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/hetero2d/manipulate/layersolver.py:
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1 | # coding: utf-8
2 | # Copyright (c) CMD Lab Development Team.
3 | # Distributed under the terms of the GNU License.
4 |
5 | """
6 | Analyze an existing structure and parse it based on atomic layers. The cutoff can be changed but defaults to 0.5
7 | Angstroms. Returns a LayeredStructure dictionary.
8 | """
9 | import numpy as np
10 | from copy import deepcopy
11 | from operator import itemgetter
12 |
13 | from pymatgen.core.structure import Structure
14 | from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
15 |
16 |
17 | __author__ = "Sydney Olson"
18 | __copyright__ = "Copyright 2022, CMD Lab"
19 | __maintainer__ = "Tara M. Boland"
20 | __email__ = "tboland1@asu.edu, snolson1@asu.edu"
21 | __date__ = "June 9, 2022"
22 |
23 |
24 | def LayerSolver(structure, cutoff=0.5):
25 | """
26 | Group sites in a structure into layers according to z-coordinate. Return layer specific data such as the
27 | z-coordinate of layer, a list of sites, the species of elements in the layer and the atom indices of that layer.
28 |
29 | Args:
30 | structure (Structure): Input structure to be analyzed.
31 | cutoff (float): The inter-layer separation distance that the algorithm searches for.
32 |
33 | Returns:
34 | Layers dictionary returning layer specific information: each layer information is encoded with dictionary key
35 | num_layers (int): number of layers in the structure and Layer{i} with sub-keys
36 | avg_z (float): average z-coordinate of the layer
37 | sites (list of PeriodicSite): PeriodicSites for each site within the layer
38 | species (list): elemental species of each site within the layer
39 | site_idx (list): atom indices for species within the layer
40 | wyckoffs (list): wyckoff symbols for each site in the layer
41 | """
42 | # ensure structure is pymatgen structure obj
43 | if not isinstance(structure, Structure):
44 | # return print('Structure must be a pymatgen structure object.')
45 | print('Structure must be a pymatgen structure object.')
46 |
47 | # add wyckoff to site_property
48 | sga = SpacegroupAnalyzer(structure)
49 | sym_data = sga.get_symmetry_dataset()
50 | wyckoffs = sym_data['wyckoffs']
51 | structure.add_site_property('wyckoffs', values=wyckoffs)
52 |
53 | # add site indices & z_value to sort structure & track sites
54 | dict_structure = structure.as_dict() # dictionary rep of struct
55 | [site.update({'index': idx, 'z_value': site['xyz'][2]})
56 | for idx, site in enumerate(dict_structure['sites'])]
57 |
58 | # sort sites based on z value
59 | dict_structure['sites'] = sorted(dict_structure['sites'], key=itemgetter('z_value'))
60 |
61 | # get lower & upper z value searching bounds
62 | z0 = dict_structure['sites'][0]['z_value']
63 | z1 = dict_structure['sites'][-1]['z_value']
64 |
65 | # initialized return data and layer counter
66 | n = 0 # number of layers to track
67 | z = deepcopy(z0) # starting z value
68 | layered_structure = {} # layer dependent dict
69 |
70 | while z <= z1:
71 | layer_indices = [] # layer atom indices
72 | layer_sites = [] # site dictionary object
73 | layer_wyc = [] # site wyckoff labels for each atom
74 |
75 | # search for all sites within [z,z+cutoff]
76 | # all sites found within this range compose a layer
77 | for site in dict_structure['sites']:
78 | if z <= site['z_value'] <= z + cutoff:
79 | layer_indices.append(site['index'])
80 | layer_sites.append(structure[site['index']])
81 | layer_wyc.append(site['properties']['wyckoffs'])
82 |
83 | # only analyze data if it exists
84 | if layer_indices:
85 | # compute: average z-coordinate for all layer sites &
86 | # return layer species
87 |
88 | z_cords = [layer_site.z for layer_site in layer_sites]
89 | layer_species = [layer_site.species_string for layer_site in layer_sites]
90 | average_z = sum(z_cords) / len(z_cords)
91 |
92 | # dictionary of layer information computed
93 | layered_structure["Layer{}".format(n)] = {'avg_z': average_z,
