Changeset 1489
- Timestamp:
- Sep 7, 2014 1:37:26 PM (7 years ago)
- Location:
- trunk
- Files:
-
- 8 edited
-
GSASIIimage.py (modified) (1 diff)
-
GSASIIlattice.py (modified) (2 diffs)
-
GSASIImapvars.py (modified) (4 diffs)
-
GSASIIphsGUI.py (modified) (1 diff)
-
GSASIIspc.py (modified) (5 diffs)
-
GSASIIstrIO.py (modified) (7 diffs)
-
GSASIIstrMain.py (modified) (1 diff)
-
GSASIIstrMath.py (modified) (4 diffs)
Legend:
- Unmodified
- Added
- Removed
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trunk/GSASIIimage.py
r1485 r1489 830 830 numAzms = data['outAzimuths'] 831 831 numChans = data['outChannels'] 832 azmOff = data['azmthOff'] 832 833 Dazm = (LRazm[1]-LRazm[0])/numAzms 833 # LRazm += Dazm/2.834 834 if 'log(q)' in data['binType']: 835 835 lutth = np.log(4.*np.pi*npsind(LUtth/2.)/data['wavelength']) -
trunk/GSASIIlattice.py
r1475 r1489 268 268 """ 269 269 U = np.array([ 270 [U6[0], U6[3] , U6[4]],271 [U6[3] , U6[1], U6[5]],272 [U6[4] , U6[5], U6[2]]])270 [U6[0], U6[3]/2., U6[4]/2.], 271 [U6[3]/2., U6[1], U6[5]/2.], 272 [U6[4]/2., U6[5]/2., U6[2]]]) 273 273 return U 274 274 … … 277 277 NB: there is a non numpy version in GSASIIspc: Uij2U 278 278 """ 279 U6 = np.array([U[0][0],U[1][1],U[2][2],U[0][1] ,U[0][2],U[1][2]])279 U6 = np.array([U[0][0],U[1][1],U[2][2],U[0][1]*2.,U[0][2]*2.,U[1][2]*2.]) 280 280 return U6 281 281 -
trunk/GSASIImapvars.py
r1276 r1489 396 396 errmsg += '\t'+ s + '\n' 397 397 equivVarList = list(set(indepVarList).union(set(depVarList))) 398 #print 'equivVarList',equivVarList398 if debug: print 'equivVarList',equivVarList 399 399 inboth = set(fixVlist).intersection(set(equivVarList)) 400 400 if len(inboth) > 0: … … 604 604 msg += str(mv) + " => " + s + '\n' 605 605 606 #print 'indepVarList',indepVarList607 #print 'depVarList',depVarList606 if debug: print 'indepVarList',indepVarList 607 if debug: print 'depVarList',depVarList 608 608 # check for errors: 609 609 inboth = set(indepVarList).intersection(set(depVarList)) … … 933 933 j = 0 934 934 for v,m in zip(varlist,invmultarr): 935 #printv,m[0]935 if debug: print 'v,m[0]: ',v,m[0] 936 936 if j > 0: s += ' & ' 937 937 j += 1 … … 984 984 if multarr is None: 985 985 for v,m in zip(varlist,invmultarr): 986 #print 'add derv',v,'/',m[0],'to derv',name 986 if debug: print 'start dMdv',dMdv[varyList.index(name)] 987 if debug: print 'add derv',v,'/',m[0],'to derv',name,'add=',derivDict[v] / m[0] 987 988 if m == 0: continue 988 989 dMdv[varyList.index(name)] += derivDict[v] / m[0] 989 990 else: 990 991 for v,m in zip(varlist,multarr[i,:]): 991 #print 'add derv',v,'*',m,'to derv',name 992 if debug: print 'start dMdv',dMdv[varyList.index(name)] 993 if debug: print 'add derv',v,'*',m,'to derv',name,'add=',m * derivDict[v] 992 994 if m == 0: continue 993 995 dMdv[varyList.index(name)] += m * derivDict[v] -
trunk/GSASIIphsGUI.py
