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Re: [lammps-users] lammps-users Digest, Vol 133, Issue 118


From: alberto <voodoo.bender@...24...>
Date: Thu, 29 Jun 2017 12:07:54 +0200



2017-06-29 2:46 GMT+02:00 <lammps-users-request@lists.sourceforge.net>:
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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 <jdmoore@...4292...2...>
To: Axel Kohlmeyer <akohlmey@...1125.....>
Cc: LAMMPS <lammps-users@...396...sourceforge.net>
Subject: Re: [lammps-users] Setting per-atom masses with fix
        property/atom rmass
Message-ID: <D2995185-6C09-4AE3-8282-56F90E6DB8DD@...1442...>
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

> On Jun 28, 2017, at 6:09 AM, Axel Kohlmeyer <akohlmey@...24...> wrote:
>
>
>
>> On Tue, Jun 27, 2017 at 9:16 PM, Joshua Moore <jdmoore@...1442...> wrote:
>> 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
>> lammps-users@...396...sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/lammps-users
>>
>
>
>
> --
> Dr. Axel Kohlmeyer  akohlmey@...24...  http://goo.gl/1wk0
> 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 <akohlmey@...43...4...>
To: Joshua Moore <jdmoore@...2175.....>
Cc: LAMMPS <lammps-users@...396...sourceforge.net>
Subject: Re: [lammps-users] Setting per-atom masses with fix
        property/atom rmass
Message-ID:
        <CADTmJ6Ex0+3wsmXtUg+mv9zi2izm7x2FN05Wtuq0NKjHitEWdw@...25...>
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.

On Wed, Jun 28, 2017 at 6:09 AM, Axel Kohlmeyer <akohlmey@...24...> wrote:
>
>
> On Tue, Jun 27, 2017 at 9:16 PM, Joshua Moore <jdmoore@...1442...> wrote:
>>
>> 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
>> lammps-users@...396...sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/lammps-users
>>
>
>
>
> --
> Dr. Axel Kohlmeyer  akohlmey@...24...  http://goo.gl/1wk0
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.



--
Dr. Axel Kohlmeyer  akohlmey@...43...4...  http://goo.gl/1wk0
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 <quang.t.ha.20@...24...>
To: LAMMPS Users Mailing List <lammps-users@...396...sourceforge.net>
Subject: [lammps-users] question regarding post-processing for LAMMPS
        output
Message-ID:
        <CAGfE9+PGYmZ1mf=9VLqJFWiEGAkkC5jZpSg0jsWW+VLmJFtNUg@...3019...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 <akohlmey@...43...4...>
To: Quang Ha <quang.t.ha.20@...33....24...>
Cc: LAMMPS Users Mailing List <lammps-users@...396...sourceforge.net>
Subject: Re: [lammps-users] question regarding post-processing for
        LAMMPS output
Message-ID:
        <CADTmJ6FrzKyifoYY-PpV6T1T2NDLYdoUnvD+b-c=-AH3D2qvdw@...25...>
Content-Type: text/plain; charset="UTF-8"

On Wed, Jun 28, 2017 at 3:44 PM, Quang Ha <quang.t.ha.20@...24...> wrote:
> 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
> lammps-users@...12...396...sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/lammps-users
>



--
Dr. Axel Kohlmeyer  akohlmey@...43...4...  http://goo.gl/1wk0
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" <athomps@...3...>
To: "hyzlvxg@...516..." <hyzlvxg@...516...>
Cc: lammps/lammps LAMMPS Users List
        <lammps-users@...396...sourceforge.net>
Subject: Re: [lammps-users] [EXTERNAL] Fwd: Temperature control in fix
        gcmc with fix rigid/nvt/small
Message-ID: <6D1DDE39-7003-43D8-8690-86F7110902C5@...3...>
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


 

There were some recent improvements made to fix gcmc that might resolve the issues you describe here. If not, please post a *small* example that demonstrates the problem.

