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update thermostats
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Signed-off-by: Conrad Hübler <[email protected]>
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@conradhuebler
conradhuebler committed Sep 1, 2024
1 parent a403f4a commit d84f329
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Showing 5 changed files with 95 additions and 90 deletions.
144 changes: 63 additions & 81 deletions src/capabilities/simplemd.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -185,10 +185,12 @@ void SimpleMD::LoadControlJson()
m_rescue = Json2KeyWord<bool>(m_defaults, "rescue");
m_wall_render = Json2KeyWord<bool>(m_defaults, "wall_render");
m_coupling = Json2KeyWord<double>(m_defaults, "coupling");
m_anderson = Json2KeyWord<double>(m_defaults, "anderson");

m_threads = Json2KeyWord<double>(m_defaults, "threads");
/* if (m_coupling < m_dT)
m_coupling = m_dT;
*/
if (m_coupling < m_dT)
m_coupling = m_dT;

/* RMSD Metadynamik block */
/* this one is used to recover https://doi.org/10.1021/acs.jctc.9b00143 */
m_rmsd_mtd = Json2KeyWord<bool>(m_defaults, "rmsd_mtd");
Expand Down Expand Up @@ -402,12 +404,7 @@ bool SimpleMD::Initialise()
m_rmass[3 * i + 2] = 1 / m_mass[3 * i + 2];
}
}
if (!m_restart) {
InitVelocities(m_scale_velo);
m_xi.resize(m_chain_length, 0.0);
m_Q.resize(m_chain_length, mass); // Setze eine geeignete Masse für jede Kette
m_eta = 0.0;
}

m_molecule.setCharge(m_charge);
m_molecule.setSpin(m_spin);
m_interface->setMolecule(m_molecule);
Expand All @@ -425,6 +422,17 @@ bool SimpleMD::Initialise()

InitConstrainedBonds();
InitialiseWalls();
if (!m_restart) {
InitVelocities(m_scale_velo);
m_xi.resize(m_chain_length, 0.0);
m_Q.resize(m_chain_length, 100); // Setze eine geeignete Masse für jede Kette
for (int i = 0; i < m_chain_length; ++i) {
m_xi[i] = pow(10.0, double(i)) - 1;
m_Q[i] = pow(10, i) * kb_Eh * m_T0 * m_dof * 100;
std::cout << m_xi[i] << " " << m_Q[i] << std::endl;
}
m_eta = 0.0;
}
if (m_writeinit) {
json init = WriteRestartInformation();
std::ofstream result_file;
Expand Down Expand Up @@ -497,6 +505,7 @@ bool SimpleMD::Initialise()

void SimpleMD::InitConstrainedBonds()
{

if (m_rattle) {
auto m = m_molecule.DistanceMatrix();
m_topo_initial = m.second;
Expand All @@ -517,6 +526,7 @@ void SimpleMD::InitConstrainedBonds()
}
}
}

std::cout << m_dof << " initial degrees of freedom " << std::endl;
std::cout << m_bond_constrained.size() << " constrains active" << std::endl;
m_dof -= m_bond_constrained.size();
Expand All @@ -527,33 +537,19 @@ void SimpleMD::InitVelocities(double scaling)
{
static std::default_random_engine generator;
for (size_t i = 0; i < m_natoms; ++i) {
std::uniform_real_distribution<double> uniform_dist(0.0, 1.0);
std::normal_distribution<double> distribution(0.0, std::sqrt(kb_Eh * m_T0 / m_mass[i]));
std::normal_distribution<double> distribution(0.0, std::sqrt(kb_Eh * m_T0 * m_rmass[i]));
m_velocities[3 * i + 0] = distribution(generator);
m_velocities[3 * i + 1] = distribution(generator);
m_velocities[3 * i + 2] = distribution(generator);
}

/*
static std::random_device rd{};
static std::mt19937 gen{ rd() };
std::normal_distribution<> d{ 0, 1 };
double Px = 0.0, Py = 0.0, Pz = 0.0;
for (int i = 0; i < m_natoms; ++i) {
double v0 = sqrt(kb_Eh * m_T0 * amu2au / (m_mass[i])) * scaling / fs2amu;
m_velocities[3 * i + 0] = v0 * d(gen);
m_velocities[3 * i + 1] = v0 * d(gen);
m_velocities[3 * i + 2] = v0 * d(gen);
Px += m_velocities[3 * i + 0] * m_mass[i];
Py += m_velocities[3 * i + 1] * m_mass[i];
Pz += m_velocities[3 * i + 2] * m_mass[i];
}*/
/*
for (int i = 0; i < m_natoms; ++i) {
m_velocities[3 * i + 0] -= Px / (m_mass[i] * m_natoms);
m_velocities[3 * i + 1] -= Py / (m_mass[i] * m_natoms);
m_velocities[3 * i + 2] -= Pz / (m_mass[i] * m_natoms);
}*/
RemoveRotation(m_velocities);
EKin();
double coupling = m_coupling;
m_coupling = m_dT;
Berendson();
Berendson();
EKin();
m_coupling = coupling;
}

void SimpleMD::InitialiseWalls()
Expand Down Expand Up @@ -969,9 +965,9 @@ void SimpleMD::start()
}

m_Epot = Energy(gradient);
m_Ekin = EKin();
EKin();
m_Etot = m_Epot + m_Ekin;

