APBS  3.0.0
pbamparm.c
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1 
57 #include "pbamparm.h"
58 
59 VEMBED(rcsid="$Id$")
60 
61 #if !defined(VINLINE_MGPARM)
62 
63 #endif /* if !defined(VINLINE_MGPARM) */
64 
65 
67 
68  /* Set up the structure */
69  PBAMparm *thee = VNULL;
70  thee = (PBAMparm*)Vmem_malloc(VNULL, 1, sizeof(PBAMparm));
71  VASSERT( thee != VNULL);
72  VASSERT( PBAMparm_ctor2(thee, type) == VRC_SUCCESS );
73 
74  return thee;
75 }
76 
77 VPUBLIC Vrc_Codes PBAMparm_ctor2(PBAMparm *thee, PBAMparm_CalcType type) {
78 
79  int i;
80 
81  if (thee == VNULL) return VRC_FAILURE;
82 
83  thee->parsed = 0;
84  thee->type = type;
85  thee->salt = 0;
86 
87  thee->setsalt = 0;
88  thee->setruntype = 0;
89  thee->setrunname = 0;
90  thee->setunits = 0;
91 
92  thee->setrandorient = 0;
93 
94  thee->setpbcs = 0;
95  thee->pbcboxlen = 1e15;
96 
97  // Electrostatics
98  thee->gridpt = 15;
99  printf("Found a pts flag in ctor: %d\n", thee->gridpt);
100  thee->setgridpt = 0;
101  thee->set3dmap = 0;
102  thee->setgrid2Dname = 0;
103  thee->grid2Dct = 0;
104  thee->setdxname = 0;
105 
106  //Dynamics
107  thee->ntraj = 1;
108  thee->setntraj = 0;
109 
110  thee->settermcombine = 0;
111  thee->diffct = 0;
112 
113  thee->termct = 0;
114  thee->setterm = 0;
115 
116  thee->setxyz = 0;
117  for (i = 0; i<PBAMPARM_MAXMOL; i++) thee->xyzct[i] = 0;
118 
119  return VRC_SUCCESS;
120 }
121 
122 VPUBLIC void PBAMparm_dtor(PBAMparm **thee) {
123  if ((*thee) != VNULL) {
124  PBAMparm_dtor2(*thee);
125  Vmem_free(VNULL, 1, sizeof(PBAMparm), (void **)thee);
126  (*thee) = VNULL;
127  }
128 }
129 
130 VPUBLIC void PBAMparm_dtor2(PBAMparm *thee) { ; }
131 
132 VPUBLIC Vrc_Codes PBAMparm_check(PBAMparm *thee) {
133 
134  Vrc_Codes rc;
135 
136  rc = VRC_SUCCESS;
137 
138  Vnm_print(0, "PBAMparm_check: checking PBAMparm object of type %d.\n",
139  thee->type);
140 
141  /* Check to see if we were even filled... */
142  if (!thee->parsed) {
143  Vnm_print(2, "PBAMparm_check: not filled!\n");
144  return VRC_FAILURE;
145  }
146 
147 
148  /* Check type settings */
149  if(thee->type != PBAMCT_AUTO) {
150  Vnm_print(2,"PBAMparm_check: type not set");
151  rc = VRC_FAILURE;
152  }
153 
154  return rc;
155 }
156 
157 VPUBLIC void PBAMparm_copy(PBAMparm *thee, PBAMparm *parm) {
158  int i, j, k;
159  VASSERT(thee != VNULL);
160  VASSERT(parm != VNULL);
161 
162  thee->type = parm->type;
163  thee->parsed = parm->parsed;
164 
165  thee->salt = parm->salt;
166  thee->setsalt = parm->setsalt;
167  for (i=0; i<CHR_MAXLEN; i++) thee->runtype[i] = parm->runtype[i];
168  thee->setruntype = parm->setruntype;
169 
170  for (i=0; i<CHR_MAXLEN; i++) thee->runname[i] = parm->runname[i];
171  thee->setrunname = parm->setrunname;
172 
173  thee->setrandorient = parm->setrandorient;
174 
175  thee->setpbcs = parm->setpbcs;
176  thee->pbcboxlen = parm->pbcboxlen;
177 
178  for (i=0; i<CHR_MAXLEN; i++) thee->units[i] = parm->units[i];
179  thee->setunits = parm->setunits;
180 
181  // Electrostatic parts
182  thee->gridpt = parm->gridpt;
183  thee->setgridpt = parm->setgridpt;
184  for (i=0; i<CHR_MAXLEN; i++) thee->map3dname[i] = parm->map3dname[i];
185  thee->set3dmap = parm->set3dmap;
186 
