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 nlambda)
 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     init_df_history(&state->dfhist, nlambda);
 193     init_swapstate(&state->swapstate);
 194     state->ddp_count       = 0;
 195     state->ddp_count_cg_gl = 0;
 196     state->cg_gl           = NULL;
 197     state->cg_gl_nalloc    = 0;
 198 }
 199
 200 void done_state(t_state *state)
 201 {
 202     if (state->x)
 203     {
 204         sfree(state->x);
 205     }
 206     if (state->v)
 207     {
 208         sfree(state->v);
 209     }
 210     if (state->cg_p)
 211     {
 212         sfree(state->cg_p);
 213     }
 214     state->nalloc = 0;
 215     if (state->cg_gl)
 216     {
 217         sfree(state->cg_gl);
 218     }
 219     state->cg_gl_nalloc = 0;
 220     if (state->lambda)
 221     {
 222         sfree(state->lambda);
 223     }
 224     if (state->ngtc > 0)
 225     {
 226         sfree(state->nosehoover_xi);
 227         sfree(state->nosehoover_vxi);
 228         sfree(state->therm_integral);
 229     }
 230 }
 231
 232 t_state *serial_init_local_state(t_state *state_global)
 233 {
 234     int      i;
 235     t_state *state_local;
 236
 237     snew(state_local, 1);
 238
 239     /* Copy all the contents */
 240     *state_local = *state_global;
 241     snew(state_local->lambda, efptNR);
 242     /* local storage for lambda */
 243     for (i = 0; i < efptNR; i++)
 244     {
 245         state_local->lambda[i] = state_global->lambda[i];
 246     }
 247
 248     return state_local;
 249 }
 250
 251 void comp_state(const t_state *st1, const t_state *st2,
 252                 gmx_bool bRMSD, real ftol, real abstol)
 253 {
 254     int i, j, nc;
 255
 256     fprintf(stdout, "comparing flags\n");
 257     cmp_int(stdout, "flags", -1, st1->flags, st2->flags);
 258     fprintf(stdout, "comparing box\n");
 259     cmp_rvecs(stdout, "box", DIM, st1->box, st2->box, FALSE, ftol, abstol);
 260     fprintf(stdout, "comparing box_rel\n");
 261     cmp_rvecs(stdout, "box_rel", DIM, st1->box_rel, st2->box_rel, FALSE, ftol, abstol);
 262     fprintf(stdout, "comparing boxv\n");
 263     cmp_rvecs(stdout, "boxv", DIM, st1->boxv, st2->boxv, FALSE, ftol, abstol);
 264     if (st1->flags & (1<<estSVIR_PREV))
 265     {
 266         fprintf(stdout, "comparing shake vir_prev\n");
 267         cmp_rvecs(stdout, "svir_prev", DIM, st1->svir_prev, st2->svir_prev, FALSE, ftol, abstol);
 268     }
 269     if (st1->flags & (1<<estFVIR_PREV))
 270     {
 271         fprintf(stdout, "comparing force vir_prev\n");
 272         cmp_rvecs(stdout, "fvir_prev", DIM, st1->fvir_prev, st2->fvir_prev, FALSE, ftol, abstol);
 273     }
 274     if (st1->flags & (1<<estPRES_PREV))
 275     {
 276         fprintf(stdout, "comparing prev_pres\n");
 277         cmp_rvecs(stdout, "pres_prev", DIM, st1->pres_prev, st2->pres_prev, FALSE, ftol, abstol);
 278     }
 279     cmp_int(stdout, "ngtc", -1, st1->ngtc, st2->ngtc);
 280     cmp_int(stdout, "nhchainlength", -1, st1->nhchainlength, st2->nhchainlength);
 281     if (st1->ngtc == st2->ngtc && st1->nhchainlength == st2->nhchainlength)
 282     {
 283         for (i = 0; i < st1->ngtc; i++)
 284         {
 285             nc = i*st1->nhchainlength;
 286             for (j = 0; j < nc; j++)
 287             {
 288                 cmp_real(stdout, "nosehoover_xi",
 289                          i, st1->nosehoover_xi[nc+j], st2->nosehoover_xi[nc+j], ftol, abstol);
 290             }
 291         }
 292     }
 293     cmp_int(stdout, "nnhpres", -1, st1->nnhpres, st2->nnhpres);
 294     if (st1->nnhpres == st2->nnhpres && st1->nhchainlength == st2->nhchainlength)
 295     {
 296         for (i = 0; i < st1->nnhpres; i++)
 297         {
 298             nc = i*st1->nhchainlength;
 299             for (j = 0; j < nc; j++)
 300             {
 301                 cmp_real(stdout, "nosehoover_xi",
 302                          i, st1->nhpres_xi[nc+j], st2->nhpres_xi[nc+j], ftol, abstol);
 303             }
 304         }
 305     }
 306
 307     cmp_int(stdout, "natoms", -1, st1->natoms, st2->natoms);
 308     if (st1->natoms == st2->natoms)
 309     {
 310         if ((st1->flags & (1<<estX)) && (st2->flags & (1<<estX)))
 311         {
 312             fprintf(stdout, "comparing x\n");
 313             cmp_rvecs(stdout, "x", st1->natoms, st1->x, st2->x, bRMSD, ftol, abstol);
 314         }
 315         if ((st1->flags & (1<<estV)) && (st2->flags & (1<<estV)))
 316         {
 317             fprintf(stdout, "comparing v\n");
 318             cmp_rvecs(stdout, "v", st1->natoms, st1->v, st2->v, bRMSD, ftol, abstol);
 319         }
 320     }
 321 }