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nomad-lab
parser-cp2k
Commits
73e24472
Commit
73e24472
authored
Jun 20, 2016
by
Lauri Himanen
Browse files
Fixed an issue with simulation cell parsing, added cell files to unittests.
parent
a2b5aed6
Changes
7
Hide whitespace changes
Inline
Side-by-side
.gitignore
View file @
73e24472
...
...
@@ -56,7 +56,6 @@ env/
# CP2K files
test/**/*.wfn
test/**/*.cube
test/**/*.cell
test/**/*.restart
test/**/*.restart.bak-1
test/**/*.restart.bak-2
...
...
parser/parser-cp2k/cp2kparser/versions/cp2k262/commonmatcher.py
View file @
73e24472
...
...
@@ -402,7 +402,7 @@ class CommonMatcher(object):
"""
self
.
section_system_index
=
gIndex
self
.
cache_service
.
push_value
(
"number_of_atoms"
)
self
.
cache_service
.
push_array_values
(
"simulation_cell"
,
unit
=
"angstrom"
)
#
self.cache_service.push_array_values("simulation_cell", unit="angstrom")
self
.
cache_service
.
push_array_values
(
"configuration_periodic_dimensions"
)
self
.
cache_service
.
push_array_values
(
"atom_labels"
)
...
...
parser/parser-cp2k/cp2kparser/versions/cp2k262/geooptparser.py
View file @
73e24472
...
...
@@ -245,6 +245,9 @@ class CP2KGeoOptParser(MainHierarchicalParser):
if
energy
is
not
None
:
self
.
cache_service
[
"frame_sequence_potential_energy"
].
append
(
energy
[
0
])
def
onClose_section_system
(
self
,
backend
,
gIndex
,
section
):
self
.
cache_service
.
push_array_values
(
"simulation_cell"
,
unit
=
"angstrom"
)
def
onClose_section_method
(
self
,
backend
,
gIndex
,
section
):
traj_file
=
self
.
file_service
.
get_file_by_id
(
"trajectory"
)
traj_format
=
self
.
cache_service
[
"trajectory_format"
]
...
...
parser/parser-cp2k/cp2kparser/versions/cp2k262/mdparser.py
View file @
73e24472
...
...
@@ -33,6 +33,7 @@ class CP2KMDParser(MainHierarchicalParser):
self
.
energy_freq
=
None
self
.
cell_freq
=
None
self
.
md_quicksteps
=
[]
self
.
ensemble
=
None
#=======================================================================
# Globally cached values
...
...
@@ -156,6 +157,7 @@ class CP2KMDParser(MainHierarchicalParser):
}
sampling
=
sampling_map
.
get
(
sampling
)
if
sampling
is
not
None
:
self
.
ensemble
=
sampling
backend
.
addValue
(
"ensemble_type"
,
sampling
)
# Sampling type
...
...
@@ -274,6 +276,11 @@ class CP2KMDParser(MainHierarchicalParser):
systemGID
=
backend
.
openSection
(
"section_system"
)
single_conf_gids
.
append
(
sectionGID
)
# If NPT is run, and the cell file is not available, output the
# simulation cel only on the first step to section_system
if
i_step
==
0
and
self
.
ensemble
==
"NPT"
and
self
.
cell_iterator
is
None
:
self
.
cache_service
.
push_array_values
(
"simulation_cell"
,
unit
=
"angstrom"
)
# Trajectory
if
freqs
[
"trajectory"
][
1
]
and
self
.
traj_iterator
is
not
None
:
if
(
i_step
+
1
)
%
freqs
[
"trajectory"
][
0
]
==
0
or
(
i_step
==
last_step
and
add_last_traj
):
...
...
@@ -320,7 +327,8 @@ class CP2KMDParser(MainHierarchicalParser):
if
(
i_step
+
1
)
%
freqs
[
"cell"
][
0
]
==
0
:
line
=
next
(
self
.
cell_iterator
)
cell
=
np
.
reshape
(
line
,
(
3
,
3
))
self
.
cache_service
[
"simulation_cell"
]
=
cell
self
.
backend
.
addArrayValues
(
"simulation_cell"
,
cell
,
unit
=
"angstrom"
)
# self.cache_service["simulation_cell"] = cell
# Output file
if
md_steps
:
...
...
parser/parser-cp2k/cp2kparser/versions/cp2k262/singlepointparser.py
View file @
73e24472
...
...
@@ -91,6 +91,7 @@ class CP2KSinglePointParser(MainHierarchicalParser):
let's get it dynamically just in case there's something wrong.
