def qmRunAll(inp_list, root=None, **kwargs):
if 'block_size' not in kwargs:
kwargs['block_size'] = 1
job = []
for inp in inp_list:
job.append([inp, inp.molecule.name])
inp = inp_list[0]
if inp.setting['threads'] != 1 and 'threads' not in kwargs:
kwargs['threads'] = setting.cpu_count / inp.setting['threads']
if root is None:
qtk.parallelize(qtk.qmRunJob, job, **kwargs)
else:
if os.path.exists(root):
if 'overwrite' in kwargs and kwargs['overwrite']:
qtk.warning("overwrite existing folder %s" % root)
shutil.rmtree(root)
os.makedirs(root)
else:
qtk.warning("%s exists, " % root +\
"joining calculations with other threads")
else:
os.makedirs(root)
cwd = os.getcwd()
os.chdir(root)
qtk.parallelize(qtk.qmRunJob, job, **kwargs)
os.chdir(cwd)
def qmRunAll(inp_list, root=None,**kwargs):
if 'block_size' not in kwargs:
kwargs['block_size'] = 1
job = []
for inp in inp_list:
job.append([inp, inp.molecule.name])
inp = inp_list[0]
if inp.setting['threads'] != 1 and 'threads' not in kwargs:
kwargs['threads'] = setting.cpu_count / inp.setting['threads']
if root is None:
qtk.parallelize(qtk.qmRunJob, job, **kwargs)
else:
if os.path.exists(root):
if 'overwrite' in kwargs and kwargs['overwrite']:
qtk.warning("overwrite existing folder %s" % root)
shutil.rmtree(root)
os.makedirs(root)
else:
qtk.warning("%s exists, " % root +\
"joining calculations with other threads")
else:
os.makedirs(root)
cwd = os.getcwd()
os.chdir(root)
qtk.parallelize(qtk.qmRunJob, job, **kwargs)
os.chdir(cwd)
def loadCubeList(cls, path_list, program=qtk.setting.qmcode):
if program == 'cpmd':
cls._file_list = path_list
_para = [[name] for name in cls._file_list]
if len(_para)<3*qtk.setting.cpu_count:
cls._cube_list = qtk.parallelize(qtk.CUBE, _para,
block_size=1)
else:
cls._cube_list = qtk.parallelize(qtk.CUBE, _para)
else:
qtk.exit("density of alchemical path is "\
+"not yet implemented for %s" % self.program)
def loadAllCube(cls, path, pattern,
program=qtk.setting.qmcode):
"""
centralized parallel CUBE loading
"""
if program == 'cpmd':
cls._file_list = sorted(glob.glob(
path + "/" + pattern + "/*.cube"))
_para = [[name] for name in cls._file_list]
if len(_para)<3*qtk.setting.cpu_count:
cls._cube_list = qtk.parallelize(qtk.CUBE, _para,
block_size=1)
else:
cls._cube_list = qtk.parallelize(qtk.CUBE, _para)
else:
qtk.exit("density of alchemical path is "\
+"not yet implemented for %s" % self.program)
def fitness(self, pop_list):
if self.threads == 1:
fit = []
for coord in pop_list:
out = self.evaluate(coord, self.target_input)
fit.append(out)
output = np.array(fit).T.tolist()
return output
else:
job = []
for coord in pop_list:
job.append([coord, self.target_input])
out = qtk.parallelize(
self.evaluate, job, n_output=2, threads=self.threads
)
return out
def loadCube(self):
# cpmd implemetation
if self.program == 'cpmd':
self.cube_name = sorted(glob.glob(
self.path + "/" + self.pattern + "/*.cube"))
if len(PathData._cube_list) > 0:
_clist = PathData._cube_list
_nlist = PathData._file_list
self.cube_list = [_clist[_nlist.index(name)]\
for name in self.cube_name]
else:
_para = [[name] for name in self.cube_name]
self.cube_list = qtk.parallelize(qtk.CUBE, _para,
block_size=1)
else:
qtk.exit("density of alchemical path is "\
+"not yet implemented for %s" % self.program)
def setDescriptor(self, descriptor, **kwargs):
self.descriptor = descriptor
if 'threads' in kwargs:
self.threads = int(kwargs['threads'])
else:
self.threads = 1
qtk.report("DataSet", "reading folder", self.path)
qtk.report("Descriptor", self.descriptor)
if descriptor == 'CoulombMatrix':
if 'matrix_size' not in kwargs:
qtk.warning("matrix size not assigend, " + \
"using default value")
qtk.warning("matrix size WILL CHANGE " + \
"according to numer of atoms in the molecule")
self.matrix_size = 0
else:
self.matrix_size = kwargs['matrix_size']
else:
qtk.exit("descriptor" + descriptor + "is not implemented")
if self.threads > 1:
data_list = []
for data in sorted(\
glob.glob(self.path + '/' + self.pattern)):
data_list.append([descriptor,
self.matrix_size,
{'xyz':data}])
self.data = qtk.parallelize(DataPoint,
data_list,
threads=self.threads)
else:
for data in sorted(\
glob.glob(self.path + '/' + self.pattern)):
self.data.append(\
DataPoint(descriptor, self.matrix_size, xyz=data)\
)
self.data_size = len(self.data)
def setDescriptor(self, descriptor, **kwargs):
self.descriptor = descriptor
if 'threads' in kwargs:
self.threads = int(kwargs['threads'])
else:
self.threads = 1
qtk.report("DataSet", "reading folder", self.path)
qtk.report("Descriptor", self.descriptor)
if descriptor == 'CoulombMatrix':
if 'matrix_size' not in kwargs:
qtk.warning("matrix size not assigend, " + \
"using default value")
qtk.warning("matrix size WILL CHANGE " + \
"according to numer of atoms in the molecule")
self.matrix_size = 0
else:
self.matrix_size = kwargs['matrix_size']
else:
qtk.exit("descriptor" + descriptor + "is not implemented")
if self.threads > 1:
data_list = []
for data in sorted(\
glob.glob(self.path + '/' + self.pattern)):
data_list.append([descriptor, self.matrix_size, {'xyz': data}])
self.data = qtk.parallelize(DataPoint,
data_list,
threads=self.threads)
else:
for data in sorted(\
glob.glob(self.path + '/' + self.pattern)):
self.data.append(\
DataPoint(descriptor, self.matrix_size, xyz=data)\
)
self.data_size = len(self.data)
