├── .gitignore ├── IO ├── Makefile ├── __init__.py ├── check_file.py ├── reader.py ├── src │ ├── dcd_reader_mod.f90 │ ├── txt_reader_mod.f90 │ └── xyz_reader_mod.f90 ├── type_conversion.py └── writer.py ├── Makefile ├── Q4_W4.png ├── README.md ├── algorithm ├── Makefile └── src │ ├── linked_list_mod.f90 │ ├── linspace_mod.f90 │ ├── single_linkage_cluster.f90 │ └── sort_mod.f90 ├── general ├── Makefile └── src │ ├── constants_mod.f90 │ └── system_mod.f90 ├── mathlib ├── Makefile ├── math_API.py ├── src │ ├── distribution.f90 │ ├── factorial_mod.f90 │ ├── spherical_harmonics_mod.f90 │ ├── statistics.f90 │ └── wigner3j_symobol_mod.f90 └── test │ ├── test_spherical_harmonics.py │ └── test_wigner3j.py ├── order_parameter ├── Makefile ├── op_lib.py ├── src │ ├── CHILL_mod.f90 │ ├── HMC_mod.f90 │ ├── Li_et_al_mod.f90 │ ├── Russo_Romano_Tanaka_mod.f90 │ ├── compile_oplib_f2py │ ├── nb_list_mod.f90 │ ├── oplib_q3_only.f90 │ ├── oplib_ql.f90 │ ├── order_parameter_mod.f90 │ ├── sph_op_mod.f90 │ ├── test_Ql_Wl.f90 │ └── tetrahedral_op_mod.f90 └── test │ ├── Russo_Romano_Tanaka │ ├── P_connection.png │ ├── dot_product_Q12.png │ └── test_order_parameter.py │ ├── test_HMC │ ├── README.md │ ├── compile_oplib_f2py │ ├── hmc_umbrella_Q6_rho.py │ ├── oplib.f90 │ ├── test_order_parameter.py │ └── test_traj.dcd │ ├── test_Q6_FFS_Li_et_al │ ├── Li_et_al_PQ6.png │ └── test_Li_et_al.py │ └── test_Ql_Wl │ ├── bcc.xyz │ ├── fcc.xyz │ ├── sc.xyz │ └── test_Ql_Wl.py ├── pair_correlation ├── Makefile ├── calc_pair_correlation.py └── src │ ├── compute_rdf_mod.f90 │ └── compute_sf_mod.f90 ├── pub1 ├── Bhatia_Thornton.py ├── Makefile ├── README ├── src │ └── bhatia_thornton_analysis.f90 └── test │ ├── All │ └── run_bhatia_thornton.py │ ├── HDL-LDL │ └── run_bhatia_thornton.py │ ├── LDL-LDL │ └── run_bhatia_thornton.py │ ├── check_pair_correlation │ ├── Tutorial_01_How_to_run_Bhatia_Thornton_analysis.ipynb │ ├── bhatia │ │ ├── Tutorial_03.ipynb │ │ ├── fig1a.png │ │ └── fig2b.png │ ├── 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