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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4584 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2010-08-24 18:32:11 +00:00
parent 763f2aac79
commit 55d76e6c22
7 changed files with 235 additions and 67 deletions
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4
src/atom.cpp
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@ -1584,13 +1584,11 @@ void Atom::update_callback(int ifix)
/* ----------------------------------------------------------------------
return a pointer to a named internal variable
if don't recognize name, return NULL
customize by adding names
------------------------------------------------------------------------- */
void *Atom::extract(char *name)
{
if (strcmp(name,"natoms") == 0) return (void *) &natoms;
if (strcmp(name,"nlocal") == 0) return (void *) &nlocal;
if (strcmp(name,"id") == 0) return (void *) tag;
if (strcmp(name,"type") == 0) return (void *) type;
if (strcmp(name,"x") == 0) return (void *) x;

1
src/compute.h
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@ -107,7 +107,6 @@ class Compute : protected Pointers {
int matchstep(int);
void clearstep();
virtual void *extract(char *) {return NULL;}
virtual double memory_usage() {return 0.0;}
protected:

1
src/fix.h
View File

@ -149,7 +149,6 @@ class Fix : protected Pointers {
virtual int modify_param(int, char **) {return 0;}
virtual void *extract(char *) {return NULL;}
virtual double memory_usage() {return 0.0;}
protected:

233
src/library.cpp
View File

@ -12,17 +12,23 @@
------------------------------------------------------------------------- */
// C or Fortran style library interface to LAMMPS
// new LAMMPS-specific functions can be added
// customize by adding new LAMMPS-specific functions
#include "mpi.h"
#include "string.h"
#include "stdlib.h"
#include "library.h"
#include "lammps.h"
#include "input.h"
#include "atom.h"
#include "update.h"
#include "domain.h"
#include "update.h"
#include "group.h"
#include "input.h"
#include "variable.h"
#include "modify.h"
#include "compute.h"
#include "fix.h"
using namespace LAMMPS_NS;
@ -70,22 +76,22 @@ char *lammps_command(void *ptr, char *str)
/* ----------------------------------------------------------------------
add LAMMPS-specific library functions
all must receive LAMMPS pointer as argument
customize by adding a function here and in library.h header file
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
extract a pointer to an internal LAMMPS value or data structure
category: 0 = general, 1 = atom, 2 = fix, 3 = compute
id = ID of fix or compute (else not used, just pass NULL)
name = desired quantity, e.g. x or dt
returns a void pointer which the caller can cast to the desired data type
returns a NULL if LAMMPS does not recognize the name
extract a pointer to an internal LAMMPS global entity
name = desired quantity, e.g. dt or boxyhi or natoms
returns a void pointer to the entity
which the caller can cast to the proper data type
returns a NULL if name not listed below
customize by adding names
------------------------------------------------------------------------- */
void *lammps_extract(void *ptr, int category, char *id, char *name)
void *lammps_extract_global(void *ptr, char *name)
{
LAMMPS *lmp = (LAMMPS *) ptr;
if (category == 0) {
if (strcmp(name,"dt") == 0) return (void *) &lmp->update->dt;
if (strcmp(name,"boxxlo") == 0) return (void *) &lmp->domain->boxlo[0];
if (strcmp(name,"boxxhi") == 0) return (void *) &lmp->domain->boxhi[0];
@ -93,12 +99,213 @@ void *lammps_extract(void *ptr, int category, char *id, char *name)
if (strcmp(name,"boxyhi") == 0) return (void *) &lmp->domain->boxhi[1];
if (strcmp(name,"boxzlo") == 0) return (void *) &lmp->domain->boxlo[2];
if (strcmp(name,"boxzhi") == 0) return (void *) &lmp->domain->boxhi[2];
if (strcmp(name,"natoms") == 0) return (void *) &lmp->atom->natoms;
if (strcmp(name,"nlocal") == 0) return (void *) &lmp->atom->nlocal;
return NULL;
}
/* ----------------------------------------------------------------------
extract a pointer to an internal LAMMPS atom-based entity
name = desired quantity, e.g. x or mass
returns a void pointer to the entity
which the caller can cast to the proper data type
returns a NULL if Atom::extract() does not recognize the name
customize by adding names to Atom::extract()
------------------------------------------------------------------------- */
void *lammps_extract_atom(void *ptr, char *name)
{
LAMMPS *lmp = (LAMMPS *) ptr;
return lmp->atom->extract(name);
}
/* ----------------------------------------------------------------------
extract a pointer to an internal LAMMPS compute-based entity
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
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
IMPORTANT: if the compute is not current it will be invoked
LAMMPS cannot easily check if it is valid to invoke the compute,
so caller must insure that it is OK
------------------------------------------------------------------------- */
void *lammps_extract_compute(void *ptr, char *id, int style, int type)
{
LAMMPS *lmp = (LAMMPS *) ptr;
int icompute = lmp->modify->find_compute(id);
if (icompute < 0) return NULL;
Compute *compute = lmp->modify->compute[icompute];
if (style == 0) {
if (type == 0) {
if (!compute->scalar_flag) return NULL;
if (compute->invoked_scalar != lmp->update->ntimestep)
compute->compute_scalar();
return (void *) &compute->scalar;
}
if (type == 1) {
if (!compute->vector_flag) return NULL;
if (compute->invoked_vector != lmp->update->ntimestep)
compute->compute_vector();
return (void *) compute->vector;
}
if (type == 2) {
if (!compute->array_flag) return NULL;
if (compute->invoked_array != lmp->update->ntimestep)
compute->compute_array();
return (void *) compute->array;
}
}
if (category == 1) return lmp->atom->extract(name);
if (category == 2) return lmp->modify->extract_fix(id,name);
if (category == 3) return lmp->modify->extract_compute(id,name);
if (style == 1) {
if (!compute->peratom_flag) return NULL;
if (type == 1) {
if (compute->invoked_peratom != lmp->update->ntimestep)
compute->compute_peratom();
return (void *) compute->vector_atom;
}
if (type == 2) {
if (compute->invoked_peratom != lmp->update->ntimestep)
compute->compute_peratom();
return (void *) compute->array_atom;
}
}
if (style == 2) {
if (!compute->local_flag) return NULL;
if (type == 1) {
if (compute->invoked_local != lmp->update->ntimestep)
compute->compute_local();
return (void *) compute->vector_local;
}
if (type == 2) {
if (compute->invoked_local != lmp->update->ntimestep)
compute->compute_local();
return (void *) compute->array_local;
}
}
return NULL;
}
/* ----------------------------------------------------------------------
extract a pointer to an internal LAMMPS fix-based entity
id = fix 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
i,j = indices needed only to specify which global vector or array value
for global data, returns a pointer to a memory location
which is allocated by this function
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
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,
so the caller must free this memory to avoid a leak, e.g.
double *dptr = (double *) lammps_extract_fix();
double value = *dptr;
free(dptr);
IMPORTANT: LAMMPS cannot easily check when info extracted from
the fix is valid, so caller must insure that it is OK
------------------------------------------------------------------------- */
void *lammps_extract_fix(void *ptr, char *id, int style, int type,
int i, int j)
{
LAMMPS *lmp = (LAMMPS *) ptr;
int ifix = lmp->modify->find_fix(id);
if (ifix < 0) return NULL;
Fix *fix = lmp->modify->fix[ifix];
if (style == 0) {
double *dptr = (double *) malloc(sizeof(double));
if (type == 0) {
if (!fix->scalar_flag) return NULL;
*dptr = fix->compute_scalar();
return (void *) dptr;
}
if (type == 1) {
if (!fix->vector_flag) return NULL;
*dptr = fix->compute_vector(i);
return (void *) dptr;
}
if (type == 2) {
if (!fix->array_flag) return NULL;
*dptr = fix->compute_array(i,j);
return (void *) dptr;
}
}
if (style == 1) {
if (!fix->peratom_flag) return NULL;
if (type == 1) return (void *) fix->vector_atom;
if (type == 2) return (void *) fix->array_atom;
}
if (style == 2) {
if (!fix->local_flag) return NULL;
if (type == 1) return (void *) fix->vector_local;
if (type == 2) return (void *) fix->array_local;
}
return NULL;
}
/* ----------------------------------------------------------------------
extract a pointer to an internal LAMMPS evaluated variable
name = variable name, must be equal-style or atom-style variable
group = group ID for evaluating an atom-style variable, else NULL
for equal-style variable, returns a pointer to a memory location
which is allocated by this function
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
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
so the caller must free this memory to avoid a leak
e.g. for equal-style variables
double *dptr = (double *) lammps_extract_variable();
double value = *dptr;
free(dptr);
e.g. for atom-style variables
double *vector = (double *) lammps_extract_variable();
use the vector values
free(vector);
IMPORTANT: LAMMPS cannot easily check when it is valid to evaluate
the variable or any fixes or computes or thermodynamic info it references,
so caller must insure that it is OK
------------------------------------------------------------------------- */
void *lammps_extract_variable(void *ptr, char *name, char *group)
{
LAMMPS *lmp = (LAMMPS *) ptr;
int ivar = lmp->input->variable->find(name);
if (ivar < 0) return NULL;
if (lmp->input->variable->equalstyle(ivar)) {
double *dptr = (double *) malloc(sizeof(double));
*dptr = lmp->input->variable->compute_equal(ivar);
return (void *) dptr;
}
if (lmp->input->variable->atomstyle(ivar)) {
int igroup = lmp->group->find(group);
if (igroup < 0) return NULL;
int nlocal = lmp->atom->nlocal;
double *vector = (double *) malloc(nlocal*sizeof(double));
lmp->input->variable->compute_atom(ivar,igroup,vector,1,0);
return (void *) vector;
}
return NULL;
}

