git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5002 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/create_atoms.cpp

@@ -19,6 +19,7 @@
 #include "atom_vec.h"
 #include "comm.h"
 #include "modify.h"
+#include "fix.h"
 #include "domain.h"
 #include "lattice.h"
 #include "region.h"
@@ -151,6 +152,16 @@ void CreateAtoms::command(int narg, char **arg)
   else if (style == RANDOM) add_random();
   else add_lattice();
 
+  // invoke set_arrays() for fixes that need initialization of new atoms
+
+  int nlocal = atom->nlocal;
+  for (int m = 0; m < modify->nfix; m++) {
+    Fix *fix = modify->fix[m];
+    if (fix->create_attribute)
+      for (int i = nlocal_previous; i < nlocal; i++)
+	fix->set_arrays(i);
+  }
+
   // clean up
 
   if (domain->lattice) delete [] basistype;

src/fix_move.cpp

@@ -47,6 +47,7 @@ FixMove::FixMove(LAMMPS *lmp, int narg, char **arg) :
   peratom_freq = 1;
   time_integrate = 1;
   time_depend = 1;
+  create_attribute = 1;
 
   // parse args
 
@@ -847,6 +848,78 @@ void FixMove::copy_arrays(int i, int j)
   xoriginal[j][2] = xoriginal[i][2];
 }
 
+/* ----------------------------------------------------------------------
+   initialize one atom's array values, called when atom is created
+------------------------------------------------------------------------- */
+
+void FixMove::set_arrays(int i)
+{
+  double **x = atom->x;
+  int *image = atom->image;
+  int *mask = atom->mask;
+
+  // particle not in group
+
+  if (!(mask[i] & groupbit)) {
+    xoriginal[i][0] = xoriginal[i][1] = xoriginal[i][2] = 0.0;
+    return;
+  }
+
+  // current time still equal fix creation time
+
+  if (update->ntimestep == time_origin) {
+    domain->unmap(x[i],image[i],xoriginal[i]);
+    return;
+  }
+
+  // backup particle to time_origin
+
+  if (mstyle == VARIABLE)
+    error->all("Cannot add atoms to fix move variable after");
+
+  domain->unmap(x[i],image[i],xoriginal[i]);
+  double delta = (update->ntimestep - time_origin) * update->dt;
+
+  if (mstyle == LINEAR) {
+    if (vxflag) xoriginal[i][0] -= vx * delta;
+    if (vyflag) xoriginal[i][1] -= vy * delta;
+    if (vzflag) xoriginal[i][2] -= vz * delta;
+  } else if (mstyle == WIGGLE) {
+    double arg = omega_rotate * delta;
+    double sine = sin(arg);
+    double cosine = cos(arg);
+    if (axflag) xoriginal[i][0] -= ax*sine;
+    if (ayflag) xoriginal[i][1] -= ay*sine;
+    if (azflag) xoriginal[i][2] -= az*sine;
+  } else if (mstyle == ROTATE) {
+    double a[3],b[3],c[3],d[3],disp[3],ddotr;
+    double arg = - omega_rotate * delta;
+    double sine = sin(arg);
+    double cosine = cos(arg);
+    d[0] = x[i][0] - point[0];
+    d[1] = x[i][1] - point[1];
+    d[2] = x[i][2] - point[2];
+    ddotr = d[0]*runit[0] + d[1]*runit[1] + d[2]*runit[2];
+    c[0] = ddotr*runit[0];
+    c[1] = ddotr*runit[1];
+    c[2] = ddotr*runit[2];
+    
+    a[0] = d[0] - c[0];
+    a[1] = d[1] - c[1];
+    a[2] = d[2] - c[2];
+    b[0] = runit[1]*a[2] - runit[2]*a[1];
+    b[1] = runit[2]*a[0] - runit[0]*a[2];
+    b[2] = runit[0]*a[1] - runit[1]*a[0];
+    disp[0] = a[0]*cosine  + b[0]*sine;
+    disp[1] = a[1]*cosine  + b[1]*sine;
+    disp[2] = a[2]*cosine  + b[2]*sine;
+    
+    xoriginal[i][0] = point[0] + c[0] + disp[0];
+    xoriginal[i][1] = point[1] + c[1] + disp[1];
+    xoriginal[i][2] = point[2] + c[2] + disp[2];
+  }
+}
+
 /* ----------------------------------------------------------------------
    pack values in local atom-based array for exchange with another proc
 ------------------------------------------------------------------------- */
@@ -920,3 +993,10 @@ int FixMove::size_restart(int nlocal)
 {
   return 4;
 }
+
+/* ---------------------------------------------------------------------- */
+
+void FixMove::reset_dt()
+{
+  error->all("Resetting timestep is not allowed with fix move");
+}

src/fix_move.h

@@ -41,6 +41,7 @@ class FixMove : public Fix {
   void restart(char *);
   void grow_arrays(int);
   void copy_arrays(int, int);
+  void set_arrays(int);
   int pack_exchange(int, double *);
   int unpack_exchange(int, double *);
   int pack_restart(int, double *);
@@ -48,6 +49,8 @@ class FixMove : public Fix {
   int maxsize_restart();
   int size_restart(int);
 
+  void reset_dt();
+
  private:
   char *xvarstr,*yvarstr,*zvarstr,*vxvarstr,*vyvarstr,*vzvarstr;
   int mstyle;