Commit 0d76b171 authored by Markus Scheidgen's avatar Markus Scheidgen
Browse files

Merged parser integration.

parents 67c887c3 022a56d7
Pipeline #43710 failed with stages
in 1 minute and 13 seconds
......@@ -45,3 +45,9 @@
[submodule "dependencies/parsers/parser-band"]
path = dependencies/parsers/band
url = git@gitlab.mpcdf.mpg.de:nomad-lab/parser-band.git
[submodule "dependencies/parsers/gaussian"]
path = dependencies/parsers/gaussian
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-gaussian
[submodule "dependencies/parsers/quantum-espresso"]
path = dependencies/parsers/quantum-espresso
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-quantum-espresso
......@@ -87,7 +87,26 @@
"-sv", "tests/test_normalizing.py::test_normalizer[parsers/wien2k-tests/data/parsers/wien2k/AlN/AlN_ZB.scf]"
]
},
{
"name": "Python: gaussian normalizer test",
"type": "python",
"request": "launch",
"cwd": "${workspaceFolder}",
"program": "${workspaceFolder}/.pyenv/bin/pytest",
"args": [
"-sv", "tests/test_normalizing.py::test_normalizer[parsers/gaussian-tests/data/parsers/gaussian/Al.out]"
]
},
{
"name": "Python: aniline gaussian normalizer test",
"type": "python",
"request": "launch",
"cwd": "${workspaceFolder}",
"program": "${workspaceFolder}/.pyenv/bin/pytest",
"args": [
"-sv", "tests/test_normalizing.py::test_normalizer[parsers/gaussian-tests/data/parsers/gaussian/al-1.out]"
]
},
{
"name": "Python: test_parsing match test",
"type": "python",
......@@ -118,6 +137,17 @@
"-sv", "tests/test_normalizing.py::test_normalizer[parsers/vasp-tests/data/parsers/vasp/vasp.xml]"
]
},
{
"name": "Python: Quantum Espresso",
"type": "python",
"request": "launch",
"cwd": "${workspaceFolder}",
"program": "${workspaceFolder}/.pyenv/bin/pytest",
"args": [
"-sv", "tests/test_parsing.py::test_parser[parsers/quantumespresso-tests/data/parsers/quantum-espresso/W.out]"
]
},
{
"name": "Python: Current File",
"type": "python",
......
Subproject commit 02c301eb0621d8676e46d4d86ac1ed85a9531eb3
Subproject commit acdd533b20022130b7cf87c765596d1d91d3b0fe
Subproject commit 03899751624694c7099d5bc3e5b48971d924bc32
Subproject commit 7547643f594f612752e0d96d77fd3705c2a809b2
Subproject commit f03817034886e2c7225806e284a1eb8ecd8b3e25
Subproject commit 2a59119a6635454eba33c268d8cf8caa6eecd204
......@@ -61,14 +61,12 @@ class RepositoryNormalizer(Normalizer):
def normalize(self, logger=None) -> None:
super().normalize(logger)
b = self._backend
repository_info_context = '/section_repository_info/0'
try:
b.openContext(repository_info_context)
except BadContextURI:
b.openNonOverlappingSection('section_repository_info')
repository_info_context = None
b.openNonOverlappingSection('section_repository_parserdata')
b.addValue('repository_checksum', b.get_value('calc_hash', 0))
......@@ -77,7 +75,6 @@ class RepositoryNormalizer(Normalizer):
'repository_code_version',
self.simplify_version(b.get_value('program_version', 0)))
b.addValue('repository_parser_id', b.get_value('parser_name', 0))
b.addValue('repository_chemical_formula', b.get_value('chemical_composition_bulk_reduced', 0))
atom_labels = b.get_value('atom_labels', 0)
b.addValue('repository_atomic_elements', list(set(atom_labels)))
......
......@@ -308,4 +308,5 @@ class SystemNormalizer(SystemBasedNormalizer):
if nomad_classification == 'Atom' and (len(self.atom_labels) > 1):
nomad_classification = 'Molecule / Cluster'
return nomad_classification
......@@ -201,31 +201,31 @@ parsers = [
name='parsers/bigdft',
parser_class_name='bigdftparser.BigDFTParser',
mainfile_contents_re=(
r'__________________________________ A fast and precise DFT wavelet code\s*'
r'\| \| \| \| \| \|\s*'
r'\| \| \| \| \| \| BBBB i gggggg\s*'
r'\|_____\|_____\|_____\|_____\|_____\| B B g\s*'
r'\| \| : \| : \| \| \| B B i g\s*'
r'\| \|-0\+--\|-0\+--\| \| \| B B i g g\s*'
# r'__________________________________ A fast and precise DFT wavelet code\s*'
# r'\| \| \| \| \| \|\s*'
# r'\| \| \| \| \| \| BBBB i gggggg\s*'
# r'\|_____\|_____\|_____\|_____\|_____\| B B g\s*'
# r'\| \| : \| : \| \| \| B B i g\s*'
# r'\| \|-0\+--\|-0\+--\| \| \| B B i g g\s*'
r'\|_____\|__:__\|__:__\|_____\|_____\|___ BBBBB i g g\s*'
r'\| : \| \| \| : \| \| B B i g g\s*'
r'\|--\+0-\| \| \|-0\+--\| \| B B iiii g g\s*'
r'\|__:__\|_____\|_____\|__:__\|_____\| B B i g g\s*'
r'\| \| : \| : \| \| \| B BBBB i g g\s*'
r'\| \|-0\+--\|-0\+--\| \| \| B iiiii gggggg\s*'
r'\|_____\|__:__\|__:__\|_____\|_____\|__BBBBB\s*'
r'\| \| \| \| : \| \| TTTTTTTTT\s*'
r'\| \| \| \|--\+0-\| \| DDDDDD FFFFF T\s*'
r'\|_____\|_____\|_____\|__:__\|_____\| D D F TTTT T\s*'
r'\| \| \| \| : \| \|D D F T T\s*'
r'\| \| \| \|--\+0-\| \|D D FFFF T T\s*'
r'\|_____\|_____\|_____\|__:__\|_____\|D___ D F T T\s*'
r'\| \| \| : \| \| \|D D F TTTTT\s*'
r'\| \| \|--\+0-\| \| \| D D F T T\s*'
r'\|_____\|_____\|__:__\|_____\|_____\| D F T T\s*'
r'\| \| \| \| \| \| D T T\s*'
r'\| \| \| \| \| \| DDDDDD F TTTT\s*'
r'\|_____\|_____\|_____\|_____\|_____\|______ www\.bigdft\.org'
# r'\| : \| \| \| : \| \| B B i g g\s*'
# r'\|--\+0-\| \| \|-0\+--\| \| B B iiii g g\s*'
# r'\|__:__\|_____\|_____\|__:__\|_____\| B B i g g\s*'
# r'\| \| : \| : \| \| \| B BBBB i g g\s*'
# r'\| \|-0\+--\|-0\+--\| \| \| B iiiii gggggg\s*'
# r'\|_____\|__:__\|__:__\|_____\|_____\|__BBBBB\s*'
# r'\| \| \| \| : \| \| TTTTTTTTT\s*'
# r'\| \| \| \|--\+0-\| \| DDDDDD FFFFF T\s*'
# r'\|_____\|_____\|_____\|__:__\|_____\| D D F TTTT T\s*'
# r'\| \| \| \| : \| \|D D F T T\s*'
# r'\| \| \| \|--\+0-\| \|D D FFFF T T\s*'
# r'\|_____\|_____\|_____\|__:__\|_____\|D___ D F T T\s*'
# r'\| \| \| : \| \| \|D D F TTTTT\s*'
# r'\| \| \|--\+0-\| \| \| D D F T T\s*'
# r'\|_____\|_____\|__:__\|_____\|_____\| D F T T\s*'
# r'\| \| \| \| \| \| D T T\s*'
# r'\| \| \| \| \| \| DDDDDD F TTTT\s*'
# r'\|_____\|_____\|_____\|_____\|_____\|______ www\.bigdft\.org'
)
