src/mdlib/init.c

   1 /*
   2  *
   3  *                This source code is part of
   4  *
   5  *                 G   R   O   M   A   C   S
   6  *
   7  *          GROningen MAchine for Chemical Simulations
   8  *
   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
  16  * modify it under the terms of the GNU General Public License
  17  * as published by the Free Software Foundation; either version 2
  18  * of the License, or (at your option) any later version.
  19  *
  20  * If you want to redistribute modifications, please consider that
  21  * scientific software is very special. Version control is crucial -
  22  * bugs must be traceable. We will be happy to consider code for
  23  * inclusion in the official distribution, but derived work must not
  24  * be called official GROMACS. Details are found in the README & COPYING
  25  * files - if they are missing, get the official version at www.gromacs.org.
  26  *
  27  * To help us fund GROMACS development, we humbly ask that you cite
  28  * the papers on the package - you can find them in the top README file.
  29  *
  30  * For more info, check our website at http://www.gromacs.org
  31  *
  32  * And Hey:
  33  * GROwing Monsters And Cloning Shrimps
  34  */
  35 #ifdef HAVE_CONFIG_H
  36 #include <config.h>
  37 #endif
  38
  39 #include <stdio.h>
  40 #include "typedefs.h"
  41 #include "tpxio.h"
  42 #include "smalloc.h"
  43 #include "vec.h"
  44 #include "main.h"
  45 #include "mvdata.h"
  46 #include "gmx_fatal.h"
  47 #include "symtab.h"
  48 #include "txtdump.h"
  49 #include "mdatoms.h"
  50 #include "mdrun.h"
  51 #include "statutil.h"
  52 #include "names.h"
  53 #include "calcgrid.h"
  54 #include "gmx_random.h"
  55 #include "update.h"
  56 #include "mdebin.h"
  57
  58 #define BUFSIZE 256
  59
  60 #define NOT_FINISHED(l1,l2) \
  61   printf("not finished yet: lines %d .. %d in %s\n",l1,l2,__FILE__)
  62
  63 static char *int_title(const char *title,int nodeid,char buf[], int size)
  64 {
  65   sprintf(buf,"%s (%d)",title,nodeid);
  66
  67   return buf;
  68 }
  69
  70 static void set_state_entries(t_state *state,t_inputrec *ir,int nnodes)
  71 {
  72   int nnhpres;
  73
  74   /* The entries in the state in the tpx file might not correspond
  75    * with what is needed, so we correct this here.
  76    */
  77   state->flags = 0;
  78   if (ir->efep != efepNO)
  79     state->flags |= (1<<estLAMBDA);
  80   state->flags |= (1<<estX);
  81   if (state->x == NULL)
  82     snew(state->x,state->nalloc);
  83   if (EI_DYNAMICS(ir->eI)) {
  84     state->flags |= (1<<estV);
  85     if (state->v == NULL)
  86       snew(state->v,state->nalloc);
  87   }
  88   if (ir->eI == eiSD2) {
  89     state->flags |= (1<<estSDX);
  90     if (state->sd_X == NULL) {
  91       /* sd_X is not stored in the tpx file, so we need to allocate it */
  92       snew(state->sd_X,state->nalloc);
  93     }
  94   }
  95   if (ir->eI == eiCG) {
  96     state->flags |= (1<<estCGP);
  97   }
  98   if (EI_SD(ir->eI) || ir->eI == eiBD || ir->etc == etcVRESCALE) {
  99     state->nrng  = gmx_rng_n();
 100     state->nrngi = 1;
 101     if (EI_SD(ir->eI) || ir->eI == eiBD) {
 102       /* This will be correct later with DD */
 103       state->nrng  *= nnodes;
 104       state->nrngi *= nnodes;
 105     }
 106     state->flags |= ((1<<estLD_RNG) | (1<<estLD_RNGI));
 107     snew(state->ld_rng, state->nrng);
