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From: Jacopo L. <jac...@sn...> - 2019-09-10 09:25:18
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Dear all, I'm writing to you because I have a problem with the execution of a MESMER job. I've constructed the input file by your GUI but when I run it it gives me this error "Too many iterations in TQLIT". I attach the input file. Any suggestion or help would be very appreciated. -- Jacopo Lupi PhD Student in Methods and Models for Molecular Sciences SMART Laboratory Scuola Normale Superiore Piazza dei Cavalieri 7, 56126 Pisa (Italy) |
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From: Bala G. <bal...@gm...> - 2016-12-19 10:10:45
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From: Sourav G. <sou...@gm...> - 2016-09-19 08:25:24
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Is there any server problem running in the given URL site: www.cce.tsinghua.edu.cn:8000? The above site is not working in my Firefox. Please resolve my problem. With Regards Sourav Ghoshal Kolkata India |
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From: Sourav G. <sou...@gm...> - 2016-09-14 06:55:49
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Dear sir/madam, The MESMER GUI site is not opening in my PC since 10 days. Is there any problem in that site? Please resolve this problem. With Regards Sourav Ghoshal Saha Institute of Nuclear Physics Kolkata India |
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From: Sourav G. <sou...@gm...> - 2016-07-22 16:06:25
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---------- Forwarded message ---------- From: Sourav Ghoshal <sou...@gm...> Date: Fri, Jul 22, 2016 at 7:45 PM Subject: Is this possible to calculate the forward and backward equilibrium constant values for the reaction A + B = AB (complex) reaction To: mes...@li... Hello, Myself Sourav Ghoshal, Senior research fellow in Saha Institute of Nuclear Physics, Kolkata, India. I have already installed Mesmer in my windows OS. My purpose of using MESMER, is to calculate the forward and backward rate constants of simple A + B = AB H-bonded complex formation reaction, where AB is a hydrogen bonded complex which formed from the isolated reactants A and B. It is known that the equilibrium constant value (Keq) of a complex formation reaction (A + B = AB), can be calculated from the relative gibbs free energy value (del G = GAB - GA -GB) by the equation of Keq = exp(-del G/ RT). The problem is that although it will give the value of Keq, but it cannot give separately the values of K1 (forward equilibrium constant) and K-1 (backward equilibrium constant), as the Keq = K1/K-1. I want to calculate both the two values of K1 and K-1. I want to know that is it possible to calculate separately K1 and K-1 and then Keq value by using MESMER? If it possible, Could anyone initially guide me how to do it? Thank you very much in an advance!!! With Regards Sourav Ghoshal Saha Institute of Nuclear Physics Kolkata India |
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From: SourceForge.net <no...@so...> - 2011-09-10 11:04:46
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Bugs item #3406422, was opened at 2011-09-08 17:15 Message generated for change (Comment added) made by chrismorl You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=894764&aid=3406422&group_id=180832 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None >Status: Closed >Resolution: Fixed Priority: 9 Private: No Submitted By: struanr (struanr) Assigned to: struanr (struanr) Summary: Parameters not associated with species in fitting report. Initial Comment: The fitting methods output detail from the covariance matrix but if, for example, the fit involves the adjustment of two zero point energy values it is not clear as to which species these are associated with making interpretation of the results difficult. This hould be fixed before the release of Mesmer 0.3. ---------------------------------------------------------------------- >Comment By: Chris Morley (chrismorl) Date: 2011-09-10 11:04 Message: Fixed in r682. The names of the range variables now include the name of the molecule or the reaction. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=894764&aid=3406422&group_id=180832 |
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From: SourceForge.net <no...@so...> - 2011-09-08 17:15:15
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Bugs item #3406422, was opened at 2011-09-08 17:15 Message generated for change (Tracker Item Submitted) made by struanr You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=894764&aid=3406422&group_id=180832 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Resolution: None Priority: 9 Private: No Submitted By: struanr (struanr) Assigned to: struanr (struanr) Summary: Parameters not associated with species in fitting report. Initial Comment: The fitting methods output detail from the covariance matrix but if, for example, the fit involves the adjustment of two zero point energy values it is not clear as to which species these are associated with making interpretation of the results difficult. This hould be fixed before the release of Mesmer 0.3. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=894764&aid=3406422&group_id=180832 |
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From: SourceForge.net <no...@so...> - 2010-06-13 09:38:30
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Bugs item #2790895, was opened at 2009-05-12 21:32 Message generated for change (Comment added) made by struanr You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=894764&aid=2790895&group_id=180832 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None >Status: Closed Resolution: None Priority: 5 Private: No Submitted By: struanr (struanr) Assigned to: Nobody/Anonymous (nobody) Summary: Reaction ILT data should have own class Initial Comment: I wonder if we might tidy up the Reaction class a little by moving all of the ILT type data into a separate class, that is only instantiated if an ILT method is specified. As it is, the Reaction class is a little cultered and its fundemental role obscured. ---------------------------------------------------------------------- >Comment By: struanr (struanr) Date: 2010-06-13 09:38 Message: ILT code has now been removed from reaction.h and placed in the ILT code classes thenselves. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=894764&aid=2790895&group_id=180832 |
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From: SourceForge.net <no...@so...> - 2009-12-09 11:11:31
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Bugs item #2911326, was opened at 2009-12-09 11:11 Message generated for change (Tracker Item Submitted) made by alvynliang You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=894764&aid=2911326&group_id=180832 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Chi-Hsiu Liang (alvynliang) Assigned to: Nobody/Anonymous (nobody) Summary: Source term DeltaEDown Initial Comment: The source term doesn't need a valid deltaEDown, but MESMER complain about it when deltaEDown is not set for a source term. In propene: No value of me:deltaEDown was supplied and the default value NEEDS TO BE CHECKED** ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=894764&aid=2911326&group_id=180832 |
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From: SourceForge.net <no...@so...> - 2009-07-15 18:25:27
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Bugs item #2818103, was opened at 2009-07-07 16:36 Message generated for change (Comment added) made by chrismorl You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=894764&aid=2818103&group_id=180832 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None >Status: Closed >Resolution: Fixed Priority: 5 Private: No Submitted By: Chi-Hsiu Liang (alvynliang) Assigned to: Chris Morley (chrismorl) Summary: Problem in assigning activation energie in grid search mode Initial Comment: The current build has a problem in assigning ILT activation energies under grid search mode. If user give a range to the activation energy in grid search mode, the program returns an error saying "There is only one point for this varaible." and ask to remove the range. I guess this is due to changes made after the creaction of DPoint class, but I am not very sure what the problem is. This should be easy to resolve but I need to focus on getting the LogExp class work first. I will look at this problem in a few days if no one else has time to look at it. ---------------------------------------------------------------------- >Comment By: Chris Morley (chrismorl) Date: 2009-07-15 18:25 Message: Problem was floating point rounding errors. Fixed (with other related mods) in r415 ---------------------------------------------------------------------- Comment By: Chi-Hsiu Liang (alvynliang) Date: 2009-07-08 10:11 Message: I have uploaded the example file here. It's simply a modification to the input file of Acetyl_O2_association.xml Please have a look. Thanks Chris!! ---------------------------------------------------------------------- Comment By: Chris Morley (chrismorl) Date: 2009-07-08 09:43 Message: I can look at this. Have you a data file that shows the problem? Chris ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=894764&aid=2818103&group_id=180832 |
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From: SourceForge.net <no...@so...> - 2009-07-08 10:11:19
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Bugs item #2818103, was opened at 2009-07-07 16:36 Message generated for change (Comment added) made by alvynliang You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=894764&aid=2818103&group_id=180832 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Chi-Hsiu Liang (alvynliang) Assigned to: Chris Morley (chrismorl) Summary: Problem in assigning activation energie in grid search mode Initial Comment: The current build has a problem in assigning ILT activation energies under grid search mode. If user give a range to the activation energy in grid search mode, the program returns an error saying "There is only one point for this varaible." and ask to remove the range. I guess this is due to changes made after the creaction of DPoint class, but I am not very sure what the problem is. This should be easy to resolve but I need to focus on getting the LogExp class work first. I will look at this problem in a few days if no one else has time to look at it. ---------------------------------------------------------------------- >Comment By: Chi-Hsiu Liang (alvynliang) Date: 2009-07-08 10:11 Message: I have uploaded the example file here. It's simply a modification to the input file of Acetyl_O2_association.xml Please have a look. Thanks Chris!! ---------------------------------------------------------------------- Comment By: Chris Morley (chrismorl) Date: 2009-07-08 09:43 Message: I can look at this. Have you a data file that shows the problem? Chris ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=894764&aid=2818103&group_id=180832 |
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From: SourceForge.net <no...@so...> - 2009-07-08 09:44:02
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Bugs item #2818103, was opened at 2009-07-07 16:36 Message generated for change (Comment added) made by chrismorl You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=894764&aid=2818103&group_id=180832 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Chi-Hsiu Liang (alvynliang) >Assigned to: Chris Morley (chrismorl) Summary: Problem in assigning activation energie in grid search mode Initial Comment: The current build has a problem in assigning ILT activation energies under grid search mode. If user give a range to the activation energy in grid search mode, the program returns an error saying "There is only one point for this varaible." and ask to remove the range. I guess this is due to changes made after the creaction of DPoint class, but I am not very sure what the problem is. This should be easy to resolve but I need to focus on getting the LogExp class work first. I will look at this problem in a few days if no one else has time to look at it. ---------------------------------------------------------------------- >Comment By: Chris Morley (chrismorl) Date: 2009-07-08 09:43 Message: I can look at this. Have you a data file that shows the problem? Chris ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=894764&aid=2818103&group_id=180832 |
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From: SourceForge.net <no...@so...> - 2009-07-07 16:36:30
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Bugs item #2818103, was opened at 2009-07-07 16:36 Message generated for change (Tracker Item Submitted) made by alvynliang You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=894764&aid=2818103&group_id=180832 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Chi-Hsiu Liang (alvynliang) Assigned to: Nobody/Anonymous (nobody) Summary: Problem in assigning activation energie in grid search mode Initial Comment: The current build has a problem in assigning ILT activation energies under grid search mode. If user give a range to the activation energy in grid search mode, the program returns an error saying "There is only one point for this varaible." and ask to remove the range. I guess this is due to changes made after the creaction of DPoint class, but I am not very sure what the problem is. This should be easy to resolve but I need to focus on getting the LogExp class work first. I will look at this problem in a few days if no one else has time to look at it. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=894764&aid=2818103&group_id=180832 |
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From: SourceForge.net <no...@so...> - 2009-06-29 14:17:18
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Bugs item #2808685, was opened at 2009-06-18 21:58 Message generated for change (Comment added) made by alvynliang You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=894764&aid=2808685&group_id=180832 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Closed Resolution: Fixed Priority: 5 Private: No Submitted By: Josh Allen (jwallen85) Assigned to: Nobody/Anonymous (nobody) Summary: Compiling MESMER on Linux Initial Comment: I have recently compiled MESMER on Linux. Compilation of TinyXML and QD worked out of the box, but there was an error during compilation of MESMER proper. After investigating I determined that the bug is on line 109 of IrreversibleExchangeReaction.h; the fix is to replace virtual void IrreversibleExchangeReaction::calcFluxFirstNonZeroIdx(void); with virtual void calcFluxFirstNonZeroIdx(void); After making this change MESMER compiled and executed fine. ---------------------------------------------------------------------- Comment By: Chi-Hsiu Liang (alvynliang) Date: 2009-06-29 14:17 Message: I have already updated and put it in the current release. Cheers! ---------------------------------------------------------------------- Comment By: Chi-Hsiu Liang (alvynliang) Date: 2009-06-19 09:13 Message: Thanks for the spotting! I have corrected it in the SVN and it will be in the next release. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=894764&aid=2808685&group_id=180832 |
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From: SourceForge.net <no...@so...> - 2009-06-29 10:07:27
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Bugs item #2813862, was opened at 2009-06-29 10:07 Message generated for change (Tracker Item Submitted) made by alvynliang You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=894764&aid=2813862&group_id=180832 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Chi-Hsiu Liang (alvynliang) Assigned to: Chris Morley (chrismorl) Summary: OpenBabel import error Initial Comment: I forward this message on behalf of Liu Zhen, a postdoc researcher in SPEME. I am not familiar with OpenBabel part of the code so I put it here and assign it to Chris in the mean time. -------- I am working on converting a Gaussian output into a mesmer recognized XML file, but a few problem arose when I followed the attached tutorial with mesmer, as listed below 1. The openbabel software I downloaded from the link provided by the tutorial seems not working in use of both the GUI and the dos command. 2. No files of .log format can be found in the folder example\acetylO2 as indicated by the tutorial 3. When I run the command ‘’babel ..\mesmerTemplate.text *.log acetylO2.ck -ocmlr acetylO2.xml -aL -e -xp -xx --add MW’’, the following ************************************** C:\Program Files (x86)\OpenBabel-2.3.0cm>babel ..\Mesmer-0.1\examples\AcetylO2\MesmerTemplate.text *.log acetylO2.ck -ocmlr acety02.xml -aL -e -xp -xx --add MW ============================== *** Open Babel Error in OpenBabel::OBConversion::LoadFormatFiles C:\Program Files (x86)\OpenBabel-2.3.0cm\OBInchi.obf did not load properly 4 reactions converted 1 errors 30 audit log messages ************************************** All the problems hinder me from kick off with any further work on this. Please help!! ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=894764&aid=2813862&group_id=180832 |
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From: SourceForge.net <no...@so...> - 2009-06-19 09:13:36
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Bugs item #2808685, was opened at 2009-06-18 21:58 Message generated for change (Settings changed) made by alvynliang You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=894764&aid=2808685&group_id=180832 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None >Status: Closed Resolution: Fixed Priority: 5 Private: No Submitted By: Josh Allen (jwallen85) Assigned to: Nobody/Anonymous (nobody) Summary: Compiling MESMER on Linux Initial Comment: I have recently compiled MESMER on Linux. Compilation of TinyXML and QD worked out of the box, but there was an error during compilation of MESMER proper. After investigating I determined that the bug is on line 109 of IrreversibleExchangeReaction.h; the fix is to replace virtual void IrreversibleExchangeReaction::calcFluxFirstNonZeroIdx(void); with virtual void calcFluxFirstNonZeroIdx(void); After making this change MESMER compiled and executed fine. ---------------------------------------------------------------------- Comment By: Chi-Hsiu Liang (alvynliang) Date: 2009-06-19 09:13 Message: Thanks for the spotting! I have corrected it in the SVN and it will be in the next release. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=894764&aid=2808685&group_id=180832 |
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From: SourceForge.net <no...@so...> - 2009-06-19 09:13:20
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Bugs item #2808685, was opened at 2009-06-18 21:58 Message generated for change (Comment added) made by alvynliang You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=894764&aid=2808685&group_id=180832 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open >Resolution: Fixed Priority: 5 Private: No Submitted By: Josh Allen (jwallen85) Assigned to: Nobody/Anonymous (nobody) Summary: Compiling MESMER on Linux Initial Comment: I have recently compiled MESMER on Linux. Compilation of TinyXML and QD worked out of the box, but there was an error during compilation of MESMER proper. After investigating I determined that the bug is on line 109 of IrreversibleExchangeReaction.h; the fix is to replace virtual void IrreversibleExchangeReaction::calcFluxFirstNonZeroIdx(void); with virtual void calcFluxFirstNonZeroIdx(void); After making this change MESMER compiled and executed fine. ---------------------------------------------------------------------- >Comment By: Chi-Hsiu Liang (alvynliang) Date: 2009-06-19 09:13 Message: Thanks for the spotting! I have corrected it in the SVN and it will be in the next release. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=894764&aid=2808685&group_id=180832 |
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From: SourceForge.net <no...@so...> - 2009-06-18 21:58:16
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Bugs item #2808685, was opened at 2009-06-18 17:58 Message generated for change (Tracker Item Submitted) made by jwallen85 You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=894764&aid=2808685&group_id=180832 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Josh Allen (jwallen85) Assigned to: Nobody/Anonymous (nobody) Summary: Compiling MESMER on Linux Initial Comment: I have recently compiled MESMER on Linux. Compilation of TinyXML and QD worked out of the box, but there was an error during compilation of MESMER proper. After investigating I determined that the bug is on line 109 of IrreversibleExchangeReaction.h; the fix is to replace virtual void IrreversibleExchangeReaction::calcFluxFirstNonZeroIdx(void); with virtual void calcFluxFirstNonZeroIdx(void); After making this change MESMER compiled and executed fine. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=894764&aid=2808685&group_id=180832 |
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From: SourceForge.net <no...@so...> - 2009-06-18 11:23:57
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Feature Requests item #2792116, was opened at 2009-05-15 08:53 Message generated for change (Comment added) made by chrismorl You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=894767&aid=2792116&group_id=180832 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None >Status: Closed Priority: 5 Private: No Submitted By: Chris Morley (chrismorl) Assigned to: Chris Morley (chrismorl) Summary: Species time profile Initial Comment: In the Firefox output add a plot which displays the species population v time (probably log(pop) v log t). ---------------------------------------------------------------------- >Comment By: Chris Morley (chrismorl) Date: 2009-06-18 11:22 Message: Duplicate ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=894767&aid=2792116&group_id=180832 |
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From: SourceForge.net <no...@so...> - 2009-06-18 09:57:15
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Feature Requests item #2808268, was opened at 2009-06-18 09:55 Message generated for change (Settings changed) made by alvynliang You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=894767&aid=2808268&group_id=180832 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Priority: 5 Private: No Submitted By: Chi-Hsiu Liang (alvynliang) >Assigned to: Chi-Hsiu Liang (alvynliang) Summary: Infinite precision in diagonalization Initial Comment: Write a class performs infinite precision operation to be used in diagonalization. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=894767&aid=2808268&group_id=180832 |
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From: SourceForge.net <no...@so...> - 2009-06-18 09:56:05
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Feature Requests item #2808268, was opened at 2009-06-18 09:55 Message generated for change (Tracker Item Submitted) made by alvynliang You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=894767&aid=2808268&group_id=180832 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Priority: 5 Private: No Submitted By: Chi-Hsiu Liang (alvynliang) Assigned to: Nobody/Anonymous (nobody) Summary: Infinite precision in diagonalization Initial Comment: Write a class performs infinite precision operation to be used in diagonalization. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=894767&aid=2808268&group_id=180832 |
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From: SourceForge.net <no...@so...> - 2009-06-11 10:17:56
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Bugs item #2804147, was opened at 2009-06-10 13:31 Message generated for change (Comment added) made by alvynliang You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=894764&aid=2804147&group_id=180832 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open >Resolution: Fixed Priority: 5 Private: No Submitted By: Chi-Hsiu Liang (alvynliang) Assigned to: Chi-Hsiu Liang (alvynliang) Summary: Exchange reaction in Benzene system causes two errors Initial Comment: I have observed two bugs when I run P/T depBenzene oxidation system from Dave. One of these is the ZPE and lowest barrier height calculation in ReactionManager.cpp for IrreversibleExchangeReaction. I will fix it asap. The second error is in approximately Line 1204 of ReactionManager.cpp which is inside BartisWidomPhenomenologicalRates(). It seems for some reason the vector index is out of range. ---------------------------------------------------------------------- >Comment By: Chi-Hsiu Liang (alvynliang) Date: 2009-06-11 10:17 Message: Resolved. I will keep working on IrreversibleAssociationReaction. ---------------------------------------------------------------------- Comment By: Chi-Hsiu Liang (alvynliang) Date: 2009-06-10 13:36 Message: KofEsTemp was not populated so the vector is out of range when executing this line sm += assymEigenVec[rxnMatrixLoc+j][nchemIdx+i] * KofEsTemp[j]; ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=894764&aid=2804147&group_id=180832 |
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From: SourceForge.net <no...@so...> - 2009-06-10 13:36:51
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Bugs item #2804147, was opened at 2009-06-10 13:31 Message generated for change (Comment added) made by alvynliang You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=894764&aid=2804147&group_id=180832 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Resolution: Accepted Priority: 5 Private: No Submitted By: Chi-Hsiu Liang (alvynliang) Assigned to: Chi-Hsiu Liang (alvynliang) Summary: Exchange reaction in Benzene system causes two errors Initial Comment: I have observed two bugs when I run P/T depBenzene oxidation system from Dave. One of these is the ZPE and lowest barrier height calculation in ReactionManager.cpp for IrreversibleExchangeReaction. I will fix it asap. The second error is in approximately Line 1204 of ReactionManager.cpp which is inside BartisWidomPhenomenologicalRates(). It seems for some reason the vector index is out of range. ---------------------------------------------------------------------- >Comment By: Chi-Hsiu Liang (alvynliang) Date: 2009-06-10 13:36 Message: KofEsTemp was not populated so the vector is out of range when executing this line sm += assymEigenVec[rxnMatrixLoc+j][nchemIdx+i] * KofEsTemp[j]; ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=894764&aid=2804147&group_id=180832 |
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From: SourceForge.net <no...@so...> - 2009-06-10 13:32:16
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Bugs item #2804147, was opened at 2009-06-10 13:31 Message generated for change (Settings changed) made by alvynliang You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=894764&aid=2804147&group_id=180832 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open >Resolution: Accepted Priority: 5 Private: No Submitted By: Chi-Hsiu Liang (alvynliang) Assigned to: Chi-Hsiu Liang (alvynliang) Summary: Exchange reaction in Benzene system causes two errors Initial Comment: I have observed two bugs when I run P/T depBenzene oxidation system from Dave. One of these is the ZPE and lowest barrier height calculation in ReactionManager.cpp for IrreversibleExchangeReaction. I will fix it asap. The second error is in approximately Line 1204 of ReactionManager.cpp which is inside BartisWidomPhenomenologicalRates(). It seems for some reason the vector index is out of range. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=894764&aid=2804147&group_id=180832 |
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From: SourceForge.net <no...@so...> - 2009-06-10 13:31:47
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Bugs item #2804147, was opened at 2009-06-10 13:31 Message generated for change (Tracker Item Submitted) made by alvynliang You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=894764&aid=2804147&group_id=180832 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Chi-Hsiu Liang (alvynliang) Assigned to: Chi-Hsiu Liang (alvynliang) Summary: Exchange reaction in Benzene system causes two errors Initial Comment: I have observed two bugs when I run P/T depBenzene oxidation system from Dave. One of these is the ZPE and lowest barrier height calculation in ReactionManager.cpp for IrreversibleExchangeReaction. I will fix it asap. The second error is in approximately Line 1204 of ReactionManager.cpp which is inside BartisWidomPhenomenologicalRates(). It seems for some reason the vector index is out of range. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=894764&aid=2804147&group_id=180832 |