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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10842 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2013-10-01 14:12:06 +00:00
parent 72d59c438d
commit 35eb67c68e
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646
src/USER-REAXC/compute_spec_atom.cpp Normal file
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Labo0ratories
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 "math.h"
#include "string.h"
#include "compute_spec_atom.h"
#include "math_extra.h"
#include "atom.h"
#include "update.h"
#include "force.h"
#include "domain.h"
#include "memory.h"
#include "error.h"
#include "reaxc_defs.h"
#include "reaxc_types.h"
#include "pair_reax_c.h"
using namespace LAMMPS_NS;
enum{KEYWORD,COMPUTE,FIX,VARIABLE};
/* ---------------------------------------------------------------------- */
ComputeSpecAtom::ComputeSpecAtom(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg < 4) error->all(FLERR,"Illegal compute reax/c/atom command");
peratom_flag = 1;
nvalues = narg - 3;
if (nvalues == 1) size_peratom_cols = 0;
else size_peratom_cols = nvalues;
// Initiate reaxc
reaxc = (PairReaxC *) force->pair_match("reax/c",1);
pack_choice = new FnPtrPack[nvalues];
int i;
for (int iarg = 3; iarg < narg; iarg++) {
i = iarg-3;
// standard lammps attributes
if (strcmp(arg[iarg],"q") == 0) {
pack_choice[i] = &ComputeSpecAtom::pack_q;
} else if (strcmp(arg[iarg],"x") == 0) {
pack_choice[i] = &ComputeSpecAtom::pack_x;
} else if (strcmp(arg[iarg],"y") == 0) {
pack_choice[i] = &ComputeSpecAtom::pack_y;
} else if (strcmp(arg[iarg],"z") == 0) {
pack_choice[i] = &ComputeSpecAtom::pack_z;
} else if (strcmp(arg[iarg],"vx") == 0) {
pack_choice[i] = &ComputeSpecAtom::pack_vx;
} else if (strcmp(arg[iarg],"vy") == 0) {
pack_choice[i] = &ComputeSpecAtom::pack_vy;
} else if (strcmp(arg[iarg],"vz") == 0) {
pack_choice[i] = &ComputeSpecAtom::pack_vz;
// from pair_reax_c
} else if (strcmp(arg[iarg],"abo01") == 0) {
pack_choice[i] = &ComputeSpecAtom::pack_abo01;
} else if (strcmp(arg[iarg],"abo02") == 0) {
pack_choice[i] = &ComputeSpecAtom::pack_abo02;
} else if (strcmp(arg[iarg],"abo03") == 0) {
pack_choice[i] = &ComputeSpecAtom::pack_abo03;
} else if (strcmp(arg[iarg],"abo04") == 0) {
pack_choice[i] = &ComputeSpecAtom::pack_abo04;
} else if (strcmp(arg[iarg],"abo05") == 0) {
pack_choice[i] = &ComputeSpecAtom::pack_abo05;
} else if (strcmp(arg[iarg],"abo06") == 0) {
pack_choice[i] = &ComputeSpecAtom::pack_abo06;
} else if (strcmp(arg[iarg],"abo07") == 0) {
pack_choice[i] = &ComputeSpecAtom::pack_abo07;
} else if (strcmp(arg[iarg],"abo08") == 0) {
pack_choice[i] = &ComputeSpecAtom::pack_abo08;
} else if (strcmp(arg[iarg],"abo09") == 0) {
pack_choice[i] = &ComputeSpecAtom::pack_abo09;
} else if (strcmp(arg[iarg],"abo10") == 0) {
pack_choice[i] = &ComputeSpecAtom::pack_abo10;
} else if (strcmp(arg[iarg],"abo11") == 0) {
pack_choice[i] = &ComputeSpecAtom::pack_abo11;
} else if (strcmp(arg[iarg],"abo12") == 0) {
pack_choice[i] = &ComputeSpecAtom::pack_abo12;
} else if (strcmp(arg[iarg],"abo13") == 0) {
pack_choice[i] = &ComputeSpecAtom::pack_abo13;
} else if (strcmp(arg[iarg],"abo14") == 0) {
pack_choice[i] = &ComputeSpecAtom::pack_abo14;
} else if (strcmp(arg[iarg],"abo15") == 0) {
pack_choice[i] = &ComputeSpecAtom::pack_abo15;
} else if (strcmp(arg[iarg],"abo16") == 0) {
pack_choice[i] = &ComputeSpecAtom::pack_abo16;
} else if (strcmp(arg[iarg],"abo17") == 0) {
pack_choice[i] = &ComputeSpecAtom::pack_abo17;
} else if (strcmp(arg[iarg],"abo18") == 0) {
pack_choice[i] = &ComputeSpecAtom::pack_abo18;
} else if (strcmp(arg[iarg],"abo19") == 0) {
pack_choice[i] = &ComputeSpecAtom::pack_abo19;
