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fix import of pyspg (binary module); redo spg & lattice unit tests
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@briantoby
briantoby committed Jan 19, 2025
1 parent 10c9f03 commit b4dbfcc
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Showing 5 changed files with 3,653 additions and 7,044 deletions.
358 changes: 0 additions & 358 deletions GSASII/GSASIIlattice.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3005,361 +3005,3 @@ def textureIndex(SHCoef):

cellUlbl = ('a','b','c',u'\u03B1',u'\u03B2',u'\u03B3')
'unicode labels for a, b, c, alpha, beta, gamma'

# self-test materials follow.
selftestlist = []
'''Defines a list of self-tests'''
selftestquiet = True
def _ReportTest():
'Report name and doc string of current routine when ``selftestquiet`` is False'
if not selftestquiet:
import inspect
caller = inspect.stack()[1][3]
doc = eval(caller).__doc__
if doc is not None:
print('testing '+__file__+' with '+caller+' ('+doc+')')
else:
print('testing '+__file__()+" with "+caller)
NeedTestData = True
def TestData():
array = np.array
global NeedTestData
NeedTestData = False
global CellTestData
# output from uctbx computed on platform darwin on 2010-05-28
CellTestData = [
# cell, g, G, cell*, V, V*
[(4, 4, 4, 90, 90, 90),
array([[ 1.60000000e+01, 9.79717439e-16, 9.79717439e-16],
[ 9.79717439e-16, 1.60000000e+01, 9.79717439e-16],
[ 9.79717439e-16, 9.79717439e-16, 1.60000000e+01]]), array([[ 6.25000000e-02, 3.82702125e-18, 3.82702125e-18],
[ 3.82702125e-18, 6.25000000e-02, 3.82702125e-18],
[ 3.82702125e-18, 3.82702125e-18, 6.25000000e-02]]), (0.25, 0.25, 0.25, 90.0, 90.0, 90.0), 64.0, 0.015625],
# cell, g, G, cell*, V, V*
[(4.0999999999999996, 5.2000000000000002, 6.2999999999999998, 100, 80, 130),
array([[ 16.81 , -13.70423184, 4.48533243],
[-13.70423184, 27.04 , -5.6887143 ],
[ 4.48533243, -5.6887143 , 39.69 ]]), array([[ 0.10206349, 0.05083339, -0.00424823],
[ 0.05083339, 0.06344997, 0.00334956],
[-0.00424823, 0.00334956, 0.02615544]]), (0.31947376387537696, 0.25189277536327803, 0.16172643497798223, 85.283666420376008, 94.716333579624006, 50.825714168082683), 100.98576357983838, 0.0099023858863968445],
# cell, g, G, cell*, V, V*
[(3.5, 3.5, 6, 90, 90, 120),
array([[ 1.22500000e+01, -6.12500000e+00, 1.28587914e-15],
[ -6.12500000e+00, 1.22500000e+01, 1.28587914e-15],
[ 1.28587914e-15, 1.28587914e-15, 3.60000000e+01]]), array([[ 1.08843537e-01, 5.44217687e-02, 3.36690552e-18],
[ 5.44217687e-02, 1.08843537e-01, 3.36690552e-18],
[ 3.36690552e-18, 3.36690552e-18, 2.77777778e-02]]), (0.32991443953692895, 0.32991443953692895, 0.16666666666666669, 90.0, 90.0, 60.000000000000021), 63.652867178156257, 0.015710211406520427],
]
