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fix_go-model.cpp
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/* ----------------------------------------------------------------------
Copyright (2010) Aram Davtyan and Garegin Papoian
Papoian's Group, University of Maryland at Collage Park
http://papoian.chem.umd.edu/
Gaussian Contacts Potential was contributed by Weihua Zheng
Last Update: 03/23/2011
------------------------------------------------------------------------- */
#include <math.h>
#include <stdlib.h>
#include <string.h>
#include "fix_go-model.h"
#include "atom.h"
#include "atom_vec_awsemmd.h"
#include "timer.h"
#include "output.h"
#include "update.h"
#include "respa.h"
#include "comm.h"
#include "error.h"
#include "group.h"
#include "domain.h"
#include "random_park.h"
#include <fstream>
#include <time.h>
using std::ifstream;
using namespace LAMMPS_NS;
using namespace FixConst;
/* ---------------------------------------------------------------------- */
// {"ALA", "ARG", "ASN", "ASP", "CYS", "GLN", "GLU", "GLY", "HIS", "ILE", "LEU", "LYS", "MET", "PHE", "PRO", "SER", "THR", "TRP", "TYR", "VAL"};
// {"A", "R", "N", "D", "C", "Q", "E", "G", "H", "I", "L", "K", "M", "F", "P", "S", "T", "W", "Y", "V"};
//int se_map[] = {0, 0, 4, 3, 6, 13, 7, 8, 9, 0, 11, 10, 12, 2, 0, 14, 5, 1, 15, 16, 0, 19, 17, 0, 18, 0};
inline void FixGoModel::print_log(char *line)
{
if (screen) fprintf(screen, line);
if (logfile) fprintf(logfile, line);
}
FixGoModel::FixGoModel(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg != 4) error->all(FLERR,"Illegal fix go-model command");
efile = fopen("energyGO.log", "w");
char eheader[] = "Step\tBond\tAngle\tDihedral\tContacts\tNative\tVTotal\n";
fprintf(efile, "%s", eheader);
restart_global = 1;
char force_file_name[] = "forcesGO.dat";
fout = fopen(force_file_name,"w");
efout = fopen("epsilon.dat","w");
scalar_flag = 1;
vector_flag = 1;
thermo_energy = 1;
size_vector = nEnergyTerms;
global_freq = 1;
extscalar = 1;
extvector = 1;
force_flag = 0;
for (int i=0;i<nEnergyTerms;++i) energy[i] = 0.0;
n = (int)(group->count(igroup)+1e-12);
seed = time(NULL);
// seed = 1;
allocated = false;
allocate();
bonds_flag = angles_flag = dihedrals_flag = contacts_flag = contacts_dev_flag = lj_contacts_flag = gaussian_contacts_flag = 0;
dev_type = DT_NONE;
epsilon = epsilon2 = 1.0;
n_basins = 1;
rmin_cutoff = 4.0 ;
int i, j, k;
double r0_tmp, theta0_tmp, phi0_tmp;
char varsection[100];
ifstream in(arg[3]);
if (!in) error->all(FLERR,"Coefficient file was not found!");
while (!in.eof()) {
in >> varsection;
if (strcmp(varsection, "[Go-Model_LJ]")==0) {
if(gaussian_contacts_flag || bonds_flag || angles_flag || dihedrals_flag || contacts_flag ) error->all(FLERR,"Conflict in definition of contact potential !!");
lj_contacts_flag = 1;
print_log("LJ Go-Model flag on\n");
allocate_contact();
in >> epsilon >> epsilon2 ;
} else if (strcmp(varsection, "[Go-Model_Gaussian]")==0) {
if(lj_contacts_flag || bonds_flag || angles_flag || dihedrals_flag || contacts_flag ) error->all(FLERR,"Conflict in definition of contact potential !!");
gaussian_contacts_flag = 1;
print_log("Gaussian Go-Model flag on\n");
in >> epsilon >> epsilon2 ;
in >> n_basins;
allocate_contact();
for(i=0; i<n_basins; ++i){
in >> A[i];
}
in >> gaussian_width;
g_w_sq_inv = 1.0/gaussian_width/gaussian_width ;
in >> rmin_cutoff ;
} else if (strcmp(varsection, "[Bonds]")==0) {
bonds_flag = 1;
print_log("Bonds flag on\n");
in >> k_bonds;
for(i=0;i<n_basins; ++i) {
for (j=0;j<n-1;++j) {
if(i==0) r0[j]=0.0;
in >> r0_tmp;
r0[j] += r0_tmp;
if(i==n_basins -1) r0[j] /= n_basins;
}
}
} else if (strcmp(varsection, "[Angles]")==0) {
angles_flag = 1;
print_log("Angles flag on\n");
in >> k_angles;
for(i=0;i<n_basins; ++i) {
for (j=0;j<n-2;++j) {
if(i==0) theta0[j]=0.0;
in >> theta0_tmp;
theta0[j] += theta0_tmp;
if(i==n_basins -1) theta0[j] /= n_basins;
}
}
} else if (strcmp(varsection, "[Dihedrals]")==0) {
dihedrals_flag = 1;
print_log("Dihedrals flag on\n");
in >> k_dihedrals[0] >> k_dihedrals[1];
for(i=0;i<n_basins; ++i) {
for (j=0;j<n-3;++j) {
if(i==0) phi0[j]=0.0;
in >> phi0_tmp;
phi0[j] += phi0_tmp;
if(i==n_basins -1) phi0[j] /= n_basins;
}
}
} else if (strcmp(varsection, "[Contacts]")==0) {
if (!lj_contacts_flag && !gaussian_contacts_flag) error->all(FLERR,"Conflict in definition of contact potential !!");
//allocate_contact();
contacts_flag = 1;
print_log("Contacts flag on\n");
if(lj_contacts_flag){
for (i=0;i<n-4;++i) for (j=i;j<n-4;++j) in >> isNative[i][j];
for (i=0;i<n-4;++i) for (j=i;j<n-4;++j) in >> sigma[i][j];
for (i=0;i<n-4;++i) for (j=i;j<n-4;++j) sigma_sq[i][j] = sigma[i][j]*sigma[i][j];
} else { //gaussian_contacts_flag
for(k=0;k<n_basins;++k){
for (i=0;i<n-4;++i) for (j=i;j<n-4;++j) in >> isNative_mb[k][i][j];
for (i=0;i<n-4;++i) for (j=i;j<n-4;++j) in >> sigma_mb[k][i][j];
}
}
} else if (strcmp(varsection, "[Contacts_Deviation]")==0) {
contacts_dev_flag = 1;
dev_type = DT_CORR;
print_log("Contacts_Deviation flag on\n");
in >> sdivf; // Standart deviation in epsilon fractions
in >> tcorr; // Correlation time in femtoseconds
in >> dev0; // Deviation on t=0
} else if (strcmp(varsection, "[Harmonic_Contacts_Deviation]")==0) {
contacts_dev_flag = 1;
dev_type = DT_SIN;
print_log("Harmonic_Contacts_Deviation flag on\n");
in >> sdivf; // Amplitud
in >> tcorr; // Period
in >> dev0; // Phase on t=0 in half periods
} else if (strcmp(varsection, "[Constant_Contacts_Deviation]")==0) {
contacts_dev_flag = 1;
dev_type = DT_CONST;
print_log("Constant_Contacts_Deviation flag on\n");
in >> sdivf; // Deviation in epsilon fractions
}
varsection[0]='\0';
}
in.close();
print_log("\n");
if (dev_type==DT_CORR) {
xi = 1/tcorr;
w = sqrt(xi)*epsilon*sdivf;
dev = dev0;
devA = w*sqrt(2*update->dt);
devB = xi*update->dt;
devC = (1 - xi*update->dt/2);
} else if (dev_type==DT_SIN) {
devA = epsilon*sdivf/sqrt(0.5);
devB = 2*M_PI*update->dt/tcorr;
devC = M_PI*dev0;
dev = devA*sin(devC);
} else if (dev_type==DT_CONST) {
dev = devA = epsilon*sdivf;
}
x = atom->x;
f = atom->f;
image = atom->image;
prd[0] = domain->xprd;
prd[1] = domain->yprd;
