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# Computational Molecular and Material Design Environment (CMMDE) |
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|
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## Introduction |
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This software is developed for decreasing the barrier in using popular open-source computational chemistry software. Currently, CMMDE can use the following software: |
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|
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1. [Orca](https://orcaforum.kofo.mpg.de/app.php/portal) |
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2. [DFTB+](https://dftbplus.org/) |
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3. [GROMACS](https://manual.gromacs.org/current/download.html) |
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4. [DOCK6](https://dock.compbio.ucsf.edu/DOCK_6/index.htm) |
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5. [DCDFTBMD](http://www.chem.waseda.ac.jp/dcdftbmd/?lang=en) |
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6. [Quantum Espresso](https://www.quantum-espresso.org/) |
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7. [xTB via Orca](https://github.com/grimme-lab/xtb) |
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|
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## Installation |
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1. Cloning the repository: |
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```bash |
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git clone https://github.com/aditchemist/CMMDE |
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``` |
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2. Change directory to CMMDE: |
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```bash |
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cd CMMDE |
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``` |
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3. Install the code: |
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```bash |
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chmod +x install.sh |
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./install.sh |
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``` |
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#!/usr/bin/env python3 |
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import sys |
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import os |
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import argparse |
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from cmmde_orca import orca |
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from cmmde_dcdftb import dcdftb |
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from cmmde_dock import readpdb, splitpdb, addH, addcharge, sphgen, showsphere, gridgen, rigiddock,flexdock, translig, sdf2xyz, multiopt, checkopt, multiflexdock |
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from cmmde_mdpro import proprep, ligprep |
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from cmmde_dftb import poscar2gen, vasp2gen, dftb |
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from cmmde_qe import qe |
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from cmmde_nw import nwchem |
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import time |
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|
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parser = argparse.ArgumentParser(description='Computational Molecular & Material Design Interface') |
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# Input Geometri, tanpa ini perhitungan tidak akan berjalan. |
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parser.add_argument('-i','--input',type=str,default='geom.xyz',help='Input geometri dalam koordinat Cartesian') |
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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.') |
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# Informasi muatan dan multiplisitas spin molekul. |
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parser.add_argument('-c','--charge',type=int,default=0, help='Muatan molekul') |
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parser.add_argument('-mult','--mult',type=int,default=1, help='Multiplisitas molekul') |
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# Input yang berkaitan dengan software, metode, dan jenis pekerjaan |
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parser.add_argument('-s','--software',type=str,default='orca',help='Software yang digunakan. Pilihan: orca, dcdftb, gromacs') |
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parser.add_argument('-j','--job',type=str,default='sp',help='Jenis perhitungan yang dilakukan. Pilihan: sp, opt, freq, md, mtd, td, dock.') |
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parser.add_argument('-m','--method',type=str,default='XTB2',help='Metode yang digunakan dalam perhitungan. Pilihan: XTB, XTB2, DFTB, DFTB2, DFTB3-diag, dan sebagainya.') |
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# Input yang berkaitan dengan perhitungan frekuensi menggunakan software Orca |
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parser.add_argument('-sfreq','--scalefreq',type=float,default=1, help='Faktor skala frekuensi yang digunakan.') |
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# Input yang berkaitan dengan perhitungan menggunakan software DCDFTBMD |
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parser.add_argument('-disp','--dispersion',type=str,default='None', help='Model koreksi dispersi jika menggunakan software DCDFTB. Pilihan: None, D3, D3BJ, D3H5.') |
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parser.add_argument('-para','--parapath',type=str,default='/home/adit/opt/dftbplus-21.2/external/slakos/origin/3ob-3-1',help='Lokasi folder berisikan himpunan parameter DFTB yang akan digunakan.') |
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parser.add_argument('-iter','--iter',type=int,default=500, help='Jumlah iterasi dalam optimasi geometri dan jenis perhitungan lainnya') |
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parser.add_argument('-ens','--ensembel',type=str,default='NVE', help='Ensembel yang digunakan dalam simulasi dinamika molekul. Pilihan: NVE, NVT, dan NPT.') |
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parser.add_argument('-tstat','--thermostat',type=str,default='andersen', help='Termostat yang digunakan dalam simulasi NVT. Pilihan: andersen,berendsen,dan nose') |
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parser.add_argument('-t','--temp', type=float, default=298.15,help='Suhu yang digunakan dalam perhitungan frekuensi maupun simulasi MD dalam satuan Kelvin.') |
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parser.add_argument('-dt','--deltat',type=float, default=1.0, help='Selang waktu integrasi dalam simulasi dinamika molekul dalam satuan femtodetik.') |
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parser.add_argument('-mdprint','--mdprint',type=int,default=10, help='Berapa step sekali struktur dicetak. Default=10.') |
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parser.add_argument('-rest','--restart',type=str,default='false',help='Apakah dilakukan restart simulasi MD?') |
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parser.add_argument('-nvtdir','--nvtdir',type=str,default='../NVT') |
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parser.add_argument('-ns','--nstep', type=int, default=50000,help='Banyaknya step dalam simulasi MD.') |
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parser.add_argument('-np','--nproc',type=int,default=1, help='Jumlah CPU yang digunakan') |
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# Opsi kondisi PBC |
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parser.add_argument('-a1','--a1',type=float, default=0, help='panjang vektor a1') |
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parser.add_argument('-a2','--a2',type=float, default=0, help='panjang vektor a2') |
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parser.add_argument('-a3','--a3',type=float, default=0, help='panjang vektor a3') |
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parser.add_argument('-b1','--b1',type=float, default=0, help='panjang vektor b1') |
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parser.add_argument('-b2','--b2',type=float, default=0, help='panjang vektor b2') |
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parser.add_argument('-b3','--b3',type=float, default=0, help='panjang vektor b3') |
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parser.add_argument('-c1','--c1',type=float, default=0, help='panjang vektor c1') |
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parser.add_argument('-c2','--c2',type=float, default=0, help='panjang vektor c2') |
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parser.add_argument('-c3','--c3',type=float, default=0, help='panjang vektor c3') |
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# Input spesifik program DFTB+ |
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parser.add_argument('-hcorr','--hcorr',type=str, default='hdamp',help='Koreksi ikatan hidrogen. Default: hdamp. Pilihan: H5.') |
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# Input yang berkaitan dengan penyiapan sistem larutan |
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parser.add_argument('-mt', '--terlarut', type=str, help='Nama file molekul terlarut dalam format .xyz (ditulis tanpa ekstensi).') |
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parser.add_argument('-ct', '--c_terlarut', type=str, help='Muatan bersih molekul terlarut.',default=0) |
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parser.add_argument('-pt', '--persen_terlarut', type=str, default=50, help='Persen massa terlarut. Jika lebih dari satu terlarut, pisahkan dengan koma.') |
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parser.add_argument('-pp', '--persen_pelarut', type=str, default=50, help='Persen massa pelarut. Default:50') |
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parser.add_argument('-l', '--lapang', type=float, default=5, help='Panjang tambahan (Angstrom) pada rusuk kubus untuk menghindari bad contact. Default: 10.0.') |
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parser.add_argument('-gen','--generate_dftbinp',type=str,default='false',help='Apakah ingin mengkonversi ke dalam format koordinat xyz?') |
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parser.add_argument('-mp', '--pelarut', type=str, help='Nama file molekul pelarut dalam format .xyz (ditulis tanpa ekstensi).') |
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parser.add_argument('-nequil','--nequil',type=int, default=50000, help='Jumlah step pada saat ekuilibrasi.') |
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parser.add_argument('-nprod','--nprod',type=int, default=400000, help='Jumlah step pada saat production.') |
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parser.add_argument('-prod', '--production', type=str, default='None', help='Ensembel yang digunakan dalam production run. Pilihan:nve,npt,nvt.') |
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parser.add_argument('-cp', '--c_pelarut', type=int, default=0, help='Muatan bersih molekul pelarut') |
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parser.add_argument('-ctype','--charge_type',type=str, default='gas', help='Tipe muatan yang digunakan untuk parameterisasi muatan.') |
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parser.add_argument('-Nump','--NumPelarut', type=int, default=100, help='Jumlah molekul pelarut maksimum dalam sistem larutan. Default = 100.') |
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parser.add_argument('-cat','--cation',type=str, default='none',help='Kation yang digunakan untuk menetralkan muatan sistem larutan.') |
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parser.add_argument('-p', '--pressure', default=1.0, type=float, help='Tekanan dalam satuan bar') |
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parser.add_argument('--packmol', type=str, default='/home/adit/opt/packmol/packmol') |
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# Opsi untuk melakukan restart simulasi MD |
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parser.add_argument('-traj','--traject',type=str, default='../NVT/traject',help='File trayektori dari simulasi sebelumnya') |
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parser.add_argument('-vel','--velocity',type=str, default='../NVT/velocity',help='File kecepatan atom dari simulasi sebelumnya') |
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parser.add_argument('-inp','--dftbinp',type=str, default='../NVT/dftb.inp',help='File dftb.inp dari simulasi sebelumnya.') |
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# Opsi untuk dinding potensial virtual |
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parser.add_argument('-soft','--soft',type=str,default='false',help='Apakah dinding potensial akan digunakan?. Pilihan: true, false.') |
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parser.add_argument('-softtype','--softtype',type=str,default='SPHERE',help='Jenis dinding apakah yang akan anda pakai? Baca lebih lanjut manual DCDFTBMD.') |
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parser.add_argument('-softrange','--softrange',type=float,default=10,help='Ukuran dinding potensial yang anda gunakan. Default = 10 angstrom') |
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parser.add_argument('-softcenter','--softcenter',type=str,default='COM',help='Jenis pusat koordinat dinding potensial. Default = COM') |
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parser.add_argument('-metarest','--metarest',type=str,default='false',help='Apakah dilakukan restart simulasi metadinamika?. Pilihan: true, false.') |
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parser.add_argument('-metafreq','--metafreq',type=int,default=100, help='Dalam berapa step sekali potensial Gaussian ditambahkan?') |
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parser.add_argument('-metaheight','--metaheight',type=float,default=3.0e-3,help='Ketinggian potensial Gaussian dalam satuan Hartree. Default = 3.0e-3') |
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parser.add_argument('-cv','--cvtype',type=str,default='coordnum',help='Pilihan collective variable (CV) yang digunakan. Pilihan: coordnum, distance, angle, dihedral, distancediff, distanceadd, meandistance, pointplanedistance.') |
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parser.add_argument('-metawidth','--metawidth',type=float,default=0.1,help='Lebar potensial Gaussian yang digunakan (dalam satuan yang sama dengan satuan cv). Default = 0.1') |
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parser.add_argument('-pow1','--pow1',type=float,default=6,help='Nilai pangkat pertama pada definisi bilangan koordinasi rasional. Default = 6') |
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parser.add_argument('-pow2','--pow2',type=float,default=12,help='Nilai pangkat kedua pada definisi bilangan koordinasi rasional. Default = 12') |
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parser.add_argument('-rcut','--rcut',type=float,default=1.6,help='Jarak cutoff pada definisi bilangan koordinasi dalam satuan angstrom. Default = 1.6') |
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parser.add_argument('-fesstart','--fesstart',type=float,default=0, help='Titik minimum CV. Default = 0.') |
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parser.add_argument('-fesend','--fesend',type=float,default=1, help='Titik maksimum CV. Defalt = 1.') |
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parser.add_argument('-fesbin','--fesbin',type=float,default=0.01,help='Selang CV. Default = 0.01') |
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parser.add_argument('-ag1','--ag1',type=str,help='Grup atom pertama dalam sebuah CV.') |
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parser.add_argument('-ag2','--ag2',type=str,help='Grup atom kedua dalam sebuah CV.') |
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parser.add_argument('-ag3','--ag3',type=str,help='Grup atom ketiga dalam sebuah CV.') |
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parser.add_argument('-ag4','--ag4',type=str,help='Grup atom keempat dalam sebuah CV.') |
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# Input terkait DC setup |
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parser.add_argument('-bufrad','--bufrad',type=float,default=3.0,help='Radius buffer yang digunakan dalam sebuah subsistem. Default: 3.0') |
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parser.add_argument('-delta','--delta',type=float,default=3.0,help='Panjang rusuk kubus virual yang dibuat untuk membelah-belah subsistem. Default: 3.0') |
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parser.add_argument('-opttype','--opttype',type=str,default='bfgs', help='Jenis algoritma optimasi geometri yang digunakan dalam program DFTBUP maupun DCDFTBMD. Default: bfgs. Pilihan: sd, cg, qm, fire.') |
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parser.add_argument('-freqtype','--freqtype',type=int,default=1, help='Jenis perhitungan frekuensi vibrasi yang dilakukan, analitik (1) atau numerik (2). Default: 1, pilihan: 2.') |
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parser.add_argument('-econv','--econv',type=float,default=1e-6, help='Batas konvergensi perhitungan energi.') |
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parser.add_argument('-dconv','--dconv',type=float,default=1e-6, help='Batas konvergensi perhitungan gradien.') |
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# Input yang berkaitan dengan persiapan docking |
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parser.add_argument('-ligname','--ligname',type=str,help='Nama ligan yang ingin diekstrak strukturnya') |
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parser.add_argument('-ligand','--ligand',type=str,help='File ligand dalam format .mol2. Format harus .xyz jika ligand bukan merupakan native ligand.') |
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parser.add_argument('-dockrange','--dockrange',type=float,default=10,help='Radius yang diperhitungkan sebagai sisi aktif di sekitar ligan asli.') |
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parser.add_argument('-chargetype','--chargetype',type=str,default='qtpie',help='Tipe muatan parsial untuk ligan. Pilihan: qtpie, gasteiger, eem, eem2015ba, eem2015bm, eem2015bn, eem2015ha, eem2015hm, eem2015hn, eqeq, mmff94, dan qeq.') |
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parser.add_argument('-calcrmsd','--calcrmsd',type=str,default='no',help='Apakah ingin menghitung RMSD saat docking?') |
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parser.add_argument('-nlig','--nligands',type=int,help='Jumlah ligan yang akan didocking.') |
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# Model Pelarut Implisit |
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parser.add_argument('-solvent','--solvent',type=str,default='none',help='Pelarut yang digunakan dalam perhitungan.') |
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# Input untuk simulasi MD sistem protein |
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parser.add_argument('-protein','--protein',type=str,help='Struktur protein dalam format pdb') |
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# Input untuk perhitungan bergantung waktu |
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parser.add_argument('-nr','--nroots',type=int,default=5,help='Jumlah orbital aktif yang diperhitungkan dalam perhitungan bergantung waktu.') |
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parser.add_argument('-tda','--tda',type=str,default='false',help='Apakah akan digunakan pendekatan Tamm-Dancoff. Default = false.') |
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# Input untuk perhitungan TD-DFTB |
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parser.add_argument('-ts','--targetstate',type=int,default=0, help='Target orbital transisi yang dituju.') |
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parser.add_argument('-multtrans','--multtrans',type=int,default=1, help='Multiplisitas spin transisi elektronik.') |
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parser.add_argument('-ocsstr','--ocsstr',type=str,default='true', help='Menghitung osscilator strength dan momen dipol transisi elektronik.') |
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parser.add_argument('-wt','--writetrans',type=str,default='true', help='Menulis informasi detail mengenai transisi elektronik yang terjadi.') |
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parser.add_argument('-lc','--longrange',type=str,default='false', help='Apakah akan dilakukan koreksi interaksi jarak jauh.') |
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# Input untuk metode multiskala |
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parser.add_argument('-qmatoms','--qmatoms',type=str,default='None',help='Indeks dari atom-atom di lapisan QM. Indeks dimulai dari nol.') |
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parser.add_argument('-activeatoms','--activeatoms',type=str,default='1:-1',help='Indeks atom aktif yang digunakan untuk perhitungan.') |
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parser.add_argument('-hessfile','--hessfile',type=str,default='None',help='File Hessian hasil optimasi geometri atau berbagai perhitungan sebelumnya.') |
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parser.add_argument('-tc','--totalcharge',type=int,default=0,help='Muatan total molekul.') |
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parser.add_argument('-tmult','--totalmult',type=int,default=1,help='Multiplisitas spin total molekul.') |
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parser.add_argument('-qm2method','--qm2method',type=str,default='None',help='Custom method untuk lapisan QM2') |
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parser.add_argument('-qm2basis','--qm2basis',type=str,default='None',help='Custom himpunan basis untuk lapisan QM2') |
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# Informasi input padatan |
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parser.add_argument('-kpts','--kpts',type=str,default='1x1x1',help='Informasi K-points yang digunakan. Ditulis sebagai: 1x1x1, 2x2x2, dsb.') |
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# Input terkait perhitungan Atom in Molecules |
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parser.add_argument('-aim','--aim',type=str, default='false',help='Apakah akan dilakukan perhitungan AIM untuk interaksi non-kovalen?') |
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# Input terkait penggunaan Quantum-Espresso |
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parser.add_argument('-mode','--mode',type=str,default='from_scratch',help='Mode perhiungan dalam software Quantum-Espresso. Default: from_scratch. Pilihan: from_scratch, restart. ') |
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parser.add_argument('-pseudo','--pseudo',type=str,default='/home/adit/opt/qe-7.0/pseudo',help='Folder tempat menyimpan file pseudo potential.') |
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parser.add_argument('-outdir','--outdir',type=str,default='./out',help='Folder tempat menyimpan output.') |
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parser.add_argument('-unit','--unit',type=str,default='angstrom',help='Satuan yang digunakan dalam mendefinisikan parameter sel dan posisi atom. Default: angstrom. Pilihan: angstrom, bohr') |
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parser.add_argument('-bravais','--bravais',type=int,default=0,help='Indeks Bravais yang diperlukan untuk mengidentifikasi kristal pada software Quantum-Espresso.') |
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parser.add_argument('-ecutwfc','--ecutwfc',type=float,default=60.0,help='Cutoff energi kinetik untuk fungsi gelombang dalam satuan Ry. Default: 60.0 Ry.') |
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parser.add_argument('-ecutrho','--ecutrho',type=float,default=720.0,help='Cutoff energi kinetikr untuk rapat muatan dan potensial. Default: 720.0 Ry.') |
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parser.add_argument('-mix','--mixing_beta',type=float,default=0.7,help='Koefisien mixing untuk self-consistency.') |
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parser.add_argument('-conv_thr','--conv_thr',type=float,default=1e-8,help='Batas nilai konvergensi.') |
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parser.add_argument('-dftfunc','--dftfunc',type=str,default='pbe',help='Fungsional DFT yang digunakan. Default: pbe') |
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parser.add_argument('-extpseudo','--extpseudo',type=str,default='UPF',help='Ekstensi dari file pseudopotensial. Default: UPF.') |
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parser.add_argument('-optalgo','--optalgo',type=str,default='bfgs',help='Algoritma untuk optimasi geometri. Default: bfgs. Pilihan: damp, fire, verlet, langevin, langevin-smc, beeman.') |
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parser.add_argument('-cpress','--cellpress',type=float,default=0.0,help='Tekanan sel dalam satuan kilobar yang digunakan dalam Quantum-Espresso. Default:0.0.') |
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parser.add_argument('-press_conv','--press_conv_thr',type=float,default=0.5,help='Kriteria konvergensi untuk tekanan sel. Default=0.5 kbar.') |
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parser.add_argument('-nband','--nband',type=int,default=8,help='Jumlah tingkat energi yang ingin diplot dalam DOS.') |
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parser.add_argument('-occ','--occ',type=str,default='tetrahedra',help='Metode smearing yang digunakan. Default: tetrahedra. Pilihan: smearing, tetrahedra_lin, tetrahedra_opt, fixed, from_input.') |
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opt=parser.parse_args(sys.argv[1:]) |
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# Menggunakan molekul dengan format smiles |
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if ('.xyz' or '.pdb' or 'POSCAR' or '.vasp' or '.poscar') in opt.input: |
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geom = opt.input |
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elif '.mol2' in opt.input: |
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with open('run_babel.sh','w') as fout: |
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print("""#!/bin/bash |
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#SBATCH --nodes=1 |
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#SBATCH --ntasks=1 |
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#SBATCH --cpus-per-task=1 |
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#SBATCH --time=168:0:0 |
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export OMP_NUM_THREADS={} |
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cd $PWD |
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obabel {} -O geom.xyz""".format(opt.nproc,opt.input),file=fout) |
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os.system('sbatch run_babel.sh') |
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geom = 'geom.xyz' |
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elif ('.mol2' not in opt.input and '.xyz' not in opt.input and '.pdb' not in opt.input and '.vasp' not in opt.input and '.poscar' not in opt.input and 'POSCAR' not in opt.input and '.gen' not in opt.input): |
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os.system("echo '{}' > geom.smi".format(opt.input)) |
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with open('run_babel.sh','w') as fout: |
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print("""#!/bin/bash |
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#SBATCH --nodes=1 |
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#SBATCH --ntasks=1 |
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#SBATCH --cpus-per-task=1 |
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#SBATCH --time=168:0:0 |
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export OMP_NUM_THREADS={} |
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cd $PWD |
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obabel geom.smi -O geom.xyz --gen3d""".format(opt.nproc),file=fout) |
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os.system('sbatch run_babel.sh') |
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while not os.path.exists('geom.xyz'): |
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time.sleep(3) |
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geom = 'geom.xyz' |
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### ORCA |
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if opt.software == 'orca': |
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orca(opt.job,opt.method,opt.nproc,geom,opt.charge,opt.mult,opt.scalefreq,opt.temp,opt.pressure,opt.nroots,opt.tda,opt.solvent,opt.constraints,opt.qmatoms,opt.totalcharge,opt.totalmult,opt.qm2method,opt.qm2basis,opt.activeatoms,opt.hessfile,opt.dispersion,opt.aim) |
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|
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### NWChem |
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if opt.software == 'nwchem': |
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nwchem(opt.job,opt.method,opt.nproc,geom,opt.charge,opt.mult,opt.scalefreq,opt.restart,opt.conv_thr,opt.iter) |
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|
||||
### DCDFTBMD |
||||
if opt.software == 'dcdftb': |
||||
dcdftb(opt.job,opt.method,geom,opt.charge,opt.mult,opt.dispersion,opt.parapath,opt.temp,opt.pressure,opt.ensembel,opt.thermostat,opt.deltat,opt.nstep,opt.mdprint,opt.a1,opt.a2,opt.a3,opt.b1,opt.b2,opt.b3,opt.c1,opt.c2,opt.c3,opt.restart,opt.traject,opt.velocity,opt.dftbinp,opt.soft,opt.softtype,opt.softrange,opt.softcenter,opt.metarest,opt.metafreq,opt.metaheight,opt.cvtype,opt.metawidth,opt.pow1,opt.pow2,opt.rcut,opt.fesstart,opt.fesend,opt.fesbin,opt.ag1,opt.ag2,opt.ag3,opt.ag4,opt.solvent,opt.nroots,opt.targetstate,opt.multtrans,opt.ocsstr,opt.writetrans,opt.longrange,opt.bufrad,opt.delta,opt.opttype,opt.freqtype,opt.econv, opt.dconv) |
||||
|
||||
if opt.software == 'dock': |
||||
if opt.job == 'readpdb': |
||||
readpdb(opt.input) |
||||
if opt.job == 'splitpdb': |
||||
splitpdb(opt.input,opt.ligname) |
||||
if opt.job == 'addH': |
||||
addH(opt.input) |
||||
if opt.job == 'addcharge': |
||||
addcharge(opt.input,opt.chargetype) |
||||
if opt.job == 'sphgen': |
||||
sphgen(opt.input) |
||||
with open('run_sphgen.sh','w') as fout: |
||||
print("""#!/bin/bash |
||||
#SBATCH --nodes=1 |
||||
#SBATCH --ntasks=1 |
||||
#SBATCH --cpus-per-task=1 |
||||
#SBATCH --time=168:0:0 |
||||
export OMP_NUM_THREADS={} |
||||
cd $PWD |
||||
$DOCK_DIR/sphgen |
||||
$DOCK_DIR/sphere_selector protein.sph {} {}""".format(opt.nproc,opt.ligand,opt.dockrange),file=fout) |
||||
os.system("sbatch run_sphgen.sh") |
||||
|
||||
if opt.job == 'showsphere': |
||||
showsphere() |
||||
if opt.job == 'gridgen': |
||||
gridgen(opt.input) |
||||
with open('run_grid.sh','w') as fout: |
||||
print("""#!/bin/bash |
||||
#SBATCH --nodes=1 |
||||
#SBATCH --ntasks=1 |
||||
#SBATCH --cpus-per-task=1 |
||||
#SBATCH --time=168:0:0 |
||||
export OMP_NUM_THREADS={} |
||||
cd $PWD |
||||
$DOCK_DIR/grid -i grid.in""".format(opt.nproc),file=fout) |
||||
os.system("sbatch run_grid.sh") |
||||
|
||||
if opt.job == 'rigiddock': |
||||
rigiddock(opt.ligand,opt.calcrmsd) |
||||
with open('run_rigiddock.sh','w') as fout: |
||||
print("""#!/bin/bash |
||||
#SBATCH --nodes=1 |
||||
#SBATCH --ntasks=1 |
||||
#SBATCH --cpus-per-task=1 |
||||
#SBATCH --time=168:0:0 |
||||
export OMP_NUM_THREADS={} |
||||
cd $PWD |
||||
$DOCK_DIR/dock6 -i rigid.in -o rigid.out""".format(opt.nproc),file=fout) |
||||
os.system("sbatch run_rigiddock.sh") |
||||
if opt.job == 'flexdock': |
||||
flexdock(opt.ligand,opt.calcrmsd) |
||||
with open('run_flexdock.sh','w') as fout: |
||||
print("""#!/bin/bash |
||||
#SBATCH --nodes=1 |
||||
#SBATCH --ntasks=1 |
||||
#SBATCH --cpus-per-task=1 |
||||
#SBATCH --time=168:0:0 |
||||
export OMP_NUM_THREADS={} |
||||
cd $PWD |
||||
$DOCK_DIR/dock6 -i flex.in -o flex.out""".format(opt.nproc),file=fout) |
||||
os.system("sbatch run_flexdock.sh") |
||||
if opt.job == 'translig': |
||||
translig(opt.ligand) |
||||
|
||||
if opt.job=='sdf2xyz' and opt.software == 'dock': |
||||
sdf2xyz(opt.ligand) |
||||
|
||||
if opt.job == 'multiflexdock' and opt.software == 'dock': |
||||
multiflexdock(opt.nligands,opt.chargetype) |
||||
|
||||
if opt.job == 'multiopt' and opt.software == 'dock': |
||||
multiopt(opt.nligands) |
||||
if opt.job == 'checkopt' and opt.software == 'dock': |
||||
checkopt(opt.nligands) |
||||
|
||||
if opt.software == 'dftb': |
||||
if '.xyz' in opt.input: |
||||
geom = opt.input |
||||
elif 'POSCAR' in opt.input or '.poscar' in opt.input: |
||||
poscar2gen(opt.input) |
||||
geom = 'in.gen' |
||||
elif 'vasp' in opt.input: |
||||
vasp2gen(opt.input) |
||||
geom = 'in.gen' |
||||
|
||||
dftb(geom,opt.job,opt.activeatoms,opt.method,opt.parapath,opt.dispersion,opt.kpts,opt.hcorr) |
||||
with open('run.sh','w') as fout: |
||||
print("""#!/bin/bash |
||||
#SBATCH --nodes=1 |
||||
#SBATCH --ntasks=1 |
||||
#SBATCH --cpus-per-task=1 |
||||
#SBATCH --time=168:0:0 |
||||
export OMP_NUM_THREADS={} |
||||
cd $PWD |
||||
cp cmmd.in dftb_in.hsd |
||||
$DFTB_COMMAND cmmd.in > cmmd.out""".format(opt.nproc),file=fout) |
||||
os.system('sbatch run.sh') |
||||
|
||||
|
||||
if opt.software == 'qe': |
||||
qe(opt.input,opt.job,opt.mode,opt.pseudo,opt.outdir,opt.bravais,opt.unit,opt.ecutwfc,opt.ecutrho,opt.mixing_beta,opt.conv_thr,opt.dftfunc,opt.extpseudo,opt.kpts,opt.optalgo,opt.cellpress,opt.press_conv_thr,opt.nband,opt.occ) |
||||
|
||||
# RUNNING SCRIPT |
||||
if opt.software == 'orca': |
||||
with open('run.sh','w') as fout: |
||||
print("""#!/bin/bash |
||||
#SBATCH --nodes=1 |
||||
#SBATCH --ntasks=1 |
||||
#SBATCH --cpus-per-task={} |
||||
#SBATCH --time=168:0:0 |
||||
export LD_LIBRARY_PATH=/home/adit/opt/openmpi411/lib:$LD_LIBRARY_PATH |
||||
export PATH=/home/adit/opt/openmpi411/bin:$PATH |
||||
export OMP_NUM_THREADS=1 |
||||
cd $PWD |
||||
$ORCA_COMMAND cmmd.in > cmmd.out --oversubscribe""".format(opt.nproc),file=fout) |
||||
os.system('sbatch run.sh') |
||||
|
||||
if opt.software == 'nwchem': |
||||
with open('run.sh','w') as fout: |
||||
print("""#!/bin/bash |
||||
#SBATCH --nodes=1 |
||||
#SBATCH --ntasks=1 |
||||
#SBATCH --cpus-per-task={} |
||||
#SBATCH --time=168:0:0 |
||||
export LD_LIBRARY_PATH=/home/adit/opt/openmpi411/lib:$LD_LIBRARY_PATH |
||||
export PATH=/home/adit/opt/openmpi411/bin:$PATH |
||||
export OMP_NUM_THREADS=1 |
||||
cd $PWD |
||||
$NWCHEM_COMMAND cmmd.in > cmmd.out""".format(opt.nproc),file=fout) |
||||
os.system('sbatch run.sh') |
||||
|
||||
if opt.software == 'qe': |
||||
with open('run.sh','w') as fout: |
||||
print("""#!/bin/bash |
||||
#SBATCH --nodes=1 |
||||
#SBATCH --ntasks=1 |
||||
#SBATCH --cpus-per-task={} |
||||
#SBATCH --time=168:0:0 |
||||
export OMP_NUM_THREADS=1 |
||||
cd $PWD |
||||
mpirun -np {} $QE_COMMAND < cmmd.in > cmmd.out""".format(opt.nproc,opt.nproc),file=fout) |
||||
os.system('sbatch run.sh') |
||||
|
||||
if opt.software == 'dcdftb': |
||||
os.system("cp cmmd.in dftb.inp") |
||||
with open('run.sh','w') as fout: |
||||
print("""#!/bin/bash |
||||
#SBATCH --nodes=1 |
||||
#SBATCH --ntasks=1 |
||||
#SBATCH --cpus-per-task=1 |
||||
#SBATCH --time=168:0:0 |
||||
export OMP_NUM_THREADS={} |
||||
cd $PWD |
||||
$DCDFTB_COMMAND |
||||
mv dftb.out cmmd.out |
||||
mv traject traject.xyz""".format(opt.nproc),file=fout) |
||||
os.system('sbatch run.sh') |
||||
|
||||
if opt.software == 'gromacs': |
||||
with open('run.sh','w') as fout: |
||||
print("""#!/bin/bash |
||||
#SBATCH --nodes=1 |
||||
#SBATCH --ntasks=1 |
||||
#SBATCH --cpus-per-task=1 |
||||
#SBATCH --time=168:0:0 |
||||
export OMP_NUM_THREADS={} |
||||
cd $PWD |
||||
$GROMACS_COMMAND -mt {} -mp {} -ct {} -pt {} -pp {} -l {} -cat {} -gen {} -Nump {} -prod {} -nprod {} -nequil {} -dt {} -ctype {}""".format(opt.nproc, opt.terlarut,opt.pelarut,opt.c_terlarut,opt.persen_terlarut,opt.persen_pelarut,opt.lapang,opt.cation,opt.generate_dftbinp,opt.NumPelarut,opt.production,opt.nprod,opt.nequil,opt.deltat,opt.charge_type),file=fout) |
||||
os.system('sbatch run.sh') |
||||
|
||||
if opt.job == 'proprep' and opt.software == 'gmx': |
||||
proprep(opt.protein) |
||||
if opt.job == 'ligprep' and opt.software == 'gmx': |
||||
ligprep(opt.ligand,opt.charge) |
||||
@ -0,0 +1,85 @@ |
||||
#!/usr/bin/env python3 |
||||
import pymatgen.analysis.adsorption as pa |
||||
import pymatgen.core.structure as st |
||||
from pymatgen.core import Structure |
||||
import argparse |
||||
import sys |
||||
import warnings |
||||
warnings.filterwarnings("ignore") |
||||
parser = argparse.ArgumentParser(description='Build possible adsorbate-adsorbent interactions for the surface reaction') |
||||
parser.add_argument('-s', '--slab', type=str, help='structure POSCAR of the surface' ) |
||||
parser.add_argument('-height','--height', type=float, help='height criteria for selection of surface sites' ) |
||||
parser.add_argument('-d','--distance', type=float, help='distance from the coordinating ensemble of atoms along the miller index for the site (i. e. the distance from the slab itself)' ) |
||||
parser.add_argument('-pi','--put_inside', default=True, type=bool, help='whether to put the site inside the cell ' ) |
||||
parser.add_argument('-sr','--symm_reduce', type=float, default=0.1, help='symmetry reduction threshold' ) |
||||
parser.add_argument('-nr','--near_reduce', type=float, default=0.1, help='near reduction threshold' ) |
||||
parser.add_argument('-noh','--no_obtuse_hollow', type=bool, default=True, help='flag to indicate whether to include obtuse triangular ensembles in hollow sites' ) |
||||
parser.add_argument('-sel','--selective_dynamics', type=bool, default=True, help='create the selective dynamics options for VASP calculations') |
||||
parser.add_argument('-dyn','--dyn', type=float, default=3.50, help='Height for dynamical atoms selections') |
||||
parser.add_argument('-t','--type', type=str, help='Type of adsorption site based on the list' ) |
||||
parser.add_argument('-ad','--ad', type=str, help='Structure of adsorbate from file' ) |
||||
parser.add_argument('-all','--all', type=bool, default=False, help='Print all possible structures') |
||||
|
||||
opt = parser.parse_args(sys.argv[1:]) |
||||
|
||||
