Commit 69a0e206 authored by rym's avatar rym
Browse files

Updated UniqueStructureGetter() so the smallest structures found are returned

parent 72d39eb0

tests/.ipynb_checkpoints/Bi2Se3-checkpoint.vasp

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Original line number Diff line number Diff line 
Bi6 Se9

1.0

   2.0956832629406277   -3.6298298879848936    0.0000000000000000

   2.0956832629406277    3.6298298879848936    0.0000000000000000

   0.0000000000000000    0.0000000000000000   29.9286872022096198

Bi Se

6 9

direct

   0.6666666666666666    0.3333333333333333    0.7317683333333331 Bi

   0.6666666666666667    0.3333333333333333    0.9348983333333335 Bi

   0.3333333333333333    0.6666666666666666    0.0651016666666664 Bi

   0.3333333333333335    0.6666666666666666    0.2682316666666669 Bi

   0.0000000000000000    0.0000000000000000    0.3984349999999997 Bi

   0.0000000000000000    0.0000000000000000    0.6015650000000001 Bi

   0.0000000000000000    0.0000000000000000    0.0000000000000000 Se

   0.3333333333333333    0.6666666666666666    0.8823816666666666 Se

   0.0000000000000000    0.0000000000000000    0.7842850000000000 Se

   0.6666666666666666    0.3333333333333333    0.3333333333333333 Se

   0.0000000000000000    0.0000000000000000    0.2157149999999999 Se

   0.6666666666666666    0.3333333333333333    0.1176183333333334 Se

   0.3333333333333333    0.6666666666666666    0.6666666666666666 Se

   0.6666666666666666    0.3333333333333333    0.5490483333333334 Se

   0.3333333333333333    0.6666666666666666    0.4509516666666666 Se

tests/.ipynb_checkpoints/BiSe2-checkpoint.vasp

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Bi1 Se2                                 

   1.0000000000000000     

     2.1374500927939288   -3.7021721593618948    0.0000000000000001

     2.1374500927939288    3.7021721593618948   -0.0000000000000000

     0.0000000000000002    0.0000000000000005    5.2079269346228720

   Bi   Se

     1     2

Direct

 -0.0000000000000000 -0.0000000000000000  0.4999996996133689

  0.3333333333333357  0.6666666666666643  0.1834668511024066

  0.6666666666666643  0.3333333333333357  0.8165331488975933



  0.00000000E+00  0.00000000E+00  0.00000000E+00

  0.00000000E+00  0.00000000E+00  0.00000000E+00

  0.00000000E+00  0.00000000E+00  0.00000000E+00
 
 No newline at end of file

tests/.ipynb_checkpoints/example-checkpoint.ipynb

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%% Cell type:code id:5647de5b-5ac4-41a1-b215-b319b8a75844 tags:



``` python

# package imports

from pymatgen.analysis.interfaces.zsl import ZSLGenerator

from pymatgen.core.structure import Structure

from ase.visualize import view

import numpy as np

from datetime import datetime



# class imports

from vdW_structures.vdW_structure import VdWStructure

from vdW_structures.vdW_heterostructure import VdWHeterostructureGenerator

from vdW_structures.layer_shifter import LayerShifter

from vdW_structures.unique_structures import UniqueStructureGetter

```



%% Cell type:markdown id:98fe58e1-bd90-43ee-8c96-cdfac46bf82d tags:



## Input Bulk Structures



%% Cell type:code id:4e69fc4f-4bee-4553-9018-1de3d3b190d8 tags:



``` python

bise2 = Structure.from_file('original_structures/BiSe2.vasp')

bi2se3 = Structure.from_file('original_structures/Bi2Se3.vasp')

bi3se4 = Structure.from_file('original_structures/Bi3Se4.vasp')

bi4se3 = Structure.from_file('original_structures/Bi4Se3.vasp')

test = bi3se4

```



%% Cell type:markdown id:039df08c-8f63-4d5a-8857-6bd2866a0e59 tags:



## Generate Starting vdW Subunits for BiSe2, Bi2Se3, Bi3Se4



%% Cell type:code id:fb3ed4e8-ecf3-4d15-a168-e9a979b8b20b tags:



``` python

vdW_bi2se3 = VdWStructure(bi2se3, minimum_vdW_gap=2.4)

vdW_bi3se4 = VdWStructure(bi3se4, minimum_vdW_gap=2.4)

vdW_bise2 = VdWStructure(bise2, minimum_vdW_gap=1.9)



# Note: the vdW_bise2 structure has a smaller minimum vdW gap than vdW_bi2se3 and vdW_bi3se4, which could cause issues

# To make this VdWStructure commensurate, create a vdW_gap in bise2 that is > 2.4



#This can be done two ways (equivalent for this system):



# Add vacuum to vdW_bise2. This works because bise2 is a single vdW unit.

vdW_bise2_first = VdWStructure(vdW_bise2.set_vacuum(vacuum=2.41).structure, minimum_vdW_gap=2.4)

print(vdW_bise2_first.vdW_layers, vdW_bise2_first.vdW_spacings)



# Or, add padding to vdW layer 0 in vdW_bise2. This is how to change layer distances when multiple layers exist in a structure.

vdW_bise2_second = VdWStructure(vdW_bise2.z_solve_shift_vdW_layers(layer_inds=0,

                                                            solve_shift=2.41,

                                                            adjust_z_cell=True).structure,

                         minimum_vdW_gap=2.4)

print(vdW_bise2_second.vdW_layers, vdW_bise2_second.vdW_spacings)

```



%% Output



    [[1, 0, 2]] [2.41]

    [[1, 0, 2]] [2.41]



%% Cell type:code id:a2e9d9d3-16bb-4741-a8fa-222e7fc03ab8 tags:



``` python

# Look at the arrangement of vdW layers (by structure indices) and interlayer distances between the layers

print(vdW_bi2se3.vdW_layers, vdW_bi2se3.vdW_spacings)

print(vdW_bi3se4.vdW_layers, vdW_bi3se4.vdW_spacings)

print(vdW_bise2_second.vdW_layers, vdW_bise2_second.vdW_spacings)

```



%% Output



    [[10, 3, 9, 4, 14], [13, 5, 12, 0, 8], [7, 1, 6, 2, 11]] [2.9359044522460795, 2.9359044522460938, 2.9359044522460884]

    [[9, 1, 12, 3, 15, 5, 14], [13, 4, 16, 6, 19, 8, 18], [17, 7, 20, 0, 11, 2, 10]] [3.0050793718446416, 3.0050793718446407, 3.0050793718446407]

    [[1, 0, 2]] [2.41]



%% Cell type:code id:e850ce93-92fb-4e41-b253-31feeaaee138 tags:



``` python

# View the vdW_bise2_second structure

view(vdW_bise2_second.structure.to_ase_atoms(), viewer='ngl')

```



%% Output





    HBox(children=(NGLWidget(), VBox(children=(Dropdown(description='Show', options=('All', 'Bi', 'Se'), value='Al…



%% Cell type:code id:f2231b75-695b-4efd-be44-d91bfcf0e2e4 tags:



``` python

# Choose which layers you'd like to include in the heterostructure construction

# For the current example, it's sufficient to use a single vdW layer from each structure



subunit_vdW_bi2se3_0 = vdW_bi2se3.extend_vdW_layers([0])

subunit_vdW_bi3se4_1 = vdW_bi3se4.extend_vdW_layers([1])

subunit_vdW_bise2_0 = vdW_bise2_second.extend_vdW_layers([0])

```



%% Cell type:code id:237268a4-e426-43b5-8a5e-01e64b9bb055 tags:



``` python

# Look at the Bi2Se3 subunit, with the appropriate vdW gap across the PBC

view(subunit_vdW_bi2se3_0.structure.to_ase_atoms(), viewer='ngl')

```



%% Output



    HBox(children=(NGLWidget(), VBox(children=(Dropdown(description='Show', options=('All', 'Bi', 'Se'), value='Al…



%% Cell type:markdown id:54ad7b33-ecd1-4ec3-b5e7-25335651a5e8 tags:



## Generate vdW Heterostructures



%% Cell type:code id:3e53c9c7-8847-4bce-b865-1681a1c6fdde tags:



``` python

# This requires you to specify a ZSLGenerator structure, with the tolerances passed dictating the size(s) of vdW heterostructures generated



# This ZSL object yields four unique heterostructures for Bi2Se3 on Bi3Se4



bi2se3_bi3se4_zsl = ZSLGenerator(max_area_ratio_tol=0.5,

                                 max_area=150,

                                 max_length_tol=0.05,

                                 max_angle_tol=0.05)



vsg = VdWHeterostructureGenerator()

start = datetime.now()

vdW_heterostructures_bi2se3_bi3se4 = vsg.generate_unique_vdW_heterostructures(film=subunit_vdW_bi2se3_0,

                                                                              substrate=subunit_vdW_bi3se4_1,

                                                                              zsl_generator=bi2se3_bi3se4_zsl,

                                                                              n_chunks=4,

                                                                              ltol=0.2, stol=0.3, angle_tol=5)

end = datetime.now()

print(end - start)

# Print the lengths of the unique heterostructures

s_vdW_heterostructures_bi2se3_bi3se4 = sorted(vdW_heterostructures_bi2se3_bi3se4, key=lambda obj: len(obj.structure))





print([len(heterostructure.structure) for heterostructure in s_vdW_heterostructures_bi2se3_bi3se4])

