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1"""Module to read and write atoms in xtl file format for the prismatic and

2computem software.

4See https://prism-em.com/docs-inputs for an example of this format and the

5documentation of prismatic.

7See https://sourceforge.net/projects/computem/ for the source code of the

8computem software.

9"""

11import numpy as np

13from ase.atoms import Atoms, symbols2numbers

15from .utils import verify_cell_for_export, verify_dictionary

20 r"""Import prismatic and computem xyz input file as an Atoms object.

22 Reads cell, atom positions, occupancies and Debye Waller factor.

23 The occupancy values and the Debye Waller factors are obtained using the

24 get_array method and the occupancies and debye_waller_factors keys,

25 respectively. The root means square (RMS) values from the

26 prismatic/computem xyz file are converted to Debye-Waller factors (B) in Å²

27 by:

29 .. math::

31 B = RMS^2 * 8\pi^2

33 """

37 # Read unit cell parameters:

38 cellpar = [float(i) for i in fd.readline().split()]

40 # Read all data at once

43 # Convert from RMS to Debye-Waller factor

44 RMS = read_data[:, 5]**2 * 8 * np.pi**2

48 cell=cellpar,

49 )

51 atoms.set_array('debye_waller_factors', RMS)

53 return atoms

56class XYZPrismaticWriter:

57 """ See the docstring of the write_prismatic function.

58 """

60 def __init__(self, atoms, debye_waller_factors=None, comments=None):

61 verify_cell_for_export(atoms.get_cell())

63 self.atoms = atoms.copy()

64 self.atom_types = set(atoms.symbols)

67 self.occupancies = self._get_occupancies()

68 debye_waller_factors = self._get_debye_waller_factors(

69 debye_waller_factors)

70 self.RMS = np.sqrt(debye_waller_factors / (8 * np.pi**2))

72 def _get_occupancies(self):

73 if 'occupancies' in self.atoms.arrays:

74 occupancies = self.atoms.get_array('occupancies', copy=False)

75 else:

76 occupancies = np.ones_like(self.atoms.numbers)

78 return occupancies

80 def _get_debye_waller_factors(self, DW):

81 if np.isscalar(DW):

82 if len(self.atom_types) > 1:

83 raise ValueError('This cell contains more then one type of '

84 'atoms and the Debye-Waller factor needs to '

85 'be provided for each atom using a '

86 'dictionary.')

87 DW = np.ones_like(self.atoms.numbers) * DW

88 elif isinstance(DW, dict):

89 verify_dictionary(self.atoms, DW, 'DW')

90 # Get the arrays of DW from mapping the DW defined by symbol

91 DW = {symbols2numbers(k)[0]: v for k, v in DW.items()}

92 DW = np.vectorize(DW.get)(self.atoms.numbers)

93 else:

94 for name in ['DW', 'debye_waller_factors']:

95 if name in self.atoms.arrays:

96 DW = self.atoms.get_array(name)

98 if DW is None:

99 raise ValueError('Missing Debye-Waller factors. It can be '

100 'provided as a dictionary with symbols as key or '

101 'can be set for each atom by using the '

102 'set_array("debye_waller_factors", values) of '

103 'the Atoms object.')

105 return DW

108 # 1st line: comment line

110 s = "{0} atoms with chemical formula: {1}.".format(

111 len(self.atoms),

112 self.atoms.get_chemical_formula())

113 else:

116 s = s.strip()

117 s += " generated by the ase library.\n"

118 # 2nd line: lattice parameter

119 s += "{} {} {}".format(

120 *self.atoms.cell.cellpar()[:3])

122 return s

124 def write_to_file(self, f):

125 data_array = np.vstack((self.atoms.numbers,

126 self.atoms.positions.T,

127 self.occupancies,

128 self.RMS)

129 ).T

131 np.savetxt(fname=f,

132 X=data_array,

133 fmt='%.6g',

135 newline='\n',

136 footer='-1',

138 )

141def write_prismatic(fd, *args, **kwargs):

142 r"""Write xyz input file for the prismatic and computem software. The cell

143 needs to be orthorhombric. If the cell contains the occupancies and

144 debye_waller_factors arrays (see the set_array method to set them),

145 these array will be written to the file.

146 If the occupancies is not specified, the default value will be set to 0.

148 Parameters:

150 atoms: Atoms object

152 debye_waller_factors: float or dictionary of float or None (optional).

153 If float, set this value to all

154 atoms. If dictionary, each atom needs to specified with the symbol as

155 key and the corresponding Debye-Waller factor as value.

156 If None, the debye_waller_factors array of the Atoms object needs to

157 be set (see the set_array method to set them), otherwise raise a

158 ValueError. Since the prismatic/computem software use root means square

159 (RMS) displacements, the Debye-Waller factors (B) needs to be provided

160 in Å² and these values are converted to RMS displacement by:

162 .. math::

164 RMS = \sqrt{\frac{B}{8\pi^2}}

166 Default is None.

168 comment: str (optional)

169 Comments to be written in the first line of the file. If not

170 provided, write the total number of atoms and the chemical formula.

172 """

174 writer = XYZPrismaticWriter(*args, **kwargs)

175 writer.write_to_file(fd)