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compute_dihedral_local.cpp
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Tue, Feb 18, 23:59

compute_dihedral_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_dihedral_local.h"
#include "atom.h"
#include "atom_vec.h"
#include "molecule.h"
#include "update.h"
#include "domain.h"
#include "force.h"
#include "dihedral.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
/* ---------------------------------------------------------------------- */
ComputeDihedralLocal::ComputeDihedralLocal(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg),
vector(NULL), array(NULL)
{
if (narg < 4) error->all(FLERR,"Illegal compute dihedral/local command");
if (atom->avec->dihedrals_allow == 0)
error->all(FLERR,
"Compute dihedral/local used when dihedrals are not allowed");
local_flag = 1;
nvalues = narg - 3;
if (nvalues == 1) size_local_cols = 0;
else size_local_cols = nvalues;
pflag = -1;
nvalues = 0;
for (int iarg = 3; iarg < narg; iarg++) {
if (strcmp(arg[iarg],"phi") == 0) pflag = nvalues++;
else error->all(FLERR,"Invalid keyword in compute dihedral/local command");
}
nmax = 0;
}
/* ---------------------------------------------------------------------- */
ComputeDihedralLocal::~ComputeDihedralLocal()
{
memory->destroy(vector);
memory->destroy(array);
}
/* ---------------------------------------------------------------------- */
void ComputeDihedralLocal::init()
{
if (force->dihedral == NULL)
error->all(FLERR,"No dihedral style is defined for compute dihedral/local");
// do initial memory allocation so that memory_usage() is correct
ncount = compute_dihedrals(0);
if (ncount > nmax) reallocate(ncount);
size_local_rows = ncount;
}
/* ---------------------------------------------------------------------- */
void ComputeDihedralLocal::compute_local()
{
invoked_local = update->ntimestep;
// count local entries and compute dihedral info
ncount = compute_dihedrals(0);
if (ncount > nmax) reallocate(ncount);
size_local_rows = ncount;
ncount = compute_dihedrals(1);
}
/* ----------------------------------------------------------------------
count dihedrals on this proc
only count if 2nd atom is the one storing the dihedral
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 dihedral
------------------------------------------------------------------------- */
int ComputeDihedralLocal::compute_dihedrals(int flag)
{
int i,m,n,nd,atom1,atom2,atom3,atom4,imol,iatom;
tagint tagprev;
double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,vb2xm,vb2ym,vb2zm;
double ax,ay,az,bx,by,bz,rasq,rbsq,rgsq,rg,ra2inv,rb2inv,rabinv;
double s,c;
double *pbuf;
double **x = atom->x;
tagint *tag = atom->tag;
int *num_dihedral = atom->num_dihedral;
tagint **dihedral_atom1 = atom->dihedral_atom1;
tagint **dihedral_atom2 = atom->dihedral_atom2;
tagint **dihedral_atom3 = atom->dihedral_atom3;
tagint **dihedral_atom4 = atom->dihedral_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 (pflag >= 0) pbuf = vector;
} else {
if (pflag >= 0 && array) pbuf = &array[0][pflag];
else pbuf = NULL;
}
}
m = n = 0;
for (atom2 = 0; atom2 < nlocal; atom2++) {
if (!(mask[atom2] & groupbit)) continue;
if (molecular == 1) nd = num_dihedral[atom2];
else {
if (molindex[atom2] < 0) continue;
imol = molindex[atom2];
iatom = molatom[atom2];
nd = onemols[imol]->num_dihedral[iatom];
}
for (i = 0; i < nd; i++) {
if (molecular == 1) {
if (tag[atom2] != dihedral_atom2[atom2][i]) continue;
atom1 = atom->map(dihedral_atom1[atom2][i]);
atom3 = atom->map(dihedral_atom3[atom2][i]);
atom4 = atom->map(dihedral_atom4[atom2][i]);
} else {
if (tag[atom2] != onemols[imol]->dihedral_atom2[atom2][i]) continue;
tagprev = tag[atom2] - iatom - 1;
atom1 = atom->map(onemols[imol]->dihedral_atom1[atom2][i]+tagprev);
atom3 = atom->map(onemols[imol]->dihedral_atom3[atom2][i]+tagprev);
atom4 = atom->map(onemols[imol]->dihedral_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) {
// phi calculation from dihedral style harmonic
if (pflag >= 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);
vb2xm = -vb2x;
vb2ym = -vb2y;
vb2zm = -vb2z;
domain->minimum_image(vb2xm,vb2ym,vb2zm);
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);
ax = vb1y*vb2zm - vb1z*vb2ym;
ay = vb1z*vb2xm - vb1x*vb2zm;
az = vb1x*vb2ym - vb1y*vb2xm;
bx = vb3y*vb2zm - vb3z*vb2ym;
by = vb3z*vb2xm - vb3x*vb2zm;
bz = vb3x*vb2ym - vb3y*vb2xm;
rasq = ax*ax + ay*ay + az*az;
rbsq = bx*bx + by*by + bz*bz;
rgsq = vb2xm*vb2xm + vb2ym*vb2ym + vb2zm*vb2zm;
rg = sqrt(rgsq);
ra2inv = rb2inv = 0.0;
if (rasq > 0) ra2inv = 1.0/rasq;
if (rbsq > 0) rb2inv = 1.0/rbsq;
rabinv = sqrt(ra2inv*rb2inv);
c = (ax*bx + ay*by + az*bz)*rabinv;
s = rg*rabinv*(ax*vb3x + ay*vb3y + az*vb3z);
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
pbuf[n] = 180.0*atan2(s,c)/MY_PI;
}
n += nvalues;
}
m++;
}
}
return m;
}
/* ---------------------------------------------------------------------- */
void ComputeDihedralLocal::reallocate(int n)
{
// grow vector or array and indices array
while (nmax < n) nmax += DELTA;
if (nvalues == 1) {
memory->destroy(vector);
memory->create(vector,nmax,"bond/local:vector");
vector_local = vector;
} else {
memory->destroy(array);
memory->create(array,nmax,nvalues,"bond/local:array");
array_local = array;
}
}
/* ----------------------------------------------------------------------
memory usage of local data
------------------------------------------------------------------------- */
double ComputeDihedralLocal::memory_usage()
{
double bytes = nmax*nvalues * sizeof(double);
return bytes;
}

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