mirror of https://github.com/lammps/lammps.git
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@283 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
523bf8c7cb
commit
d8e3722af2
|
|
@ -0,0 +1,86 @@
|
|||
<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>compute command
|
||||
</H3>
|
||||
<P><B>Syntax:</B>
|
||||
</P>
|
||||
<PRE>compute ID group-ID style args
|
||||
</PRE>
|
||||
<UL><LI>ID = user-assigned name for the computation
|
||||
<LI>group-ID = ID of the group of atoms to perform the computation on
|
||||
<LI>style = one of a list of possible style names (see below)
|
||||
<LI>args = arguments used by a particular style
|
||||
</UL>
|
||||
<P><B>Examples:</B>
|
||||
</P>
|
||||
<PRE>compute 1 all temp
|
||||
compute newtemp flow temp/partial 1 1 0
|
||||
compute 3 all ke/atom
|
||||
</PRE>
|
||||
<P><B>Description:</B>
|
||||
</P>
|
||||
<P>Create a computation that will be performed on a group of atoms.
|
||||
</P>
|
||||
<P>In LAMMPS, a "compute" is used in several ways. Computes that
|
||||
calculate one or more values for the entire group of atoms can output
|
||||
those values via the <A HREF = "thermo_style.html">thermo_style custom</A> command.
|
||||
Or the values can be referenced in a <A HREF = "variable.html">variable equal</A>
|
||||
command. Computes that calculate a temperature or pressure are used
|
||||
by fixes that do thermostatting or barostatting and when atom
|
||||
velocities are created. Computes that calculate one or more values
|
||||
for each atom in the group can output those values via the <A HREF = "dump.html">dump
|
||||
custom</A> command.
|
||||
</P>
|
||||
<P>LAMMPS creates its own computes for thermodynamic output and dumping
|
||||
atom snapshots. Likewise fixes that compute temperature or pressure
|
||||
create their own computes. These are discussed in the documentation
|
||||
for <A HREF = "thermo_style.html">thermo_style</A>, <A HREF = "dump.html">dump custom</A>, and
|
||||
specific <A HREF = "fix.html">fix</A> commands.
|
||||
</P>
|
||||
<P>In all these cases, the default computes can be replaced by computes
|
||||
defined in the input script, as described by the
|
||||
<A HREF = "thermo_modify.html">thermo_modify</A> and <A HREF = "fix_modify.html">fix modify</A>
|
||||
commands. Code for new computes can also be added to LAMMPS (see
|
||||
<A HREF = "Section_modify.html">this section</A> of the manaul) and their
|
||||
calculations accessed in the various ways described above.
|
||||
</P>
|
||||
<P>Properties of a compute can be modified via the
|
||||
<A HREF = "compute_modify.html">compute_modify</A> command.
|
||||
</P>
|
||||
<P>Compute can be deleted with the <A HREF = "uncompute.html">uncompute</A> command.
|
||||
</P>
|
||||
<P>Each compute style has its own doc page which describes its arguments
|
||||
and what it does. Here is an alphabetic list of compute styles
|
||||
defined in LAMMPS:
|
||||
</P>
|
||||
<UL><LI><A HREF = "compute_centro_atom.html">centro/atom</A> - centro-symmetry parameter for each atom
|
||||
<LI><A HREF = "compute_epair_atom.html">epair/atom</A> - pairwise energy for each atom
|
||||
<LI><A HREF = "compute_etotal_atom.html">etotal/atom</A> - total energy (ke + epair) for each atom
|
||||
<LI><A HREF = "compute_ke_atom.html">ke/atom</A> - kinetic energy for each atom
|
||||
<LI><A HREF = "compute_pressure.html">pressure</A> - total pressure and pressure tensor
|
||||
<LI><A HREF = "compute_rotate_dipole.html">rotate/dipole</A> - rotational energy of dipolar atoms
|
||||
<LI><A HREF = "compute_rotate_gran.html">rotate/gran</A> - rotational energy of granular atoms
|
||||
<LI><A HREF = "compute_stress_atom.html">stress/atom</A> - stress tensor for each atom
|
||||
<LI><A HREF = "compute_temp.html">temp</A> - temperature of group of atoms
|
||||
<LI><A HREF = "compute_temp_partial.html">temp/partial</A> - temperature excluding one or more dimensions of velocity
|
||||
<LI><A HREF = "compute_temp_ramp.html">temp/ramp</A> - temperature after subtracting a ramped velocity component
|
||||
<LI><A HREF = "compute_temp_region.html">temp/region</A> - temperature of a region of atoms
|
||||
</UL>
|
||||
<P><B>Restrictions:</B> none
|
||||
</P>
|
||||
<P><B>Related commands:</B>
|
||||
</P>
|
||||
<P><A HREF = "uncompute.html">uncompute</A>, <A HREF = "compute_modify.html">compute_modify</A>
|
||||
</P>
|
||||
<P><B>Default:</B> none
|
||||
</P>
|
||||
</HTML>
|
||||
|
|
@ -0,0 +1,81 @@
|
|||
"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
|
||||
|
||||
compute command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
compute ID group-ID style args :pre
|
||||
|
||||
ID = user-assigned name for the computation
|
||||
group-ID = ID of the group of atoms to perform the computation on
|
||||
style = one of a list of possible style names (see below)
|
||||
args = arguments used by a particular style :ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
compute 1 all temp
|
||||
compute newtemp flow temp/partial 1 1 0
|
||||
compute 3 all ke/atom :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Create a computation that will be performed on a group of atoms.
|
||||
|
||||
In LAMMPS, a "compute" is used in several ways. Computes that
|
||||
calculate one or more values for the entire group of atoms can output
|
||||
those values via the "thermo_style custom"_thermo_style.html command.
|
||||
Or the values can be referenced in a "variable equal"_variable.html
|
||||
command. Computes that calculate a temperature or pressure are used
|
||||
by fixes that do thermostatting or barostatting and when atom
|
||||
velocities are created. Computes that calculate one or more values
|
||||
for each atom in the group can output those values via the "dump
|
||||
custom"_dump.html command.
|
||||
|
||||
LAMMPS creates its own computes for thermodynamic output and dumping
|
||||
atom snapshots. Likewise fixes that compute temperature or pressure
|
||||
create their own computes. These are discussed in the documentation
|
||||
for "thermo_style"_thermo_style.html, "dump custom"_dump.html, and
|
||||
specific "fix"_fix.html commands.
|
||||
|
||||
In all these cases, the default computes can be replaced by computes
|
||||
defined in the input script, as described by the
|
||||
"thermo_modify"_thermo_modify.html and "fix modify"_fix_modify.html
|
||||
commands. Code for new computes can also be added to LAMMPS (see
|
||||
"this section"_Section_modify.html of the manaul) and their
|
||||
calculations accessed in the various ways described above.
|
||||
|
||||
Properties of a compute can be modified via the
|
||||
"compute_modify"_compute_modify.html command.
|
||||
|
||||
Compute can be deleted with the "uncompute"_uncompute.html command.
|
||||
|
||||
Each compute style has its own doc page which describes its arguments
|
||||
and what it does. Here is an alphabetic list of compute styles
|
||||
defined in LAMMPS:
|
||||
|
||||
"centro/atom"_compute_centro_atom.html - centro-symmetry parameter for each atom
|
||||
"epair/atom"_compute_epair_atom.html - pairwise energy for each atom
|
||||
"etotal/atom"_compute_etotal_atom.html - total energy (ke + epair) for each atom
|
||||
"ke/atom"_compute_ke_atom.html - kinetic energy for each atom
|
||||
"pressure"_compute_pressure.html - total pressure and pressure tensor
|
||||
"rotate/dipole"_compute_rotate_dipole.html - rotational energy of dipolar atoms
|
||||
"rotate/gran"_compute_rotate_gran.html - rotational energy of granular atoms
|
||||
"stress/atom"_compute_stress_atom.html - stress tensor for each atom
|
||||
"temp"_compute_temp.html - temperature of group of atoms
|
||||
"temp/partial"_compute_temp_partial.html - temperature excluding one or more dimensions of velocity
|
||||
"temp/ramp"_compute_temp_ramp.html - temperature after subtracting a ramped velocity component
|
||||
"temp/region"_compute_temp_region.html - temperature of a region of atoms :ul
|
||||
|
||||
[Restrictions:] none
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"uncompute"_uncompute.html, "compute_modify"_compute_modify.html
|
||||
|
||||
[Default:] none
|
||||
|
|
@ -0,0 +1,61 @@
|
|||
<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>compute ke/atom command
|
||||
</H3>
|
||||
<P><B>Syntax:</B>
|
||||
</P>
|
||||
<PRE>compute ID group-ID ke/atom
|
||||
</PRE>
|
||||
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
|
||||
<LI>ke/atom = style name of this compute command
|
||||
</UL>
|
||||
<P><B>Examples:</B>
|
||||
</P>
|
||||
<PRE>compute 1 all ke/atom
|
||||
</PRE>
|
||||
<P><B>Description:</B>
|
||||
</P>
|
||||
<P>Define a computation that calculates the centro-symmetry parameter for
|
||||
each atom in a group. This can be output via the <A HREF = "dump.html">dump
|
||||
custom</A> command.
|
||||
</P>
|
||||
<P>This parameter is computed using the following formula from
|
||||
<A HREF = "#Kelchner">(Kelchner)</A>
|
||||
</P>
|
||||
<CENTER><IMG SRC = "Eqs/centro_symmetry.jpg">
|
||||
</CENTER>
|
||||
<P>where the 12 nearest neighbors are found and Ri and Ri+6 are the
|
||||
vectors from the central atom to the opposite pair of nearest
|
||||
neighbors. In solid state systems this is a useful measure of the
|
||||
local lattice disorder around an atom and can be used to characterize
|
||||
whether the atom is part of a perfect lattice, a local defect (e.g. a
|
||||
dislocation or stacking fault), or at a surface.
|
||||
</P>
|
||||
<P>The neighbor list needed to compute this quantity is constructed each
|
||||
time the calculation is performed (i.e. each time a snapshot of atoms
|
||||
is dumped). Thus it can be inefficient to compute/dump this quantity
|
||||
too frequently or to have multiple compute/dump commands, each of a
|
||||
<I>centro/atom</I> style.
