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fix_pimdb.cpp
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, [email protected]
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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Package FixPIMDB
Purpose Quantum Path Integral Algorithm for Quantum Chemistry
Copyright Voth Group @ University of Chicago
Authors Chris Knight & Yuxing Peng (yuxing at uchicago.edu)
Updated Oct-01-2011
Version 1.0
------------------------------------------------------------------------- */
#include <cmath>
#include <cstring>
#include <cstdlib>
#include <chrono>
#include <iostream>
#include <fstream>
#include "fix_pimdb.h"
#include "universe.h"
#include "comm.h"
#include "force.h"
#include "atom.h"
#include "domain.h"
#include "update.h"
#include "memory.h"
#include "error.h"
#include <algorithm>
using namespace LAMMPS_NS;
using namespace FixConst;
enum{PIMD,NMPIMD,CMD};
/* ---------------------------------------------------------------------- */
FixPIMDB::FixPIMDB(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
{
method = PIMD;
fmass = 1.0;
nhc_temp = 298.15;
nhc_nchain = 2;
sp = 1.0;
nevery = 100;
E_kn = std::vector<double>((atom->nlocal * (atom->nlocal + 1) / 2),0.0);
V = std::vector<double>((atom->nlocal + 1),0.0);
for(int i=3; i<narg-1; i+=2)
{
if(strcmp(arg[i],"method")==0)
{
if(strcmp(arg[i+1],"pimd")==0) method=PIMD;
else if(strcmp(arg[i+1],"nmpimd")==0) method=NMPIMD;
else if(strcmp(arg[i+1],"cmd")==0) method=CMD;
else error->universe_all(FLERR,"Unkown method parameter for fix pimd-B");
}
else if(strcmp(arg[i],"fmass")==0)
{
fmass = atof(arg[i+1]);
if(fmass<0.0 || fmass>1.0) error->universe_all(FLERR,"Invalid fmass value for fix pimd-B");
}
else if(strcmp(arg[i],"sp")==0)
{
sp = atof(arg[i+1]);
if(fmass<0.0) error->universe_all(FLERR,"Invalid sp value for fix pimd-B");
}
else if(strcmp(arg[i],"temp")==0)
{
nhc_temp = atof(arg[i+1]);
if(nhc_temp<0.0) error->universe_all(FLERR,"Invalid temp value for fix pimd-B");
}
else if(strcmp(arg[i],"nhc")==0)
{
nhc_nchain = atoi(arg[i+1]);
if(nhc_nchain<2) error->universe_all(FLERR,"Invalid nhc value for fix pimd-B");
}
else error->universe_all(arg[i],i+1,"Unkown keyword for fix pimd-B");
}
/* Initiation */
max_nsend = 0;
tag_send = NULL;
buf_send = NULL;
max_nlocal = 0;
buf_recv = NULL;
buf_beads = NULL;
size_plan = 0;
plan_send = plan_recv = NULL;
M_x2xp = M_xp2x = M_f2fp = M_fp2f = NULL;
lam = NULL;
mode_index = NULL;
mass = NULL;
array_atom = NULL;
nhc_eta = NULL;
nhc_eta_dot = NULL;
nhc_eta_dotdot = NULL;
nhc_eta_mass = NULL;
size_peratom_cols = 12 * nhc_nchain + 3;
nhc_offset_one_1 = 3 * nhc_nchain;
nhc_offset_one_2 = 3 * nhc_nchain +3;
nhc_size_one_1 = sizeof(double) * nhc_offset_one_1;
nhc_size_one_2 = sizeof(double) * nhc_offset_one_2;
restart_peratom = 1;
peratom_flag = 1;
peratom_freq = 1;
global_freq = 1;
thermo_energy = 1;
vector_flag = 1;
size_vector = 2;
extvector = 1;
comm_forward = 3;
atom->add_callback(0); // Call LAMMPS to allocate memory for per-atom array
atom->add_callback(1); // Call LAMMPS to re-assign restart-data for per-atom array
grow_arrays(atom->nmax);
// some initilizations
nhc_ready = false;
}
/* ---------------------------------------------------------------------- */
int FixPIMDB::setmask()
{
int mask = 0;
mask |= POST_FORCE;
mask |= INITIAL_INTEGRATE;
mask |= FINAL_INTEGRATE;
mask |= END_OF_STEP;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixPIMDB::init()
{
if (atom->map_style == 0)
error->all(FLERR,"Fix pimd-B requires an atom map, see atom_modify");
if(universe->me==0 && screen) fprintf(screen,"Fix pimd-B initializing Path-Integral ...\n");
// prepare the constants
np = universe->nworlds;
inverse_np = 1.0 / np;
/* The first solution for the force constant, using SI units
const double Boltzmann = 1.3806488E-23; // SI unit: J/K
const double Plank = 6.6260755E-34; // SI unit: m^2 kg / s
double hbar = Plank / ( 2.0 * M_PI ) * sp;
double beta = 1.0 / ( Boltzmann * input.nh_temp);
// - P / ( beta^2 * hbar^2) SI unit: s^-2
double _fbond = -1.0 / (beta*beta*hbar*hbar) * input.nbeads;
// convert the units: s^-2 -> (kcal/mol) / (g/mol) / (A^2)
fbond = _fbond * 4.184E+26;
*/
/* The current solution, using LAMMPS internal real units */
const double Boltzmann = force->boltz;
const double Plank = force->hplanck;
double hbar = Plank / ( 2.0 * M_PI );
double beta = 1.0 / (Boltzmann * nhc_temp);
double _fbond = 1.0 * np / (beta*beta*hbar*hbar) ;
omega_np = sqrt(np) / (hbar * beta) * sqrt(force->mvv2e);
fbond = - _fbond * force->mvv2e;
if(universe->me==0)
printf("Fix pimd-B -P/(beta^2 * hbar^2) = %20.7lE (kcal/mol/A^2)\n\n", fbond);
dtv = update->dt;
dtf = 0.5 * update->dt * force->ftm2v;
comm_init();
mass = new double [atom->ntypes+1];
if(method==CMD || method==NMPIMD) nmpimd_init();
else for(int i=1; i<=atom->ntypes; i++) mass[i] = atom->mass[i] / np * fmass;
if(!nhc_ready) nhc_init();
}
/* ---------------------------------------------------------------------- */
void FixPIMDB::setup(int vflag)
{
if(universe->me==0 && screen) fprintf(screen,"Setting up Path-Integral ...\n");
post_force(vflag);
end_of_step();
}
/* ---------------------------------------------------------------------- */
void FixPIMDB::initial_integrate(int /*vflag*/)
{
nhc_update_v();
nhc_update_x();
}
/* ---------------------------------------------------------------------- */
void FixPIMDB::final_integrate()
{
nhc_update_v();
}
/* ---------------------------------------------------------------------- */
void FixPIMDB::post_force(int /*flag*/)
{
for(int i=0; i<atom->nlocal; i++) for(int j=0; j<3; j++) atom->f[i][j] /= np;
comm_exec(atom->x);
spring_force();
if(method==CMD || method==NMPIMD)
{
/* forward comm for the force on ghost atoms */
nmpimd_fill(atom->f);
/* inter-partition comm */
comm_exec(atom->f);
/* normal-mode transform */
nmpimd_transform(buf_beads, atom->f, M_f2fp[universe->iworld]);
}
}
/* ----------------------------------------------------------------------
Nose-Hoover Chains
------------------------------------------------------------------------- */
void FixPIMDB::nhc_init()
{
double tau = 1.0 / omega_np;
double KT = force->boltz * nhc_temp;
double mass0 = KT * tau * tau;
int max = 3 * atom->nlocal;
for(int i=0; i<max; i++)
{
for(int ichain=0; ichain<nhc_nchain; ichain++)
{
nhc_eta[i][ichain] = 0.0;
nhc_eta_dot[i][ichain] = 0.0;
nhc_eta_dot[i][ichain] = 0.0;
nhc_eta_dotdot[i][ichain] = 0.0;
nhc_eta_mass[i][ichain] = mass0;
if((method==CMD || method==NMPIMD) && universe->iworld==0) ; else nhc_eta_mass[i][ichain] *= fmass;
}
nhc_eta_dot[i][nhc_nchain] = 0.0;
for(int ichain=1; ichain<nhc_nchain; ichain++)
nhc_eta_dotdot[i][ichain] = (nhc_eta_mass[i][ichain-1] * nhc_eta_dot[i][ichain-1]
* nhc_eta_dot[i][ichain-1] * force->mvv2e - KT) / nhc_eta_mass[i][ichain];
}
// Zero NH acceleration for CMD
if(method==CMD && universe->iworld==0) for(int i=0; i<max; i++)
for(int ichain=0; ichain<nhc_nchain; ichain++) nhc_eta_dotdot[i][ichain] = 0.0;
nhc_ready = true;
}
/* ---------------------------------------------------------------------- */
void FixPIMDB::nhc_update_x()
{
int n = atom->nlocal;
double **x = atom->x;
double **v = atom->v;
if(method==CMD || method==NMPIMD)
{
nmpimd_fill(atom->v);
comm_exec(atom->v);
/* borrow the space of atom->f to store v in cartisian */
v = atom->f;
nmpimd_transform(buf_beads, v, M_xp2x[universe->iworld]);
}
for(int i=0; i<n; i++)
{
x[i][0] += dtv * v[i][0];
x[i][1] += dtv * v[i][1];
x[i][2] += dtv * v[i][2];
}
}
/* ---------------------------------------------------------------------- */
void FixPIMDB::nhc_update_v()
{
int n = atom->nlocal;
int *type = atom->type;
double **v = atom->v;
double **f = atom->f;
for(int i=0; i<n; i++)
{
double dtfm = dtf / mass[type[i]];
v[i][0] += dtfm * f[i][0];
v[i][1] += dtfm * f[i][1];
v[i][2] += dtfm * f[i][2];
}
t_sys = 0.0;
if(method==CMD && universe->iworld==0) return;
double expfac;
int nmax = 3 * atom->nlocal;
double KT = force->boltz * nhc_temp;
double kecurrent, t_current;
double dthalf = 0.5 * update->dt;
double dt4 = 0.25 * update->dt;
double dt8 = 0.125 * update->dt;
for(int i=0; i<nmax; i++)
{
int iatm = i/3;
int idim = i%3;
double *vv = v[iatm];
kecurrent = mass[type[iatm]] * vv[idim]* vv[idim] * force->mvv2e;
t_current = kecurrent / force->boltz;
double *eta = nhc_eta[i];
double *eta_dot = nhc_eta_dot[i];
double *eta_dotdot = nhc_eta_dotdot[i];
eta_dotdot[0] = (kecurrent - KT) / nhc_eta_mass[i][0];
for(int ichain=nhc_nchain-1; ichain>0; ichain--)
{
expfac = exp(-dt8 * eta_dot[ichain+1]);
eta_dot[ichain] *= expfac;
eta_dot[ichain] += eta_dotdot[ichain] * dt4;
eta_dot[ichain] *= expfac;
}
expfac = exp(-dt8 * eta_dot[1]);
eta_dot[0] *= expfac;
eta_dot[0] += eta_dotdot[0] * dt4;
eta_dot[0] *= expfac;
// Update particle velocities half-step
double factor_eta = exp(-dthalf * eta_dot[0]);
vv[idim] *= factor_eta;
t_current *= (factor_eta * factor_eta);
kecurrent = force->boltz * t_current;
eta_dotdot[0] = (kecurrent - KT) / nhc_eta_mass[i][0];
for(int ichain=0; ichain<nhc_nchain; ichain++)
eta[ichain] += dthalf * eta_dot[ichain];
eta_dot[0] *= expfac;
eta_dot[0] += eta_dotdot[0] * dt4;
eta_dot[0] *= expfac;
for(int ichain=1; ichain<nhc_nchain; ichain++)
{
expfac = exp(-dt8 * eta_dot[ichain+1]);
eta_dot[ichain] *= expfac;
eta_dotdot[ichain] = (nhc_eta_mass[i][ichain-1] * eta_dot[ichain-1] * eta_dot[ichain-1]
- KT) / nhc_eta_mass[i][ichain];
eta_dot[ichain] += eta_dotdot[ichain] * dt4;
eta_dot[ichain] *= expfac;
}
t_sys += t_current;
}
t_sys /= nmax;
}
/* ----------------------------------------------------------------------
Normal Mode PIMD
------------------------------------------------------------------------- */
void FixPIMDB::nmpimd_init()
{
memory->create(M_x2xp, np, np, "fix_feynman:M_x2xp");
memory->create(M_xp2x, np, np, "fix_feynman:M_xp2x");
memory->create(M_f2fp, np, np, "fix_feynman:M_f2fp");
memory->create(M_fp2f, np, np, "fix_feynman:M_fp2f");
lam = (double*) memory->smalloc(sizeof(double)*np, "FixPIMDB::lam");
// Set up eigenvalues
lam[0] = 0.0;
if(np%2==0) lam[np-1] = 4.0 * np;
for(int i=2; i<=np/2; i++)
{
lam[2*i-3] = lam[2*i-2] = 2.0 * np * (1.0 - 1.0 *cos(2.0*M_PI*(i-1)/np));
}
// Set up eigenvectors for non-degenerated modes
for(int i=0; i<np; i++)
{
M_x2xp[0][i] = 1.0 / np;
if(np%2==0) M_x2xp[np-1][i] = 1.0 / np * pow(-1.0, i);
}
// Set up eigenvectors for degenerated modes
for(int i=0; i<(np-1)/2; i++) for(int j=0; j<np; j++)
{
M_x2xp[2*i+1][j] = sqrt(2.0) * cos ( 2.0 * M_PI * (i+1) * j / np) / np;
M_x2xp[2*i+2][j] = - sqrt(2.0) * sin ( 2.0 * M_PI * (i+1) * j / np) / np;
}
// Set up Ut
for(int i=0; i<np; i++)
for(int j=0; j<np; j++)
{
M_xp2x[i][j] = M_x2xp[j][i] * np;
M_f2fp[i][j] = M_x2xp[i][j] * np;
M_fp2f[i][j] = M_xp2x[i][j];
}
// Set up masses
int iworld = universe->iworld;
for(int i=1; i<=atom->ntypes; i++)
{
mass[i] = atom->mass[i];
if(iworld)
{
mass[i] *= lam[iworld];
mass[i] *= fmass;
}
}
}
/* ---------------------------------------------------------------------- */
void FixPIMDB::nmpimd_fill(double **ptr)
{
comm_ptr = ptr;
comm->forward_comm_fix(this);
}
/* ---------------------------------------------------------------------- */
void FixPIMDB::nmpimd_transform(double** src, double** des, double *vector)
{
int n = atom->nlocal;
int m = 0;
for(int i=0; i<n; i++) for(int d=0; d<3; d++)
{
des[i][d] = 0.0;
for(int j=0; j<np; j++) { des[i][d] += (src[j][m] * vector[j]); }
m++;
}
}
//dE_n^(k) is a function of k atoms (R_n-k+1,...,R_n) for a given n and k.
std::vector<double> FixPIMDB::Evaluate_dEkn_on_atom(const int n, const int k, const int atomnum)
{
//dE_n^(k)(R_n-k+1,...,R_n) is a function of k atoms
if (atomnum < n-k or atomnum > n-1 ) { return std::vector<double>(3, 0.0); }
else {
//bead is the bead number of current replica. bead = 0,...,np-1.
int bead = universe->iworld;
double **x = atom->x;
double *_mass = atom->mass;
int *type = atom->type;
int nlocal = atom->nlocal;
//xnext is a pointer to first element of buf_beads[x_next].
//See in FixPIMDB::comm_init() for the definition of x_next.
//x_next is basically (bead + 1) for bead in (0,...,np-2) and 0 for bead = np-1.
//buf_beads[j] is a 1-D array of length 3*nlocal x0^j,y0^j,z0^j,...,x_(nlocal-1)^j,y_(nlocal-1)^j,z_(nlocal-1)^j.
double *xnext = buf_beads[x_next];
double *xlast = buf_beads[x_last];
//omega^2, could use fbond instead?
double omega_sq = omega_np * omega_np;
//dE_n^(k)(R_n-k+1,...,R_n) is a function of k atoms
//But derivative if for atom atomnum
xnext += 3 * (atomnum);
xlast += 3 * (atomnum);
//np is total number of beads
if (bead == np - 1 && k > 1){
atomnum == n - 1 ? (xnext-= 3*(k - 1)) : (xnext += 3);
}
if (bead == 0 && k > 1){
atomnum == n-k ? (xlast+= 3*(k - 1)) : (xlast -= 3);
}
//if (bead == np - 1 && k > 1) xnext += 3;
//if (bead == 0 && k > 1) xlast -= 3;
/*
if(bead==3 && n==1 && k==1) {
std::cout << "atom " << atomnum + 1 << ", bead" << bead + 1 << ": " << x[atomnum][0] << " " << x[atomnum][1] << " " << x[atomnum][2]
<< std::endl;
std::cout << "next " << atomnum + 1 << ", bead" << bead + 1 << ": " << xnext[0] << " " << xnext[1] << " " << xnext[2]
<< std::endl;
}*/
std::vector<double> res(3);
/*
std::cout<< "atom " << atomnum+1 << ", bead" << bead + 1 << ": " << x[atomnum][0] << " " << x[atomnum][1] << " " << x[atomnum][2] << std::endl;
std::cout<< "next " << atomnum+1 << ", bead" << bead + 1 << ": " << xnext[0] << " " << xnext[1] << " " << xnext[2] << std::endl;
std::cout<< "last " << atomnum+1 << ", bead" << bead + 1 << ": " << xlast[0] << " " << xlast[1] << " " << xlast[2] << std::endl;
*/
double delx1 = xnext[0] - x[atomnum][0];
double dely1 = xnext[1] - x[atomnum][1];
double delz1 = xnext[2] - x[atomnum][2];
domain->minimum_image(delx1, dely1, delz1);
double delx2 = xlast[0] - x[atomnum][0];
//std::cout<< xnext[0] << std::endl;
double dely2 = xlast[1] - x[atomnum][1];
double delz2 = xlast[2] - x[atomnum][2];
domain->minimum_image(delx2, dely2, delz2);
double dx = -1.0*(delx1 + delx2);
double dy = -1.0*(dely1 + dely2);
double dz = -1.0*(delz1 + delz2);
//std::cout << delx << " " <<dely << " " << delz << std::endl;
//std::cout << _mass[type[i]] << " " << omega_sq << " " << delx*delx << std::endl;
res.at(0) = _mass[type[atomnum]] * omega_sq * dx;
res.at(1) = _mass[type[atomnum]] * omega_sq * dy;
res.at(2) = _mass[type[atomnum]] * omega_sq * dz;
//std::cout << bead << ": " << res.at(0) << " " << res.at(1) << " " << res.at(2) << std::endl;
return res;
}
}
/* ---------------------------------------------------------------------- */
//E_n^(k) is a function of k atoms (R_n-k+1,...,R_n) for a given n and k.
double FixPIMDB::Evaluate_Ekn(const int n, const int k)
{
//bead is the bead number of current replica. bead = 0,...,np-1.
int bead = universe->iworld;
double **x = atom->x;
double* _mass = atom->mass;
int* type = atom->type;
int nlocal = atom->nlocal;
//xnext is a pointer to first element of buf_beads[x_next].
//See in FixPIMDB::comm_init() for the definition of x_next.
//x_next is basically (bead + 1) for bead in (0,...,np-2) and 0 for bead = np-1.
//buf_beads[j] is a 1-D array of length 3*nlocal x0^j,y0^j,z0^j,...,x_(nlocal-1)^j,y_(nlocal-1)^j,z_(nlocal-1)^j.
double* xnext = buf_beads[x_next];
//omega^2, could use fbond instead?
double omega_sq = omega_np*omega_np;
//E_n^(k)(R_n-k+1,...,R_n) is a function of k atoms
xnext += 3*(n-k);
//np is total number of beads
if(bead == np-1 && k > 1) xnext += 3;
spring_energy = 0.0;
for (int i = n-k; i < n ; ++i) {
/*if(bead==3 && n==2 && k==2) {
std::cout << "atom " << i + 1 << ", bead" << bead + 1 << ": " << x[i][0] << " " << x[i][1] << " " << x[i][2]
<< std::endl;
std::cout << "next " << i + 1 << ", bead" << bead + 1 << ": " << xnext[0] << " " << xnext[1] << " " << xnext[2]
<< std::endl;
}*/
double delx = xnext[0] - x[i][0];
//std::cout<< xnext[0] << std::endl;
double dely = xnext[1] - x[i][1];
double delz = xnext[2] - x[i][2];
domain->minimum_image(delx, dely, delz);
if (bead == np - 1 && i == n - 2) {
/*if(bead==3 && n==2 && k==2) {
std::cout<<"I AM HERE"<<std::endl;
std::cout << "next " << i + 1 << ", bead" << bead + 1 << ": " << xnext[0] << " " << xnext[1] << " " << xnext[2]
<< std::endl;
}*/
xnext = buf_beads[x_next];
/*if(bead==3 && n==2 && k==2) {
std::cout<<"NOW I AM HERE"<<std::endl;
std::cout << "next " << i + 1 << ", bead" << bead + 1 << ": " << xnext[0] << " " << xnext[1] << " " << xnext[2]
<< std::endl;
}*/
//std::cout<<bead<<std::endl;
//std::cout<< xnext[0] << " " << xnext[1]<< " " << xnext[2] << std::endl;
xnext += 3*(n - k);
} else xnext += 3;
//std::cout << delx << " " <<dely << " " << delz << std::endl;
//std::cout << _mass[type[i]] << " " << omega_sq << " " << delx*delx << std::endl;
spring_energy += 0.5*_mass[type[i]]*omega_sq*(delx*delx + dely*dely + delz*delz);
}
double energy_all = 0.0;
double energy_local = spring_energy;
//double energy_local = 0.0;
//if(bead==0 && n==2 && k==2)
//std::cout<< universe->iworld << " " << spring_energy <<" " << energy_all <<std::endl;
//MPI_Allreduce(&spring_energy,&energy_local,1,MPI_DOUBLE,MPI_SUM,world);
//MPI_Allreduce(&energy_local,&energy_all,1,MPI_DOUBLE,MPI_SUM,universe->uworld);
MPI_Allreduce(MPI_IN_PLACE,&energy_local,1,MPI_DOUBLE,MPI_SUM,universe->uworld);
if(isnan(spring_energy) || isnan(energy_all)){
std::cout<< universe->iworld << " " << spring_energy <<" " << energy_all <<std::endl;
exit(0);}
//return energy_all;
return energy_local;
}
std::vector<std::vector<double>>
FixPIMDB::Evaluate_dVBn(const std::vector<double> &V, const std::vector<double> &save_E_kn, const int n) {
const double Boltzmann = force->boltz;
double beta = 1.0 / (Boltzmann * nhc_temp);
int bead = universe->iworld;
double **f = atom->f;
int nlocal = atom->nlocal;
std::vector<std::vector<double>> dV_all(n, std::vector<double>(3,0.0));
//std::cout<<dV_all.at(0).size()<<std::endl;
for (int atomnum = 0; atomnum < nlocal; ++atomnum) {
std::vector<std::vector<double>> dV(n+1, std::vector<double>(3,0.0));
dV.at(0) = {0.0,0.0,0.0};
for (int m = 1; m < n + 1; ++m) {
std::vector<double> sig(3,0.0);
if (atomnum > m-1) {
dV.at(m) = {0.0,0.0,0.0};
}else{
//for (int k = 1; k < m + 1; ++k) {
int count = m*(m-1)/2;
//!BH! I had to add 0.5 below in order to not get sigma which is zero or inf for large systems
double Elongest = 0.5*(save_E_kn.at(m*(m-1)/2)+V.at(m-1));
//double Elongest = save_E_kn.at(m*(m-1)/2);
//std::cout<<"Elongest: "<<Elongest<<std::endl;
/*
for (int k = m; k > 0; --k) {
std::vector<double> dE_kn(3,0.0);
dE_kn = Evaluate_dEkn_on_atom(m,k,atomnum);
sig.at(0) += (dE_kn.at(0) + dV.at(m - k).at(0)) * exp(-beta * (save_E_kn.at(count) + V.at(m - k)-Elongest));
sig.at(1) += (dE_kn.at(1) + dV.at(m - k).at(1)) * exp(-beta * (save_E_kn.at(count) + V.at(m - k)-Elongest));
sig.at(2) += (dE_kn.at(2) + dV.at(m - k).at(2)) * exp(-beta * (save_E_kn.at(count) + V.at(m - k)-Elongest));
count++;
}
std::vector<double> num(3,0.0);
num.at(0) = Elongest-1.0/beta*log(sig.at(0));
num.at(1) = Elongest-1.0/beta*log(sig.at(1));
num.at(2) = Elongest-1.0/beta*log(sig.at(2));
//double denom = -1.0/beta*log((double)m)+ V.at(m);
//std::cout<<m<<" "<<beta<<" "<<V.at(m)<<std::endl;
//std::cout<<"sig[0] is: " << sig[0] << " V.at(m) is: "<< V.at(m) <<std::endl;
//dV.at(m).at(0) = exp(-beta*(num.at(0)-denom));
//dV.at(m).at(1) = exp(-beta*(num.at(1)-denom));
//dV.at(m).at(2) = exp(-beta*(num.at(2)-denom));
double sig_denom_m = (double)m*exp(-beta*V.at(m));
dV.at(m).at(0) = sig.at(0) / sig_denom_m;
dV.at(m).at(1) = sig.at(1) / sig_denom_m;
dV.at(m).at(2) = sig.at(2) / sig_denom_m;
*/
//std::cout<<"m: " << m<<" beta: "<<beta <<" num[0]: " <<num.at(0)<<" denom: "<<denom<<std::endl;
//exit(1);
for (int k = m; k > 0; --k) {
std::vector<double> dE_kn(3,0.0);
dE_kn = Evaluate_dEkn_on_atom(m,k,atomnum);
/*
if(bead==0 && atomnum==1) {
std::cout << "m: " << m << " k: " << k <<" Ekn:" << save_E_kn.at(count)* 2625.499638
<<" V_k-m:" << V.at(m - k)* 2625.499638 << std::endl;
}*/
sig.at(0) += (dE_kn.at(0) + dV.at(m - k).at(0)) * exp(-beta * (save_E_kn.at(count) + V.at(m - k)-Elongest));
sig.at(1) += (dE_kn.at(1) + dV.at(m - k).at(1)) * exp(-beta * (save_E_kn.at(count) + V.at(m - k)-Elongest));
sig.at(2) += (dE_kn.at(2) + dV.at(m - k).at(2)) * exp(-beta * (save_E_kn.at(count) + V.at(m - k)-Elongest));
count++;
}
double sig_denom_m = (double)m*exp(-beta*(V.at(m)-Elongest));
if(sig_denom_m ==0 || isnan(sig_denom_m) || isinf(sig_denom_m) || isnan(sig.at(0)) || isinf(sig.at(0))) {
if (universe->iworld ==0){
std::cout << "m is: "<< m << " Elongest is: " << Elongest << " V.at(m-1) is " <<V.at(m-1)<< " beta is: " << beta << " sig_denom_m is: " <<sig_denom_m << std::endl;
}
}
//std::cout<<m<<" "<<beta<<" "<<V.at(m)<<std::endl;
//std::cout<<"sig[0] is: " <<sig.at(0)<<" sig_denom_m is: "<<sig_denom_m<<std::endl;
dV.at(m).at(0) = sig.at(0) / sig_denom_m;
dV.at(m).at(1) = sig.at(1) / sig_denom_m;
dV.at(m).at(2) = sig.at(2) / sig_denom_m;
if(isinf(dV.at(m).at(0)) || isnan(dV.at(m).at(0))) {
if (universe->iworld ==0){
std::cout << "sig_denom_m is: " << sig_denom_m << " Elongest is: " << Elongest
<< " V.at(m) is " << V.at(m) << " beta is " << beta << std::endl;}
exit(0);
}
}
}
/*if(bead==0 &&atomnum==0)
std::cout <<"atom: " << atomnum+1 <<" bead: "<< bead+1 << " dV: " << dV.at(n).at(0)<<" "<< dV.at(n).at(1)<< " "<<dV.at(n).at(2) <<std::endl;
*/
//std::cout<<"index: " <<(atomnum)*np + (bead)<<std::endl;
dV_all.at((atomnum)).at(0) = dV.at(n).at(0);
dV_all.at((atomnum)).at(1) = dV.at(n).at(1);
dV_all.at((atomnum)).at(2) = dV.at(n).at(2);
/*if(bead==0)
std::cout <<"atom: " << atomnum+1 <<" bead: "<< bead+1 << " fbefore: " << f[atomnum][0]<<" "<< f[atomnum][1]<< " "<<f[atomnum][2] <<std::endl;
*/
f[atomnum][0] -= dV.at(n).at(0);
f[atomnum][1] -= dV.at(n).at(1);
f[atomnum][2] -= dV.at(n).at(2);
/*if(bead==0)
std::cout <<"atom: " << atomnum+1 <<" bead: "<< bead+1 << " fafter: " << f[atomnum][0]<<" "<< f[atomnum][1]<< " "<<f[atomnum][2] <<std::endl;
*/
}
return dV_all;
}
std::vector<double> FixPIMDB::Evaluate_VBn(std::vector <double>& V, const int n)
{
const double Boltzmann = force->boltz;
double beta = 1.0 / (Boltzmann * nhc_temp);
std::vector<double> save_E_kn(n*(n+1)/2);
int count = 0;
for (int m = 1; m < n+1; ++m) {
double sig_denom = 0.0;
double Elongest=0.0;
//for (int k = 1; k < m+1; ++k) {
for (int k = m; k > 0; --k) {
double E_kn;
E_kn = Evaluate_Ekn(m,k);
if(k==m){
//!BH! I had to add 0.5 below in order to not get sigma which is zero or inf for large systems
Elongest = 0.5*(E_kn+V.at(m-1));
//Elongest = E_kn;
//Elongest = 0.5*E_kn;
//Elongest = 0.5*(std::max(E_kn,V.at(m-1)));
}
//std::cout<<"Elongest: "<<Elongest<<std::endl;
sig_denom += exp(-beta*(E_kn + V.at(m-k)-Elongest));
//save_E_kn.push_back(E_kn);
save_E_kn.at(count) = E_kn;
count++;
if(sig_denom ==0 || isnan(sig_denom) || isinf(sig_denom)) {
if (universe->iworld ==0){
std::cout << "m is: "<<m << " k is: " <<k << " E_kn is: " << E_kn << " V.at(m-k) is: " << V.at(m - k) << " Elongest is: " << Elongest
<< " V.at(m-1) is " <<V.at(m-1)<< " beta is: " << beta << " sig_denom is: " <<sig_denom << std::endl;}
}
}
V.at(m) = Elongest-1.0/beta*log(sig_denom / (double)m);
if(isinf(V.at(m)) || isnan(V.at(m))) {
if (universe->iworld ==0){
std::cout << "sig_denom is: " << sig_denom << " Elongest is: " << Elongest
<< std::endl;}
exit(0);
}
//std::cout<< sig_denom << " " << log (sig_denom / (double)m) << " " << beta <<std::endl;
}
return save_E_kn;
}
/* ---------------------------------------------------------------------- */
void FixPIMDB::spring_force() {
int nlocal = atom->nlocal;
V.at(0) = 0.0;
std::vector<std::vector<double>> dV(nlocal * universe->nworlds, std::vector<double>(3, 0.0));
//if(universe->iworld ==0)
//std::cout<<"replica\tn\tt_V[microsec]\tt_dV[microsec]"<<std::endl;
//auto start = std::chrono::high_resolution_clock::now();
E_kn = Evaluate_VBn(V, nlocal);
//auto elapsed = std::chrono::high_resolution_clock::now() - start;
//long long microseconds = std::chrono::duration_cast<std::chrono::microseconds>(elapsed).count();
////std::cout<<nlocal<<"\t"<<microseconds<<";"<<std::endl;
//auto start_d = std::chrono::high_resolution_clock::now();
dV = Evaluate_dVBn(V,E_kn,nlocal);
//auto elapsed_d = std::chrono::high_resolution_clock::now() - start_d;
//long long microseconds_d = std::chrono::duration_cast<std::chrono::microseconds>(elapsed_d).count();
////std::cout<<nlocal<<"\t"<<microseconds_d<<";"<<std::endl;
//std::cout<<universe->iworld <<"\t"<<nlocal<<"\t"<<microseconds<<"\t"<<microseconds_d<<";"<<std::endl;
//PRINTING FOR DEBUGGING/
/*
if(universe->iworld ==0) {
//std::cout<<nlocal<<"\t"<<microseconds<<"\t"<<microseconds_d<<";"<<std::endl;
for (double val : V)
std::cout << val << std::endl;
std::cout << "" << std::endl;
for (double val : E_kn)
std::cout << val << std::endl;
std::cout << "" << std::endl;
for(std::vector<double> vec: dV) {
std::cout << vec[0] <<" " <<vec[1] <<" " <<vec[2] <<std::endl;
std::cout << std::endl;
}
}
*/
/*
int atomnum =1;
int beadnum =3;
if (universe->iworld ==beadnum) {
for (int m = 1; m < atom->nlocal + 1; ++m) {
for (int k = 1; k < m + 1; ++k) {
std::vector<double> dE = Evaluate_dEkn_on_atom(m, k, atomnum);
std::cout <<"atom " << atomnum+1 << " bead " << universe->iworld +1 << " n " << m << " k " << k << " " << dE.at(0) << " " << dE.at(1) << " " << dE.at(2) << std::endl;
}
}
}*/
//double E = Evaluate_Ekn(3,3);
//std::vector<double> dE = Evaluate_dEkn_on_atom(3,3,0);
}
/* ----------------------------------------------------------------------
OLD spring_force!!!!!!!!!!!!!!!!!!!!!!
---------------------------------------------------------------------- */
/*
void FixPIMDB::spring_force()
{
spring_energy = 0.0;
double **x = atom->x;
double **f = atom->f;
double* _mass = atom->mass;
int* type = atom->type;
int nlocal = atom->nlocal;
double* xlast = buf_beads[x_last];
double* xnext = buf_beads[x_next];
for(int i=0; i<nlocal; i++)
{
double delx1 = xlast[0] - x[i][0];
double dely1 = xlast[1] - x[i][1];
double delz1 = xlast[2] - x[i][2];
xlast += 3;
domain->minimum_image(delx1, dely1, delz1);
double delx2 = xnext[0] - x[i][0];
double dely2 = xnext[1] - x[i][1];
double delz2 = xnext[2] - x[i][2];
xnext += 3;
domain->minimum_image(delx2, dely2, delz2);
double ff = fbond * _mass[type[i]];
double dx = delx1+delx2;
double dy = dely1+dely2;
double dz = delz1+delz2;
f[i][0] -= (dx) * ff;
f[i][1] -= (dy) * ff;
f[i][2] -= (dz) * ff;
spring_energy += (dx*dx+dy*dy+dz*dz);
}
}
*/
//FOR PRINTING ENERGIES AND POTENTIALS FOR PIMD-B
void FixPIMDB::end_of_step() {
if (universe->iworld == 0) {
//std::cout << "E1\tE12\tE2\tE123\tE23\tE3\tVB0\tVB1\tVB2\tVB3" <<std::endl;
//#! FIELDS time E1 E2 E12 E3 E23 E123 VB1 VB2 VB3 E_ox3 Vr.bias
std::ofstream myfile;
myfile.open ("pimdb.log", std::ios::out | std::ios::app);
for (double val: E_kn)
myfile << val * 2625.499638 << " ";
for (double val: V)
myfile << val * 2625.499638 << " ";
myfile << std::endl;
myfile.close();