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root/OpenMD/trunk/src/applications/dynamicProps/DynamicPropsCmd.cpp
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Comparing trunk/src/applications/dynamicProps/DynamicPropsCmd.cpp (file contents):
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC vs.
Revision 2024 by gezelter, Thu Oct 16 19:13:51 2014 UTC

# Line 43 | Line 43 | const char *gengetopt_args_info_help[] = {
43    "      --sele1=selection script  select first stuntdouble set",
44    "      --sele2=selection script  select second stuntdouble set (if sele2 is not \n                                  set, use script from sele1)",
45    "      --order=INT               Lengendre Polynomial Order",
46 +  "  -z, --nzbins=INT              Number of Z bins  (default=`100')",
47    "  -m, --memory=memory specification\n                                Available memory (defaults to 2G)  \n                                  (default=`2G')",
48    "\n Group: dynamicProps\n   an option of this group is required",
49    "  -s, --selecorr                selection correlation function",
50    "  -r, --rcorr                   rmsd",
51    "  -v, --vcorr                   velocity correlation function",
52 +  "      --vcorrZ                  velocity correlation function along z-axis",
53 +  "      --vcorrR                  velocity correlation function projected \n                                  radially",
54    "  -d, --dcorr                   dipole correlation function",
55    "  -l, --lcorr                   Lengendre correlation function",
56 +  "      --lcorrZ                  Lengendre correlation function binned by Z",
57 +  "      --cohZ                    Lengendre correlation function for OH bond \n                                  vectors binned by Z",
58    "  -M, --sdcorr                  System dipole correlation function",
59    "      --r_rcorr                 Radial rmsd",
60    "      --thetacorr               Angular rmsd",
# Line 57 | Line 62 | const char *gengetopt_args_info_help[] = {
62    "      --helfandEcorr            Helfand moment for thermal conductvity",
63    "  -p, --momentum                Helfand momentum for viscosity",
64    "      --stresscorr              Stress tensor correlation function",
65 +  "  -b, --bondcorr                Bond extension correlation function",
66 +  "  -f, --freqfluccorr            Frequency Fluctuation correlation function",
67      0
68   };
69  
# Line 90 | Line 97 | void clear_given (struct gengetopt_args_info *args_inf
97    args_info->sele1_given = 0 ;
98    args_info->sele2_given = 0 ;
99    args_info->order_given = 0 ;
100 +  args_info->nzbins_given = 0 ;
101    args_info->memory_given = 0 ;
102    args_info->selecorr_given = 0 ;
103    args_info->rcorr_given = 0 ;
104    args_info->vcorr_given = 0 ;
105 +  args_info->vcorrZ_given = 0 ;
106 +  args_info->vcorrR_given = 0 ;
107    args_info->dcorr_given = 0 ;
108    args_info->lcorr_given = 0 ;
109 +  args_info->lcorrZ_given = 0 ;
110 +  args_info->cohZ_given = 0 ;
111    args_info->sdcorr_given = 0 ;
112    args_info->r_rcorr_given = 0 ;
113    args_info->thetacorr_given = 0 ;
# Line 103 | Line 115 | void clear_given (struct gengetopt_args_info *args_inf
115    args_info->helfandEcorr_given = 0 ;
116    args_info->momentum_given = 0 ;
117    args_info->stresscorr_given = 0 ;
118 +  args_info->bondcorr_given = 0 ;
119 +  args_info->freqfluccorr_given = 0 ;
120    args_info->dynamicProps_group_counter = 0 ;
121   }
122  
# Line 119 | Line 133 | void clear_args (struct gengetopt_args_info *args_info
133    args_info->sele2_arg = NULL;
134    args_info->sele2_orig = NULL;
135    args_info->order_orig = NULL;
136 +  args_info->nzbins_arg = 100;
137 +  args_info->nzbins_orig = NULL;
138    args_info->memory_arg = gengetopt_strdup ("2G");
139    args_info->memory_orig = NULL;
140    
# Line 136 | Line 152 | void init_args_info(struct gengetopt_args_info *args_i
152    args_info->sele1_help = gengetopt_args_info_help[4] ;
153    args_info->sele2_help = gengetopt_args_info_help[5] ;
