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add the ability to save the TDC and the mean TDC from classical simul…
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@tjira
tjira committed Nov 12, 2024
1 parent 5ea8878 commit e8d19d8
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Showing 14 changed files with 117 additions and 29 deletions.
2 changes: 1 addition & 1 deletion include/classicaldynamics.h
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Expand Up @@ -9,7 +9,7 @@
class ClassicalDynamics {
public:
struct TrajectoryData {
Eigen::VectorXi state; Eigen::MatrixXd position, velocity; std::vector<Eigen::MatrixXd> diabatic_potential, adiabatic_potential; std::vector<Eigen::VectorXd> hopping_geometry; std::vector<double> hopping_time;
Eigen::VectorXi state; Eigen::MatrixXd position, velocity; std::vector<Eigen::MatrixXd> diabatic_potential, adiabatic_potential, tdc; std::vector<Eigen::VectorXd> hopping_geometry; std::vector<double> hopping_time;
};

ClassicalDynamics(const Input::ClassicalDynamics& input) : input(input) {}
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11 changes: 10 additions & 1 deletion include/fewestswitches.h
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Expand Up @@ -4,6 +4,8 @@
#include <unsupported/Eigen/MatrixFunctions>
#include <random>

// #include "export.h"

class FewestSwitches {
public:
FewestSwitches(const Input::ClassicalDynamics::SurfaceHopping& input, bool adiabatic, int seed);
Expand All @@ -14,7 +16,14 @@ class FewestSwitches {
static Eigen::VectorXcd calculate_population_product(const Eigen::VectorXcd& population, const Eigen::VectorXd& potential, const Eigen::MatrixXd& derivative_coupling);
static Eigen::VectorXcd propagate_population(const Eigen::VectorXcd& population, const Eigen::VectorXd& potential, const Eigen::MatrixXd& derivative_coupling, double time_step);

std::tuple<Eigen::VectorXcd, int> jump(Eigen::VectorXcd population, const std::vector<Eigen::MatrixXd>& phi_vector, const std::vector<Eigen::MatrixXd>& potential_vector, int iteration, int state, double time_step);
std::tuple<Eigen::MatrixXd, Eigen::VectorXcd, int> jump(Eigen::VectorXcd population, const std::vector<Eigen::MatrixXd>& phi_vector, const std::vector<Eigen::MatrixXd>& potential_vector, int iteration, int state, double time_step);

// ~FewestSwitches() {
// Eigen::VectorXd data = Eigen::Map<Eigen::VectorXd>(offtdc.data(), offtdc.size());
//
// Export::EigenMatrixDouble(std::string("OFFTDC-") + (input.kappa ? "K" : "") + "FSSH.mat", data, Eigen::VectorXd::LinSpaced(offtdc.size(), 1, offtdc.size()));
// }
// std::vector<double> offtdc;

