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pair_3spn2.cpp
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pair_3spn2.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: Daniel Hinckley (Wisconsin/UChicago) dhinckley@wisc.edu
------------------------------------------------------------------------- */
#include "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "string.h"
#include "pair_3spn2.h"
#include "atom.h"
#include "comm.h"
#include "domain.h"
#include "force.h"
#include "fix.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "math_const.h"
#include "memory.h"
#include "modify.h"
#include "error.h"
//#include "base_pair.h"
#define _SF_ 8.908987181403393E-1
#define _EEF1_ 0.17958712212516656 // 1/pi^(3/2);used in solvation calculation
#define _KB_ 1.3806505E-23
#define _NA_ 6.0221415E23
#define _EC_ 1.60217653E-19
#define _PV_ 8.8541878176E-22
#define EMPTY -12345
#define FOUR 4
#define SIX 6
using namespace LAMMPS_NS;
using namespace MathConst;
/* ---------------------------------------------------------------------- */
Pair3spn2::Pair3spn2(LAMMPS *lmp) : Pair(lmp) {
// An array to store additional quantities for energy calculations
nextra = 6;
pvector = new double[nextra];
basepair = new BasePair(lmp);
}
/* ---------------------------------------------------------------------- */
Pair3spn2::~Pair3spn2()
{
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
memory->destroy(cut_lj);
memory->destroy(cut_ljsq);
memory->destroy(cut_coul);
memory->destroy(cut_coulsq);
memory->destroy(epsilon);
memory->destroy(sigma);
memory->destroy(lj1);
memory->destroy(lj2);
memory->destroy(lj3);
memory->destroy(lj4);
memory->destroy(ljeps);
memory->destroy(param);
memory->destroy(angle);
memory->destroy(bp_array);
memory->destroy(R_solv);
memory->destroy(lambda);
memory->destroy(DGsolv);
memory->destroy(volu);
delete [] pvector;
}
}
/* ---------------------------------------------------------------------- */
void Pair3spn2::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul, ebp, ecstk, ebasepair,
ecrossstack, fpair, eexcl,engy;
double rsq,r2inv,r6inv,forcecoul,forcelj,factor_coul,factor_lj;
int stea, steb, stec, sted, stee, stef, steg, steh, myitype, myjtype;
int *ilist,*jlist,*numneigh,**firstneigh;
int icg, ich;
eexcl = ecoul = ebp = ecstk = ebasepair = ecrossstack = engy = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
double **x = atom->x;
double **f = atom->f;
double *q = atom->q;
int *type = atom->type;
int *tag = atom->tag;
int *molecule = atom->molecule;
int nlocal = atom->nlocal;
//double *special_coul = force->special_coul;
//double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
double qqr2e = force->qqr2e;
double dr, drsi, r, rinv, screening;
int itag, jtag, iflag,bpflag;
double bp_cutoff = 0.8;
nbps = 0;
nbps_inter = 0; // Interstrand base pairs
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
itag = tag[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
//factor_lj = special_lj[sbmask(j)];
//factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
dr = sqrt(rsq);
drsi = 1.0 / rsq;
jtype = type[j];
jtag = tag[j];
iflag = 0;
bpflag = 0;
// Set flags for determining pair interactions
if (molecule[i] != molecule[j]) // If different molecules
{
iflag = 1;
if (bp_array[itype-1][jtype-1]) bpflag = 1;
}
else
{
if (abs(jtag - itag) > 4) iflag = 1;
if (bp_array[itype-1][jtype-1])
{
if (abs(jtag-itag) > 10) bpflag = 1;
}
}
ebasepair = 0;
ecrossstack = 0.0;
forcecoul = 0.0;
forcelj = 0.0;
