forked from lijiext/lammps
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@ -3,7 +3,7 @@
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<!-- HTML_ONLY -->
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<HEAD>
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<TITLE>LAMMPS Users Manual</TITLE>
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<META NAME="docnumber" CONTENT="3 Sep 2015 version">
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<META NAME="docnumber" CONTENT="4 Sep 2015 version">
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<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
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<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
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</HEAD>
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@ -21,7 +21,7 @@
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<P><CENTER><H3>LAMMPS Documentation
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</H3></CENTER>
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<CENTER><H4>3 Sep 2015 version
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<CENTER><H4>4 Sep 2015 version
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</H4></CENTER>
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<H4>Version info:
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</H4>
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Binary file not shown.
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@ -511,18 +511,19 @@ KOKKOS, o = USER-OMP, t = OPT.
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<TR ALIGN="center"><TD ><A HREF = "pair_line_lj.html">line/lj (o)</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm (cko)</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm/implicit (cko)</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long (cgiko)</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/msm</A></TD><TD ><A HREF = "pair_class2.html">lj/class2 (cgko)</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/cut (cko)</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/long (cgko)</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_lj_cubic.html">lj/cubic (go)</A></TD><TD ><A HREF = "pair_lj.html">lj/cut (cgikot)</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/cut (cgko)</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/debye (cgko)</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/coul/dsf (gko)</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long (cgikot)</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/msm (go)</A></TD><TD ><A HREF = "pair_dipole.html">lj/cut/dipole/cut (go)</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_dipole.html">lj/cut/dipole/long</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/tip4p/cut (o)</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/tip4p/long (ot)</A></TD><TD ><A HREF = "pair_lj_expand.html">lj/expand (cgko)</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_gromacs.html">lj/gromacs (cgko)</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs/coul/gromacs (cko)</A></TD><TD ><A HREF = "pair_lj_long.html">lj/long/coul/long (o)</A></TD><TD ><A HREF = "pair_dipole.html">lj/long/dipole/long</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_lj_long.html">lj/long/tip4p/long</A></TD><TD ><A HREF = "pair_lj_smooth.html">lj/smooth (co)</A></TD><TD ><A HREF = "pair_lj_smooth_linear.html">lj/smooth/linear (o)</A></TD><TD ><A HREF = "pair_lj96.html">lj96/cut (cgo)</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_lubricate.html">lubricate (o)</A></TD><TD ><A HREF = "pair_lubricate.html">lubricate/poly (o)</A></TD><TD ><A HREF = "pair_lubricateU.html">lubricateU</A></TD><TD ><A HREF = "pair_lubricateU.html">lubricateU/poly</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_meam.html">meam (o)</A></TD><TD ><A HREF = "pair_mie.html">mie/cut (o)</A></TD><TD ><A HREF = "pair_morse.html">morse (cgot)</A></TD><TD ><A HREF = "pair_nb3b_harmonic.html">nb3b/harmonic (o)</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_nm.html">nm/cut (o)</A></TD><TD ><A HREF = "pair_nm.html">nm/cut/coul/cut (o)</A></TD><TD ><A HREF = "pair_nm.html">nm/cut/coul/long (o)</A></TD><TD ><A HREF = "pair_peri.html">peri/eps</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_peri.html">peri/lps (o)</A></TD><TD ><A HREF = "pair_peri.html">peri/pmb (o)</A></TD><TD ><A HREF = "pair_peri.html">peri/ves</A></TD><TD ><A HREF = "pair_polymorphic.html">polymorphic</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_reax.html">reax</A></TD><TD ><A HREF = "pair_airebo.html">rebo (o)</A></TD><TD ><A HREF = "pair_resquared.html">resquared (go)</A></TD><TD ><A HREF = "pair_snap.html">snap</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_soft.html">soft (go)</A></TD><TD ><A HREF = "pair_sw.html">sw (cgkio)</A></TD><TD ><A HREF = "pair_table.html">table (gko)</A></TD><TD ><A HREF = "pair_tersoff.html">tersoff (cgko)</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_tersoff_mod.html">tersoff/mod (ko)</A></TD><TD ><A HREF = "pair_tersoff_zbl.html">tersoff/zbl (ko)</A></TD><TD ><A HREF = "pair_coul.html">tip4p/cut (o)</A></TD><TD ><A HREF = "pair_coul.html">tip4p/long (o)</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_tri_lj.html">tri/lj (o)</A></TD><TD ><A HREF = "pair_yukawa.html">yukawa (go)</A></TD><TD ><A HREF = "pair_yukawa_colloid.html">yukawa/colloid (go)</A></TD><TD ><A HREF = "pair_zbl.html">zbl (go)</A>
