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Added triclinic cell keywords and tilt factor scaling options 

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@6431 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
athomps 2011-06-16 16:25:06 +00:00
parent 0511b7caa1
commit c4df1d931a
2 changed files with 34 additions and 18 deletions
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26
doc/fix_nh.html
View File

@ -290,16 +290,24 @@ situations.
<P>IMPORTANT NOTE: Using a barostat coupled to tilt dimensions <I>xy</I>, <P>IMPORTANT NOTE: Using a barostat coupled to tilt dimensions <I>xy</I>,
<I>xz</I>, <I>yz</I> can sometimes result in arbitrarily large values of the <I>xz</I>, <I>yz</I> can sometimes result in arbitrarily large values of the
tilt dimensions, i.e. a dramatically deformed simulation box. LAMMPS tilt dimensions, i.e. a dramatically deformed simulation box. LAMMPS
imposes reasonable limits on how large the tilt values can be, and allows the tilt factors to grow a little beyond the normal limit
exits with an error if these are exceeded. This error typically of half the box length (0.6 times the box length), and then performs
flipping or re-shaping to an equivalent periodic cell. The re-shaping
operation is described in more detail in the doc page for
<A HREF = "fix_deform.html">fix deform</A>. Both the barostat dynamics and
the atom trajectories are unaffected by this operation. However,
if a tilt factor is incremented by a large amount (1.5 times the
box length) on a single timestep, LAMMPS can not accomodate
this event and will terminate the simulation
with an error. This error typically
indicates that there is something badly wrong with how the simulation indicates that there is something badly wrong with how the simulation
was constructed. The three most common sources of this error are was constructed, such as specifying values of <I>Pstart</I> that are
using keyword <I>tri</I> on a liquid system, specifying an external shear too far from the current stress value, or specifying a timestep that
stress tensor that exceeds the yield stress of the solid, and is too large. Triclinic barostatting should be used with
specifying values of <I>Pstart</I> that are too far from the current stress care. This also is true for other barostat styles, although they tend
value. In other words, triclinic barostatting should be used with to be more forgiving of insults. In particular, it is important to
care. This also is true for other barostat styles, although they tend recognize that equilibrium liquids can not support a shear stress and
to be more forgiving of insults. that equilibrium solids can not support shear stresses that exceed the yield stress.
</P> </P>
<P>IMPORTANT NOTE: Unlike the <A HREF = "fix_temp_berendsen.html">fix <P>IMPORTANT NOTE: Unlike the <A HREF = "fix_temp_berendsen.html">fix
temp/berendsen</A> command which performs temp/berendsen</A> command which performs

26
doc/fix_nh.txt
View File

@ -280,16 +280,24 @@ situations.
IMPORTANT NOTE: Using a barostat coupled to tilt dimensions {xy}, IMPORTANT NOTE: Using a barostat coupled to tilt dimensions {xy},
{xz}, {yz} can sometimes result in arbitrarily large values of the {xz}, {yz} can sometimes result in arbitrarily large values of the
tilt dimensions, i.e. a dramatically deformed simulation box. LAMMPS tilt dimensions, i.e. a dramatically deformed simulation box. LAMMPS
imposes reasonable limits on how large the tilt values can be, and allows the tilt factors to grow a little beyond the normal limit
exits with an error if these are exceeded. This error typically of half the box length (0.6 times the box length), and then performs
flipping or re-shaping to an equivalent periodic cell. The re-shaping
operation is described in more detail in the doc page for
"fix deform"_fix_deform.html. Both the barostat dynamics and
the atom trajectories are unaffected by this operation. However,
if a tilt factor is incremented by a large amount (1.5 times the
box length) on a single timestep, LAMMPS can not accomodate
this event and will terminate the simulation
with an error. This error typically
indicates that there is something badly wrong with how the simulation indicates that there is something badly wrong with how the simulation
was constructed. The three most common sources of this error are was constructed, such as specifying values of {Pstart} that are
using keyword {tri} on a liquid system, specifying an external shear too far from the current stress value, or specifying a timestep that
stress tensor that exceeds the yield stress of the solid, and is too large. Triclinic barostatting should be used with
specifying values of {Pstart} that are too far from the current stress care. This also is true for other barostat styles, although they tend
value. In other words, triclinic barostatting should be used with to be more forgiving of insults. In particular, it is important to
care. This also is true for other barostat styles, although they tend recognize that equilibrium liquids can not support a shear stress and
to be more forgiving of insults. that equilibrium solids can not support shear stresses that exceed the yield stress.
IMPORTANT NOTE: Unlike the "fix IMPORTANT NOTE: Unlike the "fix
temp/berendsen"_fix_temp_berendsen.html command which performs temp/berendsen"_fix_temp_berendsen.html command which performs