r1486 r1489 1157 1157 Atoms.SetReadOnly(row,colSS+1,True) #Mult 1158 1158 if Atoms.GetCellValue(row,colIA) == 'A': 1159 CSI = G2spc.GetCSuinel(atomData[row][colLabels.index('site sym')]) 1159 try: #patch for sytsym name changes 1160 CSI = G2spc.GetCSuinel(atomData[row][colSS]) 1161 except KeyError: 1162 Sytsym = G2spc.SytSym(atomData[row][colX:colX+3],SGData)[0] 1163 atomData[row][colSS] = Sytsym 1164 CSI = G2spc.GetCSuinel(Sytsym) 1160 1165 Atoms.SetCellStyle(row,colUiso,VERY_LIGHT_GREY,True) 1161 1166 Atoms.SetCellTextColour(row,colUiso,VERY_LIGHT_GREY) -
trunk/GSASIIspc.py
r1480 r1489 447 447 'Needs a doc string' 448 448 KNsym = { 449 '0' :' 1 ','1' :' -1 ','64' :' 2(100)','32' :' m(100)',450 '97' :' 2/m(100)','16' :' 2(010)','8' :' m(010)','25' :'2/m(010)',451 '2' :' 2(001)','4' :' m(001)','7' :'2/m(001)','134217728' :' 2(011)',452 '67108864' :' m(011)','201326593' :'2/m(011)','2097152' :' 2(0+-)','1048576' :' m(0+-)',453 '3145729' :'2/m(0+-)','8388608' :' 2(101)','4194304' :' m(101)','12582913' :'2/m(101)',454 '524288' :' 2(+0-)','262144' :' m(+0-)','796433' :'2/m(+0-)','1024' :' 2(110)',455 '512' :' m(110)','1537' :'2/m(110)','256' :' 2(+-0)','128' :' m(+-0)',456 '385' :'2/m(+-0)','76' :' mm2(100)','52' :'mm2(010)','42' :'mm2(001)',457 '135266336' :' mm2(011)','69206048' :'mm2(0+-)','8650760' :'mm2(101)','4718600' :'mm2(+0-)',458 '1156' :' mm2(110)','772' :'mm2(+-0)','82' :' 222 ','136314944' :'222(100)',459 '8912912' :' 222(010)','1282' :'222(001)','127' :' mmm ','204472417' :'mmm(100)',460 '13369369' :' mmm(010)','1927' :'mmm(001)','33554496' :' 4(100)','16777280' :' -4(100)',449 '0' :' 1 ','1' :' -1 ','64' :' 2(x)','32' :' m(x)', 450 '97' :' 2/m(x)','16' :' 2(y)','8' :' m(y)','25' :' 2/m(y)', 451 '2' :' 2(z)','4' :' m(z)','7' :' 2/m(z)','134217728' :' 2(yz)', 452 '67108864' :' m(yz)','201326593' :' 2/m(yz)','2097152' :' 2(0+-)','1048576' :' m(0+-)', 453 '3145729' :'2/m(0+-)','8388608' :' 2(xz)','4194304' :' m(xz)','12582913' :' 2/m(xz)', 454 '524288' :' 2(+0-)','262144' :' m(+0-)','796433' :'2/m(+0-)','1024' :' 2(xy)', 455 '512' :' m(xy)','1537' :' 2/m(xy)','256' :' 2(+-0)','128' :' m(+-0)', 456 '385' :'2/m(+-0)','76' :' mm2(x)','52' :' mm2(y)','42' :' mm2(z)', 457 '135266336' :' mm2(yz)','69206048' :'mm2(0+-)','8650760' :' mm2(xz)','4718600' :'mm2(+0-)', 458 '1156' :' mm2(xy)','772' :'mm2(+-0)','82' :' 222 ','136314944' :' 222(x)', 459 '8912912' :' 222(y)','1282' :' 222(z)','127' :' mmm ','204472417' :' mmm(x)', 460 '13369369' :' mmm(y)','1927' :' mmm(z)','33554496' :' 4(100)','16777280' :' -4(100)', 461 461 '50331745' :'4/m(100)','169869394' :'422(100)','84934738' :'-42m 100','101711948' :'4mm(100)', 462 462 '254804095' :'4/mmm100','536870928 ':' 4(010)','268435472' :' -4(010)','805306393' :'4/m (10)', … … 491 491 'Needs a doc string' 492 492 NXUPQsym = { 493 ' 1 ':(28,29,28,28),' -1 ':( 1,29,28, 0),' 2(100)':(12,18,12,25),' m(100)':(25,18,12,25),494 ' 2/m(100)':( 