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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3610 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2009-12-22 01:06:46 +00:00
parent 2f2c512426
commit 81dbacf3be
3 changed files with 4 additions and 259 deletions
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214
src/fix_coord_original.cpp
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@ -1,214 +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_coord_original.h"
#include "atom.h"
#include "domain.h"
#include "group.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
FixCoordOriginal::FixCoordOriginal(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg < 3) error->all("Illegal fix coord/original 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 coord/original 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 coord/original command");
iarg += 2;
} else error->all("Illegal fix coord/original 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;
}
}
/* ---------------------------------------------------------------------- */
FixCoordOriginal::~FixCoordOriginal()
{
// unregister callbacks to this fix from Atom class
atom->delete_callback(id,0);
atom->delete_callback(id,1);
// delete locally stored array
memory->destroy_2d_double_array(xoriginal);
}
/* ---------------------------------------------------------------------- */
int FixCoordOriginal::setmask()
{
int mask = 0;
return mask;
}
/* ----------------------------------------------------------------------
memory usage of local atom-based array
------------------------------------------------------------------------- */
double FixCoordOriginal::memory_usage()
{
double bytes = atom->nmax*3 * sizeof(double);
return bytes;
}
/* ----------------------------------------------------------------------
allocate atom-based array
------------------------------------------------------------------------- */
void FixCoordOriginal::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 FixCoordOriginal::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 FixCoordOriginal::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 FixCoordOriginal::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 FixCoordOriginal::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 FixCoordOriginal::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 FixCoordOriginal::maxsize_restart()
{
return 4;
}
/* ----------------------------------------------------------------------
size of atom nlocal's restart data
------------------------------------------------------------------------- */
int FixCoordOriginal::size_restart(int nlocal)
{
return 4;
}

43
src/fix_coord_original.h
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@ -1,43 +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.
------------------------------------------------------------------------- */
#ifndef FIX_COORD_ORIGINAL_H
#define FIX_COORD_ORIGINAL_H
#include "fix.h"
namespace LAMMPS_NS {
class FixCoordOriginal : public Fix {
public:
FixCoordOriginal(class LAMMPS *, int, char **);
~FixCoordOriginal();
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

6
src/style.h
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@ -189,7 +189,6 @@ DumpStyle(xyz,DumpXYZ)
#include "fix_ave_spatial.h" #include "fix_ave_spatial.h"
#include "fix_ave_time.h" #include "fix_ave_time.h"
#include "fix_box_relax.h" #include "fix_box_relax.h"
#include "fix_coord_original.h"
#include "fix_deform.h" #include "fix_deform.h"
#include "fix_deposit.h" #include "fix_deposit.h"
#include "fix_drag.h" #include "fix_drag.h"
@ -228,6 +227,8 @@ DumpStyle(xyz,DumpXYZ)
#include "fix_spring.h" #include "fix_spring.h"
#include "fix_spring_rg.h" #include "fix_spring_rg.h"
#include "fix_spring_self.h" #include "fix_spring_self.h"
#include "fix_store_coord.h"
#include "fix_store_force.h"
#include "fix_temp_berendsen.h" #include "fix_temp_berendsen.h"
#include "fix_temp_rescale.h" #include "fix_temp_rescale.h"
#include "fix_thermal_conductivity.h" #include "fix_thermal_conductivity.h"
@ -248,7 +249,6 @@ FixStyle(ave/histo,FixAveHisto)
FixStyle(ave/spatial,FixAveSpatial) FixStyle(ave/spatial,FixAveSpatial)
FixStyle(ave/time,FixAveTime) FixStyle(ave/time,FixAveTime)
FixStyle(box/relax,FixBoxRelax) FixStyle(box/relax,FixBoxRelax)
FixStyle(coord/original,FixCoordOriginal)
FixStyle(deform,FixDeform) FixStyle(deform,FixDeform)
FixStyle(deposit,FixDeposit) FixStyle(deposit,FixDeposit)
FixStyle(drag,FixDrag) FixStyle(drag,FixDrag)
@ -287,6 +287,8 @@ FixStyle(SHEAR_HISTORY,FixShearHistory)
FixStyle(spring,FixSpring) FixStyle(spring,FixSpring)
FixStyle(spring/rg,FixSpringRG) FixStyle(spring/rg,FixSpringRG)
FixStyle(spring/self,FixSpringSelf) FixStyle(spring/self,FixSpringSelf)
FixStyle(store/coord,FixStoreCoord)
FixStyle(store/force,FixStoreForce)
FixStyle(temp/berendsen,FixTempBerendsen) FixStyle(temp/berendsen,FixTempBerendsen)
FixStyle(temp/rescale,FixTempRescale) FixStyle(temp/rescale,FixTempRescale)
FixStyle(thermal/conductivity,FixThermalConductivity) FixStyle(thermal/conductivity,FixThermalConductivity)