ONETEP

https://docs.onetep.org
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### tinktep.config File Example for QM/MM

Source: https://docs.onetep.org/_sources/tinktep.rst

An example tinktep.config file that controls the QM/MM calculation setup between ONETEP and TINKER. It specifies computational resources, QM/MM interface parameters, and how ONETEP and TINKER handle different physical terms like electrostatics and bonding.

```TINKTEP Configuration
jobname water_dimer

# *** Computational environment set-up ***
tinker_nthreads 8
onetep_nranks 2
onetep_nthreads 8
onetep_executable ./onetep.RH7
mpirun_executable mpirun

# *** Nuts and bolts of the QM/MM interface ***
qm_mm_polscal 6.0
qm_polarisability
qm_thole_polarisability
renumber_offset 500

# *** Physics ***

# Undamped fixed, permanent multipoles using the full density representation,
# and Thole-damped induced dipoles using the QM* representation. MM repulsive potential.
onetep_perm_mpoles     perm_fix_rep potential_coulombic_smeared energy_from_potential
onetep_induced_dipoles ind_qmstar   potential_thole_damped      energy_from_potential

# TINKER handles all bonded (valence) terms between MM atoms.
tinker_bond_energy 1
tinker_angle_energy 1
tinker_ureybrad_energy 1

# TINKER handles MM electrostatics.
tinker_mm_perm_energy 1
tinker_mm_pol_energy 1

# ONETEP handles QM/MM electrostatics.

```

--------------------------------

### Example HFx Calculation Setup

Source: https://docs.onetep.org/hfx

A complete ONETEP input file demonstrating a basic Hartree-Fock exchange calculation using the B3LYP functional for a water molecule. This example includes essential blocks for SWRI, species, lattice, positions, and species potentials, alongside the mandatory HFx keywords.

```input
xc_functional B3LYP
cutoff_energy 800 eV

%block swri
  for_hfx 3 10 V 10 10 WE
%endblock swri

%block species_swri-for_hfx
O
H
%endblock species_swri-for_hfx

hfx_use_ri for_hfx
hfx_max_l 3
hfx_max_q 10

%block lattice_cart
  25.00     0.00     0.00
   0.00    25.00     0.00
   0.00     0.00    25.00
%endblock lattice_cart

%block positions_abs
ang
O 5.79564200 7.40742600 6.63194300
H 5.19938100 8.05407400 6.24141400
H 5.16429100 6.74016800 6.88482600
%endblock positions_abs

%block species
O O 8 4 8.0
H H 1 1 8.0
%endblock species

%block species_pot
O "oxygen.recpot"
H "hydrogen.recpot"
%endblock species_pot

```

--------------------------------

### ONETEP .dat.template Example

Source: https://docs.onetep.org/_sources/tinktep.rst

A basic ONETEP .dat.template file for a QM/MM calculation, demonstrating essential keywords for species, potentials, lattice, and DMA/polarizable embedding setup. This template is used by TINKTEP to generate the final ONETEP .dat file, excluding atom positions.

```ONETEP Configuration
! --- usual ONETEP keywords ---
%block species_atomic_set                                                       
H  "SOLVE"
O  "SOLVE"
%endblock species_atomic_set                                                    

%block species                                                                  
H  H 1 1 7.0
O  O 8 4 7.0
%endblock species                                                               

%block species_pot
H  'H_04.recpot'
O  'O_02.recpot'
%endblock species_pot

%block lattice_cart
30.0  0.0  0.0
 0.0 30.0  0.0
 0.0  0.0 30.0
%endblock lattice_cart                                                          

cutoff_energy 1000 eV
charge 0
xc_functional PBE
dispersion 1

! --- cutoff Coulomb to enforce OBCs in ONETEP ---
coulomb_cutoff_type SPHERE
coulomb_cutoff_radius 40.0 bohr
coulomb_cutoff_write_int F

! --- DMA setup, needed for QM/MM. Consult DMA manual for details ---
%block swri
  for_dma 1 12 V 12 12 W
%endblock swri

%block species_swri-for_dma
H
O
%endblock species_swri-for_dma

dma_calculate T 
dma_use_ri for_dma
dma_max_l 1
dma_max_q 12
dma_metric ELECTROSTATIC
dma_bessel_averaging T
dma_scale_charge F

! --- Polarisable embedding, needed for QM/MM. See further text. ---
pol_emb_dma_min_l 0
pol_emb_dma_max_l 1
pol_emb_mpole_exclusion_radius 1.00 bohr
pol_emb_repulsive_mm_pot_cutoff 10.0 bohr

%block mm_rep_params
H   35 2.400 ! follows TINKTEP-2 paper
O  550 1.580 ! follows TINKTEP-2 paper
%endblock mm_rep_params
```

