lammps-users Digest, Vol 60, Issue 23

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Today's Topics:

1. Re: RDF for very different cutoffs (Steve Plimpton)
2. Re: LAMMPS compilation on cluster (Steve Plimpton)
3. Re: question about create_box and region (Steve Plimpton)
4. Re: periodic boundary conditions for polymers (Steve Plimpton)
5. Re: LAMMPS compilation on cluster (Laurent Joly)
6. Re: periodic boundary conditions for polymers (Laurent Joly)

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

Message: 1
Date: Fri, 6 May 2011 07:58:20 -0600
From: Steve Plimpton <[email protected]>
Subject: Re: [lammps-users] RDF for very different cutoffs
To: ??? <[email protected]>
Cc: [email protected]
Message-ID: <BANLkTikFg9BLnv7B7C2zW[email protected]>
Content-Type: text/plain; charset="euc-kr"

Use more bins?
You can also define multiple compute rdf commands,
one for one pair, another for another pair, etc.

Steve

Steve

2011/5/5 ??? <[email protected]>

> Is it possible to calculate RDF for very different cuoffs?
>
>
>
> I will explain more. I used the following command:
>
>
>
> pair_style colloid
>
> pair_coeff 1 2 75 1 10 0 12.5
>
> pair_coeff 2 2 140 1 0 0 2.5
>
>
>
> compute myrdf mygroup rdf 100 2 1 2 2
>
>
>
> However, the calculated results are all over 0<r<12.5, which means
> that between the species 2 2, I had only nonzero values over 0<r<2.5, and
> all others were zero. I want more detailed infomation over 0<r<2.5 between
> the species 2 2. How Can I do that?
>
>
> ------------------------------------------------------------------------------
> WhatsUp Gold - Download Free Network Management Software
> The most intuitive, comprehensive, and cost-effective network
> management toolset available today. Delivers lowest initial
> acquisition cost and overall TCO of any competing solution.
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Message: 2
Date: Fri, 6 May 2011 08:00:29 -0600
From: Steve Plimpton <[email protected]>
Subject: Re: [lammps-users] LAMMPS compilation on cluster
To: karan saini <[email protected]>
Cc: [email protected]
Message-ID: <[email protected]>
Content-Type: text/plain; charset=windows-1252

There is no reason to use sudo to build LAMMPS as root:

sudo make linux

The error you get is that it can't find g++, which means
you have bigger problems than building LAMMPS.

Steve

On Thu, May 5, 2011 at 10:52 PM, karan saini <[email protected]> wrote:
> I have made cluster using openmpi-1.4.1-2? instead of mpich1 using the
> procedure as mentioned at using ubuntu 10.04
> http://www.linux.com/community/blogs/Building-a-Beowulf-Cluster-in-just-13-steps-.html
>
> I have not included LD_LIBRARY_PATH as mentioned as mentioned there (let me
> know how to do that also )
>
> I am trying to compile lammps on the cluster
>
> After uncompressing lammps.tar.gz,(actually, libs for LAMMPS is part of
> lammps.tar.gz)
>
> cd lib/reax
> Change gfortran to mpif77 in Makefile.gfortran
> sudo make -f Makefile.gfortran`` > > cd lib/meam > Change gfortran to mpif77 in Makefile.gfortran > sudo make -f Makefile.gfortran > > cd lib/poems > Change g++ to mpicxx in Makefile.g++ > sudo make -f Makefile.g++ > > LAMMPS > cd src > > Check which packages are included > sudo make package-status > > Choose all standard packages to be included > sudo make yes-standard > > If you don’t have GPU, then exclude gpu package. Otherwise, you will see > tons of error message when you compile it. > sudo make no-gpu > > Edit MAKE/Makefile.linux > > CC = mpicxx > CCFLAGS = -g ?O > DEPFLAGS = -M > LINK = mpicxx > LINKFLAGS = -g ?O > LIB = > FFT_INC = -I/application/fftw-2.1.5-gnu/ > include -DFFT_FFTW > FFT_PATH = -L/application/fftw-2.1.5-gnu/lib > FFT_LIB = -lfftw > > > MPI_INC = -I/application/openmpi-1.4.2-gnu/include -DMPICH_IGNORE_CXX_SEEK > MPI_PATH = -L/application/openmpi-1.4.2-gnu/lib > MPI_LIB =? -lpthread ?lmpi > > > > Build LAMMPS as an executable and library as well > > sudo make linux > > then i get the following error (last few lines) > > Makefile:96: temper.d: No such file or directory > Makefile:96: thermo.d: No such file or directory > Makefile:96: timer.d: No such file or directory > Makefile:96: universe.d: No such file or directory > mpicxx -g ?O -DLAMMPS_GZIP -I…/…/lib/reax -I…/…/lib/poems > -I…/…/lib/meam? -I/application/openmpi-1.4.1-2-gnu/include > -DMPICH_IGNORE_CXX_SEEK -I/application/fftw-2.1.5-gnu/include -DFFT_FFTW -M > universe.cpp > universe.d > g++: ?O: No such file or directory > make[1]: *** [universe.d] Error 1 > make[1]: Leaving directory /home/mpiuser/lammps-15Mar11/src/Obj_linux'
> make: *** [linux] Error 2
>
>
>
> Please let me know how to make LAMMPS executable
>
>
>
> --
> With thanks and regards'
>
> Karan Saini
> +91-9988 400 533
>
>
> ------------------------------------------------------------------------------
> WhatsUp Gold - Download Free Network Management Software
> The most intuitive, comprehensive, and cost-effective network
> management toolset available today. ?Delivers lowest initial
> acquisition cost and overall TCO of any competing solution.
> http://p.sf.net/sfu/whatsupgold-sd
> _______________________________________________
> lammps-users mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/lammps-users
>
>

