--- trunk/src/applications/staticProps/StaticPropsCmd.c 2010/04/29 14:41:48 1440 +++ trunk/src/applications/staticProps/StaticPropsCmd.cpp 2014/04/29 17:32:31 1993 @@ -1,7 +1,7 @@ /* - File autogenerated by gengetopt version 2.22 + File autogenerated by gengetopt version 2.22.4 generated with the following command: - gengetopt -F StaticPropsCmd -u + gengetopt --file-name=StaticPropsCmd --unamed-opts The developers of gengetopt consider the fixed text that goes in all gengetopt output files to be in the public domain: @@ -17,8 +17,16 @@ #include #include -#include "getopt.h" +#ifndef FIX_UNUSED +#define FIX_UNUSED(X) (void) (X) /* avoid warnings for unused params */ +#endif +#ifdef WIN32 +#include "utils/wingetopt.h" +#else +#include +#endif + #include "StaticPropsCmd.h" const char *gengetopt_args_info_purpose = ""; @@ -38,22 +46,28 @@ const char *gengetopt_args_info_help[] = { " -y, --nbins_y=INT number of bins in y axis (default=`100')", " --nbins_z=INT number of bins in z axis (default=`100')", " -a, --nanglebins=INT number of bins for cos(angle) (default=`50')", - " --length=DOUBLE maximum length (Defaults to 1/2 smallest length \n of first frame)", " -c, --rcut=DOUBLE cutoff radius (rcut)", + " --dz=DOUBLE slab width (dz)", + " --length=DOUBLE maximum length (Defaults to 1/2 smallest length \n of first frame)", + " --zlength=DOUBLE maximum length (Defaults to 1/2 smallest length \n of first frame)", " -z, --zoffset=DOUBLE Where to set the zero for the slab_density \n calculation (default=`0')", " --sele1=selection script select the first stuntdouble set", " --sele2=selection script select the second stuntdouble set", " --sele3=selection script select the third stuntdouble set", " --refsele=selection script\n select reference (use and only use with --gxyz)", " --comsele=selection script\n select stunt doubles for center-of-mass \n reference point", + " --seleoffset=INT global index offset for a second object (used \n to define a vector between sites in molecule)", + " --seleoffset2=INT global index offset for a third object (used to \n define a vector between sites in molecule)", " --molname=STRING molecule name", " --begin=INT begin internal index", " --end=INT end internal index", " --radius=DOUBLE nanoparticle radius", "\n Group: staticProps\n an option of this group is required", " --bo bond order parameter (--rcut must be specified)", - " --bor bond order parameter as a function of radius \n (--rcut must be specified)", + " --ior icosahedral bond order parameter as a function \n of radius (--rcut must be specified)", + " --for FCC bond order parameter as a function of \n radius (--rcut must be specified)", " --bad N(theta) bond angle density within (--rcut must \n be specified)", + " --count count of molecules matching selection criteria \n (and associated statistics)", " -g, --gofr g(r)", " --gofz g(z)", " --r_theta g(r, cos(theta))", @@ -61,15 +75,24 @@ const char *gengetopt_args_info_help[] = { " --r_z g(r, z)", " --theta_omega g(cos(theta), cos(omega))", " --gxyz g(x, y, z)", - " -p, --p2 p2 order parameter (--sele1 and --sele2 must be \n specified)", + " --twodgofr 2D g(r) (Slab width --dz must be specified)", + " -p, --p2 p2 order parameter (--sele1 must be specified, \n --sele2 is optional)", " --rp2 rp2 order parameter (--sele1 and --sele2 must \n be specified)", " -s, --scd scd order parameter (either --sele1, --sele2, \n --sele3 are specified or --molname, --begin, \n --end are specified)", " -d, --density density plot", " --slab_density slab density", - " --p_angle p(cos(theta))", + " --p_angle p(cos(theta)) (--sele1 must be specified, \n --sele2 is optional)", " --hxy hxy", " --rho_r rho of R", + " --angle_r angle of R", " --hullvol hull volume of nanoparticle", + " --rodlength length of nanorod", + " -Q, --tet_param tetrahedrality order parameter (Qk)", + " --tet_param_z spatially-resolved tetrahedrality order \n parameter Qk(z)", + " --rnemdz slab-resolved RNEMD statistics (temperature, \n density, velocity)", + " --rnemdr shell-resolved RNEMD statistics (temperature, \n density, angular velocity)", + " --rnemdrt shell and angle-resolved RNEMD statistics \n (temperature, density, angular velocity)", + " --uFreqMap electrostatic potential to frequency map based \n on the Cho nitrile fits", 0 }; @@ -85,7 +108,7 @@ static int void clear_args (struct gengetopt_args_info *args_info); static int -cmdline_parser_internal (int argc, char * const *argv, struct gengetopt_args_info *args_info, +cmdline_parser_internal (int argc, char **argv, struct gengetopt_args_info *args_info, struct cmdline_parser_params *params, const char *additional_error); static int @@ -107,21 +130,27 @@ void clear_given (struct gengetopt_args_info *args_inf args_info->nbins_y_given = 0 ; args_info->nbins_z_given = 0 ; args_info->nanglebins_given = 0 ; - args_info->length_given = 0 ; args_info->rcut_given = 0 ; + args_info->dz_given = 0 ; + args_info->length_given = 0 ; + args_info->zlength_given = 0 ; args_info->zoffset_given = 0 ; args_info->sele1_given = 0 ; args_info->sele2_given = 0 ; args_info->sele3_given = 0 ; args_info->refsele_given = 0 ; args_info->comsele_given = 0 ; + args_info->seleoffset_given = 0 ; + args_info->seleoffset2_given = 0 ; args_info->molname_given = 0 ; args_info->begin_given = 0 ; args_info->end_given = 0 ; args_info->radius_given = 0 ; args_info->bo_given = 0 ; - args_info->bor_given = 0 ; + args_info->ior_given = 0 ; + args_info->for_given = 0 ; args_info->bad_given = 0 ; + args_info->count_given = 0 ; args_info->gofr_given = 0 ; args_info->gofz_given = 0 ; args_info->r_theta_given = 0 ; @@ -129,6 +158,7 @@ void clear_given (struct gengetopt_args_info *args_inf args_info->r_z_given = 0 ; args_info->theta_omega_given = 0 ; args_info->gxyz_given = 0 ; + args_info->twodgofr_given = 0 ; args_info->p2_given = 0 ; args_info->rp2_given = 0 ; args_info->scd_given = 0 ; @@ -137,13 +167,22 @@ void clear_given (struct gengetopt_args_info *args_inf args_info->p_angle_given = 0 ; args_info->hxy_given = 0 ; args_info->rho_r_given = 0 ; + args_info->angle_r_given = 0 ; args_info->hullvol_given = 0 ; + args_info->rodlength_given = 0 ; + args_info->tet_param_given = 0 ; + args_info->tet_param_z_given = 0 ; + args_info->rnemdz_given = 0 ; + args_info->rnemdr_given = 0 ; + args_info->rnemdrt_given = 0 ; + args_info->uFreqMap_given = 0 ; args_info->staticProps_group_counter = 0 ; } static void clear_args (struct gengetopt_args_info *args_info) { + FIX_UNUSED (args_info); args_info->input_arg = NULL; args_info->input_orig = NULL; args_info->output_arg = NULL; @@ -160,8 +199,10 @@ void clear_args (struct gengetopt_args_info *args_info args_info->nbins_z_orig = NULL; args_info->nanglebins_arg = 50; args_info->nanglebins_orig = NULL; - args_info->length_orig = NULL; args_info->rcut_orig = NULL; + args_info->dz_orig = NULL; + args_info->length_orig = NULL; + args_info->zlength_orig = NULL; args_info->zoffset_arg = 0; args_info->zoffset_orig = NULL; args_info->sele1_arg = NULL; @@ -174,6 +215,8 @@ void clear_args (struct gengetopt_args_info *args_info args_info->refsele_orig = NULL; args_info->comsele_arg = NULL; args_info->comsele_orig = NULL; + args_info->seleoffset_orig = NULL; + args_info->seleoffset2_orig = NULL; args_info->molname_arg = NULL; args_info->molname_orig = NULL; args_info->begin_orig = NULL; @@ -197,44 +240,61 @@ void init_args_info(struct gengetopt_args_info *args_i args_info->nbins_y_help = gengetopt_args_info_help[7] ; args_info->nbins_z_help = gengetopt_args_info_help[8] ; args_info->nanglebins_help = gengetopt_args_info_help[9] ; - args_info->length_help = gengetopt_args_info_help[10] ; - args_info->rcut_help = gengetopt_args_info_help[11] ; - args_info->zoffset_help = gengetopt_args_info_help[12] ; - args_info->sele1_help = gengetopt_args_info_help[13] ; - args_info->sele2_help = gengetopt_args_info_help[14] ; - args_info->sele3_help = gengetopt_args_info_help[15] ; - args_info->refsele_help = gengetopt_args_info_help[16] ; - args_info->comsele_help = gengetopt_args_info_help[17] ; - args_info->molname_help = gengetopt_args_info_help[18] ; - args_info->begin_help = gengetopt_args_info_help[19] ; - args_info->end_help = gengetopt_args_info_help[20] ; - args_info->radius_help = gengetopt_args_info_help[21] ; - args_info->bo_help = gengetopt_args_info_help[23] ; - args_info->bor_help = gengetopt_args_info_help[24] ; - args_info->bad_help = gengetopt_args_info_help[25] ; - args_info->gofr_help = gengetopt_args_info_help[26] ; - args_info->gofz_help = gengetopt_args_info_help[27] ; - args_info->r_theta_help = gengetopt_args_info_help[28] ; - args_info->r_omega_help = gengetopt_args_info_help[29] ; - args_info->r_z_help = gengetopt_args_info_help[30] ; - args_info->theta_omega_help = gengetopt_args_info_help[31] ; - args_info->gxyz_help = gengetopt_args_info_help[32] ; - args_info->p2_help = gengetopt_args_info_help[33] ; - args_info->rp2_help = gengetopt_args_info_help[34] ; - args_info->scd_help = gengetopt_args_info_help[35] ; - args_info->density_help = gengetopt_args_info_help[36] ; - args_info->slab_density_help = gengetopt_args_info_help[37] ; - args_info->p_angle_help = gengetopt_args_info_help[38] ; - args_info->hxy_help = gengetopt_args_info_help[39] ; - args_info->rho_r_help = gengetopt_args_info_help[40] ; - args_info->hullvol_help = gengetopt_args_info_help[41] ; + args_info->rcut_help = gengetopt_args_info_help[10] ; + args_info->dz_help = gengetopt_args_info_help[11] ; + args_info->length_help = gengetopt_args_info_help[12] ; + args_info->zlength_help = gengetopt_args_info_help[13] ; + args_info->zoffset_help = gengetopt_args_info_help[14] ; + args_info->sele1_help = gengetopt_args_info_help[15] ; + args_info->sele2_help = gengetopt_args_info_help[16] ; + args_info->sele3_help = gengetopt_args_info_help[17] ; + args_info->refsele_help = gengetopt_args_info_help[18] ; + args_info->comsele_help = gengetopt_args_info_help[19] ; + args_info->seleoffset_help = gengetopt_args_info_help[20] ; + args_info->seleoffset2_help = gengetopt_args_info_help[21] ; + args_info->molname_help = gengetopt_args_info_help[22] ; + args_info->begin_help = gengetopt_args_info_help[23] ; + args_info->end_help = gengetopt_args_info_help[24] ; + args_info->radius_help = gengetopt_args_info_help[25] ; + args_info->bo_help = gengetopt_args_info_help[27] ; + args_info->ior_help = gengetopt_args_info_help[28] ; + args_info->for_help = gengetopt_args_info_help[29] ; + args_info->bad_help = gengetopt_args_info_help[30] ; + args_info->count_help = gengetopt_args_info_help[31] ; + args_info->gofr_help = gengetopt_args_info_help[32] ; + args_info->gofz_help = gengetopt_args_info_help[33] ; + args_info->r_theta_help = gengetopt_args_info_help[34] ; + args_info->r_omega_help = gengetopt_args_info_help[35] ; + args_info->r_z_help = gengetopt_args_info_help[36] ; + args_info->theta_omega_help = gengetopt_args_info_help[37] ; + args_info->gxyz_help = gengetopt_args_info_help[38] ; + args_info->twodgofr_help = gengetopt_args_info_help[39] ; + args_info->p2_help = gengetopt_args_info_help[40] ; + args_info->rp2_help = gengetopt_args_info_help[41] ; + args_info->scd_help = gengetopt_args_info_help[42] ; + args_info->density_help = gengetopt_args_info_help[43] ; + args_info->slab_density_help = gengetopt_args_info_help[44] ; + args_info->p_angle_help = gengetopt_args_info_help[45] ; + args_info->hxy_help = gengetopt_args_info_help[46] ; + args_info->rho_r_help = gengetopt_args_info_help[47] ; + args_info->angle_r_help = gengetopt_args_info_help[48] ; + args_info->hullvol_help = gengetopt_args_info_help[49] ; + args_info->rodlength_help = gengetopt_args_info_help[50] ; + args_info->tet_param_help = gengetopt_args_info_help[51] ; + args_info->tet_param_z_help = gengetopt_args_info_help[52] ; + args_info->rnemdz_help = gengetopt_args_info_help[53] ; + args_info->rnemdr_help = gengetopt_args_info_help[54] ; + args_info->rnemdrt_help = gengetopt_args_info_help[55] ; + args_info->uFreqMap_help = gengetopt_args_info_help[56] ; } void cmdline_parser_print_version (void) { - printf ("%s %s\n", CMDLINE_PARSER_PACKAGE, CMDLINE_PARSER_VERSION); + printf ("%s %s\n", + (strlen(CMDLINE_PARSER_PACKAGE_NAME) ? CMDLINE_PARSER_PACKAGE_NAME : CMDLINE_PARSER_PACKAGE), + CMDLINE_PARSER_VERSION); } static void print_help_common(void) { @@ -249,7 +309,7 @@ static void print_help_common(void) { printf("\n"); if (strlen(gengetopt_args_info_description) > 0) - printf("%s\n", gengetopt_args_info_description); + printf("%s\n\n", gengetopt_args_info_description); } void @@ -268,7 +328,7 @@ cmdline_parser_init (struct gengetopt_args_info *args_ clear_args (args_info); init_args_info (args_info); - args_info->inputs = NULL; + args_info->inputs = 0; args_info->inputs_num = 0; } @@ -319,8 +379,10 @@ cmdline_parser_release (struct gengetopt_args_info *ar free_string_field (&(args_info->nbins_y_orig)); free_string_field (&(args_info->nbins_z_orig)); free_string_field (&(args_info->nanglebins_orig)); - free_string_field (&(args_info->length_orig)); free_string_field (&(args_info->rcut_orig)); + free_string_field (&(args_info->dz_orig)); + free_string_field (&(args_info->length_orig)); + free_string_field (&(args_info->zlength_orig)); free_string_field (&(args_info->zoffset_orig)); free_string_field (&(args_info->sele1_arg)); free_string_field (&(args_info->sele1_orig)); @@ -332,6 +394,8 @@ cmdline_parser_release (struct gengetopt_args_info *ar free_string_field (&(args_info->refsele_orig)); free_string_field (&(args_info->comsele_arg)); free_string_field (&(args_info->comsele_orig)); + free_string_field (&(args_info->seleoffset_orig)); + free_string_field (&(args_info->seleoffset2_orig)); free_string_field (&(args_info->molname_arg)); free_string_field (&(args_info->molname_orig)); free_string_field (&(args_info->begin_orig)); @@ -350,8 +414,9 @@ static void static void -write_into_file(FILE *outfile, const char *opt, const char *arg, char *values[]) +write_into_file(FILE *outfile, const char *opt, const char *arg, const char *values[]) { + FIX_UNUSED (values); if (arg) { fprintf(outfile, "%s=\"%s\"\n", opt, arg); } else { @@ -391,10 +456,14 @@ cmdline_parser_dump(FILE *outfile, struct gengetopt_ar write_into_file(outfile, "nbins_z", args_info->nbins_z_orig, 0); if (args_info->nanglebins_given) write_into_file(outfile, "nanglebins", args_info->nanglebins_orig, 0); - if (args_info->length_given) - write_into_file(outfile, "length", args_info->length_orig, 0); if (args_info->rcut_given) write_into_file(outfile, "rcut", args_info->rcut_orig, 0); + if (args_info->dz_given) + write_into_file(outfile, "dz", args_info->dz_orig, 0); + if (args_info->length_given) + write_into_file(outfile, "length", args_info->length_orig, 0); + if (args_info->zlength_given) + write_into_file(outfile, "zlength", args_info->zlength_orig, 0); if (args_info->zoffset_given) write_into_file(outfile, "zoffset", args_info->zoffset_orig, 0); if (args_info->sele1_given) @@ -407,6 +476,10 @@ cmdline_parser_dump(FILE *outfile, struct gengetopt_ar write_into_file(outfile, "refsele", args_info->refsele_orig, 0); if (args_info->comsele_given) write_into_file(outfile, "comsele", args_info->comsele_orig, 0); + if (args_info->seleoffset_given) + write_into_file(outfile, "seleoffset", args_info->seleoffset_orig, 0); + if (args_info->seleoffset2_given) + write_into_file(outfile, "seleoffset2", args_info->seleoffset2_orig, 0); if (args_info->molname_given) write_into_file(outfile, "molname", args_info->molname_orig, 0); if (args_info->begin_given) @@ -417,10 +490,14 @@ cmdline_parser_dump(FILE *outfile, struct gengetopt_ar write_into_file(outfile, "radius", args_info->radius_orig, 0); if (args_info->bo_given) write_into_file(outfile, "bo", 0, 0 ); - if (args_info->bor_given) - write_into_file(outfile, "bor", 0, 0 ); + if (args_info->ior_given) + write_into_file(outfile, "ior", 0, 0 ); + if (args_info->for_given) + write_into_file(outfile, "for", 0, 0 ); if (args_info->bad_given) write_into_file(outfile, "bad", 0, 0 ); + if (args_info->count_given) + write_into_file(outfile, "count", 0, 0 ); if (args_info->gofr_given) write_into_file(outfile, "gofr", 0, 0 ); if (args_info->gofz_given) @@ -435,6 +512,8 @@ cmdline_parser_dump(FILE *outfile, struct gengetopt_ar write_into_file(outfile, "theta_omega", 0, 0 ); if (args_info->gxyz_given) write_into_file(outfile, "gxyz", 0, 0 ); + if (args_info->twodgofr_given) + write_into_file(outfile, "twodgofr", 0, 0 ); if (args_info->p2_given) write_into_file(outfile, "p2", 0, 0 ); if (args_info->rp2_given) @@ -451,8 +530,24 @@ cmdline_parser_dump(FILE *outfile, struct gengetopt_ar write_into_file(outfile, "hxy", 0, 0 ); if (args_info->rho_r_given) write_into_file(outfile, "rho_r", 0, 0 ); + if (args_info->angle_r_given) + write_into_file(outfile, "angle_r", 0, 0 ); if (args_info->hullvol_given) write_into_file(outfile, "hullvol", 0, 0 ); + if (args_info->rodlength_given) + write_into_file(outfile, "rodlength", 0, 0 ); + if (args_info->tet_param_given) + write_into_file(outfile, "tet_param", 0, 0 ); + if (args_info->tet_param_z_given) + write_into_file(outfile, "tet_param_z", 0, 0 ); + if (args_info->rnemdz_given) + write_into_file(outfile, "rnemdz", 0, 0 ); + if (args_info->rnemdr_given) + write_into_file(outfile, "rnemdr", 0, 0 ); + if (args_info->rnemdrt_given) + write_into_file(outfile, "rnemdrt", 