lammps-users Digest, Vol 133, Issue 118

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Today's Topics:

   1. Re: Setting per-atom masses with fix property/atom rmass
      (Joshua Moore)
   2. Re: Setting per-atom masses with fix property/atom rmass
      (Axel Kohlmeyer)
   3. question regarding post-processing for LAMMPS output (Quang Ha)
   4. Re: question regarding post-processing for LAMMPS output
      (Axel Kohlmeyer)
   5. Re: [EXTERNAL] Fwd: Temperature control in fix gcmc with fix
      rigid/nvt/small (Thompson, Aidan)
   6. Problem installing lammps-1Feb14 in Ubuntu 16.04
      (Carlos Azael Alvarez Zambrano)
   7. How can I update LAMMPS via homebrew and git? (Wusheng Zhang)
   8. Re: Problem installing lammps-1Feb14 in Ubuntu 16.04
      (Axel Kohlmeyer)
   9. Re: How can I update LAMMPS via homebrew and git? (Axel Kohlmeyer)
  10. Re: How can I update LAMMPS via homebrew and git? (Wusheng Zhang)
  11. Fwd: Re: Problem installing lammps-1Feb14 in Ubuntu 16.04
      (Carlos Azael Alvarez Zambrano)

----------------------------------------------------------------------

Message: 1
Date: Wed, 28 Jun 2017 12:59:00 -0400
From: Joshua Moore <[email protected]...>
To: Axel Kohlmeyer <[email protected]>
Cc: LAMMPS <[email protected]>
Subject: Re: [lammps-users] Setting per-atom masses with fix
        property/atom rmass
Message-ID: <[email protected]...>
Content-Type: text/plain; charset="us-ascii"

Thanks.

velocity.cpp (if you set velocities) and atom.cpp call check_mass in
atom.cpp which only checks if the per-type masses are set and gives the
error if they are not. It doesn't pass with just per-atom masses set. It
appears the check_mass in atom.cpp is always called so long as init is
called.

Could there be a switch of error checks in atom.cpp and velocity.cpp based
on if the rmass is set? If rmass is set then check that the per-atom masses
are set instead of per-type masses?

However, it appears that the per-type masses aren't used in anything I'm
doing when the per-atom masses are set so seems safe to set per-type masses
to any arbitrary value.

Thanks.

Josh

Sent from my iPhone

>
>
>
>> Hello,
>>
>> When using fix/property rmass to set a per-atom mass, do the per-type
masses still need to be initialized first?
>>
>> For example, from the the manual, with (using full atom_style)
>>
>> fix Isotopes all property/atom rmass ghost yes
>> read_data tip4p-isotopes.data fix Isotopes NULL Isotopes
>>
>> I get "ERROR: Not all per-type masses are set" unless I also set the
per-type masses before using fix property/atom rmass.
>
> you will get that error message depending on certain constructs in other
parts of your input, that you are not showing here.
> not all of the features in LAMMPS support per-atom masses and some that
do, still have checks in place from the time where only per-type masses
were available.
>
> axel.
>
>
>>
>> Thank you.
>>
>> Josh
>>
>>
>> ------------------------------------------------------------
------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> _______________________________________________
>> lammps-users mailing list
>> [email protected]
>> https://lists.sourceforge.net/lists/listinfo/lammps-users
>>
>
>
>
> --
> Dr. Axel Kohlmeyer [email protected] Homepage of Axel Kohlmeyer
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.
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Message: 2
Date: Wed, 28 Jun 2017 13:53:04 -0400
From: Axel Kohlmeyer <[email protected]>
To: Joshua Moore <[email protected]...>
Cc: LAMMPS <[email protected]>
Subject: Re: [lammps-users] Setting per-atom masses with fix
        property/atom rmass
Message-ID:
        <CADTmJ6Ex0+3wsmXtUg+mv9zi2izm7x2FN05Wtuq0NKjHitEWd
[email protected]...>
Content-Type: text/plain; charset="UTF-8"

FYI, i've looked into those cases, and found a straightforward way to
move the test for using per-atom masses inside the per-type mass
check. this should make it into the next LAMMPS patch, to be released
in a week or two.

axel.

