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131, 132, 134, 135, 139, 145, 146, 148, 149, 150, 151, 152, 154, 155, 156, 157, 159, 160, 161, 163, 165], "calcul": [0, 1, 2, 6, 7, 10, 11, 15, 17, 20, 27, 28, 30, 31, 32, 37, 38, 39, 42, 44, 45, 49, 52, 53, 54, 56, 57, 59, 62, 63, 64, 65, 66, 67, 70, 74, 78, 81, 83, 84, 85, 87, 88, 90, 92, 97, 98, 100, 101, 102, 105, 106, 107, 108, 113, 119, 121, 122, 124, 125, 127, 129, 139, 141, 142, 143, 144, 148, 149, 150, 151, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 166], "molecular": [0, 1, 2, 3, 6, 10, 12, 13, 14, 15, 16, 28, 29, 32, 33, 34, 38, 45, 50, 55, 69, 74, 78, 79, 81, 87, 88, 97, 104, 106, 124, 125, 132, 133, 135, 139, 141, 150, 157, 160], "dynam": [0, 1, 3, 8, 12, 13, 14, 20, 24, 29, 33, 34, 48, 50, 55, 65, 79, 81, 87, 88, 91, 102, 124, 125, 133, 135, 139, 157, 160], "simpl": [0, 1, 4, 7, 10, 12, 13, 23, 24, 26, 33, 34, 42, 45, 50, 51, 55, 57, 69, 70, 78, 82, 83, 85, 88, 90, 91, 93, 94, 97, 106, 111, 118, 125, 128, 131, 132, 134, 135, 139, 143, 145, 150, 151, 153, 156, 158, 159, 160, 164], "straightforward": [0, 64, 85, 139, 145, 151], "can": [0, 2, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50, 51, 53, 54, 55, 56, 57, 58, 59, 62, 63, 64, 65, 66, 67, 69, 70, 71, 74, 76, 78, 79, 80, 81, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 94, 97, 98, 99, 100, 101, 103, 104, 105, 106, 107, 108, 110, 111, 112, 114, 115, 117, 118, 120, 121, 122, 123, 124, 125, 127, 128, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 143, 144, 145, 146, 147, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 163, 164], "via": [0, 2, 3, 7, 8, 13, 26, 33, 40, 42, 46, 47, 48, 50, 55, 57, 85, 87, 99, 104, 109, 112, 124, 139, 150, 153, 160], "graphic": [0, 71, 74, 76, 78, 79, 90, 106, 108, 136], "user": [0, 3, 4, 6, 9, 26, 31, 32, 33, 38, 39, 41, 42, 47, 48, 50, 51, 57, 74, 81, 85, 86, 88, 97, 108, 109, 110, 112, 116, 117, 123, 124, 125, 131, 136, 137, 138, 139, 144, 151, 154], "interfac": [0, 1, 7, 10, 13, 16, 17, 18, 19, 20, 21, 22, 24, 26, 27, 28, 29, 32, 33, 34, 38, 39, 40, 41, 42, 45, 47, 51, 74, 76, 78, 81, 87, 88, 97, 102, 106, 108, 111, 113, 119, 121, 124, 125, 128, 132, 133, 135, 136, 139, 145, 154, 164], "command": [0, 1, 8, 9, 12, 13, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 32, 33, 34, 38, 40, 41, 42, 44, 45, 47, 48, 51, 57, 70, 74, 76, 78, 79, 86, 88, 93, 94, 106, 111, 112, 113, 116, 117, 122, 125, 130, 132, 133, 134, 135, 136, 139, 143, 151, 152, 156, 158, 164], "line": [0, 1, 2, 9, 12, 13, 17, 18, 19, 20, 22, 24, 27, 28, 32, 33, 34, 38, 42, 45, 47, 48, 51, 55, 56, 57, 58, 60, 63, 64, 74, 78, 80, 85, 86, 88, 91, 93, 94, 106, 112, 116, 120, 123, 125, 127, 130, 134, 135, 136, 138, 139, 144, 145, 151, 152, 154, 155, 156, 157, 158, 164], "tool": [0, 1, 4, 6, 35, 52, 55, 57, 63, 71, 74, 78, 84, 85, 86, 88, 103, 106, 112, 115, 120, 123, 124, 128, 134, 135, 136, 139, 143, 144, 149, 154, 158, 161, 164, 165], "script": [0, 2, 8, 11, 13, 14, 21, 27, 28, 30, 39, 48, 50, 51, 57, 71, 75, 78, 79, 86, 88, 108, 110, 116, 117, 121, 123, 125, 127, 129, 130, 131, 132, 133, 136, 138, 139, 142, 144, 146, 149, 150, 151, 152, 153, 154, 157, 159, 160, 161, 164, 165], "ar": [0, 3, 4, 5, 7, 8, 9, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 32, 33, 34, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 62, 63, 64, 65, 66, 70, 71, 72, 76, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 91, 92, 94, 96, 97, 98, 99, 100, 102, 103, 104, 107, 110, 111, 112, 113, 115, 116, 117, 118, 120, 121, 122, 123, 125, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 141, 144, 145, 146, 147, 150, 151, 152, 153, 154, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165], "follow": [0, 3, 7, 8, 12, 13, 14, 16, 17, 18, 22, 24, 25, 26, 27, 28, 30, 32, 33, 34, 38, 41, 43, 45, 46, 50, 51, 52, 53, 55, 56, 57, 62, 63, 64, 65, 66, 67, 69, 70, 78, 81, 82, 83, 85, 86, 87, 88, 106, 107, 108, 111, 112, 114, 115, 117, 120, 121, 122, 123, 128, 131, 133, 135, 136, 137, 138, 139, 141, 142, 145, 147, 150, 151, 152, 153, 154, 159, 160, 162, 164, 165], "see": [0, 2, 3, 4, 6, 7, 8, 16, 17, 19, 24, 25, 26, 27, 28, 32, 33, 34, 35, 38, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51, 52, 54, 55, 56, 57, 62, 63, 65, 70, 71, 72, 78, 79, 82, 83, 85, 86, 87, 88, 90, 91, 92, 97, 98, 99, 100, 104, 107, 108, 110, 112, 114, 117, 121, 122, 125, 127, 128, 130, 132, 133, 134, 136, 139, 140, 141, 144, 145, 148, 150, 151, 152, 153, 154, 156, 157, 158, 159, 160, 161, 164, 167], "what": [0, 1, 3, 6, 7, 8, 14, 16, 18, 38, 42, 49, 53, 64, 82, 85, 88, 90, 92, 111, 112, 113, 117, 120, 127, 129, 131, 132, 133, 134, 135, 144, 150, 154, 156, 160, 161, 163, 165], "short": [0, 13, 22, 57, 65, 85, 108, 114, 120, 132, 150, 151, 153, 160, 163], "introduct": [0, 12, 33, 61, 107, 112, 129, 135, 138, 165], "It": [0, 3, 6, 7, 8, 11, 13, 14, 15, 16, 20, 24, 25, 28, 29, 33, 34, 36, 39, 40, 41, 42, 44, 47, 48, 51, 53, 55, 56, 57, 63, 66, 69, 74, 78, 81, 83, 85, 87, 88, 91, 92, 99, 100, 101, 104, 106, 112, 114, 117, 120, 122, 124, 134, 138, 139, 144, 145, 151, 154, 157, 160, 161], "new": [0, 1, 3, 7, 13, 22, 26, 38, 42, 48, 50, 52, 57, 63, 65, 68, 70, 71, 76, 82, 85, 86, 87, 88, 90, 92, 93, 94, 102, 108, 112, 113, 118, 122, 127, 132, 133, 134, 138, 139, 144, 150, 151, 152, 153, 154, 160], "get": [0, 1, 3, 4, 6, 11, 12, 14, 19, 24, 29, 33, 35, 43, 44, 49, 50, 51, 52, 54, 56, 57, 62, 63, 64, 65, 67, 70, 71, 78, 82, 83, 85, 86, 87, 90, 94, 100, 101, 102, 103, 104, 107, 108, 109, 111, 115, 120, 122, 123, 127, 131, 132, 133, 134, 135, 136, 139, 140, 144, 146, 151, 152, 153, 154, 155, 158, 160, 161, 163, 164], "access": [0, 3, 12, 13, 15, 32, 33, 42, 47, 50, 51, 56, 57, 70, 79, 87, 88, 99, 103, 104, 109, 112, 133, 134, 139, 145], "all": [0, 1, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 19, 20, 22, 24, 25, 29, 32, 33, 35, 36, 38, 41, 44, 46, 47, 48, 49, 50, 51, 53, 54, 55, 56, 57, 62, 63, 65, 66, 70, 71, 72, 76, 78, 79, 81, 82, 83, 85, 86, 87, 88, 89, 92, 93, 97, 99, 101, 102, 103, 104, 108, 110, 111, 112, 116, 117, 118, 120, 121, 122, 125, 128, 130, 131, 132, 133, 135, 136, 138, 139, 141, 144, 145, 146, 150, 151, 152, 154, 156, 157, 158, 160, 161, 162, 163, 164, 166], "function": [0, 1, 3, 4, 7, 8, 9, 10, 12, 13, 15, 17, 18, 19, 20, 21, 22, 24, 25, 27, 28, 32, 33, 35, 38, 40, 41, 43, 44, 47, 50, 52, 53, 54, 55, 56, 57, 63, 64, 66, 67, 69, 70, 71, 72, 76, 78, 79, 81, 85, 86, 87, 89, 90, 91, 92, 94, 97, 98, 99, 102, 103, 104, 106, 107, 112, 114, 117, 120, 121, 122, 124, 125, 127, 128, 131, 132, 133, 134, 135, 139, 145, 146, 147, 151, 152, 153, 154, 155, 156, 159, 160, 161, 164, 165], "flexibl": [0, 4, 85, 87, 124, 125, 133, 139], "sinc": [0, 11, 12, 13, 14, 15, 22, 33, 41, 42, 48, 49, 53, 55, 57, 70, 78, 83, 85, 87, 88, 91, 97, 111, 112, 116, 118, 127, 133, 134, 139, 145, 151, 152, 154, 157, 160, 162, 163], "base": [0, 1, 3, 4, 8, 9, 10, 12, 13, 18, 19, 24, 25, 27, 28, 32, 38, 41, 47, 51, 53, 55, 56, 57, 60, 63, 65, 76, 78, 83, 85, 86, 87, 88, 91, 92, 93, 94, 97, 99, 100, 104, 105, 106, 107, 112, 113, 114, 117, 122, 127, 133, 135, 136, 139, 150, 151, 152], "possibl": [0, 3, 4, 6, 7, 8, 15, 16, 18, 19, 20, 25, 28, 32, 40, 41, 44, 47, 48, 50, 51, 55, 57, 63, 64, 66, 68, 70, 71, 72, 76, 78, 81, 82, 84, 85, 86, 87, 101, 104, 106, 117, 120, 125, 130, 131, 135, 139, 145, 152, 154, 156, 157, 160, 164], "perform": [0, 13, 14, 15, 16, 20, 24, 26, 28, 30, 33, 34, 35, 38, 41, 44, 47, 48, 49, 50, 51, 55, 65, 66, 69, 85, 86, 88, 93, 104, 107, 111, 124, 125, 128, 131, 132, 133, 134, 135, 139, 141, 147, 148, 150, 151, 153, 154, 156, 160, 162], "veri": [0, 3, 6, 7, 13, 20, 29, 33, 40, 42, 43, 47, 55, 85, 88, 111, 112, 114, 120, 125, 131, 132, 134, 138, 139, 145, 150, 151, 152, 154, 158, 160], "complic": [0, 4, 6, 33, 57], "task": [0, 6, 8, 13, 36, 37, 38, 40, 48, 50, 78, 85, 88, 125, 150, 160, 162], "without": [0, 6, 8, 12, 13, 14, 20, 21, 24, 26, 47, 48, 50, 51, 55, 57, 63, 70, 78, 79, 85, 86, 87, 88, 93, 94, 106, 112, 115, 121, 125, 132, 133, 139, 151, 154, 156, 158], "ani": [0, 2, 3, 6, 8, 10, 12, 13, 14, 16, 20, 22, 24, 26, 28, 32, 33, 39, 40, 44, 46, 47, 48, 49, 50, 51, 52, 57, 62, 65, 70, 78, 79, 81, 83, 87, 88, 89, 94, 100, 103, 106, 107, 109, 111, 112, 114, 122, 129, 132, 134, 136, 138, 139, 145, 150, 154, 156, 158, 160, 163, 164, 165], "code": [0, 1, 3, 8, 9, 12, 14, 17, 18, 19, 21, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 44, 45, 47, 50, 51, 56, 57, 65, 66, 72, 75, 81, 84, 85, 86, 88, 98, 99, 106, 107, 108, 110, 111, 113, 114, 117, 118, 122, 124, 125, 127, 128, 132, 135, 136, 139, 146, 150, 160, 165], "modif": [0, 50, 57, 73, 88, 91, 112, 114, 121], "For": [0, 3, 4, 6, 7, 8, 12, 16, 17, 19, 20, 21, 22, 27, 28, 29, 30, 32, 33, 34, 38, 41, 42, 43, 46, 47, 48, 50, 51, 52, 55, 56, 57, 59, 62, 63, 65, 69, 70, 71, 72, 76, 78, 79, 81, 83, 85, 86, 87, 88, 89, 91, 92, 93, 94, 97, 98, 102, 106, 107, 108, 109, 112, 120, 121, 123, 125, 128, 132, 133, 134, 135, 136, 138, 139, 141, 145, 147, 148, 150, 151, 152, 153, 154, 155, 158, 161, 162, 164, 165, 167], "exampl": [0, 1, 2, 3, 4, 7, 9, 10, 12, 14, 15, 16, 17, 32, 33, 35, 36, 37, 41, 42, 46, 48, 49, 52, 54, 55, 56, 57, 58, 59, 62, 63, 64, 65, 66, 68, 70, 71, 76, 78, 85, 86, 87, 88, 89, 90, 93, 94, 96, 98, 99, 100, 102, 103, 104, 106, 111, 112, 113, 114, 119, 120, 121, 122, 123, 125, 127, 128, 131, 132, 133, 135, 137, 138, 139, 145, 147, 148, 150, 151, 153, 156, 157, 158, 160, 163, 164], "sequenc": [0, 2, 3, 6, 15, 16, 26, 36, 43, 51, 52, 53, 55, 68, 70, 79, 92, 93, 94, 96, 106, 125, 138, 139, 141, 145, 162], "mai": [0, 2, 3, 4, 12, 13, 14, 19, 20, 21, 22, 24, 28, 33, 35, 38, 39, 41, 44, 47, 48, 49, 50, 51, 52, 53, 55, 56, 57, 62, 63, 64, 68, 70, 78, 79, 81, 82, 83, 84, 85, 86, 87, 88, 91, 93, 94, 97, 98, 101, 103, 106, 110, 111, 114, 117, 120, 121, 122, 123, 125, 129, 133, 134, 135, 136, 139, 144, 150, 153, 165], "loop": [0, 14, 48, 51, 57, 79, 85, 112, 120, 125, 132, 134, 144, 152, 154, 156, 164], "There": [0, 3, 13, 22, 24, 25, 28, 32, 33, 34, 36, 39, 41, 43, 44, 46, 53, 57, 65, 70, 78, 83, 87, 88, 92, 93, 98, 99, 103, 109, 116, 117, 120, 122, 139, 150, 151, 152, 159, 160], "exist": [0, 3, 6, 13, 14, 39, 44, 50, 51, 57, 65, 71, 73, 78, 79, 81, 82, 85, 86, 88, 93, 94, 103, 117, 122, 124, 135, 139, 145, 151, 152], "modul": [0, 4, 6, 12, 15, 25, 32, 33, 34, 35, 38, 40, 44, 47, 50, 51, 53, 55, 64, 65, 66, 68, 71, 79, 81, 83, 85, 86, 88, 91, 93, 94, 97, 98, 99, 100, 104, 106, 107, 108, 114, 120, 121, 124, 125, 127, 131, 133, 134, 135, 136, 137, 139, 141, 144, 146, 150, 154, 156, 160, 165], "mani": [0, 3, 12, 13, 14, 15, 16, 22, 23, 32, 42, 48, 51, 65, 66, 71, 79, 83, 86, 87, 88, 92, 97, 100, 112, 114, 117, 120, 121, 124, 125, 128, 132, 133, 134, 135, 139, 150, 151, 152, 154, 158, 164], "standard": [0, 3, 4, 6, 8, 12, 16, 22, 24, 28, 32, 33, 41, 45, 47, 50, 52, 55, 56, 65, 66, 70, 75, 78, 79, 83, 85, 86, 88, 97, 102, 103, 111, 112, 113, 118, 119, 120, 125, 132, 134, 135, 139, 145, 150, 159], "customiz": [0, 106, 158], "structur": [0, 1, 2, 3, 6, 7, 10, 13, 15, 24, 25, 30, 32, 38, 44, 45, 50, 54, 55, 56, 59, 61, 64, 66, 69, 70, 78, 79, 80, 85, 91, 97, 98, 100, 101, 102, 103, 104, 106, 108, 111, 124, 125, 127, 129, 130, 132, 135, 139, 143, 145, 147, 148, 151, 152, 157, 158, 159, 160, 164, 165], "intend": [0, 81, 83, 85, 93, 94, 104, 136, 139, 144, 153], "differ": [0, 2, 3, 4, 6, 7, 13, 15, 16, 22, 25, 26, 27, 28, 30, 32, 33, 34, 36, 38, 39, 40, 41, 44, 47, 48, 50, 52, 53, 55, 56, 65, 66, 69, 70, 71, 72, 74, 76, 78, 81, 82, 85, 86, 87, 88, 91, 93, 98, 99, 102, 103, 105, 111, 114, 121, 124, 127, 130, 131, 132, 133, 134, 135, 138, 139, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 156, 157, 160, 163], "purpos": [0, 2, 3, 13, 15, 23, 28, 36, 40, 51, 52, 55, 70, 85, 86, 88, 111, 114, 121, 129, 139, 152, 153, 159, 160, 163], "ase": [0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 58, 59, 62, 63, 64, 65, 66, 67, 68, 69, 70, 72, 74, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 96, 97, 98, 99, 100, 101, 102, 103, 104, 106, 107, 108, 109, 110, 111, 112, 115, 116, 117, 120, 121, 122, 123, 125, 126, 127, 128, 130, 131, 132, 133, 134, 135, 136, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 164, 166, 167], "forc": [0, 1, 2, 3, 6, 10, 11, 12, 13, 14, 15, 17, 18, 20, 21, 22, 24, 28, 29, 32, 33, 34, 37, 38, 41, 43, 48, 49, 50, 55, 57, 66, 71, 74, 76, 77, 78, 81, 85, 86, 88, 91, 102, 103, 111, 112, 117, 122, 124, 125, 131, 132, 133, 135, 139, 141, 143, 144, 148, 150, 151, 157, 158, 160, 161, 162, 163], "stress": [0, 3, 12, 13, 14, 15, 20, 24, 33, 43, 48, 49, 55, 57, 78, 81, 85, 111, 117, 123, 125, 134, 135, 139, 165], "md": [0, 1, 3, 11, 12, 29, 41, 43, 48, 55, 70, 79, 85, 88, 131, 135, 139, 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41, 42, 44, 47, 50, 51, 54, 59, 62, 63, 64, 65, 78, 88, 93, 94, 118, 126, 127, 128, 132, 134, 135, 139, 144, 154, 159, 164, 166], "data": [1, 12, 14, 22, 24, 25, 27, 33, 41, 50, 51, 52, 53, 54, 61, 65, 70, 74, 76, 79, 81, 82, 83, 84, 85, 90, 93, 95, 102, 103, 104, 106, 107, 131, 135, 137, 139, 146, 150, 151, 152, 153, 154, 155, 160], "formula": [1, 3, 6, 22, 57, 78, 85, 90, 92, 96, 97, 100, 107, 118, 135, 139, 144, 147, 151, 164], "ga": [1, 3, 51, 69, 70, 85, 88, 135, 139, 152, 160], "geometri": [1, 3, 4, 7, 8, 10, 12, 13, 16, 27, 28, 33, 37, 38, 39, 40, 45, 47, 48, 52, 54, 55, 56, 75, 78, 79, 83, 88, 97, 124, 133, 135, 139, 141, 145, 147, 150, 153], "gui": [1, 3, 19, 27, 28, 38, 39, 40, 57, 72, 75, 86, 88, 106, 108, 122, 127, 130, 131, 132, 133, 134, 135, 136, 139, 143, 144, 149, 151, 156, 158, 161, 164], "io": [1, 3, 6, 10, 13, 14, 18, 19, 24, 26, 28, 29, 34, 41, 48, 51, 57, 58, 63, 71, 78, 79, 80, 81, 82, 84, 85, 86, 88, 89, 91, 92, 100, 102, 106, 108, 111, 115, 125, 126, 127, 130, 131, 132, 133, 134, 135, 139, 140, 141, 146, 148, 149, 150, 151, 153, 154, 155, 156, 158, 162], "lattic": [1, 3, 4, 6, 12, 13, 19, 22, 24, 26, 30, 32, 33, 40, 51, 52, 53, 63, 70, 78, 80, 91, 92, 97, 100, 106, 117, 123, 127, 130, 131, 134, 135, 139, 144, 145, 149, 150, 151, 152, 156, 159, 164, 165], "neb": [1, 6, 55, 66, 74, 89, 108, 126, 135, 139, 143, 165], "neighborlist": [1, 22, 43, 70, 87, 135, 139], "parallel": [1, 3, 4, 9, 12, 15, 20, 26, 33, 34, 40, 41, 42, 47, 48, 52, 53, 55, 62, 70, 76, 79, 85, 88, 92, 97, 114, 128, 135, 136, 139, 144, 162], "phasediagram": [1, 90, 126, 135, 151], "phonon": [1, 13, 79, 85, 97, 135, 139], "spacegroup": [1, 3, 4, 7, 55, 70, 84, 97, 106, 126, 134, 135, 139], "spectrum": [1, 63, 65, 85, 93, 94, 102, 104, 127, 134, 135, 139], "symbol": [1, 2, 3, 4, 6, 7, 27, 30, 32, 40, 47, 53, 55, 57, 58, 68, 71, 73, 76, 78, 79, 83, 87, 90, 92, 94, 107, 118, 131, 132, 133, 135, 139, 140, 144, 146, 148, 150, 151, 156, 157, 159], "transport": [1, 84, 85, 102, 103, 135], "thermochemistri": [1, 135], "unit": [1, 2, 4, 6, 7, 12, 13, 14, 19, 21, 24, 33, 35, 39, 41, 44, 47, 48, 49, 50, 51, 52, 53, 55, 56, 57, 62, 63, 65, 67, 68, 70, 76, 77, 78, 79, 81, 83, 85, 87, 88, 91, 92, 97, 100, 103, 106, 111, 112, 117, 130, 131, 132, 134, 135, 139, 141, 143, 145, 146, 149, 150, 151, 153, 155, 156, 160, 162], "util": [1, 12, 20, 24, 30, 55, 70, 84, 88, 106, 107, 108, 112, 116, 135, 139, 146, 150, 151, 153, 154, 157], "vibrat": [1, 28, 45, 47, 55, 78, 85, 91, 93, 97, 102, 104, 107, 124, 135, 139, 150, 162, 165], "visual": [1, 3, 6, 39, 50, 63, 65, 71, 74, 80, 84, 130, 132, 133, 134, 135, 139, 143, 147, 154, 157, 158, 164], "tutori": [1, 25, 26, 46, 50, 55, 64, 65, 67, 69, 79, 85, 86, 88, 115, 123, 128, 129, 132, 133, 134, 135, 139, 141, 143, 144, 146, 148, 151, 152, 153, 154, 158, 160, 162, 164], "sourc": [1, 2, 3, 4, 5, 6, 7, 8, 11, 12, 13, 14, 15, 17, 18, 19, 21, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 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83, 93, 94, 99, 102, 111, 118, 134, 135, 138, 139, 153, 164], "ad": [1, 4, 7, 8, 13, 16, 24, 25, 28, 34, 38, 43, 46, 47, 50, 51, 52, 57, 63, 70, 78, 82, 83, 85, 86, 88, 93, 94, 102, 106, 113, 118, 120, 122, 124, 130, 132, 133, 135, 136, 137, 139, 144, 151, 152, 153, 154, 160], "other": [1, 4, 5, 7, 12, 13, 14, 16, 17, 18, 20, 24, 32, 33, 38, 39, 40, 41, 44, 45, 46, 47, 48, 50, 51, 52, 53, 55, 66, 68, 70, 78, 79, 81, 83, 85, 86, 87, 88, 89, 93, 99, 100, 103, 104, 107, 110, 114, 117, 118, 124, 125, 127, 128, 131, 132, 133, 134, 135, 138, 139, 145, 150, 151, 152, 154, 157, 161, 163, 165], "chang": [1, 2, 3, 8, 10, 12, 13, 14, 19, 28, 29, 33, 38, 39, 40, 41, 42, 48, 49, 50, 51, 53, 55, 68, 70, 71, 77, 79, 80, 81, 82, 85, 86, 91, 100, 103, 111, 113, 115, 116, 117, 120, 122, 123, 130, 135, 136, 138, 139, 144, 150, 151, 153, 154, 158], "codata": [1, 13, 135, 139], "input": [1, 7, 10, 13, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 38, 39, 40, 41, 42, 44, 45, 47, 48, 50, 51, 52, 55, 56, 57, 70, 72, 80, 93, 94, 97, 111, 115, 117, 121, 128, 132, 133, 135, 139, 152, 154, 160], "output": [1, 11, 12, 13, 15, 16, 19, 20, 27, 28, 32, 33, 34, 37, 38, 39, 40, 46, 47, 51, 52, 58, 59, 63, 70, 87, 88, 93, 94, 97, 100, 103, 106, 111, 112, 117, 128, 132, 133, 135, 136, 139, 142, 154, 158, 160, 161], "read": [1, 3, 10, 12, 13, 14, 19, 21, 22, 28, 33, 35, 37, 39, 41, 44, 47, 48, 49, 51, 54, 55, 57, 63, 64, 65, 66, 71, 78, 79, 80, 81, 82, 86, 88, 89, 91, 97, 102, 103, 111, 112, 113, 114, 115, 117, 120, 123, 125, 127, 128, 129, 130, 131, 132, 133, 135, 139, 140, 146, 148, 149, 150, 152, 154, 155, 158, 160, 161], "iread": [1, 79, 132, 135, 139], "write": [1, 3, 6, 12, 13, 14, 15, 18, 19, 20, 21, 25, 26, 30, 33, 34, 35, 39, 40, 41, 44, 45, 47, 48, 49, 51, 55, 63, 64, 65, 67, 74, 78, 79, 80, 81, 82, 85, 86, 88, 89, 90, 91, 92, 98, 100, 102, 103, 104, 106, 111, 113, 115, 117, 122, 125, 127, 128, 130, 131, 132, 133, 134, 135, 139, 140, 141, 144, 146, 148, 149, 150, 151, 152, 153, 154, 155, 156, 160, 162, 166], "read_cube_data": [1, 79, 135], "format": [1, 3, 9, 10, 12, 16, 20, 22, 25, 29, 32, 33, 40, 41, 48, 50, 51, 54, 56, 57, 67, 68, 70, 71, 74, 81, 82, 87, 89, 93, 94, 96, 103, 108, 115, 122, 128, 131, 132, 133, 134, 135, 139, 144, 145, 146, 150, 151, 152, 153, 154, 160, 164], "thing": [1, 8, 12, 41, 51, 57, 112, 117, 123, 132, 133, 134, 135, 138, 150, 163], "surfac": [1, 4, 26, 53, 55, 64, 66, 69, 75, 85, 86, 88, 92, 97, 107, 108, 131, 135, 139, 148, 150, 151, 153, 154, 156, 157, 159, 160], "separ": [1, 4, 30, 32, 33, 47, 51, 56, 57, 63, 66, 78, 79, 80, 85, 88, 97, 106, 112, 131, 133, 135, 136, 145, 147, 152, 154, 157], "molecul": [1, 2, 3, 6, 8, 12, 13, 16, 19, 21, 27, 28, 37, 38, 39, 40, 44, 45, 46, 47, 48, 50, 51, 55, 56, 57, 58, 70, 72, 78, 79, 80, 85, 86, 87, 88, 90, 96, 97, 98, 101, 104, 108, 118, 121, 127, 128, 130, 131, 132, 135, 139, 141, 142, 150, 153, 159, 160, 162, 163, 165, 166], "common": [1, 3, 15, 20, 28, 47, 52, 55, 56, 78, 84, 86, 92, 93, 94, 100, 112, 117, 120, 127, 131, 133, 134, 135, 139, 145, 150], "bulk": [1, 2, 6, 7, 20, 22, 24, 26, 33, 39, 47, 48, 51, 52, 54, 63, 65, 67, 69, 78, 79, 85, 88, 91, 97, 98, 100, 108, 127, 135, 139, 145, 146, 149, 151, 153, 155, 164, 165], "crystal": [1, 6, 7, 12, 25, 46, 54, 69, 70, 79, 88, 91, 92, 106, 124, 127, 129, 131, 135, 139, 145, 146, 156, 160, 164, 165], "nanotub": [1, 75, 135], "graphen": [1, 40, 75, 135, 139], "nanoribbon": [1, 75, 135], "attach": [1, 3, 8, 12, 13, 14, 19, 20, 33, 35, 36, 44, 49, 51, 55, 57, 58, 66, 67, 73, 78, 81, 85, 86, 88, 97, 111, 117, 131, 132, 134, 135, 139, 141, 142, 154, 155, 156, 162], "equat": [1, 22, 26, 47, 65, 85, 97, 108, 123, 135, 139, 146, 155, 163, 165], "state": [1, 10, 12, 14, 15, 25, 26, 28, 34, 39, 40, 50, 54, 61, 64, 65, 66, 78, 85, 86, 88, 95, 97, 98, 101, 103, 104, 108, 111, 117, 123, 131, 132, 133, 135, 139, 146, 148, 150, 155, 158, 159, 161, 165], "equationofst": [1, 67, 135, 146, 149, 152], "calculate_eo": [1, 67, 135, 139, 144], "chemic": [1, 2, 3, 4, 6, 7, 36, 41, 53, 56, 57, 65, 69, 71, 78, 79, 90, 100, 118, 124, 132, 133, 135, 139, 150, 151, 152, 154], "type": [1, 3, 4, 6, 8, 9, 13, 16, 17, 18, 19, 22, 26, 27, 28, 30, 32, 33, 34, 38, 40, 41, 44, 46, 47, 50, 51, 53, 55, 56, 57, 63, 69, 70, 71, 78, 80, 81, 82, 83, 88, 92, 102, 103, 104, 106, 112, 125, 132, 133, 134, 135, 137, 139, 146, 147, 150, 151, 152, 157, 160, 161, 162], "s22": [1, 50, 135, 139, 160], "databas": [1, 3, 4, 9, 14, 47, 50, 56, 69, 79, 81, 83, 90, 92, 108, 135, 139, 147, 150, 151, 153, 154, 160], "weakli": [1, 56, 85, 135, 139, 160], "dimer": [1, 22, 50, 55, 56, 135, 139, 157, 160, 165], "complex": [1, 13, 14, 47, 56, 82, 87, 88, 91, 122, 125, 135, 138, 139, 152, 160], "deltacodesdft": [1, 135, 139, 146], "g2": [1, 4, 39, 56, 71, 135, 139], "neutral": [1, 50, 91, 135, 160], "test": [1, 8, 11, 12, 13, 17, 18, 19, 22, 23, 25, 29, 33, 38, 41, 46, 47, 48, 50, 63, 70, 83, 84, 85, 88, 108, 112, 113, 116, 119, 120, 122, 133, 135, 139, 150, 151, 153, 154, 162], "s26": [1, 135, 139], "s22x5": [1, 135, 139], "local": [1, 3, 8, 12, 13, 16, 40, 41, 44, 57, 61, 64, 85, 98, 99, 112, 122, 123, 132, 133, 134, 135, 136, 150, 152, 153, 154, 157, 164, 166], "precondit": [1, 86, 135, 139], "global": [1, 3, 15, 23, 33, 50, 55, 57, 69, 79, 87, 99, 112, 135, 139, 150, 152, 153, 154], "choos": [1, 12, 13, 14, 41, 43, 44, 50, 66, 71, 72, 120, 125, 135, 139, 143, 149, 150, 151, 152, 161, 164], "time": [1, 3, 6, 7, 12, 13, 14, 34, 47, 48, 50, 51, 55, 56, 57, 65, 66, 68, 70, 78, 79, 81, 83, 86, 88, 91, 92, 97, 99, 100, 103, 112, 120, 121, 122, 123, 127, 131, 132, 133, 134, 135, 137, 138, 139, 144, 151, 152, 153, 154, 156, 157, 159, 160, 162, 164], "step": [1, 6, 11, 14, 16, 25, 26, 28, 29, 39, 48, 50, 55, 64, 65, 66, 71, 78, 81, 86, 87, 88, 104, 113, 115, 116, 122, 128, 131, 132, 133, 135, 139, 148, 150, 153, 154, 156, 157, 160], "log": [1, 9, 12, 20, 27, 28, 33, 39, 41, 46, 48, 55, 78, 81, 88, 112, 116, 133, 135, 139, 141, 150, 153, 157, 159, 160, 162], "constant": [1, 3, 4, 6, 13, 14, 24, 26, 43, 46, 50, 51, 53, 55, 64, 70, 78, 83, 86, 91, 97, 98, 99, 107, 123, 124, 134, 135, 139, 144, 145, 149, 150, 151, 152, 164, 165], "nve": [1, 12, 88, 135], "microcanon": [1, 135], "ensembl": [1, 19, 40, 97, 124, 135], "nvt": [1, 12, 135], "canon": [1, 52, 70, 97, 135, 139], "npt": [1, 62, 81, 91, 93, 94, 97, 102, 103, 127, 134, 135, 139], "isotherm": [1, 135], "isobar": [1, 135], "veloc": [1, 3, 19, 34, 53, 76, 77, 78, 88, 135, 139, 156], "distribut": [1, 3, 4, 27, 29, 51, 57, 62, 70, 86, 87, 114, 135, 136, 139, 150, 151, 154], "post": [1, 33, 41, 50, 51, 135], "analysi": [1, 6, 12, 26, 33, 61, 65, 78, 87, 94, 96, 97, 127, 134, 135, 139, 145, 149, 150, 152, 153, 156, 158, 165], "fixatom": [1, 13, 24, 47, 66, 78, 131, 135, 143, 144, 148, 154, 157, 158, 159], "class": [1, 2, 3, 8, 12, 13, 14, 15, 16, 17, 18, 20, 21, 23, 27, 28, 33, 34, 35, 36, 37, 38, 41, 43, 44, 45, 46, 48, 49, 51, 52, 53, 54, 57, 61, 62, 63, 64, 66, 67, 68, 70, 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164], "unitcellfilt": [1, 20, 24, 135, 139], "strainfilt": [1, 135, 155], "expcellfilt": [1, 48, 134, 135, 139, 164], "fixsymmetri": [1, 135], "subpackag": [1, 135], "reduc": [1, 3, 7, 24, 26, 51, 52, 62, 63, 64, 65, 66, 68, 70, 78, 86, 91, 97, 100, 135, 139, 151, 153, 159], "basi": [1, 4, 6, 7, 8, 9, 15, 16, 17, 18, 20, 21, 27, 28, 38, 41, 44, 45, 47, 48, 50, 51, 52, 54, 56, 63, 65, 66, 70, 76, 78, 83, 88, 97, 98, 102, 104, 118, 127, 132, 133, 134, 135, 139], "neighbor": [1, 4, 22, 32, 43, 70, 78, 86, 98, 135, 139, 145, 148, 151, 155], "api": [1, 4, 32, 44, 56, 68, 70, 78, 106, 112, 124, 135, 139], "cell_to_cellpar": [1, 52, 70, 135, 139], "cellpar_to_cel": [1, 52, 70, 135, 139], "complete_cel": [1, 70, 135, 139], "conditional_find_m": [1, 70, 135], "distanc": [1, 3, 4, 7, 22, 24, 32, 43, 46, 55, 56, 57, 63, 65, 70, 71, 76, 78, 83, 85, 86, 87, 91, 92, 107, 132, 135, 139, 141, 145, 148, 150, 153, 154, 155, 157, 159, 160, 162], "find_mic": [1, 70, 135], "get_angl": [1, 3, 55, 70, 133, 135, 139], "get_angles_deriv": [1, 70, 135], "get_dihedr": [1, 3, 55, 70, 135, 139], "get_dihedrals_deriv": [1, 70, 135], "get_dist": [1, 3, 40, 70, 92, 135, 139], "get_distances_deriv": [1, 70, 135], "get_duplicate_atom": [1, 70, 135, 139], "get_lay": [1, 53, 70, 135], "is_minkowski_reduc": [1, 70, 135], "is_orthorhomb": [1, 70, 135, 139], "minkowski_reduc": [1, 52, 70, 135], "orthorhomb": [1, 3, 4, 6, 34, 39, 52, 60, 63, 70, 83, 100, 135, 139], "permute_ax": [1, 52, 70, 135], "wrap_posit": [1, 3, 70, 135, 139], "A": [1, 3, 6, 7, 9, 10, 12, 13, 16, 22, 24, 25, 26, 27, 28, 29, 32, 34, 38, 41, 46, 47, 50, 52, 53, 54, 55, 56, 62, 63, 65, 66, 67, 68, 69, 70, 71, 76, 78, 79, 80, 81, 83, 85, 86, 87, 88, 91, 92, 94, 96, 97, 98, 100, 102, 103, 104, 106, 107, 110, 111, 112, 115, 117, 118, 122, 123, 124, 125, 127, 130, 132, 134, 135, 137, 138, 139, 145, 147, 149, 150, 151, 152, 153, 156, 159, 160, 163, 164], "integr": [1, 4, 12, 15, 24, 29, 48, 50, 51, 56, 62, 63, 70, 85, 94, 97, 102, 103, 116, 124, 131, 135, 139, 154, 156, 160], "part": [1, 7, 11, 12, 13, 29, 43, 46, 53, 65, 66, 74, 82, 85, 87, 91, 97, 112, 116, 117, 123, 131, 134, 135, 139, 150, 151, 154, 160], "brows": [1, 32, 123, 135, 165], "browser": [1, 78, 106, 135, 164], "run": [1, 4, 10, 12, 14, 15, 16, 17, 18, 19, 20, 21, 24, 27, 28, 29, 30, 32, 33, 