Multiwfn forum

Dear Tian,
As you nicely did guide me to use CDA for obtaining the value of Pauli repulsion between occupied orbitals of two interacting fragments (and, evaluating corresponding overlap), I did follow the below steps one-by-one. Please, if possible, let me know if my approach is quite correct:

1- The TS structure is fully optimized using, for instance, M062X/def2TZVPP level (TS includes two interacting fragments f1 and f2 which include some very heavy atoms such as Sn and, thus, I employed this basis set so that pseudo potentials are applied for such atoms).
2- After full optimization of TS, I changed number of atoms so that the electron-donor fragment (f1) to be the first fragment and electron-acceptor (f2) to be the second fragment.
3- Taking fully optimized TS structure, a SP is performed using "M062X/def2TZVPP nosymm pop=full iop(3/33=1)" keywords and, generated "chk" file is converted into "fch".
4- Taking the fully optimized structure of TS (whose atom numbering has been changed as described), f1 and f2 will be generated following a SP over each fragment using "M062X/def2-TZVPP nosymm pop=full" keywords and, "chk" files are converted into "fch" ones.
5-Multiwfn boots up, and the "fch" file of TS is loaded. Then 16 is chosen. I also enter 2 as there are two fragments. Then, the "fch" file of f1 (electron-donor) and "fch" file of f2 will be entered, respectively. The below data are presented:

Orb.      Occ.          d           b        d - b          r
       1    2.000000   -0.000003    0.000025   -0.000029    0.000014
       2    2.000000   -0.000005   -0.000212    0.000206   -0.000071
       3    2.000000   -0.000004   -0.000086    0.000082   -0.000026
       4    2.000000    0.000445   -0.000000    0.000445    0.000024
       5    2.000000    0.000304   -0.000001    0.000305    0.000043
       6    2.000000   -0.000006   -0.000178    0.000171   -0.000065
       7    2.000000   -0.000114   -0.001880    0.001766    0.022417
       8    2.000000    0.005204    0.000709    0.004495    0.065189
       9    2.000000    0.000370    0.002808   -0.002438   -0.003814
      10    2.000000   -0.001802   -0.008178    0.006376   -0.011103
      11    2.000000    0.003259    0.002135    0.001124    0.106547
      12    2.000000   -0.005901   -0.000438   -0.005464   -0.101433
      13    2.000000   -0.001358   -0.002066    0.000708    0.041290
      14    2.000000    0.002171   -0.000691    0.002862    0.006158
      15    2.000000   -0.001241   -0.001562    0.000321   -0.032240
      16    2.000000    0.000064    0.002083   -0.002020    0.018551
      17    2.000000    0.003422   -0.001551    0.004973    0.128120
      18    2.000000    0.001397   -0.000052    0.001449    0.025455
      19    2.000000    0.008062   -0.001752    0.009813   -0.089066
      20    2.000000    0.018289    0.016942    0.001347   -0.159743
      21    2.000000    0.051780   -0.002916    0.054697   -0.403971
      22    2.000000   -0.000894    0.062648   -0.063542   -0.141167
-------------------------------------------------------------------
Sum:      44.000000    0.083437    0.065789    0.017649   -0.528892

As can be seen, the last four MO orbitals of complex (TS), 19-22, display a significant negative "r" value. So, one can conclude that the fragments orbitals participating in these MOs are responsible for the Pauli repulsion. Consequently, we should first decompose MOs 19-22 to the fragments orbitals. Now, we should select option "6, Decompose complex orbital contribution to CDA" to find which fragments orbital participate in the formation of MO 19. Once we select 6 followed by 19, and enter a threshold value such as 0.005, the following information is displayed:

Occupation number of orbital    19 of the complex:  2.00000000
FragA Orb(Occ.)  FragB Orb(Occ.)      d           b        d - b          r
    6( 2.0000)       7( 2.0000)    0.000000    0.000000    0.000000   -0.009978
    6( 2.0000)       9( 2.0000)    0.000000    0.000000    0.000000   -0.026962
    6( 2.0000)      10( 2.0000)    0.000000    0.000000    0.000000   -0.014043
    6( 2.0000)      12( 2.0000)    0.000000    0.000000    0.000000   -0.021881
    7( 2.0000)       7( 2.0000)    0.000000    0.000000    0.000000   -0.007323
    7( 2.0000)       9( 2.0000)    0.000000    0.000000    0.000000   -0.005278
    7( 2.0000)      12( 2.0000)    0.000000    0.000000    0.000000    0.007499
    7( 2.0000)      13( 2.0000)    0.000000    0.000000    0.000000   -0.008777

Among NEGATIVE "r" values, the MOST NEGATIVE "r" is -0.026962 associated with a Pauli repulsion between orbital 6 of f1 and orbital 9 of f2. If we again repeat this calculation for orbitals 20, 21, 22 of TS and look for the most negative "r" value, we finally find that:

MO-19----> O-6_f1+O-9_f2
MO-20----> O-7_f1+O-13_f2
MO-21----> O-7_f1+O-13_f2
MO-22----> O-7_f1+O-15_f2

A simple visualization of the f1-orbitals (f1.fch is loaded into gview) one can see that orbitals 6 and 7 in f1 are HOMO-1 and HOM, respectively. These two orbitals are degenerate located over pi-orbitals of C-C triple bond of acetylene. On the other hand, a simple visualization of the f2-orbitals (f2.fch is loaded into gview), one can see that orbitals 9, 13, and 15 f2 are HOMO-6, HOMO-2, and HOMO, respectively. We should compute the value of S(i,j), the overlap integral, between:

orbital 6 of f1 and orbital 9 of f2
and
orbital 7 of f1 and each of orbitals 13 and 15 of f2.

To compute S(i,j) for f1 orbitals and f2 orbitals mentioned above, we should initially save TS.fch, f1.fch, and f2.fch as gaussian input files (gjf). Then, a SP is performed over TS.gjf using "M062X/def2TZVPP nosymm guess(save,only pop=none)" keywords and, corresponding chk file is converted into fch. A SP is also performed over each of f1.gjf and f2.gjf using "M062X/def2TZVPP nosymm" keywords and generated chk files are converted into fch ones. Now, Multiwfn boots up and TS.fch (newly generated as explained) is loaded. Then we select 100 followed by 15. The f1.fch and f2.fch is loaded, respectively and finally we enter 6,9. Then, we generate "whole overlap integral matrix to ovlpint.txt in current folder". From this file, one can see that:

S(6,9)= 0.056
S(7,13)= -0.126
S(7,15)= -0.031

We should consider the absolute value for negative S(I,j). Consequently, the Pauli repulsion between fragments orbitals at the TS structure increases as:
7,15<6,9<7,13

Please accept my highest apology for such a lengthy explanation.

Best Regards,
Saeed

Dear Tian,
If possible and you kindly let me, I am going to repecfully ask a question.
Please, first, let me present a short explanation about what I am looking for. Consider a given Diels-Alder reaction which is further catalyzed with a catalyst. Suppose our analyses reveal that the catalyzed reaction is preferred over the uncatalyzed reaction due to the least Puli repulsion in the TS associated with the catalyzed reaction (I have performed an EDA such as sobEDA over both TSs to find this matter). Now, I want to find the appropriate occupied fragments orbitals at the TS structure, which are responsible for Pauli repulsion (for example HOMO-n to HOMO from one fragment vs. HOMO-m to HOMO of the other fragment). I do not know how Multiwfn able to perform such a nice analysis. In addition, I want to compute the overlap (S_i,j) between occupied orbitals of two fragments which are responsible for the most Pauli repulsion (If, for example, we can sort the pair orbitals responsibiling for the to 10 values of Pauli repulsion, S(I,j) needs to be computed in these top 10 interactions).
While I hope you kindly accept my highest apology for taking your valuable time with explanations, I would be highly grateful if you guide me to know how such a purpose can be reached by Multiwfn.

Best regards,
Saeed

Dear Tian,
It is well known that M06-2X functional has already been somewhat corrected during parametrization. So, to include dispersion corrections into this functional, one just needs to use "em=gd3". Please let me know has M05-2X also already been corrected to some extent during parametrization. If so, to include dispersion corrections, this functional also needs "em=gd3" keyword. Do you agree and confirm this statement?

In addition, I am computing solvation energy for a set of compounds at M05-2X/6-31G(d) level together with SMD solvation model as recommended by Truhlar and, as you also confirmed in one of your highly valuable blog articles. Please let me know if there are any problems regarding the accuracy of these calculations.

Sincerely yours,
Saeed

Dear Tian,
Please let me ask a question regarding an issue I saw in an interesting article.
Please suppose one wants to draw BCPs together with the Laplacian isosurface exactly as presented in the attached picture.
As you can see, the Laplacian isosurface corresponding to isovalue 0.00 (namely reactive surface) and also BCPs are portrayed together. If possible, please let me know how one can reach such a picture using Multiwfn. Indeed, while I know how to draw Laplacian isosurface (5 Output and plot specific property within a spatial region and...), I do not know how to include BCPs at the same time.

Sincerely,
Saeed

Dear Tian,
I hope you are doing well and, like always, kindly let me ask a question on my problem about SAPT analysis.
Please suppose one wants to perform SAPT analysis on a dimer, including heavy elements, for which using "def2" bases is mandatory. Let us take "def2-TZVPP" as the desirable basis set for such a give analysis.
It seems in the recent versions of PSI4 one should use "def2-universal-jkfit" instead of "def2-TZVPP-jkfit". The question is:
Is it also mandatory to employ "def2-universal-ri" instead of "def2-tzvpp-ri"? In other words, which of the below input files are reasonable and should be used (As I checked, the results are somewhat different:

File 1:

memory 55 gb

molecule {
0 1
C                 -1.56109100   -1.20061800   -0.00000400
C                 -0.17334400   -1.20786600    0.00002200
C                  0.50607200   -0.00007600    0.00002300
C                 -0.17333700    1.20786200    0.00001700
C                 -1.56097000    1.20068700   -0.00000300
C                 -2.25745700    0.00000900   -0.00001500
H                 -2.09690700   -2.13988300   -0.00002400
H                  0.37960100   -2.13607100    0.00000800
H                  0.37980500    2.13594700    0.00001000
H                 -2.09684600    2.13992100   -0.00001000
H                 -3.33850200    0.00010300   -0.00001600
Cl                 2.24080100    0.00000000   -0.00001200
--
2 1
Hg                -0.77409920   -0.36639646   -1.52722807

units angstrom
no_reorient
symmetry c1
}

set {
    basis def2-tzvpp
    df_basis_scf  def2-universal-jkfit
    df_basis_sapt def2-tzvpp-ri
    scf_type DF
    guess sad
    freeze_core True
}

set_num_threads(8)

energy('sapt2')
/////////////////////////////////////
File 2:

memory 55 gb

molecule {
0 1
C                 -1.56109100   -1.20061800   -0.00000400
C                 -0.17334400   -1.20786600    0.00002200
C                  0.50607200   -0.00007600    0.00002300
C                 -0.17333700    1.20786200    0.00001700
C                 -1.56097000    1.20068700   -0.00000300
C                 -2.25745700    0.00000900   -0.00001500
H                 -2.09690700   -2.13988300   -0.00002400
H                  0.37960100   -2.13607100    0.00000800
H                  0.37980500    2.13594700    0.00001000
H                 -2.09684600    2.13992100   -0.00001000
H                 -3.33850200    0.00010300   -0.00001600
Cl                 2.24080100    0.00000000   -0.00001200
--
2 1
Hg                -0.77409920   -0.36639646   -1.52722807

units angstrom
no_reorient
symmetry c1
}

set {
    basis def2-tzvpp
    df_basis_scf  def2-universal-jkfit
    df_basis_sapt universal-ri
    scf_type DF
    guess sad
    freeze_core True
}

set_num_threads(8)

energy('sapt2')
//////////////////////////////////////////////

In advance, your highly valuable guidance is very appreciated and, please excuse me for bothering you.

Sincerely yours,
Saeed

Dear Tian,
If possible, please let me state that I have frequently faced problems since upgrading my Orca 5.0.3 to 6.0.1; I have never encountered such problems with the older version.

Please let me ask a question regarding a new problem. The below Orca task was ran:
***********************************************************************************************************************
! ExtrapolateEP2(3/4,def2,MP2) tightSCF noautostart miniprint
%pal nprocs   8 end
%maxcore     6000
* xyz   0   1
C     -3.00886523   -0.60110479    0.00000305
H     -3.83275726    0.09558074    0.00003101
H     -3.13625859   -1.67101162   -0.00011453
N     -1.81764115   -0.14353739    0.00008421
H     -0.98978097   -0.78273714   -0.00002296
O     -1.48821106    1.09766974    0.00016013
C      1.46382272   -0.12319892   -0.00021950
O      0.71189603   -1.08884815   -0.00013887
C      2.95709267   -0.26671500    0.00015158
H      3.36553743    0.23708253   -0.87460156
H      3.36370189    0.22895946    0.88045529
H      3.23148130   -1.31574290   -0.00408829
O      1.05435101    1.11577850   -0.00024573
H      0.02497543    1.16194217   -0.00006346
*

$new_job
! ExtrapolateEP2(3/4,def2,MP2) tightSCF noautostart miniprint Pmodel
%pal nprocs   8 end
%maxcore     6000
* xyz   0   1
C     -3.00886523   -0.60110479    0.00000305
H     -3.83275726    0.09558074    0.00003101
H     -3.13625859   -1.67101162   -0.00011453
N     -1.81764115   -0.14353739    0.00008421
H     -0.98978097   -0.78273714   -0.00002296
O     -1.48821106    1.09766974    0.00016013
C :     1.46382272   -0.12319892   -0.00021950
O :     0.71189603   -1.08884815   -0.00013887
C :     2.95709267   -0.26671500    0.00015158
H :     3.36553743    0.23708253   -0.87460156
H :     3.36370189    0.22895946    0.88045529
H :     3.23148130   -1.31574290   -0.00408829
O :     1.05435101    1.11577850   -0.00024573
H :     0.02497543    1.16194217   -0.00006346
*

$new_job
! ExtrapolateEP2(3/4,def2,MP2) tightSCF noautostart miniprint Pmodel
%pal nprocs   8 end
%maxcore     6000
* xyz   0   1
C :    -3.00886523   -0.60110479    0.00000305
H :    -3.83275726    0.09558074    0.00003101
H :    -3.13625859   -1.67101162   -0.00011453
N :    -1.81764115   -0.14353739    0.00008421
H :    -0.98978097   -0.78273714   -0.00002296
O :    -1.48821106    1.09766974    0.00016013
C      1.46382272   -0.12319892   -0.00021950
O      0.71189603   -1.08884815   -0.00013887
C      2.95709267   -0.26671500    0.00015158
H      3.36553743    0.23708253   -0.87460156
H      3.36370189    0.22895946    0.88045529
H      3.23148130   -1.31574290   -0.00408829
O      1.05435101    1.11577850   -0.00024573
H      0.02497543    1.16194217   -0.00006346
*

$new_job
! ExtrapolateEP2(3/4,def2,MP2) tightSCF noautostart miniprint Pmodel
%pal nprocs   8 end
%maxcore     6000
* xyz   0   1
C     -3.00886523   -0.60110479    0.00000305
H     -3.83275726    0.09558074    0.00003101
H     -3.13625859   -1.67101162   -0.00011453
N     -1.81764115   -0.14353739    0.00008421
H     -0.98978097   -0.78273714   -0.00002296
O     -1.48821106    1.09766974    0.00016013
*

$new_job
! ExtrapolateEP2(3/4,def2,MP2) tightSCF noautostart miniprint Pmodel
%pal nprocs   8 end
%maxcore     6000
* xyz   0   1
C      1.46382272   -0.12319892   -0.00021950
O      0.71189603   -1.08884815   -0.00013887
C      2.95709267   -0.26671500    0.00015158
H      3.36553743    0.23708253   -0.87460156
H      3.36370189    0.22895946    0.88045529
H      3.23148130   -1.31574290   -0.00408829
O      1.05435101    1.11577850   -0.00024573
H      0.02497543    1.16194217   -0.00006346
*
******************************************************************************************************************************************************************
But after a long time, the task was terminated and the below message was displayed on the screen:

--------------------------------------------------------------------------
Primary job  terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun noticed that process rank 2 with PID 0 on node saeed exited on signal 9 (Killed).
--------------------------------------------------------------------------
[file orca_tools/qcmsg.cpp, line 394]:
  .... aborting the run
***************************************************************************************************************************************************************
Moreover, at the bottom of the output file, one can see:

Maximum memory used throughout the entire LEANSCF-calculation: 57.2 MB

           ************************************************************
           *        Program running with 8 parallel MPI-processes     *
           *              working on a common directory               *
           ************************************************************

------------------------------------------------------------------------------
                                ORCA  MP2
------------------------------------------------------------------------------

Freezing NCore=14 chemical core electrons

----------
MP2 ENERGY (disk based algorithm)
----------

Dimension of the basis                      ...  609
Memory devoted to MP2                       ... 6000 MB   
Data format for buffers                     ... DOUBLE
Compression type for matrix containers      ... UNCOMPRESSED

-------------------------
SHARK HALF TRANSFORMATION (Exchange order)
-------------------------

Number of basis functions                   ...    609
Number of operators                         ...      1
   Operator  0:    7-  27 (p-index in (p*|q*))
   Operator  0:    7-  27 (q-index in (p*|q*)
Integral generator used                     ... SHARK
Contraction scheme used                     ... SEGMENTED CONTRACTION
MaxCore in resort                           ...   6000 MB

Half transformed integrals for op=   0      ... R1_S.SHARK_MNPQ0.tmp
Resorted half transformed integrals         ... R1_S.KAO_aa.tmp

ORCA finished by error termination in MP2
Calling Command: mpirun -np 8  /home/saeed/orca-6.0.1/orca_mp2_mpi R1_S.mp2inp.tmp R1_S
[file orca_tools/qcmsg.cpp, line 394]:
  .... aborting the run

Please, if possible and like always, make me benefit of your highest kindness and let me know how I can resolve this problem.

In advance, many thanks for your valuable time and energy and, please excuse me for bothering you.

Sincerely,
Saeed

Dear Tian,
I have a structure for which the ELF colored-filled mao is going to be generated (4--->9--->1--->1 (XY plane)). Indeed, the generated picture is larger than that can be fixed between X and Y axes. In other words, some parts of figure are covered by the X and Y axes and, I need to extend these axes so that all parts of figure are evidently seen. If possible, please let me know how I can resolve this problem.

Sincerely,
Saeed