40 |
|
printf(" -i, --input=filename input dump file\n"); |
41 |
|
printf(" -o, --output=filename output file name\n"); |
42 |
|
printf(" -n, --frame=INT print every n frame (default=`1')\n"); |
43 |
– |
printf(" -d, --dipole print the dipole moments (default=off)\n"); |
43 |
|
printf(" -w, --water skip the the waters (default=off)\n"); |
44 |
|
printf(" -m, --periodicBox map to the periodic box (default=off)\n"); |
45 |
|
printf(" -z, --zconstraint replace the atom types of zconstraint \n molecules (default=off)\n"); |
46 |
|
printf(" -r, --rigidbody add a pseudo COM atom to rigidbody \n (default=off)\n"); |
47 |
|
printf(" -t, --watertype replace the atom type of water model \n (default=on)\n"); |
48 |
< |
printf(" -g, --ignore=atomtype ignore the atom types\n"); |
50 |
< |
printf(" -s, --selection=selection script selection syntax:\n" |
51 |
< |
" select DMPC -- select DMPC molecule\n" |
52 |
< |
" select DMPC.* -- select all atoms and all rigidbodies belong to DMPC molecule(same as above)\n" |
53 |
< |
" select not DMPC -- select all atoms and all rigidbodies do not belong to DMPC molecule\n" |
54 |
< |
" select C* and 4 to 7 -- select stuntdoubles which match C* and which index is between [4, 7)\n" |
55 |
< |
" select 5 -- select stuntdobule whose global index is 5\n" |
56 |
< |
" select within (5.0, HDP or PO4) -- select stuntdoubles which is within 5 A to HDP or PO4\n" |
57 |
< |
" select DMPC.3 -- select stuntdouble which internal index is 3\n" |
58 |
< |
" select DMPC.DMPC_RB_*.* --select atoms belong to rigid body inside DMPC molecule \n"); |
48 |
> |
printf(" -s, --selection=selection script general selection syntax\n"); |
49 |
|
printf(" --originsele=selection script select origin\n"); |
50 |
|
printf(" --refsele=selection script select reference\n"); |
51 |
|
printf(" --repeatX=INT The number of images to repeat in the x \n direction (default=`0')\n"); |
72 |
|
cmdline_parser (int argc, char * const *argv, struct gengetopt_args_info *args_info) |
73 |
|
{ |
74 |
|
int c; /* Character of the parsed option. */ |
85 |
– |
int i; /* Counter */ |
86 |
– |
struct ignore_list |
87 |
– |
{ |
88 |
– |
char * ignore_arg; |
89 |
– |
struct ignore_list * next; |
90 |
– |
}; |
91 |
– |
struct ignore_list * ignore_list = NULL,* ignore_new = NULL; |
92 |
– |
|
75 |
|
int missing_required_options = 0; |
76 |
|
|
77 |
|
args_info->help_given = 0 ; |
79 |
|
args_info->input_given = 0 ; |
80 |
|
args_info->output_given = 0 ; |
81 |
|
args_info->frame_given = 0 ; |
100 |
– |
args_info->dipole_given = 0 ; |
82 |
|
args_info->water_given = 0 ; |
83 |
|
args_info->periodicBox_given = 0 ; |
84 |
|
args_info->zconstraint_given = 0 ; |
85 |
|
args_info->rigidbody_given = 0 ; |
86 |
|
args_info->watertype_given = 0 ; |
106 |
– |
args_info->ignore_given = 0 ; |
87 |
|
args_info->selection_given = 0 ; |
88 |
|
args_info->originsele_given = 0 ; |
89 |
|
args_info->refsele_given = 0 ; |
94 |
|
args_info->input_arg = NULL; \ |
95 |
|
args_info->output_arg = NULL; \ |
96 |
|
args_info->frame_arg = 1 ;\ |
117 |
– |
args_info->dipole_flag = 0;\ |
97 |
|
