def test_qeparser_header(self):
# Header for PH configuration files is mandatory
parser = QEParser(configText = fixtures.textHeader, type="ph")
parser.parse()
self.assertEqual(parser.toString(), fixtures.assertHeader)
def test_qeparser_type(self):
# Type of configuration file recognizes specific namelists and card only!
parser = QEParser(configText = fixtures.textHeader, type="pw")
parser.parse()
self.assertEqual(parser.toString(), '') # namelist 'INPUTPH' is not recognized
def test_qeparser_card(self):
# Card
parser = QEParser(configText = fixtures.textCards)
parser.parse()
self.assertEqual(parser.toString(), fixtures.assertCards)
def test_qeparser_comma(self):
# Parameters on the same line separated by comma - does not parse as it
# should (intentionally)
parser = QEParser(configText = fixtures.textComma, type="matdyn")
parser.parse()
self.assertEqual(parser.toString(), fixtures.assertComma)
def test_qeparser_dynmat(self):
# Slash and name of namelist on the same line with parameters
parser = QEParser(configText=fixtures.textDynmat, type="dynmat")
parser.parse()
self.assertEqual(parser.toString(), fixtures.assertDynmat)
def test_qeparser_file(self):
# Configuration file
parser = QEParser(filename = "ni.scf.in")
parser.parse()
self.assertEqual(parser.toString(), fixtures.assertFile)
def test_qeparser_comments(self):
# Filters out comments
parser = QEParser(filename="ph.mgb2.in", type="ph")
parser.parse()
self.assertEqual(parser.toString(), fixtures.assertMgB2)
class QEInput(object):
"""Quantum Espresso configuration class. It can:
- Parse existing configuration file
- Add, Edit or Remove parameters from/to namelist or card
"""
# Either filename or config (not both) can be specified
def __init__(self, filename=None, config=None, type='pw'):
self.header = None
self.filename = filename
self.config = config
self.parser = QEParser(filename, config, type)
self.type = type
self.namelists = OrderedDict()
self.cards = OrderedDict()
self.attach = None # Specific for 'matdyn', 'dynmat'
self.namelistRef = None
self.cardRef = None
self.qe = [self.header, self.namelists, self.cards, self.attach]
def parse(self):
""" Parses the configuration file and stores the values in qe dictionary """
(self.header, self.namelists, self.cards,
self.attach) = self.parser.parse()
def createNamelist(self, name):
"""Creates namelist and adds to QEInput. """
nl = Namelist(name)
self.namelists[name] = nl
return nl
def addNamelist(self, namelist):
"""Adds namelist. """
self.namelists[namelist.name()] = namelist
def removeNamelist(self, name):
try:
del (self.namelists[name])
except KeyError: # parameter is not present
return
def namelist(self, name):
"Returns namelist specified by name if exists or create a new one"
if self.namelistExists(name): # If exists, return namelist
return self.namelists[name]
return self.createNamelist(name) # otherwise create a new one
def namelistExists(self, name):
"Checks if namelist specified by name exists"
return self._exists(name, self.namelists.keys())
def createCard(self, name):
"Creates card and adds to QEInput. "
card = Card(name)
self.cards[name] = card
return card
def addCard(self, card):
"Adds card"
self.cards[card.name()] = card
def removeCard(self, name):
try:
del (self.cards[name])
except KeyError: # parameter is not present
return
def attach(self):
"Returns attachment"
return self.attach
def addAttach(self, text):
"""
Sets attachment to some string.
If attachment is not None it still will be overwritten
"""
self.attach = text
def removeAttach(self):
"Sets attachment to None"
self.attach = None
def card(self, name):
"Returns card specified by name if exists or create a new one"
if self.cardExists(name): # If exists, return card
return self.cards[name]
return self.createCard(name)
def cardExists(self, name):
"Checks if card specified by name exists"
return self._exists(name, self.cards.keys())
def getObject(self, name, dict):
"""Returns object that corresponds to 'name'"""
for n in dict.values():
if n.name() == name:
return dict[name]
return None
def save(self, filename=None):
""" Saves the QEInput to the configuration file"""
default = "config.out"
if filename is None:
if self.filename is not None:
filename = self.filename
else:
filename = default
f = open(filename, "w")
f.write(self.toString())
f.close()
def type(self):
return self.type
def structure(self):
"""Returns basic structure information as list tuples
Example: [('Ni', '52.98', 'Ni.pbe-nd-rrkjus.UPF'), (...)]
"""
# Hard to extract structure not from pw type input
# TODO: Should also have "atomic_species" card
if self.type != "pw":
return None
list = [] # list of structure
card = self.card("atomic_species")
for l in card.lines(
): # Should have format: "<Label> <Mass> <Pseudo-Potential>"
l = l.strip()
if l == "": # Empty line
continue
list.append(l.split())
return list
def toString(self):
(self.namelistRef, self.cardRef) = self.parser.setReferences()
s = ''
if self.header: # Add header
s += "%s\n" % self.header
for name in self.namelistRef: # Add namelists
nl = self.getObject(name, self.namelists)
if nl is not None:
s += nl.toString()
for name in self.cardRef: # Add cards
c = self.getObject(name, self.cards)
if c is not None:
s += c.toString()
if self.attach: # Add attribute (e.g. for type='matdyn')
s += self.attach
return s
def _exists(self, name, list):
if name in list:
return True
return False
def test_qeparser_header(self):
# Header for PH configuration files is mandatory
parser = QEParser(configText=fixtures.textHeader, type="ph")
parser.parse()
self.assertEqual(parser.toString(), fixtures.assertHeader)
def test_qeparser_type(self):
# Type of configuration file recognizes specific namelists and card only!
parser = QEParser(configText=fixtures.textHeader, type="pw")
parser.parse()
self.assertEqual(parser.toString(),
'') # namelist 'INPUTPH' is not recognized
def test_qeparser_comma(self):
# Parameters on the same line separated by comma - does not parse as it
# should (intentionally)
parser = QEParser(configText=fixtures.textComma, type="matdyn")
parser.parse()
self.assertEqual(parser.toString(), fixtures.assertComma)
def test_qeparser_card(self):
# Card
parser = QEParser(configText=fixtures.textCards)
parser.parse()
self.assertEqual(parser.toString(), fixtures.assertCards)
def test_qeparser_file(self):
# Configuration file
parser = QEParser(filename="ni.scf.in")
parser.parse()
self.assertEqual(parser.toString(), fixtures.assertFile)
def test_qeparser_comments(self):
# Filters out comments
parser = QEParser(filename = "ph.mgb2.in", type="ph")
parser.parse()
self.assertEqual(parser.toString(), fixtures.assertMgB2)
def test_qeparser_matdyn(self):
# Attachment after card
parser = QEParser(configText = fixtures.textMatdyn, type="matdyn")
parser.parse()
self.assertEqual(parser.toString(), fixtures.assertMatdyn)
class QEInput(object):
"""Quantum Espresso configuration class. It can:
- Parse existing configuration file
- Add, Edit or Remove parameters from/to namelist or card
"""
# Either filename or config (not both) can be specified
def __init__(self, filename=None, config=None, type='pw'):
self.header = None
self.filename = filename
self.config = config
self.parser = QEParser(filename, config, type)
self.type = type
self.namelists = OrderedDict()
self.cards = OrderedDict()
self.attach = None # Specific for 'matdyn'
self.namelistRef = None
self.cardRef = None
self.qe = [self.header, self.namelists, self.cards, self.attach]
def parse(self):
""" Parses the configuration file and stores the values in qe dictionary """
(self.header, self.namelists, self.cards, self.attach) = self.parser.parse()
def createNamelist(self, name):
"""Creates namelist and adds to QEInput. """
nl = Namelist(name)
self.namelists[name] = nl
def addNamelist(self, namelist):
"""Adds namelist. """
self.namelists[namelist.name()] = namelist
def removeNamelist(self, name):
try:
del(self.namelists[name])
except KeyError: # parameter is not present
return
def namelist(self, name):
# Do I need editNamelist()?
try:
return self.namelists[name]
except KeyError: # parameter is not present
raise
def createCard(self, name):
"""Creates card and adds to QEInput. """
self.cards[name] = Card(name)
def addCard(self, card):
"""Adds card. """
self.cards[card.name()] = card
def removeCard(self, name):
try:
del(self.cards[name])
except KeyError: # parameter is not present
return
def card(self, name):
# Do I need editNamelist()?
try:
return self.cards[name]
except KeyError: # parameter is not present
raise
def toString(self):
(self.namelistRef, self.cardRef) = self.parser.setReferences()
s = ''
if self.header: # Add header
s += self.header
for name in self.namelistRef: # Add namelists
nl = self.getObject(name, self.namelists)
if nl is not None:
s += nl.toString()
for name in self.cardRef: # Add cards
c = self.getObject(name, self.cards)
if c is not None:
s += c.toString()
if self.attach: # Add attribute (e.g. for type='matdyn')
s += self.attach
return s
def getObject(self, name, dict):
"""Returns object that corresponds to 'name'"""
for n in dict.values():
if n.name() == name:
return dict[name]
return None
def save(self, filename=None):
""" Saves the QEInput to the configuration file"""
default = "config.out"
if filename is None:
if self.filename is not None:
filename = self.filename
else:
filename = default
f = open(filename, "w")
f.write(self.toString())
f.close()
def type(self):
return self.type
def test_qeparser_dynmat(self):
# Slash and name of namelist on the same line with parameters
parser = QEParser(configText = fixtures.textDynmat, type="dynmat")
parser.parse()
self.assertEqual(parser.toString(), fixtures.assertDynmat)
class QEInput(object):
"""Quantum Espresso configuration class. It can:
- Parse existing configuration file
- Add, Edit or Remove parameters from/to namelist or card
"""
# Either filename or config (not both) can be specified
def __init__(self, filename=None, config=None, type='pw'):
self.header = None
self.filename = filename
self.config = config
self.parser = QEParser(filename, config, type)
self.type = type
self.namelists = OrderedDict()
self.cards = OrderedDict()
self.attach = None # Specific for 'matdyn'
self.namelistRef = None
self.cardRef = None
self.qe = [self.header, self.namelists, self.cards, self.attach]
def parse(self):
""" Parses the configuration file and stores the values in qe dictionary """
(self.header, self.namelists, self.cards,
self.attach) = self.parser.parse()
def createNamelist(self, name):
"""Creates namelist and adds to QEInput. """
nl = Namelist(name)
self.namelists[name] = nl
def addNamelist(self, namelist):
"""Adds namelist. """
self.namelists[namelist.name()] = namelist
def removeNamelist(self, name):
try:
del (self.namelists[name])
except KeyError: # parameter is not present
return
def namelist(self, name):
# Do I need editNamelist()?
try:
return self.namelists[name]
except KeyError: # parameter is not present
raise
def createCard(self, name):
"""Creates card and adds to QEInput. """
self.cards[name] = Card(name)
def addCard(self, card):
"""Adds card. """
self.cards[card.name()] = card
def removeCard(self, name):
try:
del (self.cards[name])
except KeyError: # parameter is not present
return
def card(self, name):
# Do I need editNamelist()?
try:
return self.cards[name]
except KeyError: # parameter is not present
raise
def toString(self):
(self.namelistRef, self.cardRef) = self.parser.setReferences()
s = ''
if self.header: # Add header
s += self.header
for name in self.namelistRef: # Add namelists
nl = self.getObject(name, self.namelists)
if nl is not None:
s += nl.toString()
for name in self.cardRef: # Add cards
c = self.getObject(name, self.cards)
if c is not None:
s += c.toString()
if self.attach: # Add attribute (e.g. for type='matdyn')
s += self.attach
return s
def getObject(self, name, dict):
"""Returns object that corresponds to 'name'"""
for n in dict.values():
if n.name() == name:
return dict[name]
return None
def save(self, filename=None):
""" Saves the QEInput to the configuration file"""
default = "config.out"
if filename is None:
if self.filename is not None:
filename = self.filename
else:
filename = default
f = open(filename, "w")
f.write(self.toString())
f.close()
def type(self):
return self.type
def test_qeparser_matdyn(self):
# Attachment after card
parser = QEParser(configText=fixtures.textMatdyn, type="matdyn")
parser.parse()
self.assertEqual(parser.toString(), fixtures.assertMatdyn)
