Add initial INP-generation
This commit is contained in:
rasmusvt
parent
51e2928472
commit
ace44cb48f
3 changed files with 251 additions and 44 deletions
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@ -17,12 +17,13 @@ import nafuma.auxillary as aux
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def make_initial_inp(data: dict, options={}):
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def make_initial_inp(data: dict, options={}):
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required_options = ['filename', 'overwrite', 'include', 'save_results', 'topas_options', 'background', 'capillary', 'start', 'finish', 'exclude']
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required_options = ['filename', 'overwrite', 'include', 'save_results', 'save_dir', 'topas_options', 'background', 'capillary', 'start', 'finish', 'exclude']
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default_options = {
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default_options = {
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'filename': 'start.inp',
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'filename': 'start.inp',
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'overwrite': False,
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'overwrite': False,
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'save_results': False,
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'save_results': False,
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'save_dir': 'results/',
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'include': [], # Any files that should be included with #include
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'include': [], # Any files that should be included with #include
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'topas_options': {},
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'topas_options': {},
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'background': 7,
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'background': 7,
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@ -41,15 +42,34 @@ def make_initial_inp(data: dict, options={}):
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with open(options['filename'], 'w') as fout:
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with open(options['filename'], 'w') as fout:
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write_headers(fout=fout, options=options)
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write_headers(fout=fout, options=options)
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fout.write('\n\'------------------------------------------------------------------------------------------------------------------------------------------\n')
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fout.write('\n\'------------------------------------------------------------------------------------------------------------------------------------------\n')
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fout.write('rw_p 0 r_exp 0 r_p 0 r_wp_dash 0 r_p_dash 0 r_exp_dash 0 weighted_Durbin_Watson 0 gof 0')
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fout.write('\'START OF INP - XXXX')
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fout.write('\n\'------------------------------------------------------------------------------------------------------------------------------------------\n')
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fout.write('\n\'------------------------------------------------------------------------------------------------------------------------------------------\n')
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fout.write('r_wp 0 r_exp 0 r_p 0 r_wp_dash 0 r_p_dash 0 r_exp_dash 0 weighted_Durbin_Watson 0 gof 0')
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fout.write('\n\'------------------------------------------------------------------------------------------------------------------------------------------\n')
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fout.write('\n\'------------------------------------------------------------------------------------------------------------------------------------------\n')
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write_xdd(fout=fout, data=data, options=options)
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write_xdd(fout=fout, data=data, options=options)
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for str in data['str']:
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fout.write('\n\'------------------------------------------------------------------------------------------------------------------------------------------\n')
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fout.write('\'PARAMETER DEFINITONS')
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fout.write('\n\'------------------------------------------------------------------------------------------------------------------------------------------\n')
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for i, str in enumerate(data['str']):
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fout.write('\n\n')
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fout.write('\n\n')
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write_str(fout=fout, str=str, options=options)
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write_params(fout=fout, data=data, options=options, index=i)
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fout.write('\n\'------------------------------------------------------------------------------------------------------------------------------------------\n')
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fout.write('\'STR DEFINITIONS')
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fout.write('\n\'------------------------------------------------------------------------------------------------------------------------------------------\n')
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for i, str in enumerate(data['str']):
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fout.write('\n\n')
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write_str(fout=fout, data=data, options=options, index=i)
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@ -66,6 +86,19 @@ def write_xdd(fout, data, options):
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fout.write(f'xdd "{data["xdd"]}"\n')
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fout.write(f'xdd "{data["xdd"]}"\n')
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fout.write('\t'+snippets['calculation_step'].format(topas_options['convolution_step'])+'\n')
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fout.write('\t'+snippets['calculation_step'].format(topas_options['convolution_step'])+'\n')
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for include in options['include']:
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if 'peak_width' in include:
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with open(include, 'r') as f:
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lines = f.readlines()
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peak_width_params = []
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for line in lines:
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param = line.split()[1][1:]
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peak_width_params.append(param)
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fout.write('\t'+snippets['gauss_fwhm'].format(peak_width_params[0], peak_width_params[1], peak_width_params[2])+'\n')
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# Write background
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# Write background
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fout.write('\tbkg @ ')
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fout.write('\tbkg @ ')
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for i in range(options['background']):
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for i in range(options['background']):
