elseif(NOT SPHINX_FOUND)
set(MANUAL_BUILD_IS_POSSIBLE OFF)
set(MANUAL_BUILD_NOT_POSSIBLE_REASON "Sphinx has not been found and is needed to create the LaTex input files")
- elseif(NOT PDFLATEX_COMPILER OR NOT IMAGE_CONVERT_POSSIBLE)
+ elseif(NOT PDFLATEX_COMPILER)
set(MANUAL_BUILD_IS_POSSIBLE OFF)
- set(MANUAL_BUILD_NOT_POSSIBLE_REASON "pdflatex or some other dependency (ImageMagick convert) is not available")
- if (NOT IMAGE_CONVERT_POSSIBLE)
- set(NO_IMAGE_CONVERT_REASON "Can not convert files for online or pdf manual")
- endif()
+ set(MANUAL_BUILD_NOT_POSSIBLE_REASON "pdflatex is not available")
+ elseif(NOT IMAGE_CONVERT_POSSIBLE)
+ set(MANUAL_BUILD_IS_POSSIBLE OFF)
+ set(MANUAL_BUILD_NOT_POSSIBLE_REASON "a working form of ImageMagick convert is not available")
+ set(NO_IMAGE_CONVERT_REASON "Can not convert files for online or pdf manual")
# TODO Later, identify other dependencies like bibtex,
# make_index, date, some graphics conversion program,
# etc. Perhaps patch UseLATEX.cmake and contribute upstream.
reference-manual/special/qmmm.rst
reference-manual/special/vmd-imd.rst
reference-manual/special/membrane-embedding.rst
+ reference-manual/special/mimic-qmmm.rst
# Analysis chapter
reference-manual/analysis.rst
reference-manual/analysis/using-groups.rst
dev-manual/includestyle.rst
dev-manual/index.rst
dev-manual/jenkins.rst
+ dev-manual/known-issues.rst
dev-manual/language-features.rst
dev-manual/naming.rst
dev-manual/overview.rst
how-to/visualize.rst
install-guide/index.rst
release-notes/index.rst
+ release-notes/highlights.rst
+ release-notes/features.rst
+ release-notes/performance.rst
+ release-notes/tools.rst
+ release-notes/bugs-fixed.rst
+ release-notes/removed-functionality.rst
+ release-notes/deprecated-functionality.rst
+ release-notes/portability.rst
+ release-notes/miscellaneous.rst
release-notes/2019/major/highlights.rst
release-notes/2019/major/features.rst
release-notes/2019/major/performance.rst
* a microstate for gmxapi interfaces.
*/
- // Note: these output options normalize the file names, but not their
- // paths. gmxapi 0.0.7 changes working directory for each session, so the
- // relative paths are appropriate, but a near-future version will avoid
- // changing directories once the process starts and manage file paths explicitly.
- using gmxapi::c_majorVersion;
- using gmxapi::c_minorVersion;
- using gmxapi::c_patchVersion;
- static_assert(!(c_majorVersion != 0 || c_minorVersion != 0 || c_patchVersion > 7),
- "Developer notice: check assumptions about working directory and relative file paths for this "
- "software version.");
-
// Set input TPR name
mdArgs_.emplace_back("-s");
mdArgs_.emplace_back(filename);
+
// Set checkpoint file name
mdArgs_.emplace_back("-cpi");
mdArgs_.emplace_back("state.cpt");
+ /* Note: we normalize the checkpoint file name, but not its full path.
+ * Through version 0.0.8, gmxapi clients change working directory
+ * for each session, so relative path(s) below are appropriate.
+ * A future gmxapi version should avoid changing directories once the
+ * process starts and instead manage files (paths) in an absolute and
+ * immutable way, with abstraction provided through the Context chain-of-responsibility.
+ * TODO: API abstractions for initializing simulations that may be new or partially complete.
