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From: Mengjie L. <mj...@mi...> - 2018-12-11 21:02:12
|
Dear RMG users, In an effort to improve communication with people who use or are interested in the Reaction Mechanism Generator software, we have created a new mailing list for occasional announcements related to RMG. These will include announcements about new releases and any workshops we hold, such as the upcoming training in January. If you are receiving this email, that means you may have contacted us directly in the past, have registered an account on the RMG website (rmg.mit.edu), or are subscribed to the old SourceForge mailing list for RMG-Java. - For members of the new mailing list, you can unsubscribe or change your subscription options from the mailing list web page here: http://mailman.mit.edu/mailman/listinfo/rmg-users. You can also request to be removed from the mailing list by emailing me directly. - For members of the old mailing list, we will no longer be sending email to that list in the future. If you would like to continue receiving RMG news, I encourage you to subscribe to the new mailing list via the link above. - If you are unsure which mailing list you are a part of, please email me directly for assistance. Thank you very much for your interest and support of RMG. Please let us know if you have any questions or concerns. Best regards, Max Liu ___________________________ RMG Lead Developer PhD Candidate | Green Group MIT Chemical Engineering |
From: Kehang H. <hk...@mi...> - 2016-09-17 20:47:29
|
Dear RMG Users and Developers, RMG v2.0.0 and RMG-database v2.0.0 have just been released! Instructions of installation from Binary and Source code can be found at http://reactionmechanismgenerator.github.io/ <http://reactionmechanismgenerator.github.io/>. Please let us know how you like the new version. Your feedback helps us improve RMG for all users. Feel free to post issues to our Github issues page at http://www.github.com/ReactionMechanismGenerator/RMG-Py/issues <http://www.github.com/ReactionMechanismGenerator/RMG-Py/issues> or ask RMG developers related questions in our Gitter chatting room <https://gitter.im/ReactionMechanismGenerator/RMG-Py>. The release notes for v2.0.0 are below (also found here <http://reactionmechanismgenerator.github.io/RMG-Py/users/rmg/releaseNotes.html>). RMG-Py v2.0.0 Release Notes Parallelization finally introduced in RMG: Generates reactions during enlarge step in parallel fashion (rmgpy.rmg.react) Enables concurrent computing for QMTP thermochemistry calculations (rmgpy.thermo.thermoengine) Instructions of running RMG parallel mode can be found here for SLURM scheduler <https://github.com/ReactionMechanismGenerator/RMG-Py/wiki/Running-RMG-in-parallel-with-a-SLURM-scheduler> and here for SGE scheduler <https://github.com/ReactionMechanismGenerator/RMG-Py/wiki/Running-RMG-in-parallel-with-a-SGE-scheduler>. Polycyclic thermochemistry estimation improved: Extends group additivity method for polycyclics and estimates polycyclics of any large sizes by a heuristic method (bicyclics decomposition) New tree averaging for kinetics: Fixes previous issue of imcomplete generation of cross-level rate rules Implements Euclidean distance algorithm for the selection of the best rate rules to use in estimateKinetics Streamlines storage of kinetics comments for averaged rules, which can be analyzed by extractSourceFromComments Database entry accessibility tests: Adds entry accessibility tests for future entries (testing.databaseTest) Fixes bugs fluxdiagram generation is now fixed, one can use it to generate short video of fluxdigram evolution mac environment yml file is introduced to make sure smooth RMG-Py installation and jobs on mac fixes failure of checkForExistingSpecies for polyaromatics species fixes execution failure when both pruning and pDep are turned on fixes pDep irreversible reactions fixes issue of valency of Cbf atom by dynamic benzene bond order assignment RMG-database v2.0.0 Release Notes In conjunction with the release of RMG-Py v2.0.0, an updated package for the RMG-database has also been released. This release brings some new additions and fixes: Polycyclic thermochemistry estimation improved: polycyclic database reorganized and more entries added in systematic way (input.thermo.groups.polycyclic) Database entry accessibility tests: Fixes existing inaccessible entries in solvation/statmech/thermo of RMG-database Thank you, Kehang Han (Lead Developer, hk...@mi... <mailto:hk...@mi...>) and the RMG Development Team (rm...@mi... <mailto:rm...@mi...>) |
From: Connie G. <co...@mi...> - 2016-02-01 22:50:49
|
Dear RMG Users and Developers, *RMG v1.0.2* and *RMG-database v1.0.2* have just been released and you can find out how to download and install it here: *http://reactionmechanismgenerator.github.io* <http://reactionmechanismgenerator.github.io/> Some of you who are familiar with the Java version may be wondering why the version number has gone down, and it’s because we have completely rewritten RMG in Python (The Java version on Sourceforge is no longer actively developed). Please let us know how you like the new version. Your feedback helps us improve RMG for all users. You can feel free to post issues to our Github issues page at http://www.github.com/ReactionMechanismGenerator/RMG-Py/issues or email us at rm...@mi.... The release notes for v1.0.2 are below (also found here <http://reactionmechanismgenerator.github.io/RMG-Py/users/rmg/releaseNotes.html#rmg-py-version-1-0-2> ). *RMG-Py v1.0.2 Release Notes* - Windows users can rejoice: RMG is now available in binary format on the Anaconda platform. Building by source is also much easier now through the Anaconda managed python environment for dependencies. See the updated Installation Page <http://reactionmechanismgenerator.github.io/RMG-Py/users/rmg/installation/index.html#installation> for more details - Reaction filtering for speeding up model generation has now been added. It has been shown to speed up model convergence by 7-10x. See more details about how to use it in your RMG job here <http://reactionmechanismgenerator.github.io/RMG-Py/users/rmg/input.html#filterreactions>. Learn more about the theory and algorithm on the Rate-based Model Enlarging Algorithm <http://reactionmechanismgenerator.github.io/RMG-Py/theory/rmg/enlarger.html> page. - The RMG native scripts <http://reactionmechanismgenerator.github.io/RMG-Py/users/rmg/modules/index.html> are now organized under the rmgpy.tools submodule for developer ease and better extensibility in external scripts. - InChI conversion is now more robust for singlets and triplets, and augmented InChIs and InChI keys are now possible with new radical electron, lone