def hsd_node_factory(classtype, classes, node, query):
'''Creates an object depending on the node and a class dictionary.
Parameters
----------
classtype : str
Textual name of the class to create for error messages
(e.g. 'twocenter calculator')
classes : dict
Contains classes (not instances!) with their corresponding hsd-name.
Each must have a `fromhsd(node, query)` class method.
node : Element
HSD representation of the node.
query : query object
Query object to use.
Returns
-------
node : Element or None
Returns the element created using the hsd input in the node or None
if the node passed was None.
'''
if node is None:
return None
myclass = classes.get(node.tag)
if myclass is None:
raise hsd.HSDInvalidTagException(
"Unknown {} '{}'".format(classtype, node.tag))
return myclass.fromhsd(node, query)
def get_shellvalues(node, query):
'''Returns dictionary with the values assigned to individual shells.
Args:
node (Element): parent node
query (HSDQuery): queries an HSD-tree
Returns:
values (dict): dictionary with the values assigned to individual shells
'''
values = {}
for child in node:
try:
shell = shell_name_to_ind(child.tag)
except ValueError:
raise hsd.HSDInvalidTagException(
msg="Invalid shell name '{}'".format(child.tag), node=child)
value = query.getvalue(child, '.', conv.float0)
values[shell] = value
return values
def getshellvalues(node, query):
"""Returns dictionary with the values assigned to individual shells."""
values = {}
for child in node:
try:
shell = shell_name_to_ind(child.tag)
except ValueError:
raise hsd.HSDInvalidTagException(
msg="Invalid shell name '{}'".format(child.tag), node=child)
value = query.getvalue(child, ".", conv.float0)
values[shell] = value
return values
def fromhsd(cls, root, query):
myself = cls()
for shellnode in root:
try:
nn, ll = sc.shell_name_to_ind(shellnode.tag)
except ValueError:
raise hsd.HSDInvalidTagException(
"Invalid shell name '{}'".format(shellnode.tag), shellnode)
wavecompr = sc.hsd_node_factory(
'wavefunction compression', COMPRESSIONS,
query.getvaluenode(shellnode, '.'), query)
myself[(nn, ll)] = wavecompr
return myself
def findchild(self, node, name, optional=False):
"""Finds a child of a node with a given name.
Parameters
----------
node : Element
Parent node.
name : string
Name of the child to look for.
optional : bool, optional
Whether the child is optional only.
Returns
-------
child : Element or None
A hsd node if child has been found or None.
Raises
-------
HSDMissingTagException
If child was not found and the optional flag was False.
HSDInvalidTagException
Iff there are duplicates of the child and the query object was
initialized with `check_uniqueness=True`.
"""
if self.chkunique:
children = node.findall("./" + name)
if len(children) > 1:
raise hsd.HSDInvalidTagException(
node=children[1],
msg="Double occurance of unique tag '{}'.".format(name))
child = children[0] if children else None
else:
child = node.find("./" + name)
if child is None and not optional:
raise hsd.HSDMissingTagException(
msg="Required tag '{}' not found.".format(name), node=node)
self.markprocessed(child)
return child
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))
def getvaluenode(self,
node,
name,
defvalue=None,
defvaluename=None,
defattribs=None,
hsdblock=False,
allowtextvalue=False,
returnchild=False):
"""Returns the value node stored in a child with a given
name. The child should contain either no nodes at all or only this one.
Parameters
----------
node : Element
Parent node.
name : string
Name of the child to look for.
defvalue : Element, optional
If child is not found, it will be created and contain the specified
node as subnode.
defvaluename : string, optional
If child is not found, it will be created and contain a subnode
with the given name. If name is "", the child node will not
contain a subnode. It is ignored, if defvalue had been specified.
defattribs : dict, optional
Default attribute dictionary used if child has not been found.
hsdblock : bool, optional
Whether the given value should be added in hsd block notation
(enclosed in curly braces) instead of an assignment.
allowtextvalue : bool, optional
If set to yes, the child (if it exists) is allowed to have
no subnode, but a text value instead. In that case the text
value will be deleted and converted into an empty node.
returnchild : bool, optional
Returns
-------
node : Element or None
The child node's first child or a node with the specified default
name if child had not been found. In latter case, an
appropriate child node with this as subnode is inserted into the
tree.
child : Element, optional
The child not itself. Only returned if `returnchild=Yes` was set.
Raises
------
HSDMissingTagException
If child was not found and no default value had been specified.
HSDInvalidTagException
If child has more than one child.
Notes
-----
This routine should be used, if the child is not a leaf but
contains a further child.
"""
optional = defvalue is not None or defvaluename is not None
child = self.findchild(node, name, optional)
if child is not None:
if len(child) > 1:
raise hsd.HSDInvalidTagException(
"Tag '{}' is not allowed to have"
" more than one child".format(child.tag),
node=child)
self.markprocessed(child)
if len(child):
self.markprocessed(child[0])
return (child[0], child) if returnchild else child[0]
elif allowtextvalue and child.text:
valuenode = Element(child.text)
child.text = ""
child.append(valuenode)
self.markprocessed(valuenode)
return (valuenode, child) if returnchild else valuenode
else:
return (None, child) if returnchild else None
else:
if defvalue is None:
defvalue = Element(defvaluename)
child, valuenode = self.setvaluenode(node, name, defvalue,
defattribs, hsdblock)
return (valuenode, child) if returnchild else valuenode
def getvalue(self,
node,
name,
converter=None,
defvalue=None,
attribs=None,
defattribs=None,
hsdblock=False,
returnchild=False):
"""Returns the converted value of the data stored in a child with a
given name.
Parameters
----------
node : Element
Parent node.
name : string
Name of the child to look for.
converter : converter object
Object with methods fromhsd() and tohsd() which can
convert between the hsd element and the desired type. See
converters in hsd.converter for examples.
defvalue : arbitrary, optional
Default value used if child has not been found. It will be
converted to text by the tohsd() method of the converter.
attribs : frozen set
Set of attributes the node is allowed to have.
defattribs: dict, optional
Default attribute dictionary used if child has not been found.
hsdblock : bool, optional
Whether the given value should be added in hsd block notation
(enclosed in curly braces) instead of an assignment.
returnchild : bool, optional
Whether not only the value but also the child node should be
returned.
Returns
-------
value : arbitrary
The converted value of the child node's text or the default value
if the child had not been found. In latter case, an appropriate
node with the appropriate text representation of the default
value is inserted into the tree.
child : Element, optional
Child node. Only returned, if `returnchild=True` was set.
Raises
------
HSDMissingTagException
If child was not found and no default value had been specified.
HSDInvalidTagValueException
If conversion from tag values was unsuccessful.
HSDInvalidAttributeException
If node posses an attribute which is not allowed.
Notes
-----
This method may store a reference to the converter object.
Make sure you pass something which does not change afterwards.
"""
optional = defvalue is not None
child = self.findchild(node, name, optional)
if child is not None:
if len(child):
raise hsd.HSDInvalidTagException("Unexpected children")
self._checkattribs(child, attribs)
if converter:
try:
value = converter.fromhsd(child.text)
except ValueError as ex:
raise hsd.HSDInvalidTagValueException(
msg="Conversion error: " + str(ex), node=child)
else:
value = child.text
return (value, child) if returnchild else value
else:
child = self.setvalue(node, name, converter, defvalue, defattribs,
hsdblock)
return (defvalue, child) if returnchild else defvalue