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10
doc/Manual.html
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@ -33,7 +33,7 @@ National Laboratories, a US Department of Energy facility, with
funding from the DOE. It is an open-source code, distributed freely
under the terms of the GNU Public License (GPL).
</P>
<P>The primary developers of LAMMPS are <A HREF = "http://www.cs.sandia.gov/~sjplimp">Steve Plimpton</A>, Paul
<P>The primary developers of LAMMPS are <A HREF = "http://www.sandia.gov/~sjplimp">Steve Plimpton</A>, Paul
Crozier, and Aidan Thompson who can be contacted at
sjplimp,pscrozi,athomps at sandia.gov. The <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> at
http://lammps.sandia.gov has more information about the code and its
@ -100,7 +100,7 @@ listed above.
<BR>
2.8 <A HREF = "Section_start.html#2_8">Running on GPUs</A>
<BR>
2.9 <A HREF = "2_9">Tips for users of previous versions</A>
2.9 <A HREF = "Section_start.html#2_9">Tips for users of previous versions</A>
<BR></UL>
<LI><A HREF = "Section_commands.html">Commands</A>
@ -148,7 +148,7 @@ listed above.
<BR>
4.16 <A HREF = "Section_howto.html#4_16">Thermostatting, barostatting, and compute temperature</A>
<BR>
4.17 <A HREF = "4_17">Walls</A>
4.17 <A HREF = "Section_howto.html#4_17">Walls</A>
<BR></UL>
<LI><A HREF = "Section_example.html">Example problems</A>
@ -247,6 +247,10 @@ listed above.

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doc/Manual.txt
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@ -36,7 +36,7 @@ sjplimp,pscrozi,athomps at sandia.gov. The "LAMMPS WWW Site"_lws at
http://lammps.sandia.gov has more information about the code and its
uses.
:link(sjp,http://www.cs.sandia.gov/~sjplimp)
:link(sjp,http://www.sandia.gov/~sjplimp)
:line
@ -134,6 +134,7 @@ listed above.
:link(2_6,Section_start.html#2_6)
:link(2_7,Section_start.html#2_7)
:link(2_8,Section_start.html#2_8)
:link(2_9,Section_start.html#2_9)
:link(3_1,Section_commands.html#3_1)
:link(3_2,Section_commands.html#3_2)
@ -157,6 +158,7 @@ listed above.
:link(4_14,Section_howto.html#4_14)
:link(4_15,Section_howto.html#4_15)
:link(4_16,Section_howto.html#4_16)
:link(4_17,Section_howto.html#4_17)
:link(9_1,Section_errors.html#9_1)
:link(9_2,Section_errors.html#9_2)

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doc/Section_howto.html
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@ -639,12 +639,12 @@ files. The second is the <A HREF = "Section_tools.html#arc">lmp2arc tool</A> wh
converts LAMMPS dump files into Accelrys' Insight MD program files.
The third is the <A HREF = "Section_tools.html#cfg">lmp2cfg tool</A> which converts
LAMMPS dump files into CFG files which can be read into the
<A HREF = "http://164.107.79.177/Archive/Graphics/A">AtomEye</A> visualizer.
<A HREF = "http://mt.seas.upenn.edu/Archive/Graphics/A">AtomEye</A> visualizer.
</P>
<P>A Python-based toolkit distributed by our group can read native LAMMPS
dump files, including custom dump files with additional columns of
user-specified atom information, and convert them to various formats
or pipe them into visualization software directly. See the <A HREF = "http://www.cs.sandia.gov/~sjplimp/pizza.html">Pizza.py
or pipe them into visualization software directly. See the <A HREF = "http://www.sandia.gov/~sjplimp/pizza.html">Pizza.py
WWW site</A> for details. Specifically, Pizza.py can convert
LAMMPS dump files into PDB, XYZ, <A HREF = "http://www.ensight.com">Ensight</A>, and VTK formats.
Pizza.py can pipe LAMMPS dump files directly into the Raster3d and
@ -861,7 +861,7 @@ that generate torque:
<LI><A HREF = "pair_gran.html">pair_style gran/no_history</A>
<LI><A HREF = "pair_dipole.html">pair_style dipole/cut</A>
<LI><A HREF = "pair_gayberne.html">pair_style gayberne</A>
<LI><A HREF = "pair_resuared.html">pair_style resquared</A>
<LI><A HREF = "pair_resquared.html">pair_style resquared</A>
<LI><A HREF = "pair_lubricate.html">pair_style lubricate</A>
</UL>
<P>The <A HREF = "pair_gran.html">granular pair styles</A> are used with <A HREF = "atom_style.html">atom_style
@ -1254,7 +1254,7 @@ pressure</A> command calculates pressure.
</UL>
<P>All but the first 3 calculate velocity biases (i.e. advection
velocities) that are removed when computing the thermal temperature.
<A HREF = "fix_temp_sphere.html">Fix temp/sphere</A> and <A HREF = "fix_temp_asphere.html">fix
<A HREF = "compute_temp_sphere.html">Compute temp/sphere</A> and <A HREF = "compute_temp_asphere.html">compute
temp/asphere</A> compute kinetic energy for
extended particles that includes rotational degrees of freedom. They
both allow, as an extra argument, which is another temperature compute

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doc/Section_howto.txt
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@ -662,10 +662,10 @@ LAMMPS can create XTC files directly (via "dump xtc") which is GROMACS
file format which can also be read by "VMD"_vmd for visualization.
See the "dump"_dump.html command for more information on XTC files.
:link(pizza,http://www.cs.sandia.gov/~sjplimp/pizza.html)
:link(pizza,http://www.sandia.gov/~sjplimp/pizza.html)
:link(vmd,http://www.ks.uiuc.edu/Research/vmd)
:link(ensight,http://www.ensight.com)
:link(atomeye,http://164.107.79.177/Archive/Graphics/A)
:link(atomeye,http://mt.seas.upenn.edu/Archive/Graphics/A)
:line
@ -854,7 +854,7 @@ that generate torque:
"pair_style gran/no_history"_pair_gran.html
"pair_style dipole/cut"_pair_dipole.html
"pair_style gayberne"_pair_gayberne.html
"pair_style resquared"_pair_resuared.html
"pair_style resquared"_pair_resquared.html
"pair_style lubricate"_pair_lubricate.html :ul
The "granular pair styles"_pair_gran.html are used with "atom_style
@ -1243,8 +1243,8 @@ pressure"_compute_pressure.html command calculates pressure.
All but the first 3 calculate velocity biases (i.e. advection
velocities) that are removed when computing the thermal temperature.
"Fix temp/sphere"_fix_temp_sphere.html and "fix
temp/asphere"_fix_temp_asphere.html compute kinetic energy for
"Compute temp/sphere"_compute_temp_sphere.html and "compute
temp/asphere"_compute_temp_asphere.html compute kinetic energy for
extended particles that includes rotational degrees of freedom. They
both allow, as an extra argument, which is another temperature compute
that subtracts a velocity bias. This allows the translational

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doc/Section_intro.html
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@ -237,7 +237,7 @@ molecular dynamics options:
<LI><A HREF = "temper.html">parallel tempering</A>
<LI><A HREF = "prd.html">parallel replica dynamics</A>
<LI><A HREF = "pair_dsmc.html">Direct Simulation Monte Carlo</A> for low-density fluids
<LI><A HREF = "pair_peri.html">Peridynamics mesoscale modeling</A>
<LI><A HREF = "pair_peri_pmb.html">Peridynamics mesoscale modeling</A>
<LI><A HREF = "fix_tmd.html">targeted</A> and <A HREF = "fix_smd.html">steered</A> molecular dynamics
<LI><A HREF = "fix_ttm.html">two-temperature electron model</A>
</UL>
@ -485,7 +485,7 @@ add it to the Publications page of the <A HREF = "http://lammps.sandia.gov">LAMM
for a picture or movie for the Pictures or Movies pages.
</P>
<P>The core group of LAMMPS developers is at Sandia National Labs. They
include <A HREF = "http://www.cs.sandia.gov/~sjplimp">Steve Plimpton</A>, Paul Crozier, and Aidan Thompson and can
include <A HREF = "http://www.sandia.gov/~sjplimp">Steve Plimpton</A>, Paul Crozier, and Aidan Thompson and can
be contacted via email: sjplimp, pscrozi, athomps at sandia.gov.
</P>
<P>Here are various folks who have made significant contributions to

