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@ -3,7 +3,7 @@
<!-- HTML_ONLY -->
<HEAD>
<TITLE>LAMMPS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="19 Aug 2015 version">
<META NAME="docnumber" CONTENT="28 Aug 2015 version">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD>
@ -21,7 +21,7 @@
<P><CENTER><H3>LAMMPS Documentation
</H3></CENTER>
<CENTER><H4>19 Aug 2015 version
<CENTER><H4>28 Aug 2015 version
</H4></CENTER>
<H4>Version info:
</H4>

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@ -478,8 +478,8 @@ package</A>.
<TR ALIGN="center"><TD ><A HREF = "compute_meso_rho_atom.html">meso_rho/atom</A></TD><TD ><A HREF = "compute_meso_t_atom.html">meso_t/atom</A></TD><TD ><A HREF = "compute_saed.html">saed</A></TD><TD ><A HREF = "compute_smd_contact_radius.html">smd/contact/radius</A></TD><TD ><A HREF = "compute_smd_damage.html">smd/damage</A></TD><TD ><A HREF = "compute_smd_hourglass_error.html">smd/hourglass/error</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_smd_internal_energy.html">smd/internal/energy</A></TD><TD ><A HREF = "compute_smd_plastic_strain.html">smd/plastic/strain</A></TD><TD ><A HREF = "compute_smd_plastic_strain_rate.html">smd/plastic/strain/rate</A></TD><TD ><A HREF = "compute_smd_rho.html">smd/rho</A></TD><TD ><A HREF = "compute_smd_tlsph_defgrad.html">smd/tlsph/defgrad</A></TD><TD ><A HREF = "compute_smd_tlsph_dt.html">smd/tlsph/dt</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_smd_tlsph_num_neighs.html">smd/tlsph/num/neighs</A></TD><TD ><A HREF = "compute_smd_tlsph_shape.html">smd/tlsph/shape</A></TD><TD ><A HREF = "compute_smd_tlsph_strain.html">smd/tlsph/strain</A></TD><TD ><A HREF = "compute_smd_tlsph_strain_rate.html">smd/tlsph/strain/rate</A></TD><TD ><A HREF = "compute_smd_tlsph_stress.html">smd/tlsph/stress</A></TD><TD ><A HREF = "compute_smd_triangle_mesh_vertices.html">smd/triangle/mesh/vertices</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_smd_ulsph_num_neighs.html">smd/ulsph/num/neighs</A></TD><TD ><A HREF = "compute_smd_ulsph_strain.html">smd/ulsph/strain</A></TD><TD ><A HREF = "compute_smd_ulsph_strain_rate.html">smd/ulsph/strain/rate</A></TD><TD ><A HREF = "compute_smd_ulsph_stress.html">smd/ulsph/stress</A></TD><TD ><A HREF = "compute_smd_vol.html">smd/vol</A></TD><TD ><A HREF = "compute_temp_drude.html">temp/drude</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_temp_eff.html">temp/eff</A></TD><TD ><A HREF = "compute_temp_deform_eff.html">temp/deform/eff</A></TD><TD ><A HREF = "compute_temp_region_eff.html">temp/region/eff</A></TD><TD ><A HREF = "compute_temp_rotate.html">temp/rotate</A></TD><TD ><A HREF = "compute_xrd.html">xrd</A>
<TR ALIGN="center"><TD ><A HREF = "compute_smd_ulsph_num_neighs.html">smd/ulsph/num/neighs</A></TD><TD ><A HREF = "compute_smd_ulsph_strain.html">smd/ulsph/strain</A></TD><TD ><A HREF = "compute_smd_ulsph_strain_rate.html">smd/ulsph/strain/rate</A></TD><TD ><A HREF = "compute_smd_ulsph_stress.html">smd/ulsph/stress</A></TD><TD ><A HREF = "compute_smd_vol.html">smd/vol</A></TD><TD ><A HREF = "compute_tally.html">tally</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_temp_drude.html">temp/drude</A></TD><TD ><A HREF = "compute_temp_eff.html">temp/eff</A></TD><TD ><A HREF = "compute_temp_deform_eff.html">temp/deform/eff</A></TD><TD ><A HREF = "compute_temp_region_eff.html">temp/region/eff</A></TD><TD ><A HREF = "compute_temp_rotate.html">temp/rotate</A></TD><TD ><A HREF = "compute_xrd.html">xrd</A>
</TD></TR></TABLE></DIV>
<HR>

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@ -282,9 +282,18 @@ class. See compute.h for details.
<TR><TD >remove_bias_all</TD><TD > remove velocity bias from all atoms in group (optional)</TD></TR>
<TR><TD >restore_bias</TD><TD > restore velocity bias for one atom after remove_bias (optional)</TD></TR>
<TR><TD >restore_bias_all</TD><TD > same as before, but for all atoms in group (optional)</TD></TR>
<TR><TD >pair_tally_callback</TD><TD > callback function for <I>tally</I>-style computes (optional).</TD></TR>
<TR><TD >memory_usage</TD><TD > tally memory usage (optional)
</TD></TR></TABLE></DIV>
<P>Tally-style computes are a special case, as their computation is done
in two stages: the callback function is registered with the pair style
and then called from the Pair::ev_tally() function, which is called for
each pair after force and energy has been computed for this pair. Then
the tallied values are retrieved with the standard compute_scalar or
compute_vector or compute_peratom methods. The USER-TALLY package
provides <I>examples</I>_compute_tally.html for utilizing this mechanism.
</P>
<HR>
<A NAME = "mod_4"></A><H4>10.4 Dump styles

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@ -131,7 +131,7 @@ on how to build LAMMPS with both kinds of auxiliary libraries.
<TR ALIGN="center"><TD >USER-DRUDE</TD><TD > Drude oscillators</TD><TD > Dequidt & Devemy & Padua (3)</TD><TD > <A HREF = "tutorial_drude.html">tutorial</A></TD><TD > USER/drude</TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >USER-EFF</TD><TD > electron force field</TD><TD > Andres Jaramillo-Botero (Caltech)</TD><TD > <A HREF = "pair_eff.html">pair_style eff/cut</A></TD><TD > USER/eff</TD><TD > <A HREF = "http://lammps.sandia.gov/movies.html#eff">eff</A></TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >USER-FEP</TD><TD > free energy perturbation</TD><TD > Agilio Padua (U Blaise Pascal Clermont-Ferrand)</TD><TD > <A HREF = "compute_fep.html">compute fep</A></TD><TD > USER/fep</TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >USER-H5MD</TD><TD > dump output via HDF5</TD><TD > Pierre de Buyl (KU Leuven)</TD><TD > <A HREF = "dump_h5md.html">dump h5md</A></TD><TD > -</TD><TD > -</TD><TD > h5md</TD></TR>
<TR ALIGN="center"><TD >USER-H5MD</TD><TD > dump output via HDF5</TD><TD > Pierre de Buyl (KU Leuven)</TD><TD > <A HREF = "dump_h5md.html">dump h5md</A></TD><TD > -</TD><TD > -</TD><TD > lib/h5md</TD></TR>
<TR ALIGN="center"><TD >USER-INTEL</TD><TD > Vectorized CPU and Intel(R) coprocessor styles</TD><TD > W. Michael Brown (Intel)</TD><TD > <A HREF = "accelerate_intel.html">Section accelerate</A></TD><TD > examples/intel</TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >USER-LB</TD><TD > Lattice Boltzmann fluid</TD><TD > Colin Denniston (U Western Ontario)</TD><TD > <A HREF = "fix_lb_fluid.html">fix lb/fluid</A></TD><TD > USER/lb</TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >USER-MISC</TD><TD > single-file contributions</TD><TD > USER-MISC/README</TD><TD > USER-MISC/README</TD><TD > -</TD><TD > -</TD><TD > -</TD></TR>
@ -144,6 +144,7 @@ on how to build LAMMPS with both kinds of auxiliary libraries.
<TR ALIGN="center"><TD >USER-REAXC</TD><TD > C version of ReaxFF</TD><TD > Metin Aktulga (LBNL)</TD><TD > <A HREF = "pair_reax_c.html">pair_style reaxc</A></TD><TD > reax</TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >USER-SMD</TD><TD > smoothed Mach dynamics</TD><TD > Georg Ganzenmuller (EMI)</TD><TD > <A HREF = "PDF/SMD_LAMMPS_userguide.pdf">userguide.pdf</A></TD><TD > USER/smd</TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >USER-SPH</TD><TD > smoothed particle hydrodynamics</TD><TD > Georg Ganzenmuller (EMI)</TD><TD > <A HREF = "PDF/SPH_LAMMPS_userguide.pdf">userguide.pdf</A></TD><TD > USER/sph</TD><TD > <A HREF = "http://lammps.sandia.gov/movies.html#sph">sph</A></TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >USER-TALLY</TD><TD > Pairwise tallied computes</TD><TD > Axel Kohlmeyer (Temple U)</TD><TD > <A HREF = "compute_tally.html">compute <...>/tally</A></TD><TD > USER/tally</TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >
</TD></TR></TABLE></DIV>

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<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>compute force/tally command
</H3>
<H3>compute pe/tally command
</H3>
<H3>compute stress/tally command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID style group2-ID
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>style = <I>force/tally</I> or <I>pe/tally</I> or <I>stress/tally</I>
<LI>group2-ID = group ID of second (or same) group
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 lower force/tally upper
compute 1 left pe/tally right
compute 1 lower stress/tally lower
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates properties between two groups of
atoms by accumulating them from pairwise non-bonded computations. The
two groups can be the same. This is similar to <A HREF = "compute_group_group.html">compute
group/group</A> only that the data is
accumulated directly during the non-bonded force computation. The
computes <I>force/tally</I>, <I>pe/tally</I>, <I>stress/tally</I>, and
<I>heat/flux/tally</I> are primarily provided as example how to program
additional, more sophisticated computes using the tally mechanism.
</P>
<HR>
<P>The pairwise contributions are computing via a callback that the
compute registers with the non-bonded pairwise force computation.
This limits the use to systems that have no bonds, no Kspace, and no
manybody interactions. On the other hand, the computation does not
have to compute forces or energies a second time and thus can be much
more efficient. The callback mechanism allows to write more complex
pairwise property computations.
</P>
<HR>
<P><B>Output info:</B>
</P>
<P>Compute <I>pe/tally</I> calculates a global scalar (the energy) and a per
atom scalar (the contributions of the single atom to the global
scalar). Compute <I>force/tally</I> calculates a global scalar (the force
magnitude) and a per atom 3-element vector (force contribution from
each atom). Compute <I>stress/tally</I> calculates a global scalar
(average of the diagonal elements of the stress tensor) and a per atom
vector (the 6 elements of stress tensor contributions from the
individual atom).
</P>
<P>Both the scalar and vector values calculated by this compute are
"extensive".
</P>
<P><B>Restrictions:</B>
</P>
<P>This compute is part of the USER-TALLY package. It is only enabled
if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P>Not all pair styles can be evaluated in a pairwise mode as required by
this compute. For example, 3-body and other many-body potentials,
such as <A HREF = "pair_tersoff.html">Tersoff</A> and
<A HREF = "pair_sw.html">Stillinger-Weber</A> cannot be used. <A HREF = "pair_eam.html">EAM</A>
potentials only include the pair potential portion of the EAM
interaction when used by this compute, not the embedding term. Also
bonded or Kspace interactions do not contribute to this compute.
