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dihedral.cpp
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Sat, Nov 16, 23:31

dihedral.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 "dihedral.h"
#include "atom.h"
#include "atom.h"
#include "force.h"
#include "pair.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ----------------------------------------------------------------------
set dihedral contribution to Vdwl and Coulombic energy to 0.0
DihedralCharmm will override this
------------------------------------------------------------------------- */
Dihedral::Dihedral(LAMMPS *lmp) : Pointers(lmp)
{
energy = 0.0;
allocated = 0;
PI = 4.0*atan(1.0);
maxeatom = maxvatom = 0;
eatom = NULL;
vatom = NULL;
}
/* ---------------------------------------------------------------------- */
Dihedral::~Dihedral()
{
memory->sfree(eatom);
memory->destroy_2d_double_array(vatom);
}
/* ----------------------------------------------------------------------
check if all coeffs are set
------------------------------------------------------------------------- */
void Dihedral::init()
{
if (!allocated) error->all("Dihedral coeffs are not set");
for (int i = 1; i <= atom->ndihedraltypes; i++)
if (setflag[i] == 0) error->all("All dihedral coeffs are not set");
init_style();
}
/* ----------------------------------------------------------------------
setup for energy, virial computation
see integrate::ev_set() for values of eflag (0-3) and vflag (0-6)
------------------------------------------------------------------------- */
void Dihedral::ev_setup(int eflag, int vflag)
{
int i,n;
evflag = 1;
eflag_either = eflag;
eflag_global = eflag % 2;
eflag_atom = eflag / 2;
vflag_either = vflag;
vflag_global = vflag % 4;
vflag_atom = vflag / 4;
// reallocate per-atom arrays if necessary
if (eflag_atom && atom->nmax > maxeatom) {
maxeatom = atom->nmax;
memory->sfree(eatom);
eatom = (double *) memory->smalloc(maxeatom*sizeof(double),"bond:eatom");
}
if (vflag_atom && atom->nmax > maxvatom) {
maxvatom = atom->nmax;
memory->destroy_2d_double_array(vatom);
vatom = memory->create_2d_double_array(maxvatom,6,"bond:vatom");
}
// zero accumulators
if (eflag_global) energy = 0.0;
if (vflag_global) for (i = 0; i < 6; i++) virial[i] = 0.0;
if (eflag_atom) {
n = atom->nlocal;
if (force->newton_bond) n += atom->nghost;
for (i = 0; i < n; i++) eatom[i] = 0.0;
}
if (vflag_atom) {
n = atom->nlocal;
if (force->newton_bond) n += atom->nghost;
for (i = 0; i < n; i++) {
vatom[i][0] = 0.0;
vatom[i][1] = 0.0;
vatom[i][2] = 0.0;
vatom[i][3] = 0.0;
vatom[i][4] = 0.0;
vatom[i][5] = 0.0;
}
}
}
/* ----------------------------------------------------------------------
tally energy and virial into global and per-atom accumulators
virial = r1F1 + r2F2 + r3F3 + r4F4 = (r1-r2) F1 + (r3-r2) F3 + (r4-r2) F4
= (r1-r2) F1 + (r3-r2) F3 + (r4-r3 + r3-r2) F4
= vb1*f1 + vb2*f3 + (vb3+vb2)*f4
------------------------------------------------------------------------- */
void Dihedral::ev_tally(int i1, int i2, int i3, int i4,
int nlocal, int newton_bond,
