"energy_delta_h_start_time",
"energy_delta_h_start_lambda" };
-static const char* ePullhNames[epullhNR] = { "pullhistory_numcoordinates", "pullhistory_numgroups",
+static const char* ePullhNames[epullhNR] = { "pullhistory_numcoordinates",
+ "pullhistory_numgroups",
"pullhistory_numvaluesinxsum",
"pullhistory_numvaluesinfsum" };
#if !GMX_DOUBLE
if (cptElementType == CptElementType::real3)
{
- pr_rvecs(list, 0, entryName(part, ecpt),
- reinterpret_cast<const rvec*>(data.data()), nf / 3);
+ pr_rvecs(list, 0, entryName(part, ecpt), reinterpret_cast<const rvec*>(data.data()), nf / 3);
}
else
#endif
{
/* Note: With double precision code dumping a single precision rvec will produce float iso rvec print, but that's a minor annoyance */
- pr_fvec(list, 0, entryName(part, ecpt),
- reinterpret_cast<const float*>(data.data()), nf, TRUE);
+ pr_fvec(list, 0, entryName(part, ecpt), reinterpret_cast<const float*>(data.data()), nf, TRUE);
}
break;
case xdr_datatype_double:
#if GMX_DOUBLE
if (cptElementType == CptElementType::real3)
{
- pr_rvecs(list, 0, entryName(part, ecpt),
- reinterpret_cast<const rvec*>(data.data()), nf / 3);
+ pr_rvecs(list, 0, entryName(part, ecpt), reinterpret_cast<const rvec*>(data.data()), nf / 3);
}
else
#endif
{
/* Note: With single precision code dumping a double precision rvec will produce float iso rvec print, but that's a minor annoyance */
- pr_dvec(list, 0, entryName(part, ecpt),
- reinterpret_cast<const double*>(data.data()), nf, TRUE);
+ pr_dvec(list, 0, entryName(part, ecpt), reinterpret_cast<const double*>(data.data()), nf, TRUE);
}
break;
default: GMX_RELEASE_ASSERT(false, "Data type not implemented for listing");
{
gmx_fatal(FARGS,
"Count mismatch for state entry %s, code count is %d, file count is %d\n",
- entryName(part, ecpt), nval, numElemInTheFile);
+ entryName(part, ecpt),
+ nval,
+ numElemInTheFile);
}
}
else if (nptr != nullptr)
if (!typesMatch)
{
char buf[STRLEN];
- sprintf(buf, "mismatch for state entry %s, code precision is %s, file precision is %s",
- entryName(part, ecpt), xdr_datatype_names[xdrTypeInTheCode],
+ sprintf(buf,
+ "mismatch for state entry %s, code precision is %s, file precision is %s",
+ entryName(part, ecpt),
+ xdr_datatype_names[xdrTypeInTheCode],
xdr_datatype_names[xdrTypeInTheFile]);
/* Matching int and real should never occur, but check anyhow */
if (xdrTypeInTheFile == xdr_datatype_int || xdrTypeInTheCode == xdr_datatype_int)
{
gmx_fatal(FARGS,
- "Type %s: incompatible checkpoint formats or corrupted checkpoint file.", buf);
+ "Type %s: incompatible checkpoint formats or corrupted checkpoint file.",
+ buf);
}
}
{
snew(vChar, numElemInTheFile * sizeOfXdrType(xdrTypeInTheFile));
}
- res = xdr_vector(xd, vChar, numElemInTheFile, sizeOfXdrType(xdrTypeInTheFile),
- xdrProc(xdrTypeInTheFile));
+ res = xdr_vector(
+ xd, vChar, numElemInTheFile, sizeOfXdrType(xdrTypeInTheFile), xdrProc(xdrTypeInTheFile));
if (res == 0)
{
return -1;
static int
doVector(XDR* xd, StatePart part, int ecpt, int sflags, std::vector<T>* vector, FILE* list, int numElements = -1)
{
- return doVectorLow<T>(xd, part, ecpt, sflags, numElements, nullptr, nullptr, vector, list,
- CptElementType::real);
+ return doVectorLow<T>(
+ xd, part, ecpt, sflags, numElements, nullptr, nullptr, vector, list, CptElementType::real);
}
//! \brief Read/Write an ArrayRef<real>.
