Recent Posts

1

Molecular Properties, Wavefunction Analysis, and Interfaces to Visualization Tools / Re: Population analysis new vs old (moloch)

« Last post by Arnim on September 28, 2023, 06:20:05 PM »

Hello Robin,

for 1 and 3, I don't really know. But for point 2, please note, that you can run 'ridft -proper', if you have converged orbitals. This will skip the SCF part.

Cheers,
Arnim

2

Ridft, Rdgrad, Dscf, Grad / Re: Severe Error during Ridft HFC Calculations

« Last post by jcardol on September 27, 2023, 12:41:52 AM »

Hi!

Thanks for your advice and insights Uwe  ,

1. I've changed the tcsh script code for the one you have written.

2. I follow the Turbomole 7.7 User Guide (Section 18.1) where it starts with a UHF/UKS calculation employing the X2C ($rx2c) and finite nucleus model ($finnuc). So I ran a dscf and afterwards through the use of gtensprep.sh a ridft calc was prepared and sent for each vector (x,y and z), so I guess these would be two consecutive ridft calculations then?

3. I've implemented your cleaner code changes to the script as well.


I've run a test with your changes in the script and works perfectly.
Thank you for your time!

Joan

3

Riper / Re: NumForce using riper

« Last post by uwe on September 26, 2023, 06:12:21 PM »

Hi,

oh, Antti already pointed to phonopy in your other post...

Thanks, Antti!!

4

Riper / Re: NumForce using riper

« Last post by uwe on September 26, 2023, 06:10:55 PM »

Hello,

just a hint: If you are interested in vibrations/phonons of periodic systems please see: https://phonopy.github.io/phonopy/

Best regards, Uwe

5

TmoleX - general topics / Re: NMR only calculates H atoms

« Last post by uwe on September 26, 2023, 04:06:41 PM »

Hello,
that seems to be a bug that needs to be fixed. The $nucsel keyword stays in the control file even if an NMR shieldings calculation is started.
I'd recommend to send a bug report to BIOVIA support.

6

TmoleX - general topics / NMR only calculates H atoms

« Last post by Michael_Patzschke on September 26, 2023, 02:19:05 PM »

Hello,

I am trying to use TMoleX for NMR shielding calculations. When I choose NMR in the "Start JOB" part, there are no further options to choose the nuclei the shielding tensor should be calculated for. The program automatically chooses $nucsel "h" and there seems to be no way to change this behaviour. Is there any way to choose the nuclei or at least to calculate the shielding for all nuclei? I know, I could use a text editor to change the nucsel line before submitting, but this somehow seems to defeat the purpose of a GUI.

I am using the latest version of Turbomole and TMoleX.

Kind regards,
Michael

7

Ridft, Rdgrad, Dscf, Grad / Re: Severe Error during Ridft HFC Calculations

« Last post by uwe on September 25, 2023, 07:14:04 PM »

Hello,

you are running Turbomole in an SMP environment, not using more than one node. So it is usually more efficient not to use the MPI version but the SMP one.

1. Please set in your tcsh script instead of:

Code: [Select]

module load turbomole/7.7_mpi
setenv PARA_ARCH MPI
setenv PARNODES 16
setenv OMP_NUM_THREADS 1
this here:

Code: [Select]

module load turbomole/7.7_mpi
setenv PARA_ARCH SMP
setenv PARNODES 16
source $TURBODIR/Config_turbo_env.csh
This will start the SMP versions of the Turbomole modules instead of the MPI ones.

2. Next: Your input

Please add

Code: [Select]

$rij
to the control file. Two-component calculations are all done with the module ridft (not dscf), thus $rij is required in the control file.

3. Finally replace the call

Code: [Select]

nohup dscf -np 16 > output
by

Code: [Select]

ridft > output
the -np option can be skipped as you already set $PARNODES to the number of cores you want to use for the calculation. nohup is not required within a script.

Hope this helps

8

Ridft, Rdgrad, Dscf, Grad / Severe Error during Ridft HFC Calculations

« Last post by jcardol on September 25, 2023, 06:02:04 PM »

Dear Turbomole Users,

I'm running into an error when using Turbomole 7.7 ridft module alongside x2c method to calculate HFCC (HyperFine Coupling Constants) while employing the MPI version.

