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lammps/src/USER-CGDNA/bond_oxdna_fene.cpp
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bond_oxdna_fene.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: Oliver Henrich (University of Strathclyde, Glasgow)
------------------------------------------------------------------------- */
#include <math.h>
#include <stdlib.h>
#include "bond_oxdna_fene.h"
#include "atom.h"
#include "neighbor.h"
#include "domain.h"
#include "comm.h"
#include "update.h"
#include "force.h"
#include "memory.h"
#include "error.h"
#include "atom_vec_ellipsoid.h"
#include "math_extra.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
BondOxdnaFene::BondOxdnaFene(LAMMPS *lmp) : Bond(lmp)
{
}
/* ---------------------------------------------------------------------- */
BondOxdnaFene::~BondOxdnaFene()
{
if (allocated) {
memory->destroy(setflag);
memory->destroy(k);
memory->destroy(Delta);
memory->destroy(r0);
}
}
/* ----------------------------------------------------------------------
compute vector COM-sugar-phosphate backbone interaction site in oxDNA
------------------------------------------------------------------------- */
void BondOxdnaFene::compute_interaction_sites(double e1[3],
double e2[3], double r[3])
{
double d_cs=-0.4;
r[0] = d_cs*e1[0];
r[1] = d_cs*e1[1];
r[2] = d_cs*e1[2];
}
/* ----------------------------------------------------------------------
compute function for oxDNA FENE-bond interaction
s=sugar-phosphate backbone site, b=base site, st=stacking site
------------------------------------------------------------------------- */
void BondOxdnaFene::compute(int eflag, int vflag)
{
int a,b,in,type;
double delf[3],delta[3],deltb[3]; // force, torque increment;;
double delr[3],ebond,fbond;
double rsq,Deltasq,rlogarg;
double r,rr0,rr0sq;
// vectors COM-backbone site in lab frame
double ra_cs[3],rb_cs[3];
double *qa,ax[3],ay[3],az[3];
double *qb,bx[3],by[3],bz[3];
double **x = atom->x;
double **f = atom->f;
double **torque = atom->torque;
AtomVecEllipsoid *avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
AtomVecEllipsoid::Bonus *bonus = avec->bonus;
int **bondlist = neighbor->bondlist;
int nbondlist = neighbor->nbondlist;
int nlocal = atom->nlocal;
int newton_bond = force->newton_bond;
ebond = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = 0;
// loop over FENE bonds
for (in = 0; in < nbondlist; in++) {
a = bondlist[in][1];
b = bondlist[in][0];
type = bondlist[in][2];
qa=bonus[a].quat;
MathExtra::q_to_exyz(qa,ax,ay,az);
qb=bonus[b].quat;
MathExtra::q_to_exyz(qb,bx,by,bz);
// vector COM-backbone site a and b
compute_interaction_sites(ax,ay,ra_cs);
compute_interaction_sites(bx,by,rb_cs);
// vector backbone site b to a
delr[0] = x[a][0] + ra_cs[0] - x[b][0] - rb_cs[0];
delr[1] = x[a][1] + ra_cs[1] - x[b][1] - rb_cs[1];
delr[2] = x[a][2] + ra_cs[2] - x[b][2] - rb_cs[2];
rsq = delr[0]*delr[0] + delr[1]*delr[1] + delr[2]*delr[2];
r = sqrt(rsq);
rr0 = r - r0[type];
rr0sq = rr0*rr0;
Deltasq = Delta[type] * Delta[type];
rlogarg = 1.0 - rr0sq/Deltasq;
// if r -> Delta, then rlogarg < 0.0 which is an error
// issue a warning and reset rlogarg = epsilon
// if r > 2*Delta something serious is wrong, abort
if (rlogarg < 0.1) {
char str[128];
sprintf(str,"FENE bond too long: " BIGINT_FORMAT " "
TAGINT_FORMAT " " TAGINT_FORMAT " %g",
update->ntimestep,atom->tag[a],atom->tag[b],r);
error->warning(FLERR,str,0);
if (rlogarg <= -3.0) error->one(FLERR,"Bad FENE bond");
}
fbond = -k[type]*rr0/rlogarg/Deltasq/r;
delf[0] = delr[0]*fbond;
delf[1] = delr[1]*fbond;
delf[2] = delr[2]*fbond;
// energy
if (eflag) {
ebond = -0.5 * k[type]*log(rlogarg);
}
// apply force and torque to each of 2 atoms
if (newton_bond || a < nlocal) {
f[a][0] += delf[0];
f[a][1] += delf[1];
f[a][2] += delf[2];
MathExtra::cross3(ra_cs,delf,delta);
torque[a][0] += delta[0];
torque[a][1] += delta[1];
torque[a][2] += delta[2];
}
if (newton_bond || b < nlocal) {
f[b][0] -= delf[0];
f[b][1] -= delf[1];
f[b][2] -= delf[2];
MathExtra::cross3(rb_cs,delf,deltb);
torque[b][0] -= deltb[0];
torque[b][1] -= deltb[1];
torque[b][2] -= deltb[2];
}
// increment energy and virial
if (evflag) ev_tally(a,b,nlocal,newton_bond,ebond,fbond,delr[0],delr[1],delr[2]);
}
}