static int doRealArrayRef(XDR* xd, StatePart part, int ecpt, int sflags, gmx::ArrayRef<real> vector, FILE* list)
{
real* v_real = vector.data();
- return doVectorLow<real, std::allocator<real>>(xd, part, ecpt, sflags, vector.size(), nullptr,
- &v_real, nullptr, list, CptElementType::real);
+ return doVectorLow<real, std::allocator<real>>(
+ xd, part, ecpt, sflags, vector.size(), nullptr, &v_real, nullptr, list, CptElementType::real);
}
//! Convert from view of RVec to view of real.
// allocator from RVec to real.
using realAllocator =
typename std::allocator_traits<typename PaddedVectorOfRVecType::allocator_type>::template rebind_alloc<real>;
- return doVectorLow<real, realAllocator>(xd, part, ecpt, sflags, numReals, nullptr, nullptr,
- nullptr, list, CptElementType::real);
+ return doVectorLow<real, realAllocator>(
+ xd, part, ecpt, sflags, numReals, nullptr, nullptr, nullptr, list, CptElementType::real);
}
}
*/
static int do_cpte_reals(XDR* xd, StatePart part, int ecpt, int sflags, int n, real** v, FILE* list)
{
- return doVectorLow<real, std::allocator<real>>(xd, part, ecpt, sflags, n, nullptr, v, nullptr,
- list, CptElementType::real);
+ return doVectorLow<real, std::allocator<real>>(
+ xd, part, ecpt, sflags, n, nullptr, v, nullptr, list, CptElementType::real);
}
/* This function does the same as do_cpte_reals,
*/
static int do_cpte_n_reals(XDR* xd, StatePart part, int ecpt, int sflags, int* n, real** v, FILE* list)
{
- return doVectorLow<real, std::allocator<real>>(xd, part, ecpt, sflags, -1, n, v, nullptr, list,
- CptElementType::real);
+ return doVectorLow<real, std::allocator<real>>(
+ xd, part, ecpt, sflags, -1, n, v, nullptr, list, CptElementType::real);
}
static int do_cpte_real(XDR* xd, StatePart part, int ecpt, int sflags, real* r, FILE* list)
{
- return doVectorLow<real, std::allocator<real>>(xd, part, ecpt, sflags, 1, nullptr, &r, nullptr,
- list, CptElementType::real);
+ return doVectorLow<real, std::allocator<real>>(
+ xd, part, ecpt, sflags, 1, nullptr, &r, nullptr, list, CptElementType::real);
}
static int do_cpte_ints(XDR* xd, StatePart part, int ecpt, int sflags, int n, int** v, FILE* list)
{
- return doVectorLow<int, std::allocator<int>>(xd, part, ecpt, sflags, n, nullptr, v, nullptr,
- list, CptElementType::integer);
+ return doVectorLow<int, std::allocator<int>>(
+ xd, part, ecpt, sflags, n, nullptr, v, nullptr, list, CptElementType::integer);
}
static int do_cpte_int(XDR* xd, StatePart part, int ecpt, int sflags, int* i, FILE* list)
static int do_cpte_doubles(XDR* xd, StatePart part, int ecpt, int sflags, int n, double** v, FILE* list)
{
- return doVectorLow<double, std::allocator<double>>(xd, part, ecpt, sflags, n, nullptr, v,
- nullptr, list, CptElementType::real);
+ return doVectorLow<double, std::allocator<double>>(
+ xd, part, ecpt, sflags, n, nullptr, v, nullptr, list, CptElementType::real);
}