4
doc/Section_intro.txt
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@ -233,7 +233,7 @@ coupled rigid body integration via the "POEMS"_fix_poems.html library
"parallel tempering"_temper.html
"parallel replica dynamics"_prd.html
"Direct Simulation Monte Carlo"_pair_dsmc.html for low-density fluids
"Peridynamics mesoscale modeling"_pair_peri.html
"Peridynamics mesoscale modeling"_pair_peri_pmb.html
"targeted"_fix_tmd.html and "steered"_fix_smd.html molecular dynamics
"two-temperature electron model"_fix_ttm.html :ul
@ -478,7 +478,7 @@ Here are various folks who have made significant contributions to
features in LAMMPS. The most recent contributions are at the top of
the list.
:link(sjp,http://www.cs.sandia.gov/~sjplimp)
:link(sjp,http://www.sandia.gov/~sjplimp)
pair yukawa/colloid : Randy Schunk (Sandia)
fix wall/colloid : Jeremy Lechman (Sandia)

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doc/Section_tools.html
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@ -20,9 +20,9 @@ additional tools are provided with the LAMMPS distribution and are
described in this section.
</P>
<P>Our group has also written and released a separate toolkit called
<A HREF = "http://www.cs.sandia.gov/~sjplimp/pizza.html">Pizza.py</A> which provides tools for doing setup, analysis,
<A HREF = "http://www.sandia.gov/~sjplimp/pizza.html">Pizza.py</A> which provides tools for doing setup, analysis,
plotting, and visualization for LAMMPS simulations. Pizza.py is
written in <A HREF = "http://www.python.org">Python</A> and is available for download from <A HREF = "http://www.cs.sandia.gov/~sjplimp/pizza.html">the
written in <A HREF = "http://www.python.org">Python</A> and is available for download from <A HREF = "http://www.sandia.gov/~sjplimp/pizza.html">the
Pizza.py WWW site</A>.
</P>
@ -172,7 +172,7 @@ Greathouse at Sandia (jagreat at sandia.gov).
</H4>
<P>The lmp2cfg sub-directory contains a tool for converting LAMMPS output
files into a series of *.cfg files which can be read into the
<A HREF = "http://164.107.79.177/Archive/Graphics/A">AtomEye</A> visualizer. See
<A HREF = "http://mt.seas.upenn.edu/Archive/Graphics/A">AtomEye</A> visualizer. See
the README file for more information.
</P>
<P>This tool was written by Ara Kooser at Sandia (askoose at sandia.gov).
@ -281,7 +281,7 @@ that perform common LAMMPS post-processing tasks, like
<LI>sort the snapshots in a dump file by atom ID
<LI>convert dump files into XYZ, CFG, or PDB format for viz by other packages
</UL>
<P>These are simple scripts built on <A HREF = "http://www.cs.sandia.gov/~sjplimp/pizza.html">Pizza.py</A> modules. See the
<P>These are simple scripts built on <A HREF = "http://www.sandia.gov/~sjplimp/pizza.html">Pizza.py</A> modules. See the
README for more info on Pizza.py and how to use these scripts.
</P>
<HR>

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doc/Section_tools.txt
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@ -22,7 +22,7 @@ plotting, and visualization for LAMMPS simulations. Pizza.py is
written in "Python"_python and is available for download from "the
Pizza.py WWW site"_pizza.
:link(pizza,http://www.cs.sandia.gov/~sjplimp/pizza.html)
:link(pizza,http://www.sandia.gov/~sjplimp/pizza.html)
:link(python,http://www.python.org)
Note that many users write their own setup or analysis tools or use
@ -168,7 +168,7 @@ lmp2cfg tool :h4,link(cfg)
The lmp2cfg sub-directory contains a tool for converting LAMMPS output
files into a series of *.cfg files which can be read into the
"AtomEye"_http://164.107.79.177/Archive/Graphics/A visualizer. See
"AtomEye"_http://mt.seas.upenn.edu/Archive/Graphics/A visualizer. See
the README file for more information.
This tool was written by Ara Kooser at Sandia (askoose at sandia.gov).

2
doc/compute_displace_atom.html
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@ -40,7 +40,7 @@ command had been issued:
</P>
<PRE>fix compute-ID_store_coord group-ID store/coord
</PRE>
<P>See the <A HREF = "fix_coord_original.html">fix store/coord</A> command for details.
<P>See the <A HREF = "fix_store_coord.html">fix store/coord</A> command for details.
Note that the ID of the new fix is the compute-ID + underscore +
"store_coord", and the group for the new fix is the same as the
compute group.

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doc/compute_displace_atom.txt
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@ -37,7 +37,7 @@ command had been issued:
fix compute-ID_store_coord group-ID store/coord :pre
See the "fix store/coord"_fix_coord_original.html command for details.
See the "fix store/coord"_fix_store_coord.html command for details.
Note that the ID of the new fix is the compute-ID + underscore +
"store_coord", and the group for the new fix is the same as the
compute group.

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doc/compute_erotate_asphere.html
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@ -63,7 +63,7 @@ particles, but they can be aspherical or spherical.
</P>
<P><B>Related commands:</B> none
</P>
<P><A HREF = "compute_rotate_sphere.html">compute erotate/sphere</A>
<P><A HREF = "compute_erotate_sphere.html">compute erotate/sphere</A>
</P>
<P><B>Default:</B> none
</P>

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doc/compute_erotate_asphere.txt
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@ -60,6 +60,6 @@ particles, but they can be aspherical or spherical.
[Related commands:] none
"compute erotate/sphere"_compute_rotate_sphere.html
"compute erotate/sphere"_compute_erotate_sphere.html
[Default:] none

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doc/compute_erotate_sphere.html
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@ -56,7 +56,7 @@ contribute to the rotational energy.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_rotate_asphere.html">compute erotate/asphere</A>
<P><A HREF = "compute_erotate_asphere.html">compute erotate/asphere</A>
</P>
<P><B>Default:</B> none
</P>

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doc/compute_erotate_sphere.txt
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@ -53,6 +53,6 @@ contribute to the rotational energy.
[Related commands:]
"compute erotate/asphere"_compute_rotate_asphere.html
"compute erotate/asphere"_compute_erotate_asphere.html
[Default:] none

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doc/compute_heat_flux.html
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@ -34,7 +34,7 @@ or to calculate a thermal conductivity using the Green-Kubo formalism.
</P>
<P>See the <A HREF = "fix_thermal_conductivity.html">fix thermal/conductivity</A>
command for details on how to compute thermal conductivity in an
alternate way, via the Muller-Plathe method. See the <A HREF = "fix_heat">fix
alternate way, via the Muller-Plathe method. See the <A HREF = "fix_heat.html">fix
heat</A> command for a way to control the heat added or
subtracted to a group of atoms.
</P>

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doc/compute_heat_flux.txt
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@ -32,7 +32,7 @@ or to calculate a thermal conductivity using the Green-Kubo formalism.
See the "fix thermal/conductivity"_fix_thermal_conductivity.html
command for details on how to compute thermal conductivity in an
alternate way, via the Muller-Plathe method. See the "fix
heat"_fix_heat command for a way to control the heat added or
heat"_fix_heat.html command for a way to control the heat added or
subtracted to a group of atoms.
The compute takes three arguments which are IDs of other

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doc/compute_modify.html
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@ -47,7 +47,7 @@ this option. The default is 2 or 3 for <A HREF = "dimension.html">2d or 3d
systems</A> which is a correction factor for an ensemble
of velocities with zero total linear momentum. You can use a negative
number for the <I>extra</I> parameter if you need to add
degrees-of-freedom. See the <A HREF = "compute_temp_aspher.html">compute
degrees-of-freedom. See the <A HREF = "compute_temp_asphere.html">compute
temp/asphere</A> command for an example.
</P>
<P>The <I>dynamic</I> keyword determines whether the number of atoms N in the

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doc/compute_modify.txt
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@ -41,7 +41,7 @@ systems"_dimension.html which is a correction factor for an ensemble
of velocities with zero total linear momentum. You can use a negative
number for the {extra} parameter if you need to add
degrees-of-freedom. See the "compute
temp/asphere"_compute_temp_aspher.html command for an example.
temp/asphere"_compute_temp_asphere.html command for an example.
The {dynamic} keyword determines whether the number of atoms N in the
compute group is re-computed each time a temperature is computed.

