mkits is a python written tool containing many helpful initial- or post-processing commands for some popular first-principles calculation codes.
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install from pip
pip install mkits -
build and install from source
sudo python3 setup.py bdist_wheel pip3 install dist/thebuild.whl
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build quasi-crystalline structures with NGT tiling June 16rd 2023
A new class of NGT canvas has been added to builder.py, which can be used to generate different tiling based on provided patterns. A pattern can be defined with a xyz structure file:
8 rhombus Sr 0.000000000000000 0.000000000000000 0.570133113075200 Sr 6.700000001664639 0.000000000000000 0.570133113075200 Sr 12.502370208508770 3.350000000832320 0.570133113075200 Sr 5.802370206844132 3.350000000832320 0.570133113075200 Ti 3.720469533952320 0.811662040359627 0.000000000000000 Ti 9.000535361468776 2.349738153970408 0.000000000000000 O 5.085002927088206 1.225916194572862 0.944989785403200 O 7.634468076562175 2.039944845316493 0.944989785403200Here are three examples of patterns with different shapes (rhombus, square and triangle):
By using three patterns, a simple tiling from Cockayne-σ model can be plotted and the red dash lines indicate the boder of crystals.
Then we can try to generate whole NGT tiling and truncate crystals from it:
The next target is try to recognize the target tiling automatically and plot the canvas.
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nanotube builder May 23rd 2023
mkits: my DFT helper
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|----builder
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|----vasp_init
| |--------param : additional parameters
| |----❀---kgen : generate odd KPOINTS
| |----❀---vasp_gen_input : generate input files for VASP
| |--------dryrun : generate inputs for VASP, show details
| |--------dft : choose the functional
| |--------potpath : path to directory containing POTCAR
| |--------poscar : specify the structure file
| |--------prec : specify the calculation precision
| |--------wpath : specify the working path
| |--------execode : specify the mpirun code
| |----❀---gen2d : generate 2dimensional structures
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|----vasp_post
| |--------param : additional parameters
| |--------fname : input file name
| |----❀---extract_band : extract eigen value from vasprun.xml
| |----❀---extract_dos : extract total and partial DOS from vasprun.xml
| |----❀---structdiff : check the difference between 2 structures in angstrom
| |----❀---extract_conv_test: extract data from convergence test (vasp_init)
| |--------wpath : specify the working path
| |----❀---extract_xdatcar : extract the i-th structure from XDATCAR
| |----❀---mse_xdatcar : calculate the mean squared error
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|----wien_init
| |--------fpath : specify the working directory
| |--------fname : input file name
| |--------struct : input structure name
| |--------params : additional parameters
| |----❀---gen_born_struct : generate input files for BORN effective charge
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|----wien_post
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|----structgen
| |--------node_num : maximum nodes number of the layer
| |--------node_type : trigonal, layered structure
| |--------block_num : give the block number
| |--------fix_block : fix block
| |--------block_type : specify the block
| |--------random_kation : give the kation
| |--------random_anion : give the anion
| |--------test_strgen : do some test
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|----boltz2
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|----critic2
| |----❀---extract_gvh : extract the data from
| |--------inp : input files
| |--------out : specify the name of the output file
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|----fdmnes
| |----❀---gen_input : generate the input file for FDMNES
| |--------struct_file : path to the structure file
| |--------fpath : path to save output files
| |--------findex : specify the index
| |--------params : additional parameters
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k-mesh
kfix: 3 numbers separated by blank space. If redundant numbers are given, only the first three numbers will be considered. This parameter is to fix k-mesh in specific direction to a given number. "-1 -1 -1" means no fix, whereas "-1 -1 1" means fix the k-mesh in z-axis direction to 1.
kspacing: determines the number of k points.
$k_1 = 2\pi/a_1/\text{kspacing}$