From 1bfb8d7ad589cb2bcfe59dda48bc28d19602a14e Mon Sep 17 00:00:00 2001 From: Tuguldur T Odbadrakh Date: Tue, 14 Apr 2026 08:45:09 -0400 Subject: [PATCH 1/5] Starting the software/q-e-sirius docs --- software/index.rst | 1 + software/quantum_espresso/index.rst | 29 +++++++++++++++++++++++++++++ 2 files changed, 30 insertions(+) create mode 100644 software/quantum_espresso/index.rst diff --git a/software/index.rst b/software/index.rst index 7042f90b..94f97114 100644 --- a/software/index.rst +++ b/software/index.rst @@ -21,3 +21,4 @@ Software jupyter_on_frontier containers_on_frontier debugging/index + quantum_espresso/index \ No newline at end of file diff --git a/software/quantum_espresso/index.rst b/software/quantum_espresso/index.rst new file mode 100644 index 00000000..1800fde5 --- /dev/null +++ b/software/quantum_espresso/index.rst @@ -0,0 +1,29 @@ +.. _quantum_espresso: + +***************************** +Quantum ESPRESSO Introduction +***************************** + +Overview +======== + +This document provides an introduction to the Quantum ESPRESSO software package installed on Frontier. +Quantum ESPRESSO is a plane-wave DFT code plus various utilities for electronic structure calculations +and materials modeling, and post-processing tools. + +.. note:: + + The current implementation of Quantum ESPRESSO is the + `GPU-enabled version `_ which utilizes the + `SIRIUS library `_ for efficient GPU computations. + This version is not the same as the standard CPU-only version of Quantum ESPRESSO, and is missing + some functionality, but has much better performance characteristics. + +**Currently installed version of Quantum ESPRESSO and its dependencies:** + ++-----------------------------+--------+ +| ``Quantum ESPRESSO-SIRIUS`` | 1.0.2 | ++=============================+========+ +| SIRIUS Library | 7.10.0 | ++-----------------------------+--------+ + From 26f63b13ac6a67a794ae36996cb868ce61592e76 Mon Sep 17 00:00:00 2001 From: Tuguldur T Odbadrakh Date: Thu, 28 May 2026 09:45:15 -0400 Subject: [PATCH 2/5] sample commit --- software/chem/cp2k/index.rst | 80 ++++++++++++++++++ software/chem/index.rst | 20 +++++ software/chem/quantum_espresso/index.rst | 102 +++++++++++++++++++++++ software/chem/vasp/index.rst | 35 ++++++++ software/index.rst | 2 +- 5 files changed, 238 insertions(+), 1 deletion(-) create mode 100644 software/chem/cp2k/index.rst create mode 100644 software/chem/index.rst create mode 100644 software/chem/quantum_espresso/index.rst create mode 100644 software/chem/vasp/index.rst diff --git a/software/chem/cp2k/index.rst b/software/chem/cp2k/index.rst new file mode 100644 index 00000000..857c435a --- /dev/null +++ b/software/chem/cp2k/index.rst @@ -0,0 +1,80 @@ +.. _cp2k: + +**** +CP2K +**** + +.. contents:: On this page + :local: + :depth: 2 + +Overview +======== + +CP2K is a quantum chemistry and solid state physics software package that performs atomistic simulations of +solid state, liquid, molecular, and biological systems. It provides two main methods for electronic structure +calculations: the Quickstep method for Gaussian and plane-wave (GPW) and Gaussian and augmented plane-wave +(GAPW) calculations, and SIRIUS for plane-wave DFT calculations. Both methods are GPU-accelerated and can +be used as the basis for ab-initio molecular dynamics simulations. + +Package Details +=============== + ++-----------------------------+---------+--------------------------------------------------------------+ +| Application or Library | Version | Short Description | ++=============================+=========+==============================================================+ +| CP2K | 2026.1 | Quantum chemistry and molecular simulations | ++-----------------------------+---------+--------------------------------------------------------------+ +| DBCSR | 2.9.1 | Sparse matrix operations library | ++-----------------------------+---------+--------------------------------------------------------------+ +| SIRIUS | 7.10.0 | Plane-wave DFT library | ++-----------------------------+---------+--------------------------------------------------------------+ +| ROCm | 7.0.2 | AMD GPU runtime | ++-----------------------------+---------+--------------------------------------------------------------+ +| Cray MPICH | 9.1.0 | MPI implementation for parallel execution | ++-----------------------------+---------+--------------------------------------------------------------+ + +Using CP2K +========== + +To use CP2K, load the required modules first: + +.. code-block:: bash + + module load gcc-native/14.2 + module load cray-mpich/9.1.0 + module load rocm/7.0.2 + module load cp2k/2026.1-gpu-mpi-omp + +then invoke the executable with ``srun``: + +.. code-block:: bash + + srun cp2k.psmp -i input.in > output.out + +A typical submit script for a calculation utilizing one node with 8 MPI ranks, +each bound to one GPU and 7 OpenMP threads, would look like this: + +.. code-block:: bash + + #!