| 1 | #GSASII cell indexing program: variation on that of A. Coehlo |
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| 2 | # includes cell refinement from peak positions (not zero as yet) |
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| 3 | ########### SVN repository information ################### |
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| 4 | # $Date: 2011-11-28 16:32:08 +0000 (Mon, 28 Nov 2011) $ |
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| 5 | # $Author: vondreele $ |
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| 6 | # $Revision: 429 $ |
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| 7 | # $URL: branch/MPbranch/GSASIIindex.py $ |
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| 8 | # $Id: GSASIIindex.py 429 2011-11-28 16:32:08Z vondreele $ |
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| 9 | ########### SVN repository information ################### |
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| 10 | import math |
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| 11 | import wx |
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| 12 | import time |
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| 13 | import numpy as np |
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| 14 | import numpy.linalg as nl |
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| 15 | import GSASIIpath |
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| 16 | import GSASIIlattice as G2lat |
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| 17 | import scipy.optimize as so |
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| 18 | |
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| 19 | # trig functions in degrees |
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| 20 | sind = lambda x: math.sin(x*math.pi/180.) |
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| 21 | asind = lambda x: 180.*math.asin(x)/math.pi |
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| 22 | tand = lambda x: math.tan(x*math.pi/180.) |
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| 23 | atand = lambda x: 180.*math.atan(x)/math.pi |
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| 24 | atan2d = lambda y,x: 180.*math.atan2(y,x)/math.pi |
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| 25 | cosd = lambda x: math.cos(x*math.pi/180.) |
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| 26 | acosd = lambda x: 180.*math.acos(x)/math.pi |
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| 27 | rdsq2d = lambda x,p: round(1.0/math.sqrt(x),p) |
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| 28 | #numpy versions |
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| 29 | npsind = lambda x: np.sin(x*np.pi/180.) |
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| 30 | npasind = lambda x: 180.*np.arcsin(x)/math.pi |
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| 31 | npcosd = lambda x: np.cos(x*math.pi/180.) |
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| 32 | nptand = lambda x: np.tan(x*math.pi/180.) |
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| 33 | npatand = lambda x: 180.*np.arctan(x)/np.pi |
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| 34 | npatan2d = lambda y,x: 180.*np.arctan2(y,x)/np.pi |
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| 35 | |
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| 36 | def scaleAbyV(A,V): |
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| 37 | v = G2lat.calc_V(A) |
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| 38 | scale = math.exp(math.log(v/V)/3.)**2 |
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| 39 | for i in range(6): |
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| 40 | A[i] *= scale |
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| 41 | |
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| 42 | def ranaxis(dmin,dmax): |
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| 43 | import random as rand |
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| 44 | return rand.random()*(dmax-dmin)+dmin |
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| 45 | |
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| 46 | def ran2axis(k,N): |
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| 47 | import random as rand |
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| 48 | T = 1.5+0.49*k/N |
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| 49 | # B = 0.99-0.49*k/N |
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| 50 | # B = 0.99-0.049*k/N |
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| 51 | B = 0.99-0.149*k/N |
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| 52 | R = (T-B)*rand.random()+B |
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| 53 | return R |
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| 54 | |
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| 55 | #def ranNaxis(k,N): |
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| 56 | # import random as rand |
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| 57 | # T = 1.0+1.0*k/N |
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| 58 | # B = 1.0-1.0*k/N |
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| 59 | # R = (T-B)*rand.random()+B |
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| 60 | # return R |
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| 61 | |
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| 62 | def ranAbyV(Bravais,dmin,dmax,V): |
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| 63 | cell = [0,0,0,0,0,0] |
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| 64 | bad = True |
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| 65 | while bad: |
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| 66 | bad = False |
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| 67 | cell = rancell(Bravais,dmin,dmax) |
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| 68 | G,g = G2lat.cell2Gmat(cell) |
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| 69 | A = G2lat.Gmat2A(G) |
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| 70 | if G2lat.calc_rVsq(A) < 1: |
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| 71 | scaleAbyV(A,V) |
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| 72 | cell = G2lat.A2cell(A) |
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| 73 | for i in range(3): |
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| 74 | bad |= cell[i] < dmin |
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| 75 | return A |
