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nomad-lab
parser-elk
Commits
d20ec712
Commit
d20ec712
authored
Oct 13, 2016
by
Pardini, Lorenzo (lopa)
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fixed bugs with atomic structure, total energy, xc functional
parent
4820d09d
Pipeline
#7795
passed with stage
in 12 minutes and 11 seconds
Changes
1
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1
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1 changed file
with
50 additions
and
47 deletions
+50
-47
parser/parser-elk/parser_elk.py
parser/parser-elk/parser_elk.py
+50
-47
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parser/parser-elk/parser_elk.py
View file @
d20ec712
...
...
@@ -30,6 +30,7 @@ class ElkContext(object):
cell
=
[[
latticeX
[
0
],
latticeY
[
0
],
latticeZ
[
0
]],
[
latticeX
[
1
],
latticeY
[
1
],
latticeZ
[
1
]],
[
latticeX
[
2
],
latticeY
[
2
],
latticeZ
[
2
]]]
# print ("celll= ", cell)
backend
.
addValue
(
"simulation_cell"
,
cell
)
def
onClose_x_elk_section_reciprocal_lattice_vectors
(
self
,
backend
,
gIndex
,
section
):
...
...
@@ -45,14 +46,14 @@ class ElkContext(object):
xcNr
=
section
[
"x_elk_xc_functional"
][
0
]
xc_internal_map
=
{
2
:
[
'LDA_C_PZ'
,
'LDA_X_PZ'
],
3
:
[
'LDA_C_PW'
],
3
:
[
'LDA_C_PW'
,
'LDA_X_PZ'
],
4
:
[
'LDA_C_XALPHA'
],
5
:
[
'LDA_C_VBH'
],
20
:
[
'GGA_C_PBE'
],
21
:
[
'GGA_X_PBE_R'
],
22
:
[
'GGA_C_PBE_SOL'
],
26
:
[
'GGA_X_WC'
],
30
:
[
'GGA_C_AM05'
]
20
:
[
'GGA_C_PBE'
,
'GGA_X_PBE'
],
21
:
[
'GGA_
C_PBE'
,
'GGA_
X_PBE_R'
],
22
:
[
'GGA_C_PBE_SOL'
,
'GGA_X_PBE_SOL'
],
26
:
[
'GGA_
C_PBE'
,
'GGA_
X_WC'
],
30
:
[
'GGA_C_AM05'
,
'GGA_X_AM05'
]
}
for
xcName
in
xc_internal_map
[
xcNr
]:
gi
=
backend
.
openSection
(
"section_XC_functionals"
)
...
...
@@ -87,26 +88,17 @@ class ElkContext(object):
eigvalKpoint
=
[]
eigvalVal
=
[]
eigvalOcc
=
[]
# eigvalVal=[[],[]]
# eigvalOcc=[[],[]]
fromH
=
unit_conversion
.
convert_unit_function
(
"hartree"
,
"J"
)
while
1
:
s
=
g
.
readline
()
if
not
s
:
break
s
=
s
.
strip
()
# print ("s= ", s)
# print ("len(s)= ", len(s))
if
len
(
s
)
<
20
:
continue
elif
len
(
s
)
>
50
:
eigvalVal
.
append
([])
eigvalOcc
.
append
([])
# eigvalVal[0].append([])
# eigvalVal[1].append([])
# eigvalOcc[0].append([])
# eigvalOcc[1].append([])
eigvalKpoint
.
append
(
list
(
map
(
float
,
s
.
split
()[
1
:
4
])))
# print ("eigvalKpoint= ", eigvalKpoint)
else
:
try
:
int
(
s
[
0
])
except
ValueError
:
...
...