} else if (strcmp(arg[iarg],"abo20") == 0) {
pack_choice[i] = &ComputeSpecAtom::pack_abo20;
} else if (strcmp(arg[iarg],"abo21") == 0) {
pack_choice[i] = &ComputeSpecAtom::pack_abo21;
} else if (strcmp(arg[iarg],"abo22") == 0) {
pack_choice[i] = &ComputeSpecAtom::pack_abo22;
} else if (strcmp(arg[iarg],"abo23") == 0) {
pack_choice[i] = &ComputeSpecAtom::pack_abo23;
} else if (strcmp(arg[iarg],"abo24") == 0) {
pack_choice[i] = &ComputeSpecAtom::pack_abo24;
} else error->all(FLERR,"Invalid keyword in compute reax/c/atom command");
}
nmax = 0;
vector = NULL;
array = NULL;
}
/* ---------------------------------------------------------------------- */
ComputeSpecAtom::~ComputeSpecAtom()
{
delete [] pack_choice;
memory->destroy(vector);
memory->destroy(array);
}
/* ---------------------------------------------------------------------- */
void ComputeSpecAtom::compute_peratom()
{
invoked_peratom = update->ntimestep;
// grow vector or array if necessary
if (atom->nlocal > nmax) {
nmax = atom->nmax;
if (nvalues == 1) {
memory->destroy(vector);
memory->create(vector,nmax,"property/atom:vector");
vector_atom = vector;
} else {
memory->destroy(array);
memory->create(array,nmax,nvalues,"property/atom:array");
array_atom = array;
}
}
// fill vector or array with per-atom values
if (nvalues == 1) {
buf = vector;
(this->*pack_choice[0])(0);
} else {
if (nmax > 0) {
buf = &array[0][0];
for (int n = 0; n < nvalues; n++)
(this->*pack_choice[n])(n);
}
}
}
/* ----------------------------------------------------------------------
memory usage of local atom-based array
------------------------------------------------------------------------- */
double ComputeSpecAtom::memory_usage()
{
double bytes = nmax*nvalues * sizeof(double);
return bytes;
}
/* ----------------------------------------------------------------------
one method for every keyword compute property/atom can output
the atom property is packed into buf starting at n with stride nvalues
customize a new keyword by adding a method
------------------------------------------------------------------------- */
/* ---------------------------------------------------------------------- */
void ComputeSpecAtom::pack_q(int n)
{
double *q = atom->q;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = q[i];
else buf[n] = 0.0;
n += nvalues;
}
}
/* ---------------------------------------------------------------------- */
void ComputeSpecAtom::pack_x(int n)
{
double **x = atom->x;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = x[i][0];
else buf[n] = 0.0;
n += nvalues;
}
}
/* ---------------------------------------------------------------------- */
void ComputeSpecAtom::pack_y(int n)
{
double **x = atom->x;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = x[i][1];
else buf[n] = 0.0;
n += nvalues;
}
}
/* ---------------------------------------------------------------------- */
void ComputeSpecAtom::pack_z(int n)
{
double **x = atom->x;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = x[i][2];
else buf[n] = 0.0;
n += nvalues;
}
}
/* ---------------------------------------------------------------------- */
void ComputeSpecAtom::pack_vx(int n)
{
double **v = atom->v;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = v[i][0];
else buf[n] = 0.0;
n += nvalues;
}
}
/* ---------------------------------------------------------------------- */
void ComputeSpecAtom::pack_vy(int n)
{
double **v = atom->v;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = v[i][1];
else buf[n] = 0.0;
n += nvalues;
}
}
/* ---------------------------------------------------------------------- */
void ComputeSpecAtom::pack_vz(int n)
{
double **v = atom->v;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = v[i][2];
else buf[n] = 0.0;
