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__pycache__
__pycache__
 
 
_build
_build
 
 
find_shared_pairs
find_shared_pairs
 
 
pyenergydiagram
pyenergydiagram
 
 
reference_files
reference_files
 
 
.gitignore
.gitignore
 
 
ASE processing.ipynb
ASE processing.ipynb
 
 
Adsorption ML.ipynb
Adsorption ML.ipynb
 
 
Amorphous adsorption ML.ipynb
Amorphous adsorption ML.ipynb
 
 
Bond distribution visualization.ipynb
Bond distribution visualization.ipynb
 
 
C focus.ipynb
C focus.ipynb
 
 
Cooling analysis.ipynb
Cooling analysis.ipynb
 
 
Elemental distribution.ipynb
Elemental distribution.ipynb
 
 
Energy diagramming.ipynb
Energy diagramming.ipynb
 
 
Fluorine loading analysis.ipynb
Fluorine loading analysis.ipynb
 
 
GAP fitting - Si example.ipynb
GAP fitting - Si example.ipynb
 
 
GAP fitting - SiN.ipynb
GAP fitting - SiN.ipynb
 
 
High throughput analysis - fluoromethanes.ipynb
High throughput analysis - fluoromethanes.ipynb
 
 
High throughput analysis-SiN bombardment.ipynb
High throughput analysis-SiN bombardment.ipynb
 
 
High throughput generation.ipynb
High throughput generation.ipynb
 
 
Keras.ipynb
Keras.ipynb
 
 
Makefile
Makefile
 
 
Metadynamics analysis.ipynb
Metadynamics analysis.ipynb
 
 
README.md
README.md
 
 
Repulsive potential fitting.ipynb
Repulsive potential fitting.ipynb
 
 
Si focus.ipynb
Si focus.ipynb
 
 
Trajectory analysis.ipynb
Trajectory analysis.ipynb
 
 
agg2lammps.py
agg2lammps.py
 
 
analysis.py
analysis.py
 
 
bond_dist.py
bond_dist.py
 
 
box_notation.py
box_notation.py
 
 
cart2dir.py
cart2dir.py
 
 
conf.py
conf.py
 
 
development.ipynb
development.ipynb
 
 
eigenval_analyze.py
eigenval_analyze.py
 
 
energyanimator.py
energyanimator.py
 
 
energydiagram.py
energydiagram.py
 
 
gap_si_surface.ipynb
gap_si_surface.ipynb
 
 
gapfit_tutorial.ipynb
gapfit_tutorial.ipynb
 
 
gen2pos.py
gen2pos.py
 
 
genvis.py
genvis.py
 
 
index.rst
index.rst
 
 
input_generation.py
input_generation.py
 
 
krr_utils.py
krr_utils.py
 
 
latticeconstmod.py
latticeconstmod.py
 
 
makewaterbox.py
makewaterbox.py
 
 
measure_damage_depth.py
measure_damage_depth.py
 
 
pbcprettify.py
pbcprettify.py
 
 
periodicprocess.py
periodicprocess.py
 
 
placeadsorbates.py
placeadsorbates.py
 
 
postprocessing.py
postprocessing.py
 
 
random_velos.py
random_velos.py
 
 
refstructs.py
refstructs.py
 
 
sandbox.ipynb
sandbox.ipynb
 
 
scratchwork.ipynb
scratchwork.ipynb
 
 
seed_monolayer.py
seed_monolayer.py
 
 
stitching.py
stitching.py
 
 
structure.py
structure.py
 
 
test.ipynb
test.ipynb
 
 
train_krr.py
train_krr.py
 
 
translatepos.py
translatepos.py
 
 
transmute.py
transmute.py
 
 
trim.py
trim.py
 
 
trimandseed.py
trimandseed.py
 
 
utils.py
utils.py
 
 
velos_extract_dftb
velos_extract_dftb
 
 
visualization.py
visualization.py
 
 
xyz2pos.py
xyz2pos.py
 
 
xyztopos.py
xyztopos.py
 
 

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researchscripts

A collection of Python3 scripts for working with simulation data from VASP and DFTB+.

Dependencies:

  • ASE
  • sklearn
  • numpy
  • pandas
  • dscribe

Documentation can be found here.

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