Commit 8fae0d40 authored by Daniel Speckhard's avatar Daniel Speckhard
Browse files

Added QMEspresso working for benchmark.out

parent 6fd747c9
......@@ -46,3 +46,6 @@
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
......@@ -137,6 +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 f07c719036248b4d74bff67c118187cfda167f01
......@@ -13,7 +13,6 @@
# limitations under the License.
import re
import json
from nomad.parsing import BadContextURI
......@@ -62,7 +61,9 @@ class RepositoryNormalizer(Normalizer):
def normalize(self, logger=None) -> None:
super().normalize(logger)
b = self._backend
# Don't check this in!
with open("test_file_quantum_espresso.json", "wt") as file:
b.write_json(file)
repository_info_context = '/section_repository_info/0'
try:
b.openContext(repository_info_context)
......
......@@ -203,14 +203,9 @@ parsers = [
),
LegacyParser(
name='parsers/quantumespresso',
parser_class_name='gaussianparser.GaussianParser',
main_file_re=r'^.*\.out$',
main_contents_re=(
r'\s*Cite this work as:'
r'\s*Gaussian [0-9]+, Revision [A-Za-z0-9.]*,'
r'\s\*\*\*\*\*\*\*\*\*\*\*\**'
r'\s*Gaussian\s*(?P<program_version>[0-9]+):\s*(?P<x_gaussian_program_implementation>[A-Za-z0-9-.]+)\s*(?P<x_gaussian_program_release_date>[0-9][0-9]?\-[A-Z][a-z][a-z]\-[0-9]+)'
r'\s*(?P<x_gaussian_program_execution_date>[0-9][0-9]?\-[A-Z][a-z][a-z]\-[0-9]+)')
parser_class_name='quantumespressoparser.QuantumEspressoParserPWSCF',
main_file_re=r'^.*\.out$', # It's not clear what type of extensions we should handler (.log?), either *star or .log,
main_contents_re=r"^PWSCF$"
)
]
......
......@@ -121,9 +121,15 @@ class LegacyParser(Parser):
kwargs = {key: value for key, value in kwargs.items() if key in init_signature.args}
with utils.legacy_logger(logger):
print('keyword arguments')
print(kwargs)
print("parser name")
print(str(Parser))
self.parser = Parser(**kwargs)
with patch.object(sys, 'argv', []):
print("mainfile is:")
print(mainfile)
backend = self.parser.parse(mainfile)
if backend is None or not hasattr(backend, 'status'):
......
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&control
calculation='relax'
restart_mode='from_scratch',
tstress = .true.
tprnfor = .true.
forc_conv_thr = 4.0D-5
prefix='W',
disk_io='low',
wfcdir='/tmp',
pseudo_dir = './',
outdir='./'
/
&system
ibrav=0,
celldm(1) = 1.889726134,
nat= 135,
ntyp= 1,
degauss=0.02,
smearing='mp',
occupations='smearing',
ecutwfc =30.0
ecutrho =120.0
nosym=.TRUE.
/
&electrons
conv_thr = 5.0d-7
mixing_beta = 0.02
electron_maxstep = 150
/
&ions
bfgs_ndim = 3,
pot_extrapolation = "second_order",
wfc_extrapolation = "second_order",
/
ATOMIC_SPECIES
W 183.84 W.UPF
K_POINTS AUTOMATIC
1 2 16 0 0 0
CELL_PARAMETERS (alat)
40.726845520 0.000000000 0.000000000
20.363422760 21.162289701 -0.95322
0.000000000 0.000000000 2.879822864
ATOMIC_POSITIONS (crystal)
W 0.000129325 0.000043551 0.150779369
W 0.043653260 0.112082569 0.111833490
W 0.977882480 0.111391782 0.500045938
W 0.132252115 0.000575545 0.396305718
W 0.066108340 0.000533820 0.769233363
W 0.109925083 0.111725433 0.748913556
W 0.890153629 0.220847719 0.247718102
W 0.932119180 0.335802298 0.105098636
W 0.865588168 0.335391726 0.491200435
W 0.020995804 0.223649468 0.442198105
W 0.954665238 0.223696960 0.826102374
W -0.000667763 0.334516042 0.768714052
W 0.777338489 0.447642844 0.919673033
W 0.822091523 0.558115257 0.077963591
W 0.755249309 0.558030600 0.349534600
W 0.911040692 0.446314489 0.425003873
W 0.844536544 0.447982510 0.722261684
W 0.889331843 0.556938353 0.775315294
W 0.666191268 0.667948985 1.006460192
W 0.711568913 0.778456666 0.130318783
W 0.644350597 0.778550969 0.417392789
W 0.800493680 0.668046701 0.449199016
W 0.733231300 0.668394906 0.738855603
W 0.778670202 0.778465243 0.828856706
W 0.555557085 0.888878258 0.104884669
W 0.689846755 0.889047066 0.527500102
W 0.622756488 0.888960840 0.820727959
W 0.198835132 0.000068384 0.041758538
W 0.243461742 0.110301247 0.073848238
W 0.176623727 0.110933908 0.402988745
W 0.332442903 -0.000698476 0.381315228
