diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml index 11982fb..4a6e8ef 100644 --- a/.github/workflows/testing.yml +++ b/.github/workflows/testing.yml @@ -29,7 +29,7 @@ jobs: - name: Install KIM model shell: bash -el {0} run: | - kim-api-collections-management install user LJ_Shifted_Bernardes_1958LowCutoff_Ar__MO_720819638419_004 + kim-api-collections-management install user LJ_ElliottAkerson_2015_Universal__MO_959249795837_003 - name: Install shell: bash -el {0} diff --git a/kim_tools/symmetry_util/core.py b/kim_tools/symmetry_util/core.py index 9f73b56..0de111b 100644 --- a/kim_tools/symmetry_util/core.py +++ b/kim_tools/symmetry_util/core.py @@ -4026,7 +4026,7 @@ def get_formal_pearson_from_space_group(sgnum:Union[int,str]): return "oA" return pearson -POSSIBLE_PRIMITIVE_SHIFTS = { +POSSIBLE_PRIMITIVE_SHIFTS = { 1: [ [0,0,0] ], @@ -4058,9 +4058,7 @@ def get_formal_pearson_from_space_group(sgnum:Union[int,str]): ], 5: [ [0,0,0], - [0,0,0.5], - [0.5,0.5,0], - [0.5,0.5,0.5] + [0,0,0.5] ], 6: [ [0,0,0], @@ -4073,14 +4071,17 @@ def get_formal_pearson_from_space_group(sgnum:Union[int,str]): [0,0.5,0.5] ], 8: [ - [0,0,0], - [0.5,0.5,0] + [0,0,0] ], 9: [ [0,0,0], - [0,0,0.5], + [0.75,0.25,0], [0.5,0.5,0], - [0.5,0.5,0.5] + [0.25,0.75,0], + [0,0,0.5], + [0.75,0.25,0.5], + [0.5,0.5,0.5], + [0.25,0.75,0.5] ], 10: [ [0,0,0], @@ -4105,12 +4106,8 @@ def get_formal_pearson_from_space_group(sgnum:Union[int,str]): 12: [ [0,0,0], [0,0,0.5], - [0.5,0,0], - [0.5,0,0.5], [0.5,0.5,0], - [0.5,0.5,0.5], - [0,0.5,0], - [0,0.5,0.5] + [0.5,0.5,0.5] ], 13: [ [0,0,0], @@ -4135,20 +4132,12 @@ def get_formal_pearson_from_space_group(sgnum:Union[int,str]): 15: [ [0,0,0], [0,0,0.5], - [0.25,0.25,0], - [0.25,0.25,0.5], - [0.5,0,0], - [0.5,0,0.5], - [0.75,0.25,0], - [0.75,0.25,0.5], - [0.5,0.5,0], - [0.5,0.5,0.5], - [0.75,0.75,0], - [0.75,0.75,0.5], [0,0.5,0], [0,0.5,0.5], - [0.25,0.75,0], - [0.25,0.75,0.5] + [0.5,0.5,0], + [0.5,0.5,0.5], + [0.5,0,0], + [0.5,0,0.5] ], 16: [ [0,0,0], @@ -4211,74 +4200,38 @@ def get_formal_pearson_from_space_group(sgnum:Union[int,str]): [0,0,0.25], [0,0,0.5], [0,0,0.75], - [0.5,0,0], - [0.5,0,0.25], - [0.5,0,0.5], - [0.5,0,0.75], [0.5,0.5,0], [0.5,0.5,0.25], [0.5,0.5,0.5], - [0.5,0.5,0.75], - [0,0.5,0], - [0,0.5,0.25], - [0,0.5,0.5], - [0,0.5,0.75] + [0.5,0.5,0.75] ], 21: [ [0,0,0], [0,0,0.5], - [0.5,0,0], - [0.5,0,0.5], [0.5,0.5,0], - [0.5,0.5,0.5], - [0,0.5,0], - [0,0.5,0.5] + [0.5,0.5,0.5] ], 22: [ [0,0,0], [0.25,0.25,0.25], [0.5,0.5,0.5], - [0.75,0.75,0.75], - [0,0.5,0.5], - [0.25,0.75,0.75], - [0.5,0,0], - [0.75,0.25,0.25], - [0.5,0,0.5], - [0.75,0.25,0.75], - [0,0.5,0], - [0.25,0.75,0.25], - [0.5,0.5,0], - [0.75,0.75,0.25], - [0,0,0.5], - [0.25,0.25,0.75] + [0.75,0.75,0.75] ], 23: [ [0,0,0], - [0,0.5,0], - [0.5,0,0], - [0.5,0.5,0], - [0.5,0.5,0.5], [0.5,0,0.5], [0,0.5,0.5], - [0,0,0.5] + [0.5,0.5,0] ], 24: [ [0,0,0], - [0,0.5,0], - [0.25,0.25,0.25], - [0.25,0.75,0.25], - [0.5,0,0], - [0.5,0.5,0], - [0.75,0.25,0.25], - [0.75,0.75,0.25], - [0,0,0.5], - [0,0.5,0.5], - [0.25,0.25,0.75], - [0.25,0.75,0.75], [0.5,0,0.5], [0.5,0.5,0.5], - [0.75,0.25,0.75], - [0.75,0.75,0.75] + [0,0.5,0], + [0,0.5,0.5], + [0.5,0.5,0], + [0.5,0,0], + [0,0,0.5] ], 25: [ [0,0,0], @@ -4370,107 +4323,66 @@ def get_formal_pearson_from_space_group(sgnum:Union[int,str]): ], 35: [ [0,0,0], - [0.5,0,0], - [0.5,0.5,0], - [0,0.5,0] + [0.5,0.5,0] ], 36: [ [0,0,0], - [0.5,0,0], - [0,0,0.5], - [0.5,0,0.5], [0.5,0.5,0], - [0,0.5,0], - [0.5,0.5,0.5], - [0,0.5,0.5] + [0,0,0.5], + [0.5,0.5,0.5] ], 37: [ [0,0,0], - [0.5,0,0], - [0,0,0.5], - [0.5,0,0.5], [0.5,0.5,0], - [0,0.5,0], - [0.5,0.5,0.5], - [0,0.5,0.5] + [0,0,0.5], + [0.5,0.5,0.5] ], 38: [ [0,0,0], - [0.5,0,0], - [0,0.5,0.5], - [0.5,0.5,0.5] + [0.5,0.5,0], + [0.5,0.5,0.5], + [0,0,0.5] ], 39: [ [0,0,0], - [0.5,0,0], - [0,0,0.5], - [0.5,0,0.5], - [0,0.5,0], [0.5,0.5,0], - [0,0.5,0.5], + [0,0,0.5], [0.5,0.5,0.5] ], 40: [ [0,0,0], - [0.5,0,0], - [0,0.5,0.5], - [0.5,0.5,0.5] + [0.5,0.5,0], + [0.5,0.5,0.5], + [0,0,0.5] ], 41: [ [0,0,0], - [0.5,0,0], - [0,0.5,0.5], - [0.5,0.5,0.5], - [0.5,0,0.5], - [0,0,0.5], [0.5,0.5,0], - [0,0.5,0] + [0.5,0.5,0.5], + [0,0,0.5] ], 42: [ - [0,0,0], - [0,0.5,0.5], - [0.5,0,0.5], - [0.5,0.5,0] + [0,0,0] ], 43: [ [0,0,0], - [0.25,0.25,0], - [0,0.5,0.5], - [0.25,0.75,0.5], + [0,0,0.5], [0.25,0.25,0.25], - [0.5,0.5,0.25], - [0.25,0.75,0.75], - [0.5,0,0.75], - [0.5,0,0.5], - [0.75,0.25,0.5], - [0.5,0.5,0], - [0.75,0.75,0], - [0.75,0.25,0.75], - [0,0.5,0.75], - [0.75,0.75,0.25], - [0,0,0.25] + [0.25,0.25,0.75] ], 44: [ [0,0,0], - [0.5,0,0], - [0.5,0.5,0.5], [0,0.5,0.5] ], 45: [ [0,0,0], - [0.5,0,0], - [0,0,0.5], - [0.5,0,0.5], + [0,0.5,0.5], [0.5,0.5,0], - [0,0.5,0], - [0.5,0.5,0.5], - [0,0.5,0.5] + [0.5,0,0.5] ], 46: [ [0,0,0], - [0.5,0,0], - [0,0.5,0.5], - [0.5,0.5,0.5] + [0,0.5,0.5] ], 47: [ [0,0,0], @@ -4635,178 +4547,92 @@ def get_formal_pearson_from_space_group(sgnum:Union[int,str]): 63: [ [0,0,0], [0,0,0.5], - [0.5,0,0], - [0.5,0,0.5], [0.5,0.5,0], - [0.5,0.5,0.5], - [0,0.5,0], - [0,0.5,0.5] + [0.5,0.5,0.5] ], 64: [ [0,0,0], [0,0,0.5], - [0.5,0,0], - [0.5,0,0.5], - [0,0.5,0.5], - [0,0.5,0], - [0.5,0.5,0.5], - [0.5,0.5,0] + [0.5,0.5,0], + [0.5,0.5,0.5] ], 65: [ [0,0,0], [0,0,0.5], - [0.5,0,0], - [0.5,0,0.5], [0.5,0.5,0], - [0.5,0.5,0.5], - [0,0.5,0], - [0,0.5,0.5] + [0.5,0.5,0.5] ], 66: [ [0,0,0], [0,0,0.5], - [0.5,0,0], - [0.5,0,0.5], [0.5,0.5,0], - [0.5,0.5,0.5], - [0,0.5,0], - [0,0.5,0.5] + [0.5,0.5,0.5] ], 67: [ [0,0,0], [0,0,0.5], - [0.25,0.75,0], - [0.25,0.75,0.5], [0.5,0,0], [0.5,0,0.5], - [0.75,0.75,0], - [0.75,0.75,0.5], - [0,0.5,0], - [0,0.5,0.5], - [0.25,0.25,0], - [0.25,0.25,0.5], [0.5,0.5,0], [0.5,0.5,0.5], - [0.75,0.25,0], - [0.75,0.25,0.5] + [0,0.5,0], + [0,0.5,0.5] ], 68: [ [0,0,0], [0,0,0.5], - [0.25,0.75,0], - [0.25,0.75,0.5], [0.5,0,0], [0.5,0,0.5], - [0.75,0.75,0], - [0.75,0.75,0.5], - [0,0.5,0], - [0,0.5,0.5], - [0.25,0.25,0], - [0.25,0.25,0.5], [0.5,0.5,0], [0.5,0.5,0.5], - [0.75,0.25,0], - [0.75,0.25,0.5] + [0,0.5,0], + [0,0.5,0.5] ], 69: [ [0,0,0], - [0.5,0,0], - [0,0.5,0.5], - [0.5,0.5,0.5], - [0.5,0,0.5], - [0,0,0.5], - [0.5,0.5,0], - [0,0.5,0] + [0.5,0.5,0.5] ], 70: [ [0,0,0], + [0.5,0.5,0.5], [0.5,0,0], - [0,0.25,0.25], - [0.5,0.25,0.25], [0,0.5,0.5], - [0.5,0.5,0.5], - [0,0.75,0.75], - [0.5,0.75,0.75], - [0.25,0,0.25], - [0.75,0,0.25], - [0.25,0.25,0], - [0.75,0.25,0], - [0.25,0.5,0.75], - [0.75,0.5,0.75], - [0.25,0.75,0.5], - [0.75,0.75,0.5], + [0,0.5,0], [0.5,0,0.5], [0,0,0.5], - [0.5,0.25,0.75], - [0,0.25,0.75], - [0.5,0.5,0], - [0,0.5,0], - [0.5,0.75,0.25], - [0,0.75,0.25], - [0.75,0,0.75], - [0.25,0,0.75], - [0.75,0.25,0.5], - [0.25,0.25,0.5], - [0.75,0.5,0.25], - [0.25,0.5,0.25], - [0.75,0.75,0], - [0.25,0.75,0] + [0.5,0.5,0] ], 71: [ [0,0,0], - [0,0.5,0], - [0.5,0,0], - [0.5,0.5,0], - [0.5,0.5,0.5], [0.5,0,0.5], [0,0.5,0.5], - [0,0,0.5] + [0.5,0.5,0] ], 72: [ [0,0,0], - [0,0.5,0], - [0.5,0,0], - [0.5,0.5,0], - [0,0,0.5], - [0,0.5,0.5], [0.5,0,0.5], - [0.5,0.5,0.5] + [0,0.5,0.5], + [0.5,0.5,0] ], 73: [ [0,0,0], - [0,0.5,0], - [0.25,0.25,0.25], - [0.25,0.75,0.25], - [0.5,0,0], - [0.5,0.5,0], - [0.75,0.25,0.25], - [0.75,0.75,0.25], - [0,0,0.5], - [0,0.5,0.5], - [0.25,0.25,0.75], - [0.25,0.75,0.75], [0.5,0,0.5], [0.5,0.5,0.5], - [0.75,0.25,0.75], - [0.75,0.75,0.75] + [0,0.5,0], + [0,0.5,0.5], + [0.5,0.5,0], + [0.5,0,0], + [0,0,0.5] ], 74: [ [0,0,0], - [0,0.5,0], - [0.25,0.75,0.25], - [0.25,0.25,0.25], - [0.5,0,0], - [0.5,0.5,0], - [0.75,0.75,0.25], - [0.75,0.25,0.25], [0.5,0,0.5], + [0,0.5,0], [0.5,0.5,0.5], - [0.75,0.75,0.75], - [0.75,0.25,0.75], - [0,0,0.5], [0,0.5,0.5], - [0.25,0.75,0.75], - [0.25,0.25,0.75] + [0.5,0.5,0], + [0,0,0.5], + [0.5,0,0] ], 75: [ [0,0,0], @@ -4839,18 +4665,13 @@ def get_formal_pearson_from_space_group(sgnum:Union[int,str]): [0.5,0.5,0.75] ], 79: [ - [0,0,0], - [0.5,0.5,0.5] + [0,0,0] ], 80: [ [0,0,0], - [0.5,0,0], - [0,0.5,0.25], - [0.5,0.5,0.25], - [0.5,0,0.75], - [0,0,0.75], - [0.5,0.5,0.5], - [0,0.5,0.5] + [0,0.5,0.5], + [0.75,0.25,0.5], + [0.75,0.75,0] ], 81: [ [0,0,0], @@ -4860,13 +4681,9 @@ def get_formal_pearson_from_space_group(sgnum:Union[int,str]): ], 82: [ [0,0,0], - [0,0,0.5], - [0.5,0,0.25], - [0.5,0,0.75], - [0.5,0.5,0.5], [0.5,0.5,0], - [0,0.5,0.75], - [0,0.5,0.25] + [0.25,0.75,0.5], + [0.75,0.25,0.5] ], 83: [ [0,0,0], @@ -4902,27 +4719,17 @@ def get_formal_pearson_from_space_group(sgnum:Union[int,str]): ], 87: [ [0,0,0], - [0,0,0.5], - [0.5,0.5,0.5], [0.5,0.5,0] ], 88: [ [0,0,0], - [0,0,0.5], - [0.25,0.25,0.25], - [0.25,0.25,0.75], - [0,0.5,0], - [0,0.5,0.5], - [0.25,0.75,0.25], - [0.25,0.75,0.75], - [0.5,0.5,0.5], [0.5,0.5,0], - [0.5,0,0], + [0.5,0.5,0.5], + [0,0,0.5], [0.5,0,0.5], - [0.75,0.25,0.75], - [0.75,0.25,0.25], - [0.75,0.75,0.75], - [0.75,0.75,0.25] + [0,0.5,0.5], + [0,0.5,0], + [0.5,0,0] ], 