Mechanical Engineering Commons^™

Software For Extracting Deformation Gradient And Stress From Md Simulations: Simulations Using The Charmm Force Field, Mehrdad Negahban, Lili Zhang, Zesheng Zhang, John Jasa, Antoine Jérusalem

Department of Mechanical and Materials Engineering: Faculty Publications

Software was developed, and is provided under a general use license, to calculate continuum level deformation gradient and stress for any group of atoms in an MD simulation that uses the Charmm force fields. This software can also calculate the interaction stress applied by one group of atoms on any other group. To obtain deformation gradient and stress, the user needs to provide the selected group(s) of atoms in an atom group identification file, and provide the associated LAMMPS format files and force field parameter file. An example is included to demonstrate the use of the software.