+ * Reference gmxapi milestone 13 at https://redmine.gromacs.org/issues/2585
+ */
// Create a mock argv. Note that argv[0] is expected to hold the program name.
const int offset = 1;
options_.logFileGuard = openLogFile(ftp2fn(efLOG,
options_.filenames.size(),
options_.filenames.data()),
- options_.mdrunOptions.continuationOptions.appendFiles,
- options_.cr->nodeid,
- options_.cr->nnodes);
+ options_.mdrunOptions.continuationOptions.appendFiles);
}
auto simulationContext = createSimulationContext(options_.cr);
#include "gromacs/gmxlib/nonbonded/nonbonded.h"
#include "gromacs/gpu_utils/gpu_utils.h"
#include "gromacs/hardware/hw_info.h"
- #include "gromacs/listed-forces/listed-forces.h"
+ #include "gromacs/listed-forces/gpubonded.h"
#include "gromacs/listed-forces/manage-threading.h"
#include "gromacs/listed-forces/pairs.h"
#include "gromacs/math/functions.h"
{
a0 = cgs->index[cg];
a1 = cgs->index[cg+1];
- if (getGroupType(&mtop->groups, egcENER, a_offset+am+a0) !=
- getGroupType(&mtop->groups, egcENER, a_offset +a0))
+ if (getGroupType(mtop->groups, egcENER, a_offset+am+a0) !=
+ getGroupType(mtop->groups, egcENER, a_offset +a0))
{
bId = FALSE;
}
a1 = cgs->index[cg+1];
/* Store the energy group in cginfo */
- gid = getGroupType(&mtop->groups, egcENER, a_offset+am+a0);
+ gid = getGroupType(mtop->groups, egcENER, a_offset+am+a0);
SET_CGINFO_GID(cginfo[cgm+cg], gid);
/* Check the intra/inter charge group exclusions */
init_bonded_threading(fp, mtop->groups.grps[egcENER].nr,
&fr->bondedThreading);
- if (useGpuForBonded)
- {
- fr->gpuBondedLists = new GpuBondedLists;
- }
-
fr->nthread_ewc = gmx_omp_nthreads_get(emntBonded);
snew(fr->ewc_t, fr->nthread_ewc);
if (useGpuForBonded)
{
- init_gpu_bonded(fr->gpuBondedLists,
- mtop->ffparams,
- DOMAINDECOMP(cr) ?
- nbnxn_gpu_get_command_stream(fr->nbv->gpu_nbv, eintNonlocal) :
- nbnxn_gpu_get_command_stream(fr->nbv->gpu_nbv, eintLocal));
+ auto stream = DOMAINDECOMP(cr) ?
+ nbnxn_gpu_get_command_stream(fr->nbv->gpu_nbv, eintNonlocal) :
+ nbnxn_gpu_get_command_stream(fr->nbv->gpu_nbv, eintLocal);
+ // TODO the heap allocation is only needed while
+ // t_forcerec lacks a constructor.
+ fr->gpuBonded = new gmx::GpuBonded(mtop->ffparams,
+ stream);
}
}
{
/* free nbnxn data in GPU memory */
nbnxn_gpu_free(fr->nbv->gpu_nbv);
-
- if (fr->gpuBondedLists)
- {
- delete fr->gpuBondedLists;
- fr->gpuBondedLists = nullptr;
- }
+ delete fr->gpuBonded;
+ fr->gpuBonded = nullptr;
}
/* With tMPI we need to wait for all ranks to finish deallocation before
done_ns(fr->ns, numEnergyGroups);
sfree(fr->ewc_t);
tear_down_bonded_threading(fr->bondedThreading);
- GMX_RELEASE_ASSERT(fr->gpuBondedLists == nullptr, "Should have been deleted earlier, when used");
+ GMX_RELEASE_ASSERT(fr->gpuBonded == nullptr, "Should have been deleted earlier, when used");
fr->bondedThreading = nullptr;
sfree(fr);
}
/* Update mdebin with energy history if appending to output files */
if (continuationOptions.appendFiles)
{
- restore_energyhistory_from_state(mdebin, observablesHistory->energyHistory.get());
- }
- else
- {
- if (observablesHistory->energyHistory != nullptr)
+ /* If no history is available (because a checkpoint is from before
+ * it was written) make a new one later, otherwise restore it.
+ */
+ if (observablesHistory->energyHistory)
{
- /* We might have read an energy history from checkpoint.
