def fromfile(cls, fileobj):
parser = HSDParser()
builder = VariableTreeBuilder()
treebuilder = HSDTreeBuilder(parser=parser, builder=builder)
openclose = isinstance(fileobj, str)
if openclose:
fp = open(fileobj, "r")
else:
fp = fileobj
tree = treebuilder.build(fp)
if openclose:
fp.close()
query = HSDQuery(checkuniqueness=True, markprocessed=True)
return cls.fromhsd(tree, query)
def _test_module():
from sktools.hsd.treebuilder import HSDTreeBuilder
from sktools.hsd.query import HSDQuery
from sktools.hsd.parser import HSDParser
parser = HSDParser(lowertagnames=True)
treebuilder = HSDTreeBuilder(parser=parser)
fp = open("skdefs.hsd", "r")
tree = treebuilder.build(fp)
fp.close()
query = HSDQuery(checkuniqueness=True, markprocessed=True)
skdefs = Skdef.fromhsd(tree, query)
print(skdefs.onecenterparameters["n"].calculator.exponents)
print(skdefs.onecenterparameters["n"].deltafilling)
unprocessed_list = query.findunprocessednodes(tree)
for unprocessed in unprocessed_list:
print("Unprocessed element '{}' at line {:d}!".format(
unprocessed.hsdattrib[hsd.HSDATTR_TAG],
unprocessed.hsdattrib[hsd.HSDATTR_LINE] + 1))
def fromfile(cls, fileobj):
"""Initializes an SkgenPaths instance from a file.
Args:
fileobj: File name or file like object containing the text
representation of a path tree.
Returns:
Initialized instance.
"""
parser = HSDParser()
builder = VariableTreeBuilder()
treebuilder = HSDTreeBuilder(parser=parser, builder=builder)
openclose = isinstance(fileobj, str)
if openclose:
fp = open(fileobj, "r")
else:
fp = fileobj
tree = treebuilder.build(fp)
if openclose:
fp.close()
query = HSDQuery(checkuniqueness=True)
myself = cls(tree, query)
return myself
def _test_module():
"""Testing module capabilities."""
from io import StringIO
from sktools.hsd.treebuilder import HSDTreeBuilder
from sktools.hsd.parser import HSDParser
from sktools.hsd.tree import HSDTree
import sktools.hsd.converter as conv
unit_attr = "unit"
unit_only = frozenset([unit_attr])
parser = HSDParser(defattrib=unit_attr)
builder = HSDTreeBuilder(parser=parser)
# Defining force type (scalar, list)
force_units = {"ev/aa": 0.0194469050555}
# Trivial unit conversion routine.
def multiply_unit(child, value, unitattr, units):
unit = child.get(unitattr)
convfact = units.get(unit.lower(), None)
if convfact is None:
hsd.HSDInvalidAttributeValueException(
node=child, msg="Invalid unit '{}'".format(unit))
return value * convfact
stream = StringIO("""
# Various driver possibilities
# # No driver specification
#Driver {} # Use the default driver (whatever it is)
#Driver = None {} # Use the driver None {}
#Driver = None
Driver = ConjugateGradient {
MaxForceComponent [eV/AA] = 1e-2
}
Hamiltonian = DFTB {
# SCC = True
# SCCTolerance = 1e-4
# MaxSCCIterations = 100
MaxAngularMomentum {
O = "p"
H = "s"
}
Mixer = Broyden
#Mixer = Broyden {
# MixingParameter = 0.3
#}
#ReadInitialCharges = No
KPointsAndWeights {
0.0 0.0 0.0 0.25
0.25 0.25 0.25 0.75
}
}
Options {
WriteAutotestTag = Yes
UnknownOption = No
}
#ParserOptions {
# ParserVersion = 4
#}
""")
root = builder.build(stream)
qy = HSDQuery(markprocessed=True)
# A complex case: If driver was not specified, it defaults to None {}
# If it was specified but nothing was assinged to it (no child)
# it defaults to ConjugateGradient {}.
dtype, driver = qy.getvaluenode(root,
"Driver",
"None",
allowtextvalue=True,
returnchild=True)
# Since the in the previous getvaluenode() call a default had been specified
# dtype can only be None, if "Driver" was in the input, but had no
# child (e.g. 'Driver {}' or 'Driver = ;'). In this case we set
# it to ConjugateGradient
if dtype is None:
dtype = qy.getchild(driver, "ConjugateGradient", optional=True)
if dtype.tag == "None":
pass
elif dtype.tag == "ConjugateGradient":
forcetol, child = qy.getvalue(dtype,
"MaxForceComponent",
conv.float0,
1e-4,
returnchild=True,
attribs=unit_only)
multiply_unit(child, forcetol, unit_attr, force_units)
elif dtype.tag == "SteepestDescent":
forcetol, child = qy.getvalue(dtype,
"MaxForceComponent",
conv.float0,
1e-4,
returnchild=True,
attribs=unit_only)
multiply_unit(child, forcetol, unit_attr, force_units)
stepsize = qy.getvalue(dtype, "StepSize", conv.float0, 40.0)
pass
else:
raise hsd.HSDInvalidTagException(node=dtype,
msg="Unknown driver type '{}'".format(
dtype.tag))
ham = qy.getchild(root, "Hamiltonian")
dftb = qy.getchild(ham, "DFTB")
scc = qy.getvalue(dftb, "SCC", conv.bool0, True)
scctol = qy.getvalue(dftb, "SCCTolerance", conv.float0, 1e-4)
scciter = qy.getvalue(dftb, "MaxSCCIterations", conv.int0, 100)
mangmom = qy.getchild(dftb, "MaxAngularMomentum")
maxangs = [
qy.getvalue(mangmom, species, conv.str0) for species in ["O", "H"]
]
mixer = qy.getvaluenode(dftb, "Mixer", "Broyden", allowtextvalue=True)
if mixer.tag == "Broyden":
mixparam = qy.getvalue(mixer, "MixingParameter", conv.float0, 0.2)
else:
raise hsd.HSDInvalidTagException(node=mixer,
msg="Unknown mixer type '{}'.".format(
mixer.tag))
readcharges = qy.getvalue(dftb, "ReadInitalCharges", conv.bool0, False)
kpoints = qy.getvalue(dftb, "KPointsAndWeights", conv.float1)
if len(kpoints) % 4:
raise hsd.HSDInvalidTagValueException(node=kpoints,
msg="Incorrect number of floats")
options = qy.getchild(root, "Options", optional=True)
autotest = qy.getvalue(options, "WriteAutotestTag", conv.bool0, False)
parseroptions = qy.getchild(root, "ParserOptions", optional=True)
parserversion = qy.getvalue(parseroptions, "ParserVersion", conv.int0, 4)
tree = HSDTree(root)
tree.writehsd()
print("\nUnprocessed: ", qy.findunprocessednodes(root))