Recent Posts

1

TURBOMOLE Forum General / Re: Running same method calculation on multiple molecules.

« Last post by prasanta13 on June 14, 2022, 01:17:16 PM »

Sure, Tmolex offers an excellent choice. But there are only a few issues.
1. The program crashes if large number of molecules are present.

2. The choice of methods (basis set and other properties) are limited in Tmolex.

I used Tmolex extensively for few purposes, single-point calculation etc. However, I need to do calculations with aug-cc-pVQZ (Tmolex only has def2 basis).

2

ccsdf12 / There is at least one positive pair energy in the explicitly correlated part!

« Last post by prasanta13 on June 14, 2022, 08:00:42 AM »

Hi there,
I am trying to calculate ccsd(t)/aug-cc-pVQZ single point energy for a small molecule.
First I ran dscf (worked well) followed by ccsdf12 (still running).
Looking at ccsdf12 output file, I got this bizarre statement. A snap of the output is given below,

Code: [Select]

  ++ Starting calculation of pair energies.++


     Total noinv-RI-MP2-F12/A contr.: -0.081634802627


Positive pair energy detected:   110.41930994654157E-04
Positive pair energy detected:   220.11159410834232E-05
Positive pair energy detected:   370.28960788488212E-05
Positive pair energy detected:   460.74514191790383E-06
 
 =============== Warning ===================
 There is at least one positive pair energy
 in the explicitly correlated part!
 The positive pair energies are set to NaN.
 ===========================================
 
     Total fixed-RI-MP2-F12/A contr.:             NaN


 CAREFUL!
 We have computed a crappy correlation
 energy! Amplitudes are not stored!!!
 In order to be able to check what could be
 going on, we continue until the energy is
 printed... Check your basis sets!
     Total noinv-RI-MP2-F12/B contr.: -0.077050407447


Positive pair energy detected:   110.16344501857815E-03
Positive pair energy detected:   220.47808455928281E-05
Positive pair energy detected:   290.12783358776923E-03
Positive pair energy detected:   370.19127225718180E-03
Positive pair energy detected:   460.18193945420737E-04
 
 =============== Warning ===================
 There is at least one positive pair energy
 in the explicitly correlated part!
 The positive pair energies are set to NaN.
 ===========================================
 
     Total fixed-RI-MP2-F12/B contr.:             NaN


 CAREFUL!
 We have computed a crappy correlation
 energy! Amplitudes are not stored!!!
 In order to be able to check what could be
 going on, we continue until the energy is
 printed... Check your basis sets!


     time in mp2 energy    cpu:  0.17 sec    wall:  0.00 sec    ratio: 63.4
 
     time in mp2 (NRG)     cpu:  4.48 sec    wall:  0.07 sec    ratio: 63.9
     time in mp2 (all)     cpu: 17 min 48 s  wall:  0 min 21 s  ratio: 51.2


     **********************************************************************
     *             the CCSD(F12*) approximation will be used              *
     **********************************************************************


     time in resort(f12)   cpu:  4.71 sec    wall:  4.78 sec    ratio:  1.0
     threshold for screening of F12 V intermediate: 0.45E-17
     time in Vijmn         cpu:   1 d 17 h 43 min  wall:   0 d  0 h 42 min  ratio: 59.3
     time in Vijmn->Vijkl  cpu:  0.33 sec    wall:  0.32 sec    ratio:  1.0

     Calculate additional intermediates for fixed geminal coefficients

     time in c*V contr.    cpu: 24.61 sec    wall:  0.93 sec    ratio: 26.5
     time in r12 t-amp.    cpu: 19.58 sec    wall:  1.25 sec    ratio: 15.7
     time in 3idx,ccsdint  cpu:  6 min 48 s  wall:  0 min 23 s  ratio: 18.0