private:
bool adiabatic; std::uniform_real_distribution<double> dist; std::mt19937 mt; Input::ClassicalDynamics::SurfaceHopping input;
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4 changes: 2 additions & 2 deletions include/input.h
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Expand Up @@ -45,7 +45,7 @@ struct Input {
} quantum_dynamics;
struct ClassicalDynamics {
struct DataExport {
bool diabatic_population, adiabatic_population, total_energy, total_energy_mean, position, position_mean, momentum, momentum_mean, potential_energy, potential_energy_mean, kinetic_energy, kinetic_energy_mean, hopping_geometry, hopping_time;
bool diabatic_population, adiabatic_population, total_energy, total_energy_mean, position, position_mean, momentum, momentum_mean, potential_energy, potential_energy_mean, kinetic_energy, kinetic_energy_mean, hopping_geometry, hopping_time, tdc, tdc_mean;
} data_export;
struct InitialConditions {
std::vector<std::vector<double>> positions, momenta, position_distribution, momentum_distribution; int diabatic_state; int adiabatic_state; int mass;
Expand Down Expand Up @@ -75,7 +75,7 @@ NLOHMANN_DEFINE_TYPE_NON_INTRUSIVE(Input::HartreeFock::MollerPlesset, order);
NLOHMANN_DEFINE_TYPE_NON_INTRUSIVE(Input::HartreeFock, diis_size, max_iter, threshold, configuration_interaction, coupled_cluster, moller_plesset, generalized, gradient);
NLOHMANN_DEFINE_TYPE_NON_INTRUSIVE(Input::QuantumDynamics::DataExport, diabatic_wavefunction, adiabatic_wavefunction, diabatic_density, adiabatic_density, diabatic_population, adiabatic_population, diabatic_potential, adiabatic_potential, total_energy, position, momentum, acf, potential_energy, kinetic_energy);
NLOHMANN_DEFINE_TYPE_NON_INTRUSIVE(Input::QuantumDynamics, potential, constants, imaginary, real, iterations, time_step, data_export);
NLOHMANN_DEFINE_TYPE_NON_INTRUSIVE(Input::ClassicalDynamics::DataExport, total_energy, position, momentum, diabatic_population, adiabatic_population, total_energy_mean, position_mean, momentum_mean, potential_energy, potential_energy_mean, kinetic_energy, kinetic_energy_mean, hopping_geometry, hopping_time);
NLOHMANN_DEFINE_TYPE_NON_INTRUSIVE(Input::ClassicalDynamics::DataExport, total_energy, position, momentum, diabatic_population, adiabatic_population, total_energy_mean, position_mean, momentum_mean, potential_energy, potential_energy_mean, kinetic_energy, kinetic_energy_mean, hopping_geometry, hopping_time, tdc, tdc_mean);
NLOHMANN_DEFINE_TYPE_NON_INTRUSIVE(Input::ClassicalDynamics::InitialConditions, positions, momenta, diabatic_state, adiabatic_state, mass, position_distribution, momentum_distribution);
NLOHMANN_DEFINE_TYPE_NON_INTRUSIVE(Input::ClassicalDynamics::SurfaceHopping, kappa, type, quantum_step_factor);
NLOHMANN_DEFINE_TYPE_NON_INTRUSIVE(Input::ClassicalDynamics, potential, constants, iterations, trajectories, time_step, data_export, seed, adiabatic, surface_hopping, log_interval_step, log_interval_traj, initial_conditions);
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6 changes: 3 additions & 3 deletions research/fssh_vs_lzsh/fssh_vs_lzsh.sh
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Expand Up @@ -256,13 +256,13 @@ for MODEL in ${MODELS[@]}; do
$PLOT_1D POTENTIAL-ENERGY_EXACT-REAL_1.mat POTENTIAL-ENERGY-MEAN_FS-ADIABATIC.mat POTENTIAL-ENERGY-MEAN_KFS-ADIABATIC.mat POTENTIAL-ENERGY-MEAN_LZ-ADIABATIC.mat --legend "EXACT" "FSSH" "KFSSH" "LZSH" --title "POTENTIAL ENERGY: ${MODEL}" --xlabel "Time (a.u.)" --ylabel "ENERGY (a.u.)" --output "POTENTIAL-ENERGY_${MODEL}_P=${MOMENTUM}" --png

