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improper_fourier.cpp
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Fri, Nov 1, 10:39

improper_fourier.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: Loukas D. Peristeras (Scienomics SARL)
[ based on improper_umbrella.cpp Tod A Pascal (Caltech) ]
------------------------------------------------------------------------- */
#include <mpi.h>
#include <math.h>
#include <stdlib.h>
#include <string.h>
#include "improper_fourier.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
/* ---------------------------------------------------------------------- */
ImproperFourier::ImproperFourier(LAMMPS *lmp) : Improper(lmp) {}
/* ---------------------------------------------------------------------- */
ImproperFourier::~ImproperFourier()
{
if (allocated) {
memory->destroy(setflag);
memory->destroy(k);
memory->destroy(C0);
memory->destroy(C1);
memory->destroy(C2);
}
}
/* ---------------------------------------------------------------------- */
void ImproperFourier::compute(int eflag, int vflag)
{
int i1,i2,i3,i4,n,type;
double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = 0;
double **x = atom->x;
int **improperlist = neighbor->improperlist;
int nimproperlist = neighbor->nimproperlist;
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];
// 1st bond
vb1x = x[i2][0] - x[i1][0];
vb1y = x[i2][1] - x[i1][1];
vb1z = x[i2][2] - x[i1][2];
// 2nd bond
vb2x = x[i3][0] - x[i1][0];
vb2y = x[i3][1] - x[i1][1];
vb2z = x[i3][2] - x[i1][2];
// 3rd bond
vb3x = x[i4][0] - x[i1][0];
vb3y = x[i4][1] - x[i1][1];
vb3z = x[i4][2] - x[i1][2];
addone(i1,i2,i3,i4, type,evflag,eflag,
vb1x, vb1y, vb1z,
vb2x, vb2y, vb2z,
vb3x, vb3y, vb3z);
if ( all[type] ) {
addone(i1,i4,i2,i3, type,evflag,eflag,
vb3x, vb3y, vb3z,
vb1x, vb1y, vb1z,
vb2x, vb2y, vb2z);
addone(i1,i3,i4,i2, type,evflag,eflag,
vb2x, vb2y, vb2z,
vb3x, vb3y, vb3z,
vb1x, vb1y, vb1z);
}
}
}
void ImproperFourier::addone(const int &i1,const int &i2,const int &i3,const int &i4,
const int &type,const int &evflag,const int &eflag,
const double &vb1x, const double &vb1y, const double &vb1z,
const double &vb2x, const double &vb2y, const double &vb2z,
const double &vb3x, const double &vb3y, const double &vb3z)
{
double eimproper,f1[3],f2[3],f3[3],f4[3];
double c,c2,a,s,projhfg,dhax,dhay,dhaz,dahx,dahy,dahz,cotphi;
double ax,ay,az,ra2,rh2,ra,rh,rar,rhr,arx,ary,arz,hrx,hry,hrz;
double **x = atom->x;
double **f = atom->f;
int nlocal = atom->nlocal;
int newton_bond = force->newton_bond;
eimproper = 0.0;
// c0 calculation
// A = vb1 X vb2 is perpendicular to IJK plane
ax = vb1y*vb2z-vb1z*vb2y;
ay = vb1z*vb2x-vb1x*vb2z;
az = vb1x*vb2y-vb1y*vb2x;
ra2 = ax*ax+ay*ay+az*az;
rh2 = vb3x*vb3x+vb3y*vb3y+vb3z*vb3z;
ra = sqrt(ra2);
rh = sqrt(rh2);
if (ra < SMALL) ra = SMALL;
if (rh < SMALL) rh = SMALL;
rar = 1/ra;
rhr = 1/rh;
arx = ax*rar;
ary = ay*rar;
arz = az*rar;
hrx = vb3x*rhr;
hry = vb3y*rhr;
hrz = vb3z*rhr;
c = arx*hrx+ary*hry+arz*hrz;
// error check
if (c > 1.0 + TOLERANCE || c < (-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]);
}
}
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
s = sqrt(1.0 - c*c);
if (s < SMALL) s = SMALL;
cotphi = c/s;
projhfg = (vb3x*vb1x+vb3y*vb1y+vb3z*vb1z) /
sqrt(vb1x*vb1x+vb1y*vb1y+vb1z*vb1z);
projhfg += (vb3x*vb2x+vb3y*vb2y+vb3z*vb2z) /
sqrt(vb2x*vb2x+vb2y*vb2y+vb2z*vb2z);
if (projhfg > 0.0) {
s *= -1.0;
cotphi *= -1.0;
}
// force and energy
// E = k ( C0 + C1 cos(w) + C2 cos(w)
c2 = 2.0*s*s-1.0;
if (eflag) eimproper = k[type]*(C0[type]+C1[type]*s+C2[type]*c2);
// dhax = diffrence between H and A in X direction, etc
a = k[type]*(C1[type]+4.0*C2[type]*s)*cotphi;
dhax = hrx-c*arx;
dhay = hry-c*ary;
dhaz = hrz-c*arz;
dahx = arx-c*hrx;
dahy = ary-c*hry;
dahz = arz-c*hrz;
f2[0] = (dhay*vb1z - dhaz*vb1y)*rar;
f2[1] = (dhaz*vb1x - dhax*vb1z)*rar;
f2[2] = (dhax*vb1y - dhay*vb1x)*rar;
f3[0] = (-dhay*vb2z + dhaz*vb2y)*rar;
f3[1] = (-dhaz*vb2x + dhax*vb2z)*rar;
f3[2] = (-dhax*vb2y + dhay*vb2x)*rar;
f4[0] = dahx*rhr;
f4[1] = dahy*rhr;
f4[2] = dahz*rhr;
f1[0] = -(f2[0] + f3[0] + f4[0]);
f1[1] = -(f2[1] + f3[1] + f4[1]);
f1[2] = -(f2[2] + f3[2] + f4[2]);
// apply force to each of 4 atoms
if (newton_bond || i1 < nlocal) {
f[i1][0] += f1[0]*a;
f[i1][1] += f1[1]*a;
f[i1][2] += f1[2]*a;
}
if (newton_bond || i2 < nlocal) {
f[i2][0] += f3[0]*a;
f[i2][1] += f3[1]*a;
f[i2][2] += f3[2]*a;
}
if (newton_bond || i3 < nlocal) {
f[i3][0] += f2[0]*a;
f[i3][1] += f2[1]*a;
f[i3][2] += f2[2]*a;
}
if (newton_bond || i4 < nlocal) {
f[i4][0] += f4[0]*a;
f[i4][1] += f4[1]*a;
f[i4][2] += f4[2]*a;
}
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 ImproperFourier::allocate()
{
allocated = 1;
int n = atom->nimpropertypes;
memory->create(k,n+1,"improper:k");
memory->create(C0,n+1,"improper:C0");
memory->create(C1,n+1,"improper:C1");
memory->create(C2,n+1,"improper:C2");
memory->create(all,n+1,"improper:C2");
memory->create(setflag,n+1,"improper:setflag");
for (int i = 1; i <= n; i++) setflag[i] = 0;
}
/* ----------------------------------------------------------------------
set coeffs for one type
------------------------------------------------------------------------- */
void ImproperFourier::coeff(int narg, char **arg)
{
if ( narg != 5 && narg != 6 ) 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 C0_one = force->numeric(FLERR,arg[2]);
double C1_one = force->numeric(FLERR,arg[3]);
double C2_one = force->numeric(FLERR,arg[4]);
int all_one = 1;
if ( narg == 6 ) all_one = force->inumeric(FLERR,arg[5]);
// convert w0 from degrees to radians
int count = 0;
for (int i = ilo; i <= ihi; i++) {
k[i] = k_one;
C0[i] = C0_one;
C1[i] = C1_one;
C2[i] = C2_one;
all[i] = all_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 ImproperFourier::write_restart(FILE *fp)
{
fwrite(&k[1],sizeof(double),atom->nimpropertypes,fp);
fwrite(&C0[1],sizeof(double),atom->nimpropertypes,fp);
fwrite(&C1[1],sizeof(double),atom->nimpropertypes,fp);
fwrite(&C2[1],sizeof(double),atom->nimpropertypes,fp);
fwrite(&all[1],sizeof(int),atom->nimpropertypes,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void ImproperFourier::read_restart(FILE *fp)
{
allocate();
if (comm->me == 0) {
fread(&k[1],sizeof(double),atom->nimpropertypes,fp);
fread(&C0[1],sizeof(double),atom->nimpropertypes,fp);
fread(&C1[1],sizeof(double),atom->nimpropertypes,fp);
fread(&C2[1],sizeof(double),atom->nimpropertypes,fp);
fread(&all[1],sizeof(int),atom->nimpropertypes,fp);
}
MPI_Bcast(&k[1],atom->nimpropertypes,MPI_DOUBLE,0,world);
MPI_Bcast(&C0[1],atom->nimpropertypes,MPI_DOUBLE,0,world);
MPI_Bcast(&C1[1],atom->nimpropertypes,MPI_DOUBLE,0,world);
MPI_Bcast(&C2[1],atom->nimpropertypes,MPI_DOUBLE,0,world);
MPI_Bcast(&all[1],atom->nimpropertypes,MPI_INT,0,world);
for (int i = 1; i <= atom->nimpropertypes; i++) setflag[i] = 1;
}

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