The error is:

Code: [Select]

SEVERE ERROR from node:   0 parallel densao, flag.eq.2 untested

I manually setup the control file through define to write this input:

Code: [Select]

$title
sctest
$symmetry c1
$coord    file=coord
$optimize
 internal   off
 redundant  off
 cartesian  on
$atoms
    basis =x2c-QZVPPall
$basis    file=basis
$ecp    file=basis
$uhfmo_alpha   file=alpha
$uhfmo_beta   file=beta
$uhf
$alpha shells
 a       1-60                                   ( 1 )
$beta shells
 a       1-59                                   ( 1 )
$scfiterlimit      300
$scfdamp   start=1.000  step=0.050  min=0.100
$scfdump
$scfdiis
$maxcor    500 MiB  per_core
$energy    file=energy
$grad    file=gradient
$rx2c
$finnuc
$dft
    functional   b3-lyp
    gridsize   5a
$scfconv   9
$scforbitalshift  closedshell=.05
$rundimensions
   natoms=6
$last step     define
$end

To then run a script which launches the calculations:

Code: [Select]

#!/bin/tcsh
#$ -S /bin/csh
#$ -N sctest
#$ -pe smp 16
#$ -cwd

#Set Path
set dir = $cwd

source /etc/profile.d/modules.csh
module load turbomole/7.7_mpi
setenv PARA_ARCH MPI
setenv PARNODES 16
setenv OMP_NUM_THREADS 1

cp * $TMPDIR/
cd $TMPDIR

#Execute job
nohup dscf -np 16 > output

cp -pr * $dir

/aplic/turbomole/turbomole-7.7/TURBOMOLE/scripts/gtensprep.sh -msnso -hfc

cd x/
nohup ridft -np 16 > output
cd ../y/
nohup ridft -np 16 > output
cd ../z/
nohup ridft -np 16 > output

cd ../
cp -pr * $dir

exit

The script seems to run successfully up until the first ridft, the dscf manages to compute it correctly, but another message from the outputs was declaring 'Missing spinor shell occupation number declaration!' due to the fact that no spinor.i nor spinor.r files were created during the process is what I'm guessing but I don't know why.

Any help would be greatly appreciated.

Best regards!

                     Joan

9

Escf and Egrad / Error during GW calculation with symmetry

« Last post by fbHRO on September 25, 2023, 03:31:00 PM »

Hi,

I have tried to perform a GW calculation for a transition metal complex using the gw and rigw features. However, whenever I attempted to apply a symmetry to the molecule, I received the following error message, regardless of the applied point group. (every symmetry fails besides c1)

               --------------------------------------------------
               ---------------- full GW response ----------------
               --------------------------------------------------

 starting diagonalization of block: ag  using method 2 (1=QR,2=D&C)
 starting diagonalization of block: b1g using method 2 (1=QR,2=D&C)
 starting diagonalization of block: b2g using method 2 (1=QR,2=D&C)
 starting diagonalization of block: b3g using method 2 (1=QR,2=D&C)
 starting diagonalization of block: au  using method 2 (1=QR,2=D&C)
 starting diagonalization of block: b1u using method 2 (1=QR,2=D&C)
 starting diagonalization of block: b2u using method 2 (1=QR,2=D&C)
 starting diagonalization of block: b3u using method 2 (1=QR,2=D&C)
inconsistency in modtrace:
 module    gw_n6engine_sym exits but current
 module is gw_n6engine

========================
 internal module stack:
------------------------
    escf
    escfgwsetup
    gw_n6engine
========================

 modtrace: inconsistency
 escf ended abnormally

This example is done with d2h symmetry.
Has anyone ever seen this error message? Am I doing something wrong? What should I do to solve this problem?

Regards,
Florian

10

ccsdf12 / CCSD single and doubles amplitudes

« Last post by prasanta13 on September 08, 2023, 01:00:54 PM »

How can I obtain the CCSD singles and doubles amplitudes? I need them to create a 2particle density matrix.