Closed tobigithub closed 3 years ago
JayTheDog
commented
3 years ago As discussed in issue #18 , the option is now inside the source code. @tobigithub , you can pull, compile and test it. If it works, I will close this issue and leave issue #18 open for now.
tobigithub
commented
3 years ago Currently testing qcxms v5.1.2, so compilation works, and orca 3.0 is not supported anymore, orca 4.0 works fine. Orca 5.0.1 fails: test case ethanol protonated, DFT with ORCA 5.0.1
$cat qcxms.in
orca
pbe
sv
cid
elab 40
maxcoll 1
noesi
ntraj 3and running qcxms
qcxms
Wed Sep 1 14:23:58 PDT 2021
*********************************************
* *
* Q C x M S *
* *
* V5.1.2 *
* *
* S. Grimme *
* Mulliken Center for Theoretical Chemistry *
* Universitaet Bonn *
* 2008-21 *
* Aug 27 10:30:00 CEST 2021 *
* *
*********************************************
QCxMS is free software: you can redistribute it and/or modify it under
the terms of the GNU Lesser General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
QCxMS is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU Lesser General Public License for more details.
Cite this work as:
S.Grimme, Angew.Chem.Int.Ed. 52 (2013) 6306-6312.
for the CID module:
J. Koopman, S. Grimme, J. Am. Soc. Mass Spectrom., (2021), DOI: 10.1021/jasms.1c00098
for the GFN1-xTB implementation:
V. Asgeirsson, C.Bauer, S. Grimme, Chem. Sci. 8 (2017) 4879
for the GFN2-xTB implementation:
J. Koopman, S. Grimme, ACS Omega 4 (12) (2019) 15120-15133, DOI: 10.1021/acsomega.9b02011
--------------------------------------------------
Current Dev. : J. Koopman
Former Dev. : V.Asgeirsson, C.Bauer
--------------------------------------------------
changed by input:
>orca
>pbe
>sv
>cid
>elab 40
>maxcoll 1
>noesi
>ntraj 3
************************************************************
Mode: Collision Induced Dissociation (CID)
Positive Ion mode
************************************************************
----- Internal program parameters -----
QC Program : ORCA
QC Level : PBE/SV
QC Level for IPs : PBE/SV
Dispersion : D3
total traj. (ntraj) : 3
time steps (tstep) : 0.50 fs
max. sim. time (tmax) : 5.00 ps
Initial temp. (tinit) : 500.00 K
----------- CID settings -----------
Collision Gas : Ar
E (LAB) : 40.00 eV
Run - Type : Manual
Maximum collisions : 1
--------------------------------------------
qc path /usr/local/bin/
--------------------------------------------
molecule:
1 0.889669 0.055092 -1.147109 C 12.0107
2 2.252889 1.551244 0.960635 C 12.0107
3 3.063910 4.420376 0.038847 O 15.9994
4 -0.417502 1.371467 -2.323004 H 1.0079
5 -0.416852 -0.830932 0.120487 H 1.0079
6 1.792282 -1.395510 -2.397677 H 1.0079
7 4.140774 1.069094 1.608792 H 1.0079
8 1.109262 1.997746 2.619163 H 1.0079
9 1.852010 5.762194 0.435150 H 1.0079
10 3.068213 4.641244 -1.824980 H 1.0079
reading qcxms.gs ...
--- Checking QC method for ions ---
initializing ORCA ...
