src/kernel/convparm.c

   1 /*
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  35 /* This file is completely threadsafe - keep it that way! */
  36 #ifdef HAVE_CONFIG_H
  37 #include <config.h>
  38 #endif
  39
  40 #include <math.h>
  41 #include "sysstuff.h"
  42 #include "physics.h"
  43 #include "vec.h"
  44 #include "smalloc.h"
  45 #include "typedefs.h"
  46 #include "gmx_fatal.h"
  47 #include "topio.h"
  48 #include "toputil.h"
  49 #include "convparm.h"
  50 #include "names.h"
  51 #include "gpp_atomtype.h"
  52
  53 static int round_check(real r,int limit,int ftype,const char *name)
  54 {
  55   int i;
  56
  57   if (r >= 0)
  58     i = (int)(r + 0.5);
  59   else
  60     i = (int)(r - 0.5);
  61
  62   if (r-i > 0.01 || r-i < -0.01)
  63     gmx_fatal(FARGS,"A non-integer value (%f) was supplied for '%s' in %s",
  64               r,name,interaction_function[ftype].longname);
  65
  66   if (i < limit)
  67     gmx_fatal(FARGS,"Value of '%s' in %s is %d, which is smaller than the minimum of %d",
  68               name,interaction_function[ftype].longname,i,limit);
  69
  70   return i;
  71 }
  72
  73 static void set_ljparams(int comb,double reppow,real v,real w,
  74                          real *c6,real *c12)
  75 {
  76   if (comb == eCOMB_ARITHMETIC || comb == eCOMB_GEOM_SIG_EPS) {
  77     if (v >= 0) {
  78       *c6  = 4*w*pow(v,6.0);
  79       *c12 = 4*w*pow(v,reppow);
  80     } else {
  81       /* Interpret negative sigma as c6=0 and c12 with -sigma */
  82       *c6  = 0;
  83       *c12 = 4*w*pow(-v,reppow);
  84     }
  85   } else {
  86     *c6  = v;
  87     *c12 = w;
  88   }
  89 }
  90
  91 static void assign_param(t_functype ftype,t_iparams *newparam,
  92                          real old[MAXFORCEPARAM],int comb,double reppow)
  93 {
  94   int  i,j;
  95   real tmp;
  96
  97   /* Set to zero */
  98   for(j=0; (j<MAXFORCEPARAM); j++)
  99     {
 100       newparam->generic.buf[j]=0.0;
 101     }
 102   switch (ftype) {
 103   case F_G96ANGLES:
 104     /* Post processing of input data: store cosine iso angle itself */
 105     newparam->harmonic.rA =cos(old[0]*DEG2RAD);
 106     newparam->harmonic.krA=old[1];
 107     newparam->harmonic.rB =cos(old[2]*DEG2RAD);
 108     newparam->harmonic.krB=old[3];
 109     break;
 110   case F_G96BONDS:
 111     /* Post processing of input data: store square of length itself */
 112     newparam->harmonic.rA =sqr(old[0]);
 113     newparam->harmonic.krA=old[1];
 114     newparam->harmonic.rB =sqr(old[2]);
 115     newparam->harmonic.krB=old[3];
 116     break;
 117   case F_FENEBONDS:
 118     newparam->fene.bm=old[0];
 119     newparam->fene.kb=old[1];
 120     break;
 121   case F_RESTRBONDS:
 122     newparam->restraint.lowA = old[0];
 123     newparam->restraint.up1A = old[1];
 124     newparam->restraint.up2A = old[2];
 125     newparam->restraint.kA   = old[3];
 126     newparam->restraint.lowB = old[4];
