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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4481 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2010-08-12 23:10:38 +00:00
parent 42d50bb8fa
commit 6ec5653000
26 changed files with 169 additions and 169 deletions
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10
doc/dump_modify.html
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@ -83,11 +83,11 @@ atom types.
the <A HREF = "dump.html">dump</A> command to a new value. The every keyword can be
specified in one of two ways. It can be a numeric value in which case
it must be > 0. Or it can be 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 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
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 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() 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

10
doc/dump_modify.txt
View File

@ -76,11 +76,11 @@ The {every} keyword changes the dump frequency originally specified by
the "dump"_dump.html command to a new value. The every keyword can be
specified in one of two ways. It can be a numeric value in which case
it must be > 0. Or it can be 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 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
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 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() 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

52
doc/fix_adapt.html
View File

@ -25,23 +25,23 @@
<LI>keyword = <I>pair</I> or <I>atom</I>
<PRE> <I>pair</I> args = pstyle param I J variable
<PRE> <I>pair</I> args = pstyle pparam I J v_name
pstyle = pair style name, e.g. lj/cut
pparam = parameter to adapt over time
I,J = type pair(s) to set parameter for
pvariable = name of variable that calculates value of parameter
<I>atom</I> args = param variable
v_name = variable with name that calculates value of pparam
<I>atom</I> args = aparam v_name
aparam = parameter to adapt over time
avariable = name of variable that calculates value of parameter
v_name = variable with name that calculates value of aparam
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 1 all adapt 1 pair soft a 1 1 prefactor
fix 1 all adapt 1 pair soft a 2* 3 prefactor
fix 1 all adapt 1 pair soft a * * prefactor soft a 3 3 prefactor2
fix 1 all adapt 10 atom diameter size
<PRE>fix 1 all adapt 1 pair soft a 1 1 v_prefactor
fix 1 all adapt 1 pair soft a 2* 3 v_prefactor
fix 1 all adapt 1 pair soft a * * v_prefactor soft a 3 3 v_prefactor2
fix 1 all adapt 10 atom diameter v_size
</PRE>
<P><B>Description:</B>
</P>
@ -101,13 +101,14 @@ asterisks imply type pairs where J < I, they are ignored.
<P>If a global parameter is specified, the <I>I</I> and <I>J</I> settings still
need to be specified, but are ignored.
</P>
<P>The <I>pvariable</I> argument is the name of an equal-style
<A HREF = "variable.html">variable</A> which will be evaluated each time this fix is
invoked to set the parameter to a new value. Equal-style variables
can specify formulas with various mathematical functions, and include
<A HREF = "thermo_style.html">thermo_style</A> command keywords for the simulation
box parameters and timestep and elapsed time. Thus it is easy to
specify parameters that change as a function of time or span
<P>The <I>v_name</I> argument for keyword <I>pair</I> is the name of an
<A HREF = "variable.html">equal-style variable</A> which will be evaluated each time
this fix is invoked to set the parameter to a new value. It should be
specified as v_name, where name is the variable name. Equal-style
variables can specify formulas with various mathematical functions,
and include <A HREF = "thermo_style.html">thermo_style</A> command keywords for the
simulation box parameters and timestep and elapsed time. Thus it is
easy to specify parameters that change as a function of time or span
consecutive runs in a continuous fashion. For the latter, see the
<I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command and the
<I>elaplong</I> keyword of <A HREF = "thermo_style.html">thermo_style custom</A> for
@ -118,7 +119,7 @@ the <A HREF = "pair_soft.html">pair_style soft</A> potential from 10.0 to 30.0 i
linear fashion over the course of a simulation:
</P>
<PRE>variable prefactor equal ramp(10,30)
fix 1 all adapt 1 pair soft a * * prefactor
fix 1 all adapt 1 pair soft a * * v_prefactor
</PRE>
<P>The <I>atom</I> keyword enables various atom properties to be changed. The
<I>aparam</I> argument is the name of the parameter to change. This is the
@ -126,21 +127,20 @@ current list of atom parameters that can be varied by this fix:
</P>
<UL><LI>diameter = diameter of particle
</UL>
<P>The <I>avariable</I> argument is the name of an equal-style
<A HREF = "variable.html">variable</A> which will be evaluated each time this fix is
invoked to set the parameter to a new value. See the discussion above
describing the formulas associated with equal-style variables. The
new value is assigned to the corresponding attribute for all atoms in
the fix group.
<P>The <I>v_name</I> argument of the <I>atom</I> keyword is the name of an
<A HREF = "variable.html">equal-style variable</A> which will be evaluated each time
this fix is invoked to set the parameter to a new value. It should be
specified as v_name, where name is the variable name. See the
discussion above describing the formulas associated with equal-style
variables. The new value is assigned to the corresponding attribute
for all atoms in the fix group.
</P>
<P>For example, these commands would shrink the diameter of all granular
particles in the "center" group from 1.0 to 0.1 in a linear fashion
over the course of a 1000-step simulation:
</P>
<PRE>variable start equal 1.0
variable stop equal 0.1
variable size equal ramp(1.0,0.1)
fix 1 center adapt 10 atom diameter size
<PRE>variable size equal ramp(1.0,0.1)
fix 1 center adapt 10 atom diameter v_size
</PRE>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>

