--- trunk/src/applications/staticProps/StaticPropsCmd.c 2006/05/12 21:34:43 955 +++ trunk/src/applications/staticProps/StaticPropsCmd.c 2006/09/26 01:30:32 1052 @@ -43,11 +43,12 @@ void clear_given (struct gengetopt_args_info *args_inf args_info->input_given = 0 ; args_info->output_given = 0 ; args_info->step_given = 0 ; - args_info->nrbins_given = 0 ; + args_info->nbins_given = 0 ; args_info->nbins_x_given = 0 ; args_info->nbins_y_given = 0 ; args_info->nanglebins_given = 0 ; args_info->length_given = 0 ; + args_info->rcut_given = 0 ; args_info->zoffset_given = 0 ; args_info->sele1_given = 0 ; args_info->sele2_given = 0 ; @@ -56,12 +57,14 @@ void clear_given (struct gengetopt_args_info *args_inf args_info->molname_given = 0 ; args_info->begin_given = 0 ; args_info->end_given = 0 ; + args_info->bo_given = 0 ; args_info->gofr_given = 0 ; args_info->r_theta_given = 0 ; args_info->r_omega_given = 0 ; args_info->theta_omega_given = 0 ; args_info->gxyz_given = 0 ; args_info->p2_given = 0 ; + args_info->rp2_given = 0 ; args_info->scd_given = 0 ; args_info->density_given = 0 ; args_info->slab_density_given = 0 ; @@ -78,8 +81,8 @@ void clear_args (struct gengetopt_args_info *args_info args_info->output_orig = NULL; args_info->step_arg = 1; args_info->step_orig = NULL; - args_info->nrbins_arg = 100; - args_info->nrbins_orig = NULL; + args_info->nbins_arg = 100; + args_info->nbins_orig = NULL; args_info->nbins_x_arg = 100; args_info->nbins_x_orig = NULL; args_info->nbins_y_arg = 100; @@ -87,6 +90,7 @@ void clear_args (struct gengetopt_args_info *args_info args_info->nanglebins_arg = 50; args_info->nanglebins_orig = NULL; args_info->length_orig = NULL; + args_info->rcut_orig = NULL; args_info->zoffset_arg = 0; args_info->zoffset_orig = NULL; args_info->sele1_arg = NULL; @@ -120,30 +124,33 @@ cmdline_parser_print_help (void) printf("%s\n"," -i, --input=filename input dump file"); printf("%s\n"," -o, --output=filename output file name"); printf("%s\n"," -n, --step=INT process every n frame (default=`1')"); - printf("%s\n"," -x, --nbins_x=INT number of bins in x axis (default=`100')"); - printf("%s\n"," -y , --nbins_y=INT number of bins in y axis (default=`100')"); - printf("%s\n"," -r, --nrbins=INT number of bins for distance (default=`100')"); + printf("%s\n"," -b, --nbins=INT number of bins (general purpose) \n (default=`100')"); + printf("%s\n"," -x, --nbins_x=INT number of bins in x axis (default=`100')"); + printf("%s\n"," -y, --nbins_y=INT number of bins in y axis (default=`100')"); printf("%s\n"," -a, --nanglebins=INT number of bins for cos(angle) (default=`50')"); - printf("%s\n"," -l, --length=DOUBLE maximum length (Defaults to 1/2 smallest length \n of first frame)"); + printf("%s\n"," --length=DOUBLE maximum length (Defaults to 1/2 smallest length \n of first frame)"); + printf("%s\n"," -c, --rcut=DOUBLE cutoff radius (rcut)"); printf("%s\n"," -z, --zoffset=DOUBLE Where to set the zero for the slab_density \n calculation (default=`0')"); printf("%s\n"," --sele1=selection script select the first stuntdouble set"); printf("%s\n"," --sele2=selection script select the second stuntdouble set"); printf("%s\n"," --sele3=selection script select the third stuntdouble set"); printf("%s\n"," --refsele=selection script\n select reference (use and only use with --gxyz)"); printf("%s\n"," --molname=STRING molecule name"); - printf("%s\n"," --begin=INT begin interanl