|
||||
</P>
|
||||
<P><B>Restrictions:</B> none
|
||||
</P>
|
||||
<P><B>Related commands:</B> none
|
||||
</P>
|
||||
<P><B>Default:</B> none
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<A NAME = "Kelchner"></A>
|
||||
|
||||
<P><B>(Kelchner)</B> Kelchner, Plimpton, Hamilton, Phys Rev B, 58, 11085 (1998).
|
||||
</P>
|
||||
</HTML>
|
||||
|
|
@ -0,0 +1,55 @@
|
|||
"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
|
||||
|
||||
compute ke/atom command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
compute ID group-ID ke/atom :pre
|
||||
|
||||
ID, group-ID are documented in "compute"_compute.html command
|
||||
ke/atom = style name of this compute command :ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
compute 1 all ke/atom :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Define a computation that calculates the centro-symmetry parameter for
|
||||
each atom in a group. This can be output via the "dump
|
||||
custom"_dump.html command.
|
||||
|
||||
This parameter is computed using the following formula from
|
||||
"(Kelchner)"_#Kelchner
|
||||
|
||||
:c,image(Eqs/centro_symmetry.jpg)
|
||||
|
||||
where the 12 nearest neighbors are found and Ri and Ri+6 are the
|
||||
vectors from the central atom to the opposite pair of nearest
|
||||
neighbors. In solid state systems this is a useful measure of the
|
||||
local lattice disorder around an atom and can be used to characterize
|
||||
whether the atom is part of a perfect lattice, a local defect (e.g. a
|
||||
dislocation or stacking fault), or at a surface.
|
||||
|
||||
The neighbor list needed to compute this quantity is constructed each
|
||||
time the calculation is performed (i.e. each time a snapshot of atoms
|
||||
is dumped). Thus it can be inefficient to compute/dump this quantity
|
||||
too frequently or to have multiple compute/dump commands, each of a
|
||||
{centro/atom} style.
|
||||
|
||||
[Restrictions:] none
|
||||
|
||||
[Related commands:] none
|
||||
|
||||
[Default:] none
|
||||
|
||||
:line
|
||||
|
||||
:link(Kelchner)
|
||||
[(Kelchner)] Kelchner, Plimpton, Hamilton, Phys Rev B, 58, 11085 (1998).
|
||||
|
|
@ -0,0 +1,52 @@
|
|||
<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>compute epair/atom command
|
||||
</H3>
|
||||
<P><B>Syntax:</B>
|
||||
</P>
|
||||
<PRE>compute ID group-ID epair/atom
|
||||
</PRE>
|
||||
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
|
||||
<LI>epair/atom = style name of this compute command
|
||||
</UL>
|
||||
<P><B>Examples:</B>
|
||||
</P>
|
||||
<PRE>compute 1 all epair/atom
|
||||
</PRE>
|
||||
<P><B>Description:</B>
|
||||
</P>
|
||||
<P>Define a computation that computes the per-atom pairwise energy for
|
||||
each atom in a group. This can be output via the <A HREF = "dump.html">dump
|
||||
custom</A> command.
|
||||
</P>
|
||||
<P>The pairwise energy for each atom is computed by looping over its
|
||||
neighbors and computing the energy associated with the defined
|
||||
<A HREF = "pair_style.html">pair_style</A> command for each IJ pair (divided by 2).
|
||||
Thus the sum of per-atom energy for all atoms should give the total
|
||||
pairwise energy of the system.
|
||||
</P>
|
||||
<P>For force fields that include a contribution to the pairwise energy
|
||||
that is computed as part of dihedral terms (i.e. 1-4 interactions),
|
||||
this contribution is not included in the per-atom pairwise energy.
|
||||
</P>
|
||||
<P>Computation of per-atom pairwise energy requires a loop thru the
|
||||
neighbor list and inter-processor communication, so it can be
|
||||
inefficient to compute/dump this quantity too frequently or to have
|
||||
multiple compute/dump commands, each of a <I>epair/atom</I> style.
|
||||
</P>
|
||||
<P><B>Restrictions:</B> none
|
||||
</P>
|
||||
<P><B>Related commands:</B> none
|
||||
</P>
|
||||
<P><B>Default:</B> none
|
||||
</P>
|
||||
</HTML>
|
||||
|
|
@ -0,0 +1,47 @@
|
|||
"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
|
||||
|
||||
compute epair/atom command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
compute ID group-ID epair/atom :pre
|
||||
|
||||
ID, group-ID are documented in "compute"_compute.html command
|
||||
epair/atom = style name of this compute command :ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
compute 1 all epair/atom :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Define a computation that computes the per-atom pairwise energy for
|
||||
each atom in a group. This can be output via the "dump
|
||||
custom"_dump.html command.
|
||||
|
||||
The pairwise energy for each atom is computed by looping over its
|
||||
neighbors and computing the energy associated with the defined
|
||||
"pair_style"_pair_style.html command for each IJ pair (divided by 2).
|
||||
Thus the sum of per-atom energy for all atoms should give the total
|
||||
pairwise energy of the system.
|
||||
|
||||
For force fields that include a contribution to the pairwise energy
|
||||
that is computed as part of dihedral terms (i.e. 1-4 interactions),
|
||||
this contribution is not included in the per-atom pairwise energy.
|
||||
|
||||
Computation of per-atom pairwise energy requires a loop thru the
|
||||
neighbor list and inter-processor communication, so it can be
|
||||
inefficient to compute/dump this quantity too frequently or to have
|
||||
multiple compute/dump commands, each of a {epair/atom} style.
|
||||
|
||||
[Restrictions:] none
|
||||
|
||||
[Related commands:] none
|
||||
|
||||
[Default:] none
|
||||
|
|
@ -0,0 +1,50 @@
|
|||
<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>compute etotal/atom command
|
||||
</H3>
|
||||
<P><B>Syntax:</B>
|
||||
</P>
|
||||
<PRE>compute ID group-ID etotal/atom compute-ID
|
||||
</PRE>
|
||||
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
|
||||
<LI>etotal/atom = style name of this compute command
|
||||
<LI>compute-ID = ID of compute that calculates per-atom pairwise energy
|
||||
</UL>
|
||||
<P><B>Examples:</B>
|
||||
</P>
|
||||
<PRE>compute 1 all etotal/atom atomEng
|
||||
</PRE>
|
||||
<P><B>Description:</B>
|
||||
</P>
|
||||
<P>Define a computation that computes the total energy (kinetic +
|
||||
pairwise) for each atom in a group. This can be output via the <A HREF = "dump.html">dump
|
||||
custom</A> command.
|
||||
</P>
|
||||
<P>The kinetic energy for each atom is computed the same way as in the
|
||||
<A HREF = "compute_ke_atom.html">compute ke/atom</A> command, namely as 1/2 m v^2.
|
||||
</P>
|
||||
<P>The pairwise energy is not calculated by this compute, but rather by
|
||||
the <A HREF = "compute_epair_atom.html">epair/atom compute</A> specified as the last
|
||||
argument of the command.
|
||||
</P>
|
||||
<P>Note that the total energy per atom as defined here does not include
|
||||
contributions due to bonds, angles, etc that the atom is part of.
|
||||
</P>
|
||||
<P><B>Restrictions:</B> none
|
||||
</P>
|
||||
<P><B>Related commands:</B>
|
||||
</P>
|
||||
<P><A HREF = "compute_epair_atom.html">compute epair/atom</A>
|
||||
</P>
|
||||
<P><B>Default:</B> none
|
||||
</P>
|
||||
</HTML>
|
||||
|
|
@ -0,0 +1,45 @@
|
|||
"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
|
||||
|
||||
compute etotal/atom command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
compute ID group-ID etotal/atom compute-ID :pre
|
||||
|
||||
ID, group-ID are documented in "compute"_compute.html command
|
||||
etotal/atom = style name of this compute command
|
||||
compute-ID = ID of compute that calculates per-atom pairwise energy :ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
compute 1 all etotal/atom atomEng :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Define a computation that computes the total energy (kinetic +
|
||||
pairwise) for each atom in a group. This can be output via the "dump
|
||||
custom"_dump.html command.
|
||||
|
||||
The kinetic energy for each atom is computed the same way as in the
|
||||
"compute ke/atom"_compute_ke_atom.html command, namely as 1/2 m v^2.
|
||||
|
||||
The pairwise energy is not calculated by this compute, but rather by
|
||||
the "epair/atom compute"_compute_epair_atom.html specified as the last
|
||||
argument of the command.
|
||||
|
||||
Note that the total energy per atom as defined here does not include
|
||||
contributions due to bonds, angles, etc that the atom is part of.
|
||||
|
||||
[Restrictions:] none
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"compute epair/atom"_compute_epair_atom.html
|
||||
|
||||
[Default:] none
|
||||
|
|
@ -0,0 +1,42 @@
|
|||
<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>compute ke/atom command
|
||||
</H3>
|
||||
<P><B>Syntax:</B>
|
||||
</P>
|
||||
<PRE>compute ID group-ID ke/atom
|
||||
</PRE>
|
||||
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
|
||||
<LI>ke/atom = style name of this compute command
|
||||
</UL>
|
||||
<P><B>Examples:</B>
|
||||
</P>
|
||||
<PRE>compute 1 all ke/atom
|
||||
</PRE>
|
||||
<P><B>Description:</B>
|
||||
</P>
|
||||
<P>Define a computation that calculates the per-atom kinetic energy for
|
||||
each atom in a group. This can be output via the <A HREF = "dump.html">dump
|
||||
custom</A> command.
|
||||
</P>
|
||||
<P>The kinetic energy is simply 1/2 m v^2, where m is the mass and v is
|
||||
the velocity of each atom.
|
||||
</P>
|
||||
<P><B>Restrictions:</B> none
|
||||
</P>
|
||||
<P><B>Related commands:</B>
|
||||
</P>
|
||||
<P><A HREF = "dump.html">dump custom</A>
|
||||
</P>
|
||||
<P><B>Default:</B> none
|
||||
</P>
|
||||
</HTML>
|
||||
|
|
@ -0,0 +1,37 @@
|
|||
"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
|
||||
|
||||
compute ke/atom command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
compute ID group-ID ke/atom :pre
|
||||
|
||||
ID, group-ID are documented in "compute"_compute.html command
|
||||
ke/atom = style name of this compute command :ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
compute 1 all ke/atom :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Define a computation that calculates the per-atom kinetic energy for
|
||||
each atom in a group. This can be output via the "dump
|
||||
custom"_dump.html command.