>
>
>>
>> Hello,
>>
>> When using fix/property rmass to set a per-atom mass, do the per-type
>> masses still need to be initialized first?
>>
>> For example, from the the manual, with (using full atom_style)
>>
>> fix Isotopes all property/atom rmass ghost yes
>> read_data tip4p-isotopes.data fix Isotopes NULL Isotopes
>>
>>
>> I get "ERROR: Not all per-type masses are set" unless I also set the
>> per-type masses before using fix property/atom rmass.
>
>
> you will get that error message depending on certain constructs in other
> parts of your input, that you are not showing here.
> not all of the features in LAMMPS support per-atom masses and some that
do,
> still have checks in place from the time where only per-type masses were
> available.
>
> axel.
>
>
>>
>>
>> Thank you.
>>
>> Josh
>>
>>
>>
>>
>> ------------------------------------------------------------
------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> _______________________________________________
>> lammps-users mailing list
>> [email protected]
>> https://lists.sourceforge.net/lists/listinfo/lammps-users
>>
>
>
>
> --
> Dr. Axel Kohlmeyer [email protected] Homepage of Axel Kohlmeyer
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.

--
Dr. Axel Kohlmeyer [email protected] Homepage of Axel Kohlmeyer
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.

------------------------------

Message: 3
Date: Wed, 28 Jun 2017 15:44:21 -0400
From: Quang Ha <[email protected]...>
To: LAMMPS Users Mailing List <[email protected]>
Subject: [lammps-users] question regarding post-processing for LAMMPS
        output
Message-ID:
        <[email protected]...
gmail.com>
Content-Type: text/plain; charset="utf-8"

Hi all,

After running the LAMMPS to obtain the output, I can easily view it with
OVITO. However building with USER-VTK doesn't seem to work 100% (I can
revisit it in about an hour or two).

Again, I don't know if this question is right to be posed here, but I want
to visualise the simulated flow through some form of either isosurface or
contour - just to present a more 'continuous' solution instead (I know this
contradicts the motivation of LAMMMPS... sorry to be the traitor...). Which
framework is recommended? Is it vtk output -> Paraview -> some form of
rendering there? I have heard of Blender but would it work as well?

Thanks,
Quang
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Message: 4
Date: Wed, 28 Jun 2017 17:08:21 -0400
From: Axel Kohlmeyer <[email protected]>
To: Quang Ha <[email protected]...>
Cc: LAMMPS Users Mailing List <[email protected]>
Subject: Re: [lammps-users] question regarding post-processing for
        LAMMPS output
Message-ID:
        <CADTmJ6FrzKyifoYY-PpV6T1T2NDLYdoUnvD+b-c=-AH3D2q
[email protected]...>
Content-Type: text/plain; charset="UTF-8"

> Hi all,
>
> After running the LAMMPS to obtain the output, I can easily view it with
> OVITO. However building with USER-VTK doesn't seem to work 100% (I can
> revisit it in about an hour or two).

vtk libraries come in different generations/versions requiring a
different set of libraries to link to.

> Again, I don't know if this question is right to be posed here, but I
want
> to visualise the simulated flow through some form of either isosurface or
> contour - just to present a more 'continuous' solution instead (I know
this
> contradicts the motivation of LAMMMPS... sorry to be the traitor...).
Which
> framework is recommended? Is it vtk output -> Paraview -> some form of
> rendering there? I have heard of Blender but would it work as well?

this is very special requirement, and i am not sure, if that is
actually practical. what you are looking for is a good match for
continuum models, but at the scale of where LAMMPS is typically
operating with particle simulations, you will have very noisy
"density" data unless you do significant spatial and temporal
averaging. since the resulting gridded data, will typically require
much more storage as particle based data, i would recommend looking
into writing some post processing tool.

that said, VMD already has a tool/plugin included (volmap) that can
convert particle data into grids with different rules that can be
rendered as (static) isosurface or saved as (IBM data explorer format)
.dx files and it has a very efficient isosurface renderer (quicksurf)
for generating a simplified particle density isosurface on-the-fly.

if you want to go beyond that, you are definitely in the realm of
ParaView, VisIt and alike. personally, i am quite content with doing
particle based representations, they can be made to be very
informative and good looking visualization.

axel.

>
> Thanks,
> Quang
>
> ------------------------------------------------------------
------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> lammps-users mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/lammps-users
>

--
Dr. Axel Kohlmeyer [email protected] Homepage of Axel Kohlmeyer
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.

------------------------------

Message: 5
Date: Wed, 28 Jun 2017 22:36:39 +0000
From: "Thompson, Aidan" <[email protected]>
To: "[email protected]..." <[email protected]...>
Cc: lammps/lammps LAMMPS Users List
        <[email protected]>
Subject: Re: [lammps-users] [EXTERNAL] Fwd: Temperature control in fix
        gcmc with fix rigid/nvt/small
Message-ID: <[email protected]...>
Content-Type: text/plain; charset="utf-8"

​Hi,
in my personal experience, also following the example in gcmc, I found that
to fix temperature there are two ways:

- define correctly ​

​lattice (in example sc spacing is 5 and l box is 10)
- set co​rrectly velocity: I obtained good performance with 'dist uniform
and loop'

wthat setting are you using?

Al