Activity for MESMER
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struanr posted a comment on discussion Open Discussion
Hello, Apologies for my slow response. “In my system, I am modeling the association of reactants to a pre-reactive complex. I obtained temperature-dependent high-pressure-limit rate constants from POLYRATE (CVT/SCT calculations) and attempted to parameterize these rates in MESMER using the ILT formalism.” I am not sure I understand what you are doing, I think you mean that you have canonical rate coefficients from POLYRATE and wish to invert these to get microcanonical rate coefficients. “When fitting...
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IEU posted a comment on discussion Open Discussion
Hi all I am currently using MESMER to model a barrierless association reaction and had a question regarding the use of the ILT method for the entrance channel. In my system, I am modeling the association of reactants to a pre-reactive complex. I obtained temperature-dependent high-pressure-limit rate constants from POLYRATE (CVT/SCT calculations) and attempted to parameterize these rates in MESMER using the ILT formalism. When fitting the rate constants to the ILT parameters, the effective activation...
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Hi Stella, Firstly, sincere apologies for my tardy response. Regarding your points: 1) Since you have an association reaction I would recommend ILT. There are variants of RRKM that can be used with barrierless reactions, such as FTST, but they typically require a lot more information about the potential energy surface. 2) I am always wary about negative activation energies. I know some authors are happy to cite them but when it comes to ILT such numbers can mean that you end up with negative or undefined...
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Stella Lee posted a comment on discussion Open Discussion
Hi Struan, I am studying a radical barrierless association reaction in which I was able to obtain optimised energies of the starting materials, transition state and the intermediate. The transition state is 14 kcal/mol below the starting materials. I note that my question has some similarities to this thread (https://sourceforge.net/p/mesmer/discussion/627433/thread/2e1b7ced7c/), but I am unable to use the suggestions from that discussion because I was unable to isolate a stable pre-reactive complex....
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Dear Stella, Thank-you for your reply and sorry for my slow response. It is good to read that you have been able to make progress. I did post a question on the OpenBabel discussion forum but have not yet received a response and suspect that this board is not being monitored. I will try to contact the team directly and let you know if I hear anything. With regards, Struan On Fri, 28 Nov 2025 at 05:42, Stella Lee stellal@users.sourceforge.net wrote: Hi Struan, Thank you for your reply, and my apologies...
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Hi Struan, Thank you for your reply, and my apologies for the delayed response. I was still unable to generate the .xml file with OpenBabel 2.4.1, but could do so with a later version (OpenBabel 3.1.0). I still had the following error despite the output file being successfully generated. ============================== *** Open Babel Error in OpenAndSetFormat Cannot open ..mesmerTemplate.text 4 reactions converted I then tried to open the output file in Firefox, but had to modify the file slightly...
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Hi Struan, Thank you for your reply, and my apologies for the delayed response. I was still unable to generate the .xml file with OpenBabel 2.4.1, but could do so with a later version (OpenBabel 3.1.0). I still had the following error despite the output file being successfully generated. ============================== *** Open Babel Error in OpenAndSetFormat Cannot open ..mesmerTemplate.text 4 reactions converted I then tried to open the output file in Firefox, but had to modify the file slightly...
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Hi Stella, Thanks for getting in touch. I have downloaded OpenBabel 2.4.1 and run it as described in the MESMER notes and observed the same error as you did. I also observed that an output file was produced and that it gave a sensible rendering of the reaction scheme in FireFox. This file would almost certainly require some further adjustment to work properly but I think it has most of the data requried. In short I think that OpenBabel 2.4.1. is largely working but I agree the error message is a...
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Hi Struan, I encountered errors with openbabel while following the tutorial "Constructing a Datafile from Gaussian output", under the section "Coverting to a basic data file using OpenBabel". Running "obabel ..\mesmerTemplate.text .log acetylO2.ck -ocmlr -O acetylO2.xml -aL -e -xp -xx" on terminal produces the error "obabel: cannot write output format". I am currently using obabel version 2.4.1 and noted that the tutorial specifies any obabel version later than 2.3.1 should be possible. Obabel's...
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Dear Dr. Abbes, Thank-you for your message and for using MESMER. Unfortunately, the above command will not do what you wish, it would be nice if it could! The above command can only tell you where there are things missing, you must fill these items in yourself. I attach a revised pe.xml file with some suggestions of suitable content to add, but I suspect this will need a lot more work before it can be run. I hope this helps. Regards, Struan
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Mohammed Mounsif ABBES posted a comment on discussion Open Discussion
Hello Mesmer Community, I'm having trouble adding Mesmer features to the input file using the command: mesmer X.xml -p -n Even though the terminal displays which model will be used and gives warnings the .xml file does not change at all. Please find the input file attached below.
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Dear Dr. Szalay, Firstly, thank-you for using MESMER and sorry for my slow response. I have reproduced the problem and I agree the reaction between 7A and 7B is problematic though I also find problems with the reaction between 7C and 7D. Considering the reaction of 7A and 7B in isolation and inspecting the eigenvalues shows that the eigenvalue of smallest magnitude, which should be zero as defined by the the selected precision, is about 20 orders of magnitude larger than it should be and it is this...
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Máté Szalay posted a comment on discussion Open Discussion
Dear All, Recently I bumped into some problem with my MESMER calculations. After some time the total isomer population are decreasing, reaching 0. Previously I have encounterd this problem in other systems, where I have tested each elementary reaction step to see in which the problem occurs. Usually it occured in the reactionsteps with the low barriers (10-20 kJ/mol or less), which I could just overestimate by increasing the size of the barrier or just simply exclude it. Although in my new system...
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Dear Dr. Pilar Redondo, Thank-you for using MESMER! I have had a quick look at the attached file. It is difficult for me to get a clear idea of your system, however, I did notice that the definition of the MesmerILT method is not what I would expect and should be more like the following: <me:mcrcmethod xsi:type="me:MesmerILT"> <me:preexponential units="cm3molecule-1s-1">4.241e-9</me:preexponential> <me:activationenergy units="kJ/mol">0.0</me:activationenergy> <me:ninfinity>0.0</me:ninfinity> <me:tinfinity>298</me:tinfinity>...
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Pilar Redondo Cristóbal posted a comment on discussion Open Discussion
We are trying to use the mesmer program to calculate the kinetic constants and products ratio of the OH +HCS+ reaction. This reaction is of interest to us in the context of interstellar chemistry. Therefore, we want to calculate these values at temperatures of 100K and 150K and pressures of 1e4, 1e5 and 1e7 PPCC. We consider OH as an excess reactant with a concentration 1e2 times higher than that of HCS+. Our problem is that in our results we do not obtain any significant variation with pressure...
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Dear Rui, First, my apologies for this slow response. We have used OpenMolcas to compute the MECP and MECI points, and verified the reactant and product structures using MEP and LIIC methods. We are interested in investigating the branching ratios of multiple reaction pathways that pass through these points. However, we have not used MESMER or performed calculations related to branching ratios before. We would like to ask for your guidance on how to carry out such calculations. We noticed that in...
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liurui modified a comment on discussion Open Discussion
Dear all, We have used OpenMolcas to compute the MECP and MECI points, and verified the reactant and product structures using MEP and LIIC methods. We are interested in investigating the branching ratios of multiple reaction pathways that pass through these points. However, we have not used MESMER or performed calculations related to branching ratios before. We would like to ask for your guidance on how to carry out such calculations. We noticed that in the MESMER examples, there are two files in...
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Dear all, We have used OpenMolcas to compute the MECP and MECI points, and verified the reactant and product structures using MEP and LIIC methods. We are interested in investigating the branching ratios of multiple reaction pathways that pass through these points. However, we have not used MESMER or performed calculations related to branching ratios before. We would like to ask for your guidance on how to carry out such calculations. We noticed that in the MESMER examples, there are two files in...
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Dear all, We have used OpenMolcas to compute the MECP and MECI points, and verified the reactant and product structures using MEP and LIIC methods. We are interested in investigating the branching ratios of multiple reaction pathways that pass through these points. However, we have not used MESMER or performed calculations related to branching ratios before. We would like to ask for your guidance on how to carry out such calculations. We noticed that in the MESMER examples, there are two files in...