```



%% Output



    /Users/rym/miniconda3/lib/python3.9/site-packages/spglib/spglib.py:115: DeprecationWarning: dict interface (SpglibDataset['wyckoffs']) is deprecated.Use attribute interface ({self.__class__.__name__}.{key}) instead

      warnings.warn(

    /Users/rym/miniconda3/lib/python3.9/site-packages/spglib/spglib.py:115: DeprecationWarning: dict interface (SpglibDataset['equivalent_atoms']) is deprecated.Use attribute interface ({self.__class__.__name__}.{key}) instead

      warnings.warn(



    Unique structures: 2

    Unique structures: 2

    Unique structures: 4

    Unique structures: 4

    Unique structures: 4

    0:00:12.435890

    [12, 24, 84, 84]



%% Cell type:code id:43caf0bd-7abe-42e7-8fba-5f1146767bf0 tags:



``` python

# We'll use the first heterostructure returned, which has the fewest # of atoms

view(vdW_heterostructures_bi2se3_bi3se4[0].structure.to_ase_atoms(), viewer='ngl')

```



%% Output



    HBox(children=(NGLWidget(), VBox(children=(Dropdown(description='Show', options=('All', 'Bi', 'Se'), value='Al…



%% Cell type:code id:ce0f96a9-4fe7-4760-bc73-c7bfedc730c0 tags:



``` python

# Add a BiSe2 film to this substrate

bise2_bi2se3_bi3se4_zsl = ZSLGenerator(max_area_ratio_tol=0.5,

                                 max_area=150,

                                 max_length_tol=0.05,

                                 max_angle_tol=0.05)



vdW_heterostructures_bise2_bi2se3_bi3se4 = vsg.generate_unique_vdW_heterostructures(film=subunit_vdW_bise2_0,

                                                                              substrate=vdW_heterostructures_bi2se3_bi3se4[0],

                                                                              zsl_generator=bise2_bi2se3_bi3se4_zsl)



# Print the lengths of the unique heterostructures

print([len(heterostructure.structure) for heterostructure in vdW_heterostructures_bise2_bi2se3_bi3se4])

```



%% Output



    /Users/rym/miniconda3/lib/python3.9/site-packages/spglib/spglib.py:115: DeprecationWarning: dict interface (SpglibDataset['wyckoffs']) is deprecated.Use attribute interface ({self.__class__.__name__}.{key}) instead

      warnings.warn(

    /Users/rym/miniconda3/lib/python3.9/site-packages/spglib/spglib.py:115: DeprecationWarning: dict interface (SpglibDataset['equivalent_atoms']) is deprecated.Use attribute interface ({self.__class__.__name__}.{key}) instead

      warnings.warn(



    Unique structures: 6

    Unique structures: 6

    Unique structures: 7

    Unique structures: 7

    Unique structures: 7

    [15, 30, 30, 45, 45, 60, 105]



%% Cell type:code id:8957dbcd-3039-4927-b582-c29b373eec41 tags:



``` python

# And view the first heterostructure generated

view(vdW_heterostructures_bise2_bi2se3_bi3se4[0].structure.to_ase_atoms(), viewer='ngl')

```



%% Output



    HBox(children=(NGLWidget(), VBox(children=(Dropdown(description='Show', options=('All', 'Bi', 'Se'), value='Al…



%% Cell type:code id:d44dfd9c-1d4a-41a9-9ae4-76d4fab4b50b tags:



``` python

# Generate a cubic supercell for easier viewing



from pymatgen.transformations.advanced_transformations import CubicSupercellTransformation

cst = CubicSupercellTransformation(force_90_degrees=True)



# Choose the heterostruture at index 3

index = 1

sc_heterostructure = VdWStructure(cst.apply_transformation(vdW_heterostructures_bise2_bi2se3_bi3se4[index].structure),

                                            vdW_heterostructures_bise2_bi2se3_bi3se4[index].minimum_vdW_gap)

```



%% Cell type:code id:63157904-a7fa-4597-baf4-f39e1b374c79 tags:



``` python

view(sc_heterostructure.structure.to_ase_atoms(), viewer='ngl')

```



%% Output



    HBox(children=(NGLWidget(), VBox(children=(Dropdown(description='Show', options=('All', 'Bi', 'Se'), value='Al…



%% Cell type:code id:d73e497e-abd2-4f7b-aad0-4dec4159e287 tags:



``` python

len(sc_heterostructure.structure)