 127     newparam->restraint.up1B = old[5];
 128     newparam->restraint.up2B = old[6];
 129     newparam->restraint.kB   = old[7];
 130     break;
 131   case F_TABBONDS:
 132   case F_TABBONDSNC:
 133   case F_TABANGLES:
 134   case F_TABDIHS:
 135     newparam->tab.table = round_check(old[0],0,ftype,"table index");
 136     newparam->tab.kA    = old[1];
 137     newparam->tab.kB    = old[3];
 138     break;
 139   case F_CROSS_BOND_BONDS:
 140     newparam->cross_bb.r1e=old[0];
 141     newparam->cross_bb.r2e=old[1];
 142     newparam->cross_bb.krr=old[2];
 143     break;
 144   case F_CROSS_BOND_ANGLES:
 145     newparam->cross_ba.r1e=old[0];
 146     newparam->cross_ba.r2e=old[1];
 147     newparam->cross_ba.r3e=old[2];
 148     newparam->cross_ba.krt=old[3];
 149     break;
 150   case F_UREY_BRADLEY:
 151     newparam->u_b.theta=old[0];
 152     newparam->u_b.ktheta=old[1];
 153     newparam->u_b.r13=old[2];
 154     newparam->u_b.kUB=old[3];
 155     break;
 156   case F_QUARTIC_ANGLES:
 157     newparam->qangle.theta=old[0];
 158     for(i=0; i<5; i++)
 159       newparam->qangle.c[i]=old[i+1];
 160     break;
 161   case F_ANGLES:
 162   case F_BONDS:
 163   case F_HARMONIC:
 164   case F_IDIHS:
 165     newparam->harmonic.rA =old[0];
 166     newparam->harmonic.krA=old[1];
 167     newparam->harmonic.rB =old[2];
 168     newparam->harmonic.krB=old[3];
 169     break;
 170   case F_MORSE:
 171     newparam->morse.b0    =old[0];
 172     newparam->morse.cb    =old[1];
 173     newparam->morse.beta  =old[2];
 174     break;
 175   case F_CUBICBONDS:
 176     newparam->cubic.b0    =old[0];
 177     newparam->cubic.kb    =old[1];
 178     newparam->cubic.kcub  =old[2];
 179     break;
 180   case F_CONNBONDS:
 181     break;
 182   case F_POLARIZATION:
 183     newparam->polarize.alpha = old[0];
 184     break;
 185   case F_WATER_POL:
 186     newparam->wpol.al_x   =old[0];
 187     newparam->wpol.al_y   =old[1];
 188     newparam->wpol.al_z   =old[2];
 189     newparam->wpol.rOH    =old[3];
 190     newparam->wpol.rHH    =old[4];
 191     newparam->wpol.rOD    =old[5];
 192     break;
 193   case F_THOLE_POL:
 194     newparam->thole.a      = old[0];
 195     newparam->thole.alpha1 = old[1];
 196     newparam->thole.alpha2 = old[2];
 197     if ((old[1] > 0) && (old[2] > 0))
 198       newparam->thole.rfac = old[0]*pow(old[1]*old[2],-1.0/6.0);
 199     else
 200       newparam->thole.rfac = 1;
 201     break;
 202   case F_BHAM:
 203     newparam->bham.a = old[0];
 204     newparam->bham.b = old[1];
 205     newparam->bham.c = old[2];
 206     break;
 207   case F_LJ14:
 208     set_ljparams(comb,reppow,old[0],old[1],&newparam->lj14.c6A,&newparam->lj14.c12A);
 209     set_ljparams(comb,reppow,old[2],old[3],&newparam->lj14.c6B,&newparam->lj14.c12B);
 210     break;
 211   case F_LJC14_Q:
 212     newparam->ljc14.fqq = old[0];
 213     newparam->ljc14.qi  = old[1];
 214     newparam->ljc14.qj  = old[2];
 215     set_ljparams(comb,reppow,old[3],old[4],&newparam->ljc14.c6,&newparam->ljc14.c12);
 216     break;
 217   case F_LJC_PAIRS_NB:
 218     newparam->ljcnb.qi = old[0];
 219     newparam->ljcnb.qj = old[1];
 220     set_ljparams(comb,reppow,old[2],old[3],&newparam->ljcnb.c6,&newparam->ljcnb.c12);
 221     break;
 222   case F_LJ:
 223     set_ljparams(comb,reppow,old[0],old[1],&newparam->lj.c6,&newparam->lj.c12);
 224     break;
 225   case F_PDIHS:
 226   case F_ANGRES:
 227   case F_ANGRESZ:
 228     newparam->pdihs.phiA = old[0];
 229     newparam->pdihs.cpA  = old[1];
 230
 231     /* Dont do any checks if all parameters are zero (such interactions will be removed) */
 232     tmp=fabs(old[0])+fabs(old[1])+fabs(old[2])+fabs(old[3])+fabs(old[4]);
 233     newparam->pdihs.mult = (tmp < GMX_REAL_MIN) ? 0 : round_check(old[2],1,ftype,"multiplicity");
 234
 235     newparam->pdihs.phiB = old[3];
 236     newparam->pdihs.cpB  = old[4];
 237     break;
 238   case F_POSRES:
 239     newparam->posres.fcA[XX]   = old[0];
 240     newparam->posres.fcA[YY]   = old[1];
 241     newparam->posres.fcA[ZZ]   = old[2];
 242     newparam->posres.fcB[XX]   = old[3];
 243     newparam->posres.fcB[YY]   = old[4];
 244     newparam->posres.fcB[ZZ]   = old[5];
 245     newparam->posres.pos0A[XX] = old[6];
 246     newparam->posres.pos0A[YY] = old[7];
 247     newparam->posres.pos0A[ZZ] = old[8];
 248     newparam->posres.pos0B[XX] = old[9];
 249     newparam->posres.pos0B[YY] = old[10];
 250     newparam->posres.pos0B[ZZ] = old[11];
 251     break;
 252   case F_DISRES:
 253     newparam->disres.label = round_check(old[0],0,ftype,"label");
 254     newparam->disres.type  = round_check(old[1],1,ftype,"type'");
 255     newparam->disres.low   = old[2];
 256     newparam->disres.up1   = old[3];
 257     newparam->disres.up2   = old[4];
 258     newparam->disres.kfac  = old[5];
 259     break;
 260   case F_ORIRES:
 261     newparam->orires.ex    = round_check(old[0],1,ftype,"experiment") - 1;
 262     newparam->orires.label = round_check(old[1],1,ftype,"label");
 263     newparam->orires.power = round_check(old[2],0,ftype,"power");
 264     newparam->orires.c     = old[3];
 265     newparam->orires.obs   = old[4];
 266     newparam->orires.kfac  = old[5];
 267     break;
 268   case F_DIHRES:
 269     newparam->dihres.label = round_check(old[0],0,ftype,"label");
 270     newparam->dihres.phi   = old[1];
 271     newparam->dihres.dphi  = old[2];
 272     newparam->dihres.kfac  = old[3];
 273     newparam->dihres.power = round_check(old[4],0,ftype,"power");
 274     break;
 275   case F_RBDIHS:
 276     for (i=0; (i<NR_RBDIHS); i++) {
 277       newparam->rbdihs.rbcA[i]=old[i];
 278       newparam->rbdihs.rbcB[i]=old[NR_RBDIHS+i];
 279     }
 280     break;
 281   case F_FOURDIHS:
 282     /* Read the dihedral parameters to temporary arrays,
 283      * and convert them to the computationally faster
 284      * Ryckaert-Bellemans form.
