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root/OpenMD/trunk/src/applications/staticProps/StaticPropsCmd.h
Revision: 2049
Committed: Tue Jan 6 21:44:10 2015 UTC (10 years, 4 months ago) by gezelter
Content type: text/plain
File size: 22101 byte(s)
Log Message: 
Added Geometric HBond StaticProps module.

File Contents

# User Rev Content
1 gezelter 1390 /** @file StaticPropsCmd.h
2     * @brief The header file for the command line option parser
3 kstocke1 1531 * generated by GNU Gengetopt version 2.22.4
4 gezelter 1390 * http://www.gnu.org/software/gengetopt.
5     * DO NOT modify this file, since it can be overwritten
6     * @author GNU Gengetopt by Lorenzo Bettini */
7 tim 310
8     #ifndef STATICPROPSCMD_H
9     #define STATICPROPSCMD_H
10    
11     /* If we use autoconf. */
12     #ifdef HAVE_CONFIG_H
13     #include "config.h"
14     #endif
15    
16 gezelter 1390 #include <stdio.h> /* for FILE */
17    
18 tim 310 #ifdef __cplusplus
19     extern "C" {
20     #endif /* __cplusplus */
21    
22     #ifndef CMDLINE_PARSER_PACKAGE
23 kstocke1 1531 /** @brief the program name (used for printing errors) */
24 tim 311 #define CMDLINE_PARSER_PACKAGE "StaticProps"
25 tim 310 #endif
26    
27 kstocke1 1531 #ifndef CMDLINE_PARSER_PACKAGE_NAME
28     /** @brief the complete program name (used for help and version) */
29     #define CMDLINE_PARSER_PACKAGE_NAME "StaticProps"
30     #endif
31    
32 tim 310 #ifndef CMDLINE_PARSER_VERSION
33 gezelter 1390 /** @brief the program version */
34 tim 310 #define CMDLINE_PARSER_VERSION "1.00"
35     #endif
36    
37 gezelter 1390 /** @brief Where the command line options are stored */
38 tim 543 struct gengetopt_args_info
39     {
40 gezelter 1390 const char *help_help; /**< @brief Print help and exit help description. */
41     const char *version_help; /**< @brief Print version and exit help description. */
42     char * input_arg; /**< @brief input dump file. */
43     char * input_orig; /**< @brief input dump file original value given at command line. */
44     const char *input_help; /**< @brief input dump file help description. */
45     char * output_arg; /**< @brief output file name. */
46     char * output_orig; /**< @brief output file name original value given at command line. */
47     const char *output_help; /**< @brief output file name help description. */
48     int step_arg; /**< @brief process every n frame (default='1'). */
49     char * step_orig; /**< @brief process every n frame original value given at command line. */
50     const char *step_help; /**< @brief process every n frame help description. */
51     int nbins_arg; /**< @brief number of bins (general purpose) (default='100'). */
52     char * nbins_orig; /**< @brief number of bins (general purpose) original value given at command line. */
53     const char *nbins_help; /**< @brief number of bins (general purpose) help description. */
54     int nbins_x_arg; /**< @brief number of bins in x axis (default='100'). */
55     char * nbins_x_orig; /**< @brief number of bins in x axis original value given at command line. */
56     const char *nbins_x_help; /**< @brief number of bins in x axis help description. */
57     int nbins_y_arg; /**< @brief number of bins in y axis (default='100'). */
58     char * nbins_y_orig; /**< @brief number of bins in y axis original value given at command line. */
59     const char *nbins_y_help; /**< @brief number of bins in y axis help description. */
60 gezelter 1440 int nbins_z_arg; /**< @brief number of bins in z axis (default='100'). */
61     char * nbins_z_orig; /**< @brief number of bins in z axis original value given at command line. */
62     const char *nbins_z_help; /**< @brief number of bins in z axis help description. */
63 gezelter 1390 int nanglebins_arg; /**< @brief number of bins for cos(angle) (default='50'). */
64     char * nanglebins_orig; /**< @brief number of bins for cos(angle) original value given at command line. */
65     const char *nanglebins_help; /**< @brief number of bins for cos(angle) help description. */
66 chuckv 1445 double rcut_arg; /**< @brief cutoff radius (rcut). */
67     char * rcut_orig; /**< @brief cutoff radius (rcut) original value given at command line. */
