Add a bunch of stuff to refinement
This commit is contained in:
rasmusvt
parent
83f4f6a155
commit
f1ec9df9b4
2 changed files with 202 additions and 27 deletions
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@ -16,19 +16,25 @@ import nafuma.auxillary as aux
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def make_initial_inp(data: dict, options={}):
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required_options = ['filename', 'overwrite', 'include', 'save_results', 'save_dir', 'topas_options', 'background', 'capillary', 'th2_offset', 'fit_peak_width', 'start', 'finish', 'exclude']
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required_options = ['filename', 'overwrite', 'include', 'save_results', 'save_dir', 'instrument', 'topas_options', 'background', 'capillary', 'th2_offset', 'fit_peak_width', 'simple_axial_model', 'TCHZ_Peak_Type', 'start', 'finish', 'exclude', 'magnetic_atoms', 'radiation', 'magnetic_space_group', 'interval']
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default_options = {
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'filename': 'start.inp',
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'overwrite': False,
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'save_results': False,
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'save_dir': 'results/',
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'instrument': None,
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'radiation': 'synchrotron',
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'magnetic_space_group': None,
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'magnetic_atoms': [],
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'include': [], # Any files that should be included with #include
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'topas_options': {},
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'background': 7,
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'capillary': False,
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'th2_offset': False,
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'fit_peak_width': False,
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'simple_axial_model': False,
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'TCHZ_Peak_Type': False,
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'interval': [None, None], # Start and finish values that TOPAS should refine on. Overrides 'start' and 'finish'
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'start': None, # Start value only. Overridden by 'interval' if this is set.
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'finish': None, # Finish value only. Overridden by 'interval' if this is set.
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@ -72,6 +78,16 @@ def make_initial_inp(data: dict, options={}):
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write_str(fout=fout, data=data, options=options, index=i)
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if 'peak' in data.keys():
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fout.write('\n\'------------------------------------------------------------------------------------------------------------------------------------------\n')
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fout.write('\'PEAK PHASES')
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fout.write('\n\'------------------------------------------------------------------------------------------------------------------------------------------\n')
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write_peaks(fout=fout, data=data, options=options, index=i)
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with open(options['filename'], 'r') as fin:
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lines = []
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@ -124,8 +140,21 @@ def write_xdd(fout, data, options):
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# Write wavelength and LP-factor
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fout.write('\n\n')
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if options['instrument'] == 'RECX2':
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options['radiation'] = 'MoKa'
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for line in snippets['RECX2']:
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fout.write('\t'+line+'\n')
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if options['radiation'] == 'synchrotron':
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fout.write('\t'+snippets['synchrotron'].format(data['wavelength'])+'\n')
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if options['radiation'] == 'neutron':
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fout.write('\t'+snippets['neutron'][0].format(data['wavelength']) +'\n')
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fout.write('\t'+snippets['neutron'][1] + '\n')
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if options['radiation'] == 'MoKa':
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for line in snippets['MoKa']:
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fout.write('\t'+line+'\n')
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fout.write('\t'+snippets['wavelength'].format(data['wavelength'])+'\n')
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fout.write('\t'+snippets['lp_factor'].format(topas_options['lp_factor'])+'\n')
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if options['th2_offset']:
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@ -190,21 +219,21 @@ def write_params(fout, data, options, index=0):
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# If start_values is defined:
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fout.write(f'#ifdef start_values_{label}\n')
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data['define_statements'].append(f'start_values_{label}')
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lpa = f'local !lpa_{label} {a} ;: {a}'
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lpb = f'local !lpb_{label} {b} ;: {b}'
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lpc = f'local !lpc_{label} {c} ;: {c}'
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lpa = f'local !lpa_{label} = {a} ;: {a}'
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lpb = f'local !lpb_{label} = {b} ;: {b}'
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lpc = f'local !lpc_{label} = {c} ;: {c}'
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fout.write('{: <55} {: <55} {: <55}\n'.format(lpa, lpb, lpc))
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lpal = f'local !lpal_{label} {alpha} ;: {alpha}'
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lpbe = f'local !lpbe_{label} {beta} ;: {beta}'
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lpga = f'local !lpga_{label} {gamma} ;: {gamma}'
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lpal = f'local !lpal_{label} = {alpha} ;: {alpha}'
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lpbe = f'local !lpbe_{label} = {beta} ;: {beta}'
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lpga = f'local !lpga_{label} = {gamma} ;: {gamma}'
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fout.write('{: <55} {: <55} {: <55}\n'.format(lpal, lpbe, lpga))
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# Otherwise
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fout.write('\n')
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fout.write('#else\n')
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lpa = f'local !lpa_{label} {a}'
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lpb = f'local !lpb_{label} {b}'
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lpc = f'local !lpc_{label} {c}'
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lpa = f'local !lpa_{label} = {a} ;: {a}'
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lpb = f'local !lpb_{label} = {b} ;: {b}'
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lpc = f'local !lpc_{label} = {c} ;: {c}'
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fout.write('{: <55} {: <55} {: <55}\n'.format(lpa, lpb, lpc))
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lpal = f'local !lpal_{label} {alpha}'
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lpbe = f'local !lpbe_{label} {beta}'
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@ -224,6 +253,7 @@ def write_params(fout, data, options, index=0):
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# WRITE SITE PARAMETERS
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mag = []
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for site in sites:
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params = []
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@ -232,13 +262,30 @@ def write_params(fout, data, options, index=0):
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value = atoms["atoms"][site][attr].split("(")[0]
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value = value if value != '.' else 0.
