SIESTAstepper

SIESTAstepper runs SIESTA step by step, designed for constrained calculations.

Installation

Use the package manager pip to install SIESTAstepper.

pip install SIESTAstepper

Usage

All SIESTA working directories must be named as i1, i2, i3 ... and so on.

In code

import SIESTAstepper

#Sets the path of the working directory
SIESTAstepper.cwd = "path/to/working/directory"

#Sets the name of SIESTA log files (default is "log")
SIESTAstepper.log = "log"

#Sets number of cores for parallel run
SIESTAstepper.cores = 4

#Sets Anaconda environment
SIESTAstepper.conda = "envir"

# Runs SIESTA step by step
SIESTAstepper.run("graphene")

# Converts last geometry of an ANI to FDF by using the previous FDF and ANI files
SIESTAstepper.ani_to_fdf("path/to/ANI", "path/to/FDF", "path/to/newFDF")

# Converts XYZ to FDF by using the previous FDF and XYZ files
SIESTAstepper.xyz_to_fdf("path/to/XYZ", "path/to/FDF", "path/to/newFDF")

#Merges ANI files
SIESTAstepper.merge_ani(label = "graphene")

#Merges ANI files by setting a path
SIESTAstepper.merge_ani(label = "graphene", path = "path/to/i*/ANI/files")

#Merges ANI files by setting a missing files path
SIESTAstepper.merge_ani(label = "graphene", missing="path/to/i*/missing/ANI/files")

# Runs SIESTA a for given step
SIESTAstepper.run_next("1", "graphene")

# Plots and returns energies from log files
SIESTAstepper.analysis()

# Returns energies from log files without plotting
SIESTAstepper.analysis(plot_ = False)

# Plots and returns energies from log files by setting a path
SIESTAstepper.analysis(path = "path/to/i*/log/files")

# Plots and returns energies from log files by setting a missing files path
SIESTAstepper.analysis(missing = "path/to/i*/missing/log/files")

In terminal

python -m SIESTAstepper run log

python -m SIESTAstepper run log mpirun=4

python -m SIESTAstepper run log conda=envir

python -m SIESTAstepper run_next log 1 graphene

python -m SIESTAstepper run_next log 1 graphene mpirun=4

python -m SIESTAstepper run_next log 1 graphene conda=envir

python -m SIESTAstepper ani_to_fdf path/to/ANI path/to/FDF path/to/newFDF

python -m SIESTAstepper xyz_to_fdf path/to/XYZ path/to/FDF path/to/newFDF

python -m SIESTAstepper merge_ani graphene

python -m SIESTAstepper merge_ani graphene path=path/to/i*/ANI/files

python -m SIESTAstepper merge_ani graphene missing=path/to/i*/missing/ANI/files

python -m SIESTAstepper analysis log

python -m SIESTAstepper analysis log noplot

python -m SIESTAstepper analysis log path=path/to/i*/log/files

python -m SIESTAstepper analysis log missing=path/to/i*/missing/log/files

Contributing

Pull requests are welcome. For major changes, please open an issue first to discuss what you would like to change.

Please make sure to update tests as appropriate.

Citation

@software{eftal_gezer_2022_7062764,
  author       = {Eftal Gezer},
  title        = {eftalgezer/SIESTAstepper: v0.4.2},
  month        = sep,
  year         = 2022,
  publisher    = {Zenodo},
  version      = {v0.4.2},
  doi          = {10.5281/zenodo.7062764},
  url          = {https://doi.org/10.5281/zenodo.7062764}
}

License

GNU General Public License v3.0