double edihedral, double *f1, double *f3, double *f4,
double vb1x, double vb1y, double vb1z,
double vb2x, double vb2y, double vb2z,
double vb3x, double vb3y, double vb3z)
{
double edihedralquarter,v[6];
if (eflag_either) {
if (eflag_global) {
if (newton_bond) energy += edihedral;
else {
edihedralquarter = 0.25*edihedral;
if (i1 < nlocal) energy += edihedralquarter;
if (i2 < nlocal) energy += edihedralquarter;
if (i3 < nlocal) energy += edihedralquarter;
if (i4 < nlocal) energy += edihedralquarter;
}
}
if (eflag_atom) {
edihedralquarter = 0.25*edihedral;
if (newton_bond || i1 < nlocal) eatom[i1] += edihedralquarter;
if (newton_bond || i2 < nlocal) eatom[i2] += edihedralquarter;
if (newton_bond || i3 < nlocal) eatom[i3] += edihedralquarter;
if (newton_bond || i4 < nlocal) eatom[i4] += edihedralquarter;
}
}
if (vflag_either) {
v[0] = vb1x*f1[0] + vb2x*f3[0] + (vb3x+vb2x)*f4[0];
v[1] = vb1y*f1[1] + vb2y*f3[1] + (vb3y+vb2y)*f4[1];
v[2] = vb1z*f1[2] + vb2z*f3[2] + (vb3z+vb2z)*f4[2];
v[3] = vb1x*f1[1] + vb2x*f3[1] + (vb3x+vb2x)*f4[1];
v[4] = vb1x*f1[2] + vb2x*f3[2] + (vb3x+vb2x)*f4[2];
v[5] = vb1y*f1[2] + vb2y*f3[2] + (vb3y+vb2y)*f4[2];
if (vflag_global) {
if (newton_bond) {
virial[0] += v[0];
virial[1] += v[1];
virial[2] += v[2];
virial[3] += v[3];
virial[4] += v[4];
virial[5] += v[5];
} else {
if (i1 < nlocal) {
virial[0] += 0.25*v[0];
virial[1] += 0.25*v[1];
virial[2] += 0.25*v[2];
virial[3] += 0.25*v[3];
virial[4] += 0.25*v[4];
virial[5] += 0.25*v[5];
}
if (i2 < nlocal) {
virial[0] += 0.25*v[0];
virial[1] += 0.25*v[1];
virial[2] += 0.25*v[2];
virial[3] += 0.25*v[3];
virial[4] += 0.25*v[4];
virial[5] += 0.25*v[5];
}
if (i3 < nlocal) {
virial[0] += 0.25*v[0];
virial[1] += 0.25*v[1];
virial[2] += 0.25*v[2];
virial[3] += 0.25*v[3];
virial[4] += 0.25*v[4];
virial[5] += 0.25*v[5];
}
if (i4 < nlocal) {
virial[0] += 0.25*v[0];
virial[1] += 0.25*v[1];
virial[2] += 0.25*v[2];
virial[3] += 0.25*v[3];
virial[4] += 0.25*v[4];
virial[5] += 0.25*v[5];
}
}
}
if (vflag_atom) {
if (newton_bond || i1 < nlocal) {
vatom[i1][0] += 0.25*v[0];
vatom[i1][1] += 0.25*v[1];
vatom[i1][2] += 0.25*v[2];
vatom[i1][3] += 0.25*v[3];
vatom[i1][4] += 0.25*v[4];
vatom[i1][5] += 0.25*v[5];
}
if (newton_bond || i2 < nlocal) {
vatom[i2][0] += 0.25*v[0];
vatom[i2][1] += 0.25*v[1];
vatom[i2][2] += 0.25*v[2];
vatom[i2][3] += 0.25*v[3];
vatom[i2][4] += 0.25*v[4];
vatom[i2][5] += 0.25*v[5];
}
if (newton_bond || i3 < nlocal) {
vatom[i3][0] += 0.25*v[0];
vatom[i3][1] += 0.25*v[1];
vatom[i3][2] += 0.25*v[2];
vatom[i3][3] += 0.25*v[3];
vatom[i3][4] += 0.25*v[4];
vatom[i3][5] += 0.25*v[5];
}
if (newton_bond || i4 < nlocal) {
vatom[i4][0] += 0.25*v[0];
vatom[i4][1] += 0.25*v[1];
vatom[i4][2] += 0.25*v[2];
vatom[i4][3] += 0.25*v[3];
vatom[i4][4] += 0.25*v[4];
vatom[i4][5] += 0.25*v[5];
}
}
}
}
/* ---------------------------------------------------------------------- */
double Dihedral::memory_usage()
{
double bytes = maxeatom * sizeof(double);
bytes += maxvatom*6 * sizeof(double);
return bytes;
}

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