def __init__(self,
arg0=None,
infile_name=None,
outfile_name=None,
pw2c_outfile_name=None,
analyze=False):
if isinstance(arg0, Simulation):
sim = arg0
path = sim.locdir
self.infile_name = sim.infile
self.outfile_name = sim.outfile
elif arg0 != None:
path = arg0
self.infile_name = infile_name
self.outfile_name = outfile_name
else:
return
#end if
self.path = path
self.abspath = os.path.abspath(path)
self.pw2c_outfile_name = pw2c_outfile_name
self.input = PwscfInput(os.path.join(self.path, self.infile_name))
if analyze:
self.analyze()
def __init__(self,arg0=None,infile_name=None,outfile_name=None,pw2c_outfile_name=None,analyze=False,xml=False,warn=False):
if isinstance(arg0,Simulation):
sim = arg0
path = sim.locdir
infile_name = sim.infile
outfile_name= sim.outfile
elif arg0!=None:
if infile_name!=None:
path = arg0
else:
path,infile_name = os.path.split(arg0)
#end if
if outfile_name is None:
outfile_name = infile_name.rsplit('.',1)[0]+'.out'
#end if
else:
return
#end if
self.infile_name = infile_name
self.outfile_name = outfile_name
self.path = path
self.abspath = os.path.abspath(path)
self.pw2c_outfile_name = pw2c_outfile_name
self.info = obj(xml=xml,warn=warn)
self.input = PwscfInput(os.path.join(self.path,self.infile_name))
self.input_structure = sim.system.structure
if analyze:
self.analyze()
def __init__(self,
arg0=None,
infile_name=None,
outfile_name=None,
pw2c_outfile_name=None,
analyze=False,
xml=False,
warn=False,
md_only=False):
if isinstance(arg0, Simulation):
sim = arg0
path = sim.locdir
infile_name = sim.infile
outfile_name = sim.outfile
self.input_structure = sim.system.structure
elif arg0 is not None:
path = arg0
if not os.path.exists(path):
self.error(
'path to QE data does not exist\npath provided: {}'.format(
path))
#end if
if os.path.isfile(path):
filepath = path
path, filename = os.path.split(filepath)
if filename.endswith('.in'):
infile_name = filename
elif filename.endswith('.out'):
outfile_name = filename
else:
self.error(
'could not determine whether file is QE input or output\nfile provided: {}'
.format(filepath))
#end if
#end if
if outfile_name is None:
outfile_name = infile_name.rsplit('.', 1)[0] + '.out'
#end if
else:
return
#end if
self.infile_name = infile_name
self.outfile_name = outfile_name
self.path = path
self.abspath = os.path.abspath(path)
self.pw2c_outfile_name = pw2c_outfile_name
self.info = obj(xml=xml, warn=warn, md_only=md_only)
self.input = None
if self.infile_name is not None:
self.input = PwscfInput(os.path.join(self.path, self.infile_name))
#end if
if analyze:
self.analyze()
#! /usr/bin/env python
from pwscf_input import PwscfInput
from nexus import read_input
# read the input from a file
pw = PwscfInput('./Fe_start_ns_eig.in')
# reading this way also works
pw = read_input('./Fe_start_ns_eig.in', format='pwscf')
# manipulate and write
for ecut in [100, 120, 140, 160]:
pw.system.ecutwfc = ecut
pw.write('scf_04_ecut_{0}.in'.format(ecut))
#end for
#! /usr/bin/env python
from numpy import array
from generic import obj
from pwscf_input import PwscfInput
# directly compose input in Nexus internal representation
pw = PwscfInput()
pw.control.set(
calculation='scf',
restart_mode='from_scratch',
wf_collect=True,
outdir='./output',
pseudo_dir='../pseudo/',
prefix='fe',
etot_conv_thr=1.0e-9,
forc_conv_thr=1.0e-6,
tstress=True,
tprnfor=True,
)
pw.system.set(
ibrav=1,
celldm={1: 15},
nat=2,
ntyp=1,
ecutwfc=100,
ecutrho=300,
nbnd=18,
occupations='smearing',
degauss=0.0005,
def test_input():
# imports
import os
import numpy as np
import pwscf_input as pwi
from generic import obj
from structure import read_structure
from physical_system import generate_physical_system
from pwscf_input import check_new_variables,check_section_classes
from pwscf_input import PwscfInput,generate_pwscf_input
# directories
tpath = testing.setup_unit_test_output_directory('pwscf_input','test_input')
# files
files = get_files()
# divert logging function
divert_nexus_log()
# definitions
def check_pw_same(pw1_,pw2_,l1='pw1',l2='pw2'):
pw_same = object_eq(pw1_,pw2_,int_as_float=True)
if not pw_same:
d,d1,d2 = object_diff(pw1_,pw2_,full=True,int_as_float=True)
diff = obj({l1:obj(d1),l2:obj(d2)})
failed(str(diff))
#end if
#end def check_pw_same
# test internal spec
check_new_variables(exit=False)
check_section_classes(exit=False)
# test compose
compositions = obj()
# based on sample_inputs/Fe_start_ns_eig.in
pw = PwscfInput()
pw.control.set(
calculation = 'scf' ,
restart_mode = 'from_scratch' ,
wf_collect = True ,
outdir = './output' ,
pseudo_dir = '../pseudo/' ,
prefix = 'fe' ,
etot_conv_thr = 1.0e-9 ,
forc_conv_thr = 1.0e-6 ,
tstress = True ,
tprnfor = True ,
)
pw.system.set(
ibrav = 1,
nat = 2,
ntyp = 1,
ecutwfc = 100 ,
ecutrho = 300 ,
nbnd = 18,
occupations = 'smearing',
degauss = 0.0005 ,
smearing = 'methfessel-paxton' ,
nspin = 2 ,
assume_isolated = 'martyna-tuckerman',
lda_plus_u = True ,
)
pw.system.set({
'celldm(1)' : 15,
'starting_magnetization(1)' : 0.9,
'hubbard_u(1)' : 3.1,
'starting_ns_eigenvalue(1,2,1)' : 0.0,
'starting_ns_eigenvalue(2,2,1)' : 0.0476060,
'starting_ns_eigenvalue(3,2,1)' : 0.0476060,
'starting_ns_eigenvalue(4,2,1)' : 0.9654373,
'starting_ns_eigenvalue(5,2,1)' : 0.9954307,
})
pw.electrons.set(
conv_thr = 1.0e-9 ,
mixing_beta = 0.7 ,
diagonalization = 'david' ,
mixing_fixed_ns = 500,
)
pw.atomic_species.set(
atoms = ['Fe'],
masses = obj(Fe=58.69000),
pseudopotentials = obj(Fe='Fe.pbe-nd-rrkjus.UPF'),
)
pw.atomic_positions.set(
specifier = 'angstrom',
atoms = ['Fe','Fe'],
positions = np.array([
[2.070000000, 0.000000000, 0.000000000],
[0.000000000, 0.000000000, 0.000000000],
]),
)
pw.k_points.set(
specifier = 'automatic',
grid = np.array((1,1,1)),
shift = np.array((1,1,1)),
)
compositions['Fe_start_ns_eig.in'] = pw
# test read
pwr = PwscfInput(files['Fe_start_ns_eig.in'])
pwc = pw.copy()
pwc.standardize_types()
check_pw_same(pwc,pwr,'compose','read')
# test write
infile = os.path.join(tpath,'pwscf.in')
pw.write(infile)
pw2 = PwscfInput()
pw2.read(infile)
check_pw_same(pw2,pwr)
# test read/write/read
reads = obj()
for infile in input_files:
read_path = files[infile]
write_path = os.path.join(tpath,infile)
if os.path.exists(write_path):
os.remove(write_path)
#end if
pw = PwscfInput(read_path)
pw.write(write_path)
pw2 = PwscfInput(write_path)
check_pw_same(pw,pw2,'read','write/read')
reads[infile] = pw
#end for
# test generate
generations = obj()
# based on sample_inputs/VO2_M1_afm.in
infile = 'VO2_M1_afm.in'
struct_file = files['VO2_M1_afm.xsf']
read_path = files[infile]
write_path = os.path.join(tpath,infile)
s = read_structure(struct_file)
s.elem[0] = 'V1'
s.elem[1] = 'V2'
s.elem[2] = 'V1'
s.elem[3] = 'V2'
vo2 = generate_physical_system(
structure = s,
V1 = 13,
V2 = 13,
O = 6,
)
pw = generate_pwscf_input(
selector = 'generic',
calculation = 'scf',
disk_io = 'low',
verbosity = 'high',
wf_collect = True,
input_dft = 'lda',
hubbard_u = obj(V1=3.5,V2=3.5),
ecutwfc = 350,
bandfac = 1.3,
nosym = True,
occupations = 'smearing',
smearing = 'fermi-dirac',
degauss = 0.0001,
nspin = 2,
start_mag = obj(V1=1.0,V2=-1.0),
diagonalization = 'david',
conv_thr = 1e-8,
mixing_beta = 0.2,
electron_maxstep = 1000,
system = vo2,
pseudos = ['V.opt.upf','O.opt.upf'],
kgrid = (6,6,6),
kshift = (0,0,0),
# added for reverse compatibility
celldm = {1:1.0},
cell_option = 'alat',
positions_option = 'alat',
)
generations[infile] = pw
if os.path.exists(write_path):
os.remove(write_path)
#end if
pw.write(write_path)
pw2 = PwscfInput(read_path)
pw3 = PwscfInput(write_path)
check_pw_same(pw2,pw3,'generate','read')
# based on sample_inputs/Fe_start_ns_eig.in
infile = 'Fe_start_ns_eig.in'
read_path = files[infile]
write_path = os.path.join(tpath,infile)
pw = generate_pwscf_input(
selector = 'generic',
calculation = 'scf',
restart_mode = 'from_scratch',
wf_collect = True,
outdir = './output',
pseudo_dir = '../pseudo/',
prefix = 'fe',
etot_conv_thr = 1.0e-9,
forc_conv_thr = 1.0e-6,
tstress = True,
tprnfor = True,
ibrav = 1,
nat = 2,
ntyp = 1,
ecutwfc = 100,
ecutrho = 300,
nbnd = 18,
occupations = 'smearing',
degauss = 0.0005,
smearing = 'methfessel-paxton',
nspin = 2,
assume_isolated = 'martyna-tuckerman',
lda_plus_u = True,
conv_thr = 1.0e-9,
mixing_beta = 0.7,
diagonalization = 'david',
mixing_fixed_ns = 500,
mass = obj(Fe=58.69000),
pseudos = ['Fe.pbe-nd-rrkjus.UPF'],
elem = ['Fe','Fe'],
pos = [[2.070000000, 0.000000000, 0.000000000],
[0.000000000, 0.000000000, 0.000000000]],
pos_specifier = 'angstrom',
kgrid = np.array((1,1,1)),
kshift = np.array((1,1,1)),
)
pw.system.set({
'celldm(1)' : 15,
'starting_magnetization(1)' : 0.9,
'hubbard_u(1)' : 3.1,
'starting_ns_eigenvalue(1,2,1)' : 0.0,
'starting_ns_eigenvalue(2,2,1)' : 0.0476060,
'starting_ns_eigenvalue(3,2,1)' : 0.0476060,
'starting_ns_eigenvalue(4,2,1)' : 0.9654373,
'starting_ns_eigenvalue(5,2,1)' : 0.9954307,
})
generations[infile] = pw
pw2 = compositions[infile]
check_pw_same(pw,pw2,'generate','compose')
if os.path.exists(write_path):
os.remove(write_path)
#end if
pw.write(write_path)
pw3 = PwscfInput(write_path)
pw4 = reads[infile]
check_pw_same(pw3,pw4,'generate','read')
# based on sample_inputs/Fe_start_ns_eig.in
# variant that uses direct pwscf array input
pw = generate_pwscf_input(
selector = 'generic',
calculation = 'scf',
restart_mode = 'from_scratch',
wf_collect = True,
outdir = './output',
pseudo_dir = '../pseudo/',
prefix = 'fe',
etot_conv_thr = 1.0e-9,
forc_conv_thr = 1.0e-6,
tstress = True,
tprnfor = True,
ibrav = 1,
nat = 2,
ntyp = 1,
ecutwfc = 100,
ecutrho = 300,
nbnd = 18,
occupations = 'smearing',
degauss = 0.0005,
smearing = 'methfessel-paxton',
nspin = 2,
assume_isolated = 'martyna-tuckerman',
lda_plus_u = True,
conv_thr = 1.0e-9,
mixing_beta = 0.7,
diagonalization = 'david',
mixing_fixed_ns = 500,
mass = obj(Fe=58.69000),
pseudos = ['Fe.pbe-nd-rrkjus.UPF'],
elem = ['Fe','Fe'],
pos = [[2.070000000, 0.000000000, 0.000000000],
[0.000000000, 0.000000000, 0.000000000]],
pos_specifier = 'angstrom',
kgrid = np.array((1,1,1)),
kshift = np.array((1,1,1)),
starting_ns_eigenvalue = {(1,2,1) : 0.0,
(2,2,1) : 0.0476060,
(3,2,1) : 0.0476060,
(4,2,1) : 0.9654373,
(5,2,1) : 0.9954307,},
celldm = {1 : 15 },
starting_magnetization = {1 : 0.9},
hubbard_u = {1 : 3.1},
)
pwg = pw.copy()
pwg.standardize_types()
generations[infile] = pw
pw2 = compositions[infile].copy()
pw2.standardize_types()
check_pw_same(pwg,pw2,'generate','compose')
pw3 = reads[infile]
check_pw_same(pwg,pw3,'generate','read')
if os.path.exists(write_path):
os.remove(write_path)
#end if
pw.write(write_path)
pw4 = PwscfInput(write_path)
check_pw_same(pwg,pw3,'generate','write')
# restore logging function
restore_nexus_log()