     Calculate integrals (ia|jb) for MP2 start guess



     **********************************************************************
     *                                                                    *
     *   RHF  energy                             :   -132.2965497240      *
     *   correction to HF from CABS singles      :     -0.0012818953      *
     *   corrected RHF  energy                   :   -132.2978316193      *
     *                                                                    *
     *   MP2 correlation energy (doubles)        :     -0.6051224995      *
     *   fixed-RI-MP2-F12/2B [F+K] contr.        :               NaN      *
     *   total correlation energy                :               NaN      *
     *                                                                    *
     *   Final MP2-F12 energy                    :               NaN      *
     *   (MP2 energy w/o F12, CABS singles       :   -132.9016722235)     *
     *                                                                    *
     *    E(S)   =     -0.4039616899      E(T)   =     -0.2011608096      *
     *    E(OS)  =     -0.4710152931      E(SS)  =     -0.1341072064      *
     *    F12(S) =               NaN      F12(T) =     -0.0046820586      *
     *    F12(OS)=               NaN      F12(SS)=     -0.0031213724      *
     *                                                                    *
     *   SCS-MP2-F12 energy                      :               NaN      *
     *   (SCS-MP2 energy w/o F12                 :   -132.9064704779)     *
     *   (computed with  C(OS) =   1.2000  and  C(SS) =   0.3333)         *
     *                                                                    *
     *   SOS-MP2-F12 energy                      :               NaN      *
     *   (SOS-MP2 energy w/o F12                 :   -132.9088696051)     *
     *   (computed with  C(OS) =   1.3000)                                *
     *                                                                    *
     *   Norm of MP1 T2 amplitudes               :      0.2220257492      *
     *                                                                    *
     **********************************************************************

     time in ccsdint       cpu:   1 d 18 h  2 min  wall:   0 d  0 h 43 min  ratio: 58.6


   **************************************************************************
   *                                                                        *
   *          OPTIMIZATION OF THE GROUND STATE CLUSTER AMPLITUDES           *
   *                                                                        *
   **************************************************************************I am also sharing the control file.

Code: [Select]

$title
$symmetry c1
$user-defined bonds    file=coord
$coord    file=coord
$optimize
 internal   off
 redundant  off
 cartesian  on
 global     off
 basis      off
$atoms
    basis =aug-cc-pVQZ
    cabs  =aug-cc-pVQZ
    cbas  =aug-cc-pVQZ
    jkbas =aug-cc-pVQZ
$basis    file=basis
$scfmo   file=mos
$closed shells
 a       1-10                                   ( 2 )
$scfiterlimit       30
$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
$maxcor    500 MiB  per_core
$scforbitalshift  automatic=.1
$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
$denconv     0.10000000E-06
$rir12
  ansatz      2
  ccsdapprox  ccsd(f12*)
  no_f12metric
  r12model    B
  comaprox    F+K
  cabs        svd  1.0000E-08
  examp       fixed  noflip
  corrfac     LCG
  cabsingles  on
$lcg
  nlcg    6
  slater  1.4000
$ricc2
  ccsd(t)
$rundimensions
   natoms=7
   nbf(CAO)=485
   nbf(AO)=390
$actual step      ccsdf12
$last SCF energy change = -.45088200E-09
$charge from dscf
         -0.000 (not to be modified here)
$dipole from dscf
  x    -0.00000000000002    y     0.52841373220459    z     1.29921323297381    a.u.
   | dipole | =    3.5649802707  debye
$cabs file=auxbasis
$jkbas file=auxbasis
$cbas file=auxbasis
$last CCSD(T) energy change= -.68838301
$orbital_max_rnorm 0.22364354438859E-05
$end

What is the source of this problem, and what is the solution?
Thanks in advance.
Prasanta

3

TURBOMOLE Forum General / Re: Running same method calculation on multiple molecules.

« Last post by uwe on June 13, 2022, 08:15:01 PM »

Hi,

sure, there are quite a number of options which all allow running calculations on lists of molecules. But before I start to list those, it seems that you would prefer to use TmoleX.

So let me first ask why you want to run TmoleX on a remote machine at all. While there are remote desktop solutions like RDP, VNC, Nomachine, Teamviewer or even the good old X11 server still works, it is highly recommended to install and use the graphical user interface locally on the machine you are using as a desktop. That guarantees a responsive user interface.

Is the machine you want to run the calculation on accessible by secure shell (ssh)? If yes, you can use the Run(network) button in TmoleX instead of the Run(Local) one when starting jobs. It asks you for the name of the remote machine, user name, password and the installation directory of the command line version of Turbomole on that machine. If you have all that, you can run jobs the same way you are used to on your local machine.
Queuing systems like PBS, SLURM, LSF, etc. are supported and jobs can be submitted to those from TmoleX too.

Would that be an option?

4

TURBOMOLE Forum General / Running same method calculation on multiple molecules.

« Last post by prasanta13 on June 13, 2022, 07:50:36 AM »

Hi,
I want to run PBE/def2-TZVP calculation on 1200 molecules. Now it can be done with Tmolex, but I have a problem with the graphic driver (probably) and it doesn't work as expected. Starting define module for each system is not a way. Is there any other way available so I can generate the input and run Turbomole in one go?

5

Molecular Properties, Wavefunction Analysis, and Interfaces to Visualization Tools / TDDFT-Transition densities

« Last post by Pandiselvi on May 19, 2022, 08:39:52 AM »

Dear all,


         I'm trying to plot the transition densities for a molecule having C1 symmetry with $soes 3 . By default the first excited state (of the first irrep)  is printed with the file name (vcao_td_a_001.1.plt).
   
 $curswitchdisengage
 $pointval transdens
 $tdlist
   irrep1 num1
   irrep1 num2
Those are the keywords I'm using to plot the transition densities (which is given in the manual) but still, the higher excited state is not printed having the same irrep a . How to sort out this ??
Thanks in advance

6

Ridft, Rdgrad, Dscf, Grad / Re: Manualy define DFT-D4 ($disp4) parameters

« Last post by mradon on May 16, 2022, 12:30:38 PM »

Dear Uwe:
Good to hear that this functionality will be implemented soon. It is very much needed.

Best wishes,
Mariusz

7

Molecular Properties, Wavefunction Analysis, and Interfaces to Visualization Tools / Re: plt tool mislabelling atoms with ECPs

« Last post by uwe on May 14, 2022, 10:18:52 PM »

Hello,

you are right, cub files generated directly by the keyword

$pointval fmt=cub ...

do add the charge of the nuclei which in case of ECPs is not correct. Should be fixed in the next major release.

You could write standard plt format instead (just remove the fmt=cub option) and then use 'plt2cub' from here:

https://www.turbomole.org/turbomole/utilities/

to do the conversion. plt2cub should write the correct element identifiers also in case of ECPs.

8

Ridft, Rdgrad, Dscf, Grad / Re: Manualy define DFT-D4 ($disp4) parameters

« Last post by uwe on May 14, 2022, 10:09:43 PM »

Hi,
the official versions do not yet offer the possibility to manually set parameters for D4, I'm afraid.

The developer version does recognize
$disp4 --param <s6> <s8> <a1> <a2>
just as the stand-alone version of DFT-D4.

Thus, this functionality will be available in the next major release later this year (2022).
Regards, Uwe

9

Ridft, Rdgrad, Dscf, Grad / Manualy define DFT-D4 ($disp4) parameters

« Last post by mradon on May 13, 2022, 12:51:57 AM »

Dear Turbomole experts:

I am trying to use a relatively new functional LH20t, for which the D4 correction was parametrized (10.1021/acs.jctc.0c00498). This functional is available in Turbomole 7.5.1, but it appears that the dispersion parameters are not available:
           ------------------
           density functional
           ------------------
 Lh20t local hybrid functional

(...)
      -----------------------------------------------------------
     |                   =====================                   |
     |                        D F T - D 4                        |
     |                   =====================                   |
     |                         S. Grimme                         |
     |          Mulliken Center for Theoretical Chemistry        |
     |                    University of Bonn                     |
      -----------------------------------------------------------


========================
 internal module stack:
------------------------
    ridft
    allone
    dftd4
========================

 DFA lh20t unknown
 ridft ended abnormally

The parameters of the D4 model (s8, a1, a2) for this functional are known and they are given in the original paper.

I wonder, is there a way I can manually supply the values for the D4 parameters? (of course without recompiling Turbomole).

Thank you in advance.

Regards,
Mariusz

10

Molecular Properties, Wavefunction Analysis, and Interfaces to Visualization Tools / plt tool mislabelling atoms with ECPs

« Last post by Dempsey on May 05, 2022, 01:13:05 PM »

Dear Developers,

I have come across a minor problem with the plt tool. For calculations using ECP basis sets the plt tool presents any atoms as Z - Nelectrons in the ECP. For example, my molecule has ⁹⁴Pu and I am using the Dolg 60 electron ECP so the cub file created by the plt tool presents the ⁹⁴Pu as ³⁴Se. I double-checked and ⁹³Np becomes ³³As in the cub file confirming my suspicions about the interaction of plt with the ECP.

