def test_molecular():
global outstructs
global outstrings
print(
"=== Testing generation of molecular 3D crystals. This may take some time. ==="
)
from time import time
from spglib import get_symmetry_dataset
from pyxtal.symmetry import get_wyckoffs
from pyxtal.crystal import cellsize
from pyxtal.molecular_crystal import molecular_crystal
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
slow = []
failed = []
print(" Spacegroup # |Generated (SPG)|Generated (PMG)| Time Elapsed")
skip = (
[]
) # [24, 183, 202, 203, 209, 210, 216, 219, 225, 226, 227, 228, 229, 230] #slow
for sg in range(1, 231):
if sg not in skip:
multiplicity = len(get_wyckoffs(sg)[0]) / cellsize(
sg) # multiplicity of the general position
start = time()
rand_crystal = molecular_crystal(sg, ["H2O"], [multiplicity], 2.5)
end = time()
timespent = np.around((end - start), decimals=2)
t = str(timespent)
if len(t) == 3:
t += "0"
t += " s"
if timespent >= 1.0:
t += " ~"
if timespent >= 3.0:
t += "~"
if timespent >= 10.0:
t += "~"
if timespent >= 60.0:
t += "~"
slow.append(sg)
if rand_crystal.valid:
check = False
ans1 = get_symmetry_dataset(rand_crystal.spg_struct,
symprec=1e-1)
if ans1 is None:
ans1 = "???"
else:
ans1 = ans1["number"]
sga = SpacegroupAnalyzer(rand_crystal.struct)
ans2 = "???"
if sga is not None:
try:
ans2 = sga.get_space_group_number()
except:
ans2 = "???"
if ans2 is None:
ans2 = "???"
# Compare expected and detected groups
if ans1 == "???" and ans2 == "???":
check = True
elif ans1 == "???":
if int(ans2) > sg:
pass
elif ans2 == "???":
if int(ans1) > sg:
pass
else:
if ans1 < sg and ans2 < sg:
if compare_wyckoffs(sg, ans1) or compare_wyckoffs(
sg, ans2):
pass
else:
check = True
# output cif files for incorrect space groups
if check is True:
if check_struct_group(rand_crystal, sg, dim=3):
pass
else:
t += " xxxxx"
outstructs.append(rand_crystal.struct)
outstrings.append(
str("3D_Molecular_" + str(sg) + ".vasp"))
print("\t" + str(sg) + "\t|\t" + str(ans1) + "\t|\t" +
str(ans2) + "\t|\t" + t)
else:
print("~~~~ Error: Could not generate space group " + str(sg) +
" after " + t)
failed.append(sg)
if slow != []:
print(
"~~~~ The following space groups took more than 60 seconds to generate:"
)
for i in slow:
print(" " + str(i))
if failed != []:
print("~~~~ The following space groups failed to generate:")
for i in failed:
print(" " + str(i))
def test_molecular_2D():
global outstructs
global outstrings
print("=== Testing generation of molecular 2D crystals. This may take some time. ===")
from time import time
from spglib import get_symmetry_dataset
from pyxtal.symmetry import get_layer
from pyxtal.crystal import cellsize
from pyxtal.molecular_crystal import molecular_crystal_2D
from pyxtal.database.layergroup import Layergroup
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
slow = []
failed = []
print(" Layergroup | sg # Expected |Generated (SPG)|Generated (PMG)|Time Elapsed")
skip = []#12, 64, 65, 80] #slow to generate
for num in range(1, 81):
if num not in skip:
sg = Layergroup(num).sgnumber
multiplicity = len(get_layer(num)[0]) / cellsize(sg) #multiplicity of the general position
start = time()
rand_crystal = molecular_crystal_2D(num, ['H2O'], [multiplicity], 4.0)
end = time()
timespent = np.around((end - start), decimals=2)
t = str(timespent)
if len(t) == 3:
t += "0"
t += " s"
if timespent >= 1.0:
t += " ~"
if timespent >= 3.0:
t += "~"
if timespent >= 10.0:
t += "~"
if timespent >= 60.0:
t += "~"
slow.append(num)
if rand_crystal.valid:
check = False
ans1 = get_symmetry_dataset(rand_crystal.spg_struct, symprec=1e-1)
if ans1 is None:
ans1 = "???"
else:
ans1 = ans1['number']
sga = SpacegroupAnalyzer(rand_crystal.struct)
ans2 = "???"
if sga is not None:
try:
ans2 = sga.get_space_group_number()
except: ans2 = "???"
if ans2 is None:
ans2 = "???"
#Compare expected and detected groups
if ans1 == "???" and ans2 == "???":
check = True
elif ans1 == "???":
if int(ans2) > sg: pass
elif ans2 == "???":
if int(ans1) > sg: pass
else:
if ans1 < sg and ans2 < sg:
if compare_wyckoffs(sg, ans1) or compare_wyckoffs(sg, ans2): pass
else: check = True
#output cif files for incorrect space groups
if check is True:
if check_struct_group(rand_crystal.struct, num, dim=2):
pass
else:
t += " xxxxx"
outstructs.append(rand_crystal.struct)
outstrings.append(str("2D_Molecular_"+str(num)+".vasp"))
print("\t"+str(num)+"\t|\t"+str(sg)+"\t|\t"+str(ans1)+"\t|\t"+str(ans2)+"\t|\t"+t)
else:
print("~~~~ Error: Could not generate layer group "+str(num)+" after "+t)
failed.append(num)
if slow != []:
print("~~~~ The following layer groups took more than 60 seconds to generate:")
for i in slow:
print(" "+str(i))
if failed != []:
print("~~~~ The following layer groups failed to generate:")
for i in failed:
print(" "+str(i))