// If not within one nucleotide of each other
if (iflag) {
if (rsq < cutsq[itype][jtype]) {
r2inv = 1.0/rsq;
if (rsq < cut_ljsq[itype][jtype])
{
// Calculate the base pairing interaction
if (bpflag)
{
// Set the global IDs of the sites we are working with
steb = itag;
sted = jtag;
if (steb < sted)
{
myitype = itype;
myjtype = jtype;
}
else
{
int tmp = sted;
sted = steb;
steb = tmp;
myitype = jtype;
myjtype = itype;
}
stea = steb - 1;
stec = sted - 1;
stee = sted - 3;
stef = steb + 3;
// Now I map them to local coordinates
int index[6] = {atom->map(stea), atom->map(steb), atom->map(stec),atom->map(sted),atom->map(stee), atom->map(stef)};
int site_type[6], mytype;
for (int q = 0; q < SIX; q++)
{
if (index[q] != -1){
mytype = atom->type[index[q]];
if (mytype <= 14){
//make sure its a dna site
site_type[q] = (mytype - 3) % 4;
}
else{
site_type[q] = EMPTY;
}
}
else{
site_type[q] = EMPTY;
}
}
// Initializing the distances used for cross stacking
basepair->assign(index, site_type ,param, angle, x);
// Calculating each cross stacking interaction
// Calculate first cross stacking interaction if site d is
// not a terminal base
if (!(bp_array[myitype-1][myjtype-1] % 2))
{
ecrossstack = basepair->cross_stacking(0,f); // Interaction 1
}
// Calcuate second cross stacking interaction if site b is
// not a terminal base
if (!(bp_array[myitype-1][myjtype-1] % 3))
{
ecrossstack += basepair->cross_stacking(1,f); // Interaction 2
}
// Calculating the base pair interaction
ebasepair = basepair->base_pairing(f); // Interaction 3
// Determine whether or not this is indeed a base pair
if (ebasepair < -bp_cutoff * basepair->epsi[2]) nbps++;
if ((ebasepair < -bp_cutoff * basepair->epsi[2]) && (molecule[i] != molecule[j])) nbps_inter++;
//Calculate complementary crosstacking interaction
steg = sted + 3;
steh = steb - 3;
stea = steb - 1;
stec = sted - 1;
{int tmp = myitype;
myitype = myjtype;
myjtype = tmp;}
//Make sure steg and steh are in atom list
if (steg > atom->natoms) {
icg = -1;
} else {
icg = atom->map(steg);
}
if (steh < 1) {
ich = -1;
} else {
ich = atom->map(steh);
}
// Now I map them to local coordinates
int index_complement[6] = {atom->map(stec), atom->map(sted), atom->map(stea),atom->map(steb),ich, icg};
int site_type_complement[6], mytype_complement;
for (int q = 0; q < SIX; q++)
{
if (index_complement[q] != -1){
mytype_complement = atom->type[index_complement[q]];
if (mytype_complement <= 14){
//make sure its a dna site
site_type_complement[q] = (mytype_complement - 3) % 4;
}
else{
site_type_complement[q] = EMPTY;
}
}
else{
site_type_complement[q] = EMPTY;
}
}
// Initializing the distances used for cross stacking
basepair->assign(index_complement, site_type_complement ,param, angle, x);
// Calculating each cross stacking interaction
// Calculate first cross stacking interaction if site d is
// not a terminal base
if (!(bp_array[myitype-1][myjtype-1] % 2))
{
ecrossstack += basepair->cross_stacking(0,f); // Interaction 1
}
// Calcuate second cross stacking interaction if site b is
// not a terminal base
if (!(bp_array[myitype-1][myjtype-1] % 3))
{
ecrossstack += basepair->cross_stacking(1,f); // Interaction 2
}
}
else
{
// Excluded volume interaction
if (dr * _SF_ < sigma[itype][jtype])
{
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
if (eflag) eexcl += r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) + ljeps[itype][jtype];
}
else forcelj = 0.0;
}
if (eflag)
{
ebp += ebasepair;
ecstk += ecrossstack;
}
}
