Commit 131ad4a9 authored by Markus Scheidgen's avatar Markus Scheidgen
Browse files

Added actual parsers qbox, fleur, molcas, dmol. Other parser related fixed....

Added actual parsers qbox, fleur, molcas,  dmol. Other parser related fixed. Processing catching sys.exit in tasks and parsers.
parent fb04e0e0
......@@ -48,81 +48,108 @@
[submodule "dependencies/parsers/gaussian"]
path = dependencies/parsers/gaussian
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-gaussian.git
branch = nomad-fair
[submodule "dependencies/parsers/quantum-espresso"]
path = dependencies/parsers/quantum-espresso
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-quantum-espresso.git
branch = nomad-fair
[submodule "dependencies/parsers/abinit"]
path = dependencies/parsers/abinit
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-abinit.git
branch = nomad-fair
[submodule "dependencies/parsers/orca"]
path = dependencies/parsers/orca
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-orca.git
branch = nomad-fair
[submodule "dependencies/parsers/castep"]
path = dependencies/parsers/castep
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-castep.git
branch = nomad-fair
[submodule "dependencies/parsers/dl-poly"]
path = dependencies/parsers/dl-poly
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-dl-poly.git
branch = nomad-fair
[submodule "dependencies/parsers/lib-atoms"]
path = dependencies/parsers/lib-atoms
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-lib-atoms.git
branch = nomad-fair
[submodule "dependencies/parsers/octopus"]
path = dependencies/parsers/octopus
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-octopus.git
branch = nomad-fair
[submodule "dependencies/parsers/phonopy"]
path = dependencies/parsers/phonopy
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-phonopy.git
branch = nomad-fair
[submodule "dependencies/parsers/phonopy-library"]
path = dependencies/parsers/phonopy-library
url = https://gitlab.mpcdf.mpg.de/nomad-lab/phonopy.git
branch = nomad-fair
[submodule "dependencies/parsers/gpaw"]
path = dependencies/parsers/gpaw
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-gpaw.git
branch = nomad-fair
[submodule "dependencies/parsers/atk"]
path = dependencies/parsers/atk
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-atk.git
branch = nomad-fair
[submodule "dependencies/parsers/gulp"]
path = dependencies/parsers/gulp
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-gulp.git
branch = nomad-fair
[submodule "dependencies/parsers/siesta"]
path = dependencies/parsers/siesta
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-siesta.git
branch = nomad-fair
[submodule "dependencies/parsers/elk"]
path = dependencies/parsers/elk
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-elk.git
branch = nomad-fair
[submodule "dependencies/parsers/elastic"]
path = dependencies/parsers/elastic
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-elastic.git
branch = nomad-fair
[submodule "dependencies/parsers/gamess"]
path = dependencies/parsers/gamess
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-gamess.git
branch = nomad-fair
[submodule "dependencies/parsers/turbomole"]
path = dependencies/parsers/turbomole
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-turbomole.git
branch = nomad-fair
[submodule "dependencies/parsers/photoemission"]
path = dependencies/parsers/photoemission
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-photoemission.git
branch = nomad-fair
[submodule "dependencies/parsers/skeleton"]
path = dependencies/parsers/skeleton
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-skeleton.git
branch = nomad-fair
[submodule "dependencies/parsers/mpes"]
path = dependencies/parsers/mpes
url = https://gitlab.mpcdf.mpg.de/rpx/parser-mpes.git
branch = nomad-fair
[submodule "dependencies/parsers/aptfim"]
path = dependencies/parsers/aptfim
url = https://gitlab.mpcdf.mpg.de/mkuehbac/parser-aptfim.git
branch = nomad-fair
[submodule "dependencies/parsers/dmol3"]
path = dependencies/parsers/dmol3
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-dmol3.git
branch = nomad-fair
[submodule "dependencies/parsers/fleur"]
path = dependencies/parsers/fleur
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-fleur.git
branch = nomad-fair
[submodule "dependencies/parsers/molcas"]
path = dependencies/parsers/molcas
