lammps-users Digest, Vol 60, Issue 93


Dear Steve, thanks for answer,

exactly the problem is: I am going to sketch the stress-strain diagram for bulk silicon in 300 K. But the stress of the atoms dosnt have a trend and changes (negative and positive). Actuallty before this i sketched the stress-strain diagram in zero tempreture (exactly by using that input file with 5.43 A for lattice constant) and the stress of the atoms had its own trend in tensile and compress, but in 300 K it doesnt have. Even i ran for 5 melion steps it didnt relax and changes. i dont know why?!!
What i am doing wrong? or i have to do another process when i have the tempreture?

thanks



— On Mon, 5/23/11, [email protected] [email protected] wrote:



> From: [email protected] [email protected]
> Subject: lammps-users Digest, Vol 60, Issue 93
> To: [email protected]
> Date: Monday, May 23, 2011, 6:03 PM
>
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> Today’s Topics:
>
> 1. Re: Question on fracture of angle potential (Steve Plimpton)
> 2. Re: ERROR: Mismatched compute in variable formula (Steve Plimpton)
> 3. Re: Fwd: Neighbor list overflow, boost neigh_modify one or
> page (Steve Plimpton)
> 4. Re: problem with thermostat a region (Steve Plimpton)
> 5. Re: help (Steve Plimpton)
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 23 May 2011 07:27:28 -0600
> From: Steve Plimpton <[email protected]>
> Subject: Re: [lammps-users] Question on fracture of angle potential
> To: ?? <[email protected]…24…>
> Cc: [email protected]
> Message-ID: <[email protected]…25…>
> Content-Type: text/plain; charset=UTF-8
>
> There is a bond/break and bond/quartic potential that does this.
> If you wanted something similar for an angle potential, you
> would have to code it up. You need to do it in a way, that
> you do not inject a large amount of energy into your system
> at the moment the angle breaks. This is what bond/quartic does.
>
> Steve
>
> On Sat, May 21, 2011 at 8:21 PM, ?? <[email protected]…24…> wrote:
> > Dear all,
> >
> > I am recently trying to do fracture simulation with modified morse
> > potential, such that morse potential added with a angle potential term. For
> > simplicity, I just chose harmonic angle style. The morse bond will break
> > beyond its cut off radius, but the angle interaction remains. I wonder is
> > there any way to set a cut off to angle potential? For example, the angle is
> > denoted as \theta_ijk, where j is the center atom, can I set that once r_ij
> > or r_jk is larger than a critical value, which may be the same value as that
> > of morse, the angle interaction is turned off?
> >
> > I am not sure whether this can be achieved through the command in the input
> > script?
> >
> > Thanks a lot.
> >
> > Best,
> >
> > Teng
> >
> > ------------------------------------------------------------------------------
> > What Every C/C++ and Fortran developer Should Know!
> > Read this article and learn how Intel has extended the reach of its
> > next-generation tools to help Windows* and Linux* C/C++ and Fortran
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> > https://lists.sourceforge.net/lists/listinfo/lammps-users
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> >
>
> ------------------------------
>
> Message: 2
> Date: Mon, 23 May 2011 07:28:06 -0600
> From: Steve Plimpton <[email protected]…92…>
> Subject: Re: [lammps-users] ERROR: Mismatched compute in variable
> formula
> To: “Li,LiLi” <[email protected]…1037…>, LAMMPS
> <[email protected]…459…ourceforge.net>
> Message-ID: <BANLkTi=[email protected]…25…>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Probably - I would upgrade to the current version.
>
> Steve
>
> On Sun, May 22, 2011 at 7:02 AM, Li,LiLi <[email protected]…1037…> wrote:
> > Hi, Steve
> >
> > I am using version of 2009, which the workstation of university installed. Is it because of the LAMMPS version?
