Centre for Computational Science (UCL)

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32 repositories

TIES
Public
Topology Superimposition based on joint graph traversal
Python
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MIT License
•1•6•8•0•Updated Jan 23, 2025Jan 23, 2025
EasyVVUQ
Public
Python 3 framework to facilitate verification, validation and uncertainty quantification (VVUQ) for a wide variety of simulations.
simulation hpc-applications vvuq python verification uncertainty-quantification
Jupyter Notebook
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GNU Lesser General Public License v3.0
•28•89•22•3•Updated Jan 21, 2025Jan 21, 2025
Nbed
Public
Python package to reduce the qubit requirements of quantum simulation by embedding into DFT.
chemistry quantum quantum-computing quantum-chemistry embedding
Python
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Other
•2•8•13•1•Updated Jan 9, 2025Jan 9, 2025
kinetic_NMI
Public
MIT License
•0•0•0•0•Updated Dec 30, 2024Dec 30, 2024
QSVDD
Public
0•0•0•0•Updated Dec 24, 2024Dec 24, 2024
HemePure
Public
HemeLB version with improved memory, compilation and scaling
C++
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BSD 3-Clause "New" or "Revised" License
•9•9•2•0•Updated Nov 21, 2024Nov 21, 2024
HemePure_tools
Public
C++
•
BSD 3-Clause "New" or "Revised" License
•4•0•0•0•Updated Sep 4, 2024Sep 4, 2024
HemePure-GPU
Public
GPU version of HemeLB code (HemePure)
C++
•
BSD 3-Clause "New" or "Revised" License
•9•5•4•0•Updated May 8, 2024May 8, 2024
HemePure_SelfCoupled
Public
Self-coupled version of HemeLB
C++
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BSD 3-Clause "New" or "Revised" License
•2•0•0•0•Updated Apr 18, 2024Apr 18, 2024
hemeXtract
Public
Reads and analyses HemeLB .xtr output files
C++
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BSD 3-Clause "New" or "Revised" License
•4•1•0•1•Updated Apr 18, 2024Apr 18, 2024
PINN-WM-LBM
Public
Jupyter Notebook
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MIT License
•2•4•0•0•Updated Feb 22, 2024Feb 22, 2024
TIES_MD
Public
Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.
simulation molecular-dynamics
Python
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GNU Lesser General Public License v3.0
•6•32•3•0•Updated Dec 10, 2023Dec 10, 2023
QuantumTools
Public
Random useful quantum computing for chemistry things.
Python
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GNU General Public License v3.0
•0•2•1•0•Updated Nov 21, 2023Nov 21, 2023
FabMD
Public
FabMD is a FabSim3 plugin for automated LAMMPS-based simulations.
python3 high-performance-computing lammps namd gromacs multiscale-simulation
Python
•1•1•4•0•Updated Mar 20, 2023Mar 20, 2023
LongTimescaleStudy
Public
Data associated with the long timescale study.
Creative Commons Zero v1.0 Universal
•0•0•0•0•Updated Nov 7, 2022Nov 7, 2022
FabNEPTUNE
Public
FabNEPTUNE is a FabSim3 plugin for automated NEPTUNE (UKAEA’s fusion project)-based simulations
high-performance-computing uncertainty-quantification convection2d-and-convection3d steady-and-turbulence-models
C++
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GNU General Public License v3.0
•4•2•0•0•Updated Jun 24, 2022Jun 24, 2022
DRTNN
Public
Deep Residual Transformer Neural Network (DRTNN)
neural-network transformer residual-network surrogate-model
Python
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GNU General Public License v3.0
•1•0•0•0•Updated May 21, 2022May 21, 2022
FabSCEMa
Public
FabSCEMa is a FabSim3 plugin for automated SCEMa-based simulations.
high-performance-computing uncertainty-quantification heterogeneous-multiscale-method coupled-simulation-models
Python
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GNU General Public License v3.0
•1•1•0•0•Updated May 16, 2022May 16, 2022
SCEMa
Public
HMM implementation featuring Deal.II (FE) and LAMMPS (MD)
molecular-dynamics dealii multiscale-simulation finite-element-methods lammps
C++
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GNU General Public License v3.0
•7•16•4•0•Updated Mar 20, 2022Mar 20, 2022
LargeScaleTIES
Public
2•2•0•0•Updated Feb 9, 2022Feb 9, 2022
ML-PB-Covid-drug
Public
Other
•0•0•0•0•Updated Jul 22, 2021Jul 22, 2021
UQ_NAMD
Public
High-dimension parameters sensitivity analysis of binding affinity simulations with NAMD using EasyVVUQ and EasyPJ
Jupyter Notebook
•0•0•1•0•Updated Jun 20, 2021Jun 20, 2021
HemeLBData_FistulaInputs50um
Public
HemeLB input data for 50um resolution arteriovenous fistula study
0•0•0•0•Updated Jun 10, 2021Jun 10, 2021
bac-docker
Public
Apache License 2.0
•0•1•0•0•Updated Aug 21, 2020Aug 21, 2020
BAC2
Public
A tool for the automation of molecular simulations using multiple engines, focusing on binding affinity calculations
Python
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Apache License 2.0
•1•4•19•0•Updated Mar 24, 2020Mar 24, 2020
ldha-diverse-esmacs
Public
Data from the paper "Application of ESMACS binding free energy protocols to diverse ligand datasets: lactate dehydogenase A"
Python
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Other
•0•0•0•0•Updated Jul 2, 2019Jul 2, 2019
FabSim
Public
Superseded by FabSim3.
Python
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BSD 3-Clause "New" or "Revised" License
•5•14•0•0•Updated Jun 11, 2019Jun 11, 2019
ParmEd
Public
Parameter/topology editor and molecular simulator
Python
•150•0•6•0•Updated Nov 20, 2018Nov 20, 2018
brd4-diverse-esmacs
Public
Data from the paper "Application of ESMACS binding free energy protocols to diverse ligand datasets:Bromodomain-containing protein 4"
Other
•0•0•0•0•Updated Nov 13, 2018Nov 13, 2018
esmacs-input-creation-docs
Public
Description of methods to create BAC compatible protein-ligand system descriptions for ESMACS simulations
0•0•0•0•Updated Jul 12, 2017Jul 12, 2017