// Calculate the screened Coulombic interactions
if (qtmp)
{
if (q[j])
{
if (rsq < cut_coulsq[itype][jtype])
{
rinv = 1.0/dr;
double ldbi = 1.0 / ldby;
screening = exp(-dr * ldbi)/ dielectric;
engy = qqr2e * qtmp*q[j]*screening * rinv;
forcecoul = engy * dr * (ldbi + rinv);
if (eflag) ecoul += engy;
}
}
}
}
//if ((itype == 1) && (jtype == 1)) printf("forcecoul=%lf\n", forcecoul);
fpair = (forcecoul + forcelj) * r2inv;
/*
if (fpair > 100.0)
{
printf("Large force i=%d, j=%d,itag=%d, jtag=%d,r=%lf\n",i,j,itag,jtag,dr);
printf("forecoul=%lf, forcelj=%lf\n",forcecoul,forcelj);
}
*/
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (newton_pair || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
}
}
}
}
pvector[0] = ebp;
pvector[1] = ecstk;
pvector[2] = eexcl;
pvector[3] = ecoul;
pvector[4] = nbps;
pvector[5] = nbps_inter;
evdwl = ebp + ecstk + eexcl;
// This correctly adds the potential energy. However, the virial is not calculated properly
if (evflag) ev_tally(i,j,nlocal,newton_pair,evdwl,ecoul,fpair,delx,dely,delz);
if (vflag_fdotr) virial_fdotr_compute();
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void Pair3spn2::allocate()
{
allocated = 1;
int n = atom->ntypes;
n = 40; // Large enought to accomodate extra site types, including proteins
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(cut_lj,n+1,n+1,"pair:cut_lj");
memory->create(cut_ljsq,n+1,n+1,"pair:cut_ljsq");
memory->create(cut_coul,n+1,n+1,"pair:cut_coul");
memory->create(cut_coulsq,n+1,n+1,"pair:cut_coulsq");
memory->create(epsilon,n+1,n+1,"pair:epsilon");
memory->create(sigma,n+1,n+1,"pair:sigma");
memory->create(lj1,n+1,n+1,"pair:lj1");
memory->create(lj2,n+1,n+1,"pair:lj2");
memory->create(lj3,n+1,n+1,"pair:lj3");
memory->create(lj4,n+1,n+1,"pair:lj4");
memory->create(ljeps,n+1,n+1,"pair:ljeps");
memory->create(param,13,5,5,"pair:param");
memory->create(angle,7,5,5,"pair:angle");
memory->create(bp_array,n+1,n+1,"pair:bp_array");
memory->create(R_solv,n+1,"pair:R_solv");
memory->create(lambda,n+1,"pair:lambda");
memory->create(DGsolv,n+1,"pair:DGsolv");
memory->create(volu,n+1,"pair:volu");
//
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void Pair3spn2::settings(int narg, char **arg)
{
if (narg != 5) error->all(FLERR,"Illegal pair_style command");
if (!allocated) allocate();
int i,j,k;
int n = 40; // Hardcoded number of sites
/* Args:
Temperature -
Salt Concentration (mM)
Short-range cutoff
Long-range cutoff
*/
sprintf(dna_type,"%s",arg[0]); // The y
temp = force->numeric(FLERR,arg[1]);
salt_conc = force->numeric(FLERR,arg[2]) / 1000.0; // Convert to [M]
// Calculate solution dielectric (salt concentration is in M)
dielectric = 249.4 - 7.88E-01 * temp + 7.20E-04 * temp * temp;
dielectric *= (1.000 - (0.2551 * salt_conc) + (0.05151 * salt_conc * salt_conc) - (0.006889 * salt_conc * salt_conc * salt_conc));
// Calculate Deybe length
ldby = sqrt(dielectric * _PV_ * _KB_ * temp * 1.0E27 / (2.0 * _NA_ * _EC_ * _EC_ * salt_conc));
cut_lj_global = force->numeric(FLERR,arg[3]);
cut_coul_global = force->numeric(FLERR,arg[4]); // This cutoff must be the same as that for coul/long
// Hard-coded values (used to be pair_style arguments
scale_Santalucia = 0.70; //scale factor applied to Santalucia parameters
hbond_scaling = 0.694; // scale factor applied to epsilon to get AT base pairing strength
bp_ratio = 1.266; // ratio between G:C and A:T base pairing
/*
With this information, we can proceeding to initialize a number
of important variable that must be hard-coded.
