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EChemDID
(Find up-to-date versions of EChemDID on my GitHUB)
The electrochemical dynamics with implicit degrees of freedom (EChemDID) method enables the application of an external voltage to metallic electrodes in reactive MD simulations. Validation tests show that the method provides an accurate description of the electric fields generated by the applied voltage and the driving force for electrochemical reactions.
Adding EChemDID to LAMMPS. EChemDID comes as a USER-package compatible with LAMMPS and can be downloaded here. The EChemDID method includes a LAMMPS compute’ that solves the Laplacian and a “fix” that integrates the voltage diffusion in time. The whole implementation is consistent with the parallel scheme employed in LAMMPS. The modifications are independent to the actual LAMMPS program, only a minor modification to the reax/c package allows switching from regular QEq (with constant electronegativity) to dynamical electronegativity in EChemDID. The archive contains the following directories:
- USER-ECHEMDID
- examples
The date in the name of the package corresponds to the LAMMPS version. Just copy the EChemDID user-package to the src/ directory and compile LAMMPS as:
make yes-user-reaxc
make yes-user-echemdid
make yes-rigid
make foo
Note: load reaxc BEFORE loading echemdid
Running EChemDID. The input files are self documented however we will discuss here the principal commands to include in the input file. The EChemDID code makes use of the fix & compute/property commands to add additional dynamical variables to each atom. These variables have to be initialized. The fix EChemDID contains a minimum of 12 parameters with in order: fix-ID, group, echemdid, frequency, k, k-value, cut, cut-value, norm, norm-value, nelec, nelec-value. 5 additional parameters can be input: boundary, group-left, group-right, chi-left, chi-right.
- Onofrio, Nicolas and Guzman, David and Strachan, Alejandro.
Atomistic simulations of electrochemical metallization cells: mechanisms of ultra-fast resistance switching in nanoscale devices . NANOSCALE, 8, 2016 10.1039/c6nr01335j - Onofrio, Nicolas and Guzman, David and Strachan, Alejandro.
Atomic origin of ultrafast resistance switching in nanoscale electrometallization cells . NATURE MATERIALS, 14, 2015 10.1038/NMAT4221 - Guzman, David M. and Onofrio, Nicolas and Strachan, Alejandro.
Stability and migration of small copper clusters in amorphous dielectrics . JOURNAL OF APPLIED PHYSICS, 117, 2015 10.1063/1.4921059 - Onofrio, Nicolas and Strachan, Alejandro.
Voltage equilibration for reactive atomistic simulations of electrochemical processes . JOURNAL OF CHEMICAL PHYSICS, 143, 2015 10.1063/1.4927562
The ORCAtool
The ORCAtool is an ab initio and density functional theory calculations online tool dedicated to molecular systems. Levels of theory range from post-Hartree-Fock methods to density functional theory including various functional and basis sets. The tool allows geometry optimizations with or without constrains, normal modes analysis and automatic ionization energy calculation. The ORCAtool is powered by ORCA an ab initio, DFT and semiempirical SCF-MO package from Max-Planck-Institute for Chemical Energy Conversion, Germany.
- Neese, Frank.
The ORCA program system . COMPUTATIONAL MOLECULAR SCIENCE, 2, 2012 10.1002/wcms.81 - Onofrio, Nicolas and Strachan, Alejandro.
ab initio simulations with ORCA . https://nanohub.org/resources/orcatool, 2016 10.4231/D3VT1GR06