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alexvakimov committed Jun 5, 2022
2 parents 01c7f4d + 20bf3bf commit 6eb3f5d
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9 changes: 6 additions & 3 deletions CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -96,9 +96,12 @@ SET(EIGEN3_INCLUDE_DIRS "${EIGEN3_INCLUDE_DIR}")

# Libint2 2.7.0 CONFIG REQUIRED COMPONENTS shared gss e5 g5
#FIND_PACKAGE(Libint2 MODULE 2.7.0)
FIND_PACKAGE(Libint2 CONFIG 2.7.0 REQUIRED COMPONENTS shared gss e5 g5)
#find_package(Libint2)
FIND_PACKAGE(Libint2 CONFIG 2.7.1 REQUIRED COMPONENTS shared gss impure_sh onebody_d0_l6 g12_d0_l4 g12_d1_l4 eri_c4_d0_l5 eri_c4_d1_l4) #gss e5 g5)
IF(Libint2_FOUND)
INCLUDE_DIRECTORIES("${Libint2_INCLUDE_DIRS}")
#INCLUDE_DIRECTORIES("${Libint2_INCLUDE_DIRS}")
INCLUDE_DIRECTORIES(Libint2::int2 Libint2::cxx Libint2::int2-cxx Libint2::impure_sh Libint2::gss Libint2::onebody_d0_l6 Libint::g12_d0_l4 Libint2::g12_d1_l4 Libint2::shared Libint2::cxx_ho Libint2::c Libint2::eri_c4_d0_l5 Libint2::eri_c4_d1_l4)
MESSAGE("${LIBINT2_INCLUDE_DIR}")
MESSAGE("Found Libint2 include directory: ")
MESSAGE("${Libint2_INCLUDE_DIRS}")
MESSAGE("Found Libint2_LIBRARIES: ")
Expand Down Expand Up @@ -136,7 +139,7 @@ ENDIF()
#
# Set the libraries
#
SET( ext_libs ${Boost_LIBRARIES} ${PYTHON_LIBRARIES} )
SET( ext_libs ${Boost_LIBRARIES} ${PYTHON_LIBRARIES})



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16 changes: 15 additions & 1 deletion README.md
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Expand Up @@ -26,6 +26,20 @@ for all users with the intent:
knowledge and skills with others;


## Installation Videotutorials (as of 5/16/2022)

* [Installing WSL2](https://ub.hosted.panopto.com/Panopto/Pages/Embed.aspx?id=02184b70-7745-4eb4-a776-ae92014c652a&autoplay=false&offerviewer=true&showtitle=true&showbrand=true&captions=false&interactivity=all)

* [Installing WSL2: After reboot](https://ub.hosted.panopto.com/Panopto/Pages/Embed.aspx?id=972aef79-e235-4a90-9ce1-ae92014d34db&autoplay=false&offerviewer=true&showtitle=true&showbrand=true&captions=false&interactivity=all)

* [Installing Ubuntu on Windows 11](https://ub.hosted.panopto.com/Panopto/Pages/Embed.aspx?id=31a63536-f333-4242-9b56-ae92015ece64&autoplay=false&offerviewer=true&showtitle=true&showbrand=true&captions=false&interactivity=all)

* [Creating Conda environment for Libra](https://ub.hosted.panopto.com/Panopto/Pages/Embed.aspx?id=d6ada23e-7e16-4b7a-b290-ae920188627c&autoplay=false&offerviewer=true&showtitle=true&showbrand=true&captions=false&interactivity=all)

* [Installing Libra](https://ub.hosted.panopto.com/Panopto/Pages/Embed.aspx?id=7f8dd8c4-9f58-4ca0-a8cb-ae930166b7ec&autoplay=false&offerviewer=true&showtitle=true&showbrand=true&captions=false&interactivity=all)



## Installation (as of after 5/14/2021)

### 1. Install miniconda (for Python 3.8) and activate Conda
Expand Down Expand Up @@ -131,7 +145,7 @@ We need to downgrade Python version here to 3.6 to enable Psi4 installation
You can install Jupyter notebook using the following command. This will be useful and you can set up and access the Jupyter notebook
remotely from a cluster and load the tutorials

conda install -c conda-forge jupyterlab
conda install -c anaconda jupyter


Used in some of the tutorials
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102 changes: 62 additions & 40 deletions src/dyn/Dynamics.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -248,7 +248,7 @@ CMATRIX transform_amplitudes(int rep_in, int rep_out, CMATRIX& C, nHamiltonian&


//vector<CMATRIX> compute_St(nHamiltonian& ham, CMATRIX** Uprev){
vector<CMATRIX> compute_St(nHamiltonian& ham, vector<CMATRIX>& Uprev){
vector<CMATRIX> compute_St(nHamiltonian& ham, vector<CMATRIX>& Uprev, int isNBRA){
/**
This function computes the time-overlap matrices for all trajectories
Expand All @@ -258,16 +258,26 @@ vector<CMATRIX> compute_St(nHamiltonian& ham, vector<CMATRIX>& Uprev){
int ntraj = ham.children.size();

vector<CMATRIX> St(ntraj, CMATRIX(nst, nst));

if(isNBRA==1){
St[0] = Uprev[0].H() * ham.children[0]->get_basis_transform();
}
else{
for(int traj=0; traj<ntraj; traj++){
St[traj] = Uprev[traj].H() * ham.children[traj]->get_basis_transform();
}

}
return St;

}

vector<CMATRIX> compute_St(nHamiltonian& ham){
vector<CMATRIX> compute_St(nHamiltonian& ham, vector<CMATRIX>& Uprev){

int is_nbra = 0;
return compute_St(ham, Uprev, is_nbra);

}

vector<CMATRIX> compute_St(nHamiltonian& ham, int isNBRA){
/**
This function computes the time-overlap matrices for all trajectories
Expand All @@ -277,16 +287,23 @@ vector<CMATRIX> compute_St(nHamiltonian& ham){
int ntraj = ham.children.size();

vector<CMATRIX> St(ntraj, CMATRIX(nst, nst));

if(isNBRA==1){
St[0] = ham.children[0]->get_time_overlap_adi();
}
else{
for(int traj=0; traj<ntraj; traj++){
St[traj] = ham.children[traj]->get_time_overlap_adi();
}

}
return St;

}

vector<CMATRIX> compute_St(nHamiltonian& ham){
int is_nbra = 1;

return compute_St(ham, is_nbra);
}


void apply_afssh(dyn_variables& dyn_var, CMATRIX& C, vector<int>& act_states, MATRIX& invM,
Expand Down Expand Up @@ -487,20 +504,20 @@ void compute_dynamics(MATRIX& q, MATRIX& p, MATRIX& invM, CMATRIX& C, vector<CMA




dyn_control_params prms;
prms.set_parameters(dyn_params);

int i,j;
int cdof;
int ndof = q.n_rows;
int ntraj = q.n_cols;
int ntraj1;
int nst = C.n_rows;
int traj, dof, idof;
int n_therm_dofs;
int num_el = prms.num_electronic_substeps;
double dt_el = prms.dt / num_el;

//cout << "Flag 1 isNBRA " << prms.isNBRA << endl;

//dyn_variables dyn_var(nst, nst, ndof, ntraj);

Expand All @@ -510,11 +527,22 @@ void compute_dynamics(MATRIX& q, MATRIX& p, MATRIX& invM, CMATRIX& C, vector<CMA
vector<int> project_out_states(ntraj); // for DISH

vector<CMATRIX> Uprev;
vector<CMATRIX> St(ntraj, CMATRIX(nst, nst));
vector<CMATRIX> Eadi(ntraj, CMATRIX(nst, nst));
vector<MATRIX> decoherence_rates(ntraj, MATRIX(nst, nst));
vector<double> Ekin(ntraj, 0.0);
vector<MATRIX> prev_ham_dia(ntraj, MATRIX(nst, nst));
// Defining ntraj1 as a reference for making these matrices
// ntraj is defined as q.n_cols as since it would be large in NBRA
// we can define another variable like ntraj1 and build the matrices based on that.
// We can make some changes where q is generated but this seems to be a bit easier
if(prms.isNBRA==1){
ntraj1 = 1;
}
else{
ntraj1 = ntraj;
}
// Defining matrices based on ntraj1
vector<CMATRIX> St(ntraj1, CMATRIX(nst, nst));
vector<CMATRIX> Eadi(ntraj1, CMATRIX(nst, nst));
vector<MATRIX> decoherence_rates(ntraj1, MATRIX(nst, nst));
vector<double> Ekin(ntraj1, 0.0);
vector<MATRIX> prev_ham_dia(ntraj1, MATRIX(nst, nst));
MATRIX gamma(ndof, ntraj);
MATRIX p_traj(ndof, 1);
vector<int> t1(ndof, 0); for(dof=0;dof<ndof;dof++){ t1[dof] = dof; }
Expand All @@ -535,13 +563,14 @@ void compute_dynamics(MATRIX& q, MATRIX& p, MATRIX& invM, CMATRIX& C, vector<CMA
}



if(prms.tsh_method == 3){ // DISH
for(traj=0; traj<ntraj; traj++){
if(prms.tsh_method == 3){ // DISH
// prev_ham_dia[0] = ham.children[0]->get_ham_dia().real();
//}
//else{
for(traj=0; traj<ntraj1; traj++){
prev_ham_dia[traj] = ham.children[traj]->get_ham_dia().real();
}
}

//============ Update the Hamiltonian object =============
// In case, we may need phase correction & state reordering
// prepare the temporary files
Expand All @@ -562,13 +591,12 @@ void compute_dynamics(MATRIX& q, MATRIX& p, MATRIX& invM, CMATRIX& C, vector<CMA

//============== Electronic propagation ===================
// Evolve electronic DOFs for all trajectories
// Adding the prms.isNBRA to the propagate electronic
for(i=0; i<num_el; i++){
propagate_electronic(0.5*dt_el, C, projectors, ham.children, prms.rep_tdse);
propagate_electronic(0.5*dt_el, C, projectors, ham.children, prms.rep_tdse, prms.isNBRA);
}


//============== Nuclear propagation ===================

// NVT dynamics
if(prms.ensemble==1){
for(idof=0; idof<n_therm_dofs; idof++){
Expand All @@ -578,9 +606,7 @@ void compute_dynamics(MATRIX& q, MATRIX& p, MATRIX& invM, CMATRIX& C, vector<CMA
}// traj
}// idof
}

p = p + aux_get_forces(prms, C, projectors, act_states, ham) * 0.5 * prms.dt;

// Kinetic constraint
for(cdof = 0; cdof < prms.constrained_dofs.size(); cdof++){
p.scale(prms.constrained_dofs[cdof], -1, 0.0);
Expand All @@ -591,7 +617,6 @@ void compute_dynamics(MATRIX& q, MATRIX& p, MATRIX& invM, CMATRIX& C, vector<CMA
if(prms.entanglement_opt==22){
gamma = ETHD3_friction(q, p, invM, prms.ETHD3_alpha, prms.ETHD3_beta);
}

// Update coordinates of nuclei for all trajectories
for(traj=0; traj<ntraj; traj++){
for(dof=0; dof<ndof; dof++){
Expand All @@ -615,9 +640,10 @@ void compute_dynamics(MATRIX& q, MATRIX& p, MATRIX& invM, CMATRIX& C, vector<CMA

if(prms.state_tracking_algo > 0 || prms.do_phase_correction){

if(prms.time_overlap_method==0){ St = compute_St(ham, Uprev); }
else if(prms.time_overlap_method==1){ St = compute_St(ham); }

if(prms.time_overlap_method==0){
St = compute_St(ham, Uprev, prms.isNBRA);
}
else if(prms.time_overlap_method==1){ St = compute_St(ham, prms.isNBRA); }
Eadi = get_Eadi(ham); // these are raw properties
update_projectors(prms, projectors, Eadi, St, rnd);

Expand Down Expand Up @@ -645,7 +671,6 @@ void compute_dynamics(MATRIX& q, MATRIX& p, MATRIX& invM, CMATRIX& C, vector<CMA
p.scale(prms.constrained_dofs[cdof], -1, 0.0);
}


// NVT dynamics
if(prms.ensemble==1){
for(idof=0; idof<n_therm_dofs; idof++){
Expand All @@ -656,13 +681,13 @@ void compute_dynamics(MATRIX& q, MATRIX& p, MATRIX& invM, CMATRIX& C, vector<CMA
}// idof
}


//============== Electronic propagation ===================
// Evolve electronic DOFs for all trajectories
update_Hamiltonian_p(prms, ham, p, invM);
for(i=0; i<num_el; i++){
propagate_electronic(0.5*dt_el, C, projectors, ham.children, prms.rep_tdse);
propagate_electronic(0.5*dt_el, C, projectors, ham.children, prms.rep_tdse, prms.isNBRA);
}
CMATRIX Hvib(ham.children[0]->nadi, ham.children[0]->nadi); Hvib = ham.children[0]->get_hvib_adi();


//============== Begin the TSH part ===================
Expand All @@ -684,27 +709,25 @@ void compute_dynamics(MATRIX& q, MATRIX& p, MATRIX& invM, CMATRIX& C, vector<CMA
}



//================= Update decoherence rates & times ================
//MATRIX decoh_rates(*prms.decoh_rates);
// exit(0);

if(prms.decoherence_times_type==-1){
for(traj=0; traj<ntraj; traj++){ decoherence_rates[traj] = 0.0; }
for(traj=0; traj<ntraj1; traj++){ decoherence_rates[traj] = 0.0; }
}

/// mSDM
/// Just use the plain times given from the input, usually the
/// mSDM formalism
else if(prms.decoherence_times_type==0){
for(traj=0; traj<ntraj; traj++){ decoherence_rates[traj] = *prms.decoherence_rates; }
for(traj=0; traj<ntraj1; traj++){ decoherence_rates[traj] = *prms.decoherence_rates; }
}

/// Compute the dephasing rates according the original energy-based formalism
else if(prms.decoherence_times_type==1){
Eadi = get_Eadi(ham);
Ekin = compute_kinetic_energies(p, invM);
decoherence_rates = edc_rates(Eadi, Ekin, prms.decoherence_C_param, prms.decoherence_eps_param);
decoherence_rates = edc_rates(Eadi, Ekin, prms.decoherence_C_param, prms.decoherence_eps_param, prms.isNBRA);
}

else if(prms.decoherence_times_type==2){
Expand All @@ -720,14 +743,13 @@ void compute_dynamics(MATRIX& q, MATRIX& p, MATRIX& invM, CMATRIX& C, vector<CMA
if(prms.dephasing_informed==1){
Eadi = get_Eadi(ham);
MATRIX ave_gaps(*prms.ave_gaps);
dephasing_informed_correction(decoherence_rates, Eadi, ave_gaps);
dephasing_informed_correction(decoherence_rates, Eadi, ave_gaps, prms.isNBRA);
}


//============ Apply decoherence corrections ==================
// SDM and alike methods
if(prms.decoherence_algo==0){
Coeff = sdm(Coeff, prms.dt, act_states, decoherence_rates, prms.sdm_norm_tolerance);
Coeff = sdm(Coeff, prms.dt, act_states, decoherence_rates, prms.sdm_norm_tolerance, prms.isNBRA);
}
// BCSH
else if(prms.decoherence_algo==3){
Expand All @@ -737,7 +759,7 @@ void compute_dynamics(MATRIX& q, MATRIX& p, MATRIX& invM, CMATRIX& C, vector<CMA

else if(prms.decoherence_algo==4){
// MATRIX decoh_rates(ndof, ntraj);
Coeff = mfsd(p, Coeff, invM, prms.dt, decoherence_rates, ham, rnd);
Coeff = mfsd(p, Coeff, invM, prms.dt, decoherence_rates, ham, rnd, prms.isNBRA);
}

// exit(0);
Expand Down Expand Up @@ -801,6 +823,7 @@ void compute_dynamics(MATRIX& q, MATRIX& p, MATRIX& invM, CMATRIX& C, vector<CMA

/// New version, as of 8/3/2020
vector<int> old_states(act_states);
//cout << "Flag before dish" << endl;
act_states = dish(prms, q, p, invM, Coeff, projectors, ham, act_states, coherence_time, decoherence_rates, rnd);

/// Velocity rescaling
Expand Down Expand Up @@ -841,7 +864,6 @@ void compute_dynamics(MATRIX& q, MATRIX& p, MATRIX& invM, CMATRIX& C, vector<CMA
}

// exit(0);

St.clear();
Eadi.clear();
decoherence_rates.clear();
Expand All @@ -852,13 +874,13 @@ void compute_dynamics(MATRIX& q, MATRIX& p, MATRIX& invM, CMATRIX& C, vector<CMA


// exit(0);

}






}// namespace libdyn
}// liblibra

5 changes: 4 additions & 1 deletion src/dyn/Dynamics.h
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Original file line number Diff line number Diff line change
Expand Up @@ -74,8 +74,11 @@ void update_Hamiltonian_p(bp::dict prms, nHamiltonian& ham, MATRIX& p, MATRIX& i

CMATRIX transform_amplitudes(int rep_in, int rep_out, CMATRIX& C, nHamiltonian& ham);


// Adding the NBRA flag to the functions in the header
vector<CMATRIX> compute_St(nHamiltonian& ham, int isNBRA);
vector<CMATRIX> compute_St(nHamiltonian& ham);

vector<CMATRIX> compute_St(nHamiltonian& ham, vector<CMATRIX>& Uprev, int isNBRA);
vector<CMATRIX> compute_St(nHamiltonian& ham, vector<CMATRIX>& Uprev);


Expand Down
3 changes: 2 additions & 1 deletion src/dyn/dyn_control_params.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -53,7 +53,7 @@ dyn_control_params::dyn_control_params(){
convergence = 0;
max_number_attempts = 100;
min_probability_reordering = 0.0;

isNBRA = 0;

///================= Surface hopping: proposal, acceptance =======================
tsh_method = 0;
Expand Down Expand Up @@ -187,6 +187,7 @@ void dyn_control_params::set_parameters(bp::dict params){
else if(key=="convergence") { convergence = bp::extract<int>(params.values()[i]); }
else if(key=="max_number_attempts") { max_number_attempts = bp::extract<int>(params.values()[i]); }
else if(key=="min_probability_reordering") { min_probability_reordering = bp::extract<double>(params.values()[i]); }
else if(key=="isNBRA") { isNBRA = bp::extract<int>(params.values()[i]); }

///================= Surface hopping: proposal, acceptance =======================
else if(key=="tsh_method") { tsh_method = bp::extract<int>(params.values()[i]); }
Expand Down
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