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I will send you a PM since it's unpublished research.

11

I will send you a PM since it's unpublished research.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

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

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

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

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

Can you provide the coord file?

16

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.

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.

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

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

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

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

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.

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.