1,18, 0,-1),' 2(010)':(13,17,13,24),' m(010)':(24,17,13,24),'2/m(010)':( 1,17, 0,-1),495 ' 2(001)':(14,16,14,23),' m(001)':(23,16,14,23),'2/m(001)':( 1,16, 0,-1),' 2(011)':(10,23,10,22),496 ' m(011)':(22,23,10,22),'2/m(011)':( 1,23, 0,-1),' 2(0+-)':(11,24,11,21),' m(0+-)':(21,24,11,21),497 '2/m(0+-)':( 1,24, 0,-1),' 2(101)':( 8,21, 8,20),' m(101)':(20,21, 8,20),'2/m(101)':( 1,21, 0,-1),498 ' 2(+0-)':( 9,22, 9,19),' m(+0-)':(19,22, 9,19),'2/m(+0-)':( 1,22, 0,-1),' 2(110)':( 6,19, 6,18),499 ' m(110)':(18,19, 6,18),'2/m(110)':( 1,19, 0,-1),' 2(+-0)':( 7,20, 7,17),' m(+-0)':(17,20, 7,17),500 '2/m(+-0)':( 1,20, 0,-1),' mm2(100)':(12,10, 0,-1),'mm2(010)':(13,10, 0,-1),'mm2(001)':(14,10, 0,-1),501 ' mm2(011)':(10,13, 0,-1),'mm2(0+-)':(11,13, 0,-1),'mm2(101)':( 8,12, 0,-1),'mm2(+0-)':( 9,12, 0,-1),502 ' mm2(110)':( 6,11, 0,-1),'mm2(+-0)':( 7,11, 0,-1),' 222 ':( 1,10, 0,-1),'222(100)':( 1,13, 0,-1),503 ' 222(010)':( 1,12, 0,-1),'222(001)':( 1,11, 0,-1),' mmm ':( 1,10, 0,-1),'mmm(100)':( 1,13, 0,-1),504 ' mmm(010)':( 1,12, 0,-1),'mmm(001)':( 1,11, 0,-1),' 4(100)':(12, 4,12, 0),' -4(100)':( 1, 4,12, 0),493 ' 1 ':(28,29,28,28),' -1 ':( 1,29,28, 0),' 2(x)':(12,18,12,25),' m(x)':(25,18,12,25), 494 ' 2/m(x)':( 1,18, 0,-1),' 2(y)':(13,17,13,24),' m(y)':(24,17,13,24),' 2/m(y)':( 1,17, 0,-1), 495 ' 2(z)':(14,16,14,23),' m(z)':(23,16,14,23),' 2/m(z)':( 1,16, 0,-1),' 2(yz)':(10,23,10,22), 496 ' m(yz)':(22,23,10,22),' 2/m(yz)':( 1,23, 0,-1),' 2(0+-)':(11,24,11,21),' m(0+-)':(21,24,11,21), 497 '2/m(0+-)':( 1,24, 0,-1),' 2(xz)':( 8,21, 8,20),' m(xz)':(20,21, 8,20),' 2/m(xz)':( 1,21, 0,-1), 498 ' 2(+0-)':( 9,22, 9,19),' m(+0-)':(19,22, 9,19),'2/m(+0-)':( 1,22, 0,-1),' 2(xy)':( 6,19, 6,18), 499 ' m(xy)':(18,19, 6,18),' 2/m(xy)':( 1,19, 0,-1),' 2(+-0)':( 7,20, 7,17),' m(+-0)':(17,20, 7,17), 500 '2/m(+-0)':( 1,20, 0,-1),' mm2(x)':(12,10, 0,-1),' mm2(y)':(13,10, 0,-1),' mm2(z)':(14,10, 0,-1), 501 ' mm2(yz)':(10,13, 0,-1),'mm2(0+-)':(11,13, 0,-1),' mm2(xz)':( 8,12, 0,-1),'mm2(+0-)':( 9,12, 0,-1), 502 ' mm2(xy)':( 6,11, 0,-1),'mm2(+-0)':( 7,11, 0,-1),' 222 ':( 1,10, 0,-1),' 222(x)':( 1,13, 0,-1), 503 ' 222(y)':( 1,12, 0,-1),' 222(z)':( 1,11, 0,-1),' mmm ':( 1,10, 0,-1),' mmm(x)':( 1,13, 0,-1), 504 ' mmm(y)':( 1,12, 0,-1),' mmm(z)':( 1,11, 0,-1),' 4(100)':(12, 4,12, 0),' -4(100)':( 1, 4,12, 0), 505 505 '4/m(100)':( 1, 4,12,-1),'422(100)':( 1, 4, 0,-1),'-42m 100':( 1, 4, 0,-1),'4mm(100)':(12, 4, 0,-1), 506 506 '4/mmm100':( 1, 4, 0,-1),' 4(010)':(13, 3,13, 0),' -4(010)':( 1, 3,13, 0),'4/m (10)':( 1, 3,13,-1), … … 535 535 'Needs a doc string' 536 536 CSxinel = [[], # 0th empty - indices are Fortran style 537 [[0,0,0],[ 0.0, 0.0, 0.0]], # 0 0 0538 [[1,1,1],[ 1.0, 1.0, 1.0]], # X X X539 [[1,1,1],[ 1.0, 1.0,-1.0]], # X X -X540 [[1,1,1],[ 1.0,-1.0, 1.0]], # X -X X541 [[1,1,1],[ 1.0,-1.0,-1.0]], # -X X X542 [[1,1,0],[ 1.0, 1.0, 0.0]], # X X 0543 [[1,1,0],[ 1.0,-1.0, 0.0]], # X -X 0544 [[1,0,1],[ 1.0, 0.0, 1.0]], # X 0 X545 [[1,0,1],[ 1.0, 0.0,-1.0]], # X 0 -X546 [[0,1,1],[ 0.0, 1.0, 1.0]], # 0 Y Y547 [[0,1,1],[ 0.0, 1.0,-1.0]], # 548 [[1,0,0],[ 1.0, 0.0, 0.0]], # X 0 0549 [[0,1,0],[ 0.0, 1.0, 0.0]], # 0 Y 0550 [[0,0,1],[ 0.0, 0.0, 1.0]], # 0 0 Z551 [[1,1,0],[ 1.0, 2.0, 0.0]], # X 2X 0552 [[1,1,0],[ 2.0, 1.0, 0.0]], # 2X X 0553 [[1,1,2],[ 1.0, 1.0, 1.0]], # X X Z554 [[1,1,2],[ 1.0,-1.0, 1.0]], # X -X Z555 [[1,2,1],[ 1.0, 1.0, 1.0]], # X Y X556 [[1,2,1],[ 1.0, 1.0,-1.0]], # X Y -X557 [[1,2,2],[ 1.0, 1.0, 1.0]], # X Y Y558 [[1,2,2],[ 1.0, 1.0,-1.0]], # X Y -Y559 [[1,2,0],[ 1.0, 1.0, 0.0]], # X Y 0560 [[1,0,2],[ 1.0, 0.0, 1.0]], # X 0 Z561 [[0,1,2],[ 0.0, 1.0, 1.0]], # 0 Y Z562 [[1,1,2],[ 1.0, 2.0, 1.0]], # X 2X Z563 [[1,1,2],[ 2.0, 1.0, 1.0]], # 2X X Z564 [[1,2,3],[ 1.0, 1.0, 1.0]], # X Y Z537 [[0,0,0],[ 0.0, 0.0, 0.0]], #1 0 0 0 538 [[1,1,1],[ 1.0, 1.0, 1.0]], #2 X X X 539 [[1,1,1],[ 1.0, 1.0,-1.0]], #3 X X -X 540 [[1,1,1],[ 1.0,-1.0, 1.0]], #4 X -X X 541 [[1,1,1],[ 1.0,-1.0,-1.0]], #5 -X X X 542 [[1,1,0],[ 1.0, 1.0, 0.0]], #6 X X 0 543 [[1,1,0],[ 1.0,-1.0, 0.0]], #7 X -X 0 544 [[1,0,1],[ 1.0, 0.0, 1.0]], #8 X 0 X 545 [[1,0,1],[ 1.0, 0.0,-1.0]], #9 X 0 -X 546 [[0,1,1],[ 0.0, 1.0, 1.0]], #10 0 Y Y 547 [[0,1,1],[ 0.0, 1.0,-1.0]], #11 0 Y -Y 548 [[1,0,0],[ 1.0, 0.0, 0.0]], #12 X 0 0 549 [[0,1,0],[ 0.0, 1.0, 0.0]], #13 0 Y 0 550 [[0,0,1],[ 0.0, 0.0, 1.0]], #14 0 0 Z 551 [[1,1,0],[ 1.0, 2.0, 0.0]], #15 X 2X 0 552 [[1,1,0],[ 2.0, 1.0, 0.0]], #16 2X X 0 553 [[1,1,2],[ 1.0, 1.0, 1.0]], #17 X X Z 554 [[1,1,2],[ 1.0,-1.0, 1.0]], #18 X -X Z 555 [[1,2,1],[ 1.0, 1.0, 1.0]], #19 X Y X 556 [[1,2,1],[ 1.0, 1.0,-1.0]], #20 X Y -X 557 [[1,2,2],[ 1.0, 1.0, 1.0]], #21 X Y Y 558 [[1,2,2],[ 1.0, 1.0,-1.0]], #22 X Y -Y 559 [[1,2,0],[ 1.0, 1.0, 0.0]], #23 X Y 0 560 [[1,0,2],[ 1.0, 0.0, 1.0]], #24 X 0 Z 561 [[0,1,2],[ 0.0, 1.0, 1.0]], #25 0 Y Z 562 [[1,1,2],[ 1.0, 2.0, 1.0]], #26 X 2X Z 563 [[1,1,2],[ 2.0, 1.0, 1.0]], #27 2X X Z 564 [[1,2,3],[ 1.0, 1.0, 1.0]], #28 X Y Z 565 565 ] 566 566 indx = GetNXUPQsym(siteSym) … … 570 570 "returns Uij terms, multipliers, GUI flags & Uiso2Uij multipliers" 571 571 CSuinel = [[], # 0th empty - indices are Fortran style 572 [[1,1,1,0,0,0],[ 1.0, 1.0, 1.0, 0.0, 0.0, 0.0],[1,0,0,0,0,0],[1.0,1.0,1.0,0.0,0.0,0.0]], # A A A 0 0 0573 [[1,1,2,0,0,0],[ 1.0, 1.0, 1.0, 0.0, 0.0, 0.0],[1,0,1,0,0,0],[1.0,1.0,1.0,0.0,0.0,0.0]], # A A C 0 0 0574 [[1,2,1,0,0,0],[ 1.0, 1.0, 1.0, 0.0, 0.0, 0.0],[1,1,0,0,0,0],[1.0,1.0,1.0,0.0,0.0,0.0]], # A B A 0 0 0575 [[1,2,2,0,0,0],[ 1.0, 1.0, 1.0, 0.0, 0.0, 0.0],[1,1,0,0,0,0],[1.0,1.0,1.0,0.0,0.0,0.0]], # A B B 0 0 0576 [[1,1,1,2,2,2],[ 1.0, 1.0, 1.0, 1.0, 1.0, 1.0],[1,0,0,1,0,0],[1.0,1.0,1.0,0.0,0.0,0.0]], # A A A D D D577 [[1,1,1,2,2,2],[ 1.0, 1.0, 1.0, 1.0,-1.0,-1.0],[1,0,0,1,0,0],[1.0,1.0,1.0,0.0,0.0,0.0]], # A A A D -D -D578 [[1,1,1,2,2,2],[ 1.0, 1.0, 1.0, 1.0,-1.0, 