@@ -115,17 +107,28 @@ class ElkContext(object):
n
,
e
,
occ
=
s
.
split
()
eigvalVal
[
-
1
].
append
(
fromH
(
float
(
e
)))
eigvalOcc
[
-
1
].
append
(
float
(
occ
))
# eigvalVal[0][-1].append(int(n))
# eigvalVal[1][-1].append(fromH(float(e)))
# eigvalOcc[0][-1].append(int(n))
# eigvalOcc[1][-1].append(float(occ))
# print ("eigvalOcc= ", eigvalOcc)
backend
.
addArrayValues
(
"eigenvalues_kpoints"
,
np
.
asarray
(
eigvalKpoint
))
backend
.
addArrayValues
(
"eigenvalues_values"
,
np
.
asarray
(
eigvalVal
))
backend
.
addArrayValues
(
"eigenvalues_occupation"
,
np
.
asarray
(
eigvalOcc
))
def
onClose_section_system
(
self
,
backend
,
gIndex
,
section
):
backend
.
addArrayValues
(
'configuration_periodic_dimensions'
,
np
.
asarray
([
True
,
True
,
True
]))
self
.
secSystemDescriptionIndex
=
gIndex
atom_pos
=
[]
for
i
in
[
'x'
,
'y'
,
'z'
]:
api
=
section
[
'x_elk_geometry_atom_positions_'
+
i
]
if
api
is
not
None
:
atom_pos
.
append
(
api
)
if
atom_pos
:
backend
.
addArrayValues
(
'atom_positions'
,
np
.
transpose
(
np
.
asarray
(
atom_pos
)))
atom_labels
=
section
[
'x_elk_geometry_atom_labels'
]
if
atom_labels
is
not
None
:
backend
.
addArrayValues
(
'atom_labels'
,
np
.
asarray
(
atom_labels
))
def
onClose_section_scf_iteration
(
self
,
backend
,
gIndex
,
section
):
Etot
=
section
[
"energy_total_scf_iteration"
]
backend
.
addValue
(
"energy_total"
,
Etot
)
# description of the input
mainFileDescription
=
\
...
...
@@ -222,33 +225,33 @@ mainFileDescription = \
SM
(
r"\s*core\s*:\s*(?P<x_elk_core_charge_scf_iteration>[-0-9.]+)"
),
SM
(
r"\s*valence\s*:\s*(?P<x_elk_valence_charge_scf_iteration>[-0-9.]+)"
),
SM
(
r"\s*interstitial\s*:\s*(?P<x_elk_interstitial_charge_scf_iteration>[-0-9.]+)"
),
]),
SM
(
name
=
"final_quantities"
,
startReStr
=
r"\sConvergence targets achieved\s*\+"
,
endReStr
=
r"\| Self-consistent loop stopped\s*\|\+"
,
subMatchers
=
[
SM
(
r"\s*Fermi\s*:\s*(?P<x_elk_fermi_energy__hartree>[-0-9.]+)"
),
SM
(
r"\s*sum of eigenvalues\s*:\s*(?P<energy_sum_eigenvalues__hartree>[-0-9.]+)"
),
SM
(
r"\s*electron kinetic\s*:\s*(?P<electronic_kinetic_energy__hartree>[-0-9.]+)"
),
SM
(
r"\s*core electron kinetic\s*:\s*(?P<x_elk_core_electron_kinetic_energy__hartree>[-0-9.]+)"
),
SM
(
r"\s*Coulomb\s*:\s*(?P<x_elk_coulomb_energy__hartree>[-0-9.]+)"
),
SM
(
r"\s*Coulomb potential\s*:\s*(?P<x_elk_coulomb_potential_energy__hartree>[-0-9.]+)"
),
SM
(
r"\s*nuclear-nuclear\s*:\s*(?P<x_elk_nuclear_nuclear_energy__hartree>[-0-9.]+)"
),
SM
(
r"\s*electron-nuclear\s*:\s*(?P<x_elk_electron_nuclear_energy__hartree>[-0-9.]+)"
),
SM
(
r"\s*Hartree\s*:\s*(?P<x_elk_hartree_energy__hartree>[-0-9.]+)"
),
SM
(
r"\s*Madelung\s*:\s*(?P<x_elk_madelung_energy__hartree>[-0-9.]+)"
),
SM
(
r"\s*xc potential\s*:\s*(?P<energy_XC_potential__hartree>[-0-9.]+)"
