def __init__(self, root=None, query=None):
"""Initializes an SkgenPaths instance.
Args:
root: Root of the hsd tree storing the paths (default=None).
query: Query object to use to query the path tree (default=None).
"""
if root is None:
self._root = Element("hsd")
else:
self._root = root
if query is None:
self._query = HSDQuery(checkuniqueness=True)
else:
self._query = query
self._onecenter_nodes = {}
self._twocenter_nodes = {}
self._store_nodes()
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):
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 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
class SkgenPaths:
"""Stores working paths used by skgen."""
def __init__(self, root=None, query=None):
"""Initializes an SkgenPaths instance.
Args:
root: Root of the hsd tree storing the paths (default=None).
query: Query object to use to query the path tree (default=None).
"""
if root is None:
self._root = Element("hsd")
else:
self._root = root
if query is None:
self._query = HSDQuery(checkuniqueness=True)
else:
self._query = query
self._onecenter_nodes = {}
self._twocenter_nodes = {}
self._store_nodes()
@classmethod
def fromhsd(cls, root, query):
"""Initializes an SkgenPaths instance from an existing HSD tree.
Args:
root: Root of the hsd tree storing the paths.
query: Query object to use to query the path tree.
Returns:
Initialized instance.
"""
myself = cls(root, query)
return myself
@classmethod
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 get_onecenter_workdir(self, elem, calctype, default):
"""Delivers working directory for a onecenter calculation.
Args:
elem: Element to process (must be lower case!)
calctype: Type of the calculation (e.g. 'atom', 'potcomp', ...)
default: Directory to return (and store), if no directory was
found in the path tree yet.
Returns:
Working directory for the given calculation type.
"""
elemnode = self._onecenter_nodes.get(elem)
if elemnode is None:
elemnode = SubElement(self._root, elem)
self._onecenter_nodes[elem] = elemnode
workdir = self._query.getvalue(elemnode, calctype, defvalue=default)
return workdir
def get_twocenter_workdir(self, elem1, elem2, calctype, default):
"""Delivers working directory for a two-center calculation.
Args:
elem1: First element (must be lower case!)
elem2: Second element (must be lower case!)
calctype: Type of the calculation (e.g. 'atom', 'potcomp', ...)
default: Directory to return (and store), if no directory was
found in the path tree yet.
Returns:
Working directory for the given calculation type.
"""
elem1, elem2 = min(elem1, elem2), max(elem1, elem2)
elemnode = self._twocenter_nodes.get((elem1, elem2))
if elemnode is None:
name = elem1 + "-" + elem2
elemnode = SubElement(self._root, name)
self._twocenter_nodes[elem1, elem2] = elemnode
workdir = self._query.getvalue(elemnode, calctype, defvalue=default)
return workdir
def get_paths(self):
"""Returns an hsd-tree with the stored paths.
"""
return self._root
def _store_nodes(self):
"""Sort out nodes into one-center and two-center ones.
"""
for child in self._query.findchildren(self._root, "*"):
name = child.tag
match = _PATTERN_TWOCENTER_TAG.match(name)
if match:
elem1, elem2 = match.groups()
elem1, elem2 = (min(elem1, elem2), max(elem1, elem2))
if (elem1, elem2) in self._twocenter_nodes:
msg = "Multiple two-center defintions for {}-{}".format(
elem1, elem2)
raise sc.SkgenException(msg)
self._twocenter_nodes[elem1, elem2] = child
else:
match = _PATTERN_ONECENTER_TAG.match(name)
if match:
elem = match.groups(0)
if elem in self._onecenter_nodes:
msg = "Multiple one-center defintions for {}".format(
elem)
raise sc.SkgenException(msg)
self._onecenter_nodes[elem] = child
else:
msg = "Invalid node name '{}'".format(name)
raise sc.SkgenException(msg)