),
LegacyParser(
......@@ -236,7 +236,24 @@ parsers = [
LegacyParser(
name='parsers/band',
parser_class_name='bandparser.BANDParser',
mainfile_contents_re=r' +\* +Amsterdam Density Functional +\(ADF\)'
mainfile_contents_re=r' +\* +Amsterdam Density Functional +\(ADF\)'),
LegacyParser(
name='parsers/gaussian',
parser_class_name='gaussianparser.GaussianParser',
mainfile_contents_re=(
r'\s*Cite this work as:'
r'\s*Gaussian [0-9]+, Revision [A-Za-z0-9.]*,'
r'\s\*\*\*\*\*\*\*\*\*\*\*\**'
r'\s*Gaussian\s*([0-9]+):\s*([A-Za-z0-9-.]+)\s*([0-9][0-9]?\-[A-Z][a-z][a-z]\-[0-9]+)'
r'\s*([0-9][0-9]?\-[A-Z][a-z][a-z]\-[0-9]+)')
),
LegacyParser(
name='parsers/quantumespresso',
parser_class_name='quantumespressoparser.QuantumEspressoParserPWSCF',
mainfile_contents_re=(
r'^\s*Program (\S+)\s+v\.(\S+)(?:\s+\(svn\s+rev\.\s+'
r'(\d+)\s*\))?\s+starts[^\n]+'
r'(?:\s*\n?)*This program is part of the open-source Quantum')
)
]
......
This source diff could not be displayed because it is too large. You can view the blob instead.
Program PWSCF v.5.2.1 (svn rev. 11920) starts on 26Dec2015 at 14:30:49
This program is part of the open-source Quantum ESPRESSO suite
for quantum simulation of materials; please cite
"P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
URL http://www.quantum-espresso.org",
in publications or presentations arising from this work. More details at
http://www.quantum-espresso.org/quote
Serial multi-threaded version, running on 4 processor cores
Reading input from dft1.in
Current dimensions of program PWSCF are:
Max number of different atomic species (ntypx) = 10
Max number of k-points (npk) = 40000
Max angular momentum in pseudopotentials (lmaxx) = 3
IMPORTANT: XC functional enforced from input :
Exchange-correlation = PW91 ( 1 4 2 2 0 0)
Any further DFT definition will be discarded
Please, verify this is what you really want
G-vector sticks info
--------------------
sticks: dense smooth PW G-vecs: dense smooth PW
Sum 163 163 55 1459 1459 283
bravais-lattice index = 2
lattice parameter (alat) = 10.2000 a.u.