AverageQuantities();
int m_step = 0;

#ifdef USE_Plumed
Expand Down Expand Up @@ -1045,6 +1041,7 @@ void SimpleMD::start()
}
PrintStatus();

/* Start MD Lopp here */
for (; m_currentStep < m_maxtime;) {
auto step0 = std::chrono::system_clock::now();

Expand Down Expand Up @@ -1073,8 +1070,7 @@ void SimpleMD::start()
}

Integrator(gradient);
// ThermostatFunction();
m_Ekin = EKin();
AverageQuantities();

if (m_mtd) {
if (!m_eval_mtd) {
Expand Down Expand Up @@ -1103,7 +1099,7 @@ void SimpleMD::start()
m_molecule.GetFragments();
InitVelocities(-1);
Energy(gradient);
m_Ekin = EKin();
EKin();
m_Etot = m_Epot + m_Ekin;
m_current_rescue++;
PrintStatus();
Expand Down Expand Up @@ -1141,7 +1137,7 @@ void SimpleMD::start()

if (m_impuls > m_T) {
InitVelocities(m_scale_velo * m_impuls_scaling);
m_Ekin = EKin();
EKin();
// PrintStatus();
m_time_step = 0;
}
Expand Down Expand Up @@ -1199,6 +1195,8 @@ void SimpleMD::start()

void SimpleMD::Verlet(double* grad)
{
double ekin = 0;

for (int i = 0; i < m_natoms; ++i) {
m_current_geometry[3 * i + 0] = m_current_geometry[3 * i + 0] + m_dT * m_velocities[3 * i + 0] - 0.5 * grad[3 * i + 0] * m_rmass[3 * i + 0] * m_dt2;
m_current_geometry[3 * i + 1] = m_current_geometry[3 * i + 1] + m_dT * m_velocities[3 * i + 1] - 0.5 * grad[3 * i + 1] * m_rmass[3 * i + 1] * m_dt2;
Expand All @@ -1207,10 +1205,13 @@ void SimpleMD::Verlet(double* grad)
m_velocities[3 * i + 0] = m_velocities[3 * i + 0] - 0.5 * m_dT * grad[3 * i + 0] * m_rmass[3 * i + 0];
m_velocities[3 * i + 1] = m_velocities[3 * i + 1] - 0.5 * m_dT * grad[3 * i + 1] * m_rmass[3 * i + 1];
m_velocities[3 * i + 2] = m_velocities[3 * i + 2] - 0.5 * m_dT * grad[3 * i + 2] * m_rmass[3 * i + 2];
ekin += m_mass[i] * (m_velocities[3 * i] * m_velocities[3 * i] + m_velocities[3 * i + 1] * m_velocities[3 * i + 1] + m_velocities[3 * i + 2] * m_velocities[3 * i + 2]);
}
ekin *= 0.5;
m_T = 2.0 * ekin / (kb_Eh * m_dof);
m_Ekin = ekin;
ThermostatFunction();
m_Epot = Energy(grad);

if (m_rmsd_mtd) {
if (m_step % m_mtd_steps == 0) {
ApplyRMSDMTD(grad);
Expand Down Expand Up @@ -1239,7 +1240,7 @@ void SimpleMD::Verlet(double* grad)
}
#endif
WallPotential(grad);
double ekin = 0.0;
ekin = 0.0;

for (int i = 0; i < m_natoms; ++i) {
m_velocities[3 * i + 0] -= 0.5 * m_dT * grad[3 * i + 0] * m_rmass[3 * i + 0];
Expand All @@ -1255,7 +1256,9 @@ void SimpleMD::Verlet(double* grad)
double T = 2.0 * ekin / (kb_Eh * m_dof);
m_unstable = T > 10000 * m_T;
m_T = T;
m_Ekin = ekin;
ThermostatFunction();
EKin();
}

void SimpleMD::Rattle(double* grad)
Expand Down Expand Up @@ -1337,14 +1340,20 @@ void SimpleMD::Rattle(double* grad)
if (active == 0)
break;
}
double ekin = 0;

