src/gromacs/mdtypes/state.cpp

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  38 /* This file is completely threadsafe - keep it that way! */
  39 #include "gmxpre.h"
  40
  41 #include "state.h"
  42
  43 #include <cstring>
  44
  45 #include <algorithm>
  46
  47 #include "gromacs/math/paddedvector.h"
  48 #include "gromacs/math/vec.h"
  49 #include "gromacs/math/veccompare.h"
  50 #include "gromacs/mdtypes/awh_history.h"
  51 #include "gromacs/mdtypes/df_history.h"
  52 #include "gromacs/mdtypes/inputrec.h"
  53 #include "gromacs/mdtypes/md_enums.h"
  54 #include "gromacs/mdtypes/pull_params.h"
  55 #include "gromacs/mdtypes/swaphistory.h"
  56 #include "gromacs/pbcutil/boxutilities.h"
  57 #include "gromacs/pbcutil/pbc.h"
  58 #include "gromacs/utility/compare.h"
  59 #include "gromacs/utility/gmxassert.h"
  60 #include "gromacs/utility/smalloc.h"
  61 #include "gromacs/utility/stringutil.h"
  62
  63 #include "checkpointdata.h"
  64
  65 /* The source code in this file should be thread-safe.
  66       Please keep it that way. */
  67
  68 history_t::history_t() :
  69     disre_initf(0),
  70     ndisrepairs(0),
  71     disre_rm3tav(nullptr),
  72     orire_initf(0),
  73     norire_Dtav(0),
  74     orire_Dtav(nullptr)
  75 {
  76 }
  77
  78 ekinstate_t::ekinstate_t() :
  79     bUpToDate(FALSE),
  80     ekin_n(0),
  81     ekinh(nullptr),
  82     ekinf(nullptr),
  83     ekinh_old(nullptr),
  84     ekin_total(),
  85
  86     dekindl(0),
  87     mvcos(0)
  88 {
  89     clear_mat(ekin_total);
  90 }
  91
  92 namespace
  93 {
  94 /*!
  95  * \brief Enum describing the contents ekinstate_t writes to modular checkpoint
  96  *
  97  * When changing the checkpoint content, add a new element just above Count, and adjust the
  98  * checkpoint functionality.
  99  */
 100 enum class CheckpointVersion
 101 {
 102     Base, //!< First version of modular checkpointing
 103     Count //!< Number of entries. Add new versions right above this!
 104 };
 105 constexpr auto c_currentVersion = CheckpointVersion(int(CheckpointVersion::Count) - 1);
 106 } // namespace
 107
 108 template<gmx::CheckpointDataOperation operation>
 109 void ekinstate_t::doCheckpoint(gmx::CheckpointData<operation> checkpointData)
 110 {
 111     gmx::checkpointVersion(&checkpointData, "ekinstate_t version", c_currentVersion);
 112
 113     checkpointData.scalar("bUpToDate", &bUpToDate);
 114     if (!bUpToDate)
 115     {
 116         return;
 117     }
 118     auto numOfTensors = ekin_n;
 119     checkpointData.scalar("ekin_n", &numOfTensors);
 120     if (operation == gmx::CheckpointDataOperation::Read)
 121     {
 122         // If this isn't matching, we haven't allocated the right amount of data
 123         GMX_RELEASE_ASSERT(numOfTensors == ekin_n,
 124                            "ekinstate_t checkpoint reading: Tensor size mismatch.");
 125     }
 126     for (int idx = 0; idx < numOfTensors; ++idx)
 127     {
 128         checkpointData.tensor(gmx::formatString("ekinh %d", idx), ekinh[idx]);
 129         checkpointData.tensor(gmx::formatString("ekinf %d", idx), ekinf[idx]);
 130         checkpointData.tensor(gmx::formatString("ekinh_old %d", idx), ekinh_old[idx]);
 131     }
 132     checkpointData.arrayRef("ekinscalef_nhc", gmx::makeCheckpointArrayRef<operation>(ekinscalef_nhc));
