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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5018 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2010-10-11 17:03:34 +00:00
parent 50fb5e430b
commit 1f68ebab80
2 changed files with 36 additions and 8 deletions
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22
doc/fix_nh.html
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@ -93,12 +93,19 @@ a bias velocity removed before thermostatting takes place; see the
description below. The desired temperature at each timestep is a description below. The desired temperature at each timestep is a
ramped value during the run from <I>Tstart</I> to <I>Tstop</I>. The <I>Tdamp</I> ramped value during the run from <I>Tstart</I> to <I>Tstop</I>. The <I>Tdamp</I>
parameter is specified in time units and determines how rapidly the parameter is specified in time units and determines how rapidly the
temperature is relaxed. For example, a value of 100.0 means to relax temperature is relaxed. For example, a value of 10.0 means to relax
the temperature in a timespan of (roughly) 100 time units (tau or the temperature in a timespan of (roughly) 10 time units (e.g. tau or
fmsec or psec - see the <A HREF = "units.html">units</A> command). The atoms in the fmsec or psec - see the <A HREF = "units.html">units</A> command). The atoms in the
fix group are the only ones whose velocities and positions are updated fix group are the only ones whose velocities and positions are updated
by the velocity/position update portion of the integration. by the velocity/position update portion of the integration.
</P> </P>
<P>IMPORTANT NOTE: A Nose-Hoover thermostat will not work well for
arbitrary values of <I>Tdamp</I>. If <I>Tdamp</I> is too small, the temperature
can fluctuate wildly; if it is too large, the temperature will take a
very long time to equilibrate. A good choice for many models is a
<I>Tdamp</I> of around 100 timesteps. Note that this is NOT the same as
100 time units for most <A HREF = "units.html">units</A> settings.
</P>
<HR> <HR>
<P>The barostat for fix styles <I>npt</I> and <I>nph</I> is specified using one or <P>The barostat for fix styles <I>npt</I> and <I>nph</I> is specified using one or
@ -137,10 +144,17 @@ simulation box must be triclinic, even if its initial tilt factors are
</P> </P>
<P>For all barostat keywords, the <I>Pdamp</I> parameter operates like the <P>For all barostat keywords, the <I>Pdamp</I> parameter operates like the
<I>Tdamp</I> parameter, determining the time scale on which pressure is <I>Tdamp</I> parameter, determining the time scale on which pressure is
relaxed. For example, a value of 1000.0 means to relax the pressure relaxed. For example, a value of 10.0 means to relax the pressure in
in a timespan of (roughly) 1000 time units (tau or fmsec or psec - see a timespan of (roughly) 10 time units (e.g. tau or fmsec or psec - see
the <A HREF = "units.html">units</A> command). the <A HREF = "units.html">units</A> command).
</P> </P>
<P>IMPORTANT NOTE: A Nose-Hoover barostat will not work well for
arbitrary values of <I>Pdamp</I>. If <I>Pdamp</I> is too small, the pressure
and volume can fluctuate wildly; if it is too large, the pressure will
take a very long time to equilibrate. A good choice for many models
is a <I>Pdamp</I> of around 1000 timesteps. Note that this is NOT the same
as 1000 time units for most <A HREF = "units.html">units</A> settings.
</P>
<P>Regardless of what atoms are in the fix group, a global pressure or <P>Regardless of what atoms are in the fix group, a global pressure or
stress tensor is computed for all atoms. Similarly, when the size of stress tensor is computed for all atoms. Similarly, when the size of
the simulation box is changed, all atoms are re-scaled to new the simulation box is changed, all atoms are re-scaled to new

22
doc/fix_nh.txt
View File

@ -85,12 +85,19 @@ a bias velocity removed before thermostatting takes place; see the
description below. The desired temperature at each timestep is a description below. The desired temperature at each timestep is a
ramped value during the run from {Tstart} to {Tstop}. The {Tdamp} ramped value during the run from {Tstart} to {Tstop}. The {Tdamp}
parameter is specified in time units and determines how rapidly the parameter is specified in time units and determines how rapidly the
temperature is relaxed. For example, a value of 100.0 means to relax temperature is relaxed. For example, a value of 10.0 means to relax
the temperature in a timespan of (roughly) 100 time units (tau or the temperature in a timespan of (roughly) 10 time units (e.g. tau or
fmsec or psec - see the "units"_units.html command). The atoms in the fmsec or psec - see the "units"_units.html command). The atoms in the
fix group are the only ones whose velocities and positions are updated fix group are the only ones whose velocities and positions are updated
by the velocity/position update portion of the integration. by the velocity/position update portion of the integration.
IMPORTANT NOTE: A Nose-Hoover thermostat will not work well for
arbitrary values of {Tdamp}. If {Tdamp} is too small, the temperature
can fluctuate wildly; if it is too large, the temperature will take a
very long time to equilibrate. A good choice for many models is a
{Tdamp} of around 100 timesteps. Note that this is NOT the same as
100 time units for most "units"_units.html settings.
:line :line
The barostat for fix styles {npt} and {nph} is specified using one or The barostat for fix styles {npt} and {nph} is specified using one or
@ -129,10 +136,17 @@ simulation box must be triclinic, even if its initial tilt factors are
For all barostat keywords, the {Pdamp} parameter operates like the For all barostat keywords, the {Pdamp} parameter operates like the
{Tdamp} parameter, determining the time scale on which pressure is {Tdamp} parameter, determining the time scale on which pressure is
relaxed. For example, a value of 1000.0 means to relax the pressure relaxed. For example, a value of 10.0 means to relax the pressure in
in a timespan of (roughly) 1000 time units (tau or fmsec or psec - see a timespan of (roughly) 10 time units (e.g. tau or fmsec or psec - see
the "units"_units.html command). the "units"_units.html command).
IMPORTANT NOTE: A Nose-Hoover barostat will not work well for
arbitrary values of {Pdamp}. If {Pdamp} is too small, the pressure
and volume can fluctuate wildly; if it is too large, the pressure will
take a very long time to equilibrate. A good choice for many models
is a {Pdamp} of around 1000 timesteps. Note that this is NOT the same
as 1000 time units for most "units"_units.html settings.
Regardless of what atoms are in the fix group, a global pressure or Regardless of what atoms are in the fix group, a global pressure or
stress tensor is computed for all atoms. Similarly, when the size of stress tensor is computed for all atoms. Similarly, when the size of
the simulation box is changed, all atoms are re-scaled to new the simulation box is changed, all atoms are re-scaled to new