68     const char *rcut_help; /**< @brief cutoff radius (rcut) help description. */
69 gezelter 2049 double thetacut_arg; /**< @brief cutoff angle (thetacut). */
70     char * thetacut_orig; /**< @brief cutoff angle (thetacut) original value given at command line. */
71     const char *thetacut_help; /**< @brief cutoff angle (thetacut) help description. */
72 gezelter 1454 double dz_arg; /**< @brief slab width (dz). */
73     char * dz_orig; /**< @brief slab width (dz) original value given at command line. */
74     const char *dz_help; /**< @brief slab width (dz) help description. */
75 gezelter 1390 double length_arg; /**< @brief maximum length (Defaults to 1/2 smallest length of first frame). */
76     char * length_orig; /**< @brief maximum length (Defaults to 1/2 smallest length of first frame) original value given at command line. */
77     const char *length_help; /**< @brief maximum length (Defaults to 1/2 smallest length of first frame) help description. */
78 chuckv 1445 double zlength_arg; /**< @brief maximum length (Defaults to 1/2 smallest length of first frame). */
79     char * zlength_orig; /**< @brief maximum length (Defaults to 1/2 smallest length of first frame) original value given at command line. */
80     const char *zlength_help; /**< @brief maximum length (Defaults to 1/2 smallest length of first frame) help description. */
81 gezelter 1390 double zoffset_arg; /**< @brief Where to set the zero for the slab_density calculation (default='0'). */
82     char * zoffset_orig; /**< @brief Where to set the zero for the slab_density calculation original value given at command line. */
83     const char *zoffset_help; /**< @brief Where to set the zero for the slab_density calculation help description. */
84     char * sele1_arg; /**< @brief select the first stuntdouble set. */
85     char * sele1_orig; /**< @brief select the first stuntdouble set original value given at command line. */
86     const char *sele1_help; /**< @brief select the first stuntdouble set help description. */
87     char * sele2_arg; /**< @brief select the second stuntdouble set. */
88     char * sele2_orig; /**< @brief select the second stuntdouble set original value given at command line. */
89     const char *sele2_help; /**< @brief select the second stuntdouble set help description. */
90     char * sele3_arg; /**< @brief select the third stuntdouble set. */
91     char * sele3_orig; /**< @brief select the third stuntdouble set original value given at command line. */
92     const char *sele3_help; /**< @brief select the third stuntdouble set help description. */
93     char * refsele_arg; /**< @brief select reference (use and only use with --gxyz). */
94     char * refsele_orig; /**< @brief select reference (use and only use with --gxyz) original value given at command line. */
95     const char *refsele_help; /**< @brief select reference (use and only use with --gxyz) help description. */
96     char * comsele_arg; /**< @brief select stunt doubles for center-of-mass reference point. */
97     char * comsele_orig; /**< @brief select stunt doubles for center-of-mass reference point original value given at command line. */
98     const char *comsele_help; /**< @brief select stunt doubles for center-of-mass reference point help description. */
99 gezelter 1819 int seleoffset_arg; /**< @brief global index offset for a second object (used to define a vector between sites in molecule). */
100     char * seleoffset_orig; /**< @brief global index offset for a second object (used to define a vector between sites in molecule) original value given at command line. */
101     const char *seleoffset_help; /**< @brief global index offset for a second object (used to define a vector between sites in molecule) help description. */
102 gezelter 1991 int seleoffset2_arg; /**< @brief global index offset for a third object (used to define a vector between sites in molecule). */
103     char * seleoffset2_orig; /**< @brief global index offset for a third object (used to define a vector between sites in molecule) original value given at command line. */
104     const char *seleoffset2_help; /**< @brief global index offset for a third object (used to define a vector between sites in molecule) help description. */
105 gezelter 1390 char * molname_arg; /**< @brief molecule name. */
