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11
Riper / Re: Plotting orbitals not working
« Last post by luyj on October 20, 2017, 10:04:38 pm »
I will send you a PM since it's unpublished research.
12
Dear All,

With the continuation of the previous message, the vibrational reduced masses is missing in the control file. I am using Tmolex 4.2.1 version to generate the input.  I am not sure why it is not writing into the input file.

Following lines are missing in the control file
$dipgrad    file=dipgrad
$hessian (projected)    file=hessian
$vibrational normal modes    file=vib_normal_modes
$vibrational reduced masses

Is there a way to manually add the vibrational reduced masses into the control file without using Tmolex ?

Regards,
Chandra
13
Dear All,

I am calculating the vibrational frequcencies for a molecule (with 40 atoms) using M06-2X functional. But the job stops at following:

--------------------------------------------------------------------
CONSTRUCTING G(a,i)[S(k,l)xi]              -> RHS
              G(i,j)[S(k,l)xi]*S(i,j)chi    -> Hessian

         Maximum core memory set to         1000 MB
         This corresponds to         604 vectors in CAO basis.
-------------------------------------------------------------------------------

Following is my control file and the start-job file.

control file:
----------------------------------------------------------------------------
$lastdiag
$rundimensions
dim(fock,dens)=108423
   natoms=48
   nshell=212
   nbf(CAO)=464
   dim(trafo[SAO<-->AO/CAO])=508
   rhfshells=1
$energy    file=energy
$scfdump
$drvopt
cartesian  on
   basis      off
   global     off
   hessian    on
   dipole     on
   nuclear polarizability
$maxcor    1000
$dft
 functional m062x
 gridsize m4
$subtitle
SP,DFT/no-RI,M062X,charge 0,c1,6-31G**,FREQ
$dipole from dscf
  x     2.84920221414984    y     0.56454024245295    z     0.77330933912435    a.u.
   | dipole | =    7.6399685176  debye
$scfiterlimit    30
$coord    file=coord
$jbas    file=auxbasis
$thime    5
$scfconv    6
$charge from dscf
         -0.000 (not to be modified here)
$scforbitalshift    automatic=.1
$grad    file=gradient
$optimize
 internal off
 redundant off
 cartesian on
 global off
$symmetry    c1
$tmole
$basis    file=basis
$cosmo_out    file=job_notRun_503.cosmo
$scfmo   file=mos
$title    tmolecal
$atoms
o 35 \
   basis = o 6-31G**
s 34 \
   basis = s 6-31G**
h 13-32,36,44-48 \
   basis = h 6-31G**
n 33-33,41-43 \
   basis = n 6-31G**
c 1-12,37-40 \
   basis = c 6-31G**
$scfdamp     start=0.700 step=0.050 min=0.100
$operating system unix
$thize    0.10000000E-04
$scfintunit
unit=30       size=0        file=twoint
$scfdiis
$last SCF energy change = -1317.4457
$closed shells
 a       1-87                                   ( 2 )
$actual step      force
$orbital_max_rnorm 0.33944529946641E-05
$restart  off
$end
------------------------------------------------------------------

Start-job file

------------------------------------------------------------
#!/bin/sh

ulimit -s unlimited
export PARA_ARCH=SMP
export PARNODES=16
export PATH=$TURBODIR/bin/`sysname`:$PATH

dscf >dscf.out
aoforce >aoforce.out
-------------------------------------------------------------------

ulimit -a
------------------------------------------------------
core file size          (blocks, -c) 0
data seg size           (kbytes, -d) unlimited
scheduling priority             (-e) 0
file size               (blocks, -f) unlimited
pending signals                 (-i) 1027610
max locked memory       (kbytes, -l) unlimited
max memory size         (kbytes, -m) unlimited
open files                      (-n) 1024
pipe size            (512 bytes, -p) 8
POSIX message queues     (bytes, -q) 819200
real-time priority              (-r) 0
stack size              (kbytes, -s) unlimited
cpu time               (seconds, -t) 3600
max user processes              (-u) 4096
virtual memory          (kbytes, -v) 8388608
file locks                      (-x) unlimited
-----------------------------------------------------------

I have changed the $maxcore value to 1000, 2000 ...5000 but there is no change. Please help me to sort out the issue.

Thank you very much.

With Regards,
Chandra


14
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.

--regards--
M. Ansari
15
Riper / Re: Plotting orbitals not working
« Last post by turbomaster on October 12, 2017, 01:55:18 pm »
Can you provide the coord file?
16
Statpt / jobex -trans failure after one cycle
« Last post by jkirk on October 10, 2017, 03:04:43 pm »
Hello,

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:
$statpt
   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.
17
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.

Regards,
R.

18
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).

Regards,

Uwe
19
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,
Evgeniy
20
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,

R.
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