38, 39, 40, 41, 44, 45, 47, 50, 51, 55, 66, 71, 72, 74, 78, 81, 85, 86, 88, 89, 91, 97, 101, 102, 103, 104, 107, 108, 113, 114, 116, 117, 121, 122, 124, 125, 127, 130, 131, 132, 133, 134, 135, 136, 139, 141, 142, 143, 144, 148, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164], "postgresql": [1, 79, 135, 139], "mysql": [1, 79, 135, 139], "interpol": [1, 7, 13, 22, 52, 61, 62, 70, 71, 134, 135, 139, 148, 151, 158, 165], "trajectori": [1, 3, 18, 19, 20, 21, 26, 28, 39, 48, 55, 66, 67, 70, 74, 76, 78, 79, 85, 88, 89, 91, 103, 106, 108, 115, 127, 131, 132, 133, 134, 135, 139, 141, 143, 146, 149, 151, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163], "restart": [1, 8, 12, 14, 15, 16, 17, 18, 19, 24, 27, 33, 34, 35, 37, 38, 41, 44, 45, 49, 66, 79, 85, 88, 103, 106, 111, 117, 135, 139, 166], "climb": [1, 135], "imag": [1, 3, 47, 51, 61, 66, 70, 71, 76, 78, 79, 85, 87, 91, 92, 106, 115, 116, 132, 134, 135, 139, 148, 161, 165], "scale": [1, 3, 5, 7, 12, 20, 33, 34, 40, 41, 46, 52, 55, 63, 65, 70, 78, 81, 85, 87, 88, 91, 92, 100, 102, 106, 130, 135, 139, 145, 147, 150, 152, 157], "over": [1, 12, 24, 28, 51, 54, 57, 65, 78, 81, 82, 85, 88, 97, 102, 103, 120, 121, 127, 132, 133, 134, 135, 138, 139, 144, 150, 156, 160], "share": [1, 32, 51, 88, 93, 117, 135, 158], "autoneb": [1, 135], "genet": [1, 135, 139, 165], "algorithm": [1, 7, 48, 50, 51, 55, 70, 72, 85, 86, 87, 88, 92, 117, 131, 133, 135, 139, 147, 156, 157, 159, 165], "determin": [1, 6, 7, 12, 22, 27, 28, 32, 38, 47, 52, 63, 65, 66, 69, 70, 78, 85, 86, 87, 88, 91, 92, 97, 98, 100, 135, 137, 139, 141, 147, 150, 152, 154, 159, 165], "convex": [1, 69, 90, 135, 165], "hull": [1, 69, 90, 135, 165], "search": 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154, 160], "keyword": [1, 2, 3, 4, 6, 10, 13, 15, 17, 18, 19, 20, 22, 24, 26, 27, 28, 30, 33, 34, 38, 39, 40, 42, 44, 45, 47, 48, 50, 51, 55, 57, 63, 65, 66, 68, 78, 79, 81, 85, 86, 88, 90, 91, 92, 102, 103, 106, 111, 117, 118, 125, 127, 131, 132, 133, 134, 135, 138, 139, 150, 152, 153, 164], "electron": [1, 2, 3, 8, 10, 13, 15, 16, 22, 24, 25, 41, 44, 45, 49, 50, 51, 59, 62, 63, 64, 65, 78, 85, 93, 94, 97, 99, 101, 106, 117, 125, 127, 132, 134, 135, 152, 160], "densiti": [1, 8, 9, 12, 13, 15, 16, 17, 18, 19, 21, 22, 24, 25, 26, 27, 28, 38, 40, 47, 50, 52, 54, 63, 64, 65, 69, 70, 72, 78, 83, 95, 97, 98, 102, 103, 106, 117, 122, 124, 125, 133, 135, 139, 141, 152, 154, 160, 162, 163], "theori": [1, 6, 7, 8, 9, 12, 13, 15, 16, 24, 25, 26, 28, 38, 41, 47, 48, 50, 51, 54, 65, 66, 69, 78, 86, 88, 91, 100, 102, 103, 122, 124, 125, 127, 131, 135, 150, 152, 154, 156], "brillouin": [1, 12, 15, 19, 24, 52, 61, 70, 78, 83, 91, 134, 135, 139], "zone": [1, 7, 12, 15, 19, 24, 52, 61, 70, 78, 83, 91, 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152, 158, 162, 164, 166], "rai": [1, 100, 135], "scatter": [1, 100, 102, 135], "opencew": [1, 100, 135, 139], "seterr": [1, 100, 135], "plural": [1, 100, 135], "formula_hil": [1, 100, 135, 139], "formula_met": [1, 100, 135, 139], "convert_string_to_fd": [1, 100, 135], "workdir": [1, 26, 100, 135, 139], "timer": [1, 100, 135, 139], "symmetri": [1, 6, 21, 26, 38, 44, 51, 53, 55, 61, 64, 65, 78, 85, 91, 92, 97, 104, 134, 135, 136, 145, 150, 151, 152], "equival": [1, 3, 6, 13, 24, 27, 51, 55, 56, 58, 78, 85, 90, 92, 93, 94, 97, 117, 118, 132, 135, 139, 140, 145, 152], "checker": [1, 135], "paropen": [1, 89, 135], "parprint": [1, 89, 135], "broadcast": [1, 12, 48, 79, 89, 135, 139], "parallel_funct": [1, 89, 135, 139], "parallel_gener": [1, 89, 135, 139], "dimercontrol": [1, 66, 135], "minmodeatom": [1, 66, 135], "minmodetransl": [1, 66, 135], "dimereigenmodesearch": [1, 66, 135], "from": [1, 3, 4, 6, 7, 8, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53, 54, 55, 58, 62, 63, 64, 65, 66, 67, 68, 70, 74, 76, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 110, 111, 112, 114, 115, 116, 117, 120, 121, 124, 127, 128, 130, 131, 132, 133, 134, 135, 137, 138, 139, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 164, 166], "transportcalcul": [1, 98, 135], "qmmm": [1, 12, 42, 135, 139, 160], "explicit": [1, 12, 19, 33, 47, 50, 51, 78, 117, 135, 160], "subtract": [1, 12, 63, 135, 137, 150, 151, 152, 160], "qm": [1, 11, 12, 19, 29, 42, 43, 50, 135, 139, 162, 165], "mm": [1, 11, 12, 19, 42, 43, 50, 135, 139, 162, 165], "legaci": [1, 51, 56, 125, 135], "call": [2, 3, 5, 6, 8, 9, 12, 13, 14, 15, 16, 20, 22, 26, 29, 38, 39, 43, 45, 48, 49, 50, 51, 53, 57, 65, 66, 67, 70, 71, 78, 79, 81, 83, 85, 86, 87, 88, 91, 93, 94, 97, 100, 103, 106, 108, 111, 112, 117, 128, 130, 131, 132, 133, 134, 137, 138, 139, 145, 152, 154, 155, 156, 157, 161, 163], "handl": [2, 14, 16, 20, 39, 49, 51, 57, 78, 97, 100, 111, 117, 118, 122, 125, 128, 139, 154], "like": [2, 3, 6, 7, 9, 12, 13, 14, 15, 21, 24, 25, 26, 27, 28, 30, 39, 41, 44, 49, 50, 51, 52, 55, 56, 57, 62, 63, 64, 65, 70, 71, 78, 79, 80, 81, 83, 85, 86, 87, 88, 90, 92, 94, 96, 100, 106, 108, 111, 112, 113, 114, 117, 119, 120, 122, 123, 127, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 144, 145, 147, 151, 152, 154, 155, 157, 158, 160, 163, 164], "thi": [2, 3, 4, 6, 7, 8, 9, 10, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 62, 63, 64, 65, 66, 67, 68, 70, 71, 76, 77, 78, 79, 81, 82, 83, 85, 86, 87, 88, 90, 91, 92, 93, 94, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 108, 111, 112, 114, 115, 116, 117, 118, 120, 121, 122, 123, 124, 125, 127, 128, 129, 130, 131, 132, 133, 134, 136, 138, 139, 141, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164], "import": [2, 3, 4, 6, 7, 8, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57, 58, 62, 63, 64, 65, 66, 67, 68, 70, 71, 78, 79, 80, 81, 82, 83, 85, 86, 87, 88, 89, 90, 91, 92, 94, 96, 97, 98, 99, 100, 101, 102, 103, 104, 106, 107, 114, 115, 116, 120, 121, 125, 127, 128, 130, 131, 132, 133, 134, 135, 137, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 162, 164, 166], "a1": [2, 3, 4, 7, 20, 55, 70, 108, 139, 150, 152, 153, 154, 157, 159], "si": [2, 4, 7, 38, 39, 47, 48, 51, 63, 78, 80, 91, 117, 164], "0": [2, 3, 4, 6, 7, 8, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 43, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 59, 62, 63, 64, 65, 66, 67, 70, 71, 76, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 97, 98, 99, 100, 101, 102, 103, 104, 106, 107, 111, 115, 116, 117, 118, 121, 125, 127, 130, 131, 132, 133, 134, 135, 137, 138, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 162, 164, 166], "a2": [2, 3, 4, 7, 20, 55, 70, 108, 139, 150, 152, 153, 154, 157, 159], "h": [2, 3, 4, 6, 7, 19, 23, 24, 28, 30, 33, 41, 47, 48, 51, 53, 54, 55, 56, 57, 62, 63, 65, 66, 68, 71, 78, 79, 80, 86, 87, 90, 91, 96, 97, 98, 100, 104, 106, 108, 118, 129, 130, 131, 133, 135, 137, 140, 144, 145, 147, 150, 152, 159, 163, 164, 166], "3": [2, 3, 4, 6, 7, 11, 12, 13, 14, 16, 17, 19, 20, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 43, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 59, 63, 64, 65, 66, 67, 70, 71, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 90, 91, 92, 93, 94, 96, 97, 98, 99, 100, 102, 103, 104, 106, 107, 111, 115, 116, 117, 121, 123, 125, 130, 132, 133, 134, 135, 136, 137, 138, 140, 141, 143, 144, 145, 146, 147, 148, 150, 151, 152, 153, 154, 155, 156, 158, 159, 160, 162, 164, 166], "mass": [2, 3, 4, 7, 22, 33, 53, 55, 56, 57, 78, 81, 85, 88, 97, 99, 118, 135, 139, 141, 144, 151, 156], "a3": [2, 3, 4, 55, 70, 139, 150, 152, 153, 154], "14": [2, 16, 48, 55, 57, 80, 82, 83, 134, 135, 144, 146, 147, 150, 159], "posit": [2, 3, 6, 7, 12, 13, 14, 18, 19, 28, 29, 30, 32, 33, 35, 39, 41, 43, 44, 48, 49, 50, 51, 52, 53, 54, 55, 57, 64, 65, 66, 70, 71, 76, 78, 81, 82, 85, 86, 87, 88, 92, 100, 104, 106, 111, 117, 118, 130, 131, 132, 133, 134, 135, 139, 140, 141, 144, 145, 147, 148, 150, 151, 154, 156, 157, 159, 160, 162, 163, 166], "same": [2, 3, 6, 7, 8, 12, 13, 14, 16, 17, 18, 27, 28, 38, 41, 44, 48, 51, 53, 55, 56, 57, 62, 65, 68, 70, 71, 75, 78, 79, 81, 83, 85, 86, 87, 88, 89, 92, 93, 94, 97, 104, 112, 117, 118, 121, 122, 128, 130, 131, 133, 134, 135, 137, 138, 139, 147, 150, 151, 152, 153, 157, 160, 161, 162], "tag": [2, 3, 6, 7, 16, 25, 40, 47, 53, 57, 66, 70, 73, 77, 78, 81, 82, 116, 118, 136, 141, 143, 147, 150, 153, 158, 162], "none": [2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 19, 20, 21, 24, 25, 27, 28, 32, 33, 34, 35, 36, 37, 38, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 55, 57, 59, 62, 63, 64, 65, 66, 67, 68, 70, 78, 79, 81, 82, 83, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 97, 98, 100, 101, 102, 103, 104, 106, 107, 111, 117, 118, 137, 139, 144, 147, 150, 151, 153, 154, 160, 166], "momentum": [2, 3, 85, 88, 91, 156], "magmom": [2, 3, 12, 14, 49, 50, 51, 53, 57, 78, 81, 111], "charg": [2, 3, 8, 12, 14, 15, 18, 19, 21, 28, 29, 38, 41, 43, 44, 46, 49, 50, 51, 53, 57, 58, 77, 78, 80, 81, 91, 106, 111, 114, 117, 135, 139, 144], "index": [2, 3, 4, 5, 6, 7, 17, 27, 51, 53, 54, 55, 56, 57, 65, 70, 78, 79, 81, 82, 83, 85, 87, 91, 94, 97, 106, 107, 118, 123, 130, 132, 135, 138, 157], "repres": [2, 3, 6, 7, 10, 22, 27, 38, 52, 55, 63, 70, 78, 83, 85, 93, 94, 97, 98, 118, 132, 133, 134, 139, 141, 145, 150, 151, 157, 161, 163], "singl": [2, 3, 4, 6, 7, 8, 12, 13, 14, 16, 20, 22, 23, 29, 30, 32, 33, 37, 38, 41, 44, 47, 53, 55, 57, 59, 63, 64, 65, 66, 69, 71, 73, 78, 79, 81, 82, 85, 86, 87, 88, 94, 97, 103, 107, 114, 115, 120, 127, 134, 135, 139, 141, 144, 146, 150, 151, 154, 160, 164], "paramet": [2, 3, 4, 6, 7, 8, 12, 13, 14, 16, 17, 18, 20, 23, 26, 32, 33, 34, 35, 37, 39, 40, 43, 46, 48, 49, 52, 53, 55, 56, 57, 59, 63, 66, 68, 70, 78, 79, 80, 81, 83, 85, 86, 87, 88, 91, 92, 93, 94, 97, 98, 99, 100, 103, 104, 106, 107, 111, 113, 119, 121, 124, 127, 132, 133, 134, 135, 139, 144, 146, 147, 150, 151, 152, 154, 157, 158, 160, 164], "str": [2, 3, 4, 6, 7, 8, 12, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 32, 33, 35, 37, 38, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, 56, 57, 63, 66, 67, 68, 70, 78, 79, 81, 82, 83, 85, 86, 87, 88, 90, 91, 92, 93, 94, 98, 99, 102, 103, 111, 115, 138, 146, 147, 150], "int": [2, 3, 4, 6, 7, 8, 12, 15, 16, 24, 26, 28, 38, 41, 44, 45, 46, 49, 50, 51, 52, 53, 56, 57, 59, 62, 63, 64, 66, 67, 68, 70, 78, 79, 82, 85, 86, 87, 91, 92, 93, 94, 97, 98, 102, 103, 104, 132, 138, 150, 160], "float": [2, 3, 4, 6, 7, 8, 12, 15, 16, 24, 26, 32, 36, 41, 43, 46, 47, 48, 50, 51, 52, 53, 55, 57, 59, 62, 63, 66, 67, 70, 78, 81, 82, 83, 85, 86, 87, 88, 90, 91, 92, 93, 94, 97, 98, 100, 102, 103, 106, 107, 138, 146, 147, 150], "magnet": [2, 3, 4, 12, 16, 24, 26, 27, 28, 51, 57, 73, 76, 77, 78, 117], "moment": [2, 3, 4, 12, 16, 24, 26, 27, 28, 29, 41, 50, 51, 57, 62, 73, 76, 77, 78, 97, 102, 112, 117], "first": [2, 3, 6, 7, 13, 14, 15, 16, 17, 18, 26, 28, 32, 33, 34, 38, 41, 44, 45, 46, 49, 51, 52, 53, 55, 57, 63, 66, 68, 69, 70, 71, 78, 79, 81, 82, 83, 85, 86, 87, 88, 91, 93, 97, 98, 100, 101, 102, 103, 104, 111, 113, 118, 122, 123, 124, 130, 131, 132, 133, 134, 135, 138, 139, 141, 142, 144, 145, 148, 149, 150, 151, 152, 154, 155, 157, 158, 160, 162, 164], "argument": [2, 3, 4, 6, 7, 8, 9, 12, 14, 15, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 32, 33, 35, 38, 44, 45, 47, 49, 50, 51, 52, 53, 55, 56, 57, 62, 63, 65, 70, 78, 79, 81, 82, 83, 85, 87, 88, 90, 91, 92, 93, 94, 100, 103, 104, 106, 111, 117, 118, 130, 131, 135, 138, 139, 142, 145, 150, 153], "constructor": [2, 12, 13, 15, 50, 65, 87, 91, 92, 117, 118, 135, 138, 139], "second": [2, 3, 6, 16, 41, 48, 50, 51, 52, 55, 57, 63, 70, 71, 78, 79, 82, 83, 85, 86, 87, 88, 93, 97, 99, 102, 103, 104, 121, 128, 138, 143, 144, 148, 150, 152, 156, 157, 158, 163], "\u00e5": [2, 3, 6, 12, 52, 70, 85, 99, 102, 107, 117, 130, 132, 139, 145, 153, 160], "length": [2, 3, 4, 6, 7, 25, 33, 41, 46, 51, 52, 53, 55, 57, 62, 63, 70, 76, 78, 82, 83, 85, 87, 88, 94, 97, 100, 104, 107, 120, 134, 135, 137, 139, 141, 142, 148, 150, 153, 160, 161], "three": [2, 3, 4, 6, 7, 12, 16, 19, 20, 22, 26, 28, 46, 52, 53, 55, 57, 63, 64, 70, 71, 78, 79, 83, 85, 86, 87, 90, 91, 92, 93, 97, 112, 117, 118, 130, 133, 134, 135, 139, 140, 141, 144, 145, 146, 147, 150, 151, 154, 155, 157, 158, 163, 164, 166], "properti": [2, 3, 12, 14, 20, 21, 25, 28, 32, 36, 47, 49, 52, 57, 62, 63, 69, 70, 76, 78, 80, 81, 83, 85, 87, 97, 98, 104, 107, 111, 124, 127, 128, 134, 135, 139, 145, 150, 152, 154], "also": [2, 3, 6, 7, 8, 9, 12, 13, 15, 16, 19, 22, 24, 25, 27, 28, 32, 33, 34, 38, 40, 41, 42, 43, 44, 47, 48, 50, 51, 52, 55, 57, 62, 63, 65, 70, 71, 72, 74, 76, 77, 78, 79, 80, 83, 85, 86, 87, 88, 89, 90, 92, 93, 94, 97, 99, 101, 102, 104, 106, 109, 110, 111, 112, 117, 118, 121, 123, 124, 125, 127, 128, 130, 131, 132, 133, 134, 136, 138, 139, 140, 144, 145, 150, 151, 152, 153, 154, 155, 156, 157, 158, 160, 161, 164], "done": [2, 32, 33, 38, 44, 47, 48, 53, 55, 56, 57, 65, 70, 71, 78, 81, 85, 86, 87, 92, 103, 112, 131, 133, 138, 141, 144, 150, 154, 156, 160, 164], "abov": [2, 3, 6, 7, 9, 12, 14, 22, 25, 38, 39, 41, 48, 53, 54, 55, 57, 65, 78, 79, 80, 81, 82, 85, 86, 87, 88, 97, 104, 106, 112, 114, 116, 127, 131, 133, 134, 136, 145, 150, 154, 156, 158, 159, 160, 161, 164], "more": [2, 3, 4, 6, 7, 8, 12, 13, 14, 16, 22, 23, 27, 28, 32, 33, 34, 35, 40, 41, 42, 44, 46, 47, 48, 49, 50, 51, 53, 54, 55, 56, 61, 64, 65, 66, 69, 70, 71, 78, 79, 81, 85, 86, 87, 88, 90, 91, 92, 95, 97, 98, 100, 106, 111, 112, 114, 117, 120, 121, 122, 125, 128, 132, 133, 134, 135, 136, 137, 139, 144, 145, 147, 148, 150, 151, 152, 154, 156, 158, 161, 162, 164, 165], "o": [2, 3, 4, 6, 11, 12, 14, 15, 19, 23, 24, 25, 29, 30, 38, 40, 46, 51, 54, 55, 63, 68, 71, 78, 80, 81, 88, 90, 92, 94, 106, 108, 113, 115, 117, 119, 125, 129, 133, 134, 135, 136, 139, 144, 146, 150, 157, 160, 162, 163], "b": [2, 3, 4, 7, 24, 46, 47, 50, 51, 52, 55, 57, 63, 67, 68, 69, 70, 71, 78, 79, 82, 83, 85, 86, 87, 88, 91, 92, 93, 97, 100, 102, 103, 104, 107, 112, 115, 122, 123, 126, 134, 136, 138, 139, 144, 145, 146, 147, 149, 150, 151, 152, 153, 154, 160], "8": [2, 3, 4, 6, 15, 19, 20, 22, 24, 25, 27, 29, 40, 41, 48, 54, 55, 78, 79, 80, 81, 82, 88, 90, 91, 97, 102, 107, 122, 130, 134, 135, 138, 143, 146, 147, 148, 150, 151, 152, 153, 154, 155, 157, 158, 166], "c": [2, 3, 4, 6, 7, 12, 13, 14, 20, 23, 29, 30, 33, 38, 40, 41, 44, 51, 52, 54, 55, 59, 62, 64, 67, 68, 70, 71, 78, 79, 80, 82, 83, 85, 86, 87, 88, 91, 92, 97, 100, 104, 106, 107, 108, 115, 117, 118, 125, 134, 138, 139, 140, 141, 144, 145, 150, 152, 153, 155, 157, 160, 162, 164], "print": [2, 4, 6, 8, 10, 12, 13, 15, 17, 18, 22, 24, 27, 30, 32, 33, 34, 37, 41, 44, 48, 50, 51, 52, 53, 54, 55, 57, 58, 59, 63, 67, 70, 78, 82, 83, 85, 87, 88, 89, 90, 91, 92, 99, 107, 108, 115, 128, 131, 132, 133, 134, 137, 138, 139, 142, 143, 146, 147, 148, 149, 150, 151, 152, 153, 154, 156, 158, 160, 164, 166], "42": [2, 4, 12, 39, 48, 56, 57, 82, 87, 138, 146], "li": [2, 4, 51, 127, 134], "If": [2, 3, 4, 5, 6, 7, 10, 12, 13, 14, 15, 16, 17, 18, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 41, 43, 44, 46, 47, 48, 50, 51, 52, 53, 55, 56, 57, 62, 63, 65, 66, 70, 71, 78, 79, 81, 82, 83, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 97, 98, 99, 100, 103, 106, 107, 110, 111, 112, 116, 117, 120, 121, 122, 123, 124, 125, 129, 131, 132, 133, 134, 136, 138, 139, 144, 150, 151, 152, 154, 155, 160, 161, 163, 164, 165], "belong": [2, 7, 13, 46, 70, 87, 92, 150, 153], "assign": [2, 13, 24, 30, 32, 33, 39, 43, 51, 78, 85, 132, 138, 141, 160], "valu": [2, 3, 6, 7, 8, 9, 12, 13, 14, 15, 16, 17, 18, 20, 22, 25, 26, 27, 28, 29, 32, 33, 34, 36, 37, 38, 39, 40, 41, 43, 44, 46, 47, 50, 51, 53, 54, 55, 57, 62, 63, 65, 66, 67, 70, 78, 79, 81, 82, 83, 85, 86, 87, 88, 90, 91, 93, 94, 97, 98, 99, 106, 107, 117, 118, 124, 132, 134, 135, 138, 139, 144, 145, 147, 150, 152, 155, 156, 157, 160, 162, 165], "correspond": [2, 3, 4, 6, 7, 10, 15, 25, 27, 30, 32, 41, 47, 48, 51, 53, 55, 62, 64, 65, 66, 70, 78, 80, 83, 85, 86, 87, 91, 92, 93, 94, 97, 101, 102, 123, 125, 131, 133, 139, 145, 147, 150, 152, 156, 163], "oh": [2, 4, 68, 123], "get_initial_charg": [2, 3, 135, 139], "anoth": [2, 3, 30, 33, 43, 50, 57, 63, 79, 83, 85, 86, 110, 112, 113, 115, 120, 122, 127, 135, 138, 151, 152, 156, 161, 164], "ni": [2, 23, 26, 33, 135, 144, 146, 152, 155], "7": [2, 3, 6, 7, 9, 16, 21, 22, 26, 29, 34, 38, 43, 47, 48, 49, 51, 55, 57, 65, 79, 80, 82, 87, 90, 91, 98, 102, 103, 104, 106, 116, 117, 118, 121, 134, 135, 138, 143, 144, 146, 147, 150, 152, 153, 154, 157, 158, 159, 162], "initi": [2, 3, 8, 12, 13, 17, 19, 27, 29, 32, 33, 39, 47, 48, 50, 51, 57, 65, 66, 70, 71, 78, 82, 85, 86, 88, 91, 92, 103, 117, 133, 135, 139, 148, 154, 155, 158, 160, 161, 165], "obtain": [2, 3, 4, 7, 8, 15, 17, 18, 19, 27, 28, 32, 44, 47, 50, 56, 76, 78, 86, 88, 91, 104, 105, 112, 131, 145, 148, 150, 152], "y": [2, 3, 6, 22, 46, 57, 62, 64, 71, 76, 78, 79, 83, 85, 86, 87, 91, 100, 103, 104, 106, 115, 116, 136, 138, 147, 157, 158, 166], "z": [2, 3, 4, 6, 22, 38, 46, 47, 55, 57, 64, 65, 71, 76, 78, 79, 83, 85, 87, 88, 91, 97, 102, 103, 115, 116, 118, 130, 139, 145, 147, 150, 153, 157], "5": [2, 3, 4, 5, 6, 7, 8, 12, 13, 19, 22, 25, 29, 30, 32, 34, 38, 40, 43, 46, 47, 48, 51, 52, 53, 55, 56, 57, 59, 63, 65, 66, 67, 70, 71, 76, 78, 79, 83, 85, 86, 87, 88, 90, 91, 92, 97, 98, 100, 102, 103, 104, 106, 107, 114, 115, 116, 117, 120, 121, 127, 128, 130, 132, 134, 135, 137, 138, 142, 143, 144, 145, 146, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 162, 166], "That": [2, 8, 48, 85, 112, 160], "last": [2, 3, 6, 12, 13, 14, 22, 49, 56, 57, 71, 78, 79, 81, 85, 86, 87, 103, 111, 112, 115, 116, 131, 132, 138, 143, 150, 154, 158], "some": [2, 4, 6, 7, 13, 15, 24, 26, 27, 28, 32, 33, 34, 39, 41, 43, 47, 48, 50, 51, 55, 56, 57, 65, 78, 79, 80, 83, 85, 86, 87, 90, 92, 93, 97, 106, 108, 112, 116, 117, 118, 122, 131, 132, 133, 134, 136, 138, 139, 144, 150, 151, 152, 158, 159, 160, 161, 162, 163, 164], "similar": [2, 3, 22, 32, 34, 38, 43, 46, 51, 69, 71, 78, 81, 85, 86, 88, 112, 128, 137, 139, 145, 150, 151, 152, 153], "set_initial_magnetic_mo": [2, 3, 78, 132, 135], "refer": [2, 3, 7, 8, 24, 41, 43, 44, 48, 54, 55, 63, 66, 78, 85, 86, 87, 90, 100, 106, 112, 125, 128, 132, 134, 135, 138, 150, 151, 154, 156, 159], "mutabl": [2, 94, 138], "so": [2, 3, 4, 6, 9, 14, 20, 22, 26, 28, 29, 32, 33, 42, 43, 48, 50, 51, 55, 56, 65, 70, 78, 79, 83, 85, 86, 87, 88, 91, 97, 98, 99, 102, 107, 110, 111, 112, 114, 115, 116, 123, 127, 128, 130, 132, 133, 134, 138, 139, 145, 148, 150, 151, 152, 153, 154, 155, 156, 160, 161, 162, 164], "case": [2, 3, 6, 8, 12, 13, 16, 19, 22, 26, 27, 32, 33, 39, 41, 43, 45, 46, 48, 50, 51, 55, 57, 63, 65, 70, 78, 79, 85, 87, 88, 89, 91, 94, 97, 103, 107, 111, 114, 115, 117, 122, 127, 128, 132, 133, 134, 139, 144, 145, 147, 150, 151, 152, 154, 158, 161, 164], "you": [2, 3, 4, 6, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 22, 23, 27, 28, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 51, 53, 55, 56, 57, 58, 59, 62, 63, 65, 66, 70, 71, 78, 79, 81, 83, 85, 86, 88, 89, 90, 92, 98, 99, 103, 106, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 120, 121, 122, 123, 124, 125, 127, 128, 129, 131, 132, 133, 134, 136, 138, 139, 144, 150, 154, 155, 156, 157, 158, 159, 160, 161, 162, 164, 165], "want": [2, 3, 6, 10, 13, 14, 23, 27, 32, 33, 38, 41, 42, 46, 47, 48, 49, 55, 57, 63, 70, 71, 78, 85, 90, 92, 103, 111, 112, 122, 123, 124, 127, 128, 129, 132, 133, 134, 136, 139, 144, 148, 153, 154, 155, 156, 159, 160, 164, 165], "order": [2, 3, 7, 8, 10, 12, 13, 14, 16, 23, 26, 28, 32, 33, 43, 46, 48, 50, 51, 55, 62, 66, 67, 68, 78, 79, 80, 83, 85, 87, 88, 89, 91, 92, 97, 100, 101, 103, 104, 117, 124, 131, 138, 139, 140, 145, 150, 151, 152, 153, 154, 158, 164], "avoid": [2, 7, 13, 15, 28, 39, 43, 44, 47, 56, 78, 86, 87, 92, 93, 94, 115, 120, 122, 133, 139, 152], "accid": 2, "return": [2, 3, 4, 5, 7, 12, 13, 14, 20, 30, 32, 33, 36, 48, 50, 51, 52, 53, 55, 56, 57, 59, 62, 63, 64, 65, 67, 68, 70, 78, 79, 81, 82, 83, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 97, 99, 100, 102, 103, 106, 107, 111, 117, 120, 131, 132, 133, 134, 138, 139, 144, 146, 147, 150, 151, 154, 160, 164], "still": [2, 12, 33, 34, 48, 55, 65, 66, 84, 85, 88, 112, 115, 127, 135, 139, 145, 150, 152, 160], "rememb": [2, 33, 112, 121, 133, 151, 161, 164], "modifi": [2, 3, 26, 32, 38, 43, 50, 51, 55, 56, 66, 70, 74, 85, 91, 97, 114, 122, 133, 135, 138, 144, 152, 159, 161], "ch4": [2, 4, 47, 105, 135, 140], "get_posit": [2, 3, 55, 86, 121, 135, 147, 154], "629118": 2, "62911799999999996": 2, "inform": [2, 3, 7, 12, 13, 14, 19, 26, 27, 32, 33, 41, 46, 47, 48, 50, 51, 53, 55, 56, 57, 63, 65, 66, 70, 77, 78, 79, 80, 83, 86, 87, 88, 90, 92, 97, 105, 106, 108, 110, 111, 112, 121, 128, 131, 133, 134, 135, 136, 139, 148, 150, 153, 154, 156, 167], "how": [2, 3, 8, 12, 15, 19, 20, 27, 28, 30, 32, 38, 39, 46, 47, 50, 51, 55, 57, 63, 65, 66, 69, 79, 81, 82, 83, 85, 86, 87, 91, 92, 97, 98, 100, 110, 113, 114, 117, 118, 120, 123, 124, 127, 128, 131, 132, 133, 134, 135, 139, 141, 150, 151, 152, 153, 154, 156, 158, 159, 160, 161, 162, 163, 164], "here": [3, 6, 8, 11, 12, 13, 19, 27, 28, 29, 30, 32, 33, 38, 40, 46, 47, 48, 51, 52, 53, 54, 55, 57, 65, 66, 69, 70, 78, 79, 85, 86, 87, 88, 90, 91, 97, 110, 111, 112, 118, 120, 121, 123, 124, 125, 128, 131, 132, 134, 136, 137, 138, 139, 143, 144, 145, 146, 147, 150, 151, 152, 153, 154, 156, 160, 161, 164], "co": [3, 4, 7, 13, 18, 68, 79, 85, 88, 90, 92, 107, 112, 150, 157, 162], "d": [3, 7, 13, 18, 22, 27, 28, 29, 34, 38, 41, 42, 43, 46, 51, 55, 57, 62, 63, 64, 65, 69, 70, 71, 76, 78, 79, 82, 85, 86, 87, 88, 90, 91, 94, 97, 100, 102, 104, 106, 111, 112, 115, 118, 122, 123, 125, 127, 131, 132, 134, 138, 139, 141, 142, 143, 145, 148, 150, 153, 154, 160], "specifi": [3, 4, 5, 6, 7, 8, 9, 13, 14, 16, 24, 25, 26, 27, 32, 38, 39, 40, 41, 42, 46, 47, 48, 50, 51, 53, 55, 57, 62, 65, 78, 79, 81, 83, 85, 86, 87, 88, 91, 92, 93, 97, 98, 99, 103, 106, 107, 117, 120, 124, 131, 132, 133, 134, 139, 150, 151, 152, 154, 164], "we": [3, 6, 8, 12, 13, 14, 29, 32, 41, 43, 44, 47, 48, 51, 53, 55, 57, 63, 80, 82, 83, 84, 85, 87, 90, 92, 101, 104, 107, 110, 111, 112, 114, 117, 118, 121, 122, 123, 125, 127, 128, 130, 131, 132, 133, 134, 136, 138, 139, 141, 143, 144, 145, 146, 148, 150, 151, 152, 153, 154, 155, 156, 157, 159, 160, 161, 162, 163, 164], "momenta": [3, 53, 55, 57, 70, 81, 85, 88, 118, 139, 156], "could": [3, 6, 13, 26, 32, 51, 57, 65, 76, 83, 85, 90, 112, 117, 118, 124, 127, 128, 133, 134, 138, 139, 144, 151, 152, 154, 160, 161, 165], "infinit": [3, 4, 48, 98], "gold": [3, 6, 69, 97, 125, 143, 154], "wire": 3, "bond": [3, 4, 5, 22, 55, 56, 65, 70, 71, 78, 79, 80, 85, 87, 88, 92, 97, 124, 139, 142, 147, 148, 150, 153, 159, 160], "9": [3, 6, 7, 29, 38, 40, 53, 55, 56, 57, 65, 70, 78, 90, 92, 98, 102, 118, 130, 135, 138, 142, 144, 146, 148, 152, 154, 155, 157, 159, 163, 166], "l": [3, 6, 25, 41, 51, 53, 55, 57, 63, 65, 69, 70, 83, 85, 86, 88, 91, 97, 98, 115, 134, 138, 141, 145, 150, 154, 164, 167], "10": [3, 6, 13, 15, 19, 22, 26, 29, 43, 47, 51, 54, 55, 56, 57, 62, 63, 66, 67, 70, 71, 78, 81, 82, 85, 86, 87, 88, 90, 91, 97, 102, 103, 104, 107, 115, 118, 125, 130, 131, 134, 135, 137, 141, 142, 144, 145, 146, 148, 150, 151, 152, 153, 154, 156, 157, 159, 160], "au": [3, 6, 19, 23, 30, 32, 52, 57, 79, 83, 90, 97, 106, 127, 134, 139, 143, 144, 145, 146, 152, 154, 158], "pbc": [3, 4, 6, 14, 20, 21, 25, 29, 30, 34, 47, 49, 52, 53, 55, 57, 65, 70, 78, 79, 80, 83, 87, 92, 97, 100, 111, 130, 134, 135, 139, 140, 144, 147, 149, 150, 153, 156, 160, 166], "two": [3, 4, 6, 7, 8, 12, 16, 19, 20, 22, 25, 26, 28, 32, 33, 36, 41, 42, 43, 46, 51, 53, 55, 56, 57, 58, 62, 68, 70, 71, 76, 78, 81, 83, 85, 86, 87, 88, 90, 91, 92, 97, 98, 100, 101, 102, 104, 106, 112, 114, 115, 116, 117, 120, 128, 130, 131, 132, 134, 139, 140, 146, 147, 148, 150, 151, 152, 154, 157, 160, 161], "were": [3, 13, 14, 56, 85, 94, 99, 104, 116, 122, 127, 132, 134, 139, 157], "size": [3, 6, 7, 13, 20, 29, 32, 40, 46, 47, 50, 53, 55, 56, 63, 65, 66, 69, 78, 83, 85, 86, 88, 91, 92, 98, 106, 107, 127, 130, 131, 139, 143, 145, 148, 151, 152, 154, 156, 158, 159, 163, 165, 166], "six": [3, 14, 49, 52, 55, 70, 85, 111, 163], "legth": 3, "angl": [3, 4, 7, 30, 52, 55, 57, 66, 70, 71, 76, 77, 78, 80, 83, 85, 88, 92, 100, 107, 125, 133, 135, 139, 150], "degre": [3, 4, 52, 55, 70, 81, 83, 85, 92, 97, 100, 102, 106, 107, 130, 134, 139, 148, 150, 153, 162, 163, 166], "default": [3, 4, 6, 7, 8, 9, 10, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 53, 55, 56, 57, 59, 62, 63, 65, 66, 67, 70, 74, 76, 77, 78, 79, 81, 82, 83, 85, 86, 87, 88, 90, 91, 92, 93, 94, 97, 102, 103, 106, 107, 108, 111, 115, 117, 118, 123, 128, 130, 131, 133, 134, 135, 136, 138, 139, 146, 147, 150, 152, 156, 161], "90": [3, 7, 16, 19, 55, 57, 92, 97, 130, 134, 139, 146, 154], "mean": [3, 6, 8, 12, 13, 21, 24, 32, 39, 41, 43, 44, 46, 47, 50, 53, 54, 55, 65, 66, 70, 78, 79, 81, 85, 88, 112, 114, 117, 121, 133, 134, 138, 139, 147, 150, 151, 154, 163, 164], "vector": [3, 4, 6, 7, 12, 19, 22, 33, 43, 51, 52, 55, 63, 65, 66, 70, 76, 78, 79, 83, 85, 87, 88, 91, 92, 100, 107, 