Class Scine::Utils::MDIntegrator

class MDIntegrator

Subclassed by Scine::Utils::EulerMD, Scine::Utils::LeapFrogMD, Scine::Utils::VelocityVerletMD

Public Functions

MDIntegrator()

Constructor that sets the default time step of 1 fs.

virtual Utils::DisplacementCollection calculateDisplacements(const Utils::GradientCollection &gradients) = 0

Calculates the displacements from the gradients.

void setElementTypes(const Utils::ElementTypeCollection &elements)

Sets the masses, initializes the velocities and accelerations to zero.

Parameters

• elements: The element types of the molecular system.

void resetVelocities()

Resets velocities to zero.

void setVelocities(const Utils::DisplacementCollection &velocities)

Setter for the velocities.

Utils::DisplacementCollection getVelocities() const

Getter for the velocities.

void setTimeStepInFemtoseconds(double fs)

Sets the time step in the unit femtoseconds.

void setRelaxationTimeFactor(double factor)

The temperature bath relaxation time in units of the chosen time step.

void setTargetTemperatureInKelvin(double T)

Sets the target temperature in Kelvin.

void setSeed(int seed)

Sets a seed for the random initial velocities.

void removeCenterOfMassLinearMomentum(const Eigen::MatrixX3d &positions)

Removes the center of mass motion.

void removeCenterOfMassAngularMomentum(const Eigen::MatrixX3d &positions)

Removes the center of mass motion.

Protected Functions

void calculateAccelerationsFromGradients(const Utils::GradientCollection &gradients)

Updates the accelerations according to the given gradients.

void rescaleVelocitiesForTemperatureBath()

Berendsen thermostat.

void sampleVelocitiesFromBoltzmannDistribution()

Method to sample initial velocities from a Maxwell-Boltzmann distribution.