shirtsgroup / lattice_dynamics Goto Github PK

Change all os.system calls to subprocess.call.

When using a pdb file, the properties recorded can get messed up due to rounding error. Things like volume and lattice parameter should be used directly from the spline and not pulled from the pdb file.

Give some examples in the README about how to call the programs to do particular calculations, so that I (or other users) can replicate your results. You can give example results in an example file so that people can check they are using the code correctly to replicate results.

Both test systems should have the parameter files included

sphinx or readthedocs could work well

Eigenvectors should be saved from the gruneisen parameter

There should be more consistent warning when the wave numbers are bad.
Tolerance of wavenumbers shouldn't just be a "more negative" criterion. They should be inclusive of just a general tolerance from zero (ie. catch positive ones as well).

When running Runge-Kutta, the final gradient at T_max does not receive the same output as previous runs and is not separated nicely.
When running Euler there is no separation between gradient calculations, which makes it hard to read.

Right now dG/dC is printed into numerical_checks.out. It would be nice to see dU_dC and dAv_dC there as well to help troubleshoot.

In the input.yaml file, if 'vol_fraction' and 'matrix_fractions' is unspecified, than the program will run a sensitivity analysis to determine the appropriate step size. These step sizes are used in the numerical calculation of the crystals thermal expansion when using the gradient approach.

The 'matrix_fractions' value is automatically updated in the .yaml file once they are determined. That is not the case for 'vol_fraction' and there is no place to save the lambda values. This would increase computational speed when re-running the simulation.

If the structure is not at a minimum the program can:

1. Go back to the previous step and take a smaller step size.
   OR
2. Will bail out and end the computation from continuing on.

Should be a set dV that is used across the entire run, which is not the case.

Move program specific functions into one files so that they're easy for people to edit

Right now, there are no flags or errors thrown if NumAnalysis_step is larger than Gradient_MaxTemp. Python returns an error, but the user wouldn't know what to do with this.

If one were to run 1D GaQg than the user would know if the lambda value is minimized, but it would be nice to know that it's at a minimum in 6D. A simple check at Tmax could be run to determine if the final structure is truly at a 6D minimum or just at a 1D minimum.

The saving of properties for phase diagrams or just temperature are in two different places. Bring them together to improve them.

Suggest changing the current 0README.txt to Markdown formatting and renaming it to README.md, so it pops up automatically in the GitHub web page.

During gradient runs, if we set:
Temperature = 0,100
But the numerical step size is 50, the output properties will be 0, 50, 100. Not the specified temperatures.

Computation of the Gruneisen Parameter or other approximations of the phonons should done prior to the division of methods

All properties are saved in the _raw.npy file, so sometimes we won't need the specific Gibbs free energy files or volume files. If output properties are left blank, than an error is raised. The _raw.npy file is still given.

Right now isotropic gradient, anisotropic gradient, and 1D-anisotropic gradient follow three separate paths.

1. Isotropic expansion can be written in terms of lattice parameters.
2. There are parts where the code can overlay better.

Run_LatticeDynamics.py requires a Properties.py, but that's not uploaded?

The EoS are only set-up to work for the pressure setup. They need to be implemented in the gradient approach.

Input file should be using JSON or YAML

The following files have general names during output:
numerical_checks.out, minimization.out, GRU_wvn.npy, GRU_eigen.npy

These should include the output tag '_' at the beginning so they aren't overwritten or re-used when user are trying to do multiple runs in a single directory.

numerical_outputs.out is not deleted after subsequent runs

Just an example here:

Assumptions made would prevent co-crystals to be computed w/o some type of error.

If there are temperatures in 'Temperature' higher than 'Gradient_MaxTemp' then the outputed data will include extra 0 values at the of the array, after Tmax.
This make plotting difficult and should be corrected (most likely in the spline section).

The *_Gru_organized_wavenumbers scripts can be condensed together. Also, the name is misleading, this doesn't have to do anything with the Gruneisen parameter specifically (it's just used in the process, but it can be multi-functional).

This one, I think, is legitimately not added :)