Commit 923ee610 authored by sjplimp's avatar sjplimp
Browse files

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1926 f3b2605a-c512-4ea7-a41b-209d697bcdaa
parent 48995a8f
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+19 −11
Original line number Original line Diff line number Diff line
@@ -23,7 +23,7 @@


<LI>edim = <I>x</I> or <I>y</I> or <I>z</I> = direction of kinetic energy transfer 
<LI>edim = <I>x</I> or <I>y</I> or <I>z</I> = direction of kinetic energy transfer 


<LI>Nbin = # of layers in edim direction 
<LI>Nbin = # of layers in edim direction (must be even number) 


<LI>zero or more keyword/value pairs may be appended 
<LI>zero or more keyword/value pairs may be appended 


@@ -53,16 +53,17 @@ Muller-Plathe method, the heat flux is imposed, and the temperature
gradient is the system's response.
gradient is the system's response.
</P>
</P>
<P>The simulation box is divided into <I>Nbin</I> layers in the <I>edim</I>
<P>The simulation box is divided into <I>Nbin</I> layers in the <I>edim</I>
direction.  Every N steps, Nswap pairs of atoms are chosen in the
direction, where the layer 1 is at the low end of that dimension and
following manner.  Only atoms in the fix group are considered.  The
the layer <I>Nbin</I> is at the high end.  Every N steps, Nswap pairs of
hottest Nswap atoms in the bottom layer are selected.  Similarly, the
atoms are chosen in the following manner.  Only atoms in the fix group
coldest Nswap atoms in the middle later are selected.  The two sets of
are considered.  The hottest Nswap atoms in layer 1 are selected.
Nswap atoms are paired up and their velocities are exchanged.  This
Similarly, the coldest Nswap atoms in the "middle" layer (see below)
effectively swaps their kinetic energies, assuming their masses are
are selected.  The two sets of Nswap atoms are paired up and their
the same.  Over time, this induces a temperature gradient in the
velocities are exchanged.  This effectively swaps their kinetic
system which can be measured using commands such as the following,
energies, assuming their masses are the same.  Over time, this induces
which writes the temperature profile (assuming z = edim) to the file
a temperature gradient in the system which can be measured using
tmp.profile:
commands such as the following, which writes the temperature profile
(assuming z = edim) to the file tmp.profile:
</P>
</P>
<PRE>compute   ke all ke/atom
<PRE>compute   ke all ke/atom
variable  temp atom c_ke<B></B>/1.5
variable  temp atom c_ke<B></B>/1.5
@@ -75,6 +76,13 @@ conjunction with the swap rate N, allows the heat flux to be adjusted
across a wide range of values, and the kinetic energy to be exchanged
across a wide range of values, and the kinetic energy to be exchanged
in large chunks or more smoothly.
in large chunks or more smoothly.
</P>
</P>
<P>The "middle" layer for velocity swapping is defined as the <I>Nbin</I>/2 +
1 layer.  Thus if <I>Nbin</I> = 20, the two swapping layers are 1 and 11.
This should lead to a symmetric temperature profile since the two
layers are separated by the same distance in both directions in a
periodic sense.  This is why <I>Nbin</I> is restricted to being an even
number.
</P>
<P>As described below, the total kinetic energy transferred by these
<P>As described below, the total kinetic energy transferred by these
swaps is computed by the fix and can be output.  Dividing this
swaps is computed by the fix and can be output.  Dividing this
quantity by time and the cross-sectional area of the simulation box
quantity by time and the cross-sectional area of the simulation box
+19 −11
Original line number Original line Diff line number Diff line
@@ -16,7 +16,7 @@ ID, group-ID are documented in "fix"_fix.html command :ulb,l
thermal/conductivity = style name of this fix command :l
thermal/conductivity = style name of this fix command :l
N = perform kinetic energy exchange every N steps :l
N = perform kinetic energy exchange every N steps :l
edim = {x} or {y} or {z} = direction of kinetic energy transfer :l
edim = {x} or {y} or {z} = direction of kinetic energy transfer :l
Nbin = # of layers in edim direction :l
Nbin = # of layers in edim direction (must be even number) :l


zero or more keyword/value pairs may be appended :l
zero or more keyword/value pairs may be appended :l
keyword = {swap} :l
keyword = {swap} :l
@@ -43,16 +43,17 @@ Muller-Plathe method, the heat flux is imposed, and the temperature
gradient is the system's response.
gradient is the system's response.


The simulation box is divided into {Nbin} layers in the {edim}
The simulation box is divided into {Nbin} layers in the {edim}
direction.  Every N steps, Nswap pairs of atoms are chosen in the
direction, where the layer 1 is at the low end of that dimension and
following manner.  Only atoms in the fix group are considered.  The
the layer {Nbin} is at the high end.  Every N steps, Nswap pairs of
hottest Nswap atoms in the bottom layer are selected.  Similarly, the
atoms are chosen in the following manner.  Only atoms in the fix group
coldest Nswap atoms in the middle later are selected.  The two sets of
are considered.  The hottest Nswap atoms in layer 1 are selected.
Nswap atoms are paired up and their velocities are exchanged.  This
Similarly, the coldest Nswap atoms in the "middle" layer (see below)
effectively swaps their kinetic energies, assuming their masses are
are selected.  The two sets of Nswap atoms are paired up and their
the same.  Over time, this induces a temperature gradient in the
velocities are exchanged.  This effectively swaps their kinetic
system which can be measured using commands such as the following,
energies, assuming their masses are the same.  Over time, this induces
which writes the temperature profile (assuming z = edim) to the file
a temperature gradient in the system which can be measured using
tmp.profile:
commands such as the following, which writes the temperature profile
(assuming z = edim) to the file tmp.profile:


compute   ke all ke/atom
compute   ke all ke/atom
variable  temp atom c_ke[]/1.5
variable  temp atom c_ke[]/1.5
@@ -65,6 +66,13 @@ conjunction with the swap rate N, allows the heat flux to be adjusted
across a wide range of values, and the kinetic energy to be exchanged
across a wide range of values, and the kinetic energy to be exchanged
in large chunks or more smoothly.
in large chunks or more smoothly.


The "middle" layer for velocity swapping is defined as the {Nbin}/2 +
1 layer.  Thus if {Nbin} = 20, the two swapping layers are 1 and 11.
This should lead to a symmetric temperature profile since the two
layers are separated by the same distance in both directions in a
periodic sense.  This is why {Nbin} is restricted to being an even
number.

As described below, the total kinetic energy transferred by these
As described below, the total kinetic energy transferred by these
swaps is computed by the fix and can be output.  Dividing this
swaps is computed by the fix and can be output.  Dividing this
quantity by time and the cross-sectional area of the simulation box
quantity by time and the cross-sectional area of the simulation box
+20 −13
Original line number Original line Diff line number Diff line
@@ -25,7 +25,7 @@


<LI>pdim = <I>x</I> or <I>y</I> or <I>z</I> = direction of momentum transfer 
<LI>pdim = <I>x</I> or <I>y</I> or <I>z</I> = direction of momentum transfer 


<LI>Nbin = # of layers in pdim direction 
<LI>Nbin = # of layers in pdim direction (must be even number) 


<LI>zero or more keyword/value pairs may be appended 
<LI>zero or more keyword/value pairs may be appended 


@@ -57,18 +57,19 @@ momentum flux is imposed, and the shear velocity profile is the
system's response.
system's response.
</P>
</P>
<P>The simulation box is divided into <I>Nbin</I> layers in the <I>pdim</I>
<P>The simulation box is divided into <I>Nbin</I> layers in the <I>pdim</I>
direction.  Every N steps, Nswap pairs of atoms are chosen in the
direction, where the layer 1 is at the low end of that dimension and
following manner.  Only atoms in the fix group are considered.  Nswap
the layer <I>Nbin</I> is at the high end.  Every N steps, Nswap pairs of
atoms in the bottom layer with positive velocity components in the
atoms are chosen in the following manner.  Only atoms in the fix group
<I>vdim</I> direction closest to the target value <I>V</I> are selected.
are considered.  Nswap atoms in layer 1 with positive velocity
Similarly, Nswap atoms in the middle later with negative velocity
components in the <I>vdim</I> direction closest to the target value <I>V</I> are
components in the <I>vdim</I> direction closest to the negative of the
selected.  Similarly, Nswap atoms in the "middle" layer (see below) with
target value <I>V</I> are selected.  The two sets of Nswap atoms are paired
negative velocity components in the <I>vdim</I> direction closest to the
up and their <I>vdim</I> momenta components are swapped within each pair.
negative of the target value <I>V</I> are selected.  The two sets of Nswap
This resets their velocities, typically in opposite directions.  Over
atoms are paired up and their <I>vdim</I> momenta components are swapped
time, this induces a shear velocity profile in the system which can be
within each pair.  This resets their velocities, typically in opposite
measured using commands such as the following, which writes the
directions.  Over time, this induces a shear velocity profile in the
profile to the file tmp.profile:
system which can be measured using commands such as the following,
which writes the profile to the file tmp.profile:
</P>
</P>
<PRE>fix f1 all ave/spatial 100 10 1000 z lower 0.05 vx &
<PRE>fix f1 all ave/spatial 100 10 1000 z lower 0.05 vx &
    file tmp.profile units reduced 
    file tmp.profile units reduced 
@@ -81,6 +82,12 @@ conjunction with the swap rate N, allows the momentum flux rate to be
adjusted across a wide range of values, and the momenta to be
adjusted across a wide range of values, and the momenta to be
exchanged in large chunks or more smoothly.
exchanged in large chunks or more smoothly.
</P>
</P>
<P>The "middle" layer for momenta swapping is defined as the <I>Nbin</I>/2 + 1
layer.  Thus if <I>Nbin</I> = 20, the two swapping layers are 1 and 11.
This should lead to a symmetric velocity profile since the two layers
are separated by the same distance in both directions in a periodic
sense.  This is why <I>Nbin</I> is restricted to being an even number.
</P>
<P>As described below, the total momentum transferred by these velocity
<P>As described below, the total momentum transferred by these velocity
swaps is computed by the fix and can be output.  Dividing this
swaps is computed by the fix and can be output.  Dividing this
quantity by time and the cross-sectional area of the simulation box
quantity by time and the cross-sectional area of the simulation box
+20 −13
Original line number Original line Diff line number Diff line
@@ -17,7 +17,7 @@ viscosity = style name of this fix command :l
N = perform momentum exchange every N steps :l
N = perform momentum exchange every N steps :l
vdim = {x} or {y} or {z} = which momentum component to exchange :l
vdim = {x} or {y} or {z} = which momentum component to exchange :l
pdim = {x} or {y} or {z} = direction of momentum transfer :l
pdim = {x} or {y} or {z} = direction of momentum transfer :l
Nbin = # of layers in pdim direction :l
Nbin = # of layers in pdim direction (must be even number) :l


zero or more keyword/value pairs may be appended :l
zero or more keyword/value pairs may be appended :l
keyword = {swap} or {target} :l
keyword = {swap} or {target} :l
@@ -46,18 +46,19 @@ momentum flux is imposed, and the shear velocity profile is the
system's response.
system's response.


The simulation box is divided into {Nbin} layers in the {pdim}
The simulation box is divided into {Nbin} layers in the {pdim}
direction.  Every N steps, Nswap pairs of atoms are chosen in the
direction, where the layer 1 is at the low end of that dimension and
following manner.  Only atoms in the fix group are considered.  Nswap
the layer {Nbin} is at the high end.  Every N steps, Nswap pairs of
atoms in the bottom layer with positive velocity components in the
atoms are chosen in the following manner.  Only atoms in the fix group
{vdim} direction closest to the target value {V} are selected.
are considered.  Nswap atoms in layer 1 with positive velocity
Similarly, Nswap atoms in the middle later with negative velocity
components in the {vdim} direction closest to the target value {V} are
components in the {vdim} direction closest to the negative of the
selected.  Similarly, Nswap atoms in the "middle" layer (see below) with
target value {V} are selected.  The two sets of Nswap atoms are paired
negative velocity components in the {vdim} direction closest to the
up and their {vdim} momenta components are swapped within each pair.
negative of the target value {V} are selected.  The two sets of Nswap
This resets their velocities, typically in opposite directions.  Over
atoms are paired up and their {vdim} momenta components are swapped
time, this induces a shear velocity profile in the system which can be
within each pair.  This resets their velocities, typically in opposite
measured using commands such as the following, which writes the
directions.  Over time, this induces a shear velocity profile in the
profile to the file tmp.profile:
system which can be measured using commands such as the following,
which writes the profile to the file tmp.profile:


fix f1 all ave/spatial 100 10 1000 z lower 0.05 vx &
fix f1 all ave/spatial 100 10 1000 z lower 0.05 vx &
    file tmp.profile units reduced :pre
    file tmp.profile units reduced :pre
@@ -70,6 +71,12 @@ conjunction with the swap rate N, allows the momentum flux rate to be
adjusted across a wide range of values, and the momenta to be
adjusted across a wide range of values, and the momenta to be
exchanged in large chunks or more smoothly.
exchanged in large chunks or more smoothly.


The "middle" layer for momenta swapping is defined as the {Nbin}/2 + 1
layer.  Thus if {Nbin} = 20, the two swapping layers are 1 and 11.
This should lead to a symmetric velocity profile since the two layers
are separated by the same distance in both directions in a periodic
sense.  This is why {Nbin} is restricted to being an even number.

As described below, the total momentum transferred by these velocity
As described below, the total momentum transferred by these velocity
swaps is computed by the fix and can be output.  Dividing this
swaps is computed by the fix and can be output.  Dividing this
quantity by time and the cross-sectional area of the simulation box
quantity by time and the cross-sectional area of the simulation box
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