SIESTAstepper

SIESTAstepper

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

Installation

Use the package manager pip to install SIESTAstepper.

$ pip install SIESTAstepper

# to make sure you have the latest version
$ pip install -U SIESTAstepper

# latest available code base
$ pip install -U git+https://github.com/eftalgezer/SIESTAstepper.git

Tutorial

• SIESTAstepper v1.0.0 tutorial
• SIESTAstepper v1.1.0 tutorial
• What is new in SIESTAstepper v1.2.0?
• SIESTAstepper v2.0.0 tutorial

Usage

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

In code

Simple usage

SIESTAstepper.run("graphene")

Advance usage

import SIESTAstepper

# Sets the path of the working directory
SIESTAstepper.settings.set_cwd("path/to/working/directory")

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

# Sets number of cores for parallel run
SIESTAstepper.settings.set_cores(4)

# Sets Anaconda environment
SIESTAstepper.settings.set_conda("envir")

# Sets the subfolder name for interrupted calculations (default is "continue")
SIESTAstepper.settings.set_cont("continue")

# Sets the SIESTA command name (default is "siesta")
SIESTAstepper.settings.set_siesta("siesta_p")

#Sets the file type to continue next step (default is "log", possible values are "log", "XV", "ANI")
SIESTAstepper.settings.set_contfrom("ANI")

# Sets the filenames to copy (useful for interrupted calculations)
SIESTAstepper.settings.contfiles.extend(["file1", "file2"])

# Sets the extensions to copy (useful for interrupted calculations, default is ["psf, "fdf"]
SIESTAstepper.settings.contextensions.extend(["DM", "XV", "CG", "LWF"])

# 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")

# Creates GIF file from a given ANI
SIESTAstepper.ani_to_gif(anifile="graphene.ANI")

# Creates GIF file from a given ANI by setting width and height (defaults are 1920 and 1080, respectively)
SIESTAstepper.ani_to_gif(anifile="graphene.ANI", width=1920, height=1080)

# Creates GIF file from a given ANI by setting the bonds between atoms (default is 1.3)
SIESTAstepper.ani_to_gif(anifile="graphene.ANI", bonds_param=1.3)

# Creates GIF file from a given ANI by setting loop (default is 0; 0 means loop, 1 means no loop)
SIESTAstepper.ani_to_gif(anifile="graphene.ANI", loop=1)

# Creates GIF file from a given ANI by setting camera
SIESTAstepper.ani_to_gif(anifile="graphene.ANI", camera=((40, 0, 0),
                                                        (0, 0, 0),
                                                        (0, 1, 0)))

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

# Runs SIESTA for a given step without continuing to next step
SIESTAstepper.single_run("1", "graphene")

# Continues to an interrupted calculation without continuing to next step
SIESTAstepper.single_run_interrupted("1", "graphene")

# Continues to an interrupted calculation
SIESTAstepper.run_interrupted("1", "graphene")

# Creates folders named i1, i2, i3, i4, i5, ...
SIESTAstepper.make_directories(5)

# Copies files from i1 to i2
SIESTAstepper.copy_files(["psf", "fdf", "XV", "DM"], "graphene", "path/to/i1", "path/to/i2")

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

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

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

# Calculates the energy differences between minima and maxima
SIESTAstepper.energy_diff()

# Calculates the energy differences between minima and maxima by setting a path
SIESTAstepper.energy_diff(path = "path/to/i*/log/files")

# Plots and returns forces from log files (defaults are "Tot" and "atomic", respectively)
SIESTAstepper.force_analysis(atomindex="Tot", forcetype="atomic")

# Returns forces from log files without plotting
SIESTAstepper.force_analysis(plot_ = False)

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

# Calculates the force differences between minima and maxima (defaults are "Tot" and "atomic", respectively)
SIESTAstepper.force_diff(atomindex="Tot", forcetype="atomic")

# Calculates the force differences between minima and maxima by setting a path
SIESTAstepper.force_diff(path = "path/to/i*/log/files")

# Calculates the pair correlation function
SIESTAstepper.pair_correlation_function(label="graphene")

# Calculates the pair correlation function without plotting
SIESTAstepper.pair_correlation_function(label="graphene", plot_=True)

# Calculates the pair correlation function by setting a path
SIESTAstepper.pair_correlation_function(label="graphene", path="path/to/i*")

