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angle_cg_cmm.cpp
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rLAMMPS lammps
angle_cg_cmm.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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Special Angle Potential for the CMM coarse grained MD potentials.
Contributing author: Axel Kohlmeyer <akohlmey@gmail.com>
------------------------------------------------------------------------- */
#include "math.h"
#include "stdlib.h"
#include "angle_cg_cmm.h"
#include "atom.h"
#include "neighbor.h"
#include "domain.h"
#include "comm.h"
#include "force.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace MathConst;
#define SMALL 0.001
/* ---------------------------------------------------------------------- */
AngleCGCMM::AngleCGCMM(LAMMPS *lmp) : Angle(lmp) {}
/* ---------------------------------------------------------------------- */
AngleCGCMM::~AngleCGCMM()
{
if (allocated) {
memory->destroy(setflag);
memory->destroy(k);
memory->destroy(theta0);
memory->destroy(cg_type);
memory->destroy(epsilon);
memory->destroy(sigma);
memory->destroy(rcut);
}
}
/* ---------------------------------------------------------------------- */
void AngleCGCMM::ev_tally_lj13(int i, int j, int nlocal, int newton_bond,
double evdwl, double fpair,
double delx, double dely, double delz)
{
double v[6];
if (eflag_either) {
if (eflag_global) {
if (newton_bond) {
energy += evdwl;
} else {
if (i < nlocal)
energy += 0.5*evdwl;
if (j < nlocal)
energy += 0.5*evdwl;
}
}
if (eflag_atom) {
if (newton_bond || i < nlocal) eatom[i] += 0.5*evdwl;
if (newton_bond || j < nlocal) eatom[i] += 0.5*evdwl;
}
}
if (vflag_either) {
v[0] = delx*delx*fpair;
v[1] = dely*dely*fpair;
v[2] = delz*delz*fpair;
v[3] = delx*dely*fpair;
v[4] = delx*delz*fpair;
v[5] = dely*delz*fpair;
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 (i < nlocal) {
virial[0] += 0.5*v[0];
virial[1] += 0.5*v[1];
virial[2] += 0.5*v[2];
virial[3] += 0.5*v[3];
virial[4] += 0.5*v[4];
virial[5] += 0.5*v[5];
}
if (j < nlocal) {
virial[0] += 0.5*v[0];
virial[1] += 0.5*v[1];
virial[2] += 0.5*v[2];
virial[3] += 0.5*v[3];
virial[4] += 0.5*v[4];
virial[5] += 0.5*v[5];
}
}
}
if (vflag_atom) {
if (newton_bond || i < nlocal) {
vatom[i][0] += 0.5*v[0];
vatom[i][1] += 0.5*v[1];
vatom[i][2] += 0.5*v[2];
vatom[i][3] += 0.5*v[3];
vatom[i][4] += 0.5*v[4];
vatom[i][5] += 0.5*v[5];
}
if (newton_bond || j < nlocal) {
vatom[j][0] += 0.5*v[0];
vatom[j][1] += 0.5*v[1];
vatom[j][2] += 0.5*v[2];
vatom[j][3] += 0.5*v[3];
vatom[j][4] += 0.5*v[4];
vatom[j][5] += 0.5*v[5];
}
}
}
}
/* ---------------------------------------------------------------------- */
void AngleCGCMM::compute(int eflag, int vflag)
{
int i1,i2,i3,n,type;
double delx1,dely1,delz1,delx2,dely2,delz2,delx3,dely3,delz3;
double eangle,f1[3],f3[3],e13,f13;
double dtheta,tk;
double rsq1,rsq2,rsq3,r1,r2,r3,c,s,a,a11,a12,a22;
eangle = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = 0;
double **x = atom->x;
double **f = atom->f;
int **anglelist = neighbor->anglelist;
int nanglelist = neighbor->nanglelist;
int nlocal = atom->nlocal;
int newton_bond = force->newton_bond;
for (n = 0; n < nanglelist; n++) {
i1 = anglelist[n][0];
i2 = anglelist[n][1];
i3 = anglelist[n][2];
type = anglelist[n][3];
// 1st bond
delx1 = x[i1][0] - x[i2][0];
dely1 = x[i1][1] - x[i2][1];
delz1 = x[i1][2] - x[i2][2];
rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1;
r1 = sqrt(rsq1);
// 2nd bond
delx2 = x[i3][0] - x[i2][0];
dely2 = x[i3][1] - x[i2][1];
delz2 = x[i3][2] - x[i2][2];
rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2;
r2 = sqrt(rsq2);
// angle (cos and sin)
c = delx1*delx2 + dely1*dely2 + delz1*delz2;
c /= r1*r2;
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;
s = 1.0/s;
// 1-3 LJ interaction.
// we only want to use the repulsive part,
// so this has to be done here and not in the
// general non-bonded code.
delx3 = x[i1][0] - x[i3][0];
dely3 = x[i1][1] - x[i3][1];
delz3 = x[i1][2] - x[i3][2];
rsq3 = delx3*delx3 + dely3*dely3 + delz3*delz3;
r3 = sqrt(rsq3);
f13=0.0;
e13=0.0;
if (r3 < rcut[type]) {
const int cgt = cg_type[type];
const double cgpow1 = cg_pow1[cgt];
const double cgpow2 = cg_pow2[cgt];
const double cgpref = cg_prefact[cgt];
const double ratio = sigma[type]/r3;
const double eps = epsilon[type];
f13 = cgpref*eps / rsq3 * (cgpow1*pow(ratio,cgpow1)
- cgpow2*pow(ratio,cgpow2));
if (eflag) e13 = eps + cgpref*eps * (pow(ratio,cgpow1)
- pow(ratio,cgpow2));
}
// force & energy
dtheta = acos(c) - theta0[type];
tk = k[type] * dtheta;
if (eflag) eangle = tk*dtheta;
a = -2.0 * tk * s;
a11 = a*c / rsq1;
a12 = -a / (r1*r2);
a22 = a*c / rsq2;
f1[0] = a11*delx1 + a12*delx2;
f1[1] = a11*dely1 + a12*dely2;
f1[2] = a11*delz1 + a12*delz2;
f3[0] = a22*delx2 + a12*delx1;
f3[1] = a22*dely2 + a12*dely1;
f3[2] = a22*delz2 + a12*delz1;
// apply force to each of 3 atoms
if (newton_bond || i1 < nlocal) {
f[i1][0] += f1[0] + f13*delx3;
f[i1][1] += f1[1] + f13*dely3;
f[i1][2] += f1[2] + f13*delz3;
}
if (newton_bond || i2 < nlocal) {
f[i2][0] -= f1[0] + f3[0];
f[i2][1] -= f1[1] + f3[1];
f[i2][2] -= f1[2] + f3[2];
}
if (newton_bond || i3 < nlocal) {
f[i3][0] += f3[0] - f13*delx3;
f[i3][1] += f3[1] - f13*dely3;
f[i3][2] += f3[2] - f13*delz3;
}
if (evflag) ev_tally(i1,i2,i3,nlocal,newton_bond,eangle,f1,f3,
delx1,dely1,delz1,delx2,dely2,delz2);
if (evflag) ev_tally_lj13(i1,i3,nlocal,newton_bond,
e13,f13,delx3,dely3,delz3);
}
}
/* ---------------------------------------------------------------------- */
void AngleCGCMM::allocate()
{
allocated = 1;
int n = atom->nangletypes;
memory->create(k,n+1,"angle:k");
memory->create(theta0,n+1,"angle:theta0");
memory->create(epsilon,n+1,"angle:epsilon");
memory->create(sigma,n+1,"angle:sigma");
memory->create(rcut,n+1,"angle:rcut");
memory->create(cg_type,n+1,"angle:cg_type");
memory->create(setflag,n+1,"angle:setflag");
for (int i = 1; i <= n; i++) {
cg_type[i] = CG_NOT_SET;
setflag[i] = 0;
}
}
/* ----------------------------------------------------------------------
set coeffs for one or more types
------------------------------------------------------------------------- */
void AngleCGCMM::coeff(int narg, char **arg)
{
if (narg != 6) error->all(FLERR,"Incorrect args for angle coefficients");
if (!allocated) allocate();
int ilo,ihi;
force->bounds(arg[0],atom->nangletypes,ilo,ihi);
double k_one = atof(arg[1]);
double theta0_one = atof(arg[2]);
int cg_type_one=find_cg_type(arg[3]);
if (cg_type_one == CG_NOT_SET) error->all(FLERR,"Error reading CG type flag.");
double epsilon_one = atof(arg[4]);
double sigma_one = atof(arg[5]);
// find minimum of LJ potential. we only want to include
// the repulsive part of the 1-3 LJ.
