├── LICENSE ├── README.rst ├── docs ├── Makefile ├── README.rst ├── make.bat └── source │ ├── _static │ └── custom.css │ ├── conf.py │ ├── diagrams │ ├── pcoh.png │ ├── pcomp.png │ ├── pnacme.png │ ├── ppop.png │ ├── ptraj.png │ ├── pyunixmd_file_tree.png │ └── pyunixmd_structure.png │ ├── install.rst │ ├── modules │ └── main.rst │ ├── objects │ ├── main.rst │ ├── mm │ │ ├── main.rst │ │ └── prog_tinker.rst │ ├── mqc │ │ ├── bomd.rst │ │ ├── ct.rst │ │ ├── eh.rst │ │ ├── main.rst │ │ ├── sh.rst │ │ └── shxf.rst │ ├── mqc_qed │ │ ├── bomd.rst │ │ ├── main.rst │ │ ├── sh.rst │ │ └── shxf.rst │ ├── qed │ │ ├── jaynes_cummings.rst │ │ └── main.rst │ ├── qm │ │ ├── main.rst │ │ ├── model.rst │ │ ├── prog_columbus.rst │ │ ├── prog_dftbplus.rst │ │ ├── prog_gaussian09.rst │ │ ├── prog_molpro.rst │ │ ├── prog_qchem.rst │ │ ├── prog_terachem.rst │ │ └── prog_turbomole.rst │ └── system_bath │ │ ├── main.rst │ │ ├── molecule.rst │ │ ├── polariton.rst │ │ └── thermostat.rst │ ├── overview.rst │ ├── quick_start.rst │ ├── references │ ├── main.rst │ └── reference.bib │ ├── unixmd.rst │ ├── utility_scripts.rst │ └── workflow.rst ├── examples └── qm │ ├── SH-Shin_Metiu │ ├── RESTART.bin │ ├── log │ ├── md │ │ ├── BOCOH │ │ ├── BOPOP │ │ ├── FINAL.xyz │ │ ├── MDENERGY │ │ ├── MOVIE.xyz │ │ ├── NACME │ │ ├── SHPROB │ │ └── SHSTATE │ └── run.py │ └── SHXF-Shin_Metiu │ ├── RESTART.bin │ ├── log │ ├── md │ ├── BOCOH │ ├── BOPOP │ ├── FINAL.xyz │ ├── MDENERGY │ ├── MOVIE.xyz │ ├── NACME │ ├── SHPROB │ └── SHSTATE │ └── run.py ├── image └── logo.svg ├── run.py.template ├── setup.py ├── src ├── cpa │ ├── __init__.py │ ├── cpa.py │ ├── sh.py │ └── shxf.py ├── lib │ ├── cioverlap │ │ ├── cioverlap.pyx │ │ └── tdnac.c │ ├── mqc │ │ ├── derivs.h │ │ ├── derivs_ct.h │ │ ├── derivs_xf.h │ │ ├── el_propagator.pyx │ │ ├── el_propagator_ct.pyx │ │ ├── el_propagator_xf.pyx │ │ ├── exponential.c │ │ ├── rk4.c │ │ ├── rk4_ct.c │ │ └── rk4_xf.c │ └── mqc_qed │ │ ├── derivs.h │ │ ├── derivs_xf.h │ │ ├── el_propagator.pyx │ │ ├── el_propagator_xf.pyx │ │ ├── exponential.c │ │ ├── exponential_xf.c │ │ ├── rk4.c │ │ ├── rk4_xf.c │ │ └── transform.h ├── misc.py ├── mm │ ├── __init__.py │ ├── mm_calculator.py │ └── tinker.py ├── molecule.py ├── mqc │ ├── __init__.py │ ├── bomd.py │ ├── ct.py │ ├── eh.py │ ├── ehxf.py │ ├── mqc.py │ ├── sh.py │ └── shxf.py ├── mqc_qed │ ├── __init__.py │ ├── bomd.py │ ├── ct.py │ ├── eh.py │ ├── mqc.py │ ├── sh.py │ └── shxf.py ├── polariton.py ├── qed │ ├── __init__.py │ ├── jaynes_cummings.py │ └── qed_calculator.py ├── qm │ ├── __init__.py │ ├── columbus │ │ ├── __init__.py │ │ ├── casscf.py │ │ ├── colbasis.py │ │ ├── columbus.py │ │ └── mrci.py │ ├── dftbplus │ │ ├── __init__.py │ │ ├── dftb.py │ │ ├── dftbpar.py │ │ ├── dftbplus.py │ │ └── ssr.py │ ├── gamess │ │ ├── __init__.py │ │ ├── gamess.py │ │ └── ssr.py │ ├── gaussian09 │ │ ├── __init__.py │ │ ├── dft.py │ │ └── gaussian09.py │ ├── model │ │ ├── __init__.py │ │ ├── dac.py │ │ ├── dag.py │ │ ├── ecr.py │ │ ├── file_io.py │ │ ├── model.py │ │ ├── sac.py │ │ └── shin_metiu.py │ ├── molpro │ │ ├── __init__.py │ │ ├── casscf.py │ │ └── molpro.py │ ├── qchem │ │ ├── __init__.py │ │ ├── dft.py │ │ └── qchem.py │ ├── qm_calculator.py │ ├── terachem │ │ ├── __init__.py │ │ ├── dft.py │ │ ├── ssr.py │ │ └── terachem.py │ └── turbomole │ │ ├── __init__.py │ │ ├── dft.py │ │ └── turbomole.py ├── thermostat.py └── trajectory.py └── util ├── extract_initial_conditions_from_MD.py ├── input_gen.py ├── motion_analysis.py └── statistical_analysis.py /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/skmin-lab/unixmd/HEAD/LICENSE -------------------------------------------------------------------------------- /README.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/skmin-lab/unixmd/HEAD/README.rst 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