unit-cell volume = 265.3020 (a.u.)^3
number of atoms/cell = 2
number of atomic types = 1
number of electrons = 8.00
number of Kohn-Sham states= 4
kinetic-energy cutoff = 12.0000 Ry
charge density cutoff = 48.0000 Ry
convergence threshold = 1.0E-06
mixing beta = 0.7000
number of iterations used = 8 plain mixing
Exchange-correlation = PW91 ( 1 4 2 2 0 0)
celldm(1)= 10.200000 celldm(2)= 0.000000 celldm(3)= 0.000000
celldm(4)= 0.000000 celldm(5)= 0.000000 celldm(6)= 0.000000
crystal axes: (cart. coord. in units of alat)
a(1) = ( -0.500000 0.000000 0.500000 )
a(2) = ( 0.000000 0.500000 0.500000 )
a(3) = ( -0.500000 0.500000 0.000000 )
reciprocal axes: (cart. coord. in units 2 pi/alat)
b(1) = ( -1.000000 -1.000000 1.000000 )
b(2) = ( 1.000000 1.000000 1.000000 )
b(3) = ( -1.000000 1.000000 -1.000000 )
PseudoPot. # 1 for Si read from file:
/home/fs395/scratch/QE/espresso/pseudo/Si.pz-vbc.UPF
MD5 check sum: 6dfa03ddd5817404712e03e4d12deb78
Pseudo is Norm-conserving, Zval = 4.0
Generated by new atomic code, or converted to UPF format
Using radial grid of 431 points, 2 beta functions with:
l(1) = 0
l(2) = 1
atomic species valence mass pseudopotential
Si 4.00 28.08600 Si( 1.00)
24 Sym. Ops. (no inversion) found
(note: 24 additional sym.ops. were found but ignored
their fractional translations are incommensurate with FFT grid)
Cartesian axes
site n. atom positions (alat units)
1 Si tau( 1) = ( 0.0000000 0.0000000 0.0000000 )
2 Si tau( 2) = ( 0.2500000 0.2500000 0.2500000 )
number of k points= 2
cart. coord. in units 2pi/alat
k( 1) = ( 0.2500000 0.2500000 0.2500000), wk = 0.5000000
k( 2) = ( 0.2500000 0.2500000 0.7500000), wk = 1.5000000
Dense grid: 1459 G-vectors FFT dimensions: ( 15, 15, 15)
Largest allocated arrays est. size (Mb) dimensions
Kohn-Sham Wavefunctions 0.01 Mb ( 186, 4)
NL pseudopotentials 0.02 Mb ( 186, 8)
Each V/rho on FFT grid 0.05 Mb ( 3375)
Each G-vector array 0.01 Mb ( 1459)
G-vector shells 0.00 Mb ( 43)
Largest temporary arrays est. size (Mb) dimensions
Auxiliary wavefunctions 0.05 Mb ( 186, 16)
Each subspace H/S matrix 0.00 Mb ( 16, 16)
Each <psi_i|beta_j> matrix 0.00 Mb ( 8, 4)
Arrays for rho mixing 0.41 Mb ( 3375, 8)
Initial potential from superposition of free atoms
starting charge 7.99901, renormalised to 8.00000
Starting wfc are 8 randomized atomic wfcs
total cpu time spent up to now is 0.0 secs
per-process dynamical memory: 1.6 Mb
Self-consistent Calculation
iteration # 1 ecut= 12.00 Ry beta=0.70
Davidson diagonalization with overlap
ethr = 1.00E-02, avg # of iterations = 2.0
Threshold (ethr) on eigenvalues was too large:
Diagonalizing with lowered threshold
Davidson diagonalization with overlap
ethr = 8.69E-04, avg # of iterations = 1.0
total cpu time spent up to now is 0.1 secs
total energy = -15.83023308 Ry
Harris-Foulkes estimate = -15.84661698 Ry
estimated scf accuracy < 0.06968502 Ry
iteration # 2 ecut= 12.00 Ry beta=0.70
Davidson diagonalization with overlap
ethr = 8.71E-04, avg # of iterations = 1.0
total cpu time spent up to now is 0.1 secs
total energy = -15.83307152 Ry
Harris-Foulkes estimate = -15.83307032 Ry
estimated scf accuracy < 0.00305818 Ry
iteration # 3 ecut= 12.00 Ry beta=0.70
Davidson diagonalization with overlap
