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VsevolodXVsevolodX
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Merge pull request #230 from Exabyte-io/feature/SOF-7643
feature/SOF 7643
2 parents fa70d51 + 3bd56ae commit 217d20f

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5 files changed

+120
-87
lines changed

5 files changed

+120
-87
lines changed

‎other/materials_designer/create_adatom_defect.ipynb

Lines changed: 17 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -141,20 +141,28 @@
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"metadata": {},
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"cell_type": "code",
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"source": [
144-
"from mat3ra.made.tools.build.slab import SlabConfiguration, get_terminations, create_slab\n",
144+
"from mat3ra.made.tools.analyze.lattice_planes import CrystalLatticePlanesMaterialAnalyzer\n",
145+
"from mat3ra.made.tools.build.slab.helpers import create_slab\n",
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"from utils.visualize import visualize_materials as visualize\n",
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"\n",
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"material = materials[0]\n",
148-
"slab_config = SlabConfiguration(\n",
149-
" bulk=material,\n",
149+
"# Create analyzer to get terminations\n",
150+
"analyzer = CrystalLatticePlanesMaterialAnalyzer(material=material, miller_indices=MILLER_INDICES)\n",
151+
"slab_terminations = analyzer.terminations\n",
152+
"# Get termination from analyzer\n",
153+
"terminations = analyzer.terminations\n",
154+
"termination = terminations[0] # Use first termination\n",
155+
"\n",
156+
"slab = create_slab(\n",
157+
" crystal=material,\n",
158+
" termination=termination,\n",
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" miller_indices=MILLER_INDICES,\n",
151-
" number_of_layers=SLAB_THICKNESS,\n",
152-
" vacuum=VACUUM,\n",
153-
" use_orthogonal_z=True,\n",
154-
" xy_supercell_matrix=SUPERCELL_MATRIX\n",
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" number_of_layers=1,\n",
161+
" vacuum=0,\n",
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" xy_supercell_matrix=[[1, 0], [0, 1]],\n",
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" use_orthogonal_c=True,\n",
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" use_conventional_cell=True\n",
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")\n",
156-
"termination = get_terminations(slab_config)[0]\n",
157-
"slab = create_slab(slab_config, termination)\n",
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"visualize([{\"material\": slab, \"rotation\": \"0x\"}, {\"material\": slab, \"rotation\": \"-90x\"}], repetitions=[1, 1, 1])"
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],
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"id": "8ea8b4402aef0cf0",

