src/kernel/gctio.c

   1 /*
   2  *
   3  *                This source code is part of
   4  *
   5  *                 G   R   O   M   A   C   S
   6  *
   7  *          GROningen MAchine for Chemical Simulations
   8  *
   9  *                        VERSION 3.2.0
  10  * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
  11  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  12  * Copyright (c) 2001-2004, The GROMACS development team,
  13  * check out http://www.gromacs.org for more information.
  14
  15  * This program is free software; you can redistribute it and/or
  16  * modify it under the terms of the GNU General Public License
  17  * as published by the Free Software Foundation; either version 2
  18  * of the License, or (at your option) any later version.
  19  *
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  26  *
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  29  *
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  34  */
  35 #ifdef HAVE_CONFIG_H
  36 #include <config.h>
  37 #endif
  38
  39 #include "typedefs.h"
  40 #include "xmdrun.h"
  41 #include "futil.h"
  42 #include "xvgr.h"
  43 #include "macros.h"
  44 #include "physics.h"
  45 #include "network.h"
  46 #include "smalloc.h"
  47 #include "string2.h"
  48 #include "readinp.h"
  49 #include "readir.h"
  50 #include "filenm.h"
  51 #include "names.h"
  52 #include "gmxfio.h"
  53
  54 const char *eoNames[eoNR] = {
  55   "Pres", "Epot", "Vir", "Dist", "Mu", "Force", "Fx", "Fy", "Fz",
  56   "Px", "Py", "Pz",
  57   "Polarizability", "Dipole", "Memory", "UseEinter", "UseVirial",
  58   "CombinationRule"
  59 };
  60
  61 static int Name2eo(char *s)
  62 {
  63   int i,res;
  64
  65   res=-1;
  66
  67   for(i=0; (i<eoNR); i++)
  68     if (gmx_strcasecmp(s,eoNames[i]) == 0) {
  69       res=i;
  70       fprintf(stderr,"Coupling to observable %d (%s)\n",res,eoNames[res]);
  71       break;
  72     }
  73
  74   return res;
  75 }
  76
  77 #define  block_bc(cr,   d) gmx_bcast(     sizeof(d),     &(d),(cr))
  78 #define nblock_bc(cr,nr,d) gmx_bcast((nr)*sizeof((d)[0]), (d),(cr))
  79 #define   snew_bc(cr,d,nr) { if (!MASTER(cr)) snew((d),(nr)); }
  80
  81 static void low_comm_tcr(t_commrec *cr,t_coupl_rec *tcr)
  82 {
  83   nblock_bc(cr,eoObsNR,tcr->ref_value);
  84
  85   block_bc(cr,tcr->nLJ);
  86   snew_bc(cr,tcr->tcLJ,tcr->nLJ);
  87   nblock_bc(cr,tcr->nLJ,tcr->tcLJ);
  88
  89   block_bc(cr,tcr->nBU);
  90   snew_bc(cr,tcr->tcBU,tcr->nBU);
  91   nblock_bc(cr,tcr->nBU,tcr->tcBU);
  92
  93   block_bc(cr,tcr->nQ);
  94   snew_bc(cr,tcr->tcQ,tcr->nQ);
  95   nblock_bc(cr,tcr->nQ,tcr->tcQ);
  96
  97   block_bc(cr,tcr->nmemory);
  98   block_bc(cr,tcr->bInter);
  99   block_bc(cr,tcr->bVirial);
 100   block_bc(cr,tcr->combrule);
 101 }
 102
 103 void comm_tcr(FILE *log,t_commrec *cr,t_coupl_rec **tcr)
 104 {
 105   if (!MASTER(cr))
 106     snew(*tcr,1);
 107
 108   low_comm_tcr(cr,*tcr);
 109 }
 110
 111 static void clear_lj(t_coupl_LJ *tc)
 112 {
 113   tc->at_i   = 0;
 114   tc->at_j   = 0;
 115   tc->eObs   = -1;
 116   tc->bPrint = TRUE;
 117   tc->c6     = 0.0;
 118   tc->c12    = 0.0;
 119   tc->xi_6   = 0.0;
 120   tc->xi_12  = 0.0;
 121 }
 122
 123 static void clear_bu(t_coupl_BU *tc)
 124 {
 125   tc->at_i   = 0;
 126   tc->at_j   = 0;
 127   tc->eObs   = -1;
 128   tc->bPrint = TRUE;
 129   tc->a      = 0.0;
 130   tc->b      = 0.0;
 131   tc->c      = 0.0;
 132   tc->xi_a   = 0.0;
 133   tc->xi_b   = 0.0;
 134   tc->xi_c   = 0.0;
 135 }
 136
 137 static void clear_q(t_coupl_Q *tc)
 138 {
 139   tc->at_i   = 0;
 140   tc->eObs   = -1;
 141   tc->bPrint = TRUE;
 142   tc->Q      = 0.0;
 143   tc->xi_Q   = 0.0;
 144 }
 145
 146 void copy_ff(t_coupl_rec *tcr,t_forcerec *fr,t_mdatoms *md,t_idef *idef)
 147 {
 148   int        i,j,ati,atj,type;
 149   t_coupl_LJ *tclj;
 150   t_coupl_BU *tcbu;
 151   t_coupl_Q  *tcq;
 152
 153   /* Save values for printing */
 154   for(i=0; (i<tcr->nLJ); i++) {
 155     tclj = &(tcr->tcLJ[i]);
 156
 157     ati  = tclj->at_i;
 158     atj  = tclj->at_j;
 159     if (atj == -1)
 160       atj = ati;
 161     tclj->c6  = C6(fr->nbfp,fr->ntype,ati,atj);
 162     tclj->c12 = C12(fr->nbfp,fr->ntype,ati,atj);
 163   }
 164
 165   for(i=0; (i<tcr->nBU); i++) {
 166     tcbu = &(tcr->tcBU[i]);
 167
 168     ati  = tcbu->at_i;
 169     atj  = tcbu->at_j;
 170     if (atj == -1)
 171       atj = ati;
 172     tcbu->a = BHAMA(fr->nbfp,fr->ntype,ati,atj);
 173     tcbu->b = BHAMB(fr->nbfp,fr->ntype,ati,atj);
 174     tcbu->c = BHAMC(fr->nbfp,fr->ntype,ati,atj);
 175   }
 176
 177   for(i=0; (i<tcr->nQ); i++) {
 178     tcq = &(tcr->tcQ[i]);
 179     for(j=0; (j<md->nr); j++) {
 180       if (md->typeA[j] == tcq->at_i) {
 181         tcr->tcQ[i].Q = md->chargeA[j];
 182         break;
 183       }
 184     }
 185   }
 186   for(i=0; (i<tcr->nIP); i++) {
 187     /* Let's just copy the whole struct !*/
 188     type = tcr->tIP[i].type;
 189     tcr->tIP[i].iprint=idef->iparams[type];
 190   }
 191 }
 192
 193 void write_gct(const char *fn,t_coupl_rec *tcr,t_idef *idef)
 194 {
 195   FILE *fp;
 196   int  i,ftype;
 197
 198   fp=gmx_fio_fopen(fn,"w");
 199   nice_header(fp,fn);
 200   fprintf(fp,"%-15s = %12g  ; Reference pressure for coupling\n",
 201           eoNames[eoPres],tcr->ref_value[eoPres]);
 202   fprintf(fp,"%-15s = %12g  ; Reference potential energy\n",
 203           eoNames[eoEpot],tcr->ref_value[eoEpot]);
 204   fprintf(fp,"%-15s = %12g  ; Reference distance\n",
 205           eoNames[eoDist],tcr->ref_value[eoDist]);
 206   fprintf(fp,"%-15s = %12g  ; Reference dipole\n",
 207           eoNames[eoMu],tcr->ref_value[eoMu]);
 208   fprintf(fp,"%-15s = %12g  ; Reference force\n",
 209           eoNames[eoForce],tcr->ref_value[eoForce]);
 210   fprintf(fp,"%-15s = %12g  ; Reference force in X dir\n",
 211           eoNames[eoFx],tcr->ref_value[eoFx]);
 212   fprintf(fp,"%-15s = %12g  ; Reference force in Y dir\n",
 213           eoNames[eoFy],tcr->ref_value[eoFy]);
 214   fprintf(fp,"%-15s = %12g  ; Reference force in Z dir\n",
 215           eoNames[eoFz],tcr->ref_value[eoFz]);
 216   fprintf(fp,"%-15s = %12g  ; Reference pres in X dir\n",
 217           eoNames[eoPx],tcr->ref_value[eoPx]);
 218   fprintf(fp,"%-15s = %12g  ; Reference pres in Y dir\n",
 219           eoNames[eoPy],tcr->ref_value[eoPy]);
 220   fprintf(fp,"%-15s = %12g  ; Reference pres in Z dir\n",
 221           eoNames[eoPz],tcr->ref_value[eoPz]);
 222   fprintf(fp,"%-15s = %12g  ; Polarizability used for the Epot correction\n",
 223           eoNames[eoPolarizability],tcr->ref_value[eoPolarizability]);
 224   fprintf(fp,"%-15s = %12g  ; Gas phase dipole moment used for Epot correction\n",
 225           eoNames[eoDipole],tcr->ref_value[eoDipole]);
 226   fprintf(fp,"%-15s = %12d  ; Memory for coupling. Makes it converge faster.\n",
 227           eoNames[eoMemory],tcr->nmemory);
 228   fprintf(fp,"%-15s = %12s  ; Use intermolecular Epot only (LJ+Coul)\n",
 229           eoNames[eoInter],yesno_names[tcr->bInter]);
 230   fprintf(fp,"%-15s = %12s  ; Use virial iso pressure\n",
 231           eoNames[eoUseVirial],yesno_names[tcr->bVirial]);
 232   fprintf(fp,"%-15s = %12d  ; Combination rule, same coding as in grompp.\n",
 233           eoNames[eoCombRule],tcr->combrule);
 234
 235   fprintf(fp,"\n; Q-Coupling   %6s  %12s\n","type","xi");
 236   for(i=0; (i<tcr->nQ); i++) {
 237     fprintf(fp,"%-8s = %8s  %6d  %12g\n",
 238             "Q",eoNames[tcr->tcQ[i].eObs],tcr->tcQ[i].at_i,tcr->tcQ[i].xi_Q);
 239   }
 240
 241   fprintf(fp,"\n; %8s %8s  %6s  %6s  %12s  %12s\n","Couple","To",
 242           "i-type","j-type","xi-c6","xi-c12");
 243   fprintf(fp,"; j-type == -1 means mixing rules will be applied!\n");
 244   for(i=0; (i<tcr->nLJ); i++) {
 245     fprintf(fp,"%-8s = %8s  %6d  %6d  %12g  %12g\n",
 246             "LJ",eoNames[tcr->tcLJ[i].eObs],
 247             tcr->tcLJ[i].at_i,tcr->tcLJ[i].at_j,
 248             tcr->tcLJ[i].xi_6,tcr->tcLJ[i].xi_12);
 249   }
 250
 251   fprintf(fp,"\n; %8s %8s  %6s  %6s  %12s  %12s  %12s\n","Couple","To",
 252           "i-type","j-type","xi-A","xi-B","xi-C");
 253   fprintf(fp,"; j-type == -1 means mixing rules will be applied!\n");
 254   for(i=0; (i<tcr->nBU); i++) {
 255     fprintf(fp,"%-8s = %8s  %6d  %6d  %12g  %12g  %12g\n",
 256             "BU",eoNames[tcr->tcBU[i].eObs],
 257             tcr->tcBU[i].at_i,tcr->tcBU[i].at_j,
 258             tcr->tcBU[i].xi_a,tcr->tcBU[i].xi_b,tcr->tcBU[i].xi_c);
 259   }
 260
 261   fprintf(fp,"\n; More Coupling\n");
 262   for(i=0; (i<tcr->nIP); i++) {
 263     ftype=idef->functype[tcr->tIP[i].type];
 264     switch (ftype) {
 265     case F_BONDS:
 266       fprintf(fp,"%-15s = %-8s  %4d  %12g  %12g\n",
 267               "Bonds",eoNames[tcr->tIP[i].eObs],tcr->tIP[i].type,
 268               tcr->tIP[i].xi.harmonic.krA,
 269               tcr->tIP[i].xi.harmonic.rA);
 270       break;
 271     default:
 272       fprintf(stderr,"ftype %s not supported (yet)\n",
 273               interaction_function[ftype].longname);
 274     }
 275   }
 276   gmx_fio_fclose(fp);
 277 }
 278
 279 static gmx_bool add_lj(int *nLJ,t_coupl_LJ **tcLJ,char *s,gmx_bool bObsUsed[])
 280 {
 281   int       j,ati,atj,eo;
 282   char      buf[256];
 283   double    xi6,xi12;
 284
 285   if (sscanf(s,"%s%d%d%lf%lf",buf,&ati,&atj,&xi6,&xi12) != 5)
 286     return TRUE;
 287   if ((eo=Name2eo(buf)) == -1)
 288     gmx_fatal(FARGS,"Invalid observable for LJ coupling: %s",buf);
 289
 290   for(j=0; (j<*nLJ); j++) {
 291     if ((((*tcLJ)[j].at_i == ati) && ((*tcLJ)[j].at_j == atj)) &&
 292         ((*tcLJ)[j].xi_6 || (*tcLJ)[j].xi_12) &&
 293         ((*tcLJ)[j].eObs == eo))
 294       break;
 295   }
 296   if (j == *nLJ) {
 297     ++(*nLJ);
 298     srenew((*tcLJ),*nLJ);
 299   }
 300   else
 301     fprintf(stderr,"\n*** WARNING: overwriting entry for LJ coupling '%s'\n",s);
 302
 303   clear_lj(&((*tcLJ)[j]));
 304   if (((*tcLJ)[j].eObs = eo) == -1) {
 305     gmx_fatal(FARGS,"Invalid observable for LJ coupling: %s",buf);
 306   }
 307   (*tcLJ)[j].at_i   = ati;
 308   (*tcLJ)[j].at_j   = atj;
 309   (*tcLJ)[j].xi_6   = xi6;
 310   (*tcLJ)[j].xi_12  = xi12;
 311   bObsUsed[eo] = TRUE;
 312
 313   return FALSE;
 314 }
 315
 316 static gmx_bool add_bu(int *nBU,t_coupl_BU **tcBU,char *s,gmx_bool bObsUsed[])
 317 {
 318   int       j,ati,atj,eo;
 319   char      buf[256];
 320   double    xia,xib,xic;
 321
 322   if (sscanf(s,"%s%d%d%lf%lf%lf",buf,&ati,&atj,&xia,&xib,&xic) != 6)
 323     return TRUE;
 324   if ((eo=Name2eo(buf)) == -1)
 325     gmx_fatal(FARGS,"Invalid observable for BU coupling: %s",buf);
 326
 327   for(j=0; (j<*nBU); j++) {
 328     if ((((*tcBU)[j].at_i == ati) && ((*tcBU)[j].at_j == atj)) &&
 329         ((*tcBU)[j].xi_a || (*tcBU)[j].xi_b || (*tcBU)[j].xi_c ) &&
 330         ((*tcBU)[j].eObs == eo))
 331       break;
 332   }
 333   if (j == *nBU) {
 334     ++(*nBU);
 335     srenew((*tcBU),*nBU);
 336   }
 337   else
 338     fprintf(stderr,"\n*** WARNING: overwriting entry for BU coupling '%s'\n",s);
 339
 340   clear_bu(&((*tcBU)[j]));
 341   if (((*tcBU)[j].eObs = eo) == -1) {
 342     gmx_fatal(FARGS,"Invalid observable for BU coupling: %s",buf);
 343   }
 344   (*tcBU)[j].at_i   = ati;
 345   (*tcBU)[j].at_j   = atj;
 346   (*tcBU)[j].xi_a   = xia;
 347   (*tcBU)[j].xi_b   = xib;
 348   (*tcBU)[j].xi_c   = xic;
 349   bObsUsed[eo] = TRUE;
 350
 351   return FALSE;
 352 }
 353
 354 static gmx_bool add_ip(int *nIP,t_coupl_iparams **tIP,char *s,int ftype,gmx_bool bObsUsed[])
 355 {
 356   int    i,eo,type;
 357   char   buf[256];
 358   double kb,b0;
 359
 360   switch (ftype) {
 361   case F_BONDS:
 362     /* Pick out the type */
 363     if (sscanf(s,"%s%d",buf,&type) != 2)
 364       return TRUE;
 365     if ((eo=Name2eo(buf)) == -1)
 366       gmx_fatal(FARGS,"Invalid observable for IP coupling: %s",buf);
 367
 368     /* Check whether this entry is there already */
 369     for(i=0; (i<*nIP); i++) {
 370       if ((*tIP)[i].type == type)
 371         break;
 372     }
 373     if (i < *nIP) {
 374       fprintf(stderr,"*** WARNING: overwriting entry for type %d\n",type);
 375     }
 376     else {
 377       i=*nIP;
 378       srenew((*tIP),i+1);
 379       (*nIP)++;
 380     }
 381     if (sscanf(s,"%s%d%lf%lf",buf,&type,&kb,&b0) != 4)
 382       return TRUE;
 383     (*tIP)[i].type=type;
 384     (*tIP)[i].eObs=eo;
 385     (*tIP)[i].xi.harmonic.krA = kb;
 386     (*tIP)[i].xi.harmonic.rA  = b0;
 387     bObsUsed[eo] = TRUE;
 388     break;
 389   default:
 390     fprintf(stderr,"ftype %s not supported (yet)\n",
 391             interaction_function[ftype].longname);
 392     return TRUE;
 393   }
 394   return FALSE;
 395 }
 396
 397 static gmx_bool add_q(int *nQ,t_coupl_Q **tcQ,char *s,gmx_bool bObsUsed[])
 398 {
 399   int       j,ati,eo;
 400   char      buf[256];
 401   double    xiQ;
 402
 403   if (sscanf(s,"%s%d%lf",buf,&ati,&xiQ) != 3)
 404     return TRUE;
 405
 406   for(j=0; (j<*nQ); j++) {
 407     if ((*tcQ)[j].at_i == ati)
 408       break;
 409   }
 410   if (j == *nQ) {
 411     ++(*nQ);
 412     srenew((*tcQ),*nQ);
 413   }
 414   else
 415     fprintf(stderr,"\n*** WARNING: overwriting entry for Q coupling '%s'\n",s);
 416
 417   clear_q(&((*tcQ)[j]));
 418   eo = (*tcQ)[j].eObs = Name2eo(buf);
 419   if ((*tcQ)[j].eObs == -1) {
 420     gmx_fatal(FARGS,"Invalid observable for Q coupling: %s",buf);
 421   }
 422   (*tcQ)[j].at_i   = ati;
 423   (*tcQ)[j].xi_Q  = xiQ;
 424   bObsUsed[eo] = TRUE;
 425
 426   return FALSE;
 427 }
 428
 429 void read_gct(const char *fn,t_coupl_rec *tcr)
 430 {
 431   warninp_t wi;
 432   t_inpfile *inp;
 433   int       i,j,ninp,nQ,nLJ,nBU,nIP;
 434   gmx_bool      bWrong;
 435
 436   wi = init_warning(FALSE,0);
 437
 438   inp=read_inpfile(fn,&ninp,NULL,wi);
 439
 440   for(i=0; (i<eoObsNR); i++) {
 441     tcr->bObsUsed[i] = FALSE;
 442     RTYPE (eoNames[i],  tcr->ref_value[i],      0.0);
 443   }
 444   ITYPE (eoNames[eoMemory],     tcr->nmemory,   1);
 445   ETYPE (eoNames[eoInter],      tcr->bInter,    yesno_names);
 446   ETYPE (eoNames[eoUseVirial],  tcr->bVirial,   yesno_names);
 447   ITYPE (eoNames[eoCombRule],   tcr->combrule,  1);
 448   tcr->tcLJ=NULL;
 449   tcr->tcBU=NULL;
 450   tcr->tcQ=NULL;
 451   tcr->tIP=NULL;
 452   nQ=nLJ=nBU=nIP=0;
 453
 454   for(i=0; (i<ninp); i++) {
 455     bWrong=FALSE;
 456     if (gmx_strcasecmp(inp[i].name,"LJ") == 0)
 457       bWrong=add_lj(&nLJ,&(tcr->tcLJ),inp[i].value,tcr->bObsUsed);
 458     else if (gmx_strcasecmp(inp[i].name,"BU") == 0)
 459       bWrong=add_bu(&nBU,&(tcr->tcBU),inp[i].value,tcr->bObsUsed);
 460     else if (gmx_strcasecmp(inp[i].name,"Q") == 0)
 461       bWrong=add_q(&nQ,&(tcr->tcQ),inp[i].value,tcr->bObsUsed);
 462     else if (gmx_strcasecmp(inp[i].name,"Bonds") == 0)
 463       bWrong=add_ip(&nIP,&(tcr->tIP),inp[i].value,F_BONDS,tcr->bObsUsed);
 464
 465     if (bWrong)
 466       fprintf(stderr,"Wrong line in %s: '%s = %s'\n",
 467               fn,inp[i].name,inp[i].value);
 468     /*sfree(inp[i].name);
 469       sfree(inp[i].value);*/
 470   }
 471   /* Check which ones have to be printed */
 472   for(i=1; (i<nQ); i++)
 473     for(j=0; (j<i); j++) {
 474       if (tcr->tcQ[i].at_i == tcr->tcQ[j].at_i)
 475         tcr->tcQ[j].bPrint=FALSE;
 476     }
 477   for(i=1; (i<nLJ); i++)
 478     for(j=0; (j<i); j++) {
 479       if (((tcr->tcLJ[i].at_i == tcr->tcLJ[j].at_i) &&
 480            (tcr->tcLJ[i].at_j == tcr->tcLJ[j].at_j)) ||
 481           ((tcr->tcLJ[i].at_i == tcr->tcLJ[j].at_j) &&
 482            (tcr->tcLJ[i].at_j == tcr->tcLJ[j].at_i)))
 483         tcr->tcLJ[j].bPrint=FALSE;
 484     }
 485
 486   for(i=1; (i<nBU); i++)
 487     for(j=0; (j<i); j++) {
 488       if (((tcr->tcBU[i].at_i == tcr->tcBU[j].at_i) &&
 489            (tcr->tcBU[i].at_j == tcr->tcBU[j].at_j)) ||
 490           ((tcr->tcBU[i].at_i == tcr->tcBU[j].at_j) &&
 491            (tcr->tcBU[i].at_j == tcr->tcBU[j].at_i)))
 492         tcr->tcBU[j].bPrint=FALSE;
 493     }
 494
 495   tcr->nQ  = nQ;
 496   tcr->nLJ = nLJ;
 497   tcr->nBU = nBU;
 498   tcr->nIP = nIP;
 499
 500   sfree(inp);
 501
 502   done_warning(wi,FARGS);
 503 }
 504