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Nexus: make tiling more robust #1432

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Mar 12, 2019
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Nexus: make tiling more robust #1432

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2f6c621
nexus: add function to check tiling
jtkrogel Mar 8, 2019
c424126
nexus: add structure initialization tests
jtkrogel Mar 9, 2019
1c5c4c5
nexus: add tiling tests and fix
jtkrogel Mar 11, 2019
17cd808
Merge branch 'develop' into nx_fix_tiling
markdewing Mar 11, 2019
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274 changes: 273 additions & 1 deletion nexus/bin/nxs-test
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Original file line number Diff line number Diff line change
Expand Up @@ -2410,12 +2410,283 @@ def machines():



def structure():
# divert logging function
nlog_divert()

nlabel('imports')
from generic import obj
from structure import Structure,Crystal
from structure import generate_structure
from structure import read_structure


nlabel('definitions')
def structure_same(s1,s2):
keys = ('units','elem','pos','axes','kpoints','kweights','kaxes')
o1 = s1.obj(keys)
o2 = s2.obj(keys)
return object_eq(o1,o2)
#end def structure_same

def structure_diff(s1,s2):
keys = ('units','elem','pos','axes','kpoints','kweights','kaxes')
o1 = s1.obj(keys)
o2 = s2.obj(keys)
return object_diff(o1,o2,full=True)
#end def structure_diff


nlabel('empty_init')
s1 = Structure()
s2 = generate_structure('empty')
nassert(object_eq(s1,s2))


nlabel('ref_inputs')
ref_in = obj()
ref_in.diamond_prim = obj(
units = 'A',
axes = [[1.785, 1.785, 0. ],
[0. , 1.785, 1.785],
[1.785, 0. , 1.785]],
elem = ['C','C'],
pos = [[0. , 0. , 0. ],
[0.8925, 0.8925, 0.8925]],
)
ref_in.diamond_conv = obj(
units = 'A',
axes = [[3.57, 0 , 0. ],
[0. , 3.57, 0. ],
[0 , 0. , 3.57]],
elem = ['C','C','C','C','C','C','C','C'],
pos = [[0.0000, 0.0000, 0.0000],
[0.8925, 0.8925, 0.8925],
[0.0000, 1.7850, 1.7850],
[0.8925, 2.6775, 2.6775],
[1.7850, 0.0000, 1.7850],
[2.6775, 0.8925, 2.6775],
[1.7850, 1.7850, 0.0000],
[2.6775, 2.6775, 0.8925]],
)
ref_in.wurtzite_prim = obj(
units = 'A',
axes = [[ 3.350, 0.00000000, 0.00],
[-1.675, 2.90118510, 0.00],
[ 0.000, 0.00000000, 5.22]],
elem = ['Zn','O','Zn','O'],
pos = [[0.00000000e+00, 0.00000000e+00, 3.26250000e+00],
[0.00000000e+00, 0.00000000e+00, 0.00000000e+00],
[1.67500000e+00, 9.67061701e-01, 6.52500000e-01],
[1.67500000e+00, 9.67061701e-01, 2.61000000e+00]],
)
ref_in.oxygen_prim = obj(
units = 'A',
axes = [[ 2.70150000e+00, -1.71450000e+00, 0.00000000e+00],
[ 2.70150000e+00, 1.71450000e+00, 0.00000000e+00],
[-3.43801471e+00, 0.00000000e+00, 3.74799291e+00]],
elem = ['O','O'],
pos = [[ 0., 0., 0.575],
[ 0., 0., -0.575]],
)
ref_in.CuO_prim = obj(
units = 'A',
axes = [[ 2.34150000e+00, -1.71100000e+00, 0.00000000e+00],
[ 2.34150000e+00, 1.71100000e+00, 0.00000000e+00],
[-8.49894838e-01, 0.00000000e+00, 5.05708046e+00]],
elem = ['Cu','O','Cu','O'],
pos = [[ 1.17075 , 0.8555 , 0. ],
[-0.21247371, 1.430396, 1.26427011],
[ 0.74580258, 2.5665 , 2.52854023],
[ 1.70407887, 0.280604, 3.79281034]],
)
ref_in.Ca2CuO3_prim = obj(
units = 'A',
axes = [[ 1.885, 1.625, -6.115],
[-1.885, 1.625, 6.115],
[ 1.885, -1.625, 6.115]],
elem = ['Cu','O','O','O','Ca','Ca'],
pos = [[0.000, 0.000, 0.000],
[1.885, 0.000, 0.000],
[0.000, 0.000, 1.960],
[0.000, 0.000, 10.270],
[0.000, 0.000, 4.290],
[0.000, 0.000, 7.940]],
)
ref_in.La2CuO4_prim = obj(
units = 'A',
axes = [[ 1.9045, 1.9045, -6.5845],
[-1.9045, 1.9045, 6.5845],
[ 1.9045, -1.9045, 6.5845]],
elem = ['Cu','O','O','O','O','La','La'],
pos = [[ 0. , 0. , 0. ],
[ 0.95225 , 0.95225 , -3.29225 ],
[-0.95225 , 0.95225 , 3.29225 ],
[ 0.346619, -0.346619, 1.198379],
[-0.346619, 0.346619, -1.198379],
[ 0.689429, -0.689429, 2.383589],
[-0.689429, 0.689429, -2.383589]],
)
ref_in.graphene_prim = obj(
units = 'A',
axes = [[ 2.462, 0.00000000, 0.00],
[-1.231, 2.13215454, 0.00],
[ 0.000, 0.00000000, 15.00]],
elem = ['C','C'],
pos = [[0. , 0. , 0. ],
[1.231, 0.71071818, 0. ]],
)


