def __init__(self):
self.control = Control()
self.system = System()
self.electrons = Electrons()
self.ions = Ions()
self.cell = Cell()
self.atomic_species = AtomicSpecies()
self.atomic_positions = AtomicPositions()
self.k_points = KPoints()
self.cell_parameters = CellParameters()
# Not Implemented (Card not a class)
#self.occupations = Card("OCCUPATIONS")
#self.constrains = Card("CONTRAINTS")
#self.atomicforces = Card("ATOMIC_FORCES")
self.namelist_asoc = {
"control": self.control,
"system": self.system,
"electrons": self.electrons,
"ions": self.ions,
"cell": self.cell
}
class PWBase:
"""
PW Quantum Espresso Base
From this class you can:
- initialize the input
- create inputfile
- validate input
- run pw.x
"""
def __init__(self):
self.control = Control()
self.system = System()
self.electrons = Electrons()
self.ions = Ions()
self.cell = Cell()
self.atomic_species = AtomicSpecies()
self.atomic_positions = AtomicPositions()
self.k_points = KPoints()
self.cell_parameters = CellParameters()
# Not Implemented (Card not a class)
#self.occupations = Card("OCCUPATIONS")
#self.constrains = Card("CONTRAINTS")
#self.atomicforces = Card("ATOMIC_FORCES")
self.namelist_asoc = {
"control": self.control,
"system": self.system,
"electrons": self.electrons,
"ions": self.ions,
"cell": self.cell
}
def add_keypairs_to_namelist(self, qe_keypairs):
""" Adds the respective keys to each namelist
"""
for name, keypairs in qe_keypairs.items():
namelist = self.namelist_asoc.get(name.lower())
if namelist:
namelist.add_keypairs(keypairs)
else:
error_str = "{0} is not valid namelist"
raise Exception(error_str.format(name))
def to_string(self, header=True):
qe_str = ""
if (header == True):
qe_str += "! File Autogenerated from Python QE\n"
## NameLists
qe_str += self.control.to_string()
qe_str += self.system.to_string()
qe_str += self.electrons.to_string()
qe_str += self.ions.to_string()
qe_str += self.cell.to_string()
## Cards
qe_str += str(self.atomic_species)
qe_str += str(self.atomic_positions)
qe_str += str(self.k_points)
# Only needed if unitcell is not defined
# By ibrav
if self.system.get_current_value("ibrav") == 0:
qe_str += str(self.cell_parameters)
# Not Implemented
# qe_str += str(self.occupations)
# qe_str += str(self.contraints)
# qe_str += str(self.atomic_forces)
return qe_str
def to_file(self, filename, input_format="fortran"):
""" Writes QE configuration to <filename> in format
specified. Currently only supports the Fortran style.
"""
if input_format == "fortran":
with open(filename, "w") as qefile:
qefile.write(self.to_string())
else:
raise Exception("xml input specification not supported")
def run(self, infile="", outfile="", errfile=""):
"""Runs QE pw.x.
If stdin, stdout, stderr filenames are not defined
no file is created for the given input or output.
If 'infile' is defined the program will run from the
file rather than stdin via '-i'.
Notice:
QE will still create the save files in the directory
specified by 'outfile' and 'errfile' in control namelist
"""
from subprocess import Popen, PIPE
from time import time
from pyqe import config
start_time = time()
if infile != "":
self.to_file(infile)
pw_command = config.prefix + ["pw.x", '-i', infile] + config.postfix
proc = Popen(pw_command, stdout=PIPE, stderr=PIPE)
pw_output = proc.communicate()
else:
pw_input = self.to_string()
pw_command = config.prefix + ["pw.x"] + config.postfix
proc = Popen(pw_command, stdin=PIPE, stdout=PIPE, stderr=PIPE)
pw_output = proc.communicate(pw_input.encode())
proc.wait()
end_time = time()
pw_out = pw_output[0].decode()
pw_err = pw_output[1].decode()
if outfile != "":
with open(outfile, "w") as f:
f.write(pw_out)
if errfile != "":
with open(errfile, "w") as f:
f.write(pw_err)
if proc.returncode != 0:
with open("CRASH", "r") as f:
print("Quantum Espresso CRASH FILE:\n{0}".format(f.read()))
raise Exception("pw.x CRASHED")
from pyqe.io import read_out_file, read_data_file
results = read_out_file(pw_out)
# Read save file output
prefix = self.control.get_current_value("prefix")
outdir = self.control.get_current_value("outdir")
if outdir[-1] == '/':
data_file = outdir + prefix + '.save/data-file.xml'
else:
data_file = outdir + '/' + prefix + '.save/data-file.xml'
results.update({"data-file": read_data_file(data_file)})
# Add run related info
results.update({'time': end_time - start_time})
return results
def validate(self):
""" Each Namelist and Card will validate its contents.
Sometimes they will need access to global information. (not
sure how to handle this yet) """
self.control.validate(self)
self.system.validate(self)
self.electrons.validate(self)
self.ions.validate(self)
self.cell.validate(self)
self.atomic_species.validate()
self.atomic_positions.validate()
self.k_points.validate()
self.cell_parameters.validate()