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Gromacs
2025.3
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#include "gmxpre.h"#include <cinttypes>#include <cmath>#include <cstdio>#include <cstdlib>#include <algorithm>#include <array>#include <filesystem>#include <memory>#include <numeric>#include <optional>#include <string>#include <utility>#include <vector>#include "gromacs/applied_forces/awh/awh.h"#include "gromacs/applied_forces/awh/read_params.h"#include "gromacs/commandline/filenm.h"#include "gromacs/compat/pointers.h"#include "gromacs/domdec/collect.h"#include "gromacs/domdec/dlbtiming.h"#include "gromacs/domdec/domdec.h"#include "gromacs/domdec/domdec_network.h"#include "gromacs/domdec/domdec_struct.h"#include "gromacs/domdec/gpuhaloexchange.h"#include "gromacs/domdec/localtopologychecker.h"#include "gromacs/domdec/mdsetup.h"#include "gromacs/domdec/partition.h"#include "gromacs/essentialdynamics/edsam.h"#include "gromacs/ewald/pme_load_balancing.h"#include "gromacs/ewald/pme_pp.h"#include "gromacs/fileio/enxio.h"#include "gromacs/fileio/trxio.h"#include "gromacs/gmxlib/network.h"#include "gromacs/gmxlib/nrnb.h"#include "gromacs/gpu_utils/device_stream_manager.h"#include "gromacs/gpu_utils/gpu_utils.h"#include "gromacs/gpu_utils/hostallocator.h"#include "gromacs/imd/imd.h"#include "gromacs/listed_forces/listed_forces.h"#include "gromacs/listed_forces/listed_forces_gpu.h"#include "gromacs/math/arrayrefwithpadding.h"#include "gromacs/math/boxmatrix.h"#include "gromacs/math/functions.h"#include "gromacs/math/matrix.h"#include "gromacs/math/paddedvector.h"#include "gromacs/math/vec.h"#include "gromacs/math/vectypes.h"#include "gromacs/mdlib/checkpointhandler.h"#include "gromacs/mdlib/compute_io.h"#include "gromacs/mdlib/constr.h"#include "gromacs/mdlib/coupling.h"#include "gromacs/mdlib/ebin.h"#include "gromacs/mdlib/enerdata_utils.h"#include "gromacs/mdlib/energyoutput.h"#include "gromacs/mdlib/expanded.h"#include "gromacs/mdlib/force.h"#include "gromacs/mdlib/force_flags.h"#include "gromacs/mdlib/forcerec.h"#include "gromacs/mdlib/freeenergyparameters.h"#include "gromacs/mdlib/md_support.h"#include "gromacs/mdlib/mdatoms.h"#include "gromacs/mdlib/mdgraph_gpu.h"#include "gromacs/mdlib/mdoutf.h"#include "gromacs/mdlib/membed.h"#include "gromacs/mdlib/resethandler.h"#include "gromacs/mdlib/sighandler.h"#include "gromacs/mdlib/simulationsignal.h"#include "gromacs/mdlib/stat.h"#include "gromacs/mdlib/stophandler.h"#include "gromacs/mdlib/tgroup.h"#include "gromacs/mdlib/trajectory_writing.h"#include "gromacs/mdlib/update.h"#include "gromacs/mdlib/update_constrain_gpu.h"#include "gromacs/mdlib/update_vv.h"#include "gromacs/mdlib/vcm.h"#include "gromacs/mdlib/vsite.h"#include "gromacs/mdrunutility/freeenergy.h"#include "gromacs/mdrunutility/handlerestart.h"#include "gromacs/mdrunutility/mdmodulesnotifiers.h"#include "gromacs/mdrunutility/multisim.h"#include "gromacs/mdrunutility/printtime.h"#include "gromacs/mdtypes/awh_history.h"#include "gromacs/mdtypes/awh_params.h"#include "gromacs/mdtypes/commrec.h"#include "gromacs/mdtypes/df_history.h"#include "gromacs/mdtypes/enerdata.h"#include "gromacs/mdtypes/energyhistory.h"#include "gromacs/mdtypes/fcdata.h"#include "gromacs/mdtypes/forcebuffers.h"#include "gromacs/mdtypes/forcerec.h"#include "gromacs/mdtypes/group.h"#include "gromacs/mdtypes/iforceprovider.h"#include "gromacs/mdtypes/inputrec.h"#include "gromacs/mdtypes/interaction_const.h"#include "gromacs/mdtypes/locality.h"#include "gromacs/mdtypes/md_enums.h"#include "gromacs/mdtypes/mdatom.h"#include "gromacs/mdtypes/mdrunoptions.h"#include "gromacs/mdtypes/multipletimestepping.h"#include "gromacs/mdtypes/observableshistory.h"#include "gromacs/mdtypes/observablesreducer.h"#include "gromacs/mdtypes/pull_params.h"#include "gromacs/mdtypes/pullhistory.h"#include "gromacs/mdtypes/simulation_workload.h"#include "gromacs/mdtypes/state.h"#include "gromacs/mdtypes/state_propagator_data_gpu.h"#include "gromacs/modularsimulator/energydata.h"#include "gromacs/nbnxm/gpu_data_mgmt.h"#include "gromacs/nbnxm/nbnxm.h"#include "gromacs/pbcutil/pbc.h"#include "gromacs/pulling/output.h"#include "gromacs/pulling/pull.h"#include "gromacs/swap/swapcoords.h"#include "gromacs/taskassignment/include/gromacs/taskassignment/decidesimulationworkload.h"#include "gromacs/timing/wallcycle.h"#include "gromacs/timing/walltime_accounting.h"#include "gromacs/topology/atoms.h"#include "gromacs/topology/idef.h"#include "gromacs/topology/ifunc.h"#include "gromacs/topology/mtop_util.h"#include "gromacs/topology/topology.h"#include "gromacs/topology/topology_enums.h"#include "gromacs/trajectory/trajectoryframe.h"#include "gromacs/utility/arrayref.h"#include "gromacs/utility/basedefinitions.h"#include "gromacs/utility/cstringutil.h"#include "gromacs/utility/enumerationhelpers.h"#include "gromacs/utility/fatalerror.h"#include "gromacs/utility/gmxassert.h"#include "gromacs/utility/logger.h"#include "gromacs/utility/real.h"#include "gromacs/utility/smalloc.h"#include "legacysimulator.h"#include "replicaexchange.h"#include "shellfc.h"Implements the integrator for normal molecular dynamics simulations.
1.8.5