src/kernel/readpull.c

   1 /*
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   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
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  35 #ifdef HAVE_CONFIG_H
  36 #include <config.h>
  37 #endif
  38
  39 #include <string.h>
  40 #include <stdlib.h>
  41 #include "sysstuff.h"
  42 #include "princ.h"
  43 #include "futil.h"
  44 #include "statutil.h"
  45 #include "vec.h"
  46 #include "smalloc.h"
  47 #include "typedefs.h"
  48 #include "names.h"
  49 #include "gmx_fatal.h"
  50 #include "macros.h"
  51 #include "rdgroup.h"
  52 #include "symtab.h"
  53 #include "readir.h"
  54 #include "string.h"
  55 #include "mdatoms.h"
  56 #include "pbc.h"
  57 #include "pull.h"
  58
  59
  60 static char pulldim[STRLEN];
  61
  62 static void string2dvec(char buf[], dvec nums)
  63 {
  64   if (sscanf(buf,"%lf%lf%lf",&nums[0],&nums[1],&nums[2]) != 3)
  65     gmx_fatal(FARGS,"Expected three numbers at input line %s",buf);
  66 }
  67
  68 static void init_pullgrp(t_pullgrp *pg,char *wbuf,
  69                          bool bRef,int eGeom,char *s_vec)
  70 {
  71   double d;
  72   int    n,m;
  73   dvec   vec;
  74
  75   pg->nweight = 0;
  76   while (sscanf(wbuf,"%lf %n",&d,&n) == 1) {
  77     if (pg->nweight % 100 == 0) {
  78       srenew(pg->weight,pg->nweight+100);
  79     }
  80     pg->weight[pg->nweight++] = d;
  81     wbuf += n;
  82   }
  83   if (!bRef) {
  84     if (eGeom == epullgDIST) {
  85       clear_dvec(vec);
  86     } else {
  87       string2dvec(s_vec,vec);
  88       if (eGeom == epullgDIR || eGeom == epullgCYL ||
  89           (eGeom == epullgPOS && dnorm(vec) != 0))
  90         /* Normalize the direction vector */
  91         dsvmul(1/dnorm(vec),vec,vec);
  92     }
  93     for(m=0; m<DIM; m++)
  94       pg->vec[m] = vec[m];
  95   }
  96 }
  97
  98 char **read_pullparams(int *ninp_p,t_inpfile **inp_p,
  99                        t_pull *pull,bool *bStart,int *nerror_p)
 100 {
 101   int  ninp,nerror,i,nchar,ndim,nscan,m;
 102   t_inpfile *inp;
 103   const char *tmp;
 104   char **grpbuf;
 105   char dummy[STRLEN],buf[STRLEN],init[STRLEN];
 106   const char *init_def1="0.0",*init_def3="0.0 0.0 0.0";
 107   char wbuf[STRLEN],VecTemp[STRLEN];
 108   dvec vec;
 109
 110   t_pullgrp *pgrp;
 111
 112   ninp   = *ninp_p;
 113   inp    = *inp_p;
 114   nerror = *nerror_p;
 115
 116   /* read pull parameters */
 117   CTYPE("Pull geometry: distance, direction, cylinder or position");
 118   EETYPE("pull_geometry",   pull->eGeom, epullg_names, &nerror, TRUE);
 119   CTYPE("Select components for the pull vector. default: Y Y Y");
 120   STYPE("pull_dim",         pulldim, "Y Y Y");
 121   CTYPE("Cylinder radius for dynamic reaction force groups (nm)");
 122   RTYPE("pull_r1",          pull->cyl_r1, 1.0);
 123   CTYPE("Switch from r1 to r0 in case of dynamic reaction force");
 124   RTYPE("pull_r0",          pull->cyl_r0, 1.5);
 125   RTYPE("pull_constr_tol",  pull->constr_tol, 1E-6);
 126   EETYPE("pull_start",      *bStart, yesno_names, &nerror, TRUE);
 127   ITYPE("pull_nstxout",     pull->nstxout, 10);
 128   ITYPE("pull_nstfout",     pull->nstfout,  1);
 129   CTYPE("Number of pull groups");
 130   ITYPE("pull_ngroups",     pull->ngrp,1);
 131
 132   if (pull->cyl_r1 > pull->cyl_r0) {
 133     fprintf(stderr,"ERROR: pull_r1 > pull_r0\n");
 134     nerror++;
 135   }
 136
 137   if (pull->ngrp < 1) {
 138     gmx_fatal(FARGS,"pull_ngroups should be >= 1");
 139   }
 140
 141   snew(pull->grp,pull->ngrp+1);
 142
 143   if (pull->eGeom == epullgPOS) {
 144     ndim = 3;
 145   } else {
 146     ndim = 1;
 147   }
 148
 149   /* pull group options */
 150   CTYPE("Group name, weight (default all 1), vector, init, rate (nm/ps), kJ/(mol*nm^2)");
 151   /* Read the pull groups */
 152   snew(grpbuf,pull->ngrp+1);
 153   for(i=0; i<pull->ngrp+1; i++) {
 154     pgrp = &pull->grp[i];
 155     snew(grpbuf[i],STRLEN);
 156     sprintf(buf,"pull_group%d",i);
 157     STYPE(buf,              grpbuf[i], "");
 158     sprintf(buf,"pull_weights%d",i);
 159     STYPE(buf,              wbuf, "");
 160     sprintf(buf,"pull_pbcatom%d",i);
 161     ITYPE(buf,              pgrp->pbcatom, 0);
 162     if (i > 0) {
 163       sprintf(buf,"pull_vec%d",i);
 164       STYPE(buf,              VecTemp, "0.0 0.0 0.0");
 165       sprintf(buf,"pull_init%d",i);
 166       STYPE(buf,              init, ndim==1 ? init_def1 : init_def3);
 167       nscan = sscanf(init,"%lf %lf %lf",&vec[0],&vec[1],&vec[2]);
 168       if (nscan != ndim) {
 169         fprintf(stderr,"ERROR: %s should have %d components\n",buf,ndim);
 170         nerror++;
 171       }
 172       for(m=0; m<DIM; m++) {
 173         pgrp->init[m] = (m<ndim ? vec[m] : 0.0);
 174       }
 175       sprintf(buf,"pull_rate%d",i);
 176       RTYPE(buf,              pgrp->rate, 0.0);
 177       sprintf(buf,"pull_k%d",i);
 178       RTYPE(buf,              pgrp->k, 0.0);
 179       sprintf(buf,"pull_kB%d",i);
 180       RTYPE(buf,              pgrp->kB, pgrp->k);
 181     }
 182
 183     /* Initialize the pull group */
 184     init_pullgrp(pgrp,wbuf,i==0,pull->eGeom,VecTemp);
 185   }
 186
 187   *ninp_p   = ninp;
 188   *inp_p    = inp;
 189   *nerror_p = nerror;
 190
 191   return grpbuf;
 192 }
 193
 194 void make_pull_groups(t_pull *pull,char **pgnames,t_blocka *grps,char **gnames)
 195 {
 196   int  d,nchar,g,ig=-1,i;
 197   char *ptr,pulldim1[STRLEN];
 198   t_pullgrp *pgrp;
 199
 200   ptr = pulldim;
 201   i = 0;
 202   for(d=0; d<DIM; d++) {
 203     if (sscanf(ptr,"%s%n",pulldim1,&nchar) != 1)
 204       gmx_fatal(FARGS,"Less than 3 pull dimensions given in pull_dim: '%s'",
 205                 pulldim);
 206
 207     if (strncasecmp(pulldim1,"N",1) == 0) {
 208       pull->dim[d] = 0;
 209     } else if (strncasecmp(pulldim1,"Y",1) == 0) {
 210       pull->dim[d] = 1;
 211       i++;
 212     } else {
 213       gmx_fatal(FARGS,"Please use Y(ES) or N(O) for pull_dim only (not %s)",
 214                 pulldim1);
 215     }
 216     ptr += nchar;
 217   }
 218   if (i == 0)
 219     gmx_fatal(FARGS,"All entries in pull_dim are N");
 220
 221   for(g=0; g<pull->ngrp+1; g++) {
 222     pgrp = &pull->grp[g];
 223     if (g == 0 && strcmp(pgnames[g],"") == 0) {
 224       pgrp->nat = 0;
 225     } else {
 226       ig = search_string(pgnames[g],grps->nr,gnames);
 227       pgrp->nat = grps->index[ig+1] - grps->index[ig];
 228     }
 229     if (pgrp->nat > 0) {
 230       fprintf(stderr,"Pull group %d '%s' has %d atoms\n",
 231               g,pgnames[g],pgrp->nat);
 232       snew(pgrp->ind,pgrp->nat);
 233       for(i=0; i<pgrp->nat; i++)
 234         pgrp->ind[i] = grps->a[grps->index[ig]+i];
 235
 236       if (pull->eGeom == epullgCYL && g == 0 && pgrp->nweight > 0)
 237         gmx_fatal(FARGS,"Weights are not supported for the reference group with cylinder pulling");
 238       if (pgrp->nweight > 0 && pgrp->nweight != pgrp->nat)
 239         gmx_fatal(FARGS,"Number of weights (%d) for pull group %d '%s' does not match the number of atoms (%d)",
 240                   pgrp->nweight,g,pgnames[g],pgrp->nat);
 241
 242       if (pgrp->nat == 1) {