8
src/library.h
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@ -29,7 +29,12 @@ void lammps_close(void *);
void lammps_file(void *, char *);
char *lammps_command(void *, char *);
void *lammps_extract(void *, int, char *, char *);
void *lammps_extract_global(void *, char *);
void *lammps_extract_atom(void *, char *);
void *lammps_extract_compute(void *, char *, int, int);
void *lammps_extract_fix(void *, 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 *);
@ -37,4 +42,3 @@ void lammps_put_coords(void *, double *);
#ifdef __cplusplus
}
#endif

36
src/modify.cpp
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@ -1062,42 +1062,6 @@ void Modify::list_init_compute()
if (compute[i]->timeflag) list_timeflag[n_timeflag++] = i;
}
/* ----------------------------------------------------------------------
return a pointer to a named internal variable owned by fix ID
if don't recognize ID, return NULL
------------------------------------------------------------------------- */
void *Modify::extract_fix(char *id, char *name)
{
int ifix = find_fix(id);
if (ifix < 0) return NULL;
if (strcmp(name,"index") == 0) {
index_permanent = ifix;
return (void *) &index_permanent;
}
return fix[ifix]->extract(name);
}
/* ----------------------------------------------------------------------
return a pointer to a named internal variable owned by compute ID
if don't recognize ID, return NULL
------------------------------------------------------------------------- */
void *Modify::extract_compute(char *id, char *name)
{
int icompute = find_compute(id);
if (icompute < 0) return NULL;
if (strcmp(name,"index") == 0) {
index_permanent = icompute;
return (void *) &index_permanent;
}
return compute[icompute]->extract(name);
}
/* ----------------------------------------------------------------------
return # of bytes of allocated memory from all fixes
------------------------------------------------------------------------- */

3
src/modify.h
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@ -91,9 +91,6 @@ class Modify : protected Pointers {
int read_restart(FILE *);
void restart_deallocate();
void *extract_fix(char *, char *);
void *extract_compute(char *, char *);
double memory_usage();
private: