LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Mailing List Archives
[lammps-users] Running LAMMPS from PYTHON via python interface to Lammps
[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

[lammps-users] Running LAMMPS from PYTHON via python interface to Lammps


From: Dundar Yilmaz <duy42@...122...>
Date: Wed, 18 Oct 2017 13:43:24 -0400

Hi,
In a project I am trying to run lammps from python and between each simulation step I would like to do some analysis.
In a loop:
lmp=lammps()
for i in range(10000):
lmp.command(“ run 1”)
analysis_function ( lmp)

Assuming that analysis function wont take much time is it a good approach? Is there any overhead running lammps step by step?
I tested this for a very small system:

lmp.command(“ run 10000)

vs
for i in range(10000):
lmp.command(“run 1”)

Time spent for the latter case was three times of the first one.

To be more specific I would like to compare bonding information at each step to detect chemical reactions. If there is a way to access fix reax/bond data through lammps during the simulation
I could save it to a different variable and analyze it after the md simulation.

Thanks for your time.


Dundar Yilmaz, Ph. D.
Post Doctoral Researcher 
Department of Mechanical and Nuclear Engineering 
138 Research East Building 
Penn State University 
University Park, PA 16802




On Oct 18, 2017, at 12:14, lammps-users-request@lists.sourceforge.net wrote:

Send lammps-users mailing list submissions to
lammps-users@lists.sourceforge.net

To subscribe or unsubscribe via the World Wide Web, visit
https://lists.sourceforge.net/lists/listinfo/lammps-users
or, via email, send a message with subject or body 'help' to
lammps-users-request@lists.sourceforge.net

You can reach the person managing the list at
lammps-users-owner@...430...orge.net

When replying, please edit your Subject line so it is more specific
than "Re: Contents of lammps-users digest..."
Today's Topics:

  1. Re: [EXTERNAL] Re: Cannot fetch emails from mail list anymore
     (Moore, Stan)
  2. units metal vs real -Reaxff (Alexandra Davila)
  3. Re: units metal vs real -Reaxff (Axel Kohlmeyer)
  4. Re: RATTLE in version 2017! (Axel Kohlmeyer)
  5. Re: Angle Harmonic Gradients question (Axel Kohlmeyer)
  6. Re: RATTLE in version 2017! (Hai Hoang)
  7. Re: bond atom missing in image check (Stefan Paquay)
  8. Re: bond atom missing in image check (Stefan Paquay)
  9. Re: bond atom missing in image check (Stefan Paquay)
 10. Re: [EXTERNAL] hi about the potential parameters of latte
     (Steve Plimpton)

From: "Moore, Stan" <stamoor@...3...>
Subject: Re: [lammps-users] [EXTERNAL] Re: Cannot fetch emails from mail list anymore
Date: October 18, 2017 at 09:39:40 EDT
To: Axel Kohlmeyer <akohlmey@...24...>, Wenqiang Liu <liulammps@...127...>
Cc: "lammps-users@...371...et" <lammps-users@lists.sourceforge.net>


I had the same thing happen. I was able to unsubscribe from the list and then subscribe again with the same email address, and now I get the emails again.

Stan

-----Original Message-----
From: Axel Kohlmeyer [mailto:akohlmey@...24...]
Sent: Tuesday, October 17, 2017 9:02 PM
To: Wenqiang Liu <liulammps@...127...>
Cc: lammps-users@lists.sourceforge.net
Subject: [EXTERNAL] Re: [lammps-users] Cannot fetch emails from mail list anymore

On Tue, Oct 17, 2017 at 10:22 PM, Wenqiang Liu <liulammps@...127...> wrote:
Hello everyone,
I have subscribed to Lammps mail list maybe two or three years ago
with this email address, and I successfully received the posts from
the mail list until several months ago.
However, I found that recently there is no new emails from the mail
list appeared anymore in my email box. I have tried to re-subscribe to
the mail list, however, an error poppoed up. Please see the attached
figure. I am sorry that I did not find any instructions on the
subscribing page or on http://lammps.sandia.gov/mail.html.
Could you please give me some guides to fix this problem?

sourceforge recently removed the ability to manage users for mailing list admins.
mailing list adminst now cannot see who is subscribed or not and logically also cannot change their status.

you have to contact sourceforge support directly for help with this issue.

sorry,
   axel.