187 
188  thee->grid2Dct = parm->grid2Dct;
189  for (i=0; i<PBAMPARM_MAXWRITE; i++)
190  {
191  for (j=0; j<CHR_MAXLEN; j++)
192  {
193  thee->grid2Dname[i][j] = parm->grid2Dname[i][j];
194  thee->grid2Dax[i][j] = parm->grid2Dax[i][j];
195  }
196  thee->grid2Dloc[i] = parm->grid2Dloc[i];
197  }
198 
199  for (i=0; i<CHR_MAXLEN; i++) thee->dxname[i] = parm->dxname[i];
200  thee->setdxname = parm->setdxname;
201 
202  // Dynamics parts
203  thee->ntraj = parm->ntraj;
204  thee->setntraj = parm->setntraj;
205 
206  for (i=0; i<CHR_MAXLEN; i++) thee->termcombine[i] = parm->termcombine[i];
207  thee->settermcombine = parm->settermcombine;
208 
209  thee->diffct = parm->diffct;
210 
211  for (i=0; i<PBAMPARM_MAXMOL; i++)
212  {
213  for (j=0; j<CHR_MAXLEN; j++)
214  {
215  thee->moveType[i][j] = parm->moveType[i][j];
216  }
217  thee->transDiff[i] = parm->transDiff[i];
218  thee->rotDiff[i] = parm->rotDiff[i];
219  }
220 
221  thee->termct = parm->termct;
222  thee->setterm = parm->setterm;
223  thee->confilct = parm->confilct;
224 
225  for (i=0; i<PBAMPARM_MAXWRITE; i++)
226  {
227  for (j=0; j<CHR_MAXLEN; j++)
228  {
229  thee->termnam[i][j] = parm->termnam[i][j];
230  thee->confil[i][j] = parm->confil[i][j];
231  }
232  thee->termVal[i] = parm->termVal[i];
233  thee->termnu[i][0] = parm->termnu[i][0];
234  }
235 
236  thee->setxyz = parm->setxyz;
237  for (i = 0; i<PBAMPARM_MAXMOL; i++)
238  {
239  thee->xyzct[i] = parm->xyzct[i];
240  for (j = 0; j<PBAMPARM_MAXWRITE; j++)
241  {
242  for (k = 0; k<CHR_MAXLEN; k++)
243  {
244  thee->xyzfil[i][j][k] = parm->xyzfil[i][j][k];
245  }
246  }
247  }
248 
249 }
250 
251 
252 VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock){
253  const char* name = "salt";
254  char tok[VMAX_BUFSIZE];
255  double tf;
256  if(Vio_scanf(sock, "%s", tok) == 0) {
257  Vnm_print(2, "parsePBAM: ran out of tokens on %s!\n", name);
258  return VRC_WARNING;
259  }
260 
261  if (sscanf(tok, "%lf", &tf) == 0){
262  Vnm_print(2, "NOsh: Read non-float (%s) while parsing %s keyword!\n", tok, name);
263  return VRC_WARNING;
264  }else{
265  thee->salt = tf;
266  }
267  thee->setsalt = 1;
268  return VRC_SUCCESS;
269 }
270 
271 VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock){
272  const char* name = "runtype";
273  char tok[VMAX_BUFSIZE];
274 
275  if(Vio_scanf(sock, "%s", tok) == 0) {
276  Vnm_print(2, "parsePBAM: ran out of tokens on %s!\n", name);
277  return VRC_WARNING;
278  } else if(Vstring_strcasecmp(tok, "dynamics") == 0){
279  Vnm_print(2, "parsePBAM: Dynamics has been moved out of the ELEC section!\n");
280  return VRC_WARNING;
281  } else {
282  strncpy(thee->runtype, tok, CHR_MAXLEN);
283  thee->setruntype=1;
284  }
285 
286  return VRC_SUCCESS;
287 }
288 
289 VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock){
290  const char* name = "runname";
291  char tok[VMAX_BUFSIZE];
292 
293  if(Vio_scanf(sock, "%s", tok) == 0) {
294  Vnm_print(2, "parsePBAM: ran out of tokens on %s!\n", name);
295  return VRC_WARNING;
296  } else {
297  strncpy(thee->runname, tok, CHR_MAXLEN);
298  thee->setrunname=1;
299  }
300 
301  return VRC_SUCCESS;
302 }
303 
304 VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock){