# plot the hopping geometries
$PLOT_1D HOPPING-GEOMETRIES_FS-ADIABATIC.mat HOPPING-GEOMETRIES_KFS-ADIABATIC.mat --bins 100 --legend "FSSH" "KFSSH" --title "HOPPING GEOMETRIES: ${MODEL}" --xlabel "Coordinate (a.u.)" --ylabel "Relative Count" --output "HOPPING-GEOMETRIES_${MODEL}" --histogram --png
$PLOT_1D HOPPING-TIMES_FS-ADIABATIC.mat HOPPING-TIMES_KFS-ADIABATIC.mat --bins 100 --legend "FSSH" "KFSSH" --title "HOPPING TIMES: ${MODEL}" --xlabel "Time (a.u.)" --ylabel "Relative Count" --output "HOPPING-TIMES_${MODEL}" --histogram --png
$PLOT_1D HOPPING-GEOMETRIES_FS-ADIABATIC.mat HOPPING-GEOMETRIES_KFS-ADIABATIC.mat --bins 100 --legend "FSSH" "KFSSH" --title "HOPPING GEOMETRIES: ${MODEL}" --xlabel "Coordinate (a.u.)" --ylabel "Relative Count" --output "HOPPING-GEOMETRIES_${MODEL}_P=${MOMENTUM}" --histogram --png
$PLOT_1D HOPPING-TIMES_FS-ADIABATIC.mat HOPPING-TIMES_KFS-ADIABATIC.mat --bins 100 --legend "FSSH" "KFSSH" --title "HOPPING TIMES: ${MODEL}" --xlabel "Time (a.u.)" --ylabel "Relative Count" --output "HOPPING-TIMES_${MODEL}_P=${MOMENTUM}" --histogram --png

# make the trajectory analysis image
montage "POTENTIAL-ADIABATIC_${MODEL}.png" "POPULATION-ADIABATIC_${MODEL}_P=${MOMENTUM}.png" "POSITION_${MODEL}_P=${MOMENTUM}.png" "MOMENTUM_${MODEL}_P=${MOMENTUM}.png" -mode concatenate -tile x1 "TRAJECTORIES-GENERAL_${MODEL}_P=${MOMENTUM}.png"
montage "POTENTIAL-ADIABATIC_${MODEL}.png" "KINETIC-ENERGY_${MODEL}_P=${MOMENTUM}.png" "POTENTIAL-ENERGY_${MODEL}_P=${MOMENTUM}.png" "TOTAL-ENERGY_${MODEL}_P=${MOMENTUM}.png" -mode concatenate -tile x1 "TRAJECTORIES-ENERGETICS_${MODEL}_P=${MOMENTUM}.png"
montage "POTENTIAL-ADIABATIC_${MODEL}.png" "HOPPING-GEOMETRIES_${MODEL}.png" "HOPPING-TIMES_${MODEL}.png" -mode concatenate -tile x1 "TRAJECTORIES-TRANSITIONS_${MODEL}_P=${MOMENTUM}.png"
montage "POTENTIAL-ADIABATIC_${MODEL}.png" "HOPPING-GEOMETRIES_${MODEL}_P=${MOMENTUM}.png" "HOPPING-TIMES_${MODEL}_P=${MOMENTUM}.png" -mode concatenate -tile x1 "TRAJECTORIES-TRANSITIONS_${MODEL}_P=${MOMENTUM}.png"
done

# plot the population dependence on momentum
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36 changes: 36 additions & 0 deletions research/sodium_iodide/check/fssh-check.json
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@@ -0,0 +1,36 @@
{
"classical_dynamics" : {
"initial_conditions" : {
"positions" : [
[4.966781744519960462]
],
"momenta" : [
[-7.511477096479932669]
],
"adiabatic_state" : 2,
"mass" : 35480.251398
},
"potential" : [
["((A2+(B2/(x*au2a))^8)*exp(-(x*au2a)/rho)-e2/(x*au2a)-e2*(lp+lm)/2/(x*au2a)^4-C2/(x*au2a)^6-2*e2*lm*lp/(x*au2a)^7+de)/au2ev", "A12*exp(-beta12*((x*au2a)-Rx)^2)/au2ev"],
["A12*exp(-beta12*((x*au2a)-Rx)^2)/au2ev", "A1*exp(-beta1*((x*au2a)-R0))/au2ev" ]
],
"constants" : {
"A2" : 2760, "B2" : 2.398, "C2" : 11.3, "rho" : 0.3489, "e2" : 14.3996, "lp" : 0.408, "lm" : 6.431,
"A1" : 0.813, "beta1" : 4.08, "A12" : 0.055, "beta12" : 0.6931, "R0" : 2.67, "Rx" : 6.93, "de" : 2.075,

