From bbd16d0f9430f75b36b60d226c85013459a84ade Mon Sep 17 00:00:00 2001 From: matthias muntwiler Date: Wed, 22 Nov 2017 14:55:20 +0100 Subject: [PATCH] add files for public distribution based on internal repository 0a462b6 2017-11-22 14:41:39 +0100 --- .gitattributes | 23 + .gitignore | 15 + NOTICE.md | 14 + README.md | 70 + bin/pmsco.ra.template | 157 + bin/pmsco.sge.template | 178 + bin/qpmsco.ra.sh | 145 + bin/qpmsco.sge | 128 + docs/.gitignore | 3 + docs/config.dox | 2396 + docs/makefile | 26 + docs/readme.txt | 7 + docs/src/commandline.dox | 144 + docs/src/concepts.dox | 153 + docs/src/dataflow.dot | 84 + docs/src/execution.dox | 87 + docs/src/installation.dox | 168 + docs/src/introduction.dox | 61 + docs/src/modules.dot | 51 + docs/src/processes.dot | 27 + docs/src/tasks.dot | 95 + docs/src/tasks_legend.dot | 10 + makefile | 36 + pmsco/__init__.py | 0 pmsco/__main__.py | 17 + pmsco/calculator.py | 131 + pmsco/cluster.py | 785 + pmsco/data.py | 840 + pmsco/dispatch.py | 972 + pmsco/edac/.gitignore | 3 + pmsco/edac/__init__.py | 1 + pmsco/edac/edac.i | 7 + pmsco/edac/edac_all.patch | 130 + pmsco/edac/makefile | 52 + pmsco/edac/setup.py | 20 + pmsco/edac_calculator.py | 223 + pmsco/files.py | 324 + pmsco/gradient.py | 280 + pmsco/grid.py | 409 + pmsco/handlers.py | 948 + pmsco/helpers.py | 8 + pmsco/loess/.gitignore | 2 + pmsco/loess/README | 115 + pmsco/loess/S.h | 31 + pmsco/loess/__init__.py | 1 + pmsco/loess/air.c | 78 + pmsco/loess/changes | 168 + pmsco/loess/cloess.ps | 33320 ++++++++++++++ pmsco/loess/depend.ps | 117 + pmsco/loess/dqrsl.f | 274 + pmsco/loess/dsvdc.f | 481 + pmsco/loess/ethanol.c | 93 + pmsco/loess/fix_main.c | 7 + pmsco/loess/galaxy.c | 204 + pmsco/loess/gas.c | 69 + pmsco/loess/loess.c | 327 + pmsco/loess/loess.h | 70 + pmsco/loess/loess.i | 284 + pmsco/loess/loess.m | 75 + pmsco/loess/loessc.c | 347 + pmsco/loess/loessf.f | 2198 + pmsco/loess/loessf.m | 201 + pmsco/loess/madeup.c | 172 + pmsco/loess/makefile | 77 + pmsco/loess/misc.c | 349 + pmsco/loess/numpy.i | 3161 ++ pmsco/loess/predict.c | 175 + pmsco/loess/predict.m | 77 + pmsco/loess/setup.py | 55 + pmsco/loess/struct.m | 163 + pmsco/loess/supp.f | 206 + pmsco/makefile | 33 + pmsco/msc/.gitignore | 1 + pmsco/msc/__init__.py | 1 + pmsco/msc/makefile | 49 + pmsco/msc_calculator.py | 112 + pmsco/mufpot/__init__.py | 1 + pmsco/mufpot/makefile | 46 + pmsco/pmsco.py | 381 + pmsco/project.py | 995 + pmsco/swarm.py | 909 + projects/__init__.py | 1 + projects/common/empty-hemiscan.etpi | 16376 +++++++ projects/demo/__init__.py | 1 + projects/demo/demo_alpha_scan.etpai | 181 + projects/demo/demo_holo_scan.etpi | 16376 +++++++ projects/demo/fcc.py | 284 + projects/twoatom/__init__.py | 1 + projects/twoatom/twoatom.py | 249 + projects/twoatom/twoatom_energy_alpha.etpai | 36019 ++++++++++++++++ projects/twoatom/twoatom_energy_theta_0p.etpi | 36019 ++++++++++++++++ .../twoatom/twoatom_energy_theta_180p.etpi | 36019 ++++++++++++++++ projects/twoatom/twoatom_hemi_215e.etpi | 16376 +++++++ projects/twoatom/twoatom_hemi_250e.etpi | 16376 +++++++ requirements.txt | 7 + tests/__init__.py | 1 + tests/test_cluster.py | 321 + tests/test_data.py | 428 + tests/test_files.py | 104 + tests/test_hbncu.py | 48 + tests/test_swarm.py | 364 + tests/test_swarm.setup_with_results.1.dat | 5 + 102 files changed, 230209 insertions(+) create mode 100644 .gitattributes create mode 100644 .gitignore create mode 100644 NOTICE.md create mode 100644 bin/pmsco.ra.template create mode 100644 bin/pmsco.sge.template create mode 100755 bin/qpmsco.ra.sh create mode 100755 bin/qpmsco.sge create mode 100644 docs/.gitignore create mode 100644 docs/config.dox create mode 100644 docs/makefile create mode 100644 docs/readme.txt create mode 100644 docs/src/commandline.dox create mode 100644 docs/src/concepts.dox create mode 100644 docs/src/dataflow.dot create mode 100644 docs/src/execution.dox create mode 100644 docs/src/installation.dox create mode 100644 docs/src/introduction.dox create mode 100644 docs/src/modules.dot create mode 100644 docs/src/processes.dot create mode 100644 docs/src/tasks.dot create mode 100644 docs/src/tasks_legend.dot create mode 100644 makefile create mode 100644 pmsco/__init__.py create mode 100644 pmsco/__main__.py create mode 100644 pmsco/calculator.py create mode 100644 pmsco/cluster.py create mode 100644 pmsco/data.py create mode 100644 pmsco/dispatch.py create mode 100644 pmsco/edac/.gitignore create mode 100644 pmsco/edac/__init__.py create mode 100644 pmsco/edac/edac.i create mode 100644 pmsco/edac/edac_all.patch create mode 100644 pmsco/edac/makefile create mode 100644 pmsco/edac/setup.py create mode 100644 pmsco/edac_calculator.py create mode 100644 pmsco/files.py create mode 100644 pmsco/gradient.py create mode 100644 pmsco/grid.py create mode 100644 pmsco/handlers.py create mode 100644 pmsco/helpers.py create mode 100644 pmsco/loess/.gitignore create mode 100644 pmsco/loess/README create mode 100644 pmsco/loess/S.h create mode 100644 pmsco/loess/__init__.py create mode 100644 pmsco/loess/air.c create mode 100644 pmsco/loess/changes create mode 100644 pmsco/loess/cloess.ps create mode 100644 pmsco/loess/depend.ps create mode 100644 pmsco/loess/dqrsl.f create mode 100644 pmsco/loess/dsvdc.f create mode 100644 pmsco/loess/ethanol.c create mode 100644 pmsco/loess/fix_main.c create mode 100644 pmsco/loess/galaxy.c create mode 100644 pmsco/loess/gas.c create mode 100644 pmsco/loess/loess.c create mode 100644 pmsco/loess/loess.h create mode 100644 pmsco/loess/loess.i create mode 100644 pmsco/loess/loess.m create mode 100644 pmsco/loess/loessc.c create mode 100644 pmsco/loess/loessf.f create mode 100644 pmsco/loess/loessf.m create mode 100644 pmsco/loess/madeup.c create mode 100644 pmsco/loess/makefile create mode 100644 pmsco/loess/misc.c create mode 100644 pmsco/loess/numpy.i create mode 100644 pmsco/loess/predict.c create mode 100644 pmsco/loess/predict.m create mode 100644 pmsco/loess/setup.py create mode 100644 pmsco/loess/struct.m create mode 100644 pmsco/loess/supp.f create mode 100644 pmsco/makefile create mode 100644 pmsco/msc/.gitignore create mode 100644 pmsco/msc/__init__.py create mode 100644 pmsco/msc/makefile create mode 100644 pmsco/msc_calculator.py create mode 100644 pmsco/mufpot/__init__.py create mode 100644 pmsco/mufpot/makefile create mode 100755 pmsco/pmsco.py create mode 100644 pmsco/project.py create mode 100644 pmsco/swarm.py create mode 100644 projects/__init__.py create mode 100644 projects/common/empty-hemiscan.etpi create mode 100644 projects/demo/__init__.py create mode 100644 projects/demo/demo_alpha_scan.etpai create mode 100644 projects/demo/demo_holo_scan.etpi create mode 100644 projects/demo/fcc.py create mode 100644 projects/twoatom/__init__.py create mode 100644 projects/twoatom/twoatom.py create mode 100644 projects/twoatom/twoatom_energy_alpha.etpai create mode 100644 projects/twoatom/twoatom_energy_theta_0p.etpi create mode 100644 projects/twoatom/twoatom_energy_theta_180p.etpi create mode 100644 projects/twoatom/twoatom_hemi_215e.etpi create mode 100644 projects/twoatom/twoatom_hemi_250e.etpi create mode 100644 requirements.txt create mode 100644 tests/__init__.py create mode 100644 tests/test_cluster.py create mode 100644 tests/test_data.py create mode 100644 tests/test_files.py create mode 100644 tests/test_hbncu.py create mode 100644 tests/test_swarm.py create mode 100644 tests/test_swarm.setup_with_results.1.dat diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 0000000..7e185b0 --- /dev/null +++ b/.gitattributes @@ -0,0 +1,23 @@ +# Set the default behavior, in case people don't have core.autocrlf set. +* text=auto + +# Explicitly declare text files you want to always be normalized and converted +# to native line endings on checkout. +*.c text +*.cpp text +*.f text +*.h text +*.i text +*.m text +*.py text +*.pyf text +makefile text +README text + +# Declare files that will always have CRLF line endings on checkout. +*.bat text eol=crlf +*.vc text eol=crlf + +# Denote all files that are truly binary and should not be modified. +*.png binary +*.jpg binary diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..8e3dfdf --- /dev/null +++ b/.gitignore @@ -0,0 +1,15 @@ +work/* +debug/* +lib/* +*.pyc +*.o +*.so +*.exe +*.x +*~ +*.log +.idea/* +.eric4project/* +.eric5project/* +.ropeproject/* +.fuse* diff --git a/NOTICE.md b/NOTICE.md new file mode 100644 index 0000000..47e6075 --- /dev/null +++ b/NOTICE.md @@ -0,0 +1,14 @@ +List of Contributors +==================== + + +Original Author +--------------- + +Matthias Muntwiler, + + +Contributors +------------ + + diff --git a/README.md b/README.md index e69de29..e674e3e 100644 --- a/README.md +++ b/README.md @@ -0,0 +1,70 @@ +Introduction +============ + +PMSCO stands for PEARL multiple-scattering cluster calculations and structural optimization. +It is a collection of computer programs to calculate photoelectron diffraction patterns, +and to optimize structural models based on measured data. + +The actual scattering calculation is done by code developed by other parties. +PMSCO wraps around that program and facilitates parameter handling, cluster building, structural optimization and parallel processing. +In the current version, the [EDAC](http://garciadeabajos-group.icfo.es/widgets/edac/) code +developed by F. J. García de Abajo, M. A. Van Hove, and C. S. Fadley (1999) is used for scattering calculations. +Other code can be integrated as well. + +Highlights +---------- + +- angle or energy scanned XPD. +- various scanning modes including energy, polar angle, azimuthal angle, analyser angle. +- averaging over multiple symmetries (domains or emitters). +- global optimization of multiple scans. +- structural optimization algorithms: particle swarm optimization, grid search, gradient search. +- calculation of the modulation function. +- calculation of the weighted R-factor. +- automatic parallel processing using OpenMPI. + + +Installation +============ + +PMSCO is written in Python 2.7. +The code will run in any recent Linux environment on a workstation or in a virtual machine. +Scientific Linux, CentOS7, [Ubuntu](https://www.ubuntu.com/) +and [Lubuntu](http://lubuntu.net/) (recommended for virtual machine) have been tested. +For optimization jobs, a cluster with 20-50 available processor cores is recommended. +The code requires about 2 GB of RAM per process. + +Detailed installation instructions and dependencies can be found in the documentation +(docs/src/installation.dox). +A [Doxygen](http://www.stack.nl/~dimitri/doxygen/index.html) compiler with Doxypy is required to generate the documentation in HTML or LaTeX format. + +The public distribution of PMSCO does not contain the [EDAC](http://garciadeabajos-group.icfo.es/widgets/edac/) code. +Please obtain the EDAC source code from the original author, copy it to the pmsco/edac directory, and apply the edac_all.patch patch. + + +License +======= + +The source code of PMSCO is licensed under the [Apache License, Version 2.0](http://www.apache.org/licenses/LICENSE-2.0). +Please read and respect the license agreement. + +Please share your extensions of the code with the original author. +The gitlab facility can be used to create forks and to submit pull requests. +Attribution notices for your contributions shall be added to the NOTICE.md file. + + +Author +------ + +Matthias Muntwiler, + +Copyright +--------- + +Copyright 2015-2017 by [Paul Scherrer Institut](http://www.psi.ch) + + +Release Notes +============= + + diff --git a/bin/pmsco.ra.template b/bin/pmsco.ra.template new file mode 100644 index 0000000..fa11504 --- /dev/null +++ b/bin/pmsco.ra.template @@ -0,0 +1,157 @@ +#!