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-molcas.git
branch = nomad-fair
[submodule "dependencies/parsers/qbox"]
path = dependencies/parsers/qbox
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-qbox.git
branch = nomad-fair
[submodule "dependencies/parsers/onetep"]
path = dependencies/parsers/onetep
url = git@gitlab.mpcdf.mpg.de:nomad-lab/parser-onetep
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-onetep.git
branch = nomad-fair
Subproject commit 71f7a2ad0d77d376e30d3c1a8ae55920fc7d7e5c
Subproject commit cd354f066cb8b85904a2725bb93abf7c443b3fdf
Subproject commit c99f640b45db448ae0551f8d1f5bb629b1320463
Subproject commit d7ac806d8301d2d218fde1f59c94ba433b8ecc9f
Subproject commit ae86931a771b057413509156f2eed00c8a344e40
Subproject commit 05eac2c24d6bc81d5e0585d46bc0e098bf4a0dd4
Subproject commit 92d5084cb99c23b5f41f615813ff64278d2b1aa9
Subproject commit 6b536f8f244da0fb7177d17d21543a922f7bff8f
Subproject commit 801fd628bbdcf6f7db32c05dd56eb682e94972e9
Subproject commit b932711d741c2457a80bf2447c180ce49c23e6c9
Subproject commit be07b5592a2da940ee31ddf02bdf63f7d556a084
Subproject commit ae1f7175bea210eff43d52a30a454f4f9acce30b
Subproject commit 3e58c0dd55681c6f719b80dac3eeade2da9a3608
Subproject commit f914e0c0bafc0922ab77a4347462a15b62d2efa7
......@@ -375,31 +375,39 @@ parsers = [
mainfile_mime_re=r'(application/json)|(text/.*)',
mainfile_name_re=(r'.*.aptfim')
),
MissingParser(
LegacyParser(
name='parsers/qbox', code_name='qbox', domain='DFT',
parser_class_name='qboxparser.QboxParser',
mainfile_mime_re=r'(application/xml)|(text/.*)',
mainfile_contents_re=(r'http://qboxcode.org')
),
MissingParser(
LegacyParser(
name='parsers/dmol', code_name='DMol3', domain='DFT',
mainfile_name_re=r'.*\.outmol'
parser_class_name='dmol3parser.Dmol3Parser',
mainfile_name_re=r'.*\.outmol',
mainfile_contents_re=r'Materials Studio DMol\^3'
),
MissingParser(
LegacyParser(
name='parser/fleur', code_name='fleur', domain='DFT',
parser_class_name='fleurparser.FleurParser',
mainfile_contents_re=r'This output is generated by fleur.'
),
MissingParser(
LegacyParser(
name='parser/molcas', code_name='MOLCAS', domain='DFT',
parser_class_name='molcasparser.MolcasParser',
mainfile_contents_re=r'M O L C A S'
),
MissingParser(
LegacyParser(
name='parser/onetep', code_name='ONETEP', domain='DFT',
parser_class_name='onetepparser.OnetepParser',
mainfile_contents_re=r'####### # # ####### ####### ####### ######'
),
# These are supposedly octopus files, but they do not look like octopus files at all
MissingParser(
name='parser/octopus', code_name='Octopus', domain='DFT',
mainfile_name_re=r'(inp)|(.*/inp)'
),
# TODO We have migrated the wrong octopus mainfiles .. this should be removed now
# MissingParser(
# name='parser/octopus', code_name='Octopus', domain='DFT',
# mainfile_name_re=r'(inp)|(.*/inp)'
# ),
# We already have crystal with mainfile_contents_re, but this one does not always properly match
LegacyParser(
name='parsers/crystal', code_name='Crystal',
......
......@@ -491,6 +491,8 @@ def proc_task(task, cls_name, self_id, func_attr):
self.fail(e)
except Exception as e:
self.fail(e)
except SystemExit as e:
self.fail(e)
finally:
if deleted is None or not deleted:
self.process_status = PROCESS_COMPLETED
......
......@@ -274,6 +274,11 @@ class Calc(Proc):
'parser failed with exception', level=logging.ERROR,
exc_info=e, error=str(e), **context)
return
except SystemExit:
self.fail(
'parser raised system exit', level=logging.ERROR,
error='system exit', **context)
return
# add the non code specific calc metadata to the backend
# all other quantities have been determined by parsers/normalizers
......@@ -659,17 +664,16 @@ class Upload(Proc):
if parser is None:
logger.warn(
'no parser matches during re-process, use old parser',
calc_id=calc.calcid)
calc_id=calc.calc_id)
elif calc.parser != parser.name:
calc.parser = parser.name
logger.info(
'different parser matches during re-process, use new parser',
calc_id=calc.calcid, parser=parser.name)
calc_id=calc.calc_id, parser=parser.name)
calc.re_process_calc()
except Exception as e:
# try to remove the staging copy in failure case
staging_upload_files = self.upload_files.to_staging_upload_files()
if staging_upload_files.exist():
if staging_upload_files is not None and staging_upload_files.exists():
staging_upload_files.delete()
raise e
......
