Gromacs
2020.2
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#include "gmxpre.h"
#include "listed_forces.h"
#include <cassert>
#include <algorithm>
#include <array>
#include "gromacs/gmxlib/network.h"
#include "gromacs/gmxlib/nrnb.h"
#include "gromacs/listed_forces/bonded.h"
#include "gromacs/listed_forces/disre.h"
#include "gromacs/listed_forces/orires.h"
#include "gromacs/listed_forces/pairs.h"
#include "gromacs/listed_forces/position_restraints.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdlib/enerdata_utils.h"
#include "gromacs/mdlib/force.h"
#include "gromacs/mdtypes/commrec.h"
#include "gromacs/mdtypes/fcdata.h"
#include "gromacs/mdtypes/forcerec.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/mdtypes/simulation_workload.h"
#include "gromacs/pbcutil/ishift.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/timing/wallcycle.h"
#include "gromacs/topology/topology.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
#include "listed_internal.h"
#include "utilities.h"
This file defines high-level functions for mdrun to compute energies and forces for listed interactions.
Macros | |
#define | MAX_BONDED_THREADS 256 |
The max thread number is arbitrary, we used a fixed number to avoid memory management. Using more than 16 threads is probably never useful performance wise. | |
Functions | |
bool | anonymous_namespace{listed_forces.cpp}::isPairInteraction (int ftype) |
Return true if ftype is an explicit pair-listed LJ or COULOMB interaction type: bonded LJ (usually 1-4), or special listed non-bonded for FEP. | |
void | anonymous_namespace{listed_forces.cpp}::zero_thread_output (f_thread_t *f_t) |
Zero thread-local output buffers. | |
void | anonymous_namespace{listed_forces.cpp}::reduce_thread_forces (int n, gmx::ArrayRef< gmx::RVec > force, const bonded_threading_t *bt, int nthreads) |
Reduce thread-local force buffers. | |
void | anonymous_namespace{listed_forces.cpp}::reduce_thread_output (int n, gmx::ForceWithShiftForces *forceWithShiftForces, real *ener, gmx_grppairener_t *grpp, real *dvdl, const bonded_threading_t *bt, const gmx::StepWorkload &stepWork) |
Reduce thread-local forces, shift forces and energies. | |
BondedKernelFlavor | anonymous_namespace{listed_forces.cpp}::selectBondedKernelFlavor (const gmx::StepWorkload &stepWork, const bool useSimdKernels, const bool havePerturbedInteractions) |
Returns the bonded kernel flavor. More... | |
real | anonymous_namespace{listed_forces.cpp}::calc_one_bond (int thread, int ftype, const t_idef *idef, const WorkDivision &workDivision, const rvec x[], rvec4 f[], rvec fshift[], const t_forcerec *fr, const t_pbc *pbc, const t_graph *g, gmx_grppairener_t *grpp, t_nrnb *nrnb, const real *lambda, real *dvdl, const t_mdatoms *md, t_fcdata *fcd, const gmx::StepWorkload &stepWork, int *global_atom_index) |
Calculate one element of the list of bonded interactions for this thread. | |
static void | calcBondedForces (const t_idef *idef, const rvec x[], const t_forcerec *fr, const t_pbc *pbc_null, const t_graph *g, rvec *fshiftMasterBuffer, gmx_enerdata_t *enerd, t_nrnb *nrnb, const real *lambda, real *dvdl, const t_mdatoms *md, t_fcdata *fcd, const gmx::StepWorkload &stepWork, int *global_atom_index) |
Compute the bonded part of the listed forces, parallelized over threads. | |
bool | haveRestraints (const t_idef &idef, const t_fcdata &fcd) |
Returns true if there are position, distance or orientation restraints. | |
bool | haveCpuBondeds (const t_forcerec &fr) |
Returns true if there are CPU (i.e. not GPU-offloaded) bonded interactions to compute. | |
bool | haveCpuListedForces (const t_forcerec &fr, const t_idef &idef, const t_fcdata &fcd) |
Returns true if there are listed interactions to compute. More... | |
void | calc_listed (const t_commrec *cr, const gmx_multisim_t *ms, struct gmx_wallcycle *wcycle, const t_idef *idef, const rvec x[], history_t *hist, gmx::ForceOutputs *forceOutputs, const t_forcerec *fr, const struct t_pbc *pbc, const struct t_pbc *pbc_full, const struct t_graph *g, gmx_enerdata_t *enerd, t_nrnb *nrnb, const real *lambda, const t_mdatoms *md, t_fcdata *fcd, int *global_atom_index, const gmx::StepWorkload &stepWork) |
Calculates all listed force interactions. More... | |
void | calc_listed_lambda (const t_idef *idef, const rvec x[], const t_forcerec *fr, const struct t_pbc *pbc, const struct t_graph *g, gmx_grppairener_t *grpp, real *epot, t_nrnb *nrnb, const real *lambda, const t_mdatoms *md, t_fcdata *fcd, int *global_atom_index) |
As calc_listed(), but only determines the potential energy for the perturbed interactions. More... | |
void | do_force_listed (struct gmx_wallcycle *wcycle, const matrix box, const t_lambda *fepvals, const t_commrec *cr, const gmx_multisim_t *ms, const t_idef *idef, const rvec x[], history_t *hist, gmx::ForceOutputs *forceOutputs, const t_forcerec *fr, const struct t_pbc *pbc, const struct t_graph *graph, gmx_enerdata_t *enerd, t_nrnb *nrnb, const real *lambda, const t_mdatoms *md, t_fcdata *fcd, int *global_atom_index, const gmx::StepWorkload &stepWork) |
Do all aspects of energy and force calculations for mdrun on the set of listed interactions. | |
void calc_listed | ( | const t_commrec * | cr, |
const gmx_multisim_t * | ms, | ||
struct gmx_wallcycle * | wcycle, | ||
const t_idef * | idef, | ||
const rvec | x[], | ||
history_t * | hist, | ||
gmx::ForceOutputs * | forceOutputs, | ||
const t_forcerec * | fr, | ||
const struct t_pbc * | pbc, | ||
const struct t_pbc * | pbc_full, | ||
const struct t_graph * | g, | ||
gmx_enerdata_t * | enerd, | ||
t_nrnb * | nrnb, | ||
const real * | lambda, | ||
const t_mdatoms * | md, | ||
struct t_fcdata * | fcd, | ||
int * | ddgatindex, | ||
const gmx::StepWorkload & | stepWork | ||
) |
Calculates all listed force interactions.
Note that pbc_full is used only for position restraints, and is not initialized if there are none.
void calc_listed_lambda | ( | const t_idef * | idef, |
const rvec | x[], | ||
const t_forcerec * | fr, | ||
const struct t_pbc * | pbc, | ||
const struct t_graph * | g, | ||
gmx_grppairener_t * | grpp, | ||
real * | epot, | ||
t_nrnb * | nrnb, | ||
const real * | lambda, | ||
const t_mdatoms * | md, | ||
struct t_fcdata * | fcd, | ||
int * | global_atom_index | ||
) |
As calc_listed(), but only determines the potential energy for the perturbed interactions.
The shift forces in fr are not affected.
bool haveCpuListedForces | ( | const t_forcerec & | fr, |
const t_idef & | idef, | ||
const t_fcdata & | fcd | ||
) |
Returns true if there are listed interactions to compute.
NOTE: the current implementation returns true if there are position restraints or any bonded interactions computed on the CPU.