/bin/bash +# +# Slurm script template for PMSCO calculations on the Ra cluster +# based on run_mpi_HPL_nodes-2.sl by V. Markushin 2016-03-01 +# +# Use: +# - enter the appropriate parameters and save as a new file. +# - call the sbatch command to pass the job script. +# request a specific number of nodes and tasks. +# example: +# sbatch --nodes=2 --ntasks-per-node=24 --time=02:00:00 run_pmsco.sl +# +# PMSCO arguments +# copy this template to a new file, and set the arguments +# +# PMSCO_WORK_DIR +# path to be used as working directory. +# contains the script derived from this template. +# receives output and temporary files. +# +# PMSCO_PROJECT_FILE +# python module that declares the project and starts the calculation. +# must include the file path relative to $PMSCO_WORK_DIR. +# +# PMSCO_SOURCE_DIR +# path to the pmsco source directory +# (the directory which contains the bin, lib, pmsco sub-directories) +# +# PMSCO_SCAN_FILES +# list of scan files. +# +# PMSCO_OUT +# name of output file. should not include a path. +# +# all paths are relative to $PMSCO_WORK_DIR or (better) absolute. +# +# +# Further arguments +# +# PMSCO_JOBNAME (required) +# the job name is the base name for output files. +# +# PMSCO_WALLTIME_HR (integer, required) +# wall time limit in hours. must be integer, minimum 1. +# this value is passed to PMSCO. +# it should specify the same amount of wall time as requested from the scheduler. +# +# PMSCO_MODE (optional) +# calculation mode: single, swarm, grid, gradient +# +# PMSCO_CODE (optional) +# calculation code: edac, msc, test +# +# PMSCO_LOGLEVEL (optional) +# request log level: DEBUG, INFO, WARNING, ERROR +# create a log file based on the job name. +# +# PMSCO_PROJECT_ARGS (optional) +# extra arguments that are parsed by the project module. +# +#SBATCH --job-name="_PMSCO_JOBNAME" +#SBATCH --output="_PMSCO_JOBNAME.o.%j" +#SBATCH --error="_PMSCO_JOBNAME.e.%j" + +PMSCO_WORK_DIR="_PMSCO_WORK_DIR" +PMSCO_JOBNAME="_PMSCO_JOBNAME" +PMSCO_WALLTIME_HR=_PMSCO_WALLTIME_HR + +PMSCO_PROJECT_FILE="_PMSCO_PROJECT_FILE" +PMSCO_MODE="_PMSCO_MODE" +PMSCO_CODE="_PMSCO_CODE" +PMSCO_SOURCE_DIR="_PMSCO_SOURCE_DIR" +PMSCO_SCAN_FILES="_PMSCO_SCAN_FILES" +PMSCO_OUT="_PMSCO_JOBNAME" +PMSCO_LOGLEVEL="_PMSCO_LOGLEVEL" +PMSCO_PROJECT_ARGS="_PMSCO_PROJECT_ARGS" + +module load psi-python27/2.4.1 +module load gcc/4.8.5 +module load openmpi/1.10.2 +source activate pmsco + +echo '================================================================================' +echo "=== Running $0 at the following time and place:" +date +/bin/hostname +cd $PMSCO_WORK_DIR +pwd +ls -lA +#the intel compiler is currently not compatible with mpi4py. -mm 170131 +#echo +#echo '================================================================================' +#echo "=== Setting the environment to use Intel Cluster Studio XE 2016 Update 2 intel/16.2:" +#cmd="source /opt/psi/Programming/intel/16.2/bin/compilervars.sh intel64" +#echo $cmd +#$cmd +echo +echo '================================================================================' +echo "=== The environment is set as following:" +env +echo +echo '================================================================================' +echo "BEGIN test" +echo "=== Intel native mpirun will get the number of nodes and the machinefile from Slurm" +which mpirun +cmd="mpirun /bin/hostname" +echo $cmd +$cmd +echo "END test" +echo +echo '================================================================================' +echo "BEGIN mpirun pmsco" +echo "Intel native mpirun will get the number of nodes and the machinefile from Slurm" +echo +echo "code revision" +cd "$PMSCO_SOURCE_DIR" +git log --pretty=tformat:'%h %ai %d' -1 +python -m compileall pmsco +python -m compileall projects +cd "$PMSCO_WORK_DIR" +echo + +PMSCO_CMD="python $PMSCO_PROJECT_FILE" +PMSCO_ARGS="$PMSCO_PROJECT_ARGS" +if [ -n "$PMSCO_SCAN_FILES" ]; then + PMSCO_ARGS="-s $PMSCO_SCAN_FILES $PMSCO_ARGS" +fi +if [ -n "$PMSCO_CODE" ]; then + PMSCO_ARGS="-c $PMSCO_CODE $PMSCO_ARGS" +fi +if [ -n "$PMSCO_MODE" ]; then + PMSCO_ARGS="-m $PMSCO_MODE $PMSCO_ARGS" +fi +if [ -n "$PMSCO_OUT" ]; then + PMSCO_ARGS="-o $PMSCO_OUT $PMSCO_ARGS" +fi +if [ "$PMSCO_WALLTIME_HR" -ge 1 ]; then + PMSCO_ARGS="-t $PMSCO_WALLTIME_HR $PMSCO_ARGS" +fi +if [ -n "$PMSCO_LOGLEVEL" ]; then + PMSCO_ARGS="--log-level $PMSCO_LOGLEVEL --log-file $PMSCO_JOBNAME.log $PMSCO_ARGS" +fi + +which mpirun +ls -l "$PMSCO_SOURCE_DIR" +ls -l "$PMSCO_PROJECT_FILE" +# Do no use the OpenMPI specific options, like "-x LD_LIBRARY_PATH", with the Intel mpirun. +cmd="mpirun $PMSCO_CMD $PMSCO_ARGS" +echo $cmd +$cmd +echo "END mpirun pmsco" +echo '================================================================================' +date +ls -lAtr +echo '================================================================================' + +exit 0 diff --git a/bin/pmsco.sge.template b/bin/pmsco.sge.template new file mode 100644 index 0000000..d53c363 --- /dev/null +++ b/bin/pmsco.sge.template @@ -0,0 +1,178 @@ +#!/bin/bash +# +# SGE script template for MSC calculations +# +# This script uses the tight integration of openmpi-1.4.5-gcc-4.6.3 in SGE +# using the parallel environment (PE) "orte". +# This script must be used only with qsub command - do NOT run it as a stand-alone +# shell script because it will start all processes on the local node. +# +# PhD arguments +# copy this template to a new file, and set the arguments +# +# PHD_WORK_DIR +# path to be used as working directory. +# contains the SGE script derived from this template. +# receives output and temporary files. +# +# PHD_PROJECT_FILE +# python module that declares the project and starts the calculation. +# must include the file path relative to $PHD_WORK_DIR. +# +# PHD_SOURCE_DIR +# path to the pmsco source directory +# (the directory which contains the bin, lib, pmsco sub-directories) +# +# PHD_SCAN_FILES +# list of scan files. +# +# PHD_OUT +# name of output file. should not include a path. +# +# all paths are relative to $PHD_WORK_DIR or (better) absolute. +# +# +# Further arguments +# +# PHD_JOBNAME (required) +# the job name is the base name for output files. +# +# PHD_NODES (required) +# number of computing nodes (processes) to allocate for the job. +# +# PHD_WALLTIME_HR (required) +# wall time limit (hours) +# +# PHD_WALLTIME_MIN (required) +# wall time limit (minutes) +# +# PHD_MODE (optional) +# calculation mode: single, swarm, grid, gradient +# +# PHD_CODE (optional) +# calculation code: edac, msc, test +# +# PHD_LOGLEVEL (optional) +# request log level: DEBUG, INFO, WARNING, ERROR +# create a log file based on the job name. +# +# PHD_PROJECT_ARGS (optional) +# extra arguments that are parsed by the project module. +# + +PHD_WORK_DIR="_PHD_WORK_DIR" +PHD_JOBNAME="_PHD_JOBNAME" +PHD_NODES=_PHD_NODES +PHD_WALLTIME_HR=_PHD_WALLTIME_HR +PHD_WALLTIME_MIN=_PHD_WALLTIME_MIN + +PHD_PROJECT_FILE="_PHD_PROJECT_FILE" +PHD_MODE="_PHD_MODE" +PHD_CODE="_PHD_CODE" +PHD_SOURCE_DIR="_PHD_SOURCE_DIR" +PHD_SCAN_FILES="_PHD_SCAN_FILES" +PHD_OUT="_PHD_JOBNAME" +PHD_LOGLEVEL="_PHD_LOGLEVEL" +PHD_PROJECT_ARGS="_PHD_PROJECT_ARGS" + +# Define your job name, parallel environment with the number of slots, and run time: +#$ -cwd +#$ -N _PHD_JOBNAME.job +#$ -pe orte _PHD_NODES +#$ -l ram=2G +#$ -l s_rt=_PHD_WALLTIME_HR:_PHD_WALLTIME_MIN:00 +#$ -l h_rt=_PHD_WALLTIME_HR:_PHD_WALLTIME_MIN:30 +#$ -V + +################################################### +# Fix the SGE environment-handling bug (bash): +source /usr/share/Modules/init/sh +export -n -f module + +# Load the environment modules for this job (the order may be important): +module load python/python-2.7.5 +module load gcc/gcc-4.6.3 +module load mpi/openmpi-1.4.5-gcc-4.6.3 +module load blas/blas-20110419-gcc-4.6.3 +module load lapack/lapack-3.4.2-gcc-4.6.3 +export LD_LIBRARY_PATH=$PHD_SOURCE_DIR/lib/:$LD_LIBRARY_PATH + +################################################### +# Set the environment variables: +MPIEXEC=$OPENMPI/bin/mpiexec +# OPENMPI is set by the mpi/openmpi-* module. + +export OMP_NUM_THREADS=1 +export OMPI_MCA_btl='openib,sm,self' +# export OMPI_MCA_orte_process_binding=core + +############## +# BEGIN DEBUG +# Print the SGE environment on master host: +echo "================================================================" +echo "=== SGE job JOB_NAME=$JOB_NAME JOB_ID=$JOB_ID" +echo "================================================================" +echo DATE=`date` +echo HOSTNAME=`hostname` +echo PWD=`pwd` +echo "NSLOTS=$NSLOTS" +echo "PE_HOSTFILE=$PE_HOSTFILE" +cat $PE_HOSTFILE +echo "================================================================" +echo "Running environment:" +env +echo "================================================================" +echo "Loaded environment modules:" +module list 2>&1 +echo +# END DEBUG +############## + +############## +# Setup +cd "$PHD_SOURCE_DIR" +python -m compileall . + +cd "$PHD_WORK_DIR" +ulimit -c 0 + +################################################### +# The command to run with mpiexec: +CMD="python $PHD_PROJECT_FILE" +ARGS="$PHD_PROJECT_ARGS" + +if [ -n "$PHD_SCAN_FILES" ]; then + ARGS="-s $PHD_SCAN_FILES -- $ARGS" +fi + +if [ -n "$PHD_CODE" ]; then + ARGS="-c $PHD_CODE $ARGS" +fi + +if [ -n "$PHD_MODE" ]; then + ARGS="-m $PHD_MODE $ARGS" +fi + +if [ -n "$PHD_OUT" ]; then + ARGS="-o $PHD_OUT $ARGS" +fi + +if [ "$PHD_WALLTIME_HR" -ge 1 ] +then + ARGS="-t $PHD_WALLTIME_HR $ARGS" +else + ARGS="-t 0.5 $ARGS" +fi + +if [ -n "$PHD_LOGLEVEL" ]; then + ARGS="--log-level $PHD_LOGLEVEL --log-file $PHD_JOBNAME.log $ARGS" +fi + +# The MPI command to run: +MPICMD="$MPIEXEC --prefix $OPENMPI -x PATH -x LD_LIBRARY_PATH -x OMP_NUM_THREADS -x OMPI_MCA_btl -np $NSLOTS $CMD $ARGS" +echo "Command to run:" +echo "$MPICMD" +echo +exec $MPICMD + +exit 0 diff --git a/bin/qpmsco.ra.sh b/bin/qpmsco.ra.sh new file mode 100755 index 0000000..ddf9280 --- /dev/null +++ b/bin/qpmsco.ra.sh @@ -0,0 +1,145 @@ +#!/bin/sh +# +# submission script for PMSCO calculations on the Ra cluster + +if [ $# -lt 1 ]; then + echo "Usage: $0 [NOSUB] JOBNAME NODES TASKS_PER_NODE WALLTIME:HOURS PROJECT MODE [ARGS [ARGS [...]]]" + echo "" + echo " NOSUB (optional): do not submit the script to the queue. default: submit." + echo " JOBNAME (text): name of job. use only alphanumeric characters, no spaces." + echo " NODES (integer): number of computing nodes. (1 node = 24 or 32 processors)." + echo " do not specify more than 2." + echo " TASKS_PER_NODE (integer): 1...24, or 32." + echo " 24 or 32 for full-node allocation." + echo " 1...23 for shared node allocation." + echo " WALLTIME:HOURS (integer): requested wall time." + echo " 1...24 for day partition" + echo " 24...192 for week partition" + echo " 1...192 for shared partition" + echo " PROJECT: python module (file path) that declares the project and starts the calculation." + echo " MODE: PMSCO calculation mode (single|swarm|gradient|grid)." + echo " ARGS (optional): any number of further PMSCO or project arguments (except mode and time)." + echo "" + echo "the job script complete with the program code and input/output data is generated in ~/jobs/\$JOBNAME" + exit 1 +fi + +# location of the pmsco package is derived from the path of this script +SCRIPTDIR="$(dirname $(readlink -f $0))" +SOURCEDIR="$SCRIPTDIR/.." +PMSCO_SOURCE_DIR="$SOURCEDIR" + +# read arguments +if [ "$1" == "NOSUB" ]; then + NOSUB="true" + shift +else + NOSUB="false" +fi + +PMSCO_JOBNAME=$1 +shift + +PMSCO_NODES=$1 +PMSCO_TASKS_PER_NODE=$2 +PMSCO_TASKS=$(expr $PMSCO_NODES \* $PMSCO_TASKS_PER_NODE) +shift 2 + +PMSCO_WALLTIME_HR=$1 +PMSCO_WALLTIME_MIN=$(expr $PMSCO_WALLTIME_HR \* 60) +shift + +# select partition +if [ $PMSCO_WALLTIME_HR -ge 25 ]; then + PMSCO_PARTITION="week" +else + PMSCO_PARTITION="day" +fi +if [ $PMSCO_TASKS_PER_NODE -lt 24 ]; then + PMSCO_PARTITION="shared" +fi + +PMSCO_PROJECT_FILE="$(readlink -f $1)" +shift + +PMSCO_MODE="$1" +shift + +PMSCO_PROJECT_ARGS="$*" + +# use defaults, override explicitly in PMSCO_PROJECT_ARGS if necessary +PMSCO_SCAN_FILES="" +PMSCO_LOGLEVEL="" +PMSCO_CODE="" + +# set