├── .github ├── dependabot.yml └── workflows │ ├── anaconda-publish.yml │ ├── build.yml │ └── pypi-publish.yml ├── .readthedocs.yaml ├── CODE_OF_CONDUCT.md ├── LICENSE ├── README.md ├── conda └── meta.yaml ├── docs ├── Makefile ├── logo.png ├── make.bat ├── requirements.txt └── source │ ├── conf.py │ ├── getting_started │ └── installation.rst │ ├── index.rst │ └── usage │ ├── command_line_interface.rst │ └── programming_interface.rst ├── examples ├── blender.ipynb ├── blender_color.py ├── blender_model_llto.py ├── free_energy_surface.ipynb └── trajectory_operations.ipynb ├── pyproject.toml ├── tests ├── __init__.py ├── data │ ├── blender │ │ ├── md.gro │ │ └── md.tpr │ ├── hillspot │ │ ├── HILLSPOT_1D │ │ ├── HILLSPOT_2D │ │ └── HILLSPOT_3D │ ├── npy │ │ ├── fes_2d.npy │ │ └── fes_3d.npy │ ├── oszicar │ │ ├── OSZICAR_01 │ │ └── OSZICAR_02 │ ├── outcar │ │ └── OUTCAR │ ├── pdb │ │ └── h2o.pdb │ ├── plumed │ │ ├── dat │ │ │ └── fes_bias.dat │ │ └── hills │ │ │ └── HILLS │ ├── poscar │ │ └── llto.poscar │ ├── vasprun │ │ ├── POTCAR │ │ └── vasprun.xml │ ├── xdatcar │ │ ├── XDATCAR_01 │ │ ├── XDATCAR_02 │ │ └── XDATCAR_03 │ └── xyz │ │ └── trj.xyz ├── test_bash01_bias.py ├── test_f01_xdc_aggregate.py ├── test_f02_xdc_unwrap.py ├── test_f03_xyz_unwrap.py ├── test_fmtd04_xdc2xtc.py └── test_fmtd07_neb.py └── xdatbus ├── __init__.py ├── c01_xdc_aggregate.py ├── c02a_xdc_unwrap.py ├── c02b_xyz_unwarp.py ├── c03_thermal_report.py ├── c04_xml2xyz.py ├── c05_sum_hills.py ├── fcli.py ├── fun_bld.py ├── fun_com.py ├── fun_mtd.py ├── resources ├── __init__.py ├── sum_hills.sh └── vis_data.yaml ├── utils.py └── utils_bpy.py /.github/dependabot.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jcwang587/xdatbus/HEAD/.github/dependabot.yml -------------------------------------------------------------------------------- /.github/workflows/anaconda-publish.yml: 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