diff --git a/doc/thermo.html b/doc/thermo.html
index 3255ee61b..aa36e9eb5 100644
--- a/doc/thermo.html
+++ b/doc/thermo.html
@@ -1,49 +1,64 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>thermo command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>thermo N
</PRE>
-<UL><LI>N = output thermodynamics every N timesteps
+<UL><LI>N = output thermodynamics every N timesteps
+<LI>N can be a variable (see below)
</UL>
<P><B>Examples:</B>
</P>
<PRE>thermo 100
</PRE>
<P><B>Description:</B>
</P>
<P>Compute and print thermodynamic info (e.g. temperature, energy,
pressure) on timesteps that are a multiple of N and at the beginning
and end of a simulation. A value of 0 will only print thermodynamics
at the beginning and end.
</P>
<P>The content and format of what is printed is controlled by the
<A HREF = "thermo_style.html">thermo_style</A> and
<A HREF = "thermo_modify.html">thermo_modify</A> commands.
</P>
-<P>The timesteps on which thermo output is written can also be controlled
-by a <A HREF = "variable.html">variable</A>. See the <A HREF = "thermo_modify.html">thermo_modify
-every</A> command.
+<P>Instead of a numeric value, N can be specifed as an <A HREF = "variable.html">equal-style
+variable</A>, which should be specified as v_name, where
+name is the variable name. In this case, the variable is evaluated at
+the beginning of a run to determine the next timestep at which
+thermodynamic info will be written out. On that timestep, the
+variable will be evaluated again to determine the next timestep, etc.
+Thus the variable should return timestep values. See the stagger()
+and logfreq() and stride() math functions for <A HREF = "variable.html">equal-style
+variables</A>, as examples of useful functions to use in
+this context. Other similar math functions could easily be added as
+options for <A HREF = "variable.html">equal-style variables</A>.
</P>
+<P>For example, the following commands will output thermodynamic info at
+timesteps 0,10,20,30,100,200,300,1000,2000,etc:
+</P>
+<PRE>variable s equal logfreq(10,3,10)
+thermo v_s
+</PRE>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "thermo_style.html">thermo_style</A>, <A HREF = "thermo_modify.html">thermo_modify</A>
</P>
<P><B>Default:</B>
</P>
<PRE>thermo 0
</PRE>
</HTML>
diff --git a/doc/thermo.txt b/doc/thermo.txt
index 345637a90..5001fb3c2 100644
--- a/doc/thermo.txt
+++ b/doc/thermo.txt
@@ -1,44 +1,59 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
thermo command :h3
[Syntax:]
thermo N :pre
-N = output thermodynamics every N timesteps :ul
+N = output thermodynamics every N timesteps
+N can be a variable (see below) :ul
[Examples:]
thermo 100 :pre
[Description:]
Compute and print thermodynamic info (e.g. temperature, energy,
pressure) on timesteps that are a multiple of N and at the beginning
and end of a simulation. A value of 0 will only print thermodynamics
at the beginning and end.
The content and format of what is printed is controlled by the
"thermo_style"_thermo_style.html and
"thermo_modify"_thermo_modify.html commands.
-The timesteps on which thermo output is written can also be controlled
-by a "variable"_variable.html. See the "thermo_modify
-every"_thermo_modify.html command.
+Instead of a numeric value, N can be specifed as an "equal-style
+variable"_variable.html, which should be specified as v_name, where
+name is the variable name. In this case, the variable is evaluated at
+the beginning of a run to determine the next timestep at which
+thermodynamic info will be written out. On that timestep, the
+variable will be evaluated again to determine the next timestep, etc.
+Thus the variable should return timestep values. See the stagger()
+and logfreq() and stride() math functions for "equal-style
+variables"_variable.html, as examples of useful functions to use in
+this context. Other similar math functions could easily be added as
+options for "equal-style variables"_variable.html.
+
+For example, the following commands will output thermodynamic info at
+timesteps 0,10,20,30,100,200,300,1000,2000,etc:
+
+variable s equal logfreq(10,3,10)
+thermo v_s :pre
[Restrictions:] none
[Related commands:]
"thermo_style"_thermo_style.html, "thermo_modify"_thermo_modify.html
[Default:]
thermo 0 :pre
diff --git a/doc/thermo_modify.html b/doc/thermo_modify.html
index 90842ab0f..bca7aa633 100644
--- a/doc/thermo_modify.html
+++ b/doc/thermo_modify.html
@@ -1,193 +1,161 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>thermo_modify command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>thermo_modify keyword value ...
</PRE>
<UL><LI>one or more keyword/value pairs may be listed
-<LI>keyword = <I>lost</I> or <I>norm</I> or <I>flush</I> or <I>line</I> or <I>format</I> or <I>temp</I> or <I>press</I> or <I>every</I>
-
-<PRE> <I>lost</I> value = <I>error</I> or <I>warn</I> or <I>ignore</I>
+keyword = <I>lost</I> or <I>norm</I> or <I>flush</I> or <I>line</I> or <I>format</I> or <I>temp</I> or <I>press</I>:l
+ <I>lost</I> value = <I>error</I> or <I>warn</I> or <I>ignore</I>
<I>norm</I> value = <I>yes</I> or <I>no</I>
<I>flush</I> value = <I>yes</I> or <I>no</I>
<I>line</I> value = <I>one</I> or <I>multi</I>
<I>format</I> values = <I>int</I> string or <I>float</I> string or M string
M = integer from 1 to N, where N = # of quantities being printed
string = C-style format string
<I>temp</I> value = compute ID that calculates a temperature
<I>press</I> value = compute ID that calculates a pressure
- <I>every</I> value = v_name
- v_name = an equal-style variable name
-</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>thermo_modify lost ignore flush yes
thermo_modify temp myTemp format 3 %15.8g
thermo_modify line multi format float %g
</PRE>
<P><B>Description:</B>
</P>
<P>Set options for how thermodynamic information is computed and printed
by LAMMPS.
</P>
<P>IMPORTANT NOTE: These options apply to the currently defined thermo
style. When you specify a <A HREF = "thermo_style.html">thermo_style</A> command,
all thermodynamic settings are restored to their default values,
including those previously reset by a thermo_modify command. Thus if
your input script specifies a thermo_style command, you should use the
thermo_modify command after it.
</P>
<P>The <I>lost</I> keyword determines whether LAMMPS checks for lost atoms
each time it computes thermodynamics and what it does if atoms are
lost. An atom can be "lost" if it moves across a non-periodic
simulation box <A HREF = "boundary.html">boundary</A> or if it moves more than a box
length outside the simulation domain (or more than a processor
sub-domain length) before reneighboring occurs. The latter case is
typically due to bad dynamics, e.g. too large a timestep or huge
forces and velocities. If the value is <I>ignore</I>, LAMMPS does not
check for lost atoms. If the value is <I>error</I> or <I>warn</I>, LAMMPS
checks and either issues an error or warning. The code will exit with
an error and continue with a warning. A warning will only be issued
once, the first time an atom is lost. This can be a useful debugging
option.
</P>
<P>The <I>norm</I> keyword determines whether various thermodynamic output
values are normalized by the number of atoms or not, depending on
whether it is set to <I>yes</I> or <I>no</I>. Different unit styles have
different defaults for this setting (see below). Even if <I>norm</I> is
set to <I>yes</I>, a value is only normalized if it is an "extensive"
quantity, meaning that it scales with the number of atoms in the
system. For the thermo keywords described by the doc page for the
<A HREF = "thermo_style.html">thermo_style</A> command, all energy-related keywords
are extensive, such as <I>pe</I> or <I>ebond</I> or <I>enthalpy</I>. Other keywords
such as <I>temp</I> or <I>press</I> are "intensive" meaning their value is
independent (in a statistical sense) of the number of atoms in the
system and thus are never normalized. For thermodynamic output values
extracted from fixes and computes in a <A HREF = "thermo_style.html">thermo_style
custom</A> command, the doc page for the individual
<A HREF = "fix.html">fix</A> or <A HREF = "compute.html">compute</A> lists whether the value is
"extensive" or "intensive" and thus whether it is normalized.
Thermodynamic output values calculated by a variable formula are
assumed to be "intensive" and thus are never normalized. You can
always include a divide by the number of atoms in the variable formula
if this is not the case.
</P>
<P>The <I>flush</I> keyword invokes a flush operation after thermodynamic info
is written to the log file. This insures the output in that file is
current (no buffering by the OS), even if LAMMPS halts before the
simulation completes.