305  const char* name = "randorient";
306  thee->setrandorient=1;
307  return VRC_SUCCESS;
308 }
309 
310 VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock){
311  const char* name = "pbc";
312  char tok[VMAX_BUFSIZE];
313  double tf;
314  int td;
315  if(Vio_scanf(sock, "%s", tok) == 0) {
316  Vnm_print(2, "parsePBAM: ran out of tokens on %s!\n", name);
317  return VRC_WARNING;
318  }
319 
320  if (sscanf(tok, "%d", &td) == 0) {
321  Vnm_print(2, "parsePBAM: Read non-int (%s) while parsing pbc keyword!\n", tok);
322  return VRC_FAILURE;
323  } else{
324  thee->setpbcs = td;
325  }
326 
327  if (sscanf(tok, "%lf", &tf) == 0){
328  Vnm_print(2, "NOsh: Read non-float (%s) while parsing %s keyword!\n", tok, name);
329  return VRC_WARNING;
330  }else{
331  thee->pbcboxlen = tf;
332  }
333  return VRC_SUCCESS;
334 }
335 
336 VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock){
337  const char* name = "units";
338  char tok[VMAX_BUFSIZE];
339 
340  if(Vio_scanf(sock, "%s", tok) == 0) {
341  Vnm_print(2, "parsePBAM: ran out of tokens on %s!\n", name);
342  return VRC_WARNING;
343  } else {
344  strncpy(thee->units, tok, CHR_MAXLEN);
345  thee->setunits=1;
346  }
347 
348  return VRC_SUCCESS;
349 }
350 
351 VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock){
352  const char* name = "dime";
353  char tok[VMAX_BUFSIZE];
354  int td;
355  if(Vio_scanf(sock, "%s", tok) == 0) {
356  Vnm_print(2, "parsePBAM: ran out of tokens on %s!\n", name);
357  return VRC_WARNING;
358  }
359 
360  if (sscanf(tok, "%d", &td) == 0){
361  Vnm_print(2, "NOsh: Read non-integer (%s) while parsing %s keyword!\n", tok, name);
362  return VRC_WARNING;
363  }else{
364  printf("Found a dime flag in parse: %d\n", td);
365  thee->gridpt = td;
366  }
367  thee->setgridpt = 1;
368  return VRC_SUCCESS;
369 }
370 
371 VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock){
372  const char* name = "3dmap";
373  char tok[VMAX_BUFSIZE];
374 
375  Vnm_print(2, "PBAM: 3dmap keyword has been deprecated! Please use in conjuction with the write keyword.");
376  return VRC_FAILURE;
377 
378  /*
379  if(Vio_scanf(sock, "%s", tok) == 0) {
380  Vnm_print(2, "parsePBAM: ran out of tokens on %s!\n", name);
381  return VRC_WARNING;
382  } else {
383  strncpy(thee->map3dname, tok, CHR_MAXLEN);
384  thee->set3dmap=1;
385  }
386 
387  return VRC_SUCCESS;
388  */
389 }
390 
391 VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock){
392  const char* name = "grid2d";
393  char tok[VMAX_BUFSIZE];
394  double tf;
395 
396  if(Vio_scanf(sock, "%s", tok) == 0) {
397  Vnm_print(2, "parsePBAM: ran out of tokens on %s!\n", name);
398  return VRC_WARNING;
399  } else {
400  strncpy(thee->grid2Dname[thee->grid2Dct], tok, CHR_MAXLEN);
401  thee->setgrid2Dname=1;
402  }
403 
404  if(Vio_scanf(sock, "%s", tok) == 0) {
405  Vnm_print(2, "parsePBAM: ran out of tokens on %s!\n", name);
406  return VRC_WARNING;
407  } else {
408  strncpy(thee->grid2Dax[thee->grid2Dct], tok, CHR_MAXLEN);
409  }
410 
411  if(Vio_scanf(sock, "%s", tok) == 0) {
412  Vnm_print(2, "parsePBAM: ran out of tokens on %s!\n", name);
413  return VRC_WARNING;
414  }
415 
416  if (sscanf(tok, "%lf", &tf) == 0){
417  Vnm_print(2, "NOsh: Read non-float (%s) while parsing %s keyword!\n", tok, name);
418  return VRC_WARNING;
419  }else{
420  thee->grid2Dloc[thee->grid2Dct] = tf;
421  thee->grid2Dct = thee->grid2Dct+1;
422  }
423  return VRC_SUCCESS;
424 }
425 
426 VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock){
427  Vnm_print(2, "PBAM's dx keyword is deprecated. Please use the write keyword!\n");
428  return VRC_FAILURE;
429  /*
430  const char* name = "dx";
431  char tok[VMAX_BUFSIZE];
432 
433  if(Vio_scanf(sock, "%s", tok) == 0) {
434  Vnm_print(2, "parsePBAM: ran out of tokens on %s!\n", name);
435  return VRC_WARNING;
436  } else {
437  strncpy(thee->dxname, tok, CHR_MAXLEN);
438  thee->setdxname=1;
439  }
440  return VRC_SUCCESS;
441  */
442 }
443 
444 VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock){
445  const char* name = "termcombine";
446  char tok[VMAX_BUFSIZE];
447 
448  if(Vio_scanf(sock, "%s", tok) == 0) {
449  Vnm_print(2, "parsePBAM: ran out of tokens on %s!\n", name);
450  return VRC_WARNING;
451  } else {
452  strncpy(thee->termcombine, tok, CHR_MAXLEN);
453  thee->settermcombine=1;
454  }
455  return VRC_SUCCESS;
456 }
457 
458 VPRIVATE Vrc_Codes PBAMparm_parseNtraj(PBAMparm *thee, Vio *sock){
459  const char* name = "ntraj";
460  char tok[VMAX_BUFSIZE];
461  int td;
462  if(Vio_scanf(sock, "%s", tok) == 0) {
463  Vnm_print(2, "parsePBAM: ran out of tokens on %s!\n", name);
464  return VRC_WARNING;
465  }
466 
467  if (sscanf(tok, "%d", &td) == 0){
468  Vnm_print(2, "NOsh: Read non-integer (%s) while parsing %s keyword!\n", tok, name);
469  return VRC_WARNING;
470  }else{
471  thee->ntraj = td;
472  }
473  thee->setntraj = 1;
474  return VRC_SUCCESS;
475 }
476 
477 VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock){
478  const char* name = "diff";
479  char tok[VMAX_BUFSIZE];
480  int molind;
481  double tf;
482 
483  if(Vio_scanf(sock, "%s", tok) == 0) {
484  Vnm_print(2, "parsePBAM: ran out of tokens on %s!\n", name);
485  return VRC_WARNING;
486  }
487 
488  // // looking for index
489  if (sscanf(tok, "%d", &molind) == 0){
490  Vnm_print(2, "NOsh: Read non-int (%s) while parsing %s keyword!\n", tok, name);
491  return VRC_WARNING;
492  }
493 
494  molind -= 1;
495  // looking for move type = move, stat, rot
496  if(Vio_scanf(sock, "%s", tok) == 0) {
497  Vnm_print(2, "parsePBAM: ran out of tokens on %s!\n", name);
498  return VRC_WARNING;
499  } else {
500  strncpy(thee->moveType[molind], tok, CHR_MAXLEN);
501  thee->diffct += 1;
502  }
503 
504  if (strncmp(thee->moveType[molind], "move", 4) == 0)
505  {
506  if(Vio_scanf(sock, "%s", tok) == 0) {
507  Vnm_print(2, "parsePBAM: ran out of tokens on %s!\n", name);
508  return VRC_WARNING;
509  }
510  if (sscanf(tok, "%lf", &tf) == 0){
511  Vnm_print(2, "NOsh: Read non-float (%s) while parsing %s keyword!\n", tok, name);
512  return VRC_WARNING;
513  }else{
514  thee->transDiff[molind] = tf;
515  }
516 
517  // rot diffusion coeff
518  if(Vio_scanf(sock, "%s", tok) == 0) {
519  Vnm_print(2, "parsePBAM: ran out of tokens on %s!\n", name);
520  return VRC_WARNING;
521  }
522  if (sscanf(tok, "%lf", &tf) == 0){
523  Vnm_print(2, "NOsh: Read non-float (%s) while parsing %s keyword!\n", tok, name);
524  return VRC_WARNING;
525  }else{
526  thee->rotDiff[molind] = tf;
527  }
528  } else if (strncmp(thee->moveType[molind], "rot", 3) == 0)
529  {
530  if(Vio_scanf(sock, "%s", tok) == 0) {
531  Vnm_print(2, "parsePBAM: ran out of tokens on %s!\n", name);
532  return VRC_WARNING;
533  }
534  if (sscanf(tok, "%lf", &tf) == 0){
535  Vnm_print(2, "NOsh: Read non-float (%s) while parsing %s keyword!\n", tok, name);
536  return VRC_WARNING;
537  }else{
538  thee->rotDiff[molind] = tf;
539  thee->transDiff[molind] = 0.0;
540  }
541  } else{
542  thee->transDiff[molind] = 0.0;
543  thee->rotDiff[molind] = 0.0;
544  }
545 
546  return VRC_SUCCESS;
547 }
548 
549 VPRIVATE Vrc_Codes PBAMparm_parseTerm(PBAMparm *thee, Vio *sock){
550  const char* name = "term";
551  char tok[VMAX_BUFSIZE];
552  double tf;
553  int td;
554 
555  // looking for term name
556  if(Vio_scanf(sock, "%s", tok) == 0) {
557  Vnm_print(2, "parsePBAM: ran out of tokens on %s!\n", name);
558  return VRC_WARNING;
559  }else {
560  if(strncmp(tok, "position", 8)==0){
561  return PBAMparm_parseTerm(thee, sock);
562  }else{
563  strncpy(thee->termnam[thee->termct], tok, CHR_MAXLEN);
564  }
565  }
566 
567  if (strncmp(thee->termnam[thee->termct], "contact", 7) == 0)
568  {
569  if(Vio_scanf(sock, "%s", tok) == 0) {
570  Vnm_print(2, "parsePBAM: ran out of tokens on %s!\n", name);
571  return VRC_WARNING;
572  }else{
573  strncpy(thee->confil[thee->confilct], tok, CHR_MAXLEN);
574  }
575 
576  if(Vio_scanf(sock, "%s", tok) == 0) {
577  Vnm_print(2, "parsePBAM: ran out of tokens on %s!\n", name);
578  return VRC_WARNING;
579  }
580  if (sscanf(tok, "%lf", &tf) == 0){
581  Vnm_print(2, "NOsh: Read non-float (%s) while parsing %s keyword!\n", tok, name);
582  return VRC_WARNING;
583  }else
584  {
585  thee->termVal[thee->termct] = tf;
586  thee->termnu[thee->termct][0] = 0;
587  thee->confilct += 1;
588  }
589  } else if (strncmp(thee->termnam[thee->termct], "time", 4) == 0)
590  {
591  if(Vio_scanf(sock, "%s", tok) == 0) {
592  Vnm_print(2, "parsePBAM: ran out of tokens on %s!\n", name);
593  return VRC_WARNING;
594  }
595  if (sscanf(tok, "%lf", &tf) == 0){
596  Vnm_print(2, "NOsh: Read non-float (%s) while parsing %s keyword!\n", tok, name);
597  return VRC_WARNING;
598  }else{
599  thee->termVal[thee->termct] = tf;
600  thee->termnu[thee->termct][0] = 0;
601  }
602  } else //if (strncmp(thee->termnam[thee->termct], "position", 8) == 0)
603  {
604  if(Vio_scanf(sock, "%s", tok) == 0) {
605  Vnm_print(2, "parsePBAM: ran out of tokens on %s!\n", name);
606  return VRC_WARNING;
607  }
608  if (sscanf(tok, "%lf", &tf) == 0){
609  Vnm_print(2, "NOsh: Read non-float (%s) while parsing %s keyword!\n", tok, name);
610  return VRC_WARNING;
611  }else{
612  thee->termVal[thee->termct] = tf;
613  }
614 
615  if(Vio_scanf(sock, "%s", tok) == 0) {
616  Vnm_print(2, "parsePBAM: ran out of tokens on %s!\n", name);
617  return VRC_WARNING;
618  }
619  if (sscanf(tok, "%d", &td) == 0){
620  Vnm_print(2, "NOsh: Read non-float (%s) while parsing %s keyword!\n", tok, name);
621  return VRC_WARNING;
622  }else{
623  thee->termnu[thee->termct][0] = td-1;
624  }
625  }
626 
627  thee->setterm = 1;
628  thee->termct += 1;
629  return VRC_SUCCESS;
630 }
631 
632 VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock){
633  const char* name = "xyz";
634  char tok[VMAX_BUFSIZE];
635  int td, mol;
636 
637  if(Vio_scanf(sock, "%s", tok) == 0) {
638  Vnm_print(2, "parsePBAM: ran out of tokens on %s!\n", name);
639  return VRC_WARNING;
640  }
641 
642  // // looking for index
643  if (sscanf(tok, "%d", &td) == 0){
644  Vnm_print(2, "NOsh: Read non-int (%s) while parsing %s keyword!\n", tok, name);
645  return VRC_WARNING;
646  } else{
647  printf("This is my mol in parseXYZ: %d", td);
648  mol = td-1;
649  }
650 
651  // looking for move type = move, stat, rot
652  if(Vio_scanf(sock, "%s", tok) == 0) {
653  Vnm_print(2, "parsePBAM: ran out of tokens on %s!\n", name);
654  return VRC_WARNING;
655  } else {
656  strncpy(thee->xyzfil[mol][thee->xyzct[mol]], tok, CHR_MAXLEN);
657  thee->xyzct[mol] += 1;
658  }
659  return VRC_SUCCESS;
660 }
661 
662 VPUBLIC Vrc_Codes PBAMparm_parseToken(PBAMparm *thee, char tok[VMAX_BUFSIZE],
663  Vio *sock) {
664 
665  if (thee == VNULL) {
666  Vnm_print(2, "parsePBAM: got NULL thee!\n");
667  return VRC_WARNING;
668  }
669  if (sock == VNULL) {
670  Vnm_print(2, "parsePBAM: got NULL socket!\n");
671  return VRC_WARNING;
672  }
673 
674  Vnm_print(0, "PBAMparm_parseToken: trying %s...\n", tok);
675 
676  // General terms to parse
677  if (Vstring_strcasecmp(tok, "salt") == 0) {
678  return PBAMparm_parseSalt(thee, sock);
679  }else if (Vstring_strcasecmp(tok, "runtype") == 0) {
680  return PBAMparm_parseRunType(thee, sock);
681  }else if (Vstring_strcasecmp(tok, "runname") == 0) {
682  return PBAMparm_parseRunName(thee, sock);
683  }else if (Vstring_strcasecmp(tok, "randorient") == 0) {
684  return PBAMparm_parseRandorient(thee, sock);
685  }else if (Vstring_strcasecmp(tok, "pbc") == 0) {
686  return PBAMparm_parsePBCS(thee, sock);
687  }else if (Vstring_strcasecmp(tok, "units") == 0) {
688  return PBAMparm_parseUnits(thee, sock);
689  }
690 
691  // Electrostatic parsing
692  else if (Vstring_strcasecmp(tok, "dime") == 0) {
693  return PBAMparm_parseGridPts(thee, sock);
694  }else if (Vstring_strcasecmp(tok, "3dmap") == 0) {
695  return PBAMparm_parse3Dmap(thee, sock);
696  }else if (Vstring_strcasecmp(tok, "grid2d") == 0) {
697  return PBAMparm_parseGrid2D(thee, sock);
698  }else if (Vstring_strcasecmp(tok, "dx") == 0) {
699  return PBAMparm_parseDX(thee, sock);
700  }
701 
702  // Dynamics parsing
703  else if (Vstring_strcasecmp(tok, "ntraj") == 0) {
704  return PBAMparm_parseNtraj(thee, sock);
705  }else if (Vstring_strcasecmp(tok, "termcombine") == 0) {
706  return PBAMparm_parseTermcombine(thee, sock);
707  }else if (Vstring_strcasecmp(tok, "diff") == 0) {
708  return PBAMparm_parseDiff(thee, sock);
709  }else if (Vstring_strcasecmp(tok, "term") == 0) {
710  return PBAMparm_parseTerm(thee, sock);
711  }else if (Vstring_strcasecmp(tok, "xyz") == 0) {
712  return PBAMparm_parseXYZ(thee, sock);
713  }
714 
715 
716  else
717  return 0;
718 
719  /*else {
720  Vnm_print(2, "parsePBAM: Unrecognized keyword (%s)!\n", tok);
721  return VRC_WARNING;
722  }
723  return VRC_FAILURE;
724  */
725 }
VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock)
Find 3D map filename and save it.
Definition: pbamparm.c:371
VPUBLIC void PBAMparm_dtor2(PBAMparm *thee)
FORTRAN stub for object destructor ?????????!!!!!!!!!!!!
Definition: pbamparm.c:130
enum ePBAMparm_CalcType PBAMparm_CalcType
Declare PBAMparm_CalcType type.
Definition: pbamparm.h:95
VPUBLIC void PBAMparm_copy(PBAMparm *thee, PBAMparm *parm)
copy PBAMparm object int thee.
Definition: pbamparm.c:157
VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock)
Find DX filename and save it.
Definition: pbamparm.c:426
VPUBLIC void PBAMparm_dtor(PBAMparm **thee)
Object destructor.
Definition: pbamparm.c:122
VPUBLIC Vrc_Codes PBAMparm_ctor2(PBAMparm *thee, PBAMparm_CalcType type)
FORTRAN stub to construct PBAMparm object ?????????!!!!!!!
Definition: pbamparm.c:77
VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock)
Find PBC flag and save the type and the boxlength.
Definition: pbamparm.c:310
VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock)
Find Termination logic and save it.
Definition: pbamparm.c:444
VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock)
Find Grid points and save them.
Definition: pbamparm.c:351
VPUBLIC Vrc_Codes PBAMparm_check(PBAMparm *thee)
Consistency check for parameter values stored in object.
Definition: pbamparm.c:132
VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock)
Find salt conc and save it as a structure variable.
Definition: pbamparm.c:252
#define CHR_MAXLEN
Number of things that can be written out in a single calculation.
Definition: pbamparm.h:76
VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock)
Find 2D grid filename and save it.
Definition: pbamparm.c:391
VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock)
Find xyz files for each molecule for each traj and save them.
Definition: pbamparm.c:632
VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock)
Find diffusion coeffs for each molecule and save them.
Definition: pbamparm.c:477
VPUBLIC Vrc_Codes PBAMparm_parseToken(PBAMparm *thee, char tok[VMAX_BUFSIZE], Vio *sock)
Parse an MG keyword from an input file.
Definition: pbamparm.c:662
VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock)
Find runType and save it as a structure variable.
Definition: pbamparm.c:271
VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock)
Find runName and save it as a structure variable.
Definition: pbamparm.c:289
VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock)
Find randomorientation flag and save it as a boolean.
Definition: pbamparm.c:304
VPUBLIC PBAMparm * PBAMparm_ctor(PBAMparm_CalcType type)
Construct PBAMparm object.
Definition: pbamparm.c:66
VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock)
Find units flag and save units.
Definition: pbamparm.c:336
@ PBAMCT_AUTO
Definition: pbamparm.h:87
#define VEMBED(rctag)
Allows embedding of RCS ID tags in object files.
Definition: vhal.h:556
@ VRC_FAILURE
Definition: vhal.h:69
@ VRC_SUCCESS
Definition: vhal.h:70
VPUBLIC int Vstring_strcasecmp(const char *s1, const char *s2)
Case-insensitive string comparison (BSD standard)
Definition: vstring.c:66
Contains declarations for class PBAMparm.
Parameter structure for PBAM-specific variables from input files.
Definition: pbamparm.h:105
int parsed
Definition: pbamparm.h:108
PBAMparm_CalcType type
Definition: pbamparm.h:107