94 | 'sites': layer_sites, 'species': list(np.unique(layer_species)),
95 | 'site_idx': layer_indices, 'wyckoffs': layer_wyc}
96 | n += 1 # increment the layer number
97 |
98 | # add cutoff to z to search next z area
99 | z += cutoff
100 | layered_structure['num_layers'] = n
101 |
102 | return layered_structure
103 |
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77 | Welcome to Hetero2d’s documentation!¶
69 |
70 |
76 | Contents:
71 |-
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- Project Introduction 73 |
- Documentation 74 |
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87 | Indices and tables¶
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102 | Project Introduction¶
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- Introduction
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- Package Description 80 |
- Examples 81 |
- How to cite Hetero2d 82 |
- License 83 |
- About the Team 84 |
- Copyright Policy 85 |
87 | - Installing Hetero2d
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91 | - Development Team
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96 | - References 97 |
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107 | References¶
77 |Some of Hetero2d’s functionality is based on scientific advances / principles developed by various scientists. If you use Hetero2d in your research, you may wish to consider citing the following works:
78 |79 |104 |Shyue Ping Ong, William Davidson Richards, Anubhav Jain, Geoffroy 80 | Hautier, Michael Kocher, Shreyas Cholia, Dan Gunter, Vincent 81 | Chevrier, Kristin A. Persson, Gerbrand Ceder. Python Materials 82 | Genomics (pymatgen) : A Robust, Open-Source Python Library for 83 | Materials Analysis. Computational Materials Science, 2013, 68, 314– 84 | 319. doi:10.1016/j.commatsci.2012.10.028
85 |Mathew, K., Singh, A. K., Gabriel, J. J., Choudhary, K., Sinnott, 86 | S. B., Davydov, A. V, Hennig, R. G. MPInterfaces : A Materials 87 | Project based Python tool for high-throughput computational screening 88 | of interfacial systems. Computational Materials Science, 2016, 122, 89 | 183–190. dio:10.1016/j.commatsci.2016.05.020
90 |Zur, A., & McGill, T. C. Lattice match: An application to 91 | heteroepitaxy. Journal of Applied Physics, 1984, 55, 378–386. 92 | dio:10.1063/1.333084
93 |Mathew, K., Montoya, J. H., Faghaninia, A., Dwarakanath, S., 94 | Aykol, M., Tang, H., Chu, I., Smidt, T., Bocklund, B., Horton, M., 95 | Dagdelen, J., Wood, B., Liu, Z.-K., Neaton, J., Ong, S. P., 96 | Persson, K., Jain, A. Atomate: A high-level interface to generate, 97 | execute, and analyze computational materials science workflows. 98 | Comput. Mater. Sci. 2017, 139, 140–152.
99 |Singh, A. K., Zhuang, H. L., & Hennig, R. G. Ab initio synthesis 100 | of single-layer III-V materials. Physical Review B - Condensed 101 | Matter and Materials Physics, 2014, 89, 1–10. 102 | dio:10.1103/PhysRevB.89.245431
103 |
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112 | hetero2d¶
68 |
69 |
109 | -
70 |
- Project Introduction
-
71 |
- Introduction
-
72 |
- Package Description 73 |
- Examples 74 |
- How to cite Hetero2d 75 |
- License 76 |
- About the Team 77 |
- Copyright Policy 78 |
80 | - Installing Hetero2d
-
81 |
- Setting up dependancies 82 |
84 | - Development Team
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85 |
- Lead Maintainers 86 |
- List of Developers (A-Z) 87 |
89 | - References 90 |
92 | - Introduction
- Documentation
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93 |
- hetero2d package
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94 |
- Subpackages
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95 |
- hetero2d.firetasks package 96 |
- hetero2d.fireworks package 97 |
- hetero2d.io package 98 |
- hetero2d.manipulate package 99 |
- hetero2d.workflow package 100 |
102 | - Module contents 103 |
105 | - Subpackages
107 | - hetero2d package
25 |
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80 |
103 |
104 |
105 | Development Team¶
81 |Hetero2d currently has a small development team.
