38 |
|
printf(" -h, --help Print help and exit\n"); |
39 |
|
printf(" -V, --version Print version and exit\n"); |
40 |
|
printf(" -i, --input=filename input dump file\n"); |
41 |
< |
printf(" -o, --output=STRING output file name\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"); |
44 |
|
printf(" -w, --water skip the the waters (default=off)\n"); |
45 |
|
printf(" -m, --periodicBox map to the periodic box (default=off)\n"); |
46 |
< |
printf(" -r, --replace replace the atom types of zconstraint molecules \n (default=off)\n"); |
46 |
> |
printf(" -z, --zconstraint replace the atom types of zconstraint molecules \n (default=off)\n"); |
47 |
> |
printf(" -r, --rigidbody add a pseudo COM atom to rigidbody (default=off)\n"); |
48 |
> |
printf(" -t, --watertype replace the atom type of water model (default=on)\n"); |
49 |
|
printf(" -s, --ignore=atomtype ignore the atom types\n"); |
50 |
|
printf(" --repeatX=INT The number of images to repeat in the x direction \n (default=`0')\n"); |
51 |
|
printf(" --repeatY=INT The number of images to repeat in the y direction \n (default=`0')\n"); |
89 |
|
args_info->dipole_given = 0 ; |
90 |
|
args_info->water_given = 0 ; |
91 |
|
args_info->periodicBox_given = 0 ; |
92 |
< |
args_info->replace_given = 0 ; |
92 |
> |
args_info->zconstraint_given = 0 ; |
93 |
> |
args_info->rigidbody_given = 0 ; |
94 |
> |
args_info->watertype_given = 0 ; |
95 |
|
args_info->ignore_given = 0 ; |
96 |
|
args_info->repeatX_given = 0 ; |
97 |
|
args_info->repeatY_given = 0 ; |
103 |
|
args_info->dipole_flag = 0;\ |
104 |
|
args_info->water_flag = 0;\ |
105 |
|
args_info->periodicBox_flag = 0;\ |
106 |
< |
args_info->replace_flag = 0;\ |
106 |
> |
args_info->zconstraint_flag = 0;\ |
107 |
> |
args_info->rigidbody_flag = 0;\ |
108 |
> |
args_info->watertype_flag = 1;\ |
109 |
|
args_info->ignore_arg = NULL; \ |
110 |
|
args_info->repeatX_arg = 0 ;\ |
111 |
|
args_info->repeatY_arg = 0 ;\ |
133 |
|
{ "dipole", 0, NULL, 'd' }, |
134 |
|
{ "water", 0, NULL, 'w' }, |
135 |
|
{ "periodicBox", 0, NULL, 'm' }, |
136 |
< |
{ "replace", 0, NULL, 'r' }, |
136 |
> |
{ "zconstraint", 0, NULL, 'z' }, |
137 |
> |
{ "rigidbody", 0, NULL, 'r' }, |
138 |
> |
{ "watertype", 0, NULL, 't' }, |
139 |
|
{ "ignore", 1, NULL, 's' }, |
140 |
|
{ "repeatX", 1, NULL, 0 }, |
141 |
|
{ "repeatY", 1, NULL, 0 }, |
144 |
|
}; |
145 |
|
|
146 |
|
stop_char = 0; |
147 |
< |
c = getopt_long (argc, argv, "hVi:o:n:dwmrs:", long_options, &option_index); |
147 |
> |
c = getopt_long (argc, argv, "hVi:o:n:dwmzrts:", long_options, &option_index); |
148 |
|
|
149 |
|
if (c == -1) break; /* Exit from `while (1)' loop. */ |
150 |
|
|
226 |
|
args_info->periodicBox_flag = !(args_info->periodicBox_flag); |
227 |
|
break; |
228 |
|
|
229 |
< |
case 'r': /* replace the atom types of zconstraint molecules. */ |
230 |
< |
if (args_info->replace_given) |
229 |
> |
case 'z': /* replace the atom types of zconstraint molecules. */ |
230 |
> |
if (args_info->zconstraint_given) |
231 |
|
{ |
232 |
< |
fprintf (stderr, "%s: `--replace' (`-r') option given more than once\n", CMDLINE_PARSER_PACKAGE); |
232 |
> |
fprintf (stderr, "%s: `--zconstraint' (`-z') option given more than once\n", CMDLINE_PARSER_PACKAGE); |
233 |
> |
clear_args (); |
234 |
> |
exit (EXIT_FAILURE); |
235 |
> |
} |
236 |
> |
args_info->zconstraint_given = 1; |
237 |
> |
args_info->zconstraint_flag = !(args_info->zconstraint_flag); |
238 |
> |
break; |
239 |
> |
|
240 |
> |
case 'r': /* add a pseudo COM atom to rigidbody. */ |
241 |
> |
if (args_info->rigidbody_given) |
242 |
> |
{ |
243 |
> |
fprintf (stderr, "%s: `--rigidbody' (`-r') option given more than once\n", CMDLINE_PARSER_PACKAGE); |
244 |
|
clear_args (); |
245 |
|
exit (EXIT_FAILURE); |
246 |
|
} |
247 |
< |
args_info->replace_given = 1; |
248 |
< |
args_info->replace_flag = !(args_info->replace_flag); |
247 |
> |
args_info->rigidbody_given = 1; |
248 |
> |
args_info->rigidbody_flag = !(args_info->rigidbody_flag); |
249 |
|
break; |
250 |
|
|
251 |
+ |
case 't': /* replace the atom type of water model. */ |
252 |
+ |
if (args_info->watertype_given) |
253 |
+ |
{ |
254 |
+ |
fprintf (stderr, "%s: `--watertype' (`-t') option given more than once\n", CMDLINE_PARSER_PACKAGE); |
255 |
+ |
clear_args (); |
256 |
+ |
exit (EXIT_FAILURE); |
257 |
+ |
} |
258 |
+ |
args_info->watertype_given = 1; |
259 |
+ |
args_info->watertype_flag = !(args_info->watertype_flag); |
260 |
+ |
break; |
261 |
+ |
|
262 |
|
case 's': /* ignore the atom types. */ |
263 |
|
args_info->ignore_given++; |
264 |
|
ignore_new = (struct ignore_list *) malloc (sizeof (struct ignore_list)); |