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params.append('{: <20} {: <20}'.format(f'local !{attrs[attr]}_{site}_{label}', f' = {value} ;: {value}'))
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#fout.write(f'local {attrs[attr]}_{site}_{label}\t\t =\t {value} \t ;= \t\t\t\t\t')
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if options['magnetic_space_group']:
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for mag_atom in options['magnetic_atoms']:
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if mag_atom in site:
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mag.append(site)
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fout.write('{: <55} {: <55} {: <55} {: <55} {: <55}\n'.format(*params))
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fout.write('\n')
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if options['magnetic_space_group']:
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mag = list(dict.fromkeys(mag)) # remove duplicates
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for m in mag:
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fout.write('{: <55} {: <55} {: <55}\n'.format(
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f'local !ml_x_{m}_{label}_XXXX = 0 ;: 0',
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f'local !ml_y_{m}_{label}_XXXX = 0 ;: 0',
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f'local !ml_z_{m}_{label}_XXXX = 0 ;: 0'
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))
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fout.write('\n')
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fout.write('{: <55} {: <55} {: <55} {: <55}\n'.format(
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f'local !csgc_{label}_XXXX = 200 ;: 200',
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f'local !cslc_{label}_XXXX = 200 ;: 200',
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@ -277,7 +324,10 @@ def write_str(fout, data, options, index=0):
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fout.write('\tstr\n')
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fout.write(f'\t\tphase_name "{atoms["_chemical_name_common"]} ({atoms["_space_group_name_H-M_alt"]})"\n'.replace('\'', ''))
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fout.write(f'\t\tspace_group {atoms["_space_group_IT_number"]}\n')
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if options['magnetic_space_group']:
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fout.write(f'\t\tmag_space_group {options["magnetic_space_group"]}\n')
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else:
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fout.write(f'\t\tspace_group {atoms["_space_group_IT_number"]}\n')
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fout.write(f'\t\ta = lpa_{label} ;\n')
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fout.write(f'\t\tb = lpb_{label} ;\n')
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fout.write(f'\t\tc = lpc_{label} ;\n')
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@ -287,8 +337,11 @@ def write_str(fout, data, options, index=0):
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fout.write('\n')
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fout.write(f'\t\tcell_volume\t vol_{label}_XXXX {atoms["_cell_volume"]}\n')
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fout.write(f'\t\tcell_mass\t mass_{label}_XXXX 1\n')
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fout.write(f'\t\tweight_percent\t wp_{label}_XXXX 100\n\n')
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fout.write('\n')
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fout.write(f'\t\tweight_percent\t wp_{label}_XXXX 100\n\n\n')
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if options['simple_axial_model']:
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fout.write(f'\t\t{snippets["Simple_Axial_Model"]}\n')
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if options['TCHZ_Peak_Type']:
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fout.write(f'\t\t{snippets["TCHZ_Peak_Type"]}\n\n\n')
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fout.write('\t\tscale @ 1.0\n')
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fout.write('\t\tr_bragg 1.0\n\n')
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if options['fit_peak_width']:
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@ -342,6 +395,11 @@ def write_str(fout, data, options, index=0):
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fout.write('\t\t{: <9} {: <30}; {: <30}; {: <30}; {: <30}; {: <30};'.format(site, x, y, z, occ, beq))
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fout.write('\n')
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if options['magnetic_space_group']:
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for mag_atom in options['magnetic_atoms']:
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if mag_atom in atom:
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fout.write('\t\t'+snippets['magnetic_moment_str'].format(atom, label, atom, label, atom, label)+'\n')
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if options['save_results']:
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@ -364,11 +422,13 @@ def write_output(fout, data, options, index=0):
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fout.write('#ifdef output\n')
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fout.write(f'\t\tOut_Riet({options["save_dir"]}/{filename}_{label}_XXXX_riet.xy)\n')
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fout.write(f'\t\tOut_CIF_STR({options["save_dir"]}/{filename}_{label}_XXXX.cif)\n')
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fout.write(f'\t\tOut_CIF_ADPs({options["save_dir"]}/{filename}_{label}_XXXX.cif)\n')
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fout.write(f'\t\tOut_CIF_Bonds_Angles({options["save_dir"]}/{filename}_{label}_XXXX.cif)\n')
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fout.write(f'\t\tCreate_hklm_d_Th2_Ip_file({options["save_dir"]}/{filename}_{label}_XXXX_hkl.dat)\n')
