ONIOM on MC-AFIR
Taiki Kato
Nov. 27, 2018, 10:40 a.m.
#71
Dear Prof. Maeda & laboratory people,
I'm trying ONIOM method on MC-AFIR.
But, I don't understand the exact format of the ONIOM layer & MC-AFIR part.
This is my input file with error calculation log.
---------------------------------------------------------------------------------------
# MC-AFIR/ONIOM(uwb97xd/6-31G : upm6) integral(coarsegrid)
0 1
H -5.09198232 1.46148646 0.64415956 H 1
H -5.05103711 1.51846702 -1.80580446 H 1
H -5.08619301 3.61195144 -0.53172902 H 1
H -3.07552771 2.21038282 -0.53072587 H 1
Si -4.57617575 2.2005746 -0.55601978 H 1
Si 0.92262713 -0.42951851 -0.06586408 H 2
H 0.32586471 0.89377867 0.44846657 H 2
H 0.92141623 -0.4283995 -1.60585939 H 2
Si -0.36596427 -2.22060001 0.71381911 H 2
Si 0.54148635 -4.23086015 -0.06762047 H 2
...
Si 7.89452207 2.71361008 -0.0662665 L H 16 2
Si 6.60446476 0.92311796 3.05275285 L H 16 2
Si 3.11867252 -0.64788568 3.05254379 L H 12 2
Si -2.56235026 -2.00324774 -0.06393534 L H 9 2
Si 1.83058292 -2.4396089 3.83181251 L H 19 2
Si 1.45021923 -6.24149307 3.83086153 L H 19 2
Si -0.74565359 -6.02268238 0.7123408 L H 10 2
Si 2.35719613 -8.2514615 3.04887994 L H 23 2
Si 4.55185684 -8.47158271 3.82932265 L H 33 2
External Atoms
Si 7.50985596 -1.08833081 6.95223274 L 2
Si 7.12790465 -4.89067932 6.95082004 L 2
Si 8.03487102 -6.90152356 6.17032595 L 2
Si 8.41640895 -3.09947186 6.17176893 L 2
...
H 6.74535629 -8.6930865 8.48930406 L 2
H 7.50965005 -1.08890581 8.4922214 L 2
H 4.02610987 -2.65912846 8.49169783 L 2
H 3.64455597 -6.46260745 8.4899976 L 2
H 0.54408428 -4.23167248 8.4928424 L 2
Options
MicroIt = (MMOnly)
GauProc = 4
NSample = 20
MinFC = -1
MC = ReactivePathOnly
Add Interaction
Fragm.1 = 1-5
Fragm.2 = 6-43
Fragm.3 = 66-145
1 2
1 3 -
GAMMA = 600
END
-------------------------------------------------------------------------------------
I think that the number order of ONIOM layer or MC-AFIR part is not good.
Please teach me the exact number order of ONIOM layer & MC-AFIR part.
Best regards
1
Metal Element Containing Surface Reaction Analysis
Taiki Kato
Nov. 8, 2018, 5:30 p.m.
#67
Dear Prof. Maeda & Laboratory People
I'm struggling to analyze metal element containing surface reaction analysis
such as { TiCl4 on TiN }, { EtOH on HfO2 }, { SiH4 on Ru } and so on.
I uses GRRM17 which is not feasible PBC surface model.
Then, I uses cluster surface model on these metal element containing surfaces.
However, it is difficult for me to converge these surfaces { TiN, HfO2, Ru } SCF calculation by Gaussian.
I also uses Materials Studio DMol3 which is easy to converge SCF calculation but not suitable for GRRM.
Please teach me how to converge these SCF calculation by Gaussian
or some alternative convergent technology.
Sencerely
Re:
Satoshi Maeda
Although GRRM17 doesn't contain an interface with DMol3, GRRM17 can be used together with any energy computation code if a user prepare a simple interface script. Please see the following page:
Other QM code trial
Taiki Kato
Thank you for your kind reply.
I'll consider the GRRM application trial not only on Gaussian but also on the other QM codes.
DMol3 doesn't have any analytical hessian calculation method.
Therefore, I think that DMol3 may be very slow on GRRM.
And I hope to choice more established way because I'm a biginner on these operations.
How is the performance of SIESTA (or Turbomole) on cluster model analysis ?
Will you please teach me SIESTA (or Turbomole) setting manuals ?
If you know good QM-codes, please give me some advice.
1
SC-AFIR option 'SC=NegativeON'
Ayako Furuhama
Aug. 8, 2018, 7:25 a.m.
#64
Dear Professor Maeda and his group members;
SC-AFIR calculation is performing to obtain various initial reactants of a reaction. But the following calculation is not stopped. [I do not know the reasons... Maybe 'SC=NegativeON' (?) This was used in previous calculations.] In this case, I will not follow PT structures and their TS structures due to computational cost.
Please let us know the additional or unnecessary options for such calculations. input_PARAM.rrm is following:
INPUT DATA SET OF THE GRRM VER. 13.x
-------------------------------------------------------------------------
Energy Calculation = GAUSSIAN03
-------------------------------------------------------------------------
-------------------------------------------------------------------------
Job type = 16
-------------------------------------------------------------------------
UB3LYP/6-31G*
-------------------------------------------------------------------------
0 1 XX XX 0
-------------------------------------------------------------------------
XYZ coordinate
-------------------------------------------------------------------------
-------------------------------------------------------------------------
-------------------------------------------------------------------------
-------------------------------------------------------------------------
NRun = 32
IniStr = Random
GauMem = XXX (MW)
GauProc = X
ADD INTERACTION
SC = NegativeON
DownDC = 15
RandDC = 15
STABLE = OPT
READ BOND CONDITION
Thank you very much!
