AFIRサンプル

  1. Home
  2. Forum

Boards:39 Issue

New Issue

Try to find the reaction path which is assisted by catalyst
Yutaka Oya May 18, 2022, 8 p.m. #155

Dear all，

I found the DS-AFIR can be used to find the path for the certain reactant and product. Here I try to use this method to find the reaction path for that three methyl cyanates (Me-OCN) are synthesized into a triazine ring where the water is taken as a catalyst. After the calculation, I found that the water did not participate the reaction.

(1) My first question is that if the DS-AFIR method could be used to investigate the reaction path which is involved with the catalyst？

(2) My second question is that if not, which method would be suitable to solve this problem?

The attached files are the input.file and the output.files, could you please give me a hand?

 

 

IN.rar

1 Syntax error
昌裕 山本 April 14, 2022, 10:52 a.m. #152

Dear all

 

I have question for executing of GRRM20 with GAMESS.

The following error occurs when executing GRRM20.

 

sh: 1: Syntax error: Bad fd number

Segmentation fault

 

What is the cause of this problem?

 

 

  • Need details
    Satoshi Maeda

    I need more information to answer your question. Could you check below?
    1. Does the GRRM20 run with the other Program Package?
    2. Does the GAMESS run alone?　

    Also, could you check if xxxx_GmsJOB.inp was generated?
    (xxxx is from xxxx.com of the GRRM input file)

Can we use GRRM-GDSP for the result of surface reaction?
Yuri Ichioka April 12, 2022, 3:54 p.m. #151

I calculated Surface Reaction Path Search and I executed the following command:

$ GRRM_GDSP -Cfile=Pt111_MeOH_SCAFIR

but got the following error:

GRRMrootDir:/home/GRRM20/
TS_enp.txt copied from GRRM-GDSP root
GDSP operations: grrMap=1 TsDisp=1 enp=1
wrong GRRM data

I could use GRRM-GDSP for the molecule reaction.

Can we use GRRM-GDSP for the surface reacrion?

If we can use, do we need any other settings?

  • Contact IQCE
    Satoshi Maeda

    GRRM-GDSP is not supported by this website.
    Please contact the NPO IQCE.

1 Surface Reaction of GRRM20 Tutorial made wrong result
Yuri Ichioka March 31, 2022, 8:50 a.m. #148

I did following Surface Reaction of GRRM20 Tutorial.

①CO Adsorption on the Pt(111) Surface

②CO Dissociative Adsorption on the Pt(111) Surface

③Surface Reaction Path Search

But all of their results shows Spin(**2) is more than 100.

What is wrong?

For example, I attach input files and output file of ②. 

input1 input2 output

3 GRRM20 with SIESTA generates error message
Yuri Ichioka Feb. 16, 2022, 2:47 p.m. #142

I have been facing error messages when using GRRM20 with SIESTA.

I did MIN calculation of water molecule of this manual( https://afir.sci.hokudai.ac.jp/documents/tutorial/87 ), but I got the following error in "h2o_min_message_ERROR.rrm" file:

The h2o_min_message_CONTINUE.rrm file doesn't exist...

I put h2o_min.com, h2o_min.inp, H.psf, and O.psf in the same directory, and execute the command:

$ GRRM20p h2o_min -p1 -s3600

What's wrong?

  • Re: GRRM20 with SIESTA generates error message
    Satoshi Maeda

    The most likely cause is that the SIESTA program did not start. To verify this, refer to the SIESTA log file that you have generated in the same directory to see if the SIESTA calculation was successful. Then, test whether the same SIESTA calculation can be performed using $subsiesta.

    • Re: Re: GRRM20 with SIESTA generates error message
      Yuri Ichioka

      I can not find the SIESTA log file, and

      $subsiesta < h2o_min.inp

      was successful.

      Are there any other possible problems?

    • Re:Re:Re: GRRM20 with SIESTA generates error message
      Yuri Ichioka

      In the first place, according to the manual, GRRM calls the command:

      ${submpi} -np N -machinefile XXX_Machine.rrm ${subsiesta} < XXX_SiestaJOB.fdf > XXX_SiestaJOB.out

      but nothing is written in the created "h2o_min_SiestaJOB.fdf" file...

      • Try uploading files
        Satoshi Maeda

        I suggest you compress all files on the working directory using tar and upload them. At that time, please hide personal information such as the server information, using "xxxx", etc.

        • This problem seems to have been solved
          Yuri Ichioka

          Thank you for your comment.

          This problem was just solved.

          I found error in my script file.

          I apologize for taking your time.

Cannot find route between reactant and product.
Shinya Abe Jan. 18, 2022, noon #140

Dear GRRM developer 

 

I have a question for the reaction route network obtained by the SCAFIR.

I'm now calculating the two molecular reaction such as A+B -> C+D.
The SCAFIR calculation has been stared from the reactant A+B by using GRRM20 and GAMESS.
We have found the expected product C+D at end of the calculation.
We cannot find the route between A+B and C+D from the calculation.
What is the problem about this program?

 

  • Re: Cannot find route between reactant and product
    Satoshi Maeda

    I understand your statement about not being able to find the route means the corresponding TS cannot be found.  The possible causes are the SCF does not converge near the TS, or the TS optimization does not converge. The former case requires complex solutions, such as changing the calculation level and the SCF convergence method. The latter case can be solved by performing the RePATH calculation with the PTOnly option when reading the results of the SC-AFIR calculation. Please refer to Figure 1 and related descriptions in [J. Comput. Chem. , 2018, 39, 233] for the detailed procedures.  

GRRM20 with ORCA generates error messages
Ryohei Kakuchi Nov. 17, 2021, 9:47 p.m. #138

Dear GRRM developing team,

 

I have been facing error messages when using GRRM20 with ORCA.

When Gaussian 16 Rev.C as the calculation engine, we have been able to use it without any particular errors.
On the other hand, when ORCA (4.2.1 or 5.0.1) is used as the calculation engine, the calculation itself can be performed and seems no problem (I get calculation results), but error messages are continuingly generated.
Spesifically, I am using nohup to run the calculation and I get the following message in nohup outputs.
"cp: cannot stat 'repath_AFIR_Passerini_P9/repath_AFIR_Passerini_P9_OrcaJOB.hess': No such file or directory"
In the case of a 66-hours calculation, the error message is about 13MB.
GRRM20 is installed in my home directory, so I think the permissions are fine.
In addition, both Gaussian and ORCA themseves are executed without any problems, so I think their permissions are also appropriate.
May I ask you how I can improve the situation ?

 

Best regards,

Ryohei Kakuchi

  • This is a harmless error message.
    Satoshi Maeda

    This is a harmless error message. When Orca computes Hessian in addition to energy and gradient, GRRM copies the Hessian output to the working directory. GRRM does this also when Orca does not compute Hessian. The error message appears when GRRM attempts to copy the Hessian output which does not exist. This does not at all affect the search or geometry optimization by GRRM.

1 Regarding GRRM20 with ORCA 5
Ryohei Kakuchi Oct. 5, 2021, 5:05 p.m. #135

Dear developing team,

 

I have been using GRRM20 with a ORCA5 calculation engine.

I have two questions about the orca output file when GRRM20 is calculated using orca as an interface.

I was checking the Orca file, and I noticed that the keyword "Engrad Freq" was added to the generated orca input file. Is this automatically added so that GRRM can handle calculattions with Orca as an interface?

Also, when I checked the log files of GRRM and orca output (log0 file) after the calculation, I found a difference in the calculation results. May I ask you what would be the reason for this?

The associated zipped input and output files are attached. (The input file of GRRM cannot be sent due to security reasons, so it has been rewritten from .com format to .txt format.)

I would be grateful if you could kindly let me know these points.

 

Best regards,

Ryohei Kakuchi

Opt_freq_b3lyp_trifluoro_OrcaJOB.zip

  • Re: Regarding GRRM20 with ORCA 5
    Satoshi Maeda

    "Engrad Freq" is put when GRRM needs energy, gradient, and Hessian.
    The difference in the final Gibbs energy would be due to differences in the treatment of rotational degrees of freedom. In GRRM, rotational components that should be zero at exact stationary points are eliminated explicitly before diagonalizing the Hessian.

    • Re: Regarding GRRM20 with ORCA 5
      Ryohei Kakuchi

      Dear Prof. Maeda,

       

      Thank you so much for your kind reply.

      Regarding this, may I further confirm this point ?

      The differences in both (Gibbs) Energy and frequency results between GRRM and ORCA stemms from the differences in the algolisms. Would this understanding be correct ? (frequency results from GRRM are also a bit different from the ORCA log0 result)

       

      Best regards,

      Ryohei Kakuchi

GRRM TS is not derived from Gaussian
Taiki Kato Aug. 6, 2021, 2:24 p.m. #133

I've got a TS from GRRM17 (below input).

 

********GRRM Input File********************

# SADDLE/UB3LYP/6-311G(d,p)

0 1
C 1.340489908442000 -0.312063894385000 -0.253155660263000
C 0.076739145081000 0.305609907331000 0.202005019480000
C -1.235807629082000 0.068840008793000 -0.280240177008000
H 0.216854356903000 1.250939614893000 0.726503453695000
H -1.464101386545000 -0.788592245625000 -0.901844638389000
H -2.059369537206000 0.664559278247000 0.086679428840000
H 0.315398532399000 -0.522844725917000 0.999207939120000
H 2.259688516806000 -0.029439208358000 0.240604755912000
H 1.319707093205000 -1.234922734967000 -0.819760121384000
Options
Stable = Opt
GauProc = 16
SADDLE+IRC

******************************************

 

But, Gaussian 16, Revision A.03 can't find the TS (below input).

 

********Gaussian Input File********************

%nprocshared=16
%chk=1et
%mem=10GB
# ub3lyp/6-311g** opt=(ts,noeigentest,calcfc) freq scf=xqc

Winmostar

0 1
C 1.340489908442000 -0.312063894385000 -0.253155660263000
C 0.076739145081000 0.305609907331000 0.202005019480000
C -1.235807629082000 0.068840008793000 -0.280240177008000
H 0.216854356903000 1.250939614893000 0.726503453695000
H -1.464101386545000 -0.788592245625000 -0.901844638389000
H -2.059369537206000 0.664559278247000 0.086679428840000
H 0.315398532399000 -0.522844725917000 0.999207939120000
H 2.259688516806000 -0.029439208358000 0.240604755912000
H 1.319707093205000 -1.234922734967000 -0.819760121384000

******************************************

 

How should I consider this phenomenon ?

Which is correct, GRRM or Gaussian ?

  • RE: GRRM TS is not derived from Gaussian
    Satoshi Maeda

    The TS has an open-shell singlet character. Therefore, when optimizing this TS with Gaussian, one needs to prepare initial MOs having an open-shell singlet character. In GRRM, such MO guesses are prepared automatically when the "Stable = Opt" option is given. If one prepares an appropriate initial MOs and reads them by the "guess=read" option, then one can obtain the TS obtained by GRRM even with Gaussian.

2 TURBOMOLE
jiancheng ruan July 8, 2021, 11:19 p.m. #129

Dear all

If I want to use ADDF and AFIR methond with TURBOMOLE, how can I prepare mu input file?

  • TURBOMOLE
    jiancheng ruan

    Dear all

    My job seems have an error,but I can not find.Can you help me?

    GRRM-T.zip

  • Solved
    jiancheng ruan

    Dear all

    I have alreadly solved,thanks

↑