106     char * molname_orig; /**< @brief molecule name original value given at command line. */
107     const char *molname_help; /**< @brief molecule name help description. */
108     int begin_arg; /**< @brief begin internal index. */
109     char * begin_orig; /**< @brief begin internal index original value given at command line. */
110     const char *begin_help; /**< @brief begin internal index help description. */
111     int end_arg; /**< @brief end internal index. */
112     char * end_orig; /**< @brief end internal index original value given at command line. */
113     const char *end_help; /**< @brief end internal index help description. */
114     double radius_arg; /**< @brief nanoparticle radius. */
115     char * radius_orig; /**< @brief nanoparticle radius original value given at command line. */
116     const char *radius_help; /**< @brief nanoparticle radius help description. */
117 gezelter 2015 double voxelSize_arg; /**< @brief voxel size (angstroms). */
118     char * voxelSize_orig; /**< @brief voxel size (angstroms) original value given at command line. */
119     const char *voxelSize_help; /**< @brief voxel size (angstroms) help description. */
120     double gaussWidth_arg; /**< @brief Gaussian width (angstroms). */
121     char * gaussWidth_orig; /**< @brief Gaussian width (angstroms) original value given at command line. */
122     const char *gaussWidth_help; /**< @brief Gaussian width (angstroms) help description. */
123 gezelter 1390 const char *bo_help; /**< @brief bond order parameter (--rcut must be specified) help description. */
124 gezelter 1992 const char *ior_help; /**< @brief icosahedral bond order parameter as a function of radius (--rcut must be specified) help description. */
125     const char *for_help; /**< @brief FCC bond order parameter as a function of radius (--rcut must be specified) help description. */
126 gezelter 1390 const char *bad_help; /**< @brief N(theta) bond angle density within (--rcut must be specified) help description. */
127 gezelter 1513 const char *count_help; /**< @brief count of molecules matching selection criteria (and associated statistics) help description. */
128 gezelter 1390 const char *gofr_help; /**< @brief g(r) help description. */
129     const char *gofz_help; /**< @brief g(z) help description. */
130     const char *r_theta_help; /**< @brief g(r, cos(theta)) help description. */
131     const char *r_omega_help; /**< @brief g(r, cos(omega)) help description. */
132 gezelter 1440 const char *r_z_help; /**< @brief g(r, z) help description. */
133 gezelter 1390 const char *theta_omega_help; /**< @brief g(cos(theta), cos(omega)) help description. */
134     const char *gxyz_help; /**< @brief g(x, y, z) help description. */
135 gezelter 1454 const char *twodgofr_help; /**< @brief 2D g(r) (Slab width --dz must be specified) help description. */
136 gezelter 1542 const char *p2_help; /**< @brief p2 order parameter (--sele1 must be specified, --sele2 is optional) help description. */
137 gezelter 1390 const char *rp2_help; /**< @brief rp2 order parameter (--sele1 and --sele2 must be specified) help description. */
138     const char *scd_help; /**< @brief scd order parameter (either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified) help description. */
139     const char *density_help; /**< @brief density plot help description. */
140     const char *slab_density_help; /**< @brief slab density help description. */
141 gezelter 1979 const char *p_angle_help; /**< @brief p(cos(theta)) (--sele1 must be specified, --sele2 is optional) help description. */
142 gezelter 1390 const char *hxy_help; /**< @brief hxy help description. */
143     const char *rho_r_help; /**< @brief rho of R help description. */
144 kstocke1 1522 const char *angle_r_help; /**< @brief angle of R help description. */
145 gezelter 1390 const char *hullvol_help; /**< @brief hull volume of nanoparticle help description. */
146 gezelter 1585 const char *rodlength_help; /**< @brief length of nanorod help description. */
147 gezelter 1843 const char *tet_param_help; /**< @brief tetrahedrality order parameter (Qk) help description. */
148     const char *tet_param_z_help; /**< @brief spatially-resolved tetrahedrality order parameter Qk(z) help description. */
