TMMC Class

The TMMC class serves as the main interface for handling TMMC simulation logic.

class flames.tmmc.TMMC(model, framework_atoms, adsorbates, temperature, pressure, device, vdw_radii, vdw_factor=0.6, max_overlap_tries=100, max_deltaE=25.0, save_frequency=100, output_to_file=True, output_folder=None, debug=False, random_seed=None, cutoff_radius=6.0)[source]

Bases: BaseSimulator

Base class for transition matrix Monte Carlo (TMMC) simulations using ASE.

This class implements TMMC deletion/insertion moves, recording the deletion/insertion energies of the adsorbate.

Parameters:

  • model (ase.calculators.calculator.Calculator) – The calculator to use for energy calculations. Can be any ASE-compatible calculator. The output of the calculator should be in eV.

  • framework_atoms (ase.Atoms) – The framework structure as an ASE Atoms object.

  • adsorbates (Adsorbate | list[Adsorbate]) – The adsorbate structure(s) as an Adsorbate object or list of Adsorbate objects.

  • temperature (float) – Temperature of the ideal reservoir in Kelvin.

  • pressure (float) – Pressure of the ideal reservoir in Pascal.

  • device (str) – Device to run the simulation on, e.g., 'cpu' or 'cuda'.

  • vdw_radii (np.ndarray) – Van der Waals radii for the atoms in the framework and adsorbate. Should be an array of the same length as the number of atomic numbers in ASE.

  • vdw_factor (float, optional) – Factor to scale the Van der Waals radii. Default is 0.6.

  • save_frequency (int, optional) – Frequency at which to save the simulation state and results. Default is 100.

  • output_to_file (bool, optional) – If True, writes the output to a file named output_{temperature}_{pressure}.out in the results directory. Default is True.

  • output_folder (str or None, optional) – Folder to save the output files. If None, a folder named results_<T>_<P> will be created.

  • debug (bool, optional) – If True, prints detailed debug information during the simulation. Default is False.

  • random_seed (int or None, optional) – Random seed for reproducibility. Default is None and will generate a random seed automatically if not provided.

  • cutoff_radius (float, optional) – Interaction potential cut-off radius used to estimate the minimum unit cell. Default is 6.0.

Max_overlap_tries:

Maximum tries for the insertion move. Default is 100.

get_adsorbates_index(tag=None)[source]

Get a list of indices of the adsorbate molecules in the current system.

Return type:

list[list]

get_framework_mass()

Calculate the mass of the framework in kg.

Returns:

The mass of the framework in kg.

Return type:

float

get_macrostate_str()[source]

Return a string representation of the current multi-component macrostate. Example: For a binary mixture with 1 CO2 and 2 H2O, returns “0001_0002”.

Return type:

str

get_number_of_adsorbates(system=None)[source]

Get the number of adsorbates in the current system. It considers the possibility of having multiple adsorbate species in the simulation.

Return type:

dict[str, int]

load_state(state_file)[source]

Load the state of the simulation from a file.

Parameters:

state_file (str) – Path to the file containing the saved state of the simulation.

Return type:

None

md(nsteps, atoms=None, time_step=0.5, ensemble='NVT', thermostat='NoseHoover', output_interval=100, movie_interval=100, calculator=None, update_state=True, trajectory_file=None, set_momenta=True, **kwargs)

Run a molecular dynamics simulation using the specified ensemble and thermostat.

Parameters:

  • nsteps (int) – Number of steps to run the MD simulation.

  • time_step (float, optional) – Time step for the MD simulation in femtoseconds (default is 0.5 fs).

  • ensemble (str, optional) – The ensemble to use for the MD simulation (default is “NVT”). Can be one of “NVT” or “NPT”.

  • thermostat (str, optional) – The thermostat to use for the MD simulation (default is “NoseHoover”). For NVT, can be one of “Berendsen”, “NoseHoover”, or “Langevin”. For NPT, can be one of “Berendsen”, “NoseHoover”, or “MTKNPT”.

  • output_interval (int, optional) – The interval for logging output (default is 100 steps).

  • movie_interval (int, optional) – The interval for saving trajectory frames (default is 100 steps).

  • calculator (ase.calculators.calculator.Calculator or None, optional) – The calculator to use for energy calculations. If None, the default model will be used.

  • update_state (bool, optional) – If True, updates the current state of the simulation with the final state after MD. If False, returns the final state without updating. This difference is important for using the same method in the GCMC simulations when a MD step is used as a move. Default is True.