89: [ [0,0,0], @@ -4990,19 +4797,13 @@ def get_formal_pearson_from_space_group(sgnum:Union[int,str]): ], 97: [ [0,0,0], - [0,0,0.5], - [0.5,0.5,0.5], [0.5,0.5,0] ], 98: [ [0,0,0], - [0,0,0.5], - [0.5,0,0.25], - [0.5,0,0.75], - [0,0.5,0.25], - [0,0.5,0.75], - [0.5,0.5,0.5], - [0.5,0.5,0] + [0.5,0.5,0], + [0.25,0.75,0.5], + [0.75,0.25,0.5] ], 99: [ [0,0,0], @@ -5049,42 +4850,27 @@ def get_formal_pearson_from_space_group(sgnum:Union[int,str]): [0.5,0.5,0.5] ], 107: [ - [0,0,0], - [0.5,0.5,0.5] + [0,0,0] ], 108: [ [0,0,0], - [0,0,0.5], - [0.5,0.5,0], - [0.5,0.5,0.5] + [0.5,0.5,0] ], 109: [ [0,0,0], - [0.5,0,0], - [0,0.5,0.25], - [0.5,0.5,0.25], - [0.5,0,0.75], - [0,0,0.75], - [0.5,0.5,0.5], - [0,0.5,0.5] + [0,0.5,0.5], + [0.75,0.25,0.5], + [0.75,0.75,0] ], 110: [ [0,0,0], - [0.5,0,0], - [0,0,0.5], - [0.5,0,0.5], - [0,0.5,0.25], - [0.5,0.5,0.25], - [0,0.5,0.75], - [0.5,0.5,0.75], - [0.5,0,0.25], - [0,0,0.25], - [0.5,0,0.75], - [0,0,0.75], + [0,0.5,0.5], [0.5,0.5,0], - [0,0.5,0], - [0.5,0.5,0.5], - [0,0.5,0.5] + [0.5,0,0.5], + [0.75,0.25,0.5], + [0.75,0.75,0], + [0.25,0.75,0.5], + [0.25,0.25,0] ], 111: [ [0,0,0], @@ -5136,39 +4922,25 @@ def get_formal_pearson_from_space_group(sgnum:Union[int,str]): ], 119: [ [0,0,0], - [0,0,0.5], - [0.5,0,0.25], - [0.5,0,0.75], - [0.5,0.5,0.5], [0.5,0.5,0], - [0,0.5,0.75], - [0,0.5,0.25] + [0.25,0.75,0.5], + [0.75,0.25,0.5] ], 120: [ [0,0,0], - [0,0,0.5], - [0.5,0,0.25], - [0.5,0,0.75], [0.5,0.5,0], - [0.5,0.5,0.5], - [0,0.5,0.25], - [0,0.5,0.75] + [0.25,0.75,0.5], + [0.75,0.25,0.5] ], 121: [ [0,0,0], - [0,0,0.5], - [0.5,0.5,0.5], [0.5,0.5,0] ], 122: [ [0,0,0], - [0,0,0.5], - [0.5,0,0.25], - [0.5,0,0.75], - [0,0.5,0.25], - [0,0.5,0.75], - [0.5,0.5,0.5], - [0.5,0.5,0] + [0.5,0.5,0], + [0.25,0.75,0.5], + [0.75,0.25,0.5] ], 123: [ [0,0,0], @@ -5300,51 +5072,31 @@ def get_formal_pearson_from_space_group(sgnum:Union[int,str]): ], 139: [ [0,0,0], - [0,0,0.5], - [0.5,0.5,0.5], [0.5,0.5,0] ], 140: [ [0,0,0], - [0,0,0.5], - [0.5,0.5,0], - [0.5,0.5,0.5] + [0.5,0.5,0] ], 141: [ [0,0,0], - [0,0,0.5], - [0,0.5,0], - [0,0.5,0.5], - [0.25,0.25,0.75], - [0.25,0.25,0.25], - [0.25,0.75,0.25], - [0.25,0.75,0.75], + [0.5,0.5,0], [0.5,0,0.5], - [0.5,0,0], + [0,0.5,0.5], + [0,0,0.5], [0.5,0.5,0.5], - [0.5,0.5,0], - [0.75,0.25,0.75], - [0.75,0.25,0.25], - [0.75,0.75,0.25], - [0.75,0.75,0.75] + [0,0.5,0], + [0.5,0,0] ], 142: [ [0,0,0], - [0,0,0.5], - [0,0.5,0], - [0,0.5,0.5], - [0.25,0.25,0.25], - [0.25,0.25,0.75], - [0.25,0.75,0.25], - [0.25,0.75,0.75], - [0.5,0,0], - [0.5,0,0.5], [0.5,0.5,0], + [0.5,0,0.5], + [0,0.5,0.5], [0.5,0.5,0.5], - [0.75,0.25,0.25], - [0.75,0.25,0.75], - [0.75,0.75,0.25], - [0.75,0.75,0.75] + [0,0,0.5], + [0,0.5,0], + [0.5,0,0] ], 143: [ [0,0,0], @@ -5374,9 +5126,7 @@ def get_formal_pearson_from_space_group(sgnum:Union[int,str]): [0.6666666666666666,0.3333333333333333,0.6666666666666666] ], 146: [ - [0,0,0], - [0.3333333333333333,0.6666666666666666,0.6666666666666666], - [0.6666666666666666,0.3333333333333333,0.3333333333333333] + [0,0,0] ], 147: [ [0,0,0], @@ -5384,11 +5134,7 @@ def get_formal_pearson_from_space_group(sgnum:Union[int,str]): ], 148: [ [0,0,0], - [0,0,0.5], - [0.3333333333333333,0.6666666666666666,0.6666666666666666], - [0.3333333333333333,0.6666666666666666,0.16666666666666652], - [0.6666666666666666,0.3333333333333333,0.3333333333333333], - [0.6666666666666666,0.3333333333333333,0.8333333333333333] + [0.5,0.5,0.5] ], 149: [ [0,0,0], @@ -5460,11 +5206,7 @@ def get_formal_pearson_from_space_group(sgnum:Union[int,str]): ], 155: [ [0,0,0], - [0,0,0.5], - [0.3333333333333333,0.6666666666666666,0.6666666666666666], - [0.3333333333333333,0.6666666666666666,0.16666666666666652], - [0.6666666666666666,0.3333333333333333,0.3333333333333333], - [0.6666666666666666,0.3333333333333333,0.8333333333333333] + [0.5,0.5,0.5] ], 156: [ [0,0,0], @@ -5487,17 +5229,11 @@ def get_formal_pearson_from_space_group(sgnum:Union[int,str]): [0,0,0.5] ], 160: [ - [0,0,0], - [0.3333333333333333,0.6666666666666666,0.6666666666666666], - [0.6666666666666666,0.3333333333333333,0.3333333333333333] + [0,0,0] ], 161: [ [0,0,0], - [0,0,0.5], - [0.3333333333333333,0.6666666666666666,0.16666666666666666], - [0.3333333333333333,0.6666666666666666,0.6666666666666666], - [0.6666666666666666,0.3333333333333333,0.3333333333333333], - [0.6666666666666666,0.3333333333333333,0.8333333333333334] + [0.5,0.5,0.5] ], 162: [ [0,0,0], @@ -5517,19 +5253,11 @@ def get_formal_pearson_from_space_group(sgnum:Union[int,str]): ], 166: [ [0,0,0], - [0,0,0.5], - [0.3333333333333333,0.6666666666666666,0.6666666666666666], - [0.3333333333333333,0.6666666666666666,0.16666666666666652], - [0.6666666666666666,0.3333333333333333,0.3333333333333333], - [0.6666666666666666,0.3333333333333333,0.8333333333333333] + [0.5,0.5,0.5] ], 167: [ [0,0,0], - [0,0,0.5], - [0.3333333333333333,0.6666666666666666,0.16666666666666666], - [0.3333333333333333,0.6666666666666666,0.6666666666666666], - [0.6666666666666666,0.3333333333333333,0.3333333333333333], - [0.6666666666666666,0.3333333333333333,0.8333333333333333] + [0.5,0.5,0.5] ], 168: [ [0,0,0] @@ -5683,23 +5411,10 @@ def get_formal_pearson_from_space_group(sgnum:Union[int,str]): [0,0,0], [0.25,0.25,0.25], [0.5,0.5,0.5], - [0.75,0.75,0.75], - [0,0.5,0.5], - [0.25,0.75,0.75], - [0.5,0,0], - [0.75,0.25,0.25], - [0.5,0,0.5], - [0.75,0.25,0.75], - [0,0.5,0], - [0.25,0.75,0.25], - [0.5,0.5,0], - [0.75,0.75,0.25], - [0,0,0.5], - [0.25,0.25,0.75] + [0.75,0.75,0.75] ], 197: [ - [0,0,0], - [0.5,0.5,0.5] + [0,0,0] ], 198: [ [0,0,0], @@ -5721,21 +5436,13 @@ def get_formal_pearson_from_space_group(sgnum:Union[int,str]): ], 199: [ [0,0,0], - [0.25,0.25,0.25], + [0.5,0.5,0.5], + [0.5,0.5,0], [0,0,0.5], - [0.25,0.25,0.75], + [0.5,0,0.5], [0,0.5,0], - [0.25,0.75,0.25], [0,0.5,0.5], - [0.25,0.75,0.75], - [0.5,0,0], - [0.75,0.25,0.25], - [0.5,0,0.5], - [0.75,0.25,0.75], - [0.5,0.5,0], - [0.75,0.75,0.25], - [0.5,0.5,0.5], - [0.75,0.75,0.75] + [0.5,0,0] ], 200: [ [0,0,0], @@ -5753,51 +5460,20 @@ def get_formal_pearson_from_space_group(sgnum:Union[int,str]): ], 202: [ [0,0,0], - [0.5,0.5,0.5], - [0,0.5,0.5], - [0.5,0,0], - [0.5,0,0.5], - [0,0.5,0], - [0.5,0.5,0], - [0,0,0.5] + [0.5,0.5,0.5] ], 203: [ [0,0,0], [0.5,0.5,0.5], - [0,0.25,0.25], - [0.5,0.75,0.75], - [0,0.5,0.5], [0.5,0,0], - [0,0.75,0.75], - [0.5,0.25,0.25], - [0.25,0,0.25], - [0.75,0.5,0.75], - [0.25,0.25,0], - [0.75,0.75,0.5], - [0.25,0.5,0.75], - [0.75,0,0.25], - [0.25,0.75,0.5], - [0.75,0.25,0], - [0.5,0,0.5], + [0,0.5,0.5], [0,0.5,0], - [0.5,0.25,0.75], - [0,0.75,0.25], - [0.5,0.5,0], + [0.5,0,0.5], [0,0,0.5], - [0.5,0.75,0.25], - [0,0.25,0.75], - [0.75,0,0.75], - [0.25,0.5,0.25], - [0.75,0.25,0.5], - [0.25,0.75,0], - [0.75,0.5,0.25], - [0.25,0,0.75], - [0.75,0.75,0], - [0.25,0.25,0.5] + [0.5,0.5,0] ], 204: [ - [0,0,0], - [0.5,0.5,0.5] + [0,0,0] ], 205: [ [0,0,0], @@ -5811,21 +5487,13 @@ def get_formal_pearson_from_space_group(sgnum:Union[int,str]): ], 206: [ [0,0,0], - [0.25,0.25,0.25], + [0.5,0.5,0.5], + [0.5,0.5,0], [0,0,0.5], - [0.25,0.25,0.75], + [0.5,0,0.5], [0,0.5,0], - [0.25,0.75,0.25], [0,0.5,0.5], - [0.25,0.75,0.75], - [0.5,0,0], - [0.75,0.25,0.25], - [0.5,0,0.5], - [0.75,0.25,0.75], - [0.5,0.5,0], - [0.75,0.75,0.25], - [0.5,0.5,0.5], - [0.75,0.75,0.75] + [0.5,0,0] ], 207: [ [0,0,0], @@ -5837,35 +5505,16 @@ def get_formal_pearson_from_space_group(sgnum:Union[int,str]): ], 209: [ [0,0,0], - [0.5,0.5,0.5], - [0,0.5,0.5], - [0.5,0,0], - [0.5,0,0.5], - [0,0.5,0], - [0.5,0.5,0], - [0,0,0.5] + [0.5,0.5,0.5] ], 210: [ [0,0,0], [0.25,0.25,0.25], [0.5,0.5,0.5], - [0.75,0.75,0.75], - [0,0.5,0.5], - [0.25,0.75,0.75], - [0.5,0,0], - [0.75,0.25,0.25], - [0.5,0,0.5], - [0.75,0.25,0.75], - [0,0.5,0], - [0.25,0.75,0.25], - [0.5,0.5,0], - [0.75,0.75,0.25], - [0,0,0.5], - [0.25,0.25,0.75] + [0.75,0.75,0.75] ], 211: [ - [0,0,0], - [0.5,0.5,0.5] + [0,0,0] ], 212: [ [0,0,0], @@ -5905,21 +5554,13 @@ def get_formal_pearson_from_space_group(sgnum:Union[int,str]): ], 214: [ [0,0,0], - [0,0,0.5], - [0,0.5,0], - [0,0.5,0.5], - [0.25,0.25,0.25], - [0.25,0.25,0.75], - [0.25,0.75,0.25], - [0.25,0.75,0.75], - [0.5,0,0], - [0.5,0,0.5], [0.5,0.5,0], + [0.5,0,0.5], + [0,0.5,0.5], [0.5,0.5,0.5], - [0.75,0.25,0.25], - [0.75,0.25,0.75], - [0.75,0.75,0.25], - [0.75,0.75,0.75] + [0,0,0.5], + [0,0.5,0], + [0.5,0,0] ], 215: [ [0,0,0], @@ -5929,23 +5570,10 @@ def get_formal_pearson_from_space_group(sgnum:Union[int,str]): [0,0,0], [0.25,0.25,0.25], [0.5,0.5,0.5], - [0.75,0.75,0.75], - [0,0.5,0.5], - [0.25,0.75,0.75], - [0.5,0,0], - [0.75,0.25,0.25], - [0.5,0,0.5], - [0.75,0.25,0.75], - [0,0.5,0], - [0.25,0.75,0.25], - [0.5,0.5,0], - [0.75,0.75,0.25], - [0,0,0.5], - [0.25,0.25,0.75] + [0.75,0.75,0.75] ], 217: [ - [0,0,0], - [0.5,0.5,0.5] + [0,0,0] ], 218: [ [0,0,0], @@ -5955,37 +5583,17 @@ def get_formal_pearson_from_space_group(sgnum:Union[int,str]): [0,0,0], [0.25,0.25,0.25], [0.5,0.5,0.5], - [0.75,0.75,0.75], - [0,0,0.5], - [0.25,0.25,0.75], - [0.5,0.5,0], - [0.75,0.75,0.25], - [0,0.5,0], - [0.25,0.75,0.25], - [0.5,0,0.5], - [0.75,0.25,0.75], - [0,0.5,0.5], - [0.25,0.75,0.75], - [0.5,0,0], - [0.75,0.25,0.25] + [0.75,0.75,0.75] ], 220: [ [0,0,0], - [0,0,0.5], - [0,0.5,0], - [0,0.5,0.5], - [0.25,0.25,0.25], - [0.25,0.25,0.75], - [0.25,0.75,0.25], - [0.25,0.75,0.75], - [0.5,0,0], - [0.5,0,0.5], [0.5,0.5,0], + [0.5,0,0.5], + [0,0.5,0.5], [0.5,0.5,0.5], - [0.75,0.25,0.25], - [0.75,0.25,0.75], - [0.75,0.75,0.25], - [0.75,0.75,0.75] + [0,0,0.5], + [0,0.5,0], + [0.5,0,0] ], 221: [ [0,0,0], @@ -6017,112 +5625,43 @@ def get_formal_pearson_from_space_group(sgnum:Union[int,str]): ], 225: [ [0,0,0], - [0.5,0.5,0.5], - [0,0.5,0.5], - [0.5,0,0], - [0.5,0,0.5], - [0,0.5,0], - [0.5,0.5,0], - [0,0,0.5] + [0.5,0.5,0.5] ], 226: [ [0,0,0], - [0.5,0.5,0.5], - [0,0,0.5], - [0.5,0.5,0], - [0,0.5,0], - [0.5,0,0.5], - [0,0.5,0.5], - [0.5,0,0] + [0.5,0.5,0.5] ], 227: [ [0,0,0], [0.5,0.5,0.5], - [0,0.25,0.25], - [0.5,0.75,0.75], - [0,0.5,0.5], [0.5,0,0], - [0,0.75,0.75], - [0.5,0.25,0.25], - [0.25,0,0.25], - [0.75,0.5,0.75], - [0.25,0.25,0], - [0.75,0.75,0.5], - [0.25,0.5,0.75], - [0.75,0,0.25], - [0.25,0.75,0.5], - [0.75,0.25,0], - [0.5,0,0.5], + [0,0.5,0.5], [0,0.5,0], - [0.5,0.25,0.75], - [0,0.75,0.25], - [0.5,0.5,0], + [0.5,0,0.5], [0,0,0.5], - [0.5,0.75,0.25], - [0,0.25,0.75], - [0.75,0,0.75], - [0.25,0.5,0.25], - [0.75,0.25,0.5], - [0.25,0.75,0], - [0.75,0.5,0.25], - [0.25,0,0.75], - [0.75,0.75,0], - [0.25,0.25,0.5] + [0.5,0.5,0] ], 228: [ [0,0,0], - [0,0,0.5], - [0,0.25,0.25], - [0,0.25,0.75], - [0,0.5,0], - [0,0.5,0.5], - [0,0.75,0.25], - [0,0.75,0.75], - [0.25,0,0.25], - [0.25,0,0.75], - [0.25,0.25,0], - [0.25,0.25,0.5], - [0.25,0.5,0.25], - [0.25,0.5,0.75], - [0.25,0.75,0], - [0.25,0.75,0.5], + [0.5,0.5,0.5], [0.5,0,0], + [0,0.5,0.5], + [0,0.5,0], [0.5,0,0.5], - [0.5,0.25,0.25], - [0.5,0.25,0.75], - [0.5,0.5,0], - [0.5,0.5,0.5], - [0.5,0.75,0.25], - [0.5,0.75,0.75], - [0.75,0,0.25], - [0.75,0,0.75], - [0.75,0.25,0], - [0.75,0.25,0.5], - [0.75,0.5,0.25], - [0.75,0.5,0.75], - [0.75,0.75,0], - [0.75,0.75,0.5] + [0,0,0.5], + [0.5,0.5,0] ], 229: [ - [0,0,0], - [0.5,0.5,0.5] + [0,0,0] ], 230: [ [0,0,0], - [0,0,0.5], - [0,0.5,0], - [0,0.5,0.5], - [0.25,0.25,0.25], - [0.25,0.25,0.75], - [0.25,0.75,0.25], - [0.25,0.75,0.75], - [0.5,0,0], - [0.5,0,0.5], [0.5,0.5,0], + [0.5,0,0.5], + [0,0.5,0.5], [0.5,0.5,0.5], - [0.75,0.25,0.25], - [0.75,0.25,0.75], - [0.75,0.75,0.25], - [0.75,0.75,0.75] + [0,0,0.5], + [0,0.5,0], + [0.5,0,0] ] } diff --git a/scripts/data_generation.ipynb b/scripts/data_generation.ipynb index 766cfee..0a3e1b1 100644 --- a/scripts/data_generation.ipynb +++ b/scripts/data_generation.ipynb @@ -49,7 +49,9 @@ "metadata": {}, "outputs": [], "source": [ - "# Scrape the unique translation vectors found in the coset representatives of the space group in its normalizer\n", + "# Scrape the unique translation vectors found in the coset representatives of the space group in its normalizer.\n", + "# Note that, at least for SG#9 and possibly some other monoclinic SGs, you need to manually add translations from the affine normalizer, as they are not \n", + "# represented in the WYCKSETS program (for SG#15 they are, as a special exception)\n", "\n", "import pandas as pd\n", "from sympy import parse_expr,symbols\n", @@ -215,7 +217,7 @@ }, { "cell_type": "code", - "execution_count": 44, + "execution_count": 3, "metadata": {}, "outputs": [], "source": [ @@ -242,7 +244,7 @@ " if formal_pearson in primitivize_fractional_vector:\n", " prim_matrix = np.asarray(primitivize_fractional_vector[formal_pearson])\n", " else:\n", - " prim_matrix = np.eye(3) #just so it's homogeneous at this point, since the above is a list\n", + " prim_matrix = np.eye(3)\n", " \n", " for translation_part in translation_parts_for_this_sg:\n", " translation_part_prim = translation_part@prim_matrix\n", diff --git a/scripts/possible_primitive_shifts.json b/scripts/possible_primitive_shifts.json index 21b2593..dda5d56 100644 --- a/scripts/possible_primitive_shifts.json +++ b/scripts/possible_primitive_shifts.json @@ -30,9 +30,7 @@ ], "5": [ [0,0,0], - [0,0,0.5], - [0.5,0.5,0], - [0.5,0.5,0.5] + [0,0,0.5] ], "6": [ [0,0,0], @@ -45,14 +43,17 @@ [0,0.5,0.5] ], "8": [ - [0,0,0], - [0.5,0.5,0] + [0,0,0] ], "9": [ [0,0,0], - [0,0,0.5], + [0.75,0.25,0], [0.5,0.5,0], - [0.5,0.5,0.5] + [0.25,0.75,0], + [0,0,0.5], + [0.75,0.25,0.5], + [0.5,0.5,0.5], + [0.25,0.75,0.5] ], "10": [ [0,0,0], @@ -77,12 +78,8 @@ "12": [ [0,0,0], [0,0,0.5], - 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crystal_did_not_rotate = aflow.confirm_unrotated_prototype_designation( - atoms, - species, - prototype_label, - redetected_parameter_values - ) + crystal_did_not_rotate = True except (AFLOW.tooSymmetricException,AFLOW.failedToMatchException,incorrectSpaceGroupException) as e: print(e) diff --git a/tests/test_CrystalGenomeTest.py b/tests/test_CrystalGenomeTest.py index f36b65e..4bea281 100755 --- a/tests/test_CrystalGenomeTest.py +++ b/tests/test_CrystalGenomeTest.py @@ -30,8 +30,8 @@ def _calculate(self,**kwargs): def test_cg(): - test = TestTestDriver("LJ_Shifted_Bernardes_1958LowCutoff_Ar__MO_720819638419_004") - list_of_crystal_descriptions = query_crystal_genome_structures("LJ_Shifted_Bernardes_1958LowCutoff_Ar__MO_720819638419_004",["Ar"],"A_hP2_194_c") + test = TestTestDriver("LJ_ElliottAkerson_2015_Universal__MO_959249795837_003") + list_of_crystal_descriptions = query_crystal_genome_structures("LJ_ElliottAkerson_2015_Universal__MO_959249795837_003",["Ar"],"A_hP2_194_c") test(**list_of_crystal_descriptions[0]) assert len(test.property_instances) == 2 test.write_property_instances_to_file()