Any help would be much appreciated!

With My Best Regards,
Liu

----------------------------------------------------------------------
-------- 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@...13...ge.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.

------------------------------------------------------------------------------
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@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/lammps-users





From: Alexandra Davila <davila@...6924...>
Subject: [lammps-users] units metal vs real -Reaxff
Date: October 18, 2017 at 09:46:16 EDT
To: LAMMPS Users Mailing List <lammps-users@lists.sourceforge.net>


Hi lammps-users,

I have been calculating with reax force field some gold systems, I have always used units real.

By error I did a calculation of the lattice with units metal, I was wondering why the output of the potential energy for both runs (with real and metal units) are the same. For real units energy should be printed in kcal/mol and for metal in eV, or with reax the default is real units (I think not)?

Probably I am making a very dummy mistake!

I attach the *in file!

thanks for the help!

lammps version:  Stable version (11 Aug 2017)


<calc_fcc.in>


From: Axel Kohlmeyer <akohlmey@...24...>
Subject: Re: [lammps-users] units metal vs real -Reaxff
Date: October 18, 2017 at 10:15:16 EDT
To: Alexandra Davila <davila@...6924...>
Cc: LAMMPS Users Mailing List <lammps-users@lists.sourceforge.net>


On Wed, Oct 18, 2017 at 9:46 AM, Alexandra Davila
<davila@...6924...> wrote:
Hi lammps-users,

I have been calculating with reax force field some gold systems, I have
always used units real.

By error I did a calculation of the lattice with units metal, I was
wondering why the output of the potential energy for both runs (with real
and metal units) are the same. For real units energy should be printed in
kcal/mol and for metal in eV, or with reax the default is real units (I
think not)?

i think yes. the reaxff force field parameter files contain parameters
in real units.
so if you set units to metal in your input, they will be interpreted
as if they were in metal units instead, which may lead to all kinds of
funny behavior and outputs unless you convert the entries in the
parameter file to be in metal units as well (which is horribly tedious
to get done correctly)

axel.


Probably I am making a very dummy mistake!

I attach the *in file!

thanks for the help!

lammps version:  Stable version (11 Aug 2017)



------------------------------------------------------------------------------
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@lists.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.





From: Axel Kohlmeyer <akohlmey@...24...>
Subject: Re: [lammps-users] RATTLE in version 2017!
Date: October 18, 2017 at 10:19:40 EDT
To: Hai Hoang <hhoang052@...24...>
Cc: LAMMPS Users Mailing List <lammps-users@lists.sourceforge.net>


you can see which changes were done to fix rattle by examining the
file history in the LAMMPS git repository:
https://github.com/lammps/lammps/commits/master/src/RIGID/fix_rattle.cpp

for more details, you should contact the author of this style.

please note, that the information you provide is very vague (including
the LAMMPS version, there were lots of released LAMMPS versions in
both 2015 and 2017).
please check out: http://lammps.sandia.gov/guidelines.html

axel.

On Wed, Oct 18, 2017 at 4:25 AM, Hai Hoang <hhoang052@...24...> wrote:
Dear all,

I have employed RATTLE method to constrain the rigid bonds in water
molecules and to count the number of freedom for generating initial
velocities of atoms as:

--------------------------------
   # Fix rigid bonds
   fix shake_bond    fluid shake 1.0e-5 200 0 b 1 a 1

   # Creat the velocity
   velocity fluid create ${Temp_imp} ${Iseed_imp} mom yes rot yes dist
gaussian

   # Transient duration
   timestep ${dt}
   reset_timestep 0

   fix npt_md fluid npt temp ${Temp_imp} ${Temp_imp} ${Damp_temp} iso
${Press_imp} ${Press_imp} ${Damp_press}
---------------------------------

If I used versions 2015, it works well, i.e. it exports the temperature at
t=0 is exactly equal to ${Temp_imp}. However, with version 2017, it shows
that at t=0, the temperature does not remove number of constraints in
computing the temperature, i.e. temperature at t=0 is not equal ${Temp_imp}.

