- 32-bit floating point numbers (\c h5_float32_t)
- 64-bit integers (\c h5_int64_t)
- 32-bit integers (\c h5_int32_t)
\defgroup h5block_attrib Attaching attributes to field data
Field attributes are small datasets that can be used to
describe specific properties of a field like origin, spacing
or coordinates. The H5hut API provides functions to attach
(write), read and inquire file attributes.
@}
@}
*/
/*!
\defgroup f90_api Fortran90 API
@{
\defgroup h5_f90_api H5
@{
\defgroup h5_file_f file interface
\defgroup h5_model_f setting up the data model
\defgroup h5_file_attribs_f reading and writing file attributes
\defgroup h5_step_attribs_f reading and writing step attributes
\defgroup h5_log_f control verbosity level
\defgroup h5_debug_f control debug output
\defgroup h5_error_f error handling interface
@}
\defgroup h5part_f90_api H5Part
@{
\defgroup h5part_model_f setting up the data model
\defgroup h5part_io_f reading and writing datasets
@}
\defgroup h5block_f90_api H5Block
@{
\defgroup h5block_model_f setting up the data model
\defgroup h5block_io_f reading and writing datasets
\defgroup h5block_attrib_f reading and writing attributes
@}
@}
*/
doc/H5PartExpress.html
-14
View File
@@ -1,14 +0,0 @@
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<title>Put your title here!!</title>
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
<meta name="keywords" content="scientific visualization">
<meta name="sitemap" content="put a brief descriptive phrase here that will show up in the site map:foo">
<div id="maincenter">
Under construction, will be here soon.
</div>
doc/H5PartIDL.html
-15
View File
@@ -1,15 +0,0 @@
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<title>Put your title here!!</title>
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
<meta name="keywords" content="scientific visualization">
<meta name="sitemap" content="put a brief descriptive phrase here that will show up in the site map:foo">
<div id="maincenter">
Under construction, will be here soon.
</div>
doc/H5PartParaview.html
-15
View File
@@ -1,15 +0,0 @@
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<title>Put your title here!!</title>
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
<meta name="keywords" content="scientific visualization">
<meta name="sitemap" content="put a brief descriptive phrase here that will show up in the site map:foo">
<div id="maincenter">
Under construction, will be here soon.
</div>
doc/H5PartTools.html
-99
View File
@@ -1,99 +0,0 @@
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<title>Put your title here!!</title>
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
<meta name="keywords" content="scientific visualization">
<meta name="sitemap" content="put a brief descriptive phrase here that will show up in the site map:foo">
<!--#include virtual="/include/topIncludes.html"-->
<div id="maincenter">
<head>
<title>H5Part Utility Tools</title>
</head>
<body bgcolor="#F0F0F0">
<font face="arial,helvetica" size="+2" color="#555588"><h2>H5Part Utility Tools</h2></font>
<UL>
<LI><a href="h5pAttrib">h5pAttrib</a>
<LI><a href="h5pToGNUplot">h5pToGNUplot</a>
</UL>
<hr>
<a name="h5pAttrib">
<h2>h5pAttrib</h2>
</a>
<b>h5pAttrib</b> is an inspection tool that prints to stdout the number of timesteps in a file
the file attributes, the step attributes, the dataset names and their values. It's simpler to use than h5dump.
Usage options are given by typing:
<br><br>
<PRE>
% ./h5pAttrib -h
usage: h5pAttrib [OPTIONS] file
OPTIONS
-h, --help Print help page
-n, --nstep Print number of steps
-A, --fileA Print file attributes
-a, --stepA Print step attributes & values for time step n
-d, --dataset Print data sets names & values for time step n
-H, --header Print shorter version without the values
</PRE>
<h3>Examples</h3>
<OL>
<LI>
Show file attribute names & values of sample.h5part
</LI>
h5pAttrib -A sample.h5part
<LI>
Show step attribute names for time step 5 of sample.h5part
</LI>
h5pAttrib -a 5 -H sample.h5part
</OL>
<a name="h5pToGNUplot">
<h2>h5pToGNUplot</h2>
</a>
<b>h5pToGNUplot</b> is a converter from H5Part to two column ASCII text format for loading into GNUplot. Usage options are given by typing:
<br><br>
<PRE>
% ./h5pToGNUplot -h
usage: h5pToGNUplot -t TIMESTEP -1 VARIABLE#1 -2 VARIABLE#2 -i INPUTFILE [OPTIONAL_FLAGS]
FLAGS
-h, --help Print help page
-1, --1var (REQUIRED) Takes first variable parameter
-2, --2var (REQUIRED) Takes second variable parameter
-i, --input (REQUIRED) Takes input file name
-t, --timestep (REQUIRED) Sets the timestep (Value -1 will result in dumping values of all timesteps.)
-o, --output (OPTIONAL) Takes output file name (without this flag, the program will print to stdout)
-n, --number (OPTIONAL) Sets number of output points
-s, --start (OPTIONAL) Sets the starting particle index
</PRE>
<h3>Examples</h3>
<OL>
<LI>
Create a GNU plot file output.txt from sample.h5part by ploting x vs px for timestep 54
</LI>
h5pToGNUplot -t 54 -1 x -2 px -i sample.h5part -o output.txt
<LI>
Create a GNU plot file output.txt from sample.h5part by ploting x vs px for timestep 54
using 1200 points from particle index 76
</LI>
h5pToGNUplot -t 54 -1 x -2 px -i sample.h5part -o output.txt -s 76 -n 1200
</OL>
</div>
<!--#include virtual="/include/dateFooter.html"-->
doc/H5PartVisIt.html
-75
View File
@@ -1,75 +0,0 @@
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<title>H5Part: VisIt Plugins</title>
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
<meta name="keywords" content="scientific visualization">
<meta name="sitemap" content="put a brief descriptive phrase here that will show up in the site map:foo">
<div id="maincenter">
<font face="arial,helvetica"><h1>H5Part: VisIt Plugins</h1></font>
<font face="arial,helvetica" color="#555588"><h2>Introduction</h2></font>
<P>
<a href="http://www.llnl.gov/visit">VisIt</a> is an open source point-and-click 3D scientific visualization application that supports most of the common visualization techniques on structured and unstructured grids. One of its advantages is that it employs a distributed and parallel architecture in order to handle extremely large data sets interactively. VisIt's rendering and data processing capabilities are split into viewer and engine components that may be distributed across multiple machines. See this link for <a href="http://vis.lbl.gov/NERSC/Software/visit/">details</a> on how to run VisIt in NERSC.
</P>
<P>
VisIt achieves extensibility through the use of dynamically loaded plugins. All of VisIt's plots, operators, and database readers are implemented as plugins and are loaded at run-time from the plugin directory. New plugins can be added simply by installing them in this directory. VisIt comes with a graphical plugin creation tool, which greatly simplifies the process of creating new plugins. The user describes the properties of the plugin and then the tool generates most of the code necessary to implement the plugin. For example, in the case of an operator, the plugin creation tool creates the code necessary for the graphical user interface attribute window; the C++, Python, and Java interfaces; and the code necessary to interface to VisIt. The only code you need to write is the C++ code that actually performs the operation.
</P>
<font face="arial,helvetica" color="#555588"><h2>H5Part in VisIt</h2></font>
<font face="arial,helvetica" color="#555588"><h3>Database Reader Plugin</h3></font>
<P>
We wrote a Multiple Time Step Multiple Domain database reader to read H5Part data into VisIt. H5Part datasets should be named with the extension <font color=red>".h5part"</font> to be recognized by the reader since VisIt does not have a format selection mechanism at the time of reading. Figure 1 shows a Pseudocolor plot of a data set and Figure 2 shows a Scatter plot x-y (any combination of x, px, y, py, z, pz, id are possible).
</P>
<P>
<TABLE>
<TR>
<TD>
<a href="H5PartVisIt/cloud_visit.png"><img src="H5PartVisIt/cloud_visit.s.png" width=400 height=300></a>
</TD
></TR>
<TR>
<TD width=300>
Figure 1. VisIt User interface showing an H5Part particle file rendered as spheres using the Pseudocolor plot.
</TD>
</TR>
<TR>
<TD>
<a href="H5PartVisIt/cloud_visit_2D.png"><img src="H5PartVisIt/cloud_visit_2D.s.png" width=300 height=300></a>
</TD>
</TR>
<TR>
<TD>
Figure 2. A Scatter plot of the x-y projection of the particles.
</TD>
</TR>
</TABLE>
</P>
<P>
VisIt provides a Query interface, for single time steps and for time series. Figure 3 shows the query interace over time for the sum of the x position and the z position of the particoes.
</P>
<P>
<TABLE>
<TR>
<TD>
<a href="H5PartVisIt/visit_query1.png"><img src="H5PartVisIt/visit_query1.s.png" width=400 height=300></a>
</TD
></TR>
<TR>
<TD width=300>
Figure 3. VisIt's Time Query Output.
</TD>
</TR>
</TABLE>
</p>
<font face="arial,helvetica" color="#555588"><h2>Operator Plugins</h2></font>
<P>
<font face="arial,helvetica" color="#555588"><h3>Particle Random Sampler</h3></font>
</P>
<P>
<font face="arial,helvetica" color="#555588"><h3>Particle Binner</h3></font>
</P>
</div>
doc/H5PartVisIt/cloud_visit.png
BIN
View File
Binary file not shown.
Side by Side

Before

Width:  |  Height:  |  Size: 329 KiB

doc/H5PartVisIt/cloud_visit.s.png
BIN
View File
Binary file not shown.
Side by Side

Before

Width:  |  Height:  |  Size: 107 KiB

doc/H5PartVisIt/cloud_visit_2D.png
BIN
View File
Binary file not shown.
Side by Side

Before

Width:  |  Height:  |  Size: 243 KiB

doc/H5PartVisIt/cloud_visit_2D.s.png
BIN
View File
Binary file not shown.
Side by Side

Before

Width:  |  Height:  |  Size: 72 KiB

doc/H5PartVisIt/visit_query1.png
BIN
View File
Binary file not shown.
Side by Side

Before

Width:  |  Height:  |  Size: 181 KiB

doc/H5PartVisIt/visit_query1.s.png
BIN
View File
Binary file not shown.
Side by Side