Option for SC-AFIR
Ayako Furuhama
Dear Prof. Maeda,
I am sorry but I clarify my question.
I search TS and EQ structures for the initial reaction of A + B system by using SC-AFIR/UB3LYP/6-31G(p).
A is a tri-atomic molecule and B is an organic molecule including one nitrogen and some carbon and hydrogen atoms.
After one month starting a SC-AFIR calculation (B= one nitrogen + three carbons with some hydorgens) with options (i.e. NRUN=32,GauMem=1000,GauProc=4,Add Interaction,and Gamma=100 alog with SC=NegativeON,SC=LUP-ON,NoBondRearrange,DownDC=15,RandDC=15,Stable=OPT), 343EQ and 629TS (as well as 5900 TS in PT_list) were found. But this job does not done yet. EQ and TS searches are not stopping.
Could you please inform how to finish the SC-AFIR calculation properly? Should I perporm FirstOnly calculations in advance to found out proper initial conformation?
Thank you very much in advance.
Ayako Furuhama
Re:
Satoshi Maeda
I don't know your system well, but I guess that many similar (but slightly different) EQs are generated in the flat regions of the PES in your calculation. This often happens when a spin unrestricted DFT method is used as an energy calculation method.
One can avoid this situation by one of the following three ways.
1. By increasing the grid density in DFT calculations.
E.g.) UB3LYP/6-31G(d) Int(Grid=99590)
This would be the most straightforward way, but DFT calculations with dense grids will be computational demanding.
2. By using a structural clustering option.
E.g.) MatchDecScale = 3.0
See the option list about this option: https://afir.sci.hokudai.ac.jp/documents/manual/51
3. By applying a weak force between all atom pairs.
E.g.) A simple case for CO+OH is shown below:
# SC-AFIR/UB3LYP/D95V
0 2
C 0.0 0.0 0.0 1
O 1.2 0.0 0.0 1
O 3.0 0.0 0.0 2
H 4.0 0.0 0.0 2
Options
Add Interaction
Fragm.1=1
Fragm.2=2
Fragm.3=3
Fragm.4=4
1 2 3.33
1 3 3.33
1 4 3.33
2 3 3.33
2 4 3.33
3 4 3.33
Gamma=200.0
END
EQOnly
KeepLUPPATH
With the above input, a weak force with Gamma=3.33 kJ/mol is added to all atom pairs during the SC-AFIR calculation with Gamma=200.0 kJ/mol. A recommended value of the weak force is 10.0/(N-1) kJ/mol, where N is the number of atoms in the system. All EQs and TSs obtained are those on the AFIR function consisting of these force terms and thus are not actual ones. Therefore, after the initial SC-AFIR calculation, one needs to perform a RePATH calculation reading the results of the initial SC-AFIR calculation to eliminate the weak force. Since TSs obtained by the initial SC-AFIR calculation are not actual TSs, it is recommended to avoid computing TSs accurately during the initial search using the EQOnly and KeepLUPPATH options (also see ReadBareEnergy option).
When the weak force is added, local minima for weak complexes between two molecules are formed in regions where the two molecules have sufficient interactions. When DFT grids that are not dense enough are used in spin unrestricted DFT calculations, many imaginably local minima can be created in the flat regions of the PES where two molecules are arranged far away from each other. The weak force help avoids this problem. I emphasize again that the weak force must be eliminated afterward by the additional RePATH calculation.
An example input for the RePATH calculation is also shown below:
%infile=xxx
# RePATH/UB3LYP/D95V
0 2
C 0.0 0.0 0.0 1
O 1.2 0.0 0.0 1
O 3.0 0.0 0.0 2
H 4.0 0.0 0.0 2
DS-AFIR issue 2
Seiji Mori
July 27, 2018, 11:33 a.m.
#57
Re:
Satoshi Maeda
DS-AFIR issue
Seiji Mori
July 12, 2018, 3:19 p.m.
#55
Re:
Satoshi Maeda
In general, I recommend to do RePATH in which the previous DS-AFIR results are read.
The ridge point will be used as the TS guess only when the DS = SingleSTEP option is used. Without this option, LUP is performed after the AFIR path is obtained, and energy maxima along the final LUP path are used as the TS guesses.
1
GUI software for Gaussian outputs generated by AFIR
Seiji Mori
July 6, 2018, 3:24 p.m.
#53
Re:
Satoshi Maeda
We usually convert EQ_list and TS_list into the xyz format and see allthe structures through a software which can read the xyz format.
SAFIRE can be used to draw the network of reaction pathways. It will be uploaded to GitHub in the near future, once all required documents are available.
Another software is Visomin (http://www.science-technology.jp/index.html). But, I have never used it by myself.
Thank you
Seiji Mori
Thank you very much for your comments.
1
Energy oscillating issue during geometry optimization
Seiji Mori
July 6, 2018, 9:52 a.m.
#52
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!!
Re:
Satoshi Maeda
Please see the bottom of the following page: https://afir.sci.hokudai.ac.jp/documents/manual/9
Thank you very much.
Seiji Mori
Prof. Maeda, Thank you very much for your kindful responses, through you are alwasys very busy.