You can not select more than 25 topics
Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.
80 lines
2.9 KiB
80 lines
2.9 KiB
# 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](https://orcaforum.kofo.mpg.de/app.php/portal) |
|
2. [DFTB+](https://dftbplus.org/) |
|
3. [GROMACS](https://manual.gromacs.org/current/download.html) |
|
4. [DOCK6](https://dock.compbio.ucsf.edu/DOCK_6/index.htm) |
|
5. [DCDFTBMD](http://www.chem.waseda.ac.jp/dcdftbmd/?lang=en) |
|
6. [Quantum Espresso](https://www.quantum-espresso.org/) |
|
7. [xTB](https://github.com/grimme-lab/xtb) |
|
8. [Open Babel](http://openbabel.org/wiki/Main_Page) |
|
|
|
## 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: Adit, Atthar, Hasan, MAM, Tommy |
|
- Contributors: Athiya MH, Arifin, Daniel |
|
- Core reviewers: Igun, Imam, Parsaoran |
|
- Committed users: Yusthinus, Veli, Mirella, Riyanto, Badra, Hilda, Rustaman, Edu |
|
|
|
Tahap kedua peluncuran CMMDE, didahului workshop: |
|
|
|
|
|
**Selasa, 16 Agustus 2022 (13:00 WIB):**</br> |
|
Workshop on Text-Based CMMDE</br> |
|
Tautan: [https://mki.ac/CMMDE-text]( https://mki.ac/CMMDE-text) |
|
|
|
**Rabu, 17 Agustus 2022 (13:00 WIB):**</br> |
|
Workshop on Web-Based CMMDE</br> |
|
Tautan: [https://mki.ac/CMMDE-web]( https://mki.ac/CMMDE-web) |
|
|
|
**Rabu, 17 Agustus 2022 (16:00 WIB)**:</br> |
|
Launching CMMDE: Web-Based Version</br> |
|
Launching Consortium on Computational Science Development</br> |
|
(Konsorsium Pengembangan Sains Komputasi)</br> |
|
Tautan: [https://mki.ac/ccsd-launch]( https://mki.ac/ccsd-launch) |
|
|
|
**Senin, 5 September 2022 (13:00 WIB):**</br> |
|
Penyiapan Server Komputasi</br> |
|
Tautan: [https://mki.ac/CMMD-server](https://mki.ac/CMMD-server) |
|
|
|
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 [slurm](https://) |
|
|
|
## Installation |
|
1. Cloning the repository: |
|
```bash |
|
git clone https://git.mki.or.id/coredev/cmmde |
|
``` |
|
2. Change directory to CMMDE: |
|
```bash |
|
cd cmmde |
|
``` |
|
3. Install CMMDE dengan mengetik: |
|
```bash |
|
./install.sh |
|
``` |
|
Jika ditemukan _error_: |
|
```bash |
|
FileNotFoundError: [Errno 2] No such file or directory: '/usr/bin/pip3.9' |
|
``` |
|
Lakukan: |
|
```bash |
|
ln -s /usr/bin/pip /usr/bin/pip3.9 |
|
``` |
|
4. Jika ingin menjalankan program cmmde-gui: |
|
```bash |
|
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`. |
|
```bash |
|
pip install -Iv panel-chemistry==0.0.11 |
|
```
|
|
|