W 0.265619341 -0.000499220 0.702654817
W 0.310614875 0.109719826 0.760975558
W 0.087778043 0.222778282 0.092889720
W 0.133240679 0.332546230 0.104439829
W 0.066225270 0.333465602 0.435538656
W 0.221785076 0.220835528 0.434835796
W 0.154727271 0.221792432 0.756435252
W 0.200079663 0.331465244 0.785211697
W 0.977878362 0.445238050 0.105680484
W 0.023344041 0.555011034 0.117270253
W 0.956392185 0.555988331 0.453671691
W 0.111786965 0.443270820 0.441498346
W 0.044893741 0.444322771 0.774616403
W 0.090123221 0.554150004 0.768047333
W 0.867650325 0.667468557 0.136340269
W 0.912281831 0.777712574 0.168409651
W 0.845496711 0.778273185 0.507496589
W 0.001193263 0.666067806 0.461235696
W 0.934491942 0.666842997 0.807158117
W 0.978861142 0.777223683 0.813810333
W 0.756645280 0.889278895 0.215932610
W 0.890014892 0.888755906 0.536292371
W 0.823394787 0.889156556 0.885176440
W 0.399541465 -0.000695175 0.079756286
W 0.444931453 0.109800412 0.203518938
W 0.377884280 0.109357817 0.471300120
W 0.533891452 -0.000620140 0.514244533
W 0.466764028 -0.000795932 0.792528302
W 0.512103297 0.109752728 0.933660810
W 0.289026256 0.219644315 0.132234780
W 0.333761741 0.330088980 0.289578022
W 0.266585568 0.329782110 0.488099642
W 0.422985770 0.220694725 0.637877243
W 0.355880058 0.219700675 0.860475848
W 0.402954110 0.329584481 0.111237984
W 0.178999054 0.441981056 0.105113615
W 0.220958954 0.556941834 0.962311893
W 0.156445940 0.554105955 0.384145887
W 0.309170628 0.446293604 0.147389981
W 0.245535972 0.442379941 0.719037840
W 0.287784602 0.556208593 0.543611663
W 0.067465109 0.665727758 0.098327251
W 0.110978039 0.777785639 0.059198117
W 0.045002454 0.777283605 0.440818848
W 0.199483694 0.667022680 0.312278948
W 0.133228111 0.666433199 0.710071122
W 0.177217065 0.777885611 0.674709233
W 0.956323858 0.888696322 0.171768962
W 0.088556326 0.889118576 0.414068847
W 0.022548226 0.888707746 0.795903899
W 0.601018294 -0.000422455 0.228631004
W 0.645833185 0.110829546 0.343732187
W 0.579206219 0.109998748 0.649303619
W 0.734606924 0.000166356 0.610728823
W 0.667948646 -0.000115053 0.929253239
W 0.712323750 0.111307719 0.015655336
W 0.490426320 0.219977188 0.381429208
W 0.534022121 0.332675282 0.536380130
W 0.468274175 0.331524737 0.843270252
W 0.623231550 0.221957677 0.771864877
W 0.556932946 0.221014521 0.087316025
W 0.600291741 0.333438643 0.214230760
W 0.377655741 0.442333391 0.673260474
W 0.421475908 0.555004513 0.772726917
W 0.355007973 0.554615380 0.135070003
W 0.510784574 0.444316283 0.996192296
W 0.444501788 0.443369352 0.323200777
W 0.487866687 0.555796064 0.438421748
W 0.266023339 0.666527235 0.919177181
W 0.309995600 0.777486191 0.937622783
W 0.243631227 0.777555955 0.297441623
W 0.398794711 0.666459322 0.194456548
W 0.332486168 0.666193341 0.543693827
W 0.376523542 0.777602055 0.599214256
W 0.154786383 0.889117477 0.038261417
W 0.287729891 0.888623959 0.324910144
W 0.221104692 0.889041448 0.673816075
W 0.801131007 0.000297041 0.272400636
W 0.845088126 0.111279247 0.290943187
W 0.778627485 0.111592116 0.666473232
W 0.933893372 -0.000061417 0.535333176
W 0.867486170 0.000251342 0.912612896
W 0.911624677 0.110798606 0.897767192
W 0.689617268 0.222759348 0.437669956
W 0.733408248 0.335446602 0.537804638
W 0.666572541 0.334389897 0.887356528
W 0.823302890 0.221620177 0.667152254
W 0.756084004 0.223168525 0.075537053
W 0.801858162 0.331587915 0.065734088
W 0.577056096 0.445075874 0.674003517
W 0.620685685 0.557767939 0.828634989
W 0.554172236 0.556731898 0.122892264
W 0.708146637 0.448167756 0.098372263
W 0.642819633 0.446216996 0.366963613
W 0.688130900 0.557053507 0.571858767
W 0.465289175 0.666923587 0.866340092
W 0.510109746 0.778174892 0.981257641
W 0.443179771 0.777878080 0.280670840
W 0.599020830 0.667997325 0.276225009
W 0.531918858 0.667747842 0.560660506
W 0.577228861 0.778371964 0.695570315
W 0.354479774 0.888489623 0.994103665
W 0.488360999 0.888795253 0.389134930
W 0.421273266 0.888715273 0.682460861
This diff is collapsed.