# Calculates the pair correlation function by setting infinitesimal dr parameter
SIESTAstepper.pair_correlation_function(label="graphene", dr=0.1)

In terminal

Simple usage

$ python -m SIESTAstepper run log graphene

Advance usage

$ python -m SIESTAstepper run log graphene

$ python -m SIESTAstepper run log graphene contfiles=file1,file2 contextensions=DM,XV,CG,LWF

$ python -m SIESTAstepper run log graphene mpirun=4

$ python -m SIESTAstepper run log graphene conda=envir

$ python -m SIESTAstepper run log graphene siesta=siesta_p

$ python -m SIESTAstepper run_next log 1 graphene

$ python -m SIESTAstepper run_next log 1 graphene contfiles=file1,file2 contextensions=DM,XV,CG,LWF

$ python -m SIESTAstepper run_next log 1 graphene mpirun=4

$ python -m SIESTAstepper run_next log 1 graphene conda=envir

$ python -m SIESTAstepper run_next log 1 graphene siesta=siesta_p

$ python -m SIESTAstepper single_run log 1 graphene

$ python -m SIESTAstepper single_run log 1 graphene mpirun=4

$ python -m SIESTAstepper single_run log 1 graphene conda=envir

$ python -m SIESTAstepper single_run log 1 graphene siesta=siesta_p

$ python -m SIESTAstepper run_interrupted log 1 graphene cont=continue

$ python -m SIESTAstepper run_interrupted log 1 graphene cont=continue contfiles=file1,file2 contextensions=DM,XV,CG,LWF

$ python -m SIESTAstepper run_interrupted log 1 graphene mpirun=4 cont=continue

$ python -m SIESTAstepper run_interrupted log 1 graphene conda=envir cont=continue

$ python -m SIESTAstepper run_interrupted log 1 graphene siesta=siesta_p cont=continue

$ python -m SIESTAstepper single_run_interrupted log 1 graphene cont=continue

$ python -m SIESTAstepper single_run_interrupted log 1 graphene mpirun=4 cont=continue

$ python -m SIESTAstepper single_run_interrupted log 1 graphene conda=envir cont=continue

$ python -m SIESTAstepper single_run_interrupted log 1 graphene siesta=siesta_p cont=continue

$ python -m SIESTAstepper make_directories 5

$ python -m SIESTAstepper copy_files graphene path/to/i1 path/to/i2 psf fdf XV DM

$ python -m SIESTAstepper copy_files graphene path/to/i1 path/to/i2 psf fdf XV DM

$ 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 cont=continue

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

$ python -m SIESTAstepper ani_to_gif graphene.ANI 1920 1080 1 1.3

$ python -m SIESTAstepper ani_to_gif graphene.ANI 1920 1080 1 1.3 camera=40,0,0,0,0,0,0,1,0

$ python -m SIESTAstepper energy_analysis log

$ python -m SIESTAstepper energy_analysis log cont=continue

$ python -m SIESTAstepper energy_analysis log noplot

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

$ python -m SIESTAstepper energy_diff log

$ python -m SIESTAstepper energy_diff log cont=continue

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

$ python -m SIESTAstepper force_analysis log atomic Tot

$ python -m SIESTAstepper force_analysis log atomic Tot cont=continue

$ python -m SIESTAstepper force_analysis log atomic Tot noplot

$ python -m SIESTAstepper force_analysis log atomic Tot path=path/to/i*/log/files

$ python -m SIESTAstepper force_diff log atomic Tot

$ python -m SIESTAstepper energy_diff log atomic Tot cont=continue

$ python -m SIESTAstepper energy_diff log atomic Tot path=path/to/i*/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

If you are using SIESTAstepper, please citate relevant version. You can find the relevant citation here.

@software{eftal_gezer_2022_7212472,
  author       = {Eftal Gezer},
  title        = {eftalgezer/SIESTAstepper: v2.1.0},
  month        = oct,
  year         = 2022,
  publisher    = {Zenodo},
  version      = {v2.1.0},
  doi          = {10.5281/zenodo.7212472},
  url          = {https://doi.org/10.5281/zenodo.7212472}
}

License

GNU General Public License v3.0

Acknowledgments

ani_to_gif function uses ANIAnimator.

References

Eftal Gezer. (2022). eftalgezer/ANIAnimator: v0.2.1 (v0.2.1). Zenodo. https://doi.org/10.5281/zenodo.7182193