Recent Posts

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21
Riper / Re: Convergence problem
« Last post by eliseo on February 20, 2019, 05:31:48 pm »
Thanks Uwe for the suggestion about the geometry, I had a problem with the unit cell.
Now, the calculation reaches the convergence in 26 cycles but I am trying to optimize
cell parameters and coordinates together and I have the following message:

 Keyword $statpt not found - using default options

        ***************  Stationary point options ******************
        ************************************************************
           Maximum allowed trust radius:           3.000000E-01
           Minimum allowed trust radius:           1.000000E-03
           Initial trust radius:                   1.500000E-01
           GDIIS used if gradient norm <           1.000000E-02
           Number of previous steps for GDIIS:       5
           Hessian update method:                  BFGS
                        *** Convergence criteria ***
           Threshold for energy change:            1.000000E-06
           Threshold for max displacement element: 1.000000E-03
           Threshold for max gradient element :    1.000000E-03
           Threshold for RMS of displacement:      5.000000E-04
           Threshold for RMS of gradient:          5.000000E-04
        ************************************************************


 keyword $statp missing in file <control>

  Keyword $statpt not found - using default options

 <getgrd> : data group $grad  is missing


========================
 internal module stack:
------------------------
    statpt
========================

 error reading energy and gradient in rdcor
 statpt ended abnormally
statpt step ended abnormally
next step = statpt

Any advice about this problem reading energy and gradient??

    best wishes,

             Eliseo
22
Parallel Runs / Parallel MPI execution: license issue
« Last post by Glxblt76 on February 20, 2019, 08:47:36 am »
Dear Turbomole developers and users,

I'm facing an issue when trying to launch Turbomole calculations on the cluster of my laboratory. I'm doing Turbomole calculations in China and my university bought the software to the local reseller. The reseller generated a license file based on the machine number of the master node of the cluster, in which the software is installed. However, we have to use a queuing system to carry out our calculations. bsub is used. After setting the environment variables as explained >> here <<, I tried to run the calculate script using the following shell script for a set of xyz files:
Code: ("script.sh") [Select]
#!/bin/bash
#BSUB -J 1
#BSUB -W 300:00
#BSUB -n 24
#BSUB -e errors.test.hybrid     # error file name in which test is replaced by the job ID
#BSUB -o output.test.hybrid     # output file name in which test is replaced by the job ID

ls *.xyz > list
calculate -l list -m BP-TZVP-COSMO-CART -f xyz > test.log

I ran this script using the following command:

bsub < script.sh

The script was successfully run, but then upon examining the output, the optimization froze in the running state after a few cycles. In the job.last, I found the following error message repeated several times:

ERROR: unknown host !
License file is NOT valid, please contact your local reseller or COSMOlogic


The same job did work, however, when I ran it directly on the master node (I am not supposed to do it this way, I am supposed to do my calculations on the other nodes of the cluster).

What should I do?

Best regards!
23
Riper / Re: Convergence problem
« Last post by uwe on February 19, 2019, 12:18:06 pm »
Hi,

from what I have heard (not just rumors), convergence problems can be a hint that the input structure is not reasonable. Some popular builder for crystal structures export xyz files which are not defined in a way riper expects it. Especially if you build in symmetry and then export to xyz.

Did you check the structure by visual inspection within Turbomole, i.e. by running TmoleX and view the unit cell plus replicates? Does that look reasonable?

You could try to import the structure directly from a cif file (using TmoleX) and check if you see a similar behavior.

If the structure is OK, and if you have tried changing the other typical parameters already, I'd recommend to contact the Turbomole support.

Regards,

Uwe
24
Riper / Re: Convergence problem
« Last post by eliseo on February 19, 2019, 08:32:20 am »
I was using TURBOMOLE V7.3 ( 22142 )

     thanks,

         Eliseo
25
Hi,
I calculated ADC(2) excitation using Turbomole 7.2 and 7.3 and needed to visualize difference densities between excited and ground states. I confused by some inconsistency between my results and the recommendation of the Turbomole manual.
I used control with a "min setting"
$excitations
  irrep=a nexc=12
  spectrum states=all operators=diplen,qudlen
but didn't receive the needed files. 