global CoordTestData
CoordTestData = [
# cell, ((frac, ortho),...)
((4,4,4,90,90,90,), [
((0.10000000000000001, 0.0, 0.0),(0.40000000000000002, 0.0, 0.0)),
((0.0, 0.10000000000000001, 0.0),(2.4492935982947065e-17, 0.40000000000000002, 0.0)),
((0.0, 0.0, 0.10000000000000001),(2.4492935982947065e-17, -2.4492935982947065e-17, 0.40000000000000002)),
((0.10000000000000001, 0.20000000000000001, 0.29999999999999999),(0.40000000000000013, 0.79999999999999993, 1.2)),
((0.20000000000000001, 0.29999999999999999, 0.10000000000000001),(0.80000000000000016, 1.2, 0.40000000000000002)),
((0.29999999999999999, 0.20000000000000001, 0.10000000000000001),(1.2, 0.80000000000000004, 0.40000000000000002)),
((0.5, 0.5, 0.5),(2.0, 1.9999999999999998, 2.0)),
]),
# cell, ((frac, ortho),...)
((4.1,5.2,6.3,100,80,130,), [
((0.10000000000000001, 0.0, 0.0),(0.40999999999999998, 0.0, 0.0)),
((0.0, 0.10000000000000001, 0.0),(-0.33424955703700043, 0.39834311042186865, 0.0)),
((0.0, 0.0, 0.10000000000000001),(0.10939835193016617, -0.051013289294572106, 0.6183281045774256)),
((0.10000000000000001, 0.20000000000000001, 0.29999999999999999),(0.069695941716497567, 0.64364635296002093, 1.8549843137322766)),
((0.20000000000000001, 0.29999999999999999, 0.10000000000000001),(-0.073350319180835066, 1.1440160419710339, 0.6183281045774256)),
((0.29999999999999999, 0.20000000000000001, 0.10000000000000001),(0.67089923785616512, 0.74567293154916525, 0.6183281045774256)),
((0.5, 0.5, 0.5),(0.92574397446582857, 1.7366491056364828, 3.0916405228871278)),
]),
# cell, ((frac, ortho),...)
((3.5,3.5,6,90,90,120,), [
((0.10000000000000001, 0.0, 0.0),(0.35000000000000003, 0.0, 0.0)),
((0.0, 0.10000000000000001, 0.0),(-0.17499999999999993, 0.3031088913245536, 0.0)),
((0.0, 0.0, 0.10000000000000001),(3.6739403974420595e-17, -3.6739403974420595e-17, 0.60000000000000009)),
((0.10000000000000001, 0.20000000000000001, 0.29999999999999999),(2.7675166561703527e-16, 0.60621778264910708, 1.7999999999999998)),
((0.20000000000000001, 0.29999999999999999, 0.10000000000000001),(0.17500000000000041, 0.90932667397366063, 0.60000000000000009)),
((0.29999999999999999, 0.20000000000000001, 0.10000000000000001),(0.70000000000000018, 0.6062177826491072, 0.60000000000000009)),
((0.5, 0.5, 0.5),(0.87500000000000067, 1.5155444566227676, 3.0)),
]),
]
global LaueTestData #generated by GSAS
LaueTestData = {
'R 3 m':[(4.,4.,6.,90.,90.,120.),((1,0,1,6),(1,0,-2,6),(0,0,3,2),(1,1,0,6),(2,0,-1,6),(2,0,2,6),
(1,1,3,12),(1,0,4,6),(2,1,1,12),(2,1,-2,12),(3,0,0,6),(1,0,-5,6),(2,0,-4,6),(3,0,-3,6),(3,0,3,6),
(0,0,6,2),(2,2,0,6),(2,1,4,12),(2,0,5,6),(3,1,-1,12),(3,1,2,12),(1,1,6,12),(2,2,3,12),(2,1,-5,12))],
'R 3':[(4.,4.,6.,90.,90.,120.),((1,0,1,6),(1,0,-2,6),(0,0,3,2),(1,1,0,6),(2,0,-1,6),(2,0,2,6),(1,1,3,6),