n += nvalues;
}
}
/* ---------------------------------------------------------------------- */
void ComputeSpecAtom::pack_abo01(int n)
{
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = reaxc->tmpbo[i][0];
else buf[n] = 0.0;
n += nvalues;
}
}
/* ---------------------------------------------------------------------- */
void ComputeSpecAtom::pack_abo02(int n)
{
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = reaxc->tmpbo[i][1];
else buf[n] = 0.0;
n += nvalues;
}
}
/* ---------------------------------------------------------------------- */
void ComputeSpecAtom::pack_abo03(int n)
{
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = reaxc->tmpbo[i][2];
else buf[n] = 0.0;
n += nvalues;
}
}
/* ---------------------------------------------------------------------- */
void ComputeSpecAtom::pack_abo04(int n)
{
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = reaxc->tmpbo[i][3];
else buf[n] = 0.0;
n += nvalues;
}
}
/* ---------------------------------------------------------------------- */
void ComputeSpecAtom::pack_abo05(int n)
{
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = reaxc->tmpbo[i][4];
else buf[n] = 0.0;
n += nvalues;
}
}
/* ---------------------------------------------------------------------- */
void ComputeSpecAtom::pack_abo06(int n)
{
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = reaxc->tmpbo[i][5];
else buf[n] = 0.0;
n += nvalues;
}
}
/* ---------------------------------------------------------------------- */
void ComputeSpecAtom::pack_abo07(int n)
{
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = reaxc->tmpbo[i][6];
else buf[n] = 0.0;
n += nvalues;
}
}
/* ---------------------------------------------------------------------- */
void ComputeSpecAtom::pack_abo08(int n)
{
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = reaxc->tmpbo[i][7];
else buf[n] = 0.0;
n += nvalues;
}
}
/* ---------------------------------------------------------------------- */
void ComputeSpecAtom::pack_abo09(int n)
{
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = reaxc->tmpbo[i][8];
else buf[n] = 0.0;
n += nvalues;
}
}
/* ---------------------------------------------------------------------- */
void ComputeSpecAtom::pack_abo10(int n)
{
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = reaxc->tmpbo[i][9];
else buf[n] = 0.0;
n += nvalues;
}
}
/* ---------------------------------------------------------------------- */
void ComputeSpecAtom::pack_abo11(int n)
{
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = reaxc->tmpbo[i][10];
else buf[n] = 0.0;
n += nvalues;
}
}
/* ---------------------------------------------------------------------- */
void ComputeSpecAtom::pack_abo12(int n)
{
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = reaxc->tmpbo[i][11];
else buf[n] = 0.0;
n += nvalues;
}
}
/* ---------------------------------------------------------------------- */
void ComputeSpecAtom::pack_abo13(int n)
{
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = reaxc->tmpbo[i][12];
else buf[n] = 0.0;
n += nvalues;
}
}
/* ---------------------------------------------------------------------- */
void ComputeSpecAtom::pack_abo14(int n)
{
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = reaxc->tmpbo[i][13];
else buf[n] = 0.0;
n += nvalues;
}
}
/* ---------------------------------------------------------------------- */
void ComputeSpecAtom::pack_abo15(int n)
{
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = reaxc->tmpbo[i][14];
else buf[n] = 0.0;
n += nvalues;
}
}
/* ---------------------------------------------------------------------- */
void ComputeSpecAtom::pack_abo16(int n)
{
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = reaxc->tmpbo[i][15];
else buf[n] = 0.0;