- * As we are not appending, we want to restart the statistics.
- * Free the allocated memory and reset the counts.
- */
- observablesHistory->energyHistory = {};
+ restore_energyhistory_from_state(mdebin, observablesHistory->energyHistory.get());
}
+ }
+ else if (observablesHistory->energyHistory)
+ {
+ /* We might have read an energy history from checkpoint.
+ * As we are not appending, we want to restart the statistics.
+ * Free the allocated memory and reset the counts.
+ */
+ observablesHistory->energyHistory = {};
/* We might have read a pull history from checkpoint.
* We will still want to keep the statistics, so that the files
* can be joined and still be meaningful.
* should not be reset.
*/
}
- if (ir->pull && ir->pull->bSetPbcRefToPrevStepCOM)
- {
- /* Copy the pull group COM of the previous step from the checkpoint state to the pull state */
- setPrevStepPullComFromState(ir->pull_work, state);
- }
}
- else if (ir->pull && ir->pull->bSetPbcRefToPrevStepCOM)
- {
- allocStatePrevStepPullCom(state, ir->pull_work);
- t_pbc pbc;
- set_pbc(&pbc, ir->ePBC, state->box);
- initPullComFromPrevStep(cr, ir->pull_work, mdatoms, &pbc, as_rvec_array(state->x.data()));
- updatePrevStepCom(ir->pull_work);
- setStatePrevStepPullCom(ir->pull_work, state);
- }
- if (observablesHistory->energyHistory == nullptr)
+ if (!observablesHistory->energyHistory)
{
observablesHistory->energyHistory = compat::make_unique<energyhistory_t>();
}
- if (observablesHistory->pullHistory == nullptr)
+ if (!observablesHistory->pullHistory)
{
observablesHistory->pullHistory = compat::make_unique<PullHistory>();
}
update_energyhistory(observablesHistory->energyHistory.get(), mdebin);
}
+ preparePrevStepPullCom(ir, mdatoms, state, state_global, cr, startingFromCheckpoint);
+
// TODO: Remove this by converting AWH into a ForceProvider
auto awh = prepareAwhModule(fplog, *ir, state_global, cr, ms, startingFromCheckpoint,
shellfc != nullptr,
constr, enerd, fcd,
state, f.arrayRefWithPadding(), force_vir, mdatoms,
nrnb, wcycle, graph, groups,
- shellfc, fr, t, mu_tot,
+ shellfc, fr, ppForceWorkload, t, mu_tot,
vsite,
ddOpenBalanceRegion, ddCloseBalanceRegion);
}
state->box, state->x.arrayRefWithPadding(), &state->hist,
f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd,
state->lambda, graph,
- fr, vsite, mu_tot, t, ed ? ed->getLegacyED() : nullptr,
+ fr, ppForceWorkload, vsite, mu_tot, t, ed ? ed->getLegacyED() : nullptr,
(bNS ? GMX_FORCE_NS : 0) | force_flags,
ddOpenBalanceRegion, ddCloseBalanceRegion);
}
state, graph,
nrnb, wcycle, upd, constr);
- if (MASTER(cr) && ir->bPull && ir->pull->bSetPbcRefToPrevStepCOM)
+ if (ir->bPull && ir->pull->bSetPbcRefToPrevStepCOM)
{
- updatePrevStepCom(ir->pull_work);
- setStatePrevStepPullCom(ir->pull_work, state);
+ updatePrevStepPullCom(ir->pull_work, state);
}
if (ir->eI == eiVVAK)
walltime_accounting_set_nsteps_done(walltime_accounting, step_rel);
destroy_enerdata(enerd);
+
sfree(enerd);
+
+ /* Clean up topology. top->atomtypes has an allocated pointer if no domain decomposition*/
+ if (!DOMAINDECOMP(cr))
+ {
+ done_atomtypes(&top->atomtypes);
+ }
sfree(top);
}
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/mdtypes/mdatom.h"
+ #include "gromacs/mdtypes/state.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/topology/mtop_lookup.h"
#include "gromacs/topology/topology.h"
comm->bParticipate = bWillParticipate;
comm->nparticipate = count[0];
+
+ /* When we use the previous COM for PBC, we need to broadcast
+ * the previous COM to ranks that have joined the communicator.
