git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4232 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/compute_displace_atom.cpp

@@ -35,19 +35,23 @@ ComputeDisplaceAtom::ComputeDisplaceAtom(LAMMPS *lmp, int narg, char **arg) :
   peratom_flag = 1;
   size_peratom_cols = 4;
 
-  // create a new fix store/coord style
+  // create a new fix store  style
-  // id = compute-ID + store_coord, fix group = compute group
+  // id = compute-ID + store, fix group = compute group
 
-  int n = strlen(id) + strlen("_store_coord") + 1;
+  int n = strlen(id) + strlen("_store") + 1;
   id_fix = new char[n];
   strcpy(id_fix,id);
-  strcat(id_fix,"_store_coord");
+  strcat(id_fix,"_store");
 
-  char **newarg = new char*[3];
+  char **newarg = new char*[7];
   newarg[0] = id_fix;
   newarg[1] = group->names[igroup];
-  newarg[2] = (char *) "store/coord";
+  newarg[2] = (char *) "store";
-  modify->add_fix(3,newarg);
+  newarg[3] = (char *) "0";
+  newarg[4] = (char *) "xu";
+  newarg[5] = (char *) "yu";
+  newarg[6] = (char *) "zu";
+  modify->add_fix(7,newarg);
   delete [] newarg;
 
   nmax = 0;

src/compute_msd.cpp

@@ -49,22 +49,26 @@ ComputeMSD::ComputeMSD(LAMMPS *lmp, int narg, char **arg) :
     } else error->all("Illegal compute msd command");
   }
 
-  // create a new fix store/coord style with or without com keyword
+  // create a new fix store style with or without com keyword
-  // id = compute-ID + store_coord, fix group = compute group
+  // id = compute-ID + store, fix group = compute group
 
-  int n = strlen(id) + strlen("_store_coord") + 1;
+  int n = strlen(id) + strlen("_store") + 1;
   id_fix = new char[n];
   strcpy(id_fix,id);
-  strcat(id_fix,"_store_coord");
+  strcat(id_fix,"_store");
 
-  char **newarg = new char*[5];
+  char **newarg = new char*[9];
   newarg[0] = id_fix;
   newarg[1] = group->names[igroup];
-  newarg[2] = (char *) "store/coord";
+  newarg[2] = (char *) "store";
-  newarg[3] = (char *) "com";
+  newarg[3] = (char *) "0";
-  newarg[4] = (char *) "yes";
+  newarg[4] = (char *) "xu";
-  if (comflag) modify->add_fix(5,newarg);
+  newarg[5] = (char *) "yu";
-  else modify->add_fix(3,newarg);
+  newarg[6] = (char *) "zu";
+  newarg[7] = (char *) "com";
+  newarg[8] = (char *) "yes";
+  if (comflag) modify->add_fix(9,newarg);
+  else modify->add_fix(7,newarg);
   delete [] newarg;
 
   vector = new double[4];

src/compute_property_atom.cpp

@@ -21,15 +21,6 @@
 
 using namespace LAMMPS_NS;
 
-// customize by adding keyword
-// same as in dump_custom.cpp
-
-enum{ID,MOL,TYPE,MASS,
-       X,Y,Z,XS,YS,ZS,XSTRI,YSTRI,ZSTRI,XU,YU,ZU,XUTRI,YUTRI,ZUTRI,IX,IY,IZ,
-       VX,VY,VZ,FX,FY,FZ,
-       Q,MUX,MUY,MUZ,RADIUS,OMEGAX,OMEGAY,OMEGAZ,ANGMOMX,ANGMOMY,ANGMOMZ,
-       QUATW,QUATI,QUATJ,QUATK,TQX,TQY,TQZ};
-
 /* ---------------------------------------------------------------------- */
 
 ComputePropertyAtom::ComputePropertyAtom(LAMMPS *lmp, int narg, char **arg) :
@@ -42,6 +33,9 @@ ComputePropertyAtom::ComputePropertyAtom(LAMMPS *lmp, int narg, char **arg) :
   if (nvalues == 1) size_peratom_cols = 0;
   else size_peratom_cols = nvalues;
 
+  // parse input values
+  // customize a new keyword by adding to if statement
+
   pack_choice = new FnPtrPack[nvalues];
 
   int i;
@@ -249,7 +243,7 @@ void ComputePropertyAtom::compute_peratom()
     buf = vector;
     (this->*pack_choice[0])(0);
   } else {
-    if (array) buf = &array[0][0];
+    buf = &array[0][0];
     for (int n = 0; n < nvalues; n++)
       (this->*pack_choice[n])(n);
   }

src/fix_store.h

@@ -0,0 +1,115 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under 
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef FIX_CLASS
+
+FixStyle(store,FixStore)
+
+#else
+
+#ifndef LMP_FIX_STORE_H
+#define LMP_FIX_STORE_H
+
+#include "fix.h"
+
+namespace LAMMPS_NS {
+
+class FixStore : public Fix {
+ public:
+  FixStore(class LAMMPS *, int, char **);
+  ~FixStore();
+  int setmask();
+  void init();
+  void setup(int);
+  void end_of_step();
+
+  double memory_usage();
+  void grow_arrays(int);
+  void copy_arrays(int, int);
+  int pack_exchange(int, double *);
+  int unpack_exchange(int, double *);
+  int pack_restart(int, double *);
+  void unpack_restart(int, int);
+  int size_restart(int);
+  int maxsize_restart();
+
+ private:
+  int nvalues;
+  int *which,*argindex,*value2index;
+  char **ids;
+  double **values;         // archived atom properties
+  double *buf;             // 1d ptr to values
+
+  int comflag;
+  double cm[3];            // center of mass
+
+  int kflag,cfv_flag,firstflag;
+  int cfv_any;             // 1 if any compute/fix/variable specified
+
+  typedef void (FixStore::*FnPtrPack)(int);
+  FnPtrPack *pack_choice;              // ptrs to pack functions
+
+  void pack_id(int);
+  void pack_molecule(int);
+  void pack_type(int);
+  void pack_mass(int);
+
+  void pack_x(int);
+  void pack_y(int);
+  void pack_z(int);
+  void pack_xs(int);
+  void pack_ys(int);
+  void pack_zs(int);
+  void pack_xs_triclinic(int);
+  void pack_ys_triclinic(int);
+  void pack_zs_triclinic(int);
+  void pack_xu(int);
+  void pack_yu(int);
+  void pack_zu(int);
+  void pack_xu_triclinic(int);
+  void pack_yu_triclinic(int);
+  void pack_zu_triclinic(int);
+  void pack_ix(int);
+  void pack_iy(int);
+  void pack_iz(int);
+
+  void pack_vx(int);
+  void pack_vy(int);
+  void pack_vz(int);
+  void pack_fx(int);
+  void pack_fy(int);
+  void pack_fz(int);
+  void pack_q(int);
+  void pack_mux(int);
+  void pack_muy(int);
+  void pack_muz(int);
+  void pack_radius(int);
+  void pack_omegax(int);
+  void pack_omegay(int);
+  void pack_omegaz(int);
+  void pack_angmomx(int);
+  void pack_angmomy(int);
+  void pack_angmomz(int);
+  void pack_quatw(int);
+  void pack_quati(int);
+  void pack_quatj(int);
+  void pack_quatk(int);
+  void pack_tqx(int);
+  void pack_tqy(int);
+  void pack_tqz(int);
+};
+
+}
+
+#endif
+#endif

src/fix_store_coord.cpp

@@ -1,212 +0,0 @@
-/* ----------------------------------------------------------------------
-   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@sandia.gov
-
-   Copyright (2003) Sandia Corporation.  Under the terms of Contract
-   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
-   certain rights in this software.  This software is distributed under 
-   the GNU General Public License.
-
-   See the README file in the top-level LAMMPS directory.
-------------------------------------------------------------------------- */
-
-#include "stdlib.h"
-#include "string.h"
-#include "fix_store_coord.h"
-#include "atom.h"
-#include "domain.h"
-#include "group.h"
-#include "memory.h"
-#include "error.h"
-
-using namespace LAMMPS_NS;
-
-/* ---------------------------------------------------------------------- */
-
-FixStoreCoord::FixStoreCoord(LAMMPS *lmp, int narg, char **arg) :
-  Fix(lmp, narg, arg)
-{
-  if (narg < 3) error->all("Illegal fix store/coord command");
-
-  restart_peratom = 1;
-  peratom_flag = 1;
-  size_peratom_cols = 3;
-  peratom_freq = 1;
-
-  // optional args
-
-  int comflag = 0;
-
-  int iarg = 3;
-  while (iarg < narg) {
-    if (strcmp(arg[iarg],"com") == 0) {
-      if (iarg+2 > narg) error->all("Illegal fix store/coord command");
-      if (strcmp(arg[iarg+1],"no") == 0) comflag = 0;
-      else if (strcmp(arg[iarg+1],"yes") == 0) comflag = 1;
-      else error->all("Illegal fix store/coord command");
-      iarg += 2;
-    } else error->all("Illegal fix store/coord command");
-  }
-
-  // perform initial allocation of atom-based array
-  // register with Atom class
-
-  xoriginal = NULL;
-  grow_arrays(atom->nmax);
-  atom->add_callback(0);
-  atom->add_callback(1);
-
-  // cm = original center of mass
-
-  double cm[3];
-  if (comflag) {
-    double masstotal = group->mass(igroup);
-    group->xcm(igroup,masstotal,cm);
-  }
-
-  // xoriginal = initial unwrapped positions of atoms
-  // relative to center of mass if comflag is set
-
-  double **x = atom->x;
-  int *mask = atom->mask;
-  int *image = atom->image;
-  int nlocal = atom->nlocal;
-
-  for (int i = 0; i < nlocal; i++) {
-    if (mask[i] & groupbit) {
-      domain->unmap(x[i],image[i],xoriginal[i]);
-      if (comflag) {
-	xoriginal[i][0] -= cm[0];
-	xoriginal[i][1] -= cm[1];
-	xoriginal[i][2] -= cm[2];
-      }
-    } else xoriginal[i][0] = xoriginal[i][1] = xoriginal[i][2] = 0.0;
-  }
-}
-
-/* ---------------------------------------------------------------------- */
-
-FixStoreCoord::~FixStoreCoord()
-{
-  // unregister callbacks to this fix from Atom class
- 
-  atom->delete_callback(id,0);
-  atom->delete_callback(id,1);
-
-  memory->destroy_2d_double_array(xoriginal);
-}
-
-/* ---------------------------------------------------------------------- */
-
-int FixStoreCoord::setmask()
-{
-  int mask = 0;
-  return mask;
-}
-
-/* ----------------------------------------------------------------------
-   memory usage of local atom-based array
-------------------------------------------------------------------------- */
-
-double FixStoreCoord::memory_usage()
-{
-  double bytes = atom->nmax*3 * sizeof(double);
-  return bytes;
-}
-
-/* ----------------------------------------------------------------------
-   allocate atom-based array
-------------------------------------------------------------------------- */
-
-void FixStoreCoord::grow_arrays(int nmax)
-{
-  xoriginal =
-    memory->grow_2d_double_array(xoriginal,nmax,3,"fix_msd:xoriginal");
-  array_atom = xoriginal;
-}
-
-/* ----------------------------------------------------------------------
-   copy values within local atom-based array
-------------------------------------------------------------------------- */
-
-void FixStoreCoord::copy_arrays(int i, int j)
-{
-  xoriginal[j][0] = xoriginal[i][0];
-  xoriginal[j][1] = xoriginal[i][1];
-  xoriginal[j][2] = xoriginal[i][2];
-}
-
-/* ----------------------------------------------------------------------
-   pack values in local atom-based array for exchange with another proc
-------------------------------------------------------------------------- */
-
-int FixStoreCoord::pack_exchange(int i, double *buf)
-{
-  buf[0] = xoriginal[i][0];
-  buf[1] = xoriginal[i][1];
-  buf[2] = xoriginal[i][2];
-  return 3;
-}
-
-/* ----------------------------------------------------------------------
-   unpack values in local atom-based array from exchange with another proc
-------------------------------------------------------------------------- */
-
-int FixStoreCoord::unpack_exchange(int nlocal, double *buf)
-{
-  xoriginal[nlocal][0] = buf[0];
-  xoriginal[nlocal][1] = buf[1];
-  xoriginal[nlocal][2] = buf[2];
-  return 3;
-}
-
-/* ----------------------------------------------------------------------
-   pack values in local atom-based arrays for restart file
-------------------------------------------------------------------------- */
-
-int FixStoreCoord::pack_restart(int i, double *buf)
-{
-  buf[0] = 4;
-  buf[1] = xoriginal[i][0];
-  buf[2] = xoriginal[i][1];
-  buf[3] = xoriginal[i][2];
-  return 4;
-}
-
-/* ----------------------------------------------------------------------
-   unpack values from atom->extra array to restart the fix
-------------------------------------------------------------------------- */
-
-void FixStoreCoord::unpack_restart(int nlocal, int nth)
-{
-  double **extra = atom->extra;
-
-  // skip to Nth set of extra values
-
-  int m = 0;
-  for (int i = 0; i < nth; i++) m += static_cast<int> (extra[nlocal][m]);
-  m++;
-
-  xoriginal[nlocal][0] = extra[nlocal][m++];
-  xoriginal[nlocal][1] = extra[nlocal][m++];
-  xoriginal[nlocal][2] = extra[nlocal][m++];
-}
-
-/* ----------------------------------------------------------------------
-   maxsize of any atom's restart data
-------------------------------------------------------------------------- */
-
-int FixStoreCoord::maxsize_restart()
-{
-  return 4;
-}
-
-/* ----------------------------------------------------------------------
-   size of atom nlocal's restart data
-------------------------------------------------------------------------- */
-
-int FixStoreCoord::size_restart(int nlocal)
-{
-  return 4;
-}