Before

Width:  |  Height:  |  Size: 79 KiB

doc/H5X_File_Format.txt
+170
View File
@@ -0,0 +1,170 @@
Proposal for a more general file format used by H5Part/H5Block
Authors: Achim Gsell
Status: Draft
1. Introduction
H5X is the file format used by H5Part and H5Block. H5X is designed on
top of HDF5: A H5X file is a very special HDF5 file.
+--------------------+
| Application |
+--------------------+
| H5Part/H5Block API |
+--------------------+
| H5X API |
+--------------------+
| HDF5 API |
+--------------------+
| Filesystem of OS |
+--------------------+
2. H5X file format specification
2.1 The root group
2.1.1 File attributes
Attributes of the HDF5 root group are called "file attributes". There
are no restrictions on file attribute names. Names with "__" as prefix and
postfix are intended for internal use. Supported values for file attributes
are scalars and arrays of 64bit integer and 64bit floating point number as
well as string values. Arrays of strings are not supported.
2.1.1.1 Predefined file attributes
__stepname__ (optional)
See below.
__stepnumwidth__ (optional)
See below.
2.1.2 Members of the root group
Members of the root group are special formated HDF5 groups called
"step groups". The name of a step group is "<name>#<number>".
Whereby <name> is either defined by the optional file attribute
__stepname__ or set to "Step" by default. <number> is an
unsigned integer less than 2^63.
/
+- Step#0
+- Step#1
...
+- Step#n
+- StepProperties [NEW]
+- Mesh [NEW]
The optional file attribute __stepnumwidth__ defines the minimum width
of <number> in the name of the step group. The number is padded with
'0'. The minimum width defaults to zero, so that no paddings occurs.
Example: With __stepnumwidth__ := 5 the name of the step group with
number 42 is "Step#00042", with __stepnumwidth__ := 0 the name is
"Step#42".
Step groups may be unsorted in the HDF5 file und needn't be number
consecutively.
2.1.3 Other members of the root group
Other sub-groups of the root group are allowed, but the group names are restricted
to names not matching "Step#.*".
2.2 Format of a step group
2.2.1 Step attributes
Step attributes are HDF5 attributes asigned to a step group. There
are no restrictions on step attribute names. As with file attributes names
enclosed in "__" are intended for internal use. Supported values are the same
as for file attributes:
* 64bit integer value
* arrays of 64bit integer values
* 64bit floating point number
* array of 64bit floating point number
* strings
Note that array of strings are not supported!
2.2.2 Predefined step attributes
No predefined step attributes exists.
2.2.3 Members of a step group
Members of a step group are HDF5 datasets and optional one HDF5 group
with the name "Block". HDF5 datasets in a step group are called "step
datasets". The optional block group is called "block data".
Mesh?!
2.2.4 Step datasets
Step datasets are arrays of rank 1. The dataset size must be the same
for all datasets inside a step. The size of the dataset may vary
from step to step. Array values are 64bit integer or 64bit floating
point numbers. No limitations (other than given by HDF5) are given on
step dataset names.
2.2.5 Block Data
The block data group is a container for an arbitrary number of field
data. A field is a data structure to store arrays of rank m with
n-dimensional vector values. Fields are represented within HDF5
groups. The HDF5 group name is the unique identifier for a field in
the current step.
2.2.5.1 m-rank fields with n-dimensional-vector values
Values are stored per dimension in separate datasets. Thus we have n
datasets for a field with n-dimensional vector values. Each dataset
corresponse to one dimension. The datasets are numbered from '0' to
'n-1'. Arrays are stored in column major order (Fortran indexing
scheme).
/ # HDF5 root group
...
+- Step#<i> # HDF5 group
|
+- Block # HDF5 group
|
+- <field name> # HDF5 group
|
+- 0 # HDF5 dataset, first dim of vector
+- 1 # HDF5 dataset, second dim of vector
...
+- n-1 # HDF5 dataset, last dim of vector
...
2.2.5.2 m-rank fields with scalar values
Fields with scalar values are stored as special case of fields with
n-dimensional vector values with n := 1.
/ # HDF5 root group
...
+- Step#<i> # HDF5 group
|
+- Block # HDF5 group
|
+- <field name> # HDF5 group
|
+- 0 # HDF5 dataset, scalar value
...
2.3 Step properties [NEW]
Why? Much faster than step attributes if you need to access consecutive values
Group of root group with name "StepProperties"
Members are datasets
Supported values are the same as for step attributes
Mapping of value to step via object index of step group
doc/H5tools/H5tools.htm
-417
View File
@@ -1,417 +0,0 @@
<html><head><title>H5Part Tools How-to</title>
<meta http-equiv="Content-Type" content="text/html; charset=euc-kr"></head>
<body bgcolor="#ffffff" text="#000000">
<table border="0" cellpadding="0" cellspacing="0" width="987">
<tbody><tr>
<td height="6050" width="27"></td>
<td colspan="3" valign="top">
<div id="body">
<div id="mainleft"><font face="Arial, Helvetica, sans-serif"><a name="TOP"></a>
</font></div>
<div id="maincenter"> <font face="arial,helvetica">
<h1 align="center"><font face="Arial, Helvetica, sans-serif"><b><font color="#666699">H5Part
Tools How-to</font></b></font></h1>
</font><font color="#555588" face="arial,helvetica">
<h2><font color="#666699" face="Arial, Helvetica, sans-serif">Table
of Contents</font></h2>
</font>
<p><font face="Arial, Helvetica, sans-serif"><b><a href="#Quick%20Guide">
[1] Quick Guide</a></b> </font></p>
<p><font face="Arial, Helvetica, sans-serif" size="+1"><b><font color="#999999">---
For h5pAttrib</font></b></font><font face="Arial, Helvetica, sans-serif"><br>
<b><br>
<a href="#timesteps">[2] To see number of timesteps in a h5part file</a><br>
<br>
<a href="#file%20attributes">[3] To see file attributes in a h5part
file</a><br>
<br>
<a href="#step%20attributes"> [4] To see step attributes in a h5part
file</a><br>
<br>
<a href="#dataset">[5] To see dataset in a h5part file</a><br>
<br>
<a href="#flags">[6] Providing more than one flag at once for h5pAttrib</a></b></font></p>
<p><font face="Arial, Helvetica, sans-serif" size="+1"><b><font color="#999999">---
For h5pToGNUplot</font></b></font><font face="Arial, Helvetica, sans-serif"><br>
<br>
<b><a href="#parameters">[7] What parameters to provide</a><br>
<br>
<a href="#input%20file">[8] How to create an input file to GNUplot</a></b></font></p>
<p>&nbsp;</p>
<p align="center"><font face="Arial, Helvetica, sans-serif"><a href="#TOP">&lt;back
to top&gt;</a></font></p>
<p>&nbsp;</p>
<h2><font color="#555588" face="Arial, Helvetica, sans-serif"><a name="Quick Guide">[1]
Quick Guide</a></font></h2>
<p><font face="Arial, Helvetica, sans-serif">Executing the program with
-h option will display a concise help page.</font></p>
<p><font face="Arial, Helvetica, sans-serif"><b><font face="Courier New, Courier, mono" size="+1">$&gt;</font></b><font face="Courier New, Courier, mono">./h5pAttrib
-h</font></font></p>
<p><font face="Courier New, Courier, mono">usage: h5pAttrib [OPTIONS]
file</font></p>
<p><font face="Courier New, Courier, mono"> OPTIONS<br>
-h, --help Print help page<br>
-n, --nstep Print number of steps<br>
-A, --fileA Print file attributes<br>
-a n, --stepA n Print step attributes &amp; values for time step n<br>
-d n, --dataset n Print data sets names &amp; values for time step
n<br>
-H, --header Print shorter version without the values</font></p>
<p><font face="Courier New, Courier, mono"> Examples:</font></p>
<p><font face="Courier New, Courier, mono"> 1) Show file attribute names
&amp; values of sample.h5part</font></p>
<p><font face="Courier New, Courier, mono"> h5pAttrib -A sample.h5part<br>
OR<br>
h5pAttrib --fileA sample.h5part</font></p>
<p><font face="Courier New, Courier, mono"> 2) Show step attribute names
for time step 5 of sample.h5part</font></p>
<p><font face="Courier New, Courier, mono"> h5pAttrib -a 5 -H sample.h5part<br>
OR<br>
h5pAttrib --stepA 5 -H sample.h5part</font></p>
<p><font face="Courier New, Courier, mono"><br>
<b><font size="+1">$&gt;</font></b> ./h5pToGNUplot -h</font></p>
<p><font face="Courier New, Courier, mono">usage: h5pToGNUplot -t TIMESTEP
-1 VARIABLE#1 -2 VARIABLE#2 -i INPUTFILE [OPTIONAL_FLAGS]</font></p>
<p><font face="Courier New, Courier, mono"> FLAGS<br>
-h, --help Print help page</font><br>
<font face="Courier New, Courier, mono">-1 par, --1var par (REQUIRED)
Takes first variable parameter to "par"<br>
-2 par, --2var par (REQUIRED) Takes second variable parameter to "par"<br>
-i file, --input file (REQUIRED) Takes input file name to "file"<br>
</font><font face="Courier New, Courier, mono">-t step, --timestep
step (REQUIRED) Sets the timestep to "step" (Value -1 will
result in dumping values of all timesteps.)<br>
-o file, --output file (OPTIONAL) Takes output file name to "file"
(without this flag, the program will print to stdout)<br>
-n num, --number num (OPTIONAL) Sets number of output points to "num"<br>
-s idx, --start idx (OPTIONAL) Sets the starting particle index to
"idx"</font></p>
<p><font face="Courier New, Courier, mono"><br>
Examples:</font></p>
<p><font face="Courier New, Courier, mono"> 1) Create GNU plot file
output.txt from sample.h5part by ploting x vs px for timestep 54</font></p>
<p><font face="Courier New, Courier, mono"> h5pToGNUplot -t 54 -1 x
-2 px -i sample.h5part -o output.txt</font></p>
<p><font face="Courier New, Courier, mono"> 2) Create GNU plot file
output.txt from sample.h5part by ploting x vs px for timestep 54<br>
using 1200 points from particle index 76</font></p>
<p><font face="Courier New, Courier, mono"> h5pToGNUplot -t 54 -1 x
-2 px -i sample.h5part -o output.txt -s 76 -n 1200</font></p>
<p>&nbsp;</p>
<p align="center"><font face="Arial, Helvetica, sans-serif"><a href="#TOP">&lt;back
to top&gt;</a></font></p>
<p>&nbsp;</p>
<p><font face="Arial, Helvetica, sans-serif" size="+1"><b><font color="#999999">---
For h5pAttrib</font></b></font></p>
<p>&nbsp;</p>
<h2><font color="#555588" face="Arial, Helvetica, sans-serif"><a name="timesteps">[2]
To see number of timesteps in a h5part file</a></font></h2>
<p>Executing the program h5pAttrib with -n flag will display the number
of timesteps in the file.</p>
<p><font face="Arial, Helvetica, sans-serif"><b>EXAMPLE&gt;&gt;</b></font></p>
<p><font face="Arial, Helvetica, sans-serif" size="+1"><b><font face="Courier New, Courier, mono">$&gt;</font></b></font><font face="Courier New, Courier, mono">
./h5pAttrib -n sample.h5part</font></p>
<p><font face="Courier New, Courier, mono">++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</font></p>
<p><font face="Courier New, Courier, mono">Printing number of timesteps
for: sample.h5part ...</font></p>
<p><font face="Courier New, Courier, mono">There are total 252 number
of timesteps.<br>
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</font></p>
<p><font face="Courier New, Courier, mono">done</font><font face="Arial, Helvetica, sans-serif"><br>
</font></p>
<p>&nbsp; </p>
<p align="center"><font face="Arial, Helvetica, sans-serif"><a href="#TOP">&lt;back
to top&gt;</a></font></p>
<h2><font color="#666699" face="Arial, Helvetica, sans-serif"><br>
<font color="#555588"><a name="file attributes">[3] To see file attributes
in a h5part file</a></font></font></h2>
<p>File attribute contains information about the file. (file description
etc...) Executing the program h5pAttrib with -A flag will display
the file attributes in the file.</p>
<p><font face="Arial, Helvetica, sans-serif"><b>EXAMPLE&gt;&gt;</b></font></p>
<p><font face="Arial, Helvetica, sans-serif" size="+1"><b><font face="Courier New, Courier, mono">$&gt;</font></b></font><font face="Courier New, Courier, mono">
./h5pAttrib -A sample.h5part</font></p>
<p><font face="Courier New, Courier, mono">++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</font></p>
<p><font face="Courier New, Courier, mono">Printing file attributes
for: sample.h5part ...</font></p>
<p><font face="Courier New, Courier, mono">The number of file attributes
for file sample.h5part is 0 ...<br>
There are no file attributes.<br>
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</font></p>
<p><font face="Courier New, Courier, mono">done</font></p>
<p><font face="Arial, Helvetica, sans-serif"><br>
<i>NOTE: -H option will omit the list of values of file attributes.</i></font></p>
<p>&nbsp; </p>
<p align="center"><font face="Arial, Helvetica, sans-serif"><a href="#TOP">&lt;back
to top&gt;</a></font></p>
<p align="center">&nbsp;</p>
<h2><font color="#555588" face="Arial, Helvetica, sans-serif"><a name="step attributes">[4]
To see step attributes in a h5part file</a></font></h2>
<p>Step attribute contains information that belongs to a specific step.
(step name, timestep number, etc...) Executing the program h5pAttrib
with -a flag will display the step attributes in the file.<br>
Note that the timestep index should follow -a flag.</p>
<p><font face="Arial, Helvetica, sans-serif"><b>EXAMPLE&gt;&gt;</b></font></p>
<p><font face="Arial, Helvetica, sans-serif"><b><font face="Courier New, Courier, mono" size="+1">$&gt;</font></b><font face="Courier New, Courier, mono">
./h5pAttrib -a 2 sample.h5part</font></font></p>
<p><font face="Courier New, Courier, mono">++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</font></p>
<p><font face="Courier New, Courier, mono">Printing step attributes
for: sample.h5part ...</font></p>
<p><font face="Courier New, Courier, mono">The number of step attributes
for timestep #2 is 10 ...</font></p>
<p><font face="Courier New, Courier, mono">Attribute #0 = Step<br>
There are 1 elements in the attribute<br>
Attribute Type is H5T_NATIVE_INT64<br>
Printing 1 element value(s):<br>
COUNT[0]: 2</font></p>
<p><font face="Courier New, Courier, mono">Attribute #1 = Spos<br>
There are 1 elements in the attribute<br>
Attribute Type is H5T_NATIVE_DOUBLE<br>
Printing 1 element value(s):<br>
COUNT[0]: 0.143580</font></p>
<p><font face="Courier New, Courier, mono">Attribute #2 = structLen<br>
There are 1 elements in the attribute<br>
Attribute Type is H5T_NATIVE_DOUBLE<br>
Printing 1 element value(s):<br>
COUNT[0]: 2.393000</font></p>
<p><font face="Courier New, Courier, mono">.<br>
.<br>
.</font></p>
<p><font face="Courier New, Courier, mono"><br>
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</font></p>
<p><font face="Courier New, Courier, mono">done</font></p>
<p><font face="Arial, Helvetica, sans-serif"><br>
<i>NOTE: -H option will omit the list of values of step attributes.</i></font></p>
<p>&nbsp; </p>
<p align="center"><font face="Arial, Helvetica, sans-serif"><a href="#TOP">&lt;back
to top&gt;</a></font></p>
<h2><font color="#555588" face="Arial, Helvetica, sans-serif"><br>
<a name="dataset">[5] To see dataset in a h5part file</a></font></h2>
<p>Executing the program h5pAttrib with -d flag will display the datasets
information in the file. (dataset name, type, number of elements,
etc...) Executing the program h5pAttrib with -d flag will display
the datasets information in the file.<br>
Note that the timestep index should follow -d flag.</p>
<p><font face="Arial, Helvetica, sans-serif"><b>EXAMPLE&gt;&gt;</b></font></p>
<p><font face="Arial, Helvetica, sans-serif" size="+1"><b><font face="Courier New, Courier, mono">$&gt;</font></b></font><font face="Courier New, Courier, mono">
./h5pAttrib -d 2 -H sample.h5part</font></p>
<p><font face="Courier New, Courier, mono">++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</font></p>
<p><font face="Courier New, Courier, mono">Printing names of datasets
for: sample.h5part ...</font></p>
<p><font face="Courier New, Courier, mono">The number of datasets for
timestep #2 is 7 ...</font></p>
<p><font face="Courier New, Courier, mono">Dataset Name #0 = id<br>
Dataset Type is H5T_NATIVE_INT64<br>
Number of elements: 67587</font></p>
<p><font face="Courier New, Courier, mono">Dataset Name #1 = px<br>
Dataset Type is H5T_NATIVE_DOUBLE<br>
Number of elements: 67587</font></p>
<p><font face="Courier New, Courier, mono">Dataset Name #2 = py<br>
Dataset Type is H5T_NATIVE_DOUBLE<br>
Number of elements: 67587</font></p>
<p><font face="Courier New, Courier, mono">Dataset Name #3 = pz<br>
Dataset Type is H5T_NATIVE_DOUBLE<br>
Number of elements: 67587</font></p>
<p><font face="Courier New, Courier, mono">Dataset Name #4 = x<br>
Dataset Type is H5T_NATIVE_DOUBLE<br>
Number of elements: 67587</font></p>
<p><font face="Courier New, Courier, mono">Dataset Name #5 = y<br>
Dataset Type is H5T_NATIVE_DOUBLE<br>
Number of elements: 67587</font></p>
<p><font face="Courier New, Courier, mono">Dataset Name #6 = z<br>
Dataset Type is H5T_NATIVE_DOUBLE<br>
Number of elements: 67587</font></p>
<p><font face="Courier New, Courier, mono">++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</font></p>
<p><font face="Courier New, Courier, mono">done</font></p>
<p><font face="Arial, Helvetica, sans-serif"><br>
<i>NOTE: -H option will omit the list of values of datasets.</i></font></p>
<p>&nbsp; </p>
<p align="center"><font face="Arial, Helvetica, sans-serif"><a href="#TOP">&lt;back
to top&gt;</a></font></p>
<p>&nbsp;</p>
<h2><font color="#555588" face="Arial, Helvetica, sans-serif"><a name="flags">[6]
Providing more than one flag at once</a></font></h2>
<p><font face="Arial, Helvetica, sans-serif">When more than one flags
are provided, one result after another will be displayed.</font></p>
<p><font face="Arial, Helvetica, sans-serif"><b>EXAMPLE&gt;&gt;</b></font></p>
<p><font face="Arial, Helvetica, sans-serif" size="+1"><b><font face="Courier New, Courier, mono">$&gt;</font></b></font><font face="Courier New, Courier, mono">
./h5pAttrib -H -a 1 -d 1 sample.h5part</font></p>
<p><font face="Courier New, Courier, mono">++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</font></p>
<p><font face="Courier New, Courier, mono">Printing step attributes
for: sample.h5part ...</font></p>
<p><font face="Courier New, Courier, mono">The number of step attributes
for timestep #1 is 10 ...</font></p>
<p><font face="Courier New, Courier, mono">Attribute #0 = Step<br>
Attribute #1 = Spos<br>
Attribute #2 = structLen<br>
Attribute #3 = org<br>
Attribute #4 = maxX<br>
Attribute #5 = minX<br>
Attribute #6 = maxP<br>
Attribute #7 = minP<br>
Attribute #8 = centroid<br>
Attribute #9 = nloc<br>
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</font></p>
<p><font face="Courier New, Courier, mono"><br>
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</font></p>
<p><font face="Courier New, Courier, mono">Printing names of datasets
for: sample.h5part ...</font></p>
<p><font face="Courier New, Courier, mono">The number of datasets for
timestep #1 is 7 ...</font></p>
<p><font face="Courier New, Courier, mono">Dataset Name #0 = id<br>
Dataset Type is H5T_NATIVE_INT64<br>
Number of elements: 60214</font></p>
<p><font face="Courier New, Courier, mono">Dataset Name #1 = px<br>
Dataset Type is H5T_NATIVE_DOUBLE<br>
Number of elements: 60214</font></p>
<p><font face="Courier New, Courier, mono">Dataset Name #2 = py<br>
Dataset Type is H5T_NATIVE_DOUBLE<br>
Number of elements: 60214</font></p>
<p><font face="Courier New, Courier, mono">Dataset Name #3 = pz<br>
Dataset Type is H5T_NATIVE_DOUBLE<br>
Number of elements: 60214</font></p>
<p><font face="Courier New, Courier, mono">Dataset Name #4 = x<br>
Dataset Type is H5T_NATIVE_DOUBLE<br>
Number of elements: 60214</font></p>
<p><font face="Courier New, Courier, mono">Dataset Name #5 = y<br>
Dataset Type is H5T_NATIVE_DOUBLE<br>
Number of elements: 60214</font></p>
<p><font face="Courier New, Courier, mono">Dataset Name #6 = z<br>
Dataset Type is H5T_NATIVE_DOUBLE<br>
Number of elements: 60214</font></p>
<p><font face="Courier New, Courier, mono">++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</font></p>
<p><font face="Courier New, Courier, mono">done</font></p>
<p>&nbsp;</p>
<div align="center"><font face="Arial, Helvetica, sans-serif"><a href="#TOP">&lt;back
to top&gt;</a></font></div>
</div>
</div>
</td>
</tr>
<tr>
<td height="80"></td>
<td colspan="3" valign="top">
<h2><font face="Arial, Helvetica, sans-serif" size="+1"><b><font color="#999999">---
For h5pToGNUplot</font></b></font></h2>
<h2><font color="#555588" face="Arial, Helvetica, sans-serif"><a name="parameters">[7]
What parameters to provide</a></font></h2>
<p><font face="Arial, Helvetica, sans-serif">When you execute the program
with -h option, it displays what flags are necessary and what flags are
optional.</font></p>
</td>
</tr>
<tr>
<td height="200"></td>
<td valign="top" width="137">
<p align="left"><b><font face="Arial, Helvetica, sans-serif">Short Version</font></b></p>
<p><font face="Arial, Helvetica, sans-serif">-h<br>
-1<br>
-2<br>
-i<br>
-t<br>
-o<br>
-n<br>
-s </font></p>
</td>
<td valign="top" width="144">
<p align="left"><b><font face="Arial, Helvetica, sans-serif">Long Version</font></b></p>
<p><font face="Arial, Helvetica, sans-serif">--help<br>
--1var<br>
--2var<br>
--input<br>
--timestep<br>
--output<br>
--number<br>
--start </font></p>
</td>
<td valign="top" width="679">
<p align="left"><b><font face="Arial, Helvetica, sans-serif">Meanings</font></b></p>
<p><font face="Arial, Helvetica, sans-serif">Print help page<br>
(REQUIRED) Takes first variable parameter<br>
(REQUIRED) Takes second variable parameter<br>
(REQUIRED) Takes input file name<br>
(REQUIRED) Sets the timestep (Value -1 will result in dumping values of
all timesteps.)<br>
(OPTIONAL) Takes output file name (without this flag, the program will
print to stdout)<br>
(OPTIONAL) Sets number of output points<br>
(OPTIONAL) Sets the starting particle index</font> </p>
</td>
</tr>
<tr>
<td height="1786"></td>
<td colspan="3" valign="top">
<p>&nbsp;</p>
<p align="center"><font face="Arial, Helvetica, sans-serif"><a href="#TOP">&lt;back
to top&gt;</a></font></p>
<h2><font color="#555588" face="Arial, Helvetica, sans-serif"><br>
<a name="input file">[8] How to create an input file to GNUplot</a></font></h2>
<p><font face="Arial, Helvetica, sans-serif"><b>EXAMPLE&gt;&gt;</b><br>
<i>Create input file to GNUplot that plots x vs. y.</i></font></p>
<p><font face="Arial, Helvetica, sans-serif"><b><font face="Courier New, Courier, mono" size="+1">$&gt;</font></b><font face="Courier New, Courier, mono">
./h5pToGNUplot -1 x -2 y -t 1 -i sample.h5part -o output.txt<br>
<b><font size="+1">$&gt;</font></b> cat output.txt<br>
-0.390779 -0.254793<br>
-0.396527 -0.252781<br>
-0.375362 -0.285137<br>
-0.396527 -0.252781<br>
-0.379917 -0.283147<br>
-0.390779 -0.254793<br>
-0.387536 -0.287346<br>
-0.371787 -0.319797<br>
-0.379917 -0.283147<br>
-0.378967 -0.326058<br>
-0.378976 -0.326078<br>
-0.387536 -0.287346<br>
-0.378957 -0.326069<br>
-0.379917 -0.283147<br>
-0.388762 -0.265390<br>
-0.371787 -0.319797<br>
-0.390779 -0.254793<br>
-0.376825 -0.266804<br>
-0.379917 -0.283147<br>
-0.375362 -0.285137<br>
...</font></font></p>
<p><font face="Courier New, Courier, mono"><i>Then run GNUplot...</i></font></p>
<p><font face="Courier New, Courier, mono"><b><font size="+1">$&gt;</font></b>
gnuplot</font></p>
<p><font face="Courier New, Courier, mono"> G N U P L O T<br>
Version 4.0 patchlevel 0<br>
last modified Thu Apr 15 14:44:22 CEST 2004<br>
System: Linux 2.6.11.4-21.11-smp</font></p>
<p><font face="Courier New, Courier, mono"> Copyright (C) 1986 - 1993, 1998,
2004<br>
Thomas Williams, Colin Kelley and many others</font></p>
<p><font face="Courier New, Courier, mono"> This is gnuplot version 4.0.
Please refer to the documentation<br>
for command syntax changes. The old syntax will be accepted<br>
throughout the 4.0 series, but all save files use the new syntax.</font></p>
<p><font face="Courier New, Courier, mono"> Type `help` to access the on-line
reference manual.<br>
The gnuplot FAQ is available from<br>
http://www.gnuplot.info/faq/</font></p>
<p><font face="Courier New, Courier, mono"> Send comments and requests for
help to<br>
&lt;gnuplot-info@lists.sourceforge.net&gt;<br>
Send bugs, suggestions and mods to<br>
&lt;gnuplot-bugs@lists.sourceforge.net&gt;</font></p>
<p><font face="Courier New, Courier, mono"><br>
Terminal type set to 'x11'<br>
<font size="+1"><b>gnuplot&gt;</b></font> plot "output.txt"</font></p>
<p><font face="Arial, Helvetica, sans-serif"><i>This will open a GNUplot
window that plots output.txt.</i></font></p>
<p align="center"><img src="H5tools_files/snapshot1.jpg" height="541" width="672"><br>
<font face="Arial, Helvetica, sans-serif">&lt;Sample screen shot of GNUplot
with input datafile generated by h5pToGNUplot&gt;</font></p>
</td>
</tr>
<tr>
<td height="44"></td>
<td></td>
<td></td>
<td></td>
</tr>
</tbody></table>
</body></html>
doc/H5tools/H5tools_files/snapshot1.jpg
BIN
View File
Binary file not shown.
Side by Side

Before

Width:  |  Height:  |  Size: 239 KiB

doc/H5xxx/H5xxx.tex
-345
View File
@@ -1,345 +0,0 @@
\documentclass[acus]{JAC2003}
%%
%% Use \documentclass[boxit]{JAC2003}
%% to draw a frame with the correct margins on the output.
%%
%% Use \documentclass[acus]{JAC2003}
%% for US letter paper layout
%%
\usepackage{graphicx}
%%
%% VARIABLE HEIGHT FOR THE TITLE BOX (default 35mm)
%%
\setlength{\titleblockheight}{40mm}
\begin{document}
\title{H5Pie: A Portable High Performance Parallel Data Interface for Electromagnetics Simulations Including Particles\thanks{
This work (LBNL-57607) was supported by the Director, Office of Science, Office of Advanced Scientific Computing Research, of the U.S. Department of Energy under Contract No. DE-AC03-76SF00098 and the DOE SciDAC project on ``Advanced Computing for 21st Century Accelerator Science and Technology.''.
}}
\author{A. Adelmann, A. Gsell, B. Oswald, PSI, Villigen, Switzerland \\
R.D. Ryne, LBNL/AFR, Berkeley, California, USA\\
W. Bethel, J.M. Shalf, C. Siegerist, LBNL/NERSC, Berkeley, California, USA}
\maketitle
\begin{abstract}
The very largest parallel particle simulations, for problems
involving six dimensional phase space,
generate vast quantities of data. It is desirable to
store such enormous datasets efficiently and also to share data
effortlessly between data analysis tools
such as VisIt or ParaView
among other groups who are working on particle-based accelerator
simulations. We define a very simple file schema built on top of HDF5~\cite{hdf5hp}
(Hierarchical Data Format version 5) as well as an API that simplifies
the reading/writing of the data to the HDF5 file format. HDF5 offers a
self-describing machine-independent binary file format that supports
scalable parallel I/O performance for MPI codes on computer systems
ranging from laptops to supercomputers.
H5Pie is actually a composition of three parts. On a very abstract view we have,
H5Part which handles the macro particles of a simulation. H5Mesh defines the (spatial) geometry of the
computational domain and H5Fields represents scalar and vector filds. (H5Pie = H5{\bf P} art + H5F{\bf i}eld+ H5M{\bf e}sh)
The sample H5Pie
API will be available for C, C++, and Fortran codes.
The common file format will enable groups that
use completely different simulation implementations to transparently share
datasets.
\end{abstract}
\section{Motivation}
The motivation for this undertaking is to create a file format that is
suitable for large-scale parallel simulation codes.
A suitable data format must have the following properties:
it must be a machine-independent binary representation that is
self-describing, easily extensible, language independent, efficient
(both for serial and parallel), and produces files that are seamlessly sharable
between different programs. In the following sections we describe
the motivation for these features and how they can be accomplished
using the proposed implementation.
\subsection{Machine Independence}
Processor architectures use different binary representations
for data. While the IEEE 754 standard has decreased the number of
differing floating point number represenations, byte-order still remains
a source of incompatibility. While it is trivial to byte-swap a file from
a programming standpoint, it creates a number of long-term file management
difficulties for groups that are sharing or maintaining a repository of simulation
data. Given files that store data structures with differently sized elements,
one must know the storage format precisely in order to apply byte-swapping
properly.
HDF5 does not suffer from these problems because the file format is completely
self-describing and the internal binary structures are all machine independent.
The HDF5 library is able to convert data that is stored in any native machine
represenation in the data file into a native binary representation in memory
as part of the reading process with little performance penalty.
\subsection{Language Independence}
The three most common languages used for implementing applications
in the arena of computational sciences are
Fortran, C and C++. The file format and associated API must hide
differences in the binary file-storage conventions of these languages
as well as offering native API bindings for each of these
programming languages.
For instance, Fortran unformatted binary files contain integer fields
at the beginning and the end of each record that describe the length
of the record. The size of these integer tags is usually 32-bits, but some
fortran compiler implementations will use larger tags in order to represent
larger record sizes. C and C++ binary files have no such convention for
record-oriented storage. The language-dependent differences in
binary storage layout conventions
can cause difficulties for scientists who wish to share data files between
Fortran and C/C++ implementations of a code, or with visualization tools
that are primarily written in C/C++. The API bindings and underlying file format
provided by the H5Part API and the underlying HDF5 file format are able to
hide these differences in order to provide symmetric access via all languages.
\subsection{Self-Describing}
The data is accessed by names, for example, one might ask for `the
column of data called $p_x$' -- affording a layer of file-layout independence.
In other words, self-describing data is
not accessed by a position in a file but by name of the datasets. Various attributes
of the data that may be necessary to using it are available. For
example, one can ask ``what are the units of column $p_x$?'.
There are a number of examples of self-describing file formats. Examples include HDF earlier HDF implementations leading up to HDF version 5 and the Unidata NetCDF format. Another
very popular approach is the Self Describing Data Sets (SDDS) \cite{SDDS} although it
is only serial in nature. HDF5 is a complete rewrite of the HDF file format that supports
parallel I/O and offers a much leaner, more flexible interface.
Because it is self-describing, the entire contents of an HDF5 file can be
browsed and even converted to ASCII text, including XML syntax text files,
using the built-in 'h5ls' and 'h5dump'
tools without specific knowledge of the internal file format.
\begin{figure}[htb]
\begin{minipage}[b]{0.5\textwidth}
%\includegraphics[scale=0.095]{./partview1.eps}
%\includegraphics[scale=0.097]{./density70.eps}
\end{minipage}
\caption{color: A common self-describing file format allows different codes to share a common set of visualization and data analysis tools. PartView and AVS/Express, pictured above, are able to read and display contents of an H5Part/HDF5 file written on any machine in any language, regardless of how many processors are used.}
\label{fig:vis}
\end{figure}
The primary advantage of accessing data and its attributes is that one
can then construct more flexible data manipulation tools that are capable
of surviving the natural evolution of file formats. Data formats can be extended
to include additional information without breaking older file readers.
Self-describing data contains all the information
that analysis tools need to manipulate various types of data
correctly. Two examples of such tools using the proposed file format
are shown in Figure ~\ref{fig:vis} As a result, data exchange between different simulations tools is
much simpler, robust and better defined by using self-describing data sets.
\subsection{High Performance}
The HDF5 file format allows data elements to be written to disk in the
native binary representation. The file format stores a description of
the native data representation of the machine that wrote the data so
that it can be automatically translated to the native binary
representation of the machine that reading the data (eg. if the byte
order differs). In contrast to XDR, where the data always gets
translated to/from an intermediate machine-neutral format, the HDF5
data conversion only occurs if the stored data represenation is
different from the native binary representation of the machine that is
reading the file, so there is no performance penalty if the machines
have the compatible binary data formats. [ada: need work] In general, HDF5 offers
performance that is very close to what can be achieved by writing an
ad-hoc machine-dependent binary for F77 unformatted data file.
\subsection{Parallel I/O}
HDF5 also supports parallel I/O capabilities for MPI programs.
The naive approach to writing data from a parallel program is to
write one file per processor. While this is simple to implement and
very efficient on most cluster filesystems, it leads to file management
headaches when it comes the time to analyze the data. One must either
recombine these separate files into a single file or create ponderous
user-interfaces that allow a data analysis application to read from a
directory full of files instead of just one file.
Parallel I/O methods, allow you to write data into a single file from all
of the tasks of a parallel program. The performance is typically lower
than that of writing one-file-per-processor, but it makes data management
much simpler after the program has finished. No additional recombining
steps are required to make the file accessible by vis-tools or for
restarting a simulation using a different number of processors.
Parallel HDF5 uses MPI-I/O for its low-level implementation. The
mechanics of using MPI-I/O are all hidden from the user by our
H5Part file API (the code looks nearly identical to reading/writing the data
from a serial program). While the performance is not as good as
writing one-file-per-processor, we demonstrate that writing files
with Parallel HDF5 is consistently faster than writing the data
in raw/native binary using the MPI-I/O library. This efficiency is
made possible through sophisticated HDF5 tuning directives that
control data alignment and caching within the HDF5 layer.
Therefore, we argue that it would be difficult to match
HDF5 performance even using a home-grown binary file format.
\section{H5Mesh File Organization and API}
\section{H5Field File Organization and API}
\section{H5Part File Organization and API}
The proposed file storage format uses HDF5 for the low-level file
storage and a simple API to provide a high-level interface to that
file format. A programmer can either use the H5Part API to access
the data files or write directly to the file format using some simple
conventions for organizing and naming the objects stored in the
file.
The HDF5 format, its benefits, and its file organization is decribed
at \cite{hdf5hp}. The file format was also adopted by the DOE
ASCI-VIEWS effort, so the library has been tuned and adapted to read
and write data efficiently on large-scale parallel computing
systems. We adopted HDF5 for our file storage needs because it offers
all that is needed as stipulated in the motivation section.
We describe now the H5Part conventions for storing
objects in the HDF5 file as well as some examples of the API.
\subsection{H5Part File Organization}
In order to store Particle Data in the HDF5 file format, we have
formalized the hierarchical arrangement of the datasets and naming
conventions for the groups and associated datasets. The sample H5Part API formally
encodes these conventions in order to provide a simple and uniform
way to access these files from C, C++, and Fortran codes. The API makes
it easier to write very portable data adaptors for visualization tools in order to
expand the number of tools available to access the data. Even so,
anyone can use the HDF5 $h5ls$ utility to examine the organization
of the H5Part files and even write their own HDF5-based interface for reading and writing the
file format. The standards offered by the sample API are completely independent of the
standard for organizing data within the file.
The file format supports the storage of multiple timesteps of
datasets that contain multiple fields. The fields correspond to different properties of
the particles at that particular time step -- for instance,
the 3-dimensional cartesian position of the particles
$(X,Y,Z)$ as well as the 3-dimensional phase of each
particle $(PX,PY,PZ)$. These two degrees of freedom
are organized such that the timesteps are groups (time groups) that are added sequentially
to the root group (``/''). The fields are datasets that are nested within the
time groups. The convention for naming the time group is $Particles<integer>$ where $<integer>$ is a monotonically increasing counter for the number of timesteps stored in the file.
The fields contained within a given time group are simply named for the property of the particle they represent. For instance, the phase of the particle stored in a simulation variable called 'px' is simply named $``px''$. The field names are user-defined and
can be understood automatically by the visualization
tools that read the file. The only other convention is that each time group must contain the same set of fields -- the contents of the fields will change, but the set of names for these fields must remain the same for all timesteps.
The fields can be either integer or real data types. Initially, the file format supports double precision float and 64-bit integers in order to simplify the requirements for file readers, but HDF5 is capable of automatically down-converting to 32-bit data types upon request. The API will be extended accordingly to support these conversions.
Finally, the file, the individual timesteps, and the individual data arrays can contain {\em attributes} that provide additional information about the data. For instance, the datasets can be annotated with attributes containing {\em units} for a given data field, simulation parameters, or code revision information. The {\em attributes} are key-value pairs where the $key$ is a string that is associated with the file, group, or dataset, and the $value$ is either a string, a real value, or an integer associated with that key.
%Visualization and data analysis tools can take advantage of this additional information if they are programmed to recognize it, but less-sophisticated tools can safely ignore it without compromising their ability to read the file format.