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<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/coul/dsf (gko)</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long (cgikot)</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/cs</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/msm (go)</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_dipole.html">lj/cut/dipole/cut (go)</A></TD><TD ><A HREF = "pair_dipole.html">lj/cut/dipole/long</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/tip4p/cut (o)</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/tip4p/long (ot)</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_lj_expand.html">lj/expand (cgko)</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs (cgko)</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs/coul/gromacs (cko)</A></TD><TD ><A HREF = "pair_lj_long.html">lj/long/coul/long (o)</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_dipole.html">lj/long/dipole/long</A></TD><TD ><A HREF = "pair_lj_long.html">lj/long/tip4p/long</A></TD><TD ><A HREF = "pair_lj_smooth.html">lj/smooth (co)</A></TD><TD ><A HREF = "pair_lj_smooth_linear.html">lj/smooth/linear (o)</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_lj96.html">lj96/cut (cgo)</A></TD><TD ><A HREF = "pair_lubricate.html">lubricate (o)</A></TD><TD ><A HREF = "pair_lubricate.html">lubricate/poly (o)</A></TD><TD ><A HREF = "pair_lubricateU.html">lubricateU</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_lubricateU.html">lubricateU/poly</A></TD><TD ><A HREF = "pair_meam.html">meam (o)</A></TD><TD ><A HREF = "pair_mie.html">mie/cut (o)</A></TD><TD ><A HREF = "pair_morse.html">morse (cgot)</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_nb3b_harmonic.html">nb3b/harmonic (o)</A></TD><TD ><A HREF = "pair_nm.html">nm/cut (o)</A></TD><TD ><A HREF = "pair_nm.html">nm/cut/coul/cut (o)</A></TD><TD ><A HREF = "pair_nm.html">nm/cut/coul/long (o)</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_peri.html">peri/eps</A></TD><TD ><A HREF = "pair_peri.html">peri/lps (o)</A></TD><TD ><A HREF = "pair_peri.html">peri/pmb (o)</A></TD><TD ><A HREF = "pair_peri.html">peri/ves</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_polymorphic.html">polymorphic</A></TD><TD ><A HREF = "pair_reax.html">reax</A></TD><TD ><A HREF = "pair_airebo.html">rebo (o)</A></TD><TD ><A HREF = "pair_resquared.html">resquared (go)</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_snap.html">snap</A></TD><TD ><A HREF = "pair_soft.html">soft (go)</A></TD><TD ><A HREF = "pair_sw.html">sw (cgkio)</A></TD><TD ><A HREF = "pair_table.html">table (gko)</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_tersoff.html">tersoff (cgko)</A></TD><TD ><A HREF = "pair_tersoff_mod.html">tersoff/mod (ko)</A></TD><TD ><A HREF = "pair_tersoff_zbl.html">tersoff/zbl (ko)</A></TD><TD ><A HREF = "pair_coul.html">tip4p/cut (o)</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_coul.html">tip4p/long (o)</A></TD><TD ><A HREF = "pair_tri_lj.html">tri/lj (o)</A></TD><TD ><A HREF = "pair_yukawa.html">yukawa (go)</A></TD><TD ><A HREF = "pair_yukawa_colloid.html">yukawa/colloid (go)</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_zbl.html">zbl (go)</A>
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</TD></TR></TABLE></DIV>
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<P>These are additional pair styles in USER packages, which can be used
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@ -1897,10 +1897,10 @@ and free all its memory.
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<P>The lammps_version() function can be used to determined the specific
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version of the underlying LAMMPS code. This is particularly useful
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when loading LAMMPS as a shared library via dlopen(). The code using
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the library interface can than use this information to adapt to changes
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to the LAMMPS command syntax between versions. The returned LAMMPS
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version code is an integer (e.g. 2 Sep 2015 results in 20150902) that
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is growing with every new LAMMPS version.
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the library interface can than use this information to adapt to
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changes to the LAMMPS command syntax between versions. The returned
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LAMMPS version code is an integer (e.g. 2 Sep 2015 results in
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20150902) that grows with every new LAMMPS version.
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</P>
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<P>The lammps_file() and lammps_command() functions are used to pass a
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file or string to LAMMPS as if it were an input script or single
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@ -2566,11 +2566,18 @@ specified between cores.