nlabel('direct_init')
ref = obj()
for name,inputs in ref_in.iteritems():
ref[name] = Structure(**inputs)
#end for


nlabel('generate_init')
gen = obj()
for name,inputs in ref_in.iteritems():
gen[name] = generate_structure(**inputs)
#end for


nlabel('crystal_init')
crys = obj()
for (latt,cell),inputs in Crystal.known_crystals.iteritems():
s = generate_structure(structure=latt,cell=cell)
crys[latt+'_'+cell] = s
#end for


nlabel('check_generate_init')
for name,s in ref.iteritems():
nassert(structure_same(s,gen[name]))
#end for


nlabel('check_crystal_init')
for name,s in ref.iteritems():
nassert(structure_same(s,crys[name]))
#end for


nlabel('diagonal_tiling')
diag_tilings = [
(1, 1, 1),
(1, 2, 3),
(1, 2, 4),
(1, 3, 1),
(1, 3, 2),
(1, 3, 3),
(1, 5, 3),
(1, 5, 5),
(1, 5, 6),
(2, 1, 2),
(2, 1, 3),
(2, 2, 2),
(2, 3, 1),
(2, 3, 2),
(2, 3, 3),
(2, 4, 4),
(2, 5, 1),
(2, 5, 2),
(2, 5, 3),
(3, 1, 1),
(3, 1, 2),
(3, 1, 3),
(3, 2, 1),
(3, 2, 3),
(3, 3, 6),
(4, 6, 4),
(5, 5, 1),
(5, 5, 5),
(6, 2, 6),
(6, 3, 1),
(6, 3, 6),
(6, 4, 6),
(6, 6, 4),
]
for name,s in ref.iteritems():
for tvec in diag_tilings:
st = s.tile(tvec)
st.check_tiling()
#end for
#end for