2
doc/compute_temp_com.html
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@ -57,7 +57,7 @@ that performs thermostatting then this bias will be subtracted from
each atom, thermostatting of the remaining thermal velocity will be
performed, and the bias will be added back in. Thermostatting fixes
that work in this way include <A HREF = "fix_nh.html">fix nvt</A>, <A HREF = "fix_temp_rescale.html">fix
temp/rescale</A>, <A HREF = "fix_temp_berendsen">fix
temp/rescale</A>, <A HREF = "fix_temp_berendsen.html">fix
temp/berendsen</A>, and <A HREF = "fix_langevin.html">fix
langevin</A>.
</P>

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doc/compute_temp_com.txt
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@ -55,7 +55,7 @@ each atom, thermostatting of the remaining thermal velocity will be
performed, and the bias will be added back in. Thermostatting fixes
that work in this way include "fix nvt"_fix_nh.html, "fix
temp/rescale"_fix_temp_rescale.html, "fix
temp/berendsen"_fix_temp_berendsen, and "fix
temp/berendsen"_fix_temp_berendsen.html, and "fix
langevin"_fix_langevin.html.
This compute subtracts out degrees-of-freedom due to fixes that

2
doc/compute_temp_deform.html
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@ -81,7 +81,7 @@ command that performs thermostatting then this bias will be subtracted
from each atom, thermostatting of the remaining thermal velocity will
be performed, and the bias will be added back in. Thermostatting
fixes that work in this way include <A HREF = "fix_nh.html">fix nvt</A>, <A HREF = "fix_temp_rescale.html">fix
temp/rescale</A>, <A HREF = "fix_temp_berendsen">fix
temp/rescale</A>, <A HREF = "fix_temp_berendsen.html">fix
temp/berendsen</A>, and <A HREF = "fix_langevin.html">fix
langevin</A>.
</P>

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doc/compute_temp_deform.txt
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@ -79,7 +79,7 @@ from each atom, thermostatting of the remaining thermal velocity will
be performed, and the bias will be added back in. Thermostatting
fixes that work in this way include "fix nvt"_fix_nh.html, "fix
temp/rescale"_fix_temp_rescale.html, "fix
temp/berendsen"_fix_temp_berendsen, and "fix
temp/berendsen"_fix_temp_berendsen.html, and "fix
langevin"_fix_langevin.html.
This compute subtracts out degrees-of-freedom due to fixes that

2
doc/compute_temp_partial.html
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@ -57,7 +57,7 @@ that performs thermostatting then this bias will be subtracted from
each atom, thermostatting of the remaining thermal velocity will be
performed, and the bias will be added back in. Thermostatting fixes
that work in this way include <A HREF = "fix_nh.html">fix nvt</A>, <A HREF = "fix_temp_rescale.html">fix
temp/rescale</A>, <A HREF = "fix_temp_berendsen">fix
temp/rescale</A>, <A HREF = "fix_temp_berendsen.html">fix
temp/berendsen</A>, and <A HREF = "fix_langevin.html">fix
langevin</A>.
</P>

2
doc/compute_temp_partial.txt
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@ -55,7 +55,7 @@ each atom, thermostatting of the remaining thermal velocity will be
performed, and the bias will be added back in. Thermostatting fixes
that work in this way include "fix nvt"_fix_nh.html, "fix
temp/rescale"_fix_temp_rescale.html, "fix
temp/berendsen"_fix_temp_berendsen, and "fix
temp/berendsen"_fix_temp_berendsen.html, and "fix
langevin"_fix_langevin.html.
This compute subtracts out degrees-of-freedom due to fixes that

2
doc/compute_temp_profile.html
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@ -95,7 +95,7 @@ command that performs thermostatting then this bias will be subtracted
from each atom, thermostatting of the remaining thermal velocity will
be performed, and the bias will be added back in. Thermostatting
fixes that work in this way include <A HREF = "fix_nh.html">fix nvt</A>, <A HREF = "fix_temp_rescale.html">fix
temp/rescale</A>, <A HREF = "fix_temp_berendsen">fix
temp/rescale</A>, <A HREF = "fix_temp_berendsen.html">fix
temp/berendsen</A>, and <A HREF = "fix_langevin.html">fix
langevin</A>.
</P>

2
doc/compute_temp_profile.txt
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@ -88,7 +88,7 @@ from each atom, thermostatting of the remaining thermal velocity will
be performed, and the bias will be added back in. Thermostatting
fixes that work in this way include "fix nvt"_fix_nh.html, "fix
temp/rescale"_fix_temp_rescale.html, "fix
temp/berendsen"_fix_temp_berendsen, and "fix
temp/berendsen"_fix_temp_berendsen.html, and "fix
langevin"_fix_langevin.html.
This compute subtracts out degrees-of-freedom due to fixes that

2
doc/compute_temp_ramp.html
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@ -76,7 +76,7 @@ command that performs thermostatting then this bias will be subtracted
from each atom, thermostatting of the remaining thermal velocity will
be performed, and the bias will be added back in. Thermostatting
fixes that work in this way include <A HREF = "fix_nh.html">fix nvt</A>, <A HREF = "fix_temp_rescale.html">fix
temp/rescale</A>, <A HREF = "fix_temp_berendsen">fix
temp/rescale</A>, <A HREF = "fix_temp_berendsen.html">fix
temp/berendsen</A>, and <A HREF = "fix_langevin.html">fix
langevin</A>.
</P>

2
doc/compute_temp_ramp.txt
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@ -73,7 +73,7 @@ from each atom, thermostatting of the remaining thermal velocity will
be performed, and the bias will be added back in. Thermostatting
fixes that work in this way include "fix nvt"_fix_nh.html, "fix
temp/rescale"_fix_temp_rescale.html, "fix
temp/berendsen"_fix_temp_berendsen, and "fix
temp/berendsen"_fix_temp_berendsen.html, and "fix
langevin"_fix_langevin.html.
This compute subtracts out degrees-of-freedom due to fixes that

2
doc/compute_temp_region.html
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@ -66,7 +66,7 @@ compute is used with a fix command that performs thermostatting then
this bias will be subtracted from each atom, thermostatting of the
remaining thermal velocity will be performed, and the bias will be
added back in. Thermostatting fixes that work in this way include
<A HREF = "fix_nh.html">fix nvt</A>, <A HREF = "fix_temp_rescale.html">fix temp/rescale</A>, <A HREF = "fix_temp_berendsen">fix
<A HREF = "fix_nh.html">fix nvt</A>, <A HREF = "fix_temp_rescale.html">fix temp/rescale</A>, <A HREF = "fix_temp_berendsen.html">fix
temp/berendsen</A>, and <A HREF = "fix_langevin.html">fix
langevin</A>. This means any of the thermostatting
fixes can operate on a geometric region of atoms, as defined by this

2
doc/compute_temp_region.txt
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@ -64,7 +64,7 @@ this bias will be subtracted from each atom, thermostatting of the
remaining thermal velocity will be performed, and the bias will be
added back in. Thermostatting fixes that work in this way include
"fix nvt"_fix_nh.html, "fix temp/rescale"_fix_temp_rescale.html, "fix
temp/berendsen"_fix_temp_berendsen, and "fix
temp/berendsen"_fix_temp_berendsen.html, and "fix
langevin"_fix_langevin.html. This means any of the thermostatting
fixes can operate on a geometric region of atoms, as defined by this
compute.

2
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@ -123,7 +123,7 @@ individual values and the file itself.
<P>The <I>atom</I>, <I>local</I>, and <I>custom</I> styles create files in a simple text
format that is self-explanatory when viewing a dump file. Many of the
LAMMPS <A HREF = "Section_tools.html">post-processing tools</A>, including
<A HREF = "http://www.cs.sandia.gov/~sjplimp/pizza.html">Pizza.py</A>, work with
<A HREF = "http://www.sandia.gov/~sjplimp/pizza.html">Pizza.py</A>, work with
this format.
</P>
<P>For post-processing purposes the <I>atom</I> and <I>custom</I> text files are

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doc/dump.txt
View File

@ -113,7 +113,7 @@ individual values and the file itself.
The {atom}, {local}, and {custom} styles create files in a simple text
format that is self-explanatory when viewing a dump file. Many of the
LAMMPS "post-processing tools"_Section_tools.html, including
"Pizza.py"_http://www.cs.sandia.gov/~sjplimp/pizza.html, work with
"Pizza.py"_http://www.sandia.gov/~sjplimp/pizza.html, work with
this format.
For post-processing purposes the {atom} and {custom} text files are

12
doc/fix_addforce.html
View File

@ -47,12 +47,12 @@ the group. This command can be used to give an additional push to
atoms in a simulation, such as for a simulation of Poiseuille flow in
a channel.
</P>
<P>Any of the 3 quantities defining the force components can be
specified as an equal-style or atom-style <A HREF = "variable">variable</A>, namely
<I>fx</I>, <I>fy</I>, <I>fz</I>. If the value is a variable, it should be specified
as v_ID, where ID is the variable ID. In this case, the variable will
be evaluated each timestep, and its value used to determine the
force component.
<P>Any of the 3 quantities defining the force components can be specified
as an equal-style or atom-style <A HREF = "variable.html">variable</A>, namely <I>fx</I>,
<I>fy</I>, <I>fz</I>. If the value is a variable, it should be specified as
v_ID, where ID is the variable ID. In this case, the variable will be
evaluated each timestep, and its value used to determine the force
component.
</P>
<P>Equal-style variables can specify formulas with various mathematical
functions, and include <A HREF = "thermo_style.html">thermo_style</A> command

12
doc/fix_addforce.txt
View File

@ -37,12 +37,12 @@ the group. This command can be used to give an additional push to
atoms in a simulation, such as for a simulation of Poiseuille flow in
a channel.
Any of the 3 quantities defining the force components can be
specified as an equal-style or atom-style "variable"_variable, namely
{fx}, {fy}, {fz}. If the value is a variable, it should be specified
as v_ID, where ID is the variable ID. In this case, the variable will
be evaluated each timestep, and its value used to determine the
force component.
Any of the 3 quantities defining the force components can be specified
as an equal-style or atom-style "variable"_variable.html, namely {fx},
{fy}, {fz}. If the value is a variable, it should be specified as
v_ID, where ID is the variable ID. In this case, the variable will be
evaluated each timestep, and its value used to determine the force
component.
Equal-style variables can specify formulas with various mathematical
functions, and include "thermo_style"_thermo_style.html command

4
doc/fix_atc.html
View File

@ -205,7 +205,7 @@ conditions.
</P>
<UL><LI><A HREF = "USER/atc/man_hardy_fields.html">fix_modify AtC transfer fields</A>
<LI><A HREF = "USER/atc/man_hardy_gradients.html">fix_modify AtC transfer gradients</A>
<LI><A HREF = "USER/atc/man_hardy_rates.htm">fix_modify AtC transfer rates</A>
<LI><A HREF = "USER/atc/man_hardy_rates.html">fix_modify AtC transfer rates</A>
<LI><A HREF = "USER/atc/man_hardy_computes.html">fix_modify AtC transfer computes</A>
<LI><A HREF = "USER/atc/man_hardy_set.html">fix_modify AtC set</A>
<LI><A HREF = "USER/atc/man_hardy_on_the_fly.html">fix_modify AtC transfer on_the_fly</A>
@ -214,7 +214,7 @@ conditions.
</UL>
<P>miscellaneous fix_modify commands:
</P>
<UL><LI><A HREF = "USER/atc/man_atom_element_map.htm">fix_modify AtC transfer atom_element_map</A>
<UL><LI><A HREF = "USER/atc/man_atom_element_map.html">fix_modify AtC transfer atom_element_map</A>
<LI><A HREF = "USER/atc/man_neighbor_reset_frequency.html">fix_modify AtC transfer neighbor_reset_frequency</A>
</UL>
<P><B>Default:</B> none

4
doc/fix_atc.txt
View File

@ -198,7 +198,7 @@ fix_modify commands for post-processing:
"fix_modify AtC transfer fields"_USER/atc/man_hardy_fields.html
"fix_modify AtC transfer gradients"_USER/atc/man_hardy_gradients.html
"fix_modify AtC transfer rates"_USER/atc/man_hardy_rates.htm
"fix_modify AtC transfer rates"_USER/atc/man_hardy_rates.html
"fix_modify AtC transfer computes"_USER/atc/man_hardy_computes.html
"fix_modify AtC set"_USER/atc/man_hardy_set.html
"fix_modify AtC transfer on_the_fly"_USER/atc/man_hardy_on_the_fly.html
@ -207,7 +207,7 @@ fix_modify commands for post-processing:
miscellaneous fix_modify commands:
"fix_modify AtC transfer atom_element_map"_USER/atc/man_atom_element_map.htm
"fix_modify AtC transfer atom_element_map"_USER/atc/man_atom_element_map.html
"fix_modify AtC transfer neighbor_reset_frequency"_USER/atc/man_neighbor_reset_frequency.html :ul
[Default:] none

6
doc/fix_aveforce.html
View File

@ -56,9 +56,9 @@ same as specifying a 0.0 value, since that sets all forces to the same
average value without adding in any additional force.
</P>
<P>Any of the 3 quantities defining the force components can be specified
as an equal-style <A HREF = "variable">variable</A>, namely <I>fx</I>, <I>fy</I>, <I>fz</I>. If
the value is a variable, it should be specified as v_ID, where ID is
the variable ID. In this case, the variable will be evaluated each
as an equal-style <A HREF = "variable.html">variable</A>, namely <I>fx</I>, <I>fy</I>, <I>fz</I>.
If the value is a variable, it should be specified as v_ID, where ID
is the variable ID. In this case, the variable will be evaluated each
timestep, and its value used to determine the average force.
</P>
<P>Equal-style variables can specify formulas with various mathematical

6
doc/fix_aveforce.txt
View File

@ -46,9 +46,9 @@ same as specifying a 0.0 value, since that sets all forces to the same
average value without adding in any additional force.
Any of the 3 quantities defining the force components can be specified
as an equal-style "variable"_variable, namely {fx}, {fy}, {fz}. If
the value is a variable, it should be specified as v_ID, where ID is
the variable ID. In this case, the variable will be evaluated each
as an equal-style "variable"_variable.html, namely {fx}, {fy}, {fz}.
If the value is a variable, it should be specified as v_ID, where ID
is the variable ID. In this case, the variable will be evaluated each
timestep, and its value used to determine the average force.
Equal-style variables can specify formulas with various mathematical

2
doc/fix_deform.html
View File

@ -419,7 +419,7 @@ not remapped even if <I>remap</I> is set to <I>v</I>, since <A HREF = "fix_nvt_s
nvt/sllod</A> does not currently do anything special
for rigid particles. If you wish to perform a NEMD simulation of
rigid particles, you can either thermostat them independently or
include a background fluid and thermostat the fluid via <A HREF = "fix_nvt_sllod">fix
include a background fluid and thermostat the fluid via <A HREF = "fix_nvt_sllod.html">fix
nvt/sllod</A>.
</P>
<P>The <I>units</I> keyword determines the meaning of the distance units used

2
doc/fix_deform.txt
View File

@ -410,7 +410,7 @@ nvt/sllod"_fix_nvt_sllod.html does not currently do anything special
for rigid particles. If you wish to perform a NEMD simulation of
rigid particles, you can either thermostat them independently or
include a background fluid and thermostat the fluid via "fix
nvt/sllod"_fix_nvt_sllod.
nvt/sllod"_fix_nvt_sllod.html.
The {units} keyword determines the meaning of the distance units used
to define various arguments. A {box} value selects standard distance

4
doc/fix_heat.html
View File

@ -67,8 +67,8 @@ or <A HREF = "fix_temp_rescale.html">fix temp/rescale</A> in that energy is
added/subtracted continually. Thus if there isn't another mechanism
in place to counterbalance this effect, the entire system will heat or
cool continuously. You can use multiple heat fixes so that the net
energy change is 0.0 or use <A HREF = "fix_viscous">fix viscous</A> to drain energy
from the system.
energy change is 0.0 or use <A HREF = "fix_viscous.html">fix viscous</A> to drain
energy from the system.
</P>
<P>This fix does not change the coordinates of its atoms; it only scales
their velocities. Thus you must still use an integration fix

4
doc/fix_heat.txt
View File

@ -57,8 +57,8 @@ or "fix temp/rescale"_fix_temp_rescale.html in that energy is
added/subtracted continually. Thus if there isn't another mechanism
in place to counterbalance this effect, the entire system will heat or
cool continuously. You can use multiple heat fixes so that the net
energy change is 0.0 or use "fix viscous"_fix_viscous to drain energy
from the system.
energy change is 0.0 or use "fix viscous"_fix_viscous.html to drain
energy from the system.
This fix does not change the coordinates of its atoms; it only scales
their velocities. Thus you must still use an integration fix

6
doc/fix_indent.html
View File

@ -98,13 +98,13 @@ the plane's current position will feel no force. Vice versa if <I>side</I>
is specified as <I>hi</I>.
</P>
<P>Any of the 4 quantities defining a spherical indenter's geometry can
be specified as an equal-style <A HREF = "variable">variable</A>, namely <I>x</I>, <I>y</I>,
<I>z</I>, or <I>R</I>. Similarly, for a cylindrical indenter, any of <I>c1</I>,
be specified as an equal-style <A HREF = "variable.html">variable</A>, namely <I>x</I>,
<I>y</I>, <I>z</I>, or <I>R</I>. Similarly, for a cylindrical indenter, any of <I>c1</I>,
<I>c2</I>, or <I>R</I>, can be a variable. For a planar indenter, <I>pos</I> can be
a variable. If the value is a variable, it should be specified as
v_ID, where ID is the variable ID. In this case, the variable will be
evaluated each timestep, and its value used to define the indenter
geometry.
geometry.
</P>
<P>Note that equal-style variables can specify formulas with various
mathematical functions, and include <A HREF = "thermo_style.html">thermo_style</A>

6
doc/fix_indent.txt
View File

@ -89,13 +89,13 @@ the plane's current position will feel no force. Vice versa if {side}
is specified as {hi}.
Any of the 4 quantities defining a spherical indenter's geometry can
be specified as an equal-style "variable"_variable, namely {x}, {y},
{z}, or {R}. Similarly, for a cylindrical indenter, any of {c1},
be specified as an equal-style "variable"_variable.html, namely {x},
{y}, {z}, or {R}. Similarly, for a cylindrical indenter, any of {c1},
{c2}, or {R}, can be a variable. For a planar indenter, {pos} can be
a variable. If the value is a variable, it should be specified as
v_ID, where ID is the variable ID. In this case, the variable will be
evaluated each timestep, and its value used to define the indenter
geometry.
geometry.
Note that equal-style variables can specify formulas with various
mathematical functions, and include "thermo_style"_thermo_style.html

2
doc/fix_nh.html
View File

@ -51,7 +51,7 @@ keyword = <I>temp</I> or <I>iso</I> or <I>aniso</I> or <I>tri</I> or <I>x</I> or
<PRE>fix 1 all nvt temp 300.0 300.0 100.0
fix 1 water npt temp 300.0 300.0 100.0 iso 0.0 0.0 1000.0
fix 2 jello npt temp 300.0 300.0 100.0 tri 5.0 5.0 1000.0
fix 2 ice nph temp 273.15 273.15 x 1.0 1.0 0.5 y 2.0 2.0 0.5 z 3.0 3.0 0.5 yz 0.1 0.1 0.5 xz 0.2 0.2 0.5 xy 0.3 0.3 0.5 nreset 1000
fix 2 ice nph x 1.0 1.0 0.5 y 2.0 2.0 0.5 z 3.0 3.0 0.5 yz 0.1 0.1 0.5 xz 0.2 0.2 0.5 xy 0.3 0.3 0.5 nreset 1000
</PRE>
<P><B>Description:</B>
</P>

2
doc/fix_nh.txt
View File

@ -43,7 +43,7 @@ keyword = {temp} or {iso} or {aniso} or {tri} or {x} or {y} or {z} or {xy} or {y
fix 1 all nvt temp 300.0 300.0 100.0
fix 1 water npt temp 300.0 300.0 100.0 iso 0.0 0.0 1000.0
fix 2 jello npt temp 300.0 300.0 100.0 tri 5.0 5.0 1000.0
fix 2 ice nph temp 273.15 273.15 x 1.0 1.0 0.5 y 2.0 2.0 0.5 z 3.0 3.0 0.5 yz 0.1 0.1 0.5 xz 0.2 0.2 0.5 xy 0.3 0.3 0.5 nreset 1000 :pre
fix 2 ice nph x 1.0 1.0 0.5 y 2.0 2.0 0.5 z 3.0 3.0 0.5 yz 0.1 0.1 0.5 xz 0.2 0.2 0.5 xy 0.3 0.3 0.5 nreset 1000 :pre
[Description:]

8
doc/fix_press_berendsen.html
View File

@ -75,10 +75,10 @@ thermostatting and barostatting.
ability to specify the 3 diagonal components of an external stress
tensor, and to couple various of these components together so that the
dimensions they represent are varied together during a
constant-pressure simulation. Unlike the <A HREF = "fix_npt.html">fix npt</A> and
<A HREF = "fix_nph.html">fix nph</A> commands, this fix cannot be used with
triclinic (non-orthogonal) simulation boxes to control all 6
components of the general pressure tensor.
constant-pressure simulation. Unlike the <A HREF = "fix_nh.html">fix npt</A> and
<A HREF = "fix_nh.html">fix nph</A> commands, this fix cannot be used with triclinic
(non-orthogonal) simulation boxes to control all 6 components of the
general pressure tensor.
</P>
<P>The target pressures for each of the 3 diagonal components of the
stress tensor can be specified independently via the <I>x</I>, <I>y</I>, <I>z</I>,

8
doc/fix_press_berendsen.txt
View File

@ -69,10 +69,10 @@ The barostat is specified using one or more of the {iso}, {aniso},
ability to specify the 3 diagonal components of an external stress
tensor, and to couple various of these components together so that the
dimensions they represent are varied together during a
constant-pressure simulation. Unlike the "fix npt"_fix_npt.html and
"fix nph"_fix_nph.html commands, this fix cannot be used with
triclinic (non-orthogonal) simulation boxes to control all 6
components of the general pressure tensor.
constant-pressure simulation. Unlike the "fix npt"_fix_nh.html and
"fix nph"_fix_nh.html commands, this fix cannot be used with triclinic
(non-orthogonal) simulation boxes to control all 6 components of the
general pressure tensor.
The target pressures for each of the 3 diagonal components of the
stress tensor can be specified independently via the {x}, {y}, {z},

6
doc/fix_rigid.html
View File

@ -251,14 +251,14 @@ modified when the center-of-mass of the rigid body moves across a
periodic boundary. They are not incremented/decremented as they would
be for non-rigid atoms. This change does not affect dynamics, but
means that any diagnostic computation based on the atomic image flag
values must be adjusted accordingly. For example, the <A HREF = "fix_msd.html">fix
values must be adjusted accordingly. For example, the <A HREF = "compute_msd.html">compute
msd</A> will not compute the expected mean-squared
displacement for such atoms, and the image flag values written to a
<A HREF = "dump.html">dump file</A> will be different than they would be if the
atoms were not in a rigid body. It also means that if you have bonds
between a pair of rigid bodies and the bond straddles a periodic
boundary, you cannot use the <A HREF = "replicate">replicate</A> command to increase
the system size.
boundary, you cannot use the <A HREF = "replicate.html">replicate</A> command to
increase the system size.
</P>
<HR>

8
doc/fix_rigid.txt
View File

@ -240,14 +240,14 @@ modified when the center-of-mass of the rigid body moves across a
periodic boundary. They are not incremented/decremented as they would
be for non-rigid atoms. This change does not affect dynamics, but
means that any diagnostic computation based on the atomic image flag
values must be adjusted accordingly. For example, the "fix
msd"_fix_msd.html will not compute the expected mean-squared
values must be adjusted accordingly. For example, the "compute
msd"_compute_msd.html will not compute the expected mean-squared
displacement for such atoms, and the image flag values written to a
"dump file"_dump.html will be different than they would be if the
atoms were not in a rigid body. It also means that if you have bonds
between a pair of rigid bodies and the bond straddles a periodic
boundary, you cannot use the "replicate"_replicate command to increase
the system size.
boundary, you cannot use the "replicate"_replicate.html command to
increase the system size.
:line

