first experimentatl version of h5 to VTK for dark current simulations
This commit is contained in:
@@ -56,6 +56,7 @@ test/H5testFpar.f90 -text
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test/Makefile.am -text
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tools/Makefile.am -text
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tools/README -text
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tools/h5ToVtk.cc -text
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tools/h5pAttrib.cc -text
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tools/h5pToGNUplot.cc -text
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tools/homdynToH5p.cc -text
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@@ -48,6 +48,13 @@ h5pToGNUplot_SOURCES = h5pToGNUplot.cc
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# Specific building instruction (What compilers to use...)
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# ------------ Build Tools ------------
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h5ToVtk.o: h5ToVtk.cc
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$(TOOLS_CXX) $(CFLAGS) $(INC) -g -c h5ToVtk.cc
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h5ToVtk: h5ToVtk.o
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$(TOOLS_CXX) -o h5ToVtk h5ToVtk.o $(H5PLIB) $(LIBS)
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h5pAttrib: h5pAttrib.o
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$(TOOLS_CXX) -o h5pAttrib h5pAttrib.o $(H5PLIB) $(LIBS)
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Executable
+424
@@ -0,0 +1,424 @@
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/* h5pToGNUplot.cc
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Antino Kim
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This utility will output a GNU Plot input file accodring to the flags provided from the command line.
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The parser was imported from the example of h5dump utility with slight modifications.
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*/
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#include <stdio.h>
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#include <stdlib.h>
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#include <cctype>
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#include <string.h>
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#include <hdf5.h>
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#include "H5Part.h"
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#include <iostream>
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#include <fstream>
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#include <string>
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#include <vector>
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#include <sstream>
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#include <iomanip>
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#include <cassert>
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using namespace std;
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#define MAX_LEN 100
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/* Function headers */
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int get_option(int argc, const char **argv, const char *opts, const struct long_options *l_opts);
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static void print_help();
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static void variable_assign(int argc, const char *argv[]);
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/* Global variables */
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static char* var_1 = NULL;
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static char* var_2 = NULL;
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static char* input_name = NULL;
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static char* output_name = NULL;
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static char* timestep = NULL;
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static char* start = NULL;
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static char* npoints = NULL;
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static int print_all = 0;
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/* `get_option' variables */
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int opt_err = 1; /*get_option prints errors if this is on */
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int opt_ind = 1; /*token pointer */
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const char *opt_arg = NULL; /*flag argument (or value) */
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/* indication whether the flag (option) requires an argument or not */
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enum {
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no_arg = 0, /* doesn't take an argument */
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require_arg, /* requires an argument */
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};
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/* struct for flags (options) */
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typedef struct long_options
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{
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const char *name; /* name of the long option */
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int has_arg; /* whether we should look for an arg */
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char shortval; /* the shortname equivalent of long arg
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* this gets returned from get_option */
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} long_options;
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/* List of options in single characters */
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static const char *s_opts = "h1:2:i:o:n:t:s:";
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/* List of options in full words */
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static struct long_options l_opts[] =
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{
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{ "help", no_arg, 'h' }, // Print help page
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{ "1var", require_arg, '1' }, // Takes first variable parameter
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{ "2var", require_arg, '2' }, // Takes second variable parameter
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{ "input", require_arg, 'i' }, // Takes input file name
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{ "output", require_arg, 'o' }, // Takes output file name (without this flag, the program will print to stdout)
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{ "number", require_arg, 'n' }, // Sets number of output points
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{ "start", require_arg, 's' }, // Sets the starting particle index
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{ "timestep", require_arg, 't' }, // Sets the timestep
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{ NULL, 0, '\0' }
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};
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/************************************************************************************
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*********************************** FUNCTIONS *************************************
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*************************************************************************************/
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string convert2Int(int number) {
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stringstream ss;
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ss << setw(5) << setfill('0') << number;
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return ss.str();
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}
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/* get_option is the parsing function that was majorly ported from h5dump utility */
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int get_option(int argc, const char **argv, const char *opts, const struct long_options *l_opts) {
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static int sp = 1; /* character index in current token */
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int opt_opt = '?'; /* option character passed back to user */
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if (sp == 1)
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{
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/* check for more flag-like tokens */
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if (opt_ind >= argc || argv[opt_ind][0] != '-' || argv[opt_ind][1] == '\0')
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{
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return EOF;
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}
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else if (strcmp(argv[opt_ind], "--") == 0)
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{
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opt_ind++;
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return EOF;
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}
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}
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if (sp == 1 && argv[opt_ind][0] == '-' && argv[opt_ind][1] == '-')
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{
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/* long command line option */
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const char *arg = &argv[opt_ind][2];
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int i;
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for (i = 0; l_opts && l_opts[i].name; i++)
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{
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size_t len = strlen(l_opts[i].name);
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if (strncmp(arg, l_opts[i].name, len) == 0)
