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update test
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@qzhu2017
qzhu2017 committed Dec 8, 2023
1 parent 675ab83 commit ce9bef9
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23 changes: 23 additions & 0 deletions pyxtal/miscellaneous/test_atom_mole.py
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Original file line number Diff line number Diff line change
@@ -0,0 +1,23 @@
from pyxtal.db import database

db = database('pyxtal/database/mech.db')

c = db.get_pyxtal('DAHMUX')
rep = c.get_1D_representation()
a = c.to_atomic_xtal()

dicts = c.mol_sites[0].to_1D_dicts()
b = a.to_molecular_xtal([c.mol_sites[0].molecule],
reflects = [dicts['reflect']],
oris = [dicts['orientation']])
d = rep.to_pyxtal()


import pymatgen.analysis.structure_matcher as sm

pmg1 = c.to_pymatgen()
pmg2 = b.to_pymatgen()
pmg3 = d.to_pymatgen()
print(sm.StructureMatcher().get_rms_dist(pmg1, pmg2))
print(sm.StructureMatcher().get_rms_dist(pmg1, pmg3))
print(sm.StructureMatcher().get_rms_dist(pmg2, pmg3))
81 changes: 42 additions & 39 deletions pyxtal/test_all.py
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Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
# python -m unittest pyxtal/test_all.py
import unittest
import os

from random import choice, shuffle
import numpy as np
Expand Down Expand Up @@ -39,7 +40,7 @@ def test_list_wyckoff_combinations(self):
g = Group(64)
a1, _, _ = g.list_wyckoff_combinations([4, 2])
self.assertTrue(len(a1) == 0)
a2, _, _ = g.list_wyckoff_combinations([4, 8], quick=False)
a2, _, _ = g.list_wyckoff_combinations([4, 8], quick=False)
self.assertTrue(len(a2) == 8)

def test_print_group_and_dof(self):
Expand Down Expand Up @@ -82,7 +83,7 @@ def test_check_compatible(self):
self.assertTrue(Group(19).check_compatible([6]) == (False, False))

def test_search_supergroup_paths(self):
paths = Group(59, quick=True).search_supergroup_paths(139, 2)
paths = Group(59, quick=True).search_supergroup_paths(139, 2)
self.assertTrue(paths == [[71, 139], [129, 139], [137, 139]])

def test_get_splitters(self):
Expand Down Expand Up @@ -144,7 +145,7 @@ def test_make_pyxtal(self):
sols = my.search_supergroup(max_solutions=1)
for sol in sols:
struc_high = my.make_pyxtal_in_supergroup(sol)
strucs = my.make_pyxtals_in_subgroup(sol, 3)
strucs = my.make_pyxtals_in_subgroup(sol, 3)
pmg1 = struc_high.to_pymatgen()
pmg2 = strucs[-1].to_pymatgen()
rms = sm.StructureMatcher().get_rms_dist(pmg1, pmg2)[0]
Expand Down Expand Up @@ -280,7 +281,7 @@ def test_similarity(self):
strucs, _, _, _ = s2.get_transition(s1)

if strucs is None:
print("Problem between ", cif1, cif2)
print("Problem between ", cif1, cif2)
else:
struc_G_in_H = strucs[-1]
s3 = pyxtal()
Expand Down Expand Up @@ -315,7 +316,7 @@ def test_atomic(self):
c2.optimize_lattice(1)
pmg2 = c2.to_pymatgen()
self.assertTrue(sm.StructureMatcher().fit(pmg1, pmg2))

c3 = pyxtal()
c3.from_seed(cif_path + "LiCs.cif")
pmg3 = c3.to_pymatgen()
Expand Down Expand Up @@ -349,9 +350,9 @@ def test_molecular_nonstd(self):
sgs = [5, 7, 8, 9, 12, 13, 14, 15]
c1 = pyxtal(molecular=True)
for sg in sgs:
hns = Hall(sg).hall_numbers
hns = Hall(sg).hall_numbers
for hn in hns[1:]:
c1.from_random(3, hn, ["aspirin"], use_hall=True)
c1.from_random(3, hn, ["aspirin"], use_hall=True)
pmg1 = c1.to_pymatgen()
c2 = c1.copy()
c2.optimize_lattice(1)
Expand All @@ -365,7 +366,7 @@ def test_molecular(self):
c1 = pyxtal(molecular=True)
for i in range(20):
sg = choice(sgs)
c1.from_random(3, sg, ["aspirin"])
c1.from_random(3, sg, ["aspirin"])
pmg1 = c1.to_pymatgen()
c2 = c1.copy()
c2.optimize_lattice(1)
Expand Down Expand Up @@ -396,12 +397,12 @@ def test_transforms(self):
(9.4913, 8.5844, 5.3358, 90.0000, 110.0035, 90.0000, 'monoclinic', 3),
(3.7727, 6.7490, 7.6446, 64.4392, 77.9087, 75.7214, 'triclinic', 1),
(3.7297, 6.5421, 7.9915, 73.9361, 71.5867, 103.2590, 'triclinic', 1),
(5.5740, 7.0902, 11.4529, 96.5703, 90.0224, 108.1857, 'triclinic', 2),
(5.5740, 7.0902, 11.4529, 96.5703, 90.0224, 108.1857, 'triclinic', 2),
(5.5487, 7.1197, 11.4349, 83.0223, 89.8479, 72.0003, 'triclinic', 2),
(5.7985, 30.6352, 7.6374, 90.0000, 112.2615, 90.0000, 'monoclinic', 3),
(5.7985, 30.6352, 7.6374, 90.0000, 112.2615, 90.0000, 'monoclinic', 3),
(5.8280, 30.5992, 7.6373, 90.0000, 112.6020, 90.0000, 'monoclinic', 3),
]

for i in range(int(len(paras)/2)):
(a1, b1, c1, alpha1, beta1, gamma1, ltype1, N) = paras[i*2]
(a2, b2, c2, alpha2, beta2, gamma2, ltype2, N) = paras[i*2+1]
Expand Down Expand Up @@ -444,16 +445,16 @@ def test_wp_check_translation(self):
pass

def test_wp_site_symm(self):
data = [(143, 1, '3 . .'),
(230, 6, '. 3 2'),
data = [(143, 1, '3 . .'),
(230, 6, '. 3 2'),
(160, 1, '. . m'),
(160, 2, '3 m .')]
for d in data:
(sg, i, symbol) = d
wp = Group(sg)[i]
wp.get_site_symmetry()
self.assertTrue(wp.site_symm == symbol)

def test_wp_dof(self):
for sg in range(1, 231):
g = Group(sg)
Expand Down Expand Up @@ -534,12 +535,12 @@ def check_error(spg, pt, cell):
for i in range(len(wp)):
op0 = wp[i]
p1 = op0.operate(pt)

op1 = wp.get_euclidean_generator(cell.matrix, i)
if wp.euclidean:
p2 = np.dot(op1.operate(p0), cell.inv_matrix)
else:
p2 = np.dot(op1.apply_rotation_only(p0), cell.inv_matrix)
p2 = np.dot(op1.apply_rotation_only(p0), cell.inv_matrix)
p2 += op1.translation_vector

diff = p1-p2
Expand All @@ -556,29 +557,29 @@ def check_error(spg, pt, cell):


pt = [0.1333, 0.1496, 0.969]

cell = Lattice.from_para(9.395, 7.395, 8.350, 91, 101, 92, ltype='triclinic')
self.assertTrue(check_error(range(1, 3), pt, cell))

cell = Lattice.from_para(9.395, 7.395, 8.350, 90, 101, 90, ltype='monoclinic')
self.assertTrue(check_error(range(3, 16), pt, cell))

cell = Lattice.from_para(9.395, 7.395, 8.350, 90, 90, 90, ltype='orthorhombic')
self.assertTrue(check_error(range(16, 74), pt, cell))

cell = Lattice.from_para(9.395, 9.395, 8.350, 90, 90, 90, ltype='tetragonal')
self.assertTrue(check_error(range(74, 143), pt, cell))

cell = Lattice.from_para(9.395, 9.395, 8.350, 90, 90, 120, ltype='hexagonal')
self.assertTrue(check_error(range(143, 195), pt, cell))

cell = Lattice.from_para(9.395, 9.395, 9.395, 90, 90, 90, ltype='cubic')
self.assertTrue(check_error(range(195, 231), pt, cell))


class TestDof(unittest.TestCase):
def test_atomic(self):
s = pyxtal()
s = pyxtal()
s.from_random(3, 225, ['C'], [8])
ans = s.get_dof()
self.assertTrue(s.lattice.dof == 1)
Expand Down Expand Up @@ -694,7 +695,7 @@ def test_distance(self):
AgC2N2H
Ag 4.30800 8.26300 -0.2200
"""

C2N2H7_xyz = """12
AgC2N2H
H 5.95800 5.80600 -0.9530
Expand All @@ -713,12 +714,14 @@ def test_distance(self):
f.write(Ag_xyz)
with open('C2N2H7.xyz', "w") as f:
f.write(C2N2H7_xyz)

for i in range(10):
c = pyxtal(molecular=True)
c.from_random(3, 9, ['Ag.xyz', 'C2N2H7.xyz'], [12, 12])
short_bonds = c.check_short_distances(r=1.1)
self.assertTrue(len(short_bonds)==0)
os.remove('Ag.xyz')
os.remove('C2N2H7.xyz')

def test_molecular_2d(self):
# print("test_molecular_2d")
Expand Down Expand Up @@ -785,7 +788,7 @@ def test_read_spglib(self):
self.assertTrue(sm.StructureMatcher().fit(pmg_struc, pmg1))
# more space groups
for name in ['I41amd', 'P4nmm', 'Pmmn', 'Pn3m', 'Fd3', 'Pn3']:
cif_file = cif_path + name + ".vasp"
cif_file = cif_path + name + ".vasp"
pmg1 = Structure.from_file(cif_file)
struc = pyxtal()
struc.from_seed(seed=cif_file, style='spglib')
Expand Down Expand Up @@ -885,7 +888,7 @@ class TestSymmetry(unittest.TestCase):
def test_from_symops_wo_grou(self):
data = [
(["x, y, z", "-x, y+1/2, -z"], 4, 6),
(["x, y, z", "-x+1/2, -y, z+1/2", "-x, y, z", "x+1/2, -y, z+1/2"], 31, 155),
(["x, y, z", "-x+1/2, -y, z+1/2", "-x, y, z", "x+1/2, -y, z+1/2"], 31, 155),
(["x, y, z", "-x, -y, -z", "-x+1/2, y+1/2, -z", "x+1/2, -y+1/2, z"], 14, 83),
(["x, y, z", "-x, -y, -z", "-x+1/2, y+1/2, -z+1/2", "x+1/2, -y+1/2, z+1/2"], 14, 82),
]
Expand All @@ -898,7 +901,7 @@ def test_from_symops_wo_grou(self):
def test_from_symops(self):
data = [
(["x, y, z", "-x, y+1/2, -z"], 4, 6),
(["x, y, z", "-x+1/2, -y, z+1/2", "-x, y, z", "x+1/2, -y, z+1/2"], 31, 155),
(["x, y, z", "-x+1/2, -y, z+1/2", "-x, y, z", "x+1/2, -y, z+1/2"], 31, 155),
]
for d in data:
(strs, spg, hall) = d
Expand All @@ -924,14 +927,14 @@ def test_packing(self):
("xxvi", 15),
("resorcinol", 14),
]:

(name, CN) = data
c.from_seed(seed=cif_path+name+".cif", molecules=[name])
ds, _, _, _, engs = c.get_neighboring_molecules(0, 1.5)
#print(engs)
#print(name, CN, len(ds))
self.assertTrue(len(ds) == CN)

class TestSubgroup(unittest.TestCase):
def test_cubic_cubic(self):
sites = ['8a', '32e']
Expand All @@ -945,7 +948,7 @@ def test_cubic_cubic(self):
for C2 in C2s:
pmg_s2 = C2.to_pymatgen()
#sga2 = SpacegroupAnalyzer(pmg_s2).get_space_group_symbol()
# prevent some numerical error
# prevent some numerical error
if not sm.StructureMatcher().fit(pmg_s1, pmg_s2):
C12 = pyxtal(); C12.from_seed(pmg_s2); pmg_12 = C12.to_pymatgen()
self.assertTrue(sm.StructureMatcher().fit(pmg_s1, pmg_12))
Expand All @@ -965,7 +968,7 @@ def test_from_seed(self):
pmg_s1 = s1.to_pymatgen()
pmg_s2 = s2.to_pymatgen()
self.assertTrue(sm.StructureMatcher().fit(pmg_s1, pmg_s2))

def test_molecules(self):
for name in ["aspirin", "resorcinol", "coumarin", "HAHCOI", "xxvi",\
"WEXBOS", "MERQIM", "LAGNAL", "YICMOP", "LUFHAW", \
Expand Down Expand Up @@ -997,7 +1000,7 @@ def test_special(self):
struc.from_seed(seed=cif)
for i in range(100):
s = struc.subgroup_once(0.2, None, None, 't+k', 2)

class TestPXRD(unittest.TestCase):
def test_similarity(self):
sites = ['8a']
Expand All @@ -1010,7 +1013,7 @@ def test_similarity(self):
p2 = xrd2.get_profile()
s = Similarity(p1, p2, x_range=[15, 90])
self.assertTrue( 0.9 <s.value <1.001)


C2.apply_perturbation(1e-3, 1e-3)
xrd3 = C2.get_XRD()
Expand Down Expand Up @@ -1060,7 +1063,7 @@ def test_Al2SiO5(self):
{"4g": [0.2458, 0.2522, 0.0000]},
{"4g": [0.4241, 0.3636, 0.0000]}, #partial info on O
]

s = pyxtal()
s.from_random(3, spg, elements, composition, lattice=cell, sites=sites2)
self.assertTrue(s.valid)
Expand All @@ -1077,7 +1080,7 @@ def test_molecule(self):
struc.mol_sites = [struc.mol_sites[i] for i in l]
struc.resort()
N2 = len(struc.mol_sites)
self.assertTrue(N1 == N2)
self.assertTrue(N1 == N2)

def test_atom(self):
cif = cif_path + "aspirin.cif"
Expand Down Expand Up @@ -1125,7 +1128,7 @@ def test_inverse(self):
'-y/2+1/2,-z,0',
'-z,-x/2+1/2,0',
]

for i, xyz in enumerate(xyzs):
op = SymmOp.from_xyz_str(xyz)
inv_op = get_inverse(op)
Expand All @@ -1143,7 +1146,7 @@ def test_swap_wp(self):
g = Group(38)
wp = g[4]
wp1, trans = wp.swap_axis([1,0,2])

g = Group(71)
wp = g[5]
wp1, trans = wp.swap_axis([0,2,1])
Expand All @@ -1169,7 +1172,7 @@ def test_trans(self):
np.array([[1,0,1],[0,1,0],[0,0,1]]),
np.array([[1,0,-1],[0,1,0],[0,0,1]]),
]

for n in range(3, 16):
hns = Hall(n).hall_numbers
for hn in hns:
Expand Down

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