===============================================================
Materials Studio DMol^3 version 3.0
compiled on Nov 12 2003 20:18:37
===============================================================
===============================================================
Density Functional Theory Electronic Structure Program
Copyright (c) 2003, Accelrys Inc. All rights reserved.
Cite work using this program as:
B. Delley, J. Chem. Phys. 92, 508 (1990).
B. Delley, J. Chem. Phys. 113, 7756 (2000).
DMol^3 is available as part of Materials Studio.
===============================================================
DATE: Dec 11 08:56:39 2006
Basis set is read from file:
/usr/local/MSI/MaterialsStudio/Data/Resources/Quantum/DMol3/BASFILE_v3.5
Message: License checkout of MS_dmol successful
Message: Number of licenses checked out 1
Geometry is read from file: h2o.car
INCOOR, atomic coordinates in au (for archive):
______________________________________________________________________>8
$coordinates
O 7.54901398831680 1.61628477909110 -17.16613954807418
H 9.32081624695849 1.54791826093793 -16.71026343953801
H 7.13570372523706 -0.12556968978838 -17.54885237517080
$end
______________________________________________________________________>8
N_atoms = 3 N_atom_types = 2
INPUT_DMOL keywords (for archive):
______________________________________________________________________>8
# <--
# Input for DMol3, v1.0 generated by Cerius2 <--
# <--
# Title: DMol3 calculation from Cerius2 <--
<--
<--
# ----- Type of Calculation: <--
<--
#Calculate optimize <--
#Calculate energy <--
Calculate optimize_frequency <--
#Calculate ts_search <--
#Calculate frequency <--
#Calculate gradient <--
#Calculate Molecular_Dynamics <--
#Calculate Simulated_Annealing <--
<--
<--
Functional gga <--
#Functional pwc <--
#Functional ks <--
#Functional jmw <--
#Functional vwn <--
#Functional vwn-bp <--
#Functional bp <--
#Functional blyp <--
#Functional_Post_LDA off <--
#Functional_Post_LDA BLYP <--
<--
<--
Pseudopotential none <--
#Pseudopotential ecp <--
#Pseudopotential vpsr <--
<--
#Harris on <--
<--
#MD_Atom_Mass Physical_Mass <--
#MD_Time_Step 0.463 <--
#MD_Velocity Random 0 <--
<--
#MD_Fixed_Coordinate 2 <--
#1 XYZ <--
#2 X <--
<--
#MD_SimAnn_Panel 5 <--
#1 200 MD_NVT 300 2.0 <--
#2 100 MD_NVE Continue <--
#3 100 Melt 300 1000 <--
#4 100 Quench Continue <--
#5 100 damp 100 0.2 Continue <--
<--
<--
# Environment Keywords <--
#Cosmo on <--
#Cosmo_Dielectric 78.4 <--
<--
<--
#Atom_Calculation inatom <--
<--
#Basis min <--
#Basis dn <--
#Basis dnd <--
Basis dnp <--
#Basis extended <--
#Basis all <--
#Basis user <--
# 1 7 0 0 0 0 2 2 2 <--
# 6 11 0 0 0 0 0 0 0 2 2 2 2 <--
# 7 11 0 0 0 0 0 0 0 2 2 2 2 <--
# 8 11 0 0 0 0 0 0 0 2 2 2 2 <--
# 44 15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 <--
<--
Spin_Polarization restricted <--
#Spin_Polarization unrestricted <--
<--
# Number of unpaired electrons: <--
Spin 0 <--
<--
Atom_Rcut 6.0 <--
<--
#Integration_Grid fine <--
#Integration_Grid xfine <--
Integration_Grid medium <--
#Integration_Grid coarse <--
#Integration_Grid xcoarse <--
<--
#Aux_Partition 1 <--
<--
#Aux_Density monopole <--
#Aux_Density dipole <--
#Aux_Density quadrupole <--
#Aux_Density octupole <--
#Aux_Density hexadecapole <--
#Aux_Density user <--
# 44 5 <--
# 6 4 <--
# 7 4 <--
# 8 4 <--
# 1 3 <--
<--
<--
Max_Memory 256 <--
Max_Loop 128 <--
#Memory_Check off <--
<--
Charge 0.000 <--
<--
#Symmetry c2 <--
#Symmetry auto <--
Symmetry off <--
<--
<--
# ----- Properties Keywords <--
<--
#Bond_Order on <--
<--
Mulliken_Analysis charge <--
#Mulliken_Analysis population <--
#Mulliken_Analysis full <--
<--
Hirshfeld_Analysis charge <--
#Hirshfeld_Analysis dipole <--
#Hirshfeld_Analysis quadrupole <--
<--
esp_fit on <--
<--
#Partial_Dos on <--
<--
#Electrostatic_Moments on <--
Electrostatic_Moments off <--
<--
#Nuclear_EFG on <--
Nuclear_EFG off <--
<--
Optical_Absorption off <--
#Optical_Absorption on <--
# Possible units: Ry au eV cm-1 nm <--
#Lower_Energy_Limit 1.000E+04 cm-1 <--
#Upper_Energy_Limit 2.500E+06 cm-1 <--
<--
#Electric_Field 0.0 0.0001 0.0 <--
<--
Plot homo lumo deformation density potential <--
#Plot alphadensity betadensity spindensity differen<--
Plot orbital 1 2 3 4 5 6 <--
Plot orbital 7 8 9 10 11 12 13 14 15 16 <--
Plot fermi 2 <--
<--
Grid box 3 -60 -60 -60 3.0 <--
<--
Kpoints off <--
<--
# ----- Vibrational calculation options: <--
<--
#Vibration_steps 2 0.01 <--
Vibration_steps 1 0.01 <--
<--
Vibration_Project off <--
Vibration_restart off <--
<--
<--
# ----- SCF keywords: <--
<--
SCF_Density_Convergence 1.0e-06 <--
SCF_Spin_Mixing 0.5 <--
SCF_Charge_Mixing 0.20 10 <--
#SCF_DIIS 6 kresse <--
SCF_DIIS 10 pulay <--
SCF_Iterations 150 <--
SCF_Number_Bad_Steps 13 <--
#SCF_Direct off <--
SCF_Direct on <--
#SCF_Restart off <--
SCF_Restart on <--
SCF Restart file does not exist
SCF will start from scratch
<--
# Problems with SCF try "Thermal" <--
# Level_Shift good when HOMO LUMO interchange on SCF <--
# Level_Track Max proj on occupied subspace <--
# Fixed Read from file (I5,2E22.14) <--
Occupation Fermi <--
#Occupation Thermal 0.02 <--
#Occupation Smear 0.01 <--
#Occupation Level_Shift 0.25 <--
#Occupation Level_Track <--
#Occupation Fixed <--
<--
<--
# ----- Optimization keywords: <--
<--
OPT_Energy_Convergence 1.0e-05 <--
OPT_Gradient_Convergence 0.000100000 <--
#OPT_Displacement_Convergence 0.00300000 <--
OPT_Displacement_Convergence 0.003000000 <--
OPT_Iterations 200 <--
<--
OPT_Coordinate_System cartesian <--
#OPT_Coordinate_System internal_only <--
#OPT_Coordinate_System auto <--
<--
#OPT_Hessian_Update BFGS <--
#OPT_Hessian_Update BFGS_safe <--
#OPT_Hessian_Update powell <--
<--
#OPT_Gdiis off <--
OPT_Gdiis on <--
<--
OPT_Max_Displacement 0.25000000 <--
OPT_Steep_Tol 0.30000000 <--
OPT_Hessian_Project on <--
#OPT_Hessian_Project trans <--
#opt_ts_mode 5 <--
<--
#OPT_Restart file <--
#ho2.hessian <--
<--
# ----- Optimization Constraints: <--
<--
#Opt_Constraint_Method off <--
#Opt_Constraint_Method Lagrange_Penalty <--
#Opt_Constraint_Method Penalty_Lagrange <--
#Opt_Constraint_Method Penalty <--
#Opt_Constraint_Method Lagrange <--
<--
# (4i4,f20.10) <--
#Opt_Constraint <--
# 48 49 4.00 <--
<--
# (i4,2x,a3) <--
#Opt_Fixed <--
# 1 XYZ <--
# 2 XYZ <--
# 3 XYZ <--
# 4 XYZ <--
<--
# ----- Print options: <--
<--
#Print SCF Brief <--
Print SCF Normal <--
#Print SCF Extensive <--
Print OPT Normal <--
#Print OPT Brief <--
#Print OPT Extensive <--
Print Eigval_Last_It <--
#Print Eigval_Each_It <--
#Print Eigenvectors <--
#Print Vib_hess <--
#Print Debug <--
<--
______________________________________________________________________>8
Density functional:
Perdew 1991 exchange
gradient corrected exchange potential used in SCF
Perdew 1991 correlation
gradient corrected correlation potential used in SCF
Calculation is Spin_restricted
Symmetry group of the molecule: c1
**WARNING** BFGS_safe update will be used for GDIIS
Specifications for basis set selection:
Hydrogen nbas= 1, z= 1, nrfn= 3, rcut= 6.00, e_ref= -0.046131 Ha
n=1 L=0 occ= 1.00 e= -0.222910Ha -6.0657eV
n=1 L=0 occ= 0.00 e= -0.844526Ha -22.9807eV
n=2 L=1 occ= 0.00 e= -1.999912Ha -54.4204eV
Oxygen nbas= 2, z= 8, nrfn= 7, rcut= 6.00, e_ref= -0.060781 Ha
n=1 L=0 occ= 2.00 e= -18.896548Ha -514.2014eV
n=2 L=0 occ= 2.00 e= -0.868840Ha -23.6424eV
n=2 L=1 occ= 4.00 e= -0.322562Ha -8.7774eV
n=2 L=0 occ= 0.00 e= -2.144678Ha -58.3597eV
n=2 L=1 occ= 0.00 e= -1.593751Ha -43.3682eV
n=3 L=2 occ= 0.00 e= -2.722082Ha -74.0717eV
n=3 L=2 occ= 0.00 e= -1.383811Ha -37.6554eV eliminated
Symmetry orbitals
n norb representation
1 24 a
total number of valence orbitals: 24
molecule charge= 0.0 active electron number= 10.0
including core= 10.0 (without charge= 10.0)
Integration points and checksum: 5517 10.000050 194
extra disk use on option Direct_scf off= 7.0Mbytes
Warning: Loop_goal was redefined
New Loop_goal is 194 Old was 128
d_diis workspace defines Max_memory requirements
complex matrix assembly wksp defines Max_memory requirements
----------------------------------------------------------------------
Memory Stack Information
----------------------------------------------------------------------
Number of elements Mbytes
integer arrays 24445 0.1
real arrays 1123086 8.6
total 1147531 8.7
----------------------------------------------------------------------
+++ Entering Optimization Section +++
Message: Entering optimization section
~~~~~~~~~~~~~~~~~~~~ Start Computing SCF Energy/Gradient ~~~~~~~~~~~~~~~~~~~~
----------------------------------------------------------------------
----------------------------------------------------------------------
Message: Start SCF iterations
Total E (au) Binding E (au) Convergence Time (m) Iter
-----------------------------------------------------------------------------
Ef -76.5013384 -0.4476592 0.17E+00 0.009 1
Ef -76.4484558 -0.3947765 0.96E-01 0.010 2
Ef -76.4363833 -0.3827040 0.60E-01 0.011 3
Ef -76.4368522 -0.3831730 0.27E-01 0.012 4
Ef -76.4352468 -0.3815675 0.17E-02 0.013 5
Ef -76.4352414 -0.3815621 0.81E-03 0.015 6
Ef -76.4352322 -0.3815530 0.59E-03 0.016 7
Ef -76.4352283 -0.3815491 0.50E-04 0.017 8
Ef -76.4352287 -0.3815494 0.22E-04 0.019 9
Ef -76.4352288 -0.3815495 0.16E-05 0.020 10
Ef -76.4352288 -0.3815495 0.68E-06 0.021 11
Message: SCF converged
Energy of Highest Occupied Molecular Orbital -0.24872Ha -6.768eV
HOMO is orbital number 5
LUMO is orbital number 6
state eigenvalue occupation
(au) (ev)
1 + 1 a -18.752696 -510.287 2.000
2 + 2 a -0.914403 -24.882 2.000
3 + 3 a -0.469606 -12.779 2.000
4 + 4 a -0.328826 -8.948 2.000
5 + 5 a -0.248722 -6.768 2.000
6 + 6 a 0.042721 1.162 0.000
7 + 7 a 0.108565 2.954 0.000
8 + 8 a 0.587888 15.997 0.000