├── .cardboardlint.yml ├── .coveragerc ├── .gitattributes ├── .github ├── ISSUE_TEMPLATE │ ├── bug-report.md │ ├── feature-request.md │ └── question.md └── pull_request_template.md ├── .gitignore ├── .gitmodules ├── .pycodestylerc ├── .pydocstylerc ├── .pylintrc ├── .travis.yml ├── AUTHORS ├── HEADER ├── LICENSE ├── README.md ├── chemtools ├── __init__.py ├── conceptual │ ├── __init__.py │ ├── base.py │ ├── cubic.py │ ├── exponential.py │ ├── general.py │ ├── leastnorm.py │ ├── linear.py │ ├── mixed.py │ ├── quadratic.py │ ├── rational.py │ ├── squareroot.py │ ├── test │ │ ├── __init__.py │ │ ├── test_base.py │ │ ├── test_cubic.py │ │ ├── test_exponential.py │ │ ├── test_general.py │ │ ├── test_least_norm.py │ │ ├── test_linear.py │ │ ├── test_mixed.py │ │ ├── test_quadratic.py │ │ ├── test_rational.py │ │ └── test_squareroot.py │ └── utils.py ├── data │ ├── README │ ├── __init__.py │ ├── atom_01_H_N01_M2_ub3lyp_ccpvtz_g09.fchk │ ├── atom_08_O_N08_M3_ub3lyp_ccpvtz_g09.fchk │ ├── atom_08_O_N09_M2_ub3lyp_ccpvtz_g09.fchk │ ├── c3h2o_q+0_ub3lyp_augccpvdz.fchk │ ├── c4h4_ub3lyp_ccpvdz.fchk │ ├── ch4_rhf_ccpvdz.fchk │ ├── ch4_uhf_ccpvdz.fchk │ ├── ch4_uhf_ccpvdz.wfn │ ├── data_cubegen_g09_C01_ch4_uhf_ccpvdz.npz │ ├── data_elf_nciplot_h2o_dimer_pbe_sto3g.npz │ ├── data_fortran_ch4_uhf_ccpvdz.npz │ ├── data_horton_fchk_ch4_uhf_ccpvdz.npz │ ├── data_horton_fchk_h2o_ub3lyp_ccpvtz.npz │ ├── data_multiwfn36_fchk_c3h2o_q+0_ub3lyp_augccpvdz.npz │ ├── data_multiwfn36_fchk_c4h4_ub3lyp_ccpvdz.npz │ ├── data_multiwfn36_fchk_h2o_q+0_ub3lyp_ccpvtz.npz │ ├── data_multiwfn36_fchk_li2_q+0_ub3lyp_ccpvdz.npz │ ├── examples │ │ ├── __init__.py │ │ ├── acrolein_q+0.fchk │ │ ├── acrolein_q+1.fchk │ │ ├── acrolein_q-1.fchk │ │ ├── aniline_protonated_q+0.fchk │ │ ├── aniline_protonated_q+1.fchk │ │ ├── aniline_protonated_q+2.fchk │ │ ├── aniline_q+0.fchk │ │ ├── aniline_q+1.fchk │ │ ├── aniline_q-1.fchk │ │ ├── atom_kr.fchk │ │ ├── benzene_q+0.fchk │ │ ├── benzene_q+1.fchk │ │ ├── benzene_q-1.fchk │ │ ├── c4h4.fchk │ │ ├── ch2nh2_q+0.fchk │ │ ├── ch2nh2_q+1.fchk │ │ ├── ch2nh2_q+2.fchk │ │ ├── ch2o_q+0.fchk │ │ ├── ch2o_q+1.fchk │ │ ├── ch2o_q-1.fchk │ │ ├── ch4.fchk │ │ ├── coh2_q+0_ub3lyp_6311g.fchk │ │ ├── coh2_q+1_ub3lyp_6311g.fchk │ │ ├── coh2_q-1_ub3lyp_6311g.fchk │ │ ├── cyclobutadiene_q+0.fchk │ │ ├── cyclobutadiene_q+1.fchk │ │ ├── cyclobutadiene_q-1.fchk │ │ ├── cyclooctatetraene_boat_q+0.fchk │ │ ├── cyclooctatetraene_boat_q+1.fchk │ │ ├── cyclooctatetraene_boat_q-1.fchk │ │ ├── cyclooctatetraene_planer_q+0.fchk │ │ ├── cyclooctatetraene_planer_q+1.fchk │ │ ├── cyclooctatetraene_planer_q-1.fchk │ │ ├── cyclopropenium_oxide.fchk │ │ ├── cyclopropenium_q+0.fchk │ │ ├── cyclopropenium_q+1.fchk │ │ ├── cyclopropenium_q+2.fchk │ │ ├── cyclopropenium_q-1.fchk │ │ ├── dichloropyrazine25.fchk │ │ ├── dichloropyridine26_q+0.fchk │ │ ├── dichloropyridine26_q+1.fchk │ │ ├── dichloropyridine26_q-1.fchk │ │ ├── ethane.fchk │ │ ├── ethene.fchk │ │ ├── ethyne.fchk │ │ ├── formamide_q+0.fchk │ │ ├── formamide_q+1.fchk │ │ ├── formamide_q-1.fchk │ │ ├── formic_acid_dimer.fchk │ │ ├── furan_q+0.fchk │ │ ├── furan_q+1.fchk │ │ ├── furan_q-1.fchk │ │ ├── h2o.fchk │ │ ├── h2o_dimer.fchk │ │ ├── images │ │ │ ├── ch2o-ff_fmo.jpg │ │ │ ├── ch2o-ffm_fd.jpg │ │ │ ├── ch2o_dual_fmo.jpg │ │ │ ├── elf080_ch2o_q+0.jpg │ │ │ ├── elf080_chonh2_hyperbolic.jpg │ │ │ ├── elf080_h2o_dimer.jpg │ │ │ ├── esp_dichloropyridine26_q+0.png │ │ │ ├── esp_scl2.png │ │ │ ├── local_ip.jpg │ │ │ ├── lol055_ch2o_q+0.jpg │ │ │ ├── lol055_chonh2.jpg │ │ │ ├── lol055_chonh2_hyperbolic.jpg │ │ │ ├── mo0037_38_dichloropyridine.jpg │ │ │ ├── mo0045_h2o.png │ │ │ ├── nci_formic_acid_dimer.jpg │ │ │ ├── nci_h2o_dimer.jpg │ │ │ └── top_c4h4.jpg │ │ ├── malondialdehyde_enol.fchk │ │ ├── malondialdehyde_keto.fchk │ │ ├── nh3.fchk │ │ ├── pyridine_q+0.fchk │ │ ├── pyridine_q+1.fchk │ │ ├── pyridine_q-1.fchk │ │ ├── pyrrole_q+0.fchk │ │ ├── pyrrole_q+1.fchk │ │ ├── pyrrole_q-1.fchk │ │ ├── scl2.fchk │ │ ├── secl2.fchk │ │ └── sefbr.fchk │ ├── h2o_ab_basis_map_alpha.npy │ ├── h2o_ab_basis_map_beta.npy │ ├── h2o_coeff_ab_mo_alpha.npy │ ├── h2o_coeff_ab_mo_beta.npy │ ├── h2o_dimer_pbe_sto3g-dens.cube │ ├── h2o_dimer_pbe_sto3g-elf.cube │ ├── h2o_dimer_pbe_sto3g-grad.cube │ ├── h2o_dimer_pbe_sto3g.fchk │ ├── h2o_dimer_pbe_sto3g.wfn │ ├── h2o_occupations_alpha.npy │ ├── h2o_occupations_beta.npy │ ├── h2o_olp_ab_ab_alpha.npy │ ├── h2o_olp_ab_ab_beta.npy │ ├── h2o_q+0_ub3lyp_ccpvtz.fchk │ ├── h2o_q+1_ub3lyp_ccpvtz.fchk │ ├── h2o_q-1_ub3lyp_ccpvtz.fchk │ ├── li2_q+0_ub3lyp_ccpvdz.fchk │ ├── naclo4_ab_atom_indices.npy │ ├── naclo4_coeff_ab_mmo.npy │ ├── naclo4_coeff_ab_mo.npy │ ├── naclo4_coeff_ab_quambo.npy │ ├── naclo4_coeff_ab_quao.npy │ ├── naclo4_occupations.npy │ ├── naclo4_olp_aao_aao.npy │ ├── naclo4_olp_aao_ab.npy │ ├── naclo4_olp_ab_ab.npy │ ├── naclo4_qab_atom_indices.npy │ ├── o2_uhf.fchk │ ├── o2_uhf.wfn │ ├── o2_uhf_virtual.fchk │ ├── o2_uhf_virtual.wfn │ └── water_b3lyp_sto3g.fchk ├── denstools │ ├── __init__.py │ ├── densbased.py │ └── test │ │ ├── __init__.py │ │ └── test_densbased.py ├── orbstools │ ├── __init__.py │ ├── orthogonalization.py │ ├── partition.py │ ├── quasi.py │ └── tests │ │ ├── test_orthogonalization.py │ │ ├── test_partition.py │ │ └── test_quasi.py ├── outputs │ ├── __init__.py │ ├── plot.py │ ├── test │ │ ├── __init__.py │ │ └── test_vmd.py │ └── vmd.py ├── scripts │ ├── __init__.py │ ├── chemtools_conceptual.py │ ├── chemtools_elf.py │ ├── chemtools_esp.py │ ├── chemtools_lol.py │ ├── chemtools_mot.py │ ├── chemtools_nci.py │ ├── common.py │ └── main.py ├── toolbox │ ├── __init__.py │ ├── conceptual.py │ ├── densbased.py │ ├── dftbased.py │ ├── interactions.py │ ├── kinetic.py │ ├── motbased.py │ ├── oxidation.py │ ├── test │ │ ├── __init__.py │ │ ├── test_conceptual_condensed.py │ │ ├── test_conceptual_global.py │ │ ├── test_conceptual_local.py │ │ ├── test_densbased.py │ │ ├── test_dftbased.py │ │ ├── test_elf.py │ │ ├── test_kinetic.py │ │ ├── test_nci.py │ │ ├── test_oxidation.py │ │ ├── test_partition.py │ │ ├── test_topology.py │ │ └── test_utils.py │ ├── topology.py │ └── utils.py ├── topology │ ├── __init__.py │ ├── critical.py │ ├── point.py │ └── test │ │ ├── __init__.py │ │ ├── test_critical.py │ │ └── test_point.py ├── utils │ ├── __init__.py │ ├── cube.py │ ├── mesh.py │ ├── test │ │ ├── __init__.py │ │ ├── test_cube.py │ │ ├── test_mesh.py │ │ └── test_utils.py │ └── utils.py └── wrappers │ ├── __init__.py │ ├── grid.py │ ├── molecule.py │ ├── part.py │ └── test │ ├── test_grid.py │ ├── test_molecule.py │ └── test_part.py ├── doc ├── Makefile ├── _static │ ├── CDFT-GCP.png │ ├── CDFT.png │ ├── H2O-CH4-BCO-nci.jpg │ ├── H2O_dimer_dens_rdg.jpg │ ├── chemtools_favicon.ico │ ├── chemtools_logo.png │ ├── chemtools_logo2.png │ ├── chemtools_white_bg_logo.png │ └── nci-sdens-vs-rdg.jpg ├── _templates │ └── autosummary │ │ ├── attribute.rst │ │ ├── base.rst │ │ ├── class.rst │ │ ├── function.rst │ │ ├── method.rst │ │ └── module.rst ├── conf.py ├── hover_win_generator.py ├── index.rst ├── intro_about.rst ├── intro_citing.rst ├── intro_conduct.rst ├── intro_contact.rst ├── intro_license.rst ├── make.bat ├── references.bib ├── sci_doc_conceptual.rst ├── sci_doc_condensedtool.rst ├── sci_doc_dftbased.rst ├── sci_doc_dftbased_dens.rst ├── sci_doc_dftbased_esp.rst ├── sci_doc_dftbased_it.rst ├── sci_doc_dftbased_ked.rst ├── sci_doc_global_exponential.rst ├── sci_doc_global_general.rst ├── sci_doc_global_linear.rst ├── sci_doc_global_quadratic.rst ├── sci_doc_global_rational.rst ├── sci_doc_globaltool.rst ├── sci_doc_local_linear.rst ├── sci_doc_local_quadratic.rst ├── sci_doc_localtool.rst ├── sci_doc_nci.rst ├── sci_doc_orbitaltool.rst ├── sci_doc_zref.rst ├── tech_api.rst ├── tech_dev.rst ├── usr_doc_installation.rst └── usr_doc_quick_start.rst ├── examples ├── README.txt ├── conceptual │ ├── README.txt │ ├── ex001_gloabl_quadratic_energy_fmo.py │ ├── ex002_global_quadratic_energy_fd.py │ ├── ex003_global_linear_energy_fmo.py │ ├── ex004_global_linear_energy_fd.py │ ├── ex005_local_linear_ff_fmo_plot.py │ ├── ex006_local_linear_ff_fd_plot.py │ ├── ex007_local_linear_dual_fmo_plot.py │ ├── ex008_global_energy_models_fmo_plot.py │ ├── ex009_global_energy_models_fd_plot.py │ └── ex010_local_quadratic_ff_fmo_contour_plot.py ├── density │ ├── README.txt │ └── ex001_local_ip_plot.py ├── elf │ ├── README.txt │ ├── ex001_elf_plot.py │ ├── ex002_elf_plot.py │ ├── ex003_elf_plot.py │ └── ex004_elf_plot.py ├── esp │ ├── README.txt │ ├── ex001_esp_plot.py │ └── ex002_esp_plot.py ├── lol │ ├── README.txt │ ├── ex001_lol_plot.py │ ├── ex002_lol_plot.py │ └── ex003_lol_plot.py ├── nci │ ├── README.txt │ ├── ex001_nci_plot.py │ ├── ex002_nci_plot.py │ └── ex003_nci_plot.py ├── orbital │ ├── README.txt │ ├── ex001_mot_plot.py │ └── ex002_mot_plot.py └── topology │ ├── README.txt │ └── ex001_top_plot.py ├── setup.py ├── tools ├── __init__.py ├── 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