  • trajectory_file (str or None, optional) – If provided, saves the trajectory to the specified file instead of the default trajectory.

  • set_momenta (bool, optional) – Whether to set the atomic momenta to a Maxwell-Boltzmann distribution of the simulation temperature.

  • **kwargs (optional) –

    Additional parameters passed directly to the specific MD thermostat (e.g., taut, tdamp, friction).

    NVT Berendsen:
    • tautfloat, optional

      Time constant for the Berendsen thermostat in fs (default is 1.0 fs).

    NVT Nose-Hoover:
    • tdampfloat, optional

      Time constant for the Nose-Hoover thermostat in fs (default is 50.0 fs).

    • tchainint, optional

      Number of thermostats in the Nose-Hoover chain (default is 3).

    • tloopint, optional

      Number of loops for the Nose-Hoover chain (default is 1).

    NVT Langevin:
    • frictionfloat, optional

      Friction coefficient for the Langevin dynamics (default is 0.01).

    NPT Berendsen:
    • isotropicbool, optional

      Whether to use isotropic pressure coupling (default is True).

    • compressibilityfloat, optional

      Compressibility of the material in bar^-1 (default is 1e-4 bar^-1).

    • tautfloat, optional

      Time constant for the Berendsen thermostat in fs (default is 10.0 fs).

    • taupfloat, optional

      Time constant for the Berendsen barostat in fs (default is 500.0 fs).

    NPT Nose-Hoover:
    • ttimefloat, optional

      Time constant for the Nose-Hoover thermostat in fs (default is 25.0 fs).

    • ptimefloat, optional

      Time constant for the Parrinello-Rahman barostat in fs (default is 75.0 fs).

    • bulk_modulusfloat, optional

      Bulk modulus of the material in GPa (default is 30.0 GPa).

    NPT MTK:
    • tdampfloat, optional

      Time constant for the Nose-Hoover thermostat in fs (default is 50.0 fs).

    • pdampfloat, optional

      Time constant for the Nose-Hoover barostat in fs (default is 500.0 fs).

    • tchainint, optional

      Number of thermostats in the Nose-Hoover chain (default is 3).

    • pchainint, optional

      Number of barostats in the Nose-Hoover chain (default is 3).

    • tloopint, optional

      Number of loops for the Nose-Hoover thermostat chain (default is 1).

    • ploopint, optional

      Number of loops for the Nose-Hoover barostat chain (default is 1).

    • vol_constraintbool, optional

      If True, the (N, V, sigma_a = 0, T)-ensemble is sampled, which allows for full cell fluctuations while keeping the cell volume fixed (default is False).

Return type:

None | Atoms

npt(nsteps, time_step=0.5, mode='iso_shape', driver='MTKNPT', set_momenta=True, output_interval=100, movie_interval=100, calculator=None, **kwargs)

Run a NPT simulation using the Berendsen thermostat and barostat.

Parameters:

  • nsteps (int) – Number of steps to run the NPT simulation.

  • time_step (float, optional) – Time step for the NPT simulation (default is 0.5 fs).

  • mode (str, optional) – The mode of the NPT simulation (default is “iso_shape”). Can be one of “iso_shape”, “aniso_shape”, or “aniso_flex”.

  • driver (str, optional) – The driver to use for the NPT simulation. Can be Berendsen, NoseHoover or MTKNPT (default is “MTKNPT”).

  • set_momenta (bool, optional) – Whether to set the atomic momenta to a Maxwell-Boltzmann distribution of the simulation temperature.

  • output_interval (int, optional) – The interval for logging output (default is 100 steps).

  • movie_interval (int, optional) – The interval for saving trajectory frames (default is 100 step).

  • calculator (ase.calculators.calculator.Calculator or None, optional) – The calculator to use for energy calculations. If None, the default model will be used.

  • kwargs (optional) – Arguments passed to the ase molecular dynamics class.

Return type:

None | Atoms

nvt(nsteps, time_step=0.5, set_momenta=True, driver='NoseHoover', output_interval=100, movie_interval=100, calculator=None, **kwargs)

Run a NVT simulation using the Berendsen thermostat.

Parameters:

  • nsteps (int) – Number of steps to run the NVT simulation.

  • time_step (float, optional) – Time step for the NVT simulation in femtoseconds (default is 0.5 fs).