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@ -76,14 +109,15 @@ 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['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['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['capillary']:
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if options['capillary']:
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fout.write('\n')
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fout.write('\n')
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for i, line in enumerate(snippets['capillary']):
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for i, line in enumerate(snippets['capillary']):
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if i == 0:
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if i == 0:
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line.format(topas_options['packing_density'])
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line = line.format(topas_options['packing_density'])
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if i == 1:
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if i == 1:
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line.format(topas_options['capdia'])
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line = line.format(topas_options['capdia'])
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fout.write('\t'+line+'\n')
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fout.write('\t'+line+'\n')
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@ -103,10 +137,19 @@ def write_xdd(fout, data, options):
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def write_str(fout, str, options):
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def write_params(fout, data, options, index=0):
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atoms = read_cif(str)
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print(atoms["atoms"]["Fe1"].keys())
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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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else:
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label = index
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fout.write('\n\'------------------------------------------------------------------------------------------------------------------------------------------\n')
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fout.write(atoms['_chemical_name_common'] + f'({atoms["_space_group_name_H-M_alt"]}) - Parameters')
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fout.write('\n\'------------------------------------------------------------------------------------------------------------------------------------------\n')
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a = float(atoms['_cell_length_a'].split('(')[0])
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a = float(atoms['_cell_length_a'].split('(')[0])
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b = float(atoms['_cell_length_b'].split('(')[0])
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b = float(atoms['_cell_length_b'].split('(')[0])
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@ -116,67 +159,231 @@ def write_str(fout, str, options):
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gamma = float(atoms['_cell_angle_gamma'].split('(')[0])
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gamma = float(atoms['_cell_angle_gamma'].split('(')[0])
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fout.write('#ifdef start_values\n')
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# WRITE LATTICE PARAMETERS
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fout.write(f'local lpa \t{a} \t;:\n')
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# If start_values is defined:
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fout.write(f'local lpb \t{b} \t;:\n')
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fout.write(f'#ifdef start_values_{label}\n')
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fout.write(f'local lpc \t{c} \t;:\n')
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lpa = f'local lpa_{label} {a} ;: {a}'
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fout.write(f'local lpal \t{alpha} \t;:\n')
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lpb = f'local lpb_{label} {b} ;: {b}'
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fout.write(f'local lpbe \t{beta} \t;:\n')
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lpc = f'local lpc_{label} {c} ;: {c}'
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fout.write(f'local lpga \t{gamma} \t;:\n\n')
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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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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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fout.write('#else\n')
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fout.write(f'local lpa \t{a}\n')
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lpa = f'local lpa_{label} {a}'
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fout.write(f'local lpb \t{b}\n')
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lpb = f'local lpb_{label} {b}'
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fout.write(f'local lpc \t{c}\n')
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lpc = f'local lpc_{label} {c}'
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fout.write(f'local lpal \t{alpha}\n')
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fout.write('{: <55} {: <55} {: <55}\n'.format(lpa, lpb, lpc))
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fout.write(f'local lpbe \t{beta}\n')
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lpal = f'local lpal_{label} {alpha}'
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fout.write(f'local lpga \t{gamma}\n')
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lpbe = f'local lpbe_{label} {beta}'
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lpga = f'local lpga_{label} {gamma}'
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fout.write('{: <55} {: <55} {: <55}\n'.format(lpal, lpbe, lpga))
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fout.write('#endif\n\n')
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fout.write('#endif\n\n')
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sites = list(atoms['atoms'].keys())
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sites = list(atoms['atoms'].keys())
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attrs = {'_atom_site_fract_x': 'x', '_atom_site_fract_y': 'y', '_atom_site_fract_z': 'z', '_atom_site_B_iso_or_equiv': 'beq'}
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attrs = {
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'_atom_site_fract_x': 'x',
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'_atom_site_fract_y': 'y',
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'_atom_site_fract_z': 'z',
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'_atom_site_occupancy': '!occ',
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'_atom_site_B_iso_or_equiv': '!beq'
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}
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for attr in attrs:
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for site in sites:
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# WRITE SITE PARAMETERS
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for site in sites:
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params = []
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for attr in attrs:
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if attr in atoms["atoms"][site].keys():
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if attr in atoms["atoms"][site].keys():
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value = atoms["atoms"][site][attr].split("(")[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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value = value if value != '.' else 0.