82 |
83 |
95 | Lead Maintainers¶
84 |
85 |
89 | Arunima K. Singh 
86 | Assistant Professor, Department of Physics
87 | Arizona State University, Tempe
88 |
90 |
94 | Tara M. Boland
91 | PhD Candidate, Materials Science and Engineering
92 | Arizona State University, Tempe
93 |
96 |
102 | List of Developers (A-Z)¶
97 |
98 |
101 | Syd Olson
99 | Arizona State University, Tempe
100 |
26 |
48 |
49 |
53 |
54 |
182 |
183 |
188 |
189 |
190 |
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161 |
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163 |
164 | Python Module Index
70 | 71 |
72 | h
73 |
74 |
75 | | 78 | h | ||
| 82 | |
83 | hetero2d | 84 | |
| 87 | |
88 | hetero2d.firetasks | 89 | |
| 92 | |
93 | hetero2d.firetasks.heteroiface_tasks | 94 | |
| 97 | |
98 | hetero2d.firetasks.parse_outputs | 99 | |
| 102 | |
103 | hetero2d.firetasks.run_calc | 104 | |
| 107 | |
108 | hetero2d.firetasks.write_inputs | 109 | |
| 112 | |
113 | hetero2d.fireworks | 114 | |
| 117 | |
118 | hetero2d.fireworks.core | 119 | |
| 122 | |
123 | hetero2d.io | 124 | |
| 127 | |
128 | hetero2d.io.VaspInterfaceSet | 129 | |
| 132 | |
133 | hetero2d.manipulate | 134 | |
| 137 | |
138 | hetero2d.manipulate.heterotransmuter | 139 | |
| 142 | |
143 | hetero2d.manipulate.layersolver | 144 | |
| 147 | |
148 | hetero2d.manipulate.utils | 149 | |
| 152 | |
153 | hetero2d.workflow | 154 | |
| 157 | |
158 | hetero2d.workflow.core | 159 | |
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151 |
152 |
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/hetero2d/firetasks/write_inputs.py:
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1 | # coding: utf-8
2 | # Copyright (c) CMD Lab Development Team.
3 | # Distributed under the terms of the GNU License.
4 |
5 | """
6 | These classes write the vasp input sets used to control VASP tags.
7 | """
8 | from __future__ import division, print_function, unicode_literals, absolute_import
9 |
10 | import os
11 | from importlib import import_module
12 |
13 | from atomate.utils.utils import get_logger
14 | from fireworks.core.firework import FiretaskBase
15 | from fireworks.utilities.fw_utilities import explicit_serialize
16 | from pymatgen.alchemy.materials import TransformedStructure
17 | from pymatgen.alchemy.transmuters import StandardTransmuter
18 | from pymatgen.core import Structure
19 | from pymatgen.io.vasp import Poscar
20 | from pymatgen.transformations.site_transformations import AddSitePropertyTransformation
21 |
22 | from hetero2d.io import CMDLElectronicSet
23 | from hetero2d.manipulate.utils import set_sd_flags
24 |
25 | __author__ = 'Tara M. Boland'
26 | __email__ = 'tboland1@asu.edu'
27 | __copyright__ = "Copyright 2022, CMD Lab"
28 | __maintainer__ = "Tara M. Boland"
29 | __date__ = "June 09, 2022"
30 |
31 | logger = get_logger(__name__)
32 |
33 | @explicit_serialize
34 | class WriteVaspElectronicFromPrev(FiretaskBase):
35 | """
36 | Writes input files to perform bader analysis, density of states, and charge
37 | density difference calculations.
38 |
39 | Args:
40 | dedos (float): Automatically set nedos using the total energy range
41 | which will be divided by the energy step dedos. Default 0.05 eV.
42 | grid_density (float): Distance between grid points for the NGXF,Y,Z grids.
43 | Defaults to 0.03 Angs; NGXF,Y,Z are ~2x > default. For charge
44 | density difference calculations the parent grid density is used for all
45 | children fireworks.
46 | dos (bool): If True, sets INCAR tags for high quality site-orbital projected
47 | density of states. Defaults to True.
48 | bader (bool): If True, sets INCAR tags to generate bader analysis files.
49 | cdd (bool): If True, ensures the grid density matches between the parent
50 | and child Fireworks. Default set to False.
51 |
52 | Other Parameters:
53 | **kwargs (keyword arguments): Dict of any keyword arguments supported by the
54 | CMDLRelaxSet.from_prev_calc().
55 |
56 | """
57 | required_params = ["dedos", "grid_density", "dos", "bader", "cdd"]
58 |
59 | optional_params = ["prev_calc_dir", "small_gap_multiply", "nbands_factor", "electronic_set_overrides"]
60 |
61 | def run_task(self, fw_spec):
62 | # get previous calculation information and increase accuracy
63 | vis_orig = CMDLElectronicSet.from_prev_calc(prev_calc_dir=self.get("prev_calc_dir", "."),
64 | dedos=self.get("dedos", 0.05),
65 | grid_density=self.get("grid_density", 0.03),
66 | dos=self.get("dos", True ),
67 | bader=self.get("bader", True),
68 | cdd=self.get("cdd", False),
69 | nbands_factor=self.get("nbands_factor", 1),
70 | small_gap_multiply=self.get("small_gap_multiply", None),
71 | **self.get("electronic_set_overrides", {}))
72 |
73 | vis_dict = vis_orig.as_dict() # make changes to vis in dict format
74 | vis_orig.write_input(".")
75 |
76 | @explicit_serialize
77 | class WriteSlabStructureIOSet(FiretaskBase):
78 | """
79 | Apply the provided transformations to the input structure and write the
80 | input set for that structure. Reads structure from POSCAR if no structure
81 | provided. Note that if a transformation yields many structures from one,
82 | only the last structure in the list is used.
83 |
84 | Args:
85 | structure (Structure): Input structure.
86 | transformations (list): List of names of transformation classes as defined
87 | in the modules in pymatgen.transformations.
88 | vasp_input_set (VaspInputSet): VASP input set.
89 |
90 | Other Parameters:
91 | transformation_params (list): List of dicts where each dict specifies the
92 | input parameters to instantiate the transformation class in the
93 | transformations list.
94 | override_default_vasp_params (dict): Additional user input settings.
95 | prev_calc_dir (str): Path to previous calculation if using structure
96 | from another calculation.
97 |
98 | Returns:
99 | none
100 | """
101 |
102 | required_params = ["structure", "transformations", "vasp_input_set"]
103 | optional_params = ["prev_calc_dir", "transformation_params", "override_default_vasp_params"]
104 |
105 | def run_task(self, fw_spec):
106 | """
107 | Execute the transformations and write the input files for the calculation.
108 | """
109 | transformations = []
110 | transformation_params = self.get("transformation_params",
111 | [{} for i in range(len(self["transformations"]))])
112 | for t in self["transformations"]:
113 | found = False
114 | for m in ["advanced_transformations", "defect_transformations",
115 | "site_transformations", "standard_transformations"]:
116 | mod = import_module("pymatgen.transformations.{}".format(m))
117 | try:
118 | t_cls = getattr(mod, t)
119 | except AttributeError:
120 | continue
121 | t_obj = t_cls(**transformation_params.pop(0))
122 | transformations.append(t_obj)
123 | found = True
124 | if not found:
125 | raise ValueError("Could not find transformation: {}".format(t))
126 |
127 | structure = self['structure'] if not self.get('prev_calc_dir', None) else \
128 | Poscar.from_file(os.path.join(self['prev_calc_dir'], 'POSCAR')).structure
129 | ts = TransformedStructure(structure)
130 | transmuter = StandardTransmuter([ts], transformations)
131 | trans_structure = transmuter.transformed_structures[-1].final_structure.copy()
132 |
133 | # add selective dynamics tags
134 | aspt = AddSitePropertyTransformation({'selective_dynamics': set_sd_flags(
135 | interface=trans_structure, n_layers=fw_spec.get('nlayers_sub'),
136 | top=True, bottom=False)})
137 | final_structure = aspt.apply_transformation(trans_structure)
138 |
139 | # update vasp input with user overrides
140 | vis_orig = self["vasp_input_set"]
141 | vis_dict = vis_orig.as_dict()
142 | vis_dict["structure"] = final_structure.as_dict()
143 | vis_dict.update(self.get("override_default_vasp_params", {}) or {})
144 | vis = vis_orig.__class__.from_dict(vis_dict)
145 | vis.write_input(".")
146 |
147 | @explicit_serialize
148 | class WriteHeteroStructureIOSet(FiretaskBase):
149 | """
150 | Apply the provided transformations to the input 2D structure and
151 | substrate slab then write the input set for that simulation. Reads
152 | structure from POSCAR if no structure provided.
153 |
154 | Args:
155 | structure (Slab): 2D input structure to place on substrate. Valid
156 | parameters include all pymatgen structure objects.
157 |
158 | Other Parameters:
159 | vasp_input_set (VaspInputSet): VASP input set for the transformed 2d on sub-slab.
160 | override_default_vasp_params (dict): Additional user input settings.
161 | user_incar_settings (dict): Additional incar settings to add to the calculation.
162 |
163 | Returns:
164 | None
165 | """
166 | required_params = ["structure", "nlayers_sub", "nlayers_2d"]
167 | optional_params = ["user_incar_settings", "override_default_vasp_params",
168 | "vasp_input_set"]
169 |
170 | def run_task(self, fw_spec):
171 | '''
172 | Write the selective dynamics tags for the 2d-substrate heterostructure
173 | configuration and all calculation input file to the specified directory.
