src/mdlib/wall.c

   1 /*
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  34
  35 #ifdef HAVE_CONFIG_H
  36 #include <config.h>
  37 #endif
  38
  39 #include <math.h>
  40 #include <string.h>
  41 #include "maths.h"
  42 #include "sysstuff.h"
  43 #include "typedefs.h"
  44 #include "macros.h"
  45 #include "smalloc.h"
  46 #include "force.h"
  47 #include "filenm.h"
  48 #include "nrnb.h"
  49 #include "vec.h"
  50
  51 void make_wall_tables(FILE *fplog,const output_env_t oenv,
  52                       const t_inputrec *ir,const char *tabfn,
  53                       const gmx_groups_t *groups,
  54                       t_forcerec *fr)
  55 {
  56   int  w,negp_pp,egp,i,j;
  57   int  *nm_ind;
  58   char buf[STRLEN];
  59   t_forcetable *tab;
  60
  61   negp_pp = ir->opts.ngener - ir->nwall;
  62   nm_ind  = groups->grps[egcENER].nm_ind;
  63
  64   if (fplog) {
  65     fprintf(fplog,"Reading user tables for %d energy groups with %d walls\n",
  66             negp_pp,ir->nwall);
  67   }
  68
  69   snew(fr->wall_tab,ir->nwall);
  70   for(w=0; w<ir->nwall; w++) {
  71     snew(fr->wall_tab[w],negp_pp);
  72     for(egp=0; egp<negp_pp; egp++) {
  73       /* If the energy group pair is excluded, we don't need a table */
  74       if (!(fr->egp_flags[egp*ir->opts.ngener+negp_pp+w] & EGP_EXCL)) {
  75         tab = &fr->wall_tab[w][egp];
  76         sprintf(buf,"%s",tabfn);
  77         sprintf(buf + strlen(tabfn) - strlen(ftp2ext(efXVG)) - 1,"_%s_%s.%s",
  78                 *groups->grpname[nm_ind[egp]],
  79                 *groups->grpname[nm_ind[negp_pp+w]],
  80                 ftp2ext(efXVG));
  81         *tab = make_tables(fplog,oenv,fr,FALSE,buf,0,GMX_MAKETABLES_FORCEUSER);
  82         /* Since wall have no charge, we can compress the table */
  83         for(i=0; i<=tab->n; i++)
  84           for(j=0; j<8; j++)
  85             tab->tab[8*i+j] = tab->tab[12*i+4+j];
  86       }
  87     }
  88   }
  89 }
  90
  91 static void wall_error(int a,rvec *x,real r)
  92 {
  93   gmx_fatal(FARGS,
  94             "An atom is beyond the wall: coordinates %f %f %f, distance %f\n"
  95             "You might want to use the mdp option wall_r_linpot",
  96             x[a][XX],x[a][YY],x[a][ZZ],r);
  97 }
  98
  99 real do_walls(t_inputrec *ir,t_forcerec *fr,matrix box,t_mdatoms *md,
 100               rvec x[],rvec f[],real lambda,real Vlj[],t_nrnb *nrnb)
 101 {
 102   int  nwall,w,lam,i;
 103   int  ntw[2],at,ntype,ngid,ggid,*egp_flags,*type;
 104   real *nbfp,lamfac,fac_d[2],fac_r[2],Cd,Cr,Vtot,Fwall[2];
 105   real wall_z[2],r,mr,r1,r2,r4,Vd,Vr,V,Fd,Fr,F,dvdlambda;
 106   dvec xf_z;
 107   int  n0,nnn;
 108   real tabscale,*VFtab,rt,eps,eps2,Yt,Ft,Geps,Heps,Heps2,Fp,VV,FF;
 109   unsigned short *gid=md->cENER;
 110   t_forcetable *tab;
 111
 112   nwall     = ir->nwall;
 113   ngid      = ir->opts.ngener;
 114   ntype     = fr->ntype;
 115   nbfp      = fr->nbfp;
 116   egp_flags = fr->egp_flags;
 117
 118   for(w=0; w<nwall; w++) {
 119     ntw[w] = 2*ntype*ir->wall_atomtype[w];
 120     if (ir->wall_type == ewt93) {
 121       fac_d[w] = ir->wall_density[w]*M_PI/6;
 122       fac_r[w] = ir->wall_density[w]*M_PI/45;
 123     } else if (ir->wall_type == ewt104) {
 124       fac_d[w] = ir->wall_density[w]*M_PI/2;
 125       fac_r[w] = ir->wall_density[w]*M_PI/5;
 126     }
 127     Fwall[w] = 0;
 128   }
 129   wall_z[0] = 0;
 130   wall_z[1] = box[ZZ][ZZ];
 131
 132   Vtot = 0;
 133   dvdlambda = 0;
 134   clear_dvec(xf_z);
 135   for(lam=0; lam<(md->nPerturbed ? 2 : 1); lam++) {
 136     if (md->nPerturbed) {
 137       if (lam == 0) {
 138         lamfac = 1 - lambda;
 139         type = md->typeA;
 140       } else {
 141         lamfac = 0;
 142         type = md->typeB;
 143       }
 144     } else {
 145       lamfac = 1;
 146       type = md->typeA;
 147     }
 148     for(i=md->start; i<md->start+md->homenr; i++) {
 149       for(w=0; w<nwall; w++) {
 150         /* The wall energy groups are always at the end of the list */
