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Commit 2409a22f authored by fanding2000's avatar fanding2000
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Format fix. More options in readme

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basic_function/format_parser.py
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basic_function/operation.py
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basic_function/packaged_function.py
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from basic_function import format_parser
from basic_function import CSP_generator_normal
import os
import concurrent.futures
import sys
def process_crystal(seed, sg, molecules,output_path,add_name):
aaa = CSP_generator_normal.CrystalGenerator(molecules, space_group=sg)
molecules_number = sum(len(molecule.atoms) for molecule in molecules)
new_crystal = aaa.generate(seed=seed)
sys.stdout.flush()
if new_crystal is not None:
cif_out = format_parser.write_cif_file(new_crystal)
with open(f"{output_path}/structures/{add_name}_{sg}_{seed}_z{len(molecules)}_{molecules_number}.cif", 'w') as target:
target.writelines(cif_out)
return True
return False
def CSP_generater_parallel(molecules,output_path,need_structure = 100, space_group_list=[1],max_workers=8,add_name='',start_seed=1):
space_groups = space_group_list
accept_count = need_structure
try:
os.makedirs("{}/structures".format(output_path))
except:
print("Warning, these is already an structures folder in this path, skip mkdir")
for sg in space_groups:
accept = 0
seed = start_seed
with concurrent.futures.ProcessPoolExecutor(max_workers=max_workers) as executor:
futures = {}
while accept < accept_count:
# submit new task
while len(futures) < max_workers and accept + len(futures) < accept_count:
future = executor.submit(process_crystal, seed, sg, molecules, output_path,add_name)
futures[future] = seed
seed += 1
# check the finished task
done, _ = concurrent.futures.wait(futures, return_when=concurrent.futures.FIRST_COMPLETED)
for future in done:
if future.result():
accept += 1
# remove it from list, no matter what result it is
del futures[future]
# cancel all task if the number need is arrived.
if accept >= accept_count:
for future in futures:
future.cancel()
break
def CSP_generater_serial(molecules,output_path,need_structure = 100, densely_pack_method=False, space_group_list=[1]):
"""
:param molecules: a list [molecule1, molecule2, ...]
:param output_path: a str indicate the path of output folder
:param need_structure: int
:param space_group_list:a list indicate the space group need to search
"""
try:
os.makedirs("{}\\structures".format(output_path))
except:
print("Warning, these is already an structures folder in this path, skip mkdir")
for sg in space_group_list:
aaa = CSP_generator_normal.CrystalGenerator(molecules, space_group=sg)
accept=0
i=1
while accept<need_structure:
new_crystal = aaa.generate(seed=i,densely_pack_method=densely_pack_method)
if new_crystal==None:
i += 1
continue
cif_out = format_parser.write_cif_file(new_crystal)
target = open("{}\\structures\\{}_{}.cif".format(output_path,sg,i), 'w')
target.writelines(cif_out)
target.close()
accept+=1
i += 1
def CSP_generater_one_test(molecules,output_path,space_group=1,seed=1):
"""
used to test the generator for a given space group and seed
:param molecules: a list [molecule1, molecule2, ...]
