src/mdlib/init.c

   1 /* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
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   4  *                This source code is part of
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   8  *          GROningen MAchine for Chemical Simulations
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  10  *                        VERSION 3.2.0
  11  * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
  12  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  13  * Copyright (c) 2001-2004, The GROMACS development team,
  14  * check out http://www.gromacs.org for more information.
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  35  */
  36 #ifdef HAVE_CONFIG_H
  37 #include <config.h>
  38 #endif
  39
  40 #include <stdio.h>
  41 #include "typedefs.h"
  42 #include "tpxio.h"
  43 #include "smalloc.h"
  44 #include "vec.h"
  45 #include "main.h"
  46 #include "mvdata.h"
  47 #include "gmx_fatal.h"
  48 #include "symtab.h"
  49 #include "txtdump.h"
  50 #include "mdatoms.h"
  51 #include "mdrun.h"
  52 #include "statutil.h"
  53 #include "names.h"
  54 #include "calcgrid.h"
  55 #include "gmx_random.h"
  56 #include "update.h"
  57 #include "mdebin.h"
  58
  59 #define BUFSIZE 256
  60
  61 #define NOT_FINISHED(l1,l2) \
  62   printf("not finished yet: lines %d .. %d in %s\n",l1,l2,__FILE__)
  63
  64 static char *int_title(const char *title,int nodeid,char buf[], int size)
  65 {
  66   sprintf(buf,"%s (%d)",title,nodeid);
  67
  68   return buf;
  69 }
  70
  71 void set_state_entries(t_state *state,const t_inputrec *ir,int nnodes)
  72 {
  73   int nnhpres;
  74
  75   /* The entries in the state in the tpx file might not correspond
  76    * with what is needed, so we correct this here.
  77    */
  78   state->flags = 0;
  79   if (ir->efep != efepNO)
  80     state->flags |= (1<<estLAMBDA);
  81   state->flags |= (1<<estX);
  82   if (state->x == NULL)
  83     snew(state->x,state->nalloc);
  84   if (EI_DYNAMICS(ir->eI)) {
  85     state->flags |= (1<<estV);
  86     if (state->v == NULL)
  87       snew(state->v,state->nalloc);
  88   }
  89   if (ir->eI == eiSD2) {
  90     state->flags |= (1<<estSDX);
  91     if (state->sd_X == NULL) {
  92       /* sd_X is not stored in the tpx file, so we need to allocate it */
  93       snew(state->sd_X,state->nalloc);
  94     }
  95   }
  96     if (ir->eI == eiCG)
  97     {
  98         state->flags |= (1<<estCGP);
  99         if (state->cg_p == NULL)
 100         {
 101             /* cg_p is not stored in the tpx file, so we need to allocate it */
 102             snew(state->cg_p,state->nalloc);
 103         }
 104     }
 105   if (EI_SD(ir->eI) || ir->eI == eiBD || ir->etc == etcVRESCALE) {
 106     state->nrng  = gmx_rng_n();
 107     state->nrngi = 1;
 108     if (EI_SD(ir->eI) || ir->eI == eiBD) {
 109       /* This will be correct later with DD */
 110       state->nrng  *= nnodes;
 111       state->nrngi *= nnodes;
 112     }
 113     state->flags |= ((1<<estLD_RNG) | (1<<estLD_RNGI));
 114     snew(state->ld_rng, state->nrng);
 115     snew(state->ld_rngi,state->nrngi);
 116   } else {
 117     state->nrng = 0;
 118   }
 119   state->nnhpres = 0;
 120   if (ir->ePBC != epbcNONE) {
 121     state->flags |= (1<<estBOX);
 122     if (PRESERVE_SHAPE(*ir)) {
 123       state->flags |= (1<<estBOX_REL);
 124     }
 125     if ((ir->epc == epcPARRINELLORAHMAN) || (ir->epc == epcMTTK)) {
 126       state->flags |= (1<<estBOXV);
 127     }
 128     if (ir->epc != epcNO) {
 129       if (IR_NPT_TROTTER(ir)) {
 130         state->nnhpres = 1;
 131         state->flags |= (1<<estNHPRES_XI);
 132         state->flags |= (1<<estNHPRES_VXI);
 133         state->flags |= (1<<estSVIR_PREV);
 134         state->flags |= (1<<estFVIR_PREV);
 135         state->flags |= (1<<estVETA);
 136         state->flags |= (1<<estVOL0);
 137       } else {
 138         state->flags |= (1<<estPRES_PREV);
 139       }
 140     }
 141   }
 142
 143   if (ir->etc == etcNOSEHOOVER) {
 144     state->flags |= (1<<estNH_XI);
 145     state->flags |= (1<<estNH_VXI);
 146   }
 147
 148   if (ir->etc == etcVRESCALE) {
 149     state->flags |= (1<<estTC_INT);
 150   }
 151
 152   init_gtc_state(state,state->ngtc,state->nnhpres,ir->opts.nhchainlength); /* allocate the space for nose-hoover chains */
 153   init_ekinstate(&state->ekinstate,ir);
 154
 155   init_energyhistory(&state->enerhist);
 156 }
 157
 158
 159 void init_parallel(FILE *log, t_commrec *cr, t_inputrec *inputrec,
 160                    gmx_mtop_t *mtop)
 161 {
 162   bcast_ir_mtop(cr,inputrec,mtop);
 163
 164
 165   if (inputrec->eI == eiBD || EI_SD(inputrec->eI)) {
 166     /* Make sure the random seeds are different on each node */
 167     inputrec->ld_seed += cr->nodeid;
 168   }
 169 }
 170
 171