Dear All,
I have performed MC-AFIR calculations on a periodic boundary system (Siesta),
but I am having trouble with the subsequent RePath calculations.
The input files are as attached.
I would appreciate any advice you can give me.
Thank you in advance.
Dear all,
I am using ADDF method with input file like attached.
Is it possible to specify functions like pm6 or pm7 or Hartree Fock instead of B3LYP/6-31g* ?
The intention is that the calculation takes too long and we want to low the calculation level.
I felt that the calculation would not progress just by entering pm6.
I would appreciate it if you could tell me the specific command if possible.
thank you very much.
Please tell me about the derivation of the reaction rate between EQ-UDC and EQ-TS-DDC by RCMC.
I think the RCMC method analyzes the reaction rate between EQ and TS(PT) with TST(Transition State Theory).
However, how is the reaction rate between EQ and UDC (Upward Dissociation Channel) derived?
I don't think TST can be applied between EQ-UDC because it is difficult to determine a clear transition state.
Also, am I correct in understanding that the reaction rate between EQ-TS-DDC (Downward Dissociation Channel) is derived by TST only for the dissociation reaction and not for the association reaction?
Please tell me about the derivation of reaction rates between EQ-UDC and EQ-TS-DDC by RCMC.
Thank you in advance.
Dear all.
I would like to know the reaction rate in the surface reaction after GRRM.
I am concerned that the distribution function may be treated differently for gas phase and surface reactions.
(I think the distribution function is used for Gibbs energy derivation.)
Is the distribution function of GRRM RCMC treated as gas phase reaction in the Slab model?
Or are they adjusted for surface reactions?
If surface reactions are treated with the gas-phase partition function, then
If so, how large is the error?
If you have any benchmarks that show that the error is not significant, we would appreciate it if you could let us know.
Thank you in advance.
Sorry, it is a partition function, not a distribution function.
I do not need exact benchmarks, and would appreciate comments on algorithm specifications and experience.
I've tried surface SC-AFIR2 search & got reaction network.
I tried RCMC analysis by RCMC1.txt input file.
But, it only gave RCMC1_sim.log_0 file.
RCMC1_sim.log_1 & RCMC1_sim.log_2 files weren't generated.
And RCMC1_EQ_popl.rrm_* files weren't generated, too.
Will you please give me some advice about RCMC1.txt modification ?
Best regards.
That's due to a simple mistake in the input. The option "ReadCommonGeometry" should be provided in the Options section and should end with the "END" keyword. Please see the usage in the GRRM20 manual carefully: https://afir.sci.hokudai.ac.jp/documents/tutorial/98
It is also requested to attach the "xxx_PARAM.rrm" file to identify such a mistake quickly.
Thank you for your detailed lecture.
I found inappropriate coordinate setting in RCMC1_PARAM.rrm.
I modified the input file (RCMC2.txt) and got appropriate outputs.
Thank you very much.
And I have another question.
I hope to know how to get major reaction paths & major reaction network survey diagram ?
Will you please give me some advice again ?
Best regards
I hope to try DS-AFIR with GRRM20-Siesta combination.
It may need GRRM *.com & Siesta *.inp files.
How to prepare Siesta *.inp file ?
Must I prepare *.inp file for the reactant or the product ? (or both?)
Will you please give me some advice ?
Each user needs to prepare a SIESTA input based on the SIESTA program manual. An example included in the GRRM20 program manual could work in many cases. Please refer to the SIESTA program manual for the meaning and usage of each SIESTA option.
Since GRRM20 rewrites the atomic coordinates of the SIESTA input, as long as the number and order of atoms are correct, anything will do (even all zeros). GRRM20 also rewrites cell vectors accordingly if TV is specified in a GRRM20 input. If TV is not specified in the GRRM20 input, the values given in the SIESTA input are used throughout.
Thank you for your kind lecture.
I've succeeded in PBC DS-AFIR on GRRM20-Siesta.
Attached may be the appropriate files.
Thank you very much.
Dear Prof Maeda and group members,
I would like to ask a question about MC-AFIR and RePATH job.
I tried to find possible reaction pathways from phenol oxidation with hydroxyl radical using MC-AFIR, but keep getting an error when I tried to do RePATH job. The message is "error... No structure to be refined...". This is the input for MC-AFIR and RePATH are attached.
Then I tried to do the MC-AFIR example from the tutorial and example input from GRRM school test job. However, I still got the same error as my original input.
Is there anything I can do to fix this issue? Thank you in advance.
RePATH selects only the EQs that match the conditions and applies the calculation. The calculation using the MC-AFIR input you provided will result in many stabilized products in which radical species take away hydrogen atoms. Since they are considered decomposition products, they are not regarded as qualifying EQs and thus the calculation is not applied. To avoid this, you need to change the definition of DC (dissociation channel) (please refer to https://afir.sci.hokudai.ac.jp/documents/tutorial/90). In the RePATH input, please add DownDC=15.
Thank you Prof Maeda for the answer.
I have studied and tried your suggestions by adding DownDC=15 as an input, but the error still persists. I attached the log files from MC-AFIR and RePATH job. My intention is to get the TS and EQ connection to build reaction pathways, so I followed the tutorial and manuals on the website. However, the output from MC-AFIR job did not include the connection (as seen in the attachment). The log file for DC and PT lists are also empty. Is there something else I miss in the calculation procedure and how should I fix this issue?
Thank you for your help, looking forward to your answer again.
This is probably caused by the difference between the input file name in MC-AFIR and the %infile specification in RePATH.
Please change the first line of RePATH from "%infile=phenol_ox_mcafir" to "%infile=phenol_ox_mcafir_hf" and execute RePATH again.
Thank you Prof. Maeda for your answer.
I have tried your suggestions and the followings settings:
1. changing the value of DownDC based on the formula in the reference
2. changing the molecule coordinates
3. changing the level of theory to B3LYP and PM6
4. trying to use the same input as in the tutorial and examples from GRRM school test job
All trials failed to produce an output and the error message was always "error... No structure to be refined...".
I would be glad to hear about how to fix this issue.
Thank you always.
I have tested the following input files in our environment. The calculation was successful and there were no difficulties. It is required that all the input and output files of the first calculation exist in the working directory in which the second calculation is running. I suppose that this requirement is violated in your environment. Please consult with an admin on your PC.
---First calculation (file name should be test.com)---
# MC-AFIR/B3LYP/6-31G
0 2
C -0.268408351665 -0.455721597488 0.585690563955 1
C 1.211018814399 -0.227444532107 0.441318429356 1
C 1.748559363650 1.007475159159 0.187725543083 1
C 0.931853921972 2.164881669210 0.065891111543 1
C -0.473007641993 2.055856721968 0.232771408925 1
C -1.040272392062 0.835010365106 0.485779696441 1
H -0.616960824546 -1.111669636780 -0.240520922383 1
H 1.836898757315 -1.105141845122 0.560790721678 1
H 2.824726090704 1.111461518709 0.086031669698 1
H 1.377612729030 3.132716428089 -0.132723061716 1
H -1.094841275377 2.946286612991 0.166642673367 1
O -2.400696866990 0.615496351463 0.680556099924 1
H -2.920622260213 1.442417916911 0.662969507136 1
O -0.514876584176 -1.134615985643 1.817855771704 2
H -1.480703470044 -1.267105596467 1.922839097295 2
Options
NFault = 5
Add Interaction
Fragm.1 = 1-13
Fragm.2 = 14-15
1 2
GAMMA = 200
END
GauMem=200
GauProc=4
---Second calculation (any name is OK)---
%infile=test
# Repath/B3LYP/6-31G*
0 2
C -0.268408351665 -0.455721597488 0.585690563955 1
C 1.211018814399 -0.227444532107 0.441318429356 1
C 1.748559363650 1.007475159159 0.187725543083 1
C 0.931853921972 2.164881669210 0.065891111543 1
C -0.473007641993 2.055856721968 0.232771408925 1
C -1.040272392062 0.835010365106 0.485779696441 1
H -0.616960824546 -1.111669636780 -0.240520922383 1
H 1.836898757315 -1.105141845122 0.560790721678 1
H 2.824726090704 1.111461518709 0.086031669698 1
H 1.377612729030 3.132716428089 -0.132723061716 1
H -1.094841275377 2.946286612991 0.166642673367 1
O -2.400696866990 0.615496351463 0.680556099924 1
H -2.920622260213 1.442417916911 0.662969507136 1
O -0.514876584176 -1.134615985643 1.817855771704 2
H -1.480703470044 -1.267105596467 1.922839097295 2
Options
GauMem=200
GauProc=4
I am having trouble understanding how to read the RCMC output.
■ Input : RCMC1.txt
■ Output : RCMC1_sim.log_0
1. I got RCMC1_sim.log_0 as output from RCMC1.com (RCMC1.txt), but
The following block appears frequently in the file.
*************************************************************************
Contraction of the reaction path network
The V-max parameter = 1.66667e-02 / s-1
Delta-G-max value = 192.34 / kJ mol-1
Temperature = 673.15 / K
*************************************************************************
What do V-max and Delta-G-max mean and why do they appear repeatedly?
V-max and Delta-G-max and why they appear repeatedly.
(Should I select the one from these sections ? or check the state transition ?)
2. Is it correct to assume that the information in "SS to which each EQ contributes the most:" is just replaced by a matrix of 0s and 1s?
3. what is the unit of "Rate constant matrix (SS-n --> SS-m):"?
4. what does "Traffic volume for EQ - ***" mean?
5. 9 SSs are obtained, is it possible to visualize them properly?
I see five EQs in "Five representative EQs in SS 0:"
Are there different proportions of the magnitude of each contribution? (is it possible to figure out?)
SS 0 involves 5 EQs, EQ1, 0, 2, 3, 13, but
EQ1, 0, 2, and 3 will have nearly the same structure while EQ13 is very different.
Is it necessary to ascertain the contribution from each EQ in such a case?
I would be very grateful if you could enlighten me.
Thank you in advance.
When I create an input file, the file extension is .xyz, .cif, .pdb, and so on.
How convert from these file extensions to .com and .inp (input file of GRRM20 with SIESTA) ?