nlabel('matrix_tiling')
matrix_tilings = [
(-3,-2, 0,-2,-2,-3, 3, 2,-1),
(-3,-1, 3, 0, 1, 1,-3, 3,-3),
(-3, 0,-2,-3, 0, 3, 2,-3, 0),
(-3, 1, 0,-3, 3,-3, 0,-2, 1),
(-2,-1, 2, 3,-3,-3,-2, 2,-2),
(-2, 0, 3,-2, 1,-1,-3, 0, 1),
(-2, 1,-3,-3, 0, 3, 2, 0, 3),
(-2, 2,-3,-1, 0, 1,-1,-2, 3),
(-1, 3, 2,-3, 2,-2, 3,-3,-1),
(-1, 3, 3,-3, 3, 0,-3,-1, 1),
( 0,-1,-2, 2, 3, 1, 3,-2, 0),
( 0, 1, 3,-2, 3, 1, 2, 1, 2),
( 0, 3,-1,-1,-1, 2, 2, 3, 2),
( 1,-3,-3,-3, 3, 0,-2, 2,-2),
( 1,-2, 2, 1, 1, 1, 3, 2,-1),
( 1, 0, 1,-3, 2, 1, 1, 2,-2),
( 1, 2, 1,-2, 1,-1,-2, 3, 2),
( 1, 2, 1, 2, 1,-1, 3, 2, 2),
( 1, 2, 2,-2, 1, 0, 1, 0,-1),
( 1, 2, 2, 1, 0, 1,-3, 0,-2),
( 1, 3,-1, 0, 1,-2, 1, 0, 2),
( 1, 3, 0,-1, 0,-3, 2, 0, 2),
( 1, 3, 0, 0,-2,-2,-1,-1, 1),
( 1, 3, 1,-3, 2, 0, 0, 0, 2),
( 2,-3, 0, 2, 2,-3,-1,-2, 0),
( 2,-2, 1, 3, 3,-2,-2, 1,-3),
( 2,-1, 2,-1, 0,-3, 2, 0, 1),
( 2,-1, 2, 0,-2, 0,-2, 0, 0),
( 2,-1, 3, 2, 1, 2, 1,-1,-3),
( 2, 1, 2, 0,-3,-2,-2,-3,-1),
( 2, 2, 1,-3,-2,-3, 2,-1,-2),
( 2, 3,-3, 1, 3, 1, 2,-2,-1),
( 3,-3, 0, 1,-2, 3, 2, 1, 1),
( 3,-2, 3, 3,-3,-3, 0, 0,-1),
( 3,-1, 2,-3, 2,-2, 3, 2,-1),
( 3, 0,-3, 0, 2,-1, 3,-2,-1),
( 3, 0, 2, 3,-2,-3,-3,-2, 1),
( 3, 1, 1,-2,-1,-3, 3, 1, 0),
( 3, 2,-3,-2, 2, 1, 1, 0,-1),
( 3, 2,-2,-1,-3,-1, 3, 3, 2),
( 3, 2, 3,-1, 2, 2, 0,-1, 0),
( 3, 3,-1, 0,-3, 2,-3,-1, 0),
( 3, 3, 1,-3,-2,-3, 2,-3, 3),
( 3, 3, 1, 1,-2, 2, 2,-2, 0),
]
#for name in sorted(ref.keys()):
for name in ['diamond_prim']:
s = ref[name]
npass = 0
for tmat in matrix_tilings:
tmat = array(tmat,dtype=int)
tmat.shape = 3,3
st = s.tile(tmat)
st.check_tiling()
#end for
#end for

# restore logging function
nlog_restore()
#end def structure



def pwscf_input():
# divert logging function
nlog_divert()

nlabel('directories')
loc_test_dir = os.path.join(test_dir,'pwscf_input')
loc_test_dir = os.path.join(test_dir,'pwscf_input')
sample_inputs = os.path.join(loc_test_dir,'sample_inputs')
sample_structures = os.path.join(loc_test_dir,'sample_structures')

Expand Down Expand Up @@ -2974,6 +3245,7 @@ NexusTest( generic_extensions )
NexusTest( nexus_imports )
NexusTest( settings_operation , 'settings' )
NexusTest( machines )
NexusTest( structure )
NexusTest( pwscf_input )

for label in example_information.keys():
Expand Down
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