Does it improve if you leave out the --log and if you use -O myfile.cml instead?
- Noel On 8 April 2013 20:28, Marcus D. Hanwell <marcus.hanw...@kitware.com> wrote: > Hi, > > We are using obabel to perform geometry optimizations etc on the > command line, and we are hitting a bug that seems to only present > itself on the Mac. If the input and output formats are the same then > the operation fails, for example, > > obabel -icml -ocml --minimize --log --ff UFF > > That is using standard in/out, but it also seems to happen when using > files. This works as expected on Linux and Windows, are we diverging > from expected use too much or is this a bug. This is the same in 2.3.2 > and master, using 10.6.8 and GCC 4.2.1. > > The full output is below, compared with using xyz as the output (we > could of course work around this issue by using different formats). > There is a SMARTS error I just noticed too, but that seems unrelated > to this bug on the Mac. > > $ obabel -icml ethane.cml -ocml --minimize --log --ff UFF > ============================== > *** Open Babel Error in RegisterOptionParam > The number of parameters needed by option "t" in The LPMD file > format. differs from an earlier registration. > ============================== > *** Open Babel Error in SMARTSError > SMARTS Error: > [#6+:1](~N:2)(~N:3)* > ^ > > > A T O M T Y P E S > > IDX TYPE RING > 1 H_ NO > 2 C_3 NO > 3 H_ NO > 4 H_ NO > 5 C_3 NO > 6 H_ NO > 7 H_ NO > 8 H_ NO > > S E T T I N G U P C A L C U L A T I O N S > > SETTING UP BOND CALCULATIONS... > SETTING UP ANGLE CALCULATIONS... > SETTING UP TORSION CALCULATIONS... > SETTING UP OOP CALCULATIONS... > SETTING UP VAN DER WAALS CALCULATIONS... > > C O N J U G A T E G R A D I E N T S > > STEPS = 2500 > > STEP n E(n) E(n-1) > -------------------------------- > 1 2.378 4.699 > 4 1.069 1.069 > CONJUGATE GRADIENTS HAS CONVERGED > 0 molecules converted > > $ obabel -icml ethane.cml -oxyz --minimize --log --ff UFF > ============================== > *** Open Babel Error in RegisterOptionParam > The number of parameters needed by option "t" in The LPMD file > format. differs from an earlier registration. > ============================== > *** Open Babel Error in SMARTSError > SMARTS Error: > [#6+:1](~N:2)(~N:3)* > ^ > > > A T O M T Y P E S > > IDX TYPE RING > 1 H_ NO > 2 C_3 NO > 3 H_ NO > 4 H_ NO > 5 C_3 NO > 6 H_ NO > 7 H_ NO > 8 H_ NO > > S E T T I N G U P C A L C U L A T I O N S > > SETTING UP BOND CALCULATIONS... > SETTING UP ANGLE CALCULATIONS... > SETTING UP TORSION CALCULATIONS... > SETTING UP OOP CALCULATIONS... > SETTING UP VAN DER WAALS CALCULATIONS... > > C O N J U G A T E G R A D I E N T S > > STEPS = 2500 > > STEP n E(n) E(n-1) > -------------------------------- > 1 2.378 4.699 > 4 1.069 1.069 > CONJUGATE GRADIENTS HAS CONVERGED > 8 > Ethane > H 1.17997 -0.00310 1.00769 > C 0.76583 -0.02288 -0.02125 > H 1.16144 0.85024 -0.57962 > H 1.10906 -0.95033 -0.52388 > C -0.76582 0.02291 0.02127 > H -1.16141 -0.85054 0.57913 > H -1.10918 0.95009 0.52435 > H -1.17989 0.00361 -1.00770 > 1 molecule converted > > ------------------------------------------------------------------------------ > Precog is a next-generation analytics platform capable of advanced > analytics on semi-structured data. The platform includes APIs for building > apps and a phenomenal toolset for data science. Developers can use > our toolset for easy data analysis & visualization. Get a free account! > http://www2.precog.com/precogplatform/slashdotnewsletter > _______________________________________________ > OpenBabel-Devel mailing list > OpenBabel-Devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-devel ------------------------------------------------------------------------------ Precog is a next-generation analytics platform capable of advanced analytics on semi-structured data. The platform includes APIs for building apps and a phenomenal toolset for data science. Developers can use our toolset for easy data analysis & visualization. Get a free account! http://www2.precog.com/precogplatform/slashdotnewsletter _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
