diff --git a/bin/cmmde.py b/bin/cmmde.py index 817ebd4..76e9f33 100755 --- a/bin/cmmde.py +++ b/bin/cmmde.py @@ -14,17 +14,17 @@ import time parser = argparse.ArgumentParser(description='Computational Molecular & Material Design Interface') -# Input Geometri, tanpa ini perhitungan tidak akan berjalan. +# Geometry input file, without this, your calculation won't proceed. parser.add_argument('-i','--input',type=str,default='geom.xyz',help='Input geometri dalam koordinat Cartesian') parser.add_argument('-cons','--constraints',type=str,default='None',help='Membekukan ikatan, sudut ikatan, dan sebagainya selama proses optimasi geometri. Periksa manual Orca 5.0 lebih lanjut mengenai ini.') -# Informasi muatan dan multiplisitas spin molekul. +# Charge and spin multiplicity of the molecule. parser.add_argument('-c','--charge',type=int,default=0, help='Muatan molekul') parser.add_argument('-mult','--mult',type=int,default=1, help='Multiplisitas molekul') -# Input yang berkaitan dengan software, metode, dan jenis pekerjaan +# Inputs about the software, type of job, and computational methods. parser.add_argument('-s','--software',type=str,default='orca',help='Software yang digunakan. Pilihan: orca, dcdftb, gromacs') parser.add_argument('-j','--job',type=str,default='sp',help='Jenis perhitungan yang dilakukan. Pilihan: sp, opt, freq, md, mtd, td, dock.') parser.add_argument('-m','--method',type=str,default='XTB2',help='Metode yang digunakan dalam perhitungan. Pilihan: XTB, XTB2, DFTB, DFTB2, DFTB3-diag, dan sebagainya.') -# Input yang berkaitan dengan perhitungan frekuensi menggunakan software Orca +# Inputs about the frequency calculations in Orca. parser.add_argument('-sfreq','--scalefreq',type=float,default=1, help='Faktor skala frekuensi yang digunakan.') # Input yang berkaitan dengan perhitungan menggunakan software DCDFTBMD parser.add_argument('-disp','--dispersion',type=str,default='None', help='Model koreksi dispersi jika menggunakan software DCDFTB. Pilihan: None, D3, D3BJ, D3H5.') diff --git a/lib/__pycache__/cmmde_dcdftb.cpython-310.pyc b/lib/__pycache__/cmmde_dcdftb.cpython-310.pyc new file mode 100644 index 0000000..28b898a Binary files /dev/null and b/lib/__pycache__/cmmde_dcdftb.cpython-310.pyc differ diff --git a/lib/__pycache__/cmmde_dcdftb.cpython-312.pyc b/lib/__pycache__/cmmde_dcdftb.cpython-312.pyc new file mode 100644 index 0000000..74ccf70 Binary files /dev/null and b/lib/__pycache__/cmmde_dcdftb.cpython-312.pyc differ diff --git a/lib/__pycache__/cmmde_dftb.cpython-310.pyc b/lib/__pycache__/cmmde_dftb.cpython-310.pyc new file mode 100644 index 0000000..f3f8d97 Binary files /dev/null and b/lib/__pycache__/cmmde_dftb.cpython-310.pyc differ diff --git a/lib/__pycache__/cmmde_dftb.cpython-312.pyc b/lib/__pycache__/cmmde_dftb.cpython-312.pyc new file mode 100644 index 0000000..f51bc6d Binary files /dev/null and b/lib/__pycache__/cmmde_dftb.cpython-312.pyc differ diff --git a/lib/__pycache__/cmmde_dock.cpython-310.pyc b/lib/__pycache__/cmmde_dock.cpython-310.pyc new file mode 100644 index 0000000..af8e349 Binary files /dev/null and b/lib/__pycache__/cmmde_dock.cpython-310.pyc differ diff --git a/lib/__pycache__/cmmde_dock.cpython-312.pyc b/lib/__pycache__/cmmde_dock.cpython-312.pyc new file mode 100644 index 0000000..696ae5b Binary files /dev/null and b/lib/__pycache__/cmmde_dock.cpython-312.pyc differ diff --git a/lib/__pycache__/cmmde_hubbard.cpython-310.pyc b/lib/__pycache__/cmmde_hubbard.cpython-310.pyc new file mode 100644 index 0000000..a3db6d5 Binary files /dev/null and b/lib/__pycache__/cmmde_hubbard.cpython-310.pyc differ diff --git