154    args_info->order_help = gengetopt_args_info_help[6] ;
155 <  args_info->memory_help = gengetopt_args_info_help[7] ;
156 <  args_info->selecorr_help = gengetopt_args_info_help[9] ;
157 <  args_info->rcorr_help = gengetopt_args_info_help[10] ;
158 <  args_info->vcorr_help = gengetopt_args_info_help[11] ;
159 <  args_info->dcorr_help = gengetopt_args_info_help[12] ;
160 <  args_info->lcorr_help = gengetopt_args_info_help[13] ;
161 <  args_info->sdcorr_help = gengetopt_args_info_help[14] ;
162 <  args_info->r_rcorr_help = gengetopt_args_info_help[15] ;
163 <  args_info->thetacorr_help = gengetopt_args_info_help[16] ;
164 <  args_info->drcorr_help = gengetopt_args_info_help[17] ;
165 <  args_info->helfandEcorr_help = gengetopt_args_info_help[18] ;
166 <  args_info->momentum_help = gengetopt_args_info_help[19] ;
167 <  args_info->stresscorr_help = gengetopt_args_info_help[20] ;
155 >  args_info->nzbins_help = gengetopt_args_info_help[7] ;
156 >  args_info->memory_help = gengetopt_args_info_help[8] ;
157 >  args_info->selecorr_help = gengetopt_args_info_help[10] ;
158 >  args_info->rcorr_help = gengetopt_args_info_help[11] ;
159 >  args_info->vcorr_help = gengetopt_args_info_help[12] ;
160 >  args_info->vcorrZ_help = gengetopt_args_info_help[13] ;
161 >  args_info->vcorrR_help = gengetopt_args_info_help[14] ;
162 >  args_info->dcorr_help = gengetopt_args_info_help[15] ;
163 >  args_info->lcorr_help = gengetopt_args_info_help[16] ;
164 >  args_info->lcorrZ_help = gengetopt_args_info_help[17] ;
165 >  args_info->cohZ_help = gengetopt_args_info_help[18] ;
166 >  args_info->sdcorr_help = gengetopt_args_info_help[19] ;
167 >  args_info->r_rcorr_help = gengetopt_args_info_help[20] ;
168 >  args_info->thetacorr_help = gengetopt_args_info_help[21] ;
169 >  args_info->drcorr_help = gengetopt_args_info_help[22] ;
170 >  args_info->helfandEcorr_help = gengetopt_args_info_help[23] ;
171 >  args_info->momentum_help = gengetopt_args_info_help[24] ;
172 >  args_info->stresscorr_help = gengetopt_args_info_help[25] ;
173 >  args_info->bondcorr_help = gengetopt_args_info_help[26] ;
174 >  args_info->freqfluccorr_help = gengetopt_args_info_help[27] ;
175    
176   }
177  
# Line 241 | Line 264 | cmdline_parser_release (struct gengetopt_args_info *ar
264    free_string_field (&(args_info->sele2_arg));
265    free_string_field (&(args_info->sele2_orig));
266    free_string_field (&(args_info->order_orig));
267 +  free_string_field (&(args_info->nzbins_orig));
268    free_string_field (&(args_info->memory_arg));
269    free_string_field (&(args_info->memory_orig));
270    
# Line 292 | Line 316 | cmdline_parser_dump(FILE *outfile, struct gengetopt_ar
316      write_into_file(outfile, "sele2", args_info->sele2_orig, 0);
317    if (args_info->order_given)
318      write_into_file(outfile, "order", args_info->order_orig, 0);
319 +  if (args_info->nzbins_given)
320 +    write_into_file(outfile, "nzbins", args_info->nzbins_orig, 0);
321    if (args_info->memory_given)
322      write_into_file(outfile, "memory", args_info->memory_orig, 0);
323    if (args_info->selecorr_given)
# Line 300 | Line 326 | cmdline_parser_dump(FILE *outfile, struct gengetopt_ar
326      write_into_file(outfile, "rcorr", 0, 0 );
327    if (args_info->vcorr_given)
328      write_into_file(outfile, "vcorr", 0, 0 );
329 +  if (args_info->vcorrZ_given)
330 +    write_into_file(outfile, "vcorrZ", 0, 0 );
331 +  if (args_info->vcorrR_given)
332 +    write_into_file(outfile, "vcorrR", 0, 0 );
333    if (args_info->dcorr_given)
334      write_into_file(outfile, "dcorr", 0, 0 );
335    if (args_info->lcorr_given)
336      write_into_file(outfile, "lcorr", 0, 0 );
337 +  if (args_info->lcorrZ_given)
338 +    write_into_file(outfile, "lcorrZ", 0, 0 );
339 +  if (args_info->cohZ_given)
340 +    write_into_file(outfile, "cohZ", 0, 0 );
341    if (args_info->sdcorr_given)
342      write_into_file(outfile, "sdcorr", 0, 0 );
343    if (args_info->r_rcorr_given)
# Line 318 | Line 352 | cmdline_parser_dump(FILE *outfile, struct gengetopt_ar
352      write_into_file(outfile, "momentum", 0, 0 );
