Skip to content

Commit

Permalink
Merge branch 'develop' into opengrid
Browse files Browse the repository at this point in the history
  • Loading branch information
@qiaojunfeng
qiaojunfeng committed Sep 14, 2021
2 parents 7b6c525 + f59c95d commit 02d42bb
Show file tree
Hide file tree
Showing 7 changed files with 2,716 additions and 0 deletions.
14 changes: 14 additions & 0 deletions aiida_quantumespresso/parsers/parse_xml/parse.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -75,6 +75,20 @@ def parse_xml_post_6_2(xml):
# xml_dictionary['key']['@attr'] returns its attribute 'attr'
# xml_dictionary['key']['nested_key'] goes one level deeper.

# Fix a bug of QE 6.8: the output XML is not consistent with schema, see
# https://github.com/aiidateam/aiida-quantumespresso/pull/717
xml_creator = xml.find('./general_info/creator')
if xml_creator is not None and 'VERSION' in xml_creator.attrib:
creator_version = xml_creator.attrib['VERSION']
if creator_version == '6.8':
root = xml.getroot()
timing_info = root.find('./timing_info')
partial_pwscf = timing_info.find("partial[@label='PWSCF'][@calls='0']")
try:
timing_info.remove(partial_pwscf)
except (TypeError, ValueError):
pass

xml_dictionary, errors = xsd.to_dict(xml, validation='lax')
if errors:
logs.error.append(f'{len(errors)} XML schema validation error(s) schema: {schema_filepath}:')
Expand Down
1,033 changes: 1,033 additions & 0 deletions aiida_quantumespresso/parsers/parse_xml/schemas/qes_210716.xsd
View file

Large diffs are not rendered by default.

2 changes: 2 additions & 0 deletions aiida_quantumespresso/workflows/pw/base.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -217,6 +217,8 @@ def get_builder_from_protocol(
builder.pw['structure'] = structure
builder.pw['parameters'] = orm.Dict(dict=parameters)
builder.pw['metadata'] = inputs['pw']['metadata']
if 'settings' in inputs['pw']:
builder.pw['settings'] = orm.Dict(dict=inputs['pw']['settings'])
if 'parallelization' in inputs['pw']:
builder.pw['parallelization'] = orm.Dict(dict=inputs['pw']['parallelization'])
builder.clean_workdir = orm.Bool(inputs['clean_workdir'])
Expand Down
340 changes: 340 additions & 0 deletions tests/parsers/fixtures/pw/default_xml_210716/aiida.out
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,340 @@

Program PWSCF v.6.8 starts on 20Aug2021 at 20:51:49

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);
"P. Giannozzi et al., J. Phys.:Condens. Matter 29 465901 (2017);
"P. Giannozzi et al., J. Chem. Phys. 152 154105 (2020);
URL http://www.quantum-espresso.org",
in publications or presentations arising from this work. More details at
http://www.quantum-espresso.org/quote

Parallel version (MPI), running on 1 processors

MPI processes distributed on 1 nodes
18083 MiB available memory on the printing compute node when the environment starts

Reading input from aiida.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) = 4
Message from routine volume:
axis vectors are left-handed
Message from routine setup:
using ibrav=0 with symmetry is DISCOURAGED, use correct ibrav instead

Subspace diagonalization in iterative solution of the eigenvalue problem:
a serial algorithm will be used


G-vector sticks info
--------------------
sticks: dense smooth PW G-vecs: dense smooth PW
Sum 859 433 127 16889 5985 965

Using Slab Decomposition



bravais-lattice index = 0
lattice parameter (alat) = 7.2558 a.u.
unit-cell volume = 270.1072 (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 = 30.0000 Ry
charge density cutoff = 240.0000 Ry
scf 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 0)

celldm(1)= 7.255773 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) = ( 0.707107 0.707107 0.000000 )
a(2) = ( 0.707107 0.000000 0.707107 )
a(3) = ( 0.000000 0.707107 0.707107 )

reciprocal axes: (cart. coord. in units 2 pi/alat)
b(1) = ( 0.707107 0.707107 -0.707107 )
b(2) = ( 0.707107 -0.707107 0.707107 )
b(3) = ( -0.707107 0.707107 0.707107 )


PseudoPot. # 1 for Si read from file:
./pseudo/Si.pbe-n-rrkjus_psl.1.0.0.UPF
MD5 check sum: 0b0bb1205258b0d07b9f9672cf965d36
Pseudo is Ultrasoft + core correction, Zval = 4.0
Generated using "atomic" code by A. Dal Corso v.5.1
Using radial grid of 1141 points, 6 beta functions with:
l(1) = 0
l(2) = 0
l(3) = 1
l(4) = 1
l(5) = 2
l(6) = 2
Q(r) pseudized with 0 coefficients


atomic species valence mass pseudopotential
Si 4.00 28.08550 Si( 1.00)