up working directory +cd ~ +if [ ! -d "jobs" ]; then + mkdir jobs +fi +cd jobs +if [ ! -d "$PMSCO_JOBNAME" ]; then + mkdir "$PMSCO_JOBNAME" +fi +cd "$PMSCO_JOBNAME" +WORKDIR="$(pwd)" +PMSCO_WORK_DIR="$WORKDIR" + +# provide revision information, requires git repository +cd "$SOURCEDIR" +PMSCO_REV=$(git log --pretty=format:"Data revision %h, %ai" -1) +if [ $? -ne 0 ]; then + PMSCO_REV="Data revision unknown, "$(date +"%F %T %z") +fi +cd "$WORKDIR" +echo "$PMSCO_REV" > revision.txt + +# generate job script from template +sed -e "s:_PMSCO_WORK_DIR:$PMSCO_WORK_DIR:g" \ + -e "s:_PMSCO_JOBNAME:$PMSCO_JOBNAME:g" \ + -e "s:_PMSCO_NODES:$PMSCO_NODES:g" \ + -e "s:_PMSCO_WALLTIME_HR:$PMSCO_WALLTIME_HR:g" \ + -e "s:_PMSCO_PROJECT_FILE:$PMSCO_PROJECT_FILE:g" \ + -e "s:_PMSCO_PROJECT_ARGS:$PMSCO_PROJECT_ARGS:g" \ + -e "s:_PMSCO_CODE:$PMSCO_CODE:g" \ + -e "s:_PMSCO_MODE:$PMSCO_MODE:g" \ + -e "s:_PMSCO_SOURCE_DIR:$PMSCO_SOURCE_DIR:g" \ + -e "s:_PMSCO_SCAN_FILES:$PMSCO_SCAN_FILES:g" \ + -e "s:_PMSCO_LOGLEVEL:$PMSCO_LOGLEVEL:g" \ + "$SCRIPTDIR/pmsco.ra.template" > $PMSCO_JOBNAME.job + +chmod u+x "$PMSCO_JOBNAME.job" + +# request nodes and tasks +# +# The option --ntasks-per-node is meant to be used with the --nodes option. +# (For the --ntasks option, the default is one task per node, use the --cpus-per-task option to change this default.) +# +# sbatch options +# --cores-per-socket=16 +# 32 cores per node +# --partition=[shared|day|week] +# --time=8-00:00:00 +# override default time limit (2 days in long queue) +# time formats: "minutes", "minutes:seconds", "hours:minutes:seconds", "days-hours", "days-hours:minutes", "days-hours:minutes:seconds" +# --mail-type=ALL +# --test-only +# check script but do not submit +# +SLURM_ARGS="--nodes=$PMSCO_NODES --ntasks-per-node=$PMSCO_TASKS_PER_NODE" + +if [ $PMSCO_TASKS_PER_NODE -gt 24 ]; then + SLURM_ARGS="--cores-per-socket=16 $SLURM_ARGS" +fi + +SLURM_ARGS="--partition=$PMSCO_PARTITION $SLURM_ARGS" + +SLURM_ARGS="--time=$PMSCO_WALLTIME_HR:00:00 $SLURM_ARGS" + +CMD="sbatch $SLURM_ARGS $PMSCO_JOBNAME.job" +echo $CMD +if [ "$NOSUB" != "true" ]; then + $CMD +fi + +exit 0 diff --git a/bin/qpmsco.sge b/bin/qpmsco.sge new file mode 100755 index 0000000..d9f6ff9 --- /dev/null +++ b/bin/qpmsco.sge @@ -0,0 +1,128 @@ +#!/bin/sh +# +# submission script for PMSCO calculations on Merlin cluster +# + +if [ $# -lt 1 ]; then + echo "Usage: $0 [NOSUB] JOBNAME NODES WALLTIME:HOURS PROJECT MODE [LOG_LEVEL]" + echo "" + echo " NOSUB (optional): do not submit the script to the queue. default: submit." + echo " WALLTIME:HOURS (integer): sets the wall time limits." + echo " soft limit = HOURS:00:00" + echo " hard limit = HOURS:00:30" + echo " for short.q: HOURS = 0 (-> MINUTES=30)" + echo " for all.q: HOURS <= 24" + echo " for long.q: HOURS <= 96" + echo " PROJECT: python module (file path) that declares the project and starts the calculation." + echo " MODE: PMSCO calculation mode (single|swarm|gradient|grid)." + echo " LOG_LEVEL (optional): one of DEBUG, INFO, WARNING, ERROR if log files should be produced." + echo "" + echo "the job script complete with the program code and input/output data is generated in ~/jobs/\$JOBNAME" + exit 1 +fi + +# location of the pmsco package is derived from the path of this script +SCRIPTDIR="$(dirname $(readlink -f $0))" +SOURCEDIR="$SCRIPTDIR/.." +PHD_SOURCE_DIR="$SOURCEDIR" + +PHD_CODE="edac" + +# read arguments +if [ "$1" == "NOSUB" ]; then + NOSUB="true" + shift +else + NOSUB="false" +fi + +PHD_JOBNAME=$1 +shift + +PHD_NODES=$1 +shift + +PHD_WALLTIME_HR=$1 +PHD_WALLTIME_MIN=0 +shift + +PHD_PROJECT_FILE="$(readlink -f $1)" +PHD_PROJECT_ARGS="" +shift + +PHD_MODE="$1" +shift + +PHD_LOGLEVEL="" +if [ "$1" == "DEBUG" ] || [ "$1" == "INFO" ] || [ "$1" == "WARNING" ] || [ "$1" == "ERROR" ]; then + PHD_LOGLEVEL="$1" + shift +fi + +# ignore remaining arguments +PHD_SCAN_FILES="" + +# select allowed queues +QUEUE=short.q,all.q,long.q + +# for short queue (limit 30 minutes) +if [ "$PHD_WALLTIME_HR" -lt 1 ]; then + PHD_WALLTIME_HR=0 + PHD_WALLTIME_MIN=30 +fi + +# set up working directory +cd ~ +if [ ! -d "jobs" ]; then + mkdir jobs +fi +cd jobs +if [ ! -d "$PHD_JOBNAME" ]; then + mkdir "$PHD_JOBNAME" +fi +cd "$PHD_JOBNAME" +WORKDIR="$(pwd)" +PHD_WORK_DIR="$WORKDIR" + +# provide revision information, requires git repository +cd "$SOURCEDIR" +PHD_REV=$(git log --pretty=format:"Data revision %h, %ad" --date=iso -1) +if [ $? -ne 0 ]; then + PHD_REV="Data revision unknown, "$(date +"%F %T %z") +fi +cd "$WORKDIR" +echo "$PHD_REV" > revision.txt + +# generate job script from template +sed -e "s:_PHD_WORK_DIR:$PHD_WORK_DIR:g" \ + -e "s:_PHD_JOBNAME:$PHD_JOBNAME:g" \ + -e "s:_PHD_NODES:$PHD_NODES:g" \ + -e "s:_PHD_WALLTIME_HR:$PHD_WALLTIME_HR:g" \ + -e "s:_PHD_WALLTIME_MIN:$PHD_WALLTIME_MIN:g" \ + -e "s:_PHD_PROJECT_FILE:$PHD_PROJECT_FILE:g" \ + -e "s:_PHD_PROJECT_ARGS:$PHD_PROJECT_ARGS:g" \ + -e "s:_PHD_CODE:$PHD_CODE:g" \ + -e "s:_PHD_MODE:$PHD_MODE:g" \ + -e "s:_PHD_SOURCE_DIR:$PHD_SOURCE_DIR:g" \ + -e "s:_PHD_SCAN_FILES:$PHD_SCAN_FILES:g" \ + -e "s:_PHD_LOGLEVEL:$PHD_LOGLEVEL:g" \ + "$SCRIPTDIR/pmsco.sge.template" > $PHD_JOBNAME.job + +chmod u+x "$PHD_JOBNAME.job" + +if [ "$NOSUB" != "true" ]; then + +# suppress bash error [stackoverflow.com/questions/10496758] +unset module + +# submit the job script +# EMAIL must be defined in the environment +if [ -n "$EMAIL" ]; then + qsub -q $QUEUE -m ae -M $EMAIL $PHD_JOBNAME.job +else + qsub -q $QUEUE $PHD_JOBNAME.job +fi + +fi + +exit 0 diff --git a/docs/.gitignore b/docs/.gitignore new file mode 100644 index 0000000..edb19d4 --- /dev/null +++ b/docs/.gitignore @@ -0,0 +1,3 @@ +doxygen*.db +html/* +latex/* diff --git a/docs/config.dox b/docs/config.dox new file mode 100644 index 0000000..9f93057 --- /dev/null +++ b/docs/config.dox @@ -0,0 +1,2396 @@ +# Doxyfile 1.8.9.1 + +# This file describes the settings to be used by the documentation system +# doxygen (www.doxygen.org) for a project. +# +# All text after a double hash (##) is considered a comment and is placed in +# front of the TAG it is preceding. +# +# All text after a single hash (#) is considered a comment and will be ignored. +# The format is: +# TAG = value [value, ...] +# For lists, items can also be appended using: +# TAG += value [value, ...] +# Values that contain spaces should be placed between quotes (\" \"). + +#--------------------------------------------------------------------------- +# Project related configuration options +#--------------------------------------------------------------------------- + +# This tag specifies the encoding used for all characters in the config file +# that follow. The default is UTF-8 which is also the encoding used for all text +# before the first occurrence of this tag. Doxygen uses libiconv (or the iconv +# built into libc) for the transcoding. See http://www.gnu.org/software/libiconv +# for the list of possible encodings. +# The default value is: UTF-8. + +DOXYFILE_ENCODING = UTF-8 + +# The PROJECT_NAME tag is a single word (or a sequence of words surrounded by +# double-quotes, unless you are using Doxywizard) that should identify the +# project for which the documentation is generated. This name is used in the +# title of most generated pages and in a few other places. +# The default value is: My Project. + +PROJECT_NAME = "PEARL MSCO" + +# The PROJECT_NUMBER tag can be used to enter a project or revision number. This +# could be handy for archiving the generated documentation or if some version +# control system is used. + +PROJECT_NUMBER = + +# Using the PROJECT_BRIEF tag one can provide an optional one line description +# for a project that appears at the top of each page and should give viewer a +# quick idea about the purpose of the project. Keep the description short. + +PROJECT_BRIEF = "PEARL multiple scattering calculations and optimizations" + +# With the PROJECT_LOGO tag one can specify a logo or an icon that is included +# in the documentation. The maximum height of the logo should not exceed 55 +# pixels and the maximum width should not exceed 200 pixels. Doxygen will copy +# the logo to the output directory. + +PROJECT_LOGO = + +# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) path +# into which the generated documentation will be written. If a relative path is +# entered, it will be relative to the location where doxygen was started. If +# left blank the current directory will be used. + +OUTPUT_DIRECTORY = + +# If the CREATE_SUBDIRS tag is set to YES then doxygen will create 4096 sub- +# directories (in 2 levels) under the output directory of each output format and +# will distribute the generated files over these directories. Enabling this +# option can be useful when feeding doxygen a huge amount of source files, where +# putting all generated files in the same directory would otherwise causes +# performance problems for the file system. +# The default value is: NO. + +CREATE_SUBDIRS = NO + +# If the ALLOW_UNICODE_NAMES tag is set to YES, doxygen will allow non-ASCII +# characters to appear in the names of generated files. If set to NO, non-ASCII +# characters will be escaped, for example _xE3_x81_x84 will be used for Unicode +# U+3044. +# The default value is: NO. + +ALLOW_UNICODE_NAMES = NO + +# The OUTPUT_LANGUAGE tag is used to specify the language in which all +# documentation generated by doxygen is written. Doxygen will use this +# information to generate all constant output in the proper language. +# Possible values are: Afrikaans, Arabic, Armenian, Brazilian, Catalan, Chinese, +# Chinese-Traditional, Croatian, Czech, Danish, Dutch, English (United States), +# Esperanto, Farsi (Persian), Finnish, French, German, Greek, Hungarian, +# Indonesian, Italian, Japanese, Japanese-en (Japanese with English messages), +# Korean, Korean-en (Korean with English messages), Latvian, Lithuanian, +# Macedonian, Norwegian, Persian (Farsi), Polish, Portuguese, Romanian, Russian, +# Serbian, Serbian-Cyrillic, Slovak, Slovene, Spanish, Swedish, Turkish, +# Ukrainian and Vietnamese. +# The default value is: English. + +OUTPUT_LANGUAGE = English + +# If the BRIEF_MEMBER_DESC tag is set to YES, doxygen will include brief member +# descriptions after the members that are listed in the file and class +# documentation (similar to Javadoc). Set to NO to disable this. +# The default value is: YES. + +BRIEF_MEMBER_DESC = YES + +# If the REPEAT_BRIEF tag is set to YES, doxygen will prepend the brief +# description of a member or function before the detailed description +# +# Note: If both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the +# brief descriptions will be completely suppressed. +# The default value is: YES. + +REPEAT_BRIEF = YES + +# This tag implements a quasi-intelligent brief description abbreviator that is +# used to form the text in various listings. Each string in this list, if found +# as the leading text of the brief description, will be stripped from the text +# and the result, after processing the whole list, is used as the annotated +# text. Otherwise, the brief description is used as-is. If left blank, the +# following values are used ($name is automatically replaced with the name of +# the entity):The $name class, The $name widget, The $name file, is, provides, +# specifies, contains, represents, a, an and the. + +ABBREVIATE_BRIEF = + +# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then +# doxygen will generate a detailed section even if there is only a brief +# description. +# The default value is: NO. + +ALWAYS_DETAILED_SEC = NO + +# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all +# inherited members of a class in the documentation of that class as if those +# members were ordinary class members. Constructors, destructors and assignment +# operators of the base classes will not be shown. +# The default value is: NO. + +INLINE_INHERITED_MEMB = NO + +# If the FULL_PATH_NAMES tag is set to YES, doxygen will prepend the full path +# before files name in the file list and in the header files. If set to NO the +# shortest path that makes the file name unique will be used +# The default value is: YES. + +FULL_PATH_NAMES = NO + +# The STRIP_FROM_PATH tag can be used to strip a user-defined part of the path. +# Stripping is only done if one of the specified strings matches the left-hand +# part of the path. The tag can be used to show relative paths in the file list. +# If left blank the directory from which doxygen is run is used as the path to +# strip. +# +# Note that you can specify absolute paths here, but also relative paths, which +# will be relative from the directory where doxygen is started. +# This tag requires that the tag FULL_PATH_NAMES is set to YES. + +STRIP_FROM_PATH = + +# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of the +# path mentioned in the documentation of a class, which tells the reader which +# header file to include in order to use a class. If left blank only the name of +# the header file containing the class definition is used. Otherwise one should +# specify the list of include paths that are normally passed to the compiler +# using the -I flag. + +STRIP_FROM_INC_PATH = + +# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter (but +# less readable) file names. This can be useful is your file systems doesn't +# support long names like on DOS, Mac, or CD-ROM. +# The default value is: NO. + +SHORT_NAMES = NO + +# If the JAVADOC_AUTOBRIEF tag is set to YES then doxygen will interpret the +# first line (until the first dot) of a Javadoc-style comment as the brief +# description. If set to NO, the Javadoc-style will behave just like regular Qt- +# style comments (thus requiring an explicit @brief command for a brief +# description.) +# The default value is: NO. + +JAVADOC_AUTOBRIEF = YES + +# If the QT_AUTOBRIEF tag is set to YES then doxygen will interpret the first +# line (until the first dot) of a Qt-style comment as the brief description. If +# set to NO, the Qt-style will behave just like regular Qt-style comments (thus +# requiring an explicit \brief command for a brief description.) +# The default value is: NO. + +QT_AUTOBRIEF = NO + +# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make doxygen treat a +# multi-line C++ special comment block (i.e. a block of //! or /// comments) as +# a brief description. This used to be the default behavior. The new default is +# to treat a multi-line C++ comment block as a detailed description. Set this +# tag to YES if you prefer the old behavior instead. +# +# Note that setting this tag to YES also means that rational rose comments are +# not recognized any more. +# The default value is: NO. + +MULTILINE_CPP_IS_BRIEF = NO + +# If the INHERIT_DOCS tag is set to YES then an undocumented member inherits the +# documentation from any documented member that it re-implements. +# The default value is: YES. + +INHERIT_DOCS = YES + +# If the SEPARATE_MEMBER_PAGES tag is set to YES then doxygen will produce a new +# page for each member. If set to NO, the documentation of a member will be part +# of the file/class/namespace that contains it. +# The default value is: NO. + +SEPARATE_MEMBER_PAGES = NO + +# The TAB_SIZE tag can be used to set the number of spaces in a tab. Doxygen +# uses this value to replace tabs by spaces in code fragments. +# Minimum value: 1, maximum value: 16, default value: 4. + +TAB_SIZE = 4 + +# This tag can be used to specify a number of aliases that act as commands in +# the documentation. An alias has the form: +# name=value +# For example adding +# "sideeffect=@par Side Effects:\n" +# will allow you to put the command \sideeffect (or @sideeffect) in the +# documentation, which will result in a user-defined paragraph with heading +# "Side Effects:". You can put \n's in the value part of an alias to insert +# newlines. + +ALIASES = + +# This tag can be used to specify a number of word-keyword mappings (TCL only). +# A mapping has the form "name=value". For example adding "class=itcl::class" +# will allow you to use the command class in the itcl::class meaning. + +TCL_SUBST = + +# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C sources +# only. Doxygen will then generate output that is more tailored for C. For +# instance, some of the names that are used will be different. The list of all +# members will be omitted, etc. +# The default value is: NO. + +OPTIMIZE_OUTPUT_FOR_C = NO + +# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java or +# Python sources only. Doxygen will then generate output that is more tailored +# for that language. For instance, namespaces will be presented as packages, +# qualified scopes will look different, etc. +# The default value is: NO. + +OPTIMIZE_OUTPUT_JAVA = YES + +# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran +# sources. Doxygen will then generate output that is tailored for Fortran. +# The default value is: NO. + +OPTIMIZE_FOR_FORTRAN = NO + +# Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL +# sources. Doxygen will then generate output that is tailored for VHDL. +# The default value is: NO. + +OPTIMIZE_OUTPUT_VHDL = NO + +# Doxygen selects the parser to use depending on the extension of the files it +# parses. With this tag you can assign which parser to use for a given +# extension. Doxygen has a built-in mapping, but you can override or extend it +# using this tag. The format is ext=language, where ext is a file extension, and +# language is one of the parsers supported by doxygen: IDL, Java, Javascript, +# C#, C, C++, D, PHP, Objective-C, Python, Fortran (fixed format Fortran: +# FortranFixed, free formatted Fortran: FortranFree, unknown formatted Fortran: +# Fortran. In the later case the parser tries to guess whether the code is fixed +# or free formatted code, this is the default for Fortran type files), VHDL. For +# instance to make doxygen treat .inc files as Fortran files (default is PHP), +# and .f files as C (default is Fortran), use: inc=Fortran f=C. +# +# Note: For files without extension you can use no_extension as a placeholder. +# +# Note that for custom extensions you also need to set FILE_PATTERNS otherwise +# the files are not read by doxygen. + +EXTENSION_MAPPING = + +# If the MARKDOWN_SUPPORT tag is enabled then doxygen pre-processes all comments +# according to the Markdown format, which allows for more readable +# documentation. See http://daringfireball.net/projects/markdown/ for details. +# The output of markdown processing is further processed by doxygen, so you can +# mix doxygen, HTML, and XML commands with Markdown formatting. Disable only in +# case of backward compatibilities issues. +# The default value is: YES. + +MARKDOWN_SUPPORT = YES + +# When enabled doxygen tries to link words that correspond to documented +# classes, or namespaces to their corresponding documentation. Such a link can +# be prevented in individual cases by putting a % sign in front of the word or +# globally by setting AUTOLINK_SUPPORT to NO. +# The default value is: YES. + +AUTOLINK_SUPPORT = YES + +# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want +# to include (a tag file for) the STL sources as input, then you should set this +# tag to YES in order to let doxygen match functions declarations and +# definitions whose arguments contain STL classes (e.g. func(std::string); +# versus func(std::string) {}). This also make the inheritance and collaboration +# diagrams that involve STL classes more complete and accurate. +# The default value is: NO. + +BUILTIN_STL_SUPPORT = NO + +# If you use Microsoft's C++/CLI language, you should set this option to YES to +# enable parsing support. +# The default value is: NO. + +CPP_CLI_SUPPORT = NO + +# Set the SIP_SUPPORT tag to YES if your project consists of sip (see: +# http://www.riverbankcomputing.co.uk/software/sip/intro) sources only. Doxygen +# will parse them like normal C++ but will assume all classes use public instead +# of private inheritance when no explicit protection keyword is present. +# The default value is: NO. + +SIP_SUPPORT = NO + +# For Microsoft's IDL there are propget and propput attributes to indicate +# getter and setter methods for a property. Setting this option to YES will make +# doxygen to replace the get and set methods by a property in the documentation. +# This will only work if the methods are indeed getting or setting a simple +# type. If this is not the case, or you want to show the methods anyway, you +# should set this option to NO. +# The default value is: YES. + +IDL_PROPERTY_SUPPORT = YES + +# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC +# tag is set to YES then doxygen will reuse the documentation of the first +# member in the group (if any) for the other members of the group. By default +# all members of a group must be documented explicitly. +# The default value is: NO. + +DISTRIBUTE_GROUP_DOC = NO + +# Set the SUBGROUPING tag to YES to allow class member groups of the same type +# (for instance a group of public functions) to be put as a subgroup of that +# type (e.g. under the Public Functions section). Set it to NO to prevent +# subgrouping. Alternatively, this can be done per class using the +# \nosubgrouping command. +# The default value is: YES. + +SUBGROUPING = YES + +# When the INLINE_GROUPED_CLASSES tag is set to YES, classes, structs and unions +# are shown inside the group in which they are included (e.g. using \ingroup) +# instead of on a separate page (for HTML and Man pages) or section (for LaTeX +# and RTF). +# +# Note that this feature does not work in combination with +# SEPARATE_MEMBER_PAGES. +# The default value is: NO. + +INLINE_GROUPED_CLASSES = NO + +# When the INLINE_SIMPLE_STRUCTS tag is set to YES, structs, classes, and unions +# with only public data fields or simple typedef fields will be shown inline in +# the documentation of the scope in which they are defined (i.e. file, +# namespace, or group documentation), provided this scope is documented. If set +# to NO, structs, classes, and unions are shown on a separate page (for HTML and +# Man pages) or section (for LaTeX and RTF). +# The default value is: NO. + +INLINE_SIMPLE_STRUCTS = NO + +# When TYPEDEF_HIDES_STRUCT tag is enabled, a typedef of a struct, union, or +# enum is documented as struct, union, or enum with the name of the typedef. So +# typedef struct TypeS {} TypeT, will appear in the documentation as a struct +# with name TypeT. When disabled the typedef will appear as a member of a file, +# namespace, or class. And the struct will be named TypeS. This can typically be +# useful for C code in case the coding convention dictates that all compound +# types are typedef'ed and only the typedef is referenced, never the tag name. +# The default value is: NO. + +TYPEDEF_HIDES_STRUCT = NO + +# The size of the symbol lookup cache can be set using LOOKUP_CACHE_SIZE. This +# cache is used to resolve symbols given their name and scope. Since this can be +# an expensive process and often the same symbol appears multiple times in the +# code, doxygen keeps a cache of pre-resolved symbols. If the cache is too small +# doxygen will become slower. If the cache is too large, memory is wasted. The +# cache size is given by this formula: 2^(16+LOOKUP_CACHE_SIZE). The valid range +# is 0..9, the default is 0, corresponding to a cache size of 2^16=65536 +# symbols. At the end of a run doxygen will report the cache usage and suggest +# the optimal cache size from a speed point of view. +# Minimum value: 0, maximum value: 9, default value: 0. + +LOOKUP_CACHE_SIZE = 0 + +#--------------------------------------------------------------------------- +# Build related configuration options +#--------------------------------------------------------------------------- + +# If