void State::run_md(Nuclear& mol, Electronic& el, Hamiltonian& ham){
if(md==NULL) { std::cout<<"Error: MD parameters have not been defined\n"; exit(1);}
if(!is_md_initialized){ std::cout<<"Error: Need to call init_md() first. MD is not initialized\n"; exit(2); }
int is_thermostat, is_barostat;
is_thermostat = ((thermostat!=NULL) && ((md->ensemble=="NVT")||(md->ensemble=="NPT")||(md->ensemble=="NPT_FLEX")));
is_barostat = ((barostat!=NULL) && ((md->ensemble=="NPT")||(md->ensemble=="NPT_FLEX")||(md->ensemble=="NPH")||(md->ensemble=="NPH_FLEX")));
double dt = md->dt;
double dt_half = 0.5*md->dt;
double Nf = syst->Nf_t + syst->Nf_r;
int Nf_b = 0;
if(is_barostat) {Nf_b = barostat->get_Nf_b();}
double scl,sc3,sc4,ksi_r;
MATRIX3x3 S,I,sc1,sc2;
while(md->curr_step<md->max_step){
// Operator NHCB(dt/2)
if(is_thermostat){
double ekin_baro = 0.0;
if(is_barostat){ ekin_baro = barostat->ekin_baro(); }
thermostat->update_thermostat_forces(syst->ekin_tr(),syst->ekin_rot(),ekin_baro);
thermostat->propagate_nhc(dt_half,syst->ekin_tr(),syst->ekin_rot(),ekin_baro);
}
if(is_thermostat){ thermostat->propagate_sPs(dt_half); }
//bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb
// Operator B(dt/2)
if(is_barostat){
if(md->ensemble=="NPT"||md->ensemble=="NPH"){ barostat->update_barostat_forces(syst->ekin_tr(),syst->ekin_rot(),curr_V,curr_P); }
else if(md->ensemble=="NPT_FLEX"||md->ensemble=="NPH_FLEX"){ barostat->update_barostat_forces(syst->ekin_tr(),syst->ekin_rot(),curr_V,curr_P_tens); }
scl = 0.0; if(is_thermostat){ scl = thermostat->get_ksi_b(); }
barostat->propagate_velocity(dt_half,scl);
}
//bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb
double s_var,Ps,dt_half_s,dt_over_s,dt_over_s2;
s_var = 1.0; Ps = 0.0;
dt_half_s = dt_half;
dt_over_s = dt;
dt_over_s2 = dt;
if(md->ensemble=="NVT"||md->ensemble=="NPT"||md->ensemble=="NPT_FLEX"||md->ensemble=="NPH"||md->ensemble=="NPH_FLEX"){
if(is_thermostat){
s_var = thermostat->get_s_var();
dt_half_s = dt_half*s_var;
dt_over_s = (dt/s_var);
dt_over_s2 = (dt_over_s/s_var);
}
}
//aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
// Operator A(dt/2)
//-------------------- Linear momentum propagation --------------------
S = 0.0; I.identity();
if(is_barostat){
if(Nf_b==9){ S = barostat->ksi_eps + (barostat->ksi_eps.tr()/(barostat->get_Nf_t()/*+barostat->get_Nf_r()*/))*I; }
else if(Nf_b==1){S = barostat->ksi_eps_iso * I + (3.0*barostat->ksi_eps_iso/(barostat->get_Nf_t()/*+barostat->get_Nf_r()*/))*I; }
}
if(is_thermostat){ S = S + thermostat->get_ksi_t() * I; }
sc1 = (exp_(S,-dt_half));//.symmetrized();
sc2 = dt_half*(exp1_(S,-dt_half*0.5));//.symmetrized()*dt_half;
//------------------- Angular momentum propagation -----------------------
if(is_thermostat){ ksi_r = thermostat->get_ksi_r();}else{ ksi_r = 0.0;}
sc3 = exp(-dt_half*ksi_r);
sc4 = dt_half*exp(-0.5*dt_half*ksi_r)*sinh_(0.5*dt_half*ksi_r);
for(int i=0;i<syst->Number_of_fragments;i++){
RigidBody& top = syst->Fragments[i].Group_RB;
//-------------------- Linear momentum propagation --------------------
top.scale_linear_(sc1);
top.apply_force(sc2);
//------------------- Angular momentum propagation -----------------------
top.scale_angular_(sc3);
top.apply_torque(sc4);
}// for i
// if(is_thermostat){
// thermostat->propagate_Ps(-dt_half*E_pot);
// }
//aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
if(is_thermostat){ thermostat->propagate_Ps(-dt_half*E_pot); }
//ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
//ccccccccccccccccccccccccccccccc Core part ccccccccccccccccccccccccccccccccccccc
sc1.identity();
sc2.identity();
sc2 = sc2 * dt;
if(is_barostat){
sc1 = (barostat->pos_scale(dt));
sc2 = dt*barostat->vpos_scale(dt);
}
for(i=0;i<syst->Number_of_fragments;i++){
RigidBody& top = syst->Fragments[i].Group_RB;
if(is_thermostat){ thermostat->propagate_Ps( 0.5*dt_over_s2*(top.ekin_rot()+top.ekin_tr()) ); }
double Ps,s_var;
s_var = 1.0; if(is_thermostat){ s_var = thermostat->s_var; }
Ps = 0.0;
if(md->integrator=="Jacobi") { top.propagate_exact_rb(dt_over_s); }
else if(md->integrator=="DLML") { top.propagate_dlml(dt_over_s,Ps); }
else if(md->integrator=="Terec") { top.propagate_terec(dt_over_s);}
else if(md->integrator=="qTerec") { top.propagate_qterec(dt_over_s);}
else if(md->integrator=="NO_SQUISH"){ top.propagate_no_squish(dt_over_s);}
else if(md->integrator=="KLN") { top.propagate_kln(dt_over_s);}
else if(md->integrator=="Omelyan"){ top.propagate_omelyan(dt_over_s);}
if(is_thermostat){ thermostat->propagate_Ps( 0.5*dt_over_s2*(top.ekin_rot()+top.ekin_tr()) ); }
if(is_barostat) {
top.scale_position(sc1);
top.shift_position(sc2*top.rb_p*top.rb_iM);
}
else{
top.shift_position(dt_over_s*top.rb_p*top.rb_iM);
}
}// for i - all fragments
if(is_thermostat){ thermostat->propagate_Ps(dt*( H0 - Nf*boltzmann*thermostat->Temperature*(log(thermostat->s_var)+1.0) ) ); }
// Update cell shape
if(is_barostat){
if(syst->is_Box) {
VECTOR t1_n,t2_n,t3_n; // new
VECTOR t1_o,t2_o,t3_o; // old
syst->Box = barostat->pos_scale(dt) * syst->Box;
/*
system->Boxold.get_vectors(t1_o,t2_o,t3_o);
system->Box.get_vectors(t1_n,t2_n,t3_n);
// Find minimal heights of old and new boxes
double h1_n,h2_n,h3_n;
double h1_o,h2_o,h3_o;
double V_n, V_o; // Volume
double max_n,min_n,max_o,min_o; // maximal and minimal heights new and old
V_n = fabs(system->Box.Determinant());
V_o = fabs(system->Boxold.Determinant());
VECTOR S;
S.cross(t2_n,t3_n); h1_n = V_n/fabs(S.length());
S.cross(t3_n,t1_n); h2_n = V_n/fabs(S.length());
S.cross(t1_n,t2_n); h3_n = V_n/fabs(S.length());
max_n = (h1_n>=h2_n)?h1_n:h2_n; min_n = (h1_n<=h2_n)?h1_n:h2_n;
max_n = (max_n>=h3_n)?max_n:h3_n; min_n = (min_n<=h3_n)?min_n:h3_n;
S.cross(t2_o,t3_o); h1_o = V_o/fabs(S.length());
S.cross(t3_o,t1_o); h2_o = V_o/fabs(S.length());
S.cross(t1_o,t2_o); h3_o = V_o/fabs(S.length());
max_o = (h1_o>=h2_o)?h1_o:h2_o; min_o = (h1_o<=h2_o)?h1_o:h2_o;
max_o = (max_o>=h3_o)?max_o:h3_o; min_o = (min_o<=h3_o)?min_o:h3_o;
int n_max = ceil((12.0+2.0)/min_n)+1;
int o_max = ceil((12.0+2.0)/min_o)+1;
n_max = (n_max>=o_max)?n_max:o_max;
double dt1,dt2;
dt1 = (max_n - min_o); dt1 = dt1*dt1;
dt2 = (max_o - min_n); dt2 = dt2*dt2;
system->dT_2 = 4.0*3.0*n_max*n_max*((dt1>=dt2)?dt1:dt2);
*/
}
}
// Update atomic positions and calculate interactions
for(i=0;i<syst->Number_of_fragments;i++){ syst->update_atoms_for_fragment(i); }
syst->zero_forces_and_torques();
//!!!!!!!!!!!!!!!!1 E_pot = system->energy(); !!!!!!!!!!!!!!!!1
syst->extract_atomic_q(mol.q); // syst -> mol
// E_pot = compute_potential_energy(mol, el, ham, 1); // # 1 - FSSH forces
E_pot = compute_forces(mol, el, ham, 1);
syst->set_atomic_f(mol.f); // mol -> syst
// Update rigid-body variables
syst->update_fragment_forces_and_torques();
//cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
//aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
// Operator A(dt/2)
E_kin = 0.0;
//-------------------- Linear momentum propagation --------------------
S = 0.0; I.identity();
if(is_barostat){
if(Nf_b==9){ S = barostat->ksi_eps + (barostat->ksi_eps.tr()/(barostat->get_Nf_t()/*+barostat->get_Nf_r()*/))*I; }
else if(Nf_b==1){S = barostat->ksi_eps_iso * I + (3.0*barostat->ksi_eps_iso/(barostat->get_Nf_t()/*+barostat->get_Nf_r()*/))*I; }
}
if(is_thermostat){ S = S + thermostat->get_ksi_t() * I; }
sc1 = (exp_(S,-dt_half));//.symmetrized();
sc2 = dt_half*(exp1_(S,-dt_half*0.5));//.symmetrized()*dt_half;
//------------------- Angular momentum propagation -----------------------
if(is_thermostat){ ksi_r = thermostat->get_ksi_r();}else{ ksi_r = 0.0;}
sc3 = exp(-dt_half*ksi_r);
sc4 = dt_half*exp(-0.5*dt_half*ksi_r)*sinh_(0.5*dt_half*ksi_r);
for(i=0;i<syst->Number_of_fragments;i++){
RigidBody& top = syst->Fragments[i].Group_RB;
//-------------------- Linear momentum propagation --------------------
top.scale_linear_(sc1);
top.apply_force(sc2);
//------------------- Angular momentum propagation -----------------------
top.scale_angular_(sc3);
top.apply_torque(sc4);
E_kin += (top.ekin_rot() + top.ekin_tr());
}// for i
//aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
if(is_thermostat){ thermostat->propagate_Ps( -dt_half*E_pot); }
//------- Update state variables ------------
curr_P_tens = syst->pressure_tensor();
curr_P = (curr_P_tens.tr()/3.0);
curr_V = syst->volume();
// curr_P_tens = 0.0;
// curr_P = 0.0;
// curr_V = 1e+10;
//-------------------------------------------
//bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb
// Operator B(dt/2)
if(is_barostat){
if(md->ensemble=="NPT"||md->ensemble=="NPH"){ barostat->update_barostat_forces(syst->ekin_tr(),syst->ekin_rot(),curr_V,curr_P); }
else if(md->ensemble=="NPT_FLEX"||md->ensemble=="NPH_FLEX"){ barostat->update_barostat_forces(syst->ekin_tr(),syst->ekin_rot(),curr_V,curr_P_tens); }
scl = 0.0; if(is_thermostat){ scl = thermostat->get_ksi_b(); }
barostat->propagate_velocity(dt_half,scl);
}
//bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb
if(is_thermostat){thermostat->propagate_sPs(dt_half); }
// Operator NHCB(dt/2)
if(is_thermostat){
double ekin_baro = 0.0;
if(is_barostat){ ekin_baro = barostat->ekin_baro(); }
thermostat->update_thermostat_forces(syst->ekin_tr(),syst->ekin_rot(),ekin_baro);
thermostat->propagate_nhc(dt_half,syst->ekin_tr(),syst->ekin_rot(),ekin_baro);
}
if(md->ensemble=="NVE"){ s_var = 1.0; Ps = 0.0;}
if(is_thermostat){ E_kin/=(thermostat->s_var*thermostat->s_var); }
E_kin_tr = syst->ekin_tr();
E_kin_rot = syst->ekin_rot();
E_tot = E_kin + E_pot;
// if(!is_H0){ H0 = E_tot + thermostat->energy(); is_H0 = 1;}
if(md->ensemble=="NVE"){ H_NP = E_tot; }
else if(md->ensemble=="NVT"){
if(is_thermostat){
if(!is_H0){ H0 = E_tot + thermostat->energy(); is_H0 = 1;}
if(thermostat->thermostat_type=="Nose-Poincare"){ H_NP = thermostat->s_var*(E_tot + thermostat->energy() - H0); }
else if(thermostat->thermostat_type=="Nose-Hoover"){ H_NP = E_tot + thermostat->energy(); }
}
}
else if(md->ensemble=="NPH"||md->ensemble=="NPH_FLEX"){
if(is_barostat){ H_NP = E_tot + barostat->ekin_baro() + curr_V * barostat->Pressure; }
}
else if(md->ensemble=="NPT" || md->ensemble=="NPT_FLEX"){
if(is_barostat){ H_NP = E_tot + barostat->ekin_baro() + curr_V * barostat->Pressure; }
if(is_thermostat){ H_NP += thermostat->energy(); }
}
curr_T = 2.0*E_kin/(Nf*(boltzmann/hartree));
//------------- Angular velocity --------------
L_tot = 0.0;
P_tot = 0.0;
for(i=0;i<syst->Number_of_fragments;i++){
RigidBody& top = syst->Fragments[i].Group_RB;
VECTOR tmp; tmp.cross(top.rb_cm,top.rb_p);
L_tot += top.rb_A_I_to_e_T * top.rb_l_e + tmp;
P_tot += top.rb_p;
}
md->curr_step++;
md->curr_time+=dt;
}// for s
md->curr_step = 0;
md->curr_time = 0.0;
}
inline void operator()(typename Exp::argument_type val) const {
print_(exp_(val));
}
