Source Code for Module diffpy.srrietveld.atom

  1  ############################################################################## 
  2  # 
  3  # diffpy.srrietveld by DANSE Diffraction group 
  4  #                   Simon J. L. Billinge 
  5  #                   (c) 2009 Trustees of the Columbia University 
  6  #                   in the City of New York.  All rights reserved. 
  7  # 
  8  # File coded by:    Yingrui Shang 
  9  # 
 10  # See AUTHORS.txt for a list of people who contributed. 
 11  # See LICENSE.txt for license information. 
 12  # 
 13  ############################################################################## 
 14  """ 
 15  This package contains the Atom class in SrRietveld, which is an script interface 
 16  to access the atom information 
 17  """ 
 18   
 19  __id__ = "$Id: atom.py 6726 2011-08-25 09:36:23Z yshang $" 
 20   
 21  from diffpy.refinementdata.refinable import Refinable 
 22  from diffpy.srrietveld.paramnames import PARAMNAMES 
 23   
 24 -class Atom(Refinable): 
 25       
 26      """Atom is a Refinable component which contains multiple parameters. 
 27      A composite function may also contain other functions. 
 28       
 29      data member: 
 30           
 31          formula: a string of the function definition in C style 
 32          variables: a space separated string of all variables in the formula 
 33      """ 
 34 -    def __init__(self, owner, name=None, handle=None, formula=None, variables=None, shape=None): 
 35          """Initialization. 
 36           
 37          @type owner:    a data project 
 38          @param owner:    the owner, which is usually a refinement. 
 39          @type name:    string 
 40          @param name     the name of the pattern 
 41          @type handle:    a HDF5Handle object 
 42          @param handle: a HDF5Handle pointing to the underlying HDF5 node.   
 43          @type formula:    string 
 44          @param formula:    a string of the function definition in C style 
 45          @type variables:    a space separated string 
 46          @param variables:    a space separated string of all variables  
 47   
 48          A name is passed to the initialization method when creating a node. 
 49           
 50          A handle is passed to the inialization method in two cases: 
 51              1.  when loading from a HDF5 file; 
 52              2.  when creating a HDF5 file but the object is a hard link to  
 53                  a preexisiting one. 
 54                   
 55          In the case when both name and handle are given, name will be simply ignored. 
 56          In the case when neither name nor handle is given, an exception will be raised. 
 57           
 58          Generally, in the scripting interface, users do not have to call this  
 59          constructor directly 
 60          """ 
 61          Refinable.__init__(self, owner, name, handle, shape) 
 62          return 
 63       
 64       
 65 -    def getEngineType(self): 
 66          '''Get the engine type for this refinement 
 67           
 68          @return:    the string of the engine type, for example I{"gsas"} or I{"fullprof"}''' 
 69           
 70          return self.owner.owner.getEngineType() 
 71       
 72 -    def getBiso(self): 
 73          ''' 
 74          Get the Biso values 
 75           
 76          @return: the Biso values 
 77          ''' 
 78          return self.getByPath(PARAMNAMES[self.getEngineType()]["Biso"]) 
 79       
 80 -    def getBisoSigma(self): 
 81          ''' 
 82          Get the Biso standard deviations 
 83           
 84          @return: the Biso standard deviations 
 85          ''' 
 86          return self.getSigmaByPath(PARAMNAMES[self.getEngineType()]["Biso"]) 
 87       
 88 -    def getName(self): 
 89          ''' 
 90          Get atom name. The atom name is the atom type with the id number  
 91           
 92          @return: the atom name string 
 93          ''' 
 94          return self.getByPath(PARAMNAMES[self.getEngineType()]["name"]).first() 
 95           
 96 -    def getOccupation(self): 
 97          ''' 
 98          Get the occupations of the atom 
 99           
100          @return: the occupation values 
101          ''' 
102          return self.getByPath(PARAMNAMES[self.getEngineType()]["occupation"]) 
103       
104 -    def getType(self): 
105          ''' 
106          Get atom type 
107           
108          @return: the atoms type 
109          ''' 
110          return self.getByPath(PARAMNAMES[self.getEngineType()]["type"]).first() 
111           
112 -    def getUiso(self): 
113          ''' 
114          Get the Uiso values 
115           
116          @return: the Uiso values 
117          ''' 
118          return self.getByPath(PARAMNAMES[self.getEngineType()]["Uiso"]) 
119       
120 -    def getUisoSigma(self): 
121          ''' 
122          Get the Uiso standard deviations 
123           
124          @return: the Uiso standard deviations 
125          ''' 
126          return self.getSigmaByPath(PARAMNAMES[self.getEngineType()]["Uiso"]) 
127       
128 -    def getX(self): 
129          ''' 
130          Get the x fractional coordinates 
131           
132          @return: the x fractional coordinate values 
133          ''' 
134          return self.getByPath(PARAMNAMES[self.getEngineType()]["X"]) 
135       
136 -    def getXSigma(self): 
137          ''' 
138          Get the x fractional coordinate standard deviations 
139           
140          @return: the x fractional coordinate standard deviations 
141          ''' 
142          return self.getSigmaByPath(PARAMNAMES[self.getEngineType()]["X"]) 
143           
144 -    def getY(self): 
145          ''' 
146          Get the y fractional coordinates 
147           
148          @return: the y fractional coordinate values 
149          ''' 
150          return self.getByPath(PARAMNAMES[self.getEngineType()]["Y"]) 
151       
152 -    def getYSigma(self): 
153          ''' 
154          Get the y fractional coordinate standard deviations 
155           
156          @return: the y fractional coordinate standard deviations 
157          ''' 
158          return self.getSigmaByPath(PARAMNAMES[self.getEngineType()]["Y"]) 
159           
160 -    def getZ(self): 
161          ''' 
162          Get the z fractional coordinates 
163           
164          @return: the z fractional coordinate values 
165          ''' 
166          return self.getByPath(PARAMNAMES[self.getEngineType()]["Z"]) 
167           
168 -    def getZSigma(self): 
169          ''' 
170          Get the z fractional coordinate standard deviations 
171           
172          @return: the z fractional coordinate standard deviations 
173          ''' 
174          return self.getSigmaByPath(PARAMNAMES[self.getEngineType()]["Z"]) 
175