├── .github └── workflows │ └── docs-build.yaml ├── .gitignore ├── .travis.yml ├── LICENSE ├── MC_MD_steps.tex ├── Makefile ├── Makefile.arch ├── NS_1d_ising_model.ipynb ├── NS_publications.bib ├── README.rst ├── RngStream.c ├── RngStream.h ├── TODO ├── Wang_LJ_model.F90 ├── Wang_LJ_params_mod.F90 ├── analyze_basins.py ├── ase_patches ├── gen_chemical_symb.patch └── lammpsdata.patch ├── check_memory.py ├── convergence ├── .gitignore ├── Au_melting_temperatures_with_fit.pdf ├── Au_melting_temperatures_with_fit_1_over_N.pdf ├── NOTES ├── analyze_tests ├── inputs.test.cluster.MC.TEMPLATE ├── inputs.test.cluster.MD.TEMPLATE ├── inputs.test.periodic.MC.TEMPLATE ├── mW-fig.pdf ├── melting_convergence.tex ├── prep_jobs ├── prep_scan ├── test.postscript └── test.script ├── docs ├── MC_MD_steps.txt ├── Makefile ├── NS_PES_animation.gif ├── conf.py ├── doc_figure_mlh.jpg ├── doc_figure_tutorial_120_cv.jpg ├── doc_figure_tutorial_LJ6.jpg ├── getstart.rst ├── index.rst ├── install.rst ├── intro.rst ├── junk ├── lammpslib.rst ├── ns_rng.rst ├── ns_run.rst ├── requirements.txt ├── rngstream.rst ├── stacktrace.rst └── tutorial.rst ├── environment.yml ├── example_CollapsingSpheres_model.F90 ├── example_CollapsingSpheres_params_mod.F90 ├── example_Jagla_model.F90 ├── example_Jagla_params_mod.F90 ├── example_Jaglasmooth_model.F90 ├── example_LJ_min_image_model.F90 ├── example_LJ_model.F90 ├── example_LJ_params_mod.F90 ├── example_bead_spring_polymer_model.F90 ├── example_bead_spring_polymer_params_mod.F90 ├── example_inputs ├── LJ38_7adatom_starting_walkers.extxyz ├── LJ_surface_MC.inp ├── inputs.test.2D_periodic.MC.fortran ├── inputs.test.cluster.MC.fortran ├── inputs.test.cluster.MC.fortran.converged ├── inputs.test.cluster.MC.fortran.read_initial_config ├── inputs.test.cluster.MD.lammps.polymer ├── inputs.test.cluster.MD.quip ├── inputs.test.periodic.GMC.fortran ├── inputs.test.periodic.MD.lammps ├── inputs.test.periodic.MD.lammps.converged ├── inputs.test.periodic_binary.MD.FORTRAN_LJ ├── inputs.test.periodic_binary_semiGC_dmu_0.1.MD.FORTRAN_LJ ├── quip_params.cluster.xml ├── test_start_config.xyz └── test_start_config_polymer.xyz ├── example_mat_mod.F90 ├── example_noninteracting_model.F90 ├── fortranMCMDpy.py ├── fortran_MC_MD.F90 ├── fortran_energy_calc.py ├── lammps_patches ├── communicator_self.patch ├── create_improper.cpp ├── create_improper.h ├── fix_gmc.cpp └── fix_gmc.h ├── lammpslib.py ├── make_thermal_average_xrd_rdfd_lenhisto.py ├── misc_calc_lib.py ├── nested_sampling_of_2D_function.ipynb ├── ns_T_dependent_analysis ├── ns_analyse ├── ns_analyse.py ├── ns_process_traj ├── ns_profile_analyse ├── ns_rng.py ├── ns_run ├── ns_run.py ├── ns_run_analyzers ├── __init__.py ├── config_enthalpy_distribution.py ├── ns_analyzers_util.py └── polymer.py ├── ns_set_analysis_weights ├── ns_step_naming_scheme.txt ├── pick_interconnected_clump.py ├── quip_params.xml ├── rngstream.py ├── stacktrace.py ├── test_fortran_model.py 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