1 | """ |
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2 | This module intends to compute the neutron scattering length density |
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3 | of a molecule. It uses methods of the periodictable package to provide |
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4 | easy user interface for Sld calculator applications. |
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5 | """ |
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6 | |
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7 | import periodictable |
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8 | from periodictable import formula |
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9 | from periodictable.xsf import xray_energy, xray_sld_from_atoms |
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10 | from periodictable.constants import avogadro_number |
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11 | import periodictable.nsf |
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12 | neutron_sld_from_atoms= periodictable.nsf.neutron_sld_from_atoms |
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13 | |
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14 | class SldCalculator(object): |
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15 | """ |
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16 | Given a molecule, a density and a wavelength, this class |
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17 | determine scattering length density. |
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18 | """ |
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19 | def __init__(self): |
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20 | self.wavelength = 6.0 |
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21 | self.coherence = 0.0 |
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22 | self.absorption = 0.0 |
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23 | self.incoherence = 0.0 |
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24 | self.sld_formula = None |
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25 | self.volume = 0.0 |
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26 | self.density = None |
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27 | self.length= 0.0 |
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28 | |
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29 | def set_value(self, user_formula, density, wavelength=6.0): |
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30 | """ |
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31 | Store values into the sld calculator and compute the corresponding |
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32 | volume. |
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33 | """ |
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34 | self.wavelength = wavelength |
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35 | self.density = float(density) |
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36 | self.sld_formula = formula(str(user_formula), density=self.density) |
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37 | |
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38 | if self.density == 0: |
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39 | raise ZeroDivisionError("integer division or modulo\ |
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40 | by zero for density") |
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41 | self.volume = (self.sld_formula.mass / self.density) / avogadro_number\ |
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42 | *1.0e24 |
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43 | |
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44 | |
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45 | def calculate_xray_sld(self, element): |
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46 | """ |
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47 | Get an element and compute the corresponding SLD for a given formula |
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48 | @param element: elementis a string of existing atom |
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49 | """ |
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50 | myformula = formula(str(element)) |
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51 | if len(myformula.atoms) != 1: |
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52 | return |
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53 | element = myformula.atoms.keys()[0] |
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54 | energy = xray_energy(element.K_alpha) |
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55 | atom = self.sld_formula.atoms |
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56 | atom_reel, atom_im = xray_sld_from_atoms(atom, |
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57 | density= self.density, |
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58 | energy= energy) |
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59 | return atom_reel, atom_im |
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60 | |
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61 | |
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62 | def calculate_neutron_sld(self): |
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63 | """ |
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64 | Compute the neutron SLD for a given molecule |
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65 | @return absorp: absorption |
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66 | return coh: coherence cross section |
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67 | @return inc: incoherence cross section |
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68 | """ |
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69 | if self.density == 0: |
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70 | raise ZeroDivisionError("integer division or modulo\ |
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71 | by zero for density") |
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72 | return |
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73 | atom = self.sld_formula.atoms |
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74 | coh, absorp, inc = neutron_sld_from_atoms(atom, self.density, |
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75 | self.wavelength) |
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76 | #Don't know if value is return in cm or cm^(-1).assume return in cm |
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77 | # to match result of neutron inc of Alan calculator |
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78 | self.incoherence = inc |
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79 | self.absorption = absorp |
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80 | self.coherence = coh |
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81 | return self.coherence, self.absorption, self.incoherence |
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82 | |
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83 | |
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84 | def calculate_length(self): |
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85 | """ |
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86 | Compute the neutron 1/e length |
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87 | """ |
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88 | self.length = (self.coherence + self.absorption +\ |
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89 | self.incoherence) / self.volume |
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90 | return self.length |
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91 | |
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92 | |
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93 | def calculate_coherence_im(self): |
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94 | """ |
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95 | Compute imaginary part of the absorption |
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96 | """ |
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97 | atom = self.sld_formula.atoms |
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98 | #im: imaginary part of neutron SLD |
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99 | im = 0 |
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100 | for el, count in atom.iteritems(): |
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101 | if el.neutron.b_c_i is not None: |
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102 | im += el.neutron.b_c_i * count |
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103 | |
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104 | if self.volume != 0: |
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105 | im = im/self.volume |
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106 | else: |
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107 | raise ZeroDivisionError("integer division or modulo\ |
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108 | by zero for volume") |
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109 | return im |
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