static int do_cpte_double(XDR* xd, StatePart part, int ecpt, int sflags, double* r, FILE* list)
int ret;
vr = &(v[0][0]);
- ret = doVectorLow<real, std::allocator<real>>(xd, part, ecpt, sflags, DIM * DIM, nullptr, &vr,
- nullptr, nullptr, CptElementType::matrix3x3);
+ ret = doVectorLow<real, std::allocator<real>>(
+ xd, part, ecpt, sflags, DIM * DIM, nullptr, &vr, nullptr, nullptr, CptElementType::matrix3x3);
if (list && ret == 0)
{
}
for (i = 0; i < n; i++)
{
- reti = doVectorLow<real, std::allocator<real>>(xd, part, ecpt, sflags, n, nullptr, &(v[i]),
- nullptr, nullptr, CptElementType::matrix3x3);
+ reti = doVectorLow<real, std::allocator<real>>(
+ xd, part, ecpt, sflags, n, nullptr, &(v[i]), nullptr, nullptr, CptElementType::matrix3x3);
if (list && reti == 0)
{
sprintf(name, "%s[%d]", entryName(part, ecpt), i);
}
if (list == nullptr && nf != n)
{
- gmx_fatal(FARGS, "Count mismatch for state entry %s, code count is %d, file count is %d\n",
- entryName(part, ecpt), n, nf);
+ gmx_fatal(FARGS,
+ "Count mismatch for state entry %s, code count is %d, file count is %d\n",
+ entryName(part, ecpt),
+ n,
+ nf);
}
if (list || !(sflags & (1 << ecpt)))
{
}
}
}
- ret = doVectorLow<real, std::allocator<real>>(xd, part, ecpt, sflags, nf * DIM * DIM, nullptr,
- &vr, nullptr, nullptr, CptElementType::matrix3x3);
+ ret = doVectorLow<real, std::allocator<real>>(
+ xd, part, ecpt, sflags, nf * DIM * DIM, nullptr, &vr, nullptr, nullptr, CptElementType::matrix3x3);
for (i = 0; i < nf; i++)
{
for (j = 0; j < DIM; j++)
gmx_fatal(FARGS,
"Start of file magic number mismatch, checkpoint file has %d, should be %d\n"
"The checkpoint file is corrupted or not a checkpoint file",
- magic, CPT_MAGIC1);
+ magic,
+ CPT_MAGIC1);
}
char fhost[255];
if (!bRead)
{
gmx_fatal(FARGS,
"Attempting to read a checkpoint file of version %d with code of version %d\n",
- contents->file_version, cpt_version);
+ contents->file_version,
+ cpt_version);
}
if (contents->file_version >= 13)
{
if (contents->file_version >= cptv_ModularSimulator)
{
- do_cpt_bool_err(xd, "Is modular simulator checkpoint",
- &contents->isModularSimulatorCheckpoint, list);
+ do_cpt_bool_err(
+ xd, "Is modular simulator checkpoint", &contents->isModularSimulatorCheckpoint, list);
}
else
{
{
case estLAMBDA:
ret = doRealArrayRef(
- xd, part, i, sflags,
+ xd,
+ part,
+ i,
+ sflags,
gmx::arrayRefFromArray<real>(state->lambda.data(), state->lambda.size()),
list);
break;
ret = do_cpte_real(xd, part, i, sflags, &state->hist.disre_initf, list);
break;
case estDISRE_RM3TAV:
- ret = do_cpte_n_reals(xd, part, i, sflags, &state->hist.ndisrepairs,
- &state->hist.disre_rm3tav, list);
+ ret = do_cpte_n_reals(
+ xd, part, i, sflags, &state->hist.ndisrepairs, &state->hist.disre_rm3tav, list);
break;
case estORIRE_INITF:
ret = do_cpte_real(xd, part, i, sflags, &state->hist.orire_initf, list);
break;
case estORIRE_DTAV:
- ret = do_cpte_n_reals(xd, part, i, sflags, &state->hist.norire_Dtav,
