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nomad-lab
parser-gpaw
Commits
b639b34c
Commit
b639b34c
authored
8 years ago
by
Mikkel Strange
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parser for new type (aff) GPAW output files
parent
9f96d449
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parser/parser-gpaw/default_parameters.py
+39
-0
39 additions, 0 deletions
parser/parser-gpaw/default_parameters.py
parser/parser-gpaw/parser2.py
+162
-0
162 additions, 0 deletions
parser/parser-gpaw/parser2.py
with
201 additions
and
0 deletions
parser/parser-gpaw/default_parameters.py
0 → 100644
+
39
−
0
View file @
b639b34c
import
numpy
as
np
parameters
=
{
'
mode
'
:
'
fd
'
,
'
xc
'
:
'
LDA
'
,
'
occupations
'
:
None
,
'
poissonsolver
'
:
None
,
'
h
'
:
None
,
# Angstrom
'
gpts
'
:
None
,
'
kpts
'
:
[(
0.0
,
0.0
,
0.0
)],
'
nbands
'
:
None
,
'
charge
'
:
0
,
'
setups
'
:
{},
'
basis
'
:
{},
'
spinpol
'
:
None
,
'
fixdensity
'
:
False
,
'
filter
'
:
None
,
'
mixer
'
:
None
,
'
eigensolver
'
:
None
,
'
background_charge
'
:
None
,
'
external
'
:
None
,
'
random
'
:
False
,
'
hund
'
:
False
,
'
maxiter
'
:
333
,
'
idiotproof
'
:
True
,
'
symmetry
'
:
{
'
point_group
'
:
True
,
'
time_reversal
'
:
True
,
'
symmorphic
'
:
True
,
'
tolerance
'
:
1e-7
},
'
convergence
'
:
{
'
energy
'
:
0.0005
,
# eV / electron
'
density
'
:
1.0e-4
,
'
eigenstates
'
:
4.0e-8
,
# eV^2
'
bands
'
:
'
occupied
'
,
'
forces
'
:
np
.
inf
},
# eV / Ang
'
dtype
'
:
None
,
# Deprecated
'
width
'
:
None
,
# Deprecated
'
verbose
'
:
0
}
This diff is collapsed.
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parser/parser-gpaw/parser2.py
0 → 100644
+
162
−
0
View file @
b639b34c
from
__future__
import
division
import
os
from
contextlib
import
contextmanager
import
numpy
as
np
from
ase
import
units
from
ase.data
import
chemical_symbols
from
ase.io.aff
import
affopen
#from ase.io.trajectory import read_atoms
from
ase.data
import
atomic_masses
from
ase.units
import
Rydberg
import
setup_paths
from
nomadcore.unit_conversion.unit_conversion
import
convert_unit
as
cu
from
nomadcore.local_meta_info
import
loadJsonFile
,
InfoKindEl
from
nomadcore.parser_backend
import
JsonParseEventsWriterBackend
from
libxc_names
import
get_libxc_name
from
default_parameters
import
parameters
as
parms
@contextmanager
def
open_section
(
p
,
name
):
gid
=
p
.
openSection
(
name
)
yield
gid
p
.
closeSection
(
name
,
gid
)
def
c
(
value
,
unit
=
None
):
"""
Dummy function for unit conversion
"""
return
value
return
cu
(
value
,
unit
)
parser_info
=
{
"
name
"
:
"
parser2_gpaw
"
,
"
version
"
:
"
1.0
"
}
path
=
'
../../../../nomad-meta-info/meta_info/nomad_meta_info/
'
+
\
'
gpaw.nomadmetainfo.json
'
metaInfoPath
=
os
.
path
.
normpath
(
os
.
path
.
join
(
os
.
path
.
dirname
(
os
.
path
.
abspath
(
__file__
)),
path
))
metaInfoEnv
,
warns
=
loadJsonFile
(
filePath
=
metaInfoPath
,
dependencyLoader
=
None
,
extraArgsHandling
=
InfoKindEl
.
