39 |
|
args_info->version_given = 0 ; |
40 |
|
args_info->input_given = 0 ; |
41 |
|
args_info->bandwidth_given = 0 ; |
42 |
+ |
args_info->tolerance_given = 0 ; |
43 |
|
args_info->charmm_given = 0 ; |
44 |
|
args_info->amber_given = 0 ; |
45 |
|
args_info->lj_given = 0 ; |
53 |
|
{ |
54 |
|
args_info->input_arg = NULL; |
55 |
|
args_info->bandwidth_arg = 8 ; |
56 |
+ |
args_info->tolerance_arg = 0.01 ; |
57 |
|
} |
58 |
|
|
59 |
|
void |
69 |
|
printf("\n" |
70 |
|
"Usage: %s [OPTIONS]...\n", CMDLINE_PARSER_PACKAGE); |
71 |
|
printf("\n"); |
72 |
< |
printf("%s\n"," -h, --help Print help and exit"); |
73 |
< |
printf("%s\n"," -V, --version Print version and exit"); |
74 |
< |
printf("%s\n"," -i, --input=filename input file name"); |
75 |
< |
printf("%s\n"," -b, --bandwidth=INT The step detail for the potential grids - typically a \n power of 2 (default=`8')"); |
72 |
> |
printf("%s\n"," -h, --help Print help and exit"); |
73 |
> |
printf("%s\n"," -V, --version Print version and exit"); |
74 |
> |
printf("%s\n"," -i, --input=filename input file name"); |
75 |
> |
printf("%s\n"," -b, --bandwidth=INT The step detail for the potential grids - typically \n a power of 2 (default=`8')"); |
76 |
> |
printf("%s\n"," -t, --tolerance=DOUBLE The tolerance for recognition of spherical harmonic \n terms (default=`0.01')"); |
77 |
|
printf("\n"); |
78 |
|
printf(" Group: ForceField A Force Field must be specified\n"); |
79 |
< |
printf("%s\n"," -c, --charmm Use CHARMM 27 parameters"); |
80 |
< |
printf("%s\n"," -a, --amber Use Amber99 parameters"); |
81 |
< |
printf("%s\n"," -l, --lj Use Lennard-Jones parameters"); |
82 |
< |
printf("%s\n"," -g, --gaff Use GAFF parameters"); |
83 |
< |
printf("%s\n"," -o, --opls Use OPLS/AA parameters"); |
79 |
> |
printf("%s\n"," -c, --charmm Use CHARMM 27 parameters"); |
80 |
> |
printf("%s\n"," -a, --amber Use Amber99 parameters"); |
81 |
> |
printf("%s\n"," -l, --lj Use Lennard-Jones parameters"); |
82 |
> |
printf("%s\n"," -g, --gaff Use GAFF parameters"); |
83 |
> |
printf("%s\n"," -o, --opls Use OPLS/AA parameters"); |
84 |
|
} |
85 |
|
|
86 |
|
void |
187 |
|
{ "version", 0, NULL, 'V' }, |
188 |
|
{ "input", 1, NULL, 'i' }, |
189 |
|
{ "bandwidth", 1, NULL, 'b' }, |
190 |
+ |
{ "tolerance", 1, NULL, 't' }, |
191 |
|
{ "charmm", 0, NULL, 'c' }, |
192 |
|
{ "amber", 0, NULL, 'a' }, |
193 |
|
{ "lj", 0, NULL, 'l' }, |
197 |
|
}; |
198 |
|
|
199 |
|
stop_char = 0; |
200 |
< |
c = getopt_long (argc, argv, "hVi:b:calgo", long_options, &option_index); |
200 |
> |
c = getopt_long (argc, argv, "hVi:b:t:calgo", long_options, &option_index); |
201 |
|
|
202 |
|
if (c == -1) break; /* Exit from `while (1)' loop. */ |
203 |
|
|
237 |
|
local_args_info.bandwidth_given = 1; |
238 |
|
args_info->bandwidth_given = 1; |
239 |
|
args_info->bandwidth_arg = strtol (optarg,&stop_char,0); |
240 |
+ |
break; |
241 |
+ |
|
242 |
+ |
case 't': /* The tolerance for recognition of spherical harmonic terms. */ |
243 |
+ |
if (local_args_info.tolerance_given) |
244 |
+ |
{ |
245 |
+ |
fprintf (stderr, "%s: `--tolerance' (`-t') option given more than once%s\n", CMDLINE_PARSER_PACKAGE, (additional_error ? additional_error : "")); |
246 |
+ |
goto failure; |
247 |
+ |
} |
248 |
+ |
if (args_info->tolerance_given && ! override) |
249 |
+ |
continue; |
250 |
+ |
local_args_info.tolerance_given = 1; |
251 |
+ |
args_info->tolerance_given = 1; |
252 |
+ |
args_info->tolerance_arg = strtod (optarg, NULL); |
253 |
|
break; |
254 |
|
|
255 |
|
case 'c': /* Use CHARMM 27 parameters. */ |