Merge pull request #350 from WMD-group/structure_prediction_mp_fixes

Updated MP test files for the Structure prediction module
WMD-group · Dec 18, 2024 · 276a9d5 · 276a9d5
2 parents c48a02f + dca0c39
commit 276a9d5
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Showing 7 changed files with 207 additions and 99 deletions.
diff --git a/pyproject.toml b/pyproject.toml
@@ -99,10 +99,9 @@ optional = [
     "seaborn>=0.13.2",
     "pymatgen>=2024.2.20",
     "matminer>=0.9.2",
-    "umap-learn>=0.5.3",
     "kaleido>=0.2.1",
     "ase>=3.22.0",
-    "numpy",
+    "llvmlite>=0.40",
     "ElementEmbeddings>=0.4",
     "dash>=2.18.2",
 

diff --git a/smact/tests/files/BaTiO3.txt b/smact/tests/files/BaTiO3.txt
@@ -1,18 +1,18 @@
 Ba2+ O2- Ti4+
 1.0
-5.287674 -2.670508 0.0
-5.287674 2.670508 0.0
-3.93895 0.0 4.424453
+-2.68573015 2.68573015 3.89611961
+2.68573015 -2.68573015 3.89611961
+2.68573015 2.68573015 -3.89611961
 Ba O Ti
 2 6 2
 Cartesian
-9.240948736342 6.062109608251377e-17 2.8169563115870004 Ba2+
-5.273349263658 4.9761495873212886e-17 1.6074966884130002 Ba2+
-7.807412346486 1.0122213407960001 4.306620967704 O2-
-8.357867072605998 -2.1021357708359996 2.500868964814 O2-
-5.645214628605999 -1.0899144300399997 3.600615426947 O2-
-8.869083371394 1.08991443004 0.823837573053 O2-
-6.156430927393999 2.1021357708359996 1.923584035186 O2-
-6.706885653513999 -1.0122213407959997 0.11783203229599999 O2-
-12.348663138314 2.6002918693279753e-16 3.7642936412290005 Ti4+
-2.1656348616859997 1.752656922349161e-17 0.660159358771 Ti4+
+2.68573015 0.0 1.948059805 Ba2+
+-2.220446049250313e-16 2.6857301500000004 1.948059805 Ba2+
+-1.027577758921372 1.658152391078628 3.89611961 O2-
+1.027577758921372 1.658152391078628 2.220446049250313e-16 O2-
+1.658152391078628 1.027577758921372 3.8961196100000004 O2-
+3.7133079089213714 1.0275777589213722 7.014688707853907e-17 O2-
+-1.1102230246251565e-16 1.1102230246251565e-16 5.844179415 O2-
+0.0 0.0 1.948059805 O2-
+0.0 0.0 3.89611961 Ti4+
+0.0 0.0 0.0 Ti4+
diff --git a/smact/tests/files/CaTiO3.json b/smact/tests/files/CaTiO3.json
@@ -4,90 +4,90 @@
   "charge": 0,
   "lattice": {
     "matrix": [
-      [5.287674, -2.670508, 0.0],
-      [5.287674, 2.670508, 0.0],
-      [3.93895, 0.0, 4.424453]
+      [-2.68573015, 2.68573015, 3.89611961],
+      [2.68573015, -2.68573015, 3.89611961],
+      [2.68573015, 2.68573015, -3.89611961]
     ],
     "pbc": [true, true, true],
-    "a": 5.923774920465834,
-    "b": 5.923774920465834,
-    "c": 5.923775101378259,
-    "alpha": 53.59156916755366,
-    "beta": 53.59156916755366,
-    "gamma": 53.5915681815752,
-    "volume": 124.95341697913328
+    "a": 5.441143344248945,
+    "b": 5.441143344248945,
+    "c": 5.441143344248945,
+    "alpha": 120.84549073210634,
+    "beta": 120.84549073210634,
+    "gamma": 88.54170096725916,
+    "volume": 112.41312515722095
   },
   "properties": {},
   "sites": [
     {
       "species": [{ "element": "Ca", "occu": 1 }],
-      "abc": [0.6366789999999999, 0.6366789999999999, 0.6366790000000001],
+      "abc": [0.25, 0.75, 0.5],
       "properties": {},
       "label": "Ca",
-      "xyz": [9.240948736342, 6.062109608251377e-17, 2.8169563115870004]
+      "xyz": [2.68573015, 0.0, 1.948059805]
     },
     {
       "species": [{ "element": "Ca", "occu": 1 }],
-      "abc": [0.36332099999999995, 0.36332099999999995, 0.36332100000000006],
+      "abc": [0.7500000000000001, 0.24999999999999994, 0.5],
       "properties": {},
       "label": "Ca",
-      "xyz": [5.273349263658, 4.9761495873212886e-17, 1.6074966884130002]
+      "xyz": [-2.220446049250313e-16, 2.6857301500000004, 1.9480598050000004]
     },
     {
       "species": [{ "element": "O", "occu": 1 }],
-      "abc": [0.18620099999999998, 0.565238, 0.9733680000000001],
+      "abc": [0.80869676, 0.30869676, 0.11739352000000002],
       "properties": {},
       "label": "O",
-      "xyz": [7.807412346486, 1.0122213407960001, 4.306620967704]
+      "xyz": [-1.027577758921372, 1.658152391078628, 3.89611961]
     },
     {
       "species": [{ "element": "O", "occu": 1 }],
-      "abc": [0.9733679999999998, 0.18620099999999995, 0.565238],
+      "abc": [0.30869676000000007, 0.19130324, 0.5],
       "properties": {},
       "label": "O",
-      "xyz": [8.357867072605998, -2.1021357708359996, 2.500868964814]
+      "xyz": [1.0275777589213717, 1.6581523910786282, 4.440892098500626e-16]
     },
     {
       "species": [{ "element": "O", "occu": 1 }],
-      "abc": [0.4347619999999998, 0.026631999999999944, 0.813799],
+      "abc": [0.69130324, 0.80869676, 0.5],
       "properties": {},
       "label": "O",
-      "xyz": [5.645214628605999, -1.0899144300399997, 3.600615426947]
+      "xyz": [1.658152391078628, 1.027577758921372, 3.8961196100000004]
     },
     {
       "species": [{ "element": "O", "occu": 1 }],
-      "abc": [0.5652379999999999, 0.9733679999999999, 0.186201],
+      "abc": [0.19130324, 0.6913032399999999, 0.8826064799999999],
       "properties": {},
       "label": "O",
-      "xyz": [8.869083371394, 1.08991443004, 0.823837573053]
+      "xyz": [3.713307908921371, 1.027577758921372, 5.861384700003497e-17]
     },
     {
       "species": [{ "element": "O", "occu": 1 }],
-      "abc": [0.02663199999999999, 0.8137989999999999, 0.43476200000000004],
+      "abc": [0.75, 0.75, 0.0],
       "properties": {},
       "label": "O",
-      "xyz": [6.156430927393999, 2.1021357708359996, 1.923584035186]
+      "xyz": [-1.1102230246251565e-16, 1.1102230246251565e-16, 5.844179415]
     },
     {
       "species": [{ "element": "O", "occu": 1 }],
-      "abc": [0.8137989999999999, 0.4347619999999999, 0.026632],
+      "abc": [0.25, 0.25, 0.0],
       "properties": {},
       "label": "O",
-      "xyz": [6.706885653513999, -1.0122213407959997, 0.11783203229599999]
+      "xyz": [0.0, 0.0, 1.948059805]
     },
     {
       "species": [{ "element": "Ti", "occu": 1 }],
-      "abc": [0.8507929999999999, 0.850793, 0.8507930000000001],
+      "abc": [0.5, 0.5, 0.0],
       "properties": {},
       "label": "Ti",
-      "xyz": [12.348663138314, 2.6002918693279753e-16, 3.7642936412290005]
+      "xyz": [0.0, 0.0, 3.89611961]
     },
     {
       "species": [{ "element": "Ti", "occu": 1 }],
-      "abc": [0.14920699999999998, 0.14920699999999998, 0.149207],
+      "abc": [0.0, 0.0, 0.0],
       "properties": {},
       "label": "Ti",
-      "xyz": [2.1656348616859997, 1.752656922349161e-17, 0.660159358771]
+      "xyz": [0.0, 0.0, 0.0]
     }
   ]
 }
diff --git a/smact/tests/files/CaTiO3.txt b/smact/tests/files/CaTiO3.txt
@@ -1,18 +1,18 @@
 Ca2+ O2- Ti4+
 1.0
-5.287674 -2.670508 0.0
-5.287674 2.670508 0.0
-3.93895 0.0 4.424453
+-2.68573015 2.68573015 3.89611961
+2.68573015 -2.68573015 3.89611961
+2.68573015 2.68573015 -3.89611961
 Ca O Ti
 2 6 2
 Cartesian
-9.240948736342 -8.69821668629811e-17 2.816956311587 Ca2+
-5.273349263658 -2.4040135599534552e-17 1.607496688413 Ca2+
-7.807412346486 1.012221340796 4.306620967704 O2-
-8.357867072606 -2.102135770836 2.500868964814 O2-
-5.645214628606 -1.0899144300399999 3.600615426947 O2-
-8.869083371394 1.0899144300399999 0.823837573053 O2-
-6.156430927394 2.102135770836 1.9235840351859999 O2-
-6.706885653514 -1.0122213407960001 0.11783203229599999 O2-
-12.348663138314 -1.840600229172651e-16 3.764293641229 Ti4+
-2.165634861686 -1.937424651288211e-17 0.660159358771 Ti4+
+2.68573015 0.0 1.948059805 Ca2+
+-2.220446049250313e-16 2.6857301500000004 1.948059805 Ca2+
+-1.027577758921372 1.658152391078628 3.89611961 O2-
+1.027577758921372 1.658152391078628 2.220446049250313e-16 O2-
+1.658152391078628 1.027577758921372 3.8961196100000004 O2-
+3.7133079089213714 1.0275777589213722 7.014688707853907e-17 O2-
+-1.1102230246251565e-16 1.1102230246251565e-16 5.844179415 O2-
+0.0 0.0 1.948059805 O2-
+0.0 0.0 3.89611961 Ti4+
+0.0 0.0 0.0 Ti4+
diff --git a/smact/tests/files/Fe.txt b/smact/tests/files/Fe.txt
@@ -1,9 +1,108 @@
 Fe
 1.0
--0.0 -0.0 -2.39034144
--1.24450189 -2.15554064 -0.0
--1.24450189 2.15554064 0.0
+10.405638 0.047555 -0.110237999999999
+0.044125 10.706984 0.18323
+-0.107483 0.189423999999999 10.453721999999999
 Fe
-1
+100
 Cartesian
-0.0 0.0 0.0 Fe
+5.863563436178 5.080385271678999 6.335455793802001 Fe
+8.51949344302699 2.7592447016559998 3.8482885591860008 Fe
+8.828771561939 8.983934274137988 7.772769237526001 Fe
+1.6870097303409997 7.204525939467989 10.142400312658 Fe
+8.113528983554 2.209977440294 6.043720699904 Fe
+7.323228020297 8.27356419617199 1.3377856462819901 Fe
+3.9917797092189904 4.953482352543989 7.749054994738 Fe
+-0.0014796709199998892 5.295775811737 8.20830868360199 Fe
+10.055293968587998 3.9002559101899887 5.653209523164 Fe
+0.27381150830499995 3.2446840493269993 10.103660222108 Fe
+2.14138162563299 4.701564285988999 9.428682418999989 Fe
+1.5190845387729999 1.095959690387 0.892037649372 Fe
+9.350404404555 2.8507687823049994 7.964419977996 Fe
+0.255911942375 0.9378995999379885 9.139905314549999 Fe
+1.332388443732 6.677420159852001 2.6004299454799997 Fe
+4.198817355689 6.008497803690989 9.952115506916 Fe
+4.28946429978 1.9506895944309994 5.042163307082 Fe
+0.868089390683 9.072403401184 8.79819227939 Fe
+8.287475317412 2.0825147844129988 9.974203481082 Fe
+5.926306630629001 10.671396231908 2.3969275220340003 Fe
+6.180195935798 7.1913641934829995 5.342453267630001 Fe
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+2.8899943865649997 5.391533623342 1.3216707014220002 Fe
+5.19248779554799 2.3253870906979994 2.883342401976 Fe
+1.8865575346939998 0.15418094922099954 4.950987424298 Fe
+6.62014673322399 0.5583834926179883 9.065555375147989 Fe
+4.015350863451999 8.520048906919 5.158918086558001 Fe
+6.241180487124 3.190607067801 4.980548527962 Fe
+8.48350617855 0.6425300117649992 7.872932238066 Fe
+9.461534811021998 9.741348283272 2.1580893643000008 Fe
+9.716037627741 1.2971612258999998 1.4731910394860006 Fe
+3.448247872227 3.9009208624859997 3.129511912642 Fe
+0.41746930854998965 2.3100666881319993 3.7135813490719998 Fe
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+2.577834948724 8.798042781078001 3.37278010324399 Fe
+7.676000136616 9.387678837088998 3.5642128378780007 Fe
+3.8375134940300004 4.2574679949959995 5.32226981802 Fe
+9.101376091528 3.525028048995 1.2754563774180006 Fe
+7.14719067149599 4.254072421665 2.6012767683419904 Fe
+10.026171957295999 6.28231947065299 4.902153190638001 Fe
+0.2599066999289897 8.778529535507 4.305501360627989 Fe
+2.493513698255 10.36639670343399 10.15829226216599 Fe
+4.378262254671999 10.67421300863 4.1606766874759895 Fe
+5.917285848281 9.508388863344999 7.709245513448 Fe
+0.006035716342989711 1.4469431945209992 6.2474593330599895 Fe
+5.621347221534 6.439554227872001 1.5920584747080002 Fe
+9.412666103321989 7.369629363809999 9.65736823146 Fe
+9.445455383019988 9.909481889699 10.16835885290199 Fe
+3.6342840692289897 6.535613553068 3.444642496578 Fe
+6.193972384353 5.065822701727989 8.593133009946 Fe
+3.355187054145 2.6581507540739997 1.0676981460540003 Fe
+2.6883421098610003 1.648183130530989 3.1717197142159996 Fe
+6.621449816964 2.7836945796349992 8.186908060122 Fe
+8.597744806072 4.772627407188989 9.446032891578001 Fe
+6.8671783211 3.7572843514169896 0.20290903338200045 Fe
+2.495151868975 6.901140090271 7.926636217184 Fe
+9.658528038131001 4.912791087839 3.0461839995359905 Fe
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+7.986260489981991 4.383163369705989 7.11043184563999 Fe
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+5.464825711416999 5.2218804396389995 3.8435799797800003 Fe
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+6.80231921472599 0.9739640898749994 4.16588043520599 Fe
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+7.88235462809199 6.746318061986999 7.4219081559980005 Fe
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+2.0019167996459895 0.49174565321199903 7.546917775511989 Fe
+5.13397643074699 9.882697125389 0.23498579132800057 Fe
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+9.543631087816 7.44634181234299 2.2687884587900005 Fe
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+1.835606695123 7.06599270912099 5.07616808298 Fe
+1.0820746908189898 8.86014556814999 1.2571436517499894 Fe
+3.7244187984229895 2.6396858043349885 7.261217467263999 Fe
+7.87546408340899 5.133448868687989 4.91007656168199 Fe
+2.5515590764600002 2.1122117045469992 9.425030531521989 Fe
+4.406326853805989 0.8140431066979991 8.668970823159999 Fe
+1.7470050999209998 5.056374240533 6.51595789822 Fe
+1.2523917448219897 3.578873999775 1.8870555130739897 Fe
+8.211695777265001 5.787521410621999 1.1374892043779903 Fe
+5.21854652469199 7.202216187232 7.800625650264 Fe
+0.01868758143499996 9.857541253939988 6.468135835745999 Fe
diff --git a/smact/tests/files/NaCl.txt b/smact/tests/files/NaCl.txt
@@ -1,10 +1,20 @@
 Cl1- Na1+
 1.0
-3.50219 0.0 0.0
-0.0 3.50219 0.0
-0.0 0.0 3.50219
+6.799634 0.0 0.0
+-3.399818 5.888656 0.0
+0.0 0.0 7.094838
 Cl Na
-1 1
+6 6
 Cartesian
-1.751095 1.751095 1.751095 Cl1-
-0.0 0.0 0.0 Na1+
+3.3998200664840006 1.962883370448 1.7768808925859998 Cl1-
+3.3998200664840006 1.962883370448 5.317957107413993 Cl1-
+-4.066484000077238e-06 3.925772629552 5.317957107413993 Cl1-
+-4.066484000077238e-06 3.925772629552 1.7768808925859998 Cl1-
+0.0 0.0 5.327598992255993 Cl1-
+0.0 0.0 1.7672390077439932 Cl1-
+-2.2751582056 3.9406885952 3.547419 Na1+
+1.1246591328000004 1.9479674048000002 3.547419 Na1+
+4.5503150728 0.0 3.547419 Na1+
+-1.144280144078 1.981950838576 0.0 Na1+
+2.2555365290639973 3.9067051614239943 0.0 Na1+
+2.288559615014 0.0 0.0 Na1+