APBS  1.5
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 {
279  strncpy(thee->runtype, tok, CHR_MAXLEN);
280  thee->setruntype=1;
281  }
282 
283  return VRC_SUCCESS;
284 }
285 
286 VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock){
287  const char* name = "runname";
288  char tok[VMAX_BUFSIZE];
289 
290  if(Vio_scanf(sock, "%s", tok) == 0) {
291  Vnm_print(2, "parsePBAM: ran out of tokens on %s!\n", name);
292  return VRC_WARNING;
293  } else {
294  strncpy(thee->runname, tok, CHR_MAXLEN);
295  thee->setrunname=1;
296  }
297 
298  return VRC_SUCCESS;
299 }
300 
301 VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock){
302  const char* name = "randorient";
303  thee->setrandorient=1;
304  return VRC_SUCCESS;
305 }
306 
307 VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock){
308  const char* name = "pbc";
309  char tok[VMAX_BUFSIZE];
310  double tf;
311  int td;
312  if(Vio_scanf(sock, "%s", tok) == 0) {
313  Vnm_print(2, "parsePBAM: ran out of tokens on %s!\n", name);
314  return VRC_WARNING;
315  }
316 
317  if (sscanf(tok, "%d", &td) == 0) {
318  Vnm_print(2, "parsePBAM: Read non-int (%s) while parsing pbc keyword!\n", tok);
319  return VRC_FAILURE;
320  } else{
321  thee->setpbcs = td;
322  }
323 
324  if (sscanf(tok, "%lf", &tf) == 0){
325  Vnm_print(2, "NOsh: Read non-float (%s) while parsing %s keyword!\n", tok, name);
326  return VRC_WARNING;
327  }else{
328  thee->pbcboxlen = tf;
329  }
330  return VRC_SUCCESS;
331 }
332 
333 VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock){
334  const char* name = "units";
335  char tok[VMAX_BUFSIZE];
336 
337  if(Vio_scanf(sock, "%s", tok) == 0) {
338  Vnm_print(2, "parsePBAM: ran out of tokens on %s!\n", name);
339  return VRC_WARNING;
340  } else {
341  strncpy(thee->units, tok, CHR_MAXLEN);
342  thee->setunits=1;
343  }
344 
345  return VRC_SUCCESS;
346 }
347 
348 VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock){
349  const char* name = "gridpts";
350  char tok[VMAX_BUFSIZE];
351  int td;
352  if(Vio_scanf(sock, "%s", tok) == 0) {
353  Vnm_print(2, "parsePBAM: ran out of tokens on %s!\n", name);
354  return VRC_WARNING;
355  }
356 
357  if (sscanf(tok, "%d", &td) == 0){
358  Vnm_print(2, "NOsh: Read non-integer (%s) while parsing %s keyword!\n", tok, name);
359  return VRC_WARNING;
360  }else{
361  printf("Found a pts flag in parse: %d\n", td);
362  thee->gridpt = td;
363  }
364  thee->setgridpt = 1;
365  return VRC_SUCCESS;
366 }
367 
368 VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock){
369  const char* name = "3dmap";
370  char tok[VMAX_BUFSIZE];
371 
372  if(Vio_scanf(sock, "%s", tok) == 0) {
373  Vnm_print(2, "parsePBAM: ran out of tokens on %s!\n", name);
374  return VRC_WARNING;
375  } else {
376  strncpy(thee->map3dname, tok, CHR_MAXLEN);
377  thee->set3dmap=1;
378  }
379 
380  return VRC_SUCCESS;
381 }
382 
383 VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock){
384  const char* name = "grid2d";
385  char tok[VMAX_BUFSIZE];
386  double tf;
387 
388  if(Vio_scanf(sock, "%s", tok) == 0) {
389  Vnm_print(2, "parsePBAM: ran out of tokens on %s!\n", name);
390  return VRC_WARNING;
391  } else {
392  strncpy(thee->grid2Dname[thee->grid2Dct], tok, CHR_MAXLEN);
393  thee->setgrid2Dname=1;
394  }
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->grid2Dax[thee->grid2Dct], tok, CHR_MAXLEN);
401  }
402 
403  if(Vio_scanf(sock, "%s", tok) == 0) {
404  Vnm_print(2, "parsePBAM: ran out of tokens on %s!\n", name);
405  return VRC_WARNING;
406  }
407 
408  if (sscanf(tok, "%lf", &tf) == 0){
409  Vnm_print(2, "NOsh: Read non-float (%s) while parsing %s keyword!\n", tok, name);
410  return VRC_WARNING;
411  }else{
412  thee->grid2Dloc[thee->grid2Dct] = tf;
413  thee->grid2Dct = thee->grid2Dct+1;
414  }
415  return VRC_SUCCESS;
416 }
417 
418 VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock){
419  const char* name = "dx";
420  char tok[VMAX_BUFSIZE];
421 
422  if(Vio_scanf(sock, "%s", tok) == 0) {
423  Vnm_print(2, "parsePBAM: ran out of tokens on %s!\n", name);
424  return VRC_WARNING;
425  } else {
426  strncpy(thee->dxname, tok, CHR_MAXLEN);
427  thee->setdxname=1;
428  }
429  return VRC_SUCCESS;
430 }
431 
432 VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock){
433  const char* name = "termcombine";
434  char tok[VMAX_BUFSIZE];
435 
436  if(Vio_scanf(sock, "%s", tok) == 0) {
437  Vnm_print(2, "parsePBAM: ran out of tokens on %s!\n", name);
438  return VRC_WARNING;
439  } else {
440  strncpy(thee->termcombine, tok, CHR_MAXLEN);
441  thee->settermcombine=1;
442  }
443  return VRC_SUCCESS;
444 }
445 
446 VPRIVATE Vrc_Codes PBAMparm_parseNtraj(PBAMparm *thee, Vio *sock){
447  const char* name = "ntraj";
448  char tok[VMAX_BUFSIZE];
449  int td;
450  if(Vio_scanf(sock, "%s", tok) == 0) {
451  Vnm_print(2, "parsePBAM: ran out of tokens on %s!\n", name);
452  return VRC_WARNING;
453  }
454 
455  if (sscanf(tok, "%d", &td) == 0){
456  Vnm_print(2, "NOsh: Read non-integer (%s) while parsing %s keyword!\n", tok, name);
457  return VRC_WARNING;
458  }else{
459  thee->ntraj = td;
460  }
461  thee->setntraj = 1;
462  return VRC_SUCCESS;
463 }
464 
465 VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock){
466  const char* name = "diff";
467  char tok[VMAX_BUFSIZE];
468  int molind;
469  double tf;
470 
471  if(Vio_scanf(sock, "%s", tok) == 0) {
472  Vnm_print(2, "parsePBAM: ran out of tokens on %s!\n", name);
473  return VRC_WARNING;
474  }
475 
476  // // looking for index
477  if (sscanf(tok, "%d", &molind) == 0){
478  Vnm_print(2, "NOsh: Read non-int (%s) while parsing %s keyword!\n", tok, name);
479  return VRC_WARNING;
480  }
481 
482  molind -= 1;
483  // looking for move type = move, stat, rot
484  if(Vio_scanf(sock, "%s", tok) == 0) {
485  Vnm_print(2, "parsePBAM: ran out of tokens on %s!\n", name);
486  return VRC_WARNING;
487  } else {
488  strncpy(thee->moveType[molind], tok, CHR_MAXLEN);
489  thee->diffct += 1;
490  }
491 
492  if (strncmp(thee->moveType[molind], "move", 4) == 0)
493  {
494  if(Vio_scanf(sock, "%s", tok) == 0) {
495  Vnm_print(2, "parsePBAM: ran out of tokens on %s!\n", name);
496  return VRC_WARNING;
497  }
498  if (sscanf(tok, "%lf", &tf) == 0){
499  Vnm_print(2, "NOsh: Read non-float (%s) while parsing %s keyword!\n", tok, name);
500  return VRC_WARNING;
501  }else{
502  thee->transDiff[molind] = tf;
503  }
504 
505  // rot diffusion coeff
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->rotDiff[molind] = tf;
515  }
516  } else if (strncmp(thee->moveType[molind], "rot", 3) == 0)
517  {
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  thee->transDiff[molind] = 0.0;
528  }
529  } else{
530  thee->transDiff[molind] = 0.0;
531  thee->rotDiff[molind] = 0.0;
532  }
533 
534  return VRC_SUCCESS;
535 }
536 
537 VPRIVATE Vrc_Codes PBAMparm_parseTerm(PBAMparm *thee, Vio *sock){
538  const char* name = "term";
539  char tok[VMAX_BUFSIZE];
540  double tf;
541  int td;
542 
543  // looking for term name
544  if(Vio_scanf(sock, "%s", tok) == 0) {
545  Vnm_print(2, "parsePBAM: ran out of tokens on %s!\n", name);
546  return VRC_WARNING;
547  }else {
548  strncpy(thee->termnam[thee->termct], tok, CHR_MAXLEN);
549  }
550 
551  if (strncmp(thee->termnam[thee->termct], "contact", 7) == 0)
552  {
553  if(Vio_scanf(sock, "%s", tok) == 0) {
554  Vnm_print(2, "parsePBAM: ran out of tokens on %s!\n", name);
555  return VRC_WARNING;
556  }else{
557  strncpy(thee->confil[thee->confilct], tok, CHR_MAXLEN);
558  }
559 
560  if(Vio_scanf(sock, "%s", tok) == 0) {
561  Vnm_print(2, "parsePBAM: ran out of tokens on %s!\n", name);
562  return VRC_WARNING;
563  }
564  if (sscanf(tok, "%lf", &tf) == 0){
565  Vnm_print(2, "NOsh: Read non-float (%s) while parsing %s keyword!\n", tok, name);
566  return VRC_WARNING;
567  }else
568  {
569  thee->termVal[thee->termct] = tf;
570  thee->termnu[thee->termct][0] = 0;
571  thee->confilct += 1;
572  }
573  } else if (strncmp(thee->termnam[thee->termct], "time", 4) == 0)
574  {
575  if(Vio_scanf(sock, "%s", tok) == 0) {
576  Vnm_print(2, "parsePBAM: ran out of tokens on %s!\n", name);
577  return VRC_WARNING;
578  }
579  if (sscanf(tok, "%lf", &tf) == 0){
580  Vnm_print(2, "NOsh: Read non-float (%s) while parsing %s keyword!\n", tok, name);
581  return VRC_WARNING;
582  }else{
583  thee->termVal[thee->termct] = tf;
584  thee->termnu[thee->termct][0] = 0;
585  }
586  } else
587  {
588  if(Vio_scanf(sock, "%s", tok) == 0) {
589  Vnm_print(2, "parsePBAM: ran out of tokens on %s!\n", name);
590  return VRC_WARNING;
591  }
592  if (sscanf(tok, "%lf", &tf) == 0){
593  Vnm_print(2, "NOsh: Read non-float (%s) while parsing %s keyword!\n", tok, name);
594  return VRC_WARNING;
595  }else{
596  thee->termVal[thee->termct] = tf;
597  }
598 
599  if(Vio_scanf(sock, "%s", tok) == 0) {
600  Vnm_print(2, "parsePBAM: ran out of tokens on %s!\n", name);
601  return VRC_WARNING;
602  }
603  if (sscanf(tok, "%d", &td) == 0){
604  Vnm_print(2, "NOsh: Read non-float (%s) while parsing %s keyword!\n", tok, name);
605  return VRC_WARNING;
606  }else{
607  thee->termnu[thee->termct][0] = td-1;
608  }
609  }
610 
611  thee->setterm = 1;
612  thee->termct += 1;
613  return VRC_SUCCESS;
614 }
615 
616 VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock){
617  const char* name = "xyz";
618  char tok[VMAX_BUFSIZE];
619  int td, mol;
620 
621  if(Vio_scanf(sock, "%s", tok) == 0) {
622  Vnm_print(2, "parsePBAM: ran out of tokens on %s!\n", name);
623  return VRC_WARNING;
624  }
625 
626  // // looking for index
627  if (sscanf(tok, "%d", &td) == 0){
628  Vnm_print(2, "NOsh: Read non-int (%s) while parsing %s keyword!\n", tok, name);
629  return VRC_WARNING;
630  } else{
631  printf("This is my mol in parseXYZ: %d", td);
632  mol = td-1;
633  }
634 
635  // looking for move type = move, stat, rot
636  if(Vio_scanf(sock, "%s", tok) == 0) {
637  Vnm_print(2, "parsePBAM: ran out of tokens on %s!\n", name);
638  return VRC_WARNING;
639  } else {
640  strncpy(thee->xyzfil[mol][thee->xyzct[mol]], tok, CHR_MAXLEN);
641  thee->xyzct[mol] += 1;
642  }
643  return VRC_SUCCESS;
644 }
645 
646 VPUBLIC Vrc_Codes PBAMparm_parseToken(PBAMparm *thee, char tok[VMAX_BUFSIZE],
647  Vio *sock) {
648 
649  if (thee == VNULL) {
650  Vnm_print(2, "parsePBAM: got NULL thee!\n");
651  return VRC_WARNING;
652  }
653  if (sock == VNULL) {
654  Vnm_print(2, "parsePBAM: got NULL socket!\n");
655  return VRC_WARNING;
656  }
657 
658  Vnm_print(0, "PBAMparm_parseToken: trying %s...\n", tok);
659 
660  // General terms to parse
661  if (Vstring_strcasecmp(tok, "salt") == 0) {
662  return PBAMparm_parseSalt(thee, sock);
663  }else if (Vstring_strcasecmp(tok, "runtype") == 0) {
664  return PBAMparm_parseRunType(thee, sock);
665  }else if (Vstring_strcasecmp(tok, "runname") == 0) {
666  return PBAMparm_parseRunName(thee, sock);
667  }else if (Vstring_strcasecmp(tok, "randorient") == 0) {
668  return PBAMparm_parseRandorient(thee, sock);
669  }else if (Vstring_strcasecmp(tok, "pbc") == 0) {
670  return PBAMparm_parsePBCS(thee, sock);
671  }else if (Vstring_strcasecmp(tok, "units") == 0) {
672  return PBAMparm_parseUnits(thee, sock);
673  }
674 
675  // Electrostatic parsing
676  else if (Vstring_strcasecmp(tok, "gridpts") == 0) {
677  return PBAMparm_parseGridPts(thee, sock);
678  }else if (Vstring_strcasecmp(tok, "3dmap") == 0) {
679  return PBAMparm_parse3Dmap(thee, sock);
680  }else if (Vstring_strcasecmp(tok, "grid2d") == 0) {
681  return PBAMparm_parseGrid2D(thee, sock);
682  }else if (Vstring_strcasecmp(tok, "dx") == 0) {
683  return PBAMparm_parseDX(thee, sock);
684  }
685 
686  // Dynamics parsing
687  else if (Vstring_strcasecmp(tok, "ntraj") == 0) {
688  return PBAMparm_parseNtraj(thee, sock);
689  }else if (Vstring_strcasecmp(tok, "termcombine") == 0) {
690  return PBAMparm_parseTermcombine(thee, sock);
691  }else if (Vstring_strcasecmp(tok, "diff") == 0) {
692  return PBAMparm_parseDiff(thee, sock);
693  }else if (Vstring_strcasecmp(tok, "term") == 0) {
694  return PBAMparm_parseTerm(thee, sock);
695  }else if (Vstring_strcasecmp(tok, "xyz") == 0) {
696  return PBAMparm_parseXYZ(thee, sock);
697  }
698 
699 
700  else
701  return 0;
702 
703  /*else {
704  Vnm_print(2, "parsePBAM: Unrecognized keyword (%s)!\n", tok);
705  return VRC_WARNING;
706  }
707  return VRC_FAILURE;
708  */
709 }
VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock)
Find 2D grid filename and save it.
Definition: pbamparm.c:383
VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock)
Find 3D map filename and save it.
Definition: pbamparm.c:368
#define CHR_MAXLEN
Number of things that can be written out in a single calculation.
Definition: pbamparm.h:76
VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock)
Find randomorientation flag and save it as a boolean.
Definition: pbamparm.c:301
VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock)
Find diffusion coeffs for each molecule and save them.
Definition: pbamparm.c:465
Parameter structure for PBAM-specific variables from input files.
Definition: pbamparm.h:105
VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock)
Find DX filename and save it.
Definition: pbamparm.c:418
VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock)
Find runName and save it as a structure variable.
Definition: pbamparm.c:286
VPUBLIC void PBAMparm_dtor(PBAMparm **thee)
Object destructor.
Definition: pbamparm.c:122
VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock)
Find runType and save it as a structure variable.
Definition: pbamparm.c:271
enum ePBAMparm_CalcType PBAMparm_CalcType
Declare PBAMparm_CalcType type.
Definition: pbamparm.h:95
PBAMparm_CalcType type
Definition: pbamparm.h:107
VPUBLIC void PBAMparm_copy(PBAMparm *thee, PBAMparm *parm)
copy PBAMparm object int thee.
Definition: pbamparm.c:157
Contains declarations for class PBAMparm.
int parsed
Definition: pbamparm.h:108
#define VEMBED(rctag)
Allows embedding of RCS ID tags in object files.
Definition: vhal.h:556
VPUBLIC int Vstring_strcasecmp(const char *s1, const char *s2)
Case-insensitive string comparison (BSD standard)
Definition: vstring.c:66
VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock)
Find salt conc and save it as a structure variable.
Definition: pbamparm.c:252
VPUBLIC Vrc_Codes PBAMparm_ctor2(PBAMparm *thee, PBAMparm_CalcType type)
FORTRAN stub to construct PBAMparm object ?????????!!!!!!!
Definition: pbamparm.c:77
VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock)
Find Termination logic and save it.
Definition: pbamparm.c:432
VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock)
Find PBC flag and save the type and the boxlength.
Definition: pbamparm.c:307
VPUBLIC void PBAMparm_dtor2(PBAMparm *thee)
FORTRAN stub for object destructor ?????????!!!!!!!!!!!!
Definition: pbamparm.c:130
VPUBLIC Vrc_Codes PBAMparm_parseToken(PBAMparm *thee, char tok[VMAX_BUFSIZE], Vio *sock)
Parse an MG keyword from an input file.
Definition: pbamparm.c:646
VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock)
Find units flag and save units.
Definition: pbamparm.c:333
VPUBLIC PBAMparm * PBAMparm_ctor(PBAMparm_CalcType type)
Construct PBAMparm object.
Definition: pbamparm.c:66
VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock)
Find Grid points and save them.
Definition: pbamparm.c:348
VPUBLIC Vrc_Codes PBAMparm_check(PBAMparm *thee)
Consistency check for parameter values stored in object.
Definition: pbamparm.c:132
VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock)
Find xyz files for each molecule for each traj and save them.
Definition: pbamparm.c:616