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{
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/* we've found a matching long command line flag */
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opt_opt = l_opts[i].shortval;
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if (l_opts[i].has_arg != no_arg)
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{
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if (arg[len] == '=')
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{
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opt_arg = &arg[len + 1];
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}
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else if (opt_ind < (argc - 1) && argv[opt_ind + 1][0] != '-')
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{
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opt_arg = argv[++opt_ind];
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}
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else if (l_opts[i].has_arg == require_arg)
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{
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if (opt_err)
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fprintf(stderr, "%s: option required for \"--%s\" flag\n", argv[0], arg);
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opt_opt = '?';
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}
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}
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else
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{
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if (arg[len] == '=')
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{
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if (opt_err)
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fprintf(stderr, "%s: no option required for \"%s\" flag\n", argv[0], arg);
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opt_opt = '?';
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}
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opt_arg = NULL;
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}
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break;
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}
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}
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if (l_opts[i].name == NULL)
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{
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/* exhausted all of the l_opts we have and still didn't match */
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if (opt_err)
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fprintf(stderr, "%s: unknown option \"%s\"\n", argv[0], arg);
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opt_opt = '?';
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}
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opt_ind++;
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sp = 1;
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}
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else
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{
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register char *cp; /* pointer into current token */
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/* short command line option */
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opt_opt = argv[opt_ind][sp];
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if (opt_opt == ':' || (cp = strchr(opts, opt_opt)) == 0)
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{
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if (opt_err)
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fprintf(stderr, "%s: unknown option \"%c\"\n", argv[0], opt_opt);
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/* if no chars left in this token, move to next token */
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if (argv[opt_ind][++sp] == '\0')
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{
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opt_ind++;
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sp = 1;
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}
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return '?';
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}
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if (*++cp == ':')
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{
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/* if a value is expected, get it */
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if (argv[opt_ind][sp + 1] != '\0')
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{
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/* flag value is rest of current token */
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opt_arg = &argv[opt_ind++][sp + 1];
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}
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else if (++opt_ind >= argc)
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{
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if (opt_err)
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{
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fprintf(stderr, "%s: value expected for option \"%c\"\n", argv[0], opt_opt);
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}
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opt_opt = '?';
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}
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else
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{
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/* flag value is next token */
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opt_arg = argv[opt_ind++];
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}
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sp = 1;
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}
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else
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{
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/* set up to look at next char in token, next time */
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if (argv[opt_ind][++sp] == '\0')
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{
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/* no more in current token, so setup next token */
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opt_ind++;
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sp = 1;
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}
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opt_arg = NULL;
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}
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}
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/* return the current flag character found */
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return opt_opt;
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}
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/* Assigns functions according to the parsed result */
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static void variable_assign(int argc, const char *argv[])
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{
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int option;
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/* set options according to the command line */
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while ((option = get_option(argc, argv, s_opts, l_opts)) != EOF)
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{
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switch ((char)option)
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{
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case 'h': // Print help page
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print_help();
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exit(1);
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case '1': // Print file attributes
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var_1 = strdup(opt_arg);
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break;
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case '2': // Print step attributes & values for time step n
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var_2 = strdup(opt_arg);
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break;
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case 'i': // Print data sets names & values for time step n
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input_name = strdup(opt_arg);
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break;
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case 'o': // Print number of steps
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output_name = strdup(opt_arg);
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break;
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case 'n': // Print shorter version without the values
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npoints = strdup(opt_arg);
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break;
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case 's': // Print shorter version without the values
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start = strdup(opt_arg);
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break;
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case 't': // Print shorter version without the values
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timestep = strdup(opt_arg);
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if(atoi(timestep)==-1)
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{
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print_all = 1;
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}
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break;
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default:
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print_help();
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exit(1);
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}
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}
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}
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/* For printing help page */
