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A series of Python3 script to lower the barrier of computing and simulating molecular and material systems.
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Aditya Wibawa Sakti 5110c9d0d5
Correct the freezing bond for GOAT-REACT 		1 month ago
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README.md

Computational Molecular and Material Design Environment (CMMDE)

Background

This software is developed for decreasing the barrier in using popular open-source computational chemistry software. Currently, CMMDE can use the following software:

  1. Orca
  2. DFTB+
  3. GROMACS
  4. DOCK6
  5. DCDFTBMD
  6. Quantum Espresso
  7. xTB
  8. Open Babel

About CMMDE

CMMDE is a set of tools based on Python for running computational jobs, as well as analyzing, visualizing, and post-processing the results in free/libre and open source applications for computational molecular & material design.

  • Core developers: Aditya Wibawa Sakti, Atthar Luqman Ivansyah, Hasan Al Rasyid, Muhamad Abdulkadir Martoprawiro, Aulia Sukma Hutama
  • Contributors: Athiya Mahmud Hanna, Arifin, Daniel Sethio
  • Core reviewers: Rahmat Gunawan, Imam Siswanto, Parsaoran Siahaan, Nova Pratiwi Indriyani
  • Committed users: Yusthinus Thobias Male, Veliyana Londong, Mirella Fonda, Riyanto, Badra Sanditya Rattyananda, Suci Zulaikha Hildayani, Rustaman, Eduardus

CMMDE telah diluncurkan dan akan diikuti oleh serangkaian lokakarya:

Sabtu, 17 September 2022 (10:00 WIB):
Penyiapan Server Komputasi
Tautan: https://mki.ac/CMMD-server

Sabtu, 24 September 2022 (10:00 WIB):
Workshop on Text-Based CMMDE
Tautan: https://mki.ac/CMMDE-text

Sabtu, 1 Oktober 2022 (10:00 WIB):
Workshop on Web-Based CMMDE
Tautan: https://mki.ac/CMMDE-web

Informasi lebih lanjut: cmmde@mki.or.id

Requirements

Sebelum menginstall CMMDE, perhatikan bahwa anda harus terlebih dahulu menginstall slurm untuk mengatur pengiriman pekerjaan komputasi anda ke suatu sistem antrian. Salah satu metode yang paling mudah untuk menginstall slurm dapat ditemukan di sini.

Installation

  1. Cloning the repository:
git clone https://git.mki.or.id/coredev/cmmde
  1. Change directory to CMMDE:
cd cmmde
  1. Install CMMDE dengan mengetik:
./install.sh

Jika ditemukan error:

FileNotFoundError: [Errno 2] No such file or directory: '/usr/bin/pip3.9'

Lakukan:

ln -s /usr/bin/pip /usr/bin/pip3.9
  1. Jika ingin menjalankan program cmmde-gui:
cd cmmde_gui
panel serve gui.py --autoreload

Catatan

Jika hanya ingin menginstall CMMDE versi text-based, cukup lakukan langkah 1-3. Langkah 4 hanya dilakukan jika ingin menjalankan CMMDE versi graphical user interface. Namun versi ini perlu menginstall panel-chemistry versi 0.0.11.

 pip install -Iv panel-chemistry==0.0.11