src/gromacs/mdtypes/state.cpp

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  37 /* This file is completely threadsafe - keep it that way! */
  38 #include "gmxpre.h"
  39
  40 #include "state.h"
  41
  42 #include <cstring>
  43
  44 #include <algorithm>
  45
  46 #include "gromacs/math/vec.h"
  47 #include "gromacs/math/veccompare.h"
  48 #include "gromacs/mdtypes/df_history.h"
  49 #include "gromacs/mdtypes/energyhistory.h"
  50 #include "gromacs/mdtypes/inputrec.h"
  51 #include "gromacs/mdtypes/md_enums.h"
  52 #include "gromacs/utility/compare.h"
  53 #include "gromacs/utility/smalloc.h"
  54
  55 /* The source code in this file should be thread-safe.
  56       Please keep it that way. */
  57
  58 static void zero_history(history_t *hist)
  59 {
  60     hist->disre_initf  = 0;
  61     hist->ndisrepairs  = 0;
  62     hist->disre_rm3tav = NULL;
  63     hist->orire_initf  = 0;
  64     hist->norire_Dtav  = 0;
  65     hist->orire_Dtav   = NULL;
  66 }
  67
  68 static void zero_ekinstate(ekinstate_t *eks)
  69 {
  70     eks->ekin_n         = 0;
  71     eks->ekinh          = NULL;
  72     eks->ekinf          = NULL;
  73     eks->ekinh_old      = NULL;
  74     eks->ekinscalef_nhc = NULL;
  75     eks->ekinscaleh_nhc = NULL;
  76     eks->vscale_nhc     = NULL;
  77     eks->dekindl        = 0;
  78     eks->mvcos          = 0;
  79 }
  80
  81 static void init_swapstate(swapstate_t *swapstate)
  82 {
  83     /* Ion/water position swapping */
  84     swapstate->eSwapCoords            = 0;
  85     swapstate->nIonTypes              = 0;
  86     swapstate->nAverage               = 0;
  87     swapstate->fluxleak               = 0;
  88     swapstate->fluxleak_p             = NULL;
  89     swapstate->bFromCpt               = 0;
  90     swapstate->nat[eChan0]            = 0;
  91     swapstate->nat[eChan1]            = 0;
  92     swapstate->xc_old_whole[eChan0]   = NULL;
  93     swapstate->xc_old_whole[eChan1]   = NULL;
  94     swapstate->xc_old_whole_p[eChan0] = NULL;
  95     swapstate->xc_old_whole_p[eChan1] = NULL;
  96     swapstate->ionType                = NULL;
  97 }
  98
  99 void init_gtc_state(t_state *state, int ngtc, int nnhpres, int nhchainlength)
 100 {
 101     int i, j;
 102
 103     state->ngtc          = ngtc;
 104     state->nnhpres       = nnhpres;
 105     state->nhchainlength = nhchainlength;
 106     if (state->ngtc > 0)
 107     {
 108         snew(state->nosehoover_xi, state->nhchainlength*state->ngtc);
 109         snew(state->nosehoover_vxi, state->nhchainlength*state->ngtc);
 110         snew(state->therm_integral, state->ngtc);
 111         for (i = 0; i < state->ngtc; i++)
 112         {
 113             for (j = 0; j < state->nhchainlength; j++)
 114             {
 115                 state->nosehoover_xi[i*state->nhchainlength + j]   = 0.0;
 116                 state->nosehoover_vxi[i*state->nhchainlength + j]  = 0.0;
 117             }
 118         }
 119         for (i = 0; i < state->ngtc; i++)
 120         {
 121             state->therm_integral[i]  = 0.0;
 122         }
 123     }
 124     else
 125     {
 126         state->nosehoover_xi  = NULL;
 127         state->nosehoover_vxi = NULL;
 128         state->therm_integral = NULL;
 129     }
 130
 131     if (state->nnhpres > 0)
 132     {
 133         snew(state->nhpres_xi, state->nhchainlength*nnhpres);
 134         snew(state->nhpres_vxi, state->nhchainlength*nnhpres);
 135         for (i = 0; i < nnhpres; i++)
 136         {
 137             for (j = 0; j < state->nhchainlength; j++)
 138             {
 139                 state->nhpres_xi[i*nhchainlength + j]   = 0.0;
 140                 state->nhpres_vxi[i*nhchainlength + j]  = 0.0;
 141             }
 142         }
 143     }
 144     else
 145     {
 146         state->nhpres_xi  = NULL;
 147         state->nhpres_vxi = NULL;
 148     }
 149 }
 150
 151
 152 void init_state(t_state *state, int natoms, int ngtc, int nnhpres, int nhchainlength, int dfhistNumLambda)
 153 {
 154     int i;
 155
 156     state->natoms    = natoms;
 157     state->flags     = 0;
 158     state->fep_state = 0;
 159     state->lambda    = 0;
 160     snew(state->lambda, efptNR);
 161     for (i = 0; i < efptNR; i++)
 162     {
 163         state->lambda[i] = 0;
 164     }
 165     state->veta   = 0;
 166     clear_mat(state->box);
 167     clear_mat(state->box_rel);
 168     clear_mat(state->boxv);
 169     clear_mat(state->pres_prev);
 170     clear_mat(state->svir_prev);
 171     clear_mat(state->fvir_prev);
 172     init_gtc_state(state, ngtc, nnhpres, nhchainlength);
 173     state->nalloc = state->natoms;
 174     if (state->nalloc > 0)
 175     {
 176         /* We need to allocate one element extra, since we might use
 177          * (unaligned) 4-wide SIMD loads to access rvec entries.
