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/inputrec.h"
  50 #include "gromacs/mdtypes/md_enums.h"
  51 #include "gromacs/utility/compare.h"
  52 #include "gromacs/utility/gmxassert.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 history_t::history_t() : disre_initf(0),
  59                          ndisrepairs(0),
  60                          disre_rm3tav(nullptr),
  61                          orire_initf(0),
  62                          norire_Dtav(0),
  63                          orire_Dtav(nullptr)
  64 {
  65 };
  66
  67 ekinstate_t::ekinstate_t() : bUpToDate(FALSE),
  68                              ekin_n(0),
  69                              ekinh(nullptr),
  70                              ekinf(nullptr),
  71                              ekinh_old(nullptr),
  72                              ekin_total(),
  73                              ekinscalef_nhc(),
  74                              ekinscaleh_nhc(),
  75                              vscale_nhc(),
  76                              dekindl(0),
  77                              mvcos(0)
  78 {
  79     clear_mat(ekin_total);
  80 };
  81
  82 static void init_swapstate(swapstate_t *swapstate)
  83 {
  84     /* Ion/water position swapping */
  85     swapstate->eSwapCoords            = 0;
  86     swapstate->nIonTypes              = 0;
  87     swapstate->nAverage               = 0;
  88     swapstate->fluxleak               = 0;
  89     swapstate->fluxleak_p             = nullptr;
  90     swapstate->bFromCpt               = 0;
  91     swapstate->nat[eChan0]            = 0;
  92     swapstate->nat[eChan1]            = 0;
  93     swapstate->xc_old_whole[eChan0]   = nullptr;
  94     swapstate->xc_old_whole[eChan1]   = nullptr;
  95     swapstate->xc_old_whole_p[eChan0] = nullptr;
  96     swapstate->xc_old_whole_p[eChan1] = nullptr;
  97     swapstate->ionType                = nullptr;
  98 }
  99
 100 void init_gtc_state(t_state *state, int ngtc, int nnhpres, int nhchainlength)
 101 {
 102     state->ngtc          = ngtc;
 103     state->nnhpres       = nnhpres;
 104     state->nhchainlength = nhchainlength;
 105     state->nosehoover_xi.resize(state->nhchainlength*state->ngtc, 0);
 106     state->nosehoover_vxi.resize(state->nhchainlength*state->ngtc, 0);
 107     state->therm_integral.resize(state->ngtc, 0);
 108     state->nhpres_xi.resize(state->nhchainlength*nnhpres, 0);
 109     state->nhpres_vxi.resize(state->nhchainlength*nnhpres, 0);
 110 }
 111
 112
 113 /* Checkpoint code relies on this function having no effect if
 114    state->natoms is > 0 and passed as natoms. */
 115 void state_change_natoms(t_state *state, int natoms)
 116 {
 117     state->natoms = natoms;
 118     if (state->natoms > 0)
 119     {
 120         /* We need to allocate one element extra, since we might use
 121          * (unaligned) 4-wide SIMD loads to access rvec entries.
 122          */
 123         if (state->flags & (1 << estX))
 124         {
 125             state->x.resize(state->natoms + 1);
 126         }
 127         if (state->flags & (1 << estV))
 128         {
 129             state->v.resize(state->natoms + 1);
 130         }
 131         if (state->flags & (1 << estCGP))
 132         {
 133             state->cg_p.resize(state->natoms + 1);
 134         }
 135     }
 136     else
 137     {
 138         state->x.resize(0);
 139         state->v.resize(0);
 140         state->cg_p.resize(0);
 141     }
 142 }
 143
 144 void init_dfhist_state(t_state *state, int dfhistNumLambda)
 145 {
 146     if (dfhistNumLambda > 0)
 147     {
 148         snew(state->dfhist, 1);
 149         init_df_history(state->dfhist, dfhistNumLambda);
 150     }
 151     else
 152     {
 153         state->dfhist = nullptr;
 154     }
 155 }
 156
 157 void comp_state(const t_state *st1, const t_state *st2,
 158                 gmx_bool bRMSD, real ftol, real abstol)
 159 {
 160     int i, j, nc;
 161
 162     fprintf(stdout, "comparing flags\n");
 163     cmp_int(stdout, "flags", -1, st1->flags, st2->flags);
 164     fprintf(stdout, "comparing box\n");
 165     cmp_rvecs(stdout, "box", DIM, st1->box, st2->box, FALSE, ftol, abstol);
 166     fprintf(stdout, "comparing box_rel\n");
 167     cmp_rvecs(stdout, "box_rel", DIM, st1->box_rel, st2->box_rel, FALSE, ftol, abstol);
 168     fprintf(stdout, "comparing boxv\n");
 169     cmp_rvecs(stdout, "boxv", DIM, st1->boxv, st2->boxv, FALSE, ftol, abstol);
 170     if (st1->flags & (1<<estSVIR_PREV))
 171     {
 172         fprintf(stdout, "comparing shake vir_prev\n");
 173         cmp_rvecs(stdout, "svir_prev", DIM, st1->svir_prev, st2->svir_prev, FALSE, ftol, abstol);
 174     }
 175     if (st1->flags & (1<<estFVIR_PREV))
 176     {
 177         fprintf(stdout, "comparing force vir_prev\n");
 178         cmp_rvecs(stdout, "fvir_prev", DIM, st1->fvir_prev, st2->fvir_prev, FALSE, ftol, abstol);
 179     }
 180     if (st1->flags & (1<<estPRES_PREV))
 181     {
 182         fprintf(stdout, "comparing prev_pres\n");
 183         cmp_rvecs(stdout, "pres_prev", DIM, st1->pres_prev, st2->pres_prev, FALSE, ftol, abstol);
 184     }
 185     cmp_int(stdout, "ngtc", -1, st1->ngtc, st2->ngtc);
 186     cmp_int(stdout, "nhchainlength", -1, st1->nhchainlength, st2->nhchainlength);
 187     if (st1->ngtc == st2->ngtc && st1->nhchainlength == st2->nhchainlength)
 188     {
 189         for (i = 0; i < st1->ngtc; i++)
 190         {
 191             nc = i*st1->nhchainlength;
 192             for (j = 0; j < nc; j++)
 193             {
 194                 cmp_real(stdout, "nosehoover_xi",
 195                          i, st1->nosehoover_xi[nc+j], st2->nosehoover_xi[nc+j], ftol, abstol);
 196             }
 197         }
 198     }
 199     cmp_int(stdout, "nnhpres", -1, st1->nnhpres, st2->nnhpres);
 200     if (st1->nnhpres == st2->nnhpres && st1->nhchainlength == st2->nhchainlength)
 201     {
 202         for (i = 0; i < st1->nnhpres; i++)
 203         {
 204             nc = i*st1->nhchainlength;
 205             for (j = 0; j < nc; j++)
 206             {
 207                 cmp_real(stdout, "nosehoover_xi",
 208                          i, st1->nhpres_xi[nc+j], st2->nhpres_xi[nc+j], ftol, abstol);
 209             }
 210         }
 211     }
 212
 213     cmp_int(stdout, "natoms", -1, st1->natoms, st2->natoms);
 214     if (st1->natoms == st2->natoms)
 215     {
 216         if ((st1->flags & (1<<estX)) && (st2->flags & (1<<estX)))
 217         {
 218             fprintf(stdout, "comparing x\n");
 219             cmp_rvecs(stdout, "x", st1->natoms, as_rvec_array(st1->x.data()), as_rvec_array(st2->x.data()), bRMSD, ftol, abstol);
 220         }
 221         if ((st1->flags & (1<<estV)) && (st2->flags & (1<<estV)))
 222         {
 223             fprintf(stdout, "comparing v\n");
 224             cmp_rvecs(stdout, "v", st1->natoms, as_rvec_array(st1->v.data()), as_rvec_array(st2->v.data()), bRMSD, ftol, abstol);
 225         }
 226     }
 227 }
 228
 229 rvec *getRvecArrayFromPaddedRVecVector(const PaddedRVecVector *v,
 230                                        unsigned int            n)
 231 {
 232     GMX_ASSERT(v->size() >= n, "We can't copy more elements than the vector size");
 233
 234     rvec *dest;
 235
 236     snew(dest, n);
 237
 238     const rvec *vPtr = as_rvec_array(v->data());
 239     for (unsigned int i = 0; i < n; i++)
 240     {
 241         copy_rvec(vPtr[i], dest[i]);
 242     }
 243
 244     return dest;
 245 }
 246
 247 t_state::t_state() : natoms(0),
 248                      ngtc(0),
 249                      nnhpres(0),
 250                      nhchainlength(0),
 251                      flags(0),
 252                      fep_state(0),
 253                      lambda(),
 254                      nosehoover_xi(),
 255                      nosehoover_vxi(),
 256                      nhpres_xi(),
 257                      nhpres_vxi(),
 258                      therm_integral(),
 259                      veta(0),
 260                      vol0(0),
 261                      x(),
 262                      v(),
 263                      cg_p(),
 264                      ekinstate(),
 265                      hist(),
 266                      swapstate(nullptr),
 267                      dfhist(nullptr),
 268                      edsamstate(nullptr),
 269                      ddp_count(0),
 270                      ddp_count_cg_gl(0),
 271                      cg_gl()
 272 {
 273     // It would be nicer to initialize these with {} or {{0}} in the
 274     // above initialization list, but uncrustify doesn't understand
 275     // that.
 276     // TODO Fix this if we switch to clang-format some time.
 277     // cppcheck-suppress useInitializationList
 278     lambda = {{ 0 }};
 279     clear_mat(box);
 280     clear_mat(box_rel);
 281     clear_mat(boxv);
 282     clear_mat(pres_prev);
 283     clear_mat(svir_prev);
 284     clear_mat(fvir_prev);
 285 }