pair, and multiplicity flags. - Output HTML for visualizing models are now cleaned up and also more functional, including features to display thermo comments, display enthalpy, entropy, and free energy of reaction, as well as filter reactions by species. You can use this new visualization format either by running a job in RMG v1.0.2 or revisualizing your CHEMKIN file and species dictionary using the visualization web tool <http://rmg.mit.edu/simulate/chemkin> *RMG-database v1.0.2 Release Notes* - New thermo group additivity values for oxitene, oxerene, oexpane, and furan ring groups - Improvements to sulfur chemistry: - Restructuring of radical trees in the kinetics families SubstitutionS and intra_substitutionCS_cyclization - A reaction library for di-tert-butyl sulfide - Improvements for the R_Addition_Multiple_Bond kinetics family through new rate rules for the addition of allyl radical to double bonds in ethene, propene, and butene-like compounds, based on CBS-QB3 estimates from K. Wang, S.M. Villano, A.M. Dean, “Reactions of allylic radicals that impact molecular weight growth kinetics”, *PCCP*, 6255-6273 (2015). - Several new thermodynamic and kinetics libraries for molecules associated with the pyrolysis of cyclopentadiene in the presence of ethene, based off of calculations from A.G. Vandeputte, S.S. Merchant, M.R. Djokic, K.M. Van Geem, G.B. Marin, W. H. Green, “Detailed study of cyclopentadiene pyrolysis in the presence of ethene: realistic pathways from C5H5 to naphthalene” (2016) Thank you, Connie Gao (Lead Developer, co...@mi...) and the RMG Development Team ( rm...@mi...) |
From: Antonio T. <ant...@gm...> - 2013-11-24 18:52:39
|
-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On 11/24/2013 12:04 AM, West, Richard wrote: > > On Nov 23, 2013, at 5:56 PM, Antonio Trande > <ant...@gm...> wrote: > >> Are they used in the same directory of RMG.jar file or they can >> be located into another dir ? > > > I believe they must be in $RMG/bin/ or else they won't be found. > (Where $RMG is your RMG environment variable). The Makefile should > put them in the correct place. You could run the jar from somewhere > else if you wanted, but we usually leave that in $RMG/bin too. > > Richard > Thanks to all for the replies. - -- Antonio Trande mailto: sag...@fe... http://www.fedoraos.worpress.com https://fedoraproject.org/wiki/User:Sagitter GPG Key: D400D6C4 -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.15 (GNU/Linux) Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/ iQIcBAEBAgAGBQJSkkrZAAoJED2vIvfUANbEsUEP/AikfGpkQmYbLSrFLWI8Jo3V hMrPtW4JEhOP7JfDEakYJ6pAlvcdVNzO6Po/6a5cnbzuyFerKiWLAH+Ka/dC8Gen kG12hcKxOMebKHfUqedd17wKVM0iIOpQOUVxjg5te33DnFLY1o5brV1UiXHJuoFK fb2BB+hVBmyhtFYutJQtTxnBLHdth/7666+KITCHy859hnzxD1DH1yX/gIb6KIBM 0F8oa4l3UHpqIfykPPj38lIXzubUkbU6sKf3EEHSjPSXYhIL9bOeRLrDN/XybNsl YM0aeDHUrfWLS+NC7Eof1f7VRhSMCJXGQ0RFV2VcUMSrerQj/OhsF13foH769B/H k3L4bAfUT0fXZ8CfQ2srNi0mECz5bRdDl0fLKfInmsV4cwW3CLjWd8SVnH+2Ff7+ eo1ioxO3rox1S+j0J8KSJvIqeUcpkBbWIu4vNZSZNaZoakRtOpMjaOqbzQcw2nnk DCiYm8ps3QNXDnfGTa/NR+1S2qa0s6+WtTEEiZ0WnM8h1EVo79ThuUyIcYyEzfbh IFCUoIgmT4hhU6bRwB+rY/zk2imAHHkJXTYSNVGdkWmXkl0jsawh5GlhmCvz4TzJ 44sP16NH3ljymePNb7n1a4bIqmie0ybeqEpVCcVlklhiZNRPAzw3S7v1tvkU++AB haRybeFsqPOMdngIyR/0 =N2bO -----END PGP SIGNATURE----- |
From: West, R. <R....@ne...> - 2013-11-23 23:04:20
|
On Nov 23, 2013, at 5:56 PM, Antonio Trande <ant...@gm...> wrote: > Are they used in the same directory of RMG.jar file or they can be > located into another dir ? I believe they must be in $RMG/bin/ or else they won't be found. (Where $RMG is your RMG environment variable). The Makefile should put them in the correct place. You could run the jar from somewhere else if you wanted, but we usually leave that in $RMG/bin too. Richard |
From: Antonio T. <ant...@gm...> - 2013-11-23 22:56:27
|
-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On 11/23/2013 11:40 PM, Detlev Mielczarek wrote: > I'm guessing your surprise is at the ".exe" file suffix, which is > indeed unusual on Linux. We name them that for consistency across > all > platforms; having executable files is not unusual on Linux, they just > aren't usually called "something.exe". Maybe I would have write "these executable *.exe files" to be more clear. :) Are they used in the same directory of RMG.jar file or they can be located into another dir ? -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.15 (GNU/Linux) Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/ iQIcBAEBAgAGBQJSkTKRAAoJED2vIvfUANbEKmwP/0jj/tqMA7g/RNvV+YM9b7Ku ktfbYwIgdRb90ZNSN1SPr8kedF0nU0O36P8lWcwMI7hv5oiv5yWZaFodTFNoal94 MmwKou80lqNl4+YEgpjwTGH9t4QjOLR/w4Q7OweVdL9TGS2NNBTCQyU2MFvVJKcO 7tYmzmtnd7MksFES9zpgbHtmluX5lQpHNjfZHVXqDBvd9sbmVJZXe0Vt0bWzRZoR 08QSirYBmbqxUoQr+MhTbejmlpPADPtVuuvHqWSgM4nuFlsTz2YAW8VEnI+BvmT3 ieA4tgDbT54QhZJKZBxiJr279ogKHCBQQqcJUSdpbqJ9q3TR6QHlBOZdoTgAjK8r Fy8OYTFcObVnLbtk3h2cwvD9rsoZ4ORP6WsRxRdrmdJI++le7aeOi5u1mZSpGPAY Ml5YvixXdz7+Emq56EmsUe+bTFZGKx1Z8tb+Dn8ui4czhnnux8CcQJzcynBrn3Mv X1Tnbf6I1Jvy8c+OAgYaqVy36MYv1vFg3zL0yv0Datrbg6BjMiHFbluNTKen9tSx 7Qy3QwG+NkscJ2ydFs8vSGV7IrYfrxAJ5S5fCMAK8ZAjefpzptjOJwTTOfQ6dOgh pNMVz00RXfOtVz7laEPLty8+zhJRSrvrfRaBmMhm1t1z08S9EjV8WvlczO/oiqRL oDjQ8C6kNQwEeBrKucsj =4eXy -----END PGP SIGNATURE----- |
From: West, R. <R....@ne...> - 2013-11-23 22:37:53
|
Dear Antonio, I'm guessing your surprise is at the ".exe" file suffix, which is indeed unusual on Linux. We name them that for consistency across all platforms; having executable files is not unusual on Linux, they just aren't usually called "something.exe". dasslAUTO.exe is the differential/algebraic equation solver used to run the simulations. frankie.exe is used to fit vibrational frequency estimates to match heat capacity data. GATPfit.exe is used to fit NASA-formatted polynomial expressions to thermodynamic data. fame.exe is used to solve the Master Equation for pressure-dependent reaction networks. These are all written in FORTRAN, and are necessary for RMG to function. (Technically, you may get away without frankie.exe and fame.exe if you do not use pressure-dependence). The Java code (which is compiled into RMG.jar by the Ant script) calls these executables and passes data back and forth. You will find there are also some parts written in Python, in the scripts folder. These are used for the quantum mechanics thermochemistry calculations (optional, but recommended if you have fused ring species). Does this help clarify things? Best, Richard -- Richard H. West, Ph.D. Assistant Professor, Department of Chemical Engineering, Northeastern University, 360 Huntington Ave, Boston, MA 02115 http://neu.edu/comocheng Phone: 617-373-5163 On Nov 23, 2013, at 5:24 PM, Antonio Trande <ant...@gm...> wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > Hi all. > > I'm compiling RMG in Linux (Fedora 64 bit). It seems to me that > 'gfortran' compiler builds just some .exe files, 'ant' builds the > 'RMG.jar' file. > > I'm astounded of these executable files which shouldn't be useful in > Linux. > Am I in wrong ? > What are they ? > > Thanks. > > - -- > > > Antonio Trande > > mailto: sag...@fe... > http://www.fedoraos.worpress.com > https://fedoraproject.org/wiki/User:Sagitter > GPG Key: D400D6C4 > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.15 (GNU/Linux) > Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/ > > iQIcBAEBAgAGBQJSkSssAAoJED2vIvfUANbEMbcP+wWWD72Eszcg7osWFHtp9f1o > JFPe+3M+tKY5xNL0SVu5IElwLDzYcmTfgqMnE6kmd/CAjjyKpSCfSsaGwTf33+/u > 7zfN6L7kDEpPPjHtJF+73ZOS+v8dANiyM7bDWWw2MbmrjKkbV+lVwldq+utnKwLD > RkYNWADeIznEbULnR2NjQ6nXfqfz0lb5K3ISiaVS34DCcsvxjBQWSOyJHZfFlc5O > 3jAxDHu3P1ffDUS3T69Assxf7ahWmRMurg8pt3Gvx3bvBTqTukDpEwLA+LTX/ZBE > JyUbpJ/1D9NiZe/lrinCaWN9FJeA1cim1UaRYSYy+pHTpFLGz1QoX1miIJJoKXMU > wxs5q91hkgrlxt6Am3550PdYXM+aHuRtrKHZLTU/YmVlUTGIgJyFkPZEMz9ezCbY > FJryisgcxXYNPKP9VnS8b3a6nvyMFDjZzdu6vskZPnuwmTQlIGKQa3PIuq4s+S3r > SAps6Qs7yvlLtb4rlL7ZSJOMOke7UXSd8eEK7WnGZ29Efl3ueZDTlOlS6FDqo0lz > +j8rOfXwSKcQexDIn79H8fSXMEEvEInpoOJXU3V2qSiNo3fxYaTxo8z3acFk24o0 > A4jVCIZXvsNIwL+7y6yE9ubejDn94qwZAFK12yOcDRhKtSIzPVq404Ivqo83mA4H > h9TiT1mMa0Yhv4n/3QOj > =8z+0 > -----END PGP SIGNATURE----- > > ------------------------------------------------------------------------------ > Shape the Mobile Experience: Free Subscription > Software experts and developers: Be at the forefront of tech innovation. > Intel(R) Software Adrenaline delivers strategic insight and game-changing > conversations that shape the rapidly evolving mobile landscape. Sign up now. > http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk > _______________________________________________ > RMG-users mailing list > RMG...@li... > https://lists.sourceforge.net/lists/listinfo/rmg-users |
From: Antonio T. <ant...@gm...> - 2013-11-23 22:25:06
|
-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi all. I'm compiling RMG in Linux (Fedora 64 bit). It seems to me that 'gfortran' compiler builds just some .exe files, 'ant' builds the 'RMG.jar' file. I'm astounded of these executable files which shouldn't be useful in Linux. Am I in wrong ? What are they ? Thanks. - -- Antonio Trande mailto: sag...@fe... http://www.fedoraos.worpress.com https://fedoraproject.org/wiki/User:Sagitter GPG Key: D400D6C4 -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.15 (GNU/Linux) Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/ iQIcBAEBAgAGBQJSkSssAAoJED2vIvfUANbEMbcP+wWWD72Eszcg7osWFHtp9f1o JFPe+3M+tKY5xNL0SVu5IElwLDzYcmTfgqMnE6kmd/CAjjyKpSCfSsaGwTf33+/u 7zfN6L7kDEpPPjHtJF+73ZOS+v8dANiyM7bDWWw2MbmrjKkbV+lVwldq+utnKwLD RkYNWADeIznEbULnR2NjQ6nXfqfz0lb5K3ISiaVS34DCcsvxjBQWSOyJHZfFlc5O 3jAxDHu3P1ffDUS3T69Assxf7ahWmRMurg8pt3Gvx3bvBTqTukDpEwLA+LTX/ZBE JyUbpJ/1D9NiZe/lrinCaWN9FJeA1cim1UaRYSYy+pHTpFLGz1QoX1miIJJoKXMU wxs5q91hkgrlxt6Am3550PdYXM+aHuRtrKHZLTU/YmVlUTGIgJyFkPZEMz9ezCbY FJryisgcxXYNPKP9VnS8b3a6nvyMFDjZzdu6vskZPnuwmTQlIGKQa3PIuq4s+S3r SAps6Qs7yvlLtb4rlL7ZSJOMOke7UXSd8eEK7WnGZ29Efl3ueZDTlOlS6FDqo0lz +j8rOfXwSKcQexDIn79H8fSXMEEvEInpoOJXU3V2qSiNo3fxYaTxo8z3acFk24o0 A4jVCIZXvsNIwL+7y6yE9ubejDn94qwZAFK12yOcDRhKtSIzPVq404Ivqo83mA4H h9TiT1mMa0Yhv4n/3QOj =8z+0 -----END PGP SIGNATURE----- |
From: Connie G. <connieg@MIT.EDU> - 2013-05-07 01:10:58
|
Dear RMG Users and Developers, RMG v4.0.1 has just been released and can be downloaded from http://rmg.sourceforge.net in either tarball or Windows executable format. This version is a bug-fix release, primarily addressing a problem with liquid phase solvation energy predictions. Changes since RMG 4.0 include: - Fix a bug predicting thermochemistry of species in solution at temperatures other than 298 K. (Prior versions had an incorrect enthalpy of solvation leading to erroneous temperature dependence, although the Gibbs free energy at 298 K would have been correct). - Solvation parameter predictions improved for several classes of species. - Example input files for using the stand-alone Abraham parameter estimator (for solvation predictions) are now provided. - Seed mechanisms may now contain reactions with up to four products. Please let us know how you like the new version - your feedback helps us improve RMG for all users. Any bugs or feedback should be sent to rm...@mi... Thank you, The RMG Developers rm...@mi... |
From: Connie G. <connieg@MIT.EDU> - 2013-01-23 19:43:13
|
We are proud to announce the release of RMG version 4.0. Changes since the previous version (3.3) include: - Support for sulfur (divalent) has been added, including many new thermo groups and reaction families. - Improved support for automatic MM4 calculations to estimate the thermochemistry of cyclic molecules, including a new hybrid mode for reducing the number of MM4 calculations by first checking an existing database for corrections. - A new reaction family for R group substitution on ethers has been added. - RMG can now be constrained to only run pressure dependence for small molecules. - Some Fortran modules now run as listener subprocesses to reduce the overhead of forking new processes, making RMG jobs run quite a bit faster. - A new method for restarting jobs has been added, via saving of a new condition file on output with all of the final model core species. - Some settings can now be optionally controlled using environment variables, particularly in the setting of output and scratch directories. - Many new rate rules have been added, corrected, or otherwise improved. - Many other bugfixes Please let us know how you like the new version - your feedback helps us improve RMG for all users. Any bugs or feedback should be sent to rm...@mi.... You can download RMG v4.0 at http://rmg.sourceforge.net in either tarball or windows executable format. Happy new year! Thank you, The RMG Developers rm...@mi... |
From: Mandhapati R. <ra...@gm...> - 2012-02-14 20:13:00
|
