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Commit 16705cce authored by Daniel Speckhard's avatar Daniel Speckhard
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Added elk, elastic parsers.

parent b36b8e87
Pipeline #45361 failed with stages
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.gitmodules
View file @ 16705cce
......@@ -82,3 +82,15 @@
[submodule "dependencies/parsers/atk"]
path = dependencies/parsers/atk
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-atk
[submodule "dependencies/parsers/gulp"]
path = dependencies/parsers/gulp
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-gulp
[submodule "dependencies/parsers/siesta"]
path = dependencies/parsers/siesta
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-siesta
[submodule "dependencies/parsers/elk"]
path = dependencies/parsers/elk
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-elk
[submodule "dependencies/parsers/elastic"]
path = dependencies/parsers/elastic
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-elastic
.vscode/launch.json
View file @ 16705cce
......@@ -197,6 +197,16 @@
"-sv", "tests/test_normalizing.py::test_normalizer[parsers/octopus-tests/data/parsers/octopus/stdout.txt]"
]
},
{
"name": "GULP Normalizer",
"type": "python",
"request": "launch",
"cwd": "${workspaceFolder}",
"program": "${workspaceFolder}/.pyenv/bin/pytest",
"args": [
"-sv", "tests/test_normalizing.py::test_normalizer[parsers/gulp-tests/data/parsers/gulp/example6.got]"
]
},
{
"name": "Python: Current File",
"type": "python",
......
nomad-meta-info @ 8c917126
Compare b232a5fd...8c917126
Subproject commit b232a5fdd11c344656ff1e6ec7a2ed6f787cf49f
Subproject commit 8c917126279cbbecb7adb7e30fc7d641d9a31a78
elastic @ 118e1383
Subproject commit 118e1383844c64d521a04be1c5bb26337af8c97f
elk @ c8966450
Subproject commit c89664504361ee2a06f0c9f2961f169af5dae43f
gulp @ ceb9a09e
Subproject commit ceb9a09e031016b0fc366667d79c9b44ea8a5c7f
siesta @ 63c52686
Subproject commit 63c5268677f9dfd6a75ee5a8816778975c97109f
nomad/files.py
View file @ 16705cce
......@@ -423,6 +423,7 @@ class StagingUploadFiles(UploadFiles):
target_dir = target_dir.join_dir(prefix, create=True)
ext = os.path.splitext(path)[1]
if force_archive or ext == '.zip':
print("Here's a zip!")
try:
with ZipFile(path) as zf:
zf.extractall(target_dir.os_path)
......
nomad/parsing/__init__.py
View file @ 16705cce
......@@ -316,7 +316,35 @@ parsers = [
mainfile_name_re=r'^.*\.nc',
# The previously used mime type r'application/x-netcdf' wasn't found by magic library.
mainfile_mime_re=r'application/octet-stream'
),
LegacyParser(
name='parsers/gulp',
parser_class_name='gulpparser.GULPParser',
mainfile_contents_re=(
r'\s*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*'
r'\*\*\*\*\*\*\*\*\*\*\*\*\*\s*'
r'\s*\*\s*GENERAL UTILITY LATTICE PROGRAM\s*\*\s*')
),
LegacyParser(
name='parsers/siesta',
parser_class_name='siestaparser.SiestaParser',
mainfile_contents_re=(
r'(Siesta Version: siesta-|SIESTA [0-9]\.[0-9]\.[0-9])')
),
LegacyParser(
name='parsers/elk',
parser_class_name='elkparser.ElkParser',
mainfile_contents_re=(
r'\s*\+-----------+\+\s*'
r'\s*\| Elk version (P?<version>[0-9.a-zA-Z]+) started \|\s*'
r'\s*\+----------+\+\s*')
),
LegacyParser(
name='parsers/elastic',
parser_class_name='elasticparser.ElasticParser',
mainfile_contents_re=r'\s*Order of elastic constants\s*=\s*[0-9]+\s*'
)
]
""" Instanciation and constructor based config of all parsers. """
......
tests/data/parsers/elk/Al/DTOTENERGY.OUT 0 → 100644
View file @ 16705cce
0.1198769544E-02
0.2799643479E-02
0.1175652643E-01
0.2392171444E-01
0.3584530053E-01
0.4335915746E-01
0.4394082265E-01
0.3804421405E-01
0.2847828394E-01
0.1859043836E-01
0.1066293543E-01
0.5410512229E-02
0.2441357323E-02
0.9817180543E-03
0.3518649715E-03
0.1126689946E-03
0.3257301847E-04
tests/data/parsers/elk/Al/EIGVAL.OUT 0 → 100644
View file @ 16705cce
10 : nkpt
9 : nstsv
1 0.1250000000 0.1250000000 0.1250000000 : k-point, vkl
(state, eigenvalue and occupancy below)
1 -2.122364679 2.000000000
2 -2.122259438 2.000000000
3 -2.122259438 2.000000000
4 -0.1286748619 2.000000000
5 0.5745589210 0.000000000
6 0.7051658566 0.000000000
7 0.7051658566 0.000000000
8 0.8151136384 0.000000000
9 0.8605767411 0.000000000
2 0.3750000000 0.1250000000 0.1250000000 : k-point, vkl
(state, eigenvalue and occupancy below)
1 -2.122741574 2.000000000
2 -2.122411847 2.000000000
3 -2.122334851 2.000000000
4 -0.4678368645E-01 2.000000000
5 0.3448210862 0.000000000
6 0.5063335941 0.000000000
7 0.6997894076 0.000000000
8 0.7856802707 0.000000000
9 0.8006252452 0.000000000
3 0.6250000000 0.1250000000 0.1250000000 : k-point, vkl
(state, eigenvalue and occupancy below)
1 -2.122993479 2.000000000
2 -2.122438302 2.000000000
3 -2.122380402 2.000000000
4 0.7353923216E-01 2.000000000
5 0.1525458423 2.000000000
6 0.5441924906 0.000000000
7 0.5896331272 0.000000000
8 0.6650293833 0.000000000
9 0.8356862943 0.000000000
4 0.8750000000 0.1250000000 0.1250000000 : k-point, vkl
(state, eigenvalue and occupancy below)
1 -2.122581428 2.000000000
2 -2.122336125 2.000000000
3 -2.122330979 2.000000000
4 -0.8756585904E-01 2.000000000
5 0.4593570587 0.000000000
6 0.5896431645 0.000000000
7 0.6561578100 0.000000000
8 0.6997691538 0.000000000
9 0.7958323137 0.000000000
5 0.3750000000 0.3750000000 0.1250000000 : k-point, vkl
(state, eigenvalue and occupancy below)
1 -2.122790135 2.000000000
2 -2.122463957 2.000000000
3 -2.122434744 2.000000000
4 -0.6380235792E-02 2.000000000
5 0.3817063939 0.000000000
6 0.4690786282 0.000000000
7 0.5148235813 0.000000000
8 0.5802200862 0.000000000
9 0.7261290494 0.000000000
6 0.6250000000 0.3750000000 0.1250000000 : k-point, vkl
(state, eigenvalue and occupancy below)
1 -2.122869897 2.000000000
2 -2.122682147 2.000000000
3 -2.122510464 2.000000000
4 0.1507310056 2.000000000
5 0.2285441300 2.000000000
6 0.3154891470 0.2728059484E-20
7 0.3936611581 0.000000000
8 0.7117965260 0.000000000
9 0.8710552053 0.000000000
7 0.8750000000 0.3750000000 0.1250000000 : k-point, vkl
(state, eigenvalue and occupancy below)
1 -2.122864752 2.000000000
2 -2.122537526 2.000000000
3 -2.122409389 2.000000000
4 0.3373996622E-01 2.000000000
5 0.2674457264 0.9997884984
6 0.4306935410 0.000000000
7 0.5070639965 0.000000000
8 0.7471363675 0.000000000
9 0.8351001601 0.000000000
8 0.6250000000 0.6250000000 0.1250000000 : k-point, vkl
(state, eigenvalue and occupancy below)
1 -2.122963098 2.000000000
2 -2.122576667 2.000000000
3 -2.122517646 2.000000000
4 0.1117263429 2.000000000
5 0.2759063707 0.4230028254E-03
6 0.3436488571 0.000000000
7 0.4781416554 0.000000000
8 0.5396484561 0.000000000
9 0.6904329374 0.000000000
9 0.3750000000 0.3750000000 0.3750000000 : k-point, vkl
(state, eigenvalue and occupancy below)
1 -2.122916936 2.000000000
2 -2.122351729 2.000000000
3 -2.122351729 2.000000000
4 -0.6328542043E-02 2.000000000
5 0.2305217279 2.000000000
6 0.6637824424 0.000000000
7 0.6637824424 0.000000000
8 0.7556756622 0.000000000
9 0.7556756622 0.000000000
10 0.6250000000 0.3750000000 0.3750000000 : k-point, vkl
(state, eigenvalue and occupancy below)
1 -2.122892972 2.000000000
2 -2.122646630 2.000000000
3 -2.122429945 2.000000000
4 0.1129446001 2.000000000
5 0.1900341612 2.000000000
6 0.3547527304 0.000000000
7 0.5520317928 0.000000000
8 0.6304422575 0.000000000
9 0.9658781777 0.000000000
tests/data/parsers/elk/Al/EQATOMS.OUT 0 → 100644
View file @ 16705cce
Species : 1 (Al)
atom 1 is equivalent to atom(s)
1
tests/data/parsers/elk/Al/EVALCORE.OUT 0 → 100644
View file @ 16705cce
Species : 1 (Al), atom : 1
n = 1, l = 0, k = 1 : -54.83607356
n = 2, l = 0, k = 1 : -3.511752279
tests/data/parsers/elk/Al/FERMIDOS.OUT 0 → 100644
View file @ 16705cce
93.79381046
93.79313701
93.79231979
93.79151253
93.79083328
93.79033045
93.78999830
93.78980281
93.78970213
93.78965849
93.78964396
93.78964136
93.78964213
93.78964311
93.78964363
93.78964384
93.78964390
93.78964393
93.78964393
tests/data/parsers/elk/Al/GAP.OUT 0 → 100644
View file @ 16705cce
0.367907732220E-01
0.368044960624E-01
0.368228800917E-01
0.368434558093E-01
0.368638235136E-01
0.368819830650E-01
0.368966956680E-01
0.369075704624E-01
0.369149057106E-01
0.369194078453E-01
0.369219071736E-01
0.369231504502E-01
0.369236975143E-01
0.369239069369E-01
0.369239752487E-01
0.369239937401E-01
0.369239977553E-01
0.369239984296E-01
0.369239985193E-01
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