(1,1,-3,6),(1,0,4,6),(3,-1,1,6),(2,1,1,6),(3,-1,-2,6),(2,1,-2,6),(3,0,0,6),(1,0,-5,6),(2,0,-4,6),
(2,2,0,6),(3,0,3,6),(3,0,-3,6),(0,0,6,2),(3,-1,4,6),(2,0,5,6),(2,1,4,6),(4,-1,-1,6),(3,1,-1,6),
(3,1,2,6),(4,-1,2,6),(2,2,-3,6),(1,1,-6,6),(1,1,6,6),(2,2,3,6),(2,1,-5,6),(3,-1,-5,6))],
'P 3':[(4.,4.,6.,90.,90.,120.),((0,0,1,2),(1,0,0,6),(1,0,1,6),(0,0,2,2),(1,0,-1,6),(1,0,2,6),(1,0,-2,6),
(1,1,0,6),(0,0,3,2),(1,1,1,6),(1,1,-1,6),(1,0,3,6),(1,0,-3,6),(2,0,0,6),(2,0,-1,6),(1,1,-2,6),
(1,1,2,6),(2,0,1,6),(2,0,-2,6),(2,0,2,6),(0,0,4,2),(1,1,-3,6),(1,1,3,6),(1,0,-4,6),(1,0,4,6),
(2,0,-3,6),(2,1,0,6),(2,0,3,6),(3,-1,0,6),(2,1,1,6),(3,-1,-1,6),(2,1,-1,6),(3,-1,1,6),(1,1,4,6),
(3,-1,2,6),(3,-1,-2,6),(1,1,-4,6),(0,0,5,2),(2,1,2,6),(2,1,-2,6),(3,0,0,6),(3,0,1,6),(2,0,4,6),
(2,0,-4,6),(3,0,-1,6),(1,0,-5,6),(1,0,5,6),(3,-1,-3,6),(2,1,-3,6),(2,1,3,6),(3,-1,3,6),(3,0,-2,6),
(3,0,2,6),(1,1,5,6),(1,1,-5,6),(2,2,0,6),(3,0,3,6),(3,0,-3,6),(0,0,6,2),(2,0,-5,6),(2,1,-4,6),
(2,2,-1,6),(3,-1,-4,6),(2,2,1,6),(3,-1,4,6),(2,1,4,6),(2,0,5,6),(1,0,-6,6),(1,0,6,6),(4,-1,0,6),
(3,1,0,6),(3,1,-1,6),(3,1,1,6),(4,-1,-1,6),(2,2,2,6),(4,-1,1,6),(2,2,-2,6),(3,1,2,6),(3,1,-2,6),
(3,0,4,6),(3,0,-4,6),(4,-1,-2,6),(4,-1,2,6),(2,2,-3,6),(1,1,6,6),(1,1,-6,6),(2,2,3,6),(3,-1,5,6),
(2,1,5,6),(2,1,-5,6),(3,-1,-5,6))],
'P 3 m 1':[(4.,4.,6.,90.,90.,120.),((0,0,1,2),(1,0,0,6),(1,0,-1,6),(1,0,1,6),(0,0,2,2),(1,0,-2,6),
(1,0,2,6),(1,1,0,6),(0,0,3,2),(1,1,1,12),(1,0,-3,6),(1,0,3,6),(2,0,0,6),(1,1,2,12),(2,0,1,6),
(2,0,-1,6),(0,0,4,2),(2,0,-2,6),(2,0,2,6),(1,1,3,12),(1,0,-4,6),(1,0,4,6),(2,0,3,6),(2,1,0,12),
(2,0,-3,6),(2,1,1,12),(2,1,-1,12),(1,1,4,12),(2,1,2,12),(0,0,5,2),(2,1,-2,12),(3,0,0,6),(1,0,-5,6),
(3,0,1,6),(3,0,-1,6),(1,0,5,6),(2,0,4,6),(2,0,-4,6),(2,1,3,12),(2,1,-3,12),(3,0,-2,6),(3,0,2,6),
(1,1,5,12),(3,0,-3,6),(0,0,6,2),(2,2,0,6),(3,0,3,6),(2,1,4,12),(2,2,1,12),(2,0,5,6),(2,1,-4,12),
(2,0,-5,6),(1,0,-6,6),(1,0,6,6),(3,1,0,12),(3,1,-1,12),(3,1,1,12),(2,2,2,12),(3,1,2,12),
(3,0,4,6),(3,1,-2,12),(3,0,-4,6),(1,1,6,12),(2,2,3,12))],
'P 3 1 m':[(4.,4.,6.,90.,90.,120.),((0,0,1,2),(1,0,0,6),(0,0,2,2),(1,0,1,12),(1,0,2,12),(1,1,0,6),
(0,0,3,2),(1,1,-1,6),(1,1,1,6),(1,0,3,12),(2,0,0,6),(2,0,1,12),(1,1,2,6),(1,1,-2,6),(2,0,2,12),
(0,0,4,2),(1,1,-3,6),(1,1,3,6),(1,0,4,12),(2,1,0,12),(2,0,3,12),(2,1,1,12),(2,1,-1,12),(1,1,-4,6),
(1,1,4,6),(0,0,5,2),(2,1,-2,12),(2,1,2,12),(3,0,0,6),(1,0,5,12),(2,0,4,12),(3,0,1,12),(2,1,-3,12),
(2,1,3,12),(3,0,2,12),(1,1,5,6),(1,1,-5,6),(3,0,3,12),(0,0,6,2),(2,2,0,6),(2,1,-4,12),(2,0,5,12),
(2,2,-1,6),(2,2,1,6),(2,1,4,12),(3,1,0,12),(1,0,6,12),(2,2,2,6),(3,1,-1,12),(2,2,-2,6),(3,1,1,12),
(3,1,-2,12),(3,0,4,12),(3,1,2,12),(1,1,-6,6),(2,2,3,6),(2,2,-3,6),(1,1,6,6))],
}

