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lammps/src/CG-DNA/pair_oxdna_excv.cpp
Axel Kohlmeyer efaec31a84 rename USER-CGDNA and USER-CGSDK to CG-DNA and CG-SDK
2021-06-29 15:28:27 -04:00

831 lines
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// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, 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 "pair_oxdna_excv.h"
#include "atom.h"
#include "atom_vec_ellipsoid.h"
#include "comm.h"
#include "error.h"
#include "force.h"
#include "math_extra.h"
#include "memory.h"
#include "mf_oxdna.h"
#include "neigh_list.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;
using namespace MFOxdna;
/* ---------------------------------------------------------------------- */
PairOxdnaExcv::PairOxdnaExcv(LAMMPS *lmp) : Pair(lmp)
{
single_enable = 0;
writedata = 1;
}
/* ---------------------------------------------------------------------- */
PairOxdnaExcv::~PairOxdnaExcv()
{
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
memory->destroy(epsilon_ss);
memory->destroy(sigma_ss);
memory->destroy(cut_ss_ast);
memory->destroy(b_ss);
memory->destroy(cut_ss_c);
memory->destroy(lj1_ss);
memory->destroy(lj2_ss);
memory->destroy(cutsq_ss_ast);
memory->destroy(cutsq_ss_c);
memory->destroy(epsilon_sb);
memory->destroy(sigma_sb);
memory->destroy(cut_sb_ast);
memory->destroy(b_sb);
memory->destroy(cut_sb_c);
memory->destroy(lj1_sb);
memory->destroy(lj2_sb);
memory->destroy(cutsq_sb_ast);
memory->destroy(cutsq_sb_c);
memory->destroy(epsilon_bb);
memory->destroy(sigma_bb);
memory->destroy(cut_bb_ast);
memory->destroy(b_bb);
memory->destroy(cut_bb_c);
memory->destroy(lj1_bb);
memory->destroy(lj2_bb);
memory->destroy(cutsq_bb_ast);
memory->destroy(cutsq_bb_c);
}
}
/* ----------------------------------------------------------------------
compute vector COM-excluded volume interaction sites in oxDNA
------------------------------------------------------------------------- */
void PairOxdnaExcv::compute_interaction_sites(double e1[3], double /*e2*/[3],
double /*e3*/[3], double rs[3], double rb[3])
{
double d_cs=-0.4, d_cb=+0.4;
rs[0] = d_cs*e1[0];
rs[1] = d_cs*e1[1];
rs[2] = d_cs*e1[2];
rb[0] = d_cb*e1[0];
rb[1] = d_cb*e1[1];
rb[2] = d_cb*e1[2];
}
/* ----------------------------------------------------------------------
compute function for oxDNA pair interactions
s=sugar-phosphate backbone site, b=base site, st=stacking site
------------------------------------------------------------------------- */
void PairOxdnaExcv::compute(int eflag, int vflag)
{
double delf[3],delta[3],deltb[3]; // force, torque increment;
double evdwl,fpair,factor_lj;
double rtmp_s[3],rtmp_b[3];
double delr_ss[3],rsq_ss,delr_sb[3],rsq_sb;
double delr_bs[3],rsq_bs,delr_bb[3],rsq_bb;