50
doc/fix_adapt.txt
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@ -16,22 +16,22 @@ adapt = style name of this fix command :l
N = adapt simulation settings every this many timesteps :l
one or more keyword/value pairs may be appended :l
keyword = {pair} or {atom} :l
{pair} args = pstyle param I J variable
{pair} args = pstyle pparam I J v_name
pstyle = pair style name, e.g. lj/cut
pparam = parameter to adapt over time
I,J = type pair(s) to set parameter for
pvariable = name of variable that calculates value of parameter
{atom} args = param variable
v_name = variable with name that calculates value of pparam
{atom} args = aparam v_name
aparam = parameter to adapt over time
avariable = name of variable that calculates value of parameter :pre
v_name = variable with name that calculates value of aparam :pre
:ule
[Examples:]
fix 1 all adapt 1 pair soft a 1 1 prefactor
fix 1 all adapt 1 pair soft a 2* 3 prefactor
fix 1 all adapt 1 pair soft a * * prefactor soft a 3 3 prefactor2
fix 1 all adapt 10 atom diameter size :pre
fix 1 all adapt 1 pair soft a 1 1 v_prefactor
fix 1 all adapt 1 pair soft a 2* 3 v_prefactor
fix 1 all adapt 1 pair soft a * * v_prefactor soft a 3 3 v_prefactor2
fix 1 all adapt 10 atom diameter v_size :pre
[Description:]
@ -89,13 +89,14 @@ asterisks imply type pairs where J < I, they are ignored.
If a global parameter is specified, the {I} and {J} settings still
need to be specified, but are ignored.
The {pvariable} argument is the name of an equal-style
"variable"_variable.html which will be evaluated each time this fix is
invoked to set the parameter to a new value. Equal-style variables
can specify formulas with various mathematical functions, and include
"thermo_style"_thermo_style.html command keywords for the simulation
box parameters and timestep and elapsed time. Thus it is easy to
specify parameters that change as a function of time or span
The {v_name} argument for keyword {pair} is the name of an
"equal-style variable"_variable.html which will be evaluated each time
this fix is invoked to set the parameter to a new value. It should be
specified as v_name, where name is the variable name. Equal-style
variables can specify formulas with various mathematical functions,
and include "thermo_style"_thermo_style.html command keywords for the
simulation box parameters and timestep and elapsed time. Thus it is
easy to specify parameters that change as a function of time or span
consecutive runs in a continuous fashion. For the latter, see the
{start} and {stop} keywords of the "run"_run.html command and the
{elaplong} keyword of "thermo_style custom"_thermo_style.html for
@ -106,7 +107,7 @@ the "pair_style soft"_pair_soft.html potential from 10.0 to 30.0 in a
linear fashion over the course of a simulation:
variable prefactor equal ramp(10,30)
fix 1 all adapt 1 pair soft a * * prefactor :pre
fix 1 all adapt 1 pair soft a * * v_prefactor :pre
The {atom} keyword enables various atom properties to be changed. The
{aparam} argument is the name of the parameter to change. This is the
@ -114,21 +115,20 @@ current list of atom parameters that can be varied by this fix:
diameter = diameter of particle :ul
The {avariable} argument is the name of an equal-style
"variable"_variable.html which will be evaluated each time this fix is
invoked to set the parameter to a new value. See the discussion above
describing the formulas associated with equal-style variables. The
new value is assigned to the corresponding attribute for all atoms in
the fix group.
The {v_name} argument of the {atom} keyword is the name of an
"equal-style variable"_variable.html which will be evaluated each time
this fix is invoked to set the parameter to a new value. It should be
specified as v_name, where name is the variable name. See the
discussion above describing the formulas associated with equal-style
variables. The new value is assigned to the corresponding attribute
for all atoms in the fix group.
For example, these commands would shrink the diameter of all granular
particles in the "center" group from 1.0 to 0.1 in a linear fashion
over the course of a 1000-step simulation:
variable start equal 1.0
variable stop equal 0.1
variable size equal ramp(1.0,0.1)
fix 1 center adapt 10 atom diameter size :pre
fix 1 center adapt 10 atom diameter v_size :pre
[Restart, fix_modify, output, run start/stop, minimize info:]

