Commit 6fbcee59 authored by sjplimp's avatar sjplimp
Browse files 

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3009 f3b2605a-c512-4ea7-a41b-209d697bcdaa
parent f3ddb773

src/atom.cpp

+21 −0
Original line number Diff line number Diff line
@@ -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

src/atom.h

+2 −0
Original line number Diff line number Diff line
@@ -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 *);

src/compute.h

+1 −0
Original line number Diff line number Diff line
@@ -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:

src/fix.h

+1 −0
Original line number Diff line number Diff line
@@ -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:

src/library.cpp

+55 −20
Original line number Diff line number Diff line
@@ -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];

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