src/fix_store_coord.h

@@ -1,50 +0,0 @@
-/* ----------------------------------------------------------------------
-   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@sandia.gov
-
-   Copyright (2003) Sandia Corporation.  Under the terms of Contract
-   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
-   certain rights in this software.  This software is distributed under 
-   the GNU General Public License.
-
-   See the README file in the top-level LAMMPS directory.
-------------------------------------------------------------------------- */
-
-#ifdef FIX_CLASS
-
-FixStyle(store/coord,FixStoreCoord)
-
-#else
-
-#ifndef LMP_FIX_STORE_COORD_H
-#define LMP_FIX_STORE_COORD_H
-
-#include "fix.h"
-
-namespace LAMMPS_NS {
-
-class FixStoreCoord : public Fix {
- public:
-  FixStoreCoord(class LAMMPS *, int, char **);
-  ~FixStoreCoord();
-  int setmask();
-
-  double memory_usage();
-  void grow_arrays(int);
-  void copy_arrays(int, int);
-  int pack_exchange(int, double *);
-  int unpack_exchange(int, double *);
-  int pack_restart(int, double *);
-  void unpack_restart(int, int);
-  int size_restart(int);
-  int maxsize_restart();
-
- private:
-  double **xoriginal;         // original coords of atoms
-};
-
-}
-
-#endif
-#endif