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Miscellaneous / Re: visualizing natural orbitals
« Last post by mansaribhu on October 16, 2017, 11:54:48 am »
Dear Sir/Madam

I do not have TURBOMOLE software but I want to calculate spin natural orbitals. If you have any solutions please help me.

M. Ansari
Riper / Re: Plotting orbitals not working
« Last post by turbomaster on October 12, 2017, 01:55:18 pm »
Can you provide the coord file?
Statpt / jobex -trans failure after one cycle
« Last post by jkirk on October 10, 2017, 03:04:43 pm »

I am searching for a transition state that involves two molybdenum species end-on bridged by an N2 molecule transition to a side-on bridged conformation. I generated a "guess" at the transition state, performed an ridft, rdgrad, and NumForce -ri -c. I received three negative frequencies, the lowest of which corresponding to my rotation/elongation of N2.

I then have my control file and hessian file generated from the NumForce calculation. However, when I go to perform my jobex -trans -ri, it performs one optimization cycle, then crashes.

The final lines at the end of my job.last file are:

"fine, there is no data group "$actual step"
next step = rdgrad"

Am I missing a step, or should I try itvc 2 instead?

Here are the current lines in my control:
   itrvec      1
   hssfreq      1

Again, here is a summary of all the calculations performed on this system:
- I took an optimized structure and edited the Mo-N-N-Mo motif to an initial guess for the TS structure
- ridft
- rdgrad
- NumForce -ri -c
- jobex -trans -ri (crashes after one cycle, and the ridft for this first cycle converges after 3 iterations)

Final note: I have tried the same calculation but freezing every atom except the four main ones involved: 2 Mo, 2 N. And I receive the same result.

Any help or guidance is appreciated.
Problem solved.
I was missunderstanding the results and effect on control file of promowa module.
It was my fault.
The comparison with Su&Li is good.


Hi Evgeniy,

the what you call 'next' geometry can not or should not be much different to the geometry before, since if the convergence criteria are met, the gradient norm and the maximum displacement are small. Changes can thus happen only within the accuracy of the given convergence criteria.

I think the main reason why an additional gradient step is not done, is because this data is not needed  by (almost) any subsequent calculation or post-processing tool. So it simply saves time.

The question which data is most reasonable to be stored in which file or data group is probably not a trivial one, though. What TM does is to make sure that coordinates, orbitals and energy are consistent. Those are needed for all subsequent jobs, and since in TM every job is a restart job (so to say), it is important to always have the right starting point for the next step. The gradients, on the other hand, are only needed for a few other properties, e.g. for frequency calculations when the gradients are not exactly zero. That's why the coordinates are stored in addition to the gradients for each step of an optimization in the gradient file - frequency jobs will use (for the terms which include the gradients) the correct matching coordinates.

But - as usual - you can easily adapt Turbomole such that it does what you want. jobex is a script which can be modified such that the convergence is checked after the gradient step and not after the energy step (search for the appearance of checkconv).


Dear Developers of TM,

I wonder why after successful geometry optimization the geometry
in the coord file corresponds to the "next" geometry predicted by the
optimizer (statpt or relax). This is not exactly the geometry for which
the gradients were calculated and all the optimization thresholds were
reached. Although one can find the "faithful" optimal geometry in the gradient
file I think it would be reasonable to have that geometry also in the coord
file; the additional evaluation of energy at the "next" geometry could be
then omitted.

Best regards,
Ridft, Rdgrad, Dscf, Grad / Troubling results in Energy Descomposition Analysis (EDA)
« Last post by romarine on September 27, 2017, 01:26:38 pm »
Dear all,
I would like to perform an energy decomposition analysis (EDA) on a system with biological interest.

To know if I follow the procedure correctly I tried to reproduce previous calculations.
Turbomole manual (v 7.1, section 6.6) indicates the paper of Su and Li (J, Chem. Phys. 130, 014104 (2009)) for further details.