In addition, use of RATTLE in version 2017 is not stable, i.e. i mean that
all input and script are the same, but run independently one of them has
error, others are not. Such situations donot occur with version 2015.

(Note that: if use of SHAKE, all are correct with both versions 2015 and
2017)

So, anyone can tell me what changed in RATTLE of version 2015 and 2017? Or
explain me what happen?

Thanks,


------------------------------------------------------------------------------
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@lists.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.





From: Axel Kohlmeyer <akohlmey@...24...>
Subject: Re: [lammps-users] Angle Harmonic Gradients question
Date: October 18, 2017 at 10:27:24 EDT
To: Matthew Wander <mcfwander@...43...4...>
Cc: LAMMPS Users Mailing List <lammps-users@...431...ceforge.net>


On Tue, Oct 17, 2017 at 9:32 AM, Matthew Wander <mcfwander@...24...> wrote:
I have a question about lines 115-120 of angle_harmonic.cpp. I would have
thought the gradients would have been a series of cross products of the bond
vectors: r12 x (r32 x r12) appropriately normalized multiplied by the force
constants etc. . However this is something very different. I tried checking
the manual for a reference but there was none. What is going on here?

i didn't have the time to work though the code in detail, so here is
just an educated guess:

it looks to me as if the angle force is decomposed into pairwise force
components in the molecule centered frame with the center of mass
being the origin:
one force component that moves the two outer atoms as if there was a
bond between them, and a second component that moves them up or down
with the central atom moving in the opposite direction of the outer
atoms.
the rest looks like projecting these force components on the real
space distance vectors in a similar fashion as it is done with
pairwise forces.

axel.


thanks
matthew


------------------------------------------------------------------------------
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@...371...et
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.





From: Hai Hoang <hhoang052@...29....>
Subject: Re: [lammps-users] RATTLE in version 2017!
Date: October 18, 2017 at 10:50:14 EDT
To: Axel Kohlmeyer <akohlmey@...24...>
Cc: LAMMPS Users Mailing List <lammps-users@lists.sourceforge.net>


Dear Axel,

Thank you so much for your quick response. Versions I have tested lammps-10Aug15 and lammps-31Mar17 (even the current one).


 

On Wed, Oct 18, 2017 at 4:19 PM, Axel Kohlmeyer <akohlmey@...24...> wrote:
you can see which changes were done to fix rattle by examining the
file history in the LAMMPS git repository:
https://github.com/lammps/lammps/commits/master/src/RIGID/fix_rattle.cpp

for more details, you should contact the author of this style.

please note, that the information you provide is very vague (including
the LAMMPS version, there were lots of released LAMMPS versions in
both 2015 and 2017).
please check out: http://lammps.sandia.gov/guidelines.html

axel.

On Wed, Oct 18, 2017 at 4:25 AM, Hai Hoang <hhoang052@...24...> wrote:
> Dear all,
>
> I have employed RATTLE method to constrain the rigid bonds in water
> molecules and to count the number of freedom for generating initial
> velocities of atoms as:
>
> --------------------------------
>     # Fix rigid bonds
>     fix shake_bond    fluid shake 1.0e-5 200 0 b 1 a 1
>
>     # Creat the velocity
>     velocity fluid create ${Temp_imp} ${Iseed_imp} mom yes rot yes dist
> gaussian
>
>     # Transient duration
>     timestep ${dt}
>     reset_timestep 0
>
>     fix npt_md fluid npt temp ${Temp_imp} ${Temp_imp} ${Damp_temp} iso
> ${Press_imp} ${Press_imp} ${Damp_press}
> ---------------------------------
>
>  If I used versions 2015, it works well, i.e. it exports the temperature at
> t=0 is exactly equal to ${Temp_imp}. However, with version 2017, it shows
> that at t=0, the temperature does not remove number of constraints in
> computing the temperature, i.e. temperature at t=0 is not equal ${Temp_imp}.
>
> In addition, use of RATTLE in version 2017 is not stable, i.e. i mean that
> all input and script are the same, but run independently one of them has
> error, others are not. Such situations donot occur with version 2015.
>
> (Note that: if use of SHAKE, all are correct with both versions 2015 and
> 2017)
>
> So, anyone can tell me what changed in RATTLE of version 2015 and 2017? Or
> explain me what happen?
>
> Thanks,
>
>
> ------------------------------------------------------------------------------
> 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.