// vectors COM-backbone site, COM-base site in lab frame
double ra_cs[3],ra_cb[3];
double rb_cs[3],rb_cb[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 *special_lj = force->special_lj;
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;
AtomVecEllipsoid *avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
AtomVecEllipsoid::Bonus *bonus = avec->bonus;
int *ellipsoid = atom->ellipsoid;
int a,b,ia,ib,anum,bnum,atype,btype;
evdwl = 0.0;
ev_init(eflag,vflag);
anum = list->inum;
alist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over pair interaction neighbors of my atoms
for (ia = 0; ia < anum; ia++) {
a = alist[ia];
atype = type[a];
qa=bonus[ellipsoid[a]].quat;
MathExtra::q_to_exyz(qa,ax,ay,az);
// vector COM - backbone and base site a
compute_interaction_sites(ax,ay,az,ra_cs,ra_cb);
rtmp_s[0] = x[a][0] + ra_cs[0];
rtmp_s[1] = x[a][1] + ra_cs[1];
rtmp_s[2] = x[a][2] + ra_cs[2];
rtmp_b[0] = x[a][0] + ra_cb[0];
rtmp_b[1] = x[a][1] + ra_cb[1];
rtmp_b[2] = x[a][2] + ra_cb[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 neighbors
b &= NEIGHMASK;
btype = type[b];
qb=bonus[ellipsoid[b]].quat;
MathExtra::q_to_exyz(qb,bx,by,bz);
// vector COM - backbone and base site b
compute_interaction_sites(bx,by,bz,rb_cs,rb_cb);
// vector backbone site b to a
delr_ss[0] = rtmp_s[0] - (x[b][0] + rb_cs[0]);
delr_ss[1] = rtmp_s[1] - (x[b][1] + rb_cs[1]);
delr_ss[2] = rtmp_s[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];
// vector base site b to backbone site a
delr_sb[0] = rtmp_s[0] - (x[b][0] + rb_cb[0]);
delr_sb[1] = rtmp_s[1] - (x[b][1] + rb_cb[1]);
delr_sb[2] = rtmp_s[2] - (x[b][2] + rb_cb[2]);
rsq_sb = delr_sb[0]*delr_sb[0] + delr_sb[1]*delr_sb[1] + delr_sb[2]*delr_sb[2];
// vector backbone site b to base site a
delr_bs[0] = rtmp_b[0] - (x[b][0] + rb_cs[0]);
delr_bs[1] = rtmp_b[1] - (x[b][1] + rb_cs[1]);
delr_bs[2] = rtmp_b[2] - (x[b][2] + rb_cs[2]);
rsq_bs = delr_bs[0]*delr_bs[0] + delr_bs[1]*delr_bs[1] + delr_bs[2]*delr_bs[2];
// vector base site b to a
delr_bb[0] = rtmp_b[0] - (x[b][0] + rb_cb[0]);
delr_bb[1] = rtmp_b[1] - (x[b][1] + rb_cb[1]);
delr_bb[2] = rtmp_b[2] - (x[b][2] + rb_cb[2]);
rsq_bb = delr_bb[0]*delr_bb[0] + delr_bb[1]*delr_bb[1] + delr_bb[2]*delr_bb[2];
// excluded volume interaction
// backbone-backbone
if (rsq_ss < cutsq_ss_c[atype][btype]) {
evdwl = F3(rsq_ss,cutsq_ss_ast[atype][btype],cut_ss_c[atype][btype],lj1_ss[atype][btype],
lj2_ss[atype][btype],epsilon_ss[atype][btype],b_ss[atype][btype],fpair);
// knock out nearest-neighbor interaction between ss
fpair *= factor_lj;
evdwl *= factor_lj;
delf[0] = delr_ss[0]*fpair;
delf[1] = delr_ss[1]*fpair;
delf[2] = delr_ss[2]*fpair;
// increment energy and virial
// NOTE: The virial is calculated on the 'molecular' basis.
