Recent Posts

Pages: 1 2 [3] 4 5 ... 10
21
Riper / Re: RIPER display negative root while Cholesky factorization failed
« Last post by Marek Sierka on November 08, 2018, 04:42:07 pm »
What Turbomole version do you use?
22
Riper / RIPER display negative root while Cholesky factorization failed
« Last post by skundu07 on November 07, 2018, 06:31:14 pm »
Hi, I am doing Single Point Energy Calculation via RIPER. I have 48 metal atoms with an adsorbed moiety on top of that. I have auxiliary basis sets (auxbasis), basis and molecular orbitals (alpha, beta) defined and a coord file where first two layer of metal atoms are fixed. Following is my control file, where I have used RIPER with periodic lattice defined, matrix diagonalization on.

$title
$operating system unix
$symmetry c1
$user-defined bonds    file=coord
$coord    file=coord
$periodic 3
$lattice
  8.38324586     0.00000000     0.00000000
  0.00000000    11.17766115     0.00000000
  0.00000000     0.00000000    20.92784999
$kpoints
  nkpoints 3 3 1
$riper
  thrints    1.0d-12
  lenonly    off
  lchgprj    on
  sigma      0.20
  northol    5
  pqmatdiag  on
  pqsingtol  1.0d-8
$optimize
 internal   off
 redundant  off
 cartesian  on
 global     off
 basis      off
$atoms
c  1                                                                           \
   basis =c def2-TZVP                                                          \
   jbas  =c def2-TZVP
o  2                                                                           \
   basis =o def2-TZVP                                                          \
   jbas  =o def2-TZVP
pd 3-50                                                                        \
   basis =pd ecp-28-mwb-TZVP                                                   \
   ecp   =pd ecp-28-mwb                                                        \
   jbas  =pd ecp-28-mwb-TZVP
$basis    file=basis
$ecp    file=basis
$rundimensions
   dim(fock,dens)=1296396
   natoms=50
   nshell=550
   nbf(CAO)=1608
   dim(trafo[SAO<-->AO/CAO])=1916
   rhfshells=2
   nbf(AO)=1454
$uhfmo_alpha   file=alpha
$uhfmo_beta   file=beta
$uhf
$alpha shells
 a       1-450                                  ( 1 )
$beta shells
 a       1-428                                  ( 1 )
$scfiterlimit       6000
$thize     0.10000000E-04
$thime        5

$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 b-p
   gridsize   m4
$scfconv   7
$scfdamp   start=0.700  step=0.050  min=0.050
$scforbitalshift  closedshell=0.3   automatic! 0.3
$ricore      500
$rij
$jbas    file=auxbasis
$last step     define
$end


But in my riper.out output file it is saying riper ended abnormally

              +--------------------------------------------------+
              |      SCREENING OF BASIS FUNCTION PRODUCTS        |
              +--------------------------------------------------+
               
         Threshold for shell products neglect:          0.1E-11
         Tolerance for shell products extents:          0.1E-06
         Number of {mu,nu,L} shell products:            2817642
         Number of primitive basis function products:   3867397
       
               
              +--------------------------------------------------+
              |             INITIAL ORBITALS/BANDS               |
              +--------------------------------------------------+
               

 reading orbital data $uhfmo_alpha  from file alpha
 orbital characterization : expanded

 reading orbital data $uhfmo_beta  from file beta
 orbital characterization : expanded

========================
 internal module stack:
------------------------
    riper
========================

 Cholesky factorization failed in <ztritrn>... negative root
 riper ended abnormally


Could anyone suggest me how to fix that?

Thanks
Subrata
23
Riper / RIPER
« Last post by skundu07 on November 06, 2018, 08:27:51 pm »
Hi, I am trying to do Single Point Energy (SPE) calculation with RIPER  module in Turbomole 7.2.1.

I have an optimized structure with 48 metal atoms (4 layers of atoms - each layer with 12 atoms) with a adsorbed molecule on top of that. I optimized that structure with VASP. But now I am trying to do periodic SPE calculation using RIPER module in Turbomole 7.2.1. I have couple of questions-

1. Do I use same structure (48 atoms which is transforms to coord) for RIPER calculation? Or do I need to transform that structure to a non-periodic coord file with 51 cluster metal atoms ( 2 Layers of Atoms - 30 in the first layer and 21 in the second layer) with adsorbed moiety with $lattice command in control file?

Subrata
24
Define / Re: Analysis of MOs in terms of particular AOs (basis funcstions)
« Last post by uwe on September 10, 2018, 09:45:45 pm »
Hi,

if you just want to know in which order the coefficients are printed to the mos (or alpha/beta) file, simply call define, go to the molecular orbital menu (say 'y' if you are asked if you want to enter the menu) and enter 'infsao'.

This will ask for a file name where the information will be written to. Just enter a name here, or a '0' (zero) to print it to screen. The resulting file will look like that:

 SYMMETRIZED ATOMIC ORBITALS (SAOS) EXPRESSED IN TERMS OF AOS


 representation a   contains 1 *149 basis functions

 cumulative   within current              atom  shell type    coefficient
 SAO-index   symmetry species
     1              1                      1 c     1 s         1.000000
     2              2                      1 c     2 s         1.000000
     3              3                      1 c     3 s         1.000000
     4              4                      1 c     4 s         1.000000
     5              5                      1 c     5 s         1.000000
     6              6                      1 c     1 px        1.000000
     7              7                      1 c     1 py        1.000000
     8              8                      1 c     1 pz        1.000000
     9              9                      1 c     2 px        1.000000
    10             10                      1 c     2 py        1.000000
    11             11                      1 c     2 pz        1.000000
    12             12                      1 c     3 px        1.000000
    13             13                      1 c     3 py        1.000000
    14             14                      1 c     3 pz        1.000000
    15             15                      1 c     1 d0        1.000000
    16             16                      1 c     1 d1a       1.000000
    17             17                      1 c     1 d1b       1.000000
    18             18                      1 c     1 d2a       1.000000
    19             19                      1 c     1 d2b       1.000000
    20             20                      2 n     1 s         1.000000
    21             21                      2 n     2 s         1.000000
    22             22                      2 n     3 s         1.000000

and so on. The d0, d1a, etc. terms (and higher ones if present) are described at the end of the file, e.g.:

 d0  = (-xx-yy+2zz)/sqrt(12)
 d1a = xz
 d1b = yz
 d2a = xy
 d2b = (xx-yy)/2

Then you can identify which number in each molecular orbital belongs to the AO you are interested in.

Regards,

Uwe
25
Define / Re: Analysis of MOs in terms of particular AOs (basis funcstions)
« Last post by evgeniy on September 10, 2018, 07:24:26 pm »
Dear Uwe,

Many thanks for your reply. I tried the way you suggested in your previous messages, that is,

tm2molden mostat ...

This would be perfect if for some reasons I had not got stars, i.e. ******* for the contributaion of certain basis
(atomic) functions in some cases, for example like this:

contribution of AO   1 ir    2 px       is: ****** %
contribution of AO   1 ir    1 dy2      is: 30.007 %
contribution of AO   1 ir    1 dx2      is: 30.007 %
contribution of AO   1 ir    1 dxy      is: 18.705 %
contribution of AO   1 ir    5 px       is: 18.695 %
contribution of AO   1 ir    3 px       is:  9.933 %


Some different questions:
Maybe you know if there is a way just to print out the MO coefficients in a more or less readable way from the mos file?
I do not want to use the molden file for that as there are Cartesian d-, f- etc. functions instead of spherical ones.

Best regards,
Evgeniy
26
Define / B97-3c
« Last post by chemistza on September 10, 2018, 03:25:07 pm »
Hi,

The new composite B97-3c method available in TM 7.3 does not yet appear to be documented. I assume it is defined with functional name: b97-3c; is the dispersion specified similarly to PBEh-3c (i.e. $disp3 -bj -abc) in the control file?

Many thanks
Chris
27
Define / Re: Analysis of MOs in terms of particular AOs (basis funcstions)
« Last post by uwe on September 07, 2018, 10:40:13 pm »
Dear Evgeniy,

that is a known problem with Mulliken population analysis. Well, not really a problem... this approach is just a model and one gets very different numbers just be changing the basis set size. There are plenty of papers about this topic out there.

Regards,

Uwe
28
Define / Re: Analysis of MOs in terms of particular AOs (basis funcstions)
« Last post by evgeniy on September 06, 2018, 07:46:41 pm »
Dear Uwe,

Thanks for your reply. I will try that way.

By the way, I have a related question.  Don't you happen to know
why there are sometimes negative contributions from the basis functions
in the Mulleken population analysis. For example like this:

    22a'       energy/a.u.:     -0.4962665
   1ir     0.20219   0.20063   0.00000   0.00068   0.00087   0.00001
   2c      0.13295  -0.00256   0.12903   0.00624   0.00024
   3c      0.13295  -0.00256   0.12903   0.00624   0.00024
   4c      0.13295  -0.00256   0.12903   0.00624   0.00024
   5c      0.13295  -0.00256   0.12903   0.00624   0.00024
   6c      0.13295  -0.00256   0.12903   0.00624   0.00024
   7c      0.13295  -0.00256   0.12903   0.00624   0.00024
   8c      0.18431   0.00269   0.17219   0.00926   0.00017
   9c      0.18431   0.00269   0.17219   0.00926   0.00017

Normally, there shouldn't be negative contributions. So,  I guess, it is sort of an artefact due to the Mulliken anlysis.

Best regards,
Evgeniy
29
Define / Re: Analysis of MOs in terms of particular AOs (basis funcstions)
« Last post by uwe on September 06, 2018, 03:39:19 pm »
Hi,

in principle you could use the tool tm2molden with the mostat option:

tm2molden mostat

or

tm2molden mostat 149-153,155

to print the data just from the list of selected molecular orbitals (use the eiger script to see which numbers are virtual).

But this will print the contributions only if they are larger than 1%. To change the threshold, add another option to tm2molden:

tm2molden mostat 150-160 above 0.00001

or

tm2molden mostat 150-160 above 1e-5

(smaller than 1e-5 will not help anymore as the print format  is "0.001 %")

If you run into problems or if the output does not help as expected, just contact the Turbomole support to get a modified version (email address as usual).

Regards,
Uwe

30
Define / Analysis of MOs in terms of particular AOs (basis funcstions)
« Last post by evgeniy on September 05, 2018, 05:12:08 pm »
Hello,

I am intrested in analysis of a HF MO in terms of atomic orbitals (basis funstions)  contributions.
More precisely, I am interested in the weight of certain (diffuse) basis functions in different virtual orbitals.
How could one do this best? I tried to separate those basis funstions, setting them on
a ghost atom and running just dscf with Mulliken population analysis ($pop mo ...). However, in this case
the ghost atom coincides with a real atom and Turbomole does not seem to be able to handle such
a situiation - I could not make it run. I wonder if there is some other way, except for doing it manually.

Best regards,
Evgeniy
Pages: 1 2 [3] 4 5 ... 10