),
SM
(
r"\s*exchange\s*:\s*(?P<x_elk_exchange_energy__hartree>[-0-9.]+)"
),
SM
(
r"\s*correlation\s*:\s*(?P<x_elk_correlation_energy__hartree>[-0-9.]+)"
),
SM
(
r"\s*electron entropic\s*:\s*(?P<x_elk_electron_entropic_energy__hartree>[-0-9.]+)"
),
SM
(
r"\s*total energy\s*:\s*(?P<energy_total__hartree>[-0-9.]+)"
),
SM
(
r"\s*Density of states at Fermi energy\s*:\s*(?P<x_elk_dos_fermi__hartree_1>[-0-9.]+)"
),
SM
(
r"\s*Estimated indirect band gap\s*:\s*(?P<x_elk_indirect_gap__hartree>[-0-9.]+)"
),
SM
(
r"\s*Estimated direct band gap\s*:\s*(?P<x_elk_direct_gap__hartree>[-0-9.]+)"
),
SM
(
r"\s*core\s*:\s*(?P<x_elk_core_charge_final>[-0-9.]+)"
),
SM
(
r"\s*valence\s*:\s*(?P<x_elk_valence_charge_final>[-0-9.]+)"
),
SM
(
r"\s*interstitial\s*:\s*(?P<x_elk_interstitial_charge_final>[-0-9.]+)"
)
])
])
#
,
#
SM(name="final_quantities",
#
startReStr = r"\sConvergence targets achieved\s*\+",
#
endReStr = r"\| Self-consistent loop stopped\s*\|\+",
#
subMatchers = [
#
SM(r"\s*Fermi\s*:\s*(?P<x_elk_fermi_energy__hartree>[-0-9.]+)"),
#
SM(r"\s*sum of eigenvalues\s*:\s*(?P<energy_sum_eigenvalues__hartree>[-0-9.]+)"),
#
SM(r"\s*electron kinetic\s*:\s*(?P<electronic_kinetic_energy__hartree>[-0-9.]+)"),
#
SM(r"\s*core electron kinetic\s*:\s*(?P<x_elk_core_electron_kinetic_energy__hartree>[-0-9.]+)"),
#
SM(r"\s*Coulomb\s*:\s*(?P<x_elk_coulomb_energy__hartree>[-0-9.]+)"),
#
SM(r"\s*Coulomb potential\s*:\s*(?P<x_elk_coulomb_potential_energy__hartree>[-0-9.]+)"),
#
SM(r"\s*nuclear-nuclear\s*:\s*(?P<x_elk_nuclear_nuclear_energy__hartree>[-0-9.]+)"),
#
SM(r"\s*electron-nuclear\s*:\s*(?P<x_elk_electron_nuclear_energy__hartree>[-0-9.]+)"),
#
SM(r"\s*Hartree\s*:\s*(?P<x_elk_hartree_energy__hartree>[-0-9.]+)"),
#
SM(r"\s*Madelung\s*:\s*(?P<x_elk_madelung_energy__hartree>[-0-9.]+)"),
#
SM(r"\s*xc potential\s*:\s*(?P<energy_XC_potential__hartree>[-0-9.]+)"),
#
SM(r"\s*exchange\s*:\s*(?P<x_elk_exchange_energy__hartree>[-0-9.]+)"),
#
SM(r"\s*correlation\s*:\s*(?P<x_elk_correlation_energy__hartree>[-0-9.]+)"),
#
SM(r"\s*electron entropic\s*:\s*(?P<x_elk_electron_entropic_energy__hartree>[-0-9.]+)"),
#
SM(r"\s*total energy\s*:\s*(?P<energy_total__hartree>[-0-9.]+)"),
#
SM(r"\s*Density of states at Fermi energy\s*:\s*(?P<x_elk_dos_fermi__hartree_1>[-0-9.]+)"),
#
SM(r"\s*Estimated indirect band gap\s*:\s*(?P<x_elk_indirect_gap__hartree>[-0-9.]+)"),
#
SM(r"\s*Estimated direct band gap\s*:\s*(?P<x_elk_direct_gap__hartree>[-0-9.]+)"),
#
SM(r"\s*core\s*:\s*(?P<x_elk_core_charge_final>[-0-9.]+)"),
#
SM(r"\s*valence\s*:\s*(?P<x_elk_valence_charge_final>[-0-9.]+)"),
#
SM(r"\s*interstitial\s*:\s*(?P<x_elk_interstitial_charge_final>[-0-9.]+)")
#
])
]
)
])
...
...
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