*/
// Santalucia base step enthalpies as taken from J. Santalucia, PNAS, 1996.
// A - 0, T - 1, G - 2, C - 3
double Santalucia[4][4];
Santalucia[0][0] = -7.6; // AA base step
Santalucia[0][1] = -7.2;
Santalucia[0][2] = -7.8;
Santalucia[0][3] = -8.4;
Santalucia[1][0] = -7.2;
Santalucia[1][1] = -7.6;
Santalucia[1][2] = -8.5;
Santalucia[1][3] = -8.2;
Santalucia[2][0] = -8.2;
Santalucia[2][1] = -8.4;
Santalucia[2][2] = -8.0;
Santalucia[2][3] = -9.8;
Santalucia[3][0] = -8.5;
Santalucia[3][1] = -7.8;
Santalucia[3][2] = -10.5;
Santalucia[3][3] = -8.0;
eps = 0.0;
for (i = 0; i < 4; i++) {
for (j = 0; j < 4; j++) {
Santalucia[i][j] = -Santalucia[i][j] * scale_Santalucia;
eps += Santalucia[i][j];
}
}
eps /= 16.0;
// Assign angles
assign_angles(dna_type,angle);
// Setting all of the equilibrium distances
assign_distances(dna_type,param);
// Now setting the values of alphas for the Morse potential
for (i = 0; i < FOUR; i++) {
for (j = 0; j < FOUR; j++) {
param[3][i][j] = 4.0; // Cross stacking 1
param[4][i][j] = 4.0; // Cross stacking 2
param[5][i][j] = 2.0; // Base pairing
}
}
// Now setting the ranges for angle-modulation
for (i = 0; i < FOUR; i++) {
for (j = 0; j < FOUR; j++) {
param[6][i][j] = 8.0; // Cross stacking 1
param[7][i][j] = 8.0; // Cross stacking 2
param[8][i][j] = 12.0; // Base pairing
}
}
// An array that we use to set the cross stacking values
int WC[4] = {1,0,3,2};
double hbond[4];
double ref_hbond_energy, avg_bp_energy, cstk_scale_factor;
double curv_scale_factor = 1.0;
if (strcmp("bdna/curv",dna_type) == 0) curv_scale_factor = 0.861;
ref_hbond_energy = eps * hbond_scaling;
hbond[0] = ref_hbond_energy;
hbond[1] = ref_hbond_energy;
hbond[2] = ref_hbond_energy * bp_ratio;
hbond[3] = ref_hbond_energy * bp_ratio;
// Calculating the average base pairing strength
avg_bp_energy = ref_hbond_energy * (1.0 + bp_ratio) / 2.0;
// Specifying epsilon_BP
param[11][0][0] = EMPTY;
param[11][0][1] = ref_hbond_energy * curv_scale_factor;
param[11][0][2] = EMPTY;
param[11][0][3] = EMPTY;
param[11][1][0] = ref_hbond_energy * curv_scale_factor;
param[11][1][1] = EMPTY;
param[11][1][2] = EMPTY;
param[11][1][3] = EMPTY;
param[11][2][0] = EMPTY;
param[11][2][1] = EMPTY;
param[11][2][2] = EMPTY;
param[11][2][3] = bp_ratio * ref_hbond_energy * curv_scale_factor;
param[11][3][0] = EMPTY;
param[11][3][1] = EMPTY;
param[11][3][2] = bp_ratio * ref_hbond_energy * curv_scale_factor;
param[11][3][3] = EMPTY;
//printf("AT=%lf\n", param[11][0][1]*4.184);
double cstk[FOUR][FOUR];
for (i = 0; i < FOUR; i++) {
for (j = 0; j < FOUR; j++) {
cstk[i][j] = Santalucia[i][j] - 0.5 * (hbond[i] + hbond[j]);
}
}
double avg_cstk = 0.0;
for (i = 0; i < FOUR; i++) {
for (j = 0; j < FOUR; j++) {