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

Message: 3
Date: Fri, 6 May 2011 08:04:14 -0600
From: Steve Plimpton <[email protected]>
Subject: Re: [lammps-users] question about create_box and region
To: Gemma Safont Camprub? <[email protected]>
Cc: [email protected]
Message-ID: <[email protected]>
Content-Type: text/plain; charset=ISO-8859-1

The manual says:

If a region is defined before the simulation box has been created (via
create_box or read_data or read_restart commands), then an EDGE or INF
parameter cannot be used.

This is b/c it doesn't know where the edge of the box is at that point.
You can use a region to create_box to define the simulation
box but it can't be an INF region. That makes no sense.

Periodic boundaries are altogether different. The simulation
box is still of finite size even with PBC.

Steve

On Fri, May 6, 2011 at 2:44 AM, Gemma Safont Camprub?
<[email protected]> wrote:
> Dear all,
>
> I would like to simulate a nanowire, so I need periodic boundary conditions
> and a region that is INF in x direction for example.
>
> I don't understand a part of the manual that says that if I want to use INF
> as xlo and xhi I have to use first the create_box command. But in the
> create_box command says that I have to define a region first.
>
> Which of both commands I have to use first?
>
> I have tried this and doesn't work:
>
> lattice fcc ${latparam}
> region whole block 0 3 0 3 INF INF
> create_box 1 whole
> create_atoms 1 region whole
>
> Can anybody explain me the exact difference between region and box?
>
> Thank you,
>
> Gemma
> ------------------------------------------------------------------------------
> WhatsUp Gold - Download Free Network Management Software
> The most intuitive, comprehensive, and cost-effective network
> management toolset available today. ?Delivers lowest initial
> acquisition cost and overall TCO of any competing solution.
> http://p.sf.net/sfu/whatsupgold-sd
> _______________________________________________
> lammps-users mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/lammps-users
>
>

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

Message: 4
Date: Fri, 6 May 2011 08:05:57 -0600
From: Steve Plimpton <[email protected]>
Subject: Re: [lammps-users] periodic boundary conditions for polymers
To: Kourosh Rad <[email protected]>
Cc: "[email protected]"
<[email protected]>
Message-ID: <[email protected].>
Content-Type: text/plain; charset=ISO-8859-1

Comments below.

Steve

On Fri, May 6, 2011 at 6:54 AM, Kourosh Rad <[email protected]> wrote:
> Dear LAMMPS users,
> I am modeling a polymeric system. I have two separate questions:
> 1- I am going to stretch the plymer to obtain its Young's modulus. In
> addition, I need to run my system under periodic boundary conditions. I was
> wondering if it is possible to use periodic boundary conditions and stretch
> the system using displace_atoms command at the same time. As I read in the
> manual the only way to change the size of the system under periodic boundary
> conditions is using change in pressure or using deform command.

I think you want fix deform. It stretches both the simulation box and
displaces the atoms.

> 2- when you run a system containing bonds like polymers under periodic
> conditions if an atom crosses one side of the boundary it practically
> re-enters from the other side even if it is bonded to another atom which is
> steel in its original place. It is practically means that there is huge
> distance between the two atoms which are bonded together. As long as you run
> your system under periodic boundary it does not seem to be a problem.
> However, if after a while you want to continue the modelling using other
> types of boundaries like shrink? you get the error "bond atom %%% %%%
> missing". IS there anyway to solve this problem or we simply should not run
> the polymeric system under periodic boundary conditions.