</P>
<P>The <I>line</I> keyword determines whether thermodynamics will be printed
as a series of numeric values on one line or in a multi-line format
with 3 quantities with text strings per line and a dashed-line header
containing the timestep and CPU time. This modify option overrides
the <I>one</I> and <I>multi</I> thermo_style settings.
</P>
<P>The <I>format</I> keyword sets the numeric format of individual printed
quantities. The <I>int</I> and <I>float</I> keywords set the format for all
integer or floating-point quantities printed. The setting with a
numeric value M (e.g. format 5 %10.4g) sets the format of the Mth
value printed in each output line, e.g. the 5th column of output in
this case. If the format for a specific column has been set, it will
take precedent over the <I>int</I> or <I>float</I> setting.
</P>
<P>IMPORTANT NOTE: The thermo output values <I>step</I> and <I>atoms</I> are stored
internally as 8-byte signed integers, rather than the usual 4-byte
signed integers. When specifying the "format int" keyword you can use
a "%d"-style format identifier in the format string and LAMMPS will
convert this to the corresponding "%lu" form when it is applied to
those keywords. However, when specifying the "format M string"
keyword for <I>step</I> and <I>natoms</I>, you should specify a string
appropriate for an 8-byte signed integer, e.g. one with "%ld".
</P>
<P>The <I>temp</I> keyword is used to determine how thermodynamic temperature
is calculated, which is used by all thermo quantities that require a
temperature ("temp", "press", "ke", "etotal", "enthalpy", "pxx", etc).
The specified compute ID must have been previously defined by the user
via the <A HREF = "compute.html">compute</A> command and it must be a style of
compute that calculates a temperature. As described in the
<A HREF = "thermo_style.html">thermo_style</A> command, thermo output uses a default
compute for temperature with ID = <I>thermo_temp</I>. This option allows
the user to override the default.
</P>
<P>The <I>press</I> keyword is used to determine how thermodynamic pressure is
calculated, which is used by all thermo quantities that require a
pressure ("press", "enthalpy", "pxx", etc). The specified compute ID
must have been previously defined by the user via the
<A HREF = "compute.html">compute</A> command and it must be a style of compute that
calculates a pressure. As described in the
<A HREF = "thermo_style.html">thermo_style</A> command, thermo output uses a default
compute for pressure with ID = <I>thermo_press</I>. This option allows the
user to override the default.
</P>
<P>IMPORTANT NOTE: If both the <I>temp</I> and <I>press</I> keywords are used in a
single thermo_modify command (or in two separate commands), then the
order in which the keywords are specified is important. Note that a
<A HREF = "compute_pressure.html">pressure compute</A> defines its own temperature
compute as an argument when it is specified. The <I>temp</I> keyword will
override this (for the pressure compute being used by thermodynamics),
but only if the <I>temp</I> keyword comes after the <I>press</I> keyword. If
the <I>temp</I> keyword comes before the <I>press</I> keyword, then the new
pressure compute specified by the <I>press</I> keyword will be unaffected
by the <I>temp</I> setting.
</P>
-<P>The <I>every</I> keyword allows a variable to be specified which will
-determine which timesteps thermodynamic output is generated. It must
-be an <A HREF = "variable.html">equal-style variable</A>, and is specified as
-v_name, where name is the variable name. The variable is evaluated at
-the beginning of a run to determine the next timestep at which a dump
-snapshot will be written out. On that timestep, the variable will be
-evaluated again to determine the next timestep, etc. Thus the
-variable should return timestep values. See the stagger() and
-logfreq() and stride() math functions for <A HREF = "variable.html">equal-style
-variables</A>, as examples of useful functions to use in
-this context. Other similar math functions could easily be added as
-options for <A HREF = "variable.html">equal-style variables</A>. In addition,
-thermodynamic output will always occur on the first and last timestep
-of each run.
-</P>
-<P>For example, the following commands will output thermodynamic info at
-timesteps 0,10,20,30,100,200,300,1000,2000,etc:
-</P>
-<PRE>variable s equal logfreq(10,3,10)
-thermo_modify 1 every v_s
-</PRE>
-<P>Note that the <I>every</I> keyword overrides the output frequency setting
-made by the <A HREF = "thermo.html">thermo</A> command, by setting it to 0. If the
-<A HREF = "thermo.html">thermo</A> command is later used to set the output frequency
-to a non-zero value, then the variable setting of the thermo_modify
-every command will be overridden.