Aidan


---------- Forwarded message ----------
From: Youzhi Hao <hyzlvxg@...516...>
Date: Thu, Jun 22, 2017 at 9:36 PM
Subject: Re: [lammps-users] Temperature control in fix gcmc with fix rigid/nvt/small
To: Mohammad Rafat Sadat <msadat@...33....3324...>
Cc: LAMMPS Users Mailing List <lammps-users@...396...sourceforge.net>

Hi Mohammad,
   This is update information for the question as I mentioned before as:
?2) Unfix gcmc after some time which the system was filled with some methane, then let the fix rigid/nvt/small do the thermostat alone.
However, the temperature was still not thermostat correctly, i.e. the temperature seemed not affected by this fix.?
?
Recently, I tried a different way to tackle the problem described above:
When unfix gcmc, also unfix ?rigid/nvt/small, then create a new fix rigid/nvt/small.
By doing this, the system is well thermostated. It seems that fix rigid/nvt/small functions well when fully detached from fix gcmc.
?
However, this question still troubles me:
Fix gcmc combined with fix rigid/nvt/small does not thermostat the system as user-specified temperature T.
This leads the system temperature differs greatly from the ideal gas reservoir?s temperature, which is not a uvt ensemble.
?
?
From: Youzhi Hao [mailto:hyzlvxg@...3639...51...cn]
Sent: Monday, June 19, 2017 8:20 PM
To: 'Mohammad Rafat Sadat' <msadat@...3324...>

Cc: 'LAMMPS Users Mailing List' <lammps-users@...396...sourceforge.net>
Subject: Re: [lammps-users] Temperature control in fix gcmc with fix rigid/nvt/small
?
Hi Mohammad,
???????? I?ve tested in three simulation scenarios:
1)????? Using fix gcmc to fill the clay structure with methane, combined with fix rigid/nvt/small.? During this process, the system temperature was not well controlled.
Specially, the system temperature ?was always much higher than the specified temperature, because the large amount of continuous filling of methane molecules.
2)????? Unfix gcmc after some time which the system was filled with some methane, then let the fix rigid/nvt/small do the thermostat alone.
However, the temperature was still not thermostat correctly, i.e. the temperature seemed not affected by this fix.
3)????? Then let?s just start with a new simulation, with a methane pre-filled simulation system, by using fix rigid/nvt/small, then the temperature was finely thermostat!
As you can see, this indeed may be related to the fix gcmc command, but I cannot figure out the reason, could someone take a look at this?
?
regards,
Youzhi
?
From: Mohammad Rafat Sadat [mailto:msadat@...6897...edu]
Sent: Monday, June 19, 2017 6:00 PM
To: Youzhi Hao <hyzlvxg@...516...>
Cc: LAMMPS Users Mailing List <lammps-users@...396...sourceforge.net>
Subject: Re: [lammps-users] Temperature control in fix gcmc with fix rigid/nvt/small
?
Hi Youzhi,
?
I also observed similar phenomena for my water adsorption onto silicate systems where the temperature is not controlled as speciefied in gcmc command. However, I went ahead with the simulation and equilibrated the system separately once the final configuration was achieved from the gcmc run. Not really sure if this is to be expected from gcmc. So I look forward for any other user's comments on this. Thanks!
?
?


Mohammad Rafat Sadat
Graduate Assistant?(PhD?candidate)
Department of Civil Engineering and Engineering Mechanics,
University of Arizona,
PO Box 210072 ? 1209 E. Second Street, Room 207A, Tucson, AZ 85721
?
On Mon, Jun 19, 2017 at 1:27 AM, Youzhi Hao <hyzlvxg@...516...> wrote:
hi,
I?m trying to do gcmc simulation of rigid CH4 molecules adsorption isotherms in clay minerals
by using fix gcmc with fix rigid/nvt/small.
The coulomb potential was calculated by PPPM.
The fix rigid/nvt/small was combined with fix_modify dynamic/dof yes
and fix_modify temp as the LAMMPS Manuals says.
?
However, as the simulation going on (after a long time), the CH4 molecules were just kept adding to the system,
leading the pressure far higher than the pressure specified in fix gcmc command.
Also, the system temperature continues increasing up, higher than the specified temperature.
The fix rigid/nvt/small command seems did not thermostat well.
So, what?s the reason lying beneath this unusual phenomenon?
?
Part of my input file is :
variable temp? equal ?363.15
variable press? equal ?100.00
variable fug_coeff equal 0.934
molecule ?ch4 ?mol.ch4.txt? #full atom methane molecule
compute Temp_methane methane temp/com
compute_modify Temp_methane dynamic/dof yes
fix? mrsnvt? methane ?rigid/nvt/small ?molecule ?temp ${temp} ${temp} 100.0? mol ch4
fix_modify ?mrsnvt? dynamic/dof ?yes
fix_modify ?mrsnvt? temp ?Temp_methane
fix? 1? methane ?gcmc? 1000? 1000 500 0 2949499 ${temp} -0.28 0.5 mol ch4? &
??????maxangle 180 rigid mrsnvt pressure ${press} ?fugacity_coeff ${ fug_coeff } full_energy
run 5000000
?
Best regards.
Youzhi Hao
?

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?

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

Message: 6
Date: Wed, 28 Jun 2017 19:28:55 -0300
From: Carlos Azael Alvarez Zambrano <calvarez@...6950...>
To: lammps-users@...429...96...sourceforge.net
Subject: [lammps-users] Problem installing lammps-1Feb14 in Ubuntu
        16.04
Message-ID:
        <CAMGrhr_SKp_GoEmnzevWYVgTXB_A9VGYDe2U0MJysQ-=DjeqxQ@...3019...gmail.com>
Content-Type: text/plain; charset="utf-8"

Dear LAMMPS users,

I am a new user in lammps and I am trying to install a previous version,
lammps-1Feb14, on my computer. It uses Ubuntu 16.04 LTS, 64-bit. I have
tried to create a make file, in accordance with lammps documentation (
http://lammps.sandia.gov/doc/Manual.html), but I din not to get to work it.
Can someone help me with this issue? Any suggestions would be welcome.
Thanks in advance.

Regards,

--

*Carlos A. Alvarez Z.*
Ph.D. Student
School of Mechanical Engineering
University of Campinas - UNICAMP
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Message: 7
Date: Wed, 28 Jun 2017 19:08:54 -0400
From: Wusheng Zhang <minky.k.jiang@...24...>
To: LAMMPS - post questions <lammps-users@...396...sourceforge.net>
Subject: [lammps-users] How can I update LAMMPS via homebrew and git?
Message-ID:
        <CADZEWxzdkr-M5VEiRh6eTxuG=oHNfjOjVx2hZ_+Z+JLBNz-95Q@...36.....3019...gmail.com>
Content-Type: text/plain; charset="utf-8"

Dear LAMMPS users,

I installed LAMMPS via homebrew on MacOS system on Aug 2016, and now I
intend to update it for using functions like pair_style python. I know this
seems like not a good question here, but I tried to search update
lammps homebrew on google but got nothing useful. So do you have any
suggestions on updating latest stable version of LAMMPS?

Besides, I install LAMMPS via homebrew because I want to have a stable and
updated LAMMPS. I also "git clone" LAMMPS from github - named it as "LAMMPS
for test", because I intend to modify some source files like MAX_BODY. I
know I can save my modified source files separately, and push them back
after git clone the newest LAMMPS. But is there any easy way to update my
"LAMMPS for test"?

Thank you very much for paying attention to such a basic question.

Best regards,
zjgbz
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Message: 8
Date: Wed, 28 Jun 2017 19:57:59 -0400
From: Axel Kohlmeyer <akohlmey@...43...4...>
To: Carlos Azael Alvarez Zambrano <calvarez@...6950...>
Cc: LAMMPS Users Mailing List <lammps-users@...396...sourceforge.net>
Subject: Re: [lammps-users] Problem installing lammps-1Feb14 in Ubuntu
        16.04
Message-ID:
        <CADTmJ6H2hbBwoRNpzvJF9ze4rz15G9QKPuLMe2jMh8rAPtLsvw@...3019...gmail.com>
Content-Type: text/plain; charset="UTF-8"

On Wed, Jun 28, 2017 at 6:28 PM, Carlos Azael Alvarez Zambrano
<calvarez@...6950...> wrote:
> Dear LAMMPS users,
>
> I am a new user in lammps and I am trying to install a previous version,
> lammps-1Feb14, on my computer. It uses Ubuntu 16.04 LTS, 64-bit. I have
> tried to create a make file, in accordance with lammps documentation
> (http://lammps.sandia.gov/doc/Manual.html), but I din not to get to work it.
> Can someone help me with this issue? Any suggestions would be welcome.

the online version of the manual always reflects the latest
development version of LAMMPS.
if you are installing an old version (which i strongly advise against,
and where you are not likely to get much help from this list) you need
to consult the manual that *matches* your version. things keep
changing and improving in LAMMPS all the time.

axel.