149 gezelter 2015 const char *tet_param_xyz_help; /**< @brief volume-resolved tetrahedrality order parameter Qk(x,y,z). (voxelSize, rcut, and gaussWidth must be specified) help description. */
150 gezelter 1879 const char *rnemdz_help; /**< @brief slab-resolved RNEMD statistics (temperature, density, velocity) help description. */
151     const char *rnemdr_help; /**< @brief shell-resolved RNEMD statistics (temperature, density, angular velocity) help description. */
152 gezelter 1953 const char *rnemdrt_help; /**< @brief shell and angle-resolved RNEMD statistics (temperature, density, angular velocity) help description. */
153 gezelter 1994 const char *nitrile_help; /**< @brief electrostatic potential to frequency map based on the Cho nitrile fits help description. */
154 gezelter 1999 const char *multipole_help; /**< @brief average multipole moments contained within cutoff spheres as a function of radius help description. */
155 jmichalk 2031 const char *surfDiffusion_help; /**< @brief X, Y, and R (surface diffusion if Z exposed and bulk immobile) diffusion help description. */
156 gezelter 2049 const char *hbond_help; /**< @brief Hydrogen Bonding statistics using geometric criteria (rcut and thetacut must be specified) help description. */
157 gezelter 929
158 gezelter 1390 unsigned int help_given ; /**< @brief Whether help was given. */
159     unsigned int version_given ; /**< @brief Whether version was given. */
160     unsigned int input_given ; /**< @brief Whether input was given. */
161     unsigned int output_given ; /**< @brief Whether output was given. */
162     unsigned int step_given ; /**< @brief Whether step was given. */
163     unsigned int nbins_given ; /**< @brief Whether nbins was given. */
164     unsigned int nbins_x_given ; /**< @brief Whether nbins_x was given. */
165     unsigned int nbins_y_given ; /**< @brief Whether nbins_y was given. */
166 gezelter 1440 unsigned int nbins_z_given ; /**< @brief Whether nbins_z was given. */
167 gezelter 1390 unsigned int nanglebins_given ; /**< @brief Whether nanglebins was given. */
168 chuckv 1445 unsigned int rcut_given ; /**< @brief Whether rcut was given. */
169 gezelter 2049 unsigned int thetacut_given ; /**< @brief Whether thetacut was given. */
170 gezelter 1454 unsigned int dz_given ; /**< @brief Whether dz was given. */
171 gezelter 1390 unsigned int length_given ; /**< @brief Whether length was given. */
172 chuckv 1445 unsigned int zlength_given ; /**< @brief Whether zlength was given. */
173 gezelter 1390 unsigned int zoffset_given ; /**< @brief Whether zoffset was given. */
174     unsigned int sele1_given ; /**< @brief Whether sele1 was given. */
175     unsigned int sele2_given ; /**< @brief Whether sele2 was given. */
176     unsigned int sele3_given ; /**< @brief Whether sele3 was given. */
177     unsigned int refsele_given ; /**< @brief Whether refsele was given. */
178     unsigned int comsele_given ; /**< @brief Whether comsele was given. */
179 gezelter 1819 unsigned int seleoffset_given ; /**< @brief Whether seleoffset was given. */
180 gezelter 1991 unsigned int seleoffset2_given ; /**< @brief Whether seleoffset2 was given. */
181 gezelter 1390 unsigned int molname_given ; /**< @brief Whether molname was given. */
182     unsigned int begin_given ; /**< @brief Whether begin was given. */
183     unsigned int end_given ; /**< @brief Whether end was given. */
184     unsigned int radius_given ; /**< @brief Whether radius was given. */
185 gezelter 2015 unsigned int voxelSize_given ; /**< @brief Whether voxelSize was given. */
186     unsigned int gaussWidth_given ; /**< @brief Whether gaussWidth was given. */
187 gezelter 1390 unsigned int bo_given ; /**< @brief Whether bo was given. */
188 gezelter 1992 unsigned int ior_given ; /**< @brief Whether ior was given. */
189     unsigned int for_given ; /**< @brief Whether for was given. */
190 gezelter 1390 unsigned int bad_given ; /**< @brief Whether bad was given. */
191 gezelter 1513 unsigned int count_given ; /**< @brief Whether count was given. */
192 gezelter 1390 unsigned int gofr_given ; /**< @brief Whether gofr was given. */
193     unsigned int gofz_given ; /**< @brief Whether gofz was given. */
