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2
doc/Section_accelerate.html
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@ -69,7 +69,7 @@ The speed-up due to GPU usage depends on a variety of factors, as
discussed below.
</P>
<P>To see what styles are currently available in each of the accelerated
packages, see <A HREF = "Section_commands.html#cmd_5">this section</A> of the
packages, see <A HREF = "Section_commands.html#cmd_5">Section_commands 5</A> of the
manual. A list of accelerated styles is included in the pair, fix,
compute, and kspace sections.
</P>

2
doc/Section_accelerate.txt
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@ -66,7 +66,7 @@ The speed-up due to GPU usage depends on a variety of factors, as
discussed below.
To see what styles are currently available in each of the accelerated
packages, see "this section"_Section_commands.html#cmd_5 of the
packages, see "Section_commands 5"_Section_commands.html#cmd_5 of the
manual. A list of accelerated styles is included in the pair, fix,
compute, and kspace sections.

14
doc/Section_howto.html
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@ -674,9 +674,9 @@ of the Python wrapper provided with LAMMPS that operates through the
LAMMPS library interface.
</P>
<P>The files src/library.cpp and library.h contain the C-style interface
to LAMMPS. See <A HREF = "Section_howto.html#howto_19">this section</A> of the manual
for a description of the interface and how to extend it for your
needs.
to LAMMPS. See <A HREF = "Section_howto.html#howto_19">Section_howto 19</A> of the
manual for a description of the interface and how to extend it for
your needs.
</P>
<P>Note that the lammps_open() function that creates an instance of
LAMMPS takes an MPI communicator as an argument. This means that
@ -1658,10 +1658,10 @@ converge and requires careful post-processing <A HREF = "#Shinoda">(Shinoda)</A>
<A NAME = "howto_19"></A><H4>6.19 Library interface to LAMMPS
</H4>
<P>As described in <A HREF = "Section_start.html#start_4">this section</A>, LAMMPS can
be built as a library, so that it can be called by another code, used
in a <A HREF = "Section_howto.html#howto_10">coupled manner</A> with other codes, or
driven through a <A HREF = "Section_python.html">Python interface</A>.
<P>As described in <A HREF = "Section_start.html#start_4">Section_start 4</A>, LAMMPS
can be built as a library, so that it can be called by another code,
used in a <A HREF = "Section_howto.html#howto_10">coupled manner</A> with other
codes, or driven through a <A HREF = "Section_python.html">Python interface</A>.
</P>
<P>All of these methodologies use a C-style interface to LAMMPS that is
provided in the files src/library.cpp and src/library.h. The

14
doc/Section_howto.txt
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@ -668,9 +668,9 @@ of the Python wrapper provided with LAMMPS that operates through the
LAMMPS library interface.
The files src/library.cpp and library.h contain the C-style interface
to LAMMPS. See "this section"_Section_howto.html#howto_19 of the manual
for a description of the interface and how to extend it for your
needs.
to LAMMPS. See "Section_howto 19"_Section_howto.html#howto_19 of the
manual for a description of the interface and how to extend it for
your needs.
Note that the lammps_open() function that creates an instance of
LAMMPS takes an MPI communicator as an argument. This means that
@ -1645,10 +1645,10 @@ converge and requires careful post-processing "(Shinoda)"_#Shinoda
6.19 Library interface to LAMMPS :link(howto_19),h4
As described in "this section"_Section_start.html#start_4, LAMMPS can
be built as a library, so that it can be called by another code, used
in a "coupled manner"_Section_howto.html#howto_10 with other codes, or
driven through a "Python interface"_Section_python.html.
As described in "Section_start 4"_Section_start.html#start_4, LAMMPS
can be built as a library, so that it can be called by another code,
used in a "coupled manner"_Section_howto.html#howto_10 with other
codes, or driven through a "Python interface"_Section_python.html.
All of these methodologies use a C-style interface to LAMMPS that is
provided in the files src/library.cpp and src/library.h. The

8
doc/Section_intro.html
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@ -51,8 +51,8 @@ LAMMPS performance and scalability, or the Benchmarks section of the
</P>
<P>LAMMPS is a freely-available open-source code, distributed under the
terms of the <A HREF = "http://www.gnu.org/copyleft/gpl.html">GNU Public License</A>, which means you can use or
modify the code however you wish. See <A HREF = "#intro_4">this section</A> for a brief
discussion of the open-source philosophy.
modify the code however you wish. See <A HREF = "#intro_4">this section</A> for a
brief discussion of the open-source philosophy.
</P>
@ -421,8 +421,8 @@ Site</A>, or have a suggestion for something to clarify or include,
send an email to the
<A HREF = "http://lammps.sandia.gov/authors.html">developers</A>.
<LI>If you find a bug, <A HREF = "Section_errors.html#err_2">this section</A> describes
how to report it.
<LI>If you find a bug, <A HREF = "Section_errors.html#err_2">Section_errors 2</A>
describes how to report it.
<LI>If you publish a paper using LAMMPS results, send the citation (and
any cool pictures or movies if you like) to add to the Publications,

8
doc/Section_intro.txt
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@ -47,8 +47,8 @@ LAMMPS performance and scalability, or the Benchmarks section of the
LAMMPS is a freely-available open-source code, distributed under the
terms of the "GNU Public License"_gnu, which means you can use or
modify the code however you wish. See "this section"_#intro_4 for a brief
discussion of the open-source philosophy.
modify the code however you wish. See "this section"_#intro_4 for a
brief discussion of the open-source philosophy.
:link(gnu,http://www.gnu.org/copyleft/gpl.html)
@ -410,8 +410,8 @@ Site"_lws, or have a suggestion for something to clarify or include,
send an email to the
"developers"_http://lammps.sandia.gov/authors.html. :l
If you find a bug, "this section"_Section_errors.html#err_2 describes
how to report it. :l
If you find a bug, "Section_errors 2"_Section_errors.html#err_2
describes how to report it. :l
If you publish a paper using LAMMPS results, send the citation (and
any cool pictures or movies if you like) to add to the Publications,

2
doc/Section_packages.html
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@ -25,7 +25,7 @@ molecular systems or granular systems are in packages. You can see
the list of all packages by typing "make package" from within the src
directory of the LAMMPS distribution.
</P>
<P>See <A HREF = "Section_start.html#start_3">this section</A> of the manual for
<P>See <A HREF = "Section_start.html#start_3">Section_start 3</A> of the manual for
details on how to include/exclude specific packages as part of the
LAMMPS build process, and for more details about the differences
between standard packages and user packages in LAMMPS.

2
doc/Section_packages.txt
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@ -22,7 +22,7 @@ molecular systems or granular systems are in packages. You can see
the list of all packages by typing "make package" from within the src
directory of the LAMMPS distribution.
See "this section"_Section_start.html#start_3 of the manual for
See "Section_start 3"_Section_start.html#start_3 of the manual for
details on how to include/exclude specific packages as part of the
LAMMPS build process, and for more details about the differences
between standard packages and user packages in LAMMPS.

8
doc/Section_python.html
View File

@ -34,8 +34,8 @@ packages. It can be used to glue multiple pieces of software
together, e.g. to run a coupled or multiscale model. See <A HREF = "Section_howto.html#howto_10">this
section</A> of the manual and the couple
directory of the distribution for more ideas about coupling LAMMPS to
other codes. See <A HREF = "Section_start.html#start_4">this section</A> about how
to build LAMMPS as a library, and <A HREF = "Section_howto.html#howto_19">this
other codes. See <A HREF = "Section_start.html#start_4">Section_start 4</A> about
how to build LAMMPS as a library, and <A HREF = "Section_howto.html#howto_19">this
section</A> for a description of the library
interface provided in src/library.cpp and src/library.h and how to
extend it for your needs. As described below, that interface is what
@ -502,7 +502,7 @@ subscripting. The one exception is that for a fix that calculates a
global vector or array, a single double value from the vector or array
is returned, indexed by I (vector) or I and J (array). I,J are
zero-based indices. The I,J arguments can be left out if not needed.
See <A HREF = "Section_howto.html#howto_15">this section</A> of the manual for a
See <A HREF = "Section_howto.html#howto_15">Section_howto 15</A> of the manual for a
discussion of global, per-atom, and local data, and of scalar, vector,
and array data types. See the doc pages for individual
<A HREF = "compute.html">computes</A> and <A HREF = "fix.html">fixes</A> for a description of what
@ -582,7 +582,7 @@ following steps:
src/library.h.
<LI>Verify the new function is syntactically correct by building LAMMPS as
a library - see <A HREF = "Section_start.html#start_4">this section</A> of the
a library - see <A HREF = "Section_start.html#start_4">Section_start 4</A> of the
manual.
<LI>Add a wrapper method in the Python LAMMPS module to python/lammps.py

8
doc/Section_python.txt
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@ -31,8 +31,8 @@ packages. It can be used to glue multiple pieces of software
together, e.g. to run a coupled or multiscale model. See "this
section"_Section_howto.html#howto_10 of the manual and the couple
directory of the distribution for more ideas about coupling LAMMPS to
other codes. See "this section"_Section_start.html#start_4 about how
to build LAMMPS as a library, and "this
other codes. See "Section_start 4"_Section_start.html#start_4 about
how to build LAMMPS as a library, and "this
section"_Section_howto.html#howto_19 for a description of the library
interface provided in src/library.cpp and src/library.h and how to
extend it for your needs. As described below, that interface is what
@ -497,7 +497,7 @@ subscripting. The one exception is that for a fix that calculates a
global vector or array, a single double value from the vector or array
is returned, indexed by I (vector) or I and J (array). I,J are
zero-based indices. The I,J arguments can be left out if not needed.
See "this section"_Section_howto.html#howto_15 of the manual for a
See "Section_howto 15"_Section_howto.html#howto_15 of the manual for a
discussion of global, per-atom, and local data, and of scalar, vector,
and array data types. See the doc pages for individual
"computes"_compute.html and "fixes"_fix.html for a description of what
@ -577,7 +577,7 @@ Add a new interface function to src/library.cpp and
src/library.h. :ulb,l
Verify the new function is syntactically correct by building LAMMPS as
a library - see "this section"_Section_start.html#start_4 of the
a library - see "Section_start 4"_Section_start.html#start_4 of the
manual. :l
Add a wrapper method in the Python LAMMPS module to python/lammps.py

12
doc/Section_start.html
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@ -717,13 +717,13 @@ src/library.cpp and src/library.h.
<P>See the sample codes couple/simple/simple.cpp and simple.c as examples
of C++ and C codes that invoke LAMMPS thru its library interface.
There are other examples as well in the couple directory which are
discussed in <A HREF = "Section_howto.html#howto_10">this section</A> of the manual.
See <A HREF = "Section_python.html">Section_python</A> of the manual for a
discussed in <A HREF = "Section_howto.html#howto_10">Section_howto 10</A> of the
manual. See <A HREF = "Section_python.html">Section_python</A> of the manual for a
description of the Python wrapper provided with LAMMPS that operates
through the LAMMPS library interface.
</P>
<P>The files src/library.cpp and library.h contain the C-style interface
to LAMMPS. See <A HREF = "Section_howto.html#howto_19">this section</A> of the
to LAMMPS. See <A HREF = "Section_howto.html#howto_19">Section_howto 19</A> of the
manual for a description of the interface and how to extend it for
your needs.
</P>
@ -938,9 +938,9 @@ installed on a machine (e.g. your desktop), you can run on more
(virtual) processors than you have physical processors.
</P>
<P>To run multiple independent simulatoins from one input script, using
multiple partitions, see <A HREF = "Section_howto.html#howto_4">this section</A> of
the manual. World- and universe-style <A HREF = "variable.html">variables</A> are
useful in this context.
multiple partitions, see <A HREF = "Section_howto.html#howto_4">Section_howto 4</A>
of the manual. World- and universe-style <A HREF = "variable.html">variables</A>
are useful in this context.
</P>
<PRE>-plog file
</PRE>

12
doc/Section_start.txt
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@ -711,13 +711,13 @@ src/library.cpp and src/library.h.
See the sample codes couple/simple/simple.cpp and simple.c as examples
of C++ and C codes that invoke LAMMPS thru its library interface.
There are other examples as well in the couple directory which are
discussed in "this section"_Section_howto.html#howto_10 of the manual.
See "Section_python"_Section_python.html of the manual for a
discussed in "Section_howto 10"_Section_howto.html#howto_10 of the
manual. See "Section_python"_Section_python.html of the manual for a
description of the Python wrapper provided with LAMMPS that operates
through the LAMMPS library interface.
The files src/library.cpp and library.h contain the C-style interface
to LAMMPS. See "this section"_Section_howto.html#howto_19 of the
to LAMMPS. See "Section_howto 19"_Section_howto.html#howto_19 of the
manual for a description of the interface and how to extend it for
your needs.
@ -929,9 +929,9 @@ installed on a machine (e.g. your desktop), you can run on more
(virtual) processors than you have physical processors.
To run multiple independent simulatoins from one input script, using
multiple partitions, see "this section"_Section_howto.html#howto_4 of
the manual. World- and universe-style "variables"_variable.html are
useful in this context.
multiple partitions, see "Section_howto 4"_Section_howto.html#howto_4
of the manual. World- and universe-style "variables"_variable.html
are useful in this context.
-plog file :pre

4
doc/compute_ackland_atom.html
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@ -53,8 +53,8 @@ which computes this quantity.-
</P>
<P>This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
<A HREF = "Section_howto.html#howto_15">this section</A> for an overview of LAMMPS
output options.
<A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an overview of
LAMMPS output options.
</P>
<P><B>Restrictions:</B>
</P>

4
doc/compute_ackland_atom.txt
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@ -50,8 +50,8 @@ which computes this quantity.-
This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
"this section"_Section_howto.html#howto_15 for an overview of LAMMPS
output options.
"Section_howto 15"_Section_howto.html#howto_15 for an overview of
LAMMPS output options.
[Restrictions:]

4
doc/compute_centro_atom.html
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@ -79,8 +79,8 @@ too frequently or to have multiple compute/dump commands, each with a
</P>
<P>This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
<A HREF = "Section_howto.html#howto_15">this section</A> for an overview of LAMMPS
output options.
<A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an overview of
LAMMPS output options.
</P>
<P>The per-atom vector values are unitless values >= 0.0. Their
magnitude depends on the lattice style due to the number of

4
doc/compute_centro_atom.txt
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@ -75,8 +75,8 @@ too frequently or to have multiple compute/dump commands, each with a
This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
"this section"_Section_howto.html#howto_15 for an overview of LAMMPS
output options.
"Section_howto 15"_Section_howto.html#howto_15 for an overview of
LAMMPS output options.
The per-atom vector values are unitless values >= 0.0. Their
magnitude depends on the lattice style due to the number of

4
doc/compute_cluster_atom.html
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@ -46,8 +46,8 @@ too frequently or to have multiple compute/dump commands, each of a
</P>
<P>This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
<A HREF = "Section_howto.html#howto_15">this section</A> for an overview of LAMMPS
output options.
<A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an overview of
LAMMPS output options.
</P>
<P>The per-atom vector values will be an ID > 0, as explained above.
</P>

4
doc/compute_cluster_atom.txt
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@ -43,8 +43,8 @@ too frequently or to have multiple compute/dump commands, each of a
This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
"this section"_Section_howto.html#howto_15 for an overview of LAMMPS
output options.
"Section_howto 15"_Section_howto.html#howto_15 for an overview of
LAMMPS output options.
The per-atom vector values will be an ID > 0, as explained above.