index"); + printf("%s\n"," --begin=INT begin internal index"); printf("%s\n"," --end=INT end internal index"); printf("%s\n","\n Group: staticProps\n an option of this group is required"); - printf("%s\n"," --gofr g(r)"); + printf("%s\n"," --bo bond order parameter (--rcut must be specified"); + printf("%s\n"," -g, --gofr g(r)"); printf("%s\n"," --r_theta g(r, cos(theta))"); printf("%s\n"," --r_omega g(r, cos(omega))"); printf("%s\n"," --theta_omega g(cos(theta), cos(omega))"); printf("%s\n"," --gxyz g(x, y, z)"); - printf("%s\n"," --p2 p2 order parameter (--sele1 and --sele2 must be \n specified)"); - printf("%s\n"," --scd scd order parameter(either --sele1, --sele2, \n --sele3 are specified or --molname, --begin, \n --end are specified)"); - printf("%s\n"," --density density plot (--sele1 must be specified)"); - printf("%s\n"," --slab_density slab density (--sele1 must be specified)"); - printf("%s\n"," --hxy hxy (--sele1 must be specified)"); + printf("%s\n"," -p, --p2 p2 order parameter (--sele1 and --sele2 must be \n specified)"); + printf("%s\n"," --rp2 rp2 order parameter (--sele1 and --sele2 must \n be specified)"); + printf("%s\n"," -s, --scd scd order parameter (either --sele1, --sele2, \n --sele3 are specified or --molname, --begin, \n --end are specified)"); + printf("%s\n"," -d, --density density plot"); + printf("%s\n"," --slab_density slab density"); + printf("%s\n"," --hxy hxy"); } @@ -183,12 +190,12 @@ cmdline_parser_release (struct gengetopt_args_info *ar free (args_info->step_orig); /* free previous argument */ args_info->step_orig = 0; } - if (args_info->nrbins_orig) + if (args_info->nbins_orig) { - free (args_info->nrbins_orig); /* free previous argument */ - args_info->nrbins_orig = 0; + free (args_info->nbins_orig); /* free previous argument */ + args_info->nbins_orig = 0; } - if (args_info->nbins_x_orig) + if (args_info->nbins_x_orig) { free (args_info->nbins_x_orig); /* free previous argument */ args_info->nbins_x_orig = 0; @@ -198,7 +205,6 @@ cmdline_parser_release (struct gengetopt_args_info *ar free (args_info->nbins_y_orig); /* free previous argument */ args_info->nbins_y_orig = 0; } - if (args_info->nanglebins_orig) { free (args_info->nanglebins_orig); /* free previous argument */ @@ -209,6 +215,11 @@ cmdline_parser_release (struct gengetopt_args_info *ar free (args_info->length_orig); /* free previous argument */ args_info->length_orig = 0; } + if (args_info->rcut_orig) + { + free (args_info->rcut_orig); /* free previous argument */ + args_info->rcut_orig = 0; + } if (args_info->zoffset_orig) { free (args_info->zoffset_orig); /* free previous argument */ @@ -319,11 +330,11 @@ cmdline_parser_file_save(const char *filename, struct fprintf(outfile, "%s\n", "step"); } } - if (args_info->nrbins_given) { - if (args_info->nrbins_orig) { - fprintf(outfile, "%s=\"%s\"\n", "nrbins", args_info->nrbins_orig); + if (args_info->nbins_given) { + if (args_info->nbins_orig) { + fprintf(outfile, "%s=\"%s\"\n", "nbins", args_info->nbins_orig); } else { - fprintf(outfile, "%s\n", "nrbins"); + fprintf(outfile, "%s\n", "nbins"); } } if (args_info->nbins_x_given) { @@ -352,6 +363,13 @@ cmdline_parser_file_save(const char *filename, struct fprintf(outfile, "%s=\"%s\"\n", "length", args_info->length_orig); } else { fprintf(outfile, "%s\n", "length"); + } + } + if (args_info->rcut_given) { + if (args_info->rcut_orig) { + fprintf(outfile, "%s=\"%s\"\n", "rcut", args_info->rcut_orig); + } else { + fprintf(outfile, "%s\n", "rcut"); } } if (args_info->zoffset_given) { @@ -410,6 +428,9 @@ cmdline_parser_file_save(const char *filename, struct fprintf(outfile, "%s\n", "end"); } } + if (args_info->bo_given) { + fprintf(outfile, "%s\n", "bo"); + } if (args_info->gofr_given) { fprintf(outfile, "%s\n", "gofr"); } @@ -428,6 +449,9 @@ cmdline_parser_file_save(const char *filename, struct if (args_info->p2_given) { fprintf(outfile, "%s\n", "p2"); } + if (args_info->rp2_given) { + fprintf(outfile, "%s\n", "rp2"); + } if (args_info->scd_given) { fprintf(outfile, "%s\n", "scd"); } @@ -440,6 +464,7 @@ cmdline_parser_file_save(const char *filename, struct if (args_info->hxy_given) { fprintf(outfile, "%s\n", "hxy"); } + fclose (outfile); i = EXIT_SUCCESS; @@ -478,16 +503,18 @@ reset_group_staticProps(struct gengetopt_args_info *ar if (! args_info->staticProps_group_counter) return; + args_info->bo_given = 0 ; args_info->gofr_given = 0 ; args_info->r_theta_given = 0 ; args_info->r_omega_given = 0 ; args_info->theta_omega_given = 0 ; args_info->gxyz_given = 0 ; args_info->p2_given = 0 ; + args_info->rp2_given = 0 ; args_info->scd_given = 0 ; args_info->density_given = 0 ; args_info->slab_density_given = 0 ; - args_info->hxy_given= 0 ; + args_info->hxy_given = 0 ; args_info->staticProps_group_counter = 0; } @@ -580,9 +607,12 @@ cmdline_parser_internal (int argc, char * const *argv, { "input", 1, NULL, 'i' }, { "output", 1, NULL, 'o' }, { "step", 1, NULL, 'n' }, - { "nrbins", 1, NULL, 'r' }, + { "nbins", 1, NULL, 'b' }, + { "nbins_x", 1, NULL, 'x' }, + { "nbins_y", 1, NULL, 'y' }, { "nanglebins", 1, NULL, 'a' }, - { "length", 1, NULL, 'l' }, + { "length", 1, NULL, 0 }, + { "rcut", 1, NULL, 'c' }, { "zoffset", 1, NULL, 'z' }, { "sele1", 1, NULL, 0 }, { "sele2", 1, NULL, 0 }, @@ -591,21 +621,23 @@ cmdline_parser_internal (int argc, char * const *argv, { "molname", 1, NULL, 0 }, { "begin", 1, NULL, 0 }, { "end", 1, NULL, 0 }, - { "gofr", 0, NULL, 0 }, + { "bo", 0, NULL, 0 }, + { "gofr", 0, NULL, 'g' }, { "r_theta", 0, NULL, 0 }, { "r_omega", 0, NULL, 0 }, { "theta_omega", 0, NULL, 0 }, { "gxyz", 0, NULL, 0 }, - { "p2", 0, NULL, 0 }, - { "scd", 0, NULL, 0 }, - { "density", 0, NULL, 0 }, + { "p2", 0, NULL, 'p' }, + { "rp2", 0, NULL, 0 }, + { "scd", 0, NULL, 's' }, + { "density", 0, NULL, 'd' }, { "slab_density", 0, NULL, 0 }, { "hxy", 0, NULL, 0 }, { NULL, 0, NULL, 0 } }; stop_char = 0; - c = getopt_long (argc, argv, "hVi:o:n:r:a:l:z:", long_options, &option_index); + c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:c:z:gpsd", long_options, &option_index); if (c == -1) break; /* Exit from `while (1)' loop. */ @@ -677,30 +709,30 @@ cmdline_parser_internal (int argc, char * const *argv, args_info->step_orig = gengetopt_strdup (optarg); break; - case 'r': /* number of bins for distance. */ - if (local_args_info.nrbins_given) + case 'b': /* number of bins (general purpose). */ + if (local_args_info.nbins_given) { - fprintf (stderr, "%s: `--nrbins' (`-r') option given more than once%s\n", argv[0], (additional_error ? additional_error : "")); + fprintf (stderr, "%s: `--nbins' (`-b') option given more than once%s\n", argv[0], (additional_error ? additional_error : "")); goto failure; } - if (args_info->nrbins_given && ! override) + if (args_info->nbins_given && ! override) continue; - local_args_info.nrbins_given = 1; - args_info->nrbins_given = 1; - args_info->nrbins_arg = strtol (optarg, &stop_char, 0); + local_args_info.nbins_given = 1; + args_info->nbins_given = 1; + args_info->nbins_arg = strtol (optarg, &stop_char, 0); if (!