...... SYMMETRIES REMOVED

Cartesian axes

site n. atom positions (alat units)
1 Si tau( 1) = ( 0.0000000 0.0000000 0.0000000 )
2 Si tau( 2) = ( 0.3535534 0.3535534 0.3535534 )

Crystallographic axes

site n. atom positions (cryst. coord.)
1 Si tau( 1) = ( 0.0000000 0.0000000 0.0000000 )
2 Si tau( 2) = ( 0.2500000 0.2500000 0.2500000 )

number of k points= 3
cart. coord. in units 2pi/alat
k( 1) = ( 0.0000000 0.0000000 0.0000000), wk = 0.2500000
k( 2) = ( 0.3535534 -0.3535534 -0.3535534), wk = 1.0000000
k( 3) = ( 0.0000000 0.0000000 -0.7071068), wk = 0.7500000

cryst. coord.
k( 1) = ( 0.0000000 0.0000000 0.0000000), wk = 0.2500000
k( 2) = ( 0.0000000 0.0000000 -0.5000000), wk = 1.0000000
k( 3) = ( 0.0000000 -0.5000000 -0.5000000), wk = 0.7500000

Dense grid: 16889 G-vectors FFT dimensions: ( 36, 36, 36)

Smooth grid: 5985 G-vectors FFT dimensions: ( 32, 32, 32)

Dynamical RAM for wfc: 0.05 MB

Dynamical RAM for wfc (w. buffer): 0.18 MB

Dynamical RAM for str. fact: 0.26 MB

Dynamical RAM for local pot: 0.00 MB

Dynamical RAM for nlocal pot: 0.41 MB

Dynamical RAM for qrad: 1.24 MB

Dynamical RAM for rho,v,vnew: 1.84 MB

Dynamical RAM for rhoin: 0.61 MB

Dynamical RAM for rho*nmix: 4.12 MB

Dynamical RAM for G-vectors: 1.01 MB

Dynamical RAM for h,s,v(r/c): 0.00 MB

Dynamical RAM for <psi|beta>: 0.00 MB

Dynamical RAM for psi: 0.09 MB

Dynamical RAM for hpsi: 0.09 MB

Dynamical RAM for spsi: 0.09 MB

Dynamical RAM for wfcinit/wfcrot: 0.18 MB

Dynamical RAM for addusdens: 48.45 MB

Estimated static dynamical RAM per process > 7.86 MB

Estimated max dynamical RAM per process > 60.43 MB

Initial potential from superposition of free atoms

starting charge 7.99888, renormalised to 8.00000
Starting wfcs are 8 randomized atomic wfcs

total cpu time spent up to now is 0.9 secs

Self-consistent Calculation

iteration # 1 ecut= 30.00 Ry beta= 0.70
Davidson diagonalization with overlap

---- Real-time Memory Report at c_bands before calling an iterative solver
140 MiB given to the printing process from OS
0 MiB allocation reported by mallinfo(arena+hblkhd)
18064 MiB available memory on the node where the printing process lives
------------------
ethr = 1.00E-02, avg # of iterations = 2.0

total cpu time spent up to now is 1.1 secs

total energy = -22.64483140 Ry
estimated scf accuracy < 0.09763908 Ry

iteration # 2 ecut= 30.00 Ry beta= 0.70
Davidson diagonalization with overlap

---- Real-time Memory Report at c_bands before calling an iterative solver
146 MiB given to the printing process from OS
0 MiB allocation reported by mallinfo(arena+hblkhd)
18057 MiB available memory on the node where the printing process lives
------------------
ethr = 1.22E-03, avg # of iterations = 1.3

total cpu time spent up to now is 1.3 secs

total energy = -22.64982164 Ry
estimated scf accuracy < 0.00605427 Ry

iteration # 3 ecut= 30.00 Ry beta= 0.70
Davidson diagonalization with overlap

---- Real-time Memory Report at c_bands before calling an iterative solver
147 MiB given to the printing process from OS
0 MiB allocation reported by mallinfo(arena+hblkhd)
18057 MiB available memory on the node where the printing process lives
------------------
ethr = 7.57E-05, avg # of iterations = 3.0

total cpu time spent up to now is 1.4 secs

total energy = -22.65158389 Ry
estimated scf accuracy < 0.00017276 Ry

iteration # 4 ecut= 30.00 Ry beta= 0.70
Davidson diagonalization with overlap

---- Real-time Memory Report at c_bands before calling an iterative solver
147 MiB given to the printing process from OS
0 MiB allocation reported by mallinfo(arena+hblkhd)
18057 MiB available memory on the node where the printing process lives
------------------
ethr = 2.16E-06, avg # of iterations = 3.7

total cpu time spent up to now is 1.6 secs

total energy = -22.65169763 Ry
estimated scf accuracy < 0.00003757 Ry

iteration # 5 ecut= 30.00 Ry beta= 0.70
Davidson diagonalization with overlap

---- Real-time Memory Report at c_bands before calling an iterative solver
147 MiB given to the printing process from OS
0 MiB allocation reported by mallinfo(arena+hblkhd)
18057 MiB available memory on the node where the printing process lives
------------------
ethr = 4.70E-07, avg # of iterations = 2.7

total cpu time spent up to now is 1.7 secs

End of self-consistent calculation

k = 0.0000 0.0000 0.0000 ( 749 PWs) bands (ev):

-5.5135 6.5081 6.5081 6.5081

occupation numbers
1.0000 1.0000 1.0000 1.0000

k = 0.3536-0.3536-0.3536 ( 754 PWs) bands (ev):

-3.1616 -0.5346 5.2782 5.2782

occupation numbers
1.0000 1.0000 1.0000 1.0000

k = 0.0000 0.0000-0.7071 ( 740 PWs) bands (ev):

-1.3466 -1.3466 3.5874 3.5874

occupation numbers
1.0000 1.0000 1.0000 1.0000

highest occupied level (ev): 6.5081

! total energy = -22.65170438 Ry
estimated scf accuracy < 0.00000032 Ry

The total energy is the sum of the following terms:
one-electron contribution = 5.27239738 Ry
hartree contribution = 1.26896101 Ry
xc contribution = -12.39411904 Ry
ewald contribution = -16.79894374 Ry

convergence has been achieved in 5 iterations

Writing output data file ./out/aiida.save/

init_run : 0.58s CPU 0.64s WALL ( 1 calls)
electrons : 0.66s CPU 0.78s WALL ( 1 calls)

Called by init_run:
wfcinit : 0.01s CPU 0.01s WALL ( 1 calls)
wfcinit:atom : 0.00s CPU 0.00s WALL ( 3 calls)
wfcinit:wfcr : 0.01s CPU 0.01s WALL ( 3 calls)
potinit : 0.04s CPU 0.05s WALL ( 1 calls)
hinit0 : 0.48s CPU 0.50s WALL ( 1 calls)

Called by electrons:
c_bands : 0.14s CPU 0.14s WALL ( 5 calls)
sum_band : 0.28s CPU 0.33s WALL ( 5 calls)
v_of_rho : 0.10s CPU 0.10s WALL ( 6 calls)
v_h : 0.00s CPU 0.01s WALL ( 6 calls)
v_xc : 0.09s CPU 0.10s WALL ( 6 calls)
newd : 0.21s CPU 0.27s WALL ( 6 calls)
mix_rho : 0.00s CPU 0.01s WALL ( 5 calls)

Called by c_bands:
init_us_2 : 0.01s CPU 0.01s WALL ( 33 calls)
cegterg : 0.07s CPU 0.07s WALL ( 15 calls)

Called by sum_band:
sum_band:wei : 0.00s CPU 0.00s WALL ( 5 calls)
sum_band:loo : 0.02s CPU 0.02s WALL ( 5 calls)
sum_band:buf : 0.00s CPU 0.00s WALL ( 15 calls)
sum_band:ini : 0.01s CPU 0.01s WALL ( 15 calls)
sum_band:cal : 0.00s CPU 0.00s WALL ( 15 calls)
sum_band:bec : 0.00s CPU 0.00s WALL ( 15 calls)
addusdens : 0.24s CPU 0.29s WALL ( 5 calls)
addusd:skk : 0.00s CPU 0.00s WALL ( 5 calls)
addusd:dgemm : 0.04s CPU 0.09s WALL ( 5 calls)
addusd:qvan2 : 0.17s CPU 0.17s WALL ( 5 calls)

Called by *egterg:
cdiaghg : 0.00s CPU 0.00s WALL ( 53 calls)
cegterg:over : 0.00s CPU 0.00s WALL ( 38 calls)
cegterg:upda : 0.00s CPU 0.00s WALL ( 38 calls)
cegterg:last : 0.00s CPU 0.00s WALL ( 34 calls)
h_psi : 0.07s CPU 0.07s WALL ( 56 calls)
s_psi : 0.00s CPU 0.00s WALL ( 56 calls)
g_psi : 0.00s CPU 0.00s WALL ( 38 calls)

Called by h_psi:
h_psi:calbec : 0.00s CPU 0.00s WALL ( 56 calls)
vloc_psi : 0.06s CPU 0.06s WALL ( 56 calls)
add_vuspsi : 0.00s CPU 0.00s WALL ( 56 calls)

General routines
calbec : 0.00s CPU 0.00s WALL ( 71 calls)
fft : 0.02s CPU 0.05s WALL ( 76 calls)
ffts : 0.00s CPU 0.00s WALL ( 11 calls)
fftw : 0.03s CPU 0.03s WALL ( 454 calls)
interpolate : 0.00s CPU 0.00s WALL ( 6 calls)

Parallel routines

PWSCF : 1.32s CPU 1.73s WALL


This run was terminated on: 20:51:51 20Aug2021

=------------------------------------------------------------------------------=
JOB DONE.
=------------------------------------------------------------------------------=
Loading

0 comments on commit 02d42bb

Please sign in to comment.