Unable to read CUBE files in ECCE6.4
Just Got Here
5:26:01 PM PDT - Mon, Sep 10th 2012
Hi,
I just installed ECCE 6.4 binary in a SLES11 64-bit system. The installation seems to work fine, and all the pre-requisite packages were found.
Builder seems to run fine.
I can load and visualize a molecular structure from an xyz file, but when I tried to read in a CUBE file using "Import Chemical System", I got an error message: "Unable to parse input data".

With an older (ECCE 6.1 binary) version, I can load the same CUBE file, but none of the menu nor tool buttons for creating or visualizing an isosurface seems to work.

Can ECCE read a CUBE file and generate isosurfaces? The only documentation and example I could find is for an old version:
http://ecce.pnl.gov/docs/manual/Ecce_v3.2.2_Users_Manual.pdf

Thanks,
--Harsono

Gets Around
10:46:17 AM PDT - Tue, Sep 11th 2012
Hi Harsono,

I did see that our release notes for ECCE v3.0 and v3.2 describe Gaussian Cube format files. However, those ECCE versions were about 10 years ago and since then the Calculation Viewer application has been completely reimplemented to be based on wxWidgets and as a shared builder/viewer visualization capability. So, paying any attention to those or what you found I'm sure would cause confusion.

However, I do see that we still have some capability to import cube files (and hopefully we still automatically detect any that are generated from a calculation run under ECCE as well). But, you would not do this by importing it as a chemical system. You would want to use the "Open in New Context..." File menu option. Note when you select this that the file selection dialog shows "Cube" as one of the available file types. Try opening your cube file that way. If it works you will see a "Cube File" property panel. It should list the MOs (isosurfaces) in a scrolling list. You would select one of those and then you can use the drop-down slider to change the isosurface value. There is also a way to combine multiple isosurfaces scaling each of them separately. I honestly didn't recall that we had this capability, but I assume it is useful in some situations or it wouldn't be there.

If it doesn't work for you, then perhaps something has changed in the format of a cube file, although hopefully that wouldn't happen. I'm sure we implemented this originally for Gaussian 98 and to support the cube files that NWChem would create back then. I just tried it with some cube files dating back to 2002 when we first implemented it in the previous ECCE Viewer and it worked for me in the latest ECCE 6.4 as described above.

Gary

Just Got Here
5:44:24 PM PDT - Thu, Sep 13th 2012
This is to summarize what I can find out using ECCE 6.4, with the help of Gary and others (thank you!) I hope it's useful to others exploring the tool...

ECCE 6.4 can read a cube file (generated by G03) using the steps described by Gary (see previous post). To get an isosurface created, one has to first select / click on the name of the header shown on the Cube panel. An isosurface will be generated and displayed. The value on the slider is the logarithm of the value in the cube file. For example, to generate an 0.01 isosurface of from a cube file containing electron density, choose the value "-2". To generate an isosurface for 0.1, choose the value "-1", etc.




Quote:Gary Sep 11th 10:46 am
Hi Harsono,

I did see that our release notes for ECCE v3.0 and v3.2 describe Gaussian Cube format files. However, those ECCE versions were about 10 years ago and since then the Calculation Viewer application has been completely reimplemented to be based on wxWidgets and as a shared builder/viewer visualization capability. So, paying any attention to those or what you found I'm sure would cause confusion.

However, I do see that we still have some capability to import cube files (and hopefully we still automatically detect any that are generated from a calculation run under ECCE as well). But, you would not do this by importing it as a chemical system. You would want to use the "Open in New Context..." File menu option. Note when you select this that the file selection dialog shows "Cube" as one of the available file types. Try opening your cube file that way. If it works you will see a "Cube File" property panel. It should list the MOs (isosurfaces) in a scrolling list. You would select one of those and then you can use the drop-down slider to change the isosurface value. There is also a way to combine multiple isosurfaces scaling each of them separately. I honestly didn't recall that we had this capability, but I assume it is useful in some situations or it wouldn't be there.

If it doesn't work for you, then perhaps something has changed in the format of a cube file, although hopefully that wouldn't happen. I'm sure we implemented this originally for Gaussian 98 and to support the cube files that NWChem would create back then. I just tried it with some cube files dating back to 2002 when we first implemented it in the previous ECCE Viewer and it worked for me in the latest ECCE 6.4 as described above.

Gary


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