- &state->hist.orire_Dtav, list);
+ ret = do_cpte_n_reals(
+ xd, part, i, sflags, &state->hist.norire_Dtav, &state->hist.orire_Dtav, list);
break;
case estPULLCOMPREVSTEP:
ret = doVector<double>(xd, part, i, sflags, &state->pull_com_prev_step, list);
}
else
{
- do_cpt_n_rvecs_err(xd, "Ch0 whole x", swapstate->nat[eChan0],
- *swapstate->xc_old_whole_p[eChan0], list);
- do_cpt_n_rvecs_err(xd, "Ch1 whole x", swapstate->nat[eChan1],
- *swapstate->xc_old_whole_p[eChan1], list);
+ do_cpt_n_rvecs_err(
+ xd, "Ch0 whole x", swapstate->nat[eChan0], *swapstate->xc_old_whole_p[eChan0], list);
+ do_cpt_n_rvecs_err(
+ xd, "Ch1 whole x", swapstate->nat[eChan1], *swapstate->xc_old_whole_p[eChan1], list);
}
return 0;
return ret;
}
- GMX_RELEASE_ASSERT(enerhist != nullptr,
- "With energy history, we need a valid enerhist pointer");
+ GMX_RELEASE_ASSERT(enerhist != nullptr, "With energy history, we need a valid enerhist pointer");
/* This is stored/read for backward compatibility */
int energyHistoryNumEnergies = 0;
if (bRead)
{
- initCorrelationGridHistory(corrGrid, corrGrid->numCorrelationTensors, corrGrid->tensorSize,
- corrGrid->blockDataListSize);
+ initCorrelationGridHistory(
+ corrGrid, corrGrid->numCorrelationTensors, corrGrid->tensorSize, corrGrid->blockDataListSize);
}
for (gmx::CorrelationBlockDataHistory& blockData : corrGrid->blockDataBuffer)
do_cpt_step_err(xd, eawhh_names[i], &(state->numUpdates), list);
break;
case eawhhFORCECORRELATIONGRID:
- ret = do_cpt_correlation_grid(xd, bRead, fflags,
- &biasHistory->forceCorrelationGrid, list, i);
+ ret = do_cpt_correlation_grid(
+ xd, bRead, fflags, &biasHistory->forceCorrelationGrid, list, i);
break;
default: gmx_fatal(FARGS, "Unknown awh history entry %d\n", i);
}
{
return -1;
}
- if (do_cpt_u_chars(xd, "file_checksum", outputfile.checksum.size(),
- outputfile.checksum.data(), list)
+ if (do_cpt_u_chars(xd, "file_checksum", outputfile.checksum.size(), outputfile.checksum.data(), list)
!= 0)
{
return -1;
if ((do_cpt_state(gmx_fio_getxdr(fp), state->flags, state, nullptr) < 0)
|| (do_cpt_ekinstate(gmx_fio_getxdr(fp), headerContents.flags_eks, &state->ekinstate, nullptr) < 0)
|| (do_cpt_enerhist(gmx_fio_getxdr(fp), FALSE, headerContents.flags_enh, enerhist, nullptr) < 0)
- || (doCptPullHist(gmx_fio_getxdr(fp), FALSE, headerContents.flagsPullHistory, pullHist,
- StatePart::pullHistory, nullptr)
+ || (doCptPullHist(gmx_fio_getxdr(fp), FALSE, headerContents.flagsPullHistory, pullHist, StatePart::pullHistory, nullptr)
< 0)
- || (do_cpt_df_hist(gmx_fio_getxdr(fp), headerContents.flags_dfh, headerContents.nlambda,
- &state->dfhist, nullptr)
+ || (do_cpt_df_hist(gmx_fio_getxdr(fp), headerContents.flags_dfh, headerContents.nlambda, &state->dfhist, nullptr)
< 0)
- || (do_cpt_EDstate(gmx_fio_getxdr(fp), FALSE, headerContents.nED,
- observablesHistory->edsamHistory.get(), nullptr)
+ || (do_cpt_EDstate(
+ gmx_fio_getxdr(fp), FALSE, headerContents.nED, observablesHistory->edsamHistory.get(), nullptr)
< 0)
|| (do_cpt_awh(gmx_fio_getxdr(fp), FALSE, headerContents.flags_awhh, state->awhHistory.get(), nullptr) < 0)
- || (do_cpt_swapstate(gmx_fio_getxdr(fp), FALSE, headerContents.eSwapCoords,
- observablesHistory->swapHistory.get(), nullptr)
+ || (do_cpt_swapstate(gmx_fio_getxdr(fp),
+ FALSE,
+ headerContents.eSwapCoords,
+ observablesHistory->swapHistory.get(),
+ nullptr)
< 0)
|| (do_cpt_files(gmx_fio_getxdr(fp), FALSE, outputfiles, nullptr, headerContents.file_version) < 0))
{
if (reproducibilityRequested)
{
- check_string(fplog, "Program name", gmx::getProgramContext().fullBinaryPath(),
- headerContents.fprog, &mm);
+ check_string(
+ fplog, "Program name", gmx::getProgramContext().fullBinaryPath(), headerContents.fprog, &mm);
check_int(fplog, "#ranks", cr->nnodes, headerContents.nnodes, &mm);
}
gmx_fatal(FARGS,
"Checkpoint file is for a system of %d atoms, while the current system consists "
"of %d atoms",
- headerContents->natoms, state->natoms);
+ headerContents->natoms,
+ state->natoms);
}
if (headerContents->ngtc != state->ngtc)
{
gmx_fatal(FARGS,
"Checkpoint file is for a system of %d T-coupling groups, while the current "
"system consists of %d T-coupling groups",
- headerContents->ngtc, state->ngtc);
+ headerContents->ngtc,
+ state->ngtc);
}
if (headerContents->nnhpres != state->nnhpres)
{
gmx_fatal(FARGS,
"Checkpoint file is for a system of %d NH-pressure-coupling variables, while the "
"current system consists of %d NH-pressure-coupling variables",
- headerContents->nnhpres, state->nnhpres);
+ headerContents->nnhpres,
+ state->nnhpres);
}
int nlambdaHistory = (state->dfhist ? state->dfhist->nlambda : 0);
gmx_fatal(FARGS,
"Checkpoint file is for a system with %d lambda states, while the current system "
"consists of %d lambda states",
- headerContents->nlambda, nlambdaHistory);
+ headerContents->nlambda,
+ nlambdaHistory);
}
- init_gtc_state(state, state->ngtc, state->nnhpres,
+ init_gtc_state(state,
+ state->ngtc,
+ state->nnhpres,
headerContents->nhchainlength); /* need to keep this here to keep the tpr format working */
/* write over whatever was read; we use the number of Nose-Hoover chains from the checkpoint */
{
observablesHistory->energyHistory = std::make_unique<energyhistory_t>();
}
- ret = do_cpt_enerhist(gmx_fio_getxdr(fp), TRUE, headerContents->flags_enh,
- observablesHistory->energyHistory.get(), nullptr);
+ ret = do_cpt_enerhist(
+ gmx_fio_getxdr(fp), TRUE, headerContents->flags_enh, observablesHistory->energyHistory.get(), nullptr);
if (ret)
{
cp_error();
{
observablesHistory->pullHistory = std::make_unique<PullHistory>();
}
- ret = doCptPullHist(gmx_fio_getxdr(fp), TRUE, headerContents->flagsPullHistory,
- observablesHistory->pullHistory.get(), StatePart::pullHistory, nullptr);
+ ret = doCptPullHist(gmx_fio_getxdr(fp),
+ TRUE,
+ headerContents->flagsPullHistory,
+ observablesHistory->pullHistory.get(),
