new library functions

examples/COUPLE/simple/in.lj

@@ -20,4 +20,6 @@ neigh_modify	delay 0 every 20 check no
 
 fix		1 all nve
 
+variable        fx atom fx
+
 run		10

examples/COUPLE/simple/simple.c

@@ -71,8 +71,8 @@ int main(int narg, char **arg)
      (could just send it to proc 0 of comm_lammps and let it Bcast)
      all LAMMPS procs call lammps_command() on the line */
 
-  void *ptr;
-  if (lammps == 1) lammps_open(0,NULL,comm_lammps,&ptr);
+  void *lmp = NULL;
+  if (lammps == 1) lammps_open(0,NULL,comm_lammps,&lmp);
 
   int n;
   char line[1024];
@@ -85,7 +85,7 @@ int main(int narg, char **arg)
     MPI_Bcast(&n,1,MPI_INT,0,MPI_COMM_WORLD);
     if (n == 0) break;
     MPI_Bcast(line,n,MPI_CHAR,0,MPI_COMM_WORLD);
-    if (lammps == 1) lammps_command(ptr,line);
+    if (lammps == 1) lammps_command(lmp,line);
   }
 
   /* run 10 more steps
@@ -94,23 +94,72 @@ int main(int narg, char **arg)
      put coords back into LAMMPS
      run a single step with changed coords */
 
-  if (lammps == 1) {
-    lammps_command(ptr,"run 10");
+  double *x = NULL;
+  double *v = NULL;
 
-    int natoms = lammps_get_natoms(ptr);
-    double *x = (double *) malloc(3*natoms*sizeof(double));
-    lammps_gather_atoms(ptr,"x",1,3,x);
+  if (lammps == 1) {
+    lammps_command(lmp,"run 10");
+
+    int natoms = lammps_get_natoms(lmp);
+    x = (double *) malloc(3*natoms*sizeof(double));
+    lammps_gather_atoms(lmp,"x",1,3,x);
+    v = (double *) malloc(3*natoms*sizeof(double));
+    lammps_gather_atoms(lmp,"v",1,3,v);
     double epsilon = 0.1;
     x[0] += epsilon;
-    lammps_scatter_atoms(ptr,"x",1,3,x);
-    free(x);
+    lammps_scatter_atoms(lmp,"x",1,3,x);
 
-    lammps_command(ptr,"run 1");
+    lammps_command(lmp,"run 1");
   }
 
-  if (lammps == 1) lammps_close(ptr);
+  // extract force on single atom two different ways
+
+  if (lammps == 1) {
+    double **f = (double **) lammps_extract_atom(lmp,"f");
+    printf("Force on 1 atom via extract_atom: %g\n",f[0][0]);
+
+    double *fx = (double *) lammps_extract_variable(lmp,"fx","all");
+    printf("Force on 1 atom via extract_variable: %g\n",fx[0]);
+  }
+
+  /* use commands_string() and commands_list() to invoke more commands */
+
+  char *strtwo = "run 10\nrun 20";
+  if (lammps == 1) lammps_commands_string(lmp,strtwo);
+
+  char *cmds[2];
+  cmds[0] = "run 10";
+  cmds[1] = "run 20";
+  if (lammps == 1) lammps_commands_list(lmp,2,cmds);
+
+  /* delete all atoms
+     create_atoms() to create new ones with old coords, vels
+     initial thermo should be same as step 20 */
+
+  int *type = NULL;
+
+  if (lammps == 1) {
+    int natoms = lammps_get_natoms(lmp);
+    type = (int *) malloc(natoms*sizeof(double));
+    int i;
+    for (i = 0; i < natoms; i++) type[i] = 1;
+
+    lammps_command(lmp,"delete_atoms group all");
+    lammps_create_atoms(lmp,natoms,NULL,type,x,v);
+    lammps_command(lmp,"run 10");
+  }
+
+  if (x) free(x);
+  if (v) free(v);
+  if (type) free(type);
+
+  // close down LAMMPS
+
+  lammps_close(lmp);
 
   /* close down MPI */
 
+  if (lammps == 1) MPI_Comm_free(&comm_lammps);
+  MPI_Barrier(MPI_COMM_WORLD);
   MPI_Finalize();
 }

examples/COUPLE/simple/simple.cpp

@@ -77,7 +77,7 @@ int main(int narg, char **arg)
   // (could just send it to proc 0 of comm_lammps and let it Bcast)
   // all LAMMPS procs call input->one() on the line
   
-  LAMMPS *lmp;
+  LAMMPS *lmp = NULL;
   if (lammps == 1) lmp = new LAMMPS(0,NULL,comm_lammps);
 
   int n;
@@ -91,7 +91,7 @@ int main(int narg, char **arg)
     MPI_Bcast(&n,1,MPI_INT,0,MPI_COMM_WORLD);
     if (n == 0) break;
     MPI_Bcast(line,n,MPI_CHAR,0,MPI_COMM_WORLD);
-    if (lammps == 1) lmp->input->one(line);
+    if (lammps == 1) lammps_command(lmp,line);
   }
 
   // run 10 more steps
@@ -100,23 +100,74 @@ int main(int narg, char **arg)
   // put coords back into LAMMPS
   // run a single step with changed coords
 
+  double *x = NULL;
+  double *v = NULL;
+
   if (lammps == 1) {
     lmp->input->one("run 10");
 
     int natoms = static_cast<int> (lmp->atom->natoms);
-    double *x = new double[3*natoms];
+    x = new double[3*natoms];
+    v = new double[3*natoms];
     lammps_gather_atoms(lmp,"x",1,3,x);
+    lammps_gather_atoms(lmp,"v",1,3,v);
     double epsilon = 0.1;
     x[0] += epsilon;
     lammps_scatter_atoms(lmp,"x",1,3,x);
-    delete [] x;
 
+    // these 2 lines are the same
+
+    // lammps_command(lmp,"run 1");
     lmp->input->one("run 1");
   }
 
-  if (lammps == 1) delete lmp;
+  // extract force on single atom two different ways
+
+  if (lammps == 1) {
+    double **f = (double **) lammps_extract_atom(lmp,"f");
+    printf("Force on 1 atom via extract_atom: %g\n",f[0][0]);
+
+    double *fx = (double *) lammps_extract_variable(lmp,"fx","all");
+    printf("Force on 1 atom via extract_variable: %g\n",fx[0]);
+  }
+
+  // use commands_string() and commands_list() to invoke more commands
+
+  char *strtwo = "run 10\nrun 20";
+  if (lammps == 1) lammps_commands_string(lmp,strtwo);
+
+  char *cmds[2];
+  cmds[0] = "run 10";
+  cmds[1] = "run 20";
+  if (lammps == 1) lammps_commands_list(lmp,2,cmds);
+
+  // delete all atoms
+  // create_atoms() to create new ones with old coords, vels
+  // initial thermo should be same as step 20
+
+  int *type = NULL;
+
+  if (lammps == 1) {
+    int natoms = static_cast<int> (lmp->atom->natoms);
+    type = new int[natoms];
+    for (int i = 0; i < natoms; i++) type[i] = 1;
+
+    lmp->input->one("delete_atoms group all");
+    lammps_create_atoms(lmp,natoms,NULL,type,x,v);
+    lmp->input->one("run 10");
+  }
+
+  delete [] x;
+  delete [] v;
+  delete [] type;
+
+  // close down LAMMPS
+
+  delete lmp;
 
   // close down MPI
 
+  if (lammps == 1) MPI_Comm_free(&comm_lammps);
+  MPI_Barrier(MPI_COMM_WORLD);
   MPI_Finalize();
 }