</P>
<P><B>Related commands:</B>
</P>
<P><I>compute group/group</I>_compute_group_group.html, <I>compute
heat/flux</I>_compute_heat_flux.html
</P>
<P><B>Default:</B> none
</P>
</HTML>

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@ -17,12 +17,12 @@
</PRE>
<LI><I>args</I> = one or more of <I>off</I> or <I>loop</I> or <I>normal</I> or <I>full</I> or <I>sync</I> or <I>nosync</I>
<PRE> <I>off</I> = do not collect and print timing information
<PRE> <I>off</I> = do not collect or print any timing information
<I>loop</I> = collect only the total time for the simulation loop
<I>normal</I> = collect timer information broken down in sections (default)
<I>normal</I> = collect timer information broken down by sections (default)
<I>full</I> = like <I>normal</I> but also include CPU and thread utilzation
<I>sync</I> = explicitly synchronize MPI tasks between sections
<I>nosync</I> = do not synchronize MPI tasks when collecting timer info (default)
<I>nosync</I> = do not synchronize MPI tasks between sections (default)
</PRE>
<P><B>Examples:</B>
</P>
@ -31,44 +31,46 @@ timer loop
</PRE>
<P><B>Description:</B>
</P>
<P>Select to which level of detail LAMMPS is performing internal profiling.
<P>Select the level of detail LAMMPS performs its CPU timings.
</P>
<P>During regular runs LAMMPS will collect information about how much
<P>During a simulation run LAMMPS collects information about how much
time is spent in different sections of the code and thus can provide
valuable information for determining performance and load imbalance
problems. This can be done at different levels of detail and
accuracy. For more information about the timing output, please have a
look at the <A HREF = "Section_start.html#start_8">discussion of screen output</A>.
accuracy. For more information about the timing output, see this
<A HREF = "Section_start.html#start_8">discussion of screen output</A>.
</P>
<P>The <I>off</I> setting will turn all time measurements off. The <I>loop</I>
setting will only measure the total time of run loop and not collect
any detailed per section information. With the <I>normal</I> setting,
timing information for individual sections of the code are collected
and also information about load imbalances inside those sections
presented. The <I>full</I> setting adds information about CPU utilization
and thread utilization, when multi-threading is enabled.
setting will only measure the total time for a run and not collect any
detailed per section information. With the <I>normal</I> setting, timing
information for portions of the timestep (pairwise calculations,
neighbor list construction, output, etc) are collected as well as
information about load imbalances for those sections across
procsessors. The <I>full</I> setting adds information about CPU
utilization and thread utilization, when multi-threading is enabled.
</P>
<P>With the <I>sync</I> setting, all MPI tasks are synchronized at each timer
call and thus allowing to study load imbalance more accuractly, but
this usually has some performance impact. Using the <I>nosync</I> setting
this can be turned off (which is the default).
call which meaures load imbalance more accuractly, though it can also
slow down the simulation. Using the <I>nosync</I> setting (which is the
default) turns off this synchronization.
</P>
<P>Multiple keywords can be provided and for keywords that are mutually
exclusive, the last one in that group is taking effect.
<P>Multiple keywords can be specified. For keywords that are mutually
exclusive, the last one specified takes effect.
</P>
<P>IMPORTANT NOTE: Using the <I>full</I> and <I>sync</I> options provides the most
detailed and accurate timing information, but also can have a
significant negative performance impact due to the overhead of the
many required system calls. It is thus recommended to use these
settings only when making tests to identify the performance. For
calculations with few atoms or a very large number of performance,
even using the <I>normal</I> setting can have a measurable performance
impact. In those cases just use the <I>loop</I> or <I>off</I> setting.
detailed and accurate timing information, but can also have a negative
performance impact due to the overhead of the many required system
calls. It is thus recommended to use these settings only when testing
tests to identify performance bottlenecks. For calculations with few
atoms or a very large number of processors, even the <I>normal</I> setting
can have a measurable negative performance impact. In those cases you
can just use the <I>loop</I> or <I>off</I> setting.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
<A HREF = "run.html">run post no</A>, <A HREF = "kspace_modify.html">kspace_modify fftbench</A>
</P>
<P><A HREF = "run.html">run post no</A>, <A HREF = "kspace_modify.html">kspace_modify fftbench</A>
</P>
<P><B>Default:</B>
</P>