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21
Define / Turbomole parallel error
« Last post by kshatresh on February 01, 2018, 11:33:33 am »
Dear Users,

I am using Turbomole 7.2.1 for QM/MM using chemshell interface. The script runs fine for serial version but it gives an error during mpi run, as below:

Parallel program dscf_mpi will be taken out of the TURBODIR directory.
STARTING dscf ON 48 PROCESSORS!
RUNNING PROGRAM /hpc2n/eb/software/Core/Turbomole/7.2.1-mpi/bin/em64t-unknown-linux-gnu_mpi/dscf_mpi.
PLEASE WAIT UNTIL dscf HAS FINISHED.
Look for the output in slave1.output.
MACHINEFILE is /pfs/nobackup/home/k/kddubey/HisA/QM-MM-setup/kdd-MD/SNAP-12621/TURBOMOLE/TS-OPT/B3LYP/FREQ/machinelist.used
 this is node-proc. number 1 running on node b-cn0313.hpc2n.umu.se
 the total number of node-proc. spawned is  50
  parallel platform: MPP or cluster with fast interconnect

 data group $actual step is not empty
 due to the abend of dscf

Error: statistics runs not possible with MPI binaries...
       delete $statistics from control file or use sequential binary

========================
 internal module stack:
------------------------
    dscf
    turbo_setup
========================

 fatal error for MPI rank    1

 statistics run not possible with MPI binaries!
 dscf ended abnormally

Please help me to fix this issue.

Regards
Kshatresh
22
Fast and Robust Quantum Chemistry
TURBOMOLE Users Meet Developers
20 - 22 September 2018 in Jena, Germany
www.meeting2018.sierkalab.com

We are pleased to announce the Turbomole users and developers meeting “Fast and Robust Quantum Chemistry”, which will be held in Germany, at the Friedrich Schiller University of Jena, from September 20 to 22, 2018.

This meeting will bring together the community of Turbomole developers and users to highlight selected applications demonstrating new features and capabilities of the code, present new theoretical developments, identify new user needs, and discuss future directions.

Hands-on sessions will cover the most important methods available in Turbomole with emphasis on new approaches and features which make Turbomole applicable to an ever widening spectrum of research applications.

Program
The meeting will start on September 20 with registration (starting 4:00 pm) and a Welcome Diner (starting 7:00 pm). The end of the meeting is planned about 2:00 pm on September 22.
The meeting will include five presentations (30 minutes) given by the main developers of Turbomole. In addition, there will be 15 talks (20 minutes including discussion) invited or selected from the contributed abstracts and a poster session.

Venue
The meeting “Fast and Robust Quantum Chemistry” will take place at the Friedrich Schiller University of Jena, Germany, in the “Rosensäle” located in Fürstengraben 27. This is one of the historical, recently nicely renovated buildings you find throughout the heart of Jena city.

Registration
There is no registration fee for the meeting. The number of participants is limited. Registration will be closed once the limit is reached.

Please visit http://www.meeting2018.sierkalab.com for more information and registration.

The  deadline for the abstract submission is 30.06.2018
23
TURBOMOLE Forum General / Re: IRC in turbomole
« Last post by Arnim on January 15, 2018, 01:54:24 pm »
You can also plot the energy versus the time step. If you run log2egy, you will get these values. You have to reorder the data for displaced_plus and displaced_minus, however, to get a continuous plot.

But selecting and plotting internal coordinate should be straightforward and would be more informative in a discussion.

24
TURBOMOLE Forum General / Re: IRC in turbomole
« Last post by inozerox on January 12, 2018, 08:54:29 pm »
I meant I want to obtain a graphical like this



Cheers
25
TURBOMOLE Forum General / Re: IRC in turbomole
« Last post by inozerox on January 12, 2018, 06:19:17 pm »
Thanks for answering again Arnim.

> Can I use those tools when I used cartesians coordinates?

In that question I meant I am not using internal coordinates (bond length, bond angles, dihedral angles) in my work. I am using x,y,z coordinates instead of internal ones.

About the second answer. Thank you for the piece of advice you gave me. But, I have a question related with that. is it necessary to select some couple of atoms to do that? (I guess you select some couple of atoms to see the change of some internal coordinates when the reaction is working)

what does it happend if I do not specify any atom? like Gaussian programm.

Cheers and thank you again



26
TURBOMOLE Forum General / Re: IRC in turbomole
« Last post by Arnim on January 12, 2018, 10:27:08 am »

> Can I use those tools when I used cartesians coordinates?

I don't know what that should mean.

> Does it existe any form to obtain a graphical Energy Versus IRC (Intrinsic Reaction Coordinate)?

Yes. E.g. with the evalgrad and gnuplot commands I mentioned.
You could also use Excel/LibreOffice, if you are not familiar the gnuplot.
27
TURBOMOLE Forum General / Re: IRC in turbomole
« Last post by inozerox on January 11, 2018, 07:58:28 pm »
Thank you Arnim for answering me

I am going to tell you what I obtained.

When I applied the command DRC -i -c (number of cycles) I obtained two new folders.

when I checked the file with Tmolex. I saw the gradient information and I could find the results. But the program made a graphical energy versus cycle step (like every gradient graphical)

I have some questions related with the things you answered me in your reply.

Can I use those tools when I used cartesians coordinates?

Does it existe any form to obtain a graphical Energy Versus IRC (Intrinsic Reaction Coordinate)?

Cheers
28
Ricc2 / Crash on the calculation of excited state with ADC(2)/COSMO
« Last post by bin on January 11, 2018, 06:55:10 pm »
Hello,

I'm using TM6.6(don't have a higher version) to calculate the excited state energy and oscillator strength with ADC(2)/COSMO/def2-TZVP. But I have one problem.
It always crashes when the ricc2_omp to calculate the part of  "CALCULATION OF COUPLED CLUSTER RESPONSE PROPERTIES", and there is no error information on the ricc2.out file. And if I restart the ricc2 calculation or do a new calculation from dscf, it will crash at the same point.
And sometimes on the error file of system, I can find this information:"bin/em64t-unknown-linux-gnu_smp/ricc2: line 39: 30867 Segmentation fault      (core dumped) $TURBODIR/bin/`sysname`/ricc2_omp ", but this error doesn't  always appear when crashes. Most time there is no any error information in the system error file.

I think there is no mistake in my input file, because I changed the basis set to def-SV(P), and ricc2 ended normally. And, in the gas phase, there is no problem.

This is the last part of ricc2.out:

 ======== LINEAR CC RESPONSE SOLVER ========

    threshold for convergence: 0.32E-01
    maximum number of simultaneous jacoby matrix transformations:  1
                                               
     summary of start vectors generation:
     -------------------------------------------
     type of solution vectors      : l0o
     symmetry                      : a 
     number of vectors requested   :     1
     number of vectors generated   :     1
     -------------------------------------------
                                               

    Iter  #Vectors  time (min)    max. residual
    --------------------------------------------
 COSMO cphf update


this is my contronl file:
$cosmo
  epsilon=    4.711
  rsolv= 1.30
  refind=   1.4459
  cosmorel state=(x)
$cosmo_atoms
# radii in Angstrom units
n  1,11,23,35                                                                  \
   radius=  1.8300
c  2-5,7-10,12-19,22,24-30,33-34,36-42                                         \
   radius=  2.0000
o  6,20-21,31-32,43                                                            \
   radius=  1.7200
h  44-79                                                                       \
   radius=  1.3000
# nofast
$cosmo_out file=out.ccf
$cosmo_correlated
$title
br-adc2-solvent
$operating system unix
$symmetry c1
$redundant    file=coord
$coord    file=coord
$user-defined bonds    file=coord
$atoms
n  1,11,23,35                                                                  \
   basis =n def2-TZVP                                                          \
   cbas  =n def2-TZVP
c  2-5,7-10,12-19,22,24-30,33-34,36-42                                         \
   basis =c def2-TZVP                                                          \
   cbas  =c def2-TZVP
o  6,20-21,31-32,43                                                            \
   basis =o def2-TZVP                                                          \
   cbas  =o def2-TZVP
h  44-79                                                                       \
   basis =h def2-TZVP                                                          \
   cbas  =h def2-TZVP
$basis    file=basis
$rundimensions
   dim(fock,dens)=1560450
   natoms=79
   nshell=617
   nbf(CAO)=1764
   nbf(AO)=1549
   dim(trafo[SAO<-->AO/CAO])=2194
   rhfshells=1
$scfmo   file=mos
$scfiterlimit       50
$scfconv        7
$thize     0.10000000E-04
$thime        5
$scfdamp   start=0.300  step=0.050  min=0.100
$scfdump
$scfintunit
 unit=30       size=0        file=twoint
$scfdiis
$scforbitalshift  automatic=.1
$drvopt
   cartesian  on
   basis      off
   global     off
   hessian    on
   dipole     on
   nuclear polarizability
$interconversion  off
   qconv=1.d-7
   maxiter=25
$optimize
   internal   on
   redundant  on
   cartesian  off
   global     off
   basis      off   logarithm
$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
$lock off
$maxcor    10000
$denconv     0.10000000E-06
$cbas    file=auxbasis
$ricc2
  adc(2)
$excitations
  irrep=a  multiplicity=  1  nexc=  4  npre=  4  nstart=  4
  exprop relaxed states=all
  spectrum  states=all  operators=diplen,qudlen
$response
  fop relaxed
$closed shells
 a       1-155                                  ( 2 )
$last step     define
$end

I don't know how to solve this problem, can anyone help me with this.
Thank you in advance.

29
Aoforce and Numforce / Re: Vibrational spectrum of first excited state
« Last post by Arnim on January 08, 2018, 03:17:43 pm »
When you are looking for a transition state with triplet occupation, you can do that similar to the singlet case.
Since you have computed already the Hessian of the triplet state, you could open the control file in TmoleX and visualize the vibrational frequencies. Then distort the molecule along the mode, which you can identify as your hydrogen transfer reaction mode and run jobex -trans for that structure.

Hope that helps,

Arnim
30
Aoforce and Numforce / Re: Vibrational spectrum of first excited state
« Last post by luyj on January 08, 2018, 02:57:34 pm »
Hello,

I just ran energy and gradient calculations with your input and noticed that gradient for the triplet is not zero (also not for the singlet, btw). Therefore, this structure of course can not be a minimum of the triplet state, regardless of the second derivative.

Cheers,

Arnim

Hello,

that is right I am looking for the transition state. To use statpt itrvec I need some guess for the imaginary mode, but there is none. The input structure is the TS of the singlet case.
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