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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8626 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2012-08-13 21:41:28 +00:00
parent 9b2440a0ab
commit 6304a8c9bf
4 changed files with 165 additions and 36 deletions
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2
src/MAKE/Makefile.g++
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@ -28,7 +28,7 @@ SHLIBFLAGS = -shared
# LAMMPS ifdef settings, OPTIONAL
# see possible settings in doc/Section_start.html#2_2 (step 4)
LMP_INC = -DLAMMPS_GZIP -DLAMMPS_JPEG
LMP_INC = -DLAMMPS_GZIP #-DLAMMPS_JPEG
# MPI library, REQUIRED
# see discussion in doc/Section_start.html#2_2 (step 5)

13
src/atom.cpp
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@ -1384,14 +1384,25 @@ void Atom::update_callback(int ifix)
void *Atom::extract(char *name)
{
if (strcmp(name,"mass") == 0) return (void *) mass;
if (strcmp(name,"id") == 0) return (void *) tag;
if (strcmp(name,"type") == 0) return (void *) type;
if (strcmp(name,"mask") == 0) return (void *) mask;
if (strcmp(name,"image") == 0) return (void *) image;
if (strcmp(name,"x") == 0) return (void *) x;
if (strcmp(name,"v") == 0) return (void *) v;
if (strcmp(name,"f") == 0) return (void *) f;
if (strcmp(name,"mass") == 0) return (void *) mass;
if (strcmp(name,"molecule") == 0) return (void *) molecule;
if (strcmp(name,"q") == 0) return (void *) q;
if (strcmp(name,"mu") == 0) return (void *) mu;
if (strcmp(name,"omega") == 0) return (void *) omega;
if (strcmp(name,"amgmom") == 0) return (void *) angmom;
if (strcmp(name,"torque") == 0) return (void *) torque;
if (strcmp(name,"radius") == 0) return (void *) radius;
if (strcmp(name,"rmass") == 0) return (void *) rmass;
if (strcmp(name,"vfrac") == 0) return (void *) vfrac;
if (strcmp(name,"s0") == 0) return (void *) s0;
return NULL;
}