ethr = 3.82E-05, avg # of iterations = 2.0
total cpu time spent up to now is 0.1 secs
total energy = -15.83337170 Ry
Harris-Foulkes estimate = -15.83337540 Ry
estimated scf accuracy < 0.00006493 Ry
iteration # 4 ecut= 12.00 Ry beta=0.70
Davidson diagonalization with overlap
ethr = 8.12E-07, avg # of iterations = 3.0
total cpu time spent up to now is 0.1 secs
total energy = -15.83340518 Ry
Harris-Foulkes estimate = -15.83340525 Ry
estimated scf accuracy < 0.00000104 Ry
iteration # 5 ecut= 12.00 Ry beta=0.70
Davidson diagonalization with overlap
ethr = 1.30E-08, avg # of iterations = 2.0
total cpu time spent up to now is 0.1 secs
End of self-consistent calculation
k = 0.2500 0.2500 0.2500 ( 180 PWs) bands (ev):
-4.8500 2.3922 5.5060 5.5060
k = 0.2500 0.2500 0.7500 ( 186 PWs) bands (ev):
-2.9166 -0.0593 2.7215 4.0318
highest occupied level (ev): 5.5060
! total energy = -15.83340547 Ry
Harris-Foulkes estimate = -15.83340547 Ry
estimated scf accuracy < 0.00000004 Ry
The total energy is the sum of the following terms:
one-electron contribution = 4.81204927 Ry
hartree contribution = 1.12419003 Ry
xc contribution = -4.86988619 Ry
ewald contribution = -16.89975858 Ry
convergence has been achieved in 5 iterations
Writing output data file pwscf.save
init_run : 0.04s CPU 0.03s WALL ( 1 calls)
electrons : 0.12s CPU 0.03s WALL ( 1 calls)
Called by init_run:
wfcinit : 0.01s CPU 0.00s WALL ( 1 calls)
potinit : 0.01s CPU 0.00s WALL ( 1 calls)
Called by electrons:
c_bands : 0.05s CPU 0.01s WALL ( 6 calls)
sum_band : 0.02s CPU 0.00s WALL ( 6 calls)
v_of_rho : 0.05s CPU 0.01s WALL ( 6 calls)
mix_rho : 0.00s CPU 0.00s WALL ( 6 calls)
Called by c_bands:
init_us_2 : 0.00s CPU 0.00s WALL ( 26 calls)
cegterg : 0.05s CPU 0.01s WALL ( 12 calls)
Called by sum_band:
Called by *egterg:
h_psi : 0.04s CPU 0.01s WALL ( 36 calls)
g_psi : 0.00s CPU 0.00s WALL ( 22 calls)
cdiaghg : 0.01s CPU 0.00s WALL ( 32 calls)
Called by h_psi:
add_vuspsi : 0.00s CPU 0.00s WALL ( 36 calls)
General routines
calbec : 0.01s CPU 0.00s WALL ( 36 calls)
fft : 0.00s CPU 0.00s WALL ( 67 calls)
fftw : 0.03s CPU 0.01s WALL ( 328 calls)
davcio : 0.00s CPU 0.00s WALL ( 2 calls)
PWSCF : 0.19s CPU 0.09s WALL
This run was terminated on: 14:30:49 26Dec2015
=------------------------------------------------------------------------------=
JOB DONE.
=------------------------------------------------------------------------------=
......@@ -39,14 +39,16 @@ parser_examples = [
('parsers/nwchem', 'tests/data/parsers/nwchem/single_point/output.out'),
('parsers/bigdft', 'tests/data/parsers/bigdft/n2_output.out'),
('parsers/wien2k', 'tests/data/parsers/wien2k/AlN/AlN_ZB.scf'),
('parsers/band', 'tests/data/parsers/band_adf.out')
('parsers/band', 'tests/data/parsers/band_adf.out'),
('parsers/gaussian', 'tests/data/parsers/gaussian/aniline.out'),
('parsers/quantumespresso', 'tests/data/parsers/quantum-espresso/benchmark.out')
]
faulty_unknown_one_d_matid_example = [
('parsers/template', 'tests/data/normalizers/no_sim_cell_boolean_positions.json')
]
correct_num_output_files = 18
correct_num_output_files = 19
class TestLocalBackend(object):
......
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