for (int i = 0; i < m_natoms; ++i) {
m_current_geometry[3 * i + 0] = coord[3 * i + 0];
m_current_geometry[3 * i + 1] = coord[3 * i + 1];
m_current_geometry[3 * i + 2] = coord[3 * i + 2];
ekin += m_mass[i] * (m_velocities[3 * i] * m_velocities[3 * i] + m_velocities[3 * i + 1] * m_velocities[3 * i + 1] + m_velocities[3 * i + 2] * m_velocities[3 * i + 2]);
}
ekin *= 0.5;
m_T = 2.0 * ekin / (kb_Eh * m_dof);
m_Ekin = ekin;
ThermostatFunction();

m_Epot = Energy(grad);

if (m_rmsd_mtd) {
if (m_step % m_mtd_steps == 0) {
ApplyRMSDMTD(grad);
Expand Down Expand Up @@ -1373,7 +1382,6 @@ void SimpleMD::Rattle(double* grad)
}
#endif
WallPotential(grad);
double ekin = 0.0;

for (int i = 0; i < m_natoms; ++i) {
m_velocities[3 * i + 0] -= 0.5 * m_dT * grad[3 * i + 0] * m_rmass[3 * i + 0];
Expand Down Expand Up @@ -1431,6 +1439,7 @@ void SimpleMD::Rattle(double* grad)
m_unstable = T > 10000 * m_T;
m_T = T;
ThermostatFunction();
EKin();
}

void SimpleMD::ApplyRMSDMTD(double* grad)
Expand Down Expand Up @@ -1914,16 +1923,19 @@ double SimpleMD::FastEnergy(double* grad)
return Energy;
}

double SimpleMD::EKin()
void SimpleMD::EKin()
{
double ekin = 0;

for (int i = 0; i < m_natoms; ++i) {
ekin += m_mass[i] * (m_velocities[3 * i] * m_velocities[3 * i] + m_velocities[3 * i + 1] * m_velocities[3 * i + 1] + m_velocities[3 * i + 2] * m_velocities[3 * i + 2]);
}
ekin *= 0.5;
m_Ekin = ekin;
m_T = 2.0 * ekin / (kb_Eh * m_dof);
}

void SimpleMD::AverageQuantities()
{
m_aver_Temp = (m_T + (m_currentStep)*m_aver_Temp) / (m_currentStep + 1);
m_aver_Epot = (m_Epot + (m_currentStep)*m_aver_Epot) / (m_currentStep + 1);
m_aver_Ekin = (m_Ekin + (m_currentStep)*m_aver_Ekin) / (m_currentStep + 1);
Expand All @@ -1933,8 +1945,6 @@ double SimpleMD::EKin()
}
m_average_wall_potential = (m_wall_potential + (m_currentStep)*m_average_wall_potential) / (m_currentStep + 1);
m_average_virial_correction = (m_virial_correction + (m_currentStep)*m_average_virial_correction) / (m_currentStep + 1);

return ekin;
}

bool SimpleMD::WriteGeometry()
Expand Down Expand Up @@ -1971,70 +1981,48 @@ void SimpleMD::None()

void SimpleMD::Berendson()
{
double kinetic_energy = 0.0;

double lambda = sqrt(1 + (m_dT * (m_T0 - m_T)) / (m_T * m_coupling));
double lambda = sqrt(1 + (m_dT / 2.0 * (m_T0 - m_T)) / (m_T * m_coupling));
for (int i = 0; i < m_natoms; ++i) {
// m_velocities[i] *= alpha;
m_velocities[3 * i + 0] *= lambda;
m_velocities[3 * i + 1] *= lambda;
m_velocities[3 * i + 2] *= lambda;
kinetic_energy += 0.5 * m_mass[i] * (m_velocities[3 * i] * m_velocities[3 * i] + m_velocities[3 * i + 1] * m_velocities[3 * i + 1] + m_velocities[3 * i + 2] * m_velocities[3 * i + 2]);
}
kinetic_energy *= 0.5;
double T = 2.0 * kinetic_energy / (kb_Eh * m_dof);
m_unstable = T > 10000 * m_T;
m_T = T;
}

void SimpleMD::CSVR()
{
double Ekin_target = 0.5 * kb_Eh * (m_T0)*m_dof;
double c = exp(-(m_dT * m_respa) / m_coupling);
double c = exp(-(m_dT / 2.0 * m_respa) / m_coupling);
static std::default_random_engine rd{};
static std::mt19937 gen{ rd() };
static std::normal_distribution<> d{ 0, 1 };
static std::chi_squared_distribution<float> dchi{ m_dof };
double kinetic_energy = 0.0;

