def getInputParam(text, param):
"Gets input string, sets param value and returns updated string"
# XXX: Parameters should be from "SYSTEM" namelist (extend for K-points)
input = QEInput(config=text)
input.parse()
nl = input.namelist("system")
return nl.param(param)
class Q2RGenerator(object):
def __init__(self, director, inventory):
self._director = director
self._inv = inventory
self._input = None
def setInput(self):
"Set namelist 'input'"
self._input = QEInput(type='q2r')
nl = self._input.namelist("input")
zasr = ZASR[ZASRLIST[int(self._inv.zasr)]]
nl.set("fildyn", self.fildyn()) # from PH results
nl.set("zasr", zasr)
nl.set("flfrc", FLFRC)
def fildyn(self):
"Returns fildyn parameter from PH results"
phresults = PHResult(self._director, self._inv.id)
return phresults.fildyn()
def toString(self):
return self._input.toString()
def getInputParam(text, param):
"Gets input string, sets param value and returns updated string"
# XXX: Parameters should be from "SYSTEM" namelist (extend for K-points)
input = QEInput(config=text)
input.parse()
nl = input.namelist("system")
return nl.param(param)
def setInput(self):
"Set namelist 'input'"
self._input = QEInput(type='q2r')
nl = self._input.namelist("input")
zasr = ZASR[ZASRLIST[int(self._inv.zasr)]]
nl.set("fildyn", self.fildyn()) # from PH results
nl.set("zasr", zasr)
nl.set("flfrc", FLFRC)
def setInput(self):
"Set namelist 'input'"
self._input = QEInput(type='dynmat')
nl = Namelist("input")
self._input.addNamelist(nl)
nl.add("fildyn", self._phresults.fildyn()) # from PH results
self._addAsr(nl)
self._addQPoint(nl)
def _inputFromRecord(self):
"Set input object from input configuration"
inputs = self._director.clerk.getQEConfigurations(where="taskid='%s'" %
self._emTaskId())
if len(inputs) == 0: # No input created
return
input = inputs[0]
fname = defaultInputName(input.type)
inputStr = readRecordFile(self._director.dds, input, fname)
self._input = QEInput(config=inputStr, type="cp")
self._input.parse()
class BANDSGenerator(object):
def __init__(self, director, inventory):
self._director = director
self._inv = inventory
self._input = None
def setInputpp(self):
self._input = QEInput(type="bands")
nl = self._input.namelist("inputpp")
nl.add("filband", FILBAND)
nl.add("lsym", LSIM)
def toString(self):
return self._input.toString()
class DOSGenerator(object):
def __init__(self, director, inventory):
self._director = director
self._inv = inventory
self._input = None
def setInputpp(self):
self._input = QEInput(type="dos")
nl = self._input.namelist("inputpp")
nl.add("Emin", self._inv.emin)
nl.add("Emax", self._inv.emax)
nl.add("DeltaE", self._inv.deltae)
def toString(self):
return self._input.toString()
def filterInput(self, director):
"Default behaviour: standard filtering"
input = QEInput(config=self.inventory.text, type=self.inventory.type)
filter = filters.filterFactory(self.inventory.type) # Creating filter
filter.apply(input) # Apply filter to input
fconfig = input.toString() # Filtered config input
return director.redirect(actor = 'material_simulations/espresso/input-create',
routine = 'createRecord',
text = fconfig,
id = self.inventory.id,
taskid = self.inventory.taskid,
type = self.inventory.type,
subtype = self.inventory.subtype,
fname = self.inventory.fname,
description = self.inventory.description)
class BANDSGenerator(object):
def __init__(self, director, inventory):
self._director = director
self._inv = inventory
self._input = None
def setInputpp(self):
self._input = QEInput(type="bands")
nl = self._input.namelist("inputpp")
nl.add("filband", FILBAND)
nl.add("lsym", LSIM)
def toString(self):
return self._input.toString()
class DOSGenerator(object):
def __init__(self, director, inventory):
self._director = director
self._inv = inventory
self._input = None
def setInputpp(self):
self._input = QEInput(type="dos")
nl = self._input.namelist("inputpp")
nl.add("Emin", self._inv.emin)
nl.add("Emax", self._inv.emax)
nl.add("DeltaE", self._inv.deltae)
def toString(self):
return self._input.toString()
def filterInput(self, director):
"Default behaviour: standard filtering"
input = QEInput(config=self.inventory.text, type=self.inventory.type)
filter = filters.filterFactory(self.inventory.type) # Creating filter
filter.apply(input) # Apply filter to input
fconfig = input.toString() # Filtered config input
return director.redirect(
actor='material_simulations/espresso/input-create',
routine='createRecord',
text=fconfig,
id=self.inventory.id,
taskid=self.inventory.taskid,
type=self.inventory.type,
subtype=self.inventory.subtype,
fname=self.inventory.fname,
description=self.inventory.description)
def setInput(self):
"Set namelist 'input'"
self._input = QEInput(type='q2r')
nl = self._input.namelist("input")
zasr = ZASR[ZASRLIST[int(self._inv.zasr)]]
nl.set("fildyn", self.fildyn()) # from PH results
nl.set("zasr", zasr)
nl.set("flfrc", FLFRC)
class DYNMATGenerator(object):
def __init__(self, director, inventory):
self._director = director
self._inv = inventory
self._input = None
self._phresults = PHResult(self._director, self._inv.id)
def setInput(self):
"Set namelist 'input'"
self._input = QEInput(type='dynmat')
nl = Namelist("input")
self._input.addNamelist(nl)
nl.add("fildyn", self._phresults.fildyn()) # from PH results
self._addAsr(nl)
self._addQPoint(nl)
def fildyn(self):
"Returns fildyn parameter from PH results"
return self._phresults.fildyn()
def _addAsr(self, nl):
"Adds 'asr' parameter for gamma point only"
if self._phresults.isGammaPoint():
asr = ZASR[ZASRLIST[int(self._inv.asr)]]
nl.add("asr", asr)
def _addQPoint(self, nl):
"Adds q point"
kp = self._phresults.kCoord()
if not kp or type(kp) != list:
nl.add("q(#)", "ERROR: Phonon coordinate (Kx, Ky, Kz) are not set in PH input")
for i in range(len(kp)):
nl.add("q(%s)" % str(i+1), kp[i])
def toString(self):
return self._input.toString()
def _inputFromRecord(self):
"Set input object from input configuration"
inputs = self._director.clerk.getQEConfigurations(where="taskid='%s'" % self._emTaskId())
if len(inputs) == 0: # No input created
return
input = inputs[0]
fname = defaultInputName(input.type)
inputStr = readRecordFile(self._director.dds, input, fname)
self._input = QEInput(config = inputStr, type = "cp")
self._input.parse()
class Q2RGenerator(object):
def __init__(self, director, inventory):
self._director = director
self._inv = inventory
self._input = None
def setInput(self):
"Set namelist 'input'"
self._input = QEInput(type='q2r')
nl = self._input.namelist("input")
zasr = ZASR[ZASRLIST[int(self._inv.zasr)]]
nl.set("fildyn", self.fildyn()) # from PH results
nl.set("zasr", zasr)
nl.set("flfrc", FLFRC)
def fildyn(self):
"Returns fildyn parameter from PH results"
phresults = PHResult(self._director, self._inv.id)
return phresults.fildyn()
def toString(self):
return self._input.toString()
def setInputph(self):
"Sets inputph depending on the simulation type"
self._input = QEInput(type='ph')
self._input.header = "phonon simulation\n"
nl = Namelist("inputph")
self._input.addNamelist(nl)
self._simtype = self._simtype()
if not self._simtype: # no simtype, no inputph population
return
if self._simtype == SIMTYPE["multiple-phonon"]:
self._multiPhonInput() # population of inputph for multiple phonon
elif self._simtype == SIMTYPE["single-phonon"]:
self._singlePhonInput() # population of inputph for single phonon
def setInputpp(self):
self._input = QEInput(type="dos")
nl = self._input.namelist("inputpp")
nl.add("Emin", self._inv.emin)
nl.add("Emax", self._inv.emax)
nl.add("DeltaE", self._inv.deltae)
class PHGenerator(object):
def __init__(self, director, inventory):
self._director = director
self._inv = inventory
self._input = None
self._pwresult = PWResult(self._director, self._inv.id)
# XXX: Handle prefix properly (should be same as in pw input)
def setInputph(self):
"Sets inputph depending on the simulation type"
self._input = QEInput(type='ph')
self._input.header = "phonon simulation\n"
nl = Namelist("inputph")
self._input.addNamelist(nl)
self._simtype = self._simtype()
if not self._simtype: # no simtype, no inputph population
return
if self._simtype == SIMTYPE["multiple-phonon"]:
self._multiPhonInput() # population of inputph for multiple phonon
elif self._simtype == SIMTYPE["single-phonon"]:
self._singlePhonInput() # population of inputph for single phonon
def toString(self):
if not self._input:
return ""
return self._input.toString()
def amasses(self):
"""Returns list of tuples with amass label and mass value from PW input configuration
Example: [("amass(1)", "35.5"), ("amass(2)", "54.3")]
"""
species = self._pwresult.species() # Example: masses = [("Al", "29.7"), ("Ni", "56.7") ...]
if not species:
return None # No masses, no amasses :)
list = [] # amass list
for l in range(len(species)):
list.append(("amass(%s)" % str(l+1), species[l][1]))
return list
def isGammaPoint(self):
"Checks if phonon point is gamma point"
# Rudimentary filter
if self._inv.kx == '' or self._inv.ky == '' or self._inv.kz == '':
return False
return float(self._inv.kx) == 0.0 and float(self._inv.ky) == 0.0 and float(self._inv.kz) == 0.0
# XXX: Reset parameters 'prefix', 'outdir', 'fildyn'
def _singlePhonInput(self):
"Takes namelist and populates inputph for single phonon"
nl = self._input.namelist("inputph")
nl.add("tr2_ph", TR2_PH)
nl.add("trans", TRANS)
self._addAmasses(nl)
self._addEpsil(nl) # for isolator only
self._addLnscf(nl) # for non-Gamma point
self._input.addAttach("%s %s %s" % (self._inv.kx, self._inv.ky, self._inv.kz))
def _multiPhonInput(self):
"Takes namelist and populates inputph for multiple phonons"
nl = self._input.namelist("inputph")
nl.add("nq1", self._inv.nq1)
nl.add("nq2", self._inv.nq2)
nl.add("nq3", self._inv.nq3)
nl.add("tr2_ph", TR2_PH)
nl.add("ldisp", LDISP)
#nl.add("prefix", QE_PREFIX)
self._addAmasses(nl)
self._addEpsil(nl) # for isolator only
def _addAmasses(self, nl):
"Takes namelist and adds amasses"
masses = self.amasses()
if not masses: # In case if not masses are found in PW input
nl.add("amass", "ERROR: masses not defined in PW input file!")
return
for m in masses:
nl.add(m[0], m[1])
def _addLnscf(self, nl):
"Adds 'lnscf' parameter for non-Gamma point"
if not self.isGammaPoint():
nl.add("lnscf", LNSCF)
def _addEpsil(self, nl):
"Add 'epsil' parameter for isolators only. Do nothing otherwise"
if self._pwresult.isIsolator():
nl.add("epsil", EPSIL)
def _simtype(self):
"Be cautious in case if inventory doesn't have simtype"
try:
simtype = self._inv.simtype
except AttributeError:
return None
return simtype
class CPGenerator(object):
"Generator for CP molecular dynamics tasks"
def __init__(self, director, inventory, input = None):
self._director = director
self._inv = inventory
self._input = input
self._init()
def setInput(self):
"Update input"
self.setControl()
self.setSystem()
self.setElectrons()
self.setIons()
self.setCell()
self.setExtra()
# Methods which should be overwritten in subclasses!
def setControl(self):
"CONTROL namelist"
pass
def setSystem(self):
"SYSTEM namelist"
pass
def setElectrons(self):
"ELECTRONS namelist"
pass
def setIons(self):
"IONS namelist"
pass
def setCell(self):
"CELL namelist"
pass
def setExtra(self):
"Extra parameters not specified by other namelists or cards"
pass
def _init(self):
self._inputFromRecord()
# Note:
# - Change to _inputFromResult() if you want to get input from result!
def _inputFromRecord(self):
"Set input object from input configuration"
inputs = self._director.clerk.getQEConfigurations(where="taskid='%s'" % self._emTaskId())
if len(inputs) == 0: # No input created
return
input = inputs[0]
fname = defaultInputName(input.type)
inputStr = readRecordFile(self._director.dds, input, fname)
self._input = QEInput(config = inputStr, type = "cp")
self._input.parse()
def _inputFromResult(self):
"Set input object from electron-min result"
if not self._input:
self._input = self._cpInput()
def _cpInput(self):
"Take input file from results and create QEInput object"
result = CPResult(self._director, self._inv.id, linkorder = EM_LINKORDER)
return result.input()
def _emTaskId(self):
"Returns electron-min task id"
simtasks = self._director.clerk.getQESimulationTasks(where="simulationid='%s'" % self._inv.id)
for st in simtasks:
if st:
task = self._director.clerk.getQETasks(id=st.taskid)
if task.linkorder == 0:
return task.id
return None
def toString(self):
if not self._input:
return "CP Generator: Electronic Minimization input is not created!"
return self._input.toString()
class CPGenerator(object):
"Generator for CP molecular dynamics tasks"
def __init__(self, director, inventory, input=None):
self._director = director
self._inv = inventory
self._input = input
self._init()
def setInput(self):
"Update input"
self.setControl()
self.setSystem()
self.setElectrons()
self.setIons()
self.setCell()
self.setExtra()
# Methods which should be overwritten in subclasses!
def setControl(self):
"CONTROL namelist"
pass
def setSystem(self):
"SYSTEM namelist"
pass
def setElectrons(self):
"ELECTRONS namelist"
pass
def setIons(self):
"IONS namelist"
pass
def setCell(self):
"CELL namelist"
pass
def setExtra(self):
"Extra parameters not specified by other namelists or cards"
pass
def _init(self):
self._inputFromRecord()
# Note:
# - Change to _inputFromResult() if you want to get input from result!
def _inputFromRecord(self):
"Set input object from input configuration"
inputs = self._director.clerk.getQEConfigurations(where="taskid='%s'" %
self._emTaskId())
if len(inputs) == 0: # No input created
return
input = inputs[0]
fname = defaultInputName(input.type)
inputStr = readRecordFile(self._director.dds, input, fname)
self._input = QEInput(config=inputStr, type="cp")
self._input.parse()
def _inputFromResult(self):
"Set input object from electron-min result"
if not self._input:
self._input = self._cpInput()
def _cpInput(self):
"Take input file from results and create QEInput object"
result = CPResult(self._director, self._inv.id, linkorder=EM_LINKORDER)
return result.input()
def _emTaskId(self):
"Returns electron-min task id"
simtasks = self._director.clerk.getQESimulationTasks(
where="simulationid='%s'" % self._inv.id)
for st in simtasks:
if st:
task = self._director.clerk.getQETasks(id=st.taskid)
if task.linkorder == 0:
return task.id
return None
def toString(self):
if not self._input:
return "CP Generator: Electronic Minimization input is not created!"
return self._input.toString()
def setInputpp(self):
self._input = QEInput(type="dos")
nl = self._input.namelist("inputpp")
nl.add("Emin", self._inv.emin)
nl.add("Emax", self._inv.emax)
nl.add("DeltaE", self._inv.deltae)
def setInputpp(self):
self._input = QEInput(type="bands")
nl = self._input.namelist("inputpp")
nl.add("filband", FILBAND)
nl.add("lsym", LSIM)
def setInputpp(self):
self._input = QEInput(type="bands")
nl = self._input.namelist("inputpp")
nl.add("filband", FILBAND)
nl.add("lsym", LSIM)