print('Begin searching for adsorption sites...') |
||||
# Defining the slab coordinate |
||||
slab_coord = Structure.from_file(opt.slab) |
||||
|
||||
# Searching the active sites |
||||
check_site = pa.AdsorbateSiteFinder(slab_coord, height=opt.height) |
||||
# Preparing the adsorbate molecules in xyz cartesian format |
||||
ad = st.Molecule.from_file(opt.ad) |
||||
|
||||
# Defining thke protocol for selective dynamics. Here you need to manually specify the height measured from the top of your slab structure. The default value is 3.50 Angstroms. |
||||
adsorbent = pa.AdsorbateSiteFinder(slab_coord, height=opt.dyn, selective_dynamics=opt.selective_dynamics) |
||||
adsorbent.slab.to(filename='adsorbent.vasp', fmt='poscar') |
||||
# Here, I assume that you want to generate one by one the adsorption types. The choices are 'ontop', 'hollow', and 'bridge' types. |
||||
if (opt.all == False): |
||||
sites = check_site.find_adsorption_sites(distance=opt.distance, put_inside=opt.put_inside, symm_reduce=opt.symm_reduce, near_reduce=opt.near_reduce, positions=[opt.type], no_obtuse_hollow=opt.no_obtuse_hollow) |
||||
site_coord = sites.get(opt.type) |
||||
index = 0 |
||||
site_all = [] |
||||
for site in site_coord: |
||||
adsorbed = adsorbent.add_adsorbate(ad, site, repeat=None, reorient=True) |
||||
adsorbed.to(filename='{}_{}.vasp'.format(opt.type,index), fmt='poscar') |
||||
index += 1 |
||||
site_all.append(site.tolist()) |
||||
# adsorbed = adsorbent.add_adsorbate(ad, site_all, repeat=None, reorient=True) |
||||
# adsorbed.to(filename='{}_all.vasp'.format(opt.type), fmt='poscar') |
||||
print('{}: {}'.format(opt.type, len(site_coord))) |
||||
print('Done for all possibilities of {} adsorption mode!'.format(opt.type)) |
||||
# The following if in case you want to generate all possible adsorption sites. |
||||
else: |
||||
sites = check_site.find_adsorption_sites(distance=opt.distance, put_inside=opt.put_inside, symm_reduce=opt.symm_reduce, near_reduce=opt.near_reduce, positions=['hollow','ontop','bridge'], no_obtuse_hollow=opt.no_obtuse_hollow) |
||||
hollow_coord = sites.get('hollow') |
||||
bridge_coord = sites.get('bridge') |
||||
ontop_coord = sites.get('ontop') |
||||
hollow_ind = 0 |
||||
bridge_ind = 0 |
||||
ontop_ind = 0 |
||||
|
||||
for site in hollow_coord: |
||||
adsorbed = adsorbent.add_adsorbate(ad, site, repeat=None, reorient=True) |
||||
elements = adsorbed.types_of_specie |
||||
element = [str(x) for x in elements] |
||||
sorted_ads = adsorbed.get_sorted_structure(key=lambda x: element.index(str(x.specie))) |
||||
sorted_ads.to(filename='hollow_{}.vasp'.format(hollow_ind), fmt='poscar') |
||||
hollow_ind += 1 |
||||
for site in ontop_coord: |
||||
adsorbed = adsorbent.add_adsorbate(ad, site, repeat=None, reorient=True) |
||||
elements = adsorbed.types_of_specie |
||||
element = [str(x) for x in elements] |
||||
sorted_ads = adsorbed.get_sorted_structure(key=lambda x: element.index(str(x.specie))) |
||||
sorted_ads.to(filename='ontop_{}.vasp'.format(ontop_ind), fmt='poscar') |
||||
ontop_ind += 1 |
||||
for site in bridge_coord: |
||||
adsorbed = adsorbent.add_adsorbate(ad, site, repeat=None, reorient=True) |
||||
elements = adsorbed.types_of_specie |
||||
element = [str(x) for x in elements] |
||||
sorted_ads = adsorbed.get_sorted_structure(key=lambda x: element.index(str(x.specie))) |
||||
sorted_ads.to(filename='bridge_{}.vasp'.format(bridge_ind), fmt='poscar') |
||||
bridge_ind += 1 |
||||
print('###############THE LIST OF ADSORPTION SITES####################') |
||||
print('hollow:{}, bridge:{}, ontop:{}'.format(len(hollow_coord), len(bridge_coord), len(ontop_coord))) |
||||
print('Done for all possibilities of adsorption modes!') |
||||
@ -0,0 +1,60 @@ |
||||
#!/usr/bin/env ruby |
||||
|
||||
require 'matrix' |
||||
|
||||
|
||||
genfile = ARGV[0] |
||||
|
||||
type = "C" |
||||
|
||||
symbols = [] |
||||
index = [] |
||||
coords = [] |
||||
nat = 0 |
||||
|
||||
lat_vector = [] |
||||
|
||||
File.open(genfile, "r") do |file| |
||||
line = file.gets |
||||
arr = line.split |
||||
if arr.size > 1 |
||||
type = arr[1] |
||||
end |
||||
nat = arr[0].to_i |
||||
symbols = file.gets.split |
||||
(1..nat).each do |i| |
||||
line = file.gets |
||||
arr = line.split |
||||
index << arr[1].to_i |
||||
coords << Vector.elements(arr[2..4].map{|x| x.to_f}) |
||||
end |
||||
if ( type.upcase != "C") |
||||
file.gets |
||||
(1..3).each do |i| |
||||
arr = file.gets.split.map{|x| x.to_f} |
||||
lat_vector << Vector.elements(arr) |
||||
end |
||||
end |
||||
end |
||||
|
||||
|
||||
puts nat |
||||
puts |
||||
if type.upcase == "C" |
||||
(1..nat).each do |i| |
||||
puts [symbols[index[i-1]-1], coords[i-1].to_a].to_a.join(" ") |
||||
end |
||||
elsif type.upcase == "F" |
||||
(1..nat).each do |i| |
||||
puts [symbols[index[i-1]-1], (coords[i-1][0]*lat_vector[0]+coords[i-1][1]*lat_vector[1]+coords[i-1][2]*lat_vector[2]).to_a.map{|x| "%16.12f"%x}].join(" ") |
||||
end |
||||
elsif type.upcase == "S" |
||||
(1..nat).each do |i| |
||||
puts [symbols[index[i-1]-1], coords[i-1].to_a.map{|x| "%16.12f"%x}.join(" ")].to_a.join(" ") |
||||
end |
||||
end |
||||
if ( type.upcase != "C") |
||||
puts "TV #{lat_vector[0].to_a.map{|x| "%16.12f"%x}.join(" ")}" |
||||
puts "TV #{lat_vector[1].to_a.map{|x| "%16.12f"%x}.join(" ")}" |
||||
puts "TV #{lat_vector[2].to_a.map{|x| "%16.12f"%x}.join(" ")}" |
||||
end |
||||
@ -0,0 +1,81 @@ |
||||
#!/usr/bin/env ruby |
||||
|
||||
|
||||
require 'matrix' |
||||
|
||||
lines = [] |
||||
while line = gets |
||||
lines << line |
||||
end |
||||
|
||||
|
||||
title = lines.shift |
||||
|
||||
factor = lines.shift.to_f |
||||
basis_vectors = [] |
||||
3.times do |
||||
basis_vectors << lines.shift |
||||
end |
||||
|
||||
basis = basis_vectors.map{|x| x.split.map{|y| y.to_f}} |
||||
|
||||
typenames = lines.shift.split |
||||
nats = lines.shift.split.map{|x|x.to_i} |
||||
|
||||
|
||||
selective_dynamics = false |
||||
|
||||
if (lines[0].downcase().start_with?("selective")) |
||||
selective_dynamics = true |
||||
lines.shift |
||||
end |
||||
|
||||
mode_str = lines.shift |
||||
mode_type = "S" |
||||
if mode_str[0..0].upcase == "D" |
||||
mode_name = "Relative" |
||||
mode_type = "F" |
||||
else |
||||
mode_name = "Angstrom" |
||||
end |
||||
|
||||
coords = [] |
||||
nats.each_with_index do |n, i| |
||||
n.times do |
||||
line = lines.shift.split(" ") |
||||
coords << [i+1, line[0..2]] |
||||
end |
||||
end |
||||
|
||||
|
||||
final = basis.map{|line| (Vector.elements(line)*factor).to_a} |
||||
|
||||
nat = nats.inject(0){|sum,x| sum + x } |
||||
|
||||
puts "#{nat} #{mode_type}" |
||||
puts "#{typenames.join(" ")}" |
||||
coords.each_with_index do |line, j| |
||||
puts "#{j+1} #{line.join(" ")}" |
||||
end |
||||
|
||||
puts "0.0 0.0 0.0" |
||||
final.each do |line| |
||||
puts line.map{|x| "%20.14f" % x}.join(" ") |
||||
end |
||||
exit |
||||
|
||||
puts " |
||||
TypeNames = { #{typenames.join(" ") } } |
||||
TypesAndCoordinates [#{mode}] = { |
||||
" |
||||
coords.each do |line| |
||||
puts " #{line.join(" ")}" |
||||
end |
||||
puts " } |
||||
Periodic = Yes |
||||
LatticeVectors [Angstrom] = { |
||||
" |
||||
puts " } |
||||
" |
||||
|
||||
|
||||
@ -0,0 +1,90 @@ |
||||
#!/usr/bin/env ruby |
||||
|
||||
require 'ostruct' |
||||
|
||||
input_file = ARGV[0] |
||||
|
||||
def parsexyz(infile) |
||||
|
||||
res = OpenStruct.new |
||||
res.coords = [] |
||||
res.symbols = [] |
||||
res.natoms = 0 |
||||
res.title = "POSCAR" |
||||
res.tv = [] |
||||
res.succ = true |
||||
res.nats = [] |
||||
|
||||
counting_map = {} |
||||
counting_map.default = 0 |
||||
|
||||
natoms = infile.gets.split[0].to_i |
||||
title = infile.gets |
||||
natoms.times do |
||||
line = infile.gets |
||||
arr = line.split |
||||
res.symbols << arr[0] |
||||
res.coords << arr |
||||
counting_map[arr[0]] += 1 |
||||
end |
||||
3.times do |
||||
if line = infile.gets and line.include?("TV") |
||||
res.tv << line.split(" ")[1..-1] |
||||
else |
||||
res.tv = [ [20.0, 0.0, 0.0], [0.0, 20.0, 0.0], [0.0, 0.0, 20.0] ] |
||||
break |
||||
end |
||||
end |
||||
res.symbols.uniq! |
||||
res.symbols.each do |sym| |
||||
res.nats << counting_map[sym] |
||||
end |
||||
return res |
||||
end |
||||
|
||||
|
||||
def writePOSCAR(res) |
||||
if (res.title.size == 0) |
||||
puts "POSCAR" |
||||
else |
||||
puts res.title |
||||
end |
||||
puts 1.0 |
||||
(0..2).each do |i| |
||||
puts res.tv[i].map{|x| "%16.12f" % x}.join(" ") |
||||
end |
||||
puts res.symbols.join(" ") |
||||
puts res.nats.join(" ") |
||||
puts "Cart" |
||||
res.coords.each do |line| |
||||
puts "#{line[1..-1].map{|x| "%16.12f" % x}.join(" ")} #{line[0]}" |
||||
end |
||||
end |
||||
|
||||
|
||||
|
||||
|
||||
File.open(input_file) do |infile| |
||||
num = 0 |
||||
last_obj = OpenStruct.new |
||||
while infile.eof? == false |
||||
obj = parsexyz(infile) |
||||
num += 1 |
||||
if obj.succ |
||||
last_obj = obj |
||||
# last_obj.marshal_load(obj.marshal_dump()) |
||||
end |
||||
end |
||||
writePOSCAR(last_obj) |
||||
end |
||||
exit |
||||
|
||||
|
||||
File.open(output_file, "w") do |outfile| |
||||
|
||||
outfile.puts [natoms, "C"].join(" ") |
||||
outfile.puts symbols.join(" ") |
||||
lines.each_with_index do |line, index| |
||||
outfile.puts [index+1, symbols.index(line[0])+1, line[1..3]].join(" ") |
||||
end |
||||
end |
||||
File diff suppressed because it is too large
Load Diff
@ -0,0 +1,197 @@ |
||||
#!/usr/bin/env python3 |
||||
import os |
||||
import argparse |
||||
import sys |
||||
from cmmde_dftb import xyz2gen |
||||
import numpy as np |
||||
from cmmde_surface import surface |
||||
from cmmde_formats import read, write |
||||
from cmmde_dftb import xyz2gen |
||||
from cmmde_tools import sort |
||||
from cmmde_decahedron import Decahedron |
||||
from cmmde_icosahedron import Icosahedron |
||||
from cmmde_tetrahedron import Tetrahedron |
||||
from cmmde_cubic import FaceCenteredCubic, SimpleCubic, BodyCenteredCubic |
||||
import pymatgen.analysis.adsorption as pa |
||||
import pymatgen.core.structure as st |
||||
from pymatgen.core import Structure |
||||
import argparse |
||||
import sys |
||||
import warnings |
||||
warnings.filterwarnings("ignore") |
||||
|
||||
parser = argparse.ArgumentParser(description='CMMDEPRE: Program untuk modifikasi input file') |
||||
parser.add_argument('-i','--input', type=str, default='',help='Input geometri dalam berbagai format. Format yang didukung: .smi, .mol2, dan semua format yang didukung oleh openbabel.') |
||||
parser.add_argument('-j','--job', type=str, default='sp',help='Jenis pekerjaan yang dilakukan.') |
||||
parser.add_argument('-s','--size',type=str,help='Ukuran supersel yang ingin dibuat.') |
||||
parser.add_argument('-hkl','--hkl',type=str,help='Indeks Miller (hkl) permukaan yang akan dibuat.') |
||||
parser.add_argument('-v', '--vacuum', type=float, default=20, help='Tebal lapisan vakum yang dibuat (dalam angstrom). Default: 20 Angstrom.') |
||||
parser.add_argument('-n', '--layer', type=int, help='Jumlah lapisan permukaan atau klaster yang akan dibuat.') |
||||
parser.add_argument('-ads','--ads',type=str, help='File koordinat Cartesian berisikan molekul adsorbat') |
||||
parser.add_argument('-d','--distance',type=float,default=1.5,help='Jarak adsorbat dari lapisan teratas permukaan (Angstrom). Default: 1.5 Angstrom.') |
||||
parser.add_argument('-height','--height',type=float,default=2.0, help='Tebal lapisan sisi aktif (Angstrom). Default: 2.0.') |
||||
parser.add_argument('-dyn','--dyn',type=float,default=3.0, help='Tebal lapisan bawah permukaan yang dibuat kaku (Angstrom). Default: 3.0.') |
||||
parser.add_argument('-e', '--element', type=str, help='Unsur yang akan dibuat klaster' ) |
||||
parser.add_argument('-t', '--type', type=str, help='Tipe klaster yang akan dibuat. Pilihan: decahedron dan icosahedron') |
||||
parser.add_argument('-lc', '--lc', type=float, help='Panjang sel satuan kristal ruah jika dianggap kubus.' ) |
||||
# Setup untuk klaster decahedron |
||||
parser.add_argument('-npar', '--parallel', type=int, help='Jumlah atom pada sisi sejajar dengan ekuatorial.' ) |
||||
parser.add_argument('-nper', '--perpendicular', type=int, help='Jumlah atom pada sisi tegak lurus dengan ekuatorial.' ) |
||||
opt = parser.parse_args(sys.argv[1:]) |
||||
|
||||
|
||||
opt = parser.parse_args(sys.argv[1:]) |
||||
|
||||
|
||||
if opt.job == 'smi2xyz': |
||||
os.system("echo '{}' > geom.smi".format(opt.input)) |
||||
with open('run_babel.sh', 'w') as fout: |
||||
print("""#!/bin/bash |
||||
#SBATCH --nodes=1 |
||||
#SBATCH --ntasks=1 |
||||
#SBATCH --cpus-per-task=1 |
||||
#SBATCH --time=168:0:0 |
||||
export OMP_NUM_THREADS=1 |
||||
cd $PWD |
||||
obabel geom.smi -O geom.xyz --gen3d""",file=fout) |
||||
os.system('sbatch run_babel.sh') |
||||
if opt.job == 'mol2xyz' or opt.job == 'pdb2xyz': |
||||
with open('run_babel.sh', 'w') as fout: |
||||
print("""#!/bin/bash |
||||
#SBATCH --nodes=1 |
||||
#SBATCH --ntasks=1 |
||||
#SBATCH --cpus-per-task=1 |
||||
#SBATCH --time=168:0:0 |
||||
export OMP_NUM_THREADS=1 |
||||
cd $PWD |
||||
obabel {} -O geom.xyz""".format(opt.input),file=fout) |
||||
os.system('sbatch run_babel.sh') |
||||
if opt.job == 'gen2poscar': |
||||
from cmmde_gen2poscar import gen2poscar |
||||
gen2poscar(opt.input) |
||||
|
||||
if '.mol2' in opt.input and 'charge' in opt.job: |
||||
charges = [] |
||||
with open(opt.input,'r') as f: |
||||
lines = f.readlines() |
||||
Natom = int(lines[2].split()[0]) |
||||
for i in range(1,Natom+1): |
||||
charges.append(float(lines[7+i].split()[8])) |
||||
charges = np.array(charges) |
||||
print("Muatan total = {}".format(round(sum(charges)))) |
||||
|
||||
if opt.job == 'combinexyz': |
||||
xyz = opt.input.split(' ') |
||||
natom = 0 |
||||
coord = [] |
||||
for i in xyz: |
||||
with open(i, 'r') as f: |
||||
natom+=int(next(f)) |
||||
next(f) |
||||
for line in f: |
||||
coord.append(line.strip()) |
||||
with open('geom.xyz','w') as f: |
||||
print(natom,file=f) |
||||
print('Complex file generated by CMMDE',file=f) |
||||
for i in coord: |
||||
print(i,file=f) |
||||
|
||||
if opt.job == 'supercell': |
||||
cell = opt.size.split('x') |
||||
filename = opt.input.split('.')[0] |
||||
os.system('aflow --supercell={},{},{} < {} > {}_{}{}{}.vasp'.format(cell[0],cell[1],cell[2],opt.input,filename,cell[0],cell[1],cell[2])) |
||||
|
||||
if opt.job == 'surface': |
||||
hkl = [int(x) for x in str(opt.hkl)] |
||||
|
||||
bulk = read(opt.input) |
||||
|
||||
slab = surface(bulk, (hkl[0],hkl[1],hkl[2]), opt.layer, vacuum=opt.vacuum) |
||||
size = opt.size.split('x') |
||||
superslab = slab*(int(size[0]),int(size[1]),1) |
||||
superslab_sorted = sort(superslab) |
||||
|
||||
write('slab_{}{}{}.xyz'.format(hkl[0],hkl[1],hkl[2]), superslab_sorted) |
||||
# write('slab.vasp', slab*(int(size[0]),int(size[1]),1)) |
||||
x = [] |
||||
y = [] |
||||
z = [] |
||||
sym = [] |
||||
a1 = 0 |
||||
b1 = 0 |
||||
c1 = 0 |
||||
a2 = 0 |
||||
b2 = 0 |
||||
c2 = 0 |
||||
a3 = 0 |
||||
b3 = 0 |
||||
c3 = 0 |
||||
with open('slab_{}{}{}.xyz'.format(hkl[0],hkl[1],hkl[2]),'r') as f: |
||||
Natoms = int(next(f)) |
||||
lat = next(f).split('Lattice=')[1].split() |
||||
a1+=float(lat[0].strip('"')) |
||||
a2+=float(lat[1]) |
||||
a3+=float(lat[2]) |
||||
b1+=float(lat[3]) |
||||
b2+=float(lat[4]) |
||||
b3+=float(lat[5]) |
||||
c1+=float(lat[6]) |
||||
c2+=float(lat[7]) |
||||
c3+=float(lat[8].strip('"')) |
||||
xyz2gen('slab_{}{}{}.xyz'.format(hkl[0],hkl[1],hkl[2]),a1,a2,a3,b1,b2,b3,c1,c2,c3) |
||||
from cmmde_gen2poscar import gen2poscar |
||||
gen2poscar("in.gen") |
||||
os.system("mv in.vasp slab_{}{}{}.vasp".format(hkl[0],hkl[1],hkl[2])) |
||||
|
||||
|
||||
if opt.job == 'adsorb': |
||||
os.system('cmmde_adsorbate.py -s {} -ad {} -all true -dyn {} -height {} -d {}'.format(opt.input,opt.ads,opt.dyn, opt.height, opt.distance)) |
||||
|
||||
if opt.job == 'clusadsorb': |
||||
os.system('cmmde_xyz2poscar.rb {} > POSCAR'.format(opt.input)) |
||||
os.system('cmmde_adsorbate.py -s POSCAR -ad {} -all true -dyn {} -height {} -d {}'.format(opt.ads,opt.dyn, opt.height, opt.distance)) |
||||
|
||||
if opt.job == 'poscar2xyz': |
||||
os.system('cmmde_poscar2gen.rb {} > in.gen'.format(opt.input)) |
||||
filename = opt.input.split('.')[0] |
||||
os.system('cmmde_gen2xyz.rb in.gen > {}.xyz'.format(filename)) |
||||
|
||||
if opt.job == 'surfinfo': |
||||
moveatoms = [] |
||||
frozen = [] |
||||
index = 0 |
||||
with open(opt.input, 'r') as f: |
||||
next(f) |
||||
next(f) |
||||
next(f) |
||||
next(f) |
||||
next(f) |
||||
next(f) |
||||
next(f) |
||||
next(f) |
||||
next(f) |
||||
for line in f: |
||||
arr = line.split() |
||||
index += 1 |
||||
if (arr[3] == "T" and arr[4] == "T" and arr[5] == "T"): |
||||
moveatoms.append(index) |
||||
else: |
||||
frozen.append(index) |
||||
print('Serial Atom-atom beku:') |
||||
for i in frozen: |
||||
print(i, end=' ') |
||||
print('') |
||||
print('Serial Atom-atom aktif:') |
||||
for i in moveatoms: |
||||
print(i, end=' ') |
||||
print('') |
||||
|
||||
if opt.job == 'cluster': |
||||
if (opt.type == "icosahedron"): |
||||
struct = Icosahedron(opt.element,opt.layer, opt.lc) |
||||
struct.write("{}_{}_{}.xyz".format(opt.element,opt.type,opt.layer)) |
||||
if (opt.type == "decahedron"): |
||||
struct = Decahedron(opt.element,opt.perpendicular,opt.parallel,0,opt.lc) |
||||
struct.write("{}_{}_{}_{}.xyz".format(opt.element,opt.type,opt.parallel,opt.perpendicular)) |
||||
if (opt.type == "tetrahedron"): |
||||
struct = Tetrahedron(opt.element) |
||||
@ -0,0 +1,125 @@ |
||||
#!/usr/bin/env python3 |
||||
# pylint: disable=missing-function-docstring |
||||
from __future__ import print_function |
||||
import panel as pn |
||||
|
||||
from panel_chemistry.widgets import JSMEEditor |
||||
from panel.interact import interact |
||||
import os |
||||
import sys |
||||
from panel_chemistry.pane import NGLViewer |
||||
from panel_chemistry.pane.ngl_viewer import EXTENSIONS |
||||
import py3Dmol |
||||
from panel_chemistry.pane import Py3DMol |
||||
# from iodata import IOData |
||||
|
||||
|
||||
def test_can_construct(): |
||||
JSMEEditor() |
||||
|
||||
|
||||
def cmmde_gui(): |
||||
geom = '' |
||||
pn.extension("jsme", sizing_mode="stretch_width") |
||||
|
||||
editor = JSMEEditor(value = " ",height=500,format="smiles",subscriptions=['smiles']) |
||||
|
||||
|
||||
|
||||
# Terminal widget |
||||
terminal = pn.widgets.Terminal( |
||||
"Computational Molecular and Material Design Environment\n Authors:\n Universitas Pertamina\n Institut Teknologi Sumatera\n Masyarakat Komputasi Indonesia\n\n", |
||||
options = {"cursorBlink": True}, |
||||
height = 200, sizing_mode = 'stretch_width' |
||||
) |
||||
# CMMDE software options |
||||
software_btn = pn.widgets.MultiSelect(name="Software selections",value=['Orca'],options=['Orca','GROMACS','Dcdftbmd','Quantum Espresso']) |
||||
software = {'Orca':'orca','GROMACS':'gromacs','Dcdftbmd':'dcdftb','Quantum Espresso':'qe'} |
||||
|
||||
|
||||
|
||||
# CMMDE job options |
||||
job_btn = pn.widgets.MultiChoice(name="Job selections",value=['Single point calculation'],options=['Single point calculation','Geometry optimization','Frequency calculation','Molecular dynamics','Metadynamics']) |
||||
job = {'Single point calculation':'sp','Geometry optimization':'opt','Frequency calculation':'freq','Molecular dynamics':'md','Metadynamics':'mtd'} |
||||
# CMMDE method options |
||||
method_btn = pn.widgets.MultiChoice(name="Method selections",value=['GFN2-xTB'],options=['GFN2-xTB','GFN1-xTB','DFTB2','DFTB2-gammah','DFTB3','DFTB3-diag']) |
||||
method = {'GFN2-xTB':'XTB2', 'GFN1-xTB':'XTB1','DFTB2':'DFTB2','DFTB2-gammah':'DFTB2_gammah','DFTB3':'DFTB3','DFTB3-diag':'DFTB3-diag'} |
||||
|
||||
# Name your molecule/material |
||||
Name_input = pn.widgets.TextInput(name="Molecule name") |
||||
|
||||
# CMMDE running button |
||||
Run_btn = pn.widgets.Button(name="Run CMMDE!",button_type='primary') |
||||
|
||||
def run(event): |
||||
os.makedirs(Name_input.value) |
||||
os.chdir(Name_input.value) |
||||
terminal.subprocess.run("cmmde.py","-i{}".format(editor.value),"-s{}".format(software[software_btn.value[0]]), "-j{}".format(job[job_btn.value[0]]), "-m{}".format(method[method_btn.value[0]])) |
||||
|
||||
Run_btn.on_click(run) |
||||
# Post calculations |
||||
post_btn = pn.widgets.MultiChoice(name="Post calculation",value=['Frequency calculation'], options=['Frequency calculation','Radial distribution function', 'Mean Square Displacement','Time-dependent calculation','Thermochemistry calculation']) |
||||
post_calc = {'Frequency calculation':'freq', 'Radial distribution function':'rdf','Mean Square Displacement':'msd','Time-dependent calculation':'td','Thermochemistry':'thermo'} |
||||
def post_calculation(event): |
||||
os.makedirs(post_calc[post_btn.value[0]]) |
||||
os.chdir(post_calc[post_btn.value[0]]) |
||||
if post_calc[post_btn.value[0]] == 'thermo' and software[software_btn.value[0]] == 'orca': |
||||
terminal.subprocess.run("cmmdepost.py","-j{}".format(post_calc[post_btn.value[0]]),"-s{}".format(software[software_btn.value[0]])) |
||||
else: |
||||
terminal.subprocess.run("cmmde.py","-i{}".format("../cmmd.xyz"),"-s{}".format(software[software_btn.value[0]]), "-j{}".format(post_calc[post_btn.value[0]]), "-m{}".format(method[method_btn.value[0]])) |
||||
runpost_btn = pn.widgets.Button(name="Run post calculation!",button_type='primary') |
||||
runpost_btn.on_click(post_calculation) |
||||
# Check the progress |
||||
def progress(event): |
||||
terminal.subprocess.run("squeue") |
||||
Progress_btn = pn.widgets.Button(name="Check calculation",button_type='primary') |
||||
Progress_btn.on_click(progress) |
||||
|
||||
# Visualize the results |
||||
xyzview = py3Dmol.view() |
||||
xyzview.setBackgroundColor('0xeeeeee') |
||||
xyzview.zoomTo() |
||||
xyzviewer = Py3DMol(xyzview, height=400, sizing_mode="stretch_width",name="CMMDE viewer") |
||||
def visualize(event): |
||||
with open('cmmd.xyz','r') as f: |
||||
xyz = f.read() |
||||
xyzview.addModel(xyz,'xyz') |
||||
xyzview.setStyle('stick') |
||||
xyzviewer.object = xyzview |
||||
|
||||
# xyzviewer.object = xyzview |
||||
|
||||
visual_btn = pn.widgets.Button(name="Visualize!", button_type='primary') |
||||
visual_btn.on_click(visualize) |
||||
|
||||
def set_background(color='0xeeeeee'): |
||||
xyzview.setBackgroundColor(color) |
||||
xyzviewer.param.trigger("object") |
||||
set_background("#e6f6ff") |
||||
|
||||
accent = "#0072B5" |
||||
|
||||
# background = pn.widgets.ColorPicker(value="#e6f6ff", name="Background") |
||||
# pn.bind(set_background, color=background, watch=True) |
||||
# def set_style(style="stick"): |
||||
# xyzview.setStyle({style: {}}) |
||||
# xyzview.zoomTo() |
||||
# xyzviewer.param.trigger("object") |
||||
|
||||
# set_style("stick") |
||||
# style=pn.widgets.RadioButtonGroup(value="stick", options=["stick", "sphere"], name="Style", button_type="success") |
||||
# set_style=pn.bind(set_style, style=style, watch=True) |
||||
|
||||
|
||||
#### Wrap them all together ########## |
||||
return pn.template.FastListTemplate( |
||||
site="CMMDE-GUI", |
||||
title="CMMDE Editor", |
||||
main=[editor, terminal, terminal.subprocess.param.running,visual_btn,pn.Tabs(xyzviewer)], |
||||
sidebar=[pn.Row(software_btn,height=200),Name_input,pn.Column(job_btn, height=400),pn.Column(method_btn,height=400),pn.Row(Run_btn,Progress_btn),pn.Column(post_btn,height=400),pn.Row(runpost_btn,Progress_btn)], |
||||
header_background=accent, accent_base_color=accent |
||||
) |
||||
|
||||
|
||||
if __name__.startswith("bokeh"): |
||||
cmmde_gui().servable() |
||||
Binary file not shown.
File diff suppressed because it is too large
Load Diff
@ -0,0 +1,34 @@ |
||||
# |
||||
# Number of atoms |
||||
# |
||||
5 |
||||
# |
||||
# The current total energy in Eh |
||||
# |
||||
-4.174453278190 |
||||
# |
||||
# The current gradient in Eh/bohr |
||||
# |
||||
-0.000009007707 |
||||
-0.000001022543 |
||||
-0.000028029012 |
||||
0.011370019952 |
||||
0.000004146566 |
||||
0.000007643366 |
||||
-0.003786329235 |
||||
0.003636059856 |
||||
-0.010072248687 |
||||
-0.003784129718 |
||||
0.006913091591 |
||||
0.008198977151 |
||||
-0.003790553292 |
||||
-0.010552275470 |
||||
0.001893657182 |
||||
# |
||||
# The atomic numbers and current coordinates in Bohr |
||||
# |
||||
6 1.8082282 -0.1155039 -0.1255024 |
||||
1 3.8862633 -0.1154577 -0.1253829 |
||||
1 1.1155667 0.5496500 -1.9682689 |
||||
1 1.1156455 1.1478457 1.3720151 |
||||
1 1.1155587 -2.0439966 0.2199578 |
||||
Binary file not shown.
@ -0,0 +1,192 @@ |
||||
|
||||
$orca_hessian_file |
||||
|
||||
$act_atom |
||||
0 |
||||
|
||||
$act_coord |
||||
0 |
||||
|
||||
$act_energy |
||||
-4.174453 |
||||
|
||||
$hessian |
||||
15 |
||||
0 1 2 3 4 |
||||
0 4.7636737984E-01 9.8065926338E-06 4.0509474611E-05 -2.6387163902E-01 -4.9481781065E-06 |
||||
1 9.8065926338E-06 4.7636874797E-01 -3.5322753161E-05 -4.4553523828E-06 -4.6712723347E-02 |
||||
2 4.0509474611E-05 -3.5322753161E-05 4.7642267416E-01 -1.2244706595E-05 1.3445702371E-06 |
||||
3 -2.6387163902E-01 -4.4553523828E-06 -1.2244706595E-05 3.0569963803E-01 3.1934909046E-06 |
||||
4 -4.9481781065E-06 -4.6712723347E-02 1.3445702371E-06 3.1934909046E-06 4.9654687555E-02 |
||||
5 -1.3149822728E-05 1.3436762125E-06 -4.6713637453E-02 1.0441682149E-05 5.2350354108E-07 |
||||
6 -7.0839334605E-02 2.3174998109E-02 -6.4209878747E-02 -1.3938723600E-02 1.0841749785E-02 |
||||
7 2.3175171407E-02 -6.8961088744E-02 6.1660244645E-02 6.2463766555E-04 -1.9733379734E-04 |
||||
8 -6.4209650586E-02 6.1659527473E-02 -2.1753160526E-01 -1.7300159651E-03 6.4963338353E-04 |
||||
9 -7.0831022262E-02 4.3995634311E-02 5.2150044298E-02 -1.3942892159E-02 2.0594374742E-02 |
||||
10 4.3995912265E-02 -1.2696536462E-01 -9.5129410929E-02 1.1882102059E-03 -8.0894314407E-04 |
||||
11 5.2150455969E-02 -9.5129546775E-02 -1.5947516242E-01 1.4084470151E-03 -1.0045758742E-03 |
||||
12 -7.0837646203E-02 -6.7175983361E-02 1.2031570067E-02 -1.3939157729E-02 -3.1434370036E-02 |
||||
13 -6.7175915060E-02 -2.3374165050E-01 3.3503139526E-02 -1.8110895566E-03 -1.9348846781E-03 |
||||
14 1.2031855740E-02 3.3503990448E-02 -5.2714172578E-02 3.2464202323E-04 3.5307530516E-04 |
||||
5 6 7 8 9 |
||||
0 -1.3149822728E-05 -7.0839334605E-02 2.3175171407E-02 -6.4209650586E-02 -7.0831022262E-02 |
||||
1 1.3436762125E-06 2.3174998109E-02 -6.8961088744E-02 6.1659527473E-02 4.3995634311E-02 |
||||
2 -4.6713637453E-02 -6.4209878747E-02 6.1660244645E-02 -2.1753160526E-01 5.2150044298E-02 |
||||
3 1.0441682149E-05 -1.3938723600E-02 6.2463766555E-04 -1.7300159651E-03 -1.3942892159E-02 |
||||
4 5.2350354108E-07 1.0841749785E-02 -1.9733379734E-04 6.4963338353E-04 2.0594374742E-02 |
||||
5 4.9655550291E-02 -3.0037506737E-02 6.5000245392E-04 -1.7635556184E-03 2.4410415586E-02 |
||||
6 -3.0037506737E-02 7.8101558840E-02 -2.7323500177E-02 7.5703379066E-02 3.3391028845E-03 |
||||
7 6.5000245392E-04 -2.7323500177E-02 7.5886724901E-02 -7.2696444954E-02 -6.1280276453E-03 |
||||
8 -1.7635556184E-03 7.5703379066E-02 -7.2696444954E-02 2.5105105304E-01 -7.7284477870E-03 |
||||
9 2.4410415586E-02 3.3391028845E-03 -6.1280276453E-03 -7.7284477870E-03 7.8097057948E-02 |
||||
10 -1.0046717260E-03 -3.0650673504E-03 5.6305999555E-03 6.6430798619E-03 -5.1877079575E-02 |
||||
11 -1.1518223626E-03 9.3745302500E-03 -1.7929175053E-02 -2.4869250248E-02 -6.1492402669E-02 |
||||
12 5.6297988854E-03 3.3390756247E-03 9.6509362855E-03 -2.0330968182E-03 3.3394321869E-03 |
||||
13 3.5280279411E-04 -3.6290316847E-03 -1.2357232660E-02 3.7418875799E-03 -6.5863631195E-03 |
||||
14 -2.5744191699E-05 9.1708936904E-03 2.8314023659E-02 -6.8818696287E-03 -7.3415421228E-03 |
||||
10 11 12 13 14 |
||||
0 4.3995912265E-02 5.2150455969E-02 -7.0837646203E-02 -6.7175915060E-02 1.2031855740E-02 |
||||
1 -1.2696536462E-01 -9.5129546775E-02 -6.7175983361E-02 -2.3374165050E-01 3.3503990448E-02 |
||||
2 -9.5129410929E-02 -1.5947516242E-01 1.2031570067E-02 3.3503139526E-02 -5.2714172578E-02 |
||||
3 1.1882102059E-03 1.4084470151E-03 -1.3939157729E-02 -1.8110895566E-03 3.2464202323E-04 |
||||
4 -8.0894314407E-04 -1.0045758742E-03 -3.1434370036E-02 -1.9348846781E-03 3.5307530516E-04 |
||||
5 -1.0046717260E-03 -1.1518223626E-03 5.6297988854E-03 3.5280279411E-04 -2.5744191699E-05 |
||||
6 -3.0650673504E-03 9.3745302500E-03 3.3390756247E-03 -3.6290316847E-03 9.1708936904E-03 |
||||
7 5.6305999555E-03 -1.7929175053E-02 9.6509362855E-03 -1.2357232660E-02 2.8314023659E-02 |
||||
8 6.6430798619E-03 -2.4869250248E-02 -2.0330968182E-03 3.7418875799E-03 -6.8818696287E-03 |
||||
9 -5.1877079575E-02 -6.1492402669E-02 3.3394321869E-03 -6.5863631195E-03 -7.3415421228E-03 |
||||
10 1.4428067706E-01 1.1216627263E-01 9.7565379841E-03 -2.2133354919E-02 -2.2671723378E-02 |
||||
11 1.1216627263E-01 1.8260820267E-01 -1.4427922682E-03 1.9002273053E-03 2.8931816346E-03 |
||||
12 9.7565379841E-03 -1.4427922682E-03 7.8099975098E-02 7.9204668253E-02 -1.4186255518E-02 |
||||
13 -2.2133354919E-02 1.9002273053E-03 7.9204668253E-02 2.7017311542E-01 -3.9500247375E-02 |
||||
14 -2.2671723378E-02 2.8931816346E-03 -1.4186255518E-02 -3.9500247375E-02 5.6729796094E-02 |
||||
|
||||
$vibrational_frequencies |
||||
15 |
||||
0 0.000000 |
||||
1 0.000000 |
||||
2 0.000000 |
||||
3 0.000000 |
||||
4 0.000000 |
||||
5 0.000000 |
||||
6 1411.894158 |
||||
7 1411.942387 |
||||
8 1411.989208 |
||||
9 1567.724975 |
||||
10 1567.756664 |
||||
11 2918.147432 |
||||
12 2930.722274 |
||||
13 2930.813685 |
||||
14 2930.996046 |
||||
|
||||
$normal_modes |
||||
15 15 |
||||
0 1 2 3 4 |
||||
0 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 |
||||
1 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 |
||||
2 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 |
||||
3 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 |
||||
4 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 |
||||
5 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 |
||||
6 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 |
||||
7 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 |
||||
8 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 |
||||
9 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 |
||||
10 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 |
||||
11 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 |
||||
12 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 |
||||
13 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 |
||||
14 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 |
||||
5 6 7 8 9 |
||||
0 0.0000000000E+00 9.6477903682E-02 6.9838285112E-02 5.0247657476E-02 1.0285495508E-05 |
||||
1 0.0000000000E+00 -6.5244195857E-02 1.0860033168E-01 -2.5674116800E-02 -1.0798405126E-05 |
||||
2 0.0000000000E+00 -5.6088574999E-02 -6.1989041273E-03 1.1629676616E-01 -7.5696185494E-06 |
||||
3 0.0000000000E+00 4.2224433199E-02 3.0585059656E-02 2.2027491770E-02 1.1770838068E-05 |
||||
4 0.0000000000E+00 3.0574268985E-01 -5.0895242725E-01 1.2037823767E-01 4.2177266162E-01 |
||||
5 0.0000000000E+00 2.6292699701E-01 2.9150057128E-02 -5.4508701960E-01 -2.6859136081E-01 |
||||
6 0.0000000000E+00 -4.4663913988E-01 -3.5644404675E-01 -1.6705301932E-02 3.7314153890E-01 |
||||
7 0.0000000000E+00 3.0044265391E-01 -4.8132377619E-01 -8.9851299978E-02 -2.4247029500E-01 |
||||
8 0.0000000000E+00 2.7795616746E-01 -4.8141902391E-02 3.7122287366E-02 -2.2777215718E-01 |
||||
9 0.0000000000E+00 -2.6047059427E-01 -3.9261870970E-01 -3.2337347124E-01 6.2793968834E-02 |
||||
10 0.0000000000E+00 -4.3850669339E-02 -3.8972868840E-01 2.8067701807E-01 -3.6444449307E-01 |
||||
11 0.0000000000E+00 -1.5166137869E-01 1.7045603953E-01 -3.5509072322E-01 3.3649266944E-01 |
||||
12 0.0000000000E+00 -4.8471400571E-01 -1.1369258345E-01 -2.8068345465E-01 -4.3606983719E-01 |
||||
13 0.0000000000E+00 2.1509393316E-01 8.5958677760E-02 -5.2795342450E-03 1.8527079673E-01 |
||||
14 0.0000000000E+00 2.7911142286E-01 -7.7600069791E-02 -5.2269896754E-01 1.5996104566E-01 |
||||
10 11 12 13 14 |
||||
0 1.9204652077E-05 -5.4805850258E-05 -4.1798508139E-02 -6.7803732330E-02 3.4456264823E-02 |
||||
1 2.0564924792E-05 6.8646694199E-05 6.0729309089E-02 -5.3425545265E-02 -3.1456376564E-02 |
||||
2 9.6100321186E-06 -6.9645773690E-04 4.5782854569E-02 8.9593147936E-03 7.3181607166E-02 |
||||
3 2.5534976406E-05 5.0051084360E-01 4.1636224744E-01 6.7286481475E-01 -3.3775125382E-01 |
||||
4 -2.6872468668E-01 3.7454611147E-05 2.9774155047E-02 -2.6169302021E-02 -1.5414189686E-02 |
||||
5 -4.2176170002E-01 -3.2676870747E-04 2.2463737380E-02 4.4214525483E-03 3.5838244132E-02 |
||||
6 2.8791652277E-01 -1.6441255022E-01 -4.6171136093E-02 -4.1860475240E-02 -2.8431296913E-01 |
||||
7 4.0677554581E-01 1.5789223761E-01 5.4429591353E-02 -1.7893642594E-02 2.7381977344E-01 |
||||
8 3.8608146478E-02 -4.3768539857E-01 -4.5893125785E-02 -1.8572459712E-02 -7.6545794522E-01 |
||||
9 -4.6732937548E-01 -1.6820033754E-01 2.6974086174E-01 -4.5257667378E-02 9.2311851128E-02 |
||||
10 -1.5748775713E-01 3.0678667384E-01 -4.9963292343E-01 -4.2590214260E-03 -1.5299492287E-01 |
||||
11 -8.3277284963E-02 3.6326100083E-01 -6.0508221964E-01 3.0380954142E-02 -1.2722379425E-01 |
||||
12 1.7915848135E-01 -1.6724490716E-01 -1.4187455121E-01 2.2218053919E-01 1.1918273215E-01 |
||||
13 1.9191853047E-02 -4.6553433773E-01 -3.0820150894E-01 6.8492337892E-01 2.6941328644E-01 |
||||
14 4.6631632849E-01 8.3049930218E-02 8.2978010602E-02 -1.2298622673E-01 -1.5164722587E-02 |
||||
|
||||
# |
||||
# The atoms: label mass x y z (in bohrs) |
||||
# |
||||
$atoms |
||||
5 |
||||
C 12.01100 1.808228232708 -0.115503926643 -0.125502358011 |
||||
H 1.00800 3.886263342700 -0.115457665877 -0.125382884353 |
||||
H 1.00800 1.115566681275 0.549649980043 -1.968268883378 |
||||
H 1.00800 1.115645469129 1.147845717277 1.372015106814 |
||||
H 1.00800 1.115558681105 -2.043996616803 0.219957812341 |
||||
|
||||
$actual_temperature |
||||
0.000000 |
||||
|
||||
$frequency_scale_factor |
||||
1.000000 |
||||
|
||||
$dipole_derivatives |
||||
15 |
||||
0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 |
||||
0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 |
||||
0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 |
||||
-2.0000000000E-01 0.0000000000E+00 0.0000000000E+00 |
||||
0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 |
||||
0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 |
||||
0.0000000000E+00 0.0000000000E+00 -0.0000000000E+00 |
||||
0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 |
||||
-0.0000000000E+00 0.0000000000E+00 -2.0000000000E-01 |
||||
0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 |
||||
0.0000000000E+00 -0.0000000000E+00 -1.0000000000E-01 |
||||
0.0000000000E+00 -0.0000000000E+00 -0.0000000000E+00 |
||||
0.0000000000E+00 -0.0000000000E+00 0.0000000000E+00 |
||||
-0.0000000000E+00 -2.0000000000E-01 0.0000000000E+00 |
||||
0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 |
||||
|
||||
# |
||||
# The IR spectrum |
||||
# wavenumber eps Int TX TY TZ |
||||
# |
||||
$ir_spectrum |
||||
15 |
||||
0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000 |
||||
0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000 |
||||
0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000 |
||||
0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000 |
||||
0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000 |
||||
0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000 |
||||
1411.89 0.00073546 3.71673613 -0.001597 -0.008137 -0.009685 |
||||
1411.94 0.00043621 2.20441932 -0.001157 -0.003252 0.009192 |
||||
1411.99 0.00020721 1.04716171 -0.000833 0.000200 -0.006713 |
||||
1567.72 0.00154955 7.83078993 -0.000000 -0.007232 0.016004 |
||||
1567.76 0.00001515 0.07656697 -0.000001 -0.000749 0.001567 |
||||
2918.15 0.00419539 21.20180047 -0.014320 0.013320 0.008134 |
||||
2930.72 0.00251671 12.71842438 -0.011427 0.008458 0.008116 |
||||
2930.81 0.00652390 32.96909208 -0.018466 -0.018797 0.000568 |
||||
2931.00 0.00633467 32.01283832 0.009269 -0.007394 0.023106 |
||||
|
||||
|
||||
$end |
||||
|
||||
@ -0,0 +1,13 @@ |
||||
#CMMDE generated Orca input file |
||||
!XTB2 Numfreq |
||||
%pal |
||||
nprocs 1 |
||||
end |
||||
|
||||
*xyzfile 0 1 cmmd.xyz |
||||
|
||||
%freq |
||||
scalfreq 1 |
||||
Temp 298.15 |
||||
Pressure 1.0 |
||||
end |
||||
@ -0,0 +1,164 @@ |
||||
|
||||
$orca_opt_file |
||||
|
||||
$trust |
||||
0.300000000000 |
||||
|
||||
$epredict |
||||
0.000000000000 |
||||
|
||||
$ediffsc |
||||
1000.000000000000 |
||||
|
||||
$ctyp |
||||
3 |
||||
|
||||
$coordinates |
||||
2 15 |
||||
1.80826004 -0.11550006 -0.12544002 3.87220003 -0.11550006 -0.12544002 |
||||
1.12026745 0.54514820 -1.95577206 1.12026745 1.13931589 1.36186893 |
||||
1.12026745 -2.03092647 0.21760196 |
||||
1.80823704 -0.11549999 -0.12548122 3.88617549 -0.11547122 -0.12540627 |
||||
1.11560506 0.54961930 -1.96816875 1.11565113 1.14779680 1.37193952 |
||||
1.11559369 -2.04390740 0.21993552 |
||||
|
||||
# redundant internal coordinates |
||||
# nbonds nangles ndihedrals nimpropers ncartesians |
||||
# bond definitions A B |
||||
# angle definitions A B C |
||||
# dihedral definitions A B C D |
||||
# improper torsion definitions A B C D |
||||
# cartesian definitions A x/y/z |
||||
$redundant_internals |
||||
4 6 0 0 0 |
||||
1 0 0 |
||||
2 0 0 |
||||
3 0 0 |
||||
4 0 0 |
||||
1 0 3 0 0 |
||||
2 0 3 0 0 |
||||
1 0 4 0 0 |
||||
2 0 4 0 0 |
||||
3 0 4 0 0 |
||||
1 0 2 0 0 |
||||
$energies |
||||
2 |
||||
-40.4517849381878705 |
||||
-40.4519245409608246 |
||||
|
||||
$gradients |
||||
2 15 |
||||
0.0000281120249107 -0.0000037064411669 0.0000525165778874 -0.0049990129430250 |
||||
-0.0000045316433501 0.0000098634302251 0.0016701552391622 -0.0015882790949084 |
||||
0.0044334055573350 0.0016586340354712 -0.0030330170283499 -0.0035893738581539 |
||||
0.0016688694657209 0.0046447102314975 -0.0008246575087751 |
||||
0.0000109936929351 0.0000063540709450 0.0000318229732579 -0.0000294208486349 |
||||
-0.0000021914169169 0.0000138398073834 0.0000203548871545 -0.0000037180473361 |
||||
0.0000440886074016 0.0000094316758080 -0.0000186102122881 -0.0000130949132512 |
||||
0.0000130715741403 0.0000344084933163 0.0000033464078443 |
||||
|
||||
$redundant_coords |
||||
2 10 |
||||
2.0639399862074517 2.0639538051479716 2.0639730605185891 2.0639452371510258 |
||||
1.9106340448094910 1.9106237183363008 1.9106388109628560 1.9106351045974839 |
||||
1.9106303954694328 1.9106373432471970 |
||||
2.0779384518561348 2.0778883651837607 2.0779467901700923 2.0779371257260508 |
||||
1.9105645779003646 1.9106531722343145 1.9106392975229700 1.9106648467042662 |
||||
1.9106137724204406 1.9106637475244237 |
||||
|
||||
$redundant_gradients |
||||
2 10 |
||||
-0.0050043645066456 -0.0049813849297886 -0.0049952006081833 -0.0050019622241142 |
||||
0.0000201718064817 -0.0000085529895258 -0.0000001414303179 -0.0000086367530628 |
||||
0.0000048268874594 -0.0000076675152472 |
||||
-0.0000343072826948 -0.0000322949407078 -0.0000357710991749 -0.0000337494803822 |
||||
0.0000116868532667 -0.0000047060577191 -0.0000004911749077 -0.0000044784875371 |
||||
0.0000028621663169 -0.0000048722788676 |
||||
|
||||
$hessian_approx |
||||
15 15 |
||||
