From ea76d9b37f78315bbf93f93fa56460c7dfe0652a Mon Sep 17 00:00:00 2001 From: Sebastiaan Huber Date: Wed, 11 Sep 2024 23:27:27 +0200 Subject: [PATCH 1/2] CLI: Fix bug in `aiida-quantumespresso workflow launc pw-base` (#1039) The command would not specify the `CONTROL` key for the input parameters resulting in an exception in the upload step. This was not discovered by tests because the workflow is not actually run and the exception is only hit when the calcjob is actually executed. --- src/aiida_quantumespresso/cli/workflows/pw/base.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/src/aiida_quantumespresso/cli/workflows/pw/base.py b/src/aiida_quantumespresso/cli/workflows/pw/base.py index 6880eea19..75deb6e26 100755 --- a/src/aiida_quantumespresso/cli/workflows/pw/base.py +++ b/src/aiida_quantumespresso/cli/workflows/pw/base.py @@ -42,6 +42,9 @@ def launch_workflow( cutoff_wfc, cutoff_rho = pseudo_family.get_recommended_cutoffs(structure=structure, unit='Ry') parameters = { + 'CONTROL': { + 'calculation': 'scf', + }, 'SYSTEM': { 'ecutwfc': ecutwfc or cutoff_wfc, 'ecutrho': ecutrho or cutoff_rho, From 57e7463c5727775d6a0470a41d1aca0ec4083b9a Mon Sep 17 00:00:00 2001 From: Marnik Bercx Date: Fri, 27 Sep 2024 14:23:39 +0200 Subject: [PATCH 2/2] =?UTF-8?q?=E2=9C=A8=20`PwParser`:=20Add=20the=20XML?= =?UTF-8?q?=20schema=20for=20Quantum=20ESPRESSO=20v7.3.1?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit In the new schema, the `number_of_atomic_wfc` is moved to the `atomic_structure` tag as an attribute. In case the former is not present, we extract the value from the latter. --- .../parsers/parse_xml/parse.py | 4 +- .../parsers/parse_xml/schemas/qes_240411.xsd | 1391 +++++++++++++++++ .../fixtures/pw/default_xml_240411/aiida.out | 1259 +++++++++++++++ .../default_xml_240411/data-file-schema.xml | 989 ++++++++++++ tests/parsers/test_pw.py | 21 +- .../test_pw/test_pw_default_xml_240411_.yml | 199 +++ 6 files changed, 3853 insertions(+), 10 deletions(-) create mode 100644 src/aiida_quantumespresso/parsers/parse_xml/schemas/qes_240411.xsd create mode 100644 tests/parsers/fixtures/pw/default_xml_240411/aiida.out create mode 100644 tests/parsers/fixtures/pw/default_xml_240411/data-file-schema.xml create mode 100644 tests/parsers/test_pw/test_pw_default_xml_240411_.yml diff --git a/src/aiida_quantumespresso/parsers/parse_xml/parse.py b/src/aiida_quantumespresso/parsers/parse_xml/parse.py index ef5994e82..df2bcfadc 100644 --- a/src/aiida_quantumespresso/parsers/parse_xml/parse.py +++ b/src/aiida_quantumespresso/parsers/parse_xml/parse.py @@ -295,7 +295,9 @@ def parse_xml_post_6_2(xml): num_k_points = band_structure['nks'] num_electrons = band_structure['nelec'] - num_atomic_wfc = band_structure['num_of_atomic_wfc'] + + # In schema v240411 (QE v7.3.1), the `number_of_atomic_wfc` is moved to the `atomic_structure` tag as an attribute + num_atomic_wfc = band_structure.get('num_of_atomic_wfc', None) or outputs['atomic_structure']['@num_of_atomic_wfc'] num_bands = band_structure.get('nbnd', None) num_bands_up = band_structure.get('nbnd_up', None) num_bands_down = band_structure.get('nbnd_dw', None) diff --git a/src/aiida_quantumespresso/parsers/parse_xml/schemas/qes_240411.xsd b/src/aiida_quantumespresso/parsers/parse_xml/schemas/qes_240411.xsd new file mode 100644 index 000000000..160930fb2 --- /dev/null +++ b/src/aiida_quantumespresso/parsers/parse_xml/schemas/qes_240411.xsd @@ -0,0 +1,1391 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/tests/parsers/fixtures/pw/default_xml_240411/aiida.out b/tests/parsers/fixtures/pw/default_xml_240411/aiida.out new file mode 100644 index 000000000..d70675ff7 --- /dev/null +++ b/tests/parsers/fixtures/pw/default_xml_240411/aiida.out @@ -0,0 +1,1259 @@ + + Program PWSCF v.7.3.1 starts on 24Jul2024 at 16:39:13 + + 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 12 processors + + MPI processes distributed on 1 nodes + 35534 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 setup: + using ibrav=0 with symmetry is DISCOURAGED, use correct ibrav instead + + K-points division: npool = 3 + R & G space division: proc/nbgrp/npool/nimage = 4 + Subspace diagonalization in iterative solution of the eigenvalue problem: + a serial algorithm will be used + + + Parallelization info + -------------------- + sticks: dense smooth PW G-vecs: dense smooth PW + Min 219 109 37 4315 1545 284 + Max 220 110 38 4316 1546 285 + Sum 877 439 151 17261 6183 1139 + + Using Slab Decomposition + + + + bravais-lattice index = 0 + lattice parameter (alat) = 7.3075 a.u. + unit-cell volume = 275.9279 (a.u.)^3 + number of atoms/cell = 2 + number of atomic types = 1 + number of electrons = 8.00 + number of Kohn-Sham states= 8 + kinetic-energy cutoff = 30.0000 Ry + charge density cutoff = 240.0000 Ry + scf convergence threshold = 8.0E-10 + mixing beta = 0.4000 + number of iterations used = 8 plain mixing + energy convergence thresh.= 2.0E-04 + force convergence thresh. = 1.0E-03 + press convergence thresh. = 5.0E-01 + Exchange-correlation= PBESOL + ( 1 4 10 8 0 0 0) + nstep = 50 + + + celldm(1)= 7.307523 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) = ( 0.500000 0.866025 0.000000 ) + a(3) = ( 0.500000 0.288675 0.816497 ) + + reciprocal axes: (cart. coord. in units 2 pi/alat) + b(1) = ( 1.000000 -0.577350 -0.408248 ) + b(2) = ( 0.000000 1.154701 -0.408248 ) + b(3) = ( 0.000000 0.000000 1.224745 ) + + + PseudoPot. # 1 for Si read from file: + ./pseudo/Si.pbesol-n-rrkjus_psl.1.0.0.UPF + MD5 check sum: c4212819de858c94c3a1644338846ac9 + Pseudo is Ultrasoft + core correction, Zval = 4.0 + Generated using "atomic" code by A. Dal Corso v.6.0 svn rev. 13079 + 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 28.08500 Si( 1.00) + + 12 Sym. Ops., with inversion, found ( 6 have fractional translation) + + + s frac. trans. + +--- SYMMETRIES REMOVED --- + +--- K-POINTS REMOVED --- + +--- MEMORY