0, 0 ); + if (args_info->uFreqMap_given) + write_into_file(outfile, "uFreqMap", 0, 0 ); i = EXIT_SUCCESS; @@ -489,7 +584,7 @@ gengetopt_strdup (const char *s) char * gengetopt_strdup (const char *s) { - char *result = NULL; + char *result = 0; if (!s) return result; @@ -507,8 +602,10 @@ reset_group_staticProps(struct gengetopt_args_info *ar return; args_info->bo_given = 0 ; - args_info->bor_given = 0 ; + args_info->ior_given = 0 ; + args_info->for_given = 0 ; args_info->bad_given = 0 ; + args_info->count_given = 0 ; args_info->gofr_given = 0 ; args_info->gofz_given = 0 ; args_info->r_theta_given = 0 ; @@ -516,6 +613,7 @@ reset_group_staticProps(struct gengetopt_args_info *ar args_info->r_z_given = 0 ; args_info->theta_omega_given = 0 ; args_info->gxyz_given = 0 ; + args_info->twodgofr_given = 0 ; args_info->p2_given = 0 ; args_info->rp2_given = 0 ; args_info->scd_given = 0 ; @@ -524,23 +622,31 @@ reset_group_staticProps(struct gengetopt_args_info *ar args_info->p_angle_given = 0 ; args_info->hxy_given = 0 ; args_info->rho_r_given = 0 ; + args_info->angle_r_given = 0 ; args_info->hullvol_given = 0 ; + args_info->rodlength_given = 0 ; + args_info->tet_param_given = 0 ; + args_info->tet_param_z_given = 0 ; + args_info->rnemdz_given = 0 ; + args_info->rnemdr_given = 0 ; + args_info->rnemdrt_given = 0 ; + args_info->uFreqMap_given = 0 ; args_info->staticProps_group_counter = 0; } int -cmdline_parser (int argc, char * const *argv, struct gengetopt_args_info *args_info) +cmdline_parser (int argc, char **argv, struct gengetopt_args_info *args_info) { return cmdline_parser2 (argc, argv, args_info, 0, 1, 1); } int -cmdline_parser_ext (int argc, char * const *argv, struct gengetopt_args_info *args_info, +cmdline_parser_ext (int argc, char **argv, struct gengetopt_args_info *args_info, struct cmdline_parser_params *params) { int result; - result = cmdline_parser_internal (argc, argv, args_info, params, NULL); + result = cmdline_parser_internal (argc, argv, args_info, params, 0); if (result == EXIT_FAILURE) { @@ -552,7 +658,7 @@ int } int -cmdline_parser2 (int argc, char * const *argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required) +cmdline_parser2 (int argc, char **argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required) { int result; struct cmdline_parser_params params; @@ -563,7 +669,7 @@ cmdline_parser2 (int argc, char * const *argv, struct params.check_ambiguity = 0; params.print_errors = 1; - result = cmdline_parser_internal (argc, argv, args_info, ¶ms, NULL); + result = cmdline_parser_internal (argc, argv, args_info, ¶ms, 0); if (result == EXIT_FAILURE) { @@ -579,7 +685,7 @@ cmdline_parser_required (struct gengetopt_args_info *a { int result = EXIT_SUCCESS; - if (cmdline_parser_required2(args_info, prog_name, NULL) > 0) + if (cmdline_parser_required2(args_info, prog_name, 0) > 0) result = EXIT_FAILURE; if (result == EXIT_FAILURE) @@ -595,6 +701,7 @@ cmdline_parser_required2 (struct gengetopt_args_info * cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error) { int error = 0; + FIX_UNUSED (additional_error); /* checks for required options */ if (! args_info->input_given) @@ -605,7 +712,7 @@ cmdline_parser_required2 (struct gengetopt_args_info * if (args_info->staticProps_group_counter == 0) { - fprintf (stderr, "%s: %d options of group staticProps were given. One is required.%s\n", prog_name, args_info->staticProps_group_counter, (additional_error ? additional_error : "")); + fprintf (stderr, "%s: %d options of group staticProps were given. One is required%s.\n", prog_name, args_info->staticProps_group_counter, (additional_error ? additional_error : "")); error = 1; } @@ -639,7 +746,8 @@ int update_arg(void *field, char **orig_field, static int update_arg(void *field, char **orig_field, unsigned int *field_given, unsigned int *prev_given, - char *value, char *possible_values[], const char *default_value, + char *value, const char *possible_values[], + const char *default_value, cmdline_parser_arg_type arg_type, int check_ambiguity, int override, int no_free, int multiple_option, @@ -650,6 +758,7 @@ int update_arg(void *field, char **orig_field, const char *val = value; int found; char **string_field; + FIX_UNUSED (field); stop_char = 0; found = 0; @@ -667,6 +776,7 @@ int update_arg(void *field, char **orig_field, return 