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nomad-lab
parser-gpaw
Commits
00fb8efd
Commit
00fb8efd
authored
Jan 26, 2019
by
Mohamed, Fawzi Roberto (fawzi)
Browse files
meta 2.0 changes
parent
2a39c1f0
Changes
4
Hide whitespace changes
Inline
Side-by-side
parser/parser-gpaw/parser.py
View file @
00fb8efd
...
...
@@ -100,7 +100,7 @@ def parse(filename):
p
.
addValue
(
'x_gpaw_fix_magnetic_moment'
,
r
.
FixMagneticMoment
)
if
r
.
FixMagneticMoment
:
p
.
addValue
(
'x_gpaw_fixed_spin_
S
z'
,
p
.
addValue
(
'x_gpaw_fixed_spin_
s
z'
,
r
.
MagneticMoments
.
sum
()
/
2.
)
if
'FermiWidth'
in
r
:
p
.
addValue
(
'smearing_kind'
,
'fermi'
)
...
...
@@ -129,22 +129,25 @@ def parse(filename):
xc_names
=
get_libxc_xc_names
(
r
.
XCFunctional
)
for
name
in
xc_names
.
values
():
if
name
is
not
None
:
with
o
(
p
,
'section_
XC
_functionals'
):
p
.
addValue
(
'
XC
_functional_name'
,
name
)
with
o
(
p
,
'section_
xc
_functionals'
):
p
.
addValue
(
'
xc
_functional_name'
,
name
)
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'
,
p
.
addValue
(
'single_configuration_calculation_
to_
method_ref'
,
method_gid
)
p
.
addRealValue
(
'energy_total'
,
c
(
r
.
Epot
,
'hartree'
))
p
.
addRealValue
(
'energy_
XC
'
,
c
(
r
.
Exc
,
'hartree'
))
p
.
addRealValue
(
'energy_
xc
'
,
c
(
r
.
Exc
,
'hartree'
))
p
.
addRealValue
(
'electronic_kinetic_energy'
,
c
(
r
.
Ekin
,
'hartree'
))
p
.
addRealValue
(
'energy_correction_entropy'
,
c
(
r
.
S
,
'hartree'
))
if
'CartesianForces'
in
r
:
p
.
addArrayValues
(
'atom_forces_free'
,
fId
=
p
.
openSection
(
'section_atom_forces'
)
p
.
addValue
(
'atom_forces_quantity'
,
'energy_free'
)
p
.
addArrayValues
(
'atom_forces'
,
c
(
r
.
CartesianForces
,
'bohr/hartree'
))
p
.
closeSection
(
'section_atom_forces'
,
fId
)
p
.
addArrayValues
(
'x_gpaw_magnetic_moments'
,
r
.
MagneticMoments
)
p
.
addRealValue
(
'x_gpaw_spin_
S
z'
,
r
.
MagneticMoments
.
sum
()
/
2.0
)
p
.
addRealValue
(
'x_gpaw_spin_
s
z'
,
r
.
MagneticMoments
.
sum
()
/
2.0
)
#p.addArrayValues('x_gpaw_atomic_density_matrices',
# r.AtomicDensityMatrices)
#p.addArrayValues('x_gpaw_projections_real', r.Projections.real)
...
...
parser/parser-gpaw/parser2.py
View file @
00fb8efd
...
...
@@ -114,7 +114,7 @@ def parse(filename):
p
.
addValue
(
'scf_threshold_energy_change'
,
c
(
parms
[
'convergence'
][
'energy'
],
'eV'
))
# eV / electron
#if r.FixMagneticMoment:
# p.addValue('x_gpaw_fixed_spin_
S
z',
# p.addValue('x_gpaw_fixed_spin_
s
z',
# r.MagneticMoments.sum() / 2.)
if
parms
[
'occupations'
]
is
None
:
# use default values
if
tuple
(
parms
[
'kpts'
])
==
(
1
,
1
,
1
):
...
...
@@ -127,13 +127,13 @@ def parse(filename):
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'
,
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'
,
p
.
addValue
(
'single_configuration_calculation_
to_
method_ref'
,
method_gid
)
p
.
addValue
(
'single_configuration_calculation_converged'
,
r
.
scf
.
converged
)
...
...
@@ -141,7 +141,7 @@ def parse(filename):
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
(
'energy_
xc
'
,
c
(
r
.
hamiltonian
.
e_xc
,
'eV'
))
p
.
addRealValue
(
'electronic_kinetic_energy'
,
c
(
r
.
hamiltonian
.
e_kinetic
,
'eV'
))
p
.
addRealValue
(
'energy_correction_entropy'
,
...
...
@@ -185,12 +185,16 @@ def parse(filename):
unit
=
'eV*angstrom**(-3)'
)
if
'forces'
in
r
.
results
:
p
.
addArrayValues
(
'atom_forces_free_raw'
,
fId
=
p
.
openSection
(
'section_atom_forces'
)
p
.
addValue
(
'atom_forces_quantity'
,
'energy_free'
)
p
.
addValue
(
'atom_forces_constraints'
,
'raw'
)
p
.
addArrayValues
(
'atom_forces'
,
c
(
r
.
results
.
forces
,
'eV/angstrom'
))
p
.
closeSection
(
'section_atom_forces'
,
fId
)
if
'magmons'
in
r
.
results
:
p
.
addArrayValues
(
'x_gpaw_magnetic_moments'
,
r
.
results
.
magmoms
)
p
.
addRealValue
(
'x_gpaw_spin_
S
z'
,
r
.
results
.
magmoms
.
sum
()
/
2.0
)
p
.
addRealValue
(
'x_gpaw_spin_
s
z'
,
r
.
results
.
magmoms
.
sum
()
/
2.0
)
#p.addArrayValues('x_gpaw_atomic_density_matrices',
# r.AtomicDensityMatrices)
#p.addArrayValues('x_gpaw_projections_real', r.Projections.real)
...
...
src/main/scala/eu/nomad_lab/parsers/GpawParser.scala
View file @
00fb8efd
...
...
@@ -46,7 +46,7 @@ object GpawParser extends SimpleExternalParserGenerator(
"parser-gpaw/setup_paths.py"
,
"nomad_meta_info/public.nomadmetainfo.json"
,
"nomad_meta_info/common.nomadmetainfo.json"
,
"nomad_meta_info/meta
_types
.nomadmetainfo.json"
,
"nomad_meta_info/meta.nomadmetainfo.json"
,
"nomad_meta_info/gpaw.nomadmetainfo.json"
)
++
lab
.
DefaultPythonInterpreter
.
commonFiles
(),
dirMap
=
Map
(
...
...
src/main/scala/eu/nomad_lab/parsers/GpawParser2.scala
View file @
00fb8efd
...
...
@@ -49,7 +49,7 @@ object GpawParser2 extends SimpleExternalParserGenerator(
"parser-gpaw/setup_paths.py"
,
"nomad_meta_info/public.nomadmetainfo.json"
,
"nomad_meta_info/common.nomadmetainfo.json"
,
"nomad_meta_info/meta
_types
.nomadmetainfo.json"
,
"nomad_meta_info/meta.nomadmetainfo.json"
,
"nomad_meta_info/gpaw.nomadmetainfo.json"
)
++
lab
.
DefaultPythonInterpreter
.
commonFiles
(),
dirMap
=
Map
(
...
...
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