22
doc/fix_addforce.html
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@ -29,8 +29,8 @@
<PRE> <I>region</I> value = region-ID
region-ID = ID of region atoms must be in to have added force
<I>energy</I> value = variable-ID
variable-ID = ID of variable that calculates the potential energy of each atom in the added force field
<I>energy</I> value = v_name
v_name = variable with name that calculates the potential energy of each atom in the added force field
</PRE>
</UL>
@ -38,7 +38,7 @@
</P>
<PRE>fix kick flow addforce 1.0 0.0 0.0
fix kick flow addforce 1.0 0.0 v_oscillate
fix ff boundary addforce 0.0 0.0 v_push energy espace
fix ff boundary addforce 0.0 0.0 v_push energy v_espace
</PRE>
<P><B>Description:</B>
</P>
@ -50,9 +50,9 @@ a channel.
<P>Any of the 3 quantities defining the force components can be specified
as an equal-style or atom-style <A HREF = "variable.html">variable</A>, namely <I>fx</I>,
<I>fy</I>, <I>fz</I>. If the value is a variable, it should be specified as
v_ID, where ID is the variable ID. In this case, the variable will be
evaluated each timestep, and its value used to determine the force
component.
v_name, where name is the variable name. In this case, the variable
will be evaluated each timestep, and its value used to determine the
force component.
</P>
<P>Equal-style variables can specify formulas with various mathematical
functions, and include <A HREF = "thermo_style.html">thermo_style</A> command
@ -91,11 +91,11 @@ the energy to 0.0, which is typically fine for dynamics.
</P>
<P>The <I>energy</I> keyword is required if the added force is defined with
one or more variables, and you are performing energy minimization via
the "minimize" command. The keyword specifies the ID of an atom-style
<A HREF = "variable.html">variable</A> which is used to compute the energy of each
atom as function of its position. Unlike variables used for <I>fx</I>,
<I>fy</I>, <I>fz</I>, the energy variable is specified by ID only, without a
"v_" prefix.
the "minimize" command. The keyword specifies the name of an
atom-style <A HREF = "variable.html">variable</A> which is used to compute the
energy of each atom as function of its position. Like variables used
for <I>fx</I>, <I>fy</I>, <I>fz</I>, the energy variable is specified as v_name,
where name is the variable name.
</P>
<P>Note that when the <I>energy</I> keyword is used during an energy
minimization, you must insure that the formula defined for the

22
doc/fix_addforce.txt
View File

@ -20,15 +20,15 @@ zero or more keyword/value pairs may be appended to args :l
keyword = {region} :l
{region} value = region-ID
region-ID = ID of region atoms must be in to have added force
{energy} value = variable-ID
variable-ID = ID of variable that calculates the potential energy of each atom in the added force field :pre
{energy} value = v_name
v_name = variable with name that calculates the potential energy of each atom in the added force field :pre
:ule
[Examples:]
fix kick flow addforce 1.0 0.0 0.0
fix kick flow addforce 1.0 0.0 v_oscillate
fix ff boundary addforce 0.0 0.0 v_push energy espace :pre
fix ff boundary addforce 0.0 0.0 v_push energy v_espace :pre
[Description:]
@ -40,9 +40,9 @@ a channel.
Any of the 3 quantities defining the force components can be specified
as an equal-style or atom-style "variable"_variable.html, namely {fx},
{fy}, {fz}. If the value is a variable, it should be specified as
v_ID, where ID is the variable ID. In this case, the variable will be
evaluated each timestep, and its value used to determine the force
component.
v_name, where name is the variable name. In this case, the variable
will be evaluated each timestep, and its value used to determine the
force component.
Equal-style variables can specify formulas with various mathematical
functions, and include "thermo_style"_thermo_style.html command
@ -81,11 +81,11 @@ the energy to 0.0, which is typically fine for dynamics.
The {energy} keyword is required if the added force is defined with
one or more variables, and you are performing energy minimization via
the "minimize" command. The keyword specifies the ID of an atom-style
"variable"_variable.html which is used to compute the energy of each
atom as function of its position. Unlike variables used for {fx},
{fy}, {fz}, the energy variable is specified by ID only, without a
"v_" prefix.
the "minimize" command. The keyword specifies the name of an
atom-style "variable"_variable.html which is used to compute the
energy of each atom as function of its position. Like variables used
for {fx}, {fy}, {fz}, the energy variable is specified as v_name,
where name is the variable name.
Note that when the {energy} keyword is used during an energy
minimization, you must insure that the formula defined for the

4
doc/fix_ave_histo.html
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@ -81,8 +81,8 @@ commands</A>, and can also be written to a file.
<P>The group specified with this command is ignored for global and local
input values. For per-atom input values, only atoms in the group
contribute to the histogram. Note that regardless of the specified
group, calculations may be performed by computes and fixes which store
their own "group" definition.
group, specified values may represent calculations performed by
computes and fixes which store their own "group" definition.
</P>
<P>A histogram is simply a count of the number of values that fall within
a histogram bin. <I>Nbins</I> are defined, with even spacing between <I>lo</I>

4
doc/fix_ave_histo.txt
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@ -69,8 +69,8 @@ commands"_Section_howto.html#4_15, and can also be written to a file.
The group specified with this command is ignored for global and local
input values. For per-atom input values, only atoms in the group
contribute to the histogram. Note that regardless of the specified
group, calculations may be performed by computes and fixes which store
their own "group" definition.
group, specified values may represent calculations performed by
computes and fixes which store their own "group" definition.
A histogram is simply a count of the number of values that fall within
a histogram bin. {Nbins} are defined, with even spacing between {lo}

8
doc/fix_ave_time.html
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@ -46,7 +46,7 @@
filename = name of file to output time averages to
<I>ave</I> args = <I>one</I> or <I>running</I> or <I>window M</I>
one = output a new average value every Nfreq steps
running = output cumulative average of all previous Nfreq steps
running = output cummulative average of all previous Nfreq steps
window M = output average of M most recent Nfreq steps
<I>start</I> args = Nstart
Nstart = start averaging on this timestep
@ -79,8 +79,8 @@ used as a convenient way to simply output one or more global values to
a file.
</P>
<P>The group specified with this command is ignored. However, note that
calculations may be performed by computes and fixes which store their
own "group" definitions.
specified values may represent calculations performed by computes and
fixes which store their own "group" definitions.
</P>
<P>Each input value can be the result of a <A HREF = "compute.html">compute</A> or
<A HREF = "fix.html">fix</A> or the evaluation of an equal-style
@ -209,7 +209,7 @@ output as-is without further averaging.
</P>
<P>If the <I>ave</I> setting is <I>running</I>, then the values produced on
timesteps that are multiples of <I>Nfreq</I> are summed and averaged in a
cumulative sense before being output. Each output value is thus the
cummulative sense before being output. Each output value is thus the
average of the value produced on that timestep with all preceding
values. This running average begins when the fix is defined; it can
only be restarted by deleting the fix via the <A HREF = "unfix.html">unfix</A>

