├── .eggs └── README.txt ├── .github └── workflows │ ├── mirror_gitee.yml │ ├── pipy_release.yml │ └── test.yml ├── .gitignore ├── .readthedocs.yaml ├── LICENSE ├── README.md ├── docs ├── .eggs │ └── README.txt ├── Makefile ├── make.bat ├── pics │ ├── mcmc_ala_1cv.png │ ├── mcmc_ala_2cv.png │ └── rid_workflow.jpg ├── requirements.txt └── source │ ├── _static │ └── .gitkeep │ ├── conf.py │ ├── index.rst │ ├── install.md │ ├── install_dp.md │ ├── mcmc_configuration.md │ ├── prepare_files.md │ ├── rid_configuration.md │ ├── rid_download.md │ ├── rid_machine.md │ ├── troubleshooting │ ├── index.rst │ ├── installation.md │ ├── minikube.md │ └── submit.md │ ├── tutorial.ipynb │ └── tutorial.md ├── examples ├── README.md ├── ala2_input │ ├── ala2.gro │ └── ala2.top ├── chignolin_input │ ├── charmm36-mar2019.ff │ │ ├── atomtypes.atp │ │ ├── cmap.itp │ │ ├── ffbonded.itp │ │ ├── ffnonbonded.itp │ │ ├── forcefield.doc │ │ ├── forcefield.itp │ │ ├── gb.itp │ │ ├── ions.itp │ │ ├── merged.arn │ │ ├── merged.c.tdb │ │ ├── merged.hdb │ │ ├── merged.n.tdb │ │ ├── merged.r2b │ │ ├── merged.rtp │ │ ├── merged.vsd │ │ ├── nbfix.itp │ │ ├── old_c36_cmap.itp │ │ ├── spc.itp │ │ ├── spce.itp │ │ ├── tip3p.itp │ │ ├── tip4p.itp │ │ └── watermodels.dat │ ├── npt.gro │ └── topol.top ├── hfo2_input │ ├── colvar │ ├── conf0.gro │ ├── dp000.pb │ ├── hfo2.top │ ├── index.ndx │ ├── index.raw │ ├── input.json │ ├── make_index.sh │ ├── plmpath.pdb │ └── type.raw ├── install-linux-cn.sh ├── machine_bohrium_k8s.json ├── quick-start-postgres-stable-cn.yaml ├── rid_json_files │ ├── rid_ala2.json │ ├── rid_chignolin.json │ └── rid_hfo2.json └── tutorial.ipynb ├── install ├── DeePFE.cpp ├── README.md ├── gmx_exploration.dockerfile ├── gmx_plumed.dockerfile ├── gmx_tf.Dockerfile ├── lmp_exploration_dp.dockerfile ├── tf_cpu.dockerfile └── tf_gpu.Dockerfile ├── requirements.txt ├── rid ├── __about__.py ├── __init__.py ├── __main__.py ├── common │ ├── __init__.py │ ├── gromacs │ │ ├── __init__.py │ │ ├── command.py │ │ ├── gmx_constant.py │ │ ├── mdp.py │ │ └── trjconv.py │ ├── lammps │ │ ├── __init__.py │ │ ├── command.py │ │ └── lmp_constant.py │ ├── mol.py │ ├── mol_dpdata.py │ ├── plumed │ │ ├── __init__.py │ │ ├── check_plumed.py │ │ ├── make_plumed.py │ │ └── plumed_constant.py │ ├── sampler │ │ ├── __init__.py │ │ └── command.py │ └── tensorflow │ │ ├── __init__.py │ │ └── graph.py ├── constants.py ├── entrypoint │ ├── __init__.py │ ├── cli.py │ ├── download.py │ ├── explore.py │ ├── info.py │ ├── label.py │ ├── main.py │ ├── redim.py │ ├── relabel.py │ ├── reredim.py │ ├── resubmit.py │ ├── server.py │ ├── submit.py │ └── train.py ├── flow │ ├── __init__.py │ └── loop.py ├── main.py ├── mcmc │ ├── __init__.py │ └── walker.py ├── nn │ ├── __init__.py │ ├── freeze.py │ ├── model.py │ └── train_net.py ├── op │ ├── __init__.py │ ├── adjust_trust_level.py │ ├── label_stats.py │ ├── mcmc_plot.py │ ├── mcmc_run.py │ ├── prep_data.py │ ├── prep_exploration.py │ ├── prep_label.py │ ├── prep_rid.py │ ├── prep_select.py │ ├── recorder.py │ ├── run_exploration.py │ ├── run_label.py │ ├── run_model_devi.py │ ├── run_select.py │ └── run_train.py ├── select │ ├── __init__.py │ ├── cluster.py │ ├── conf_select.py │ └── model_devi.py ├── superop │ ├── __init__.py │ ├── blocks.py │ ├── data.py │ ├── exploration.py │ ├── label.py │ ├── mcmc.py │ └── selector.py ├── task │ ├── __init__.py │ ├── builder.py │ └── task.py ├── template │ ├── machine_bohrium.json │ ├── machine_bohrium_k8s.json │ ├── machine_bohrium_k8s_mcmc.json │ ├── machine_local_k8s.json │ ├── machine_slurm_k8s.json │ ├── machine_slurm_k8s_mcmc.json │ ├── machine_slurm_local.json │ ├── machine_slurm_local_mcmc.json │ ├── rid_gmx_custom.json │ ├── rid_gmx_dih.json │ ├── rid_gmx_dis.json │ ├── rid_gmx_dp.json │ ├── rid_lmp_dp.json │ ├── rid_lmp_gmx_dp.json │ ├── rid_mcmc_cv_dih.json │ ├── rid_mcmc_cv_dis.json │ └── rid_mcmc_path.json ├── tools │ ├── __init__.py │ └── estimator.py └── utils │ ├── __init__.py │ ├── command.py │ ├── files.py │ ├── format.py │ ├── path.py │ └── set_config.py ├── setup.py └── tests ├── context.py ├── data ├── 000 │ ├── conf.gro │ └── topol.top ├── 001 │ ├── conf.gro │ ├── plumed.dat │ └── topol.top ├── centers.out ├── cls_sel.ndx ├── cls_sel.out ├── conf.gro ├── conf.json ├── cv_forces.out ├── kappa.out ├── models │ ├── model_000.pb │ ├── model_001.pb │ ├── model_002.pb │ └── model_003.pb ├── plm.out ├── plm_label.out ├── plumed.dat ├── rid.json ├── topol.top └── traj_comp.xtc ├── mocked_ops.py ├── op ├── context.py ├── test_adjust_trust_l.py ├── test_prep_data.py ├── test_prep_explore.py ├── test_prep_label.py ├── test_prep_rid.py ├── test_prep_select.py ├── test_recorder.py ├── test_run_explore.py ├── test_run_label.py ├── test_run_select.py ├── test_run_train.py └── utils.py ├── test_data.py ├── test_exploration.py ├── test_init-block.py ├── test_iter-block.py ├── test_label.py └── test_select.py /.eggs/README.txt: 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