I compared the wavefunctions generated by both plt and tm2molden and they appear to be the same. The ECP atoms can be fixed manually by editing the cub file e.g. changing 34 to 94 but maybe you could implement a fix for this?

I should also note that I am using Turbomole 7.3, this may be fixed in newer versions?

Code: [Select]

$title
$operating system unix
$symmetry c1
$redundant    file=coord
$user-defined bonds    file=coord
$coord    file=coord
$optimize
 internal   on
 redundant  on
 cartesian  off
 global     off
 basis      off
$atoms
pu 1                                                                           \
   basis =pu def-SV(P)                                                         \
   ecp   =pu def-ecp                                                           \
   jbas  =pu def-SV(P)
o  2,5,8,11,14,17,20,23                                                        \
   basis =o def2-SVP                                                           \
   jbas  =o def2-SVP
h  3-4,6-7,9-10,12-13,15-16,18-19,21-22,24-25                                  \
   basis =h def2-SVP                                                           \
   jbas  =h def2-SVP
$basis    file=basis
$ecp    file=basis
$newecp
$rundimensions
   dim(fock,dens)=52606
   natoms=25
   nshell=125
   nbf(CAO)=322
   dim(trafo[SAO<-->AO/CAO])=385
   rhfshells=2
   nbf(AO)=291
$uhfmo_alpha   file=alpha
$uhfmo_beta   file=beta
$uhf
$scfiterlimit       3000
$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 pbe0
   gridsize   m4
$disp3 -bj
$scfconv   8
$scfdamp   start=0.700  step=0.050  min=0.050
$scforbitalshift  automatic=.1
$ricore      500
$rij
$jbas    file=auxbasis
$marij
$last SCF energy change = -.40488317E-06
$ssquare from ridft
          6.025 (not to be modified here)
$charge from ridft
          4.000 (not to be modified here)
$dipole from ridft
  x     0.12195769945513    y     0.00426054814190    z     0.06652229715999    a.u.
   | dipole | =    0.3532693012  debye
$alpha shells
 a       1-57                                   ( 1 )
$beta shells
 a       1-53                                   ( 1 )
$pointval fmt=cub mo 110
$last step     ridft
$orbital_max_rnorm 0.27147188038346E-04
$subenergy  Etot         E1                  Ej                Ex                 Ec                 En                 Disp
-1161.602293901    -3945.264799283     1745.918486321    -77.06141850395    -4.307684619003     1119.137232935    -.2411075074845E-01
$end


Code: [Select]

amplitude of MO   57a      a      -1.06731a.u.
OUTER/INNER/MIDDLE LOOP: X,Y,Z
   25   -7.163758   -8.035522   -8.200891
   72    0.203215    0.000000    0.000000
   81    0.000000    0.202709    0.000000
   81    0.000000    0.000000    0.202628
   34    0.000000    0.040324    0.008193    0.009549
    8    0.000000    3.146616   -2.432724   -2.180174
    1    0.000000    2.745017   -2.158459   -3.593451
    1    0.000000    2.635920   -3.810491   -1.906671
    8    0.000000    3.076968    2.296790    2.447402
    1    0.000000    2.549683    2.045558    3.823159
    1    0.000000    2.658780    3.697589    2.136379
    8    0.000000    3.264512    2.244631   -2.227628
    1    0.000000    2.824009    3.651637   -1.982379
    1    0.000000    2.848885    1.962346   -3.635260
    8    0.000000    2.623040   -2.448840    2.415281
    1    0.000000    2.134659   -3.832814    2.132511
    1    0.000000    2.109782   -2.143523    3.785392
    8    0.000000   -3.163758    0.121235    3.191230
    1    0.000000   -2.760680   -1.062833    4.009380
    1    0.000000   -2.701127    1.299839    3.985409
    8    0.000000   -3.114510   -3.223036   -0.080960
    1    0.000000   -2.622558   -4.035522   -1.234956
    1    0.000000   -2.717292   -4.009175    1.126541
    8    0.000000   -2.898531    0.047471   -3.420261
    1    0.000000   -2.372725    1.208506   -4.200891
    1    0.000000   -2.432278   -1.154166   -4.176920
    8    0.000000   -2.947779    3.391742   -0.148071
    1    0.000000   -2.416113    4.154849   -1.318053
    1    0.000000   -2.510847    4.181195    1.043445

Best,
Dempsey