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Bidentate #1

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5e9dc93
Update nmf.py
pparanja Mar 15, 2023
47c4ed6
Update nmf.py
pparanja Mar 15, 2023
68b5425
Update nmf.py
pparanja Mar 16, 2023
fecf763
Update nmf.py
pparanja Mar 16, 2023
3fab8c1
Update graphs.py
pparanja Apr 7, 2023
3432352
Fixed minor issues
sawantk Apr 19, 2023
24f2346
added multidentate
sawantk May 2, 2023
c558559
fixed multidentate
sawantk May 3, 2023
71ab878
get_theta & graphs
pparanja May 8, 2023
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95 changes: 71 additions & 24 deletions nmf/graphs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -8,18 +8,18 @@

#1d Graph square symmetry
c_1d = nx.Graph()
c_1d.add_node(0,typ="c")
c_1d.add_node(1,typ="e1")
c_1d.add_node(2,typ="e1")
c_1d.add_node(0,typ1 = "t", typ2 ="c1")
c_1d.add_node(1,typ1 = "t", typ2 ="e1")
c_1d.add_node(2,typ1 = "t", typ2 ="e1")
c_1d.add_weighted_edges_from([(0, 2, 1), (0, 1, 1)])

#2d Graph square symmetry
c_2d = nx.Graph()
c_2d.add_node(0,typ="c")
c_2d.add_node(1,typ="e1")
c_2d.add_node(2,typ="e1")
c_2d.add_node(3,typ="e1")
c_2d.add_node(4,typ="e1")
c_2d.add_node(0,typ1 = "t", typ2 ="c1")
c_2d.add_node(1,typ1 = "t", typ2 ="e1")
c_2d.add_node(2,typ1 = "t", typ2 ="e1")
c_2d.add_node(3,typ1 = "t", typ2 ="e1")
c_2d.add_node(4,typ1 = "t", typ2 ="e1")
c_2d.add_weighted_edges_from([(0, 2, 1), (0, 1, 1), (0, 3, 1), (0, 4, 1)])

#2d Graph with edge nodes connected to each other
Expand All @@ -28,13 +28,13 @@

#2d Graph Hexagonal symmetry
c_2d_hex = nx.Graph()
c_2d_hex.add_node(0,typ="c")
c_2d_hex.add_node(1,typ="e1")
c_2d_hex.add_node(2,typ="e1")
c_2d_hex.add_node(3,typ="e1")
c_2d_hex.add_node(4,typ="e1")
c_2d_hex.add_node(5,typ="e1")
c_2d_hex.add_node(6,typ="e1")
c_2d_hex.add_node(0,typ1 = "t", typ2 ="c1")
c_2d_hex.add_node(1,typ1 = "t", typ2 ="e1")
c_2d_hex.add_node(2,typ1 = "t", typ2 ="e1")
c_2d_hex.add_node(3,typ1 = "t", typ2 ="e1")
c_2d_hex.add_node(4,typ1 = "t", typ2 ="e1")
c_2d_hex.add_node(5,typ1 = "t", typ2 ="e1")
c_2d_hex.add_node(6,typ1 = "t", typ2 ="e1")
c_2d_hex.add_weighted_edges_from([(0, 2, 1), (0, 1, 1), (0, 3, 1), (0, 4, 1), (0, 5, 1), (0, 6, 1)])

