Feature request: Custom atom form factors #32

Activity

1. DanPorter commented on Apr 28, 2025

   

   DanPorter

   on Apr 28, 2025

   OwnerAuthor

   More actions

   You could probably hack the current code by adding  your pseudo-atom name to ELEMENT_LIST, then adding the parameters to for this to "data/Dans Element Properties.txt" and "data/atomic_scattering_factors.npy".

   The following untested code should be roughly right:

   """
   Dans_Diffraction example
   Alter the element properties files
   
   14/4/2025
   """
   import os
   import numpy as np
   import Dans_Diffraction as dif
   from Dans_Diffraction.functions_crystallography import ATOMFILE, datadir
   
   
   # 1. Add pseudo-atom label to ELEMENT_LIST in functions_crystallography.py:
   #    'c', 'i', 'p', 'h', 's', 'n', 'o',
   #    'D', 'd',  # add Deuterium
   #    'ClO',  # this must match other labels for this atom below.
   #]
   
   # 2. Edit Element Properties
   print(f"Location of element properties file: {ATOMFILE}")
   
   # all of these parameters must be filled in, but most don't need to mean anything
   new_properties = {
       'Z': 27,
       'Element': 'ClO',  # this one is used to select the atom
       'Name': 'myClO4',  # this one will be printed
       'Group': 9,
       'Period': 4,
       'Block': 'd',
       'ValenceE': 2,
       'Config': '1s2.2s2.2p6.3s2.3p6.3d7.4s2',
       'Radii': 135.,
       'Weight': 58.9332,
       'Coh_b': 2.49,  # used for neutron scattering
       'Inc_b': -6.2,
       'Nabs': 37.18,
       'Nscat': 5.6,
       'a1': 12.2841,  # a1-c are used for x-ray scattering, if unsure, put a1==sum(Z) and the rest to zero.
       'b1': 4.2791,
       'a2': 7.3409,
       'b2': 0.2784,
       'a3': 4.0034,
       'b3': 13.5359,
       'a4': 2.3488,
       'b4': 71.1692,
       'c': 1.0118,
       'j0_A': 0.4139,
       'j0_a': 16.1616,
       'j0_B': 0.6013,
       'j0_b': 4.7805,
       'j0_C': -0.1518,
       'j0_c': 0.021,
       'j0_D': 0.1345,
       'K': 7.709,
       'L1': 0.925,
       'L2': 0.793,
       'L3': 0.778,
       'M1': 0.101,
       'M2': 0.059,
       'M3': 0.06,
       'M4': 0.,
       'M5': 0.,
       'N1': 0.,
       'N2': 0.,
       'N3': 0.,
   }
   
   # edit atom file
   with open(ATOMFILE, 'r') as f:
       atomfile_str = f.read()
   
   # make a backup
   backup = ATOMFILE.replace('.txt', '_backup.txt')
   if not os.path.isfile(backup):
       with open(backup, 'w') as f:
           f.write(atomfile_str)
   
   # add extra line
   atomfile_str += ' '.join(new_properties.values()) + '\n'
   with open(ATOMFILE, 'w') as f:
       f.write(atomfile_str)
   
   
   # 3. add values to atomic scattering factors file
   asf_file = os.path.join(datadir, 'atomic_scattering_factors.npy')
   asf = np.load(asf_file, allow_pickle=True)
   asf = asf.item()
   
   # make a backup
   asf_backup = asf_file.replace('.npy', '_backup.npy')
   if not os.path.isfile(backup):
       np.save(asf_backup, asf, allow_pickle=True)
   
   new_asf = {
       'Z': 27,
       'energy': [10.0, 10.1, 30000.0],  # energy values in eV
       'f1': [1, 1, 1],  # all lists should be the same length. Typically, about 500 values
       'f2': [0, 0, 0],
   }
   
   # add extra line
   asf['ClO'] = new_asf  # should have the same name as 'Element' above
   np.save(asf, asf, allow_pickle=True)
   
   
   # 4. Make new crystal
   xtl = dif.Crystal()
   xtl.Atoms.addatom(0, 0, 0, 'ClO')
   xtl.generate_structure()
   
   print(xtl)  # if all goes well - this will work!
2. DanPorter

   self-assigned this

   on Apr 28, 2025
3. DanPorter commented on Aug 9, 2025

   

   DanPorter

   on Aug 9, 2025

   OwnerAuthor

   More actions

   Added custom form factor functions in current feature branch: adbeb52

   Example usage:

   import numpy as np
   import Dans_Diffraction as dif
   
   xtl = dif.Crystal('file.cif')
   
   # add custom element 
   name = 'Co3+'
   # custom analytical coefficients for the form factor (a1, b1, a2, b2, a3, b3, a4, b4, c, 0)
   coefs = (12.2841,  4.5791,  7.4409,  0.6784,  4.2034, 12.5359,  2.2488, 72.1692,  1.1118,  0.)
   # custom dispersion corrections as a table of [energy_kev, f1, f2]
   # the dispersion corrections are only used when calculating structure factors with energy defined
   table = np.array([
       [7.7, 7.71, 7.72, 7.73, 7.74, 7.75, 7.76, 7.77, 7.78, 7.79],  # keV
       [-9.6866, -11.0362, -10.1969, -9.3576, -8.5184, -7.6791, -6.8398, -6.0005, -5.1613, -4.322],  # f1
       [-0.4833, -3.7933, -3.7862, -3.7791, -3.772, -3.765, -3.7579, -3.7508, -3.7437, -3.7367]  # f2
   ])
   # add the new element to the internal table (this is lost when python is closed)
   dif.fc.add_custom_form_factor_coefs(name, *coefs, dispersion_table=table)
   # Change one of the atoms in the crystal to the new atom
   xtl.Structure.changeatom(3, type=name)
   
   # Calculate custom structure factors
   en = np.arange(7.7, 7.8, 0.01)  # this must be within the range of the table
   ref = [0, 0, 3]
   inten = xtl.Scatter.intensity(ref, 'custom', energy_kev=en)
4. DanPorter

   linked a pull request that will close this issue32 feature request custom atom form factors #34on Aug 22, 2025
5. DanPorter

   closed this as completedin #34on Sep 15, 2025