avg_cstk += 0.5 * cstk[WC[i]][j];
avg_cstk += 0.5 * cstk[i][WC[j]];
}
}
avg_cstk /= 32.0;
cstk_scale_factor = avg_bp_energy * 100/88.0 * 0.12/avg_cstk * curv_scale_factor;
for (i = 0; i < FOUR; i++) {
for (j = 0; j < FOUR; j++) {
// cstk_1
param[9][i][j] = 0.5 * cstk_scale_factor * 0.5 * cstk[i][WC[j]]; //Scaled back crosstacking interaction to account for complement chain
// cstk_2
param[10][i][j] = 0.5 * cstk_scale_factor * 0.5 * cstk[WC[i]][j]; //Scaled back crosstacking interaction to account for complement chain
//printf("cstk1[%d][%d]=%lf\n", i,j,param[9][i][j]*4.184);
}
}
/* Initializing the base pair array (contains flags that determine whether
or not cross stacking interactions are calculated) */
// Initialize all to zero
for (int i = 0; i < n; i++) {
for (int j = 0; j < n; j++) {
bp_array[i][j] = 0;
}
}
/*
flag non-zero - calculate base pairing
flag divisible by 2 calculate the base pair interaction b--e
flag divisible by 3 calculate the base pair interaction d--f
*/
bp_array[2][3] = bp_array[2][11] = 6; bp_array[2][7] = 3; // A
bp_array[3][2] = bp_array[3][10] = 6; bp_array[3][6] = 3; // T
bp_array[4][5] = bp_array[4][13] = 6; bp_array[4][9] = 3; // G
bp_array[5][4] = bp_array[5][12] = 6; bp_array[5][8] = 3; // C
bp_array[6][3] = bp_array[6][11] = 6; bp_array[6][7] = 3; // 5A
bp_array[7][2] = bp_array[7][10] = 6; bp_array[7][6] = 3; // 5T
bp_array[8][5] = bp_array[8][13] = 6; bp_array[8][9] = 3; // 5G
bp_array[9][4] = bp_array[9][12] = 6; bp_array[9][8] = 3; // 5C
bp_array[10][3] = bp_array[10][11] = 2; bp_array[10][7] = 7; // 3A
bp_array[11][2] = bp_array[11][10] = 2; bp_array[11][6] = 7; // 3T
bp_array[12][5] = bp_array[12][13] = 2; bp_array[12][9] = 7; // 3G
bp_array[13][4] = bp_array[13][12] = 2; bp_array[13][8] = 7; // 3C
/*
bp_array[14][14] = {{0,0,0,0,0,0,0,0,0,0,0,0,0,0}, // P
{0,0,0,0,0,0,0,0,0,0,0,0,0,0}, // S
{0,0,0,6,0,0,0,3,0,0,0,6,0,0}, // A
{0,0,6,0,0,0,3,0,0,0,6,0,0,0}, // T
{0,0,0,0,0,6,0,0,0,3,0,0,0,6}, // G
{0,0,0,0,6,0,0,0,3,0,0,0,6,0}, // C
{0,0,0,6,0,0,0,3,0,0,0,6,0,0}, // 5A
{0,0,6,0,0,0,3,0,0,0,6,0,0,0}, // 5T
{0,0,0,0,0,6,0,0,0,3,0,0,0,6}, // 5G
{0,0,0,0,6,0,0,0,3,0,0,0,6,0}, // 5C
{0,0,0,2,0,0,0,7,0,0,0,2,0,0}, //3A
{0,0,2,0,0,0,7,0,0,0,2,0,0,0}, //3T
{0,0,0,0,0,2,0,0,0,7,0,0,0,2}, //3G
{0,0,0,0,2,0,0,0,7,0,0,0,2,0}}; //3C
*/
if (allocated) {
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
if (setflag[i][j]) {
cut_lj[i][j] = cut_lj_global;
cut_coul[i][j] = cut_coul_global;
}
}
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void Pair3spn2::coeff(int narg, char **arg)
{
if (narg != 4) error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
int n = atom->ntypes;
int ilo,ihi,jlo,jhi;
force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi);