% ada: to philosophic for a 3 page paper, although it is very important and of course right!
%The ability to ignore such information is arguably one of the most powerful capabilities of the HDF5 file format. Whereas changes to headers or data layout in conventional, non-self-describing file formats can render an older reader interface useless, one can continuously add new descriptive information to the HDF5 file without having any detrimental effect on readers that were designed to work with older versions of the file format. This provides enormous benefits for the long term maintenance and evolution of the file format.
\section{GENERAL FORM IN PSEUDOCODE}
In Figure \ref{fig:usage} we show the very simple API for writing
data. The API for reading is almost symmetric. It is also worth to
note that there are minimal differences whether one read/write serial
or in parallel. The API consists of a small number of C, C++ and
Fortran functions and will be described elsewhere.
In the parallel case the original domain decomposition can be used or
the data can be decomposed according to the new number of processor
nodes available.
The resulting HDF5 file will contains a simple directory structure that can be navigated using the generic 'h5ls' utility;
\begin{figure}[h!] \label{fig:sbendVect}
\newsavebox{\gogo}
\setbox\gogo=\hbox{%
\begin{minipage}{0.4\textwidth}
\small
\begin{tabbing}
111111\=aaaa\=aaaa\=aaaa\=\kill
\texttt{if(not parallel);}\\
\quad\texttt{filehandle=OpenFile(filename,mode)} \\
\texttt{else}\\
\quad\texttt{filehandle=OpenFile(filename,mode,mpicomm)} \\
\texttt{SetNumberOfParticles(filehandle);}\\
\texttt{loop(step=1,NSteps);}\\
\quad\texttt{SetStep(filehandle,step);}\\
\quad\texttt{WriteData(filehandle,fieldname1,data1);}\\
\centerline{\texttt{{\bf write more data}}}\\
\quad\texttt{WriteData(filehandle,fieldname<n>,data<n>);}\\
\texttt{CloseFile(filehandle);}
\end{tabbing}
\end{minipage}
}
\fbox{\usebox{\gogo}}
\caption{Usage of H5Part in pseudo-code}
\label{fig:usage}
\end{figure}
% \begin{figure}[h!] \label{fig:sbendVect}
% \newsavebox{\gugu}
% \setbox\gugu=\hbox{%
% \begin{minipage}{0.4\textwidth}
% \small
% \begin{tabbing}
% 111111\=aaaa\=aaaa\=aaaa\=\kill
%\texttt{/Particles1/fieldname1 } \\
%\texttt{/Particles1/fieldname2} \\
%\texttt{ . . . } \\
%\texttt{/Particles1/fieldname<n> } \\
%\texttt{/Particles2/fieldname1} \\
%\texttt{ . . .}\\
%\texttt{ /Particles<nsteps>/fieldname<n>}
%\end{tabbing}
%\end{minipage}
%}
%\fbox{\usebox{\gugu}}
%\end{figure}
\vspace{-5mm}
\section{PERFORMANCE}
% [ada] We also have data for 4 procs
% [ada] name for one file per proc
Preliminary performance estimations, looking at global (GD) and local data (LD)
rates, suggests that our HDF5 writing has a very good performance even
with respect to raw mpi, as shown in Table \ref{tab:perf}.
\begin{table}[h!]
\begin{flushleft} \footnotesize
\begin{tabular}{|l|l|l|}
\hline
\bf Mode & \bf GD [MB/s] & \bf LD [MB/s]\\
\hline
mpi-io (one file) & 241 & 3.7 \\
\hline
one file per proc & 1288 & 20 \\
\hline
H5Part/pHDFf5 (one file) & 773 & 12 \\
\hline
\end{tabular}
\end{flushleft}
\caption{\label{tab:perf}{64 IBM SP-3 nodes writing $51e6$ particles (6D). }}
%, each having 6 double-precision floating point fields for 64 timesteps over 3 trials.}}
\end{table}
\vspace{-4mm}
\section{Conclusions and Future Work}
The file format will be extended in the near future to integrate fast bitmap indexing
technology~\cite{DEX} in order to provide accelerated queries of data
stored in the file. With fastbit technolgy, a user can efficiently extract subsets of data
using compound query expressions such
as {\it $(velocity > 1e6)$ AND $(0.4 < phase < 1.0)$}.
%Such a query-driven approach offers advantages over scalable technologies aimed at visualizing ever-larger datasets.
We are also constantly tuning the performance of the parallel data
file format implementation. We will also be porting the H5Part reader
to a wider variety of visualization tools.
%in order to expand the arena
%of tools available for analyzing the stored particle data.
\begin{thebibliography}{9} % Use for 1-9 references
\bibitem{FPAT082}
A. Adelmann, R.D Ryne, C. Siegerist, J. Shalf, "From Visualization to Data Mining With Large Datasets," PAC, 2005.
\bibitem{hdf5hp}
HDF5 Home Page, http://hdf.ncsa.uiuc.edu/HDF5.
\bibitem{SDDS}
Definitions and libraries for SDDS implementation may be found at the link http://www.aps.anl.gov/asd/oag/oagPackages.shtml.
\bibitem{DEX}
K. Stockinger, J. Shalf, W. Bethel, K. Wu. "DEX: Increasing the Capability of Scientific Data Analysis Pipelines by Using Efficient Bitmap Indices to Accelerate Scientific Visualization." Scientific and Statistical Database Management Conference (SDDBM), 2005.
\end{thebibliography}
\end{document}
doc/H5xxx/JAC2003.cls
-217
View File
@@ -1,217 +0,0 @@
%%
%% This file has been developed as a common template for papers
%% destined for electronic production using Adobe Acrobat
%% software for Accelerator Conferences
%%
%% See the JACo Website for more information
%%
%% http://www.cern.ch/accelconf/
%%
% Special thanks to John Jowett and Michel Goossens from CERN and
% Martin Comyn at TRIUMF for their significant contributions to
% this class file over the period 1996 to 2000.
% John Poole
% March 2000
% JAC2001.cls is a modified version of JAC2000.cls to produce indented
% first paragraphs after section, subsection and subsubsection headings.
%
% Martin Comyn April 2001
\def\fileversion{1.2}
\def\filedate{2003/03/10}
\def\docdate {2003/03/10}
\newlength{\dsep}
\newlength{\dwid}
\newlength{\dht}
\NeedsTeXFormat{LaTeX2e}
\ProvidesClass{JAC2003}[\filedate\space Version \fileversion]
\DeclareOption{acus}
{\setlength{\dwid}{6mm}%
\setlength{\dht}{-18mm}
\setlength{\paperheight}{11in}
\setlength{\paperwidth}{8.5in}
\typeout{Setup for US LETTER PAPER}}
\DeclareOption{aca4}
{\setlength{\dwid}{0mm}%
\setlength{\dht}{0mm}}
\DeclareOption{boxit}
%%
%% This option draws a box on the output text with the correct margins
%%
{\special{!userdict begin /bop-hook{
gsave
newpath
58 55 moveto
58 737 lineto
539 737 lineto
539 55 lineto
closepath
stroke
grestore
}def end}}
\DeclareOption*{\PassOptionsToClass{\CurrentOption}{article}}
\ExecuteOptions{aca4}
\ProcessOptions
\LoadClass[10pt]{article}
%%
%% Using Times fonts produces a Uniform, compact document
%% suitable for the Acrobat Software and printable anywhere.
%%
%% In a 'modern' TeX installation
%% e.g TeXLive Version 3 or later (more information on the JACo Website)
%% one can use the following command
%%
\renewcommand{\rmdefault}{ptm}
%%
%% Older installations may require
%% \RequirePackage{times}
%%
\typeout{------------------------------------------------------------------------}
\typeout{LaTeX2e Class file for Accelerator Conference publication for LaTeX2e users}
\typeout{ }
\typeout{Use the boxit option to draw a box on page showing the correct margins}
\typeout{ }
\typeout{Itemize, Enumerate and Description environments are compact versions}
\typeout{------------------------------------------------------------------------}
\typeout{ }
%
% DIMENSION OF TEXT:
\setlength{\textheight}{241mm}
\setlength{\textwidth}{170mm}
\setlength{\topmargin}{23mm}
\addtolength{\topmargin}{\dht}
\setlength{\oddsidemargin}{20mm}
\setlength{\evensidemargin}{20mm}
\setlength{\columnsep}{5mm}
\hoffset -25.4mm
\voffset -25.4mm
\columnseprule 0pt % Width of rule between columns.
% Use Michel Goossens' dense lists
% Prevent infinite loops
\let\Otemize =\itemize
\let\Onumerate =\enumerate
\let\Oescription =\description
% Zero the vertical spacing parameters
\def\Nospacing{\itemsep=0pt\topsep=0pt\partopsep=0pt\parskip=0pt\parsep=0pt}
% Redefine the environments in terms of the original values
\newenvironment{Itemize}{\Otemize\Nospacing}{\endlist}
\newenvironment{Enumerate}{\Onumerate\Nospacing}{\endlist}
\newenvironment{Description}{\Oescription\Nospacing}{\endlist}
\renewcommand{\topfraction}{.95}
\renewcommand{\bottomfraction}{.95}
\renewcommand{\textfraction}{0.1}
\renewcommand{\floatpagefraction}{0.8}
\def\@oddhead{}\def\@evenhead{}
\def\@oddfoot{}
\def\@evenfoot{\@oddfoot}
%-----------------------------------------------------------------------
% We acknowledge the borrowing of the clever part of
% Steven Gildea's definition of \section
% from geophysi.sty.
%
% \section is tricky because we want to both support \section* and have
% the section title uppercased.
\def\section{\secdef\@sectionb\@sections}
\def\@sectionb[#1]#2{\@sections{#2}}
\def\@sections#1{\@startsection {section}{1}{\z@}
{2.8ex plus 0.8ex minus .1ex}{1.5ex plus .2ex}
{\large\bf\boldmath\centering}{\uppercase{#1}}}
% Should there be any problem with this, we can revert to the following
% but then the onus is on the user to type the argument of \section in
% uppercase in the input file.
%
%\def\section{\@startsection {section}{1}{\z@}{2.8ex plus 0.8ex minus.1ex}
% {1.5ex plus .2ex}{\large\bf\boldmath\centering}}
\def\subsection{\@startsection{subsection}{2}{\z@}{2.6ex plus .8ex minus
.17ex}{1.2ex plus .17ex}{\large\it}}
\def\subsubsection{\@startsection{subsubsection}{3}{\parindent}
{2.5ex plus .7ex minus .17ex}{-1em}{\normalsize\bf}}
\def\paragraph{\@startsection
{paragraph}{4}{\z@}{2.5ex plus .7ex minus .17ex}{-1em}{\normalsize\it}}
\def\subparagraph{\@startsection
{subparagraph}{4}{\parindent}{2.25ex plus .7ex minus
.17ex}{-1em}{\normalsize\bf}}
\setcounter{secnumdepth}{0}
% This definition of \maketitle taken from article.sty, and has been
% somewhat modified.
\def\maketitle{\par
\begingroup
\def\thefootnote{\fnsymbol{footnote}}
\def\@makefnmark{\hbox
to 5pt{$^{\@thefnmark}$\hss}}
\twocolumn[\@maketitle]
\@thanks
\endgroup
\setcounter{footnote}{0}
\let\maketitle\relax
\let\@maketitle\relax
\gdef\@thanks{}\gdef\@author{}\gdef\@title{}\let\thanks\relax}
\newlength{\titleblockheight} % so user can change it if need be
\setlength{\titleblockheight}{3.5cm}
\def\@maketitle{\vbox to \titleblockheight {\hsize\textwidth
\linewidth\hsize \vskip 3pt \centering
{\Large\bf \@title \par}
\vskip 2em % Vertical space after title.
{\large\begin{tabular}[t]{@{}c@{}}\@author \end{tabular}\par}
\vfil}}
% The \copyrightspace command is used to produce a blank space in the first
% column where a copyright notice may go. It works by producing a
% blank footnote of the appropriate size. Note that it should appear
% after any \footnote commands that produce footnotes for the first
% column. Adjusted to leave just 1cm.
\def\copyrightspace{\footnotetext[0]{\mbox{}\vrule height 1cm width 0pt}}
\def\abstract{\subsection*{Abstract}}
\def\endabstract{\par}
% Redefine to use smaller fonts
\def\thebibliography#1{\setlength{\itemsep}{0pt}\setlength{\parsep}{0pt}
\section*{REFERENCES\@mkboth
{REFERENCES}{REFERENCES}}\small\list
{[\arabic{enumi}]}{\settowidth\labelwidth{[#1]}\leftmargin\labelwidth
\advance\leftmargin\labelsep
\usecounter{enumi}}
\def\newblock{\hskip .11em plus .33em minus .07em}
\sloppy\clubpenalty4000\widowpenalty4000
\sfcode`\.=1000\relax}
\let\endthebibliography=\endlist
\twocolumn
\sloppy
\parindent 1em
\leftmargini 2em
\leftmargin\leftmargini
\leftmarginv .5em
\leftmarginvi .5em
\flushbottom
%-----------------------------------------------------------------------
doc/H5xxx/makefile
-14
View File
@@ -1,14 +0,0 @@
#################################################
##BEGIN OF makefile "makefile" - using the gnu-compiler g++
##This file is used by the Make command.
###################################################
FILE=H5xxx
all: $(FILE).tex
latex $(FILE).tex
#bibtex $(FILE)
dvips -j0 $(FILE).dvi -o $(FILE).ps
# dvips $(FILE).dvi -o $(FILE).ps -x 1200 -O 10mm,15mm
clean:
rm *~ *.bbl *.aux *.blg *.log *.dvi *.ps
doc/InternalLayout.html
-54
View File
@@ -1,54 +0,0 @@
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<title>H5Part, Logical Internal HDF5 File Layout</title>
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
<meta name="keywords" content="scientific visualization">
<meta name="sitemap" content="put a brief descriptive phrase here that will show up in the site map:foo">
<div id="maincenter">
<font face="arial,helvetica"><h1>H5Part: Logical Internal HDF5 File Layout</h1></font>
<P>
HDF5 is extremely flexible in the sense that it allows the user to define a higher level data model to describe domain-specific data relationships. This flexibility however makes it necessary to develop an agreement on the logical layout of the data. The H5Part data model consists of Particle groups corresponding to the simulation time steps, each with seven datasets corresponding to x, px, y, py, z, pz, id for each particle. Attributes can be added to the file and to the datasets.
</P>
<center><img src="layout.png"></center>
<PRE>
HDF5 "parttest.h5" {
GROUP "/" {
GROUP "Particles#0" {
DATASET "id" {
DATATYPE H5T_STD_I64LE
DATASPACE SIMPLE { ( 10 ) / ( 10 ) }
}
DATASET "px" {
DATATYPE H5T_IEEE_F64LE
DATASPACE SIMPLE { ( 10 ) / ( 10 ) }
}
DATASET "py" {
DATATYPE H5T_IEEE_F64LE
DATASPACE SIMPLE { ( 10 ) / ( 10 ) }
}
DATASET "pz" {
DATATYPE H5T_IEEE_F64LE
DATASPACE SIMPLE { ( 10 ) / ( 10 ) }
}
DATASET "x" {
DATATYPE H5T_IEEE_F64LE
DATASPACE SIMPLE { ( 10 ) / ( 10 ) }
}
DATASET "y" {
DATATYPE H5T_IEEE_F64LE
DATASPACE SIMPLE { ( 10 ) / ( 10 ) }
}
DATASET "z" {
DATATYPE H5T_IEEE_F64LE
DATASPACE SIMPLE { ( 10 ) / ( 10 ) }
}
}
</PRE>
<P>
See <a href="http://www-vis.lbl.gov/Publications/2002/hdf5.pdf">hdf5.pdf</a> for an introduction on the use of HDF5.
</P>
</div>
doc/Makefile.am
+14
View File
@@ -0,0 +1,14 @@
EXTRA_DIST = \
Doxyfile \
H5.dox
all:
doc:
doxydoc:
doxygen
clean-local:
$(RM) -r ReferencePages TWiki
$(RM) *~
doc/ReferencePages/H5PartF_8c.html
-2181
View File
File diff suppressed because it is too large Load Diff
doc/ReferencePages/H5Part_8c.html
-2205
View File
File diff suppressed because it is too large Load Diff
doc/ReferencePages/H5Part_8h-source.html
-146
View File
@@ -1,146 +0,0 @@
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html><head><meta http-equiv="Content-Type" content="text/html;charset=iso-8859-1">
<title>H5Part: H5Part.h Source File</title>
<link href="doxygen.css" rel="stylesheet" type="text/css">
</head><body>
<!-- Generated by Doxygen 1.4.4 -->