174 | '''
175 | structure = self['structure']
176 |
177 | # set selective dynamics for the 2D sub slab iface
178 | sd_flags = set_sd_flags(
179 | interface=structure,
180 | n_layers=self['nlayers_sub'] + self['nlayers_2d'],
181 | top=True, bottom=False)
182 | for idx, sd in enumerate(sd_flags):
183 | sd_flags[idx] = [True if j == 1.0 else False for j in sd]
184 | structure.add_site_property('selective_dynamics', sd_flags)
185 |
186 | # write vasp input
187 | vis_orig = self["vasp_input_set"] # get vis passed to FW
188 | vis_dict = vis_orig.as_dict() # editable
189 | vis_dict["structure"] = structure.as_dict() # update structure
190 | vis_dict.update(self.get("override_default_vasp_params",
191 | {}) or {}) # override defaults
192 | vis_dict['user_incar_settings'].update(self.get("user_incar_settings", {})) # uis
193 | vis = vis_orig.__class__.from_dict(vis_dict) # update the vis
194 | vis.write_input(".")
195 |
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72 |
120 |
121 |
122 | hetero2d¶
73 |
74 |
119 | -
75 |
- hetero2d package
-
76 |
- Subpackages
-
77 |
- hetero2d.firetasks package 85 | 86 |
- hetero2d.fireworks package
-
87 |
- Submodules 88 |
- hetero2d.fireworks.core module 89 |
- Module contents 90 |
92 | - hetero2d.io package
-
93 |
- Submodules 94 |
- hetero2d.io.VaspInterfaceSet module 95 |
- Module contents 96 |
98 | - hetero2d.manipulate package
-
99 |
- Submodules 100 |
- hetero2d.manipulate.heterotransmuter module 101 |
- hetero2d.manipulate.layersolver module 102 |
- hetero2d.manipulate.utils module 103 |
- Module contents 104 |
106 | - hetero2d.workflow package
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107 |
- Submodules 108 |
- hetero2d.workflow.core module 109 |
- Module contents 110 |
112 |
114 | - Module contents 115 |
117 | - Subpackages
25 |
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66 |
67 |
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156 |
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162 |
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131 |
132 |
133 | hetero2d package¶
85 |
86 |
127 | Subpackages¶
87 |
88 |
126 | -
89 |
- hetero2d.firetasks package 97 | 98 |
- hetero2d.fireworks package
-
99 |
- Submodules 100 |
- hetero2d.fireworks.core module 101 |
- Module contents 102 |
104 | - hetero2d.io package
-
105 |
- Submodules 106 |
- hetero2d.io.VaspInterfaceSet module 107 |
- Module contents 108 |
110 | - hetero2d.manipulate package
-
111 |
- Submodules 112 |
- hetero2d.manipulate.heterotransmuter module 113 |
- hetero2d.manipulate.layersolver module 114 |
- hetero2d.manipulate.utils module 115 |
- Module contents 116 |
118 | - hetero2d.workflow package
-
119 |
- Submodules 120 |
- hetero2d.workflow.core module 121 |
- Module contents 122 |
124 |
128 |
130 | Module contents¶
129 |
25 |
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1 | /*
2 | * doctools.js
3 | * ~~~~~~~~~~~
4 | *
5 | * Sphinx JavaScript utilities for all documentation.
6 | *
7 | * :copyright: Copyright 2007-2020 by the Sphinx team, see AUTHORS.
8 | * :license: BSD, see LICENSE for details.
9 | *
10 | */
11 |
12 | /**
13 | * select a different prefix for underscore
14 | */
15 | $u = _.noConflict();
16 |
17 | /**
18 | * make the code below compatible with browsers without
19 | * an installed firebug like debugger
20 | if (!window.console || !console.firebug) {
21 | var names = ["log", "debug", "info", "warn", "error", "assert", "dir",
22 | "dirxml", "group", "groupEnd", "time", "timeEnd", "count", "trace",
23 | "profile", "profileEnd"];
24 | window.console = {};
25 | for (var i = 0; i < names.length; ++i)
26 | window.console[names[i]] = function() {};
27 | }
28 | */
29 |
30 | /**
31 | * small helper function to urldecode strings
32 | */
33 | jQuery.urldecode = function(x) {
34 | return decodeURIComponent(x).replace(/\+/g, ' ');
35 | };
36 |
37 | /**
38 | * small helper function to urlencode strings
39 | */
40 | jQuery.urlencode = encodeURIComponent;
41 |
42 | /**
43 | * This function returns the parsed url parameters of the
44 | * current request. Multiple values per key are supported,
45 | * it will always return arrays of strings for the value parts.
