Recent Posts

31

Ridft, Rdgrad, Dscf, Grad / Re: Density plots from DSCF

« Last post by chris.hol on March 13, 2024, 09:26:21 PM »

Hi Cody,

as far as I can remember, gOpenMol can read "cube" densities. On the Turbomole website under utilities (https://www.turbomole.org/turbomole/utilities/) you can download a "plt2cub" binary, that can convert your .plt files to such a .cube file. Download it, put it somewhere were you can execute it, and simply execute

/path/to/plt2cub td.plt > td.cube

in the directory where td.plt resides to obtain a cube file. Same is possible for sd.plt.

Best,
Christof

32

Ridft, Rdgrad, Dscf, Grad / Density plots from DSCF

« Last post by cwoods7 on March 13, 2024, 06:16:46 PM »

Hello,

I was wondering how to read the files sd.plt and td.plt from running dscf with $pointval dens. Has anyone had success with gOpenMol?

Best,

Cody

33

Parallel Runs / Re: ricc2 dipole moment calculation problem for MPI+amd nodes

« Last post by uwe on March 08, 2024, 07:53:37 PM »

Hello,

Christof found out what the problem is: The MPI version that is used in newer Turbomole releases is too new. Intel MPI 2019/2021 reduced the maximum allowed number for MPI tags (that's an implementation detail and can only be changed when building ricc2, not during runtime).

Turbomole 7.5.1 came with an older Intel MPI version which still works. So as a workaround, if you have older Turbomole releases available, use 7.5.1 (or older) for this job. Alternative is of course to use the latest version but SMP and not MPI.

A fix will be available in one of the next official releases of Turbomole.

Sorry for the inconvenience...

34

Statpt / statpt - geoired.f: lowest eigenvalue is too small

« Last post by jmkormanik on February 27, 2024, 01:31:51 PM »

Hello everyone,

I am working with short peptides (~400-500 atoms). When I am doing a minimization using jobex in TurboMole 7.7, usually in ired, sometimes I get this error during statpt: "geoired.f: lowest eigenvalue is too small". I was unable to find any information or what this means.

I am wondering why this is and if there is a way to fix it. Things we have tried and somewhat worked:
- small displacements of atoms before the start of the optimization (within 0.1 A)
- $redund_inp keyword in control set to "metric 2" (this works in majority of cases, but also occasionally fails)
- starting optimization in cartesian coordinates (without ired) for a few steps (tested 25) and then continuing in ired.

Despite all of these workarounds, which mostly work, statpt still occasionally fails in some cases (~1%) and I'm not sure whether this can be fixed or how to fix it. Can someone please elaborate what this error means and what I can do with it?

I'm attaching the control and coord files, as well as statpt output. cood.non_displaced.inp are the original coordinates of the structure, which was pre-optimized using xTB-GFN2 method. Upon visual inspection, I didn't notice any glaring issues with the structure itself. The structure is supposed to have certain restraints (to keep certain atoms together; a tetrahedron created by atoms 52, 118, 400 and 447), which might play some role, but in other similar calculations this didn't cause issues.

Thank you for your time and responses,

jmkormanik

35

Parallel Runs / Re: ricc2 dipole moment calculation problem for MPI+amd nodes

« Last post by glebreto on February 21, 2024, 09:10:19 AM »

Hello,

Thanks for your suggestions. How should I run on 2 cores in parallel using MPI in a machine that has 32 cores? In the above input, I set:

export PARNODES=2
export OMP_NUM_THREADS=2

and I do not have 2 processes starting but 33.
 

I also tried on Anliline or on this molecule:

$coord
   -8.31772213412044      2.35528661159307      0.00000566917837       c
   -5.74708611281726      1.68082068100064      0.00002456643962       c
   -5.02669605794417     -0.91132420305303      0.00001322808287       c
   -6.84130556911606     -2.84734483827988     -0.00004346370087       c
   -9.35925035688630     -2.15343929504342     -0.00006236096211       c
  -10.07869932814933      0.42537357120101     -0.00002834589187       c
   -2.35207029772896     -0.84979094098296      0.00002267671350       c
   -1.73118377194804      1.77591925849631     -0.00000377945225       n
   -3.71886196051766      3.29465057088330      0.00003401507024       n
   -0.61420256447812     -2.62628089676891      0.00004913287924       n
    1.73137274456050     -1.77546383450027      0.00001133835675       n
    2.35210053334695      0.84903127108086     -0.00000188972612       c
    0.61405138638815      2.62631302211303      0.00003968424862       n
    5.02651086478396      0.91116546605856      0.00007180959274       c
    5.74706154637764     -1.68116650088145      0.00005858150986       c
    8.31808685126249     -2.35518456638234      0.00002456643962       c
   10.07865208499621     -0.42515436297056     -0.00005291233149       c
    9.35889319864875      2.15379267382873     -0.00006803014049       c
    6.84105045608924      2.84742798622936     -0.00004157397474       c
    3.71926825163446     -3.29486977911375     -0.00000566917837       n
  -10.81255368166037     -3.59482033769723     -0.00009826575848       h
   -6.27814639699021     -4.81502594499871     -0.00006614041436       h
   -8.87810151911696      4.32341369367732      0.00003212534412       h
    6.27756436134383      4.81503161417709     -0.00006614041436       h
   10.81221731041019      3.59517182675641     -0.00013606028097       h
    8.87871190065522     -4.32324739777835      0.00004913287924       h
   12.07361327805014     -0.89154632943269     -0.00008692740173       h
  -12.07358493215827      0.89215293151870     -0.00003590479637       h
$end

and get similar issues.

If it may help, in the meantime I also had memory issues while performing CC2/ADC2 geometry optimization at the same step of the calculation: while calling the CC density Module using MPI. Note that it worked fine in SMP.

Best,
Guillaume

36

Parallel Runs / Re: ricc2 dipole moment calculation problem for MPI+amd nodes

« Last post by uwe on February 20, 2024, 05:03:03 PM »

Hello,

if the number of processes is large but the input small, some MPI processes will not get any tasks to do in some parts of the code. That might result in messaging problems. It should of course not happen, so it is good to get a bug report.
 
Depending on how the parallelization is done, the limiting factor for size of the input could be something like the number of occupied orbitals - which is 9 in your HCl case. You tried to run the job on 33 cores which is most likely too much for a two-atom input where the serial version just runs a couple of seconds.

Your input runs fine for me on 2 cores in parallel using MPI, but I'd recommend to try a larger input for testing.

Best Regards

37

Ridft, Rdgrad, Dscf, Grad / Re: DSCF No Exchange Energy

« Last post by chris.hol on February 17, 2024, 10:35:04 AM »

Hi Cody,

"Exc" and the "2e-ENERGY" should be reported in each iteration in dscf, just below the line with the iteration number. They are not reported in the end, but one can simply take the one from the last iteration. For a pure functional (without exact exchange, so non-hybrid functionals), the 2e-energy - Exc is actually the Coulomb energy. If a hybrid functional was used, no way leads around the route of using ridft for a single iteration if the Coulomb energy needs to be extracted.

An example PBE/def2-TZVP calculation on water is attached to this post. There, the 2e-energy in the last iteration is 37.577393, and Exc is -9.264745, leading to a Coulomb energy of 46.842138 Hartree.

Best,
Christof

38

Ridft, Rdgrad, Dscf, Grad / Re: DSCF No Exchange Energy

« Last post by cwoods7 on February 16, 2024, 09:11:31 PM »

Thank you Christof!

I am still a little confused about the subtraction from the "2e-Energy". I have used dscf for some more complex systems and both the "Exc" and exchange terms are absent. Essentially, all I am looking for is the Coulomb energy to do a density analysis. Is there a way to just extract the coulomb energy for dscf of both HF and DFT methods? If not, I will try to run the single ridft for all of my calculations.

Best,

Cody

39

Ridft, Rdgrad, Dscf, Grad / Re: DSCF No Exchange Energy

« Last post by chris.hol on February 16, 2024, 06:13:16 PM »

Hi,

in dscf, Coulomb + Exchange energies (and matrices!) are calculated at the same time using 4-center electron repulsion integrals. Therefore, they cannot be easily separated. You can extract the combined Coulomb + Exchange energy from the "2e-ENERGY" by subtracting the exchange-correlation energy ("Exc"). If you want to further separate them, an easy workaround is to run a single ridft iteration. For this, just change "$scfiterlimit" to 1, add $rij and run ridft, preferably in a separate directory. This will then yield the converged Coulomb + exchange energies at the dscf density.

Best regards,
Christof

40

Ridft, Rdgrad, Dscf, Grad / DSCF No Exchange Energy

« Last post by cwoods7 on February 16, 2024, 05:42:06 PM »

Hello,

I am fairly new to TURBOMOLE and am trying to run a test calculation on hydrogen for HF and DFT methods. I am trying to extract the exchange energy and the coulomb energy from the dscf calculation, but it is not appearing for me. Is there any special thing I should put in the control file so that it shows me these energies? Or is there something I should look for in the output file? They seem to be present in ridft, but not in dscf. I have already done a bunch of calculations for various systems using dscf and it would be a shame if I have to re-run these calculations especially since I have the total energies anyway. Any help would be much appreciated.