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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9251 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2013-01-08 20:26:00 +00:00
parent 405ed17338
commit 9d9587cb96
4 changed files with 78 additions and 42 deletions
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4
doc/fix_addforce.html
View File

@ -53,8 +53,8 @@ a channel.
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_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.
will be evaluated each timestep, and its value(s) 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

4
doc/fix_addforce.txt
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@ -42,8 +42,8 @@ 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_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.
will be evaluated each timestep, and its value(s) used to determine
the force component.
Equal-style variables can specify formulas with various mathematical
functions, and include "thermo_style"_thermo_style.html command

56
doc/fix_heat.html
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@ -42,11 +42,11 @@ fix 4 qout heat 1 -1.0 region top
</PRE>
<P><B>Description:</B>
</P>
<P>Add non-translational kinetic energy (heat) to a group of atoms such
that their aggregate momentum is conserved. Two of these fixes can be
used to establish a temperature gradient across a simulation domain by
adding heat (energy) to one group of atoms (hot reservoir) and
subtracting heat from another (cold reservoir). E.g. a simulation
<P>Add non-translational kinetic energy (heat) to a group of atoms in a
manner that conserves their aggregate momentum. Two of these fixes
can be used to establish a temperature gradient across a simulation
domain by adding heat (energy) to one group of atoms (hot reservoir)
and subtracting heat from another (cold reservoir). E.g. a simulation
sampling from the McDLT ensemble.
</P>
<P>If the <I>region</I> keyword is used, the atom must be in both the group
@ -55,27 +55,43 @@ energy added or subtracted to it. If not specified, then the atoms in
the group are affected wherever they may move to.
</P>
<P>Heat addition/subtraction is performed every N timesteps. The <I>eflux</I>
parameter determines the change in aggregate energy of the entire
group of atoms per unit time, e.g. in eV/psec for <A HREF = "units.html">metal
units</A>. Thus it is an "extensive" quantity, meaning its
magnitude should be scaled with the number of atoms in the group.
Since <I>eflux</I> is independent of N or the <A HREF = "timestep.html">timestep</A>, a
larger value of N will add/subtract a larger amount of energy each
time the fix is invoked. If heat is subtracted from the system too
aggressively so that the group's kinetic energy would go to zero,
LAMMPS halts with an error message.
parameter can be specified as a numeric constant or as a variable (see
below). If it is a numeric constant or equal-style variable which
evaluates to a scalar value, then the <I>eflux</I> determines the change in
aggregate energy of the entire group of atoms per unit time, e.g. in
eV/psec for <A HREF = "units.html">metal units</A>. In this case it is an
"extensive" quantity, meaning its magnitude should be scaled with the
number of atoms in the group. Note that since <I>eflux</I> has per-time
units (i.e. it is a flux), this means that a larger value of N will
add/subtract a larger amount of energy each time the fix is invoked.
</P>
<P>The <I>eflux</I> parameter can be specified as an equal-style
<A HREF = "variable.html">variable</A>. 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 flux.
<P>If <I>eflux</I> is specified as an atom-style variable (see below), then
the variable computes one value per atom. In this case, each value is
the energy flux for a single atom, again in units of energy per unit
time. In this case, each value is an "intensive" quantity, which need
not be scaled with the number of atoms in the group.
</P>
<P>As mentioned above, the <I>eflux</I> parameter can be specified as an
equal-style or atom_style <A HREF = "variable.html">variable</A>. 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(s) used to determine the flux.
</P>
<P>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 flux.
</P>
<P>Atom-style variables can specify the same formulas as equal-style
variables but can also include per-atom values, such as atom
coordinates. Thus it is easy to specify a spatially-dependent flux
with optional time-dependence as well.
</P>
<P>IMPORTANT NOTE: If heat is subtracted from the system too aggressively
so that the group's kinetic energy would go to zero, or any individual
atom's kinetic energy would go to zero for the case where <I>eflux</I> is
an atom-style variable, then LAMMPS will halt with an error message.
</P>
<P>Fix heat is different from a thermostat such as <A HREF = "fix_nh.html">fix nvt</A>
or <A HREF = "fix_temp_rescale.html">fix temp/rescale</A> in that energy is
added/subtracted continually. Thus if there isn't another mechanism
@ -102,6 +118,8 @@ are relevant to this fix.
most recent value by which velocites were scaled. The scalar value
calculated by this fix is "intensive".
</P>
<P>// NOTE: what is the scalar output for an atom-style variable?
</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
minimization</A>.

56
doc/fix_heat.txt
View File

@ -31,11 +31,11 @@ fix 4 qout heat 1 -1.0 region top :pre
[Description:]
Add non-translational kinetic energy (heat) to a group of atoms such
that their aggregate momentum is conserved. Two of these fixes can be
used to establish a temperature gradient across a simulation domain by
adding heat (energy) to one group of atoms (hot reservoir) and
subtracting heat from another (cold reservoir). E.g. a simulation
Add non-translational kinetic energy (heat) to a group of atoms in a
manner that conserves their aggregate momentum. Two of these fixes
can be used to establish a temperature gradient across a simulation
domain by adding heat (energy) to one group of atoms (hot reservoir)
and subtracting heat from another (cold reservoir). E.g. a simulation
sampling from the McDLT ensemble.
If the {region} keyword is used, the atom must be in both the group
@ -44,27 +44,43 @@ energy added or subtracted to it. If not specified, then the atoms in
the group are affected wherever they may move to.
Heat addition/subtraction is performed every N timesteps. The {eflux}
parameter determines the change in aggregate energy of the entire
group of atoms per unit time, e.g. in eV/psec for "metal
units"_units.html. Thus it is an "extensive" quantity, meaning its
magnitude should be scaled with the number of atoms in the group.
Since {eflux} is independent of N or the "timestep"_timestep.html, a
larger value of N will add/subtract a larger amount of energy each
time the fix is invoked. If heat is subtracted from the system too
aggressively so that the group's kinetic energy would go to zero,
LAMMPS halts with an error message.
parameter can be specified as a numeric constant or as a variable (see
below). If it is a numeric constant or equal-style variable which
evaluates to a scalar value, then the {eflux} determines the change in
aggregate energy of the entire group of atoms per unit time, e.g. in
eV/psec for "metal units"_units.html. In this case it is an
"extensive" quantity, meaning its magnitude should be scaled with the
number of atoms in the group. Note that since {eflux} has per-time
units (i.e. it is a flux), this means that a larger value of N will
add/subtract a larger amount of energy each time the fix is invoked.
The {eflux} parameter can be specified as an equal-style
"variable"_variable.html. 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 flux.
If {eflux} is specified as an atom-style variable (see below), then
the variable computes one value per atom. In this case, each value is
the energy flux for a single atom, again in units of energy per unit
time. In this case, each value is an "intensive" quantity, which need
not be scaled with the number of atoms in the group.
As mentioned above, the {eflux} parameter can be specified as an
equal-style or atom_style "variable"_variable.html. 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(s) used to determine the flux.
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 flux.
Atom-style variables can specify the same formulas as equal-style
variables but can also include per-atom values, such as atom
coordinates. Thus it is easy to specify a spatially-dependent flux
with optional time-dependence as well.
IMPORTANT NOTE: If heat is subtracted from the system too aggressively
so that the group's kinetic energy would go to zero, or any individual
atom's kinetic energy would go to zero for the case where {eflux} is
an atom-style variable, then LAMMPS will halt with an error message.
Fix heat is different from a thermostat such as "fix nvt"_fix_nh.html
or "fix temp/rescale"_fix_temp_rescale.html in that energy is
added/subtracted continually. Thus if there isn't another mechanism
@ -91,6 +107,8 @@ This fix computes a global scalar which can be accessed by various
most recent value by which velocites were scaled. The scalar value
calculated by this fix is "intensive".
// NOTE: what is the scalar output for an atom-style variable?
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
minimization"_minimize.html.