46 | */
47 | jQuery.getQueryParameters = function(s) {
48 | if (typeof s === 'undefined')
49 | s = document.location.search;
50 | var parts = s.substr(s.indexOf('?') + 1).split('&');
51 | var result = {};
52 | for (var i = 0; i < parts.length; i++) {
53 | var tmp = parts[i].split('=', 2);
54 | var key = jQuery.urldecode(tmp[0]);
55 | var value = jQuery.urldecode(tmp[1]);
56 | if (key in result)
57 | result[key].push(value);
58 | else
59 | result[key] = [value];
60 | }
61 | return result;
62 | };
63 |
64 | /**
65 | * highlight a given string on a jquery object by wrapping it in
66 | * span elements with the given class name.
67 | */
68 | jQuery.fn.highlightText = function(text, className) {
69 | function highlight(node, addItems) {
70 | if (node.nodeType === 3) {
71 | var val = node.nodeValue;
72 | var pos = val.toLowerCase().indexOf(text);
73 | if (pos >= 0 &&
74 | !jQuery(node.parentNode).hasClass(className) &&
75 | !jQuery(node.parentNode).hasClass("nohighlight")) {
76 | var span;
77 | var isInSVG = jQuery(node).closest("body, svg, foreignObject").is("svg");
78 | if (isInSVG) {
79 | span = document.createElementNS("http://www.w3.org/2000/svg", "tspan");
80 | } else {
81 | span = document.createElement("span");
82 | span.className = className;
83 | }
84 | span.appendChild(document.createTextNode(val.substr(pos, text.length)));
85 | node.parentNode.insertBefore(span, node.parentNode.insertBefore(
86 | document.createTextNode(val.substr(pos + text.length)),
87 | node.nextSibling));
88 | node.nodeValue = val.substr(0, pos);
89 | if (isInSVG) {
90 | var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect");
91 | var bbox = node.parentElement.getBBox();
92 | rect.x.baseVal.value = bbox.x;
93 | rect.y.baseVal.value = bbox.y;
94 | rect.width.baseVal.value = bbox.width;
95 | rect.height.baseVal.value = bbox.height;
96 | rect.setAttribute('class', className);
97 | addItems.push({
98 | "parent": node.parentNode,
99 | "target": rect});
100 | }
101 | }
102 | }
103 | else if (!jQuery(node).is("button, select, textarea")) {
104 | jQuery.each(node.childNodes, function() {
105 | highlight(this, addItems);
106 | });
107 | }
108 | }
109 | var addItems = [];
110 | var result = this.each(function() {
111 | highlight(this, addItems);
112 | });
113 | for (var i = 0; i < addItems.length; ++i) {
114 | jQuery(addItems[i].parent).before(addItems[i].target);
115 | }
116 | return result;
117 | };
118 |
119 | /*
120 | * backward compatibility for jQuery.browser
121 | * This will be supported until firefox bug is fixed.
122 | */
123 | if (!jQuery.browser) {
124 | jQuery.uaMatch = function(ua) {
125 | ua = ua.toLowerCase();
126 |
127 | var match = /(chrome)[ \/]([\w.]+)/.exec(ua) ||
128 | /(webkit)[ \/]([\w.]+)/.exec(ua) ||
129 | /(opera)(?:.*version|)[ \/]([\w.]+)/.exec(ua) ||
130 | /(msie) ([\w.]+)/.exec(ua) ||
131 | ua.indexOf("compatible") < 0 && /(mozilla)(?:.*? rv:([\w.]+)|)/.exec(ua) ||
132 | [];
133 |
134 | return {
135 | browser: match[ 1 ] || "",
136 | version: match[ 2 ] || "0"
137 | };
138 | };
139 | jQuery.browser = {};
140 | jQuery.browser[jQuery.uaMatch(navigator.userAgent).browser] = true;
141 | }
142 |
143 | /**
144 | * Small JavaScript module for the documentation.