+ */
+ for (pull_group_work_t &group : pull->group)
+ {
+ if (group.epgrppbc == epgrppbcPREVSTEPCOM)
+ {
+ GMX_ASSERT(comm->bParticipate || !MASTER(cr),
+ "The master rank has to participate, as it should pass an up to date prev. COM "
+ "to bcast here as well as to e.g. checkpointing");
+
+ gmx_bcast(sizeof(dvec), group.x_prev_step, cr);
+ }
+ }
}
}
/* In parallel, store we need to extract localWeights from weights at DD time */
std::vector<real> &weights = ((cr && PAR(cr)) ? pg->globalWeights : pg->localWeights);
- const gmx_groups_t *groups = &mtop->groups;
+ const gmx_groups_t &groups = mtop->groups;
/* Count frozen dimensions and (weighted) mass */
int nfrozen = 0;
}
else
{
- if (groups->grpnr[egcTC] == nullptr)
+ if (groups.grpnr[egcTC] == nullptr)
{
mbd = ir->delta_t/ir->opts.tau_t[0];
}
else
{
- mbd = ir->delta_t/ir->opts.tau_t[groups->grpnr[egcTC][ii]];
+ mbd = ir->delta_t/ir->opts.tau_t[groups.grpnr[egcTC][ii]];
}
}
w *= m/mbd;
/* Set up the global to local atom mapping for PBC atoms */
for (pull_group_work_t &group : pull->group)
{
- if (group.epgrppbc == epgrppbcREFAT)
+ if (group.epgrppbc == epgrppbcREFAT || group.epgrppbc == epgrppbcPREVSTEPCOM)
{
/* pbcAtomSet consists of a single atom */
group.pbcAtomSet = gmx::compat::make_unique<gmx::LocalAtomSet>(atomSets->add({&group.params.pbcatom, &group.params.pbcatom + 1}));
pull->bFOutAverage = pull_params->bFOutAverage;
GMX_RELEASE_ASSERT(pull->group[0].params.nat == 0, "pull group 0 is an absolute reference group and should not contain atoms");
- pull->group[0].x_prev_step[XX] = NAN;
pull->numCoordinatesWithExternalPotential = 0;
init_pull_group_index(fplog, cr, g, pgrp,
bConstraint, pulldim_con,
mtop, ir, lambda);
-
- pgrp->x_prev_step[XX] = NAN;
}
else
{
}
comm->pbcAtomBuffer.resize(pull->group.size());
- comm->comBuffer.resize(pull->group.size()*DIM);
+ comm->comBuffer.resize(pull->group.size()*c_comBufferStride);
if (pull->bCylinder)
{
comm->cylinderBuffer.resize(pull->coord.size()*c_cylinderBufferStride);
delete pull;
}
+ void preparePrevStepPullCom(const t_inputrec *ir, const t_mdatoms *md, t_state *state, const t_state *state_global, const t_commrec *cr, bool startingFromCheckpoint)
+ {
+ if (!ir->pull || !ir->pull->bSetPbcRefToPrevStepCOM)
+ {
+ return;
+ }
+ allocStatePrevStepPullCom(state, ir->pull_work);
+ if (startingFromCheckpoint)
+ {
+ if (MASTER(cr))
+ {
+ state->pull_com_prev_step = state_global->pull_com_prev_step;
+ }
+ if (PAR(cr))
+ {
+ /* Only the master rank has the checkpointed COM from the previous step */
+ gmx_bcast(sizeof(double) * state->pull_com_prev_step.size(), &state->pull_com_prev_step[0], cr);
+ }
+ setPrevStepPullComFromState(ir->pull_work, state);
+ }
+ else
+ {
+ t_pbc pbc;
+ set_pbc(&pbc, ir->ePBC, state->box);
+ initPullComFromPrevStep(cr, ir->pull_work, md, &pbc, state->x.rvec_array());
+ updatePrevStepPullCom(ir->pull_work, state);
+ }
+ }
+
void finish_pull(struct pull_t *pull)
{
check_external_potential_registration(pull);
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff