No idea what's happening there, but you can run ctest with -V to see
the process output for the failing tests.
Dave
On Mon, Feb 8, 2016 at 8:28 AM, David van der Spoel
wrote:
> Hi,
>
> if I compiled OB with -DCMAKE_BUILD_TYPE=Debug on my mac (OSX Mavericks,
> gcc 4.9) many
Congrats, Geoff! It's great news that your tenure has been accepted! :-)
Dave
On Wed, Oct 30, 2013 at 4:10 PM, Geoffrey Hutchison geo...@pitt.edu wrote:
Dear everyone,
My department voted recently to recommend me for tenure here at Pitt.
While this still needs approval from the Dean, it’s
Dr. Tsafack,
I've forward your error message to the openbabel development mailing
list. Perhaps someone there may know what's going on with the shared
pointer classes?
OB devs, he is following the instructions at
http://xtalopt.openmolecules.net/wiki/index.fcgi/wiki/Installation
for building
(Moving this to the openbabel developers list)
Can you provide a full sample file that demonstrates the issue?
Thanks,
Dave
On Mon, Apr 29, 2013 at 2:39 PM, Cohen, Ron rco...@carnegiescience.edu wrote:
It fails when the typeat goes over two lines, as in:
typat 1 1 1 1 1 1
It seems to run OK.
Ron
On Mon, Apr 29, 2013 at 2:41 PM, David Lonie lonieda...@gmail.com wrote:
(Moving this to the openbabel developers list)
Can you provide a full sample file that demonstrates the issue?
Thanks,
Dave
On Mon, Apr 29, 2013 at 2:39 PM, Cohen, Ron rco...@carnegiescience.edu
It seems to run OK.
Ron
On Mon, Apr 29, 2013 at 2:41 PM, David Lonie lonieda...@gmail.com
wrote:
(Moving this to the openbabel developers list)
Can you provide a full sample file that demonstrates the issue?
Thanks,
Dave
On Mon, Apr 29, 2013 at 2:39 PM, Cohen, Ron
rco
On Thu, Feb 28, 2013 at 6:16 PM, Geoffrey Hutchison geo...@pitt.edu wrote:
If you'd like to access and/or write changes, you'll need to use GitHub.
Hurray! What is the workflow for submitting a patch to github? Will the SVN
committers have write access to openbabel/openbabel, or should we fork
On Fri, Mar 1, 2013 at 2:17 AM, David van der Spoel sp...@xray.bmc.uu.sewrote:
So how does one (re)gain access to git other than anonymous
git clone g...@github.com:openbabel/openbabel.git
I'm getting
Permission denied (publickey).
Someone (Geoff, I assume) will need to give you
Hi list,
Is there a way to perceive bonds in a collection of atoms with obabel? I
looked though the documentation, but don't see an explicit operation for
this.
We thought maybe converting cml -- cml might trigger bond perception, but
this doesn't seem to work either. Are there any
On Tue, Feb 12, 2013 at 12:00 PM, Noel O'Boyle baoille...@gmail.com wrote:
Try the xyz format.
That was our next guess, just wanted to make sure that I wasn't overlooking
anything more straightforward.
--
Free Next-Gen
Hi list,
We're in the process of developing Avogadro 2, and I'm currently adding an
interface to perform the obabel minimize operation on a molecule.
My question: Is there a heuristic that can be used to select the best
forcefield for a given molecule? As I understand it:
* Ghemical is good for
On Mon, Feb 4, 2013 at 11:22 AM, David van der Spoel sp...@xray.bmc.uu.se
wrote:
On 2013-02-04 17:18, Geoffrey Hutchison wrote:
* Are there cases where MMFF94s should be preferred to Ghemical?
Everything. The heuristic should be something like MMFF94 if it works,
UFF otherwise. Ghemical is
I'll take a look at the sources and see if I can figure out when they'll
fail, and use GAFF-MMFF94-UFF.
Thanks for the feedback!
Dave
On Mon, Feb 4, 2013 at 1:22 PM, Geoffrey Hutchison
geoff.hutchi...@gmail.com wrote:
Speed? Should make no difference at all. Lennard Jones + Coulomb on
On Tue, May 15, 2012 at 2:02 PM, Igor Filippov [Contr]
filipp...@mail.nih.gov wrote:
(master) $ git checkout -b myNewBranch
(myNewBranch) $ emacs someSourceCode.cpp #edit
(myNewBranch) $ git commit
(myNewBranch) $ git checkout master
(master) $ git merge myNewBranch
One important
On Mon, May 14, 2012 at 3:34 PM, My Th rei4...@gmail.com wrote:
By the way, is a general migration to git still off the table?
I'm OK with this, but I think we'd need a more comprehensive vote.
That is two, how about others? :)
Make that three ;-)
A better question may be, who wants
On Wed, May 9, 2012 at 8:57 AM, Noel O'Boyle baoille...@gmail.com wrote:
On 9 May 2012 13:22, David Lonie david.lo...@kitware.com wrote:
On Wed, May 9, 2012 at 7:42 AM, David Lonie david.lo...@kitware.comwrote:
On Wed, May 9, 2012 at 4:42 AM, Noel O'Boyle baoille...@gmail.comwrote
/openbabel-2.0, so
OPENBABEL2_INCLUDE_DIR is C:/Program Files
(x86)/openbabel/include/openbabel-2.0
OPENBABEL2_LIBRARIES is C:/Program Files (x86)/openbabel/bin/openbabel-2.lib
Dave
- Noel
On 8 May 2012 23:18, David Lonie david.lo...@kitware.com wrote:
On Tue, May 8, 2012 at 2:49 PM, Craig
On Wed, May 9, 2012 at 7:42 AM, David Lonie david.lo...@kitware.com wrote:
On Wed, May 9, 2012 at 4:42 AM, Noel O'Boyle baoille...@gmail.com wrote:
In the OB docs, there's an example C++ program. Can you edit this so that
it reproduces the problem?
I'll give this a try.
Surprisingly, I
Hi all,
I'm setting up a new windows build environment using Windows 7 and MSVC
2010 C++ express, and my application is unable to find some of the symbols
from openbabel, namely etab and obErrorLog:
2 Creating library
C:/src/xtalopt/build/src/xtalopt/Release/xtalopt.lib and object
On Tue, May 8, 2012 at 2:05 PM, Craig James cja...@emolecules.com wrote:
On Tue, May 8, 2012 at 10:04 AM, David Lonie david.lo...@kitware.comwrote:
Hi all,
I'm setting up a new windows build environment using Windows 7 and MSVC
2010 C++ express, and my application is unable to find some
I'm having an issue compiling the latest avogadro, and it looks like an
issue with the new OBConformerSearch class. Can anyone reproduce? This is
with a fresh checkout/build of both avogadro and openbabel.
Linking CXX shared module ../../../lib/forcefieldextension.so
Hi Geoff, List,
I'm working with a student to implement a BFGS minimizer for the
OBForceFields. Do any utilities already exist to test these
minimizers, or is there a test system that anyone can recommend?
My current plan is to grab some structures from the MMFF94 test set,
distort and
Hi Jean,
On Tue, Mar 27, 2012 at 2:58 PM, Jean Brefort
jean.bref...@normalesup.org wrote:
Can someone test attached patch? It fixes the space groups list (adding
variants for groups #1 and #2, accepts unknown groups, and understand
the symmetry operations from the CIF file (they changed the
On Sun, Feb 5, 2012 at 4:28 PM, Chris Morley c.mor...@gaseq.co.uk wrote:
On 05/02/2012 19:16, Ian Kirker wrote:
So, I've been working on a fuller Turbomole format reader (I won't
promise anything, I'm pretty new to proper C++ and it's probably going
to take me a Good While to get to finishing
On Tue, Jan 3, 2012 at 11:09 PM, Geoff Hutchison
ge...@geoffhutchison.net wrote:
On Jan 3, 2012, at 2:45 PM, David Lonie wrote:
beyond the trust radius. I didn't track down which is happening, but
switching to the Newton2Num line-search method fixes the problem for
me (see OBForceField
On Wed, Jan 4, 2012 at 8:47 AM, Noel O'Boyle baoille...@gmail.com wrote:
On 4 January 2012 12:53, David Lonie lonieda...@gmail.com wrote:
On Tue, Jan 3, 2012 at 11:09 PM, Geoff Hutchison
ge...@geoffhutchison.net wrote:
On Jan 3, 2012, at 2:45 PM, David Lonie wrote:
beyond the trust radius. I
On Wed, Jan 4, 2012 at 11:04 AM, Geoffrey Hutchison
ge...@geoffhutchison.net wrote:
On Jan 4, 2012, at 9:19 AM, David Lonie wrote:
If there is an easily parsed / imported / OBConv-ertable database of
structures somewhere, it wouldn't be too difficult to come up with a
test.
I think
On Wed, Jan 4, 2012 at 12:48 PM, Jiahao Chen jia...@mit.edu wrote:
Long email ahead, but here is my implementation of BFGS and L-BFGS in
Python from one of my research code, if anyone is interested in going
down that route:
https://gist.github.com/1561144
This is a good summary of various
Hi Geoff,
Thanks for moving this -- I should check autocompleted mailing list
addresses more closely ;-)
On Tue, Jan 3, 2012 at 11:51 AM, Geoffrey Hutchison
ge...@geoffhutchison.net wrote:
On Jan 3, 2012, at 11:44 AM, David Lonie wrote:
which copies the data in _gradientPtr to _grad1. Trouble
On Tue, Jan 3, 2012 at 12:12 PM, David Lonie lonieda...@gmail.com wrote:
I'm trying to track down a bug somewhere in the forcefields that is
causing this to happen:
C O N J U G A T E G R A D I E N T S
STEPS = 250
STEP n E(n) E(n-1)
1
On Wed, Dec 21, 2011 at 10:16 AM, Marcus D. Hanwell
marcus.hanw...@kitware.com wrote:
The SBIR gives us a couple of years to really engineer the components
needed for cross-platform open chemistry. What we develop will be
released under permissive licenses, such as the 3-clause BSD license,
Hi list,
I'm looking for a way to store a molecular structure and it's
conformers as a string, so I figured I'd look through the support
openbabel formats and try to find a standard one that supports
conformers. Explicit specification of bonds is another requirement
that is causing issues. A
On Tue, Nov 15, 2011 at 5:23 PM, Marcus D. Hanwell
marcus.hanw...@kitware.com wrote:
On Tue, Nov 15, 2011 at 5:12 PM, David Lonie lonieda...@gmail.com wrote:
Hi all,
I'm attempting to build a relocatable avogadro installation, and I'm
having trouble with OpenBabel's plugin handling
Hi list,
In atom.h, there are the following three functions:
//! \return the internal atom index (e.g., inside an OBMol)
unsigned int GetIdx() const { return((int)_idx); }
unsigned int GetIndex() const { return _idx - 1; }
unsigned long GetId() const { return
On Thu, Nov 10, 2011 at 11:51 AM, Geoffrey Hutchison geo...@pitt.edu wrote:
On Nov 10, 2011, at 11:47 AM, My Th wrote:
The idea is to use everywhere zero-based indices in future [1], but the
library is in the state of transition, so there is quite a mess with
this. It's a task assigned to
On Thu, Nov 10, 2011 at 12:13 PM, Chris Morley c.mor...@gaseq.co.uk wrote:
On 10/11/2011 15:35, David Lonie wrote:
The confusion caused by too much choice and the deficiencies in all of
the above mean that MolCore API (the proposed re-writing of the central
part of the toolkit) deserves better
Hi list,
I'm using OBForceFields to perform quick preoptimizations in my code,
and I've noticed that when I try to run multiple preoptimizations
simultaneously using threads, I get random segfaults, usually in
portions of OpenBabel that assign hybridizations to atoms (This
happens during the call
On Fri, Oct 14, 2011 at 12:04 PM, My Th rei4...@gmail.com wrote:
Here is a patch for plugin constructors. It is a bit big because I
decompacted the macros to make them readable, but there is really only
one change - an if statement which checks if the ID is already in the
Map() and only if not
On Wed, Oct 12, 2011 at 6:39 PM, My Th rei4...@gmail.com wrote:
T , 2011-10-12 17:17 -0400, David Lonie rakstīja:
On Wed, Oct 12, 2011 at 4:53 PM, My Th rei4...@gmail.com wrote:
The reason it breaks on making second instance is that you invalidate
plugin map pointers by deleting
Hi list,
I've written a routine that makes a copy of the UFF forcefield with
MakeNewInstance() and caches it in a member variable of the my class.
The function's definition is:
bool MyClass::setupForcefield()
{
QMutexLocker locker (this-m_ffMutex);
// already setup!
if (m_ff !=
On Wed, Oct 12, 2011 at 3:25 PM, David Lonie lonieda...@gmail.com wrote:
Hi list,
I've written a routine that makes a copy of the UFF forcefield with
MakeNewInstance() and caches it in a member variable of the my class.
snip
This works perfectly the first time it is used -- the forcefield
On Wed, Oct 12, 2011 at 4:53 PM, My Th rei4...@gmail.com wrote:
T , 2011-10-12 15:42 -0400, David Lonie rakstīja:
On Wed, Oct 12, 2011 at 3:25 PM, David Lonie lonieda...@gmail.com wrote:
Hi list,
I've written a routine that makes a copy of the UFF forcefield with
MakeNewInstance
On Wed, Oct 5, 2011 at 4:37 PM, Chris Morley c.mor...@gaseq.co.uk wrote:
The recent changes in OBUnitCell constantness mean that the SWIG
bindings do not compile in Visual C++ 9:
1..\..\..\scripts\java\openbabel-java.cpp(2945) : error C2668:
'OpenBabel::OBUnitCell::WrapFractionalCoordinate' :
On Tue, Aug 23, 2011 at 8:26 PM, David Lonie lonieda...@gmail.com wrote:
Hi list,
I'm trying to build openbabel-2.lib using trunk with MSVC 2008.
Leaving BUILD_SHARED on produces openbabel-2.dll without any problem,
but I need the static .lib for avogadro to link against.
I found a bit more
Hi Peter,
On Wed, Jul 6, 2011 at 7:35 PM, Peter Schellenberg
peter.schellenb...@fisica.uminho.pt wrote:
I wonder how Avogadro recognizes double bonds. The concrete problem is
as follows: I loaded gaussian log files (results from DFT geometry
opt.) of molecules with conjugated bonds into
Hi OpenBabel'ers, Avogadro'ers,
On Fri, Nov 5, 2010 at 12:09 PM, David Lonie lonieda...@gmail.com wrote:
On Thu, Nov 4, 2010 at 1:52 PM, Louis Ricard
louis.ric...@polytechnique.edu wrote:
Hi all.
I started testing the Windows installer shortly after David's message.
I was puzzled by absence
On Wed, Oct 13, 2010 at 11:47 AM, Geoffrey Hutchison
ge...@geoffhutchison.net wrote:
I'm getting a segfault on MSVC when I delete a pointer to an
OBForceField (or indeed an OBOp). But this should work okay right?
No. These are static unique objects. We don't delete formats or other plugins
Hi Tim,
I just received this message after pushing a change to trunk. I can't
figure out what would be conflicting -- I made a change to a single
format file, and it seems to be complaining about CMakeList.txt?
Dave
-- Forwarded message --
From: CDash ad...@www.cdash.org
Date:
On Tue, Aug 24, 2010 at 1:51 PM, Noel O'Boyle baoille...@gmail.com wrote:
On 24 August 2010 18:22, David Lonie lonieda...@gmail.com wrote:
On Tue, Aug 24, 2010 at 1:20 PM, Geoffrey Hutchison
ge...@geoffhutchison.net wrote:
This has happened a few times recently -- Is Eigen now an
official
On Wed, Aug 11, 2010 at 11:34 PM, Geoffrey Hutchison
ge...@geoffhutchison.net wrote:
I've always wondered why OBRandom exists -- I would assume that the
built in standard random number generators would be decent on each
platform?
No, that's not true. In fact, the BSD and Mac man pages for
On Wed, Aug 11, 2010 at 7:26 AM, Chris Morley c.mor...@gaseq.co.uk wrote:
Although it has been touched on previously in the mailing lists, I
think we need to clarify what OBMol::_energy contains. It is accessed
in OBMol::SetEnergy(double) and by OBMol::GetEnergy().
Note that
On Fri, Jul 30, 2010 at 7:49 PM, Tim Vandermeersch
tim.vandermeer...@gmail.com wrote:
On Sat, Jul 31, 2010 at 1:40 AM, David Lonie lonieda...@gmail.com wrote:
On Fri, Jul 30, 2010 at 1:06 PM, Geoffrey Hutchison geo...@pitt.edu wrote:
Hans De Winter and Silicos whipped up a 2-page quick
On Wed, Mar 3, 2010 at 4:33 AM, Vincent Favre-Nicolin
vinc...@users.sourceforge.net wrote:
See the attached POSCAR and POTCAR. When opened in Avogadro, the cell
is displayed as shown in the screenshot. The atoms are given in
fractional coordinates -- there should not be any outside the cell! At
On Wed, Mar 3, 2010 at 2:04 PM, Geoffrey Hutchison
ge...@geoffhutchison.net wrote:
Note that this could potentially break programs that use
GetOrthoMatrix and GetFractionalMatrix to convert between cartesian
and fractional coordinates, since the ortho and fractional matrices
may be rotated
On Tue, Mar 2, 2010 at 4:16 PM, Geoffrey Hutchison
ge...@geoffhutchison.net wrote:
Is there some method to this that I'm missing? Would anyone object to
the change I propose?
The main requirement is that you don't remove API. Otherwise, I think we'd
all be happy to see improvements.
Ok -- I
Hi Jonas,
On Mon, Mar 1, 2010 at 2:03 PM, Jonas Baltrusaitis jasiu...@yahoo.com wrote:
I was going to try ORCA and CRYSTAL input/output implementation in OB. What's
your approach when you take new format? How do you begin? What do you look
for and how do you proceed? How do you test it
On Mon, Mar 1, 2010 at 5:00 PM, David Osguthorpe
david.osgutho...@gmail.com wrote:
On Mon, Mar 01, 2010 at 01:33:06PM -0800, Jonas Baltrusaitis wrote:
I second Konstantin. Typical calculations yields values of, say,
-1000.00 Hartrees, in kcal it would be x627.5 which would be
I forgot to reply to all...
On Thu, Jan 14, 2010 at 4:18 PM, Geoffrey Hutchison
ge...@geoffhutchison.net wrote:
The attached gamout file crashes when OB tries to read it.
What version of OB are you using? Trunk?
Yes, though I seem to remember this happening with 2.2.x also.
Dave
Hi Geoff,
On Mon, Nov 30, 2009 at 5:51 PM, Geoffrey Hutchison
ge...@geoffhutchison.net wrote:
I was taking some time to review new classes in the trunk and I wanted to ask
about the electronic transition data (i.e., for UV/Vis spectra or computed
excitation energies). Is there are reason you
Hi list,
I've been using OB in a multithreaded environment for a while, and a
common headache comes from the abundance of singleton classes in OB,
namely for error handling/logging. If two concurrent threads call two
OB functions and the logging functions are accessed at the same time,
the
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