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improper_distance.cpp
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Wed, Jul 3, 03:44

improper_distance.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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Paolo Raiteri (Curtin University)
------------------------------------------------------------------------- */
#include <mpi.h>
#include <math.h>
#include <stdlib.h>
#include "improper_distance.h"
#include "atom.h"
#include "comm.h"
#include "neighbor.h"
#include "domain.h"
#include "force.h"
#include "update.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define TOLERANCE 0.05
#define SMALL 0.001
/* ---------------------------------------------------------------------- */
ImproperDistance::ImproperDistance(LAMMPS *lmp) : Improper(lmp) {}
/* ---------------------------------------------------------------------- */
ImproperDistance::~ImproperDistance()
{
if (allocated) {
memory->destroy(setflag);
memory->destroy(k);
memory->destroy(chi);
}
}
/* ---------------------------------------------------------------------- */
void ImproperDistance::compute(int eflag, int vflag)
{
int i1,i2,i3,i4,n,type;
double xab, yab, zab; // bond 1-2
double xac, yac, zac; // bond 1-3
double xad, yad, zad; // bond 1-4
double xbc, ybc, zbc; // bond 2-3
double xbd, ybd, zbd; // bond 2-4
double xna, yna, zna, rna; // normal
double da;
double eimproper,f1[3],f2[3],f3[3],f4[3];
// double ss1,ss2,ss3,r1,r2,r3,c0,c1,c2,s1,s2;
// double s12,c,s,domega,a,a11,a22,a33,a12,a13,a23;
double domega,a;
eimproper = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = 0;
double **x = atom->x;
double **f = atom->f;
int **improperlist = neighbor->improperlist;
int nimproperlist = neighbor->nimproperlist;
int nlocal = atom->nlocal;
int newton_bond = force->newton_bond;
for (n = 0; n < nimproperlist; n++) {
i1 = improperlist[n][0];
i2 = improperlist[n][1];
i3 = improperlist[n][2];
i4 = improperlist[n][3];
type = improperlist[n][4];
// geometry of 4-body
// 1 is the central atom
// 2-3-4 are ment to be equivalent
// I need the bonds between 2-3 and 2-4 to get the plane normal
// Then I need the bond 1-2 to project it onto the normal to the plane
// bond 1->2
xab = x[i2][0] - x[i1][0];
yab = x[i2][1] - x[i1][1];
zab = x[i2][2] - x[i1][2];
domain->minimum_image(xab,yab,zab);
// bond 1->3
xac = x[i3][0] - x[i1][0];
yac = x[i3][1] - x[i1][1];
zac = x[i3][2] - x[i1][2];
domain->minimum_image(xac,yac,zac);
// bond 1->4
xad = x[i4][0] - x[i1][0];
yad = x[i4][1] - x[i1][1];
zad = x[i4][2] - x[i1][2];
domain->minimum_image(xad,yad,zad);
// bond 2-3
xbc = x[i3][0] - x[i2][0];
ybc = x[i3][1] - x[i2][1];
zbc = x[i3][2] - x[i2][2];
domain->minimum_image(xbc,ybc,zbc);
// bond 2-4
xbd = x[i4][0] - x[i2][0];
ybd = x[i4][1] - x[i2][1];
zbd = x[i4][2] - x[i2][2];
domain->minimum_image(xbd,ybd,zbd);
xna = ybc*zbd - zbc*ybd;
yna = -(xbc*zbd - zbc*xbd);
zna = xbc*ybd - ybc*xbd;
rna = 1.0 / sqrt(xna*xna+yna*yna+zna*zna);
xna *= rna;
yna *= rna;
zna *= rna;
da = xna*xab + yna*yab + zna*zab;
domega = k[type]*da*da + chi[type]*da*da*da*da;
//printf("%3i %3i %3i %3i %10.5f %10.5f \n",i1,i2,i3,i4,da,domega);
a = 2.0* (k[type]*da + 2.0*chi[type]*da*da*da);
if (eflag) eimproper = domega;
f1[0] = a*( xna);
f1[1] = a*( yna);
f1[2] = a*( zna);