(stop_char && *stop_char == '\0')) { fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg); goto failure; } - if (args_info->nrbins_orig) - free (args_info->nrbins_orig); /* free previous string */ - args_info->nrbins_orig = gengetopt_strdup (optarg); + if (args_info->nbins_orig) + free (args_info->nbins_orig); /* free previous string */ + args_info->nbins_orig = gengetopt_strdup (optarg); break; case 'x': /* number of bins in x axis. */ if (local_args_info.nbins_x_given) { - fprintf (stderr, "%s: `--nbins_x' (`-r') option given more than once%s\n", argv[0], (additional_error ? additional_error : "")); + fprintf (stderr, "%s: `--nbins_x' (`-x') option given more than once%s\n", argv[0], (additional_error ? additional_error : "")); goto failure; } if (args_info->nbins_x_given && ! override) @@ -720,7 +752,7 @@ cmdline_parser_internal (int argc, char * const *argv, case 'y': /* number of bins in y axis. */ if (local_args_info.nbins_y_given) { - fprintf (stderr, "%s: `--nbins_y' (`-r') option given more than once%s\n", argv[0], (additional_error ? additional_error : "")); + fprintf (stderr, "%s: `--nbins_y' (`-y') option given more than once%s\n", argv[0], (additional_error ? additional_error : "")); goto failure; } if (args_info->nbins_y_given && ! override) @@ -757,24 +789,24 @@ cmdline_parser_internal (int argc, char * const *argv, args_info->nanglebins_orig = gengetopt_strdup (optarg); break; - case 'l': /* maximum length (Defaults to 1/2 smallest length of first frame). */ - if (local_args_info.length_given) + case 'c': /* cutoff radius (rcut). */ + if (local_args_info.rcut_given) { - fprintf (stderr, "%s: `--length' (`-l') option given more than once%s\n", argv[0], (additional_error ? additional_error : "")); + fprintf (stderr, "%s: `--rcut' (`-c') option given more than once%s\n", argv[0], (additional_error ? additional_error : "")); goto failure; } - if (args_info->length_given && ! override) + if (args_info->rcut_given && ! override) continue; - local_args_info.length_given = 1; - args_info->length_given = 1; - args_info->length_arg = strtod (optarg, &stop_char); + local_args_info.rcut_given = 1; + args_info->rcut_given = 1; + args_info->rcut_arg = strtod (optarg, &stop_char); if (!(stop_char && *stop_char == '\0')) { fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg); goto failure; } - if (args_info->length_orig) - free (args_info->length_orig); /* free previous string */ - args_info->length_orig = gengetopt_strdup (optarg); + if (args_info->rcut_orig) + free (args_info->rcut_orig); /* free previous string */ + args_info->rcut_orig = gengetopt_strdup (optarg); break; case 'z': /* Where to set the zero for the slab_density calculation. */ @@ -797,10 +829,91 @@ cmdline_parser_internal (int argc, char * const *argv, args_info->zoffset_orig = gengetopt_strdup (optarg); break; + case 'g': /* g(r). */ + if (local_args_info.gofr_given) + { + fprintf (stderr, "%s: `--gofr' (`-g') option given more than once%s\n", argv[0], (additional_error ? additional_error : "")); + goto failure; + } + if (args_info->gofr_given && ! override) + continue; + local_args_info.gofr_given = 1; + args_info->gofr_given = 1; + if (args_info->staticProps_group_counter && override) + reset_group_staticProps (args_info); + args_info->staticProps_group_counter += 1; + break; + case 'p': /* p2 order parameter (--sele1 and --sele2 must be specified). */ + if (local_args_info.p2_given) + { + fprintf (stderr, "%s: `--p2' (`-p') option given more than once%s\n", argv[0], (additional_error ? additional_error : "")); + goto failure; + } + if (args_info->p2_given && ! override) + continue; + local_args_info.p2_given = 1; + args_info->p2_given = 1; + if (args_info->staticProps_group_counter && override) + reset_group_staticProps (args_info); + args_info->staticProps_group_counter += 1; + break; + + case 's': /* scd order parameter (either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified). */ + if (local_args_info.scd_given) + { + fprintf (stderr, "%s: `--scd' (`-s') option given more than once%s\n", argv[0], (additional_error ? additional_error : "")); + goto failure; + } + if (args_info->scd_given && ! override) + continue; + local_args_info.scd_given = 1; + args_info->scd_given = 1; + if (args_info->staticProps_group_counter && override) + reset_group_staticProps (args_info); + args_info->staticProps_group_counter += 1; + break; + + case 'd': /* density plot. */ + if (local_args_info.density_given) + { + fprintf (stderr, "%s: `--density' (`-d') option given more than once%s\n", argv[0], (additional_error ? additional_error : "")); + goto failure; + } + if (args_info->density_given && ! override) + continue; + local_args_info.density_given = 1; + args_info->density_given = 1; + if (args_info->staticProps_group_counter && override) + reset_group_staticProps (args_info); + args_info->staticProps_group_counter += 1; + break; + + case 0: /* Long option with no short option */ + /* maximum length (Defaults to 1/2 smallest length of first frame). */ + if (strcmp (long_options[option_index].name, "length") == 0) + { + if (local_args_info.length_given) + { + fprintf (stderr, "%s: `--length' option given more than once%s\n", argv[0], (additional_error ? additional_error : "")); + goto failure; + } + if (args_info->length_given && ! override) + continue; + local_args_info.length_given = 1; + args_info->length_given = 1; + args_info->length_arg = strtod (optarg, &stop_char); + if (!(stop_char && *stop_char == '\0')) { + fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg); + goto failure; + } + if (args_info->length_orig) + free (args_info->length_orig); /* free previous string */ + args_info->length_orig = gengetopt_strdup (optarg); + } /* select the first stuntdouble set. */ - if (strcmp (long_options[option_index].name, "sele1") == 0) + else if (strcmp (long_options[option_index].name, "sele1") == 0) { if (local_args_info.sele1_given) { @@ -894,7 +1007,7 @@ cmdline_parser_internal (int argc, char * const *argv, free (args_info->molname_orig); /* free previous string */ args_info->molname_orig = gengetopt_strdup (optarg); } - /* begin interanl index. */ + /* begin internal index. */ else if (strcmp (long_options[option_index].name, "begin") == 0) { if (local_args_info.begin_given) @@ -936,18 +1049,18 @@ cmdline_parser_internal (int argc, char * const *argv, free (args_info->end_orig); /* free previous string */ args_info->end_orig = gengetopt_strdup (optarg); } - /* g(r). */ - else if (strcmp (long_options[option_index].name, "gofr") == 0) + /* bond order parameter (--rcut must be specified. */ + else if (strcmp (long_options[option_index].name, "bo") == 