1. Which minimum set of keywords should I add to control for getting files like
cc1td-<type>-<mult><irrep>-<number> ?
They should be something like
cc1td-cc2-gs-1a1-001
cc1td-adc2-xs-1a1-00*, where *=1,2,3,...
as it's described in "Default density analysis and visualization" for the canonical SCF orbitals.
if I want EDD for second singlet but I don't see such files to continue with
$anadens
calc my_favourite_diffden from
1d0 cc1td-adc2-xs-1a1-002
-1d0 cc1td-cc2-gs-1a1-001
$pointval

2. I tried to apply a recommendation from your forum that is a "max setting" for me
$excitations
 irrep=a multiplicity=1  nexc=8  npre=8  nstart=8
 spectrum states=all operators=diplen,qudlen
 exprop  states=all  operators=diplen,qudlen
 xgrad states=(a 1-3)
$response
  semicano
  fop relaxed  operators=diplen,qudlen
This calculation was more than twice longer in comparing with the min setting but returned me several interesting files
cc2-gsdn-1a-000-total.cao and 3 files of
cc2-xsdn-1a-00*-total.cao, where *=1,2,3 that corresponds to number from xgrad states=(a 1-3)
The job run CC2 instead of I required ADC(2) that is strange
$ricc2
adc(2)
Nevertheless, I used these files to try EDD according to  the $anadens described above.
The results were similar "Difference densities based on natural transition orbitals"
I could obtain such difference because CCRE0-1--1---* are created even with the min setting.

3. Just an extra question is for my common knowledge. Could you explain me the meanings of the following files:
adcp2-tm0f-1a-00* which appeared with my 1st min setting and even I tried to use them for EDD and obtained quite reasonable pictures;
cc2-tmf0-1a-00* which appeared with the max setting and has the main difference of tmf0 vs tm0f. {I required adc(2) but have got cc2}
cc2-xs1d-ur-1a-00*  which also appeared with the max setting. {the same calculation where I required adc(2) but have got cc2.}

4. The last note is about MOs. There is an inconsistency between the required numbering of states and returned data.
For instance, $pointval mo 33,34 could return 33a and 35a, though, as I checked, these 33a and 35a correspond to these numbers.

I apology for long detailed questions but I should describe all my attempt to present the most clear picture.
Thank you for any incoming answer.

 
26
Riper / Re: Convergence problem
« Last post by antti_karttunen on February 18, 2019, 08:40:36 pm »
Hi,

which TM version you are using? Periodic calculations are much more robust with TM 7.3.

Best,
Antti
27
Riper / Convergence problem
« Last post by eliseo on February 18, 2019, 12:06:11 pm »
Hi all,

  I am trying to perform some riper calculations of the unit cell of a metal complex, Fe(II) mononuclear system, with two molecules in the unit cell.
I was trying PBE or SCAN functionals wit  basis = pob-TZVP and jbas  = dhf-TZVP but always I have convergence problems and after 8-9 scf cycles the energy explodes...

              | TOTAL ENERGY         =       -6433.0146972943    |
              | TOTAL ENERGY         =       -6047.3950058257    |
              | TOTAL ENERGY         =       -6377.5263506254    |
              | TOTAL ENERGY         =       -6623.9976990770    |
              | TOTAL ENERGY         =       -6518.7293471434    |
              | TOTAL ENERGY         =       -6574.3035042539    |
              | TOTAL ENERGY         =       -6627.6332493572    |
              | TOTAL ENERGY         =       -6606.1255709050    |
              | TOTAL ENERGY         =       -6294.1403523448    |
              | TOTAL ENERGY         =       -6545.2222578067    |
              | TOTAL ENERGY         =       -6586.3762207693    |
              | TOTAL ENERGY         =       -4334.0223948992    |
              | TOTAL ENERGY         =       -4101.3356070603    |
              | TOTAL ENERGY         =       -4514.5430856829    |
              | TOTAL ENERGY         =       -2667.6707907154    |