Hello, I am new to RMG. I am trying to generate a n-butane reaction mechanism using RMG. I did get a mechanism but when I try to match the ignition delay prediction of this mechanism, it does not even ignite. See the condition.txt file below. I guess I am not doing something right. Any help would be appreciated. Database: RMG_database //MaxCarbonNumberPerSpecies: //MaxOxygenNumberPerSpecies: //MaxRadicalNumberPerSpecies: //MaxSulfurNumberPerSpecies: //MaxSiliconNumberPerSpecies: //MaxHeavyAtomPerSpecies: PrimaryThermoLibrary: Name: GRIMech3.0 Location: GRI-Mech3.0 Name: RMG-minimal Location: primaryThermoLibrary END PrimaryTransportLibrary: Name: GRIMech3.0 Location: GRI-Mech3.0 END ForbiddenStructures: END ReadRestart: no WriteRestart: yes TemperatureModel: Constant (K) 800 1000 2000 PressureModel: Constant (atm) 15 20 30 InitialStatus: C4H10 (mol/cm3) 0.4 0.7 1.0 1 C 0 {2,S} 2 C 0 {1,S} {3,S} 3 C 0 {2,S} {4,S} 4 C 0 {3,S} O2 (mol/cm3) 6.5 6.5 6.5 1 O 1 {2,S} 2 O 1 {1,S} END InertGas: N2 (mol/cm3) 24.399 24.399 24.399 Ar (mol/cm3) 0 0 0 END SpectroscopicDataEstimator: off PressureDependence: off //PressureDependence: ModifiedStrongCollision //PDepKineticsModel: Chebyshev FinishController: (1) Goal Conversion: C4H10 0.75 (2) Error Tolerance: 0.1 DynamicSimulator: DASSL //Conversions: AUTO Conversions: AUTOPRUNE TerminationTolerance: 1000 PruningTolerance: 1.0E-18 MinSpeciesForPruning: 1000 MaxEdgeSpeciesAfterPruning: 10000 Atol: 1e-18 Rtol: 1e-8 PrimaryKineticLibrary: //Name: RMG-example //Location: RMG_database/primaryReactionLibrary/Example END ReactionLibrary: END SeedMechanism: //Name: Leeds //Location: RMG_database/SeedMechanisms/combustion_core/version5 //GenerateReactions: yes Name: GRIMech3.0 Location: GRI-Mech3.0 GenerateReactions: yes //Name: Glarborg //Location: RMG_database\SeedMechanisms\Glarborg\C3_light //GenerateReactions: yes END I tried running the mechanism that got generated in Cantera at 1000K, 20 bar and 0.5 equivalence ratio. I do not even see ignition where as the experimental data shows an ignition delay in the range of milliseconds. thanks, Raju. |
From: Richard W. <rwest@MIT.EDU> - 2011-03-09 21:27:49
|
We are pleased to announce the release of RMG version 3.3. This version includes better support for liquid phase systems, and other important improvements and bug fixes. We recommend upgrading for all users of RMG. We have also overhauled the installation instructions. Please let us know how you get on with the new version - your feedback helps us improve RMG for all users. You can find RMG 3.3 at http://rmg.sourceforge.net/ Thank you, The RMG Developers. rm...@mi... |
From: Richard W. <rwest@MIT.EDU> - 2010-08-20 19:56:11
|
Dear Nick, I'm afraid we do not have such unit tests in the RMG Java code. I agree that they would be useful. If you are familiar with JUnit testing and feel comfortable adding the required framework and a few examples, then I'm sure the rest of us can add a few more once we see how it's done. Feel free to fork the project on github - that way we can easily pull in your commits. We're sorry that the code is hard to learn - we have all discovered this the hard way. On the bright side, the Python version of RMG (still under development) has many unit tests! Richard On Aug 20, 2010, at 3:44 PM, Nick Vandewiele wrote: > Hi, > > I was wondering if RMG developers added junit tests to RMG to test specific functionalities of RMG? I haven’t noticed those tests in the distribution on github nor on SF, but maybe you stored them somewhere else? I am asking because I find JUnit tests particularly useful to get to know software libraries like RMG in an efficient way... > > Thanks in advance, > > Nick VANDEWIELE > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by > > Make an app they can't live without > Enter the BlackBerry Developer Challenge > http://p.sf.net/sfu/RIM-dev2dev _______________________________________________ > Rmg-users mailing list > Rmg...@li... > https://lists.sourceforge.net/lists/listinfo/rmg-users |
From: Nick V. <Nick.Vandewiele@UGent.be> - 2010-08-20 19:44:42
|
Hi, I was wondering if RMG developers added junit tests to RMG to test specific functionalities of RMG? I haven't noticed those tests in the distribution on github nor on SF, but maybe you stored them somewhere else? I am asking because I find JUnit tests particularly useful to get to know software libraries like RMG in an efficient way... Thanks in advance, Nick VANDEWIELE |
From: Gregory M. <gmagoon@MIT.EDU> - 2010-07-30 23:39:13
|
Hello manojkumar, Thanks for your interest in RMG. We are currently limited in our ability to handle elements besides H, C, O, S, and Si, partly due to a lack of good rate estimates for species with other elements. Also, RMG is currently designed to handle gas phase chemistry, and to a certain extent, liquid phase chemistry, and it isn't currently designed to handle surface chemistry. There are however, some people in our research group who have done surface chemistry work like this (not using RMG), so if you are interested, we can put you in touch with them. Greg Quoting manojkumar <man...@re...>: > hi, > > I am a new member to RMG group.I need reaction mechanism of nheptane > with nitrogen chemistry on any metal surface or metal oxide > surface.any body can help me > > manojkumar |
From: manojkumar <man...@re...> - 2010-07-29 10:49:22
|
hi, I am a new member to RMG group.I need reaction mechanism of nheptane with nitrogen chemistry on any metal surface or metal oxide surface.any body can help me manojkumar |
From: Michael F. <inf...@gm...> - 2010-04-23 18:35:25
|
Thanks for the reply. I have been busy with other projects but will reply at greater length later. Regards, Michael Flora InfinET LLC On Wed, Apr 21, 2010 at 4:10 PM, Michael Harper <mic...@gm...> wrote: > Hi Michael, > > Thanks for the email. Getting RMG to converge in a reasonable time, > especially for C14 species, is no easy task. Depending on the options > specified, the RMG developers have seen simulations run as long as ~10 days. > Some "tricks" that could be helpful (in no particular order): > 1) Setting the maximum number of carbons (or oxygens, heavy atoms, etc.) in > a species, if you're focusing on the species decomposition (the default > value is 100). > 2) Run RMG for a single temperature / pressure (these are the values in the > TemperatureModel and PressureModel fields). > 3) If you are running RMG w/pressure dependence, consider trying the less > accurate (but faster) ModifiedStrongCollision option. > 4) Relax the error tolerance. NOTE: This parameter is the most important in > determining the size of the final mechanism (and the total runtime). The > error tolerance instructs RMG which species to consider significant (and > therefore explore their pathways). When RMG is determining if a species is > important, it compares the rate of formation of that species to the root > mean square of the (already determined) significant species' flux, > multiplied by the error tolerance. A conservative value is 0.9 > 5) (This is for the RMG-Java version located at github) If you are using a > Seed Mechanism, set the GenerateReactions field to off. > These are some general tricks at getting simulations to run faster. > However, if you send us the condition file you are running (and the version > of RMG you are using), we can hopefully give you some other options to try > for your specific case. > Best Regards, > Mike > Michael Harper > Ph.D. Candidate > Department of Chemical Engineering | MIT > Email: mrh...@mi... > Office: (617) 253-6554 > > > On Wed, Apr 21, 2010 at 9:49 AM, Michael Flora <inf...@gm...> > wrote: >> >> Hi, I am not an RMG expert by any means. I am still on a learning >> curve. So, pardon me if there is an easy answer to this problem. I >> am reacting some relatively simple molecules with 14 or less C atoms. >> RMG does not terminate. I specify reaction times of 10 minutes, 1 >> minute, or 1 second, but it doesn't matter. On my computer (1.6GHZ, >> 2GB RAM) RMG is still running after 1-2 days real time, and I just run >> out of patience. I have tried changing concentrations of reactants >> and also changing the simulator from DASSL to DASPK without success. >> Is there some obvious way to get these runs to terminate in a >> reasonable amount of time or do I just need a supercomputer :) ? >> >> Regards, >> M.R.F. >> >> >> ------------------------------------------------------------------------------ >> _______________________________________________ >> Rmg-users mailing list >> Rmg...@li... >> https://lists.sourceforge.net/lists/listinfo/rmg-users > > |
From: Michael F. <inf...@gm...> - 2010-04-21 13:49:32
|
Hi, I am not an RMG expert by any means. I am still on a learning curve. So, pardon me if there is an easy answer to this problem. I am reacting some relatively simple molecules with 14 or less C atoms. RMG does not terminate. I specify reaction times of 10 minutes, 1 minute, or 1 second, but it doesn't matter. On my computer (1.6GHZ, 2GB RAM) RMG is still running after 1-2 days real time, and I just run out of patience. I have tried changing concentrations of reactants and also changing the simulator from DASSL to DASPK without success. Is there some obvious way to get these runs to terminate in a reasonable amount of time or do I just need a supercomputer :) ? Regards, M.R.F. |
From: Michael F. <inf...@gm...> - 2010-03-03 15:23:01
|
Hey, Michael, thanks for the reply. I believe you have addressed the issue I am having. As I said I am a novice with RMG and am climbing the learning curve. Thanks, M.R. Flora On Wed, Mar 3, 2010 at 8:56 AM, Michael Harper <mic...@gm...> wrote: > Hi Michael, > Thanks for the email. When you say "simple carbon", do you mean carbon atom > (with no hydrogens and 4 radicals)? If so, you can supply RMG with the > following in the input file: > Carbon > 1 C 4 > This would resolve RMG automatically placing hydrogens with the carbon. If > not, please let me know what you were referring to and I will help resolve > the issue. > Best Regards, > Mike > > Begin forwarded message: > >> From: Michael Flora <inf...@gm...> >> Date: 3 March 2010 09:39:33 EST >> To: rmg...@li... >> Subject: [Rmg-users] Hello and a question >> >> Hello, I am a new user of RMG and organic chemistry is not my strong >> suit. I am trying to react simple carbon with various compounds but >> RMG always adds H to my carbons, which I do not want. Is there a way >> around this? >> >> Thanks, >> M.R. Flora >> >> >> ------------------------------------------------------------------------------ >> Download Intel® Parallel Studio Eval >> Try the new software tools for yourself. Speed compiling, find bugs >> proactively, and fine-tune applications for parallel performance. >> See why Intel Parallel Studio got high marks during beta. >> http://p.sf.net/sfu/intel-sw-dev >> _______________________________________________ >> Rmg-users mailing list >> Rmg...@li... >> https://lists.sourceforge.net/lists/listinfo/rmg-users > > > |
From: Michael F. <inf...@gm...> - 2010-03-03 14:39:40
|
Hello, I am a new user of RMG and organic chemistry is not my strong suit. I am trying to react simple carbon with various compounds but RMG always adds H to my carbons, which I do not want. Is there a way around this? Thanks, M.R. Flora |
From: Gregory M. <gmagoon@MIT.EDU> - 2007-05-29 14:56:01
|
----- Forwarded message from her...@ll... ----- Date: Fri, 25 May 2007 14:39:05 -0700 From: Olivier Herbinet <her...@ll...> Reply-To: Olivier Herbinet <her...@ll...> Subject: Re: new question about RMG To: Gregory Magoon <gm...@mi...> Hi Greg I found a little bug in the Chemkin file generated by RMG. Argon appears as "AR" in the species declaration whereas it appears as "Ar" in the other sections of the mechanism . The Chemkin Interpreter doesn't like it because it is case sensitive. Have a nice weekend. Olivier At 11:16 AM 5/7/2007, you wrote: >Hello Olivier, > The model edge contains species whose rates/fluxes are relatively >insignificant. If a species in the model edge is determined to have a >significant flux during the process of mechanism generation, it is >moved to the >model core. In the RMG version on SourceForge, the species in the >model edge are >not sent to a file for output. If you would like to see the contents of the >model edge, we should be able to adjust to code to do so without too >much work. >Another option is to reduce the "Error tolerance" in the condition.txt file; >this should tend to move more of the species from the model edge to the model >core during mechanism generation. > >Thanks, >Greg Magoon > >Quoting Olivier Herbinet <her...@ll...>: > >>Hi Greg. >> >>While using RMG I noticed in the output file that there are two >>kinds of models in RMG: >>1/ the model edge >>2/ the model core >>It seems to me that the model core is a part of the model edge >>since it has less reactions and species. >>When I generate a mechanism I would be interested by seeing the >>model edge. But I can't find the corresponding file. >>Do you know where to find it? >>Thank you for your help. >> >>Olivier ----- End forwarded message ----- |
From: Gregory M. <gmagoon@MIT.EDU> - 2007-05-07 18:17:23
|
Hello Olivier, The model edge contains species whose rates/fluxes are relatively insignificant. If a species in the model edge is determined to have a significant flux during the process of mechanism generation, it is moved to the model core. In the RMG version on SourceForge, the species in the model edge are not sent to a file for output. If you would like to see the contents of the model edge, we should be able to adjust to code to do so without too much work. Another option is to reduce the "Error tolerance" in the condition.txt file; this should tend to move more of the species from the model edge to the model core during mechanism generation. Thanks, Greg Magoon Quoting Olivier Herbinet <her...@ll...>: > Hi Greg. > > While using RMG I noticed in the output file that there are two kinds > of models in RMG: > 1/ the model edge > 2/ the model core > It seems to me that the model core is a part of the model edge since > it has less reactions and species. > When I generate a mechanism I would be interested by seeing the model > edge. But I can't find the corresponding file. > Do you know where to find it? > Thank you for your help. > > Olivier > |
