Main Features
===============

1. Structure Analysis
   
   - `Ackland Jones Analysis <https://mdapy.readthedocs.io/en/latest/mdapy.html#module-mdapy.ackland_jones_analysis>`_
   - `Atomic Shear Strain <https://mdapy.readthedocs.io/en/latest/mdapy.html#module-mdapy.atomic_strain>`_
   - `CentroSymmetry Parameter <https://mdapy.readthedocs.io/en/latest/mdapy.html#module-mdapy.centro_symmetry_parameter>`_ 
   - `Common Neighbor Analysis <https://mdapy.readthedocs.io/en/latest/mdapy.html#module-mdapy.common_neighbor_analysis>`_ 
   - `Common Neighbor Parameter <https://mdapy.readthedocs.io/en/latest/mdapy.html#module-mdapy.common_neighbor_parameter>`_
   - `Atomic Structure Entropy <https://mdapy.readthedocs.io/en/latest/mdapy.html#module-mdapy.entropy>`_ 
   - `Steinhardt Bondorder <https://mdapy.readthedocs.io/en/latest/mdapy.html#module-mdapy.steinhardt_bond_orientation>`_ 
   - `Radiul Distribution Function <https://mdapy.readthedocs.io/en/latest/mdapy.html#module-mdapy.pair_distribution>`_
   - `Polyhedral Template Matching <https://mdapy.readthedocs.io/en/latest/mdapy.html#module-mdapy.polyhedral_template_matching>`_
   - `Identify stacking faults (SFs) and twinning boundary (TBs) <https://mdapy.readthedocs.io/en/latest/mdapy.html#module-mdapy.identify_SFs_TBs>`_
   - `Identify Diamond structure <https://mdapy.readthedocs.io/en/latest/mdapy.html#module-mdapy.identify_diamond_structure>`_
   - `Bond Analysis <https://mdapy.readthedocs.io/en/latest/mdapy.html#module-mdapy.bond_analysis>`_

2. Potential Analysis 

   - `Generate EAM/alloy Potential <https://mdapy.readthedocs.io/en/latest/mdapy.html#module-mdapy.eam_generate>`_
   - `Read EAM/alloy Potential <https://mdapy.readthedocs.io/en/latest/mdapy.html#module-mdapy.potential>`_
   - `Average EAM/alloy Potential <https://mdapy.readthedocs.io/en/latest/mdapy.html#module-mdapy.eam_average>`_
   - `Calculate Atomic Force and Energy by EAM/alloy <https://mdapy.readthedocs.io/en/latest/mdapy.html#mdapy.potential.EAM>`_

3. Phonon Calculation
   
   - `Cell optimization <https://mdapy.readthedocs.io/en/latest/mdapy.html#module-mdapy.cell_opt>`_
   - `Calculate phonon dispersion, dos and thermal properties, supporting any kind of potential formats <https://mdapy.readthedocs.io/en/latest/mdapy.html#module-mdapy.phonon>`_

4. Melting Analysis 

   - `Mean Squared Displacement <https://mdapy.readthedocs.io/en/latest/mdapy.html#module-mdapy.mean_squared_displacement>`_
   - `Lindemann Parameter <https://mdapy.readthedocs.io/en/latest/mdapy.html#module-mdapy.lindemann_parameter>`_
   - `Identify Solid/Liquid Phase <https://mdapy.readthedocs.io/en/latest/mdapy.html#module-mdapy.steinhardt_bond_orientation>`_

5. Deep Learning Potential Database Preparing
   
   - `Generate perturbation models <https://mdapy.readthedocs.io/en/latest/mdapy.html#module-mdapy.perturb_model>`_
   - `Extract DFT data to XYZ format for NEP training <https://mdapy.readthedocs.io/en/latest/mdapy.html#module-mdapy.dft2nepxyz>`_
   - `Calculate Atomic Force and Energy by NEP <https://mdapy.readthedocs.io/en/latest/mdapy.html#mdapy.potential.NEP>`_

6. Geometry Structure Creation 

   - `Generate Standard Lattice Structure <https://mdapy.readthedocs.io/en/latest/mdapy.html#module-mdapy.lattice_maker>`_
   - `Generate Polycrystal <https://mdapy.readthedocs.io/en/latest/mdapy.html#mdapy.create_polycrystalline.CreatePolycrystalline>`_

7. Neighbor Search 

   - `Neighbor Atoms within Fixed Distance <https://mdapy.readthedocs.io/en/latest/mdapy.html#module-mdapy.neighbor>`_
   - `Neighbor Atoms within Fixed Number <https://mdapy.readthedocs.io/en/latest/mdapy.html#module-mdapy.nearest_neighbor>`_

8. I/O
   
   - `Load Dump, Data, POSCAR, XYZ, cif format <https://mdapy.readthedocs.io/en/latest/mdapy.html#mdapy.system.System>`_
   - `Export Dump, Data, POSCAR, XYZ, cif format <https://mdapy.readthedocs.io/en/latest/mdapy.html#mdapy.system.System>`_

9. Other 

   - `Void Distribution <https://mdapy.readthedocs.io/en/latest/mdapy.html#module-mdapy.void_distribution>`_
   - `Cluster Analysis <https://mdapy.readthedocs.io/en/latest/mdapy.html#module-mdapy.cluser_analysis>`_
   - `Replication <https://mdapy.readthedocs.io/en/latest/mdapy.html#module-mdapy.replicate>`_
   - `Warren Cowley Parameter <https://mdapy.readthedocs.io/en/latest/mdapy.html#module-mdapy.warren_cowley_parameter>`_
   - `Identify species <https://mdapy.readthedocs.io/en/latest/mdapy.html#mdapy.system.System>`_
   - `Average Atomic Temperature <https://mdapy.readthedocs.io/en/latest/mdapy.html#module-mdapy.temperature>`_
   - `Atomic Voronoi Volume <https://mdapy.readthedocs.io/en/latest/mdapy.html#module-mdapy.voronoi_analysis>`_
   - `Multi-dimensional Spatial Binning <https://mdapy.readthedocs.io/en/latest/mdapy.html#module-mdapy.spatial_binning>`_
   - `Parallelly Compress file to .gz format <https://mdapy.readthedocs.io/en/latest/mdapy.html#module-mdapy.pigz>`_
   - `Split xyz/dump trajectories into seperate xyz/dump files <https://mdapy.readthedocs.io/en/latest/mdapy.html#mdapy.tool_function.split_dump>`_
   - `Minimization <https://mdapy.readthedocs.io/en/latest/mdapy.html#module-mdapy.minimizer>`_
   - `OrthogonalBox <https://mdapy.readthedocs.io/en/latest/mdapy.html#module-mdapy.orthogonal_box>`_