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pair_oxdna2_coaxstk.cpp
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Sun, Jun 9, 07:52

pair_oxdna2_coaxstk.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 <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "pair_oxdna2_coaxstk.h"
#include "mf_oxdna.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "update.h"
#include "integrate.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
#include "atom_vec_ellipsoid.h"
#include "math_extra.h"
using namespace LAMMPS_NS;
using namespace MathConst;
using namespace MFOxdna;
/* ---------------------------------------------------------------------- */
PairOxdna2Coaxstk::PairOxdna2Coaxstk(LAMMPS *lmp) : Pair(lmp)
{
single_enable = 0;
writedata = 1;
}
/* ---------------------------------------------------------------------- */
PairOxdna2Coaxstk::~PairOxdna2Coaxstk()
{
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
memory->destroy(k_cxst);
memory->destroy(cut_cxst_0);
memory->destroy(cut_cxst_c);
memory->destroy(cut_cxst_lo);
memory->destroy(cut_cxst_hi);
memory->destroy(cut_cxst_lc);
memory->destroy(cut_cxst_hc);
memory->destroy(b_cxst_lo);
memory->destroy(b_cxst_hi);
memory->destroy(a_cxst1);
memory->destroy(theta_cxst1_0);
memory->destroy(dtheta_cxst1_ast);
memory->destroy(b_cxst1);
memory->destroy(dtheta_cxst1_c);
memory->destroy(a_cxst4);
memory->destroy(theta_cxst4_0);
memory->destroy(dtheta_cxst4_ast);
memory->destroy(b_cxst4);
memory->destroy(dtheta_cxst4_c);
memory->destroy(a_cxst5);
memory->destroy(theta_cxst5_0);
memory->destroy(dtheta_cxst5_ast);
memory->destroy(b_cxst5);
memory->destroy(dtheta_cxst5_c);
memory->destroy(a_cxst6);
memory->destroy(theta_cxst6_0);
memory->destroy(dtheta_cxst6_ast);
memory->destroy(b_cxst6);
memory->destroy(dtheta_cxst6_c);
memory->destroy(AA_cxst1);
memory->destroy(BB_cxst1);
}
}
/* ----------------------------------------------------------------------
compute function for oxDNA pair interactions
st=stacking site
------------------------------------------------------------------------- */
void PairOxdna2Coaxstk::compute(int eflag, int vflag)
{
double delf[3],delt[3],delta[3],deltb[3]; // force, torque increment;
double evdwl,fpair,finc,tpair,factor_lj;
double v1tmp[3],v2tmp[3],v3tmp[3];
double delr_ss[3],delr_ss_norm[3],rsq_ss,r_ss,rinv_ss;
double delr_st[3],delr_st_norm[3],rsq_st,r_st,rinv_st;
double theta1,theta1p,t1dir[3],cost1;
double theta4,t4dir[3],cost4;
double theta5,theta5p,t5dir[3],cost5;
double theta6,theta6p,t6dir[3],cost6;
double cosphi3;
double gamma,gammacub,rinv_ss_cub,fac;
double aybx,azbx,rax,ray,raz,rbx;
double dcdr,dcdrbx;
double dcdaxbx,dcdaybx,dcdazbx;
double dcdrax,dcdray,dcdraz;
// distances COM-backbone site, COM-stacking site
double d_cs=-0.4, d_cst=+0.34;
// vectors COM-backbone site, COM-stacking site in lab frame
double ra_cs[3],ra_cst[3];
double rb_cs[3],rb_cst[3];
// quaternions and Cartesian unit vectors in lab frame
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;
int *type = atom->type;
int nlocal = atom->nlocal;
int newton_pair = force->newton_pair;
int *alist,*blist,*numneigh,**firstneigh;
double *special_lj = force->special_lj;
AtomVecEllipsoid *avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
AtomVecEllipsoid::Bonus *bonus = avec->bonus;
int a,b,ia,ib,anum,bnum,atype,btype;
double f2,f4f6t1,f4t4,f4t5,f4t6;
double df2,df4f6t1,df4t4,df4t5,df4t6,rsint;
evdwl = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
anum = list->inum;
alist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over pair interaction neighbours of my atoms
for (ia = 0; ia < anum; ia++) {
a = alist[ia];
atype = type[a];
qa=bonus[a].quat;
MathExtra::q_to_exyz(qa,ax,ay,az);
// vector COM a - stacking site a
ra_cst[0] = d_cst*ax[0];
ra_cst[1] = d_cst*ax[1];
ra_cst[2] = d_cst*ax[2];
// vector COM a - backbone site a
ra_cs[0] = d_cs*ax[0];
ra_cs[1] = d_cs*ax[1];
ra_cs[2] = d_cs*ax[2];
blist = firstneigh[a];
bnum = numneigh[a];
for (ib = 0; ib < bnum; ib++) {
b = blist[ib];
factor_lj = special_lj[sbmask(b)]; // = 0 for nearest neighbours
b &= NEIGHMASK;
btype = type[b];
qb=bonus[b].quat;
MathExtra::q_to_exyz(qb,bx,by,bz);
// vector COM b - stacking site b
rb_cst[0] = d_cst*bx[0];
rb_cst[1] = d_cst*bx[1];
rb_cst[2] = d_cst*bx[2];
// vector stacking site b to a
delr_st[0] = x[a][0] + ra_cst[0] - x[b][0] - rb_cst[0];
delr_st[1] = x[a][1] + ra_cst[1] - x[b][1] - rb_cst[1];
delr_st[2] = x[a][2] + ra_cst[2] - x[b][2] - rb_cst[2];
rsq_st = delr_st[0]*delr_st[0] + delr_st[1]*delr_st[1] + delr_st[2]*delr_st[2];
r_st = sqrt(rsq_st);
rinv_st = 1.0/r_st;
delr_st_norm[0] = delr_st[0] * rinv_st;
delr_st_norm[1] = delr_st[1] * rinv_st;
delr_st_norm[2] = delr_st[2] * rinv_st;
// vector COM b - backbone site b
rb_cs[0] = d_cs*bx[0];
rb_cs[1] = d_cs*bx[1];
rb_cs[2] = d_cs*bx[2];
// vector backbone site b to a
delr_ss[0] = (x[a][0] + ra_cs[0] - x[b][0] - rb_cs[0]);
delr_ss[1] = (x[a][1] + ra_cs[1] - x[b][1] - rb_cs[1]);
delr_ss[2] = (x[a][2] + ra_cs[2] - x[b][2] - rb_cs[2]);
rsq_ss = delr_ss[0]*delr_ss[0] + delr_ss[1]*delr_ss[1] + delr_ss[2]*delr_ss[2];
r_ss = sqrt(rsq_ss);
rinv_ss = 1.0/r_ss;
delr_ss_norm[0] = delr_ss[0] * rinv_ss;
delr_ss_norm[1] = delr_ss[1] * rinv_ss;
delr_ss_norm[2] = delr_ss[2] * rinv_ss;
cost1 = -1.0*MathExtra::dot3(ax,bx);
if (cost1 > 1.0) cost1 = 1.0;
if (cost1 < -1.0) cost1 = -1.0;
theta1 = acos(cost1);
theta1p = 2 * MY_PI - theta1;
f4f6t1 = F4(theta1, a_cxst1[atype][btype], theta_cxst1_0[atype][btype], dtheta_cxst1_ast[atype][btype],
b_cxst1[atype][btype], dtheta_cxst1_c[atype][btype]) +
F6(theta1, AA_cxst1[atype][btype], BB_cxst1[atype][btype]);
// early rejection criterium
if (f4f6t1) {
cost4 = MathExtra::dot3(az,bz);
if (cost4 > 1.0) cost4 = 1.0;
if (cost4 < -1.0) cost4 = -1.0;
theta4 = acos(cost4);
f4t4 = F4(theta4, a_cxst4[atype][btype], theta_cxst4_0[atype][btype], dtheta_cxst4_ast[atype][btype],
b_cxst4[atype][btype], dtheta_cxst4_c[atype][btype]);
// early rejection criterium
if (f4t4) {
cost5 = MathExtra::dot3(delr_st_norm,az);
if (cost5 > 1.0) cost5 = 1.0;
if (cost5 < -1.0) cost5 = -1.0;
theta5 = acos(cost5);
theta5p = MY_PI - theta5;
f4t5 = F4(theta5, a_cxst5[atype][btype], theta_cxst5_0[atype][btype], dtheta_cxst5_ast[atype][btype],
b_cxst5[atype][btype], dtheta_cxst5_c[atype][btype]) +
F4(theta5p, a_cxst5[atype][btype], theta_cxst5_0[atype][btype], dtheta_cxst5_ast[atype][btype],
b_cxst5[atype][btype], dtheta_cxst5_c[atype][btype]);
// early rejection criterium
if (f4t5) {
cost6 = MathExtra::dot3(delr_st_norm,bz);
if (cost6 > 1.0) cost6 = 1.0;
if (cost6 < -1.0) cost6 = -1.0;
theta6 = acos(cost6);
theta6p = MY_PI - theta6;
f4t6 = F4(theta6, a_cxst6[atype][btype], theta_cxst6_0[atype][btype], dtheta_cxst6_ast[atype][btype],
b_cxst6[atype][btype], dtheta_cxst6_c[atype][btype]) +
F4(theta6p, a_cxst6[atype][btype], theta_cxst6_0[atype][btype], dtheta_cxst6_ast[atype][btype],
b_cxst6[atype][btype], dtheta_cxst6_c[atype][btype]);
MathExtra::cross3(delr_ss_norm,ax,v1tmp);
cosphi3 = MathExtra::dot3(delr_st_norm,v1tmp);
if (cosphi3 > 1.0) cosphi3 = 1.0;
if (cosphi3 < -1.0) cosphi3 = -1.0;
f2 = F2(r_st, k_cxst[atype][btype], cut_cxst_0[atype][btype],
cut_cxst_lc[atype][btype], cut_cxst_hc[atype][btype], cut_cxst_lo[atype][btype], cut_cxst_hi[atype][btype],
b_cxst_lo[atype][btype], b_cxst_hi[atype][btype], cut_cxst_c[atype][btype]);
evdwl = f2 * f4f6t1 * f4t4 * f4t5 * f4t6 * factor_lj;
// early rejection criterium
if (evdwl) {
df2 = DF2(r_st, k_cxst[atype][btype], cut_cxst_0[atype][btype],
cut_cxst_lc[atype][btype], cut_cxst_hc[atype][btype], cut_cxst_lo[atype][btype], cut_cxst_hi[atype][btype],
b_cxst_lo[atype][btype], b_cxst_hi[atype][btype]);
rsint = 1.0/sin(theta1);
df4f6t1 = DF4(theta1, a_cxst1[atype][btype], theta_cxst1_0[atype][btype], dtheta_cxst1_ast[atype][btype],
b_cxst1[atype][btype], dtheta_cxst1_c[atype][btype])*rsint +
DF6(theta1, AA_cxst1[atype][btype], BB_cxst1[atype][btype])*rsint;
df4t4 = DF4(theta4, a_cxst4[atype][btype], theta_cxst4_0[atype][btype], dtheta_cxst4_ast[atype][btype],
b_cxst4[atype][btype], dtheta_cxst4_c[atype][btype])/sin(theta4);
rsint = 1.0/sin(theta5);
df4t5 = DF4(theta5, a_cxst5[atype][btype], theta_cxst5_0[atype][btype], dtheta_cxst5_ast[atype][btype],
b_cxst5[atype][btype], dtheta_cxst5_c[atype][btype])*rsint -
DF4(theta5p, a_cxst5[atype][btype], theta_cxst5_0[atype][btype], dtheta_cxst5_ast[atype][btype],
b_cxst5[atype][btype], dtheta_cxst5_c[atype][btype])*rsint;
rsint = 1.0/sin(theta6);
df4t6 = DF4(theta6, a_cxst6[atype][btype], theta_cxst6_0[atype][btype], dtheta_cxst6_ast[atype][btype],
b_cxst6[atype][btype], dtheta_cxst6_c[atype][btype])*rsint -
DF4(theta6p, a_cxst6[atype][btype], theta_cxst6_0[atype][btype], dtheta_cxst6_ast[atype][btype],
b_cxst6[atype][btype], dtheta_cxst6_c[atype][btype])*rsint;
// force, torque and virial contribution for forces between stacking sites
fpair = 0.0;
delf[0] = 0.0;
delf[1] = 0.0;
delf[2] = 0.0;
delta[0] = 0.0;
delta[1] = 0.0;
delta[2] = 0.0;
deltb[0] = 0.0;
deltb[1] = 0.0;
deltb[2] = 0.0;
// radial force
finc = -df2 * f4f6t1 * f4t4 * f4t5 * f4t6 * rinv_st * factor_lj;
fpair += finc;
delf[0] += delr_st[0] * finc;
delf[1] += delr_st[1] * finc;
delf[2] += delr_st[2] * finc;
// theta5 force
if (theta5 && theta5p) {
finc = -f2 * f4f6t1 * f4t4 * df4t5 * f4t6 * rinv_st * factor_lj;
fpair += finc;
delf[0] += (delr_st_norm[0]*cost5 - az[0]) * finc;
delf[1] += (delr_st_norm[1]*cost5 - az[1]) * finc;
delf[2] += (delr_st_norm[2]*cost5 - az[2]) * finc;
}
// theta6 force
if (theta6 && theta6p) {
finc = -f2 * f4f6t1* f4t4 * f4t5 * df4t6 * rinv_st * factor_lj;
fpair += finc;
delf[0] += (delr_st_norm[0]*cost6 - bz[0]) * finc;
delf[1] += (delr_st_norm[1]*cost6 - bz[1]) * finc;
delf[2] += (delr_st_norm[2]*cost6 - bz[2]) * finc;
}
// increment forces and torques
f[a][0] += delf[0];
f[a][1] += delf[1];
f[a][2] += delf[2];
MathExtra::cross3(ra_cst,delf,delta);
torque[a][0] += delta[0];
torque[a][1] += delta[1];
torque[a][2] += delta[2];
if (newton_pair || b < nlocal) {
f[b][0] -= delf[0];
f[b][1] -= delf[1];
f[b][2] -= delf[2];
MathExtra::cross3(rb_cst,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_pair,evdwl,0.0,fpair,delr_st[0],delr_st[1],delr_st[2]);
// pure torques not expressible as r x f
delta[0] = 0.0;
delta[1] = 0.0;
delta[2] = 0.0;
deltb[0] = 0.0;
deltb[1] = 0.0;
deltb[2] = 0.0;
// theta1 torque
if (theta1 && theta1p) {
tpair = -f2 * df4f6t1 * f4t4 * f4t5 * f4t6 * factor_lj;
MathExtra::cross3(ax,bx,t1dir);
delta[0] += t1dir[0]*tpair;
delta[1] += t1dir[1]*tpair;
delta[2] += t1dir[2]*tpair;
deltb[0] += t1dir[0]*tpair;
deltb[1] += t1dir[1]*tpair;
deltb[2] += t1dir[2]*tpair;
}
// theta4 torque
if (theta4) {
tpair = -f2 * f4f6t1 * df4t4 * f4t5 * f4t6 * factor_lj;
MathExtra::cross3(bz,az,t4dir);
delta[0] += t4dir[0]*tpair;
delta[1] += t4dir[1]*tpair;
delta[2] += t4dir[2]*tpair;
deltb[0] += t4dir[0]*tpair;
deltb[1] += t4dir[1]*tpair;
deltb[2] += t4dir[2]*tpair;
}
// theta5 torque
if (theta5 && theta5p) {
tpair = -f2 * f4f6t1 * f4t4 * df4t5 * f4t6 * factor_lj;
MathExtra::cross3(delr_st_norm,az,t5dir);
delta[0] += t5dir[0] * tpair;
delta[1] += t5dir[1] * tpair;
delta[2] += t5dir[2] * tpair;
}
// theta6 torque
if (theta6 && theta6p) {
tpair = -f2 * f4f6t1 * f4t4 * f4t5 * df4t6 * factor_lj;
MathExtra::cross3(delr_st_norm,bz,t6dir);
deltb[0] -= t6dir[0] * tpair;
deltb[1] -= t6dir[1] * tpair;
deltb[2] -= t6dir[2] * tpair;
}
// increment torques
torque[a][0] += delta[0];
torque[a][1] += delta[1];
torque[a][2] += delta[2];
if (newton_pair || b < nlocal) {
torque[b][0] -= deltb[0];
torque[b][1] -= deltb[1];
torque[b][2] -= deltb[2];
}
}
}
}
}// end early rejection criteria
}
}
if (vflag_fdotr) virial_fdotr_compute();
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairOxdna2Coaxstk::allocate()
{
allocated = 1;
int n = atom->ntypes;
memory->create(setflag,n+1,n+1,"pair:setflag");
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
setflag[i][j] = 0;
memory->create(cutsq,n+1,n+1,"pair:cutsq");
memory->create(k_cxst,n+1,n+1,"pair:k_cxst");
memory->create(cut_cxst_0,n+1,n+1,"pair:cut_cxst_0");
memory->create(cut_cxst_c,n+1,n+1,"pair:cut_cxst_c");
memory->create(cut_cxst_lo,n+1,n+1,"pair:cut_cxst_lo");
memory->create(cut_cxst_hi,n+1,n+1,"pair:cut_cxst_hi");
memory->create(cut_cxst_lc,n+1,n+1,"pair:cut_cxst_lc");
memory->create(cut_cxst_hc,n+1,n+1,"pair:cut_cxst_hc");
memory->create(b_cxst_lo,n+1,n+1,"pair:b_cxst_lo");
memory->create(b_cxst_hi,n+1,n+1,"pair:b_cxst_hi");
memory->create(cutsq_cxst_hc,n+1,n+1,"pair:cutsq_cxst_hc");
memory->create(a_cxst1,n+1,n+1,"pair:a_cxst1");
memory->create(theta_cxst1_0,n+1,n+1,"pair:theta_cxst1_0");
memory->create(dtheta_cxst1_ast,n+1,n+1,"pair:dtheta_cxst1_ast");
memory->create(b_cxst1,n+1,n+1,"pair:b_cxst1");
memory->create(dtheta_cxst1_c,n+1,n+1,"pair:dtheta_cxst1_c");
memory->create(a_cxst4,n+1,n+1,"pair:a_cxst4");
memory->create(theta_cxst4_0,n+1,n+1,"pair:theta_cxst4_0");
memory->create(dtheta_cxst4_ast,n+1,n+1,"pair:dtheta_cxst4_ast");
memory->create(b_cxst4,n+1,n+1,"pair:b_cxst4");
memory->create(dtheta_cxst4_c,n+1,n+1,"pair:dtheta_cxst4_c");
memory->create(a_cxst5,n+1,n+1,"pair:a_cxst5");
memory->create(theta_cxst5_0,n+1,n+1,"pair:theta_cxst5_0");
memory->create(dtheta_cxst5_ast,n+1,n+1,"pair:dtheta_cxst5_ast");
memory->create(b_cxst5,n+1,n+1,"pair:b_cxst5");
memory->create(dtheta_cxst5_c,n+1,n+1,"pair:dtheta_cxst5_c");
memory->create(a_cxst6,n+1,n+1,"pair:a_cxst6");
memory->create(theta_cxst6_0,n+1,n+1,"pair:theta_cxst6_0");
memory->create(dtheta_cxst6_ast,n+1,n+1,"pair:dtheta_cxst6_ast");
memory->create(b_cxst6,n+1,n+1,"pair:b_cxst6");
memory->create(dtheta_cxst6_c,n+1,n+1,"pair:dtheta_cxst6_c");
memory->create(AA_cxst1,n+1,n+1,"pair:AA_cxst1");
memory->create(BB_cxst1,n+1,n+1,"pair:BB_cxst1");
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairOxdna2Coaxstk::settings(int narg, char **arg)
{
if (narg != 0) error->all(FLERR,"Illegal pair_style command");
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairOxdna2Coaxstk::coeff(int narg, char **arg)
{
int count;
if (narg != 21) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/coaxstk");
if (!allocated) allocate();
int ilo,ihi,jlo,jhi;
force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi);
force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi);
// cross-stacking interaction
count = 0;
double k_cxst_one, cut_cxst_0_one, cut_cxst_c_one, cut_cxst_lo_one, cut_cxst_hi_one;
double b_cxst_lo_one, b_cxst_hi_one, cut_cxst_lc_one, cut_cxst_hc_one;
double a_cxst1_one, theta_cxst1_0_one, dtheta_cxst1_ast_one;
double b_cxst1_one, dtheta_cxst1_c_one;
double a_cxst4_one, theta_cxst4_0_one, dtheta_cxst4_ast_one;
double b_cxst4_one, dtheta_cxst4_c_one;
double a_cxst5_one, theta_cxst5_0_one, dtheta_cxst5_ast_one;
double b_cxst5_one, dtheta_cxst5_c_one;
double a_cxst6_one, theta_cxst6_0_one, dtheta_cxst6_ast_one;
double b_cxst6_one, dtheta_cxst6_c_one;
double AA_cxst1_one, BB_cxst1_one;
k_cxst_one = force->numeric(FLERR,arg[2]);
cut_cxst_0_one = force->numeric(FLERR,arg[3]);
cut_cxst_c_one = force->numeric(FLERR,arg[4]);
cut_cxst_lo_one = force->numeric(FLERR,arg[5]);
cut_cxst_hi_one = force->numeric(FLERR,arg[6]);
a_cxst1_one = force->numeric(FLERR,arg[7]);
theta_cxst1_0_one = force->numeric(FLERR,arg[8]);
dtheta_cxst1_ast_one = force->numeric(FLERR,arg[9]);
a_cxst4_one = force->numeric(FLERR,arg[10]);
theta_cxst4_0_one = force->numeric(FLERR,arg[11]);
dtheta_cxst4_ast_one = force->numeric(FLERR,arg[12]);
a_cxst5_one = force->numeric(FLERR,arg[13]);
theta_cxst5_0_one = force->numeric(FLERR,arg[14]);
dtheta_cxst5_ast_one = force->numeric(FLERR,arg[15]);
a_cxst6_one = force->numeric(FLERR,arg[16]);
theta_cxst6_0_one = force->numeric(FLERR,arg[17]);
dtheta_cxst6_ast_one = force->numeric(FLERR,arg[18]);
AA_cxst1_one = force->numeric(FLERR,arg[19]);
BB_cxst1_one = force->numeric(FLERR,arg[20]);
b_cxst_lo_one = 0.25 * (cut_cxst_lo_one - cut_cxst_0_one) * (cut_cxst_lo_one - cut_cxst_0_one)/
(0.5 * (cut_cxst_lo_one - cut_cxst_0_one) * (cut_cxst_lo_one - cut_cxst_0_one) -
k_cxst_one * 0.5 * (cut_cxst_0_one -cut_cxst_c_one) * (cut_cxst_0_one - cut_cxst_c_one)/k_cxst_one);
cut_cxst_lc_one = cut_cxst_lo_one - 0.5 * (cut_cxst_lo_one - cut_cxst_0_one)/b_cxst_lo_one;;
b_cxst_hi_one = 0.25 * (cut_cxst_hi_one - cut_cxst_0_one) * (cut_cxst_hi_one - cut_cxst_0_one)/
(0.5 * (cut_cxst_hi_one - cut_cxst_0_one) * (cut_cxst_hi_one - cut_cxst_0_one) -
k_cxst_one * 0.5 * (cut_cxst_0_one -cut_cxst_c_one) * (cut_cxst_0_one - cut_cxst_c_one)/k_cxst_one);
cut_cxst_hc_one = cut_cxst_hi_one - 0.5* (cut_cxst_hi_one - cut_cxst_0_one)/b_cxst_hi_one;
b_cxst1_one = a_cxst1_one*a_cxst1_one*dtheta_cxst1_ast_one*dtheta_cxst1_ast_one/(1-a_cxst1_one*dtheta_cxst1_ast_one*dtheta_cxst1_ast_one);
dtheta_cxst1_c_one = 1/(a_cxst1_one*dtheta_cxst1_ast_one);
b_cxst4_one = a_cxst4_one*a_cxst4_one*dtheta_cxst4_ast_one*dtheta_cxst4_ast_one/(1-a_cxst4_one*dtheta_cxst4_ast_one*dtheta_cxst4_ast_one);
dtheta_cxst4_c_one = 1/(a_cxst4_one*dtheta_cxst4_ast_one);
b_cxst5_one = a_cxst5_one*a_cxst5_one*dtheta_cxst5_ast_one*dtheta_cxst5_ast_one/(1-a_cxst5_one*dtheta_cxst5_ast_one*dtheta_cxst5_ast_one);
dtheta_cxst5_c_one = 1/(a_cxst5_one*dtheta_cxst5_ast_one);
b_cxst6_one = a_cxst6_one*a_cxst6_one*dtheta_cxst6_ast_one*dtheta_cxst6_ast_one/(1-a_cxst6_one*dtheta_cxst6_ast_one*dtheta_cxst6_ast_one);
dtheta_cxst6_c_one = 1/(a_cxst6_one*dtheta_cxst6_ast_one);
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j <= jhi; j++) {
k_cxst[i][j] = k_cxst_one;
cut_cxst_0[i][j] = cut_cxst_0_one;
cut_cxst_c[i][j] = cut_cxst_c_one;
cut_cxst_lo[i][j] = cut_cxst_lo_one;
cut_cxst_hi[i][j] = cut_cxst_hi_one;
cut_cxst_lc[i][j] = cut_cxst_lc_one;
cut_cxst_hc[i][j] = cut_cxst_hc_one;
b_cxst_lo[i][j] = b_cxst_lo_one;
b_cxst_hi[i][j] = b_cxst_hi_one;
a_cxst1[i][j] = a_cxst1_one;
theta_cxst1_0[i][j] = theta_cxst1_0_one;
dtheta_cxst1_ast[i][j] = dtheta_cxst1_ast_one;
b_cxst1[i][j] = b_cxst1_one;
dtheta_cxst1_c[i][j] = dtheta_cxst1_c_one;
a_cxst4[i][j] = a_cxst4_one;
theta_cxst4_0[i][j] = theta_cxst4_0_one;
dtheta_cxst4_ast[i][j] = dtheta_cxst4_ast_one;
b_cxst4[i][j] = b_cxst4_one;
dtheta_cxst4_c[i][j] = dtheta_cxst4_c_one;
a_cxst5[i][j] = a_cxst5_one;
theta_cxst5_0[i][j] = theta_cxst5_0_one;
dtheta_cxst5_ast[i][j] = dtheta_cxst5_ast_one;
b_cxst5[i][j] = b_cxst5_one;
dtheta_cxst5_c[i][j] = dtheta_cxst5_c_one;
a_cxst6[i][j] = a_cxst6_one;
theta_cxst6_0[i][j] = theta_cxst6_0_one;
dtheta_cxst6_ast[i][j] = dtheta_cxst6_ast_one;
b_cxst6[i][j] = b_cxst6_one;
dtheta_cxst6_c[i][j] = dtheta_cxst6_c_one;
AA_cxst1[i][j] = AA_cxst1_one;
BB_cxst1[i][j] = BB_cxst1_one;
setflag[i][j] = 1;
count++;
}
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/coaxstk");
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairOxdna2Coaxstk::init_style()
{
int irequest;
// request regular neighbor lists
irequest = neighbor->request(this,instance_me);
}
/* ----------------------------------------------------------------------
neighbor callback to inform pair style of neighbor list to use regular
------------------------------------------------------------------------- */
void PairOxdna2Coaxstk::init_list(int id, NeighList *ptr)
{
if (id == 0) list = ptr;
if (id > 0) error->all(FLERR,"Respa not supported");
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairOxdna2Coaxstk::init_one(int i, int j)
{
if (setflag[i][j] == 0) {
error->all(FLERR,"Coefficient mixing not defined in oxDNA");
}
if (offset_flag) {
error->all(FLERR,"Offset not supported in oxDNA");
}
k_cxst[j][i] = k_cxst[i][j];
cut_cxst_0[j][i] = cut_cxst_0[i][j];
cut_cxst_c[j][i] = cut_cxst_c[i][j];
cut_cxst_lo[j][i] = cut_cxst_lo[i][j];
cut_cxst_hi[j][i] = cut_cxst_hi[i][j];
b_cxst_lo[j][i] = b_cxst_lo[i][j];
b_cxst_hi[j][i] = b_cxst_hi[i][j];
cut_cxst_lc[j][i] = cut_cxst_lc[i][j];
cut_cxst_hc[j][i] = cut_cxst_hc[i][j];
a_cxst1[j][i] = a_cxst1[i][j];
theta_cxst1_0[j][i] = theta_cxst1_0[i][j];
dtheta_cxst1_ast[j][i] = dtheta_cxst1_ast[i][j];
b_cxst1[j][i] = b_cxst1[i][j];
dtheta_cxst1_c[j][i] = dtheta_cxst1_c[i][j];
a_cxst4[j][i] = a_cxst4[i][j];
theta_cxst4_0[j][i] = theta_cxst4_0[i][j];
dtheta_cxst4_ast[j][i] = dtheta_cxst4_ast[i][j];
b_cxst4[j][i] = b_cxst4[i][j];
dtheta_cxst4_c[j][i] = dtheta_cxst4_c[i][j];
a_cxst5[j][i] = a_cxst5[i][j];
theta_cxst5_0[j][i] = theta_cxst5_0[i][j];
dtheta_cxst5_ast[j][i] = dtheta_cxst5_ast[i][j];
b_cxst5[j][i] = b_cxst5[i][j];
dtheta_cxst5_c[j][i] = dtheta_cxst5_c[i][j];
a_cxst6[j][i] = a_cxst6[i][j];
theta_cxst6_0[j][i] = theta_cxst6_0[i][j];
dtheta_cxst6_ast[j][i] = dtheta_cxst6_ast[i][j];
b_cxst6[j][i] = b_cxst6[i][j];
dtheta_cxst6_c[j][i] = dtheta_cxst6_c[i][j];
AA_cxst1[j][i] = AA_cxst1[i][j];
BB_cxst1[j][i] = BB_cxst1[i][j];
cutsq_cxst_hc[i][j] = cut_cxst_hc[i][j]*cut_cxst_hc[i][j];
cutsq_cxst_hc[j][i] = cutsq_cxst_hc[i][j];
// set the master list distance cutoff
return cut_cxst_hc[i][j];
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairOxdna2Coaxstk::write_restart(FILE *fp)
{
write_restart_settings(fp);
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
fwrite(&k_cxst[i][j],sizeof(double),1,fp);
fwrite(&cut_cxst_0[i][j],sizeof(double),1,fp);
fwrite(&cut_cxst_c[i][j],sizeof(double),1,fp);
fwrite(&cut_cxst_lo[i][j],sizeof(double),1,fp);
fwrite(&cut_cxst_hi[i][j],sizeof(double),1,fp);
fwrite(&cut_cxst_lc[i][j],sizeof(double),1,fp);
fwrite(&cut_cxst_hc[i][j],sizeof(double),1,fp);
fwrite(&b_cxst_lo[i][j],sizeof(double),1,fp);
fwrite(&b_cxst_hi[i][j],sizeof(double),1,fp);
fwrite(&a_cxst1[i][j],sizeof(double),1,fp);
fwrite(&theta_cxst1_0[i][j],sizeof(double),1,fp);
fwrite(&dtheta_cxst1_ast[i][j],sizeof(double),1,fp);
fwrite(&b_cxst1[i][j],sizeof(double),1,fp);
fwrite(&dtheta_cxst1_c[i][j],sizeof(double),1,fp);
fwrite(&a_cxst4[i][j],sizeof(double),1,fp);
fwrite(&theta_cxst4_0[i][j],sizeof(double),1,fp);
fwrite(&dtheta_cxst4_ast[i][j],sizeof(double),1,fp);
fwrite(&b_cxst4[i][j],sizeof(double),1,fp);
fwrite(&dtheta_cxst4_c[i][j],sizeof(double),1,fp);
fwrite(&a_cxst5[i][j],sizeof(double),1,fp);
fwrite(&theta_cxst5_0[i][j],sizeof(double),1,fp);
fwrite(&dtheta_cxst5_ast[i][j],sizeof(double),1,fp);
fwrite(&b_cxst5[i][j],sizeof(double),1,fp);
fwrite(&dtheta_cxst5_c[i][j],sizeof(double),1,fp);
fwrite(&a_cxst6[i][j],sizeof(double),1,fp);
fwrite(&theta_cxst6_0[i][j],sizeof(double),1,fp);
fwrite(&dtheta_cxst6_ast[i][j],sizeof(double),1,fp);
fwrite(&b_cxst6[i][j],sizeof(double),1,fp);
fwrite(&dtheta_cxst6_c[i][j],sizeof(double),1,fp);
fwrite(&AA_cxst1[i][j],sizeof(double),1,fp);
fwrite(&BB_cxst1[i][j],sizeof(double),1,fp);
}
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairOxdna2Coaxstk::read_restart(FILE *fp)
{
read_restart_settings(fp);
allocate();
int i,j;
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
if (me == 0) {
fread(&k_cxst[i][j],sizeof(double),1,fp);
fread(&cut_cxst_0[i][j],sizeof(double),1,fp);
fread(&cut_cxst_c[i][j],sizeof(double),1,fp);
fread(&cut_cxst_lo[i][j],sizeof(double),1,fp);
fread(&cut_cxst_hi[i][j],sizeof(double),1,fp);
fread(&cut_cxst_lc[i][j],sizeof(double),1,fp);
fread(&cut_cxst_hc[i][j],sizeof(double),1,fp);
fread(&b_cxst_lo[i][j],sizeof(double),1,fp);
fread(&b_cxst_hi[i][j],sizeof(double),1,fp);
fread(&a_cxst1[i][j],sizeof(double),1,fp);
fread(&theta_cxst1_0[i][j],sizeof(double),1,fp);
fread(&dtheta_cxst1_ast[i][j],sizeof(double),1,fp);
fread(&b_cxst1[i][j],sizeof(double),1,fp);
fread(&dtheta_cxst1_c[i][j],sizeof(double),1,fp);
fread(&a_cxst4[i][j],sizeof(double),1,fp);
fread(&theta_cxst4_0[i][j],sizeof(double),1,fp);
fread(&dtheta_cxst4_ast[i][j],sizeof(double),1,fp);
fread(&b_cxst4[i][j],sizeof(double),1,fp);
fread(&dtheta_cxst4_c[i][j],sizeof(double),1,fp);
fread(&a_cxst5[i][j],sizeof(double),1,fp);
fread(&theta_cxst5_0[i][j],sizeof(double),1,fp);
fread(&dtheta_cxst5_ast[i][j],sizeof(double),1,fp);
fread(&b_cxst5[i][j],sizeof(double),1,fp);
fread(&dtheta_cxst5_c[i][j],sizeof(double),1,fp);
fread(&a_cxst6[i][j],sizeof(double),1,fp);
fread(&theta_cxst6_0[i][j],sizeof(double),1,fp);
fread(&dtheta_cxst6_ast[i][j],sizeof(double),1,fp);
fread(&b_cxst6[i][j],sizeof(double),1,fp);
fread(&dtheta_cxst6_c[i][j],sizeof(double),1,fp);
fread(&AA_cxst1[i][j],sizeof(double),1,fp);
fread(&BB_cxst1[i][j],sizeof(double),1,fp);
}
MPI_Bcast(&k_cxst[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_cxst_0[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_cxst_c[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_cxst_lo[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_cxst_hi[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_cxst_lc[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_cxst_hc[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&b_cxst_lo[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&b_cxst_hi[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&a_cxst1[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&theta_cxst1_0[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&dtheta_cxst1_ast[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&b_cxst1[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&dtheta_cxst1_c[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&a_cxst4[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&theta_cxst4_0[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&dtheta_cxst4_ast[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&b_cxst4[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&dtheta_cxst4_c[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&a_cxst5[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&theta_cxst5_0[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&dtheta_cxst5_ast[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&b_cxst5[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&dtheta_cxst5_c[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&a_cxst6[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&theta_cxst6_0[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&dtheta_cxst6_ast[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&b_cxst6[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&dtheta_cxst6_c[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&AA_cxst1[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&BB_cxst1[i][j],1,MPI_DOUBLE,0,world);
}
}
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairOxdna2Coaxstk::write_restart_settings(FILE *fp)
{
fwrite(&offset_flag,sizeof(int),1,fp);
fwrite(&mix_flag,sizeof(int),1,fp);
fwrite(&tail_flag,sizeof(int),1,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairOxdna2Coaxstk::read_restart_settings(FILE *fp)
{
int me = comm->me;
if (me == 0) {
fread(&offset_flag,sizeof(int),1,fp);
fread(&mix_flag,sizeof(int),1,fp);
fread(&tail_flag,sizeof(int),1,fp);
}
MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
MPI_Bcast(&tail_flag,1,MPI_INT,0,world);
}
/* ----------------------------------------------------------------------
proc 0 writes to data file
------------------------------------------------------------------------- */
void PairOxdna2Coaxstk::write_data(FILE *fp)
{
for (int i = 1; i <= atom->ntypes; i++)
fprintf(fp,"%d\
%g %g %g %g %g\
%g %g %g %g\