1.0],[1,0,0,1,0,0],[1.0,1.0,1.0,0.0,0.0,0.0]], # A A A D -D D579 [[1,1,1,2,2,2],[ 1.0, 1.0, 1.0, 1.0, 1.0,-1.0],[1,0,0,1,0,0],[1.0,1.0,1.0,0.0,0.0,0.0]], # A A A D D -D580 [[1,1,2,1,0,0],[ 1.0, 1.0, 1.0, 0.5, 0.0, 0.0],[1,0,1,0,0,0],[1.0,1.0,1.0,0.5,0.0,0.0]], # A A C A/2 0 0581 [[1,2,3,0,0,0],[ 1.0, 1.0, 1.0, 0.0, 0.0, 0.0],[1,1,1,0,0,0],[1.0,1.0,1.0,0.0,0.0,0.0]], # A B C 0 0 0582 [[1,1,2,3,0,0],[ 1.0, 1.0, 1.0, 1.0, 0.0, 0.0],[1,0,1,1,0,0],[1.0,1.0,1.0,0.0,0.0,0.0]], # A A C D 0 0583 [[1,2,1,0,3,0],[ 1.0, 1.0, 1.0, 0.0, 1.0, 0.0],[1,1,0,0,1,0],[1.0,1.0,1.0,0.0,0.0,0.0]], # A B A 0 E 0584 [[1,2,2,0,0,3],[ 1.0, 1.0, 1.0, 0.0, 0.0, 1.0],[1,1,0,0,0,1],[1.0,1.0,1.0,0.0,0.0,0.0]], # A B B 0 0 F585 [[1,2,3,2,0,0],[ 1.0, 1.0, 1.0, 0.5, 0.0, 0.0],[1,1,1,0,0,0],[1.0,1.0,1.0,0.0,0.5,0.0]], # A B C B/2 0 0586 [[1,2,3,1,0,0],[ 1.0, 1.0, 1.0, 0.5, 0.0, 0.0],[1,1,1,0,0,0],[1.0,1.0,1.0,0.0,0.5,0.0]], # A B C A/2 0 0587 [[1,2,3,4,0,0],[ 1.0, 1.0, 1.0, 1.0, 0.0, 0.0],[1,1,1,1,0,0],[1.0,1.0,1.0,0.0,0.0,0.0]], # A B C D 0 0588 [[1,2,3,0,4,0],[ 1.0, 1.0, 1.0, 0.0, 1.0, 0.0],[1,1,1,0,1,0],[1.0,1.0,1.0,0.0,0.0,0.0]], # A B C 0 E 0589 [[1,2,3,0,0,4],[ 1.0, 1.0, 1.0, 0.0, 0.0, 1.0],[1,1,1,0,0,1],[1.0,1.0,1.0,0.0,0.0,0.0]], # A B C 0 0 F590 [[1,1,2,3,4,4],[ 1.0, 1.0, 1.0, 1.0, 1.0,-1.0],[1,0,1,1,1,0],[1.0,1.0,1.0,0.0,0.0,0.0]], # A A C D E -E591 [[1,1,2,3,4,4],[ 1.0, 1.0, 1.0, 1.0, 1.0, 1.0],[1,0,1,1,1,0],[1.0,1.0,1.0,0.0,0.0,0.0]], # A A C D E E592 [[1,2,1,3,4,3],[ 1.0, 1.0, 1.0, 1.0, 1.0,-1.0],[1,1,0,1,1,0],[1.0,1.0,1.0,0.0,0.0,0.0]], # A B A D E -D593 [[1,2,1,3,4,3],[ 1.0, 1.0, 1.0, 1.0, 1.0, 1.0],[1,1,0,1,1,0],[1.0,1.0,1.0,0.0,0.0,0.0]], # A B A D E D594 [[1,2,2,3,3,4],[ 1.0, 1.0, 1.0, 1.0,-1.0, 1.0],[1,1,0,1,0,1],[1.0,1.0,1.0,0.0,0.0,0.0]], # A B B D -D F595 [[1,2,2,3,3,4],[ 1.0, 1.0, 1.0, 1.0, 1.0, 1.0],[1,1,0,1,0,1],[1.0,1.0,1.0,0.0,0.0,0.0]], # A B B D D F596 [[1,2,3,2,4,4],[ 1.0, 1.0, 1.0, 0.5, 0.5, 1.0],[1,1,1,0,0,1],[1.0,1.0,1.0,0.5,0.0,0.0]], # A B C B/2 F/2 F597 [[1,2,3,1,0,4],[ 1.0, 1.0, 1.0, 0.5, 0.0, 1.0],[1,1,1,0,0,1],[1.0,1.0,1.0,0.5,0.0,0.0]], # A B C A/2 0 F598 [[1,2,3,2,4,0],[ 1.0, 1.0, 1.0, 0.5, 1.0, 0.0],[1,1,1,0,1,0],[1.0,1.0,1.0,0.5,0.0,0.0]], # A B C B/2 E 0599 [[1,2,3,1,4,4],[ 1.0, 1.0, 1.0, 0.5, 1.0, 0.5],[1,1,1,0,1,0],[1.0,1.0,1.0,0.5,0.0,0.0]], # A B C A/2 E E/2600 [[1,2,3,4,5,6],[ 1.0, 1.0, 1.0, 1.0, 1.0, 1.0],[1,1,1,1,1,1],[1.0,1.0,1.0,0.0,0.0,0.0]], # A B C D E F572 [[1,1,1,0,0,0],[ 1.0, 1.0, 1.0, 0.0, 0.0, 0.0],[1,0,0,0,0,0],[1.0,1.0,1.0,0.0,0.0,0.0]], #1 A A A 0 0 0 573 [[1,1,2,0,0,0],[ 1.0, 1.0, 1.0, 0.0, 0.0, 0.0],[1,0,1,0,0,0],[1.0,1.0,1.0,0.0,0.0,0.0]], #2 A A C 0 0 0 574 [[1,2,1,0,0,0],[ 1.0, 1.0, 1.0, 0.0, 0.0, 0.0],[1,1,0,0,0,0],[1.0,1.0,1.0,0.0,0.0,0.0]], #3 A B A 0 0 0 575 [[1,2,2,0,0,0],[ 1.0, 1.0, 1.0, 0.0, 0.0, 0.0],[1,1,0,0,0,0],[1.0,1.0,1.0,0.0,0.0,0.0]], #4 A B B 0 0 0 576 [[1,1,1,2,2,2],[ 1.0, 1.0, 1.0, 1.0, 1.0, 1.0],[1,0,0,1,0,0],[1.0,1.0,1.0,0.0,0.0,0.0]], #5 A A A D D D 577 [[1,1,1,2,2,2],[ 1.0, 1.0, 1.0, 1.0,-1.0,-1.0],[1,0,0,1,0,0],[1.0,1.0,1.0,0.0,0.0,0.0]], #6 A A A D -D -D 578 [[1,1,1,2,2,2],[ 1.0, 1.0, 1.0, 1.0,-1.0, 1.0],[1,0,0,1,0,0],[1.0,1.0,1.0,0.0,0.0,0.0]], #7 A A A D -D D 579 [[1,1,1,2,2,2],[ 1.0, 1.0, 1.0, 1.0, 1.0,-1.0],[1,0,0,1,0,0],[1.0,1.0,1.0,0.0,0.0,0.0]], #8 A A A D D -D 580 [[1,1,2,1,0,0],[ 1.0, 1.0, 1.0, 0.5, 0.0, 0.0],[1,0,1,0,0,0],[1.0,1.0,1.0,0.5,0.0,0.0]], #9 A A C A/2 0 0 581 [[1,2,3,0,0,0],[ 1.0, 1.0, 1.0, 0.0, 0.0, 0.0],[1,1,1,0,0,0],[1.0,1.0,1.0,0.0,0.0,0.0]], #10 A B C 0 0 0 582 [[1,1,2,3,0,0],[ 1.0, 1.0, 1.0, 1.0, 0.0, 0.0],[1,0,1,1,0,0],[1.0,1.0,1.0,0.0,0.0,0.0]], #11 A A C D 0 0 583 [[1,2,1,0,3,0],[ 1.0, 1.0, 1.0, 0.0, 1.0, 0.0],[1,1,0,0,1,0],[1.0,1.0,1.0,0.0,0.0,0.0]], #12 A B A 0 E 0 584 [[1,2,2,0,0,3],[ 1.0, 1.0, 1.0, 0.0, 0.0, 1.0],[1,1,0,0,0,1],[1.0,1.0,1.0,0.0,0.0,0.0]], #13 A B B 0 0 F 585 [[1,2,3,2,0,0],[ 1.0, 1.0, 1.0, 0.5, 0.0, 0.0],[1,1,1,0,0,0],[1.0,1.0,1.0,0.0,0.5,0.0]], #14 A B C B/2 0 0 586 [[1,2,3,1,0,0],[ 1.0, 1.0, 1.0, 0.5, 0.0, 0.0],[1,1,1,0,0,0],[1.0,1.0,1.0,0.0,0.5,0.0]], #15 A B C A/2 0 0 587 [[1,2,3,4,0,0],[ 1.0, 1.0, 1.0, 1.0, 0.0, 0.0],[1,1,1,1,0,0],[1.0,1.0,1.0,0.0,0.0,0.0]], #16 A B C D 0 0 588 [[1,2,3,0,4,0],[ 1.0, 1.0, 1.0, 0.0, 1.0, 0.0],[1,1,1,0,1,0],[1.0,1.0,1.0,0.0,0.0,0.0]], #17 A B C 0 E 0 589 [[1,2,3,0,0,4],[ 1.0, 1.0, 1.0, 0.0, 0.0, 1.0],[1,1,1,0,0,1],[1.0,1.0,1.0,0.0,0.0,0.0]], #18 A B C 0 0 F 590 [[1,1,2,3,4,4],[ 1.0, 1.0, 1.0, 1.0, 1.0,-1.0],[1,0,1,1,1,0],[1.0,1.0,1.0,0.0,0.0,0.0]], #19 A A C D E -E 591 [[1,1,2,3,4,4],[ 1.0, 1.0, 1.0, 1.0, 1.0, 1.0],[1,0,1,1,1,0],[1.0,1.0,1.0,0.0,0.0,0.0]], #20 A A C D E E 592 [[1,2,1,3,4,3],[ 1.0, 1.0, 1.0, 1.0, 1.0,-1.0],[1,1,0,1,1,0],[1.0,1.0,1.0,0.0,0.0,0.0]], #21 A B A D E -D 593 [[1,2,1,3,4,3],[ 1.0, 1.0, 1.0, 1.0, 1.0, 1.0],[1,1,0,1,1,0],[1.0,1.0,1.0,0.0,0.0,0.0]], #22 A B A D E D 594 [[1,2,2,3,3,4],[ 1.0, 1.0, 1.0, 1.0,-1.0, 1.0],[1,1,0,1,0,1],[1.0,1.0,1.0,0.0,0.0,0.0]], #23 A B B D -D F 595 [[1,2,2,3,3,4],[ 1.0, 1.0, 1.0, 1.0, 1.0, 1.0],[1,1,0,1,0,1],[1.0,1.0,1.0,0.0,0.0,0.0]], #24 A B B D D F 596 [[1,2,3,2,4,4],[ 1.0, 1.0, 1.0, 0.5, 0.5, 1.0],[1,1,1,0,0,1],[1.0,1.0,1.0,0.5,0.0,0.0]], #25 A B C B/2 F/2 F 597 [[1,2,3,1,0,4],[ 1.0, 1.0, 1.0, 0.5, 0.0, 1.0],[1,1,1,0,0,1],[1.0,1.0,1.0,0.5,0.0,0.0]], #26 A B C A/2 0 F 598 [[1,2,3,2,4,0],[ 1.0, 1.0, 1.0, 0.5, 1.0, 0.0],[1,1,1,0,1,0],[1.0,1.0,1.0,0.5,0.0,0.0]], #27 A B C B/2 E 0 599 [[1,2,3,1,4,4],[ 1.0, 1.0, 1.0, 0.5, 1.0, 0.5],[1,1,1,0,1,0],[1.0,1.0,1.0,0.5,0.0,0.0]], #28 A B C A/2 E E/2 600 [[1,2,3,4,5,6],[ 1.0, 1.0, 1.0, 1.0, 1.0, 1.0],[1,1,1,1,1,1],[1.0,1.0,1.0,0.0,0.0,0.0]], #29 A B C D E F 601 601 ] 602 602 indx = GetNXUPQsym(siteSym) … … 954 954 def U2Uij(U): 955 955 #returns the UIJ vector U11,U22,U33,U12,U13,U23 from tensor U 956 return [U[0][0],U[1][1],U[2][2], U[0][1],U[0][2],U[1][2]]956 return [U[0][0],U[1][1],U[2][2],2.*U[0][1],2.*U[0][2],2.*U[1][2]] 957 957 958 958 def Uij2U(Uij): 959 959 #returns the thermal motion tensor U from Uij as numpy array 960 return np.array([[Uij[0],Uij[3] ,Uij[4]],[Uij[3],Uij[1],Uij[5]],[Uij[4],Uij[5],Uij[2]]])960 return np.array([[Uij[0],Uij[3]/2.,Uij[4]/2.],[Uij[3]/2.,Uij[1],Uij[5]/2.],[Uij[4]/2.,Uij[5]/2.,Uij[2]]]) 961 961 962 962 def StandardizeSpcName(spcgroup): -
trunk/GSASIIstrIO.py
r1483 r1489 831 831 '%10.5f'%(at[cx+2])+'%8.3f'%(at[cx+3])+'%7s'%(at[cs])+'%5d'%(at[cs+1])+'%5s'%(at[cia]) 832 832 if at[cia] == 'I': 833 line += '%8. 4f'%(at[cia+1])+48*' '833 line += '%8.5f'%(at[cia+1])+48*' ' 834 834 else: 835 835 line += 8*' ' 836 836 for j in range(6): 837 line += '%8. 4f'%(at[cia+1+j])837 line += '%8.5f'%(at[cia+2+j]) 838 838 print >>pFile,line 839 839 elif General['Type'] == 'macromolecular': … … 847 847 line += 8*' ' 848 848 for j in range(6): 849 line += '%8.4f'%(at[cia+ 1+j])849 line += '%8.4f'%(at[cia+2+j]) 850 850 print >>pFile,line 851 851 … … 999 999 phaseVary.append(pfx+'Afrac:'+str(i)) 1000 1000 if 'X' in at[ct+1]: 1001 try: #patch for sytsym name changes 1002 xId,xCoef = G2spc.GetCSxinel(at[cs]) 1003 except KeyError: 1004 Sytsym = G2spc.SytSym(at[cx:cx+3],SGData)[0] 1005 at[cs] = Sytsym 1006 xId,xCoef = G2spc.GetCSxinel(at[cs]) 1001 1007 xId,xCoef = G2spc.GetCSxinel(at[cs]) 1002 1008 names = [pfx+'dAx:'+str(i),pfx+'dAy:'+str(i),pfx+'dAz:'+str(i)] … … 1009 1015 if len(equiv) > 1: 1010 1016 name = equiv[0][0] 1017 coef = equiv[0][1] 1011 1018 for eqv in equiv[1:]: 1019 eqv[1] /= coef 1012 1020 G2mv.StoreEquivalence(name,(eqv,)) 1013 1021 if 'U' in at[ct+1]: … … 1015 1023 phaseVary.append(pfx+'AUiso:'+str(i)) 1016 1024 else: 1025 try: #patch for sytsym name changes 1026 uId,uCoef = G2spc.GetCSuinel(at[cs])[:2] 1027 except KeyError: 1028 Sytsym = G2spc.SytSym(at[cx:cx+3],SGData)[0] 1029 at[cs] = Sytsym 1030 uId,uCoef = G2spc.GetCSuinel(at[cs])[:2] 1017 1031 uId,uCoef = G2spc.GetCSuinel(at[cs])[:2] 1018 1032 names = [pfx+'AU11:'+str(i),pfx+'AU22:'+str(i),pfx+'AU33:'+str(i), … … 1026 1040 if len(equiv) > 1: 1027 1041 name = equiv[0][0] 1042 coef = equiv[0][1] 1028 1043 for eqv in equiv[1:]: 1029 G2mv.StoreEquivalence(name,(eqv,)) 1044 eqv[1] /= coef 1045 G2mv.StoreEquivalence(name,equiv[1:]) 1030 1046 # elif General['Type'] == 'magnetic': 1031 1047 # elif General['Type'] == 'macromolecular': … … 1293 1309 elif General['Type'] == 'macromolecular': 1294 1310 line = ' res no residue chain '+line 1311 cx,ct,cs,cia = General['AtomPtrs'] 1295 1312 print >>pFile,line 1296 1313 if General['Type'] == 'nuclear': -
trunk/GSASIIstrMain.py
r1474 r1489 173 173 #if warnmsg: print 'Warnings',warnmsg 174 174 raise Exception(' *** Refine aborted ***') 175 #print G2mv.VarRemapShow(varyList)175 # print G2mv.VarRemapShow(varyList) 176 176 177 177 ifPrint = True -
trunk/GSASIIstrMath.py
r1484 r1489 764 764 dfadua = np.sum(-Hij*fa[:,:,:,np.newaxis],axis=2) 765 765 dfadba = np.sum(-cosp*(occ*Tcorr)[:,np.newaxis],axis=1) 766 #NB: the above have been checked against PA(1:10,1:2) in strfctr.for 766 #NB: the above have been checked against PA(1:10,1:2) in strfctr.for for al2O3! 767 767 dFdfr[iref] = 2.*(fas[0]*dfadfr[0]+fas[1]*dfadfr[1])*Mdata/len(Uniq) 768 768 dFdx[iref] = 2.*(fas[0]*dfadx[0]+fas[1]*dfadx[1]) … … 2014 2014 depDerivDict[var][iref] = w*dFdvDict[var][iref]*parmDict[phfx+'Scale']*ref[11] #*dervCor 2015 2015 if phfx+'Scale' in varylist: 2016 dMdvh[varylist.index(phfx+'Scale')][iref] = w*ref[9]* dervCor2016 dMdvh[varylist.index(phfx+'Scale')][iref] = w*ref[9]*ref[11] #*dervCor 2017 2017 elif phfx+'Scale' in dependentVars: 2018 depDerivDict[phfx+'Scale'][iref] = w*ref[9]* dervCor2018 depDerivDict[phfx+'Scale'][iref] = w*ref[9]*ref[11] #*dervCor 2019 2019 for item in ['Ep','Es','Eg']: 2020 2020 if phfx+item in varylist and dervDict: 2021 dMdvh[varylist.index(phfx+item)][iref] = w*dervDict[phfx+item]/ dervCor2021 dMdvh[varylist.index(phfx+item)][iref] = w*dervDict[phfx+item]/ref[11] #/dervCor 2022 2022 elif phfx+item in dependentVars and dervDict: 2023 depDerivDict[phfx+item][iref] = w*dervDict[phfx+item]/ dervCor2023 depDerivDict[phfx+item][iref] = w*dervDict[phfx+item]/ref[11] #/dervCor 2024 2024 for item in ['BabA','BabU']: 2025 2025 if phfx+item in varylist: … … 2038 2038 for j,var in enumerate(varylist): 2039 2039 if var in dFdvDict: 2040 dMdvh[j][iref] = w*dFdvDict[var][iref]*parmDict[phfx+'Scale']* ref[11] #*dervCor2040 dMdvh[j][iref] = w*dFdvDict[var][iref]*parmDict[phfx+'Scale']*dervCor #*ref[11] 2041 2041 for var in dependentVars: 2042 2042 if var in dFdvDict: 2043 depDerivDict[var][iref] = w*dFdvDict[var][iref]*parmDict[phfx+'Scale']* ref[11] #*dervCor2043 depDerivDict[var][iref] = w*dFdvDict[var][iref]*parmDict[phfx+'Scale']*dervCor #*ref[11] 2044 2044 if phfx+'Scale' in varylist: 2045 dMdvh[varylist.index(phfx+'Scale')][iref] = w*ref[9]* ref[11] #*dervCor2045 dMdvh[varylist.index(phfx+'Scale')][iref] = w*ref[9]*dervCor #*ref[11] 2046 2046 elif phfx+'Scale' in dependentVars: 2047 depDerivDict[phfx+'Scale'][iref] = w*ref[9]* ref[11] #*dervCor2047 depDerivDict[phfx+'Scale'][iref] = w*ref[9]*dervCor #*ref[11] 2048 2048 for item in ['Ep','Es','Eg']: 2049 2049 if phfx+item in varylist and dervDict: … … 2085 2085 Limits = calcControls[hfx+'Limits'] 2086 2086 x,y,w,yc,yb,yd = Histogram['Data'] 2087 W = wtFactor*w2088 2087 xB = np.searchsorted(x,Limits[0]) 2089 2088 xF = np.searchsorted(x,Limits[1]) 2090 dMdvh = np.sqrt( W[xB:xF])*getPowderProfileDerv(parmDict,x[xB:xF],2089 dMdvh = np.sqrt(w[xB:xF])*getPowderProfileDerv(parmDict,x[xB:xF], 2091 2090 varylist,Histogram,Phases,rigidbodyDict,calcControls,pawleyLookup) 2092 2091 elif 'HKLF' in histogram[:4]:
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