|
||||
|
||||
The kinetic energy is simply 1/2 m v^2, where m is the mass and v is
|
||||
the velocity of each atom.
|
||||
|
||||
[Restrictions:] none
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"dump custom"_dump.html
|
||||
|
||||
[Default:] none
|
||||
|
|
@ -9,13 +9,13 @@
|
|||
|
||||
<HR>
|
||||
|
||||
<H3>temp_modify command
|
||||
<H3>compute_modify command
|
||||
</H3>
|
||||
<P><B>Syntax:</B>
|
||||
</P>
|
||||
<PRE>temp_modify temp-ID keyword value ...
|
||||
<PRE>compute_modify compute-ID keyword value ...
|
||||
</PRE>
|
||||
<UL><LI>temp-ID = ID of temperature to modify
|
||||
<UL><LI>compute-ID = ID of the compute to modify
|
||||
|
||||
<LI>one or more keyword/value pairs may be listed
|
||||
|
||||
|
|
@ -30,25 +30,25 @@
|
|||
</UL>
|
||||
<P><B>Examples:</B>
|
||||
</P>
|
||||
<PRE>temp_modify mine extra 0
|
||||
temp_modify mine dynamic yes
|
||||
<PRE>compute_modify myTemp extra 0
|
||||
compute_modify newtemp dynamic yes extra 600
|
||||
</PRE>
|
||||
<P><B>Description:</B>
|
||||
</P>
|
||||
<P>Modify the parameters of a previously defined temperature method.
|
||||
This can either be the default temperature defined by LAMMPS (ID =
|
||||
<I>default</I>) or a user-defined temperature created by using the
|
||||
<A HREF = "temperature.html">temperature</A> command.
|
||||
<P>Modify one or more parameters of a previously defined compute. Not
|
||||
all compute styles support all parameters.
|
||||
</P>
|
||||
<P>The <I>extra</I> keyword refers to how many degrees-of-freedom are
|
||||
subtracted (typically from 3N) as a normalizing factor in the
|
||||
temperature computation. The default is 3 which is a correction
|
||||
factor for an ensemble of velocities with zero total linear momentum.
|
||||
subtracted (typically from 3N) as a normalizing factor in a
|
||||
temperature computation. Only computes that compute a temperature use
|
||||
this option. The default is 3 which is a correction factor for an
|
||||
ensemble of velocities with zero total linear momentum.
|
||||
</P>
|
||||
<P>The <I>dynamic</I> keyword determines whether the number of atoms N in the
|
||||
temperature group is re-computed each time the temperature is
|
||||
computed. By default, N is assumed to be constant. If you are adding
|
||||
atoms to the system (see the <A HREF = "fix_pour.html">fix pour</A> or <A HREF = "fix_deposit.html">fix
|
||||
compute group is re-computed each time a temperature is computed.
|
||||
Only compute styles that compute a temperature use this option. By
|
||||
default, N is assumed to be constant. If you are adding atoms to the
|
||||
system (see the <A HREF = "fix_pour.html">fix pour</A> or <A HREF = "fix_deposit.html">fix
|
||||
deposit</A> commands) or expect atoms to be lost
|
||||
(e.g. due to evaporation), then this option can be used to insure the
|
||||
temperature is correctly normalized.
|
||||
|
|
@ -57,7 +57,7 @@ temperature is correctly normalized.
|
|||
</P>
|
||||
<P><B>Related commands:</B>
|
||||
</P>
|
||||
<P><A HREF = "temperature.html">temperature</A>
|
||||
<P><A HREF = "compute.html">compute</A>
|
||||
</P>
|
||||
<P><B>Default:</B>
|
||||
</P>
|
||||
|
|
@ -6,13 +6,13 @@
|
|||
|
||||
:line
|
||||
|
||||
temp_modify command :h3
|
||||
compute_modify command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
temp_modify temp-ID keyword value ... :pre
|
||||
compute_modify compute-ID keyword value ... :pre
|
||||
|
||||
temp-ID = ID of temperature to modify :ulb,l
|
||||
compute-ID = ID of the compute to modify :ulb,l
|
||||
one or more keyword/value pairs may be listed :l
|
||||
keyword = {extra} or {dynamic} :l
|
||||
{extra} value = N
|
||||
|
|
@ -23,25 +23,25 @@ keyword = {extra} or {dynamic} :l
|
|||
|
||||
[Examples:]
|
||||
|
||||
temp_modify mine extra 0
|
||||
temp_modify mine dynamic yes :pre
|
||||
compute_modify myTemp extra 0
|
||||
compute_modify newtemp dynamic yes extra 600 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Modify the parameters of a previously defined temperature method.
|
||||
This can either be the default temperature defined by LAMMPS (ID =
|
||||
{default}) or a user-defined temperature created by using the
|
||||
"temperature"_temperature.html command.
|
||||
Modify one or more parameters of a previously defined compute. Not
|
||||
all compute styles support all parameters.
|
||||
|
||||
The {extra} keyword refers to how many degrees-of-freedom are
|
||||
subtracted (typically from 3N) as a normalizing factor in the
|
||||
temperature computation. The default is 3 which is a correction
|
||||
factor for an ensemble of velocities with zero total linear momentum.
|
||||
subtracted (typically from 3N) as a normalizing factor in a
|
||||
temperature computation. Only computes that compute a temperature use
|
||||
this option. The default is 3 which is a correction factor for an
|
||||
ensemble of velocities with zero total linear momentum.
|
||||
|
||||
The {dynamic} keyword determines whether the number of atoms N in the
|
||||
temperature group is re-computed each time the temperature is
|
||||
computed. By default, N is assumed to be constant. If you are adding
|
||||
atoms to the system (see the "fix pour"_fix_pour.html or "fix
|
||||
compute group is re-computed each time a temperature is computed.
|
||||
Only compute styles that compute a temperature use this option. By
|
||||
default, N is assumed to be constant. If you are adding atoms to the
|
||||
system (see the "fix pour"_fix_pour.html or "fix
|
||||
deposit"_fix_deposit.html commands) or expect atoms to be lost
|
||||
(e.g. due to evaporation), then this option can be used to insure the
|
||||
temperature is correctly normalized.
|
||||
|
|
@ -50,7 +50,7 @@ temperature is correctly normalized.
|
|||
|
||||
[Related commands:]
|
||||
|
||||
"temperature"_temperature.html
|
||||
"compute"_compute.html
|
||||
|
||||
[Default:]
|
||||
|
||||
|
|
@ -0,0 +1,70 @@
|
|||
<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>compute pressure command
|
||||
</H3>
|
||||
<P><B>Syntax:</B>
|
||||
</P>
|
||||
<PRE>compute ID group-ID pressure compute-ID
|
||||
</PRE>
|
||||
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
|
||||
<LI>pressure = style name of this compute command
|
||||
<LI>compute-ID = ID of compute that calculates temperature
|
||||
</UL>
|
||||
<P><B>Examples:</B>
|
||||
</P>
|
||||
<PRE>compute 1 all pressure myTemp
|
||||
</PRE>
|
||||
<P><B>Description:</B>
|
||||
</P>
|
||||
<P>Define a computation that calculates the pressure of atoms averaged
|
||||
over the entire system. The specified group must be "all". See the
|
||||
<A HREF = "dump.html">dump custom</A> command for how to dump the per-atom stress
|
||||
tensor if you want more localized information about pressure (stress)
|
||||
in your system.
|
||||
</P>
|
||||
<P>The pressure is computed by the standard formula
|
||||
</P>
|
||||
<CENTER><IMG SRC = "Eqs/pressure.jpg">
|
||||
</CENTER>
|
||||
<P>where N is the number of atoms in the system (see discussion of DOF
|
||||
below), Kb is the Boltzmann constant, T is the temperature, V is the
|
||||
system volume, and the second term is the virial, computed within
|
||||
LAMMPS for all pairwise as well as 2-body, 3-body, 4-body bonded
|
||||
interactions.
|
||||
</P>
|
||||
<P>A 6-component pressure tensor is also calculated by this compute which
|
||||
can be output by the <A HREF = "thermo_style.html">thermo_style custom</A> command.
|
||||
The formula for the components of the tensor is the same as in above
|
||||
formula, except that the first term uses the components of the kinetic
|
||||
energy tensor (vx * vy instead of v^2 for temperature) and the second
|
||||
term uses Rx * Fy for the Wxy component of the virial tensor, etc.
|
||||
</P>
|
||||
<P>The temperature and kinetic energy tensor is not calculated by this
|
||||
compute, but rather by the temperature compute specified as the last
|
||||
argument of the command. Normally this compute should calculate the
|
||||
temperature of all atoms for consistency with the virial term, but any
|
||||
compute style that calculates temperature can be used, e.g. one that
|
||||
excludes frozen atoms or other degrees of freedom.
|
||||
</P>
|
||||
<P>Note that the N is the above formula is really degrees-of-freedom/3
|
||||
where the DOF is specified by the temperature compute. See the
|
||||
various <A HREF = "compute.html">compute temperature</A> styles for details.
|
||||
</P>
|
||||
<P><B>Restrictions:</B> none
|
||||
</P>
|
||||
<P><B>Related commands:</B>
|
||||
</P>
|
||||
<P><A HREF = "compute_temp.html">compute temp</A>, <A HREF = "themo_style.html">thermo_style</A>
|
||||
</P>
|
||||
<P><B>Default:</B> none
|
||||
</P>
|
||||
</HTML>
|
||||
|
|
@ -0,0 +1,65 @@
|
|||
"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
|
||||
|
||||
compute pressure command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
compute ID group-ID pressure compute-ID :pre
|
||||
|
||||
ID, group-ID are documented in "compute"_compute.html command
|
||||
pressure = style name of this compute command
|
||||
compute-ID = ID of compute that calculates temperature :ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
compute 1 all pressure myTemp :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Define a computation that calculates the pressure of atoms averaged
|
||||
over the entire system. The specified group must be "all". See the
|
||||
"dump custom"_dump.html command for how to dump the per-atom stress
|
||||
tensor if you want more localized information about pressure (stress)
|
||||
in your system.
|
||||
|
||||
The pressure is computed by the standard formula
|
||||
|
||||
:c,image(Eqs/pressure.jpg)
|
||||
|
||||
where N is the number of atoms in the system (see discussion of DOF
|
||||
below), Kb is the Boltzmann constant, T is the temperature, V is the
|
||||
system volume, and the second term is the virial, computed within
|
||||
LAMMPS for all pairwise as well as 2-body, 3-body, 4-body bonded
|
||||
interactions.
|
||||
|
||||
A 6-component pressure tensor is also calculated by this compute which
|
||||
can be output by the "thermo_style custom"_thermo_style.html command.
|
||||
The formula for the components of the tensor is the same as in above
|
||||
formula, except that the first term uses the components of the kinetic
|
||||
energy tensor (vx * vy instead of v^2 for temperature) and the second
|
||||
term uses Rx * Fy for the Wxy component of the virial tensor, etc.
|
||||
|
||||
The temperature and kinetic energy tensor is not calculated by this
|
||||
compute, but rather by the temperature compute specified as the last
|
||||
argument of the command. Normally this compute should calculate the
|
||||
temperature of all atoms for consistency with the virial term, but any
|
||||
compute style that calculates temperature can be used, e.g. one that
|
||||
excludes frozen atoms or other degrees of freedom.
|
||||
|
||||
Note that the N is the above formula is really degrees-of-freedom/3
|
||||
where the DOF is specified by the temperature compute. See the
|
||||
various "compute temperature"_compute.html styles for details.
|
||||
|
||||
[Restrictions:] none
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"compute temp"_compute_temp.html, "thermo_style"_themo_style.html
|
||||
|
||||
[Default:] none
|
||||
|
|
@ -0,0 +1,40 @@
|
|||
<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>compute rotate/dipole command
|
||||
</H3>
|
||||
<P><B>Syntax:</B>
|
||||
</P>
|
||||
<PRE>compute ID group-ID rotate/dipole
|
||||
</PRE>
|
||||
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
|
||||
<LI>rotate/dipole = style name of this compute command
|
||||
</UL>
|
||||
<P><B>Examples:</B>
|
||||
</P>
|
||||
<PRE>compute 1 all rotate/dipole
|
||||
</PRE>
|
||||
<P><B>Description:</B>
|
||||
</P>
|
||||
<P>Define a computation that calculates the total rotational energy of a
|
||||
group of dipolar atoms.
|
||||
</P>
|
||||
<P>The rotational energy is calculated as the sum of 1/2 I w^2 over all
|
||||
the atoms in the group, where I is the moment of inertia of a
|
||||
disk/spherical (2d/3d) particle, and w is its angular velocity.
|
||||
</P>
|
||||
<P><B>Restrictions:</B> none
|
||||
</P>
|
||||
<P><B>Related commands:</B> none
|
||||
</P>
|
||||
<P><B>Default:</B> none
|
||||
</P>
|
||||
</HTML>
|
||||
|
|
@ -0,0 +1,35 @@
|
|||
"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
|
||||
|
||||
compute rotate/dipole command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
compute ID group-ID rotate/dipole :pre
|
||||
|
||||
ID, group-ID are documented in "compute"_compute.html command
|
||||
rotate/dipole = style name of this compute command :ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
compute 1 all rotate/dipole :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Define a computation that calculates the total rotational energy of a
|
||||
group of dipolar atoms.
|
||||
|
||||
The rotational energy is calculated as the sum of 1/2 I w^2 over all
|
||||
the atoms in the group, where I is the moment of inertia of a
|
||||
disk/spherical (2d/3d) particle, and w is its angular velocity.
|
||||
|
||||
[Restrictions:] none
|
||||
|
||||
[Related commands:] none
|
||||
|
||||
[Default:] none
|
||||
|
|
@ -0,0 +1,40 @@
|
|||
<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>compute rotate/gran command
|
||||
</H3>
|
||||
<P><B>Syntax:</B>
|
||||
</P>
|
||||
<PRE>compute ID group-ID rotate/gran
|
||||
</PRE>
|
||||
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
|
||||
<LI>rotate/gran = style name of this compute command
|
||||
</UL>
|
||||
<P><B>Examples:</B>
|
||||
</P>
|
||||
<PRE>compute 1 all rotate/gran
|
||||
</PRE>
|
||||
<P><B>Description:</B>
|
||||
</P>
|
||||
<P>Define a computation that calculates the total rotational energy of a
|
||||
group of granular atoms.
|
||||
</P>
|
||||
<P>The rotational energy is calculated as the sum of 1/2 I w^2 over all
|
||||
the atoms in the group, where I is the moment of inertia of a
|
||||
disk/spherical (2d/3d) particle, and w is its angular velocity.
|
||||
</P>
|
||||
<P><B>Restrictions:</B> none
|
||||
</P>
|
||||
<P><B>Related commands:</B> none
|
||||
</P>
|
||||
<P><B>Default:</B> none
|
||||
</P>
|
||||
</HTML>
|
||||
|
|
@ -0,0 +1,35 @@
|
|||
"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
|
||||
|
||||
compute rotate/gran command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
compute ID group-ID rotate/gran :pre
|
||||
|
||||
ID, group-ID are documented in "compute"_compute.html command
|
||||
rotate/gran = style name of this compute command :ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
compute 1 all rotate/gran :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Define a computation that calculates the total rotational energy of a
|
||||
group of granular atoms.
|
||||
|
||||
The rotational energy is calculated as the sum of 1/2 I w^2 over all
|
||||
the atoms in the group, where I is the moment of inertia of a
|
||||
disk/spherical (2d/3d) particle, and w is its angular velocity.
|
||||
|
||||
[Restrictions:] none
|
||||
|
||||
[Related commands:] none
|
||||
|
||||
[Default:] none
|
||||
|
|
@ -0,0 +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>compute stress/atom command
|
||||
</H3>
|
||||
<P><B>Syntax:</B>
|
||||
</P>
|
||||
<PRE>compute ID group-ID stress/atom
|
||||
</PRE>
|
||||
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
|
||||
<LI>stress/atom = style name of this compute command
|
||||
</UL>
|
||||
<P><B>Examples:</B>
|
||||
</P>
|
||||
<PRE>compute 1 mobile stress/atom
|
||||
</PRE>
|
||||
<P><B>Description:</B>
|
||||
</P>
|
||||
<P>Define a computation that computes the per-atom stress tensor for each
|
||||
atom in a group. The 6 components can be output via the <A HREF = "dump.html">dump
|
||||
custom</A> command.
|
||||
</P>
|
||||
<P>The stress tensor is computed for only pairwise forces where the <I>ab</I>
|
||||
component of stress on atom <I>i</I> is given by
|
||||
</P>
|
||||
<CENTER><IMG SRC = "Eqs/stress_tensor.jpg">
|
||||
</CENTER>
|
||||
<P>where the first term is a kinetic energy component for atom <I>i</I>, <I>j</I>
|
||||
loops over the <I>N</I> neighbors of atom <I>i</I>, and <I>Fb</I> is one of 3
|
||||
components of force on atom <I>i</I> due to atom <I>j</I>. Both <I>a</I> and <I>b</I>
|
||||
take on values x,y,z to generate the 6 components of the symmetric
|
||||
tensor.
|
||||
</P>
|
||||
<P>Note that this formula for stress does not include virial
|
||||
contributions from intra-molecular interactions (e.g. bonds, angles,
|
||||
torsions, etc). Also note that this quantity is the negative of the
|
||||
per-atom pressure tensor. It is also really a stress-volume
|
||||
formulation. It would need to be divided by a per-atom volume to have
|
||||
units of stress, but an individual atom's volume is not easy to
|
||||
compute in a deformed solid. Thus, if you sum the diagonal components
|
||||
of the per-atom stress tensor for all atoms in the system and divide
|
||||
the sum by 3V, where V is the volume of the system, you should get -P,
|
||||
where P is the total pressure of the system.
|
||||
</P>
|
||||
<P>Computation of per-atom stress tensor components requires a loop thru
|
||||
the neighbor list and inter-processor communication, so it can be
|
||||
inefficient to compute/dump this quantity too frequently or to have
|
||||
multiple compute/dump commands, each of a <I>stress/atom</I> style.
|
||||
</P>
|
||||
<P><B>Restrictions:</B> none
|
||||
</P>
|
||||
<P><B>Related commands:</B> none
|
||||
</P>
|
||||
<P><B>Default:</B> none
|
||||
</P>
|
||||
</HTML>
|
||||
|
|
@ -0,0 +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
|
||||
|
||||
compute stress/atom command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
compute ID group-ID stress/atom :pre
|
||||
|
||||
ID, group-ID are documented in "compute"_compute.html command
|
||||
stress/atom = style name of this compute command :ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
compute 1 mobile stress/atom :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Define a computation that computes the per-atom stress tensor for each
|
||||
atom in a group. The 6 components can be output via the "dump
|
||||
custom"_dump.html command.
|
||||
|
||||
The stress tensor is computed for only pairwise forces where the {ab}
|
||||
component of stress on atom {i} is given by
|
||||
|
||||
:c,image(Eqs/stress_tensor.jpg)
|
||||
|
||||
where the first term is a kinetic energy component for atom {i}, {j}
|
||||
loops over the {N} neighbors of atom {i}, and {Fb} is one of 3
|
||||
components of force on atom {i} due to atom {j}. Both {a} and {b}
|
||||
take on values x,y,z to generate the 6 components of the symmetric
|
||||
tensor.
|
||||
|
||||
Note that this formula for stress does not include virial
|
||||
contributions from intra-molecular interactions (e.g. bonds, angles,
|
||||
torsions, etc). Also note that this quantity is the negative of the
|
||||
per-atom pressure tensor. It is also really a stress-volume
|
||||
formulation. It would need to be divided by a per-atom volume to have
|
||||
units of stress, but an individual atom's volume is not easy to
|
||||
compute in a deformed solid. Thus, if you sum the diagonal components
|
||||
of the per-atom stress tensor for all atoms in the system and divide
|
||||
the sum by 3V, where V is the volume of the system, you should get -P,
|
||||
where P is the total pressure of the system.
|
||||
|
||||
Computation of per-atom stress tensor components requires a loop thru
|
||||
the neighbor list and inter-processor communication, so it can be
|
||||
inefficient to compute/dump this quantity too frequently or to have
|
||||
multiple compute/dump commands, each of a {stress/atom} style.
|
||||
|
||||
[Restrictions:] none
|
||||
|
||||
[Related commands:] none
|
||||
|
||||
[Default:] none
|
||||
|
|
@ -0,0 +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>compute temp command
|
||||
</H3>
|
||||
<P><B>Syntax:</B>
|
||||
</P>
|
||||
<PRE>compute ID group-ID temp
|
||||
</PRE>
|
||||
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
|
||||
<LI>temp = style name of this compute command
|
||||
</UL>
|
||||
<P><B>Examples:</B>
|
||||
</P>
|
||||
<PRE>compute 1 all temp
|
||||
compute myTemp mobile temp
|
||||
</PRE>
|
||||
<P><B>Description:</B>
|
||||
</P>
|
||||
<P>Define a computation that calculates the temperature of a group of
|
||||
atoms. A compute of this style can be used by any command that
|
||||
computes a temperature, e.g. <A HREF = "thermo_modify.html">thermo_modify</A>, <A HREF = "fix_temp_rescale.html">fix
|
||||
temp/rescale</A>, <A HREF = "fix_npt.html">fix npt</A>, etc.
|
||||
</P>
|
||||
<P>The temperature is calculated by the formula KE = dim/2 N k T, where
|
||||
KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2),
|
||||
dim = 2 or 3 = dimensionality of the simulation, N = number of atoms
|
||||
in the group, k = Boltzmann constant, and T = temperature.
|
||||
</P>
|
||||
<P>A 6-component kinetic energy tensor is also calculated by this compute
|
||||
for use in the computation of a pressure tensor. The formula for the
|
||||
components of the tensor is the same as the above formula, except that
|
||||
v^2 is replaced by vx * vy for the xy component, etc.
|
||||
</P>
|
||||
<P>The number of atoms contributing to the temperature is assumed to be
|
||||
constant for the duration of the run; use the <I>dynamic</I> option of the
|
||||
<A HREF = "compute_modify.html">compute_modify</A> command if this is not the case.
|
||||
</P>
|
||||
<P>This compute subtracts out degrees-of-freedom due to fixes that
|
||||
constrain molecular motion, such as <A HREF = "fix_shake.html">fix shake</A> and
|
||||
<A HREF = "fix_rigid.html">fix rigid</A>. This means the temperature of groups of
|
||||
atoms that include these constraints will be computed correctly. If
|
||||
needed, the subtracted degrees-of-freedom can be altered using the
|
||||
<I>extra</I> option of the <A HREF = "compute_modify.html">compute_modify</A> command.
|
||||
</P>
|
||||
<P><B>Restrictions:</B> none
|
||||
</P>
|
||||
<P><B>Related commands:</B>
|
||||
</P>
|
||||
<P><A HREF = "compute_temp_partial.html">compute temp/partial</A>, <A HREF = "compute_temp_region.html">compute
|
||||
temp/region</A>, <A HREF = "compute_pressure.html">compute
|
||||
pressure</A>
|
||||
</P>
|
||||
<P><B>Default:</B> none
|
||||
</P>
|
||||
</HTML>
|
||||
|
|
@ -0,0 +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
|
||||
|
||||
compute temp command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
compute ID group-ID temp :pre
|
||||
|
||||
ID, group-ID are documented in "compute"_compute.html command
|
||||
temp = style name of this compute command :ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
compute 1 all temp
|
||||
compute myTemp mobile temp :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Define a computation that calculates the temperature of a group of
|
||||
atoms. A compute of this style can be used by any command that
|
||||
computes a temperature, e.g. "thermo_modify"_thermo_modify.html, "fix
|
||||
temp/rescale"_fix_temp_rescale.html, "fix npt"_fix_npt.html, etc.
|
||||
|
||||
The temperature is calculated by the formula KE = dim/2 N k T, where
|
||||
KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2),
|
||||
dim = 2 or 3 = dimensionality of the simulation, N = number of atoms
|
||||
in the group, k = Boltzmann constant, and T = temperature.
|
||||
|
||||
A 6-component kinetic energy tensor is also calculated by this compute
|
||||
for use in the computation of a pressure tensor. The formula for the
|
||||
components of the tensor is the same as the above formula, except that
|
||||
v^2 is replaced by vx * vy for the xy component, etc.
|
||||
|
||||
The number of atoms contributing to the temperature is assumed to be
|
||||
constant for the duration of the run; use the {dynamic} option of the
|
||||
"compute_modify"_compute_modify.html command if this is not the case.
|
||||
|
||||
This compute subtracts out degrees-of-freedom due to fixes that
|
||||
constrain molecular motion, such as "fix shake"_fix_shake.html and
|
||||
"fix rigid"_fix_rigid.html. This means the temperature of groups of
|
||||
atoms that include these constraints will be computed correctly. If
|
||||
needed, the subtracted degrees-of-freedom can be altered using the
|
||||
{extra} option of the "compute_modify"_compute_modify.html command.
|
||||
|
||||
[Restrictions:] none
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"compute temp/partial"_compute_temp_partial.html, "compute
|
||||
temp/region"_compute_temp_region.html, "compute
|
||||
pressure"_compute_pressure.html
|
||||
|
||||
[Default:] none
|
||||
|
|
@ -0,0 +1,68 @@
|
|||
<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>compute temp/partial command
|
||||
</H3>
|
||||
<P><B>Syntax:</B>
|
||||
</P>
|
||||
<PRE>compute ID group-ID temp/partial xflag yflag zflag
|
||||
</PRE>
|
||||
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
|
||||
<LI>temp/partial = style name of this compute command
|
||||
<LI>xflag,yflag,zflag = 0/1 for whether to exclude/include this dimension
|
||||
</UL>
|
||||
<P><B>Examples:</B>
|
||||
</P>
|
||||
<PRE>compute newT flow temp/partial 1 1 0
|
||||
</PRE>
|
||||
<P><B>Description:</B>
|
||||
</P>
|
||||
<P>Define a compute to calculate the temperature of a group of atoms,
|
||||
after excluding one or more velocity components. A compute of this
|
||||
style can be used by any command that computes a temperature,
|
||||
e.g. <A HREF = "thermo_modify.html">thermo_modify</A>, <A HREF = "fix_temp_rescale.html">fix
|
||||
temp/rescale</A>, <A HREF = "fix_npt.html">fix npt</A>, etc.
|
||||
</P>
|
||||
<P>The temperature is calculated by the formula KE = dim/2 N k T, where
|
||||
KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2),
|
||||
dim = dimensionality of the simulation, N = number of atoms in the
|
||||
group, k = Boltzmann constant, and T = temperature. The calculation
|
||||
of KE excludes the x, y, or z dimensions if xflag, yflag, or zflag =
|
||||
0. The dim parameter is adjusted to give the correct number of
|
||||
degrees of freedom.
|
||||
</P>
|
||||
<P>A 6-component kinetic energy tensor is also calculated by this compute
|
||||
for use in the calculation of a pressure tensor. The formula for the
|
||||
components of the tensor is the same as the above formula, except that
|
||||
v^2 is replaced by vx * vy for the xy component, etc.
|
||||
</P>
|
||||
<P>The number of atoms contributing to the temperature is assumed to be
|
||||
constant for the duration of the run; use the <I>dynamic</I> option of the
|
||||
<A HREF = "compute_modify.html">compute_modify</A> command if this is not the case.
|
||||
</P>
|
||||
<P>This compute subtracts out degrees-of-freedom due to fixes that
|
||||
constrain molecular motion, such as <A HREF = "fix_shake.html">fix shake</A> and
|
||||
<A HREF = "fix_rigid.html">fix rigid</A>. This means the temperature of groups of
|
||||
atoms that include these constraints will be computed correctly. If
|
||||
needed, the subtracted degrees-of-freedom can be altered using the
|
||||
<I>extra</I> option of the <A HREF = "compute_modify.html">compute_modify</A> command.
|
||||
</P>
|
||||
<P><B>Restrictions:</B> none
|
||||
</P>
|
||||
<P><B>Related commands:</B>
|
||||
</P>
|
||||
<P><A HREF = "compute_temp.html">compute temp</A>, <A HREF = "compute_temp_region.html">compute
|
||||
temp/region</A>, <A HREF = "compute_pressure.html">compute
|
||||
pressure</A>
|
||||
</P>
|
||||
<P><B>Default:</B> none
|
||||
</P>
|
||||
</HTML>
|
||||
|
|
@ -0,0 +1,63 @@
|
|||
"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
|
||||
|
||||
compute temp/partial command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
compute ID group-ID temp/partial xflag yflag zflag :pre
|
||||
|
||||
ID, group-ID are documented in "compute"_compute.html command
|
||||
temp/partial = style name of this compute command
|
||||
xflag,yflag,zflag = 0/1 for whether to exclude/include this dimension :ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
compute newT flow temp/partial 1 1 0 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Define a compute to calculate the temperature of a group of atoms,
|
||||
after excluding one or more velocity components. A compute of this
|
||||
style can be used by any command that computes a temperature,
|
||||
e.g. "thermo_modify"_thermo_modify.html, "fix
|
||||
temp/rescale"_fix_temp_rescale.html, "fix npt"_fix_npt.html, etc.
|
||||
|
||||
The temperature is calculated by the formula KE = dim/2 N k T, where
|
||||
KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2),
|
||||
dim = dimensionality of the simulation, N = number of atoms in the
|
||||
group, k = Boltzmann constant, and T = temperature. The calculation
|
||||
of KE excludes the x, y, or z dimensions if xflag, yflag, or zflag =
|
||||
0. The dim parameter is adjusted to give the correct number of
|
||||
degrees of freedom.
|
||||
|
||||
A 6-component kinetic energy tensor is also calculated by this compute
|
||||
for use in the calculation of a pressure tensor. The formula for the
|
||||
components of the tensor is the same as the above formula, except that
|
||||
v^2 is replaced by vx * vy for the xy component, etc.
|
||||
|
||||
The number of atoms contributing to the temperature is assumed to be
|
||||
constant for the duration of the run; use the {dynamic} option of the
|
||||
"compute_modify"_compute_modify.html command if this is not the case.
|
||||
|
||||
This compute subtracts out degrees-of-freedom due to fixes that
|
||||
constrain molecular motion, such as "fix shake"_fix_shake.html and
|
||||
"fix rigid"_fix_rigid.html. This means the temperature of groups of
|
||||
atoms that include these constraints will be computed correctly. If
|
||||
needed, the subtracted degrees-of-freedom can be altered using the
|
||||
{extra} option of the "compute_modify"_compute_modify.html command.
|
||||
|
||||
[Restrictions:] none
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"compute temp"_compute_temp.html, "compute
|
||||
temp/region"_compute_temp_region.html, "compute
|
||||
pressure"_compute_pressure.html
|
||||
|
||||
[Default:] none
|
||||
|
|
@ -0,0 +1,82 @@
|
|||
<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>compute temp/ramp command
|
||||
</H3>
|
||||
<P><B>Syntax:</B>
|
||||
</P>
|
||||
<PRE>compute ID group-ID temp/ramp vdim vlo vhi dim clo chi keyword value ...
|
||||
</PRE>
|
||||
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
|
||||
<LI>temp/ramp = style name of this compute command
|
||||
<LI>vdim = <I>vx</I> or <I>vy</I> or <I>vz</I>
|
||||
<LI>vlo,vhi = subtract velocities between vlo and vhi (velocity units)
|
||||
<LI>dim = <I>x</I> or <I>y</I> or <I>z</I>
|
||||
<LI>clo,chi = lower and upper bound of domain to subtract from (distance units)
|
||||
<LI>zero or more keyword/value pairs may be appended to the args
|
||||
<LI>keyword = <I>units</I>
|
||||
</UL>
|
||||
<PRE> <I>units</I> value = <I>lattice</I> or <I>box</I>
|
||||
</PRE>
|
||||
<P><B>Examples:</B>
|
||||
</P>
|
||||
<PRE>temperature 2nd middle ramp vx 0 8 y 2 12 units lattice
|
||||
</PRE>
|
||||
<P><B>Description:</B>
|
||||
</P>
|
||||
<P>Define a computation that calculates the temperature of a group of
|
||||
atoms, while subtracting out an imposed velocity on the system before
|
||||
computing the kinetic energy. A compute of this style can be used by
|
||||
any command that computes a temperature,
|
||||
e.g. <A HREF = "thermo_modify.html">thermo_modify</A>, <A HREF = "fix_temp_rescale.html">fix
|
||||
temp/rescale</A>, <A HREF = "fix_npt.html">fix npt</A>, etc.
|
||||
</P>
|
||||
<P>The meaning of the arguments for this command is the same as for the
|
||||
<A HREF = "velocity.html">velocity</A> command which was presumably used to impose
|
||||
the velocity.
|
||||
</P>
|
||||
<P>The <I>units</I> keyword determines the meaning of the distance units used
|
||||
for coordinates (c1,c2) and velocities (vlo,vhi). A <I>box</I> value
|
||||
selects standard distance units as defined by the <A HREF = "units.html">units</A>
|
||||
command, e.g. Angstroms for units = real or metal. A <I>lattice</I> value
|
||||
means the distance units are in lattice spacings; e.g. velocity =
|
||||
lattice spacings / tau. The <A HREF = "lattice.html">lattice</A> command must have
|
||||
been previously used to define the lattice spacing.
|
||||
</P>
|
||||
<P>A 6-component kinetic energy tensor is also calculated by this compute
|
||||
for use in the calculation of a pressure tensor. The formula for the
|
||||
components of the tensor is the same as the above formula, except that
|
||||
v^2 is replaced by vx * vy for the xy component, etc.
|
||||
</P>
|
||||
<P>The number of atoms contributing to the temperature is assumed to be
|
||||
constant for the duration of the run; use the <I>dynamic</I> option of the
|
||||
<A HREF = "compute_modify.html">compute_modify</A> command if this is not the case.
|
||||
</P>
|
||||
<P>This compute subtracts out degrees-of-freedom due to fixes that
|
||||
constrain molecular motion, such as <A HREF = "fix_shake.html">fix shake</A> and
|
||||
<A HREF = "fix_rigid.html">fix rigid</A>. This means the temperature of groups of
|
||||
atoms that include these constraints will be computed correctly. If
|
||||
needed, the subtracted degrees-of-freedom can be altered using the
|
||||
<I>extra</I> option of the <A HREF = "compute_modify.html">compute_modify</A> command.
|
||||
</P>
|
||||
<P><B>Restrictions:</B> none
|
||||
</P>
|
||||
<P><B>Related commands:</B>
|
||||
</P>
|
||||
<P><A HREF = "compute_temp.html">compute temp</A>, <A HREF = "compute_temp_region.html">compute
|
||||
temp/region</A>, <A HREF = "compute_pressure.html">compute
|
||||
pressure</A>
|
||||
</P>
|
||||
<P><B>Default:</B>
|
||||
</P>
|
||||
<P>The option default is units = lattice.
|
||||
</P>
|
||||
</HTML>
|
||||
|
|
@ -0,0 +1,77 @@
|
|||
"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
|
||||
|
||||
compute temp/ramp command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
compute ID group-ID temp/ramp vdim vlo vhi dim clo chi keyword value ... :pre
|
||||
|
||||
ID, group-ID are documented in "compute"_compute.html command
|
||||
temp/ramp = style name of this compute command
|
||||
vdim = {vx} or {vy} or {vz}
|
||||
vlo,vhi = subtract velocities between vlo and vhi (velocity units)
|
||||
dim = {x} or {y} or {z}
|
||||
clo,chi = lower and upper bound of domain to subtract from (distance units)
|
||||
zero or more keyword/value pairs may be appended to the args
|
||||
keyword = {units} :ul
|
||||
{units} value = {lattice} or {box} :pre
|
||||
|
||||
[Examples:]
|
||||
|
||||
temperature 2nd middle ramp vx 0 8 y 2 12 units lattice :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Define a computation that calculates the temperature of a group of
|
||||
atoms, while subtracting out an imposed velocity on the system before
|
||||
computing the kinetic energy. A compute of this style can be used by
|
||||
any command that computes a temperature,
|
||||
e.g. "thermo_modify"_thermo_modify.html, "fix
|
||||
temp/rescale"_fix_temp_rescale.html, "fix npt"_fix_npt.html, etc.
|
||||
|
||||
The meaning of the arguments for this command is the same as for the
|
||||
"velocity"_velocity.html command which was presumably used to impose
|
||||
the velocity.
|
||||
|
||||
The {units} keyword determines the meaning of the distance units used
|
||||
for coordinates (c1,c2) and velocities (vlo,vhi). A {box} value
|
||||
selects standard distance units as defined by the "units"_units.html
|
||||
command, e.g. Angstroms for units = real or metal. A {lattice} value
|
||||
means the distance units are in lattice spacings; e.g. velocity =
|
||||
lattice spacings / tau. The "lattice"_lattice.html command must have
|
||||
been previously used to define the lattice spacing.
|
||||
|
||||
A 6-component kinetic energy tensor is also calculated by this compute
|
||||
for use in the calculation of a pressure tensor. The formula for the
|
||||
components of the tensor is the same as the above formula, except that
|
||||
v^2 is replaced by vx * vy for the xy component, etc.
|
||||
|
||||
The number of atoms contributing to the temperature is assumed to be
|
||||
constant for the duration of the run; use the {dynamic} option of the
|
||||
"compute_modify"_compute_modify.html command if this is not the case.
|
||||
|
||||
This compute subtracts out degrees-of-freedom due to fixes that
|
||||
constrain molecular motion, such as "fix shake"_fix_shake.html and
|
||||
"fix rigid"_fix_rigid.html. This means the temperature of groups of
|
||||
atoms that include these constraints will be computed correctly. If
|
||||
needed, the subtracted degrees-of-freedom can be altered using the
|
||||
{extra} option of the "compute_modify"_compute_modify.html command.
|
||||
|
||||
[Restrictions:] none
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"compute temp"_compute_temp.html, "compute
|
||||
temp/region"_compute_temp_region.html, "compute
|
||||
pressure"_compute_pressure.html
|
||||
|
||||
[Default:]
|
||||
|
||||
The option default is units = lattice.
|
||||
|
||||
|
|
@ -0,0 +1,76 @@
|
|||
<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>compute temp/region command
|
||||
</H3>
|
||||
<P><B>Syntax:</B>
|
||||
</P>
|
||||
<PRE>compute ID group-ID temp/region region-ID
|
||||
</PRE>
|
||||
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
|
||||
<LI>temp/region = style name of this compute command
|
||||
<LI>region-ID = ID of region to use for choosing atoms
|
||||
</UL>
|
||||
<P><B>Examples:</B>
|
||||
</P>
|
||||
<PRE>temperature mine flow region boundary
|
||||
</PRE>
|
||||
<P><B>Description:</B>
|
||||
</P>
|
||||
<P>Define a computation that calculates the temperature of a group of
|
||||
atoms in a geometric region. This can be useful for thermostatting
|
||||
one portion of the simulation box. E.g. a McDLT simulation where one
|
||||
side is cooled, and the other side is heated. A compute of this style
|
||||
can be used by any command that computes a temperature,
|
||||
e.g. <A HREF = "thermo_modify.html">thermo_modify</A>, <A HREF = "fix_temp_rescale.html">fix
|
||||
temp/rescale</A>, etc.
|
||||
</P>
|
||||
<P>Note that a <I>region</I>-style temperature can be used to thermostat with
|
||||
<A HREF = "fix_temp_rescale.html">fix temp/rescale</A> or <A HREF = "fix_langevin.html">fix
|
||||
langevin</A>, but should probably not be used with
|
||||
Nose/Hoover style fixes (<A HREF = "fix_nvt.html<A HREF = "fix_npt.html">>fix nvt</A>, fix
|
||||
npt</A>, or <A HREF = "fix_nph.html">fix nph</A>), if the
|
||||
degrees-of-freedom included in the computed T varies with time.
|
||||
</P>
|
||||
<P>The temperature is calculated by the formula KE = dim/2 N k T, where
|
||||
KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2),
|
||||
dim = 2 or 3 = dimensionality of the simulation, N = number of atoms
|
||||
in both the group and region, k = Boltzmann constant, and T =
|
||||
temperature.
|
||||
</P>
|
||||
<P>A 6-component kinetic energy tensor is also calculated by this compute
|
||||
for use in the computation of a pressure tensor. The formula for the
|
||||
components of the tensor is the same as the above formula, except that
|
||||
v^2 is replaced by vx * vy for the xy component, etc.
|
||||
</P>
|
||||
<P>The number of atoms contributing to the temperature is compute each
|
||||
time the temperature is evaluated since it is assumed atoms can
|
||||
enter/leave the region. Thus there is no need to use the <I>dynamic</I>
|
||||
option of the <A HREF = "compute_modify.html">compute_modify</A> command for this
|
||||
compute style.
|
||||
</P>
|
||||
<P>Unlike other compute styles that calculate temperature, this compute
|
||||
does NOT currently subtract out degrees-of-freedom due to fixes that
|
||||
constrain molecular motion, such as <A HREF = "fix_shake.html">fix shake</A> and
|
||||
<A HREF = "fix_rigid.html">fix rigid</A>. If needed the subtracted
|
||||
degrees-of-freedom can be altered using the <I>extra</I> option of the
|
||||
<A HREF = "compute_modify.html">compute_modify</A> command.
|
||||
</P>
|
||||
<P><B>Restrictions:</B> none
|
||||
</P>
|
||||
<P><B>Related commands:</B>
|
||||
</P>
|
||||
<P><A HREF = "compute_temp.html">compute temp</A>, <A HREF = "compute_pressure.html">compute
|
||||
pressure</A>
|
||||
</P>
|
||||
<P><B>Default:</B> none
|
||||
</P>
|
||||
</HTML>
|
||||
|
|
@ -0,0 +1,71 @@
|
|||
"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
|
||||
|
||||
compute temp/region command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
compute ID group-ID temp/region region-ID :pre
|
||||
|
||||
ID, group-ID are documented in "compute"_compute.html command
|
||||
temp/region = style name of this compute command
|
||||
region-ID = ID of region to use for choosing atoms :ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
temperature mine flow region boundary :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Define a computation that calculates the temperature of a group of
|
||||
atoms in a geometric region. This can be useful for thermostatting
|
||||
one portion of the simulation box. E.g. a McDLT simulation where one
|
||||
side is cooled, and the other side is heated. A compute of this style
|
||||
can be used by any command that computes a temperature,
|
||||
e.g. "thermo_modify"_thermo_modify.html, "fix
|
||||
temp/rescale"_fix_temp_rescale.html, etc.
|
||||
|
||||
Note that a {region}-style temperature can be used to thermostat with
|
||||
"fix temp/rescale"_fix_temp_rescale.html or "fix
|
||||
langevin"_fix_langevin.html, but should probably not be used with
|
||||
Nose/Hoover style fixes ("fix nvt"_fix_nvt.html, fix
|
||||
npt"_fix_npt.html, or "fix nph"_fix_nph.html), if the
|
||||
degrees-of-freedom included in the computed T varies with time.
|
||||
|
||||
The temperature is calculated by the formula KE = dim/2 N k T, where
|
||||
KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2),
|
||||
dim = 2 or 3 = dimensionality of the simulation, N = number of atoms
|
||||
in both the group and region, k = Boltzmann constant, and T =
|
||||
temperature.
|
||||
|
||||
A 6-component kinetic energy tensor is also calculated by this compute
|
||||
for use in the computation of a pressure tensor. The formula for the
|
||||
components of the tensor is the same as the above formula, except that
|
||||
v^2 is replaced by vx * vy for the xy component, etc.
|
||||
|
||||
The number of atoms contributing to the temperature is compute each
|
||||
time the temperature is evaluated since it is assumed atoms can
|
||||
enter/leave the region. Thus there is no need to use the {dynamic}
|
||||
option of the "compute_modify"_compute_modify.html command for this
|
||||
compute style.
|
||||
|
||||
Unlike other compute styles that calculate temperature, this compute
|
||||
does NOT currently subtract out degrees-of-freedom due to fixes that
|
||||
constrain molecular motion, such as "fix shake"_fix_shake.html and
|
||||
"fix rigid"_fix_rigid.html. If needed the subtracted
|
||||
degrees-of-freedom can be altered using the {extra} option of the
|
||||
"compute_modify"_compute_modify.html command.
|
||||
|
||||
[Restrictions:] none
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"compute temp"_compute_temp.html, "compute
|
||||
pressure"_compute_pressure.html
|
||||
|
||||
[Default:] none
|
||||
|
|
@ -58,7 +58,7 @@ Lennard-Jones 12/6) given by
|
|||
<P>Rc is the cutoff.
|
||||
</P>
|
||||
<P>The <I>buck/coul/cut</I> and <I>buck/coul/long</I> styles add a Coulombic term
|
||||
as described for the <A HREF = "pair_style_lj.html">lj/cut</A> pair styles.
|
||||
as described for the <A HREF = "pair_lj.html">lj/cut</A> pair styles.
|
||||
</P>
|
||||
<P>The following coefficients must be defined for each pair of atoms
|
||||
types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
|
||||
|
|
@ -52,7 +52,7 @@ Lennard-Jones 12/6) given by
|
|||
Rc is the cutoff.
|
||||
|
||||
The {buck/coul/cut} and {buck/coul/long} styles add a Coulombic term
|
||||
as described for the "lj/cut"_pair_style_lj.html pair styles.
|
||||
as described for the "lj/cut"_pair_lj.html pair styles.
|
||||
|
||||
The following coefficients must be defined for each pair of atoms
|
||||
types via the "pair_coeff"_pair_coeff.html command as in the examples
|
||||
|
|
@ -15,11 +15,13 @@
|
|||
</H3>
|
||||
<H3>pair_style lj/charmm/coul/long command
|
||||
</H3>
|
||||
<H3>pair_style lj/charmm/coul/long/opt command
|
||||
</H3>
|
||||
<P><B>Syntax:</B>
|
||||
</P>
|
||||
<PRE>pair_style style args
|
||||
</PRE>
|
||||
<UL><LI>style = <I>lj/charmm/coul/charmm</I> or <I>lj/charmm/coul/charmm/implicit</I> or <I>lj/charmm/coul/long</I>
|
||||
<UL><LI>style = <I>lj/charmm/coul/charmm</I> or <I>lj/charmm/coul/charmm/implicit</I> or <I>lj/charmm/coul/long</I> or <I>lj/charmm/coul/long/opt</I>
|
||||
<LI>args = list of arguments for a particular style
|
||||
</UL>
|
||||
<PRE> <I>lj/charmm/coul/charmm</I> args = inner outer (inner2) (outer2)
|
||||
|
|
@ -45,6 +47,7 @@ pair_coeff * * 100.0 2.0
|
|||
pair_coeff 1 1 100.0 2.0 150.0 3.5
|
||||
</PRE>
|
||||
<PRE>pair_style lj/charmm/coul/long 8.0 10.0
|
||||
pair_style lj/charmm/coul/long/opt 8.0 10.0
|
||||
pair_style lj/charmm/coul/long 8.0 10.0 9.0
|
||||
pair_coeff * * 100.0 2.0
|
||||
pair_coeff 1 1 100.0 2.0 150.0 3.5
|
||||
|
|
@ -83,6 +86,11 @@ applied to the Coulombic term, as in the discussion for pair style
|
|||
command, then the outer LJ cutoff is used as the single Coulombic
|
||||
cutoff.
|
||||
</P>
|
||||
<P>Style <I>lj/charmm/coul/long/opt</I> is an optimized version of style
|
||||
<I>lj/charmm/coul/long</I> that should give identical answers. Depending
|
||||
on system size and the processor you are running on, it may be 5-25%
|
||||
faster (for the pairwise portion of the run time).
|
||||
</P>
|
||||
<P>The following coefficients must be defined for each pair of atoms
|
||||
types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
|
||||
above, or in the data file or restart files read by the
|
||||
|
|
@ -109,9 +117,11 @@ the pair_style command.
|
|||
</P>
|
||||
<P>The <I>lj/charmm/coul/charmm</I> and <I>lj/charmm/coul/charmm/implicit</I>
|
||||
styles are part of the "molecule" package. The <I>lj/charmm/coul/long</I>
|
||||
style is part of the "kspace" package. They are only enabled if
|
||||
LAMMPS was built with those package(s). See the <A HREF = "Section_start.html#2_2">Making
|
||||
LAMMPS</A> section for more info.
|
||||
style is part of the "kspace" package. The <I>lj/charmm/coul/long/opt</I>
|
||||
style is part of the "opt" package and also requires the "kspace"
|
||||
package. They are only enabled if LAMMPS was built with those
|
||||
package(s). See the <A HREF = "Section_start.html#2_3">Making LAMMPS</A> section
|
||||
for more info.
|
||||
</P>
|
||||
<P>On some 64-bit machines, compiling with -O3 appears to break the
|
||||
Coulombic tabling option used by the <I>lj/charmm/coul/long</I> style. See
|
||||
|
|
@ -9,12 +9,13 @@
|
|||
pair_style lj/charmm/coul/charmm command :h3
|
||||
pair_style lj/charmm/coul/charmm/implicit command :h3
|
||||
pair_style lj/charmm/coul/long command :h3
|
||||
pair_style lj/charmm/coul/long/opt command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
pair_style style args :pre
|
||||
|
||||
style = {lj/charmm/coul/charmm} or {lj/charmm/coul/charmm/implicit} or {lj/charmm/coul/long}
|
||||
style = {lj/charmm/coul/charmm} or {lj/charmm/coul/charmm/implicit} or {lj/charmm/coul/long} or {lj/charmm/coul/long/opt}
|
||||
args = list of arguments for a particular style :ul
|
||||
{lj/charmm/coul/charmm} args = inner outer (inner2) (outer2)
|
||||
inner, outer = global switching cutoffs for Lennard Jones (and Coulombic if only 2 args)
|
||||
|
|
@ -39,6 +40,7 @@ pair_coeff * * 100.0 2.0
|
|||
pair_coeff 1 1 100.0 2.0 150.0 3.5 :pre
|
||||
|
||||
pair_style lj/charmm/coul/long 8.0 10.0
|
||||
pair_style lj/charmm/coul/long/opt 8.0 10.0
|
||||
pair_style lj/charmm/coul/long 8.0 10.0 9.0
|
||||
pair_coeff * * 100.0 2.0
|
||||
pair_coeff 1 1 100.0 2.0 150.0 3.5 :pre
|
||||
|
|
@ -77,6 +79,11 @@ applied to the Coulombic term, as in the discussion for pair style
|
|||
command, then the outer LJ cutoff is used as the single Coulombic
|
||||
cutoff.
|
||||
|
||||
Style {lj/charmm/coul/long/opt} is an optimized version of style
|
||||
{lj/charmm/coul/long} that should give identical answers. Depending
|
||||
on system size and the processor you are running on, it may be 5-25%
|
||||
faster (for the pairwise portion of the run time).
|
||||
|
||||
The following coefficients must be defined for each pair of atoms
|
||||
types via the "pair_coeff"_pair_coeff.html command as in the examples
|
||||
above, or in the data file or restart files read by the
|
||||
|
|
@ -103,9 +110,11 @@ the pair_style command.
|
|||
|
||||
The {lj/charmm/coul/charmm} and {lj/charmm/coul/charmm/implicit}
|
||||
styles are part of the "molecule" package. The {lj/charmm/coul/long}
|
||||
style is part of the "kspace" package. They are only enabled if
|
||||
LAMMPS was built with those package(s). See the "Making
|
||||
LAMMPS"_Section_start.html#2_2 section for more info.
|
||||
style is part of the "kspace" package. The {lj/charmm/coul/long/opt}
|
||||
style is part of the "opt" package and also requires the "kspace"
|
||||
package. They are only enabled if LAMMPS was built with those
|
||||
package(s). See the "Making LAMMPS"_Section_start.html#2_3 section
|
||||
for more info.
|
||||
|
||||
On some 64-bit machines, compiling with -O3 appears to break the
|
||||
Coulombic tabling option used by the {lj/charmm/coul/long} style. See
|
||||
|
|
@ -57,7 +57,7 @@ pair_coeff 1 1 100.0 3.5 9.0
|
|||
<P>Rc is the cutoff.
|
||||
</P>
|
||||
<P>The <I>lj/class2/coul/cut</I> and <I>lj/class2/coul/long</I> styles add a
|
||||
Coulombic term as described for the <A HREF = "pair_style_lj.html">lj/cut</A> pair
|
||||
Coulombic term as described for the <A HREF = "pair_lj.html">lj/cut</A> pair
|
||||
styles.
|
||||
</P>
|
||||
<P>See <A HREF = "#Sun">(Sun)</A> for a description of the COMPASS class2 force field.
|
||||
|
|
@ -51,7 +51,7 @@ The {lj/class2} styles compute a 6/9 Lennard-Jones potential given by
|
|||
Rc is the cutoff.
|
||||
|
||||
The {lj/class2/coul/cut} and {lj/class2/coul/long} styles add a
|
||||
Coulombic term as described for the "lj/cut"_pair_style_lj.html pair
|
||||
Coulombic term as described for the "lj/cut"_pair_lj.html pair
|
||||
styles.
|
||||
|
||||
See "(Sun)"_#Sun for a description of the COMPASS class2 force field.
|
||||
|
|
@ -19,18 +19,21 @@
|
|||
</P>
|
||||
<PRE>pair_style style
|
||||
</PRE>
|
||||
<UL><LI>style = <I>eam</I> or <I>eam/alloy</I> or <I>eam/fs</I>
|
||||
<UL><LI>style = <I>eam</I> or <I>eam/alloy</I> or <I>eam/fs</I> or <I>eam/opt</I> or <I>eam/alloy/opt</I> or <I>eam/fs/opt</I>
|
||||
</UL>
|
||||
<P><B>Examples:</B>
|
||||
</P>
|
||||
<PRE>pair_style eam
|
||||
pair_style eam/opt
|
||||
pair_coeff * * cuu3
|
||||
pair_coeff 1*3 1*3 niu3.eam
|
||||
</PRE>
|
||||
<PRE>pair_style eam/alloy
|
||||
pair_style eam/alloy/opt
|
||||
pair_coeff * * ../potentials/nialhjea.eam.alloy Ni Al Ni Ni
|
||||
</PRE>
|
||||
<PRE>pair_style eam/fs
|
||||
pair_style eam/fs/opt
|
||||
pair_coeff * * nialhjea.eam.fs Ni Al Ni Ni
|
||||
</PRE>
|
||||
<P><B>Description:</B>
|
||||
|
|
@ -48,6 +51,11 @@ nature of the EAM potential is a result of the embedding energy term.
|
|||
Both summations in the formula are over all neighbors J of atom I
|
||||
within the cutoff distance.
|
||||
</P>
|
||||
<P>Style <I>eam/opt</I> is an optimized version of style <I>eam</I> that should
|
||||
give identical answers. Depending on system size and the processor
|
||||
you are running on, it may be 5-25% faster (for the pairwise portion
|
||||
of the run time).
|
||||
</P>
|
||||
<P>The cutoff distance and the tabulated values of the functionals F,
|
||||
rho, and phi are listed in one or more files which are specified by
|
||||
the <A HREF = "pair_coeff.html">pair_coeff</A> command. These are ASCII text files
|
||||
|
|
@ -145,6 +153,11 @@ above, <I>setfl</I> files contain explicit tabulated values for alloy
|
|||
interactions. Thus they allow more generality than <I>funcfl</I> files for
|
||||
modeling alloys.
|
||||
</P>
|
||||
<P>Style <I>eam/alloy/opt</I> is an optimized version of style <I>eam/alloy</I>
|
||||
that should give identical answers. Depending on system size and the
|
||||
processor you are running on, it may be 5-25% faster (for the pairwise
|
||||
portion of the run time).
|
||||
</P>
|
||||
<P>For style <I>eam/alloy</I>, potential values are read from a file that is
|
||||
in the DYNAMO multi-element <I>setfl</I> format, except that element names
|
||||
(Ni, Cu, etc) are added to one of the lines in the file. If the
|
||||
|
|
@ -236,6 +249,11 @@ so that different elements can contribute differently to the total
|
|||
electron density at an atomic site depending on the identity of the
|
||||
element at that atomic site.
|
||||
</P>
|
||||
<P>Style <I>eam/fs/opt</I> is an optimized version of style <I>eam/fs</I> that
|
||||
should give identical answers. Depending on system size and the
|
||||
processor you are running on, it may be 5-25% faster (for the pairwise
|
||||
portion of the run time).
|
||||
</P>
|
||||
<P>The associated <A HREF = "pair_coeff.html">pair_coeff</A> command for style <I>eam/fs</I>
|
||||
reads a DYNAMO <I>setfl</I> file that has been extended to include
|
||||
additional rho_alpha_beta arrays of tabulated values. A discussion of
|
||||
|
|
@ -298,7 +316,11 @@ are listed.
|
|||
</P>
|
||||
<HR>
|
||||
|
||||
<P><B>Restrictions:</B> none
|
||||
<P><B>Restrictions:</B>
|
||||
</P>
|
||||
<P>The <I>opt</I> styles are part of the "opt" package. They are only enabled
|
||||
if LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
|
||||
LAMMPS</A> section for more info.
|
||||
</P>
|
||||
<P><B>Related commands:</B>
|
||||
</P>
|
||||
|
|
@ -14,18 +14,21 @@ pair_style eam/fs command :h3
|
|||
|
||||
pair_style style :pre
|
||||
|
||||
style = {eam} or {eam/alloy} or {eam/fs} :ul
|
||||
style = {eam} or {eam/alloy} or {eam/fs} or {eam/opt} or {eam/alloy/opt} or {eam/fs/opt} :ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
pair_style eam
|
||||
pair_style eam/opt
|
||||
pair_coeff * * cuu3
|
||||
pair_coeff 1*3 1*3 niu3.eam :pre
|
||||
|
||||
pair_style eam/alloy
|
||||
pair_style eam/alloy/opt
|
||||
pair_coeff * * ../potentials/nialhjea.eam.alloy Ni Al Ni Ni :pre
|
||||
|
||||
pair_style eam/fs
|
||||
pair_style eam/fs/opt
|
||||
pair_coeff * * nialhjea.eam.fs Ni Al Ni Ni :pre
|
||||
|
||||
[Description:]
|
||||
|
|
@ -43,6 +46,11 @@ nature of the EAM potential is a result of the embedding energy term.
|
|||
Both summations in the formula are over all neighbors J of atom I
|
||||
within the cutoff distance.
|
||||
|
||||
Style {eam/opt} is an optimized version of style {eam} that should
|
||||
give identical answers. Depending on system size and the processor
|
||||
you are running on, it may be 5-25% faster (for the pairwise portion
|
||||
of the run time).
|
||||
|
||||
The cutoff distance and the tabulated values of the functionals F,
|
||||
rho, and phi are listed in one or more files which are specified by
|
||||
the "pair_coeff"_pair_coeff.html command. These are ASCII text files
|
||||
|
|
@ -140,6 +148,11 @@ above, {setfl} files contain explicit tabulated values for alloy
|
|||
interactions. Thus they allow more generality than {funcfl} files for
|
||||
modeling alloys.
|
||||
|
||||
Style {eam/alloy/opt} is an optimized version of style {eam/alloy}
|
||||
that should give identical answers. Depending on system size and the
|
||||
processor you are running on, it may be 5-25% faster (for the pairwise
|
||||
portion of the run time).
|
||||
|
||||
For style {eam/alloy}, potential values are read from a file that is
|
||||
in the DYNAMO multi-element {setfl} format, except that element names
|
||||
(Ni, Cu, etc) are added to one of the lines in the file. If the
|
||||
|
|
@ -231,6 +244,11 @@ so that different elements can contribute differently to the total
|
|||
electron density at an atomic site depending on the identity of the
|
||||
element at that atomic site.
|
||||
|
||||
Style {eam/fs/opt} is an optimized version of style {eam/fs} that
|
||||
should give identical answers. Depending on system size and the
|
||||
processor you are running on, it may be 5-25% faster (for the pairwise
|
||||
portion of the run time).
|
||||
|
||||
The associated "pair_coeff"_pair_coeff.html command for style {eam/fs}
|
||||
reads a DYNAMO {setfl} file that has been extended to include
|
||||
additional rho_alpha_beta arrays of tabulated values. A discussion of
|
||||
|
|
@ -293,7 +311,11 @@ are listed.
|
|||
|
||||
:line
|
||||
|
||||
[Restrictions:] none
|
||||
[Restrictions:]
|
||||
|
||||
The {opt} styles are part of the "opt" package. They are only enabled
|
||||
if LAMMPS was built with that package. See the "Making
|
||||
LAMMPS"_Section_start.html#2_3 section for more info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
Some files were not shown because too many files have changed in this diff Show More
Loading…
Reference in New Issue