From a963c78c43065585cb3548085024004fdfe3482a Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Tue, 9 Oct 2007 18:24:42 +0000
Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@989
f3b2605a-c512-4ea7-a41b-209d697bcdaa
---
doc/Section_howto.html | 63 +++++++++++++++++--------------
doc/Section_howto.txt | 63 +++++++++++++++++--------------
doc/compute.html | 3 ++
doc/compute.txt | 3 ++
doc/dihedral_charmm.html | 2 +-
doc/dihedral_charmm.txt | 2 +-
doc/fix.html | 8 ++++
doc/fix.txt | 8 ++++
doc/fix_ave_time.html | 78 ++++++++++++++++++++++-----------------
doc/fix_ave_time.txt | 77 +++++++++++++++++++++-----------------
doc/fix_indent.html | 7 ++--
doc/fix_indent.txt | 7 ++--
doc/fix_nph.html | 6 +--
doc/fix_nph.txt | 6 +--
doc/fix_npt.html | 6 +--
doc/fix_npt.txt | 6 +--
doc/fix_npt_asphere.html | 6 +--
doc/fix_npt_asphere.txt | 6 +--
doc/fix_nvt.html | 6 +--
doc/fix_nvt.txt | 6 +--
doc/fix_nvt_asphere.html | 6 +--
doc/fix_nvt_asphere.txt | 6 +--
doc/fix_nvt_sllod.html | 6 +--
doc/fix_nvt_sllod.txt | 6 +--
doc/fix_orient_fcc.html | 7 ++--
doc/fix_orient_fcc.txt | 7 ++--
doc/fix_setforce.html | 13 ++-----
doc/fix_setforce.txt | 13 ++-----
doc/fix_temp_rescale.html | 7 +++-
doc/fix_temp_rescale.txt | 7 +++-
doc/fix_wall_lj126.html | 7 ++--
doc/fix_wall_lj126.txt | 7 ++--
doc/fix_wall_lj93.html | 7 ++--
doc/fix_wall_lj93.txt | 7 ++--
doc/run.html | 2 +-
doc/run.txt | 2 +-
doc/thermo_style.html | 57 ++++++++++++++++------------
doc/thermo_style.txt | 57 ++++++++++++++++------------
doc/variable.html | 25 +++++++++++--
doc/variable.txt | 25 +++++++++++--
40 files changed, 373 insertions(+), 270 deletions(-)
diff --git a/doc/Section_howto.html b/doc/Section_howto.html
index cbb90b0cb1..2506f650e9 100644
--- a/doc/Section_howto.html
+++ b/doc/Section_howto.html
@@ -796,18 +796,20 @@ lj/cut</A>.
<A NAME = "4_15"></A><H4>4.15 Output from LAMMPS
</H4>
-<P>There are two basic kinds of LAMMPS output. The first is
-thermodynamic output, which is a list of quantities printed every few
-timesteps to the screen and logfile. The second is dump files, which
+<P>Aside from <A HREF = "restart.html">restart files</A>, there are two basic kinds of
+LAMMPS output. The first is <A HREF = "thermo_style.html">thermodynamic output</A>,
+which is a list of quantities printed every few timesteps to the
+screen and logfile. The second is <A HREF = "dump.html">dump files</A>, which
contain snapshots of atoms and various per-atom values and are written
at a specified frequency. A simulation prints one set of
thermodynamic output; it may generate zero, or one, or multiple dump
files. LAMMPS gives you a variety of ways to determine what
quantities are computed and printed when thermodynamic info or dump
files are output. There are also two fixes which perform time and
-spatial averaging of user-defined quantities, fix ave/time and fix
-ave/spatial. These produce their own output files and are described
-below.
+spatial averaging of user-defined quantities, <A HREF = "fix_ave_time.html">fix
+ave/time</A> and <A HREF = "fix_ave_spatial.html">fix
+ave/spatial</A>. These produce their own output
+files and are described below.
</P>
<P>The frequency and format of thermodynamic output is set by the
<A HREF = "thermo.html">thermo</A>, <A HREF = "thermo_style.html">thermo_style</A>, and
@@ -830,12 +832,13 @@ the compute is used along with an optional subscript as part of the
single scalar value generated by the compute; c_myTemp[2] would
output the 2nd vector value.
</P>
-<P><A HREF = "fix.html">Fixes</A> can also generate values to output with thermodynamic
-output, e.g. the energy of an indenter's interaction with the
-simulation atoms. These values are accessed via the same format as
-compute's values, as f_ID or f_ID[N]. See the doc pages for
-individual fix commands to see which ones generate global values that
-can be output with thermodynamic info.
+<P><A HREF = "fix.html">Fixes</A> can also generate global scalar or vector values
+which can be output with thermodynamic output, e.g. the energy of an
+indenter's interaction with the simulation atoms. These values are
+accessed via the same format as a compute's values, as f_ID or
+f_ID[N]. See the doc pages for individual fix commands to see which
+ones generate global values that can be output with thermodynamic
+info.
</P>
<P>Input script variables of various kinds are defined by the
<A HREF = "variable.html">variable</A> command. All kinds except the atom-style
@@ -846,9 +849,9 @@ variable can be used for thermodynamic output. A variable with name
functions (add, exp, etc), atom values (x[N], fx[N]), groups
quantities (mass(), vcm(), etc), references to thermodynamic
quantities (e.g. temp, volume, etc), or references to other variables
-or <A HREF = "compute.html">computes</A>. Thus a variable is the most general way
-to define some quantity you want calculated and output with
-thermodynamic info.
+or <A HREF = "compute.html">computes</A> or <A HREF = "fix.html">fixes</A>. Thus a variable is
+the most general way to define some quantity you want calculated and
+output with thermodynamic info.
</P>
<P>Dump file output is specified by the <A HREF = "dump.html">dump</A> and
<A HREF = "dump_modify.html">dump_modify</A> commands. There are several
@@ -862,34 +865,38 @@ values to be output.
<P><A HREF = "compute.html">Computes</A> that generate per-atom values can be accessed
by the dump custom command. These are computes that have the word
"atom" in their style name, e.g. ke/atom, stress/atom, etc. The
-values are accessed as described above: c_myKE or c_myStress[2].
-The <A HREF = "compute_variable_atom.html">compute variable/atom</A> command takes a
+values are accessed as c_myKE for a scalar per-atom quantity or as
+c_myStress[2] for a component of a vector per-atom quantity. The
+<A HREF = "compute_variable_atom.html">compute variable/atom</A> command takes a
user-defined atom-style <A HREF = "variable.html">variable</A> as input and
calculates its value for each atom. Since this compute can be
accessed by the dump custom command, this is a general way to define
some quantity you want calculated and output in a dump file.
</P>
-<P><A HREF = "fix.html">Fixes</A> can also generate values to output to dump files.
-For example, the <A HREF = "fix_ave_atom.html">fix ave/atom</A> command does
-time-averaging of atom quantites, such as velocity or energy or stress
-which can then be output in a dump file. These values are accessed as
-describe above, as f_ID or f_ID[N].
+<P><A HREF = "fix.html">Fixes</A> can also generate per-atom values to output to dump
+files. For example, the <A HREF = "fix_ave_atom.html">fix ave/atom</A> command does
+time-averaging of atom quantities, such as velocity or energy or
+stress which can then be output in a dump file. These values are
+accessed as f_myKE for a scalar per-atom quantity or as
+f_myStress[2] for a component of a vector per-atom quantity.
</P>
<P>Two other fixes are of particular note for output. Neither produces
-values for thermodynamic or dump output, rather they output their
+values for thermodynamic or dump output. Instead they output their
results directly to a file.
</P>
<P>The <A HREF = "fix_ave_time.html">fix ave/time</A> command enables time-averaging of
global quantities like temperature or pressure. The global quantities
-are calculated by a <A HREF = "compute.html">compute</A>.
+are calculated by a <A HREF = "compute.html">compute</A> or a <A HREF = "fix.html">fix</A>. The
+compute or fix must generate global scalar or vector quantities.
</P>
<P>The <A HREF = "fix_ave_spatial.html">fix ave/spatial</A> command enables
spatial-averaging of per-atom quantities like per-atom energy or
stress. The per-atom quantities can be atom density (mass or number)
-or be calculated by a by a <A HREF = "compute.html">compute</A>. They can also be
-quantities calculated by <A HREF = "fix_ave_atom.html">fix ave/atom</A>, which means
-you are effectively calculating a time average of a spatial average of
-a time-averaged per-atom quantity.