From: Gregory M. <gmagoon@MIT.EDU> - 2007-04-24 18:39:28
|
Hi Olivier, See the following instructions and the attached files for a fix for the molecule size limitation issue you encountered in RMG: ----- Forwarded message from sandeeps@MIT.EDU ----- Date: Tue, 24 Apr 2007 14:15:32 -0400 From: Sandeep Sharma <sandeeps@MIT.EDU> Reply-To: Sandeep Sharma <sandeeps@MIT.EDU> Subject: chemgreen.java and chemgreen.class To: Gregory Magoon <gm...@mi...> Just replace the chemgreen.java and chemgreen.class in the directory $RMG/software/RMG/jing/chem with the new files in this folder and it should allow you to generate species with upto 30 carbon atoms. sandeep. ----- End forwarded message ----- Let me know if you have any further questions, comments, or problems. Greg Quoting Olivier Herbinet <her...@ll...>: > Hi Greg. > > I tried to generate models for the oxidation of methyl esters. > I obtained results (RMG works perfectly now) but It seems that the > number of atoms in the reactants is limited. > I found a maximum of 8 for carbon atoms. > I would be interested by knowing the limitations of the software > (maybe there is paper dealing with that). > Thank you very much for you help for the installation of the software > (your explanations were very clear and I learned a lot about unix > commands thanks to you). > > Olivier > > > At 12:40 PM 4/17/2007, you wrote: >> Hi Olivier, >> I have attached a "condition.txt" file. If this works (whereas your >> original >> condition file does not work) you can send the one that doesn't work >> to me, and >> I can take a look at it to see why it isn't working. If the attached >> test file >> doesn't work, please let me know, and I will try to figure out the problem. >> >> Greg >> >> Quoting Olivier Herbinet <her...@ll...>: >> >>> Hi Greg. >>> >>> It works now. >>> But I have a new issue : "can't find database" >>> Maybe you can send me a "condition.txt" file to do a test if you have one. >>> Thank you. >>> >>> Olivier >>> >>> >>> At 11:42 AM 4/17/2007, you wrote: >>>> Hi Olivier, >>>> I would suggest you try the following: >>>> Instead of beginning the command-line call for RMG with "java >>>> ...", replace >>>> "java" with the directory of the new version of Java (with >>>> /bin/java at the >>>> end); the rest of the line can be the same. >>>> >>>> If this works, we may be able to adjust the ordering of the path >>>> variable to >>>> cause the new version of Java to be called by default with "java". >>>> (That way >>>> you won't have to include the entire directory path every time you >>>> want to call >>>> RMG.) >>>> >>>> Greg >>>> >>>> Quoting Olivier Herbinet <her...@ll...>: >>>> >>>> > Hi Greg. >>>> > >>>> > Here is what I got: >>>> > >>>> > yana4{herbinet}21: which java >>>> > /usr/bin/java >>>> > >>>> > This is the location of the "old" java version. >>>> > >>>> > Olivier >>>> > >>>> > At 11:03 AM 4/17/2007, you wrote: >>>> > Hi Olivier, >>>> > Try typing "which java" to see which version of Java it is >>>> > referencing. Please >>>> > let me know what you find out. >>>> > >>>> > Greg >>>> > >>>> > Quoting Olivier Herbinet <her...@ll...>: >>>> > >>>> > Hi Greg. >>>> > >>>> > I performed the installation of the Java Platform but I still get a >>>> > similar error message: >>>> > >>>> > yana4{herbinet}99: java -Xmx500m -classpath >>>> > /g/g92/herbinet/RMG/RMG_2_00/software/RMG RMG condition.txt > output >>>> > & >>>> > The java class could not be loaded. >>>> > java.lang.UnsupportedClassVersionError: (RMG) bad major version at >>>> > offset=6 >>>> > >>>> > If you have an idea why it doesn't work, let me know (maybe I have to >>>> > create a link to specify where the software is installed). >>>> > Thank you for your help. >>>> > >>>> > Olivier. >>>> > >>>> > P.S.: feel free to forward our correspondance. >>>> > >>>> > At 06:33 PM 4/16/2007, you wrote: >>>> > Hi Olivier, >>>> > Good job getting Steps 4 and 5 to work. I can understand your >>>> > difficulty with >>>> > the Java versions, as the multitude of options can be confusing. As I >>>> > understand it, there are two main options: JRE (Java Runtime >>>> > Environment) or >>>> > JDK (Java (Software) Development Kit). Basically, the JRE allows you >>>> > to run >>>> > Java applications, while JDK provides additional Java development >>>> > capabilities >>>> > (compiling, etc.); the JDK also includes the JRE components for >>>> > running Java >>>> > applications. Unless you plan on writing or modifying Java code, JRE >>>> > should be >>>> > adequate. >>>> > Another potential point of confusion is the version numbering: for >>>> > instance, >>>> > Java 5 and Java 1.5 are the same, while Java 6 and Java 1.6 are also >>>> > the same. >>>> > In my experience, the newest version of RMG will not work with Java >>>> > 5/1.5, but >>>> > will work with Java 6/1.6. >>>> > So to make a long story short, I would recommend downloading JRE 6. >>>> > It is >>>> > available at http://java.sun.com/javase/downloads/index.jsp[1[1]] >>>> > under >>>> > "Java Runtime >>>> > Environment (JRE) 6u1" (a little more than halfway down the page). >>>> > Let me know >>>> > if you need any further assistance with this. >>>> > As an aside, would you mind if I forwarded some of our >>>> > correspondence to the >>>> > RMG users mailing list (hosted and archived on SourceForge.net) so >>>> > that others >>>> > with similar problems can benefit? >>>> > >>>> > Greg >>>> > >>>> > Quoting Olivier Herbinet <her...@ll...>: >>>> > >>>> > Hi Greg. >>>> > >>>> > I have good news. >>>> > We have a Fortran 90 compiler on our machine (the list of the >>>> > available compilers was not updated...). The command is "pathf90". I >>>> > was able to complete the steps 4 and 5 of the installation process. >>>> > So now the software is installed. >>>> > >>>> > I have a new problem. It seems that the version of java is not the >>>> > good one. >>>> > Can you tell me what version is necessary to run RMG? I looked on the >>>> > website of Sun but there are many available kits. I don't know which >>>> > one is the good one. >>>> > Thank you for your help. >>>> > >>>> > Olivier >>>> > >>>> > Here is the error message I got this afternoon: >>>> > >>>> > yana4{herbinet}78: java -Xmx500m -classpath >>>> > /g/g92/herbinet/RMG/RMG_2_00/software/RMG RMG condition.txt > output >>>> > & >>>> > [1] 18101 >>>> > yana4{herbinet}79: The java class could not be loaded. >>>> > java.lang.UnsupportedClassVersionError: (RMG) bad major version at >>>> > offset=6 >>>> > >>>> > Links: >>>> > ------ >>>> > [1] http://java.sun.com/javase/downloads/index.jsp[2] >>>> > >>>> > >>>> > >>>> > Links: >>>> > ------ >>>> > [1] http://java.sun.com/javase/downloads/index.jsp%5B1 >>>> > [2] http://java.sun.com/javase/downloads/index.jsp >>>> > >>> >> >> >> >> > > |