12
doc/fix_setforce.html
View File

@ -49,12 +49,12 @@ force, assuming their initial velocity zero.
<P>Any of the fx,fy,fz values can be specified as NULL which means do not
alter the force component in that dimension.
</P>
<P>Any of the 3 quantities defining the force components can be
specified as an equal-style or atom-style <A HREF = "variable">variable</A>, namely
<I>fx</I>, <I>fy</I>, <I>fz</I>. If the value is a variable, it should be specified
as v_ID, where ID is the variable ID. In this case, the variable will
be evaluated each timestep, and its value used to determine the
force component.
<P>Any of the 3 quantities defining the force components can be specified
as an equal-style or atom-style <A HREF = "variable.html">variable</A>, namely <I>fx</I>,
<I>fy</I>, <I>fz</I>. If the value is a variable, it should be specified as
v_ID, where ID is the variable ID. In this case, the variable will be
evaluated each timestep, and its value used to determine the force
component.
</P>
<P>Equal-style variables can specify formulas with various mathematical
functions, and include <A HREF = "thermo_style.html">thermo_style</A> command

12
doc/fix_setforce.txt
View File

@ -39,12 +39,12 @@ force, assuming their initial velocity zero.
Any of the fx,fy,fz values can be specified as NULL which means do not
alter the force component in that dimension.
Any of the 3 quantities defining the force components can be
specified as an equal-style or atom-style "variable"_variable, namely
{fx}, {fy}, {fz}. If the value is a variable, it should be specified
as v_ID, where ID is the variable ID. In this case, the variable will
be evaluated each timestep, and its value used to determine the
force component.
Any of the 3 quantities defining the force components can be specified
as an equal-style or atom-style "variable"_variable.html, namely {fx},
{fy}, {fz}. If the value is a variable, it should be specified as
v_ID, where ID is the variable ID. In this case, the variable will be
evaluated each timestep, and its value used to determine the force
component.
Equal-style variables can specify formulas with various mathematical
functions, and include "thermo_style"_thermo_style.html command

2
doc/fix_store_coord.html
View File

@ -87,7 +87,7 @@ minimization</A>.
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_msd.html">compute msd</A>, <A HREF = "compute_displace_atom.html">compute
displace/atom</A>, <A HREF = "compute_store_force.html">compute
displace/atom</A>, <A HREF = "fix_store_force.html">fix
store/force</A>
</P>
<P><B>Default:</B>

4
doc/fix_store_coord.txt
View File

@ -79,8 +79,8 @@ minimization"_minimize.html.
[Related commands:]
"compute msd"_compute_msd.html, "compute
displace/atom"_compute_displace_atom.html, "compute
store/force"_compute_store_force.html
displace/atom"_compute_displace_atom.html, "fix
store/force"_fix_store_force.html
[Default:]

2
doc/fix_store_force.html
View File

@ -70,7 +70,7 @@ minimization</A>.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_store_coord.html">compute store/coord</A>
<P><A HREF = "fix_store_coord.html">fix store/coord</A>
</P>
<P><B>Default:</B> none
</P>

2
doc/fix_store_force.txt
View File

@ -67,6 +67,6 @@ minimization"_minimize.html.
[Related commands:]
"compute store/coord"_compute_store_coord.html
"fix store/coord"_fix_store_coord.html
[Default:] none

2
doc/fix_ttm.html
View File

@ -192,7 +192,7 @@ minimization</A>.
<P><B>Restrictions:</B>
</P>
<P>This fix can only be used for 3d simulations and orthogonal
simlulation boxes. You must use periodic <A HREF = "doc/boundary.html">boundary</A>
simlulation boxes. You must use periodic <A HREF = "boundary.html">boundary</A>
conditions with this fix.
</P>
<P><B>Related commands:</B>

2
doc/fix_ttm.txt
View File

@ -189,7 +189,7 @@ minimization"_minimize.html.
[Restrictions:]
This fix can only be used for 3d simulations and orthogonal
simlulation boxes. You must use periodic "boundary"_doc/boundary.html
simlulation boxes. You must use periodic "boundary"_boundary.html
conditions with this fix.
[Related commands:]

4
doc/fix_wall_reflect.html
View File

@ -60,14 +60,14 @@ This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>
<P>A reflecting wall should not be used with rigid bodies such as those
defined by a "fix rigid" command. This is because the wall/reflect
displaces atoms directly rather than exerts a force on them. For
rigid bodies, use a soft wall instead, such as <A HREF = "fix_wall_lj93.html">fix
rigid bodies, use a soft wall instead, such as <A HREF = "fix_wall.html">fix
wall/lj93</A>. LAMMPS will flag the use of a rigid
fix with fix wall/reflect with a warning, but will not generate an
error.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_wall_lj93.html">fix wall/lj93</A> command
<P><A HREF = "fix_wall.html">fix wall/lj93</A> command
</P>
<P><B>Default:</B> none
</P>

4
doc/fix_wall_reflect.txt
View File

@ -58,13 +58,13 @@ A reflecting wall should not be used with rigid bodies such as those
defined by a "fix rigid" command. This is because the wall/reflect
displaces atoms directly rather than exerts a force on them. For
rigid bodies, use a soft wall instead, such as "fix
wall/lj93"_fix_wall_lj93.html. LAMMPS will flag the use of a rigid
wall/lj93"_fix_wall.html. LAMMPS will flag the use of a rigid
fix with fix wall/reflect with a warning, but will not generate an
error.
[Related commands:]
"fix wall/lj93"_fix_wall_lj93.html command
"fix wall/lj93"_fix_wall.html command
[Default:] none

2
doc/group.html
View File

@ -106,7 +106,7 @@ group. This group cannot be deleted.
<P><B>Related commands:</B>
</P>
<P><A HREF = "dump.html">dump</A>, <A HREF = "fix.html">fix</A>, <A HREF = "region.html">region</A>,
<A HREF = "temperature.html">temperature</A>, <A HREF = "velocity.html">velocity</A>
<A HREF = "velocity.html">velocity</A>
</P>
<P><B>Default:</B>
</P>

2
doc/group.txt
View File

@ -101,7 +101,7 @@ There can be no more than 32 groups defined at one time, including
[Related commands:]
"dump"_dump.html, "fix"_fix.html, "region"_region.html,
"temperature"_temperature.html, "velocity"_velocity.html
"velocity"_velocity.html
[Default:]

7
doc/kspace_style.html
View File

@ -108,9 +108,10 @@ style <I>pppm/tip4p</I> and vice versa.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "kspace_modify.html">kspace_modify</A>, <A HREF = "pair_style.html">pair_style</A>
lj/cut/coul/long, <A HREF = "pair_style.html">pair_style</A> lj/charmm/coul/long,
<A HREF = "pair_style">pair_style</A> lj/coul, <A HREF = "pair_style">pair_style</A> buck/coul
<P><A HREF = "kspace_modify.html">kspace_modify</A>, <A HREF = "pair_lj.html">pair_style
lj/cut/coul/long</A>, <A HREF = "pair_charmm.html">pair_style
lj/charmm/coul/long</A>, <A HREF = "pair_lj_coul.html">pair_style
lj/coul</A>, <A HREF = "pair_buck.html">pair_style buck/coul/long</A>
</P>
<P><B>Default:</B>
</P>

7
doc/kspace_style.txt
View File

@ -103,9 +103,10 @@ style {pppm/tip4p} and vice versa.
[Related commands:]
"kspace_modify"_kspace_modify.html, "pair_style"_pair_style.html
lj/cut/coul/long, "pair_style"_pair_style.html lj/charmm/coul/long,
"pair_style"_pair_style lj/coul, "pair_style"_pair_style buck/coul
"kspace_modify"_kspace_modify.html, "pair_style
lj/cut/coul/long"_pair_lj.html, "pair_style
lj/charmm/coul/long"_pair_charmm.html, "pair_style
lj/coul"_pair_lj_coul.html, "pair_style buck/coul/long"_pair_buck.html
[Default:]

2
doc/lattice.html
View File

@ -127,7 +127,7 @@ simulation box.
scaled when mapping it into the simulation box. I.e. it determines a
multiplicative factor to apply to the unit cell, to convert it to a
lattice of the desired size and distance units in the simulation box.
The meaning of the <I>scale</I> argument depends on the <A HREF = "unit.html">units</A>
The meaning of the <I>scale</I> argument depends on the <A HREF = "units.html">units</A>
being used in your simulation.
</P>
<P>For all unit styles except <I>lj</I>, the scale argument is specified in

