├── .gitignore ├── PYXAID ├── __init__.py ├── aux.py ├── average.py ├── dev_modules │ └── combine.py ├── diff.py ├── distribute.py ├── excitation_spectrum.py ├── filesys.py ├── lazy.py ├── out2inp.py ├── out2pdb.py ├── out2xyz.py ├── pdos.py ├── proj_dos.py ├── runMD.py ├── runMD1.py ├── spectrum.py ├── src_cpp │ ├── ElectronicStructure.cpp │ ├── ElectronicStructure.h │ ├── InputStructure.cpp │ ├── InputStructure.h │ ├── Makefile │ ├── aux.cpp │ ├── aux.h │ ├── io.cpp │ ├── io.h │ ├── matrix.cpp │ ├── matrix.h │ ├── namd.cpp │ ├── namd.h │ ├── namd_export.cpp │ ├── namd_export.h │ ├── pyxaid_core.cpp │ ├── random.cpp │ ├── random.h │ ├── state.cpp │ ├── state.h │ ├── units.h │ ├── wfc.h │ ├── wfc_QE_methods.cpp │ ├── wfc_VASP_methods.cpp │ ├── wfc_basic_methods.cpp │ ├── wfc_export.cpp │ ├── wfc_export.h │ └── wfc_functions.cpp ├── td_map.py ├── test.py └── xdatcar2inp.py ├── README.md ├── __init__.py ├── code_level3 ├── plotting │ ├── plt_map │ ├── plt_map1 │ ├── plt_relax │ ├── plt_spectr │ └── plt_td_map ├── py-scr2.py ├── py-scr3.py ├── py-scr4.py ├── py-scr5.py ├── py-scr6.py ├── py-scr7.py └── submit_templ.pbs └── tutorials ├── Tut1_basics ├── step1 │ ├── py-scr5.py │ ├── submit.pbs │ └── x.md.in ├── step2 │ ├── py-scr2.py │ ├── py-scr6.py │ ├── py-scr7.py │ ├── submit_templ.pbs │ ├── x0.exp.in │ ├── x0.scf.in │ ├── x1.exp.in │ └── x1.scf.in └── step3 │ ├── py-scr3.py │ ├── py-scr4.py │ └── submit_namd.pbs ├── Tut2_small ├── step1 │ ├── py-scr5.py │ ├── submit.slm │ └── x.md.in ├── step2 │ ├── py-scr2.py │ ├── py-scr6.py │ ├── py-scr7.py │ ├── res.tar.bz2 │ ├── spectr.tar.bz2 │ ├── submit_templ.slm │ ├── x.md.out │ ├── x0.exp.in │ └── x0.scf.in └── step3 │ ├── macro.tar.bz2 │ ├── out.tar.bz2 │ ├── py-scr3.py │ ├── py-scr4.py │ └── submit_namd.slm ├── Tut2_small_copy ├── step1 │ ├── C.pbe-rrkjus.UPF │ ├── H.pbe-rrkjus.UPF │ ├── py-scr5.py │ ├── submit.pbs │ ├── submit.slm │ └── x.md.in ├── step2 │ ├── py-scr2.py │ ├── py-scr6.py │ ├── py-scr7.py │ ├── res.tar.bz2 │ ├── spectr.tar.bz2 │ ├── submit.pbs │ ├── submit_templ.pbs │ ├── submit_templ.slm │ ├── x.md.out │ ├── x0.exp.in │ └── x0.scf.in └── step3 │ ├── macro.tar.bz2 │ ├── out.tar.bz2 │ ├── py-scr3.py │ ├── py-scr4.py │ └── submit_namd.slm ├── Tut3_code_level2_NAC └── Tut3.1 │ ├── out │ ├── Ham_original__im │ ├── Ham_original__re │ ├── Ham_original_complete_2x2_im │ ├── Ham_original_complete_2x2_re │ ├── Ham_original_complete_5x5_im │ ├── Ham_original_complete_5x5_re │ ├── Ham_original_complete_im │ ├── Ham_original_complete_re │ ├── Ham_original_normalize_im │ ├── Ham_original_normalize_re │ ├── x0.exp.out │ ├── x0.scf.out │ ├── x1.exp.out │ └── x1.scf.out │ ├── submit.slm │ ├── tut3.1.py │ ├── x0.exp.in │ ├── x0.scf.in │ ├── x1.exp.in │ └── x1.scf.in └── Tut4_coding_with_Pyxaid ├── NOTE.txt └── step2 ├── py-scr2.py ├── py-scr6.py ├── py-scr7.py ├── res.tar.bz2 ├── spectr.tar.bz2 ├── spectr ├── ab_spectrx.dat ├── ab_spectrx_conv.dat ├── spectr.plt └── spectr.png ├── 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