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