> Hi Miguel, > > Echoing the input deck is indeed an option in NWChem (it is called > echo, and can be seen in the input deck itself). I was wondering > whether the 'argument' would be specific enough to pick up the nwchem > output file.
Yes. Look for the phrase " argument 1" (space argument space space 1) at the beginning of the line. > NWChem has another problem, I think, in that you can very easily do all > kinds of things in a single input file. I haven't figured out how the > go about trying to unravel which pieces one should pick. OK > I have a question, similar to Nicholas Vervelle about how to possibly > contribute to Jmol. I am not very familiar with the CVS system and > worry that what I write may not necessarily be acceptable by other > people. I understand that it allows one to go back to a previous > version and get rid of bad stuff I may have added, but my unfamiliarity > with it makes me worried about messing things up. Which is why I passed > my modification to you so you can act as a gatekeeper, which does mean > more work for you. Sorry :-). So far I only dealt with a single file, > but if I were to make modifications to the ModelResolver and > ModelReader too, it may become trickier. Sending enhancements through me is fine until everyone is comfortable. You are right that CVS allows us to roll back in case of problems. But it is sometimes painful and it is always a waste of time. > Part of the problem is also that I am not completely sure of the > direction that Jmol goes with dealing with multiple structures, > vibrations and other meta information for a particular nuclear > arrangement. We still need to think these things through and get them resolved. Multiple models may mean different things, depending upon the context. For example, there is generally no way to distinguish between a multi-frame animation and different vibrational frequencies. > That was the reason I tried looking at the CML format, > hoping that it would allow me to define the information in a very > hierarchical fashion by encapsulating molecular structures (i.e., the > vibration, with the symmetry, energy, transition moment etc) and > optimization steps as a different set of structures within a molecular > structure (the final optimized geometry, which has its energy, > symmetry, orbital energies, dipole moment, quadrupole moment and all > kinds of other things). By allowing a list of those, one could handle a > run where a particular run does a scan over a nuclear coordinate (e.g. > a changing bond distance) and have each geometry optimization as a set > of structures associated with the final geometry for each of the steps > in the scan (and possibly also a frequency analysis for each step, if > one calculated that too). I can't see from the current Readers how that > may be done, and I haven't been able to figure that out from the > adapter either. (A lot of code to look through and try to understand > :-). It is important to understand that the functionality of the core JmolViewer is quite separate from the specific file format Readers. The JmolViewer reads all of its molecular model data through the ModelAdapter API. Therefore, if you need to add something *new*, then it must first be added to the ModelAdapter. Any change of this type demands thought and coordination. Look at the org/jmol/api/ModelAdapter.java code and see if the functionality you want is in there. Then let's talk ... > About the filename extension, do you think I should give it a try to do > a 'pre-resolving' based on an extension? No. At this point it would be best for you to look for ' argument 1' Miguel ------------------------------------------------------- This SF.net email is sponsored by: IT Product Guide on ITManagersJournal Use IT products in your business? Tell us what you think of them. Give us Your Opinions, Get Free ThinkGeek Gift Certificates! Click to find out more http://productguide.itmanagersjournal.com/guidepromo.tmpl _______________________________________________ Jmol-developers mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-developers