prd[2] = domain->zprd;
half_prd[0] = prd[0]/2;
half_prd[1] = prd[1]/2;
half_prd[2] = prd[2]/2;
periodicity = domain->periodicity;
Step = 0;
sStep=0, eStep=0;
ifstream in_rs("record_steps");
in_rs >> sStep >> eStep;
in_rs.close();
avec = (AtomVecAWSEM *) atom->style_match("awsemmd");
if (!avec) error->all(FLERR,"Fix gomodel requires atom style awsemmd");
Construct_Computational_Arrays();
}
/* ---------------------------------------------------------------------- */
FixGoModel::~FixGoModel()
{
if (allocated) {
for (int i=0;i<n;i++) {
delete [] xca[i];
}
delete [] r0;
delete [] theta0;
delete [] phi0;
delete [] alpha_carbons;
delete [] xca;
delete [] res_no;
delete [] chain_no;
delete [] res_info;
delete random;
}
if (contacts_allocated) {
if(lj_contacts_flag){
for (int i=0;i<n-4;i++) {
delete [] sigma[i];
delete [] sigma_sq[i];
delete [] isNative[i];
}
delete [] sigma;
delete [] sigma_sq;
delete [] isNative;
} else { //gaussian_contacts_flag
delete [] G;
delete [] A;
for(int k=0; k<n_basins; ++k){
for(int i=0; i<n-4; ++i){
delete [] sigma_mb[k][i];
delete [] isNative_mb[k][i];
}
delete [] sigma_mb[k];
delete [] isNative_mb[k];
}
delete [] sigma_mb;
delete [] isNative_mb;
}
}
}
/* ---------------------------------------------------------------------- */
inline bool FixGoModel::isFirst(int index)
{
if (res_no[index]==1) return true;
return false;
}
inline bool FixGoModel::isLast(int index)
{
if (res_no[index]==n) return true;
return false;
}
int FixGoModel::Tag(int index) {
if (index==-1) return -1;
return atom->tag[index];
}
inline void FixGoModel::Construct_Computational_Arrays()
{
int *mask = atom->mask;
int nlocal = atom->nlocal;
int nall = atom->nlocal + atom->nghost;
int *mol_tag = atom->molecule;
int *res_tag = avec->residue;
int i, j, js;
// Creating index arrays for Alpha_Carbons
nn = 0;
int last = 0;
for (i = 0; i < n; ++i) {
int min = -1, jm = -1;
for (int j = 0; j < nall; ++j) {
if (i==0 && res_tag[j]<=0)
error->all(FLERR,"Residue index must be positive in fix go-model");
if ( (mask[j] & groupbit) && res_tag[j]>last ) {
if (res_tag[j]<min || min==-1) {
min = res_tag[j];
jm = j;
}
}
}
if (min==-1) break;
alpha_carbons[nn] = jm;
res_no[nn] = min;
last = min;
nn++;
}
int nMinNeighbours = 3;
int iLastLocal = -1;
int lastResNo = -1;
int lastResType = NONE;
int nlastType = 0;
// Checking sequance and marking residues
for (i = 0; i < nn; ++i) {
chain_no[i] = -1;
if (lastResNo!=-1 && lastResNo!=res_no[i]-1) {
if (lastResType==LOCAL && res_no[i]!=n)
error->all(FLERR,"Missing neighbor atoms in fix go-model (code: 001)");
if (lastResType==GHOST) {
if (iLastLocal!=-1 && i-nMinNeighbours<=iLastLocal)
error->all(FLERR,"Missing neighbor atoms in fix go-model (code: 002)");
}
iLastLocal = -1;
lastResNo = -1;
lastResType = NONE;
nlastType = 0;
}
if (alpha_carbons[i]!=-1) {
chain_no[i] = mol_tag[alpha_carbons[i]];
if (alpha_carbons[i]<nlocal) {
if ( lastResType==OFF || (lastResType==GHOST && nlastType<nMinNeighbours && nlastType!=res_no[i]-1) ) {
error->all(FLERR,"Missing neighbor atoms in fix go-model (code: 003)");