:param output_path: a str indicate the path of output folder
:param space_group: a list indicate the space group need to search
:param seed: int
:return: write out a cif
"""
aaa = CSP_generator_normal.CrystalGenerator(molecules, space_group=space_group)
new_crystal = aaa.generate(seed=seed, test=True)
if new_crystal==None:
print("Return failed generate")
else:
cif_out = format_parser.write_cif_file(new_crystal,sym=True)
target = open("{}\\{}_{}.cif".format(output_path,space_group,seed), 'w')
target.writelines(cif_out)
target.close()
from basic_function import format_parser
from basic_function import CSP_generator_normal
import os
import concurrent.futures
import sys
def process_crystal(seed, sg, molecules,output_path,add_name):
aaa = CSP_generator_normal.CrystalGenerator(molecules, space_group=sg)
molecules_number = sum(len(molecule.atoms) for molecule in molecules)
new_crystal = aaa.generate(seed=seed)
sys.stdout.flush()
if new_crystal is not None:
cif_out = format_parser.write_cif_file(new_crystal)
with open(f"{output_path}/structures/{add_name}_{sg}_{seed}_z{len(molecules)}_{molecules_number}.cif", 'w') as target:
target.writelines(cif_out)
return True
return False
def CSP_generater_parallel(molecules,output_path,need_structure = 100, space_group_list=[1],max_workers=8,add_name='',start_seed=1):
space_groups = space_group_list
accept_count = need_structure
try:
os.makedirs("{}/structures".format(output_path))
except:
print("Warning, these is already an structures folder in this path, skip mkdir")
for sg in space_groups:
accept = 0
seed = start_seed
with concurrent.futures.ProcessPoolExecutor(max_workers=max_workers) as executor:
futures = {}
while accept < accept_count:
# submit new task
while len(futures) < max_workers and accept + len(futures) < accept_count:
future = executor.submit(process_crystal, seed, sg, molecules, output_path,add_name)
futures[future] = seed
seed += 1
# check the finished task
done, _ = concurrent.futures.wait(futures, return_when=concurrent.futures.FIRST_COMPLETED)
for future in done:
if future.result():
accept += 1
# remove it from list, no matter what result it is
del futures[future]
# cancel all task if the number need is arrived.
if accept >= accept_count:
for future in futures:
future.cancel()
break
def CSP_generater_serial(molecules,output_path,need_structure = 100, densely_pack_method=False, space_group_list=[1]):
"""
:param molecules: a list [molecule1, molecule2, ...]
:param output_path: a str indicate the path of output folder
:param need_structure: int
:param space_group_list:a list indicate the space group need to search
"""
try:
os.makedirs("{}\\structures".format(output_path))
except:
print("Warning, these is already an structures folder in this path, skip mkdir")
for sg in space_group_list:
aaa = CSP_generator_normal.CrystalGenerator(molecules, space_group=sg)
accept=0
i=1
while accept<need_structure:
new_crystal = aaa.generate(seed=i,densely_pack_method=densely_pack_method)
if new_crystal==None:
i += 1
continue
cif_out = format_parser.write_cif_file(new_crystal)
target = open("{}\\structures\\{}_{}.cif".format(output_path,sg,i), 'w')
target.writelines(cif_out)
target.close()
accept+=1
i += 1
def CSP_generater_one_test(molecules,output_path,space_group=1,seed=1):
"""
used to test the generator for a given space group and seed
:param molecules: a list [molecule1, molecule2, ...]
:param output_path: a str indicate the path of output folder
:param space_group: a list indicate the space group need to search
:param seed: int
:return: write out a cif
"""
aaa = CSP_generator_normal.CrystalGenerator(molecules, space_group=space_group)
new_crystal = aaa.generate(seed=seed, test=True)
if new_crystal==None:
print("Return failed generate")
else:
cif_out = format_parser.write_cif_file(new_crystal,sym=True)
target = open("{}\\{}_{}.cif".format(output_path,space_group,seed), 'w')
target.writelines(cif_out)
target.close()
basic_function/unit_cell_parser.py
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csp.sh
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mace-bench/3rdparty/SevenNet/sevenn/__init__.py
View file @ 2409a22f
from importlib.metadata import version
from packaging.version import Version
__version__ = version('sevenn')
from e3nn import __version__ as e3nn_ver
if Version(e3nn_ver) < Version('0.5.0'):
raise ValueError(
'The e3nn version MUST be 0.5.0 or later due to changes in CG coefficient '
'convention.'
)
from importlib.metadata import version
from packaging.version import Version
__version__ = version('sevenn')
from e3nn import __version__ as e3nn_ver
if Version(e3nn_ver) < Version('0.5.0'):
raise ValueError(
'The e3nn version MUST be 0.5.0 or later due to changes in CG coefficient '
'convention.'
)
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