+or be calculated by a <A HREF = "compute.html">compute</A> or a <A HREF = "fix.html">fix</A>. The
+compute or fix must generate per-atom scalar or vector quantities.
+Note that if you use the <A HREF = "fix_ave_atom.html">fix ave/atom</A> command with
+fix ave/spatial, it means you are effectively calculating a time
+average of a spatial average of a time-averaged per-atom quantity.
</P>
<HR>
diff --git a/doc/Section_howto.txt b/doc/Section_howto.txt
index a3f5a9e9a8..1a74e6c6ba 100644
--- a/doc/Section_howto.txt
+++ b/doc/Section_howto.txt
@@ -789,18 +789,20 @@ lj/cut"_pair_lj.html.
4.15 Output from LAMMPS :link(4_15),h4
-There are two basic kinds of LAMMPS output. The first is
-thermodynamic output, which is a list of quantities printed every few
-timesteps to the screen and logfile. The second is dump files, which
+Aside from "restart files"_restart.html, there are two basic kinds of
+LAMMPS output. The first is "thermodynamic output"_thermo_style.html,
+which is a list of quantities printed every few timesteps to the
+screen and logfile. The second is "dump files"_dump.html, which
contain snapshots of atoms and various per-atom values and are written
at a specified frequency. A simulation prints one set of
thermodynamic output; it may generate zero, or one, or multiple dump
files. LAMMPS gives you a variety of ways to determine what
quantities are computed and printed when thermodynamic info or dump
files are output. There are also two fixes which perform time and
-spatial averaging of user-defined quantities, fix ave/time and fix
-ave/spatial. These produce their own output files and are described
-below.
+spatial averaging of user-defined quantities, "fix
+ave/time"_fix_ave_time.html and "fix
+ave/spatial"_fix_ave_spatial.html. These produce their own output
+files and are described below.
The frequency and format of thermodynamic output is set by the
"thermo"_thermo.html, "thermo_style"_thermo_style.html, and
@@ -823,12 +825,13 @@ the compute is used along with an optional subscript as part of the
single scalar value generated by the compute; c_myTemp\[2\] would
output the 2nd vector value.
-"Fixes"_fix.html can also generate values to output with thermodynamic
-output, e.g. the energy of an indenter's interaction with the
-simulation atoms. These values are accessed via the same format as
-compute's values, as f_ID or f_ID\[N\]. See the doc pages for
-individual fix commands to see which ones generate global values that
-can be output with thermodynamic info.
+"Fixes"_fix.html can also generate global scalar or vector values
+which can be output with thermodynamic output, e.g. the energy of an
+indenter's interaction with the simulation atoms. These values are
+accessed via the same format as a compute's values, as f_ID or
+f_ID\[N\]. See the doc pages for individual fix commands to see which
+ones generate global values that can be output with thermodynamic
+info.
Input script variables of various kinds are defined by the
"variable"_variable.html command. All kinds except the atom-style
@@ -839,9 +842,9 @@ The variable formula defined in the input script can contain math
functions (add, exp, etc), atom values (x\[N\], fx\[N\]), groups
quantities (mass(), vcm(), etc), references to thermodynamic
quantities (e.g. temp, volume, etc), or references to other variables
-or "computes"_compute.html. Thus a variable is the most general way
-to define some quantity you want calculated and output with
-thermodynamic info.
+or "computes"_compute.html or "fixes"_fix.html. Thus a variable is
+the most general way to define some quantity you want calculated and
+output with thermodynamic info.
Dump file output is specified by the "dump"_dump.html and
"dump_modify"_dump_modify.html commands. There are several
@@ -855,34 +858,38 @@ values to be output.
"Computes"_compute.html that generate per-atom values can be accessed
by the dump custom command. These are computes that have the word
"atom" in their style name, e.g. ke/atom, stress/atom, etc. The
-values are accessed as described above: c_myKE or c_myStress\[2\].
-The "compute variable/atom"_compute_variable_atom.html command takes a
+values are accessed as c_myKE for a scalar per-atom quantity or as
+c_myStress\[2\] for a component of a vector per-atom quantity. The
+"compute variable/atom"_compute_variable_atom.html command takes a
user-defined atom-style "variable"_variable.html as input and
calculates its value for each atom. Since this compute can be
accessed by the dump custom command, this is a general way to define
some quantity you want calculated and output in a dump file.
-"Fixes"_fix.html can also generate values to output to dump files.
-For example, the "fix ave/atom"_fix_ave_atom.html command does
-time-averaging of atom quantites, such as velocity or energy or stress
-which can then be output in a dump file. These values are accessed as
-describe above, as f_ID or f_ID\[N\].
+"Fixes"_fix.html can also generate per-atom values to output to dump
+files. For example, the "fix ave/atom"_fix_ave_atom.html command does
+time-averaging of atom quantities, such as velocity or energy or
+stress which can then be output in a dump file. These values are
+accessed as f_myKE for a scalar per-atom quantity or as
+f_myStress\[2\] for a component of a vector per-atom quantity.
Two other fixes are of particular note for output. Neither produces
-values for thermodynamic or dump output, rather they output their
+values for thermodynamic or dump output. Instead they output their
results directly to a file.
The "fix ave/time"_fix_ave_time.html command enables time-averaging of
global quantities like temperature or pressure. The global quantities
-are calculated by a "compute"_compute.html.
+are calculated by a "compute"_compute.html or a "fix"_fix.html. The
+compute or fix must generate global scalar or vector quantities.
The "fix ave/spatial"_fix_ave_spatial.html command enables
spatial-averaging of per-atom quantities like per-atom energy or
stress. The per-atom quantities can be atom density (mass or number)
-or be calculated by a by a "compute"_compute.html. They can also be
-quantities calculated by "fix ave/atom"_fix_ave_atom.html, which means
-you are effectively calculating a time average of a spatial average of
-a time-averaged per-atom quantity.
+or be calculated by a "compute"_compute.html or a "fix"_fix.html. The
+compute or fix must generate per-atom scalar or vector quantities.
+Note that if you use the "fix ave/atom"_fix_ave_atom.html command with
+fix ave/spatial, it means you are effectively calculating a time
+average of a spatial average of a time-averaged per-atom quantity.
:line
diff --git a/doc/compute.html b/doc/compute.html
index bfe35ef64e..3c2b969228 100644
--- a/doc/compute.html
+++ b/doc/compute.html
@@ -50,6 +50,9 @@ be time-averaged via the <A HREF = "fix_ave_atom.html">fix ave/atom</A> command
then output via the <A HREF = "dump.html">dump custom</A> or <A HREF = "fix_ave_spatial.html">fix
ave/spatial</A> commands.
</P>
+<P>See this <A HREF = "Section_howto.html#4_15">howto section</A> for a summary of
+various LAMMPS output options.
+</P>
<P>LAMMPS creates its own global computes for thermodynamic output. Two
computes are always created, named "thermo_temp" and
"thermo_pressure", as if these commands had been invoked:
diff --git a/doc/compute.txt b/doc/compute.txt
index 67c53d3be4..2f6b1c2367 100644
--- a/doc/compute.txt
+++ b/doc/compute.txt
@@ -47,6 +47,9 @@ be time-averaged via the "fix ave/atom"_fix_ave_atom.html command and
then output via the "dump custom"_dump.html or "fix
ave/spatial"_fix_ave_spatial.html commands.
+See this "howto section"_Section_howto.html#4_15 for a summary of
+various LAMMPS output options.
+
LAMMPS creates its own global computes for thermodynamic output. Two
computes are always created, named "thermo_temp" and
"thermo_pressure", as if these commands had been invoked:
diff --git a/doc/dihedral_charmm.html b/doc/dihedral_charmm.html
index 809afe4723..668b6e759e 100644
--- a/doc/dihedral_charmm.html
+++ b/doc/dihedral_charmm.html
@@ -43,7 +43,7 @@ or <A HREF = "read_restart.html">read_restart</A> commands:
</UL>
<P>The weighting factor is applied to pairwise interaction between the
1st and 4th atoms in the dihedral. Note that this weighting factor is
-unrelated to the weighting factor specified by the <A HREF = "doc/special_bonds.html">special
+unrelated to the weighting factor specified by the <A HREF = "special_bonds.html">special
bonds</A> command which applies to all 1-4
interactions in the system.