 243         /* No pbc is required for this group */
 244         pgrp->pbcatom = -1;
 245       } else {
 246         if (pgrp->pbcatom > 0) {
 247           pgrp->pbcatom -= 1;
 248         } else if (pgrp->pbcatom == 0) {
 249           pgrp->pbcatom = pgrp->ind[(pgrp->nat-1)/2];
 250         } else {
 251           /* Use cosine weighting */
 252           pgrp->pbcatom = -1;
 253         }
 254       }
 255
 256       if (g > 0 && pull->eGeom != epullgDIST) {
 257         for(d=0; d<DIM; d++) {
 258           if (pgrp->vec[d] != 0 && pull->dim[d] == 0) {
 259             gmx_fatal(FARGS,"ERROR: pull_vec%d has non-zero %c-component while pull_dim in N\n",g,'x'+d);
 260           }
 261         }
 262       }
 263
 264       if ((pull->eGeom == epullgDIR || pull->eGeom == epullgCYL) &&
 265           g > 0 && norm2(pgrp->vec) == 0)
 266         gmx_fatal(FARGS,"pull_vec%d can not be zero with geometry %s",
 267                   g,EPULLGEOM(pull->eGeom));
 268       if ((pull->eGeom == epullgPOS) && pgrp->rate != 0 &&
 269           g > 0 && norm2(pgrp->vec) == 0)
 270         gmx_fatal(FARGS,"pull_vec%d can not be zero with geometry %s and non-zero rate",
 271                   g,EPULLGEOM(pull->eGeom));
 272     } else {
 273       if (g == 0) {
 274         if (pull->eGeom == epullgCYL)
 275           gmx_fatal(FARGS,"Absolute reference groups are not supported with geometry %s",EPULLGEOM(pull->eGeom));
 276       } else {
 277         gmx_fatal(FARGS,"Pull group %d '%s' is empty",g,pgnames[g]);
 278       }
 279       pgrp->pbcatom = -1;
 280     }
 281   }
 282 }
 283
 284 void set_pull_init(t_inputrec *ir,gmx_mtop_t *mtop,rvec *x,matrix box,
 285                    const output_env_t oenv,bool bStart)
 286 {
 287   t_mdatoms *md;
 288   t_pull    *pull;
 289   t_pullgrp *pgrp;
 290   t_pbc     pbc;
 291   int       ndim,g,m;
 292   double    t_start,tinvrate;
 293   rvec      init;
 294   dvec      dr,dev;
 295
 296   init_pull(NULL,ir,0,NULL,mtop,NULL,oenv,FALSE,0);
 297   md = init_mdatoms(NULL,mtop,ir->efep);
 298   atoms2md(mtop,ir,0,NULL,0,mtop->natoms,md);
 299   if (ir->efep)
 300     update_mdatoms(md,ir->init_lambda);
 301
 302   pull = ir->pull;
 303   if (pull->eGeom == epullgPOS)
 304     ndim = 3;
 305   else
 306     ndim = 1;
 307
 308   set_pbc(&pbc,ir->ePBC,box);
 309
 310   t_start = ir->init_t + ir->init_step*ir->delta_t;
 311
 312   pull_calc_coms(NULL,pull,md,&pbc,t_start,x,NULL);
 313
 314   fprintf(stderr,"Pull group  natoms  pbc atom  distance at start     reference at t=0\n");
 315   for(g=0; g<pull->ngrp+1; g++) {
 316     pgrp = &pull->grp[g];
 317     fprintf(stderr,"%8d  %8d  %8d ",g,pgrp->nat,pgrp->pbcatom+1);
 318     copy_rvec(pgrp->init,init);
 319     clear_rvec(pgrp->init);
 320     if (g > 0) {
 321       if (pgrp->rate == 0)
 322         tinvrate = 0;
 323       else
 324         tinvrate = t_start/pgrp->rate;
 325       get_pullgrp_distance(pull,&pbc,g,0,dr,dev);
 326       for(m=0; m<DIM; m++) {
 327         if (m < ndim)
 328           fprintf(stderr," %6.3f",dev[m]);
 329         else
 330           fprintf(stderr,"       ");
 331       }
 332       fprintf(stderr," ");
 333       for(m=0; m<DIM; m++) {
 334         if (bStart)
 335           pgrp->init[m] = init[m] + dev[m]
 336             - tinvrate*(pull->eGeom==epullgPOS ? pgrp->vec[m] : 1);
 337         else
 338           pgrp->init[m] = init[m];
 339         if (m < ndim)
 340           fprintf(stderr," %6.3f",pgrp->init[m]);
 341         else
 342           fprintf(stderr,"       ");
 343       }
 344     }
 345     fprintf(stderr,"\n");
 346   }
 347 }