Reax ff #122
Reax ff #122
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| # set environment for LAMMPS and msi2lmp executables | ||
| # to find potential and force field files | ||
| if ( "$?LAMMPS_POTENTIALS" == 0 ) setenv LAMMPS_POTENTIALS /home/brandon/.local/share/lammps/potentials | ||
| if ( "$?MSI2LMP_LIBRARY" == 0 ) setenv MSI2LMP_LIBRARY /home/brandon/.local/share/lammps/frc_files |
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Personal files such as these can be added to .git/info/exclude
| volume = 38, | ||
| pages = {245--259} | ||
| } | ||
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Files like this which may be accidentally created could be added to .gitignore (a line with log.cite would do)
| "atom_modify map array", // store all positions in an array | ||
| "atom_modify sort 0 0.0", // don't reorder atoms during simulation | ||
| ])?; | ||
| if &(pair_style.to_string())[..17] == "pair_style reax/c"{ |
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This can be simplified to
if pair_style.to_string().starts_with("pair_style reax/c") {More importantly, however, rather than checking these things here, it would be preferrable to make it possible to handle these changes by adding methods to abstract over this to the rsp2_lammps_wrap::Potential trait. For now though, until we are certain what methods are needed, I am okay with this hack.
| pub fn a() -> f64 { 1.0 } | ||
| pub fn vacuum_sep() -> f64 { 10.0 } | ||
| pub fn layer_sep() -> Either<f64, Vec<f64>> { Either::A(1.0) } | ||
| pub fn layer_sep() -> Either<f64, Vec<f64>> { Either::A(1.5) } |
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Try and see if adding layer-sep: 1.5 to your layers.yaml files works, rather than changing the default.
src/io/structure/layers_yaml.rs
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| // Number of unique images to generate along each layer lattice vector | ||
| #[serde(default = "defaults::layer::repeat")] | ||
| pub repeat: [u32; 2], | ||
| pub site_atoms: Vec<String>, |
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If you make this Vec<Element> then you shouldn't need the conversion loop.
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Also I think "atoms" is vague. For a public interface like this I think the preferred name would be site-symbols. elements would also work.
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Did you try Vec<Element> here? What happens? I know I also suggested this before submitting the PR.
This would be what I intended to work, so if this produces a missing trait impl error then that's a bug in Element.
| ) => bail!("cannot scale layer separations when layers have not been determined"), | ||
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| ( | ||
| &cfg::Scalable::UniformLayerSep { ref mask, .. } | &cfg::Scalable::LayerSeps { ref mask, .. }, |
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hmmm I wonder why these changes are showing up here, did I not merge them into master?
src/tasks/filetypes/eigensols.rs
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| // Conversion factor phonopy uses to scale the eigenvalues to THz angular momentum. | ||
| // = sqrt(eV/amu)/angstrom/(2*pi)/THz | ||
| const SQRT_EIGENVALUE_TO_THZ: f64 = 15.6333043006705; | ||
| const SQRT_EIGENVALUE_TO_THZ: f64 = 15.6333043006705 * 0.208; |
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Yikes! We'll definitely need to figure out a better way to adjust this.
(also, you should document where the 0.208 comes from)
| } | ||
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| Ok(()) | ||
| } |
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Hmm I'll have to try and recall what the deal with this was, but I'd like to avoid just deleting this...
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