8
doc/fix_ave_time.txt
View File

@ -34,7 +34,7 @@ keyword = {mode} or {file} or {ave} or {start} or {off} or {title1} or {title2}
filename = name of file to output time averages to
{ave} args = {one} or {running} or {window M}
one = output a new average value every Nfreq steps
running = output cumulative average of all previous Nfreq steps
running = output cummulative average of all previous Nfreq steps
window M = output average of M most recent Nfreq steps
{start} args = Nstart
Nstart = start averaging on this timestep
@ -66,8 +66,8 @@ used as a convenient way to simply output one or more global values to
a file.
The group specified with this command is ignored. However, note that
calculations may be performed by computes and fixes which store their
own "group" definitions.
specified values may represent calculations performed by computes and
fixes which store their own "group" definitions.
Each input value can be the result of a "compute"_compute.html or
"fix"_fix.html or the evaluation of an equal-style
@ -196,7 +196,7 @@ output as-is without further averaging.
If the {ave} setting is {running}, then the values produced on
timesteps that are multiples of {Nfreq} are summed and averaged in a
cumulative sense before being output. Each output value is thus the
cummulative sense before being output. Each output value is thus the
average of the value produced on that timestep with all preceding
values. This running average begins when the fix is defined; it can
only be restarted by deleting the fix via the "unfix"_unfix.html

7
doc/fix_aveforce.html
View File

@ -57,9 +57,10 @@ average value without adding in any additional force.
</P>
<P>Any of the 3 quantities defining the force components can be specified
as an equal-style <A HREF = "variable.html">variable</A>, namely <I>fx</I>, <I>fy</I>, <I>fz</I>.
If the value is a variable, it should be specified as v_ID, where ID
is the variable ID. In this case, the variable will be evaluated each
timestep, and its value used to determine the average force.
If the value is a variable, it should be specified as v_name, where
name is the variable name. In this case, the variable will be
evaluated each timestep, and its value used to determine the average
force.
</P>
<P>Equal-style variables can specify formulas with various mathematical
functions, and include <A HREF = "thermo_style.html">thermo_style</A> command

7
doc/fix_aveforce.txt
View File

@ -47,9 +47,10 @@ average value without adding in any additional force.
Any of the 3 quantities defining the force components can be specified
as an equal-style "variable"_variable.html, namely {fx}, {fy}, {fz}.
If the value is a variable, it should be specified as v_ID, where ID
is the variable ID. In this case, the variable will be evaluated each
timestep, and its value used to determine the average force.
If the value is a variable, it should be specified as v_name, where
name is the variable name. In this case, the variable will be
evaluated each timestep, and its value used to determine the average
force.
Equal-style variables can specify formulas with various mathematical
functions, and include "thermo_style"_thermo_style.html command

4
doc/fix_efield.html
View File

@ -33,8 +33,8 @@ external electric field being applied to the system.
<P>Any of the 3 quantities defining the E-field components can be
specified as an equal-style or atom-style <A HREF = "variable.html">variable</A>,
namely <I>ex</I>, <I>ey</I>, <I>ez</I>. If the value is a variable, it should be
specified as v_ID, where ID is the variable ID. In this case, the
variable will be evaluated each timestep, and its value used to
specified as v_name, where name is the variable name. In this case,
the variable will be evaluated each timestep, and its value used to
determine the E-field component.
</P>
<P>Equal-style variables can specify formulas with various mathematical

4
doc/fix_efield.txt
View File

@ -30,8 +30,8 @@ external electric field being applied to the system.
Any of the 3 quantities defining the E-field components can be
specified as an equal-style or atom-style "variable"_variable.html,
namely {ex}, {ey}, {ez}. If the value is a variable, it should be
specified as v_ID, where ID is the variable ID. In this case, the
variable will be evaluated each timestep, and its value used to
specified as v_name, where name is the variable name. In this case,
the variable will be evaluated each timestep, and its value used to
determine the E-field component.
Equal-style variables can specify formulas with various mathematical

6
doc/fix_indent.html
View File

@ -102,9 +102,9 @@ be specified as an equal-style <A HREF = "variable.html">variable</A>, namely <I
<I>y</I>, <I>z</I>, or <I>R</I>. Similarly, for a cylindrical indenter, any of <I>c1</I>,
<I>c2</I>, or <I>R</I>, can be a variable. For a planar indenter, <I>pos</I> can be
a variable. If the value is a variable, it should be specified as
v_ID, where ID is the variable ID. In this case, the variable will be
evaluated each timestep, and its value used to define the indenter
geometry.
v_name, where name is the variable name. In this case, the variable
will be evaluated each timestep, and its value used to define the
indenter geometry.
</P>
<P>Note that equal-style variables can specify formulas with various
mathematical functions, and include <A HREF = "thermo_style.html">thermo_style</A>

6
doc/fix_indent.txt
View File

@ -93,9 +93,9 @@ be specified as an equal-style "variable"_variable.html, namely {x},
{y}, {z}, or {R}. Similarly, for a cylindrical indenter, any of {c1},
{c2}, or {R}, can be a variable. For a planar indenter, {pos} can be
a variable. If the value is a variable, it should be specified as
v_ID, where ID is the variable ID. In this case, the variable will be
evaluated each timestep, and its value used to define the indenter
geometry.
v_name, where name is the variable name. In this case, the variable
will be evaluated each timestep, and its value used to define the
indenter geometry.
Note that equal-style variables can specify formulas with various
mathematical functions, and include "thermo_style"_thermo_style.html

4
doc/fix_move.html
View File

@ -126,8 +126,8 @@ rotation.
<P>The <I>variable</I> style allows the position and velocity components of
each atom to be set by formulas specified via the
<A HREF = "variable.html">variable</A> command. Each of the 6 variables is
specified as an argument to the fix as v_name, where <I>name</I> is the
name of the variable that appears elsewhere in the input script.
specified as an argument to the fix as v_name, where name is the
variable name that is defined elsewhere in the input script.
</P>
<P>Each variable must be of either the <I>equal</I> or <I>atom</I> style.
<I>Equal</I>-style variables compute a single numeric quantity, that can be

4
doc/fix_move.txt
View File

@ -117,8 +117,8 @@ rotation.
The {variable} style allows the position and velocity components of
each atom to be set by formulas specified via the
"variable"_variable.html command. Each of the 6 variables is
specified as an argument to the fix as v_name, where {name} is the
name of the variable that appears elsewhere in the input script.
specified as an argument to the fix as v_name, where name is the
variable name that is defined elsewhere in the input script.
Each variable must be of either the {equal} or {atom} style.
{Equal}-style variables compute a single numeric quantity, that can be

6
doc/fix_setforce.html
View File

@ -52,9 +52,9 @@ alter the force component in that dimension.
<P>Any of the 3 quantities defining the force components can be specified
as an equal-style or atom-style <A HREF = "variable.html">variable</A>, namely <I>fx</I>,
<I>fy</I>, <I>fz</I>. If the value is a variable, it should be specified as
v_ID, where ID is the variable ID. In this case, the variable will be
evaluated each timestep, and its value used to determine the force
component.
v_name, where name is the variable name. In this case, the variable
will be evaluated each timestep, and its value used to determine the
force component.
</P>
<P>Equal-style variables can specify formulas with various mathematical
functions, and include <A HREF = "thermo_style.html">thermo_style</A> command

6
doc/fix_setforce.txt
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@ -42,9 +42,9 @@ alter the force component in that dimension.
Any of the 3 quantities defining the force components can be specified
as an equal-style or atom-style "variable"_variable.html, namely {fx},
{fy}, {fz}. If the value is a variable, it should be specified as
v_ID, where ID is the variable ID. In this case, the variable will be
evaluated each timestep, and its value used to determine the force
component.
v_name, where name is the variable name. In this case, the variable
will be evaluated each timestep, and its value used to determine the
force component.
Equal-style variables can specify formulas with various mathematical
functions, and include "thermo_style"_thermo_style.html command

16
doc/fix_wall_reflect.html
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@ -78,14 +78,14 @@ EDGE is used, then the corresponding boundary of the current
simulation box is used. If a numeric constant is specified then the
wall is placed at that position in the appropriate dimension (x, y, or
z). In both the EDGE and constant cases, the wall will never move.
If the face position is specified with a variable name v_ID, then ID
should be the name of an <A HREF = "variable.html">equal-style variable</A>. In
this case the variable is evaluated each timestep and the result
becomes the current position of the reflecting wall. Equal-style
variables can specify formulas with various mathematical functions,
and include <A HREF = "thermo_style.html">thermo_style</A> command keywords for the
simulation box parameters and timestep and elapsed time. Thus it is
easy to specify a time-dependent wall position.
If the face position is a variable, it should be specified as v_name,
where name is an <A HREF = "variable.html">equal-style variable</A> name. In this
case the variable is evaluated each timestep and the result becomes
the current position of the reflecting wall. Equal-style variables
can specify formulas with various mathematical functions, and include
<A HREF = "thermo_style.html">thermo_style</A> command keywords for the simulation
box parameters and timestep and elapsed time. Thus it is easy to
specify a time-dependent wall position.
</P>
<P>The <I>units</I> keyword determines the meaning of the distance units used
to define a face position, but only when a numeric constant is used.

16
doc/fix_wall_reflect.txt
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@ -67,14 +67,14 @@ EDGE is used, then the corresponding boundary of the current
simulation box is used. If a numeric constant is specified then the
wall is placed at that position in the appropriate dimension (x, y, or
z). In both the EDGE and constant cases, the wall will never move.
If the face position is specified with a variable name v_ID, then ID
should be the name of an "equal-style variable"_variable.html. In
this case the variable is evaluated each timestep and the result
becomes the current position of the reflecting wall. Equal-style
variables can specify formulas with various mathematical functions,
and include "thermo_style"_thermo_style.html command keywords for the
simulation box parameters and timestep and elapsed time. Thus it is
easy to specify a time-dependent wall position.
If the face position is a variable, it should be specified as v_name,
where name is an "equal-style variable"_variable.html name. In this
case the variable is evaluated each timestep and the result becomes
the current position of the reflecting wall. Equal-style variables
can specify formulas with various mathematical functions, and include
"thermo_style"_thermo_style.html command keywords for the simulation
box parameters and timestep and elapsed time. Thus it is easy to
specify a time-dependent wall position.
The {units} keyword determines the meaning of the distance units used
to define a face position, but only when a numeric constant is used.

25
doc/thermo_modify.html
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@ -137,19 +137,18 @@ 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. The
variable 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() 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.
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() 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:

25
doc/thermo_modify.txt
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@ -131,19 +131,18 @@ 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. The
variable 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() 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.
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() 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:

6
doc/thermo_style.html
View File

@ -279,9 +279,9 @@ when output, depending on the <A HREF = "thermo_modify.html">thermo_modify norm<
option being used.
</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 name
of the variable that has been defined elsewhere in the input script.
Only equal-style variables can be referenced. See the
output. The name in the keyword should be replaced by the variable
name that has been defined elsewhere in the input script. Only
equal-style variables can be referenced. See the
<A HREF = "variable.html">variable</A> command for details. Variables of style
<I>equal</I> can reference per-atom properties or thermodynamic keywords,
or they can invoke other computes, fixes, or variables when evaluated,

6
doc/thermo_style.txt
View File

@ -273,9 +273,9 @@ when output, depending on the "thermo_modify norm"_thermo_modify.html
option being used.
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 name
of the variable that has been defined elsewhere in the input script.
Only equal-style variables can be referenced. See the
output. The name in the keyword should be replaced by the variable
name that has been defined elsewhere in the input script. Only
equal-style variables can be referenced. See the
"variable"_variable.html command for details. Variables of style
{equal} can reference per-atom properties or thermodynamic keywords,
or they can invoke other computes, fixes, or variables when evaluated,