msm_defn.h File Reference

#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include <math.h>
#include <strings.h>
#include "msm.h"
#include "wkfutils.h"

Go to the source code of this file.

Classes
struct	NL_Msm_t

Macros
#define	X   0
#define	Y   1
#define	Z   2
#define	Q   3
#define	NELEMS(arr)   (sizeof(arr)/sizeof(arr[0]))
#define	GRID_TEMPLATE(TYPE)
#define	GRID_INIT(_p)
#define	GRID_DONE(_p)   free((_p)->buffer)
#define	GRID_INDEX(_p, _i, _j, _k)   (((_k)*((_p)->nj) + (_j))*((_p)->ni) + (_i))
#define	GRID_POINTER(_p, _i, _j, _k)   ((_p)->data + GRID_INDEX(_p, _i, _j, _k))
#define	GRID_RESIZE(_p, TYPE, __i0, __ni, __j0, __nj, __k0, __nk)
#define	GRID_ZERO(_p)   memset((_p)->buffer, 0, (_p)->numbytes) /* ; */
#define	ASSERT(expr)
#define	GRID_INDEX_CHECK(a, _i, _j, _k)
#define	DEFAULT_GRIDSPACING   2.5
#define	DEFAULT_APPROX   NL_MSM_APPROX_CUBIC
#define	DEFAULT_SPLIT   NL_MSM_SPLIT_TAYLOR2
#define	DEFAULT_NLEVELS   0 /* set number of levels as needed */
#define	DEFAULT_DENSITY   0.1
#define	DEFAULT_BINFILL   0.8
#define	DEFAULT_NBINSLOTS   8
#define	SPOLY(pg, pdg, ra, split)
#define	SPOLY_SPREC(pg, pdg, ra, split)

Functions
	GRID_TEMPLATE (double)
	GRID_TEMPLATE (float)
void	NL_msm_cleanup (NL_Msm *pm)
int	NL_msm_compute_short_range (NL_Msm *pm)
int	NL_msm_compute_long_range (NL_Msm *pm)
int	NL_msm_compute_short_range_sprec (NL_Msm *pm)
int	NL_msm_compute_long_range_sprec (NL_Msm *pm)

Macro Definition Documentation

ASSERT

#define ASSERT

(

expr

)

Definition at line 113 of file msm_defn.h.

DEFAULT_APPROX

#define DEFAULT_APPROX   NL_MSM_APPROX_CUBIC

Definition at line 120 of file msm_defn.h.

Referenced by NL_msm_create().

DEFAULT_BINFILL

#define DEFAULT_BINFILL   0.8

Definition at line 125 of file msm_defn.h.

Referenced by NL_msm_create().

DEFAULT_DENSITY

#define DEFAULT_DENSITY   0.1

Definition at line 124 of file msm_defn.h.

Referenced by NL_msm_create().

DEFAULT_GRIDSPACING

#define DEFAULT_GRIDSPACING   2.5

Default MSM parameters

Definition at line 119 of file msm_defn.h.

Referenced by NL_msm_create().

DEFAULT_NBINSLOTS

#define DEFAULT_NBINSLOTS   8

Definition at line 126 of file msm_defn.h.

Referenced by NL_msm_create().

DEFAULT_NLEVELS

#define DEFAULT_NLEVELS   0 /* set number of levels as needed */

Definition at line 122 of file msm_defn.h.

Referenced by NL_msm_create().

DEFAULT_SPLIT

#define DEFAULT_SPLIT   NL_MSM_SPLIT_TAYLOR2

Definition at line 121 of file msm_defn.h.

Referenced by NL_msm_create().

GRID_DONE

#define GRID_DONE

(

_p

)

free((_p)->buffer)

Finished with grid, free its memory

Definition at line 61 of file msm_defn.h.

Referenced by NL_msm_cleanup().

GRID_INDEX

#define GRID_INDEX	(		_p,
			_i,
			_j,
			_k
	)		(((_k)*((_p)->nj) + (_j))*((_p)->ni) + (_i))

Determine the signed flattened index for 3D grid datum

Definition at line 66 of file msm_defn.h.

Referenced by anterpolation(), gridcutoff(), interpolation(), and setup_grids().

GRID_INDEX_CHECK

#define GRID_INDEX_CHECK	(		a,
			_i,
			_j,
			_k
	)

Definition at line 114 of file msm_defn.h.

Referenced by anterpolation(), gridcutoff(), interpolation(), and setup_grids().

GRID_INIT

#define GRID_INIT

(

_p

)

Value:

((_p)->buffer=NULL, (_p)->data=NULL, (_p)->numbytes=0, (_p)->maxbytes=0, \
   (_p)->i0=0, (_p)->j0=0, (_p)->k0=0, (_p)->ni=0, (_p)->nj=0, (_p)->nk=0)

Initialize grid to empty

Definition at line 55 of file msm_defn.h.

Referenced by setup_grids().

GRID_POINTER

#define GRID_POINTER	(		_p,
			_i,
			_j,
			_k
	)		((_p)->data + GRID_INDEX(_p, _i, _j, _k))

Obtain pointer to 3D grid datum

Definition at line 71 of file msm_defn.h.

GRID_RESIZE

#define GRID_RESIZE	(		_p,
			TYPE,
			__i0,
			__ni,
			__j0,
			__nj,
			__k0,
			__nk
	)

Value:

do { \
    int _i0=(__i0), _ni=(__ni); \
    int _j0=(__j0), _nj=(__nj); \
    int _k0=(__k0), _nk=(__nk); \
    size_t _numbytes = (_nk * _nj) * (size_t) _ni * sizeof((_p)->buffer[0]); \
    if ((_p)->maxbytes < _numbytes) { \
      void *_t = realloc((_p)->buffer, _numbytes); \
      if (NULL == _t) return NL_MSM_ERROR_MALLOC; \
      (_p)->buffer = (TYPE *) _t; \
      (_p)->maxbytes = _numbytes; \
    } \
    (_p)->numbytes = _numbytes; \
    (_p)->i0 = _i0, (_p)->ni = _ni; \
    (_p)->j0 = _j0, (_p)->nj = _nj; \
    (_p)->k0 = _k0, (_p)->nk = _nk; \
    (_p)->data = (_p)->buffer + GRID_INDEX((_p), -_i0, -_j0, -_k0); \
  } while (0)

Resize 3D grid buffer, setup its indexing. Grab more memory when needed (must be used within function returning int).

Definition at line 77 of file msm_defn.h.

Referenced by setup_grids().

GRID_TEMPLATE

#define GRID_TEMPLATE

(

TYPE

)

Value:

typedef struct NL_Msmgrid_##TYPE##_t { \
    TYPE *buffer;       /* raw buffer */ \
    TYPE *data;         /* data access offset from buffer */ \
    size_t numbytes;    /* number of bytes in use by buffer */ \
    size_t maxbytes;    /* actual allocation for buffer */ \
    int i0, j0, k0;     /* starting index value for each dimension */ \
    int ni, nj, nk;     /* number of elements in each dimension */ \
  } NL_Msmgrid_##TYPE

Template to create a 3D grid to access data of given TYPE

Definition at line 43 of file msm_defn.h.

GRID_ZERO

#define GRID_ZERO

(

_p

)

memset((_p)->buffer, 0, (_p)->numbytes) /* ; */

Definition at line 98 of file msm_defn.h.

Referenced by anterpolation().

NELEMS

#define NELEMS

(

arr

)

(sizeof(arr)/sizeof(arr[0]))

Return number of elements in static array

Definition at line 39 of file msm_defn.h.

Referenced by NL_msm_approx(), NL_msm_approx_name(), NL_msm_split(), and NL_msm_split_name().

Q

#define Q   3

Definition at line 35 of file msm_defn.h.

Referenced by bin_evaluation_1away(), and bin_evaluation_k_away().

SPOLY

#define SPOLY	(		pg,
			pdg,
			ra,
			split
	)

SPOLY() calculates the polynomial part of the normalized smoothing of 1/r.

Returns g(R), where R=r/a, and (d/dR)g(R).

pg - float*, points to variable to receive g(R) pdg - float*, points to variable to receive (d/dR)g(R) ra - (r/a), assumed to be between 0 and 1 split - identify the type of smoothing used to split the potential

Definition at line 140 of file msm_defn.h.

Referenced by bin_evaluation_1away(), bin_evaluation_k_away(), ComputeNonbondedUtil::select(), and setup_grids().

SPOLY_SPREC

#define SPOLY_SPREC	(		pg,
			pdg,
			ra,
			split
	)

SPOLY_SPREC() calculates the polynomial part of the normalized smoothing of 1/r. Single precision version.

Returns g(R), where R=r/a, and (d/dR)g(R).

pg - float*, points to variable to receive g(R) pdg - float*, points to variable to receive (d/dR)g(R) ra - (r/a), assumed to be between 0 and 1 split - identify the type of smoothing used to split the potential

Definition at line 351 of file msm_defn.h.

Referenced by bin_evaluation_1away(), and bin_evaluation_k_away().

X

#define X   0

Index vectors for x,y,z,q coordinates

Definition at line 29 of file msm_defn.h.

Referenced by bin_evaluation_1away(), bin_evaluation_k_away(), ETITLE(), FEPTITLE(), FEPTITLE2(), FEPTITLE_BACK(), FORMAT(), QMETITLE(), setup_bins_1away(), setup_bins_k_away(), setup_cell_vectors(), spatial_hashing(), TITITLE(), write_dcdstep(), and write_dcdstep_par_slave().

Y

#define Y   1

Definition at line 31 of file msm_defn.h.

Referenced by bin_evaluation_1away(), bin_evaluation_k_away(), setup_bins_1away(), setup_bins_k_away(), setup_cell_vectors(), spatial_hashing(), write_dcdstep(), and write_dcdstep_par_slave().

Z

#define Z   2

Definition at line 33 of file msm_defn.h.

Referenced by bin_evaluation_1away(), bin_evaluation_k_away(), setup_bins_1away(), setup_bins_k_away(), setup_cell_vectors(), spatial_hashing(), write_dcdstep(), and write_dcdstep_par_slave().

Function Documentation

GRID_TEMPLATE() [1/2]

GRID_TEMPLATE

(

double

)

GRID_TEMPLATE() [2/2]

GRID_TEMPLATE

(

float

)

NL_msm_cleanup()

void NL_msm_cleanup

(

NL_Msm *

pm

)

Definition at line 7 of file msm_setup.c.

References NL_Msm_t::eh, NL_Msm_t::eh_f, NL_Msm_t::gc, NL_Msm_t::gc_f, GRID_DONE, NL_Msm_t::lyzd, NL_Msm_t::lyzd_f, NL_Msm_t::lzd, NL_Msm_t::lzd_f, NL_Msm_t::maxlevels, NL_Msm_t::msmflags, NL_MSM_COMPUTE_CUDA_GRID_CUTOFF, NL_MSM_COMPUTE_SPREC, NL_Msm_t::qh, and NL_Msm_t::qh_f.

Referenced by NL_msm_destroy().