> >
> > Lily
> >
> > ________________________________________
> > From: Steve Plimpton [[email protected]]
> > Sent: Thursday, May 19, 2011 9:58 AM
> > To: Li,LiLi
> > Cc: [email protected]…452…sts.sourceforge.net
> > Subject: Re: [lammps-users] ERROR: Mismatched compute in variable formula
> >
> > If I add those 3 lines to bench/in.lj and change matrix
> > to all, it works fine. ?Are you using the current version
> > of LAMMPS?
> >
> > Steve
> >
> > On Thu, May 19, 2011 at 1:54 AM, Li,LiLi <[email protected]…1037…> wrote:
> >> Hi,
> >>
> >> I am trying to use compute stress/atom command as followed:
> >>
> >> compute as matrix stress/atom
> >> variable as atom
> >> sqrt((c_as[1]-c_as[2])^2+(c_as[2]-c_as[3])^2+(c_as[3]-c_as[1])^2)
> >> dump 3 matrix custom 2000 dumpas.lammpstrj id type x y z c_as[1] c_as[2]
> >> c_as[3] c_as[4] c_as[5] c_as[6] v_as
> >>
> >> ERROR: Mismatched compute in variable formula
> >>
> >> could anyone tell me where I did wrong? ?Thanks a lot!!
> >>
> >> lily
> >>
> >> ------------------------------------------------------------------------------
> >> What Every C/C++ and Fortran developer Should Know!
> >> Read this article and learn how Intel has extended the reach of its
> >> next-generation tools to help Windows* and Linux* C/C++ and Fortran
> >> developers boost performance applications - including clusters.
> >> http://p.sf.net/sfu/intel-dev2devmay
> >> _______________________________________________
> >> lammps-users mailing list
> >> [email protected]
> >> https://lists.sourceforge.net/lists/listinfo/lammps-users
> >>
> >>
>
> ------------------------------
>
> Message: 3
> Date: Mon, 23 May 2011 07:29:28 -0600
> From: Steve Plimpton <[email protected]>
> Subject: Re: [lammps-users] Fwd: Neighbor list overflow, boost
> neigh_modify one or page
> To: saly jackson <[email protected]…24…>
> Cc: LAMMPS <[email protected]>
> Message-ID: <BANLkTi=Qc9f5Mg0+oTAjDwOqFg+[email protected]…25…>
> Content-Type: text/plain; charset=ISO-8859-1
>
> The neigh_modify limits are large. 2000 neighbors per atom.
> You can set them larger if you like. But you should ask yourself
> why your system is exceeding those limits It is porbably an
> error in your setup.
>
> Steve
>
> On Sun, May 22, 2011 at 7:19 AM, saly jackson <[email protected]…24…> wrote:
> > Hi all
> >
> > In my simulation when there are about 1000 atoms I have no error, but when
> > there are about 4000 atoms I have the following error:
> >
> > Neighbor list overflow, boost neigh_modify one or page
> > --------------------------------------------------------------------------
> > MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
> > with errorcode 1.
> >
> > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> > You may or may not see output from other processes, depending on
> > exactly when Open MPI kills them.
> >
> > Also I used
> >
> > neigh_modify??? delay 10 every 2 check yes page 100000
> >
> > but still I have the error
> >
> > Also in visually all things are correct.
> >
> > Would you please help me?
> >
> > Elena
> >
> > ------------------------------------------------------------------------------
> > Achieve unprecedented app performance and reliability
> > What every C/C++ and Fortran developer should know.
> > Learn how Intel has extended the reach of its next-generation tools
> > to help boost performance applications - inlcuding clusters.
> > http://p.sf.net/sfu/intel-dev2devmay
> > _______________________________________________
> > lammps-users mailing list
> > [email protected]…459…ourceforge.net
> > https://lists.sourceforge.net/lists/listinfo/lammps-users
> >
> >
> >
> > ------------------------------------------------------------------------------
> > What Every C/C++ and Fortran developer Should Know!