 108     snew(state->ld_rngi,state->nrngi);
 109   } else {
 110     state->nrng = 0;
 111   }
 112   state->nnhpres = 0;
 113   if (ir->ePBC != epbcNONE) {
 114     state->flags |= (1<<estBOX);
 115     if (PRESERVE_SHAPE(*ir)) {
 116       state->flags |= (1<<estBOX_REL);
 117     }
 118     if ((ir->epc == epcPARRINELLORAHMAN) || (ir->epc == epcMTTK)) {
 119       state->flags |= (1<<estBOXV);
 120     }
 121     if (ir->epc != epcNO) {
 122       if (IR_NPT_TROTTER(ir)) {
 123         state->nnhpres = 1;
 124         state->flags |= (1<<estNHPRES_XI);
 125         state->flags |= (1<<estNHPRES_VXI);
 126         state->flags |= (1<<estSVIR_PREV);
 127         state->flags |= (1<<estFVIR_PREV);
 128         state->flags |= (1<<estVETA);
 129         state->flags |= (1<<estVOL0);
 130       } else {
 131         state->flags |= (1<<estPRES_PREV);
 132       }
 133     }
 134   }
 135
 136   if (ir->etc == etcNOSEHOOVER) {
 137     state->flags |= (1<<estNH_XI);
 138     state->flags |= (1<<estNH_VXI);
 139   }
 140
 141   if (ir->etc == etcVRESCALE) {
 142     state->flags |= (1<<estTC_INT);
 143   }
 144
 145   init_gtc_state(state,state->ngtc,state->nnhpres,ir->opts.nhchainlength); /* allocate the space for nose-hoover chains */
 146   init_ekinstate(&state->ekinstate,ir);
 147
 148   init_energyhistory(&state->enerhist);
 149 }
 150
 151 void init_single(FILE *fplog,t_inputrec *inputrec,
 152                  const char *tpxfile,gmx_mtop_t *mtop,
 153                  t_state *state)
 154 {
 155   read_tpx_state(tpxfile,inputrec,state,NULL,mtop);
 156   set_state_entries(state,inputrec,1);
 157
 158   if (fplog)
 159     pr_inputrec(fplog,0,"Input Parameters",inputrec,FALSE);
 160 }
 161
 162 void init_parallel(FILE *log,const char *tpxfile,t_commrec *cr,
 163                    t_inputrec *inputrec,gmx_mtop_t *mtop,
 164                    t_state *state,
 165                    int list)
 166 {
 167   char buf[256];
 168
 169   if (MASTER(cr)) {
 170     init_inputrec(inputrec);
 171     read_tpx_state(tpxfile,inputrec,state,NULL,mtop);
 172     /* When we will be doing domain decomposition with separate PME nodes
 173      * the rng entries will be too large, we correct for this later.
 174      */
 175     set_state_entries(state,inputrec,cr->nnodes);
 176   }
 177   bcast_ir_mtop(cr,inputrec,mtop);
 178
 179   if (inputrec->eI == eiBD || EI_SD(inputrec->eI)) {
 180     /* Make sure the random seeds are different on each node */
 181     inputrec->ld_seed += cr->nodeid;
 182   }
 183
 184   /* Printing */
 185   if (list!=0 && log!=NULL)
 186   {
 187           if (list&LIST_INPUTREC)
 188                   pr_inputrec(log,0,"parameters of the run",inputrec,FALSE);
 189           if (list&LIST_X)
 190                   pr_rvecs(log,0,"box",state->box,DIM);
 191           if (list&LIST_X)
 192                   pr_rvecs(log,0,"box_rel",state->box_rel,DIM);
 193           if (list&LIST_V)
 194                   pr_rvecs(log,0,"boxv",state->boxv,DIM);
 195           if (list&LIST_X)
 196                   pr_rvecs(log,0,int_title("x",0,buf,255),state->x,state->natoms);
 197           if (list&LIST_V)
 198                   pr_rvecs(log,0,int_title("v",0,buf,255),state->v,state->natoms);
 199           if (list&LIST_TOP)
 200                   pr_mtop(log,0,int_title("topology",cr->nodeid,buf,255),mtop,TRUE);
 201           fflush(log);
 202   }
 203 }
 204
 205