Optimization potential interaction parameters for ion mobility spectrometry

This repository contains a set of source code and input scripts that allows to optimization of Lennard-Jones parameters to perform collision cross section (CCS) calculations. We developed optimization methods for force field parameters in order to improve "MassCCS" accuracy. Our optimization method uses the differential evolution algorithm and "OMPC" to reduce computation time.

The repository contents:

src: This directory contains massccs-ompc source codes to perform a bunch of CCS calculations using MassCCS and OMPC.

N2_gas: This directory contains inputs, scripts and outputs for optimization Lennard-Jones parameters using N2 buffer gas.

CO2_gas: This directory contains inputs, scripts and outputs for optimization Lennard-Jones parameters using CO2 buffer gas.

Installation

Download the MassCCS-OMPC or clone the repository on your computer:

git clone https://github.com/cces-cepid/opt-massccs.git

Required Software

MassCCS-OMPC depends on the following software:

• Singularity
• OpenMP Cluster container image
• MPI compiler

On Ubuntu/Debian, you can simply run the following commands to dowlonad the last version of OMPC:

sudo apt-get install singularity-container  
singularity pull docker://ompcluster/runtime

Installing

On your terminal, run the following commands to compile the source code:

$ cd massccs-ompc
$ singularity shell ./runtime_latest.sif # execute the OMPC container
Singularity> mkdir build # Create build directory 
Singularity> cd build
Singularity> export CC=clang CXX=clang++ # export Clang compiler 
Singularity> cmake .. # Generate Makefiles
Singularity> make  # Compile the program to create the massccs-ompc executable called massccs

Author & Contact:

Samuel Cajahuaringa - [email protected]