 133     checkpointData.arrayRef("ekinscaleh_nhc", gmx::makeCheckpointArrayRef<operation>(ekinscaleh_nhc));
 134     checkpointData.arrayRef("vscale_nhc", gmx::makeCheckpointArrayRef<operation>(vscale_nhc));
 135     checkpointData.scalar("dekindl", &dekindl);
 136     checkpointData.scalar("mvcos", &mvcos);
 137
 138     if (operation == gmx::CheckpointDataOperation::Read)
 139     {
 140         hasReadEkinState = true;
 141     }
 142 }
 143
 144 // Explicit template instantiation
 145 template void ekinstate_t::doCheckpoint(gmx::CheckpointData<gmx::CheckpointDataOperation::Read> checkpointData);
 146 template void ekinstate_t::doCheckpoint(gmx::CheckpointData<gmx::CheckpointDataOperation::Write> checkpointData);
 147
 148 void init_gtc_state(t_state* state, int ngtc, int nnhpres, int nhchainlength)
 149 {
 150     state->ngtc          = ngtc;
 151     state->nnhpres       = nnhpres;
 152     state->nhchainlength = nhchainlength;
 153     state->nosehoover_xi.resize(state->nhchainlength * state->ngtc, 0);
 154     state->nosehoover_vxi.resize(state->nhchainlength * state->ngtc, 0);
 155     state->therm_integral.resize(state->ngtc, 0);
 156     state->baros_integral = 0.0;
 157     state->nhpres_xi.resize(state->nhchainlength * nnhpres, 0);
 158     state->nhpres_vxi.resize(state->nhchainlength * nnhpres, 0);
 159 }
 160
 161
 162 /* Checkpoint code relies on this function having no effect if
 163    state->natoms is > 0 and passed as natoms. */
 164 void state_change_natoms(t_state* state, int natoms)
 165 {
 166     state->natoms = natoms;
 167
 168     /* We need padding, since we might use SIMD access, but the
 169      * containers here all ensure that. */
 170     if (state->flags & (1 << estX))
 171     {
 172         state->x.resizeWithPadding(natoms);
 173     }
 174     if (state->flags & (1 << estV))
 175     {
 176         state->v.resizeWithPadding(natoms);
 177     }
 178     if (state->flags & (1 << estCGP))
 179     {
 180         state->cg_p.resizeWithPadding(natoms);
 181     }
 182 }
 183
 184 void init_dfhist_state(t_state* state, int dfhistNumLambda)
 185 {
 186     if (dfhistNumLambda > 0)
 187     {
 188         snew(state->dfhist, 1);
 189         init_df_history(state->dfhist, dfhistNumLambda);
 190     }
 191     else
 192     {
 193         state->dfhist = nullptr;
 194     }
 195 }
 196
 197 void comp_state(const t_state* st1, const t_state* st2, gmx_bool bRMSD, real ftol, real abstol)
 198 {
 199     int i, j, nc;
 200
 201     fprintf(stdout, "comparing flags\n");
 202     cmp_int(stdout, "flags", -1, st1->flags, st2->flags);
 203     fprintf(stdout, "comparing box\n");
 204     cmp_rvecs(stdout, "box", DIM, st1->box, st2->box, FALSE, ftol, abstol);
 205     fprintf(stdout, "comparing box_rel\n");
 206     cmp_rvecs(stdout, "box_rel", DIM, st1->box_rel, st2->box_rel, FALSE, ftol, abstol);
 207     fprintf(stdout, "comparing boxv\n");
 208     cmp_rvecs(stdout, "boxv", DIM, st1->boxv, st2->boxv, FALSE, ftol, abstol);
 209     if (st1->flags & (1 << estSVIR_PREV))
 210     {
 211         fprintf(stdout, "comparing shake vir_prev\n");
 212         cmp_rvecs(stdout, "svir_prev", DIM, st1->svir_prev, st2->svir_prev, FALSE, ftol, abstol);
 213     }
 214     if (st1->flags & (1 << estFVIR_PREV))
 215     {
 216         fprintf(stdout, "comparing force vir_prev\n");
 217         cmp_rvecs(stdout, "fvir_prev", DIM, st1->fvir_prev, st2->fvir_prev, FALSE, ftol, abstol);
 218     }
 219     if (st1->flags & (1 << estPRES_PREV))
 220     {
 221         fprintf(stdout, "comparing prev_pres\n");
 222         cmp_rvecs(stdout, "pres_prev", DIM, st1->pres_prev, st2->pres_prev, FALSE, ftol, abstol);
 223     }
 224     cmp_int(stdout, "ngtc", -1, st1->ngtc, st2->ngtc);
 225     cmp_int(stdout, "nhchainlength", -1, st1->nhchainlength, st2->nhchainlength);
 226     if (st1->ngtc == st2->ngtc && st1->nhchainlength == st2->nhchainlength)
 227     {
 228         for (i = 0; i < st1->ngtc; i++)
 229         {
 230             nc = i * st1->nhchainlength;
 231             for (j = 0; j < nc; j++)
 232             {
 233                 cmp_real(stdout, "nosehoover_xi", i, st1->nosehoover_xi[nc + j],
 234                          st2->nosehoover_xi[nc + j], ftol, abstol);
 235             }
 236         }
 237     }
 238     cmp_int(stdout, "nnhpres", -1, st1->nnhpres, st2->nnhpres);
 239     if (st1->nnhpres == st2->nnhpres && st1->nhchainlength == st2->nhchainlength)
 240     {
 241         for (i = 0; i < st1->nnhpres; i++)
 242         {
 243             nc = i * st1->nhchainlength;
 244             for (j = 0; j < nc; j++)
 245             {
 246                 cmp_real(stdout, "nosehoover_xi", i, st1->nhpres_xi[nc + j], st2->nhpres_xi[nc + j],
 247                          ftol, abstol);
 248             }
 249         }
 250     }
 251
 252     cmp_int(stdout, "natoms", -1, st1->natoms, st2->natoms);
 253     if (st1->natoms == st2->natoms)
 254     {
 255         if ((st1->flags & (1 << estX)) && (st2->flags & (1 << estX)))
 256         {
 257             fprintf(stdout, "comparing x\n");
 258             cmp_rvecs(stdout, "x", st1->natoms, st1->x.rvec_array(), st2->x.rvec_array(), bRMSD,
 259                       ftol, abstol);
 260         }
 261         if ((st1->flags & (1 << estV)) && (st2->flags & (1 << estV)))
 262         {
 263             fprintf(stdout, "comparing v\n");
 264             cmp_rvecs(stdout, "v", st1->natoms, st1->v.rvec_array(), st2->v.rvec_array(), bRMSD,
 265                       ftol, abstol);
 266         }
 267     }
 268 }
 269
 270 rvec* makeRvecArray(gmx::ArrayRef<const gmx::RVec> v, gmx::index n)
 271 {
 272     GMX_ASSERT(v.ssize() >= n, "We can't copy more elements than the vector size");
 273
 274     rvec* dest;
 275
 276     snew(dest, n);
 277
 278     const rvec* vPtr = as_rvec_array(v.data());
 279     for (gmx::index i = 0; i < n; i++)
 280     {
 281         copy_rvec(vPtr[i], dest[i]);
 282     }
 283
 284     return dest;
 285 }
 286
 287 t_state::t_state() :
 288     natoms(0),
 289     ngtc(0),
 290     nnhpres(0),
 291     nhchainlength(0),
 292     flags(0),
 293     fep_state(0),
 294     lambda(),
 295
 296     baros_integral(0),
 297     veta(0),
 298     vol0(0),
 299
 300     ekinstate(),
 301     hist(),
 302     dfhist(nullptr),
 303     awhHistory(nullptr),
 304     ddp_count(0),
 305     ddp_count_cg_gl(0)
 306
 307 {
 308     // It would be nicer to initialize these with {} or {{0}} in the
 309     // above initialization list, but uncrustify doesn't understand
 310     // that.
