From NWChem
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| 4:57:00 PM PDT - Thu, May 31st 2012 |
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Gary,
thanks for all that information and help!
I have to admit that I've been somewhat lax in reading the documentation. To some extent I blame the presence of somewhat outdated information on the EMSL site, but mostly it's a real oversight from my part and I will amend this in the future.
In particular the main node-sub node hop part is very interesting since it'd be much easier to set up for non-technical users. Luckily, I'm about to help another research group set up ECCE management of their cluster so will have the opportunity to explore that in more detail -- I'll post my experience on the blog and will link here once it's up.
EDIT: Here's how to use node hopping [blog http://verahill.blogspot.com.au/2012/06/ecce-and-inaccessible-cluster-nodes.html]. The example shows how to access a node on a cluster directly without SGE, but modifying it for the remote site example that precipitated my first set of questions is just as easy.
Which brings me to a somewhat related item:
I understand that ECCE is going full open source this summer, which sounds like a great thing, in particular if the community picks it up and become active contributors. I also understand that there hasn't been adequate funding (if any) for maintaining the documentation of ECCE for many years, and I'd suspect that this has been a bit of a hurdle in terms of adoption. Certainly this won't change. However, has any thought been given to the possibility of creating a wiki-type documentation for ECCE? The general documentation of NWChem on this site is halfways there, but editing isn't open to forum members. I'm sure there's a lot of people like myself who run into problems, find a solution and would like to share it with future/other users. Creating a post on a forum isn't quite the same thing, since you'd primarily do that if you have a question rather than a solution. I also acknowledge that policing posts can potentially become a real problem very quickly if the restrictions are too lax.
Finally, what's the preferred way of communicating minor bugs at the moment? Or is everything on hold until the open source transition? Two things that come to mind are:
- In the ECCE NWChem editor, if you look at the Theory overview (just what's listed in the overview i.e. not clicking on Details) choosing a DFT method doesn't change "SCF Max Iterations" to "DFT Max iterations", even though this is what you actually set when you click on Details/SCF Max Iterations -- i.e. there's a bit mislabelling going on. Secondly, there should be a separate field for SCF maxiter when doing DFT since 30 cycles often isn't enough for reasonably large, inorganic species. It's easily compensated for by editing the input file, and I suspect (wildly guessing) that editing the codereg/*.py files may solve this.
- If you're setting up an MD simulation: if (in the viewer/builder) you draw the backbone of the molecule first and then add the protons by hand AMBER will sort out the atom types automatically. If you hit "Add H" the H's are inserted between the backbone molecule in the atoms list i.e. instead of
1 C 0 0 0
2 C 0 1 0
3 H 0 -1 0
4 H 0 20
you get
1 C 0 0 0
2 H 0 -1 0
3 C 0 1 0
4 H 0 20
and AMBER doesn't know what to do half the time in terms of assigning atom types (I've had the problem with oxygen atoms in particular). I'm not saying that automatically assigning atomtypes is a safe thing to do, but it's an observation.
I apologise for all the unrelated questions above -- but I didn't feel they warranted separate threads.
Anyway, again thank you for all the help!
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Edited On 5:59:50 PM PDT - Fri, Jun 1st 2012 by Ohlincha
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