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Finished changes to fix nphug docs

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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@6924 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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athomps
2011-09-02 19:15:20 +00:00
parent 8280970bee
commit 3da41b83f9
5 changed files with 50 additions and 50 deletions
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doc/Eqs/fix_nphug.tex Normal file
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@ -0,0 +1,9 @@
\documentstyle[12pt]{article}
\begin{document}
$$
T_t - T = \frac{\left(\frac{1}{2}\left(P + P_0\right)\left(V_0 - V\right) + E_0 - E\right)}{N_{dof} k_B } = Delta
$$
\end{document}

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doc/fix.txt
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@ -188,6 +188,7 @@ list of fix styles available in LAMMPS:
"nph"_fix_nh.html - constant NPH time integration via Nose/Hoover
"nph/asphere"_fix_nph_asphere.html - NPH for aspherical particles
"nph/sphere"_fix_nph_sphere.html - NPH for spherical particles
"nphug"_fix_nphug.html - Constant-stress Hugoniostat integration
"npt"_fix_nh.html - constant NPT time integration via Nose/Hoover
"npt/asphere"_fix_npt_asphere.html - NPT for aspherical particles
"npt/sphere"_fix_npt_sphere.html - NPT for spherical particles

49
doc/fix_nphug.html
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@ -45,9 +45,9 @@ keyword = <I>temp</I> or <I>iso</I> or <I>aniso</I> or <I>tri</I> or <I>x</I> or
</UL>
<P><B>Examples:</B>
</P>
<P>fix myhug all nphug temp 1.0 1.0 10.0 z 40.0 40.0 70.0
<PRE>fix myhug all nphug temp 1.0 1.0 10.0 z 40.0 40.0 70.0
fix myhug all nphug temp 1.0 1.0 10.0 iso 40.0 40.0 70.0 drag 200.0 tchain 1 pchain 0
</P>
</PRE>
<P><B>Description:</B>
</P>
<P>This command is a variant of the Nose-Hoover
@ -61,8 +61,8 @@ jump conditions for steady shocks.
</P>
<P>The compression can be performed
either
hydrostatically (using keyword iso, aniso, or tri) or uniaxially
(using keywords x, y, or z). In the hydrostatic case,
hydrostatically (using keyword <I>iso</I>, <I>aniso</I>, or <I>tri</I>) or uniaxially
(using keywords <I>x</I>, <I>y</I>, or <I>z</I>). In the hydrostatic case,
the cell dimensions change dynamically so that the average axial stress
in all three directions converges towards the specified target value.
In the uniaxial case, the chosen cell dimension changes dynamically
@ -72,34 +72,30 @@ other two cell dimensions are kept fixed (zero lateral strain).
</P>
<P>This leads to the following additional restrictions on the keywords:
</P>
<P>One and only one of the following keywords should be used: iso, aniso, tri, x, y, z,
</P>
<P>The specified initial and final target pressures must be the same.
</P>
<P>The keywords xy, xz, yz may not be used.
</P>
<P>The only admissible value for the couple keyword is xyz,
which has the same effect as keyword iso
</P>
<UL><LI>The temp keyword must be used in order to specify the time constant for
<LI>kinetic energy relaxation, but initial and final target temperature values
<LI>are ignored.
<UL><LI>One and only one of the following keywords should be used: <I>iso</I>, <I>aniso</I>, <I>tri</I>, <I>x</I>, <I>y</I>, <I>z</I>
<LI>The specified initial and final target pressures must be the same.
<LI>The keywords <I>xy</I>, <I>xz</I>, <I>yz</I> may not be used.
<LI>The only admissible value for the couple keyword is <I>xyz</I>, which has the same effect as keyword <I>iso</I>
<LI>The <I>temp</I> keyword must be used to specify the time constant for kinetic energy relaxation, but initial and final target temperature values are ignored.
</UL>
<P>Essentially, a Hugoniostat simulation is an NPT simulation in which the
user-specified target temperature is replaced with a time-dependent
target temperature Tt obtained from the following equation:
</P>
<P>Tt - T = (0.5*(P+P0)(V0-V)+E0-E)/(Ndof kB) = Delta
</P>
<CENTER><IMG SRC = "Eqs/fix_nphug.jpg">
</CENTER>
<P>where T and Tt are the instantaneous and target temperatures,
P and P0 are the instantaneous and reference pressure or axial stress,
P and P0 are the instantaneous and reference pressures or axial stresses,
depending on whether hydrostatic or uniaxial compression is being
performed, V and V0 are the instantaneous and reference volumes,
E and E0 are the instantaneous and reference internal energy (potential
plus kinetic), Ndof is the number of degrees of freedom used in the
definition of temperature, and kB is the Boltzmann constant. Delta is the
negative deviation of the instantaneous temperature from the target temperature.
The values of E0, V0, and P0 are the instantaneous values at the start of
When the system reaches a stable equilibrium, the value of Delta should
fluctuate about zero.
</P>
<P>The values of E0, V0, and P0 are the instantaneous values at the start of
the simulation. These can be overridden using the fix_modify keywords <I>e0</I>,
<I>v0</I>, and <I>p0</I> described below.
</P>
@ -117,7 +113,7 @@ commands.
</P>
<HR>
<P>This fix compute a temperature and pressure each timestep. To do
<P>This fix computes a temperature and pressure at each timestep. To do
this, the fix creates its own computes of style "temp" and "pressure",
as if one of these two sets of commands had been issued:
</P>
@ -130,8 +126,7 @@ compute fix-ID_press all pressure fix-ID_temp
<P>See the <A HREF = "compute_temp.html">compute temp</A> and <A HREF = "compute_pressure.html">compute
pressure</A> commands for details. Note that the
IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID
+ underscore + "press". For fix nvt, the group for the new computes
is the same as the fix group. For fix nph and fix npt, the group for
+ underscore + "press". The group for
the new computes is "all" since pressure is computed for the entire
system.
</P>
@ -157,8 +152,8 @@ a fix in an input script that reads a restart file, so that the
operation of the fix continues in an uninterrupted fashion.
</P>
<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>e0</I>, <I>v0</I> and <I>p0</I> keywords
can be used to define the values of these quantities. Note the
the values for <I>e0</I> and <I>v0</I> are extensive, and so must correspond
can be used to define the values of E0, V0, and P0. Note the
the values for <I>e0</I> and <I>p0</I> are extensive, and so must correspond
to the total energy and volume of the entire system, not energy and
volume per atom. If any of these quantities are not specified, then the
instanteous value in the system at the start of the simulation is used.
@ -190,8 +185,8 @@ these fixes is "extensive"; the vector values are "intensive".
followed by all the internal Nose/Hoover thermostat and barostat
variables defined for <A HREF = "fix_nh.html">fix_style npt</A>. Delta is the deviation
of the temperature from the target temperature, given by the above equation.
Us and up are the shock and particle velocity correspponding to a steady
shock calculated from the Rh conditions. They have units of distance/time.
Us and up are the shock and particle velocity corresponding to a steady
shock calculated from the RH conditions. They have units of distance/time.
</P>
<P><B>Restrictions:</B>
</P>

41
doc/fix_nphug.txt
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@ -41,7 +41,7 @@ keyword = {temp} or {iso} or {aniso} or {tri} or {x} or {y} or {z} or {couple} o
[Examples:]
fix myhug all nphug temp 1.0 1.0 10.0 z 40.0 40.0 70.0
fix myhug all nphug temp 1.0 1.0 10.0 iso 40.0 40.0 70.0 drag 200.0 tchain 1 pchain 0
fix myhug all nphug temp 1.0 1.0 10.0 iso 40.0 40.0 70.0 drag 200.0 tchain 1 pchain 0 :pre
[Description:]
@ -56,8 +56,8 @@ jump conditions for steady shocks.
The compression can be performed
either
hydrostatically (using keyword iso, aniso, or tri) or uniaxially
(using keywords x, y, or z). In the hydrostatic case,
hydrostatically (using keyword {iso}, {aniso}, or {tri}) or uniaxially
(using keywords {x}, {y}, or {z}). In the hydrostatic case,
the cell dimensions change dynamically so that the average axial stress
in all three directions converges towards the specified target value.
In the uniaxial case, the chosen cell dimension changes dynamically
@ -67,33 +67,29 @@ other two cell dimensions are kept fixed (zero lateral strain).
This leads to the following additional restrictions on the keywords:
One and only one of the following keywords should be used: iso, aniso, tri, x, y, z,
One and only one of the following keywords should be used: {iso}, {aniso}, {tri}, {x}, {y}, {z}
The specified initial and final target pressures must be the same.
The keywords xy, xz, yz may not be used.
The only admissible value for the couple keyword is xyz,
which has the same effect as keyword iso
The temp keyword must be used in order to specify the time constant for
kinetic energy relaxation, but initial and final target temperature values
are ignored. :ul
The keywords {xy}, {xz}, {yz} may not be used.
The only admissible value for the couple keyword is {xyz}, which has the same effect as keyword {iso}
The {temp} keyword must be used to specify the time constant for kinetic energy relaxation, but initial and final target temperature values are ignored. :ul
Essentially, a Hugoniostat simulation is an NPT simulation in which the
user-specified target temperature is replaced with a time-dependent
target temperature Tt obtained from the following equation:
Tt - T = (0.5*(P+P0)(V0-V)+E0-E)/(Ndof kB) = Delta
:c,image(Eqs/fix_nphug.jpg)
where T and Tt are the instantaneous and target temperatures,
P and P0 are the instantaneous and reference pressure or axial stress,
P and P0 are the instantaneous and reference pressures or axial stresses,
depending on whether hydrostatic or uniaxial compression is being
performed, V and V0 are the instantaneous and reference volumes,
E and E0 are the instantaneous and reference internal energy (potential
plus kinetic), Ndof is the number of degrees of freedom used in the
definition of temperature, and kB is the Boltzmann constant. Delta is the
negative deviation of the instantaneous temperature from the target temperature.
When the system reaches a stable equilibrium, the value of Delta should
fluctuate about zero.
The values of E0, V0, and P0 are the instantaneous values at the start of
the simulation. These can be overridden using the fix_modify keywords {e0},
{v0}, and {p0} described below.
@ -112,7 +108,7 @@ commands.
:line
This fix compute a temperature and pressure each timestep. To do
This fix computes a temperature and pressure at each timestep. To do
this, the fix creates its own computes of style "temp" and "pressure",
as if one of these two sets of commands had been issued:
@ -125,8 +121,7 @@ compute fix-ID_press all pressure fix-ID_temp :pre
See the "compute temp"_compute_temp.html and "compute
pressure"_compute_pressure.html commands for details. Note that the
IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID
+ underscore + "press". For fix nvt, the group for the new computes
is the same as the fix group. For fix nph and fix npt, the group for
+ underscore + "press". The group for
the new computes is "all" since pressure is computed for the entire
system.
@ -152,8 +147,8 @@ a fix in an input script that reads a restart file, so that the
operation of the fix continues in an uninterrupted fashion.
The "fix_modify"_fix_modify.html {e0}, {v0} and {p0} keywords
can be used to define the values of these quantities. Note the
the values for {e0} and {v0} are extensive, and so must correspond
can be used to define the values of E0, V0, and P0. Note the
the values for {e0} and {p0} are extensive, and so must correspond
to the total energy and volume of the entire system, not energy and
volume per atom. If any of these quantities are not specified, then the
instanteous value in the system at the start of the simulation is used.
@ -185,8 +180,8 @@ The vector stores three quantities unique to this fix (Delta, Us, and up),
followed by all the internal Nose/Hoover thermostat and barostat
variables defined for "fix_style npt"_fix_nh.html. Delta is the deviation
of the temperature from the target temperature, given by the above equation.
Us and up are the shock and particle velocity correspponding to a steady
shock calculated from the Rh conditions. They have units of distance/time.
Us and up are the shock and particle velocity corresponding to a steady
shock calculated from the RH conditions. They have units of distance/time.
[Restrictions:]