2
doc/lattice.txt
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@ -119,7 +119,7 @@ The {scale} argument determines how the size of the unit cell will be
scaled when mapping it into the simulation box. I.e. it determines a
multiplicative factor to apply to the unit cell, to convert it to a
lattice of the desired size and distance units in the simulation box.
The meaning of the {scale} argument depends on the "units"_unit.html
The meaning of the {scale} argument depends on the "units"_units.html
being used in your simulation.
For all unit styles except {lj}, the scale argument is specified in

2
doc/min_style.html
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@ -1,5 +1,5 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Page</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Chapter_commands.html#comm">LAMMPS Commands</A>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Page</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>

2
doc/min_style.txt
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@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Chapter_commands.html#comm)
:link(lc,Section_commands.html#comm)
:line
min_style command :h3

15
doc/minimize.html
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@ -170,13 +170,14 @@ minimum to the specified energy or force tolerance.
</P>
<P>Note that a cutoff Lennard-Jones potential (and others) can be shifted
so that its energy is 0.0 at the cutoff via the
<A HREF = "pair_modify">pair_modify</A> command. See the doc pages for inidividual
<A HREF = "pair_style.html">pair styles</A> for details. Note that Coulombic
potentials always have a cutoff, unless versions with a long-range
component are used (e.g. <A HREF = "pair_lj.html">pair_style lj/cut/coul/long</A>).
The CHARMM potentials go to 0.0 at the cutoff (e.g. <A HREF = "pair_charmm.html</I>">pair_style
lj/charmm/coul/charmm</A>, as do the GROMACS potentials
(e.g. <A HREF = "pair_gromacs.html</I>">pair_style lj/gromacs</A>.
<A HREF = "pair_modify.html">pair_modify</A> command. See the doc pages for
inidividual <A HREF = "pair_style.html">pair styles</A> for details. Note that
Coulombic potentials always have a cutoff, unless versions with a
long-range component are used (e.g. <A HREF = "pair_lj.html">pair_style
lj/cut/coul/long</A>). The CHARMM potentials go to 0.0 at
the cutoff (e.g. <A HREF = "pair_charmm.html">pair_style lj/charmm/coul/charmm</A>),
as do the GROMACS potentials (e.g. <A HREF = "pair_gromacs.html">pair_style
lj/gromacs</A>).
</P>
<P>If a soft potential (<A HREF = "pair_soft.html">pair_style soft</A>) is used the
Astop value is used for the prefactor (no time dependence).

15
doc/minimize.txt
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@ -167,13 +167,14 @@ minimum to the specified energy or force tolerance.
Note that a cutoff Lennard-Jones potential (and others) can be shifted
so that its energy is 0.0 at the cutoff via the
"pair_modify"_pair_modify command. See the doc pages for inidividual
"pair styles"_pair_style.html for details. Note that Coulombic
potentials always have a cutoff, unless versions with a long-range
component are used (e.g. "pair_style lj/cut/coul/long"_pair_lj.html).
The CHARMM potentials go to 0.0 at the cutoff (e.g. "pair_style
lj/charmm/coul/charmm"_pair_charmm.html}, as do the GROMACS potentials
(e.g. "pair_style lj/gromacs"_pair_gromacs.html}.
"pair_modify"_pair_modify.html command. See the doc pages for
inidividual "pair styles"_pair_style.html for details. Note that
Coulombic potentials always have a cutoff, unless versions with a
long-range component are used (e.g. "pair_style
lj/cut/coul/long"_pair_lj.html). The CHARMM potentials go to 0.0 at
the cutoff (e.g. "pair_style lj/charmm/coul/charmm"_pair_charmm.html),
as do the GROMACS potentials (e.g. "pair_style
lj/gromacs"_pair_gromacs.html).
If a soft potential ("pair_style soft"_pair_soft.html) is used the
Astop value is used for the prefactor (no time dependence).

3
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@ -120,8 +120,7 @@ LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "fix_nve_dipole.html">fix nve/dipole</A>,
<A HREF = "compute_temp_dipole.html">compute temp/dipole</A>
<P><A HREF = "pair_coeff.html">pair_coeff</A>
</P>
<P><B>Default:</B> none
</P>

3
doc/pair_dipole.txt
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@ -117,8 +117,7 @@ LAMMPS"_Section_start.html#2_3 section for more info.
[Related commands:]
"pair_coeff"_pair_coeff.html, "fix nve/dipole"_fix_nve_dipole.html,
"compute temp/dipole"_compute_temp_dipole.html
"pair_coeff"_pair_coeff.html
[Default:] none

22
doc/pair_hybrid.html
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@ -105,7 +105,7 @@ as described below.
</P>
<P>If you want there to be no interactions between a particular pair of
atom types, you have 3 choices. You can assign the type pair to some
sub-style and use the <A HREF = "neigh_modify">neigh_modify exclude type</A>
sub-style and use the <A HREF = "neigh_modify.html">neigh_modify exclude type</A>
command. You can assign it to some sub-style and set the coefficients
so that there is effectively no interaction (e.g. epsilon = 0.0 in a
LJ potential). Or, for <I>hybrid</I> and <I>hybrid/overlay</I> simulations, you
@ -147,11 +147,11 @@ associated sub-style supports it.
</P>
<P>For the hybrid pair styles, the list of sub-styles and their
respective settings are written to <A HREF = "restart.html">binary restart
files</A>, so a pair_style command does not need to
specified in an input script that reads a restart file. However, the
coefficient information is not stored in the restart file. Thus,
pair_coeff commands need to be re-specified in the restart input
script.
files</A>, so a <A HREF = "pair_style.html">pair_style</A> command does
not need to specified in an input script that reads a restart file.
However, the coefficient information is not stored in the restart
file. Thus, pair_coeff commands need to be re-specified in the
restart input script.
</P>
<P>These pair styles support the use of the <I>inner</I>, <I>middle</I>, and
<I>outer</I> keywords of the <A HREF = "run_style.html">run_style respa</A> command, if
@ -160,11 +160,11 @@ their sub-styles do.
<P><B>Restrictions:</B>
</P>
<P>When using a long-range Coulombic solver (via the
<A HREF = "kspace_style">kspace_style</A> command) with a hybrid pair_style, one or
more sub-styles will be of the "long" variety, e.g. <I>lj/cut/coul/long</I>
or <I>buck/coul/long</I>. You must insure that the short-range Coulombic
cutoff used by each of these long pair styles is the same or else
LAMMPS will generate an error.
<A HREF = "kspace_style.html">kspace_style</A> command) with a hybrid pair_style,
one or more sub-styles will be of the "long" variety,
e.g. <I>lj/cut/coul/long</I> or <I>buck/coul/long</I>. You must insure that the
short-range Coulombic cutoff used by each of these long pair styles is
the same or else LAMMPS will generate an error.
</P>
<P><B>Related commands:</B>
</P>

22
doc/pair_hybrid.txt
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@ -101,7 +101,7 @@ as described below.
If you want there to be no interactions between a particular pair of
atom types, you have 3 choices. You can assign the type pair to some
sub-style and use the "neigh_modify exclude type"_neigh_modify
sub-style and use the "neigh_modify exclude type"_neigh_modify.html
command. You can assign it to some sub-style and set the coefficients
so that there is effectively no interaction (e.g. epsilon = 0.0 in a
LJ potential). Or, for {hybrid} and {hybrid/overlay} simulations, you
@ -143,11 +143,11 @@ associated sub-style supports it.
For the hybrid pair styles, the list of sub-styles and their
respective settings are written to "binary restart
files"_restart.html, so a pair_style command does not need to
specified in an input script that reads a restart file. However, the
coefficient information is not stored in the restart file. Thus,
pair_coeff commands need to be re-specified in the restart input
script.
files"_restart.html, so a "pair_style"_pair_style.html command does
not need to specified in an input script that reads a restart file.
However, the coefficient information is not stored in the restart
file. Thus, pair_coeff commands need to be re-specified in the
restart input script.
These pair styles support the use of the {inner}, {middle}, and
{outer} keywords of the "run_style respa"_run_style.html command, if
@ -156,11 +156,11 @@ their sub-styles do.
[Restrictions:]
When using a long-range Coulombic solver (via the
"kspace_style"_kspace_style command) with a hybrid pair_style, one or
more sub-styles will be of the "long" variety, e.g. {lj/cut/coul/long}
or {buck/coul/long}. You must insure that the short-range Coulombic
cutoff used by each of these long pair styles is the same or else
LAMMPS will generate an error.
"kspace_style"_kspace_style.html command) with a hybrid pair_style,
one or more sub-styles will be of the "long" variety,
e.g. {lj/cut/coul/long} or {buck/coul/long}. You must insure that the
short-range Coulombic cutoff used by each of these long pair styles is
the same or else LAMMPS will generate an error.
[Related commands:]

2
doc/prd.html
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@ -280,7 +280,7 @@ for dephasing.
of elapsed time to perform time-dependent operations. Examples
include the "ave" fixes such as <A HREF = "fix_ave_spatial.html">fix
ave/spatial</A>. Also <A HREF = "fix_dt_reset.html">fix
dt/reset</A> and <A HREF = "fix_deposity.html">fix deposit</A>.
dt/reset</A> and <A HREF = "fix_deposit.html">fix deposit</A>.
</P>
<P><B>Related commands:</B>
</P>

2
doc/prd.txt
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@ -267,7 +267,7 @@ This command cannot be used when any fixes are defined that keep track
of elapsed time to perform time-dependent operations. Examples
include the "ave" fixes such as "fix
ave/spatial"_fix_ave_spatial.html. Also "fix
dt/reset"_fix_dt_reset.html and "fix deposit"_fix_deposity.html.
dt/reset"_fix_dt_reset.html and "fix deposit"_fix_deposit.html.
[Related commands:]

2
doc/reset_timestep.html
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@ -49,7 +49,7 @@ given after the reset_timestep command is used.
of elapsed time to perform time-dependent operations. Examples
include the "ave" fixes such as <A HREF = "fix_ave_spatial.html">fix
ave/spatial</A>. Also <A HREF = "fix_dt_reset.html">fix
dt/reset</A> and <A HREF = "fix_deposity.html">fix deposit</A>.
dt/reset</A> and <A HREF = "fix_deposit.html">fix deposit</A>.
</P>
<P>This command cannot be used when any dynamic regions are defined via
the <A HREF = "region.html">region</A> command, which have time-dependent position

2
doc/reset_timestep.txt
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@ -46,7 +46,7 @@ This command cannot be used when any fixes are defined that keep track
of elapsed time to perform time-dependent operations. Examples
include the "ave" fixes such as "fix
ave/spatial"_fix_ave_spatial.html. Also "fix
dt/reset"_fix_dt_reset.html and "fix deposit"_fix_deposity.html.
dt/reset"_fix_dt_reset.html and "fix deposit"_fix_deposit.html.
This command cannot be used when any dynamic regions are defined via
the "region"_region.html command, which have time-dependent position

15
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@ -171,13 +171,14 @@ value for that dimension is unchanged.
atoms have diffused one or more box lengths in various directions.
This command can then reset the image values for atoms so that they
are effectively inside the simulation box, e.g if a diffusion
coefficient is about to be measured via the <A HREF = "fix_msd.html">fix msd</A>
command. Care should be taken not to reset the image flags of two
atoms in a bond to the same value if the bond straddles a periodic
boundary (rather they should be different by +/- 1). This will not
affect the dynamics of a simulation, but may mess up analysis of the
trajectories if a LAMMPS diagnostic or your own analysis relies on the
image flags to unwrap a molecule which straddles the periodic box.
coefficient is about to be measured via the <A HREF = "compute_msd.html">compute
msd</A> command. Care should be taken not to reset the
image flags of two atoms in a bond to the same value if the bond
straddles a periodic boundary (rather they should be different by +/-
1). This will not affect the dynamics of a simulation, but may mess
up analysis of the trajectories if a LAMMPS diagnostic or your own
analysis relies on the image flags to unwrap a molecule which
straddles the periodic box.
</P>
<P>For the <I>diameter</I> and <I>density</I> and <I>volume</I> keywords, the <A HREF = "atom_style.html">atom
style</A> being used must support the use of those

15
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@ -166,13 +166,14 @@ This command can be useful after a system has been equilibrated and
atoms have diffused one or more box lengths in various directions.
This command can then reset the image values for atoms so that they
are effectively inside the simulation box, e.g if a diffusion
coefficient is about to be measured via the "fix msd"_fix_msd.html
command. Care should be taken not to reset the image flags of two
atoms in a bond to the same value if the bond straddles a periodic
boundary (rather they should be different by +/- 1). This will not
affect the dynamics of a simulation, but may mess up analysis of the
trajectories if a LAMMPS diagnostic or your own analysis relies on the
image flags to unwrap a molecule which straddles the periodic box.
coefficient is about to be measured via the "compute
msd"_compute_msd.html command. Care should be taken not to reset the
image flags of two atoms in a bond to the same value if the bond
straddles a periodic boundary (rather they should be different by +/-
1). This will not affect the dynamics of a simulation, but may mess
up analysis of the trajectories if a LAMMPS diagnostic or your own
analysis relies on the image flags to unwrap a molecule which
straddles the periodic box.
For the {diameter} and {density} and {volume} keywords, the "atom
style"_atom_style.html being used must support the use of those

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@ -181,7 +181,7 @@ components of velocity and/or include different degrees of freedom
</P>
<P>The potential energy of the system <I>pe</I> will include contributions
from fixes if the <A HREF = "fix_modify.html">fix_modify thermo</A> option is set
for a fix that calculates such a contribution. For example, the <A HREF = "fix_wall_lj93">fix
for a fix that calculates such a contribution. For example, the <A HREF = "fix_wall.html">fix
wall/lj93</A> fix calculates the energy of atoms
interacting with the wall. See the doc pages for "individual fixes"
to see which ones contribute.

2
doc/thermo_style.txt
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@ -176,7 +176,7 @@ components of velocity and/or include different degrees of freedom
The potential energy of the system {pe} will include contributions
from fixes if the "fix_modify thermo"_fix_modify.html option is set
for a fix that calculates such a contribution. For example, the "fix
wall/lj93"_fix_wall_lj93 fix calculates the energy of atoms
wall/lj93"_fix_wall.html fix calculates the energy of atoms
interacting with the wall. See the doc pages for "individual fixes"
to see which ones contribute.

4
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@ -76,7 +76,7 @@ which when evaluated produces a single numeric value which can be
output either directly (see the <A HREF = "print.html">print</A>, <A HREF = "fix_print.html">fix
print</A>, and <A HREF = "run.html">run every</A> commands) or as part
of thermodynamic output (see the <A HREF = "thermo_style.html">thermo_style</A>
command), or used as input to an averaging fix (see the <A HREF = "fix_ave/time">fix
command), or used as input to an averaging fix (see the <A HREF = "fix_ave_time">fix
ave/time</A> command). Variables of style <I>atom</I> store a
formula which when evaluated produces one numeric value per atom which
can be output to a dump file (see the <A HREF = "dump.html">dump custom</A> command)
@ -328,7 +328,7 @@ return components of the position and velocity of the center of mass
of the group. Fcm() returns a component of the total force on the
group of atoms. Bound() returns the min/max of a particular
coordinate for all atoms in the group. Gyration() computes the
radius-of-gyration of the group of atoms. See the <A HREF = "fix_gyration.html">fix
radius-of-gyration of the group of atoms. See the <A HREF = "compute_gyration.html">compute
gyration</A> command for a definition of the formula.
</P>
<P>Region functions are exactly the same as group functions except they

6
doc/variable.txt
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@ -71,7 +71,7 @@ output either directly (see the "print"_print.html, "fix
print"_fix_print.html, and "run every"_run.html commands) or as part
of thermodynamic output (see the "thermo_style"_thermo_style.html
command), or used as input to an averaging fix (see the "fix
ave/time"_fix_ave/time command). Variables of style {atom} store a
ave/time"_fix_ave_time command). Variables of style {atom} store a
formula which when evaluated produces one numeric value per atom which
can be output to a dump file (see the "dump custom"_dump.html command)
or used as input to an averaging fix (see the "fix
@ -323,8 +323,8 @@ return components of the position and velocity of the center of mass
of the group. Fcm() returns a component of the total force on the
group of atoms. Bound() returns the min/max of a particular
coordinate for all atoms in the group. Gyration() computes the
radius-of-gyration of the group of atoms. See the "fix
gyration"_fix_gyration.html command for a definition of the formula.
radius-of-gyration of the group of atoms. See the "compute
gyration"_compute_gyration.html command for a definition of the formula.
Region functions are exactly the same as group functions except they
take an extra argument which is the region ID. The function is