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turn-off the Coulombic interaction within core/shell pairs, since that
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interaction is set by the bond spring. This is done using the
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<A HREF = "special_bonds.html">special_bonds</A> command with a 1-2 weight = 0.0,
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which is the default value.
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which is the default value. It needs to be considered whether one has
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to adjust the <A HREF = "special_bonds.html">special_bonds</A> weighting according
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to the molecular topology since the interactions of the shells are
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bypassed over an extra bond.
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</P>
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<P>Note that this core/shell implementation does not require all ions to
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be polarized. One can mix core/shell pairs and ions without a
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satellite particle if desired.
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</P>
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<P>Since the core/shell model permits distances of r = 0.0 between the
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core and shell, a pair style with a "cs" suffix needs to be used to
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implement a valid long-range Coulombic correction. Several such pair
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implement a valid long-rangeCoulombic correction. Several such pair
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styles are provided in the CORESHELL package. See <A HREF = "pair_cs.html">this doc
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page</A> for details. All of the core/shell enabled pair
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styles require the use of a long-range Coulombic solver, as specified
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@ -2602,15 +2609,20 @@ temp/cs</A> command can be used, in conjunction with
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any of the thermostat fixes, such as <A HREF = "fix_nh.html">fix nvt</A> or <A HREF = "fix_langevin">fix
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langevin</A>. This compute uses the center-of-mass velocity
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of the core/shell pairs to calculate a temperature, and insures that
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velocity is what is rescaled for thermostatting purposes. The
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velocity is what is rescaled for thermostatting purposes. This
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compute also works for a system with both core/shell pairs and
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non-polarized ions (ions without an attached satellite particle). The
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<A HREF = "compute_temp_cs.html">compute temp/cs</A> command requires input of two
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groups, one for the core atoms, another for the shell atoms. These
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can be defined using the <A HREF = "group.html">group <I>type</I></A> command. Note that
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to perform thermostatting using this definition of temperature, the
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<A HREF = "fix_modify.html">fix modify temp</A> command should be used to assign the
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comptue to the thermostat fix. Likewise the <A HREF = "thermo_modify.html">thermo_modify
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temp</A> command can be used to make this temperature
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be output for the overall system.
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groups, one for the core atoms, another for the shell atoms.
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Non-polarized ions which might also be included in the treated system
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should not be included into either of these groups, they are taken
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into account by the <I>group-ID</I> (2nd argument) of the compute. The
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groups can be defined using the <A HREF = "group.html">group <I>type</I></A> command.
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Note that to perform thermostatting using this definition of
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temperature, the <A HREF = "fix_modify.html">fix modify temp</A> command should be
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used to assign the comptue to the thermostat fix. Likewise the
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<A HREF = "thermo_modify.html">thermo_modify temp</A> command can be used to make
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this temperature be output for the overall system.
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</P>
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<P>For the NaCl example, this can be done as follows:
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</P>
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@ -2649,19 +2661,19 @@ energy can be monitored using the <A HREF = "compute_chunk_atom.html">compute
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chunk/atom</A> and <A HREF = "compute_temp_chunk.html">compute
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temp/chunk</A> commands. The internal kinetic
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energies of each core/shell pair can then be summed using the sum()
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special functino of the <A HREF = "variable.html">variable</A> command. Or they can
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special function of the <A HREF = "variable.html">variable</A> command. Or they can
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be time/averaged and output using the <A HREF = "fix_ave_time.html">fix ave/time</A>
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command. To use these commands, each core/shell pair must be defined
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as a "chunk". If each core/shell pair is defined as its own molecule,
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the molecule ID can be used to define the chunks. If cores are bonded
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to each other to form larger molecules, then another way to define the
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chunks is to use the <A HREF = "fix_property_atom.html">fix property/atom</A> to
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assign a core/shell ID to each atom via a special field in the data
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file read by the <A HREF = "read_data.html">read_data</A> command. This field can
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then be accessed by the <A HREF = "compute_property_atom.html">compute
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property/atom</A> command, to use as input to
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the <A HREF = "compute_chunk_atom.html">compute chunk/atom</A> command to define the
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core/shell pairs as chunks.
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to each other to form larger molecules, the chunks can be identified
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by the <A HREF = "fix_property_atom.html">fix property/atom</A> via assigning a
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core/shell ID to each atom using a special field in the data file read
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by the <A HREF = "read_data.html">read_data</A> command. This field can then be
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accessed by the <A HREF = "compute_property_atom.html">compute property/atom</A>
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command, to use as input to the <A HREF = "compute_chunk_atom.html">compute
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chunk/atom</A> command to define the core/shell
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pairs as chunks.