// (see G. Ciccotti and J.P. Ryckaert, Comp. Phys. Rep. 4, 345-392 (1986))
if (evflag) ev_tally_xyz(a,b,nlocal,newton_pair,evdwl,0.0,
delf[0],delf[1],delf[2],x[a][0]-x[b][0],x[a][1]-x[b][1],x[a][2]-x[b][2]);
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_pair || 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];
}
}
// backbone-base
if (rsq_sb < cutsq_sb_c[atype][btype]) {
evdwl = F3(rsq_sb,cutsq_sb_ast[atype][btype],cut_sb_c[atype][btype],lj1_sb[atype][btype],
lj2_sb[atype][btype],epsilon_sb[atype][btype],b_sb[atype][btype],fpair);
delf[0] = delr_sb[0]*fpair;
delf[1] = delr_sb[1]*fpair;
delf[2] = delr_sb[2]*fpair;
// increment energy and virial
if (evflag) ev_tally_xyz(a,b,nlocal,newton_pair,evdwl,0.0,
delf[0],delf[1],delf[2],x[a][0]-x[b][0],x[a][1]-x[b][1],x[a][2]-x[b][2]);
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_pair || b < nlocal) {
f[b][0] -= delf[0];
f[b][1] -= delf[1];
f[b][2] -= delf[2];
MathExtra::cross3(rb_cb,delf,deltb);
torque[b][0] -= deltb[0];
torque[b][1] -= deltb[1];
torque[b][2] -= deltb[2];
}
}
// base-backbone
if (rsq_bs < cutsq_sb_c[atype][btype]) {
evdwl = F3(rsq_bs,cutsq_sb_ast[atype][btype],cut_sb_c[atype][btype],lj1_sb[atype][btype],
lj2_sb[atype][btype],epsilon_sb[atype][btype],b_sb[atype][btype],fpair);
delf[0] = delr_bs[0]*fpair;
delf[1] = delr_bs[1]*fpair;
delf[2] = delr_bs[2]*fpair;
// increment energy and virial
if (evflag) ev_tally_xyz(a,b,nlocal,newton_pair,evdwl,0.0,
delf[0],delf[1],delf[2],x[a][0]-x[b][0],x[a][1]-x[b][1],x[a][2]-x[b][2]);
f[a][0] += delf[0];
f[a][1] += delf[1];
f[a][2] += delf[2];
MathExtra::cross3(ra_cb,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_cs,delf,deltb);
torque[b][0] -= deltb[0];
torque[b][1] -= deltb[1];
torque[b][2] -= deltb[2];
}
}
// base-base
if (rsq_bb < cutsq_bb_c[atype][btype]) {
evdwl = F3(rsq_bb,cutsq_bb_ast[atype][btype],cut_bb_c[atype][btype],lj1_bb[atype][btype],
lj2_bb[atype][btype],epsilon_bb[atype][btype],b_bb[atype][btype],fpair);
delf[0] = delr_bb[0]*fpair;
delf[1] = delr_bb[1]*fpair;
delf[2] = delr_bb[2]*fpair;
// increment energy and virial
if (evflag) ev_tally_xyz(a,b,nlocal,newton_pair,evdwl,0.0,
delf[0],delf[1],delf[2],x[a][0]-x[b][0],x[a][1]-x[b][1],x[a][2]-x[b][2]);
f[a][0] += delf[0];
f[a][1] += delf[1];
f[a][2] += delf[2];
MathExtra::cross3(ra_cb,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_cb,delf,deltb);
torque[b][0] -= deltb[0];
torque[b][1] -= deltb[1];
torque[b][2] -= deltb[2];
}
}
// end excluded volume interaction
}
}
if (vflag_fdotr) virial_fdotr_compute();
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairOxdnaExcv::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(epsilon_ss,n+1,n+1,"pair:epsilon_ss");
memory->create(sigma_ss,n+1,n+1,"pair:sigma_ss");
memory->create(cut_ss_ast,n+1,n+1,"pair:cut_ss_ast");
memory->create(b_ss,n+1,n+1,"pair:b_ss");
memory->create(cut_ss_c,n+1,n+1,"pair:cut_ss_c");
memory->create(lj1_ss,n+1,n+1,"pair:lj1_ss");
memory->create(lj2_ss,n+1,n+1,"pair:lj2_ss");
memory->create(cutsq_ss_ast,n+1,n+1,"pair:cutsq_ss_ast");
memory->create(cutsq_ss_c,n+1,n+1,"pair:cutsq_ss_c");