the EXTRACT_ALL tag is set to YES, doxygen will assume all entities in +# documentation are documented, even if no documentation was available. Private +# class members and static file members will be hidden unless the +# EXTRACT_PRIVATE respectively EXTRACT_STATIC tags are set to YES. +# Note: This will also disable the warnings about undocumented members that are +# normally produced when WARNINGS is set to YES. +# The default value is: NO. + +EXTRACT_ALL = YES + +# If the EXTRACT_PRIVATE tag is set to YES, all private members of a class will +# be included in the documentation. +# The default value is: NO. + +EXTRACT_PRIVATE = YES + +# If the EXTRACT_PACKAGE tag is set to YES, all members with package or internal +# scope will be included in the documentation. +# The default value is: NO. + +EXTRACT_PACKAGE = YES + +# If the EXTRACT_STATIC tag is set to YES, all static members of a file will be +# included in the documentation. +# The default value is: NO. + +EXTRACT_STATIC = YES + +# If the EXTRACT_LOCAL_CLASSES tag is set to YES, classes (and structs) defined +# locally in source files will be included in the documentation. If set to NO, +# only classes defined in header files are included. Does not have any effect +# for Java sources. +# The default value is: YES. + +EXTRACT_LOCAL_CLASSES = YES + +# This flag is only useful for Objective-C code. If set to YES, local methods, +# which are defined in the implementation section but not in the interface are +# included in the documentation. If set to NO, only methods in the interface are +# included. +# The default value is: NO. + +EXTRACT_LOCAL_METHODS = YES + +# If this flag is set to YES, the members of anonymous namespaces will be +# extracted and appear in the documentation as a namespace called +# 'anonymous_namespace{file}', where file will be replaced with the base name of +# the file that contains the anonymous namespace. By default anonymous namespace +# are hidden. +# The default value is: NO. + +EXTRACT_ANON_NSPACES = NO + +# If the HIDE_UNDOC_MEMBERS tag is set to YES, doxygen will hide all +# undocumented members inside documented classes or files. If set to NO these +# members will be included in the various overviews, but no documentation +# section is generated. This option has no effect if EXTRACT_ALL is enabled. +# The default value is: NO. + +HIDE_UNDOC_MEMBERS = NO + +# If the HIDE_UNDOC_CLASSES tag is set to YES, doxygen will hide all +# undocumented classes that are normally visible in the class hierarchy. If set +# to NO, these classes will be included in the various overviews. This option +# has no effect if EXTRACT_ALL is enabled. +# The default value is: NO. + +HIDE_UNDOC_CLASSES = NO + +# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, doxygen will hide all friend +# (class|struct|union) declarations. If set to NO, these declarations will be +# included in the documentation. +# The default value is: NO. + +HIDE_FRIEND_COMPOUNDS = NO + +# If the HIDE_IN_BODY_DOCS tag is set to YES, doxygen will hide any +# documentation blocks found inside the body of a function. If set to NO, these +# blocks will be appended to the function's detailed documentation block. +# The default value is: NO. + +HIDE_IN_BODY_DOCS = NO + +# The INTERNAL_DOCS tag determines if documentation that is typed after a +# \internal command is included. If the tag is set to NO then the documentation +# will be excluded. Set it to YES to include the internal documentation. +# The default value is: NO. + +INTERNAL_DOCS = NO + +# If the CASE_SENSE_NAMES tag is set to NO then doxygen will only generate file +# names in lower-case letters. If set to YES, upper-case letters are also +# allowed. This is useful if you have classes or files whose names only differ +# in case and if your file system supports case sensitive file names. Windows +# and Mac users are advised to set this option to NO. +# The default value is: system dependent. + +CASE_SENSE_NAMES = YES + +# If the HIDE_SCOPE_NAMES tag is set to NO then doxygen will show members with +# their full class and namespace scopes in the documentation. If set to YES, the +# scope will be hidden. +# The default value is: NO. + +HIDE_SCOPE_NAMES = NO + +# If the HIDE_COMPOUND_REFERENCE tag is set to NO (default) then doxygen will +# append additional text to a page's title, such as Class Reference. If set to +# YES the compound reference will be hidden. +# The default value is: NO. + +HIDE_COMPOUND_REFERENCE= NO + +# If the SHOW_INCLUDE_FILES tag is set to YES then doxygen will put a list of +# the files that are included by a file in the documentation of that file. +# The default value is: YES. + +SHOW_INCLUDE_FILES = YES + +# If the SHOW_GROUPED_MEMB_INC tag is set to YES then Doxygen will add for each +# grouped member an include statement to the documentation, telling the reader +# which file to include in order to use the member. +# The default value is: NO. + +SHOW_GROUPED_MEMB_INC = NO + +# If the FORCE_LOCAL_INCLUDES tag is set to YES then doxygen will list include +# files with double quotes in the documentation rather than with sharp brackets. +# The default value is: NO. + +FORCE_LOCAL_INCLUDES = NO + +# If the INLINE_INFO tag is set to YES then a tag [inline] is inserted in the +# documentation for inline members. +# The default value is: YES. + +INLINE_INFO = YES + +# If the SORT_MEMBER_DOCS tag is set to YES then doxygen will sort the +# (detailed) documentation of file and class members alphabetically by member +# name. If set to NO, the members will appear in declaration order. +# The default value is: YES. + +SORT_MEMBER_DOCS = YES + +# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the brief +# descriptions of file, namespace and class members alphabetically by member +# name. If set to NO, the members will appear in declaration order. Note that +# this will also influence the order of the classes in the class list. +# The default value is: NO. + +SORT_BRIEF_DOCS = NO + +# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen will sort the +# (brief and detailed) documentation of class members so that constructors and +# destructors are listed first. If set to NO the constructors will appear in the +# respective orders defined by SORT_BRIEF_DOCS and SORT_MEMBER_DOCS. +# Note: If SORT_BRIEF_DOCS is set to NO this option is ignored for sorting brief +# member documentation. +# Note: If SORT_MEMBER_DOCS is set to NO this option is ignored for sorting +# detailed member documentation. +# The default value is: NO. + +SORT_MEMBERS_CTORS_1ST = NO + +# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the hierarchy +# of group names into alphabetical order. If set to NO the group names will +# appear in their defined order. +# The default value is: NO. + +SORT_GROUP_NAMES = NO + +# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be sorted by +# fully-qualified names, including namespaces. If set to NO, the class list will +# be sorted only by class name, not including the namespace part. +# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES. +# Note: This option applies only to the class list, not to the alphabetical +# list. +# The default value is: NO. + +SORT_BY_SCOPE_NAME = NO + +# If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to do proper +# type resolution of all parameters of a function it will reject a match between +# the prototype and the implementation of a member function even if there is +# only one candidate or it is obvious which candidate to choose by doing a +# simple string match. By disabling STRICT_PROTO_MATCHING doxygen will still +# accept a match between prototype and implementation in such cases. +# The default value is: NO. + +STRICT_PROTO_MATCHING = NO + +# The GENERATE_TODOLIST tag can be used to enable (YES) or disable (NO) the todo +# list. This list is created by putting \todo commands in the documentation. +# The default value is: YES. + +GENERATE_TODOLIST = YES + +# The GENERATE_TESTLIST tag can be used to enable (YES) or disable (NO) the test +# list. This list is created by putting \test commands in the documentation. +# The default value is: YES. + +GENERATE_TESTLIST = YES + +# The GENERATE_BUGLIST tag can be used to enable (YES) or disable (NO) the bug +# list. This list is created by putting \bug commands in the documentation. +# The default value is: YES. + +GENERATE_BUGLIST = YES + +# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or disable (NO) +# the deprecated list. This list is created by putting \deprecated commands in +# the documentation. +# The default value is: YES. + +GENERATE_DEPRECATEDLIST= YES + +# The ENABLED_SECTIONS tag can be used to enable conditional documentation +# sections, marked by \if ... \endif and \cond +# ... \endcond blocks. + +ENABLED_SECTIONS = + +# The MAX_INITIALIZER_LINES tag determines the maximum number of lines that the +# initial value of a variable or macro / define can have for it to appear in the +# documentation. If the initializer consists of more lines than specified here +# it will be hidden. Use a value of 0 to hide initializers completely. The +# appearance of the value of individual variables and macros / defines can be +# controlled using \showinitializer or \hideinitializer command in the +# documentation regardless of this setting. +# Minimum value: 0, maximum value: 10000, default value: 30. + +MAX_INITIALIZER_LINES = 30 + +# Set the SHOW_USED_FILES tag to NO to disable the list of files generated at +# the bottom of the documentation of classes and structs. If set to YES, the +# list will mention the files that were used to generate the documentation. +# The default value is: YES. + +SHOW_USED_FILES = YES + +# Set the SHOW_FILES tag to NO to disable the generation of the Files page. This +# will remove the Files entry from the Quick Index and from the Folder Tree View +# (if specified). +# The default value is: YES. + +SHOW_FILES = YES + +# Set the SHOW_NAMESPACES tag to NO to disable the generation of the Namespaces +# page. This will remove the Namespaces entry from the Quick Index and from the +# Folder Tree View (if specified). +# The default value is: YES. + +SHOW_NAMESPACES = YES + +# The FILE_VERSION_FILTER tag can be used to specify a program or script that +# doxygen should invoke to get the current version for each file (typically from +# the version control system). Doxygen will invoke the program by executing (via +# popen()) the command command input-file, where command is the value of the +# FILE_VERSION_FILTER tag, and input-file is the name of an input file provided +# by doxygen. Whatever the program writes to standard output is used as the file +# version. For an example see the documentation. + +FILE_VERSION_FILTER = "git log --pretty=format:\"revision %h, %ad\" --date=iso -1" + +# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed +# by doxygen. The layout file controls the global structure of the generated +# output files in an output format independent way. To create the layout file +# that represents doxygen's defaults, run doxygen with the -l option. You can +# optionally specify a file name after the option, if omitted DoxygenLayout.xml +# will be used as the name of the layout file. +# +# Note that if you run doxygen from a directory containing a file called +# DoxygenLayout.xml, doxygen will parse it automatically even if the LAYOUT_FILE +# tag is left empty. + +LAYOUT_FILE = + +# The CITE_BIB_FILES tag can be used to specify one or more bib files containing +# the reference definitions. This must be a list of .bib files. The .bib +# extension is automatically appended if omitted. This requires the bibtex tool +# to be installed. See also http://en.wikipedia.org/wiki/BibTeX for more info. +# For LaTeX the style of the bibliography can be controlled using +# LATEX_BIB_STYLE. To use this