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lammps/src/compute_improper_local.cpp
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compute_improper_local.cpp
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/* ----------------------------------------------------------------------
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 <math.h>
#include <string.h>
#include "compute_improper_local.h"
#include "atom.h"
#include "atom_vec.h"
#include "molecule.h"
#include "update.h"
#include "domain.h"
#include "force.h"
#include "improper.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace MathConst;
#define DELTA 10000
#define SMALL 0.001
/* ---------------------------------------------------------------------- */
ComputeImproperLocal::ComputeImproperLocal(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg),
vlocal(NULL), alocal(NULL)
{
if (narg < 4) error->all(FLERR,"Illegal compute improper/local command");
if (atom->avec->impropers_allow == 0)
error->all(FLERR,
"Compute improper/local used when impropers are not allowed");
local_flag = 1;
nvalues = narg - 3;
if (nvalues == 1) size_local_cols = 0;
else size_local_cols = nvalues;
cflag = -1;
nvalues = 0;
for (int iarg = 3; iarg < narg; iarg++) {
if (strcmp(arg[iarg],"chi") == 0) cflag = nvalues++;
else error->all(FLERR,"Invalid keyword in compute improper/local command");
}
nmax = 0;
vlocal = NULL;
alocal = NULL;
}
/* ---------------------------------------------------------------------- */
ComputeImproperLocal::~ComputeImproperLocal()
{
memory->destroy(vlocal);
memory->destroy(alocal);
}
/* ---------------------------------------------------------------------- */
void ComputeImproperLocal::init()
{
if (force->improper == NULL)
error->all(FLERR,"No improper style is defined for compute improper/local");
// do initial memory allocation so that memory_usage() is correct
ncount = compute_impropers(0);
if (ncount > nmax) reallocate(ncount);
size_local_rows = ncount;
}
/* ---------------------------------------------------------------------- */
void ComputeImproperLocal::compute_local()
{
invoked_local = update->ntimestep;
// count local entries and compute improper info
ncount = compute_impropers(0);
if (ncount > nmax) reallocate(ncount);
size_local_rows = ncount;
ncount = compute_impropers(1);
}
/* ----------------------------------------------------------------------
count impropers on this proc
only count if 2nd atom is the one storing the improper
all atoms in interaction must be in group
all atoms in interaction must be known to proc
if flag is set, compute requested info about improper
------------------------------------------------------------------------- */
int ComputeImproperLocal::compute_impropers(int flag)
{
int i,m,n,ni,atom1,atom2,atom3,atom4,imol,iatom;
tagint tagprev;
double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z;
double ss1,ss2,ss3,r1,r2,r3,c0,c1,c2,s1,s2;
double s12,c;
double *cbuf;
double **x = atom->x;
tagint *tag = atom->tag;
int *num_improper = atom->num_improper;
tagint **improper_atom1 = atom->improper_atom1;
tagint **improper_atom2 = atom->improper_atom2;
tagint **improper_atom3 = atom->improper_atom3;
tagint **improper_atom4 = atom->improper_atom4;
int *mask = atom->mask;
int *molindex = atom->molindex;
int *molatom = atom->molatom;
Molecule **onemols = atom->avec->onemols;
int nlocal = atom->nlocal;
int molecular = atom->molecular;
if (flag) {
if (nvalues == 1) {
if (cflag >= 0) cbuf = vlocal;
} else {
if (cflag >= 0 && alocal) cbuf = &alocal[0][cflag];
else cbuf = NULL;
}
}
m = n = 0;
for (atom2 = 0; atom2 < nlocal; atom2++) {
if (!(mask[atom2] & groupbit)) continue;
if (molecular == 1) ni = num_improper[atom2];
else {
if (molindex[atom2] < 0) continue;
imol = molindex[atom2];
iatom = molatom[atom2];
ni = onemols[imol]->num_improper[iatom];
}
for (i = 0; i < ni; i++) {
if (molecular == 1) {
if (tag[atom2] != improper_atom2[atom2][i]) continue;
atom1 = atom->map(improper_atom1[atom2][i]);
atom3 = atom->map(improper_atom3[atom2][i]);
atom4 = atom->map(improper_atom4[atom2][i]);
} else {
if (tag[atom2] != onemols[imol]->improper_atom2[atom2][i]) continue;
tagprev = tag[atom2] - iatom - 1;
atom1 = atom->map(onemols[imol]->improper_atom1[atom2][i]+tagprev);
atom3 = atom->map(onemols[imol]->improper_atom3[atom2][i]+tagprev);
atom4 = atom->map(onemols[imol]->improper_atom4[atom2][i]+tagprev);
}
if (atom1 < 0 || !(mask[atom1] & groupbit)) continue;
if (atom3 < 0 || !(mask[atom3] & groupbit)) continue;
if (atom4 < 0 || !(mask[atom4] & groupbit)) continue;
if (flag) {
// chi calculation from improper style harmonic
if (cflag >= 0) {
vb1x = x[atom1][0] - x[atom2][0];
vb1y = x[atom1][1] - x[atom2][1];
vb1z = x[atom1][2] - x[atom2][2];
domain->minimum_image(vb1x,vb1y,vb1z);
vb2x = x[atom3][0] - x[atom2][0];
vb2y = x[atom3][1] - x[atom2][1];
vb2z = x[atom3][2] - x[atom2][2];
domain->minimum_image(vb2x,vb2y,vb2z);
vb3x = x[atom4][0] - x[atom3][0];
vb3y = x[atom4][1] - x[atom3][1];
vb3z = x[atom4][2] - x[atom3][2];
domain->minimum_image(vb3x,vb3y,vb3z);
ss1 = 1.0 / (vb1x*vb1x + vb1y*vb1y + vb1z*vb1z);
ss2 = 1.0 / (vb2x*vb2x + vb2y*vb2y + vb2z*vb2z);
ss3 = 1.0 / (vb3x*vb3x + vb3y*vb3y + vb3z*vb3z);
r1 = sqrt(ss1);
r2 = sqrt(ss2);
r3 = sqrt(ss3);
c0 = (vb1x * vb3x + vb1y * vb3y + vb1z * vb3z) * r1 * r3;
c1 = (vb1x * vb2x + vb1y * vb2y + vb1z * vb2z) * r1 * r2;
c2 = -(vb3x * vb2x + vb3y * vb2y + vb3z * vb2z) * r3 * r2;
s1 = 1.0 - c1*c1;
if (s1 < SMALL) s1 = SMALL;
s1 = 1.0 / s1;
s2 = 1.0 - c2*c2;
if (s2 < SMALL) s2 = SMALL;
s2 = 1.0 / s2;
s12 = sqrt(s1*s2);
c = (c1*c2 + c0) * s12;
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
cbuf[n] = 180.0*acos(c)/MY_PI;
}
n += nvalues;
}
m++;
}
}
return m;
}
/* ---------------------------------------------------------------------- */
void ComputeImproperLocal::reallocate(int n)
{
// grow vector_local or array_local
while (nmax < n) nmax += DELTA;
if (nvalues == 1) {
memory->destroy(vlocal);
memory->create(vlocal,nmax,"improper/local:vector_local");
vector_local = vlocal;
} else {
memory->destroy(alocal);
memory->create(alocal,nmax,nvalues,"improper/local:array_local");
array_local = alocal;
}
}
/* ----------------------------------------------------------------------
memory usage of local data
------------------------------------------------------------------------- */
double ComputeImproperLocal::memory_usage()
{
double bytes = nmax*nvalues * sizeof(double);
return bytes;
}
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