 285      */
 286     /* Use conversion formula for OPLS to Ryckaert-Bellemans: */
 287     newparam->rbdihs.rbcA[0]=old[1]+0.5*(old[0]+old[2]);
 288     newparam->rbdihs.rbcA[1]=0.5*(3.0*old[2]-old[0]);
 289     newparam->rbdihs.rbcA[2]=4.0*old[3]-old[1];
 290     newparam->rbdihs.rbcA[3]=-2.0*old[2];
 291     newparam->rbdihs.rbcA[4]=-4.0*old[3];
 292     newparam->rbdihs.rbcA[5]=0.0;
 293
 294     newparam->rbdihs.rbcB[0]=old[NR_FOURDIHS+1]+0.5*(old[NR_FOURDIHS+0]+old[NR_FOURDIHS+2]);
 295     newparam->rbdihs.rbcB[1]=0.5*(3.0*old[NR_FOURDIHS+2]-old[NR_FOURDIHS+0]);
 296     newparam->rbdihs.rbcB[2]=4.0*old[NR_FOURDIHS+3]-old[NR_FOURDIHS+1];
 297     newparam->rbdihs.rbcB[3]=-2.0*old[NR_FOURDIHS+2];
 298     newparam->rbdihs.rbcB[4]=-4.0*old[NR_FOURDIHS+3];
 299     newparam->rbdihs.rbcB[5]=0.0;
 300     break;
 301   case F_CONSTR:
 302   case F_CONSTRNC:
 303     newparam->constr.dA = old[0];
 304     newparam->constr.dB = old[1];
 305     break;
 306   case F_SETTLE:
 307     newparam->settle.doh=old[0];
 308     newparam->settle.dhh=old[1];
 309     break;
 310   case F_VSITE2:
 311   case F_VSITE3:
 312   case F_VSITE3FD:
 313   case F_VSITE3OUT:
 314   case F_VSITE4FD:
 315   case F_VSITE4FDN:
 316     newparam->vsite.a=old[0];
 317     newparam->vsite.b=old[1];
 318     newparam->vsite.c=old[2];
 319     newparam->vsite.d=old[3];
 320     newparam->vsite.e=old[4];
 321     newparam->vsite.f=old[5];
 322     break;
 323   case F_VSITE3FAD:
 324     newparam->vsite.a=old[1] * cos(DEG2RAD * old[0]);
 325     newparam->vsite.b=old[1] * sin(DEG2RAD * old[0]);
 326     newparam->vsite.c=old[2];
 327     newparam->vsite.d=old[3];
 328     newparam->vsite.e=old[4];
 329     newparam->vsite.f=old[5];
 330     break;
 331   case F_VSITEN:
 332     newparam->vsiten.n = round_check(old[0],1,ftype,"number of atoms");
 333     newparam->vsiten.a = old[1];
 334     break;
 335   case F_CMAP:
 336     newparam->cmap.cmapA=old[0];
 337     newparam->cmap.cmapB=old[1];
 338     break;
 339   case F_GB12:
 340   case F_GB13:
 341   case F_GB14:
 342     newparam->gb.sar  = old[0];
 343     newparam->gb.st   = old[1];
 344     newparam->gb.pi   = old[2];
 345     newparam->gb.gbr  = old[3];
 346     newparam->gb.bmlt = old[4];
 347     break;
 348   default:
 349     gmx_fatal(FARGS,"unknown function type %d in %s line %d",
 350               ftype,__FILE__,__LINE__);
 351   }
 352 }
 353
 354 static int enter_params(gmx_ffparams_t *ffparams, t_functype ftype,
 355                         real forceparams[MAXFORCEPARAM],int comb,real reppow,
 356                         int start,bool bAppend)
 357 {
 358   t_iparams newparam;
 359   int       type;
 360
 361   assign_param(ftype,&newparam,forceparams,comb,reppow);
 362   if (!bAppend) {
 363     for (type=start; (type<ffparams->ntypes); type++) {
 364       if (ffparams->functype[type]==ftype) {
 365         if (memcmp(&newparam,&ffparams->iparams[type],(size_t)sizeof(newparam)) == 0)
 366           return type;
 367       }
 368     }
 369   }
 370   else {
 371     type = ffparams->ntypes;
 372   }
 373   if (debug)
 374     fprintf(debug,"copying newparam to ffparams->iparams[%d] (ntypes=%d)\n",
 375             type,ffparams->ntypes);
 376   memcpy(&ffparams->iparams[type],&newparam,(size_t)sizeof(newparam));
 377