‎other/materials_designer/create_cluster_sphere.ipynb

Lines changed: 24 additions & 15 deletions
Original file line numberDiff line numberDiff line change
@@ -38,7 +38,6 @@
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},
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{
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"cell_type": "code",
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"outputs": [],
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"source": [
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"RADIUS = 4.5 # in Angstroms\n",
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"VACUUM = 10.0 # in Angstroms on each side\n",
@@ -48,6 +47,7 @@
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"collapsed": false
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},
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"id": "9d8b1890b34d850a",
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"outputs": [],
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"execution_count": null
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},
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{
@@ -63,7 +63,6 @@
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},
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{
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"cell_type": "code",
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"outputs": [],
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"source": [
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"import sys\n",
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"\n",
@@ -80,6 +79,7 @@
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"collapsed": false
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},
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"id": "ef664b14457530fd",
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"outputs": [],
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"execution_count": null
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},
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{
@@ -94,7 +94,6 @@
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},
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{
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"cell_type": "code",
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"outputs": [],
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"source": [
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"from utils.jupyterlite import get_materials\n",
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"\n",
@@ -104,6 +103,7 @@
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"collapsed": false
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},
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"id": "be38fdda1984c654",
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"outputs": [],
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"execution_count": null
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},
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{
@@ -118,21 +118,29 @@
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},
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{
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"cell_type": "code",
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"outputs": [],
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"source": [
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"from mat3ra.made.tools.build.supercell import create_supercell\n",
124-
"from mat3ra.made.tools.build.slab import create_slab, SlabConfiguration\n",
123+
"from mat3ra.made.tools.analyze.lattice_planes import CrystalLatticePlanesMaterialAnalyzer\n",
124+
"from mat3ra.made.tools.build.slab.helpers import create_slab\n",
125125
"from utils.visualize import visualize_materials as visualize\n",
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"\n",
127-
"slab_config = SlabConfiguration(\n",
128-
" bulk=materials[0],\n",
127+
"# Create analyzer to get terminations\n",
128+
"analyzer = CrystalLatticePlanesMaterialAnalyzer(material=materials[0], miller_indices=Z_ORIENTATION)\n",
129+
"\n",
130+
"# Get termination from analyzer\n",
131+
"terminations = analyzer.terminations\n",
132+
"termination = terminations[0] # Use first termination\n",
133+
"\n",
134+
"slab = create_slab(\n",
135+
" crystal=materials[0],\n",
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" termination=termination,\n",
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" miller_indices=Z_ORIENTATION,\n",
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" number_of_layers=1,\n",
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" vacuum=0,\n",
132-
" use_orthogonal_z=True\n",
140+
" xy_supercell_matrix=[[1, 0], [0, 1]],\n",
141+
" use_orthogonal_c=True,\n",
142+
" use_conventional_cell=True\n",
133143
")\n",
134-
"\n",
135-
"slab = create_slab(slab_config)\n",
136144
"length = slab.lattice.a\n",
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"sufficient_n = int(2 * RADIUS / length) + 1\n",
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"\n",
@@ -145,6 +153,7 @@
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"collapsed": false
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},
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"id": "7fcb1e02e84c5f35",
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"outputs": [],
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"execution_count": null
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},
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{
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},
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{
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"cell_type": "code",
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"outputs": [],
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"source": [
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"from mat3ra.made.tools.modify import filter_by_sphere, add_vacuum, add_vacuum_sides\n",
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"\n",
@@ -172,6 +180,7 @@
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"collapsed": false
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},
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"id": "a990fa35742d7269",
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"outputs": [],
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"execution_count": null
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},
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{
@@ -186,11 +195,10 @@
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},
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{
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"cell_type": "code",
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"outputs": [],
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"source": [
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"from mat3ra.made.lattice import Lattice\n",
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"\n",
193-
"current_vector_1, current_vector_2, current_vector_3 = cluster.lattice.vectors\n",
201+
"current_vector_1, current_vector_2, current_vector_3 = cluster.lattice.vector_arrays\n",
194202
"cubic_vector_1 = [current_vector_1[0], 0, 0]\n",
195203
"cubic_vector_2 = [0, current_vector_2[1], 0]\n",
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"cubic_vector_3 = [0, 0, current_vector_3[2]]\n",
@@ -200,6 +208,7 @@
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"collapsed": false
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},
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"id": "4f78c4743b370c3b",
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"outputs": [],
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"execution_count": null
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},
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{
@@ -214,7 +223,6 @@
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},
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{
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"cell_type": "code",
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"outputs": [],
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"source": [
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"visualize([{\"material\": slab, \"title\": \"Original material\"},\n",
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" {\"material\": cluster, \"title\": f\"Cluster\"}])\n",
@@ -226,6 +234,7 @@
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"collapsed": false
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},
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"id": "509b18661a069e42",
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"outputs": [],
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"execution_count": null
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},
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{
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},
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{
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"cell_type": "code",
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"outputs": [],
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"source": [
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"from utils.jupyterlite import set_materials\n",
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"\n",
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"collapsed": false
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},
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"id": "61daa5afcbc078a9",
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"outputs": [],
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"execution_count": null
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}
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],

