gnrs.optimize¶

gnrs.optimize.optimization_task¶

This module provides the GeometryOptimizationTask class for performing geometry optimization tasks.

This source code is licensed under the BSD-3-Clause license found in the LICENSE file in the root directory of this source tree.

class gnrs.optimize.optimization_task.GeometryOptimizationTask[source]¶

Bases: TaskABC

Task for relaxing geometry of crystal structures.

Initialize the geometry optimization task.

Parameters:

comm – MPI communicator
config – Config dictionary
gnrs_info – Genarris info dictionary
optimizer – Optimizer
energy_method – Energy calculator(optional)

__init__(comm, config, gnrs_info, optimizer, energy_method=None)[source]¶

Initialize the geometry optimization task.

Parameters:

comm (mpi4py.MPI.Comm) – MPI communicator
config (dict) – Config dictionary
gnrs_info (dict) – Genarris info dictionary
optimizer (str) – Optimizer
energy_method (str | None) – Energy calculator(optional)

Return type:

None

initialize()[source]¶

Initialize the optimization task.

Return type:: None

pack_settings()[source]¶

Pack settings for the optimization task.

Returns:: Task settings dictionary
Return type:: dict

print_settings(task_set)[source]¶

Print the task settings.

Parameters:: task_set (dict) – Task settings dictionary
Return type:: None

create_folders()[source]¶

Create the necessary folders for the optimization task.

Return type:: None

perform_task(task_set)[source]¶

Perform the optimization task.

Parameters:: task_set (dict) – Task settings dictionary
Return type:: None

collect_results()[source]¶: Collect and save the results of the task.

analyze()[source]¶

Analyze the results of the optimization task.

Return type:: None

finalize()[source]¶

Finalize the optimization task.

Return type:: None

gnrs.optimize.bfgs¶

This module provides a wrapper around the BFGS implementation from ASE.

This source code is licensed under the BSD-3-Clause license found in the LICENSE file in the root directory of this source tree.

class gnrs.optimize.bfgs.BFGSOptimizer[source]¶

Bases: GeometryOptimizerABC

Limited-memory BFGS optimization using ASE’s BFGS implementation.

fmax¶: Maximum force tolerance for convergence criterion

steps¶: Maximum number of optimization steps to perform

fix_sym¶: Whether to fix the symmetry of the structure

cell_opt¶: Whether to optimize the cell parameters as well

opt_name¶: Name of the optimizer for storing in the crystal info

converged¶: Whether the optimization successfully converged

Initialize the geometry optimizer.

Parameters:

comm – MPI communicator for parallel computation
task_set – Optimization settings
opt_name – Optimizer
energy_method – Energy calculation method

__init__(*args)[source]¶

Initialize the geometry optimizer.

Parameters:

comm – MPI communicator for parallel computation
task_set – Optimization settings
opt_name – Optimizer
energy_method – Energy calculation method

optimize(xtal)[source]¶

Performs geometry optimization using BFGS algorithm.

Parameters:: xtal (ase.atoms.Atoms) – ASE Atoms object
Return type:: None

update(xtal)[source]¶

Update the optimizer with the new structure.

Parameters:: xtal (ase.atoms.Atoms)
Return type:: None

gnrs.optimize.lbfgs¶

This module provides a wrapper around the LBFGS implementation from ASE.

This source code is licensed under the BSD-3-Clause license found in the LICENSE file in the root directory of this source tree.

class gnrs.optimize.lbfgs.LBFGSOptimizer[source]¶

Bases: GeometryOptimizerABC

Limited-memory BFGS optimization using ASE’s LBFGS implementation.

fmax¶: Maximum force tolerance for convergence criterion

steps¶: Maximum number of optimization steps to perform

fix_sym¶: Whether to fix the symmetry of the structure

cell_opt¶: Whether to optimize the cell parameters as well

opt_name¶: Name of the optimizer for storing in the crystal info

converged¶: Whether the optimization successfully converged

Initialize the geometry optimizer.

Parameters:

comm – MPI communicator for parallel computation
task_set – Optimization settings
opt_name – Optimizer
energy_method – Energy calculation method

__init__(*args)[source]¶

Initialize the geometry optimizer.

Parameters:

comm – MPI communicator for parallel computation
task_set – Optimization settings
opt_name – Optimizer
energy_method – Energy calculation method

optimize(xtal)[source]¶

Performs geometry optimization using LBFGS algorithm.

Parameters:: xtal (ase.atoms.Atoms) – ASE Atoms object
Return type:: None

update(xtal)[source]¶

Update the optimizer with the new structure.

Parameters:: xtal (ase.atoms.Atoms)
Return type:: None

gnrs.optimize.rigid_press¶

This module provides a wrapper around the rigid_press C code.

This source code is licensed under the BSD-3-Clause license found in the LICENSE file in the root directory of this source tree.

class gnrs.optimize.rigid_press.RIGID_PRESSOptimizer[source]¶

Bases: GeometryOptimizerABC

Optimizes structure using rigid_press C code.

Initialize the geometry optimizer.

Parameters:

comm – MPI communicator for parallel computation
task_set – Optimization settings
opt_name – Optimizer
energy_method – Energy calculation method

__init__(*args)[source]¶

Initialize the geometry optimizer.

Parameters:

comm – MPI communicator for parallel computation
task_set – Optimization settings
opt_name – Optimizer
energy_method – Energy calculation method

initialize()[source]¶

Initialize the optimizer.

Return type:: None

optimize(xtal)[source]¶

Optimize the structure using rigid_press C code.

Parameters:: xtal (ase.Atoms)
Return type:: None

update(xtal)[source]¶

Update the optimizer with the new structure.

Parameters:: xtal (ase.Atoms)
Return type:: None

gnrs.optimize.symm_rigid_press¶

This module provides a wrapper around the Rigid Press implementation with symmetry constraints.

This source code is licensed under the BSD-3-Clause license found in the LICENSE file in the root directory of this source tree.

class gnrs.optimize.symm_rigid_press.SYMM_RIGID_PRESSOptimizer[source]¶

Bases: GeometryOptimizerABC

Optimizes crystal structures using rigid_press algorithm with symmetry constraints.

This optimizer uses van der Waals cutoff matrices for tight molecular packing and preserves symmetry during optimization.

opt_name¶: Name identifier for the optimizer

int_scale¶: Interaction scale factor

method¶: Optimization method to use

tol¶: Convergence tolerance

maxiter¶: Maximum number of iterations

vol_tol¶: Volume tolerance

debug_flag¶: Whether to enable debug output

Initialize the symmetry-preserving rigid press optimizer.

__init__(*args)[source]¶: Initialize the symmetry-preserving rigid press optimizer.

initialize()[source]¶

Initialize the optimizer.

Return type:: None

optimize(xtal)[source]¶

Perform structure optimization using the RigidPressSymm algorithm.

Parameters:: xtal (ase.Atoms) – ASE Atoms object
Return type:: None

update(xtal)[source]¶

Update crystal info with optimization status.

Parameters:: xtal (ase.Atoms) – ASE Atoms object
Return type:: None