#2d Hexagonal Graph with edge nodes connected to each other
Expand All @@ -44,17 +44,64 @@
#2d Graph with asymmetric bridge sites
custom_1 = nx.Graph()
custom_1 = nx.Graph()
custom_1.add_node(0,typ="c")
custom_1.add_node(2,typ="e1")
custom_1.add_node(4,typ="e1")
custom_1.add_node(6,typ="e1")
custom_1.add_node(8,typ="e1")
custom_1.add_node(1,typ="e2")
custom_1.add_node(5,typ="e2")
custom_1.add_node(3,typ="e3")
custom_1.add_node(7,typ="e3")
custom_1.add_node(0,typ1 = "b",typ2="c1")
custom_1.add_node(2,typ1 = "b",typ2="e1")
custom_1.add_node(4,typ1 = "b",typ2="e1")
custom_1.add_node(6,typ1 = "b",typ2="e1")
custom_1.add_node(8,typ1 = "b",typ2="e1")
custom_1.add_node(1,typ1 = "b",typ2="e2")
custom_1.add_node(5,typ1 = "b",typ2="e2")
custom_1.add_node(3,typ1 = "b",typ2="e3")
custom_1.add_node(7,typ1 = "b",typ2="e3")
custom_1.add_weighted_edges_from([ (0, 1, 2), (0, 7, 1), (0, 3, 1), (0, 5, 2),
(8, 2, 1), (2, 4, 2), (6, 4, 1), (6, 8, 2),
(2, 1, 0), (2, 3, 0), (3, 4, 0), (4, 5, 0),
(5, 6, 0), (6, 7, 0), (7, 8, 0), (8, 1, 0),
(2, 0, 0), (4, 0, 0), (6, 0, 0), (8, 0, 0)])

#2d graph for bidentates
c_2d_9 = nx.Graph()
c_2d_9.add_node(0,typ1 = "t", typ2 ="c1")
c_2d_9.add_node(1,typ1 = "t", typ2 ="e1")
c_2d_9.add_node(2,typ1 = "t", typ2 ="e1")
c_2d_9.add_node(3,typ1 = "t", typ2 ="e1")
c_2d_9.add_node(4,typ1 = "t", typ2 ="e1")
c_2d_9.add_node(5,typ1 = "t", typ2 ="e1")
c_2d_9.add_node(6,typ1 = "t", typ2 ="e1")
c_2d_9.add_node(7,typ1 = "t", typ2 ="e1")
c_2d_9.add_node(8,typ1 = "t", typ2 ="e1")
c_2d_9.add_weighted_edges_from([(0,1,1),(0,3,1),(0,5,1),(0,7,1),
(8,1,1),(8,7,1),(1,2,1),(2,3,1),
(7,6,1),(6,5,1),(5,4,1),(3,4,1)])
#2d graph Bridge-Top
c_tb = nx.Graph()
c_tb.add_node(0,typ = "c1")
c_tb.add_node(1,typ ="c2")
c_tb.add_node(18,typ ="c2")
c_tb.add_node(19,typ ="c2")
c_tb.add_node(20,typ ="c2")
c_tb.add_node(2,typ ="e1")
c_tb.add_node(4,typ ="e1")
c_tb.add_node(6,typ ="e1")
c_tb.add_node(8,typ ="e1")
c_tb.add_node(9,typ ="e2")
c_tb.add_node(10,typ ="e1")
c_tb.add_node(11,typ ="e2")
c_tb.add_node(12,typ ="e1")
c_tb.add_node(13,typ ="e2")
c_tb.add_node(14,typ ="e1")
c_tb.add_node(15,typ ="e2")
c_tb.add_node(16,typ ="e1")
c_tb.add_node(17,typ ="e2")
c_tb.add_node(3,typ = "e2")
c_tb.add_node(7,typ = "e2")
for i in range(0,c_tb.number_of_nodes()):
c_tb.add_weighted_edges_from([(i,i+1,0)]) #no adjacent top-bridge
if i%2 == 0 and i<15:
c_tb.add_weighted_edges_from([(i,i+2,1)])#top-top bond type
c_tb.add_weighted_edges_from([(0,i,1) for i in range(2,16,4)])#remaining top-top
c_tb.add_weighted_edges_from([(0,l,0) for l in range(18,21)]) #Remaining adjacent sites
c_tb.add_weighted_edges_from([(1,3,0),(3,5,0),(5,20,0),(20,1,0),(20,7,0),(7,9,0),(9,19,0),
(11,19,0),(19,18,0),(18,13,0),(11,13,0),(1,18,0),(18,15,0),(15,17,0),(17,1,0)]) #no adjacent bridges
c_tb.add_weighted_edges_from([(6,20,0),(18,14,0),(10,19,0)]) #remaining adjacent top-bridge