0) { - if (local_args_info.gofr_given) + if (local_args_info.bo_given) { - fprintf (stderr, "%s: `--gofr' option given more than once%s\n", argv[0], (additional_error ? additional_error : "")); + fprintf (stderr, "%s: `--bo' option given more than once%s\n", argv[0], (additional_error ? additional_error : "")); goto failure; } - if (args_info->gofr_given && ! override) + if (args_info->bo_given && ! override) continue; - local_args_info.gofr_given = 1; - args_info->gofr_given = 1; + local_args_info.bo_given = 1; + args_info->bo_given = 1; if (args_info->staticProps_group_counter && override) reset_group_staticProps (args_info); args_info->staticProps_group_counter += 1; @@ -1021,58 +1134,24 @@ cmdline_parser_internal (int argc, char * const *argv, args_info->staticProps_group_counter += 1; break; } - /* p2 order parameter (--sele1 and --sele2 must be specified). */ - else if (strcmp (long_options[option_index].name, "p2") == 0) + /* rp2 order parameter (--sele1 and --sele2 must be specified). */ + else if (strcmp (long_options[option_index].name, "rp2") == 0) { - if (local_args_info.p2_given) + if (local_args_info.rp2_given) { - fprintf (stderr, "%s: `--p2' option given more than once%s\n", argv[0], (additional_error ? additional_error : "")); + fprintf (stderr, "%s: `--rp2' option given more than once%s\n", argv[0], (additional_error ? additional_error : "")); goto failure; } - if (args_info->p2_given && ! override) + if (args_info->rp2_given && ! override) continue; - local_args_info.p2_given = 1; - args_info->p2_given = 1; + local_args_info.rp2_given = 1; + args_info->rp2_given = 1; if (args_info->staticProps_group_counter && override) reset_group_staticProps (args_info); args_info->staticProps_group_counter += 1; break; } - /* scd order parameter(either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified). */ - else if (strcmp (long_options[option_index].name, "scd") == 0) - { - if (local_args_info.scd_given) - { - fprintf (stderr, "%s: `--scd' option given more than once%s\n", argv[0], (additional_error ? additional_error : "")); - goto failure; - } - if (args_info->scd_given && ! override) - continue; - local_args_info.scd_given = 1; - args_info->scd_given = 1; - if (args_info->staticProps_group_counter && override) - reset_group_staticProps (args_info); - args_info->staticProps_group_counter += 1; - break; - } - /* density plot (--sele1 must be specified). */ - else if (strcmp (long_options[option_index].name, "density") == 0) - { - if (local_args_info.density_given) - { - fprintf (stderr, "%s: `--density' option given more than once%s\n", argv[0], (additional_error ? additional_error : "")); - goto failure; - } - if (args_info->density_given && ! override) - continue; - local_args_info.density_given = 1; - args_info->density_given = 1; - if (args_info->staticProps_group_counter && override) - reset_group_staticProps (args_info); - args_info->staticProps_group_counter += 1; - break; - } - /* slab density (--sele1 must be specified). */ + /* slab density. */ else if (strcmp (long_options[option_index].name, "slab_density") == 0) { if (local_args_info.slab_density_given) @@ -1089,7 +1168,7 @@ cmdline_parser_internal (int argc, char * const *argv, args_info->staticProps_group_counter += 1; break; } - /* hxy (--sele1 must be specified). */ + /* hxy. */ else if (strcmp (long_options[option_index].name, "hxy") == 0) { if (local_args_info.hxy_given)