API参考
Atom
Atom.id
Atom.symbol
Atom.mass_amu
Atom.mass
Atom.position
Atom.velocity
Atom.force
Atom.__init__()
Atom.move_by()
Atom.accelerate_by()
Atom.copy()
Cell
Cell.lattice_vectors
Cell.atoms
Cell.volume
Cell.pbc_enabled
Cell.lattice_locked
Cell.lattice_inv
Cell.num_atoms
Cell.apply_periodic_boundary()
Cell.minimum_image()
Cell.calculate_temperature()
Cell.build_supercell()
Cell.__init__()
Cell.calculate_volume()
Cell.get_box_lengths()
Cell.calculate_stress_tensor()
Cell.lock_lattice_vectors()
Cell.unlock_lattice_vectors()
Cell.apply_deformation()
Cell.copy()
Cell.calculate_kinetic_energy()
Cell.get_positions()
Cell.get_velocities()
Cell.get_forces()
Cell.get_com_velocity()
Cell.remove_com_motion()
Cell.get_com_position()
Cell.set_lattice_vectors()
Cell.get_fractional_coordinates()
Cell.set_fractional_coordinates()
Cell.set_positions()
Cell.get_volume()
Cell.scale_lattice()
ConfigManager
ConfigManager.config
ConfigManager.__init__()
ConfigManager.load_config()
ConfigManager.get()
DeformationResult
StructureRelaxer
ZeroTempDeformationCalculator
ElasticConstantsSolver
ShearDeformationMethod
calculate_zero_temp_elastic_constants()
FiniteTempElasticityWorkflow
StressCalculator
StressCalculator.__init__()
StressCalculator.calculate_kinetic_stress()
StressCalculator.calculate_virial_stress()
StressCalculator.calculate_total_stress()
StressCalculator.calculate_finite_difference_stress()
StressCalculator.calculate_lattice_stress()
StressCalculator.get_all_stress_components()
StressCalculator.compute_stress()
StressCalculator.calculate_virial_kinetic_stress()
StressCalculator.calculate_stress_basic()
StressCalculator.validate_tensor_symmetry()
StrainCalculator
StrainCalculator.compute_strain()
MDComponent
Propagator
Propagator.propagate()
IntegrationScheme
IntegrationScheme.step()
ThermostatInterface
ThermostatInterface.apply()
BarostatInterface
BarostatInterface.apply()
PositionPropagator
PositionPropagator.propagate()
VelocityPropagator
VelocityPropagator.propagate()
ForcePropagator
ForcePropagator.__init__()
ForcePropagator.propagate()
BerendsenThermostatPropagator
BerendsenThermostatPropagator.__init__()
BerendsenThermostatPropagator.propagate()
BerendsenThermostatPropagator.get_statistics()
BerendsenThermostatPropagator.reset_statistics()
AndersenThermostatPropagator
AndersenThermostatPropagator.__init__()
AndersenThermostatPropagator.propagate()
AndersenThermostatPropagator.get_statistics()
AndersenThermostatPropagator.reset_statistics()
NoseHooverChainPropagator
NoseHooverChainPropagator.__init__()
NoseHooverChainPropagator.propagate()
NoseHooverChainPropagator.get_conserved_energy()
NoseHooverChainPropagator.get_statistics()
NoseHooverChainPropagator.reset_statistics()
NoseHooverChainPropagator.reset_thermostat_state()
create_nve_propagators()
LangevinThermostatPropagator
LangevinThermostatPropagator.__init__()
LangevinThermostatPropagator.propagate()
LangevinThermostatPropagator.get_statistics()
LangevinThermostatPropagator.reset_statistics()
LangevinThermostatPropagator.set_friction()
LangevinThermostatPropagator.get_effective_parameters()
exprel()
MTKBarostatPropagator
MTKBarostatPropagator.__init__()
MTKBarostatPropagator.propagate()
MTKBarostatPropagator.integrate_momenta()