<div class="qindex"><a class="qindex" href="index.html">Main&nbsp;Page</a> | <a class="qindex" href="annotated.html">Class&nbsp;List</a> | <a class="qindex" href="files.html">File&nbsp;List</a> | <a class="qindex" href="functions.html">Class&nbsp;Members</a> | <a class="qindex" href="globals.html">File&nbsp;Members</a></div>
<h1>H5Part.h</h1><a href="H5Part_8h.html">Go to the documentation of this file.</a><div class="fragment"><pre class="fragment"><a name="l00001"></a>00001 <span class="preprocessor">#ifndef _H5Part_H_</span>
<a name="l00002"></a>00002 <span class="preprocessor"></span><span class="preprocessor">#define _H5Part_H_</span>
<a name="l00003"></a>00003 <span class="preprocessor"></span>
<a name="l00004"></a>00004 <span class="preprocessor">#include &lt;hdf5.h&gt;</span>
<a name="l00005"></a>00005 <span class="preprocessor">#ifdef PARALLEL_IO</span>
<a name="l00006"></a>00006 <span class="preprocessor"></span><span class="preprocessor">#include &lt;mpi.h&gt;</span>
<a name="l00007"></a>00007 <span class="preprocessor">#endif</span>
<a name="l00008"></a>00008 <span class="preprocessor"></span>
<a name="l00016"></a><a class="code" href="structH5PartFile.html">00016</a> <span class="keyword">typedef</span> <span class="keyword">struct </span><a class="code" href="structH5PartFile.html">H5PartFile</a> {
<a name="l00017"></a><a class="code" href="structH5PartFile.html#o0">00017</a> hid_t <a class="code" href="structH5PartFile.html#o0">file</a>;
<a name="l00018"></a><a class="code" href="structH5PartFile.html#o1">00018</a> <span class="keywordtype">int</span> <a class="code" href="structH5PartFile.html#o1">timestep</a>;
<a name="l00019"></a>00019
<a name="l00020"></a><a class="code" href="structH5PartFile.html#o2">00020</a> hid_t <a class="code" href="structH5PartFile.html#o2">timegroup</a>;
<a name="l00021"></a><a class="code" href="structH5PartFile.html#o3">00021</a> hid_t <a class="code" href="structH5PartFile.html#o3">properties</a>;
<a name="l00022"></a><a class="code" href="structH5PartFile.html#o4">00022</a> hsize_t <a class="code" href="structH5PartFile.html#o4">nparticles</a>;
<a name="l00023"></a><a class="code" href="structH5PartFile.html#o5">00023</a> hid_t <a class="code" href="structH5PartFile.html#o5">shape</a>;
<a name="l00024"></a><a class="code" href="structH5PartFile.html#o6">00024</a> <span class="keywordtype">unsigned</span> <a class="code" href="structH5PartFile.html#o6">mode</a>;
<a name="l00025"></a><a class="code" href="structH5PartFile.html#o7">00025</a> <span class="keywordtype">int</span> <a class="code" href="structH5PartFile.html#o7">maxstep</a>;
<a name="l00026"></a><a class="code" href="structH5PartFile.html#o8">00026</a> hid_t <a class="code" href="structH5PartFile.html#o8">xfer_prop</a>,<a class="code" href="structH5PartFile.html#o9">create_prop</a>,<a class="code" href="structH5PartFile.html#o10">access_prop</a>;
<a name="l00027"></a><a class="code" href="structH5PartFile.html#o12">00027</a> hid_t <a class="code" href="structH5PartFile.html#o11">diskshape</a>,<a class="code" href="structH5PartFile.html#o12">memshape</a>; <span class="comment">/* for parallel I/O (this is on-disk) H5S_ALL </span>
<a name="l00028"></a>00028 <span class="comment"> if serial I/O */</span>
<a name="l00029"></a><a class="code" href="structH5PartFile.html#o13">00029</a> <span class="keywordtype">long</span> <span class="keywordtype">long</span> <a class="code" href="structH5PartFile.html#o13">viewstart</a>,<a class="code" href="structH5PartFile.html#o14">viewend</a>; <span class="comment">/* -1 if no view is available: A "view" looks at a subset of the data. */</span>
<a name="l00030"></a>00030
<a name="l00031"></a>00031 <span class="preprocessor">#ifdef PARALLEL_IO</span>
<a name="l00032"></a>00032 <span class="preprocessor"></span> <span class="keywordtype">long</span> <span class="keywordtype">long</span> *pnparticles; <span class="comment">/* the number of particles in each processor.</span>
<a name="l00033"></a>00033 <span class="comment"> With respect to the "VIEW", these numbers</span>
<a name="l00034"></a>00034 <span class="comment"> can be regarded as non-overlapping subsections</span>
<a name="l00035"></a>00035 <span class="comment"> of the particle array stored in the file.</span>
<a name="l00036"></a>00036 <span class="comment"> So they can be used to compute the offset of</span>
<a name="l00037"></a>00037 <span class="comment"> the view for each processor */</span>
<a name="l00038"></a>00038 MPI_Comm comm;
<a name="l00039"></a>00039 <span class="keywordtype">int</span> nprocs,myproc;
<a name="l00040"></a>00040 <span class="preprocessor">#endif</span>
<a name="l00041"></a>00041 <span class="preprocessor"></span>}<a class="code" href="structH5PartFile.html">H5PartFile</a>;
<a name="l00042"></a>00042
<a name="l00043"></a><a class="code" href="H5Part_8h.html#a0">00043</a> <span class="preprocessor">#define H5PART_READ 0x01</span>
<a name="l00044"></a><a class="code" href="H5Part_8h.html#a1">00044</a> <span class="preprocessor"></span><span class="preprocessor">#define H5PART_WRITE 0x02</span>
<a name="l00045"></a>00045 <span class="preprocessor"></span>
<a name="l00046"></a>00046 <span class="comment">/*========== File Opening/Closing ===============*/</span>
<a name="l00047"></a>00047 <span class="preprocessor">#ifdef PARALLEL_IO</span>
<a name="l00048"></a>00048 <span class="preprocessor"></span><span class="preprocessor">#include &lt;mpi.h&gt;</span>
<a name="l00049"></a>00049 <a class="code" href="structH5PartFile.html">H5PartFile</a> *<a class="code" href="H5Part_8c.html#a3">H5PartOpenFileParallel</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> *filename,
<a name="l00050"></a>00050 <span class="keywordtype">unsigned</span> flags,
<a name="l00051"></a>00051 MPI_Comm communicator);
<a name="l00052"></a>00052 <span class="preprocessor">#endif</span>
<a name="l00053"></a><a class="code" href="H5Part_8h.html#a2">00053</a> <span class="preprocessor"></span><span class="preprocessor">#define H5PartOpenFileSerial(x,y) H5PartOpenFile(x,y)</span>
<a name="l00054"></a>00054 <span class="preprocessor"></span>
<a name="l00055"></a>00055 <a class="code" href="structH5PartFile.html">H5PartFile</a> *<a class="code" href="H5Part_8c.html#a4">H5PartOpenFile</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> *filename, <span class="comment">/* name of datafile */</span>
<a name="l00056"></a>00056 <span class="keywordtype">unsigned</span> flags); <span class="comment">/* H5PART_READ | H5PART_WRITE */</span>
<a name="l00057"></a>00057 <span class="keywordtype">int</span> <a class="code" href="H5Part_8c.html#a5">H5PartFileIsValid</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f);
<a name="l00058"></a>00058 <span class="keywordtype">void</span> <a class="code" href="H5Part_8c.html#a6">H5PartCloseFile</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f);
<a name="l00059"></a>00059
<a name="l00060"></a>00060
<a name="l00061"></a>00061 <span class="comment">/*============== File Writing Functions ==================== */</span>
<a name="l00062"></a>00062 <span class="keywordtype">void</span> <a class="code" href="H5Part_8c.html#a7">H5PartSetNumParticles</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f,<span class="keywordtype">long</span> <span class="keywordtype">long</span> nparticles);
<a name="l00063"></a>00063 <span class="keywordtype">int</span> <a class="code" href="H5Part_8c.html#a8">H5PartWriteDataFloat64</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f,<span class="keywordtype">char</span> *name,<span class="keywordtype">double</span> *array);
<a name="l00064"></a>00064 <span class="keywordtype">int</span> <a class="code" href="H5Part_8c.html#a9">H5PartWriteDataInt64</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f,<span class="keywordtype">char</span> *name,<span class="keywordtype">long</span> <span class="keywordtype">long</span> *array);
<a name="l00065"></a>00065
<a name="l00066"></a>00066 <span class="comment">/*================== File Reading Routines =================*/</span>
<a name="l00067"></a>00067 <span class="keywordtype">void</span> <a class="code" href="H5Part_8c.html#a24">H5PartSetStep</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f, <span class="comment">/* file handle */</span>
<a name="l00068"></a>00068 <span class="keywordtype">int</span> step); <span class="comment">/* current timestep to select (0 to n-1) */</span>
<a name="l00069"></a>00069 <span class="keywordtype">int</span> <a class="code" href="H5Part_8c.html#a27">H5PartGetNumSteps</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f);
<a name="l00070"></a>00070 <span class="keywordtype">int</span> <a class="code" href="H5Part_8c.html#a28">H5PartGetNumDatasets</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f);
<a name="l00071"></a>00071 <span class="keywordtype">int</span> <a class="code" href="H5Part_8c.html#a29">H5PartGetDatasetName</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f,<span class="keywordtype">int</span> index,<span class="keywordtype">char</span> *name,<span class="keywordtype">int</span> maxlen);
<a name="l00072"></a>00072 <span class="keywordtype">long</span> <span class="keywordtype">long</span> <a class="code" href="H5Part_8c.html#a33">H5PartGetNumParticles</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f);
<a name="l00073"></a>00073 <span class="keywordtype">void</span> <a class="code" href="H5Part_8c.html#a34">H5PartSetView</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f,<span class="keywordtype">long</span> <span class="keywordtype">long</span> start,<span class="keywordtype">long</span> <span class="keywordtype">long</span> end);
<a name="l00074"></a><a class="code" href="H5Part_8h.html#a3">00074</a> <span class="preprocessor">#define H5PartResetView(f) H5PartSetView(f,-1,-1)</span>
<a name="l00075"></a><a class="code" href="H5Part_8h.html#a4">00075</a> <span class="preprocessor"></span><span class="preprocessor">#define H5PartHasView(f) ((f-&gt;viewstart&lt;0||f-&gt;viewend&lt;0)?0:1)</span>
<a name="l00076"></a>00076 <span class="preprocessor"></span><span class="keywordtype">int</span> <a class="code" href="H5Part_8c.html#a35">H5PartGetView</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f,<span class="keywordtype">long</span> <span class="keywordtype">long</span> *start,<span class="keywordtype">long</span> <span class="keywordtype">long</span> *end);
<a name="l00077"></a>00077 <span class="keywordtype">void</span> <a class="code" href="H5Part_8c.html#a36">H5PartSetCanonicalView</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f);
<a name="l00078"></a>00078
<a name="l00079"></a>00079 <span class="keywordtype">int</span> <a class="code" href="H5Part_8c.html#a37">H5PartReadDataFloat64</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f,
<a name="l00080"></a>00080 <span class="keywordtype">char</span> *name, <span class="comment">/* name of the array to read</span>
<a name="l00081"></a>00081 <span class="comment"> "x"=position in x direction (y,z)</span>
<a name="l00082"></a>00082 <span class="comment"> "vx"=velocity in x directio (y,z)</span>
<a name="l00083"></a>00083 <span class="comment"> "px"=position in x dir (y,z) */</span>
<a name="l00084"></a>00084 <span class="keywordtype">double</span> *array); <span class="comment">/* array to read data into */</span>
<a name="l00085"></a>00085 <span class="keywordtype">int</span> <a class="code" href="H5Part_8c.html#a38">H5PartReadDataInt64</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f,
<a name="l00086"></a>00086 <span class="keywordtype">char</span> *name, <span class="comment">/* name of the array to read</span>
<a name="l00087"></a>00087 <span class="comment"> "x"=position in x direction (y,z)</span>
<a name="l00088"></a>00088 <span class="comment"> "vx"=velocity in x directio (y,z)</span>
<a name="l00089"></a>00089 <span class="comment"> "px"=position in x dir (y,z) */</span>
<a name="l00090"></a>00090 <span class="keywordtype">long</span> <span class="keywordtype">long</span> *array); <span class="comment">/* array to read data into */</span>
<a name="l00091"></a>00091
<a name="l00092"></a>00092 <span class="comment">/* the following is a back-door for extensions to the data writing */</span>
<a name="l00093"></a>00093 <span class="preprocessor">#if 0</span>
<a name="l00094"></a>00094 <span class="preprocessor"></span><span class="keywordtype">int</span> H5PartReadData(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f,<span class="keywordtype">char</span> *name,<span class="keywordtype">void</span> *array,hid_t type);
<a name="l00095"></a>00095 <span class="keywordtype">int</span> H5PartWriteData(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f,<span class="keywordtype">char</span> *name,<span class="keywordtype">void</span> *array,hid_t type);
<a name="l00096"></a>00096 <span class="preprocessor">#endif</span>
<a name="l00097"></a>00097 <span class="preprocessor"></span><span class="keywordtype">int</span> <a class="code" href="H5Part_8c.html#a39">H5PartReadParticleStep</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f, <span class="comment">/* filehandle */</span>
<a name="l00098"></a>00098 <span class="keywordtype">int</span> step, <span class="comment">/* selects timestep to read from*/</span>
<a name="l00099"></a>00099 <span class="keywordtype">double</span> *x,<span class="keywordtype">double</span> *y,<span class="keywordtype">double</span> *z, <span class="comment">/* particle positions */</span>
<a name="l00100"></a>00100 <span class="keywordtype">double</span> *px,<span class="keywordtype">double</span> *py,<span class="keywordtype">double</span> *pz, <span class="comment">/* particle momenta */</span>
<a name="l00101"></a>00101 <span class="keywordtype">long</span> <span class="keywordtype">long</span> *<span class="keywordtype">id</span>); <span class="comment">/* and phase */</span>
<a name="l00102"></a>00102 <span class="comment">/**********==============Attributes Interface============***************/</span>
<a name="l00103"></a>00103 <span class="comment">/* currently there is file attributes: Attributes bound to the file</span>
<a name="l00104"></a>00104 <span class="comment"> and step attributes which are bound to the current timestep. You </span>