117, 134, 137, 139, 150, 153, 154, 163], "period": [3, 4, 6, 7, 11, 12, 16, 20, 21, 26, 32, 33, 52, 57, 63, 65, 70, 77, 78, 83, 86, 87, 88, 91, 92, 97, 98, 107, 112, 130, 134, 135, 139, 144, 145, 147, 150, 152, 157, 160], "fals": [3, 4, 6, 7, 12, 13, 14, 15, 16, 20, 23, 24, 25, 29, 30, 32, 34, 35, 38, 41, 43, 44, 45, 47, 48, 50, 51, 52, 53, 55, 56, 57, 59, 64, 65, 66, 67, 68, 70, 71, 78, 79, 81, 82, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 96, 98, 100, 102, 103, 104, 107, 111, 117, 125, 130, 138, 139, 140, 146, 150, 152, 153, 154, 156, 158, 159, 166], "true": [3, 4, 6, 7, 12, 13, 15, 16, 17, 18, 20, 21, 23, 24, 25, 27, 29, 32, 33, 34, 38, 39, 40, 41, 43, 44, 46, 47, 48, 50, 51, 52, 53, 55, 57, 59, 65, 66, 67, 68, 70, 71, 78, 79, 81, 85, 86, 87, 88, 89, 90, 91, 92, 96, 97, 100, 102, 103, 104, 107, 111, 114, 115, 117, 121, 125, 128, 130, 133, 134, 137, 138, 139, 140, 141, 146, 147, 149, 150, 151, 152, 153, 154, 156, 158, 160, 162, 163, 164, 166], "would": [3, 13, 16, 17, 18, 28, 33, 38, 46, 47, 50, 51, 55, 65, 78, 83, 86, 90, 93, 97, 112, 127, 132, 133, 134, 139, 151, 152, 157, 160, 164], "give": [3, 6, 13, 15, 23, 25, 41, 47, 55, 56, 57, 65, 76, 78, 83, 85, 86, 87, 89, 91, 92, 97, 102, 103, 104, 106, 112, 114, 121, 123, 125, 131, 132, 134, 138, 139, 145, 150, 154, 161], "along": [3, 4, 6, 7, 14, 17, 18, 22, 33, 51, 52, 55, 57, 63, 66, 70, 75, 78, 83, 85, 86, 88, 91, 97, 139, 143, 147, 150, 157, 161, 163], "ax": [3, 4, 6, 52, 57, 67, 70, 71, 78, 83, 85, 86, 90, 91, 93, 94, 106, 107, 127, 132, 134, 150, 151, 157, 158], "boolean": [3, 13, 33, 41, 45, 55, 57, 66, 76, 78, 85, 86, 88, 107, 134, 138, 139, 140, 147, 150], "specif": [3, 4, 7, 8, 12, 13, 19, 21, 27, 28, 32, 36, 38, 41, 46, 47, 48, 49, 50, 51, 55, 57, 63, 65, 66, 69, 71, 79, 83, 86, 87, 88, 91, 106, 112, 114, 127, 128, 131, 134, 135, 139, 150, 154, 156, 160], "set_pbc": [3, 135, 141, 147, 148, 160, 162], "set_cel": [3, 26, 47, 88, 115, 130, 135, 139, 141, 146, 149, 151, 152, 159, 162], "get_cel": [3, 26, 79, 87, 115, 121, 135, 139, 143, 149, 150, 154, 158, 159], "get_pbc": [3, 79, 135], "address": [3, 8, 13, 48, 57, 85, 112, 125, 153], "n3": [3, 12, 19, 62, 65, 76, 117], "set_posit": [3, 55, 135], "full": [3, 8, 12, 20, 25, 26, 28, 42, 44, 51, 55, 70, 78, 86, 90, 93, 97, 106, 114, 128, 132, 133, 139, 151, 152, 154, 159, 160], "oper": [3, 32, 44, 52, 55, 63, 64, 69, 70, 78, 85, 92, 94, 112, 115, 118, 120, 122, 135, 138, 139, 153, 154], "onc": [3, 7, 13, 44, 57, 70, 79, 81, 88, 97, 112, 122, 127, 128, 132, 133, 134, 138, 145, 151, 154, 162], "quantiti": [3, 12, 33, 48, 51, 70, 71, 76, 78, 81, 85, 87, 88, 97, 125, 133, 134, 139], "one": [3, 4, 6, 7, 8, 9, 12, 13, 14, 15, 16, 20, 22, 25, 26, 28, 29, 30, 32, 33, 35, 41, 44, 46, 47, 48, 49, 50, 51, 52, 53, 55, 56, 57, 58, 63, 65, 66, 68, 70, 75, 77, 78, 79, 80, 81, 82, 85, 86, 87, 88, 89, 90, 92, 93, 94, 97, 98, 100, 103, 106, 108, 109, 111, 112, 116, 117, 120, 121, 122, 130, 131, 132, 133, 134, 135, 138, 139, 141, 142, 144, 145, 150, 151, 152, 153, 154, 156, 157, 158, 159, 160, 161, 164, 166], "each": [3, 5, 6, 7, 10, 12, 13, 14, 19, 22, 24, 25, 28, 30, 32, 34, 36, 39, 40, 41, 46, 47, 48, 51, 52, 53, 55, 56, 57, 63, 65, 70, 71, 76, 78, 83, 85, 86, 87, 88, 92, 97, 98, 101, 102, 103, 112, 117, 121, 122, 132, 133, 134, 139, 141, 145, 146, 147, 148, 150, 151, 152, 153, 154, 157, 158, 160, 161, 162, 163, 164], "take": [3, 6, 8, 12, 13, 14, 20, 23, 28, 32, 44, 51, 53, 57, 63, 66, 70, 78, 85, 88, 92, 94, 97, 102, 103, 106, 111, 112, 117, 123, 130, 131, 133, 134, 136, 139, 144, 150, 151, 152, 153, 154, 159, 160, 161], "e": [3, 7, 8, 9, 12, 13, 14, 15, 16, 19, 24, 26, 27, 28, 30, 32, 33, 38, 41, 42, 43, 44, 46, 47, 48, 50, 51, 52, 53, 55, 56, 57, 62, 65, 67, 70, 71, 76, 78, 79, 81, 83, 85, 86, 87, 88, 90, 91, 92, 93, 94, 97, 104, 106, 112, 114, 115, 117, 120, 121, 122, 124, 125, 127, 128, 132, 134, 138, 139, 141, 144, 145, 146, 147, 150, 151, 152, 153, 154, 160, 161, 163, 166], "g": [3, 7, 8, 9, 13, 14, 15, 16, 19, 24, 25, 26, 28, 30, 32, 33, 38, 41, 42, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55, 56, 63, 65, 66, 70, 71, 76, 78, 79, 81, 83, 85, 86, 87, 88, 91, 92, 93, 94, 97, 106, 112, 114, 115, 120, 122, 124, 132, 134, 139, 141, 145, 147, 150, 151, 152, 153, 154, 160], "n": [3, 4, 7, 12, 13, 22, 23, 24, 25, 28, 29, 38, 40, 46, 51, 55, 56, 57, 59, 63, 64, 65, 66, 68, 70, 71, 76, 78, 79, 81, 82, 83, 85, 86, 87, 88, 91, 97, 98, 100, 103, 106, 116, 117, 118, 122, 125, 131, 132, 135, 136, 137, 138, 142, 143, 144, 145, 148, 150, 151, 152, 153, 154, 160, 163, 166], "get_atomic_numb": [3, 135], "integ": [3, 4, 7, 13, 24, 25, 33, 41, 44, 47, 48, 53, 57, 64, 70, 78, 83, 85, 87, 91, 92, 97, 118, 138, 150, 151], "These": [3, 6, 12, 18, 19, 28, 32, 33, 38, 39, 47, 51, 56, 57, 64, 76, 78, 79, 83, 84, 88, 101, 104, 111, 112, 120, 121, 122, 124, 127, 132, 133, 134, 139, 144, 147, 150, 152, 153, 156], "intern": [3, 4, 13, 14, 21, 22, 28, 30, 32, 33, 37, 50, 55, 57, 71, 72, 78, 81, 85, 86, 88, 92, 97, 111, 120, 139, 150, 153, 158, 162], "thu": [3, 27, 41, 44, 65, 78, 81, 86, 88, 92, 97, 98, 99, 104, 120, 133, 137, 145, 151, 152, 154, 160], "safe": [3, 89, 94, 112, 116], "set_atomic_numb": [3, 135], "set_initial_charg": [3, 135, 139], "get_charg": [3, 50, 135, 139], "get_chemical_symbol": [3, 7, 40, 54, 56, 92, 118, 135, 140, 151, 152], "set_chemical_symbol": [3, 40, 135, 151, 152], "get_initial_magnetic_mo": [3, 78, 135], "get_magnetic_mo": [3, 12, 51, 78, 135], "get_mass": [3, 135, 141], "set_mass": [3, 56, 135, 139, 141], "get_momenta": [3, 135], "set_momenta": [3, 135], "get_forc": [3, 10, 11, 12, 22, 40, 44, 48, 50, 57, 101, 132, 135, 144, 150], "get_potential_energi": [3, 10, 12, 13, 14, 19, 20, 21, 22, 24, 26, 28, 30, 32, 33, 37, 39, 40, 44, 47, 50, 51, 57, 63, 66, 97, 117, 127, 128, 131, 132, 134, 135, 142, 144, 146, 148, 149, 151, 152, 154, 155, 156, 160, 164, 166], "get_scaled_posit": [3, 135, 139], "set_scaled_posit": [3, 135], "get_stress": [3, 12, 34, 111, 134, 135, 139, 164], "get_tag": [3, 6, 40, 82, 135], "set_tag": [3, 40, 47, 135, 147, 153], "get_veloc": [3, 135, 139], "set_veloc": [3, 19, 135], "get_calcul": [3, 135, 139], "set_calcul": [3, 135, 139], "get_cell_lengths_and_angl": [3, 135, 139], "get_center_of_mass": [3, 102, 135], "get_kinetic_energi": [3, 131, 132, 135, 156], "get_global_number_of_atom": [3, 135], "get_total_energi": [3, 135], "get_volum": [3, 24, 87, 135, 144, 146, 149], "hold": [3, 40, 47, 62, 92, 137, 142], "resembl": [3, 52, 70, 139], "3x3": [3, 7, 8, 52, 55, 62, 63, 70, 78, 83, 85, 87, 92, 139], "matrix": [3, 7, 38, 41, 47, 50, 51, 52, 55, 63, 65, 70, 78, 85, 87, 88, 91, 92, 98, 102, 103, 109, 137, 139, 145, 150, 163], "when": [3, 6, 7, 12, 13, 14, 15, 16, 19, 21, 22, 25, 28, 33, 35, 36, 38, 39, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, 55, 56, 57, 63, 64, 66, 78, 81, 82, 83, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 111, 112, 113, 115, 117, 121, 122, 128, 130, 131, 132, 133, 135, 138, 139, 144, 145, 150, 151, 152, 154, 156, 161, 164], "arithmet": [3, 39], "doe": [3, 6, 8, 9, 13, 14, 20, 22, 24, 29, 48, 51, 52, 53, 56, 65, 70, 78, 79, 81, 83, 85, 86, 88, 97, 103, 112, 114, 115, 117, 120, 121, 128, 131, 133, 134, 136, 139, 145, 157, 161], "per": [3, 12, 13, 27, 33, 50, 51, 52, 53, 54, 63, 66, 70, 78, 79, 81, 85, 86, 87, 90, 97, 100, 102, 103, 117, 120, 139, 146, 150, 156, 160], "move": [3, 13, 22, 43, 48, 55, 57, 65, 66, 70, 74, 84, 85, 86, 87, 88, 97, 117, 132, 135, 139, 143, 144, 148, 152, 161], "np": [3, 4, 7, 8, 9, 14, 15, 18, 20, 21, 22, 25, 26, 30, 34, 41, 44, 45, 47, 49, 50, 55, 56, 63, 70, 82, 85, 87, 88, 90, 98, 100, 107, 111, 130, 137, 139, 141, 145, 146, 147, 148, 149, 151, 152, 153, 154, 155, 158, 159, 160, 162, 166], "ident": [3, 12, 13, 28, 50, 55, 65, 85, 86, 88, 93, 98, 112, 120, 135, 137, 145, 150, 151, 153, 157, 161], "howev": [3, 7, 8, 14, 21, 22, 26, 28, 33, 40, 41, 43, 44, 51, 56, 78, 79, 85, 88, 97, 99, 114, 131, 133, 138, 139, 141, 145, 150, 153, 156, 159, 162, 163, 164], "scale_atom": [3, 47, 130, 146, 149, 151, 152, 159], "whether": [3, 6, 13, 15, 32, 33, 38, 47, 48, 50, 52, 70, 78, 85, 92, 111, 134, 139, 150, 151, 152, 154], "direct": [3, 4, 6, 7, 8, 13, 22, 24, 26, 28, 33, 46, 47, 52, 53, 55, 59, 64, 65, 70, 76, 78, 83, 85, 87, 88, 91, 92, 97, 98, 102, 103, 104, 106, 111, 112, 115, 130, 133, 134, 139, 145, 147, 150, 154, 156, 159, 161, 163], "slab": [3, 6, 7, 16, 22, 55, 66, 79, 83, 106, 131, 135, 139, 143, 144, 147, 148, 150, 151, 153, 154, 157, 158, 159], "free": [3, 11, 12, 29, 42, 49, 55, 63, 78, 83, 85, 97, 103, 107, 109, 114, 127, 132, 139], "through": [3, 15, 16, 26, 27, 31, 32, 33, 40, 44, 47, 48, 51, 69, 78, 81, 85, 87, 88, 92, 97, 116, 125, 132, 133, 134, 135, 139, 154, 160, 164], "directli": [3, 13, 22, 27, 32, 33, 38, 39, 47, 48, 50, 51, 52, 55, 57, 63, 70, 71, 79, 85, 86, 93, 94, 106, 108, 110, 112, 121, 122, 131, 133, 136, 145, 152, 158], "2nd": [3, 62, 97, 150], "count": [3, 57, 68, 70, 87, 92, 100, 106, 135, 138, 147, 151, 152], "becaus": [3, 13, 15, 20, 22, 29, 32, 33, 83, 87, 88, 91, 114, 120, 122, 132, 133, 134, 139, 150, 151, 153, 154, 156, 157, 163], "start": [3, 12, 19, 26, 28, 33, 37, 38, 41, 42, 45, 48, 50, 57, 65, 66, 70, 71, 78, 85, 86, 87, 88, 92, 100, 102, 103, 104, 111, 112, 117, 121, 122, 128, 131, 133, 135, 136, 138, 139, 144, 147, 150, 151, 152, 153, 154, 156], "zero": [3, 7, 11, 12, 14, 16, 20, 26, 43, 46, 49, 51, 52, 53, 55, 56, 57, 63, 70, 78, 82, 85, 87, 88, 91, 93, 94, 97, 102, 103, 106, 107, 111, 134, 137, 139, 150, 156], "13": [3, 6, 19, 22, 50, 51, 55, 63, 70, 80, 116, 135, 166], "al": [3, 4, 6, 7, 22, 23, 33, 54, 55, 56, 70, 85, 88, 91, 92, 100, 104, 135, 139, 143, 144, 146, 147, 152, 158, 165], "shortcut": [3, 106, 122, 134, 139], "aln2": 3, "cu": [3, 4, 23, 33, 53, 54, 55, 56, 57, 63, 67, 68, 71, 78, 79, 83, 88, 90, 107, 127, 131, 134, 144, 146, 148, 151, 152, 156, 157], "alncu": 3, "29": [3, 8, 56, 71, 125, 146], "check": [3, 7, 8, 12, 13, 15, 20, 22, 33, 41, 43, 50, 55, 57, 63, 68, 70, 78, 81, 83, 85, 88, 91, 93, 97, 111, 112, 113, 116, 117, 121, 123, 135, 137, 139, 144, 150, 151, 152, 153, 154, 164], "dtype": [3, 30, 79, 82, 87, 88, 90, 96, 140], "bool": [3, 4, 6, 7, 8, 12, 14, 15, 16, 17, 18, 19, 25, 30, 32, 33, 34, 35, 38, 41, 43, 44, 46, 47, 49, 50, 51, 52, 53, 55, 57, 59, 64, 66, 68, 70, 78, 79, 81, 82, 85, 86, 87, 88, 90, 91, 92, 93, 94, 96, 98, 100, 103, 111, 138, 140, 146, 150], "hexagon": [3, 6, 40, 60, 63, 83, 145, 153], "15": [3, 29, 47, 51, 54, 55, 57, 62, 65, 78, 86, 97, 102, 106, 107, 111, 135, 144, 146, 150, 153, 157, 158, 166], "120": [3, 80, 88, 92, 97, 130, 150], "calc": [3, 8, 10, 11, 12, 13, 14, 16, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 57, 59, 62, 63, 65, 66, 67, 78, 86, 88, 91, 97, 98, 101, 102, 104, 117, 118, 127, 128, 131, 132, 133, 134, 135, 139, 141, 142, 143, 144, 146, 148, 151, 152, 154, 155, 156, 157, 158, 159, 160, 162, 164, 166], "after": [3, 6, 7, 8, 14, 15, 24, 25, 28, 33, 42, 47, 48, 50, 51, 55, 56, 57, 67, 71, 76, 78, 79, 81, 86, 88, 97, 112, 120, 122, 127, 131, 133, 139, 145, 148, 150, 151, 152, 153, 154, 156, 164], "appropri": [3, 13, 28, 32, 38, 40, 48, 51, 81, 85, 88, 94, 122, 132, 136, 139, 153, 154], "term": [3, 7, 8, 22, 43, 46, 55, 65, 85, 97, 98, 104, 145, 152, 159, 160, 162], "potenti": [3, 8, 9, 10, 12, 13, 14, 15, 19, 20, 21, 23, 25, 26, 30, 32, 33, 34, 38, 39, 41, 42, 43, 45, 46, 47, 51, 55, 57, 66, 76, 78, 85, 86, 87, 88, 90, 97, 98, 106, 118, 122, 124, 128, 132, 134, 135, 139, 141, 143, 144, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 160, 162, 165], "includ": [3, 7, 8, 9, 10, 12, 13, 14, 19, 20, 22, 23, 24, 27, 28, 32, 34, 48, 50, 51, 52, 53, 57, 64, 65, 66, 70, 77, 78, 79, 85, 86, 87, 88, 91, 92, 94, 97, 102, 104, 111, 113, 114, 117, 123, 124, 128, 134, 135, 136, 139, 145, 150, 152, 154, 156, 160, 162, 164], "kinet": [3, 51, 76, 85, 88, 132, 156], "electrostat": [3, 19, 46, 106, 135, 145], "exchang": [3, 8, 10, 12, 15, 27, 28, 38, 41, 47, 128, 135, 161], "correl": [3, 8, 10, 12, 15, 27, 28, 38, 41, 47, 128, 135, 150], "reason": [3, 4, 12, 19, 32, 51, 55, 70, 81, 84, 85, 86, 87, 114, 117, 134, 139, 141, 145, 150, 154, 157], "might": [3, 7, 13, 27, 33, 34, 43, 44, 50, 51, 76, 78, 79, 87, 88, 92, 101, 123, 127, 134, 152, 160], "have": [3, 4, 6, 7, 8, 12, 13, 14, 15, 20, 23, 24, 26, 29, 30, 32, 33, 34, 38, 39, 40, 41, 43, 44, 46, 47, 48, 50, 51, 55, 57, 62, 63, 64, 65, 67, 69, 78, 81, 82, 85, 86, 87, 88, 90, 92, 93, 94, 98, 102, 103, 104, 106, 109, 111, 112, 115, 117, 122, 123, 125, 127, 128, 130, 131, 132, 133, 134, 136, 139, 141, 144, 145, 147, 148, 150, 151, 152, 153, 154, 158, 160, 161, 162, 163, 164], "nuclei": [3, 132, 160], "In": [3, 6, 8, 9, 12, 13, 14, 16, 19, 22, 26, 27, 32, 38, 39, 41, 43, 46, 48, 50, 51, 53, 55, 57, 63, 65, 71, 78, 79, 80, 81, 82, 85, 88, 89, 91, 97, 102, 104, 107, 111, 112, 114, 115, 117, 122, 123, 125, 127, 131, 132, 133, 134, 138, 139, 140, 141, 143, 144, 145, 146, 147, 148, 150, 151, 152, 153, 154, 156, 157, 158, 160, 161, 163, 164], "exactli": [3, 8, 53, 57, 65, 78, 85, 133, 143], "result": [3, 6, 7, 13, 14, 16, 17, 19, 20, 22, 25, 26, 27, 28, 33, 39, 43, 47, 49, 50, 51, 53, 55, 56, 57, 62, 65, 70, 78, 85, 86, 87, 91, 93, 94, 97, 107, 111, 114, 115, 117, 121, 123, 128, 133, 135, 137, 139, 143, 144, 145, 146, 147, 149, 150, 151, 152, 154, 155, 156, 158, 159, 161], "finit": [3, 38, 46, 66, 83, 85, 91, 101, 102, 103, 105, 107, 111, 135, 145, 156, 163], "temperatur": [3, 41, 50, 55, 56, 76, 85, 88, 90, 91, 97, 99, 101, 135, 139, 141, 162], "smear": [3, 8, 12, 15, 16, 26, 41, 50, 51, 62, 93, 94, 117, 127, 134, 150], "occup": [3, 12, 50, 78, 91, 92, 101, 104, 127, 139], "extrapol": [3, 12, 48, 56, 66, 84, 85, 88, 97, 139, 145], "found": [3, 6, 12, 13, 14, 16, 25, 29, 31, 32, 33, 47, 50, 51, 56, 66, 69, 78, 79, 83, 84, 88, 89, 97, 103, 132, 136, 138, 139, 143, 150, 154, 155, 157, 160, 161, 163], "onli": [3, 4, 6, 8, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 26, 30, 32, 33, 34, 38, 39, 41, 47, 48, 50, 51, 53, 54, 55, 56, 57, 58, 59, 65, 66, 68, 70, 78, 79, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 98, 102, 103, 104, 106, 107, 112, 114, 122, 128, 130, 131, 132, 133, 134, 135, 139, 143, 144, 145, 147, 150, 151, 152, 153, 154, 157, 160, 164, 166], "Not": [3, 12, 14, 33, 35, 44, 49, 51, 78, 81, 85, 92, 97, 111, 118, 135], "wire2": 3, "extend": [3, 7, 22, 32, 50, 65, 78, 79, 80, 92, 96, 106, 115, 118, 120, 124, 130, 135, 139, 145, 151, 157], "append": [3, 13, 57, 66, 78, 79, 81, 82, 85, 86, 88, 89, 92, 100, 108, 117, 122, 123, 130, 132, 135, 138, 139, 146, 151, 152, 154, 158, 159, 164], "wire3": 3, "repeat": [3, 4, 6, 7, 46, 64, 65, 68, 71, 74, 83, 85, 91, 92, 98, 106, 115, 130, 134, 135, 137, 139, 141, 143, 145, 150, 160, 162], "len": [3, 14, 24, 40, 49, 52, 54, 55, 57, 62, 70, 86, 87, 88, 92, 111, 140, 144, 146, 147, 150, 151, 152, 153, 154, 156, 158, 162, 166], "del": [3, 55, 57, 88, 139, 140, 144], "pop": [3, 131, 135, 151, 152, 153], "oxygen": [3, 19, 30, 56, 57, 90, 135, 160], "note": [3, 4, 6, 7, 8, 12, 14, 15, 19, 20, 25, 26, 27, 28, 33, 39, 44, 48, 51, 52, 53, 55, 56, 57, 65, 66, 68, 70, 78, 79, 81, 83, 85, 86, 87, 88, 97, 99, 100, 103, 114, 116, 121, 128, 131, 132, 133, 134, 135, 136, 148, 150, 151, 152, 153, 154, 156, 157, 159, 163], "power": [3, 11, 112, 120, 125, 137, 152, 154], "style": [3, 12, 33, 78, 80, 112, 116, 120, 122, 123, 124, 139, 151], "comprehens": [3, 45, 120, 124], "select": [3, 9, 16, 20, 30, 32, 34, 41, 46, 50, 51, 53, 57, 70, 72, 74, 76, 77, 78, 81, 85, 90, 92, 93, 94, 99, 107, 115, 118, 125, 128, 133, 135, 139, 144, 147, 151, 152, 154, 158, 160, 164], "delet": [3, 34, 48, 50, 57, 70, 81, 97, 103, 112, 116, 135, 140, 144, 160], "within": [3, 7, 8, 13, 14, 27, 30, 32, 33, 40, 48, 50, 55, 65, 70, 75, 78, 85, 86, 87, 91, 92, 102, 103, 120, 121, 130, 132, 133, 134, 139, 150, 151, 152, 154, 156, 157], "below": [3, 6, 8, 15, 16, 19, 26, 27, 28, 29, 32, 34, 38, 39, 41, 44, 45, 47, 48, 50, 51, 53, 55, 63, 65, 66, 72, 78, 79, 83, 84, 86, 88, 92, 97, 98, 104, 111, 112, 116, 117, 122, 131, 134, 136, 137, 140, 145, 146, 147, 151, 154, 156, 157, 158, 159], "ethanol": [3, 39, 56], "subsequ": [3, 14, 28, 39, 86, 91, 103, 133, 139, 152], "strip": 3, "hydrogen": [3, 4, 6, 47, 54, 55, 56, 57, 78, 85, 104, 107, 135, 141, 160], "ch3ch2oh": [3, 4, 39, 87, 96, 133], "center": [3, 4, 6, 7, 13, 18, 19, 38, 39, 40, 51, 53, 55, 62, 65, 66, 70, 76, 78, 83, 85, 91, 103, 121, 127, 128, 130, 132, 133, 135, 139, 141, 143, 145, 154, 156, 158, 160, 162, 166], "wrap": [3, 7, 12, 14, 20, 63, 70, 78, 87, 112, 130, 133, 134, 135, 139, 164], "rotat": [3, 4, 6, 7, 12, 52, 65, 66, 70, 71, 74, 78, 79, 85, 86, 91, 92, 97, 100, 106, 115, 125, 130, 135, 137, 139, 141, 150, 159, 163], "euler_rot": [3, 19, 135, 139], "set_dihedr": [3, 135, 139], "rotate_dihedr": [3, 135, 139], "rattl": [3, 20, 39, 48, 55, 85, 88, 117, 135, 150, 160, 162], "set_constraint": [3, 55, 66, 131, 135, 141, 143, 148, 154, 157, 158, 159, 162], "set_dist": [3, 135], "get_all_dist": [3, 135, 139], "scaled_posit": [3, 6, 52, 53, 70, 130, 135], "celldisp": [3, 53], "info": [3, 42, 46, 53, 57, 78, 79, 83, 92, 93, 94, 108, 115, 132, 133, 139, 150, 151, 152, 154, 160, 162], "isol": [3, 57, 127, 131, 132, 135, 142, 144, 147, 150, 154], "store": [3, 12, 13, 14, 16, 22, 28, 50, 53, 57, 63, 66, 78, 79, 80, 81, 82, 83, 87, 88, 93, 94, 112, 116, 117, 123, 128, 135, 139, 142, 144, 150, 152, 154, 156, 164], "ndarrai": [3, 52, 59, 62, 63, 66, 70, 78, 82, 83, 85, 87, 91, 92, 94, 98, 106, 137, 138, 139, 140], "string": [3, 4, 6, 8, 13, 16, 25, 27, 28, 30, 32, 33, 34, 38, 39, 40, 41, 42, 47, 48, 50, 51, 52, 53, 56, 57, 63, 66, 68, 70, 78, 82, 83, 85, 86, 87, 88, 90, 91, 92, 94, 96, 100, 103, 104, 107, 111, 117, 118, 120, 122, 138, 139, 147, 150, 151], "h2o": [3, 4, 11, 12, 17, 18, 19, 21, 27, 28, 38, 40, 44, 48, 56, 57, 68, 88, 90, 135], "copt12": 3, "ne": [3, 22], "xyz": [3, 10, 12, 18, 19, 20, 29, 47, 66, 71, 79, 87, 102, 130, 131, 135, 139, 140], "anyth": [3, 8, 12, 44, 47, 57, 78, 87, 132, 134], "convert": [3, 7, 13, 19, 24, 25, 39, 45, 47, 52, 56, 63, 68, 70, 76, 78, 79, 82, 85, 86, 87, 92, 97, 100, 103, 108, 111, 115, 123, 135, 139, 144, 164], "shape": [3, 6, 7, 12, 22, 38, 53, 57, 59, 62, 63, 66, 70, 78, 82, 85, 87, 91, 106, 107, 124, 133, 135, 137, 139, 150, 159, 161], "do": [3, 8, 10, 12, 13, 14, 23, 25, 28, 29, 33, 34, 35, 37, 38, 39, 42, 43, 44, 46, 48, 49, 50, 51, 52, 53, 55, 57, 62, 63, 65, 66, 67, 70, 78, 82, 85, 86, 87, 88, 90, 91, 92, 93, 94, 97, 98, 100, 103, 104, 106, 108, 110, 111, 112, 114, 115, 117, 120, 121, 122, 123, 127, 128, 131, 132, 133, 134, 135, 139, 144, 148, 149, 151, 152, 154, 155, 156, 158, 160, 161, 163, 164], "x1": [3, 87, 93, 94, 159], "y1": [3, 83, 87, 93, 94, 159], "z1": [3, 87, 159], "x2": [3, 87, 93, 94, 159], "y2": [3, 87, 91, 93, 94, 159], "z2": [3, 87, 159], "given": [3, 4, 6, 7, 10, 12, 13, 17, 18, 22, 24, 25, 30, 32, 33, 39, 41, 47, 48, 50, 51, 52, 53, 55, 56, 57, 63, 64, 65, 66, 70, 76, 78, 79, 81, 83, 85, 86, 87, 88, 90, 91, 92, 93, 94, 97, 99, 100, 102, 103, 104, 107, 117, 120, 133, 134, 138, 139, 145, 147, 148, 150, 151, 154, 156], "either": [3, 4, 6, 7, 8, 17, 18, 20, 22, 24, 27, 32, 33, 40, 43, 44, 46, 47, 48, 50, 51, 53, 54, 55, 65, 70, 76, 78, 83, 85, 92, 97, 98, 103, 112, 120, 136, 139, 147, 150, 151, 152, 153, 156, 164], "collinear": [3, 47], "6": [3, 4, 7, 8, 9, 13, 14, 16, 17, 22, 24, 26, 27, 28, 29, 34, 38, 40, 41, 43, 44, 45, 47, 49, 50, 51, 52, 53, 55, 57, 67, 68, 70, 71, 76, 78, 80, 83, 85, 86, 87, 88, 90, 92, 96, 97, 102, 103, 106, 107, 111, 118, 130, 134, 135, 136, 137, 140, 144, 145, 146, 157, 159, 160, 162, 166], "just": [3, 7, 13, 14, 23, 29, 32, 44, 46, 51, 57, 70, 76, 78, 81, 85, 88, 97, 99, 112, 114, 121, 122, 127, 132, 133, 151, 152, 156, 160, 163], "where": [3, 6, 7, 8, 9, 11, 12, 13, 14, 16, 19, 22, 26, 27, 32, 33, 43, 44, 46, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57, 59, 62, 63, 64, 65, 70, 78, 81, 85, 86, 87, 88, 91, 92, 93, 94, 97, 98, 99, 101, 104, 106, 107, 112, 114, 117, 120, 122, 128, 129, 133, 136, 139, 141, 144, 145, 146, 150, 151, 152, 153, 154, 156, 160, 163, 164], "between": [3, 4, 7, 15, 22, 24, 28, 32, 43, 46, 47, 48, 50, 52, 53, 55, 56, 57, 63, 65, 70, 71, 74, 76, 78, 79, 81, 85, 86, 87, 88, 91, 97, 98, 100, 104, 107, 108, 114, 124, 125, 130, 134, 135, 139, 141, 145, 146, 148, 150, 151, 154, 157, 158, 159, 160, 161], "them": [3, 5, 9, 10, 14, 16, 24, 30, 36, 47, 51, 52, 55, 57, 65, 70, 71, 78, 84, 85, 86, 88, 101, 112, 114, 117, 121, 122, 132, 133, 136, 139, 144, 150, 151, 152, 153, 154, 160, 164], "lie": [3, 63, 70, 134, 150, 153], "xy": [3, 6, 33, 55, 102], "plane": [3, 4, 6, 7, 9, 12, 15, 24, 26, 38, 40, 41, 51, 55, 70, 76, 92, 102, 117, 128, 130, 139, 143, 147, 150, 151, 159, 164], "third": [3, 6, 55, 63, 67, 78, 81, 83, 102, 139, 143, 158, 161], "subspac": 3, "displac": [3, 7, 24, 50, 66, 78, 85, 86, 91, 101, 102, 103, 104, 111, 132, 139, 150, 163], "To": [3, 4, 6, 9, 13, 15, 32, 33, 38, 41, 47, 48, 51, 52, 53, 55, 56, 57, 63, 70, 71, 78, 82, 83, 85, 86, 88, 90, 92, 97, 100, 106, 112, 121, 123, 127, 128, 132, 133, 139, 145, 150, 151, 152, 154, 159, 160, 161, 164], "around": [3, 32, 43, 46, 51, 53, 55, 85, 86, 87, 88, 110, 114, 117, 120, 127, 130, 132, 133, 134, 139, 147, 159, 161, 163, 164], "system": [3, 4, 6, 7, 10, 12, 13, 15, 16, 18, 19, 20, 21, 24, 27, 28, 29, 30, 32, 33, 34, 38, 40, 41, 43, 44, 47, 50, 51, 55, 56, 57, 59, 65, 66, 67, 71, 72, 74, 78, 81, 83, 85, 86, 87, 88, 91, 92, 97, 98, 104, 107, 108, 111, 117, 122, 130, 131, 133, 134, 135, 138, 139, 147, 150, 151, 152, 156, 162, 163], "flag": [3, 6, 15, 45, 51, 57, 78, 92, 107, 112, 122], "appli": [3, 7, 13, 25, 26, 41, 47, 51, 55, 56, 57, 63, 70, 76, 83, 85, 86, 87, 88, 115, 137, 139, 150, 153], "dure": [3, 14, 36, 47, 55, 66, 70, 81, 86, 88, 112, 121, 139, 153, 157], "dict": [3, 8, 10, 14, 17, 18, 19, 24, 25, 26, 27, 32, 33, 38, 46, 47, 48, 49, 50, 51, 52, 54, 57, 63, 68, 70, 78, 79, 82, 83, 87, 90, 92, 93, 94, 99, 104, 106, 111, 138, 139, 146, 147, 150, 151], "kei": [3, 4, 17, 18, 25, 27, 28, 38, 41, 50, 51, 54, 57, 76, 78, 82, 83, 92, 93, 94, 97, 99, 112, 122, 138, 139, 144, 147, 151, 152, 160], "pair": [3, 12, 15, 22, 25, 33, 46, 55, 57, 78, 86, 87, 88, 94, 97, 99, 132, 135, 139, 144, 150, 152, 153, 154, 165], "dictionari": [3, 10, 12, 13, 14, 24, 26, 27, 33, 38, 41, 47, 49, 50, 51, 52, 54, 56, 57, 63, 68, 70, 78, 79, 82, 83, 87, 92, 94, 99, 106, 107, 111, 135, 138, 139, 145, 150, 152, 154], "addit": [3, 4, 6, 7, 12, 19, 24, 28, 32, 33, 34, 38, 50, 51, 53, 55, 63, 76, 77, 78, 79, 81, 86, 91, 92, 93, 94, 99, 102, 106, 112, 117, 121, 128, 134, 135, 139, 144, 150, 151, 152, 164], "instanc": [3, 7, 8, 12, 13, 22, 25, 30, 32, 46, 47, 51, 55, 63, 70, 71, 83, 86, 87, 89, 92, 103, 106, 138, 150, 151, 152, 154, 161], "unit_cel": 3, "convent": [3, 6, 52, 56, 63, 70, 78, 83, 86, 87, 92, 112, 113, 134, 135, 137, 139, 145], "primit": [3, 4, 6, 60, 63, 78, 83, 87, 88, 92, 100, 124, 134, 139, 145, 150], "adsorbate_info": 3, "adsorpt": [3, 6, 131, 135, 139], "site": [3, 6, 43, 50, 78, 88, 92, 97, 100, 130, 141, 143, 148, 158], "item": [3, 54, 56, 82, 87, 93, 94, 146, 147, 150, 153], "surviv": 3, "slice": [3, 46, 70, 78, 79, 139], "retriev": [3, 14, 32, 47, 50, 56, 57, 70, 78, 79, 132, 139, 150, 151, 152, 164], "json": [3, 13, 51, 54, 57, 63, 64, 79, 82, 91, 92, 103, 134, 139, 144, 145, 146, 150, 164], "compat": [3, 8, 19, 22, 28, 32, 33, 34, 39, 48, 55, 57, 78, 81, 85, 88, 91, 112, 114, 115, 118, 120, 122, 139, 145, 160, 162], "its": [3, 6, 7, 8, 12, 14, 19, 20, 22, 27, 28, 32, 33, 35, 44, 49, 51, 53, 55, 56, 57, 66, 73, 78, 81, 85, 86, 87, 88, 92, 96, 97, 98, 106, 111, 114, 117, 121, 131, 132, 134, 139, 147, 150, 154, 157, 158, 160, 163, 164], "One": [3, 6, 8, 25, 48, 53, 55, 57, 70, 71, 78, 86, 112, 122, 127, 130, 136, 145, 154, 155], "should": [3, 6, 7, 8, 9, 12, 13, 14, 15, 19, 20, 21, 23, 25, 26, 27, 28, 29, 32, 33, 34, 38, 41, 44, 46, 47, 48, 49, 50, 51, 53, 55, 56, 57, 70, 78, 79, 80, 81, 83, 85, 86, 87, 88, 92, 94, 97, 99, 102, 103, 104, 106, 107, 111, 112, 113, 117, 118, 120, 121, 122, 123, 124, 127, 128, 130, 131, 132, 133, 134, 135, 136, 139, 145, 147, 150, 151, 152, 153, 154, 157, 158, 159, 160, 163, 164], "assumpt": [3, 127, 153], "104": [3, 88, 139], "n2": [3, 4, 12, 19, 47, 62, 65, 76, 97, 98, 103, 117, 118, 128, 131, 132, 148, 153], "bondlength": 3, "4": [3, 4, 6, 7, 8, 9, 11, 15, 16, 17, 19, 22, 25, 27, 29, 30, 32, 34, 38, 39, 40, 41, 43, 47, 51, 52, 54, 55, 56, 59, 63, 65, 66, 67, 68, 69, 70, 76, 78, 79, 80, 83, 85, 86, 87, 88, 90, 91, 92, 97, 102, 103, 104, 106, 107, 115, 120, 121, 125, 127, 130, 131, 134, 135, 138, 140, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 158, 159, 160, 162, 164, 166], "05": [3, 4, 7, 10, 20, 22, 26, 30, 39, 48, 50, 52, 55, 57, 63, 70, 78, 86, 88, 91, 92, 97, 100, 104, 131, 132, 133, 134, 139, 143, 145, 148, 149, 150, 152, 153, 154, 158, 159, 160, 164, 166], "end": [3, 7, 10, 11, 15, 24, 27, 33, 38, 42, 48, 50, 57, 63, 66, 78, 79, 81, 86, 87, 97, 98, 102, 103, 104, 112, 115, 121, 135, 138, 145, 147, 152, 157, 160], "manipul": [3, 57, 74, 96, 106, 108, 129, 135, 139, 144], "vacuum": [3, 4, 6, 39, 46, 48, 53, 66, 79, 83, 121, 127, 128, 130, 131, 132, 133, 139, 143, 151, 154, 156, 157, 158, 159, 160, 166], "axi": [3, 4, 6, 7, 41, 53, 57, 63, 70, 83, 85, 93, 94, 97, 106, 121, 130, 134, 139, 143, 147, 150, 157, 158, 166], "amount": [3, 4, 6, 22, 44, 46, 53, 65, 66, 70, 83, 87, 88], "side": [3, 4, 6, 7, 48, 55, 63, 83, 91, 98, 106, 141, 143], "adjust": [3, 7, 43, 50, 55, 76, 86, 87, 88, 132, 133, 151, 156, 157], "angstrom": [3, 4, 6, 7, 13, 22, 32, 33, 46, 50, 55, 56, 63, 64, 65, 67, 70, 71, 76, 78, 83, 91, 100, 107, 150, 153, 157], "act": [3, 41, 44, 48, 55, 81, 85, 134, 150], "interpret": [3, 4, 10, 19, 24, 47, 51, 53, 64, 76, 78, 81, 86, 97, 114, 125, 138, 158, 159, 164], "origin": [3, 8, 15, 22, 33, 43, 46, 51, 52, 54, 55, 56, 57, 65, 66, 70, 78, 81, 86, 98, 112, 122, 123, 134, 147, 151], "conflict": [3, 64, 121, 122], "lead": [3, 43, 78, 85, 88, 98, 104, 118, 145, 157], "undesir": 3, "behaviour": [3, 23, 39, 56, 71, 78, 79, 85, 133, 139], "aris": [3, 83], "pre": [3, 51, 72, 81, 102], "certain": [3, 7, 33, 38, 39, 40, 48, 71, 79, 85, 86, 87, 97, 99, 122, 136, 139, 150, 151, 153], "incompat": [3, 7, 32, 78, 86, 112, 136, 139], "backend": [3, 81, 87, 132, 139], "while": [3, 6, 7, 13, 14, 20, 21, 27, 32, 33, 41, 43, 47, 48, 50, 51, 55, 56, 57, 78, 85, 86, 88, 92, 93, 104, 122, 134, 139, 141, 144, 145, 150, 151, 152, 153, 154, 157, 161], "try": [3, 4, 13, 14, 22, 57, 63, 71, 78, 79, 88, 112, 115, 120, 122, 125, 128, 133, 134, 138, 139, 150, 151, 152, 155, 156], "insid": [3, 14, 63, 70, 82, 121, 139, 144, 156], "circumv": [3, 71], "pleas": [3, 8, 14, 33, 35, 39, 44, 47, 48, 49, 51, 55, 57, 78, 81, 89, 109, 110, 111, 112, 114, 120, 122, 124, 125, 127, 128, 129, 131, 134, 136, 139, 150, 165, 167], "gtk": [3, 115, 139], "befor": [3, 6, 19, 20, 26, 47, 48, 50, 53, 55, 56, 57, 65, 72, 78, 81, 85, 92, 99, 103, 112, 116, 122, 132, 134, 136, 139, 148, 150, 151, 152, 154, 155, 156, 159, 160], "phi": [3, 22, 55, 139, 150, 153], "theta": [3, 19, 97, 107, 139], "psi": [3, 135, 139, 150, 153], "euler": 3, "mathworld": 3, "wolfram": [3, 107], "com": [3, 7, 10, 12, 17, 24, 28, 43, 54, 55, 78, 79, 109, 112, 116, 120, 135, 136, 139, 146], "eulerangl": 3, "html": [3, 17, 32, 48, 68, 79, 100, 123, 134, 163, 164], "explan": [3, 32, 44, 112, 164], "point": [3, 6, 7, 8, 9, 12, 13, 16, 19, 21, 22, 24, 25, 26, 28, 30, 38, 41, 46, 47, 49, 52, 53, 55, 56, 57, 59, 61, 62, 64, 65, 66, 67, 70, 78, 81, 83, 85, 86, 87, 88, 91, 93, 94, 97, 98, 100, 102, 103, 107, 112, 114, 117, 124, 127, 128, 132, 134, 135, 138, 139, 151, 152, 154, 156, 158, 160, 161, 164], "coordin": [3, 4, 6, 7, 12, 13, 15, 20, 29, 33, 48, 50, 52, 55, 63, 64, 65, 70, 76, 78, 79, 87, 88, 91, 92, 97, 101, 102, 103, 124, 130, 132, 133, 135, 139, 150, 157, 158, 159, 160, 163], "cop": [3, 19], "cou": 3, "1st": [3, 14, 62, 150], "classmethod": [3, 52, 63, 70, 81, 83, 93], "fromdict": [3, 12, 51, 135], "dct": [3, 51, 54, 57, 68, 146, 151, 152], "rebuild": [3, 87], "represent": [3, 51, 63, 68, 70, 78, 87, 92, 122, 134, 139], "todict": [3, 50, 51, 135], "mic": [3, 55, 70, 87, 135, 139, 154], "minimum": [3, 24, 26, 39, 41, 43, 55, 63, 66, 67, 70, 78, 83, 86, 87, 88, 92, 93, 94, 134, 139, 144, 150, 152, 155, 157, 159, 161], "form": [3, 13, 22, 32, 38, 39, 48, 51, 52, 53, 55, 63, 70, 78, 93, 94, 97, 104, 106, 107, 108, 112, 117, 122, 127, 134, 145, 150, 151, 152, 153], "across": [3, 27, 43, 81, 89, 161], "indic": [3, 5, 6, 12, 13, 15, 32, 33, 38, 47, 50, 53, 55, 59, 64, 65, 70, 78, 81, 83, 85, 87, 90, 91, 102, 103, 112, 120, 122, 130, 134, 139, 144, 145, 150, 157, 160], "multipl": [3, 6, 7, 12, 13, 22, 27, 28, 32, 36, 38, 44, 47, 50, 55, 65, 66, 70, 78, 79, 85, 88, 94, 122, 127, 132, 133, 137, 139, 147, 154], "group": [3, 12, 20, 38, 40, 44, 46, 50, 51, 57, 66, 78, 91, 92, 118, 139, 141, 150, 151, 159], "row": [3, 70, 87, 93, 135, 137, 139, 144, 151, 161, 164], "get_angular_momentum": [3, 135], "angular": [3, 22, 55, 85, 107, 156], "respect": [3, 13, 16, 28, 33, 43, 50, 53, 55, 56, 57, 62, 78, 88, 91, 93, 97, 104, 107, 134, 139, 145, 148, 150, 151, 160, 163], "get_arrai": [3, 78, 135], "name": [3, 4, 8, 12, 13, 14, 15, 16, 18, 20, 22, 24, 25, 27, 28, 29, 32, 33, 35, 38, 40, 41, 44, 47, 48, 49, 50, 51, 52, 54, 56, 57, 63, 64, 66, 70, 71, 78, 79, 80, 81, 82, 83, 85, 86, 88, 89, 90, 91, 97, 98, 100, 101, 102, 103, 104, 106, 111, 112, 115, 117, 120, 121, 127, 133, 138, 139, 145, 146, 147, 150, 154, 164], "unless": [3, 13, 38, 39, 41, 51, 65, 70, 87, 88, 93, 94, 112, 133, 139], "current": [3, 6, 13, 14, 15, 20, 22, 26, 32, 33, 38, 41, 46, 50, 51, 53, 57, 64, 65, 66, 72, 76, 77, 78, 81, 82, 83, 85, 86, 88, 90, 91, 92, 97, 103, 111, 112, 118, 122, 138, 139, 150, 151, 152, 154, 160, 162], "instead": [3, 4, 6, 7, 13, 14, 24, 33, 35, 38, 41, 44, 48, 49, 50, 51, 52, 53, 55, 64, 65, 66, 70, 71, 76, 78, 79, 81, 83, 85, 86, 88, 92, 103, 111, 112, 114, 120, 122, 123, 133, 134, 139, 141, 144, 150, 151, 152, 154, 156, 158, 162, 165], "complet": [3, 13, 46, 47, 52, 53, 54, 55, 70, 76, 83, 86, 122, 128, 132, 135, 139, 148, 150, 151, 152, 153, 154, 161], "j": [3, 6, 7, 13, 22, 40, 43, 46, 47, 51, 52, 54, 55, 56, 62, 63, 66, 69, 70, 85, 86, 87, 88, 91, 92, 97, 98, 107, 125, 135, 137, 144, 150, 152, 158, 159, 162, 163], "jth": [3, 9, 40, 52, 70], "cartesian": [3, 51, 52, 63, 70, 78, 85, 87, 92, 102, 103, 130, 163], "ith": [3, 52, 70], "get_celldisp": [3, 135], "get_chemical_formula": [3, 135, 151], "hill": [3, 68], "empir": [3, 27, 42, 100, 121, 134], "four": [3, 12, 57, 71, 83, 92, 97, 106, 120, 130, 139, 152, 154], "contract": [3, 55], "becom": [3, 16, 48, 55, 57, 81, 87, 88, 139, 154], "chhhoh": 3, "element": [3, 4, 6, 13, 22, 23, 24, 25, 26, 27, 32, 38, 40, 47, 50, 51, 52, 53, 54, 55, 56, 63, 65, 70, 78, 80, 85, 87, 90, 91, 92, 96, 97, 98, 100, 107, 109, 112, 132, 134, 135, 138, 139, 144, 146, 150, 151, 152, 157, 160, 163], "chhhochhh": 3, "ch3och3": [3, 4], "notat": [3, 4, 14], "alphabet": [3, 33, 41, 68, 100, 124], "c2h6o": 3, "soohoho": 3, "h2o4": 3, "metal": [3, 6, 22, 23, 33, 34, 68, 69, 78, 85, 100, 127, 134, 135, 139, 146, 151, 152], "divid": [3, 12, 70, 78, 88, 100, 151], "greatest": [3, 100], "divisor": [3, 100, 150], "yield": [3, 43, 48, 56, 70, 78, 79, 89, 92, 94, 97, 100, 103, 145, 151, 160], "a0": [3, 47, 70, 78, 88, 155], "dihedr": [3, 55, 70, 71, 76, 78, 80, 88, 139], "get_dipole_mo": [3, 50, 102, 135], "electr": [3, 41, 57], "dipol": [3, 8, 14, 17, 22, 41, 49, 50, 57, 81, 102, 111, 117], "No": [3, 22, 48, 69, 70, 71, 84, 90, 106, 120, 139, 144, 152, 160], "self": [3, 13, 14, 24, 26, 49, 51, 55, 57, 68, 70, 71, 85, 87, 88, 89, 91, 93, 94, 100, 111, 133, 135, 138, 145, 157, 164, 165], "apply_constraint": [3, 78, 139], "ask": [3, 12, 27, 28, 53, 55, 92, 111, 114, 117, 122, 132, 135, 139, 154, 167], "raw": [3, 86, 94, 150, 151, 152, 153], "don": [3, 12, 13, 14, 19, 33, 35, 38, 44, 47, 49, 51, 56, 57, 111, 112, 117, 120, 121, 123, 132, 133, 136, 148, 157, 163], "t": [3, 12, 13, 14, 18, 19, 27, 28, 32, 33, 35, 38, 40, 41, 44, 46, 47, 49, 51, 54, 55, 56, 57, 62, 67, 69, 70, 71, 76, 78, 80, 81, 84, 85, 87, 88, 90, 97, 98, 102, 103, 107, 111, 112, 115, 117, 120, 121, 123, 124, 132, 133, 136, 137, 138, 139, 148, 150, 152, 155, 156, 157, 160, 163], "holonom": [3, 55, 139], "rigid": [3, 55, 85, 141, 160, 162], "linear": [3, 10, 12, 25, 26, 36, 40, 47, 55, 62, 65, 85, 86, 87, 88, 97, 104, 134, 137, 139, 141, 154, 156, 159, 163], "triatom": [3, 55, 141], "redistribut": [3, 27, 43, 55, 160], "tripl": [3, 20, 55, 120, 141], "requir": [3, 4, 6, 7, 8, 12, 13, 15, 19, 22, 24, 30, 32, 33, 36, 38, 40, 42, 43, 44, 46, 48, 51, 55, 57, 65, 66, 76, 78, 79, 81, 85, 86, 87, 88, 89, 91, 92, 94, 98, 99, 100, 112, 114, 121, 123, 124, 128, 132, 134, 135, 139, 141, 145, 150, 151, 156, 159], "NOT": [3, 29, 51, 78, 112], "know": [3, 6, 13, 32, 33, 56, 57, 83, 86, 92, 122, 124, 128, 133, 134, 140, 161, 164], "normal": [3, 6, 7, 12, 20, 28, 48, 52, 55, 70, 71, 78, 83, 85, 91, 92, 97, 102, 103, 122, 127, 128, 132, 133, 135, 145, 150, 159], "asap": [3, 12, 23, 32, 89, 114, 128, 135, 139, 150, 156], "easier": [3, 6, 125, 133, 134, 139, 152, 153, 154], "maintain": [3, 28, 55, 83, 84, 85, 110, 113, 135, 139], "few": [3, 7, 16, 28, 45, 70, 81, 83, 91, 106, 112, 114, 122, 127, 132, 134, 144, 150, 151, 153, 154], "place": [3, 4, 13, 28, 51, 65, 72, 78, 94, 99, 112, 116, 123, 138, 139, 150, 152, 154, 159, 160], "typic": [3, 7, 13, 24, 33, 34, 38, 41, 43, 48, 55, 57, 63, 78, 81, 85, 86, 88, 93, 94, 111, 112, 117, 123, 124, 133, 134, 135, 138, 151, 153, 154], "freedom": [3, 43, 55, 85, 97, 102, 134, 139, 148, 150, 153, 162, 163, 166], "situat": [3, 112, 114, 154], "get_moments_of_inertia": [3, 135], "inertia": [3, 97], "princip": [3, 98], "comput": [3, 7, 8, 10, 14, 24, 27, 28, 32, 38, 41, 42, 46, 47, 50, 54, 63, 69, 72, 76, 78, 85, 86, 87, 88, 90, 91, 97, 100, 114, 122, 125, 132, 133, 135, 136, 144, 145, 150, 151, 152], "eigenvalu": [3, 12, 41, 59, 62, 63, 65, 66, 85, 91, 94, 137, 139, 163], "symmetr": [3, 38, 43, 55, 85, 87, 91, 97, 100, 124, 135, 139, 146, 152, 161], "inerti": 3, "tensor": [3, 15, 20, 22, 55, 57, 85, 91, 111, 117, 123, 134, 135, 139, 165], "ignor": [3, 12, 13, 14, 16, 17, 19, 27, 33, 35, 39, 41, 44, 48, 49, 51, 55, 56, 66, 78, 81, 92, 94, 107, 111, 117, 150], "amu": [3, 85, 91, 97, 102], "get_number_of_atom": [3, 135], "deprec": [3, 8, 12, 14, 33, 35, 44, 49, 51, 55, 85, 111, 112, 135, 139], "probabl": [3, 6, 13, 38, 39, 55, 78, 85, 86, 92, 110, 114, 120, 127, 133, 134, 139, 150, 151, 152, 156, 160, 164], "Or": [3, 40, 46, 92, 132, 138], "wrap_kw": 3, "back": [3, 15, 32, 33, 52, 57, 66, 70, 78, 87, 88, 114, 121, 132, 163], "pretty_transl": [3, 70, 139], "ep": [3, 6, 41, 46, 52, 63, 65, 67, 70, 71, 79, 106, 107, 137, 152, 155, 166], "classic": [3, 11, 12, 14, 15, 20, 22, 29, 32, 33, 34, 46, 85, 86, 88, 141], "force_consist": [3, 12, 66, 85, 88], "kelvin": [3, 12, 50, 85, 90, 99, 139, 156], "consist": [3, 6, 12, 24, 26, 32, 51, 55, 63, 66, 78, 83, 85, 86, 88, 94, 120, 121, 124, 127, 133, 139, 150, 153, 154, 164], "get_properti": [3, 10, 50, 111, 113, 135], "experiment": [3, 6, 13, 33, 53, 54, 56, 64, 88, 90, 111, 135, 139, 142, 146, 151], "get_reciprocal_cel": [3, 135, 139], "reciproc": [3, 12, 13, 19, 24, 51, 52, 63, 70, 78, 83, 91, 92, 108, 117, 134, 135, 139], "commonli": [3, 38, 78, 97, 145], "pi": [3, 18, 48, 52, 70, 78, 85, 87, 88, 97, 107, 133, 139, 150, 153, 162], "fourier": [3, 91], "transform": [3, 7, 52, 55, 63, 65, 70, 83, 87, 88, 91, 100, 135, 145], "rel": [3, 4, 7, 12, 13, 16, 17, 18, 38, 47, 51, 56, 62, 63, 65, 71, 78, 86, 92, 100, 101, 112, 130, 139, 150, 156], "outsid": [3, 14, 86, 87, 134], "those": [3, 4, 8, 12, 28, 30, 39, 47, 48, 55, 63, 65, 70, 78, 87, 90, 92, 103, 114, 117, 120, 127, 139, 144, 150, 152, 154], "long": [3, 6, 13, 20, 28, 33, 57, 85, 88, 114, 120, 123, 133, 145, 156], "span": [3, 52, 63, 65, 70, 92, 145, 154], "voigt": [3, 111, 134], "include_ideal_ga": [3, 55, 139], "independ": [3, 8, 55, 65, 81, 83, 86, 97, 103, 114, 145], "compon": [3, 22, 55, 57, 66, 78, 85, 86, 90, 97, 134, 147, 154], "tradit": [3, 152], "xx": [3, 55], "yy": [3, 55], "zz": [3, 55], "yz": [3, 33, 55, 85, 143], "xz": [3, 33, 55, 79, 85], "even": [3, 6, 7, 13, 15, 33, 47, 48, 79, 85, 92, 114, 121, 122, 133, 136, 139, 152], "arbitrari": [3, 4, 6, 14, 22, 36, 55, 65, 81, 87, 91, 124, 138, 139, 145], "get_temperatur": [3, 135], "plu": [3, 4, 22, 24, 55, 90, 97, 98, 125], "volum": [3, 7, 52, 53, 54, 55, 57, 62, 63, 67, 70, 85, 97, 100, 125, 135, 144, 145, 146, 149, 150, 152, 153, 154], "must": [3, 4, 6, 7, 9, 12, 16, 17, 18, 22, 24, 26, 27, 28, 30, 32, 33, 40, 41, 43, 47, 48, 50, 51, 55, 57, 62, 63, 65, 66, 67, 68, 70, 78, 81, 82, 83, 85, 86, 87, 89, 90, 91, 92, 94, 97, 98, 102, 103, 111, 117, 118, 120, 128, 132, 134, 141, 145, 150, 152, 153, 162], "initial_magmom": [3, 14, 49, 57, 111, 118], "initial_charg": [3, 14, 28, 49, 57, 78, 111, 118], "new_arrai": [3, 25, 135], "add": [3, 6, 8, 9, 12, 14, 24, 30, 38, 40, 42, 46, 51, 68, 74, 78, 79, 81, 82, 86, 87, 90, 100, 108, 112, 113, 115, 117, 118, 123, 130, 131, 135, 136, 139, 144, 148, 150, 151, 152, 153, 155, 157, 159, 164], "number_of_lattice_vector": [3, 135, 139], "stdev": [3, 20, 39, 48], "001": [3, 50, 53, 66, 70, 91, 92, 111, 143, 156, 158], "seed": [3, 13, 20, 39, 48, 66, 87, 139], "rng": [3, 4, 65, 85, 150], "randomli": [3, 4, 85, 150, 152, 153, 154], "random": [3, 4, 20, 39, 57, 65, 66, 85, 137, 139, 150, 151, 152, 153, 154, 156, 157], "account": [3, 43, 91, 97, 107, 112, 134, 151, 154], "drawn": [3, 85, 150], "deviat": [3, 7, 66, 85, 145, 150], "processor": [3, 38, 41, 45, 51, 86, 110], "rep": [3, 46, 147], "r": [3, 7, 22, 43, 46, 51, 53, 64, 65, 70, 71, 76, 78, 79, 80, 81, 82, 85, 86, 88, 89, 91, 98, 102, 104, 106, 115, 125, 127, 130, 139, 145, 150, 160, 166], 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91, 97, 103, 107, 139, 141, 153], "hhcchh": 3, "210": [3, 57, 67], "By": [3, 7, 10, 12, 13, 14, 17, 19, 28, 33, 35, 39, 40, 41, 44, 48, 49, 51, 78, 85, 86, 88, 111, 145, 150, 153, 154, 159], "assum": [3, 8, 27, 28, 30, 47, 52, 56, 57, 63, 70, 78, 81, 87, 97, 98, 104, 107, 121, 128, 131, 136, 150, 152, 154, 162], "togeth": [3, 7, 47, 55, 76, 94, 114, 128, 132, 135, 139, 151, 157], "everi": [3, 14, 15, 41, 47, 48, 57, 67, 70, 71, 78, 81, 85, 86, 87, 88, 150, 154, 156, 164], "spin": [3, 8, 12, 15, 19, 24, 28, 41, 44, 47, 49, 59, 62, 65, 78, 97, 106, 132, 135, 139], "newposit": [3, 55], "honor": [3, 81], "except": [3, 7, 13, 14, 22, 28, 33, 50, 54, 71, 81, 82, 96, 120, 121, 138, 144, 152, 162], "nx3": 3, "filenam": [3, 13, 14, 15, 19, 24, 30, 37, 48, 51, 54, 57, 63, 64, 66, 67, 78, 79, 81, 82, 85, 93, 94, 100, 104, 107, 108, 120, 150, 154], "kwarg": [3, 4, 5, 8, 12, 14, 15, 17, 18, 19, 24, 25, 27, 28, 33, 37, 38, 41, 43, 44, 45, 47, 48, 49, 51, 56, 57, 63, 66, 70, 78, 79, 81, 82, 83, 85, 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"brief": 154, "same": 154, "comput": 154, "togeth": 154, "que": 154, "parameteris": 154, "screen": 154, "stress": 155, "tensor": 155, "temperatur": 156, "isol": 156, "particl": 156, "constrain": 157, "mpi": 158, "pair": 159, "improv": 159, "guess": 159, "ethan": 159, "n": 159, "edg": 159, "electrostat": 160, "embed": 160, "ljinteractionsgener": 160, "For": 160, "intric": 160, "eiqmmm": 160, "And": 160, "charg": 160, "counterion": 160, "self": 161, "al": 161, "110": 161, "tipnp": 162, "inspect": 164, "open": 164, "entri": 164, "exist": 164, "metal": 164, "tutori": 165, "uncategor": 165, "video": 165, "partli": 166, "occupi": 166, "workshop": 167, "softwar": 167, "chalmer": 167, "2019": 167, "program": 167, "registr": 167, "organ": 167}, "envversion": {"sphinx.domains.c": 2, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 8, "sphinx.domains.index": 1, "sphinx.domains.javascript": 2, "sphinx.domains.math": 2, "sphinx.domains.python": 3, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.viewcode": 1, "sphinx.ext.intersphinx": 1, "sphinx": 57}, "alltitles": {"About": [[0, "about"]], "Modules": [[1, "modules"]], "The Atom object": [[2, "the-atom-object"]], "Getting an Atom from an Atoms object": [[2, "getting-an-atom-from-an-atoms-object"]], "The Atoms object": [[3, "the-atoms-object"]], "Working with the array methods of Atoms objects": [[3, "working-with-the-array-methods-of-atoms-objects"]], "Unit cell and boundary conditions": [[3, "unit-cell-and-boundary-conditions"]], "Special attributes": [[3, "special-attributes"]], "Adding a calculator": [[3, "adding-a-calculator"]], "List-methods": [[3, "list-methods"]], "Other methods": [[3, "other-methods"]], "List of all Methods": [[3, "list-of-all-methods"], [91, "list-of-all-methods"]], "Building things": [[4, "building-things"]], "Molecules": [[4, "molecules"]], "Common bulk crystals": [[4, "common-bulk-crystals"]], "Nanotubes": [[4, "nanotubes"]], "Graphene nanoribbons": [[4, "graphene-nanoribbons"]], "Attaching structures": [[4, "attaching-structures"]], "Separation of structures": [[5, "separation-of-structures"]], "Surfaces": [[6, "surfaces"]], "Common surfaces": [[6, "common-surfaces"]], "Example": [[6, "example"], [6, "id2"], [8, "example"], [21, "example"], [30, "example"], [34, "example"], [47, "example"], [83, "example"], [91, "example"], [97, "example"], [97, "id1"], [97, "id2"], [107, "example"]], "Utility functions for setting up surfaces": [[6, "utility-functions-for-setting-up-surfaces"]], "The following functions are provided": [[6, "the-following-functions-are-provided"]], "Create root cuts of surfaces": [[6, "create-root-cuts-of-surfaces"]], "Adding adsorbates": [[6, "adding-adsorbates"]], "Create specific non-common surfaces": [[6, "create-specific-non-common-surfaces"]], "Tools for building things": [[7, "tools-for-building-things"]], "FHI-aims": [[8, "fhi-aims"]], "Introduction": [[8, "introduction"], [9, "introduction"], [11, "introduction"], [13, "introduction"], [16, "introduction"], [19, "introduction"], [20, "introduction"], [22, "introduction"], [25, "introduction"], [26, "introduction"], [29, "introduction"], [34, "introduction"], [39, "introduction"], [40, "introduction"], [41, "introduction"], [47, "introduction"], [48, "introduction"], [51, "introduction"], [65, "introduction"]], "Running the Calculator": [[8, "running-the-calculator"], [13, "running-the-calculator"], [22, "running-the-calculator"]], "List of keywords": [[8, "list-of-keywords"]], "Volumetric Data Output": [[8, "volumetric-data-output"]], "ABINIT": [[9, "abinit"]], "Environment variables": [[9, "environment-variables"], [16, "environment-variables"], [18, "environment-variables"], [19, "environment-variables"], [21, "environment-variables"], [26, "environment-variables"], [34, "environment-variables"], [40, "environment-variables"], [41, "environment-variables"], [47, "environment-variables"], [51, "environment-variables"], [136, "environment-variables"]], "ABINIT Calculator": [[9, "abinit-calculator"]], "Pseudopotentials": [[9, "pseudopotentials"], [47, "pseudopotentials"], [51, "pseudopotentials"]], "ACE-Molecule": [[10, "ace-molecule"]], "Setup": [[10, "setup"], [24, "setup"], [27, "setup"], [28, "setup"], [38, "setup"], [44, "setup"], [45, "setup"], [75, "setup"]], "Parameters": [[10, "parameters"], [19, "parameters"], [24, "parameters"], [27, "parameters"], [28, "parameters"], [29, "parameters"], [38, "parameters"], [44, "parameters"], [50, "parameters"]], "Amber": [[11, "amber"]], "Water example": [[11, "water-example"]], "Calculators": [[12, "calculators"], [132, "calculators"]], "Supported calculators": [[12, "supported-calculators"]], "Calculator keywords": [[12, "calculator-keywords"]], "Calculator interface": [[12, "calculator-interface"]], "Electronic structure calculators": [[12, "electronic-structure-calculators"]], "CASTEP": [[13, "castep"]], "Getting Started:": [[13, "getting-started"]], "Arguments:": [[13, "arguments"]], "Additional Settings": [[13, "additional-settings"]], "Special features:": [[13, "special-features"]], "Notes/Issues:": [[13, "notes-issues"]], "Example:": [[13, "example"], [22, "example"]], "Checkpointing": [[14, "checkpointing"]], "Manual checkpointing": [[14, "manual-checkpointing"]], "Automatic checkpointing with the checkpoint calculator": [[14, "automatic-checkpointing-with-the-checkpoint-calculator"]], "CP2K": [[15, "cp2k"]], "CRYSTAL14": [[16, "crystal14"]], "CRYSTAL Calculator (a FileIOCalculator)": [[16, "crystal-calculator-a-fileiocalculator"]], "Exchange-correlation functionals": [[16, "exchange-correlation-functionals"], [51, "exchange-correlation-functionals"]], "Setups": [[16, "setups"], [51, "setups"]], "Spin-polarized calculation": [[16, "spin-polarized-calculation"], [26, "spin-polarized-calculation"], [51, "spin-polarized-calculation"]], "Brillouin-zone sampling": [[16, "brillouin-zone-sampling"], [51, "brillouin-zone-sampling"]], "Reading an external wave function": [[16, "reading-an-external-wave-function"]], "Code related keywords": [[16, "code-related-keywords"]], "Demon": [[17, "demon"]], "deMon-Nano": [[18, "demon-nano"]], "deMon-Nano Calculator (a FileIOCalculator)": [[18, "demon-nano-calculator-a-fileiocalculator"]], "Example: Geometry Optimization with ASE": [[18, "example-geometry-optimization-with-ase"]], "DFTB+": [[19, "dftb"]], "Examples": [[19, "examples"], [20, "examples"], [26, "examples"], [27, "examples"], [28, "examples"], [38, "examples"], [39, "examples"], [40, "examples"], [44, "examples"], [45, "examples"], [50, "examples"], [51, "examples"], [53, "examples"], [79, "examples"], [81, "examples"], [118, "examples"]], "Geometry optimization by ASE": [[19, "geometry-optimization-by-ase"]], "Geometry optimization by DFTB+": [[19, "geometry-optimization-by-dftb"]], "NVE-MD followed by NVT-MD (both by DFTB+)": [[19, "nve-md-followed-by-nvt-md-both-by-dftb"]], "DFTB+ calculator class": [[19, "dftb-calculator-class"]], "DFT-D3": [[20, "dft-d3"]], "Additional information": [[20, "additional-information"], [39, "additional-information"]], "Caveats": [[20, "caveats"]], "DMol3": [[21, "dmol3"]], "DMol3 Calculator": [[21, "dmol3-calculator"]], "File formats": [[21, "file-formats"]], "EAM": [[22, "eam"]], "Theory": [[22, "theory"], [107, "theory"]], "Arguments": [[22, "arguments"]], "Additional parameters for writing potential files": [[22, "additional-parameters-for-writing-potential-files"]], "Special features": [[22, "special-features"]], "Notes/Issues": [[22, "notes-issues"]], "Pure Python EMT calculator": [[23, "pure-python-emt-calculator"]], "Espresso": [[24, "espresso"]], "Alternative Calculators": [[24, "alternative-calculators"]], "Espresso Calculator Class": [[24, "espresso-calculator-class"]], "exciting": [[25, "exciting"], [78, "exciting"]], "Constructor with Groundstate Keywords": [[25, "constructor-with-groundstate-keywords"]], "Parameter Dictionary": [[25, "parameter-dictionary"]], "Muffin Tin Radius": [[25, "muffin-tin-radius"]], "Exciting Calculator Class": [[25, "exciting-calculator-class"]], "FLEUR": [[26, "fleur"]], "FLEUR Calculator": [[26, "fleur-calculator"]], "Utility functions": [[26, "utility-functions"]], "GAMESS-US": [[27, "gamess-us"]], "Gaussian": [[28, "gaussian"]], "GaussianOptimizer and GaussianIRC": [[28, "gaussianoptimizer-and-gaussianirc"]], "Gromacs": [[29, "gromacs"]], "Gromacs Calculator": [[29, "gromacs-calculator"]], "Environmental variables:": [[29, "environmental-variables"]], "Example: MM-only geometry optimization of a histidine molecule": [[29, "example-mm-only-geometry-optimization-of-a-histidine-molecule"]], "GULP": [[30, "gulp"]], "Instructions": [[30, "instructions"]], "Jacapo - ASE python interface for Dacapo": [[31, "jacapo-ase-python-interface-for-dacapo"]], "KIM": [[32, "kim"]], "Overview": [[32, "overview"]], "Implementation": [[32, "implementation"], [117, "implementation"]], "Advanced Usage": [[32, "advanced-usage"]], "LAMMPS Calculators": [[33, "lammps-calculators"]], "LAMMPSrun": [[34, "lammpsrun"]], "LAMMPS Calculator": [[34, "lammps-calculator"]], "Setting up an OPLS calculation": [[34, "setting-up-an-opls-calculation"]], "Logging Calculator": [[35, "logging-calculator"]], "Mixing Calculators": [[36, "mixing-calculators"]], "Mopac": [[37, "mopac"]], "NWChem": [[38, "nwchem"]], "Octopus": [[39, "octopus"]], "Structure optimization": [[39, "structure-optimization"], [88, "module-ase.optimize"]], "Periodic system": [[39, "periodic-system"]], "Time-dependent density functional theory": [[39, "time-dependent-density-functional-theory"]], "Hints": [[39, "hints"]], "Bugs and misbehaviour": [[39, "bugs-and-misbehaviour"]], "ONETEP": [[40, "onetep"]], "ONETEP Calculator": [[40, "onetep-calculator"]], "Species Definitions": [[40, "species-definitions"]], "OpenMX": [[41, "openmx"]], "Keyword Arguments of OpenMX objects": [[41, "keyword-arguments-of-openmx-objects"]], "Calculator parameters": [[41, "calculator-parameters"]], "Density of States": [[41, "density-of-states"], [51, "density-of-states"]], "Methods of OpenMX objects": [[41, "methods-of-openmx-objects"]], "ORCA": [[42, "orca"]], "Setup and usage": [[42, "setup-and-usage"]], "Other built-in calculators": [[43, "module-ase.calculators.tip3p"]], "TIP3P": [[43, "tip3p"]], "TIP4P": [[43, "tip4p"]], "Lennard-Jones": [[43, "lennard-jones"]], "Morse": [[43, "morse"]], "psi4": [[44, "psi4"]], "Parallelization": [[44, "parallelization"]], "Q-Chem": [[45, "q-chem"]], "QMMM": [[46, "qmmm"]], "Explicit Interaction QMMM": [[46, "explicit-interaction-qmmm"]], "Simple, subtractive QMMM calculations": [[46, "simple-subtractive-qmmm-calculations"]], "Force-based QM/MM": [[46, "force-based-qm-mm"]], "SIESTA": [[47, "siesta"]], "SIESTA Calculator": [[47, "siesta-calculator"]], "Extra FDF parameters": [[47, "extra-fdf-parameters"]], "Defining Custom Species": [[47, "defining-custom-species"]], "Restarting from an old Calculation": [[47, "restarting-from-an-old-calculation"]], "Choosing the coordinate format": [[47, "choosing-the-coordinate-format"]], "Siesta Calculator Class": [[47, "siesta-calculator-class"]], "Excited states calculations": [[47, "excited-states-calculations"]], "Raman