MTKBarostatPropagator.propagate_positions_and_cell()
MTKBarostatPropagator.get_barostat_energy()
MTKBarostatPropagator.get_current_pressure()
MTKBarostatPropagator.get_statistics()
NVEScheme
NVEScheme.__init__()
NVEScheme.step()
NVEScheme.get_statistics()
NVEScheme.reset_statistics()
BerendsenNVTScheme
BerendsenNVTScheme.__init__()
BerendsenNVTScheme.step()
BerendsenNVTScheme.get_statistics()
BerendsenNVTScheme.reset_statistics()
BerendsenNVTScheme.get_current_temperature()
AndersenNVTScheme
AndersenNVTScheme.__init__()
AndersenNVTScheme.step()
AndersenNVTScheme.get_statistics()
AndersenNVTScheme.reset_statistics()
AndersenNVTScheme.get_current_temperature()
AndersenNVTScheme.get_collision_statistics()
NoseHooverNVTScheme
NoseHooverNVTScheme.__init__()
NoseHooverNVTScheme.step()
NoseHooverNVTScheme.get_statistics()
NoseHooverNVTScheme.reset_statistics()
NoseHooverNVTScheme.reset_thermostat_state()
NoseHooverNVTScheme.get_current_temperature()
NoseHooverNVTScheme.get_thermostat_variables()
LangevinNVTScheme
LangevinNVTScheme.__init__()
LangevinNVTScheme.step()
LangevinNVTScheme.get_statistics()
LangevinNVTScheme.reset_statistics()
LangevinNVTScheme.get_current_temperature()
LangevinNVTScheme.set_friction()
LangevinNVTScheme.get_thermostat_parameters()
LangevinNVTScheme.get_energy_balance_info()
create_nose_hoover_nvt_scheme()
create_andersen_nvt_scheme()
create_berendsen_nvt_scheme()
create_langevin_nvt_scheme()
create_nve_scheme()
MTKNPTScheme
MTKNPTScheme.__init__()
MTKNPTScheme.step()
MTKNPTScheme.get_statistics()
MTKNPTScheme.get_current_state()
create_mtk_npt_scheme()
Thermostat
Thermostat.__init__()
Thermostat.apply()
Thermostat.get_kinetic_energy()
Thermostat.get_temperature()
Thermostat.remove_com_motion()
Thermostat.record_state()
BerendsenThermostat
BerendsenThermostat.__init__()
BerendsenThermostat.apply()
AndersenThermostat
AndersenThermostat.__init__()
AndersenThermostat.apply()
NoseHooverThermostat
NoseHooverThermostat.__init__()
NoseHooverThermostat.apply()
NoseHooverChainThermostat
NoseHooverChainThermostat.__init__()
NoseHooverChainThermostat.apply()
NoseHooverChainThermostat.get_chain_state()
Barostat
Barostat.__init__()
Barostat.apply()
Barostat.calculate_internal_pressure()
Barostat.record_state()
ParrinelloRahmanHooverBarostat
ParrinelloRahmanHooverBarostat.__init__()
ParrinelloRahmanHooverBarostat.apply()
ParrinelloRahmanHooverBarostat.calculate_internal_pressure()
BerendsenBarostat
BerendsenBarostat.__init__()
BerendsenBarostat.apply()
AndersenBarostat
AndersenBarostat.__init__()
AndersenBarostat.apply()
MDSimulator
MDSimulator.__init__()
MDSimulator.run_nve()
MDSimulator.run_nvt()
MDSimulator.run_npt()
MDSimulator.run()
MDSimulator.calculate_total_energy()
MDSimulator.plot_temperature()
MDSimulator.plot_pressure()
Potential
Potential.__init__()
Potential.calculate_forces()
Potential.calculate_energy()
EAMAl1Potential
EAMAl1Potential.__init__()
EAMAl1Potential.calculate_forces()
EAMAl1Potential.calculate_energy()
EAMCu1Potential
EAMCu1Potential.__init__()
EAMCu1Potential.calculate_forces()
EAMCu1Potential.calculate_energy()
LennardJonesPotential
LennardJonesPotential.__init__()
LennardJonesPotential.calculate_forces()