From: Stefan Paquay <stefanpaquay@...24...>
Subject: Re: [lammps-users] bond atom missing in image check
Date: October 18, 2017 at 11:07:11 EDT
To: Hossein Geraili <geraili.hsn@...24...>
Cc: LAMMPS Users Mailing List <lammps-users@lists.sourceforge.net>


No. What probably goes wrong is that an xyz file does not store box images, so when LAMMPS tries to reconstruct the actual position of atoms that are straddled across the periodic boundary it cannot do so. You need the periodic images. If you want to resume from a dump file, you need to also dump the periodic images. Alternatively, use a write_restart or write_data to restart from.

On Tue, Oct 17, 2017 at 10:31 PM, Hossein Geraili <geraili.hsn@...24...> wrote:

Just tell me, if I run for more timestep I can use .xyz coordinations or restart. Because actually, I did not exit the simulation in the parallel simulation on my computer whenever internet is disconnected tthe simulation would be exited. This is the third time that I am going near 100 microsecond and simulation exits. Please help me, so I can finish simulation for 1 nanoseconds.
Best regards


On Oct 17, 2017 9:06 PM, "Hossein Geraili" <geraili.hsn@...24...> wrote:
Dear all,
I am running in NPT ensemble for 300 molecules of ionic liquid with AMber force field. I ran for a small number of steps about 50 microseconds and then I wanted to use atom positions in this state which seems to be equilibrated state for next simulations. I used positions in .xyz file of dump command and substitute them in the data file. First I ran it serial and the warning of bond/angle/dihedral extent > half of periodic box length showed up and after that error of bond atom missing error occurred. In the parallel simulation, the simulation was exited with the error of bond atom missing in image check. Also, I tried using restart, but it exited with the error of did not assign all restart atoms correctly, and I even used remap command but it did not work. 
All the bonded and nonbonded energy are in good agreement with the article data.
what is wrong?
best
--
Hosein Geraili Daronkola
M.Sc.Graduated of physical chemistry
Physical Chemistry,
Department of Chemistry,
Sharif University of Technology.
geraili_hosein@...7110...



Sent with Mailtrack

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





From: Stefan Paquay <stefanpaquay@...24...>
Subject: Re: [lammps-users] bond atom missing in image check
Date: October 18, 2017 at 11:08:02 EDT
To: Hossein Geraili <geraili.hsn@...24...>
Cc: LAMMPS Users Mailing List <lammps-users@lists.sourceforge.net>


Also, there are ways to make sure the simulation keeps running even after your connection drops (e.g., tmux or GNU screen or a simple nohup and a &).

On Wed, Oct 18, 2017 at 11:07 AM, Stefan Paquay <stefanpaquay@...24...> wrote:
No. What probably goes wrong is that an xyz file does not store box images, so when LAMMPS tries to reconstruct the actual position of atoms that are straddled across the periodic boundary it cannot do so. You need the periodic images. If you want to resume from a dump file, you need to also dump the periodic images. Alternatively, use a write_restart or write_data to restart from.