Calculations with SIESTA and PyNAO": [[47, "raman-calculations-with-siesta-and-pynao"]], "Further Examples": [[47, "further-examples"]], "Siesta lrtddft Class": [[47, "siesta-lrtddft-class"]], "Siesta RamanCalculatorInterface Calculator Class": [[47, "siesta-ramancalculatorinterface-calculator-class"]], "Communication with calculators over sockets": [[48, "communication-with-calculators-over-sockets"]], "Which codes can be used with socket I/O calculators?": [[48, "which-codes-can-be-used-with-socket-i-o-calculators"]], "How to use the ASE socket I/O interface": [[48, "how-to-use-the-ase-socket-i-o-interface"]], "Run server and client manually": [[48, "run-server-and-client-manually"]], "Module documentation": [[48, "module-documentation"]], "Stuff for testing things": [[49, "stuff-for-testing-things"]], "TURBOMOLE": [[50, "turbomole"]], "Setting up the environment": [[50, "setting-up-the-environment"]], "Using the calculator": [[50, "using-the-calculator"]], "Python interface": [[50, "python-interface"]], "Command-line interface": [[50, "command-line-interface"]], "Reading output": [[50, "reading-output"]], "Properties": [[50, "properties"]], "Metadata": [[50, "metadata"], [57, "metadata"]], "Restart mode": [[50, "restart-mode"]], "Policies for files in the working directory": [[50, "policies-for-files-in-the-working-directory"]], "Single-point energy calculation": [[50, "single-point-energy-calculation"]], "Nudged elastic band calculation": [[50, "nudged-elastic-band-calculation"]], "Single-point gradient calculation of Au13-": [[50, "single-point-gradient-calculation-of-au13"]], "Geometry optimization using TurbomoleOptimizer (recommended)": [[50, "geometry-optimization-using-turbomoleoptimizer-recommended"]], "Geometry optimization and normal mode analysis for H2O": [[50, "geometry-optimization-and-normal-mode-analysis-for-h2o"]], "QMMM simulation": [[50, "qmmm-simulation"]], "Deprecated, non-implemented and unsupported features": [[50, "deprecated-non-implemented-and-unsupported-features"]], "Deprecated but still accepted parameters": [[50, "deprecated-but-still-accepted-parameters"]], "Not implemented parameters": [[50, "not-implemented-parameters"]], "Unsupported methods and features": [[50, "unsupported-methods-and-features"]], "VASP": [[51, "vasp"]], "Table of Conents": [[51, "table-of-conents"]], "VASP execution": [[51, "vasp-execution"]], "VASP Calculator": [[51, "id2"]], "Single-parameter schemes": [[51, "single-parameter-schemes"]], "Three-parameter scheme": [[51, "three-parameter-scheme"]], "Explicitly listing the k-points": [[51, "explicitly-listing-the-k-points"]], "Band structure paths": [[51, "band-structure-paths"]], "LD(S)A+U": [[51, "ld-s-a-u"]], "Restart old calculation": [[51, "restart-old-calculation"]], "Storing the calculator state": [[51, "storing-the-calculator-state"]], "Band structure with VASP": [[51, "band-structure-with-vasp"]], "The Cell object": [[52, "the-cell-object"]], "Nanoparticles and clusters": [[53, "nanoparticles-and-clusters"]], "Layer specification": [[53, "layer-specification"]], "Wulff construction": [[53, "wulff-construction"]], "Creating a nanoparticle": [[53, "creating-a-nanoparticle"]], "Possible crystal structures": [[53, "possible-crystal-structures"]], "Collections": [[54, "collections"]], "S22 database of weakly interacting dimers and complexes": [[54, "s22-database-of-weakly-interacting-dimers-and-complexes"]], "DeltaCodesDFT": [[54, "deltacodesdft"]], "G2 neutral test set of molecules": [[54, "g2-neutral-test-set-of-molecules"]], "Constraints": [[55, "constraints"], [76, "constraints"]], "The FixAtoms class": [[55, "the-fixatoms-class"]], "The FixBondLength class": [[55, "the-fixbondlength-class"]], "The FixBondLengths class": [[55, "the-fixbondlengths-class"]], "The FixLinearTriatomic class": [[55, "the-fixlineartriatomic-class"]], "The FixedLine class": [[55, "the-fixedline-class"]], "The FixedPlane class": [[55, "the-fixedplane-class"]], "The FixedMode class": [[55, "the-fixedmode-class"]], "The FixCom class": [[55, "the-fixcom-class"]], "The Hookean class": [[55, "the-hookean-class"]], "The ExternalForce class": [[55, "the-externalforce-class"]], "The FixInternals class": [[55, "the-fixinternals-class"]], "Combining constraints": [[55, "combining-constraints"]], "Making your own constraint class": [[55, "making-your-own-constraint-class"]], "The Filter class": [[55, "the-filter-class"]], "The UnitCellFilter class": [[55, "the-unitcellfilter-class"]], "The StrainFilter class": [[55, "the-strainfilter-class"]], "The ExpCellFilter class": [[55, "the-expcellfilter-class"]], "The FixSymmetry class": [[55, "the-fixsymmetry-class"]], "The data module": [[56, "the-data-module"]], "Atomic data": [[56, "atomic-data"]], "How to extract isotope data from NIST": [[56, "how-to-extract-isotope-data-from-nist"]], "Molecular data": [[56, "molecular-data"]], "S22, s26, and s22x5 data": [[56, "s22-s26-and-s22x5-data"]], "A database for atoms": [[57, "a-database-for-atoms"]], "Contents": [[57, "contents"], [81, "contents"], [114, "contents"], [135, "contents"], [140, "contents"], [145, "contents"], [152, "contents"]], "What\u2019s in the database?": [[57, "what-s-in-the-database"]], "ase db": [[57, "ase-db"]], "Querying": [[57, "querying"]], "Integration with other parts of ASE": [[57, "integration-with-other-parts-of-ase"]], "Browse database with your web-browser": [[57, "browse-database-with-your-web-browser"]], "Python Interface": [[57, "module-ase.db.core"]], "Description of a row": [[57, "description-of-a-row"]], "Extracting Atoms objects from the database": [[57, "extracting-atoms-objects-from-the-database"]], "Add additional data": [[57, "add-additional-data"]], "Row objects": [[57, "row-objects"]], "Writing and updating many rows efficiently": [[57, "writing-and-updating-many-rows-efficiently"]], "Writing rows in parallel": [[57, "writing-rows-in-parallel"]], "More details": [[57, "more-details"], [62, "more-details"], [93, "more-details"], [94, "more-details"]], "External Tables": [[57, "external-tables"]], "Running a PostgreSQL server": [[57, "running-a-postgresql-server"]], "Running a MySQL server": [[57, "running-a-mysql-server"]], "Bader Analysis": [[58, "bader-analysis"]], "Band gap": [[59, "band-gap"]], "Brillouin zone data": [[60, "brillouin-zone-data"], [63, "brillouin-zone-data"]], "Density Functional Theory": [[61, "density-functional-theory"]], "Density of states": [[62, "density-of-states"], [127, "density-of-states"], [134, "density-of-states"]], "Brillouin zone sampling": [[63, "brillouin-zone-sampling"]], "Monkhorst-Pack": [[63, "monkhorst-pack"]], "Special points in the Brillouin zone": [[63, "special-points-in-the-brillouin-zone"]], "Band path": [[63, "band-path"]], "Band structure": [[63, "band-structure"], [134, "band-structure"]], "Interpolation": [[63, "interpolation"], [86, "interpolation"]], "High symmetry paths": [[63, "high-symmetry-paths"]], "Chadi-Cohen": [[63, "chadi-cohen"]], "STM images": [[64, "stm-images"]], "Maximally localized Wannier functions": [[65, "maximally-localized-wannier-functions"]], "The Wannier class": [[65, "the-wannier-class"]], "Dimer method": [[66, "module-ase.dimer"]], "Equation of state": [[67, "equation-of-state"], [134, "equation-of-state"]], "Chemical formula type": [[68, "chemical-formula-type"]], "Genetic Algorithm": [[69, "genetic-algorithm"]], "Geometry tools": [[70, "module-ase.geometry"]], "Analysis tools": [[70, "analysis-tools"]], "ase-gui basics and command line options": [[71, "ase-gui-basics-and-command-line-options"]], "General use": [[71, "general-use"]], "Files": [[71, "files"]], "Selecting part of a trajectory": [[71, "selecting-part-of-a-trajectory"]], "Writing files": [[71, "writing-files"]], "Interactive use": [[71, "interactive-use"]], "NEB calculations": [[71, "neb-calculations"]], "Plotting data from the command line": [[71, "plotting-data-from-the-command-line"]], "Defaults": [[71, "defaults"]], "High contrast settings": [[71, "high-contrast-settings"]], "Calculate": [[72, "calculate"]], "Set calculator": [[72, "set-calculator"]], "Energy and forces": [[72, "energy-and-forces"]], "Energy minimization": [[72, "energy-minimization"]], "Edit": [[73, "edit"]], "Add atoms": [[73, "add-atoms"]], "Modify": [[73, "modify"]], "ASE\u2019s GUI": [[74, "ase-s-gui"]], "Tools": [[76, "tools"]], "Graphs": [[76, "graphs"]], "Movie": [[76, "movie"]], "Render scene": [[76, "render-scene"]], "Move atoms": [[76, "move-atoms"]], "View": [[77, "view"]], "Repeat": [[77, "repeat"]], "Rotate": [[77, "rotate"]], "Colors": [[77, "colors"]], "Settings": [[77, "settings"]], "Format Specific Options": [[78, "format-specific-options"]], "abinit-in": [[78, "abinit-in"]], "abinit-out": [[78, "abinit-out"]], "acemolecule-input": [[78, "acemolecule-input"]], "acemolecule-out": [[78, "acemolecule-out"]], "aims": [[78, "aims"]], "aims-output": [[78, "aims-output"]], "bundletrajectory": [[78, "bundletrajectory"]], "castep-castep": [[78, "castep-castep"]], "castep-cell": [[78, "castep-cell"]], "castep-geom": [[78, "castep-geom"]], "castep-md": [[78, "castep-md"]], "castep-phonon": [[78, "castep-phonon"]], "cfg": [[78, "cfg"]], "cif": [[78, "cif"]], "cmdft": [[78, "cmdft"]], "cml": [[78, "cml"]], "cp2k-dcd": [[78, "cp2k-dcd"]], "cp2k-restart": [[78, "cp2k-restart"]], "crystal": [[78, "crystal"]], "cube": [[78, "cube"]], "dacapo-text": [[78, "dacapo-text"]], "db": [[78, "db"]], "dftb": [[78, "dftb"]], "dlp-history": [[78, "dlp-history"]], "dlp4": [[78, "dlp4"]], "dmol-arc": [[78, "dmol-arc"]], "dmol-car": [[78, "dmol-car"]], "dmol-incoor": [[78, "dmol-incoor"]], "elk": [[78, "elk"]], "elk-in": [[78, "elk-in"]], "eon": [[78, "eon"]], "eps": [[78, "eps"]], "espresso-in": [[78, "espresso-in"]], "espresso-out": [[78, "espresso-out"]], "extxyz": [[78, "extxyz"]], "findsym": [[78, "findsym"]], "gamess-us-in": [[78, "gamess-us-in"]], "gamess-us-out": [[78, "gamess-us-out"]], "gamess-us-punch": [[78, "gamess-us-punch"]], "gaussian-in": [[78, "gaussian-in"]], "gaussian-out": [[78, "gaussian-out"]], "gen": [[78, "gen"]], "gif": [[78, "gif"]], "gpaw-out": [[78, "gpaw-out"]], "gpumd": [[78, "gpumd"]], "gpw": [[78, "gpw"]], "gromacs": [[78, "gromacs"]], "gromos": [[78, "gromos"]], "html": [[78, "html"]], "json": [[78, "json"]], "jsv": [[78, "jsv"]], "lammps-data": [[78, "lammps-data"]], "lammps-dump-binary": [[78, "lammps-dump-binary"]], "lammps-dump-text": [[78, "lammps-dump-text"]], "magres": [[78, "magres"]], "mol": [[78, "mol"]], "mp4": [[78, "mp4"]], "mustem": [[78, "mustem"]], "mysql": [[78, "mysql"]], "netcdftrajectory": [[78, "netcdftrajectory"]], "nomad-json": [[78, "nomad-json"]], "nwchem-in": [[78, "nwchem-in"]], "nwchem-out": [[78, "nwchem-out"]], "octopus-in": [[78, "octopus-in"]], "png": [[78, "png"]], "postgresql": [[78, "postgresql"]], "pov": [[78, "pov"]], "prismatic": [[78, "prismatic"]], "proteindatabank": [[78, "proteindatabank"]], "py": [[78, "py"]], "qbox": [[78, "qbox"]], "res": [[78, "res"]], "rmc6f": [[78, "rmc6f"]], "sdf": [[78, "sdf"]], "siesta-xv": [[78, "siesta-xv"]], "struct": [[78, "struct"]], "struct_out": [[78, "struct-out"]], "sys": [[78, "sys"]], "traj": [[78, "traj"]], "turbomole": [[78, "turbomole"]], "turbomole-gradient": [[78, "turbomole-gradient"]], "v-sim": [[78, "v-sim"]], "vasp": [[78, "vasp"]], "vasp-out": [[78, "vasp-out"]], "vasp-xdatcar": [[78, "vasp-xdatcar"]], "vasp-xml": [[78, "vasp-xml"]], "vti": [[78, "vti"]], "vtu": [[78, "vtu"]], "wout": [[78, "wout"]], "x3d": [[78, "x3d"]], "xsd": [[78, "xsd"]], "xsf": [[78, "xsf"]], "xtd": [[78, "xtd"]], "xyz": [[78, "xyz"]], "File input and output": [[79, "file-input-and-output"]], "Adding a new file-format to ASE": [[79, "adding-a-new-file-format-to-ase"]], "Setting up an OPLS force field calculation": [[80, "module-ase.io.opls"]], "Modified xyz": [[80, "modified-xyz"]], "Defining the force field": [[80, "defining-the-force-field"]], "Trajectory files": [[81, "trajectory-files"]], "Trajectory": [[81, "trajectory"]], "The TrajectoryReader and TrajectoryWriter objects": [[81, "the-trajectoryreader-and-trajectorywriter-objects"]], "PickleTrajectory": [[81, "pickletrajectory"]], "Converting old PickleTrajectory files to new Trajectory files": [[81, "converting-old-pickletrajectory-files-to-new-trajectory-files"]], "BundleTrajectory": [[81, "bundletrajectory"]], "See also": [[81, "see-also"]], "ULM files": [[82, "ulm-files"]], "File layout": [[82, "file-layout"]], "More examples": [[82, "more-examples"]], "Versions": [[82, "versions"]], "Bravais lattices": [[83, "module-ase.lattice"]], "General crystal structures and surfaces": [[83, "general-crystal-structures-and-surfaces"]], "Available crystal lattices": [[83, "available-crystal-lattices"]], "Usage": [[83, "usage"]], "Defining new lattices": [[83, "defining-new-lattices"]], "Lattices with more than one element": [[83, "lattices-with-more-than-one-element"]], "Legacy functionality": [[84, "legacy-functionality"]], "Molecular dynamics": [[85, "module-ase.md"], [131, "molecular-dynamics"], [156, "molecular-dynamics"]], "Choosing the time step": [[85, "choosing-the-time-step"]], "File output": [[85, "file-output"]], "Logging": [[85, "logging"]], "Constant NVE simulations (the microcanonical ensemble)": [[85, "constant-nve-simulations-the-microcanonical-ensemble"]], "Velocity Verlet dynamics": [[85, "module-ase.md.verlet"]], "Constant NVT simulations (the canonical ensemble)": [[85, "constant-nvt-simulations-the-canonical-ensemble"]], "Langevin dynamics": [[85, "module-ase.md.langevin"]], "Andersen dynamics": [[85, "module-ase.md.andersen"]], "Nos\u00e9-Hoover dynamics": [[85, "nose-hoover-dynamics"]], "Berendsen NVT dynamics": [[85, "module-ase.md.nvtberendsen"]], "Constant NPT simulations (the isothermal-isobaric ensemble)": [[85, "module-ase.md.npt"]], "Berendsen NPT dynamics": [[85, "module-ase.md.nptberendsen"]], "Contour Exploration": [[85, "module-ase.md.contour_exploration"]], "Velocity distributions": [[85, "velocity-distributions"]], "Post-simulation Analysis": [[85, "post-simulation-analysis"]], "Nudged elastic band": [[86, "module-ase.neb"]], "The NEB class": [[86, "the-neb-class"]], "Trajectories": [[86, "trajectories"], [140, "trajectories"]], "Restarting": [[86, "restarting"]], "Climbing image": [[86, "climbing-image"]], "Scaled and dynamic optimizations": [[86, "scaled-and-dynamic-optimizations"]], "Parallelization over images": [[86, "parallelization-over-images"]], "Using Shared Calculators": [[86, "using-shared-calculators"]], "Analysis of output": [[86, "analysis-of-output"]], "AutoNEB": [[86, "autoneb"]], "Building neighbor-lists": [[87, "building-neighbor-lists"]], "API": [[87, "module-ase.neighborlist"]], "Local optimization": [[88, "local-optimization"]], "BFGS": [[88, "bfgs"]], "LBFGS": [[88, "lbfgs"]], "GPMin": [[88, "gpmin"]], "FIRE": [[88, "fire"]], "MDMin": [[88, "mdmin"]], "SciPy optimizers": [[88, "scipy-optimizers"]], "BFGSLineSearch": [[88, "bfgslinesearch"]], "Pyberny": [[88, "pyberny"]], "Preconditioned optimizers": [[88, "preconditioned-optimizers"]], "Global optimization": [[88, "global-optimization"], [165, "global-optimization"]], "Basin hopping": [[88, "module-ase.optimize.basin"]], "Minima hopping": [[88, "minima-hopping"]], "Parallel calculations": [[89, "parallel-calculations"]], "Phase diagrams and Pourbaix diagrams": [[90, "phase-diagrams-and-pourbaix-diagrams"]], "Pourbaix diagrams": [[90, "pourbaix-diagrams"]], "Phonon calculations": [[91, "phonon-calculations"]], "Using the spacegroup subpackage": [[92, "using-the-spacegroup-subpackage"]], "Examples of setting up bulk structures": [[92, "examples-of-setting-up-bulk-structures"]], "Aluminium (fcc)": [[92, "aluminium-fcc"]], "Iron (bcc)": [[92, "iron-bcc"]], "Magnesium (hcp)": [[92, "magnesium-hcp"]], "Diamond": [[92, "diamond"]], "Sodium chloride": [[92, "sodium-chloride"]], "Rutile": [[92, "rutile"]], "CoSb3 skutterudite": [[92, "cosb3-skutterudite"]], "The Spacegroup class": [[92, "the-spacegroup-class"]], "Getting a reduced atomic basis": [[92, "getting-a-reduced-atomic-basis"]], "Density of states collections": [[93, "density-of-states-collections"]], "Density of states data": [[94, "density-of-states-data"]], "Spectrum tools": [[95, "spectrum-tools"]], "Chemical symbols": [[96, "chemical-symbols"]], "Thermochemistry": [[97, "thermochemistry"]], "Ideal-gas limit": [[97, "ideal-gas-limit"]], "Harmonic limit": [[97, "harmonic-limit"], [97, "id3"]], "Hindered translator / hindered rotor model": [[97, "hindered-translator-hindered-rotor-model"]], "Crystals": [[97, "crystals"]], "Background": [[97, "background"], [145, "background"]], "Ideal gas": [[97, "ideal-gas"]], "Hindered translator / hindered rotor": [[97, "hindered-translator-hindered-rotor"]], "Crystalline solid": [[97, "crystalline-solid"]], "Electron transport": [[98, "electron-transport"]], "Units": [[99, "units"], [107, "units"]], "Changing the CODATA version": [[99, "changing-the-codata-version"]], "Utillity functions and classes": [[100, "utillity-functions-and-classes"]], "Symmetry equivalence checker": [[100, "symmetry-equivalence-checker"]], "Symmetry analysis": [[100, "symmetry-analysis"]], "Phonons": [[100, "phonons"]], "Evaluation of Franck-Condon factors": [[101, "evaluation-of-franck-condon-factors"]], "Franck-Condon factors in CH4": [[101, "franck-condon-factors-in-ch4"]], "Forces": [[101, "forces"]], "Vibrational properties": [[101, "vibrational-properties"]], "Huang-Rhys factors": [[101, "huang-rhys-factors"]], "Franck-Condon factors": [[101, "franck-condon-factors"]], "Infrared intensities": [[102, "infrared-intensities"]], "Vibrational modes": [[103, "vibrational-modes"]], "Old calculations": [[103, "old-calculations"]], "Resonant and non-resonant Raman spectra": [[104, "resonant-and-non-resonant-raman-spectra"]], "1. Finite difference calculations": [[104, "finite-difference-calculations"]], "1a. Forces and excitations": [[104, "a-forces-and-excitations"]], "1b. More accurate forces": [[104, "b-more-accurate-forces"]], "1c. Overlaps": [[104, "c-overlaps"]], "2. Analysis of the results": [[104, "analysis-of-the-results"]], "Placzek": [[104, "placzek"]], "Albrecht": [[104, "albrecht"]], "Vibration analysis": [[105, "vibration-analysis"]], "Visualization": [[106, "visualization"], [131, "visualization"]], "Viewer for Jupyter notebooks": [[106, "viewer-for-jupyter-notebooks"]], "Plotting iso-surfaces with Mayavi": [[106, "plotting-iso-surfaces-with-mayavi"]], "Matplotlib": [[106, "matplotlib"]], "X-ray scattering simulation": [[107, "x-ray-scattering-simulation"]], "Further details": [[107, "further-details"]], "XrDebye class members": [[107, "xrdebye-class-members"]], "References": [[107, "references"]], "Command line tool": [[108, "command-line-tool"]], "Help": [[108, "help"]], "Bash completion": [[108, "bash-completion"]], "Python -m tricks": [[108, "python-m-tricks"]], "Contact": [[109, "contact"]], "Mailing List": [[109, "mailing-list"]], "Chat": [[109, "chat"]], "Forum": [[109, "forum"]], "GitLab": [[109, "gitlab"]], "Bugs!": [[110, "bugs"]], "Bug report": [[110, "bug-report"]], "Known bugs": [[110, "known-bugs"]], "Adding new calculators": [[111, "adding-new-calculators"]], "Description of base-classes": [[111, "description-of-base-classes"]], "The Calculator base-class": [[111, "the-calculator-base-class"]], "The FileIOCalculator class": [[111, "the-fileiocalculator-class"]], "How to contribute": [[112, "how-to-contribute"]], "GitLab repository": [[112, "gitlab-repository"]], "Proposed git workflow": [[112, "proposed-git-workflow"]], "Aliases": [[112, "aliases"]], "The first steps as a developer": [[112, "the-first-steps-as-a-developer"]], "Making changes": [[112, "making-changes"]], "Adding corrections to be included in a merge request": [[112, "adding-corrections-to-be-included-in-a-merge-request"]], "Making small changes": [[112, "making-small-changes"]], "Writing the commit message": [[112, "writing-the-commit-message"]], "Code review": [[112, "code-review"]], "Development": [[113, "development"]], "License": [[114, "license"]], "Human-readable version": [[114, "human-readable-version"]], "Legal version of the license": [[114, "legal-version-of-the-license"]], "What happens when ASE Calculators are under another license?": [[114, "what-happens-when-ase-calculators-are-under-another-license"]], "Making movies": [[115, "making-movies"]], "using recordmydesktop": [[115, "using-recordmydesktop"]], "using avconf to collect png files": [[115, "using-avconf-to-collect-png-files"]], "New release": [[116, "new-release"]], "Calculator interface proposal": [[117, "calculator-interface-proposal"]], "Behavior": [[117, "behavior"]], "Standards parameters": [[117, "standards-parameters"]], "ABC calculator example": [[117, "abc-calculator-example"]], "Testing": [[117, "testing"]], "Labels for atoms": [[118, "labels-for-atoms"]], "Why?": [[118, "why"]], "Proposal": [[118, "proposal"]], "List-like objects": [[118, "list-like-objects"]], "Atom objects": [[118, "atom-objects"]], "I/O": [[118, "i-o"]], "ASE enhancement proposals": [[119, "ase-enhancement-proposals"]], "Coding Conventions": [[120, "coding-conventions"]], "General advice": [[120, "general-advice"]], "Writing documentation in the code": [[120, "writing-documentation-in-the-code"]], "Run flake8 on your code": [[120, "run-flake8-on-your-code"]], "Run autopep8.py on your code": [[120, "run-autopep8-py-on-your-code"]], "Testing the code": [[121, "testing-the-code"]], "How to add a test": [[121, "how-to-add-a-test"]], "How to fail successfully": [[121, "how-to-fail-successfully"]], "Translate ASE": [[122, "translate-ase"]], "How to translate": [[122, "how-to-translate"]], "Check and commit your translation": [[122, "check-and-commit-your-translation"]], "Maintaining translations": [[122, "maintaining-translations"]], "Writing documentation": [[123, "writing-documentation"]], "Installing Docutils and Sphinx": [[123, "installing-docutils-and-sphinx"]], "Using Sphinx": [[123, "using-sphinx"]], "Extensions to Sphinx": [[123, "extensions-to-sphinx"]], "Running Python code to create figures": [[123, "running-python-code-to-create-figures"]], "reStructedText in emacs": [[123, "restructedtext-in-emacs"]], "ASE ecosystem": [[124, "ase-ecosystem"]], "Frequently Asked Questions": [[125, "frequently-asked-questions"]], "ASE-GUI": [[125, "ase-gui"]], "How do I export images from a trajectory to png or pov files?": [[125, "how-do-i-export-images-from-a-trajectory-to-png-or-pov-files"]], "General": [[125, "general"]], "How should I cite ASE?": [[125, "how-should-i-cite-ase"]], "Gallery": [[126, "gallery"]], "Dissociation of oxygen on Pt(100)": [[126, "dissociation-of-oxygen-on-pt-100"]], "Phase diagrams": [[126, "phase-diagrams"]], "Brillouin zones": [[126, "brillouin-zones"]], "Band-structure": [[126, "band-structure"]], "Nudged elastic band calculations": [[126, "nudged-elastic-band-calculations"]], "Nanoparticle": [[126, "nanoparticle"], [127, "nanoparticle"]], "Pretty pictures": [[126, "pretty-pictures"]], "Periodic table": [[126, "periodic-table"]], "Build and optimise nanoparticle": [[127, "build-and-optimise-nanoparticle"]], "Exercise": [[127, null], [127, null], [127, null], [127, null], [127, null], [132, null], [132, null], [132, null], [132, null], [133, null], [133, null], [133, null], [133, null], [133, null], [134, null], [134, null], [134, null], [134, null], [134, null], [134, null], [134, null], [134, null], [134, null], [163, null], [164, null], [164, null], [164, null], [164, null], [164, null]], "Ground state": [[127, "ground-state"]], "Solutions": [[127, "solutions"], [132, "solutions"], [133, "solutions"], [134, "solutions"], [164, "solutions"]], "External calculators": [[128, "external-calculators"]], "Setting up an external calculator with ASE": [[128, "setting-up-an-external-calculator-with-ase"]], "Setting up": [[128, "setting-up"]], "Your first run": [[128, "your-first-run"]], "Getting started": [[129, "getting-started"]], "Manipulating atoms": [[130, "manipulating-atoms"]], "Ag adatom on Ni slab": [[130, "ag-adatom-on-ni-slab"]], "Interface building": [[130, "interface-building"]], "Introduction: Nitrogen on copper": [[131, "introduction-nitrogen-on-copper"]], "Atoms": [[131, "atoms"], [132, "atoms"]], "Adding calculator": [[131, "adding-calculator"]], "Structure relaxation": [[131, "structure-relaxation"]], "Input-output": [[131, "input-output"]], "Atoms and calculators": [[132, "atoms-and-calculators"]], "Python": [[132, "python"], [165, "python"]], "Binding curve": [[132, "binding-curve"]], "Optional exercise": [[132, null], [133, null]], "Structure optimization: H2O": [[133, "structure-optimization-h2o"]], "Optimizers": [[133, "optimizers"]], "G2 molecule dataset": [[133, "g2-molecule-dataset"]], "Use another calculator": [[133, "use-another-calculator"]], "Appendix: Communication between calculators and codes": [[133, "appendix-communication-between-calculators-and-codes"]], "Crystals and band structure": [[134, "crystals-and-band-structure"]], "Setting up bulk structures": [[134, "setting-up-bulk-structures"]], "Bulk calculation": [[134, "bulk-calculation"]], "Complex crystals and cell optimisation": [[134, "complex-crystals-and-cell-optimisation"]], "Atomic Simulation Environment": [[135, "atomic-simulation-environment"]], "Supported Calculators": [[135, "supported-calculators"]], "News": [[135, "news"]], "Installation": [[136, "installation"]], "Requirements": [[136, "requirements"]], "Installation using system package managers": [[136, "installation-using-system-package-managers"]], "Linux": [[136, "linux"]], "Max OSX (Homebrew)": [[136, "max-osx-homebrew"]], "Installation using pip": [[136, "installation-using-pip"]], "Installation from source": [[136, "installation-from-source"]], "Test your installation": [[136, "test-your-installation"]], "Numeric arrays in Python": [[137, "numeric-arrays-in-python"]], "What is Python?": [[138, "what-is-python"]], "Executing Python code": [[138, "executing-python-code"]], "Types": [[138, "types"]], "Loops": [[138, "loops"]], "Functions and classes": [[138, "functions-and-classes"]], "Importing modules": [[138, "importing-modules"]], "Release notes": [[139, "release-notes"]], "Git master branch": [[139, "git-master-branch"]], "Version 3.22.1": [[139, "version-3-22-1"]], "Version 3.22.0": [[139, "version-3-22-0"]], "Version 3.21.1": [[139, "version-3-21-1"]], "Version 3.21.0": [[139, "version-3-21-0"]], "Version 3.20.1": [[139, "version-3-20-1"]], "Version 3.19.3": [[139, "version-3-19-3"]], "Version 3.20.0": [[139, "version-3-20-0"]], "Version 3.19.2": [[139, "version-3-19-2"]], "Version 3.19.1": [[139, "version-3-19-1"]], "Version 3.19.0": [[139, "version-3-19-0"]], "Version 3.18.2": [[139, "version-3-18-2"]], "Version 3.18.1": [[139, "version-3-18-1"]], "Version 3.18.0": [[139, "version-3-18-0"]], "Version 3.17.0": [[139, "version-3-17-0"]], "Version 3.16.2": [[139, "version-3-16-2"]], "Version 3.16.0": [[139, "version-3-16-0"]], "Version 3.15.0": [[139, "version-3-15-0"]], "Version 3.14.1": [[139, "version-3-14-1"]], "Version 3.14.0": [[139, "version-3-14-0"]], "Version 3.13.0": [[139, "version-3-13-0"]], "Version 3.12.0": [[139, "version-3-12-0"]], "Version 3.11.0": [[139, "version-3-11-0"]], "Version 3.10.0": [[139, "version-3-10-0"]], "Version 3.9.1": [[139, "version-3-9-1"]], "Version 3.9.0": [[139, "version-3-9-0"]], "Version 3.8.0": [[139, "version-3-8-0"]], "Version 3.7.0": [[139, "version-3-7-0"]], "Version 3.6.0": [[139, "version-3-6-0"]], "Version 3.5.1": [[139, "version-3-5-1"]], "Version 3.5.0": [[139, "version-3-5-0"]], "Version 3.4.1": [[139, "version-3-4-1"]], "Tips and tricks": [[140, "tips-and-tricks"]], "Atoms objects": [[140, "atoms-objects"]], "Species": [[140, "species"]], "Indexing": [[140, "indexing"]], "Sorting": [[140, "sorting"]], "Append one trajectory to the end of another": [[140, "append-one-trajectory-to-the-end-of-another"]], "Input/output": [[140, "input-output"]], "Convert from one format to another": [[140, "convert-from-one-format-to-another"]], "Equilibrating an MD box of acetonitrile": [[141, "equilibrating-an-md-box-of-acetonitrile"]], "Atomization energy": [[142, "atomization-energy"]], "Surface diffusion energy barriers using ASE constraints": [[143, "surface-diffusion-energy-barriers-using-ase-constraints"]], "Surface adsorption study using the ASE database": [[144, "surface-adsorption-study-using-the-ase-database"]], "Bulk": [[144, "bulk"]], "Adsorbates": [[144, "adsorbates"]], "Reference energies": [[144, "reference-energies"]], "Analysis": [[144, "analysis"], [155, "analysis"]], "Tools for defect calculations": [[145, "tools-for-defect-calculations"]], "Supercell creation": [[145, "supercell-creation"]], "Algorithm for finding optimal supercell shapes": [[145, "algorithm-for-finding-optimal-supercell-shapes"]], "Implementation of algorithm": [[145, "implementation-of-algorithm"]], "Generation of supercell": [[145, 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"envvar-ASE_ABINIT_COMMAND"], [12, "index-1"], [19, "index-0"], [19, "index-1"], [19, "index-2"], [26, "index-0"], [26, "index-1"], [28, "index-0"], [28, "index-1"], [34, "index-0"], [38, "index-0"], [40, "index-0"], [41, "index-0"], [41, "index-1"], [42, "index-0"], [47, "index-0"], [47, "index-1"], [51, "index-0"], [51, "index-1"], [51, "index-2"], [51, "index-3"], [51, "index-4"], [51, "index-5"], [51, "index-6"], [51, "index-7"], [123, "index-0"], [123, "index-1"], [123, "index-2"], [128, "index-0"], [128, "index-1"], [128, "index-2"], [136, "envvar-PATH"], [136, "envvar-PYTHONPATH"], [136, "index-1"], [136, "index-2"], [136, "index-3"], [136, "index-4"], [136, "index-6"], [138, "index-0"]], "ase.calculators.acemolecule": [[10, "module-ase.calculators.acemolecule"]], "ase.calculators.amber": [[11, "module-ase.calculators.amber"]], "ase_abc_command": [[12, "index-1"]], "calculator (class in ase.calculators.interface)": [[12, "ase.calculators.interface.Calculator"]], "d3": [[12, "index-0"]], "dftcalculator (class in ase.calculators.interface)": [[12, "ase.calculators.interface.DFTCalculator"]], "grimme": [[12, "index-0"]], "ase.calculators": [[12, "module-ase.calculators"]], "calculation_required() (ase.calculators.interface.calculator method)": [[12, "ase.calculators.interface.Calculator.calculation_required"]], "get_bz_k_points() (ase.calculators.interface.dftcalculator method)": [[12, "ase.calculators.interface.DFTCalculator.get_bz_k_points"]], "get_effective_potential() (ase.calculators.interface.dftcalculator method)": [[12, "ase.calculators.interface.DFTCalculator.get_effective_potential"]], "get_eigenvalues() (ase.calculators.interface.dftcalculator method)": [[12, "ase.calculators.interface.DFTCalculator.get_eigenvalues"]], "get_fermi_level() (ase.calculators.interface.dftcalculator method)": [[12, "ase.calculators.interface.DFTCalculator.get_fermi_level"]], "get_forces() (ase.calculators.interface.calculator method)": [[12, "ase.calculators.interface.Calculator.get_forces"]], "get_ibz_k_points() (ase.calculators.interface.dftcalculator method)": [[12, "ase.calculators.interface.DFTCalculator.get_ibz_k_points"]], "get_k_point_weights() (ase.calculators.interface.dftcalculator method)": [[12, "ase.calculators.interface.DFTCalculator.get_k_point_weights"]], "get_magnetic_moment() (ase.calculators.interface.dftcalculator method)": [[12, "ase.calculators.interface.DFTCalculator.get_magnetic_moment"]], "get_number_of_bands() (ase.calculators.interface.dftcalculator method)": [[12, "ase.calculators.interface.DFTCalculator.get_number_of_bands"]], "get_number_of_grid_points() (ase.calculators.interface.dftcalculator method)": [[12, "ase.calculators.interface.DFTCalculator.get_number_of_grid_points"]], "get_number_of_spins() (ase.calculators.interface.dftcalculator method)": [[12, "ase.calculators.interface.DFTCalculator.get_number_of_spins"]], "get_occupation_numbers() (ase.calculators.interface.dftcalculator method)": [[12, "ase.calculators.interface.DFTCalculator.get_occupation_numbers"]], "get_potential_energy() (ase.calculators.interface.calculator method)": [[12, "ase.calculators.interface.Calculator.get_potential_energy"]], "get_pseudo_density() (ase.calculators.interface.dftcalculator method)": [[12, "ase.calculators.interface.DFTCalculator.get_pseudo_density"]], "get_pseudo_wave_function() (ase.calculators.interface.dftcalculator method)": [[12, "ase.calculators.interface.DFTCalculator.get_pseudo_wave_function"]], "get_spin_polarized() (ase.calculators.interface.dftcalculator method)": [[12, "ase.calculators.interface.DFTCalculator.get_spin_polarized"]], "get_stress() (ase.calculators.interface.calculator method)": [[12, "ase.calculators.interface.Calculator.get_stress"]], "get_wannier_localization_matrix() (ase.calculators.interface.dftcalculator method)": [[12, "ase.calculators.interface.DFTCalculator.get_wannier_localization_matrix"]], "get_xc_functional() (ase.calculators.interface.dftcalculator method)": [[12, "ase.calculators.interface.DFTCalculator.get_xc_functional"]], "initial_wannier() (ase.calculators.interface.dftcalculator method)": [[12, "ase.calculators.interface.DFTCalculator.initial_wannier"]], "set() (in module ase.calculators)": [[12, "ase.calculators.set"]], "castep (class in ase.calculators.castep)": [[13, "ase.calculators.castep.Castep"]], "ase.calculators.castep": [[13, "module-ase.calculators.castep"]], "checkpoint (class in ase.calculators.checkpoint)": [[14, "ase.calculators.checkpoint.Checkpoint"]], "checkpointcalculator (class in ase.calculators.checkpoint)": [[14, "ase.calculators.checkpoint.CheckpointCalculator"]], "ase.calculators.checkpoint": [[14, "module-ase.calculators.checkpoint"]], "calculate() (ase.calculators.checkpoint.checkpointcalculator method)": [[14, "ase.calculators.checkpoint.CheckpointCalculator.calculate"]], "default_parameters (ase.calculators.checkpoint.checkpointcalculator attribute)": [[14, "ase.calculators.checkpoint.CheckpointCalculator.default_parameters"]], "flush() (ase.calculators.checkpoint.checkpoint method)": [[14, "ase.calculators.checkpoint.Checkpoint.flush"]], "implemented_properties (ase.calculators.checkpoint.checkpointcalculator attribute)": [[14, "ase.calculators.checkpoint.CheckpointCalculator.implemented_properties"]], "load() (ase.calculators.checkpoint.checkpoint method)": [[14, "ase.calculators.checkpoint.Checkpoint.load"]], "save() (ase.calculators.checkpoint.checkpoint method)": [[14, "ase.calculators.checkpoint.Checkpoint.save"]], "cp2k (class in ase.calculators.cp2k)": [[15, "ase.calculators.cp2k.CP2K"]], "ase.calculators.cp2k": [[15, "module-ase.calculators.cp2k"]], "ase.calculators.crystal": [[16, "module-ase.calculators.crystal"]], "demon (class in ase.calculators.demon)": [[17, "ase.calculators.demon.Demon"]], "ase.calculators.demon": [[17, "module-ase.calculators.demon"]], "demonnano (class in ase.calculators.demonnano)": [[18, "ase.calculators.demonnano.DemonNano"]], "ase.calculators.demonnano": [[18, "module-ase.calculators.demonnano"]], "ase_dftb_command": [[19, "index-0"]], "dftb_command": [[19, "index-1"]], "dftb_prefix": [[19, "index-2"]], "dftb (class in ase.calculators.dftb)": [[19, "ase.calculators.dftb.Dftb"]], "ase.calculators.dftb": [[19, "module-ase.calculators.dftb"]], "ase.calculators.dftd3": [[20, "module-ase.calculators.dftd3"]], "dmol3 (class in ase.calculators.dmol)": [[21, "ase.calculators.dmol.DMol3"]], "ase.calculators.dmol": [[21, "module-ase.calculators.dmol"]], "ase.calculators.eam": [[22, "module-ase.calculators.eam"]], "emt (class in ase.calculators.emt)": [[23, "ase.calculators.emt.EMT"]], "ase.calculators.emt": [[23, "module-ase.calculators.emt"]], "espresso (class in ase.calculators.espresso)": [[24, "ase.calculators.espresso.Espresso"]], "ase.calculators.espresso": [[24, "module-ase.calculators.espresso"]], "exciting (class in ase.calculators.exciting)": [[25, "ase.calculators.exciting.Exciting"]], "ase.calculators.exciting": [[25, "module-ase.calculators.exciting"]], "fleur": [[26, "index-1"]], "fleur_inpgen": [[26, "index-0"]], "ase.calculators.fleur": [[26, "module-ase.calculators.fleur"]], "calculate() (ase.calculators.fleur.fleur method)": [[26, "ase.calculators.fleur.FLEUR.calculate"]], "initialize_density() (ase.calculators.fleur.fleur method)": [[26, "ase.calculators.fleur.FLEUR.initialize_density"]], "relax() (ase.calculators.fleur.fleur method)": [[26, "ase.calculators.fleur.FLEUR.relax"]], "write_inp() (ase.calculators.fleur.fleur method)": [[26, "ase.calculators.fleur.FLEUR.write_inp"]], "gamessus (class in ase.calculators.gamess_us)": [[27, "ase.calculators.gamess_us.GAMESSUS"]], "ase.calculators.gamess_us": [[27, "module-ase.calculators.gamess_us"]], "ase_gaussian_command": [[28, "index-1"]], "gaussian (class in ase.calculators.gaussian)": [[28, "ase.calculators.gaussian.Gaussian"]], "path": [[28, "index-0"], [123, "index-0"], [123, "index-2"], [136, "envvar-PATH"], [136, "index-1"], [136, "index-3"], [136, "index-4"], [136, "index-6"]], "ase.calculators.gaussian": [[28, "module-ase.calculators.gaussian"]], "ase.calculators.gromacs": [[29, "module-ase.calculators.gromacs"]], "ase.calculators.gulp": [[30, "module-ase.calculators.gulp"]], "kim() (in module ase.calculators.kim.kim)": [[32, "ase.calculators.kim.kim.KIM"]], "ase.calculators.kim": [[32, "module-ase.calculators.kim"]], "lammps (class in ase.calculators.lammpsrun)": [[33, "ase.calculators.lammpsrun.LAMMPS"], [34, "ase.calculators.LAMMPSrun.LAMMPS"]], "lammpslib (class in ase.calculators.lammpslib)": [[33, "ase.calculators.lammpslib.LAMMPSlib"]], "ase.calculators.lammps": [[33, "module-ase.calculators.lammps"]], "ase_lammpsrun_command": [[34, "index-0"]], "ase.calculators.lammpsrun": [[34, "module-ase.calculators.LAMMPSrun"]], "loggingcalculator (class in ase.calculators.loggingcalc)": [[35, "ase.calculators.loggingcalc.LoggingCalculator"]], "ase.calculators.loggingcalc": [[35, "module-ase.calculators.loggingcalc"]], "averagecalculator (class in ase.calculators.mixing)": [[36, "ase.calculators.mixing.AverageCalculator"]], "linearcombinationcalculator (class in ase.calculators.mixing)": [[36, "ase.calculators.mixing.LinearCombinationCalculator"]], "sumcalculator (class in ase.calculators.mixing)": [[36, "ase.calculators.mixing.SumCalculator"]], "ase.calculators.mixing": [[36, "module-ase.calculators.mixing"]], "mopac (class in ase.calculators.mopac)": [[37, "ase.calculators.mopac.MOPAC"]], "ase.calculators.mopac": [[37, "module-ase.calculators.mopac"]], "ase_nwchem_command": [[38, "index-0"]], "nwchem (class in ase.calculators.nwchem)": [[38, "ase.calculators.nwchem.NWChem"]], "ase.calculators.nwchem": [[38, "module-ase.calculators.nwchem"]], "ase.calculators.octopus": [[39, "module-ase.calculators.octopus"]], "ase_onetep_command": [[40, "index-0"]], "ase.calculators.onetep": [[40, "module-ase.calculators.onetep"]], "ase_openmx_command": [[41, "index-0"]], "openmx_dft_data_path": [[41, "index-1"]], "openmx (class in ase.calculators.openmx)": [[41, "ase.calculators.openmx.OpenMX"]], "ase.calculators.openmx": [[41, "module-ase.calculators.openmx"]], "$ase_orca_command": [[42, "index-0"]], "ase.calculators.orca": [[42, "module-ase.calculators.orca"]], "lennardjones (class in ase.calculators.lj)": [[43, "ase.calculators.lj.LennardJones"]], "morsepotential (class in ase.calculators.morse)": [[43, "ase.calculators.morse.MorsePotential"]], "tip3p (class in ase.calculators.tip3p)": [[43, "ase.calculators.tip3p.TIP3P"]], "tip4p (class in ase.calculators.tip4p)": [[43, "ase.calculators.tip4p.TIP4P"]], "ase.calculators.lj": [[43, "module-ase.calculators.lj"]], "ase.calculators.morse": [[43, "module-ase.calculators.morse"]], "ase.calculators.tip3p": [[43, "module-ase.calculators.tip3p"]], "ase.calculators.tip4p": [[43, "module-ase.calculators.tip4p"]], "psi4 (class in ase.calculators.psi4)": [[44, "ase.calculators.psi4.Psi4"]], "ase.calculators.psi4": [[44, "module-ase.calculators.psi4"]], "qchem (class in ase.calculators.qchem)": [[45, "ase.calculators.qchem.QChem"]], "ase.calculators.qchem": [[45, "module-ase.calculators.qchem"]], "eiqmmm (class in ase.calculators.qmmm)": [[46, "ase.calculators.qmmm.EIQMMM"]], "embedding (class in ase.calculators.qmmm)": [[46, "ase.calculators.qmmm.Embedding"]], "forceqmmm (class in ase.calculators.qmmm)": [[46, "ase.calculators.qmmm.ForceQMMM"]], "ljinteractions (class in ase.calculators.qmmm)": [[46, "ase.calculators.qmmm.LJInteractions"]], "ljinteractionsgeneral (class in ase.calculators.qmmm)": [[46, "ase.calculators.qmmm.LJInteractionsGeneral"]], "simpleqmmm (class in ase.calculators.qmmm)": [[46, "ase.calculators.qmmm.SimpleQMMM"]], "ase.calculators.qmmm": [[46, "module-ase.calculators.qmmm"]], "ase_siesta_command": [[47, "index-0"]], "ramancalculatorinterface (class in ase.calculators.siesta.siesta_lrtddft)": [[47, "ase.calculators.siesta.siesta_lrtddft.RamanCalculatorInterface"]], "siesta_pp_path": [[47, "index-1"]], "siesta (class in ase.calculators.siesta.siesta)": [[47, "ase.calculators.siesta.siesta.Siesta"]], "siestalrtddft (class in ase.calculators.siesta.siesta_lrtddft)": [[47, "ase.calculators.siesta.siesta_lrtddft.SiestaLRTDDFT"]], "ase.calculators.siesta": [[47, "module-ase.calculators.siesta"]], "socketclient (class in ase.calculators.socketio)": [[48, "ase.calculators.socketio.SocketClient"]], "socketiocalculator (class in ase.calculators.socketio)": [[48, "ase.calculators.socketio.SocketIOCalculator"]], "socketserver (class in ase.calculators.socketio)": [[48, "ase.calculators.socketio.SocketServer"]], "ase.calculators.socketio": [[48, "module-ase.calculators.socketio"]], "freeelectrons (class in ase.calculators.test)": [[49, "ase.calculators.test.FreeElectrons"]], "ase.calculators.test": [[49, "module-ase.calculators.test"]], "calculate() (ase.calculators.test.freeelectrons method)": [[49, "ase.calculators.test.FreeElectrons.calculate"]], "default_parameters (ase.calculators.test.freeelectrons attribute)": [[49, "ase.calculators.test.FreeElectrons.default_parameters"]], "get_eigenvalues() (ase.calculators.test.freeelectrons method)": [[49, "ase.calculators.test.FreeElectrons.get_eigenvalues"]], "get_fermi_level() (ase.calculators.test.freeelectrons method)": [[49, "ase.calculators.test.FreeElectrons.get_fermi_level"]], "get_ibz_k_points() (ase.calculators.test.freeelectrons method)": [[49, "ase.calculators.test.FreeElectrons.get_ibz_k_points"]], "get_number_of_spins() (ase.calculators.test.freeelectrons method)": [[49, "ase.calculators.test.FreeElectrons.get_number_of_spins"]], "implemented_properties (ase.calculators.test.freeelectrons attribute)": [[49, "ase.calculators.test.FreeElectrons.implemented_properties"]], "ase.calculators.turbomole": [[50, "module-ase.calculators.turbomole"]], "ase_vasp_command": [[51, "index-0"], [51, "index-5"], [128, "index-0"], [128, "index-2"]], "ase_vasp_vdw": [[51, "index-4"]], "vasp_command": [[51, "index-1"], [51, "index-6"]], "vasp_pp_path": [[51, "index-3"], [128, "index-1"]], "vasp_script": [[51, "index-2"], [51, "index-7"]], "vasp (class in ase.calculators.vasp)": [[51, "ase.calculators.vasp.Vasp"]], "asdict() (ase.calculators.vasp.vasp method)": [[51, "ase.calculators.vasp.Vasp.asdict"]], "ase.calculators.vasp": [[51, "module-ase.calculators.vasp"]], "fromdict() (ase.calculators.vasp.vasp method)": [[51, "ase.calculators.vasp.Vasp.fromdict"]], "read_json() (ase.calculators.vasp.vasp method)": [[51, "ase.calculators.vasp.Vasp.read_json"]], "write_json() (ase.calculators.vasp.vasp method)": [[51, "ase.calculators.vasp.Vasp.write_json"]], "cell (class in ase.cell)": [[52, "ase.cell.Cell"]], "angles() (ase.cell.cell method)": [[52, "ase.cell.Cell.angles"]], "ascell() (ase.cell.cell class method)": [[52, "ase.cell.Cell.ascell"]], "ase.cell": [[52, "module-ase.cell"]], "bandpath() (ase.cell.cell method)": [[52, "ase.cell.Cell.bandpath"]], "cartesian_positions() (ase.cell.cell method)": [[52, "ase.cell.Cell.cartesian_positions"]], "cellpar() (ase.cell.cell method)": [[52, "ase.cell.Cell.cellpar"]], "complete() (ase.cell.cell method)": [[52, "ase.cell.Cell.complete"]], "copy() (ase.cell.cell method)": [[52, "ase.cell.Cell.copy"]], "fromcellpar() (ase.cell.cell class method)": [[52, "ase.cell.Cell.fromcellpar"]], "get_bravais_lattice() (ase.cell.cell method)": [[52, "ase.cell.Cell.get_bravais_lattice"]], "handedness (ase.cell.cell property)": [[52, "ase.cell.Cell.handedness"]], "lengths() (ase.cell.cell method)": [[52, "ase.cell.Cell.lengths"]], "minkowski_reduce() (ase.cell.cell method)": [[52, "ase.cell.Cell.minkowski_reduce"]], "new() (ase.cell.cell class method)": [[52, "ase.cell.Cell.new"]], "niggli_reduce() (ase.cell.cell method)": [[52, "ase.cell.Cell.niggli_reduce"]], "orthorhombic (ase.cell.cell property)": [[52, "ase.cell.Cell.orthorhombic"]], "permute_axes() (ase.cell.cell method)": [[52, "ase.cell.Cell.permute_axes"]], "rank (ase.cell.cell property)": [[52, "ase.cell.Cell.rank"]], "reciprocal() (ase.cell.cell method)": [[52, "ase.cell.Cell.reciprocal"]], "scaled_positions() (ase.cell.cell method)": [[52, "ase.cell.Cell.scaled_positions"]], "standard_form() (ase.cell.cell method)": [[52, "ase.cell.Cell.standard_form"]], "uncomplete() (ase.cell.cell method)": [[52, "ase.cell.Cell.uncomplete"]], "volume (ase.cell.cell property)": [[52, "ase.cell.Cell.volume"]], "cluster (class in ase.cluster)": [[53, "ase.cluster.Cluster"]], "decahedron() (in module ase.cluster)": [[53, "ase.cluster.Decahedron"]], "icosahedron() (in module ase.cluster)": [[53, "ase.cluster.Icosahedron"]], "octahedron() (in module ase.cluster)": [[53, "ase.cluster.Octahedron"]], "ase.cluster": [[53, "module-ase.cluster"]], "copy() (ase.cluster.cluster method)": [[53, "ase.cluster.Cluster.copy"]], "get_diameter() (ase.cluster.cluster method)": [[53, "ase.cluster.Cluster.get_diameter"]], "get_layers() (ase.cluster.cluster method)": [[53, "ase.cluster.Cluster.get_layers"]], "get_surfaces() (ase.cluster.cluster method)": [[53, "ase.cluster.Cluster.get_surfaces"]], "wulff_construction() (in module ase.cluster)": [[53, "ase.cluster.wulff_construction"]], "collection (class in ase.collections.collection)": [[54, "ase.collections.collection.Collection"]], "ase.collections": [[54, "module-ase.collections"]], "dcdft (in module ase.collections)": [[54, "ase.collections.dcdft"]], "g2 (in module ase.collections)": [[54, "ase.collections.g2"]], "s22 (in module ase.collections)": [[54, "ase.collections.s22"]], "expcellfilter (class in ase.constraints)": [[55, "ase.constraints.ExpCellFilter"]], "externalforce (class in ase.constraints)": [[55, "ase.constraints.ExternalForce"]], "filter (class in ase.constraints)": [[55, "ase.constraints.Filter"]], "fixatoms (class in ase.constraints)": [[55, "ase.constraints.FixAtoms"]], "fixbondlength (class in ase.constraints)": [[55, "ase.constraints.FixBondLength"]], "fixbondlengths (class in ase.constraints)": [[55, "ase.constraints.FixBondLengths"]], "fixcom (class in ase.constraints)": [[55, "ase.constraints.FixCom"]], "fixinternals (class in ase.constraints)": [[55, "ase.constraints.FixInternals"]], "fixlineartriatomic (class in ase.constraints)": [[55, "ase.constraints.FixLinearTriatomic"]], "fixsymmetry (class in ase.spacegroup.symmetrize)": [[55, "ase.spacegroup.symmetrize.FixSymmetry"]], "fixedline (class in ase.constraints)": [[55, "ase.constraints.FixedLine"]], "fixedmode (class in ase.constraints)": [[55, "ase.constraints.FixedMode"]], "fixedplane (class in ase.constraints)": [[55, "ase.constraints.FixedPlane"]], "strainfilter (class in ase.constraints)": [[55, "ase.constraints.StrainFilter"]], "unitcellfilter (class in ase.constraints)": [[55, "ase.constraints.UnitCellFilter"]], "adjust_forces() (in module ase.constraints)": [[55, "ase.constraints.adjust_forces"]], "adjust_momenta() (in module ase.constraints)": [[55, "ase.constraints.adjust_momenta"]], "adjust_positions() (in module ase.constraints)": [[55, "ase.constraints.adjust_positions"]], "adjust_potential_energy() (in module ase.constraints)": [[55, "ase.constraints.adjust_potential_energy"]], "ase.constraints": [[55, "module-ase.constraints"]], "ase.spacegroup.symmetrize": [[55, "module-ase.spacegroup.symmetrize"]], "check_symmetry() (in module ase.spacegroup.symmetrize)": [[55, "ase.spacegroup.symmetrize.check_symmetry"]], "refine_symmetry() (in module ase.spacegroup.symmetrize)": [[55, "ase.spacegroup.symmetrize.refine_symmetry"]], "ase.data": [[56, "module-ase.data"]], "atomic_masses (in module ase.data)": [[56, "ase.data.atomic_masses"]], "atomic_masses_iupac2016 (in module ase.data)": [[56, "ase.data.atomic_masses_iupac2016"]], "atomic_masses_legacy (in module ase.data)": [[56, "ase.data.atomic_masses_legacy"]], "atomic_names (in module ase.data)": [[56, "ase.data.atomic_names"]], "atomic_numbers (in module ase.data)": [[56, "ase.data.atomic_numbers"]], "chemical_symbols (in module ase.data)": [[56, "ase.data.chemical_symbols"]], "covalent_radii (in module ase.data)": [[56, "ase.data.covalent_radii"]], "cpk_colors (in module ase.data)": [[56, "ase.data.cpk_colors"]], "download_isotope_data() (in module ase.data.isotopes)": [[56, "ase.data.isotopes.download_isotope_data"]], "pubchem_atoms_conformer_search() (in module ase.data.pubchem)": [[56, "ase.data.pubchem.pubchem_atoms_conformer_search"]], "pubchem_atoms_search() (in module ase.data.pubchem)": [[56, "ase.data.pubchem.pubchem_atoms_search"]], "pubchem_conformer_search() (in module ase.data.pubchem)": [[56, "ase.data.pubchem.pubchem_conformer_search"]], "pubchem_search() (in module ase.data.pubchem)": [[56, "ase.data.pubchem.pubchem_search"]], "reference_states (in module ase.data)": [[56, "ase.data.reference_states"]], "vdw_radii (in module ase.data)": [[56, "ase.data.vdw_radii"]], "atomsrow (class in ase.db.row)": [[57, "ase.db.row.AtomsRow"]], "database (class in ase.db.core)": [[57, "ase.db.core.Database"]], "ase.db": [[57, "module-ase.db"]], "ase.db.core": [[57, "module-ase.db.core"]], "charge (ase.db.row.atomsrow property)": [[57, "ase.db.row.AtomsRow.charge"]], "connect() (in module ase.db.core)": [[57, "ase.db.core.connect"]], "constrained_forces (ase.db.row.atomsrow property)": [[57, "ase.db.row.AtomsRow.constrained_forces"]], "constraints (ase.db.row.atomsrow property)": [[57, "ase.db.row.AtomsRow.constraints"]], "count() (ase.db.core.database method)": [[57, "ase.db.core.Database.count"]], "count_atoms() (ase.db.row.atomsrow method)": [[57, "ase.db.row.AtomsRow.count_atoms"]], "data (ase.db.row.atomsrow property)": [[57, "ase.db.row.AtomsRow.data"]], "delete() (ase.db.core.database method)": [[57, "ase.db.core.Database.delete"]], "fmax (ase.db.row.atomsrow property)": [[57, "ase.db.row.AtomsRow.fmax"]], "formula (ase.db.row.atomsrow property)": [[57, "ase.db.row.AtomsRow.formula"]], "get() (ase.db.core.database method)": [[57, "ase.db.core.Database.get"]], "get() (ase.db.row.atomsrow method)": [[57, "ase.db.row.AtomsRow.get"]], "get_atoms() (ase.db.core.database method)": [[57, "ase.db.core.Database.get_atoms"]], "key_value_pairs (ase.db.row.atomsrow property)": [[57, "ase.db.row.AtomsRow.key_value_pairs"]], "mass (ase.db.row.atomsrow property)": [[57, "ase.db.row.AtomsRow.mass"]], "metadata (ase.db.core.database attribute)": [[57, "ase.db.core.Database.metadata"]], "natoms (ase.db.row.atomsrow property)": [[57, "ase.db.row.AtomsRow.natoms"]], "reserve() (ase.db.core.database method)": [[57, "ase.db.core.Database.reserve"]], "select() (ase.db.core.database method)": [[57, "ase.db.core.Database.select"]], "smax (ase.db.row.atomsrow property)": [[57, "ase.db.row.AtomsRow.smax"]], "symbols (ase.db.row.atomsrow property)": [[57, "ase.db.row.AtomsRow.symbols"]], "toatoms() (ase.db.row.atomsrow method)": [[57, "ase.db.row.AtomsRow.toatoms"]], "update() (ase.db.core.database method)": [[57, "ase.db.core.Database.update"]], "volume (ase.db.row.atomsrow property)": [[57, "ase.db.row.AtomsRow.volume"]], "write() (ase.db.core.database method)": [[57, "ase.db.core.Database.write"]], "ase.dft.bandgap": [[59, "module-ase.dft.bandgap"]], "bandgap() (in module ase.dft.bandgap)": [[59, "ase.dft.bandgap.bandgap"]], "ase.dft": [[61, "module-ase.dft"]], "dos (class in ase.dft.dos)": [[62, "ase.dft.dos.DOS"]], "ase.dft.dos": [[62, "module-ase.dft.dos"]], "get_distribution_moment() (in module ase.dft)": [[62, "ase.dft.get_distribution_moment"]], "get_dos() (ase.dft.dos.dos method)": [[62, "ase.dft.dos.DOS.get_dos"]], "get_energies() (ase.dft.dos.dos method)": [[62, "ase.dft.dos.DOS.get_energies"]], "linear_tetrahedron_integration() (in module ase.dft.dos)": [[62, "ase.dft.dos.linear_tetrahedron_integration"]], "bandpath (class in ase.dft.kpoints)": [[63, "ase.dft.kpoints.BandPath"]], "bandstructure (class in ase.spectrum.band_structure)": [[63, "ase.spectrum.band_structure.BandStructure"]], "ase.dft.kpoints": [[63, "module-ase.dft.kpoints"]], "bandpath() (in module ase.dft.kpoints)": [[63, "ase.dft.kpoints.bandpath"]], "cartesian_kpts() (ase.dft.kpoints.bandpath method)": [[63, "ase.dft.kpoints.BandPath.cartesian_kpts"]], "cc12_2x3 (in module ase.dft.kpoints)": [[63, "ase.dft.kpoints.cc12_2x3"]], "cc162_1x1 (in module ase.dft.kpoints)": [[63, "ase.dft.kpoints.cc162_1x1"]], "cc162_sq3xsq3 (in module ase.dft.kpoints)": [[63, "ase.dft.kpoints.cc162_sq3xsq3"]], "cc18_1x1 (in module ase.dft.kpoints)": [[63, "ase.dft.kpoints.cc18_1x1"]], "cc18_sq3xsq3 (in module ase.dft.kpoints)": [[63, "ase.dft.kpoints.cc18_sq3xsq3"]], "cc54_1x1 (in module ase.dft.kpoints)": [[63, "ase.dft.kpoints.cc54_1x1"]], "cc54_sq3xsq3 (in module ase.dft.kpoints)": [[63, "ase.dft.kpoints.cc54_sq3xsq3"]], "cc6_1x1 (in module ase.dft.kpoints)": [[63, "ase.dft.kpoints.cc6_1x1"]], "cell (ase.dft.kpoints.bandpath property)": [[63, "ase.dft.kpoints.BandPath.cell"]], "energies (ase.spectrum.band_structure.bandstructure property)": [[63, "ase.spectrum.band_structure.BandStructure.energies"]], "free_electron_band_structure() (ase.dft.kpoints.bandpath method)": [[63, "ase.dft.kpoints.BandPath.free_electron_band_structure"]], "get_labels() (ase.spectrum.band_structure.bandstructure method)": [[63, "ase.spectrum.band_structure.BandStructure.get_labels"]], "get_linear_kpoint_axis() (ase.dft.kpoints.bandpath method)": [[63, "ase.dft.kpoints.BandPath.get_linear_kpoint_axis"]], "get_monkhorst_pack_size_and_offset() (in module ase.dft.kpoints)": [[63, "ase.dft.kpoints.get_monkhorst_pack_size_and_offset"]], "get_special_points() (in module ase.dft.kpoints)": [[63, "ase.dft.kpoints.get_special_points"]], "icell (ase.dft.kpoints.bandpath property)": [[63, "ase.dft.kpoints.BandPath.icell"]], "interpolate() (ase.dft.kpoints.bandpath method)": [[63, "ase.dft.kpoints.BandPath.interpolate"]], "kpts (ase.dft.kpoints.bandpath property)": [[63, "ase.dft.kpoints.BandPath.kpts"]], "labels_from_kpts() (in module ase.dft.kpoints)": [[63, "ase.dft.kpoints.labels_from_kpts"]], "monkhorst_pack() (in module ase.dft.kpoints)": [[63, "ase.dft.kpoints.monkhorst_pack"]], "monkhorst_pack_interpolate() (in module ase.dft.kpoints)": [[63, "ase.dft.kpoints.monkhorst_pack_interpolate"]], "parse_path_string() (in module ase.dft.kpoints)": [[63, "ase.dft.kpoints.parse_path_string"]], "path (ase.dft.kpoints.bandpath property)": [[63, "ase.dft.kpoints.BandPath.path"]], "path (ase.spectrum.band_structure.bandstructure property)": [[63, "ase.spectrum.band_structure.BandStructure.path"]], "plot() (ase.dft.kpoints.bandpath method)": [[63, "ase.dft.kpoints.BandPath.plot"]], "plot() (ase.spectrum.band_structure.bandstructure method)": [[63, "ase.spectrum.band_structure.BandStructure.plot"]], "read() (ase.dft.kpoints.bandpath class method)": [[63, "ase.dft.kpoints.BandPath.read"]], "read() (ase.spectrum.band_structure.bandstructure class method)": [[63, "ase.spectrum.band_structure.BandStructure.read"]], "reference (ase.spectrum.band_structure.bandstructure property)": [[63, "ase.spectrum.band_structure.BandStructure.reference"]], "special_paths (in module ase.dft.kpoints)": [[63, "ase.dft.kpoints.special_paths"]], "special_points (ase.dft.kpoints.bandpath property)": [[63, "ase.dft.kpoints.BandPath.special_points"]], "special_points (in module ase.dft.kpoints)": [[63, "ase.dft.kpoints.special_points"]], "subtract_reference() (ase.spectrum.band_structure.bandstructure method)": [[63, "ase.spectrum.band_structure.BandStructure.subtract_reference"]], "transform() (ase.dft.kpoints.bandpath method)": [[63, "ase.dft.kpoints.BandPath.transform"]], "write() (ase.dft.kpoints.bandpath method)": [[63, "ase.dft.kpoints.BandPath.write"]], "write() (ase.spectrum.band_structure.bandstructure method)": [[63, "ase.spectrum.band_structure.BandStructure.write"]], "stm (class in ase.dft.stm)": [[64, "ase.dft.stm.STM"]], "calculate_ldos() (ase.dft.stm.stm method)": [[64, "ase.dft.stm.STM.calculate_ldos"]], "find_current() (ase.dft.stm.stm method)": [[64, "ase.dft.stm.STM.find_current"]], "get_averaged_current() (ase.dft.stm.stm method)": [[64, "ase.dft.stm.STM.get_averaged_current"]], "linescan() (ase.dft.stm.stm method)": [[64, "ase.dft.stm.STM.linescan"]], "pointcurrent() (ase.dft.stm.stm method)": [[64, "ase.dft.stm.STM.pointcurrent"]], "scan() (ase.dft.stm.stm method)": [[64, "ase.dft.stm.STM.scan"]], "scan2() (ase.dft.stm.stm method)": [[64, "ase.dft.stm.STM.scan2"]], "sts() (ase.dft.stm.stm method)": [[64, "ase.dft.stm.STM.sts"]], "write() (ase.dft.stm.stm method)": [[64, "ase.dft.stm.STM.write"]], "wannier (class in ase.dft.wannier)": [[65, "ase.dft.wannier.Wannier"]], "ase.dft.wannier": [[65, "module-ase.dft.wannier"]], "distances() (ase.dft.wannier.wannier method)": [[65, "ase.dft.wannier.Wannier.distances"]], "get_centers() (ase.dft.wannier.wannier method)": [[65, "ase.dft.wannier.Wannier.get_centers"]], "get_function() (ase.dft.wannier.wannier method)": [[65, "ase.dft.wannier.Wannier.get_function"]], "get_functional_value() (ase.dft.wannier.wannier method)": [[65, "ase.dft.wannier.Wannier.get_functional_value"]], "get_hamiltonian() (ase.dft.wannier.wannier method)": [[65, "ase.dft.wannier.Wannier.get_hamiltonian"]], "get_hamiltonian_kpoint() (ase.dft.wannier.wannier method)": [[65, "ase.dft.wannier.Wannier.get_hamiltonian_kpoint"]], "get_hopping() (ase.dft.wannier.wannier method)": [[65, "ase.dft.wannier.Wannier.get_hopping"]], "get_pdos() (ase.dft.wannier.wannier method)": [[65, "ase.dft.wannier.Wannier.get_pdos"]], "get_radii() (ase.dft.wannier.wannier method)": [[65, "ase.dft.wannier.Wannier.get_radii"]], "initialize() (ase.dft.wannier.wannier method)": [[65, "ase.dft.wannier.Wannier.initialize"]], "localize() (ase.dft.wannier.wannier method)": [[65, "ase.dft.wannier.Wannier.localize"]], "save() (ase.dft.wannier.wannier method)": [[65, "ase.dft.wannier.Wannier.save"]], "translate() (ase.dft.wannier.wannier method)": [[65, "ase.dft.wannier.Wannier.translate"]], "translate_all_to_cell() (ase.dft.wannier.wannier method)": [[65, "ase.dft.wannier.Wannier.translate_all_to_cell"]], "translate_to_cell() (ase.dft.wannier.wannier method)": [[65, "ase.dft.wannier.Wannier.translate_to_cell"]], "write_cube() (ase.dft.wannier.wannier method)": [[65, "ase.dft.wannier.Wannier.write_cube"]], "dimercontrol (class in ase.dimer)": [[66, "ase.dimer.DimerControl"]], "dimereigenmodesearch (class in ase.dimer)": [[66, "ase.dimer.DimerEigenmodeSearch"]], "minmodeatoms (class in ase.dimer)": [[66, "ase.dimer.MinModeAtoms"]], "minmodetranslate (class in ase.dimer)": [[66, "ase.dimer.MinModeTranslate"]], "ase.dimer": [[66, "module-ase.dimer"]], "bulk modulus": [[67, "index-0"]], "equationofstate (class in ase.eos)": [[67, "ase.eos.EquationOfState"]], "ase.eos": [[67, "module-ase.eos"]], "calculate_eos() (in module ase.eos)": [[67, "ase.eos.calculate_eos"]], "fit() (ase.eos.equationofstate method)": [[67, "ase.eos.EquationOfState.fit"]], "plot() (ase.eos.equationofstate method)": [[67, "ase.eos.EquationOfState.plot"]], "formula (class in ase.formula)": [[68, "ase.formula.Formula"]], "__add__() (ase.formula.formula method)": [[68, "ase.formula.Formula.__add__"]], "__contains__() (ase.formula.formula method)": [[68, "ase.formula.Formula.__contains__"]], "__divmod__() (ase.formula.formula method)": [[68, "ase.formula.Formula.__divmod__"]], "__eq__() (ase.formula.formula method)": [[68, "ase.formula.Formula.__eq__"]], "__format__() (ase.formula.formula method)": [[68, "ase.formula.Formula.__format__"]], "__getitem__() (ase.formula.formula method)": [[68, "ase.formula.Formula.__getitem__"]], "__len__() (ase.formula.formula method)": [[68, "ase.formula.Formula.__len__"]], "__mul__() (ase.formula.formula method)": [[68, "ase.formula.Formula.__mul__"]], "ase.formula": [[68, "module-ase.formula"]], "convert() (ase.formula.formula method)": [[68, "ase.formula.Formula.convert"]], "count() (ase.formula.formula method)": [[68, "ase.formula.Formula.count"]], "format() (ase.formula.formula method)": [[68, "ase.formula.Formula.format"]], "from_dict() (ase.formula.formula static method)": [[68, "ase.formula.Formula.from_dict"]], "from_list() (ase.formula.formula static method)": [[68, "ase.formula.Formula.from_list"]], "reduce() (ase.formula.formula method)": [[68, "ase.formula.Formula.reduce"]], "stoichiometry() (ase.formula.formula method)": [[68, "ase.formula.Formula.stoichiometry"]], "ase.ga": [[69, "module-ase.ga"]], "analysis (class in ase.geometry.analysis)": [[70, "ase.geometry.analysis.Analysis"]], "cell (class in ase.geometry)": [[70, "ase.geometry.Cell"]], "adjacency_matrix (ase.geometry.analysis.analysis property)": [[70, "ase.geometry.analysis.Analysis.adjacency_matrix"]], "all_angles (ase.geometry.analysis.analysis property)": [[70, "ase.geometry.analysis.Analysis.all_angles"]], "all_bonds (ase.geometry.analysis.analysis property)": [[70, "ase.geometry.analysis.Analysis.all_bonds"]], "all_dihedrals (ase.geometry.analysis.analysis property)": [[70, "ase.geometry.analysis.Analysis.all_dihedrals"]], "angles() (ase.geometry.cell method)": [[70, "ase.geometry.Cell.angles"]], "ascell() (ase.geometry.cell class method)": [[70, "ase.geometry.Cell.ascell"]], "ase.geometry": [[70, "module-ase.geometry"]], "bandpath() (ase.geometry.cell method)": [[70, "ase.geometry.Cell.bandpath"]], "cartesian_positions() (ase.geometry.cell method)": [[70, "ase.geometry.Cell.cartesian_positions"]], "cell_to_cellpar() (in module ase.geometry)": [[70, "ase.geometry.cell_to_cellpar"]], "cellpar() (ase.geometry.cell method)": [[70, "ase.geometry.Cell.cellpar"]], "cellpar_to_cell() (in module ase.geometry)": [[70, "ase.geometry.cellpar_to_cell"]], "clear_cache() (ase.geometry.analysis.analysis method)": [[70, "ase.geometry.analysis.Analysis.clear_cache"]], "complete() (ase.geometry.cell method)": [[70, "ase.geometry.Cell.complete"]], "complete_cell() (in module ase.geometry)": [[70, "ase.geometry.complete_cell"]], "conditional_find_mic() (in module ase.geometry)": [[70, "ase.geometry.conditional_find_mic"]], "copy() (ase.geometry.cell method)": [[70, "ase.geometry.Cell.copy"]], "distance() (in module ase.geometry)": [[70, "ase.geometry.distance"]], "distance_matrix (ase.geometry.analysis.analysis property)": [[70, "ase.geometry.analysis.Analysis.distance_matrix"]], "find_mic() (in module ase.geometry)": [[70, "ase.geometry.find_mic"]], "fromcellpar() (ase.geometry.cell class method)": [[70, "ase.geometry.Cell.fromcellpar"]], "get_angle_value() (ase.geometry.analysis.analysis method)": [[70, "ase.geometry.analysis.Analysis.get_angle_value"]], "get_angles() (ase.geometry.analysis.analysis method)": [[70, "ase.geometry.analysis.Analysis.get_angles"]], "get_angles() (in module ase.geometry)": [[70, "ase.geometry.get_angles"]], "get_angles_derivatives() (in module ase.geometry)": [[70, "ase.geometry.get_angles_derivatives"]], "get_bond_value() (ase.geometry.analysis.analysis method)": [[70, "ase.geometry.analysis.Analysis.get_bond_value"]], "get_bonds() (ase.geometry.analysis.analysis method)": [[70, "ase.geometry.analysis.Analysis.get_bonds"]], "get_bravais_lattice() (ase.geometry.cell method)": [[70, "ase.geometry.Cell.get_bravais_lattice"]], "get_dihedral_value() (ase.geometry.analysis.analysis method)": [[70, "ase.geometry.analysis.Analysis.get_dihedral_value"]], "get_dihedrals() (ase.geometry.analysis.analysis method)": [[70, "ase.geometry.analysis.Analysis.get_dihedrals"]], "get_dihedrals() (in module ase.geometry)": [[70, "ase.geometry.get_dihedrals"]], "get_dihedrals_derivatives() (in module ase.geometry)": [[70, "ase.geometry.get_dihedrals_derivatives"]], "get_distances() (in module ase.geometry)": [[70, "ase.geometry.get_distances"]], "get_distances_derivatives() (in module ase.geometry)": [[70, "ase.geometry.get_distances_derivatives"]], "get_duplicate_atoms() (in module ase.geometry)": [[70, "ase.geometry.get_duplicate_atoms"]], "get_layers() (in module ase.geometry)": [[70, "ase.geometry.get_layers"]], "get_rdf() (ase.geometry.analysis.analysis method)": [[70, "ase.geometry.analysis.Analysis.get_rdf"]], "get_values() (ase.geometry.analysis.analysis method)": [[70, "ase.geometry.analysis.Analysis.get_values"]], "handedness (ase.geometry.cell property)": [[70, "ase.geometry.Cell.handedness"]], "images (ase.geometry.analysis.analysis property)": [[70, "ase.geometry.analysis.Analysis.images"]], "is_minkowski_reduced() (in module ase.geometry)": [[70, "ase.geometry.is_minkowski_reduced"]], "is_orthorhombic() (in module ase.geometry)": [[70, "ase.geometry.is_orthorhombic"]], "lengths() (ase.geometry.cell method)": [[70, "ase.geometry.Cell.lengths"]], "minkowski_reduce() (ase.geometry.cell method)": [[70, "ase.geometry.Cell.minkowski_reduce"]], "minkowski_reduce() (in module ase.geometry)": [[70, "ase.geometry.minkowski_reduce"]], "nimages (ase.geometry.analysis.analysis property)": [[70, "ase.geometry.analysis.Analysis.nImages"]], "new() (ase.geometry.cell class method)": [[70, "ase.geometry.Cell.new"]], "niggli_reduce() (ase.geometry.cell method)": [[70, "ase.geometry.Cell.niggli_reduce"]], "nl (ase.geometry.analysis.analysis property)": [[70, "ase.geometry.analysis.Analysis.nl"]], "orthorhombic (ase.geometry.cell property)": [[70, "ase.geometry.Cell.orthorhombic"]], "orthorhombic() (in module ase.geometry)": [[70, "ase.geometry.orthorhombic"]], "permute_axes() (ase.geometry.cell method)": [[70, "ase.geometry.Cell.permute_axes"]], "permute_axes() (in module ase.geometry)": [[70, "ase.geometry.permute_axes"]], "rank (ase.geometry.cell property)": [[70, "ase.geometry.Cell.rank"]], "reciprocal() (ase.geometry.cell method)": [[70, "ase.geometry.Cell.reciprocal"]], "scaled_positions() (ase.geometry.cell method)": [[70, "ase.geometry.Cell.scaled_positions"]], "standard_form() (ase.geometry.cell method)": [[70, "ase.geometry.Cell.standard_form"]], "uncomplete() (ase.geometry.cell method)": [[70, "ase.geometry.Cell.uncomplete"]], "unique_angles (ase.geometry.analysis.analysis property)": [[70, "ase.geometry.analysis.Analysis.unique_angles"]], "unique_bonds (ase.geometry.analysis.analysis property)": [[70, "ase.geometry.analysis.Analysis.unique_bonds"]], "unique_dihedrals (ase.geometry.analysis.analysis property)": [[70, "ase.geometry.analysis.Analysis.unique_dihedrals"]], "volume (ase.geometry.cell property)": [[70, "ase.geometry.Cell.volume"]], "wrap_positions() (in module ase.geometry)": [[70, "ase.geometry.wrap_positions"]], "repeat_poll() (ase.gui.gui.gui method)": [[71, "ase.gui.gui.GUI.repeat_poll"]], "ag": [[74, "index-0"]], "ase-gui": [[74, "index-0"]], "ase.gui": [[74, "module-ase.gui"]], "gui": [[74, "index-0"]], "read_abinit_in() (in module ase.io.abinit)": [[78, "ase.io.abinit.read_abinit_in"]], "read_abinit_out() (in module ase.io.abinit)": [[78, "ase.io.abinit.read_abinit_out"]], "read_acemolecule_input() (in module ase.io.acemolecule)": [[78, "ase.io.acemolecule.read_acemolecule_input"]], "read_acemolecule_out() (in module ase.io.acemolecule)": [[78, "ase.io.acemolecule.read_acemolecule_out"]], "read_aims() (in module ase.io.aims)": [[78, "ase.io.aims.read_aims"]], "read_aims_output() (in module ase.io.aims)": [[78, "ase.io.aims.read_aims_output"]], "read_bundletrajectory() (in module ase.io.bundletrajectory)": [[78, "ase.io.bundletrajectory.read_bundletrajectory"]], "read_castep_castep() (in module ase.io.castep)": [[78, "ase.io.castep.read_castep_castep"]], "read_castep_cell() (in module ase.io.castep)": [[78, "ase.io.castep.read_castep_cell"]], "read_castep_geom() (in module ase.io.castep)": [[78, "ase.io.castep.read_castep_geom"]], "read_castep_md() (in module ase.io.castep)": [[78, "ase.io.castep.read_castep_md"]], "read_castep_phonon() (in module ase.io.castep)": [[78, "ase.io.castep.read_castep_phonon"]], "read_cfg() (in module ase.io.cfg)": [[78, "ase.io.cfg.read_cfg"]], "read_cif() (in module ase.io.cif)": [[78, "ase.io.cif.read_cif"]], "read_cmdft() (in module ase.io.cmdft)": [[78, "ase.io.cmdft.read_cmdft"]], "read_cml() (in module ase.io.cml)": [[78, "ase.io.cml.read_cml"]], "read_cp2k_dcd() (in module ase.io.cp2k)": [[78, "ase.io.cp2k.read_cp2k_dcd"]], "read_cp2k_restart() (in module ase.io.cp2k)": [[78, "ase.io.cp2k.read_cp2k_restart"]], "read_crystal() (in module ase.io.crystal)": [[78, "ase.io.crystal.read_crystal"]], "read_cube() (in module ase.io.cube)": [[78, "ase.io.cube.read_cube"]], "read_dacapo_text() (in module ase.io.dacapo)": [[78, "ase.io.dacapo.read_dacapo_text"]], "read_db() (in module ase.io.db)": [[78, "ase.io.db.read_db"]], "read_dftb() (in module ase.io.dftb)": [[78, "ase.io.dftb.read_dftb"]], "read_dlp4() (in module ase.io.dlp4)": [[78, "ase.io.dlp4.read_dlp4"]], "read_dlp_history() (in module ase.io.dlp4)": [[78, "ase.io.dlp4.read_dlp_history"]], "read_dmol_arc() (in module ase.io.dmol)": [[78, "ase.io.dmol.read_dmol_arc"]], "read_dmol_car() (in module ase.io.dmol)": [[78, "ase.io.dmol.read_dmol_car"]], "read_dmol_incoor() (in module ase.io.dmol)": [[78, "ase.io.dmol.read_dmol_incoor"]], "read_elk() (in module ase.io.elk)": [[78, "ase.io.elk.read_elk"]], "read_eon() (in module ase.io.eon)": [[78, "ase.io.eon.read_eon"]], "read_espresso_in() (in module ase.io.espresso)": [[78, "ase.io.espresso.read_espresso_in"]], "read_espresso_out() (in module ase.io.espresso)": [[78, "ase.io.espresso.read_espresso_out"]], "read_exciting() (in module ase.io.exciting)": [[78, "ase.io.exciting.read_exciting"]], "read_extxyz() (in module ase.io.extxyz)": [[78, "ase.io.extxyz.read_extxyz"]], "read_gamess_us_out() (in module ase.io.gamess_us)": [[78, "ase.io.gamess_us.read_gamess_us_out"]], "read_gamess_us_punch() (in module ase.io.gamess_us)": [[78, "ase.io.gamess_us.read_gamess_us_punch"]], "read_gaussian_in() (in module ase.io.gaussian)": [[78, "ase.io.gaussian.read_gaussian_in"]], "read_gaussian_out() (in module ase.io.gaussian)": [[78, "ase.io.gaussian.read_gaussian_out"]], "read_gen() (in module ase.io.gen)": [[78, "ase.io.gen.read_gen"]], "read_gpaw_out() (in module ase.io.gpaw_out)": [[78, "ase.io.gpaw_out.read_gpaw_out"]], "read_gpumd() (in module ase.io.gpumd)": [[78, "ase.io.gpumd.read_gpumd"]], "read_gpw() (in module ase.io.gpw)": [[78, "ase.io.gpw.read_gpw"]], "read_gromacs() (in module ase.io.gromacs)": [[78, "ase.io.gromacs.read_gromacs"]], "read_gromos() (in module ase.io.gromos)": [[78, "ase.io.gromos.read_gromos"]], "read_json() (in module ase.io.db)": [[78, "ase.io.db.read_json"]], "read_jsv() (in module ase.io.jsv)": [[78, "ase.io.jsv.read_jsv"]], "read_lammps_data() (in module ase.io.lammpsdata)": [[78, "ase.io.lammpsdata.read_lammps_data"]], "read_lammps_dump_binary() (in module ase.io.lammpsrun)": [[78, "ase.io.lammpsrun.read_lammps_dump_binary"]], "read_lammps_dump_text() (in module ase.io.lammpsrun)": [[78, "ase.io.lammpsrun.read_lammps_dump_text"]], "read_magres() (in module ase.io.magres)": [[78, "ase.io.magres.read_magres"]], "read_mol() (in module ase.io.mol)": [[78, "ase.io.mol.read_mol"]], "read_mustem() (in module ase.io.mustem)": [[78, "ase.io.mustem.read_mustem"]], "read_mysql() (in module ase.io.db)": [[78, "ase.io.db.read_mysql"]], "read_netcdftrajectory() (in module ase.io.netcdftrajectory)": [[78, "ase.io.netcdftrajectory.read_netcdftrajectory"]], "read_nomad_json() (in module ase.io.nomad_json)": [[78, "ase.io.nomad_json.read_nomad_json"]], "read_nwchem_in() (in module ase.io.nwchem)": [[78, "ase.io.nwchem.read_nwchem_in"]], "read_nwchem_out() (in module ase.io.nwchem)": [[78, "ase.io.nwchem.read_nwchem_out"]], "read_octopus_in() (in module ase.io.octopus)": [[78, "ase.io.octopus.read_octopus_in"]], "read_postgresql() (in module ase.io.db)": [[78, "ase.io.db.read_postgresql"]], "read_prismatic() (in module ase.io.prismatic)": [[78, "ase.io.prismatic.read_prismatic"]], "read_proteindatabank() (in module ase.io.proteindatabank)": [[78, "ase.io.proteindatabank.read_proteindatabank"]], "read_qbox() (in module ase.io.qbox)": [[78, "ase.io.qbox.read_qbox"]], "read_res() (in module ase.io.res)": [[78, "ase.io.res.read_res"]], "read_rmc6f() (in module ase.io.rmc6f)": [[78, "ase.io.rmc6f.read_rmc6f"]], "read_sdf() (in module ase.io.sdf)": [[78, "ase.io.sdf.read_sdf"]], "read_siesta_xv() (in module ase.io.siesta)": [[78, "ase.io.siesta.read_siesta_xv"]], "read_struct() (in module ase.io.wien2k)": [[78, "ase.io.wien2k.read_struct"]], "read_struct_out() (in module ase.io.siesta)": [[78, "ase.io.siesta.read_struct_out"]], "read_sys() (in module ase.io.sys)": [[78, "ase.io.sys.read_sys"]], "read_traj() (in module ase.io.trajectory)": [[78, "ase.io.trajectory.read_traj"]], "read_turbomole() (in module ase.io.turbomole)": [[78, "ase.io.turbomole.read_turbomole"]], "read_turbomole_gradient() (in module ase.io.turbomole)": [[78, "ase.io.turbomole.read_turbomole_gradient"]], "read_v_sim() (in module ase.io.v_sim)": [[78, "ase.io.v_sim.read_v_sim"]], "read_vasp() (in module ase.io.vasp)": [[78, "ase.io.vasp.read_vasp"]], "read_vasp_out() (in module ase.io.vasp)": [[78, "ase.io.vasp.read_vasp_out"]], "read_vasp_xdatcar() (in module ase.io.vasp)": [[78, "ase.io.vasp.read_vasp_xdatcar"]], "read_vasp_xml() (in module ase.io.vasp)": [[78, "ase.io.vasp.read_vasp_xml"]], "read_wout() (in module ase.io.wannier90)": [[78, "ase.io.wannier90.read_wout"]], "read_xsd() (in module ase.io.xsd)": [[78, "ase.io.xsd.read_xsd"]], "read_xsf() (in module ase.io.xsf)": [[78, "ase.io.xsf.read_xsf"]], "read_xtd() (in module ase.io.xtd)": [[78, "ase.io.xtd.read_xtd"]], "read_xyz() (in module ase.io.xyz)": [[78, "ase.io.xyz.read_xyz"]], "write_abinit_in() (in module ase.io.abinit)": [[78, "ase.io.abinit.write_abinit_in"]], "write_aims() (in module ase.io.aims)": [[78, "ase.io.aims.write_aims"]], "write_bundletrajectory() (in module ase.io.bundletrajectory)": [[78, "ase.io.bundletrajectory.write_bundletrajectory"]], "write_castep_cell() (in module ase.io.castep)": [[78, "ase.io.castep.write_castep_cell"]], "write_cfg() (in module ase.io.cfg)": [[78, "ase.io.cfg.write_cfg"]], "write_cif() (in module ase.io.cif)": [[78, "ase.io.cif.write_cif"]], "write_crystal() (in module ase.io.crystal)": [[78, "ase.io.crystal.write_crystal"]], "write_cube() (in module ase.io.cube)": [[78, "ase.io.cube.write_cube"]], "write_db() (in module ase.io.db)": [[78, "ase.io.db.write_db"]], "write_dftb() (in module ase.io.dftb)": [[78, "ase.io.dftb.write_dftb"]], "write_dlp4() (in module ase.io.dlp4)": [[78, "ase.io.dlp4.write_dlp4"]], "write_dmol_arc() (in module ase.io.dmol)": [[78, "ase.io.dmol.write_dmol_arc"]], "write_dmol_car() (in module ase.io.dmol)": [[78, "ase.io.dmol.write_dmol_car"]], "write_dmol_incoor() (in module ase.io.dmol)": [[78, "ase.io.dmol.write_dmol_incoor"]], "write_elk_in() (in module ase.io.elk)": [[78, "ase.io.elk.write_elk_in"]], "write_eon() (in module ase.io.eon)": [[78, "ase.io.eon.write_eon"]], "write_eps() (in module ase.io.eps)": [[78, "ase.io.eps.write_eps"]], "write_espresso_in() (in module ase.io.espresso)": [[78, "ase.io.espresso.write_espresso_in"]], "write_exciting() (in module ase.io.exciting)": [[78, "ase.io.exciting.write_exciting"]], "write_extxyz() (in module ase.io.extxyz)": [[78, "ase.io.extxyz.write_extxyz"]], "write_findsym() (in module ase.io.findsym)": [[78, "ase.io.findsym.write_findsym"]], "write_gamess_us_in() (in module ase.io.gamess_us)": [[78, "ase.io.gamess_us.write_gamess_us_in"]], "write_gaussian_in() (in module ase.io.gaussian)": [[78, "ase.io.gaussian.write_gaussian_in"]], "write_gen() (in module ase.io.gen)": [[78, "ase.io.gen.write_gen"]], "write_gif() (in module ase.io.animation)": [[78, "ase.io.animation.write_gif"]], "write_gpumd() (in module ase.io.gpumd)": [[78, "ase.io.gpumd.write_gpumd"]], "write_gromacs() (in module ase.io.gromacs)": [[78, "ase.io.gromacs.write_gromacs"]], "write_gromos() (in module ase.io.gromos)": [[78, "ase.io.gromos.write_gromos"]], "write_html() (in module ase.io.x3d)": [[78, "ase.io.x3d.write_html"]], "write_json() (in module ase.io.db)": [[78, "ase.io.db.write_json"]], "write_jsv() (in module ase.io.jsv)": [[78, "ase.io.jsv.write_jsv"]], "write_lammps_data() (in module ase.io.lammpsdata)": [[78, "ase.io.lammpsdata.write_lammps_data"]], "write_magres() (in module ase.io.magres)": [[78, "ase.io.magres.write_magres"]], "write_mp4() (in module ase.io.animation)": [[78, "ase.io.animation.write_mp4"]], "write_mustem() (in module ase.io.mustem)": [[78, "ase.io.mustem.write_mustem"]], "write_mysql() (in module ase.io.db)": [[78, "ase.io.db.write_mysql"]], "write_netcdftrajectory() (in module ase.io.netcdftrajectory)": [[78, "ase.io.netcdftrajectory.write_netcdftrajectory"]], "write_nwchem_in() (in module ase.io.nwchem)": [[78, "ase.io.nwchem.write_nwchem_in"]], "write_png() (in module ase.io.png)": [[78, "ase.io.png.write_png"]], "write_postgresql() (in module ase.io.db)": [[78, "ase.io.db.write_postgresql"]], "write_pov() (in module ase.io.pov)": [[78, "ase.io.pov.write_pov"]], "write_prismatic() (in module ase.io.prismatic)": [[78, "ase.io.prismatic.write_prismatic"]], "write_proteindatabank() (in module ase.io.proteindatabank)": [[78, "ase.io.proteindatabank.write_proteindatabank"]], "write_py() (in module ase.io.py)": [[78, "ase.io.py.write_py"]], "write_res() (in module ase.io.res)": [[78, "ase.io.res.write_res"]], "write_rmc6f() (in module ase.io.rmc6f)": [[78, "ase.io.rmc6f.write_rmc6f"]], "write_struct() (in module ase.io.wien2k)": [[78, "ase.io.wien2k.write_struct"]], "write_sys() (in module ase.io.sys)": [[78, "ase.io.sys.write_sys"]], "write_traj() (in module ase.io.trajectory)": [[78, "ase.io.trajectory.write_traj"]], "write_turbomole() (in module ase.io.turbomole)": [[78, "ase.io.turbomole.write_turbomole"]], "write_v_sim() (in module ase.io.v_sim)": [[78, "ase.io.v_sim.write_v_sim"]], "write_vasp() (in module ase.io.vasp)": [[78, "ase.io.vasp.write_vasp"]], "write_vasp_xdatcar() (in module ase.io.vasp)": [[78, "ase.io.vasp.write_vasp_xdatcar"]], "write_vti() (in module ase.io.vtkxml)": [[78, "ase.io.vtkxml.write_vti"]], "write_vtu() (in module ase.io.vtkxml)": [[78, "ase.io.vtkxml.write_vtu"]], "write_x3d() (in module ase.io.x3d)": [[78, "ase.io.x3d.write_x3d"]], "write_xsd() (in module ase.io.xsd)": [[78, "ase.io.xsd.write_xsd"]], "write_xsf() (in module ase.io.xsf)": [[78, "ase.io.xsf.write_xsf"]], "write_xtd() (in module ase.io.xtd)": [[78, "ase.io.xtd.write_xtd"]], "write_xyz() (in module ase.io.xyz)": [[78, "ase.io.xyz.write_xyz"]], "ase.io": [[79, "module-ase.io"]], "iread() (in module ase.io)": [[79, "ase.io.iread"]], "read() (in module ase.io)": [[79, "ase.io.read"]], "read_cube_data() (in module ase.io)": [[79, "ase.io.read_cube_data"]], "write() (in module ase.io)": [[79, "ase.io.write"]], "ase.io.opls": 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"ase.io.bundletrajectory.BundleTrajectory.is_bundle"]], "is_empty_bundle() (ase.io.bundletrajectory.bundletrajectory static method)": [[81, "ase.io.bundletrajectory.BundleTrajectory.is_empty_bundle"]], "log() (ase.io.bundletrajectory.bundletrajectory method)": [[81, "ase.io.bundletrajectory.BundleTrajectory.log"]], "post_write_attach() (ase.io.bundletrajectory.bundletrajectory method)": [[81, "ase.io.bundletrajectory.BundleTrajectory.post_write_attach"]], "pre_write_attach() (ase.io.bundletrajectory.bundletrajectory method)": [[81, "ase.io.bundletrajectory.BundleTrajectory.pre_write_attach"]], "read_extra_data() (ase.io.bundletrajectory.bundletrajectory method)": [[81, "ase.io.bundletrajectory.BundleTrajectory.read_extra_data"]], "select_data() (ase.io.bundletrajectory.bundletrajectory method)": [[81, "ase.io.bundletrajectory.BundleTrajectory.select_data"]], "set_extra_data() (ase.io.bundletrajectory.bundletrajectory method)": [[81, "ase.io.bundletrajectory.BundleTrajectory.set_extra_data"]], "write() (ase.io.bundletrajectory.bundletrajectory method)": [[81, "ase.io.bundletrajectory.BundleTrajectory.write"]], "write() (ase.io.trajectory.trajectorywriter method)": [[81, "ase.io.trajectory.TrajectoryWriter.write"]], "invalidulmfileerror": [[82, "ase.io.ulm.InvalidULMFileError"]], "reader (class in ase.io.ulm)": [[82, "ase.io.ulm.Reader"]], "writer (class in ase.io.ulm)": [[82, "ase.io.ulm.Writer"]], "add_array() (ase.io.ulm.writer method)": [[82, "ase.io.ulm.Writer.add_array"]], "asdict() (ase.io.ulm.reader method)": [[82, "ase.io.ulm.Reader.asdict"]], "ase.io.ulm": [[82, "module-ase.io.ulm"]], "child() (ase.io.ulm.writer method)": [[82, "ase.io.ulm.Writer.child"]], "close() (ase.io.ulm.writer method)": [[82, "ase.io.ulm.Writer.close"]], "fill() (ase.io.ulm.writer method)": [[82, "ase.io.ulm.Writer.fill"]], "get() (ase.io.ulm.reader method)": [[82, "ase.io.ulm.Reader.get"]], "get_tag() (ase.io.ulm.reader method)": [[82, "ase.io.ulm.Reader.get_tag"]], "keys() (ase.io.ulm.reader method)": [[82, "ase.io.ulm.Reader.keys"]], "open() (in module ase.io.ulm)": [[82, "ase.io.ulm.open"]], "sync() (ase.io.ulm.writer method)": [[82, "ase.io.ulm.Writer.sync"]], "write() (ase.io.ulm.writer method)": [[82, "ase.io.ulm.Writer.write"]], "bravaislattice (class in ase.lattice)": [[83, "ase.lattice.BravaisLattice"]], "ase.lattice": [[83, "module-ase.lattice"]], "bandpath() (ase.lattice.bravaislattice method)": [[83, "ase.lattice.BravaisLattice.bandpath"]], "cellpar() (ase.lattice.bravaislattice method)": [[83, "ase.lattice.BravaisLattice.cellpar"]], "conventional() (ase.lattice.bravaislattice method)": [[83, "ase.lattice.BravaisLattice.conventional"]], "description() (ase.lattice.bravaislattice method)": [[83, "ase.lattice.BravaisLattice.description"]], "get_special_points() (ase.lattice.bravaislattice method)": [[83, "ase.lattice.BravaisLattice.get_special_points"]], "get_special_points_array() (ase.lattice.bravaislattice method)": [[83, "ase.lattice.BravaisLattice.get_special_points_array"]], "plot_bz() (ase.lattice.bravaislattice method)": [[83, "ase.lattice.BravaisLattice.plot_bz"]], "special_path (ase.lattice.bravaislattice property)": [[83, "ase.lattice.BravaisLattice.special_path"]], "special_point_names (ase.lattice.bravaislattice property)": [[83, "ase.lattice.BravaisLattice.special_point_names"]], "tocell() (ase.lattice.bravaislattice method)": [[83, "ase.lattice.BravaisLattice.tocell"]], "type_description() (ase.lattice.bravaislattice class method)": [[83, "ase.lattice.BravaisLattice.type_description"]], "variant (ase.lattice.bravaislattice property)": [[83, "ase.lattice.BravaisLattice.variant"]], "vars() (ase.lattice.bravaislattice method)": [[83, "ase.lattice.BravaisLattice.vars"]], "andersen (class in ase.md.andersen)": [[85, "ase.md.andersen.Andersen"]], "contourexploration (class in ase.md.contour_exploration)": [[85, "ase.md.contour_exploration.ContourExploration"]], "diffusioncoefficient (class in ase.md.analysis)": [[85, "ase.md.analysis.DiffusionCoefficient"]], "langevin (class in ase.md.langevin)": [[85, "ase.md.langevin.Langevin"]], "mdlogger (class in ase.md)": [[85, "ase.md.MDLogger"]], "maxwellboltzmanndistribution() (in module ase.md.velocitydistribution)": [[85, "ase.md.velocitydistribution.MaxwellBoltzmannDistribution"]], "npt (class in ase.md.npt)": [[85, "ase.md.npt.NPT"]], "nptberendsen (class in ase.md.nptberendsen)": [[85, "ase.md.nptberendsen.NPTBerendsen"]], "nvtberendsen (class in ase.md.nvtberendsen)": [[85, "ase.md.nvtberendsen.NVTBerendsen"]], "phononharmonics() (in module ase.md.velocitydistribution)": [[85, "ase.md.velocitydistribution.PhononHarmonics"]], "stationary() (in module ase.md.velocitydistribution)": [[85, "ase.md.velocitydistribution.Stationary"]], "velocityverlet (class in ase.md.verlet)": [[85, "ase.md.verlet.VelocityVerlet"]], "zerorotation() (in module ase.md.velocitydistribution)": [[85, "ase.md.velocitydistribution.ZeroRotation"]], "ase.md": [[85, "module-ase.md"]], "ase.md.analysis": [[85, "module-ase.md.analysis"]], "ase.md.andersen": [[85, "module-ase.md.andersen"]], "ase.md.contour_exploration": [[85, "module-ase.md.contour_exploration"]], "ase.md.langevin": [[85, "module-ase.md.langevin"]], "ase.md.npt": [[85, "module-ase.md.npt"]], "ase.md.nptberendsen": [[85, "module-ase.md.nptberendsen"]], "ase.md.nvtberendsen": [[85, "module-ase.md.nvtberendsen"]], "ase.md.velocitydistribution": [[85, "module-ase.md.velocitydistribution"]], "ase.md.verlet": [[85, "module-ase.md.verlet"]], "attach() (ase.md.npt.npt method)": [[85, "ase.md.npt.NPT.attach"]], "get_gibbs_free_energy() (ase.md.npt.npt method)": [[85, "ase.md.npt.NPT.get_gibbs_free_energy"]], "get_strain_rate() (ase.md.npt.npt method)": [[85, "ase.md.npt.NPT.get_strain_rate"]], "get_time() (ase.md.npt.npt method)": [[85, "ase.md.npt.NPT.get_time"]], "initialize() (ase.md.npt.npt method)": [[85, "ase.md.npt.NPT.initialize"]], "phonon_harmonics() (in module ase.md.velocitydistribution)": [[85, "ase.md.velocitydistribution.phonon_harmonics"]], "run() (ase.md.npt.npt method)": [[85, "ase.md.npt.NPT.run"]], "set_fraction_traceless() (ase.md.npt.npt method)": [[85, "ase.md.npt.NPT.set_fraction_traceless"]], "set_mask() (ase.md.npt.npt method)": [[85, "ase.md.npt.NPT.set_mask"]], "set_strain_rate() (ase.md.npt.npt method)": [[85, "ase.md.npt.NPT.set_strain_rate"]], "set_stress() (ase.md.npt.npt method)": [[85, "ase.md.npt.NPT.set_stress"]], "set_temperature() (ase.md.npt.npt method)": [[85, "ase.md.npt.NPT.set_temperature"]], "zero_center_of_mass_momentum() (ase.md.npt.npt method)": [[85, "ase.md.npt.NPT.zero_center_of_mass_momentum"]], "autoneb (class in ase.autoneb)": [[86, "ase.autoneb.AutoNEB"]], "dyneb (class in ase.dyneb)": [[86, "ase.dyneb.DyNEB"]], "neb (class in ase.neb)": [[86, "ase.neb.NEB"]], "nebtools (class in ase.neb)": [[86, "ase.neb.NEBTools"]], "ase.neb": [[86, "module-ase.neb"]], "get_barrier() (ase.neb.nebtools method)": [[86, "ase.neb.NEBTools.get_barrier"]], "get_fmax() (ase.neb.nebtools method)": [[86, "ase.neb.NEBTools.get_fmax"]], "idpp_interpolate() (in module ase.neb)": [[86, "ase.neb.idpp_interpolate"]], "interpolate() (in module ase.neb)": [[86, "ase.neb.interpolate"]], "plot_band() (ase.neb.nebtools method)": [[86, "ase.neb.NEBTools.plot_band"]], "plot_bands() (ase.neb.nebtools method)": [[86, "ase.neb.NEBTools.plot_bands"]], "neighborlist (class in ase.neighborlist)": [[87, "ase.neighborlist.NeighborList"]], "newprimitiveneighborlist (class in ase.neighborlist)": [[87, "ase.neighborlist.NewPrimitiveNeighborList"]], "primitiveneighborlist (class in ase.neighborlist)": [[87, "ase.neighborlist.PrimitiveNeighborList"]], "ase.neighborlist": [[87, "module-ase.neighborlist"]], "build() (ase.neighborlist.newprimitiveneighborlist method)": [[87, "ase.neighborlist.NewPrimitiveNeighborList.build"]], "build() (ase.neighborlist.primitiveneighborlist method)": [[87, "ase.neighborlist.PrimitiveNeighborList.build"]], "build_neighbor_list() (in module ase.neighborlist)": [[87, "ase.neighborlist.build_neighbor_list"]], "first_neighbors() (in module ase.neighborlist)": [[87, "ase.neighborlist.first_neighbors"]], "get_connectivity_matrix() (ase.neighborlist.neighborlist method)": [[87, "ase.neighborlist.NeighborList.get_connectivity_matrix"]], "get_connectivity_matrix() (in module ase.neighborlist)": [[87, "ase.neighborlist.get_connectivity_matrix"]], "get_distance_indices() (in module ase.neighborlist)": [[87, "ase.neighborlist.get_distance_indices"]], "get_distance_matrix() (in module ase.neighborlist)": [[87, "ase.neighborlist.get_distance_matrix"]], "get_neighbors() (ase.neighborlist.neighborlist method)": [[87, "ase.neighborlist.NeighborList.get_neighbors"]], "get_neighbors() (ase.neighborlist.newprimitiveneighborlist method)": [[87, "ase.neighborlist.NewPrimitiveNeighborList.get_neighbors"]], "get_neighbors() (ase.neighborlist.primitiveneighborlist method)": [[87, "ase.neighborlist.PrimitiveNeighborList.get_neighbors"]], "mic() (in module ase.neighborlist)": [[87, "ase.neighborlist.mic"]], "natural_cutoffs() (in module ase.neighborlist)": [[87, "ase.neighborlist.natural_cutoffs"]], "neighbor_list() (in module ase.neighborlist)": [[87, "ase.neighborlist.neighbor_list"]], "nneighbors (ase.neighborlist.neighborlist property)": [[87, "ase.neighborlist.NeighborList.nneighbors"]], "npbcneighbors (ase.neighborlist.neighborlist property)": [[87, "ase.neighborlist.NeighborList.npbcneighbors"]], "nupdates (ase.neighborlist.neighborlist property)": [[87, "ase.neighborlist.NeighborList.nupdates"]], "primitive_neighbor_list() (in module ase.neighborlist)": [[87, "ase.neighborlist.primitive_neighbor_list"]], "update() (ase.neighborlist.neighborlist method)": [[87, "ase.neighborlist.NeighborList.update"]], "update() (ase.neighborlist.newprimitiveneighborlist method)": [[87, "ase.neighborlist.NewPrimitiveNeighborList.update"]], "update() (ase.neighborlist.primitiveneighborlist method)": [[87, "ase.neighborlist.PrimitiveNeighborList.update"]], "bfgs (class in ase.optimize)": [[88, "ase.optimize.BFGS"]], "bfgslinesearch (class in ase.optimize)": [[88, "ase.optimize.BFGSLineSearch"]], "berny (class in ase.optimize)": [[88, "ase.optimize.Berny"]], "fire (class in ase.optimize)": [[88, "ase.optimize.FIRE"]], "gpmin (class in ase.optimize)": [[88, "ase.optimize.GPMin"]], "lbfgs (class in ase.optimize)": [[88, "ase.optimize.LBFGS"]], "lbfgslinesearch (class in ase.optimize)": [[88, "ase.optimize.LBFGSLineSearch"]], "mdmin (class in ase.optimize)": [[88, "ase.optimize.MDMin"]], "quasinewton (class in ase.optimize)": [[88, "ase.optimize.QuasiNewton"]], "scipyfminbfgs (class in ase.optimize.sciopt)": [[88, "ase.optimize.sciopt.SciPyFminBFGS"]], "scipyfmincg (class in ase.optimize.sciopt)": [[88, "ase.optimize.sciopt.SciPyFminCG"]], "ase.optimize": [[88, "module-ase.optimize"]], "ase.optimize.basin": [[88, "module-ase.optimize.basin"]], "ase.optimize.precon": [[88, "module-ase.optimize.precon"]], "ase.parallel": [[89, "module-ase.parallel"]], "broadcast() (in module ase.parallel)": [[89, "ase.parallel.broadcast"]], "parallel_function() (in module ase.parallel)": [[89, "ase.parallel.parallel_function"]], "parallel_generator() (in module ase.parallel)": [[89, "ase.parallel.parallel_generator"]], "paropen() (in module ase.parallel)": [[89, "ase.parallel.paropen"]], "parprint() (in module ase.parallel)": [[89, "ase.parallel.parprint"]], "phasediagram (class in ase.phasediagram)": [[90, "ase.phasediagram.PhaseDiagram"]], "pourbaix (class in ase.phasediagram)": [[90, "ase.phasediagram.Pourbaix"]], "ase.phasediagram": [[90, "module-ase.phasediagram"]], "decompose() (ase.phasediagram.phasediagram method)": [[90, "ase.phasediagram.PhaseDiagram.decompose"]], "decompose() (ase.phasediagram.pourbaix method)": [[90, "ase.phasediagram.Pourbaix.decompose"]], "diagram() (ase.phasediagram.pourbaix method)": [[90, "ase.phasediagram.Pourbaix.diagram"]], "plot() (ase.phasediagram.phasediagram method)": [[90, "ase.phasediagram.PhaseDiagram.plot"]], "solvated() (in module ase.phasediagram)": [[90, "ase.phasediagram.solvated"]], "phonons (class in ase.phonons)": [[91, "ase.phonons.Phonons"]], "acoustic() (ase.phonons.phonons method)": [[91, "ase.phonons.Phonons.acoustic"]], "apply_cutoff() (ase.phonons.phonons method)": [[91, "ase.phonons.Phonons.apply_cutoff"]], "ase.phonons": [[91, "module-ase.phonons"]], "band_structure() (ase.phonons.phonons method)": [[91, "ase.phonons.Phonons.band_structure"]], "check_eq_forces() (ase.phonons.phonons method)": [[91, "ase.phonons.Phonons.check_eq_forces"]], "compute_dynamical_matrix() (ase.phonons.phonons method)": [[91, "ase.phonons.Phonons.compute_dynamical_matrix"]], "dos() (ase.phonons.phonons method)": [[91, "ase.phonons.Phonons.dos"]], "get_force_constant() (ase.phonons.phonons method)": [[91, "ase.phonons.Phonons.get_force_constant"]], "read() (ase.phonons.phonons method)": [[91, "ase.phonons.Phonons.read"]], "read_born_charges() (ase.phonons.phonons method)": [[91, "ase.phonons.Phonons.read_born_charges"]], "symmetrize() (ase.phonons.phonons method)": [[91, "ase.phonons.Phonons.symmetrize"]], "write_modes() (ase.phonons.phonons method)": [[91, "ase.phonons.Phonons.write_modes"]], "spacegroup (class in ase.spacegroup)": [[92, "ase.spacegroup.Spacegroup"]], "ase.spacegroup": [[92, "module-ase.spacegroup"]], "crystal() (in module ase.spacegroup)": [[92, "ase.spacegroup.crystal"]], "get_basis() (in module ase.spacegroup)": [[92, "ase.spacegroup.get_basis"]], "get_spacegroup() (in module ase.spacegroup)": [[92, "ase.spacegroup.get_spacegroup"]], "ase.spectrum.doscollection": [[93, "module-ase.spectrum.doscollection"]], "ase.spectrum.dosdata": [[94, "module-ase.spectrum.dosdata"]], "ase.spectrum": [[95, "module-ase.spectrum"]], "symbols (class in ase.symbols)": [[96, "ase.symbols.Symbols"]], "ase.symbols": [[96, "module-ase.symbols"]], "crystalthermo (class in ase.thermochemistry)": [[97, "ase.thermochemistry.CrystalThermo"]], "harmonicthermo (class in ase.thermochemistry)": [[97, "ase.thermochemistry.HarmonicThermo"]], "hinderedthermo (class in ase.thermochemistry)": [[97, "ase.thermochemistry.HinderedThermo"]], "idealgasthermo (class in ase.thermochemistry)": [[97, "ase.thermochemistry.IdealGasThermo"]], "ase.thermochemistry": [[97, "module-ase.thermochemistry"]], "get_enthalpy() (ase.thermochemistry.idealgasthermo method)": [[97, "ase.thermochemistry.IdealGasThermo.get_enthalpy"]], "get_entropy() (ase.thermochemistry.crystalthermo method)": [[97, "ase.thermochemistry.CrystalThermo.get_entropy"]], "get_entropy() (ase.thermochemistry.harmonicthermo method)": [[97, "ase.thermochemistry.HarmonicThermo.get_entropy"]], "get_entropy() (ase.thermochemistry.hinderedthermo method)": [[97, "ase.thermochemistry.HinderedThermo.get_entropy"]], "get_entropy() (ase.thermochemistry.idealgasthermo method)": [[97, "ase.thermochemistry.IdealGasThermo.get_entropy"]], "get_gibbs_energy() (ase.thermochemistry.idealgasthermo method)": [[97, "ase.thermochemistry.IdealGasThermo.get_gibbs_energy"]], "get_helmholtz_energy() (ase.thermochemistry.crystalthermo method)": [[97, "ase.thermochemistry.CrystalThermo.get_helmholtz_energy"]], "get_helmholtz_energy() (ase.thermochemistry.harmonicthermo method)": [[97, "ase.thermochemistry.HarmonicThermo.get_helmholtz_energy"]], "get_helmholtz_energy() (ase.thermochemistry.hinderedthermo method)": [[97, "ase.thermochemistry.HinderedThermo.get_helmholtz_energy"]], "get_internal_energy() (ase.thermochemistry.crystalthermo method)": [[97, "ase.thermochemistry.CrystalThermo.get_internal_energy"]], "get_internal_energy() (ase.thermochemistry.harmonicthermo method)": [[97, "ase.thermochemistry.HarmonicThermo.get_internal_energy"]], "get_internal_energy() (ase.thermochemistry.hinderedthermo method)": [[97, "ase.thermochemistry.HinderedThermo.get_internal_energy"]], "get_zero_point_energy() (ase.thermochemistry.hinderedthermo method)": [[97, "ase.thermochemistry.HinderedThermo.get_zero_point_energy"]], "transportcalculator (class in ase.transport)": [[98, "ase.transport.TransportCalculator"]], "ase.transport": [[98, "module-ase.transport"]], "ase.units": [[99, "module-ase.units"]], "create_units() (in module ase.units)": [[99, "ase.units.create_units"]], "symmetryequivalencecheck (class in ase.utils.structure_comparator)": [[100, "ase.utils.structure_comparator.SymmetryEquivalenceCheck"]], "timer (class in ase.utils.timing)": [[100, "ase.utils.timing.Timer"], [100, "ase.utils.timing.timer"]], "ase.utils": [[100, "module-ase.utils"]], "compare() (ase.utils.structure_comparator.symmetryequivalencecheck method)": [[100, "ase.utils.structure_comparator.SymmetryEquivalenceCheck.compare"]], "convert_string_to_fd() (in module ase.utils)": [[100, "ase.utils.convert_string_to_fd"]], "formula_hill() (in module ase.utils)": [[100, "ase.utils.formula_hill"]], "formula_metal() (in module ase.utils)": [[100, "ase.utils.formula_metal"]], "opencew() (in module ase.utils)": [[100, "ase.utils.opencew"]], "plural() (in module ase.utils)": [[100, "ase.utils.plural"]], "seterr() (in module ase.utils)": [[100, "ase.utils.seterr"]], "workdir() (in module ase.utils)": [[100, "ase.utils.workdir"]], "infrared (class in ase.vibrations)": [[102, "ase.vibrations.Infrared"]], "get_spectrum() (ase.vibrations.infrared method)": [[102, "ase.vibrations.Infrared.get_spectrum"]], "write_spectra() (ase.vibrations.infrared method)": [[102, "ase.vibrations.Infrared.write_spectra"]], "vibrations (class in ase.vibrations)": [[103, "ase.vibrations.Vibrations"]], "ase.vibrations": [[103, "module-ase.vibrations"]], "clean() (ase.vibrations.vibrations method)": [[103, "ase.vibrations.Vibrations.clean"]], "combine() (ase.vibrations.vibrations method)": [[103, "ase.vibrations.Vibrations.combine"]], "fold() (ase.vibrations.vibrations method)": [[103, "ase.vibrations.Vibrations.fold"]], "get_energies() (ase.vibrations.vibrations method)": [[103, "ase.vibrations.Vibrations.get_energies"]], "get_frequencies() (ase.vibrations.vibrations method)": [[103, "ase.vibrations.Vibrations.get_frequencies"]], "get_mode() (ase.vibrations.vibrations method)": [[103, "ase.vibrations.Vibrations.get_mode"]], "get_vibrations() (ase.vibrations.vibrations method)": [[103, "ase.vibrations.Vibrations.get_vibrations"]], "iterdisplace() (ase.vibrations.vibrations method)": [[103, "ase.vibrations.Vibrations.iterdisplace"]], "iterimages() (ase.vibrations.vibrations method)": [[103, "ase.vibrations.Vibrations.iterimages"]], "run() (ase.vibrations.vibrations method)": [[103, "ase.vibrations.Vibrations.run"]], "split() (ase.vibrations.vibrations method)": [[103, "ase.vibrations.Vibrations.split"]], "write_dos() (ase.vibrations.vibrations method)": [[103, "ase.vibrations.Vibrations.write_dos"]], "write_jmol() (ase.vibrations.vibrations method)": [[103, "ase.vibrations.Vibrations.write_jmol"]], "write_mode() (ase.vibrations.vibrations method)": [[103, "ase.vibrations.Vibrations.write_mode"]], "resonantramancalculator (class in ase.vibrations.resonant_raman)": [[104, "ase.vibrations.resonant_raman.ResonantRamanCalculator"]], "ngldisplay (class in ase.visualize.ngl)": [[106, "ase.visualize.ngl.NGLDisplay"]], "ase.visualize": [[106, "module-ase.visualize"]], "ase.visualize.mlab": [[106, "module-ase.visualize.mlab"]], "ase.visualize.nglview": [[106, "module-ase.visualize.nglview"]], "custom_colors() (ase.visualize.ngl.ngldisplay method)": [[106, "ase.visualize.ngl.NGLDisplay.custom_colors"]], "plot() (in module ase.visualize.mlab)": [[106, "ase.visualize.mlab.plot"]], "view() (in module ase.visualize)": [[106, "ase.visualize.view"]], "view_ngl() (in module ase.visualize.ngl)": [[106, "ase.visualize.ngl.view_ngl"]], "xrdebye (class in ase.utils.xrdebye)": [[107, "ase.utils.xrdebye.XrDebye"]], "ase.utils.xrdebye": [[107, "module-ase.utils.xrdebye"]], "calc_pattern() (ase.utils.xrdebye.xrdebye method)": [[107, "ase.utils.xrdebye.XrDebye.calc_pattern"]], "get() (ase.utils.xrdebye.xrdebye method)": [[107, "ase.utils.xrdebye.XrDebye.get"]], "get_waasmaier() (ase.utils.xrdebye.xrdebye method)": [[107, "ase.utils.xrdebye.XrDebye.get_waasmaier"]], "plot_pattern() (ase.utils.xrdebye.xrdebye method)": [[107, "ase.utils.xrdebye.XrDebye.plot_pattern"]], "set_damping() (ase.utils.xrdebye.xrdebye method)": [[107, "ase.utils.xrdebye.XrDebye.set_damping"]], "write_pattern() (ase.utils.xrdebye.xrdebye method)": [[107, "ase.utils.xrdebye.XrDebye.write_pattern"]], "command line tools": [[108, "index-0"]], "calculator (class in ase.calculators.calculator)": [[111, "ase.calculators.calculator.Calculator"]], "fileiocalculator (class in ase.calculators.calculator)": [[111, "ase.calculators.calculator.FileIOCalculator"]], "band_structure() 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