rid package

Subpackages

• rid.common package
  • Subpackages
    • rid.common.gromacs package
      • Submodules
      • rid.common.gromacs.command module
      • rid.common.gromacs.gmx_constant module
      • rid.common.gromacs.mdp module
      • rid.common.gromacs.trjconv module
    • rid.common.lammps package
      • Submodules
      • rid.common.lammps.lmp_constant module
    • rid.common.plumed package
      • Submodules
      • rid.common.plumed.check_plumed module
      • rid.common.plumed.make_plumed module
      • rid.common.plumed.plumed_constant module
    • rid.common.sampler package
      • Submodules
      • rid.common.sampler.command module
    • rid.common.tensorflow package
      • Submodules
      • rid.common.tensorflow.graph module
  • Submodules
  • rid.common.mol module
• rid.entrypoint package
  • Submodules
  • rid.entrypoint.cli module
    • rid_ls()
    • rid_rm()
  • rid.entrypoint.info module
  • rid.entrypoint.main module
  • rid.entrypoint.resubmit module
  • rid.entrypoint.server module
    • check_port_status()
    • forward_ports()
  • rid.entrypoint.submit module
• rid.flow package
  • Submodules
  • rid.flow.loop module
    • ReinforcedDynamics
      • ReinforcedDynamics.init_keys
      • ReinforcedDynamics.input_artifacts
      • ReinforcedDynamics.input_parameters
      • ReinforcedDynamics.loop_keys
      • ReinforcedDynamics.output_artifacts
      • ReinforcedDynamics.output_parameters
    • ReinforcedDynamicsLoop
      • ReinforcedDynamicsLoop.input_artifacts
      • ReinforcedDynamicsLoop.input_parameters
      • ReinforcedDynamicsLoop.keys
      • ReinforcedDynamicsLoop.output_artifacts
      • ReinforcedDynamicsLoop.output_parameters
• rid.nn package
  • Submodules
  • rid.nn.data module
    • check_new_data()
    • collect_data()
    • make_train()
  • rid.nn.freeze module
    • freeze_model()
  • rid.nn.model module
    • Model
      • Model.build_force()
      • Model.compute_statistic()
      • Model.load_graph()
      • Model.test_error()
      • Model.test_error_mix()
      • Model.train()
    • Reader
      • Reader.get_batch_size()
      • Reader.get_data()
      • Reader.get_train_size()
      • Reader.prepare()
      • Reader.sample_train()
  • rid.nn.train_net module
    • Config
    • get_parm()
    • print_conf()
    • reset_batch_size()
    • set_conf()
    • train()
• rid.op package
  • Submodules
  • rid.op.adjust_trust_level module
    • AdjustTrustLevel
      • AdjustTrustLevel.execute()
      • AdjustTrustLevel.get_input_sign()
      • AdjustTrustLevel.get_output_sign()
  • rid.op.calc_mf module
    • CalcMF
      • CalcMF.execute()
      • CalcMF.get_input_sign()
      • CalcMF.get_output_sign()
  • rid.op.prep_data module
    • CollectData
      • CollectData.execute()
      • CollectData.get_input_sign()
      • CollectData.get_output_sign()
    • MergeData
      • MergeData.execute()
      • MergeData.get_input_sign()
      • MergeData.get_output_sign()
  • rid.op.prep_exploration module
  • rid.op.prep_label module
  • rid.op.prep_rid module
    • PrepRiD
      • PrepRiD.execute()
      • PrepRiD.get_input_sign()
      • PrepRiD.get_output_sign()
    • prep_confs()
  • rid.op.prep_select module
    • PrepSelect
      • PrepSelect.execute()
      • PrepSelect.get_input_sign()
      • PrepSelect.get_output_sign()
  • rid.op.recorder module
    • Recorder
      • Recorder.execute()
      • Recorder.get_input_sign()
      • Recorder.get_output_sign()
  • rid.op.run_exploration module
  • rid.op.run_label module
    • RunLabel
      • RunLabel.execute()
      • RunLabel.get_input_sign()
      • RunLabel.get_output_sign()
  • rid.op.run_select module
  • rid.op.run_train module
    • TrainModel
      • TrainModel.execute()
      • TrainModel.get_input_sign()
      • TrainModel.get_output_sign()
• rid.select package
  • Submodules
  • rid.select.cluster module
    • Cluster
      • Cluster.get_cluster_selection()
      • Cluster.make_threshold()
    • cv_dist()
    • mk_cluster()
    • mk_dist()
    • sel_from_cluster()
  • rid.select.conf_select module
    • ConfSelector
      • ConfSelector.select()
    • select_from_devi()
  • rid.select.model_devi module
    • compute_std()
    • make_std()
    • test_ef()
• rid.superop package
  • Submodules
  • rid.superop.blocks module
    • InitBlock
      • InitBlock.input_artifacts
      • InitBlock.input_parameters
      • InitBlock.keys
      • InitBlock.output_artifacts
      • InitBlock.output_parameters
    • IterBlock
      • IterBlock.input_artifacts
      • IterBlock.input_parameters
      • IterBlock.keys
      • IterBlock.output_artifacts
      • IterBlock.output_parameters
  • rid.superop.data module
    • DataGenerator
      • DataGenerator.input_artifacts
      • DataGenerator.input_parameters
      • DataGenerator.keys
      • DataGenerator.output_artifacts
      • DataGenerator.output_parameters
  • rid.superop.exploration module
    • Exploration
      • Exploration.input_artifacts
      • Exploration.input_parameters
      • Exploration.keys
      • Exploration.output_artifacts
      • Exploration.output_parameters
  • rid.superop.label module
    • Label
      • Label.input_artifacts
      • Label.input_parameters
      • Label.keys
      • Label.output_artifacts
      • Label.output_parameters
  • rid.superop.selector module
    • Selector
      • Selector.input_artifacts
      • Selector.input_parameters
      • Selector.keys
      • Selector.output_artifacts
      • Selector.output_parameters
• rid.task package
  • Submodules
  • rid.task.builder module
  • rid.task.task module
    • Task
      • Task.add_file()
      • Task.add_property()
      • Task.files
• rid.tools package
• rid.utils package
  • Submodules
  • rid.utils.command module
    • run_command()
  • rid.utils.files module
    • dump_json()
    • load_json()
    • load_pkl()
    • load_txt()
    • read_binary()
    • read_txt()
    • save_pkl()
    • save_txt()
    • write_binary()
    • write_txt()
  • rid.utils.format module
    • list_to_string()
  • rid.utils.path module
    • set_directory()
  • rid.utils.set_config module
    • init_executor()
    • normalize_resources()

Submodules

rid.constants module

rid.main module