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| 76 | |
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| 77 | def ranAbyR(Bravais,A,k,N,ranFunc): |
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| 78 | R = ranFunc(k,N) |
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| 79 | if Bravais in [0,1,2]: #cubic - not used |
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| 80 | A[0] = A[1] = A[2] = A[0]*R |
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| 81 | A[3] = A[4] = A[5] = 0. |
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| 82 | elif Bravais in [3,4]: #hexagonal/trigonal |
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| 83 | A[0] = A[1] = A[3] = A[0]*R |
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| 84 | A[2] *= R |
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| 85 | A[4] = A[5] = 0. |
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| 86 | elif Bravais in [5,6]: #tetragonal |
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| 87 | A[0] = A[1] = A[0]*R |
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| 88 | A[2] *= R |
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| 89 | A[3] = A[4] = A[5] = 0. |
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| 90 | elif Bravais in [7,8,9,10]: #orthorhombic |
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| 91 | A[0] *= R |
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| 92 | A[1] *= R |
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| 93 | A[2] *= R |
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| 94 | A[3] = A[4] = A[5] = 0. |
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| 95 | elif Bravais in [11,12]: #monoclinic |
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| 96 | A[0] *= R |
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| 97 | A[1] *= R |
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| 98 | A[2] *= R |
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| 99 | A[4] *= R |
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| 100 | A[3] = A[5] = 0. |
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| 101 | else: #triclinic |
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| 102 | A[0] *= R |
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| 103 | A[1] *= R |
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| 104 | A[2] *= R |
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| 105 | A[3] *= R |
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| 106 | A[4] *= R |
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| 107 | A[5] *= R |
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| 108 | return A |
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| 109 | |
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| 110 | def rancell(Bravais,dmin,dmax): |
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| 111 | if Bravais in [0,1,2]: #cubic |
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| 112 | a = b = c = ranaxis(dmin,dmax) |
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| 113 | alp = bet = gam = 90 |
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| 114 | elif Bravais in [3,4]: #hexagonal/trigonal |
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| 115 | a = b = ranaxis(dmin,dmax) |
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| 116 | c = ranaxis(dmin,dmax) |
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| 117 | alp = bet = 90 |
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| 118 | gam = 120 |
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| 119 | elif Bravais in [5,6]: #tetragonal |
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| 120 | a = b = ranaxis(dmin,dmax) |
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| 121 | c = ranaxis(dmin,dmax) |
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| 122 | alp = bet = gam = 90 |
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| 123 | elif Bravais in [7,8,9,10]: #orthorhombic - F,I,C,P - a<b<c convention |
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| 124 | abc = [ranaxis(dmin,dmax),ranaxis(dmin,dmax),ranaxis(dmin,dmax)] |
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| 125 | abc.sort() |
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| 126 | a = abc[0] |
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| 127 | b = abc[1] |
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| 128 | c = abc[2] |
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| 129 | alp = bet = gam = 90 |
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| 130 | elif Bravais in [11,12]: #monoclinic - C,P - a<c convention |
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| 131 | ac = [ranaxis(dmin,dmax),ranaxis(dmin,dmax)] |
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| 132 | ac.sort() |
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| 133 | a = ac[0] |
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| 134 | b = ranaxis(dmin,dmax) |
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| 135 | c = ac[1] |
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| 136 | alp = gam = 90 |
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| 137 | bet = ranaxis(90.,130.) |
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| 138 | else: #triclinic - a<b<c convention |
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| 139 | abc = [ranaxis(dmin,dmax),ranaxis(dmin,dmax),ranaxis(dmin,dmax)] |
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| 140 | abc.sort() |
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| 141 | a = abc[0] |
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| 142 | b = abc[1] |
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| 143 | c = abc[2] |
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| 144 | r = 0.5*b/c |
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| 145 | alp = ranaxis(acosd(r),acosd(-r)) |
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| 146 | r = 0.5*a/c |
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| 147 | bet = ranaxis(acosd(r),acosd(-r)) |
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| 148 | r = 0.5*a/b |
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| 149 | gam = ranaxis(acosd(r),acosd(-r)) |
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| 150 | return [a,b,c,alp,bet,gam] |
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| 151 | |
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| 152 | def calc_M20(peaks,HKL): |
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| 153 | diff = 0 |
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| 154 | X20 = 0 |
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| 155 | for Nobs20,peak in enumerate(peaks): |
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| 156 | if peak[3]: |
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| 157 | Qobs = 1.0/peak[7]**2 |
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| 158 | Qcalc = 1.0/peak[8]**2 |
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| 159 | diff += abs(Qobs-Qcalc) |
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| 160 | elif peak[2]: |
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| 161 | X20 += 1 |
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| 162 | if Nobs20 == 19: |
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| 163 | d20 = peak[7] |
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| 164 | break |
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| 165 | else: |
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| 166 | d20 = peak[7] |
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| 167 | Nobs20 = len(peaks) |
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| 168 | for N20,hkl in enumerate(HKL): |
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| 169 | if hkl[3] < d20: |
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| 170 | break |
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| 171 | eta = diff/Nobs20 |
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| 172 | Q20 = 1.0/d20**2 |
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| 173 | if diff: |
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| 174 | M20 = Q20/(2.0*diff) |
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| 175 | else: |
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| 176 | M20 = 0 |
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| 177 | M20 /= (1.+X20) |
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| 178 | return M20,X20 |
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| 179 | |
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| 180 | def sortM20(cells): |
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| 181 | #cells is M20,X20,Bravais,a,b,c,alp,bet,gam |
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| 182 | #sort highest M20 1st |
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| 183 | T = [] |
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| 184 | for i,M in enumerate(cells): |
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| 185 | T.append((M[0],i)) |
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| 186 | D = dict(zip(T,cells)) |
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| 187 | T.sort() |
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| 188 | T.reverse() |
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| 189 | X = [] |
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| 190 | for key in T: |
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| 191 | X.append(D[key]) |
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| 192 | return X |
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| 193 | |
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| 194 | def sortVolume(cells): |
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| 195 | #cells is M20,X20,Bravais,a,b,c,alp,bet,gam,volume |
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| 196 | #sort smallest volume 1st |
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| 197 | T = [] |
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| 198 | for i,M in enumerate(cells): |
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| 199 | T.append((M[9],i)) |
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| 200 | D = dict(zip(T,cells)) |
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| 201 | T.sort() |
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| 202 | X = [] |
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| 203 | for key in T: |
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| 204 | X.append(D[key]) |
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| 205 | return X |
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| 206 | |
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| 207 | def IndexPeaks(peaks,HKL): |
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| 208 | import bisect |
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| 209 | N = len(HKL) |
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| 210 | if N == 0: return False |
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| 211 | hklds = list(np.array(HKL).T[3])+[1000.0,0.0,] |
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| 212 | hklds.sort() # ascending sort - upper bound at end |
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| 213 | hklmax = [0,0,0] |
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| 214 | for ipk,peak in enumerate(peaks): |
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| 215 | if peak[2]: |
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| 216 | i = bisect.bisect_right(hklds,peak[7]) # find peak position in hkl list |
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| 217 | dm = peak[7]-hklds[i-1] # peak to neighbor hkls in list |
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| 218 | dp = hklds[i]-peak[7] |
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| 219 | pos = N-i # reverse the order |
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| 220 | if dp > dm: pos += 1 # closer to upper than lower |
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| 221 | if pos >= N: |
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| 222 | print pos,N |
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| 223 | break |
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| 224 | hkl = HKL[pos] # put in hkl |
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| 225 | if hkl[4] >= 0: # peak already assigned - test if this one better |
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| 226 | opeak = peaks[hkl[4]] |
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| 227 | dold = abs(opeak[7]-hkl[3]) |
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| 228 | dnew = min(dm,dp) |
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| 229 | if dold > dnew: # new better - zero out old |
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| 230 | opeak[4:7] = [0,0,0] |
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| 231 | opeak[8] = 0. |
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| 232 | else: # old better - do nothing |
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| 233 | continue |
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| 234 | hkl[4] = ipk |
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| 235 | peak[4:7] = hkl[:3] |
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| 236 | peak[8] = hkl[3] # fill in d-calc |
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| 237 | for peak in peaks: |
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| 238 | peak[3] = False |
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| 239 | if peak[2]: |
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| 240 | if peak[8] > 0.: |
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| 241 | for j in range(3): |
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| 242 | if abs(peak[j+4]) > hklmax[j]: hklmax[j] = abs(peak[j+4]) |
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| 243 | peak[3] = True |
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| 244 | if hklmax[0]*hklmax[1]*hklmax[2] > 0: |
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| 245 | return True |
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| 246 | else: |
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| 247 | return False |
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| 248 | |
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| 249 | def Values2A(ibrav,values): |
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| 250 | if ibrav in [0,1,2]: |
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| 251 | return [values[0],values[0],values[0],0,0,0] |
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| 252 | elif ibrav in [3,4]: |
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| 253 | return [values[0],values[0],values[1],values[0],0,0] |
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| 254 | elif ibrav in [5,6]: |
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| 255 | return [values[0],values[0],values[1],0,0,0] |
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| 256 | elif ibrav in [7,8,9,10]: |
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| 257 | return [values[0],values[1],values[2],0,0,0] |
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| 258 | elif ibrav in [11,12]: |
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| 259 | return [values[0],values[1],values[2],0,values[3],0] |
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| 260 | else: |
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| 261 | return list(values) |
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| 262 | |
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| 263 | def A2values(ibrav,A): |
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| 264 | if ibrav in [0,1,2]: |
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| 265 | return [A[0],] |
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| 266 | elif ibrav in [3,4,5,6]: |
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| 267 | return [A[0],A[2]] |
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| 268 | elif ibrav in [7,8,9,10]: |
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| 269 | return [A[0],A[1],A[2]] |
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| 270 | elif ibrav in [11,12]: |
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| 271 | return [A[0],A[1],A[2],A[4]] |
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| 272 | else: |
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| 273 | return A |
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| 274 | |
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| 275 | def FitHKL(ibrav,peaks,A,Pwr): |
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| 276 | |
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| 277 | def errFit(values,ibrav,d,H,Pwr): |
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| 278 | A = Values2A(ibrav,values) |
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| 279 | Qo = 1./d**2 |
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| 280 | Qc = G2lat.calc_rDsq(H,A) |
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| 281 | return (Qo-Qc)*d**Pwr |
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| 282 | |
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| 283 | Peaks = np.array(peaks).T |
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| 284 | |
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| 285 | values = A2values(ibrav,A) |
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| 286 | result = so.leastsq(errFit,values,full_output=True,ftol=0.0001, |
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| 287 | args=(ibrav,Peaks[7],Peaks[4:7],Pwr)) |
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| 288 | A = Values2A(ibrav,result[0]) |
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| 289 | return True,np.sum(errFit(result[0],ibrav,Peaks[7],Peaks[4:7],Pwr)**2),A,result |
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| 290 | |
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| 291 | def FitHKLZ(wave,ibrav,peaks,A,Z,Zref,Pwr): |
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| 292 | |
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| 293 | def errFit(values,ibrav,d,H,tth,wave,Zref,Pwr): |
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| 294 | Zero = Z |
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| 295 | if Zref: |
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| 296 | Zero = values[-1] |
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| 297 | A = Values2A(ibrav,values[:6]) |
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| 298 | Qo = 1./d**2 |
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| 299 | Qc = G2lat.calc_rDsqZ(H,A,Zero,tth,wave) |
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| 300 | return (Qo-Qc)*d**Pwr |
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| 301 | |
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| 302 | Peaks = np.array(peaks).T |
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| 303 | |
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| 304 | values = A2values(ibrav,A) |
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| 305 | if Zref: |
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| 306 | values.append(Z) |
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| 307 | result = so.leastsq(errFit,values,full_output=True,ftol=0.0001,factor=0.001, |
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| 308 | args=(ibrav,Peaks[7],Peaks[4:7],Peaks[0],wave,Zref,Pwr)) |
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| 309 | A = Values2A(ibrav,result[0][:6]) |
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| 310 | if Zref: |
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| 311 | Z = result[0][-1] |
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| 312 | |
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| 313 | return True,np.sum(errFit(result[0],ibrav,Peaks[7],Peaks[4:7],Peaks[0],wave,Zref,Pwr)**2),A,Z,result |
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| 314 | |
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| 315 | def rotOrthoA(A): |
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| 316 | return [A[1],A[2],A[0],0,0,0] |
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| 317 | |
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| 318 | def swapMonoA(A): |
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| 319 | return [A[2],A[1],A[0],0,A[4],0] |
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| 320 | |
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| 321 | def oddPeak(indx,peaks): |
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| 322 | noOdd = True |
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| 323 | for peak in peaks: |
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| 324 | H = peak[4:7] |
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| 325 | if H[indx] % 2: |
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| 326 | noOdd = False |
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| 327 | return noOdd |
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| 328 | |
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| 329 | def halfCell(ibrav,A,peaks): |
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| 330 | if ibrav in [0,1,2]: |
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| 331 | if oddPeak(0,peaks): |
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| 332 | A[0] *= 2 |
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| 333 | A[1] = A[2] = A[0] |
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| 334 | elif ibrav in [3,4,5,6]: |
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| 335 | if oddPeak(0,peaks): |
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| 336 | A[0] *= 2 |
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| 337 | A[1] = A[0] |
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| 338 | if oddPeak(2,peaks): |
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| 339 | A[2] *=2 |
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| 340 | else: |
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| 341 | if oddPeak(0,peaks): |
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| 342 | A[0] *=2 |
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| 343 | if oddPeak(1,peaks): |
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| 344 | A[1] *=2 |
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| 345 | if oddPeak(2,peaks): |
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| 346 | A[2] *=2 |
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| 347 | return A |
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| 348 | |
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| 349 | def getDmin(peaks): |
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| 350 | return peaks[-1][7] |
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| 351 | |
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| 352 | def getDmax(peaks): |
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| 353 | return peaks[0][7] |
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| 354 | |
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| 355 | def refinePeaksZ(peaks,wave,ibrav,A,Zero,ZeroRef): |
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| 356 | dmin = getDmin(peaks) |
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| 357 | OK,smin,Aref,Z,result = FitHKLZ(wave,ibrav,peaks,A,Zero,ZeroRef,0) |
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| 358 | Peaks = np.array(peaks).T |
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| 359 | H = Peaks[4:7] |
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| 360 | Peaks[8] = 1./np.sqrt(G2lat.calc_rDsqZ(H,Aref,Z,Peaks[0],wave)) |
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| 361 | peaks = Peaks.T |
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| 362 | HKL = G2lat.GenHBravais(dmin,ibrav,Aref) |
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| 363 | M20,X20 = calc_M20(peaks,HKL) |
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| 364 | return len(HKL),M20,X20,Aref,Z |
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| 365 | |
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| 366 | def refinePeaks(peaks,ibrav,A): |
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| 367 | dmin = getDmin(peaks) |
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| 368 | smin = 1.0e10 |
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| 369 | pwr = 8 |
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| 370 | maxTries = 10 |
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| 371 | OK = False |
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| 372 | tries = 0 |
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| 373 | HKL = G2lat.GenHBravais(dmin,ibrav,A) |
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| 374 | while len(HKL) > 2 and IndexPeaks(peaks,HKL): |
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| 375 | Pwr = pwr - (tries % 2) |
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| 376 | HKL = [] |
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| 377 | tries += 1 |
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| 378 | osmin = smin |
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| 379 | oldA = A[:] |
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| 380 | Vold = G2lat.calc_V(oldA) |
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| 381 | OK,smin,A,result = FitHKL(ibrav,peaks,A,Pwr) |
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| 382 | Vnew = G2lat.calc_V(A) |
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| 383 | if Vnew > 2.0*Vold or Vnew < 2.: |
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| 384 | A = ranAbyR(ibrav,oldA,tries+1,maxTries,ran2axis) |
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| 385 | OK = False |
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| 386 | continue |
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| 387 | try: |
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| 388 | HKL = G2lat.GenHBravais(dmin,ibrav,A) |
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| 389 | except FloatingPointError: |
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| 390 | A = oldA |
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| 391 | OK = False |
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| 392 | break |
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| 393 | if len(HKL) == 0: break #absurd cell obtained! |
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| 394 | rat = (osmin-smin)/smin |
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| 395 | if abs(rat) < 1.0e-5 or not OK: break |
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| 396 | if tries > maxTries: break |
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| 397 | if OK: |
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| 398 | OK,smin,A,result = FitHKL(ibrav,peaks,A,2) |
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| 399 | Peaks = np.array(peaks).T |
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| 400 | H = Peaks[4:7] |
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| 401 | try: |
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| 402 | Peaks[8] = 1./np.sqrt(G2lat.calc_rDsq(H,A)) |
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| 403 | peaks = Peaks.T |
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| 404 | except FloatingPointError: |
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| 405 | A = oldA |
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| 406 | |
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| 407 | M20,X20 = calc_M20(peaks,HKL) |
|---|
| 408 | return len(HKL),M20,X20,A |
|---|
| 409 | |
|---|
| 410 | def findBestCell(dlg,ncMax,A,Ntries,ibrav,peaks,V1): |
|---|
| 411 | # dlg & ncMax are used for wx progress bar |
|---|
| 412 | # A != 0 find the best A near input A, |
|---|
| 413 | # A = 0 for random cell, volume normalized to V1; |
|---|
| 414 | # returns number of generated hkls, M20, X20 & A for best found |
|---|
| 415 | mHKL = [3,3,3, 5,5, 5,5, 7,7,7,7, 9,9, 10] |
|---|
| 416 | dmin = getDmin(peaks)-0.05 |
|---|
| 417 | amin = 2.5 |
|---|
| 418 | amax = 5.*getDmax(peaks) |
|---|
| 419 | Asave = [] |
|---|
| 420 | GoOn = True |
|---|
| 421 | if A: |
|---|
| 422 | HKL = G2lat.GenHBravais(dmin,ibrav,A[:]) |
|---|
| 423 | if len(HKL) > mHKL[ibrav]: |
|---|
| 424 | IndexPeaks(peaks,HKL) |
|---|
| 425 | Asave.append([calc_M20(peaks,HKL),A[:]]) |
|---|
| 426 | tries = 0 |
|---|
| 427 | while tries < Ntries: |
|---|
| 428 | if A: |
|---|
| 429 | Abeg = ranAbyR(ibrav,A,tries+1,Ntries,ran2axis) |
|---|
| 430 | if ibrav in [11,12,13]: #monoclinic & triclinic |
|---|
| 431 | Abeg = ranAbyR(ibrav,A,tries/10+1,Ntries,ran2axis) |
|---|
| 432 | else: |
|---|
| 433 | Abeg = ranAbyV(ibrav,amin,amax,V1) |
|---|
| 434 | HKL = G2lat.GenHBravais(dmin,ibrav,Abeg) |
|---|
| 435 | |
|---|
| 436 | if IndexPeaks(peaks,HKL) and len(HKL) > mHKL[ibrav]: |
|---|
| 437 | Lhkl,M20,X20,Aref = refinePeaks(peaks,ibrav,Abeg) |
|---|
| 438 | Asave.append([calc_M20(peaks,HKL),Aref[:]]) |
|---|
| 439 | if ibrav == 9: #C-centered orthorhombic |
|---|
| 440 | for i in range(2): |
|---|
| 441 | Abeg = rotOrthoA(Abeg[:]) |
|---|
| 442 | Lhkl,M20,X20,Aref = refinePeaks(peaks,ibrav,Abeg) |
|---|
| 443 | HKL = G2lat.GenHBravais(dmin,ibrav,Aref) |
|---|
| 444 | IndexPeaks(peaks,HKL) |
|---|
| 445 | Asave.append([calc_M20(peaks,HKL),Aref[:]]) |
|---|
| 446 | elif ibrav == 11: #C-centered monoclinic |
|---|
| 447 | Abeg = swapMonoA(Abeg[:]) |
|---|
| 448 | Lhkl,M20,X20,Aref = refinePeaks(peaks,ibrav,Abeg) |
|---|
| 449 | HKL = G2lat.GenHBravais(dmin,ibrav,Aref) |
|---|
| 450 | IndexPeaks(peaks,HKL) |
|---|
| 451 | Asave.append([calc_M20(peaks,HKL),Aref[:]]) |
|---|
| 452 | else: |
|---|
| 453 | break |
|---|
| 454 | Nc = len(HKL) |
|---|
| 455 | if Nc >= ncMax: |
|---|
| 456 | GoOn = False |
|---|
| 457 | elif dlg: |
|---|
| 458 | GoOn = dlg.Update(Nc)[0] |
|---|
| 459 | if not GoOn: |
|---|
| 460 | break |
|---|
| 461 | tries += 1 |
|---|
| 462 | X = sortM20(Asave) |
|---|
| 463 | if X: |
|---|
| 464 | Lhkl,M20,X20,A = refinePeaks(peaks,ibrav,X[0][1]) |
|---|
| 465 | return GoOn,Lhkl,M20,X20,A |
|---|
| 466 | |
|---|
| 467 | else: |
|---|
| 468 | return GoOn,0,0,0,0 |
|---|
| 469 | |
|---|
| 470 | def monoCellReduce(ibrav,A): |
|---|
| 471 | a,b,c,alp,bet,gam = G2lat.A2cell(A) |
|---|
| 472 | G,g = G2lat.A2Gmat(A) |
|---|
| 473 | if ibrav in [11]: |
|---|
| 474 | u = [0,0,-1] |
|---|
| 475 | v = [1,0,2] |
|---|
| 476 | anew = math.sqrt(np.dot(np.dot(v,g),v)) |
|---|
| 477 | if anew < a: |
|---|
| 478 | cang = np.dot(np.dot(u,g),v)/(anew*c) |
|---|
| 479 | beta = acosd(-abs(cang)) |
|---|
| 480 | A = G2lat.cell2A([anew,b,c,90,beta,90]) |
|---|
| 481 | else: |
|---|
| 482 | u = [-1,0,0] |
|---|
| 483 | v = [1,0,1] |
|---|
| 484 | cnew = math.sqrt(np.dot(np.dot(v,g),v)) |
|---|
| 485 | if cnew < c: |
|---|
| 486 | cang = np.dot(np.dot(u,g),v)/(a*cnew) |
|---|
| 487 | beta = acosd(-abs(cang)) |
|---|
| 488 | A = G2lat.cell2A([a,b,cnew,90,beta,90]) |
|---|
| 489 | return A |
|---|
| 490 | |
|---|
| 491 | def DoIndexPeaks(peaks,inst,controls,bravais): |
|---|
| 492 | |
|---|
| 493 | delt = 0.005 #lowest d-spacing cushion - can be fixed? |
|---|
| 494 | amin = 2.5 |
|---|
| 495 | amax = 5.0*getDmax(peaks) |
|---|
| 496 | dmin = getDmin(peaks)-delt |
|---|
| 497 | bravaisNames = ['Cubic-F','Cubic-I','Cubic-P','Trigonal-R','Trigonal/Hexagonal-P', |
|---|
| 498 | 'Tetragonal-I','Tetragonal-P','Orthorhombic-F','Orthorhombic-I','Orthorhombic-C', |
|---|
| 499 | 'Orthorhombic-P','Monoclinic-C','Monoclinic-P','Triclinic'] |
|---|
| 500 | tries = ['1st','2nd','3rd','4th','5th','6th','7th','8th','9th','10th'] |
|---|
| 501 | N1s = [1,1,1, 5,5, 5,5, 50,50,50,50, 50,50, 200] |
|---|
| 502 | N2s = [1,1,1, 2,2, 2,2, 2,2,2,2, 2,2, 4] |
|---|
| 503 | Nm = [1,1,1, 1,1, 1,1, 1,1,1,1, 2,2, 4] |
|---|
| 504 | Nobs = len(peaks) |
|---|
| 505 | wave = inst[1] |
|---|
| 506 | zero,ncno = controls[1:3] |
|---|
| 507 | ncMax = Nobs*ncno |
|---|
| 508 | print "%s %8.3f %8.3f" % ('lattice parameter range = ',amin,amax) |
|---|
| 509 | print "%s %8.5f %s %.4f %s %d %s %d" % ('Wavelength =',wave,'Zero =',zero,'Nc/No max =',ncno,' Max Nc =',ncno*Nobs) |
|---|
| 510 | cells = [] |
|---|
| 511 | for ibrav in range(14): |
|---|
| 512 | begin = time.time() |
|---|
| 513 | if bravais[ibrav]: |
|---|
| 514 | print 'cell search for ',bravaisNames[ibrav] |
|---|
| 515 | print ' M20 X20 Nc a b c alpha beta gamma volume V-test' |
|---|
| 516 | V1 = controls[3] |
|---|
| 517 | bestM20 = 0 |
|---|
| 518 | topM20 = 0 |
|---|
| 519 | cycle = 0 |
|---|
| 520 | while cycle < 5: |
|---|
| 521 | dlg = wx.ProgressDialog("Generated reflections",tries[cycle]+" cell search for "+bravaisNames[ibrav],ncMax, |
|---|
| 522 | style = wx.PD_ELAPSED_TIME|wx.PD_AUTO_HIDE|wx.PD_REMAINING_TIME|wx.PD_CAN_ABORT) |
|---|
| 523 | screenSize = wx.ClientDisplayRect() |
|---|
| 524 | Size = dlg.GetSize() |
|---|
| 525 | dlg.SetPosition(wx.Point(screenSize[2]-Size[0]-305,screenSize[1]+5)) |
|---|
| 526 | try: |
|---|
| 527 | GoOn = True |
|---|
| 528 | while GoOn: #Loop over increment of volume |
|---|
| 529 | N2 = 0 |
|---|
| 530 | while N2 < N2s[ibrav]: #Table 2 step (iii) |
|---|
| 531 | if ibrav > 2: |
|---|
| 532 | if not N2: |
|---|
| 533 | A = [] |
|---|
| 534 | GoOn,Nc,M20,X20,A = findBestCell(dlg,ncMax,A,Nm[ibrav]*N1s[ibrav],ibrav,peaks,V1) |
|---|
| 535 | if A: |
|---|
| 536 | GoOn,Nc,M20,X20,A = findBestCell(dlg,ncMax,A[:],N1s[ibrav],ibrav,peaks,0) |
|---|
| 537 | else: |
|---|
| 538 | GoOn,Nc,M20,X20,A = findBestCell(dlg,ncMax,0,Nm[ibrav]*N1s[ibrav],ibrav,peaks,V1) |
|---|
| 539 | if Nc >= ncMax: |
|---|
| 540 | GoOn = False |
|---|
| 541 | break |
|---|
| 542 | elif 3*Nc < Nobs: |
|---|
| 543 | N2 = 10 |
|---|
| 544 | break |
|---|
| 545 | else: |
|---|
| 546 | if not GoOn: |
|---|
| 547 | break |
|---|
| 548 | if M20 > 1.0: |
|---|
| 549 | bestM20 = max(bestM20,M20) |
|---|
| 550 | A = halfCell(ibrav,A[:],peaks) |
|---|
| 551 | if ibrav in [12]: |
|---|
| 552 | A = monoCellReduce(ibrav,A[:]) |
|---|
| 553 | HKL = G2lat.GenHBravais(dmin,ibrav,A) |
|---|
| 554 | IndexPeaks(peaks,HKL) |
|---|
| 555 | a,b,c,alp,bet,gam = G2lat.A2cell(A) |
|---|
| 556 | V = G2lat.calc_V(A) |
|---|
| 557 | print "%10.3f %3d %3d %10.5f %10.5f %10.5f %10.3f %10.3f %10.3f %10.2f %10.2f" % (M20,X20,Nc,a,b,c,alp,bet,gam,V,V1) |
|---|
| 558 | if M20 >= 2.0: |
|---|
| 559 | cells.append([M20,X20,ibrav,a,b,c,alp,bet,gam,V,False]) |
|---|
| 560 | if not GoOn: |
|---|
| 561 | break |
|---|
| 562 | N2 += 1 |
|---|
| 563 | if ibrav < 11: |
|---|
| 564 | V1 *= 1.1 |
|---|
| 565 | elif ibrav in range(11,14): |
|---|
| 566 | V1 *= 1.05 |
|---|
| 567 | if not GoOn: |
|---|
| 568 | if bestM20 > topM20: |
|---|
| 569 | topM20 = bestM20 |
|---|
| 570 | if cells: |
|---|
| 571 | V1 = cells[0][9] |
|---|
| 572 | else: |
|---|
| 573 | V1 = 25 |
|---|
| 574 | ncMax += Nobs |
|---|
| 575 | cycle += 1 |
|---|
| 576 | print 'Restart search, new Max Nc = ',ncMax |
|---|
| 577 | else: |
|---|
| 578 | cycle = 10 |
|---|
| 579 | finally: |
|---|
| 580 | dlg.Destroy() |
|---|
| 581 | print '%s%s%s%s'%('finished cell search for ',bravaisNames[ibrav], \ |
|---|
| 582 | ', elapsed time = ',G2lat.sec2HMS(time.time()-begin)) |
|---|
| 583 | |
|---|
| 584 | if cells: |
|---|
| 585 | cells = sortM20(cells) |
|---|
| 586 | cells[0][-1] = True |
|---|
| 587 | return True,dmin,cells |
|---|
| 588 | else: |
|---|
| 589 | return False,0,0 |
|---|
| 590 | |
|---|
| 591 | |
|---|
| 592 | NeedTestData = True |
|---|
| 593 | def TestData(): |
|---|
| 594 | array = np.array |
|---|
| 595 | global NeedTestData |
|---|
| 596 | NeedTestData = False |
|---|
| 597 | global TestData |
|---|
| 598 | TestData = [12, [7.,8.70,10.86,90.,102.95,90.], [7.76006,8.706215,10.865679,90.,102.947,90.],3, |
|---|
| 599 | [[2.176562137832974, 761.60902227696033, True, True, 0, 0, 1, 10.591300714328161, 10.589436], |
|---|
| 600 | [3.0477561489789498, 4087.2956049071572, True, True, 1, 0, 0, 7.564238997554908, 7.562777], |
|---|
| 601 | [3.3254921120068524, 1707.0253890991009, True, True, 1, 0, -1, 6.932650301411212, 6.932718], |
|---|
| 602 | [3.428121546163426, 2777.5082170150563, True, True, 0, 1, 1, 6.725163158013632, 6.725106], |
|---|
| 603 | [4.0379791325512118, 1598.4321673135987, True, True, 1, 1, 0, 5.709789097440156, 5.70946], |
|---|
| 604 | [4.2511182350743937, 473.10955149057577, True, True, 1, 1, -1, 5.423637972781876, 5.42333], |
|---|
| 605 | [4.354684330373451, 569.88528280256071, True, True, 0, 0, 2, 5.2947091882172534, 5.294718], |
|---|
| 606 | [4.723324574319177, 342.73882372499997, True, True, 1, 0, -2, 4.881681587039431, 4.881592], |
|---|
| 607 | [4.9014773581253994, 5886.3516356615492, True, True, 1, 1, 1, 4.704350709093183, 4.70413], |
|---|
| 608 | [5.0970774474587275, 3459.7541692903033, True, True, 0, 1, 2, 4.523933797797693, 4.523829], |
|---|
| 609 | [5.2971997607389518, 1290.0229964239879, True, True, 0, 2, 0, 4.353139557169142, 4.353108], |
|---|
| 610 | [5.4161306205553847, 1472.5726977257755, True, True, 1, 1, -2, 4.257619398422479, 4.257944], |
|---|
| 611 | [5.7277364698554161, 1577.8791668322888, True, True, 0, 2, 1, 4.026169751907777, 4.026193], |
|---|
| 612 | [5.8500213058834163, 420.74210142657131, True, True, 1, 0, 2, 3.9420803081518443, 3.942219], |
|---|
| 613 | [6.0986764166731708, 163.02160537058708, True, True, 2, 0, 0, 3.7814965150452537, 3.781389], |
|---|
| 614 | [6.1126665157702753, 943.25461245706833, True, True, 1, 2, 0, 3.772849962062199, 3.772764], |
|---|
| 615 | [6.2559260555056957, 250.55355015505376, True, True, 1, 2, -1, 3.6865353266375283, 3.686602], |
|---|
| 616 | [6.4226243128279892, 5388.5560141098349, True, True, 1, 1, 2, 3.5909481979190283, 3.591214], |
|---|
| 617 | [6.5346132446561134, 1951.6070344509026, True, True, 0, 0, 3, 3.5294722429440584, 3.529812], |
|---|
| 618 | [6.5586952135236443, 259.65938178131034, True, True, 2, 1, -1, 3.516526936765838, 3.516784], |
|---|
| 619 | [6.6509216222783722, 93.265376597376573, True, True, 2, 1, 0, 3.4678179073694952, 3.468369], |
|---|
| 620 | [6.7152737044107722, 289.39386813803162, True, True, 1, 2, 1, 3.4346235125812807, 3.434648], |
|---|
| 621 | [6.8594130457361899, 603.54959764648322, True, True, 0, 2, 2, 3.362534044860622, 3.362553], |
|---|
| 622 | [7.0511627728884454, 126.43246447656593, True, True, 0, 1, 3, 3.2712038721790675, 3.271181], |
|---|
| 623 | [7.077700845503319, 125.49742760019636, True, True, 1, 1, -3, 3.2589538988480626, 3.259037], |
|---|
| 624 | [7.099393757363675, 416.55444885434633, True, True, 1, 2, -2, 3.2490085228959193, 3.248951], |
|---|
| 625 | [7.1623933278642742, 369.27397110921817, True, True, 2, 1, -2, 3.2204673608202383, 3.220487], |
|---|
| 626 | [7.4121734953058924, 482.84120827021826, True, True, 2, 1, 1, 3.1120858221599876, 3.112308]] |
|---|
| 627 | ] |
|---|
| 628 | global TestData2 |
|---|
| 629 | TestData2 = [12, [0.15336547830008007, 0.017345499139401827, 0.008122368657493792, 0, 0.02893538955687591, 0], 3, |
|---|
| 630 | [[2.176562137832974, 761.6090222769603, True, True, 0, 0, 1, 10.591300714328161, 11.095801], |
|---|
| 631 | [3.0477561489789498, 4087.295604907157, True, True, 0, 1, 0, 7.564238997554908, 7.592881], |
|---|
| 632 | [3.3254921120068524, 1707.025389099101, True, False, 0, 0, 0, 6.932650301411212, 0.0], |
|---|
| 633 | [3.428121546163426, 2777.5082170150563, True, True, 0, 1, 1, 6.725163158013632, 6.266192], |
|---|
| 634 | [4.037979132551212, 1598.4321673135987, True, False, 0, 0, 0, 5.709789097440156, 0.0], |
|---|
| 635 | [4.251118235074394, 473.10955149057577, True, True, 0, 0, 2, 5.423637972781876, 5.5479], |
|---|
| 636 | [4.354684330373451, 569.8852828025607, True, True, 0, 0, 2, 5.2947091882172534, 5.199754], |
|---|
| 637 | [4.723324574319177, 342.738823725, True, False, 0, 0, 0, 4.881681587039431, 0.0], |
|---|
| 638 | [4.901477358125399, 5886.351635661549, True, False, 0, 0, 0, 4.704350709093183, 0.0], |
|---|
| 639 | [5.0970774474587275, 3459.7541692903033, True, True, 0, 1, 2, 4.523933797797693, 4.479534], |
|---|
| 640 | [5.297199760738952, 1290.022996423988, True, True, 0, 1, 0, 4.353139557169142, 4.345087], |
|---|
| 641 | [5.416130620555385, 1472.5726977257755, True, False, 0, 0, 0, 4.257619398422479, 0.0], |
|---|
| 642 | [5.727736469855416, 1577.8791668322888, True, False, 0, 0, 0, 4.026169751907777, 0.0], |
|---|
| 643 | [5.850021305883416, 420.7421014265713, True, False, 0, 0, 0, 3.9420803081518443, 0.0], |
|---|
| 644 | [6.098676416673171, 163.02160537058708, True, True, 0, 2, 0, 3.7814965150452537, 3.796441], |
|---|
| 645 | [6.112666515770275, 943.2546124570683, True, False, 0, 0, 0, 3.772849962062199, 0.0], |
|---|
| 646 | [6.255926055505696, 250.55355015505376, True, True, 0, 0, 3, 3.6865353266375283, 3.6986], |
|---|
| 647 | [6.422624312827989, 5388.556014109835, True, True, 0, 2, 1, 3.5909481979190283, 3.592005], |
|---|
| 648 | [6.534613244656113, 191.6070344509026, True, True, 1, 0, -1, 3.5294722429440584, 3.546166], |
|---|
| 649 | [6.558695213523644, 259.65938178131034, True, True, 0, 0, 3, 3.516526936765838, 3.495428], |
|---|
| 650 | [6.650921622278372, 93.26537659737657, True, True, 0, 0, 3, 3.4678179073694952, 3.466503], |
|---|
| 651 | [6.715273704410772, 289.3938681380316, True, False, 0, 0, 0, 3.4346235125812807, 0.0], |
|---|
| 652 | [6.85941304573619, 603.5495976464832, True, True, 0, 1, 3, 3.362534044860622, 3.32509], |
|---|
| 653 | [7.051162772888445, 126.43246447656593, True, True, 0, 1, 2, 3.2712038721790675, 3.352121], |
|---|
| 654 | [7.077700845503319, 125.49742760019636, True, False, 0, 0, 0, 3.2589538988480626, 0.0], |
|---|
| 655 | [7.099393757363675, 416.55444885434633, True, False, 0, 0, 0, 3.2490085228959193, 0.0], |
|---|
| 656 | [7.162393327864274, 369.27397110921817, True, False, 0, 0, 0, 3.2204673608202383, 0.0], |
|---|
| 657 | [7.412173495305892, 482.84120827021826, True, True, 0, 2, 2, 3.112085822159976, 3.133096]] |
|---|
| 658 | ] |
|---|
| 659 | # |
|---|
| 660 | def test0(): |
|---|
| 661 | if NeedTestData: TestData() |
|---|
| 662 | msg = 'test FitHKL' |
|---|
| 663 | ibrav,cell,bestcell,Pwr,peaks = TestData |
|---|
| 664 | print 'best cell:',bestcell |
|---|
| 665 | print 'old cell:',cell |
|---|
| 666 | Peaks = np.array(peaks) |
|---|
| 667 | HKL = Peaks[4:7] |
|---|
| 668 | print calc_M20(peaks,HKL) |
|---|
| 669 | A = G2lat.cell2A(cell) |
|---|
| 670 | OK,smin,A,result = FitHKL(ibrav,peaks,A,Pwr) |
|---|
| 671 | print 'new cell:',G2lat.A2cell(A) |
|---|
| 672 | print 'x:',result[0] |
|---|
| 673 | print 'cov_x:',result[1] |
|---|
| 674 | print 'infodict:' |
|---|
| 675 | for item in result[2]: |
|---|
| 676 | print item,result[2][item] |
|---|
| 677 | print 'msg:',result[3] |
|---|
| 678 | print 'ier:',result[4] |
|---|
| 679 | result = refinePeaks(peaks,ibrav,A) |
|---|
| 680 | N,M20,X20,A = result |
|---|
| 681 | print 'refinePeaks:',N,M20,X20,G2lat.A2cell(A) |
|---|
| 682 | print 'compare bestcell:',bestcell |
|---|
| 683 | # |
|---|
| 684 | def test1(): |
|---|
| 685 | if NeedTestData: TestData() |
|---|
| 686 | msg = 'test FitHKL' |
|---|
| 687 | ibrav,A,Pwr,peaks = TestData2 |
|---|
| 688 | print 'bad cell:',G2lat.A2cell(A) |
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| 689 | print 'FitHKL' |
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| 690 | OK,smin,A,result = FitHKL(ibrav,peaks,A,Pwr) |
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| 691 | result = refinePeaks(peaks,ibrav,A) |
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| 692 | N,M20,X20,A = result |
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| 693 | print 'refinePeaks:',N,M20,X20,A |
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| 694 | # Peaks = np.array(peaks) |
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| 695 | # HKL = Peaks[4:7] |
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| 696 | # print calc_M20(peaks,HKL) |
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| 697 | # OK,smin,A,result = FitHKL(ibrav,peaks,A,Pwr) |
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| 698 | # print 'new cell:',G2lat.A2cell(A) |
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| 699 | # print 'x:',result[0] |
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| 700 | # print 'cov_x:',result[1] |
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| 701 | # print 'infodict:' |
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| 702 | # for item in result[2]: |
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| 703 | # print item,result[2][item] |
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| 704 | # print 'msg:',result[3] |
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| 705 | # print 'ier:',result[4] |
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| 706 | |
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| 707 | # |
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| 708 | if __name__ == '__main__': |
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| 709 | test0() |
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| 710 | test1() |
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| 711 | # test2() |
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| 712 | # test3() |
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| 713 | # test4() |
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| 714 | # test5() |
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| 715 | # test6() |
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| 716 | # test7() |
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| 717 | # test8() |
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| 718 | print "OK" |
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