n += nvalues;
}
}
/* ---------------------------------------------------------------------- */
void ComputeSpecAtom::pack_abo17(int n)
{
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = reaxc->tmpbo[i][16];
else buf[n] = 0.0;
n += nvalues;
}
}
/* ---------------------------------------------------------------------- */
void ComputeSpecAtom::pack_abo18(int n)
{
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = reaxc->tmpbo[i][17];
else buf[n] = 0.0;
n += nvalues;
}
}
/* ---------------------------------------------------------------------- */
void ComputeSpecAtom::pack_abo19(int n)
{
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = reaxc->tmpbo[i][18];
else buf[n] = 0.0;
n += nvalues;
}
}
/* ---------------------------------------------------------------------- */
void ComputeSpecAtom::pack_abo20(int n)
{
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = reaxc->tmpbo[i][19];
else buf[n] = 0.0;
n += nvalues;
}
}
/* ---------------------------------------------------------------------- */
void ComputeSpecAtom::pack_abo21(int n)
{
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = reaxc->tmpbo[i][20];
else buf[n] = 0.0;
n += nvalues;
}
}
/* ---------------------------------------------------------------------- */
void ComputeSpecAtom::pack_abo22(int n)
{
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = reaxc->tmpbo[i][21];
else buf[n] = 0.0;
n += nvalues;
}
}
/* ---------------------------------------------------------------------- */
void ComputeSpecAtom::pack_abo23(int n)
{
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = reaxc->tmpbo[i][22];
else buf[n] = 0.0;
n += nvalues;
}
}
/* ---------------------------------------------------------------------- */
void ComputeSpecAtom::pack_abo24(int n)
{
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = reaxc->tmpbo[i][23];
else buf[n] = 0.0;
n += nvalues;
}
}
/* ---------------------------------------------------------------------- */

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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Labo0ratories
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 COMPUTE_CLASS
ComputeStyle(SPEC/ATOM,ComputeSpecAtom)
#else
#ifndef LMP_COMPUTE_SPEC_ATOM_H
#define LMP_COMPUTE_SPEC_ATOM_H
#include "compute.h"
#include "pointers.h"
namespace LAMMPS_NS {
class ComputeSpecAtom : public Compute {
public:
ComputeSpecAtom(class LAMMPS *, int, char **);
~ComputeSpecAtom();
void init() {}
void compute_peratom();
double memory_usage();
private:
int nvalues;
int nmax;
double *vector;
double **array;
double *buf;
double *vbuf;
typedef void (ComputeSpecAtom::*FnPtrPack)(int);
FnPtrPack *pack_choice;
void pack_q(int);
void pack_x(int);
void pack_y(int);
void pack_z(int);
void pack_vx(int);
void pack_vy(int);
void pack_vz(int);
void pack_abo01(int);
void pack_abo02(int);
void pack_abo03(int);
void pack_abo04(int);
void pack_abo05(int);
void pack_abo06(int);
void pack_abo07(int);
void pack_abo08(int);
void pack_abo09(int);
void pack_abo10(int);
void pack_abo11(int);
void pack_abo12(int);
void pack_abo13(int);
void pack_abo14(int);
void pack_abo15(int);
void pack_abo16(int);
void pack_abo17(int);
void pack_abo18(int);
void pack_abo19(int);
void pack_abo20(int);
void pack_abo21(int);
void pack_abo22(int);
void pack_abo23(int);
void pack_abo24(int);
class PairReaxC *reaxc;
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Illegal ... command
Self-explanatory. Check the input script syntax and compare to the
documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see the offending line.
E: Compute reaxc/atom for atom reaxc that isn't allocated
Self-explanatory.
E: Invalid keyword in compute reaxc/atom command
Self-explanatory.
*/