f2[0] = a*( -xna -yab*(zbd-zbc)*rna +zab*(ybd-ybc)*rna -da*( -yna*(zbd-zbc) + zna*(ybd-ybc) )*rna);
f2[1] = a*( +xab*(zbd-zbc)*rna -yna +zab*(xbc-xbd)*rna -da*( +xna*(zbd-zbc) + zna*(xbc-xbd) )*rna);
f2[2] = a*( -xab*(ybd-ybc)*rna -yab*(xbc-xbd)*rna -zna -da*( +xna*(ybc-ybd) - yna*(xbc-xbd) )*rna);
f3[0] = a*( ( yab*zbd -zab*ybd ) *rna +da*( -yna*zbd +zna*ybd )*rna);
f3[1] = a*( ( -xab*zbd +zab*xbd ) *rna +da*( +xna*zbd -zna*xbd )*rna);
f3[2] = a*( ( +xab*ybd -yab*xbd ) *rna +da*( -xna*ybd +yna*xbd )*rna);
f4[0] = a*( ( -yab*zbc +zab*ybc ) *rna -da*( -yna*zbc +zna*ybc )*rna);
f4[1] = a*( ( +xab*zbc -zab*xbc ) *rna -da*( +xna*zbc -zna*xbc )*rna);
f4[2] = a*( ( -xab*ybc +yab*xbc ) *rna -da*( -xna*ybc +yna*xbc )*rna);
//printf("%10.5f %10.5f %10.5f \n",f1[0],f1[1],f1[2]);
//printf("%10.5f %10.5f %10.5f \n",f2[0],f2[1],f2[2]);
//printf("%10.5f %10.5f %10.5f \n",f3[0],f3[1],f3[2]);
//printf("%10.5f %10.5f %10.5f \n",f4[0],f4[1],f4[2]);
// apply force to each of 4 atoms
if (newton_bond || i1 < nlocal) {
f[i1][0] += f1[0];
f[i1][1] += f1[1];
f[i1][2] += f1[2];
}
if (newton_bond || i2 < nlocal) {
f[i2][0] += f2[0];
f[i2][1] += f2[1];
f[i2][2] += f2[2];
}
if (newton_bond || i3 < nlocal) {
f[i3][0] += f3[0];
f[i3][1] += f3[1];
f[i3][2] += f3[2];
}
if (newton_bond || i4 < nlocal) {
f[i4][0] += f4[0];
f[i4][1] += f4[1];
f[i4][2] += f4[2];
}
if (evflag)
ev_tally(i1,i2,i3,i4,nlocal,newton_bond,eimproper,f2,f3,f4,
xab,yab,zab,xac,yac,zac,xad-xac,yad-yac,zad-zac);
}
}
/* ---------------------------------------------------------------------- */
void ImproperDistance::allocate()
{
allocated = 1;
int n = atom->nimpropertypes;
memory->create(k,n+1,"improper:k");
memory->create(chi,n+1,"improper:chi");
memory->create(setflag,n+1,"improper:setflag");
for (int i = 1; i <= n; i++) setflag[i] = 0;
}
/* ----------------------------------------------------------------------
set coeffs for one type
------------------------------------------------------------------------- */
void ImproperDistance::coeff(int narg, char **arg)
{
// if (which > 0) return;
if (narg != 3) error->all(FLERR,"Incorrect args for improper coefficients");
if (!allocated) allocate();
int ilo,ihi;
force->bounds(arg[0],atom->nimpropertypes,ilo,ihi);
double k_one = force->numeric(FLERR,arg[1]);
double chi_one = force->numeric(FLERR,arg[2]);
// convert chi from degrees to radians
int count = 0;
for (int i = ilo; i <= ihi; i++) {
k[i] = k_one;
//chi[i] = chi_one/180.0 * PI;
chi[i] = chi_one;
setflag[i] = 1;
count++;
}
if (count == 0) error->all(FLERR,"Incorrect args for improper coefficients");
}
/* ----------------------------------------------------------------------
proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void ImproperDistance::write_restart(FILE *fp)
{
fwrite(&k[1],sizeof(double),atom->nimpropertypes,fp);
fwrite(&chi[1],sizeof(double),atom->nimpropertypes,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void ImproperDistance::read_restart(FILE *fp)
{
allocate();
if (comm->me == 0) {
fread(&k[1],sizeof(double),atom->nimpropertypes,fp);
fread(&chi[1],sizeof(double),atom->nimpropertypes,fp);
}
MPI_Bcast(&k[1],atom->nimpropertypes,MPI_DOUBLE,0,world);
MPI_Bcast(&chi[1],atom->nimpropertypes,MPI_DOUBLE,0,world);
for (int i = 1; i <= atom->nimpropertypes; i++) setflag[i] = 1;
}

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