                                {
  int i;
#ifdef NL_USE_CUDA
  if (pm->msmflags & NL_MSM_COMPUTE_CUDA_GRID_CUTOFF) {
    NL_msm_cuda_cleanup_gridcutoff(pm);
  }
#endif /* NL_USE_CUDA */
  if (pm->msmflags & NL_MSM_COMPUTE_SPREC) {
    for (i = 0;  i < pm->maxlevels;  i++) {
      GRID_DONE( &(pm->qh_f[i]) );
      GRID_DONE( &(pm->eh_f[i]) );
      GRID_DONE( &(pm->gc_f[i]) );
    }
  }
  else {
    for (i = 0;  i < pm->maxlevels;  i++) {
      GRID_DONE( &(pm->qh[i]) );
      GRID_DONE( &(pm->eh[i]) );
      GRID_DONE( &(pm->gc[i]) );
    }
  }
  free(pm->lzd);
  free(pm->lyzd);
  free(pm->lzd_f);
  free(pm->lyzd_f);
  free(pm->qh);
  free(pm->eh);
  free(pm->gc);
  free(pm->qh_f);
  free(pm->eh_f);
  free(pm->gc_f);
}

NL_msm_compute_long_range()

int NL_msm_compute_long_range

(

NL_Msm *

pm

)

Definition at line 52 of file msm_longrng.c.

References anterpolation(), gridcutoff(), interpolation(), NL_MSM_COMPUTE_CUDA_FALL_BACK, NL_MSM_COMPUTE_CUDA_GRID_CUTOFF, NL_MSM_COMPUTE_NONFACTORED, NL_MSM_ERROR_SUPPORT, NL_MSM_SUCCESS, prolongation(), prolongation_factored(), restriction(), restriction_factored(), wkf_timer_start(), wkf_timer_stop(), and wkf_timer_time().

Referenced by NL_msm_compute_force().

                                           {
  double time_delta;
  int rc = 0;
  int level;
  int nlevels = msm->nlevels;
  int use_cuda_gridcutoff = (msm->msmflags & NL_MSM_COMPUTE_CUDA_GRID_CUTOFF);
  int fallback_cpu = (msm->msmflags & NL_MSM_COMPUTE_CUDA_FALL_BACK);
  int use_nonfactored = (msm->msmflags & NL_MSM_COMPUTE_NONFACTORED);

  wkf_timer_start(msm->timer_longrng);
  rc = anterpolation(msm);
  if (rc) return rc;
  wkf_timer_stop(msm->timer_longrng);
  time_delta = wkf_timer_time(msm->timer_longrng);
  if (msm->report_timings) {
    printf("MSM anterpolation:  %6.3f sec\n", time_delta);
  }

  wkf_timer_start(msm->timer_longrng);
  if (use_nonfactored) {
    for (level = 0;  level < nlevels - 1;  level++) {
      rc = restriction(msm, level);
      if (rc) return rc;
    }
  }
  else {
    for (level = 0;  level < nlevels - 1;  level++) {
      rc = restriction_factored(msm, level);
      if (rc) return rc;
    }
  }
  wkf_timer_stop(msm->timer_longrng);
  time_delta = wkf_timer_time(msm->timer_longrng);
  if (msm->report_timings) {
    printf("MSM restriction:    %6.3f sec\n", time_delta);
  }

  wkf_timer_start(msm->timer_longrng);
  if (use_cuda_gridcutoff && nlevels > 1) {
#ifdef NL_USE_CUDA
    if ((rc = NL_msm_cuda_condense_qgrids(msm)) != NL_MSM_SUCCESS ||
        (rc = NL_msm_cuda_compute_gridcutoff(msm)) != NL_MSM_SUCCESS ||
        (rc = NL_msm_cuda_expand_egrids(msm)) != NL_MSM_SUCCESS) {
      if (fallback_cpu) {
        printf("Falling back on CPU for grid cutoff computation\n");
        use_cuda_gridcutoff = 0;
      }
      else return rc;
    }
#else
    if (fallback_cpu) {
      printf("Falling back on CPU for grid cutoff computation\n");
      use_cuda_gridcutoff = 0;
    }
    else return NL_MSM_ERROR_SUPPORT;
#endif
  }

  if ( ! use_cuda_gridcutoff ) {
    for (level = 0;  level < nlevels - 1;  level++) {
      rc = gridcutoff(msm, level);
      if (rc) return rc;
    }
  }

  rc = gridcutoff(msm, level);  /* top level */
  if (rc) return rc;

  wkf_timer_stop(msm->timer_longrng);
  time_delta = wkf_timer_time(msm->timer_longrng);
  if (msm->report_timings) {
    printf("MSM grid cutoff:    %6.3f sec\n", time_delta);
  }

  wkf_timer_start(msm->timer_longrng);
  if (use_nonfactored) {
    for (level--;  level >= 0;  level--) {
      rc = prolongation(msm, level);
      if (rc) return rc;
    }
  }
  else {
    for (level--;  level >= 0;  level--) {
      rc = prolongation_factored(msm, level);
      if (rc) return rc;
    }
  }
  wkf_timer_stop(msm->timer_longrng);
  time_delta = wkf_timer_time(msm->timer_longrng);
  if (msm->report_timings) {
    printf("MSM prolongation:   %6.3f sec\n", time_delta);
  }

  wkf_timer_start(msm->timer_longrng);
  rc = interpolation(msm);
  if (rc) return rc;
  wkf_timer_stop(msm->timer_longrng);
  time_delta = wkf_timer_time(msm->timer_longrng);
  if (msm->report_timings) {
    printf("MSM interpolation:  %6.3f sec\n", time_delta);
  }

  return 0;
}

NL_msm_compute_long_range_sprec()

int NL_msm_compute_long_range_sprec

(

NL_Msm *

pm

)

Definition at line 52 of file msm_longrng_sprec.c.

References anterpolation(), gridcutoff(), interpolation(), NL_MSM_COMPUTE_CUDA_FALL_BACK, NL_MSM_COMPUTE_CUDA_GRID_CUTOFF, NL_MSM_COMPUTE_NONFACTORED, NL_MSM_ERROR_SUPPORT, NL_MSM_SUCCESS, prolongation(), prolongation_factored(), restriction(), restriction_factored(), wkf_timer_start(), wkf_timer_stop(), and wkf_timer_time().

Referenced by NL_msm_compute_force_sprec().

                                                 {
  double time_delta;
  int rc = 0;
  int level;
  int nlevels = msm->nlevels;
  int use_cuda_gridcutoff = (msm->msmflags & NL_MSM_COMPUTE_CUDA_GRID_CUTOFF);
  int fallback_cpu = (msm->msmflags & NL_MSM_COMPUTE_CUDA_FALL_BACK);
  int use_nonfactored = (msm->msmflags & NL_MSM_COMPUTE_NONFACTORED);

  wkf_timer_start(msm->timer_longrng);
  rc = anterpolation(msm);
  if (rc) return rc;
  wkf_timer_stop(msm->timer_longrng);
  time_delta = wkf_timer_time(msm->timer_longrng);
  if (msm->report_timings) {
    printf("MSM anterpolation:  %6.3f sec\n", time_delta);
  }

  wkf_timer_start(msm->timer_longrng);
  if (use_nonfactored) {
    for (level = 0;  level < nlevels - 1;  level++) {
      rc = restriction(msm, level);
      if (rc) return rc;
    }
  }
  else {
    for (level = 0;  level < nlevels - 1;  level++) {
      rc = restriction_factored(msm, level);
      if (rc) return rc;
    }
  }
  wkf_timer_stop(msm->timer_longrng);
  time_delta = wkf_timer_time(msm->timer_longrng);
  if (msm->report_timings) {
    printf("MSM restriction:    %6.3f sec\n", time_delta);
  }

  wkf_timer_start(msm->timer_longrng);
  if (use_cuda_gridcutoff && nlevels > 1) {
#ifdef NL_USE_CUDA
    if ((rc = NL_msm_cuda_condense_qgrids(msm)) != NL_MSM_SUCCESS ||
        (rc = NL_msm_cuda_compute_gridcutoff(msm)) != NL_MSM_SUCCESS ||
        (rc = NL_msm_cuda_expand_egrids(msm)) != NL_MSM_SUCCESS) {
      if (fallback_cpu) {
        printf("Falling back on CPU for grid cutoff computation\n");
        use_cuda_gridcutoff = 0;
      }
      else return rc;
    }
#else
    if (fallback_cpu) {
      printf("Falling back on CPU for grid cutoff computation\n");
      use_cuda_gridcutoff = 0;
    }
    else return NL_MSM_ERROR_SUPPORT;
#endif
  }