memory->create(epsilon_sb,n+1,n+1,"pair:epsilon_sb");
memory->create(sigma_sb,n+1,n+1,"pair:sigma_sb");
memory->create(cut_sb_ast,n+1,n+1,"pair:cut_sb_ast");
memory->create(b_sb,n+1,n+1,"pair:b_sb");
memory->create(cut_sb_c,n+1,n+1,"pair:cut_sb_c");
memory->create(lj1_sb,n+1,n+1,"pair:lj1_sb");
memory->create(lj2_sb,n+1,n+1,"pair:lj2_sb");
memory->create(cutsq_sb_ast,n+1,n+1,"pair:cutsq_sb_ast");
memory->create(cutsq_sb_c,n+1,n+1,"pair:cutsq_sb_c");
memory->create(epsilon_bb,n+1,n+1,"pair:epsilon_bb");
memory->create(sigma_bb,n+1,n+1,"pair:sigma_bb");
memory->create(cut_bb_ast,n+1,n+1,"pair:cut_bb_ast");
memory->create(b_bb,n+1,n+1,"pair:b_bb");
memory->create(cut_bb_c,n+1,n+1,"pair:cut_bb_c");
memory->create(lj1_bb,n+1,n+1,"pair:lj1_bb");
memory->create(lj2_bb,n+1,n+1,"pair:lj2_bb");
memory->create(cutsq_bb_ast,n+1,n+1,"pair:cutsq_bb_ast");
memory->create(cutsq_bb_c,n+1,n+1,"pair:cutsq_bb_c");
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairOxdnaExcv::settings(int narg, char **/*arg*/)
{
if (narg != 0) error->all(FLERR,"Illegal pair_style command");
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairOxdnaExcv::coeff(int narg, char **arg)
{
int count;
if (narg != 11) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/excv");
if (!allocated) allocate();
int ilo,ihi,jlo,jhi;
utils::bounds(FLERR,arg[0],1,atom->ntypes,ilo,ihi,error);
utils::bounds(FLERR,arg[1],1,atom->ntypes,jlo,jhi,error);
count = 0;
double epsilon_ss_one, sigma_ss_one;
double cut_ss_ast_one, cut_ss_c_one, b_ss_one;
double epsilon_sb_one, sigma_sb_one;
double cut_sb_ast_one, cut_sb_c_one, b_sb_one;
double epsilon_bb_one, sigma_bb_one;
double cut_bb_ast_one, cut_bb_c_one, b_bb_one;
// Excluded volume interaction
// LJ parameters
epsilon_ss_one = utils::numeric(FLERR,arg[2],false,lmp);
sigma_ss_one = utils::numeric(FLERR,arg[3],false,lmp);
cut_ss_ast_one = utils::numeric(FLERR,arg[4],false,lmp);
// smoothing - determined through continuity and differentiability
b_ss_one = 4.0/sigma_ss_one
*(6.0*pow(sigma_ss_one/cut_ss_ast_one,7)-12.0*pow(sigma_ss_one/cut_ss_ast_one,13))
*4.0/sigma_ss_one*(6.0*pow(sigma_ss_one/cut_ss_ast_one,7)-12.0*pow(sigma_ss_one/cut_ss_ast_one,13))
/4.0/(4.0*(pow(sigma_ss_one/cut_ss_ast_one,12)-pow(sigma_ss_one/cut_ss_ast_one,6)));
cut_ss_c_one = cut_ss_ast_one
- 2.0*4.0*(pow(sigma_ss_one/cut_ss_ast_one,12)-pow(sigma_ss_one/cut_ss_ast_one,6))
/(4.0/sigma_ss_one*(6.0*pow(sigma_ss_one/cut_ss_ast_one,7)-12.0*pow(sigma_ss_one/cut_ss_ast_one,13)));
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j <= jhi; j++) {
epsilon_ss[i][j] = epsilon_ss_one;
sigma_ss[i][j] = sigma_ss_one;
cut_ss_ast[i][j] = cut_ss_ast_one;
b_ss[i][j] = b_ss_one;
cut_ss_c[i][j] = cut_ss_c_one;
setflag[i][j] = 1;
count++;
}
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/excv");
count = 0;
// LJ parameters
epsilon_sb_one = utils::numeric(FLERR,arg[5],false,lmp);
sigma_sb_one = utils::numeric(FLERR,arg[6],false,lmp);
cut_sb_ast_one = utils::numeric(FLERR,arg[7],false,lmp);
// smoothing - determined through continuity and differentiability
b_sb_one = 4.0/sigma_sb_one
*(6.0*pow(sigma_sb_one/cut_sb_ast_one,7)-12.0*pow(sigma_sb_one/cut_sb_ast_one,13))