double R = d(gen);
double SNf = dchi(gen);
double alpha2 = c + (1 - c) * (SNf + R * R) * Ekin_target / (m_dof * m_Ekin) + 2 * R * sqrt(c * (1 - c) * Ekin_target / (m_dof * m_Ekin));
m_Ekin_exchange += m_Ekin * (alpha2 - 1);
double alpha = sqrt(alpha2);
for (int i = 0; i < m_natoms; ++i) {
// m_velocities[i] *= alpha;
m_velocities[3 * i + 0] *= alpha;
m_velocities[3 * i + 1] *= alpha;
m_velocities[3 * i + 2] *= alpha;
kinetic_energy += 0.5 * m_mass[i] * (m_velocities[3 * i] * m_velocities[3 * i] + m_velocities[3 * i + 1] * m_velocities[3 * i + 1] + m_velocities[3 * i + 2] * m_velocities[3 * i + 2]);
}
kinetic_energy *= 0.5;
double T = 2.0 * kinetic_energy / (kb_Eh * m_dof);
m_unstable = T > 10000 * m_T;
m_T = T;
}

void SimpleMD::Anderson()
{
static std::default_random_engine generator;
double kinetic_energy = 0.0;
double probability = m_coupling * m_dT;
double probability = m_anderson * m_dT;
std::uniform_real_distribution<double> uniform_dist(0.0, 1.0);
for (size_t i = 0; i < m_natoms; ++i) {
std::normal_distribution<double> distribution(0.0, std::sqrt(kb_Eh * m_T0 / m_mass[i]));
if (uniform_dist(generator) < probability) {
m_velocities[3 * i + 0] = distribution(generator);
m_velocities[3 * i + 1] = distribution(generator);
m_velocities[3 * i + 2] = distribution(generator);
std::normal_distribution<double> distribution(0.0, std::sqrt(kb_Eh * m_T0 * m_rmass[i]));
m_velocities[3 * i + 0] = (m_velocities[3 * i + 0] + distribution(generator)) / 2.0;
m_velocities[3 * i + 1] = (m_velocities[3 * i + 1] + distribution(generator)) / 2.0;
m_velocities[3 * i + 2] = (m_velocities[3 * i + 2] + distribution(generator)) / 2.0;
}
kinetic_energy += 0.5 * m_mass[i] * (m_velocities[3 * i] * m_velocities[3 * i] + m_velocities[3 * i + 1] * m_velocities[3 * i + 1] + m_velocities[3 * i + 2] * m_velocities[3 * i + 2]);
}

kinetic_energy *= 0.5;
double T = 2.0 * kinetic_energy / (kb_Eh * m_dof);
m_unstable = T > 10000 * m_T;
m_T = T;
}
void SimpleMD::NoseHover()
{
Expand All @@ -2051,17 +2039,11 @@ void SimpleMD::NoseHover()

// Update der Geschwindigkeiten
double scale = exp(-m_xi[0] * m_dT);
kinetic_energy = 0.0;
for (int i = 0; i < m_natoms; ++i) {
m_velocities[3 * i + 0] *= scale;
m_velocities[3 * i + 1] *= scale;
m_velocities[3 * i + 2] *= scale;
kinetic_energy += 0.5 * m_mass[i] * (m_velocities[3 * i] * m_velocities[3 * i] + m_velocities[3 * i + 1] * m_velocities[3 * i + 1] + m_velocities[3 * i + 2] * m_velocities[3 * i + 2]);
}
kinetic_energy *= 0.5;
double T = 2.0 * kinetic_energy / (kb_Eh * m_dof);
m_unstable = T > 10000 * m_T;
m_T = T;

// Rückwärts-Update der Thermostatkette
for (int j = m_chain_length - 1; j >= 1; --j) {
Expand Down
9 changes: 7 additions & 2 deletions src/capabilities/simplemd.h
View file
Original file line number Diff line number Diff line change
Expand Up @@ -187,7 +187,8 @@ static json CurcumaMDJson{
{ "rmsd_ref_file", "none" },
{ "rmsd_fix_structure", false },
{ "rmsd_atoms", "-1" },
{ "chainlength", 3 }
{ "chainlength", 3 },
{ "anderson", 0.001 }
};

class SimpleMD : public CurcumaMethod {
Expand Down Expand Up @@ -256,7 +257,9 @@ class SimpleMD : public CurcumaMethod {
void RemoveRotation(std::vector<double>& velo);
void RemoveRotations(std::vector<double>& velo);

double EKin();
void EKin();
void AverageQuantities();

void Berendson();
void CSVR();
void None();
Expand Down Expand Up @@ -362,6 +365,8 @@ class SimpleMD : public CurcumaMethod {
double m_eta; // Variable zur Speicherung der Thermostatenergie

int m_chain_length = 3; // Länge der Thermostatkette

double m_anderson = 0.01;
};

class MDThread : public CxxThread {
Expand Down
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