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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1581 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2008-03-10 17:48:22 +00:00
parent 609a4dba91
commit c012684a4f
6 changed files with 50 additions and 45 deletions
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35
doc/fix_langevin.html
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@ -27,7 +27,7 @@
<LI>zero or more keyword/value pairs may be appended
<PRE>keyword = <I>axes</I> or <I>scale</I> or <I>region</I> or <I>weight</I>
keyword = <I>axes</I> or <I>scale</I> or <I>region</I>
<I>axes</I> values = xflag yflag zflag
xflag,yflag,zflag = 0/1 to exclude/include a dimension in the thermostat
<I>scale</I> values = type ratio
@ -35,9 +35,6 @@
ratio = factor to scale the damping coefficient by
<I>region</I> value = region-ID
region-ID = ID of region to apply thermostat to
<I>weight</I> value = factor
factor = scale factor to apply to random thermal force
</PRE>
</UL>
<P><B>Examples:</B>
@ -98,29 +95,23 @@ and Fr to. A flag of 0 means skip that dimension; a flag of 1 means
include that dimension. The default is 1 for all 3 dimensions.
</P>
<P>The keyword <I>scale</I> allows the damp factor to be scaled up or down by
the specified factor for atoms of that type. It can be used multiple
times to adjust damp for several atom types. Note that specifying a
ratio of 2 increase the relaxation time which is equivalent to the the
solvent's viscosity acting on particles with 1/2 the diameter. This
is the opposite effect of scale factors used by the <A HREF = "fix_viscous.html">fix
viscous</A> command, since the damp factor in fix
<I>langevin</I> is inversely related to the gamma factor in fix <I>viscous</I>.
Also note that the damping factor in fix <I>langevin</I> includes the
particle mass in Ff, unlike fix <I>viscous</I>. Thus the mass and size of
different atom types should be accounted for in the choice of ratio
values.
the specified factor for atoms of that type. This can be useful when
different atom types have different sizes or masses. It can be used
multiple times to adjust damp for several atom types. Note that
specifying a ratio of 2 increase the relaxation time which is
equivalent to the the solvent's viscosity acting on particles with 1/2
the diameter. This is the opposite effect of scale factors used by
the <A HREF = "fix_viscous.html">fix viscous</A> command, since the damp factor in
fix <I>langevin</I> is inversely related to the gamma factor in fix
<I>viscous</I>. Also note that the damping factor in fix <I>langevin</I>
includes the particle mass in Ff, unlike fix <I>viscous</I>. Thus the mass
and size of different atom types should be accounted for in the choice
of ratio values.
</P>
<P>The keyword <I>region</I> applies the fix only to atoms that are in the
specified geometric region (and in the fix group). Since atoms can
enter/leave a region, this test is performed each timestep.
</P>
<P>The keyword <I>weight</I> applies the specified scale factor to the Fr term
in the above equation. A value of 1.0 (the default) leaves it
unchanged. A value smaller/greater than 1.0 scales its relative
magnitude as compared to the Ff term. This can be useful for some
models of thermostatting where a different coupling to the background
solvent (coupling constant) is desired.
</P>
<P>As noted above, fix <I>langevin</I> does not update the coordinates or
velocities of its atoms, only the forces. It is normally used with a
<A HREF = "fix_nve.html">fix nve</A> that does the time integration. Fix <I>langevin</I>

34
doc/fix_langevin.txt
View File

@ -18,7 +18,7 @@ Tstart,Tstop = desired temperature at start/end of run (temperature units) :l
damp = damping parameter (time units) :l
seed = random # seed to use for white noise (positive integer) :l
zero or more keyword/value pairs may be appended :l
keyword = {axes} or {scale} or {region} or {weight}
keyword = {axes} or {scale} or {region}
{axes} values = xflag yflag zflag
xflag,yflag,zflag = 0/1 to exclude/include a dimension in the thermostat
{scale} values = type ratio
@ -26,8 +26,6 @@ keyword = {axes} or {scale} or {region} or {weight}
ratio = factor to scale the damping coefficient by
{region} value = region-ID
region-ID = ID of region to apply thermostat to
{weight} value = factor
factor = scale factor to apply to random thermal force :pre
:ule
[Examples:]
@ -88,29 +86,23 @@ and Fr to. A flag of 0 means skip that dimension; a flag of 1 means
include that dimension. The default is 1 for all 3 dimensions.
The keyword {scale} allows the damp factor to be scaled up or down by
the specified factor for atoms of that type. It can be used multiple
times to adjust damp for several atom types. Note that specifying a
ratio of 2 increase the relaxation time which is equivalent to the the
solvent's viscosity acting on particles with 1/2 the diameter. This
is the opposite effect of scale factors used by the "fix
viscous"_fix_viscous.html command, since the damp factor in fix
{langevin} is inversely related to the gamma factor in fix {viscous}.
Also note that the damping factor in fix {langevin} includes the
particle mass in Ff, unlike fix {viscous}. Thus the mass and size of
different atom types should be accounted for in the choice of ratio
values.
the specified factor for atoms of that type. This can be useful when
different atom types have different sizes or masses. It can be used
multiple times to adjust damp for several atom types. Note that
specifying a ratio of 2 increase the relaxation time which is
equivalent to the the solvent's viscosity acting on particles with 1/2
the diameter. This is the opposite effect of scale factors used by
the "fix viscous"_fix_viscous.html command, since the damp factor in
fix {langevin} is inversely related to the gamma factor in fix
{viscous}. Also note that the damping factor in fix {langevin}
includes the particle mass in Ff, unlike fix {viscous}. Thus the mass
and size of different atom types should be accounted for in the choice
of ratio values.
The keyword {region} applies the fix only to atoms that are in the
specified geometric region (and in the fix group). Since atoms can
enter/leave a region, this test is performed each timestep.
The keyword {weight} applies the specified scale factor to the Fr term
in the above equation. A value of 1.0 (the default) leaves it
unchanged. A value smaller/greater than 1.0 scales its relative
magnitude as compared to the Ff term. This can be useful for some
models of thermostatting where a different coupling to the background
solvent (coupling constant) is desired.
As noted above, fix {langevin} does not update the coordinates or
velocities of its atoms, only the forces. It is normally used with a
"fix nve"_fix_nve.html that does the time integration. Fix {langevin}

2
doc/pair_soft.html
View File

@ -66,7 +66,7 @@ the pair_modify mix value. The default mix value is <I>geometric</I>. See
the "pair_modify" command for details.
</P>
<P>This pair styles does not support the <A HREF = "pair_modify.html">pair_modify</A>
shift option, since the pair interaction is goes to 0.0 at the cutoff.
shift option, since the pair interaction goes to 0.0 at the cutoff.
</P>
<P>The <A HREF = "pair_modify.html">pair_modify</A> table and tail options are not
relevant for this pair style.

2
doc/pair_soft.txt
View File

@ -63,7 +63,7 @@ the pair_modify mix value. The default mix value is {geometric}. See
the "pair_modify" command for details.
This pair styles does not support the "pair_modify"_pair_modify.html
shift option, since the pair interaction is goes to 0.0 at the cutoff.
shift option, since the pair interaction goes to 0.0 at the cutoff.
The "pair_modify"_pair_modify.html table and tail options are not
relevant for this pair style.

11
doc/thermo_modify.html
View File

@ -102,6 +102,17 @@ calculates a pressure. As described in the
compute for pressure with ID = <I>thermo_press</I>. This option allows the
user to override the default.
</P>
<P>IMPORTANT NOTE: If both the <I>temp</I> and <I>press</I> keywords are used in a
thermo_modify command (or in two separate commands), then the order in
which the keywords are specified is important. Note that a <A HREF = "compute_pressure.html">pressure
compute</A> defines its own temperature compute as
an argument when it is specified. The <I>temp</I> keyword will override
this (for the pressure compute being used by thermodynamics), but only
if the <I>temp</I> keyword comes after the <I>press</I> keyword. If the <I>temp</I>
keyword comes before the <I>press</I> keyword, then the new pressure
compute specified by the <I>press</I> keyword will be unaffected by the
<I>temp</I> setting.
</P>
<P>The <I>drot</I> keyword is used to determine how rotational energy is
calculated for dipolar atoms, which is used by the thermo_style
keyword <I>drot</I>. The specified compute ID must have been previously

11
doc/thermo_modify.txt
View File

@ -96,6 +96,17 @@ calculates a pressure. As described in the
compute for pressure with ID = {thermo_press}. This option allows the
user to override the default.
IMPORTANT NOTE: If both the {temp} and {press} keywords are used in a
thermo_modify command (or in two separate commands), then the order in
which the keywords are specified is important. Note that a "pressure
compute"_compute_pressure.html defines its own temperature compute as
an argument when it is specified. The {temp} keyword will override
this (for the pressure compute being used by thermodynamics), but only
if the {temp} keyword comes after the {press} keyword. If the {temp}
keyword comes before the {press} keyword, then the new pressure
compute specified by the {press} keyword will be unaffected by the
{temp} setting.
The {drot} keyword is used to determine how rotational energy is
calculated for dipolar atoms, which is used by the thermo_style
keyword {drot}. The specified compute ID must have been previously