MolSimulX

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Molecular Simulation EXploration

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Any comments, suggestions, and questions? Open an issue or submit PRs!

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Overview

• Start date: 2021/11/24
• Maintainers:
  • Dr. Yawei Liu ([email protected])

This project is aiming to integrate tools/scripts used in our molecular simulations of matters. The corresponding tutorials and examples will also be given here.

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Build work platform

OS

Mac OS, Ubuntu Os and other Linux type OS are recommended. In Windows OS, you can install wsl Ubuntu, and then use the WSL Ubuntu as a subsystem in Windows OS.

• see use_wsl_ubuntu.md for a simple tutorial on how to instal WSL Ubuntu in Windows OS and to launch WSL Ubuntu in vsode (see below figure)

• more details can be found here for how to install WSL Ubuntu and here for how to use WSL Ubuntu invscode (see below figure)

Install software/packages

• before installation

  • most software/pakcages are installed via code command in Terminal

    • In Mac Os, see here for Mac Terminal
    • In Ubuntu OS, see here for Ubuntu Terminal
    • In WSL Ubuntu, you can launch WSL Ubuntu in vscode, and then open a Ubuntu Terminal from the menu bar

  • bash profile

    • a bash profile is a file used to store environment settings for your terminal, and it is
      • for bash shell
        • ~/.bash_profile in Mac and ~/.bashrc in Ubuntu (~ represents the user’s home directory)
      • for zsh shell (oh-my-zsh for zsh is highly recommanded)
        • ~/.zshrc in both Mac and Ubuntu
    • for the changes in the profile file to be applied, run the source command with the file as an argument
      • source ~/.bash_profile or
      • source ~/.bashrc or
      • source ~/.zshrc

• install compiler

  • gcc/g++
    • brew install gcc # for Mac
    • sudo apt install build-essential # for Ubuntu
    • test gcc --version
  • make
    • brew install make # for Mac
    • sudo apt install make # for Ununtu
    • test make --version
  • cmake
    • brew install cmake # for Mac
    • sudo apt install cmake # for Ununtu
    • test make --version

• git

  • install git, see here for details
    • brew install git # for mac
    • sudo apt-get install git # for Ubuntu
  • see use_git.md for basic usage of git
  • see here for more details of git

• MolSimulX

  • obtain MolSimulX
    • cd some_folder
    • git clone https://gitee.com/yliu3803/MolSimulX.git
  • update MolSimulX
    • cd MolSimulX
    • git pull

• python and python packages

  • install miniconda (recommended for limited storage space) or anaconda (most python packages are already included)

  • install pyhton packages including via conda

    conda install numpy pandas scipy matplotlib

    conda install nodejs

    conda install -c conda-forge MDanalysis MDAnalysisTests nglview

    conda install -c conda-forge freud fresnel

    pip install plato-draw

    pip install wulffpack

    pip install ase

    Tip：Packages can be install via pip or conda, see details in corresponding official documents.

• fftool

  • also can be found in ilmdtoolkit/preprocess folder

  • add fftool to the PATH environment variable

    • in bash profile, addexport PATH=path_to_fftool:$PATH

  • see use_fftool.md for basic usage of fftool

• packmol

  • also can be found in ilmdtoolkit/preprocess folder

  • expand the files and compile the package

    • tar zxvf packmol.tar.gz
    • cd packmol
    • make

  • add packmol to the PATH environment variable

    • in bash profile, add export PATH=path_to_packmol:$PATH

• lammps

  • see use_lammps.md for how to compile your own lammps

• vmd

Data processing platform

Jupyterlab is a web-based interactive development environment for notebooks, code, and data. Its flexible interface allows users to configure and arrange workflows in data science, scientific computing, computational journalism, and machine learning.

• install jupyterlab

  • conda install jupyterlab

• see use_jupyerlab.ipynb for basic usage of python and packages in jupyterlab

Other recommendations

• markdown
• latex and overleaf

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Content

preprocess # 预处理

This folder contains some tools and files used to set up a simulation system.

• folder clandp contains topology and force field files for ILs, provided by Padua Group.

• folder molecules contains topology and force field files for some small molecules.

• ions contains topology and force field files for some ions.

• folder fftool contains source codes of fftool, which, combined with packmol, can be used to build initial configrautions and data files for MD simulations carried out in, such as LAMMPS.

• packmol.tar.gz contains the source code of packmol.

on-the-fly # 即时处理

This folder contains some tools/srcipts combined with other simulation tools to perform special simulations (e.g. rare event techniques).

postprocess # 后处理

This folder contains some python scripts to analyse/visulise the simulation data (depends on numpy, pandas, scipy, etc. python packages) and to generate the final report (depends on markdown, latex).

• PyLAT has source codes of PyLAT

use_

Basics usage for some tools and packages.

• use_git.md # basic usage of git.

• use_jupyerlab.ipynb # basic usage of python and packages in jupyterlab.

• use_fftool.md # basic usage of fftool.

• use_lammps.md # how to compile your own Lammps.

• use_wsl_ubuntu.md # install WSL Ubuntu and use it with vscode

example_

Some simple examples.

• example_co2_eos: MD simulaitons to calculate the equation of state of CO$_2$, see details in co2_eos.ipynb

  python jupyterlab fftool packmol lammps mdanalysis nglview

• example_BmimPF6_ACN_CG Coarse-grained MD simulations of BmimPF6-ACN mixtures，see details in BmimPF6_ACN_mixture.ipynb

  python jupyterlab fftool packmol lammps mdanalysis nglview

• example_Wulff_Ru_cluster build Wulff cluster of Ru hcp crystal，see details in wulff_Ru.ipynb

  python jupyterlab ase wulffpack nglview

• example_water_between_two_walls build a configuration with water molecules between two different substrates, and create lammps input files，see details in water_between_two_walls.ipynb

  python jupyterlab ase fftool packmol nglview

• example_il_com_orientation compute the center-of-mass and orientation vector of cations in a ionic liquidsee details in il_com_orientation.ipynb

  python jupyterlab pandas mdanalysis nglview

• project_

  These folders contains all codes and details of our published papers.

Publications

2022

• Charged Nanochannels in Covalent Organic Framework Membranes Enabling Efficient Ion Exclusion. ACS Nano 2022, 16 (8), 11781.
• A General Method for Direct Assembly of Single Nanocrystals. Adv. Opt. Mater. 2022, 10 (14), 2200179.
• Confined Assembly of Colloidal Nanorod Superstructures by Locally Controlling Free‐Volume Entropy in Nonequilibrium Fluids. Adv. Mater. 2022, 34 (28), 2202119.
• Ultrafast Seawater Desalination with Covalent Organic Framework Membranes. Nat. Sustain. 2022, 5 (6), 518. [Cover Artical]
• Nanoscale Faceting and Ligand Shell Structure Dominate the Self‐Assembly of Nonpolar Nanoparticles into Superlattices. Adv. Mater. 2022, 34 (20), 2109093. [picked up by chemeurope.com, etc.]
• Charged Nanochannels Endow COF Membrane with Weakly Concentration-Dependent Methanol Permeability. J. Memb. Sci. 2022, 645, 120186.

2011-2021 (part)

• A Dissipative Particle Dynamics Model for Studying Dynamic Phenomena in Colloidal Rod Suspensions. J. Chem. Phys. 2021, 154 (10), 104120. [Editor's Pick]
• Direct Assembly of Vertically Oriented, Gold Nanorod Arrays. Adv. Funct. Mater. 2021, 31 (6), 2006753. [picked up by eurekalert, phys.org, etc.]
• Hamiltonian Transformation to Compute Thermo-Osmotic Forces. Phys. Rev. Lett. 2018, 121 (6), 068002.
• Molecular Simulation of Thermo-Osmotic Slip. Phys. Rev. Lett. 2017, 119 (3), 038002.
• Microscopic Marangoni Flows Cannot Be Predicted on the Basis of Pressure Gradients. Phys. Rev. Lett. 2017, 119 (22), 224502.
• A Unified Mechanism for the Stability of Surface Nanobubbles: Contact Line Pinning and Supersaturation. J. Chem. Phys. 2014, 141 (13), 134702.
• Nanobubble Stability Induced by Contact Line Pinning. J. Chem. Phys. 2013, 138 (1), 014706.
• How Nanoscale Seed Particles Affect Vapor-Liquid Nucleation. J. Chem. Phys. 2011, 135 (18), 184701.