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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.
=------------------------------------------------------------------------------=
This diff is collapsed.
Program PWSCF v.5.2.1 (svn rev. 11920) starts on 26Dec2015 at 14:41:16
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 uspp1.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
============================================================
| pseudopotential report for atomic species: 1 |
| pseudo potential version 7 3 2 |
------------------------------------------------------------
| oxygen PBE exchange-corr |
| z = 8. zv( 1) = 6. exfact = 5.00000 |
| ifpcor = 0 atomic energy = -31.58351 Ry |
| index orbital occupation energy |
| 1 200 2.00 -1.76 |
| 2 210 4.00 -0.66 |
| rinner = 0.7000 0.7000 0.7000 |
| new generation scheme: |
| nbeta = 4 kkbeta = 519 rcloc = 1.0000 |
| ibeta l epsilon rcut |
| 1 0 -1.76 1.20 |
| 2 0 -0.66 1.20 |
| 3 1 -1.76 1.20 |
| 4 1 -0.66 1.20 |
============================================================
============================================================
| pseudopotential report for atomic species: 2 |
| pseudo potential version 7 3 2 |
------------------------------------------------------------
| hydrogen PBE exchange-corr |
| z = 1. zv( 2) = 1. exfact = 5.00000 |
| ifpcor = 0 atomic energy = -0.91772 Ry |
| index orbital occupation energy |
| 1 100 1.00 -0.48 |
| rinner = 0.5000 |
| new generation scheme: |
| nbeta = 1 kkbeta = 271 rcloc = 0.6000 |
| ibeta l epsilon rcut |
| 1 0 -0.48 0.80 |
============================================================
gamma-point specific algorithms are used
G-vector sticks info
--------------------
sticks: dense smooth PW G-vecs: dense smooth PW
Sum 3181 3181 793 135043 135043 16879
Tot 1591 1591 397
bravais-lattice index = 1
lattice parameter (alat) = 20.0000 a.u.
unit-cell volume = 8000.0000 (a.u.)^3
number of atoms/cell = 3
number of atomic types = 2
number of electrons = 8.00
number of Kohn-Sham states= 4
kinetic-energy cutoff = 25.0000 Ry
charge density cutoff = 100.0000 Ry
convergence threshold = 1.0E-06
mixing beta = 0.7000
number of iterations used = 8 plain mixing
Exchange-correlation = PBE ( 1 4 3 4 0 0)
celldm(1)= 20.000000 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) = ( 1.000000 0.000000 0.000000 )
a(2) = ( 0.000000 1.000000 0.000000 )
a(3) = ( 0.000000 0.000000 1.000000 )
reciprocal axes: (cart. coord. in units 2 pi/alat)
b(1) = ( 1.000000 0.000000 0.000000 )
b(2) = ( 0.000000 1.000000 0.000000 )
b(3) = ( 0.000000 0.000000 1.000000 )
PseudoPot. # 1 for ox read from file:
/home/fs395/scratch/QE/espresso/pseudo/O_US.van
MD5 check sum: 7e325307d184e51bd80757047dcf04f9
Pseudo is Ultrasoft, Zval = 6.0
Generated by Vanderbilt code, v. 7.3.2
Using radial grid of 737 points, 4 beta functions with:
l(1) = 0
l(2) = 0
l(3) = 1
l(4) = 1
Q(r) pseudized with 8 coefficients, rinner = 0.700 0.700 0.700
PseudoPot. # 2 for hy read from file:
/home/fs395/scratch/QE/espresso/pseudo/H_US.van
MD5 check sum: a9a9bfe98ff56cf4de197d71fc46bb44
Pseudo is Ultrasoft, Zval = 1.0
Generated by Vanderbilt code, v. 7.3.2
Using radial grid of 399 points, 1 beta functions with:
l(1) = 0
Q(r) pseudized with 8 coefficients, rinner = 0.500
atomic species valence mass pseudopotential
O 6.00 16.00000 ox( 1.00)
H 1.00 2.00000 hy( 1.00)