force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi);
double epsilon_one = force->numeric(FLERR,arg[2]);
double sigma_one = force->numeric(FLERR,arg[3]);
double cut_lj_one = cut_lj_global;
double cut_coul_one = cut_coul_global;
int count = 0;
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j <= jhi; j++) {
epsilon[i][j] = epsilon_one;
sigma[i][j] = sigma_one * _SF_;
cut_lj[i][j] = cut_lj_one;
cut_coul[i][j] = cut_coul_one;
setflag[i][j] = 1;
count++;
}
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void Pair3spn2::init_style()
{
if (!atom->q_flag)
error->all(FLERR,"Pair style 3spn2 requires atom attribute q");
neighbor->request(this);
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double Pair3spn2::init_one(int i, int j)
{
if (setflag[i][j] == 0) {
// Apply mixing rules to sigma and epsilon
epsilon[i][j] = mix_energy(epsilon[i][i],epsilon[j][j],
sigma[i][i],sigma[j][j]);
sigma[i][j] = mix_distance(sigma[i][i],sigma[j][j]);
cut_lj[i][j] = mix_distance(cut_lj[i][i],cut_lj[j][j]);
cut_coul[i][j] = mix_distance(cut_coul[i][i],cut_coul[j][j]);
}
double cut = MAX(cut_lj[i][j],cut_coul[i][j]);
cut_ljsq[i][j] = cut_lj[i][j] * cut_lj[i][j];
cut_coulsq[i][j] = cut_coul[i][j] * cut_coul[i][j];
lj1[i][j] = 48.0 * epsilon[i][j] * pow(sigma[i][j],12.0);
lj2[i][j] = 24.0 * epsilon[i][j] * pow(sigma[i][j],6.0);
lj3[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],12.0);
lj4[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],6.0);
ljeps[i][j] = epsilon[i][j];
cut_ljsq[j][i] = cut_ljsq[i][j];
cut_coulsq[j][i] = cut_coulsq[i][j];
lj1[j][i] = lj1[i][j];
lj2[j][i] = lj2[i][j];
lj3[j][i] = lj3[i][j];
lj4[j][i] = lj4[i][j];
ljeps[j][i] = ljeps[i][j];
sigma[j][i] = sigma[i][j];
// Set cross terms
// compute I,J contribution to long-range tail correction
// count total # of atoms of type I and J via Allreduce
if (tail_flag) {
int *type = atom->type;
int nlocal = atom->nlocal;
double count[2],all[2];
count[0] = count[1] = 0.0;
for (int k = 0; k < nlocal; k++) {
if (type[k] == i) count[0] += 1.0;
if (type[k] == j) count[1] += 1.0;
}
MPI_Allreduce(count,all,2,MPI_DOUBLE,MPI_SUM,world);
double sig2 = sigma[i][j]*sigma[i][j];
double sig6 = sig2*sig2*sig2;
double rc3 = cut_lj[i][j]*cut_lj[i][j]*cut_lj[i][j];
double rc6 = rc3*rc3;
double rc9 = rc3*rc6;
etail_ij = 8.0*MY_PI*all[0]*all[1]*epsilon[i][j] *
sig6 * (sig6 - 3.0*rc6) / (9.0*rc9);
ptail_ij = 16.0*MY_PI*all[0]*all[1]*epsilon[i][j] *
sig6 * (2.0*sig6 - 3.0*rc6) / (9.0*rc9);
}
return cut;
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void Pair3spn2::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[i][j],sizeof(double),1,fp);
fwrite(&sigma[i][j],sizeof(double),1,fp);
