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72
doc/fix_viscosity.html
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@ -13,18 +13,33 @@
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID viscosity N vdim pdim Nbin
<PRE>fix ID group-ID viscosity N vdim pdim Nbin keyword value ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>viscosity = style name of this fix command
<LI>N = perform momentum exchange every N steps
<LI>vdim = <I>x</I> or <I>y</I> or <I>z</I> = which momentum component to exchange
<LI>pdim = <I>x</I> or <I>y</I> or <I>z</I> = direction of momentum transfer
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>viscosity = style name of this fix command
<LI>N = perform momentum exchange every N steps
<LI>vdim = <I>x</I> or <I>y</I> or <I>z</I> = which momentum component to exchange
<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>zero or more keyword/value pairs may be appended
<LI>keyword = <I>swap</I> or <I>target</I>
<PRE> <I>swap</I> value = Nswap = number of swaps to perform every N steps
<I>vtarget</I> value = V or INF = target velocity of swap partners (velocity units)
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 1 all viscosity 100 x z 20
<PRE>fix 1 all viscosity 100 x z 20
fix 1 all viscosity 50 x z 20 swap 2 vtarget 1.5
</PRE>
<P><B>Description:</B>
</P>
@ -42,27 +57,36 @@ 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, two atoms are chosen in the following
manner. Only atoms in the fix group are considered. The atom in the
bottom layer with the most positive momentum component in the <I>vdim</I>
direction is the first atom. The atom in the middle later with the
most negative momentum component in the <I>vdim</I> direction is the second
atom. The <I>vdim</I> momenta components of these two atoms are swapped,
which resets their velocities, typically in opposite directions. Over
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:
</P>
<PRE>compute c1 all attribute/atom vx
fix f1 all ave/spatial 100 10 1000 z lower 0.05 tmp.profile &
compute c1 units reduced
<PRE>fix f1 all ave/spatial 100 10 1000 z lower 0.05 vx &
file tmp.profile units reduced
</PRE>
<P>Note that by default, Nswap = 1 and vtarget = INF, though this can be
changed by the optional <I>swap</I> and <I>vtarget</I> keywords. When vtarget =
INF, one or more atoms with the most positive and negative velocity
components are selected. Setting these parameters appropriately, in
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>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
yields a momentum flux. The ratio of momentum flux to the slope of
the shear velocity profile is the viscosity of the fluid, in
appropriate units. See the <A HREF = "#Muller-Plathe">Muller-Plathe paper</A> for
appopriate units. See the <A HREF = "#Muller-Plathe">Muller-Plathe paper</A> for
details.
</P>
<P>IMPORTANT NOTE: After equilibration, if the velocity profile you
@ -73,7 +97,7 @@ the Nevery parameter.
</P>
<P>An alternative method for calculating a viscosity is to run a NEMD
simulation, as described in <A HREF = "Section_howto.html#4_13">this section</A> of
the manual. NEMD simulations deform the simulation box via the <A HREF = "fix_deform.html">fix
the manual. NEMD simulations deform the simmulation box via the <A HREF = "fix_deform.html">fix
deform</A> command. Thus they cannot be run on a charged
system using a <A HREF = "kspace_style.html">PPPM solver</A> since PPPM does not
currently support non-orthogonal boxes. Using fix viscosity keeps the
@ -85,10 +109,10 @@ box orthogonal; thus it does not suffer from this limitation.
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
are relevant to this fix.
</P>
<P>The cumulative momentum transferred between the bottom and middle of
<P>The cummulative momentum transferred between the bottom and middle of
the simulation box (in the <I>pdim</I> direction) is stored as a scalar
quantity by this fix. This quantity is zeroed when the fix is defined
and accumulates thereafter, once every N steps. The units of the
and accumlates thereafter, once every N steps. The units of the
quantity are momentum = mass*velocity. This quantity can be accessed
by various <A HREF = "Section_howto.html#4_15">output commands</A>, such as
<A HREF = "thermo_style.html">thermo_style custom</A>. The scalar value calculated
@ -115,7 +139,7 @@ See the <A HREF = "#Maginn">Maginn paper</A> for an example of using this algori
in a computation of alcohol molecule properties.
</P>
<P>When running a simulation with large, massive particles or molecules
in a background solvent, you may want to only exchange momenta between
in a background solvent, you may want to only exchange momenta bewteen
solvent particles.
</P>
<P><B>Related commands:</B>
@ -123,7 +147,9 @@ solvent particles.
<P><A HREF = "fix_ave_spatial.html">fix ave/spatial</A>, <A HREF = "fix_nvt_sllod.html">fix
nvt/sllod</A>
</P>
<P><B>Default:</B> none
<P><B>Default:</B>
</P>
<P>The option defaults are swap = 1 and vtarget = INF.
</P>
<HR>

66
doc/fix_viscosity.txt
View File

@ -10,18 +10,25 @@ fix viscosity command :h3
[Syntax:]
fix ID group-ID viscosity N vdim pdim Nbin :pre
fix ID group-ID viscosity N vdim pdim Nbin keyword value ... :pre
ID, group-ID are documented in "fix"_fix.html command
viscosity = style name of this fix command
N = perform momentum exchange every N steps
vdim = {x} or {y} or {z} = which momentum component to exchange
pdim = {x} or {y} or {z} = direction of momentum transfer
Nbin = # of layers in pdim direction :ul
ID, group-ID are documented in "fix"_fix.html command :ulb,l
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
zero or more keyword/value pairs may be appended :l
keyword = {swap} or {target} :l
{swap} value = Nswap = number of swaps to perform every N steps
{vtarget} value = V or INF = target velocity of swap partners (velocity units) :pre
:ule
[Examples:]
fix 1 all viscosity 100 x z 20 :pre
fix 1 all viscosity 100 x z 20
fix 1 all viscosity 50 x z 20 swap 2 vtarget 1.5 :pre
[Description:]
@ -39,27 +46,36 @@ 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, two atoms are chosen in the following
manner. Only atoms in the fix group are considered. The atom in the
bottom layer with the most positive momentum component in the {vdim}
direction is the first atom. The atom in the middle later with the
most negative momentum component in the {vdim} direction is the second
atom. The {vdim} momenta components of these two atoms are swapped,
which resets their velocities, typically in opposite directions. Over
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:
compute c1 all attribute/atom vx
fix f1 all ave/spatial 100 10 1000 z lower 0.05 tmp.profile &
compute c1 units reduced :pre
fix f1 all ave/spatial 100 10 1000 z lower 0.05 vx &
file tmp.profile units reduced :pre
Note that by default, Nswap = 1 and vtarget = INF, though this can be
changed by the optional {swap} and {vtarget} keywords. When vtarget =
INF, one or more atoms with the most positive and negative velocity
components are selected. Setting these parameters appropriately, in
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.
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
yields a momentum flux. The ratio of momentum flux to the slope of
the shear velocity profile is the viscosity of the fluid, in
appropriate units. See the "Muller-Plathe paper"_#Muller-Plathe for
appopriate units. See the "Muller-Plathe paper"_#Muller-Plathe for
details.
IMPORTANT NOTE: After equilibration, if the velocity profile you
@ -70,7 +86,7 @@ the Nevery parameter.
An alternative method for calculating a viscosity is to run a NEMD
simulation, as described in "this section"_Section_howto.html#4_13 of
the manual. NEMD simulations deform the simulation box via the "fix
the manual. NEMD simulations deform the simmulation box via the "fix
deform"_fix_deform.html command. Thus they cannot be run on a charged
system using a "PPPM solver"_kspace_style.html since PPPM does not
currently support non-orthogonal boxes. Using fix viscosity keeps the
@ -82,10 +98,10 @@ 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.
The cumulative momentum transferred between the bottom and middle of
The cummulative momentum transferred between the bottom and middle of
the simulation box (in the {pdim} direction) is stored as a scalar
quantity by this fix. This quantity is zeroed when the fix is defined
and accumulates thereafter, once every N steps. The units of the
and accumlates thereafter, once every N steps. The units of the
quantity are momentum = mass*velocity. This quantity can be accessed
by various "output commands"_Section_howto.html#4_15, such as
"thermo_style custom"_thermo_style.html. The scalar value calculated
@ -112,7 +128,7 @@ See the "Maginn paper"_#Maginn for an example of using this algorithm
in a computation of alcohol molecule properties.
When running a simulation with large, massive particles or molecules
in a background solvent, you may want to only exchange momenta between
in a background solvent, you may want to only exchange momenta bewteen
solvent particles.
[Related commands:]
@ -120,7 +136,9 @@ solvent particles.
"fix ave/spatial"_fix_ave_spatial.html, "fix
nvt/sllod"_fix_nvt_sllod.html
[Default:] none
[Default:]
The option defaults are swap = 1 and vtarget = INF.
:line