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</P>
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<P>For example,
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</P>
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@ -13,8 +13,8 @@
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</H3>
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<P><B>Syntax:</B>
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</P>
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<P>compute ID group-ID temp/cs group1 group2 pre
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</P>
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<PRE>compute ID group-ID temp/cs group1 group2
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</PRE>
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<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
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<LI>temp/cs = style name of this compute command
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<LI>group1 = group-ID of either cores or shells
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@ -40,11 +40,19 @@ A compute of this style can be used by any command that computes a
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temperature via <A HREF = "fix_modify.html">fix_modify</A> e.g. <A HREF = "fix_temp_rescale.html">fix
|
||||
temp/rescale</A>, <A HREF = "fix_nh.html">fix npt</A>, etc.
|
||||
</P>
|
||||
<P>Note that this compute does not require all ions to be polarized,
|
||||
hence defined as core/shell pairs. One can mix core/shell pairs and
|
||||
ions without a satellite particle if desired. The compute will
|
||||
consider the non-polarized ions according to the physical system.
|
||||
</P>
|
||||
<P>For this compute, core and shell particles are specified by two
|
||||
respective group IDs, which can be defined using the
|
||||
<A HREF = "group.html">group</A> command. The number of atoms in the two groups
|
||||
must be the same and there should be one bond defined between a pair
|
||||
of atoms in the two groups.
|
||||
of atoms in the two groups. Non-polarized ions which might also be
|
||||
included in the treated system should not be included into either of
|
||||
these groups, they are taken into account by the <I>group-ID</I> (2nd
|
||||
argument) of the compute.
|
||||
</P>
|
||||
<P>The temperature is calculated by the formula KE = dim/2 N k T, where
|
||||
KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2),
|
||||
|
|
@ -52,10 +60,7 @@ dim = 2 or 3 = dimensionality of the simulation, N = number of atoms
|
|||
in the group, k = Boltzmann constant, and T = temperature. Note that
|
||||
the velocity of each core or shell atom used in the KE calculation is
|
||||
the velocity of the center-of-mass (COM) of the core/shell pair the
|
||||
atom is part of. Note that atoms that are not core or shell particles
|
||||
are also included in the temperature calculation (if they are in the
|
||||
specified group-ID); they contribute to the total kinetic energy in
|
||||
the usual way.
|
||||
atom is part of.
|
||||
</P>
|
||||
<P>A kinetic energy tensor, stored as a 6-element vector, is also
|
||||
calculated by this compute for use in the computation of a pressure
|
||||
|
|
|
|||
|
|
@ -51,6 +51,8 @@
|
|||
</H3>
|
||||
<H3>pair_style lj/cut/coul/long command
|
||||
</H3>
|
||||
<H3>pair_style lj/cut/coul/long/cs command
|
||||
</H3>
|
||||
<H3>pair_style lj/cut/coul/long/cuda command
|
||||
</H3>
|
||||
<H3>pair_style lj/cut/coul/long/gpu command
|
||||
|
|
@ -81,7 +83,7 @@
|
|||
</P>
|
||||
<PRE>pair_style style args
|
||||
</PRE>
|
||||
<UL><LI>style = <I>lj/cut</I> or <I>lj/cut/coul/cut</I> or <I>lj/cut/coul/debye</I> or <I>lj/cut/coul/dsf</I> or <I>lj/cut/coul/long</I> or <I>lj/cut/coul/msm</I> or <I>lj/cut/tip4p/long</I>
|
||||
<UL><LI>style = <I>lj/cut</I> or <I>lj/cut/coul/cut</I> or <I>lj/cut/coul/debye</I> or <I>lj/cut/coul/dsf</I> or <I>lj/cut/coul/long</I> or <I>lj/cut/coul/long/cs</I> or <I>lj/cut/coul/msm</I> or <I>lj/cut/tip4p/long</I>
|
||||
<LI>args = list of arguments for a particular style
|
||||
</UL>
|
||||
<PRE> <I>lj/cut</I> args = cutoff
|
||||
|
|
@ -139,7 +141,9 @@ pair_coeff * * 1.0 1.0
|
|||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
</PRE>
|
||||
<PRE>pair_style lj/cut/coul/long 10.0
|
||||
pair_style lj/cut/coul/long/cs 10.0
|
||||
pair_style lj/cut/coul/long 10.0 8.0
|
||||
pair_style lj/cut/coul/long/cs 10.0 8.0
|
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pair_coeff * * 100.0 3.0
|
||||
pair_coeff 1 1 100.0 3.5 9.0
|
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</PRE>
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|
@ -212,6 +216,11 @@ specified for this style means that pairwise interactions within this
|
|||
distance are computed directly; interactions outside that distance are
|
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computed in reciprocal space.