 178          */
 179         snew(state->x, state->nalloc + 1);
 180         snew(state->v, state->nalloc + 1);
 181     }
 182     else
 183     {
 184         state->x = NULL;
 185         state->v = NULL;
 186     }
 187     state->cg_p = NULL;
 188     zero_history(&state->hist);
 189     zero_ekinstate(&state->ekinstate);
 190     snew(state->enerhist, 1);
 191     init_energyhistory(state->enerhist);
 192     if (dfhistNumLambda > 0)
 193     {
 194         snew(state->dfhist, 1);
 195         init_df_history(state->dfhist, dfhistNumLambda);
 196     }
 197     else
 198     {
 199         state->dfhist = NULL;
 200     }
 201     state->swapstate       = NULL;
 202     state->edsamstate      = NULL;
 203     state->ddp_count       = 0;
 204     state->ddp_count_cg_gl = 0;
 205     state->cg_gl           = NULL;
 206     state->cg_gl_nalloc    = 0;
 207 }
 208
 209 void done_state(t_state *state)
 210 {
 211     sfree(state->x);
 212     sfree(state->v);
 213     sfree(state->cg_p);
 214     sfree(state->enerhist);
 215     state->nalloc = 0;
 216     sfree(state->cg_gl);
 217     state->cg_gl_nalloc = 0;
 218     sfree(state->lambda);
 219     if (state->ngtc > 0)
 220     {
 221         sfree(state->nosehoover_xi);
 222         sfree(state->nosehoover_vxi);
 223         sfree(state->therm_integral);
 224     }
 225 }
 226
 227 void comp_state(const t_state *st1, const t_state *st2,
 228                 gmx_bool bRMSD, real ftol, real abstol)
 229 {
 230     int i, j, nc;
 231
 232     fprintf(stdout, "comparing flags\n");
 233     cmp_int(stdout, "flags", -1, st1->flags, st2->flags);
 234     fprintf(stdout, "comparing box\n");
 235     cmp_rvecs(stdout, "box", DIM, st1->box, st2->box, FALSE, ftol, abstol);
 236     fprintf(stdout, "comparing box_rel\n");
 237     cmp_rvecs(stdout, "box_rel", DIM, st1->box_rel, st2->box_rel, FALSE, ftol, abstol);
 238     fprintf(stdout, "comparing boxv\n");
 239     cmp_rvecs(stdout, "boxv", DIM, st1->boxv, st2->boxv, FALSE, ftol, abstol);
 240     if (st1->flags & (1<<estSVIR_PREV))
 241     {
 242         fprintf(stdout, "comparing shake vir_prev\n");
 243         cmp_rvecs(stdout, "svir_prev", DIM, st1->svir_prev, st2->svir_prev, FALSE, ftol, abstol);
 244     }
 245     if (st1->flags & (1<<estFVIR_PREV))
 246     {
 247         fprintf(stdout, "comparing force vir_prev\n");
 248         cmp_rvecs(stdout, "fvir_prev", DIM, st1->fvir_prev, st2->fvir_prev, FALSE, ftol, abstol);
 249     }
 250     if (st1->flags & (1<<estPRES_PREV))
 251     {
 252         fprintf(stdout, "comparing prev_pres\n");
 253         cmp_rvecs(stdout, "pres_prev", DIM, st1->pres_prev, st2->pres_prev, FALSE, ftol, abstol);
 254     }
 255     cmp_int(stdout, "ngtc", -1, st1->ngtc, st2->ngtc);
 256     cmp_int(stdout, "nhchainlength", -1, st1->nhchainlength, st2->nhchainlength);
 257     if (st1->ngtc == st2->ngtc && st1->nhchainlength == st2->nhchainlength)
 258     {
 259         for (i = 0; i < st1->ngtc; i++)
 260         {
 261             nc = i*st1->nhchainlength;
 262             for (j = 0; j < nc; j++)
 263             {
 264                 cmp_real(stdout, "nosehoover_xi",
 265                          i, st1->nosehoover_xi[nc+j], st2->nosehoover_xi[nc+j], ftol, abstol);
 266             }
 267         }
 268     }
 269     cmp_int(stdout, "nnhpres", -1, st1->nnhpres, st2->nnhpres);
 270     if (st1->nnhpres == st2->nnhpres && st1->nhchainlength == st2->nhchainlength)
 271     {
 272         for (i = 0; i < st1->nnhpres; i++)
 273         {
 274             nc = i*st1->nhchainlength;
 275             for (j = 0; j < nc; j++)
 276             {
 277                 cmp_real(stdout, "nosehoover_xi",
 278                          i, st1->nhpres_xi[nc+j], st2->nhpres_xi[nc+j], ftol, abstol);
 279             }
 280         }
 281     }
 282
 283     cmp_int(stdout, "natoms", -1, st1->natoms, st2->natoms);
 284     if (st1->natoms == st2->natoms)
 285     {
 286         if ((st1->flags & (1<<estX)) && (st2->flags & (1<<estX)))
 287         {
 288             fprintf(stdout, "comparing x\n");
 289             cmp_rvecs(stdout, "x", st1->natoms, st1->x, st2->x, bRMSD, ftol, abstol);
 290         }
 291         if ((st1->flags & (1<<estV)) && (st2->flags & (1<<estV)))
 292         {
 293             fprintf(stdout, "comparing v\n");
 294             cmp_rvecs(stdout, "v", st1->natoms, st1->v, st2->v, bRMSD, ftol, abstol);
 295         }
 296     }
 297 }