 378   ffparams->ntypes++;
 379   ffparams->functype[type]=ftype;
 380
 381   return type;
 382 }
 383
 384 static void append_interaction(t_ilist *ilist,
 385                                int type,int nral,atom_id a[MAXATOMLIST])
 386 {
 387   int i,where1;
 388
 389   where1     = ilist->nr;
 390   ilist->nr += nral+1;
 391
 392   ilist->iatoms[where1++]=type;
 393   for (i=0; (i<nral); i++)
 394     ilist->iatoms[where1++]=a[i];
 395 }
 396
 397 static void enter_function(t_params *p,t_functype ftype,int comb,real reppow,
 398                            gmx_ffparams_t *ffparams,t_ilist *il,
 399                            int *maxtypes,
 400                            bool bNB,bool bAppend)
 401 {
 402   int     k,type,nr,nral,delta,start;
 403
 404   start = ffparams->ntypes;
 405   nr    = p->nr;
 406
 407   for (k=0; k<nr; k++) {
 408     if (*maxtypes <= ffparams->ntypes) {
 409       *maxtypes += 1000;
 410       srenew(ffparams->functype,*maxtypes);
 411       srenew(ffparams->iparams, *maxtypes);
 412       if (debug)
 413         fprintf(debug,"%s, line %d: srenewed idef->functype and idef->iparams to %d\n",
 414                 __FILE__,__LINE__,*maxtypes);
 415     }
 416     type = enter_params(ffparams,ftype,p->param[k].c,comb,reppow,start,bAppend);
 417     if (!bNB) {
 418       nral  = NRAL(ftype);
 419       delta = nr*(nral+1);
 420       srenew(il->iatoms,il->nr+delta);
 421       append_interaction(il,type,nral,p->param[k].a);
 422     }
 423   }
 424 }
 425
 426 static void new_interaction_list(t_ilist *ilist)
 427 {
 428   int i;
 429
 430   ilist->nr=0;
 431   ilist->iatoms=NULL;
 432 }
 433
 434 void convert_params(int atnr,t_params nbtypes[],
 435                     t_molinfo *mi,int comb,double reppow,real fudgeQQ,
 436                     gmx_mtop_t *mtop)
 437 {
 438   int    i,j,maxtypes,mt;
 439   unsigned long  flags;
 440   gmx_ffparams_t *ffp;
 441   gmx_moltype_t *molt;
 442   t_params *plist;
 443
 444   maxtypes=0;
 445
 446   ffp = &mtop->ffparams;
 447   ffp->ntypes   = 0;
 448   ffp->atnr     = atnr;
 449   ffp->functype = NULL;
 450   ffp->iparams  = NULL;
 451   ffp->reppow   = reppow;
 452
 453   enter_function(&(nbtypes[F_LJ]),  (t_functype)F_LJ,    comb,reppow,ffp,NULL,
 454                  &maxtypes,TRUE,TRUE);
 455   enter_function(&(nbtypes[F_BHAM]),(t_functype)F_BHAM,  comb,reppow,ffp,NULL,
 456                  &maxtypes,TRUE,TRUE);
 457
 458   for(mt=0; mt<mtop->nmoltype; mt++) {
 459     molt = &mtop->moltype[mt];
 460     for(i=0; (i<F_NRE); i++) {
 461       molt->ilist[i].nr     = 0;
 462       molt->ilist[i].iatoms = NULL;
 463
 464       plist = mi[mt].plist;
 465
 466       flags = interaction_function[i].flags;
 467       if ((i != F_LJ) && (i != F_BHAM) && ((flags & IF_BOND) ||
 468                                            (flags & IF_VSITE) ||
 469                                            (flags & IF_CONSTRAINT))) {
 470         enter_function(&(plist[i]),(t_functype)i,comb,reppow,
 471                        ffp,&molt->ilist[i],
 472                        &maxtypes,FALSE,(i == F_POSRES));
 473       }
 474     }
 475   }
 476   if (debug) {
 477     fprintf(debug,"%s, line %d: There are %d functypes in idef\n",
 478             __FILE__,__LINE__,ffp->ntypes);
 479   }
 480
 481   ffp->fudgeQQ = fudgeQQ;
 482 }