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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). 

  • 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".

  • 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.

1 Applying artificial force in SC-AFIR
Seiji Mori June 27, 2018, 5:40 p.m. #29

 When performing an AFIR calculation (using the keyword SC-AFIR ), it is supposed that we apply an “artificial” force between fragments. In the case of the SC-AFIR, it is applied between two fragments of the same system (e.g. two atoms A and B of one molecule ACB). The parameter that we can manipulate in the input to create different SC-AFIR are the gamma value (in kJ/mol) and the chosen fragments with a keyword Target, we can define which atoms we want to involve as fragments to generate different AFIR paths. Now, I was wondering how we can define that the force that is going to be applied to the fragments is only attractive or only repulsive? It should be related to a rho parameter written in the GRRM17 paper of J. Comput. Chem. 2017, which is either -1.0 or 1.0. We found the “Adding AFIR function” page (https://afir.sci.hokudai.ac.jp/documents/manual/32) that includes adding “-“ to apply a negative force to two fragments in a MC-AFIR input file. Is there a way to do this in SC-AFIR? I can’t find the “Local search by single-component algorithm” page (https://afir.sci.hokudai.ac.jp/documents/manual/35).

We just found a keyword such as “Target = 1,4,10,12”, which keyword is different from MC-AFIR file.

 

Thank you very much for your help.

  • Re:
    Satoshi Maeda

    In SC-AFIR, paths of both attractive and repulsive forces are computed in default. There is an option to disable calculations of paths of repulsive forces (see: SC=NegativeOFF).

AFIR Web unavailable 8 - 9 Sep 2018
afiradmin June 13, 2018, 1:15 p.m. #28

Due to a planned power outage in Hokkaido University, all services on our website will be unavailable during the following date and times:

8 September 2018, 6:00 (GMT+9) - 9 September 2018, 22:00 (GMT+9)

Thank you for your cooperation.

  • AFIR Web server has been back
    afiradmin

    We were sorry that AFIR Web server was down during 6 - 9 September 2018. 

    Because we underwent the earthquake on 6th September 2018 at 3:08 a.m. (2018 Hokkaido Eastern Iburi earthquake) and the subsequent power failure until 9 September 2018.

    All services on our website are running now.

    Thank you for your patience.

About User Registration
afiradmin Dec. 8, 2017, 6:51 p.m. #26

Only GRRM17 users are eligible for the registered users of this web site.  The GRM17 program is distributed through GRRM web site. Please visit http://iqce.jp/GRRM/index_e.shtml.