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4
doc/doc2/Manual.html.html
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@ -3,7 +3,7 @@
<!-- HTML_ONLY -->
<HEAD>
<TITLE>LAMMPS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="17 Nov 2015 version">
<META NAME="docnumber" CONTENT="20 Nov 2015 version">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD>
@ -21,7 +21,7 @@
<P><CENTER><H3>LAMMPS Documentation
</H3></CENTER>
<CENTER><H4>17 Nov 2015 version
<CENTER><H4>20 Nov 2015 version
</H4></CENTER>
<H4>Version info:
</H4>

46
doc/doc2/compute_msd.html
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@ -21,16 +21,17 @@
<LI>zero or more keyword/value pairs may be appended
<LI>keyword = <I>com</I>
<LI>keyword = <I>com</I> or <I>average</I>
<PRE> <I>com</I> value = <I>yes</I> or <I>no</I>
<PRE> <I>com</I> value = <I>yes</I> or <I>no</I>
<I>average</I> value = <I>yes</I> or <I>no</I>
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all msd
compute 1 upper msd com yes
compute 1 upper msd com yes average yes
</PRE>
<P><B>Description:</B>
</P>
@ -49,13 +50,34 @@ averaged over atoms in the group.
<P>The slope of the mean-squared displacement (MSD) versus time is
proportional to the diffusion coefficient of the diffusing atoms.
</P>
<P>The displacement of an atom is from its original position at the time
the compute command was issued. The value of the displacement will be
<P>The displacement of an atom is from its reference position. This is
normally the original position at the time
the compute command was issued, unless the <I>average</I> keyword is set to <I>yes</I>.
The value of the displacement will be
0.0 for atoms not in the specified compute group.
</P>
<P>If the <I>com</I> option is set to <I>yes</I> then the effect of any drift in
the center-of-mass of the group of atoms is subtracted out before xhe
displacment of each atom is calcluated.
the center-of-mass of the group of atoms is subtracted out before the
displacment of each atom is calculated.
</P>
<P>If the <I>average</I> option is set to <I>yes</I> then the reference position of
an atom is based on the average position of that atom,
corrected for center-of-mass motion if requested.
The average position
is a running average over all previous calls to the compute, including the
current call. So on the first call
it is current position, on the second call it is the arithmetic average of the
current position and the position on the first call, and so on.
Note that when using this option, the precise value of the mean square
displacement will depend on the number of times the compute is
called. So, for example, changing the frequency of thermo output may
change the computed displacement. Also, the precise values will be
changed if a single simulation is broken up into two parts, using
either multiple run commands or a restart file. It only makes
sense to use this option if the atoms are not diffusing, so that
their average positions relative to the center of mass of the system
are stationary. The most common case is crystalline solids undergoing
thermal motion.
</P>
<P>IMPORTANT NOTE: Initial coordinates are stored in "unwrapped" form, by
using the image flags associated with each atom. See the <A HREF = "dump.html">dump
@ -70,7 +92,13 @@ to be continuous when running from a <A HREF = "read_restart.html">restart file<
then you should use the same ID for this compute, as in the original
run. This is so that the fix this compute creates to store per-atom
quantities will also have the same ID, and thus be initialized
correctly with time=0 atom coordinates from the restart file.
correctly with atom reference positions from the restart file.
When <I>average</I> is set to yes, then the atom reference positions
are restored correctly, but not the number of samples used
obtain them. As a result, the reference positions from the restart
file are combined with subsequent positions as if they were from a
single sample, instead of many, which will change the values of msd
somewhat.
</P>
<P><B>Output info:</B>
</P>
@ -94,6 +122,6 @@ msd/chunk</A>
</P>
<P><B>Default:</B>
</P>
<P>The option default is com = no.
<P>The option default are com = no, average = no.
</P>
</HTML>

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doc/doc2/compute_orientorder_atom.html
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@ -71,9 +71,11 @@ parameters. This is followed by that number of integers giving the
degree of each order parameter. Because <I>Q</I>2 and all odd-degree
order parameters are zero for atoms in cubic crystals
(see <A HREF = "#Steinhardt">Steinhardt</A>), the default order parameters
are <I>Q</I>4, <I>Q</I>6, <I>Q</I>8, <I>Q</I>10, and <I>Q</I>12. The correct
numerical values for commonly encountered high-symmetry
structures are given by <A HREF = "#Mickel">Mickel et al.</A>
are <I>Q</I>4, <I>Q</I>6, <I>Q</I>8, <I>Q</I>10, and <I>Q</I>12. For the
FCC crystal with <I>nnn</I>=12, <I>Q</I>4 = sqrt(7/3)/8 = 0.19094....
The numerical values of all order parameters up to <I>Q</I>12
for a range of commonly encountered high-symmetry structures are given
in Table I of <A HREF = "#Mickel">Mickel et al.</A>.
</P>
<P>The value of <I>Ql</I> is set to zero for atoms not in the
specified compute group, as well as for atoms that have less than

2
doc/doc2/fix_atom_swap.html
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@ -48,7 +48,7 @@
</P>
<PRE>fix 2 all atom/swap 1 1 29494 300.0 ke no types 1 2
fix myFix all atom/swap 100 1 12345 298.0 region my_swap_region types 5 6
fix SGMC all atom/swap 1 100 345 1.0 semi-grand yes types 1 2 3 mu 4.3 -5.0
fix SGMC all atom/swap 1 100 345 1.0 semi-grand yes types 1 2 3 mu 0.0 4.3 -5.0
</PRE>
<P><B>Description:</B>
</P>

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doc/doc2/fix_ave_atom.html
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@ -81,8 +81,8 @@ that are a multiple of <I>Nfreq</I>. The average is over <I>Nrepeat</I>
quantities, computed in the preceding portion of the simulation every
<I>Nevery</I> timesteps. <I>Nfreq</I> must be a multiple of <I>Nevery</I> and
<I>Nevery</I> must be non-zero even if <I>Nrepeat</I> is 1. Also, the timesteps
contributing to the average value cannot overlap, i.e. Nfreq >
(Nrepeat-1)*Nevery is required.
contributing to the average value cannot overlap,
i.e. Nrepeat*Nevery can not exceed Nfreq.
</P>
<P>For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
timesteps 90,92,94,96,98,100 will be used to compute the final average

4
doc/doc2/fix_ave_chunk.html
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@ -161,8 +161,8 @@ that are a multiples of <I>Nfreq</I>. The average is over <I>Nrepeat</I>
quantities, computed in the preceding portion of the simulation every
<I>Nevery</I> timesteps. <I>Nfreq</I> must be a multiple of <I>Nevery</I> and
<I>Nevery</I> must be non-zero even if <I>Nrepeat</I> is 1. Also, the timesteps
contributing to the average value cannot overlap, i.e. Nfreq >
(Nrepeat-1)*Nevery is required.
contributing to the average value cannot overlap,
i.e. Nrepeat*Nevery can not exceed Nfreq.
</P>
<P>For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
timesteps 90,92,94,96,98,100 will be used to compute the final average

6
doc/doc2/fix_ave_histo.html
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@ -143,9 +143,9 @@ histogram. The final histogram is generated on timesteps that are
multiple of <I>Nfreq</I>. It is averaged over <I>Nrepeat</I> histograms,
computed in the preceding portion of the simulation every <I>Nevery</I>
timesteps. <I>Nfreq</I> must be a multiple of <I>Nevery</I> and <I>Nevery</I> must
be non-zero even if <I>Nrepeat</I> is 1. Also, the timesteps contributing
to the histogram cannot overlap, i.e. Nfreq > (Nrepeat-1)*Nevery is
required.
be non-zero even if <I>Nrepeat</I> is 1. Also, the timesteps
contributing to the histogram value cannot overlap,
i.e. Nrepeat*Nevery can not exceed Nfreq.
</P>
<P>For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then input values
on timesteps 90,92,94,96,98,100 will be used to compute the final

4
doc/doc2/fix_ave_spatial.html
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@ -157,8 +157,8 @@ that are a multiples of <I>Nfreq</I>. The average is over <I>Nrepeat</I>
quantities, computed in the preceding portion of the simulation every
<I>Nevery</I> timesteps. <I>Nfreq</I> must be a multiple of <I>Nevery</I> and
<I>Nevery</I> must be non-zero even if <I>Nrepeat</I> is 1. Also, the timesteps
contributing to the average value cannot overlap, i.e. Nfreq >
(Nrepeat-1)*Nevery is required.
contributing to the average value cannot overlap,
i.e. Nrepeat*Nevery can not exceed Nfreq.
</P>
<P>For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
timesteps 90,92,94,96,98,100 will be used to compute the final average

7
doc/doc2/fix_ave_spatial_sphere.html
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@ -127,9 +127,10 @@ the average. The final averaged quantities are generated on timesteps
that are a multiples of <I>Nfreq</I>. The average is over <I>Nrepeat</I>
quantities, computed in the preceding portion of the simulation every
<I>Nevery</I> timesteps. <I>Nfreq</I> must be a multiple of <I>Nevery</I> and
<I>Nevery</I> must be non-zero even if <I>Nrepeat</I> is 1. Also, the timesteps
contributing to the average value cannot overlap, i.e. Nfreq >
(Nrepeat-1)*Nevery is required.
<I>Nevery</I> must be non-zero even if <I>Nrepeat</I> is 1.
Also, the timesteps
contributing to the average value cannot overlap,
i.e. Nrepeat*Nevery can not exceed Nfreq.
</P>
<P>For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
timesteps 90,92,94,96,98,100 will be used to compute the final average

4
doc/doc2/fix_ave_time.html
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@ -131,8 +131,8 @@ that are a mlutiple of <I>Nfreq</I>. The average is over <I>Nrepeat</I>
quantities, computed in the preceding portion of the simulation every
<I>Nevery</I> timesteps. <I>Nfreq</I> must be a multiple of <I>Nevery</I> and
<I>Nevery</I> must be non-zero even if <I>Nrepeat</I> is 1. Also, the timesteps
contributing to the average value cannot overlap, i.e. Nfreq >
(Nrepeat-1)*Nevery is required.
contributing to the average value cannot overlap,
i.e. Nrepeat*Nevery can not exceed Nfreq.
</P>
<P>For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
timesteps 90,92,94,96,98,100 will be used to compute the final average

7
doc/doc2/fix_indent.html
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@ -57,9 +57,10 @@ fix 2 flow indent 10.0 cylinder z 0.0 0.0 10.0 units box
<P><B>Description:</B>
</P>
<P>Insert an indenter within a simulation box. The indenter repels all
atoms that touch it, so it can be used to push into a material or as
an obstacle in a flow. Or it can be used as a constraining wall
around a simulation; see the discussion of the <I>side</I> keyword below.
atoms in the group that touch it, so it can be used to push into a
material or as an obstacle in a flow. Or it can be used as a
constraining wall around a simulation; see the discussion of the
<I>side</I> keyword below.
</P>
<P>The indenter can either be spherical or cylindrical or planar. You
must set one of those 3 keywords.

7
doc/doc2/fix_reaxc_species.html
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@ -102,9 +102,10 @@ order. The species analysis is performed using the average bond-order
on timesteps that are a multiple of <I>Nfreq</I>. The average is over
<I>Nrepeat</I> bond-order samples, computed in the preceding portion of the
simulation every <I>Nevery</I> timesteps. <I>Nfreq</I> must be a multiple of
<I>Nevery</I> and <I>Nevery</I> must be non-zero even if <I>Nrepeat</I> is 1. Also,
the timesteps contributing to the average bond-order cannot overlap,
i.e. Nfreq > (Nrepeat-1)*Nevery is required.
<I>Nevery</I> and <I>Nevery</I> must be non-zero even if <I>Nrepeat</I> is 1.
Also, the timesteps
contributing to the average bond-order cannot overlap,
i.e. Nrepeat*Nevery can not exceed Nfreq.
</P>
<P>For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then bond-order
values on timesteps 90,92,94,96,98,100 will be used to compute the

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doc/doc2/fix_saed_vtk.html
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@ -82,9 +82,10 @@ average. The final averaged quantities are generated on timesteps
that are a multiple of <I>Nfreq</I>. The average is over <I>Nrepeat</I>
quantities, computed in the preceding portion of the simulation every
<I>Nevery</I> timesteps. <I>Nfreq</I> must be a multiple of <I>Nevery</I> and
<I>Nevery</I> must be non-zero even if <I>Nrepeat</I> is 1. Also, the timesteps
contributing to the average value cannot overlap, i.e. Nfreq >
(Nrepeat-1)*Nevery is required.
<I>Nevery</I> must be non-zero even if <I>Nrepeat</I> is 1.
Also, the timesteps
contributing to the average value cannot overlap,
i.e. Nrepeat*Nevery can not exceed Nfreq.
</P>
<P>For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
timesteps 90,92,94,96,98,100 will be used to compute the final average