INFO REMOVED --- + + Initial potential from superposition of free atoms + + starting charge 7.9989, renormalised to 8.0000 + Starting wfcs are 8 randomized atomic wfcs + + total cpu time spent up to now is 0.4 secs + + Self-consistent Calculation + + iteration # 1 ecut= 30.00 Ry beta= 0.40 + Davidson diagonalization with overlap + +---- Real-time Memory Report at c_bands before calling an iterative solver + 102 MiB given to the printing process from OS + 0 MiB allocation reported by mallinfo(arena+hblkhd) + 35243 MiB available memory on the node where the printing process lives +------------------ + ethr = 1.00E-02, avg # of iterations = 3.6 + + Threshold (ethr) on eigenvalues was too large: + Diagonalizing with lowered threshold + + Davidson diagonalization with overlap + +---- Real-time Memory Report at c_bands before calling an iterative solver + 109 MiB given to the printing process from OS + 0 MiB allocation reported by mallinfo(arena+hblkhd) + 35231 MiB available memory on the node where the printing process lives +------------------ + ethr = 6.79E-04, avg # of iterations = 1.7 + + total cpu time spent up to now is 0.5 secs + + total energy = -22.66564781 Ry + estimated scf accuracy < 0.05850370 Ry + + iteration # 2 ecut= 30.00 Ry beta= 0.40 + Davidson diagonalization with overlap + +---- Real-time Memory Report at c_bands before calling an iterative solver + 109 MiB given to the printing process from OS + 0 MiB allocation reported by mallinfo(arena+hblkhd) + 35227 MiB available memory on the node where the printing process lives +------------------ + ethr = 7.31E-04, avg # of iterations = 1.0 + + total cpu time spent up to now is 0.5 secs + + WARNING: integrated charge= 8.00002111, expected= 8.00000000 + + total energy = -22.66198083 Ry + estimated scf accuracy < 0.01627960 Ry + + iteration # 3 ecut= 30.00 Ry beta= 0.40 + Davidson diagonalization with overlap + +---- Real-time Memory Report at c_bands before calling an iterative solver + 110 MiB given to the printing process from OS + 0 MiB allocation reported by mallinfo(arena+hblkhd) + 35226 MiB available memory on the node where the printing process lives +------------------ + ethr = 2.03E-04, avg # of iterations = 1.5 + + total cpu time spent up to now is 0.6 secs + + WARNING: integrated charge= 8.00078523, expected= 8.00000000 + + total energy = -22.66258880 Ry + estimated scf accuracy < 0.00025387 Ry + + iteration # 4 ecut= 30.00 Ry beta= 0.40 + Davidson diagonalization with overlap + +---- Real-time Memory Report at c_bands before calling an iterative solver + 110 MiB given to the printing process from OS + 0 MiB allocation reported by mallinfo(arena+hblkhd) + 35226 MiB available memory on the node where the printing process lives +------------------ + ethr = 3.17E-06, avg # of iterations = 5.5 + + total cpu time spent up to now is 0.7 secs + + WARNING: integrated charge= 8.00070298, expected= 8.00000000 + + total energy = -22.66281125 Ry + estimated scf accuracy < 0.00000803 Ry + + iteration # 5 ecut= 30.00 Ry beta= 0.40 + Davidson diagonalization with overlap + +---- Real-time Memory Report at c_bands before calling an iterative solver + 110 MiB given to the printing process from OS + 0 MiB allocation reported by mallinfo(arena+hblkhd) + 35226 MiB available memory on the node where the printing process lives +------------------ + ethr = 1.00E-07, avg # of iterations = 1.8 + + total cpu time spent up to now is 0.7 secs + + WARNING: integrated charge= 8.00060768, expected= 8.00000000 + + total energy = -22.66279546 Ry + estimated scf accuracy < 0.00000021 Ry + + iteration # 6 ecut= 30.00 Ry beta= 0.40 + Davidson diagonalization with overlap + +---- Real-time Memory Report at c_bands before calling an iterative solver + 110 MiB given to the printing process from OS + 0 MiB allocation reported by mallinfo(arena+hblkhd) + 35226 MiB available memory on the node where the printing process lives +------------------ + ethr = 2.57E-09, avg # of iterations = 3.0 + + total cpu time spent up to now is 0.8 secs + + WARNING: integrated charge= 8.00059538, expected= 8.00000000 + + total energy = -22.66279684 Ry + estimated scf accuracy < 0.00000005 Ry + + iteration # 7 ecut= 30.00 Ry beta= 0.40 + Davidson diagonalization with overlap + +---- Real-time Memory Report at c_bands before calling an iterative solver + 110 MiB given to the printing process from OS + 0 MiB allocation reported by mallinfo(arena+hblkhd) + 35226 MiB available memory on the node where the printing process lives +------------------ + ethr = 6.26E-10, avg # of iterations = 1.8 + + total cpu time spent up to now is 0.8 secs + + End of self-consistent calculation + +--- OCCUPATIONS REMOVED --- + + the Fermi energy is 6.3641 ev + + WARNING: integrated charge= 8.00060120, expected= 8.00000000 + +! total energy = -22.66279927 Ry + estimated scf accuracy < 1.5E-10 Ry + smearing contrib. (-TS) = 0.00000489 Ry + internal energy E=F+TS = -22.66280417 Ry + + The total energy is F=E-TS. E is the sum of the following terms: + one-electron contribution = 5.01865204 Ry + hartree contribution = 1.12199684 Ry + xc contribution = -12.12347470 Ry + ewald contribution = -16.67997834 Ry + + convergence has been achieved in 7 iterations + + Forces acting on atoms (cartesian axes, Ry/au): + + atom 1 type 1 force = 0.00000000 0.00000000 -0.00000092 + atom 2 type 1 force = 0.00000000 0.00000000 0.00000092 + The non-local contrib. to forces + atom 1 type 1 force = 0.00000000 0.00000000 -0.00000151 + atom 2 type 1 force = 0.00000000 -0.00000000 0.00000151 + The ionic contribution to forces + atom 1 type 1 force = -0.00000000 -0.00000000 0.00000000 + atom 2 type 1 force = 0.00000000 0.00000000 -0.00000000 + The local contribution to forces + atom 1 type 1 force = -0.00000000 0.00000000 0.00000089 + atom 2 type 1 force = -0.00000000 0.00000000 -0.00000089 + The core correction contribution