a/lib/__pycache__/cmmde_hubbard.cpython-312.pyc b/lib/__pycache__/cmmde_hubbard.cpython-312.pyc new file mode 100644 index 0000000..d149e01 Binary files /dev/null and b/lib/__pycache__/cmmde_hubbard.cpython-312.pyc differ diff --git a/lib/__pycache__/cmmde_mass.cpython-310.pyc b/lib/__pycache__/cmmde_mass.cpython-310.pyc new file mode 100644 index 0000000..1a0d312 Binary files /dev/null and b/lib/__pycache__/cmmde_mass.cpython-310.pyc differ diff --git a/lib/__pycache__/cmmde_mass.cpython-312.pyc b/lib/__pycache__/cmmde_mass.cpython-312.pyc new file mode 100644 index 0000000..01910cf Binary files /dev/null and b/lib/__pycache__/cmmde_mass.cpython-312.pyc differ diff --git a/lib/__pycache__/cmmde_mdpro.cpython-310.pyc b/lib/__pycache__/cmmde_mdpro.cpython-310.pyc new file mode 100644 index 0000000..67c62df Binary files /dev/null and b/lib/__pycache__/cmmde_mdpro.cpython-310.pyc differ diff --git a/lib/__pycache__/cmmde_mdpro.cpython-312.pyc b/lib/__pycache__/cmmde_mdpro.cpython-312.pyc new file mode 100644 index 0000000..97fc66a Binary files /dev/null and b/lib/__pycache__/cmmde_mdpro.cpython-312.pyc differ diff --git a/lib/__pycache__/cmmde_msd_com.cpython-310.pyc b/lib/__pycache__/cmmde_msd_com.cpython-310.pyc new file mode 100644 index 0000000..e7b905e Binary files /dev/null and b/lib/__pycache__/cmmde_msd_com.cpython-310.pyc differ diff --git a/lib/__pycache__/cmmde_nw.cpython-310.pyc b/lib/__pycache__/cmmde_nw.cpython-310.pyc new file mode 100644 index 0000000..4437316 Binary files /dev/null and b/lib/__pycache__/cmmde_nw.cpython-310.pyc differ diff --git a/lib/__pycache__/cmmde_nw.cpython-312.pyc b/lib/__pycache__/cmmde_nw.cpython-312.pyc new file mode 100644 index 0000000..db5d464 Binary files /dev/null and b/lib/__pycache__/cmmde_nw.cpython-312.pyc differ diff --git a/lib/__pycache__/cmmde_orca.cpython-310.pyc b/lib/__pycache__/cmmde_orca.cpython-310.pyc new file mode 100644 index 0000000..0c338f8 Binary files /dev/null and b/lib/__pycache__/cmmde_orca.cpython-310.pyc differ diff --git a/lib/__pycache__/cmmde_orca.cpython-312.pyc b/lib/__pycache__/cmmde_orca.cpython-312.pyc new file mode 100644 index 0000000..72a5789 Binary files /dev/null and b/lib/__pycache__/cmmde_orca.cpython-312.pyc differ diff --git a/lib/__pycache__/cmmde_qe.cpython-310.pyc b/lib/__pycache__/cmmde_qe.cpython-310.pyc new file mode 100644 index 0000000..f32f8e8 Binary files /dev/null and b/lib/__pycache__/cmmde_qe.cpython-310.pyc differ diff --git a/lib/__pycache__/cmmde_qe.cpython-312.pyc b/lib/__pycache__/cmmde_qe.cpython-312.pyc new file mode 100644 index 0000000..279afb2 Binary files /dev/null and b/lib/__pycache__/cmmde_qe.cpython-312.pyc differ diff --git a/lib/__pycache__/cmmde_rdf.cpython-310.pyc b/lib/__pycache__/cmmde_rdf.cpython-310.pyc new file mode 100644 index 0000000..cf39a8f Binary files /dev/null and b/lib/__pycache__/cmmde_rdf.cpython-310.pyc differ diff --git a/lib/__pycache__/cmmde_xtb.cpython-310.pyc b/lib/__pycache__/cmmde_xtb.cpython-310.pyc new file mode 100644 index 0000000..f4fcb1d Binary files /dev/null and b/lib/__pycache__/cmmde_xtb.cpython-310.pyc differ diff --git a/lib/__pycache__/cmmde_xtb.cpython-312.pyc b/lib/__pycache__/cmmde_xtb.cpython-312.pyc new file mode 100644 index 0000000..5f1cf99 Binary files /dev/null and b/lib/__pycache__/cmmde_xtb.cpython-312.pyc differ diff --git a/lib/cmmde_hubbard.py b/lib/cmmde_hubbard.py index db51236..85a2e1a 100644 --- a/lib/cmmde_hubbard.py +++ b/lib/cmmde_hubbard.py @@ -24,7 +24,8 @@ def azimuth(element): 'Co' : '3', 'Ti' : '3', 'C' : '2', - 'Si': '3' + 'Si': '3', + 'Zr': '3', } return azimuth[element]