  • set_momenta (bool, optional) – Whether to set the atomic momenta to a Maxwell-Boltzmann distribution of the simulation temperature.

  • driver (str, optional) – The driver to use for the NVT simulation. Can be “NoseHoover” (default), Langevin, or “Berendsen” (Not recommended, for testing purposes only).

  • output_interval (int, optional) – The interval for logging output (default is 100 steps).

  • movie_interval (int, optional) – The interval for saving trajectory frames (default is 100 step).

  • calculator (ase.calculators.calculator.Calculator or None, optional) – The calculator to use for energy calculations. If None, the default model will be used.

  • kwargs (optional) – Arguments passed to the ase molecular dynamics class.

  • NoseHoover (For)

  • tdamp (-) – Time constant for the thermostat in fs (default is 50.0 fs).

  • tchain (-) – Length of the Nose-Hoover chain (default is 3).

  • tloop (-) – Number of loops for the Nose-Hoover chain (default is 1).

  • Langevin (For)

  • friction (-) – Friction coefficient for the Langevin thermostat in fs^-1 (default is 0.1 fs^-1).

  • Berendsen (For)

  • tau (-) – Time constant for the Berendsen thermostat in fs (default is 1.0 fs).

optimize_adsorbate(max_steps=1000, max_force=0.05)

Optimize the adsorbate structure using the provided calculator.

Parameters:

  • max_steps (int, optional) – Maximum number of optimization steps (default is 1000).

  • symm_tol (float, optional) – Tolerance for symmetry (default is 1e-3).

  • max_force (float, optional) – Maximum force tolerance for convergence (default is 0.05 eV/Å).

Returns:

The optimized adsorbate structure.

Return type:

ase.Atoms

optimize_framework(max_steps=1000, opt_cell=True, fix_symmetry=True, hydrostatic_strain=True, symm_tol=0.001, max_force=0.05)

Optimize the framework structure using the provided calculator.

Parameters:

  • max_steps (int, optional) – Maximum number of optimization steps (default is 1000).

  • tol (float, optional) – Tolerance for convergence (default is 1e-5).

Returns:

The optimized framework structure.

Return type:

ase.Atoms

restart()[source]

Restart the simulation from the last state.

This method loads the last saved state from the trajectory file and restores the simulation to that state. It also loads the arrays handling the deletion/insertion energies.

Return type:

None

run(N)[source]

Run the transition matrix Monte Carlo simulation for N iterations.

Return type:

None

save_results(file_name=None)[source]

Save a json file with the main results of the simulation.

Parameters:

file_name (str) – Name of the output file. Default uses macrostate string format.

Return type:

None

set_adsorbates(adsorbates, adsorbate_energy=None)

Set the adsorbate structure for the simulation.

Parameters:

  • adsorbates (Adsorbate) – The list of adsorbate structure(s) as an Adsorbate object.

  • adsorbate_energy (float or None, optional) – The energy of the adsorbate in eV. If None, the energy will be calculated using the provided model.

  • n_adsorbates (int) – Number of adsorbate molecules in the framework.

Return type:

None

set_framework(framework_atoms, framework_energy=None)

Set the framework structure for the simulation.

Parameters:

  • framework_atoms (ase.Atoms) – The new framework structure as an ASE Atoms object.

  • framework_energy (float or None, optional) – The energy of the framework in eV. If None, the energy will be calculated using the provided model.

Return type:

None

set_state(state)

Set the current state of the simulation.

Parameters:

state (ase.Atoms) – The current state of the simulation as an ASE Atoms object.

Return type:

None

try_deletion(adsorbate_tag)[source]

Try to delete an adsorbate molecule from the framework. This method randomly selects an adsorbate molecule and attempts deletion.

Parameters:

adsorbate_tag (int) – The tag of the adsorbate molecule being deleted.

Returns:

Deletion energy.

Return type:

deltaE

try_insertion(adsorbate_tag)[source]

Try to insert a new adsorbate molecule into the framework. This method randomly places the adsorbate in the framework and checks for van der Waals overlap. If there is no overlap, it calculates the new potential energy and decides whether to accept the insertion based on the acceptance criteria.

If after a number of tries (self.max_overlap_tries) no valid position is found, an exception is thrown.

Parameters:

adsorbate_tag (int) – The tag of the adsorbate molecule being inserted.

Returns:

Insertion energy.

Return type:

deltaE

property base_iteration: int

Get the base iteration for the TMMC simulation.

Returns:

The base iteration count.

Return type:

int