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DS-AFIR issue
Seiji Mori July 12, 2018, 3:19 p.m. #55

 
-During a DS-AFIR calculation, AFIR program found 5 Equilibrium Structures (EQ0, EQ1, EQ2, EQ3, EQ4, where EQ4 and EQ0 are reactant and product respectively)  and 2 Transition states ,TS0 (which connects EQ0 with EQ1) and TS1 which connects EQ2 with EQ3). But, we missed  the other two TSs between EQ4- EQ3 and  between EQ2-EQ1.
 
Which option would be, in principle, more effective to find a path? To do RePATH (in the same folder where DS-AFIR was performed) or to calculate new DS-AFIRs to find the missing TSs from the each pair of EQ structures?
 
Also, another thing that caught our attention in this particular DS-AFIR output was the highlighted with a # 'hashtag' word #RIDGE-POINT (we could find this in the manual) that appears instead of "#STEP N " in the main output XXX.log . This word seems to mark the final structure in the PATH LUP   (after the structure marked with that word, the next line is this: "DS-AFIR COMPLETED, LUP-PATH OPTIMIZATION CARRIED OUT" ).  We are wondering how we  find the TS rather than the "ridge point"?
 
Thank you very much.
 

GUI software for Gaussian outputs generated by AFIR
Seiji Mori July 6, 2018, 3:24 p.m. #53

As far as we understand, the GRRM17 uses a part of the Gaussian program (or other ab initio programs associated to it) to calculate gradient vectors and Hessian matrices. So, the XXX_GauJOB.log files (Gaussian format) generated during AFIR calculations (MC-AFIR, DS-AFIR, SC-AFIR) or minimizations contain, temporarily,  the information of the Hessian.  So our question is, what kind of other information is stored in these xxx_GauJob.log files? Are they useful as an output of the AFIR calculation?  Also, when we try to visualize these files with a output GUI visualizer like Chemcraft or Gaussview,  it shows the file as a "not-finished" optimization or a "cannot-read-properly" frequency calculation.  
In a similar manner, it is not possible to visualize the output of the GRRM17 (log files)  in a chemistry visualization program like Chemcraft, Gaussview, etc. In your paper about GRRM17 ( J. Comput. Chem.201839, 233–251https://doi.org/10.1002/jcc.25106 ), you mention a visualization code of the reaction pathways, SAFIRE, but there is no more information in the AFIR website or the paper regarding how to obtain SAFIRE. For example, if a user wants to visualize the normal modes of vibration, from the xxx_TS_list.log output file, this file is not recognized by any visualizers to show explicitly how the atoms move in their respective TSs.  Which also makes me wonder how we can visualize the result obtained in all the outputs and intermediate files (to control or keep an eye on the process of the calculation, visually) ? 
 
Thank you very much for your help.
 
 

When we are doing a energy minimization in Gaussian 09, one of the issues that rise are that the energy of minimization steps will start to oscillate and never converge until one kills the calculation job or it passes a huge number of steps, wasting a computational time. So, our question is: can this kind of behavior happen in the GRRM during the minimization performed during a AFIR calculation (or other GRRM calculation that requires the minimization algorithm) that we have to keep an eye on it to avoid wasting computer time in a calculation that gets "derailed " from its original purpose?, in other words, what are those things that we should watch out during the calculation to know that something is wrong and we have to reset or change something because the calculation won't stop but it is going wrong? 

Thank you very much.

  • Re:
    Satoshi Maeda

    GRRM uses a Quasi-Newton algorithm in geometry optimization. Therefore, common problems in Quasi-Newton algorithms also occur in GRRM calculations. In AFIR path calculations, such a case is detected and the path calculation will be terminated before wasting computational time. It is also noted that such paths are not just discarded but are processed like other paths to find TSs along the paths.

1 Determining clusters of equivalent structures
Matthew Addicoat July 4, 2018, 3:48 p.m. #48

We are using MC-AFIR to look at some reactions on metal clusters, similar to the gold cluster work here: J. Phys. Chem. C, 2015, 119 , pp 11120–11130.

We're having many equivalent structures show up as new, and while we've tried various settings of MatchDecScale and MatchDecTarget, we've not had much success in cutting down the number of incorrectly identified new structures.

Are there any other recommended options to more closely identify structures as equivalent? What options were used for the MC-AFIR of Au_n + H2? 

Many thanks,
Matt

  • Re:
    Satoshi Maeda

    MatchDecScale and MatchDecTarget do not work with MC-AFIR. In SC-AFIR, when these options are used, the GRRM program does a structure clustering and avoids the SC-AFIR searches around similar structures (those belongs to the same cluster).

    In MC-AFIR, you may try StructCheckThreshold or ScaleStructCheckThreshold. My recommendation is ScaleStructCheckThreshold = 2.0 or 3.0. Please adjust the value for your system with some tests.

4 EQ list in SC-AFIR2 calculation
Ayako Furuhama July 3, 2018, 1:21 p.m. #44

Yesterday, I attended GRRM18 tutorial and have a question.

When SC-AFIR2 is performed (input name: butadiene.com ) to consider dummy EQs, how to understand the Energy in a parenthesis.

 

For example, EQ2 is dummy EQ with "Energy    = -154.769690740354 (-154.850619271653 :    0.000000000000)", please let us know the meanings of -154.769690740354 and -154.850619271653, respectively. 

%grep Ene butadiene_EQ_list.log

Energy    = -154.864576395665 (-154.864576395665 :    0.000000000000) #EQ0

Energy    = -154.859935087313 (-154.859935087313 :    0.000000000000) #EQ1

Energy    = -154.769690740354 (-154.850619271653 :    0.000000000000) #EQ2...dummy EQ

Energy    = -154.742435832251 (-154.850514028576 :    0.000000000000) #EQ3...dummy EQ

Energy    = -154.703735106368 (-154.841020263992 :    0.000000000000) #EQ4...dummy EQ

 

Thank you in advance.

  • Sorry
    Ayako Furuhama

    If my question is inappropriate, please remove the comment. 

     

  • Re:
    Satoshi Maeda

    First, it's a tutorial of GRRM17, not GRRM18.

    For the dummy EQs obtained by the SC-AFIR2 calculations, the number before the parentheses corresponds to electronic energy plus the force term of the AFIR function. The first number in the parentheses is (bare) electronic energy.

  • Thank you
    Ayako Furuhama

    Prof. Satoshi Maeda

    Thank you very much for the clear answer. I understand the differences.

    Yes, it was a tutorial for GRRM17. A. Furuhama

  • Third energy?
    Matthew Addicoat

    And what is the third energy (zero in the excerpt above, but not always)?

    Many thanks,
    Matt

2 Input file name
Seiji Mori June 27, 2018, 6:53 p.m. #35

We understand that two files are required for the submission, for example, a shell script file (ABC.sh) which is giving the orders to the queuing system and an GRRM input file (ABC.com)  in the same folder.

After we failed one GRRM calculation with an error, and modify/overwrite the input file as the name followed by resubmission, this calculation did not work. We think that the error was caused by the presence of the residual files from the previous failed calculations. Once we deleted all the extra files and left only the ABC.sh and ABC.com,  the calculation runs successfully. Why did this error happen and it is not mentioned in the manual? Is there any possibility that the presence of other files in the same folder can interfere with the GRRM calculation?

Thank you very much for  taking time on so many questions!!

 

1 Input files for MESX or MECI calculations
Seiji Mori June 27, 2018, 6:01 p.m. #34

- In the MESX or MECI calculations, (https://afir.sci.hokudai.ac.jp/documents/manual/37) we need to define a Second Input, where we explicitly specify the level of theory and the charge and spin of the other PES that is going to cross the first one. But what we don't see in the manual is how to specify the extra Gaussian input in our second Input, i.e., if we need also to repeat the specification of the extra keywords and lines, like when you define your own basis sets or add ECPs by using a GenECP keyword to the Second Input? or we do not need to repeat that and rather specify in the first input file (the ones defines in the previous GauInpB) ?

https://afir.sci.hokudai.ac.jp/documents/manual/20

 

Thank you very much again.

 

  • Re:
    Satoshi Maeda

    In OptX calculations, the common GauInpB is used  for both of the two states.

2 Meta-IRC issue
Seiji Mori June 27, 2018, 5:52 p.m. #33

-If we want to calculate the IRC trajectory of a structure, it is possible to do it with GRRM with the keyword  IRC, and it will give you the IRC path in both directions, the forward and the backwards direction to the Gradient Vector. Now, if you want only one of the directions of the IRC path, you could use the keyword Meta-IRC to compute ONLY the forward path. is there a way to compute ONLY the backward path?  I am assuming the forward and backward concept from Gaussian, in which they refer to the direction of the gradient Vector, which means that sometimes the Product path can be in the Reverse direction and not the Forward direction. 

https://afir.sci.hokudai.ac.jp/documents/manual/14

  • Re:
    Satoshi Maeda

    The meta-IRC is the steepest descent path in the mass-weighted coordinates. Therefore, it leads toward the inverse direction of the gradient vector (even when the norm of gradient vector is very small). 

  • Adding a question
    Seiji Mori

    If that is the case, that the meta IRC calculates the backward path (inverse direction) how can we calculate the ONLY the forward direction? because the IRC keyword gives me both sides, Forward and backwards, not only one of them. Thank you.
     

3 Version of Gaussian in use
Seiji Mori June 27, 2018, 5:49 p.m. #31

- Regarding the use or embedding of the Gaussian program into the GRRM, it is supposed that  through aliases and environment variables we define which version of Gaussian program is connected to the GRRM (how it is explained in the manual in the section "how to run GRRM17 (with Gaussian 09)"( https://afir.sci.hokudai.ac.jp/documents/manual/9). Now, I was checking some of the files generated during a MIN  calculation and a SC-AFIR calculation , specifically the file xxx_PARAM.rrm that is generated during the calculation says explicitly 

"INPUT DATA SET OF THE GRRM VER. 13.X 

 Energy Calculation=GAUSSIAN03"  ( It must be "GRRM VER 17. and ....=GAUSSIAN09" because I am connecting to Gaussian 09.)

  • Adding a question
    Seiji Mori

     So this part of the output made me wonder which version of Gaussian is in use? The one that we define in the aliases? the one that it seems to come with the GRRM program or is there a way or keyword to define specifically the version of Gaussian that we want to use with the GRRM?

  • Re:
    Satoshi Maeda

    GRRMp calls GRRM.out and Gaussian 03/09/16 by "subgrr" and "subgau", respectively, defined in your submission/login shell (please see: https://afir.sci.hokudai.ac.jp/documents/manual/9). You can control versions that are called from GRRMp by changing "subgrr" and "subgau".

  • Adding a question
    Seiji Mori

    That's why we find that the message of Gaussian 03 a bit odd, because we have set "subgau" and "subgrr" to gaussian 09  and  GRRM17.out,  respectively and not Gaussian 03 or another version of GRRM.
    Could they be some errors in the system? is the program reading from somewhere else?. Even more odd, we don't even have installed Gaussian 03 in our server. 
     
    Thank you very much.
     

- It is supposed that the GRRM programs can be connected to Gaussian programs when you have installed both programs in one computer. What are the commands from the Gaussian program that the GRRM is able to understand in the command line (the line that starts with the # symbol. For example, can I write in this line IOp commands, can I specify implicit solvent such as scrf=PCM, change from Cartesian functions or pure functions (for example, 5d or 6d), What about the command that have and impact (or are needed) for the extra input (which you call GauInpB)  to work? 
In the AFIR manual (“Options for Gaussian 03/09/16”)(
https://afir.sci.hokudai.ac.jp/documents/manual/43), there's only the example of the basis set with GenECP but that's it, there's no information regarding the other options such as SCRF or IOP keywords. Thank you.

  • Re:
    Satoshi Maeda

    You can put SCRF, SCF, GRID, and so on as follows:

    # MIN/B3LYP/D95V(d) SCRF=(CPCM,Solvent=Water) SCF=TIGHT INT(GRID=FINE)

    The sentence after "# MIN/" will be copied to G03/09/16 inputs.