  I was trying to increasing the scfdamp parameter but I obtain more or less the same result.
Any advice will be welcome, I add the control file at the end

     best wishes, thanks a lot

            Eliseo




$title
s13 hs scan periodic D
$operating system unix
$symmetry c1
$user-defined bonds    file=coord
$coord    file=coord
$optimize
 internal   off
 redundant  off
 cartesian  on
 global     off
 basis      off
$atoms
fe 1-2                                                                         \
   basis =fe pob-TZVP                                                          \
   jbas  =fe dhf-TZVP
n  3-6,19-20,37-40,49-52,69-70,87-90                                           \
   basis =n pob-TZVP                                                           \
   jbas  =n dhf-TZVP
c  7-8,11-12,15-16,21-24,27-28,31-32,35-36,41-42,45-46,53-54,57-58,61-62,65-66 \
   71-74,77-78,81-82,85-86,91-92,95-96,99-100                                  \
   basis =c pob-TZVP                                                           \
   jbas  =c dhf-TZVP
h  9-10,13-14,17-18,25-26,29-30,33-34,43-44,47-48,55-56,59-60,63-64,67-68,     \
   75-76,79-80,83-84,93-94,97-98,101-102                                       \
   basis =h pob-TZVP                                                           \
   jbas  =h dhf-TZVP
b  103-104,113-114                                                             \
   basis =b pob-TZVP                                                           \
   jbas  =b dhf-TZVP
f  105-112,115-122                                                             \
   basis =f pob-TZVP                                                           \
   jbas  =f dhf-TZVP
$basis    file=basis
$rundimensions
   dim(fock,dens)=1815888
   natoms=122
   nshell=844
   nbf(CAO)=1904
   dim(trafo[SAO<-->AO/CAO])=2096
   rhfshells=2
   nbf(AO)=1808
$uhfmo_alpha   file=alpha
$uhfmo_beta   file=beta
$uhf
$alpha shells
 a       1-332                                  ( 1 )
$beta shells
 a       1-324                                  ( 1 )
$scfiterlimit       230
$thize     0.10000000E-04
$thime        5
$scfdump
$scfintunit
 unit=30       size=0        file=twoint
$scfdiis
$maxcor    500 MiB  per_core
$drvopt
   cartesian  on
   basis      off
   global     off
   hessian    on
   dipole     on
   nuclear polarizability
$interconversion  off
   qconv=1.d-7
   maxiter=25
$coordinateupdate
   dqmax=0.3
   interpolate  on
   statistics    5
$forceupdate
   ahlrichs numgeo=0  mingeo=3 maxgeo=4 modus=<g|dq> dynamic fail=0.3
   threig=0.005  reseig=0.005  thrbig=3.0  scale=1.00  damping=0.0
$forceinit on
   diag=default
$energy    file=energy
$grad    file=gradient
$forceapprox    file=forceapprox
$dft
   functional pbe
   gridsize   5
   radsize    50
$scfconv   6
$scfdamp   start=0.700  step=0.050  min=0.050
$scforbitalshift  closedshell=.05
$jbas    file=auxbasis
$ricore      500
$rij
$periodic 3
$cell
8.4098 8.4731 18.2909 90.  98.575 90.
$kpoints
nkpoints 2 2 1
$riper
lenonly on
sigma 0.01
$optcell
$disp3 bj
$actual step      riper
$end

28
Hello,

Is there any way to compute Hirshfeld charges with Turbomole? I would like to compare Hirshfeld charges with NPA charges.

Thanks,
Andreas
29
TmoleX - general topics / Re: Forgot to activate cosmo file generation
« Last post by Desang on February 13, 2019, 09:29:28 pm »
Hi.

A follow up question here. I ran the geometry optimization (with 'activate' cosmo file this time) of my molecules of interest. Then, when I was trying to get the IR spectrum (vibration frequency), the button turned grey. I could not run it.

This is not the case when I run geometry optimization (without 'activate' cosmo file). I could get the IR spectrum.

Is there anything I missed out?

Thanks~
30
Miscellaneous / Re: Molecular simulation of adsorption using activated carbon
« Last post by Desang on February 13, 2019, 09:17:34 pm »
Thanks uwe.
That's helpful =)
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