4
doc/compute_cna_atom.html
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@ -77,8 +77,8 @@ too frequently or to have multiple compute/dump commands, each with a
</P>
<P>This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
<A HREF = "Section_howto.html#howto_15">this section</A> for an overview of LAMMPS
output options.
<A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an overview of
LAMMPS output options.
</P>
<P>The per-atom vector values will be a number from 0 to 5, as explained
above.

4
doc/compute_cna_atom.txt
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@ -74,8 +74,8 @@ too frequently or to have multiple compute/dump commands, each with a
This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
"this section"_Section_howto.html#howto_15 for an overview of LAMMPS
output options.
"Section_howto 15"_Section_howto.html#howto_15 for an overview of
LAMMPS output options.
The per-atom vector values will be a number from 0 to 5, as explained
above.

4
doc/compute_com_molecule.html
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@ -64,8 +64,8 @@ file</A> containing coordinates of the atoms in the bodies.
Nmolecules and the number of columns = 3 for the x,y,z center-of-mass
coordinates of each molecule. These values can be accessed by any
command that uses global array values from a compute as input. See
<A HREF = "Section_howto.html#howto_15">this section</A> for an overview of LAMMPS
output options.
<A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an overview of
LAMMPS output options.
</P>
<P>The array values are "intensive". The array values will be in
distance <A HREF = "units.html">units</A>.

4
doc/compute_com_molecule.txt
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@ -61,8 +61,8 @@ This compute calculates a global array where the number of rows =
Nmolecules and the number of columns = 3 for the x,y,z center-of-mass
coordinates of each molecule. These values can be accessed by any
command that uses global array values from a compute as input. See
"this section"_Section_howto.html#howto_15 for an overview of LAMMPS
output options.
"Section_howto 15"_Section_howto.html#howto_15 for an overview of
LAMMPS output options.
The array values are "intensive". The array values will be in
distance "units"_units.html.

4
doc/compute_coord_atom.html
View File

@ -46,8 +46,8 @@ too frequently or to have multiple compute/dump commands, each of a
</P>
<P>This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
<A HREF = "Section_howto.html#howto_15">this section</A> for an overview of LAMMPS
output options.
<A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an overview of
LAMMPS output options.
</P>
<P>The per-atom vector values will be a number >= 0.0, as explained
above.

4
doc/compute_coord_atom.txt
View File

@ -43,8 +43,8 @@ too frequently or to have multiple compute/dump commands, each of a
This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
"this section"_Section_howto.html#howto_15 for an overview of LAMMPS
output options.
"Section_howto 15"_Section_howto.html#howto_15 for an overview of
LAMMPS output options.
The per-atom vector values will be a number >= 0.0, as explained
above.

4
doc/compute_damage_atom.html
View File

@ -37,8 +37,8 @@ compute group.
</P>
<P>This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
<A HREF = "Section_howto.html#howto_15">this section</A> for an overview of LAMMPS
output options.
<A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an overview of
LAMMPS output options.
</P>
<P>The per-atom vector values will be a number >= 0.0, as explained
above.

4
doc/compute_damage_atom.txt
View File

@ -34,8 +34,8 @@ compute group.
This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
"this section"_Section_howto.html#howto_15 for an overview of LAMMPS
output options.
"Section_howto 15"_Section_howto.html#howto_15 for an overview of
LAMMPS output options.
The per-atom vector values will be a number >= 0.0, as explained
above.

5
doc/compute_displace_atom.html
View File

@ -76,8 +76,9 @@ file.
</P>
<P>This compute calculates a per-atom array with 4 columns, which can be
accessed by indices 1-4 by any command that uses per-atom values from
a compute as input. See <A HREF = "Section_howto.html#howto_15">this section</A>
for an overview of LAMMPS output options.
a compute as input. See <A HREF = "Section_howto.html#howto_15">Section_howto
15</A> for an overview of LAMMPS output
options.
</P>
<P>The per-atom array values will be in distance <A HREF = "units.html">units</A>.
</P>

5
doc/compute_displace_atom.txt
View File

@ -73,8 +73,9 @@ file.
This compute calculates a per-atom array with 4 columns, which can be
accessed by indices 1-4 by any command that uses per-atom values from
a compute as input. See "this section"_Section_howto.html#howto_15
for an overview of LAMMPS output options.
a compute as input. See "Section_howto
15"_Section_howto.html#howto_15 for an overview of LAMMPS output
options.
The per-atom array values will be in distance "units"_units.html.

4
doc/compute_erotate_asphere.html
View File

@ -43,8 +43,8 @@ inertia will be the same as in 3d.
</P>
<P>This compute calculates a global scalar (the KE). This value can be
used by any command that uses a global scalar value from a compute as
input. See <A HREF = "Section_howto.html#howto_15">this section</A> for an overview
of LAMMPS output options.
input. See <A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an
overview of LAMMPS output options.
</P>
<P>The scalar value calculated by this compute is "extensive". The
scalar value will be in energy <A HREF = "units.html">units</A>.

4
doc/compute_erotate_asphere.txt
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@ -40,8 +40,8 @@ inertia will be the same as in 3d.
This compute calculates a global scalar (the KE). This value can be
used by any command that uses a global scalar value from a compute as
input. See "this section"_Section_howto.html#howto_15 for an overview
of LAMMPS output options.
input. See "Section_howto 15"_Section_howto.html#howto_15 for an
overview of LAMMPS output options.
The scalar value calculated by this compute is "extensive". The
scalar value will be in energy "units"_units.html.

4
doc/compute_erotate_sphere.html
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@ -38,8 +38,8 @@ same as in 3d.
</P>
<P>This compute calculates a global scalar (the KE). This value can be
used by any command that uses a global scalar value from a compute as
input. See <A HREF = "Section_howto.html#howto_15">this section</A> for an overview
of LAMMPS output options.
input. See <A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an
overview of LAMMPS output options.
</P>
<P>The scalar value calculated by this compute is "extensive". The
scalar value will be in energy <A HREF = "units.html">units</A>.

4
doc/compute_erotate_sphere.txt
View File

@ -35,8 +35,8 @@ same as in 3d.
This compute calculates a global scalar (the KE). This value can be
used by any command that uses a global scalar value from a compute as
input. See "this section"_Section_howto.html#howto_15 for an overview
of LAMMPS output options.
input. See "Section_howto 15"_Section_howto.html#howto_15 for an
overview of LAMMPS output options.
The scalar value calculated by this compute is "extensive". The
scalar value will be in energy "units"_units.html.

4
doc/compute_event_displace.html
View File

@ -46,8 +46,8 @@ local atom displacements and may generate "false postives."
</P>
<P>This compute calculates a global scalar (the flag). This value can be
used by any command that uses a global scalar value from a compute as
input. See <A HREF = "Section_howto.html#howto_15">this section</A> for an overview
of LAMMPS output options.
input. See <A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an
overview of LAMMPS output options.
</P>
<P>The scalar value calculated by this compute is "intensive". The
scalar value will be a 0 or 1 as explained above.

