├── .gitignore ├── .travis.yml ├── LICENSE ├── Notes.txt ├── PSI4_SETUP.md ├── README.md ├── bin └── mbmlpg.py ├── database_setup.py ├── docs ├── CONFIG.md ├── DATABASE_SETUP.txt ├── FILTERS.md ├── PYTHON_REQUIREMENTS.txt ├── SMILES.md ├── SYSTEM_REQUIREMENTS.txt └── documentation │ ├── documentation.ipynb │ └── figures │ ├── over_underfitting.png │ └── plot_methods.png ├── examples ├── 1-co2_1b_mb-nrg │ └── 1-co2_1b_mb-nrg.ipynb ├── 2-co2_2b_ttmnrg │ └── 2-co2_2b_ttmnrg.ipynb ├── 3-co2_2b_mbnrg │ └── 3-co2_2b_mbnrg.ipynb ├── 4-co2_h2o_ttm_and_mbnrg │ └── 4-co2_h2o_ttm_and_mbnrg.ipynb ├── 5-nh4+_1b_mbnrg │ └── 5-nh4+_1b_mbnrg.ipynb ├── 6-nh4+_h2o_2b_ttm_and_mbnrg │ └── 6-nh4+_h2o_2b_ttm_and_mbnrg.ipynb └── obsolete_examples │ ├── formamide_monomer │ ├── formamide.ini │ ├── formamide.xyz │ └── general_monomer_notebook.ipynb │ ├── general_dimer_notebook │ ├── dimer_settings.ini │ ├── general_dimer_notebook.ipynb │ ├── monomer1.xyz │ ├── monomer1_settings.ini │ ├── monomer2.xyz │ └── monomer2_settings.ini │ ├── general_monomer_notebook │ ├── general_monomer_notebook.ipynb │ ├── monomer.xyz │ └── monomer_settings.ini │ ├── general_trimer_notebook │ ├── dimer_settings.ini │ ├── general_trimer_notebook.ipynb │ ├── monomer1.xyz │ ├── monomer1_settings.ini │ ├── monomer2.xyz │ ├── monomer2_settings.ini │ ├── monomer3.xyz │ ├── monomer3_settings.ini │ └── trimer_settings.ini │ ├── mb_decomp_notebook │ └── mb_decomp.ipynb │ ├── mbml_examples │ ├── N2O5_monomer │ │ ├── N2O5_optimized.xyz │ │ └── training_configs.xyz │ └── formamide_monomer │ │ ├── formamide_opt.xyz │ │ └── training_input.xyz │ ├── pyrrole_monomer │ ├── general_monomer_notebook.ipynb │ ├── pyrrole.ini │ └── pyrrole.xyz │ ├── pyrrole_monomer_out_of_order_doesnt_work │ ├── general_monomer_notebook.ipynb │ ├── pyrrole.ini │ └── pyrrole.xyz │ └── tutorial │ └── tutorial.ipynb ├── mbfit ├── __init__.py ├── calculator │ ├── __init__.py │ ├── calculator.py │ ├── calculator_utils.py │ ├── mbdecomp.py │ ├── model.py │ ├── psi4_calculator.py │ └── qchem_calculator.py ├── configurations │ ├── __init__.py │ ├── atom_distance_configuration_generator.py │ ├── configuration_generator.py │ ├── configuration_generator_2b.py │ ├── configuration_generator_nb.py │ ├── configurations_splitter.py │ ├── geometry_optimizer.py │ ├── normal_modes_configuration_generator.py │ └── normal_modes_generator.py ├── database │ ├── __init__.py │ ├── database.py │ ├── database_cleaner.py │ ├── database_filler.py │ ├── database_initializer.py │ ├── init.sql │ ├── job_handler.py │ ├── job_handler_utils.py │ ├── psi4_job_handler.py │ ├── psi4_job_template.py │ ├── qchem_job_handler.py │ ├── qchem_job_template.py │ └── training_set_generator.py ├── exceptions │ ├── __init__.py │ └── exceptions.py ├── fitting │ ├── __init__.py │ ├── config.py │ ├── evaluator.py │ ├── file_writer_nb_fitting.py │ ├── fit_visualizer.py │ ├── fitting_code_templates │ │ ├── constants.h │ │ ├── coulomb.cpp │ │ ├── coulomb.h │ │ ├── electrostatics.cpp │ │ ├── electrostatics.h │ │ ├── fit-utils.cpp │ │ ├── fit-utils.h │ │ ├── gammq.cpp │ │ ├── gammq.h │ │ ├── geom_manip.h │ │ ├── io-xyz.cpp │ │ ├── io-xyz.h │ │ ├── molecule.h │ │ ├── ps.cpp │ │ ├── ps.h │ │ ├── rwlsq.cpp │ │ ├── rwlsq.h │ │ ├── tang-toennies.cpp │ │ ├── tang-toennies.h │ │ ├── training_set.cpp │ │ ├── training_set.h │ │ ├── variable.cpp │ │ ├── variable.h │ │ ├── vsites.cpp │ │ ├── vsites.h │ │ ├── water_monomer_lp.cpp │ │ ├── water_monomer_lp.h │ │ ├── wlsq.cpp │ │ └── wlsq.h │ ├── generate_software_files.py │ ├── prepare_fitting_code.py │ ├── qchem_template │ ├── qchem_template_chelpg │ ├── utils_nb_fitting.py │ └── write_fitting_code.py ├── graphing │ ├── PCA.py │ ├── __init__.py │ └── grapher.py ├── mbfit.py ├── molecule │ ├── __init__.py │ ├── atom.py │ ├── fragment.py │ ├── molecule.py │ └── molecule_parser.py ├── polynomials │ ├── __init__.py │ ├── filters.py │ ├── generate_input_poly.py │ ├── generate_poly.py │ ├── molecule_in_parser.py │ ├── monomial.py │ ├── scripts │ │ └── clean-maple-c.pl │ └── variable.py ├── training_set │ ├── __init__.py │ ├── training_set.py │ └── training_set_element.py └── utils │ ├── __init__.py │ ├── constants.py │ ├── distribution_function │ ├── __init__.py │ └── distribution_function.py │ ├── files.py │ ├── math.py │ ├── periodic_table.py │ ├── progress_bar.py │ ├── quaternion.py │ ├── settings_reader.py │ └── system.py ├── run_tests.py ├── run_tests.sh ├── setup.py ├── sourceme.sh ├── test_file └── test_mbfit ├── __init__.py ├── test_calculator ├── __init__.py ├── reference │ ├── 36c6e9c4_2019-02-12_17-14-46.767262.out │ ├── 36c6e9c4_2019-02-12_17-18-21.567344.out │ ├── 36c6e9c4_2019-02-12_17-25-30.184407.out │ ├── 36c6e9c4_2019-02-12_17-27-48.298430.out │ ├── 59bb6335_2019-02-26_16-43-16.263184.out │ ├── 59bb6335_2019-02-26_16-47-33.759389.out │ ├── 59bb6335_2019-02-26_17-02-54.549218.log │ ├── 59bb6335_2019-02-26_17-08-15.986530.log │ ├── 869cbba7_2019-02-12_16-50-54.163398.out │ ├── 869cbba7_2019-02-12_16-54-55.906360.out │ ├── 869cbba7_2019-02-12_16-57-06.189857.out │ ├── 869cbba7_2019-02-12_17-02-55.820866.out │ ├── 87d98bce_2019-02-12_17-36-57.640340.out │ ├── 87d98bce_2019-02-12_17-54-18.734011.out │ ├── 87d98bce_2019-02-12_18-05-57.011827.log │ ├── 87d98bce_2019-02-26_17-12-02.103049.log │ └── training_set.xyz ├── resources │ ├── CN-monomer.ini │ ├── CN-monomer.xyz │ ├── CO2.ini │ ├── CO2monomer.ini │ ├── CO2monomer.xyz │ ├── bad_code.ini │ ├── configs.xyz │ ├── psi4.ini │ └── qchem.ini ├── test_calculator.py ├── test_calculator_utils.py ├── test_model.py ├── test_psi4_calculator.py └── test_qchem_calculator.py ├── test_case_with_id ├── __init__.py └── test_case_with_id.py ├── test_database ├── __init__.py ├── resources │ ├── execute_jobs.sh │ ├── water.ini │ ├── water_dimer_configs.xyz │ ├── water_dimer_psi4.ini │ ├── water_dimer_qchem.ini │ └── water_opt.xyz ├── test_database.py ├── test_database_job_reader_and_writer.py ├── test_user1.ini ├── test_user2.ini └── test_user3.ini ├── test_fitting ├── __init__.py ├── resources │ ├── A1B2 │ │ ├── config.ini │ │ ├── poly.in │ │ ├── poly │ │ │ ├── poly-direct.cpp │ │ │ ├── poly-grd.c │ │ │ ├── poly-grd.cpp │ │ │ ├── poly-grd.maple │ │ │ ├── poly-model.h │ │ │ ├── poly-nogrd.c │ │ │ ├── poly-nogrd.cpp │ │ │ ├── poly-nogrd.maple │ │ │ ├── poly.log │ │ │ └── vars.cpp │ │ ├── settings.ini │ │ └── training_set.xyz │ ├── A1B2_A1B2_MB │ │ ├── config.ini │ │ ├── poly.in │ │ ├── poly │ │ │ ├── poly-direct.cpp │ │ │ ├── poly-grd-direct.cpp │ │ │ ├── poly-grd.c │ │ │ ├── poly-grd.cpp │ │ │ ├── poly-grd.maple │ │ │ ├── poly-model.h │ │ │ ├── poly-nogrd.c │ │ │ ├── poly-nogrd.cpp │ │ │ ├── poly-nogrd.maple │ │ │ ├── poly.log │ │ │ └── vars.cpp │ │ ├── settings.ini │ │ └── training_set.xyz │ └── A1B2_A1B2_TTM │ │ ├── config.ini │ │ ├── settings.ini │ │ └── training_set.xyz └── test_fitting.py ├── test_mbfit.py ├── test_molecule ├── __init__.py ├── resources │ ├── NO2-_NO2-_dimer.ini │ ├── NO2-_NO2-_dimer.xyz │ ├── NO2-_water_water_trimer.ini │ ├── NO2-_water_water_trimer.xyz │ ├── bdc.ini │ ├── bdc.xyz │ ├── bdc2.ini │ ├── bdc2.xyz │ ├── water_monomer.ini │ └── water_monomer.xyz ├── test_atom.py ├── test_fragment.py ├── test_molecule.py └── test_molecule_parser.py ├── test_polynomials ├── __init__.py ├── reference │ ├── A1B2C2_custom_filters_degree_4 │ │ └── poly.log │ ├── A1B2X2_A1B2X2_A1B2X2_purely_inter_degree_2 │ │ └── poly.log │ ├── A1B2X2_A1B2X2_mbpol_filters_degree_4 │ │ └── poly.log │ ├── A1B2X2_A1B2X2_no_filters_degree_4 │ │ └── poly.log │ ├── A1B2_A1B2_A1B2_mbpol_filters_degree_4 │ │ └── poly.log │ ├── A1B3_no_filter_degree_4 │ │ └── poly.log │ ├── A1_B1C2_B1C2_partly_inter_degree_2 │ │ └── poly.log │ ├── A2B1_A2B1_partly_inter_degree_2 │ │ └── poly.log │ ├── A2B5_C1D2_partly_inter_degree_2 │ │ └── poly.log │ └── A4B1_no_filter_degree_4 │ │ └── poly.log ├── resources │ ├── A1B2C2_custom_filters.in │ ├── A1B2X2_A1B2X2_A1B2X2_purely_inter.in │ ├── 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