<a name="l00105"></a>00105 <span class="comment"> must set the timestep explicitly before writing the attributes (just</span>
<a name="l00106"></a>00106 <span class="comment"> as you must do when you write a new dataset. Currently there are no</span>
<a name="l00107"></a>00107 <span class="comment"> attributes that are bound to a particular data array, but this could</span>
<a name="l00108"></a>00108 <span class="comment"> easily be done if required.</span>
<a name="l00109"></a>00109 <span class="comment">*/</span>
<a name="l00110"></a>00110 <span class="keywordtype">int</span> <a class="code" href="H5Part_8c.html#a12">H5PartWriteStepAttrib</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f,<span class="keywordtype">char</span> *name,
<a name="l00111"></a>00111 hid_t type,<span class="keywordtype">void</span> *attrib,<span class="keywordtype">int</span> nelem);
<a name="l00112"></a>00112 <span class="keywordtype">int</span> <a class="code" href="H5Part_8c.html#a14">H5PartWriteFileAttrib</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f,<span class="keywordtype">char</span> *name,
<a name="l00113"></a>00113 hid_t type,<span class="keywordtype">void</span> *attrib,<span class="keywordtype">int</span> nelem);
<a name="l00114"></a>00114 <span class="keywordtype">int</span> <a class="code" href="H5Part_8c.html#a13">H5PartWriteAttrib</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f,<span class="keywordtype">char</span> *name,
<a name="l00115"></a>00115 hid_t type,<span class="keywordtype">void</span> *attrib,<span class="keywordtype">int</span> nelem); <span class="comment">/* this should be deprecated */</span>
<a name="l00116"></a>00116
<a name="l00117"></a>00117 <span class="keywordtype">int</span> <a class="code" href="H5Part_8c.html#a10">H5PartWriteFileAttribString</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f,<span class="keywordtype">char</span> *name,
<a name="l00118"></a>00118 <span class="keywordtype">char</span> *attrib);
<a name="l00119"></a>00119 <span class="keywordtype">int</span> <a class="code" href="H5Part_8c.html#a11">H5PartWriteStepAttribString</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f,<span class="keywordtype">char</span> *name,
<a name="l00120"></a>00120 <span class="keywordtype">char</span> *attrib);
<a name="l00121"></a>00121 <span class="keywordtype">int</span> <a class="code" href="H5Part_8c.html#a16">H5PartGetNumStepAttribs</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f); <span class="comment">/* for current filestep */</span>
<a name="l00122"></a>00122 <span class="keywordtype">int</span> <a class="code" href="H5Part_8c.html#a17">H5PartGetNumFileAttribs</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f);
<a name="l00123"></a>00123 <span class="keywordtype">void</span> <a class="code" href="H5Part_8c.html#a19">H5PartGetStepAttribInfo</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f,<span class="keywordtype">int</span> idx,
<a name="l00124"></a>00124 <span class="keywordtype">char</span> *name,size_t maxnamelen,
<a name="l00125"></a>00125 hid_t *type,<span class="keywordtype">int</span> *nelem);
<a name="l00126"></a>00126 <span class="keywordtype">void</span> <a class="code" href="H5Part_8c.html#a20">H5PartGetFileAttribInfo</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f,<span class="keywordtype">int</span> idx,
<a name="l00127"></a>00127 <span class="keywordtype">char</span> *name,size_t maxnamelen,
<a name="l00128"></a>00128 hid_t *type,<span class="keywordtype">int</span> *nelem);
<a name="l00129"></a>00129 <span class="keywordtype">int</span> <a class="code" href="H5Part_8c.html#a21">H5PartReadStepAttrib</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f,<span class="keywordtype">char</span> *name,<span class="keywordtype">void</span> *data);
<a name="l00130"></a>00130 <span class="keywordtype">void</span> <a class="code" href="H5Part_8c.html#a22">H5PartReadAttrib</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f,<span class="keywordtype">char</span> *name,<span class="keywordtype">void</span> *data);
<a name="l00131"></a>00131 <span class="keywordtype">int</span> <a class="code" href="H5Part_8c.html#a23">H5PartReadFileAttrib</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f,<span class="keywordtype">char</span> *name,<span class="keywordtype">void</span> *data);
<a name="l00132"></a>00132
<a name="l00133"></a>00133
<a name="l00134"></a>00134 <span class="comment">/**************** File Stashing Interfaces *************************/</span>
<a name="l00135"></a>00135 <span class="keywordtype">int</span> <a class="code" href="H5Part_8c.html#a42">H5PartStashFile</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f,<span class="keywordtype">char</span> *filename);
<a name="l00136"></a>00136 <span class="keywordtype">int</span> <a class="code" href="H5Part_8c.html#a43">H5PartUnstashFile</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f, <span class="keywordtype">char</span> *filename, <span class="keywordtype">char</span> *outputpath); <span class="comment">/* outputpath can be null for cwd */</span>
<a name="l00137"></a>00137 <span class="keywordtype">int</span> <a class="code" href="H5Part_8c.html#a44">H5PartGetNumStashFiles</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f);
<a name="l00138"></a>00138 <span class="keywordtype">int</span> <a class="code" href="H5Part_8c.html#a45">H5PartFileGetStashFileName</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f,<span class="keywordtype">int</span> nameindex,<span class="keywordtype">char</span> *filename,<span class="keywordtype">int</span> maxnamelen);
<a name="l00139"></a>00139
<a name="l00140"></a>00140
<a name="l00141"></a>00141 <span class="preprocessor">#endif</span>
</pre></div><hr size="1"><address style="align: right;"><small>Generated on Tue Jan 31 11:52:45 2006 for H5Part by&nbsp;
<a href="http://www.doxygen.org/index.html">
<img src="doxygen.png" alt="doxygen" align="middle" border="0"></a> 1.4.4 </small></address>
</body>
</html>
doc/ReferencePages/H5Part_8h.html
-1876
View File
File diff suppressed because it is too large Load Diff
doc/ReferencePages/annotated.html
-16
View File
@@ -1,16 +0,0 @@
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html><head><meta http-equiv="Content-Type" content="text/html;charset=iso-8859-1">
<title>H5Part: Class List</title>
<link href="doxygen.css" rel="stylesheet" type="text/css">
</head><body>
<!-- Generated by Doxygen 1.4.4 -->
<div class="qindex"><a class="qindex" href="index.html">Main&nbsp;Page</a> | <a class="qindexHL" href="annotated.html">Class&nbsp;List</a> | <a class="qindex" href="files.html">File&nbsp;List</a> | <a class="qindex" href="functions.html">Class&nbsp;Members</a> | <a class="qindex" href="globals.html">File&nbsp;Members</a></div>
<h1>H5Part Class List</h1>Here are the classes, structs, unions and interfaces with brief descriptions:<table>
<tr><td class="indexkey"><a class="el" href="structH5IO__getname__t.html">H5IO_getname_t</a></td><td class="indexvalue"></td></tr>
<tr><td class="indexkey"><a class="el" href="structH5PartFile.html">H5PartFile</a></td><td class="indexvalue"></td></tr>
</table>
<hr size="1"><address style="align: right;"><small>Generated on Tue Jan 31 11:52:45 2006 for H5Part by&nbsp;
<a href="http://www.doxygen.org/index.html">
<img src="doxygen.png" alt="doxygen" align="middle" border="0"></a> 1.4.4 </small></address>
</body>
</html>
doc/ReferencePages/doxygen.css
-309
View File
@@ -1,309 +0,0 @@
BODY,H1,H2,H3,H4,H5,H6,P,CENTER,TD,TH,UL,DL,DIV {
font-family: Geneva, Arial, Helvetica, sans-serif;
}
BODY,TD {
font-size: 90%;
}
H1 {
text-align: center;
font-size: 160%;
}
H2 {
font-size: 120%;
}
H3 {
font-size: 100%;
}
CAPTION { font-weight: bold }
DIV.qindex {
width: 100%;
background-color: #eeeeff;
border: 1px solid #b0b0b0;
text-align: center;
margin: 2px;
padding: 2px;
line-height: 140%;
}
DIV.nav {
width: 100%;
background-color: #eeeeff;
border: 1px solid #b0b0b0;
text-align: center;
margin: 2px;
padding: 2px;
line-height: 140%;
}
DIV.navtab {
background-color: #eeeeff;
border: 1px solid #b0b0b0;
text-align: center;
margin: 2px;
margin-right: 15px;
padding: 2px;
}
TD.navtab {
font-size: 70%;
}
A.qindex {
text-decoration: none;
font-weight: bold;
color: #1A419D;
}
A.qindex:visited {
text-decoration: none;
font-weight: bold;
color: #1A419D
}
A.qindex:hover {
text-decoration: none;
background-color: #ddddff;
}
A.qindexHL {
text-decoration: none;
font-weight: bold;
background-color: #6666cc;
color: #ffffff;
border: 1px double #9295C2;
}
A.qindexHL:hover {
text-decoration: none;
background-color: #6666cc;
color: #ffffff;
}
A.qindexHL:visited { text-decoration: none; background-color: #6666cc; color: #ffffff }
A.el { text-decoration: none; font-weight: bold }
A.elRef { font-weight: bold }
A.code:link { text-decoration: none; font-weight: normal; color: #0000FF}
A.code:visited { text-decoration: none; font-weight: normal; color: #0000FF}
A.codeRef:link { font-weight: normal; color: #0000FF}
A.codeRef:visited { font-weight: normal; color: #0000FF}
A:hover { text-decoration: none; background-color: #f2f2ff }
DL.el { margin-left: -1cm }
.fragment {
font-family: Fixed, monospace;
font-size: 95%;
}
PRE.fragment {
border: 1px solid #CCCCCC;
background-color: #f5f5f5;
margin-top: 4px;
margin-bottom: 4px;
margin-left: 2px;
margin-right: 8px;
padding-left: 6px;
padding-right: 6px;
padding-top: 4px;
padding-bottom: 4px;
}
DIV.ah { background-color: black; font-weight: bold; color: #ffffff; margin-bottom: 3px; margin-top: 3px }
TD.md { background-color: #F4F4FB; font-weight: bold; }
TD.mdPrefix {
background-color: #F4F4FB;
color: #606060;
font-size: 80%;
}
TD.mdname1 { background-color: #F4F4FB; font-weight: bold; color: #602020; }
TD.mdname { background-color: #F4F4FB; font-weight: bold; color: #602020; width: 600px; }
DIV.groupHeader {
margin-left: 16px;
margin-top: 12px;
margin-bottom: 6px;
font-weight: bold;
}
DIV.groupText { margin-left: 16px; font-style: italic; font-size: 90% }
BODY {
background: white;
color: black;
margin-right: 20px;
margin-left: 20px;
}
TD.indexkey {
background-color: #eeeeff;
font-weight: bold;
padding-right : 10px;
padding-top : 2px;
padding-left : 10px;
padding-bottom : 2px;
margin-left : 0px;
margin-right : 0px;
margin-top : 2px;
margin-bottom : 2px;
border: 1px solid #CCCCCC;
}
TD.indexvalue {
background-color: #eeeeff;
font-style: italic;
padding-right : 10px;
padding-top : 2px;
padding-left : 10px;
padding-bottom : 2px;
margin-left : 0px;
margin-right : 0px;
margin-top : 2px;
margin-bottom : 2px;
border: 1px solid #CCCCCC;
}
TR.memlist {
background-color: #f0f0f0;
}
P.formulaDsp { text-align: center; }
IMG.formulaDsp { }
IMG.formulaInl { vertical-align: middle; }
SPAN.keyword { color: #008000 }
SPAN.keywordtype { color: #604020 }
SPAN.keywordflow { color: #e08000 }
SPAN.comment { color: #800000 }
SPAN.preprocessor { color: #806020 }
SPAN.stringliteral { color: #002080 }
SPAN.charliteral { color: #008080 }
.mdTable {
border: 1px solid #868686;
background-color: #F4F4FB;
}
.mdRow {
padding: 8px 10px;
}
.mdescLeft {
padding: 0px 8px 4px 8px;
font-size: 80%;
font-style: italic;
background-color: #FAFAFA;
border-top: 1px none #E0E0E0;
border-right: 1px none #E0E0E0;
border-bottom: 1px none #E0E0E0;
border-left: 1px none #E0E0E0;
margin: 0px;
}
.mdescRight {
padding: 0px 8px 4px 8px;
font-size: 80%;
font-style: italic;
background-color: #FAFAFA;
border-top: 1px none #E0E0E0;
border-right: 1px none #E0E0E0;
border-bottom: 1px none #E0E0E0;
border-left: 1px none #E0E0E0;
margin: 0px;
}
.memItemLeft {
padding: 1px 0px 0px 8px;
margin: 4px;
border-top-width: 1px;
border-right-width: 1px;
border-bottom-width: 1px;
border-left-width: 1px;
border-top-color: #E0E0E0;
border-right-color: #E0E0E0;
border-bottom-color: #E0E0E0;
border-left-color: #E0E0E0;
border-top-style: solid;
border-right-style: none;
border-bottom-style: none;
border-left-style: none;
background-color: #FAFAFA;
font-size: 80%;
}
.memItemRight {
padding: 1px 8px 0px 8px;
margin: 4px;
border-top-width: 1px;
border-right-width: 1px;
border-bottom-width: 1px;
border-left-width: 1px;
border-top-color: #E0E0E0;
border-right-color: #E0E0E0;
border-bottom-color: #E0E0E0;
border-left-color: #E0E0E0;
border-top-style: solid;
border-right-style: none;
border-bottom-style: none;
border-left-style: none;
background-color: #FAFAFA;
font-size: 80%;
}
.memTemplItemLeft {
padding: 1px 0px 0px 8px;
margin: 4px;
border-top-width: 1px;
border-right-width: 1px;
border-bottom-width: 1px;
border-left-width: 1px;
border-top-color: #E0E0E0;
border-right-color: #E0E0E0;
border-bottom-color: #E0E0E0;
border-left-color: #E0E0E0;
border-top-style: none;
border-right-style: none;
border-bottom-style: none;
border-left-style: none;
background-color: #FAFAFA;
font-size: 80%;
}
.memTemplItemRight {
padding: 1px 8px 0px 8px;
margin: 4px;
border-top-width: 1px;
border-right-width: 1px;
border-bottom-width: 1px;
border-left-width: 1px;
border-top-color: #E0E0E0;
border-right-color: #E0E0E0;
border-bottom-color: #E0E0E0;
border-left-color: #E0E0E0;
border-top-style: none;
border-right-style: none;
border-bottom-style: none;
border-left-style: none;
background-color: #FAFAFA;
font-size: 80%;
}
.memTemplParams {
padding: 1px 0px 0px 8px;
margin: 4px;
border-top-width: 1px;
border-right-width: 1px;
border-bottom-width: 1px;
border-left-width: 1px;
border-top-color: #E0E0E0;
border-right-color: #E0E0E0;
border-bottom-color: #E0E0E0;
border-left-color: #E0E0E0;
border-top-style: solid;
border-right-style: none;
border-bottom-style: none;
border-left-style: none;
color: #606060;
background-color: #FAFAFA;
font-size: 80%;
}
.search { color: #003399;
font-weight: bold;
}
FORM.search {
margin-bottom: 0px;
margin-top: 0px;
}
INPUT.search { font-size: 75%;
color: #000080;
font-weight: normal;
background-color: #eeeeff;
}
TD.tiny { font-size: 75%;
}
a {
color: #252E78;
}
a:visited {
color: #3D2185;
}
.dirtab { padding: 4px;
border-collapse: collapse;
border: 1px solid #b0b0b0;
}
TH.dirtab { background: #eeeeff;
font-weight: bold;
}
HR { height: 1px;
border: none;
border-top: 1px solid black;
}
doc/ReferencePages/doxygen.png
BIN
View File
Binary file not shown.
Side by Side

