VeloxChem for LUMI added

docs/apps/by_discipline.md

@@ -100,6 +100,7 @@
 * [TmoleX](tmolex.md) GUI for setting up and analyzing TURBOMOLE jobs
 * [TURBOMOLE](turbomole.md) Efficient program package for electronic structure calculations
 * [VASP](vasp.md) Ab initio DFT electronic structures
+* [VeloxChem](veloxchem.md) Python-based open source quantum chemistry software 
 * [VMD](vmd.md) Molecular visualization program
 
 ## Computational Engineering

docs/apps/veloxchem.md

@@ -0,0 +1,112 @@
+---
+tags:
+  - Free
+---
+
+# VeloxChem
+
+VeloxChem is a Python-based open source quantum chemistry software for
+contemporary and future hardware architectures. It features interactive program
+access through Jupyter notebooks as well as massively parallel calculations in
+high-performance computing (HPC) environments. 
+
+## Available
+
+
+ - LUMI
+
+
+   | Version | Available modules | Notes |
+   |:-------:|:------------------|:-----:|
+   | 1.0rc4 | veloxchem/cpu   | CPU version |
+   | 1.0 | veloxchem/gpu   | GPU version |
+
+
+## License
+
+ - VeloxChem is a free software available under the 3-Clause BSD License.
+
+## Usage
+
+On LUMI, you need to first activate CSC's local software stack before you can
+see and load the module. For example:
+
+```bash
+module use /appl/local/csc/modulefiles
+module load veloxchem/cpu
+source $VLXHOME/vlxenv/bin/activate
+vlx --version
+```
+
+
+### LUMI
+
+=== "LUMI CPU script"
+
+    ```bash
+    #!/bin/bash
+    #SBATCH --account=<project>
+    #SBATCH --partition=standard
+    #SBATCH --job-name=vlx.cpu_test
+    #SBATCH --time 02:00:00
+
+    #SBATCH --nodes=2
+    #SBATCH --ntasks-per-node=8
+    #SBATCH --cpus-per-task=16
+
+    # Load VeloxChem CPU environment
+    module use /appl/local/csc/modulefiles
+    module load veloxchem/cpu
+
+    # Activate Python virtual environment
+    source $VLXHOME/vlxenv/bin/activate
+
+    # OpenMP settings (based on allocated SLURM cpus)
+    export OMP_NUM_THREADS=${SLURM_CPUS_PER_TASK}
+    export OMP_PLACES=cores
+
+    # Run VeloxChem
+    job=ecd_response
+    srun vlx ${job}.inp ${job}.out
+    ```
+
+=== "LUMI GPU script"
+
+    ```bash
+    #!/bin/bash
+    #SBATCH --account=<project>
+    #SBATCH --partition=standard-g
+    #SBATCH --job-name=vlx.gpu_test
+    #SBATCH --time 02:00:00
+
+    #SBATCH --nodes=2
+    #SBATCH --exclusive
+    #SBATCH --ntasks-per-node=1
+    #SBATCH --hint=nomultithread
+    #SBATCH --gpus-per-node=8
+
+    # Load VeloxChem GPU environment
+    module use /appl/local/csc/modulefiles
+    module load veloxchem/gpu
+
+    # Activate Python virtual environment
+    source $VLXHOME/vlxenv/bin/activate
+
+    # use one OpenMP thread per GPU device
+    export OMP_NUM_THREADS=8
+    export OMP_PLACES=cores
+    export SRUN_CPUS_PER_TASK=8
+
+    # Run VeloxChem
+    job=g-quad-neutral
+    srun python3 -m veloxchem ${job}.inp ${job}.out
+    ```
+
+## More information
+
+ - VeloxChem website: [veloxchem.org](https://veloxchem.org/)
+ - VeloxChem GitLab repository: [gitlab.com/veloxchem/veloxchem](https://gitlab.com/veloxchem/veloxchem)
+ - [VeloxChem: A Python-driven density-functional theory program for spectroscopy simulations in high-performance computing environments](https://doi.org/10.1002/wcms.1457) (introductory paper about VeloxChem) 
+ - [VeloxChem — Quantum Molecular Modelling in HPC Environments](https://www.pdc.kth.se/about/publications/pdc-newsletter-no-2-2019/veloxchem-1.945304) (article about the reasons and need for developing VeloxChem, the goals and structure of the software and its efficiency)
+ - VIAMD for VeloxChem: [github.com/scanberg/viamd/wiki](https://github.com/scanberg/viamd/wiki) 
+