--------------------------------

### ONETEP Induced Dipoles Examples (TINKTEP Setups)

Source: https://docs.onetep.org/tinktep

Illustrates various TINKTEP setups for ONETEP, demonstrating different configurations for permanent and induced multipoles, potential interactions, and energy calculations. Includes standard and non-polarisable force-field scenarios.

```text
# Usual TINKTEP2 set-up: Permanent multipoles interact Coulombically with full QM density,
#                        induced dipoles interact with QM* via Thole damping,
#                        repulsive MM potential in effect (attached to perm. multipoles)

```

```text
onetep_perm_mpoles      perm_fix_rep  potential_coulombic_smeared  energy_from_potential

```

```text
onetep_induced_dipoles  ind_qmstar    potential_thole_damped       energy_from_potential

```

```text

# Usual TINKTEP1 set-up: Permanent multipoles interact Coulombically with full QM density,
#                        induced dipoles interact with QM* via Thole damping,
#                        no repulsive MM potential in effect.

```

```text
onetep_perm_mpoles      perm_fix      potential_coulombic_smeared  energy_from_potential

```

```text
onetep_induced_dipoles  ind_qmstar    potential_thole_damped       energy_from_potential

```

```text

# TINKTEP2 set-up for a non-polarisable force-field (eg. GAFF).

```

```text
onetep_perm_mpoles      perm_fix_rep  potential_coulombic_smeared  energy_from_potential

```

```text
onetep_induced_dipoles  ind_qmstar    potential_zero               energy_from_potential

```

```text

# TINKTEP2 set-up, where both permanent and induced interactions use QM* and Thole damping

```

```text
onetep_perm_mpoles      perm_fix_rep_qmstar  potential_thole_damped  energy_from_potential

```

```text
onetep_induced_dipoles  ind_qmstar           potential_thole_damped  energy_from_potential

```

--------------------------------

### ONETEP PDOS Configuration Examples

Source: https://docs.onetep.org/_sources/ldos_calculations.rst

Examples of ONETEP input file parameters for configuring PDOS calculations. These settings control basis sets, projection quality, and summation over magnetic quantum numbers.

```text
pdos_pseudoatomic : F
pdos_reduce_sws F
pdos_max_l 3
pdos_construct_basis : F
pdos_sum_mag : F
```

--------------------------------

### Install Docker on Ubuntu

Source: https://docs.onetep.org/_sources/developer_area.rst

Provides the command to install Docker on an Ubuntu system. This is a prerequisite for using Docker containers as GitHub Actions runners on self-hosted environments.

```shell
# On Ubuntu
# ... installation commands would go here
```

--------------------------------

### Install Docker on Ubuntu/Debian

Source: https://docs.onetep.org/_sources/developer_area.rst

Installs the Docker engine and build tools on Ubuntu-based systems using apt package manager. This is the primary command for setting up Docker on these distributions.

```shell
sudo apt install docker.io docker-buildx
```

--------------------------------

### Example ONETEP Input File for Embedding Calculation

Source: https://docs.onetep.org/_sources/EMFT_in_ONETEP.rst

An example input file demonstrating the configuration for an ONETEP calculation utilizing embedding features. This includes setting up species, regions, and enabling EMFT-related options.

```fortran
!====================================================!
! Input for calculation with the ONETEP program      !
!                                                    !
! O2 and H2 form the embedded system to be treated   !
! at the higher level of theory, O1 and H1 are the   !
! environment treated at the low-level.              !
!====================================================!

%block species_ngwf_regions
O2 H2
O1 H1
%endblock species_ngwf_regions

task: SINGLEPOINT
cutoff_energy 1000 eV
write_forces: T
xc_functional: LDA
active_xc_functional: PBE

use_emft: T
use_emft_follow: T
use_emft_lnv_only: T
block_orthogonalise : T
parallel_scheme: HOUSE

%block species_atomic_set
H1 "SOLVE"
O1 "SOLVE"
H2 "SOLVE"
O2 "SOLVE"
%endblock species_atomic_set

%block species
H1 H 1 1 7.0
O1 O 8 4 7.0
H2 H 1 1 7.0
O2 O 8 4 7.0
%endblock species

%block species_pot
H1 "pseudo/hydrogen.recpot"
O1 "pseudo/oxygen.recpot"
H2 "pseudo/hydrogen.recpot"
O2 "pseudo/oxygen.recpot"
%endblock species_pot

%block lattice_cart
     30.000000000       0.000000000       0.000000000
      0.000000000      30.000000000       0.000000000
      0.000000000       0.000000000      30.000000000
%endblock lattice_cart

%block positions_abs
O1       16.203224001     15.100000000     11.536063353
H1       15.100000000     15.100000000     10.100000000
H1       15.100000000     15.100000000     12.991451046
O2       12.600158789     15.100000000     17.306583960
H2       13.051873252     13.656398529     18.308114239
H2       13.051873252     16.543601471     18.308114239
%endblock positions_abs
```

--------------------------------

### Install Rootless Podman Prerequisites on Red Hat

Source: https://docs.onetep.org/developer_area

Installs necessary packages (slirp4netns) and configures subuid/subgid for rootless Podman operation, which is an alternative to Docker. This setup is more complex than standard Docker configuration.

```bash
sudo yum install slirp4netns
usermod --add-subuids 100000-165535 --add-subgids 100000-165535 $USER

```

--------------------------------

### Start and List VirtualBox VMs

Source: https://docs.onetep.org/_sources/developer_area.rst

Shell commands to manage VirtualBox Virtual Machines (VMs). Includes listing all VMs, starting a VM in headless mode, and listing only running VMs. Ensures background execution and proper detachment from the controlling shell.

```bash
VBoxManage list vms
VBoxManage startvm "self-hosted-runner-ubuntu" --type headless
disown -ah
VBoxManage list runningvms
```

--------------------------------

### Build and Deploy Tutorials with Sphinx (YAML)

Source: https://docs.onetep.org/_sources/developer_area.rst

This workflow builds the tutorials using Sphinx and deploys them to GitHub Pages. It is defined in the 'tutorials' repository and runs on every push and pull request, as well as daily at 1 AM.

```yaml
name: tutorials

# This workflow is set up by Alin, which builds the tutorials with sphinx
# and deploys them, via GitHub pages, to tutorials.onetep.org.

on:
  push:
    branches: [ main ]
  pull_request:
    branches: [ main ]
  schedule:
    - cron: '0 1 * * *'

jobs:
  build:
    runs-on: ubuntu-latest

    steps:
    - uses: actions/checkout@v3
    - name: Set up Python
      uses: actions/setup-python@v3
      with:
        python-version: 3.9
    - name: Install dependencies
      run: |
        python -m pip install --upgrade pip
        pip install sphinx
    - name: Build documentation
      run: |
        cd tutorials
        make html
    - name: Deploy to GitHub Pages
      uses: peaceiris/actions-gh-pages@v3
      with:
        github_token: ${{ secrets.GITHUB_TOKEN }}
        publish_dir: ./tutorials/_build/html

```

--------------------------------

### Test Docker Installation

Source: https://docs.onetep.org/_sources/developer_area.rst

Executes basic Docker commands to verify the installation. 'docker images' lists available images, and 'docker pull hello-world' tests the ability to download images from a registry and run a simple container.

```shell
docker images
docker pull hello-world
```

--------------------------------

### HFx Calculation Configuration Example

Source: https://docs.onetep.org/_sources/hfx.rst

A configuration block demonstrating the setup for a High-Frequency Exchange (HFx) calculation in ONETEP. It specifies the exchange-correlation functional, cutoff energy, SWRI block for HFx, species information, lattice, and atomic positions. This example is designed for a water molecule calculation.

```text
xc_functional B3LYP
cutoff_energy 800 eV

%block swri
  for_hfx 3 10 V 10 10 WE
%endblock swri

%block species_swri-for_hfx
O
H
%endblock species_swri-for_hfx

hfx_use_ri for_hfx
hfx_max_l 3
hfx_max_q 10

%block lattice_cart
  25.00     0.00     0.00
   0.00    25.00     0.00
   0.00     0.00    25.00
%endblock lattice_cart

%block positions_abs
ang
O 5.79564200 7.40742600 6.63194300
H 5.19938100 8.05407400 6.24141400
H 5.16429100 6.74016800 6.88482600
%endblock positions_abs

%block species
O O 8 4 8.0
H H 1 1 8.0
%endblock species

%block species_pot
O "oxygen.recpot"
H "hydrogen.recpot"
%endblock species_pot

DMA
```

--------------------------------

### Enabling File Writing for Restarting

Source: https://docs.onetep.org/_sources/starting_with_onetep.rst

Demonstrates how to instruct ONETEP to write auxiliary files that can be used for restarting or continuing calculations by using 'write_[...]' keywords.

```input
write_wavefunc T
write_forces T
```

--------------------------------

### ONETEP Input File Example

Source: https://docs.onetep.org/EMFT_in_ONETEP

Example input file for the ONETEP program, demonstrating the configuration for an embedded system calculation. It includes definitions for species, pseudopotentials, lattice structure, and atomic positions. This file serves as a template for setting up complex calculations involving embedded and environment systems.

```text
!====================================================!
! Input for calculation with the ONETEP program      !
!                                                    !
! O2 and H2 form the embedded system to be treated   !
! at the higher level of theory, O1 and H1 are the   !
! environment treated at the low-level.              !
!====================================================!

%block species_ngwf_regions
O2 H2
O1 H1
%endblock species_ngwf_regions

task: SINGLEPOINT
cutoff_energy 1000 eV
write_forces: T
xc_functional: LDA
active_xc_functional: PBE

use_emft: T
use_emft_follow: T
use_emft_lnv_only: T
block_orthogonalise : T
parallel_scheme: HOUSE

%block species_atomic_set
H1 "SOLVE"
O1 "SOLVE"
H2 "SOLVE"
O2 "SOLVE"
%endblock species_atomic_set

%block species
H1 H 1 1 7.0
O1 O 8 4 7.0
H2 H 1 1 7.0
O2 O 8 4 7.0
%endblock species

%block species_pot
H1 "pseudo/hydrogen.recpot"
O1 "pseudo/oxygen.recpot"
H2 "pseudo/hydrogen.recpot"
O2 "pseudo/oxygen.recpot"
%endblock species_pot

%block lattice_cart
     30.000000000       0.000000000       0.000000000
      0.000000000      30.000000000       0.000000000
      0.000000000       0.000000000      30.000000000
%endblock lattice_cart

%block positions_abs
O1       16.203224001     15.100000000     11.536063353
H1       15.100000000     15.100000000     10.100000000
H1       15.100000000     15.100000000     12.991451046
O2       12.600158789     15.100000000     17.306583960
H2       13.051873252     13.656398529     18.308114239
H2       13.051873252     16.543601471     18.308114239
%endblock positions_abs

```

--------------------------------

### ONETEP HPC Submission Script Example

Source: https://docs.onetep.org/Geometry_Relaxation

An example SLURM submission script for running ONETEP on a high-performance computing cluster. Key parameters to modify include job name, number of nodes and tasks, memory, time limits, loaded modules, simulation root name, threads per rank, and crucially, the full path to the ONETEP installation and executable.

```bash
#!/bin/bash -l
#SBATCH  -J ethanol   # Job name on the scheduler.
#SBATCH  -p batch     # Queue (partition) type.
#SBATCH  -N 1         # Number of nodes.
#SBATCH  -n 4         # Total number of MPI ranks.
#SBATCH --mem=16G     # Max memory per node.
#SBATCH  -t 01:10:00  # Wallclock time in [hh:mm:ss].

# load modules
# Change the line below the comments to match your
# preferred compiler, mpi, mkl versions.
module load intel-compilers intel-mpi intel-mkl

# on Iridis5 you can use the following modules,
# module load intel-compilers/2021.2.0 intel-mkl/2021.2.0 \
#             intel-mpi/2021.2.0 python/3.9.7

# on ARCHER2 you can use the following modules,
# module load PrgEnv-cray/8.1.0 cce/12.0.3 cray-fftw/3.3.8.11 \
#               cray-mpich/8.1.4 cray-python/3.9.7.1

# sim ID.
# Please put a name of your preference to distinguish
# this simulation. This should be the same as the
# ONETEP input file without the .dat extension.
rootname='ethanol_geo_opt'

# Number of threads per MPI rank.
# This value can be modified, even though ONETEP
# works well with 4 threads per rank for most systems.
export OMP_NUM_THREADS=4

# ONETEP top directory full path,
# e.g., "/home/user/software/onetep".
# Need to modify this.
onetep_top="/full/path/to/onetep/"

# Relative location of the ONETEP executable file.
# e.g., ${onetep_top}/bin/onetep.x86_64_gfortran
# Need to modify the name of the executable.
onetep_exe="${onetep_top}/bin/onetep.executable"

# ONETEP launcher. No need to change this.
onetep_launcher="${onetep_top}/utils/onetep_launcher"

# Show shared libraries. No need to change this.
ldd $onetep_exe >$ldd

# If running on Iridis5, set I_MPI_PMI_LIBRARY
# environmental variable by removing the comment
# sign '#' at the start of the next couple of lines.
#export I_MPI_PMI_LIBRARY\
#/local/software/slurm/default/lib/libpmi.so

# If running on ARCHER2, export the python-related
# paths. The PYTHONUSERBASE path is an example, hence
# it should be modified to your needs as explained in
# the python section of the ARCHER2 documentation.
# You should copy the correct project code, e.g., t01,
# your username on ARCHER2, and change python3.9 to
# your version of python. You can export these paths
# by removing the comment sign '#' at the start of
# the next four lines.
#export PYTHONUSERBASE=/work/project_code/project_code/username/.local
#export PATH=$PYTHONUSERBASE/bin:$PATH
#export PYTHONPATH\
#=$PYTHONUSERBASE/lib/python3.9/site-packages:$PYTHONPATH

# Command to run ONETEP. No need to change this.
srun \
     -N $SLURM_JOB_NUM_NODES \
     -n $SLURM_NPROCS \
     -e $onetep_exe \
     -t $OMP_NUM_THREADS \
     $onetep_launcher \
     ${rootname}.dat \
     >${rootname}.out \
     2>${rootname}.err

```

--------------------------------

### Example ONETEP .dat.template File

Source: https://docs.onetep.org/_sources/tinktep.rst

This .dat.template file serves as a base for ONETEP's input .dat file. It contains keywords that will be passed to ONETEP, with TINKTEP potentially adding parameters like 'pol_emb_pot_filename' for QM/MM interactions.

```text
pol_emb_pot_filename
```

--------------------------------

### Fix CA Certificates in Dockerfile

Source: https://docs.onetep.org/_sources/developer_area.rst

Installs necessary packages within a Dockerfile to ensure proper CA certificate setup. This prevents TLS/SSL connection errors, particularly when 'git pull'ing from HTTPS sources like GitHub.

```dockerfile
apt-get install apt-transport-https ca-certificates -y
update-ca-certificates
```

--------------------------------

### ONETEP Local Execution Script Example

Source: https://docs.onetep.org/Geometry_Relaxation

A simplified bash script for running ONETEP on a local machine, instead of an HPC cluster. This script removes SLURM directives and replaces `srun` with `mpirun`. Users must ensure Intel(R) MPI Library is installed and adjust the `onetep_top` path.

```bash
#!/bin/bash -l

# sim ID.
# Please put a name of your preference to distinguish
# this simulation. This should be the same as the
# ONETEP input file without the .dat extension.
rootname='ethanol_geo_opt'

# Number of threads per MPI rank.
# This value can be modified, even though ONETEP
# works well with 4 threads per rank for most systems.
export OMP_NUM_THREADS=4

# ONETEP top directory full path.
# e.g., /home/user/software/onetep
# Need to modify this.
onetep_top="/full/path/to/onetep/top/directory"

# Relative location of the ONETEP executable file.
# e.g., ${onetep_top}/bin/onetep.x86_64_gfortran
# Need to modify the name of the executable.
onetep_exe="${onetep_top}/bin/onetep.executable"

# ONETEP launcher. No need to change this.
onetep_launcher="${onetep_top}/utils/onetep_launcher"

# Command to run ONETEP using mpirun for local execution.
mpirun \
     -n 4 \
     -e $onetep_exe \
     -t $OMP_NUM_THREADS \
     $onetep_launcher \
     ${rootname}.dat \
     >${rootname}.out \
     2>${rootname}.err

```

--------------------------------

### ONETEP SLURM Submission Script Example

Source: https://docs.onetep.org/_sources/Geometry_Relaxation.rst

A SLURM submission script for running ONETEP on an HPC cluster. It configures job parameters, loads necessary modules, sets environment variables like OMP_NUM_THREADS and the ONETEP installation path, and defines the executable and launcher paths. The script then uses 'srun' to launch the ONETEP calculation.

```bash
#!/bin/bash -l
#SBATCH  -J ethanol   # Job name on the scheduler.
#SBATCH  -p batch     # Queue (partition) type.
#SBATCH  -N 1         # Number of nodes.
#SBATCH  -n 4         # Total number of MPI ranks.
#SBATCH --mem=16G     # Max memory per node.
#SBATCH  -t 01:10:00  # Wallclock time in [hh:mm:ss]. 

# load modules
# Change the line below the comments to match your
# preferred compiler, mpi, mkl versions.
module load intel-compilers intel-mpi intel-mkl

# on Iridis5 you can use the following modules,
# module load intel-compilers/2021.2.0 intel-mkl/2021.2.0 \
#             intel-mpi/2021.2.0 python/3.9.7

# on ARCHER2 you can use the following modules,
# module load PrgEnv-cray/8.1.0 cce/12.0.3 cray-fftw/3.3.8.11 \
#                   cray-mpich/8.1.4 cray-python/3.9.7.1

# sim ID.
# Please put a name of your preference to distinguish
# this simulation. This should be the same as the
# ONETEP input file without the .dat extension.
rootname='ethanol_geo_opt'

# Number of threads per MPI rank.
# This value can be modified, even though ONETEP
# works well with 4 threads per rank for most systems.
export OMP_NUM_THREADS=4

# ONETEP top directory full path,
# e.g., "/home/user/software/onetep". 
# Need to modify this.
onetep_top="/full/path/to/onetep/"

# Relative location of the ONETEP executable file.
# e.g., ${onetep_top}/bin/onetep.x86_64_gfortran
# Need to modify the name of the executable.

# NOTE: The actual executable name might vary based on your ONETEP build.
# Common examples include: onetep.x86_64_gfortran, onetep.serial, etc.
# Please check your ONETEP installation directory for the correct name.
# For this example, we'll use a placeholder.
onetep_exe="${onetep_top}/bin/onetep.executable"

# ONETEP launcher. No need to change this.
onetep_launcher="${onetep_top}/utils/onetep_launcher"

# Show shared libraries. No need to change this.
ldd $onetep_exe >$ldd

# If running on Iridis5, set I_MPI_PMI_LIBRARY
# environmental variable by removing the comment
# sign '#' at the start of the next couple of lines.
#export I_MPI_PMI_LIBRARY\
#=/local/software/slurm/default/lib/libpmi.so

# If running on ARCHER2, export the python-related
# paths. The PYTHONUSERBASE path is an example, hence
# it should be modified to your needs as explained in
# the python section of the ARCHER2 documentation.
# You should copy the correct project code, e.g., t01, 
# your username on ARCHER2, and change python3.9 to
# your version of python. You can export these paths
# by removing the comment sign '#' at the start of
# the next four lines.
#export PYTHONUSERBASE=/work/project_code/project_code/username/.local
#export PATH=$PYTHONUSERBASE/bin:$PATH 
#export PYTHONPATH\
#=$PYTHONUSERBASE/lib/python3.9/site-packages:$PYTHONPATH

# Command to run ONETEP. No need to change this.
srun \
         -N $SLURM_JOB_NUM_NODES \
         -n $SLURM_NPROCS \
         -e $onetep_exe \
         -t $OMP_NUM_THREADS \
         $onetep_launcher \
         ${rootname}.dat \
         >${rootname}.out \
         2>${rootname}.err

```

--------------------------------

### BSUNFLD_TRANSFORMATION Example

Source: https://docs.onetep.org/_sources/spectral_function_unfolding.rst

Example of the BSUNFLD_TRANSFORMATION keyword, defining the transformation matrix from primitive to supercell. This example corresponds to a 4x4x1 supercell.

```fortran
BSUNFLD_TRANSFORMATION : 4 0 0 0 4 0 0 0 1
```

--------------------------------

### Install Docker on Red Hat

Source: https://docs.onetep.org/developer_area

Installs Docker on Red Hat-based systems. Note that this command may install Podman with Docker emulation.

```bash
sudo yum install docker

```

--------------------------------

### Launching ONETEP Processes with MPI (Bash)

Source: https://docs.onetep.org/_sources/starting_with_onetep.rst

This command demonstrates how to launch multiple ONETEP processes on a single machine using MPI. It specifies the number of processes, the ONETEP launcher script, and redirects standard output and error streams.

```bash
mpirun -np 4 ./onetep_launcher input.dat >input.out 2>input.err
```

--------------------------------

### PBS Script for Hybrid Parallelization in ONETEP

Source: https://docs.onetep.org/_sources/kpoints_and_spin.rst

An example PBS (Portable Batch System) script demonstrating a hybrid parallelization setup for ONETEP. It specifies resources for a single node, including 64 CPU cores, 16 MPI processes, and 4 OpenMP threads per MPI process, suitable for a calculation with 4 kpars, 4 MPI processes per kpar, and 4 OpenMP threads per MPI process.

```bash
#PBS -l select=1:ncpus=64:mpiprocs=16:ompthreads=4:mem=200gb
```
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