Changeset 4882


Ignore:
Timestamp:
Apr 13, 2021 7:08:28 AM (6 months ago)
Author:
toby
Message:

new routine: getCellSU

Location:
trunk
Files:
2 edited

Legend:

Unmodified
Added
Removed
  • trunk/GSASIIstrIO.py

    r4868 r4882  
    18991899       
    19001900def getCellEsd(pfx,SGData,A,covData):
    1901     'needs a doc string'
     1901    '''Compute the standard uncertainty on cell parameters
     1902   
     1903    :param str pfx: prefix of form p::
     1904    :param SGdata: space group information
     1905    :param list A: Reciprocal cell Ai terms
     1906    :param dict covData: covariance tree item
     1907    '''
    19021908    rVsq = G2lat.calc_rVsq(A)
    19031909    G,g = G2lat.A2Gmat(A)       #get recip. & real metric tensors
     
    19531959        CS[3:6] = 0.0
    19541960    return [CS[0],CS[1],CS[2],CS[5],CS[4],CS[3],sigVol]
    1955    
     1961
     1962def getCellSU(pId,hId,SGData,parmDict,covData):
     1963    '''Compute the unit cell parameters and standard uncertainties
     1964    where lattice parameters and Hstrain (Dij) may be refined
     1965   
     1966    :param pId: phase index
     1967    :param hId: histogram index
     1968    :param SGdata: space group information
     1969    :param dict parmDict: parameter dict, must have all non-zero Dij and Ai terms
     1970    :param dict covData: covariance tree item
     1971    '''
     1972
     1973    Dnames = ['{}:{}:D{}'.format(pId,hId,i) for i in ['11','22','33','12','13','23']]
     1974    Anames = ['{}::A{}'.format(pId,i) for i in range(6)]
     1975    Ai = [parmDict[i] for i in Anames]
     1976    Dij = [parmDict.get(i,0.) for i in Dnames]   
     1977    A = np.array(Ai) + np.array(Dij)
     1978    cell = list(G2lat.A2cell(A)) + [G2lat.calc_V(A)]
     1979    rVsq = G2lat.calc_rVsq(A)
     1980    G,g = G2lat.A2Gmat(A)       #get recip. & real metric tensors
     1981    varyList = covData['varyList']
     1982    covMatrix = covData['covMatrix']
     1983    if len(covMatrix):
     1984        vcov = G2mth.getVCov(Anames+Dnames,varyList,covMatrix)
     1985        for i in [0,6]:
     1986            for j in [0,6]:
     1987                if SGData['SGLaue'] in ['3', '3m1', '31m', '6/m', '6/mmm']:
     1988                    vcov[1+i,1+j] = vcov[3+i,3+j] = vcov[i,1+j] = vcov[1+i,j] = vcov[i,j]
     1989                    vcov[1+i,3+j] = vcov[3+i,1+j] = vcov[i,3+j] = vcov[3+i,j] = vcov[i,j]
     1990                    vcov[1+i,2+j] = vcov[2+i,1+j] = vcov[2+i,3+j] = vcov[3+i,2+j] = vcov[i,2+j]
     1991                elif SGData['SGLaue'] in ['m3','m3m']:
     1992                    vcov[i:3+i,j:3+j] = vcov[i,j]
     1993                elif SGData['SGLaue'] in ['4/m', '4/mmm']:
     1994                    vcov[i:2+i,j:2+j] = vcov[i,j]
     1995                    vcov[1+i,2+j] = vcov[2+i,1+j] = vcov[i,2+j]
     1996                elif SGData['SGLaue'] in ['3R','3mR']:
     1997                    vcov[i:3+j,i:3+j] = vcov[i,j]
     1998                    #        vcov[4,4] = vcov[5,5] = vcov[3,3]
     1999                    vcov[3+i:6+i,3+j:6+j] = vcov[3,3+j]
     2000                    vcov[i:3+i,3+j:6+j] = vcov[i,3+j]
     2001                    vcov[3+i:6+i,j:3+j] = vcov[3+i,j]
     2002    else:
     2003        vcov = np.eye(12)
     2004    delt = 1.e-9
     2005    drVdA = np.zeros(12)
     2006    for i in range(12):
     2007        A[i%6] += delt
     2008        drVdA[i] = G2lat.calc_rVsq(A)
     2009        A[i%6] -= 2*delt
     2010        drVdA[i] -= G2lat.calc_rVsq(A)
     2011        A[i%6] += delt
     2012    drVdA /= 2.*delt
     2013    srcvlsq = np.inner(drVdA,np.inner(drVdA,vcov))
     2014    Vol = 1/np.sqrt(rVsq)
     2015    sigVol = Vol**3*np.sqrt(srcvlsq)/2.         #ok - checks with GSAS
     2016   
     2017    dcdA = np.zeros((12,12))
     2018    for i in range(12):
     2019        pdcdA =np.zeros(12)
     2020        A[i%6] += delt
     2021        pdcdA += G2lat.A2cell(A)+G2lat.A2cell(A)
     2022        A[i%6] -= 2*delt
     2023        pdcdA -= G2lat.A2cell(A)+G2lat.A2cell(A)
     2024        A[i%6] += delt
     2025        dcdA[i] = pdcdA/(2.*delt)
     2026    sigMat = np.inner(dcdA,np.inner(dcdA,vcov))
     2027    var = np.diag(sigMat)
     2028    CS = np.where(var>0.,np.sqrt(var),0.)
     2029    if SGData['SGLaue'] in ['3', '3m1', '31m', '6/m', '6/mmm','m3','m3m','4/m','4/mmm']:
     2030        CS[3:6] = 0.0
     2031    return cell,[CS[0],CS[1],CS[2],CS[5],CS[4],CS[3],sigVol]
     2032
    19562033def SetPhaseData(parmDict,sigDict,Phases,RBIds,covData,RestraintDict=None,pFile=None):
    19572034    '''Called after a refinement to transfer parameters from the parameter dict to
  • trunk/docs/source/index.rst

    r4880 r4882  
    55=================================
    66
    7 The following documentation is intended for those wishing to code
    8 withing the GSAS-II framework, those planning to understand how
     7The documentation here is intended for those wishing to extend the
     8capabilities within the GSAS-II framework, for scientists/students
     9working to understand how
    910GSAS-II works, or for people wishing to develop scripting applications
    10 using the API (:mod:`GSASIIscriptable`). Note that many data structures
    11 used in GSAS-II are defined in module :mod:`GSASIIobj`.
     11using the GSAS-II Python API (module :mod:`GSASIIscriptable`). Note that many
     12data structures used in GSAS-II are defined in module :mod:`GSASIIobj`.
    1213
    13 For information on obtaining or learning to use GSAS-II, please see
    14 the information on the GSAS-II home page:
    15 https://subversion.xray.aps.anl.gov/trac/pyGSAS
    16 and pages referenced there.
    17 
     14For information on downloading/installing GSAS-II, please see
     15the GSAS-II home page:
     16https://subversion.xray.aps.anl.gov/trac/pyGSAS. To learn how to
     17use GSAS-II, please see the tutorials referenced in the home page.
    1818
    1919.. toctree::
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