From: Gregory M. <gmagoon@MIT.EDU> - 2007-04-18 02:21:22
|
----- Forwarded message from gm...@mi... ----- Date: Tue, 17 Apr 2007 19:22:14 -0400 From: Gregory Magoon <gm...@mi...> Reply-To: Gregory Magoon <gm...@mi...> Subject: Re: Reaction Mechanism Generator (RMG) To: Olivier Herbinet <her...@ll...> Hi Olivier, Regarding the issue with the limited number of carbon atoms, it appears that this is an unintented limitation that ended up making its way into the distribution on the web. I have talked to the lead developer and he says it should be relatively easy to fix. He will remove the unintended limitation and we will send you a replacement file with instructions (I don't think you will have to reinstall or recompile anything, as it will probably just be a replacement of one of the RMG Java files.) By the way, thank you also for your help with bringing your problems with the installation and use of RMG to our attention. Your experience will help us improve the software so others will not experience some of the problems you encountered. Greg Quoting Olivier Herbinet <her...@ll...>: > Hi Greg. > > I tried to generate models for the oxidation of methyl esters. > I obtained results (RMG works perfectly now) but It seems that the > number of atoms in the reactants is limited. > I found a maximum of 8 for carbon atoms. > I would be interested by knowing the limitations of the software > (maybe there is paper dealing with that). > Thank you very much for you help for the installation of the software > (your explanations were very clear and I learned a lot about unix > commands thanks to you). > > Olivier > > > At 12:40 PM 4/17/2007, you wrote: >> Hi Olivier, >> I have attached a "condition.txt" file. If this works (whereas your >> original >> condition file does not work) you can send the one that doesn't work >> to me, and >> I can take a look at it to see why it isn't working. If the attached >> test file >> doesn't work, please let me know, and I will try to figure out the problem. >> >> Greg >> >> Quoting Olivier Herbinet <her...@ll...>: >> >>> Hi Greg. >>> >>> It works now. >>> But I have a new issue : "can't find database" >>> Maybe you can send me a "condition.txt" file to do a test if you have one. >>> Thank you. >>> >>> Olivier >>> >>> >>> At 11:42 AM 4/17/2007, you wrote: >>>> Hi Olivier, >>>> I would suggest you try the following: >>>> Instead of beginning the command-line call for RMG with "java >>>> ...", replace >>>> "java" with the directory of the new version of Java (with >>>> /bin/java at the >>>> end); the rest of the line can be the same. >>>> >>>> If this works, we may be able to adjust the ordering of the path >>>> variable to >>>> cause the new version of Java to be called by default with "java". >>>> (That way >>>> you won't have to include the entire directory path every time you >>>> want to call >>>> RMG.) >>>> >>>> Greg >>>> >>>> Quoting Olivier Herbinet <her...@ll...>: >>>> >>>> > Hi Greg. >>>> > >>>> > Here is what I got: >>>> > >>>> > yana4{herbinet}21: which java >>>> > /usr/bin/java >>>> > >>>> > This is the location of the "old" java version. >>>> > >>>> > Olivier >>>> > >>>> > At 11:03 AM 4/17/2007, you wrote: >>>> > Hi Olivier, >>>> > Try typing "which java" to see which version of Java it is >>>> > referencing. Please >>>> > let me know what you find out. >>>> > >>>> > Greg >>>> > >>>> > Quoting Olivier Herbinet <her...@ll...>: >>>> > >>>> > Hi Greg. >>>> > >>>> > I performed the installation of the Java Platform but I still get a >>>> > similar error message: >>>> > >>>> > yana4{herbinet}99: java -Xmx500m -classpath >>>> > /g/g92/herbinet/RMG/RMG_2_00/software/RMG RMG condition.txt > output >>>> > & >>>> > The java class could not be loaded. >>>> > java.lang.UnsupportedClassVersionError: (RMG) bad major version at >>>> > offset=6 >>>> > >>>> > If you have an idea why it doesn't work, let me know (maybe I have to >>>> > create a link to specify where the software is installed). >>>> > Thank you for your help. >>>> > >>>> > Olivier. >>>> > >>>> > P.S.: feel free to forward our correspondance. >>>> > >>>> > At 06:33 PM 4/16/2007, you wrote: >>>> > Hi Olivier, >>>> > Good job getting Steps 4 and 5 to work. I can understand your >>>> > difficulty with >>>> > the Java versions, as the multitude of options can be confusing. As I >>>> > understand it, there are two main options: JRE (Java Runtime >>>> > Environment) or >>>> > JDK (Java (Software) Development Kit). Basically, the JRE allows you >>>> > to run >>>> > Java applications, while JDK provides additional Java development >>>> > capabilities >>>> > (compiling, etc.); the JDK also includes the JRE components for >>>> > running Java >>>> > applications. Unless you plan on writing or modifying Java code, JRE >>>> > should be >>>> > adequate. >>>> > Another potential point of confusion is the version numbering: for >>>> > instance, >>>> > Java 5 and Java 1.5 are the same, while Java 6 and Java 1.6 are also >>>> > the same. >>>> > In my experience, the newest version of RMG will not work with Java >>>> > 5/1.5, but >>>> > will work with Java 6/1.6. >>>> > So to make a long story short, I would recommend downloading JRE 6. >>>> > It is >>>> > available at http://java.sun.com/javase/downloads/index.jsp[1[1]] >>>> > under >>>> > "Java Runtime >>>> > Environment (JRE) 6u1" (a little more than halfway down the page). >>>> > Let me know >>>> > if you need any further assistance with this. >>>> > As an aside, would you mind if I forwarded some of our >>>> > correspondence to the >>>> > RMG users mailing list (hosted and archived on SourceForge.net) so >>>> > that others >>>> > with similar problems can benefit? >>>> > >>>> > Greg >>>> > >>>> > Quoting Olivier Herbinet <her...@ll...>: >>>> > >>>> > Hi Greg. >>>> > >>>> > I have good news. >>>> > We have a Fortran 90 compiler on our machine (the list of the >>>> > available compilers was not updated...). The command is "pathf90". I >>>> > was able to complete the steps 4 and 5 of the installation process. >>>> > So now the software is installed. >>>> > >>>> > I have a new problem. It seems that the version of java is not the >>>> > good one. >>>> > Can you tell me what version is necessary to run RMG? I looked on the >>>> > website of Sun but there are many available kits. I don't know which >>>> > one is the good one. >>>> > Thank you for your help. >>>> > >>>> > Olivier >>>> > >>>> > Here is the error message I got this afternoon: >>>> > >>>> > yana4{herbinet}78: java -Xmx500m -classpath >>>> > /g/g92/herbinet/RMG/RMG_2_00/software/RMG RMG condition.txt > output >>>> > & >>>> > [1] 18101 >>>> > yana4{herbinet}79: The java class could not be loaded. >>>> > java.lang.UnsupportedClassVersionError: (RMG) bad major version at >>>> > offset=6 >>>> > >>>> > Links: >>>> > ------ >>>> > [1] http://java.sun.com/javase/downloads/index.jsp[2] >>>> > >>>> > >>>> > >>>> > Links: >>>> > ------ >>>> > [1] http://java.sun.com/javase/downloads/index.jsp%5B1 >>>> > [2] http://java.sun.com/javase/downloads/index.jsp >>>> > >>> >> >> >> >> > > ----- End forwarded message ----- |
