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

This commit is contained in:
sjplimp 2010-06-03 23:52:37 +00:00
parent 3cafb13abe
commit a79fb73584
7 changed files with 1474 additions and 289 deletions
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18
src/compute_displace_atom.cpp
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@ -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
// id = compute-ID + store_coord, fix group = compute group
// create a new fix store style
// 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";
modify->add_fix(3,newarg);
newarg[2] = (char *) "store";
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;

24
src/compute_msd.cpp
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@ -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
// id = compute-ID + store_coord, fix group = compute group
// create a new fix store style with or without com keyword
// 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[3] = (char *) "com";
newarg[4] = (char *) "yes";
if (comflag) modify->add_fix(5,newarg);
else modify->add_fix(3,newarg);
newarg[2] = (char *) "store";
newarg[3] = (char *) "0";
newarg[4] = (char *) "xu";
newarg[5] = (char *) "yu";
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];

14
src/compute_property_atom.cpp
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@ -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);
}

1330
src/fix_store.cpp Normal file
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File diff suppressed because it is too large Load Diff

115
src/fix_store.h Normal file
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@ -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

212
src/fix_store_coord.cpp
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@ -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;
}

50
src/fix_store_coord.h
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@ -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