From 6fbcee59ee0b2d4b6705c106b1c0d537bc804793 Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Thu, 6 Aug 2009 22:21:38 +0000
Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3009
f3b2605a-c512-4ea7-a41b-209d697bcdaa
---
src/atom.cpp | 21 ++++++++++++++
src/atom.h | 2 ++
src/compute.h | 1 +
src/fix.h | 1 +
src/library.cpp | 75 ++++++++++++++++++++++++++++++++++++-------------
src/library.h | 17 +++++------
src/memory.cpp | 6 +++-
src/modify.cpp | 36 ++++++++++++++++++++++++
src/modify.h | 5 ++++
9 files changed, 135 insertions(+), 29 deletions(-)
diff --git a/src/atom.cpp b/src/atom.cpp
index 28bee5266e..563548c388 100644
--- a/src/atom.cpp
+++ b/src/atom.cpp
@@ -1369,6 +1369,27 @@ void Atom::update_callback(int ifix)
if (extra_restart[i] > ifix) extra_restart[i]--;
}
+/* ----------------------------------------------------------------------
+ return a pointer to a named internal variable
+ if don't recognize name, return NULL
+------------------------------------------------------------------------- */
+
+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;
+ 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,"rmass") == 0) return (void *) rmass;
+
+ return NULL;
+}
+
/* ----------------------------------------------------------------------
return # of bytes of allocated memory
call to avec sums per-atom vectors
diff --git a/src/atom.h b/src/atom.h
index 8325811bff..33d4668e78 100644
--- a/src/atom.h
+++ b/src/atom.h
@@ -146,6 +146,8 @@ class Atom : protected Pointers {
void delete_callback(const char *, int);
void update_callback(int);
+ void *extract(char *);
+
double memory_usage();
int memcheck(const char *);
diff --git a/src/compute.h b/src/compute.h
index effcc9462a..9f37dfdaf9 100644
--- a/src/compute.h
+++ b/src/compute.h
@@ -90,6 +90,7 @@ class Compute : protected Pointers {
int matchstep(int);
void clearstep();
+ virtual void *extract(char *) {return NULL;}
virtual double memory_usage() {return 0.0;}
protected:
diff --git a/src/fix.h b/src/fix.h
index 31ea065fbe..f869f9fc26 100644
--- a/src/fix.h
+++ b/src/fix.h
@@ -126,6 +126,7 @@ 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:
diff --git a/src/library.cpp b/src/library.cpp
index d341a33725..8a1918c98e 100644
--- a/src/library.cpp
+++ b/src/library.cpp
@@ -15,10 +15,14 @@
// new LAMMPS-specific functions can be added
#include "mpi.h"
+#include "string.h"
#include "library.h"
#include "lammps.h"
#include "input.h"
#include "atom.h"
+#include "update.h"
+#include "domain.h"
+#include "modify.h"
using namespace LAMMPS_NS;
@@ -29,8 +33,8 @@ using namespace LAMMPS_NS;
void lammps_open(int argc, char **argv, MPI_Comm communicator, void **ptr)
{
- LAMMPS *lammps = new LAMMPS(argc,argv,communicator);
- *ptr = (void *) lammps;
+ LAMMPS *lmp = new LAMMPS(argc,argv,communicator);
+ *ptr = (void *) lmp;
}
/* ----------------------------------------------------------------------
@@ -39,8 +43,8 @@ void lammps_open(int argc, char **argv, MPI_Comm communicator, void **ptr)
void lammps_close(void *ptr)
{
- LAMMPS *lammps = (LAMMPS *) ptr;
- delete lammps;
+ LAMMPS *lmp = (LAMMPS *) ptr;
+ delete lmp;
}
/* ----------------------------------------------------------------------
@@ -49,8 +53,8 @@ void lammps_close(void *ptr)
void lammps_file(void *ptr, char *str)
{
- LAMMPS *lammps = (LAMMPS *) ptr;
- lammps->input->file(str);
+ LAMMPS *lmp = (LAMMPS *) ptr;
+ lmp->input->file(str);
}
/* ----------------------------------------------------------------------
@@ -59,8 +63,8 @@ void lammps_file(void *ptr, char *str)
char *lammps_command(void *ptr, char *str)
{
- LAMMPS *lammps = (LAMMPS *) ptr;
- return lammps->input->one(str);
+ LAMMPS *lmp = (LAMMPS *) ptr;
+ return lmp->input->one(str);
}
/* ----------------------------------------------------------------------
@@ -68,12 +72,43 @@ char *lammps_command(void *ptr, char *str)
all must receive LAMMPS pointer as argument
------------------------------------------------------------------------- */
+/* ----------------------------------------------------------------------
+ extract a pointer to an internal LAMMPS value or data structure
+ category: 0 = general, 1 = fix, 2 = compute
+ id = ID of fix or compute (else not used)
+ 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