 311     // TODO Fix this if we switch to clang-format some time.
 312     lambda = { { 0 } };
 313     clear_mat(box);
 314     clear_mat(box_rel);
 315     clear_mat(boxv);
 316     clear_mat(pres_prev);
 317     clear_mat(svir_prev);
 318     clear_mat(fvir_prev);
 319 }
 320
 321 void set_box_rel(const t_inputrec* ir, t_state* state)
 322 {
 323     /* Make sure the box obeys the restrictions before we fix the ratios */
 324     correct_box(nullptr, 0, state->box);
 325
 326     clear_mat(state->box_rel);
 327
 328     if (inputrecPreserveShape(ir))
 329     {
 330         const int ndim = ir->epct == epctSEMIISOTROPIC ? 2 : 3;
 331         do_box_rel(ndim, ir->deform, state->box_rel, state->box, true);
 332     }
 333 }
 334
 335 void preserve_box_shape(const t_inputrec* ir, matrix box_rel, matrix box)
 336 {
 337     if (inputrecPreserveShape(ir))
 338     {
 339         const int ndim = ir->epct == epctSEMIISOTROPIC ? 2 : 3;
 340         do_box_rel(ndim, ir->deform, box_rel, box, false);
 341     }
 342 }
 343
 344 void printLambdaStateToLog(FILE* fplog, const gmx::ArrayRef<real> lambda, const bool isInitialOutput)
 345 {
 346     if (fplog != nullptr)
 347     {
 348         fprintf(fplog, "%s vector of lambda components:[ ", isInitialOutput ? "Initial" : "Current");
 349         for (const auto& l : lambda)
 350         {
 351             fprintf(fplog, "%10.4f ", l);
 352         }
 353         fprintf(fplog, "]\n%s", isInitialOutput ? "" : "\n");
 354     }
 355 }
 356
 357 void initialize_lambdas(FILE* fplog, const t_inputrec& ir, bool isMaster, int* fep_state, gmx::ArrayRef<real> lambda)
 358 {
 359     /* TODO: Clean up initialization of fep_state and lambda in
 360        t_state.  This function works, but could probably use a logic
 361        rewrite to keep all the different types of efep straight. */
 362
 363     if ((ir.efep == efepNO) && (!ir.bSimTemp))
 364     {
 365         return;
 366     }
 367
 368     const t_lambda* fep = ir.fepvals;
 369     if (isMaster)
 370     {
 371         *fep_state = fep->init_fep_state; /* this might overwrite the checkpoint
 372                                              if checkpoint is set -- a kludge is in for now
 373                                              to prevent this.*/
 374     }
 375
 376     for (int i = 0; i < efptNR; i++)
 377     {
 378         double thisLambda;
 379         /* overwrite lambda state with init_lambda for now for backwards compatibility */
 380         if (fep->init_lambda >= 0) /* if it's -1, it was never initialized */
 381         {
 382             thisLambda = fep->init_lambda;
 383         }
 384         else
 385         {
 386             thisLambda = fep->all_lambda[i][fep->init_fep_state];
 387         }
 388         if (isMaster)
 389         {
 390             lambda[i] = thisLambda;
 391         }
 392     }
 393     if (ir.bSimTemp)
 394     {
 395         /* need to rescale control temperatures to match current state */
 396         for (int i = 0; i < ir.opts.ngtc; i++)
 397         {
 398             if (ir.opts.ref_t[i] > 0)
 399             {
 400                 ir.opts.ref_t[i] = ir.simtempvals->temperatures[fep->init_fep_state];
 401             }
 402         }
 403     }
 404
 405     /* Send to the log the information on the current lambdas */
 406     const bool isInitialOutput = true;
 407     printLambdaStateToLog(fplog, lambda, isInitialOutput);
 408 }