‎other/materials_designer/create_cutout_box.ipynb

Lines changed: 15 additions & 16 deletions
Original file line numberDiff line numberDiff line change
@@ -41,7 +41,6 @@
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},
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{
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"cell_type": "code",
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"outputs": [],
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"source": [
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"# Box cutout parameters\n",
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"MIN_COORDINATE = [0.25, 0.25, 0.5]\n",
@@ -53,14 +52,15 @@
5352
" \"miller_indices\": (0, 0, 1),\n",
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" \"thickness\": 6,\n",
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" \"vacuum\": 10.0,\n",
56-
" \"use_orthogonal_z\": True,\n",
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" \"use_orthogonal_c\": True,\n",
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" \"xy_supercell_matrix\": [[10, 0], [0, 10]]\n",
5857
"}"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "9d8b1890b34d850a",
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"outputs": [],
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"execution_count": null
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},
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{
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},
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{
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"cell_type": "code",
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"outputs": [],
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"source": [
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"import sys\n",
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"\n",
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"collapsed": false
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},
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"id": "ef664b14457530fd",
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"outputs": [],
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"execution_count": null
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},
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{
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},
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{
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"cell_type": "code",
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"outputs": [],
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"source": [
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"from utils.jupyterlite import get_materials\n",
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"\n",
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"collapsed": false
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},
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"id": "be38fdda1984c654",
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"outputs": [],
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"execution_count": null
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},
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{
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},
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{
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"cell_type": "code",
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"outputs": [],
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"source": [
136-
"from mat3ra.made.tools.build.slab import create_slab_if_not, SlabConfiguration\n",
135+
"from mat3ra.made.tools.build.slab.helpers import create_slab\n",
137136
"\n",
138-
"default_slab_config = SlabConfiguration(\n",
139-
" bulk=materials[0],\n",
137+
"# Create analyzer to get terminations\n",
138+
"slab = create_slab(\n",
139+
" crystal=materials[0],\n",
140140
" miller_indices=DEFAULT_SLAB_PARAMETERS[\"miller_indices\"],\n",
141141
" number_of_layers=DEFAULT_SLAB_PARAMETERS[\"thickness\"],\n",
142142
" vacuum=DEFAULT_SLAB_PARAMETERS[\"vacuum\"],\n",
143-
" use_orthogonal_z=DEFAULT_SLAB_PARAMETERS[\"use_orthogonal_z\"],\n",
143+
" use_orthogonal_c=DEFAULT_SLAB_PARAMETERS[\"use_orthogonal_c\"],\n",
144144
" xy_supercell_matrix=DEFAULT_SLAB_PARAMETERS[\"xy_supercell_matrix\"]\n",
145-
")\n",
146-
"\n",
147-
"slab = create_slab_if_not(materials[0], default_slab_config)"
145+
")"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "bfce9928ba2d0c7e",
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"outputs": [],
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"execution_count": null
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},
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{
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},
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{
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"cell_type": "code",
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"outputs": [],
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"source": [
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"from utils.visualize import visualize_materials as visualize\n",
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"\n",
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"collapsed": false
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},
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"id": "7fcb1e02e84c5f35",
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"outputs": [],
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"execution_count": null
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},
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{
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},
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{
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"cell_type": "code",
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"outputs": [],
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"source": [
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"from mat3ra.made.tools.modify import filter_by_box\n",
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"\n",
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"collapsed": false
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},
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"id": "a990fa35742d7269",
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"outputs": [],
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"execution_count": null
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},
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{
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},
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{
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"cell_type": "code",
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"outputs": [],
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"source": [
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"visualize([{\"material\": slab, \"title\": \"Original material\"},\n",
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" {\"material\": slab_with_box_cutout, \"title\": f\"Cluster\"}])\n",
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"collapsed": false
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},
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"id": "509b18661a069e42",
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"outputs": [],
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"execution_count": null
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},
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{
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},
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{
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"cell_type": "code",
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"outputs": [],
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"source": [
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"from utils.jupyterlite import set_materials\n",
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"\n",
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"collapsed": false
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},
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"id": "61daa5afcbc078a9",
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"outputs": [],
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"execution_count": null
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}
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],

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