LennardJonesPotential.calculate_energy()
TersoffPotential
TersoffPotential.__init__()
TersoffPotential.calculate_forces()
TersoffPotential.calculate_energy()
MLPotential
MLPotential.__init__()
MLPotential.calculate_forces()
MLPotential.calculate_energy()
TensorConverter
TensorConverter.to_voigt()
TensorConverter.from_voigt()
DataCollector
DataCollector.__init__()
DataCollector.__del__()
DataCollector.collect()
DataCollector.save_trajectory()
NeighborList
NeighborList.__init__()
NeighborList.get_neighbor_stats()
NeighborList.build()
NeighborList.need_refresh()
NeighborList.update()
NeighborList.get_neighbors()
NeighborList.debug_neighbor_distribution()
get_atomic_mass()
Optimizer
Optimizer.optimize()
GradientDescentOptimizer
GradientDescentOptimizer.converged
GradientDescentOptimizer.trajectory
GradientDescentOptimizer.__init__()
GradientDescentOptimizer.optimize()
BFGSOptimizer
BFGSOptimizer.converged
BFGSOptimizer.trajectory
BFGSOptimizer.__init__()
BFGSOptimizer.optimize()
CGOptimizer
CGOptimizer.__init__()
CGOptimizer.optimize()
LBFGSOptimizer
LBFGSOptimizer.__init__()
LBFGSOptimizer.optimize()
TrajectoryWriter
TrajectoryWriter.__init__()
TrajectoryWriter.open()
TrajectoryWriter.initialize()
TrajectoryWriter.write_frame()
TrajectoryWriter.write_metadata()
TrajectoryWriter.close()
TrajectoryReader
TrajectoryReader.__init__()
TrajectoryReader.open()
TrajectoryReader.read_frame()
TrajectoryReader.read_frames()
TrajectoryReader.get_metadata()
TrajectoryReader.get_trajectory_info()
TrajectoryReader.close()
save_trajectory()
load_trajectory()
TrajectoryRecorder
TrajectoryRecorder.__init__()
TrajectoryRecorder.initialize()
TrajectoryRecorder.record()
TrajectoryRecorder.finalize()
LBFGSOptimizerWithTrajectory
LBFGSOptimizerWithTrajectory.__init__()
LBFGSOptimizerWithTrajectory.optimize()
create_optimizer_with_trajectory()
DeformationTrajectoryRecorder
DeformationTrajectoryRecorder.__init__()
DeformationTrajectoryRecorder.initialize()
DeformationTrajectoryRecorder.record_deformation()
DeformationTrajectoryRecorder.finalize()
Visualizer
Visualizer.__init__()
Visualizer.plot_cell_structure()
Visualizer.set_axes_equal()
Visualizer.plot_stress_strain_multiple()
Visualizer.plot_deformation_stress_strain()
Visualizer.create_optimization_animation()
Visualizer.create_stress_strain_animation()
Visualizer.create_simulation_animation()
setup_matplotlib()
get_chinese_font()
thermoelasticsim
thermoelasticsim.core.config
thermoelasticsim.core.structure
thermoelasticsim.elastic.deformation_method.finite_temp
thermoelasticsim.elastic.deformation_method.zero_temp
thermoelasticsim.elastic.fluctuation_method
thermoelasticsim.elastic.mechanics
thermoelasticsim.md.barostats
thermoelasticsim.md.interfaces
thermoelasticsim.md.md_simulator
thermoelasticsim.md.propagators
thermoelasticsim.md.schemes
thermoelasticsim.md.thermostats
thermoelasticsim.potentials.base
thermoelasticsim.potentials.eam
thermoelasticsim.potentials.lennard_jones
thermoelasticsim.potentials.mlp
thermoelasticsim.potentials.tersoff
thermoelasticsim.utils.optimizers
thermoelasticsim.utils.plot_config
thermoelasticsim.utils.trajectory
thermoelasticsim.utils.trajectory_recorder
thermoelasticsim.utils.utils
thermoelasticsim.utils.visualization