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

src/atom.cpp

@@ -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;

src/compute.h

@@ -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:

src/fix.h

@@ -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:

src/library.cpp

@@ -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;
 
@@ -70,35 +76,236 @@ 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
+   extract a pointer to an internal LAMMPS global entity
-   category: 0 = general, 1 = atom, 2 = fix, 3 = compute
+   name = desired quantity, e.g. dt or boxyhi or natoms
-   id = ID of fix or compute (else not used, just pass NULL)
+   returns a void pointer to the entity
-   name = desired quantity, e.g. x or dt
+     which the caller can cast to the proper data type
-   returns a void pointer which the caller can cast to the desired data type
+   returns a NULL if name not listed below
-   returns a NULL if LAMMPS does not recognize the name
+   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,"dt") == 0) return (void *) &lmp->update->dt;
+  if (strcmp(name,"boxxlo") == 0) return (void *) &lmp->domain->boxlo[0];
-    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,"boxxhi") == 0) return (void *) &lmp->domain->boxhi[0];
+  if (strcmp(name,"boxylo") == 0) return (void *) &lmp->domain->boxlo[1];
-    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,"boxyhi") == 0) return (void *) &lmp->domain->boxhi[1];
+  if (strcmp(name,"boxzlo") == 0) return (void *) &lmp->domain->boxlo[2];
-    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,"boxzhi") == 0) return (void *) &lmp->domain->boxhi[2];
+  if (strcmp(name,"natoms") == 0) return (void *) &lmp->atom->natoms;
-    return NULL;
+  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 (style == 1) {
-  if (category == 2) return lmp->modify->extract_fix(id,name);
+    if (!compute->peratom_flag) return NULL;
-  if (category == 3) return lmp->modify->extract_compute(id,name);
+    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;
 }

src/library.h

@@ -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
-

src/modify.cpp

@@ -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
 ------------------------------------------------------------------------- */

src/modify.h

@@ -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: