NMR calculation of Si(CH3)4 not converged

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Please upload an output file showing the problem, if applicable.
(It is not necessary to upload input files, they can be found in the output file.)

xiongyan21
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NMR calculation of Si(CH3)4 not converged

Post by xiongyan21 » 26 Jun 2020, 15:01

I am going to calculate the solvation chemical shiffs of pesticide hemexazole, thus I first calculate the shelding tensor of Si(CH3)4, which is optimized with mp2 and 6-311G++(2d,2p), and the Dalton input is
**DALTON INPUT
.RUN PROPERTIES
*PCM
.SOLVNT
H2O
.NPCMMT
0
.NESFP
6
.ICESPH
2
*PCMCAV
.INA
1
2
3
4
5
6
.RIN
1.7
1.7
1.3
1.2
1.2
1.2
.AREATS
1.2
**WAVE FUNCTIONS
.DFT
B3LYP
**PROPERTIES
.SHIELD
.SPIN-SPIN
**END OF DALTON INPUT

Although it still moves on, there are warnings

********* WARNING ORBDIA ***********
DIAGONAL ORBITAL HESSIAN HAS 137 NEGATIVE ELEMENTS

*** MICROITERATIONS STOPPED DUE TO MAX ITERATIONS REACHED.

*** WARNING : REQUESTED 1 SOLUTION VECTORS NOT CONVERGED

Convergence of RSP solution vectors, threshold = 1.00D-04
---------------------------------------------------------------
(dimension of paired reduced space: 120)
RSP solution vector no. 1; norm of residual 3.91D-01

*** RSPCTL WARNING-MAXIMUM NUMBER OF MICROITERATIONS, 60, REACHED

@ WARNING No convergence for SD 001 x. Last residual and threshold: 0.39077 0.00010
...

The same calculation of the molecule with the same geometry has been successful using DFT and 6-311G(d,p) by NWCHEM7.0.0.
Very Best Regards!
Last edited by xiongyan21 on 26 Jun 2020, 15:09, edited 2 times in total.

hjaaj
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Re: NMR calculation of Si(CH3)4 not converged

Post by hjaaj » 26 Jun 2020, 15:05

Does you calculation work without PCM?

xiongyan21
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Re: NMR calculation of Si(CH3)4 not converged

Post by xiongyan21 » 26 Jun 2020, 15:09

Sure, also in water by NWCHEM7.0.0 with DFT and 6-311G(d,p).

Very Best Regards!

xiongyan21
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Re: NMR calculation of Si(CH3)4 not converged

Post by xiongyan21 » 26 Jun 2020, 15:15

Dear Prof. Jensen

I misunderstood your saying, and I will try it without PCM with Dalton2018.

Very Best Regards!

xiongyan21
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Re: NMR calculation of Si(CH3)4 not converged

Post by xiongyan21 » 27 Jun 2020, 06:17

Dear Prof. Jensen
It works with Dalton2018 for this molecule without PCM, and the shielding constants agree well with those from GAMESS RHF and NWCHEM DFT results.
The input is
**DALTON INPUT
.RUN PROPERTIES
**WAVE FUNCTIONS
.DFT
B3LYP
**PROPERTIES
.SHIELD
.SPIN-SPIN
**END OF DALTON INPUT

Very Best Regards!

kennethruud
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Re: NMR calculation of Si(CH3)4 not converged

Post by kennethruud » 27 Jun 2020, 08:23

Could you post the entire output file? I am somewhat puzzled by your input, as you ask for 6 spheres to be used, but you have only five heavy atoms in the Si(CH3)4. You also you use a fairly large AREATS.

Kenneth

xiongyan21
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Re: NMR calculation of Si(CH3)4 not converged

Post by xiongyan21 » 27 Jun 2020, 09:26

Dear Prof. Ruud
Thanks a lot.
I will retry.
By the way, without PCM, the shielding constants of the enol form of hemexazole calcualated by Dalton 2018 with DFT agree well with those by NWCHEM7.0.0 with DFT and by GAMESS with RHF all using 6-311G, whereas in the case of the keto form, the shielding constants from Dalton 2018 DFT, GAMESS RHF and NWCHEM7.0.0 DFT agrees witth each other except for the smallest one, where those from the former two deviating from the latter by around 3 PPMs

Very Best Regards!
Last edited by xiongyan21 on 27 Jun 2020, 13:32, edited 1 time in total.

hjaaj
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Re: NMR calculation of Si(CH3)4 not converged

Post by hjaaj » 27 Jun 2020, 12:24

3 ppm can be a question about how hard the wave function and the response equations are converged, anyway, 3 ppm is less than the model errors.

xiongyan21
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Re: NMR calculation of Si(CH3)4 not converged

Post by xiongyan21 » 27 Jun 2020, 13:22

Dear Prof. Jensen
Thanks a lot, and I will try to change the input.
By the way, I have used GAMESS calculating the first three excited states of the enol form of hemexazole in water with B3lyp , aug-cc-pvdz, and aug-cc-pvtz, and found the first two excitation energies all can agree with the maximum wavelength experimentally obtained by Gao, et al. using an Agilent 1260 published in World Pesticides in China, but the first one is a Rydberg state according to the calculation.
I will use Dalton TDDFT to calculate them.

Very Best Regards!
Last edited by xiongyan21 on 03 Jul 2020, 08:51, edited 5 times in total.

xiongyan21
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Re: NMR calculation of Si(CH3)4 not converged

Post by xiongyan21 » 28 Jun 2020, 04:04

Dear Prof. Ruud
I have not seen any solvation at all using the following input
**DALTON INPUT
.RUN PROPERTIES
**DALTON INPUT
.RUN PROPERTIES
*PCM
.SOLVNT
H2O
.NPCMMT
0
.NESFP
5
.ICESPH
2
*PCMCAV
.INA
1
2
3
4
5
.RIN
1.7
1.2
1.2
1.2
1.2
.AREATS
0.6
**WAVE FUNCTIONS
.DFT
B3LYP
**PROPERTIES
.SHIELD
.SPIN-SPIN
**END OF DALTON INPUT
**WAVE FUNCTIONS
.DFT
B3LYP
**PROPERTIES
.SHIELD
.SPIN-SPIN
**END OF DALTON INPUT

I will chose 17 and retry.

By the way, using C1 symmetry, the shielding constants have negligible differences among the hydrogen atoms in Si(CH3)4 with GAMESS, NWCHEM7.0.0 and DALTON2018, respectively, and are very slightly affected by water solvation using NWCHEM7.0.0.
I will use other solvents and retry. GAMESS may can apply explicit solvation in NMR.

Very Best Regards!

xiongyan21
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Re: NMR calculation of Si(CH3)4 not converged

Post by xiongyan21 » 28 Jun 2020, 06:52

It seems although the input includes solvation, the calculation does not move through it. 17 spheres gets the same results as those from 5 and without PCM.

Yesterday, I completely removed the build clips, recompiled Dalton2018, and did the tests again.

Very Best Regards!
Last edited by xiongyan21 on 29 Jun 2020, 04:47, edited 3 times in total.

xiongyan21
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Re: NMR calculation of Si(CH3)4 not converged

Post by xiongyan21 » 28 Jun 2020, 08:16

Dear Prof. Jensen
I am very sorry for my mistakenly reading several principal components as shielding constants, however your opinion is very helpful in the evaluation of the calculated.
Actually, at the DFT level on Ubuntu18.04 using the workstation, all those from Dalton2018 are almost identical with those from NWCHEM7.0.0 both in the cases of the enol form and keto form without PCM, all of which are not greater than 0.5 ppms when compared with those from GAMESS RHF running on Mac.

Thanks very much again !

Very Best Regards!

xiongyan21
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Re: NMR calculation of Si(CH3)4 not converged

Post by xiongyan21 » 29 Jun 2020, 04:38

Test tpa_pcm_sym_CH2O_STO-3G can be repeated, but test shield_spin_C2H3LI-STO-3G can also be repeated.
The tests repeated by me are attached.

Although it is said MPI Off, I use mpirun -np 3 to do, but actually it may use one thread.
Perhaps MPI is not exported.
Originally , the workstation has been tested by HP for Red Hat Linux.

Very Best Regards!
Attachments
C2H3Li_STO-3G.log
(85.91 KiB) Downloaded 8 times
CH2O_STO-3G.log
(82.31 KiB) Downloaded 8 times
Last edited by xiongyan21 on 30 Jun 2020, 13:07, edited 4 times in total.

xiongyan21
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Re: NMR calculation of Si(CH3)4 not converged

Post by xiongyan21 » 29 Jun 2020, 05:20

Now when the input is
**DALTON INPUT
.RUN PROPERTIES
**DALTON INPUT
.RUN PROPERTIES
*PCM
.SOLVNT
H2O
.NPCMMT
0
.NESFP
5
.ICESPH
2
*PCMCAV
.INA
1
2
3
4
5
.RIN
1.7
1.2
1.2
1.2
1.2
.AREATS
0.8
**WAVE FUNCTIONS
.DFT
B3LYP
**PROPERTIES
.SHIELD
.SPIN-SPIN
**END OF DALTON INPUT

The calculation terminates at
Input for PCM solvation calculation
...
Very Best Regards!

rob
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Re: NMR calculation of Si(CH3)4 not converged

Post by rob » 29 Jun 2020, 14:57

I think you're having trouble setting up the cavity correctly. Section 14.1.1 in the manual gives details on how to do that.
You have two options:
  1. Letting the code put one sphere per atom, with the appropriate radius and scaling factor.
  2. Specifying which atoms to put spheres on, and with what radii and scaling factors.
For the former, the input would look like:

Code: Select all

**DALTON INPUT
.RUN PROPERTIES
**DALTON INPUT
.RUN PROPERTIES
*PCM
.SOLVNT
H2O
*PCMCAV
.AREATS
0.8
**WAVE FUNCTIONS
.DFT
B3LYP
**PROPERTIES
.SHIELD
.SPIN-SPIN
**END OF DALTON INPUT
For the latter, you'll have to decide on which atoms to put spheres and this depends on how the geomtry was specified in the molecule input file. I am here assuming that:
  • You want to use 5 spheres, centered on the non-hydrogen atoms.
  • The heavy atoms are the atoms 1 through 5 in your molecule input file.

Code: Select all

**DALTON INPUT
.RUN PROPERTIES
**DALTON INPUT
.RUN PROPERTIES
*PCM
.SOLVNT
H2O
.NESFP
5
.ICESPH
2
*PCMCAV
.INA
1
2
3
4
5
.RIN
2.1
1.9
1.9
1.9
1.9
.AREATS
0.8
**WAVE FUNCTIONS
.DFT
B3LYP
**PROPERTIES
.SHIELD
.SPIN-SPIN
**END OF DALTON INPUT
Here, I've used 2.1 Angstrom for silicon and 1.9 Angstrom for each carbon atom (slightly larger than the van der Waals radius reported by Bondi, due to the fact the hydrogen atoms are to be in the same sphere)

As Kenneth said, you should not have to specify .AREATS parameter for production calculations.

xiongyan21
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Re: NMR calculation of Si(CH3)4 not converged

Post by xiongyan21 » 30 Jun 2020, 00:11

Dear Prof. Di Remigio
The input specifying 5 from you, which I am just trying, can move on without any warning of the cavities, but it seems it gets stuck at
********* WARNING ORBDIA ***********
DIAGONAL ORBITAL HESSIAN HAS 56 NEGATIVE ELEMENTS,
and it also gets stuck with different negative elements when .areats is removed.


Thank you very much.

Very Best Regards!

rob
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Re: NMR calculation of Si(CH3)4 not converged

Post by rob » 30 Jun 2020, 08:53

Could you please post your entire output file?

xiongyan21
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Re: NMR calculation of Si(CH3)4 not converged

Post by xiongyan21 » 30 Jun 2020, 11:15

Dear Prof.Remigio

The information in the shell is
*******************************************
**** OUTPUT FROM DALTON SHELL SCRIPT
*******************************************

DALTON release Dalton2018.1 (2019)



*******************************************
**** OUTPUT FROM DALTON SHELL SCRIPT
*******************************************

DALTON release Dalton2018.1 (2019)

Invocation: /home/hp/dalton2018/build/dalton -o sinmr.log -mb 13000 shield_spin.dal sinmr.mol

2020年 06月 30日 星期二 18:12:01 CST

Calculation: shield_spin_sinmr (input files: shield_spin.dal and sinmr.mol)
PID : 2250
Input dir : /home/hp/dalton2018/build
Scratch dir: /home/hp/dalton2018/DALTON_scratch_hp/shield_spin_sinmr_2250

2020年 06月 30日 星期二 18:12:01 CST

Calculation: shield_spin_sinmr (input files: shield_spin.dal and sinmr.mol)
PID : 2251
Input dir : /home/hp/dalton2018/build
Scratch dir: /home/hp/dalton2018/DALTON_scratch_hp/shield_spin_sinmr_2251

2020年 06月 30日 星期二 18:12:01 CST

Calculation: shield_spin_sinmr (input files: shield_spin.dal and sinmr.mol)
PID : 2252
Input dir : /home/hp/dalton2018/build
Scratch dir: /home/hp/dalton2018/DALTON_scratch_hp/shield_spin_sinmr_2252


INFO : OMP_NUM_THREADS set to 1 because it was not defined by user
INFO : and the cores are probably used by MPI


INFO : OMP_NUM_THREADS set to 1 because it was not defined by user
INFO : and the cores are probably used by MPI


...

0: Directories for basis set searches:
/home/hp/dalton2018/build:/home/hp/dalton2018/build/basis

Node 0: --- SEVERE ERROR, PROGRAM WILL BE ABORTED ---
ERROR (GPOPEN) UPON OPENING A FILE

Program received signal SIGILL: Illegal instruction.

Backtrace for this error:
Work memory size (LMWORK+2): 1664000002 = 12.398 gigabytes; node 0

0: Directories for basis set searches:
/home/hp/dalton2018/build:/home/hp/dalton2018/build/basis


--> ERROR (GPOPEN) UPON TRYING TO OPEN FILE ON UNIT 2
--> with filename /home/hp/dalton2018/build/sinmr.log
--> IOSTAT ERROR CODE RETURNED 17


QTRACE dump of internal trace stack

========================
level module
========================
2 GPOPEN
1 DALTON main
========================

#0 0x7f362802f2ed in ???
#1 0x7f362802e503 in ???
#2 0x7f3627481f1f in ???
#3 0x55ce664936c0 in ???
#4 0x55ce664b54c3 in ???
#5 0x55ce664bd890 in ???
#6 0x55ce657983eb in ???
#7 0x55ce657974de in ???
#8 0x7f3627464b96 in ???
#9 0x55ce65797539 in ???
#10 0xffffffffffffffff in ???

SERIOUS ERROR:
/home/hp/dalton2018/build/dalton.x finished with non-zero exit code: 132

File list in scratch directory:


----------------------------------------------------------
WARNING for ERROR (DALTON program stopped with exit code 132)
- THEREFORE scratch directory /home/hp/dalton2018/DALTON_scratch_hp/shield_spin_sinmr_2251 is not deleted
by this script so you may restart the calculation, if possible
( /home/hp/dalton2018/DALTON_scratch_hp/shield_spin_sinmr_2251 may be deleted by your queueing system )
- REMEMBER to delete /home/hp/dalton2018/DALTON_scratch_hp/shield_spin_sinmr_2251 yourself !!!


2020年 06月 30日 星期二 18:12:01 CST
*****************************************
-------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code.. Per user-direction, the job has been aborted.
-------------------------------------------------------

Very Best Regards!
Last edited by xiongyan21 on 30 Jun 2020, 12:43, edited 1 time in total.

xiongyan21
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Re: NMR calculation of Si(CH3)4 not converged

Post by xiongyan21 » 30 Jun 2020, 11:48

I am using CCl4 as the solvent and retry.
Very Best Regards!
Last edited by xiongyan21 on 30 Jun 2020, 11:56, edited 3 times in total.

hjaaj
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Re: NMR calculation of Si(CH3)4 not converged

Post by hjaaj » 30 Jun 2020, 11:53

Please use "Attachments" (find it below the input field for text) for all relevant output files and log files !!!! (Do not add input files, because these are copied in the output files.)

xiongyan21
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Re: NMR calculation of Si(CH3)4 not converged

Post by xiongyan21 » 30 Jun 2020, 11:58

Using CCl4, it can move on
...
and find it can move on
...
No symmetry -> DSO by numerical integration.
Electrons: 50.0001536( 0.000154): DFTDSO time: 4.4 s

2-el. integral transformation level 4: Total CPU and WALL times (sec) 5.784 5.785

Sorting integrals to Dirac format: Total CPU and WALL times (sec) 0.142 0.142
Convergence for SD 001 x. Last residual and threshold: 0.00006 0.00010
Convergence for SD 002 x. Last residual and threshold: 0.00007 0.00010
...
But NWCHEM7.0.0 can finish using water. Tomorrow I will try solvent CCl4 using NWCHEM7.0.0, and compare the result with that from Dalton2018.

Very Best regards!
Last edited by xiongyan21 on 30 Jun 2020, 12:03, edited 1 time in total.

hjaaj
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Re: NMR calculation of Si(CH3)4 not converged

Post by hjaaj » 30 Jun 2020, 12:03

Again, please attach your output file if you want anyone to look more at your problem.

xiongyan21
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Re: NMR calculation of Si(CH3)4 not converged

Post by xiongyan21 » 01 Jul 2020, 06:56

When CCl4 is used as the solvent, Dalton2018 gives the following
1 atom shielding ...
@1 ----------------------------------------------------------------------------
@1 Si ...
@1 C ...
@1 H 33.7920
@1 H 33.7608
@1 H 33.6133
@1 C ...
@1 H 29.9833
@1 H 33.4073
@1 H 31.0855
@1 C ...
@1 H 31.1293
@1 H 29.8739
@1 H 24.4203
@1 C ...
@1 H 30.6469
@1 H 32.3443
@1 H 31.0112
If dielectric constant 2.24 , for CCl4, is used, NWCHEM7.0.0 gives those, each having negligible differences from any other one, not greater than 0.75 ppms different from those of the hydrogen atoms of the first methyl by Dalton2018. Thus, it seems symmetry or a potential is required when Dalton2018 is used for this calculation.

Very Best Regards!
Last edited by xiongyan21 on 01 Jul 2020, 10:09, edited 2 times in total.

hjaaj
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Re: NMR calculation of Si(CH3)4 not converged

Post by hjaaj » 01 Jul 2020, 08:37

Again, PLEASE attach your output file to get a response!

xiongyan21
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Re: NMR calculation of Si(CH3)4 not converged

Post by xiongyan21 » 01 Jul 2020, 11:27

Dear Prof. Jensen
I am astonished about the result of the significantly different shielding constants using the input above specifyng 5 without .areat by Dalton2018.
Could you please ask someone to repeat it if it is convenient.

Very Best Regards!
Last edited by xiongyan21 on 02 Jul 2020, 02:51, edited 1 time in total.

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