VMD-L Mailing List

From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Sat Mar 30 2019 - 01:50:26 CDT

Hey John,

  I am putting those files together and should be able to send them sometime next week. Thanks for looking at this! In the mean-time, I am also looking into TeraChem because of GPU acceleration. Is there anything like orcaviewer for TeraChem in VMD? I could just use the script I found to get the HOMO and LUMO orbital number. Just curious on the work that's being done with NAMD/VMD and TeraChem since ORCA doesn't have plans yet to implement GPU usage.

Kelly L. McGuire

PhD Candidate

Biophysics

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602

________________________________
From: John Stone <johns_at_ks.uiuc.edu>
Sent: Thursday, March 28, 2019 8:51 AM
To: McGuire, Kelly
Cc: Vermaas, Joshua; vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: Re: VMD OrcaPlugin Bug

Kelly,
  If you can send me both kinds of files, we should be able to make
the ORCA plugin tolerant of these minor variations in the output format.
The misbehavior you've seen is caused by bugs/limitations in the implementation
of the ORCA plugin that need to be fixed. Since the original author doesn't
have time to fix his code, we're trying to fix it ex post facto.

Not being an ORCA expert, it is helpful to me to have as many samples of
ORCA output to work with as possible, so if you can provide all of the inputs
that cause trouble, that'd be great!

Best,
  John Stone
  johns_at_ks.uiuc.edu

On Thu, Mar 21, 2019 at 10:34:38PM +0000, McGuire, Kelly wrote:
> Found the problem. Here is my input:
> !RI BP86 OPT def2-SVP def2/J NOSOSCF CPCM(Water) Grid5 NoFinalGrid EnGrad
> NormalSCF printbasis
> %output PrintLevel Mini Print[ P_Mulliken ] 1 Print[P_AtCharges_M] 1 end
> %output Print[ P_Basis ] 2 Print[ P_MOs ] 1 end
> %scf
> maxiter 2000
> shift shift 0.1 erroff 0 end
> damp fac 0.80 erroff 0.0001 end
> end
> Notice that I have printbasis in the input line and I have the output
> command (2nd line) with another print command. I think this was
> corrupting my output. After deleting printbasis from the input line, I
> can now open the ORCA output in VMD.
>
> Kelly L. McGuire
>
> PhD Candidate
>
> Biophysics
>
> Department of Physiology and Developmental Biology
>
> Brigham Young University
>
> LSB 3050
>
> Provo, UT 84602
>
> --------------------------------------------------------------------------
>
> From: Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
> Sent: Thursday, March 21, 2019 3:41 PM
> To: McGuire, Kelly; vmd-l_at_ks.uiuc.edu
> Subject: RE: VMD OrcaPlugin Bug
>
> Oof. This isn't nessicarily a memory leak, but could just be memory being
> accessed before it is allocated. In any event, the stack trace seems to
> indicate that the offending code/input is somewhere in the close_orca_read
> function in the plugins/molfile_plugin/src directory. Its a new plugin, so
> I suspect that the range of attempted input didn't consider your input
> format.
>
> -Josh
>
>
>
> On 2019-03-21 14:10:50-06:00 owner-vmd-l_at_ks.uiuc.edu wrote:
>
> Sometimes, the console prints this out also:
> terminate called after throwing an instance of 'std::bad_alloc'
> what(): std::bad_alloc
> Abort
> So, it seems like a memory leak? The ORCA output is only 420 KB..--_000_BYAPR01MB47440992727983CC7C8EE570FF5B0BYAPR01MB4744prod_--