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xpowder.py
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xpowder.py
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#
# example of using xraylib to get crystal data
#
# see:
# http://dx.doi.org/10.1016/j.sab.2011.09.011 (paper)
# https://github.com/tschoonj/xraylib/ (code)
# http://lvserver.ugent.be/xraylib-web (web interface, but crystals not included!)
#
#
# import block
#
import xraylib
import numpy
import scipy.constants.codata
import matplotlib.pyplot as plt
codata = scipy.constants.codata.physical_constants
codata_c, tmp1, tmp2 = codata["speed of light in vacuum"]
codata_h, tmp1, tmp2 = codata["Planck constant"]
codata_ec, tmp1, tmp2 = codata["elementary charge"]
codata_r, tmp1, tmp2 = codata["classical electron radius"]
ev2meter = codata_h*codata_c/codata_ec
#
# crystal structures
#
def structure_silicon():
cryst = {} # cryst.copy()
cryst['name'] = b"Si"
cryst['a'] = 5.430699825286865
cryst['b'] = 5.430699825286865
cryst['c'] = 5.430699825286865
cryst['alpha'] = 90.0
cryst['beta'] = 90.0
cryst['gamma'] = 90.0
cryst['n_atom'] = 8
cryst['atom'] = [ {'x': 0.0, 'y': 0.0, 'z': 0.0, 'Zatom': 14, 'fraction': 1.0, 'label':'Si'},
{'x': 0.0, 'y': 0.5, 'z': 0.5, 'Zatom': 14, 'fraction': 1.0, 'label':'Si'},
{'x': 0.5, 'y': 0.0, 'z': 0.5, 'Zatom': 14, 'fraction': 1.0, 'label':'Si'},
{'x': 0.5, 'y': 0.5, 'z': 0.0, 'Zatom': 14, 'fraction': 1.0, 'label':'Si'},
{'x': 0.25, 'y': 0.25, 'z': 0.25, 'Zatom': 14, 'fraction': 1.0, 'label':'Si'},
{'x': 0.25, 'y': 0.75, 'z': 0.75, 'Zatom': 14, 'fraction': 1.0, 'label':'Si'},
{'x': 0.75, 'y': 0.25, 'z': 0.75, 'Zatom': 14, 'fraction': 1.0, 'label':'Si'},
{'x': 0.75, 'y': 0.75, 'z': 0.25, 'Zatom': 14, 'fraction': 1.0, 'label':'Si'}]
cryst['volume'] = 160.16493225097656
return cryst
def structure_MgO():
cryst = {} # cryst.copy()
cryst['name'] = b"MgO"
cryst['a'] = 4.217
cryst['b'] = 4.217
cryst['c'] = 4.217
cryst['alpha'] = 90.0
cryst['beta'] = 90.0
cryst['gamma'] = 90.0
cryst['n_atom'] = 8
cryst['atom'] = [{'x': 0.0, 'y': 0.0, 'z': 0.0, 'Zatom': 12, 'fraction': 1.0, 'label':'Mg'},
{'x': 0.0, 'y': 0.5, 'z': 0.5, 'Zatom': 12, 'fraction': 1.0, 'label':'Mg'},
{'x': 0.5, 'y': 0.0, 'z': 0.5, 'Zatom': 12, 'fraction': 1.0, 'label':'Mg'},
{'x': 0.5, 'y': 0.5, 'z': 0.0, 'Zatom': 12, 'fraction': 1.0, 'label':'Mg'},
{'x': 0.5, 'y': 0.5, 'z': 0.5, 'Zatom': 8 , 'fraction': 1.0, 'label':'O'},
{'x': 0.5, 'y': 0.0, 'z': 0.0, 'Zatom': 8 , 'fraction': 1.0, 'label':'O'},
{'x': 0.0, 'y': 0.5, 'z': 0.0, 'Zatom': 8 , 'fraction': 1.0, 'label':'O'},
{'x': 0.0, 'y': 0.0, 'z': 0.5, 'Zatom': 8 , 'fraction': 1.0, 'label':'O'}]
cryst['volume'] = 74.99128631299997
return cryst
def structure_sepiolite():
cryst = {} # cryst.copy()
cryst['name'] = b"Sepiolite"
cryst['a'] = 13.4
cryst['b'] = 26.8
cryst['c'] = 5.28
cryst['alpha'] = 90.0
cryst['beta'] = 90.0
cryst['gamma'] = 90.0
cryst['n_atom'] = 132
cryst['atom'] = [
{'Zatom':12 ,'fraction': 1.000 ,'x': 0.000 ,'y': 0.02800 ,'z': 0.2500,'label':' Mg1'},
{'Zatom':12 ,'fraction': 1.000 ,'x': 0.5000 ,'y': 0.4720 ,'z': 0.2500,'label':' Mg1'},
{'Zatom':12 ,'fraction': 1.000 ,'x': 0.000 ,'y': 0.9720 ,'z': 0.7500,'label':' Mg1'},
{'Zatom':12 ,'fraction': 1.000 ,'x': 0.5000 ,'y': 0.5280 ,'z': 0.7500,'label':' Mg1'},
{'Zatom':12 ,'fraction': 1.000 ,'x': 0.000 ,'y': 0.9160 ,'z': 0.2500,'label':' Mg2'},
{'Zatom':12 ,'fraction': 1.000 ,'x': 0.5000 ,'y': 0.5840 ,'z': 0.2500,'label':' Mg2'},
{'Zatom':12 ,'fraction': 1.000 ,'x': -0.000 ,'y': 0.08400 ,'z': 0.7500,'label':' Mg2'},
{'Zatom':12 ,'fraction': 1.000 ,'x': 0.5000 ,'y': 0.4160 ,'z': 0.7500,'label':' Mg2'},
{'Zatom':12 ,'fraction': 1.000 ,'x': 0.000 ,'y': 0.1400 ,'z': 0.2500,'label':' Mg3'},
{'Zatom':12 ,'fraction': 1.000 ,'x': 0.5000 ,'y': 0.3600 ,'z': 0.2500,'label':' Mg3'},
{'Zatom':12 ,'fraction': 1.000 ,'x': 0.000 ,'y': 0.8600 ,'z': 0.7500,'label':' Mg3'},
{'Zatom':12 ,'fraction': 1.000 ,'x': 0.5000 ,'y': 0.6400 ,'z': 0.7500,'label':' Mg3'},
{'Zatom':12 ,'fraction': 1.000 ,'x': 0.000 ,'y': 0.8040 ,'z': 0.2500,'label':' Mg4'},
{'Zatom':12 ,'fraction': 1.000 ,'x': 0.5000 ,'y': 0.6960 ,'z': 0.2500,'label':' Mg4'},
{'Zatom':12 ,'fraction': 1.000 ,'x': -0.000 ,'y': 0.1960 ,'z': 0.7500,'label':' Mg4'},
{'Zatom':12 ,'fraction': 1.000 ,'x': 0.5000 ,'y': 0.3040 ,'z': 0.7500,'label':' Mg4'},
{'Zatom':14 ,'fraction': 1.000 ,'x': 0.2080 ,'y': 0.02800 ,'z': 0.5625,'label':' Si1'},
{'Zatom':14 ,'fraction': 1.000 ,'x': 0.7920 ,'y': 0.02800 ,'z': 0.9375,'label':' Si1'},
{'Zatom':14 ,'fraction': 1.000 ,'x': 0.7080 ,'y': 0.4720 ,'z': 0.9375,'label':' Si1'},
{'Zatom':14 ,'fraction': 1.000 ,'x': 0.2920 ,'y': 0.4720 ,'z': 0.5625,'label':' Si1'},
{'Zatom':14 ,'fraction': 1.000 ,'x': 0.7920 ,'y': 0.9720 ,'z': 0.4375,'label':' Si1'},
{'Zatom':14 ,'fraction': 1.000 ,'x': 0.2080 ,'y': 0.9720 ,'z': 0.06250,'label':' Si1'},
{'Zatom':14 ,'fraction': 1.000 ,'x': 0.2920 ,'y': 0.5280 ,'z': 0.06250,'label':' Si1'},
{'Zatom':14 ,'fraction': 1.000 ,'x': 0.7080 ,'y': 0.5280 ,'z': 0.4375,'label':' Si1'},
{'Zatom':14 ,'fraction': 1.000 ,'x': 0.2080 ,'y': 0.1400 ,'z': 0.5625,'label':' Si2'},
{'Zatom':14 ,'fraction': 1.000 ,'x': 0.7920 ,'y': 0.1400 ,'z': 0.9375,'label':' Si2'},
{'Zatom':14 ,'fraction': 1.000 ,'x': 0.7080 ,'y': 0.3600 ,'z': 0.9375,'label':' Si2'},
{'Zatom':14 ,'fraction': 1.000 ,'x': 0.2920 ,'y': 0.3600 ,'z': 0.5625,'label':' Si2'},
{'Zatom':14 ,'fraction': 1.000 ,'x': 0.7920 ,'y': 0.8600 ,'z': 0.4375,'label':' Si2'},
{'Zatom':14 ,'fraction': 1.000 ,'x': 0.2080 ,'y': 0.8600 ,'z': 0.06250,'label':' Si2'},