global FLnhTestData
FLnhTestData = [{
'C(4,0,0)': (0.965, 0.42760447),
'C(2,0,0)': (1.0122, -0.80233610),
'C(2,0,2)': (0.0061, 8.37491546E-03),
'C(6,0,4)': (-0.0898, 4.37985696E-02),
'C(6,0,6)': (-0.1369, -9.04081762E-02),
'C(6,0,0)': (0.5935, -0.18234928),
'C(4,0,4)': (0.1872, 0.16358127),
'C(6,0,2)': (0.6193, 0.27573633),
'C(4,0,2)': (-0.1897, 0.12530720)},[1,0,0]]
def test0():
if NeedTestData: TestData()
msg = 'test cell2Gmat, fillgmat, Gmat2cell'
for (cell, tg, tG, trcell, tV, trV) in CellTestData:
G, g = cell2Gmat(cell)
assert np.allclose(G,tG),msg
assert np.allclose(g,tg),msg
tcell = Gmat2cell(g)
assert np.allclose(cell,tcell),msg
tcell = Gmat2cell(G)
assert np.allclose(tcell,trcell),msg
selftestlist.append(test0)

def test1():
'test cell2A and A2Gmat'
_ReportTest()
if NeedTestData: TestData()
msg = 'test cell2A and A2Gmat'
for (cell, tg, tG, trcell, tV, trV) in CellTestData:
G, g = A2Gmat(cell2A(cell))
assert np.allclose(G,tG),msg
assert np.allclose(g,tg),msg
selftestlist.append(test1)

def test2():
'test Gmat2A, A2cell, A2Gmat, Gmat2cell'
_ReportTest()
if NeedTestData: TestData()
msg = 'test Gmat2A, A2cell, A2Gmat, Gmat2cell'
for (cell, tg, tG, trcell, tV, trV) in CellTestData:
G, g = cell2Gmat(cell)
tcell = A2cell(Gmat2A(G))
assert np.allclose(cell,tcell),msg
selftestlist.append(test2)

def test3():
'test invcell2Gmat'
_ReportTest()
if NeedTestData: TestData()
msg = 'test invcell2Gmat'
for (cell, tg, tG, trcell, tV, trV) in CellTestData:
G, g = invcell2Gmat(trcell)
assert np.allclose(G,tG),msg
assert np.allclose(g,tg),msg
selftestlist.append(test3)

def test4():
'test calc_rVsq, calc_rV, calc_V'
_ReportTest()
if NeedTestData: TestData()
msg = 'test calc_rVsq, calc_rV, calc_V'
for (cell, tg, tG, trcell, tV, trV) in CellTestData:
assert np.allclose(calc_rV(cell2A(cell)),trV), msg
assert np.allclose(calc_V(cell2A(cell)),tV), msg
selftestlist.append(test4)

def test5():
'test A2invcell'
_ReportTest()
if NeedTestData: TestData()
msg = 'test A2invcell'
for (cell, tg, tG, trcell, tV, trV) in CellTestData:
rcell = A2invcell(cell2A(cell))
assert np.allclose(rcell,trcell),msg
selftestlist.append(test5)

def test6():
'test cell2AB'
_ReportTest()
if NeedTestData: TestData()
msg = 'test cell2AB'
for (cell,coordlist) in CoordTestData:
A,B = cell2AB(cell)
for (frac,ortho) in coordlist:
to = np.inner(A,frac)
tf = np.inner(B,to)
assert np.allclose(ortho,to), msg
assert np.allclose(frac,tf), msg
to = np.sum(A*frac,axis=1)
tf = np.sum(B*to,axis=1)
assert np.allclose(ortho,to), msg
assert np.allclose(frac,tf), msg
selftestlist.append(test6)

def test7():
'test GetBraviasNum() and GenHBravais()'
_ReportTest()
import os.path
import sys
import GSASIIspc as spc
testdir = os.path.join(os.path.split(os.path.abspath( __file__ ))[0],'testinp')
if os.path.exists(testdir):
if testdir not in sys.path: sys.path.insert(0,testdir)
import sgtbxlattinp
derror = 1e-4
def indexmatch(hklin, hkllist, system):
for hklref in hkllist:
hklref = list(hklref)
# these permutations are far from complete, but are sufficient to
# allow the test to complete
if system == 'cubic':
permlist = [(1,2,3),(1,3,2),(2,1,3),(2,3,1),(3,1,2),(3,2,1),]
elif system == 'monoclinic':
permlist = [(1,2,3),(-1,2,-3)]
else:
permlist = [(1,2,3)]

for perm in permlist:
hkl = [abs(i) * hklin[abs(i)-1] / i for i in perm]
if hkl == hklref: return True
if [-i for i in hkl] == hklref: return True
else:
return False

for key in sgtbxlattinp.sgtbx7:
spdict = spc.SpcGroup(key)
cell = sgtbxlattinp.sgtbx7[key][0]
system = spdict[1]['SGSys']
center = spdict[1]['SGLatt']

bravcode = GetBraviasNum(center, system)

g2list = GenHBravais(sgtbxlattinp.dmin, bravcode, cell2A(cell))

assert len(sgtbxlattinp.sgtbx7[key][1]) == len(g2list), 'Reflection lists differ for %s' % key
for h,k,l,d,num in g2list:
for hkllist,dref in sgtbxlattinp.sgtbx7[key][1]:
if abs(d-dref) < derror:
if indexmatch((h,k,l,), hkllist, system):
break
else:
assert 0,'No match for %s at %s (%s)' % ((h,k,l),d,key)
selftestlist.append(test7)

def test8():
'test GenHLaue'
_ReportTest()
import GSASIIspc as spc
import sgtbxlattinp
derror = 1e-4
dmin = sgtbxlattinp.dmin

def indexmatch(hklin, hklref, system, axis):
# these permutations are far from complete, but are sufficient to
# allow the test to complete
if system == 'cubic':
permlist = [(1,2,3),(1,3,2),(2,1,3),(2,3,1),(3,1,2),(3,2,1),]
elif system == 'monoclinic' and axis=='b':
permlist = [(1,2,3),(-1,2,-3)]
elif system == 'monoclinic' and axis=='a':
permlist = [(1,2,3),(1,-2,-3)]
elif system == 'monoclinic' and axis=='c':
permlist = [(1,2,3),(-1,-2,3)]
elif system == 'trigonal':
permlist = [(1,2,3),(2,1,3),(-1,-2,3),(-2,-1,3)]
elif system == 'rhombohedral':
permlist = [(1,2,3),(2,3,1),(3,1,2)]
else:
permlist = [(1,2,3)]

hklref = list(hklref)
for perm in permlist:
hkl = [abs(i) * hklin[abs(i)-1] / i for i in perm]
if hkl == hklref: return True
if [-i for i in hkl] == hklref: return True
return False

for key in sgtbxlattinp.sgtbx8:
spdict = spc.SpcGroup(key)[1]
cell = sgtbxlattinp.sgtbx8[key][0]
Axis = spdict['SGUniq']
system = spdict['SGSys']

g2list = GenHLaue(dmin,spdict,cell2A(cell))
#if len(g2list) != len(sgtbxlattinp.sgtbx8[key][1]):
# print 'failed',key,':' ,len(g2list),'vs',len(sgtbxlattinp.sgtbx8[key][1])
# print 'GSAS-II:'
# for h,k,l,d in g2list: print ' ',(h,k,l),d
# print 'SGTBX:'
# for hkllist,dref in sgtbxlattinp.sgtbx8[key][1]: print ' ',hkllist,dref
assert len(g2list) == len(sgtbxlattinp.sgtbx8[key][1]), (
'Reflection lists differ for %s' % key
)
#match = True
for h,k,l,d in g2list:
for hkllist,dref in sgtbxlattinp.sgtbx8[key][1]:
if abs(d-dref) < derror:
if indexmatch((h,k,l,), hkllist, system, Axis): break
else:
assert 0,'No match for %s at %s (%s)' % ((h,k,l),d,key)
#match = False
#if not match:
#for hkllist,dref in sgtbxlattinp.sgtbx8[key][1]: print ' ',hkllist,dref
#print center, Laue, Axis, system
selftestlist.append(test8)

def test9():
'test GenHLaue'
_ReportTest()
import GSASIIspc as G2spc
if NeedTestData: TestData()
for spc in LaueTestData:
data = LaueTestData[spc]
cell = data[0]
hklm = np.array(data[1])
H = hklm[-1][:3]
hklO = hklm.T[:3].T
A = cell2A(cell)
dmin = 1./np.sqrt(calc_rDsq(H,A))
SGData = G2spc.SpcGroup(spc)[1]
hkls = np.array(GenHLaue(dmin,SGData,A))
hklN = hkls.T[:3].T
#print spc,hklO.shape,hklN.shape
err = True
for H in hklO:
if H not in hklN:
print ('%d %s'%(H,' missing from hkl from GSASII'))
err = False
assert(err)
selftestlist.append(test9)




if __name__ == '__main__':
import GSASIIpath
GSASIIpath.SetBinaryPath()
# run self-tests
selftestquiet = False
for test in selftestlist:
test()
print ("OK")
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