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</P>
|
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<P>Style <I>lj/cut/coul/long/cs</I> is identical to <I>lj/cut/coul/long</I> except
|
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that a term is added for the <A HREF = "Section_howto.html#howto_25">core/shell
|
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model</A> to allow charges on core and shell
|
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particles to be separated by r = 0.0.
|
||||
</P>
|
||||
<P>Styles <I>lj/cut/tip4p/cut</I> and <I>lj/cut/tip4p/long</I> implement the TIP4P
|
||||
water model of <A HREF = "#Jorgensen">(Jorgensen)</A>, which introduces a massless
|
||||
site located a short distance away from the oxygen atom along the
|
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@ -0,0 +1,263 @@
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<title>timestep command — LAMMPS 15 May 2015 version documentation</title>
|
||||
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|
||||
|
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|
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|
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|
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<ul>
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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
|
||||
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
|
||||
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
|
||||
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
|
||||
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
|
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<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
|
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<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
|
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<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
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<li>timestep command</li>
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<a href="http://lammps.sandia.gov">Website</a>
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<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
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<div itemprop="articleBody">
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||||
|
||||
<div class="section" id="timestep-command">
|
||||
<span id="index-0"></span><h1>timestep command<a class="headerlink" href="#timestep-command" title="Permalink to this headline">¶</a></h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline">¶</a></h2>
|
||||
<div class="highlight-python"><div class="highlight"><pre>timers args
|
||||
</pre></div>
|
||||
</div>
|
||||
<ul class="simple">
|
||||
<li><em>args</em> = one or more of <em>off</em> or <em>loop</em> or <em>normal</em> or <em>full</em> or <em>sync</em> or <em>nosync</em></li>
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>off</em> = do not collect and print timing information
|
||||
<em>loop</em> = collect only the total time for the simulation loop
|
||||
<em>normal</em> = collect timer information broken down in sections (default)
|
||||
<em>full</em> = like <em>normal</em> but also include CPU and thread utilzation
|
||||
<em>sync</em> = explicitly synchronize MPI tasks between sections
|
||||
<em>nosync</em> = do not synchronize MPI tasks when collecting timer info (default)
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
|
||||
<div class="highlight-python"><div class="highlight"><pre>timers full sync
|
||||
timers loop
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
|
||||
<p>Select to which level of detail LAMMPS is performing internal profiling.</p>
|
||||
<p>During regular runs LAMMPS will collect 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 class="reference internal" href="Section_start.html#start-8"><span>discussion of screen output</span></a>.</p>
|
||||
<p>The <em>off</em> setting will turn all time measurements off. The <em>loop</em> setting
|
||||
will only measure the total time of run loop and not collect any detailed
|
||||
per section information. With the <em>normal</em> setting, timing information for
|
||||
individual sections of the code are collected and also information about
|
||||
load imbalances inside those sections presented. The <em>full</em> setting adds
|
||||
information about CPU utilization and thread utilization, when multi-threading
|
||||
is enabled.</p>
|
||||
<p>With the <em>sync</em> 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 <em>nosync</em> setting this can be turned
|
||||
off (which is the default).</p>
|
||||
<p>Multiple keywords can be provided and for keywords that are mutually
|
||||
exclusive, the last one in that group is taking effect.</p>
|
||||
<div class="admonition warning">
|
||||
<p class="first admonition-title">Warning</p>
|
||||
<p class="last">Using the <em>full</em> and <em>sync</em> 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 <em>normal</em> setting can have
|
||||
a measurable performance impact. It is recommended in those cases to use
|
||||
the <em>loop</em> or <em>off</em> setting.</p>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="restrictions">
|
||||
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
|
||||
<blockquote>
|
||||
<div>none</div></blockquote>
|
||||
</div>
|
||||
<div class="section" id="related-commands">
|
||||
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline">¶</a></h2>
|
||||
<p><a class="reference internal" href="run.html"><em>run post no</em></a>, <a class="reference internal" href="kspace_modify.html"><em>kspace_modify fftbench</em></a></p>
|
||||
</div>
|
||||
<div class="section" id="default">
|
||||
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline">¶</a></h2>
|
||||
<p>timers normal nosync</p>
|
||||
</div>
|
||||
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|
||||
|
||||
|
||||
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|
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