Commit b36e0286 authored by speckhard's avatar speckhard
Browse files

Adding wien2k parser into nomad-faird.

parent 494767b0
......@@ -57,6 +57,17 @@
"-sv", "tests/test_normalizing.py::test_normalizer[parsers/crystal-tests/data/parsers/crystal/si.out]"
]
},
{
"name": "Python: wien2k normalizer test",
"type": "python",
"request": "launch",
"cwd": "${workspaceFolder}",
"program": "${workspaceFolder}/.pyenv/bin/pytest",
"args": [
"-sv", "tests/test_normalizing.py::test_normalizer[parsers/wien2k-tests/data/parsers/wien2k/ok/ok.scf]"
]
},
{
"name": "Python: nwchem normalizer test h2o sp test",
"type": "python",
......
......@@ -208,7 +208,11 @@ dependencies = [
PythonGit(
name='parsers/bigdft',
git_url='https://gitlab.mpcdf.mpg.de/nomad-lab/parser-big-dft',
git_branch='nomad-fair')
git_branch='nomad-fair'),
PythonGit(
name='parsers/wien2k',
git_url='https://gitlab.mpcdf.mpg.de/nomad-lab/parser-wien2k',
git_branch='master')
]
......
......@@ -108,7 +108,7 @@ parsers = [
LegacyParser(
python_git=dependencies['parsers/crystal'],
parser_class_name='crystalparser.CrystalParser',
main_file_re=r'^.*\.out$', # This looks for files with .out
main_file_re=r'^.*\.out$',
main_contents_re=(
r'\s*[\*]{22,}' # Looks for '*' 22 times or more in a row.
r'\s*\*\s{20,}\*' # Looks for a '*' sandwhiched by whitespace.
......@@ -119,7 +119,7 @@ parsers = [
LegacyParser(
python_git=dependencies['parsers/cpmd'],
parser_class_name='cpmdparser.CPMDParser',
main_file_re=r'^.*\.out$', # This looks for files with .out
main_file_re=r'^.*\.out$',
main_contents_re=(
r'\s* \*\*\*\*\*\* \*\*\*\*\*\* \*\*\*\* \*\*\*\* \*\*\*\*\*\*\s*'
r'\s* \*\*\*\*\*\*\* \*\*\*\*\*\*\* \*\*\*\*\*\*\*\*\*\* \*\*\*\*\*\*\*\s*'
......@@ -134,7 +134,7 @@ parsers = [
LegacyParser(
python_git=dependencies['parsers/nwchem'],
parser_class_name='nwchemparser.NWChemParser',
main_file_re=r'^.*\.out$', # This looks for files with .out
main_file_re=r'^.*\.out$',
main_contents_re=(
r' Northwest Computational Chemistry Package \(NWChem\) \d+\.\d+'
r' ------------------------------------------------------'
......@@ -146,7 +146,7 @@ parsers = [
LegacyParser(
python_git=dependencies['parsers/bigdft'],
parser_class_name='bigdftparser.BigDFTParser',
main_file_re=r'^.*\.out$', # This looks for files with .out
main_file_re=r'^.*\.out$',
main_contents_re=(
r'__________________________________ A fast and precise DFT wavelet code\s*'
r'\| \| \| \| \| \|\s*'
......@@ -174,8 +174,15 @@ parsers = [
r'\| \| \| \| \| \| DDDDDD F TTTT\s*'
r'\|_____\|_____\|_____\|_____\|_____\|______ www\.bigdft\.org'
)
),
LegacyParser(
python_git=dependencies['parsers/wien2k'],
parser_class_name='wien2kparser.Wien2kParser',
main_file_re=r'^.*\.scf$', # This looks for files with .scf
main_contents_re=r':ITE[0-9]+: 1. ITERATION'
)
]
""" Instanciation and constructor based config of all parsers. """
parser_dict = {parser.name: parser for parser in parsers} # type: ignore
......
TOT 19 (5:LDA, 13:PBE, 11:WC, 19:PBEsol, 28:mBJ, 29:revTPSS, 46:HTBS)
NR2V IFFT (R2V)
120 120 200 2.00 1 min IFFT-parameters, enhancement factor, iprint
WFFIL EF=-.204956810975 (WFFIL, WFPRI, ENFIL, SUPWF)
7.00 10 4 (R-MT*K-MAX; MAX L IN WF, V-NMT
-.4050839945 2 0 global e-param with N other choices, napw
0 -1.175 0.000 CONT 1
1 -0.643 0.000 CONT 1
-.4050839945 2 0 global e-param with N other choices, napw
0 -1.280 0.000 CONT 1
1 -0.736 0.000 CONT 1
-.4050839945 2 0 global e-param with N other choices, napw
0 -1.275 0.000 CONT 1
1 -0.729 0.000 CONT 1
-.4050839945 2 0 global e-param with N other choices, napw
0 -1.272 0.000 CONT 1
1 -0.724 0.000 CONT 1
-.4050839945 2 0 global e-param with N other choices, napw
0 -1.271 0.000 CONT 1
1 -0.722 0.000 CONT 1
-.4050839945 2 0 global e-param with N other choices, napw
0 -1.266 0.000 CONT 1
1 -0.713 0.000 CONT 1
-.4050839945 2 0 global e-param with N other choices, napw
0 -1.276 0.000 CONT 1
1 -0.728 0.000 CONT 1
-.4050839945 2 0 global e-param with N other choices, napw
0 -1.266 0.000 CONT 1
1 -0.718 0.000 CONT 1
-.4050839945 2 0 global e-param with N other choices, napw
0 -1.271 0.000 CONT 1
1 -0.722 0.000 CONT 1
-.4050839945 2 0 global e-param with N other choices, napw
0 -1.271 0.000 CONT 1
1 -0.722 0.000 CONT 1
-.4050839945 2 0 global e-param with N other choices, napw
0 -1.263 0.000 CONT 1
1 -0.716 0.000 CONT 1
-.4050839945 2 0 global e-param with N other choices, napw
0 -1.266 0.000 CONT 1
1 -0.715 0.000 CONT 1
-.4050839945 2 0 global e-param with N other choices, napw
0 -1.259 0.000 CONT 1
1 -0.706 0.000 CONT 1
K-VECTORS FROM UNIT:4 -9.0 2.5 198 red emin/emax/nband
TOT (TOT,FOR,QTL,EFG,FERMI)
-12.0 196.0 0.50 0.05 EMIN, NE, ESEPERMIN, ESEPER0
TETRA 0.000 (GAUSS,ROOT,TEMP,TETRA,ALL eval)
0 0 1 0 2 0 2 2 3 0 3 2 4 0 4 2 4 4 5 0 5 2 5 4 6 0 6 2 6 4 6 6
0 0 1 1 -1 1 2 0 2 2 -2 2 3 1 -3 1 3 3 -3 3 4 0 4 2 -4 2 4 4 -4 4 5 1 -5 1 5 3 -5 3 5 5 -5 5 6 0 6 2 -6 2 6 4 -6 4 6 6 -6 6
0 0 1 1 -1 1 2 0 2 2 -2 2 3 1 -3 1 3 3 -3 3 4 0 4 2 -4 2 4 4 -4 4 5 1 -5 1 5 3 -5 3 5 5 -5 5 6 0 6 2 -6 2 6 4 -6 4 6 6 -6 6
0 0 1 1 -1 1 2 0 2 2 -2 2 3 1 -3 1 3 3 -3 3 4 0 4 2 -4 2 4 4 -4 4 5 1 -5 1 5 3 -5 3 5 5 -5 5 6 0 6 2 -6 2 6 4 -6 4 6 6 -6 6
0 0 1 0 2 0 2 2 3 0 3 2 4 0 4 2 4 4 5 0 5 2 5 4 6 0 6 2 6 4 6 6
0 0 1 0 2 0 2 2 3 0 3 2 4 0 4 2 4 4 5 0 5 2 5 4 6 0 6 2 6 4 6 6
0 0 1 0 2 0 2 2 3 0 3 2 4 0 4 2 4 4 5 0 5 2 5 4 6 0 6 2 6 4 6 6
0 0 1 0 2 0 2 2 3 0 3 2 4 0 4 2 4 4 5 0 5 2 5 4 6 0 6 2 6 4 6 6
0 0 1 0 2 0 2 2 3 0 3 2 4 0 4 2 4 4 5 0 5 2 5 4 6 0 6 2 6 4 6 6
0 0 1 0 2 0 2 2 3 0 3 2 4 0 4 2 4 4 5 0 5 2 5 4 6 0 6 2 6 4 6 6
0 0 1 0 2 0 2 2 3 0 3 2 4 0 4 2 4 4 5 0 5 2 5 4 6 0 6 2 6 4 6 6
0 0 1 1 -1 1 2 0 2 2 -2 2 3 1 -3 1 3 3 -3 3 4 0 4 2 -4 2 4 4 -4 4 5 1 -5 1 5 3 -5 3 5 5 -5 5 6 0 6 2 -6 2 6 4 -6 4 6 6 -6 6
0 0 2 0 3 3 4 0 5 3 6 0 6 6
16.00 GMAX
NOFILE FILE/NOFILE write recprlist
Graphite C K edge of first atom.
ELNES # We broaden case.elnes .
1 1 0 # We use spectrum 1 out of 1
0.000000000 1.000000000 0.000000000 # split energy, weights of spectra
0.8676271836E-01 0.8676271836E-01 # core hole lifetime of two edges
1 0.000000000 # select linearly energy dependent valence broadening; edge offset
0.5000000000 # default spectrometer broadening - Gaussian FWHM
1 0.00 0 NUMBER OF ORBITALS (EXCLUDING SPIN), SHIFT, IPRINT
1,-1,2 ( N,KAPPA,OCCUP)
1 0.00 0 NUMBER OF ORBITALS (EXCLUDING SPIN), SHIFT, IPRINT
1,-1,2 ( N,KAPPA,OCCUP)
1 0.00 0 NUMBER OF ORBITALS (EXCLUDING SPIN), SHIFT, IPRINT
1,-1,2 ( N,KAPPA,OCCUP)
1 0.00 0 NUMBER OF ORBITALS (EXCLUDING SPIN), SHIFT, IPRINT
1,-1,2 ( N,KAPPA,OCCUP)
1 0.00 0 NUMBER OF ORBITALS (EXCLUDING SPIN), SHIFT, IPRINT
1,-1,2 ( N,KAPPA,OCCUP)
1 0.00 0 NUMBER OF ORBITALS (EXCLUDING SPIN), SHIFT, IPRINT
1,-1,2 ( N,KAPPA,OCCUP)
1 0.00 0 NUMBER OF ORBITALS (EXCLUDING SPIN), SHIFT, IPRINT
1,-1,2 ( N,KAPPA,OCCUP)
1 0.00 0 NUMBER OF ORBITALS (EXCLUDING SPIN), SHIFT, IPRINT
1,-1,2 ( N,KAPPA,OCCUP)
1 0.00 0 NUMBER OF ORBITALS (EXCLUDING SPIN), SHIFT, IPRINT
1,-1,2 ( N,KAPPA,OCCUP)
1 0.00 0 NUMBER OF ORBITALS (EXCLUDING SPIN), SHIFT, IPRINT
1,-1,2 ( N,KAPPA,OCCUP)
1 0.00 0 NUMBER OF ORBITALS (EXCLUDING SPIN), SHIFT, IPRINT
1,-1,2 ( N,KAPPA,OCCUP)
1 0.00 0 NUMBER OF ORBITALS (EXCLUDING SPIN), SHIFT, IPRINT
1,-1,2 ( N,KAPPA,OCCUP)
1 0.00 0 NUMBER OF ORBITALS (EXCLUDING SPIN), SHIFT, IPRINT
1,-1,2 ( N,KAPPA,OCCUP)
0
MSR1 0.0 YES (BROYD/PRATT, extra charge (+1 for additional e), norm)
0.20 mixing FACTOR for BROYD/PRATT scheme
1.00 1.00 PW and CLM-scaling factors
9999 8 idum, HISTORY
-.23076923076923076923 3.73846153846153846153
1
13 99 1 0
4 0 1 2 3
Title
-0.50 0.002 3.500 0.003 # EMIN, DE, EMAX, Gauss-broadening(>de)
13 N 0.000 # NUMBER OF DOS-CASES specified below, G/L/B broadening (Ry)
1 3 At1P # atom, case=column in qtl-header, labe
2 3 At2P
3 3 At3P
4 3 At4P
5 3 At5P
6 3 At6P
7 3 At7P
8 3 At8P
9 3 At9P
10 3 At10P
11 3 At11P
12 3 At12P
13 3 At13P
This diff is collapsed.
graphene
H LATTICE,NONEQUIV.ATOMS: 13 187 P-6m2
RELA
23.239030 23.239030 37.794538 90.000000 90.000000120.000000
ATOM -1: X=0.59987104 Y=0.40012896 Z=0.00000000
MULT= 3 ISPLIT= 8
-1: X=0.59987104 Y=0.19974208 Z=0.00000000
-1: X=0.80025792 Y=0.40012896 Z=0.00000000
C 1 NPT= 781 R0=0.00010000 RMT= 1.32 Z: 6.
LOCAL ROT MATRIX: 0.0000000 0.8660254 0.5000000
0.0000000 0.5000000-0.8660254
-1.0000000 0.0000000 0.0000000
ATOM -2: X=0.86544201 Y=0.33289950 Z=0.00000000
MULT= 6 ISPLIT= 8
-2: X=0.66710050 Y=0.53254251 Z=0.00000000
-2: X=0.46745749 Y=0.13455799 Z=0.00000000
-2: X=0.66710050 Y=0.13455799 Z=0.00000000
-2: X=0.46745749 Y=0.33289950 Z=0.00000000
-2: X=0.86544201 Y=0.53254251 Z=0.00000000
C 2 NPT= 781 R0=0.00010000 RMT= 1.32 Z: 6.
LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
0.0000000 1.0000000 0.0000000
0.0000000 0.0000000 1.0000000
ATOM -3: X=0.00020325 Y=0.40034148 Z=0.00000000
MULT= 6 ISPLIT= 8
-3: X=0.59965852 Y=0.59986177 Z=0.00000000
-3: X=0.40013823 Y=0.99979675 Z=0.00000000
-3: X=0.59965852 Y=0.99979675 Z=0.00000000
-3: X=0.40013823 Y=0.40034148 Z=0.00000000
-3: X=0.00020325 Y=0.59986177 Z=0.00000000
C 3 NPT= 781 R0=0.00010000 RMT= 1.32 Z: 6.
LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
0.0000000 1.0000000 0.0000000
0.0000000 0.0000000 1.0000000
ATOM -4: X=0.06654808 Y=0.33316015 Z=0.00000000
MULT= 6 ISPLIT= 8
-4: X=0.66683985 Y=0.73338793 Z=0.00000000
-4: X=0.26661207 Y=0.93345192 Z=0.00000000
-4: X=0.66683985 Y=0.93345192 Z=0.00000000
-4: X=0.26661207 Y=0.33316015 Z=0.00000000
-4: X=0.06654808 Y=0.73338793 Z=0.00000000
C 4 NPT= 781 R0=0.00010000 RMT= 1.32 Z: 6.
LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
0.0000000 1.0000000 0.0000000
0.0000000 0.0000000 1.0000000
ATOM -5: X=0.20002391 Y=0.40004782 Z=0.00000000
MULT= 3 ISPLIT= 8
-5: X=0.59995218 Y=0.79997609 Z=0.00000000
-5: X=0.20002391 Y=0.79997609 Z=0.00000000
C 5 NPT= 781 R0=0.00010000 RMT= 1.32 Z: 6.
LOCAL ROT MATRIX: 0.0000000 0.8660254 0.5000000
0.0000000-0.5000000 0.8660254
1.0000000 0.0000000 0.0000000
ATOM -6: X=0.80016271 Y=0.60032543 Z=0.00000000
MULT= 3 ISPLIT= 8
-6: X=0.39967457 Y=0.19983728 Z=0.00000000
-6: X=0.80016272 Y=0.19983729 Z=0.00000000
C 6 NPT= 781 R0=0.00010000 RMT= 1.32 Z: 6.
LOCAL ROT MATRIX: 0.0000000 0.8660254 0.5000000
0.0000000-0.5000000 0.8660254
1.0000000 0.0000000 0.0000000
ATOM -7: X=0.06661061 Y=0.53330531 Z=0.00000000
MULT= 3 ISPLIT= 8
-7: X=0.46669469 Y=0.53330530 Z=0.00000000
-7: X=0.46669470 Y=0.93338939 Z=0.00000000
C 7 NPT= 781 R0=0.00010000 RMT= 1.32 Z: 6.
LOCAL ROT MATRIX: 0.0000000 0.0000000 1.0000000
0.0000000 1.0000000 0.0000000
-1.0000000 0.0000000 0.0000000
ATOM -8: X=0.86659078 Y=0.73318156 Z=0.00000000
MULT= 3 ISPLIT= 8
-8: X=0.26681844 Y=0.13340922 Z=0.00000000
-8: X=0.86659078 Y=0.13340922 Z=0.00000000
C 8 NPT= 781 R0=0.00010000 RMT= 1.32 Z: 6.
LOCAL ROT MATRIX: 0.0000000 0.8660254 0.5000000
0.0000000-0.5000000 0.8660254
1.0000000 0.0000000 0.0000000
ATOM -9: X=0.20003553 Y=0.60001777 Z=0.00000000
MULT= 3 ISPLIT= 8
-9: X=0.39998223 Y=0.60001776 Z=0.00000000
-9: X=0.39998224 Y=0.79996447 Z=0.00000000
C 9 NPT= 781 R0=0.00010000 RMT= 1.32 Z: 6.
LOCAL ROT MATRIX: 0.0000000 0.0000000 1.0000000
0.0000000 1.0000000 0.0000000
-1.0000000 0.0000000 0.0000000
ATOM -10: X=0.26666892 Y=0.53333785 Z=0.00000000
MULT= 3 ISPLIT= 8
-10: X=0.46666215 Y=0.73333107 Z=0.00000000
-10: X=0.26666893 Y=0.73333108 Z=0.00000000
C 10 NPT= 781 R0=0.00010000 RMT= 1.32 Z: 6.
LOCAL ROT MATRIX: 0.0000000 0.8660254 0.5000000
0.0000000-0.5000000 0.8660254
1.0000000 0.0000000 0.0000000
ATOM -11: X=0.86666941 Y=0.93333471 Z=0.00000000
MULT= 3 ISPLIT= 8
-11: X=0.06666529 Y=0.93333470 Z=0.00000000
-11: X=0.06666530 Y=0.13333059 Z=0.00000000
C 11 NPT= 781 R0=0.00010000 RMT= 1.32 Z: 6.
LOCAL ROT MATRIX: 0.0000000 0.0000000 1.0000000
0.0000000 1.0000000 0.0000000
-1.0000000 0.0000000 0.0000000
ATOM -12: X=0.79998126 Y=0.80006772 Z=0.00000000
MULT= 6 ISPLIT= 8
-12: X=0.19993228 Y=0.99991354 Z=0.00000000
-12: X=0.00008646 Y=0.20001874 Z=0.00000000
-12: X=0.19993228 Y=0.20001874 Z=0.00000000
-12: X=0.00008646 Y=0.80006772 Z=0.00000000
-12: X=0.79998126 Y=0.99991354 Z=0.00000000
C 12 NPT= 781 R0=0.00010000 RMT= 1.32 Z: 6.
LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
0.0000000 1.0000000 0.0000000
0.0000000 0.0000000 1.0000000
ATOM -13: X=0.00000000 Y=0.00000000 Z=0.00000000
MULT= 1 ISPLIT= 4
C 13 NPT= 781 R0=0.00010000 RMT= 1.32 Z: 6.
LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
0.0000000 1.0000000 0.0000000
0.0000000 0.0000000 1.0000000
12 NUMBER OF SYMMETRY OPERATIONS
1 0 0 0.00000000
0 1 0 0.00000000
0 0 1 0.00000000
1
0-1 0 0.00000000
1-1 0 0.00000000
0 0 1 0.00000000
2
-1 1 0 0.00000000
-1 0 0 0.00000000
0 0 1 0.00000000
3
1 0 0 0.00000000
0 1 0 0.00000000
0 0-1 0.00000000
4
0-1 0 0.00000000
1-1 0 0.00000000
0 0-1 0.00000000
5
-1 1 0 0.00000000
-1 0 0 0.00000000
0 0-1 0.00000000
6
0-1 0 0.00000000
-1 0 0 0.00000000
0 0 1 0.00000000
7
-1 1 0 0.00000000
0 1 0 0.00000000
0 0 1 0.00000000
8
1 0 0 0.00000000
1-1 0 0.00000000
0 0 1 0.00000000
9
0-1 0 0.00000000
-1 0 0 0.00000000
0 0-1 0.00000000
10
-1 1 0 0.00000000
0 1 0 0.00000000
0 0-1 0.00000000
11
1 0 0 0.00000000
1-1 0 0.00000000
0 0-1 0.00000000
12
......@@ -52,6 +52,8 @@ def normalized_template_example(parsed_template_example) -> LocalBackend:
def assert_normalized(backend):
with open("test_file_name.json", "wt") as file:
backend.write_json(file)
# The assertions are based on the quanitites need for the repository.
assert backend.get_value('atom_species', 0) is not None
assert backend.get_value('system_type', 0) is not None
......@@ -83,4 +85,3 @@ def test_normalizer_faulty_matid(
assert_log(caplog, 'ERROR', unknown_class_error)
assert_log(caplog, 'ERROR', wrong_class_for_no_sim_cell)
......@@ -35,7 +35,8 @@ parser_examples = [
('parsers/crystal', 'tests/data/parsers/crystal/si.out'),
('parsers/cpmd', 'tests/data/parsers/cpmd/geo_output.out'),
('parsers/nwchem', 'tests/data/parsers/nwchem/md/output.out'),
('parsers/bigdft', 'tests/data/parsers/bigdft/n2_output.out')
('parsers/bigdft', 'tests/data/parsers/bigdft/n2_output.out'),
('parsers/wien2k', 'tests/data/parsers/wien2k/ok/ok.scf')
]
faulty_unknown_one_d_matid_example = [
......
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