Gromacs
2016
|
#include <stdio.h>
#include "gromacs/gmxlib/nrnb.h"
#include "gromacs/math/vectypes.h"
#include "gromacs/mdtypes/forcerec.h"
#include "gromacs/mdtypes/interaction_const.h"
#include "gromacs/timing/wallcycle.h"
#include "gromacs/timing/walltime_accounting.h"
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/real.h"
This file contains function declarations necessary for computing energies and forces for the PME long-ranged part (Coulomb and LJ).
Macros | |
#define | GMX_PME_SPREAD (1<<0) |
Flag values that control what gmx_pme_do() will calculate. More... | |
#define | GMX_PME_SOLVE (1<<1) |
#define | GMX_PME_CALC_F (1<<2) |
#define | GMX_PME_CALC_ENER_VIR (1<<3) |
#define | GMX_PME_CALC_POT (1<<4) |
#define | GMX_PME_DO_COULOMB (1<<13) |
#define | GMX_PME_DO_LJ (1<<14) |
#define | GMX_PME_DO_ALL_F (GMX_PME_SPREAD | GMX_PME_SOLVE | GMX_PME_CALC_F) |
Enumerations | |
enum | { GMX_SUM_GRID_FORWARD, GMX_SUM_GRID_BACKWARD } |
Functions | |
int | gmx_pme_init (struct gmx_pme_t **pmedata, struct t_commrec *cr, int nnodes_major, int nnodes_minor, t_inputrec *ir, int homenr, gmx_bool bFreeEnergy_q, gmx_bool bFreeEnergy_lj, gmx_bool bReproducible, int nthread) |
Initialize pmedata . More... | |
int | gmx_pme_destroy (FILE *log, struct gmx_pme_t **pmedata) |
Destroy the pme data structures resepectively. More... | |
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, real ewaldcoeff_q, matrix vir_lj, real ewaldcoeff_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 for the long range electrostatics and/or LJ. More... | |
int | gmx_pmeonly (struct gmx_pme_t *pme, struct t_commrec *cr, t_nrnb *mynrnb, gmx_wallcycle_t wcycle, gmx_walltime_accounting_t walltime_accounting, real ewaldcoeff_q, real ewaldcoeff_lj, t_inputrec *ir) |
Called on the nodes that do PME exclusively (as slaves) | |
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... | |
void | gmx_pme_send_parameters (struct t_commrec *cr, const interaction_const_t *ic, gmx_bool bFreeEnergy_q, gmx_bool bFreeEnergy_lj, real *chargeA, real *chargeB, real *sqrt_c6A, real *sqrt_c6B, real *sigmaA, real *sigmaB, int maxshift_x, int maxshift_y) |
Send the charges and maxshift to out PME-only node. | |
void | gmx_pme_send_coordinates (struct t_commrec *cr, matrix box, rvec *x, gmx_bool bFreeEnergy_q, gmx_bool bFreeEnergy_lj, real lambda_q, real lambda_lj, gmx_bool bEnerVir, int pme_flags, gmx_int64_t step) |
Send the coordinates to our PME-only node and request a PME calculation. | |
void | gmx_pme_send_finish (struct t_commrec *cr) |
Tell our PME-only node to finish. | |
void | gmx_pme_send_resetcounters (struct t_commrec *cr, gmx_int64_t step) |
Tell our PME-only node to reset all cycle and flop counters. | |
void | gmx_pme_receive_f (struct t_commrec *cr, rvec f[], matrix vir_q, real *energy_q, matrix vir_lj, real *energy_lj, real *dvdlambda_q, real *dvdlambda_lj, float *pme_cycles) |
PP nodes receive the long range forces from the PME nodes. | |
#define GMX_PME_SPREAD (1<<0) |
Flag values that control what gmx_pme_do() will calculate.
These can be combined with bitwise-OR if more than one thing is required.
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.
int gmx_pme_destroy | ( | FILE * | log, |
struct gmx_pme_t ** | pmedata | ||
) |
Destroy the pme data structures resepectively.
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, | ||
real | ewaldcoeff_q, | ||
matrix | vir_lj, | ||
real | ewaldcoeff_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 for the long range electrostatics and/or LJ.
The meaning of flags
is defined above, and determines which parts of the calculation are performed.
int gmx_pme_init | ( | struct gmx_pme_t ** | pmedata, |
struct t_commrec * | cr, | ||
int | nnodes_major, | ||
int | nnodes_minor, | ||
t_inputrec * | ir, | ||
int | homenr, | ||
gmx_bool | bFreeEnergy_q, | ||
gmx_bool | bFreeEnergy_lj, | ||
gmx_bool | bReproducible, | ||
int | nthread | ||
) |
Initialize pmedata
.
Return value 0 indicates all well, non zero is an error code.