to forces + atom 1 type 1 force = -0.00000000 -0.00000000 0.00000008 + atom 2 type 1 force = -0.00000000 -0.00000000 -0.00000008 + The Hubbard contrib. to forces + atom 1 type 1 force = 0.00000000 0.00000000 0.00000000 + atom 2 type 1 force = 0.00000000 0.00000000 0.00000000 + The SCF correction term to forces + atom 1 type 1 force = -0.00000000 -0.00000000 -0.00000039 + atom 2 type 1 force = 0.00000000 0.00000000 0.00000039 + + Total force = 0.000001 Total SCF correction = 0.000001 + SCF correction compared to forces is large: reduce conv_thr to get better values + + + Computing stress (Cartesian axis) and pressure + + total stress (Ry/bohr**3) (kbar) P= -11.77 + -0.00008004 0.00000000 -0.00000000 -11.77 0.00 -0.00 + 0.00000000 -0.00008004 0.00000000 0.00 -11.77 0.00 + 0.00000000 0.00000000 -0.00008004 0.00 0.00 -11.77 + + kinetic stress (kbar) 2158.74 0.00 0.00 + 0.00 2158.74 -0.00 + 0.00 -0.00 2158.74 + + local stress (kbar) 12.08 0.00 0.00 + 0.00 12.08 0.00 + 0.00 0.00 12.08 + + nonloc. stress (kbar) 1579.34 -0.00 0.00 + -0.00 1579.34 -0.00 + 0.00 -0.00 1579.34 + + hartree stress (kbar) 199.39 -0.00 -0.00 + -0.00 199.39 0.00 + -0.00 0.00 199.39 + + exc-cor stress (kbar) 2850.74 -0.00 -0.00 + -0.00 2850.74 -0.00 + -0.00 -0.00 2850.74 + + corecor stress (kbar) -3847.88 0.00 -0.00 + 0.00 -3847.88 0.00 + -0.00 0.00 -3847.88 + + ewald stress (kbar) -2964.19 0.00 0.00 + 0.00 -2964.19 -0.00 + 0.00 -0.00 -2964.19 + + hubbard stress (kbar) 0.00 0.00 0.00 + 0.00 0.00 0.00 + 0.00 0.00 0.00 + + DFT-D stress (kbar) 0.00 0.00 0.00 + 0.00 0.00 0.00 + 0.00 0.00 0.00 + + XDM stress (kbar) 0.00 0.00 0.00 + 0.00 0.00 0.00 + 0.00 0.00 0.00 + + dft-nl stress (kbar) 0.00 0.00 0.00 + 0.00 0.00 0.00 + 0.00 0.00 0.00 + + TS-vdW stress (kbar) 0.00 0.00 0.00 + 0.00 0.00 0.00 + 0.00 0.00 0.00 + + MDB stress (kbar) 0.00 0.00 0.00 + 0.00 0.00 0.00 + 0.00 0.00 0.00 + + 3D-RISM stress (kbar) 0.00 0.00 0.00 + 0.00 0.00 0.00 + 0.00 0.00 0.00 + + + BFGS Geometry Optimization + Energy error = 1.3E-04 Ry + Gradient error = 9.2E-07 Ry/Bohr + Cell gradient error = 1.2E+01 kbar + + number of scf cycles = 1 + number of bfgs steps = 0 + + enthalpy new = -22.6627992744 Ry + + new trust radius = 0.0066480062 bohr + new conv_thr = 0.0000000008 Ry + + new unit-cell volume = 274.27476 a.u.^3 ( 40.64333 Ang^3 ) + density = 2.29490 g/cm^3 + +CELL_PARAMETERS (angstrom) + 3.859236539 -0.000000000 0.000000000 + 1.929618269 3.342196882 0.000000000 + 1.929618269 1.114065627 3.151053816 + +ATOMIC_POSITIONS (angstrom) +Si 5.7888548084 3.3421968820 2.3632898762 +Si 3.8592365390 2.2281312546 1.5755273931 + + + + Writing config-only to output data dir ./out/aiida.save/ : + XML data file + NEW-OLD atomic charge density approx. for the potential + New effective cutoffs (rho, wfc): 240.49 30.06 + extrapolated charge 8.00060, renormalised to 8.00000 + + total cpu time spent up to now is 1.0 secs + + Self-consistent Calculation + + iteration # 1 ecut= 30.00 Ry beta= 0.40 + Davidson diagonalization with overlap + +---- Real-time Memory Report at c_bands before calling an iterative solver + 111 MiB given to the printing process from OS + 0 MiB allocation reported by mallinfo(arena+hblkhd) + 35195 MiB available memory on the node where the printing process lives +------------------ + ethr = 1.00E-06, avg # of iterations = 2.1 + + Threshold (ethr) on eigenvalues was too large: + Diagonalizing with lowered threshold + + Davidson diagonalization with overlap + +---- Real-time Memory Report at c_bands before calling an iterative solver + 112 MiB given to the printing process from OS + 0 MiB allocation reported by mallinfo(arena+hblkhd) + 35195 MiB available memory on the node where the printing process lives +------------------ + ethr = 2.68E-08, avg # of iterations = 3.2 + + total cpu time spent up to now is 1.0 secs + + WARNING: integrated charge= 8.00028103, expected= 8.00000000 + + total energy = -22.66285336 Ry + estimated scf accuracy < 0.00000172 Ry + + iteration # 2 ecut= 30.00 Ry beta= 0.40 + Davidson diagonalization with overlap + +---- Real-time Memory Report at c_bands before calling an iterative solver + 112 MiB given to the printing process from OS + 0 MiB allocation reported by mallinfo(arena+hblkhd) + 35272 MiB available memory on the node where the printing process lives +------------------ + ethr = 2.15E-08, avg # of iterations = 1.0 + + total cpu time spent up to now is 1.1 secs + + WARNING: integrated charge= 8.00062814, expected= 8.00000000 + + total energy = -22.66284852 Ry + estimated scf accuracy < 0.00000044 Ry + + iteration # 3 ecut= 30.00 Ry beta= 0.40 + Davidson diagonalization with overlap + +---- Real-time Memory Report at c_bands before calling an iterative solver + 112 MiB given to the printing process from OS + 0 MiB allocation reported by mallinfo(arena+hblkhd) + 35273 MiB available memory on the node where the printing process lives +------------------ + ethr = 5.53E-09, avg # of iterations = 2.0 + + total cpu time spent up to now is 1.1 secs + + WARNING: integrated charge= 8.00071091, expected= 8.00000000 + + total energy = -22.66284212 Ry + estimated scf accuracy < 9.6E-09 Ry + + iteration # 4 ecut= 30.00 Ry beta= 0.40 + Davidson diagonalization with overlap + +---- Real-time Memory Report at c_bands before calling an iterative solver + 112 MiB given to the printing process from OS + 0 MiB allocation reported by mallinfo(arena+hblkhd) + 35273 MiB available memory on the node where the printing process lives +------------------ + ethr = 1.20E-10, avg # of iterations = 2.3 + + total cpu time spent up to now is 1.2 secs + + WARNING: integrated charge= 8.00072709, expected= 8.00000000 + + total energy = -22.66284488 Ry + estimated scf accuracy < 0.00000002 Ry + + iteration # 5 ecut= 30.00 Ry beta= 0.40 + Davidson diagonalization with overlap + +---- Real-time Memory Report at c_bands before calling an iterative solver + 112 