{'Zatom':14 ,'fraction': 1.000 ,'x': 0.2920 ,'y': 0.6400 ,'z': 0.06250,'label':' Si2'},
{'Zatom':14 ,'fraction': 1.000 ,'x': 0.7080 ,'y': 0.6400 ,'z': 0.4375,'label':' Si2'},
{'Zatom':14 ,'fraction': 1.000 ,'x': 0.2080 ,'y': 0.1960 ,'z': 0.06250,'label':' Si3'},
{'Zatom':14 ,'fraction': 1.000 ,'x': 0.7920 ,'y': 0.1960 ,'z': 0.4375,'label':' Si3'},
{'Zatom':14 ,'fraction': 1.000 ,'x': 0.7080 ,'y': 0.3040 ,'z': 0.4375,'label':' Si3'},
{'Zatom':14 ,'fraction': 1.000 ,'x': 0.2920 ,'y': 0.3040 ,'z': 0.06250 ,'label':' Si3'},
{'Zatom':14 ,'fraction': 1.000 ,'x': 0.7920 ,'y': 0.8040 ,'z': 0.9375 ,'label':' Si3'},
{'Zatom':14 ,'fraction': 1.000 ,'x': 0.2080 ,'y': 0.8040 ,'z': 0.5625 ,'label':' Si3'},
{'Zatom':14 ,'fraction': 1.000 ,'x': 0.2920 ,'y': 0.6960 ,'z': 0.5625 ,'label':' Si3'},
{'Zatom':14 ,'fraction': 1.000 ,'x': 0.7080 ,'y': 0.6960 ,'z': 0.9375 ,'label':' Si3'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.2500 ,'y': 0.2500 ,'z': 0.06250 ,'label':' O1_O3'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.7500 ,'y': 0.2500 ,'z': 0.4375 ,'label':' O1_O3'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.7500 ,'y': 0.7500 ,'z': 0.9375 ,'label':' O1_O3'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.2500 ,'y': 0.7500 ,'z': 0.5625 ,'label':' O1_O3'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.08400 ,'y': 0.02800 ,'z': 0.5620 ,'label':' O2_O4'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.9160 ,'y': 0.02800 ,'z': 0.9380 ,'label':' O2_O4'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.5840 ,'y': 0.4720 ,'z': 0.9380 ,'label':' O2_O4'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.4160 ,'y': 0.4720 ,'z': 0.5620 ,'label':' O2_O4'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.9160 ,'y': 0.9720 ,'z': 0.4380 ,'label':' O2_O4'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.08400 ,'y': 0.9720 ,'z': 0.06200 ,'label':' O2_O4'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.4160 ,'y': 0.5280 ,'z': 0.06200 ,'label':' O2_O4'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.5840 ,'y': 0.5280 ,'z': 0.4380 ,'label':' O2_O4'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.08400 ,'y': 0.1400 ,'z': 0.5620 ,'label':' O3_O5'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.9160 ,'y': 0.1400 ,'z': 0.9380 ,'label':' O3_O5'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.5840 ,'y': 0.3600 ,'z': 0.9380 ,'label':' O3_O5'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.4160 ,'y': 0.3600 ,'z': 0.5620 ,'label':' O3_O5'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.9160 ,'y': 0.8600 ,'z': 0.4380 ,'label':' O3_O5'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.08400 ,'y': 0.8600 ,'z': 0.06200 ,'label':' O3_O5'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.4160 ,'y': 0.6400 ,'z': 0.06200 ,'label':' O3_O5'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.5840 ,'y': 0.6400 ,'z': 0.4380 ,'label':' O3_O5'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.08400 ,'y': 0.1960 ,'z': .06200 ,'label':' O4_O6'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.9160 ,'y': 0.1960 ,'z': 0.4380 ,'label':' O4_O6'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.5840 ,'y': 0.3040 ,'z': 0.4380 ,'label':' O4_O6'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.4160 ,'y': 0.3040 ,'z': .06200 ,'label':' O4_O6'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.9160 ,'y': 0.8040 ,'z': 0.9380 ,'label':' O4_O6'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.08400 ,'y': 0.8040 ,'z': 0.5620 ,'label':' O4_O6'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.4160 ,'y': 0.6960 ,'z': 0.5620 ,'label':' O4_O6'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.5840 ,'y': 0.6960 ,'z': 0.9380 ,'label':' O4_O6'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.2400 ,'y': 0.000 ,'z': 0.3120 ,'label':' O5_O7'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.7600 ,'y': 0.000 ,'z': 0.1880 ,'label':' O5_O7'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.7400 ,'y': 0.5000 ,'z': 0.1880 ,'label':' O5_O7'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.2600 ,'y': 0.5000 ,'z': 0.3120 ,'label':' O5_O7'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.7600 ,'y': 0.000 ,'z': 0.6880 ,'label':' O5_O7'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.2400 ,'y': 0.000 ,'z': 0.8120 ,'label':' O5_O7'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.2600 ,'y': 0.5000 ,'z': 0.8120 ,'label':' O5_O7'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.7400 ,'y': 0.5000 ,'z': 0.6880 ,'label':' O5_O7'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.2400 ,'y': 0.08400 ,'z': 0.5620 ,'label':' O6_O8'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.7600 ,'y': 0.08400 ,'z': 0.9380 ,'label':' O6_O8'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.7400 ,'y': 0.4160 ,'z': 0.9380 ,'label':' O6_O8'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.2600 ,'y': 0.4160 ,'z': 0.5620 ,'label':' O6_O8'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.7600 ,'y': 0.9160 ,'z': 0.4380 ,'label':' O6_O8'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.2400 ,'y': 0.9160 ,'z': 0.06200 ,'label':' O6_O8'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.2600 ,'y': 0.5840 ,'z': 0.06200 ,'label':' O6_O8'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.7400 ,'y': 0.5840 ,'z': 0.4380 ,'label':' O6_O8'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.2400 ,'y': 0.1680 ,'z': 0.3120 ,'label':' O7_O9'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.7600 ,'y': 0.1680 ,'z': 0.1880 ,'label':' O7_O9'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.7400 ,'y': 0.3320 ,'z': 0.1880 ,'label':' O7_O9'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.2600 ,'y': 0.3320 ,'z': 0.3120 ,'label':' O7_O9'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.7600 ,'y': 0.8320 ,'z': 0.6880 ,'label':' O7_O9'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.2400 ,'y': 0.8320 ,'z': 0.8120 ,'label':' O7_O9'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.2600 ,'y': 0.6680 ,'z': 0.8120 ,'label':' O7_O9'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.7400 ,'y': 0.6680 ,'z': 0.6880 ,'label':' O7_O9'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.2400 ,'y': 0.1680 ,'z': 0.8120 ,'label':' O8_O10'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.7600 ,'y': 0.1680 ,'z': 0.6880 ,'label':' O8_O10'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.7400 ,'y': 0.3320 ,'z': 0.6880 ,'label':' O8_O10'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.2600 ,'y': 0.3320 ,'z': 0.8120 ,'label':' O8_O10'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.7600 ,'y': 0.8320 ,'z': 0.1880 ,'label':' O8_O10'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.2400 ,'y': 0.8320 ,'z': 0.3120 ,'label':' O8_O10'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.2600 ,'y': 0.6680 ,'z': 0.3120 ,'label':' O8_O10'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.7400 ,'y': 0.6680 ,'z': 0.1880 ,'label':' O8_O10'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.08400 ,'y': 0.08400 ,'z': 0.06200 ,'label':' OH_O11'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.9160 ,'y': 0.08400 ,'z': 0.4380 ,'label':' OH_O11'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.5840 ,'y': 0.4160 ,'z': 0.4380 ,'label':' OH_O11'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.4160 ,'y': 0.4160 ,'z': 0.06200 ,'label':' OH_O11'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.9160 ,'y': 0.9160 ,'z': 0.9380 ,'label':' OH_O11'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.08400 ,'y': 0.9160 ,'z': 0.5620 ,'label':' OH_O11'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.4160 ,'y': 0.5840 ,'z': 0.5620 ,'label':' OH_O11'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.5840 ,'y': 0.5840 ,'z': 0.9380 ,'label':' OH_O11'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.08300 ,'y': 0.2500 ,'z': 0.5000 ,'label':' CW_O12'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.9170 ,'y': 0.2500 ,'z': 0.000 ,'label':' CW_O12'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.5830 ,'y': 0.2500 ,'z': 0.000 ,'label':' CW_O12'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.4170 ,'y': 0.2500 ,'z': 0.5000 ,'label':' CW_O12'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.9170 ,'y': 0.7500 ,'z': 0.5000 ,'label':' CW_O12'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.08300 ,'y': 0.7500 ,'z': 0.000 ,'label':' CW_O12'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.4170 ,'y': 0.7500 ,'z': 0.000 ,'label':' CW_O12'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.5830 ,'y': 0.7500 ,'z': 0.5000 ,'label':' CW_O12'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.08300 ,'y': 0.4160 ,'z': 0.9167 ,'label':' ZW1_O13'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.9170 ,'y': 0.4160 ,'z': 0.5833 ,'label':' ZW1_O13'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.5830 ,'y': 0.08400 ,'z': 0.5833 ,'label':' ZW1_O13'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.4170 ,'y': 0.08400 ,'z': 0.9167 ,'label':' ZW1_O13'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.9170 ,'y': 0.5840 ,'z': 0.08330 ,'label':' ZW1_O13'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.08300 ,'y': 0.5840 ,'z': 0.4167 ,'label':' ZW1_O13'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.4170 ,'y': 0.9160 ,'z': 0.4167 ,'label':' ZW1_O13'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.5830 ,'y': 0.9160 ,'z': 0.08330 ,'label':' ZW1_O13'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.000 ,'y': 0.6720 ,'z': 0.2500 ,'label':' W2_O1(4)'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.5000 ,'y': 0.8280 ,'z': 0.2500 ,'label':' W2_O1(4)'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.000 ,'y': 0.3280 ,'z': 0.7500 ,'label':' W2_O1(4)'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.5000 ,'y': 0.1720 ,'z': 0.7500 ,'label':' W2_O1(4)'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.000 ,'y': 0.4850 ,'z': 0.2500 ,'label':' W3_O2(4)'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.5000 ,'y': 0.01500 ,'z': 0.2500 ,'label':' W3_O2(4)'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.000 ,'y': 0.5150 ,'z': 0.7500 ,'label':' W3_O2(4)'},
{'Zatom':8 ,'fraction':1.000 ,'x': 0.5000 ,'y': 0.9850 ,'z': 0.7500 ,'label':' ZW3_O2(4)'} ]
cryst['volume'] = cryst['a'] * cryst['b'] * cryst['c']
return cryst
def structure_palygorskiteO():
cryst = {} # cryst.copy()
cryst['name'] = b"PalygorskiteO"
cryst['a'] = 12.78
cryst['b'] = 17.89
cryst['c'] = 5.21
cryst['alpha'] = 90.0
cryst['beta'] = 90.0
cryst['gamma'] = 90.0
cryst['n_atom'] = 84
cryst['volume'] = cryst['a'] * cryst['b'] * cryst['c']
cryst['atom'] = [
{'Zatom': 13, 'fraction': 1.000, 'x': 0.000 ,'y': 0.08333 ,'z': 0.5000 ,'label': ' Al '},
{'Zatom': 13, 'fraction': 1.000, 'x': 0.5000 ,'y': 0.4166 ,'z': 0.5000 ,'label': ' Al '},
{'Zatom': 13, 'fraction': 1.000, 'x': 0.000 ,'y': 0.9166 ,'z': 0.5000 ,'label': ' Al '},