On Tue, Oct 17, 2017 at 10:31 PM, Hossein Geraili <geraili.hsn@...24...> wrote:

Just tell me, if I run for more timestep I can use .xyz coordinations or restart. Because actually, I did not exit the simulation in the parallel simulation on my computer whenever internet is disconnected tthe simulation would be exited. This is the third time that I am going near 100 microsecond and simulation exits. Please help me, so I can finish simulation for 1 nanoseconds.
Best regards


On Oct 17, 2017 9:06 PM, "Hossein Geraili" <geraili.hsn@...24...> wrote:
Dear all,
I am running in NPT ensemble for 300 molecules of ionic liquid with AMber force field. I ran for a small number of steps about 50 microseconds and then I wanted to use atom positions in this state which seems to be equilibrated state for next simulations. I used positions in .xyz file of dump command and substitute them in the data file. First I ran it serial and the warning of bond/angle/dihedral extent > half of periodic box length showed up and after that error of bond atom missing error occurred. In the parallel simulation, the simulation was exited with the error of bond atom missing in image check. Also, I tried using restart, but it exited with the error of did not assign all restart atoms correctly, and I even used remap command but it did not work. 
All the bonded and nonbonded energy are in good agreement with the article data.
what is wrong?
best
--
Hosein Geraili Daronkola
M.Sc.Graduated of physical chemistry
Physical Chemistry,
Department of Chemistry,
Sharif University of Technology.
geraili_hosein@...7110...



Sent with Mailtrack

------------------------------------------------------------------------------
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@...655....net
https://lists.sourceforge.net/lists/listinfo/lammps-users






From: Stefan Paquay <stefanpaquay@...24...>
Subject: Re: [lammps-users] bond atom missing in image check
Date: October 18, 2017 at 11:19:00 EDT
To: Hossein Geraili <geraili.hsn@...24...>, LAMMPS <lammps-users@...44...s.sourceforge.net>


Please always include the mailing list in replies.

Restart should "just work", I do now know why it would fail in your case. You can use dump custom and write the periodic images in addition to all coordinates and atom ids/types. See the "dump custom" docs.

On Wed, Oct 18, 2017 at 11:15 AM, Hossein Geraili <geraili.hsn@...36.....24...> wrote:

Thank you Stefan,
I used write_restart and the error did not assign all restart atoms correctly occured. Do you think with write_data it would be solved. Are there any other extention besides .xyz that would save priodic images?
Best


On Oct 18, 2017 6:38 PM, "Stefan Paquay" <stefanpaquay@...24...> wrote:
Also, there are ways to make sure the simulation keeps running even after your connection drops (e.g., tmux or GNU screen or a simple nohup and a &).

On Wed, Oct 18, 2017 at 11:07 AM, Stefan Paquay <stefanpaquay@...24...> wrote:
No. What probably goes wrong is that an xyz file does not store box images, so when LAMMPS tries to reconstruct the actual position of atoms that are straddled across the periodic boundary it cannot do so. You need the periodic images. If you want to resume from a dump file, you need to also dump the periodic images. Alternatively, use a write_restart or write_data to restart from.

On Tue, Oct 17, 2017 at 10:31 PM, Hossein Geraili <geraili.hsn@...24...> wrote:

Just tell me, if I run for more timestep I can use .xyz coordinations or restart. Because actually, I did not exit the simulation in the parallel simulation on my computer whenever internet is disconnected tthe simulation would be exited. This is the third time that I am going near 100 microsecond and simulation exits. Please help me, so I can finish simulation for 1 nanoseconds.
Best regards


On Oct 17, 2017 9:06 PM, "Hossein Geraili" <geraili.hsn@...24...> wrote:
Dear all,
I am running in NPT ensemble for 300 molecules of ionic liquid with AMber force field. I ran for a small number of steps about 50 microseconds and then I wanted to use atom positions in this state which seems to be equilibrated state for next simulations. I used positions in .xyz file of dump command and substitute them in the data file. First I ran it serial and the warning of bond/angle/dihedral extent > half of periodic box length showed up and after that error of bond atom missing error occurred. In the parallel simulation, the simulation was exited with the error of bond atom missing in image check. Also, I tried using restart, but it exited with the error of did not assign all restart atoms correctly, and I even used remap command but it did not work. 
All the bonded and nonbonded energy are in good agreement with the article data.
what is wrong?
best
--
Hosein Geraili Daronkola
M.Sc.Graduated of physical chemistry
Physical Chemistry,
Department of Chemistry,
Sharif University of Technology.
geraili_hosein@...7110...



Sent with Mailtrack

------------------------------------------------------------------------------
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@...655....net
https://lists.sourceforge.net/lists/listinfo/lammps-users







From: Steve Plimpton <sjplimp@...24...>
Subject: Re: [lammps-users] [EXTERNAL] hi about the potential parameters of latte
Date: October 18, 2017 at 12:14:12 EDT
To: Oleg Sergeev <seoman@...567...>
Cc: Steve Plimpton <sjplimp@...3...>, "Song, Zhigong" <zhigong_song@...4267.....>, "cawkwell@...795..." <cawkwell@...795...>, "cnegre@...795..." <cnegre@...795...>, "lammps-users@lists.sourceforge.net" <lammps-users@lists.sourceforge.net>, "Goldman, Nir" <goldman14@...87...>


I'll leave comparisons of LATTE and DFTB+ to the experts.
I'm CCing Nir Goldman (LLNL) who has coupled DFTB+ and LAMMPS
for modeling he has done.  I believe what he did was add
some code to DFTB+ to call LAMMPS as a library.  I'm not clear on
if that version of DFTB+ is publicly available - Nir can comment.

From a software point of view the coupling of LAMMPS to the 2
codes is the inverse of each other, though both accomplish the
same thing,

For LATTE, LAMMPS is the driver, if calls LATTE as a lib each timestep,
thru fix latte as a wrapper.  It passes coords, and receives back forces.

For DFTB+, it is the driver, it calls LAMMPS as a library, and the
LAMMPS script that is run includes a fix external command, which does a callback
to DFTB+ each timestep to pass coords and receive back forces.
Nir added a new Fortran interface to the LAMMPS lib to facilitate
this - see examples/COUPLE/fortran_dftb.

Steve


On Mon, Oct 16, 2017 at 11:44 AM, Oleg Sergeev <seoman@...567...> wrote:
Dear Zhigong,
 
I believe there are also parameter files for MgO. Don't know if those are of interest to you.
 
And I also have another question of, I think, general interest to other users. As far as I know, while the LATTE interface is new, LAMMPS can be and in the past was already used with DFTB+ code for running TB simulations. From the user point of view, what are the main advantages of one code over the other?
 
Regards,
Oleg
 
16.10.2017, 20:00, "Steve Plimpton" <sjplimp@...429......>:

Hi - Marc and Christian are the right folks to answer this,
as it's really a LATTE Q. I'm also CCing this to
the LAMMPS mail list, as I think the Q/A will be of
general interest to other LAMMPS users who want
to try out tight-binding and LATTE.

Marc/Christian - if you CC the mail list address
in your replies, the info should appear there as well.

Thanks,
Steve

 

 From: "Song, Zhigong" <zhigong_song@...802...>
 Date: Sat, 14 Oct 2017 15:19:05 -0400
 Cc: cnegre@...795..., sjplimp@...3...
 Content-Type: multipart/alternative; boundary="001a113b0cc89a18ad055b86a52b"

 [1:text/plain Hide]
 This is a heavy lammps users from Brown University. I am very excited to
 find that tight-binding method is implemented with lammps and make it
 complie successfully. However, when I finished the testing in example
 directory, I realized that there are only C,H,N,O potentials within. I am
 forced on mechanical properties of materials Thus, I am just wondering if
 there are TB potentials of other elements. Or where could I get them?
 Thanks a lot for all your contributions on it,


 Best
 [2:text/html Show]


------------------------------------------------------------------------------
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@...33....396...sourceforge.net
https://lists.sourceforge.net/lists/listinfo/lammps-users


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




------------------------------------------------------------------------------
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@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/lammps-users