[file orca_main/maininp4.cpp, line 11063]:
QM code initialization failure
>>> fatal QC error. Must stop! <<<
and the created ORCA.INPUT file:
cat ORCA.INPUT
! DEF2/J SMALLPRINT NOSOSCF
! NOFINALGRID NOMAYER
! UHF
! SV
! GRID2
! PBE D3BJ
%output
Print[ P_AtPopMO_L] 1 end
%output
Print[ P_AtPopMO_M] 1 end
%method
runtyp energy
end
%elprop
dipole false
end
%scf
SmearTemp 5000.
maxcore 5000
MaxIter 400
end
* xyz 1 1
C 0.470792542713 0.029153417786 -0.607024031726
C 1.192177711979 0.820883127883 0.508346150328
O 1.621351267701 2.339162706129 0.020556957909
H -0.220932587053 0.725748909788 -1.229280636996
H -0.220588436464 -0.439710365680 0.063758771712
H 0.948434743655 -0.738472095025 -1.268795891855
H 2.191203671855 0.565740251594 0.851336185651
H 0.586996096610 1.057161930725 1.386001554286
H 0.980041477966 3.049221824277 0.230271522684
H 1.623628379946 2.456040939865 -0.965737774029
*and the orca 5.0.1 error message:
orca ORCA.INPUT
*****************
* O R C A *
*****************
#,
###
####
#####
######
########,
,,################,,,,,
,,#################################,,
,,##########################################,,
,#########################################, ''#####,
,#############################################,, '####,
,##################################################,,,,####,
,###########'''' ''''###############################
,#####'' ,,,,##########,,,, '''####''' '####
,##' ,,,,###########################,,, '##
' ,,###'''' '''############,,,
,,##'' '''############,,,, ,,,,,,###''
,#'' '''#######################'''
' ''''####''''
,#######, #######, ,#######, ##
,#' '#, ## ## ,#' '#, #''# ###### ,####,
## ## ## ,#' ## #' '# # #' '#
## ## ####### ## ,######, #####, # #
'#, ,#' ## ## '#, ,#' ,# #, ## #, ,#
'#######' ## ## '#######' #' '# #####' # '####'
#######################################################
# -***- #
# Department of theory and spectroscopy #
# Directorship and core code : Frank Neese #
# Max Planck Institute fuer Kohlenforschung #
# Kaiser Wilhelm Platz 1 #
# D-45470 Muelheim/Ruhr #
# Germany #
# #
# All rights reserved #
# -***- #
#######################################################
Program Version 5.0.1 - RELEASE -
With contributions from (in alphabetic order):
Daniel Aravena : Magnetic Suceptibility
Michael Atanasov : Ab Initio Ligand Field Theory (pilot matlab implementation)
Alexander A. Auer : GIAO ZORA, VPT2 properties, NMR spectrum
Ute Becker : Parallelization
Giovanni Bistoni : ED, misc. LED, open-shell LED, HFLD
Martin Brehm : Molecular dynamics
Dmytro Bykov : SCF Hessian
Vijay G. Chilkuri : MRCI spin determinant printing, contributions to CSF-ICE
Dipayan Datta : RHF DLPNO-CCSD density
Achintya Kumar Dutta : EOM-CC, STEOM-CC
Dmitry Ganyushin : Spin-Orbit,Spin-Spin,Magnetic field MRCI
Miquel Garcia : C-PCM and meta-GGA Hessian, CC/C-PCM, Gaussian charge scheme
Yang Guo : DLPNO-NEVPT2, F12-NEVPT2, CIM, IAO-localization
Andreas Hansen : Spin unrestricted coupled pair/coupled cluster methods
Benjamin Helmich-Paris : MC-RPA, TRAH-SCF, COSX integrals
Lee Huntington : MR-EOM, pCC
Robert Izsak : Overlap fitted RIJCOSX, COSX-SCS-MP3, EOM
Marcus Kettner : VPT2
Christian Kollmar : KDIIS, OOCD, Brueckner-CCSD(T), CCSD density, CASPT2, CASPT2-K
Simone Kossmann : Meta GGA functionals, TD-DFT gradient, OOMP2, MP2 Hessian
Martin Krupicka : Initial AUTO-CI
Lucas Lang : DCDCAS
Marvin Lechner : AUTO-CI (C++ implementation), FIC-MRCC
Dagmar Lenk : GEPOL surface, SMD
Dimitrios Liakos : Extrapolation schemes; Compound Job, initial MDCI parallelization
Dimitrios Manganas : Further ROCIS development; embedding schemes
Dimitrios Pantazis : SARC Basis sets
Anastasios Papadopoulos: AUTO-CI, single reference methods and gradients
Taras Petrenko : DFT Hessian,TD-DFT gradient, ASA, ECA, R-Raman, ABS, FL, XAS/XES, NRVS
Peter Pinski : DLPNO-MP2, DLPNO-MP2 Gradient
Christoph Reimann : Effective Core Potentials
Marius Retegan : Local ZFS, SOC
Christoph Riplinger : Optimizer, TS searches, QM/MM, DLPNO-CCSD(T), (RO)-DLPNO pert. Triples
Tobias Risthaus : Range-separated hybrids, TD-DFT gradient, RPA, STAB
Michael Roemelt : Original ROCIS implementation
Masaaki Saitow : Open-shell DLPNO-CCSD energy and density
Barbara Sandhoefer : DKH picture change effects
Avijit Sen : IP-ROCIS
Kantharuban Sivalingam : CASSCF convergence, NEVPT2, FIC-MRCI
Bernardo de Souza : ESD, SOC TD-DFT
Georgi Stoychev : AutoAux, RI-MP2 NMR, DLPNO-MP2 response
Willem Van den Heuvel : Paramagnetic NMR
Boris Wezisla : Elementary symmetry handling
Frank Wennmohs : Technical directorship
We gratefully acknowledge several colleagues who have allowed us to
interface, adapt or use parts of their codes:
Stefan Grimme, W. Hujo, H. Kruse, P. Pracht, : VdW corrections, initial TS optimization,
C. Bannwarth, S. Ehlert DFT functionals, gCP, sTDA/sTD-DF
Ed Valeev, F. Pavosevic, A. Kumar : LibInt (2-el integral package), F12 methods
Garnet Chan, S. Sharma, J. Yang, R. Olivares : DMRG
Ulf Ekstrom : XCFun DFT Library
Mihaly Kallay : mrcc (arbitrary order and MRCC methods)
Jiri Pittner, Ondrej Demel : Mk-CCSD
Frank Weinhold : gennbo (NPA and NBO analysis)
Christopher J. Cramer and Donald G. Truhlar : smd solvation model
Lars Goerigk : TD-DFT with DH, B97 family of functionals
V. Asgeirsson, H. Jonsson : NEB implementation
FAccTs GmbH : IRC, NEB, NEB-TS, DLPNO-Multilevel, CI-OPT
MM, QMMM, 2- and 3-layer-ONIOM, Crystal-QMMM,
LR-CPCM, SF, NACMEs, symmetry and pop. for TD-DFT,
nearIR, NL-DFT gradient (VV10), updates on ESD,
ML-optimized integration grids
S Lehtola, MJT Oliveira, MAL Marques : LibXC Library
Liviu Ungur et al : ANISO software
Your calculation uses the libint2 library for the computation of 2-el integrals
For citations please refer to: http://libint.valeyev.net
Your ORCA version has been built with support for libXC version: 5.1.0
For citations please refer to: https://tddft.org/programs/libxc/
This ORCA versions uses:
CBLAS interface : Fast vector & matrix operations
LAPACKE interface : Fast linear algebra routines
SCALAPACK package : Parallel linear algebra routines
Shared memory : Shared parallel matrices
BLAS/LAPACK : OpenBLAS 0.3.15 USE64BITINT DYNAMIC_ARCH NO_AFFINITY Haswell SINGLE_THREADED
Core in use : Haswell
Copyright (c) 2011-2014, The OpenBLAS Project
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
INPUT ERROR
UNRECOGNIZED OR DUPLICATED KEYWORD(S) IN SIMPLE INPUT LINE
NOFINALGRID GRID2
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
[file orca_main/maininp4.cpp, line 11063]:
[file orca_main/maininp4.cpp, line 11063]:
I see two issues here:
1) in ORCA 5.01 NOFINALGRID is now NOFINALGRIDX The ORCA 5.0.1 handbook states: "Turn off the final grid in COSX (not recommended)."
2) The ORCA 5.0.1 grids are named: DEFGRID1, DEFGRID2 (default), DEFGRID3
ORCA5 Manual: Why are my old inputs not running anymore with ORCA-5? "ORCA 5 uses new grids, optimized via machine learning and extensively benchmarked on GMTKN55 as well as for gradients, frequencies, properties. The new DefGrid2 is larger but much more robust than the previous default and the upgrade to DefGrid3 is only required in rare cases. For more information, consult section 9.3. The old grids are deprecated and the !Grid[1-7] and !GridX[1-9] keywords are no longer available! If you need to compare results to a previous version of ORCA (or indeed any other program), use sufficiently large grids in both programs"
So changing the ORCA.INPUT to the correct parameters for ORCA 5.0.1, works:
! DEF2/J SMALLPRINT NOSOSCF
! NOFINALGRIDX NOMAYER
! UHF
! SV
! DEFGRID2
! PBE D3BJ
%output
Print[ P_AtPopMO_L] 1 end
%output
Print[ P_AtPopMO_M] 1 end
%method
runtyp energy
end
%elprop
dipole false
end
%scf
SmearTemp 5000.
maxcore 5000
MaxIter 400
end
* xyz 1 1
C 0.470792542713 0.029153417786 -0.607024031726
C 1.192177711979 0.820883127883 0.508346150328
O 1.621351267701 2.339162706129 0.020556957909
H -0.220932587053 0.725748909788 -1.229280636996
H -0.220588436464 -0.439710365680 0.063758771712
H 0.948434743655 -0.738472095025 -1.268795891855
H 2.191203671855 0.565740251594 0.851336185651
H 0.586996096610 1.057161930725 1.386001554286
H 0.980041477966 3.049221824277 0.230271522684
H 1.623628379946 2.456040939865 -0.965737774029
*Hi, I think this needs to be added to the documentation (https://xtb-docs.readthedocs.io/en/latest/qcxms_doc/qcxms.html),
in qcxms.in: set orca4 or orca5 [default] for the different ORCA versionsI will rerun the examples, potentially the errors will resolve. Tobias
JayTheDog
commented
3 years ago It seems that the compilation of the new version did not work for you, because otherwise the program would state:
QC Program : ORCA 5
Here, nofinalgrid was deleted and defgrid added, it runs as expected. However, I did some tests with the new ORCA version, and some strange things are occurring for the program where I'm not sure of where they stem from. I saw that ORCA 5.0.1 has quite some major bug reports and thus I will re-set ORCA4 as the default for the next release until ORCA5 has fixed some of its issues.
tobigithub
commented
3 years ago @JayTheDog Sorry, might have been my fault, because I downloaded the tar.gz from the release 6 days ago, but I did not use git. I don't have the latest changes including:
! Set mayer and finalgrid
if ( orca_version == 4 ) write(io_orca,'(''! NOFINALGRID NOMAYER'')')
if ( orca_version == 5 ) write(io_orca,'(''! NOMAYER'')')I will add the nofinalgridx again. I don't really see the necessity for ORCA 3, but adding it should not be a problem.
tobigithub
commented
3 years ago So i cloned the latest from git and ORCA5 works with "orca5" in the qcxms in file! Thank you.
Orca 3.0.0 runs fine with qcxms v5.1.1, but with ORCA 5.0.1 there is an error.
the ORCA.INPUT file, generated by QCxMS v5.1.1:
the qcxms.in file (THF example in CID mode):
I can run ORCA 5.0.1 when deleting both grid commands "NOFINALGRID" and "! GRID2" like so:
the result when running orca ORCA.INPUT will be
when running qcxms the routine has to quit
Solution: for orca 5.0.1 acccoring to the orca_manual_5_0_1.pdf change grid definitions to "DefGrid2" T.