-</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "thermo.html">thermo</A>, <A HREF = "thermo_style.html">thermo_style</A>
</P>
<P><B>Default:</B>
</P>
<P>The option defaults are lost = error, norm = yes for unit style of
<I>lj</I>, norm = no for unit style of <I>real</I> and <I>metal</I>, flush = no,
-temp/press = compute IDs defined by thermo_style, every = non-variable
-setting provided by the <A HREF = "thermo.html">thermo</A> command.
+and temp/press = compute IDs defined by thermo_style.
</P>
<P>The defaults for the line and format options depend on the thermo
style. For styles "one" and "custom", the line and format defaults
are "one", "%8d", and "%12.8g". For style "multi", the line and
format defaults are "multi", "%8d", and "%14.4f".
</P>
</HTML>
diff --git a/doc/thermo_modify.txt b/doc/thermo_modify.txt
index 5d983afdf..ce9ceea5a 100644
--- a/doc/thermo_modify.txt
+++ b/doc/thermo_modify.txt
@@ -1,185 +1,155 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
thermo_modify command :h3
[Syntax:]
thermo_modify keyword value ... :pre
one or more keyword/value pairs may be listed :ulb,l
-keyword = {lost} or {norm} or {flush} or {line} or {format} or {temp} or {press} or {every} :l
+keyword = {lost} or {norm} or {flush} or {line} or {format} or {temp} or {press}:l
{lost} value = {error} or {warn} or {ignore}
{norm} value = {yes} or {no}
{flush} value = {yes} or {no}
{line} value = {one} or {multi}
{format} values = {int} string or {float} string or M string
M = integer from 1 to N, where N = # of quantities being printed
string = C-style format string
{temp} value = compute ID that calculates a temperature
{press} value = compute ID that calculates a pressure
- {every} value = v_name
- v_name = an equal-style variable name :pre
:ule
[Examples:]
thermo_modify lost ignore flush yes
thermo_modify temp myTemp format 3 %15.8g
thermo_modify line multi format float %g :pre
[Description:]
Set options for how thermodynamic information is computed and printed
by LAMMPS.
IMPORTANT NOTE: These options apply to the currently defined thermo
style. When you specify a "thermo_style"_thermo_style.html command,
all thermodynamic settings are restored to their default values,
including those previously reset by a thermo_modify command. Thus if
your input script specifies a thermo_style command, you should use the
thermo_modify command after it.
The {lost} keyword determines whether LAMMPS checks for lost atoms
each time it computes thermodynamics and what it does if atoms are
lost. An atom can be "lost" if it moves across a non-periodic
simulation box "boundary"_boundary.html or if it moves more than a box
length outside the simulation domain (or more than a processor
sub-domain length) before reneighboring occurs. The latter case is
typically due to bad dynamics, e.g. too large a timestep or huge
forces and velocities. If the value is {ignore}, LAMMPS does not
check for lost atoms. If the value is {error} or {warn}, LAMMPS
checks and either issues an error or warning. The code will exit with
an error and continue with a warning. A warning will only be issued
once, the first time an atom is lost. This can be a useful debugging
option.
The {norm} keyword determines whether various thermodynamic output
values are normalized by the number of atoms or not, depending on
whether it is set to {yes} or {no}. Different unit styles have
different defaults for this setting (see below). Even if {norm} is
set to {yes}, a value is only normalized if it is an "extensive"
quantity, meaning that it scales with the number of atoms in the
system. For the thermo keywords described by the doc page for the
"thermo_style"_thermo_style.html command, all energy-related keywords
are extensive, such as {pe} or {ebond} or {enthalpy}. Other keywords
such as {temp} or {press} are "intensive" meaning their value is
independent (in a statistical sense) of the number of atoms in the
system and thus are never normalized. For thermodynamic output values
extracted from fixes and computes in a "thermo_style
custom"_thermo_style.html command, the doc page for the individual
"fix"_fix.html or "compute"_compute.html lists whether the value is
"extensive" or "intensive" and thus whether it is normalized.
Thermodynamic output values calculated by a variable formula are
assumed to be "intensive" and thus are never normalized. You can
always include a divide by the number of atoms in the variable formula
if this is not the case.
The {flush} keyword invokes a flush operation after thermodynamic info
is written to the log file. This insures the output in that file is
current (no buffering by the OS), even if LAMMPS halts before the
simulation completes.
The {line} keyword determines whether thermodynamics will be printed
as a series of numeric values on one line or in a multi-line format
with 3 quantities with text strings per line and a dashed-line header
containing the timestep and CPU time. This modify option overrides
the {one} and {multi} thermo_style settings.
The {format} keyword sets the numeric format of individual printed
quantities. The {int} and {float} keywords set the format for all
integer or floating-point quantities printed. The setting with a
numeric value M (e.g. format 5 %10.4g) sets the format of the Mth
value printed in each output line, e.g. the 5th column of output in
this case. If the format for a specific column has been set, it will
take precedent over the {int} or {float} setting.
IMPORTANT NOTE: The thermo output values {step} and {atoms} are stored
internally as 8-byte signed integers, rather than the usual 4-byte
signed integers. When specifying the "format int" keyword you can use
a "%d"-style format identifier in the format string and LAMMPS will
convert this to the corresponding "%lu" form when it is applied to
those keywords. However, when specifying the "format M string"
keyword for {step} and {natoms}, you should specify a string
appropriate for an 8-byte signed integer, e.g. one with "%ld".
The {temp} keyword is used to determine how thermodynamic temperature
is calculated, which is used by all thermo quantities that require a
temperature ("temp", "press", "ke", "etotal", "enthalpy", "pxx", etc).
The specified compute ID must have been previously defined by the user
via the "compute"_compute.html command and it must be a style of
compute that calculates a temperature. As described in the
"thermo_style"_thermo_style.html command, thermo output uses a default
compute for temperature with ID = {thermo_temp}. This option allows
the user to override the default.
The {press} keyword is used to determine how thermodynamic pressure is
calculated, which is used by all thermo quantities that require a
pressure ("press", "enthalpy", "pxx", etc). The specified compute ID
must have been previously defined by the user via the
"compute"_compute.html command and it must be a style of compute that
calculates a pressure. As described in the
"thermo_style"_thermo_style.html command, thermo output uses a default
compute for pressure with ID = {thermo_press}. This option allows the
user to override the default.
IMPORTANT NOTE: If both the {temp} and {press} keywords are used in a
single thermo_modify command (or in two separate commands), then the
order in which the keywords are specified is important. Note that a
"pressure compute"_compute_pressure.html defines its own temperature
compute as an argument when it is specified. The {temp} keyword will
override this (for the pressure compute being used by thermodynamics),
but only if the {temp} keyword comes after the {press} keyword. If
the {temp} keyword comes before the {press} keyword, then the new
pressure compute specified by the {press} keyword will be unaffected
by the {temp} setting.
-The {every} keyword allows a variable to be specified which will
-determine which timesteps thermodynamic output is generated. It must
-be an "equal-style variable"_variable.html, and is specified as
-v_name, where name is the variable name. The variable is evaluated at
-the beginning of a run to determine the next timestep at which a dump
-snapshot will be written out. On that timestep, the variable will be
-evaluated again to determine the next timestep, etc. Thus the
-variable should return timestep values. See the stagger() and
-logfreq() and stride() math functions for "equal-style
-variables"_variable.html, as examples of useful functions to use in
-this context. Other similar math functions could easily be added as
-options for "equal-style variables"_variable.html. In addition,
-thermodynamic output will always occur on the first and last timestep
-of each run.
-
-For example, the following commands will output thermodynamic info at
-timesteps 0,10,20,30,100,200,300,1000,2000,etc:
-
-variable s equal logfreq(10,3,10)
-thermo_modify 1 every v_s :pre
-
-Note that the {every} keyword overrides the output frequency setting
-made by the "thermo"_thermo.html command, by setting it to 0. If the
-"thermo"_thermo.html command is later used to set the output frequency
-to a non-zero value, then the variable setting of the thermo_modify
-every command will be overridden.
-
[Restrictions:] none
[Related commands:]
"thermo"_thermo.html, "thermo_style"_thermo_style.html
[Default:]
The option defaults are lost = error, norm = yes for unit style of
{lj}, norm = no for unit style of {real} and {metal}, flush = no,
-temp/press = compute IDs defined by thermo_style, every = non-variable
-setting provided by the "thermo"_thermo.html command.
+and temp/press = compute IDs defined by thermo_style.
The defaults for the line and format options depend on the thermo
style. For styles "one" and "custom", the line and format defaults
are "one", "%8d", and "%12.8g". For style "multi", the line and
format defaults are "multi", "%8d", and "%14.4f".