ThermoElasticSim

API参考

  • 核心模块 (core)
    • 结构模块
      • 理论基础
      • Classes
      • Functions
      • 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.apply_periodic_boundary()
        • Cell.copy()
        • Cell.calculate_temperature()
        • Cell.calculate_kinetic_energy()
        • Cell.get_positions()
        • Cell.get_velocities()
        • Cell.get_forces()
        • Cell.minimum_image()
        • Cell.build_supercell()
        • Cell.get_com_velocity()
        • Cell.remove_com_motion()
        • Cell.get_com_position()
        • Cell.num_atoms
        • Cell.set_lattice_vectors()
        • Cell.get_fractional_coordinates()
        • Cell.set_fractional_coordinates()
        • Cell.set_positions()
        • Cell.get_volume()
        • Cell.scale_lattice()
    • 配置模块
      • ConfigManager
        • ConfigManager.config
        • ConfigManager.__init__()
        • ConfigManager.load_config()
        • ConfigManager.get()
  • 弹性常数计算模块 (elastic)
    • 显式形变法
      • 零温计算
        • DeformationResult
        • StructureRelaxer
        • ZeroTempDeformationCalculator
        • ElasticConstantsSolver
        • ShearDeformationMethod
        • calculate_zero_temp_elastic_constants()
      • 有限温计算
        • FiniteTempElasticityWorkflow
    • 力学计算
      • 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()
    • 涨落法(开发中)
  • 分子动力学引擎 (md)
    • 接口定义
      • MDComponent
      • Propagator
        • Propagator.propagate()
      • IntegrationScheme
        • IntegrationScheme.step()
      • ThermostatInterface
        • ThermostatInterface.apply()
      • BarostatInterface
        • BarostatInterface.apply()
    • 传播子
      • 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()
    • 积分方案
      • 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()
    • 恒温器
      • 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()
    • 恒压器
      • 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()
    • MD模拟器
      • MDSimulator
        • MDSimulator.__init__()
        • MDSimulator.run_nve()
        • MDSimulator.run_nvt()
        • MDSimulator.run_npt()
        • MDSimulator.run()
        • MDSimulator.calculate_total_energy()
        • MDSimulator.plot_temperature()
        • MDSimulator.plot_pressure()
  • 势函数模块 (potentials)
    • 基类
      • Potential
        • Potential.__init__()
        • Potential.calculate_forces()
        • Potential.calculate_energy()
    • EAM势
      • EAMAl1Potential
        • EAMAl1Potential.__init__()
        • EAMAl1Potential.calculate_forces()
        • EAMAl1Potential.calculate_energy()
      • EAMCu1Potential
        • EAMCu1Potential.__init__()
        • EAMCu1Potential.calculate_forces()
        • EAMCu1Potential.calculate_energy()
    • Lennard-Jones势
      • LennardJonesPotential
        • LennardJonesPotential.__init__()
        • LennardJonesPotential.calculate_forces()
        • LennardJonesPotential.calculate_energy()
    • Tersoff势
      • TersoffPotential
        • TersoffPotential.__init__()
        • TersoffPotential.calculate_forces()
        • TersoffPotential.calculate_energy()
    • 机器学习势(开发中)
      • MLPotential
        • MLPotential.__init__()
        • MLPotential.calculate_forces()
        • MLPotential.calculate_energy()
  • 工具模块 (utils)
    • 通用工具
      • 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()
    • 优化器
      • Optimizer
        • Optimizer.optimize()
        • 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()
    • 轨迹记录
      • 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()
    • 可视化
      • 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()
    • 绘图配置
      • setup_matplotlib()
      • get_chinese_font()
ThermoElasticSim
  • Python 模块索引

Python 模块索引

t
 
t
- 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

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