fwrite(&cut_lj[i][j],sizeof(double),1,fp);
fwrite(&cut_coul[i][j],sizeof(double),1,fp);
}
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void Pair3spn2::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(&epsilon[i][j],sizeof(double),1,fp);
fread(&sigma[i][j],sizeof(double),1,fp);
fread(&cut_lj[i][j],sizeof(double),1,fp);
fread(&cut_coul[i][j],sizeof(double),1,fp);
}
MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_lj[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_coul[i][j],1,MPI_DOUBLE,0,world);
}
}
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void Pair3spn2::write_restart_settings(FILE *fp)
{
fwrite(&cut_lj_global,sizeof(double),1,fp);
fwrite(&cut_coul_global,sizeof(double),1,fp);
fwrite(&mix_flag,sizeof(int),1,fp);
fwrite(&tail_flag,sizeof(int),1,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void Pair3spn2::read_restart_settings(FILE *fp)
{
if (comm->me == 0) {
fread(&cut_lj_global,sizeof(double),1,fp);
fread(&cut_coul_global,sizeof(double),1,fp);
fread(&mix_flag,sizeof(int),1,fp);
fread(&tail_flag,sizeof(int),1,fp);
}
MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_coul_global,1,MPI_DOUBLE,0,world);
MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
MPI_Bcast(&tail_flag,1,MPI_INT,0,world);
}
/* ---------------------------------------------------------------------- */
// This function is
double Pair3spn2::single(int i, int j, int itype, int jtype,
double rsq,
double factor_coul, double factor_lj,
double &fforce)
{
double r2inv,r6inv,forcecoul,forcelj,phicoul,philj;
r2inv = 1.0/rsq;
if (rsq < cut_coulsq[itype][jtype]) {
forcecoul = force->qqrd2e * atom->q[i]*atom->q[j]*sqrt(r2inv);
} else forcecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
} else forcelj = 0.0;
fforce = (factor_coul*forcecoul + factor_lj*forcelj) * r2inv;
double eng = 0.0;
if (rsq < cut_coulsq[itype][jtype]) {
phicoul = force->qqrd2e * atom->q[i]*atom->q[j]*sqrt(r2inv);
eng += factor_coul*phicoul;
}
if (rsq < cut_ljsq[itype][jtype]) {
philj = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
eng += factor_lj*philj;
}
return eng;
}
/* ---------------------------------------------------------------------- */
void *Pair3spn2::extract(const char *str, int &dim)
{
dim = 0;
if (strcmp(str,"cut_coul") == 0) return (void *) &cut_coul[1][1];
dim = 2;
if (strcmp(str,"epsilon") == 0) return (void *) epsilon;
return NULL;
}
void Pair3spn2::assign_angles(char *dna_type, double***angles)
{
if (strcmp(dna_type,"bdna") == 0) {
// Angle between ba and dc
angle[0][0][0] = EMPTY;
angle[0][0][1] = 116.09;
angle[0][0][2] = EMPTY;
angle[0][0][3] = EMPTY;
angle[0][1][0] = 116.09;
angle[0][1][1] = EMPTY;
angle[0][1][2] = EMPTY;
angle[0][1][3] = EMPTY;
angle[0][2][0] = EMPTY;
angle[0][2][1] = EMPTY;
angle[0][2][2] = EMPTY;
angle[0][2][3] = 124.93;
angle[0][3][0] = EMPTY;
angle[0][3][1] = EMPTY;
angle[0][3][2] = 124.93;
angle[0][3][3] = EMPTY;
// Defining the angles for cross stacking 1
angle[1][0][0] = 154.38;
angle[1][0][1] = 159.10;
angle[1][0][2] = 152.46;
angle[1][0][3] = 158.38;
angle[1][1][0] = 147.10;
angle[1][1][1] = 153.79;
angle[1][1][2] = 144.44;
angle[1][1][3] = 151.48;
angle[1][2][0] = 154.69;
angle[1][2][1] = 157.83;
angle[1][2][2] = 153.43;
angle[1][2][3] = 158.04;
angle[1][3][0] = 152.99;
angle[1][3][1] = 159.08;
angle[1][3][2] = 150.53;
angle[1][3][3] = 157.17;
// Defining the angles for cross stacking 2
angle[2][0][0] = 116.88;
angle[2][0][1] = 121.74;
angle[2][0][2] = 114.23;
angle[2][0][3] = 119.06;
angle[2][1][0] = 109.42;
angle[2][1][1] = 112.95;
angle[2][1][2] = 107.32;
angle[2][1][3] = 110.56;
angle[2][2][0] = 119.34;
angle[2][2][1] = 124.72;
angle[2][2][2] = 116.51;
angle[2][2][3] = 121.98;
angle[2][3][0] = 114.60;
angle[2][3][1] = 118.26;
angle[2][3][2] = 112.45;
angle[2][3][3] = 115.88;
// Torsion angles used in base pairing
angle[3][0][0] = EMPTY;
angle[3][0][1] = -38.35;
angle[3][0][2] = EMPTY;
angle[3][0][3] = EMPTY;
angle[3][1][0] = -38.35;
angle[3][1][1] = EMPTY;
angle[3][1][2] = EMPTY;
angle[3][1][3] = EMPTY;
angle[3][2][0] = EMPTY;
angle[3][2][1] = EMPTY;
angle[3][2][2] = EMPTY;
angle[3][2][3] = -42.98;
angle[3][3][0] = EMPTY;
angle[3][3][1] = EMPTY;
angle[3][3][2] = -42.98;
angle[3][3][3] = EMPTY;
// Theta 1 angle - (base pairing)
angle[4][0][0] = EMPTY;
angle[4][0][1] = 156.54;
angle[4][0][2] = EMPTY;
angle[4][0][3] = EMPTY;
angle[4][1][0] = 135.78;
angle[4][1][1] = EMPTY;
angle[4][1][2] = EMPTY;
angle[4][1][3] = EMPTY;
angle[4][2][0] = EMPTY;
angle[4][2][1] = EMPTY;
angle[4][2][2] = EMPTY;
angle[4][2][3] = 159.81;
angle[4][3][0] = EMPTY;
angle[4][3][1] = EMPTY;
angle[4][3][2] = 141.16;
angle[4][3][3] = EMPTY;
// Theta 2 angle (base pairing)
angle[5][0][0] = EMPTY;
angle[5][0][1] = 135.78;
angle[5][0][2] = EMPTY;
angle[5][0][3] = EMPTY;
angle[5][1][0] = 156.54;
angle[5][1][1] = EMPTY;
angle[5][1][2] = EMPTY;
angle[5][1][3] = EMPTY;
angle[5][2][0] = EMPTY;
angle[5][2][1] = EMPTY;
angle[5][2][2] = EMPTY;
angle[5][2][3] = 141.16;
angle[5][3][0] = EMPTY;
angle[5][3][1] = EMPTY;
angle[5][3][2] = 159.81;
angle[5][3][3] = EMPTY;
} else if (strcmp("bdna/curv",dna_type) == 0) {
angle[0][0][0] = EMPTY;
angle[0][0][1] = 110.92; //was bug
angle[0][0][2] = EMPTY;
angle[0][0][3] = EMPTY;
angle[0][1][0] = 110.92; //was bug
angle[0][1][1] = EMPTY;
angle[0][1][2] = EMPTY;
angle[0][1][3] = EMPTY;
angle[0][2][0] = EMPTY;
angle[0][2][1] = EMPTY;
angle[0][2][2] = EMPTY;
angle[0][2][3] = 120.45; //was bug
angle[0][3][0] = EMPTY;