From: Gregory M. <gmagoon@MIT.EDU> - 2007-04-18 02:19:01
|
----- Forwarded message from her...@ll... ----- Date: Tue, 17 Apr 2007 15:29:35 -0700 From: Olivier Herbinet <her...@ll...> Reply-To: Olivier Herbinet <her...@ll...> Subject: Re: Reaction Mechanism Generator (RMG) To: Gregory Magoon <gm...@mi...> Hi Greg. I tried to generate models for the oxidation of methyl esters. I obtained results (RMG works perfectly now) but It seems that the number of atoms in the reactants is limited. I found a maximum of 8 for carbon atoms. I would be interested by knowing the limitations of the software (maybe there is paper dealing with that). Thank you very much for you help for the installation of the software (your explanations were very clear and I learned a lot about unix commands thanks to you). Olivier At 12:40 PM 4/17/2007, you wrote: >Hi Olivier, > I have attached a "condition.txt" file. If this works (whereas your original >condition file does not work) you can send the one that doesn't work >to me, and >I can take a look at it to see why it isn't working. If the attached test file >doesn't work, please let me know, and I will try to figure out the problem. > >Greg > >Quoting Olivier Herbinet <her...@ll...>: > >>Hi Greg. >> >>It works now. >>But I have a new issue : "can't find database" >>Maybe you can send me a "condition.txt" file to do a test if you have one. >>Thank you. >> >>Olivier >> >> >>At 11:42 AM 4/17/2007, you wrote: >>>Hi Olivier, >>>I would suggest you try the following: >>> Instead of beginning the command-line call for RMG with "java >>> ...", replace >>>"java" with the directory of the new version of Java (with /bin/java at the >>>end); the rest of the line can be the same. >>> >>>If this works, we may be able to adjust the ordering of the path variable to >>>cause the new version of Java to be called by default with "java". (That way >>>you won't have to include the entire directory path every time you >>>want to call >>>RMG.) >>> >>>Greg >>> >>>Quoting Olivier Herbinet <her...@ll...>: >>> >>> > Hi Greg. >>> > >>> > Here is what I got: >>> > >>> > yana4{herbinet}21: which java >>> > /usr/bin/java >>> > >>> > This is the location of the "old" java version. >>> > >>> > Olivier >>> > >>> > At 11:03 AM 4/17/2007, you wrote: >>> > Hi Olivier, >>> > Try typing "which java" to see which version of Java it is >>> > referencing. Please >>> > let me know what you find out. >>> > >>> > Greg >>> > >>> > Quoting Olivier Herbinet <her...@ll...>: >>> > >>> > Hi Greg. >>> > >>> > I performed the installation of the Java Platform but I still get a >>> > similar error message: >>> > >>> > yana4{herbinet}99: java -Xmx500m -classpath >>> > /g/g92/herbinet/RMG/RMG_2_00/software/RMG RMG condition.txt > output >>> > & >>> > The java class could not be loaded. >>> > java.lang.UnsupportedClassVersionError: (RMG) bad major version at >>> > offset=6 >>> > >>> > If you have an idea why it doesn't work, let me know (maybe I have to >>> > create a link to specify where the software is installed). >>> > Thank you for your help. >>> > >>> > Olivier. >>> > >>> > P.S.: feel free to forward our correspondance. >>> > >>> > At 06:33 PM 4/16/2007, you wrote: >>> > Hi Olivier, >>> > Good job getting Steps 4 and 5 to work. I can understand your >>> > difficulty with >>> > the Java versions, as the multitude of options can be confusing. As I >>> > understand it, there are two main options: JRE (Java Runtime >>> > Environment) or >>> > JDK (Java (Software) Development Kit). Basically, the JRE allows you >>> > to run >>> > Java applications, while JDK provides additional Java development >>> > capabilities >>> > (compiling, etc.); the JDK also includes the JRE components for >>> > running Java >>> > applications. Unless you plan on writing or modifying Java code, JRE >>> > should be >>> > adequate. >>> > Another potential point of confusion is the version numbering: for >>> > instance, >>> > Java 5 and Java 1.5 are the same, while Java 6 and Java 1.6 are also >>> > the same. >>> > In my experience, the newest version of RMG will not work with Java >>> > 5/1.5, but >>> > will work with Java 6/1.6. >>> > So to make a long story short, I would recommend downloading JRE 6. >>> > It is >>> > available at http://java.sun.com/javase/downloads/index.jsp[1[1]] >>> > under >>> > "Java Runtime >>> > Environment (JRE) 6u1" (a little more than halfway down the page). >>> > Let me know >>> > if you need any further assistance with this. >>> > As an aside, would you mind if I forwarded some of our >>> > correspondence to the >>> > RMG users mailing list (hosted and archived on SourceForge.net) so >>> > that others >>> > with similar problems can benefit? >>> > >>> > Greg >>> > >>> > Quoting Olivier Herbinet <her...@ll...>: >>> > >>> > Hi Greg. >>> > >>> > I have good news. >>> > We have a Fortran 90 compiler on our machine (the list of the >>> > available compilers was not updated...). The command is "pathf90". I >>> > was able to complete the steps 4 and 5 of the installation process. >>> > So now the software is installed. >>> > >>> > I have a new problem. It seems that the version of java is not the >>> > good one. >>> > Can you tell me what version is necessary to run RMG? I looked on the >>> > website of Sun but there are many available kits. I don't know which >>> > one is the good one. >>> > Thank you for your help. >>> > >>> > Olivier >>> > >>> > Here is the error message I got this afternoon: >>> > >>> > yana4{herbinet}78: java -Xmx500m -classpath >>> > /g/g92/herbinet/RMG/RMG_2_00/software/RMG RMG condition.txt > output >>> > & >>> > [1] 18101 >>> > yana4{herbinet}79: The java class could not be loaded. >>> > java.lang.UnsupportedClassVersionError: (RMG) bad major version at >>> > offset=6 >>> > >>> > Links: >>> > ------ >>> > [1] http://java.sun.com/javase/downloads/index.jsp[2] >>> > >>> > >>> > >>> > Links: >>> > ------ >>> > [1] http://java.sun.com/javase/downloads/index.jsp%5B1 >>> > [2] http://java.sun.com/javase/downloads/index.jsp >>> > >> > > > > ----- End forwarded message ----- |