{'Zatom': 13, 'fraction': 1.000, 'x': 0.5000 ,'y': 0.5833 ,'z': 0.5000 ,'label': ' Al '},
{'Zatom': 12, 'fraction': 1.000, 'x': 0.000 ,'y': 0.1666 ,'z': 0.000 ,'label': ' Mg '},
{'Zatom': 12, 'fraction': 1.000, 'x': 0.5000 ,'y': 0.3333 ,'z': 0.000 ,'label': ' Mg '},
{'Zatom': 12, 'fraction': 1.000, 'x': 0.000 ,'y': 0.8333 ,'z': 0.000 ,'label': ' Mg '},
{'Zatom': 12, 'fraction': 1.000, 'x': 0.5000 ,'y': 0.6666 ,'z': 0.000 ,'label': ' Mg '},
{'Zatom': 14, 'fraction': 1.000, 'x': 0.2083 ,'y': 0.08333 ,'z': 0.8333 ,'label': ' Si1 '},
{'Zatom': 14, 'fraction': 1.000, 'x': 0.2916 ,'y': 0.4166 ,'z': 0.8333 ,'label': ' Si1 '},
{'Zatom': 14, 'fraction': 1.000, 'x': 0.7083 ,'y': 0.4166 ,'z': 0.1666 ,'label': ' Si1 '},
{'Zatom': 14, 'fraction': 1.000, 'x': 0.7916 ,'y': 0.08333 ,'z': 0.1666 ,'label': ' Si1 '},
{'Zatom': 14, 'fraction': 1.000, 'x': 0.7916 ,'y': 0.9166 ,'z': 0.1666 ,'label': ' Si1 '},
{'Zatom': 14, 'fraction': 1.000, 'x': 0.7083 ,'y': 0.5833 ,'z': 0.1666 ,'label': ' Si1 '},
{'Zatom': 14, 'fraction': 1.000, 'x': 0.2916 ,'y': 0.5833 ,'z': 0.8333 ,'label': ' Si1 '},
{'Zatom': 14, 'fraction': 1.000, 'x': 0.2083 ,'y': 0.9166 ,'z': 0.8333 ,'label': ' Si1 '},
{'Zatom': 14, 'fraction': 1.000, 'x': 0.2083 ,'y': 0.1666 ,'z': 0.3333 ,'label': ' Si2 '},
{'Zatom': 14, 'fraction': 1.000, 'x': 0.2916 ,'y': 0.3333 ,'z': 0.3333 ,'label': ' Si2 '},
{'Zatom': 14, 'fraction': 1.000, 'x': 0.7083 ,'y': 0.3333 ,'z': 0.6666 ,'label': ' Si2 '},
{'Zatom': 14, 'fraction': 1.000, 'x': 0.7916 ,'y': 0.1666 ,'z': 0.6666 ,'label': ' Si2 '},
{'Zatom': 14, 'fraction': 1.000, 'x': 0.7916 ,'y': 0.8333 ,'z': 0.6666 ,'label': ' Si2 '},
{'Zatom': 14, 'fraction': 1.000, 'x': 0.7083 ,'y': 0.6666 ,'z': 0.6666 ,'label': ' Si2 '},
{'Zatom': 14, 'fraction': 1.000, 'x': 0.2916 ,'y': 0.6666 ,'z': 0.3333 ,'label': ' Si2 '},
{'Zatom': 14, 'fraction': 1.000, 'x': 0.2083 ,'y': 0.8333 ,'z': 0.3333 ,'label': ' Si2 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.08333 ,'y': 0.000 ,'z': 0.3333 ,'label': ' OH '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.4166 ,'y': 0.5000 ,'z': 0.3333 ,'label': ' OH '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.5833 ,'y': 0.5000 ,'z': 0.6666 ,'label': ' OH '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.9166 ,'y': 0.000 ,'z': 0.6666 ,'label': ' OH '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.08333 ,'y': 0.08333 ,'z': 0.8333 ,'label': ' O1 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.4166 ,'y': 0.4166 ,'z': 0.8333 ,'label': ' O1 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.5833 ,'y': 0.4166 ,'z': 0.1666 ,'label': ' O1 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.9166 ,'y': 0.08333 ,'z': 0.1666 ,'label': ' O1 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.9166 ,'y': 0.9166 ,'z': 0.1666 ,'label': ' O1 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.5833 ,'y': 0.5833 ,'z': 0.1666 ,'label': ' O1 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.4166 ,'y': 0.5833 ,'z': 0.8333 ,'label': ' O1 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.08333 ,'y': 0.9166 ,'z': 0.8333 ,'label': ' O1 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.08333 ,'y': 0.1666 ,'z': 0.3333 ,'label': ' O2 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.4166 ,'y': 0.3333 ,'z': 0.3333 ,'label': ' O2 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.5833 ,'y': 0.3333 ,'z': 0.6666 ,'label': ' O2 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.9166 ,'y': 0.1666 ,'z': 0.6666 ,'label': ' O2 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.9166 ,'y': 0.8333 ,'z': 0.6666 ,'label': ' O2 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.5833 ,'y': 0.6666 ,'z': 0.6666 ,'label': ' O2 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.4166 ,'y': 0.6666 ,'z': 0.3333 ,'label': ' O2 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.08333 ,'y': 0.8333 ,'z': 0.3333 ,'label': ' O2 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.08333 ,'y': 0.2500 ,'z': 0.8333 ,'label': ' H2OB '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.4166 ,'y': 0.2500 ,'z': 0.8333 ,'label': ' H2OB '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.5833 ,'y': 0.2500 ,'z': 0.1666 ,'label': ' H2OB '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.9166 ,'y': 0.2500 ,'z': 0.1666 ,'label': ' H2OB '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.9166 ,'y': 0.7500 ,'z': 0.1666 ,'label': ' H2OB '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.5833 ,'y': 0.7500 ,'z': 0.1666 ,'label': ' H2OB '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.4166 ,'y': 0.7500 ,'z': 0.8333 ,'label': ' H2OB '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.08333 ,'y': 0.7500 ,'z': 0.8333 ,'label': ' H2OB '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.2500 ,'y': 0.000 ,'z': 0.8333 ,'label': ' O3 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.2500 ,'y': 0.5000 ,'z': 0.8333 ,'label': ' O3 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.7500 ,'y': 0.5000 ,'z': 0.1666 ,'label': ' O3 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.7500 ,'y': 0.000 ,'z': 0.1666 ,'label': ' O3 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.2500 ,'y': 0.2500 ,'z': 0.3333 ,'label': ' O4 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.7500 ,'y': 0.2500 ,'z': 0.6666 ,'label': ' O4 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.7500 ,'y': 0.7500 ,'z': 0.6666 ,'label': ' O4 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.2500 ,'y': 0.7500 ,'z': 0.3333 ,'label': ' O4 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.2500 ,'y': 0.1250 ,'z': 0.5833 ,'label': ' O5 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.2500 ,'y': 0.3750 ,'z': 0.5833 ,'label': ' O5 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.7500 ,'y': 0.3750 ,'z': 0.4166 ,'label': ' O5 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.7500 ,'y': 0.1250 ,'z': 0.4166 ,'label': ' O5 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.7500 ,'y': 0.8750 ,'z': 0.4166 ,'label': ' O5 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.7500 ,'y': 0.6250 ,'z': 0.4166 ,'label': ' O5 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.2500 ,'y': 0.6250 ,'z': 0.5833 ,'label': ' O5 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.2500 ,'y': 0.8750 ,'z': 0.5833 ,'label': ' O5 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.2500 ,'y': 0.1250 ,'z': 0.08333 ,'label': ' O6 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.2500 ,'y': 0.3750 ,'z': 0.08333 ,'label': ' O6 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.7500 ,'y': 0.3750 ,'z': 0.9166 ,'label': ' O6 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.7500 ,'y': 0.1250 ,'z': 0.9166 ,'label': ' O6 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.7500 ,'y': 0.8750 ,'z': 0.9166 ,'label': ' O6 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.7500 ,'y': 0.6250 ,'z': 0.9166 ,'label': ' O6 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.2500 ,'y': 0.6250 ,'z': 0.08333 ,'label': ' O6 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.2500 ,'y': 0.8750 ,'z': 0.08333 ,'label': ' O6 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.000 ,'y': 0.3333 ,'z': 0.5000 ,'label': ' ZW1 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.5000 ,'y': 0.1666 ,'z': 0.5000 ,'label': ' ZW1 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.000 ,'y': 0.6666 ,'z': 0.5000 ,'label': ' ZW1 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.5000 ,'y': 0.8333 ,'z': 0.5000 ,'label': ' ZW1 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.000 ,'y': 0.4166 ,'z': 0.000 ,'label': ' ZW2 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.5000 ,'y': 0.08333 ,'z': 0.000 ,'label': ' ZW2 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.000 ,'y': 0.5833 ,'z': 0.000 ,'label': ' ZW2 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.5000 ,'y': 0.9166 ,'z': 0.000 ,'label': ' ZW2 '} ]
cryst['volume'] = cryst['a'] * cryst['b'] * cryst['c']
return cryst
def structure_palygorskite_new():
cryst = {} # cryst.copy()
cryst['name'] = b"Palygorskite_new"
cryst['a'] = 10.99
cryst['b'] = 5.21
cryst['c'] = 10.99
cryst['alpha'] = 90.0
cryst['beta'] = 71.08
cryst['gamma'] = 90.0
cryst['n_atom'] = 52
cryst['volume'] = cryst['a'] * cryst['b'] * cryst['c']
cryst['atom'] = [
{'Zatom': 13, 'fraction': 1.000, 'x': 0.083 ,'y': 0.500 ,'z': 0.083 ,'label': ' Al '},
{'Zatom': 13, 'fraction': 1.000, 'x': 0.917 ,'y': 0.500 ,'z': 0.917 ,'label': ' Al '},
{'Zatom': 12, 'fraction': 1.000, 'x': 0.167 ,'y': 0.000 ,'z': 0.167 ,'label': ' Mg1 '},
{'Zatom': 12, 'fraction': 1.000, 'x': 0.833 ,'y': 1.000 ,'z': 0.833 ,'label': ' Mg1 '},
{'Zatom': 12, 'fraction': 1.000, 'x': 0.833 ,'y': 0.000 ,'z': 0.833 ,'label': ' Mg2 '},
{'Zatom': 12, 'fraction': 1.000, 'x': 0.167 ,'y': 1.000 ,'z': 0.167 ,'label': ' Mg2 '},
{'Zatom': 14, 'fraction': 1.000, 'x': 0.708 ,'y': 0.833 ,'z': 0.125 ,'label': ' Si1 '},
{'Zatom': 14, 'fraction': 1.000, 'x': 0.292 ,'y': 0.167 ,'z': 0.875 ,'label': ' Si1 '},
{'Zatom': 14, 'fraction': 1.000, 'x': 0.125 ,'y': 0.167 ,'z': 0.708 ,'label': ' Si2 '},
{'Zatom': 14, 'fraction': 1.000, 'x': 0.875 ,'y': 0.833 ,'z': 0.292 ,'label': ' Si2 '},
{'Zatom': 14, 'fraction': 1.000, 'x': 0.625 ,'y': 0.333 ,'z': 0.042 ,'label': ' Si3 '},
{'Zatom': 14, 'fraction': 1.000, 'x': 0.375 ,'y': 0.667 ,'z': 0.958 ,'label': ' Si3 '},
{'Zatom': 14, 'fraction': 1.000, 'x': 0.042 ,'y': 0.667 ,'z': 0.625 ,'label': ' Si4 '},
{'Zatom': 14, 'fraction': 1.000, 'x': 0.958 ,'y': 0.333 ,'z': 0.375 ,'label': ' Si4 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.917 ,'y': 0.333 ,'z': 0.083 ,'label': ' OH '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.083 ,'y': 0.667 ,'z': 0.917 ,'label': ' OH '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.167 ,'y': 0.833 ,'z': 0.000 ,'label': ' O1 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.833 ,'y': 0.167 ,'z': 1.000 ,'label': ' O1 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.833 ,'y': 0.833 ,'z': 0.000 ,'label': ' O2 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.167 ,'y': 0.167 ,'z': 1.000 ,'label': ' O2 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.000 ,'y': 0.167 ,'z': 0.833 ,'label': ' O3 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 1.000 ,'y': 0.833 ,'z': 0.167 ,'label': ' O3 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.000 ,'y': 0.167 ,'z': 0.167 ,'label': ' O4 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 1.000 ,'y': 0.833 ,'z': 0.833 ,'label': ' O4 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.250 ,'y': 0.333 ,'z': 0.083 ,'label': ' O5 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.750 ,'y': 0.667 ,'z': 0.917 ,'label': ' O5 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.083 ,'y': 0.667 ,'z': 0.250 ,'label': ' O6 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.917 ,'y': 0.333 ,'z': 0.750 ,'label': ' O6 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.333 ,'y': 0.833 ,'z': 0.167 ,'label': ' BW1 