4
doc/compute_event_displace.txt
View File

@ -43,8 +43,8 @@ local atom displacements and may generate "false postives."
This compute calculates a global scalar (the flag). This value can be
used by any command that uses a global scalar value from a compute as
input. See "this section"_Section_howto.html#howto_15 for an overview
of LAMMPS output options.
input. See "Section_howto 15"_Section_howto.html#howto_15 for an
overview of LAMMPS output options.
The scalar value calculated by this compute is "intensive". The
scalar value will be a 0 or 1 as explained above.

4
doc/compute_gyration.html
View File

@ -49,8 +49,8 @@ image</A> command.
</P>
<P>This compute calculates a global scalar (Rg). This value can be used
by any command that uses a global scalar value from a compute as
input. See <A HREF = "Section_howto.html#howto_15">this section</A> for an overview
of LAMMPS output options.
input. See <A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an
overview of LAMMPS output options.
</P>
<P>The scalar value calculated by this compute is "intensive". The
scalar value will be in distance <A HREF = "units.html">units</A>.

4
doc/compute_gyration.txt
View File

@ -46,8 +46,8 @@ image"_set.html command.
This compute calculates a global scalar (Rg). This value can be used
by any command that uses a global scalar value from a compute as
input. See "this section"_Section_howto.html#howto_15 for an overview
of LAMMPS output options.
input. See "Section_howto 15"_Section_howto.html#howto_15 for an
overview of LAMMPS output options.
The scalar value calculated by this compute is "intensive". The
scalar value will be in distance "units"_units.html.

4
doc/compute_ke.html
View File

@ -47,8 +47,8 @@ include different degrees of freedom (translational, rotational, etc).
</P>
<P>This compute calculates a global scalar (the KE). This value can be
used by any command that uses a global scalar value from a compute as
input. See <A HREF = "Section_howto.html#howto_15">this section</A> for an overview
of LAMMPS output options.
input. See <A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an
overview of LAMMPS output options.
</P>
<P>The scalar value calculated by this compute is "extensive". The
scalar value will be in energy <A HREF = "units.html">units</A>.

4
doc/compute_ke.txt
View File

@ -44,8 +44,8 @@ include different degrees of freedom (translational, rotational, etc).
This compute calculates a global scalar (the KE). This value can be
used by any command that uses a global scalar value from a compute as
input. See "this section"_Section_howto.html#howto_15 for an overview
of LAMMPS output options.
input. See "Section_howto 15"_Section_howto.html#howto_15 for an
overview of LAMMPS output options.
The scalar value calculated by this compute is "extensive". The
scalar value will be in energy "units"_units.html.

4
doc/compute_ke_atom.html
View File

@ -37,8 +37,8 @@ specified compute group.
</P>
<P>This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
<A HREF = "Section_howto.html#howto_15">this section</A> for an overview of LAMMPS
output options.
<A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an overview of
LAMMPS output options.
</P>
<P>The per-atom vector values will be in energy <A HREF = "units.html">units</A>.
</P>

4
doc/compute_ke_atom.txt
View File

@ -34,8 +34,8 @@ specified compute group.
This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
"this section"_Section_howto.html#howto_15 for an overview of LAMMPS
output options.
"Section_howto 15"_Section_howto.html#howto_15 for an overview of
LAMMPS output options.
The per-atom vector values will be in energy "units"_units.html.

4
doc/compute_ke_atom_eff.html
View File

@ -62,8 +62,8 @@ electrons) not in the specified compute group.
</P>
<P>This compute calculates a scalar quantity for each atom, which can be
accessed by any command that uses per-atom computes as input. See
<A HREF = "Section_howto.html#howto_15">this section</A> for an overview of LAMMPS
output options.
<A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an overview of
LAMMPS output options.
</P>
<P>The per-atom vector values will be in energy <A HREF = "units.html">units</A>.
</P>

4
doc/compute_ke_atom_eff.txt
View File

@ -59,8 +59,8 @@ electrons) not in the specified compute group.
This compute calculates a scalar quantity for each atom, which can be
accessed by any command that uses per-atom computes as input. See
"this section"_Section_howto.html#howto_15 for an overview of LAMMPS
output options.
"Section_howto 15"_Section_howto.html#howto_15 for an overview of
LAMMPS output options.
The per-atom vector values will be in energy "units"_units.html.

4
doc/compute_ke_eff.html
View File

@ -64,8 +64,8 @@ thermo_modify temp effTemp
</P>
<P>This compute calculates a global scalar (the KE). This value can be
used by any command that uses a global scalar value from a compute as
input. See <A HREF = "Section_howto.html#howto_15">this section</A> for an overview
of LAMMPS output options.
input. See <A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an
overview of LAMMPS output options.
</P>
<P>The scalar value calculated by this compute is "extensive". The
scalar value will be in energy <A HREF = "units.html">units</A>.

4
doc/compute_ke_eff.txt
View File

@ -61,8 +61,8 @@ See "compute temp/eff"_compute_temp_eff.html.
This compute calculates a global scalar (the KE). This value can be
used by any command that uses a global scalar value from a compute as
input. See "this section"_Section_howto.html#howto_15 for an overview
of LAMMPS output options.
input. See "Section_howto 15"_Section_howto.html#howto_15 for an
overview of LAMMPS output options.
The scalar value calculated by this compute is "extensive". The
scalar value will be in energy "units"_units.html.

4
doc/compute_meso_e_atom.html
View File

@ -41,8 +41,8 @@ specified compute group.
</P>
<P>This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
<A HREF = "Section_howto.html#4_15">this section</A> for an overview of LAMMPS
output options.
<A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an overview of
LAMMPS output options.
</P>
<P>The per-atom vector values will be in energy <A HREF = "units.html">units</A>.
</P>

4
doc/compute_meso_e_atom.txt
View File

@ -38,8 +38,8 @@ specified compute group.
This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
"this section"_Section_howto.html#4_15 for an overview of LAMMPS
output options.
"Section_howto 15"_Section_howto.html#howto_15 for an overview of
LAMMPS output options.
The per-atom vector values will be in energy "units"_units.html.

4
doc/compute_meso_rho_atom.html
View File

@ -41,8 +41,8 @@ specified compute group.
</P>
<P>This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
<A HREF = "Section_howto.html#4_15">this section</A> for an overview of LAMMPS
output options.
<A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an overview of
LAMMPS output options.
</P>
<P>The per-atom vector values will be in mass/volume <A HREF = "units.html">units</A>.
</P>

4
doc/compute_meso_rho_atom.txt
View File

@ -38,8 +38,8 @@ specified compute group.
This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
"this section"_Section_howto.html#4_15 for an overview of LAMMPS
output options.
"Section_howto 15"_Section_howto.html#howto_15 for an overview of
LAMMPS output options.
The per-atom vector values will be in mass/volume "units"_units.html.

4
doc/compute_meso_t_atom.html
View File

@ -43,8 +43,8 @@ specified compute group.
</P>
<P>This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
<A HREF = "Section_howto.html#4_15">this section</A> for an overview of LAMMPS
output options.
<A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an overview of
LAMMPS output options.
</P>
<P>The per-atom vector values will be in temperature <A HREF = "units.html">units</A>.
</P>

4
doc/compute_meso_t_atom.txt
View File

@ -40,8 +40,8 @@ specified compute group.
This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
"this section"_Section_howto.html#4_15 for an overview of LAMMPS
output options.
"Section_howto 15"_Section_howto.html#howto_15 for an overview of
LAMMPS output options.
The per-atom vector values will be in temperature "units"_units.html.

