mirror of https://github.com/lammps/lammps.git
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4029 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
7dbb6d500e
commit
00eca36fe5
|
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@ -38,7 +38,7 @@ tar xvf lammps*.tar
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<P>This will create a LAMMPS directory containing two files and several
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sub-directories:
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</P>
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<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
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<DIV ALIGN=center><TABLE BORDER=1 >
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<TR><TD >README</TD><TD > text file</TD></TR>
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<TR><TD >LICENSE</TD><TD > the GNU General Public License (GPL)</TD></TR>
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<TR><TD >bench</TD><TD > benchmark problems</TD></TR>
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@ -350,7 +350,7 @@ package".
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</P>
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<P>The current list of standard packages is as follows:
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</P>
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<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
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<DIV ALIGN=center><TABLE BORDER=1 >
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<TR><TD >asphere </TD><TD > aspherical particles and force fields</TD></TR>
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<TR><TD >class2 </TD><TD > class 2 force fields</TD></TR>
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<TR><TD >colloid </TD><TD > colloidal particle force fields</TD></TR>
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@ -762,7 +762,7 @@ output is performed.
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<P>Specify a variable that will be defined for substitution purposes when
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the input script is read. "Name" is the variable name which can be a
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single character (referenced as $x in the input script) or a full
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string (referenced as $\<I>abc\</I>). The value can be any string. Using
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string (referenced as ${abc}). The value can be any string. Using
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this command-line option is equivalent to putting the line "variable
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name index value" at the beginning of the input script. Defining an
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index variable as a command-line argument overrides any setting for
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|
|
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@ -21,18 +21,24 @@
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<LI>fx,fy,fz = force component values (force units)
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<LI>any of fx,fy,fz can be a variable (see below)
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<LI>zero or more keyword/value pairs may be appended to args
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<LI>keyword = <I>region</I>
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<PRE> <I>region</I> value = region-ID
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region-ID = ID of region atoms must be in to have added force
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region-ID = ID of region atoms must be in to have added force
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<I>energy</I> value = variable-ID
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variable-ID = ID of variable that calculates the potential energy of each atom in the added force field
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</PRE>
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>fix kick flow addforce 1.0 0.0 0.0
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<PRE>fix kick flow addforce 1.0 0.0 0.0
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fix kick flow addforce 1.0 0.0 v_oscillate
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fix ff boundary addforce 0.0 0.0 v_push energy espace
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</PRE>
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<P><B>Description:</B>
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</P>
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@ -41,10 +47,60 @@ the group. This command can be used to give an additional push to
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atoms in a simulation, such as for a simulation of Poiseuille flow in
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a channel.
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</P>
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<P>Any of the 3 quantities defining the force components can be
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specified as an equal-style or atom-style <A HREF = "variable">variable</A>, namely
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<I>fx</I>, <I>fy</I>, <I>fz</I>. If the value is a variable, it should be specified
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as v_ID, where ID is the variable ID. In this case, the variable will
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be evaluated each timestep, and its value used to determine the
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force component.
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</P>
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<P>Equal-style variables can specify formulas with various mathematical
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functions, and include <A HREF = "thermo_style.html">thermo_style</A> command
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keywords for the simulation box parameters and timestep and elapsed
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time. Thus it is easy to specify a time-dependent force field.
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</P>
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<P>Atom-style variables can specify the same formulas as equal-style
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variables but can also include per-atom values, such as atom
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coordinates. Thus it is easy to specify a spatially-dependent force
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field with optional time-dependence as well.
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</P>
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<P>If the <I>region</I> keyword is used, the atom must also be in the
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specified geometric <A HREF = "region.html">region</A> in order to have force added
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to it.
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</P>
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<P>Adding a force to atoms implies a change in their potential energy as
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they move due to the applied force field. For dynamics via the "run"
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command, this energy can be optionally added to the system's potential
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energy for thermodynamic output (see below). For energy minimization
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via the "minimize" command, this energy must be added to the system's
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potential energy to formulate a self-consistent minimization problem
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(see below).
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</P>
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<P>The <I>energy</I> keyword is not allowed if the added force is a constant
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vector F = (fx,fy,fz), with all components defined as numeric
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constants and not as variables. This is because LAMMPS can compute
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the energy for each atom directly as E = -x dot F = -(x*fx + y*fy +
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z*fz), so that -Grad(E) = F.
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</P>
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<P>The <I>energy</I> keyword is optional if the added force is defined with
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one or more variables, and if you are performing dynamics via the
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<A HREF = "run.html">run</A> command. If the keyword is not used, LAMMPS will set
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the energy to 0.0, which is typically fine for dynamics.