"""
self
.
cache_service
.
push_array_values
(
"atom_positions"
,
unit
=
"angstrom"
)
self
.
cache_service
.
push_array_values
(
"simulation_cell"
,
unit
=
"angstrom"
)
#===========================================================================
# adHoc functions
test/unittests/cp2k_2.6.2/md/npt/H2O-md-1.cell
0 → 100644
View file @
73e24472
# Step Time [fs] Ax [Angstrom] Ay [Angstrom] Az [Angstrom] Bx [Angstrom] By [Angstrom] Bz [Angstrom] Cx [Angstrom] Cy [Angstrom] Cz [Angstrom] Volume [Angstrom^3]
0 0.000 6.0000000000 0.0000000000 0.0000000000 0.0000000000 6.0000000000 0.0000000000 0.0000000000 0.0000000000 6.0000000000 216.0000000000
1 0.500 5.9995865891 -0.0006884817 -0.0010127508 -0.0006884817 6.0022063627 -0.0015429583 -0.0010127508 -0.0015429583 6.0008306670 216.0944304520
2 1.000 5.9991635661 -0.0013715242 -0.0020124634 -0.0013715223 6.0044280501 -0.0030858637 -0.0020124619 -0.0030858693 6.0016525349 216.1887100692
3 1.500 5.9987354326 -0.0020507044 -0.0030038816 -0.0020506975 6.0066631407 -0.0046293928 -0.0030038779 -0.0046294135 6.0024678974 216.2830142465
4 2.000 5.9983081311 -0.0027276709 -0.0039930111 -0.0027276548 6.0089096419 -0.0061742363 -0.0039930078 -0.0061742825 6.0032801692 216.3776082058
5 2.500 5.9978882711 -0.0034040416 -0.0049866158 -0.0034040111 6.0111656733 -0.0077211182 -0.0049866223 -0.0077211991 6.0040935434 216.4728134845
6 3.000 5.9974821459 -0.0040812622 -0.0059914363 -0.0040812103 6.0134296600 -0.0092707652 -0.0059914716 -0.0092708864 6.0049124772 216.5689609536
7 3.500 5.9970947973 -0.0047604264 -0.0070132193 -0.0047603435 6.0157005634 -0.0108238027 -0.0070133129 -0.0108239647 6.0057410535 216.6663424164
8 4.000 5.9967291987 -0.0054420965 -0.0080557344 -0.0054419694 6.0179781365 -0.0123805881 -0.0080559250 -0.0123807875 6.0065823171 216.7651664221
9 4.500 5.9963856760 -0.0061261768 -0.0091200506 -0.0061259871 6.0202631442 -0.0139410237 -0.0091203831 -0.0139412562 6.0074377769 216.8655273092
10 5.000 5.9960617905 -0.0068118798 -0.0102043036 -0.0068116027 6.0225574669 -0.0155044063 -0.0102048226 -0.0155046726 6.0083072343 216.9673985082
test/unittests/cp2k_2.6.2/md/nve/H2O-32-1.cell
0 → 100644
View file @
73e24472
# Step Time [fs] Ax [Angstrom] Ay [Angstrom] Az [Angstrom] Bx [Angstrom] By [Angstrom] Bz [Angstrom] Cx [Angstrom] Cy [Angstrom] Cz [Angstrom] Volume [Angstrom^3]
0 0.000 9.8528000000 0.0000000000 0.0000000000 0.0000000000 9.8528000000 0.0000000000 0.0000000000 0.0000000000 9.8528000000 956.4868456940
1 0.500 9.8528000000 0.0000000000 0.0000000000 0.0000000000 9.8528000000 0.0000000000 0.0000000000 0.0000000000 9.8528000000 956.4868456940
2 1.000 9.8528000000 0.0000000000 0.0000000000 0.0000000000 9.8528000000 0.0000000000 0.0000000000 0.0000000000 9.8528000000 956.4868456940
3 1.500 9.8528000000 0.0000000000 0.0000000000 0.0000000000 9.8528000000 0.0000000000 0.0000000000 0.0000000000 9.8528000000 956.4868456940
4 2.000 9.8528000000 0.0000000000 0.0000000000 0.0000000000 9.8528000000 0.0000000000 0.0000000000 0.0000000000 9.8528000000 956.4868456940
5 2.500 9.8528000000 0.0000000000 0.0000000000 0.0000000000 9.8528000000 0.0000000000 0.0000000000 0.0000000000 9.8528000000 956.4868456940
6 3.000 9.8528000000 0.0000000000 0.0000000000 0.0000000000 9.8528000000 0.0000000000 0.0000000000 0.0000000000 9.8528000000 956.4868456940
7 3.500 9.8528000000 0.0000000000 0.0000000000 0.0000000000 9.8528000000 0.0000000000 0.0000000000 0.0000000000 9.8528000000 956.4868456940
8 4.000 9.8528000000 0.0000000000 0.0000000000 0.0000000000 9.8528000000 0.0000000000 0.0000000000 0.0000000000 9.8528000000 956.4868456940
9 4.500 9.8528000000 0.0000000000 0.0000000000 0.0000000000 9.8528000000 0.0000000000 0.0000000000 0.0000000000 9.8528000000 956.4868456940
10 5.000 9.8528000000 0.0000000000 0.0000000000 0.0000000000 9.8528000000 0.0000000000 0.0000000000 0.0000000000 9.8528000000 956.4868456940
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