feature you need bibtex and perl available in the +# search path. See also \cite for info how to create references. + +CITE_BIB_FILES = + +#--------------------------------------------------------------------------- +# Configuration options related to warning and progress messages +#--------------------------------------------------------------------------- + +# The QUIET tag can be used to turn on/off the messages that are generated to +# standard output by doxygen. If QUIET is set to YES this implies that the +# messages are off. +# The default value is: NO. + +QUIET = NO + +# The WARNINGS tag can be used to turn on/off the warning messages that are +# generated to standard error (stderr) by doxygen. If WARNINGS is set to YES +# this implies that the warnings are on. +# +# Tip: Turn warnings on while writing the documentation. +# The default value is: YES. + +WARNINGS = YES + +# If the WARN_IF_UNDOCUMENTED tag is set to YES then doxygen will generate +# warnings for undocumented members. If EXTRACT_ALL is set to YES then this flag +# will automatically be disabled. +# The default value is: YES. + +WARN_IF_UNDOCUMENTED = YES + +# If the WARN_IF_DOC_ERROR tag is set to YES, doxygen will generate warnings for +# potential errors in the documentation, such as not documenting some parameters +# in a documented function, or documenting parameters that don't exist or using +# markup commands wrongly. +# The default value is: YES. + +WARN_IF_DOC_ERROR = YES + +# This WARN_NO_PARAMDOC option can be enabled to get warnings for functions that +# are documented, but have no documentation for their parameters or return +# value. If set to NO, doxygen will only warn about wrong or incomplete +# parameter documentation, but not about the absence of documentation. +# The default value is: NO. + +WARN_NO_PARAMDOC = NO + +# The WARN_FORMAT tag determines the format of the warning messages that doxygen +# can produce. The string should contain the $file, $line, and $text tags, which +# will be replaced by the file and line number from which the warning originated +# and the warning text. Optionally the format may contain $version, which will +# be replaced by the version of the file (if it could be obtained via +# FILE_VERSION_FILTER) +# The default value is: $file:$line: $text. + +WARN_FORMAT = "$file:$line: $text" + +# The WARN_LOGFILE tag can be used to specify a file to which warning and error +# messages should be written. If left blank the output is written to standard +# error (stderr). + +WARN_LOGFILE = + +#--------------------------------------------------------------------------- +# Configuration options related to the input files +#--------------------------------------------------------------------------- + +# The INPUT tag is used to specify the files and/or directories that contain +# documented source files. You may enter file names like myfile.cpp or +# directories like /usr/src/myproject. Separate the files or directories with +# spaces. +# Note: If this tag is empty the current directory is searched. + +INPUT = \ +src/introduction.dox \ +src/concepts.dox \ +src/installation.dox \ +src/execution.dox \ +src/commandline.dox \ + ../pmsco \ + ../projects \ + ../tests + +# This tag can be used to specify the character encoding of the source files +# that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses +# libiconv (or the iconv built into libc) for the transcoding. See the libiconv +# documentation (see: http://www.gnu.org/software/libiconv) for the list of +# possible encodings. +# The default value is: UTF-8. + +INPUT_ENCODING = UTF-8 + +# If the value of the INPUT tag contains directories, you can use the +# FILE_PATTERNS tag to specify one or more wildcard patterns (like *.cpp and +# *.h) to filter out the source-files in the directories. If left blank the +# following patterns are tested:*.c, *.cc, *.cxx, *.cpp, *.c++, *.java, *.ii, +# *.ixx, *.ipp, *.i++, *.inl, *.idl, *.ddl, *.odl, *.h, *.hh, *.hxx, *.hpp, +# *.h++, *.cs, *.d, *.php, *.php4, *.php5, *.phtml, *.inc, *.m, *.markdown, +# *.md, *.mm, *.dox, *.py, *.f90, *.f, *.for, *.tcl, *.vhd, *.vhdl, *.ucf, +# *.qsf, *.as and *.js. + +FILE_PATTERNS = *.py \ + *.dox + +# The RECURSIVE tag can be used to specify whether or not subdirectories should +# be searched for input files as well. +# The default value is: NO. + +RECURSIVE = YES + +# The EXCLUDE tag can be used to specify files and/or directories that should be +# excluded from the INPUT source files. This way you can easily exclude a +# subdirectory from a directory tree whose root is specified with the INPUT tag. +# +# Note that relative paths are relative to the directory from which doxygen is +# run. + +EXCLUDE = ../pmsco/edac \ + ../pmsco/loess \ + ../pmsco/msc \ + ../pmsco/mufpot + +# The EXCLUDE_SYMLINKS tag can be used to select whether or not files or +# directories that are symbolic links (a Unix file system feature) are excluded +# from the input. +# The default value is: NO. + +EXCLUDE_SYMLINKS = NO + +# If the value of the INPUT tag contains directories, you can use the +# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude +# certain files from those directories. +# +# Note that the wildcards are matched against the file with absolute path, so to +# exclude all test directories for example use the pattern */test/* + +EXCLUDE_PATTERNS = */__init__.py \ + */setup.py + +# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names +# (namespaces, classes, functions, etc.) that should be excluded from the +# output. The symbol name can be a fully qualified name, a word, or if the +# wildcard * is used, a substring. Examples: ANamespace, AClass, +# AClass::ANamespace, ANamespace::*Test +# +# Note that the wildcards are matched against the file with absolute path, so to +# exclude all test directories use the pattern */test/* + +EXCLUDE_SYMBOLS = + +# The EXAMPLE_PATH tag can be used to specify one or more files or directories +# that contain example code fragments that are included (see the \include +# command). + +EXAMPLE_PATH = + +# If the value of the EXAMPLE_PATH tag contains directories, you can use the +# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp and +# *.h) to filter out the source-files in the directories. If left blank all +# files are included. + +EXAMPLE_PATTERNS = + +# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be +# searched for input files to be used with the \include or \dontinclude commands +# irrespective of the value of the RECURSIVE tag. +# The default value is: NO. + +EXAMPLE_RECURSIVE = NO + +# The IMAGE_PATH tag can be used to specify one or more files or directories +# that contain images that are to be included in the documentation (see the +# \image command). + +IMAGE_PATH = + +# The INPUT_FILTER tag can be used to specify a program that doxygen should +# invoke to filter for each input file. Doxygen will invoke the filter program +# by executing (via popen()) the command: +# +# +# +# where is the value of the INPUT_FILTER tag, and is the +# name of an input file. Doxygen will then use the output that the filter +# program writes to standard output. If FILTER_PATTERNS is specified, this tag +# will be ignored. +# +# Note that the filter must not add or remove lines; it is applied before the +# code is scanned, but not when the output code is generated. If lines are added +# or removed, the anchors will not be placed correctly. + +INPUT_FILTER = /usr/bin/doxypy + +# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern +# basis. Doxygen will compare the file name with each pattern and apply the +# filter if there is a match. The filters are a list of the form: pattern=filter +# (like *.cpp=my_cpp_filter). See INPUT_FILTER for further information on how +# filters are used. If the FILTER_PATTERNS tag is empty or if none of the +# patterns match the file name, INPUT_FILTER is applied. + +FILTER_PATTERNS = + +# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using +# INPUT_FILTER) will also be used to filter the input files that are used for +# producing the source files to browse (i.e. when SOURCE_BROWSER is set to YES). +# The default value is: NO. + +FILTER_SOURCE_FILES = NO + +# The FILTER_SOURCE_PATTERNS tag can be used to specify source filters per file +# pattern. A pattern will override the setting for FILTER_PATTERN (if any) and +# it is also possible to disable source filtering for a specific pattern using +# *.ext= (so without naming a filter). +# This tag requires that the tag FILTER_SOURCE_FILES is set to YES. + +FILTER_SOURCE_PATTERNS = + +# If the USE_MDFILE_AS_MAINPAGE tag refers to the name of a markdown file that +# is part of the input, its contents will be placed on the main page +# (index.html). This can be useful if you have a project on for instance GitHub +# and want to reuse the introduction page also for the doxygen output. + +USE_MDFILE_AS_MAINPAGE = + +#--------------------------------------------------------------------------- +# Configuration options related to source browsing +#--------------------------------------------------------------------------- + +# If the SOURCE_BROWSER tag is set to YES then a list of source files will be +# generated. Documented entities will be cross-referenced with these sources. +# +# Note: To get rid of all source code in the generated output, make sure that +# also VERBATIM_HEADERS is set to NO. +# The default value is: NO. + +SOURCE_BROWSER = YES + +# Setting the INLINE_SOURCES tag to YES will include the body of functions, +# classes and enums directly into the documentation. +# The default value is: NO. + +INLINE_SOURCES = NO + +# Setting the STRIP_CODE_COMMENTS tag to YES will instruct doxygen to hide any +# special comment blocks from generated source code fragments. Normal C, C++ and +# Fortran comments will always remain visible. +# The default value is: YES. + +STRIP_CODE_COMMENTS = YES + +# If the REFERENCED_BY_RELATION tag is set to YES then for each documented +# function all documented functions referencing it will be listed. +# The default value is: NO. + +REFERENCED_BY_RELATION = NO + +# If the REFERENCES_RELATION tag is set to YES then for each documented function +# all documented entities called/used by that function will be listed. +# The default value is: NO. + +REFERENCES_RELATION = NO + +# If the REFERENCES_LINK_SOURCE tag is set to YES and SOURCE_BROWSER tag is set +# to YES then the hyperlinks from functions in REFERENCES_RELATION and +# REFERENCED_BY_RELATION lists will link to the source code. Otherwise they will +# link to the documentation. +# The default value is: YES. + +REFERENCES_LINK_SOURCE = YES + +# If SOURCE_TOOLTIPS is enabled (the default) then hovering a hyperlink in the +# source code will show a tooltip with additional information such as prototype, +# brief description and links to the definition and documentation. Since this +# will make the HTML file larger and loading of large files a bit slower, you +# can opt to disable this feature. +# The default value is: YES. +# This tag requires that the tag SOURCE_BROWSER is set to YES. + +SOURCE_TOOLTIPS = YES + +# If the USE_HTAGS tag is set to YES then the references to source code will +# point to the HTML generated by the htags(1) tool instead of doxygen built-in +# source browser. The htags tool is part of GNU's global source tagging system +# (see http://www.gnu.org/software/global/global.html). You will need version +# 4.8.6 or higher. +# +# To use it do the following: +# - Install the latest version of global +# - Enable SOURCE_BROWSER and USE_HTAGS in the config file +# - Make sure the INPUT points to the root of the source tree +# - Run doxygen as normal +# +# Doxygen will invoke htags (and that will in turn invoke gtags), so these +# tools must be available from the command line (i.e. in the search path). +# +# The result: instead of the source browser generated by doxygen, the links to +# source code will now point to the output of htags. +# The default value is: NO. +# This tag requires that the tag SOURCE_BROWSER is set to YES. + +USE_HTAGS = NO + +# If the VERBATIM_HEADERS tag is set the YES then doxygen will generate a +# verbatim copy of the header file for each class for which an include is +# specified. Set to NO to disable this. +# See also: Section \class. +# The default value is: YES. + +VERBATIM_HEADERS = YES + +# If the CLANG_ASSISTED_PARSING tag is set to YES then doxygen will use the +# clang parser (see: http://clang.llvm.org/) for more accurate parsing at the +# cost of reduced performance. This can be particularly helpful with template +# rich C++ code for which doxygen's built-in parser lacks the necessary type +# information. +# Note: The availability of this option depends on whether or not doxygen was +# compiled with the --with-libclang option. +# The default value is: NO. + +CLANG_ASSISTED_PARSING = NO + +# If clang assisted parsing is enabled you can provide the compiler with command +# line options that you would normally use when invoking the compiler. Note that +# the include paths will already be set by doxygen for the files and directories +# specified with INPUT and INCLUDE_PATH. +# This tag requires that the tag CLANG_ASSISTED_PARSING is set to YES. + +CLANG_OPTIONS = + +#--------------------------------------------------------------------------- +# Configuration options related to the alphabetical class index +#--------------------------------------------------------------------------- + +# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index of all +# compounds will be generated. Enable this if the project contains a lot of +# classes, structs, unions or interfaces. +# The default value is: YES. + +ALPHABETICAL_INDEX = YES + +# The COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns in +# which the alphabetical index list will be split. +# Minimum value: 1, maximum value: 20, default value: 5. +# This tag requires that the tag ALPHABETICAL_INDEX is set to YES. + +COLS_IN_ALPHA_INDEX = 8 + +# In case all classes in a project start with a common prefix, all classes will +# be put under the same header in the alphabetical index. The IGNORE_PREFIX tag +# can be used to specify a prefix (or a list of prefixes) that should be ignored +# while generating the index headers. +# This tag requires that the tag ALPHABETICAL_INDEX is set to YES. + +IGNORE_PREFIX = + +#--------------------------------------------------------------------------- +# Configuration options related to the HTML output +#--------------------------------------------------------------------------- + +# If the GENERATE_HTML tag is set to YES, doxygen will generate HTML output +# The default value is: YES. + +GENERATE_HTML = YES + +# The HTML_OUTPUT tag is used to specify where the HTML docs will be put. If a +# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of +# it. +# The default directory is: html. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_OUTPUT = html + +# The HTML_FILE_EXTENSION tag can be used to specify the file extension for each +# generated HTML page (for example: .htm, .php, .asp). +# The default value is: .html. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_FILE_EXTENSION = .html + +# The HTML_HEADER tag can be used to specify a user-defined HTML header file for +# each generated HTML page. If the tag is left blank doxygen will generate a +# standard header. +# +# To get valid HTML the header file that includes any scripts and style sheets +# that doxygen needs, which is dependent on the configuration options used (e.g. +# the setting GENERATE_TREEVIEW). It is highly recommended to start with a +# default header using +# doxygen -w html new_header.html new_footer.html new_stylesheet.css +# YourConfigFile +# and then modify the file new_header.html. See also section "Doxygen usage" +# for information on how to generate the default header that doxygen normally +# uses. +# Note: The header is subject to change so you typically have to regenerate the +# default header when upgrading to a newer version of doxygen. For a description +# of the possible markers and block names see the documentation. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_HEADER = + +# The HTML_FOOTER tag can be used to specify a user-defined HTML footer for each +# generated HTML page. If the tag is left blank doxygen will generate a standard +# footer. See HTML_HEADER for more information on how to generate a default +# footer and what special commands can be used inside the footer. See also +# section "Doxygen usage" for information on how to generate the default footer +# that doxygen normally uses. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_FOOTER = + +# The HTML_STYLESHEET tag can be used to specify a user-defined cascading style +# sheet that is used by each HTML page. It can be used to fine-tune the look of +# the HTML output. If left blank doxygen will generate a default style sheet. +# See also section "Doxygen usage" for information on how to generate the style +# sheet that doxygen normally uses. +# Note: It is recommended to use HTML_EXTRA_STYLESHEET instead of this tag, as +# it is more robust and this tag (HTML_STYLESHEET) will in the future become +# obsolete. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_STYLESHEET = + +# The HTML_EXTRA_STYLESHEET tag can be used to specify additional user-defined +# cascading style sheets that are included after the standard style sheets +# created by doxygen. Using this option one can overrule certain style aspects. +# This is preferred over using HTML_STYLESHEET since it does not replace the +# standard style sheet and is therefore more robust against future updates. +# Doxygen will copy the style sheet files to the output directory. +# Note: The order of the extra style sheet files is of importance (e.g. the last +# style sheet in the list overrules the setting of the previous ones in the +# list). For an example see the documentation. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_EXTRA_STYLESHEET = + +# The HTML_EXTRA_FILES tag can be used to specify one or more extra images or +# other source files which should be copied to the HTML output directory. Note +# that these files will be copied to the base HTML output directory. Use the +# $relpath^ marker in the HTML_HEADER and/or HTML_FOOTER files to load these +# files. In the HTML_STYLESHEET file, use the file name only. Also note that the +# files will be copied as-is; there are no commands or markers available. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_EXTRA_FILES = + +# The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. Doxygen +# will adjust the colors in the style sheet and background images according to +# this color. Hue is specified as an angle on a colorwheel, see +# http://en.wikipedia.org/wiki/Hue for more information. For instance the value +# 0 represents red, 60 is yellow, 120 is green, 180 is cyan, 240 is blue, 300 +# purple, and 360 is red again. +# Minimum value: 0, maximum value: 359, default value: 220. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_COLORSTYLE_HUE = 220 + +# The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of the colors +# in the HTML output. For a value of 0 the output will use grayscales only. A +# value of 255 will produce the most vivid colors. +# Minimum value: 0, maximum value: 255, default value: 100. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_COLORSTYLE_SAT = 100 + +# The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to the +# luminance component of the colors in the HTML output. Values below 100 +# gradually make the output lighter, whereas values above 100 make the output +# darker. The value divided by 100 is the actual gamma applied, so 80 represents +# a gamma of 0.8, The value 220 represents a gamma of 2.2, and 100 does not +# change the gamma. +# Minimum value: 40, maximum value: 240, default value: 80. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_COLORSTYLE_GAMMA = 80 + +# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML +# page will contain the date and time when the page was generated. Setting this +# to NO can help when comparing the output of multiple runs. +# The default value is: YES. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_TIMESTAMP = YES + +# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML +# documentation will contain sections that can be hidden and shown after the +# page has loaded. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_DYNAMIC_SECTIONS = NO + +# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of entries +# shown in the various tree structured indices initially; the user can expand +# and collapse entries dynamically later on. Doxygen will expand the tree to +# such a level that at most the specified number of entries are visible (unless +# a fully collapsed tree already exceeds this amount). So setting the number of +# entries 1 will produce a full collapsed tree by default. 0 is a special value +# representing an infinite number of entries and will result in a full expanded +# tree by default. +# Minimum value: 0, maximum value: 9999, default value: 100. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_INDEX_NUM_ENTRIES = 100 + +# If the GENERATE_DOCSET tag is set to YES, additional index files will be +# generated that can be used as input for Apple's Xcode 3 integrated development +# environment (see: http://developer.apple.com/tools/xcode/), introduced with +# OSX 10.5 (Leopard). To create a documentation set, doxygen will generate a +# Makefile in the HTML output directory. Running make will produce the docset in +# that directory and running make install will install the docset in +# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find it at +# startup. See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html +# for more information. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_DOCSET = NO + +# This tag determines the name of the docset feed. A documentation feed provides +# an umbrella under which multiple documentation sets from a single provider +# (such as a company or product suite) can be grouped. +# The default value is: Doxygen generated docs. +# This tag requires that the tag GENERATE_DOCSET is set to YES. + +DOCSET_FEEDNAME = "Doxygen generated docs" + +# This tag specifies a string that should uniquely identify the documentation +# set bundle. This should be a reverse domain-name style string, e.g. +# com.mycompany.MyDocSet. Doxygen will append .docset to the name. +# The default value is: org.doxygen.Project. +# This tag requires that the tag GENERATE_DOCSET is set to YES. + +DOCSET_BUNDLE_ID = org.doxygen.Project + +# The DOCSET_PUBLISHER_ID tag specifies a string that should uniquely identify +# the documentation publisher. This should be a reverse domain-name style +# string, e.g. com.mycompany.MyDocSet.documentation. +# The default value is: org.doxygen.Publisher. +# This tag requires that the tag GENERATE_DOCSET is set to YES. + +DOCSET_PUBLISHER_ID = org.doxygen.Publisher + +# The DOCSET_PUBLISHER_NAME tag identifies the documentation publisher. +# The default value is: Publisher. +# This tag requires that the tag GENERATE_DOCSET is set to YES. + +DOCSET_PUBLISHER_NAME = Publisher + +# If the GENERATE_HTMLHELP tag is set to YES then doxygen generates three +# additional HTML index files: index.hhp, index.hhc, and index.hhk. The +# index.hhp is a project file that can be read by Microsoft's HTML Help Workshop +# (see: http://www.microsoft.com/en-us/download/details.aspx?id=21138) on +# Windows. +# +# The HTML Help Workshop contains a compiler that can convert all HTML output +# generated by doxygen into a single compiled HTML file (.chm). Compiled HTML +# files are now used as the Windows 98 help format, and will replace the old +# Windows help format (.hlp) on all Windows platforms in the future. Compressed +# HTML files also contain an index, a table of contents, and you can search for +# words in the documentation. The HTML workshop also contains a viewer for +# compressed HTML files. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_HTMLHELP = NO + +# The CHM_FILE tag can be used to specify the file name of the resulting .chm +# file. You can add a path in front of the file if the result should not be +# written to the html output directory. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +CHM_FILE = + +# The HHC_LOCATION tag can be used to specify the location (absolute path +# including file name) of the HTML help compiler (hhc.exe). If non-empty, +# doxygen will try to run the HTML help compiler on the generated index.hhp. +# The file has to be specified with full path. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +HHC_LOCATION = + +# The GENERATE_CHI flag controls if a separate .chi index file is generated +# (YES) or that it should be included in the master .chm file (NO). +# The default value is: NO. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +GENERATE_CHI = NO + +# The CHM_INDEX_ENCODING is used to encode HtmlHelp index (hhk), content (hhc) +# and project file content. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +CHM_INDEX_ENCODING = + +# The BINARY_TOC flag controls whether a binary table of contents is generated +# (YES) or a normal table of contents (NO) in the .chm file. Furthermore it +# enables the Previous and Next buttons. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +BINARY_TOC = NO + +# The TOC_EXPAND flag can be set to YES to add extra items for group members to +# the table of contents of the HTML help documentation and to the tree view. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +TOC_EXPAND = NO + +# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and +# QHP_VIRTUAL_FOLDER are set, an additional index file will be generated that +# can be used as input for Qt's qhelpgenerator to generate a Qt Compressed Help +# (.qch) of the generated HTML documentation. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_QHP = NO + +# If the QHG_LOCATION tag is specified, the QCH_FILE tag can be used to specify +# the file name of the resulting .qch file. The path specified is relative to +# the HTML output folder. +# This tag requires that the tag GENERATE_QHP is set to YES. + +QCH_FILE = + +# The QHP_NAMESPACE tag specifies the namespace to use when generating Qt Help +# Project output. For more information please see Qt Help Project / Namespace +# (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#namespace). +# The default value is: org.doxygen.Project. +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_NAMESPACE = org.doxygen.Project + +# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating Qt +# Help Project output. For more information please see Qt Help Project / Virtual +# Folders (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#virtual- +# folders). +# The default value is: doc. +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_VIRTUAL_FOLDER = doc + +# If the QHP_CUST_FILTER_NAME tag is set, it specifies the name of a custom +# filter to add. For more information please see Qt Help Project / Custom +# Filters (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#custom- +# filters). +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_CUST_FILTER_NAME = + +# The QHP_CUST_FILTER_ATTRS tag specifies the list of the attributes of the +# custom filter to add. For more information please see Qt Help Project / Custom +# Filters (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#custom- +# filters). +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_CUST_FILTER_ATTRS = + +# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this +# project's filter section matches. Qt Help Project / Filter Attributes (see: +# http://qt-project.org/doc/qt-4.8/qthelpproject.html#filter-attributes). +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_SECT_FILTER_ATTRS = + +# The QHG_LOCATION tag can be used to specify the location of Qt's +# qhelpgenerator. If non-empty doxygen will try to run qhelpgenerator on the +# generated .qhp file. +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHG_LOCATION = + +# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files will be +# generated, together with the HTML files, they form an Eclipse help plugin. To +# install this plugin and make it available under the help contents menu in +# Eclipse, the contents of the directory containing the HTML and XML files needs +# to be copied into the plugins directory of eclipse. The name of the directory +# within the plugins directory should be the same as the ECLIPSE_DOC_ID value. +# After copying Eclipse needs to be restarted before the help appears. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_ECLIPSEHELP = NO + +# A unique identifier for the Eclipse help plugin. When installing the plugin +# the directory name containing the HTML and XML files should also have this +# name. Each documentation set should have its own identifier. +# The default value is: org.doxygen.Project. +# This tag requires that the tag GENERATE_ECLIPSEHELP is set to YES. + +ECLIPSE_DOC_ID = org.doxygen.Project + +# If you want full control over the layout of the generated HTML pages it might +# be necessary to disable the index and replace it with your own. The +# DISABLE_INDEX tag can be used to turn on/off the condensed index (tabs) at top +# of each HTML page. A value of NO enables the index and the value YES disables +# it. Since the tabs in the index contain the same information as the navigation +# tree, you can set this option to YES if you also set GENERATE_TREEVIEW to YES. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +DISABLE_INDEX = YES + +# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index +# structure should be generated to display hierarchical information. If the tag +# value is set to YES, a side panel will be generated containing a tree-like +# index structure (just like the one that is generated for HTML Help). For this +# to work a browser that supports JavaScript, DHTML, CSS and frames is required +# (i.e. any modern browser). Windows users are probably better off using the +# HTML help feature. Via custom style sheets (see HTML_EXTRA_STYLESHEET) one can +# further fine-tune the look of the index. As an example, the default style +# sheet generated by doxygen has an example that shows how to put an image at +# the root of the tree instead of the PROJECT_NAME. Since the tree basically has +# the same information as the tab index, you could consider setting +# DISABLE_INDEX to YES when enabling this option. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_TREEVIEW = YES + +# The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values that +# doxygen will group on one line in the generated HTML documentation. +# +# Note that a value of 0 will completely suppress the enum values from appearing +# in the overview section. +# Minimum value: 0, maximum value: 20, default value: 4. +# This tag requires that the tag GENERATE_HTML is set to YES. + +ENUM_VALUES_PER_LINE = 4 + +# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be used +# to set the initial width (in pixels) of the frame in which the tree is shown. +# Minimum value: 0, maximum value: 1500, default value: 250. +# This tag requires that the tag GENERATE_HTML is set to YES. + +TREEVIEW_WIDTH = 250 + +# If the EXT_LINKS_IN_WINDOW option is set to YES, doxygen will open links to +# external symbols imported via tag files in a separate window. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +EXT_LINKS_IN_WINDOW = NO + +# Use this tag to change the font size of LaTeX formulas included as images in +# the HTML documentation. When you change the font size after a successful +# doxygen run you need to manually remove any form_*.png images from the HTML +# output directory to force them to be regenerated. +# Minimum value: 8, maximum value: 50, default value: 10. +# This tag requires that the tag GENERATE_HTML is set to YES. + +FORMULA_FONTSIZE = 10 + +# Use the FORMULA_TRANPARENT tag to determine whether or not the images +# generated for formulas are transparent PNGs. Transparent PNGs are not +# supported properly for IE 6.0, but are supported on all modern browsers. +# +# Note that when changing this option you need to delete any form_*.png files in +# the HTML output directory before the changes have effect. +# The default value is: YES. +# This tag requires that the tag GENERATE_HTML is set to YES. + +FORMULA_TRANSPARENT = YES + +# Enable the USE_MATHJAX option to render LaTeX formulas using MathJax (see +# http://www.mathjax.org) which uses client side Javascript for the rendering +# instead of using pre-rendered bitmaps. Use this if you do not have LaTeX +# installed or if you want to formulas look prettier in the HTML output. When +# enabled you may also need to install MathJax separately and configure the path +# to it using the MATHJAX_RELPATH option. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +USE_MATHJAX = NO + +# When MathJax is enabled you can set the default output format to be used for +# the MathJax output. See the MathJax site (see: +# http://docs.mathjax.org/en/latest/output.html) for more details. +# Possible values are: HTML-CSS (which is slower, but has the best +# compatibility), NativeMML (i.e. MathML) and SVG. +# The default value is: HTML-CSS. +# This tag requires that the tag USE_MATHJAX is set to YES. + +MATHJAX_FORMAT = HTML-CSS + +# When MathJax is enabled you need to specify the location relative to the HTML +# output directory using the MATHJAX_RELPATH option. The destination directory +# should contain the MathJax.js script. For instance, if the mathjax directory +# is located at the same level as the HTML output directory, then +# MATHJAX_RELPATH should be ../mathjax. The default value points to the MathJax +# Content Delivery Network so you can quickly see the result without installing +# MathJax. However, it is strongly recommended to install a local copy of +# MathJax from http://www.mathjax.org before deployment. +# The default value is: http://cdn.mathjax.org/mathjax/latest. +# This tag requires that the tag USE_MATHJAX is set to YES. + +MATHJAX_RELPATH = http://cdn.mathjax.org/mathjax/latest + +# The MATHJAX_EXTENSIONS tag can be used to specify one or more MathJax +# extension names that should be enabled during MathJax rendering. For example +# MATHJAX_EXTENSIONS = TeX/AMSmath TeX/AMSsymbols +# This tag requires that the tag USE_MATHJAX is set to YES. + +MATHJAX_EXTENSIONS = + +# The MATHJAX_CODEFILE tag can be used to specify a file with javascript pieces +# of code that will be used on startup of the MathJax code. See the MathJax site +# (see: http://docs.mathjax.org/en/latest/output.html) for more details. For an +# example see the documentation. +# This tag requires that the tag USE_MATHJAX is set to YES. + +MATHJAX_CODEFILE = + +# When the SEARCHENGINE tag is enabled doxygen will generate a search box for +# the HTML output. The underlying search engine uses javascript and DHTML and +# should work on any modern browser. Note that when using HTML help +# (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets (GENERATE_DOCSET) +# there is already a search function so this one should typically be disabled. +# For large projects the javascript based search engine can be slow, then +# enabling SERVER_BASED_SEARCH may provide a better solution. It is possible to +# search using the keyboard; to jump to the search box use + S +# (what the is depends on the OS and browser, but it is typically +# , /