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Commit ad1dd9dd authored by Lauri Himanen's avatar Lauri Himanen
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Added new module for constants. Contains e.g. custom atomic masses that are neeed by normalizers.

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4 merge requests!115V0.8.0 beta,!113V0.8.0,!103Merging Encyclopedia functionality with v0.8.0,!102First version of EncyclopediaNormalizer
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nomad/constants.py 0 → 100644
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View file @ ad1dd9dd
# Copyright 2018 Markus Scheidgen
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an"AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
import numpy as np
# List of atomic masses (natural isotope dist.) in order, atomic mass units.
# These custom mass definitions are used because the ones provided by ASE are not
# as complete. Origin: phonopy-1.11.2.25.tar.gz:phonopy/structure/atoms.py:atom_data
NUMBER_TO_MASS_MAP_AMU = np.array([
np.nan, # 0
1.00794, # 1
4.002602, # 2
6.941, # 3
9.012182, # 4
10.811, # 5
12.0107, # 6
14.0067, # 7
15.9994, # 8
18.9984032, # 9
20.1797, # 10
22.98976928, # 11
24.3050, # 12
26.9815386, # 13
28.0855, # 14
30.973762, # 15
32.065, # 16
35.453, # 17
39.948, # 18
39.0983, # 19
40.078, # 20
44.955912, # 21
47.867, # 22
50.9415, # 23
51.9961, # 24
54.938045, # 25
55.845, # 26
58.933195, # 27
58.6934, # 28
63.546, # 29
65.38, # 30
69.723, # 31
72.64, # 32
74.92160, # 33
78.96, # 34
79.904, # 35
83.798, # 36
85.4678, # 37
87.62, # 38
88.90585, # 39
91.224, # 40
92.90638, # 41
95.96, # 42
98.9062, # 43 - NIST
101.07, # 44
102.90550, # 45
106.42, # 46
107.8682, # 47
112.411, # 48
114.818, # 49
118.710, # 50
121.760, # 51
127.60, # 52
126.90447, # 53
131.293, # 54
132.9054519, # 55
137.327, # 56
138.90547, # 57
140.116, # 58
140.90765, # 59
144.242, # 60
145, # 61 most stable isotope
150.36, # 62
151.964, # 63
157.25, # 64
158.92535, # 65
162.500, # 66
164.93032, # 67
167.259, # 68
168.93421, # 69
173.054, # 70
174.9668, # 71
178.49, # 72
180.94788, # 73
183.84, # 74
186.207, # 75
190.23, # 76
192.217, # 77
195.084, # 78
196.966569, # 79
200.59, # 80
204.3833, # 81
207.2, # 82
208.98040, # 83
209, # 84 - NIST
210, # 85 - NIST
222, # 86 - NIST
223, # 87 - NIST
226, # 88 - NIST
227, # 89 - NIST
232.03806, # 90
231.03588, # 91
238.02891, # 92
237, # 93 - NIST
244, # 94 - NIST
243, # 95 - most stable isotope
247, # 96 - most stable isotope
247, # 97 - most stable isotope
251, # 98 - most stable isotope
252, # 99 - most stable isotope
257, # 100 - most stable isotope
258, # 101 - most stable isotope
259, # 102 - most stable isotope
262, # 103 - most stable isotope
261, # 104 - most stable isotope
262, # 105 - most stable isotope
266, # 106 - most stable isotope
264, # 107 - most stable isotope
277, # 108 - most stable isotope
268, # 109 - most stable isotope
281, # 110
282, # 111
285, # 112
286, # 113
289, # 114
290, # 115
293, # 116
294, # 117
294, # 118
])
NUMBER_TO_MASS_MAP_AMU.flags.writeable = False
# List of atomic masses (natural isotope dist.) in order, SI units (kg)
NUMBER_TO_MASS_MAP_KG = NUMBER_TO_MASS_MAP_AMU * 1.6605389e-27
NUMBER_TO_MASS_MAP_KG.flags.writeable = False
nomad/normalizing/structure.py
+ 7
− 136
View file @ ad1dd9dd
...@@ -15,6 +15,8 @@ ...@@ -15,6 +15,8 @@
from typing import Dict from typing import Dict
import numpy as np import numpy as np
from nomad.constants import NUMBER_TO_MASS_MAP_KG
def get_summed_atomic_mass(atomic_numbers: np.ndarray) -> float: def get_summed_atomic_mass(atomic_numbers: np.ndarray) -> float:
"""Calculates the summed atomic mass for the given atomic numbers. """Calculates the summed atomic mass for the given atomic numbers.
...@@ -26,8 +28,7 @@ def get_summed_atomic_mass(atomic_numbers: np.ndarray) -> float: ...@@ -26,8 +28,7 @@ def get_summed_atomic_mass(atomic_numbers: np.ndarray) -> float:
The atomic mass in kilograms. The atomic mass in kilograms.
""" """
# It is assumed that the atomic numbers are valid at this point. # It is assumed that the atomic numbers are valid at this point.
masses = np.array(number_to_mass_map) mass = np.sum(NUMBER_TO_MASS_MAP_KG[atomic_numbers])
mass = np.sum(masses[atomic_numbers])
return mass return mass
...@@ -62,12 +63,12 @@ def get_lattice_parameters(normalized_cell: np.ndarray) -> np.ndarray: ...@@ -62,12 +63,12 @@ def get_lattice_parameters(normalized_cell: np.ndarray) -> np.ndarray:
"""Calculate the lattice parameters for the normalized cell. """Calculate the lattice parameters for the normalized cell.
Args: Args:
normalized_cell: The normalized cell as a 2D array. Each row is a basis normalized_cell: The normalized cell as a 3x3 array. Each row is a
vector. basis vector.
Returns: Returns:
Six parameters a, b, c, alpha, beta, gamma (in this order) as a numpy array. Six parameters a, b, c, alpha, beta, gamma (in this order) as a numpy
Here is an explanation of each parameter: array. Here is an explanation of each parameter:
a = length of first basis vector a = length of first basis vector
b = length of second basis vector b = length of second basis vector
...@@ -95,133 +96,3 @@ def get_lattice_parameters(normalized_cell: np.ndarray) -> np.ndarray: ...@@ -95,133 +96,3 @@ def get_lattice_parameters(normalized_cell: np.ndarray) -> np.ndarray:
alpha, beta, gamma = np.arccos(angles) alpha, beta, gamma = np.arccos(angles)
return [a, b, c, alpha, beta, gamma] return [a, b, c, alpha, beta, gamma]
"""List of atomic masses (natural isotope dist.) in order, atomic mass units.
origin: phonopy-1.11.2.25.tar.gz:phonopy/structure/atoms.py:atom_data
"""
number_to_mass_map_amu = np.array([
np.nan, # 0
1.00794, # 1
4.002602, # 2
6.941, # 3
9.012182, # 4
10.811, # 5
12.0107, # 6
14.0067, # 7
15.9994, # 8
18.9984032, # 9
20.1797, # 10
22.98976928, # 11
24.3050, # 12
26.9815386, # 13
28.0855, # 14
30.973762, # 15
32.065, # 16
35.453, # 17
39.948, # 18
39.0983, # 19
40.078, # 20
44.955912, # 21
47.867, # 22
50.9415, # 23
51.9961, # 24
54.938045, # 25
55.845, # 26
58.933195, # 27
58.6934, # 28
63.546, # 29
65.38, # 30
69.723, # 31
72.64, # 32
74.92160, # 33
78.96, # 34
79.904, # 35
83.798, # 36
85.4678, # 37
87.62, # 38
88.90585, # 39
91.224, # 40
92.90638, # 41
95.96, # 42
98.9062, # 43 - NIST
101.07, # 44
102.90550, # 45
106.42, # 46
107.8682, # 47
112.411, # 48
114.818, # 49
118.710, # 50
121.760, # 51
127.60, # 52
126.90447, # 53
131.293, # 54
132.9054519, # 55
137.327, # 56
138.90547, # 57
140.116, # 58
140.90765, # 59
144.242, # 60
145, # 61 most stable isotope
150.36, # 62
151.964, # 63
157.25, # 64
158.92535, # 65
162.500, # 66
164.93032, # 67
167.259, # 68
168.93421, # 69
173.054, # 70
174.9668, # 71
178.49, # 72
180.94788, # 73
183.84, # 74
186.207, # 75
190.23, # 76
192.217, # 77
195.084, # 78
196.966569, # 79
200.59, # 80
204.3833, # 81
207.2, # 82
208.98040, # 83
209, # 84 - NIST
210, # 85 - NIST
222, # 86 - NIST
223, # 87 - NIST
226, # 88 - NIST
227, # 89 - NIST
232.03806, # 90
231.03588, # 91
238.02891, # 92
237, # 93 - NIST
244, # 94 - NIST
243, # 95 - most stable isotope
247, # 96 - most stable isotope
247, # 97 - most stable isotope
251, # 98 - most stable isotope
252, # 99 - most stable isotope
257, # 100 - most stable isotope
258, # 101 - most stable isotope
259, # 102 - most stable isotope
262, # 103 - most stable isotope
261, # 104 - most stable isotope
262, # 105 - most stable isotope
266, # 106 - most stable isotope
264, # 107 - most stable isotope
277, # 108 - most stable isotope
268, # 109 - most stable isotope
281, # 110
282, # 111
285, # 112
286, # 113
289, # 114
290, # 115
293, # 116
294, # 117
294, # 118
])
"""List of atomic masses (natural isotope dist.) in order, SI units (kg)"""
number_to_mass_map = number_to_mass_map_amu * 1.6605389e-27
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