353    if (args_info->stresscorr_given)
354      write_into_file(outfile, "stresscorr", 0, 0 );
355 +  if (args_info->bondcorr_given)
356 +    write_into_file(outfile, "bondcorr", 0, 0 );
357 +  if (args_info->freqfluccorr_given)
358 +    write_into_file(outfile, "freqfluccorr", 0, 0 );
359    
360  
361    i = EXIT_SUCCESS;
# Line 374 | Line 412 | reset_group_dynamicProps(struct gengetopt_args_info *a
412    args_info->selecorr_given = 0 ;
413    args_info->rcorr_given = 0 ;
414    args_info->vcorr_given = 0 ;
415 +  args_info->vcorrZ_given = 0 ;
416 +  args_info->vcorrR_given = 0 ;
417    args_info->dcorr_given = 0 ;
418    args_info->lcorr_given = 0 ;
419 +  args_info->lcorrZ_given = 0 ;
420 +  args_info->cohZ_given = 0 ;
421    args_info->sdcorr_given = 0 ;
422    args_info->r_rcorr_given = 0 ;
423    args_info->thetacorr_given = 0 ;
# Line 383 | Line 425 | reset_group_dynamicProps(struct gengetopt_args_info *a
425    args_info->helfandEcorr_given = 0 ;
426    args_info->momentum_given = 0 ;
427    args_info->stresscorr_given = 0 ;
428 +  args_info->bondcorr_given = 0 ;
429 +  args_info->freqfluccorr_given = 0 ;
430  
431    args_info->dynamicProps_group_counter = 0;
432   }
# Line 631 | Line 675 | cmdline_parser_internal (
675          { "sele1",      1, NULL, 0 },
676          { "sele2",      1, NULL, 0 },
677          { "order",      1, NULL, 0 },
678 +        { "nzbins",     1, NULL, 'z' },
679          { "memory",     1, NULL, 'm' },
680          { "selecorr",   0, NULL, 's' },
681          { "rcorr",      0, NULL, 'r' },
682          { "vcorr",      0, NULL, 'v' },
683 +        { "vcorrZ",     0, NULL, 0 },
684 +        { "vcorrR",     0, NULL, 0 },
685          { "dcorr",      0, NULL, 'd' },
686          { "lcorr",      0, NULL, 'l' },
687 +        { "lcorrZ",     0, NULL, 0 },
688 +        { "cohZ",       0, NULL, 0 },
689          { "sdcorr",     0, NULL, 'M' },
690          { "r_rcorr",    0, NULL, 0 },
691          { "thetacorr",  0, NULL, 0 },
# Line 644 | Line 693 | cmdline_parser_internal (
693          { "helfandEcorr",       0, NULL, 0 },
694          { "momentum",   0, NULL, 'p' },
695          { "stresscorr", 0, NULL, 0 },
696 +        { "bondcorr",   0, NULL, 'b' },
697 +        { "freqfluccorr",       0, NULL, 'f' },
698          { 0,  0, 0, 0 }
699        };
700  
701 <      c = getopt_long (argc, argv, "hVi:o:m:srvdlMp", long_options, &option_index);
701 >      c = getopt_long (argc, argv, "hVi:o:z:m:srvdlMpbf", long_options, &option_index);
702  
703        if (c == -1) break;       /* Exit from `while (1)' loop.  */
704  
# Line 687 | Line 738 | cmdline_parser_internal (
738              goto failure;
739          
740            break;
741 +        case 'z':       /* Number of Z bins.  */
742 +        
743 +        
744 +          if (update_arg( (void *)&(args_info->nzbins_arg),
745 +               &(args_info->nzbins_orig), &(args_info->nzbins_given),
746 +              &(local_args_info.nzbins_given), optarg, 0, "100", ARG_INT,
747 +              check_ambiguity, override, 0, 0,
748 +              "nzbins", 'z',
749 +              additional_error))
750 +            goto failure;
751 +        
752 +          break;
753          case 'm':       /* Available memory (defaults to 2G).  */
754          
755          
# Line 804 | Line 867 | cmdline_parser_internal (
867              goto failure;
868          
869            break;
870 +        case 'b':       /* Bond extension correlation function.  */
871 +        
872 +          if (args_info->dynamicProps_group_counter && override)
873 +            reset_group_dynamicProps (args_info);
874 +          args_info->dynamicProps_group_counter += 1;
875 +        
876 +          if (update_arg( 0 ,
877 +               0 , &(args_info->bondcorr_given),
878 +              &(local_args_info.bondcorr_given), optarg, 0, 0, ARG_NO,
879 +              check_ambiguity, override, 0, 0,
880 +              "bondcorr", 'b',
881 +              additional_error))
882 +            goto failure;
883 +        
884 +          break;