That error means you probably pulled too far and things blew up. Bonds
can't be stretched indefinitely w/out huge energy excursions.

> Any help would be highly appreciated.
>
> Bests,
>
> Kourosh
>
> ------------------------------------------------------------------------------
> WhatsUp Gold - Download Free Network Management Software
> The most intuitive, comprehensive, and cost-effective network
> management toolset available today. ?Delivers lowest initial
> acquisition cost and overall TCO of any competing solution.
> http://p.sf.net/sfu/whatsupgold-sd
> _______________________________________________
> lammps-users mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/lammps-users
>
>

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

Message: 5
Date: Fri, 6 May 2011 16:14:55 +0200
From: Laurent Joly <[email protected]>
Subject: Re: [lammps-users] LAMMPS compilation on cluster
To: Steve Plimpton <[email protected]>
Cc: karan saini <[email protected]>,
[email protected]
Message-ID: <[email protected]>
Content-Type: text/plain; charset=UTF-8

Dear Karan and Steve,

>> mpicxx -g ?O -DLAMMPS_GZIP -I../../lib/reax -I../../lib/poems -I../../lib/meam -I/application/openmpi-1.4.1-2-gnu/include -DMPICH_IGNORE_CXX_SEEK -I/application/fftw-2.1.5-gnu/include -DFFT_FFTW -M universe.cpp > universe.d

>> g++: ?O: No such file or directory

I think the error comes from a typo: the minus before O is not
standard, so you should replace "?O" by "-O" in your Makefile flags.
The question is, how did this strange minus appeared in your Makefile?

Best,
Laurent

2011/5/6 Steve Plimpton <[email protected]>:
> There is no reason to use sudo to build LAMMPS as root:
>
> sudo make linux
>
> The error you get is that it can't find g++, which means
> you have bigger problems than building LAMMPS.
>
> Steve
>
> On Thu, May 5, 2011 at 10:52 PM, karan saini <[email protected]> wrote:
>> I have made cluster using openmpi-1.4.1-2? instead of mpich1 using the
>> procedure as mentioned at using ubuntu 10.04
>> http://www.linux.com/community/blogs/Building-a-Beowulf-Cluster-in-just-13-steps-.html
>>
>> I have not included LD_LIBRARY_PATH as mentioned as mentioned there (let me
>> know how to do that also )
>>
>> I am trying to compile lammps on the cluster
>>
>> After uncompressing lammps.tar.gz,(actually, libs for LAMMPS is part of
>> lammps.tar.gz)
>>
>> cd lib/reax
>> Change gfortran to mpif77 in Makefile.gfortran
>> sudo make -f Makefile.gfortran`` >> >> cd lib/meam >> Change gfortran to mpif77 in Makefile.gfortran >> sudo make -f Makefile.gfortran >> >> cd lib/poems >> Change g++ to mpicxx in Makefile.g++ >> sudo make -f Makefile.g++ >> >> LAMMPS >> cd src >> >> Check which packages are included >> sudo make package-status >> >> Choose all standard packages to be included >> sudo make yes-standard >> >> If you don’t have GPU, then exclude gpu package. Otherwise, you will see >> tons of error message when you compile it. >> sudo make no-gpu >> >> Edit MAKE/Makefile.linux >> >> CC = mpicxx >> CCFLAGS = -g ?O >> DEPFLAGS = -M >> LINK = mpicxx >> LINKFLAGS = -g ?O >> LIB = >> FFT_INC = -I/application/fftw-2.1.5-gnu/ >> include -DFFT_FFTW >> FFT_PATH = -L/application/fftw-2.1.5-gnu/lib >> FFT_LIB = -lfftw >> >> >> MPI_INC = -I/application/openmpi-1.4.2-gnu/include -DMPICH_IGNORE_CXX_SEEK >> MPI_PATH = -L/application/openmpi-1.4.2-gnu/lib >> MPI_LIB =? -lpthread ?lmpi >> >> >> >> Build LAMMPS as an executable and library as well >> >> sudo make linux >> >> then i get the following error (last few lines) >> >> Makefile:96: temper.d: No such file or directory >> Makefile:96: thermo.d: No such file or directory >> Makefile:96: timer.d: No such file or directory >> Makefile:96: universe.d: No such file or directory >> mpicxx -g ?O -DLAMMPS_GZIP -I…/…/lib/reax -I…/…/lib/poems >> -I…/…/lib/meam? -I/application/openmpi-1.4.1-2-gnu/include >> -DMPICH_IGNORE_CXX_SEEK -I/application/fftw-2.1.5-gnu/include -DFFT_FFTW -M >> universe.cpp > universe.d >> g++: ?O: No such file or directory >> make[1]: *** [universe.d] Error 1 >> make[1]: Leaving directory /home/mpiuser/lammps-15Mar11/src/Obj_linux'
>> make: *** [linux] Error 2
>>
>>
>>
>> Please let me know how to make LAMMPS executable
>>
>>
>>
>> --
>> With thanks and regards'
>>
>> Karan Saini
>> +91-9988 400 533
>>
>>
>> ------------------------------------------------------------------------------
>> WhatsUp Gold - Download Free Network Management Software
>> The most intuitive, comprehensive, and cost-effective network
>> management toolset available today. ?Delivers lowest initial
>> acquisition cost and overall TCO of any competing solution.
>> http://p.sf.net/sfu/whatsupgold-sd
>> _______________________________________________
>> lammps-users mailing list
>> [email protected]
>> https://lists.sourceforge.net/lists/listinfo/lammps-users
>>
>>
>
> ------------------------------------------------------------------------------
> WhatsUp Gold - Download Free Network Management Software
> The most intuitive, comprehensive, and cost-effective network
> management toolset available today. ?Delivers lowest initial
> acquisition cost and overall TCO of any competing solution.
> http://p.sf.net/sfu/whatsupgold-sd
> _______________________________________________
> lammps-users mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/lammps-users
>