*4.0/sigma_sb_one*(6.0*pow(sigma_sb_one/cut_sb_ast_one,7)-12.0*pow(sigma_sb_one/cut_sb_ast_one,13))
/4.0/(4.0*(pow(sigma_sb_one/cut_sb_ast_one,12)-pow(sigma_sb_one/cut_sb_ast_one,6)));
cut_sb_c_one = cut_sb_ast_one
- 2.0*4.0*(pow(sigma_sb_one/cut_sb_ast_one,12)-pow(sigma_sb_one/cut_sb_ast_one,6))
/(4.0/sigma_sb_one*(6.0*pow(sigma_sb_one/cut_sb_ast_one,7)-12.0*pow(sigma_sb_one/cut_sb_ast_one,13)));
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j <= jhi; j++) {
epsilon_sb[i][j] = epsilon_sb_one;
sigma_sb[i][j] = sigma_sb_one;
cut_sb_ast[i][j] = cut_sb_ast_one;
b_sb[i][j] = b_sb_one;
cut_sb_c[i][j] = cut_sb_c_one;
setflag[i][j] = 1;
count++;
}
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/excv");
count = 0;
// LJ parameters
epsilon_bb_one = utils::numeric(FLERR,arg[8],false,lmp);
sigma_bb_one = utils::numeric(FLERR,arg[9],false,lmp);
cut_bb_ast_one = utils::numeric(FLERR,arg[10],false,lmp);
// smoothing - determined through continuity and differentiability
b_bb_one = 4.0/sigma_bb_one
*(6.0*pow(sigma_bb_one/cut_bb_ast_one,7)-12.0*pow(sigma_bb_one/cut_bb_ast_one,13))
*4.0/sigma_bb_one*(6.0*pow(sigma_bb_one/cut_bb_ast_one,7)-12.0*pow(sigma_bb_one/cut_bb_ast_one,13))
/4.0/(4.0*(pow(sigma_bb_one/cut_bb_ast_one,12)-pow(sigma_bb_one/cut_bb_ast_one,6)));
cut_bb_c_one = cut_bb_ast_one
- 2.0*4.0*(pow(sigma_bb_one/cut_bb_ast_one,12)-pow(sigma_bb_one/cut_bb_ast_one,6))
/(4.0/sigma_bb_one*(6.0*pow(sigma_bb_one/cut_bb_ast_one,7)-12.0*pow(sigma_bb_one/cut_bb_ast_one,13)));
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j <= jhi; j++) {
epsilon_bb[i][j] = epsilon_bb_one;
sigma_bb[i][j] = sigma_bb_one;
cut_bb_ast[i][j] = cut_bb_ast_one;
b_bb[i][j] = b_bb_one;
cut_bb_c[i][j] = cut_bb_c_one;
setflag[i][j] = 1;
count++;
}
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/excv");
}
/* ----------------------------------------------------------------------
neighbor callback to inform pair style of neighbor list to use regular
------------------------------------------------------------------------- */
void PairOxdnaExcv::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 PairOxdnaExcv::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");
}
epsilon_ss[j][i] = epsilon_ss[i][j];
sigma_ss[j][i] = sigma_ss[i][j];
cut_ss_ast[j][i] = cut_ss_ast[i][j];
cut_ss_c[j][i] = cut_ss_c[i][j];
b_ss[j][i] = b_ss[i][j];
epsilon_sb[j][i] = epsilon_sb[i][j];
sigma_sb[j][i] = sigma_sb[i][j];
cut_sb_ast[j][i] = cut_sb_ast[i][j];
cut_sb_c[j][i] = cut_sb_c[i][j];
b_sb[j][i] = b_sb[i][j];
epsilon_bb[j][i] = epsilon_bb[i][j];
sigma_bb[j][i] = sigma_bb[i][j];
cut_bb_ast[j][i] = cut_bb_ast[i][j];
cut_bb_c[j][i] = cut_bb_c[i][j];
b_bb[j][i] = b_bb[i][j];
// excluded volume auxiliary parameters
lj1_ss[i][j] = 4.0 * epsilon_ss[i][j] * pow(sigma_ss[i][j],12.0);
lj2_ss[i][j] = 4.0 * epsilon_ss[i][j] * pow(sigma_ss[i][j],6.0);
lj1_sb[i][j] = 4.0 * epsilon_sb[i][j] * pow(sigma_sb[i][j],12.0);
lj2_sb[i][j] = 4.0 * epsilon_sb[i][j] * pow(sigma_sb[i][j],6.0);
lj1_bb[i][j] = 4.0 * epsilon_bb[i][j] * pow(sigma_bb[i][j],12.0);
lj2_bb[i][j] = 4.0 * epsilon_bb[i][j] * pow(sigma_bb[i][j],6.0);