Before

Width:  |  Height:  |  Size: 1.3 KiB

doc/ReferencePages/files.html
-17
View File
@@ -1,17 +0,0 @@
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html><head><meta http-equiv="Content-Type" content="text/html;charset=iso-8859-1">
<title>H5Part: File Index</title>
<link href="doxygen.css" rel="stylesheet" type="text/css">
</head><body>
<!-- Generated by Doxygen 1.4.4 -->
<div class="qindex"><a class="qindex" href="index.html">Main&nbsp;Page</a> | <a class="qindex" href="annotated.html">Class&nbsp;List</a> | <a class="qindexHL" href="files.html">File&nbsp;List</a> | <a class="qindex" href="functions.html">Class&nbsp;Members</a> | <a class="qindex" href="globals.html">File&nbsp;Members</a></div>
<h1>H5Part File List</h1>Here is a list of all files with brief descriptions:<table>
<tr><td class="indexkey"><a class="el" href="H5Part_8c.html">H5Part.c</a></td><td class="indexvalue"></td></tr>
<tr><td class="indexkey"><a class="el" href="H5Part_8h.html">H5Part.h</a> <a href="H5Part_8h-source.html">[code]</a></td><td class="indexvalue"></td></tr>
<tr><td class="indexkey"><a class="el" href="H5PartF_8c.html">H5PartF.c</a></td><td class="indexvalue"></td></tr>
</table>
<hr size="1"><address style="align: right;"><small>Generated on Tue Jan 31 11:52:45 2006 for H5Part by&nbsp;
<a href="http://www.doxygen.org/index.html">
<img src="doxygen.png" alt="doxygen" align="middle" border="0"></a> 1.4.4 </small></address>
</body>
</html>
doc/ReferencePages/functions.html
-35
View File
@@ -1,35 +0,0 @@
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html><head><meta http-equiv="Content-Type" content="text/html;charset=iso-8859-1">
<title>H5Part: Class Members</title>
<link href="doxygen.css" rel="stylesheet" type="text/css">
</head><body>
<!-- Generated by Doxygen 1.4.4 -->
<div class="qindex"><a class="qindex" href="index.html">Main&nbsp;Page</a> | <a class="qindex" href="annotated.html">Class&nbsp;List</a> | <a class="qindex" href="files.html">File&nbsp;List</a> | <a class="qindexHL" href="functions.html">Class&nbsp;Members</a> | <a class="qindex" href="globals.html">File&nbsp;Members</a></div>
<div class="qindex"><a class="qindexHL" href="functions.html">All</a> | <a class="qindex" href="functions_vars.html">Variables</a></div>
Here is a list of all class members with links to the classes they belong to:
<p>
<ul>
<li>access_prop
: <a class="el" href="structH5PartFile.html#o10">H5PartFile</a><li>count
: <a class="el" href="structH5IO__getname__t.html#o1">H5IO_getname_t</a><li>create_prop
: <a class="el" href="structH5PartFile.html#o9">H5PartFile</a><li>diskshape
: <a class="el" href="structH5PartFile.html#o11">H5PartFile</a><li>file
: <a class="el" href="structH5PartFile.html#o0">H5PartFile</a><li>index
: <a class="el" href="structH5IO__getname__t.html#o0">H5IO_getname_t</a><li>maxstep
: <a class="el" href="structH5PartFile.html#o7">H5PartFile</a><li>memshape
: <a class="el" href="structH5PartFile.html#o12">H5PartFile</a><li>mode
: <a class="el" href="structH5PartFile.html#o6">H5PartFile</a><li>name
: <a class="el" href="structH5IO__getname__t.html#o2">H5IO_getname_t</a><li>nparticles
: <a class="el" href="structH5PartFile.html#o4">H5PartFile</a><li>properties
: <a class="el" href="structH5PartFile.html#o3">H5PartFile</a><li>shape
: <a class="el" href="structH5PartFile.html#o5">H5PartFile</a><li>timegroup
: <a class="el" href="structH5PartFile.html#o2">H5PartFile</a><li>timestep
: <a class="el" href="structH5PartFile.html#o1">H5PartFile</a><li>viewend
: <a class="el" href="structH5PartFile.html#o14">H5PartFile</a><li>viewstart
: <a class="el" href="structH5PartFile.html#o13">H5PartFile</a><li>xfer_prop
: <a class="el" href="structH5PartFile.html#o8">H5PartFile</a></ul>
<hr size="1"><address style="align: right;"><small>Generated on Tue Jan 31 11:52:45 2006 for H5Part by&nbsp;
<a href="http://www.doxygen.org/index.html">
<img src="doxygen.png" alt="doxygen" align="middle" border="0"></a> 1.4.4 </small></address>
</body>
</html>
doc/ReferencePages/functions_vars.html
-35
View File
@@ -1,35 +0,0 @@
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html><head><meta http-equiv="Content-Type" content="text/html;charset=iso-8859-1">
<title>H5Part: Class Members - Variables</title>
<link href="doxygen.css" rel="stylesheet" type="text/css">
</head><body>
<!-- Generated by Doxygen 1.4.4 -->
<div class="qindex"><a class="qindex" href="index.html">Main&nbsp;Page</a> | <a class="qindex" href="annotated.html">Class&nbsp;List</a> | <a class="qindex" href="files.html">File&nbsp;List</a> | <a class="qindexHL" href="functions.html">Class&nbsp;Members</a> | <a class="qindex" href="globals.html">File&nbsp;Members</a></div>
<div class="qindex"><a class="qindex" href="functions.html">All</a> | <a class="qindexHL" href="functions_vars.html">Variables</a></div>
<p>
<ul>
<li>access_prop
: <a class="el" href="structH5PartFile.html#o10">H5PartFile</a><li>count
: <a class="el" href="structH5IO__getname__t.html#o1">H5IO_getname_t</a><li>create_prop
: <a class="el" href="structH5PartFile.html#o9">H5PartFile</a><li>diskshape
: <a class="el" href="structH5PartFile.html#o11">H5PartFile</a><li>file
: <a class="el" href="structH5PartFile.html#o0">H5PartFile</a><li>index
: <a class="el" href="structH5IO__getname__t.html#o0">H5IO_getname_t</a><li>maxstep
: <a class="el" href="structH5PartFile.html#o7">H5PartFile</a><li>memshape
: <a class="el" href="structH5PartFile.html#o12">H5PartFile</a><li>mode
: <a class="el" href="structH5PartFile.html#o6">H5PartFile</a><li>name
: <a class="el" href="structH5IO__getname__t.html#o2">H5IO_getname_t</a><li>nparticles
: <a class="el" href="structH5PartFile.html#o4">H5PartFile</a><li>properties
: <a class="el" href="structH5PartFile.html#o3">H5PartFile</a><li>shape
: <a class="el" href="structH5PartFile.html#o5">H5PartFile</a><li>timegroup
: <a class="el" href="structH5PartFile.html#o2">H5PartFile</a><li>timestep
: <a class="el" href="structH5PartFile.html#o1">H5PartFile</a><li>viewend
: <a class="el" href="structH5PartFile.html#o14">H5PartFile</a><li>viewstart
: <a class="el" href="structH5PartFile.html#o13">H5PartFile</a><li>xfer_prop
: <a class="el" href="structH5PartFile.html#o8">H5PartFile</a></ul>
<hr size="1"><address style="align: right;"><small>Generated on Tue Jan 31 11:52:45 2006 for H5Part by&nbsp;
<a href="http://www.doxygen.org/index.html">
<img src="doxygen.png" alt="doxygen" align="middle" border="0"></a> 1.4.4 </small></address>
</body>
</html>

Some files were not shown because too many files have changed in this diff Show More