double rcut_one = sigma_one*exp(
1.0/(cg_pow1[cg_type_one]-cg_pow2[cg_type_one])
*log(cg_pow1[cg_type_one]/cg_pow2[cg_type_one])
);
int count = 0;
for (int i = ilo; i <= ihi; i++) {
k[i] = k_one;
// convert theta0 from degrees to radians
theta0[i] = theta0_one/180.0 * MY_PI;
epsilon[i] = epsilon_one;
sigma[i] = sigma_one;
rcut[i] = rcut_one;
cg_type[i] = cg_type_one;
setflag[i] = 1;
count++;
}
if (count == 0) error->all(FLERR,"Incorrect args for angle coefficients");
}
/* ---------------------------------------------------------------------- */
double AngleCGCMM::equilibrium_angle(int i)
{
return theta0[i];
}
/* ----------------------------------------------------------------------
proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void AngleCGCMM::write_restart(FILE *fp)
{
fwrite(&k[1],sizeof(double),atom->nangletypes,fp);
fwrite(&theta0[1],sizeof(double),atom->nangletypes,fp);
fwrite(&epsilon[1],sizeof(double),atom->nangletypes,fp);
fwrite(&sigma[1],sizeof(double),atom->nangletypes,fp);
fwrite(&rcut[1],sizeof(double),atom->nangletypes,fp);
fwrite(&cg_type[1],sizeof(int),atom->nangletypes,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void AngleCGCMM::read_restart(FILE *fp)
{
allocate();
if (comm->me == 0) {
fread(&k[1],sizeof(double),atom->nangletypes,fp);
fread(&theta0[1],sizeof(double),atom->nangletypes,fp);
fread(&epsilon[1],sizeof(double),atom->nangletypes,fp);
fread(&sigma[1],sizeof(double),atom->nangletypes,fp);
fread(&rcut[1],sizeof(double),atom->nangletypes,fp);
fread(&cg_type[1],sizeof(int),atom->nangletypes,fp);
}
MPI_Bcast(&k[1],atom->nangletypes,MPI_DOUBLE,0,world);
MPI_Bcast(&theta0[1],atom->nangletypes,MPI_DOUBLE,0,world);
MPI_Bcast(&epsilon[1],atom->nangletypes,MPI_DOUBLE,0,world);
MPI_Bcast(&sigma[1],atom->nangletypes,MPI_DOUBLE,0,world);
MPI_Bcast(&rcut[1],atom->nangletypes,MPI_DOUBLE,0,world);
MPI_Bcast(&cg_type[1],atom->nangletypes,MPI_INT,0,world);
for (int i = 1; i <= atom->nangletypes; i++) setflag[i] = 1;
}
/* ---------------------------------------------------------------------- */
double AngleCGCMM::single(int type, int i1, int i2, int i3)
{
double **x = atom->x;
double delx1 = x[i1][0] - x[i2][0];
double dely1 = x[i1][1] - x[i2][1];
double delz1 = x[i1][2] - x[i2][2];
domain->minimum_image(delx1,dely1,delz1);
double r1 = sqrt(delx1*delx1 + dely1*dely1 + delz1*delz1);
double delx2 = x[i3][0] - x[i2][0];
double dely2 = x[i3][1] - x[i2][1];
double delz2 = x[i3][2] - x[i2][2];
domain->minimum_image(delx2,dely2,delz2);
double r2 = sqrt(delx2*delx2 + dely2*dely2 + delz2*delz2);
double c = delx1*delx2 + dely1*dely2 + delz1*delz2;
c /= r1*r2;
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
// 1-3 LJ interaction.
double delx3 = x[i1][0] - x[i3][0];
double dely3 = x[i1][1] - x[i3][1];
double delz3 = x[i1][2] - x[i3][2];
domain->minimum_image(delx3,dely3,delz3);
const double r3 = sqrt(delx3*delx3 + dely3*dely3 + delz3*delz3);
double e13=0.0;
if (r3 < rcut[type]) {
const int cgt = cg_type[type];
const double cgpow1 = cg_pow1[cgt];
const double cgpow2 = cg_pow2[cgt];
const double cgpref = cg_prefact[cgt];
const double ratio = sigma[type]/r3;
const double eps = epsilon[type];
e13 = eps + cgpref*eps * (pow(ratio,cgpow1)
- pow(ratio,cgpow2));
}
double dtheta = acos(c) - theta0[type];
double tk = k[type] * dtheta;
return tk*dtheta + e13;
}
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