VMD-L Mailing List
From: Chang, Christopher (Christopher.Chang_at_nrel.gov)
Date: Fri Feb 19 2021 - 13:35:02 CST
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Thanks John, I appreciate your time having a look at this. I sent you the link off-list.
Cheers; Chris
On 2/19/21, 1:58 AM, "owner-vmd-l_at_ks.uiuc.edu on behalf of John Stone" <owner-vmd-l_at_ks.uiuc.edu on behalf of johns_at_ks.uiuc.edu> wrote:
CAUTION: This email originated from outside of NREL. Do not click links or open attachments unless you recognize the sender and know the content is safe.
Chris,
If you can provide the Molden file(s) that are misbehaving, that would
be tremendously helpful. If you can post file(s) on Google Drive, Box, or
similar, that would be ideal.
Best regards,
John Stone
vmd_at_ks.uiuc.edu
On Tue, Feb 16, 2021 at 10:53:56PM +0000, Chang, Christopher wrote:
> Hi,
>
>
>
> I have a Molden-format file of orbitals generated by PySCF.
>
> Based on this file:
> [1]https://urldefense.com/v3/__https://gcc02.safelinks.protection.outlook.com/?url=https*3A*2F*2Fwww.ks.uiuc.edu*2FTraining*2FTutorials*2Fvmd-qmvis*2Fqmvis-tutorial.pdf&data=04*7C01*7CChristopher.Chang*40nrel.gov*7C2edbda8e04e54acb365a08d8d4b4933e*7Ca0f29d7e28cd4f5484427885aee7c080*7C0*7C0*7C637493219330284704*7CUnknown*7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0*3D*7C1000&sdata=h91HqqL5JGKx2Lsln*2Fks2544l0Bol1S9YcSfzSS4fak*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJSUl!!DZ3fjg!tVd0g51xZAXDmKtL_nW0E63astMEZ4MmP72EimrXJt5Ne4as-r7FE9M_MY6LTduTeA$ ,
> it sounds like VMD should be able to generate the volume data to plot from
> the data in the Molden file.
>
> I'm on Mac OSX 10.15, and just installed VMD 1.9.4a51 rev 9. Does this
> build support orbital visualization? When I create the Orbital
> Representation, a lot of the input widgets (OrbList, Isovalue, Draw, Show,
> Size, Grid Spacing) are grayed out. If I change the upper value of Range,
> the Isovalue changes accordingly (but stays grayed out), but I never see
> any surface plot. The atoms pop up when I load the file, so I am getting
> that far, but I could imagine that the Molden file generated by PySCF is
> not quite right. Happy to send out-of-band (as I understand it, the list
> doesn't handle attachments well?).
>
>
>
> Thanks; Chris
>
>
>
> --
> Christopher Chang
> Computational Scientist / Computational Science Center
> National Renewable Energy Laboratory (NREL)
> 15013 Denver West Parkway | Golden, CO 80401
> 303-275-3751 | M: 720-219-7696
> [2]christopher.chang_at_nrel.gov | [3]nrel.gov
>
>
>
>
>
> References
>
> Visible links
> 1. https://urldefense.com/v3/__https://gcc02.safelinks.protection.outlook.com/?url=https*3A*2F*2Fwww.ks.uiuc.edu*2FTraining*2FTutorials*2Fvmd-qmvis*2Fqmvis-tutorial.pdf&data=04*7C01*7CChristopher.Chang*40nrel.gov*7C2edbda8e04e54acb365a08d8d4b4933e*7Ca0f29d7e28cd4f5484427885aee7c080*7C0*7C0*7C637493219330284704*7CUnknown*7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0*3D*7C1000&sdata=h91HqqL5JGKx2Lsln*2Fks2544l0Bol1S9YcSfzSS4fak*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJSUl!!DZ3fjg!tVd0g51xZAXDmKtL_nW0E63astMEZ4MmP72EimrXJt5Ne4as-r7FE9M_MY6LTduTeA$
> 2. mailto:christopher.chang_at_nrel.gov
> 3. https://urldefense.com/v3/__https://gcc02.safelinks.protection.outlook.com/?url=https*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2F*2Fwww.nrel.gov*2Fresearch*2Fstaff*2Fchristopher-chang.html__*3B!!DZ3fjg!sNQVEbCGQY1l_KaxhuHwy17EFnpJYRdefnEgwvee_H4WVmZSKSinwcMORNub-0p2Pw*24&data=04*7C01*7CChristopher.Chang*40nrel.gov*7C2edbda8e04e54acb365a08d8d4b4933e*7Ca0f29d7e28cd4f5484427885aee7c080*7C0*7C0*7C637493219330284704*7CUnknown*7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0*3D*7C1000&sdata=0npoC77TLLwS8PYfDci988N24jiJX3WvYz5ImFmYh0M*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSU!!DZ3fjg!tVd0g51xZAXDmKtL_nW0E63astMEZ4MmP72EimrXJt5Ne4as-r7FE9M_MY6ioqMT7w$
--
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
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https://urldefense.com/v3/__https://gcc02.safelinks.protection.outlook.com/?url=http*3A*2F*2Fwww.ks.uiuc.edu*2FResearch*2Fvmd*2F&data=04*7C01*7CChristopher.Chang*40nrel.gov*7C2edbda8e04e54acb365a08d8d4b4933e*7Ca0f29d7e28cd4f5484427885aee7c080*7C0*7C0*7C637493219330284704*7CUnknown*7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0*3D*7C1000&sdata=1fM1YnTo*2BviqU7TGyqWlDm8pTShyl03xG2swMyKI94s*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJSU!!DZ3fjg!tVd0g51xZAXDmKtL_nW0E63astMEZ4MmP72EimrXJt5Ne4as-r7FE9M_MY62K5r7IA$
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