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Re: [lammps-users] zero barrier from NEB calculations
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Re: [lammps-users] zero barrier from NEB calculations


From: Emile Maras <e1000.3000@...24...>
Date: Mon, 25 Sep 2017 11:32:12 +0200

Hi,

The barrier might be very small so that your second image is already on the other side of the barrier.

If the computation cost is law you can increase the number of image until you get a barrier. 

The computationally most efficient way would be to use the free-end neb with the last replica being the second replica of your previous complete path. This way you will focus on the important part of your transition path.

Emile

 

Message: 6
Date: Thu, 20 Jul 2017 15:12:07 +0000 (UTC)
From: anyy zsj <zsjanyy@...16...>
To: "lammps-users@...396...sourceforge.net"
        <lammps-users@...396...sourceforge.net>
Subject: [lammps-users] zero barrier from NEB calculations
Message-ID: <795989915.1300264.1500563527071@...5436...>
Content-Type: text/plain; charset="utf-8"

Dear lammps users:
I have a question about minimization implemented in lammps. I have a defective configuration with an interstitial and a vacancy in it. After I relax it with minimization command using either cg or sd method, the defect pair finds an optimal location. Then I use NEB calculations to calculate the barrier when moving the interstitial to the vacancy. However, I always get a zero barrier like this:
3156 9.9485711e-09 7.6750495e-10 4.5723397e-12 9.9485711e-09 4.5723397e-12??????????? 0??? 5.4487092??? 3.8110102??????????? 0?? -16642.612? 0.066666667?? -16642.655?? 0.13333333?? -16642.906????????? 0.2?? -16643.173?? 0.26666667?? -16643.483?? 0.33333333?? -16643.992????????? 0.4?? -16644.533?? 0.46666667?? -16645.057?? 0.53333333?? -16645.579????????? 0.6?? -16646.098?? 0.66666667?? -16646.641?? 0.73333333?? -16647.232????????? 0.8?? -16647.695?? 0.86666667?? -16647.951?? 0.93333333?? -16648.046??????????? 1? ?-16648.061?I have tried all kinds of convergence criteria during minimization but the configuration seems stable. So why there is 0 barrier but the system cannot relax to the low energy state? What's wrong here?
If you are interested, I can provide my input files.?Thank you very much!
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Message: 7
Date: Thu, 20 Jul 2017 13:56:42 -0400
From: Yutong Bi <ybi@...1789...>
To: lammps-users@...429...96...sourceforge.net
Subject: [lammps-users] an Error when saving restart files
Message-ID:
        <CANOemPCxnCTPRy+9f_P9jKDVLQ+iuSpuwvZMFKmzCDwx2Ke6-Q@...3019...gmail.com>
Content-Type: text/plain; charset="utf-8"

Hello, I have encountered an issue while trying to save the restart file
with lammps.
The .restart-files generated after the program terminates displays an error
like this:

*Error! /home/ybi/data/GB_743_anneal/al743.140000.restart is not UTF-8
encoded.*
*Saving Disabled*
*See Console for more details.*

?Could somebody explain to me what happened and how to fix it?

Thanks!?

--
Yutong.Bi
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Message: 8
Date: Thu, 20 Jul 2017 14:43:01 -0400
From: Axel Kohlmeyer <akohlmey@...43...4...>
To: Yutong Bi <ybi@...1789...>
Cc: LAMMPS Users Mailing List <lammps-users@...396...sourceforge.net>
Subject: Re: [lammps-users] an Error when saving restart files
Message-ID:
        <CADTmJ6HdNjCr3vQ9DkXrZYjya+HtAoe+-hKK8jzy8HML3Jv10w@...3019...gmail.com>
Content-Type: text/plain; charset="UTF-8"

On Thu, Jul 20, 2017 at 1:56 PM, Yutong Bi <ybi@...1789...> wrote:
> Hello, I have encountered an issue while trying to save the restart file
> with lammps.
> The .restart-files generated after the program terminates displays an error
> like this:
>
> Error! /home/ybi/data/GB_743_anneal/al743.140000.restart is not UTF-8
> encoded.
> Saving Disabled
> See Console for more details.
>
> Could somebody explain to me what happened and how to fix it?

you have to talk to your sysadmin people. this is not an error that
LAMMPS generates.
in fact, .restart files are binary, so text encoding (ASCII, UTF-8 or
other) is irrelevant.

axel.


>
> Thanks!
>
> --
> Yutong.Bi
>
> ------------------------------------------------------------------------------
> 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: Thu, 20 Jul 2017 14:45:14 -0400
From: Cong Dai <congdai1220@...43...4...>
To: "lammps-users@...396...sourceforge.net"
        <lammps-users@...396...sourceforge.net>
Subject: [lammps-users] Errors when define a region after reading a
        data file
Message-ID: <A5601717-5A9B-446E-BF4E-6309E085D377@...24...>
Content-Type: text/plain; charset=us-ascii

Dear LAMMPS users,

  I tried many ways to solve this problem but failed, so I hope you can give me any hints.
The part of the script is:

read_data   /datafile.data
region          box block INF INF INF INF -65.0 65.0 units box
group           mobile region box
region          low block INF INF INF INF INF -65.0 units box
group           lowsurface region low
region          upper block INF INF INF INF 65.0 INF units box
group           uppersurface region upper
group               boundary union lowsurface uppersurface

and log file shows the error:
region          box block INF INF INF INF -65.0 65.0 units box
group           mobile region box
ERROR: Illegal region command (../region.cpp:397)
Last command: region            box block INF INF INF INF -65.0 65.0 units box
group           mobile region box

I tried to only define the region without defining the group and it works, then why it said that the error is in region command?

Cong




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

Message: 10
Date: Thu, 20 Jul 2017 15:01:15 -0400
From: Axel Kohlmeyer <akohlmey@...43...4...>
To: Cong Dai <congdai1220@...1125.....>
Cc: "lammps-users@...396...sourceforge.net"
        <lammps-users@...396...sourceforge.net>
Subject: Re: [lammps-users] Errors when define a region after reading
        a data file
Message-ID:
        <CADTmJ6EeUk464XeJ-UD_1OsuVB4CRwmD3LOweg9m24ZdqnHEHg@mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"

On Thu, Jul 20, 2017 at 2:45 PM, Cong Dai <congdai1220@...24...> wrote:
> Dear LAMMPS users,
>
>   I tried many ways to solve this problem but failed, so I hope you can give me any hints.
> The part of the script is:
>
> read_data   /datafile.data
> region          box block INF INF INF INF -65.0 65.0 units box
> group           mobile region box
> region          low block INF INF INF INF INF -65.0 units box
> group           lowsurface region low
> region          upper block INF INF INF INF 65.0 INF units box
> group           uppersurface region upper
> group               boundary union lowsurface uppersurface
>
> and log file shows the error:
> region          box block INF INF INF INF -65.0 65.0 units box
> group           mobile region box
> ERROR: Illegal region command (../region.cpp:397)
> Last command: region            box block INF INF INF INF -65.0 65.0 units box
> group           mobile region box
>
> I tried to only define the region without defining the group and it works, then why it said that the error is in region command?

i can add these commands to, e.g. example/micelle/in.micelle, and
there is no error.

axel.


>
> Cong
>
>
> ------------------------------------------------------------------------------
> 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.



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