145 | */
146 | var Documentation = {
147 |
148 | init : function() {
149 | this.fixFirefoxAnchorBug();
150 | this.highlightSearchWords();
151 | this.initIndexTable();
152 | if (DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) {
153 | this.initOnKeyListeners();
154 | }
155 | },
156 |
157 | /**
158 | * i18n support
159 | */
160 | TRANSLATIONS : {},
161 | PLURAL_EXPR : function(n) { return n === 1 ? 0 : 1; },
162 | LOCALE : 'unknown',
163 |
164 | // gettext and ngettext don't access this so that the functions
165 | // can safely bound to a different name (_ = Documentation.gettext)
166 | gettext : function(string) {
167 | var translated = Documentation.TRANSLATIONS[string];
168 | if (typeof translated === 'undefined')
169 | return string;
170 | return (typeof translated === 'string') ? translated : translated[0];
171 | },
172 |
173 | ngettext : function(singular, plural, n) {
174 | var translated = Documentation.TRANSLATIONS[singular];
175 | if (typeof translated === 'undefined')
176 | return (n == 1) ? singular : plural;
177 | return translated[Documentation.PLURALEXPR(n)];
178 | },
179 |
180 | addTranslations : function(catalog) {
181 | for (var key in catalog.messages)
182 | this.TRANSLATIONS[key] = catalog.messages[key];
183 | this.PLURAL_EXPR = new Function('n', 'return +(' + catalog.plural_expr + ')');
184 | this.LOCALE = catalog.locale;
185 | },
186 |
187 | /**
188 | * add context elements like header anchor links
189 | */
190 | addContextElements : function() {
191 | $('div[id] > :header:first').each(function() {
192 | $('\u00B6').
193 | attr('href', '#' + this.id).
194 | attr('title', _('Permalink to this headline')).
195 | appendTo(this);
196 | });
197 | $('dt[id]').each(function() {
198 | $('\u00B6').
199 | attr('href', '#' + this.id).
200 | attr('title', _('Permalink to this definition')).
201 | appendTo(this);
202 | });
203 | },
204 |
205 | /**
206 | * workaround a firefox stupidity
207 | * see: https://bugzilla.mozilla.org/show_bug.cgi?id=645075
208 | */
209 | fixFirefoxAnchorBug : function() {
210 | if (document.location.hash && $.browser.mozilla)
211 | window.setTimeout(function() {
212 | document.location.href += '';
213 | }, 10);
214 | },
215 |
216 | /**
217 | * highlight the search words provided in the url in the text
218 | */
219 | highlightSearchWords : function() {
220 | var params = $.getQueryParameters();
221 | var terms = (params.highlight) ? params.highlight[0].split(/\s+/) : [];
222 | if (terms.length) {
223 | var body = $('div.body');
224 | if (!body.length) {
225 | body = $('body');
226 | }
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134 | Introduction¶
85 |The Hetero2d package leverages well known computational tools: pymatgen, MPInterfaces, atomate, fireworks, and custodian to perform high-throughput ab-initio calculations. Hetero2d is tailored to addressing scientific questions regarding the stability of 2D-substrate hetero-structured materials using an all-in-one workflow approach to model the hetero-structures formed by arbitrary 2D materials and substrates. The workflow creates, computes, analyzes and stores all relevant simulation parameters and results in a queryable MongoDB database that can be accessed through our API.
86 |
87 |
91 | Package Description¶
88 |The 2D-substrate hetero-structure workflow takes a given 2D material, 3D phase (bulk) of the 2D material, and a substrate, relaxes the structures using vdW-corrected DFT and creates hetero-structures subject to user constraints. The workflow analyzes and stores energetic stability information of various 2D hetero-structured materials to predict the feasibility of a substrate stabilizing a meta-stable 2D material.
89 |Hetero2d provides automated routines for the generation of low-lattice mismatched hetero-structures for arbitrary 2D materials and substrate surfaces, the creation of van der Waals corrected density-functional theory (DFT) input files, the submission and monitoring of simulations on computing resources, the post-processing of the key parameters to compute (a) the interface interaction energy of 2D-substrate hetero-structures, (b) the identification of substrate-induced changes in interfacial structure, and (c) charge doping of the 2D material.
90 |
92 |
95 | Examples¶
93 |To get started using Hetero2d, various tutorials and examples have been created using Jupyter Notebooks. These notebooks demonstrate the basic functionality of Hetero2d to enable users to quickly learn how to use the various modules within this package. These can be found under Hetero2d/examples.
94 |
96 |
102 | How to cite Hetero2d¶
97 |If you use Hetero2d in your research, please consider citing the following work:
98 |99 |101 |Tara M. Boland, Arunima K. Singh. Computational Synthesis of 2D Materials: A High-throughput Approach to Materials Design (2021). arXiv:2112.03900.
