qzhu2017 / PyXtal

A code to generate atomic structure with symmetry
MIT License
234 stars 59 forks source link

Error in pyxtal.symmetry module #214

Closed ignaspakamore closed 1 year ago

ignaspakamore commented 1 year ago

When running the following code for certain space group numbers an error is returned:

>>> from pyxtal.symmetry import Group
>>> g = Group(int)
>>> g
-- Spacegroup --# 64 (Cmce)--
16g site symm: 1
8f  site symm: m..
8e  site symm: .2.
8d  site symm: 2..
8c  site symm: -1
4b  site symm: 2/m..
4a  site symm: 2/m..
Traceback (most recent call last):
  File "/Users/ignaspakamore/miniconda3/lib/python3.9/site-packages/pyxtal-0.5.6-py3.9.egg/pyxtal/symmetry.py", line 297, in __str__
    return self.string
AttributeError: 'Group' object has no attribute 'string'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/ignaspakamore/miniconda3/lib/python3.9/site-packages/pyxtal-0.5.6-py3.9.egg/pyxtal/symmetry.py", line 312, in __repr__
    return str(self)
  File "/Users/ignaspakamore/miniconda3/lib/python3.9/site-packages/pyxtal-0.5.6-py3.9.egg/pyxtal/symmetry.py", line 303, in __str__
    ops = ss_string_from_ops(wp.symmetry[0], self.number, dim=self.dim)
  File "/Users/ignaspakamore/miniconda3/lib/python3.9/site-packages/pyxtal-0.5.6-py3.9.egg/pyxtal/symmetry.py", line 2691, in ss_string_from_ops
    if np.isclose(abs(np.dot(opa.axis, axis)), 1):
  File "<__array_function__ internals>", line 180, in dot
TypeError: unsupported operand type(s) for *: 'NoneType' and 'float'

It seems that it doesn't run for a certain set of space groups: 143 146 147 148 149 150 152 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194

qzhu2017 commented 1 year ago

When running the following code for certain space group numbers an error is returned:


>>> from pyxtal.symmetry import Group

>>> g = Group(int)

>>> g

-- Spacegroup --# 64 (Cmce)--

16g site symm: 1

8f  site symm: m..

8e  site symm: .2.

8d  site symm: 2..

8c  site symm: -1

4b  site symm: 2/m..

4a  site symm: 2/m..

Traceback (most recent call last):

  File "/Users/ignaspakamore/miniconda3/lib/python3.9/site-packages/pyxtal-0.5.6-py3.9.egg/pyxtal/symmetry.py", line 297, in __str__

    return self.string

AttributeError: 'Group' object has no attribute 'string'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

  File "<stdin>", line 1, in <module>

  File "/Users/ignaspakamore/miniconda3/lib/python3.9/site-packages/pyxtal-0.5.6-py3.9.egg/pyxtal/symmetry.py", line 312, in __repr__

    return str(self)

  File "/Users/ignaspakamore/miniconda3/lib/python3.9/site-packages/pyxtal-0.5.6-py3.9.egg/pyxtal/symmetry.py", line 303, in __str__

    ops = ss_string_from_ops(wp.symmetry[0], self.number, dim=self.dim)

  File "/Users/ignaspakamore/miniconda3/lib/python3.9/site-packages/pyxtal-0.5.6-py3.9.egg/pyxtal/symmetry.py", line 2691, in ss_string_from_ops

    if np.isclose(abs(np.dot(opa.axis, axis)), 1):

  File "<__array_function__ internals>", line 180, in dot

TypeError: unsupported operand type(s) for *: 'NoneType' and 'float'

It seems that it doesn't run for a certain set of space groups:

143

146

147

148

149

150

152

154

155

156

157

158

159

160

161

162

163

164

165

166

167

168

173

174

175

176

177

178

179

180

181

182

183

184

185

186

187

188

189

190

191

192

193

194

Sorry for the late reply. This error is probably due to recent change. I will resolve it and get back to you asap.