/bin/bash + #SBATCH -A + #SBATCH -J + #SBATCH -N 1 + #SBATCH -p batch + #SBATCH -o %x-%j.out + #SBATCH -t + + module load gcc-native/14.2 + module load cray-mpich/9.1.0 + module load rocm/7.0.2 + module load cp2k/2026.1-gpu-mpi-omp + + srun -N 1 -n 8 -c 7 --gpus-per-task=1 --gpu-bind=closest cp2k.psmp -i .in > .out + +Links +===== + +- CP2K home: https://www.cp2k.org +- User manual: https://manual.cp2k.org/trunk/ +- In-depth review of CP2K features: https://pubs.acs.org/doi/10.1021/acs.jpcb.5c05851 diff --git a/software/chem/index.rst b/software/chem/index.rst new file mode 100644 index 00000000..0ea54a5f --- /dev/null +++ b/software/chem/index.rst @@ -0,0 +1,20 @@ +.. _computational_chemistry: + +################################################ +Quantum Chemistry and Materials Science Software +################################################ + +The Oak Ridge Leadership Computing Facility (OLCF) provides access to +production-quality software for quantum chemistry and materials science. +These packages are tuned for Frontier's AMD GPU architecture and supported +for large-scale, capability-class workloads. + +For questions about access, licensing, or performance guidance, contact +User Assistance through the support portal. + +.. toctree:: + :maxdepth: 2 + + cp2k/index + quantum_espresso/index + vasp/index \ No newline at end of file diff --git a/software/chem/quantum_espresso/index.rst b/software/chem/quantum_espresso/index.rst new file mode 100644 index 00000000..ab9f02c1 --- /dev/null +++ b/software/chem/quantum_espresso/index.rst @@ -0,0 +1,102 @@ +.. _quantum_espresso: + +**************** +Quantum ESPRESSO +**************** + +.. contents:: On this page + :local: + :depth: 2 + +Overview +======== + +Quantum ESPRESSO is a plane-wave electronic structure code and associated post-processing tools. Among +its capabilities are density functional theory (DFT) calculations and molecular dynamics simulations. + +.. note:: + + The current implementation of Quantum ESPRESSO is the + `GPU-enabled version `_ which utilizes the + `SIRIUS library `_ for efficient GPU computations. + This version is not the same as the standard CPU-only version of Quantum ESPRESSO, and is missing + some functionality, but has much better plane-wave DFT performance. + +---- + +Package Details +=============== + ++-----------------------------+---------+--------------------------------------------------------------+ +| Application or Library | Version | Short Description | ++=============================+=========+==============================================================+ +| Quantum ESPRESSO-SIRIUS | 1.0.2 | Electronic structure calculations and utilities | ++-----------------------------+---------+--------------------------------------------------------------+ +| SIRIUS | 7.10.0 | Plane-wave DFT library | ++-----------------------------+---------+--------------------------------------------------------------+ +| ROCm | 7.0.2 | AMD GPU runtime | ++-----------------------------+---------+--------------------------------------------------------------+ +| Cray MPICH | 9.1.0 | MPI implementation for parallel execution | ++-----------------------------+---------+--------------------------------------------------------------+ + +---- + +Using Quantum ESPRESSO +====================== + +To use Quantum ESPRESSO, load the required modules first: + +.. code-block:: bash + + module load gcc-native/14.2 + module load cray-mpich/9.1.0 + module load rocm/7.0.2 + module load q-e-sirius/1.0.2 + +then invoke the executable with ``srun``: + +.. code-block:: bash + + srun pw.x -in input.in > output.out + +A typical submit script for a plane-wave DFT calculation utilizing one node with 8 MPI ranks, +each bound to one GPU and 7 OpenMP threads, would look like this: + +.. code-block:: bash + + #!/bin/bash + #SBATCH -A + #SBATCH -J + #SBATCH -N 1 + #SBATCH -p batch + #SBATCH -o %x-%j.out + #SBATCH -t + + module load gcc-native/14.2 + module load cray-mpich/9.1.0 + module load rocm/7.0.2 + module load q-e-sirius/1.0.2 + + srun -N 1 -n 8 -c 7 --gpus-per-task=1 --gpu-bind=closest pw.x -in .in > .out + +---- + +Beginner's Guide +================ + +For new users of Quantum ESPRESSO, an illustration of the workflow for a plane-wave DFT calculation +is provided below. + +1. Prepare the input file (``input.in``). +2. Prepare the pseudopotentials. +3. Prepare the job submission script. +4. Submit the job to the queue with ``sbatch``. + +---- + +Helpful Links +============= + +- Documentation: https://www.quantum-espresso.org/documentation/package-specific-documentation +- Quantum ESPRESSO input generator: https://qeinputgenerator.materialscloud.io +- Standard solid-state pseudopotentials: https://legacy.materialscloud.org/discover/sssp/table/efficiency diff --git a/software/chem/vasp/index.rst b/software/chem/vasp/index.rst new file mode 100644 index 00000000..837e6c9b --- /dev/null +++ b/software/chem/vasp/index.rst @@ -0,0 +1,35 @@ +.. _vasp: + +**** +VASP +**** + +Overview +======== + +VASP (Vienna Ab initio Simulation Package) is a plane-wave DFT code for electronic structure calculations +and ab initio molecular dynamics. + +Usage +===== + +.. note:: + + Add site-specific details here (module name, version, license notes, and launch instructions). + +**Currently installed version of VASP and its dependencies:** + ++-----------------------------+---------+--------------------------------------------------------------+ +| Application or Library | Version | Short Description | ++=============================+=========+==============================================================+ +| VASP | TBD | Electronic structure calculations and molecular dynamics | ++-----------------------------+---------+--------------------------------------------------------------+ +| ROCm | TBD | GPU drivers and runtime for AMD GPUs | ++-----------------------------+---------+--------------------------------------------------------------+ +| Cray MPICH | TBD | MPI implementation for parallel execution | ++-----------------------------+---------+--------------------------------------------------------------+ + +Links +===== + +- VASP home: https://www.vasp.at diff --git a/software/index.rst b/software/index.rst index 94f97114..6c3bf2b2 100644 --- a/software/index.rst +++ b/software/index.rst @@ -21,4 +21,4 @@ Software jupyter_on_frontier containers_on_frontier debugging/index - quantum_espresso/index \ No newline at end of file + chem/index \ No newline at end of file From 93ef1a990edacf0f906c675096007d1e6d046184 Mon Sep 17 00:00:00 2001 From: Tuguldur T Odbadrakh Date: Wed, 22 Jul 2026 09:58:24 -0400 Subject: [PATCH 3/5] Added pages for CP2K, Quantum ESPRESSO, and VASP --- software/chem/cp2k/index.rst | 121 ++++++++++++++-- software/chem/quantum_espresso/index.rst | 109 ++++++++++---- software/chem/vasp/index.rst | 176 ++++++++++++++++++++--- software/quantum_espresso/index.rst | 29 ---- 4 files changed, 352 insertions(+), 83 deletions(-) delete mode 100644 software/quantum_espresso/index.rst diff --git a/software/chem/cp2k/index.rst b/software/chem/cp2k/index.rst index 857c435a..c89faf76 100644 --- a/software/chem/cp2k/index.rst +++ b/software/chem/cp2k/index.rst @@ -17,8 +17,10 @@ calculations: the Quickstep method for Gaussian and plane-wave (GPW) and Gaussia (GAPW) calculations, and SIRIUS for plane-wave DFT calculations. Both methods are GPU-accelerated and can be used as the basis for ab-initio molecular dynamics simulations. +---- + Package Details -=============== +================ +-----------------------------+---------+--------------------------------------------------------------+ | Application or Library | Version | Short Description | @@ -29,15 +31,17 @@ Package Details +-----------------------------+---------+--------------------------------------------------------------+ | SIRIUS | 7.10.0 | Plane-wave DFT library | +-----------------------------+---------+--------------------------------------------------------------+ -| ROCm | 7.0.2 | AMD GPU runtime | +| ROCm | 7.0.2 | AMD GPU runtime | +-----------------------------+---------+--------------------------------------------------------------+ | Cray MPICH | 9.1.0 | MPI implementation for parallel execution | +-----------------------------+---------+--------------------------------------------------------------+ -Using CP2K -========== +---- + +Usage +===== -To use CP2K, load the required modules first: +To use CP2K, load the required modules: .. code-block:: bash @@ -46,34 +50,123 @@ To use CP2K, load the required modules first: module load rocm/7.0.2 module load cp2k/2026.1-gpu-mpi-omp -then invoke the executable with ``srun``: +Beginner's Guide +================ + +For new users of CP2K, an illustration of the workflow for a Quickstep DFT energy calculation +is provided below. Let us use a single water molecule as an example. + +0. Prepare a working directory. +******************************** +Before running a calculation, we need a working directory with the necessary input files and +basis sets. Your project directory is a good place to start. For example, if your project +directory is ``/lustre/orion/``, you might create a working directory named +``cp2k-water-example`` in the scratch space like: .. code-block:: bash - srun cp2k.psmp -i input.in > output.out + mkdir -p /lustre/orion//scratch/cp2k-water-example + cd /lustre/orion//scratch/cp2k-water-example -A typical submit script for a calculation utilizing one node with 8 MPI ranks, -each bound to one GPU and 7 OpenMP threads, would look like this: +1. Prepare the input file (``input.in``). +****************************************** +Now, we need an input file which describes the system and the calculation parameters. A simple +input file for a single water molecule might look like this: + +.. code-block:: bash + + &GLOBAL ! calculation-wide settings + PROJECT water ! a name for the calculation, used for output files + RUN_TYPE ENERGY ! request a single-point energy calculation + PRINT_LEVEL LOW + &END GLOBAL + &FORCE_EVAL ! settings for evaluating energy and forces + METHOD Quickstep ! use the Quickstep GPW/GAPW method + &DFT + BASIS_SET_FILE_NAME BASIS_MOLOPT ! basis set file location + POTENTIAL_FILE_NAME GTH_POTENTIALS ! pseudopotential file location + &MGRID + CUTOFF 300 ! plane-wave cutoff energy in Ry + &END MGRID + &XC + &XC_FUNCTIONAL PBE ! exchange-correlation functional + &END XC_FUNCTIONAL + &END XC + &END DFT + &SUBSYS + &CELL + ABC 8.0 8.0 8.0 ! cell dimensions in Angstrom + &END CELL + &COORD ! atomic positions in Angstrom + O 0.000 0.000 0.000 + H 0.757 0.586 0.000 + H -0.757 0.586 0.000 + &END COORD + &KIND O + BASIS_SET DZVP-MOLOPT-GTH ! basis set for oxygen + POTENTIAL GTH-PBE-q6 ! pseudopotential for oxygen + &END KIND + &KIND H + BASIS_SET DZVP-MOLOPT-GTH ! basis set for hydrogen + POTENTIAL GTH-PBE-q1 ! pseudopotential for hydrogen + &END KIND + &END SUBSYS + &END FORCE_EVAL + +Note that the ``!`` symbol followed by text indicates a comment. + +2. Prepare the basis sets and pseudopotentials. +************************************************ + +A Quickstep calculation requires the ``BASIS_MOLOPT`` and ``GTH_POTENTIALS`` data files +referenced by ``BASIS_SET_FILE_NAME`` and ``POTENTIAL_FILE_NAME``. These files are provided +as part of the module and the environment variable ``CP2K_DATA_DIR`` points to their location. + +3. Prepare the job submission script. +************************************** +To submit the calculation to the queue, we need a job submission script, like: .. code-block:: bash #!/bin/bash #SBATCH -A - #SBATCH -J + #SBATCH -J water-scf #SBATCH -N 1 #SBATCH -p batch #SBATCH -o %x-%j.out - #SBATCH -t + #SBATCH -t 10:00 module load gcc-native/14.2 module load cray-mpich/9.1.0 module load rocm/7.0.2 module load cp2k/2026.1-gpu-mpi-omp - srun -N 1 -n 8 -c 7 --gpus-per-task=1 --gpu-bind=closest cp2k.psmp -i .in > .out + srun -N 1 -n 8 -c 7 --gpus-per-task=1 --gpu-bind=closest cp2k.psmp -i input.in > output.log -Links -===== +Here, we request 1 node, with 8 MPI ranks each bound to one GPU and 7 OpenMP threads, for 10 +minutes. This example calculation only takes about one minute, so the requested time is +sufficient. Adjust the resource requests and walltime as needed for larger systems. + +4. Submit the job to the queue with ``sbatch``. +************************************************* +Now we are ready to submit the job. Use the ``sbatch`` command to submit the job script to the +queue: + +.. code-block:: bash + + sbatch + +Once in the queue, you can check the job status with ``squeue -u ``. Once the job +starts running, the output will be written to the file ``output.log`` as specified in the +submit script. + +Congratulations! You have successfully run a Quickstep DFT energy calculation with CP2K on +Frontier. You can now analyze the output file and explore the results. + +---- + +Helpful Links +============= - CP2K home: https://www.cp2k.org - User manual: https://manual.cp2k.org/trunk/ diff --git a/software/chem/quantum_espresso/index.rst b/software/chem/quantum_espresso/index.rst index ab9f02c1..8fcffef3 100644 --- a/software/chem/quantum_espresso/index.rst +++ b/software/chem/quantum_espresso/index.rst @@ -41,10 +41,10 @@ Package Details ---- -Using Quantum ESPRESSO -====================== +Usage +===== -To use Quantum ESPRESSO, load the required modules first: +To use Quantum ESPRESSO, load the required modules: .. code-block:: bash @@ -53,44 +53,105 @@ To use Quantum ESPRESSO, load the required modules first: module load rocm/7.0.2 module load q-e-sirius/1.0.2 -then invoke the executable with ``srun``: +Beginner's Guide +================ + +For new users of Quantum ESPRESSO, an illustration of the workflow for a plane-wave DFT calculation +is provided below. Let us use the silicon crystal primitive cell as an example. + +0. Prepare a working directory. +******************************* +Before running a calculation, we need a working directory with the necessary input files and pseudopotentials. +Your project directory is a good place to start. For example, if your project directory is +``/lustre/orion/``, you might create a working directory named ``qe-silicon-example`` in the scratch +space like: + +.. code-block:: bash + + mkdir -p /lustre/orion//scratch/qe-silicon-example + cd /lustre/orion//scratch/qe-silicon-example + + +1. Prepare the input file (``input.in``). +***************************************** +Now, we need an input file which describes the system and the calculation parameters. A simple input file for a +silicon primitive cell might look like this: .. code-block:: bash - srun pw.x -in input.in > output.out + &control ! calculation parameters and settings + calculation = 'scf' ! request a self-consistent field energy calculation + prefix = 'silicon' ! a name for the calculation, used for output files + outdir = './tmp' ! directory for temporary files + pseudo_dir = '.' ! directory where pseudopotential files are located + / + &system ! chemical system parameters + ibrav = 2 ! Bravais lattice index for face-centered cubic lattice: only one lattice parameter is needed + celldm(1) = 10.26 ! The lattice parameter A in atomic units (1 Bohr = 0.529177 Angstroms) + nat = 2 ! Number of atoms in the unit cell + ntyp = 1 ! Number of types of atoms + ecutwfc = 30.0 ! Plane-wave cutoff energy in Ry + / + &electrons + conv_thr = 1.0d-8 ! Convergence threshold for self-consistency + / + ATOMIC_SPECIES + Si 28.0855 Si.pbe-n-kjpaw_psl.1.0.0.UPF ! Element, atomic mass, and pseudopotential file + ATOMIC_POSITIONS crystal ! Defining positions in crystal coordinates + Si 0.00 0.00 0.00 + Si 0.25 0.25 0.25 + K_POINTS automatic ! k-point grid for Brillouin zone sampling + 4 4 4 1 1 1 ! 4x4x4 grid with no shift + +Note that the ``!`` symbol followed by text indicates a comment. + +2. Prepare the pseudopotentials. +******************************** + +A plane-wave DFT calculation requires pseudopotential (PP) files for each type of atom in the system. +Download the PP file and place it in the working directory (as specified by ``pseudo_dir '.'`` in the input file). Alternatively, you can +collect your PP files in a central directory and point to it with the ``pseudo_dir`` variable. -A typical submit script for a plane-wave DFT calculation utilizing one node with 8 MPI ranks, -each bound to one GPU and 7 OpenMP threads, would look like this: +3. Prepare the job submission script. +************************************* +To submit the calculation to the queue, we need a job submission script, like: .. code-block:: bash - #!/bin/bash - #SBATCH -A - #SBATCH -J - #SBATCH -N 1 - #SBATCH -p batch - #SBATCH -o %x-%j.out - #SBATCH -t + !!/bin/bash + !SBATCH -A + !SBATCH -J Si2-scf + !SBATCH -N 1 + !SBATCH -p batch + !SBATCH -o %x-%j.out + !SBATCH -t 10:00 module load gcc-native/14.2 module load cray-mpich/9.1.0 module load rocm/7.0.2 + module load cray-hdf5-parallel/1.14.3.9 module load q-e-sirius/1.0.2 - srun -N 1 -n 8 -c 7 --gpus-per-task=1 --gpu-bind=closest pw.x -in .in > .out + srun -N 1 -n 1 -c 1 --gpus-per-task=1 --gpu-bind=closest pw.x -in input.in > output.log ----- +Here, we request 1 node, with 1 MPI rank, 1 CPU core, and 1 GPU for 10 minutes. This example calculation +only takes about one minute, so the requested time is sufficient. Adjust the resource requests and walltime +as needed for larger systems. -Beginner's Guide -================ -For new users of Quantum ESPRESSO, an illustration of the workflow for a plane-wave DFT calculation -is provided below. - -1. Prepare the input file (``input.in``). -2. Prepare the pseudopotentials. -3. Prepare the job submission script. 4. Submit the job to the queue with ``sbatch``. +*********************************************** +Now we are ready to submit the job. Use the ``sbatch`` command to submit the job script to the queue: + +.. code-block:: bash + + sbatch + +Once in the queue, you can check the job status with ``squeue -u ``. Once the job starts running, +the output will be written to the file ``output.log`` as specified in the submit script. + +Congratulations! You have successfully run a plane-wave DFT calculation with Quantum ESPRESSO on Frontier. +You can now analyze the output file and explore the results. ---- diff --git a/software/chem/vasp/index.rst b/software/chem/vasp/index.rst index 837e6c9b..498c044f 100644 --- a/software/chem/vasp/index.rst +++ b/software/chem/vasp/index.rst @@ -4,32 +4,176 @@ VASP **** +.. contents:: On this page + :local: + :depth: 2 + Overview ======== -VASP (Vienna Ab initio Simulation Package) is a plane-wave DFT code for electronic structure calculations -and ab initio molecular dynamics. +VASP (Vienna Ab initio Simulation Package) is a plane-wave electronic structure code. Among +its capabilities are density functional theory (DFT) calculations and ab initio molecular +dynamics simulations. + +.. note:: + + VASP is licensed software. OLCF cannot provide access to VASP unless you or your + organization hold a valid license. To gain access to the centrally installed module, + contact User Assistance through the support portal with proof of your license (for + example, a copy of your VASP license agreement or confirmation from the VASP team), and + you will be added to the ``vasp`` Unix group that controls access to the software and its + documentation. + +---- + +Package Details +================ + ++-----------------------------+---------+-------------------------------------------------------------------+ +| Application or Library | Version | Short Description | ++=============================+=========+===================================================================+ +| VASP | 6.6.0 | Electronic structure calculations and ab initio molecular dynamics| ++-----------------------------+---------+-------------------------------------------------------------------+ +| ROCm | 6.4.2 | AMD GPU runtime. | ++-----------------------------+---------+-------------------------------------------------------------------+ +| Cray MPICH | 9.0.1 | MPI implementation for parallel execution | ++-----------------------------+---------+-------------------------------------------------------------------+ + +---- Usage ===== -.. note:: +To use VASP, load the required modules: - Add site-specific details here (module name, version, license notes, and launch instructions). +.. code-block:: bash -**Currently installed version of VASP and its dependencies:** + module load vasp/6.6.0-gpu -+-----------------------------+---------+--------------------------------------------------------------+ -| Application or Library | Version | Short Description | -+=============================+=========+==============================================================+ -| VASP | TBD | Electronic structure calculations and molecular dynamics | -+-----------------------------+---------+--------------------------------------------------------------+ -| ROCm | TBD | GPU drivers and runtime for AMD GPUs | -+-----------------------------+---------+--------------------------------------------------------------+ -| Cray MPICH | TBD | MPI implementation for parallel execution | -+-----------------------------+---------+--------------------------------------------------------------+ +If the module is not visible with ``module avail vasp``, you have not yet been added to the +``vasp`` Unix group. See the note above for how to request access. -Links -===== +Beginner's Guide +================ + +For new users of VASP, an illustration of the workflow for a plane-wave DFT calculation is +provided below. Let us use the silicon crystal primitive cell as an example. + +0. Prepare a working directory. +******************************** +Before running a calculation, we need a working directory with the necessary input files and +pseudopotentials. Your project directory is a good place to start. For example, if your +project directory is ``/lustre/orion/``, you might create a working directory +named ``vasp-silicon-example`` in the scratch space like: + +.. code-block:: bash + + mkdir -p /lustre/orion//scratch/vasp-silicon-example + cd /lustre/orion//scratch/vasp-silicon-example + +1. Prepare the input files. +**************************** +A VASP calculation requires four input files: ``INCAR``, ``POSCAR``, ``POTCAR``, and +``KPOINTS``. + +``INCAR`` (calculation parameters and settings): + +.. code-block:: bash + + SYSTEM = Silicon primitive cell ! a name for the calculation + ISTART = 0 ! start from scratch, no previous wavefunction + ICHARG = 2 ! construct initial charge density from atomic charges + ENCUT = 300 ! plane-wave cutoff energy in eV + EDIFF = 1E-6 ! convergence threshold for self-consistency (eV) + ISMEAR = 0 ! Gaussian smearing of partial occupancies + SIGMA = 0.05 ! smearing width in eV + +``POSCAR`` (lattice geometry and atomic positions): + +.. code-block:: bash + + Silicon primitive cell + 5.43 + 0.0 0.5 0.5 + 0.5 0.0 0.5 + 0.5 0.5 0.0 + Si + 2 + Direct + 0.00 0.00 0.00 + 0.25 0.25 0.25 + +``KPOINTS`` (Brillouin zone sampling): + +.. code-block:: bash + + Automatic mesh + 0 + Gamma + 4 4 4 + 0 0 0 + +``POTCAR`` (pseudopotentials): see the next step. + +2. Prepare the pseudopotentials. +********************************* + +A VASP calculation requires a ``POTCAR`` file, which is a concatenation of pseudopotential +files for each atomic species in the order they appear in ``POSCAR``. Pseudopotentials are +distributed with your VASP license and are not provided by OLCF. For the silicon example, +concatenate the silicon pseudopotential into a file named ``POTCAR`` in the working directory: + +.. code-block:: bash + + cat /path/to/potpaw_PBE/Si/POTCAR > POTCAR + +If your system has multiple species, concatenate their ``POTCAR`` files in the same order the +species appear in ``POSCAR``. + +3. Prepare the job submission script. +************************************** +To submit the calculation to the queue, we need a job submission script, like: + +.. code-block:: bash + + #!/bin/bash + #SBATCH -A + #SBATCH -J Si2-scf + #SBATCH -N 1 + #SBATCH -p batch + #SBATCH -o %x-%j.out + #SBATCH -t 10:00 + + module load vasp/6.6.0-gpu + + srun -N 1 -n 1 -c 1 --gpus-per-task=1 --gpu-bind=closest vasp_std > output.log + +Here, we request 1 node, with 1 MPI rank, 1 CPU core, and 1 GPU for 10 minutes. This example +calculation only takes about one minute, so the requested time is sufficient. Adjust the +resource requests and walltime as needed for larger systems. + +4. Submit the job to the queue with ``sbatch``. +************************************************* +Now we are ready to submit the job. Use the ``sbatch`` command to submit the job script to the +queue: + +.. code-block:: bash + + sbatch + +Once in the queue, you can check the job status with ``squeue -u ``. Once the job +starts running, VASP writes its results to several output files, including ``OUTCAR`` (a +detailed log of the calculation) and ``vasprun.xml`` (a structured summary suitable for +post-processing), in addition to the ``output.log`` file specified in the submit script. + +Congratulations! You have successfully run a plane-wave DFT calculation with VASP on Frontier. +You can now analyze the output files and explore the results. + +---- + +Helpful Links +============= - VASP home: https://www.vasp.at +- VASP documentation wiki: https://www.vasp.at/wiki/index.php/The_VASP_Manual +- VASP forum (support and troubleshooting): https://www.vasp.at/forum/ diff --git a/software/quantum_espresso/index.rst b/software/quantum_espresso/index.rst deleted file mode 100644 index 1800fde5..00000000 --- a/software/quantum_espresso/index.rst +++ /dev/null @@ -1,29 +0,0 @@ -.. _quantum_espresso: - -***************************** -Quantum ESPRESSO Introduction -***************************** - -Overview -======== - -This document provides an introduction to the Quantum ESPRESSO software package installed on Frontier. -Quantum ESPRESSO is a plane-wave DFT code plus various utilities for electronic structure calculations -and materials modeling, and post-processing tools. - -.. note:: - - The current implementation of Quantum ESPRESSO is the - `GPU-enabled version `_ which utilizes the - `SIRIUS library `_ for efficient GPU computations. - This version is not the same as the standard CPU-only version of Quantum ESPRESSO, and is missing - some functionality, but has much better performance characteristics. - -**Currently installed version of Quantum ESPRESSO and its dependencies:** - -+-----------------------------+--------+ -| ``Quantum ESPRESSO-SIRIUS`` | 1.0.2 | -+=============================+========+ -| SIRIUS Library | 7.10.0 | -+-----------------------------+--------+ - From 35086fd2f7f1fb30b2da3360b0bbf441a2a51684 Mon Sep 17 00:00:00 2001 From: Tuguldur T Odbadrakh Date: Mon, 3 Aug 2026 14:04:27 -0400 Subject: [PATCH 4/5] finalized QE, CP2K, VASP pages --- software/chem/vasp/index.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/software/chem/vasp/index.rst b/software/chem/vasp/index.rst index 498c044f..3ff25aa1 100644 --- a/software/chem/vasp/index.rst +++ b/software/chem/vasp/index.rst @@ -32,7 +32,7 @@ Package Details +-----------------------------+---------+-------------------------------------------------------------------+ | Application or Library | Version | Short Description | +=============================+=========+===================================================================+ -| VASP | 6.6.0 | Electronic structure calculations and ab initio molecular dynamics| +| VASP | 6.6.1 | Electronic structure calculations and ab initio molecular dynamics| +-----------------------------+---------+-------------------------------------------------------------------+ | ROCm | 6.4.2 | AMD GPU runtime. | +-----------------------------+---------+-------------------------------------------------------------------+ From f71ffe97048b12c6ab837432625a2ee01cb703ce Mon Sep 17 00:00:00 2001 From: Tuguldur T Odbadrakh Date: Mon, 3 Aug 2026 14:04:55 -0400 Subject: [PATCH 5/5] Whoops, didn't add these pages in the last commit --- software/chem/cp2k/index.rst | 154 +++++++++++++++++++++++++++++------ software/chem/vasp/index.rst | 8 +- 2 files changed, 134 insertions(+), 28 deletions(-) diff --git a/software/chem/cp2k/index.rst b/software/chem/cp2k/index.rst index c89faf76..92f90611 100644 --- a/software/chem/cp2k/index.rst +++ b/software/chem/cp2k/index.rst @@ -13,7 +13,7 @@ Overview CP2K is a quantum chemistry and solid state physics software package that performs atomistic simulations of solid state, liquid, molecular, and biological systems. It provides two main methods for electronic structure -calculations: the Quickstep method for Gaussian and plane-wave (GPW) and Gaussian and augmented plane-wave +calculations: the Quickstep method for mixed Gaussian and plane-wave (GPW) and Gaussian and augmented plane-wave (GAPW) calculations, and SIRIUS for plane-wave DFT calculations. Both methods are GPU-accelerated and can be used as the basis for ab-initio molecular dynamics simulations. @@ -31,7 +31,7 @@ Package Details +-----------------------------+---------+--------------------------------------------------------------+ | SIRIUS | 7.10.0 | Plane-wave DFT library | +-----------------------------+---------+--------------------------------------------------------------+ -| ROCm | 7.0.2 | AMD GPU runtime | +| ROCm | 7.0.2 | AMD GPU runtime | +-----------------------------+---------+--------------------------------------------------------------+ | Cray MPICH | 9.1.0 | MPI implementation for parallel execution | +-----------------------------+---------+--------------------------------------------------------------+ @@ -54,7 +54,7 @@ Beginner's Guide ================ For new users of CP2K, an illustration of the workflow for a Quickstep DFT energy calculation -is provided below. Let us use a single water molecule as an example. +is provided below. Let us use a system of 32 water molecules as an example. 0. Prepare a working directory. ******************************** @@ -71,44 +71,141 @@ directory is ``/lustre/orion/``, you might create a working director 1. Prepare the input file (``input.in``). ****************************************** Now, we need an input file which describes the system and the calculation parameters. A simple -input file for a single water molecule might look like this: +input file for 32 water molecules might look like this: .. code-block:: bash - &GLOBAL ! calculation-wide settings - PROJECT water ! a name for the calculation, used for output files - RUN_TYPE ENERGY ! request a single-point energy calculation - PRINT_LEVEL LOW + &GLOBAL + PROJECT H2O-32 + RUN_TYPE ENERGY &END GLOBAL - &FORCE_EVAL ! settings for evaluating energy and forces - METHOD Quickstep ! use the Quickstep GPW/GAPW method + + &FORCE_EVAL + METHOD QS ! Quickstep method for mixed Gaussian and plane-wave calculations &DFT - BASIS_SET_FILE_NAME BASIS_MOLOPT ! basis set file location - POTENTIAL_FILE_NAME GTH_POTENTIALS ! pseudopotential file location + BASIS_SET_FILE_NAME GTH_BASIS_SETS ! The name of the file containing the basis sets + POTENTIAL_FILE_NAME POTENTIAL ! The name of the file containing the pseudopotentials &MGRID - CUTOFF 300 ! plane-wave cutoff energy in Ry + CUTOFF 280 ! Plane-wave cutoff energy in Ry &END MGRID + &SCF + SCF_GUESS ATOMIC ! Initial guess for the SCF procedure + &END SCF &XC - &XC_FUNCTIONAL PBE ! exchange-correlation functional + &XC_FUNCTIONAL PBE ! Exchange-correlation functional &END XC_FUNCTIONAL &END XC &END DFT &SUBSYS &CELL - ABC 8.0 8.0 8.0 ! cell dimensions in Angstrom + ABC 9.8528 9.8528 9.8528 ! Cell dimensions in Angstroms &END CELL - &COORD ! atomic positions in Angstrom - O 0.000 0.000 0.000 - H 0.757 0.586 0.000 - H -0.757 0.586 0.000 + # 32 H2O (TIP5P,1bar,300K) a = 9.8528 + &COORD ! Atomic coordinates + O 2.280398 9.146539 5.088696 + O 1.251703 2.406261 7.769908 + O 1.596302 6.920128 0.656695 + O 2.957518 3.771868 1.877387 + O 0.228972 5.884026 6.532308 + O 9.023431 6.119654 0.092451 + O 7.256289 8.493641 5.772041 + O 5.090422 9.467016 0.743177 + O 6.330888 7.363471 3.747750 + O 7.763819 8.349367 9.279457 + O 8.280798 3.837153 5.799282 + O 8.878250 2.025797 1.664102 + O 9.160372 0.285100 6.871004 + O 4.962043 4.134437 0.173376 + O 2.802896 8.690383 2.435952 + O 9.123223 3.549232 8.876721 + O 1.453702 1.402538 2.358278 + O 6.536550 1.146790 7.609732 + O 2.766709 0.881503 9.544263 + O 0.856426 2.075964 5.010625 + O 6.386036 1.918950 0.242690 + O 2.733023 4.452756 5.850203 + O 4.600039 9.254314 6.575944 + O 3.665373 6.210561 3.158420 + O 3.371648 6.925594 7.476036 + O 5.287920 3.270653 6.155080 + O 5.225237 6.959594 9.582991 + O 0.846293 5.595877 3.820630 + O 9.785620 8.164617 3.657879 + O 8.509982 4.430362 2.679946 + O 1.337625 8.580920 8.272484 + O 8.054437 9.221335 1.991376 + H 1.762019 9.820429 5.528454 + H 3.095987 9.107088 5.588186 + H 0.554129 2.982634 8.082024 + H 1.771257 2.954779 7.182181 + H 2.112148 6.126321 0.798136 + H 1.776389 7.463264 1.424030 + H 3.754249 3.824017 1.349436 + H 3.010580 4.524142 2.466878 + H 0.939475 5.243834 6.571945 + H 0.515723 6.520548 5.877445 + H 9.852960 6.490366 0.393593 + H 8.556008 6.860063 -0.294256 + H 7.886607 7.941321 6.234506 + H 7.793855 9.141028 5.315813 + H 4.467366 9.971162 0.219851 + H 5.758685 10.102795 0.998994 + H 6.652693 7.917443 3.036562 + H 6.711966 7.743594 4.539279 + H 7.751955 8.745180 10.150905 + H 7.829208 9.092212 8.679343 + H 8.312540 3.218330 6.528858 + H 8.508855 4.680699 6.189990 + H 9.742249 1.704975 1.922581 + H 8.799060 2.876412 2.095861 + H 9.505360 1.161677 6.701213 + H 9.920117 -0.219794 7.161006 + H 4.749903 4.186003 -0.758595 + H 5.248010 5.018415 0.403676 + H 3.576065 9.078451 2.026264 + H 2.720238 9.146974 3.273164 + H 9.085561 4.493058 9.031660 + H 9.215391 3.166305 9.749133 + H 1.999705 2.060411 1.927796 + H 1.824184 0.564565 2.081195 + H 7.430334 0.849764 7.438978 + H 6.576029 1.537017 8.482885 + H 2.415851 1.576460 8.987338 + H 2.276957 0.099537 9.289499 + H 1.160987 1.818023 4.140602 + H 0.350256 2.874437 4.860741 + H 5.768804 2.638450 0.375264 + H 7.221823 2.257514 0.563730 + H 3.260797 5.243390 5.962382 + H 3.347848 3.732214 5.988196 + H 5.328688 9.073059 5.982269 + H 5.007063 9.672150 7.334875 + H 4.566850 6.413356 3.408312 + H 3.273115 7.061666 2.963521 + H 3.878372 7.435003 6.843607 + H 3.884673 6.966316 8.283117 + H 5.918240 3.116802 5.451335 + H 5.355924 2.495093 6.711958 + H 5.071858 7.687254 10.185667 + H 6.106394 7.112302 9.241707 + H 1.637363 5.184910 4.169264 + H 0.427645 4.908936 3.301903 + H 9.971698 7.227076 3.709104 + H 10.647901 8.579244 3.629806 + H 8.046808 5.126383 2.213838 + H 7.995317 4.290074 3.474723 + H 1.872601 7.864672 7.930401 + H 0.837635 8.186808 8.987268 + H 8.314696 10.115534 2.212519 + H 8.687134 8.667252 2.448452 &END COORD - &KIND O - BASIS_SET DZVP-MOLOPT-GTH ! basis set for oxygen - POTENTIAL GTH-PBE-q6 ! pseudopotential for oxygen - &END KIND &KIND H - BASIS_SET DZVP-MOLOPT-GTH ! basis set for hydrogen - POTENTIAL GTH-PBE-q1 ! pseudopotential for hydrogen + BASIS_SET TZV2P-GTH ! Basis set for hydrogen + POTENTIAL GTH-PBE-q1 ! Pseudopotential for hydrogen + &END KIND + &KIND O + BASIS_SET TZV2P-GTH ! Basis set for oxygen + POTENTIAL GTH-PBE-q6 ! Pseudopotential for oxygen &END KIND &END SUBSYS &END FORCE_EVAL @@ -121,6 +218,13 @@ Note that the ``!`` symbol followed by text indicates a comment. A Quickstep calculation requires the ``BASIS_MOLOPT`` and ``GTH_POTENTIALS`` data files referenced by ``BASIS_SET_FILE_NAME`` and ``POTENTIAL_FILE_NAME``. These files are provided as part of the module and the environment variable ``CP2K_DATA_DIR`` points to their location. +So, the user does not need to download the standard basis sets or pseudopotentials. The user +can simply use the available ones by specifying in the input file: + +.. code-block:: bash + + BASIS_SET_FILE_NAME GTH_BASIS_SETS + POTENTIAL_FILE_NAME POTENTIAL 3. Prepare the job submission script. ************************************** diff --git a/software/chem/vasp/index.rst b/software/chem/vasp/index.rst index 3ff25aa1..ff300af4 100644 --- a/software/chem/vasp/index.rst +++ b/software/chem/vasp/index.rst @@ -119,13 +119,15 @@ A VASP calculation requires four input files: ``INCAR``, ``POSCAR``, ``POTCAR``, ********************************* A VASP calculation requires a ``POTCAR`` file, which is a concatenation of pseudopotential -files for each atomic species in the order they appear in ``POSCAR``. Pseudopotentials are -distributed with your VASP license and are not provided by OLCF. For the silicon example, +files for each atomic species in the order they appear in ``POSCAR``. Pseudopotentials distributed +with VASP are located in ``$VASP_POTENTIALS_DIR//`` where ```` +can be ``LDA`` or ``PBE``. Each directory contains element directories containing the corresponding +``POTCAR`` file. For the silicon example, concatenate the silicon pseudopotential into a file named ``POTCAR`` in the working directory: .. code-block:: bash - cat /path/to/potpaw_PBE/Si/POTCAR > POTCAR + cat $VASP_POTENTIALS_DIR/PBE/Si/POTCAR > POTCAR If your system has multiple species, concatenate their ``POTCAR`` files in the same order the species appear in ``POSCAR``.