lj1_ss[j][i] = lj1_ss[i][j];
lj2_ss[j][i] = lj2_ss[i][j];
lj1_sb[j][i] = lj1_sb[i][j];
lj2_sb[j][i] = lj2_sb[i][j];
lj1_bb[j][i] = lj1_bb[i][j];
lj2_bb[j][i] = lj2_bb[i][j];
cutsq_ss_ast[i][j] = cut_ss_ast[i][j]*cut_ss_ast[i][j];
cutsq_ss_c[i][j] = cut_ss_c[i][j]*cut_ss_c[i][j];
cutsq_sb_ast[i][j] = cut_sb_ast[i][j]*cut_sb_ast[i][j];
cutsq_sb_c[i][j] = cut_sb_c[i][j]*cut_sb_c[i][j];
cutsq_bb_ast[i][j] = cut_bb_ast[i][j]*cut_bb_ast[i][j];
cutsq_bb_c[i][j] = cut_bb_c[i][j]*cut_bb_c[i][j];
cutsq_ss_ast[j][i] = cutsq_ss_ast[i][j];
cutsq_ss_c[j][i] = cutsq_ss_c[i][j];
cutsq_sb_ast[j][i] = cutsq_sb_ast[i][j];
cutsq_sb_c[j][i] = cutsq_sb_c[i][j];
cutsq_bb_ast[j][i] = cutsq_bb_ast[i][j];
cutsq_bb_c[j][i] = cutsq_bb_c[i][j];
// set the master list distance cutoff
return cut_ss_c[i][j];
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairOxdnaExcv::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(&epsilon_ss[i][j],sizeof(double),1,fp);
fwrite(&sigma_ss[i][j],sizeof(double),1,fp);
fwrite(&cut_ss_ast[i][j],sizeof(double),1,fp);
fwrite(&b_ss[i][j],sizeof(double),1,fp);
fwrite(&cut_ss_c[i][j],sizeof(double),1,fp);
fwrite(&epsilon_sb[i][j],sizeof(double),1,fp);
fwrite(&sigma_sb[i][j],sizeof(double),1,fp);
fwrite(&cut_sb_ast[i][j],sizeof(double),1,fp);
fwrite(&b_sb[i][j],sizeof(double),1,fp);
fwrite(&cut_sb_c[i][j],sizeof(double),1,fp);
fwrite(&epsilon_bb[i][j],sizeof(double),1,fp);
fwrite(&sigma_bb[i][j],sizeof(double),1,fp);
fwrite(&cut_bb_ast[i][j],sizeof(double),1,fp);
fwrite(&b_bb[i][j],sizeof(double),1,fp);
fwrite(&cut_bb_c[i][j],sizeof(double),1,fp);
}
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairOxdnaExcv::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) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,nullptr,error);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
if (me == 0) {
utils::sfread(FLERR,&epsilon_ss[i][j],sizeof(double),1,fp,nullptr,error);
utils::sfread(FLERR,&sigma_ss[i][j],sizeof(double),1,fp,nullptr,error);
utils::sfread(FLERR,&cut_ss_ast[i][j],sizeof(double),1,fp,nullptr,error);
utils::sfread(FLERR,&b_ss[i][j],sizeof(double),1,fp,nullptr,error);
utils::sfread(FLERR,&cut_ss_c[i][j],sizeof(double),1,fp,nullptr,error);
utils::sfread(FLERR,&epsilon_sb[i][j],sizeof(double),1,fp,nullptr,error);
utils::sfread(FLERR,&sigma_sb[i][j],sizeof(double),1,fp,nullptr,error);
utils::sfread(FLERR,&cut_sb_ast[i][j],sizeof(double),1,fp,nullptr,error);
utils::sfread(FLERR,&b_sb[i][j],sizeof(double),1,fp,nullptr,error);
utils::sfread(FLERR,&cut_sb_c[i][j],sizeof(double),1,fp,nullptr,error);
utils::sfread(FLERR,&epsilon_bb[i][j],sizeof(double),1,fp,nullptr,error);
utils::sfread(FLERR,&sigma_bb[i][j],sizeof(double),1,fp,nullptr,error);
utils::sfread(FLERR,&cut_bb_ast[i][j],sizeof(double),1,fp,nullptr,error);
utils::sfread(FLERR,&b_bb[i][j],sizeof(double),1,fp,nullptr,error);
utils::sfread(FLERR,&cut_bb_c[i][j],sizeof(double),1,fp,nullptr,error);
}
MPI_Bcast(&epsilon_ss[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&sigma_ss[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_ss_ast[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&b_ss[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_ss_c[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&epsilon_sb[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&sigma_sb[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_sb_ast[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&b_sb[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_sb_c[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&epsilon_bb[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&sigma_bb[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_bb_ast[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&b_bb[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_bb_c[i][j],1,MPI_DOUBLE,0,world);
}
}
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairOxdnaExcv::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 PairOxdnaExcv::read_restart_settings(FILE *fp)
{
int me = comm->me;
if (me == 0) {
utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,nullptr,error);
utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,nullptr,error);
utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,nullptr,error);
}
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 PairOxdnaExcv::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\
\n",i,
epsilon_ss[i][i],sigma_ss[i][i],cut_ss_ast[i][i],b_ss[i][i],cut_ss_c[i][i],
epsilon_sb[i][i],sigma_sb[i][i],cut_sb_ast[i][i],b_sb[i][i],cut_sb_c[i][i],
epsilon_bb[i][i],sigma_bb[i][i],cut_bb_ast[i][i],b_bb[i][i],cut_bb_c[i][i]);
}
/* ----------------------------------------------------------------------
proc 0 writes all pairs to data file
------------------------------------------------------------------------- */
void PairOxdnaExcv::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\
\n",i,j,
epsilon_ss[i][j],sigma_ss[i][j],cut_ss_ast[i][j],b_ss[i][j],cut_ss_c[i][j],
epsilon_sb[i][j],sigma_sb[i][j],cut_sb_ast[i][j],b_sb[i][j],cut_sb_c[i][j],
epsilon_bb[i][j],sigma_bb[i][j],cut_bb_ast[i][j],b_bb[i][j],cut_bb_c[i][j]);
}
/* ---------------------------------------------------------------------- */
void *PairOxdnaExcv::extract(const char *str, int &dim)
{
dim = 2;
if (strcmp(str,"epsilon_ss") == 0) return (void *) epsilon_ss;
if (strcmp(str,"sigma_ss") == 0) return (void *) sigma_ss;
if (strcmp(str,"cut_ss_ast") == 0) return (void *) cut_ss_ast;
if (strcmp(str,"b_ss") == 0) return (void *) b_ss;
if (strcmp(str,"cut_ss_c") == 0) return (void *) cut_ss_c;
if (strcmp(str,"epsilon_sb") == 0) return (void *) epsilon_sb;
if (strcmp(str,"sigma_sb") == 0) return (void *) sigma_sb;
if (strcmp(str,"cut_sb_ast") == 0) return (void *) cut_sb_ast;
if (strcmp(str,"b_sb") == 0) return (void *) b_sb;
if (strcmp(str,"cut_sb_c") == 0) return (void *) cut_sb_c;
if (strcmp(str,"epsilon_bb") == 0) return (void *) epsilon_bb;
if (strcmp(str,"sigma_bb") == 0) return (void *) sigma_bb;
if (strcmp(str,"cut_bb_ast") == 0) return (void *) cut_bb_ast;
if (strcmp(str,"b_bb") == 0) return (void *) b_bb;
if (strcmp(str,"cut_bb_c") == 0) return (void *) cut_bb_c;
return nullptr;
}
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