%g %g %g %g %g\
%g %g %g %g %g\
%g %g %g %g %g\
%g %g %g %g %g\
%g %g\
\n",i,
k_cxst[i][i],cut_cxst_0[i][i],cut_cxst_c[i][i],cut_cxst_lo[i][i],cut_cxst_hi[i][i],
cut_cxst_lc[i][i],cut_cxst_hc[i][i],b_cxst_lo[i][i],b_cxst_hi[i][i],
a_cxst1[i][i],theta_cxst1_0[i][i],dtheta_cxst1_ast[i][i],b_cxst1[i][i],dtheta_cxst1_c[i][i],
a_cxst4[i][i],theta_cxst4_0[i][i],dtheta_cxst4_ast[i][i],b_cxst4[i][i],dtheta_cxst4_c[i][i],
a_cxst5[i][i],theta_cxst5_0[i][i],dtheta_cxst5_ast[i][i],b_cxst5[i][i],dtheta_cxst5_c[i][i],
a_cxst6[i][i],theta_cxst6_0[i][i],dtheta_cxst6_ast[i][i],b_cxst6[i][i],dtheta_cxst6_c[i][i],
AA_cxst1[i][i],BB_cxst1[i][i]);
}
/* ----------------------------------------------------------------------
proc 0 writes all pairs to data file
------------------------------------------------------------------------- */
void PairOxdna2Coaxstk::write_data_all(FILE *fp)
{
for (int i = 1; i <= atom->ntypes; i++)
for (int j = i; j <= atom->ntypes; j++)
fprintf(fp,"%d %d\
%g %g %g %g %g\
%g %g %g %g\
%g %g %g %g %g\
%g %g %g %g %g\
%g %g %g %g %g\
%g %g %g %g %g\
%g %g\
\n",i,j,
k_cxst[i][j],cut_cxst_0[i][j],cut_cxst_c[i][j],cut_cxst_lo[i][j],cut_cxst_hi[i][j],
cut_cxst_lc[i][j],cut_cxst_hc[i][j],b_cxst_lo[i][j],b_cxst_hi[i][j],
a_cxst1[i][j],theta_cxst1_0[i][j],dtheta_cxst1_ast[i][j],b_cxst1[i][j],dtheta_cxst1_c[i][j],
a_cxst4[i][j],theta_cxst4_0[i][j],dtheta_cxst4_ast[i][j],b_cxst4[i][j],dtheta_cxst4_c[i][j],
a_cxst5[i][j],theta_cxst5_0[i][j],dtheta_cxst5_ast[i][j],b_cxst5[i][j],dtheta_cxst5_c[i][j],
a_cxst6[i][j],theta_cxst6_0[i][j],dtheta_cxst6_ast[i][j],b_cxst6[i][j],dtheta_cxst6_c[i][j],
AA_cxst1[i][j],BB_cxst1[i][j]);
}
/* ---------------------------------------------------------------------- */
void *PairOxdna2Coaxstk::extract(const char *str, int &dim)
{
dim = 2;
if (strcmp(str,"k_cxst") == 0) return (void *) k_cxst;
if (strcmp(str,"cut_cxst_0") == 0) return (void *) cut_cxst_0;
if (strcmp(str,"cut_cxst_c") == 0) return (void *) cut_cxst_c;
if (strcmp(str,"cut_cxst_lo") == 0) return (void *) cut_cxst_lo;
if (strcmp(str,"cut_cxst_hi") == 0) return (void *) cut_cxst_hi;
if (strcmp(str,"cut_cxst_lc") == 0) return (void *) cut_cxst_lc;
if (strcmp(str,"cut_cxst_hc") == 0) return (void *) cut_cxst_hc;
if (strcmp(str,"b_cxst_lo") == 0) return (void *) b_cxst_lo;
if (strcmp(str,"b_cxst_hi") == 0) return (void *) b_cxst_hi;
if (strcmp(str,"a_cxst1") == 0) return (void *) a_cxst1;
if (strcmp(str,"theta_cxst1_0") == 0) return (void *) theta_cxst1_0;
if (strcmp(str,"dtheta_cxst1_ast") == 0) return (void *) dtheta_cxst1_ast;
if (strcmp(str,"b_cxst1") == 0) return (void *) b_cxst1;
if (strcmp(str,"dtheta_cxst1_c") == 0) return (void *) dtheta_cxst1_c;
if (strcmp(str,"a_cxst4") == 0) return (void *) a_cxst4;
if (strcmp(str,"theta_cxst4_0") == 0) return (void *) theta_cxst4_0;
if (strcmp(str,"dtheta_cxst4_ast") == 0) return (void *) dtheta_cxst4_ast;
if (strcmp(str,"b_cxst4") == 0) return (void *) b_cxst4;
if (strcmp(str,"dtheta_cxst4_c") == 0) return (void *) dtheta_cxst4_c;
if (strcmp(str,"a_cxst5") == 0) return (void *) a_cxst5;
if (strcmp(str,"theta_cxst5_0") == 0) return (void *) theta_cxst5_0;
if (strcmp(str,"dtheta_cxst5_ast") == 0) return (void *) dtheta_cxst5_ast;
if (strcmp(str,"b_cxst5") == 0) return (void *) b_cxst5;
if (strcmp(str,"dtheta_cxst5_c") == 0) return (void *) dtheta_cxst5_c;
if (strcmp(str,"a_cxst6") == 0) return (void *) a_cxst6;
if (strcmp(str,"theta_cxst6_0") == 0) return (void *) theta_cxst6_0;
if (strcmp(str,"dtheta_cxst6_ast") == 0) return (void *) dtheta_cxst6_ast;
if (strcmp(str,"b_cxst6") == 0) return (void *) b_cxst6;
if (strcmp(str,"dtheta_cxst6_c") == 0) return (void *) dtheta_cxst6_c;
if (strcmp(str,"AA_cxst1") == 0) return (void *) AA_cxst1;
if (strcmp(str,"BB_cxst1") == 0) return (void *) BB_cxst1;
return NULL;
}

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