args_info->water_flag = 0;\ |
98 |
|
args_info->periodicBox_flag = 0;\ |
99 |
|
args_info->zconstraint_flag = 0;\ |
100 |
|
args_info->rigidbody_flag = 0;\ |
101 |
|
args_info->watertype_flag = 1;\ |
123 |
– |
args_info->ignore_arg = NULL; \ |
102 |
|
args_info->selection_arg = NULL; \ |
103 |
|
args_info->originsele_arg = NULL; \ |
104 |
|
args_info->refsele_arg = NULL; \ |
125 |
|
{ "input", 1, NULL, 'i' }, |
126 |
|
{ "output", 1, NULL, 'o' }, |
127 |
|
{ "frame", 1, NULL, 'n' }, |
150 |
– |
{ "dipole", 0, NULL, 'd' }, |
128 |
|
{ "water", 0, NULL, 'w' }, |
129 |
|
{ "periodicBox", 0, NULL, 'm' }, |
130 |
|
{ "zconstraint", 0, NULL, 'z' }, |
131 |
|
{ "rigidbody", 0, NULL, 'r' }, |
132 |
|
{ "watertype", 0, NULL, 't' }, |
156 |
– |
{ "ignore", 1, NULL, 'g' }, |
133 |
|
{ "selection", 1, NULL, 's' }, |
134 |
|
{ "originsele", 1, NULL, 0 }, |
135 |
|
{ "refsele", 1, NULL, 0 }, |
140 |
|
}; |
141 |
|
|
142 |
|
stop_char = 0; |
143 |
< |
c = getopt_long (argc, argv, "hVi:o:n:dwmzrtg:s:", long_options, &option_index); |
143 |
> |
c = getopt_long (argc, argv, "hVi:o:n:wmzrts:", long_options, &option_index); |
144 |
|
|
145 |
|
if (c == -1) break; /* Exit from `while (1)' loop. */ |
146 |
|
|
189 |
|
args_info->frame_arg = strtol (optarg,&stop_char,0); |
190 |
|
break; |
191 |
|
|
216 |
– |
case 'd': /* print the dipole moments. */ |
217 |
– |
if (args_info->dipole_given) |
218 |
– |
{ |
219 |
– |
fprintf (stderr, "%s: `--dipole' (`-d') option given more than once\n", CMDLINE_PARSER_PACKAGE); |
220 |
– |
clear_args (); |
221 |
– |
exit (EXIT_FAILURE); |
222 |
– |
} |
223 |
– |
args_info->dipole_given = 1; |
224 |
– |
args_info->dipole_flag = !(args_info->dipole_flag); |
225 |
– |
break; |
226 |
– |
|
192 |
|
case 'w': /* skip the the waters. */ |
193 |
|
if (args_info->water_given) |
194 |
|
{ |
244 |
|
args_info->watertype_flag = !(args_info->watertype_flag); |
245 |
|
break; |
246 |
|
|
247 |
< |
case 'g': /* ignore the atom types. */ |
283 |
< |
args_info->ignore_given++; |
284 |
< |
ignore_new = (struct ignore_list *) malloc (sizeof (struct ignore_list)); |
285 |
< |
ignore_new->next = ignore_list; |
286 |
< |
ignore_list = ignore_new; |
287 |
< |
ignore_new->ignore_arg = gengetopt_strdup (optarg); |
288 |
< |
break; |
289 |
< |
|
290 |
< |
case 's': /* general selection syntax(now only support select atoms within a specified range). */ |
247 |
> |
case 's': /* general selection syntax. */ |
248 |
|
if (args_info->selection_given) |
249 |
|
{ |
250 |
|
fprintf (stderr, "%s: `--selection' (`-s') option given more than once\n", CMDLINE_PARSER_PACKAGE); |
347 |
|
if ( missing_required_options ) |
348 |
|
exit (EXIT_FAILURE); |
349 |
|
|
393 |
– |
if (args_info->ignore_given) |
394 |
– |
{ |
395 |
– |
args_info->ignore_arg = (char * *) malloc (args_info->ignore_given * sizeof (char *)); |
396 |
– |
for (i = 0; i < args_info->ignore_given; i++) |
397 |
– |
{ |
398 |
– |
args_info->ignore_arg [i] = ignore_list->ignore_arg; |
399 |
– |
ignore_list = ignore_list->next; |
400 |
– |
} |
401 |
– |
} |
402 |
– |
|
350 |
|
return 0; |
351 |
|
} |