"au2ev" : 27.21138602, "au2a" : 0.529177
},
"surface_hopping" : {
"type" : "fewest-switches",
"kappa" : false
},
"adiabatic" : true,
"iterations" : 12000,
"time_step" : 1,
"trajectories" : 1,
"log_interval_step" : 1,
"data_export" : {
"diabatic_population" : true, "adiabatic_population" : true, "tdc" : true
}
}
}
4 changes: 2 additions & 2 deletions research/sodium_iodide/kfssh-check.json → ...arch/sodium_iodide/check/kfssh-check.json
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Expand Up @@ -25,12 +25,12 @@
"kappa" : true
},
"adiabatic" : true,
"iterations" : 9000,
"iterations" : 12000,
"time_step" : 1,
"trajectories" : 1,
"log_interval_step" : 1,
"data_export" : {
"diabatic_population" : true, "adiabatic_population" : true
"diabatic_population" : true, "adiabatic_population" : true, "tdc" : true
}
}
}
4 changes: 2 additions & 2 deletions research/sodium_iodide/fssh.json
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Expand Up @@ -22,9 +22,9 @@
"type" : "fewest-switches"
},
"adiabatic" : true,
"iterations" : 9000,
"iterations" : 100000,
"time_step" : 1,
"trajectories" : 1000,
"trajectories" : 100,
"log_interval_step" : 500,
"data_export" : {
"diabatic_population" : true, "adiabatic_population" : true
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4 changes: 2 additions & 2 deletions research/sodium_iodide/kfssh.json
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Expand Up @@ -23,9 +23,9 @@
"kappa" : true
},
"adiabatic" : true,
"iterations" : 9000,
"iterations" : 100000,
"time_step" : 1,
"trajectories" : 1000,
"trajectories" : 100,
"log_interval_step" : 500,
"data_export" : {
"diabatic_population" : true, "adiabatic_population" : true
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4 changes: 2 additions & 2 deletions research/sodium_iodide/lzsh.json
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Expand Up @@ -22,9 +22,9 @@
"type" : "landau-zener"
},
"adiabatic" : true,
"iterations" : 9000,
"iterations" : 100000,
"time_step" : 1,
"trajectories" : 1000,
"trajectories" : 100,
"log_interval_step" : 500,
"data_export" : {
"diabatic_population" : true, "adiabatic_population" : true
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2 changes: 1 addition & 1 deletion research/sodium_iodide/qd.json
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Expand Up @@ -19,7 +19,7 @@
"au2ev" : 27.21138602, "au2a" : 0.529177
},
"real" : 1,
"iterations" : 9000,
"iterations" : 100000,
"time_step" : 1,
"data_export" : {
"diabatic_population" : true, "adiabatic_population" : true,
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13 changes: 8 additions & 5 deletions src/classicaldynamics.cpp
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Expand Up @@ -189,14 +189,14 @@ void ClassicalDynamics::run(const Input::Wavefunction& initial_diabatic_wavefunc
// define and initialize the surface hopping algorithms
FewestSwitches fewestswitches(input.surface_hopping, input.adiabatic, seed); LandauZener landauzener(input.surface_hopping, input.adiabatic, seed);

// define the current fssh population vector
// define the current fssh population vector and TDC
Eigen::VectorXcd fssh_population = Eigen::VectorXcd::Zero(input.potential.size()); fssh_population(state(0)) = 1;

// define the vector of hopping geometries and times
std::vector<Eigen::VectorXd> hopping_geometry_vector; std::vector<double> hopping_time_vector;

// define a vector to contain diabatic potentials and eigenvectors phi
std::vector<Eigen::MatrixXd> diabatic_potential_vector(input.iterations + 1), adiabatic_potential_vector(input.iterations + 1), phi_vector(input.iterations + 1);
std::vector<Eigen::MatrixXd> diabatic_potential_vector(input.iterations + 1), adiabatic_potential_vector(input.iterations + 1), phi_vector(input.iterations + 1), tdc_vector(input.iterations);

// propagate the current trajectory
for (int j = 0; j < input.iterations + 1; j++) {
Expand All @@ -211,7 +211,7 @@ void ClassicalDynamics::run(const Input::Wavefunction& initial_diabatic_wavefunc
if (j) {position.row(j) = position.row(j - 1) + input.time_step * (velocity.row(j) + 0.5 * acceleration.row(j) * input.time_step), state(j) = state(j - 1);}

// calculate the potential at the current point and assign it to the container and create the new state variable
Eigen::MatrixXd potential = evaluate_potential(potential_expressions, position.row(j)); diabatic_potential_vector.at(j) = potential; int new_state = state(j);
Eigen::MatrixXd potential = evaluate_potential(potential_expressions, position.row(j)), tdc; diabatic_potential_vector.at(j) = potential; int new_state = state(j);

// adiabatization block
if (input.adiabatic) {
Expand All @@ -227,7 +227,7 @@ void ClassicalDynamics::run(const Input::Wavefunction& initial_diabatic_wavefunc
if (input.surface_hopping.type == "landau-zener" && j > 1) {
new_state = landauzener.jump(input.adiabatic ? adiabatic_potential_vector : diabatic_potential_vector, j, state(j), input.time_step);
} else if (input.surface_hopping.type == "fewest-switches" && j) {
std::tie(fssh_population, new_state) = fewestswitches.jump(fssh_population, phi_vector, adiabatic_potential_vector, j, state(j), input.time_step);
std::tie(tdc, fssh_population, new_state) = fewestswitches.jump(fssh_population, phi_vector, adiabatic_potential_vector, j, state(j), input.time_step);
}

// update the velocity and the state
Expand All @@ -238,6 +238,9 @@ void ClassicalDynamics::run(const Input::Wavefunction& initial_diabatic_wavefunc
// append the hopping geometry and time
if (j && state(j) != state(j - 1) && input.data_export.hopping_geometry) hopping_geometry_vector.push_back(position.row(j));
if (j && state(j) != state(j - 1) && input.data_export.hopping_time ) hopping_time_vector.push_back(j * input.time_step);

// append the TDC
if (j && (input.data_export.tdc || input.data_export.tdc_mean)) tdc_vector.at(j - 1) = tdc;

// print the iteration info
if ((j % input.log_interval_step == 0 || (j && state(j) != state(j - 1))) && (i ? i + 1 : i) % input.log_interval_traj == 0) {
Expand All @@ -246,7 +249,7 @@ void ClassicalDynamics::run(const Input::Wavefunction& initial_diabatic_wavefunc
}

// set the trajectory data
trajectory_data_vector.at(i) = {state, position, velocity, diabatic_potential_vector, adiabatic_potential_vector, hopping_geometry_vector, hopping_time_vector};
trajectory_data_vector.at(i) = {state, position, velocity, diabatic_potential_vector, adiabatic_potential_vector, tdc_vector, hopping_geometry_vector, hopping_time_vector};
}

// create the vector of populations
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44 changes: 40 additions & 4 deletions src/export.cpp
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Expand Up @@ -241,10 +241,10 @@ void Export::ClassicalTrajectories(const Input::ClassicalDynamics& input, const
}

// transform the hopping geometries to a matrix
data_matrix = Eigen::MatrixXd::Zero(hopping_geometries.size(), hopping_geometries.front().rows()); for (size_t i = 0; i < hopping_geometries.size(); i++) data_matrix.row(i) = hopping_geometries.at(i).transpose();
if (!hopping_geometries.empty()) data_matrix = Eigen::MatrixXd::Zero(hopping_geometries.size(), hopping_geometries.front().rows()); for (size_t i = 0; i < hopping_geometries.size(); i++) data_matrix.row(i) = hopping_geometries.at(i).transpose();

// export the energy mean
Export::EigenMatrixDouble(std::string("HOPPING-GEOMETRIES_") + algorithm + (input.adiabatic ? "-ADIABATIC" : "-DIABATIC") + ".mat", data_matrix);
if (!hopping_geometries.empty()) Export::EigenMatrixDouble(std::string("HOPPING-GEOMETRIES_") + algorithm + (input.adiabatic ? "-ADIABATIC" : "-DIABATIC") + ".mat", data_matrix);
}

// export the hopping times
Expand All @@ -259,10 +259,46 @@ void Export::ClassicalTrajectories(const Input::ClassicalDynamics& input, const
}

// transform the hopping geometries to a matrix
data_matrix = Eigen::MatrixXd::Zero(hopping_times.size(), 1); for (size_t i = 0; i < hopping_times.size(); i++) data_matrix(i, 0) = hopping_times.at(i);
if (!hopping_times.empty()) data_matrix = Eigen::MatrixXd::Zero(hopping_times.size(), 1); for (size_t i = 0; i < hopping_times.size(); i++) data_matrix(i, 0) = hopping_times.at(i);

// export the energy mean
Export::EigenMatrixDouble(std::string("HOPPING-TIMES_") + algorithm + (input.adiabatic ? "-ADIABATIC" : "-DIABATIC") + ".mat", data_matrix);
if (!hopping_times.empty()) Export::EigenMatrixDouble(std::string("HOPPING-TIMES_") + algorithm + (input.adiabatic ? "-ADIABATIC" : "-DIABATIC") + ".mat", data_matrix);
}

// export the TDC
if (Eigen::VectorXd time_variable = Eigen::VectorXd::LinSpaced(input.iterations, 1, input.time_step * input.iterations); input.data_export.tdc) {

// create the matrix containing the TDC
data_matrix = Eigen::MatrixXd::Zero(input.iterations, trajectory_data_vector.size() * trajectory_data_vector.at(0).tdc.at(0).size());

// extract the tdc dimension
int dim = trajectory_data_vector.at(0).tdc.at(0).rows();

// fill the matrix with the TDC
for (int i = 0; i < input.trajectories; i++) for (int j = 0; j < input.iterations; j++) for (int k = 0; k < dim * dim; k++) {
data_matrix.row(j)(i * dim * dim + k) = trajectory_data_vector.at(i).tdc.at(j)(k / dim, k % dim);
}

// export the energy
Export::EigenMatrixDouble(std::string("TDC_") + algorithm + (input.adiabatic ? "-ADIABATIC" : "-DIABATIC") + ".mat", data_matrix, time_variable);
}

// export the mean TDC
if (Eigen::VectorXd time_variable = Eigen::VectorXd::LinSpaced(input.iterations, 1, input.time_step * input.iterations); input.data_export.tdc_mean) {

// create the matrix containing the TDC mean
data_matrix = Eigen::MatrixXd::Zero(input.iterations, trajectory_data_vector.at(0).tdc.at(0).size());

// extract the tdc dimension
int dim = trajectory_data_vector.at(0).tdc.at(0).rows();

// fill the matrix with the the TDC
for (int i = 0; i < input.trajectories; i++) for (int j = 0; j < input.iterations; j++) for (int k = 0; k < dim * dim; k++) {
data_matrix.row(j)(k) += trajectory_data_vector.at(i).tdc.at(j)(k / dim, k % dim);
}

// export the energy
Export::EigenMatrixDouble(std::string("TDC_") + algorithm + (input.adiabatic ? "-ADIABATIC" : "-DIABATIC") + ".mat", data_matrix / input.trajectories, time_variable);
}
}

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