194     unsigned int r_theta_given ; /**< @brief Whether r_theta was given. */
195     unsigned int r_omega_given ; /**< @brief Whether r_omega was given. */
196 gezelter 1440 unsigned int r_z_given ; /**< @brief Whether r_z was given. */
197 gezelter 1390 unsigned int theta_omega_given ; /**< @brief Whether theta_omega was given. */
198     unsigned int gxyz_given ; /**< @brief Whether gxyz was given. */
199 gezelter 1454 unsigned int twodgofr_given ; /**< @brief Whether twodgofr was given. */
200 gezelter 1390 unsigned int p2_given ; /**< @brief Whether p2 was given. */
201     unsigned int rp2_given ; /**< @brief Whether rp2 was given. */
202     unsigned int scd_given ; /**< @brief Whether scd was given. */
203     unsigned int density_given ; /**< @brief Whether density was given. */
204     unsigned int slab_density_given ; /**< @brief Whether slab_density was given. */
205 gezelter 1413 unsigned int p_angle_given ; /**< @brief Whether p_angle was given. */
206 gezelter 1390 unsigned int hxy_given ; /**< @brief Whether hxy was given. */
207     unsigned int rho_r_given ; /**< @brief Whether rho_r was given. */
208 kstocke1 1522 unsigned int angle_r_given ; /**< @brief Whether angle_r was given. */
209 gezelter 1390 unsigned int hullvol_given ; /**< @brief Whether hullvol was given. */
210 gezelter 1585 unsigned int rodlength_given ; /**< @brief Whether rodlength was given. */
211 kstocke1 1522 unsigned int tet_param_given ; /**< @brief Whether tet_param was given. */
212 gezelter 1782 unsigned int tet_param_z_given ; /**< @brief Whether tet_param_z was given. */
213 gezelter 2015 unsigned int tet_param_xyz_given ; /**< @brief Whether tet_param_xyz was given. */
214 gezelter 1879 unsigned int rnemdz_given ; /**< @brief Whether rnemdz was given. */
215     unsigned int rnemdr_given ; /**< @brief Whether rnemdr was given. */
216 gezelter 1953 unsigned int rnemdrt_given ; /**< @brief Whether rnemdrt was given. */
217 gezelter 1994 unsigned int nitrile_given ; /**< @brief Whether nitrile was given. */
218 gezelter 1998 unsigned int multipole_given ; /**< @brief Whether multipole was given. */
219 jmichalk 2031 unsigned int surfDiffusion_given ; /**< @brief Whether surfDiffusion was given. */
220 gezelter 2049 unsigned int hbond_given ; /**< @brief Whether hbond was given. */
221 tim 310
222 gezelter 2049 char **inputs ; /**< @brief unamed options (options without names) */
223     unsigned inputs_num ; /**< @brief unamed options number */
224 gezelter 1390 int staticProps_group_counter; /**< @brief Counter for group staticProps */
225 tim 543 } ;
226 tim 310
227 gezelter 1390 /** @brief The additional parameters to pass to parser functions */
228     struct cmdline_parser_params
229     {
230     int override; /**< @brief whether to override possibly already present options (default 0) */
231     int initialize; /**< @brief whether to initialize the option structure gengetopt_args_info (default 1) */
232     int check_required; /**< @brief whether to check that all required options were provided (default 1) */
233     int check_ambiguity; /**< @brief whether to check for options already specified in the option structure gengetopt_args_info (default 0) */
234     int print_errors; /**< @brief whether getopt_long should print an error message for a bad option (default 1) */
235     } ;
236    
237     /** @brief the purpose string of the program */
238 chuckv 1128 extern const char *gengetopt_args_info_purpose;
239 gezelter 1390 /** @brief the usage string of the program */
240 chuckv 1128 extern const char *gengetopt_args_info_usage;
241 gezelter 1390 /** @brief all the lines making the help output */
242 chuckv 1128 extern const char *gengetopt_args_info_help[];
243 tim 310
244 gezelter 1390 /**
245     * The command line parser
246     * @param argc the number of command line options
247     * @param argv the command line options
248     * @param args_info the structure where option information will be stored
249     * @return 0 if everything went fine, NON 0 if an error took place
250     */
251 kstocke1 1531 int cmdline_parser (int argc, char **argv,
252 chuckv 1128 struct gengetopt_args_info *args_info);
253 gezelter 1390
254     /**
255     * The command line parser (version with additional parameters - deprecated)