</P>
diff --git a/doc/dihedral_charmm.txt b/doc/dihedral_charmm.txt
index c9aefa7266..cf1531e770 100644
--- a/doc/dihedral_charmm.txt
+++ b/doc/dihedral_charmm.txt
@@ -41,7 +41,7 @@ weighting factor (0.0 to 1.0) :ul
The weighting factor is applied to pairwise interaction between the
1st and 4th atoms in the dihedral. Note that this weighting factor is
unrelated to the weighting factor specified by the "special
-bonds"_doc/special_bonds.html command which applies to all 1-4
+bonds"_special_bonds.html command which applies to all 1-4
interactions in the system.
For CHARMM force fields, the special_bonds 1-4 weighting factor should
diff --git a/doc/fix.html b/doc/fix.html
index c6d1437fa2..ba7101e40f 100644
--- a/doc/fix.html
+++ b/doc/fix.html
@@ -63,6 +63,14 @@ made to the old fix via the <A HREF = "fix_modify.html">fix_modify</A> command.
<P>The <A HREF = "fix_modify.html">fix modify</A> command allows settings for some
fixes to be reset. See the doc page for individual fixes for details.
</P>
+<P>Some fixes calculate a global scalar or vector quantity which can be
+accessed by various output commands, including
+<A HREF = "variable.html">variables</A>, <A HREF = "thermo_style.html">thermo_style custom</A>,
+and <A HREF = "fix_ave_time.html">fix ave/time</A>. See this <A HREF = "Section_howto.html#4_15">howto
+section</A> for a summary of various LAMMPS
+output options. See the doc pages for individual fixes for info on
+which ones calculate these quantities.
+</P>
<P>Some fixes store an internal "state" which is written to binary
restart files via the <A HREF = "restart.html">restart</A> or
<A HREF = "write_restart.html">write_restart</A> commands. This allows the fix to
diff --git a/doc/fix.txt b/doc/fix.txt
index dff6e087e9..5281912381 100644
--- a/doc/fix.txt
+++ b/doc/fix.txt
@@ -60,6 +60,14 @@ made to the old fix via the "fix_modify"_fix_modify.html command.
The "fix modify"_fix_modify.html command allows settings for some
fixes to be reset. See the doc page for individual fixes for details.
+Some fixes calculate a global scalar or vector quantity which can be
+accessed by various output commands, including
+"variables"_variable.html, "thermo_style custom"_thermo_style.html,
+and "fix ave/time"_fix_ave_time.html. See this "howto
+section"_Section_howto.html#4_15 for a summary of various LAMMPS
+output options. See the doc pages for individual fixes for info on
+which ones calculate these quantities.
+
Some fixes store an internal "state" which is written to binary
restart files via the "restart"_restart.html or
"write_restart"_write_restart.html commands. This allows the fix to
diff --git a/doc/fix_ave_time.html b/doc/fix_ave_time.html
index cd318ed159..2fb477ba44 100644
--- a/doc/fix_ave_time.html
+++ b/doc/fix_ave_time.html
@@ -13,43 +13,51 @@
</H3>
<P><B>Syntax:</B>
</P>
-<PRE>fix ID group-ID ave/time Nevery Nrepeat Nfreq compute-ID flag file
+<PRE>fix ID group-ID ave/time Nevery Nrepeat Nfreq style ID flag file
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>ave/time = style name of this fix command
<LI>Nevery = calculate property every this many timesteps
<LI>Nrepeat = # of times to repeat the Nevery calculation before averaging
<LI>Nfreq = timestep frequency at which the average value is written to file
-<LI>compute-ID = ID of compute that performs the calculation
+<LI>style = <I>compute</I> or <I>fix</I>
+<LI>ID = ID of compute or fix that performs the calculation
<LI>flag = 0 for scalar quantity, 1 for vector quantity, 2 for both
<LI>file = filename to write results to
</UL>
<P><B>Examples:</B>
</P>
-<PRE>fix 1 all ave/time 100 5 1000 myTemp 0 temp.stats
+<PRE>fix 1 all ave/time 100 5 1000 compute myTemp 0 temp.stats
+</PRE>
+<PRE>fix 1 all ave/time 1 100 1000 fix indenter 0 temp.indent
</PRE>
<P><B>Description:</B>
</P>
<P>Calculate one or more instantaneous quantities every few timesteps,
average them over a longer timescale, and print the results to a file.
-This can be used to time-average any "compute" entity in LAMMPS which
-calculates a global quantity such as a temperature or pressure.
-Per-atom computes cannot be used with this fix.
-</P>
-<P>The <I>compute-ID</I> specifies a <A HREF = "compute.html">compute</A> which calculates
-the desired property. The compute must be a "global" compute that
-calculates one or more global properties rather than a "per-atom"
-compute. The compute can be previously defined in the input script.
-Or it can be a compute defined by <A HREF = "thermo_style.html">thermodynamic
+This can be used to time-average a <A HREF = "compute.html">compute</A> which
+calculates a global quantity such as a temperature or pressure or a
+<A HREF = "fix.html">fix</A> which calculates such a global quantity. Note that
+per-atom computes cannot be used with this fix; their values can be
+averaged by the <A HREF = "fix_ave_spatial.html">fix ave/spatial</A> or <A HREF = "fix_ave_atom.html">fix
+ave/atom</A> commands.
+</P>
+<P>For style <I>compute</I> the <I>ID</I> specifies a <A HREF = "compute.html">compute</A> which
+calculates the desired property. The compute must be a "global"
+compute that calculates one or more global properties rather than a
+"per-atom" compute. The fix must be previously defined in the input
+script. Or it can be a compute defined by <A HREF = "thermo_style.html">thermodynamic
output</A> or other fixes such as <A HREF = "fix_nvt.html">fix
nvt</A> or <A HREF = "fix_temp_rescale.html">fix temp/rescale</A>. Users
-can also write code for their own compute styles and <A HREF = "Section_modify.html">add them to
+can write code for their own compute styles and <A HREF = "Section_modify.html">add them to
LAMMPS</A>.
</P>
-<P>In all these cases, the fix ave/time command uses the global scalar or
-vector calculated by the compute. See the <A HREF = "fix_ave_spatial.html">fix
-ave/spatial</A> command if you wish to average
-spatially, e.g. via a compute that calculates per-atom quantities.
+<P>For style <I>fix</I> the <I>ID</I> specifies a <A HREF = "fix.html">fix</A> which calculates
+the desired property. The fix must calculate a global scalar or
+vector quantity, which only a few fixes do. See the doc page for
+individual fix commands for details. The fix must be previously
+defined in the input script. Users can write code for their own fix
+styles and <A HREF = "Section_modify.html">add them to LAMMPS</A>.
</P>
<P>The <I>Nevery</I>, <I>Nrepeat</I>, and <I>Nfreq</I> arguments specify how the
property will be time-averaged. The final averaged value(s) are
@@ -61,22 +69,23 @@ final average written to the file on timestep 100. Similary for
timesteps 190,192,194,196,198,200 on timestep 200, etc.
</P>
<P>The <I>flag</I> argument chooses whether the scalar and/or vector
-calculation of the compute is invoked. The former computes a single
-global value. The latter computes N global values, where N is defined
-by the compute, e.g. 6 pressure tensor components. In the vector
-case, each of the N values is averaged independently and N values are
-written to the file at each output.
-</P>
-<P>Since the calculation is performed by the compute which stores its own
-"group" definition, the group specified for this fix is ignored.
-</P>
-<P>If the compute calculates pressure, it will cause the force
-computations performed by LAMMPS (pair, bond, angle, etc) to calculate
-virial terms each Nevery timesteps. If this is more frequent than
-thermodynamic output, this adds extra cost to a simulation. However,
-if a constant pressure simulation is being run (<A HREF = "fix_npt.html">fix npt</A>
-or <A HREF = "fix_nph.html">fix nph</A>), LAMMPS is already calculating virial terms
-for the pressure every timestep.
+calculation of the compute or fix is invoked. The former computes a
+single global value. The latter computes N global values, where N is
+defined by the compute or fix, e.g. 6 pressure tensor components. In
+the vector case, each of the N values is averaged independently and N
+values are written to the file at each output.
