(1) Installation

Using pip command to download autobskan

$ pip install autobskan

Or download via github, and unzip it.

$ pip install -r requirements.txt

$ python setup.py install

(2) Explanation of bskan.in input file.

MODE = CALCULATION / IMAGE / POST_PROCESSING

[tip] you can also type ca/im/po

a. Calculation Parts (Not supported yet)

VASP = command of executing VASP binary

BSKAN = command of excuting BSKAN binary

(ex. mpirun -np 8 ~/programs/VASP/norm_std.x > stdout.log)

METHOD = TH (Tersoff Hamann) / CHEN / BARDEEN (Numerical)

[tip] you can also write th(or te) / ch / ba(or nu)

BIAS = start_end_steps & value

1. If you put separator "_", it is regarded as MIN_MAX_INCREMENTS to make list of input bias values.

   For example, -0.01_0.03_0.02 will be regarded as [-0.01, 0.01, 0.03].

2. If you put separator "&", it is regarded as ingredients of lists.

   For example, 0.02 & 0.05 will be regarded as [0.02, 0.05].

3. Or you can write the combination of 1) and 2).

   For example, "-0.05_0.01_0.02 & 0.00" will give you array([-0.05, -0.03, -0.01, 0., 0.01])

+) Space will be ignored. Do not worry about this.

b. Image Parts

CURRENT = filename of CURRENT. [Default = CURRENT]

• For filenames, multiple choices are also possible. (Must be divided by "&")
• Or, following Regular expressions. (ex. '*current' indicates all files which have 'current' words in the last.)

ISO_AUTO = True / False / LOGSCALE [Default = LOGSCALE]

[tip] you can also type t/f/l

ISO = value(s) / numbers of wanted isosurface values.

1. When ISO_AUTO = True, ISO will be the number of isosurface values. [Default = 5]

   • ex) generate 5 images when ISO = 5

2. When ISO_AUTO = False, ISO will be the exact value of isosurface. (Same format of BIAS input)

   • ex1) 2500_1e4_2500 will be regarded as [2500., 5000., 7500., 10000.]
   • ex2) 1e3 & 1e4 & 1e5 will be regarded as [1000., 10000., 100000.]

3. When ISO_AUTO = LOGSCALE, ISO will be possible 10^x value

   • here, x will be set automatically from minimum to maximum. (2020.08.29 updated)
   • +) input ISO value will be ignored

CMAP = name of colormap [Default = afmhot]

Colomaps are following matplotlib.pyplot cmaps

CONTRAST = 0

• normalization factor (float). 0 is default, which is linear normalization.
• value from -1 to 1 is recommended, and usually absolte value within 0.2 is enough.

BRIGHTNESS = -1 ~ 0[Default] ~ 1

CONTOUR_RESOLUTION = 200

EXT = Wanted extension type or raw_images. [Default = png]

POSCAR = filename of structure file. vasp5 POSCAR format is supported.

ATOM_ADDINFO = If you want manual setting of Atomic size and colors, you can put the filename with atomic informations.

• Default setting is identical to default setting of VESTA program
• For example, if you want to change the size and color of hydrogen atom, to 1.5 Angstrom and white color,
• You can set ATOM_ADDINFO = element.txt in bskan.in which includes information of H by following commands,
• $echo 'H 1.5 255 255 255' > elements.txt

LAYERS = number of layers to plot from surface. [Default = 1]

RADIUS_TYPE = atomic / van der Waals / ionic radius [Default = ATOMIC]

[tip] you can also type a / v / i

SIZE_RATIO = marker size ratio of atoms [Default = 30]

c. Postprocessing Parts

POST_PROCESSING = Precede to the post_processing process or not. [Default = FALSE]

ITERATION = nx, ny [Default = 4, 4] # iterations along x / y axis

BLUR_METHOD = GAUSSIAN [Default] # For now, there is only one choice (Gaussian).

BLUR_SIGMA = Postive number [Default = 10]

GAMMA = Manual input gamma value of lattice parameter. Using in iteration process. [Default = 90]

Only when there is no POSCAR file. If POSCAR file exists, it will automatically calculate this value.