100 |
103 |
106 | License¶
104 |Hetero2d is released under the GNU General Public Version 3 License. Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>. The terms of the license can be found in the main directory in this software package under the LICENSE file.
105 |
107 |
112 | About the Team¶
108 |Arunima Singh (P.I.) of the Computational Materials Design Lab started Hetero2d in 2020, and is project lead.
109 |Currently, the main developer for this package is graduate student Tara M. Boland who has developed much of the existing Hetero2d package under the guidance of Arunima Singh.
110 |See more team details in the Development Team section.
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130 |
131 | Copyright Policy¶
114 |Hetero2d uses a shared copyright model. Each contributor maintains 115 | copyright over their contributions to pymatgen. But, it is important 116 | to note that these contributions are typically only changes to the 117 | repositories. Thus, the Hetero2d source code, in its entirety is not 118 | the copyright of any single person or institution. Instead, it is the 119 | collective copyright of the entire Hetero2d Development Team. If 120 | individual contributors want to maintain a record of what 121 | changes/contributions they have specific copyright on, they should 122 | indicate their copyright in the commit message of the change, when 123 | they commit the change to one of the pymatgen repositories.
124 |With this in mind, the following banner should be used in any source 125 | code file to indicate the copyright and license terms:
126 |# Copyright (c) CMD Lab Development Team.
127 | # Distributed under the terms of the GNU License.
128 | ' + _('Hide Search Matches') + '
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161 | Installing Hetero2d¶
80 |IMPORTANT NOTE: Atomate and FireWorks do not run on Windows OS. You need a unix-based OS (Mac or Linux) in order for these packages to run. As such, all setup instructions are given for Unix systems.
81 |-
82 |
Download the repo from the green code icon or via github’s commandline tool gh.
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85 |90 |86 |
89 |- 87 |
gh repo clone cmdlab/Hetero2d(gh must be installed)- 88 |
git clone https://github.com/cmdlab/Hetero2d.git
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91 |
Install Hetero2d in a clean enviromnent using python=3.6. I suggest using Anaconda3 to manange environments.
92 |
94 |98 |95 |
97 |- 96 |
conda create --name hetero2d python=3.6
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Activate the hetero2d environment and run the line below to install Hetero2d. Must be in the directory where Hetero2d was downloaded to.
100 |
102 |106 |103 |
105 |- 104 |
pip install -r requirements.txt
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107 |
After installation, Hetero2d needs to be added to your python path. This can be done by running the first line below OR by adding the 2nd line to your .bashrc file. This is only necessary if python cannot find the package or the setup.py failed for some reason.
108 |
110 |115 |111 |
114 |- 112 |
python setup.py developorpython setup.py install- 113 |
export PYTHONPATH="$HOME/path_to_package/Hetero2d:$PYTHONPATH"
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If this is your first time installing the package dependencies listed below, please ensure you have followed the respective setup instructions:
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119 |126 |120 |
125 |- 121 |
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To run jupyter notebooks on various resources the ipykernel has to be installed. Sometimes this isn’t enough and you need explicitly add the kernel to the list of environments.
128 |
130 |135 |131 |
134 |- 132 |
Activate your environment
conda activate hetero2d- 133 |
python -m ipykernel install --user --name hetero2d
136 |
158 | Setting up dependancies¶
137 |The Hetero2d package dependancies have a lot of documentation to look over. I will highlight the essential documentation to get started as quickly as possible.
138 |-
139 |
atomate requires the most set up. Mainly, creating a directory scaffold and writing the 5 required files to connect to the database and run jobs. (MongoDB or free Atlas MongoDB is required)
140 | pymatgen has a command line tool installed to set up default directory paths for psuedopotentials called pmg. There are 2 essential commands you have to run to use Hetero2d on any system.
141 |
143 |148 |144 |
147 |- 145 |
VASP POTCARs directory:
pmg config -p <EXTRACTED_VASP_POTCAR> <MY_PSP>- 146 |
Default pseudopotential:
pmg config --add PMG_DEFAULT_FUNCTIONAL PBE_54
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MPInterfaces has a config file similar to pymatgen. You need to set at least 2 parameters in the mpint_config.yaml file to remove the warning message. An example config file can be found on MPInterfaces github website.
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152 |157 |153 |
156 |- 154 |
mp_api: the_key_obtained_from_materialsproject
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potentials: path_to_vasp_potcar_files