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improper_cossq.cpp
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Wed, Jul 10, 00:58

improper_cossq.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: Georgios G. Vogiatzis (CoMSE, NTU Athens),
gvog@chemeng.ntua.gr
------------------------------------------------------------------------- */
#include <mpi.h>
#include <math.h>
#include <stdlib.h>
#include "improper_cossq.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"
#include "math_const.h"
using namespace LAMMPS_NS;
using namespace MathConst;
#define TOLERANCE 0.05
#define SMALL 0.001
/* ---------------------------------------------------------------------- */
ImproperCossq::ImproperCossq(LAMMPS *lmp) : Improper(lmp) {}
/* ---------------------------------------------------------------------- */
ImproperCossq::~ImproperCossq()
{
if (allocated) {
memory->destroy(setflag);
memory->destroy(k);
memory->destroy(chi);
}
}
/* ---------------------------------------------------------------------- */
void ImproperCossq::compute(int eflag, int vflag)
{
int i1,i2,i3,i4,n,type;
double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z ;
double eimproper,f1[3],f2[3],f3[3],f4[3];
double rjisq, rji, rlksq, rlk, cosphi, angfac;
double cjiji, clkji, clklk, cfact1, cfact2, cfact3;
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++) {
/* Ask the improper list for the atom types. */
i1 = improperlist[n][0];
i2 = improperlist[n][1];
i3 = improperlist[n][2];
i4 = improperlist[n][3];
type = improperlist[n][4];
/* separation vector between i1 and i2, (i2-i1) */
vb1x = x[i2][0] - x[i1][0];
vb1y = x[i2][1] - x[i1][1];
vb1z = x[i2][2] - x[i1][2];
rjisq = vb1x*vb1x + vb1y*vb1y + vb1z*vb1z ;
rji = sqrt(rjisq);
/* separation vector between i2 and i3 (i3-i2) */
vb2x = x[i3][0] - x[i2][0];
vb2y = x[i3][1] - x[i2][1];
vb2z = x[i3][2] - x[i2][2];
/* separation vector between i3 and i4, (i4-i3) */
vb3x = x[i4][0] - x[i3][0];
vb3y = x[i4][1] - x[i3][1];
vb3z = x[i4][2] - x[i3][2];
rlksq = vb3x*vb3x + vb3y*vb3y + vb3z*vb3z ;
rlk = sqrt(rlksq);
cosphi = (vb3x*vb1x + vb3y*vb1y + vb3z*vb1z)/(rji * rlk);
/* Check that cos(phi) is in the correct limits. */
if (cosphi > 1.0 + TOLERANCE || cosphi < (-1.0 - TOLERANCE))
{
int me;
MPI_Comm_rank(world,&me);
if (screen) {
char str[128];
sprintf(str,"Improper problem: %d " BIGINT_FORMAT " "
TAGINT_FORMAT " " TAGINT_FORMAT " "
TAGINT_FORMAT " " TAGINT_FORMAT,
me,update->ntimestep,
atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
error->warning(FLERR,str,0);
fprintf(screen," 1st atom: %d %g %g %g\n",me,x[i1][0],x[i1][1],x[i1][2]);
fprintf(screen," 2nd atom: %d %g %g %g\n",me,x[i2][0],x[i2][1],x[i2][2]);
fprintf(screen," 3rd atom: %d %g %g %g\n",me,x[i3][0],x[i3][1],x[i3][2]);
fprintf(screen," 4th atom: %d %g %g %g\n",me,x[i4][0],x[i4][1],x[i4][2]);
}
}
/* Apply corrections to round-off errors. */
if (cosphi > 1.0) cosphi -= SMALL;
if (cosphi < -1.0) cosphi += SMALL;
/* Calculate the angle: */