+</P>
+<P>Since the calculation is performed by the compute or fix which stores
+its own "group" definition, the group specified for with the fix
+ave/time command is ignored.
+</P>
+<P>If the style is <I>compute</I> and the compute calculates pressure, it will
+cause the force computations performed by LAMMPS (pair, bond, angle,
+etc) to calculate virial terms each Nevery timesteps. If this is more
+frequent than thermodynamic output, this adds extra cost to a
+simulation. However, if a constant pressure simulation is being run
+(<A HREF = "fix_npt.html">fix npt</A> or <A HREF = "fix_nph.html">fix nph</A>), LAMMPS is already
+calculating virial terms for the pressure every timestep.
</P>
<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
</P>
@@ -92,7 +101,8 @@ minimization</A>.
</P>
<P><B>Related commands:</B>
</P>
-<P><A HREF = "compute.html">compute</A>, <A HREF = "fix_ave_spatial.html">fix ave/spatial</A>
+<P><A HREF = "compute.html">compute</A>, <A HREF = "fix_ave_atom.html">fix ave/atom</A>, <A HREF = "fix_ave_spatial.html">fix
+ave/spatial</A>
</P>
<P><B>Default:</B> none
</P>
diff --git a/doc/fix_ave_time.txt b/doc/fix_ave_time.txt
index e603c3019c..085983ee09 100644
--- a/doc/fix_ave_time.txt
+++ b/doc/fix_ave_time.txt
@@ -10,43 +10,50 @@ fix ave/time command :h3
[Syntax:]
-fix ID group-ID ave/time Nevery Nrepeat Nfreq compute-ID flag file :pre
+fix ID group-ID ave/time Nevery Nrepeat Nfreq style ID flag file :pre
ID, group-ID are documented in "fix"_fix.html command
ave/time = style name of this fix command
Nevery = calculate property every this many timesteps
Nrepeat = # of times to repeat the Nevery calculation before averaging
Nfreq = timestep frequency at which the average value is written to file
-compute-ID = ID of compute that performs the calculation
+style = {compute} or {fix}
+ID = ID of compute or fix that performs the calculation
flag = 0 for scalar quantity, 1 for vector quantity, 2 for both
file = filename to write results to :ul
[Examples:]
-fix 1 all ave/time 100 5 1000 myTemp 0 temp.stats :pre
+fix 1 all ave/time 100 5 1000 compute myTemp 0 temp.stats :pre
+fix 1 all ave/time 1 100 1000 fix indenter 0 temp.indent :pre
[Description:]
Calculate one or more instantaneous quantities every few timesteps,
average them over a longer timescale, and print the results to a file.
-This can be used to time-average any "compute" entity in LAMMPS which
-calculates a global quantity such as a temperature or pressure.
-Per-atom computes cannot be used with this fix.
-
-The {compute-ID} specifies a "compute"_compute.html which calculates
-the desired property. The compute must be a "global" compute that
-calculates one or more global properties rather than a "per-atom"
-compute. The compute can be previously defined in the input script.
-Or it can be a compute defined by "thermodynamic
+This can be used to time-average a "compute"_compute.html which
+calculates a global quantity such as a temperature or pressure or a
+"fix"_fix.html which calculates such a global quantity. Note that
+per-atom computes cannot be used with this fix; their values can be
+averaged by the "fix ave/spatial"_fix_ave_spatial.html or "fix
+ave/atom"_fix_ave_atom.html commands.
+
+For style {compute} the {ID} specifies a "compute"_compute.html which
+calculates the desired property. The compute must be a "global"
+compute that calculates one or more global properties rather than a
+"per-atom" compute. The fix must be previously defined in the input
+script. Or it can be a compute defined by "thermodynamic
output"_thermo_style.html or other fixes such as "fix
nvt"_fix_nvt.html or "fix temp/rescale"_fix_temp_rescale.html. Users
-can also write code for their own compute styles and "add them to
+can write code for their own compute styles and "add them to
LAMMPS"_Section_modify.html.
-In all these cases, the fix ave/time command uses the global scalar or
-vector calculated by the compute. See the "fix
-ave/spatial"_fix_ave_spatial.html command if you wish to average
-spatially, e.g. via a compute that calculates per-atom quantities.
+For style {fix} the {ID} specifies a "fix"_fix.html which calculates
+the desired property. The fix must calculate a global scalar or
+vector quantity, which only a few fixes do. See the doc page for
+individual fix commands for details. The fix must be previously
+defined in the input script. Users can write code for their own fix
+styles and "add them to LAMMPS"_Section_modify.html.
The {Nevery}, {Nrepeat}, and {Nfreq} arguments specify how the
property will be time-averaged. The final averaged value(s) are
@@ -58,22 +65,23 @@ final average written to the file on timestep 100. Similary for
timesteps 190,192,194,196,198,200 on timestep 200, etc.
The {flag} argument chooses whether the scalar and/or vector
-calculation of the compute is invoked. The former computes a single
-global value. The latter computes N global values, where N is defined
-by the compute, e.g. 6 pressure tensor components. In the vector
-case, each of the N values is averaged independently and N values are
-written to the file at each output.
-
-Since the calculation is performed by the compute which stores its own
-"group" definition, the group specified for this fix is ignored.
-
-If the compute calculates pressure, it will cause the force
-computations performed by LAMMPS (pair, bond, angle, etc) to calculate
-virial terms each Nevery timesteps. If this is more frequent than
-thermodynamic output, this adds extra cost to a simulation. However,
-if a constant pressure simulation is being run ("fix npt"_fix_npt.html
-or "fix nph"_fix_nph.html), LAMMPS is already calculating virial terms
-for the pressure every timestep.
+calculation of the compute or fix is invoked. The former computes a
+single global value. The latter computes N global values, where N is
+defined by the compute or fix, e.g. 6 pressure tensor components. In
+the vector case, each of the N values is averaged independently and N
+values are written to the file at each output.
+
+Since the calculation is performed by the compute or fix which stores
+its own "group" definition, the group specified for with the fix
+ave/time command is ignored.
+
+If the style is {compute} and the compute calculates pressure, it will
+cause the force computations performed by LAMMPS (pair, bond, angle,
+etc) to calculate virial terms each Nevery timesteps. If this is more
+frequent than thermodynamic output, this adds extra cost to a
+simulation. However, if a constant pressure simulation is being run
+("fix npt"_fix_npt.html or "fix nph"_fix_nph.html), LAMMPS is already
+calculating virial terms for the pressure every timestep.
[Restart, fix_modify, thermo output, run start/stop, minimize info:]
@@ -89,6 +97,7 @@ minimization"_minimize.html.
[Related commands:]
-"compute"_compute.html, "fix ave/spatial"_fix_ave_spatial.html
+"compute"_compute.html, "fix ave/atom"_fix_ave_atom.html, "fix
+ave/spatial"_fix_ave_spatial.html
[Default:] none
diff --git a/doc/fix_indent.html b/doc/fix_indent.html
index 27605132ac..56301f6364 100644
--- a/doc/fix_indent.html
+++ b/doc/fix_indent.html
@@ -105,10 +105,9 @@ the system's potential energy as part of <A HREF = "thermo_style.html">thermodyn
output</A>. The energy of each particle interacting
with the indenter is K/3 (r - R)^3.
</P>
-<P>The atom/indenter interaction energy can be printed as part of
-thermodynamic output via the keyword f_ID, where ID is the fix-ID of
-this fix. See the <A HREF = "thermo_style.html">thermo_style custom</A> command for
-details.
+<P>This fix computes a scalar energy and a 3-vector of forces (on the
+indenter), which can be accessed by various <A HREF = "Section_howto.html#4_15">output
+commands</A>.
</P>
<P>This fix can adjust the indenter position and radius over multiple
runs, using the <I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A>
diff --git a/doc/fix_indent.txt b/doc/fix_indent.txt
index 2186996d84..232f0a6f42 100644
--- a/doc/fix_indent.txt
+++ b/doc/fix_indent.txt
@@ -96,10 +96,9 @@ the system's potential energy as part of "thermodynamic
output"_thermo_style.html. The energy of each particle interacting
with the indenter is K/3 (r - R)^3.
-The atom/indenter interaction energy can be printed as part of
-thermodynamic output via the keyword f_ID, where ID is the fix-ID of
-this fix. See the "thermo_style custom"_thermo_style.html command for
-details.
+This fix computes a scalar energy and a 3-vector of forces (on the
+indenter), which can be accessed by various "output
+commands"_Section_howto.html#4_15.
This fix can adjust the indenter position and radius over multiple
runs, using the {start} and {stop} keywords of the "run"_run.html
diff --git a/doc/fix_nph.html b/doc/fix_nph.html
index 1126337099..0c4e9a6c33 100644
--- a/doc/fix_nph.html
+++ b/doc/fix_nph.html
@@ -168,9 +168,9 @@ fix to add the energy change induced by Nose/Hoover barostatting to
the system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
output</A>.
</P>
-<P>The energy change can be printed as part of thermodynamic output via
-the keyword f_ID, where ID is the fix-ID of this fix. See the
-<A HREF = "thermo_style.html">thermo_style custom</A> command for details.
+<P>The potential energy change due to this fix is stored as a scalar
+quantity, which can be accessed by various <A HREF = "Section_howto.html#4_15">output
+commands</A>.
</P>
<P>This fix can ramp its target pressure over multiple runs, using the
<I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command. See the
diff --git a/doc/fix_nph.txt b/doc/fix_nph.txt
index 1688ea9f81..3e9a170b25 100644
--- a/doc/fix_nph.txt
+++ b/doc/fix_nph.txt
@@ -158,9 +158,9 @@ fix to add the energy change induced by Nose/Hoover barostatting to
the system's potential energy as part of "thermodynamic
output"_thermo_style.html.
-The energy change can be printed as part of thermodynamic output via
-the keyword f_ID, where ID is the fix-ID of this fix. See the
-"thermo_style custom"_thermo_style.html command for details.
+The potential energy change due to this fix is stored as a scalar
+quantity, which can be accessed by various "output
+commands"_Section_howto.html#4_15.
This fix can ramp its target pressure over multiple runs, using the
{start} and {stop} keywords of the "run"_run.html command. See the
diff --git a/doc/fix_npt.html b/doc/fix_npt.html
index fd7b031c98..c40ce4c25b 100644
--- a/doc/fix_npt.html
+++ b/doc/fix_npt.html
@@ -171,9 +171,9 @@ fix to add the energy change induced by Nose/Hoover thermostatting and
barostatting to the system's potential energy as part of
<A HREF = "thermo_style.html">thermodynamic output</A>.
</P>
-<P>The energy change can be printed as part of thermodynamic output via
-the keyword f_ID, where ID is the fix-ID of this fix. See the
-<A HREF = "thermo_style.html">thermo_style custom</A> command for details.
+<P>The potential energy change due to this fix is stored as a scalar
+quantity, which can be accessed by various <A HREF = "Section_howto.html#4_15">output
+commands</A>.
</P>
<P>This fix can ramp its target temperature and pressure over multiple
runs, using the <I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A>
diff --git a/doc/fix_npt.txt b/doc/fix_npt.txt
index 2f3244b9b5..ba2471c4a5 100644
--- a/doc/fix_npt.txt
+++ b/doc/fix_npt.txt
@@ -160,9 +160,9 @@ fix to add the energy change induced by Nose/Hoover thermostatting and
barostatting to the system's potential energy as part of
"thermodynamic output"_thermo_style.html.
-The energy change can be printed as part of thermodynamic output via
-the keyword f_ID, where ID is the fix-ID of this fix. See the
-"thermo_style custom"_thermo_style.html command for details.
+The potential energy change due to this fix is stored as a scalar
+quantity, which can be accessed by various "output
+commands"_Section_howto.html#4_15.
This fix can ramp its target temperature and pressure over multiple
runs, using the {start} and {stop} keywords of the "run"_run.html
diff --git a/doc/fix_npt_asphere.html b/doc/fix_npt_asphere.html
index b85d70acdc..6e11cd5018 100644
--- a/doc/fix_npt_asphere.html
+++ b/doc/fix_npt_asphere.html
@@ -172,9 +172,9 @@ fix to add the energy change induced by Nose/Hoover thermostatting and
barostatting to the system's potential energy as part of
<A HREF = "thermo_style.html">thermodynamic output</A>.
</P>
-<P>The energy change can be printed as part of thermodynamic output via
-the keyword f_ID, where ID is the fix-ID of this fix. See the
-<A HREF = "thermo_style.html">thermo_style custom</A> command for details.
+<P>The potential energy change due to this fix is stored as a scalar
+quantity, which can be accessed by various <A HREF = "Section_howto.html#4_15">output
+commands</A>.
</P>
<P>This fix can ramp its target temperature and pressure over multiple
runs, using the <I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A>
diff --git a/doc/fix_npt_asphere.txt b/doc/fix_npt_asphere.txt
index 745259154d..011191b05c 100755
--- a/doc/fix_npt_asphere.txt
+++ b/doc/fix_npt_asphere.txt
@@ -161,9 +161,9 @@ fix to add the energy change induced by Nose/Hoover thermostatting and
barostatting to the system's potential energy as part of
"thermodynamic output"_thermo_style.html.
-The energy change can be printed as part of thermodynamic output via
-the keyword f_ID, where ID is the fix-ID of this fix. See the
-"thermo_style custom"_thermo_style.html command for details.
+The potential energy change due to this fix is stored as a scalar
+quantity, which can be accessed by various "output
+commands"_Section_howto.html#4_15.
This fix can ramp its target temperature and pressure over multiple
runs, using the {start} and {stop} keywords of the "run"_run.html
diff --git a/doc/fix_nvt.html b/doc/fix_nvt.html
index 2238ac8095..64f1273ea6 100644
--- a/doc/fix_nvt.html
+++ b/doc/fix_nvt.html
@@ -99,9 +99,9 @@ fix to add the energy change induced by Nose/Hoover thermostatting to
the system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
output</A>.
</P>
-<P>The energy change can be printed as part of thermodynamic output via
-the keyword f_ID, where ID is the fix-ID of this fix. See the
-<A HREF = "thermo_style.html">thermo_style custom</A> command for details.
+<P>The potential energy change due to this fix is stored as a scalar
+quantity, which can be accessed by various <A HREF = "Section_howto.html#4_15">output
+commands</A>.
</P>
<P>This fix can ramp its target temperature over multiple runs, using the
<I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command. See the
diff --git a/doc/fix_nvt.txt b/doc/fix_nvt.txt
index 08350114f1..c43ff8a28f 100644
--- a/doc/fix_nvt.txt
+++ b/doc/fix_nvt.txt
@@ -90,9 +90,9 @@ fix to add the energy change induced by Nose/Hoover thermostatting to
the system's potential energy as part of "thermodynamic
output"_thermo_style.html.
-The energy change can be printed as part of thermodynamic output via
-the keyword f_ID, where ID is the fix-ID of this fix. See the
-"thermo_style custom"_thermo_style.html command for details.
+The potential energy change due to this fix is stored as a scalar
+quantity, which can be accessed by various "output
+commands"_Section_howto.html#4_15.
This fix can ramp its target temperature over multiple runs, using the
{start} and {stop} keywords of the "run"_run.html command. See the
diff --git a/doc/fix_nvt_asphere.html b/doc/fix_nvt_asphere.html
index 5da14c27bc..9b0f0efb63 100644
--- a/doc/fix_nvt_asphere.html
+++ b/doc/fix_nvt_asphere.html
@@ -100,9 +100,9 @@ fix to add the energy change induced by Nose/Hoover thermostatting to
the system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
output</A>.
</P>
-<P>The energy change can be printed as part of thermodynamic output via
-the keyword f_ID, where ID is the fix-ID of this fix. See the
-<A HREF = "thermo_style.html">thermo_style custom</A> command for details.
+<P>The potential energy change due to this fix is stored as a scalar
+quantity, which can be accessed by various <A HREF = "Section_howto.html#4_15">output
+commands</A>.
</P>
<P>This fix can ramp its target temperature over multiple runs, using the
<I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command. See the
diff --git a/doc/fix_nvt_asphere.txt b/doc/fix_nvt_asphere.txt
index 84343089a1..8a1a8fc4c1 100755
--- a/doc/fix_nvt_asphere.txt
+++ b/doc/fix_nvt_asphere.txt
@@ -91,9 +91,9 @@ fix to add the energy change induced by Nose/Hoover thermostatting to
the system's potential energy as part of "thermodynamic
output"_thermo_style.html.
-The energy change can be printed as part of thermodynamic output via
-the keyword f_ID, where ID is the fix-ID of this fix. See the
-"thermo_style custom"_thermo_style.html command for details.
+The potential energy change due to this fix is stored as a scalar
+quantity, which can be accessed by various "output
+commands"_Section_howto.html#4_15.
This fix can ramp its target temperature over multiple runs, using the
{start} and {stop} keywords of the "run"_run.html command. See the
diff --git a/doc/fix_nvt_sllod.html b/doc/fix_nvt_sllod.html
index 493b6afbb8..6a9918bf4d 100644
--- a/doc/fix_nvt_sllod.html
+++ b/doc/fix_nvt_sllod.html
@@ -126,9 +126,9 @@ fix to add the energy change induced by Nose/Hoover thermostatting to
the system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
output</A>.
</P>
-<P>The energy change can be printed as part of thermodynamic output via
-the keyword f_ID, where ID is the fix-ID of this fix. See the
-<A HREF = "thermo_style.html">thermo_style custom</A> command for details.
+<P>The potential energy change due to this fix is stored as a scalar
+quantity, which can be accessed by various <A HREF = "Section_howto.html#4_15">output
+commands</A>.
</P>
<P>This fix can ramp its target temperature over multiple runs, using the
<I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command. See the
diff --git a/doc/fix_nvt_sllod.txt b/doc/fix_nvt_sllod.txt
index 8bbf55a4e1..416970e5b0 100644
--- a/doc/fix_nvt_sllod.txt
+++ b/doc/fix_nvt_sllod.txt
@@ -117,9 +117,9 @@ fix to add the energy change induced by Nose/Hoover thermostatting to
the system's potential energy as part of "thermodynamic
output"_thermo_style.html.
-The energy change can be printed as part of thermodynamic output via
-the keyword f_ID, where ID is the fix-ID of this fix. See the
-"thermo_style custom"_thermo_style.html command for details.
+The potential energy change due to this fix is stored as a scalar
+quantity, which can be accessed by various "output
+commands"_Section_howto.html#4_15.
This fix can ramp its target temperature over multiple runs, using the
{start} and {stop} keywords of the "run"_run.html command. See the
diff --git a/doc/fix_orient_fcc.html b/doc/fix_orient_fcc.html
index 66fc8f7856..1a8cc1cf40 100644
--- a/doc/fix_orient_fcc.html
+++ b/doc/fix_orient_fcc.html
@@ -126,10 +126,9 @@ fix to add the potential energy of atom interactions with the grain
boundary driving force to the system's potential energy as part of
<A HREF = "thermo_style.html">thermodynamic output</A>.
</P>
-<P>The atom/grain-boundary interaction energy can be printed as part of
-thermodynamic output via the keyword f_ID, where ID is the fix-ID of
-this fix. See the <A HREF = "thermo_style.html">thermo_style custom</A> command for
-details.
+<P>The potential energy change due to this fix is stored as a scalar
+quantity, which can be accessed by various <A HREF = "Section_howto.html#4_15">output
+commands</A>.
</P>
<P>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
diff --git a/doc/fix_orient_fcc.txt b/doc/fix_orient_fcc.txt
index 2f586125c5..6385b1870e 100644
--- a/doc/fix_orient_fcc.txt
+++ b/doc/fix_orient_fcc.txt
@@ -123,10 +123,9 @@ fix to add the potential energy of atom interactions with the grain
boundary driving force to the system's potential energy as part of
"thermodynamic output"_thermo_style.html.
-The atom/grain-boundary interaction energy can be printed as part of
-thermodynamic output via the keyword f_ID, where ID is the fix-ID of
-this fix. See the "thermo_style custom"_thermo_style.html command for
-details.
+The potential energy change due to this fix is stored as a scalar
+quantity, which can be accessed 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. This fix is not invoked during "energy
diff --git a/doc/fix_setforce.html b/doc/fix_setforce.html
index 1d68b32c0e..9b3f905102 100644
--- a/doc/fix_setforce.html
+++ b/doc/fix_setforce.html
@@ -41,15 +41,10 @@ alter the force component in that dimension.
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
are relevant to this fix.
</P>
-<P>The total vector force on the group of atoms before it is reset is
-stored by the fix and its components can be printed as part of
-thermodynamic output via the keywords f_ID[N] where ID is the fix-ID
-of this fix and N = 1,2,3. See the <A HREF = "thermo_style.html">thermo_style
-custom</A> command for details. Note that the fix
-stores the total force on the group of atoms, but the printed value
-may be normalized by the total number of atoms in the simulation
-depending on the <A HREF = "thermo_modify.html">thermo_modify norm</A> option being
-used.
+<P>This fix computes a 3-vector of forces, which can be accessed by
+various <A HREF = "Section_howto.html#4_15">output commands</A>. This is the total
+force on the group of atoms before the forces on individual atoms are
+reset by the fix.
</P>
<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
the <A HREF = "run.html">run</A> command.
diff --git a/doc/fix_setforce.txt b/doc/fix_setforce.txt
index 6c2180792a..29d12fe152 100644
--- a/doc/fix_setforce.txt
+++ b/doc/fix_setforce.txt
@@ -38,15 +38,10 @@ 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.
-The total vector force on the group of atoms before it is reset is
-stored by the fix and its components can be printed as part of
-thermodynamic output via the keywords f_ID\[N\] where ID is the fix-ID
-of this fix and N = 1,2,3. See the "thermo_style
-custom"_thermo_style.html command for details. Note that the fix
-stores the total force on the group of atoms, but the printed value
-may be normalized by the total number of atoms in the simulation
-depending on the "thermo_modify norm"_thermo_modify.html option being
-used.
+This fix computes a 3-vector of forces, which can be accessed by
+various "output commands"_Section_howto.html#4_15. This is the total
+force on the group of atoms before the forces on individual atoms are
+reset by the fix.
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command.
diff --git a/doc/fix_temp_rescale.html b/doc/fix_temp_rescale.html
index 8ddffc5bb0..bfc8b8d139 100644
--- a/doc/fix_temp_rescale.html
+++ b/doc/fix_temp_rescale.html
@@ -111,8 +111,11 @@ fix to add the energy change implied by a velocity rescaling to the
system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
output</A>. Note that because this fix is invoked
every N steps and thermodynamic info is printed every M steps, that
-unless M is a multiple of N, the energy contribution will not be for
-the current timestep.
+unless M is a multiple of N, the energy contribution will be zero.
+</P>
+<P>The potential energy change due to this fix is stored as a scalar
+quantity, which can be accessed by various <A HREF = "Section_howto.html#4_15">output
+commands</A>.
</P>
<P>The energy change can be printed as part of thermodynamic output via
the keyword f_ID, where ID is the fix-ID of this fix. See the
diff --git a/doc/fix_temp_rescale.txt b/doc/fix_temp_rescale.txt
index d56eea6968..c0bdf97db7 100644
--- a/doc/fix_temp_rescale.txt
+++ b/doc/fix_temp_rescale.txt
@@ -107,8 +107,11 @@ fix to add the energy change implied by a velocity rescaling to the
system's potential energy as part of "thermodynamic
output"_thermo_style.html. Note that because this fix is invoked
every N steps and thermodynamic info is printed every M steps, that
-unless M is a multiple of N, the energy contribution will not be for
-the current timestep.
+unless M is a multiple of N, the energy contribution will be zero.
+
+The potential energy change due to this fix is stored as a scalar
+quantity, which can be accessed by various "output
+commands"_Section_howto.html#4_15.
The energy change can be printed as part of thermodynamic output via
the keyword f_ID, where ID is the fix-ID of this fix. See the
diff --git a/doc/fix_wall_lj126.html b/doc/fix_wall_lj126.html
index 46dae8478f..3ddf4952c0 100644
--- a/doc/fix_wall_lj126.html
+++ b/doc/fix_wall_lj126.html
@@ -54,10 +54,9 @@ fix to add the energy of interaction between atoms and the wall to the
system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
output</A>.
</P>
-<P>The atom/wall interaction energy can be printed as part of
-thermodynamic output via the keyword f_ID, where ID is the fix-ID of
-this fix. See the <A HREF = "thermo_style.html">thermo_style custom</A> command for
-details.
+<P>This fix computes a scalar energy and a 3-vector of forces (on the
+wall), which can be accessed by various <A HREF = "Section_howto.html#4_15">output
+commands</A>.
</P>
<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
the <A HREF = "run.html">run</A> command.
diff --git a/doc/fix_wall_lj126.txt b/doc/fix_wall_lj126.txt
index 3bb4f10337..2b51378601 100644
--- a/doc/fix_wall_lj126.txt
+++ b/doc/fix_wall_lj126.txt
@@ -51,10 +51,9 @@ fix to add the energy of interaction between atoms and the wall to the
system's potential energy as part of "thermodynamic
output"_thermo_style.html.
-The atom/wall interaction energy can be printed as part of
-thermodynamic output via the keyword f_ID, where ID is the fix-ID of
-this fix. See the "thermo_style custom"_thermo_style.html command for
-details.
+This fix computes a scalar energy and a 3-vector of forces (on the
+wall), which can be accessed 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.
diff --git a/doc/fix_wall_lj93.html b/doc/fix_wall_lj93.html
index 116fa5ddef..d0f9f6d744 100644
--- a/doc/fix_wall_lj93.html
+++ b/doc/fix_wall_lj93.html
@@ -55,10 +55,9 @@ fix to add the energy of interaction between atoms and the wall to the
system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
output</A>.
</P>
-<P>The atom/wall interaction energy can be printed as part of
-thermodynamic output via the keyword f_ID, where ID is the fix-ID of
-this fix. See the <A HREF = "thermo_style.html">thermo_style custom</A> command for
-details.
+<P>This fix computes a scalar energy and a 3-vector of forces (on the
+wall), which can be accessed by various <A HREF = "Section_howto.html#4_15">output
+commands</A>.
</P>
<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
the <A HREF = "run.html">run</A> command.
diff --git a/doc/fix_wall_lj93.txt b/doc/fix_wall_lj93.txt
index 49fb34872a..3807aead23 100644
--- a/doc/fix_wall_lj93.txt
+++ b/doc/fix_wall_lj93.txt
@@ -52,10 +52,9 @@ fix to add the energy of interaction between atoms and the wall to the
system's potential energy as part of "thermodynamic
output"_thermo_style.html.
-The atom/wall interaction energy can be printed as part of
-thermodynamic output via the keyword f_ID, where ID is the fix-ID of
-this fix. See the "thermo_style custom"_thermo_style.html command for
-details.
+This fix computes a scalar energy and a 3-vector of forces (on the
+wall), which can be accessed 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.
diff --git a/doc/run.html b/doc/run.html
index 1d48c29962..8ec9405480 100644
--- a/doc/run.html
+++ b/doc/run.html
@@ -48,7 +48,7 @@ run 100000 every 1000 NULL
</P>
<P>Run or continue dynamics for a specified number of timesteps.
</P>
-<P>When the <A HREF = "doc/run_style.html">run style</A> is <I>respa</I>, N refers to outer
+<P>When the <A HREF = "run_style.html">run style</A> is <I>respa</I>, N refers to outer
loop (largest) timesteps.
</P>
<P>A value of N = 0 is acceptable; only the thermodynamics of the system
diff --git a/doc/run.txt b/doc/run.txt
index a53cdc34d3..bb09ef529f 100644
--- a/doc/run.txt
+++ b/doc/run.txt
@@ -41,7 +41,7 @@ run 100000 every 1000 NULL :pre
Run or continue dynamics for a specified number of timesteps.
-When the "run style"_doc/run_style.html is {respa}, N refers to outer
+When the "run style"_run_style.html is {respa}, N refers to outer
loop (largest) timesteps.
A value of N = 0 is acceptable; only the thermodynamics of the system
diff --git a/doc/thermo_style.html b/doc/thermo_style.html
index 4d0c794878..5a03705167 100644
--- a/doc/thermo_style.html
+++ b/doc/thermo_style.html
@@ -200,33 +200,44 @@ timesteps), where N is the value set by the <I>window</I> option of the
</P>
<HR>
-<P>The <I>c_ID</I> and <I>c_ID[N]</I> keywords allow scalar or vector quantities
-calculated by a compute to be output. The ID in the keyword should be
-replaced by the actual ID of the compute that has been defined
-elsewhere in the input script. See the <A HREF = "compute.html">compute</A> command
-for details. Note that only global scalar or vector quantites
-calculated by a compute can be output as thermodynamic data; per-atom
-quantities calcalated by a compute are output by the <A HREF = "dump.html">dump
-custom</A> command.
+<P>The <I>c_ID</I> and <I>c_ID[N]</I> keywords allow global scalar or vector
+quantities calculated by a compute to be output. The ID in the
+keyword should be replaced by the actual ID of the compute that has
+been defined elsewhere in the input script. See the
+<A HREF = "compute.html">compute</A> command for details. Note that only global
+scalar or vector quantites calculated by a compute can be output as
+thermodynamic data; per-atom quantities calcalated by a compute are
+output by the <A HREF = "dump.html">dump custom</A> command. Note that computes
+typically calculate global quantities that are summed over all atoms
+in the compute group. However the value printed by thermo_style
+custom may be normalized by the total number of atoms in the
+simulation depending on the <A HREF = "thermo_modify.html">thermo_modify norm</A>
+option being used.
</P>
<P>If <I>c_ID</I> is used as a keyword, then the scalar quantity calculated by
-the compute is printed. If <I>c_ID[N]</I> is used, then N in the range
-from 1-M will print the Nth component of the M-length vector
-calculated by the compute. See the doc pages for individual compute
-styles for info on what these quantities are.
-</P>
-<P>The <I>f_ID</I> and <I>f_ID[N]</I> keywords allow scalar or vector quantities
-calculated by a fix to be output. The ID in the keyword should be
-replaced by the actual ID of the fix that has been defined elsewhere
-in the input script.
+the compute is printed. If <I>c_ID[N]</I> is used, then the compute must
+calculate a vector quantity and N must be an index from 1 to M where M
+is the length of the vector calculated by the compute. See the doc
+pages for individual compute styles for info on what these quantities
+are.
+</P>
+<P>The <I>f_ID</I> and <I>f_ID[N]</I> keywords allow global scalar or vector
+quantities calculated by a fix to be output. The ID in the keyword
+should be replaced by the actual ID of the fix that has been defined
+elsewhere in the input script. Note that fixes typically calculate
+global quantities that are summed over all atoms in the fix group.
+However the value printed by thermo_style custom may be normalized by
+the total number of atoms in the simulation depending on the
+<A HREF = "thermo_modify.html">thermo_modify norm</A> option being used.
</P>
<P>If <I>f_ID</I> is used as a keyword, then the scalar quantity calculated by
-the fix is printed. If <I>f_ID[N]</I> is used, then N in the range from
-1-M will print the Nth component of the M-length vector calculated by
-the fix. See the doc pages for individual fix styles for info on what
-these quantities are. For fixes that compute a contribution to the
-potential energy of the system, the scalar quantity f_ID is typically
-that quantity.
+the fix is printed. If <I>f_ID[N]</I> is used, then the fix must
+calculate a vector quantity and N must be an index from 1 to M where M
+is the length of the vector calculated by the fix. See the doc pages
+for individual fix styles for info on which fixes calculate these
+global quantities and what they quantities are. For fixes that
+compute a contribution to the potential energy of the system, the
+scalar quantity f_ID is typically that quantity.
</P>
<P>The <I>v_name</I> keyword allow the current value of a variable to be
output. The name in the keyword should be replaced by the actual namd
diff --git a/doc/thermo_style.txt b/doc/thermo_style.txt
index 8a5c4efc2f..9216d24252 100644
--- a/doc/thermo_style.txt
+++ b/doc/thermo_style.txt
@@ -194,33 +194,44 @@ timesteps), where N is the value set by the {window} option of the
:line
-The {c_ID} and {c_ID\[N\]} keywords allow scalar or vector quantities
-calculated by a compute to be output. The ID in the keyword should be
-replaced by the actual ID of the compute that has been defined
-elsewhere in the input script. See the "compute"_compute.html command
-for details. Note that only global scalar or vector quantites
-calculated by a compute can be output as thermodynamic data; per-atom
-quantities calcalated by a compute are output by the "dump
-custom"_dump.html command.
+The {c_ID} and {c_ID\[N\]} keywords allow global scalar or vector
+quantities calculated by a compute to be output. The ID in the
+keyword should be replaced by the actual ID of the compute that has
+been defined elsewhere in the input script. See the
+"compute"_compute.html command for details. Note that only global
+scalar or vector quantites calculated by a compute can be output as
+thermodynamic data; per-atom quantities calcalated by a compute are
+output by the "dump custom"_dump.html command. Note that computes
+typically calculate global quantities that are summed over all atoms
+in the compute group. However the value printed by thermo_style
+custom may be normalized by the total number of atoms in the
+simulation depending on the "thermo_modify norm"_thermo_modify.html
+option being used.
If {c_ID} is used as a keyword, then the scalar quantity calculated by
-the compute is printed. If {c_ID\[N\]} is used, then N in the range
-from 1-M will print the Nth component of the M-length vector
-calculated by the compute. See the doc pages for individual compute
-styles for info on what these quantities are.
-
-The {f_ID} and {f_ID\[N\]} keywords allow scalar or vector quantities
-calculated by a fix to be output. The ID in the keyword should be
-replaced by the actual ID of the fix that has been defined elsewhere
-in the input script.
+the compute is printed. If {c_ID\[N\]} is used, then the compute must
+calculate a vector quantity and N must be an index from 1 to M where M
+is the length of the vector calculated by the compute. See the doc
+pages for individual compute styles for info on what these quantities
+are.
+
+The {f_ID} and {f_ID\[N\]} keywords allow global scalar or vector
+quantities calculated by a fix to be output. The ID in the keyword
+should be replaced by the actual ID of the fix that has been defined
+elsewhere in the input script. Note that fixes typically calculate
+global quantities that are summed over all atoms in the fix group.
+However the value printed by thermo_style custom may be normalized by
+the total number of atoms in the simulation depending on the
+"thermo_modify norm"_thermo_modify.html option being used.
If {f_ID} is used as a keyword, then the scalar quantity calculated by
-the fix is printed. If {f_ID\[N\]} is used, then N in the range from
-1-M will print the Nth component of the M-length vector calculated by
-the fix. See the doc pages for individual fix styles for info on what
-these quantities are. For fixes that compute a contribution to the
-potential energy of the system, the scalar quantity f_ID is typically
-that quantity.
+the fix is printed. If {f_ID\[N\]} is used, then the fix must
+calculate a vector quantity and N must be an index from 1 to M where M
+is the length of the vector calculated by the fix. See the doc pages
+for individual fix styles for info on which fixes calculate these
+global quantities and what they quantities are. For fixes that
+compute a contribution to the potential energy of the system, the
+scalar quantity f_ID is typically that quantity.
The {v_name} keyword allow the current value of a variable to be
output. The name in the keyword should be replaced by the actual namd
diff --git a/doc/variable.html b/doc/variable.html
index 19fcaf887b..42582fd3f4 100644
--- a/doc/variable.html
+++ b/doc/variable.html
@@ -39,6 +39,7 @@
vx[], vy[], vz[],
fx[], fy[], fz[]
compute references = c_ID[0], c_ID[N]
+ fix references = f_ID[0], f_ID[N]
other variables = v_abc, v_x, etc
</PRE>
@@ -211,6 +212,7 @@ variables; the syntax of Atom vector references is different.
<TR><TD >Atom vectors for <I>equal</I></TD><TD > mass[N], x[N], y[N], z[N], vx[N], vy[N], vz[N], fx[N], fy[N], fz[N]</TD></TR>
<TR><TD >Atom vectors for <I>atom</I></TD><TD > mass[], x[], y[], z[], vx[], vy[], vz[], fx[], fy[], fz[]</TD></TR>
<TR><TD >Compute references</TD><TD > c_ID[0], c_ID[N]</TD></TR>
+<TR><TD >Fix references</TD><TD > f_ID[0], f_ID[N]</TD></TR>
<TR><TD >Other variables</TD><TD > v_abc, v_x, etc
</TD></TR></TABLE></DIV>
@@ -252,9 +254,26 @@ per-atom quantities calculated by a compute cannot be accessed this
way, but only global scalar or vector quantities.
</P>
<P>If <I>c_ID[0]</I> is used as a keyword, then the scalar quantity
-calculated by the compute is printed. If <I>c_ID[N]</I> is used, then N
-in the range from 1-M will print the Mth component of the N-length
-vector calculated by the compute.
+calculated by the compute is used. If <I>c_ID[N]</I> is used, then one
+component of the vector quantity calculated by the compute is used. N
+should be an integer from 1-M, where M is the length of the vector
+calculated by the compute.
+</P>
+<P>Fix references access scalar or vector quantities calculated by a
+<A HREF = "fix.html">fix</A>. See the doc pages for individual fixes to see which
+ones compute a scalar or vector quantity. Since the fix may not be
+invoked every timestep and compute its quantities, you should insure
+the variable is only evaluated on appropriate timesteps. The ID in
+the reference should be replaced by the actual ID of the fix defined
+elsewhere in the input script. See the <A HREF = "fix.html">fix</A> command for
+details. Note that per-atom quantities calculated by a fix cannot be
+accessed this way, but only global scalar or vector quantities.
+</P>
+<P>If <I>f_ID[0]</I> is used as a keyword, then the scalar quantity
+calculated by the fix is used. If <I>f_ID[N]</I> is used, then one
+component of the vector quantity calculated by the fix is used. N
+should be an integer from 1-M, where M is the length of the vector
+calculated by the fix.
</P>
<P>The current values of other variables can be accessed by prepending a
"v_" to the variable name. This will cause the other variable to be
diff --git a/doc/variable.txt b/doc/variable.txt
index 27d2753c6c..3ed55a90dc 100644
--- a/doc/variable.txt
+++ b/doc/variable.txt
@@ -34,6 +34,7 @@ style = {index} or {loop} or {world} or {universe} or {uloop} or {equal} or {ato
vx\[\], vy\[\], vz\[\],
fx\[\], fy\[\], fz\[\]
compute references = c_ID\[0\], c_ID\[N\]
+ fix references = f_ID\[0\], f_ID\[N\]
other variables = v_abc, v_x, etc :pre
:ule
@@ -210,6 +211,7 @@ Atom vectors for {atom}: mass\[\], x\[\], y\[\], z\[\], \
vx\[\], vy\[\], vz\[\], \
fx\[\], fy\[\], fz\[\]
Compute references: c_ID\[0\], c_ID\[N\]
+Fix references: f_ID\[0\], f_ID\[N\]
Other variables: v_abc, v_x, etc :tb(s=:)
The thermo keywords allowed in the equation are those defined by the
@@ -250,9 +252,26 @@ per-atom quantities calculated by a compute cannot be accessed this
way, but only global scalar or vector quantities.
If {c_ID\[0\]} is used as a keyword, then the scalar quantity
-calculated by the compute is printed. If {c_ID\[N\]} is used, then N
-in the range from 1-M will print the Mth component of the N-length
-vector calculated by the compute.
+calculated by the compute is used. If {c_ID\[N\]} is used, then one
+component of the vector quantity calculated by the compute is used. N
+should be an integer from 1-M, where M is the length of the vector
+calculated by the compute.
+
+Fix references access scalar or vector quantities calculated by a
+"fix"_fix.html. See the doc pages for individual fixes to see which
+ones compute a scalar or vector quantity. Since the fix may not be
+invoked every timestep and compute its quantities, you should insure
+the variable is only evaluated on appropriate timesteps. The ID in
+the reference should be replaced by the actual ID of the fix defined
+elsewhere in the input script. See the "fix"_fix.html command for
+details. Note that per-atom quantities calculated by a fix cannot be
+accessed this way, but only global scalar or vector quantities.
+
+If {f_ID\[0\]} is used as a keyword, then the scalar quantity
+calculated by the fix is used. If {f_ID\[N\]} is used, then one
+component of the vector quantity calculated by the fix is used. N
+should be an integer from 1-M, where M is the length of the vector
+calculated by the fix.
The current values of other variables can be accessed by prepending a
"v_" to the variable name. This will cause the other variable to be
--
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