0 1 2 3 4 5 |
||||
0 0.839489 0.000005 0.000001 -0.357113 0.000000 0.000001 |
||||
1 0.000005 0.839479 -0.000008 0.000060 -0.136205 0.000001 |
||||
2 0.000001 -0.000008 0.839466 0.000280 0.000001 -0.136202 |
||||
3 -0.357113 0.000060 0.000280 0.356650 -0.000050 -0.000126 |
||||
4 0.000000 -0.136205 0.000001 -0.000050 0.102153 -0.000001 |
||||
5 0.000001 0.000001 -0.136202 -0.000126 -0.000001 0.102152 |
||||
6 -0.160793 0.023559 -0.065423 0.000164 0.021816 -0.060351 |
||||
7 0.023611 -0.158825 0.062823 -0.000161 0.002601 -0.007289 |
||||
8 -0.065420 0.062681 -0.310252 0.000457 -0.007205 0.020195 |
||||
9 -0.160787 0.044765 0.052991 0.000084 0.041419 0.049116 |
||||
10 0.044847 -0.217845 -0.096648 -0.000331 0.009409 0.011112 |
||||
11 0.053157 -0.096774 -0.250752 -0.000490 0.011152 0.013170 |
||||
12 -0.160796 -0.068388 0.012151 0.000173 -0.063185 0.011361 |
||||
13 -0.068464 -0.326605 0.033831 0.000502 0.022042 -0.003822 |
||||
14 0.012261 0.034100 -0.142260 -0.000152 -0.003947 0.000685 |
||||
6 7 8 9 10 11 |
||||
0 -0.160793 0.023611 -0.065420 -0.160787 0.044847 0.053157 |
||||
1 0.023559 -0.158825 0.062681 0.044765 -0.217845 -0.096774 |
||||
2 -0.065423 0.062823 -0.310252 0.052991 -0.096648 -0.250752 |
||||
3 0.000164 -0.000161 0.000457 0.000084 -0.000331 -0.000490 |
||||
4 0.021816 0.002601 -0.007205 0.041419 0.009409 0.011152 |
||||
5 -0.060351 -0.007289 0.020195 0.049116 0.011112 0.013170 |
||||
6 0.130445 -0.027167 0.075264 0.015113 -0.017703 0.022163 |
||||
7 -0.027167 0.128238 -0.072271 -0.024314 0.028526 -0.035545 |
||||
8 0.075264 -0.072271 0.302367 -0.014531 0.017288 -0.020652 |
||||
9 0.015113 -0.024314 -0.014531 0.130495 -0.051638 -0.061174 |
||||
10 -0.017703 0.028526 0.017288 -0.051638 0.196223 0.111445 |
||||
11 0.022163 -0.035545 -0.020652 -0.061174 0.111445 0.234173 |
||||
12 0.015084 0.028017 0.004267 0.015111 0.024801 -0.013686 |
||||
13 -0.000511 -0.000534 -0.000510 -0.010238 -0.016301 0.009736 |
||||
14 0.028356 0.052273 0.008369 -0.026390 -0.043216 0.024039 |
||||
12 13 14 |
||||
0 -0.160796 -0.068464 0.012261 |
||||
1 -0.068388 -0.326605 0.034100 |
||||
2 0.012151 0.033831 -0.142260 |
||||
3 0.000173 0.000502 -0.000152 |
||||
4 -0.063185 0.022042 -0.003947 |
||||
5 0.011361 -0.003822 0.000685 |
||||
6 0.015084 -0.000511 0.028356 |
||||
7 0.028017 -0.000534 0.052273 |
||||
8 0.004267 -0.000510 0.008369 |
||||
9 0.015111 -0.010238 -0.026390 |
||||
10 0.024801 -0.016301 -0.043216 |
||||
11 -0.013686 0.009736 0.024039 |
||||
12 0.130441 0.078750 -0.014083 |
||||
13 0.078750 0.321380 -0.039205 |
||||
14 -0.014083 -0.039205 0.109162 |
||||
|
||||
$bmatrix |
||||
10 15 |
||||
0 1 2 3 4 5 |
||||
0 -1.000000 -0.000014 -0.000036 1.000000 0.000014 0.000036 |
||||
1 0.333335 -0.320094 0.886808 0.000000 0.000000 0.000000 |
||||
2 0.333303 -0.607954 -0.720625 0.000000 0.000000 0.000000 |
||||
3 0.333332 0.928039 -0.166231 0.000000 0.000000 0.000000 |
||||
4 0.453709 0.413743 0.490435 0.000018 -0.310318 -0.367832 |
||||
5 -0.453718 0.631637 -0.113097 0.000000 0.000000 0.000000 |
||||
6 0.453727 -0.631604 0.113159 -0.000003 0.473706 -0.084857 |
||||
7 -0.453744 -0.413783 -0.490432 0.000000 0.000000 0.000000 |
||||
8 -0.453692 -0.217839 0.603568 0.000000 0.000000 0.000000 |
||||
9 0.453748 0.217869 -0.603547 -0.000014 -0.163392 0.452660 |
||||
6 7 8 9 10 11 |
||||
0 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 |
||||
1 -0.333335 0.320094 -0.886808 0.000000 0.000000 0.000000 |
||||
2 0.000000 0.000000 0.000000 -0.333303 0.607954 0.720625 |
||||
3 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 |
||||
4 0.000000 0.000000 0.000000 -0.453727 -0.103425 -0.122603 |
||||
5 0.226857 -0.364801 -0.216946 0.226861 -0.266836 0.330043 |
||||
6 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 |
||||
7 0.226874 0.419254 0.066052 0.000000 0.000000 0.000000 |
||||
8 0.000000 0.000000 0.000000 0.226850 0.370268 -0.207453 |
||||
9 -0.453734 -0.054476 0.150887 0.000000 0.000000 0.000000 |
||||
12 13 14 |
||||
0 0.000000 0.000000 0.000000 |
||||
1 0.000000 0.000000 0.000000 |
||||
2 0.000000 0.000000 0.000000 |
||||
3 -0.333332 -0.928039 0.166231 |
||||
4 0.000000 0.000000 0.000000 |
||||
5 0.000000 0.000000 0.000000 |
||||
6 -0.453724 0.157898 -0.028302 |
||||
7 0.226870 -0.005472 0.424380 |
||||
8 0.226841 -0.152429 -0.396114 |
||||
9 0.000000 0.000000 0.000000 |
||||
|
||||
@ -0,0 +1,715 @@ |
||||
|
||||
***************** |
||||
* O R C A * |
||||
***************** |
||||
|
||||
#, |
||||
### |
||||
#### |
||||
##### |
||||
###### |
||||
########, |
||||
,,################,,,,, |
||||
,,#################################,, |
||||
,,##########################################,, |
||||
,#########################################, ''#####, |
||||
,#############################################,, '####, |
||||
,##################################################,,,,####, |
||||
,###########'''' ''''############################### |
||||
,#####'' ,,,,##########,,,, '''####''' '#### |
||||
,##' ,,,,###########################,,, '## |
||||
' ,,###'''' '''############,,, |
||||
,,##'' '''############,,,, ,,,,,,###'' |
||||
,#'' '''#######################''' |
||||
' ''''####'''' |
||||
,#######, #######, ,#######, ## |
||||
,#' '#, ## ## ,#' '#, #''# ###### ,####, |
||||
## ## ## ,#' ## #' '# # #' '# |
||||
## ## ####### ## ,######, #####, # # |
||||
'#, ,#' ## ## '#, ,#' ,# #, ## #, ,# |
||||
'#######' ## ## '#######' #' '# #####' # '####' |
||||
|
||||
|
||||
|
||||
####################################################### |
||||
# -***- # |
||||
# Department of theory and spectroscopy # |
||||
# Directorship and core code : Frank Neese # |
||||
# Max Planck Institute fuer Kohlenforschung # |
||||
# Kaiser Wilhelm Platz 1 # |
||||
# D-45470 Muelheim/Ruhr # |
||||
# Germany # |
||||
# # |
||||
# All rights reserved # |
||||
# -***- # |
||||
####################################################### |
||||
|
||||
|
||||
Program Version 5.0.2 - RELEASE - |
||||
|
||||
|
||||
With contributions from (in alphabetic order): |
||||
Daniel Aravena : Magnetic Suceptibility |
||||
Michael Atanasov : Ab Initio Ligand Field Theory (pilot matlab implementation) |
||||
Alexander A. Auer : GIAO ZORA, VPT2 properties, NMR spectrum |
||||
Ute Becker : Parallelization |
||||
Giovanni Bistoni : ED, misc. LED, open-shell LED, HFLD |
||||
Martin Brehm : Molecular dynamics |
||||
Dmytro Bykov : SCF Hessian |
||||
Vijay G. Chilkuri : MRCI spin determinant printing, contributions to CSF-ICE |
||||
Dipayan Datta : RHF DLPNO-CCSD density |
||||
Achintya Kumar Dutta : EOM-CC, STEOM-CC |
||||
Dmitry Ganyushin : Spin-Orbit,Spin-Spin,Magnetic field MRCI |
||||
Miquel Garcia : C-PCM and meta-GGA Hessian, CC/C-PCM, Gaussian charge scheme |
||||
Yang Guo : DLPNO-NEVPT2, F12-NEVPT2, CIM, IAO-localization |
||||
Andreas Hansen : Spin unrestricted coupled pair/coupled cluster methods |
||||
Benjamin Helmich-Paris : MC-RPA, TRAH-SCF, COSX integrals |
||||
Lee Huntington : MR-EOM, pCC |
||||
Robert Izsak : Overlap fitted RIJCOSX, COSX-SCS-MP3, EOM |
||||
Marcus Kettner : VPT2 |
||||
Christian Kollmar : KDIIS, OOCD, Brueckner-CCSD(T), CCSD density, CASPT2, CASPT2-K |
||||
Simone Kossmann : Meta GGA functionals, TD-DFT gradient, OOMP2, MP2 Hessian |
||||
Martin Krupicka : Initial AUTO-CI |
||||
Lucas Lang : DCDCAS |
||||
Marvin Lechner : AUTO-CI (C++ implementation), FIC-MRCC |
||||
Dagmar Lenk : GEPOL surface, SMD |
||||
Dimitrios Liakos : Extrapolation schemes; Compound Job, initial MDCI parallelization |
||||
Dimitrios Manganas : Further ROCIS development; embedding schemes |
||||
Dimitrios Pantazis : SARC Basis sets |
||||
Anastasios Papadopoulos: AUTO-CI, single reference methods and gradients |
||||
Taras Petrenko : DFT Hessian,TD-DFT gradient, ASA, ECA, R-Raman, ABS, FL, XAS/XES, NRVS |
||||
Peter Pinski : DLPNO-MP2, DLPNO-MP2 Gradient |
||||
Christoph Reimann : Effective Core Potentials |
||||
Marius Retegan : Local ZFS, SOC |
||||
Christoph Riplinger : Optimizer, TS searches, QM/MM, DLPNO-CCSD(T), (RO)-DLPNO pert. Triples |
||||
Tobias Risthaus : Range-separated hybrids, TD-DFT gradient, RPA, STAB |
||||
Michael Roemelt : Original ROCIS implementation |
||||
Masaaki Saitow : Open-shell DLPNO-CCSD energy and density |
||||
Barbara Sandhoefer : DKH picture change effects |
||||
Avijit Sen : IP-ROCIS |
||||
Kantharuban Sivalingam : CASSCF convergence, NEVPT2, FIC-MRCI |
||||
Bernardo de Souza : ESD, SOC TD-DFT |
||||
Georgi Stoychev : AutoAux, RI-MP2 NMR, DLPNO-MP2 response |
||||
Willem Van den Heuvel : Paramagnetic NMR |
||||
Boris Wezisla : Elementary symmetry handling |
||||
Frank Wennmohs : Technical directorship |
||||
|
||||
|
||||
We gratefully acknowledge several colleagues who have allowed us to |
||||
interface, adapt or use parts of their codes: |
||||
Stefan Grimme, W. Hujo, H. Kruse, P. Pracht, : VdW corrections, initial TS optimization, |
||||
C. Bannwarth, S. Ehlert DFT functionals, gCP, sTDA/sTD-DF |
||||
Ed Valeev, F. Pavosevic, A. Kumar : LibInt (2-el integral package), F12 methods |
||||
Garnet Chan, S. Sharma, J. Yang, R. Olivares : DMRG |
||||
Ulf Ekstrom : XCFun DFT Library |
||||
Mihaly Kallay : mrcc (arbitrary order and MRCC methods) |
||||
Jiri Pittner, Ondrej Demel : Mk-CCSD |
||||
Frank Weinhold : gennbo (NPA and NBO analysis) |
||||
Christopher J. Cramer and Donald G. Truhlar : smd solvation model |
||||
Lars Goerigk : TD-DFT with DH, B97 family of functionals |
||||
V. Asgeirsson, H. Jonsson : NEB implementation |
||||
FAccTs GmbH : IRC, NEB, NEB-TS, DLPNO-Multilevel, CI-OPT |
||||
MM, QMMM, 2- and 3-layer-ONIOM, Crystal-QMMM, |
||||
LR-CPCM, SF, NACMEs, symmetry and pop. for TD-DFT, |
||||
nearIR, NL-DFT gradient (VV10), updates on ESD, |
||||
ML-optimized integration grids |
||||
S Lehtola, MJT Oliveira, MAL Marques : LibXC Library |
||||
Liviu Ungur et al : ANISO software |
||||
|
||||
|
||||
Your calculation uses the libint2 library for the computation of 2-el integrals |
||||
For citations please refer to: http://libint.valeyev.net |
||||
|
||||
Your ORCA version has been built with support for libXC version: 5.1.0 |
||||
For citations please refer to: https://tddft.org/programs/libxc/ |
||||
|
||||
This ORCA versions uses: |
||||
CBLAS interface : Fast vector & matrix operations |
||||
LAPACKE interface : Fast linear algebra routines |
||||
SCALAPACK package : Parallel linear algebra routines |
||||
Shared memory : Shared parallel matrices |
||||
BLAS/LAPACK : OpenBLAS 0.3.15 USE64BITINT DYNAMIC_ARCH NO_AFFINITY SkylakeX SINGLE_THREADED |
||||
Core in use : SkylakeX |
||||
Copyright (c) 2011-2014, The OpenBLAS Project |
||||
|
||||
|
||||
|
||||
|
||||
*************************************** |
||||
The coordinates will be read from file: cmmd.xyz |
||||
*************************************** |
||||
|
||||
|
||||
Your calculation utilizes the semiempirical GFN2-xTB method |
||||
Please cite in your paper: |
||||
C. Bannwarth, Ehlert S., S. Grimme, J. Chem. Theory Comput., 15, (2019), 1652. |
||||
|
||||
|
||||
================================================================================ |
||||
|
||||
================================================================================ |
||||
WARNINGS |
||||
Please study these warnings very carefully! |
||||
================================================================================ |
||||
|
||||
WARNING: Old DensityContainer found on disk! |
||||
Will remove this file - |
||||
If you want to keep old densities, please start your calculation with a different basename. |
||||
|
||||
WARNING: Gradients needed for Numerical Frequencies |
||||
===> : Setting RunTyp to EnGrad |
||||
|
||||
WARNING: Found dipole moment calculation with XTB calculation |
||||
===> : Switching off dipole moment calculation |
||||
|
||||
|
||||
WARNING: TRAH-SCF for XTB is not implemented! |
||||
===> : Turning TRAH off! |
||||
|
||||
================================================================================ |
||||
INPUT FILE |
||||
================================================================================ |
||||
NAME = cmmd.in |
||||
| 1> #CMMDE generated Orca input file |
||||
| 2> !XTB2 Numfreq |
||||
| 3> %pal |
||||
| 4> nprocs 1 |
||||
| 5> end |
||||
| 6> |
||||
| 7> *xyzfile 0 1 cmmd.xyz |
||||
| 8> |
||||
| 9> %freq |
||||
| 10> scalfreq 1 |
||||
| 11> Temp 298.15 |
||||
| 12> Pressure 1.0 |
||||
| 13> end |
||||
| 14> |
||||
| 15> ****END OF INPUT**** |
||||
================================================================================ |
||||
|
||||
******************************* |
||||
* Energy+Gradient Calculation * |
||||
******************************* |
||||
|
||||
----------------------------------------------------------- |
||||
| ===================== | |
||||
| x T B | |
||||
| ===================== | |
||||
| S. Grimme | |
||||
| Mulliken Center for Theoretical Chemistry | |
||||
| University of Bonn | |
||||
| Aditya W. Sakti | |
||||
| Departemen Kimia | |
||||
| Universitas Pertamina | |
||||
----------------------------------------------------------- |
||||
|
||||
* xtb version 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54) compiled by '@Linux' on 12/03/2021 |
||||
|
||||
xtb is free software: you can redistribute it and/or modify it under |
||||
the terms of the GNU Lesser General Public License as published by |
||||
the Free Software Foundation, either version 3 of the License, or |
||||
(at your option) any later version. |
||||
|
||||
xtb is distributed in the hope that it will be useful, |
||||
but WITHOUT ANY WARRANTY; without even the implied warranty of |
||||
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
||||
GNU Lesser General Public License for more details. |
||||
|
||||
Cite this work as: |
||||
* C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht, |
||||
J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11, |
||||
e01493. DOI: 10.1002/wcms.1493 |
||||
|
||||
for GFN2-xTB: |
||||
* C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019, |
||||
15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176 |
||||
for GFN1-xTB: |
||||
* S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017, |
||||
13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118 |
||||
for GFN0-xTB: |
||||
* P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint. |
||||
DOI: 10.26434/chemrxiv.8326202.v1 |
||||
for GFN-FF: |
||||
* S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673. |
||||
DOI: 10.1002/anie.202004239 |
||||
|
||||
for ALPB and GBSA implicit solvation: |
||||
* S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput., |
||||
2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471 |
||||
|
||||
for DFT-D4: |
||||
* E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017, |
||||
147, 034112. DOI: 10.1063/1.4993215 |
||||
* E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher, |
||||
C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122. |
||||
DOI: 10.1063/1.5090222 |
||||
* E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys. |
||||
2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A |
||||
|
||||
for sTDA-xTB: |
||||
* S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103. |
||||
DOI: 10.1063/1.4959605 |
||||
|
||||
in the mass-spec context: |
||||
* V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879. |
||||
DOI: 10.1039/c7sc00601b |
||||
* J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133. |
||||
DOI: 10.1021/acsomega.9b02011 |
||||
|
||||
for metadynamics refer to: |
||||
* S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862 |
||||
DOI: 10.1021/acs.jctc.9b00143 |
||||
|
||||
for SPH calculations refer to: |
||||
* S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714 |
||||
DOI: 10.1021/acs.jctc.0c01306 |
||||
|
||||
with help from (in alphabetical order) |
||||
P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher |
||||
M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, J. Koopman |
||||
C. Lavigne, S. Lehtola, F. März, M. Müller, F. Musil, H. Neugebauer |
||||
J. Pisarek, C. Plett, P. Pracht, J. Seibert, P. Shushkov, S. Spicher |
||||
M. Stahn, M. Steiner, T. Strunk, J. Stückrath, T. Rose, and J. Unsleber |
||||
|
||||
* started run on 2022/04/28 at 11:27:15.724 |
||||
|
||||
------------------------------------------------- |
||||
| Calculation Setup | |
||||
------------------------------------------------- |
||||
|
||||
program call : /home/adit/opt/orca/otool_xtb cmmd_XTB.xyz --grad -c 0 -u 0 -P 1 --namespace cmmd --input cmmd_XTB.input.tmp --acc 1.000000 |
||||
hostname : compute |
||||
calculation namespace : cmmd |
||||
coordinate file : cmmd_XTB.xyz |
||||
number of atoms : 5 |
||||
number of electrons : 8 |
||||
charge : 0 |
||||
spin : 0.0 |
||||
first test random number : 0.45806096902679 |
||||
|
||||
ID Z sym. atoms |
||||
1 6 C 1 |
||||
2 1 H 2-5 |
||||
|
||||
------------------------------------------------- |
||||
| G F N 2 - x T B | |
||||
------------------------------------------------- |
||||
|
||||
Reference 10.1021/acs.jctc.8b01176 |
||||
* Hamiltonian: |
||||
H0-scaling (s, p, d) 1.850000 2.230000 2.230000 |
||||
zeta-weighting 0.500000 |
||||
* Dispersion: |
||||
s8 2.700000 |
||||
a1 0.520000 |
||||
a2 5.000000 |
||||
s9 5.000000 |
||||
* Repulsion: |
||||
kExp 1.500000 1.000000 |
||||
rExp 1.000000 |
||||
* Coulomb: |
||||
alpha 2.000000 |
||||
third order shell-resolved |
||||
anisotropic true |
||||
a3 3.000000 |
||||
a5 4.000000 |
||||
cn-shift 1.200000 |
||||
cn-exp 4.000000 |
||||
max-rad 5.000000 |
||||
|
||||
|
||||
................................................... |
||||
: SETUP : |
||||
:.................................................: |
||||
: # basis functions 8 : |
||||
: # atomic orbitals 8 : |
||||
: # shells 6 : |
||||
: # electrons 8 : |
||||
: max. iterations 250 : |
||||
: Hamiltonian GFN2-xTB : |
||||
: restarted? false : |
||||
: GBSA solvation false : |
||||
: PC potential false : |
||||
: electronic temp. 300.0000000 K : |
||||
: accuracy 1.0000000 : |
||||
: -> integral cutoff 0.2500000E+02 : |
||||
: -> integral neglect 0.1000000E-07 : |
||||
: -> SCF convergence 0.1000000E-05 Eh : |
||||
: -> wf. convergence 0.1000000E-03 e : |
||||
: Broyden damping 0.4000000 : |
||||
................................................... |
||||
|
||||
iter E dE RMSdq gap omega full diag |
||||
1 -4.2239587 -0.422396E+01 0.248E+00 16.90 0.0 T |
||||
2 -4.2374347 -0.134760E-01 0.912E-01 16.71 1.0 T |
||||
3 -4.2375727 -0.137987E-03 0.506E-01 16.61 1.0 T |
||||
4 -4.2376226 -0.499077E-04 0.100E-01 16.49 1.0 T |
||||
5 -4.2376226 0.183268E-07 0.539E-03 16.49 8.3 T |
||||
6 -4.2376227 -0.794093E-07 0.166E-04 16.49 269.4 T |
||||
7 -4.2376227 -0.834559E-10 0.196E-06 16.49 22792.6 T |
||||
|
||||
*** convergence criteria satisfied after 7 iterations *** |
||||
|
||||
# Occupation Energy/Eh Energy/eV |
||||
------------------------------------------------------------- |
||||
1 2.0000 -0.5788386 -15.7510 |
||||
2 2.0000 -0.4661696 -12.6851 |
||||
3 2.0000 -0.4661655 -12.6850 |
||||
4 2.0000 -0.4661594 -12.6848 (HOMO) |
||||
5 0.1398593 3.8058 (LUMO) |
||||
6 0.2020304 5.4975 |
||||
7 0.2020678 5.4985 |
||||
8 0.2021139 5.4998 |
||||
------------------------------------------------------------- |
||||
HL-Gap 0.6060187 Eh 16.4906 eV |
||||
Fermi-level -0.1631500 Eh -4.4395 eV |
||||
|
||||
SCC (total) 0 d, 0 h, 0 min, 0.023 sec |
||||
SCC setup ... 0 min, 0.000 sec ( 1.260%) |
||||
Dispersion ... 0 min, 0.000 sec ( 0.106%) |
||||
classical contributions ... 0 min, 0.000 sec ( 0.058%) |
||||
integral evaluation ... 0 min, 0.001 sec ( 2.896%) |
||||
iterations ... 0 min, 0.021 sec ( 94.189%) |
||||
molecular gradient ... 0 min, 0.000 sec ( 0.973%) |
||||
printout ... 0 min, 0.000 sec ( 0.466%) |
||||
|
||||
::::::::::::::::::::::::::::::::::::::::::::::::::::: |
||||
:: SUMMARY :: |
||||
::::::::::::::::::::::::::::::::::::::::::::::::::::: |
||||
:: total energy -4.174453278189 Eh :: |
||||
:: gradient norm 0.022735966218 Eh/a0 :: |
||||
:: HOMO-LUMO gap 16.490609280094 eV :: |
||||
::.................................................:: |
||||
:: SCC energy -4.237622656391 Eh :: |
||||
:: -> isotropic ES 0.001892323517 Eh :: |
||||
:: -> anisotropic ES 0.002670073781 Eh :: |
||||
:: -> anisotropic XC 0.004009252448 Eh :: |
||||
:: -> dispersion -0.000663926968 Eh :: |
||||
:: repulsion energy 0.063169371945 Eh :: |
||||
:: add. restraining 0.000000000000 Eh :: |
||||
:: total charge 0.000000000000 e :: |
||||
::::::::::::::::::::::::::::::::::::::::::::::::::::: |
||||
|
||||
|
||||
Property printout bound to 'properties.out' |
||||
|
||||
------------------------------------------------- |
||||
| TOTAL ENERGY -4.174453278189 Eh | |
||||
| GRADIENT NORM 0.022735966218 Eh/α | |
||||
| HOMO-LUMO GAP 16.490609280094 eV | |
||||
------------------------------------------------- |
||||
|
||||
------------------------------------------------------------------------ |
||||
* finished run on 2022/04/28 at 11:27:15.762 |
||||
------------------------------------------------------------------------ |
||||
total: |
||||
* wall-time: 0 d, 0 h, 0 min, 0.038 sec |
||||
* cpu-time: 0 d, 0 h, 0 min, 0.009 sec |
||||
* ratio c/w: 0.247 speedup |
||||
SCF: |
||||
* wall-time: 0 d, 0 h, 0 min, 0.023 sec |
||||
* cpu-time: 0 d, 0 h, 0 min, 0.002 sec |
||||
* ratio c/w: 0.094 speedup |
||||
|
||||
|
||||
------------------------- -------------------- |
||||
FINAL SINGLE POINT ENERGY -4.174453278190 |
||||
------------------------- -------------------- |
||||
|
||||
|
||||
---------------------------------------------------------------------------- |
||||
ORCA NUMERICAL FREQUENCIES |
||||
---------------------------------------------------------------------------- |
||||
|
||||
Number of atoms ... 5 |
||||
Central differences ... used |
||||
Number of displacements ... 30 |
||||
Numerical increment ... 5.000e-03 bohr |
||||
IR-spectrum generation ... on |
||||
Raman-spectrum generation ... off |
||||
Surface Crossing Hessian ... off |
||||
|
||||
The output will be reduced. Please look at the following files: |
||||
SCF program output ... >cmmd.lastscf |
||||
Integral program output ... >cmmd.lastint |
||||
Gradient program output ... >cmmd.lastgrad |
||||
Dipole moment program output ... >cmmd.lastmom |
||||
AutoCI program output ... >cmmd.lastautoci |
||||
|
||||
<< Calculating on displaced geometry 1 (of 30) >> |
||||
<< Calculating on displaced geometry 2 (of 30) >> |
||||
<< Calculating on displaced geometry 3 (of 30) >> |
||||
<< Calculating on displaced geometry 4 (of 30) >> |
||||
<< Calculating on displaced geometry 5 (of 30) >> |
||||
<< Calculating on displaced geometry 6 (of 30) >> |
||||
<< Calculating on displaced geometry 7 (of 30) >> |
||||
<< Calculating on displaced geometry 8 (of 30) >> |
||||
<< Calculating on displaced geometry 9 (of 30) >> |
||||
<< Calculating on displaced geometry 10 (of 30) >> |
||||
<< Calculating on displaced geometry 11 (of 30) >> |
||||
<< Calculating on displaced geometry 12 (of 30) >> |
||||
<< Calculating on displaced geometry 13 (of 30) >> |
||||
<< Calculating on displaced geometry 14 (of 30) >> |
||||
<< Calculating on displaced geometry 15 (of 30) >> |
||||
<< Calculating on displaced geometry 16 (of 30) >> |
||||
<< Calculating on displaced geometry 17 (of 30) >> |
||||
<< Calculating on displaced geometry 18 (of 30) >> |
||||
<< Calculating on displaced geometry 19 (of 30) >> |
||||
<< Calculating on displaced geometry 20 (of 30) >> |
||||
<< Calculating on displaced geometry 21 (of 30) >> |
||||
<< Calculating on displaced geometry 22 (of 30) >> |
||||
<< Calculating on displaced geometry 23 (of 30) >> |
||||
<< Calculating on displaced geometry 24 (of 30) >> |
||||
<< Calculating on displaced geometry 25 (of 30) >> |
||||
<< Calculating on displaced geometry 26 (of 30) >> |
||||
<< Calculating on displaced geometry 27 (of 30) >> |
||||
<< Calculating on displaced geometry 28 (of 30) >> |
||||
<< Calculating on displaced geometry 29 (of 30) >> |
||||
<< Calculating on displaced geometry 30 (of 30) >> |
||||
|
||||
----------------------- |
||||
VIBRATIONAL FREQUENCIES |
||||
----------------------- |
||||
|
||||
Scaling factor for frequencies = 1.000000000 (already applied!) |
||||
|
||||
0: 0.00 cm**-1 |
||||
1: 0.00 cm**-1 |
||||
2: 0.00 cm**-1 |
||||
3: 0.00 cm**-1 |
||||
4: 0.00 cm**-1 |
||||
5: 0.00 cm**-1 |
||||
6: 1411.89 cm**-1 |
||||
7: 1411.94 cm**-1 |
||||
8: 1411.99 cm**-1 |
||||
9: 1567.72 cm**-1 |
||||
10: 1567.76 cm**-1 |
||||
11: 2918.15 cm**-1 |
||||
12: 2930.72 cm**-1 |
||||
13: 2930.81 cm**-1 |
||||
14: 2931.00 cm**-1 |
||||
|
||||
|
||||
------------ |
||||
NORMAL MODES |
||||
------------ |
||||
|
||||
These modes are the cartesian displacements weighted by the diagonal matrix |
||||
M(i,i)=1/sqrt(m[i]) where m[i] is the mass of the displaced atom |
||||
Thus, these vectors are normalized but *not* orthogonal |
||||
|
||||
0 1 2 3 4 5 |
||||
0 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 |
||||
1 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 |
||||
2 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 |
||||
3 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 |
||||
4 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 |
||||
5 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 |
||||
6 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 |
||||
7 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 |
||||
8 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 |
||||
9 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 |
||||
10 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 |
||||
11 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 |
||||
12 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 |
||||
13 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 |
||||
14 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 |
||||
6 7 8 9 10 11 |
||||
0 0.096478 0.069838 0.050248 0.000010 0.000019 -0.000055 |
||||
1 -0.065244 0.108600 -0.025674 -0.000011 0.000021 0.000069 |
||||
2 -0.056089 -0.006199 0.116297 -0.000008 0.000010 -0.000696 |
||||
3 0.042224 0.030585 0.022027 0.000012 0.000026 0.500511 |
||||
4 0.305743 -0.508952 0.120378 0.421773 -0.268725 0.000037 |
||||
5 0.262927 0.029150 -0.545087 -0.268591 -0.421762 -0.000327 |
||||
6 -0.446639 -0.356444 -0.016705 0.373142 0.287917 -0.164413 |
||||
7 0.300443 -0.481324 -0.089851 -0.242470 0.406776 0.157892 |
||||
8 0.277956 -0.048142 0.037122 -0.227772 0.038608 -0.437685 |
||||
9 -0.260471 -0.392619 -0.323373 0.062794 -0.467329 -0.168200 |
||||
10 -0.043851 -0.389729 0.280677 -0.364444 -0.157488 0.306787 |
||||
11 -0.151661 0.170456 -0.355091 0.336493 -0.083277 0.363261 |
||||
12 -0.484714 -0.113693 -0.280683 -0.436070 0.179158 -0.167245 |
||||
13 0.215094 0.085959 -0.005280 0.185271 0.019192 -0.465534 |
||||
14 0.279111 -0.077600 -0.522699 0.159961 0.466316 0.083050 |
||||
12 13 14 |
||||
0 -0.041799 -0.067804 0.034456 |
||||
1 0.060729 -0.053426 -0.031456 |
||||
2 0.045783 0.008959 0.073182 |
||||
3 0.416362 0.672865 -0.337751 |
||||
4 0.029774 -0.026169 -0.015414 |
||||
5 0.022464 0.004421 0.035838 |
||||
6 -0.046171 -0.041860 -0.284313 |
||||
7 0.054430 -0.017894 0.273820 |
||||
8 -0.045893 -0.018572 -0.765458 |
||||
9 0.269741 -0.045258 0.092312 |
||||
10 -0.499633 -0.004259 -0.152995 |
||||
11 -0.605082 0.030381 -0.127224 |
||||
12 -0.141875 0.222181 0.119183 |
||||
13 -0.308202 0.684923 0.269413 |
||||
14 0.082978 -0.122986 -0.015165 |
||||
|
||||
|
||||
----------- |
||||
IR SPECTRUM |
||||
----------- |
||||
|
||||
Mode freq eps Int T**2 TX TY TZ |
||||
cm**-1 L/(mol*cm) km/mol a.u. |
||||
---------------------------------------------------------------------------- |
||||
6: 1411.89 0.000735 3.72 0.000163 (-0.001597 -0.008137 -0.009685) |
||||
7: 1411.94 0.000436 2.20 0.000096 (-0.001157 -0.003252 0.009192) |
||||
8: 1411.99 0.000207 1.05 0.000046 (-0.000833 0.000200 -0.006713) |
||||
9: 1567.72 0.001550 7.83 0.000308 (-0.000000 -0.007232 0.016004) |
||||
10: 1567.76 0.000015 0.08 0.000003 (-0.000001 -0.000749 0.001567) |
||||
11: 2918.15 0.004195 21.20 0.000449 (-0.014320 0.013320 0.008134) |
||||
12: 2930.72 0.002517 12.72 0.000268 (-0.011427 0.008458 0.008116) |
||||
13: 2930.81 0.006524 32.97 0.000695 (-0.018466 -0.018797 0.000568) |
||||
14: 2931.00 0.006335 32.01 0.000674 ( 0.009269 -0.007394 0.023106) |
||||
|
||||
* The epsilon (eps) is given for a Dirac delta lineshape. |
||||
** The dipole moment derivative (T) already includes vibrational overlap. |
||||
|
||||
The first frequency considered to be a vibration is 6 |
||||
The total number of vibrations considered is 9 |
||||
|
||||
|
||||
-------------------------- |
||||
THERMOCHEMISTRY AT 298.15K |
||||
-------------------------- |
||||
|
||||
Temperature ... 298.15 K |
||||
Pressure ... 1.00 atm |
||||
Total Mass ... 16.04 AMU |
||||
|
||||
Throughout the following assumptions are being made: |
||||
(1) The electronic state is orbitally nondegenerate |
||||
(2) There are no thermally accessible electronically excited states |
||||
(3) Hindered rotations indicated by low frequency modes are not |
||||
treated as such but are treated as vibrations and this may |
||||
cause some error |
||||
(4) All equations used are the standard statistical mechanics |
||||
equations for an ideal gas |
||||
(5) All vibrations are strictly harmonic |
||||
|
||||
freq. 1411.89 E(vib) ... 0.00 |
||||
freq. 1411.94 E(vib) ... 0.00 |
||||
freq. 1411.99 E(vib) ... 0.00 |
||||
freq. 1567.72 E(vib) ... 0.00 |
||||
freq. 1567.76 E(vib) ... 0.00 |
||||
freq. 2918.15 E(vib) ... 0.00 |
||||
freq. 2930.72 E(vib) ... 0.00 |
||||
freq. 2930.81 E(vib) ... 0.00 |
||||
freq. 2931.00 E(vib) ... 0.00 |
||||
|
||||
------------ |
||||
INNER ENERGY |
||||
------------ |
||||
|
||||
The inner energy is: U= E(el) + E(ZPE) + E(vib) + E(rot) + E(trans) |
||||
E(el) - is the total energy from the electronic structure calculation |
||||
= E(kin-el) + E(nuc-el) + E(el-el) + E(nuc-nuc) |
||||
E(ZPE) - the the zero temperature vibrational energy from the frequency calculation |
||||
E(vib) - the the finite temperature correction to E(ZPE) due to population |
||||
of excited vibrational states |
||||
E(rot) - is the rotational thermal energy |
||||
E(trans)- is the translational thermal energy |
||||
|
||||
Summary of contributions to the inner energy U: |
||||
Electronic energy ... -4.17445328 Eh |
||||
Zero point energy ... 0.04347196 Eh 27.28 kcal/mol |
||||
Thermal vibrational correction ... 0.00002868 Eh 0.02 kcal/mol |
||||
Thermal rotational correction ... 0.00141627 Eh 0.89 kcal/mol |
||||
Thermal translational correction ... 0.00141627 Eh 0.89 kcal/mol |
||||
----------------------------------------------------------------------- |
||||
Total thermal energy -4.12812009 Eh |
||||
|
||||
|
||||
Summary of corrections to the electronic energy: |
||||
(perhaps to be used in another calculation) |
||||
Total thermal correction 0.00286122 Eh 1.80 kcal/mol |
||||
Non-thermal (ZPE) correction 0.04347196 Eh 27.28 kcal/mol |
||||
----------------------------------------------------------------------- |
||||
Total correction 0.04633319 Eh 29.07 kcal/mol |
||||
|
||||
|
||||
-------- |
||||
ENTHALPY |
||||
-------- |
||||
|
||||
The enthalpy is H = U + kB*T |
||||
kB is Boltzmann's constant |
||||
Total free energy ... -4.12812009 Eh |
||||
Thermal Enthalpy correction ... 0.00094421 Eh 0.59 kcal/mol |
||||
----------------------------------------------------------------------- |
||||
Total Enthalpy ... -4.12717588 Eh |
||||
|
||||
|
||||
Note: Rotational entropy computed according to Herzberg |
||||
Infrared and Raman Spectra, Chapter V,1, Van Nostrand Reinhold, 1945 |
||||
Point Group: Td, Symmetry Number: 12 |
||||
Rotational constants in cm-1: 5.186502 5.186421 5.186221 |
||||
|
||||
Vibrational entropy computed according to the QRRHO of S. Grimme |
||||
Chem.Eur.J. 2012 18 9955 |
||||
|
||||
|
||||
------- |
||||
ENTROPY |
||||
------- |
||||
|
||||
The entropy contributions are T*S = T*(S(el)+S(vib)+S(rot)+S(trans)) |
||||
S(el) - electronic entropy |
||||
S(vib) - vibrational entropy |
||||
S(rot) - rotational entropy |
||||
S(trans)- translational entropy |
||||
The entropies will be listed as multiplied by the temperature to get |
||||
units of energy |
||||
|
||||
Electronic entropy ... 0.00000000 Eh 0.00 kcal/mol |
||||
Vibrational entropy ... 0.00003278 Eh 0.02 kcal/mol |
||||
Rotational entropy ... 0.00483337 Eh 3.03 kcal/mol |
||||
Translational entropy ... 0.01627961 Eh 10.22 kcal/mol |
||||
----------------------------------------------------------------------- |
||||
Final entropy term ... 0.02114577 Eh 13.27 kcal/mol |
||||
|
||||
In case the symmetry of your molecule has not been determined correctly |
||||
or in case you have a reason to use a different symmetry number we print |
||||
out the resulting rotational entropy values for sn=1,12 : |
||||
-------------------------------------------------------- |
||||
| sn= 1 | S(rot)= 0.00717958 Eh 4.51 kcal/mol| |
||||
| sn= 2 | S(rot)= 0.00652512 Eh 4.09 kcal/mol| |
||||
| sn= 3 | S(rot)= 0.00614229 Eh 3.85 kcal/mol| |
||||
| sn= 4 | S(rot)= 0.00587066 Eh 3.68 kcal/mol| |
||||
| sn= 5 | S(rot)= 0.00565998 Eh 3.55 kcal/mol| |
||||
| sn= 6 | S(rot)= 0.00548783 Eh 3.44 kcal/mol| |
||||
| sn= 7 | S(rot)= 0.00534228 Eh 3.35 kcal/mol| |
||||
| sn= 8 | S(rot)= 0.00521621 Eh 3.27 kcal/mol| |
||||
| sn= 9 | S(rot)= 0.00510500 Eh 3.20 kcal/mol| |
||||
| sn=10 | S(rot)= 0.00500552 Eh 3.14 kcal/mol| |
||||
| sn=11 | S(rot)= 0.00491553 Eh 3.08 kcal/mol| |
||||
| sn=12 | S(rot)= 0.00483337 Eh 3.03 kcal/mol| |
||||
-------------------------------------------------------- |
||||
|
||||
|
||||
------------------- |
||||
GIBBS FREE ENERGY |
||||
------------------- |
||||
|
||||
The Gibbs free energy is G = H - T*S |
||||
|
||||
Total enthalpy ... -4.12717588 Eh |
||||
Total entropy correction ... -0.02114577 Eh -13.27 kcal/mol |
||||
----------------------------------------------------------------------- |
||||
Final Gibbs free energy ... -4.14832165 Eh |
||||
|
||||
For completeness - the Gibbs free energy minus the electronic energy |
||||
G-E(el) ... 0.02613163 Eh 16.40 kcal/mol |
||||
|
||||
|
||||
|
||||
Timings for individual modules: |
||||
|
||||
Sum of individual times ... 63.124 sec (= 1.052 min) |
||||
Numerical frequency calculation ... 63.060 sec (= 1.051 min) 99.9 % |
||||
XTB module ... 0.064 sec (= 0.001 min) 0.1 % |
||||
****ORCA TERMINATED NORMALLY**** |
||||
TOTAL RUN TIME: 0 days 0 hours 1 minutes 3 seconds 189 msec |
||||
Binary file not shown.
@ -0,0 +1,7 @@ |
||||
5 |
||||
Coordinates from ORCA-job cmmd |
||||
C 0.95687316815352 -0.06112204544860 -0.06641298744721 |
||||
H 2.05652198640884 -0.06109756530571 -0.06634976471074 |
||||
H 0.59033246206982 0.29086224198130 -1.04156303288977 |
||||
H 0.59037415480610 0.60741379222750 0.72603912396949 |
||||
H 0.59032822856172 -1.08163642345449 0.11639666107824 |
||||
@ -0,0 +1,48 @@ |
||||
------------------------------------------------------------- |
||||
----------------------- !PROPERTIES! ------------------------ |
||||
------------------------------------------------------------- |
||||
# ----------------------------------------------------------- |
||||
$ THERMOCHEMISTRY_Energies |
||||
description: The Thermochemistry energies |
||||
geom. index: 0 |
||||
prop. index: 1 |
||||
Temperature (Kelvin) : 298.1500000000 |
||||
Pressure (atm) : 1.0000000000 |
||||
Total Mass (AMU) : 16.0430000000 |
||||
Spin Degeneracy : 1.0000000000 |
||||
Electronic Energy (Hartree) : -4.1744532782 |
||||
Translational Energy (Hartree) : 0.0014162714 |
||||
Rotational Energy (Hartree) : 0.0014162714 |
||||
Vibrational Energy (Hartree) : 0.0000286783 |
||||
Number of frequencies : 15 |
||||
Scaling Factor for frequencies : 1.0000000000 |
||||
Vibrational frequencies : |
||||
0 |
||||
0 0.000000 |
||||
1 0.000000 |
||||
2 0.000000 |
||||
3 0.000000 |
||||
4 0.000000 |
||||
5 0.000000 |
||||
6 1411.894158 |
||||
7 1411.942387 |
||||
8 1411.989208 |
||||
9 1567.724975 |
||||
10 1567.756664 |
||||
11 2918.147432 |
||||
12 2930.722274 |
||||
13 2930.813685 |
||||
14 2930.996046 |
||||
Zero Point Energy (Hartree) : 0.0434719647 |
||||
Inner Energy (Hartree) : -4.1281200924 |
||||
Enthalpy (Hartree) : -4.1271758833 |
||||
Electronic entropy : 0.0000000000 |
||||
Rotational entropy : 0.0048333747 |
||||
Vibrational entropy : 0.0000327813 |
||||
Translational entropy : 0.0048333747 |
||||
Entropy : 0.0211457665 |
||||
Gibbs Energy (Hartree) : -4.1483216498 |
||||
Is Linear : false |
||||
# ------------------------------------------------------------- |
||||
----------------------- !GEOMETRIES! ------------------------ |
||||
# ------------------------------------------------------------- |
||||
@ -0,0 +1,21 @@ |
||||
5 |
||||
Coordinates from ORCA-job cmmd E -40.451784938188 |
||||
C 0.956890 -0.061120 -0.066380 |
||||
H 2.049080 -0.061120 -0.066380 |
||||
H 0.592820 0.288480 -1.034950 |
||||
H 0.592820 0.602900 0.720670 |
||||
H 0.592820 -1.074720 0.115150 |
||||
5 |
||||
Coordinates from ORCA-job cmmd E -40.451924540961 |
||||
C 0.956878 -0.061120 -0.066402 |
||||
H 2.056475 -0.061105 -0.066362 |
||||
H 0.590353 0.290846 -1.041510 |
||||
H 0.590377 0.607388 0.725999 |
||||
H 0.590347 -1.081589 0.116385 |
||||
5 |
||||
Coordinates from ORCA-job cmmd E -40.451924547020 |
||||
C 0.956873 -0.061122 -0.066413 |
||||
H 2.056522 -0.061098 -0.066350 |
||||
H 0.590332 0.290862 -1.041563 |
||||
H 0.590374 0.607414 0.726039 |
||||
H 0.590328 -1.081636 0.116397 |
||||
@ -0,0 +1 @@ |
||||
C |
||||
@ -0,0 +1,7 @@ |
||||
5 |
||||
XYZ file generated by Avogadro. |
||||
C -2.23209 1.11879 -0.00000 |
||||
H -1.43210 0.87042 0.66574 |
||||
H -1.90949 1.88312 -0.67574 |
||||
H -2.51738 0.24944 -0.55475 |
||||
H -3.06940 1.47217 0.56475 |
||||
@ -0,0 +1,10 @@ |
||||
#!/bin/bash |
||||
#SBATCH --nodes=1 |
||||
#SBATCH --ntasks=1 |
||||
#SBATCH --cpus-per-task=1 |
||||
#SBATCH --time=168:0:0 |
||||
export LD_LIBRARY_PATH=/home/adit/opt/openmpi411/lib:$LD_LIBRARY_PATH |
||||
export PATH=/home/adit/opt/openmpi411/bin:$PATH |
||||
export OMP_NUM_THREADS=1 |
||||
cd $PWD |
||||
$ORCA_COMMAND cmmd.in > cmmd.out --oversubscribe |
||||
@ -0,0 +1,8 @@ |
||||
#!/bin/bash |
||||
#SBATCH --nodes=1 |
||||
#SBATCH --ntasks=1 |
||||
#SBATCH --cpus-per-task=1 |
||||
#SBATCH --time=168:0:0 |
||||
export OMP_NUM_THREADS=1 |
||||
cd $PWD |
||||
obabel geom.smi -O geom.xyz --gen3d |
||||
@ -0,0 +1 @@ |
||||
1 molecule converted |
||||
@ -0,0 +1,26 @@ |
||||
# |
||||
# Number of atoms |
||||
# |
||||
3 |
||||
# |
||||
# The current total energy in Eh |
||||
# |
||||
-10.306829455250 |
||||
# |
||||
# The current gradient in Eh/bohr |
||||
# |
||||
-0.042660634499 |
||||
-0.000000000306 |
||||
0.000000001629 |
||||
-0.000000242791 |
||||
0.000000000542 |
||||
-0.000000002879 |
||||
0.042660877290 |
||||
-0.000000000236 |
||||
0.000000001251 |
||||
# |
||||
# The atomic numbers and current coordinates in Bohr |
||||
# |
||||
8 2.0516285 0.0008882 0.1843806 |
||||
6 4.2499940 0.0008882 0.1843806 |
||||
8 6.4483597 0.0008882 0.1843806 |
||||
Binary file not shown.
@ -0,0 +1,116 @@ |
||||
|
||||
$orca_hessian_file |
||||
|
||||
$act_atom |
||||
0 |
||||
|
||||
$act_coord |
||||
0 |
||||
|
||||
$act_energy |
||||
-10.306829 |
||||
|
||||
$hessian |
||||
9 |
||||
0 1 2 3 4 |
||||
0 1.0172558866E+00 3.7717939410E-10 -2.0158590912E-09 -9.6522099886E-01 -3.3453629031E-10 |
||||
1 3.7717939410E-10 4.6257550965E-02 7.1422933750E-13 -3.9371313327E-10 -4.8415046700E-02 |
||||
2 -2.0158590912E-09 7.1422933750E-13 4.6257550963E-02 2.1016768163E-09 -2.8402779435E-12 |
||||
3 -9.6522099886E-01 -3.9371313327E-10 2.1016768163E-09 1.9304270433E+00 1.2319228909E-10 |
||||
4 -3.3453629031E-10 -4.8415046700E-02 -2.8402779435E-12 1.2319228909E-10 1.4621391619E-01 |
||||
5 1.7855160986E-09 6.4867390050E-13 -4.8415046685E-02 -6.5106717659E-10 2.0327540885E-12 |
||||
6 -5.2027873836E-02 2.2757391073E-13 1.8907040842E-12 -9.6522007231E-01 2.3591578074E-10 |
||||
7 -2.0432886188E-12 -2.2534365607E-02 2.5381625415E-12 2.6245214419E-10 -4.8415147821E-02 |
||||
8 1.3193083418E-11 -1.1466340465E-12 -2.2534365615E-02 -1.4073202047E-09 2.9823040150E-13 |
||||
5 6 7 8 |
||||
0 1.7855160986E-09 -5.2027873836E-02 -2.0432886188E-12 1.3193083418E-11 |
||||
1 6.4867390050E-13 2.2757391073E-13 -2.2534365607E-02 -1.1466340465E-12 |
||||
2 -4.8415046685E-02 1.8907040842E-12 2.5381625415E-12 -2.2534365615E-02 |
||||
3 -6.5106717659E-10 -9.6522007231E-01 2.6245214419E-10 -1.4073202047E-09 |
||||
4 2.0327540885E-12 2.3591578074E-10 -4.8415147821E-02 2.9823040150E-13 |
||||
5 1.4621391619E-01 -1.2654105292E-09 -3.1249372990E-12 -4.8415147827E-02 |
||||
6 -1.2654105292E-09 1.0172549601E+00 -2.6859343894E-10 1.4374199555E-09 |
||||
7 -3.1249372990E-12 -2.6859343894E-10 4.6257653100E-02 8.7979902001E-13 |
||||
8 -4.8415147827E-02 1.4374199555E-09 8.7979902001E-13 4.6257653101E-02 |
||||
|
||||
$vibrational_frequencies |
||||
9 |
||||
0 0.000000 |
||||
1 0.000000 |
||||
2 0.000000 |
||||
3 0.000000 |
||||
4 0.000000 |
||||
5 600.703532 |
||||
6 600.703532 |
||||
7 1328.912392 |
||||
8 2416.816551 |
||||
|
||||
$normal_modes |
||||
9 9 |
||||
0 1 2 3 4 |
||||
0 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 |
||||
1 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 |
||||
2 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 |
||||
3 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 |
||||
4 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 |
||||
5 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 |
||||
6 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 |
||||
7 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 |
||||
8 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 |
||||
5 6 7 8 |
||||
0 -2.3648407580E-09 -4.6552238897E-10 -7.0710664842E-01 -3.3154792498E-01 |
||||
1 1.2276547308E-01 -3.0798137360E-01 -2.4533875555E-10 -1.9830812166E-10 |
||||
2 -3.0798137360E-01 -1.2276547308E-01 1.3121764702E-09 1.0587844555E-09 |
||||
3 3.0553128916E-10 5.9475780235E-11 -3.5369919662E-07 8.8326227666E-01 |
||||
4 -3.2705431550E-01 8.2048017898E-01 6.5359681247E-10 5.7884064953E-11 |
||||
5 8.2048017898E-01 3.2705431550E-01 -3.4957149607E-09 -3.0583792470E-10 |
||||
6 2.1354678417E-09 4.2087184936E-10 7.0710691395E-01 -3.3154746879E-01 |
||||
7 1.2276545906E-01 -3.0798133843E-01 -2.4533886896E-10 1.5485256168E-10 |
||||
8 -3.0798133843E-01 -1.2276545906E-01 1.3121770764E-09 -8.2918139823E-10 |
||||
|
||||
# |
||||
# The atoms: label mass x y z (in bohrs) |
||||
# |
||||
$atoms |
||||
3 |
||||
O 15.99900 2.051628489027 0.000888170893 0.184380580973 |
||||
C 12.01100 4.249993991510 0.000888172063 0.184380574714 |
||||
O 15.99900 6.448359745030 0.000888170893 0.184380580973 |
||||
|
||||
$actual_temperature |
||||
0.000000 |
||||
|
||||
$frequency_scale_factor |
||||
1.000000 |
||||
|
||||
$dipole_derivatives |
||||
9 |
||||
-1.4000000000E+00 0.0000000000E+00 0.0000000000E+00 |
||||
0.0000000000E+00 -4.0000000000E-01 0.0000000000E+00 |
||||
0.0000000000E+00 0.0000000000E+00 -4.0000000000E-01 |
||||
3.0000000000E+00 0.0000000000E+00 0.0000000000E+00 |
||||
0.0000000000E+00 8.0000000000E-01 0.0000000000E+00 |
||||
0.0000000000E+00 0.0000000000E+00 8.0000000000E-01 |
||||
-1.4000000000E+00 0.0000000000E+00 0.0000000000E+00 |
||||
0.0000000000E+00 -4.0000000000E-01 0.0000000000E+00 |
||||
0.0000000000E+00 0.0000000000E+00 -4.0000000000E-01 |
||||
|
||||
# |
||||
# The IR spectrum |
||||
# wavenumber eps Int TX TY TZ |
||||
# |
||||
$ir_spectrum |
||||
9 |
||||
0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000 |
||||
0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000 |
||||
0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000 |
||||
0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000 |
||||
0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000 |
||||
600.70 0.01413744 71.44481416 0.000000 -0.031733 0.079608 |
||||
600.70 0.01413744 71.44481416 0.000000 0.079608 0.031733 |
||||
1328.91 0.00000000 0.00000000 -0.000000 0.000000 -0.000000 |
||||
2416.82 0.19163901 968.46501055 0.157305 0.000000 -0.000000 |
||||
|
||||
|
||||
$end |
||||
|
||||
@ -0,0 +1,13 @@ |
||||
#CMMDE generated Orca input file |
||||
!XTB2 Numfreq |
||||
%pal |
||||
nprocs 1 |
||||
end |
||||
|
||||
*xyzfile 0 1 cmmd.xyz |
||||
|
||||
%freq |
||||
scalfreq 1 |
||||
Temp 298.15 |
||||
Pressure 1.0 |
||||
end |
||||
@ -0,0 +1,119 @@ |
||||
|
||||
$orca_opt_file |
||||
|
||||
$trust |
||||
0.300000000000 |
||||
|
||||
$epredict |
||||
0.000000000000 |
||||
|
||||
$ediffsc |
||||
1000.000000000000 |
||||
|
||||
$ctyp |
||||
3 |
||||
|
||||
$coordinates |
||||
4 9 |
||||
1.98799189 0.00088817 0.18438058 4.24999408 0.00088817 0.18438058 |
||||
6.51199626 0.00088817 0.18438058 |
||||
2.04568896 0.00088817 0.18438058 4.24999407 0.00088817 0.18438058 |
||||
6.45429920 0.00088817 0.18438058 |
||||
2.05236544 0.00088817 0.18438058 4.24999403 0.00088817 0.18438057 |
||||
6.44762275 0.00088817 0.18438058 |
||||
2.05162112 0.00088817 0.18438058 4.24999366 0.00088817 0.18438057 |
||||
6.44836745 0.00088817 0.18438058 |
||||
|
||||
# redundant internal coordinates |
||||
# nbonds nangles ndihedrals nimpropers ncartesians |
||||
# bond definitions A B |
||||
# angle definitions A B C |
||||
# dihedral definitions A B C D |
||||
# improper torsion definitions A B C D |
||||
# cartesian definitions A x/y/z |
||||
$redundant_internals |
||||
2 2 0 0 0 |
||||
1 0 0 |
||||
2 1 0 |
||||
0 1 2 -8 0 |
||||
0 1 2 -4 0 |
||||
$energies |
||||
4 |
||||
-188.3560728084584639 |
||||
-188.3604090030537179 |
||||
-188.3604497811382998 |
||||
-188.3604503522372795 |
||||
|
||||
$gradients |
||||
4 9 |
||||
-0.0660464538439282 0.0000000053304393 0.0000000001716335 0.0000000128165979 |
||||
0.0000000022640539 0.0000000026807788 0.0660464549296912 -0.0000000161230601 |
||||
-0.0000000078716251 |
||||
-0.0068505804958569 0.0000000053495906 -0.0000000149072329 0.0000001199697298 |
||||
-0.0000000003533555 -0.0000000010682996 0.0068504632637335 0.0000000035999274 |
||||
0.0000000055705466 |
||||
0.0008590760165977 0.0000000043006531 -0.0000000143543937 0.0000014546664970 |
||||
0.0000000003891685 -0.0000000038394442 -0.0008605282115356 0.0000000010853741 |
||||
0.0000000041938126 |
||||
-0.0000082136982629 0.0000000047182270 -0.0000000144218323 -0.0000011585474631 |
||||
0.0000000026750576 -0.0000000057815938 0.0000093738124540 0.0000000018118397 |
||||
0.0000000052452088 |
||||
|
||||
$redundant_coords |
||||
4 4 |
||||
2.2620021823037382 2.2620021823037373 3.1415926535897931 3.1415926535897931 |
||||
|
||||
2.2043051168065126 2.2043051239545850 3.1415926535897931 3.1415926535897931 |
||||
|
||||
2.1976285904240038 2.1976287143764415 3.1415926535897931 3.1415926535897931 |
||||
|
||||
2.1983725358524921 2.1983737944425048 3.1415926535897931 3.1415926535897931 |
||||
|
||||
|
||||
$redundant_gradients |
||||
4 4 |
||||
0.0660464584780485 0.0660464502955709 0.0000000025534548 -0.0000000021769249 |
||||
|
||||
0.0068505814083924 0.0068504623511980 -0.0000000015947643 -0.0000000012124678 |
||||
|
||||
-0.0008590751927447 -0.0008605290353886 -0.0000000007682665 -0.0000000004112485 |
||||
|
||||
0.0000082142205056 0.0000093732902113 -0.0000000001966618 0.0000000003977327 |
||||
|
||||
|
||||
$hessian_approx |
||||
9 9 |
||||
0 1 2 3 4 5 |
||||
0 1.150980 -0.000000 0.000000 -1.136192 -0.000002 0.000001 |
||||
1 -0.000000 0.535644 -0.000000 -0.000000 -1.071288 -0.000000 |
||||
2 0.000000 -0.000000 0.535644 0.000000 -0.000000 -1.071288 |
||||
3 -1.136192 -0.000000 0.000000 2.274183 -0.000000 0.000000 |
||||
4 -0.000002 -1.071288 -0.000000 -0.000000 2.142575 -0.000000 |
||||
5 0.000001 -0.000000 -1.071288 0.000000 -0.000000 2.142575 |
||||
6 -0.014788 0.000000 -0.000000 -1.137992 0.000002 -0.000001 |
||||
7 -0.000000 0.535644 -0.000000 -0.000000 -1.071288 -0.000000 |
||||
8 -0.000001 0.000000 0.535644 -0.000000 0.000000 -1.071288 |
||||
6 7 8 |
||||
0 -0.014788 -0.000000 -0.000001 |
||||
1 0.000000 0.535644 0.000000 |
||||
2 -0.000000 -0.000000 0.535644 |
||||
3 -1.137992 -0.000000 -0.000000 |
||||
4 0.000002 -1.071288 0.000000 |
||||
5 -0.000001 -0.000000 -1.071288 |
||||
6 1.152778 0.000000 0.000001 |
||||
7 0.000000 0.535644 0.000000 |
||||
8 0.000001 0.000000 0.535644 |
||||
|
||||
$bmatrix |
||||
4 9 |
||||
0 1 2 3 4 5 |
||||
0 -1.000000 -0.000000 0.000000 1.000000 0.000000 -0.000000 |
||||
1 0.000000 0.000000 0.000000 -1.000000 0.000000 -0.000000 |
||||
2 0.000000 -1.000000 0.000000 -0.000000 2.000000 -0.000000 |
||||
3 0.000000 -0.000000 1.000000 -0.000000 0.000000 -2.000000 |
||||
6 7 8 |
||||
0 0.000000 0.000000 0.000000 |
||||
1 1.000000 -0.000000 0.000000 |
||||
2 -0.000000 -1.000000 0.000000 |
||||
3 -0.000000 0.000000 1.000000 |
||||
|
||||
@ -0,0 +1,647 @@ |
||||
|
||||
***************** |
||||
* O R C A * |
||||
***************** |
||||
|
||||
#, |
||||
### |
||||
#### |
||||
##### |
||||
###### |
||||
########, |
||||
,,################,,,,, |
||||
,,#################################,, |
||||
,,##########################################,, |
||||
,#########################################, ''#####, |
||||
,#############################################,, '####, |
||||
,##################################################,,,,####, |
||||
,###########'''' ''''############################### |
||||
,#####'' ,,,,##########,,,, '''####''' '#### |
||||
,##' ,,,,###########################,,, '## |
||||
' ,,###'''' '''############,,, |
||||
,,##'' '''############,,,, ,,,,,,###'' |
||||
,#'' '''#######################''' |
||||
' ''''####'''' |
||||
,#######, #######, ,#######, ## |
||||
,#' '#, ## ## ,#' '#, #''# ###### ,####, |
||||
## ## ## ,#' ## #' '# # #' '# |
||||
## ## ####### ## ,######, #####, # # |
||||
'#, ,#' ## ## '#, ,#' ,# #, ## #, ,# |
||||
'#######' ## ## '#######' #' '# #####' # '####' |
||||
|
||||
|
||||
|
||||
####################################################### |
||||
# -***- # |
||||
# Department of theory and spectroscopy # |
||||
# Directorship and core code : Frank Neese # |
||||
# Max Planck Institute fuer Kohlenforschung # |
||||
# Kaiser Wilhelm Platz 1 # |
||||
# D-45470 Muelheim/Ruhr # |
||||
# Germany # |
||||
# # |
||||
# All rights reserved # |
||||
# -***- # |
||||
####################################################### |
||||
|
||||
|
||||
Program Version 5.0.2 - RELEASE - |
||||
|
||||
|
||||
With contributions from (in alphabetic order): |
||||
Daniel Aravena : Magnetic Suceptibility |
||||
Michael Atanasov : Ab Initio Ligand Field Theory (pilot matlab implementation) |
||||
Alexander A. Auer : GIAO ZORA, VPT2 properties, NMR spectrum |
||||
Ute Becker : Parallelization |
||||
Giovanni Bistoni : ED, misc. LED, open-shell LED, HFLD |
||||
Martin Brehm : Molecular dynamics |
||||
Dmytro Bykov : SCF Hessian |
||||
Vijay G. Chilkuri : MRCI spin determinant printing, contributions to CSF-ICE |
||||
Dipayan Datta : RHF DLPNO-CCSD density |
||||
Achintya Kumar Dutta : EOM-CC, STEOM-CC |
||||
Dmitry Ganyushin : Spin-Orbit,Spin-Spin,Magnetic field MRCI |
||||
Miquel Garcia : C-PCM and meta-GGA Hessian, CC/C-PCM, Gaussian charge scheme |
||||
Yang Guo : DLPNO-NEVPT2, F12-NEVPT2, CIM, IAO-localization |
||||
Andreas Hansen : Spin unrestricted coupled pair/coupled cluster methods |
||||
Benjamin Helmich-Paris : MC-RPA, TRAH-SCF, COSX integrals |
||||
Lee Huntington : MR-EOM, pCC |
||||
Robert Izsak : Overlap fitted RIJCOSX, COSX-SCS-MP3, EOM |
||||
Marcus Kettner : VPT2 |
||||
Christian Kollmar : KDIIS, OOCD, Brueckner-CCSD(T), CCSD density, CASPT2, CASPT2-K |
||||
Simone Kossmann : Meta GGA functionals, TD-DFT gradient, OOMP2, MP2 Hessian |
||||
Martin Krupicka : Initial AUTO-CI |
||||
Lucas Lang : DCDCAS |
||||
Marvin Lechner : AUTO-CI (C++ implementation), FIC-MRCC |
||||
Dagmar Lenk : GEPOL surface, SMD |
||||
Dimitrios Liakos : Extrapolation schemes; Compound Job, initial MDCI parallelization |
||||
Dimitrios Manganas : Further ROCIS development; embedding schemes |
||||
Dimitrios Pantazis : SARC Basis sets |
||||
Anastasios Papadopoulos: AUTO-CI, single reference methods and gradients |
||||
Taras Petrenko : DFT Hessian,TD-DFT gradient, ASA, ECA, R-Raman, ABS, FL, XAS/XES, NRVS |
||||
Peter Pinski : DLPNO-MP2, DLPNO-MP2 Gradient |
||||
Christoph Reimann : Effective Core Potentials |
||||
Marius Retegan : Local ZFS, SOC |
||||
Christoph Riplinger : Optimizer, TS searches, QM/MM, DLPNO-CCSD(T), (RO)-DLPNO pert. Triples |
||||
Tobias Risthaus : Range-separated hybrids, TD-DFT gradient, RPA, STAB |
||||
Michael Roemelt : Original ROCIS implementation |
||||
Masaaki Saitow : Open-shell DLPNO-CCSD energy and density |
||||
Barbara Sandhoefer : DKH picture change effects |
||||
Avijit Sen : IP-ROCIS |
||||
Kantharuban Sivalingam : CASSCF convergence, NEVPT2, FIC-MRCI |
||||
Bernardo de Souza : ESD, SOC TD-DFT |
||||
Georgi Stoychev : AutoAux, RI-MP2 NMR, DLPNO-MP2 response |
||||
Willem Van den Heuvel : Paramagnetic NMR |
||||
Boris Wezisla : Elementary symmetry handling |
||||
Frank Wennmohs : Technical directorship |
||||
|
||||
|
||||
We gratefully acknowledge several colleagues who have allowed us to |
||||
interface, adapt or use parts of their codes: |
||||
Stefan Grimme, W. Hujo, H. Kruse, P. Pracht, : VdW corrections, initial TS optimization, |
||||
C. Bannwarth, S. Ehlert DFT functionals, gCP, sTDA/sTD-DF |
||||
Ed Valeev, F. Pavosevic, A. Kumar : LibInt (2-el integral package), F12 methods |
||||
Garnet Chan, S. Sharma, J. Yang, R. Olivares : DMRG |
||||
Ulf Ekstrom : XCFun DFT Library |
||||
Mihaly Kallay : mrcc (arbitrary order and MRCC methods) |
||||
Jiri Pittner, Ondrej Demel : Mk-CCSD |
||||
Frank Weinhold : gennbo (NPA and NBO analysis) |
||||
Christopher J. Cramer and Donald G. Truhlar : smd solvation model |
||||
Lars Goerigk : TD-DFT with DH, B97 family of functionals |
||||
V. Asgeirsson, H. Jonsson : NEB implementation |
||||
FAccTs GmbH : IRC, NEB, NEB-TS, DLPNO-Multilevel, CI-OPT |
||||
MM, QMMM, 2- and 3-layer-ONIOM, Crystal-QMMM, |
||||
LR-CPCM, SF, NACMEs, symmetry and pop. for TD-DFT, |
||||
nearIR, NL-DFT gradient (VV10), updates on ESD, |
||||
ML-optimized integration grids |
||||
S Lehtola, MJT Oliveira, MAL Marques : LibXC Library |
||||
Liviu Ungur et al : ANISO software |
||||
|
||||
|
||||
Your calculation uses the libint2 library for the computation of 2-el integrals |
||||
For citations please refer to: http://libint.valeyev.net |
||||
|
||||
Your ORCA version has been built with support for libXC version: 5.1.0 |
||||
For citations please refer to: https://tddft.org/programs/libxc/ |
||||
|
||||
This ORCA versions uses: |
||||
CBLAS interface : Fast vector & matrix operations |
||||
LAPACKE interface : Fast linear algebra routines |
||||
SCALAPACK package : Parallel linear algebra routines |
||||
Shared memory : Shared parallel matrices |
||||
BLAS/LAPACK : OpenBLAS 0.3.15 USE64BITINT DYNAMIC_ARCH NO_AFFINITY SkylakeX SINGLE_THREADED |
||||
Core in use : SkylakeX |
||||
Copyright (c) 2011-2014, The OpenBLAS Project |
||||
|
||||
|
||||
|
||||
|
||||
*************************************** |
||||
The coordinates will be read from file: cmmd.xyz |
||||
*************************************** |
||||
|
||||
|
||||
Your calculation utilizes the semiempirical GFN2-xTB method |
||||
Please cite in your paper: |
||||
C. Bannwarth, Ehlert S., S. Grimme, J. Chem. Theory Comput., 15, (2019), 1652. |
||||
|
||||
|
||||
================================================================================ |
||||
|
||||
================================================================================ |
||||
WARNINGS |
||||
Please study these warnings very carefully! |
||||
================================================================================ |
||||
|
||||
WARNING: Old DensityContainer found on disk! |
||||
Will remove this file - |
||||
If you want to keep old densities, please start your calculation with a different basename. |
||||
|
||||
WARNING: Gradients needed for Numerical Frequencies |
||||
===> : Setting RunTyp to EnGrad |
||||
|
||||
WARNING: Found dipole moment calculation with XTB calculation |
||||
===> : Switching off dipole moment calculation |
||||
|
||||
|
||||
WARNING: TRAH-SCF for XTB is not implemented! |
||||
===> : Turning TRAH off! |
||||
|
||||
================================================================================ |
||||
INPUT FILE |
||||
================================================================================ |
||||
NAME = cmmd.in |
||||
| 1> #CMMDE generated Orca input file |
||||
| 2> !XTB2 Numfreq |
||||
| 3> %pal |
||||
| 4> nprocs 1 |
||||
| 5> end |
||||
| 6> |
||||
| 7> *xyzfile 0 1 cmmd.xyz |
||||
| 8> |
||||
| 9> %freq |
||||
| 10> scalfreq 1 |
||||
| 11> Temp 298.15 |
||||
| 12> Pressure 1.0 |
||||
| 13> end |
||||
| 14> |
||||
| 15> ****END OF INPUT**** |
||||
================================================================================ |
||||
|
||||
******************************* |
||||
* Energy+Gradient Calculation * |
||||
******************************* |
||||
|
||||
----------------------------------------------------------- |
||||
| ===================== | |
||||
| x T B | |
||||
| ===================== | |
||||
| S. Grimme | |
||||
| Mulliken Center for Theoretical Chemistry | |
||||
| University of Bonn | |
||||
| Aditya W. Sakti | |
||||
| Departemen Kimia | |
||||
| Universitas Pertamina | |
||||
----------------------------------------------------------- |
||||
|
||||
* xtb version 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54) compiled by '@Linux' on 12/03/2021 |
||||
|
||||
xtb is free software: you can redistribute it and/or modify it under |
||||
the terms of the GNU Lesser General Public License as published by |
||||
the Free Software Foundation, either version 3 of the License, or |
||||
(at your option) any later version. |
||||
|
||||
xtb is distributed in the hope that it will be useful, |
||||
but WITHOUT ANY WARRANTY; without even the implied warranty of |
||||
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
||||
GNU Lesser General Public License for more details. |
||||
|
||||
Cite this work as: |
||||
* C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht, |
||||
J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11, |
||||
e01493. DOI: 10.1002/wcms.1493 |
||||
|
||||
for GFN2-xTB: |
||||
* C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019, |
||||
15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176 |
||||
for GFN1-xTB: |
||||
* S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017, |
||||
13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118 |
||||
for GFN0-xTB: |
||||
* P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint. |
||||
DOI: 10.26434/chemrxiv.8326202.v1 |
||||
for GFN-FF: |
||||
* S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673. |
||||
DOI: 10.1002/anie.202004239 |
||||
|
||||
for ALPB and GBSA implicit solvation: |
||||
* S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput., |
||||
2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471 |
||||
|
||||
for DFT-D4: |
||||
* E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017, |
||||
147, 034112. DOI: 10.1063/1.4993215 |
||||
* E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher, |
||||
C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122. |
||||
DOI: 10.1063/1.5090222 |
||||
* E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys. |
||||
2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A |
||||
|
||||
for sTDA-xTB: |
||||
* S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103. |
||||
DOI: 10.1063/1.4959605 |
||||
|
||||
in the mass-spec context: |
||||
* V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879. |
||||
DOI: 10.1039/c7sc00601b |
||||
* J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133. |
||||
DOI: 10.1021/acsomega.9b02011 |
||||
|
||||
for metadynamics refer to: |
||||
* S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862 |
||||
DOI: 10.1021/acs.jctc.9b00143 |
||||
|
||||
for SPH calculations refer to: |
||||
* S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714 |
||||
DOI: 10.1021/acs.jctc.0c01306 |
||||
|
||||
with help from (in alphabetical order) |
||||
P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher |
||||
M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, J. Koopman |
||||
C. Lavigne, S. Lehtola, F. März, M. Müller, F. Musil, H. Neugebauer |
||||
J. Pisarek, C. Plett, P. Pracht, J. Seibert, P. Shushkov, S. Spicher |
||||
M. Stahn, M. Steiner, T. Strunk, J. Stückrath, T. Rose, and J. Unsleber |
||||
|
||||
* started run on 2022/04/28 at 11:27:29.719 |
||||
|
||||
------------------------------------------------- |
||||
| Calculation Setup | |
||||
------------------------------------------------- |
||||
|
||||
program call : /home/adit/opt/orca/otool_xtb cmmd_XTB.xyz --grad -c 0 -u 0 -P 1 --namespace cmmd --input cmmd_XTB.input.tmp --acc 1.000000 |
||||
hostname : compute |
||||
calculation namespace : cmmd |
||||
coordinate file : cmmd_XTB.xyz |
||||
number of atoms : 3 |
||||
number of electrons : 16 |
||||
charge : 0 |
||||
spin : 0.0 |
||||
first test random number : 0.68590959901946 |
||||
|
||||
ID Z sym. atoms |
||||
1 8 O 1, 3 |
||||
2 6 C 2 |
||||
|
||||
------------------------------------------------- |
||||
| G F N 2 - x T B | |
||||
------------------------------------------------- |
||||
|
||||
Reference 10.1021/acs.jctc.8b01176 |
||||
* Hamiltonian: |
||||
H0-scaling (s, p, d) 1.850000 2.230000 2.230000 |
||||
zeta-weighting 0.500000 |
||||
* Dispersion: |
||||
s8 2.700000 |
||||
a1 0.520000 |
||||
a2 5.000000 |
||||
s9 5.000000 |
||||
* Repulsion: |
||||
kExp 1.500000 1.000000 |
||||
rExp 1.000000 |
||||
* Coulomb: |
||||
alpha 2.000000 |
||||
third order shell-resolved |
||||
anisotropic true |
||||
a3 3.000000 |
||||
a5 4.000000 |
||||
cn-shift 1.200000 |
||||
cn-exp 4.000000 |
||||
max-rad 5.000000 |
||||
|
||||
|
||||
................................................... |
||||
: SETUP : |
||||
:.................................................: |
||||
: # basis functions 12 : |
||||
: # atomic orbitals 12 : |
||||
: # shells 6 : |
||||
: # electrons 16 : |
||||
: max. iterations 250 : |
||||
: Hamiltonian GFN2-xTB : |
||||
: restarted? false : |
||||
: GBSA solvation false : |
||||
: PC potential false : |
||||
: electronic temp. 300.0000000 K : |
||||
: accuracy 1.0000000 : |
||||
: -> integral cutoff 0.2500000E+02 : |
||||
: -> integral neglect 0.1000000E-07 : |
||||
: -> SCF convergence 0.1000000E-05 Eh : |
||||
: -> wf. convergence 0.1000000E-03 e : |
||||
: Broyden damping 0.4000000 : |
||||
................................................... |
||||
|
||||
iter E dE RMSdq gap omega full diag |
||||
1 -10.3965360 -0.103965E+02 0.837E+00 8.67 0.0 T |
||||
2 -10.4101892 -0.136532E-01 0.431E+00 7.88 1.0 T |
||||
3 -10.4094776 0.711590E-03 0.204E+00 8.23 1.0 T |
||||
4 -10.4117031 -0.222544E-02 0.655E-02 7.98 1.0 T |
||||
5 -10.4117158 -0.127551E-04 0.707E-03 8.00 8.2 T |
||||
6 -10.4117158 -0.371099E-09 0.255E-03 7.99 22.6 T |
||||
7 -10.4117158 -0.126620E-07 0.789E-05 7.99 731.6 T |
||||
8 -10.4117158 0.113864E-11 0.304E-05 7.99 1897.3 T |
||||
|
||||
*** convergence criteria satisfied after 8 iterations *** |
||||
|
||||
# Occupation Energy/Eh Energy/eV |
||||
------------------------------------------------------------- |
||||
1 2.0000 -0.8071320 -21.9632 |
||||
2 2.0000 -0.7942628 -21.6130 |
||||
3 2.0000 -0.6642345 -18.0747 |
||||
4 2.0000 -0.6586945 -17.9240 |
||||
5 2.0000 -0.6586945 -17.9240 |
||||
6 2.0000 -0.6017795 -16.3753 |
||||
7 2.0000 -0.5339897 -14.5306 |
||||
8 2.0000 -0.5339897 -14.5306 (HOMO) |
||||
9 -0.2401980 -6.5361 (LUMO) |
||||
10 -0.2401980 -6.5361 |
||||
11 0.2460866 6.6964 |
||||
12 1.2242558 33.3137 |
||||
------------------------------------------------------------- |
||||
HL-Gap 0.2937917 Eh 7.9945 eV |
||||
Fermi-level -0.3870939 Eh -10.5334 eV |
||||
|
||||
SCC (total) 0 d, 0 h, 0 min, 0.008 sec |
||||
SCC setup ... 0 min, 0.000 sec ( 0.895%) |
||||
Dispersion ... 0 min, 0.000 sec ( 0.159%) |
||||
classical contributions ... 0 min, 0.000 sec ( 0.101%) |
||||
integral evaluation ... 0 min, 0.000 sec ( 2.187%) |
||||
iterations ... 0 min, 0.008 sec ( 90.726%) |
||||
molecular gradient ... 0 min, 0.000 sec ( 3.490%) |
||||
printout ... 0 min, 0.000 sec ( 2.293%) |
||||
|
||||
::::::::::::::::::::::::::::::::::::::::::::::::::::: |
||||
:: SUMMARY :: |
||||
::::::::::::::::::::::::::::::::::::::::::::::::::::: |
||||
:: total energy -10.306829455248 Eh :: |
||||
:: gradient norm 0.060331419568 Eh/a0 :: |
||||
:: HOMO-LUMO gap 7.994478852059 eV :: |
||||
::.................................................:: |
||||
:: SCC energy -10.411715834534 Eh :: |
||||
:: -> isotropic ES 0.032208314694 Eh :: |
||||
:: -> anisotropic ES 0.003353522512 Eh :: |
||||
:: -> anisotropic XC 0.000791903701 Eh :: |
||||
:: -> dispersion -0.000686207603 Eh :: |
||||
:: repulsion energy 0.104886381085 Eh :: |
||||
:: add. restraining 0.000000000000 Eh :: |
||||
:: total charge 0.000000000000 e :: |
||||
::::::::::::::::::::::::::::::::::::::::::::::::::::: |
||||
|
||||
|
||||
Property printout bound to 'properties.out' |
||||
|
||||
------------------------------------------------- |
||||
| TOTAL ENERGY -10.306829455248 Eh | |
||||
| GRADIENT NORM 0.060331419568 Eh/α | |
||||
| HOMO-LUMO GAP 7.994478852059 eV | |
||||
------------------------------------------------- |
||||
|
||||
------------------------------------------------------------------------ |
||||
* finished run on 2022/04/28 at 11:27:29.735 |
||||
------------------------------------------------------------------------ |
||||
total: |
||||
* wall-time: 0 d, 0 h, 0 min, 0.016 sec |
||||
* cpu-time: 0 d, 0 h, 0 min, 0.010 sec |
||||
* ratio c/w: 0.598 speedup |
||||
SCF: |
||||
* wall-time: 0 d, 0 h, 0 min, 0.009 sec |
||||
* cpu-time: 0 d, 0 h, 0 min, 0.002 sec |
||||
* ratio c/w: 0.249 speedup |
||||
|
||||
|
||||
------------------------- -------------------- |
||||
FINAL SINGLE POINT ENERGY -10.306829455250 |
||||
------------------------- -------------------- |
||||
|
||||
|
||||
---------------------------------------------------------------------------- |
||||
ORCA NUMERICAL FREQUENCIES |
||||
---------------------------------------------------------------------------- |
||||
|
||||
Number of atoms ... 3 |
||||
Central differences ... used |
||||
Number of displacements ... 18 |
||||
Numerical increment ... 5.000e-03 bohr |
||||
IR-spectrum generation ... on |
||||
Raman-spectrum generation ... off |
||||
Surface Crossing Hessian ... off |
||||
|
||||
The output will be reduced. Please look at the following files: |
||||
SCF program output ... >cmmd.lastscf |
||||
Integral program output ... >cmmd.lastint |
||||
Gradient program output ... >cmmd.lastgrad |
||||
Dipole moment program output ... >cmmd.lastmom |
||||
AutoCI program output ... >cmmd.lastautoci |
||||
|
||||
<< Calculating on displaced geometry 1 (of 18) >> |
||||
<< Calculating on displaced geometry 2 (of 18) >> |
||||
<< Calculating on displaced geometry 3 (of 18) >> |
||||
<< Calculating on displaced geometry 4 (of 18) >> |
||||
<< Calculating on displaced geometry 5 (of 18) >> |
||||
<< Calculating on displaced geometry 6 (of 18) >> |
||||
<< Calculating on displaced geometry 7 (of 18) >> |
||||
<< Calculating on displaced geometry 8 (of 18) >> |
||||
<< Calculating on displaced geometry 9 (of 18) >> |
||||
<< Calculating on displaced geometry 10 (of 18) >> |
||||
<< Calculating on displaced geometry 11 (of 18) >> |
||||
<< Calculating on displaced geometry 12 (of 18) >> |
||||
<< Calculating on displaced geometry 13 (of 18) >> |
||||
<< Calculating on displaced geometry 14 (of 18) >> |
||||
<< Calculating on displaced geometry 15 (of 18) >> |
||||
<< Calculating on displaced geometry 16 (of 18) >> |
||||
<< Calculating on displaced geometry 17 (of 18) >> |
||||
<< Calculating on displaced geometry 18 (of 18) >> |
||||
|
||||
----------------------- |
||||
VIBRATIONAL FREQUENCIES |
||||
----------------------- |
||||
|
||||
Scaling factor for frequencies = 1.000000000 (already applied!) |
||||
|
||||
0: 0.00 cm**-1 |
||||
1: 0.00 cm**-1 |
||||
2: 0.00 cm**-1 |
||||
3: 0.00 cm**-1 |
||||
4: 0.00 cm**-1 |
||||
5: 600.70 cm**-1 |
||||
6: 600.70 cm**-1 |
||||
7: 1328.91 cm**-1 |
||||
8: 2416.82 cm**-1 |
||||
|
||||
|
||||
------------ |
||||
NORMAL MODES |
||||
------------ |
||||
|
||||
These modes are the cartesian displacements weighted by the diagonal matrix |
||||
M(i,i)=1/sqrt(m[i]) where m[i] is the mass of the displaced atom |
||||
Thus, these vectors are normalized but *not* orthogonal |
||||
|
||||
0 1 2 3 4 5 |
||||
0 0.000000 0.000000 0.000000 0.000000 0.000000 -0.000000 |
||||
1 0.000000 0.000000 0.000000 0.000000 0.000000 0.122765 |
||||
2 0.000000 0.000000 0.000000 0.000000 0.000000 -0.307981 |
||||
3 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 |
||||
4 0.000000 0.000000 0.000000 0.000000 0.000000 -0.327054 |
||||
5 0.000000 0.000000 0.000000 0.000000 0.000000 0.820480 |
||||
6 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 |
||||
7 0.000000 0.000000 0.000000 0.000000 0.000000 0.122765 |
||||
8 0.000000 0.000000 0.000000 0.000000 0.000000 -0.307981 |
||||
6 7 8 |
||||
0 -0.000000 -0.707107 -0.331548 |
||||
1 -0.307981 -0.000000 -0.000000 |
||||
2 -0.122765 0.000000 0.000000 |
||||
3 0.000000 -0.000000 0.883262 |
||||
4 0.820480 0.000000 0.000000 |
||||
5 0.327054 -0.000000 -0.000000 |
||||
6 0.000000 0.707107 -0.331547 |
||||
7 -0.307981 -0.000000 0.000000 |
||||
8 -0.122765 0.000000 -0.000000 |
||||
|
||||
|
||||
----------- |
||||
IR SPECTRUM |
||||
----------- |
||||
|
||||
Mode freq eps Int T**2 TX TY TZ |
||||
cm**-1 L/(mol*cm) km/mol a.u. |
||||
---------------------------------------------------------------------------- |
||||
5: 600.70 0.014137 71.44 0.007344 ( 0.000000 -0.031733 0.079608) |
||||
6: 600.70 0.014137 71.44 0.007344 ( 0.000000 0.079608 0.031733) |
||||
7: 1328.91 0.000000 0.00 0.000000 (-0.000000 0.000000 -0.000000) |
||||
8: 2416.82 0.191639 968.47 0.024745 ( 0.157305 0.000000 -0.000000) |
||||
|
||||
* The epsilon (eps) is given for a Dirac delta lineshape. |
||||
** The dipole moment derivative (T) already includes vibrational overlap. |
||||
|
||||
The first frequency considered to be a vibration is 5 |
||||
The total number of vibrations considered is 4 |
||||
|
||||
|
||||
-------------------------- |
||||
THERMOCHEMISTRY AT 298.15K |
||||
-------------------------- |
||||
|
||||
Temperature ... 298.15 K |
||||
Pressure ... 1.00 atm |
||||
Total Mass ... 44.01 AMU |
||||
The molecule is recognized as being linear |
||||
|
||||
Throughout the following assumptions are being made: |
||||
(1) The electronic state is orbitally nondegenerate |
||||
(2) There are no thermally accessible electronically excited states |
||||
(3) Hindered rotations indicated by low frequency modes are not |
||||
treated as such but are treated as vibrations and this may |
||||
cause some error |
||||
(4) All equations used are the standard statistical mechanics |
||||
equations for an ideal gas |
||||
(5) All vibrations are strictly harmonic |
||||
|
||||
freq. 600.70 E(vib) ... 0.10 |
||||
freq. 600.70 E(vib) ... 0.10 |
||||
freq. 1328.91 E(vib) ... 0.01 |
||||
freq. 2416.82 E(vib) ... 0.00 |
||||
|
||||
------------ |
||||
INNER ENERGY |
||||
------------ |
||||
|
||||
The inner energy is: U= E(el) + E(ZPE) + E(vib) + E(rot) + E(trans) |
||||
E(el) - is the total energy from the electronic structure calculation |
||||
= E(kin-el) + E(nuc-el) + E(el-el) + E(nuc-nuc) |
||||
E(ZPE) - the the zero temperature vibrational energy from the frequency calculation |
||||
E(vib) - the the finite temperature correction to E(ZPE) due to population |
||||
of excited vibrational states |
||||
E(rot) - is the rotational thermal energy |
||||
E(trans)- is the translational thermal energy |
||||
|
||||
Summary of contributions to the inner energy U: |
||||
Electronic energy ... -10.30682946 Eh |
||||
Zero point energy ... 0.01127041 Eh 7.07 kcal/mol |
||||
Thermal vibrational correction ... 0.00032921 Eh 0.21 kcal/mol |
||||
Thermal rotational correction ... 0.00094418 Eh 0.59 kcal/mol |
||||
Thermal translational correction ... 0.00141627 Eh 0.89 kcal/mol |
||||
----------------------------------------------------------------------- |
||||
Total thermal energy -10.29286939 Eh |
||||
|
||||
|
||||
Summary of corrections to the electronic energy: |
||||
(perhaps to be used in another calculation) |
||||
Total thermal correction 0.00268966 Eh 1.69 kcal/mol |
||||
Non-thermal (ZPE) correction 0.01127041 Eh 7.07 kcal/mol |
||||
----------------------------------------------------------------------- |
||||
Total correction 0.01396007 Eh 8.76 kcal/mol |
||||
|
||||
|
||||
-------- |
||||
ENTHALPY |
||||
-------- |
||||
|
||||
The enthalpy is H = U + kB*T |
||||
kB is Boltzmann's constant |
||||
Total free energy ... -10.29286939 Eh |
||||
Thermal Enthalpy correction ... 0.00094421 Eh 0.59 kcal/mol |
||||
----------------------------------------------------------------------- |
||||
Total Enthalpy ... -10.29192518 Eh |
||||
|
||||
|
||||
Note: Rotational entropy computed according to Herzberg |
||||
Infrared and Raman Spectra, Chapter V,1, Van Nostrand Reinhold, 1945 |
||||
Point Group: Dinfh, Symmetry Number: 2 |
||||
Rotational constants in cm-1: 0.000000 0.389289 0.389289 |
||||
|
||||
Vibrational entropy computed according to the QRRHO of S. Grimme |
||||
Chem.Eur.J. 2012 18 9955 |
||||
|
||||
|
||||
------- |
||||
ENTROPY |
||||
------- |
||||
|
||||
The entropy contributions are T*S = T*(S(el)+S(vib)+S(rot)+S(trans)) |
||||
S(el) - electronic entropy |
||||
S(vib) - vibrational entropy |
||||
S(rot) - rotational entropy |
||||
S(trans)- translational entropy |
||||
The entropies will be listed as multiplied by the temperature to get |
||||
units of energy |
||||
|
||||
Electronic entropy ... 0.00000000 Eh 0.00 kcal/mol |
||||
Vibrational entropy ... 0.00043823 Eh 0.27 kcal/mol |
||||
Rotational entropy ... 0.00621658 Eh 3.90 kcal/mol |
||||
Translational entropy ... 0.01770880 Eh 11.11 kcal/mol |
||||
----------------------------------------------------------------------- |
||||
Final entropy term ... 0.02436361 Eh 15.29 kcal/mol |
||||
|
||||
|
||||
------------------- |
||||
GIBBS FREE ENERGY |
||||
------------------- |
||||
|
||||
The Gibbs free energy is G = H - T*S |
||||
|
||||
Total enthalpy ... -10.29192518 Eh |
||||
Total entropy correction ... -0.02436361 Eh -15.29 kcal/mol |
||||
----------------------------------------------------------------------- |
||||
Final Gibbs free energy ... -10.31628879 Eh |
||||
|
||||
For completeness - the Gibbs free energy minus the electronic energy |
||||
G-E(el) ... -0.00945933 Eh -5.94 kcal/mol |
||||
|
||||
|
||||
|
||||
Timings for individual modules: |
||||
|
||||
Sum of individual times ... 44.986 sec (= 0.750 min) |
||||
Numerical frequency calculation ... 44.913 sec (= 0.749 min) 99.8 % |
||||
XTB module ... 0.073 sec (= 0.001 min) 0.2 % |
||||
****ORCA TERMINATED NORMALLY**** |
||||
TOTAL RUN TIME: 0 days 0 hours 0 minutes 44 seconds 988 msec |
||||
Binary file not shown.
@ -0,0 +1,5 @@ |
||||
3 |
||||
Coordinates from ORCA-job cmmd |
||||
O 1.08567503629188 0.00046999979347 0.09757000110407 |
||||
C 2.24899995571885 0.00047000041305 0.09756999779185 |
||||
O 3.41232500798927 0.00046999979347 0.09757000110407 |
||||
@ -0,0 +1,42 @@ |
||||
------------------------------------------------------------- |
||||
----------------------- !PROPERTIES! ------------------------ |
||||
------------------------------------------------------------- |
||||
# ----------------------------------------------------------- |
||||
$ THERMOCHEMISTRY_Energies |
||||
description: The Thermochemistry energies |
||||
geom. index: 0 |
||||
prop. index: 1 |
||||
Temperature (Kelvin) : 298.1500000000 |
||||
Pressure (atm) : 1.0000000000 |
||||
Total Mass (AMU) : 44.0090000000 |
||||
Spin Degeneracy : 1.0000000000 |
||||
Electronic Energy (Hartree) : -10.3068294552 |
||||
Translational Energy (Hartree) : 0.0014162714 |
||||
Rotational Energy (Hartree) : 0.0009441809 |
||||
Vibrational Energy (Hartree) : 0.0003292089 |
||||
Number of frequencies : 9 |
||||
Scaling Factor for frequencies : 1.0000000000 |
||||
Vibrational frequencies : |
||||
0 |
||||
0 0.000000 |
||||
1 0.000000 |
||||
2 0.000000 |
||||
3 0.000000 |
||||
4 0.000000 |
||||
5 600.703532 |
||||
6 600.703532 |
||||
7 1328.912392 |
||||
8 2416.816551 |
||||
Zero Point Energy (Hartree) : 0.0112704051 |
||||
Inner Energy (Hartree) : -10.2928693888 |
||||
Enthalpy (Hartree) : -10.2919251798 |
||||
Electronic entropy : 0.0000000000 |
||||
Rotational entropy : 0.0062165785 |
||||
Vibrational entropy : 0.0004382285 |
||||
Translational entropy : 0.0062165785 |
||||
Entropy : 0.0243636075 |
||||
Gibbs Energy (Hartree) : -10.3162887873 |
||||
Is Linear : false |
||||
# ------------------------------------------------------------- |
||||
----------------------- !GEOMETRIES! ------------------------ |
||||
# ------------------------------------------------------------- |
||||
@ -0,0 +1,25 @@ |
||||
3 |
||||
Coordinates from ORCA-job cmmd E -188.356072808458 |
||||
O 1.052000 0.000470 0.097570 |
||||
C 2.249000 0.000470 0.097570 |
||||
O 3.446000 0.000470 0.097570 |
||||
3 |
||||
Coordinates from ORCA-job cmmd E -188.360409003054 |
||||
O 1.082532 0.000470 0.097570 |
||||
C 2.249000 0.000470 0.097570 |
||||
O 3.415468 0.000470 0.097570 |
||||
3 |
||||
Coordinates from ORCA-job cmmd E -188.360449781138 |
||||
O 1.086065 0.000470 0.097570 |
||||
C 2.249000 0.000470 0.097570 |
||||
O 3.411935 0.000470 0.097570 |
||||
3 |
||||
Coordinates from ORCA-job cmmd E -188.360450352237 |
||||
O 1.085671 0.000470 0.097570 |
||||
C 2.249000 0.000470 0.097570 |
||||
O 3.412329 0.000470 0.097570 |
||||
3 |
||||
Coordinates from ORCA-job cmmd E -188.360450353656 |
||||
O 1.085675 0.000470 0.097570 |
||||
C 2.249000 0.000470 0.097570 |
||||
O 3.412325 0.000470 0.097570 |
||||
@ -0,0 +1 @@ |
||||
O=C=O |
||||
@ -0,0 +1,5 @@ |
||||
3 |
||||
|
||||
O 1.05200 0.00047 0.09757 |
||||
C 2.24900 0.00047 0.09757 |
||||
O 3.44600 0.00047 0.09757 |
||||
@ -0,0 +1,10 @@ |
||||
#!/bin/bash |
||||
#SBATCH --nodes=1 |
||||
#SBATCH --ntasks=1 |
||||
#SBATCH --cpus-per-task=1 |
||||
#SBATCH --time=168:0:0 |
||||
export LD_LIBRARY_PATH=/home/adit/opt/openmpi411/lib:$LD_LIBRARY_PATH |
||||
export PATH=/home/adit/opt/openmpi411/bin:$PATH |
||||
export OMP_NUM_THREADS=1 |
||||
cd $PWD |
||||
$ORCA_COMMAND cmmd.in > cmmd.out --oversubscribe |
||||
@ -0,0 +1,8 @@ |
||||
#!/bin/bash |
||||
#SBATCH --nodes=1 |
||||
#SBATCH --ntasks=1 |
||||
#SBATCH --cpus-per-task=1 |
||||
#SBATCH --time=168:0:0 |
||||
export OMP_NUM_THREADS=1 |
||||
cd $PWD |
||||
obabel geom.smi -O geom.xyz --gen3d |
||||
@ -0,0 +1 @@ |
||||
1 molecule converted |
||||
@ -0,0 +1,26 @@ |
||||
# |
||||
# Number of atoms |
||||
# |
||||
3 |
||||
# |
||||
# The current total energy in Eh |
||||
# |
||||
-5.070123981300 |
||||
# |
||||
# The current gradient in Eh/bohr |
||||
# |
||||
-0.008377591894 |
||||
-0.009332836846 |
||||
-0.007297711124 |
||||
0.004688751138 |
||||
0.004388014404 |
||||
0.003431157867 |
||||
0.003688840756 |
||||
0.004944822442 |
||||
0.003866553256 |
||||
# |
||||
# The atomic numbers and current coordinates in Bohr |
||||
# |
||||
8 1.7463773 0.0986767 -0.0997319 |
||||
1 3.5707559 0.1789166 -0.0369954 |
||||
1 1.2342827 1.4804000 0.9806980 |
||||
Binary file not shown.
@ -0,0 +1,116 @@ |
||||
|
||||
$orca_hessian_file |
||||
|
||||
$act_atom |
||||
0 |
||||
|
||||
$act_coord |
||||
0 |
||||
|
||||
$act_energy |
||||
-5.070124 |
||||
|
||||
$hessian |
||||
9 |
||||
0 1 2 3 4 |
||||
0 5.0153331710E-01 -5.3060722768E-02 -4.1491079430E-02 -4.3244534659E-01 -4.0084092878E-02 |
||||
1 -5.3060722768E-02 2.8650738494E-01 2.1405136245E-01 -8.0486957880E-03 -3.0519687256E-02 |
||||
2 -4.1491079430E-02 2.1405136245E-01 1.8013792250E-01 -6.2920646425E-03 -1.8871513419E-02 |
||||
3 -4.3244534659E-01 -8.0486957880E-03 -6.2920646425E-03 4.5189264359E-01 3.9039242588E-03 |
||||
4 -4.0084092878E-02 -3.0519687256E-02 -1.8871513419E-02 3.9039242588E-03 3.0226919572E-02 |
||||
5 -3.1341920012E-02 -1.8871689535E-02 -2.1141829960E-02 3.0510466469E-03 2.0971324760E-02 |
||||
6 -6.9088148033E-02 6.1109394648E-02 4.7783125377E-02 -1.9447166108E-02 3.6180182740E-02 |
||||
7 9.3144650593E-02 -2.5598799181E-01 -1.9517992292E-01 4.1448060830E-03 2.9290278726E-04 |
||||
8 7.2832797380E-02 -1.9517987280E-01 -1.5899626281E-01 3.2410666038E-03 -2.0996758124E-03 |
||||
5 6 7 8 |
||||
0 -3.1341920012E-02 -6.9088148033E-02 9.3144650593E-02 7.2832797380E-02 |
||||
1 -1.8871689535E-02 6.1109394648E-02 -2.5598799181E-01 -1.9517987280E-01 |
||||
2 -2.1141829960E-02 4.7783125377E-02 -1.9517992292E-01 -1.5899626281E-01 |
||||
3 3.0510466469E-03 -1.9447166108E-02 4.1448060830E-03 3.2410666038E-03 |
||||
4 2.0971324760E-02 3.6180182740E-02 2.9290278726E-04 -2.0996758124E-03 |
||||
5 1.9805805652E-02 2.8290884407E-02 -2.0995584766E-03 1.3360988061E-03 |
||||
6 2.8290884407E-02 8.8535360763E-02 -9.7289446888E-02 -7.6073856331E-02 |
||||
7 -2.0995584766E-03 -9.7289446888E-02 2.5569524804E-01 1.9727954575E-01 |
||||
8 1.3360988061E-03 -7.6073856331E-02 1.9727954575E-01 1.5766025977E-01 |
||||
|
||||
$vibrational_frequencies |
||||
9 |
||||
0 0.000000 |
||||
1 0.000000 |
||||
2 0.000000 |
||||
3 0.000000 |
||||
4 0.000000 |
||||
5 0.000000 |
||||
6 1591.021914 |
||||
7 3532.222317 |
||||
8 3553.964928 |
||||
|
||||
$normal_modes |
||||
9 9 |
||||
0 1 2 3 4 |
||||
0 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 |
||||
1 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 |
||||
2 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 |
||||
3 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 |
||||
4 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 |
||||
5 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 |
||||
6 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 |
||||
7 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 |
||||
8 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 |
||||
5 6 7 8 |
||||
0 0.0000000000E+00 4.0721137498E-02 -5.6762076790E-02 -2.9045170495E-02 |
||||
1 0.0000000000E+00 4.5365698453E-02 3.1729345277E-02 -3.2146768540E-02 |
||||
2 0.0000000000E+00 3.5473218659E-02 2.4810723522E-02 -2.5136818297E-02 |
||||
3 0.0000000000E+00 2.7274520573E-02 7.0266957076E-01 7.0767482621E-01 |
||||
4 0.0000000000E+00 -5.5522727783E-01 3.0998203060E-02 -9.7397068783E-03 |
||||
5 0.0000000000E+00 -4.3415585773E-01 2.4236302572E-02 -7.6184151067E-03 |
||||
6 0.0000000000E+00 -6.7360138449E-01 1.9825946352E-01 -2.4666918856E-01 |
||||
7 0.0000000000E+00 -1.6481816815E-01 -5.3460712676E-01 5.1997398255E-01 |
||||
8 0.0000000000E+00 -1.2887591343E-01 -4.1803269704E-01 4.0659059361E-01 |
||||
|
||||
# |
||||
# The atoms: label mass x y z (in bohrs) |
||||
# |
||||
$atoms |
||||
3 |
||||
O 15.99900 1.746377337196 0.098676688290 -0.099731938722 |
||||
H 1.00800 3.570755883853 0.178916624800 -0.036995438538 |
||||
H 1.00800 1.234282723597 1.480400012035 0.980697965930 |
||||
|
||||
$actual_temperature |
||||
0.000000 |
||||
|
||||
$frequency_scale_factor |
||||
1.000000 |
||||
|
||||
$dipole_derivatives |
||||
9 |
||||
-4.0000000000E-01 0.0000000000E+00 0.0000000000E+00 |
||||
0.0000000000E+00 -6.0000000000E-01 2.0000000000E-01 |
||||
0.0000000000E+00 2.0000000000E-01 -6.0000000000E-01 |
||||
1.0000000000E-01 0.0000000000E+00 0.0000000000E+00 |
||||
-1.0000000000E-01 4.0000000000E-01 0.0000000000E+00 |
||||
0.0000000000E+00 0.0000000000E+00 4.0000000000E-01 |
||||
3.0000000000E-01 0.0000000000E+00 0.0000000000E+00 |
||||
1.0000000000E-01 2.0000000000E-01 -2.0000000000E-01 |
||||
1.0000000000E-01 -2.0000000000E-01 3.0000000000E-01 |
||||
|
||||
# |
||||
# The IR spectrum |
||||
# wavenumber eps Int TX TY TZ |
||||
# |
||||
$ir_spectrum |
||||
9 |
||||
0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000 |
||||
0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000 |
||||
0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000 |
||||
0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000 |
||||
0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000 |
||||
0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000 |
||||
1591.02 0.02402202 121.39743181 -0.035425 -0.046627 -0.035815 |
||||
3532.22 0.00068734 3.47355421 0.006792 -0.003138 -0.002177 |
||||
3553.96 0.00222411 11.23974807 0.012984 0.004205 0.003002 |
||||
|
||||
|
||||
$end |
||||
|
||||
@ -0,0 +1,13 @@ |
||||
#CMMDE generated Orca input file |
||||
!XTB2 Numfreq |
||||
%pal |
||||
nprocs 1 |
||||
end |
||||
|
||||
*xyzfile 0 1 cmmd.xyz |
||||
|
||||
%freq |
||||
scalfreq 1 |
||||
Temp 298.15 |
||||
Pressure 1.0 |
||||
end |
||||
@ -0,0 +1,108 @@ |
||||
|
||||
$orca_opt_file |
||||
|
||||
$trust |
||||
0.300000000000 |
||||
|
||||
$epredict |
||||
0.000000000000 |
||||
|
||||
$ediffsc |
||||
1000.000000000000 |
||||
|
||||
$ctyp |
||||
3 |
||||
|
||||
$coordinates |
||||
4 9 |
||||
1.74977302 0.10246095 -0.09677288 3.57882004 0.17158713 -0.04272671 |
||||
1.22282288 1.48394524 0.98347017 |
||||
1.74856683 0.10111637 -0.09782426 3.57219877 0.17628338 -0.03905449 |
||||
1.23065035 1.48059358 0.98084934 |
||||
1.74723144 0.09962851 -0.09898768 3.57099818 0.17806796 -0.03765905 |
||||
1.23318633 1.48029686 0.98061731 |
||||
1.74638369 0.09868381 -0.09972637 3.57071543 0.17893384 -0.03698198 |
||||
1.23431682 1.48037568 0.98067894 |
||||
|
||||
# redundant internal coordinates |
||||
# nbonds nangles ndihedrals nimpropers ncartesians |
||||
# bond definitions A B |
||||
# angle definitions A B C |
||||
# dihedral definitions A B C D |
||||
# improper torsion definitions A B C D |
||||
# cartesian definitions A x/y/z |
||||
$redundant_internals |
||||
2 1 0 0 0 |
||||
1 0 0 |
||||
2 0 0 |
||||
1 0 2 0 0 |
||||
$energies |
||||
4 |
||||
-76.3212379100696410 |
||||
-76.3212655904724357 |
||||
-76.3212690328680594 |
||||
-76.3212696812114473 |
||||
|
||||
$gradients |
||||
4 9 |
||||
-0.0004253922326744 -0.0005001819868337 -0.0003303905934972 0.0025973903065613 |
||||
-0.0010880141228024 -0.0008601520349792 -0.0021667166814798 0.0015671654932914 |
||||
0.0012271009412793 |
||||
0.0007834186175729 0.0008428236020004 0.0007251027461325 -0.0003236165648111 |
||||
-0.0004686022216160 -0.0003758718456999 -0.0004517894639538 -0.0003950351543238 |
||||
-0.0003081717188155 |
||||
0.0003983757946074 0.0004127842267320 0.0003916383200292 -0.0002984982162071 |
||||
-0.0001614364453191 -0.0001357999461145 -0.0000926555729789 -0.0002736661866776 |
||||
-0.0002137094933613 |
||||
0.0000160541345634 -0.0000138278483816 0.0000596139427747 -0.0000255751549404 |
||||
0.0000054195140033 -0.0000054104954291 0.0000159365342492 -0.0000150225127057 |
||||
-0.0000117004532667 |
||||
|
||||
$redundant_coords |
||||
4 3 |
||||
1.8311505801026724 1.8311472707494942 1.8147573140807562 |
||||
1.8261263372240049 1.8261247413604469 1.8060846250815792 |
||||
1.8264827030928774 1.8264814331491046 1.8015498668250125 |
||||
1.8271735622382301 1.8271728309768116 1.7990716639809692 |
||||
|
||||
$redundant_gradients |
||||
4 3 |
||||
0.0025276445547656 0.0025267987700943 0.0027615881197076 |
||||
-0.0003558507824992 -0.0003559310471405 0.0010632671904284 |
||||
-0.0003105383757455 -0.0003106763198600 0.0003530776201266 |
||||
-0.0000261697488893 -0.0000262085824290 -0.0000064837205582 |
||||
|
||||
$hessian_approx |
||||
9 9 |
||||
0 1 2 3 4 5 |
||||
0 0.572190 -0.058342 -0.045804 -0.500828 -0.043281 -0.033824 |
||||
1 -0.058342 0.322567 0.252024 -0.017583 -0.027909 -0.021805 |
||||
2 -0.045804 0.252024 0.196912 -0.014064 -0.021494 -0.016793 |
||||
3 -0.500828 -0.017583 -0.014064 0.530290 0.002073 0.001620 |
||||
4 -0.043281 -0.027909 -0.021494 0.002073 0.030371 0.023734 |
||||
5 -0.033824 -0.021805 -0.016793 0.001620 0.023734 0.018548 |
||||
6 -0.071094 0.076223 0.060101 -0.029696 0.041115 0.032133 |
||||
7 0.101880 -0.294370 -0.230307 0.015444 -0.002639 -0.002068 |
||||
8 0.079687 -0.230155 -0.180068 0.012133 -0.002116 -0.001658 |
||||
6 7 8 |
||||
0 -0.071094 0.101880 0.079687 |
||||
1 0.076223 -0.294370 -0.230155 |
||||
2 0.060101 -0.230307 -0.180068 |
||||
3 -0.029696 0.015444 0.012133 |
||||
4 0.041115 -0.002639 -0.002116 |
||||
5 0.032133 -0.002068 -0.001658 |
||||
6 0.100758 -0.117528 -0.091982 |
||||
7 -0.117528 0.296901 0.232186 |
||||
8 -0.091982 0.232186 0.181576 |
||||
|
||||
$bmatrix |
||||
3 9 |
||||
0 1 2 3 4 5 |
||||
0 -0.998445 -0.043920 -0.034340 0.998445 0.043920 0.034340 |
||||
1 0.280251 -0.756191 -0.591299 0.000000 0.000000 0.000000 |
||||
2 0.494849 0.551292 0.431077 0.030512 -0.430465 -0.336599 |
||||
6 7 8 |
||||
0 0.000000 0.000000 0.000000 |
||||
1 -0.280251 0.756191 0.591299 |
||||
2 -0.525362 -0.120827 -0.094478 |
||||
|
||||
@ -0,0 +1,657 @@ |
||||
|
||||
***************** |
||||
* O R C A * |
||||
***************** |
||||
|
||||
#, |
||||
### |
||||
#### |
||||
##### |
||||
###### |
||||
########, |
||||
,,################,,,,, |
||||
,,#################################,, |
||||
,,##########################################,, |
||||
,#########################################, ''#####, |
||||
,#############################################,, '####, |
||||
,##################################################,,,,####, |
||||
,###########'''' ''''############################### |
||||
,#####'' ,,,,##########,,,, '''####''' '#### |
||||
,##' ,,,,###########################,,, '## |
||||
' ,,###'''' '''############,,, |
||||
,,##'' '''############,,,, ,,,,,,###'' |
||||
,#'' '''#######################''' |
||||
' ''''####'''' |
||||
,#######, #######, ,#######, ## |
||||
,#' '#, ## ## ,#' '#, #''# ###### ,####, |
||||
## ## ## ,#' ## #' '# # #' '# |
||||
## ## ####### ## ,######, #####, # # |
||||
'#, ,#' ## ## '#, ,#' ,# #, ## #, ,# |
||||
'#######' ## ## '#######' #' '# #####' # '####' |
||||
|
||||
|
||||
|
||||
####################################################### |
||||
# -***- # |
||||
# Department of theory and spectroscopy # |
||||
# Directorship and core code : Frank Neese # |
||||
# Max Planck Institute fuer Kohlenforschung # |
||||
# Kaiser Wilhelm Platz 1 # |
||||
# D-45470 Muelheim/Ruhr # |
||||
# Germany # |
||||
# # |
||||
# All rights reserved # |
||||
# -***- # |
||||
####################################################### |
||||
|
||||
|
||||
Program Version 5.0.2 - RELEASE - |
||||
|
||||
|
||||
With contributions from (in alphabetic order): |
||||
Daniel Aravena : Magnetic Suceptibility |
||||
Michael Atanasov : Ab Initio Ligand Field Theory (pilot matlab implementation) |
||||
Alexander A. Auer : GIAO ZORA, VPT2 properties, NMR spectrum |
||||
Ute Becker : Parallelization |
||||
Giovanni Bistoni : ED, misc. LED, open-shell LED, HFLD |
||||
Martin Brehm : Molecular dynamics |
||||
Dmytro Bykov : SCF Hessian |
||||
Vijay G. Chilkuri : MRCI spin determinant printing, contributions to CSF-ICE |
||||
Dipayan Datta : RHF DLPNO-CCSD density |
||||
Achintya Kumar Dutta : EOM-CC, STEOM-CC |
||||
Dmitry Ganyushin : Spin-Orbit,Spin-Spin,Magnetic field MRCI |
||||
Miquel Garcia : C-PCM and meta-GGA Hessian, CC/C-PCM, Gaussian charge scheme |
||||
Yang Guo : DLPNO-NEVPT2, F12-NEVPT2, CIM, IAO-localization |
||||
Andreas Hansen : Spin unrestricted coupled pair/coupled cluster methods |
||||
Benjamin Helmich-Paris : MC-RPA, TRAH-SCF, COSX integrals |
||||
Lee Huntington : MR-EOM, pCC |
||||
Robert Izsak : Overlap fitted RIJCOSX, COSX-SCS-MP3, EOM |
||||
Marcus Kettner : VPT2 |
||||
Christian Kollmar : KDIIS, OOCD, Brueckner-CCSD(T), CCSD density, CASPT2, CASPT2-K |
||||
Simone Kossmann : Meta GGA functionals, TD-DFT gradient, OOMP2, MP2 Hessian |
||||
Martin Krupicka : Initial AUTO-CI |
||||
Lucas Lang : DCDCAS |
||||
Marvin Lechner : AUTO-CI (C++ implementation), FIC-MRCC |
||||
Dagmar Lenk : GEPOL surface, SMD |
||||
Dimitrios Liakos : Extrapolation schemes; Compound Job, initial MDCI parallelization |
||||
Dimitrios Manganas : Further ROCIS development; embedding schemes |
||||
Dimitrios Pantazis : SARC Basis sets |
||||
Anastasios Papadopoulos: AUTO-CI, single reference methods and gradients |
||||
Taras Petrenko : DFT Hessian,TD-DFT gradient, ASA, ECA, R-Raman, ABS, FL, XAS/XES, NRVS |
||||
Peter Pinski : DLPNO-MP2, DLPNO-MP2 Gradient |
||||
Christoph Reimann : Effective Core Potentials |
||||
Marius Retegan : Local ZFS, SOC |
||||
Christoph Riplinger : Optimizer, TS searches, QM/MM, DLPNO-CCSD(T), (RO)-DLPNO pert. Triples |
||||
Tobias Risthaus : Range-separated hybrids, TD-DFT gradient, RPA, STAB |
||||
Michael Roemelt : Original ROCIS implementation |
||||
Masaaki Saitow : Open-shell DLPNO-CCSD energy and density |
||||
Barbara Sandhoefer : DKH picture change effects |
||||
Avijit Sen : IP-ROCIS |
||||
Kantharuban Sivalingam : CASSCF convergence, NEVPT2, FIC-MRCI |
||||
Bernardo de Souza : ESD, SOC TD-DFT |
||||
Georgi Stoychev : AutoAux, RI-MP2 NMR, DLPNO-MP2 response |
||||
Willem Van den Heuvel : Paramagnetic NMR |
||||
Boris Wezisla : Elementary symmetry handling |
||||
Frank Wennmohs : Technical directorship |
||||
|
||||
|
||||
We gratefully acknowledge several colleagues who have allowed us to |
||||
interface, adapt or use parts of their codes: |
||||
Stefan Grimme, W. Hujo, H. Kruse, P. Pracht, : VdW corrections, initial TS optimization, |
||||
C. Bannwarth, S. Ehlert DFT functionals, gCP, sTDA/sTD-DF |
||||
Ed Valeev, F. Pavosevic, A. Kumar : LibInt (2-el integral package), F12 methods |
||||
Garnet Chan, S. Sharma, J. Yang, R. Olivares : DMRG |
||||
Ulf Ekstrom : XCFun DFT Library |
||||
Mihaly Kallay : mrcc (arbitrary order and MRCC methods) |
||||
Jiri Pittner, Ondrej Demel : Mk-CCSD |
||||
Frank Weinhold : gennbo (NPA and NBO analysis) |
||||
Christopher J. Cramer and Donald G. Truhlar : smd solvation model |
||||
Lars Goerigk : TD-DFT with DH, B97 family of functionals |
||||
V. Asgeirsson, H. Jonsson : NEB implementation |
||||
FAccTs GmbH : IRC, NEB, NEB-TS, DLPNO-Multilevel, CI-OPT |
||||
MM, QMMM, 2- and 3-layer-ONIOM, Crystal-QMMM, |
||||
LR-CPCM, SF, NACMEs, symmetry and pop. for TD-DFT, |
||||
nearIR, NL-DFT gradient (VV10), updates on ESD, |
||||
ML-optimized integration grids |
||||
S Lehtola, MJT Oliveira, MAL Marques : LibXC Library |
||||
Liviu Ungur et al : ANISO software |
||||
|
||||
|
||||
Your calculation uses the libint2 library for the computation of 2-el integrals |
||||
For citations please refer to: http://libint.valeyev.net |
||||
|
||||
Your ORCA version has been built with support for libXC version: 5.1.0 |
||||
For citations please refer to: https://tddft.org/programs/libxc/ |
||||
|
||||
This ORCA versions uses: |
||||
CBLAS interface : Fast vector & matrix operations |
||||
LAPACKE interface : Fast linear algebra routines |
||||
SCALAPACK package : Parallel linear algebra routines |
||||
Shared memory : Shared parallel matrices |
||||
BLAS/LAPACK : OpenBLAS 0.3.15 USE64BITINT DYNAMIC_ARCH NO_AFFINITY SkylakeX SINGLE_THREADED |
||||
Core in use : SkylakeX |
||||
Copyright (c) 2011-2014, The OpenBLAS Project |
||||
|
||||
|
||||
|
||||
|
||||
*************************************** |
||||
The coordinates will be read from file: cmmd.xyz |
||||
*************************************** |
||||
|
||||
|
||||
Your calculation utilizes the semiempirical GFN2-xTB method |
||||
Please cite in your paper: |
||||
C. Bannwarth, Ehlert S., S. Grimme, J. Chem. Theory Comput., 15, (2019), 1652. |
||||
|
||||
|
||||
================================================================================ |
||||
|
||||
================================================================================ |
||||
WARNINGS |
||||
Please study these warnings very carefully! |
||||
================================================================================ |
||||
|
||||
WARNING: Old DensityContainer found on disk! |
||||
Will remove this file - |
||||
If you want to keep old densities, please start your calculation with a different basename. |
||||
|
||||
WARNING: Gradients needed for Numerical Frequencies |
||||
===> : Setting RunTyp to EnGrad |
||||
|
||||
WARNING: Found dipole moment calculation with XTB calculation |
||||
===> : Switching off dipole moment calculation |
||||
|
||||
|
||||
WARNING: TRAH-SCF for XTB is not implemented! |
||||
===> : Turning TRAH off! |
||||
|
||||
================================================================================ |
||||
INPUT FILE |
||||
================================================================================ |
||||
NAME = cmmd.in |
||||
| 1> #CMMDE generated Orca input file |
||||
| 2> !XTB2 Numfreq |
||||
| 3> %pal |
||||
| 4> nprocs 1 |
||||
| 5> end |
||||
| 6> |
||||
| 7> *xyzfile 0 1 cmmd.xyz |
||||
| 8> |
||||
| 9> %freq |
||||
| 10> scalfreq 1 |
||||
| 11> Temp 298.15 |
||||
| 12> Pressure 1.0 |
||||
| 13> end |
||||
| 14> |
||||
| 15> ****END OF INPUT**** |
||||
================================================================================ |
||||
|
||||
******************************* |
||||
* Energy+Gradient Calculation * |
||||
******************************* |
||||
|
||||
----------------------------------------------------------- |
||||
| ===================== | |
||||
| x T B | |
||||
| ===================== | |
||||
| S. Grimme | |
||||
| Mulliken Center for Theoretical Chemistry | |
||||
| University of Bonn | |
||||
| Aditya W. Sakti | |
||||
| Departemen Kimia | |
||||
| Universitas Pertamina | |
||||
----------------------------------------------------------- |
||||
|
||||
* xtb version 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54) compiled by '@Linux' on 12/03/2021 |
||||
|
||||
xtb is free software: you can redistribute it and/or modify it under |
||||
the terms of the GNU Lesser General Public License as published by |
||||
the Free Software Foundation, either version 3 of the License, or |
||||
(at your option) any later version. |
||||
|
||||
xtb is distributed in the hope that it will be useful, |
||||
but WITHOUT ANY WARRANTY; without even the implied warranty of |
||||
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
||||
GNU Lesser General Public License for more details. |
||||
|
||||
Cite this work as: |
||||
* C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht, |
||||
J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11, |
||||
e01493. DOI: 10.1002/wcms.1493 |
||||
|
||||
for GFN2-xTB: |
||||
* C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019, |
||||
15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176 |
||||
for GFN1-xTB: |
||||
* S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017, |
||||
13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118 |
||||
for GFN0-xTB: |
||||
* P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint. |
||||
DOI: 10.26434/chemrxiv.8326202.v1 |
||||
for GFN-FF: |
||||
* S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673. |
||||
DOI: 10.1002/anie.202004239 |
||||
|
||||
for ALPB and GBSA implicit solvation: |
||||
* S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput., |
||||
2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471 |
||||
|
||||
for DFT-D4: |
||||
* E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017, |
||||
147, 034112. DOI: 10.1063/1.4993215 |
||||
* E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher, |
||||
C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122. |
||||
DOI: 10.1063/1.5090222 |
||||
* E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys. |
||||
2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A |
||||
|
||||
for sTDA-xTB: |
||||
* S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103. |
||||
DOI: 10.1063/1.4959605 |
||||
|
||||
in the mass-spec context: |
||||
* V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879. |
||||
DOI: 10.1039/c7sc00601b |
||||
* J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133. |
||||
DOI: 10.1021/acsomega.9b02011 |
||||
|
||||
for metadynamics refer to: |
||||
* S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862 |
||||
DOI: 10.1021/acs.jctc.9b00143 |
||||
|
||||
for SPH calculations refer to: |
||||
* S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714 |
||||
DOI: 10.1021/acs.jctc.0c01306 |
||||
|
||||
with help from (in alphabetical order) |
||||
P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher |
||||
M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, J. Koopman |
||||
C. Lavigne, S. Lehtola, F. März, M. Müller, F. Musil, H. Neugebauer |
||||
J. Pisarek, C. Plett, P. Pracht, J. Seibert, P. Shushkov, S. Spicher |
||||
M. Stahn, M. Steiner, T. Strunk, J. Stückrath, T. Rose, and J. Unsleber |
||||
|
||||
* started run on 2022/04/28 at 11:27:34.587 |
||||
|
||||
------------------------------------------------- |
||||
| Calculation Setup | |
||||
------------------------------------------------- |
||||
|
||||
program call : /home/adit/opt/orca/otool_xtb cmmd_XTB.xyz --grad -c 0 -u 0 -P 1 --namespace cmmd --input cmmd_XTB.input.tmp --acc 1.000000 |
||||
hostname : compute |
||||
calculation namespace : cmmd |
||||
coordinate file : cmmd_XTB.xyz |
||||
number of atoms : 3 |
||||
number of electrons : 8 |
||||
charge : 0 |
||||
spin : 0.0 |
||||
first test random number : 0.93951341933391 |
||||
|
||||
ID Z sym. atoms |
||||
1 8 O 1 |
||||
2 1 H 2, 3 |
||||
|
||||
------------------------------------------------- |
||||
| G F N 2 - x T B | |
||||
------------------------------------------------- |
||||
|
||||
Reference 10.1021/acs.jctc.8b01176 |
||||
* Hamiltonian: |
||||
H0-scaling (s, p, d) 1.850000 2.230000 2.230000 |
||||
zeta-weighting 0.500000 |
||||
* Dispersion: |
||||
s8 2.700000 |
||||
a1 0.520000 |
||||
a2 5.000000 |
||||
s9 5.000000 |
||||
* Repulsion: |
||||
kExp 1.500000 1.000000 |
||||
rExp 1.000000 |
||||
* Coulomb: |
||||
alpha 2.000000 |
||||
third order shell-resolved |
||||
anisotropic true |
||||
a3 3.000000 |
||||
a5 4.000000 |
||||
cn-shift 1.200000 |
||||
cn-exp 4.000000 |
||||
max-rad 5.000000 |
||||
|
||||
|
||||
................................................... |
||||
: SETUP : |
||||
:.................................................: |
||||
: # basis functions 6 : |
||||
: # atomic orbitals 6 : |
||||
: # shells 4 : |
||||
: # electrons 8 : |
||||
: max. iterations 250 : |
||||
: Hamiltonian GFN2-xTB : |
||||
: restarted? false : |
||||
: GBSA solvation false : |
||||
: PC potential false : |
||||
: electronic temp. 300.0000000 K : |
||||
: accuracy 1.0000000 : |
||||
: -> integral cutoff 0.2500000E+02 : |
||||
: -> integral neglect 0.1000000E-07 : |
||||
: -> SCF convergence 0.1000000E-05 Eh : |
||||
: -> wf. convergence 0.1000000E-03 e : |
||||
: Broyden damping 0.4000000 : |
||||
................................................... |
||||
|
||||
iter E dE RMSdq gap omega full diag |
||||
1 -5.1005103 -0.510051E+01 0.419E+00 14.71 0.0 T |
||||
2 -5.1019252 -0.141483E-02 0.240E+00 14.41 1.0 T |
||||
3 -5.1021667 -0.241498E-03 0.391E-01 14.18 1.0 T |
||||
4 -5.1022308 -0.641084E-04 0.843E-02 14.33 1.0 T |
||||
5 -5.1022332 -0.246222E-05 0.551E-02 14.28 1.0 T |
||||
6 -5.1022352 -0.194708E-05 0.107E-03 14.30 54.1 T |
||||
7 -5.1022352 0.126747E-09 0.102E-03 14.30 56.4 T |
||||
8 -5.1022352 -0.665856E-09 0.201E-05 14.30 2872.0 T |
||||
9 -5.1022352 -0.251354E-12 0.108E-07 14.30 100000.0 T |
||||
|
||||
*** convergence criteria satisfied after 9 iterations *** |
||||
|
||||
# Occupation Energy/Eh Energy/eV |
||||
------------------------------------------------------------- |
||||
1 2.0000 -0.6809644 -18.5300 |
||||
2 2.0000 -0.5645561 -15.3624 |
||||
3 2.0000 -0.5163314 -14.0501 |
||||
4 2.0000 -0.4474968 -12.1770 (HOMO) |
||||
5 0.0780978 2.1251 (LUMO) |
||||
6 0.2232972 6.0762 |
||||
------------------------------------------------------------- |
||||
HL-Gap 0.5255946 Eh 14.3022 eV |
||||
Fermi-level -0.1846995 Eh -5.0259 eV |
||||
|
||||
SCC (total) 0 d, 0 h, 0 min, 0.033 sec |
||||
SCC setup ... 0 min, 0.000 sec ( 0.138%) |
||||
Dispersion ... 0 min, 0.000 sec ( 0.017%) |
||||
classical contributions ... 0 min, 0.000 sec ( 0.015%) |
||||
integral evaluation ... 0 min, 0.000 sec ( 0.149%) |
||||
iterations ... 0 min, 0.033 sec ( 99.151%) |
||||
molecular gradient ... 0 min, 0.000 sec ( 0.289%) |
||||
printout ... 0 min, 0.000 sec ( 0.225%) |
||||
|
||||
::::::::::::::::::::::::::::::::::::::::::::::::::::: |
||||
:: SUMMARY :: |
||||
::::::::::::::::::::::::::::::::::::::::::::::::::::: |
||||
:: total energy -5.070123981303 Eh :: |
||||
:: gradient norm 0.017792229436 Eh/a0 :: |
||||
:: HOMO-LUMO gap 14.302156491823 eV :: |
||||
::.................................................:: |
||||
:: SCC energy -5.102235193405 Eh :: |
||||
:: -> isotropic ES 0.031392635975 Eh :: |
||||
:: -> anisotropic ES 0.000754364857 Eh :: |
||||
:: -> anisotropic XC -0.000693407516 Eh :: |
||||
:: -> dispersion -0.000141490641 Eh :: |
||||
:: repulsion energy 0.032111212067 Eh :: |
||||
:: add. restraining 0.000000000000 Eh :: |
||||
:: total charge 0.000000000000 e :: |
||||
::::::::::::::::::::::::::::::::::::::::::::::::::::: |
||||
|
||||
|
||||
Property printout bound to 'properties.out' |
||||
|
||||
------------------------------------------------- |
||||
| TOTAL ENERGY -5.070123981303 Eh | |
||||
| GRADIENT NORM 0.017792229436 Eh/α | |
||||
| HOMO-LUMO GAP 14.302156491823 eV | |
||||
------------------------------------------------- |
||||
|
||||
------------------------------------------------------------------------ |
||||
* finished run on 2022/04/28 at 11:27:34.626 |
||||
------------------------------------------------------------------------ |
||||
total: |
||||
* wall-time: 0 d, 0 h, 0 min, 0.039 sec |
||||
* cpu-time: 0 d, 0 h, 0 min, 0.007 sec |
||||
* ratio c/w: 0.169 speedup |
||||
SCF: |
||||
* wall-time: 0 d, 0 h, 0 min, 0.033 sec |
||||
* cpu-time: 0 d, 0 h, 0 min, 0.001 sec |
||||
* ratio c/w: 0.041 speedup |
||||
|
||||
|
||||
------------------------- -------------------- |
||||
FINAL SINGLE POINT ENERGY -5.070123981300 |
||||
------------------------- -------------------- |
||||
|
||||
|
||||
---------------------------------------------------------------------------- |
||||
ORCA NUMERICAL FREQUENCIES |
||||
---------------------------------------------------------------------------- |
||||
|
||||
Number of atoms ... 3 |
||||
Central differences ... used |
||||
Number of displacements ... 18 |
||||
Numerical increment ... 5.000e-03 bohr |
||||
IR-spectrum generation ... on |
||||
Raman-spectrum generation ... off |
||||
Surface Crossing Hessian ... off |
||||
|
||||
The output will be reduced. Please look at the following files: |
||||
SCF program output ... >cmmd.lastscf |
||||
Integral program output ... >cmmd.lastint |
||||
Gradient program output ... >cmmd.lastgrad |
||||
Dipole moment program output ... >cmmd.lastmom |
||||
AutoCI program output ... >cmmd.lastautoci |
||||
|
||||
<< Calculating on displaced geometry 1 (of 18) >> |
||||
<< Calculating on displaced geometry 2 (of 18) >> |
||||
<< Calculating on displaced geometry 3 (of 18) >> |
||||
<< Calculating on displaced geometry 4 (of 18) >> |
||||
<< Calculating on displaced geometry 5 (of 18) >> |
||||
<< Calculating on displaced geometry 6 (of 18) >> |
||||
<< Calculating on displaced geometry 7 (of 18) >> |
||||
<< Calculating on displaced geometry 8 (of 18) >> |
||||
<< Calculating on displaced geometry 9 (of 18) >> |
||||
<< Calculating on displaced geometry 10 (of 18) >> |
||||
<< Calculating on displaced geometry 11 (of 18) >> |
||||
<< Calculating on displaced geometry 12 (of 18) >> |
||||
<< Calculating on displaced geometry 13 (of 18) >> |
||||
<< Calculating on displaced geometry 14 (of 18) >> |
||||
<< Calculating on displaced geometry 15 (of 18) >> |
||||
<< Calculating on displaced geometry 16 (of 18) >> |
||||
<< Calculating on displaced geometry 17 (of 18) >> |
||||
<< Calculating on displaced geometry 18 (of 18) >> |
||||
|
||||
----------------------- |
||||
VIBRATIONAL FREQUENCIES |
||||
----------------------- |
||||
|
||||
Scaling factor for frequencies = 1.000000000 (already applied!) |
||||
|
||||
0: 0.00 cm**-1 |
||||
1: 0.00 cm**-1 |
||||
2: 0.00 cm**-1 |
||||
3: 0.00 cm**-1 |
||||
4: 0.00 cm**-1 |
||||
5: 0.00 cm**-1 |
||||
6: 1591.02 cm**-1 |
||||
7: 3532.22 cm**-1 |
||||
8: 3553.96 cm**-1 |
||||
|
||||
|
||||
------------ |
||||
NORMAL MODES |
||||
------------ |
||||
|
||||
These modes are the cartesian displacements weighted by the diagonal matrix |
||||
M(i,i)=1/sqrt(m[i]) where m[i] is the mass of the displaced atom |
||||
Thus, these vectors are normalized but *not* orthogonal |
||||
|
||||
0 1 2 3 4 5 |
||||
0 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 |
||||
1 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 |
||||
2 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 |
||||
3 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 |
||||
4 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 |
||||
5 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 |
||||
6 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 |
||||
7 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 |
||||
8 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 |
||||
6 7 8 |
||||
0 0.040721 -0.056762 -0.029045 |
||||
1 0.045366 0.031729 -0.032147 |
||||
2 0.035473 0.024811 -0.025137 |
||||
3 0.027275 0.702670 0.707675 |
||||
4 -0.555227 0.030998 -0.009740 |
||||
5 -0.434156 0.024236 -0.007618 |
||||
6 -0.673601 0.198259 -0.246669 |
||||
7 -0.164818 -0.534607 0.519974 |
||||
8 -0.128876 -0.418033 0.406591 |
||||
|
||||
|
||||
----------- |
||||
IR SPECTRUM |
||||
----------- |
||||
|
||||
Mode freq eps Int T**2 TX TY TZ |
||||
cm**-1 L/(mol*cm) km/mol a.u. |
||||
---------------------------------------------------------------------------- |
||||
6: 1591.02 0.024022 121.40 0.004712 (-0.035425 -0.046627 -0.035815) |
||||
7: 3532.22 0.000687 3.47 0.000061 ( 0.006792 -0.003138 -0.002177) |
||||
8: 3553.96 0.002224 11.24 0.000195 ( 0.012984 0.004205 0.003002) |
||||
|
||||
* The epsilon (eps) is given for a Dirac delta lineshape. |
||||
** The dipole moment derivative (T) already includes vibrational overlap. |
||||
|
||||
The first frequency considered to be a vibration is 6 |
||||
The total number of vibrations considered is 3 |
||||
|
||||
|
||||
-------------------------- |
||||
THERMOCHEMISTRY AT 298.15K |
||||
-------------------------- |
||||
|
||||
Temperature ... 298.15 K |
||||
Pressure ... 1.00 atm |
||||
Total Mass ... 18.02 AMU |
||||
|
||||
Throughout the following assumptions are being made: |
||||
(1) The electronic state is orbitally nondegenerate |
||||
(2) There are no thermally accessible electronically excited states |
||||
(3) Hindered rotations indicated by low frequency modes are not |
||||
treated as such but are treated as vibrations and this may |
||||
cause some error |
||||
(4) All equations used are the standard statistical mechanics |
||||
equations for an ideal gas |
||||
(5) All vibrations are strictly harmonic |
||||
|
||||
freq. 1591.02 E(vib) ... 0.00 |
||||
freq. 3532.22 E(vib) ... 0.00 |
||||
freq. 3553.96 E(vib) ... 0.00 |
||||
|
||||
------------ |
||||
INNER ENERGY |
||||
------------ |
||||
|
||||
The inner energy is: U= E(el) + E(ZPE) + E(vib) + E(rot) + E(trans) |
||||
E(el) - is the total energy from the electronic structure calculation |
||||
= E(kin-el) + E(nuc-el) + E(el-el) + E(nuc-nuc) |
||||
E(ZPE) - the the zero temperature vibrational energy from the frequency calculation |
||||
E(vib) - the the finite temperature correction to E(ZPE) due to population |
||||
of excited vibrational states |
||||
E(rot) - is the rotational thermal energy |
||||
E(trans)- is the translational thermal energy |
||||
|
||||
Summary of contributions to the inner energy U: |
||||
Electronic energy ... -5.07012398 Eh |
||||
Zero point energy ... 0.01976814 Eh 12.40 kcal/mol |
||||
Thermal vibrational correction ... 0.00000336 Eh 0.00 kcal/mol |
||||
Thermal rotational correction ... 0.00141627 Eh 0.89 kcal/mol |
||||
Thermal translational correction ... 0.00141627 Eh 0.89 kcal/mol |
||||
----------------------------------------------------------------------- |
||||
Total thermal energy -5.04751994 Eh |
||||
|
||||
|
||||
Summary of corrections to the electronic energy: |
||||
(perhaps to be used in another calculation) |
||||
Total thermal correction 0.00283590 Eh 1.78 kcal/mol |
||||
Non-thermal (ZPE) correction 0.01976814 Eh 12.40 kcal/mol |
||||
----------------------------------------------------------------------- |
||||
Total correction 0.02260404 Eh 14.18 kcal/mol |
||||
|
||||
|
||||
-------- |
||||
ENTHALPY |
||||
-------- |
||||
|
||||
The enthalpy is H = U + kB*T |
||||
kB is Boltzmann's constant |
||||
Total free energy ... -5.04751994 Eh |
||||
Thermal Enthalpy correction ... 0.00094421 Eh 0.59 kcal/mol |
||||
----------------------------------------------------------------------- |
||||
Total Enthalpy ... -5.04657573 Eh |
||||
|
||||
|
||||
Note: Rotational entropy computed according to Herzberg |
||||
Infrared and Raman Spectra, Chapter V,1, Van Nostrand Reinhold, 1945 |
||||
Point Group: C2v, Symmetry Number: 2 |
||||
Rotational constants in cm-1: 26.033328 14.586495 9.348515 |
||||
|
||||
Vibrational entropy computed according to the QRRHO of S. Grimme |
||||
Chem.Eur.J. 2012 18 9955 |
||||
|
||||
|
||||
------- |
||||
ENTROPY |
||||
------- |
||||
|
||||
The entropy contributions are T*S = T*(S(el)+S(vib)+S(rot)+S(trans)) |
||||
S(el) - electronic entropy |
||||
S(vib) - vibrational entropy |
||||
S(rot) - rotational entropy |
||||
S(trans)- translational entropy |
||||
The entropies will be listed as multiplied by the temperature to get |
||||
units of energy |
||||
|
||||
Electronic entropy ... 0.00000000 Eh 0.00 kcal/mol |
||||
Vibrational entropy ... 0.00000380 Eh 0.00 kcal/mol |
||||
Rotational entropy ... 0.00499716 Eh 3.14 kcal/mol |
||||
Translational entropy ... 0.01644380 Eh 10.32 kcal/mol |
||||
----------------------------------------------------------------------- |
||||
Final entropy term ... 0.02144476 Eh 13.46 kcal/mol |
||||
|
||||
In case the symmetry of your molecule has not been determined correctly |
||||
or in case you have a reason to use a different symmetry number we print |
||||
out the resulting rotational entropy values for sn=1,12 : |
||||
-------------------------------------------------------- |
||||
| sn= 1 | S(rot)= 0.00565162 Eh 3.55 kcal/mol| |
||||
| sn= 2 | S(rot)= 0.00499716 Eh 3.14 kcal/mol| |
||||
| sn= 3 | S(rot)= 0.00461433 Eh 2.90 kcal/mol| |
||||
| sn= 4 | S(rot)= 0.00434270 Eh 2.73 kcal/mol| |
||||
| sn= 5 | S(rot)= 0.00413202 Eh 2.59 kcal/mol| |
||||
| sn= 6 | S(rot)= 0.00395987 Eh 2.48 kcal/mol| |
||||
| sn= 7 | S(rot)= 0.00381433 Eh 2.39 kcal/mol| |
||||
| sn= 8 | S(rot)= 0.00368825 Eh 2.31 kcal/mol| |
||||
| sn= 9 | S(rot)= 0.00357704 Eh 2.24 kcal/mol| |
||||
| sn=10 | S(rot)= 0.00347756 Eh 2.18 kcal/mol| |
||||
| sn=11 | S(rot)= 0.00338757 Eh 2.13 kcal/mol| |
||||
| sn=12 | S(rot)= 0.00330541 Eh 2.07 kcal/mol| |
||||
-------------------------------------------------------- |
||||
|
||||
|
||||
------------------- |
||||
GIBBS FREE ENERGY |
||||
------------------- |
||||
|
||||
The Gibbs free energy is G = H - T*S |
||||
|
||||
Total enthalpy ... -5.04657573 Eh |
||||
Total entropy correction ... -0.02144476 Eh -13.46 kcal/mol |
||||
----------------------------------------------------------------------- |
||||
Final Gibbs free energy ... -5.06802049 Eh |
||||
|
||||
For completeness - the Gibbs free energy minus the electronic energy |
||||
G-E(el) ... 0.00210349 Eh 1.32 kcal/mol |
||||
|
||||
|
||||
|
||||
Timings for individual modules: |
||||
|
||||
Sum of individual times ... 43.304 sec (= 0.722 min) |
||||
Numerical frequency calculation ... 43.071 sec (= 0.718 min) 99.5 % |
||||
XTB module ... 0.232 sec (= 0.004 min) 0.5 % |
||||
****ORCA TERMINATED NORMALLY**** |
||||
TOTAL RUN TIME: 0 days 0 hours 0 minutes 43 seconds 500 msec |
||||
Binary file not shown.
@ -0,0 +1,5 @@ |
||||
3 |
||||
Coordinates from ORCA-job cmmd |
||||
O 0.92414308393591 0.05221745443381 -0.05277586891122 |
||||
H 1.88956263013796 0.09467860003036 -0.01957714288512 |
||||
H 0.65315428592613 0.78339394553583 0.51896301179633 |
||||
@ -0,0 +1,42 @@ |
||||
------------------------------------------------------------- |
||||
----------------------- !PROPERTIES! ------------------------ |
||||
------------------------------------------------------------- |
||||
# ----------------------------------------------------------- |
||||
$ THERMOCHEMISTRY_Energies |
||||
description: The Thermochemistry energies |
||||
geom. index: 0 |
||||
prop. index: 1 |
||||
Temperature (Kelvin) : 298.1500000000 |
||||
Pressure (atm) : 1.0000000000 |
||||
Total Mass (AMU) : 18.0150000000 |
||||
Spin Degeneracy : 1.0000000000 |
||||
Electronic Energy (Hartree) : -5.0701239813 |
||||
Translational Energy (Hartree) : 0.0014162714 |
||||
Rotational Energy (Hartree) : 0.0014162714 |
||||
Vibrational Energy (Hartree) : 0.0000033599 |
||||
Number of frequencies : 9 |
||||
Scaling Factor for frequencies : 1.0000000000 |
||||
Vibrational frequencies : |
||||
0 |
||||
0 0.000000 |
||||
1 0.000000 |
||||
2 0.000000 |
||||
3 0.000000 |
||||
4 0.000000 |
||||
5 0.000000 |
||||
6 1591.021914 |
||||
7 3532.222317 |
||||
8 3553.964928 |
||||
Zero Point Energy (Hartree) : 0.0197681370 |
||||
Inner Energy (Hartree) : -5.0475199415 |
||||
Enthalpy (Hartree) : -5.0465757325 |
||||
Electronic entropy : 0.0000000000 |
||||
Rotational entropy : 0.0049971600 |
||||
Vibrational entropy : 0.0000037975 |
||||
Translational entropy : 0.0049971600 |
||||
Entropy : 0.0214447594 |
||||
Gibbs Energy (Hartree) : -5.0680204919 |
||||
Is Linear : false |
||||
# ------------------------------------------------------------- |
||||
----------------------- !GEOMETRIES! ------------------------ |
||||
# ------------------------------------------------------------- |
||||
@ -0,0 +1,25 @@ |
||||
3 |
||||
Coordinates from ORCA-job cmmd E -76.321237910070 |
||||
O 0.925940 0.054220 -0.051210 |
||||
H 1.893830 0.090800 -0.022610 |
||||
H 0.647090 0.785270 0.520430 |
||||
3 |
||||
Coordinates from ORCA-job cmmd E -76.321265590472 |
||||
O 0.925302 0.053508 -0.051766 |
||||
H 1.890326 0.093285 -0.020667 |
||||
H 0.651232 0.783496 0.519043 |
||||
3 |
||||
Coordinates from ORCA-job cmmd E -76.321269032868 |
||||
O 0.924595 0.052721 -0.052382 |
||||
H 1.889691 0.094230 -0.019928 |
||||
H 0.652574 0.783339 0.518920 |
||||
3 |
||||
Coordinates from ORCA-job cmmd E -76.321269681211 |
||||
O 0.924146 0.052221 -0.052773 |
||||
H 1.889541 0.094688 -0.019570 |
||||
H 0.653172 0.783381 0.518953 |
||||
3 |
||||
Coordinates from ORCA-job cmmd E -76.321269681391 |
||||
O 0.924143 0.052217 -0.052776 |
||||
H 1.889563 0.094679 -0.019577 |
||||
H 0.653154 0.783394 0.518963 |
||||
@ -0,0 +1 @@ |
||||
O |
||||
@ -0,0 +1,5 @@ |
||||
3 |
||||
|
||||
O 0.92594 0.05422 -0.05121 |
||||
H 1.89383 0.09080 -0.02261 |
||||
H 0.64709 0.78527 0.52043 |
||||
@ -0,0 +1,10 @@ |
||||
#!/bin/bash |
||||
#SBATCH --nodes=1 |
||||
#SBATCH --ntasks=1 |
||||
#SBATCH --cpus-per-task=1 |
||||
#SBATCH --time=168:0:0 |
||||
export LD_LIBRARY_PATH=/home/adit/opt/openmpi411/lib:$LD_LIBRARY_PATH |
||||
export PATH=/home/adit/opt/openmpi411/bin:$PATH |
||||
export OMP_NUM_THREADS=1 |
||||
cd $PWD |
||||
$ORCA_COMMAND cmmd.in > cmmd.out --oversubscribe |
||||
@ -0,0 +1,8 @@ |
||||
#!/bin/bash |
||||
#SBATCH --nodes=1 |
||||
#SBATCH --ntasks=1 |
||||
#SBATCH --cpus-per-task=1 |
||||
#SBATCH --time=168:0:0 |
||||
export OMP_NUM_THREADS=1 |
||||
cd $PWD |
||||
obabel geom.smi -O geom.xyz --gen3d |
||||
@ -0,0 +1 @@ |
||||
1 molecule converted |
||||
@ -0,0 +1,22 @@ |
||||
# |
||||
# Number of atoms |
||||
# |
||||
2 |
||||
# |
||||
# The current total energy in Eh |
||||
# |
||||
-7.906649846780 |
||||
# |
||||
# The current gradient in Eh/bohr |
||||
# |
||||
0.013068499674 |
||||
-0.000000000007 |
||||
-0.000000000001 |
||||
-0.013068499674 |
||||
0.000000000007 |
||||
0.000000000001 |
||||
# |
||||
# The atomic numbers and current coordinates in Bohr |
||||
# |
||||
8 1.9411149 -0.1746107 -0.0166863 |
||||
8 4.2114933 -0.1746107 -0.0166863 |
||||
Binary file not shown.
@ -0,0 +1,94 @@ |
||||
|
||||
$orca_hessian_file |
||||
|
||||
$act_atom |
||||
0 |
||||
|
||||
$act_coord |
||||
0 |
||||
|
||||
$act_energy |
||||
-7.906650 |
||||
|
||||
$hessian |
||||
6 |
||||
0 1 2 3 4 |
||||
0 8.4758564328E-01 -1.9586528653E-13 9.9420864020E-15 -8.4758564327E-01 4.4592567559E-13 |
||||
1 -1.9586528653E-13 -5.7540195132E-03 -2.3384841278E-14 -9.0456931015E-13 5.7540195134E-03 |
||||
2 9.9420864020E-15 -2.3384841278E-14 -5.7540195132E-03 -1.1572655252E-13 2.3972966388E-14 |
||||
3 -8.4758564327E-01 -9.0456931015E-13 -1.1572655252E-13 8.4758564327E-01 6.5450892109E-13 |
||||
4 4.4592567559E-13 5.7540195134E-03 2.3972966388E-14 6.5450892109E-13 -5.7540195136E-03 |
||||
5 3.4003837488E-13 3.2581672750E-16 5.7540195134E-03 -2.3425390876E-13 -9.1394183800E-16 |
||||
5 |
||||
0 3.4003837488E-13 |
||||
1 3.2581672750E-16 |
||||
2 5.7540195134E-03 |
||||
3 -2.3425390876E-13 |
||||
4 -9.1394183800E-16 |
||||
5 -5.7540195136E-03 |
||||
|
||||
$vibrational_frequencies |
||||
6 |
||||
0 0.000000 |
||||
1 0.000000 |
||||
2 0.000000 |
||||
3 0.000000 |
||||
4 0.000000 |
||||
5 1673.234280 |
||||
|
||||
$normal_modes |
||||
6 6 |
||||
0 1 2 3 4 |
||||
0 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 |
||||
1 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 |
||||
2 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 |
||||
3 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 |
||||
4 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 |
||||
5 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 |
||||
5 |
||||
0 7.0710678119E-01 |
||||
1 0.0000000000E+00 |
||||
2 0.0000000000E+00 |
||||
3 -7.0710678119E-01 |
||||
4 0.0000000000E+00 |
||||
5 0.0000000000E+00 |
||||
|
||||
# |
||||
# The atoms: label mass x y z (in bohrs) |
||||
# |
||||
$atoms |
||||
2 |
||||
O 15.99900 1.941114862176 -0.174610694774 -0.016686281763 |
||||
O 15.99900 4.211493279168 -0.174610694774 -0.016686281763 |
||||
|
||||
$actual_temperature |
||||
0.000000 |
||||
|
||||
$frequency_scale_factor |
||||
1.000000 |
||||
|
||||
$dipole_derivatives |
||||
6 |
||||
0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 |
||||
0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 |
||||
0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 |
||||
0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 |
||||
0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 |
||||
0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 |
||||
|
||||
# |
||||
# The IR spectrum |
||||
# wavenumber eps Int TX TY TZ |
||||
# |
||||
$ir_spectrum |
||||
6 |
||||
0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000 |
||||
0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000 |
||||
0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000 |
||||
0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000 |
||||
0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000 |
||||
1673.23 0.00000000 0.00000000 0.000000 0.000000 0.000000 |
||||
|
||||
|
||||
$end |
||||
|
||||
@ -0,0 +1,13 @@ |
||||
#CMMDE generated Orca input file |
||||
!XTB2 Numfreq |
||||
%pal |
||||
nprocs 1 |
||||
end |
||||
|
||||
*xyzfile 0 1 cmmd.xyz |
||||
|
||||
%freq |
||||
scalfreq 1 |
||||
Temp 298.15 |
||||
Pressure 1.0 |
||||
end |
||||
@ -0,0 +1,90 @@ |
||||
|
||||
$orca_opt_file |
||||
|
||||
$trust |
||||
0.300000000000 |
||||
|
||||
$epredict |
||||
0.000000000000 |
||||
|
||||
$ediffsc |
||||
1000.000000000000 |
||||
|
||||
$ctyp |
||||
3 |
||||
|
||||
$coordinates |
||||
5 6 |
||||
1.86498962 -0.17461069 -0.01668628 4.28761852 -0.17461069 -0.01668628 |
||||
|
||||
1.92904409 -0.17461069 -0.01668628 4.22356405 -0.17461069 -0.01668628 |
||||
|
||||
1.94530163 -0.17461069 -0.01668628 4.20730651 -0.17461069 -0.01668628 |
||||
|
||||
1.94090974 -0.17461069 -0.01668628 4.21169840 -0.17461069 -0.01668628 |
||||
|
||||
1.94110955 -0.17461069 -0.01668628 4.21149859 -0.17461069 -0.01668628 |
||||
|
||||
|
||||
# redundant internal coordinates |
||||
# nbonds nangles ndihedrals nimpropers ncartesians |
||||
# bond definitions A B |
||||
# angle definitions A B C |
||||
# dihedral definitions A B C D |
||||
# improper torsion definitions A B C D |
||||
# cartesian definitions A x/y/z |
||||
$redundant_internals |
||||
1 0 0 0 0 |
||||
1 0 0 |
||||
$energies |
||||
5 |
||||
-150.0735671197928411 |
||||
-150.0814796331173113 |
||||
-150.0816905296451864 |
||||
-150.0817207523842285 |
||||
-150.0817208238475189 |
||||
|
||||
$gradients |
||||
5 6 |
||||
-0.0970701356891092 0.0000000037705223 -0.0000000020745829 0.0970701396000397 |
||||
0.0000000041241647 0.0000000045418583 |
||||
-0.0196664709248346 0.0000000000788218 -0.0000000002131847 0.0196664777184270 |
||||
0.0000000059598546 0.0000000058290589 |
||||
0.0072800276715361 0.0000000014684576 0.0000000012614792 -0.0072800235313076 |
||||
-0.0000000014076424 0.0000000011235850 |
||||
-0.0003470003285211 0.0000000013188094 0.0000000005114984 0.0003470040777374 |
||||
-0.0000000019503669 -0.0000000003265739 |
||||
-0.0000089794375978 0.0000000016304541 0.0000000005607051 0.0000089823666367 |
||||
-0.0000000013571736 0.0000000007610567 |
||||
|
||||
$redundant_coords |
||||
5 1 |
||||
2.4226289036870434 |
||||
2.2945199680204644 |
||||
2.2620048732196394 |
||||
2.2707886655429821 |
||||
2.2703890347982991 |
||||
|
||||
$redundant_gradients |
||||
5 1 |
||||
0.0970701376445745 |
||||
0.0196664743216308 |
||||
-0.0072800256014219 |
||||
0.0003470022031292 |
||||
0.0000089809021172 |
||||
|
||||
$hessian_approx |
||||
6 6 |
||||
0 1 2 3 4 5 |
||||
0 0.845855 0.000001 0.000000 -0.845857 0.000001 0.000003 |
||||
1 0.000001 0.000000 0.000000 -0.000001 0.000000 0.000000 |
||||
2 0.000000 0.000000 0.000000 -0.000000 0.000000 0.000000 |
||||
3 -0.845857 -0.000001 -0.000000 0.845859 -0.000001 -0.000003 |
||||
4 0.000001 0.000000 0.000000 -0.000001 0.000000 0.000000 |
||||
5 0.000003 0.000000 0.000000 -0.000003 0.000000 0.000000 |
||||
|
||||
$bmatrix |
||||
1 6 |
||||
0 1 2 3 4 5 |
||||
0 -1.000000 0.000000 0.000000 1.000000 -0.000000 -0.000000 |
||||
|
||||
@ -0,0 +1,612 @@ |
||||
|
||||
***************** |
||||
* O R C A * |
||||
***************** |
||||
|
||||
#, |
||||
### |
||||
#### |
||||
##### |
||||
###### |
||||
########, |
||||
,,################,,,,, |
||||
,,#################################,, |
||||
,,##########################################,, |
||||
,#########################################, ''#####, |
||||
,#############################################,, '####, |
||||
,##################################################,,,,####, |
||||
,###########'''' ''''############################### |
||||
,#####'' ,,,,##########,,,, '''####''' '#### |
||||
,##' ,,,,###########################,,, '## |
||||
' ,,###'''' '''############,,, |
||||
,,##'' '''############,,,, ,,,,,,###'' |
||||
,#'' '''#######################''' |
||||
' ''''####'''' |
||||
,#######, #######, ,#######, ## |
||||
,#' '#, ## ## ,#' '#, #''# ###### ,####, |
||||
## ## ## ,#' ## #' '# # #' '# |
||||
## ## ####### ## ,######, #####, # # |
||||
'#, ,#' ## ## '#, ,#' ,# #, ## #, ,# |
||||
'#######' ## ## '#######' #' '# #####' # '####' |
||||
|
||||
|
||||
|
||||
####################################################### |
||||
# -***- # |
||||
# Department of theory and spectroscopy # |
||||
# Directorship and core code : Frank Neese # |
||||
# Max Planck Institute fuer Kohlenforschung # |
||||
# Kaiser Wilhelm Platz 1 # |
||||
# D-45470 Muelheim/Ruhr # |
||||
# Germany # |
||||
# # |
||||
# All rights reserved # |
||||
# -***- # |
||||
####################################################### |
||||
|
||||
|
||||
Program Version 5.0.2 - RELEASE - |
||||
|
||||
|
||||
With contributions from (in alphabetic order): |
||||
Daniel Aravena : Magnetic Suceptibility |
||||
Michael Atanasov : Ab Initio Ligand Field Theory (pilot matlab implementation) |
||||
Alexander A. Auer : GIAO ZORA, VPT2 properties, NMR spectrum |
||||
Ute Becker : Parallelization |
||||
Giovanni Bistoni : ED, misc. LED, open-shell LED, HFLD |
||||
Martin Brehm : Molecular dynamics |
||||
Dmytro Bykov : SCF Hessian |
||||
Vijay G. Chilkuri : MRCI spin determinant printing, contributions to CSF-ICE |
||||
Dipayan Datta : RHF DLPNO-CCSD density |
||||
Achintya Kumar Dutta : EOM-CC, STEOM-CC |
||||
Dmitry Ganyushin : Spin-Orbit,Spin-Spin,Magnetic field MRCI |
||||
Miquel Garcia : C-PCM and meta-GGA Hessian, CC/C-PCM, Gaussian charge scheme |
||||
Yang Guo : DLPNO-NEVPT2, F12-NEVPT2, CIM, IAO-localization |
||||
Andreas Hansen : Spin unrestricted coupled pair/coupled cluster methods |
||||
Benjamin Helmich-Paris : MC-RPA, TRAH-SCF, COSX integrals |
||||
Lee Huntington : MR-EOM, pCC |
||||
Robert Izsak : Overlap fitted RIJCOSX, COSX-SCS-MP3, EOM |
||||
Marcus Kettner : VPT2 |
||||
Christian Kollmar : KDIIS, OOCD, Brueckner-CCSD(T), CCSD density, CASPT2, CASPT2-K |
||||
Simone Kossmann : Meta GGA functionals, TD-DFT gradient, OOMP2, MP2 Hessian |
||||
Martin Krupicka : Initial AUTO-CI |
||||
Lucas Lang : DCDCAS |
||||
Marvin Lechner : AUTO-CI (C++ implementation), FIC-MRCC |
||||
Dagmar Lenk : GEPOL surface, SMD |
||||
Dimitrios Liakos : Extrapolation schemes; Compound Job, initial MDCI parallelization |
||||
Dimitrios Manganas : Further ROCIS development; embedding schemes |
||||
Dimitrios Pantazis : SARC Basis sets |
||||
Anastasios Papadopoulos: AUTO-CI, single reference methods and gradients |
||||
Taras Petrenko : DFT Hessian,TD-DFT gradient, ASA, ECA, R-Raman, ABS, FL, XAS/XES, NRVS |
||||
Peter Pinski : DLPNO-MP2, DLPNO-MP2 Gradient |
||||
Christoph Reimann : Effective Core Potentials |
||||
Marius Retegan : Local ZFS, SOC |
||||
Christoph Riplinger : Optimizer, TS searches, QM/MM, DLPNO-CCSD(T), (RO)-DLPNO pert. Triples |
||||
Tobias Risthaus : Range-separated hybrids, TD-DFT gradient, RPA, STAB |
||||
Michael Roemelt : Original ROCIS implementation |
||||
Masaaki Saitow : Open-shell DLPNO-CCSD energy and density |
||||
Barbara Sandhoefer : DKH picture change effects |
||||
Avijit Sen : IP-ROCIS |
||||
Kantharuban Sivalingam : CASSCF convergence, NEVPT2, FIC-MRCI |
||||
Bernardo de Souza : ESD, SOC TD-DFT |
||||
Georgi Stoychev : AutoAux, RI-MP2 NMR, DLPNO-MP2 response |
||||
Willem Van den Heuvel : Paramagnetic NMR |
||||
Boris Wezisla : Elementary symmetry handling |
||||
Frank Wennmohs : Technical directorship |
||||
|
||||
|
||||
We gratefully acknowledge several colleagues who have allowed us to |
||||
interface, adapt or use parts of their codes: |
||||
Stefan Grimme, W. Hujo, H. Kruse, P. Pracht, : VdW corrections, initial TS optimization, |
||||
C. Bannwarth, S. Ehlert DFT functionals, gCP, sTDA/sTD-DF |
||||
Ed Valeev, F. Pavosevic, A. Kumar : LibInt (2-el integral package), F12 methods |
||||
Garnet Chan, S. Sharma, J. Yang, R. Olivares : DMRG |
||||
Ulf Ekstrom : XCFun DFT Library |
||||
Mihaly Kallay : mrcc (arbitrary order and MRCC methods) |
||||
Jiri Pittner, Ondrej Demel : Mk-CCSD |
||||
Frank Weinhold : gennbo (NPA and NBO analysis) |
||||
Christopher J. Cramer and Donald G. Truhlar : smd solvation model |
||||
Lars Goerigk : TD-DFT with DH, B97 family of functionals |
||||
V. Asgeirsson, H. Jonsson : NEB implementation |
||||
FAccTs GmbH : IRC, NEB, NEB-TS, DLPNO-Multilevel, CI-OPT |
||||
MM, QMMM, 2- and 3-layer-ONIOM, Crystal-QMMM, |
||||
LR-CPCM, SF, NACMEs, symmetry and pop. for TD-DFT, |
||||
nearIR, NL-DFT gradient (VV10), updates on ESD, |
||||
ML-optimized integration grids |
||||
S Lehtola, MJT Oliveira, MAL Marques : LibXC Library |
||||
Liviu Ungur et al : ANISO software |
||||
|
||||
|
||||
Your calculation uses the libint2 library for the computation of 2-el integrals |
||||
For citations please refer to: http://libint.valeyev.net |
||||
|
||||
Your ORCA version has been built with support for libXC version: 5.1.0 |
||||
For citations please refer to: https://tddft.org/programs/libxc/ |
||||
|
||||
This ORCA versions uses: |
||||
CBLAS interface : Fast vector & matrix operations |
||||
LAPACKE interface : Fast linear algebra routines |
||||
SCALAPACK package : Parallel linear algebra routines |
||||
Shared memory : Shared parallel matrices |
||||
BLAS/LAPACK : OpenBLAS 0.3.15 USE64BITINT DYNAMIC_ARCH NO_AFFINITY SkylakeX SINGLE_THREADED |
||||
Core in use : SkylakeX |
||||
Copyright (c) 2011-2014, The OpenBLAS Project |
||||
|
||||
|
||||
|
||||
|
||||
*************************************** |
||||
The coordinates will be read from file: cmmd.xyz |
||||
*************************************** |
||||
|
||||
|
||||
Your calculation utilizes the semiempirical GFN2-xTB method |
||||
Please cite in your paper: |
||||
C. Bannwarth, Ehlert S., S. Grimme, J. Chem. Theory Comput., 15, (2019), 1652. |
||||
|
||||
|
||||
================================================================================ |
||||
|
||||
================================================================================ |
||||
WARNINGS |
||||
Please study these warnings very carefully! |
||||
================================================================================ |
||||
|
||||
WARNING: Old DensityContainer found on disk! |
||||
Will remove this file - |
||||
If you want to keep old densities, please start your calculation with a different basename. |
||||
|
||||
WARNING: Gradients needed for Numerical Frequencies |
||||
===> : Setting RunTyp to EnGrad |
||||
|
||||
WARNING: Found dipole moment calculation with XTB calculation |
||||
===> : Switching off dipole moment calculation |
||||
|
||||
|
||||
WARNING: TRAH-SCF for XTB is not implemented! |
||||
===> : Turning TRAH off! |
||||
|
||||
================================================================================ |
||||
INPUT FILE |
||||
================================================================================ |
||||
NAME = cmmd.in |
||||
| 1> #CMMDE generated Orca input file |
||||
| 2> !XTB2 Numfreq |
||||
| 3> %pal |
||||
| 4> nprocs 1 |
||||
| 5> end |
||||
| 6> |
||||
| 7> *xyzfile 0 1 cmmd.xyz |
||||
| 8> |
||||
| 9> %freq |
||||
| 10> scalfreq 1 |
||||
| 11> Temp 298.15 |
||||
| 12> Pressure 1.0 |
||||
| 13> end |
||||
| 14> |
||||
| 15> ****END OF INPUT**** |
||||
================================================================================ |
||||
|
||||
******************************* |
||||
* Energy+Gradient Calculation * |
||||
******************************* |
||||
|
||||
----------------------------------------------------------- |
||||
| ===================== | |
||||
| x T B | |
||||
| ===================== | |
||||
| S. Grimme | |
||||
| Mulliken Center for Theoretical Chemistry | |
||||
| University of Bonn | |
||||
| Aditya W. Sakti | |
||||
| Departemen Kimia | |
||||
| Universitas Pertamina | |
||||
----------------------------------------------------------- |
||||
|
||||
* xtb version 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54) compiled by '@Linux' on 12/03/2021 |
||||
|
||||
xtb is free software: you can redistribute it and/or modify it under |
||||
the terms of the GNU Lesser General Public License as published by |
||||
the Free Software Foundation, either version 3 of the License, or |
||||
(at your option) any later version. |
||||
|
||||
xtb is distributed in the hope that it will be useful, |
||||
but WITHOUT ANY WARRANTY; without even the implied warranty of |
||||
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
||||
GNU Lesser General Public License for more details. |
||||
|
||||
Cite this work as: |
||||
* C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht, |
||||
J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11, |
||||
e01493. DOI: 10.1002/wcms.1493 |
||||
|
||||
for GFN2-xTB: |
||||
* C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019, |
||||
15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176 |
||||
for GFN1-xTB: |
||||
* S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017, |
||||
13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118 |
||||
for GFN0-xTB: |
||||
* P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint. |
||||
DOI: 10.26434/chemrxiv.8326202.v1 |
||||
for GFN-FF: |
||||
* S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673. |
||||
DOI: 10.1002/anie.202004239 |
||||
|
||||
for ALPB and GBSA implicit solvation: |
||||
* S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput., |
||||
2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471 |
||||
|
||||
for DFT-D4: |
||||
* E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017, |
||||
147, 034112. DOI: 10.1063/1.4993215 |
||||
* E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher, |
||||
C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122. |
||||
DOI: 10.1063/1.5090222 |
||||
* E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys. |
||||
2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A |
||||
|
||||
for sTDA-xTB: |
||||
* S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103. |
||||
DOI: 10.1063/1.4959605 |
||||
|
||||
in the mass-spec context: |
||||
* V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879. |
||||
DOI: 10.1039/c7sc00601b |
||||
* J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133. |
||||
DOI: 10.1021/acsomega.9b02011 |
||||
|
||||
for metadynamics refer to: |
||||
* S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862 |
||||
DOI: 10.1021/acs.jctc.9b00143 |
||||
|
||||
for SPH calculations refer to: |
||||
* S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714 |
||||
DOI: 10.1021/acs.jctc.0c01306 |
||||
|
||||
with help from (in alphabetical order) |
||||
P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher |
||||
M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, J. Koopman |
||||
C. Lavigne, S. Lehtola, F. März, M. Müller, F. Musil, H. Neugebauer |
||||
J. Pisarek, C. Plett, P. Pracht, J. Seibert, P. Shushkov, S. Spicher |
||||
M. Stahn, M. Steiner, T. Strunk, J. Stückrath, T. Rose, and J. Unsleber |
||||
|
||||
* started run on 2022/04/28 at 11:27:40.328 |
||||
|
||||
------------------------------------------------- |
||||
| Calculation Setup | |
||||
------------------------------------------------- |
||||
|
||||
program call : /home/adit/opt/orca/otool_xtb cmmd_XTB.xyz --grad -c 0 -u 0 -P 1 --namespace cmmd --input cmmd_XTB.input.tmp --acc 1.000000 |
||||
hostname : compute |
||||
calculation namespace : cmmd |
||||
coordinate file : cmmd_XTB.xyz |
||||
number of atoms : 2 |
||||
number of electrons : 12 |
||||
charge : 0 |
||||
spin : 0.0 |
||||
first test random number : 0.84096853316258 |
||||
|
||||
ID Z sym. atoms |
||||
1 8 O 1, 2 |
||||
|
||||
------------------------------------------------- |
||||
| G F N 2 - x T B | |
||||
------------------------------------------------- |
||||
|
||||
Reference 10.1021/acs.jctc.8b01176 |
||||
* Hamiltonian: |
||||
H0-scaling (s, p, d) 1.850000 2.230000 2.230000 |
||||
zeta-weighting 0.500000 |
||||
* Dispersion: |
||||
s8 2.700000 |
||||
a1 0.520000 |
||||
a2 5.000000 |
||||
s9 5.000000 |
||||
* Repulsion: |
||||
kExp 1.500000 1.000000 |
||||
rExp 1.000000 |
||||
* Coulomb: |
||||
alpha 2.000000 |
||||
third order shell-resolved |
||||
anisotropic true |
||||
a3 3.000000 |
||||
a5 4.000000 |
||||
cn-shift 1.200000 |
||||
cn-exp 4.000000 |
||||
max-rad 5.000000 |
||||
|
||||
|
||||
................................................... |
||||
: SETUP : |
||||
:.................................................: |
||||
: # basis functions 8 : |
||||
: # atomic orbitals 8 : |
||||
: # shells 4 : |
||||
: # electrons 12 : |
||||
: max. iterations 250 : |
||||
: Hamiltonian GFN2-xTB : |
||||
: restarted? false : |
||||
: GBSA solvation false : |
||||
: PC potential false : |
||||
: electronic temp. 300.0000000 K : |
||||
: accuracy 1.0000000 : |
||||
: -> integral cutoff 0.2500000E+02 : |
||||
: -> integral neglect 0.1000000E-07 : |
||||
: -> SCF convergence 0.1000000E-05 Eh : |
||||
: -> wf. convergence 0.1000000E-03 e : |
||||
: Broyden damping 0.4000000 : |
||||
................................................... |
||||
|
||||
iter E dE RMSdq gap omega full diag |
||||
1 -7.9155572 -0.791556E+01 0.407E+00 0.00 0.0 T |
||||
2 -7.9155697 -0.125362E-04 0.246E+00 0.00 1.0 T |
||||
3 -7.9155792 -0.944533E-05 0.542E-02 0.00 1.3 T |
||||
4 -7.9155792 -0.302522E-08 0.166E-02 0.00 4.3 T |
||||
5 -7.9155792 -0.836504E-10 0.345E-05 0.00 2049.3 T |
||||
6 -7.9155792 0.355271E-14 0.271E-07 0.00 100000.0 T |
||||
|
||||
*** convergence criteria satisfied after 6 iterations *** |
||||
|
||||
# Occupation Energy/Eh Energy/eV |
||||
------------------------------------------------------------- |
||||
1 2.0000 -0.8284027 -22.5420 |
||||
2 2.0000 -0.7371506 -20.0589 |
||||
3 2.0000 -0.6631440 -18.0451 |
||||
4 2.0000 -0.6631440 -18.0451 |
||||
5 2.0000 -0.6374674 -17.3464 |
||||
6 1.0000 -0.4399644 -11.9720 (HOMO) |
||||
7 1.0000 -0.4399644 -11.9720 (LUMO) |
||||
8 0.1444079 3.9295 |
||||
------------------------------------------------------------- |
||||
HL-Gap 0.0000000 Eh 0.0000 eV |
||||
Fermi-level -0.4399644 Eh -11.9720 eV |
||||
|
||||
SCC (total) 0 d, 0 h, 0 min, 0.050 sec |
||||
SCC setup ... 0 min, 0.000 sec ( 0.151%) |
||||
Dispersion ... 0 min, 0.000 sec ( 0.040%) |
||||
classical contributions ... 0 min, 0.000 sec ( 0.017%) |
||||
integral evaluation ... 0 min, 0.000 sec ( 0.294%) |
||||
iterations ... 0 min, 0.050 sec ( 98.980%) |
||||
molecular gradient ... 0 min, 0.000 sec ( 0.333%) |
||||
printout ... 0 min, 0.000 sec ( 0.168%) |
||||
|
||||
::::::::::::::::::::::::::::::::::::::::::::::::::::: |
||||
:: SUMMARY :: |
||||
::::::::::::::::::::::::::::::::::::::::::::::::::::: |
||||
:: total energy -7.906649846778 Eh :: |
||||
:: gradient norm 0.018481649479 Eh/a0 :: |
||||
:: HOMO-LUMO gap 0.000000000015 eV :: |
||||
::.................................................:: |
||||
:: SCC energy -7.915579172539 Eh :: |
||||
:: -> isotropic ES -0.000237652172 Eh :: |
||||
:: -> anisotropic ES 0.003738001563 Eh :: |
||||
:: -> anisotropic XC -0.007283115557 Eh :: |
||||
:: -> dispersion -0.000194539012 Eh :: |
||||
:: repulsion energy 0.008929325760 Eh :: |
||||
:: add. restraining 0.000000000000 Eh :: |
||||
:: total charge 0.000000000000 e :: |
||||
::::::::::::::::::::::::::::::::::::::::::::::::::::: |
||||
|
||||
|
||||
Property printout bound to 'properties.out' |
||||
|
||||
------------------------------------------------- |
||||
| TOTAL ENERGY -7.906649846778 Eh | |
||||
| GRADIENT NORM 0.018481649479 Eh/α | |
||||
| HOMO-LUMO GAP 0.000000000015 eV | |
||||
------------------------------------------------- |
||||
|
||||
------------------------------------------------------------------------ |
||||
* finished run on 2022/04/28 at 11:27:40.387 |
||||
------------------------------------------------------------------------ |
||||
total: |
||||
* wall-time: 0 d, 0 h, 0 min, 0.059 sec |
||||
* cpu-time: 0 d, 0 h, 0 min, 0.012 sec |
||||
* ratio c/w: 0.196 speedup |
||||
SCF: |
||||
* wall-time: 0 d, 0 h, 0 min, 0.050 sec |
||||
* cpu-time: 0 d, 0 h, 0 min, 0.003 sec |
||||
* ratio c/w: 0.058 speedup |
||||
|
||||
|
||||
------------------------- -------------------- |
||||
FINAL SINGLE POINT ENERGY -7.906649846780 |
||||
------------------------- -------------------- |
||||
|
||||
|
||||
---------------------------------------------------------------------------- |
||||
ORCA NUMERICAL FREQUENCIES |
||||
---------------------------------------------------------------------------- |
||||
|
||||
Number of atoms ... 2 |
||||
Central differences ... used |
||||
Number of displacements ... 12 |
||||
Numerical increment ... 5.000e-03 bohr |
||||
IR-spectrum generation ... on |
||||
Raman-spectrum generation ... off |
||||
Surface Crossing Hessian ... off |
||||
|
||||
The output will be reduced. Please look at the following files: |
||||
SCF program output ... >cmmd.lastscf |
||||
Integral program output ... >cmmd.lastint |
||||
Gradient program output ... >cmmd.lastgrad |
||||
Dipole moment program output ... >cmmd.lastmom |
||||
AutoCI program output ... >cmmd.lastautoci |
||||
|
||||
<< Calculating on displaced geometry 1 (of 12) >> |
||||
<< Calculating on displaced geometry 2 (of 12) >> |
||||
<< Calculating on displaced geometry 3 (of 12) >> |
||||
<< Calculating on displaced geometry 4 (of 12) >> |
||||
<< Calculating on displaced geometry 5 (of 12) >> |
||||
<< Calculating on displaced geometry 6 (of 12) >> |
||||
<< Calculating on displaced geometry 7 (of 12) >> |
||||
<< Calculating on displaced geometry 8 (of 12) >> |
||||
<< Calculating on displaced geometry 9 (of 12) >> |
||||
<< Calculating on displaced geometry 10 (of 12) >> |
||||
<< Calculating on displaced geometry 11 (of 12) >> |
||||
<< Calculating on displaced geometry 12 (of 12) >> |
||||
|
||||
----------------------- |
||||
VIBRATIONAL FREQUENCIES |
||||
----------------------- |
||||
|
||||
Scaling factor for frequencies = 1.000000000 (already applied!) |
||||
|
||||
0: 0.00 cm**-1 |
||||
1: 0.00 cm**-1 |
||||
2: 0.00 cm**-1 |
||||
3: 0.00 cm**-1 |
||||
4: 0.00 cm**-1 |
||||
5: 1673.23 cm**-1 |
||||
|
||||
|
||||
------------ |
||||
NORMAL MODES |
||||
------------ |
||||
|
||||
These modes are the cartesian displacements weighted by the diagonal matrix |
||||
M(i,i)=1/sqrt(m[i]) where m[i] is the mass of the displaced atom |
||||
Thus, these vectors are normalized but *not* orthogonal |
||||
|
||||
0 1 2 3 4 5 |
||||
0 0.000000 0.000000 0.000000 0.000000 0.000000 0.707107 |
||||
1 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 |
||||
2 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 |
||||
3 0.000000 0.000000 0.000000 0.000000 0.000000 -0.707107 |
||||
4 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 |
||||
5 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 |
||||
|
||||
|
||||
----------- |
||||
IR SPECTRUM |
||||
----------- |
||||
|
||||
Mode freq eps Int T**2 TX TY TZ |
||||
cm**-1 L/(mol*cm) km/mol a.u. |
||||
---------------------------------------------------------------------------- |
||||
5: 1673.23 0.000000 0.00 0.000000 ( 0.000000 0.000000 0.000000) |
||||
|
||||
* The epsilon (eps) is given for a Dirac delta lineshape. |
||||
** The dipole moment derivative (T) already includes vibrational overlap. |
||||
|
||||
The first frequency considered to be a vibration is 5 |
||||
The total number of vibrations considered is 1 |
||||
|
||||
|
||||
-------------------------- |
||||
THERMOCHEMISTRY AT 298.15K |
||||
-------------------------- |
||||
|
||||
Temperature ... 298.15 K |
||||
Pressure ... 1.00 atm |
||||
Total Mass ... 32.00 AMU |
||||
The molecule is recognized as being linear |
||||
|
||||
Throughout the following assumptions are being made: |
||||
(1) The electronic state is orbitally nondegenerate |
||||
(2) There are no thermally accessible electronically excited states |
||||
(3) Hindered rotations indicated by low frequency modes are not |
||||
treated as such but are treated as vibrations and this may |
||||
cause some error |
||||
(4) All equations used are the standard statistical mechanics |
||||
equations for an ideal gas |
||||
(5) All vibrations are strictly harmonic |
||||
|
||||
freq. 1673.23 E(vib) ... 0.00 |
||||
|
||||
------------ |
||||
INNER ENERGY |
||||
------------ |
||||
|
||||
The inner energy is: U= E(el) + E(ZPE) + E(vib) + E(rot) + E(trans) |
||||
E(el) - is the total energy from the electronic structure calculation |
||||
= E(kin-el) + E(nuc-el) + E(el-el) + E(nuc-nuc) |
||||
E(ZPE) - the the zero temperature vibrational energy from the frequency calculation |
||||
E(vib) - the the finite temperature correction to E(ZPE) due to population |
||||
of excited vibrational states |
||||
E(rot) - is the rotational thermal energy |
||||
E(trans)- is the translational thermal energy |
||||
|
||||
Summary of contributions to the inner energy U: |
||||
Electronic energy ... -7.90664985 Eh |
||||
Zero point energy ... 0.00381191 Eh 2.39 kcal/mol |
||||
Thermal vibrational correction ... 0.00000238 Eh 0.00 kcal/mol |
||||
Thermal rotational correction ... 0.00094418 Eh 0.59 kcal/mol |
||||
Thermal translational correction ... 0.00141627 Eh 0.89 kcal/mol |
||||
----------------------------------------------------------------------- |
||||
Total thermal energy -7.90047511 Eh |
||||
|
||||
|
||||
Summary of corrections to the electronic energy: |
||||
(perhaps to be used in another calculation) |
||||
Total thermal correction 0.00236283 Eh 1.48 kcal/mol |
||||
Non-thermal (ZPE) correction 0.00381191 Eh 2.39 kcal/mol |
||||
----------------------------------------------------------------------- |
||||
Total correction 0.00617474 Eh 3.87 kcal/mol |
||||
|
||||
|
||||
-------- |
||||
ENTHALPY |
||||
-------- |
||||
|
||||
The enthalpy is H = U + kB*T |
||||
kB is Boltzmann's constant |
||||
Total free energy ... -7.90047511 Eh |
||||
Thermal Enthalpy correction ... 0.00094421 Eh 0.59 kcal/mol |
||||
----------------------------------------------------------------------- |
||||
Total Enthalpy ... -7.89953090 Eh |
||||
|
||||
|
||||
Note: Rotational entropy computed according to Herzberg |
||||
Infrared and Raman Spectra, Chapter V,1, Van Nostrand Reinhold, 1945 |
||||
Point Group: Dinfh, Symmetry Number: 2 |
||||
Rotational constants in cm-1: 0.000000 1.459941 1.459941 |
||||
|
||||
Vibrational entropy computed according to the QRRHO of S. Grimme |
||||
Chem.Eur.J. 2012 18 9955 |
||||
|
||||
|
||||
------- |
||||
ENTROPY |
||||
------- |
||||
|
||||
The entropy contributions are T*S = T*(S(el)+S(vib)+S(rot)+S(trans)) |
||||
S(el) - electronic entropy |
||||
S(vib) - vibrational entropy |
||||
S(rot) - rotational entropy |
||||
S(trans)- translational entropy |
||||
The entropies will be listed as multiplied by the temperature to get |
||||
units of energy |
||||
|
||||
Electronic entropy ... 0.00000000 Eh 0.00 kcal/mol |
||||
Vibrational entropy ... 0.00000267 Eh 0.00 kcal/mol |
||||
Rotational entropy ... 0.00496853 Eh 3.12 kcal/mol |
||||
Translational entropy ... 0.01725741 Eh 10.83 kcal/mol |
||||
----------------------------------------------------------------------- |
||||
Final entropy term ... 0.02222861 Eh 13.95 kcal/mol |
||||
|
||||
|
||||
------------------- |
||||
GIBBS FREE ENERGY |
||||
------------------- |
||||
|
||||
The Gibbs free energy is G = H - T*S |
||||
|
||||
Total enthalpy ... -7.89953090 Eh |
||||
Total entropy correction ... -0.02222861 Eh -13.95 kcal/mol |
||||
----------------------------------------------------------------------- |
||||
Final Gibbs free energy ... -7.92175951 Eh |
||||
|
||||
For completeness - the Gibbs free energy minus the electronic energy |
||||
G-E(el) ... -0.01510966 Eh -9.48 kcal/mol |
||||
|
||||
|
||||
|
||||
Timings for individual modules: |
||||
|
||||
Sum of individual times ... 30.549 sec (= 0.509 min) |
||||
Numerical frequency calculation ... 30.380 sec (= 0.506 min) 99.4 % |
||||
XTB module ... 0.169 sec (= 0.003 min) 0.6 % |
||||
****ORCA TERMINATED NORMALLY**** |
||||
TOTAL RUN TIME: 0 days 0 hours 0 minutes 30 seconds 827 msec |
||||
Binary file not shown.
@ -0,0 +1,4 @@ |
||||
2 |
||||
Coordinates from ORCA-job cmmd |
||||
O 1.02719374375572 -0.09240000000000 -0.00883000000000 |
||||
O 2.22862625624428 -0.09240000000000 -0.00883000000000 |
||||
@ -0,0 +1,39 @@ |
||||
------------------------------------------------------------- |
||||
----------------------- !PROPERTIES! ------------------------ |
||||
------------------------------------------------------------- |
||||
# ----------------------------------------------------------- |
||||
$ THERMOCHEMISTRY_Energies |
||||
description: The Thermochemistry energies |
||||
geom. index: 0 |
||||
prop. index: 1 |
||||
Temperature (Kelvin) : 298.1500000000 |
||||
Pressure (atm) : 1.0000000000 |
||||
Total Mass (AMU) : 31.9980000000 |
||||
Spin Degeneracy : 1.0000000000 |
||||
Electronic Energy (Hartree) : -7.9066498468 |
||||
Translational Energy (Hartree) : 0.0014162714 |
||||
Rotational Energy (Hartree) : 0.0009441809 |
||||
Vibrational Energy (Hartree) : 0.0000023751 |
||||
Number of frequencies : 6 |
||||
Scaling Factor for frequencies : 1.0000000000 |
||||
Vibrational frequencies : |
||||
0 |
||||
0 0.000000 |
||||
1 0.000000 |
||||
2 0.000000 |
||||
3 0.000000 |
||||
4 0.000000 |
||||
5 1673.234280 |
||||
Zero Point Energy (Hartree) : 0.0038119082 |
||||
Inner Energy (Hartree) : -7.9004751111 |
||||
Enthalpy (Hartree) : -7.8995309021 |
||||
Electronic entropy : 0.0000000000 |
||||
Rotational entropy : 0.0049685321 |
||||
Vibrational entropy : 0.0000026695 |
||||
Translational entropy : 0.0049685321 |
||||
Entropy : 0.0222286070 |
||||
Gibbs Energy (Hartree) : -7.9217595090 |
||||
Is Linear : false |
||||
# ------------------------------------------------------------- |
||||
----------------------- !GEOMETRIES! ------------------------ |
||||
# ------------------------------------------------------------- |
||||
@ -0,0 +1,24 @@ |
||||
2 |
||||
Coordinates from ORCA-job cmmd E -150.073567119793 |
||||
O 0.986910 -0.092400 -0.008830 |
||||
O 2.268910 -0.092400 -0.008830 |
||||
2 |
||||
Coordinates from ORCA-job cmmd E -150.081479633117 |
||||
O 1.020806 -0.092400 -0.008830 |
||||
O 2.235014 -0.092400 -0.008830 |
||||
2 |
||||
Coordinates from ORCA-job cmmd E -150.081690529645 |
||||
O 1.029409 -0.092400 -0.008830 |
||||
O 2.226411 -0.092400 -0.008830 |
||||
2 |
||||
Coordinates from ORCA-job cmmd E -150.081720752384 |
||||
O 1.027085 -0.092400 -0.008830 |
||||
O 2.228735 -0.092400 -0.008830 |
||||
2 |
||||
Coordinates from ORCA-job cmmd E -150.081720823848 |
||||
O 1.027191 -0.092400 -0.008830 |
||||
O 2.228629 -0.092400 -0.008830 |
||||
2 |
||||
Coordinates from ORCA-job cmmd E -150.081720823916 |
||||
O 1.027194 -0.092400 -0.008830 |
||||
O 2.228626 -0.092400 -0.008830 |
||||
@ -0,0 +1 @@ |
||||
O=O |
||||
@ -0,0 +1,4 @@ |
||||
2 |
||||
|
||||
O 0.98691 -0.09240 -0.00883 |
||||
O 2.26891 -0.09240 -0.00883 |
||||
@ -0,0 +1,10 @@ |
||||
#!/bin/bash |
||||
#SBATCH --nodes=1 |
||||
#SBATCH --ntasks=1 |
||||
#SBATCH --cpus-per-task=1 |
||||
#SBATCH --time=168:0:0 |
||||
export LD_LIBRARY_PATH=/home/adit/opt/openmpi411/lib:$LD_LIBRARY_PATH |
||||
export PATH=/home/adit/opt/openmpi411/bin:$PATH |
||||
export OMP_NUM_THREADS=1 |
||||
cd $PWD |
||||
$ORCA_COMMAND cmmd.in > cmmd.out --oversubscribe |
||||
@ -0,0 +1,8 @@ |
||||
#!/bin/bash |
||||
#SBATCH --nodes=1 |
||||
#SBATCH --ntasks=1 |
||||
#SBATCH --cpus-per-task=1 |
||||
#SBATCH --time=168:0:0 |
||||
export OMP_NUM_THREADS=1 |
||||
cd $PWD |
||||
obabel geom.smi -O geom.xyz --gen3d |
||||
@ -0,0 +1 @@ |
||||
1 molecule converted |
||||
@ -0,0 +1,21 @@ |
||||
[ (resname_SLV) ] |
||||
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 |
||||
16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 |
||||
31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 |
||||
46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 |
||||
61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 |
||||
76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 |
||||
91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 |
||||
106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 |
||||
121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 |
||||
136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 |
||||
151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 |
||||
166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 |
||||
181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 |
||||
196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 |
||||
211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 |
||||
226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 |
||||
241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 |
||||
256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 |
||||
271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 |
||||
286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 |
||||
@ -0,0 +1,8 @@ |
||||
[ (resname_URA) ] |
||||
301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 |
||||
316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 |
||||
331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 |
||||
346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 |
||||
361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 |
||||
376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 |
||||
391 392 393 394 395 396 397 398 399 400 401 402 403 404 |
||||
@ -0,0 +1,5 @@ |
||||
; to test |
||||
; gmx grompp -f em.mdp -c system_GMX.gro -p system_GMX.top -o em.tpr -v |
||||
; gmx mdrun -ntmpi 1 -v -deffnm em |
||||
integrator = steep |
||||
nsteps = 500 |
||||
File diff suppressed because it is too large
Load Diff
@ -0,0 +1,297 @@ |
||||
log started: Thu Apr 28 23:05:06 2022 |
||||
|
||||
Log file: ./leap.log |
||||
>> # |
||||
>> # ----- leaprc for loading the general Amber Force field. |
||||
>> # This file is mostly for use with Antechamber |
||||
>> # |
||||
>> # load atom type hybridizations |
||||
>> # |
||||
>> addAtomTypes { |
||||
>> { "h1" "H" "sp3" } |
||||
>> { "h2" "H" "sp3" } |
||||
>> { "h3" "H" "sp3" } |
||||
>> { "h4" "H" "sp3" } |
||||
>> { "h5" "H" "sp3" } |
||||
>> { "ha" "H" "sp3" } |
||||
>> { "hc" "H" "sp3" } |
||||
>> { "hn" "H" "sp3" } |
||||
>> { "ho" "H" "sp3" } |
||||
>> { "hp" "H" "sp3" } |
||||
>> { "hs" "H" "sp3" } |
||||
>> { "hw" "H" "sp3" } |
||||
>> { "hx" "H" "sp3" } |
||||
>> { "o" "O" "sp2" } |
||||
>> { "o2" "O" "sp2" } |
||||
>> { "oh" "O" "sp3" } |
||||
>> { "op" "O" "sp3" } |
||||
>> { "oq" "O" "sp3" } |
||||
>> { "os" "O" "sp3" } |
||||
>> { "ow" "O" "sp3" } |
||||
>> { "c" "C" "sp2" } |
||||
>> { "c1" "C" "sp2" } |
||||
>> { "c2" "C" "sp2" } |
||||
>> { "c3" "C" "sp3" } |
||||
>> { "ca" "C" "sp2" } |
||||
>> { "cc" "C" "sp2" } |
||||
>> { "cd" "C" "sp2" } |
||||
>> { "ce" "C" "sp2" } |
||||
>> { "cf" "C" "sp2" } |
||||
>> { "cg" "C" "sp2" } |
||||
>> { "ch" "C" "sp2" } |
||||
>> { "cp" "C" "sp2" } |
||||
>> { "cq" "C" "sp2" } |
||||
>> { "cu" "C" "sp2" } |
||||
>> { "cv" "C" "sp2" } |
||||
>> { "cx" "C" "sp2" } |
||||
>> { "cy" "C" "sp2" } |
||||
>> { "cz" "C" "sp2" } |
||||
>> { "n" "N" "sp2" } |
||||
>> { "n1" "N" "sp2" } |
||||
>> { "n2" "N" "sp2" } |
||||
>> { "n3" "N" "sp3" } |
||||
>> { "n4" "N" "sp3" } |
||||
>> { "na" "N" "sp2" } |
||||
>> { "nb" "N" "sp2" } |
||||
>> { "nc" "N" "sp2" } |
||||
>> { "nd" "N" "sp2" } |
||||
>> { "ne" "N" "sp2" } |
||||
>> { "nf" "N" "sp2" } |
||||
>> { "nh" "N" "sp2" } |
||||
>> { "ni" "N" "sp2" } |
||||
>> { "nj" "N" "sp2" } |
||||
>> { "nk" "N" "sp3" } |
||||
>> { "nl" "N" "sp3" } |
||||
>> { "nm" "N" "sp2" } |
||||
>> { "nn" "N" "sp2" } |
||||
>> { "no" "N" "sp2" } |
||||
>> { "np" "N" "sp3" } |
||||
>> { "nq" "N" "sp3" } |
||||
>> { "s" "S" "sp2" } |
||||
>> { "s2" "S" "sp2" } |
||||
>> { "s3" "S" "sp3" } |
||||
>> { "s4" "S" "sp3" } |
||||
>> { "s6" "S" "sp3" } |
||||
>> { "sh" "S" "sp3" } |
||||
>> { "sp" "S" "sp3" } |
||||
>> { "sq" "S" "sp3" } |
||||
>> { "ss" "S" "sp3" } |
||||
>> { "sx" "S" "sp3" } |
||||
>> { "sy" "S" "sp3" } |
||||
>> { "p2" "P" "sp2" } |
||||
>> { "p3" "P" "sp3" } |
||||
>> { "p4" "P" "sp3" } |
||||
>> { "p5" "P" "sp3" } |
||||
>> { "pb" "P" "sp3" } |
||||
>> { "pc" "P" "sp3" } |
||||
>> { "pd" "P" "sp3" } |
||||
>> { "pe" "P" "sp3" } |
||||
>> { "pf" "P" "sp3" } |
||||
>> { "px" "P" "sp3" } |
||||
>> { "py" "P" "sp3" } |
||||
>> { "f" "F" "sp3" } |
||||
>> { "cl" "Cl" "sp3" } |
||||
>> { "br" "Br" "sp3" } |
||||
>> { "i" "I" "sp3" } |
||||
>> } |
||||
>> # |
||||
>> # Load the general force field parameter set. |
||||
>> # |
||||
>> gaff = loadamberparams gaff.dat |
||||
Loading parameters: /home/adit/miniconda3/dat/leap/parm/gaff.dat |
||||
Reading title: |
||||
AMBER General Force Field for organic molecules (Version 1.81, May 2017) |
||||
> |
||||
> loadamberparams /home/adit/miniconda3/dat/leap/parm/frcmod.ions1lm_iod |
||||
Loading parameters: /home/adit/miniconda3/dat/leap/parm/frcmod.ions1lm_iod |
||||
Reading force field modification type file (frcmod) |
||||
Reading title: |
||||
Li/Merz ion parameters of monovalent ions for TIP3P, SPC/E and TIP4P/EW water models (12-6 IOD set) |
||||
(UNKNOWN ATOM TYPE: Li+) |
||||
(UNKNOWN ATOM TYPE: Na+) |
||||
(UNKNOWN ATOM TYPE: K+) |
||||
(UNKNOWN ATOM TYPE: Rb+) |
||||
(UNKNOWN ATOM TYPE: Cs+) |
||||
(UNKNOWN ATOM TYPE: Tl+) |
||||
(UNKNOWN ATOM TYPE: Cu+) |
||||
(UNKNOWN ATOM TYPE: Ag+) |
||||
(UNKNOWN ATOM TYPE: NH4+) |
||||
(UNKNOWN ATOM TYPE: HE+) |
||||
(UNKNOWN ATOM TYPE: HZ+) |
||||
(UNKNOWN ATOM TYPE: H3O+) |
||||
(UNKNOWN ATOM TYPE: F-) |
||||
(UNKNOWN ATOM TYPE: Cl-) |
||||
(UNKNOWN ATOM TYPE: Br-) |
||||
(UNKNOWN ATOM TYPE: I-) |
||||
> loadoff ../urea/URA.lib |
||||
Loading library: ../urea/URA.lib |
||||
Loading: URA |
||||
> loadamberparams ../urea/urea.frcmod |
||||
Loading parameters: ../urea/urea.frcmod |
||||
Reading force field modification type file (frcmod) |
||||
Reading title: |
||||
Remark line goes here |
||||
> loadoff ../water/water.lib |
||||
Loading library: ../water/water.lib |
||||
Loading: SLV |
||||
> loadamberparams ../water/water.frcmod |
||||
Loading parameters: ../water/water.frcmod |
||||
Reading force field modification type file (frcmod) |
||||
Reading title: |
||||
Remark line goes here |
||||
> SYSTEM = loadpdb system_init.pdb |
||||
Loading PDB file: ./system_init.pdb |
||||
(starting new molecule for chain B) |
||||
Matching PDB residue names to LEaP variables. |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with SLV |
||||
Starting new chain with URA |
||||
Starting new chain with URA |
||||
Starting new chain with URA |
||||
Starting new chain with URA |
||||
Starting new chain with URA |
||||
Starting new chain with URA |
||||
Starting new chain with URA |
||||
Starting new chain with URA |
||||
Starting new chain with URA |
||||
Starting new chain with URA |
||||
Starting new chain with URA |
||||
Starting new chain with URA |
||||
total atoms in file: 404 |
||||
> list |
||||
SLV SYSTEM URA gaff |
||||
> saveamberparm SYSTEM system.prmtop system.inpcrd |
||||
Checking Unit. |
||||
|
||||
/home/adit/miniconda3/bin/teLeap: Warning! |
||||
The unperturbed charge of the unit (-0.013100) is not integral. |
||||
|
||||
/home/adit/miniconda3/bin/teLeap: Warning! |
||||
The unperturbed charge of the unit (-0.013100) is not zero. |
||||
|
||||
/home/adit/miniconda3/bin/teLeap: Note. |
||||
Ignoring the error and warning from Unit Checking. |
||||
|
||||
Building topology. |
||||
Building atom parameters. |
||||
Building bond parameters. |
||||
Building angle parameters. |
||||
Building proper torsion parameters. |
||||
Building improper torsion parameters. |
||||
total 39 improper torsions applied |
||||
Building H-Bond parameters. |
||||
Incorporating Non-Bonded adjustments. |
||||
Not Marking per-residue atom chain types. |
||||
Marking per-residue atom chain types. |
||||
(Residues lacking connect0/connect1 - |
||||
these don't have chain types marked: |
||||
|
||||
res total affected |
||||
|
||||
SLV 100 |
||||
URA 13 |
||||
) |
||||
(no restraints) |
||||
> savepdb SYSTEM system.pdb |
||||
Writing pdb file: system.pdb |
||||
> quit |
||||
Quit |
||||
|
||||
Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. |
||||
@ -0,0 +1,5 @@ |
||||
; to test |
||||
; gmx grompp -f md.mdp -c em.gro -p system_GMX.top -o md.tpr |
||||
; gmx mdrun -ntmpi 1 -v -deffnm md |
||||
integrator = md |
||||
nsteps = 10000 |
||||
@ -0,0 +1,312 @@ |
||||
; |
||||
; File 'mdout.mdp' was generated |
||||
; By user: unknown (1000) |
||||
; On host: compute |
||||
; At date: Thu Apr 28 23:06:12 2022 |
||||
; |
||||
; Created by: |
||||
; :-) GROMACS - gmx grompp, 2021.3 (-: |
||||
; |
||||
; Executable: /usr/local/gromacs/bin/gmx |
||||
; Data prefix: /usr/local/gromacs |
||||
; Working dir: /home/adit/MySoftware/CMMDE/test/larutan/SistemLarutan |
||||
; Command line: |
||||
; gmx -quiet grompp -c npt.gro -f nvep.mdp -maxwarn 2 -o nvep.tpr -p system_GMX.top |
||||
|
||||
; VARIOUS PREPROCESSING OPTIONS |
||||
; Preprocessor information: use cpp syntax. |
||||
; e.g.: -I/home/joe/doe -I/home/mary/roe |
||||
include = |
||||
; e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive) |
||||
define = |
||||
|
||||
; RUN CONTROL PARAMETERS |
||||
integrator = md |
||||
; Start time and timestep in ps |
||||
tinit = 0 |
||||
dt = 0.0005 |
||||
nsteps = 10000 |
||||
; For exact run continuation or redoing part of a run |
||||
init-step = 0 |
||||
; Part index is updated automatically on checkpointing (keeps files separate) |
||||
simulation-part = 1 |
||||
; Multiple time-stepping |
||||
mts = no |
||||
; mode for center of mass motion removal |
||||
comm-mode = Linear |
||||
; number of steps for center of mass motion removal |
||||
nstcomm = 100 |
||||
; group(s) for center of mass motion removal |
||||
comm-grps = |
||||
|
||||
; LANGEVIN DYNAMICS OPTIONS |
||||
; Friction coefficient (amu/ps) and random seed |
||||
bd-fric = 0 |
||||
ld-seed = -1 |
||||
|
||||
; ENERGY MINIMIZATION OPTIONS |
||||
; Force tolerance and initial step-size |
||||
emtol = 10 |
||||
emstep = 0.01 |
||||
; Max number of iterations in relax-shells |
||||
niter = 20 |
||||
; Step size (ps^2) for minimization of flexible constraints |
||||
fcstep = 0 |
||||
; Frequency of steepest descents steps when doing CG |
||||
nstcgsteep = 1000 |
||||
nbfgscorr = 10 |
||||
|
||||
; TEST PARTICLE INSERTION OPTIONS |
||||
rtpi = 0.05 |
||||
|
||||
; OUTPUT CONTROL OPTIONS |
||||
; Output frequency for coords (x), velocities (v) and forces (f) |
||||
nstxout = 500 |
||||
nstvout = 500 |
||||
nstfout = 0 |
||||
; Output frequency for energies to log file and energy file |
||||
nstlog = 500 |
||||
nstcalcenergy = 100 |
||||
nstenergy = 500 |
||||
; Output frequency and precision for .xtc file |
||||
nstxout-compressed = 0 |
||||
compressed-x-precision = 1000 |
||||
; This selects the subset of atoms for the compressed |
||||
; trajectory file. You can select multiple groups. By |
||||
; default, all atoms will be written. |
||||
compressed-x-grps = |
||||
; Selection of energy groups |
||||
energygrps = |
||||
|
||||
; NEIGHBORSEARCHING PARAMETERS |
||||
; cut-off scheme (Verlet: particle based cut-offs) |
||||
cutoff-scheme = Verlet |
||||
; nblist update frequency |
||||
nstlist = 10 |
||||
; Periodic boundary conditions: xyz, no, xy |
||||
pbc = xyz |
||||
periodic-molecules = no |
||||
; Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom, |
||||
; a value of -1 means: use rlist |
||||
verlet-buffer-tolerance = 0.005 |
||||
; nblist cut-off |
||||
rlist = 1 |
||||
; long-range cut-off for switched potentials |
||||
|
||||
; OPTIONS FOR ELECTROSTATICS AND VDW |
||||
; Method for doing electrostatics |
||||
coulombtype = PME |
||||
coulomb-modifier = Potential-shift-Verlet |
||||
rcoulomb-switch = 0 |
||||
rcoulomb = 0.7113990804113833 |
||||
; Relative dielectric constant for the medium and the reaction field |
||||
epsilon-r = 1 |
||||
epsilon-rf = 0 |
||||
; Method for doing Van der Waals |
||||
vdw-type = Cut-off |
||||
vdw-modifier = Potential-shift-Verlet |
||||
; cut-off lengths |
||||
rvdw-switch = 0 |
||||
rvdw = 0.7113990804113833 |
||||
; Apply long range dispersion corrections for Energy and Pressure |
||||
DispCorr = EnerPres |
||||
; Extension of the potential lookup tables beyond the cut-off |
||||
table-extension = 1 |
||||
; Separate tables between energy group pairs |
||||
energygrp-table = |
||||
; Spacing for the PME/PPPM FFT grid |
||||
fourierspacing = 0.16 |
||||
; FFT grid size, when a value is 0 fourierspacing will be used |
||||
fourier-nx = 0 |
||||
fourier-ny = 0 |
||||
fourier-nz = 0 |
||||
; EWALD/PME/PPPM parameters |
||||
pme_order = 4 |
||||
ewald-rtol = 1e-05 |
||||
ewald-rtol-lj = 0.001 |
||||
lj-pme-comb-rule = Geometric |
||||
ewald-geometry = 3d |
||||
epsilon-surface = 0 |
||||
implicit-solvent = no |
||||
|
||||
; OPTIONS FOR WEAK COUPLING ALGORITHMS |
||||
; Temperature coupling |
||||
tcoupl = no |
||||
nsttcouple = -1 |
||||
nh-chain-length = 10 |
||||
print-nose-hoover-chain-variables = no |
||||
; Groups to couple separately |
||||
tc-grps = |
||||
; Time constant (ps) and reference temperature (K) |
||||
tau-t = |
||||
ref-t = |
||||
; pressure coupling |
||||
pcoupl = no |
||||
pcoupltype = Isotropic |
||||
nstpcouple = -1 |
||||
; Time constant (ps), compressibility (1/bar) and reference P (bar) |
||||
tau-p = 1 |
||||
compressibility = |
||||
ref-p = |
||||
; Scaling of reference coordinates, No, All or COM |
||||
refcoord-scaling = No |
||||
|
||||
; OPTIONS FOR QMMM calculations |
||||
QMMM = no |
||||
; Groups treated with MiMiC |
||||
QMMM-grps = |
||||
|
||||
; SIMULATED ANNEALING |
||||
; Type of annealing for each temperature group (no/single/periodic) |
||||
annealing = |
||||
; Number of time points to use for specifying annealing in each group |
||||
annealing-npoints = |
||||
; List of times at the annealing points for each group |
||||
annealing-time = |
||||
; Temp. at each annealing point, for each group. |
||||
annealing-temp = |
||||
|
||||
; GENERATE VELOCITIES FOR STARTUP RUN |
||||
gen_vel = no |
||||
gen-temp = 300 |
||||
gen-seed = -1 |
||||
|
||||
; OPTIONS FOR BONDS |
||||
constraints = none |
||||
; Type of constraint algorithm |
||||
constraint-algorithm = Lincs |
||||
; Do not constrain the start configuration |
||||
continuation = yes |
||||
; Use successive overrelaxation to reduce the number of shake iterations |
||||
Shake-SOR = no |
||||
; Relative tolerance of shake |
||||
shake-tol = 0.0001 |
||||
; Highest order in the expansion of the constraint coupling matrix |
||||
lincs-order = 4 |
||||
; Number of iterations in the final step of LINCS. 1 is fine for |
||||
; normal simulations, but use 2 to conserve energy in NVE runs. |
||||
; For energy minimization with constraints it should be 4 to 8. |
||||
lincs-iter = 1 |
||||
; Lincs will write a warning to the stderr if in one step a bond |
||||
; rotates over more degrees than |
||||
lincs-warnangle = 30 |
||||
; Convert harmonic bonds to morse potentials |
||||
morse = no |
||||
|
||||
; ENERGY GROUP EXCLUSIONS |
||||
; Pairs of energy groups for which all non-bonded interactions are excluded |
||||
energygrp-excl = |
||||
|
||||
; WALLS |
||||
; Number of walls, type, atom types, densities and box-z scale factor for Ewald |
||||
nwall = 0 |
||||
wall-type = 9-3 |
||||
wall-r-linpot = -1 |
||||
wall-atomtype = |
||||
wall-density = |
||||
wall-ewald-zfac = 3 |
||||
|
||||
; COM PULLING |
||||
pull = no |
||||
|
||||
; AWH biasing |
||||
awh = no |
||||
|
||||
; ENFORCED ROTATION |
||||
; Enforced rotation: No or Yes |
||||
rotation = no |
||||
|
||||
; Group to display and/or manipulate in interactive MD session |
||||
IMD-group = |
||||
|
||||
; NMR refinement stuff |
||||
; Distance restraints type: No, Simple or Ensemble |
||||
disre = No |
||||
; Force weighting of pairs in one distance restraint: Conservative or Equal |
||||
disre-weighting = Conservative |
||||
; Use sqrt of the time averaged times the instantaneous violation |
||||
disre-mixed = no |
||||
disre-fc = 1000 |
||||
disre-tau = 0 |
||||
; Output frequency for pair distances to energy file |
||||
nstdisreout = 100 |
||||
; Orientation restraints: No or Yes |
||||
orire = no |
||||
; Orientation restraints force constant and tau for time averaging |
||||
orire-fc = 0 |
||||
orire-tau = 0 |
||||
orire-fitgrp = |
||||
; Output frequency for trace(SD) and S to energy file |
||||
nstorireout = 100 |
||||
|
||||
; Free energy variables |
||||
free-energy = no |
||||
couple-moltype = |
||||
couple-lambda0 = vdw-q |
||||
couple-lambda1 = vdw-q |
||||
couple-intramol = no |
||||
init-lambda = -1 |
||||
init-lambda-state = -1 |
||||
delta-lambda = 0 |
||||
nstdhdl = 50 |
||||
fep-lambdas = |
||||
mass-lambdas = |
||||
coul-lambdas = |
||||
vdw-lambdas = |
||||
bonded-lambdas = |
||||
restraint-lambdas = |
||||
temperature-lambdas = |
||||
calc-lambda-neighbors = 1 |
||||
init-lambda-weights = |
||||
dhdl-print-energy = no |
||||
sc-alpha = 0 |
||||
sc-power = 1 |
||||
sc-r-power = 6 |
||||
sc-sigma = 0.3 |
||||
sc-coul = no |
||||
separate-dhdl-file = yes |
||||
dhdl-derivatives = yes |
||||
dh_hist_size = 0 |
||||
dh_hist_spacing = 0.1 |
||||
|
||||
; Non-equilibrium MD stuff |
||||
acc-grps = |
||||
accelerate = |
||||
freezegrps = |
||||
freezedim = |
||||
cos-acceleration = 0 |
||||
deform = |
||||
|
||||
; simulated tempering variables |
||||
simulated-tempering = no |
||||
simulated-tempering-scaling = geometric |
||||
sim-temp-low = 300 |
||||
sim-temp-high = 300 |
||||
|
||||
; Ion/water position swapping for computational electrophysiology setups |
||||
; Swap positions along direction: no, X, Y, Z |
||||
swapcoords = no |
||||
adress = no |
||||
|
||||
; User defined thingies |
||||
user1-grps = |
||||
user2-grps = |
||||
userint1 = 0 |
||||
userint2 = 0 |
||||
userint3 = 0 |
||||
userint4 = 0 |
||||
userreal1 = 0 |
||||
userreal2 = 0 |
||||
userreal3 = 0 |
||||
userreal4 = 0 |
||||
; Electric fields |
||||
; Format for electric-field-x, etc. is: four real variables: |
||||
; amplitude (V/nm), frequency omega (1/ps), time for the pulse peak (ps), |
||||
; and sigma (ps) width of the pulse. Omega = 0 means static field, |
||||
; sigma = 0 means no pulse, leaving the field to be a cosine function. |
||||
electric-field-x = 0 0 0 0 |
||||
electric-field-y = 0 0 0 0 |
||||
electric-field-z = 0 0 0 0 |
||||
|
||||
; Density guided simulation |
||||
density-guided-simulation-active = false |
||||
Binary file not shown.
@ -0,0 +1,407 @@ |
||||
system |
||||
404 |
||||
1SLV O 1 0.682 0.076 0.216 |
||||
1SLV H 2 0.707 0.147 0.279 |
||||
1SLV H1 3 0.583 0.083 0.210 |
||||
2SLV O 4 0.361 0.189 0.582 |
||||
2SLV H 5 0.384 0.273 0.535 |
||||
2SLV H1 6 0.432 0.180 0.650 |
||||
3SLV O 7 0.020 0.744 1.097 |
||||
3SLV H 8 0.038 0.749 0.999 |
||||
3SLV H1 9 0.112 0.742 1.135 |
||||
4SLV O 10 0.355 1.129 0.948 |
||||
4SLV H 11 0.295 1.162 0.876 |
||||
4SLV H1 12 0.379 1.038 0.916 |
||||
5SLV O 13 0.087 1.162 0.060 |
||||
5SLV H 14 0.098 1.104 1.603 |
||||
5SLV H1 15 0.036 1.106 0.124 |
||||
6SLV O 16 0.134 0.823 0.010 |
||||
6SLV H 17 0.040 0.802 1.609 |
||||
6SLV H1 18 0.154 0.893 1.565 |
||||
7SLV O 19 0.079 0.809 0.826 |
||||
7SLV H 20 0.176 0.818 0.813 |
||||
7SLV H1 21 0.045 0.785 0.737 |
||||
8SLV O 22 1.173 0.813 0.137 |
||||
8SLV H 23 1.126 0.852 0.214 |
||||
8SLV H1 24 1.225 0.887 0.101 |
||||
9SLV O 25 0.563 1.519 1.520 |
||||
9SLV H 26 0.652 1.564 1.534 |
||||
9SLV H1 27 0.530 1.502 1.611 |
||||
10SLV O 28 1.336 1.262 1.030 |
||||
10SLV H 29 1.434 1.253 1.032 |
||||
10SLV H1 30 1.317 1.314 0.949 |
||||
11SLV O 31 1.019 1.340 0.333 |
||||
11SLV H 32 1.040 1.281 0.257 |
||||
11SLV H1 33 1.063 1.292 0.408 |
||||
12SLV O 34 0.193 1.213 0.738 |
||||
12SLV H 35 0.143 1.295 0.713 |
||||
12SLV H1 36 0.118 1.153 0.764 |
||||
13SLV O 37 0.752 1.306 0.021 |
||||
13SLV H 38 0.733 1.316 1.548 |
||||
13SLV H1 39 0.679 1.248 0.054 |
||||
14SLV O 40 1.175 0.828 0.973 |
||||
14SLV H 41 1.114 0.798 1.046 |
||||
14SLV H1 42 1.183 0.748 0.917 |
||||
15SLV O 43 1.469 0.539 0.098 |
||||
15SLV H 44 1.409 0.511 0.171 |
||||
15SLV H1 45 1.554 0.494 0.122 |
||||
16SLV O 46 1.152 0.062 0.652 |
||||
16SLV H 47 1.168 1.610 0.716 |
||||
16SLV H1 48 1.070 0.104 0.687 |
||||
17SLV O 49 0.465 0.804 1.547 |
||||
17SLV H 50 0.563 0.818 1.554 |
||||
17SLV H1 51 0.430 0.831 0.012 |
||||
18SLV O 52 0.169 0.223 1.492 |
||||
18SLV H 53 0.231 0.260 1.559 |
||||
18SLV H1 54 0.143 0.134 1.528 |
||||
19SLV O 55 0.757 1.249 0.391 |
||||
19SLV H 56 0.701 1.332 0.397 |
||||
19SLV H1 57 0.846 1.286 0.368 |
||||
20SLV O 58 0.411 0.068 0.238 |
||||
20SLV H 59 0.323 0.097 0.271 |
||||
20SLV H1 60 0.388 1.607 0.189 |
||||
21SLV O 61 0.366 0.854 0.179 |
||||
21SLV H 62 0.272 0.852 0.145 |
||||
21SLV H1 63 0.356 0.883 0.273 |
||||
22SLV O 64 1.061 1.354 1.597 |
||||
22SLV H 65 1.033 1.269 0.019 |
||||
22SLV H1 66 0.977 1.406 1.601 |
||||
23SLV O 67 0.081 0.406 0.163 |
||||
23SLV H 68 0.129 0.460 0.095 |
||||
23SLV H1 69 0.120 0.317 0.149 |
||||
24SLV O 70 0.352 0.532 1.025 |
||||
24SLV H 71 0.296 0.451 1.026 |
||||
24SLV H1 72 0.428 0.510 1.086 |
||||
25SLV O 73 0.549 0.964 1.188 |
||||
25SLV H 74 0.511 1.054 1.193 |
||||
25SLV H1 75 0.645 0.979 1.186 |
||||
26SLV O 76 0.099 0.038 0.657 |
||||
26SLV H 77 0.069 1.566 0.660 |
||||
26SLV H1 78 0.193 0.032 0.684 |
||||
27SLV O 79 0.007 1.274 1.375 |
||||
27SLV H 80 0.099 1.307 1.396 |
||||
27SLV H1 81 1.576 1.313 1.447 |
||||
28SLV O 82 1.605 1.078 0.850 |
||||
28SLV H 83 0.001 0.982 0.859 |
||||
28SLV H1 84 1.609 1.116 0.941 |
||||
29SLV O 85 0.636 1.173 0.838 |
||||
29SLV H 86 0.550 1.172 0.792 |
||||
29SLV H1 87 0.613 1.156 0.932 |
||||
30SLV O 88 0.562 1.084 0.064 |
||||
30SLV H 89 0.624 1.007 0.065 |
||||
30SLV H1 90 0.502 1.070 0.141 |
||||
31SLV O 91 1.134 0.145 1.269 |
||||
31SLV H 92 1.082 0.060 1.268 |
||||
31SLV H1 93 1.132 0.167 1.366 |
||||
32SLV O 94 0.693 1.345 1.342 |
||||
32SLV H 95 0.634 1.409 1.390 |
||||
32SLV H1 96 0.632 1.303 1.276 |
||||
33SLV O 97 0.427 0.546 1.453 |
||||
33SLV H 98 0.444 0.642 1.475 |
||||
33SLV H1 99 0.337 0.533 1.493 |
||||
34SLV O 100 1.448 0.232 0.875 |
||||
34SLV H 101 1.477 0.239 0.970 |
||||
34SLV H1 102 1.535 0.251 0.829 |
||||
35SLV O 103 1.582 1.621 0.335 |
||||
35SLV H 104 1.526 0.045 0.402 |
||||
35SLV H1 105 0.047 0.043 0.345 |
||||
36SLV O 106 0.086 1.584 1.544 |
||||
36SLV H 107 0.046 1.588 1.454 |
||||
36SLV H1 108 0.025 1.520 1.590 |
||||
37SLV O 109 1.341 0.336 1.573 |
||||
37SLV H 110 1.390 0.257 1.607 |
||||
37SLV H1 111 1.391 0.413 1.609 |
||||
38SLV O 112 1.316 1.190 0.002 |
||||
38SLV H 113 1.329 1.140 1.539 |
||||
38SLV H1 114 1.232 1.240 1.607 |
||||
39SLV O 115 1.065 1.058 0.813 |
||||
39SLV H 116 0.974 1.053 0.850 |
||||
39SLV H1 117 1.112 0.993 0.871 |
||||
40SLV O 118 0.347 1.457 0.099 |
||||
40SLV H 119 0.338 1.377 0.157 |
||||
40SLV H1 120 0.257 1.472 0.064 |
||||
41SLV O 121 0.568 0.106 0.755 |
||||
41SLV H 122 0.655 0.063 0.767 |
||||
41SLV H1 123 0.502 0.038 0.785 |
||||
42SLV O 124 0.094 1.018 1.443 |
||||
42SLV H 125 0.048 0.962 1.376 |
||||
42SLV H1 126 0.071 1.108 1.411 |
||||
43SLV O 127 1.186 1.559 0.396 |
||||
43SLV H 128 1.122 1.486 0.376 |
||||
43SLV H1 129 1.157 1.591 0.486 |
||||
44SLV O 130 0.185 0.109 1.228 |
||||
44SLV H 131 0.114 0.045 1.251 |
||||
44SLV H1 132 0.212 0.147 1.315 |
||||
45SLV O 133 0.003 1.218 1.101 |
||||
45SLV H 134 0.082 1.276 1.086 |
||||
45SLV H1 135 1.610 1.235 1.198 |
||||
46SLV O 136 1.133 1.470 0.837 |
||||
46SLV H 137 1.064 1.411 0.798 |
||||
46SLV H1 138 1.083 1.528 0.900 |
||||
47SLV O 139 0.178 0.177 0.365 |
||||
47SLV H 140 0.223 0.171 0.454 |
||||
47SLV H1 141 0.161 0.273 0.356 |
||||
48SLV O 142 0.920 1.572 0.139 |
||||
48SLV H 143 0.930 1.495 0.199 |
||||
48SLV H1 144 0.834 1.613 0.168 |
||||
49SLV O 145 0.462 0.101 1.367 |
||||
49SLV H 146 0.493 0.026 1.424 |
||||
49SLV H1 147 0.496 0.181 1.414 |
||||
50SLV O 148 0.815 0.017 1.511 |
||||
50SLV H 149 0.867 0.002 1.594 |
||||
50SLV H1 150 0.882 0.010 1.439 |
||||
51SLV O 151 1.138 0.639 1.436 |
||||
51SLV H 152 1.221 0.656 1.386 |
||||
51SLV H1 153 1.168 0.596 1.518 |
||||
52SLV O 154 0.751 0.619 0.456 |
||||
52SLV H 155 0.716 0.635 0.366 |
||||
52SLV H1 156 0.784 0.526 0.451 |
||||
53SLV O 157 0.450 0.560 0.165 |
||||
53SLV H 158 0.544 0.558 0.132 |
||||
53SLV H1 159 0.423 0.654 0.155 |
||||
54SLV O 160 1.261 1.512 0.090 |
||||
54SLV H 161 1.217 1.526 0.177 |
||||
54SLV H1 162 1.193 1.464 0.037 |
||||
55SLV O 163 1.361 0.703 1.273 |
||||
55SLV H 164 1.303 0.753 1.211 |
||||
55SLV H1 165 1.444 0.690 1.221 |
||||
56SLV O 166 1.006 1.131 0.121 |
||||
56SLV H 167 0.919 1.095 0.096 |
||||
56SLV H1 168 1.035 1.075 0.198 |
||||
57SLV O 169 1.434 0.109 0.114 |
||||
57SLV H 170 1.375 0.034 0.088 |
||||
57SLV H1 171 1.501 0.062 0.170 |
||||
58SLV O 172 0.280 1.229 0.244 |
||||
58SLV H 173 0.210 1.204 0.178 |
||||
58SLV H1 174 0.248 1.192 0.329 |
||||
59SLV O 175 1.456 1.358 0.439 |
||||
59SLV H 176 1.401 1.437 0.423 |
||||
59SLV H1 177 1.540 1.379 0.393 |
||||
60SLV O 178 0.420 1.105 1.450 |
||||
60SLV H 179 0.409 1.011 1.425 |
||||
60SLV H1 180 0.468 1.101 1.537 |
||||
61SLV O 181 0.337 1.575 0.820 |
||||
61SLV H 182 0.315 1.500 0.879 |
||||
61SLV H1 183 0.308 0.032 0.874 |
||||
62SLV O 184 0.377 1.537 0.530 |
||||
62SLV H 185 0.365 0.012 0.530 |
||||
62SLV H1 186 0.364 1.513 0.625 |
||||
63SLV O 187 1.014 0.045 0.997 |
||||
63SLV H 188 0.969 0.111 0.939 |
||||
63SLV H1 189 1.075 0.099 1.052 |
||||
64SLV O 190 0.567 0.317 1.514 |
||||
64SLV H 191 0.524 0.402 1.487 |
||||
64SLV H1 192 0.662 0.341 1.518 |
||||
65SLV O 193 1.337 1.053 1.383 |
||||
65SLV H 194 1.273 1.066 1.311 |
||||
65SLV H1 195 1.418 1.019 1.335 |
||||
66SLV O 196 0.176 0.556 1.571 |
||||
66SLV H 197 0.115 0.544 1.495 |
||||
66SLV H1 198 0.169 0.654 1.592 |
||||
67SLV O 199 1.375 0.123 0.483 |
||||
67SLV H 200 1.319 0.131 0.565 |
||||
67SLV H1 201 1.319 0.061 0.429 |
||||
68SLV O 202 0.289 0.765 1.174 |
||||
68SLV H 203 0.369 0.822 1.188 |
||||
68SLV H1 204 0.322 0.689 1.120 |
||||
69SLV O 205 1.274 1.189 0.288 |
||||
69SLV H 206 1.300 1.192 0.193 |
||||
69SLV H1 207 1.350 1.228 0.338 |
||||
70SLV O 208 0.975 0.407 1.224 |
||||
70SLV H 209 0.951 0.422 1.131 |
||||
70SLV H1 210 1.003 0.313 1.229 |
||||
71SLV O 211 0.550 0.490 1.214 |
||||
71SLV H 212 0.639 0.506 1.255 |
||||
71SLV H1 213 0.491 0.508 1.292 |
||||
72SLV O 214 0.614 1.483 0.396 |
||||
72SLV H 215 0.523 1.500 0.433 |
||||
72SLV H1 216 0.625 1.549 0.325 |
||||
73SLV O 217 1.326 0.339 1.197 |
||||
73SLV H 218 1.279 0.419 1.229 |
||||
73SLV H1 219 1.264 0.265 1.221 |
||||
74SLV O 220 0.505 1.263 1.139 |
||||
74SLV H 221 0.439 1.221 1.078 |
||||
74SLV H1 222 0.476 1.358 1.141 |
||||
75SLV O 223 1.393 0.459 0.718 |
||||
75SLV H 224 1.487 0.482 0.701 |
||||
75SLV H1 225 1.400 0.377 0.774 |
||||
76SLV O 226 1.104 0.330 0.237 |
||||
76SLV H 227 1.199 0.335 0.262 |
||||
76SLV H1 228 1.055 0.368 0.313 |
||||
77SLV O 229 0.931 1.573 1.256 |
||||
77SLV H 230 0.866 1.500 1.272 |
||||
77SLV H1 231 0.925 1.590 1.159 |
||||
78SLV O 232 0.457 0.907 0.811 |
||||
78SLV H 233 0.552 0.932 0.813 |
||||
78SLV H1 234 0.460 0.816 0.771 |
||||
79SLV O 235 1.579 0.257 1.114 |
||||
79SLV H 236 1.502 0.297 1.163 |
||||
79SLV H1 237 0.011 0.212 1.182 |
||||
80SLV O 238 1.121 1.241 0.589 |
||||
80SLV H 239 1.101 1.176 0.662 |
||||
80SLV H1 240 1.218 1.251 0.592 |
||||
81SLV O 241 0.685 0.436 0.741 |
||||
81SLV H 242 0.656 0.391 0.823 |
||||
81SLV H1 243 0.729 0.364 0.691 |
||||
82SLV O 244 0.483 0.649 0.709 |
||||
82SLV H 245 0.560 0.600 0.669 |
||||
82SLV H1 246 0.425 0.576 0.739 |
||||
83SLV O 247 1.380 0.327 0.289 |
||||
83SLV H 248 1.403 0.261 0.217 |
||||
83SLV H1 249 1.390 0.271 0.370 |
||||
84SLV O 250 1.613 1.398 0.685 |
||||
84SLV H 251 1.544 1.455 0.728 |
||||
84SLV H1 252 1.560 1.348 0.619 |
||||
85SLV O 253 0.272 1.336 1.422 |
||||
85SLV H 254 0.325 1.251 1.428 |
||||
85SLV H1 255 0.322 1.396 1.482 |
||||
86SLV O 256 1.440 1.601 0.752 |
||||
86SLV H 257 1.416 0.049 0.816 |
||||
86SLV H1 258 1.484 0.028 0.680 |
||||
87SLV O 259 0.205 1.414 1.161 |
||||
87SLV H 260 0.226 1.382 1.253 |
||||
87SLV H1 261 0.277 1.480 1.146 |
||||
88SLV O 262 1.570 1.589 1.266 |
||||
88SLV H 263 1.477 1.614 1.249 |
||||
88SLV H1 264 1.586 1.512 1.207 |
||||
89SLV O 265 0.456 0.350 0.360 |
||||
89SLV H 266 0.430 0.284 0.292 |
||||
89SLV H1 267 0.451 0.436 0.311 |
||||
90SLV O 268 0.452 1.549 1.148 |
||||
90SLV H 269 0.435 1.615 1.221 |
||||
90SLV H1 270 0.536 1.584 1.111 |
||||
91SLV O 271 1.035 0.744 1.192 |
||||
91SLV H 272 0.947 0.786 1.200 |
||||
91SLV H1 273 1.048 0.696 1.278 |
||||
92SLV O 274 1.212 0.540 0.521 |
||||
92SLV H 275 1.265 0.529 0.440 |
||||
92SLV H1 276 1.273 0.512 0.594 |
||||
93SLV O 277 0.055 0.298 0.741 |
||||
93SLV H 278 0.122 0.355 0.695 |
||||
93SLV H1 279 0.074 0.208 0.704 |
||||
94SLV O 280 1.508 0.750 1.536 |
||||
94SLV H 281 1.476 0.672 1.589 |
||||
94SLV H1 282 1.452 0.749 1.455 |
||||
95SLV O 283 1.101 0.207 1.542 |
||||
95SLV H 284 1.182 0.265 1.549 |
||||
95SLV H1 285 1.089 0.174 0.011 |
||||
96SLV O 286 1.545 1.382 0.002 |
||||
96SLV H 287 1.595 1.305 0.040 |
||||
96SLV H1 288 1.451 1.366 0.029 |
||||
97SLV O 289 0.249 0.168 0.968 |
||||
97SLV H 290 0.166 0.217 0.947 |
||||
97SLV H1 291 0.237 0.146 1.065 |
||||
98SLV O 292 1.550 0.968 1.221 |
||||
98SLV H 293 1.581 1.041 1.163 |
||||
98SLV H1 294 1.580 0.885 1.173 |
||||
99SLV O 295 0.347 0.318 0.067 |
||||
99SLV H 296 0.426 0.293 0.013 |
||||
99SLV H1 297 0.368 0.410 0.096 |
||||
100SLV O 298 0.772 0.512 1.384 |
||||
100SLV H 299 0.858 0.483 1.343 |
||||
100SLV H1 300 0.799 0.556 1.468 |
||||
101URA C 301 1.001 1.134 1.184 |
||||
101URA O 302 0.904 1.062 1.199 |
||||
101URA N 303 0.982 1.268 1.152 |
||||
101URA N1 304 1.122 1.080 1.143 |
||||
101URA H 305 0.889 1.307 1.161 |
||||
101URA H1 306 1.061 1.324 1.124 |
||||
101URA H2 307 1.124 0.981 1.122 |
||||
101URA H3 308 1.191 1.141 1.101 |
||||
102URA C 309 0.825 0.251 0.476 |
||||
102URA O 310 0.849 0.357 0.422 |
||||
102URA N 311 0.913 0.145 0.461 |
||||
102URA N1 312 0.693 0.213 0.493 |
||||
102URA H 313 1.002 0.161 0.416 |
||||
102URA H1 314 0.893 0.057 0.507 |
||||
102URA H2 315 0.619 0.278 0.467 |
||||
102URA H3 316 0.670 0.121 0.529 |
||||
103URA C 317 0.809 0.916 1.509 |
||||
103URA O 318 0.735 0.865 1.592 |
||||
103URA N 319 0.944 0.884 1.507 |
||||
103URA N1 320 0.779 1.044 1.463 |
||||
103URA H 321 0.975 0.796 1.547 |
||||
103URA H1 322 1.010 0.947 1.464 |
||||
103URA H2 323 0.686 1.081 1.476 |
||||
103URA H3 324 0.842 1.089 1.398 |
||||
104URA C 325 1.539 0.966 0.252 |
||||
104URA O 326 1.580 1.073 0.294 |
||||
104URA N 327 1.478 0.963 0.128 |
||||
104URA N1 328 1.606 0.851 0.288 |
||||
104URA H 329 1.437 1.048 0.090 |
||||
104URA H1 330 1.475 0.877 0.074 |
||||
104URA H2 331 0.029 0.848 0.378 |
||||
104URA H3 332 1.598 0.768 0.231 |
||||
105URA C 333 0.821 0.466 0.100 |
||||
105URA O 334 0.717 0.530 0.096 |
||||
105URA N 335 0.940 0.528 0.066 |
||||
105URA N1 336 0.818 0.330 0.075 |
||||
105URA H 337 0.946 0.629 0.070 |
||||
105URA H1 338 1.025 0.472 0.067 |
||||
105URA H2 339 0.732 0.278 0.088 |
||||
105URA H3 340 0.904 0.281 0.057 |
||||
106URA C 341 0.799 0.777 0.906 |
||||
106URA O 342 0.853 0.878 0.947 |
||||
106URA N 343 0.812 0.743 0.772 |
||||
106URA N1 344 0.682 0.733 0.966 |
||||
106URA H 345 0.883 0.791 0.717 |
||||
106URA H1 346 0.757 0.668 0.732 |
||||
106URA H2 347 0.651 0.778 1.051 |
||||
106URA H3 348 0.621 0.669 0.917 |
||||
107URA C 349 0.984 0.919 0.438 |
||||
107URA O 350 1.042 0.962 0.339 |
||||
107URA N 351 0.856 0.966 0.467 |
||||
107URA N1 352 1.006 0.787 0.475 |
||||
107URA H 353 0.829 1.059 0.435 |
||||
107URA H1 354 0.795 0.912 0.526 |
||||
107URA H2 355 1.094 0.743 0.451 |
||||
107URA H3 356 0.927 0.729 0.501 |
||||
108URA C 357 0.804 1.476 0.729 |
||||
108URA O 358 0.860 1.581 0.704 |
||||
108URA N 359 0.737 1.462 0.850 |
||||
108URA N1 360 0.857 1.357 0.682 |
||||
108URA H 361 0.736 1.540 0.916 |
||||
108URA H1 362 0.706 1.370 0.878 |
||||
108URA H2 363 0.929 1.358 0.611 |
||||
108URA H3 364 0.815 1.269 0.711 |
||||
109URA C 365 1.417 0.821 0.607 |
||||
109URA O 366 1.524 0.772 0.574 |
||||
109URA N 367 1.355 0.915 0.526 |
||||
109URA N1 368 1.389 0.833 0.742 |
||||
109URA H 369 1.392 0.932 0.433 |
||||
109URA H1 370 1.277 0.969 0.561 |
||||
109URA H2 371 1.448 0.785 0.809 |
||||
109URA H3 372 1.324 0.904 0.774 |
||||
110URA C 373 0.688 0.161 1.094 |
||||
110URA O 374 0.695 0.044 1.060 |
||||
110URA N 375 0.583 0.238 1.047 |
||||
110URA N1 376 0.732 0.196 1.221 |
||||
110URA H 377 0.523 0.200 0.974 |
||||
110URA H1 378 0.554 0.320 1.099 |
||||
110URA H2 379 0.778 0.126 1.277 |
||||
110URA H3 380 0.694 0.278 1.265 |
||||
111URA C 381 1.024 0.365 0.838 |
||||
111URA O 382 0.948 0.270 0.839 |
||||
111URA N 383 1.155 0.348 0.879 |
||||
111URA N1 384 1.002 0.470 0.751 |
||||
111URA H 385 1.187 0.258 0.910 |
||||
111URA H1 386 1.224 0.419 0.855 |
||||
111URA H2 387 0.910 0.482 0.710 |
||||
111URA H3 388 1.081 0.522 0.713 |
||||
112URA C 389 0.185 0.559 0.510 |
||||
112URA O 390 0.224 0.461 0.572 |
||||
112URA N 391 0.062 0.553 0.446 |
||||
112URA N1 392 0.223 0.685 0.553 |
||||
112URA H 393 0.034 0.468 0.400 |
||||
112URA H1 394 1.622 0.632 0.452 |
||||
112URA H2 395 0.311 0.694 0.602 |
||||
112URA H3 396 0.184 0.767 0.508 |
||||
113URA C 397 0.447 1.024 0.469 |
||||
113URA O 398 0.359 0.942 0.448 |
||||
113URA N 399 0.414 1.145 0.529 |
||||
113URA N1 400 0.553 1.031 0.380 |
||||
113URA H 401 0.333 1.150 0.589 |
||||
113URA H1 402 0.465 1.229 0.504 |
||||
113URA H2 403 0.579 0.948 0.329 |
||||
113URA H3 404 0.615 1.112 0.381 |
||||
1.62280 1.62280 1.62280 |
||||
File diff suppressed because it is too large
Load Diff
@ -0,0 +1,28 @@ |
||||
[ System ] |
||||
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 |
||||
16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 |
||||
31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 |
||||
46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 |
||||
61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 |
||||
76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 |
||||
91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 |
||||
106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 |
||||
121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 |
||||
136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 |
||||
151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 |
||||
166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 |
||||
181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 |
||||
196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 |
||||
211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 |
||||
226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 |
||||
241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 |
||||
256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 |
||||
271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 |
||||
286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 |
||||
301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 |
||||
316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 |
||||
331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 |
||||
346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 |
||||
361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 |
||||
376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 |
||||
391 392 393 394 395 396 397 398 399 400 401 402 403 404 |
||||
Binary file not shown.
Binary file not shown.
@ -0,0 +1,15 @@ |
||||
|
||||
integrator = steep ; Algorithm (steep = steepest descent minimization) |
||||
emtol = 100.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm |
||||
emstep = 0.01 ; Minimization step size |
||||
nsteps = 50000 ; Maximum number of (minimization) steps to perform |
||||
|
||||
; Parameters describing how to find the neighbors of each atom and how to calculate the interactions |
||||
nstlist = 5 ; Frequency to update the neighbor list and long range forces |
||||
ns_type = grid ; Method to determine neighbor list (simple, grid) |
||||
coulombtype = PME ; Treatment of long range electrostatic interactions |
||||
rcoulomb = 0.7113990804113833 ; Short-range electrostatic cut-off |
||||
rvdw = 0.7113990804113833 ; Short-range Van der Waals cut-off |
||||
pbc = xyz ; Periodic Boundary Conditions in all 3 dimensions |
||||
;define = -DFLEXIBLE |
||||
|
||||
@ -0,0 +1,41 @@ |
||||
# This file was created Thu Apr 28 23:06:14 2022 |
||||
# Created by: |
||||
# :-) GROMACS - gmx msd, 2021.3 (-: |
||||
# |
||||
# Executable: /home/adit/opt/gromacs-2021.3/build/bin/gmx |
||||
# Data prefix: /home/adit/opt/gromacs-2021.3 (source tree) |
||||
# Working dir: /home/adit/MySoftware/CMMDE/test/larutan/SistemLarutan |
||||
# Command line: |
||||
# gmx msd -f nvep.trr -s nvep.tpr -n SLV.ndx -o msd_SLV.xvg |
||||
# gmx msd is part of G R O M A C S: |
||||
# |
||||
# GROtesk MACabre and Sinister |
||||
# |
||||
@ title "Mean Square Displacement" |
||||
@ xaxis label "Time (ps)" |
||||
@ yaxis label "MSD (nm\S2\N)" |
||||
@TYPE xy |
||||
# MSD gathered over 5 ps with 1 restarts |
||||
# Diffusion constants fitted from time 0.5 to 4.5 ps |
||||
# D[(resname_SLV)] = 6.4232 (+/- 1.9949) (1e-5 cm^2/s) |
||||
0 0 |
||||
0.25 0.0096222 |
||||
0.5 0.0203094 |
||||
0.75 0.0339887 |
||||
1 0.0499902 |
||||
1.25 0.0581352 |
||||
1.5 0.0635697 |
||||
1.75 0.0687521 |
||||
2 0.0769021 |
||||
2.25 0.0810643 |
||||
2.5 0.0943307 |
||||
2.75 0.107156 |
||||
3 0.116171 |
||||
3.25 0.12999 |
||||
3.5 0.142552 |
||||
3.75 0.155407 |
||||
4 0.165951 |
||||
4.25 0.169858 |
||||
4.5 0.169497 |
||||
4.75 0.175091 |
||||
5 0.191759 |
||||
@ -0,0 +1,41 @@ |
||||
# This file was created Thu Apr 28 23:06:14 2022 |
||||
# Created by: |
||||
# :-) GROMACS - gmx msd, 2021.3 (-: |
||||
# |
||||
# Executable: /home/adit/opt/gromacs-2021.3/build/bin/gmx |
||||
# Data prefix: /home/adit/opt/gromacs-2021.3 (source tree) |
||||
# Working dir: /home/adit/MySoftware/CMMDE/test/larutan/SistemLarutan |
||||
# Command line: |
||||
# gmx msd -f nvep.trr -s nvep.tpr -n URA.ndx -o msd_URA.xvg |
||||
# gmx msd is part of G R O M A C S: |
||||
# |
||||
# GROtesk MACabre and Sinister |
||||
# |
||||
@ title "Mean Square Displacement" |
||||
@ xaxis label "Time (ps)" |
||||
@ yaxis label "MSD (nm\S2\N)" |
||||
@TYPE xy |
||||
# MSD gathered over 5 ps with 1 restarts |
||||
# Diffusion constants fitted from time 0.5 to 4.5 ps |
||||
# D[(resname_URA)] = 3.9640 (+/- 3.7993) (1e-5 cm^2/s) |
||||
0 0 |
||||
0.25 0.00908764 |
||||
0.5 0.0186648 |
||||
0.75 0.0266412 |
||||
1 0.0334288 |
||||
1.25 0.0384099 |
||||
1.5 0.0487507 |
||||
1.75 0.063285 |
||||
2 0.0724394 |
||||
2.25 0.0743349 |
||||
2.5 0.082415 |
||||
2.75 0.0883465 |
||||
3 0.101314 |
||||
3.25 0.103967 |
||||
3.5 0.109389 |
||||
3.75 0.110158 |
||||
4 0.102565 |
||||
4.25 0.101962 |
||||
4.5 0.104766 |
||||
4.75 0.114225 |
||||
5 0.132007 |
||||
Binary file not shown.
Binary file not shown.
@ -0,0 +1,407 @@ |
||||
system |
||||
404 |
||||
1SLV O 1 0.417 0.127 0.980 0.0096 0.4551 0.2395 |
||||
1SLV H 2 0.443 0.046 1.028 -0.4908 0.0432 -0.1579 |
||||
1SLV H1 3 0.367 0.090 0.905 -1.2084 1.4512 0.5314 |
||||
2SLV O 4 0.719 0.022 0.013 0.1280 0.5902 0.3504 |
||||
2SLV H 5 0.671 0.028 0.098 1.2760 -2.8160 1.4147 |
||||
2SLV H1 6 0.663 0.061 -0.056 1.0934 -0.3243 -1.0145 |
||||
3SLV O 7 0.435 0.495 1.480 -0.3386 0.2690 0.5433 |
||||
3SLV H 8 0.417 0.581 1.438 0.4760 -0.0779 -0.5591 |
||||
3SLV H1 9 0.358 0.448 1.445 -1.4587 2.6384 -0.3512 |
||||
4SLV O 10 1.322 1.438 1.285 -0.0325 -0.0169 -0.8243 |
||||
4SLV H 11 1.316 1.352 1.330 0.3368 -0.1374 -0.9969 |
||||
4SLV H1 12 1.377 1.494 1.342 -1.0735 -0.0692 0.2606 |
||||
5SLV O 13 0.402 1.125 0.779 -0.0377 0.1158 -0.0642 |
||||
5SLV H 14 0.321 1.148 0.827 -1.8768 0.9213 -3.2358 |
||||
5SLV H1 15 0.369 1.049 0.727 -0.4949 -0.1055 0.5324 |
||||
6SLV O 16 0.639 0.468 1.242 0.2674 -0.0961 -0.1409 |
||||
6SLV H 17 0.664 0.487 1.149 1.5826 -0.0697 0.1958 |
||||
6SLV H1 18 0.623 0.560 1.269 -2.6264 -1.0511 1.8681 |
||||
7SLV O 19 0.861 1.487 0.266 -0.3978 -0.0949 -0.4893 |
||||
7SLV H 20 0.906 1.540 0.197 -0.6303 -0.6502 -1.0846 |
||||
7SLV H1 21 0.786 1.437 0.230 -0.3109 0.2648 -1.1998 |
||||
8SLV O 22 1.538 0.751 0.539 0.1567 -0.5353 0.0748 |
||||
8SLV H 23 1.604 0.780 0.605 -1.4478 1.3947 0.9418 |
||||
8SLV H1 24 1.459 0.781 0.588 2.3119 1.0293 2.9604 |
||||
9SLV O 25 0.991 0.058 0.069 0.4452 -0.0407 0.1446 |
||||
9SLV H 26 1.033 0.069 -0.018 -0.6858 0.9859 -0.3127 |
||||
9SLV H1 27 0.897 0.065 0.043 0.0869 -1.0343 1.1053 |
||||
10SLV O 28 1.526 1.482 0.351 0.2594 0.0315 0.4005 |
||||
10SLV H 29 1.518 1.473 0.255 -1.6690 -0.7873 0.6042 |
||||
10SLV H1 30 1.540 1.390 0.379 -0.6761 0.2682 1.7446 |
||||
11SLV O 31 0.513 0.620 0.198 -0.3771 -0.3104 -0.6505 |
||||
11SLV H 32 0.514 0.523 0.205 -0.4844 -0.2264 0.9926 |
||||
11SLV H1 33 0.426 0.628 0.157 -0.8732 -1.4028 0.1449 |
||||
12SLV O 34 1.080 0.064 0.800 0.5035 -0.2350 -0.0647 |
||||
12SLV H 35 1.143 0.128 0.839 0.4072 0.4133 -0.9341 |
||||
12SLV H1 36 1.039 0.120 0.731 1.0601 -1.9131 -1.8333 |
||||
13SLV O 37 0.549 0.488 0.907 -0.2582 -0.2580 0.4263 |
||||
13SLV H 38 0.603 0.430 0.850 -0.5852 0.9054 -1.1625 |
||||
13SLV H1 39 0.526 0.558 0.843 2.9125 2.1792 1.6902 |
||||
14SLV O 40 1.104 0.651 0.029 -0.3595 0.1544 -0.1572 |
||||
14SLV H 41 1.020 0.607 0.050 -0.5154 0.3637 -0.3477 |
||||
14SLV H1 42 1.083 0.704 -0.050 -0.7755 0.5042 0.1849 |
||||
15SLV O 43 0.172 0.899 0.369 -0.7227 0.2668 -0.0252 |
||||
15SLV H 44 0.170 0.977 0.310 0.5470 0.9305 0.7705 |
||||
15SLV H1 45 0.106 0.837 0.332 -1.3565 0.4149 0.8235 |
||||
16SLV O 46 0.755 0.257 0.228 -0.3553 -0.2597 0.1931 |
||||
16SLV H 47 0.682 0.202 0.260 -2.5266 0.3928 -3.0851 |
||||
16SLV H1 48 0.729 0.278 0.136 3.2523 -0.2798 -0.9832 |
||||
17SLV O 49 1.197 1.014 0.727 0.1729 -0.4958 0.1763 |
||||
17SLV H 50 1.125 1.041 0.667 -0.9245 -0.7593 1.3310 |
||||
17SLV H1 51 1.192 0.917 0.725 -0.3712 -0.5005 1.0034 |
||||
18SLV O 52 0.369 0.395 0.162 0.1065 0.0745 -0.3991 |
||||
18SLV H 53 0.350 0.447 0.082 -0.9642 -0.4062 -0.4731 |
||||
18SLV H1 54 0.281 0.368 0.195 0.6439 -0.1138 0.9323 |
||||
19SLV O 55 1.443 1.126 0.028 0.1135 0.0053 -0.3157 |
||||
19SLV H 56 1.419 1.124 0.122 -1.1332 1.2486 -0.5784 |
||||
19SLV H1 57 1.500 1.204 0.016 -1.2280 0.8584 -1.3792 |
||||
20SLV O 58 0.400 0.909 1.040 -0.0603 -0.1365 0.1969 |
||||
20SLV H 59 0.439 0.994 1.068 -0.1259 0.4006 -1.2850 |
||||
20SLV H1 60 0.313 0.898 1.083 -0.2452 -0.5801 -0.2853 |
||||
21SLV O 61 0.581 0.882 0.818 0.4311 -1.0663 -0.9830 |
||||
21SLV H 62 0.544 0.877 0.729 -0.2625 0.9368 -0.8471 |
||||
21SLV H1 63 0.514 0.857 0.884 0.0203 -0.4787 -1.1776 |
||||
22SLV O 64 1.286 0.044 1.079 -0.4598 0.3873 0.0889 |
||||
22SLV H 65 1.342 0.047 1.159 1.8523 -1.0161 -1.3469 |
||||
22SLV H1 66 1.293 -0.047 1.044 -0.1445 0.4756 -0.0780 |
||||
23SLV O 67 0.620 0.256 0.776 0.3699 -0.9281 -0.6039 |
||||
23SLV H 68 0.614 0.192 0.703 0.0159 -0.0901 -1.3425 |
||||
23SLV H1 69 0.526 0.273 0.793 -0.0659 -0.5172 -3.0261 |
||||
24SLV O 70 0.387 1.212 0.073 -0.3622 -0.3313 -0.2897 |
||||
24SLV H 71 0.477 1.241 0.050 -0.3379 -0.0441 0.1595 |
||||
24SLV H1 72 0.354 1.285 0.127 -0.0132 1.4680 -2.3509 |
||||
25SLV O 73 1.541 0.480 0.480 0.3597 0.1768 -0.3088 |
||||
25SLV H 74 1.539 0.571 0.515 -1.2563 0.5264 -1.2041 |
||||
25SLV H1 75 1.551 0.415 0.551 2.5780 0.3991 -0.3449 |
||||
26SLV O 76 0.592 0.049 0.560 0.0861 0.2554 -0.4392 |
||||
26SLV H 77 0.560 0.127 0.512 -1.2016 0.7678 1.1630 |
||||
26SLV H1 78 0.689 0.047 0.554 0.3344 3.9848 0.1508 |
||||
27SLV O 79 0.941 0.759 1.233 0.7787 -0.2728 0.0255 |
||||
27SLV H 80 0.942 0.840 1.287 -0.2767 -0.3672 0.1941 |
||||
27SLV H1 81 0.985 0.794 1.153 -1.2311 -0.5031 -1.2457 |
||||
28SLV O 82 1.606 0.051 0.564 -0.6492 -0.3493 -0.2911 |
||||
28SLV H 83 1.614 0.002 0.480 -0.1535 -0.2180 -0.3253 |
||||
28SLV H1 84 1.624 -0.025 0.623 -0.0484 1.0302 1.3988 |
||||
29SLV O 85 0.231 1.359 0.502 -0.5673 -0.0158 0.2291 |
||||
29SLV H 86 0.295 1.367 0.575 0.6003 -0.3462 -0.7283 |
||||
29SLV H1 87 0.260 1.280 0.454 -0.3100 -0.1226 0.5604 |
||||
30SLV O 88 1.451 0.218 0.911 0.2817 0.1732 0.3031 |
||||
30SLV H 89 1.437 0.125 0.935 1.3627 -0.7664 -2.3566 |
||||
30SLV H1 90 1.364 0.261 0.912 0.8276 1.3520 -0.2257 |
||||
31SLV O 91 0.858 0.758 0.134 -0.2391 -0.1526 -0.2981 |
||||
31SLV H 92 0.948 0.722 0.147 0.4904 1.8502 0.6419 |
||||
31SLV H1 93 0.820 0.690 0.075 1.9418 -2.0834 0.3517 |
||||
32SLV O 94 0.244 0.233 0.587 0.2567 0.1140 0.9333 |
||||
32SLV H 95 0.213 0.251 0.677 -0.0448 0.2118 0.8079 |
||||
32SLV H1 96 0.155 0.218 0.551 1.0318 -0.5142 -0.9045 |
||||
33SLV O 97 1.384 1.463 0.870 0.5901 0.1708 -0.1402 |
||||
33SLV H 98 1.370 1.449 0.775 0.4862 -0.1746 -0.0729 |
||||
33SLV H1 99 1.356 1.376 0.904 -0.6637 0.4360 -0.4611 |
||||
34SLV O 100 0.818 0.259 1.250 -0.0992 -0.2427 -0.4532 |
||||
34SLV H 101 0.784 0.349 1.264 -1.6038 -0.7238 -0.8583 |
||||
34SLV H1 102 0.802 0.244 1.155 -0.4422 1.6993 -0.7440 |
||||
35SLV O 103 0.715 0.686 0.380 -0.0193 0.1075 -0.4958 |
||||
35SLV H 104 0.642 0.652 0.326 -0.8190 1.8351 -0.5785 |
||||
35SLV H1 105 0.795 0.655 0.334 -0.3895 -0.9614 -0.4344 |
||||
36SLV O 106 0.925 1.361 1.147 -0.3659 -0.0627 -0.0861 |
||||
36SLV H 107 0.950 1.453 1.125 -2.2485 0.6056 0.3796 |
||||
36SLV H1 108 0.912 1.363 1.244 -0.7789 -1.1401 -0.1176 |
||||
37SLV O 109 0.656 1.444 1.069 0.1223 0.2291 -0.2527 |
||||
37SLV H 110 0.709 1.525 1.060 0.4109 0.2744 1.5304 |
||||
37SLV H1 111 0.721 1.378 1.039 0.2843 0.0697 0.4342 |
||||
38SLV O 112 0.132 1.161 0.066 -0.5492 -0.1295 -0.1570 |
||||
38SLV H 113 0.226 1.180 0.050 -0.4262 2.8143 2.9078 |
||||
38SLV H1 114 0.119 1.067 0.047 0.5610 0.2824 -3.6320 |
||||
39SLV O 115 0.945 0.162 0.564 0.2369 -0.4457 0.1589 |
||||
39SLV H 116 0.950 0.189 0.471 -1.2440 -2.0288 -0.4412 |
||||
39SLV H1 117 0.947 0.251 0.604 0.6771 -1.1453 1.7686 |
||||
40SLV O 118 0.001 0.680 0.229 0.0960 -0.0981 -0.3446 |
||||
40SLV H 119 -0.004 0.651 0.322 3.6845 0.1325 0.0535 |
||||
40SLV H1 120 -0.070 0.637 0.179 -1.1751 0.3847 0.9620 |
||||
41SLV O 121 0.092 1.357 1.069 -0.1724 0.2945 0.9680 |
||||
41SLV H 122 0.188 1.370 1.075 0.1731 -1.4604 -0.0291 |
||||
41SLV H1 123 0.072 1.279 1.124 3.3827 -2.1762 -0.8230 |
||||
42SLV O 124 0.581 1.587 0.264 0.0761 -0.1106 -0.1031 |
||||
42SLV H 125 0.606 1.496 0.288 -0.8008 -0.0347 1.1507 |
||||
42SLV H1 126 0.519 1.602 0.337 0.9651 -1.3560 0.9537 |
||||
43SLV O 127 0.093 0.932 1.024 -0.3827 0.2486 0.0086 |
||||
43SLV H 128 0.063 1.012 1.071 1.4086 -0.1269 1.8990 |
||||
43SLV H1 129 0.076 0.952 0.930 0.4391 -1.2472 -0.4837 |
||||
44SLV O 130 0.885 1.431 1.414 -0.6600 0.6425 0.4699 |
||||
44SLV H 131 0.824 1.449 1.488 -0.0933 0.3436 1.0182 |
||||
44SLV H1 132 0.932 1.513 1.394 -0.4775 0.5194 0.3911 |
||||
45SLV O 133 1.444 0.452 1.080 -0.2396 0.3501 0.3150 |
||||
45SLV H 134 1.505 0.465 1.155 0.5154 0.1051 -0.2493 |
||||
45SLV H1 135 1.496 0.392 1.024 -1.3159 0.3942 -0.7752 |
||||
46SLV O 136 0.385 1.336 1.068 0.0801 0.2112 -0.7873 |
||||
46SLV H 137 0.422 1.246 1.060 1.0491 0.5569 -0.4114 |
||||
46SLV H1 138 0.463 1.394 1.073 -1.4488 2.2965 1.2502 |
||||
47SLV O 139 1.015 0.809 0.893 0.4886 0.1851 0.7985 |
||||
47SLV H 140 0.946 0.850 0.839 -0.6531 -0.9223 1.3671 |
||||
47SLV H1 141 1.037 0.887 0.947 -0.1378 -0.0209 1.3740 |
||||
48SLV O 142 0.636 0.367 1.603 -0.8413 -0.2207 0.4040 |
||||
48SLV H 143 0.578 0.442 1.579 -0.1368 -0.3688 -1.9657 |
||||
48SLV H1 144 0.595 0.300 1.546 1.3194 -0.7535 -0.6174 |
||||
49SLV O 145 0.642 1.256 1.569 -0.0691 0.2772 0.5096 |
||||
49SLV H 146 0.649 1.220 1.478 0.8536 -2.2547 1.4769 |
||||
49SLV H1 147 0.652 1.174 1.620 -0.7048 1.6490 3.0082 |
||||
50SLV O 148 0.049 1.488 0.788 0.0520 0.7816 -0.3860 |
||||
50SLV H 149 -0.045 1.488 0.811 0.7934 1.2247 3.2905 |
||||
50SLV H1 150 0.079 1.442 0.868 2.6303 2.5790 -0.1884 |
||||
51SLV O 151 1.551 0.296 0.670 -0.1567 0.1572 -0.4597 |
||||
51SLV H 152 1.570 0.204 0.647 -0.2677 0.3447 -1.3228 |
||||
51SLV H1 153 1.524 0.307 0.763 0.9149 1.1666 -0.2468 |
||||
52SLV O 154 1.222 1.260 1.003 -0.4894 0.1313 -0.1158 |
||||
52SLV H 155 1.192 1.228 1.090 -0.2107 -0.4777 -0.2379 |
||||
52SLV H1 156 1.183 1.202 0.935 -3.5554 0.5758 1.1078 |
||||
53SLV O 157 1.019 0.116 1.379 -0.2842 0.1889 -0.6209 |
||||
53SLV H 158 0.949 0.153 1.323 -1.1557 3.3400 2.2041 |
||||
53SLV H1 159 1.056 0.194 1.424 -0.6420 1.4595 -2.4787 |
||||
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||||
112URA N 391 1.061 0.710 0.487 -0.2898 -0.3490 0.1816 |
||||
112URA N1 392 1.244 0.578 0.453 -0.2985 0.2997 0.5757 |
||||
112URA H 393 1.048 0.806 0.455 -0.2645 0.2546 1.8846 |
||||
112URA H1 394 0.994 0.637 0.467 -1.8273 1.2608 -0.8190 |
||||
112URA H2 395 1.195 0.515 0.390 1.1268 -0.4552 0.1924 |
||||
112URA H3 396 1.344 0.567 0.456 -0.3351 -0.6010 -0.6117 |
||||
113URA C 397 1.551 1.137 0.754 0.3728 1.2113 0.4130 |
||||
113URA O 398 1.673 1.138 0.760 0.4830 -0.0422 0.1989 |
||||
113URA N 399 1.486 1.014 0.777 -0.0825 0.3621 0.0796 |
||||
113URA N1 400 1.493 1.219 0.654 -0.4069 0.1890 0.2794 |
||||
113URA H 401 1.524 0.936 0.829 -2.6709 -2.1558 -1.5287 |
||||
113URA H1 402 1.385 1.018 0.772 -0.1551 0.4102 1.3328 |
||||
113URA H2 403 1.413 1.181 0.604 1.0092 1.1549 -3.0095 |
||||
113URA H3 404 1.557 1.281 0.605 1.0733 -0.6395 1.1018 |
||||
1.60651 1.60651 1.60651 |
||||
File diff suppressed because it is too large
Load Diff
@ -0,0 +1,46 @@ |
||||
|
||||
title = NPT equilibration |
||||
; Run parameters |
||||
integrator = md ; leap-frog integrator |
||||
nsteps = 100000 ; 2 * 50000 = 100 ps |
||||
dt = 0.002 ; 2 fs |
||||
; Output control |
||||
nstxout = 500 ; save coordinates every 1.0 ps |
||||
nstvout = 500 ; save velocities every 1.0 ps |
||||
nstenergy = 500 ; save energies every 1.0 ps |
||||
nstlog = 500 ; update log file every 1.0 ps |
||||
; Bond parameters |
||||
continuation = yes ; first dynamics run |
||||
constraint_algorithm = lincs ; holonomic constraints |
||||
constraints = h-bonds ; bonds involving H are constrained |
||||
lincs_iter = 1 ; accuracy of LINCS |
||||
lincs_order = 4 ; also related to accuracy |
||||
; Neighborsearching |
||||
cutoff-scheme = Verlet |
||||
ns_type = grid ; search neighboring grid cells |
||||
nstlist = 10 ; 20 fs, largely irrelevant with Verlet scheme |
||||
rcoulomb = 0.7113990804113833 ; short-range electrostatic cutoff (in nm) |
||||
rvdw = 0.7113990804113833 ; short-range van der Waals cutoff (in nm) |
||||
; Electrostatics |
||||
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics |
||||
pme_order = 4 ; cubic interpolation |
||||
fourierspacing = 0.16 ; grid spacing for FFT |
||||
; Temperature coupling is on |
||||
tcoupl = V-rescale ; modified Berendsen thermostat |
||||
tc-grps = System ; two coupling groups - more accurate |
||||
tau_t = 0.1 ; time constant, in ps |
||||
ref_t = 298.15 ; reference temperature, one for each group, in K |
||||
; Pressure coupling is on |
||||
pcoupl = Berendsen ; Pressure coupling on in NPT |
||||
pcoupltype = isotropic ; uniform scaling of box vectors |
||||
tau_p = 2.0 ; time constant, in ps |
||||
ref_p = 1.0 ; reference pressure, in bar |
||||
compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1 |
||||
refcoord_scaling = com |
||||
; Periodic boundary conditions |
||||
pbc = xyz ; 3-D PBC |
||||
; Dispersion correction |
||||
DispCorr = EnerPres ; account for cut-off vdW scheme |
||||
; Velocity generation |
||||
gen_vel = no ; Velocity generation is off |
||||
|
||||
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Reference in new issue