![]() ![]() Potential energy diagrammes in latex using pg. Let's update out nwchem input file with the internal coordinates: The format isn't quite right (everything in red needs to go, and the V in blue should be lower case), but we can sort that out:īabel -ixyz ~/methanol.xyz -ogzmat |sed 's/\=//g s/V/v/g s/\://g' |tail -n+6 > methanol.zmat methanol.xyz:īabel -ixyz methanol.xyz -ogzmat #Put Keywords Here, check Charge and Multiplicity. Take the coordinates, and paste them into a file, e.g. ECCE for a geometry optimisation of methanol you'll end up with the following input file: Anyway, you'll understand more after this post, and it isn't important anyway.Ĭalculation using a z matrix (internal coordinates) in nwchem, with a little bit of help from openbabel:Īssuming that you set up a calculation in e.g. This particular error came about because the zmatrix module is case sensitive, and my Variables couldn't be interpreted (it should be variables). This error has not yet been assigned to a category NOR ALPHANUMERIC OR COULD NOT BE MATCHED WITH A VARIABLE. THE 3-D PIECE OF -Z- DATA FOR ATOM = 2 IS NEITHER FLOATING POINT The easiest remedy is to supply the internal coordinates directly, but there honestly aren't too many examples online showing how that's done, and I kept on getting annoying failure messages along the lines of When nwchem PES scans fail to constrain - autoz failure However, if you're doing a PES scan you'll notice that it's not proceeding as intended - the constraints are completely ignored: 511. In most cases, this isn't a cause for any real concern - the computation will continue although I think cartesian coordinates are supposed to be slightly slower. Sometimes that fails, and nwchem defaults to using cartesian coordinates. Normally you don't have to fiddle with zmatrices in nwchem - instead you'd typically supply cartesian coordinates, and nwchem would do autoz to autogenerate internal (z matrix) coordinates. I can get the same calc to run in gaussian though (gaussian has its own issues), but it'd be nice if stuff just.worked. Which is really, really, really annoying since there doesn't seem to be a real fix for it - I've tried everything suggested in. There are insufficient internal variables: expected 95 got 96 But I also get messages about the user generated z matrix, so we'll see whether my input is respected or not. Nwchem still gives errors about autoz in spite of using noautoz. In an ideal world I'd give the actual details, but quite apart from the risk of being scooped, doing so would also make it easier to identify me (not that it's impossible at this point). Not being an expert, to me it seems that there's something fundamentally difficult with the system I'm working on. ![]() Job cpu time: 0 days 22 hours 25 minutes 27.6 seconds.įile lengths (MBytes): RWF= 192 Int= 0 D2E= 0 Chk= 28 Scr= 1 NTrRot= -1 NTRed= 628 NAtoms= 34 NSkip= 532 IsLin=FĮrror termination via Lnk1e in /opt/gaussian/g09/l103.exe at Thu Sep 5 18:17:12 2013. The gaussian run failed after 14 geometry steps during the first PES point. I can now confirm that using your own z matrix still does not constrain the geometry during a PES scan, which was the original impetus for this post: ![]()
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