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static void print_help()
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{
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fflush(stdout);
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fprintf(stdout, "\nusage: h5pToGNUplot -t TIMESTEP -1 VARIABLE#1 -2 VARIABLE#2 -i INPUTFILE [OPTIONAL_FLAGS]\n");
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fprintf(stdout, "\n");
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fprintf(stdout, " FLAGS\n");
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fprintf(stdout, " -h, --help Print help page\n");
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fprintf(stdout, " -1 par, --1var par (REQUIRED) Takes first variable parameter to \"par\"\n");
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fprintf(stdout, " -2 par, --2var par (REQUIRED) Takes second variable parameter to \"par\"\n");
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fprintf(stdout, " -i file, --input file (REQUIRED) Takes input file name to \"file\"\n");
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fprintf(stdout, " -t step, --timestep step (REQUIRED) Sets the timestep to \"step\" (Value -1 will result in dumping values of all timesteps.)\n");
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fprintf(stdout, " -o file, --output file (OPTIONAL) Takes output file name to \"file\" (without this flag, the program will print to stdout)\n");
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fprintf(stdout, " -n num, --number num (OPTIONAL) Sets number of output points to \"num\"\n");
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fprintf(stdout, " -s idx, --start idx (OPTIONAL) Sets the starting particle index to \"idx\"\n");
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fprintf(stdout, "\n");
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fprintf(stdout, " Examples:\n");
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fprintf(stdout, "\n");
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fprintf(stdout, " 1) Create GNU plot file output.txt from sample.h5part by ploting x vs px for timestep 54\n");
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fprintf(stdout, "\n");
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fprintf(stdout, " h5pToGNUplot -t 54 -1 x -2 px -i sample.h5part -o output.txt\n");
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fprintf(stdout, "\n");
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fprintf(stdout, " 2) Create GNU plot file output.txt from sample.h5part by ploting x vs px for timestep 54 \n using 1200 points from particle index 76\n");
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fprintf(stdout, "\n");
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fprintf(stdout, " h5pToGNUplot -t 54 -1 x -2 px -i sample.h5part -o output.txt -s 76 -n 1200\n");
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fprintf(stdout, "\n");
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}
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int main(int argc, const char *argv[])
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{
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H5PartFile *h5file = NULL;
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std::ofstream of;
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int j;
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int num_dataset;
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int ntime_step = 0;
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variable_assign(argc, argv);
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if(input_name == NULL) {
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fprintf(stdout, "missing input file name\n");
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print_help();
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exit(1);
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}
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if(output_name == NULL) {
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fprintf(stdout, "missing output file name\n");
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print_help();
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exit(1);
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}
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string ifn = string(input_name) + string(".h5");
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h5file = H5PartOpenFile(ifn.c_str(), H5PART_READ);
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if( h5file == NULL ) {
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fprintf(stdout, "unable to open file %s\n", input_name);
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print_help();
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exit(1);
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}
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ntime_step = H5PartGetNumSteps(h5file);
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j = 0;
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for (; j<ntime_step; j++) {
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H5PartSetStep(h5file,j);
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num_dataset = H5PartGetNumDatasets(h5file);
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h5part_int64_t nparticles = H5PartGetNumParticles(h5file);
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cout << "Working on timestep " << j << " expecting " << nparticles << " particles " << endl;
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h5part_float64_t* x = (h5part_float64_t*)malloc(sizeof(h5part_float64_t)*nparticles);
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H5PartReadDataFloat64(h5file, "x", x);
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h5part_float64_t* y = (h5part_float64_t*)malloc(sizeof(h5part_float64_t)*nparticles);
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H5PartReadDataFloat64(h5file, "y", y);
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h5part_float64_t* z = (h5part_float64_t*)malloc(sizeof(h5part_float64_t)*nparticles);
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H5PartReadDataFloat64(h5file, "z", z);
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h5part_int64_t* ptype = (h5part_int64_t*)malloc(sizeof(h5part_int64_t)*nparticles);
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H5PartReadDataInt64(h5file, "ptype", ptype);
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string ffn = string("vtk/") + string(output_name) + convert2Int(j) + string(".vtk");
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of.open(ffn.c_str());
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assert(of.is_open());
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of.precision(6);
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of << setprecision(5)
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<< "# vtk DataFile Version 2.0" << endl
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<< "unstructured grid and vector field on the nodes" << endl
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<< "ASCII" << endl
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<< "DATASET UNSTRUCTURED_GRID" << endl
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<< "POINTS " << nparticles << " float" << endl;
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// Particle positions
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for(size_t i = 0; i < nparticles; i++)
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of << x[i] << " " << y[i] << " " << z[i] << endl;
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of << endl; // defining VTK_poly_vertex
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of << "CELLS " << nparticles << " " << 2 * nparticles << endl;
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for(int i = 0; i < nparticles; i++)
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of << "1 " << i << endl;
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of << endl;
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// defining Cell_types
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of << "CELL_TYPES " << nparticles << endl;
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for(int i = 0; i < nparticles; i++)
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of << "2" << endl;
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// defining Cell_types
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of << "CELL_DATA " << nparticles << endl;
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of << "SCALARS " << "cell_attribute_data" << " float " << "1" << endl;
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of << "LOOKUP_TABLE " << "default" << endl ;
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for(int i = 0; i < nparticles ; i ++)
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of << (float)(i) << endl;
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of << endl;
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of << "COLOR_SCALARS " << "ParticleColor " << 4 << endl ;
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for(int i = 0; i < nparticles ; i ++) {
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if(ptype[i] == 0)
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of << "1.0" << " 1.0 " << "0.0 " << "1.0" << endl;
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else
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of << "0" << " 1.0 " << "0.0 " << "1.0" << endl;
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}
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of << endl;
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of.close();
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free(x);
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free(x);
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free(z);
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free(ptype);
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}
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H5PartCloseFile(h5file);
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return 0;
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}
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