256     * @param argc the number of command line options
257     * @param argv the command line options
258     * @param args_info the structure where option information will be stored
259     * @param override whether to override possibly already present options
260     * @param initialize whether to initialize the option structure my_args_info
261     * @param check_required whether to check that all required options were provided
262     * @return 0 if everything went fine, NON 0 if an error took place
263     * @deprecated use cmdline_parser_ext() instead
264     */
265 kstocke1 1531 int cmdline_parser2 (int argc, char **argv,
266 chuckv 1128 struct gengetopt_args_info *args_info,
267     int override, int initialize, int check_required);
268 gezelter 1390
269     /**
270     * The command line parser (version with additional parameters)
271     * @param argc the number of command line options
272     * @param argv the command line options
273     * @param args_info the structure where option information will be stored
274     * @param params additional parameters for the parser
275     * @return 0 if everything went fine, NON 0 if an error took place
276     */
277 kstocke1 1531 int cmdline_parser_ext (int argc, char **argv,
278 gezelter 1390 struct gengetopt_args_info *args_info,
279     struct cmdline_parser_params *params);
280    
281     /**
282     * Save the contents of the option struct into an already open FILE stream.
283     * @param outfile the stream where to dump options
284     * @param args_info the option struct to dump
285     * @return 0 if everything went fine, NON 0 if an error took place
286     */
287     int cmdline_parser_dump(FILE *outfile,
288     struct gengetopt_args_info *args_info);
289    
290     /**
291     * Save the contents of the option struct into a (text) file.
292     * This file can be read by the config file parser (if generated by gengetopt)
293     * @param filename the file where to save
294     * @param args_info the option struct to save
295     * @return 0 if everything went fine, NON 0 if an error took place
296     */
297 chuckv 1128 int cmdline_parser_file_save(const char *filename,
298     struct gengetopt_args_info *args_info);
299    
300 gezelter 1390 /**
301     * Print the help
302     */
303 tim 543 void cmdline_parser_print_help(void);
304 gezelter 1390 /**
305     * Print the version
306     */
307 tim 543 void cmdline_parser_print_version(void);
308 tim 310
309 gezelter 1390 /**
310     * Initializes all the fields a cmdline_parser_params structure
311     * to their default values
312     * @param params the structure to initialize
313     */
314     void cmdline_parser_params_init(struct cmdline_parser_params *params);
315    
316     /**
317     * Allocates dynamically a cmdline_parser_params structure and initializes
318     * all its fields to their default values
319     * @return the created and initialized cmdline_parser_params structure
320     */
321     struct cmdline_parser_params *cmdline_parser_params_create(void);
322    
323     /**
324     * Initializes the passed gengetopt_args_info structure's fields
325     * (also set default values for options that have a default)
326     * @param args_info the structure to initialize
327     */
328 gezelter 929 void cmdline_parser_init (struct gengetopt_args_info *args_info);
329 gezelter 1390 /**
330     * Deallocates the string fields of the gengetopt_args_info structure
331     * (but does not deallocate the structure itself)
332     * @param args_info the structure to deallocate
333     */
334 gezelter 929 void cmdline_parser_free (struct gengetopt_args_info *args_info);
335    
336 gezelter 1390 /**
337     * Checks that all the required options were specified
338     * @param args_info the structure to check
339     * @param prog_name the name of the program that will be used to print
340     * possible errors
341     * @return
342     */
343 chuckv 1128 int cmdline_parser_required (struct gengetopt_args_info *args_info,
344     const char *prog_name);
345 gezelter 929
346    
347 tim 310 #ifdef __cplusplus
348     }
349     #endif /* __cplusplus */
350     #endif /* STATICPROPSCMD_H */

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