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fout.write(f'local {attrs[attr]}_{site}\t\t =\t {value} \t ;= \n')
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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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fout.write('{: <55} {: <55} {: <55} {: <55} {: <55}\n'.format(*params))
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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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f'local sgc_{label}_XXXX = 0 ;: 0',
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f'local slc_{label}_XXXX = 0 ;: 0',
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))
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fout.write('\n')
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# fout.write(f'local csgc_{label} ;:\t\t\t\t\t')
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# fout.write(f'local cslc_{label} ;:\t\t\t\t\t')
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# fout.write(f'local sgc_{label} ;:\t\t\t\t\t')
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# fout.write(f'local slc_{label} ;:\n')
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def write_str(fout, data, options, index=0):
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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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else:
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label = index
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fout.write('\n\'------------------------------------------------------------------------------------------------------------------------------------------\n')
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fout.write('\n\'------------------------------------------------------------------------------------------------------------------------------------------\n')
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fout.write(atoms['_chemical_name_common'] + f'({atoms["_space_group_name_H-M_alt"]})')
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fout.write('\'' + atoms['_chemical_name_common'].strip('\'') + ' ' + f'({atoms["_space_group_name_H-M_alt"]})'.replace("\'", ""))
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fout.write('\n\'------------------------------------------------------------------------------------------------------------------------------------------\n')
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fout.write('\n\'------------------------------------------------------------------------------------------------------------------------------------------\n')
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fout.write('\tstr\n')
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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')
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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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fout.write(f'\t\tspace_group {atoms["_space_group_IT_number"]}\n')
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fout.write('\t\ta = lpa ;\n')
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fout.write(f'\t\ta = lpa_{label} ;\n')
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fout.write('\t\tb = lpb ;\n')
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fout.write(f'\t\tb = lpb_{label} ;\n')
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fout.write('\t\tc = lpc ;\n')
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fout.write(f'\t\tc = lpc_{label} ;\n')
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fout.write('\t\tal = lpal ;\n')
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fout.write(f'\t\tal = lpal_{label} ;\n')
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fout.write('\t\tbe = lpbe ;\n')
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fout.write(f'\t\tbe = lpbe_{label} ;\n')
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fout.write('\t\tga = lpga ;\n')
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fout.write(f'\t\tga = lpga_{label} ;\n')
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fout.write('\n')
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fout.write('\n')
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fout.write(f'\t\tcell_volume vol_XXXX {atoms["_cell_volume"]}\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('\t\tscale @ 1.0\n')
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fout.write('\t\tr_bragg 1.0\n\n')
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fout.write(f'\t\t#ifdef crystallite_size_gaussian_{label}\n')
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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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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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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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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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for atom in atoms['atoms'].keys():
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for atom in atoms['atoms'].keys():
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atom_label = atom if len(atom) == 3 else atom+' '
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fout.write(f'\t\tsite {atom_label}\t x = x_{atom_label} ;\t y = y_{atom_label} ;\t z = z_{atom_label} ; occ {atoms["atoms"][atom]["_atom_site_occupancy"]}\t beq = beq_{atom_label} \t ;\n')