+------------------------------------------------------------------------- */
+
+void *lammps_extract(void *ptr, int category, char *id, 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];
+ if (strcmp(name,"boxylo") == 0) return (void *) &lmp->domain->boxlo[1];
+ 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];
+ return NULL;
+ }
+
+ 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);
+
+ return NULL;
+}
+
/* ---------------------------------------------------------------------- */
int lammps_get_natoms(void *ptr)
{
- LAMMPS *lammps = (LAMMPS *) ptr;
- int natoms = static_cast<int> (lammps->atom->natoms);
+ LAMMPS *lmp = (LAMMPS *) ptr;
+ int natoms = static_cast<int> (lmp->atom->natoms);
return natoms;
}
@@ -81,14 +116,14 @@ int lammps_get_natoms(void *ptr)
void lammps_get_coords(void *ptr, double *coords)
{
- LAMMPS *lammps = (LAMMPS *) ptr;
- int natoms = static_cast<int> (lammps->atom->natoms);
+ LAMMPS *lmp = (LAMMPS *) ptr;
+ 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 = lammps->atom->x;
- int *tag = lammps->atom->tag;
- int nlocal = lammps->atom->nlocal;
+ double **x = lmp->atom->x;
+ int *tag = lmp->atom->tag;
+ int nlocal = lmp->atom->nlocal;
int id,offset;
for (int i = 0; i < nlocal; i++) {
@@ -99,7 +134,7 @@ void lammps_get_coords(void *ptr, double *coords)
copy[offset+2] = x[i][2];
}
- MPI_Allreduce(copy,coords,3*natoms,MPI_DOUBLE,MPI_SUM,lammps->world);
+ MPI_Allreduce(copy,coords,3*natoms,MPI_DOUBLE,MPI_SUM,lmp->world);
delete [] copy;
}
@@ -107,14 +142,14 @@ void lammps_get_coords(void *ptr, double *coords)
void lammps_put_coords(void *ptr, double *coords)
{
- LAMMPS *lammps = (LAMMPS *) ptr;
- int natoms = static_cast<int> (lammps->atom->natoms);
+ LAMMPS *lmp = (LAMMPS *) ptr;
+ int natoms = static_cast<int> (lmp->atom->natoms);
- double **x = lammps->atom->x;
+ double **x = lmp->atom->x;
int m,offset;
for (int i = 0; i < natoms; i++) {
- if ((m = lammps->atom->map(i+1)) >= 0) {
+ if ((m = lmp->atom->map(i+1)) >= 0) {
offset = 3*i;
x[m][0] = coords[offset+0];
x[m][1] = coords[offset+1];
diff --git a/src/library.h b/src/library.h
index f97f27fdc0..9c21d7a1d2 100644
--- a/src/library.h
+++ b/src/library.h
@@ -24,14 +24,15 @@
extern "C" {
#endif
-void lammps_open(int, char **, MPI_Comm, void **); /* start-up LAMMPS */
-void lammps_close(void *); /* shut-down LAMMPS */
-void lammps_file(void *, char *); /* run an input script */
-char *lammps_command(void *, char *); /* execute a command */
-
-int lammps_get_natoms(void *); /* return # of atoms */
-void lammps_get_coords(void *, double *); /* get atom x from all procs */
-void lammps_put_coords(void *, double *); /* put atom x on all procs */
+void lammps_open(int, char **, MPI_Comm, void **);
+void lammps_close(void *);
+void lammps_file(void *, char *);
+char *lammps_command(void *, char *);
+
+void *lammps_extract(void *, int, char *, char *);
+int lammps_get_natoms(void *);
+void lammps_get_coords(void *, double *);
+void lammps_put_coords(void *, double *);
#ifdef __cplusplus
}
diff --git a/src/memory.cpp b/src/memory.cpp
index caf553120a..4e46b87b57 100644
--- a/src/memory.cpp
+++ b/src/memory.cpp
@@ -56,7 +56,11 @@ void Memory::sfree(void *ptr)
void *Memory::srealloc(void *ptr, int n, const char *name)
{
- if (n == 0) return NULL;
+ if (n == 0) {
+ sfree(ptr);
+ return NULL;
+ }
+
ptr = realloc(ptr,n);
if (ptr == NULL) {
char str[128];
diff --git a/src/modify.cpp b/src/modify.cpp
index 962536a9f9..3dace9f5d0 100644
--- a/src/modify.cpp
+++ b/src/modify.cpp
@@ -996,6 +996,42 @@ 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
------------------------------------------------------------------------- */
diff --git a/src/modify.h b/src/modify.h
index a749f010dc..067513ee6d 100644
--- a/src/modify.h
+++ b/src/modify.h
@@ -83,6 +83,9 @@ 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:
@@ -111,6 +114,8 @@ class Modify : protected Pointers {
char **style_restart_peratom;
int *index_restart_peratom;
+ int index_permanent; // fix/compute index returned to library call
+
void list_init(int, int &, int *&);
void list_init_end_of_step(int, int &, int *&);
void list_init_thermo_energy(int, int &, int *&);
--
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