├── .gitignore ├── LICENSE.md ├── README.md ├── doc ├── Makefile ├── docify.sh ├── make.bat └── source │ ├── README │ ├── conf.py │ ├── index.rst │ ├── installation.rst │ ├── manual.rst │ ├── pycdft │ ├── pycdft.atomic.rst │ ├── pycdft.common.rst │ ├── pycdft.constraint.rst │ ├── pycdft.debug.rst │ ├── pycdft.dft_driver.rst │ └── pycdft.elcoupling.rst │ ├── quickreference.rst │ └── tutorial.rst ├── examples ├── 01-he2_coupling │ ├── README │ ├── interactive │ │ ├── He2_3Ang.cif │ │ ├── He_ONCV_PBE-1.0.xml │ │ ├── gs.in │ │ ├── he2_coupling.ipynb │ │ └── he2_coupling.py │ ├── reference │ │ ├── 3.0-he2-coupling.ipynb │ │ ├── 3.0-he2-coupling.py │ │ ├── He2.cif │ │ └── gs.in │ ├── restart_example │ │ ├── run_coupling.py │ │ └── run_he2_solvers.py │ └── script │ │ ├── He2_tmp.cif │ │ ├── He_ONCV_PBE-1.0.xml │ │ ├── gs_tmp.in │ │ ├── he2_coupling-tmp.py │ │ └── run_he2_coupling ├── 02-thiophene │ ├── C_ONCV_PBE-1.0.xml │ ├── H_ONCV_PBE-1.0.xml │ ├── README │ ├── S_ONCV_PBE-1.0.xml │ ├── align.cif │ ├── align.in │ ├── run_thio_dist │ └── thiophene-coupling-tmp.ipynb └── 03-thiophene-rotated │ ├── C_ONCV_PBE-1.0.xml │ ├── H_ONCV_PBE-1.0.xml │ ├── README │ ├── S_ONCV_PBE-1.0.xml │ ├── delta0.cif │ ├── delta20.cif │ ├── delta20.in │ ├── delta40.cif │ ├── delta40.in │ ├── delta60.cif │ ├── delta60.in │ ├── delta80.cif │ ├── delta80.in │ ├── delta90.cif │ ├── delta90.in │ ├── setup_thio_delta │ ├── thio_delta_gs │ ├── thio_delta_pycdft │ └── thiophene-coupling-tmp.ipynb ├── pycdft ├── __init__.py ├── atomic │ ├── README │ ├── __init__.py │ ├── pp.py │ └── rho │ │ ├── Ag.spavr │ │ ├── Al.spavr │ │ ├── Ar.spavr │ │ ├── As.spavr │ │ ├── Au.spavr │ │ ├── B.spavr │ │ ├── Ba.spavr │ │ ├── Be.spavr │ │ ├── Bi.spavr │ │ ├── Br.spavr │ │ ├── C.spavr │ │ ├── Ca.spavr │ │ ├── Cd.spavr │ │ ├── Cl.spavr │ │ ├── Co.spavr │ │ ├── Cr.spavr │ │ ├── Cs.spavr │ │ ├── Cu.spavr │ │ ├── F.spavr │ │ ├── Fe.spavr │ │ ├── Ga.spavr │ │ ├── Ge.spavr │ │ ├── H.spavr │ │ ├── He.spavr │ │ ├── Hf.spavr │ │ ├── Hg.spavr │ │ ├── I.spavr │ │ ├── In.spavr │ │ ├── Ir.spavr │ │ ├── K.spavr │ │ ├── Kr.spavr │ │ ├── Li.spavr │ │ ├── Mg.spavr │ │ ├── Mn.spavr │ │ ├── Mo.spavr │ │ ├── N.spavr │ │ ├── Na.spavr │ │ ├── Nb.spavr │ │ ├── Ne.spavr │ │ ├── Ni.spavr │ │ ├── O.spavr │ │ ├── Os.spavr │ │ ├── P.spavr │ │ ├── Pb.spavr │ │ ├── Pd.spavr │ │ ├── Pt.spavr │ │ ├── Rb.spavr │ │ ├── Re.spavr │ │ ├── Rh.spavr │ │ ├── Ru.spavr │ │ ├── S.spavr │ │ ├── Sb.spavr │ │ ├── Sc.spavr │ │ ├── Se.spavr │ │ ├── Si.spavr │ │ ├── Sn.spavr │ │ ├── Sr.spavr │ │ ├── Ta.spavr │ │ ├── Tc.spavr │ │ ├── Te.spavr │ │ ├── Ti.spavr │ │ ├── Tl.spavr │ │ ├── V.spavr │ │ ├── W.spavr │ │ ├── Xe.spavr │ │ ├── Y.spavr │ │ ├── Zn.spavr │ │ └── Zr.spavr ├── cdft.py ├── common │ ├── __init__.py │ ├── atom.py │ ├── fragment.py │ ├── ft.py │ ├── sample.py │ ├── units.py │ └── wfc.py ├── constraint │ ├── __init__.py │ ├── base.py │ ├── charge.py │ └── charge_transfer.py ├── debug │ ├── __init__.py │ └── plot_debug.py ├── dft_driver 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