5
doc/compute_pe.html
View File

@ -83,8 +83,9 @@ more instructions on how to use the accelerated styles effectively.
</P>
<P>This compute calculates a global scalar (the potential energy). This
value can be used by any command that uses a global scalar value from
a compute as input. See <A HREF = "Section_howto.html#howto_15">this section</A>
for an overview of LAMMPS output options.
a compute as input. See <A HREF = "Section_howto.html#howto_15">Section_howto
15</A> for an overview of LAMMPS output
options.
</P>
<P>The scalar value calculated by this compute is "extensive". The
scalar value will be in energy <A HREF = "units.html">units</A>.

5
doc/compute_pe.txt
View File

@ -79,8 +79,9 @@ more instructions on how to use the accelerated styles effectively.
This compute calculates a global scalar (the potential energy). This
value can be used by any command that uses a global scalar value from
a compute as input. See "this section"_Section_howto.html#howto_15
for an overview of LAMMPS output options.
a compute as input. See "Section_howto
15"_Section_howto.html#howto_15 for an overview of LAMMPS output
options.
The scalar value calculated by this compute is "extensive". The
scalar value will be in energy "units"_units.html.

4
doc/compute_pe_atom.html
View File

@ -70,8 +70,8 @@ the system energy.
</P>
<P>This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
<A HREF = "Section_howto.html#howto_15">this section</A> for an overview of LAMMPS
output options.
<A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an overview of
LAMMPS output options.
</P>
<P>The per-atom vector values will be in energy <A HREF = "units.html">units</A>.
</P>

4
doc/compute_pe_atom.txt
View File

@ -67,8 +67,8 @@ the system energy.
This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
"this section"_Section_howto.html#howto_15 for an overview of LAMMPS
output options.
"Section_howto 15"_Section_howto.html#howto_15 for an overview of
LAMMPS output options.
The per-atom vector values will be in energy "units"_units.html.

4
doc/compute_rdf.html
View File

@ -104,8 +104,8 @@ coordinate (center of the bin), Each successive set of 2 columns has
the g(r) and coord(r) values for a specific set of <I>itypeN</I> versus
<I>jtypeN</I> interactions, as described above. These values can be used
by any command that uses a global values from a compute as input. See
<A HREF = "Section_howto.html#howto_15">this section</A> for an overview of LAMMPS
output options.
<A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an overview of
LAMMPS output options.
</P>
<P>The array values calculated by this compute are all "intensive".
</P>

4
doc/compute_rdf.txt
View File

@ -101,8 +101,8 @@ coordinate (center of the bin), Each successive set of 2 columns has
the g(r) and coord(r) values for a specific set of {itypeN} versus
{jtypeN} interactions, as described above. These values can be used
by any command that uses a global values from a compute as input. See
"this section"_Section_howto.html#howto_15 for an overview of LAMMPS
output options.
"Section_howto 15"_Section_howto.html#howto_15 for an overview of
LAMMPS output options.
The array values calculated by this compute are all "intensive".

4
doc/compute_reduce.html
View File

@ -173,8 +173,8 @@ divides by the appropriate atom count.
specified or a global vector of length N where N is the number of
inputs, and which can be accessed by indices 1 to N. These values can
be used by any command that uses global scalar or vector values from a
compute as input. See <A HREF = "Section_howto.html#howto_15">this section</A> for
an overview of LAMMPS output options.
compute as input. See <A HREF = "Section_howto.html#howto_15">Section_howto 15</A>
for an overview of LAMMPS output options.
</P>
<P>All the scalar or vector values calculated by this compute are
"intensive", except when the <I>sum</I> mode is used on per-atom or local

4
doc/compute_reduce.txt
View File

@ -160,8 +160,8 @@ This compute calculates a global scalar if a single input value is
specified or a global vector of length N where N is the number of
inputs, and which can be accessed by indices 1 to N. These values can
be used by any command that uses global scalar or vector values from a
compute as input. See "this section"_Section_howto.html#howto_15 for
an overview of LAMMPS output options.
compute as input. See "Section_howto 15"_Section_howto.html#howto_15
for an overview of LAMMPS output options.
All the scalar or vector values calculated by this compute are
"intensive", except when the {sum} mode is used on per-atom or local

5
doc/compute_stress_atom.html
View File

@ -102,8 +102,9 @@ contribution can easily be computed.
</P>
<P>This compute calculates a per-atom array with 6 columns, which can be
accessed by indices 1-6 by any command that uses per-atom values from
a compute as input. See <A HREF = "Section_howto.html#howto_15">this section</A>
for an overview of LAMMPS output options.
a compute as input. See <A HREF = "Section_howto.html#howto_15">Section_howto
15</A> for an overview of LAMMPS output
options.
</P>
<P>The per-atom array values will be in pressure*volume
<A HREF = "units.html">units</A> as discussed above.

5
doc/compute_stress_atom.txt
View File

@ -99,8 +99,9 @@ contribution can easily be computed.
This compute calculates a per-atom array with 6 columns, which can be
accessed by indices 1-6 by any command that uses per-atom values from
a compute as input. See "this section"_Section_howto.html#howto_15
for an overview of LAMMPS output options.
a compute as input. See "Section_howto
15"_Section_howto.html#howto_15 for an overview of LAMMPS output
options.
The per-atom array values will be in pressure*volume
"units"_units.html as discussed above.

5
doc/compute_ti.html
View File

@ -102,8 +102,9 @@ du/dl can be found in the paper by <A HREF = "#Eike">Eike</A>.
</P>
<P>This compute calculates a global scalar, namely dUs/dlambda. This
value can be used by any command that uses a global scalar value from
a compute as input. See <A HREF = "Section_howto.html#howto_15">this section</A>
for an overview of LAMMPS output options.
a compute as input. See <A HREF = "Section_howto.html#howto_15">Section_howto
15</A> for an overview of LAMMPS output
options.
</P>
<P>The scalar value calculated by this compute is "extensive".
</P>

5
doc/compute_ti.txt
View File

@ -94,8 +94,9 @@ du/dl can be found in the paper by "Eike"_#Eike.
This compute calculates a global scalar, namely dUs/dlambda. This
value can be used by any command that uses a global scalar value from
a compute as input. See "this section"_Section_howto.html#howto_15
for an overview of LAMMPS output options.
a compute as input. See "Section_howto
15"_Section_howto.html#howto_15 for an overview of LAMMPS output
options.
The scalar value calculated by this compute is "extensive".

6
doc/create_box.html
View File

@ -55,9 +55,9 @@ since if the maximum tilt factor is 5 (as in this example), then
configurations with tilt = ..., -15, -5, 5, 15, 25, ... are all
geometrically equivalent.
</P>
<P>See <A HREF = "Section_howto.html#howto_12">this section</A> of the doc pages for a
geometric description of triclinic boxes, as defined by LAMMPS, and
how to transform these parameters to and from other commonly used
<P>See <A HREF = "Section_howto.html#howto_12">Section_howto 12</A> of the doc pages
for a geometric description of triclinic boxes, as defined by LAMMPS,
and how to transform these parameters to and from other commonly used
triclinic representations.
</P>
<P>When a prism region is used, the simulation domain must be periodic in

6
doc/create_box.txt
View File

@ -52,9 +52,9 @@ since if the maximum tilt factor is 5 (as in this example), then
configurations with tilt = ..., -15, -5, 5, 15, 25, ... are all
geometrically equivalent.
See "this section"_Section_howto.html#howto_12 of the doc pages for a
geometric description of triclinic boxes, as defined by LAMMPS, and
how to transform these parameters to and from other commonly used
See "Section_howto 12"_Section_howto.html#howto_12 of the doc pages
for a geometric description of triclinic boxes, as defined by LAMMPS,
and how to transform these parameters to and from other commonly used
triclinic representations.
When a prism region is used, the simulation domain must be periodic in

6
doc/dump.html
View File

@ -283,9 +283,9 @@ coordinate format that many codes can read.
</P>
<P>Note that DCD, XTC, and XYZ formatted files can be read directly by
<A HREF = "http://www.ks.uiuc.edu/Research/vmd">VMD</A> (a popular molecular viewing
program). See <A HREF = "Section_tools.html#vmd">this section</A> of the manual and
the tools/lmp2vmd/README.txt file for more information about support
in VMD for reading and visualizing LAMMPS dump files.
program). See <A HREF = "Section_tools.html#vmd">Section tools</A> of the manual
and the tools/lmp2vmd/README.txt file for more information about
support in VMD for reading and visualizing LAMMPS dump files.
</P>
<HR>

6
doc/dump.txt
View File

@ -272,9 +272,9 @@ coordinate format that many codes can read.
Note that DCD, XTC, and XYZ formatted files can be read directly by
"VMD"_http://www.ks.uiuc.edu/Research/vmd (a popular molecular viewing
program). See "this section"_Section_tools.html#vmd of the manual and
the tools/lmp2vmd/README.txt file for more information about support
in VMD for reading and visualizing LAMMPS dump files.
program). See "Section tools"_Section_tools.html#vmd of the manual
and the tools/lmp2vmd/README.txt file for more information about
support in VMD for reading and visualizing LAMMPS dump files.
:line

11
doc/fix_append_atoms.html
View File

@ -87,9 +87,9 @@ define the lattice spacings.
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various <A HREF = "Section_howto.html#4_15">output
commands</A>. No parameter of this fix can be
used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
by this fix for access by various <A HREF = "Section_howto.html#howto_15">output
commands</A>. No parameter of this fix can
be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
</P>
<P><B>Restrictions:</B>
@ -98,8 +98,9 @@ This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P>The zhi boundary on which atoms are added with append_atoms must be shrink-wrapped.
The zlo boundary may be any boundary type other than periodic.
<P>The zhi boundary on which atoms are added with append_atoms must be
shrink-wrapped. The zlo boundary may be any boundary type other than
periodic.
</P>
<P><B>Related commands:</B>
</P>

9
doc/fix_append_atoms.txt
View File

@ -78,8 +78,8 @@ No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various "output
commands"_Section_howto.html#4_15. No parameter of this fix can be
used with the {start/stop} keywords of the "run"_run.html command.
commands"_Section_howto.html#howto_15. No parameter of this fix can
be used with the {start/stop} keywords of the "run"_run.html command.
This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
@ -88,8 +88,9 @@ This fix style is part of the SHOCK package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
The zhi boundary on which atoms are added with append_atoms must be shrink-wrapped.
The zlo boundary may be any boundary type other than periodic.
The zhi boundary on which atoms are added with append_atoms must be
shrink-wrapped. The zlo boundary may be any boundary type other than
periodic.
[Related commands:]

6
doc/fix_meso.html
View File

@ -37,9 +37,9 @@ LAMMPS.
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various <A HREF = "Section_howto.html#4_15">output
commands</A>. No parameter of this fix can be
used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
by this fix for access by various <A HREF = "Section_howto.html#howto_15">output
commands</A>. No parameter of this fix can
be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
</P>
<P><B>Restrictions:</B>

4
doc/fix_meso.txt
View File

@ -35,8 +35,8 @@ No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various "output
commands"_Section_howto.html#4_15. No parameter of this fix can be
used with the {start/stop} keywords of the "run"_run.html command.
commands"_Section_howto.html#howto_15. No parameter of this fix can
be used with the {start/stop} keywords of the "run"_run.html command.
This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]

6
doc/fix_meso_stationary.html
View File

@ -38,9 +38,9 @@ LAMMPS.
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various <A HREF = "Section_howto.html#4_15">output
commands</A>. No parameter of this fix can be
used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
by this fix for access by various <A HREF = "Section_howto.html#howto_15">output
commands</A>. No parameter of this fix can
be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
</P>
<P><B>Restrictions:</B>

4
doc/fix_meso_stationary.txt
View File

@ -36,8 +36,8 @@ No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various "output
commands"_Section_howto.html#4_15. No parameter of this fix can be
used with the {start/stop} keywords of the "run"_run.html command.
commands"_Section_howto.html#howto_15. No parameter of this fix can
be used with the {start/stop} keywords of the "run"_run.html command.
This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]

4
doc/fix_neb.html
View File

@ -29,8 +29,8 @@
simulation run via the <A HREF = "neb.html">neb</A> command to perform a nudged
elastic band (NEB) calculation for transition state finding. Hi-level
explanations of NEB are given with the <A HREF = "neb.html">neb</A> command and in
<A HREF = "Section_howto.html#howto_5">this section</A> of the manual. The fix neb
command must be used with the "neb" command to define how
<A HREF = "Section_howto.html#howto_5">Section_howto 5</A> of the manual. The fix
neb command must be used with the "neb" command to define how
inter-replica forces are computed.
</P>
<P>Only the N atoms in the fix group experience inter-replica forces.

4
doc/fix_neb.txt
View File

@ -26,8 +26,8 @@ Add inter-replica forces to atoms in the group for a multi-replica
simulation run via the "neb"_neb.html command to perform a nudged
elastic band (NEB) calculation for transition state finding. Hi-level
explanations of NEB are given with the "neb"_neb.html command and in
"this section"_Section_howto.html#howto_5 of the manual. The fix neb
command must be used with the "neb" command to define how
"Section_howto 5"_Section_howto.html#howto_5 of the manual. The fix
neb command must be used with the "neb" command to define how
inter-replica forces are computed.
Only the N atoms in the fix group experience inter-replica forces.

13
doc/fix_viscosity.html
View File

@ -103,12 +103,13 @@ you cannot accurately infer a viscosity and should try increasing
the Nevery parameter.
</P>
<P>An alternative method for calculating a viscosity is to run a NEMD
simulation, as described in <A HREF = "Section_howto.html#howto_13">this section</A>
of the manual. NEMD simulations deform the simmulation box via the
<A HREF = "fix_deform.html">fix deform</A> command. Thus they cannot be run on a
charged system using a <A HREF = "kspace_style.html">PPPM solver</A> since PPPM does
not currently support non-orthogonal boxes. Using fix viscosity keeps
the box orthogonal; thus it does not suffer from this limitation.
simulation, as described in <A HREF = "Section_howto.html#howto_13">Section_howto
13</A> of the manual. NEMD simulations
deform the simmulation box via the <A HREF = "fix_deform.html">fix deform</A>
command. Thus they cannot be run on a charged system using a <A HREF = "kspace_style.html">PPPM
solver</A> since PPPM does not currently support
non-orthogonal boxes. Using fix viscosity keeps the box orthogonal;
thus it does not suffer from this limitation.
</P>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>

13
doc/fix_viscosity.txt
View File

@ -92,12 +92,13 @@ you cannot accurately infer a viscosity and should try increasing
the Nevery parameter.
An alternative method for calculating a viscosity is to run a NEMD
simulation, as described in "this section"_Section_howto.html#howto_13
of the manual. NEMD simulations deform the simmulation box via the
"fix deform"_fix_deform.html command. Thus they cannot be run on a
charged system using a "PPPM solver"_kspace_style.html since PPPM does
not currently support non-orthogonal boxes. Using fix viscosity keeps
the box orthogonal; thus it does not suffer from this limitation.
simulation, as described in "Section_howto
13"_Section_howto.html#howto_13 of the manual. NEMD simulations
deform the simmulation box via the "fix deform"_fix_deform.html
command. Thus they cannot be run on a charged system using a "PPPM
solver"_kspace_style.html since PPPM does not currently support
non-orthogonal boxes. Using fix viscosity keeps the box orthogonal;
thus it does not suffer from this limitation.
[Restart, fix_modify, output, run start/stop, minimize info:]

6
doc/fix_wall_piston.html
View File

@ -101,9 +101,9 @@ define the lattice spacings.
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various <A HREF = "Section_howto.html#4_15">output
commands</A>. No parameter of this fix can be
used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
by this fix for access by various <A HREF = "Section_howto.html#howoto_15">output
commands</A>. No parameter of this fix can
be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
</P>
<P><B>Restrictions:</B>

4
doc/fix_wall_piston.txt
View File

@ -92,8 +92,8 @@ No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various "output
commands"_Section_howto.html#4_15. No parameter of this fix can be
used with the {start/stop} keywords of the "run"_run.html command.
commands"_Section_howto.html#howoto_15. No parameter of this fix can
be used with the {start/stop} keywords of the "run"_run.html command.
This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]

6
doc/if.html
View File

@ -66,9 +66,9 @@ above.
<P>IMPORTANT NOTE: If a command itself requires a quoted argument (e.g. a
<A HREF = "print.html">print</A> command), then double and single quotes can be used
and nested in the usual manner, as in the examples above and below.
See <A HREF = "Section_commands.html#cmd_2">this section</A> of the manual for more
details on using quotes in arguments. Only one of level of nesting is
allowed, but that should be sufficient for most use cases.
See <A HREF = "Section_commands.html#cmd_2">Section_commands 2</A> of the manual for
more details on using quotes in arguments. Only one of level of
nesting is allowed, but that should be sufficient for most use cases.
</P>
<P>Note that by using the line continuation character "&", the if command
can be spread across many lines, though it is still a single command:

6
doc/if.txt
View File

@ -63,9 +63,9 @@ above.
IMPORTANT NOTE: If a command itself requires a quoted argument (e.g. a
"print"_print.html command), then double and single quotes can be used
and nested in the usual manner, as in the examples above and below.
See "this section"_Section_commands.html#cmd_2 of the manual for more
details on using quotes in arguments. Only one of level of nesting is
allowed, but that should be sufficient for most use cases.
See "Section_commands 2"_Section_commands.html#cmd_2 of the manual for
more details on using quotes in arguments. Only one of level of
nesting is allowed, but that should be sufficient for most use cases.
Note that by using the line continuation character "&", the if command
can be spread across many lines, though it is still a single command:

2
doc/log.html
View File

@ -33,7 +33,7 @@ the same log file.
</P>
<P>The file "log.lammps" is the default log file for a LAMMPS run. The
name of the initial log file can also be set by the command-line
switch -log. See <A HREF = "Section_start.html#start_6">this section</A> for
switch -log. See <A HREF = "Section_start.html#start_6">Section_start 6</A> for
details.
</P>
<P><B>Restrictions:</B> none

2
doc/log.txt
View File

@ -30,7 +30,7 @@ the same log file.
The file "log.lammps" is the default log file for a LAMMPS run. The
name of the initial log file can also be set by the command-line
switch -log. See "this section"_Section_start.html#start_6 for
switch -log. See "Section_start 6"_Section_start.html#start_6 for
details.
[Restrictions:] none

10
doc/neb.html
View File

@ -42,11 +42,11 @@ follows the discussion in these 3 papers: <A HREF = "#Henkelman1">(Henkelman1)</
</P>
<P>Each replica runs on a partition of one or more processors. Processor
partitions are defined at run-time using the -partition command-line
switch; see <A HREF = "Section_start.html#start_6">this section</A> of the manual.
Note that if you have MPI installed, you can run a multi-replica
simulation with more replicas (partitions) than you have physical
processors, e.g you can run a 10-replica simulation on one or two
processors. You will simply not get the performance speed-up you
switch; see <A HREF = "Section_start.html#start_6">Section_start 6</A> of the
manual. Note that if you have MPI installed, you can run a
multi-replica simulation with more replicas (partitions) than you have
physical processors, e.g you can run a 10-replica simulation on one or
two processors. You will simply not get the performance speed-up you
would see with one or more physical processors per replica. See <A HREF = "Section_howto.html#howto_5">this
section</A> of the manual for further
discussion.

10
doc/neb.txt
View File

@ -39,11 +39,11 @@ follows the discussion in these 3 papers: "(Henkelman1)"_#Henkelman1,
Each replica runs on a partition of one or more processors. Processor
partitions are defined at run-time using the -partition command-line
switch; see "this section"_Section_start.html#start_6 of the manual.
Note that if you have MPI installed, you can run a multi-replica
simulation with more replicas (partitions) than you have physical
processors, e.g you can run a 10-replica simulation on one or two
processors. You will simply not get the performance speed-up you
switch; see "Section_start 6"_Section_start.html#start_6 of the
manual. Note that if you have MPI installed, you can run a
multi-replica simulation with more replicas (partitions) than you have
physical processors, e.g you can run a 10-replica simulation on one or
two processors. You will simply not get the performance speed-up you
would see with one or more physical processors per replica. See "this
section"_Section_howto.html#howto_5 of the manual for further
discussion.

2
doc/partition.html
View File

@ -30,7 +30,7 @@ partition yes 6* fix all nvt temp 1.0 1.0 0.1
</P>
<P>This command invokes the specified command on a subset of the
partitions of processors you have defined via the -partition
command-line switch. See <A HREF = "Section_start.html#start_6">this section</A>
command-line switch. See <A HREF = "Section_start.html#start_6">Section_start 6</A>
for an explanation of the switch.
</P>
<P>Normally, every input script command in your script is invoked by

2
doc/partition.txt
View File

@ -27,7 +27,7 @@ partition yes 6* fix all nvt temp 1.0 1.0 0.1 :pre
This command invokes the specified command on a subset of the
partitions of processors you have defined via the -partition
command-line switch. See "this section"_Section_start.html#start_6
command-line switch. See "Section_start 6"_Section_start.html#start_6
for an explanation of the switch.
Normally, every input script command in your script is invoked by

14
doc/prd.html
View File

@ -71,13 +71,13 @@ event to occur.
</P>
<P>Each replica runs on a partition of one or more processors. Processor
partitions are defined at run-time using the -partition command-line
switch; see <A HREF = "Section_start.html#start_6">this section</A> of the manual.
Note that if you have MPI installed, you can run a multi-replica
simulation with more replicas (partitions) than you have physical
processors, e.g you can run a 10-replica simulation on one or two
processors. For PRD, this makes little sense, since this offers no
effective parallel speed-up in searching for infrequent events. See
<A HREF = "Section_howto.html#howto_5">this section</A> of the manual for further
switch; see <A HREF = "Section_start.html#start_6">Section_start 6</A> of the
manual. Note that if you have MPI installed, you can run a
multi-replica simulation with more replicas (partitions) than you have
physical processors, e.g you can run a 10-replica simulation on one or
two processors. For PRD, this makes little sense, since this offers
no effective parallel speed-up in searching for infrequent events. See
<A HREF = "Section_howto.html#howto_5">Section_howto 5</A> of the manual for further
discussion.
</P>
<P>When a PRD simulation is performed, it is assumed that each replica is

14
doc/prd.txt
View File

@ -58,13 +58,13 @@ event to occur.
Each replica runs on a partition of one or more processors. Processor
partitions are defined at run-time using the -partition command-line
switch; see "this section"_Section_start.html#start_6 of the manual.
Note that if you have MPI installed, you can run a multi-replica
simulation with more replicas (partitions) than you have physical
processors, e.g you can run a 10-replica simulation on one or two
processors. For PRD, this makes little sense, since this offers no
effective parallel speed-up in searching for infrequent events. See
"this section"_Section_howto.html#howto_5 of the manual for further
switch; see "Section_start 6"_Section_start.html#start_6 of the
manual. Note that if you have MPI installed, you can run a
multi-replica simulation with more replicas (partitions) than you have
physical processors, e.g you can run a 10-replica simulation on one or
two processors. For PRD, this makes little sense, since this offers
no effective parallel speed-up in searching for infrequent events. See
"Section_howto 5"_Section_howto.html#howto_5 of the manual for further
discussion.
When a PRD simulation is performed, it is assumed that each replica is

6
doc/read_data.html
View File

@ -111,9 +111,9 @@ limitation, since if the maximum tilt factor is 5 (as in this
example), then configurations with tilt = ..., -15, -5, 5, 15, 25,
... are all geometrically equivalent.
</P>
<P>See <A HREF = "Section_howto.html#howto_12">this section</A> of the doc pages for a
geometric description of triclinic boxes, as defined by LAMMPS, and
how to transform these parameters to and from other commonly used
<P>See <A HREF = "Section_howto.html#howto_12">Section_howto 12</A> of the doc pages
for a geometric description of triclinic boxes, as defined by LAMMPS,
and how to transform these parameters to and from other commonly used
triclinic representations.
</P>
<P>When a triclinic system is used, the simulation domain must be

6
doc/read_data.txt
View File

@ -108,9 +108,9 @@ limitation, since if the maximum tilt factor is 5 (as in this
example), then configurations with tilt = ..., -15, -5, 5, 15, 25,
... are all geometrically equivalent.
See "this section"_Section_howto.html#howto_12 of the doc pages for a
geometric description of triclinic boxes, as defined by LAMMPS, and
how to transform these parameters to and from other commonly used
See "Section_howto 12"_Section_howto.html#howto_12 of the doc pages
for a geometric description of triclinic boxes, as defined by LAMMPS,
and how to transform these parameters to and from other commonly used
triclinic representations.
When a triclinic system is used, the simulation domain must be

6
doc/region.html
View File

@ -175,9 +175,9 @@ since if the maximum tilt factor is 5 (as in this example), then
configurations with tilt = ..., -15, -5, 5, 15, 25, ... are all
geometrically equivalent.
</P>
<P>See <A HREF = "Section_howto.html#howto_12">this section</A> of the doc pages for a
geometric description of triclinic boxes, as defined by LAMMPS, and
how to transform these parameters to and from other commonly used
<P>See <A HREF = "Section_howto.html#howto_12">Section_howto 12</A> of the doc pages
for a geometric description of triclinic boxes, as defined by LAMMPS,
and how to transform these parameters to and from other commonly used
triclinic representations.
</P>
<P>The <I>union</I> style creates a region consisting of the volume of all the

6
doc/region.txt
View File

@ -166,9 +166,9 @@ since if the maximum tilt factor is 5 (as in this example), then
configurations with tilt = ..., -15, -5, 5, 15, 25, ... are all
geometrically equivalent.
See "this section"_Section_howto.html#howto_12 of the doc pages for a
geometric description of triclinic boxes, as defined by LAMMPS, and
how to transform these parameters to and from other commonly used
See "Section_howto 12"_Section_howto.html#howto_12 of the doc pages
for a geometric description of triclinic boxes, as defined by LAMMPS,
and how to transform these parameters to and from other commonly used
triclinic representations.
The {union} style creates a region consisting of the volume of all the

2
doc/run_style.html
View File

@ -69,7 +69,7 @@ simulations performed by LAMMPS.
<P>The <I>verlet/split</I> style is also a velocity-Verlet integrator, but it
splits the force calculation within each timestep over 2 partitions of
processors. See <A HREF = "Section_start.html#start_6">this section</A> for an
processors. See <A HREF = "Section_start.html#start_6">Section_start 6</A> for an
explanation of the -partition command-line switch.
</P>
<P>Specifically, this style performs all computation except the

2
doc/run_style.txt
View File

@ -64,7 +64,7 @@ The {verlet} style is a standard velocity-Verlet integrator.
The {verlet/split} style is also a velocity-Verlet integrator, but it
splits the force calculation within each timestep over 2 partitions of
processors. See "this section"_Section_start.html#start_6 for an
processors. See "Section_start 6"_Section_start.html#start_6 for an
explanation of the -partition command-line switch.
Specifically, this style performs all computation except the

5
doc/tad.html
View File

@ -102,8 +102,9 @@ restricts you to having exactly one processor per replica. For more
information, see the documentation for the <A HREF = "neb.html">neb</A> command. In
the current LAMMPS implementation of TAD, all the non-NEB TAD
operations are performed on the first partition, while the other
partitions remain idle. See <A HREF = "Section_howto.html#howto_5">this section</A>
of the manual for further discussion of multi-replica simulations.
partitions remain idle. See <A HREF = "Section_howto.html#howto_5">Section_howto
5</A> of the manual for further discussion of
multi-replica simulations.
</P>
<P>A TAD run has several stages, which are repeated each time an event is
performed. The logic for a TAD run is as follows:

5
doc/tad.txt
View File

@ -91,8 +91,9 @@ restricts you to having exactly one processor per replica. For more
information, see the documentation for the "neb"_neb.html command. In
the current LAMMPS implementation of TAD, all the non-NEB TAD
operations are performed on the first partition, while the other
partitions remain idle. See "this section"_Section_howto.html#howto_5
of the manual for further discussion of multi-replica simulations.
partitions remain idle. See "Section_howto
5"_Section_howto.html#howto_5 of the manual for further discussion of
multi-replica simulations.
A TAD run has several stages, which are repeated each time an event is

10
doc/temper.html
View File

@ -35,11 +35,11 @@ replicas (ensembles) of a system. Two or more replicas must be used.
</P>
<P>Each replica runs on a partition of one or more processors. Processor
partitions are defined at run-time using the -partition command-line
switch; see <A HREF = "Section_start.html#start_6">this section</A> of the manual.
Note that if you have MPI installed, you can run a multi-replica
simulation with more replicas (partitions) than you have physical
processors, e.g you can run a 10-replica simulation on one or two
processors. You will simply not get the performance speed-up you
switch; see <A HREF = "Section_start.html#start_6">Section_start 6</A> of the
manual. Note that if you have MPI installed, you can run a
multi-replica simulation with more replicas (partitions) than you have
physical processors, e.g you can run a 10-replica simulation on one or
two processors. You will simply not get the performance speed-up you
would see with one or more physical processors per replica. See <A HREF = "Section_howto.html#howto_5">this
section</A> of the manual for further
discussion.

10
doc/temper.txt
View File

@ -32,11 +32,11 @@ replicas (ensembles) of a system. Two or more replicas must be used.
Each replica runs on a partition of one or more processors. Processor
partitions are defined at run-time using the -partition command-line
switch; see "this section"_Section_start.html#start_6 of the manual.
Note that if you have MPI installed, you can run a multi-replica
simulation with more replicas (partitions) than you have physical
processors, e.g you can run a 10-replica simulation on one or two
processors. You will simply not get the performance speed-up you
switch; see "Section_start 6"_Section_start.html#start_6 of the
manual. Note that if you have MPI installed, you can run a
multi-replica simulation with more replicas (partitions) than you have
physical processors, e.g you can run a 10-replica simulation on one or
two processors. You will simply not get the performance speed-up you
would see with one or more physical processors per replica. See "this
section"_Section_howto.html#howto_5 of the manual for further
discussion.