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</P>
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<P>The <I>energy</I> keyword is required if the added force is defined with
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one or more variables, and you are performing energy minimization via
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the "minimize" command. The keyword specifies the ID of an atom-style
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<A HREF = "variable.html">variable</A> which is used to compute the energy of each
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atom as function of its position. Unlike variables used for <I>fx</I>,
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<I>fy</I>, <I>fz</I>, the energy variable is specified by ID only, without a
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"v_" prefix.
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</P>
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<P>Note that when the <I>energy</I> keyword is used during an energy
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minimization, you must insure that the formula defined for the
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atom-style <A HREF = "variable.html">variable</A> is consistent with the force
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variable formulas, i.e. that -Grad(E) = F. If you don't, the
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minimization will not converge properly.
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</P>
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<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
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</P>
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<P>No information about this fix is written to <A HREF = "restart.html">binary restart
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@ -70,7 +126,10 @@ scalar and vector values calculated by this fix are "extensive".
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the <A HREF = "run.html">run</A> command.
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</P>
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<P>The forces due to this fix are imposed during an energy minimization,
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invoked by the <A HREF = "minimize.html">minimize</A> command.
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invoked by the <A HREF = "minimize.html">minimize</A> command. You should not
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specify force components with a variable that has time-dependence for
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use with a minimizer, since the minimizer increments the timestep as
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the iteration count during the minimization.
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</P>
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<P>IMPORTANT NOTE: If you want the fictitious potential energy associated
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with the added forces to be included in the total potential energy of
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|
|
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@ -15,15 +15,20 @@ fix ID group-ID addforce fx fy fz keyword value ... :pre
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ID, group-ID are documented in "fix"_fix.html command :ulb,l
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addforce = style name of this fix command :l
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fx,fy,fz = force component values (force units) :l
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any of fx,fy,fz can be a variable (see below) :l
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zero or more keyword/value pairs may be appended to args :l
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keyword = {region} :l
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{region} value = region-ID
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region-ID = ID of region atoms must be in to have added force :pre
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region-ID = ID of region atoms must be in to have added force
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{energy} value = variable-ID
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variable-ID = ID of variable that calculates the potential energy of each atom in the added force field :pre
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:ule
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[Examples:]
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fix kick flow addforce 1.0 0.0 0.0 :pre
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fix kick flow addforce 1.0 0.0 0.0
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fix kick flow addforce 1.0 0.0 v_oscillate
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fix ff boundary addforce 0.0 0.0 v_push energy espace :pre
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[Description:]
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||||
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||||
|
|
@ -32,10 +37,62 @@ the group. This command can be used to give an additional push to
|
|||
atoms in a simulation, such as for a simulation of Poiseuille flow in
|
||||
a channel.
|
||||
|
||||
Any of the 3 quantities defining the force components can be
|
||||
specified as an equal-style or atom-style "variable"_variable, 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.
|
||||
|
||||
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 force field.
|
||||
|
||||
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 force
|
||||
field with optional time-dependence as well.
|
||||
|
||||
If the {region} keyword is used, the atom must also be in the
|
||||
specified geometric "region"_region.html in order to have force added
|
||||
to it.
|
||||
|
||||
Adding a force to atoms implies a change in their potential energy as
|
||||
they move due to the applied force field. For dynamics via the "run"
|
||||
command, this energy can be optionally added to the system's potential
|
||||
energy for thermodynamic output (see below). For energy minimization
|
||||
via the "minimize" command, this energy must be added to the system's
|
||||
potential energy to formulate a self-consistent minimization problem
|
||||
(see below).
|
||||
|
||||
The {energy} keyword is not allowed if the added force is a constant
|
||||
vector F = (fx,fy,fz), with all components defined as numeric
|
||||
constants and not as variables. This is because LAMMPS can compute
|
||||
the energy for each atom directly as E = -x dot F = -(x*fx + y*fy +
|
||||
z*fz), so that -Grad(E) = F.
|
||||
|
||||
The {energy} keyword is optional if the added force is defined with
|
||||
one or more variables, and if you are performing dynamics via the
|
||||
"run"_run.html command. If the keyword is not used, LAMMPS will set
|
||||
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.
|
||||
|
||||
Note that when the {energy} keyword is used during an energy
|
||||
minimization, you must insure that the formula defined for the
|
||||
atom-style "variable"_variable.html is consistent with the force
|
||||
variable formulas, i.e. that -Grad(E) = F. For example, if the force
|
||||
were a spring-like F = kx, then the energy formula should be E =
|
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-0.5kx^2. If you don't do this correctly, the minimization will not
|
||||
converge properly.
|
||||
|
||||
[Restart, fix_modify, output, run start/stop, minimize info:]
|
||||
|
||||
No information about this fix is written to "binary restart
|
||||
|
|
@ -61,7 +118,10 @@ No parameter of this fix can be used with the {start/stop} keywords of
|
|||
the "run"_run.html command.
|
||||
|
||||
The forces due to this fix are imposed during an energy minimization,
|
||||
invoked by the "minimize"_minimize.html command.
|
||||
invoked by the "minimize"_minimize.html command. You should not
|
||||
specify force components with a variable that has time-dependence for
|
||||
use with a minimizer, since the minimizer increments the timestep as
|
||||
the iteration count during the minimization.
|
||||
|
||||
IMPORTANT NOTE: If you want the fictitious potential energy associated
|
||||
with the added forces to be included in the total potential energy of
|
||||
|
|
|
|||
|
|
@ -21,6 +21,8 @@
|
|||
|
||||
<LI>fx,fy,fz = force component values (force units)
|
||||
|
||||
<LI>any of fx,fy,fz can be a variable (see below)
|
||||
|
||||
<LI>zero or more keyword/value pairs may be appended to args
|
||||
|
||||
<LI>keyword = <I>region</I>
|
||||
|
|
@ -33,7 +35,8 @@
|
|||
<P><B>Examples:</B>
|
||||
</P>
|
||||
<PRE>fix pressdown topwall aveforce 0.0 -1.0 0.0
|
||||
fix 2 bottomwall aveforce NULL -1.0 0.0 region top
|
||||
fix 2 bottomwall aveforce NULL -1.0 0.0 region top
|
||||
fix 2 bottomwall aveforce NULL -1.0 v_oscillate region top
|
||||
</PRE>
|
||||
<P><B>Description:</B>
|
||||
</P>
|
||||
|
|
@ -47,10 +50,21 @@ component. The actual force on each atom is then set to the average
|
|||
value plus the component specified in this command. This means each
|
||||
atom in the group receives the same force.
|
||||
</P>
|
||||
<P>If any of the arguments is specified as NULL then the forces in that
|
||||
dimension are not changed. Note that this is not the same as
|
||||
specifying a 0.0 value, since that sets all forces to the same average
|
||||
value without adding in any additional force.
|
||||
<P>Any of the fx,fy,fz values can be specified as NULL which means the
|
||||
force in that dimension is not changed. Note that this is not the
|
||||
same as specifying a 0.0 value, since that sets all forces to the same
|
||||
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">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.
|
||||
</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 average force.
|
||||
</P>
|
||||
<P>If the <I>region</I> keyword is used, the atom must also be in the
|
||||
specified geometric <A HREF = "region.html">region</A> in order to have force added
|
||||
|
|
@ -72,7 +86,10 @@ fix are "extensive".
|
|||
the <A HREF = "run.html">run</A> command.
|
||||
</P>
|
||||
<P>The forces due to this fix are imposed during an energy minimization,
|
||||
invoked by the <A HREF = "minimize.html">minimize</A> command.
|
||||
invoked by the <A HREF = "minimize.html">minimize</A> command. You should not
|
||||
specify force components with a variable that has time-dependence for
|
||||
use with a minimizer, since the minimizer increments the timestep as
|
||||
the iteration count during the minimization.
|
||||
</P>
|
||||
<P><B>Restrictions:</B> none
|
||||
</P>
|
||||
|
|
|
|||
|
|
@ -15,6 +15,7 @@ fix ID group-ID aveforce fx fy fz keyword value ... :pre
|
|||
ID, group-ID are documented in "fix"_fix.html command :ulb,l
|
||||
aveforce = style name of this fix command :l
|
||||
fx,fy,fz = force component values (force units) :l
|
||||
any of fx,fy,fz can be a variable (see below) :l
|
||||
zero or more keyword/value pairs may be appended to args :l
|
||||
keyword = {region} :l
|
||||
{region} value = region-ID
|
||||
|
|
@ -24,7 +25,8 @@ keyword = {region} :l
|
|||
[Examples:]
|
||||
|
||||
fix pressdown topwall aveforce 0.0 -1.0 0.0
|
||||
fix 2 bottomwall aveforce NULL -1.0 0.0 region top :pre
|
||||
fix 2 bottomwall aveforce NULL -1.0 0.0 region top
|
||||
fix 2 bottomwall aveforce NULL -1.0 v_oscillate region top :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
|
|
@ -38,10 +40,21 @@ component. The actual force on each atom is then set to the average
|
|||
value plus the component specified in this command. This means each
|
||||
atom in the group receives the same force.
|
||||
|
||||
If any of the arguments is specified as NULL then the forces in that
|
||||
dimension are not changed. Note that this is not the same as
|
||||
specifying a 0.0 value, since that sets all forces to the same average
|
||||
value without adding in any additional force.
|
||||
Any of the fx,fy,fz values can be specified as NULL which means the
|
||||
force in that dimension is not changed. Note that this is not the
|
||||
same as specifying a 0.0 value, since that sets all forces to the same
|
||||
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, 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.
|
||||
|
||||
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 average force.
|
||||
|
||||
If the {region} keyword is used, the atom must also be in the
|
||||
specified geometric "region"_region.html in order to have force added
|
||||
|
|
@ -63,7 +76,10 @@ No parameter of this fix can be used with the {start/stop} keywords of
|
|||
the "run"_run.html command.
|
||||
|
||||
The forces due to this fix are imposed during an energy minimization,
|
||||
invoked by the "minimize"_minimize.html command.
|
||||
invoked by the "minimize"_minimize.html command. You should not
|
||||
specify force components with a variable that has time-dependence for
|
||||
use with a minimizer, since the minimizer increments the timestep as
|
||||
the iteration count during the minimization.
|
||||
|
||||
[Restrictions:] none
|
||||
|
||||
|
|
|
|||
|
|
@ -17,12 +17,14 @@
|
|||
</PRE>
|
||||
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
|
||||
<LI>setforce = style name of this fix command
|
||||
<LI>fx,fy,fz = force component values
|
||||
<LI>fx,fy,fz = force component values
|
||||
<LI>any of fx,fy,fz can be a variable (see below)
|
||||
</UL>
|
||||
<P><B>Examples:</B>
|
||||
</P>
|
||||
<PRE>fix freeze indenter setforce 0.0 0.0 0.0
|
||||
fix 2 edge setforce NULL 0.0 0.0
|
||||
fix 2 edge setforce NULL 0.0 0.0
|
||||
fix 2 edge setforce NULL 0.0 v_oscillate
|
||||
</PRE>
|
||||
<P><B>Description:</B>
|
||||
</P>
|
||||
|
|
@ -35,6 +37,23 @@ force, assuming their initial velocity zero.
|
|||
<P>Any of the fx,fy,fz values can be specified as NULL which means do not
|
||||
alter the force component in that dimension.
|
||||
</P>
|
||||
<P>Any of the 3 quantities defining the force components can be
|
||||
specified as an equal-style or atom-style <A HREF = "variable">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.
|
||||
</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 force field.
|
||||
</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 force
|
||||
field with optional time-dependence as well.
|
||||
</P>
|
||||
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
|
||||
</P>
|
||||
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
|
||||
|
|
@ -51,7 +70,10 @@ fix are "extensive".
|
|||
the <A HREF = "run.html">run</A> command.
|
||||
</P>
|
||||
<P>The forces due to this fix are imposed during an energy minimization,
|
||||
invoked by the <A HREF = "minimize.html">minimize</A> command.
|
||||
invoked by the <A HREF = "minimize.html">minimize</A> command. You should not
|
||||
specify force components with a variable that has time-dependence for
|
||||
use with a minimizer, since the minimizer increments the timestep as
|
||||
the iteration count during the minimization.
|
||||
</P>
|
||||
<P><B>Restrictions:</B> none
|
||||
</P>
|
||||
|
|
|
|||
|
|
@ -14,12 +14,14 @@ fix ID group-ID setforce fx fy fz :pre
|
|||
|
||||
ID, group-ID are documented in "fix"_fix.html command
|
||||
setforce = style name of this fix command
|
||||
fx,fy,fz = force component values :ul
|
||||
fx,fy,fz = force component values
|
||||
any of fx,fy,fz can be a variable (see below) :ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
fix freeze indenter setforce 0.0 0.0 0.0
|
||||
fix 2 edge setforce NULL 0.0 0.0 :pre
|
||||
fix 2 edge setforce NULL 0.0 0.0
|
||||
fix 2 edge setforce NULL 0.0 v_oscillate :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
|
|
@ -32,6 +34,23 @@ force, assuming their initial velocity zero.
|
|||
Any of the fx,fy,fz values can be specified as NULL which means do not
|
||||
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, 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.
|
||||
|
||||
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 force field.
|
||||
|
||||
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 force
|
||||
field with optional time-dependence as well.
|
||||
|
||||
[Restart, fix_modify, output, run start/stop, minimize info:]
|
||||
|
||||
No information about this fix is written to "binary restart
|
||||
|
|
@ -48,7 +67,10 @@ No parameter of this fix can be used with the {start/stop} keywords of
|
|||
the "run"_run.html command.
|
||||
|
||||
The forces due to this fix are imposed during an energy minimization,
|
||||
invoked by the "minimize"_minimize.html command.
|
||||
invoked by the "minimize"_minimize.html command. You should not
|
||||
specify force components with a variable that has time-dependence for
|
||||
use with a minimizer, since the minimizer increments the timestep as
|
||||
the iteration count during the minimization.
|
||||
|
||||
[Restrictions:] none
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue