src/kernel/convparm.c

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
   5  * Copyright (c) 2001-2004, The GROMACS development team,
   6  * check out http://www.gromacs.org for more information.
   7  * Copyright (c) 2012, by the GROMACS development team, led by
   8  * David van der Spoel, Berk Hess, Erik Lindahl, and including many
   9  * others, as listed in the AUTHORS file in the top-level source
  10  * directory and at http://www.gromacs.org.
  11  *
  12  * GROMACS is free software; you can redistribute it and/or
  13  * modify it under the terms of the GNU Lesser General Public License
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  38 /* This file is completely threadsafe - keep it that way! */
  39 #ifdef HAVE_CONFIG_H
  40 #include <config.h>
  41 #endif
  42
  43 #include <math.h>
  44 #include "sysstuff.h"
  45 #include "physics.h"
  46 #include "vec.h"
  47 #include "smalloc.h"
  48 #include "typedefs.h"
  49 #include "gmx_fatal.h"
  50 #include "topio.h"
  51 #include "toputil.h"
  52 #include "convparm.h"
  53 #include "names.h"
  54 #include "gpp_atomtype.h"
  55 #include "maths.h"
  56
  57 static int round_check(real r,int limit,int ftype,const char *name)
  58 {
  59   int i;
  60
  61   if (r >= 0)
  62     i = (int)(r + 0.5);
  63   else
  64     i = (int)(r - 0.5);
  65
  66   if (r-i > 0.01 || r-i < -0.01)
  67     gmx_fatal(FARGS,"A non-integer value (%f) was supplied for '%s' in %s",
  68               r,name,interaction_function[ftype].longname);
  69
  70   if (i < limit)
  71     gmx_fatal(FARGS,"Value of '%s' in %s is %d, which is smaller than the minimum of %d",
  72               name,interaction_function[ftype].longname,i,limit);
  73
  74   return i;
  75 }
  76
  77 static void set_ljparams(int comb,double reppow,real v,real w,
  78                          real *c6,real *c12)
  79 {
  80   if (comb == eCOMB_ARITHMETIC || comb == eCOMB_GEOM_SIG_EPS) {
  81     if (v >= 0) {
  82       *c6  = 4*w*pow(v,6.0);
  83       *c12 = 4*w*pow(v,reppow);
  84     } else {
  85       /* Interpret negative sigma as c6=0 and c12 with -sigma */
  86       *c6  = 0;
  87       *c12 = 4*w*pow(-v,reppow);
  88     }
  89   } else {
  90     *c6  = v;
  91     *c12 = w;
  92   }
  93 }
  94
  95 /* A return value of 0 means parameters were assigned successfully,
  96  * returning -1 means this is an all-zero interaction that should not be added.
  97  */
  98 static int
  99 assign_param(t_functype ftype,t_iparams *newparam,
 100                          real old[MAXFORCEPARAM],int comb,double reppow)
 101 {
 102   int  i,j;
 103   real tmp;
 104   gmx_bool all_param_zero=TRUE;
 105
 106   /* Set to zero */
 107   for(j=0; (j<MAXFORCEPARAM); j++)
 108   {
 109       newparam->generic.buf[j]=0.0;
 110       /* If all parameters are zero we might not add some interaction types (selected below).
 111        * We cannot apply this to ALL interactions, since many have valid reasons for having
 112        * zero parameters (e.g. an index to a Cmap interaction, or LJ parameters), but
 113        * we use it for angles and torsions that are typically generated automatically.
 114        */
 115       all_param_zero = (all_param_zero==TRUE) && fabs(old[j])<GMX_REAL_MIN;
 116   }
 117
 118   if(all_param_zero==TRUE)
 119   {
 120       if(IS_ANGLE(ftype) || IS_RESTRAINT_TYPE(ftype) || ftype==F_IDIHS ||
 121          ftype==F_PDIHS || ftype==F_PIDIHS || ftype==F_RBDIHS || ftype==F_FOURDIHS)
 122       {
 123           return -1;
 124       }
 125   }
 126
 127   switch (ftype) {
 128   case F_G96ANGLES:
 129     /* Post processing of input data: store cosine iso angle itself */
 130     newparam->harmonic.rA =cos(old[0]*DEG2RAD);
 131     newparam->harmonic.krA=old[1];
 132     newparam->harmonic.rB =cos(old[2]*DEG2RAD);
 133     newparam->harmonic.krB=old[3];
 134     break;
 135   case F_G96BONDS:
 136     /* Post processing of input data: store square of length itself */
 137     newparam->harmonic.rA =sqr(old[0]);
 138     newparam->harmonic.krA=old[1];
 139     newparam->harmonic.rB =sqr(old[2]);
 140     newparam->harmonic.krB=old[3];
 141     break;
 142   case F_FENEBONDS:
 143     newparam->fene.bm=old[0];
 144     newparam->fene.kb=old[1];
 145     break;
 146   case F_RESTRBONDS:
 147     newparam->restraint.lowA = old[0];
 148     newparam->restraint.up1A = old[1];
 149     newparam->restraint.up2A = old[2];
 150     newparam->restraint.kA   = old[3];
 151     newparam->restraint.lowB = old[4];
 152     newparam->restraint.up1B = old[5];
 153     newparam->restraint.up2B = old[6];
 154     newparam->restraint.kB   = old[7];
 155     break;
 156   case F_TABBONDS:
 157   case F_TABBONDSNC:
 158   case F_TABANGLES:
 159   case F_TABDIHS:
 160     newparam->tab.table = round_check(old[0],0,ftype,"table index");
 161     newparam->tab.kA    = old[1];
 162     newparam->tab.kB    = old[3];
 163     break;
 164   case F_CROSS_BOND_BONDS:
 165     newparam->cross_bb.r1e=old[0];
 166     newparam->cross_bb.r2e=old[1];
 167     newparam->cross_bb.krr=old[2];
 168     break;
 169   case F_CROSS_BOND_ANGLES:
 170     newparam->cross_ba.r1e=old[0];
 171     newparam->cross_ba.r2e=old[1];
 172     newparam->cross_ba.r3e=old[2];
 173     newparam->cross_ba.krt=old[3];
 174     break;
 175   case F_UREY_BRADLEY:
 176     newparam->u_b.thetaA=old[0];
 177     newparam->u_b.kthetaA=old[1];
 178     newparam->u_b.r13A=old[2];
 179     newparam->u_b.kUBA=old[3];
 180     newparam->u_b.thetaB=old[4];
 181     newparam->u_b.kthetaB=old[5];
 182     newparam->u_b.r13B=old[6];
 183     newparam->u_b.kUBB=old[7];
 184     break;
 185   case F_QUARTIC_ANGLES:
 186     newparam->qangle.theta=old[0];
 187     for(i=0; i<5; i++)
 188       newparam->qangle.c[i]=old[i+1];
 189     break;
 190   case F_LINEAR_ANGLES:
 191     newparam->linangle.aA    = old[0];
 192     newparam->linangle.klinA = old[1];
 193     newparam->linangle.aB    = old[2];
 194     newparam->linangle.klinB = old[3];
 195     break;
 196   case F_BONDS:
 197   case F_ANGLES:
 198   case F_HARMONIC:
 199   case F_IDIHS:
 200     newparam->harmonic.rA =old[0];
 201     newparam->harmonic.krA=old[1];
 202     newparam->harmonic.rB =old[2];
 203     newparam->harmonic.krB=old[3];
 204     break;
 205   case F_MORSE:
 206     newparam->morse.b0A    =old[0];
 207     newparam->morse.cbA    =old[1];
 208     newparam->morse.betaA  =old[2];
 209     newparam->morse.b0B    =old[3];
 210     newparam->morse.cbB    =old[4];
 211     newparam->morse.betaB  =old[5];
 212     break;
 213   case F_CUBICBONDS:
 214     newparam->cubic.b0    =old[0];
 215     newparam->cubic.kb    =old[1];
 216     newparam->cubic.kcub  =old[2];
 217     break;
 218   case F_CONNBONDS:
 219     break;
 220   case F_POLARIZATION:
 221     newparam->polarize.alpha = old[0];
 222     break;
 223   case F_ANHARM_POL:
 224     newparam->anharm_polarize.alpha = old[0];
 225     newparam->anharm_polarize.drcut = old[1];
 226     newparam->anharm_polarize.khyp  = old[2];
 227     break;
 228   case F_WATER_POL:
 229     newparam->wpol.al_x   =old[0];
 230     newparam->wpol.al_y   =old[1];
 231     newparam->wpol.al_z   =old[2];
 232     newparam->wpol.rOH    =old[3];
 233     newparam->wpol.rHH    =old[4];
 234     newparam->wpol.rOD    =old[5];
 235     break;
 236   case F_THOLE_POL:
 237     newparam->thole.a      = old[0];
 238     newparam->thole.alpha1 = old[1];
 239     newparam->thole.alpha2 = old[2];
 240     if ((old[1] > 0) && (old[2] > 0))
 241       newparam->thole.rfac = old[0]*pow(old[1]*old[2],-1.0/6.0);
 242     else
 243       newparam->thole.rfac = 1;
 244     break;
 245   case F_BHAM:
 246     newparam->bham.a = old[0];
 247     newparam->bham.b = old[1];
 248     newparam->bham.c = old[2];
 249     break;
 250   case F_LJ14:
 251     set_ljparams(comb,reppow,old[0],old[1],&newparam->lj14.c6A,&newparam->lj14.c12A);
 252     set_ljparams(comb,reppow,old[2],old[3],&newparam->lj14.c6B,&newparam->lj14.c12B);
 253     break;
 254   case F_LJC14_Q:
 255     newparam->ljc14.fqq = old[0];
 256     newparam->ljc14.qi  = old[1];
 257     newparam->ljc14.qj  = old[2];
 258     set_ljparams(comb,reppow,old[3],old[4],&newparam->ljc14.c6,&newparam->ljc14.c12);
 259     break;
 260   case F_LJC_PAIRS_NB:
 261     newparam->ljcnb.qi = old[0];
 262     newparam->ljcnb.qj = old[1];
 263     set_ljparams(comb,reppow,old[2],old[3],&newparam->ljcnb.c6,&newparam->ljcnb.c12);
 264     break;
 265   case F_LJ:
 266     set_ljparams(comb,reppow,old[0],old[1],&newparam->lj.c6,&newparam->lj.c12);
 267     break;
 268   case F_PDIHS:
 269   case F_PIDIHS:
 270   case F_ANGRES:
 271   case F_ANGRESZ:
 272           newparam->pdihs.phiA = old[0];
 273           newparam->pdihs.cpA  = old[1];
 274
 275           /* Change 20100720: Amber occasionally uses negative multiplicities (mathematically OK),
 276            * so I have changed the lower limit to -99 /EL
 277            */
 278           newparam->pdihs.phiB = old[3];
 279           newparam->pdihs.cpB  = old[4];
 280           /* If both force constants are zero there is no interaction. Return -1 to signal
 281            * this entry should NOT be added.
 282            */
 283           if( fabs(newparam->pdihs.cpA) < GMX_REAL_MIN && fabs(newparam->pdihs.cpB) < GMX_REAL_MIN )
 284           {
 285               return -1;
 286           }
 287
 288           newparam->pdihs.mult = round_check(old[2],-99,ftype,"multiplicity");
 289
 290     break;
 291   case F_POSRES:
 292     newparam->posres.fcA[XX]   = old[0];
 293     newparam->posres.fcA[YY]   = old[1];
 294     newparam->posres.fcA[ZZ]   = old[2];
 295     newparam->posres.fcB[XX]   = old[3];
 296     newparam->posres.fcB[YY]   = old[4];
 297     newparam->posres.fcB[ZZ]   = old[5];
 298     newparam->posres.pos0A[XX] = old[6];
 299     newparam->posres.pos0A[YY] = old[7];
 300     newparam->posres.pos0A[ZZ] = old[8];
 301     newparam->posres.pos0B[XX] = old[9];
 302     newparam->posres.pos0B[YY] = old[10];
 303     newparam->posres.pos0B[ZZ] = old[11];
 304     break;
 305   case F_DISRES:
 306     newparam->disres.label = round_check(old[0],0,ftype,"label");
 307     newparam->disres.type  = round_check(old[1],1,ftype,"type'");
 308     newparam->disres.low   = old[2];
 309     newparam->disres.up1   = old[3];
 310     newparam->disres.up2   = old[4];
 311     newparam->disres.kfac  = old[5];
 312     break;
 313   case F_ORIRES:
 314     newparam->orires.ex    = round_check(old[0],1,ftype,"experiment") - 1;
 315     newparam->orires.label = round_check(old[1],1,ftype,"label");
 316     newparam->orires.power = round_check(old[2],0,ftype,"power");
 317     newparam->orires.c     = old[3];
 318     newparam->orires.obs   = old[4];
 319     newparam->orires.kfac  = old[5];
 320     break;
 321   case F_DIHRES:
 322     newparam->dihres.phiA  = old[0];
 323     newparam->dihres.dphiA = old[1];
 324     newparam->dihres.kfacA = old[2];
 325     newparam->dihres.phiB   = old[3];
 326     newparam->dihres.dphiB  = old[4];
 327     newparam->dihres.kfacB  = old[5];
 328     break;
 329   case F_RBDIHS:
 330     for (i=0; (i<NR_RBDIHS); i++) {
 331       newparam->rbdihs.rbcA[i]=old[i];
 332       newparam->rbdihs.rbcB[i]=old[NR_RBDIHS+i];
 333     }
 334     break;
 335   case F_FOURDIHS:
 336     /* Read the dihedral parameters to temporary arrays,
 337      * and convert them to the computationally faster
 338      * Ryckaert-Bellemans form.
 339      */
 340     /* Use conversion formula for OPLS to Ryckaert-Bellemans: */
 341     newparam->rbdihs.rbcA[0]=old[1]+0.5*(old[0]+old[2]);
 342     newparam->rbdihs.rbcA[1]=0.5*(3.0*old[2]-old[0]);
 343     newparam->rbdihs.rbcA[2]=4.0*old[3]-old[1];
 344     newparam->rbdihs.rbcA[3]=-2.0*old[2];
 345     newparam->rbdihs.rbcA[4]=-4.0*old[3];
 346     newparam->rbdihs.rbcA[5]=0.0;
 347
 348     newparam->rbdihs.rbcB[0]=old[NR_FOURDIHS+1]+0.5*(old[NR_FOURDIHS+0]+old[NR_FOURDIHS+2]);
 349     newparam->rbdihs.rbcB[1]=0.5*(3.0*old[NR_FOURDIHS+2]-old[NR_FOURDIHS+0]);
 350     newparam->rbdihs.rbcB[2]=4.0*old[NR_FOURDIHS+3]-old[NR_FOURDIHS+1];
 351     newparam->rbdihs.rbcB[3]=-2.0*old[NR_FOURDIHS+2];
 352     newparam->rbdihs.rbcB[4]=-4.0*old[NR_FOURDIHS+3];
 353     newparam->rbdihs.rbcB[5]=0.0;
 354     break;
 355   case F_CONSTR:
 356   case F_CONSTRNC:
 357     newparam->constr.dA = old[0];
 358     newparam->constr.dB = old[1];
 359     break;
 360   case F_SETTLE:
 361     newparam->settle.doh=old[0];
 362     newparam->settle.dhh=old[1];
 363     break;
 364   case F_VSITE2:
 365   case F_VSITE3:
 366   case F_VSITE3FD:
 367   case F_VSITE3OUT:
 368   case F_VSITE4FD:
 369   case F_VSITE4FDN:
 370     newparam->vsite.a=old[0];
 371     newparam->vsite.b=old[1];
 372     newparam->vsite.c=old[2];
 373     newparam->vsite.d=old[3];
 374     newparam->vsite.e=old[4];
 375     newparam->vsite.f=old[5];
 376     break;
 377   case F_VSITE3FAD:
 378     newparam->vsite.a=old[1] * cos(DEG2RAD * old[0]);
 379     newparam->vsite.b=old[1] * sin(DEG2RAD * old[0]);
 380     newparam->vsite.c=old[2];
 381     newparam->vsite.d=old[3];
 382     newparam->vsite.e=old[4];
 383     newparam->vsite.f=old[5];
 384     break;
 385   case F_VSITEN:
 386     newparam->vsiten.n = round_check(old[0],1,ftype,"number of atoms");
 387     newparam->vsiten.a = old[1];
 388     break;
 389   case F_CMAP:
 390     newparam->cmap.cmapA=old[0];
 391     newparam->cmap.cmapB=old[1];
 392     break;
 393   case F_GB12:
 394   case F_GB13:
 395   case F_GB14:
 396     newparam->gb.sar  = old[0];
 397     newparam->gb.st   = old[1];
 398     newparam->gb.pi   = old[2];
 399     newparam->gb.gbr  = old[3];
 400     newparam->gb.bmlt = old[4];
 401     break;
 402   default:
 403     gmx_fatal(FARGS,"unknown function type %d in %s line %d",
 404               ftype,__FILE__,__LINE__);
 405   }
 406     return 0;
 407 }
 408
 409 static int enter_params(gmx_ffparams_t *ffparams, t_functype ftype,
 410                         real forceparams[MAXFORCEPARAM],int comb,real reppow,
 411                         int start,gmx_bool bAppend)
 412 {
 413   t_iparams newparam;
 414   int       type;
 415   int       rc;
 416
 417   if( (rc=assign_param(ftype,&newparam,forceparams,comb,reppow))<0 )
 418   {
 419       /* -1 means this interaction is all-zero and should not be added */
 420       return rc;
 421   }
 422
 423   if (!bAppend) {
 424     for (type=start; (type<ffparams->ntypes); type++) {
 425       if (ffparams->functype[type]==ftype) {
 426         if (F_GB13 == ftype) {
 427           /* Occasionally, the way the 1-3 reference distance is
 428            * computed can lead to non-binary-identical results, but I
 429            * don't know why. */
 430           if ((gmx_within_tol(newparam.gb.sar,  ffparams->iparams[type].gb.sar,  1e-6)) &&
 431               (gmx_within_tol(newparam.gb.st,   ffparams->iparams[type].gb.st,   1e-6)) &&
 432               (gmx_within_tol(newparam.gb.pi,   ffparams->iparams[type].gb.pi,   1e-6)) &&
 433               (gmx_within_tol(newparam.gb.gbr,  ffparams->iparams[type].gb.gbr,  1e-6)) &&
 434               (gmx_within_tol(newparam.gb.bmlt, ffparams->iparams[type].gb.bmlt, 1e-6))) {
 435             return type;
 436           }
 437         }
 438         else {
 439         if (memcmp(&newparam,&ffparams->iparams[type],(size_t)sizeof(newparam)) == 0)
 440           return type;
 441         }
 442       }
 443     }
 444   }
 445   else {
 446     type = ffparams->ntypes;
 447   }
 448   if (debug)
 449     fprintf(debug,"copying newparam to ffparams->iparams[%d] (ntypes=%d)\n",
 450             type,ffparams->ntypes);
 451   memcpy(&ffparams->iparams[type],&newparam,(size_t)sizeof(newparam));
 452
 453   ffparams->ntypes++;
 454   ffparams->functype[type]=ftype;
 455
 456   return type;
 457 }
 458
 459 static void append_interaction(t_ilist *ilist,
 460                                int type,int nral,atom_id a[MAXATOMLIST])
 461 {
 462   int i,where1;
 463
 464   where1     = ilist->nr;
 465   ilist->nr += nral+1;
 466
 467   ilist->iatoms[where1++]=type;
 468   for (i=0; (i<nral); i++)
 469     ilist->iatoms[where1++]=a[i];
 470 }
 471
 472 static void enter_function(t_params *p,t_functype ftype,int comb,real reppow,
 473                            gmx_ffparams_t *ffparams,t_ilist *il,
 474                            int *maxtypes,
 475                            gmx_bool bNB,gmx_bool bAppend)
 476 {
 477   int     k,type,nr,nral,delta,start;
 478
 479   start = ffparams->ntypes;
 480   nr    = p->nr;
 481
 482   for (k=0; k<nr; k++) {
 483     if (*maxtypes <= ffparams->ntypes) {
 484       *maxtypes += 1000;
 485       srenew(ffparams->functype,*maxtypes);
 486       srenew(ffparams->iparams, *maxtypes);
 487       if (debug)
 488         fprintf(debug,"%s, line %d: srenewed idef->functype and idef->iparams to %d\n",
 489                 __FILE__,__LINE__,*maxtypes);
 490     }
 491     type = enter_params(ffparams,ftype,p->param[k].c,comb,reppow,start,bAppend);
 492     /* Type==-1 is used as a signal that this interaction is all-zero and should not be added. */
 493     if (!bNB && type>=0) {
 494       nral  = NRAL(ftype);
 495       delta = nr*(nral+1);
 496       srenew(il->iatoms,il->nr+delta);
 497       append_interaction(il,type,nral,p->param[k].a);
 498     }
 499   }
 500 }
 501
 502 void convert_params(int atnr,t_params nbtypes[],
 503                     t_molinfo *mi,int comb,double reppow,real fudgeQQ,
 504                     gmx_mtop_t *mtop)
 505 {
 506   int    i,j,maxtypes,mt;
 507   unsigned long  flags;
 508   gmx_ffparams_t *ffp;
 509   gmx_moltype_t *molt;
 510   t_params *plist;
 511
 512   maxtypes=0;
 513
 514   ffp = &mtop->ffparams;
 515   ffp->ntypes   = 0;
 516   ffp->atnr     = atnr;
 517   ffp->functype = NULL;
 518   ffp->iparams  = NULL;
 519   ffp->reppow   = reppow;
 520
 521   enter_function(&(nbtypes[F_LJ]),  (t_functype)F_LJ,    comb,reppow,ffp,NULL,
 522                  &maxtypes,TRUE,TRUE);
 523   enter_function(&(nbtypes[F_BHAM]),(t_functype)F_BHAM,  comb,reppow,ffp,NULL,
 524                  &maxtypes,TRUE,TRUE);
 525
 526   for(mt=0; mt<mtop->nmoltype; mt++) {
 527     molt = &mtop->moltype[mt];
 528     for(i=0; (i<F_NRE); i++) {
 529       molt->ilist[i].nr     = 0;
 530       molt->ilist[i].iatoms = NULL;
 531
 532       plist = mi[mt].plist;
 533
 534       flags = interaction_function[i].flags;
 535       if ((i != F_LJ) && (i != F_BHAM) && ((flags & IF_BOND) ||
 536                                            (flags & IF_VSITE) ||
 537                                            (flags & IF_CONSTRAINT))) {
 538         enter_function(&(plist[i]),(t_functype)i,comb,reppow,
 539                        ffp,&molt->ilist[i],
 540                        &maxtypes,FALSE,(i == F_POSRES));
 541       }
 542     }
 543   }
 544   if (debug) {
 545     fprintf(debug,"%s, line %d: There are %d functypes in idef\n",
 546             __FILE__,__LINE__,ffp->ntypes);
 547   }
 548
 549   ffp->fudgeQQ = fudgeQQ;
 550 }