forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2726 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
3d1ba30578
commit
ea615ff444
Binary file not shown.
|
After Width: | Height: | Size: 3.6 KiB |
|
|
@ -0,0 +1,15 @@
|
|||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
C_e \rho_e \frac{\partial T_e}{\partial t} =
|
||||
\bigtriangledown (\kappa_e \bigtriangledown T_e) -
|
||||
g_p (T_e - T_a) + g_s T_a'
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
|
||||
|
||||
|
||||
|
||||
|
|
@ -0,0 +1,178 @@
|
|||
<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>fix ttm command
|
||||
</H3>
|
||||
<P><B>Syntax:</B>
|
||||
</P>
|
||||
<PRE>fix ID group-ID ttm seed e_specific_heat e_density e_thermal_conductivity gamma_p gamma_s v_0 nxnodes nynodes nznodes T_infile N T_outfile
|
||||
</PRE>
|
||||
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
|
||||
<LI>ttm = style name of this fix command
|
||||
<LI>seed = random number seed to use for white noise (positive integer)
|
||||
<LI>e_specific_heat = electronic specific heat (energy/(electron*temperature) units)
|
||||
<LI>e_density = electronic density (electrons/volume units)
|
||||
<LI>e_thermal_conductivity = electronic thermal conductivity (energy/(time*distance*temperature) units)
|
||||
<LI>gamma_p = friction coefficient due to electron-ion interactions (mass/time units)
|
||||
<LI>gamma_s = friction coefficient due to electronic stopping (mass/time units)
|
||||
<LI>v_0 = electronic stopping critical velocity (velocity units)
|
||||
<LI>nxnodes = number of thermal solve grid points in the x-direction (positive integer)
|
||||
<LI>nynodes = number of thermal solve grid points in the y-direction (positive integer)
|
||||
<LI>nznodes = number of thermal solve grid points in the z-direction (positive integer)
|
||||
<LI>T_infile = filename to read initial electronic temperature from
|
||||
<LI>N = dump TTM temperatures every this many timesteps, 0 = no dump
|
||||
<LI>T_outfile = filename to write TTM temperatures to (only needed if N > 0)
|
||||
</UL>
|
||||
<P><B>Examples:</B>
|
||||
</P>
|
||||
<PRE>fix 2 all ttm 699489 1.0 1.0 10 0.1 0.0 2.0 1 12 1 initialTs 1000 T.out
|
||||
fix 2 all ttm 123456 1.0 1.0 1.0 1.0 1.0 5.0 5 5 5 Te.in 1 Te.out
|
||||
</PRE>
|
||||
<P><B>Description:</B>
|
||||
</P>
|
||||
<P>Use a two-temperature model (TTM) to represent heat transfer through
|
||||
and between electronic and atomic subsystems. LAMMPS models the
|
||||
atomic subsystem as usual with a molecular dynamics model and the
|
||||
classical force field specified by the user, but the electronic
|
||||
subsystem is modeled as a continuum, or a background "gas", on a
|
||||
regular grid. Energy can be transferred spatially within the grid
|
||||
representing the electrons. Energy can also be transferred between
|
||||
the electronic and the atomic subsystems. The algorithm underlying
|
||||
this fix was derived by D. M. Duffy and A. M. Rutherford and is
|
||||
discussed in two J Physics: Condensed Matter papers: <A HREF = "#Duffy">(Duffy)</A>
|
||||
and <A HREF = "#Rutherford">(Rutherford)</A>. They used this algorithm in cascade
|
||||
simulations where a primary knock-on atom (PKA) was initialized with a
|
||||
high velocity to simulate a radiation event.
|
||||
</P>
|
||||
<P>Heat transfer between the electronic and atomic subsystems is carried
|
||||
out via an inhomogeneous Langevin thermostat. This thermostat differs
|
||||
from the regular Langevin thermostat (<A HREF = "fix_langevin.html">fix
|
||||
langevin</A>) in three important ways. First, the
|
||||
Langevin thermostat is applied uniformly to all atoms in the
|
||||
user-specified group, whereas the TTM fix applies Langevin
|
||||
thermostatting locally within the volumes represented by the
|
||||
user-specified grid points. Second, the Langevin thermostat couples
|
||||
the temperature of the atoms to an infinite heat reservoir, whereas
|
||||
the heat reservoir for fix TTM is finite and represents the local
|
||||
electrons. Third, the TTM fix allows users to specify not just one
|
||||
friction coefficient, but rather two independent friction
|
||||
coefficients: one for the electron-ion interactions and one for
|
||||
electron stopping.
|
||||
</P>
|
||||
<P>When the friction coefficient due to electron stopping, <I>gamma_s</I>, is
|
||||
non-zero, electron stopping effects are included for atoms moving
|
||||
faster than the electron stopping critical velocity, <I>v_0</I>. For
|
||||
further details about this algorithm, see <A HREF = "#Duffy">(Duffy)</A> and
|
||||
<A HREF = "#Rutherford">(Rutherford)</A>.
|
||||
</P>
|
||||
<P>Energy transport within the electronic subsystem is solved according
|
||||
to the heat diffusion equation with added source terms for heat
|
||||
transfer between the subsystems:
|
||||
</P>
|
||||
<CENTER><IMG SRC = "Eqs/fix_ttm.jpg">
|
||||
</CENTER>
|
||||
<P>where C is the specific heat, rho is the density, kappa is the thermal
|
||||
conductivity, and the "e" and "a" subscripts represent the electronic
|
||||
and atomic subsystems respectively. g_p is the coupling constant for
|
||||
the electron-ion interaction, and g_s is the electron stopping
|
||||
coupling parameter. The form of the heat diffusion equation used here
|
||||
is almost the same as that in equation 6 of <A HREF = "#Duffy">(Duffy)</A>, with the
|
||||
exception that the electronic density is explicitly reprensented,
|
||||
rather than being part of the the specific heat parameter.
|
||||
</P>
|
||||
<P>Currently, this fix assumes that none of the user-supplied parameters
|
||||
will vary with temperature. This assumption can be relaxed by
|
||||
modifying the source code to include the desired temperature
|
||||
dependency and functional form for any of the parameters. Note that
|
||||
<A HREF = "#Duffy">(Duffy)</A> used a tanh() functional form for the temperature
|
||||
dependence of the electronic specific heat, but ignored temperature
|
||||
dependencies of any of the other parameters.
|
||||
</P>
|
||||
<P>This fix requires use of periodic boundary conditions and a 3D
|
||||
simulation. Periodic boundary conditions are also used in the heat
|
||||
equation solve for the electronic subsystem. This varies from the
|
||||
approach of <A HREF = "#Rutherford">(Rutherford)</A> where the atomic subsystem was
|
||||
embedded within a larger continuum representation of the electronic
|
||||
subsystem.
|
||||
</P>
|
||||
<P>The initial electronic temperature input file, <I>T_infile</I>, is a text
|
||||
file LAMMPS reads in with no header and with four numeric columns
|
||||
(ix,iy,iz,Temp) and with a number of rows equal to the number of
|
||||
user-specified grid points (nxnodes*nynodes*nznodes). The ix,iy,iz
|
||||
are node indices from 0 to nxnodes-1, etc. For example, the initial
|
||||
electronic temperatures on a 1 by 2 by 3 grid could be specified in a
|
||||
<I>T_infile</I> as follows:
|
||||
</P>
|
||||
<PRE>0 0 0 1.0
|
||||
0 0 1 1.0
|
||||
0 0 2 1.0
|
||||
0 1 0 2.0
|
||||
0 1 1 2.0
|
||||
0 1 2 2.0
|
||||
</PRE>
|
||||
<P>where the electronic temperatures along the nynodes=0 plane have been
|
||||
set to 1.0, and the electronic temperatures along the nynodes=1 plane
|
||||
have been set to 2.0. The order of lines in this file is unimportant.
|
||||
If all the nodal values are not specified, LAMMPS will generate an
|
||||
error.
|
||||
</P>
|
||||
<P>The temperature output file, <I>T_oufile</I>, is created and written by
|
||||
this fix. Temperatures for both the electronic and atomic subsystems
|
||||
at every node and every N timesteps are output. If N is specified as
|
||||
zero, no output is generated, and no output filename is needed. The
|
||||
format of the output is as follows. One long line is written every
|
||||
output timestep. The timestep itself is given in the first column.
|
||||
The next nxnodes*nynodes*nznodes columns contain the temperatures for
|
||||
the atomic subsystem, and the final nxnodes*nynodes*nznodes columns
|
||||
contain the temperatures for the electronic subsystem. The ordering
|
||||
of the nxnodes*nynodes*nznodes columns is with the z index varing
|
||||
fastest, y the next fastest, and x the slowest.
|
||||
</P>
|
||||
<P>This fix does not change the coordinates of its atoms; it only scales
|
||||
their velocities. Thus a time integration fix (e.g. <A HREF = "fix_nve.html">fix
|
||||
nve</A>) should still be used to time integrate the affected
|
||||
atoms. This fix should not normally be used on atoms that have their
|
||||
temperature controlled by another fix - e.g. <A HREF = "fix_nvt.html">fix nvt</A> or
|
||||
<A HREF = "fix_langevin.html">fix langevin</A>.
|
||||
</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
|
||||
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
|
||||
are relevant to this fix. No global scalar or vector or per-atom
|
||||
quantities are stored by this fix for access by various <A HREF = "Section_howto.html#4_15">output
|
||||
commands</A>. No parameter of this fix can be
|
||||
used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
|
||||
This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
|
||||
</P>
|
||||
<P><B>Restrictions:</B>
|
||||
</P>
|
||||
<P>This fix can only be used for 3d simulations and orthogonal
|
||||
simlulation boxes. You must use periodic <A HREF = "doc/boundary.html">boundary</A>
|
||||
conditions with this fix.
|
||||
</P>
|
||||
<P><B>Related commands:</B>
|
||||
</P>
|
||||
<P><A HREF = "fix_langevin.html">fix langevin</A>, <A HREF = "fix_dt_reset.html">fix dt/reset</A>
|
||||
</P>
|
||||
<P><B>Default:</B> none
|
||||
</P>
|
||||
<A NAME = "Duffy"></A>
|
||||
|
||||
<P><B>(Duffy)</B> D M Duffy and A M Rutherford, J. Phys.: Condens. Matter, 19,
|
||||
016207-016218 (2007).
|
||||
</P>
|
||||
<A NAME = "Rutherford"></A>
|
||||
|
||||
<P><B>(Rutherford)</B> A M Rutherford and D M Duffy, J. Phys.:
|
||||
Condens. Matter, 19, 496201-496210 (2007).
|
||||
</P>
|
||||
</HTML>
|
||||
|
|
@ -0,0 +1,171 @@
|
|||
"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
|
||||
|
||||
fix ttm command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
fix ID group-ID ttm seed e_specific_heat e_density e_thermal_conductivity gamma_p gamma_s v_0 nxnodes nynodes nznodes T_infile N T_outfile :pre
|
||||
|
||||
ID, group-ID are documented in "fix"_fix.html command
|
||||
ttm = style name of this fix command
|
||||
seed = random number seed to use for white noise (positive integer)
|
||||
e_specific_heat = electronic specific heat (energy/(electron*temperature) units)
|
||||
e_density = electronic density (electrons/volume units)
|
||||
e_thermal_conductivity = electronic thermal conductivity (energy/(time*distance*temperature) units)
|
||||
gamma_p = friction coefficient due to electron-ion interactions (mass/time units)
|
||||
gamma_s = friction coefficient due to electronic stopping (mass/time units)
|
||||
v_0 = electronic stopping critical velocity (velocity units)
|
||||
nxnodes = number of thermal solve grid points in the x-direction (positive integer)
|
||||
nynodes = number of thermal solve grid points in the y-direction (positive integer)
|
||||
nznodes = number of thermal solve grid points in the z-direction (positive integer)
|
||||
T_infile = filename to read initial electronic temperature from
|
||||
N = dump TTM temperatures every this many timesteps, 0 = no dump
|
||||
T_outfile = filename to write TTM temperatures to (only needed if N > 0) :ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
fix 2 all ttm 699489 1.0 1.0 10 0.1 0.0 2.0 1 12 1 initialTs 1000 T.out
|
||||
fix 2 all ttm 123456 1.0 1.0 1.0 1.0 1.0 5.0 5 5 5 Te.in 1 Te.out :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Use a two-temperature model (TTM) to represent heat transfer through
|
||||
and between electronic and atomic subsystems. LAMMPS models the
|
||||
atomic subsystem as usual with a molecular dynamics model and the
|
||||
classical force field specified by the user, but the electronic
|
||||
subsystem is modeled as a continuum, or a background "gas", on a
|
||||
regular grid. Energy can be transferred spatially within the grid
|
||||
representing the electrons. Energy can also be transferred between
|
||||
the electronic and the atomic subsystems. The algorithm underlying
|
||||
this fix was derived by D. M. Duffy and A. M. Rutherford and is
|
||||
discussed in two J Physics: Condensed Matter papers: "(Duffy)"_#Duffy
|
||||
and "(Rutherford)"_#Rutherford. They used this algorithm in cascade
|
||||
simulations where a primary knock-on atom (PKA) was initialized with a
|
||||
high velocity to simulate a radiation event.
|
||||
|
||||
Heat transfer between the electronic and atomic subsystems is carried
|
||||
out via an inhomogeneous Langevin thermostat. This thermostat differs
|
||||
from the regular Langevin thermostat ("fix
|
||||
langevin"_fix_langevin.html) in three important ways. First, the
|
||||
Langevin thermostat is applied uniformly to all atoms in the
|
||||
user-specified group, whereas the TTM fix applies Langevin
|
||||
thermostatting locally within the volumes represented by the
|
||||
user-specified grid points. Second, the Langevin thermostat couples
|
||||
the temperature of the atoms to an infinite heat reservoir, whereas
|
||||
the heat reservoir for fix TTM is finite and represents the local
|
||||
electrons. Third, the TTM fix allows users to specify not just one
|
||||
friction coefficient, but rather two independent friction
|
||||
coefficients: one for the electron-ion interactions and one for
|
||||
electron stopping.
|
||||
|
||||
When the friction coefficient due to electron stopping, {gamma_s}, is
|
||||
non-zero, electron stopping effects are included for atoms moving
|
||||
faster than the electron stopping critical velocity, {v_0}. For
|
||||
further details about this algorithm, see "(Duffy)"_#Duffy and
|
||||
"(Rutherford)"_#Rutherford.
|
||||
|
||||
Energy transport within the electronic subsystem is solved according
|
||||
to the heat diffusion equation with added source terms for heat
|
||||
transfer between the subsystems:
|
||||
|
||||
:c,image(Eqs/fix_ttm.jpg)
|
||||
|
||||
where C is the specific heat, rho is the density, kappa is the thermal
|
||||
conductivity, and the "e" and "a" subscripts represent the electronic
|
||||
and atomic subsystems respectively. g_p is the coupling constant for
|
||||
the electron-ion interaction, and g_s is the electron stopping
|
||||
coupling parameter. The form of the heat diffusion equation used here
|
||||
is almost the same as that in equation 6 of "(Duffy)"_#Duffy, with the
|
||||
exception that the electronic density is explicitly reprensented,
|
||||
rather than being part of the the specific heat parameter.
|
||||
|
||||
Currently, this fix assumes that none of the user-supplied parameters
|
||||
will vary with temperature. This assumption can be relaxed by
|
||||
modifying the source code to include the desired temperature
|
||||
dependency and functional form for any of the parameters. Note that
|
||||
"(Duffy)"_#Duffy used a tanh() functional form for the temperature
|
||||
dependence of the electronic specific heat, but ignored temperature
|
||||
dependencies of any of the other parameters.
|
||||
|
||||
This fix requires use of periodic boundary conditions and a 3D
|
||||
simulation. Periodic boundary conditions are also used in the heat
|
||||
equation solve for the electronic subsystem. This varies from the
|
||||
approach of "(Rutherford)"_#Rutherford where the atomic subsystem was
|
||||
embedded within a larger continuum representation of the electronic
|
||||
subsystem.
|
||||
|
||||
The initial electronic temperature input file, {T_infile}, is a text
|
||||
file LAMMPS reads in with no header and with four numeric columns
|
||||
(ix,iy,iz,Temp) and with a number of rows equal to the number of
|
||||
user-specified grid points (nxnodes*nynodes*nznodes). The ix,iy,iz
|
||||
are node indices from 0 to nxnodes-1, etc. For example, the initial
|
||||
electronic temperatures on a 1 by 2 by 3 grid could be specified in a
|
||||
{T_infile} as follows:
|
||||
|
||||
0 0 0 1.0
|
||||
0 0 1 1.0
|
||||
0 0 2 1.0
|
||||
0 1 0 2.0
|
||||
0 1 1 2.0
|
||||
0 1 2 2.0 :pre
|
||||
|
||||
where the electronic temperatures along the nynodes=0 plane have been
|
||||
set to 1.0, and the electronic temperatures along the nynodes=1 plane
|
||||
have been set to 2.0. The order of lines in this file is unimportant.
|
||||
If all the nodal values are not specified, LAMMPS will generate an
|
||||
error.
|
||||
|
||||
The temperature output file, {T_oufile}, is created and written by
|
||||
this fix. Temperatures for both the electronic and atomic subsystems
|
||||
at every node and every N timesteps are output. If N is specified as
|
||||
zero, no output is generated, and no output filename is needed. The
|
||||
format of the output is as follows. One long line is written every
|
||||
output timestep. The timestep itself is given in the first column.
|
||||
The next nxnodes*nynodes*nznodes columns contain the temperatures for
|
||||
the atomic subsystem, and the final nxnodes*nynodes*nznodes columns
|
||||
contain the temperatures for the electronic subsystem. The ordering
|
||||
of the nxnodes*nynodes*nznodes columns is with the z index varing
|
||||
fastest, y the next fastest, and x the slowest.
|
||||
|
||||
This fix does not change the coordinates of its atoms; it only scales
|
||||
their velocities. Thus a time integration fix (e.g. "fix
|
||||
nve"_fix_nve.html) should still be used to time integrate the affected
|
||||
atoms. This fix should not normally be used on atoms that have their
|
||||
temperature controlled by another fix - e.g. "fix nvt"_fix_nvt.html or
|
||||
"fix langevin"_fix_langevin.html.
|
||||
|
||||
[Restart, fix_modify, output, run start/stop, minimize info:]
|
||||
|
||||
No information about this fix is written to "binary restart
|
||||
files"_restart.html. None of the "fix_modify"_fix_modify.html options
|
||||
are relevant to this fix. No global scalar or vector or per-atom
|
||||
quantities are stored by this fix for access by various "output
|
||||
commands"_Section_howto.html#4_15. No parameter of this fix can be
|
||||
used with the {start/stop} keywords of the "run"_run.html command.
|
||||
This fix is not invoked during "energy minimization"_minimize.html.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This fix can only be used for 3d simulations and orthogonal
|
||||
simlulation boxes. You must use periodic "boundary"_doc/boundary.html
|
||||
conditions with this fix.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"fix langevin"_fix_langevin.html, "fix dt/reset"_fix_dt_reset.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
:link(Duffy)
|
||||
[(Duffy)] D M Duffy and A M Rutherford, J. Phys.: Condens. Matter, 19,
|
||||
016207-016218 (2007).
|
||||
|
||||
:link(Rutherford)
|
||||
[(Rutherford)] A M Rutherford and D M Duffy, J. Phys.:
|
||||
Condens. Matter, 19, 496201-496210 (2007).
|
||||
Loading…
Reference in New Issue