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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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site = f'site {atom}'
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x = f'\t\tx = x_{atom}_{label}'
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y = f'\t\ty = y_{atom}_{label}'
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z = f'\t\tz = z_{atom}_{label}'
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occ = '\t\tocc {: <4} = occ_{}_{}'.format(specie, atom, label)
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#occ = f'\t\tocc {atoms["atoms"][atom]["_atom_site_type_symbol"]} occ_{atom}_{label}'
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beq = f'\t\tbeq = beq_{atom}_{label}'
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# FIXME Fix alignment here at some point
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#fout.write(f'\t\tsite {atom}\t x = x_{atom}_{label} ;\t y = y_{atom}_{label} ;\t z = z_{atom}_{label} ;\t occ {atoms["atoms"][atom]["_atom_site_type_symbol"]} occ_{atom}_{label} \t beq = beq_{atom}_{label} \t ;\n')
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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['save_results']:
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fout.write('\n\n')
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write_output(fout=fout, data=data, options=options, index=index)
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def write_output(fout, data, options, index=0):
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filename = os.path.basename(data['xdd']).split('.')[0]
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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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else:
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label = index
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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')
|
||||||
|
fout.write(f'\t\tOut_CIF_ADPs({options["save_dir"]}/{label}_XXXX.cif)\n')
|
||||||
|
fout.write(f'\t\tOut_CIF_Bonds_Angles({options["save_dir"]}/{label}_XXXX.cif)\n')
|
||||||
|
fout.write(f'\t\tCreate_hklm_d_Th2_Ip_file({options["save_dir"]}/{label}_XXXX_hkl.dat)\n')
|
||||||
|
|
||||||
fout.write('\n')
|
fout.write('\n')
|
||||||
fout.write('\t\tscale @ 0.0')
|
|
||||||
fout.write('\t\t r_bragg 1.0')
|
|
||||||
|
|
||||||
|
|
||||||
|
fout.write(f'out {options["save_dir"]}/{filename}_{label}.dat append\n')
|
||||||
|
fout.write(f'\t\tOut_String("XXXX")\n')
|
||||||
|
|
||||||
|
fout.write('\t\t{: <40} {: <40} {: <40} {: <40} {: <40} {: <40}'.format(
|
||||||
|
f'Out(Get(r_wp), "%11.5f")',
|
||||||
|
f'Out(Get(r_exp), "%11.5f")',
|
||||||
|
f'Out(Get(r_p), "%11.5f")',
|
||||||
|
f'Out(Get(r_p_dash), "%11.5f")',
|
||||||
|
f'Out(Get(r_exp_dash), "%11.5f")',
|
||||||
|
f'Out(Get(gof), "%11.5f")',
|
||||||
|
)
|
||||||
|
)
|
||||||
|
|
||||||
|
fout.write('\n')
|
||||||
|
|
||||||
|
|
||||||
|
fout.write('\t\t{: <40} {: <40} {: <40}'.format(
|
||||||
|
f'Out(vol_{label}_XXXX, "%11.5f")',
|
||||||
|
f'Out(mass_{label}_XXXX, "%11.5f")',
|
||||||
|
f'Out(wp_{label}_XXXX, "%11.5f")',
|
||||||
|
|
||||||
|
)
|
||||||
|
)
|
||||||
|
|
||||||
|
|
||||||
|
fout.write('\n')
|
||||||
|
|
||||||
|
|
||||||
|
fout.write('\t\t{: <40} {: <40} {: <40} {: <40} {: <40} {: <40}'.format(
|
||||||
|
f'Out(lpa_{label}, "%11.5f")',
|
||||||
|
f'Out(lpb_{label}, "%11.5f")',
|
||||||
|
f'Out(lpc_{label}, "%11.5f")',
|
||||||
|
f'Out(lpal_{label}, "%11.5f")',
|
||||||
|
f'Out(lpbe_{label}, "%11.5f")',
|
||||||
|
f'Out(lpga_{label}, "%11.5f")',
|
||||||
|
|
||||||
|
)
|
||||||
|
)
|
||||||
|
|
||||||
|
fout.write('\n\n')
|
||||||
|
|
||||||
|
for atom in atoms['atoms']:
|
||||||
|
fout.write('\t\t{: <40} {: <40} {: <40} {: <40} {: <40}'.format(
|
||||||
|
f'Out(x_{atom}_{label}, "%11.5f")',
|
||||||
|
f'Out(y_{atom}_{label}, "%11.5f")',
|
||||||
|
f'Out(z_{atom}_{label}, "%11.5f")',
|
||||||
|
f'Out(occ_{atom}_{label}, "%11.5f")',
|
||||||
|
f'Out(beq_{atom}_{label}, "%11.5f")',
|
||||||
|
)
|
||||||
|
)
|
||||||
|
|
||||||
|
fout.write('\n')
|
||||||
|
|
||||||
|
fout.write('\n\n')
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
fout.write('#endif')
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
|
||||||
|
|
@ -7,7 +7,7 @@
|
||||||
"local muR = (capdia/20)*linab*packing_density;",
|
"local muR = (capdia/20)*linab*packing_density;",
|
||||||
"Cylindrical_I_Correction(muR)"
|
"Cylindrical_I_Correction(muR)"
|
||||||
],
|
],
|
||||||
|
"gauss_fwhm": "gauss_fwhm = Sqrt({} Cos(2 * Th)^4 + {} Cos(2 * Th)^2 + {});",
|
||||||
"lp_factor": "LP_Factor({}) 'change the LP correction or lh value if required",
|
"lp_factor": "LP_Factor({}) 'change the LP correction or lh value if required",
|
||||||
"wavelength": "lam ymin_on_ymax 0.0001 la 1.0 lo {} lh 0.1",
|
"wavelength": "lam ymin_on_ymax 0.0001 la 1.0 lo {} lh 0.1",
|
||||||
"zero_error": "Zero_Error(zero, 0)"
|
"zero_error": "Zero_Error(zero, 0)"
|
||||||
|
|
|
||||||
|
|
@ -6,7 +6,7 @@
|
||||||
"chi2_convergence_criteria": 0.001,
|
"chi2_convergence_criteria": 0.001,
|
||||||
"conserve_memory": false,
|
"conserve_memory": false,
|
||||||
"continue_after_convergence": false,
|
"continue_after_convergence": false,
|
||||||
"convolution_step": 4,
|
"convolution_step": 1,
|
||||||
"do_errors": false,
|
"do_errors": false,
|
||||||
"iters": 100000,
|
"iters": 100000,
|
||||||
"lp_factor": 90,
|
"lp_factor": 90,
|
||||||
|
|
|
||||||
Loading…
Add table
Add a link
Reference in a new issue