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?
> From: [email protected][email protected] > Subject: lammps-users Digest, Vol 60, Issue 93 > To: [email protected] > Date: Monday, May 23, 2011, 6:03 PM > > Send lammps-users mailing list submissions to > [email protected] > > 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 > [email protected] > > You can reach the person managing the list at > [email protected] > > When replying, please edit your Subject line so it is more specific > than “Re: Contents of lammps-users digest…” > > 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: ?? <zhangteng2008@…24…> > Cc: [email protected] > Message-ID: <BANLkTikHDRYMTUtg6L0v5oi43qA-s6utRA@…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, ?? <zhangteng2008@…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 > > developers boost performance applications - including clusters. > > http://p.sf.net/sfu/intel-dev2devmay > > _______________________________________________ > > lammps-users mailing list > > lammps-users@…459…ourceforge.net > > https://lists.sourceforge.net/lists/listinfo/lammps-users > > > > > > ------------------------------ > > Message: 2 > Date: Mon, 23 May 2011 07:28:06 -0600 > From: Steve Plimpton <sjplimp@…92…> > Subject: Re: [lammps-users] ERROR: Mismatched compute in variable > formula > To: “Li,LiLi” <lil3@…1037…>, LAMMPS > <lammps-users@…459…ourceforge.net> > Message-ID: <BANLkTi=9G-XbBPyQS7OmhzPE5410fqS6pw@…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 <lil3@…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: lammps-users@…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 <lil3@…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 <saly.jackson12@…24…> > Cc: LAMMPS <[email protected]> > Message-ID: <BANLkTi=Qc9f5Mg0+oTAjDwOqFg+3CMf4Zg@…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 <saly.jackson12@…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 > > lammps-users@…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 > > lammps-users@…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]> > Subject: Re: [lammps-users] problem with thermostat a region > To: Yong Li <yonglifly@…24…> > Cc: [email protected] > Message-ID: <BANLkTikL8Sxt5-mjdvgs48ULoqxkKSPAxg@…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 <yonglifly@…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 <hossein_dormohammadi@…1152…> > Cc: [email protected] > Message-ID: <BANLkTinEpW=MU+cjqEec3DMRdUToADiboA@…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 < > hossein_dormohammadi@…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 > > lammps-users@…431…ceforge.net > > https://lists.sourceforge.net/lists/listinfo/lammps-users > > > > > -------------- next part -------------- > An HTML attachment was scrubbed… > > ------------------------------ > > ------------------------------------------------------------------------------ > 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 > > End of lammps-users Digest, Vol 60, Issue 93 > ********************************************