 151         ggid = gid[i]*ngid + ngid - nwall + w;
 152         at = type[i];
 153         Cd = nbfp[ntw[w]+2*at];
 154         Cr = nbfp[ntw[w]+2*at+1];
 155         if (!((Cd==0 && Cr==0) || egp_flags[ggid] & EGP_EXCL)) {
 156           if (w == 0) {
 157             r = x[i][ZZ];
 158           } else {
 159             r = wall_z[1] - x[i][ZZ];
 160           }
 161           if (r < ir->wall_r_linpot) {
 162             mr = ir->wall_r_linpot - r;
 163             r  = ir->wall_r_linpot;
 164           } else {
 165             mr = 0;
 166           }
 167           if (ir->wall_type == ewtTABLE) {
 168             if (r < 0)
 169               wall_error(i,x,r);
 170             tab = &(fr->wall_tab[w][gid[i]]);
 171             tabscale = tab->scale;
 172             VFtab    = tab->tab;
 173
 174             rt    = r*tabscale;
 175             n0    = rt;
 176             if (n0 >= tab->n) {
 177               /* Beyond the table range, set V and F to zero */
 178               V     = 0;
 179               F     = 0;
 180             } else {
 181               eps   = rt - n0;
 182               eps2  = eps*eps;
 183               /* Dispersion */
 184               nnn   = 8*n0;
 185               Yt    = VFtab[nnn];
 186               Ft    = VFtab[nnn+1];
 187               Geps  = VFtab[nnn+2]*eps;
 188               Heps2 = VFtab[nnn+3]*eps2;
 189               Fp    = Ft + Geps + Heps2;
 190               VV    = Yt + Fp*eps;
 191               FF    = Fp + Geps + 2.0*Heps2;
 192               Vd    = Cd*VV;
 193               Fd    = Cd*FF;
 194               /* Repulsion */
 195               nnn   = nnn + 4;
 196               Yt    = VFtab[nnn];
 197               Ft    = VFtab[nnn+1];
 198               Geps  = VFtab[nnn+2]*eps;
 199               Heps2 = VFtab[nnn+3]*eps2;
 200               Fp    = Ft + Geps + Heps2;
 201               VV    = Yt + Fp*eps;
 202               FF    = Fp + Geps + 2.0*Heps2;
 203               Vr    = Cr*VV;
 204               Fr    = Cr*FF;
 205               V     = Vd + Vr;
 206               F     = -lamfac*(Fd + Fr)*tabscale;
 207             }
 208           } else if (ir->wall_type == ewt93) {
 209             if (r <= 0)
 210               wall_error(i,x,r);
 211             r1 = 1/r;
 212             r2 = r1*r1;
 213             r4 = r2*r2;
 214             Vd = fac_d[w]*Cd*r2*r1;
 215             Vr = fac_r[w]*Cr*r4*r4*r1;
 216             V  = Vr - Vd;
 217             F  = lamfac*(9*Vr - 3*Vd)*r1;
 218           } else {
 219             if (r <= 0)
 220               wall_error(i,x,r);
 221             r1 = 1/r;
 222             r2 = r1*r1;
 223             r4 = r2*r2;
 224             Vd = fac_d[w]*Cd*r4;
 225             Vr = fac_r[w]*Cr*r4*r4*r2;
 226             V  = Vr - Vd;
 227             F  = lamfac*(10*Vr - 4*Vd)*r1;
 228           }
 229           if (mr > 0) {
 230             V += mr*F;
 231           }
 232           if (w == 1) {
 233             F = -F;
 234           }
 235           Vlj[ggid] += lamfac*V;
 236           Vtot      += V;
 237           f[i][ZZ]  += F;
 238           /* Because of the single sum virial calculation we need to add
 239            * the full virial contribution of the walls.
 240            * Since the force only has a z-component, there is only
 241            * a contribution to the z component of the virial tensor.
 242            * We could also determine the virial contribution directly,
 243            * which would be cheaper here, but that would require extra
 244            * communication for f_novirsum for with virtual sites in parallel.
 245            */
 246           xf_z[XX]  -= x[i][XX]*F;
 247           xf_z[YY]  -= x[i][YY]*F;
 248           xf_z[ZZ]  -= wall_z[w]*F;
 249         }
 250       }
 251     }
 252     if (md->nPerturbed)
 253       dvdlambda += (lam==0 ? -1 : 1)*Vtot;
 254
 255     inc_nrnb(nrnb,eNR_WALLS,md->homenr);
 256   }
 257
 258   for(i=0; i<DIM; i++) {
 259     fr->vir_wall_z[i] = -0.5*xf_z[i];
 260   }
 261
 262   return dvdlambda;
 263 }