+ StatePart::pullHistory,
+ nullptr);
if (ret)
{
cp_error();
"Continuing from checkpoint files written before GROMACS 4.5 is not supported");
}
- ret = do_cpt_df_hist(gmx_fio_getxdr(fp), headerContents->flags_dfh, headerContents->nlambda,
- &state->dfhist, nullptr);
+ ret = do_cpt_df_hist(
+ gmx_fio_getxdr(fp), headerContents->flags_dfh, headerContents->nlambda, &state->dfhist, nullptr);
if (ret)
{
cp_error();
{
observablesHistory->edsamHistory = std::make_unique<edsamhistory_t>(edsamhistory_t{});
}
- ret = do_cpt_EDstate(gmx_fio_getxdr(fp), TRUE, headerContents->nED,
- observablesHistory->edsamHistory.get(), nullptr);
+ ret = do_cpt_EDstate(
+ gmx_fio_getxdr(fp), TRUE, headerContents->nED, observablesHistory->edsamHistory.get(), nullptr);
if (ret)
{
cp_error();
{
observablesHistory->swapHistory = std::make_unique<swaphistory_t>(swaphistory_t{});
}
- ret = do_cpt_swapstate(gmx_fio_getxdr(fp), TRUE, headerContents->eSwapCoords,
- observablesHistory->swapHistory.get(), nullptr);
+ ret = do_cpt_swapstate(
+ gmx_fio_getxdr(fp), TRUE, headerContents->eSwapCoords, observablesHistory->swapHistory.get(), nullptr);
if (ret)
{
cp_error();
if (SIMMASTER(cr))
{
/* Read the state from the checkpoint file */
- read_checkpoint(fn, logfio, cr, dd_nc, ir->eI, &(ir->fepvals->init_fep_state),
- &headerContents, state, observablesHistory, reproducibilityRequested,
- mdModulesNotifier, modularSimulatorCheckpointData, useModularSimulator);
+ read_checkpoint(fn,
+ logfio,
+ cr,
+ dd_nc,
+ ir->eI,
+ &(ir->fepvals->init_fep_state),
+ &headerContents,
+ state,
+ observablesHistory,
+ reproducibilityRequested,
+ mdModulesNotifier,
+ modularSimulatorCheckpointData,
+ useModularSimulator);
}
if (PAR(cr))
{
cp_error();
}
PullHistory pullHist = {};
- ret = doCptPullHist(gmx_fio_getxdr(fp), TRUE, headerContents.flagsPullHistory, &pullHist,
- StatePart::pullHistory, nullptr);
+ ret = doCptPullHist(
+ gmx_fio_getxdr(fp), TRUE, headerContents.flagsPullHistory, &pullHist, StatePart::pullHistory, nullptr);
if (ret)
{
cp_error();
}
- ret = do_cpt_df_hist(gmx_fio_getxdr(fp), headerContents.flags_dfh, headerContents.nlambda,
- &state->dfhist, nullptr);
+ ret = do_cpt_df_hist(
+ gmx_fio_getxdr(fp), headerContents.flags_dfh, headerContents.nlambda, &state->dfhist, nullptr);
if (ret)
{
cp_error();
if (ret == 0)
{
PullHistory pullHist = {};
- ret = doCptPullHist(gmx_fio_getxdr(fp), TRUE, headerContents.flagsPullHistory, &pullHist,
- StatePart::pullHistory, out);
+ ret = doCptPullHist(
+ gmx_fio_getxdr(fp), TRUE, headerContents.flagsPullHistory, &pullHist, StatePart::pullHistory, out);
}
if (ret == 0)
{
- ret = do_cpt_df_hist(gmx_fio_getxdr(fp), headerContents.flags_dfh, headerContents.nlambda,
- &state.dfhist, out);
+ ret = do_cpt_df_hist(
+ gmx_fio_getxdr(fp), headerContents.flags_dfh, headerContents.nlambda, &state.dfhist, out);
}
if (ret == 0)
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff