From fa5d7a469e5725e66dd483a069a82d65470588e2 Mon Sep 17 00:00:00 2001 From: Kilian Cavalotti Date: Thu, 17 Oct 2024 10:39:23 -0700 Subject: [PATCH] docs: updated software list --- includes/data/software.yml | 282 ++++++++++++++++++---------------- src/docs/software/updates.xml | 9 ++ 2 files changed, 156 insertions(+), 135 deletions(-) diff --git a/includes/data/software.yml b/includes/data/software.yml index 61e57b26d..740ee35c6 100644 --- a/includes/data/software.yml +++ b/includes/data/software.yml @@ -5662,6 +5662,27 @@ software_modules: versionName: 2.0.3} - {description: Libint computes molecular integrals., markedDefault: false, versionName: 2.6.0} + - categories: chemistry, computational chemistry + defaultVersionName: g16.B01 + description: Gaussian is a general purpose computational chemistry software + package. + package: gaussian + url: https://www.gaussian.com + versions: + - description: Gaussian is a general purpose computational chemistry software + package. + markedDefault: false + properties: + arch: {gpu: 1} + license: {restricted: 1} + versionName: g16.A03 + - description: Gaussian is a general purpose computational chemistry software + package. + markedDefault: false + properties: + arch: {gpu: 1} + license: {restricted: 1} + versionName: g16.B01 - categories: chemistry, tools defaultVersionName: 3.1.1 description: Open Babel is a chemical toolbox designed to speak the many languages @@ -5823,27 +5844,6 @@ software_modules: can be used for the simulation of molecules in gases, fluids, zeolites, aluminosilicates, metal-organic frameworks, carbon nanotubes and external fields.', markedDefault: false, versionName: 2.0.3_py27} - - categories: chemistry, computational chemistry - defaultVersionName: g16.B01 - description: Gaussian is a general purpose computational chemistry software - package. - package: gaussian - url: https://www.gaussian.com - versions: - - description: Gaussian is a general purpose computational chemistry software - package. - markedDefault: false - properties: - arch: {gpu: 1} - license: {restricted: 1} - versionName: g16.A03 - - description: Gaussian is a general purpose computational chemistry software - package. - markedDefault: false - properties: - arch: {gpu: 1} - license: {restricted: 1} - versionName: g16.B01 - categories: chemistry, x-ray spectroscopy defaultVersionName: 0.9.80_py312 description: Larch is a open-source library and set of applications for processing @@ -5856,6 +5856,30 @@ software_modules: and analyzing X-ray absorption and fluorescence spectroscopy data and X-ray fluorescence and diffraction image data from synchrotron beamlines., markedDefault: false, versionName: 0.9.80_py312} + - categories: chemistry, quantum chemistry + defaultVersionName: '4.1' + description: CP2K is a quantum chemistry and solid state physics software package + that can perform atomistic simulations of solid state, liquid, molecular, + periodic, material, crystal, and biological systems. + package: cp2k + url: http://www.cp2k.org + versions: + - description: CP2K is a quantum chemistry and solid state physics software + package that can perform atomistic simulations of solid state, liquid, molecular, + periodic, material, crystal, and biological systems. + markedDefault: false + properties: + arch: {gpu: 1} + parallel: {mpi: 1} + versionName: '9.1' + - description: CP2K is a quantum chemistry and solid state physics software + package that can perform atomistic simulations of solid state, liquid, molecular, + periodic, material, crystal, and biological systems. + markedDefault: true + properties: + arch: {gpu: 1} + parallel: {mpi: 1} + versionName: '4.1' - categories: chemistry, computational chemistry defaultVersionName: 3.22.1_py39 description: The Atomic Simulation Environment (ASE) is a set of tools and Python @@ -5886,30 +5910,6 @@ software_modules: versions: - {description: APBS solves the equations of continuum electrostatics for large biomolecular assemblages., markedDefault: false, versionName: '1.5'} - - categories: chemistry, quantum chemistry - defaultVersionName: '4.1' - description: CP2K is a quantum chemistry and solid state physics software package - that can perform atomistic simulations of solid state, liquid, molecular, - periodic, material, crystal, and biological systems. - package: cp2k - url: http://www.cp2k.org - versions: - - description: CP2K is a quantum chemistry and solid state physics software - package that can perform atomistic simulations of solid state, liquid, molecular, - periodic, material, crystal, and biological systems. - markedDefault: false - properties: - arch: {gpu: 1} - parallel: {mpi: 1} - versionName: '9.1' - - description: CP2K is a quantum chemistry and solid state physics software - package that can perform atomistic simulations of solid state, liquid, molecular, - periodic, material, crystal, and biological systems. - markedDefault: true - properties: - arch: {gpu: 1} - parallel: {mpi: 1} - versionName: '4.1' - categories: chemistry, quantum chemistry defaultVersionName: 6.0.0 description: ORCA is a flexible, efficient and easy-to-use general purpose tool @@ -5941,6 +5941,33 @@ software_modules: properties: parallel: {mpi: 1} versionName: 6.0.0 + - categories: chemistry, molecular dynamics + defaultVersionName: '20230802' + description: LAMMPS is a classical molecular dynamics code that models an ensemble + of particles in a liquid, solid, or gaseous state. + package: lammps + url: http://lammps.sandia.gov + versions: + - description: LAMMPS is a classical molecular dynamics code that models an + ensemble of particles in a liquid, solid, or gaseous state. + markedDefault: false + properties: + parallel: {mpi: 1} + versionName: '20180316' + - description: LAMMPS is a classical molecular dynamics code that models an + ensemble of particles in a liquid, solid, or gaseous state. + markedDefault: false + properties: + arch: {gpu: 1} + parallel: {mpi: 1} + versionName: '20200303' + - description: LAMMPS is a classical molecular dynamics code that models an + ensemble of particles in a liquid, solid, or gaseous state. + markedDefault: false + properties: + arch: {gpu: 1} + parallel: {mpi: 1} + versionName: '20230802' - categories: chemistry, molecular dynamics defaultVersionName: '2023.1' description: GROMACS is a versatile package to perform molecular dynamics, i.e. @@ -5981,17 +6008,48 @@ software_modules: arch: {gpu: 1} parallel: {mpi: 1} versionName: '2023.1' - - categories: chemistry, molecular dynamics - defaultVersionName: 1.65.0 - description: Qbox is a First-Principles Molecular Dynamics code. - package: qbox - url: http://www.qboxcode.org + - categories: chemistry, quantum chemistry + defaultVersionName: '7.1' + description: Quantum ESPRESSO is an integrated suite of Open-Source computer + codes for electronic-structure calculations and materials modeling at the + nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials. + package: quantum-espresso + url: https://www.quantum-espresso.org versions: - - description: Qbox is a First-Principles Molecular Dynamics code. + - description: Quantum ESPRESSO is an integrated suite of Open-Source computer + codes for electronic-structure calculations and materials modeling at the + nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials. + family: qe markedDefault: false properties: parallel: {mpi: 1} - versionName: 1.65.0 + versionName: 6.2.1 + - description: Quantum ESPRESSO is an integrated suite of Open-Source computer + codes for electronic-structure calculations and materials modeling at the + nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials. + family: qe + markedDefault: false + properties: + parallel: {mpi: 1} + versionName: '6.6' + - description: Quantum ESPRESSO is an integrated suite of Open-Source computer + codes for electronic-structure calculations and materials modeling at the + nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials. + family: qe + help: https://www.sherlock.stanford.edu/docs/software/using/quantum-espresso + markedDefault: false + properties: + parallel: {mpi: 1} + versionName: '7.0' + - description: Quantum ESPRESSO is an integrated suite of Open-Source computer + codes for electronic-structure calculations and materials modeling at the + nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials. + family: qe + help: https://www.sherlock.stanford.edu/docs/software/using/quantum-espresso + markedDefault: false + properties: + parallel: {mpi: 1} + versionName: '7.1' - categories: chemistry, quantum chemistry defaultVersionName: 2.9.7 description: OCEAN is a versatile and user-friendly package for calculating @@ -6016,14 +6074,28 @@ software_modules: properties: arch: {gpu: 1} versionName: 7.1.1 + - categories: chemistry, molecular dynamicx + defaultVersionName: 0.2.2_py39 + description: FATSLiM stands for “Fast Analysis Toolbox for Simulations of Lipid + Membranes” and its goal is to provide an efficient, yet robust, tool to extract + physical parameters from MD trajectories. + package: py-fatslim + url: https://fatslim.github.io/ + versions: + - {description: 'FATSLiM stands for “Fast Analysis Toolbox for Simulations of + Lipid Membranes” and its goal is to provide an efficient, yet robust, tool + to extract physical parameters from MD trajectories.', markedDefault: false, + versionName: 0.2.2_py39} - categories: chemistry, crystallography - defaultVersionName: 2.0.20 - description: A C++ toolkit for working with macromolecular coordinate files. - package: mmdb2 - url: https://www.ccp4.ac.uk/ + defaultVersionName: 3.4.4 + description: VESTA is a 3D visualization program for structural models, volumetric + data such as electron/nuclear densities, and crystal morphologies. + package: vesta + url: http://jp-minerals.org/vesta/en/ versions: - - {description: A C++ toolkit for working with macromolecular coordinate files., - markedDefault: false, versionName: 2.0.20} + - {description: 'VESTA is a 3D visualization program for structural models, + volumetric data such as electron/nuclear densities, and crystal morphologies.', + markedDefault: false, versionName: 3.4.4} - categories: chemistry, computational chemistry defaultVersionName: 5.4.1 description: The Vienna Ab initio Simulation Package (VASP) is a computer program @@ -6077,48 +6149,6 @@ software_modules: license: {restricted: 1} parallel: {mpi: 1} versionName: 5.4.1 - - categories: chemistry, quantum chemistry - defaultVersionName: '7.1' - description: Quantum ESPRESSO is an integrated suite of Open-Source computer - codes for electronic-structure calculations and materials modeling at the - nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials. - package: quantum-espresso - url: https://www.quantum-espresso.org - versions: - - description: Quantum ESPRESSO is an integrated suite of Open-Source computer - codes for electronic-structure calculations and materials modeling at the - nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials. - family: qe - markedDefault: false - properties: - parallel: {mpi: 1} - versionName: 6.2.1 - - description: Quantum ESPRESSO is an integrated suite of Open-Source computer - codes for electronic-structure calculations and materials modeling at the - nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials. - family: qe - markedDefault: false - properties: - parallel: {mpi: 1} - versionName: '6.6' - - description: Quantum ESPRESSO is an integrated suite of Open-Source computer - codes for electronic-structure calculations and materials modeling at the - nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials. - family: qe - help: https://www.sherlock.stanford.edu/docs/software/using/quantum-espresso - markedDefault: false - properties: - parallel: {mpi: 1} - versionName: '7.0' - - description: Quantum ESPRESSO is an integrated suite of Open-Source computer - codes for electronic-structure calculations and materials modeling at the - nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials. - family: qe - help: https://www.sherlock.stanford.edu/docs/software/using/quantum-espresso - markedDefault: false - properties: - parallel: {mpi: 1} - versionName: '7.1' - categories: chemistry, computational chemistry defaultVersionName: 7.0.2 description: NWChem is an ab initio computational chemistry software package @@ -6148,33 +6178,14 @@ software_modules: versions: - {description: Crystallographic automation and complex data manipulation libraries., markedDefault: false, versionName: 2.1.20180802} - - categories: chemistry, molecular dynamics - defaultVersionName: '20230802' - description: LAMMPS is a classical molecular dynamics code that models an ensemble - of particles in a liquid, solid, or gaseous state. - package: lammps - url: http://lammps.sandia.gov + - categories: chemistry, crystallography + defaultVersionName: 2.0.20 + description: A C++ toolkit for working with macromolecular coordinate files. + package: mmdb2 + url: https://www.ccp4.ac.uk/ versions: - - description: LAMMPS is a classical molecular dynamics code that models an - ensemble of particles in a liquid, solid, or gaseous state. - markedDefault: false - properties: - parallel: {mpi: 1} - versionName: '20180316' - - description: LAMMPS is a classical molecular dynamics code that models an - ensemble of particles in a liquid, solid, or gaseous state. - markedDefault: false - properties: - arch: {gpu: 1} - parallel: {mpi: 1} - versionName: '20200303' - - description: LAMMPS is a classical molecular dynamics code that models an - ensemble of particles in a liquid, solid, or gaseous state. - markedDefault: false - properties: - arch: {gpu: 1} - parallel: {mpi: 1} - versionName: '20230802' + - {description: A C++ toolkit for working with macromolecular coordinate files., + markedDefault: false, versionName: 2.0.20} - categories: chemistry, crystallography defaultVersionName: '1.4' description: A macromolecular superposition library. @@ -6183,16 +6194,17 @@ software_modules: versions: - {description: A macromolecular superposition library., markedDefault: false, versionName: '1.4'} - - categories: chemistry, crystallography - defaultVersionName: 3.4.4 - description: VESTA is a 3D visualization program for structural models, volumetric - data such as electron/nuclear densities, and crystal morphologies. - package: vesta - url: http://jp-minerals.org/vesta/en/ + - categories: chemistry, molecular dynamics + defaultVersionName: 1.65.0 + description: Qbox is a First-Principles Molecular Dynamics code. + package: qbox + url: http://www.qboxcode.org versions: - - {description: 'VESTA is a 3D visualization program for structural models, - volumetric data such as electron/nuclear densities, and crystal morphologies.', - markedDefault: false, versionName: 3.4.4} + - description: Qbox is a First-Principles Molecular Dynamics code. + markedDefault: false + properties: + parallel: {mpi: 1} + versionName: 1.65.0 - categories: chemistry, cheminformatics defaultVersionName: 2018.09.1_py27 description: RDKit is a collection of cheminformatics and machine-learning software diff --git a/src/docs/software/updates.xml b/src/docs/software/updates.xml index 857093cf6..c4334765c 100644 --- a/src/docs/software/updates.xml +++ b/src/docs/software/updates.xml @@ -5,6 +5,15 @@ Sherlock software update feed https://www.sherlock.stanford.edu/docs/software/list + + New module: chemistry/py-fatslim version 0.2.2_py39 + FATSLiM stands for “Fast Analysis Toolbox for Simulations of Lipid Membranes” and its goal is to provide an efficient, yet robust, tool to extract physical parameters from MD trajectories. + https://fatslim.github.io/ + https://www.sherlock.stanford.edu/docs/software/list/?add:v=0.2.2_py39#py-fatslim + chemistry, molecular dynamicx + kilian@stanford.edu (Kilian Cavalotti) + Thu, 17 Oct 2024 10:36:57 -0700 + New module: math/py-ultralytics version 8.3.14_py312 Ultra YOLO11 is a cutting-edge, state-of-the-art (SOTA) model that builds upon the success of previous YOLO versions and introduces new features and improvements to further boost performance and flexibility.