1; /* failure */ } + FIX_UNUSED (default_value); if (field_given && *field_given && ! override) return 0; @@ -730,7 +840,8 @@ int int -cmdline_parser_internal (int argc, char * const *argv, struct gengetopt_args_info *args_info, +cmdline_parser_internal ( + int argc, char **argv, struct gengetopt_args_info *args_info, struct cmdline_parser_params *params, const char *additional_error) { int c; /* Character of the parsed option. */ @@ -775,21 +886,27 @@ cmdline_parser_internal (int argc, char * const *argv, { "nbins_y", 1, NULL, 'y' }, { "nbins_z", 1, NULL, 0 }, { "nanglebins", 1, NULL, 'a' }, - { "length", 1, NULL, 0 }, { "rcut", 1, NULL, 'c' }, + { "dz", 1, NULL, 0 }, + { "length", 1, NULL, 0 }, + { "zlength", 1, NULL, 0 }, { "zoffset", 1, NULL, 'z' }, { "sele1", 1, NULL, 0 }, { "sele2", 1, NULL, 0 }, { "sele3", 1, NULL, 0 }, { "refsele", 1, NULL, 0 }, { "comsele", 1, NULL, 0 }, + { "seleoffset", 1, NULL, 0 }, + { "seleoffset2", 1, NULL, 0 }, { "molname", 1, NULL, 0 }, { "begin", 1, NULL, 0 }, { "end", 1, NULL, 0 }, { "radius", 1, NULL, 0 }, { "bo", 0, NULL, 0 }, - { "bor", 0, NULL, 0 }, + { "ior", 0, NULL, 0 }, + { "for", 0, NULL, 0 }, { "bad", 0, NULL, 0 }, + { "count", 0, NULL, 0 }, { "gofr", 0, NULL, 'g' }, { "gofz", 0, NULL, 0 }, { "r_theta", 0, NULL, 0 }, @@ -797,6 +914,7 @@ cmdline_parser_internal (int argc, char * const *argv, { "r_z", 0, NULL, 0 }, { "theta_omega", 0, NULL, 0 }, { "gxyz", 0, NULL, 0 }, + { "twodgofr", 0, NULL, 0 }, { "p2", 0, NULL, 'p' }, { "rp2", 0, NULL, 0 }, { "scd", 0, NULL, 's' }, @@ -805,11 +923,19 @@ cmdline_parser_internal (int argc, char * const *argv, { "p_angle", 0, NULL, 0 }, { "hxy", 0, NULL, 0 }, { "rho_r", 0, NULL, 0 }, + { "angle_r", 0, NULL, 0 }, { "hullvol", 0, NULL, 0 }, - { NULL, 0, NULL, 0 } + { "rodlength", 0, NULL, 0 }, + { "tet_param", 0, NULL, 'Q' }, + { "tet_param_z", 0, NULL, 0 }, + { "rnemdz", 0, NULL, 0 }, + { "rnemdr", 0, NULL, 0 }, + { "rnemdrt", 0, NULL, 0 }, + { "uFreqMap", 0, NULL, 0 }, + { 0, 0, 0, 0 } }; - c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:c:z:gpsd", long_options, &option_index); + c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:c:z:gpsdQ", long_options, &option_index); if (c == -1) break; /* Exit from `while (1)' loop. */ @@ -948,7 +1074,7 @@ cmdline_parser_internal (int argc, char * const *argv, goto failure; break; - case 'p': /* p2 order parameter (--sele1 and --sele2 must be specified). */ + case 'p': /* p2 order parameter (--sele1 must be specified, --sele2 is optional). */ if (args_info->staticProps_group_counter && override) reset_group_staticProps (args_info); @@ -993,6 +1119,21 @@ cmdline_parser_internal (int argc, char * const *argv, goto failure; break; + case 'Q': /* tetrahedrality order parameter (Qk). */ + + if (args_info->staticProps_group_counter && override) + reset_group_staticProps (args_info); + args_info->staticProps_group_counter += 1; + + if (update_arg( 0 , + 0 , &(args_info->tet_param_given), + &(local_args_info.tet_param_given), optarg, 0, 0, ARG_NO, + check_ambiguity, override, 0, 0, + "tet_param", 'Q', + additional_error)) + goto failure; + + break; case 0: /* Long option with no short option */ /* number of bins in z axis. */ @@ -1009,6 +1150,20 @@ cmdline_parser_internal (int argc, char * const *argv, goto failure; } + /* slab width (dz). */ + else if (strcmp (long_options[option_index].name, "dz") == 0) + { + + + if (update_arg( (void *)&(args_info->dz_arg), + &(args_info->dz_orig), &(args_info->dz_given), + &(local_args_info.dz_given), optarg, 0, 0, ARG_DOUBLE, + check_ambiguity, override, 0, 0, + "dz", '-', + additional_error)) + goto failure; + + } /* maximum length (Defaults to 1/2 smallest length of first frame). */ else if (strcmp (long_options[option_index].name, "length") == 0) { @@ -1023,6 +1178,20 @@ cmdline_parser_internal (int argc, char * const *argv, goto failure; } + /* maximum length (Defaults to 1/2 smallest length of first frame). */ + else if (strcmp (long_options[option_index].name, "zlength") == 0) + { + + + if (update_arg( (void *)&(args_info->zlength_arg), + &(args_info->zlength_orig), &(args_info->zlength_given), + &(local_args_info.zlength_given), optarg, 0, 0, ARG_DOUBLE, + check_ambiguity, override, 0, 0, + "zlength", '-', + additional_error)) + goto failure; + + } /* select the first stuntdouble set. */ else if (strcmp (long_options[option_index].name, "sele1") == 0) { @@ -1089,6 +1258,34 @@ cmdline_parser_internal (int argc, char * const *argv, &(local_args_info.comsele_given), optarg, 0, 0, ARG_STRING, check_ambiguity, override, 0, 0, "comsele", '-', + additional_error)) + goto failure; + + } + /* global index offset for a second object (used to define a vector between sites in molecule). */ + else if (strcmp (long_options[option_index].name, "seleoffset") == 0) + { + + + if (update_arg( (void *)&(args_info->seleoffset_arg), + &(args_info->seleoffset_orig), &(args_info->seleoffset_given), + &(local_args_info.seleoffset_given), optarg, 0, 0, ARG_INT, + check_ambiguity, override, 0, 0, + "seleoffset", '-', + additional_error)) + goto failure; + + } + /* global index offset for a third object (used to define a vector between sites in molecule). */ + else if (strcmp (long_options[option_index].name, "seleoffset2") == 0) + { + + + if (update_arg( (void *)&(args_info->seleoffset2_arg), + &(args_info->seleoffset2_orig), &(args_info->seleoffset2_given), + &(local_args_info.seleoffset2_given), optarg, 0, 0, ARG_INT, + check_ambiguity, override, 0, 0, + "seleoffset2", '-', additional_error)) goto failure; @@ -1166,8 +1363,8 @@ cmdline_parser_internal (int argc, char * const *argv, goto failure; } - /* bond order parameter as a function of radius (--rcut must be specified). */ - else if (strcmp (long_options[option_index].name, "bor") == 0) + /* icosahedral bond order parameter as a function of radius (--rcut must be specified). */ + else if (strcmp (long_options[option_index].name, "ior") == 0) { if (args_info->staticProps_group_counter && override) @@ -1175,14 +1372,31 @@ cmdline_parser_internal (int argc, char * const *argv, args_info->staticProps_group_counter += 1; if (update_arg( 0 , - 0 , &(args_info->bor_given), - &(local_args_info.bor_given), optarg, 0, 0, ARG_NO, + 0 , &(args_info->ior_given), + &(local_args_info.ior_given), optarg, 0, 0, ARG_NO, check_ambiguity, override, 0, 0, - "bor", '-', + "ior", '-', additional_error)) goto failure; } + /* FCC bond order parameter as a function of radius (--rcut must be specified). */ + else if (strcmp (long_options[option_index].name, "for") == 0) + { + + if (args_info->staticProps_group_counter && override) + reset_group_staticProps (args_info); + args_info->staticProps_group_counter += 1; + + if (update_arg( 0 , + 0 , &(args_info->for_given), + &(local_args_info.for_given), optarg, 0, 0, ARG_NO, + check_ambiguity, override, 0, 0, + "for", '-', + additional_error)) + goto failure; + + } /* N(theta) bond angle density within (--rcut must be specified). */ else if (strcmp (long_options[option_index].name, "bad") == 0) { @@ -1200,6 +1414,23 @@ cmdline_parser_internal (int argc, char * const *argv, goto failure; } + /* count of molecules matching selection criteria (and associated statistics). */ + else if (strcmp (long_options[option_index].name, "count") == 0) + { + + if (args_info->staticProps_group_counter && override) + reset_group_staticProps (args_info); + args_info->staticProps_group_counter += 1; + + if (update_arg( 0 , + 0 , &(args_info->count_given), + &(local_args_info.count_given), optarg, 0, 0, ARG_NO, + check_ambiguity, override, 0, 0, + "count", '-', + additional_error)) + goto failure; + + } /* g(z). */ else if (strcmp (long_options[option_index].name, "gofz") == 0) { @@ -1298,6 +1529,23 @@ cmdline_parser_internal (int argc, char * const *argv, &(local_args_info.gxyz_given), optarg, 0, 0, ARG_NO, check_ambiguity, override, 0, 0, "gxyz", '-', + additional_error)) + goto failure; + + } + /* 2D g(r) (Slab width --dz must be specified). */ + else if (strcmp (long_options[option_index].name, "twodgofr") == 0) + { + + if (args_info->staticProps_group_counter && override) + reset_group_staticProps (args_info); + args_info->staticProps_group_counter += 1; + + if (update_arg( 0 , + 0 , &(args_info->twodgofr_given), + &(local_args_info.twodgofr_given), optarg, 0, 0, ARG_NO, + check_ambiguity, override, 0, 0, + "twodgofr", '-', additional_error)) goto failure; @@ -1336,7 +1584,7 @@ cmdline_parser_internal (int argc, char * const *argv, goto failure; } - /* p(cos(theta)). */ + /* p(cos(theta)) (--sele1 must be specified, --sele2 is optional). */ else if (strcmp (long_options[option_index].name, "p_angle") == 0) { @@ -1387,6 +1635,23 @@ cmdline_parser_internal (int argc, char * const *argv, goto failure; } + /* angle of R. */ + else if (strcmp (long_options[option_index].name, "angle_r") == 0) + { + + if (args_info->staticProps_group_counter && override) + reset_group_staticProps (args_info); + args_info->staticProps_group_counter += 1; + + if (update_arg( 0 , + 0 , &(args_info->angle_r_given), + &(local_args_info.angle_r_given), optarg, 0, 0, ARG_NO, + check_ambiguity, override, 0, 0, + "angle_r", '-', + additional_error)) + goto failure; + + } /* hull volume of nanoparticle. */ else if (strcmp (long_options[option_index].name, "hullvol") == 0) { @@ -1404,7 +1669,109 @@ cmdline_parser_internal (int argc, char * const *argv, goto failure; } + /* length of nanorod. */ + else if (strcmp (long_options[option_index].name, "rodlength") == 0) + { + if (args_info->staticProps_group_counter && override) + reset_group_staticProps (args_info); + args_info->staticProps_group_counter += 1; + + if (update_arg( 0 , + 0 , &(args_info->rodlength_given), + &(local_args_info.rodlength_given), optarg, 0, 0, ARG_NO, + check_ambiguity, override, 0, 0, + "rodlength", '-', + additional_error)) + goto failure; + + } + /* spatially-resolved tetrahedrality order parameter Qk(z). */ + else if (strcmp (long_options[option_index].name, "tet_param_z") == 0) + { + + if (args_info->staticProps_group_counter && override) + reset_group_staticProps (args_info); + args_info->staticProps_group_counter += 1; + + if (update_arg( 0 , + 0 , &(args_info->tet_param_z_given), + &(local_args_info.tet_param_z_given), optarg, 0, 0, ARG_NO, + check_ambiguity, override, 0, 0, + "tet_param_z", '-', + additional_error)) + goto failure; + + } + /* slab-resolved RNEMD statistics (temperature, density, velocity). */ + else if (strcmp (long_options[option_index].name, "rnemdz") == 0) + { + + if (args_info->staticProps_group_counter && override) + reset_group_staticProps (args_info); + args_info->staticProps_group_counter += 1; + + if (update_arg( 0 , + 0 , &(args_info->rnemdz_given), + &(local_args_info.rnemdz_given), optarg, 0, 0, ARG_NO, + check_ambiguity, override, 0, 0, + "rnemdz", '-', + additional_error)) + goto failure; + + } + /* shell-resolved RNEMD statistics (temperature, density, angular velocity). */ + else if (strcmp (long_options[option_index].name, "rnemdr") == 0) + { + + if (args_info->staticProps_group_counter && override) + reset_group_staticProps (args_info); + args_info->staticProps_group_counter += 1; + + if (update_arg( 0 , + 0 , &(args_info->rnemdr_given), + &(local_args_info.rnemdr_given), optarg, 0, 0, ARG_NO, + check_ambiguity, override, 0, 0, + "rnemdr", '-', + additional_error)) + goto failure; + + } + /* shell and angle-resolved RNEMD statistics (temperature, density, angular velocity). */ + else if (strcmp (long_options[option_index].name, "rnemdrt") == 0) + { + + if (args_info->staticProps_group_counter && override) + reset_group_staticProps (args_info); + args_info->staticProps_group_counter += 1; + + if (update_arg( 0 , + 0 , &(args_info->rnemdrt_given), + &(local_args_info.rnemdrt_given), optarg, 0, 0, ARG_NO, + check_ambiguity, override, 0, 0, + "rnemdrt", '-', + additional_error)) + goto failure; + + } + /* electrostatic potential to frequency map based on the Cho nitrile fits. */ + else if (strcmp (long_options[option_index].name, "uFreqMap") == 0) + { + + if (args_info->staticProps_group_counter && override) + reset_group_staticProps (args_info); + args_info->staticProps_group_counter += 1; + + if (update_arg( 0 , + 0 , &(args_info->uFreqMap_given), + &(local_args_info.uFreqMap_given), optarg, 0, 0, ARG_NO, + check_ambiguity, override, 0, 0, + "uFreqMap", '-', + additional_error)) + goto failure; + + } + break; case '?': /* Invalid option. */ /* `getopt_long' already printed an error message. */ @@ -1418,7 +1785,7 @@ cmdline_parser_internal (int argc, char * const *argv, if (args_info->staticProps_group_counter > 1) { - fprintf (stderr, "%s: %d options of group staticProps were given. One is required.%s\n", argv[0], args_info->staticProps_group_counter, (additional_error ? additional_error : "")); + fprintf (stderr, "%s: %d options of group staticProps were given. One is required%s.\n", argv[0], args_info->staticProps_group_counter, (additional_error ? additional_error : "")); error = 1; }