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

Message: 6
Date: Fri, 6 May 2011 16:18:43 +0200
From: Laurent Joly <[email protected]>
Subject: Re: [lammps-users] periodic boundary conditions for polymers
To: Steve Plimpton <[email protected]>
Cc: Kourosh Rad <[email protected]>,
"[email protected]"
<[email protected]>
Message-ID: <[email protected]>
Content-Type: text/plain; charset=UTF-8

If you don't use periodic boundary conditions, you have to put some
kind of wall at the boundaries to prevent atoms from exiting the box,
otherwise they will be lost.

Best,
Laurent

2011/5/6 Steve Plimpton <[email protected]>:
> Comments below.
>
> Steve
>
> On Fri, May 6, 2011 at 6:54 AM, Kourosh Rad <[email protected]> wrote:
>> Dear LAMMPS users,
>> I am modeling a polymeric system. I have two separate questions:
>> 1- I am going to stretch the plymer to obtain its Young's modulus. In
>> addition, I need to run my system under periodic boundary conditions. I was
>> wondering if it is possible to use periodic boundary conditions and stretch
>> the system using displace_atoms command at the same time. As I read in the
>> manual the only way to change the size of the system under periodic boundary
>> conditions is using change in pressure or using deform command.
>
> I think you want fix deform. ?It stretches both the simulation box and
> displaces the atoms.
>
>> 2- when you run a system containing bonds like polymers under periodic
>> conditions if an atom crosses one side of the boundary it practically
>> re-enters from the other side even if it is bonded to another atom which is
>> steel in its original place. It is practically means that there is huge
>> distance between the two atoms which are bonded together. As long as you run
>> your system under periodic boundary it does not seem to be a problem.
>> However, if after a while you want to continue the modelling using other
>> types of boundaries like shrink? you get the error "bond atom %%% %%%
>> missing". IS there anyway to solve this problem or we simply should not run
>> the polymeric system under periodic boundary conditions.
>
> That error means you probably pulled too far and things blew up. ?Bonds
> can't be stretched indefinitely w/out huge energy excursions.
>
>
>> Any help would be highly appreciated.
>>
>> Bests,
>>
>> Kourosh
>>
>> ------------------------------------------------------------------------------
>> WhatsUp Gold - Download Free Network Management Software
>> The most intuitive, comprehensive, and cost-effective network
>> management toolset available today. ?Delivers lowest initial
>> acquisition cost and overall TCO of any competing solution.
>> http://p.sf.net/sfu/whatsupgold-sd
>> _______________________________________________
>> lammps-users mailing list
>> [email protected]
>> https://lists.sourceforge.net/lists/listinfo/lammps-users
>>
>>
>
> ------------------------------------------------------------------------------
> WhatsUp Gold - Download Free Network Management Software
> The most intuitive, comprehensive, and cost-effective network
> management toolset available today. ?Delivers lowest initial
> acquisition cost and overall TCO of any competing solution.
> http://p.sf.net/sfu/whatsupgold-sd
> _______________________________________________
> lammps-users mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/lammps-users
>

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

------------------------------------------------------------------------------
WhatsUp Gold - Download Free Network Management Software
The most intuitive, comprehensive, and cost-effective network
management toolset available today. Delivers lowest initial
acquisition cost and overall TCO of any competing solution.
http://p.sf.net/sfu/whatsupgold-sd

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

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End of lammps-users Digest, Vol 60, Issue 23
********************************************