ADD_EXTRA_ARGS
,
uri
=
None
)
def
parse
(
filename
):
p
=
JsonParseEventsWriterBackend
(
metaInfoEnv
)
o
=
open_section
r
=
affopen
(
filename
)
# Reader(filename)
p
.
startedParsingSession
(
filename
,
parser_info
)
parms
.
update
(
r
.
parameters
.
asdict
())
with
o
(
p
,
'
section_run
'
):
p
.
addValue
(
'
program_name
'
,
'
GPAW
'
)
p
.
addValue
(
'
program_version
'
,
r
.
gpaw_version
)
mode
=
parms
[
'
mode
'
]
if
isinstance
(
mode
,
basestring
):
mode
=
{
'
name
'
:
mode
}
if
mode
[
'
name
'
]
==
'
pw
'
:
p
.
addValue
(
'
program_basis_set_type
'
,
'
plane waves
'
)
with
o
(
p
,
'
section_basis_set_cell_dependent
'
):
p
.
addValue
(
'
basis_set_cell_dependent_name
'
,
'
PW_%.1f_Ry
'
%
(
mode
[
'
ecut
'
]
/
r
.
ha
*
2
))
# in Ry
p
.
addRealValue
(
'
basis_set_planewave_cutoff
'
,
c
(
mode
[
'
ecut
'
],
'
eV
'
))
elif
mode
[
'
name
'
]
==
'
fd
'
:
p
.
addValue
(
'
program_basis_set_type
'
,
'
real space grid
'
)
with
o
(
p
,
'
section_basis_set_cell_dependent
'
):
cell
=
r
.
atoms
.
cell
ngpts
=
r
.
density
.
density
.
shape
h1
=
np
.
linalg
.
norm
(
cell
[
0
])
/
ngpts
[
0
]
h2
=
np
.
linalg
.
norm
(
cell
[
1
])
/
ngpts
[
1
]
h3
=
np
.
linalg
.
norm
(
cell
[
2
])
/
ngpts
[
2
]
h
=
(
h1
+
h2
+
h3
)
/
3.0
p
.
addValue
(
'
basis_set_cell_dependent_name
'
,
'
GR_%.1f
'
%
(
c
(
h
,
'
angstrom
'
)
*
1.0E15
))
# in fm
elif
mode
[
'
name
'
]
==
'
lcao
'
:
p
.
addValue
(
'
program_basis_set_type
'
,
'
numeric AOs
'
)
with
o
(
p
,
'
section_basis_set_atom_centered
'
):
p
.
addValue
(
'
basis_set_atom_centered_short_name
'
,
parms
[
'
basis
'
])
with
o
(
p
,
'
section_system
'
)
as
system_gid
:
p
.
addArrayValues
(
'
simulation_cell
'
,
c
(
r
.
atoms
.
cell
,
'
angstrom
'
))
symbols
=
np
.
array
([
chemical_symbols
[
z
]
for
z
in
r
.
atoms
.
numbers
])
p
.
addArrayValues
(
'
atom_labels
'
,
symbols
)
p
.
addArrayValues
(
'
atom_positions
'
,
c
(
r
.
atoms
.
positions
,
'
angstrom
'
))
p
.
addArrayValues
(
'
configuration_periodic_dimensions
'
,
np
.
array
(
r
.
atoms
.
pbc
,
bool
))
if
hasattr
(
r
.
atoms
,
'
momenta
'
):
masses
=
atomic_masses
[
r
.
atoms
.
numbers
]
velocities
=
r
.
atoms
.
momenta
/
masses
.
reshape
(
-
1
,
1
)
p
.
addArrayValues
(
'
atom_velocities
'
,
c
(
velocities
*
units
.
fs
/
units
.
Angstrom
,
'
angstrom/femtosecond
'
))
with
o
(
p
,
'
section_sampling_method
'
):
p
.
addValue
(
'
ensemble_type
'
,
'
NVE
'
)
with
o
(
p
,
'
section_frame_sequence
'
):
pass
with
o
(
p
,
'
section_method
'
)
as
method_gid
:
p
.
addValue
(
'
relativity_method
'
,
'
pseudo_scalar_relativistic
'
)
p
.
addValue
(
'
electronic_structure_method
'
,
'
DFT
'
)
p
.
addValue
(
'
scf_threshold_energy_change
'
,
c
(
parms
[
'
convergence
'
][
'
energy
'
],
'
eV
'
))
# eV / electron
#if r.FixMagneticMoment:
# p.addValue('x_gpaw_fixed_spin_Sz',
# r.MagneticMoments.sum() / 2.)
if
parms
[
'
occupations
'
]
is
None
:
# use default values
if
tuple
(
parms
[
'
kpts
'
])
==
(
1
,
1
,
1
):
width
=
0.0
else
:
width
=
0.1
parms
[
'
occupations
'
]
=
{
'
width
'
:
width
,
'
name
'
:
'
fermi-dirac
'
}
p
.
addValue
(
'
smearing_kind
'
,
parms
[
'
occupations
'
][
'
name
'
])
p
.
addRealValue
(
'
smearing_width
'
,
c
(
parms
[
'
occupations
'
][
'
width
'
],
'
eV
'
))
p
.
addRealValue
(
'
total_charge
'
,
parms
[
'
charge
'
])
with
o
(
p
,
'
section_XC_functionals
'
):
p
.
addValue
(
'
XC_functional_name
'
,
get_libxc_name
(
parms
[
'
xc
'
]))
with
o
(
p
,
'
section_single_configuration_calculation
'
):
p
.
addValue
(
'
single_configuration_calculation_to_system_ref
'
,
system_gid
)
p
.
addValue
(
'
single_configuration_to_calculation_method_ref
'
,
method_gid
)
p
.
addValue
(
'
single_configuration_calculation_converged
'
,
r
.
scf
.
converged
)
p
.
addRealValue
(
'
energy_total
'
,
c
(
r
.
hamiltonian
.
e_total_extrapolated
,
'
eV
'
))
p
.
addRealValue
(
'
energy_free
'
,
c
(
r
.
hamiltonian
.
e_total_free
,
'
eV
'
))
p
.
addRealValue
(
'
energy_XC
'
,
c
(
r
.
hamiltonian
.
e_xc
,
'
eV
'
))
p
.
addRealValue
(
'
electronic_kinetic_energy
'
,
c
(
r
.
hamiltonian
.
e_kinetic
,
'
eV
'
))
p
.
addRealValue
(
'
energy_correction_entropy
'
,
c
(
r
.
hamiltonian
.
e_entropy
,
'
eV
'
))
p
.
addRealValue
(
'
energy_reference_fermi
'
,
c
(
r
.
occupations
.
fermilevel
,
'
eV
'
))
p
.
addRealValue
(
'
energy_reference_fermi
'
,
c
(
r
.
occupations
.
fermilevel
,
'
eV
'
))
if
hasattr
(
r
.
results
,
'
forces
'
):
p
.
addArrayValues
(
'
atom_forces_free
'
,
c
(
r
.
results
.
forces
,
'
eV/angstrom
'
))
if
hasattr
(
r
.
results
,
'
magmoms
'
):
p
.
addArrayValues
(
'
x_gpaw_magnetic_moments
'
,
r
.
results
.
magmoms
)
p
.
addRealValue
(
'
x_gpaw_spin_Sz
'
,
r
.
results
.
magmoms
.
sum
()
/
2.0
)
#p.addArrayValues('x_gpaw_atomic_density_matrices',
# r.AtomicDensityMatrices)
#p.addArrayValues('x_gpaw_projections_real', r.Projections.real)
#p.addArrayValues('x_gpaw_projections_imag', r.Projections.imag)
with
o
(
p
,
'
section_eigenvalues
'
):
p
.
addValue
(
'
eigenvalues_kind
'
,
'
normal
'
)
p
.
addArrayValues
(
'
eigenvalues_values
'
,
c
(
r
.
wave_functions
.
eigenvalues
,
'
eV
'
))
p
.
addArrayValues
(
'
eigenvalues_occupation
'
,
r
.
wave_functions
.
occupations
)
#p.addArrayValues('eigenvalues_kpoints', r.IBZKPoints)
p
.
finishedParsingSession
(
"
ParseSuccess
"
,
None
)
if
__name__
==
'
__main__
'
:
import
sys
filename
=
sys
.
argv
[
1
]
parse
(
filename
)
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