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fout.write(f'\t\tOut_Riet({options["save_dir"]}/{filename}_{label}_riet.xy)\n')
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fout.write(f'\t\tOut_CIF_STR({options["save_dir"]}/{filename}_{label}.cif)\n')
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fout.write(f'\t\tOut_CIF_ADPs({options["save_dir"]}/{filename}_{label}.cif)\n')
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fout.write(f'\t\tOut_CIF_Bonds_Angles({options["save_dir"]}/{filename}_{label}.cif)\n')
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fout.write(f'\t\tCreate_hklm_d_Th2_Ip_file({options["save_dir"]}/{filename}_{label}_hkl.dat)\n')
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if options['magnetic_space_group']:
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fout.write(f'\t\tOut_CIF_mag({options["save_dir"]}/{filename}_{label}_magnetic.cif)\n')
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fout.write('\n')
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@ -446,7 +506,26 @@ def write_output(fout, data, options, index=0):
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fout.write('\n\n')
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def write_peaks(fout, data, options, index=0):
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import nafuma.xrd as xrd
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basedir = os.path.dirname(xrd.__file__)
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with open(os.path.join(basedir, 'snippets.json'), 'r') as snip:
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snippets = json.load(snip)
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if not isinstance(data['peak'], list):
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data['peak'] = [data['peak']]
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for peak in data['peak']:
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fout.write('\t'+snippets['peak'][0]+'\n')
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fout.write('\t\t'+snippets['peak'][1].format(peak)+'\n')
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fout.write('\t\t'+snippets['peak'][2]+'\n')
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fout.write('\t\t'+snippets['peak'][3]+'\n')
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fout.write('\t\t'+snippets['peak'][4]+'\n')
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fout.write('\n\n')
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def read_cif(path):
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@ -600,7 +679,7 @@ def make_big_inp(data: dict, options={}):
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aux.backup_file(filename=options['output'], backup_dir=options['backup_dir'])
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runlist = os.path.join(os.path.dirname(options['output']), 'runlist.txt')
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runlist = os.path.abspath(os.path.join(os.path.dirname(options['output']), f'runlist_{os.path.basename(options["output"]).split(".")[0]}.txt'))
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options['include'].append(runlist)
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with open(options['template'], 'r') as template:
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@ -615,6 +694,8 @@ def make_big_inp(data: dict, options={}):
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for i, path in enumerate(data['path']):
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path = os.path.abspath(path)
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s = make_inp_entry(template=template, xdd=path, num=i, options=options)
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output.write(s)
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output.write('\n\n')
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@ -745,6 +826,7 @@ def make_inp_entry(template: str, xdd: str, num: int, options: dict) -> str:
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# Replace diffractogram-path
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s = template.replace(temp_xdd, xdd).replace('XXXX', num_str)
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s = s.replace(os.path.basename(temp_xdd).split('.')[0], os.path.basename(xdd).split('.')[0])
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return s
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@ -867,3 +949,73 @@ def read_results(path):
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return results
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def fix_magnetic_cif(path):
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with open(path, 'r') as f:
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lines = f.readlines()
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for i, line in enumerate(lines):
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if '_magnetic_space_group_symop_operation_timereversal' in line: # last line before symmetry operations
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j = 1
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line = lines[i + j]
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while len(line) > 1:
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lines[i+j] = f'{j} ' + line
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j += 1
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line = lines[i+j]
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with open(path, 'w') as f:
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for line in lines:
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f.write(line)
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def get_magnetic_moment(path):
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with open(path, 'r') as f:
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lines = f.readlines()
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for i, line in enumerate(lines):
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if '_magnetic_atom_site_moment_crystalaxis_mz' in line: # last line before magnetic moments