> Thanks in advance.
>
> Regards,
>
> --
> Carlos A. Alvarez Z.
> Ph.D. Student
> School of Mechanical Engineering
> University of Campinas - UNICAMP
>
>
>
>
>
> ------------------------------------------------------------------------------
> 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
> lammps-users@...12...396...sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/lammps-users
>



--
Dr. Axel Kohlmeyer  akohlmey@...43...4...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.



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

Message: 9
Date: Wed, 28 Jun 2017 20:06:49 -0400
From: Axel Kohlmeyer <akohlmey@...43...4...>
To: Wusheng Zhang <minky.k.jiang@...24...>
Cc: LAMMPS - post questions <lammps-users@...396...sourceforge.net>
Subject: Re: [lammps-users] How can I update LAMMPS via homebrew and
        git?
Message-ID:
        <CADTmJ6Eq1NN97A0bN0f3gXAEamMjM2MeksOaVuKkQ4m5OO1y-A@...3019...gmail.com>
Content-Type: text/plain; charset="UTF-8"

On Wed, Jun 28, 2017 at 7:08 PM, Wusheng Zhang <minky.k.jiang@...24...> wrote:
> Dear LAMMPS users,
>
> I installed LAMMPS via homebrew on MacOS system on Aug 2016, and now I
> intend to update it for using functions like pair_style python. I know this
> seems like not a good question here, but I tried to search update lammps
> homebrew on google but got nothing useful. So do you have any suggestions on
> updating latest stable version of LAMMPS?

please contact the homebrew-science folks. they have a project on github.
you will have to learn from them how to customize your installation process.
i suspect, it may be just as well to do a manual compilation.

> Besides, I install LAMMPS via homebrew because I want to have a stable and
> updated LAMMPS. I also "git clone" LAMMPS from github - named it as "LAMMPS
> for test", because I intend to modify some source files like MAX_BODY. I
> know I can save my modified source files separately, and push them back
> after git clone the newest LAMMPS. But is there any easy way to update my
> "LAMMPS for test"?

you are contradicting yourself here. you cannot have a "stable"
version of LAMMPS and then do development and update to newer
"unstable" patches.

i would suggest that you have two versions of LAMMPS installed. the
"stable" homebrew compiled executable, and a custom that you compile
manually in your cloned git repository.
that one you can always update to the latest state of the development
master branch (or unstable patch release branch or ...). i also
strongly advise to do any development in your own personal branch (or
branches), but that depends on how deeply you want to dig into source
code management and using git to keep track of your changes.

axel.

>
> Thank you very much for paying attention to such a basic question.
>
> Best regards,
> zjgbz
>
> ------------------------------------------------------------------------------
> 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
> lammps-users@...12...396...sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/lammps-users
>



--
Dr. Axel Kohlmeyer  akohlmey@...43...4...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.



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

Message: 10
Date: Wed, 28 Jun 2017 20:12:54 -0400
From: Wusheng Zhang <minky.k.jiang@...24...>
To: Axel Kohlmeyer <akohlmey@...1125.....>
Cc: LAMMPS - post questions <lammps-users@...396...sourceforge.net>
Subject: Re: [lammps-users] How can I update LAMMPS via homebrew and
        git?
Message-ID:
        <CADZEWxxEPeF4_NBtUjZYTvcBOCYCBhi6B1FzaMQA17RDG2xLTg@...25...>
Content-Type: text/plain; charset="utf-8"

Hi Axel,

Thank you very much. Treating LAMMPS as a git project is a good way to
manage my changing.

Best regards,
zjgbz

2017-06-28 20:06 GMT-04:00 Axel Kohlmeyer <akohlmey@...24...>:

> On Wed, Jun 28, 2017 at 7:08 PM, Wusheng Zhang <minky.k.jiang@...24...>
> wrote:
> > Dear LAMMPS users,
> >
> > I installed LAMMPS via homebrew on MacOS system on Aug 2016, and now I
> > intend to update it for using functions like pair_style python. I know
> this
> > seems like not a good question here, but I tried to search update lammps
> > homebrew on google but got nothing useful. So do you have any
> suggestions on
> > updating latest stable version of LAMMPS?
>
> please contact the homebrew-science folks. they have a project on github.
> you will have to learn from them how to customize your installation
> process.
> i suspect, it may be just as well to do a manual compilation.
>
> > Besides, I install LAMMPS via homebrew because I want to have a stable
> and
> > updated LAMMPS. I also "git clone" LAMMPS from github - named it as
> "LAMMPS
> > for test", because I intend to modify some source files like MAX_BODY. I
> > know I can save my modified source files separately, and push them back
> > after git clone the newest LAMMPS. But is there any easy way to update my
> > "LAMMPS for test"?
>
> you are contradicting yourself here. you cannot have a "stable"
> version of LAMMPS and then do development and update to newer
> "unstable" patches.
>
> i would suggest that you have two versions of LAMMPS installed. the
> "stable" homebrew compiled executable, and a custom that you compile
> manually in your cloned git repository.
> that one you can always update to the latest state of the development
> master branch (or unstable patch release branch or ...). i also
> strongly advise to do any development in your own personal branch (or
> branches), but that depends on how deeply you want to dig into source
> code management and using git to keep track of your changes.
>
> axel.
>
> >
> > Thank you very much for paying attention to such a basic question.
> >
> > Best regards,
> > zjgbz
> >
> > ------------------------------------------------------------
> ------------------
> > 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
> > lammps-users@...396...sourceforge.net
> > https://lists.sourceforge.net/lists/listinfo/lammps-users
> >
>
>
>
> --
> Dr. Axel Kohlmeyer  akohlmey@...24...  http://goo.gl/1wk0
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.
>
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Message: 11
Date: Wed, 28 Jun 2017 21:16:51 -0300
From: Carlos Azael Alvarez Zambrano <calvarez@...6950...>
To: lammps-users@...429...96...sourceforge.net
Subject: [lammps-users] Fwd: Re: Problem installing lammps-1Feb14 in
        Ubuntu 16.04
Message-ID:
        <CAMGrhr99hFxWJRUSDD1pxidyqkc_ymFE8RBsDD4VtBiyuAAhCA@...3019...gmail.com>
Content-Type: text/plain; charset="utf-8"

---------- Mensagem encaminhada ----------
De: "Carlos Alvarez Zambrano" <calvarez@...6950...>
Data: 28 de jun de 2017 21:09
Assunto: Re: [lammps-users] Problem installing lammps-1Feb14 in Ubuntu 16.04
Para: "Axel Kohlmeyer" <akohlmey@...24...>
Cc:

Dear Axel,

Thanks for your response, I need to install this old version because I want
to install another program which works with that old version. Where I can
find that manual? Thank you.

Carlos

Enviado desde mi iPad

> El 28 jun 2017, a las 20:57, Axel Kohlmeyer <akohlmey@...24...> escribi?:
>
> On Wed, Jun 28, 2017 at 6:28 PM, Carlos Azael Alvarez Zambrano
> <calvarez@...6950...> wrote:
>> Dear LAMMPS users,
>>
>> I am a new user in lammps and I am trying to install a previous version,
>> lammps-1Feb14, on my computer. It uses Ubuntu 16.04 LTS, 64-bit. I have
>> tried to create a make file, in accordance with lammps documentation
>> (http://lammps.sandia.gov/doc/Manual.html), but I din not to get to work
it.
>> Can someone help me with this issue? Any suggestions would be welcome.
>
> the online version of the manual always reflects the latest
> development version of LAMMPS.
> if you are installing an old version (which i strongly advise against,
> and where you are not likely to get much help from this list) you need
> to consult the manual that *matches* your version. things keep
> changing and improving in LAMMPS all the time.
>
> axel.
>
>> Thanks in advance.
>>
>> Regards,
>>
>> --
>> Carlos A. Alvarez Z.
>> Ph.D. Student
>> School of Mechanical Engineering
>> University of Campinas - UNICAMP
>>
>>
>>
>>
>>
>> ------------------------------------------------------------
------------------
>> 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
>> lammps-users@...396...sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/lammps-users
>
>
>
> --
> Dr. Axel Kohlmeyer  akohlmey@...24...  http://goo.gl/1wk0
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.
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