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compute_angle_local.cpp
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Sat, Sep 21, 06:56

compute_angle_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_angle_local.h"
#include "atom.h"
#include "atom_vec.h"
#include "update.h"
#include "domain.h"
#include "force.h"
#include "angle.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
enum{THETA,ENERGY};
#define DELTA 10000
/* ---------------------------------------------------------------------- */
ComputeAngleLocal::ComputeAngleLocal(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg < 4) error->all("Illegal compute angle/local command");
if (atom->avec->angles_allow == 0)
error->all("Compute angle/local used when angles are not allowed");
local_flag = 1;
nvalues = narg - 3;
if (nvalues == 1) size_local_cols = 0;
else size_local_cols = nvalues;
which = new int[nvalues];
pack_choice = new FnPtrPack[nvalues];
dflag = eflag = 0;
int i;
for (int iarg = 3; iarg < narg; iarg++) {
i = iarg-3;
if (strcmp(arg[iarg],"theta") == 0) {
dflag = 1;
which[i] = THETA;
pack_choice[i] = &ComputeAngleLocal::pack_theta;
} else if (strcmp(arg[iarg],"energy") == 0) {
eflag = 1;
which[i] = ENERGY;
pack_choice[i] = &ComputeAngleLocal::pack_energy;
} else error->all("Invalid keyword in compute angle/local command");
}
nmax = 0;
theta = energy = NULL;
array = NULL;
}
/* ---------------------------------------------------------------------- */
ComputeAngleLocal::~ComputeAngleLocal()
{
delete [] which;
delete [] pack_choice;
memory->sfree(theta);
memory->sfree(energy);
memory->destroy_2d_double_array(array);
}
/* ---------------------------------------------------------------------- */
void ComputeAngleLocal::init()
{
if (force->angle == NULL)
error->all("No angle style is defined for compute angle/local");
// do initial memory allocation so that memory_usage() is correct
ncount = compute_angles(0);
if (ncount > nmax) reallocate(ncount);
size_local_rows = ncount;
}
/* ---------------------------------------------------------------------- */
void ComputeAngleLocal::compute_local()
{
invoked_local = update->ntimestep;
// count local entries and compute angle info
ncount = compute_angles(0);
if (ncount > nmax) reallocate(ncount);
size_local_rows = ncount;
ncount = compute_angles(1);
// fill array with theta/energy values
if (nvalues > 1) {
if (array) buf = array[0];
for (int n = 0; n < nvalues; n++)
(this->*pack_choice[n])(n);
}
}
/* ----------------------------------------------------------------------
count angles and compute angle info on this proc
only count angle once if newton_angle is off
all atoms in interaction must be in group
all atoms in interaction must be known to proc
if angle is deleted (type = 0), do not count
if angle is turned off (type < 0), still count
if flag is set, compute requested info about angle
------------------------------------------------------------------------- */
int ComputeAngleLocal::compute_angles(int flag)
{
int i,atom1,atom2,atom3;
double delx1,dely1,delz1,delx2,dely2,delz2;
double rsq1,rsq2,r1,r2,c;
double **x = atom->x;
int *num_angle = atom->num_angle;
int **angle_atom1 = atom->angle_atom1;
int **angle_atom2 = atom->angle_atom2;
int **angle_atom3 = atom->angle_atom3;
int **angle_type = atom->angle_type;
int *tag = atom->tag;
int *mask = atom->mask;
int nlocal = atom->nlocal;
Angle *angle = force->angle;
int m = 0;
for (atom2 = 0; atom2 < nlocal; atom2++) {
if (!(mask[atom2] & groupbit)) continue;
for (i = 0; i < num_angle[atom2]; i++) {
if (tag[atom2] != angle_atom2[atom2][i]) continue;
atom1 = atom->map(angle_atom1[atom2][i]);
if (atom1 < 0 || !(mask[atom1] & groupbit)) continue;
atom3 = atom->map(angle_atom3[atom2][i]);
if (atom3 < 0 || !(mask[atom3] & groupbit)) continue;
if (flag) {
if (dflag) {
delx1 = x[atom1][0] - x[atom2][0];
dely1 = x[atom1][1] - x[atom2][1];
delz1 = x[atom1][2] - x[atom2][2];
domain->minimum_image(delx1,dely1,delz1);
rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1;
r1 = sqrt(rsq1);
delx2 = x[atom3][0] - x[atom2][0];
dely2 = x[atom3][1] - x[atom2][1];
delz2 = x[atom3][2] - x[atom2][2];
domain->minimum_image(delx2,dely2,delz2);
rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2;
r2 = sqrt(rsq2);
// c = cosine of angle
c = delx1*delx2 + dely1*dely2 + delz1*delz2;
c /= r1*r2;
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
theta[m] = acos(c);
}
if (eflag)
energy[m] = angle->single(angle_type[atom1][i],atom1,atom2,atom3);
}
m++;
}
}
return m;
}
/* ---------------------------------------------------------------------- */
void ComputeAngleLocal::pack_theta(int n)
{
for (int m = 0; m < ncount; m++) {
buf[n] = theta[m];
n += nvalues;
}
}
/* ---------------------------------------------------------------------- */
void ComputeAngleLocal::pack_energy(int n)
{
for (int m = 0; m < ncount; m++) {
buf[n] = energy[m];
n += nvalues;
}
}
/* ---------------------------------------------------------------------- */
void ComputeAngleLocal::reallocate(int n)
{
// grow vector or array and indices array
while (nmax < n) nmax += DELTA;
if (dflag) {
memory->sfree(theta);
theta = (double *) memory->smalloc(nmax*sizeof(double),
"bond/local:theta");
}
if (eflag) {
memory->sfree(energy);
energy = (double *) memory->smalloc(nmax*sizeof(double),
"bond/local:energy");
}
if (nvalues == 1) {
if (dflag) vector_local = theta;
if (eflag) vector_local = energy;
} else {
memory->destroy_2d_double_array(array);
array = memory->create_2d_double_array(nmax,nvalues,
"bond/local:array");
array_local = array;
}
}
/* ----------------------------------------------------------------------
memory usage of local data
------------------------------------------------------------------------- */
double ComputeAngleLocal::memory_usage()
{
double bytes = 0.0;
if (dflag) bytes += nmax * sizeof(double);
if (eflag) bytes += nmax * sizeof(double);
if (nvalues > 1) bytes += nmax*nvalues * sizeof(double);
return bytes;
}

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