}
iLastLocal = i;
res_info[i] = LOCAL;
} else {
res_info[i] = GHOST;
}
} else res_info[i] = OFF;
if (lastResNo == res_no[i]) nlastType++; else nlastType = 0;
lastResNo = res_no[i];
lastResType = res_info[i];
}
if (lastResType==LOCAL && res_no[nn-1]!=n)
error->all(FLERR,"Missing neighbor atoms in fix go-model (code: 004)");
if (lastResType==GHOST) {
if (iLastLocal!=-1 && nn-nMinNeighbours<=iLastLocal)
error->all(FLERR,"Missing neighbor atoms in fix go-model (code: 005)");
}
}
void FixGoModel::allocate()
{
alpha_carbons = new int[n];
xca = new double*[n];
res_no = new int[n];
chain_no = new int[n];
res_info = new int[n];
r0 = new double[n-1];
theta0 = new double[n-2];
phi0 = new double[n-3];
for (int i = 0; i < n; ++i) {
xca[i] = new double [3];
}
random = new RanPark(lmp,seed);
allocated = true;
}
void FixGoModel::allocate_contact()
{
if(lj_contacts_flag){
sigma = new double*[n-4];
sigma_sq = new double*[n-4];
isNative = new bool*[n-4];
for (int i = 0; i < n-4; ++i) {
sigma[i] = new double[n-4];
sigma_sq[i] = new double[n-4];
isNative[i] = new bool[n-4];
}
} else { //gaussian_contacts_flag
G = new double[n_basins];
A = new double[n_basins];
sigma_mb = new double**[n_basins];
isNative_mb = new bool**[n_basins];
for (int k=0; k<n_basins; ++k){
sigma_mb[k] = new double*[n-4];
isNative_mb[k] = new bool*[n-4];
for(int i=0; i< n-4; ++i){
sigma_mb[k][i] = new double[n-4];
isNative_mb[k][i] = new bool[n-4];
}
}
}
contacts_allocated = true;
}
/* ---------------------------------------------------------------------- */
int FixGoModel::setmask()
{
int mask = 0;
mask |= POST_FORCE;
mask |= THERMO_ENERGY;
mask |= POST_FORCE_RESPA;
mask |= MIN_POST_FORCE;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixGoModel::init()
{
if (strstr(update->integrate_style,"respa"))
nlevels_respa = ((Respa *) update->integrate)->nlevels;
}
/* ---------------------------------------------------------------------- */
void FixGoModel::setup(int vflag)
{
if (strstr(update->integrate_style,"verlet"))
post_force(vflag);
else {
((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1);
post_force_respa(vflag,nlevels_respa-1,0);
((Respa *) update->integrate)->copy_f_flevel(nlevels_respa-1);
}
}
/* ---------------------------------------------------------------------- */
void FixGoModel::min_setup(int vflag)
{
post_force(vflag);
}
/* ---------------------------------------------------------------------- */
inline double adotb(double *a, double *b)
{
return (a[0]*b[0] + a[1]*b[1] + a[2]*b[2]);
}
inline double cross(double *a, double *b, int index)
{
switch (index) {
case 0:
return a[1]*b[2] - a[2]*b[1];
case 1:
return a[2]*b[0] - a[0]*b[2];
case 2:
return a[0]*b[1] - a[1]*b[0];
}
return 0;
}
inline double atan2(double y, double x)
{
if (x==0) {
if (y>0) return M_PI_2;
else if (y<0) return -M_PI_2;
else return NULL;
} else {
return atan(y/x) + (x>0 ? 0 : (y>=0 ? M_PI : -M_PI) );
}
}
inline double FixGoModel::PeriodicityCorrection(double d, int i)
{
if (!periodicity[i]) return d;
else return ( d > half_prd[i] ? d - prd[i] : (d < -half_prd[i] ? d + prd[i] : d) );
}
void FixGoModel::compute_bond(int i)
{
int i_resno = res_no[i]-1;
if (i_resno>=n-1) error->all(FLERR,"Wrong use of compute_bond() in fix go-model");
double dx[3], r, dr, force;
dx[0] = xca[i+1][0] - xca[i][0];
dx[1] = xca[i+1][1] - xca[i][1];
dx[2] = xca[i+1][2] - xca[i][2];
r = sqrt(dx[0]*dx[0]+dx[1]*dx[1]+dx[2]*dx[2]);
dr = r - r0[i_resno];
force = 2*epsilon*k_bonds*dr/r;
energy[ET_BOND] += epsilon*k_bonds*dr*dr;
f[alpha_carbons[i+1]][0] -= dx[0]*force;
f[alpha_carbons[i+1]][1] -= dx[1]*force;
f[alpha_carbons[i+1]][2] -= dx[2]*force;
f[alpha_carbons[i]][0] -= -dx[0]*force;
f[alpha_carbons[i]][1] -= -dx[1]*force;
f[alpha_carbons[i]][2] -= -dx[2]*force;
}
void FixGoModel::compute_angle(int i)
{
int i_resno = res_no[i]-1;
if (i_resno>=n-2) error->all(FLERR,"Wrong use of compute_angle() in fix go-model");
double a[3], b[3], a2, b2, A, B, AB, adb, alpha;
double theta, dtheta, force, factor[2][3];
a[0] = xca[i][0] - xca[i+1][0];
a[1] = xca[i][1] - xca[i+1][1];
a[2] = xca[i][2] - xca[i+1][2];
b[0] = xca[i+2][0] - xca[i+1][0];
b[1] = xca[i+2][1] - xca[i+1][1];
b[2] = xca[i+2][2] - xca[i+1][2];
a2 = adotb(a, a);
b2 = adotb(b, b);
adb = adotb(a, b);
A = sqrt(a2);
B = sqrt(b2);
AB = A*B;
alpha = adb/AB;
theta = acos(alpha);
dtheta = theta - theta0[i_resno];
force = 2*epsilon*k_angles*dtheta/(AB*sqrt(1-alpha*alpha));
energy[ET_ANGLE] += epsilon*k_angles*dtheta*dtheta;
factor[0][0] = (b[0] - a[0]*adb/a2);
factor[0][1] = (b[1] - a[1]*adb/a2);
factor[0][2] = (b[2] - a[2]*adb/a2);
factor[1][0] = (a[0] - b[0]*adb/b2);
factor[1][1] = (a[1] - b[1]*adb/b2);
factor[1][2] = (a[2] - b[2]*adb/b2);
f[alpha_carbons[i]][0] -= -factor[0][0]*force;
f[alpha_carbons[i]][1] -= -factor[0][1]*force;
f[alpha_carbons[i]][2] -= -factor[0][2]*force;
f[alpha_carbons[i+1]][0] -= (factor[1][0] + factor[0][0])*force;
f[alpha_carbons[i+1]][1] -= (factor[1][1] + factor[0][1])*force;
f[alpha_carbons[i+1]][2] -= (factor[1][2] + factor[0][2])*force;
f[alpha_carbons[i+2]][0] -= -factor[1][0]*force;
f[alpha_carbons[i+2]][1] -= -factor[1][1]*force;
f[alpha_carbons[i+2]][2] -= -factor[1][2]*force;
}
void FixGoModel::compute_dihedral(int i)
{
int i_resno = res_no[i]-1;
if (i_resno>=n-3) error->all(FLERR,"Wrong use of compute_dihedral() in fix go-model");
double phi, dphi, y_slope[4][3], x_slope[4][3], force, V;
double a[3], b[3], c[3];
double bxa[3], cxa[3], cxb[3];
double adb, bdc, adc, b2, bm, cdbxa;
double X, Y, X2Y2;
double dAngle_y, dAngle_x;
double h1, h2, h3;
int j, l;
a[0] = xca[i+1][0] - xca[i][0];
a[1] = xca[i+1][1] - xca[i][1];
a[2] = xca[i+1][2] - xca[i][2];
b[0] = xca[i+2][0] - xca[i+1][0];
b[1] = xca[i+2][1] - xca[i+1][1];
b[2] = xca[i+2][2] - xca[i+1][2];
c[0] = xca[i+3][0] - xca[i+2][0];
c[1] = xca[i+3][1] - xca[i+2][1];
c[2] = xca[i+3][2] - xca[i+2][2];
adb = adotb(a, b);
bdc = adotb(b, c);
adc = adotb(a, c);
b2 = adotb(b, b);
bm = sqrt(b2);
bxa[0] = cross(b, a, 0);
bxa[1] = cross(b, a, 1);
bxa[2] = cross(b, a, 2);
cxa[0] = cross(c, a, 0);
cxa[1] = cross(c, a, 1);
cxa[2] = cross(c, a, 2);
cxb[0] = cross(c, b, 0);
cxb[1] = cross(c, b, 1);
cxb[2] = cross(c, b, 2);
cdbxa = adotb(c, bxa);
Y = -bm*cdbxa;
X = adb*bdc - b2*adc;
phi = atan2(Y, X);
X2Y2 = (X*X + Y*Y);
dAngle_y = X/X2Y2;
dAngle_x = -Y/X2Y2;
for (l=0;l<3;++l) {
y_slope[0][l] = dAngle_y*bm*cxb[l];
y_slope[1][l] = dAngle_y*( b[l]*cdbxa/bm - bm*(cxb[l] + cxa[l]) );
y_slope[2][l] = dAngle_y*( -b[l]*cdbxa/bm + bm*(bxa[l] + cxa[l]) );
y_slope[3][l] = -dAngle_y*bm*bxa[l];
h1 = b[l]*bdc - c[l]*b2;
h2 = a[l]*bdc - 2*b[l]*adc + c[l]*adb;
h3 = b[l]*adb - a[l]*b2;
x_slope[0][l] = -dAngle_x*h1;
x_slope[1][l] = dAngle_x*(h1 - h2);
x_slope[2][l] = dAngle_x*(h2 - h3);
x_slope[3][l] = dAngle_x*h3;
}
for (j=0;j<2;j++) {
dphi = (2*j+1)*(phi - phi0[i_resno]);
V = epsilon*k_dihedrals[j]*(1-cos(dphi));
force = (2*j+1)*epsilon*k_dihedrals[j]*sin(dphi);
energy[ET_DIHEDRAL] += V;
for (l=0; l<3; l++) {
f[alpha_carbons[i]][l] -= force*(y_slope[0][l] + x_slope[0][l]);
f[alpha_carbons[i+1]][l] -= force*(y_slope[1][l] + x_slope[1][l]);
f[alpha_carbons[i+2]][l] -= force*(y_slope[2][l] + x_slope[2][l]);
f[alpha_carbons[i+3]][l] -= force*(y_slope[3][l] + x_slope[3][l]);
}
}
}
/* Correlated noise generator for contact potential
dev(t+dt) = dev(t) - 0.5*xi*(dev(t) + devp(t))*dt + w*sqrt(2*dt)*rand
devp(t) = dev(t) - xi*dev(t)*dt + w*sqrt(2*dt)*rand
The formula above was simplified to
dev += (w*sqrt(2*dt)*rand - xi*dt*dev)*(1 - xi*dt/2)
devA = w*sqrt(2*dt)
devB = xi*dt
devC = (1 - xi*dt/2)
<dev(t)dev(t+dt)> = w^2/xi * Exp[-xi*dt]
*/
void FixGoModel::compute_contact_deviation()
{
if (dev_type==DT_CORR) {
if (ntimestep!=0) {
rand = random->gaussian();
dev += (devA*rand - devB*dev)*devC;
}
} else if (dev_type==DT_SIN) {
dev = devA*sin(devB*ntimestep + devC);
} else if (dev_type==DT_CONST) {
dev = devA;
}
}
void FixGoModel::compute_contact(int i, int j)
{
int i_resno = res_no[i]-1;
int j_resno = res_no[j]-1;
if (i_resno>=n-4 || j_resno<=i_resno+3) error->all(FLERR,"Wrong use of compute_contact() in fix go-model");
double dx[3], rsq, sgrinvsq, sgrinv12, sgrinv10;
double V, force, contact_epsilon;
dx[0] = xca[j][0] - xca[i][0];
dx[1] = xca[j][1] - xca[i][1];
dx[2] = xca[j][2] - xca[i][2];
rsq = dx[0]*dx[0]+dx[1]*dx[1]+dx[2]*dx[2];
// r = sqrt(rsq);
if (rsq>sigma_sq[i_resno][j_resno-4]*9) return;
sgrinvsq = sigma_sq[i_resno][j_resno-4]/rsq;
sgrinv12 = pow(sgrinvsq, 6);
sgrinv10 = pow(sgrinvsq, 5);
// sgrinv = sigma[i_resno][j_resno-4]/r;
// sgrinv12 = pow(sgrinv, 12);
// sgrinv10 = pow(sgrinv, 10);
if (isNative[i_resno][j_resno-4]) {
contact_epsilon = epsilon;
if (contacts_dev_flag) contact_epsilon = epsilon + dev;
V = contact_epsilon*(5*sgrinv12 - 6*sgrinv10);
force = -60*contact_epsilon*(sgrinv12 - sgrinv10)/rsq;
energy[ET_NCONTS] += V;
} else {
V = epsilon2*sgrinv12;
force = -12*epsilon2*sgrinv12/rsq;
}
energy[ET_CONTACTS] += V;
f[alpha_carbons[j]][0] -= force*dx[0];
f[alpha_carbons[j]][1] -= force*dx[1];
f[alpha_carbons[j]][2] -= force*dx[2];
f[alpha_carbons[i]][0] -= -force*dx[0];
f[alpha_carbons[i]][1] -= -force*dx[1];
f[alpha_carbons[i]][2] -= -force*dx[2];
}
void FixGoModel::compute_contact_gaussian(int i, int j)
{
int i_resno = res_no[i]-1;
int j_resno = res_no[j]-1;
int k, l;
if (i_resno>=n-4 || j_resno<=i_resno+3) error->all(FLERR,"Wrong use of compute_contact_gaussian() in fix go-model");
double dx[3], r, dr, rsq;
double V, force, contact_epsilon;
double w_sq_inv, VTotal ;
double force_tmp, force_tmp_sum;
dx[0] = xca[j][0] - xca[i][0];
dx[1] = xca[j][1] - xca[i][1];
dx[2] = xca[j][2] - xca[i][2];
rsq = dx[0]*dx[0]+dx[1]*dx[1]+dx[2]*dx[2];
r = sqrt(rsq);
w_sq_inv = 1.0/pow( abs(i_resno - j_resno), 0.3 ) * g_w_sq_inv ; // / gaussian_width / gaussian_width ;
//V == epsilon * {Product_k(1+V_k[k]) - 1}
R = pow( (rmin_cutoff/r) , 12); //rmin_cutoff = 4.0 A
V = 1.0;
for(k=0; k<n_basins; ++k){
if(isNative_mb[k][i_resno][j_resno-4]){
dr = r - sigma_mb[k][i_resno][j_resno-4] ;
G[k]= - A[k] * exp(-dr*dr*w_sq_inv/2.0);
V *= 1.0 + G[k];
//fprintf(screen, "%f %f %f\n", xca[i][0],xca[i][1], xca[i][2]);
//fprintf(screen, "%f %f %f\n", xca[j][0],xca[j][1], xca[j][2]);
//fprintf(screen, "i %d j %d sigma %f\n", i_resno, j_resno, sigma_mb[k][i_resno][j_resno-4]);
//fprintf(screen, "r %f dr %f A %f G %e w_sq_inv %e\n", r, dr, A[k], G[k], w_sq_inv);
} else {
G[k] = 0.0;
}
}
VTotal = epsilon*((1.0 + R)*V - 1.0);
energy[ET_CONTACTS] += VTotal;
force = 12.0 * R * V / r;
//fprintf(screen, "R %f V %f f %f\n", R, V, force);
force_tmp_sum = 0.0 ;
for(k=0; k<n_basins; ++k){
if(isNative_mb[k][i_resno][j_resno-4]){
dr = r - sigma_mb[k][i_resno][j_resno-4] ;
force_tmp = G[k] * dr;
for(l=0; l<n_basins; ++l){
if(l != k ) {
force_tmp *= 1.0 + G[l];
}
}
force_tmp_sum += force_tmp ;
}
}
force_tmp_sum *= 1.0 + R ;
force += force_tmp_sum ;
//fprintf(screen, "f_tmp_sum %f force %f eps %f r %f\n", force_tmp_sum, force, epsilon, r);
force *= - epsilon / r ;
//fprintf(screen, "f_tmp_sum %f force %f\n", force_tmp_sum, force);
f[alpha_carbons[j]][0] -= force*dx[0];
//fprintf(screen, "f_tmp_sum %f force_final %f\n", force_tmp_sum, force*dx[0]);
f[alpha_carbons[j]][1] -= force*dx[1];
f[alpha_carbons[j]][2] -= force*dx[2];
f[alpha_carbons[i]][0] -= -force*dx[0];
f[alpha_carbons[i]][1] -= -force*dx[1];
f[alpha_carbons[i]][2] -= -force*dx[2];
}
void FixGoModel::out_xyz_and_force(int coord)
{
// out.precision(12);
fprintf(fout, "%d\n", Step);
fprintf(fout, "%d%d%d%d\n", bonds_flag, angles_flag, dihedrals_flag, contacts_flag);
fprintf(fout, "Number of atoms %d\n", n);
int index;
if (coord==1) {
fprintf(fout, "rca = {");
for (int i=0;i<nn;i++) {
index = alpha_carbons[i];
if (index!=-1) {
fprintf(fout, "{%.12f, %.12f, %.12f}", x[index][0], x[index][1], x[index][2]);
if (i!=nn-1) fprintf(fout, ",\n");
}
}
fprintf(fout, "};\n\n\n");
}
fprintf(fout, "fca = {");
for (int i=0;i<nn;i++) {
index = alpha_carbons[i];
if (index!=-1) {
fprintf(fout, "{%.12f, %.12f, %.12f}", f[index][0], f[index][1], f[index][2]);
if (i!=nn-1) fprintf(fout, ",\n");
}
}
fprintf(fout, "};\n\n\n\n");
}
void FixGoModel::compute_goModel()
{
ntimestep = update->ntimestep;
Step++;
if(atom->nlocal==0) return;