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j = 1
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line = lines[i+j]
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magnetic_moments = {}
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while line:
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magnetic_moments[line.split()[0]] = (float(line.split()[1]), float(line.split()[2]), float(line.split()[3]))
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j += 1
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if i+j < len(lines):
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line = lines[i+j]
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else:
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break
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return magnetic_moments
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def get_magnetic_moment_magnitude(magmom):
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magnitudes = {}
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for site in magmom.keys():
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magnitudes[site] = np.sqrt(magmom[site][0]**2+magmom[site][1]**2+magmom[site][2]**2)
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return magnitudes
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def strip_labels_from_inp(path, save_path=None):
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if not save_path:
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save_path = path
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with open(path, 'r') as fin:
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lines = fin.readlines()
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for i, line in enumerate(lines):
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lines[i] = line.replace('_XXXX', '')
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with open(save_path, 'w') as fout:
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for line in lines:
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fout.write(line)
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@ -9,13 +9,36 @@
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],
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"gauss_fwhm": "gauss_fwhm = Sqrt({} Cos(2 * Th)^4 + {} Cos(2 * Th)^2 + {});",
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"lp_factor": "LP_Factor({}) 'change the LP correction or lh value if required",
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"wavelength": "lam ymin_on_ymax 0.0001 la 1.0 lo {} lh 0.1",
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"zero_error": "Zero_Error(zero, 0)",
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"synchrotron": "lam ymin_on_ymax 0.0001 la 1.0 lo {} lh 0.1",
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"neutron": [
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"lam ymin_on_ymax 0.0001 la 1.0 lo {} lh 0.5",
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"neutron_data"
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],
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"MoKa":[
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"lam ymin_on_ymax 0.0001",
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"la 0.6533 lo 0.7093 lh 0.2695",
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"la 0.3467 lo 0.713574 lh 0.2795"
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],
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"RECX2": [
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"Rp 280",
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"Rs 280"
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],
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"zero_error": "Zero_Error(!zero, 0)",
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"th2_offset": [
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"prm zero \t\t\t0 \t\t\t\tmin = Max(Val - 20 Yobs_dx_at(X1), -100 Yobs_dx_at(X1)); max = Min(Val + 20 Yobs_dx_at(X2), 100 Yobs_dx_at(X2)); del = .01 Yobs_dx_at(X1); val_on_continue 0",
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"prm cos_shift \t\t0 \t\t\t\tmin = Val-.8; max = Val+.8; del 0.001",
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"prm sin_shift \t\t0 \t\t\t\tmin = Val-.8; max = Val+.8; del 0.001",
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"prm !zero\t\t\t= 0 ;: 0 \t\t\t\tmin = Max(Val - 20 Yobs_dx_at(X1), -100 Yobs_dx_at(X1)); max = Min(Val + 20 Yobs_dx_at(X2), 100 Yobs_dx_at(X2)); del = .01 Yobs_dx_at(X1); val_on_continue 0",
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"prm !cos_shift\t\t= 0 ;: 0 \t\t\t\tmin = Val-.8; max = Val+.8; del 0.001",
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"prm !sin_shift\t\t= 0 ;: 0 \t\t\t\tmin = Val-.8; max = Val+.8; del 0.001",
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"th2_offset = (zero) + (cos_shift) Cos(Th) + (sin_shift) Sin(Th) ;"
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],
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"fit_peak_width": "DC1( ad, 0, bd, 0, cd, 0)"
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"fit_peak_width": "DC1( ad, 0, bd, 0, cd, 0)",
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"TCHZ_Peak_Type": "TCHZ_Peak_Type(pku_1, 0, pkv_1, 0,pkw_1, 0, !pkx_1, 0.0000,pky_1, 0,!pkz_1, 0.0000)",
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"Simple_Axial_Model": "Simple_Axial_Model( axial_1, 0)",
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"magnetic_moment_str": "mlx = ml_x_{}_{}_XXXX ; \t mly = ml_y_{}_{}_XXXX ; \t mlz = ml_z_{}_{}_XXXX ; \t MM_CrystalAxis_Display( 0, 0, 0)",
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"peak": [
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"xo_Is",
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"xo @ {}",
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"peak_type fp",
|
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"LVol_FWHM_CS_G_L( 1, 0, 0.89, 0,,,@, 2)",
|
||||
"I @ 35.35632`"
|
||||
]
|
||||
}
|
||||
Loading…
Add table
Add a link
Reference in a new issue