```



%% Output



    240



%% Cell type:markdown id:c9f2ac4e-4d08-411b-8f74-d753efe3e621 tags:



## Modifying the Heterostructure



%% Cell type:markdown id:a4a15e07-dcc8-45dc-8e27-f4e5d78097b7 tags:



### Shift a layer within the fixed box



%% Cell type:code id:a14c9758-94a5-4159-8fb4-df8636c499df tags:



``` python

# Can be performed for x, y , or z directions, but we'll shift relative to z because it's easiest to visualize



z_shifted_layer_1 = sc_heterostructure.z_shift_vdW_layers(layer_inds=1,

                                                          shift=-1.0,

                                                          coords_are_cartesian=True)

view(z_shifted_layer_1.structure.to_ase_atoms(), viewer='ngl')

```



%% Output



    HBox(children=(NGLWidget(), VBox(children=(Dropdown(description='Show', options=('All', 'Bi', 'Se'), value='Al…



%% Cell type:markdown id:e2d16126-4ae8-46c0-9984-5952312e7527 tags:



### Increase interlayer distance, preserving other vdW spacings



%% Cell type:code id:59ea4315-6bfa-4b52-b4da-7e59efa05252 tags:



``` python

# Increase a layer and increase box to preserve vdW spacing

increased_gap_layer_2 = sc_heterostructure.z_solve_shift_vdW_layers(layer_inds=[2, 0],

                                                                    solve_shift=[2.8, 3.4],

                                                                    adjust_z_cell=True)

view(increased_gap_layer_2.structure.to_ase_atoms(), viewer='ngl')

```



%% Output



    HBox(children=(NGLWidget(), VBox(children=(Dropdown(description='Show', options=('All', 'Bi', 'Se'), value='Al…



%% Cell type:code id:f6ae9624-8e65-486c-a097-78dc06ff9516 tags:



``` python

print(increased_gap_layer_2.vdW_spacings)

```



%% Output



    [3.400000000000006, 2.9359044522460724, 2.7999999999999936]



%% Cell type:markdown id:beb807a4-5527-44c4-b621-8ceee62f6dc3 tags:



### Change the layering, so that it is Bi3Se4 - Bi2Se3 - BiSe2 - Bi2Se3



%% Cell type:code id:76d06136-4e29-4322-8ba0-d52fa2da6f33 tags:



``` python

modified_layering = sc_heterostructure.extend_vdW_layers([0, 1, 2, 1])

view(modified_layering.structure.to_ase_atoms(), viewer='ngl')

```



%% Output



    HBox(children=(NGLWidget(), VBox(children=(Dropdown(description='Show', options=('All', 'Bi', 'Se'), value='Al…



%% Cell type:code id:295e9f76-e8cc-4c12-952a-0d74369aac8b tags:



``` python

print(modified_layering.vdW_spacings)

```



%% Output



    [3.005079371844629, 2.935904452246076, 2.4099999999999824, 2.93590445224606]



%% Cell type:code id:e0a0322a-fdc5-4e98-b299-9a9012ffeaed tags:



``` python

```

tests/example.ipynb

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File added.

Preview size limit exceeded, changes collapsed.

tests/original_structures/Bi2Se3.vasp

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+23 −0
Original line number Diff line number Diff line 
Bi6 Se9

1.0

   2.0956832629406277   -3.6298298879848936    0.0000000000000000

   2.0956832629406277    3.6298298879848936    0.0000000000000000

   0.0000000000000000    0.0000000000000000   29.9286872022096198

Bi Se

6 9

direct

   0.6666666666666666    0.3333333333333333    0.7317683333333331 Bi

   0.6666666666666667    0.3333333333333333    0.9348983333333335 Bi

   0.3333333333333333    0.6666666666666666    0.0651016666666664 Bi

   0.3333333333333335    0.6666666666666666    0.2682316666666669 Bi

   0.0000000000000000    0.0000000000000000    0.3984349999999997 Bi

   0.0000000000000000    0.0000000000000000    0.6015650000000001 Bi

   0.0000000000000000    0.0000000000000000    0.0000000000000000 Se

   0.3333333333333333    0.6666666666666666    0.8823816666666666 Se

   0.0000000000000000    0.0000000000000000    0.7842850000000000 Se

   0.6666666666666666    0.3333333333333333    0.3333333333333333 Se

   0.0000000000000000    0.0000000000000000    0.2157149999999999 Se

   0.6666666666666666    0.3333333333333333    0.1176183333333334 Se

   0.3333333333333333    0.6666666666666666    0.6666666666666666 Se

   0.6666666666666666    0.3333333333333333    0.5490483333333334 Se

   0.3333333333333333    0.6666666666666666    0.4509516666666666 Se