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.667 ,'y': 0.167 ,'z': 0.833 ,'label': ' BW1 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.167 ,'y': 0.167 ,'z': 0.333 ,'label': ' BW2 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.833 ,'y': 0.833 ,'z': 0.667 ,'label': ' BW2 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.750 ,'y': 0.833 ,'z': 0.250 ,'label': ' O7 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.250 ,'y': 0.167 ,'z': 0.750 ,'label': ' O7 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.500 ,'y': 0.333 ,'z': 0.000 ,'label': ' O8 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.500 ,'y': 0.667 ,'z': 1.000 ,'label': ' O8 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.000 ,'y': 0.667 ,'z': 0.500 ,'label': ' O9 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 1.000 ,'y': 0.333 ,'z': 0.500 ,'label': ' O9 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.625 ,'y': 0.583 ,'z': 0.125 ,'label': ' O10 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.375 ,'y': 0.417 ,'z': 0.875 ,'label': ' O10 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.875 ,'y': 0.583 ,'z': 0.375 ,'label': ' O11 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.125 ,'y': 0.417 ,'z': 0.625 ,'label': ' O11 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.625 ,'y': 0.083 ,'z': 0.125 ,'label': ' O12 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.375 ,'y': 0.917 ,'z': 0.875 ,'label': ' O12 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.875 ,'y': 0.083 ,'z': 0.375 ,'label': ' O13 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.125 ,'y': 0.917 ,'z': 0.625 ,'label': ' O13 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.333 ,'y': 0.500 ,'z': 0.333 ,'label': ' ZW1 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.667 ,'y': 0.500 ,'z': 0.667 ,'label': ' ZW1 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.417 ,'y': 0.000 ,'z': 0.417 ,'label': ' ZW2 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.583 ,'y': 1.000 ,'z': 0.583 ,'label': ' ZW2 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.583 ,'y': 0.000 ,'z': 0.583 ,'label': ' ZW2 '},
{'Zatom': 8., 'fraction': 1.000, 'x': 0.417 ,'y': 1.000 ,'z': 0.417 ,'label': ' ZW2 '} ]
cryst['volume'] = cryst['a'] * cryst['b'] * cryst['c']
return cryst
#
# code
#
def voigt1(x,a,area=0):
xx = x - a[1]
#
# gaussian and lorentzian normalized to 1 in amplitude
#
lor = 1.0 + (xx/(0.5 * a[2]))**2
gau = numpy.exp( - (xx*2.0 * numpy.sqrt(numpy.log(2.0))/a[2])**2 )
if area == 1:
res = (a[3]/lor/numpy.pi*2+(1.0-a[3])* gau * numpy.sqrt(4.0*numpy.log(2.0)/numpy.pi) )*a[0]/a[2]
else:
res = (a[3]/lor + (1.0 - a[3])* gau )*a[0]
return res
def structure_info(cryst,verbose=0,file_out=""):
txt = ""
txt += "name: %s\n" % (cryst['name'] )
txt += "a: %f\n" % (cryst['a'] )
txt += "b: %f\n" % (cryst['b'] )
txt += "c: %f\n" % (cryst['c'] )
txt += "alpha: %f\n" % (cryst['alpha'] )
txt += "beta: %f\n" % (cryst['beta'] )
txt += "gamma: %f\n" % (cryst['gamma'] )
txt += "n_atom: %d\n" % (cryst['n_atom'])
txt += "volume: %f\n" % (cryst['volume'])
for atom in cryst['atom']:
txt += "Z=%2d f:%3.1f xyz=(%5.3f, %5.3f, %5.3f) %s \n"%(atom['Zatom'],atom['fraction'],
atom['x'],atom['y'],atom['z'],atom['label'])
if file_out != "":
f = open(file_out,'w')
f.write(txt)
f.close()
if verbose:
print(txt)
return txt
def structure_group(cryst1,cryst2,axis='a'):
cryst = {} # cryst.copy()
cryst['name'] = cryst1['name']+b"+"+cryst2['name']
if axis == 'a':
cryst['a'] = cryst1['a'] + cryst2['a']
cryst['b'] = cryst1['b']
cryst['c'] = cryst1['c']
if cryst1['b'] != cryst2['b']:
print("Warning: b axes are not the same!")
if cryst1['c'] != cryst2['c']:
print("Warning: c axes are not the same (taken the first one)!")
elif axis == 'b':
cryst['a'] = cryst1['a']
cryst['b'] = cryst1['b'] + cryst2['b']
cryst['c'] = cryst1['c']
if cryst1['a'] != cryst2['a']:
print("Warning: a axes are not the same (taken the first one)!")
if cryst1['c'] != cryst2['c']:
print("Warning: c axes are not the same (taken the first one)!")
elif axis == 'c':
cryst['a'] = cryst1['a']
cryst['b'] = cryst1['b']
cryst['c'] = cryst1['c'] + cryst2['c']
if cryst1['b'] != cryst2['b']:
print("Warning: b axes are not the same (taken the first one)!")
if cryst1['a'] != cryst2['a']:
print("Warning: a axes are not the same (taken the first one)!")
else:
raise Exception("Error: Bad grouping axis.")
cryst['alpha'] = cryst1['alpha']
cryst['beta'] = cryst1['beta']
cryst['gamma'] = cryst1['gamma']
cryst['n_atom'] = cryst1['n_atom'] + cryst2['n_atom']
tmp = []
for at1 in cryst1['atom']:
at11 = at1.copy()
if axis == 'a':
scale = cryst1['a'] / (cryst1['a'] + cryst2['a'])
at11['x'] *= scale
if axis == 'b':
scale = cryst1['b'] / (cryst1['b'] + cryst2['b'])
at11['y'] *= scale
if axis == 'c':
scale = cryst1['c'] / (cryst1['c'] + cryst2['c'])
at11['z'] *= scale
tmp.append(at11)
for at1 in cryst2['atom']:
at11 = at1.copy()
if axis == 'a':
scale = cryst2['a'] / (cryst1['a'] + cryst2['a'])
at11['x'] *= scale
at11['x'] += cryst1['a'] / (cryst1['a'] + cryst2['a'])
if axis == 'b':
scale = cryst2['b'] / (cryst1['b'] + cryst2['b'])
at11['y'] *= scale
at11['y'] += cryst1['a'] / (cryst1['a'] + cryst2['a'])
if axis == 'c':
scale = cryst2['c'] / (cryst1['c'] + cryst2['c'])
at11['z'] *= scale
at11['z'] += cryst1['a'] / (cryst1['a'] + cryst2['a'])
tmp.append(at11)
cryst['atom'] = tmp
cryst['volume'] = cryst['a'] * cryst['b'] * cryst['c']
return cryst
def lorentz(theta_bragg_deg):
tr = theta_bragg_deg * numpy.pi / 180.
polarization_factor = 0.5 * (1.0 + (numpy.cos(2.0 * tr))**2)
lorentz_factor = 1.0 / numpy.sin(2.0 * tr)
geometrical_factor = 1.0 * numpy.cos(tr) / numpy.sin(2.0 * tr)
return polarization_factor*lorentz_factor*geometrical_factor
def plot_lines(x1,y1,xtitle=r"$2\theta$",ytitle="Intensity",toptitle="",noblock=0):
fig = plt.figure()
ax = fig.add_subplot(111)
x = numpy.repeat(x1,3)
y = numpy.zeros_like(x)
idx = -1
for i in range(x1.size):
idx += 1
y[idx] = 0.0
idx += 1
y[idx] = y1[i]
idx += 1
y[idx] = 0.0
numBins = 50
ax.plot(x,y,color='green')
plt.title(toptitle)
plt.xlabel(xtitle)
plt.ylabel(ytitle)
if noblock == 0:
plt.show()
def plot_pattern(x1,y1,xtitle=r"$2\theta$",ytitle="Intensity",toptitle="",noblock=0):
fig = plt.figure()
ax = fig.add_subplot(111)
ax.plot(x1,y1,color='green')
plt.title(toptitle)
plt.xlabel(xtitle)
plt.ylabel(ytitle)
if noblock == 0:
plt.show()
def calculate_reflections(cryst,wavelength_in_A=1.0,debyeWaller=1.0,rel_angle=1.0,twotheta_max=30.0,structure_factor_min=1e-3,file_out="",verbose=1):
"""
Calculate crystal reflections
:param cryst: crystal structure
:param wavelength_in_A: photon wavelength in m (default=1A)
:param debyeWaller: Debye-Waller term (default=1.0)
:param rel_angle: for structure factors, incident angle/ Bragg angle (default=1.0)
:param twotheta_max: Maximum 2theta for simulations in degrees (default=30 deg)
:param structure_factor_min: minimum value for structure factor for considering the reflectio.
Set to a negative value to consider all reflections
:return: a numpy array [8,nreflections] with first index:
0 = miller index h
1 = miller index k
2 = miller index l
3 = dspacing in A
4 = |Real(Fh)} with Fh the structure factor
5 = 2thete: Twice the Bragg angle
6 = multiplicity of the reflection
7 = intensity (arbitrary units)
8 = intensity (% of highest reflection)
"""
photon_energy_in_keV = ev2meter / (wavelength_in_A*1e-10)
# get limits of indices
dspacingmin = wavelength_in_A / 2 / numpy.sin(twotheta_max / 2 * numpy.pi / 180)
print("dspacingmin: ",dspacingmin)
hmax = int(cryst['a']/dspacingmin)
kmax = int(cryst['b']/dspacingmin)
lmax = int(cryst['c']/dspacingmin)
# loop over all reflections
nmiller = (2*hmax+1)*(2*kmax+1)*(2*lmax+1)-1
out = numpy.zeros((9,nmiller))
print("Total number of h k l permutations: %d"%nmiller)
idx = -1
for hh in range(-hmax,hmax+1):
for kk in range(-kmax,kmax+1):
for ll in range(-lmax,lmax+1):
if hh == 0 and kk == 00 and ll == 00: continue
dspacing = xraylib.Crystal_dSpacing(cryst,hh,kk,ll )
fH = xraylib.Crystal_F_H_StructureFactor(cryst, photon_energy_in_keV, hh, kk, ll, debyeWaller, rel_angle)
idx += 1
# print("hkl: %3d %3d %3d, %5.3f A, F=%5.1f, idx:%4d"%(hh,kk,ll,dspacing, numpy.abs(numpy.real(fH)),idx))
out[0,idx] = hh
out[1,idx] = kk
out[2,idx] = ll
out[3,idx] = dspacing
out[4,idx] = numpy.abs(numpy.real(fH))
# out[5,idx] = xraylib.Bragg_angle(cryst,photon_energy_in_keV,hh,kk,ll ) * 2 * 180 / numpy.pi #2theta in deg
out[5,idx] = numpy.arcsin(wavelength_in_A/2/dspacing) * 180.0 / numpy.pi * 2
out[6,idx] = 1.0 # reserved for multiplicity
# reserved for intensity out[7,idx]
# reserved for normalized intensity out[8,idx]
n = out.shape[1]
#
# remove forbidden (or low intensity) reflections
#
if structure_factor_min >= 0:
igood = numpy.where( out[4,:] > structure_factor_min)
igood = numpy.array(igood)
igood.shape = -1
print("igood (forbiden) shape: ",igood.shape)
out = out[:,igood]
n = out.shape[1]
print("shape arter removing forbidden: ",out.shape)
#
# group by multiplicity
#
if 1:
# define a flag that distinguishes different reflections
out_flag = numpy.abs(out[0,:]) + numpy.abs(out[1,:]) * 2 + numpy.abs(out[2,:]) * 4
tmp = out[5,:] * (1.0 + out_flag * 1e-5)
shit, igood = numpy.unique(tmp, return_index=True)
igood = numpy.array(igood)
igood.shape = -1
n = igood.shape[0]
print("igood (multiplicity) shape: ",igood.shape)
out = out[:,igood]
tmp2 = tmp[igood]
# set multiplicities
for i in range(n):
print(i, numpy.array(numpy.where(tmp == tmp2[i])).size )
out[6,i] = numpy.array(numpy.where(tmp == tmp2[i])).size
#
# compute intensities
#
for i in range(n):
# M * F**2 * lorent_etc
intensity = out[6,i] * out[4,i]**2 * lorentz(0.5*out[5,i])
print("hkl, M, F, L:",out[0,i],out[1,i],out[2,i],out[6,i],out[4,i],lorentz(0.5*out[5,i]))
out[7,i] = intensity
intensity_max = out[7,:].max()
print("intensity: ", out[7,:])
print("intensity_max: ",intensity_max)
for i in range(n):
out[8,i] = 100 * out[7,i] / intensity_max
#
# remove reflections at theta >
#
igood = numpy.where( out[5,:] <= twotheta_max)
igood = numpy.array(igood)
igood.shape = -1
out = out[:,igood]
txt = ("%4s "*3+"%15s "*4+"%15s "+"%15s "+"\n")%('h','k','l','2*Theta','d-spc','|F|','M','IntAll','IntNorm')
# ,format='(3A4,4A15,A15,2A15)')
n = out.shape[1]
# 0 = miller index h
# 1 = miller index k
# 2 = miller index l
# 3 = dspacing in A
# 4 = |Real(Fh)} with Fh the structure factor
# 5 = 2thete: Twice the Bragg angle
# 6 = multiplicity of the reflection
# 7 = intensity (arbitrary units)
# 8 = intensity (% of highest reflection)
for i in range(n):
txt += "%4d %4d %4d %15.5f %15.5f %15.5f %15d %15.5f %15.5f \n"%(
out[0,i],out[1,i],out[2,i],
out[5,i],out[3,i],out[4,i],out[6,i],out[7,i],out[8,i])
if file_out != "":
f = open(file_out,'w')
f.write(txt)
f.close()
if verbose:
print(txt)
return out.copy()
def reconvert_axes(p):
p2 = p.copy()
beta = 2 * numpy.arctan(p['a']/p['b'])
p2['beta'] = beta * 180 / numpy.pi
at = p2['atom']
for i,iat in enumerate(at):
x = iat['x']
y = iat['y']
z = iat['z']
x_new = ( x + y - 1)
y_new = z
z_new =( y - x )
if x_new < 0: x_new += 1
if y_new < 0: y_new += 1
if z_new < 0: z_new += 1
iat['x'] = x_new
iat['y'] = y_new
iat['z'] = z_new
# print("%10s (%4.3f %4.3f) new: (%4.3f %4.3f) "%(iat['label'],x,y,x_new,z_new))
p2['a'] = numpy.sqrt( (p['a']/2)**2 + (p['b']/2)**2 )
p2['c'] = p2['a']
p2['b'] = p['c']
p2['name'] = p['name']+b" WITH AXES CHANGED"
return p2
def broad_peaks(out,step_in_twotheta=0.02,FWHM=0.05,eta=0.0,file_out=""):
twotheta_min = out[5,:].min()
twotheta_max = out[5,:].max()
twotheta_interval = numpy.abs(twotheta_max - twotheta_min)
epsilon = twotheta_interval * 0.01
twotheta = numpy.arange(start=twotheta_min-epsilon,stop=twotheta_max+epsilon,step=0.02)
intensity = numpy.zeros_like(twotheta)
nlines = out.shape [1]
FWHM = 0.05
eta = 0.0
# 0 = miller index h
# 1 = miller index k
# 2 = miller index l
# 3 = dspacing in A
# 4 = |Real(Fh)} with Fh the structure factor
# 5 = 2thete: Twice the Bragg angle
# 6 = multiplicity of the reflection
# 7 = intensity (arbitrary units)
# 8 = intensity (% of highest reflection)
print("nlines: ",nlines)
for i in range(nlines):
# i0 = ( out[4,i] )**2 * out[7,i] * lorentz(out[5,i]/2.)
# i0 = out[7,i]
intensity = intensity + voigt1(twotheta,[out[7,i] ,out[5,i],FWHM,eta],area=1)
intensity /= intensity.max()
intensity *= 100.0
if file_out != "":
f = open(file_out,'w')
for i in range(len(twotheta)):
f.write("%f %f \n"%(twotheta[i],intensity[i]))
f.close()
return twotheta,intensity
#
# tests
#
def test_sepiolite_pattern():
cryst = structure_sepiolite()
out = calculate_reflections(cryst, wavelength_in_A=1.0, twotheta_max=30.0, structure_factor_min=1e-3,file_out="",verbose=1)
print("out shape",out.shape)
plot_lines(out[5,:],out[8,:])
def test_group_si():
si = structure_silicon()
out = calculate_reflections(si, wavelength_in_A=1.0, twotheta_max=60.0, structure_factor_min=1e-3,file_out="",verbose=1)
plot_lines(out[5,:],out[8,:],toptitle="Si",noblock=1)
#
#
ss = structure_group(si,si,axis='a')
ss_ss = structure_group(ss,ss,axis='b')
ss_ss_ss = structure_group(ss_ss,ss_ss,axis='c')
out = calculate_reflections(ss_ss_ss, wavelength_in_A=1.0, twotheta_max=60.0, structure_factor_min=1e-3,file_out="",verbose=1)
plot_lines(out[5,:],out[8,:],toptitle="SiSi",noblock=0)
print(structure_info(si))
print(structure_info(ss_ss_ss))
def test_group_sepiolite():
s = structure_sepiolite()
out = calculate_reflections(s, wavelength_in_A=1.0, twotheta_max=15.0, structure_factor_min=1e-3,file_out="",verbose=1)
plot_lines(out[5,:],out[8,:],toptitle="Sepiolite",noblock=1)
#
#
ss = structure_group(s,s,axis='a')
ss_ss = structure_group(ss,ss,axis='b')
ss_ss_ss = structure_group(ss_ss,ss_ss,axis='c')
#
out = calculate_reflections(ss_ss_ss, wavelength_in_A=1.0, twotheta_max=15.0, structure_factor_min=1e-3,file_out="",verbose=1)
plot_lines(out[5,:],out[8,:],toptitle="Supercell",noblock=0)
print(structure_info(s))
print(structure_info(ss_ss_ss))
def test_group_ab(a=structure_sepiolite(),b=structure_palygorskiteO()):
out = calculate_reflections(a, wavelength_in_A=1.0, twotheta_max=15.0, structure_factor_min=1e-3,file_out="",verbose=1)
plot_lines(out[5,:],out[8,:],toptitle=a['name'],noblock=1)
#
#
#
ab = structure_group(a,b,axis='a')
ab_ab = structure_group(ab,ab,axis='b')
ab_ab_ab = structure_group(ab_ab,ab_ab,axis='c')
#
out = calculate_reflections(ab_ab_ab, wavelength_in_A=1.0, twotheta_max=15.0, structure_factor_min=1e-3,file_out="",verbose=1)
plot_lines(out[5,:],out[8,:],toptitle=ab_ab_ab['name'],noblock=0)
print(structure_info(ab_ab_ab))
#
# main program
#
if __name__ == "__main__":
p = structure_MgO()
out = calculate_reflections(p, wavelength_in_A=1.54, twotheta_max=70, structure_factor_min=1e-3,file_out="",verbose=1)
plot_lines(out[5,:],out[8,:],toptitle="MgO",noblock=0)
twotheta,intensity = broad_peaks(out,step_in_twotheta=0.02,FWHM=0.05,eta=0.0,file_out="tmp")
plot_pattern(twotheta,intensity)
# test_sepiolite_pattern()
# test_group_si()
# test_group_sepiolite()
# test_group_ab(a=structure_palygorskiteO(),b=structure_palygorskiteO())
# pO = structure_palygorskiteO()
# p = reconvert_axes(pO)
#
#
# p = structure_palygorskite_new()
#
#
# out = calculate_reflections(p, wavelength_in_A=0.86100131, twotheta_max=30, structure_factor_min=1e-3,file_out="",verbose=1)
#
# plot_lines(out[5,:],out[8,:],toptitle="Palygorskite_new",noblock=0)
#
# twotheta,intensity = broad_peaks(out,step_in_twotheta=0.02,FWHM=0.05,eta=0.0,file_out="tmp")
#
#
# plot_pattern(twotheta,intensity)