Scripts I use to have a better experience with file manipulation and data analysis of VASP input and output files.
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analyze.py (main) - Takes output files from vasp and returns data of interest. Requires:
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reader.py - Contains the definition of the objects that read output files
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analysisalgs.py - Contains the data analysis procedures
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myfunctions.py - Contains useful functions
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usage: analyze.py [-h] [-f F_PATH] [--sd SUBDIR] [-i IGNORE [I ...]] [--MD] [--ads ADS [ADS ...]]
[--rep {io_step,F,F_n,e_step,E0,dE,Temp,E,m}]
optional arguments:
-h, --help show this help message and exit
-f, --folder F_PATH
--sd, --subdir, --sub-directory SUBDIR
-i, --ignore [I ...] directory names to ignore
--MD Molecular Dynamic analysis
--rep REP output summary (choices: {io_step, F, F_n, e_step, E0, dE, Temp, E, m})
--ads ADS [ADS ...] perform an energy differecne calculation
usage: analyze.py [+h] [+b BULK] [+a ADS] [++area [AREA]] [+v]
[part [part ...]]
positional arguments:
part paths to directories containing output files of the parts
optional arguments:
+h, ++help show this help message and exit
+b BULK, ++bulk BULK path to outputfiles of bulk material
+a ADS, ++ads ADS path to output files of adsorbate
++area [AREA] report Ediff / area (Default: [ from a and b cell vectors ])
+v include energy of parts in output
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DOS.py (main) - Takes density of state VASP output files and returns data of interest. Requires:
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densityofstates.py - Contains the definition of the objects that read and analyze DOSCAR file
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myfunctions.py - Contains useful functions
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usage: DOS.py [-h] [-n N [N ...]] [-e E [E ...]] [-l L [L ...]] [--e-range NEG POS] [--layers LAYERS]
[--dbc] [-w] [-p {s, p, d, sum}] [--name NAME] [-v] [directories [directories ...]]
positional arguments:
directories path to directories with DOS files to read (default: getpwd())
optional arguments:
-h, --help show this help message and exit
-n N [N ...] The index number of the atoms to be read (default: [])
-e E [E ...] Read info of atoms of selected elements (default: [])
-l L [L ...] Read info of atoms in selected layers (default: [])
--e-range NEG POS Range of energies for DOS calculations (first arg will be multiplied by -1)
--layers LAYERS Number of layers in structure (default: 4)
--dbc, --d-band-center get d-band center (default: False)
-w, --write write requested DOS data (default: False)
-p, -g, --graph, --plot [PLOT ... (choices: {s, p, d, sum})]
plot DOS for the specified orbitals (default: all)
--name NAME name of DOSCAR file to read (default: DOSCAR)
These scripts work with the ASE and pymatgen modules.
fix_layers.py - Takes an atom-like file (readable with ASE) and fixes a number of desired layers for selective dynamics
usage: fix_layers.py [-h] [--fix FIX] [-l N_LAYERS] [-p PAD] [-f FORMAT] [file]
positional arguments:
file filename (default: POSCAR)
optional arguments:
-h, --help show this help message and exit
--fix Number of layers (bottom-up) to be fixed (default: 2)
-l, --layers Number of layers in slab (default: 4)
-p, --pad extra text for output filename (default: .draft)
-f, --format format of file to read (default: None)
slab.py - generates a slab structure from a bulk structure. Needs myfunctions.py, fix_layers.py and createSlab.py.
usage: slab.py [-h] [-s SIZE [SIZE ...]] [--ss SLAB_SIZE] [-f FIX]
[-l N_LAYERS] [--vac VACUUM] [--slab SLAB] [--format FORMAT]
[-p PAD]
bulk face [face ...]
positional arguments:
bulk bulk as reference for data
face build orthogonal cell
optional arguments:
-h, --help show this help message and exit
-s SIZE [SIZE ...], --size SIZE [SIZE ...]
repetitions of unit cell (default: (1, 1, 1))
--ss SLAB_SIZE, --slab_size SLAB_SIZE
height of the slab (default: 10.0)
-f FIX, --fix FIX number of layers to be fixed (default: 0)
-l N_LAYERS, --layers N_LAYERS
number of layers in slab for fixing atoms (default: 0)
--vac VACUUM, --vacuum VACUUM
separation between slabs in Angstroms (default: 13.0)
--slab SLAB existing slab to modify (default: None)
--format FORMAT fromat of input file (default: None)
-p PAD, --pad PAD extra text for output filename (default: .draft)
genSlab.py - Creates a monometallic fcc (111) structure with desired amount of vacuum and fixed layers.
usage: genSlab.py [-h] [-s SIZE SIZE SIZE] [-a A] [-c C] [-f FIX] [--layers N_LAYERS] [--vac VACUUM] [-o]
[--struct STRUCT] [--face FACE] [-p PAD] element
positional arguments:
element Symbol of element
optional arguments:
-h, --help show this help message and exit
-s SIZE SIZE SIZE, --size SIZE SIZE SIZE
times unit cell is repeated in each direction
(default: [4, 4, 4])
-a A lattice constant a in Angstroms (default: 1.0)
-c C lattice constant c in Angstroms (default: 1.0)
-f, --fix FIX number of layers to be fixed (default: 0)
--layers N_LAYERS number of layers in slab (default: 4)
--vac, --vacuum separation between slabs in Angstroms (default: 13.0)
-o, --orthogonal build orthogonal cell (default: False)
--struct, --structure Face Centered Cubic (default: fcc)
--face FACE build orthogonal cell (default: 111)
-p PAD, --pad PAD extra text for output filename (default: .draft)
convert.py - Convert between multiple file types (supported by ASE).
usage: convert.py [file] [new_format] [new_name] [-f old_format] [-n new_name]
positional arguments:
file old name (default: CONTCAR > POSCAR)
format new format (default: cif)
new_name new_name.format (default: file)
optional arguments:
-h, --help show this help message and exit
-f F old format
-n NAME, --name NAME overwrite new name
I will modify them as new functionality is needed.