pme.cpp File Reference

#include "gmxpre.h"
#include "pme.h"
#include "config.h"
#include <assert.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <cmath>
#include <algorithm>
#include "gromacs/ewald/ewald-utils.h"
#include "gromacs/fft/parallel_3dfft.h"
#include "gromacs/fileio/pdbio.h"
#include "gromacs/gmxlib/network.h"
#include "gromacs/gmxlib/nrnb.h"
#include "gromacs/math/gmxcomplex.h"
#include "gromacs/math/invertmatrix.h"
#include "gromacs/math/units.h"
#include "gromacs/math/vec.h"
#include "gromacs/math/vectypes.h"
#include "gromacs/mdtypes/commrec.h"
#include "gromacs/mdtypes/forcerec.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/timing/cyclecounter.h"
#include "gromacs/timing/wallcycle.h"
#include "gromacs/timing/walltime_accounting.h"
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxmpi.h"
#include "gromacs/utility/gmxomp.h"
#include "gromacs/utility/logger.h"
#include "gromacs/utility/real.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/stringutil.h"
#include "gromacs/utility/unique_cptr.h"
#include "calculate-spline-moduli.h"
#include "pme-gather.h"
#include "pme-gpu-internal.h"
#include "pme-grid.h"
#include "pme-internal.h"
#include "pme-redistribute.h"
#include "pme-solve.h"
#include "pme-spline-work.h"
#include "pme-spread.h"

Include dependency graph for pme.cpp:

Description

This file contains function definitions necessary for computing energies and forces for the PME long-ranged part (Coulomb and LJ).

Author

Erik Lindahl erik@.nosp@m.kth..nosp@m.se

Berk Hess hess@.nosp@m.kth..nosp@m.se

Functions
static void	setup_coordinate_communication (pme_atomcomm_t *atc)
	Set up coordinate communication.
static int	mult_up (int n, int f)
	Round n up to the next multiple of f.
static double	estimate_pme_load_imbalance (struct gmx_pme_t *pme)
	Return estimate of the load imbalance from the PME grid not being a good match for the number of PME ranks.
static void	init_atomcomm (struct gmx_pme_t *pme, pme_atomcomm_t *atc, int dimind, gmx_bool bSpread)
	Initialize atom communication data structure.
static void	destroy_atomcomm (pme_atomcomm_t *atc)
	Destroy an atom communication data structure and its child structs.
static void	init_overlap_comm (pme_overlap_t *ol, int norder, int nnodes, int nodeid, int ndata, int commplainsize)
	Initialize data structure for communication.
static void	destroy_overlap_comm (const pme_overlap_t *ol)
	Destroy data structure for communication.
int	minimalPmeGridSize (int pmeOrder)
	Return the smallest allowed PME grid size for pmeOrder.
bool	gmx_pme_check_restrictions (int pme_order, int nkx, int nky, int nkz, int nnodes_major, bool useThreads, bool errorsAreFatal)
	Check restrictions on pme_order and the PME grid nkx,nky,nkz. More...
static int	div_round_up (int enumerator, int denominator)
	Round enumerator.
gmx_pme_t *	gmx_pme_init (const t_commrec *cr, int nnodes_major, int nnodes_minor, const t_inputrec *ir, int homenr, gmx_bool bFreeEnergy_q, gmx_bool bFreeEnergy_lj, gmx_bool bReproducible, real ewaldcoeff_q, real ewaldcoeff_lj, int nthread, PmeRunMode runMode, PmeGpu *pmeGpu, gmx_device_info_t *gpuInfo, const gmx::MDLogger &)
	Construct PME data. More...
void	gmx_pme_reinit (struct gmx_pme_t **pmedata, t_commrec *cr, struct gmx_pme_t *pme_src, const t_inputrec *ir, const ivec grid_size, real ewaldcoeff_q, real ewaldcoeff_lj)
	As gmx_pme_init, but takes most settings, except the grid/Ewald coefficients, from pme_src. This is only called when the PME cut-off/grid size changes.
void	gmx_pme_calc_energy (struct gmx_pme_t *pme, int n, rvec *x, real *q, real *V)
	Calculate the PME grid energy V for n charges. More...
static void	calc_initial_lb_coeffs (struct gmx_pme_t *pme, real *local_c6, real *local_sigma)
	Calculate initial Lorentz-Berthelot coefficients for LJ-PME.
static void	calc_next_lb_coeffs (struct gmx_pme_t *pme, real *local_sigma)
	Calculate next Lorentz-Berthelot coefficients for LJ-PME.
int	gmx_pme_do (struct gmx_pme_t *pme, int start, int homenr, rvec x[], rvec f[], real chargeA[], real chargeB[], real c6A[], real c6B[], real sigmaA[], real sigmaB[], matrix box, t_commrec *cr, int maxshift_x, int maxshift_y, t_nrnb *nrnb, gmx_wallcycle_t wcycle, matrix vir_q, matrix vir_lj, real *energy_q, real *energy_lj, real lambda_q, real lambda_lj, real *dvdlambda_q, real *dvdlambda_lj, int flags)
	Do a PME calculation on a CPU for the long range electrostatics and/or LJ. More...
void	gmx_pme_destroy (gmx_pme_t *pme)
	Destroys the PME data structure.
void	gmx_pme_reinit_atoms (const gmx_pme_t *pme, const int nAtoms, const real *charges)
	This function updates the local atom data on GPU after DD (charges, coordinates, etc.). TODO: it should update the PME CPU atom data as well. (currently PME CPU call gmx_pme_do() gets passed the input pointers for each computation). More...