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Dear Struan, We have used OpenMolcas to compute the MECP and MECI points, and verified the reactant and product structures using MEP and LIIC methods. We are interested in investigating the branching ratios of multiple reaction pathways that pass through these points. However, we have not used MESMER or performed calculations related to branching ratios before. We would like to ask for your guidance on how to carry out such calculations. We noticed that in the MESMER examples, there are two files...
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Dear Dr. Qian, Thank-you for using MESMER. The calculation shows an error “WARNING: Chemically significant eigenvalues (CSE) not well separated from internal energy relaxation eigenvals (IEREs). The last CSE = -3.10654e+08 and the first IERE = -1.70469e+09 (last CSE)/(first IERE) ratio = 0.182235, which is less than an order of magnitude Results obtained from Bartis Widom eigenvalue-vector analysis may be unreliable” This is a warning not an error. The origin of this warning is the eigenvalue spectrum...
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Qian Xu posted a comment on discussion Open Discussion
Dear all, I am using mesmer to simulate the reaction of R radicals with O2 and subsequent reactions in the atmosphere, and the simulation process is as shown in the following figure. The calculation shows an error “WARNING: Chemically significant eigenvalues (CSE) not well separated from internal energy relaxation eigenvals (IEREs). The last CSE = -3.10654e+08 and the first IERE = -1.70469e+09 (last CSE)/(first IERE) ratio = 0.182235, which is less than an order of magnitude Results obtained from...
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Kalok Ho posted a comment on discussion Open Discussion
Dear Dr. Struan, Sorry for the late reply. I would like to thank you again for your patience in helping me solve my confusion. I have checked your modified file and reproduced it. In addition, you mentioned that there may be an internal rotor in it. I have also carefully checked the Gaussian output file to make sure that it is a transformation of the configuration. In addition to the reaction pathways I uploaded, there were other calculations that had the same problem. After checking them, I realised...
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Dear Kalok, Once again, sorry for my slow response. I have looked at your input file, run it and was able to reproduce your observations. There is a subtle bug in the section that calculates the equilibrium fractions of each species. I will investigate this issue further but fortunately there is a way to work around this problem by simply re-ordering the definitions of the reactions. I attached to this message a modified input file and the results I obtained. You will see that I have split the final...
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Dear Struan, Thank you so much for your response!
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Dear Kalok, Sorry for my slow response and thank-you again for supporting MESMER. Thank-you for sending your input. I see from this file that the only reaction is an irreversible exchange reaction. This reaction type is a bimolecular reaction and so the associated rate coefficient has no pressure dependence. This reaction type was added for a specific purpose, as give in section 4 on page 45 of the manual, that is to provide an alternative channel for a bimolecular source term species to be consumed,...
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Dear all, best wish for u! Recently, i had met a problem that “The total number of independent species is greater than the number of unique reactions - the system is under specified.This may be because two independent sets of reactions are being defined in one system.” it may because i have two barrierless reactions, but idont know how to deal with it though i had look for others paper( didnt mention about, sad) What is the best way to properly consider both pathways and get a branching ratio? Thanks...
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another tries
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another tries
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Dear all, I have recently calculated the rate coefficients for Irreversible exchange reactions with transition state structures by mesmer.（excess+deficient--TS-->sink+sink） In the output file, Canonical (high pressure) rate coefficients are calculated normally, but Bartis-Widom Phenomenological Rate Coefficients and species/time profiles are shown as “nan”. I tried my best to see if anything is wrong, but I failed all the day. I couldn't find a good solution , so I came to ask a question. Sorry for...
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MESMER released /mesmer/7.1/Mesmer7.1-source.tar.gz
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Hello, Thank-you for sending me your input file. I have made a few changes and run some calculations, the input file and the results are in the attached .zip file. I created an initially excited distribution of the R1 species by shifting a Boltzmann distribution by 3500 cm-1. However, I have not observed any impact of this initial distribution. This can best be seen by inspecting the mesmer_out.xml file in Firefox (see manual for details). As you will see I looked at several sets of conditions to...
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SAIKAT SADHUKHAN modified a comment on discussion Open Discussion
Thank You for your time. I am attaching a file for your convenience. I am also attaching a schematic diagram of the problem I have discussed above. Here I want to make R1 as well as comp1 vibrationally excited so that it has sufficient energy over the TS. Can you suggest a way to model this type of reaction in MESMER? Additionally, I would like to know if the following keywords may come in handy in this case. 1. electronicExcitation 2. Excitation 3. EnergyExcess
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Thank You for your time. I am attaching a file for your convenience. I am also attaching a schematic diagram of the problem I have discussed above. Here I want to make R1 as well as comp1 vibrationally excited so that it has sufficient energy over the TS. Can you suggest a way to model this type of reaction in MESMER? Additionally, I would like to know if the following keywords may come in handy in this case. 1. electronicExcitation 2. Excitation 3. EnergyExcess
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Hello, Sorry for the slow response to your request. It might be possible to model this system in MESMER. However, the shallow well and low transition state suggest that there will be convergence of eigenvalues so it is going to be difficult to extract rate coefficients. It may be better to consider a scattering code for this system such as PolyRate. If you would like to pursue this with MESMER. it would us a lot if you could share more details of the system. With regards, Struan
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Hi all, I am working with MESMER to calculate the overall rate constant of a multistep reaction such as R1+R2 (0.0+0.0) -> Comp1(-3.5) -> TS (5.0) -> Prod1(-15.5) The numbers in the parenthesis represent their zero-point corrected energies in kcal/mol unit. Here the first step (i.e. R1+R2 -> Comp1) is a bimolecular step and the second step (i.e. Comp1->TS -> Prod1) is an unimolecular reaction step. In experimental conditions, R1 has excess vibrational energy (R1 * ) around 10 kcal/mol. It is well...
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Hi all, I am working with MESMER to calculate the overall rate constant of a multistep reaction such as R1+R2 (0.0+0.0) -> Comp1(-3.5) -> TS (5.0) -> Prod1(-15.5) The numbers in the parenthesis represent their zero-point corrected energies in kcal/mol unit. Here the first step (i.e. R1+R2 -> Comp1) is a bimolecular step and the second step (i.e. Comp1->TS -> Prod1) is an unimolecular reaction step. In experimental conditions, R1 has excess vibrational energy (R1) around 10 kcal/mol. It is well known...
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Hello, I have revised the input to include the hindered rotor. The revised input and the results obtained are in the attached .zip file. I made a guess for the barrier height of the potential of 20 kJ/mol but obviously you should check this against ab initio. I also note that you were using a <delta e="">down of 300 cm-1 which, in my experience, is a little high, so I floated this parameter as well. This does result in a marginally better Chi^2 but as you will see the errors on this parameter are...
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CCM posted a comment on discussion Open Discussion
Hi Struan, Thank you for taking the time to look at my input file and making the necessary corrections. There are other experimental studies I can compare against, so I'm not too concerned with the Chi_2 statistic for this case, but I appreciate the note. Regarding the internal rotor for C2F6, the vibrational mode that corresponds to the rotor is the lowest value vibrational frequency in this case (confirmed in GaussView). I have been reading through the manual and I am a little confused on how to...
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Hello, Sorry for my slow response. I have looked at your system and found a few issues. One issue was the control section, which needed to be separated out into individual tasks, which I have done and added a third so that you can see the change in the calculated rate coefficients. I found a bug MESMER concerning the units that you were using, cm3mol-1s-1, which are clearly correct but were not being processed by MESMER properly. I will fix this for the next release of MESMER (scheduled for autumn...
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Dear Struan, Thank you for your patient and detailed reply. After receiving the file, I pondered it and ran it again and got good results. After clearing up some confusion, I will modify my other files further. Looking forward to the release of the new version! Thanks again for your help! (^-^) Best regards, Kalok
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Dear Struan, Thank you for your patient and detailed reply. After receiving the file, I pondered it and ran it again and got good results. After clearing up some confusion, I will modify my file further. Looking forward to the release of the new version! Thanks again for your help! (^-^) Best regards, Kalok
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Dear Struan, Thank you for your patient and detailed reply. After receiving the file, I pondered it and ran it again and got good results. After clearing up some confusion, I will modify my file further. Thanks again for your help! (^-^) Best regards, Kalok
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Hi! I'm trying to get pressure dependent Arrhenius parameters for some radical recombination reactions, starting with CF3 recombination. I'm using rovibrational data from electronic structure calculations I've done in Gaussian 16. There are several papers with experimental data that I would like to incorporate in addition to getting the Plog rate constants. I've tried to use the Marquardt calculation method with the rate data from a paper by Rossi & Golden (1979), but it seems like the chi squared...
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Dear Kalok, Thank-you again for supporting MESMER. Thanks also for sending your files, which I have now looked at. As you mentioned earlier, the mesmer.log file shows that there was a failure to allocate a matrix of size 4448. I think this refers to the allocation of a transition matrix and given that you are using quadruple-double precision (qd), this would equate to an allocation of 4448 by 4448 by 32 bytes or 633110528 bytes, and MESMER will need two of these matrices for a given condition set,...
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In addition, I am running it on my personal computer with 32G of RAM, but mesmer does not seem to take up much memory when running, no more than 1.2G. as well as almost 10% CPU utilization/
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Dear Struan, Thank you for your reply and concern. Here is the input file and logfile.It just stopped running. With regards, Kalok
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Dear Struan, Thank you for your reply and concern. Here is the input file and logfile.It just stopped running. With regards, Kalok
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Hello, Thank-you for getting in touch about MESMER. Unfortunately, the link to the input file you sent appears to be broken. Please could you upload the file again and I will take a look. With regards, Struan
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here is input file
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Dear all, I am new to MESMER too. I set up an input file but it cant run. In the output file, the prompt is as follows： “Matrix allocation failed for matrix of size 4448Rank 0: FUNCTION: Matrix allocation failed.” Is this a problem of insufficient memory allocation? I tried my best to see if there was a setting for memory usage, but I couldn't find it. Due to my poor programming knowledge, I couldn't find a good solution online, so I came to ask a question. Sorry for taking up your time. Thanks a...
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Addition of radiation attenuation factor.
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MultiHinderedRotorPotential.cpp: Cross terms added.
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Dear Lin, Thank-you for your email. I have now looked at both input files. The file named test2 had a few syntax errors which I think is the cause of the problems. I think the problem was in the definition of the ILT term but I need to investigate this more. I attached a revised input file with example output as test5.zip. The input named test1 in your last email also had a number of syntax errors which I have fixed. It also had negative frequencies in the transition state definition which I have...
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Lin Zhang posted a comment on discussion Open Discussion
Dear Struanr, I apologize for bothering you again. Now all test files (test1 and test2) seem to be running normally through MESMER. It is puzzling that all files have been running through 32 cores for 48 hours and still show as running. I want to know if this is normal or if there is an issue with the installation of MESMER (Iinux version). I am looking forward to your reply. With regards, Lin
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Dear struanr, Thanks a lot. I have already solved some of the current problems and the MESMER is running now. With regards, Lin
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Dear jinigxin, Thank-you for your message. I believe it may be possible to model your system but how this is done depends on the type of species represented by IM2, that is is it a true stationary point on the surface or an inflexion? To put it another way, is there a barrier between IM1 and IM2? If you can share some details of your system with me, I might be able to help a little more. With regards, Struan
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jingxin posted a comment on discussion Open Discussion
Dear all, I'm trying to run a trimolecular reaction by MESMER. The examples given in the MESMER tutorial are all bimolecular reactions. Can MESMER calculate trimolecular reactions? If so, how should I set up the input file. The reaction schematic I'm trying to set up is in attachment ( fig.jpg ). The three reactant molecules are marked in yellow. Looking forward to your reply, thanks! Regards, jinigxin
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Fix for Linux build break.
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Dear Lin, I have already modified the location of the folder containing and the input file for the unreasonable energy (attachments: test 3), but it still exists some problems: Firstly, although I have already updated the Firefox version and altered the Firefox defaults , this test file (test3.xml) still cannot be viewed for their additional graphical information using FireFox. In addition, the running of MESMER will print an error (see Fig 1). So, how should I set these two parameters in Fig2 ?...
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* gDensityOfStates.cpp: Altered .xml output statement as to limit conversion to scientific format as this cannot be processed by XSLT.
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Dear Struan, Thank you for your reply. I have already modified the location of the folder containing and the input file for the unreasonable energy (attachments: test 3), but it still exists some problems: Firstly, although I have already updated the Firefox version and altered the Firefox defaults , this test file (test3.xml) still cannot be viewed for their additional graphical information using FireFox. In addition, the running of MESMER will print an error (see Fig 1). So, how should I set these...
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* CollisionOperator.cpp: Effective radiation temperature, norm update.
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Dear Lin, Sorry for my slow reply. I have already passed the Edge “ http://www.mesmergui.cn/ and created several input files (attachments: test 1 and test 2) for MESMER, but there are some problems: Firstly, these test files cannot be viewed for their additional graphical information using FireFox. I was able to view your input files in FireFox without any modifications and I attach screen shots obtained from the two files. In addition, the running of MESMER will print an error (see Fig 1). As the...
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Dear Struan, Thank you for your reply. I have already passed the Edge “ http://www.mesmergui.cn/ and created several input files (attachments: test 1 and test 2) for MESMER, but there are some problems: Firstly, these test files cannot be viewed for their additional graphical information using FireFox. In addition, the running of MESMER will print an error (see Fig 1). I am looking forward to your reply. Regards，Lin
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Dear Lin Zhang, Thank-you for your message. I have tried the link just now and it seems to be working as expected for me. It may be an issue with the browser you are using, I was using Edge. I have also tried FireFox and the interface appears to be working with this browser. I hope this helps, but if you are still having problems please do get in touch again. Regards, Struan
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Dear all, I am new to MESMER. I would like to set up an input file according to the manual, but the page “ http://www.mesmergui.cn/ ” unable to open properly now. Is something wrong and what should i do? Thanks in advance.
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Dear Jianqin Qian, Firstly, my apologies for taking so long to respond, I have been trying to get details from colleagues but have so far been unsuccessful. The implementation of the Landau-Zener (LZ) transition in MESMER is based on earlier code developed by Jeremy Harvey, a paper by whom you cite above. Looking through the papers, the code and comparing with the derivation of the LZ transition, the "GradientReducedMass" is the reduced mass associated with the reaction coordinate, so I would suggest...
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Dear Jianqin Qian, Thank-you for your message. I will confer with colleagues and respond shortly. With regards, Struan
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Jianqin Qian posted a comment on discussion Open Discussion
Dear all, I'm new to MESMER. I would like to calculate the intersystem crossing (ISC) rate by LandauZenerCrossing mehtod implemented in MESMER. I have calculated the geometries and frequencies of reactant, product, and MECP using CASPT2//CASSCF of OpenMolcas software. However, I'm not sure how to obtain the "GradientReducedMass" and "GradientDifferenceMagnitude" needed for ISC rate calculation. According to the MESMER manual, GradientReducedMass means the reduced mass for movement along the direction...
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WUWU posted a comment on discussion Open Discussion
Thank you Struan for your help. I will have a try.
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Hello, Sorry for my slow reply. "Thank you for your reply. I have attached the input file for you. I need to get the branching ratios of all products in a range of energies at low temperature (~100K). However, when I set this temperature to run MESMER, the output file went terrible results--the reactant got 5.61E103 in 10^(-11)s. At 500K, I obtained seemingly reasonable results, but in the experiment, my reactants would remain at around 10% in 10 ^ (-5) s, while the products were quickly consumed...
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Dear Struan, Thank you for your reply. I have attached the inputfile for you. I need to get the branching ratios of all products in a range of energies at low temperature (~100K). However, when I set this temperature to run MESMER, the output file went terrible results--the reactant got 5.61E103 in 10^(-11)s. At 500K, I obtained seemingly reasonable results, but in the experiment, my reactants would remain at around 10% in 10 ^ (-5) s, while the products were quickly consumed in the calculation....
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Hello, Apologies for my slow response. Generally speaking, master equation codes have a difficulty with low temperatures because the underlying eigenvalue spectrum has such a wide range of eigenvalue moduli thus making numerical solution difficult. In your case there is the added difficulty of a large energy span. Even so I think that the value of 362 for energyabovethetophill for 100 K seems large, but I do not know the specifics of your system so it hard to judge. You mention the system is a dissociation,...
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Dear MESMER-developers, I am working in kinetics of a complex dissociation reaction using MESMER software and I have some problems with it to calculate the rate coefficient. As it is a dissociation process, I used the prior distribution instead of Boltzmann distribution to describe the energy distribution of the reactant. Meanwhile, our experiment was performed at low temperature (less than 100K). So we set the temperature parameter of MESMER input file to 100K and energyabovethetophill to 362 (The...
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Further updates to coupled hindered rotor potential.
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Improved control and reporting of coupled hindered rotor potential.
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Update of classical coupled rotors class to invoke coupled hindered rotor potential.
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Extension of coupled hindered rotor potential to include basis product terms.
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Initial implementation of coupled hindered rotor potential.
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Implementation of the effective collision-radiation temperature method.
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Mods. in preparation for the implementation of the effective collision-radiation temperature method.
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Initial outline of N-dimensional angular potential.
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Dear Soumen, You can send the input files to struanhrobertson@outlook.com. With regards, Struan
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SOUMEN posted a comment on discussion Open Discussion
Dear Struanr; Thank you very much for your reply and guidance. I am glad to say after considering hindered rotors treatment for R1, R2, Add-I, Add-II, Add-III, TS-2, and TS-3 we have been able to get rid of most of the negative frequencies. There are only two (or we can say one) negative rate coefficients so far. One is R1 (deficient reactant) to ADD-I (association product) , and the other one is the reverse of it i.e., ADD-I to R1. We can very easily neglect the second one as it is of the order...
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Dear Struan; Thank you very much for reply and guidance. I am glad to say after considering hindered rotors treatment for R1, Add-I, Add-II, Add-III, TS-2 and TS-3 we have able to get rid of most of the negative frequencies.
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Hello, “I have my last queries regarding the PES we have been talking about so far.The file "File1_withT" contains the full PES for your reference. In the PES Add-I, Add-II and Add-III are rotational isomers. A COOH group rotates about an angle slightly larger than 180° ( dihedrally) via TS-2 and TS-3. we already discussed output of this file has quite a few negative rate constants and that is due to those small rotational barriers (TS-2 and TS-3). As a way out you suggested the use of the hindered...
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Thank you for your time and effort to clarify all my doubts. I believe we are at the end of this conversation trail. So far I have learned a lot from our conversation. I have my last queries regarding the PES we have been talking about so far. The file "File1_withT" contains the full PES for your reference. In the PES Add-I, Add-II and Add-III are rotational isomers. A COOH group rotates about an angle slightly larger than 180° ( dihedrally) via TS-2 and TS-3. we already discussed output of this...
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Hello, “So, you were correct. I somehow put a wrong value of imaginary frequency for TS-5. The actual value of it is around 1006.17 cm-1. That solves the issue with tunneling.” I am pleased to read this. “Now to solve the issue with negative rate coefficients your suggestion is to treat intermediate species having low barriers as a single one and combine their states. I want your guide here. If I understood correctly one possible option is to remove Add-II and Add-III and directly connect Add-I with...
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Thank you very much for your reply. So, you were correct. I somehow put a wrong value of imaginary frequency for TS-5. The actual value of it is around 1006.17 cm-1. That solves the issue with tunneling. Now to solve the issue with negative rate coefficients your suggestion is to treat intermediate species having low barriers as a single one and combine their states. I want your guide here. If I understood correctly one possible option is to remove Add-II and Add-III and directly connect Add-I with...
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Hello, "From the output, it can be observed when tunneling was considered one of the branches getting zero Bartis-Widom phenomenological rate constants. Whereas when tunneling was not considered thats the same branch got a very small Bartis-Widom phenomenological rate constants (as that one has a relatively large barrier height i.e. consistent with PES). So I want your valuable suggestion about the consideration of tunneling. is it really necessary to consider the tunneling correction when this PES...
