git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1926 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/fix_thermal_conductivity.html

@@ -23,7 +23,7 @@
 
 <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 
 
@@ -53,16 +53,17 @@ Muller-Plathe method, the heat flux is imposed, and the temperature
 gradient is the system's response.
 </P>
 <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
-following manner.  Only atoms in the fix group are considered.  The
-hottest Nswap atoms in the bottom layer are selected.  Similarly, the
-coldest Nswap atoms in the middle later are selected.  The two sets of
-Nswap atoms are paired up and their velocities are exchanged.  This
-effectively swaps their kinetic energies, assuming their masses are
-the same.  Over time, this induces a temperature gradient in the
-system which can be measured using commands such as the following,
-which writes the temperature profile (assuming z = edim) to the file
-tmp.profile:
+direction, where the layer 1 is at the low end of that dimension and
+the layer <I>Nbin</I> is at the high end.  Every N steps, Nswap pairs of
+atoms are chosen in the following manner.  Only atoms in the fix group
+are considered.  The hottest Nswap atoms in layer 1 are selected.
+Similarly, the coldest Nswap atoms in the "middle" layer (see below)
+are selected.  The two sets of Nswap atoms are paired up and their
+velocities are exchanged.  This effectively swaps their kinetic
+energies, assuming their masses are the same.  Over time, this induces
+a temperature gradient in the system which can be measured using
+commands such as the following, which writes the temperature profile
+(assuming z = edim) to the file tmp.profile:
 </P>
 <PRE>compute   ke all ke/atom
 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
 in large chunks or more smoothly.
 </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
 swaps is computed by the fix and can be output.  Dividing this
 quantity by time and the cross-sectional area of the simulation box

doc/fix_thermal_conductivity.txt

@@ -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
 N = perform kinetic energy exchange every N steps :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
 keyword = {swap} :l
@@ -43,16 +43,17 @@ Muller-Plathe method, the heat flux is imposed, and the temperature
 gradient is the system's response.
 
 The simulation box is divided into {Nbin} layers in the {edim}
-direction.  Every N steps, Nswap pairs of atoms are chosen in the
-following manner.  Only atoms in the fix group are considered.  The
-hottest Nswap atoms in the bottom layer are selected.  Similarly, the
-coldest Nswap atoms in the middle later are selected.  The two sets of
-Nswap atoms are paired up and their velocities are exchanged.  This
-effectively swaps their kinetic energies, assuming their masses are
-the same.  Over time, this induces a temperature gradient in the
-system which can be measured using commands such as the following,
-which writes the temperature profile (assuming z = edim) to the file
-tmp.profile:
+direction, where the layer 1 is at the low end of that dimension and
+the layer {Nbin} is at the high end.  Every N steps, Nswap pairs of
+atoms are chosen in the following manner.  Only atoms in the fix group
+are considered.  The hottest Nswap atoms in layer 1 are selected.
+Similarly, the coldest Nswap atoms in the "middle" layer (see below)
+are selected.  The two sets of Nswap atoms are paired up and their
+velocities are exchanged.  This effectively swaps their kinetic
+energies, assuming their masses are the same.  Over time, this induces
+a temperature gradient in the system which can be measured using
+commands such as the following, which writes the temperature profile
+(assuming z = edim) to the file tmp.profile:
 
 compute   ke all ke/atom
 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
 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
 swaps is computed by the fix and can be output.  Dividing this
 quantity by time and the cross-sectional area of the simulation box

doc/fix_viscosity.html

@@ -25,7 +25,7 @@
 
 <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 
 
@@ -57,18 +57,19 @@ momentum flux is imposed, and the shear velocity profile is the
 system's response.
 </P>
 <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
-following manner.  Only atoms in the fix group are considered.  Nswap
-atoms in the bottom layer with positive velocity components in the
-<I>vdim</I> direction closest to the target value <I>V</I> are selected.
-Similarly, Nswap atoms in the middle later with negative velocity
-components in the <I>vdim</I> direction closest to the negative of the
-target value <I>V</I> are selected.  The two sets of Nswap atoms are paired
-up and their <I>vdim</I> momenta components are swapped within each pair.
-This resets their velocities, typically in opposite directions.  Over
-time, this induces a shear velocity profile in the system which can be
-measured using commands such as the following, which writes the
-profile to the file tmp.profile:
+direction, where the layer 1 is at the low end of that dimension and
+the layer <I>Nbin</I> is at the high end.  Every N steps, Nswap pairs of
+atoms are chosen in the following manner.  Only atoms in the fix group
+are considered.  Nswap atoms in layer 1 with positive velocity
+components in the <I>vdim</I> direction closest to the target value <I>V</I> are
+selected.  Similarly, Nswap atoms in the "middle" layer (see below) with
+negative velocity components in the <I>vdim</I> direction closest to the
+negative of the target value <I>V</I> are selected.  The two sets of Nswap
+atoms are paired up and their <I>vdim</I> momenta components are swapped
+within each pair.  This resets their velocities, typically in opposite
+directions.  Over time, this induces a shear velocity profile in the
+system which can be measured using commands such as the following,
+which writes the profile to the file tmp.profile:
 </P>
 <PRE>fix f1 all ave/spatial 100 10 1000 z lower 0.05 vx &
     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
 exchanged in large chunks or more smoothly.
 </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
 swaps is computed by the fix and can be output.  Dividing this
 quantity by time and the cross-sectional area of the simulation box

doc/fix_viscosity.txt

@@ -17,7 +17,7 @@ viscosity = style name of this fix command :l
 N = perform momentum exchange every N steps :l
 vdim = {x} or {y} or {z} = which momentum component to exchange :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
 keyword = {swap} or {target} :l
@@ -46,18 +46,19 @@ momentum flux is imposed, and the shear velocity profile is the
 system's response.
 
 The simulation box is divided into {Nbin} layers in the {pdim}
-direction.  Every N steps, Nswap pairs of atoms are chosen in the
-following manner.  Only atoms in the fix group are considered.  Nswap
-atoms in the bottom layer with positive velocity components in the
-{vdim} direction closest to the target value {V} are selected.
-Similarly, Nswap atoms in the middle later with negative velocity
-components in the {vdim} direction closest to the negative of the
-target value {V} are selected.  The two sets of Nswap atoms are paired
-up and their {vdim} momenta components are swapped within each pair.
-This resets their velocities, typically in opposite directions.  Over
-time, this induces a shear velocity profile in the system which can be
-measured using commands such as the following, which writes the
-profile to the file tmp.profile:
+direction, where the layer 1 is at the low end of that dimension and
+the layer {Nbin} is at the high end.  Every N steps, Nswap pairs of
+atoms are chosen in the following manner.  Only atoms in the fix group
+are considered.  Nswap atoms in layer 1 with positive velocity
+components in the {vdim} direction closest to the target value {V} are
+selected.  Similarly, Nswap atoms in the "middle" layer (see below) with
+negative velocity components in the {vdim} direction closest to the
+negative of the target value {V} are selected.  The two sets of Nswap
+atoms are paired up and their {vdim} momenta components are swapped
+within each pair.  This resets their velocities, typically in opposite
+directions.  Over time, this induces a shear velocity profile in the
+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 &
     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
 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
 swaps is computed by the fix and can be output.  Dividing this
 quantity by time and the cross-sectional area of the simulation box