/* ---------------------------------------------------------------------- */
void BondOxdnaFene::allocate()
{
allocated = 1;
int n = atom->nbondtypes;
memory->create(k,n+1,"bond:k");
memory->create(Delta,n+1,"bond:Delta");
memory->create(r0,n+1,"bond:r0");
memory->create(setflag,n+1,"bond:setflag");
for (int i = 1; i <= n; i++) setflag[i] = 0;
}
/* ----------------------------------------------------------------------
set coeffs for one type
------------------------------------------------------------------------- */
void BondOxdnaFene::coeff(int narg, char **arg)
{
if (narg != 4) error->all(FLERR,"Incorrect args for bond coefficients in oxdna/fene");
if (!allocated) allocate();
int ilo,ihi;
force->bounds(FLERR,arg[0],atom->nbondtypes,ilo,ihi);
double k_one = force->numeric(FLERR,arg[1]);
double Delta_one = force->numeric(FLERR,arg[2]);
double r0_one = force->numeric(FLERR,arg[3]);
int count = 0;
for (int i = ilo; i <= ihi; i++) {
k[i] = k_one;
Delta[i] = Delta_one;
r0[i] = r0_one;
setflag[i] = 1;
count++;
}
if (count == 0) error->all(FLERR,"Incorrect args for bond coefficients in oxdna/fene");
}
/* ----------------------------------------------------------------------
set special_bond settings and check if valid
------------------------------------------------------------------------- */
void BondOxdnaFene::init_style()
{
/* special bonds have to be lj = 0 1 1 and coul = 1 1 1 to exclude
the ss excluded volume interaction between nearest neighbours */
force->special_lj[1] = 0.0;
force->special_lj[2] = 1.0;
force->special_lj[3] = 1.0;
force->special_coul[1] = 1.0;
force->special_coul[2] = 1.0;
force->special_coul[3] = 1.0;
fprintf(screen,"Finding 1-2 1-3 1-4 neighbors ...\n"
" Special bond factors lj: %-10g %-10g %-10g\n"
" Special bond factors coul: %-10g %-10g %-10g\n",
force->special_lj[1],force->special_lj[2],force->special_lj[3],
force->special_coul[1],force->special_coul[2],force->special_coul[3]);
if (force->special_lj[1] != 0.0 || force->special_lj[2] != 1.0 || force->special_lj[3] != 1.0 ||
force->special_coul[1] != 1.0 || force->special_coul[2] != 1.0 || force->special_coul[3] != 1.0)
{
if (comm->me == 0)
error->warning(FLERR,"Use special bonds lj = 0,1,1 and coul = 1,1,1 with bond style oxdna/fene");
}
}
/* ---------------------------------------------------------------------- */
double BondOxdnaFene::equilibrium_distance(int i)
{
return r0[i];
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void BondOxdnaFene::write_restart(FILE *fp)
{
fwrite(&k[1],sizeof(double),atom->nbondtypes,fp);
fwrite(&Delta[1],sizeof(double),atom->nbondtypes,fp);
fwrite(&r0[1],sizeof(double),atom->nbondtypes,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void BondOxdnaFene::read_restart(FILE *fp)
{
allocate();
if (comm->me == 0) {
fread(&k[1],sizeof(double),atom->nbondtypes,fp);
fread(&Delta[1],sizeof(double),atom->nbondtypes,fp);
fread(&r0[1],sizeof(double),atom->nbondtypes,fp);
}
MPI_Bcast(&k[1],atom->nbondtypes,MPI_DOUBLE,0,world);
MPI_Bcast(&Delta[1],atom->nbondtypes,MPI_DOUBLE,0,world);
MPI_Bcast(&r0[1],atom->nbondtypes,MPI_DOUBLE,0,world);
for (int i = 1; i <= atom->nbondtypes; i++) setflag[i] = 1;
}
/* ----------------------------------------------------------------------
proc 0 writes to data file
------------------------------------------------------------------------- */
void BondOxdnaFene::write_data(FILE *fp)
{
for (int i = 1; i <= atom->nbondtypes; i++)
fprintf(fp,"%d %g %g %g\n",i,k[i],r0[i],Delta[i]);
}
/* ---------------------------------------------------------------------- */
double BondOxdnaFene::single(int type, double rsq, int i, int j,
double &fforce)
{
double r = sqrt(rsq);
double rr0 = r - r0[type];
double rr0sq = rr0*rr0;
double Deltasq = Delta[type] * Delta[type];
double rlogarg = 1.0 - rr0sq/Deltasq;
// if r -> Delta, then rlogarg < 0.0 which is an error
// issue a warning and reset rlogarg = epsilon
// if r > 2*Delta something serious is wrong, abort
if (rlogarg < 0.1) {
char str[128];
sprintf(str,"FENE bond too long: " BIGINT_FORMAT " %g",
update->ntimestep,sqrt(rsq));
error->warning(FLERR,str,0);
if (rlogarg <= -3.0) error->one(FLERR,"Bad FENE bond");
}
double eng = -0.5 * k[type]*log(rlogarg);
fforce = -k[type]*rr0/rlogarg/Deltasq/r;
return eng;
}
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