181
src/library.cpp
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@ -30,6 +30,7 @@
#include "modify.h"
#include "compute.h"
#include "fix.h"
#include "memory.h"
using namespace LAMMPS_NS;
@ -157,6 +158,14 @@ void *lammps_extract_atom(void *ptr, char *name)
id = compute ID
style = 0 for global data, 1 for per-atom data, 2 for local data
type = 0 for scalar, 1 for vector, 2 for array
for global data, returns a pointer to the
compute's internal data structure for the entity
caller should cast it to (double *) for a scalar or vector
caller should cast it to (double **) for an array
for per-atom or local data, returns a pointer to the
compute's internal data structure for the entity
caller should cast it to (double *) for a vector
caller should cast it to (double **) for an array
returns a void pointer to the compute's internal data structure
for the entity which the caller can cast to the proper data type
returns a NULL if id is not recognized or style/type not supported
@ -236,7 +245,8 @@ void *lammps_extract_compute(void *ptr, char *id, int style, int type)
which the caller can cast to a (double *) which points to the value
for per-atom or local data, returns a pointer to the
fix's internal data structure for the entity
which the caller can cast to the proper data type
caller should cast it to (double *) for a vector
caller should cast it to (double **) for an array
returns a NULL if id is not recognized or style/type not supported
IMPORTANT: for global data,
this function allocates a double to store the value in,
@ -300,7 +310,7 @@ void *lammps_extract_fix(void *ptr, char *id, int style, int type,
which the caller can cast to a (double *) which points to the value
for atom-style variable, returns a pointer to the
vector of per-atom values on each processor,
which the caller can cast to the proper data type
which the caller can cast to a (double *) which points to the values
returns a NULL if name is not recognized or not equal-style or atom-style
IMPORTANT: for both equal-style and atom-style variables,
this function allocates memory to store the variable data in
@ -343,7 +353,10 @@ void *lammps_extract_variable(void *ptr, char *name, char *group)
return NULL;
}
/* ---------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
return the total number of atoms in the system
useful before call to lammps_get_atoms() so can pre-allocate vector
------------------------------------------------------------------------- */
int lammps_get_natoms(void *ptr)
{
@ -353,9 +366,18 @@ int lammps_get_natoms(void *ptr)
return natoms;
}
/* ---------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
gather the named atom-based entity across all processors
name = desired quantity, e.g. x or charge
type = 0 for integer values, 1 for double values
count = # of per-atom values, e.g. 1 for type or charge, 3 for x or f
return atom-based values in data, ordered by count, then by atom ID
e.g. x[0][0],x[0][1],x[0][2],x[1][0],x[1][1],x[1][2],x[2][0],...
data must be allocated by caller to correct length
------------------------------------------------------------------------- */
void lammps_get_coords(void *ptr, double *coords)
void lammps_gather_atoms(void *ptr, char *name,
int type, int count, void *data)
{
LAMMPS *lmp = (LAMMPS *) ptr;
@ -365,47 +387,142 @@ void lammps_get_coords(void *ptr, double *coords)
if (lmp->atom->natoms > MAXSMALLINT) return;
int natoms = static_cast<int> (lmp->atom->natoms);
double *copy = new double[3*natoms];
for (int i = 0; i < 3*natoms; i++) copy[i] = 0.0;
double **x = lmp->atom->x;
int *tag = lmp->atom->tag;
int nlocal = lmp->atom->nlocal;
int i,j,offset;
int id,offset;
for (int i = 0; i < nlocal; i++) {
id = tag[i];
offset = 3*(id-1);
copy[offset+0] = x[i][0];
copy[offset+1] = x[i][1];
copy[offset+2] = x[i][2];
// copy = Natom length vector of per-atom values
// use atom ID to insert each atom's values into copy
// MPI_Allreduce with MPI_SUM to merge into data, ordered by atom ID
if (type == 0) {
void *vptr = lmp->atom->extract(name);
int *vector;
int **array;
if (count == 1) vector = (int *) vptr;
else array = (int **) vptr;
int *copy;
lmp->memory->create(copy,count*natoms,"lib/gather:copy");
for (i = 0; i < count*natoms; i++) copy[i] = 0;
int *tag = lmp->atom->tag;
int nlocal = lmp->atom->nlocal;
if (count == 1)
for (i = 0; i < nlocal; i++)
copy[tag[i]-1] = vector[i];
else
for (i = 0; i < nlocal; i++) {
offset = count*(tag[i]-1);
for (j = 0; j < count; j++)
copy[offset++] = array[i][0];
}
MPI_Allreduce(copy,data,count*natoms,MPI_INT,MPI_SUM,lmp->world);
lmp->memory->destroy(copy);
} else {
void *vptr = lmp->atom->extract(name);
double *vector;
double **array;
if (count == 1) vector = (double *) vptr;
else array = (double **) vptr;
double *copy;
lmp->memory->create(copy,count*natoms,"lib/gather:copy");
for (i = 0; i < count*natoms; i++) copy[i] = 0.0;
int *tag = lmp->atom->tag;
int nlocal = lmp->atom->nlocal;
if (count == 1) {
for (i = 0; i < nlocal; i++)
copy[tag[i]-1] = vector[i];
} else {
for (i = 0; i < nlocal; i++) {
offset = count*(tag[i]-1);
for (j = 0; j < count; j++)
copy[offset++] = array[i][j];
}
}
MPI_Allreduce(copy,data,count*natoms,MPI_DOUBLE,MPI_SUM,lmp->world);
lmp->memory->destroy(copy);
}
MPI_Allreduce(copy,coords,3*natoms,MPI_DOUBLE,MPI_SUM,lmp->world);
delete [] copy;
}
/* ---------------------------------------------------------------------- */
void lammps_put_coords(void *ptr, double *coords)
/* ----------------------------------------------------------------------
gather the named atom-based entity across all processors
name = desired quantity, e.g. x or charge
type = 0 for integer values, 1 for double values
count = # of per-atom values, e.g. 1 for type or charge, 3 for x or f
return atom-based values in data, ordered by count, then by atom ID
e.g. x[0][0],x[0][1],x[0][2],x[1][0],x[1][1],x[1][2],x[2][0],...
data must be allocated by caller to correct length
------------------------------------------------------------------------- */
void lammps_scatter_atoms(void *ptr, char *name,
int type, int count, void *data)
{
LAMMPS *lmp = (LAMMPS *) ptr;
// error if no map defined by LAMMPS
// error if tags are not defined or not consecutive
if (lmp->atom->map_style == 0) return;
if (lmp->atom->tag_enable == 0 || lmp->atom->tag_consecutive() == 0) return;
if (lmp->atom->natoms > MAXSMALLINT) return;
int natoms = static_cast<int> (lmp->atom->natoms);
double **x = lmp->atom->x;
int m,offset;
for (int i = 0; i < natoms; i++) {
if ((m = lmp->atom->map(i+1)) >= 0) {
offset = 3*i;
x[m][0] = coords[offset+0];
x[m][1] = coords[offset+1];
x[m][2] = coords[offset+2];
int i,j,m,offset;
// copy = Natom length vector of per-atom values
// use atom ID to insert each atom's values into copy
// MPI_Allreduce with MPI_SUM to merge into data, ordered by atom ID
if (type == 0) {
void *vptr = lmp->atom->extract(name);
int *vector;
int **array;
if (count == 1) vector = (int *) vptr;
else array = (int **) vptr;
int *dptr = (int *) data;
if (count == 1)
for (i = 0; i < natoms; i++)
if ((m = lmp->atom->map(i+1)) >= 0)
vector[m] = dptr[i];
else
for (i = 0; i < natoms; i++)
if ((m = lmp->atom->map(i+1)) >= 0) {
offset = count*i;
for (j = 0; j < count; j++)
array[m][j] = dptr[offset++];
}
} else {
void *vptr = lmp->atom->extract(name);
double *vector;
double **array;
if (count == 1) vector = (double *) vptr;
else array = (double **) vptr;
double *dptr = (double *) data;
int *tag = lmp->atom->tag;
int nlocal = lmp->atom->nlocal;
if (count == 1) {
for (i = 0; i < natoms; i++)
if ((m = lmp->atom->map(i+1)) >= 0)
vector[m] = dptr[i];
} else {
for (i = 0; i < natoms; i++) {
if ((m = lmp->atom->map(i+1)) >= 0) {
offset = count*i;
for (j = 0; j < count; j++)
array[m][j] = dptr[offset++];
}
}
}
}
}

5
src/library.h
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@ -38,12 +38,13 @@ void *lammps_extract_fix(void *, char *, int, int, int, int);
void *lammps_extract_variable(void *, char *, char *);
int lammps_get_natoms(void *);
void lammps_get_coords(void *, double *);
void lammps_put_coords(void *, double *);
void lammps_gather_atoms(void *, char *, int, int, void *);
void lammps_scatter_atoms(void *, char *, int, int, void *);
#ifdef __cplusplus
}
#endif
/* ERROR/WARNING messages:
*/