> > Read this article and learn how Intel has extended the reach of its
> > next-generation tools to help Windows* and Linux* C/C++ and Fortran
> > developers boost performance applications - including clusters.
> > http://p.sf.net/sfu/intel-dev2devmay
> > _______________________________________________
> > lammps-users mailing list
> > [email protected]…239…forge.net
> > https://lists.sourceforge.net/lists/listinfo/lammps-users
> >
> >
>
> ------------------------------
>
> Message: 4
> Date: Mon, 23 May 2011 07:31:14 -0600
> From: Steve Plimpton <[email protected]ov>
> Subject: Re: [lammps-users] problem with thermostat a region
> To: Yong Li <[email protected]…24…>
> Cc: [email protected]
> Message-ID: <[email protected]…25…>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Use compute temp/region and assign it to a thermostat.
> Section 4.16 of the manual has a good overview of this
> and other options.
>
> Steve
>
> On Sun, May 22, 2011 at 9:03 PM, Yong Li <[email protected]…24…> wrote:
> > Dear all,
> >
> > How to keep the temperature of a specific region at a constant value in
> > lammps? The region has a fixed size, while atoms can enter/leave the region.
> > I find it very difficult to define a group for this region with dynamic
> > atoms.
> >
> > I tried fix heat/region commend, but the temperature increased gradually. Is
> > there any other commends like fix heat/region that can achieve
> > thermostatting a region with dynamic atoms?
> >
> > Thanks.
> >
> > Yong
> >
> > ------------------------------------------------------------------------------
> > What Every C/C++ and Fortran developer Should Know!
> > Read this article and learn how Intel has extended the reach of its
> > next-generation tools to help Windows* and Linux* C/C++ and Fortran
> > developers boost performance applications - including clusters.
> > http://p.sf.net/sfu/intel-dev2devmay
> > _______________________________________________
> > lammps-users mailing list
> > [email protected]
> > https://lists.sourceforge.net/lists/listinfo/lammps-users
> >
> >
>
> ------------------------------
>
> Message: 5
> Date: Mon, 23 May 2011 07:33:14 -0600
> From: Steve Plimpton <[email protected]>
> Subject: Re: [lammps-users] help
> To: hossein dormohammadi <[email protected]…1152…>
> Cc: [email protected]
> Message-ID: <BANLkTinEpW=MU+[email protected]…43…5…>
> Content-Type: text/plain; charset=“iso-8859-1”
>
> You’re using fix nvt so you’re not controlling the pressure
> at all. It is what it is, and pressures fluctuate. However you
> are using 0.001 for your damping constant in fix nvt which
> is far too small. That is equiv to one timestep in metal
> units. Read the fix nvt doc page and use something more
> like 0.1.
>
> Steve
>
> On Mon, May 23, 2011 at 2:31 AM, hossein dormohammadi <
> [email protected]…16…> wrote:
>
> > Hi lammps-user,
> >
> > i am simulating bulk silicon with tempreture (300 K), static boundry
> > condition, Tersoff potential. I choose 5.445 A for the lattice constant
> > (Ref: “Molecular dyanmycs simulation of bulk silicon under strain” by H.
> > Zhao and N. R. Aluru). I would like to apply compressive load at that
> > tempreture. But the problem is: the pressure (press at thermo_style) dosnt
> > relax and it is changing even after 1 nanosecond (1melion steps) of
> > simulation time. Maybe i dont know the correct “drag” factor in “fix”
> > command!!. Could you please tell me what i am doing wrong?
> >
> > Thanks,
> >
> >
> > The input file is:
> >
> > #Si geometry creation, relaxation and compressive loading
> >
> > #set dimension and boundry condition
> > dimension 3
> > boundary s s s
> >
> > #set units type,atom type and neigborhood
> > units metal
> > atom_style atomic
> > neigh_modify every 1
> > #create big box
> > lattice diamond 5.445
> > region big block -12 12 -12 12 -12 12
> > create_box 1 big
> > #create main atoms
> > lattice diamond 5.445
> > region main block -1.5 1.5 -1.5 1.5 -1.5 1.5
> > create_atoms 1 region main
> >
> > #create sefr region
> > region sefrsefr block -1.5 -1.4 -1.5 1.5 -1.5 1.5
> > group sefr region sefrsefr
> >
> > #create bist region
> > region bistbist block 1.4 1.5 -1.5 1.5 -1.5 1.5
> > group bist region bistbist
> >
> > #create center17 region
> > region centercenter17 block -1.3 1.3 -1.5 1.5 -1.5 1.5
> > group center17 region centercenter17
> >
> > #set the mass of atoms
> > mass 1 28.0855
> >
> > #set the velocity of atoms
> > velocity all create 300.0 4928459 rot yes mom yes
> >
> > #set the velocity of atoms of left and right to zero
> > velocity sefr set 0.0 0.0 0.0
> > velocity bist set 0.0 0.0 0.0
> >
> > #set forces to sefr and bist
> > fix 144 sefr setforce 0.0 0.0 0.0
> > fix 155 bist setforce 0.0 0.0 0.0
> >
> > #define the tersoff potential
> > pair_style tersoff
> > pair_coeff * * Si.tersoff Si
> >
> > #set timestep
> > timestep 0.001
> >
> > #compute stress per atom and potential per atom
> > compute stress all stress/atom
> > compute poten all pe/atom
> >
> > compute stresscenter17x all reduce/region centercenter17
> > sum c_stress[1]
> > compute stresscenter17y all reduce/region centercenter17
> > sum c_stress[2]
> > compute stresscenter17z all reduce/region centercenter17
> > sum c_stress[3]
> >
> > dump 101 all xyz 100000 dump.xyz
> > dump 117 center17 xyz 100000 dump17.xyz
> > dump 17 center17 custom 100000 dump.center17 x y z c_stress[1]
> > c_stress[2] c_stress[3] c_stress[4] c_stress[5] c_stress[6] c_poten
> >
> > #specify values to show in run
> > thermo 10000
> > thermo_style custom step temp pe ke etotal press
> > c_stresscenter17x c_stresscenter17y C_stresscenter17z lx ly lz
> >
> > #specify the method of calculation
> > fix 201 all nvt 300.0 300.0 0.001 drag 0.5 chain no
> > run 1000000
> >
> > #strain load 1
> > fix 201 all nvt 300.0 300.0 0.001 drag 0.5 chain no
> > displace_atoms bist move -0.01 0 0 units box
> > run 100000
> >
> > #strain load 1
> > fix 201 all nvt 300.0 300.0 0.001 drag 0.5 chain no
> > displace_atoms bist move -0.01 0 0 units box
> > run
> > 100000
> > &
> > nbsp;
> >
> >
> >
> >
> >
> >
> >
> >
> > ------------------------------------------------------------------------------
> > What Every C/C++ and Fortran developer Should Know!
> > Read this article and learn how Intel has extended the reach of its
> > next-generation tools to help Windows* and Linux* C/C++ and Fortran
> > developers boost performance applications - including clusters.
> > http://p.sf.net/sfu/intel-dev2devmay
> > _______________________________________________
> > lammps-users mailing list
> > [email protected]…431…ceforge.net
> > https://lists.sourceforge.net/lists/listinfo/lammps-users
> >
> >
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>
> ------------------------------------------------------------------------------
> What Every C/C++ and Fortran developer Should Know!
> Read this article and learn how Intel has extended the reach of its
> next-generation tools to help Windows* and Linux* C/C++ and Fortran
> developers boost performance applications - including clusters.
> http://p.sf.net/sfu/intel-dev2devmay
>
> ------------------------------
>
> _______________________________________________
> lammps-users mailing list
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>
> End of lammps-users Digest, Vol 60, Issue 93
> ********************************************

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