double torangle = acos(cosphi);
cosphi = cos(torangle - chi[type]);
if (eflag) eimproper = 0.5 * k[type] * cosphi * cosphi;
/*
printf("The tags: %d-%d-%d-%d, of type %d .\n",atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4],type);
printf("The ji vector: %f, %f, %f.\nThe lk vector: %f, %f, %f.\n", vb1x,vb1y,vb1z,vb3x,vb3y,vb3z);
printf("The cosine of the angle: %-1.16e.\n", cosphi);
printf("The energy of the improper: %-1.16e with prefactor %-1.16e.\n", eimproper, 0.5*k[type]);
*/
/* Work out forces. */
angfac = - k[type] * cosphi;
cjiji = rjisq;
clklk = rlksq;
/*CLKJI = RXLK * RXJI + RYLK * RYJI + RZLK * RZJI */
clkji = vb3x*vb1x + vb3y*vb1y + vb3z*vb1z;
/*CFACT1 = CLKLK * CJIJI
CFACT1 = SQRT(CFACT1)
CFACT1 = ANGFAC / CFACT1*/
cfact1 = angfac / sqrt(clklk * cjiji);
/*CFACT2 = CLKJI / CLKLK*/
cfact2 = clkji / clklk;
/*CFACT3 = CLKJI / CJIJI*/
cfact3 = clkji / cjiji;
/*FIX = -RXLK + CFACT3 * RXJI
FIY = -RYLK + CFACT3 * RYJI
FIZ = -RZLK + CFACT3 * RZJI*/
f1[0] = - vb3x + cfact3 * vb1x;
f1[1] = - vb3y + cfact3 * vb1y;
f1[2] = - vb3z + cfact3 * vb1z;
/*FJX = -FIX
FJY = -FIY
FJZ = -FIZ*/
f2[0] = - f1[0];
f2[1] = - f1[1];
f2[2] = - f1[2];
/*FKX = CFACT2 * RXLK - RXJI
FKY = CFACT2 * RYLK - RYJI
FKZ = CFACT2 * RZLK - RZJI*/
f3[0] = cfact2 * vb3x - vb1x;
f3[1] = cfact2 * vb3y - vb1y;
f3[2] = cfact2 * vb3z - vb1z;
/*FLX = -FKX
FLY = -FKY
FLZ = -FKZ*/
f4[0] = - f3[0];
f4[1] = - f3[1];
f4[2] = - f3[2];
/*FIX = FIX * CFACT1
FIY = FIY * CFACT1
FIZ = FIZ * CFACT1*/
f1[0] *= cfact1;
f1[1] *= cfact1;
f1[2] *= cfact1;
/*FJX = FJX * CFACT1
FJY = FJY * CFACT1
FJZ = FJZ * CFACT1*/
f2[0] *= cfact1;
f2[1] *= cfact1;
f2[2] *= cfact1;
/*FKX = FKX * CFACT1
FKY = FKY * CFACT1
FKZ = FKZ * CFACT1*/
f3[0] *= cfact1;
f3[1] *= cfact1;
f3[2] *= cfact1;
/*FLX = FLX * CFACT1
FLY = FLY * CFACT1
FLZ = FLZ * CFACT1*/
f4[0] *= cfact1;
f4[1] *= cfact1;
f4[2] *= cfact1;
/* 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,f1,f3,f4,
-vb1x,-vb1y,-vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z);
}
}
/* ---------------------------------------------------------------------- */
void ImproperCossq::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 ImproperCossq::coeff(int narg, char **arg)
{
/* Check whether there exist sufficient number of arguments.
0: type of improper to be applied to
1: energetic constant
2: equilibrium angle in degrees */
if (narg != 3) error->all(FLERR,"Incorrect args for cossq 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]);
int count = 0;
for (int i = ilo; i <= ihi; i++) {
k[i] = k_one;
chi[i] = ((chi_one * MY_PI)/180.0);
setflag[i] = 1;
count++;
}
if (count == 0) error->all(FLERR,"Incorrect args for improper coefficients");
}
/* ----------------------------------------------------------------------
proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void ImproperCossq::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 ImproperCossq::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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