Add new params and add define statements
This commit is contained in:
rasmusvt
parent
4fd68eab55
commit
006cddaaa3
1 changed files with 88 additions and 11 deletions
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@ -16,7 +16,7 @@ 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', 'start', 'finish', 'exclude']
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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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default_options = {
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'filename': 'start.inp',
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@ -27,10 +27,12 @@ def make_initial_inp(data: dict, options={}):
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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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'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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'exlude': [] # Excluded regions. List of lists.
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'exclude': [] # Excluded regions. List of lists.
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}
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options = aux.update_options(options=options, required_options=required_options, default_options=default_options)
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@ -70,6 +72,23 @@ 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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with open(options['filename'], 'r') as fin:
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lines = []
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for statement in data['define_statements']:
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lines.append(f'\'#define {statement}\n')
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lines.append('\n')
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lines += fin.readlines()
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with open(options['filename'], 'w') as fout:
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for line in lines:
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fout.write(line)
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def write_xdd(fout, data, options):
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@ -108,7 +127,13 @@ def write_xdd(fout, data, options):
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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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fout.write('\t'+snippets['zero_error']+'\n')
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if options['th2_offset']:
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fout.write('\n')
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for line in snippets['th2_offset']:
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fout.write('\t'+line+'\n')
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else:
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fout.write('\t'+snippets['zero_error']+'\n')
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if options['capillary']:
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fout.write('\n')
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@ -139,6 +164,9 @@ def write_xdd(fout, data, options):
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def write_params(fout, data, options, index=0):
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# List to include #define-statements at top of INP-file
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data['define_statements'] = []
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atoms = read_cif(data['str'][index])
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if 'labels' in data.keys():
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label = data['labels'][index]
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@ -161,6 +189,7 @@ def write_params(fout, data, options, index=0):
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# WRITE LATTICE PARAMETERS
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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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@ -228,6 +257,12 @@ def write_params(fout, data, options, index=0):
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def write_str(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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atoms = read_cif(data['str'][index])
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if 'labels' in data.keys():
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label = data['labels'][index]
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@ -256,18 +291,24 @@ def write_str(fout, data, options, index=0):
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fout.write('\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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fout.write('\t\t'+snippets['fit_peak_width']+'\n\n')
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fout.write(f'\t\t#ifdef crystallite_size_gaussian_{label}\n')
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data['define_statements'].append(f'crystallite_size_gaussian_{label}')
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fout.write(f'\t\tCS_G(csgc_{label}_XXXX)\n')
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fout.write('\t\t#endif\n')
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fout.write(f'\t\t#ifdef crystallite_size_lorentzian_{label}\n')
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data['define_statements'].append(f'crystallite_size_lorentzian_{label}')
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fout.write(f'\t\tCS_L(cslc_{label}_XXXX)\n')
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fout.write('\t\t#endif\n\n')
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fout.write(f'\t\t#ifdef strain_gaussian_{label}\n')
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data['define_statements'].append(f'strain_gaussian_{label}')
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fout.write(f'\t\tStrain_G(sgc_{label}_XXXX)\n')
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fout.write('\t\t#endif\n')
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fout.write(f'\t\t#ifdef strain_lorentzian_{label}\n')
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data['define_statements'].append(f'strain_lorentzian_{label}')
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fout.write(f'\t\tStrain_L(slc_{label}_XXXX)\n')
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fout.write('\t\t#endif\n\n')
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@ -277,10 +318,16 @@ def write_str(fout, data, options, index=0):
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for atom in atoms['atoms'].keys():
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specie = '{}{}'.format(
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if 'oxidation_states' in data.keys():
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specie = '{}{}'.format(
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atoms["atoms"][atom]["_atom_site_type_symbol"],
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data['oxidation_states'][index][atoms["atoms"][atom]["_atom_site_type_symbol"]]
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)
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)
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else:
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specie = '{}'.format(
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atoms["atoms"][atom]["_atom_site_type_symbol"]
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)
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site = f'site {atom}'
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x = f'\t\tx = x_{atom}_{label}'
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@ -317,11 +364,11 @@ 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"]}/{label}_XXXX_riet.xy)\n')
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fout.write(f'\t\tOut_CIF_STR({options["save_dir"]}/{label}_XXXX.cif)\n')
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fout.write(f'\t\tOut_CIF_ADPs({options["save_dir"]}/{label}_XXXX.cif)\n')
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fout.write(f'\t\tOut_CIF_Bonds_Angles({options["save_dir"]}/{label}_XXXX.cif)\n')
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fout.write(f'\t\tCreate_hklm_d_Th2_Ip_file({options["save_dir"]}/{label}_XXXX_hkl.dat)\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('\n')
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@ -381,6 +428,20 @@ def write_output(fout, data, options, index=0):
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fout.write('\n')
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fout.write('\t\tOut_String("\\n")\n')
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if options['fit_peak_width']:
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fout.write(f'out {options["save_dir"]}/{filename}_peak_width.dat\n')
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fout.write('\t\tOut_String("prm !ad = \t\t")\n')
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fout.write('\t\tOut(ad)')
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fout.write('\tOut_String(";\\n")\n')
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fout.write('\t\tOut_String("prm !bd = \t\t")\n')
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fout.write('\t\tOut(bd)')
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fout.write('\tOut_String(";\\n")\n')
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fout.write('\t\tOut_String("prm !cd = \t\t")\n')
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fout.write('\t\tOut(cd)')
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fout.write('\tOut_String(";")\n')
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fout.write('#endif')
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fout.write('\n\n')
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@ -785,7 +846,23 @@ def refine(data: dict, options={}):
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def read_results(path):
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results = pd.read_csv(path, delim_whitespace=True, index_col=0)
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results = pd.read_csv(path, delim_whitespace=True, index_col=0, header=None)
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atoms = int((results.shape[1] - 15) / 5)
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headers = [
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'r_wp', 'r_exp', 'r_p', 'r_p_dash', 'r_exp_dash', 'gof',
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'vol', 'mass', 'wp',
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'a', 'b', 'c', 'alpha', 'beta', 'gamma',
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]
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labels = ['x', 'y', 'z', 'occ', 'beq']
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for i in range(atoms):
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for label in labels:
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headers.append(f'atom_{i+1}_{label}')
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results.columns = headers
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return results
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