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 for your attention and best wish for u！
Kalok.
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 product into two branches so I can see which pathway is the more important. Not surprisingly, it turns out that the pathway with the lowest barriers is the dominant channel. The time evolution can be seen in either the old Firefox viewer or the new MXG viewer.
I have some other observations. As the temperature is quite low, I have used quadruple-double precision. I have also altered the method of calculating the rotational density of states to classical in some cases as these molecules are quite heavy and the classical approach is quicker, but you may want to change this back to check the results. I note that the barrier heights are very low, some of them are similar to the heights of internal rotation and these should perhaps be checked. Finally, there are some very low frequencies, some of which are almost certainly related to internal rotors, and I would suggest that these are altered to internal rotors to improve the density of states calculations.
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 that it was the calculation part of the ILT section of them that had been filled in with the wrong parameters that were too far off the mark. After correction, normal results have been obtained that match the experimental values.
Thank you again and Happy New Year!!
Regards, Kalok
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
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 for your attention and best wish for u！
Kalok.
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 product into two branches so I can see which pathway is the more important. Not surprisingly, it turns out that the pathway with the lowest barriers is the dominant channel. The time evolution can be seen in either the old Firefox viewer or the new MXG viewer.
I have some other observations. As the temperature is quite low, I have used quadruple-double precision. I have also altered the method of calculating the rotational density of states to classical in some cases as these molecules are quite heavy and the classical approach is quicker, but you may want to change this back to check the results. I note that the barrier heights are very low, some of them are similar to the heights of internal rotation and these should perhaps be checked. Finally, there are some very low frequencies, some of which are almost certainly related to internal rotors, and I would suggest that these are altered to internal rotors to improve the density of states calculations.
I hope this allows you to make progress.
Regards, Struan
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 that it was the calculation part of the ILT section of them that had been filled in with the wrong parameters that were too far off the mark. After correction, normal results have been obtained that match the experimental values.
Thank you again and Happy New Year!!
Regards, Kalok