// int me,nprocs;
// MPI_Comm_rank(world,&me);
// MPI_Comm_size(world,&nprocs);
// Construct_Computational_Arrays();
x = atom->x;
f = atom->f;
image = atom->image;
int i, j, xbox, ybox, zbox;
int i_resno, j_resno;
for (int i=0;i<nEnergyTerms;++i) energy[i] = 0.0;
force_flag = 0;
for (i=0;i<nn;++i) {
// Calculating xca Ca atoms coordinates array
if ( (res_info[i]==LOCAL || res_info[i]==GHOST) ) {
if (domain->xperiodic) {
xbox = (image[alpha_carbons[i]] & 1023) - 512;
xca[i][0] = x[alpha_carbons[i]][0] + xbox*prd[0];
} else xca[i][0] = x[alpha_carbons[i]][0];
if (domain->yperiodic) {
ybox = (image[alpha_carbons[i]] >> 10 & 1023) - 512;
xca[i][1] = x[alpha_carbons[i]][1] + ybox*prd[1];
} else xca[i][1] = x[alpha_carbons[i]][1];
if (domain->zperiodic) {
zbox = (image[alpha_carbons[i]] >> 20) - 512;
xca[i][2] = x[alpha_carbons[i]][2] + zbox*prd[2];
} else xca[i][2] = x[alpha_carbons[i]][2];
}
}
// seed = random->state();
/* if (contacts_dev_flag)
compute_contact_deviation();
for (i=0;i<nn;++i) {
if (res_info[i]!=LOCAL) continue;
if (bonds_flag && res_no[i]<=n-1)
compute_bond(i);
if (angles_flag && res_no[i]<=n-2)
compute_angle(i);
if (dihedrals_flag && res_no[i]<=n-3)
compute_dihedral(i);
for (j=i+1;contacts_flag && j<nn;++j) {
if (res_info[j]!=LOCAL && res_info[j]!=GHOST) continue;
if (contacts_flag) {
if (lj_contacts_flag && res_no[i]<res_no[j]-3)
compute_contact(i, j);
if (gaussian_contacts_flag && res_no[i]<res_no[j]-3)
compute_contact_gaussian(i, j);
}
}
}*/
/* double tmp, tmp2;
double tmp_time;
int me,nprocs;
MPI_Comm_rank(world,&me);
MPI_Comm_size(world,&nprocs);
if (Step>=sStep && Step<=eStep) {
fprintf(fout, "At Start %d:\n", nn);
out_xyz_and_force(1);
}
if (contacts_dev_flag)
compute_contact_deviation();
tmp = energy[ET_BOND];
for (i=0;i<nn;i++) {
if (bonds_flag && res_info[i]==LOCAL && res_no[i]<=n-1)
compute_bond(i);
}
if (bonds_flag && Step>=sStep && Step<=eStep) {
fprintf(fout, "Bonds %d:\n", nn);
fprintf(fout, "Bonds_Energy: %.12f\n", energy[ET_BOND]-tmp);
out_xyz_and_force();
}
tmp = energy[ET_ANGLE];
for (i=0;i<nn;i++) {
if (angles_flag && res_info[i]==LOCAL && res_no[i]<=n-2)
compute_angle(i);
}
if (angles_flag && Step>=sStep && Step<=eStep) {
fprintf(fout, "Angles %d:\n", nn);
fprintf(fout, "Angles_Energy: %.12f\n", energy[ET_ANGLE]-tmp);
out_xyz_and_force();
}
tmp = energy[ET_DIHEDRAL];
for (i=0;i<nn;i++) {
if (dihedrals_flag && res_info[i]==LOCAL && res_no[i]<=n-3)
compute_dihedral(i);
}
if (dihedrals_flag && Step>=sStep && Step<=eStep) {
fprintf(fout, "Dihedrals %d:\n", nn);
fprintf(fout, "Dihedrals_Energy: %.12f\n", energy[ET_DIHEDRAL]-tmp);
out_xyz_and_force();
}
// fprintf(efout, "%.15f\n", epsilon + dev);
tmp = energy[ET_CONTACTS];
// if (contacts_flag && Step>=sStep && Step<=eStep) fprintf(fout, "\n{");
for (i=0;i<nn;i++) {
for (j=0;j<nn;j++) {
tmp2 = energy[ET_CONTACTS];
if (res_info[i]==LOCAL && (res_info[j]==LOCAL || res_info[j]==GHOST) && res_no[i]<res_no[j]-3){
if (lj_contacts_flag)
compute_contact(i, j);
if (gaussian_contacts_flag)
compute_contact_gaussian(i, j);