885 +        case 'f':       /* Frequency Fluctuation correlation function.  */
886 +        
887 +          if (args_info->dynamicProps_group_counter && override)
888 +            reset_group_dynamicProps (args_info);
889 +          args_info->dynamicProps_group_counter += 1;
890 +        
891 +          if (update_arg( 0 ,
892 +               0 , &(args_info->freqfluccorr_given),
893 +              &(local_args_info.freqfluccorr_given), optarg, 0, 0, ARG_NO,
894 +              check_ambiguity, override, 0, 0,
895 +              "freqfluccorr", 'f',
896 +              additional_error))
897 +            goto failure;
898 +        
899 +          break;
900  
901          case 0: /* Long option with no short option */
902            /* select first stuntdouble set.  */
# Line 848 | Line 941 | cmdline_parser_internal (
941                goto failure;
942            
943            }
944 +          /* velocity correlation function along z-axis.  */
945 +          else if (strcmp (long_options[option_index].name, "vcorrZ") == 0)
946 +          {
947 +          
948 +            if (args_info->dynamicProps_group_counter && override)
949 +              reset_group_dynamicProps (args_info);
950 +            args_info->dynamicProps_group_counter += 1;
951 +          
952 +            if (update_arg( 0 ,
953 +                 0 , &(args_info->vcorrZ_given),
954 +                &(local_args_info.vcorrZ_given), optarg, 0, 0, ARG_NO,
955 +                check_ambiguity, override, 0, 0,
956 +                "vcorrZ", '-',
957 +                additional_error))
958 +              goto failure;
959 +          
960 +          }
961 +          /* velocity correlation function projected radially.  */
962 +          else if (strcmp (long_options[option_index].name, "vcorrR") == 0)
963 +          {
964 +          
965 +            if (args_info->dynamicProps_group_counter && override)
966 +              reset_group_dynamicProps (args_info);
967 +            args_info->dynamicProps_group_counter += 1;
968 +          
969 +            if (update_arg( 0 ,
970 +                 0 , &(args_info->vcorrR_given),
971 +                &(local_args_info.vcorrR_given), optarg, 0, 0, ARG_NO,
972 +                check_ambiguity, override, 0, 0,
973 +                "vcorrR", '-',
974 +                additional_error))
975 +              goto failure;
976 +          
977 +          }
978 +          /* Lengendre correlation function binned by Z.  */
979 +          else if (strcmp (long_options[option_index].name, "lcorrZ") == 0)
980 +          {
981 +          
982 +            if (args_info->dynamicProps_group_counter && override)
983 +              reset_group_dynamicProps (args_info);
984 +            args_info->dynamicProps_group_counter += 1;
985 +          
986 +            if (update_arg( 0 ,
987 +                 0 , &(args_info->lcorrZ_given),
988 +                &(local_args_info.lcorrZ_given), optarg, 0, 0, ARG_NO,
989 +                check_ambiguity, override, 0, 0,
990 +                "lcorrZ", '-',
991 +                additional_error))
992 +              goto failure;
993 +          
994 +          }
995 +          /* Lengendre correlation function for OH bond vectors binned by Z.  */
996 +          else if (strcmp (long_options[option_index].name, "cohZ") == 0)
997 +          {
998 +          
999 +            if (args_info->dynamicProps_group_counter && override)
1000 +              reset_group_dynamicProps (args_info);
1001 +            args_info->dynamicProps_group_counter += 1;
1002 +          
1003 +            if (update_arg( 0 ,
1004 +                 0 , &(args_info->cohZ_given),
1005 +                &(local_args_info.cohZ_given), optarg, 0, 0, ARG_NO,
1006 +                check_ambiguity, override, 0, 0,
1007 +                "cohZ", '-',
1008 +                additional_error))
1009 +              goto failure;
1010 +          
1011 +          }
1012            /* Radial rmsd.  */
1013            else if (strcmp (long_options[option_index].name, "r_rcorr") == 0)
1014            {

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