Taking an example of this reference I performed the EDA for the Cu+(SCH3)- complex at the BLYP/ACCQ//MP2/ACCT level: EDA at BLYP/aug-cc-pVQZ level using the CuSCH3 optimized structure at MP2/aug-cc-pVTZ level (the SCH3- fragment was not reoptimized), and compared the results with the Su&Li's work (Table V of the paper).

The comparison of the results is:
                   DEele   DEex  DErep   DEpol  DEdisp  DEtotal   (kcal/mol, where D means Delta)
My Calcs: -199.37    4.77  0.000    0.001  -12.40 -207.00
Su&Li:      -257.96 -46.95 190.97 -81.21  -12.27 -207.41
I am comparing polarization and dispersion (from paper) with orbital relaxation and correlation energy differences, respectively as it is commented in the paper (as I understand from points (2) and (4) of page 2 of the paper)

As you can see that my results reproduce the total and dispersion energy differences assuming that differences are due to the use of RI approx. in my calculations (what do you think?) but I am obtaining very different values in the rest of energy differences.

But this doesn't finish here. As I am interested in solvated systems, I performed EDA of the same system using COSMO model (EDA-COSMO) and comparing with the results in J. Chem. Phys. 137, 034111 (2012) where the EDA-CPCM analysis is performed on the same system at B3LYP-cc-pVTZ level (Table II of the paper, B3LYP/CCT results).

The comparison is:

                                       DGele   DGex  DGrep   DGpol  DGdisp  DGotal   (kcal/mol, where D means Delta)
EDA-COSMO,eps=78.4):  -84.96  25.80  0.00     -0.001  -9.16  -68,20
EDA-CPCM,eps=78.4):  -264.23 -60.99  203,92 -69,44  -9,99  -67,95

EDA-COSMO,eps=1.00) -214.54  21.92    0.00     -2.75   -9.11   -204.48
EDA-CPCM,eps=1.00):  -268.16 -60.36  205.23  -67.71 -10.22  -201.22 

I must confess that in this case I have to do a deeper bibliographical analysis to confirm that both methods are comparable (for example, are free energy data the turbomole's results in the case of EDA-COSMO?), but again, the comparison in dispersion and total energy difference values are the only reasonable, although the differences for epsilon=1.00 are the biggest.

Dear community,

Am I missing something important/evident?
Is it normal that repulsion energy difference is always zero in turbomole's results?
Is there other systems (computationally fast) I can compare results with?
Any other idea?

I am using TURBOMOLE V7.1, jobex -ri -level mp2 command for MP2/aug-cc-VTZ geometry optimization, and rift command for EDA method making the modifications on control files exposed in the manual.

Thanks in advance,

Riper / Plotting orbitals not working
« Last post by luyj on September 27, 2017, 01:10:52 pm »

I tried to plot some orbitals of a 1D periodic molecule. Following the advise from the manual, I modified the control file. The calculation seemed to have finished without error. Sadly the cub files were not created in the calculation folder.

              |         Calculation of quantities on grid        |
 Creating .cub files
   *grid construction*
   *plotting orbital     1 of     5*
   calculating values on grid points
   writing orbital values to   orb_k_1_1_1_a_1_real.cub
   *plotting orbital     2 of     5*
   calculating values on grid points
   writing orbital values to   orb_k_1_1_1_a_2_real.cub
   *plotting orbital     3 of     5*
   calculating values on grid points
   writing orbital values to   orb_k_1_1_1_a_3_real.cub
   *plotting orbital     4 of     5*
   calculating values on grid points
   writing orbital values to   orb_k_1_1_1_a_4_real.cub
   *plotting orbital     5 of     5*
   calculating values on grid points
   writing orbital values to   orb_k_1_1_1_a_5_real.cub
   ****  riper : all done  ****

Maybe I did something wrong since the example is only for 3D systems.

My input:

Code: [Select]
$periodic 1
$lattice angs
     8.6727102444608981   -0.0006344509069820    0.0076449746608829
    13.0074129090911157   22.3641390786160628    0.0134372830829742
     0.0238619607550042    0.0023876986523183   27.0526534211542611
 nkpoints 1
 sigma 0.01
$scfconv   6
$scfdamp   start=0.700  step=0.050  min=0.050
$disp3 bj
$restart   off
$closed shells
 a       1-154                                  ( 2 )
$energy    file=energy
$grad    file=gradient
$last step     riper
$maxcor 1387
$pointvalper fmt=cub
 orbs 5
 k 1 1 1 a 1 r
 k 1 1 1 a 2 r
 k 1 1 1 a 3 r
 k 1 1 1 a 4 r
 k 1 1 1 a 5 r

Hopefully you can help me.
Installing the Program / Re: Newly installed Turbomole running slow
« Last post by mariavd on September 15, 2017, 11:10:21 pm »

Thank you for the quick reply. Turbomole runs fine on the CSC cluster. I had to set it up on another cluster at the university. It has about a dozen free nodes at the moment, so I guess that if the SLURM system is set up correctly, it should send the jobs to CPUs from the same node.

Yes, I allocate all CPUs from the nodes. The Xeon E5-2620 v3 is an octacore CPU with hyper-threading, so the script requests 16 tasks per node:

#SBATCH --nodes 2         # for SMP only 1 is possible
#SBATCH --ntasks-per-node=16 # Tasks per node
#SBATCH --ntasks 32      # total number of cores (processes)

The $profile option for a simple ridft run on the cyclopentadienyl cation returned the following:

    dscf profiling
             module   cpu total (s)       %  wall total (s)       %

                   1.2  100.00            18.8  100.00
        dscf.prepare                 0.1    5.60             0.8    4.27
      prepare.oneint               0.0    0.72             0.1    0.68
     prepare.moinput             0.0    1.43             0.2    1.30
     prepare.orthmos             0.0    0.52             0.1    0.30
            dscf.scf                   1.1   93.88            17.8   94.68
             scf.pre                   0.0    0.08             0.1    0.42
        scf.makedmat              0.0    0.22             0.1    0.38
          scf.shlupf                  0.8   65.94            12.5   66.40
         dscf.shloop                 0.8   63.94            10.7   56.77
          scf.symcar                 0.0    0.11             0.0    0.00
        scf.makefock               0.0    0.17             0.3    1.45
                 0.0    0.01             0.0    0.00
          scf.pardft                  0.3   21.02             3.8   20.21
        dft_grid_con                0.0    0.82             0.0    0.04
          scf.newerg                0.0    0.00             0.0    0.00
          scf.newcnv                0.0    0.35             0.1    0.72
           scf.fdiag                   0.0    1.52             0.0    0.25
         diag_tritrn                  0.0    0.29             0.0    0.02
          diag_rdiag                 0.0    1.14             0.0    0.20
          scf.modump              0.0    2.70             0.5    2.77
                     0.0    1.58             0.2    1.14
        dscf.postscf                 0.0    0.48             0.2    1.04

         total  cpu-time :   1.25 seconds
         total wall-time :  20.15 seconds

The difference between the wall clock time and CPU time is huge, which makes me think that there is some communication delay between separate nodes. I will first contact the IT support at the department, and if needed, the Turbomole support, too.

Installing the Program / Re: Newly installed Turbomole running slow
« Last post by uwe on September 15, 2017, 04:10:02 pm »

hm, was that on the SLURM cluster at the CSC in Espoo? Did you allocate all cores on the nodes?

To figure out what happens it could be useful to see the timings of the individual steps. If you add $profile to the control file and run the job, you will get detailed timings at the end of the output.

If things do not change even if all CPUs on the nodes are used, please contact the Turbomole support to get help.



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