Variables
const int	gmxCacheLineSize = 64
	Number of bytes in a cache line. More...

Function Documentation

void gmx_pme_calc_energy	(	struct gmx_pme_t *	pme,
		int	n,
		rvec *	x,
		real *	q,
		real *	V
	)

Calculate the PME grid energy V for n charges.

The potential (found in pme) must have been found already with a call to gmx_pme_do() with at least GMX_PME_SPREAD and GMX_PME_SOLVE specified. Note that the charges are not spread on the grid in the pme struct. Currently does not work in parallel or with free energy.

bool gmx_pme_check_restrictions	(	int	pme_order,
		int	nkx,
		int	nky,
		int	nkz,
		int	nnodes_major,
		bool	useThreads,
		bool	errorsAreFatal
	)

Check restrictions on pme_order and the PME grid nkx,nky,nkz.

With errorsAreFatal=true, an exception or fatal error is generated on violation of restrictions. With errorsAreFatal=false, false is returned on violation of restrictions. When all restrictions are obeyed, true is returned. Argument useThreads tells if any MPI rank doing PME uses more than 1 threads. If at calling useThreads is unknown, pass true for conservative checking.

The PME GPU restrictions are checked separately during pme_gpu_init().

int gmx_pme_do	(	struct gmx_pme_t *	pme,
		int	start,
		int	homenr,
		rvec	x[],
		rvec	f[],
		real	chargeA[],
		real	chargeB[],
		real	c6A[],
		real	c6B[],
		real	sigmaA[],
		real	sigmaB[],
		matrix	box,
		t_commrec *	cr,
		int	maxshift_x,
		int	maxshift_y,
		t_nrnb *	nrnb,
		gmx_wallcycle_t	wcycle,
		matrix	vir_q,
		matrix	vir_lj,
		real *	energy_q,
		real *	energy_lj,
		real	lambda_q,
		real	lambda_lj,
		real *	dvdlambda_q,
		real *	dvdlambda_lj,
		int	flags
	)

Do a PME calculation on a CPU for the long range electrostatics and/or LJ.

The meaning of flags is defined above, and determines which parts of the calculation are performed.

Returns

0 indicates all well, non zero is an error code.

gmx_pme_t* gmx_pme_init	(	const t_commrec *	cr,
		int	nnodes_major,
		int	nnodes_minor,
		const t_inputrec *	ir,
		int	homenr,
		gmx_bool	bFreeEnergy_q,
		gmx_bool	bFreeEnergy_lj,
		gmx_bool	bReproducible,
		real	ewaldcoeff_q,
		real	ewaldcoeff_lj,
		int	nthread,
		PmeRunMode	runMode,
		PmeGpu *	pmeGpu,
		gmx_device_info_t *	gpuInfo,
		const gmx::MDLogger &	mdlog
	)

Construct PME data.

Exceptions

gmx::InconsistentInputError

if input grid sizes/PME order are inconsistent.

Returns

Pointer to newly allocated and initialized PME data.

void gmx_pme_reinit_atoms	(	const gmx_pme_t *	pme,
		const int	nAtoms,
		const real *	charges
	)

This function updates the local atom data on GPU after DD (charges, coordinates, etc.). TODO: it should update the PME CPU atom data as well. (currently PME CPU call gmx_pme_do() gets passed the input pointers for each computation).

Parameters

[in]	pme	The PME structure.
[in]	nAtoms	The number of particles.
[in]	charges	The pointer to the array of particle charges.

Variable Documentation

const int gmxCacheLineSize = 64

Number of bytes in a cache line.

Must also be a multiple of the SIMD and SIMD4 register size, to preserve alignment.