Magmatomix/UMD package

The Magmatomix/UMD package performs post-processing of molecular-dynamics simulations. It is best suited for ab initio calculations. It is written in python, and it is open-source. We welcome contributors and collaborators!

The package can be downloaded from this page as a zip file, or from Github

And if you use the code, please cite it using:
R. Caracas, A. Kobsch, N. V Solomatova, Z. Li, F. Soubiran, J.A. Hernandez, F. Soubiran. Analyzing melts and fluids from ab initio molecular dynamics simulations with the UMD package, JoVE, 175, e61534 (2021).

UMD file format

The various parsers extract only the relevant thermodynamic information and atomic trajectories from the output of the first-principles/atomistic simulations. This info is writteni in “UMD” files. The umd files are ascii files; typical extension is .umd.dat but not mandatory. 

Each physical property is expressed on one line. Every line starts with a keyword, followed by the numerical value(s), and the unit. In this way the format is highly adaptable and allows for new properties to be added to the umd  file, all the while preserving its readability throughout versions.

Then each atom is detailed on one line, where 

  • columns 1-3 give the atomic positions expressed in reduced coordinates
  • columns 4-6 give the atomic positions expressed in cartesian units
  • columns 7-9 give the real Cartesian positions that take into account diffusion, 
  • columns 10-12 give the atomic velocities
  • columns 12-15 give the atomic forces
  • column 16 gives the atomic charges
  • column 17 gives the atomic local magnetic moment.

All the functions related to the reading and printing of the umd files are combined into one python library, umd These functions are consistently called by all the scripts of the package after proper loading.

Magmatomix/UMD workflow

The following figure shows the updated workflow of the Magmatomix/UMD pacakge.

You can perform four types if analysis:

  • Input/output to and from ab initio packages, like VASP or Qbox into umd, xyz, etc files
  • Structural analysis, like interatomic bonding, chemical speciation, lifetimes of clusters, liquid vs vapor identification, interatomic angles
  • Transport properties like diffusion coefficients and viscosity
  • Thermodynamic analysis, like internal energies, heat capacity, vibrational spectrum
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