VMD-L Mailing List

From: Caro Miguel (miguel.caro_at_aalto.fi)
Date: Tue Apr 28 2015 - 11:05:05 CDT

Dear Axel,

Thanks very much. I have VASP files but I guess it should be more or less straightforward to do the conversion.

Thanks again,
Miguel

Sent from my Windows Phone
________________________________
From: Axel Kohlmeyer
Sent: 4/28/2015 6:41 PM
To: Ryan McGreevy
Cc: Caro Miguel; Vmd l
Subject: Re: vmd-l: Setting up a truncation cutoff fro volumetric data

On Tue, Apr 28, 2015 at 11:06 AM, Ryan McGreevy
<ryanmcgreevy_at_ks.uiuc.edu> wrote:
>
> Miguel, you can truncate the density around your structure by using the
> "volmap mask" command in VMD to create a binary mask, then multiply that
> mask by your density using "volutil -mult".

i don't think that that will reduce the file size and/or storage
requirements (on the contrary).
a long time ago i wrote a utility that can perform such grid cutting
operations on gaussian style cube files.
i am attaching the (C) source code. it can do some additional
processing and trimming as well.
of course, if your grids are in a different format, you will need to
change the parts related to reading the data.

axel.

>
> On Tue, Apr 28, 2015 at 4:23 AM Miguel Caro <miguel.caro_at_aalto.fi> wrote:
>>
>> Dear all,
>>
>> I am working with charge density isosurfaces and have observed that for
>> the cell size and grid spacing I'm dealing with these become memory
>> intensive.
>>
>> I use big cells in my DFT calculations to prevent interactions with
>> periodic replicas of my molecule. This means that the cell region where the
>> wave functions are significantly different from zero is much smaller than
>> the overall cell size. I was wondering if, in order to lower the amount of
>> memory needed, I can somehow truncate the region in space where the
>> volumetric data is represented to some region around my molecule, for
>> instance by defining a spherical cutoff around some position in space.
>>
>> Many thanks,
>> Miguel
>>
>> --
>> Dr. Miguel Caro
>> Postdoctoral researcher
>> Department of Electrical Engineering and Automation,
>> and COMP Centre of Excellence in Computational Nanoscience
>> Aalto University, Finland
>> Personal email: mcaroba_at_gmail.com
>> Work: miguel.caro_at_aalto.fi
>> Website: http://mcaroba.dyndns.org 

--
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.