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ReactionMechanismGenerator / RMG-Java

The Java version of RMG: Reaction Mechanism Generator
http://rmg.sourceforge.net/
MIT License
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QMTP fails on every species and QMTP Library prints all zero values #280

Open shamelmerchant opened 11 years ago

shamelmerchant commented 11 years ago

I tried using hybrid QMTP for my butanol job, I notice two things immediately

1) QMTP fails on all species after trying 36 times. Even on species like benzene, toluene, am I doing something wrong has someone else tested this feature ?

2) QMTP library is printing junk numbers

"InChI=1/C6H6/c1-2-4-6-5-3-1/h1-6H 1000.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 gaussian03 pm3 Calculation"

This job was run on the latest master branch.

nickvandewiele commented 11 years ago

could you provide the commit hash of the "latest" master branch?

shamelmerchant commented 11 years ago

And at the commit with the hash: 4a315df37003d38427622080a77d4b6bba1295cc

On Thu, Nov 29, 2012 at 3:55 PM, nickvandewiele notifications@github.comwrote:

could you provide the commit hash of the "latest" master branch?

— Reply to this email directly or view it on GitHubhttps://github.com/GreenGroup/RMG-Java/issues/280#issuecomment-10865919.

rwest commented 11 years ago

You could try cherry-picking @nyee's latest commits: nyee@57926291fe371f3fffc82ada2d33bfeebac308ae and nyee@93bc6b382000c6c180184bd9e844803a2a0fff86

rwest commented 11 years ago

I have cherry-picked those commits onto GreenGroup/master. That should make it behave better when your QMTP jobs fail. I do not know why all your jobs are failing though. Are your environment variables etc. all set correctly? When you do figure out what it is, please improve the error messages so that it would have been more obvious to you.

nyee commented 11 years ago

The junk numbers are something that I fixed and should be in the latest commit.

I'm not exactly sure why it is failing though. I recall seeing that pm3 was the source for benzene thermo for some of the previous JP10 models, so it must have worked on benzene before.

jwallen commented 11 years ago

The problem was that SYMMETRY.exe was missing. We think that RMG should crash with an error when this happens (like it does when cInChI-1.exe is missing) and are adding an exception with a better error message.

(Aside: I notice that SYMMETRY is GPL code. I'm not sure what that means for us in terms of use of and distribution with RMG.)

(Aside 2: Our link in the documentation to the InChI webpage is no longer valid. The InChI code is LGPL, so we are fine there.)

rwest commented 11 years ago

re: aside 1: From the GNU GPL FAQ

Where's the line between two separate programs, and one program with two parts? This is a legal question, which ultimately judges will decide. We believe that a proper criterion depends both on the mechanism of communication (exec, pipes, rpc, function calls within a shared address space, etc.) and the semantics of the communication (what kinds of information are interchanged). If the modules are included in the same executable file, they are definitely combined in one program. If modules are designed to run linked together in a shared address space, that almost surely means combining them into one program. By contrast, pipes, sockets and command-line arguments are communication mechanisms normally used between two separate programs. So when they are used for communication, the modules normally are separate programs. But if the semantics of the communication are intimate enough, exchanging complex internal data structures, that too could be a basis to consider the two parts as combined into a larger program.

I think it's fair to say that we use the symmetry program, but we are not part of the same program, so I think we're OK. We don't distribute it, anyway - if you run "make symmetry" it just tries to download it.

re: aside 2: Our "make inchi" target still seems to work.