def __init__(self, name):
# Verifies if the namelist is valid
try:
if name not in configPW.namelists:
raise NameError('Not valid namelist')
except NameError:
raise
self.__name = name.lower() # keeps lower name
self.params = OrderedDict() # Replace dictionary by ordered dictionry
class Namelist():
"""Namelist class that corresponds to Namelist in QE config file"""
def __init__(self, name):
# Verifies if the namelist is valid
try:
if name not in configPW.namelists:
raise NameError('Not valid namelist')
except NameError:
raise
self.__name = name.lower() # keeps lower name
self.params = OrderedDict() # Replace dictionary by ordered dictionry
def name(self):
return self.__name
def setName(self, name):
self.__name = name.lower()
def param(self, param):
"""Returns value of parameter 'param'"""
if self.__paramExists(param):
return self.params[param]
def addParam(self, param, val):
# Add verification?
param = param.lower()
self.params[param] = val
def editParam(self, param, val):
"""Edits parameter. If it doesn't exist, it just ignores it """
if self.__paramExists(param):
self.params[param] = val
def removeParam(self, param):
"""Deletes parameter"""
if self.__paramExists(param):
del(self.params[param])
def __paramExists(self, param):
try:
param = param.lower()
self.params[param]
return True
except KeyError: # parameter is not present
return False
def toString(self, indent=" ", br="\n"):
# Dump namelist
# Should I use space?
s = '&%s%s' % (self.name().upper(), br)
for p in self.params.keys():
s += '%s%s = %s,%s' % (indent, p, self.params[p], br)
s += "/%s" % br
return s
def getCards(rawlist):
cards = OrderedDict()
cardName = None
for l in rawlist:
firstPart = l.split()[0].lower()
if firstPart in CARD_NAMES:
cardName = firstPart
cards[cardName] = []
elif cardName is not None:
cards[cardName].append(l)
return cards
def parseNamelists(text):
namelists = OrderedDict()
p = re.compile(COMMENT)
s1 = re.sub(p, '', text) # Remove comments
p2 = re.compile(NAMELIST)
matches = p2.findall(s1) # Finds all namelist blocks
for m in matches:
name = m[0]
if name in NAMELIST_NAMES:
params = parseParams(
m[1]) # Parse parameters from a namelist block
namelists[name.lower()] = params
noneparsed = re.sub(p2, '', s1)
return (namelists, noneparsed)
# Steps of job creation
STEPS = ("Create Simulation", "Create Configuration",
"Set Simulation Parameters", "Review Simulation")
SIMULATIONS = (
"Total Energy", # 0
"Electron DOS", # 1
"Electron Dispersion", # 2
"Geometry Optimization", # 3
"Single-Phonon", # 4
"Multi-Phonon DOS", # 5
"Multi-Phonon Dispersion") # 6
# Types of simulations
SIMCHAINS = OrderedDict()
SIMCHAINS[SIMULATIONS[0]] = ("PW", )
SIMCHAINS[SIMULATIONS[1]] = ("PW", "DOS")
SIMCHAINS[SIMULATIONS[2]] = ("PW", "DOS")
SIMCHAINS[SIMULATIONS[3]] = ("PW", )
SIMCHAINS[SIMULATIONS[4]] = ("PW", "PH", "DYNMAT")
SIMCHAINS[SIMULATIONS[5]] = ("PW", "PH", "Q2R", "MATDYN")
SIMCHAINS[SIMULATIONS[6]] = ("PW", "PH", "Q2R", "MATDYN")
# Available servers
SERVERS = ("foxtrot.danse.us", )
#"octopod.danse.us",
#"upgrayedd.danse.us",
#"teragrid"
# States of a job
#!/usr/bin/env python
#
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#
# Alex Dementsov
# California Institute of Technology
# (C) 2009 All Rights Reserved
#
# {LicenseText}
#
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#
from vinil.utils.orderedDict import OrderedDict
PW = OrderedDict()
# Namelist: CONTROL
NAMELIST_CONTROL = ('calculation', #: ('scf', 'nscf', 'bands', 'phonon', 'relax', 'md', 'vc-relax', 'vc-md', 'neb', 'smd', 'metadyn'),
'title', #: (''),
'verbosity', #: ('high', 'default', 'low', 'minimal'),
'restart_mode', #: ('from_scratch', 'restart'),
'wf_collect', #: ('.false.', '.true.'),
'nstep', #: ('???'),
'iprint',
'tstress',
'tprnfor',
'dt',
'outdir',
'wfcdir',
'prefix',
def __init__(self, filename=None, config=None):
self.filename = filename
self.config = config
self.namelists = OrderedDict()
self.cards = OrderedDict()
self.qe = [self.namelists, self.cards]
class QEConfig(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):
self.filename = filename
self.config = config
self.namelists = OrderedDict()
self.cards = OrderedDict()
self.qe = [self.namelists, self.cards]
def createNamelist(self, name):
"""Creates namelist and adds to QEConfig. """
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 QEConfig. """
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):
s = ''
for nl in self.namelists.values():
s += nl.toString()
for c in self.cards.values():
s += c.toString()
return s
def save(self, filename=None):
""" Saves the QEConfig 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 parse(self):
""" Parses the configuration file and stores the values in qe dictionary """
if self.filename is not None:
try:
f = open(self.filename)
except IOError:
print "I/O error"
except:
import sys
print "Unexpected error:", sys.exc_info()[0]
raise
lines = f.readlines() # Returns list of lines.
f.close()
elif self.config is not None:
lines = self.config.splitlines()
else:
print "Error: You haven't specify any config file"
lines = self.__clearLines(lines)
marks = self.__getMarks(lines)
for m in marks:
block = self.__addBlock(m[0], lines[m[1]:m[2]])
def __clearLines(self, lines):
""" Strips lines from white spaces, commas and empty lines"""
cl = [] # Lines without white spaces and empty lines
for l in lines:
l = l.strip().strip(
','
) # Remove both lead and trailing whitespace, including '\n' and comma
if l == '':
continue
cl.append(l)
return cl
def __addBlock(self, type, slice):
""" Adds block (namelist or card to ) """
# Improve calls?
if type == 'namelist':
self.__addNamelist(slice)
elif type == 'card':
self.__addCard(slice)
return
def __addNamelist(self, slice):
"""Adds namelist based on slice """
name = slice[0].strip('&')
nl = Namelist(name)
for s in slice[1:]:
p = self.getParam(s)
nl.addParam(p[0], p[1])
self.namelists[name] = nl
def __addCard(self, slice):
"""Adds card"""
name = slice[0].lower()
c = Card(name)
for s in slice[1:]:
c.addLine(s)
self.cards[name] = c
def __getMarks(self, lines):
# TODO: Cumbersome method, rewrite it
"""
Determines start and end of namelist and card blocks: [type, start, end]
E.g ['namelist', 0, 7] for CONTROL namelist
Iterate over number of lines. Empty lines are included
Not tested very well yet
"""
blocklist = []
isNamelist = False
isCard = False
size = len(lines)
for i in range(size):
l = lines[i]
# We suppose that namelists and card do not intersect
# Namelist part
# Namelist end
if l[0] == '/' and isNamelist:
isNamelist = False
block.append(i)
blocklist.append(block)
# Namelist start
if l[0] == '&' and not isNamelist:
name = l[1:].lower()
if not name in configPW.namelists:
continue # namelist is not recognizable
block = []
isNamelist = True
block.append('namelist')
block.append(i)
# Card part
line = l.lower()
# Card end
if line in configPW.cards and isCard:
#print "End: %s, line: %d" % (line, i-1)
isCard = False
block.append(i)
blocklist.append(block)
if i == size - 1 and isCard:
isCard = False
block.append(i + 1)
blocklist.append(block)
# Card start
if line in configPW.cards and not isCard:
#print "Start: %s, line: %d" % (line, i)
block = []
isCard = True
block.append('card')
block.append(i)
return blocklist
# Example return: [['namelist', 0, 7], ['namelist', 8, 20]]
def getParam(self, s):
""" Takes string like 'a = 2' and returns tuple ('a', 2) """
ss = s.split('=')
for i in range(len(ss)):
ss[i] = ss[i].strip()
val = ss[1]
# Assume that there are two values only: (variable, value) pair
assert len(ss) == 2
return (ss[0], val)
def __init__(self, filename=None, config=None):
self.filename = filename
self.config = config
self.namelists = OrderedDict()
self.cards = OrderedDict()
self.qe = [self.namelists, self.cards]
class QEConfig(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):
self.filename = filename
self.config = config
self.namelists = OrderedDict()
self.cards = OrderedDict()
self.qe = [self.namelists, self.cards]
def createNamelist(self, name):
"""Creates namelist and adds to QEConfig. """
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 QEConfig. """
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):
s = ''
for nl in self.namelists.values():
s += nl.toString()
for c in self.cards.values():
s += c.toString()
return s
def save(self, filename=None):
""" Saves the QEConfig 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 parse(self):
""" Parses the configuration file and stores the values in qe dictionary """
if self.filename is not None:
try:
f = open(self.filename)
except IOError:
print "I/O error"
except:
import sys
print "Unexpected error:", sys.exc_info()[0]
raise
lines = f.readlines() # Returns list of lines.
f.close()
elif self.config is not None:
lines = self.config.splitlines()
else:
print "Error: You haven't specify any config file"
lines = self.__clearLines(lines)
marks = self.__getMarks(lines)
for m in marks:
block = self.__addBlock(m[0], lines[m[1]:m[2]])
def __clearLines(self, lines):
""" Strips lines from white spaces, commas and empty lines"""
cl = [] # Lines without white spaces and empty lines
for l in lines:
l = l.strip().strip(',') # Remove both lead and trailing whitespace, including '\n' and comma
if l == '':
continue
cl.append(l)
return cl
def __addBlock(self, type, slice):
""" Adds block (namelist or card to ) """
# Improve calls?
if type == 'namelist':
self.__addNamelist(slice)
elif type == 'card':
self.__addCard(slice)
return
def __addNamelist(self, slice):
"""Adds namelist based on slice """
name = slice[0].strip('&')
nl = Namelist(name)
for s in slice[1:]:
p = self.getParam(s)
nl.addParam(p[0], p[1])
self.namelists[name] = nl
def __addCard(self, slice):
"""Adds card"""
name = slice[0].lower()
c = Card(name)
for s in slice[1:]:
c.addLine(s)
self.cards[name] = c
def __getMarks(self, lines):
# TODO: Cumbersome method, rewrite it
"""
Determines start and end of namelist and card blocks: [type, start, end]
E.g ['namelist', 0, 7] for CONTROL namelist
Iterate over number of lines. Empty lines are included
Not tested very well yet
"""
blocklist = []
isNamelist = False
isCard = False
size = len(lines)
for i in range(size):
l = lines[i]
# We suppose that namelists and card do not intersect
# Namelist part
# Namelist end
if l[0] == '/' and isNamelist:
isNamelist = False
block.append(i)
blocklist.append(block)
# Namelist start
if l[0] == '&' and not isNamelist:
name = l[1:].lower()
if not name in configPW.namelists:
continue # namelist is not recognizable
block = []
isNamelist = True
block.append('namelist')
block.append(i)
# Card part
line = l.lower()
# Card end
if line in configPW.cards and isCard:
#print "End: %s, line: %d" % (line, i-1)
isCard = False
block.append(i)
blocklist.append(block)
if i == size-1 and isCard:
isCard = False
block.append(i+1)
blocklist.append(block)
# Card start
if line in configPW.cards and not isCard:
#print "Start: %s, line: %d" % (line, i)
block = []
isCard = True
block.append('card')
block.append(i)
return blocklist
# Example return: [['namelist', 0, 7], ['namelist', 8, 20]]
def getParam(self, s):
""" Takes string like 'a = 2' and returns tuple ('a', 2) """
ss = s.split('=')
for i in range(len(ss)):
ss[i] = ss[i].strip()
val = ss[1]
# Assume that there are two values only: (variable, value) pair
assert len(ss) == 2
return (ss[0], val)