MiB given to the printing process from OS + 0 MiB allocation reported by mallinfo(arena+hblkhd) + 35273 MiB available memory on the node where the printing process lives +------------------ + ethr = 1.20E-10, avg # of iterations = 2.0 + + total cpu time spent up to now is 1.2 secs + + End of self-consistent calculation + +--- OCCUPATIONS REMOVED --- + + the Fermi energy is 6.4194 ev + + WARNING: integrated charge= 8.00072346, expected= 8.00000000 + +! total energy = -22.66284342 Ry + estimated scf accuracy < 2.0E-10 Ry + smearing contrib. (-TS) = 0.00000593 Ry + internal energy E=F+TS = -22.66284935 Ry + + The total energy is F=E-TS. E is the sum of the following terms: + one-electron contribution = 5.06484499 Ry + hartree contribution = 1.11681435 Ry + xc contribution = -12.13108618 Ry + ewald contribution = -16.71342250 Ry + + convergence has been achieved in 5 iterations + + Forces acting on atoms (cartesian axes, Ry/au): + + atom 1 type 1 force = -0.00000000 -0.00000000 0.00000057 + atom 2 type 1 force = 0.00000000 0.00000000 -0.00000057 + The non-local contrib. to forces + atom 1 type 1 force = -0.00000000 -0.00000000 0.00000038 + atom 2 type 1 force = 0.00000000 -0.00000000 -0.00000038 + The ionic contribution to forces + atom 1 type 1 force = 0.00000000 -0.00000000 0.00000131 + atom 2 type 1 force = 0.00000000 0.00000000 -0.00000131 + The local contribution to forces + atom 1 type 1 force = -0.00000000 0.00000000 -0.00000107 + atom 2 type 1 force = -0.00000000 0.00000000 0.00000107 + The core correction contribution to forces + atom 1 type 1 force = -0.00000000 -0.00000000 -0.00000005 + atom 2 type 1 force = -0.00000000 -0.00000000 0.00000005 + The Hubbard contrib. to forces + atom 1 type 1 force = 0.00000000 0.00000000 0.00000000 + atom 2 type 1 force = 0.00000000 0.00000000 0.00000000 + The SCF correction term to forces + atom 1 type 1 force = -0.00000000 -0.00000000 -0.00000000 + atom 2 type 1 force = -0.00000000 -0.00000000 0.00000000 + + Total force = 0.000001 Total SCF correction = 0.000000 + + + Computing stress (Cartesian axis) and pressure + + total stress (Ry/bohr**3) (kbar) P= -6.28 + -0.00004266 -0.00000000 0.00000000 -6.27 -0.00 0.00 + 0.00000000 -0.00004266 0.00000000 0.00 -6.27 0.00 + 0.00000000 0.00000000 -0.00004266 0.00 0.00 -6.28 + + kinetic stress (kbar) 2177.24 -0.00 -0.00 + -0.00 2177.24 -0.00 + -0.00 -0.00 2177.24 + + local stress (kbar) 18.44 0.00 0.00 + 0.00 18.44 0.00 + 0.00 0.00 18.45 + + nonloc. stress (kbar) 1590.97 -0.00 -0.00 + -0.00 1590.97 -0.00 + -0.00 -0.00 1590.97 + + hartree stress (kbar) 199.67 -0.00 -0.00 + -0.00 199.67 0.00 + -0.00 0.00 199.66 + + exc-cor stress (kbar) 2867.00 0.00 -0.00 + 0.00 2867.00 -0.00 + -0.00 -0.00 2867.00 + + corecor stress (kbar) -3871.57 -0.00 0.00 + -0.00 -3871.57 0.00 + 0.00 0.00 -3871.57 + + ewald stress (kbar) -2988.03 -0.00 -0.00 + -0.00 -2988.03 -0.00 + -0.00 -0.00 -2988.04 + + hubbard stress (kbar) 0.00 0.00 0.00 + 0.00 0.00 0.00 + 0.00 0.00 0.00 + + DFT-D stress (kbar) 0.00 0.00 0.00 + 0.00 0.00 0.00 + 0.00 0.00 0.00 + + XDM stress (kbar) 0.00 0.00 0.00 + 0.00 0.00 0.00 + 0.00 0.00 0.00 + + dft-nl stress (kbar) 0.00 0.00 0.00 + 0.00 0.00 0.00 + 0.00 0.00 0.00 + + TS-vdW stress (kbar) 0.00 0.00 0.00 + 0.00 0.00 0.00 + 0.00 0.00 0.00 + + MDB stress (kbar) 0.00 0.00 0.00 + 0.00 0.00 0.00 + 0.00 0.00 0.00 + + 3D-RISM stress (kbar) 0.00 0.00 0.00 + 0.00 0.00 0.00 + 0.00 0.00 0.00 + + Energy error = 4.4E-05 Ry + Gradient error = 5.7E-07 Ry/Bohr + Cell gradient error = 6.3E+00 kbar + + number of scf cycles = 2 + number of bfgs steps = 1 + + enthalpy old = -22.6627992744 Ry + enthalpy new = -22.6628434200 Ry + + CASE: enthalpy _new < enthalpy _old + + new trust radius = 0.0075145776 bohr + new conv_thr = 8.0E-12 Ry + + new unit-cell volume = 272.41241 a.u.^3 ( 40.36735 Ang^3 ) + density = 2.31059 g/cm^3 + +CELL_PARAMETERS (angstrom) + 3.850482223 0.000000000 0.000000000 + 1.925241111 3.334615422 0.000000000 + 1.925241111 1.111538474 3.143904944 + +ATOMIC_POSITIONS (angstrom) +Si 5.7757233339 3.3346154216 2.3579288575 +Si 3.8504822226 2.2230769477 1.5719523229 + + + + Writing config-only to output data dir ./out/aiida.save/ : + XML data file + NEW-OLD atomic charge density approx. for the potential + New effective cutoffs (rho, wfc): 241.59 30.20 + extrapolated charge 8.00072, renormalised to 8.00000 + + total cpu time spent up to now is 1.4 secs + + Self-consistent Calculation + + iteration # 1 ecut= 30.00 Ry beta= 0.40 + Davidson diagonalization with overlap + +---- Real-time Memory Report at c_bands before calling an iterative solver + 112 MiB given to the printing process from OS + 0 MiB allocation reported by mallinfo(arena+hblkhd) + 35273 MiB available memory on the node where the printing process lives +------------------ + ethr = 1.00E-06, avg # of iterations = 2.1 + + Threshold (ethr) on eigenvalues was too large: + Diagonalizing with lowered threshold + + Davidson diagonalization with overlap + +---- Real-time Memory Report at c_bands before calling an iterative solver + 113 MiB given to the printing process from OS + 0 MiB allocation reported by mallinfo(arena+hblkhd) + 35272 MiB available memory on the node where the printing process lives +------------------ + ethr = 3.46E-08, avg # of iterations = 3.2 + + total cpu time spent up to now is 1.5 secs + + WARNING: integrated charge= 8.00034486, expected= 8.00000000 + + total energy = -22.66281705 Ry + estimated scf accuracy < 0.00000221 Ry + + iteration # 2 ecut= 30.00 Ry beta= 0.40 + Davidson diagonalization with overlap + +---- Real-time Memory Report at c_bands before calling an iterative solver + 114 MiB given to the printing process from OS + 0 MiB allocation reported by mallinfo(arena+hblkhd) + 35272 MiB available memory on the node where the printing process lives +------------------ + ethr = 2.77E-08, avg # of iterations = 1.0 + + total cpu time spent up to now is 1.5 secs + + WARNING: integrated charge= 8.00077323, expected= 8.00000000 + + total energy = -22.66281049 Ry + estimated scf accuracy < 0.00000057 Ry + + iteration # 3 ecut= 30.00 Ry beta= 0.40 + Davidson diagonalization with overlap + +---- Real-time Memory Report at c_bands before calling an iterative solver + 114 MiB given to the printing process from OS + 0 MiB allocation reported by mallinfo(arena+hblkhd) + 35272 MiB available memory on the node where the printing process lives +------------------ + ethr = 7.18E-09, avg # of iterations = 2.0 + + total cpu time spent up to now is 1.6 secs + + WARNING: integrated charge= 8.00087311, expected= 8.00000000 + + total energy = -22.66280152 Ry + estimated scf accuracy < 0.00000001 Ry + + iteration # 4 ecut= 30.00 Ry beta= 0.40 + Davidson diagonalization with overlap + +---- Real-time Memory Report at c_bands before calling an iterative solver + 114 MiB given to the printing process from OS + 0 MiB allocation reported by mallinfo(arena+hblkhd) + 35271 MiB available memory on the node where the printing process lives +------------------ + ethr = 1.62E-10, avg # of iterations = 2.3 + + total cpu time spent up to now is 1.6 secs + + WARNING: integrated charge= 8.00089536, expected= 8.00000000 + + total energy = -22.66280547 Ry + estimated scf accuracy < 0.00000003 Ry + + iteration # 5 ecut= 30.00 Ry beta= 0.40 + Davidson diagonalization with overlap + +---- Real-time Memory Report at c_bands before calling an iterative solver + 114 MiB given to the printing process from OS + 0 MiB allocation reported by mallinfo(arena+hblkhd) + 35271 MiB available memory on the node where the printing process lives +------------------ + ethr = 1.62E-10, avg # of iterations = 2.0 + + total cpu time spent up to now is 1.7 secs + + WARNING: integrated charge= 8.00089207, expected= 8.00000000 + + total energy = -22.66280333 Ry + estimated scf accuracy < 2.7E-10 Ry + + iteration # 6 ecut= 30.00 Ry beta= 0.40 + Davidson diagonalization with overlap + +---- Real-time Memory Report at c_bands before calling an iterative solver + 114 MiB given to the printing process from OS + 0 MiB allocation reported by mallinfo(arena+hblkhd) + 35271 MiB available memory on the node where the printing process lives +------------------ + ethr = 3.33E-12, avg # of iterations = 2.5 + + total cpu time spent up to now is 1.7 secs + + WARNING: integrated charge= 8.00089129, expected= 8.00000000 + + total energy = -22.66280306 Ry + estimated scf accuracy < 5.7E-11 Ry + + iteration # 7 ecut= 30.00 Ry beta= 0.40 + Davidson diagonalization with overlap + +---- Real-time Memory Report at c_bands before calling an iterative solver + 114 MiB given to the printing process from OS + 0 MiB allocation reported by mallinfo(arena+hblkhd) + 35270 MiB available memory on the node where the printing process lives +------------------ + ethr = 7.08E-13, avg # of iterations = 1.8 + + total cpu time spent up to now is 1.8 secs + + End of self-consistent calculation + +--- OCCUPATIONS REMOVED --- + + the Fermi energy is 6.4825 ev + + WARNING: integrated charge= 8.00089101, expected= 8.00000000 + +! total energy = -22.66280318 Ry + estimated scf accuracy < 1.1E-12 Ry + smearing contrib. (-TS) = 0.00000737 Ry + internal energy E=F+TS = -22.66281055 Ry + + The total energy is F=E-TS. E is the sum of the following terms: + one-electron contribution = 5.11744330 Ry + hartree contribution = 1.11093802 Ry + xc contribution = -12.13976856 Ry + ewald contribution = -16.75142331 Ry + + convergence has been achieved in 7 iterations + + Forces acting on atoms (cartesian axes, Ry/au): + + atom 1 type 1 force = 0.00000000 0.00000000 -0.00000025 + atom 2 type 1 force = -0.00000000 -0.00000000 0.00000025 + The non-local contrib. to forces + atom 1 type 1 force = 0.00000000 0.00000000 -0.00000030 + atom 2 type 1 force = -0.00000000 -0.00000000 0.00000030 + The ionic contribution to forces + atom 1 type 1 force = -0.00000000 -0.00000000 -0.00000098 + atom 2 type 1 force = -0.00000000 0.00000000 0.00000098 + The local contribution to forces + atom 1 type 1 force = -0.00000000 0.00000000 0.00000099 + atom 2 type 1 force = -0.00000000 0.00000000 -0.00000099 + The core correction contribution to forces + atom 1 type 1 force = -0.00000000 -0.00000000 0.00000004 + atom 2 type 1 force = -0.00000000 -0.00000000 -0.00000004 + The Hubbard contrib. to forces + atom 1 type 1 force = 0.00000000 0.00000000 0.00000000 + atom 2 type 1 force = 0.00000000 0.00000000 0.00000000 + The SCF correction term to forces + atom 1 type 1 force = 0.00000000 -0.00000000 -0.00000001 + atom 2 type 1 force = -0.00000000 -0.00000000 0.00000001 + + Total force = 0.000000 Total SCF correction = 0.000000 + + + Computing stress (Cartesian axis) and pressure + + total stress (Ry/bohr**3) (kbar) P= 0.13 + 0.00000086 0.00000000 0.00000000 0.13 0.00 0.00 + 0.00000000 0.00000086 -0.00000000 0.00 0.13 -0.00 + 0.00000000 -0.00000000 0.00000086 0.00 -0.00 0.13 + + kinetic stress (kbar) 2198.44 0.00 0.00 + 0.00 2198.44 -0.00 + 0.00 -0.00 2198.44 + + local stress (kbar) 25.78 0.00 0.00 + 0.00 25.78 0.00 + 0.00 0.00 25.78 + + nonloc. stress (kbar) 1604.30 0.00 0.00 + 0.00 1604.30 -0.00 + 0.00 -0.00 1604.30 + + hartree stress (kbar) 199.97 0.00 -0.00 + 0.00 199.97 0.00 + -0.00 0.00 199.97 + + exc-cor stress (kbar) 2885.56 -0.00 -0.00 + -0.00 2885.56 -0.00 + -0.00 -0.00 2885.56 + + corecor stress (kbar) -3898.61 0.00 -0.00 + 0.00 -3898.61 0.00 + -0.00 0.00 -3898.61 + + ewald stress (kbar) -3015.31 -0.00 0.00 + -0.00 -3015.31 -0.00 + 0.00 -0.00 -3015.30 + + hubbard stress (kbar) 0.00 0.00 0.00 + 0.00 0.00 0.00 + 0.00 0.00 0.00 + + DFT-D stress (kbar) 0.00 0.00 0.00 + 0.00 0.00 0.00 + 0.00 0.00 0.00 + + XDM stress (kbar) 0.00 0.00 0.00 + 0.00 0.00 0.00 + 0.00 0.00 0.00 + + dft-nl stress (kbar) 0.00 0.00 0.00 + 0.00 0.00 0.00 + 0.00 0.00 0.00 + + TS-vdW stress (kbar) 0.00 0.00 0.00 + 0.00 0.00 0.00 + 0.00 0.00 0.00 + + MDB stress (kbar) 0.00 0.00 0.00 + 0.00 0.00 0.00 + 0.00 0.00 0.00 + + 3D-RISM stress (kbar) 0.00 0.00 0.00 + 0.00 0.00 0.00 + 0.00 0.00 0.00 + + Energy error = 4.0E-05 Ry + Gradient error = 2.5E-07 Ry/Bohr + Cell gradient error = 1.3E-01 kbar + + bfgs converged in 3 scf cycles and 2 bfgs steps + (criteria: energy < 2.0E-04 Ry, force < 1.0E-03 Ry/Bohr, cell < 5.0E-01 kbar) + + End of BFGS Geometry Optimization + + Final enthalpy = -22.6628031775 Ry + + File ./out/aiida.bfgs deleted, as requested +Begin final coordinates + new unit-cell volume = 272.41241 a.u.^3 ( 40.36735 Ang^3 ) + density = 2.31059 g/cm^3 + +CELL_PARAMETERS (angstrom) + 3.850482223 0.000000000 0.000000000 + 1.925241111 3.334615422 0.000000000 + 1.925241111 1.111538474 3.143904944 + +ATOMIC_POSITIONS (angstrom) +Si 5.7757233339 3.3346154216 2.3579288575 +Si 3.8504822226 2.2230769477 1.5719523229 +End final coordinates + + + + Writing config-only to output data dir ./out/aiida.save/ : + XML data file + + Final scf calculation at the relaxed structure. + The G-vectors are recalculated for the final unit cell + Results may differ from those at the preceding step. + + Parallelization info + -------------------- + sticks: dense smooth PW G-vecs: dense smooth PW + Min 217 108 34 4240 1495 266 + Max 219 109 35 4241 1498 267 + Sum 871 433 139 16961 5985 1067 + + Using Slab Decomposition + + + + bravais-lattice index = 0 + lattice parameter (alat) = 7.3075 a.u. + unit-cell volume = 272.4124 (a.u.)^3 + number of atoms/cell = 2 + number of atomic types = 1 + number of electrons = 8.00 + number of Kohn-Sham states= 8 + kinetic-energy cutoff = 30.0000 Ry + charge density cutoff = 240.0000 Ry + scf convergence threshold = 8.0E-12 + mixing beta = 0.4000 + number of iterations used = 8 plain mixing + press convergence thresh. = 5.0E-01 + Exchange-correlation= PBESOL + ( 1 4 10 8 0 0 0) + + celldm(1)= 7.307523 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) = ( 0.995735 0.000000 0.000000 ) + a(2) = ( 0.497868 0.862332 0.000000 ) + a(3) = ( 0.497868 0.287444 0.813014 ) + + reciprocal axes: (cart. coord. in units 2 pi/alat) + b(1) = ( 1.004283 -0.579823 -0.409997 ) + b(2) = ( -0.000000 1.159646 -0.409997 ) + b(3) = ( -0.000000 -0.000000 1.229991 ) + + + PseudoPot. # 1 for Si read from file: + ./pseudo/Si.pbesol-n-rrkjus_psl.1.0.0.UPF + MD5 check sum: c4212819de858c94c3a1644338846ac9 + Pseudo is Ultrasoft + core correction, Zval = 4.0 + Generated using "atomic" code by A. Dal Corso v.6.0 svn rev. 13079 + 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 28.08500 Si( 1.00) + + 12 Sym. Ops., with inversion, found ( 6 have fractional translation) + + + s frac. trans. + +--- SYMMETRIES REMOVED --- + + Cartesian axes + + site n. atom positions (alat units) + 1 Si tau( 1) = ( 1.4936026 0.8623319 0.6097606 ) + 2 Si tau( 2) = ( 0.9957351 0.5748879 0.4065070 ) + + Crystallographic axes + + site n. atom positions (cryst. coord.) + 1 Si tau( 1) = ( 0.7500000 0.7500000 0.7500000 ) + 2 Si tau( 2) = ( 0.5000000 0.5000000 0.5000000 ) + +--- K-POINTS REMOVED --- + +--- MEMORY INFO REMOVED --- + + Initial potential from superposition of free atoms + + starting charge 7.9989, renormalised to 8.0000 + Starting wfcs are 8 randomized atomic wfcs + + total cpu time spent up to now is 1.9 secs + + Self-consistent Calculation + + iteration # 1 ecut= 30.00 Ry beta= 0.40 + Davidson diagonalization with overlap + +---- Real-time Memory Report at c_bands before calling an iterative solver + 115 MiB given to the printing process from OS + 0 MiB allocation reported by mallinfo(arena+hblkhd) + 35236 MiB available memory on the node where the printing process lives +------------------ + ethr = 1.00E-06, avg # of iterations = 13.8 + + total cpu time spent up to now is 2.0 secs + + total energy = -22.66588974 Ry + estimated scf accuracy < 0.06115147 Ry + + iteration # 2 ecut= 30.00 Ry beta= 0.40 + Davidson diagonalization with overlap + +---- Real-time Memory Report at c_bands before calling an iterative solver + 115 MiB given to the printing process from OS + 0 MiB allocation reported by mallinfo(arena+hblkhd) + 35236 MiB available memory on the node where the printing process lives +------------------ + ethr = 7.64E-04, avg # of iterations = 1.0 + + total cpu time spent up to now is 2.1 secs + + WARNING: integrated charge= 8.00003315, expected= 8.00000000 + + total energy = -22.66218504 Ry + estimated scf accuracy < 0.01630045 Ry + + iteration # 3 ecut= 30.00 Ry beta= 0.40 + Davidson diagonalization with overlap + +---- Real-time Memory Report at c_bands before calling an iterative solver + 115 MiB given to the printing process from OS + 0 MiB allocation reported by mallinfo(arena+hblkhd) + 35236 MiB available memory on the node where the printing process lives +------------------ + ethr = 2.04E-04, avg # of iterations = 1.0 + + total cpu time spent up to now is 2.1 secs + + WARNING: integrated charge= 8.00103940, expected= 8.00000000 + + total energy = -22.66257544 Ry + estimated scf accuracy < 0.00024660 Ry + + iteration # 4 ecut= 30.00 Ry beta= 0.40 + Davidson diagonalization with overlap + +---- Real-time Memory Report at c_bands before calling an iterative solver + 115 MiB given to the printing process from OS + 0 MiB allocation reported by mallinfo(arena+hblkhd) + 35236 MiB available memory on the node where the printing process lives +------------------ + ethr = 3.08E-06, avg # of iterations = 2.8 + + total cpu time spent up to now is 2.2 secs + + WARNING: integrated charge= 8.00099504, expected= 8.00000000 + + total energy = -22.66278415 Ry + estimated scf accuracy < 0.00000131 Ry + + iteration # 5 ecut= 30.00 Ry beta= 0.40 + Davidson diagonalization with overlap + +---- Real-time Memory Report at c_bands before calling an iterative solver + 115 MiB given to the printing process from OS + 0 MiB allocation reported by mallinfo(arena+hblkhd) + 35236 MiB available memory on the node where the printing process lives +------------------ + ethr = 1.63E-08, avg # of iterations = 3.2 + + total cpu time spent up to now is 2.2 secs + + WARNING: integrated charge= 8.00086574, expected= 8.00000000 + + total energy = -22.66279009 Ry + estimated scf accuracy < 0.00000034 Ry + + iteration # 6 ecut= 30.00 Ry beta= 0.40 + Davidson diagonalization with overlap + +---- Real-time Memory Report at c_bands before calling an iterative solver + 115 MiB given to the printing process from OS + 0 MiB allocation reported by mallinfo(arena+hblkhd) + 35235 MiB available memory on the node where the printing process lives +------------------ + ethr = 4.28E-09, avg # of iterations = 1.4 + + total cpu time spent up to now is 2.3 secs + + WARNING: integrated charge= 8.00088861, expected= 8.00000000 + + total energy = -22.66279432 Ry + estimated scf accuracy < 0.00000003 Ry + + iteration # 7 ecut= 30.00 Ry beta= 0.40 + Davidson diagonalization with overlap + +---- Real-time Memory Report at c_bands before calling an iterative solver + 115 MiB given to the printing process from OS + 0 MiB allocation reported by mallinfo(arena+hblkhd) + 35235 MiB available memory on the node where the printing process lives +------------------ + ethr = 3.34E-10, avg # of iterations = 1.9 + + total cpu time spent up to now is 2.3 secs + + WARNING: integrated charge= 8.00088787, expected= 8.00000000 + + total energy = -22.66279382 Ry + estimated scf accuracy < 3.8E-10 Ry + + iteration # 8 ecut= 30.00 Ry beta= 0.40 + Davidson diagonalization with overlap + +---- Real-time Memory Report at c_bands before calling an iterative solver + 115 MiB given to the printing process from OS + 0 MiB allocation reported by mallinfo(arena+hblkhd) + 35235 MiB available memory on the node where the printing process lives +------------------ + ethr = 4.72E-12, avg # of iterations = 3.7 + + total cpu time spent up to now is 2.4 secs + + WARNING: integrated charge= 8.00088849, expected= 8.00000000 + + total energy = -22.66279392 Ry + estimated scf accuracy < 2.6E-11 Ry + + iteration # 9 ecut= 30.00 Ry beta= 0.40 + Davidson diagonalization with overlap + +---- Real-time Memory Report at c_bands before calling an iterative solver + 115 MiB given to the printing process from OS + 0 MiB allocation reported by mallinfo(arena+hblkhd) + 35235 MiB available memory on the node where the printing process lives +------------------ + ethr = 3.22E-13, avg # of iterations = 1.8 + + total cpu time spent up to now is 2.4 secs + + End of self-consistent calculation + +--- OCCUPATIONS REMOVED --- + + the Fermi energy is 6.4826 ev + + WARNING: integrated charge= 8.00088840, expected= 8.00000000 + +! total energy = -22.66279398 Ry + estimated scf accuracy < 8.2E-13 Ry + smearing contrib. (-TS) = 0.00000735 Ry + internal energy E=F+TS = -22.66280132 Ry + + The total energy is F=E-TS. E is the sum of the following terms: + one-electron contribution = 5.11745109 Ry + hartree contribution = 1.11093191 Ry + xc contribution = -12.13976101 Ry + ewald contribution = -16.75142331 Ry + + convergence has been achieved in 9 iterations + + Forces acting on atoms (cartesian axes, Ry/au): + + atom 1 type 1 force = 0.00000000 0.00000000 -0.00000023 + atom 2 type 1 force = -0.00000000 -0.00000000 0.00000023 + The non-local contrib. to forces + atom 1 type 1 force = -0.00000000 0.00000000 -0.00000040 + atom 2 type 1 force = -0.00000000 0.00000000 0.00000040 + The ionic contribution to forces + atom 1 type 1 force = 0.00000000 -0.00000000 -0.00000098 + atom 2 type 1 force = 0.00000000 0.00000000 0.00000098 + The local contribution to forces + atom 1 type 1 force = 0.00000000 0.00000000 0.00000121 + atom 2 type 1 force = 0.00000000 0.00000000 -0.00000121 + The core correction contribution to forces + atom 1 type 1 force = 0.00000000 -0.00000000 0.00000006 + atom 2 type 1 force = 0.00000000 -0.00000000 -0.00000006 + The Hubbard contrib. to forces + atom 1 type 1 force = 0.00000000 0.00000000 0.00000000 + atom 2 type 1 force = 0.00000000 0.00000000 0.00000000 + The SCF correction term to forces + atom 1 type 1 force = 0.00000000 0.00000000 -0.00000012 + atom 2 type 1 force = -0.00000000 0.00000000 0.00000012 + + Total force = 0.000000 Total SCF correction = 0.000000 + SCF correction compared to forces is large: reduce conv_thr to get better values + + + Computing stress (Cartesian axis) and pressure + + total stress (Ry/bohr**3) (kbar) P= 0.08 + 0.00000057 0.00000000 0.00000000 0.08 0.00 0.00 + 0.00000000 0.00000057 -0.00000000 0.00 0.08 -0.00 + 0.00000000 -0.00000000 0.00000057 0.00 -0.00 0.08 + + kinetic stress (kbar) 2198.43 0.00 0.00 + 0.00 2198.43 -0.00 + 0.00 -0.00 2198.43 + + local stress (kbar) 25.79 -0.00 -0.00 + -0.00 25.79 0.00 + -0.00 0.00 25.79 + + nonloc. stress (kbar) 1604.27 0.00 0.00 + 0.00 1604.27 -0.00 + 0.00 -0.00 1604.27 + + hartree stress (kbar) 199.97 0.00 0.00 + 0.00 199.97 0.00 + 0.00 0.00 199.97 + + exc-cor stress (kbar) 2885.56 0.00 -0.00 + 0.00 2885.56 -0.00 + -0.00 -0.00 2885.56 + + corecor stress (kbar) -3898.63 0.00 -0.00 + 0.00 -3898.63 0.00 + -0.00 0.00 -3898.63 + + ewald stress (kbar) -3015.31 -0.00 -0.00 + -0.00 -3015.31 -0.00 + -0.00 -0.00 -3015.30 + + hubbard stress (kbar) 0.00 0.00 0.00 + 0.00 0.00 0.00 + 0.00 0.00 0.00 + + DFT-D stress (kbar) 0.00 0.00 0.00 + 0.00 0.00 0.00 + 0.00 0.00 0.00 + + XDM stress (kbar) 0.00 0.00 0.00 + 0.00 0.00 0.00 + 0.00 0.00 0.00 + + dft-nl stress (kbar) 0.00 0.00 0.00 + 0.00 0.00 0.00 + 0.00 0.00 0.00 + + TS-vdW stress (kbar) 0.00 0.00 0.00 + 0.00 0.00 0.00 + 0.00 0.00 0.00 + + MDB stress (kbar) 0.00 0.00 0.00 + 0.00 0.00 0.00 + 0.00 0.00 0.00 + + 3D-RISM stress (kbar) 0.00 0.00 0.00 + 0.00 0.00 0.00 + 0.00 0.00 0.00 + + + Writing all to output data dir ./out/aiida.save/ : + XML data file, charge density, pseudopotentials, collected wavefunctions + +--- TIMINGS REMOVED --- + + This run was terminated on: 16:39:15 24Jul2024 + +=------------------------------------------------------------------------------= + JOB DONE. +=------------------------------------------------------------------------------= diff --git a/tests/parsers/fixtures/pw/default_xml_240411/data-file-schema.xml b/tests/parsers/fixtures/pw/default_xml_240411/data-file-schema.xml new file mode 100644 index 000000000..a22943aad --- /dev/null +++ b/tests/parsers/fixtures/pw/default_xml_240411/data-file-schema.xml @@ -0,0 +1,989 @@ + + + + + QEXSD_24.04.11 + XML file generated by PWSCF + This run was terminated on: 16:39:15 24 Jul 2024 + + + + 12 + 1 + 1 + 1 + 3 + 4 + + + + + vc-relax + from_scratch + aiida + ./pseudo/ + ./out/ + true + true + true + low + 41040 + 50 + 1.000000000000000E-004 + 5.000000000000000E-004 + 5.000000000000000E-001 + high + 100000 + false + false + + + + 2.808500000000000E+001 + Si.pbesol-n-rrkjus_psl.1.0.0.UPF + + + + + + 1.096128452905589E+001 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6.186389923095703E-002 + + + 2.314000000000149E-003 + 2.318859100341797E-003 + + + 3.138899999999989E-002 + 3.146076202392578E-002 + + + 2.511000000000152E-003 + 2.519130706787109E-003 + + + 2.426710000000001E-001 + 2.526237964630127E-001 + + + 2.217299999999978E-002 + 2.347397804260254E-002 + + + + diff --git a/tests/parsers/test_pw.py b/tests/parsers/test_pw.py index 022071080..71256ca27 100644 --- a/tests/parsers/test_pw.py +++ b/tests/parsers/test_pw.py @@ -97,15 +97,18 @@ def test_pw_default_no_xml( }) -@pytest.mark.parametrize('xml_format', [ - '190304', - '191206', - '200420', - '210716', - '211101', - '220603', - '230310', -]) +@pytest.mark.parametrize( + 'xml_format', [ + '190304', + '191206', + '200420', + '210716', + '211101', + '220603', + '230310', + '240411', + ] +) def test_pw_default_xml( fixture_localhost, generate_calc_job_node, generate_parser, generate_inputs, data_regression, xml_format ): diff --git a/tests/parsers/test_pw/test_pw_default_xml_240411_.yml b/tests/parsers/test_pw/test_pw_default_xml_240411_.yml new file mode 100644 index 000000000..d2a500efb --- /dev/null +++ b/tests/parsers/test_pw/test_pw_default_xml_240411_.yml @@ -0,0 +1,199 @@ +output_band: + array|bands: + - 13 + - 8 + array|kpoints: + - 13 + - 3 + array|occupations: + - 13 + - 8 + array|weights: + - 13 + cell: + - - 2.715 + - 2.715 + - 0.0 + - - 2.715 + - 0.0 + - 2.715 + - - 0.0 + - 2.715 + - 2.715 + label_numbers: [] + labels: [] + pbc1: true + pbc2: true + pbc3: true + units: eV +output_parameters: + beta_real_space: false + charge_density: ./charge-density.dat + constraint_mag: 0 + convergence_info: + opt_conv: + convergence_achieved: true + grad_norm: 3.231667310330838e-07 + n_opt_steps: 2 + scf_conv: + convergence_achieved: true + n_scf_steps: 9 + scf_error: 4.077374347958867e-13 + creator_name: pwscf + creator_version: 7.3.1 + degauss: 0.136056917253 + dft_exchange_correlation: PBESOL + do_magnetization: false + do_not_use_time_reversal: false + energy: -308.34298852586466 + energy_accuracy: 1.1156667214746e-11 + energy_accuracy_units: eV + energy_ewald: -227.91470151586452 + energy_ewald_units: eV + energy_hartree: 15.114997095258722 + energy_hartree_units: eV + energy_one_electron: 69.62646194984048 + energy_one_electron_units: eV + energy_smearing: 0.000100001834180955 + energy_smearing_units: eV + energy_threshold: 3.22e-13 + energy_units: eV + energy_xc: -165.16984592087658 + energy_xc_units: eV + fermi_energy: 6.4826 + fermi_energy_units: eV + fft_grid: + - 36 + - 36 + - 36 + forces_units: ev / angstrom + format_name: QEXSD + format_version: 24.04.11 + has_dipole_correction: false + has_electric_field: false + init_wall_time_seconds: 0.4 + inversion_symmetry: true + lattice_symmetries: [] + lda_plus_u_calculation: false + lkpoint_dir: false + lsda: false + magnetization_angle1: + - 0.0 + magnetization_angle2: + - 0.0 + monkhorst_pack_grid: + - 4 + - 4 + - 4 + monkhorst_pack_offset: + - 0 + - 0 + - 0 + no_time_rev_operations: false + non_colinear_calculation: false + number_ionic_steps: 2 + number_of_atomic_wfc: 8 + number_of_atoms: 2 + number_of_bands: 8 + number_of_bravais_symmetries: 12 + number_of_electrons: 8.0 + number_of_k_points: 13 + number_of_species: 1 + number_of_spin_components: 1 + number_of_symmetries: 12 + occupations: smearing + q_real_space: false + rho_cutoff: 3265.366014072 + rho_cutoff_units: eV + scf_iterations: 9 + smearing_type: mv + smooth_fft_grid: + - 32 + - 32 + - 32 + spin_orbit_calculation: false + spin_orbit_domag: false + starting_magnetization: + - 0.0 + stress_units: GPascal + symmetries: + - symmetry_number: 0 + t_rev: '0' + - symmetry_number: 3 + t_rev: '0' + - symmetry_number: 26 + t_rev: '0' + - symmetry_number: 27 + t_rev: '0' + - symmetry_number: 30 + t_rev: '0' + - symmetry_number: 31 + t_rev: '0' + - symmetry_number: 32 + t_rev: '0' + - symmetry_number: 35 + t_rev: '0' + - symmetry_number: 58 + t_rev: '0' + - symmetry_number: 59 + t_rev: '0' + - symmetry_number: 62 + t_rev: '0' + - symmetry_number: 63 + t_rev: '0' + symmetries_units: crystal + time_reversal_flag: true + total_force: 0.0 + total_force_units: ev / angstrom + total_number_of_scf_iterations: 28 + volume: 40.36735351405804 + wfc_cutoff: 408.170751759 + wfc_cutoff_units: eV +output_trajectory: + array|atomic_species_name: + - 2 + array|cells: + - 3 + - 3 + - 3 + array|energy: + - 4 + array|energy_accuracy: + - 4 + array|energy_ewald: + - 4 + array|energy_hartree: + - 4 + array|energy_one_electron: + - 4 + array|energy_smearing: + - 4 + array|energy_threshold: + - 4 + array|energy_xc: + - 4 + array|fermi_energy: + - 4 + array|forces: + - 4 + - 2 + - 3 + array|positions: + - 3 + - 2 + - 3 + array|scf_accuracy: + - 28 + array|scf_iterations: + - 4 + array|steps: + - 3 + array|stress: + - 4 + - 3 + - 3 + array|total_force: + - 4 + symbols: + - Si + - Si