  if ( ! use_cuda_gridcutoff ) {
    for (level = 0;  level < nlevels - 1;  level++) {
      rc = gridcutoff(msm, level);
      if (rc) return rc;
    }
  }

  rc = gridcutoff(msm, level);  /* top level */
  if (rc) return rc;

  wkf_timer_stop(msm->timer_longrng);
  time_delta = wkf_timer_time(msm->timer_longrng);
  if (msm->report_timings) {
    printf("MSM grid cutoff:    %6.3f sec\n", time_delta);
  }

  wkf_timer_start(msm->timer_longrng);
  if (use_nonfactored) {
    for (level--;  level >= 0;  level--) {
      rc = prolongation(msm, level);
      if (rc) return rc;
    }
  }
  else {
    for (level--;  level >= 0;  level--) {
      rc = prolongation_factored(msm, level);
      if (rc) return rc;
    }
  }
  wkf_timer_stop(msm->timer_longrng);
  time_delta = wkf_timer_time(msm->timer_longrng);
  if (msm->report_timings) {
    printf("MSM prolongation:   %6.3f sec\n", time_delta);
  }

  wkf_timer_start(msm->timer_longrng);
  rc = interpolation(msm);
  if (rc) return rc;
  wkf_timer_stop(msm->timer_longrng);
  time_delta = wkf_timer_time(msm->timer_longrng);
  if (msm->report_timings) {
    printf("MSM interpolation:  %6.3f sec\n", time_delta);
  }

  return 0;
}

NL_msm_compute_short_range()

int NL_msm_compute_short_range

(

NL_Msm *

pm

)

Definition at line 37 of file msm_shortrng.c.

References bin_evaluation_1away(), bin_evaluation_k_away(), NL_Msm_t::maxatoms, NL_Msm_t::msmflags, NL_MSM_COMPUTE_1AWAY, NL_MSM_SUCCESS, NL_Msm_t::numatoms, setup_bin_data(), and spatial_hashing().

Referenced by NL_msm_compute_force().

                                           {
  int rc = 0;  /* return code */

  if (pm->maxatoms < pm->numatoms) {
    rc = setup_bin_data(pm);
    if (rc) return rc;
  }
  rc = spatial_hashing(pm);
  if (rc) return rc;
  if (pm->msmflags & NL_MSM_COMPUTE_1AWAY) {
    rc = bin_evaluation_1away(pm);
  }
  else {
    rc = bin_evaluation_k_away(pm);
  }
  if (rc) return rc;
  return NL_MSM_SUCCESS;
}

NL_msm_compute_short_range_sprec()

int NL_msm_compute_short_range_sprec

(

NL_Msm *

pm

)

Definition at line 37 of file msm_shortrng_sprec.c.

References bin_evaluation_1away(), bin_evaluation_k_away(), NL_Msm_t::maxatoms, NL_Msm_t::msmflags, NL_MSM_COMPUTE_1AWAY, NL_MSM_SUCCESS, NL_Msm_t::numatoms, setup_bin_data(), and spatial_hashing().

Referenced by NL_msm_compute_force_sprec().

                                                 {
  int rc = 0;  /* return code */

  if (pm->maxatoms < pm->numatoms) {
    rc = setup_bin_data(pm);
    if (rc) return rc;
  }
  rc = spatial_hashing(pm);
  if (rc) return rc;
  if (pm->msmflags & NL_MSM_COMPUTE_1AWAY) {
    rc = bin_evaluation_1away(pm);
  }
  else {
    rc = bin_evaluation_k_away(pm);
  }
  if (rc) return rc;
  return NL_MSM_SUCCESS;
}