diff --git a/doc/fix_nph.html b/doc/fix_nph.html
index 825e051f0..13fde0bba 100644
--- a/doc/fix_nph.html
+++ b/doc/fix_nph.html
@@ -1,224 +1,228 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>fix nph command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID nph p-style args keyword value ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>nph = style name of this fix command
<LI>p-style = <I>xyz</I> or <I>xy</I> or <I>yz</I> or <I>xz</I> or <I>aniso</I>
<PRE> <I>xyz</I> args = Pstart Pstop Pdamp
Pstart,Pstop = desired pressure at start/end of run (pressure units)
Pdamp = pressure damping parameter (time units)
<I>xy</I> or <I>yz</I> or <I>xz</I> args = Px0 Px1 Py0 Py1 Pz0 Pz1 Pdamp
Px0,Px1,Py0,Py1,Pz0,Pz1 = desired pressure in x,y,z at
start/end (0/1) of run (pressure units)
Pdamp = pressure damping parameter (time units)
<I>aniso</I> args = Px0 Px1 Py0 Py1 Pz0 Pz1 Pdamp
Px0,Px1,Py0,Py1,Pz0,Pz1 = desired pressure in x,y,z at
start/end (0/1) of run (pressure units)
Pdamp = pressure damping parameter (time units)
</PRE>
<LI>zero or more keyword/value pairs may be appended
<LI>keyword = <I>drag</I> or <I>dilate</I>
<PRE> <I>drag</I> value = drag factor added to barostat (0.0 = no drag)
<I>dilate</I> value = <I>all</I> or <I>partial</I>
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 1 all nph xyz 0.0 0.0 1000.0
fix 2 all nph xz 5.0 5.0 NULL NULL 5.0 5.0 1000.0 drag 1.0
fix 2 all nph aniso 0.0 0.0 0.0 0.0 NULL NULL 1000.0
</PRE>
<P><B>Description:</B>
</P>
<P>Perform constant NPH integration to update positions and velocities
each timestep for atoms in the group using a Nose/Hoover pressure
barostat <A HREF = "#Hoover">(Hoover)</A>, implemented as described in
<A HREF = "#Melchionna">(Melchionna)</A>. P is pressure. This creates a system
trajectory consistent with the isobaric ensemble. Unlike <A HREF = "fix_npt.html">fix
npt</A>, temperature will not be controlled if no other fix
is used. Temperature can be controlled independently by using a
thermostatting fis such as <A HREF = "fix_langevin.html">fix langevin</A> or <A HREF = "fix_temp_rescale.html">fix
temp/rescale</A>.
</P>
<P>The atoms in the fix group are the only ones whose velocities and
positions are updated by the velocity/position update portion of the
NPT integration.
</P>
<P>Regardless of what atoms are in the fix group, a global pressure is
computed for all atoms. Similarly, when the size of the simulation
box is changed, all atoms are re-scaled to new positions, unless the
keyword <I>dilate</I> is specified with a value of <I>partial</I>, in which case
only the atoms in the fix group are re-scaled. The latter can be
useful for leaving the coordinates of atoms in a solid substrate
unchanged and controlling the pressure of a surrounding fluid.
</P>
<P>IMPORTANT NOTE: Unlike the <A HREF = "fix_press_berendsen.html">fix
press/berendsen</A> command which performs
barostatting but NO time integration, this fix performs barostatting
AND time integration. Thus you should not use any other time
integration fix, such as <A HREF = "fix_nve.html">fix nve</A> or <A HREF = "fix_nvt.html">fix
nvt</A> on atoms to which this fix is applied. Use <A HREF = "fix_npt.html">fix
npt</A> instead of this fix, if you want to control both
temperature and pressure via Nose/Hoover.
</P>
<P>See <A HREF = "Section_howto.html#4_16">this howto section</A> of the manual for a
discussion of different ways to compute temperature and perform
thermostatting and barostatting.
</P>
<HR>
<P>The pressure can be controlled in one of several styles, as specified
by the <I>p-style</I> argument. In each case, the desired pressure at each
timestep is a ramped value during the run from the starting value to
the end value.
</P>
<P>Style <I>xyz</I> means couple all dimensions together when pressure is
computed (isotropic pressure), and dilate/contract the dimensions
together.
</P>
<P>Styles <I>xy</I> or <I>yz</I> or <I>xz</I> means that the 2 specified dimensions are
coupled together, both for pressure computation and for
dilation/contraction. The 3rd dimension dilates/contracts
independently, using its pressure component as the driving force.
These styles cannot be used for a 2d simulation.
</P>
<P>For style <I>aniso</I>, all dimensions dilate/contract independently using
their individual pressure components as the driving forces.
</P>
<P>For any of the styles except <I>xyz</I>, any of the independent pressure
components (e.g. z in <I>xy</I>, or any dimension in <I>aniso</I>) can have
their target pressures (both start and stop values) specified as NULL.
This means that no pressure control is applied to that dimension so
that the box dimension remains unchanged. For a 2d simulation the z
pressure components must be specified as NULL when using style
<I>aniso</I>.
</P>
+<P>For styles <I>xy</I> and <I>yz</I> and <I>xz</I>, the starting and stopping pressures
+must be the same for the two coupled dimensions and cannot be
+specified as NULL.
+</P>
<P>In some cases (e.g. for solids) the pressure (volume) and/or
temperature of the system can oscillate undesirably when a Nose/Hoover
barostat is applied. The optional <I>drag</I> keyword will damp these
oscillations, although it alters the Nose/Hoover equations. A value
of 0.0 (no drag) leaves the Nose/Hoover formalism unchanged. A
non-zero value adds a drag term; the larger the value specified, the
greater the damping effect. Performing a short run and monitoring the
pressure is the best way to determine if the drag term is working.
Typically a value between 0.2 to 2.0 is sufficient to damp
oscillations after a few periods.
</P>
<P>For all pressure styles, the simulation box stays rectangular in
shape. Parinello-Rahman boundary condition for tilted boxes
(triclinic symmetry) are supported by other LAMMPS commands (see <A HREF = "Section_howto.html#4_12">this
section</A> of the manual), but not yet by this
command.
</P>
<P>For all styles, the <I>Pdamp</I> parameter determines the time scale on
which pressure is relaxed. For example, a value of 1000.0 means to
relax the pressure in a timespan of (roughly) 1000 time units (tau or
fmsec or psec - see the <A HREF = "units.html">units</A> command).
</P>
<HR>
<P>This fix computes a temperature and pressure each timestep. To do
this, the fix creates its own computes of style "temp" and "pressure",
as if these commands had been issued:
</P>
<PRE>compute fix-ID_temp group-ID temp
</PRE>
<PRE>compute fix-ID_press group-ID pressure fix-ID_temp
</PRE>
<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", and the group for the new computes is the same
as the fix group.
</P>
<P>Note that these are NOT the computes used by thermodynamic output (see
the <A HREF = "thermo_style.html">thermo_style</A> command) with ID = <I>thermo_temp</I>
and <I>thermo_press</I>. This means you can change the attributes of this
fix's temperature or pressure via the
<A HREF = "compute_modify.html">compute_modify</A> command or print this temperature
or pressure during thermodynamic output via the <A HREF = "thermo_style.html">thermo_style
custom</A> command using the appropriate compute-ID.
It also means that changing attributes of <I>thermo_temp</I> or
<I>thermo_press</I> will have no effect on this fix.
</P>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>This fix writes the state of the Nose/Hoover barostat to <A HREF = "restart.html">binary
restart files</A>. See the <A HREF = "read_restart.html">read_restart</A>
command for info on how to re-specify 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>temp</I> and <I>press</I> options are
supported by this fix. You can use them to assign a
<A HREF = "compute.html">compute</A> you have defined to this fix which will be used
in its thermostatting or barostatting procedure. If you do this, note
that the kinetic energy derived from the compute temperature should be
consistent with the virial term computed using all atoms for the
pressure. LAMMPS will warn you if you choose to compute temperature
on a subset of atoms.
</P>
<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
fix to add the energy change induced by Nose/Hoover barostatting to
the system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
output</A>.
</P>
<P>The potential energy change due to this fix is stored as a scalar
quantity, which can be accessed by various <A HREF = "Section_howto.html#4_15">output
commands</A>. The scalar value calculated by
this fix is "extensive", meaning it scales with the number of atoms in
the simulation.
</P>
<P>This fix can ramp its target pressure over multiple runs, using the
<I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command. See the
<A HREF = "run.html">run</A> command for details of how to do this.
</P>
<P>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
</P>
<P><B>Restrictions:</B>
</P>
<P>Any dimension being adjusted by this fix must be periodic. A
dimension whose target pressures are specified as NULL can be
non-periodic or periodic.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_nve.html">fix nve</A>, <A HREF = "fix_npt.html">fix npt</A>,
<A HREF = "fix_modify.html">fix_modify</A>
</P>
<P><B>Default:</B>
</P>
<P>The keyword defaults are drag = 0.0 and dilate = all.
</P>
<HR>
<A NAME = "Hoover"></A>
<P><B>(Hoover)</B> Hoover, Phys Rev A, 34, 2499 (1986).
</P>
<A NAME = "Melchionna"></A>
<P><B>(Melchionna)</B> Melchionna, Ciccotti, Holian, Molecular Physics, 78,
533-44 (1993).
</P>
</HTML>
diff --git a/doc/fix_nph.txt b/doc/fix_nph.txt
index b064aa76b..92a058967 100644
--- a/doc/fix_nph.txt
+++ b/doc/fix_nph.txt
@@ -1,210 +1,214 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
fix nph command :h3
[Syntax:]
fix ID group-ID nph p-style args keyword value ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
nph = style name of this fix command :l
p-style = {xyz} or {xy} or {yz} or {xz} or {aniso} :l
{xyz} args = Pstart Pstop Pdamp
Pstart,Pstop = desired pressure at start/end of run (pressure units)
Pdamp = pressure damping parameter (time units)
{xy} or {yz} or {xz} args = Px0 Px1 Py0 Py1 Pz0 Pz1 Pdamp
Px0,Px1,Py0,Py1,Pz0,Pz1 = desired pressure in x,y,z at
start/end (0/1) of run (pressure units)
Pdamp = pressure damping parameter (time units)
{aniso} args = Px0 Px1 Py0 Py1 Pz0 Pz1 Pdamp
Px0,Px1,Py0,Py1,Pz0,Pz1 = desired pressure in x,y,z at
start/end (0/1) of run (pressure units)
Pdamp = pressure damping parameter (time units) :pre
zero or more keyword/value pairs may be appended :l
keyword = {drag} or {dilate} :l
{drag} value = drag factor added to barostat (0.0 = no drag)
{dilate} value = {all} or {partial} :pre
:ule
[Examples:]
fix 1 all nph xyz 0.0 0.0 1000.0
fix 2 all nph xz 5.0 5.0 NULL NULL 5.0 5.0 1000.0 drag 1.0
fix 2 all nph aniso 0.0 0.0 0.0 0.0 NULL NULL 1000.0 :pre
[Description:]
Perform constant NPH integration to update positions and velocities
each timestep for atoms in the group using a Nose/Hoover pressure
barostat "(Hoover)"_#Hoover, implemented as described in
"(Melchionna)"_#Melchionna. P is pressure. This creates a system
trajectory consistent with the isobaric ensemble. Unlike "fix
npt"_fix_npt.html, temperature will not be controlled if no other fix
is used. Temperature can be controlled independently by using a
thermostatting fis such as "fix langevin"_fix_langevin.html or "fix
temp/rescale"_fix_temp_rescale.html.
The atoms in the fix group are the only ones whose velocities and
positions are updated by the velocity/position update portion of the
NPT integration.
Regardless of what atoms are in the fix group, a global pressure is
computed for all atoms. Similarly, when the size of the simulation
box is changed, all atoms are re-scaled to new positions, unless the
keyword {dilate} is specified with a value of {partial}, in which case
only the atoms in the fix group are re-scaled. The latter can be
useful for leaving the coordinates of atoms in a solid substrate
unchanged and controlling the pressure of a surrounding fluid.
IMPORTANT NOTE: Unlike the "fix
press/berendsen"_fix_press_berendsen.html command which performs
barostatting but NO time integration, this fix performs barostatting
AND time integration. Thus you should not use any other time
integration fix, such as "fix nve"_fix_nve.html or "fix
nvt"_fix_nvt.html on atoms to which this fix is applied. Use "fix
npt"_fix_npt.html instead of this fix, if you want to control both
temperature and pressure via Nose/Hoover.
See "this howto section"_Section_howto.html#4_16 of the manual for a
discussion of different ways to compute temperature and perform
thermostatting and barostatting.
:line
The pressure can be controlled in one of several styles, as specified
by the {p-style} argument. In each case, the desired pressure at each
timestep is a ramped value during the run from the starting value to
the end value.
Style {xyz} means couple all dimensions together when pressure is
computed (isotropic pressure), and dilate/contract the dimensions
together.
Styles {xy} or {yz} or {xz} means that the 2 specified dimensions are
coupled together, both for pressure computation and for
dilation/contraction. The 3rd dimension dilates/contracts
independently, using its pressure component as the driving force.
These styles cannot be used for a 2d simulation.
For style {aniso}, all dimensions dilate/contract independently using
their individual pressure components as the driving forces.
For any of the styles except {xyz}, any of the independent pressure
components (e.g. z in {xy}, or any dimension in {aniso}) can have
their target pressures (both start and stop values) specified as NULL.
This means that no pressure control is applied to that dimension so
that the box dimension remains unchanged. For a 2d simulation the z
pressure components must be specified as NULL when using style
{aniso}.
+For styles {xy} and {yz} and {xz}, the starting and stopping pressures
+must be the same for the two coupled dimensions and cannot be
+specified as NULL.
+
In some cases (e.g. for solids) the pressure (volume) and/or
temperature of the system can oscillate undesirably when a Nose/Hoover
barostat is applied. The optional {drag} keyword will damp these
oscillations, although it alters the Nose/Hoover equations. A value
of 0.0 (no drag) leaves the Nose/Hoover formalism unchanged. A
non-zero value adds a drag term; the larger the value specified, the
greater the damping effect. Performing a short run and monitoring the
pressure is the best way to determine if the drag term is working.
Typically a value between 0.2 to 2.0 is sufficient to damp
oscillations after a few periods.
For all pressure styles, the simulation box stays rectangular in
shape. Parinello-Rahman boundary condition for tilted boxes
(triclinic symmetry) are supported by other LAMMPS commands (see "this
section"_Section_howto.html#4_12 of the manual), but not yet by this
command.
For all styles, the {Pdamp} parameter determines the time scale on
which pressure is relaxed. For example, a value of 1000.0 means to
relax the pressure in a timespan of (roughly) 1000 time units (tau or
fmsec or psec - see the "units"_units.html command).
:line
This fix computes a temperature and pressure each timestep. To do
this, the fix creates its own computes of style "temp" and "pressure",
as if these commands had been issued:
compute fix-ID_temp group-ID temp :pre
compute fix-ID_press group-ID 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", and the group for the new computes is the same
as the fix group.
Note that these are NOT the computes used by thermodynamic output (see
the "thermo_style"_thermo_style.html command) with ID = {thermo_temp}
and {thermo_press}. This means you can change the attributes of this
fix's temperature or pressure via the
"compute_modify"_compute_modify.html command or print this temperature
or pressure during thermodynamic output via the "thermo_style
custom"_thermo_style.html command using the appropriate compute-ID.
It also means that changing attributes of {thermo_temp} or
{thermo_press} will have no effect on this fix.
[Restart, fix_modify, output, run start/stop, minimize info:]
This fix writes the state of the Nose/Hoover barostat to "binary
restart files"_restart.html. See the "read_restart"_read_restart.html
command for info on how to re-specify 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 {temp} and {press} options are
supported by this fix. You can use them to assign a
"compute"_compute.html you have defined to this fix which will be used
in its thermostatting or barostatting procedure. If you do this, note
that the kinetic energy derived from the compute temperature should be
consistent with the virial term computed using all atoms for the
pressure. LAMMPS will warn you if you choose to compute temperature
on a subset of atoms.
The "fix_modify"_fix_modify.html {energy} option is supported by this
fix to add the energy change induced by Nose/Hoover barostatting to
the system's potential energy as part of "thermodynamic
output"_thermo_style.html.
The potential energy change due to this fix is stored as a scalar
quantity, which can be accessed by various "output
commands"_Section_howto.html#4_15. The scalar value calculated by
this fix is "extensive", meaning it scales with the number of atoms in
the simulation.
This fix can ramp its target pressure over multiple runs, using the
{start} and {stop} keywords of the "run"_run.html command. See the
"run"_run.html command for details of how to do this.
This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
Any dimension being adjusted by this fix must be periodic. A
dimension whose target pressures are specified as NULL can be
non-periodic or periodic.
[Related commands:]
"fix nve"_fix_nve.html, "fix npt"_fix_npt.html,
"fix_modify"_fix_modify.html
[Default:]
The keyword defaults are drag = 0.0 and dilate = all.
:line
:link(Hoover)
[(Hoover)] Hoover, Phys Rev A, 34, 2499 (1986).
:link(Melchionna)
[(Melchionna)] Melchionna, Ciccotti, Holian, Molecular Physics, 78,
533-44 (1993).
diff --git a/doc/fix_npt.html b/doc/fix_npt.html
index 9df4e5341..0e23efcd6 100644
--- a/doc/fix_npt.html
+++ b/doc/fix_npt.html
@@ -1,270 +1,274 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>fix npt command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID npt Tstart Tstop Tdamp p-style args keyword value ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>npt = style name of this fix command
<LI>Tstart,Tstop = desired temperature at start/end of run
<LI>Tdamp = temperature damping parameter (time units)
<LI>p-style = <I>xyz</I> or <I>xy</I> or <I>yz</I> or <I>xz</I> or <I>aniso</I>
<PRE> <I>xyz</I> args = Pstart Pstop Pdamp
Pstart,Pstop = desired pressure at start/end of run (pressure units)
Pdamp = pressure damping parameter (time units)
<I>xy</I> or <I>yz</I> or <I>xz</I> or <I>aniso</I> args = Px_start Px_stop Py_start Py_stop Pz_start Pz_stop Pdamp
Px_start,Px_stop,... = desired pressure in x,y,z at start/end of run (pressure units)
Pdamp = pressure damping parameter (time units)
</PRE>
<LI>zero or more keyword/value pairs may be appended
<LI>keyword = <I>drag</I> or <I>dilate</I>
<PRE> <I>drag</I> value = drag factor added to barostat/thermostat (0.0 = no drag)
<I>dilate</I> value = <I>all</I> or <I>partial</I>
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 1 all npt 300.0 300.0 100.0 xyz 0.0 0.0 1000.0
fix 2 all npt 300.0 300.0 100.0 xz 5.0 5.0 NULL NULL 5.0 5.0 1000.0
fix 2 all npt 300.0 300.0 100.0 xz 5.0 5.0 NULL NULL 5.0 5.0 1000.0 drag 0.2
fix 2 water npt 300.0 300.0 100.0 aniso 0.0 0.0 0.0 0.0 NULL NULL 1000.0 dilate partial
</PRE>
<P><B>Description:</B>
</P>
<P>Perform constant NPT integration to update positions and velocities
each timestep for atoms in the group using a Nose/Hoover temperature
thermostat <A HREF = "#Hoover1">(Hoover1)</A> and Nose/Hoover pressure barostat
<A HREF = "#Hoover2">(Hoover2)</A>, implemented as described in
<A HREF = "#Melchionna">(Melchionna)</A>. P is pressure; T is temperature. This
creates a system trajectory consistent with the isothermal-isobaric
ensemble.
</P>
<P>The thermostat is applied to only the translational degrees of freedom
for the particles. The translational degrees of freedom can also have
a bias velocity removed from them before thermostatting takes place;
see the description below.
</P>
<P>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> parameter is specified in
time units and determines how rapidly the temperature is relaxed. For
example, a value of 100.0 means to relax the temperature in a timespan
of (roughly) 100 time units (tau or fmsec or psec - see the
<A HREF = "units.html">units</A> command).
</P>
<P>The atoms in the fix group are the only ones whose velocities and
positions are updated by the velocity/position update portion of the
NPT integration.
</P>
<P>Regardless of what atoms are in the fix group, a global pressure is
computed for all atoms. Similarly, when the size of the simulation
box is changed, all atoms are re-scaled to new positions, unless the
keyword <I>dilate</I> is specified with a value of <I>partial</I>, in which case
only the atoms in the fix group are re-scaled. The latter can be
useful for leaving the coordinates of atoms in a solid substrate
unchanged and controlling the pressure of a surrounding fluid.
</P>
<P>IMPORTANT NOTE: Unlike the <A HREF = "fix_temp_berendsen.html">fix
temp/berendsen</A> command which performs
thermostatting but NO time integration, this fix performs
thermostatting/barostatting AND time integration. Thus you should not
use any other time integration fix, such as <A HREF = "fix_nve.html">fix nve</A> on
atoms to which this fix is applied. Likewise, this fix should not
normally be used on atoms that also have their temperature controlled
by another fix - e.g. by <A HREF = "fix_nvt.html">fix langevin</A> or <A HREF = "fix_temp_rescale.html">fix
temp/rescale</A> commands.
</P>
<P>See <A HREF = "Section_howto.html#4_16">this howto section</A> of the manual for a
discussion of different ways to compute temperature and perform
thermostatting and barostatting.
</P>
<HR>
<P>The pressure can be controlled in one of several styles, as specified
by the <I>p-style</I> argument. In each case, the desired pressure at each
timestep is a ramped value during the run from the starting value to
the end value.
</P>
<P>Style <I>xyz</I> means couple all dimensions together when pressure is
computed (isotropic pressure), and dilate/contract the dimensions
together.
</P>
<P>Styles <I>xy</I> or <I>yz</I> or <I>xz</I> means that the 2 specified dimensions are
coupled together, both for pressure computation and for
dilation/contraction. The 3rd dimension dilates/contracts
independently, using its pressure component as the driving force.
These styles cannot be used for a 2d simulation.
</P>
<P>For style <I>aniso</I>, all dimensions dilate/contract independently using
their individual pressure components as the driving forces.
</P>
<P>For any of the styles except <I>xyz</I>, any of the independent pressure
components (e.g. z in <I>xy</I>, or any dimension in <I>aniso</I>) can have
their target pressures (both start and stop values) specified as NULL.
This means that no pressure control is applied to that dimension so
that the box dimension remains unchanged. For a 2d simulation the z
pressure components must be specified as NULL when using style
<I>aniso</I>.
</P>
+<P>For styles <I>xy</I> and <I>yz</I> and <I>xz</I>, the starting and stopping pressures
+must be the same for the two coupled dimensions and cannot be
+specified as NULL.
+</P>
<P>In some cases (e.g. for solids) the pressure (volume) and/or
temperature of the system can oscillate undesirably when a Nose/Hoover
barostat and thermostat is applied. The optional <I>drag</I> keyword will
damp these oscillations, although it alters the Nose/Hoover equations.
A value of 0.0 (no drag) leaves the Nose/Hoover formalism unchanged.
A non-zero value adds a drag term; the larger the value specified, the
greater the damping effect. Performing a short run and monitoring the
pressure and temperature is the best way to determine if the drag term
is working. Typically a value between 0.2 to 2.0 is sufficient to
damp oscillations after a few periods.
</P>
<P>For all pressure styles, the simulation box stays rectangular in
shape. Parinello-Rahman boundary condition for tilted boxes
(triclinic symmetry) are supported by other LAMMPS commands (see <A HREF = "Section_howto.html#4_12">this
section</A> of the manual), but not yet by this
command.
</P>
<P>For all styles, the <I>Pdamp</I> parameter operates like the <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 in a
timespan of (roughly) 1000 time units (tau or fmsec or psec - see the
<A HREF = "units.html">units</A> command).
</P>
<HR>
<P>This fix computes a temperature and pressure each timestep. To do
this, the fix creates its own computes of style "temp" and "pressure",
as if these commands had been issued:
</P>
<PRE>compute fix-ID_temp group-ID temp
compute fix-ID_press group-ID pressure fix-ID_temp
</PRE>
<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", and the group for the new computes is the same
as the fix group.
</P>
<P>Note that these are NOT the computes used by thermodynamic output (see
the <A HREF = "thermo_style.html">thermo_style</A> command) with ID = <I>thermo_temp</I>
and <I>thermo_press</I>. This means you can change the attributes of this
fix's temperature or pressure via the
<A HREF = "compute_modify.html">compute_modify</A> command or print this temperature
or pressure during thermodynamic output via the <A HREF = "thermo_style.html">thermo_style
custom</A> command using the appropriate compute-ID.
It also means that changing attributes of <I>thermo_temp</I> or
<I>thermo_press</I> will have no effect on this fix.
</P>
<P>Like other fixes that perform thermostatting, this fix can be used
with <A HREF = "compute.html">compute commands</A> that calculate a temperature
after removing a "bias" from the atom velocities. E.g. removing the
center-of-mass velocity from a group of atoms or only calculating
temperature on the x-component of velocity or only calculating
temperature for atoms in a geometric region. This is not done by
default, but only if the <A HREF = "fix_modify.html">fix_modify</A> command is used
to assign a temperature compute to this fix that includes such a bias
term. See the doc pages for individual <A HREF = "compute.html">compute
commands</A> to determine which ones include a bias. In
this case, the thermostat works in the following manner: the current
temperature is calculated taking the bias into account, bias is
removed from each atom, thermostatting is performed on the remaining
thermal degrees of freedom, and the bias is added back in.
</P>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>This fix writes the state of the Nose/Hoover thermostat and barostat
to <A HREF = "restart.html">binary restart files</A>. See the
<A HREF = "read_restart.html">read_restart</A> command for info on how to re-specify
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>temp</I> and <I>press</I> options are
supported by this fix. You can use them to assign a
<A HREF = "compute.html">compute</A> you have defined to this fix which will be used
in its thermostatting or barostatting procedure, as described above.
If you do this, note that the kinetic energy derived from the compute
temperature should be consistent with the virial term computed using
all atoms for the pressure. LAMMPS will warn you if you choose to
compute temperature on a subset of atoms.
</P>
<P>IMPORTANT NOTE: If both the <I>temp</I> and <I>press</I> keywords are used in a
single 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 fix npt), 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 <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
fix to add the energy change induced by Nose/Hoover thermostatting and
barostatting to the system's potential energy as part of
<A HREF = "thermo_style.html">thermodynamic output</A>.
</P>
<P>The potential energy change due to this fix is stored as a scalar
quantity, which can be accessed by various <A HREF = "Section_howto.html#4_15">output
commands</A>. The scalar value calculated by
this fix is "extensive", meaning it scales with the number of atoms in
the simulation.
</P>
<P>This fix can ramp its target temperature and pressure over multiple
runs, using the <I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A>
command. See the <A HREF = "run.html">run</A> command for details of how to do
this.
</P>
<P>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
</P>
<P><B>Restrictions:</B>
</P>
<P>Any dimension being adjusted by this fix must be periodic. A
dimension whose target pressures are specified as NULL can be
non-periodic or periodic.
</P>
<P>The final Tstop cannot be 0.0 since it would make the target T = 0.0
at some timestep during the simulation which is not allowed in
the Nose/Hoover formulation.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_nve.html">fix nve</A>, <A HREF = "fix_nvt.html">fix nvt</A>, <A HREF = "fix_nph.html">fix nph</A>,
<A HREF = "fix_modify.html">fix_modify</A>
</P>
<P><B>Default:</B>
</P>
<P>The keyword defaults are drag = 0.0 and dilate = all.
</P>
<HR>
<A NAME = "Hoover1"></A>
<P><B>(Hoover1)</B> Hoover, Phys Rev A, 31, 1695 (1985).
</P>
<A NAME = "Hoover2"></A>
<P><B>(Hoover2)</B> Hoover, Phys Rev A, 34, 2499 (1986).
</P>
<A NAME = "Melchionna"></A>
<P><B>(Melchionna)</B> Melchionna, Ciccotti, Holian, Molecular Physics, 78,
533-44 (1993).
</P>
</HTML>
diff --git a/doc/fix_npt.txt b/doc/fix_npt.txt
index ae36e8a7f..7b17cc66c 100644
--- a/doc/fix_npt.txt
+++ b/doc/fix_npt.txt
@@ -1,254 +1,258 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
fix npt command :h3
[Syntax:]
fix ID group-ID npt Tstart Tstop Tdamp p-style args keyword value ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
npt = style name of this fix command :l
Tstart,Tstop = desired temperature at start/end of run :l
Tdamp = temperature damping parameter (time units) :l
p-style = {xyz} or {xy} or {yz} or {xz} or {aniso} :l
{xyz} args = Pstart Pstop Pdamp
Pstart,Pstop = desired pressure at start/end of run (pressure units)
Pdamp = pressure damping parameter (time units)
{xy} or {yz} or {xz} or {aniso} args = Px_start Px_stop Py_start Py_stop Pz_start Pz_stop Pdamp
Px_start,Px_stop,... = desired pressure in x,y,z at start/end of run (pressure units)
Pdamp = pressure damping parameter (time units) :pre
zero or more keyword/value pairs may be appended :l
keyword = {drag} or {dilate} :l
{drag} value = drag factor added to barostat/thermostat (0.0 = no drag)
{dilate} value = {all} or {partial} :pre
:ule
[Examples:]
fix 1 all npt 300.0 300.0 100.0 xyz 0.0 0.0 1000.0
fix 2 all npt 300.0 300.0 100.0 xz 5.0 5.0 NULL NULL 5.0 5.0 1000.0
fix 2 all npt 300.0 300.0 100.0 xz 5.0 5.0 NULL NULL 5.0 5.0 1000.0 drag 0.2
fix 2 water npt 300.0 300.0 100.0 aniso 0.0 0.0 0.0 0.0 NULL NULL 1000.0 dilate partial :pre
[Description:]
Perform constant NPT integration to update positions and velocities
each timestep for atoms in the group using a Nose/Hoover temperature
thermostat "(Hoover1)"_#Hoover1 and Nose/Hoover pressure barostat
"(Hoover2)"_#Hoover2, implemented as described in
"(Melchionna)"_#Melchionna. P is pressure; T is temperature. This
creates a system trajectory consistent with the isothermal-isobaric
ensemble.
The thermostat is applied to only the translational degrees of freedom
for the particles. The translational degrees of freedom can also have
a bias velocity removed from them before thermostatting takes place;
see the description below.
The desired temperature at each timestep is a ramped value during the
run from {Tstart} to {Tstop}. The {Tdamp} parameter is specified in
time units and determines how rapidly the temperature is relaxed. For
example, a value of 100.0 means to relax the temperature in a timespan
of (roughly) 100 time units (tau or 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 by the velocity/position update portion of the
NPT integration.
Regardless of what atoms are in the fix group, a global pressure is
computed for all atoms. Similarly, when the size of the simulation
box is changed, all atoms are re-scaled to new positions, unless the
keyword {dilate} is specified with a value of {partial}, in which case
only the atoms in the fix group are re-scaled. The latter can be
useful for leaving the coordinates of atoms in a solid substrate
unchanged and controlling the pressure of a surrounding fluid.
IMPORTANT NOTE: Unlike the "fix
temp/berendsen"_fix_temp_berendsen.html command which performs
thermostatting but NO time integration, this fix performs
thermostatting/barostatting AND time integration. Thus you should not
use any other time integration fix, such as "fix nve"_fix_nve.html on
atoms to which this fix is applied. Likewise, this fix should not
normally be used on atoms that also have their temperature controlled
by another fix - e.g. by "fix langevin"_fix_nvt.html or "fix
temp/rescale"_fix_temp_rescale.html commands.
See "this howto section"_Section_howto.html#4_16 of the manual for a
discussion of different ways to compute temperature and perform
thermostatting and barostatting.
:line
The pressure can be controlled in one of several styles, as specified
by the {p-style} argument. In each case, the desired pressure at each
timestep is a ramped value during the run from the starting value to
the end value.
Style {xyz} means couple all dimensions together when pressure is
computed (isotropic pressure), and dilate/contract the dimensions
together.
Styles {xy} or {yz} or {xz} means that the 2 specified dimensions are
coupled together, both for pressure computation and for
dilation/contraction. The 3rd dimension dilates/contracts
independently, using its pressure component as the driving force.
These styles cannot be used for a 2d simulation.
For style {aniso}, all dimensions dilate/contract independently using
their individual pressure components as the driving forces.
For any of the styles except {xyz}, any of the independent pressure
components (e.g. z in {xy}, or any dimension in {aniso}) can have
their target pressures (both start and stop values) specified as NULL.
This means that no pressure control is applied to that dimension so
that the box dimension remains unchanged. For a 2d simulation the z
pressure components must be specified as NULL when using style
{aniso}.
+For styles {xy} and {yz} and {xz}, the starting and stopping pressures
+must be the same for the two coupled dimensions and cannot be
+specified as NULL.
+
In some cases (e.g. for solids) the pressure (volume) and/or
temperature of the system can oscillate undesirably when a Nose/Hoover
barostat and thermostat is applied. The optional {drag} keyword will
damp these oscillations, although it alters the Nose/Hoover equations.
A value of 0.0 (no drag) leaves the Nose/Hoover formalism unchanged.
A non-zero value adds a drag term; the larger the value specified, the
greater the damping effect. Performing a short run and monitoring the
pressure and temperature is the best way to determine if the drag term
is working. Typically a value between 0.2 to 2.0 is sufficient to
damp oscillations after a few periods.
For all pressure styles, the simulation box stays rectangular in
shape. Parinello-Rahman boundary condition for tilted boxes
(triclinic symmetry) are supported by other LAMMPS commands (see "this
section"_Section_howto.html#4_12 of the manual), but not yet by this
command.
For all styles, the {Pdamp} parameter operates like the {Tdamp}
parameter, determining the time scale on which pressure is relaxed.
For example, a value of 1000.0 means to relax the pressure in a
timespan of (roughly) 1000 time units (tau or fmsec or psec - see the
"units"_units.html command).
:line
This fix computes a temperature and pressure each timestep. To do
this, the fix creates its own computes of style "temp" and "pressure",
as if these commands had been issued:
compute fix-ID_temp group-ID temp
compute fix-ID_press group-ID 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", and the group for the new computes is the same
as the fix group.
Note that these are NOT the computes used by thermodynamic output (see
the "thermo_style"_thermo_style.html command) with ID = {thermo_temp}
and {thermo_press}. This means you can change the attributes of this
fix's temperature or pressure via the
"compute_modify"_compute_modify.html command or print this temperature
or pressure during thermodynamic output via the "thermo_style
custom"_thermo_style.html command using the appropriate compute-ID.
It also means that changing attributes of {thermo_temp} or
{thermo_press} will have no effect on this fix.
Like other fixes that perform thermostatting, this fix can be used
with "compute commands"_compute.html that calculate a temperature
after removing a "bias" from the atom velocities. E.g. removing the
center-of-mass velocity from a group of atoms or only calculating
temperature on the x-component of velocity or only calculating
temperature for atoms in a geometric region. This is not done by
default, but only if the "fix_modify"_fix_modify.html command is used
to assign a temperature compute to this fix that includes such a bias
term. See the doc pages for individual "compute
commands"_compute.html to determine which ones include a bias. In
this case, the thermostat works in the following manner: the current
temperature is calculated taking the bias into account, bias is
removed from each atom, thermostatting is performed on the remaining
thermal degrees of freedom, and the bias is added back in.
[Restart, fix_modify, output, run start/stop, minimize info:]
This fix writes the state of the Nose/Hoover thermostat and barostat
to "binary restart files"_restart.html. See the
"read_restart"_read_restart.html command for info on how to re-specify
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 {temp} and {press} options are
supported by this fix. You can use them to assign a
"compute"_compute.html you have defined to this fix which will be used
in its thermostatting or barostatting procedure, as described above.
If you do this, note that the kinetic energy derived from the compute
temperature should be consistent with the virial term computed using
all atoms for the pressure. LAMMPS will warn you if you choose to
compute temperature on a subset of atoms.
IMPORTANT NOTE: If both the {temp} and {press} keywords are used in a
single 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 fix npt), 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 "fix_modify"_fix_modify.html {energy} option is supported by this
fix to add the energy change induced by Nose/Hoover thermostatting and
barostatting to the system's potential energy as part of
"thermodynamic output"_thermo_style.html.
The potential energy change due to this fix is stored as a scalar
quantity, which can be accessed by various "output
commands"_Section_howto.html#4_15. The scalar value calculated by
this fix is "extensive", meaning it scales with the number of atoms in
the simulation.
This fix can ramp its target temperature and pressure over multiple
runs, using the {start} and {stop} keywords of the "run"_run.html
command. See the "run"_run.html command for details of how to do
this.
This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
Any dimension being adjusted by this fix must be periodic. A
dimension whose target pressures are specified as NULL can be
non-periodic or periodic.
The final Tstop cannot be 0.0 since it would make the target T = 0.0
at some timestep during the simulation which is not allowed in
the Nose/Hoover formulation.
[Related commands:]
"fix nve"_fix_nve.html, "fix nvt"_fix_nvt.html, "fix nph"_fix_nph.html,
"fix_modify"_fix_modify.html
[Default:]
The keyword defaults are drag = 0.0 and dilate = all.
:line
:link(Hoover1)
[(Hoover1)] Hoover, Phys Rev A, 31, 1695 (1985).
:link(Hoover2)
[(Hoover2)] Hoover, Phys Rev A, 34, 2499 (1986).
:link(Melchionna)
[(Melchionna)] Melchionna, Ciccotti, Holian, Molecular Physics, 78,
533-44 (1993).
diff --git a/doc/fix_npt_asphere.html b/doc/fix_npt_asphere.html
index d4700aa84..bf1abbacd 100644
--- a/doc/fix_npt_asphere.html
+++ b/doc/fix_npt_asphere.html
@@ -1,236 +1,240 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>fix npt/asphere command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID npt/asphere Tstart Tstop Tdamp p-style args keyword value ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>npt/asphere = style name of this fix command
<LI>Tstart,Tstop = desired temperature at start/end of run
<LI>Tdamp = temperature damping parameter (time units)
<LI>p-style = <I>xyz</I> or <I>xy</I> or <I>yz</I> or <I>xz</I> or <I>aniso</I>
<PRE> <I>xyz</I> args = Pstart Pstop Pdamp
Pstart,Pstop = desired pressure at start/end of run (pressure units)
Pdamp = pressure damping parameter (time units)
<I>xy</I> or <I>yz</I> or <I>xz</I> or <I>aniso</I> args = Px_start Px_stop Py_start Py_stop Pz_start Pz_stop Pdamp
Px_start,Px_stop,... = desired pressure in x,y,z at start/end of run (pressure units)
Pdamp = pressure damping parameter (time units)
</PRE>
<LI>zero or more keyword/value pairs may be appended
<LI>keyword = <I>drag</I> or <I>dilate</I>
<PRE> <I>drag</I> value = drag factor added to barostat/thermostat (0.0 = no drag)
<I>dilate</I> value = <I>all</I> or <I>partial</I>
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 1 all npt/asphere 300.0 300.0 100.0 xyz 0.0 0.0 1000.0
fix 2 all npt/asphere 300.0 300.0 100.0 xz 5.0 5.0 NULL NULL 5.0 5.0 1000.0
fix 2 all npt/asphere 300.0 300.0 100.0 xz 5.0 5.0 NULL NULL 5.0 5.0 1000.0 drag 0.2
fix 2 water npt/asphere 300.0 300.0 100.0 aniso 0.0 0.0 0.0 0.0 NULL NULL 1000.0 dilate partial
</PRE>
<P><B>Description:</B>
</P>
<P>Perform constant NPT integration to update position, velocity,
orientation, and angular velocity each timestep for aspherical or
ellipsoidal particles in the group using a Nose/Hoover temperature
thermostat and Nose/Hoover pressure barostat. P is pressure; T is
temperature. This creates a system trajectory consistent with the
isothermal-isobaric ensemble.
</P>
<P>The thermostat is applied to both the translational and rotational
degrees of freedom for the aspherical particles, assuming a compute is
used which calculates a temperature that includes the rotational
degrees of freedom (see below). The translational degrees of freedom
can also have a bias velocity removed from them before thermostatting
takes place; see the description below.
</P>
<P>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> parameter is specified in
time units and determines how rapidly the temperature is relaxed. For
example, a value of 100.0 means to relax the temperature in a timespan
of (roughly) 100 time units (tau or fmsec or psec - see the
<A HREF = "units.html">units</A> command).
</P>
<P>The particles in the fix group are the only ones whose velocities and
positions are updated by the velocity/position update portion of the
NPT integration.
</P>
<P>Regardless of what particles are in the fix group, a global pressure is
computed for all particles. Similarly, when the size of the simulation
box is changed, all particles are re-scaled to new positions, unless the
keyword <I>dilate</I> is specified with a value of <I>partial</I>, in which case
only the particles in the fix group are re-scaled. The latter can be
useful for leaving the coordinates of particles in a solid substrate
unchanged and controlling the pressure of a surrounding fluid.
</P>
<HR>
<P>The pressure can be controlled in one of several styles, as specified
by the <I>p-style</I> argument. In each case, the desired pressure at each
timestep is a ramped value during the run from the starting value to
the end value.
</P>
<P>Style <I>xyz</I> means couple all dimensions together when pressure is
computed (isotropic pressure), and dilate/contract the dimensions
together.
</P>
<P>Styles <I>xy</I> or <I>yz</I> or <I>xz</I> means that the 2 specified dimensions are
coupled together, both for pressure computation and for
dilation/contraction. The 3rd dimension dilates/contracts
independently, using its pressure component as the driving force.
These styles cannot be used for a 2d simulation.
</P>
<P>For style <I>aniso</I>, all dimensions dilate/contract independently using
their individual pressure components as the driving forces.
</P>
<P>For any of the styles except <I>xyz</I>, any of the independent pressure
components (e.g. z in <I>xy</I>, or any dimension in <I>aniso</I>) can have
their target pressures (both start and stop values) specified as NULL.
This means that no pressure control is applied to that dimension so
that the box dimension remains unchanged. For a 2d simulation the z
pressure components must be specified as NULL when using style
<I>aniso</I>.
</P>
+<P>For styles <I>xy</I> and <I>yz</I> and <I>xz</I>, the starting and stopping pressures
+must be the same for the two coupled dimensions and cannot be
+specified as NULL.
+</P>
<P>In some cases (e.g. for solids) the pressure (volume) and/or
temperature of the system can oscillate undesirably when a Nose/Hoover
barostat and thermostat is applied. The optional <I>drag</I> keyword will
damp these oscillations, although it alters the Nose/Hoover equations.
A value of 0.0 (no drag) leaves the Nose/Hoover formalism unchanged.
A non-zero value adds a drag term; the larger the value specified, the
greater the damping effect. Performing a short run and monitoring the
pressure and temperature is the best way to determine if the drag term
is working. Typically a value between 0.2 to 2.0 is sufficient to
damp oscillations after a few periods.
</P>
<P>For all pressure styles, the simulation box stays rectangular in
shape. Parinello-Rahman boundary conditions (tilted box) are not yet
implemented in LAMMPS.
</P>
<P>For all styles, the <I>Pdamp</I> parameter operates like the <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 in a
timespan of (roughly) 1000 time units (tau or fmsec or psec - see the
<A HREF = "units.html">units</A> command).
</P>
<HR>
<P>This fix computes a temperature and pressure each timestep. To do
this, the fix creates its own computes of style "temp/asphere" and
"pressure", as if these commands had been issued:
</P>
<PRE>compute fix-ID_temp group-ID temp/asphere
compute fix-ID_press group-ID pressure fix-ID_temp
</PRE>
<P>See the <A HREF = "compute_temp_asphere.html">compute temp/asphere</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", and the group for the new computes is the same
as the fix group.
</P>
<P>Note that these are NOT the computes used by thermodynamic output (see
the <A HREF = "thermo_style.html">thermo_style</A> command) with ID = <I>thermo_temp</I>
and <I>thermo_press</I>. This means you can change the attributes of this
fix's temperature or pressure via the
<A HREF = "compute_modify.html">compute_modify</A> command or print this temperature
or pressure during thermodynamic output via the <A HREF = "thermo_style.html">thermo_style
custom</A> command using the appropriate compute-ID.
It also means that changing attributes of <I>thermo_temp</I> or
<I>thermo_press</I> will have no effect on this fix.
</P>
<P>Like other fixes that perform thermostatting, this fix can be used
with <A HREF = "compute.html">compute commands</A> that calculate a temperature
after removing a "bias" from the atom velocities. E.g. removing the
center-of-mass velocity from a group of atoms or only calculating
temperature on the x-component of velocity or only calculating
temperature for atoms in a geometric region. This is not done by
default, but only if the <A HREF = "fix_modify.html">fix_modify</A> command is used
to assign a temperature compute to this fix that includes such a bias
term. See the doc pages for individual <A HREF = "compute.html">compute
commands</A> to determine which ones include a bias. In
this case, the thermostat works in the following manner: the current
temperature is calculated taking the bias into account, bias is
removed from each atom, thermostatting is performed on the remaining
thermal degrees of freedom, and the bias is added back in.
</P>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>This fix writes the state of the Nose/Hoover thermostat and barostat
to <A HREF = "restart.html">binary restart files</A>. See the
<A HREF = "read_restart.html">read_restart</A> command for info on how to re-specify
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>temp</I> and <I>press</I> options are
supported by this fix. You can use them to assign a
<A HREF = "compute.html">compute</A> you have defined to this fix which will be used
in its thermostatting or barostatting procedure. If you do this, note
that the kinetic energy derived from the compute temperature should be
consistent with the virial term computed using all atoms for the
pressure. LAMMPS will warn you if you choose to compute temperature
on a subset of atoms.
</P>
<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
fix to add the energy change induced by Nose/Hoover thermostatting and
barostatting to the system's potential energy as part of
<A HREF = "thermo_style.html">thermodynamic output</A>.
</P>
<P>The potential energy change due to this fix is stored as a scalar
quantity, which can be accessed by various <A HREF = "Section_howto.html#4_15">output
commands</A>.
</P>
<P>This fix can ramp its target temperature and pressure over multiple
runs, using the <I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A>
command. See the <A HREF = "run.html">run</A> command for details of how to do
this.
</P>
<P>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
</P>
<P><B>Restrictions:</B>
</P>
<P>This fix is part of the "asphere" package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
LAMMPS</A> section for more info.
</P>
<P>This fix requires that particles be represented as extended ellipsoids
and not point particles. This means they will have an angular
momentum and a shape which is determined by the <A HREF = "shape.html">shape</A>
command.
</P>
<P>Any dimension being adjusted by this fix must be periodic. A
dimension whose target pressures are specified as NULL can be
non-periodic or periodic.
</P>
<P>The final Tstop cannot be 0.0 since it would make the target T = 0.0
at some timestep during the simulation which is not allowed in
the Nose/Hoover formulation.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_npt.html">fix npt</A>, <A HREF = "fix_nve_asphere.html">fix nve_asphere</A>, <A HREF = "fix_npt_asphere.html">fix
npt_asphere</A>, <A HREF = "fix_modify.html">fix_modify</A>
</P>
<P><B>Default:</B>
</P>
<P>The keyword defaults are drag = 0.0 and dilate = all.
</P>
</HTML>
diff --git a/doc/fix_npt_asphere.txt b/doc/fix_npt_asphere.txt
index 0e4feaa93..7814388fb 100755
--- a/doc/fix_npt_asphere.txt
+++ b/doc/fix_npt_asphere.txt
@@ -1,223 +1,227 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
fix npt/asphere command :h3
[Syntax:]
fix ID group-ID npt/asphere Tstart Tstop Tdamp p-style args keyword value ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
npt/asphere = style name of this fix command :l
Tstart,Tstop = desired temperature at start/end of run :l
Tdamp = temperature damping parameter (time units) :l
p-style = {xyz} or {xy} or {yz} or {xz} or {aniso} :l
{xyz} args = Pstart Pstop Pdamp
Pstart,Pstop = desired pressure at start/end of run (pressure units)
Pdamp = pressure damping parameter (time units)
{xy} or {yz} or {xz} or {aniso} args = Px_start Px_stop Py_start Py_stop Pz_start Pz_stop Pdamp
Px_start,Px_stop,... = desired pressure in x,y,z at start/end of run (pressure units)
Pdamp = pressure damping parameter (time units) :pre
zero or more keyword/value pairs may be appended :l
keyword = {drag} or {dilate} :l
{drag} value = drag factor added to barostat/thermostat (0.0 = no drag)
{dilate} value = {all} or {partial} :pre
:ule
[Examples:]
fix 1 all npt/asphere 300.0 300.0 100.0 xyz 0.0 0.0 1000.0
fix 2 all npt/asphere 300.0 300.0 100.0 xz 5.0 5.0 NULL NULL 5.0 5.0 1000.0
fix 2 all npt/asphere 300.0 300.0 100.0 xz 5.0 5.0 NULL NULL 5.0 5.0 1000.0 drag 0.2
fix 2 water npt/asphere 300.0 300.0 100.0 aniso 0.0 0.0 0.0 0.0 NULL NULL 1000.0 dilate partial :pre
[Description:]
Perform constant NPT integration to update position, velocity,
orientation, and angular velocity each timestep for aspherical or
ellipsoidal particles in the group using a Nose/Hoover temperature
thermostat and Nose/Hoover pressure barostat. P is pressure; T is
temperature. This creates a system trajectory consistent with the
isothermal-isobaric ensemble.
The thermostat is applied to both the translational and rotational
degrees of freedom for the aspherical particles, assuming a compute is
used which calculates a temperature that includes the rotational
degrees of freedom (see below). The translational degrees of freedom
can also have a bias velocity removed from them before thermostatting
takes place; see the description below.
The desired temperature at each timestep is a ramped value during the
run from {Tstart} to {Tstop}. The {Tdamp} parameter is specified in
time units and determines how rapidly the temperature is relaxed. For
example, a value of 100.0 means to relax the temperature in a timespan
of (roughly) 100 time units (tau or fmsec or psec - see the
"units"_units.html command).
The particles in the fix group are the only ones whose velocities and
positions are updated by the velocity/position update portion of the
NPT integration.
Regardless of what particles are in the fix group, a global pressure is
computed for all particles. Similarly, when the size of the simulation
box is changed, all particles are re-scaled to new positions, unless the
keyword {dilate} is specified with a value of {partial}, in which case
only the particles in the fix group are re-scaled. The latter can be
useful for leaving the coordinates of particles in a solid substrate
unchanged and controlling the pressure of a surrounding fluid.
:line
The pressure can be controlled in one of several styles, as specified
by the {p-style} argument. In each case, the desired pressure at each
timestep is a ramped value during the run from the starting value to
the end value.
Style {xyz} means couple all dimensions together when pressure is
computed (isotropic pressure), and dilate/contract the dimensions
together.
Styles {xy} or {yz} or {xz} means that the 2 specified dimensions are
coupled together, both for pressure computation and for
dilation/contraction. The 3rd dimension dilates/contracts
independently, using its pressure component as the driving force.
These styles cannot be used for a 2d simulation.
For style {aniso}, all dimensions dilate/contract independently using
their individual pressure components as the driving forces.
For any of the styles except {xyz}, any of the independent pressure
components (e.g. z in {xy}, or any dimension in {aniso}) can have
their target pressures (both start and stop values) specified as NULL.
This means that no pressure control is applied to that dimension so
that the box dimension remains unchanged. For a 2d simulation the z
pressure components must be specified as NULL when using style
{aniso}.
+For styles {xy} and {yz} and {xz}, the starting and stopping pressures
+must be the same for the two coupled dimensions and cannot be
+specified as NULL.
+
In some cases (e.g. for solids) the pressure (volume) and/or
temperature of the system can oscillate undesirably when a Nose/Hoover
barostat and thermostat is applied. The optional {drag} keyword will
damp these oscillations, although it alters the Nose/Hoover equations.
A value of 0.0 (no drag) leaves the Nose/Hoover formalism unchanged.
A non-zero value adds a drag term; the larger the value specified, the
greater the damping effect. Performing a short run and monitoring the
pressure and temperature is the best way to determine if the drag term
is working. Typically a value between 0.2 to 2.0 is sufficient to
damp oscillations after a few periods.
For all pressure styles, the simulation box stays rectangular in
shape. Parinello-Rahman boundary conditions (tilted box) are not yet
implemented in LAMMPS.
For all styles, the {Pdamp} parameter operates like the {Tdamp}
parameter, determining the time scale on which pressure is relaxed.
For example, a value of 1000.0 means to relax the pressure in a
timespan of (roughly) 1000 time units (tau or fmsec or psec - see the
"units"_units.html command).
:line
This fix computes a temperature and pressure each timestep. To do
this, the fix creates its own computes of style "temp/asphere" and
"pressure", as if these commands had been issued:
compute fix-ID_temp group-ID temp/asphere
compute fix-ID_press group-ID pressure fix-ID_temp :pre
See the "compute temp/asphere"_compute_temp_asphere.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", and the group for the new computes is the same
as the fix group.
Note that these are NOT the computes used by thermodynamic output (see
the "thermo_style"_thermo_style.html command) with ID = {thermo_temp}
and {thermo_press}. This means you can change the attributes of this
fix's temperature or pressure via the
"compute_modify"_compute_modify.html command or print this temperature
or pressure during thermodynamic output via the "thermo_style
custom"_thermo_style.html command using the appropriate compute-ID.
It also means that changing attributes of {thermo_temp} or
{thermo_press} will have no effect on this fix.
Like other fixes that perform thermostatting, this fix can be used
with "compute commands"_compute.html that calculate a temperature
after removing a "bias" from the atom velocities. E.g. removing the
center-of-mass velocity from a group of atoms or only calculating
temperature on the x-component of velocity or only calculating
temperature for atoms in a geometric region. This is not done by
default, but only if the "fix_modify"_fix_modify.html command is used
to assign a temperature compute to this fix that includes such a bias
term. See the doc pages for individual "compute
commands"_compute.html to determine which ones include a bias. In
this case, the thermostat works in the following manner: the current
temperature is calculated taking the bias into account, bias is
removed from each atom, thermostatting is performed on the remaining
thermal degrees of freedom, and the bias is added back in.
[Restart, fix_modify, output, run start/stop, minimize info:]
This fix writes the state of the Nose/Hoover thermostat and barostat
to "binary restart files"_restart.html. See the
"read_restart"_read_restart.html command for info on how to re-specify
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 {temp} and {press} options are
supported by this fix. You can use them to assign a
"compute"_compute.html you have defined to this fix which will be used
in its thermostatting or barostatting procedure. If you do this, note
that the kinetic energy derived from the compute temperature should be
consistent with the virial term computed using all atoms for the
pressure. LAMMPS will warn you if you choose to compute temperature
on a subset of atoms.
The "fix_modify"_fix_modify.html {energy} option is supported by this
fix to add the energy change induced by Nose/Hoover thermostatting and
barostatting to the system's potential energy as part of
"thermodynamic output"_thermo_style.html.
The potential energy change due to this fix is stored as a scalar
quantity, which can be accessed by various "output
commands"_Section_howto.html#4_15.
This fix can ramp its target temperature and pressure over multiple
runs, using the {start} and {stop} keywords of the "run"_run.html
command. See the "run"_run.html command for details of how to do
this.
This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
This fix is part of the "asphere" package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info.
This fix requires that particles be represented as extended ellipsoids
and not point particles. This means they will have an angular
momentum and a shape which is determined by the "shape"_shape.html
command.
Any dimension being adjusted by this fix must be periodic. A
dimension whose target pressures are specified as NULL can be
non-periodic or periodic.
The final Tstop cannot be 0.0 since it would make the target T = 0.0
at some timestep during the simulation which is not allowed in
the Nose/Hoover formulation.
[Related commands:]
"fix npt"_fix_npt.html, "fix nve_asphere"_fix_nve_asphere.html, "fix
npt_asphere"_fix_npt_asphere.html, "fix_modify"_fix_modify.html
[Default:]
The keyword defaults are drag = 0.0 and dilate = all.
diff --git a/doc/fix_npt_sphere.html b/doc/fix_npt_sphere.html
index 18867d5df..fda875dd9 100644
--- a/doc/fix_npt_sphere.html
+++ b/doc/fix_npt_sphere.html
@@ -1,235 +1,239 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>fix npt/sphere command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID npt/sphere Tstart Tstop Tdamp p-style args keyword value ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>npt/sphere = style name of this fix command
<LI>Tstart,Tstop = desired temperature at start/end of run
<LI>Tdamp = temperature damping parameter (time units)
<LI>p-style = <I>xyz</I> or <I>xy</I> or <I>yz</I> or <I>xz</I> or <I>aniso</I>
<PRE> <I>xyz</I> args = Pstart Pstop Pdamp
Pstart,Pstop = desired pressure at start/end of run (pressure units)
Pdamp = pressure damping parameter (time units)
<I>xy</I> or <I>yz</I> or <I>xz</I> or <I>aniso</I> args = Px_start Px_stop Py_start Py_stop Pz_start Pz_stop Pdamp
Px_start,Px_stop,... = desired pressure in x,y,z at start/end of run (pressure units)
Pdamp = pressure damping parameter (time units)
</PRE>
<LI>zero or more keyword/value pairs may be appended
<LI>keyword = <I>drag</I> or <I>dilate</I>
<PRE> <I>drag</I> value = drag factor added to barostat/thermostat (0.0 = no drag)
<I>dilate</I> value = <I>all</I> or <I>partial</I>
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 1 all npt/sphere 300.0 300.0 100.0 xyz 0.0 0.0 1000.0
fix 2 all npt/sphere 300.0 300.0 100.0 xz 5.0 5.0 NULL NULL 5.0 5.0 1000.0
fix 2 all npt/sphere 300.0 300.0 100.0 xz 5.0 5.0 NULL NULL 5.0 5.0 1000.0 drag 0.2
fix 2 water npt/sphere 300.0 300.0 100.0 aniso 0.0 0.0 0.0 0.0 NULL NULL 1000.0 dilate partial
</PRE>
<P><B>Description:</B>
</P>
<P>Perform constant NPT integration to update position, velocity, and
angular velocity each timestep for extended spherical particles in the
group using a Nose/Hoover temperature thermostat and Nose/Hoover
pressure barostat. P is pressure; T is temperature. This creates a
system trajectory consistent with the isothermal-isobaric ensemble.
</P>
<P>This fix differs from the <A HREF = "fix_npt.html">fix npt</A> command, which
assumes point particles and only updates their position and velocity.
</P>
<P>The thermostat is applied to both the translational and rotational
degrees of freedom for the spherical particles, assuming a compute is
used which calculates a temperature that includes the rotational
degrees of freedom (see below). The translational degrees of freedom
can also have a bias velocity removed from them before thermostatting
takes place; see the description below.
</P>
<P>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> parameter is specified in
time units and determines how rapidly the temperature is relaxed. For
example, a value of 100.0 means to relax the temperature in a timespan
of (roughly) 100 time units (tau or fmsec or psec - see the
<A HREF = "units.html">units</A> command).
</P>
<P>The particles in the fix group are the only ones whose velocities and
positions are updated by the velocity/position update portion of the
NPT integration.
</P>
<P>Regardless of what particles are in the fix group, a global pressure is
computed for all particles. Similarly, when the size of the simulation
box is changed, all particles are re-scaled to new positions, unless the
keyword <I>dilate</I> is specified with a value of <I>partial</I>, in which case
only the particles in the fix group are re-scaled. The latter can be
useful for leaving the coordinates of particles in a solid substrate
unchanged and controlling the pressure of a surrounding fluid.
</P>
<HR>
<P>The pressure can be controlled in one of several styles, as specified
by the <I>p-style</I> argument. In each case, the desired pressure at each
timestep is a ramped value during the run from the starting value to
the end value.
</P>
<P>Style <I>xyz</I> means couple all dimensions together when pressure is
computed (isotropic pressure), and dilate/contract the dimensions
together.
</P>
<P>Styles <I>xy</I> or <I>yz</I> or <I>xz</I> means that the 2 specified dimensions are
coupled together, both for pressure computation and for
dilation/contraction. The 3rd dimension dilates/contracts
independently, using its pressure component as the driving force.
These styles cannot be used for a 2d simulation.
</P>
<P>For style <I>aniso</I>, all dimensions dilate/contract independently using
their individual pressure components as the driving forces.
</P>
<P>For any of the styles except <I>xyz</I>, any of the independent pressure
components (e.g. z in <I>xy</I>, or any dimension in <I>aniso</I>) can have
their target pressures (both start and stop values) specified as NULL.
This means that no pressure control is applied to that dimension so
that the box dimension remains unchanged. For a 2d simulation the z
pressure components must be specified as NULL when using style
<I>aniso</I>.
</P>
+<P>For styles <I>xy</I> and <I>yz</I> and <I>xz</I>, the starting and stopping pressures
+must be the same for the two coupled dimensions and cannot be
+specified as NULL.
+</P>
<P>In some cases (e.g. for solids) the pressure (volume) and/or
temperature of the system can oscillate undesirably when a Nose/Hoover
barostat and thermostat is applied. The optional <I>drag</I> keyword will
damp these oscillations, although it alters the Nose/Hoover equations.
A value of 0.0 (no drag) leaves the Nose/Hoover formalism unchanged.
A non-zero value adds a drag term; the larger the value specified, the
greater the damping effect. Performing a short run and monitoring the
pressure and temperature is the best way to determine if the drag term
is working. Typically a value between 0.2 to 2.0 is sufficient to
damp oscillations after a few periods.
</P>
<P>For all pressure styles, the simulation box stays rectangular in
shape. Parinello-Rahman boundary conditions (tilted box) are not yet
implemented in LAMMPS.
</P>
<P>For all styles, the <I>Pdamp</I> parameter operates like the <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 in a
timespan of (roughly) 1000 time units (tau or fmsec or psec - see the
<A HREF = "units.html">units</A> command).
</P>
<HR>
<P>This fix computes a temperature and pressure each timestep. To do
this, the fix creates its own computes of style "temp/asphere" and
"pressure", as if these commands had been issued:
</P>
<PRE>compute fix-ID_temp group-ID temp/sphere
compute fix-ID_press group-ID pressure fix-ID_temp
</PRE>
<P>See the <A HREF = "compute_temp_sphere.html">compute temp/sphere</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", and the group for the new computes is the same
as the fix group.
</P>
<P>Note that these are NOT the computes used by thermodynamic output (see
the <A HREF = "thermo_style.html">thermo_style</A> command) with ID = <I>thermo_temp</I>
and <I>thermo_press</I>. This means you can change the attributes of this
fix's temperature or pressure via the
<A HREF = "compute_modify.html">compute_modify</A> command or print this temperature
or pressure during thermodynamic output via the <A HREF = "thermo_style.html">thermo_style
custom</A> command using the appropriate compute-ID.
It also means that changing attributes of <I>thermo_temp</I> or
<I>thermo_press</I> will have no effect on this fix.
</P>
<P>Like other fixes that perform thermostatting, this fix can be used
with <A HREF = "compute.html">compute commands</A> that calculate a temperature
after removing a "bias" from the atom velocities. E.g. removing the
center-of-mass velocity from a group of atoms or only calculating
temperature on the x-component of velocity or only calculating
temperature for atoms in a geometric region. This is not done by
default, but only if the <A HREF = "fix_modify.html">fix_modify</A> command is used
to assign a temperature compute to this fix that includes such a bias
term. See the doc pages for individual <A HREF = "compute.html">compute
commands</A> to determine which ones include a bias. In
this case, the thermostat works in the following manner: the current
temperature is calculated taking the bias into account, bias is
removed from each atom, thermostatting is performed on the remaining
thermal degrees of freedom, and the bias is added back in.
</P>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>This fix writes the state of the Nose/Hoover thermostat and barostat
to <A HREF = "restart.html">binary restart files</A>. See the
<A HREF = "read_restart.html">read_restart</A> command for info on how to re-specify
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>temp</I> and <I>press</I> options are
supported by this fix. You can use them to assign a
<A HREF = "compute.html">compute</A> you have defined to this fix which will be used
in its thermostatting or barostatting procedure. If you do this, note
that the kinetic energy derived from the compute temperature should be
consistent with the virial term computed using all atoms for the
pressure. LAMMPS will warn you if you choose to compute temperature
on a subset of atoms.
</P>
<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
fix to add the energy change induced by Nose/Hoover thermostatting and
barostatting to the system's potential energy as part of
<A HREF = "thermo_style.html">thermodynamic output</A>.
</P>
<P>The potential energy change due to this fix is stored as a scalar
quantity, which can be accessed by various <A HREF = "Section_howto.html#4_15">output
commands</A>.
</P>
<P>This fix can ramp its target temperature and pressure over multiple
runs, using the <I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A>
command. See the <A HREF = "run.html">run</A> command for details of how to do
this.
</P>
<P>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
</P>
<P><B>Restrictions:</B>
</P>
<P>This fix requires that particles be represented as extended spheres
and not point particles. This means they will have an angular
velocity and a diameter which is determined by the <A HREF = "shape.html">shape</A>
command.
</P>
<P>Any dimension being adjusted by this fix must be periodic. A
dimension whose target pressures are specified as NULL can be
non-periodic or periodic.
</P>
<P>The final Tstop cannot be 0.0 since it would make the target T = 0.0
at some timestep during the simulation which is not allowed in
the Nose/Hoover formulation.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_npt.html">fix npt</A>, <A HREF = "fix_nve_sphere.html">fix nve_sphere</A>, <A HREF = "fix_nvt_sphere.html">fix
nvt_sphere</A>, <A HREF = "fix_npt_asphere.html">fix
npt_asphere</A>, <A HREF = "fix_modify.html">fix_modify</A>
</P>
<P><B>Default:</B>
</P>
<P>The keyword defaults are drag = 0.0 and dilate = all.
</P>
</HTML>
diff --git a/doc/fix_npt_sphere.txt b/doc/fix_npt_sphere.txt
index b65b9259a..1837e8a57 100755
--- a/doc/fix_npt_sphere.txt
+++ b/doc/fix_npt_sphere.txt
@@ -1,222 +1,226 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
fix npt/sphere command :h3
[Syntax:]
fix ID group-ID npt/sphere Tstart Tstop Tdamp p-style args keyword value ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
npt/sphere = style name of this fix command :l
Tstart,Tstop = desired temperature at start/end of run :l
Tdamp = temperature damping parameter (time units) :l
p-style = {xyz} or {xy} or {yz} or {xz} or {aniso} :l
{xyz} args = Pstart Pstop Pdamp
Pstart,Pstop = desired pressure at start/end of run (pressure units)
Pdamp = pressure damping parameter (time units)
{xy} or {yz} or {xz} or {aniso} args = Px_start Px_stop Py_start Py_stop Pz_start Pz_stop Pdamp
Px_start,Px_stop,... = desired pressure in x,y,z at start/end of run (pressure units)
Pdamp = pressure damping parameter (time units) :pre
zero or more keyword/value pairs may be appended :l
keyword = {drag} or {dilate} :l
{drag} value = drag factor added to barostat/thermostat (0.0 = no drag)
{dilate} value = {all} or {partial} :pre
:ule
[Examples:]
fix 1 all npt/sphere 300.0 300.0 100.0 xyz 0.0 0.0 1000.0
fix 2 all npt/sphere 300.0 300.0 100.0 xz 5.0 5.0 NULL NULL 5.0 5.0 1000.0
fix 2 all npt/sphere 300.0 300.0 100.0 xz 5.0 5.0 NULL NULL 5.0 5.0 1000.0 drag 0.2
fix 2 water npt/sphere 300.0 300.0 100.0 aniso 0.0 0.0 0.0 0.0 NULL NULL 1000.0 dilate partial :pre
[Description:]
Perform constant NPT integration to update position, velocity, and
angular velocity each timestep for extended spherical particles in the
group using a Nose/Hoover temperature thermostat and Nose/Hoover
pressure barostat. P is pressure; T is temperature. This creates a
system trajectory consistent with the isothermal-isobaric ensemble.
This fix differs from the "fix npt"_fix_npt.html command, which
assumes point particles and only updates their position and velocity.
The thermostat is applied to both the translational and rotational
degrees of freedom for the spherical particles, assuming a compute is
used which calculates a temperature that includes the rotational
degrees of freedom (see below). The translational degrees of freedom
can also have a bias velocity removed from them before thermostatting
takes place; see the description below.
The desired temperature at each timestep is a ramped value during the
run from {Tstart} to {Tstop}. The {Tdamp} parameter is specified in
time units and determines how rapidly the temperature is relaxed. For
example, a value of 100.0 means to relax the temperature in a timespan
of (roughly) 100 time units (tau or fmsec or psec - see the
"units"_units.html command).
The particles in the fix group are the only ones whose velocities and
positions are updated by the velocity/position update portion of the
NPT integration.
Regardless of what particles are in the fix group, a global pressure is
computed for all particles. Similarly, when the size of the simulation
box is changed, all particles are re-scaled to new positions, unless the
keyword {dilate} is specified with a value of {partial}, in which case
only the particles in the fix group are re-scaled. The latter can be
useful for leaving the coordinates of particles in a solid substrate
unchanged and controlling the pressure of a surrounding fluid.
:line
The pressure can be controlled in one of several styles, as specified
by the {p-style} argument. In each case, the desired pressure at each
timestep is a ramped value during the run from the starting value to
the end value.
Style {xyz} means couple all dimensions together when pressure is
computed (isotropic pressure), and dilate/contract the dimensions
together.
Styles {xy} or {yz} or {xz} means that the 2 specified dimensions are
coupled together, both for pressure computation and for
dilation/contraction. The 3rd dimension dilates/contracts
independently, using its pressure component as the driving force.
These styles cannot be used for a 2d simulation.
For style {aniso}, all dimensions dilate/contract independently using
their individual pressure components as the driving forces.
For any of the styles except {xyz}, any of the independent pressure
components (e.g. z in {xy}, or any dimension in {aniso}) can have
their target pressures (both start and stop values) specified as NULL.
This means that no pressure control is applied to that dimension so
that the box dimension remains unchanged. For a 2d simulation the z
pressure components must be specified as NULL when using style
{aniso}.
+For styles {xy} and {yz} and {xz}, the starting and stopping pressures
+must be the same for the two coupled dimensions and cannot be
+specified as NULL.
+
In some cases (e.g. for solids) the pressure (volume) and/or
temperature of the system can oscillate undesirably when a Nose/Hoover
barostat and thermostat is applied. The optional {drag} keyword will
damp these oscillations, although it alters the Nose/Hoover equations.
A value of 0.0 (no drag) leaves the Nose/Hoover formalism unchanged.
A non-zero value adds a drag term; the larger the value specified, the
greater the damping effect. Performing a short run and monitoring the
pressure and temperature is the best way to determine if the drag term
is working. Typically a value between 0.2 to 2.0 is sufficient to
damp oscillations after a few periods.
For all pressure styles, the simulation box stays rectangular in
shape. Parinello-Rahman boundary conditions (tilted box) are not yet
implemented in LAMMPS.
For all styles, the {Pdamp} parameter operates like the {Tdamp}
parameter, determining the time scale on which pressure is relaxed.
For example, a value of 1000.0 means to relax the pressure in a
timespan of (roughly) 1000 time units (tau or fmsec or psec - see the
"units"_units.html command).
:line
This fix computes a temperature and pressure each timestep. To do
this, the fix creates its own computes of style "temp/asphere" and
"pressure", as if these commands had been issued:
compute fix-ID_temp group-ID temp/sphere
compute fix-ID_press group-ID pressure fix-ID_temp :pre
See the "compute temp/sphere"_compute_temp_sphere.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", and the group for the new computes is the same
as the fix group.
Note that these are NOT the computes used by thermodynamic output (see
the "thermo_style"_thermo_style.html command) with ID = {thermo_temp}
and {thermo_press}. This means you can change the attributes of this
fix's temperature or pressure via the
"compute_modify"_compute_modify.html command or print this temperature
or pressure during thermodynamic output via the "thermo_style
custom"_thermo_style.html command using the appropriate compute-ID.
It also means that changing attributes of {thermo_temp} or
{thermo_press} will have no effect on this fix.
Like other fixes that perform thermostatting, this fix can be used
with "compute commands"_compute.html that calculate a temperature
after removing a "bias" from the atom velocities. E.g. removing the
center-of-mass velocity from a group of atoms or only calculating
temperature on the x-component of velocity or only calculating
temperature for atoms in a geometric region. This is not done by
default, but only if the "fix_modify"_fix_modify.html command is used
to assign a temperature compute to this fix that includes such a bias
term. See the doc pages for individual "compute
commands"_compute.html to determine which ones include a bias. In
this case, the thermostat works in the following manner: the current
temperature is calculated taking the bias into account, bias is
removed from each atom, thermostatting is performed on the remaining
thermal degrees of freedom, and the bias is added back in.
[Restart, fix_modify, output, run start/stop, minimize info:]
This fix writes the state of the Nose/Hoover thermostat and barostat
to "binary restart files"_restart.html. See the
"read_restart"_read_restart.html command for info on how to re-specify
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 {temp} and {press} options are
supported by this fix. You can use them to assign a
"compute"_compute.html you have defined to this fix which will be used
in its thermostatting or barostatting procedure. If you do this, note
that the kinetic energy derived from the compute temperature should be
consistent with the virial term computed using all atoms for the
pressure. LAMMPS will warn you if you choose to compute temperature
on a subset of atoms.
The "fix_modify"_fix_modify.html {energy} option is supported by this
fix to add the energy change induced by Nose/Hoover thermostatting and
barostatting to the system's potential energy as part of
"thermodynamic output"_thermo_style.html.
The potential energy change due to this fix is stored as a scalar
quantity, which can be accessed by various "output
commands"_Section_howto.html#4_15.
This fix can ramp its target temperature and pressure over multiple
runs, using the {start} and {stop} keywords of the "run"_run.html
command. See the "run"_run.html command for details of how to do
this.
This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
This fix requires that particles be represented as extended spheres
and not point particles. This means they will have an angular
velocity and a diameter which is determined by the "shape"_shape.html
command.
Any dimension being adjusted by this fix must be periodic. A
dimension whose target pressures are specified as NULL can be
non-periodic or periodic.
The final Tstop cannot be 0.0 since it would make the target T = 0.0
at some timestep during the simulation which is not allowed in
the Nose/Hoover formulation.
[Related commands:]
"fix npt"_fix_npt.html, "fix nve_sphere"_fix_nve_sphere.html, "fix
nvt_sphere"_fix_nvt_sphere.html, "fix
npt_asphere"_fix_npt_asphere.html, "fix_modify"_fix_modify.html
[Default:]
The keyword defaults are drag = 0.0 and dilate = all.
diff --git a/doc/fix_press_berendsen.html b/doc/fix_press_berendsen.html
index 3079e1178..c0787420d 100644
--- a/doc/fix_press_berendsen.html
+++ b/doc/fix_press_berendsen.html
@@ -1,218 +1,222 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>fix press/berendsen command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID press/berendsen p-style args keyword value ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>press/berendsen = style name of this fix command
<LI>p-style = <I>xyz</I> or <I>xy</I> or <I>yz</I> or <I>xz</I> or <I>aniso</I>
<PRE> <I>xyz</I> args = Pstart Pstop Pdamp
Pstart,Pstop = desired pressure at start/end of run (pressure units)
Pdamp = pressure damping parameter (time units)
<I>xy</I> or <I>yz</I> or <I>xz</I> args = Px0 Px1 Py0 Py1 Pz0 Pz1 Pdamp
Px0,Px1,Py0,Py1,Pz0,Pz1 = desired pressure in x,y,z at
start/end (0/1) of run (pressure units)
Pdamp = pressure damping parameter (time units)
<I>aniso</I> args = Px0 Px1 Py0 Py1 Pz0 Pz1 Pdamp
Px0,Px1,Py0,Py1,Pz0,Pz1 = desired pressure in x,y,z at
start/end (0/1) of run (pressure units)
Pdamp = pressure damping parameter (time units)
</PRE>
<LI>zero or more keyword/value pairs may be appended
<LI>keyword = <I>dilate</I> or <I>modulus</I>
<PRE> <I>dilate</I> value = <I>all</I> or <I>partial</I>
<I>modulus</I> value = bulk modulus of system (pressure units)
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 1 all press/berendsen xyz 0.0 0.0 1000.0
fix 2 all press/berendsen aniso 0.0 0.0 0.0 0.0 NULL NULL 1000.0 dilate partial
</PRE>
<P><B>Description:</B>
</P>
<P>Reset the pressure of the system by using a Berendsen barostat
<A HREF = "#Berendsen">(Berendsen)</A>, which rescales the system volume and
(optionally) the atoms coordinates withing the simulation box every
timestep.
</P>
<P>Regardless of what atoms are in the fix group, a global pressure is
computed for all atoms. Similarly, when the size of the simulation
box is changed, all atoms are re-scaled to new positions, unless the
keyword <I>dilate</I> is specified with a value of <I>partial</I>, in which case
only the atoms in the fix group are re-scaled. The latter can be
useful for leaving the coordinates of atoms in a solid substrate
unchanged and controlling the pressure of a surrounding fluid.
</P>
<P>IMPORTANT NOTE: Unlike the <A HREF = "fix_npt.html">fix npt</A> or <A HREF = "fix_nph.html">fix
nph</A> commands which perform Nose/Hoover barostatting AND
time integration, this fix does NOT perform time integration. It only
modifies the box size and atom coordinates to effect barostatting.
Thus you must use a separate time integration fix, like <A HREF = "fix_nve.html">fix
nve</A> or <A HREF = "fix_nvt.html">fix nvt</A> to actually update the
positions and velocities of atoms. This fix can be used in
conjunction with thermostatting fixes to control the temperature, such
as <A HREF = "fix_nvt.html">fix nvt</A> or <A HREF = "fix_langevin.html">fix langevin</A> or <A HREF = "fix_temp_berendsen,html">fix
temp/berendsen</A>.
</P>
<P>See <A HREF = "Section_howto.html#4_16">this howto section</A> of the manual for a
discussion of different ways to compute temperature and perform
thermostatting and barostatting.
</P>
<HR>
<P>The pressure can be controlled in one of several styles, as specified
by the <I>p-style</I> argument. In each case, the desired pressure at each
timestep is a ramped value during the run from the starting value to
the end value.
</P>
<P>Style <I>xyz</I> means couple all dimensions together when pressure is
computed (isotropic pressure), and dilate/contract the dimensions
together.
</P>
<P>Styles <I>xy</I> or <I>yz</I> or <I>xz</I> means that the 2 specified dimensions are
coupled together, both for pressure computation and for
dilation/contraction. The 3rd dimension dilates/contracts
independently, using its pressure component as the driving force.
These styles cannot be used for a 2d simulation.
</P>
<P>For style <I>aniso</I>, all dimensions dilate/contract independently using
their individual pressure components as the driving forces.
</P>
<P>For any of the styles except <I>xyz</I>, any of the independent pressure
components (e.g. z in <I>xy</I>, or any dimension in <I>aniso</I>) can have
their target pressures (both start and stop values) specified as NULL.
This means that no pressure control is applied to that dimension so
that the box dimension remains unchanged. For a 2d simulation the z
pressure components must be specified as NULL when using style
<I>aniso</I>.
</P>
+<P>For styles <I>xy</I> and <I>yz</I> and <I>xz</I>, the starting and stopping pressures
+must be the same for the two coupled dimensions and cannot be
+specified as NULL.
+</P>
<P>In some cases (e.g. for solids) the pressure (volume) and/or
temperature of the system can oscillate undesirably when a Nose/Hoover
barostat is applied. The optional <I>drag</I> keyword will damp these
oscillations, although it alters the Nose/Hoover equations. A value
of 0.0 (no drag) leaves the Nose/Hoover formalism unchanged. A
non-zero value adds a drag term; the larger the value specified, the
greater the damping effect. Performing a short run and monitoring the
pressure is the best way to determine if the drag term is working.
Typically a value between 0.2 to 2.0 is sufficient to damp
oscillations after a few periods.
</P>
<P>For all pressure styles, the simulation box stays rectangular in
shape. Parinello-Rahman boundary condition for tilted boxes
(triclinic symmetry) are supported by other LAMMPS commands (see <A HREF = "Section_howto.html#4_12">this
section</A> of the manual), but not yet by this
command.
</P>
<P>For all styles, the <I>Pdamp</I> parameter determines the time scale on
which pressure is relaxed. For example, a value of 1000.0 means to
relax the pressure in a timespan of (roughly) 1000 time units (tau or
fmsec or psec - see the <A HREF = "units.html">units</A> command).
</P>
<P>IMPORTANT NOTE: The relaxation time is actually also a function of the
bulk modulus of the system (inverse of isothermal compressibility).
The bulk modulus has units of pressure and is the amount of pressure
that would need to be applied (isotropically) to reduce the volume of
the system by a factor of 2 (assuming the bulk modulus was a constant,
independent of density, which it's not). The bulk modulus can be set
via the keyword <I>modulus</I>. The <I>Pdamp</I> parameter is effectively
multiplied by the bulk modulus, so if the pressure is relaxing faster
than expected or desired, increasing the bulk modulus has the same
effect as increasing <I>Pdamp</I>. The converse is also true. LAMMPS does
not attempt to guess a correct value of the bulk modulus; it just uses
10.0 as a default value which gives reasonable relaxation for a
Lennard-Jones liquid, but will be way off for other materials and way
too small for solids. Thus you should experiment to find appropriate
values of <I>Pdamp</I> and/or the <I>modulus</I> when using this fix.
</P>
<HR>
<P>This fix computes a temperature and pressure each timestep. To do
this, the fix creates its own computes of style "temp" and "pressure",
as if these commands had been issued:
</P>
<PRE>compute fix-ID_temp group-ID temp
compute fix-ID_press group-ID pressure fix-ID_temp
</PRE>
<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", and the group for the new computes is the same
as the fix group.
</P>
<P>Note that these are NOT the computes used by thermodynamic output (see
the <A HREF = "thermo_style.html">thermo_style</A> command) with ID = <I>thermo_temp</I>
and <I>thermo_press</I>. This means you can change the attributes of this
fix's temperature or pressure via the
<A HREF = "compute_modify.html">compute_modify</A> command or print this temperature
or pressure during thermodynamic output via the <A HREF = "thermo_style.html">thermo_style
custom</A> command using the appropriate compute-ID.
It also means that changing attributes of <I>thermo_temp</I> or
<I>thermo_press</I> will have no effect on this fix.
</P>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>.
</P>
<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>temp</I> and <I>press</I> options are
supported by this fix. You can use them to assign a
<A HREF = "compute.html">compute</A> you have defined to this fix which will be used
in its temperature and pressure calculations. If you do this, note
that the kinetic energy derived from the compute temperature should be
consistent with the virial term computed using all atoms for the
pressure. LAMMPS will warn you if you choose to compute temperature
on a subset of atoms.
</P>
<P>No global scalar or vector or per-atom quantities are stored by this
fix for access by various <A HREF = "Section_howto.html#4_15">output commands</A>.
</P>
<P>This fix can ramp its target pressure over multiple runs, using the
<I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command. See the
<A HREF = "run.html">run</A> command for details of how to do this.
</P>
<P>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
</P>
<P><B>Restrictions:</B>
</P>
<P>Any dimension being adjusted by this fix must be periodic. A
dimension whose target pressures are specified as NULL can be
non-periodic or periodic.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_nve.html">fix nve</A>, <A HREF = "fix_nph.html">fix nph</A>, <A HREF = "fix_npt.html">fix
npt</A>, <A HREF = "fix_temp_berendsen.html">fix temp/berendsen</A>,
<A HREF = "fix_modify.html">fix_modify</A>
</P>
<P><B>Default:</B>
</P>
<P>The keyword defaults are dilate = all, modulus = 10.0 in units of
pressure for whatever <A HREF = "units.html">units</A> are defined.
</P>
<HR>
<A NAME = "Berendsen"></A>
<P><B>(Berendsen)</B> Berendsen, Postma, van Gunsteren, DiNola, Haak, J Chem
Phys, 81, 3684 (1984).
</P>
</HTML>
diff --git a/doc/fix_press_berendsen.txt b/doc/fix_press_berendsen.txt
index db4d9ba32..9128b4a54 100644
--- a/doc/fix_press_berendsen.txt
+++ b/doc/fix_press_berendsen.txt
@@ -1,207 +1,211 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
fix press/berendsen command :h3
[Syntax:]
fix ID group-ID press/berendsen p-style args keyword value ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
press/berendsen = style name of this fix command :l
p-style = {xyz} or {xy} or {yz} or {xz} or {aniso} :l
{xyz} args = Pstart Pstop Pdamp
Pstart,Pstop = desired pressure at start/end of run (pressure units)
Pdamp = pressure damping parameter (time units)
{xy} or {yz} or {xz} args = Px0 Px1 Py0 Py1 Pz0 Pz1 Pdamp
Px0,Px1,Py0,Py1,Pz0,Pz1 = desired pressure in x,y,z at
start/end (0/1) of run (pressure units)
Pdamp = pressure damping parameter (time units)
{aniso} args = Px0 Px1 Py0 Py1 Pz0 Pz1 Pdamp
Px0,Px1,Py0,Py1,Pz0,Pz1 = desired pressure in x,y,z at
start/end (0/1) of run (pressure units)
Pdamp = pressure damping parameter (time units) :pre
zero or more keyword/value pairs may be appended :l
keyword = {dilate} or {modulus} :l
{dilate} value = {all} or {partial}
{modulus} value = bulk modulus of system (pressure units) :pre
:ule
[Examples:]
fix 1 all press/berendsen xyz 0.0 0.0 1000.0
fix 2 all press/berendsen aniso 0.0 0.0 0.0 0.0 NULL NULL 1000.0 dilate partial :pre
[Description:]
Reset the pressure of the system by using a Berendsen barostat
"(Berendsen)"_#Berendsen, which rescales the system volume and
(optionally) the atoms coordinates withing the simulation box every
timestep.
Regardless of what atoms are in the fix group, a global pressure is
computed for all atoms. Similarly, when the size of the simulation
box is changed, all atoms are re-scaled to new positions, unless the
keyword {dilate} is specified with a value of {partial}, in which case
only the atoms in the fix group are re-scaled. The latter can be
useful for leaving the coordinates of atoms in a solid substrate
unchanged and controlling the pressure of a surrounding fluid.
IMPORTANT NOTE: Unlike the "fix npt"_fix_npt.html or "fix
nph"_fix_nph.html commands which perform Nose/Hoover barostatting AND
time integration, this fix does NOT perform time integration. It only
modifies the box size and atom coordinates to effect barostatting.
Thus you must use a separate time integration fix, like "fix
nve"_fix_nve.html or "fix nvt"_fix_nvt.html to actually update the
positions and velocities of atoms. This fix can be used in
conjunction with thermostatting fixes to control the temperature, such
as "fix nvt"_fix_nvt.html or "fix langevin"_fix_langevin.html or "fix
temp/berendsen"_fix_temp_berendsen,html.
See "this howto section"_Section_howto.html#4_16 of the manual for a
discussion of different ways to compute temperature and perform
thermostatting and barostatting.
:line
The pressure can be controlled in one of several styles, as specified
by the {p-style} argument. In each case, the desired pressure at each
timestep is a ramped value during the run from the starting value to
the end value.
Style {xyz} means couple all dimensions together when pressure is
computed (isotropic pressure), and dilate/contract the dimensions
together.
Styles {xy} or {yz} or {xz} means that the 2 specified dimensions are
coupled together, both for pressure computation and for
dilation/contraction. The 3rd dimension dilates/contracts
independently, using its pressure component as the driving force.
These styles cannot be used for a 2d simulation.
For style {aniso}, all dimensions dilate/contract independently using
their individual pressure components as the driving forces.
For any of the styles except {xyz}, any of the independent pressure
components (e.g. z in {xy}, or any dimension in {aniso}) can have
their target pressures (both start and stop values) specified as NULL.
This means that no pressure control is applied to that dimension so
that the box dimension remains unchanged. For a 2d simulation the z
pressure components must be specified as NULL when using style
{aniso}.
+For styles {xy} and {yz} and {xz}, the starting and stopping pressures
+must be the same for the two coupled dimensions and cannot be
+specified as NULL.
+
In some cases (e.g. for solids) the pressure (volume) and/or
temperature of the system can oscillate undesirably when a Nose/Hoover
barostat is applied. The optional {drag} keyword will damp these
oscillations, although it alters the Nose/Hoover equations. A value
of 0.0 (no drag) leaves the Nose/Hoover formalism unchanged. A
non-zero value adds a drag term; the larger the value specified, the
greater the damping effect. Performing a short run and monitoring the
pressure is the best way to determine if the drag term is working.
Typically a value between 0.2 to 2.0 is sufficient to damp
oscillations after a few periods.
For all pressure styles, the simulation box stays rectangular in
shape. Parinello-Rahman boundary condition for tilted boxes
(triclinic symmetry) are supported by other LAMMPS commands (see "this
section"_Section_howto.html#4_12 of the manual), but not yet by this
command.
For all styles, the {Pdamp} parameter determines the time scale on
which pressure is relaxed. For example, a value of 1000.0 means to
relax the pressure in a timespan of (roughly) 1000 time units (tau or
fmsec or psec - see the "units"_units.html command).
IMPORTANT NOTE: The relaxation time is actually also a function of the
bulk modulus of the system (inverse of isothermal compressibility).
The bulk modulus has units of pressure and is the amount of pressure
that would need to be applied (isotropically) to reduce the volume of
the system by a factor of 2 (assuming the bulk modulus was a constant,
independent of density, which it's not). The bulk modulus can be set
via the keyword {modulus}. The {Pdamp} parameter is effectively
multiplied by the bulk modulus, so if the pressure is relaxing faster
than expected or desired, increasing the bulk modulus has the same
effect as increasing {Pdamp}. The converse is also true. LAMMPS does
not attempt to guess a correct value of the bulk modulus; it just uses
10.0 as a default value which gives reasonable relaxation for a
Lennard-Jones liquid, but will be way off for other materials and way
too small for solids. Thus you should experiment to find appropriate
values of {Pdamp} and/or the {modulus} when using this fix.
:line
This fix computes a temperature and pressure each timestep. To do
this, the fix creates its own computes of style "temp" and "pressure",
as if these commands had been issued:
compute fix-ID_temp group-ID temp
compute fix-ID_press group-ID 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", and the group for the new computes is the same
as the fix group.
Note that these are NOT the computes used by thermodynamic output (see
the "thermo_style"_thermo_style.html command) with ID = {thermo_temp}
and {thermo_press}. This means you can change the attributes of this
fix's temperature or pressure via the
"compute_modify"_compute_modify.html command or print this temperature
or pressure during thermodynamic output via the "thermo_style
custom"_thermo_style.html command using the appropriate compute-ID.
It also means that changing attributes of {thermo_temp} or
{thermo_press} will have no effect on this fix.
[Restart, fix_modify, output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html.
The "fix_modify"_fix_modify.html {temp} and {press} options are
supported by this fix. You can use them to assign a
"compute"_compute.html you have defined to this fix which will be used
in its temperature and pressure calculations. If you do this, note
that the kinetic energy derived from the compute temperature should be
consistent with the virial term computed using all atoms for the
pressure. LAMMPS will warn you if you choose to compute temperature
on a subset of atoms.
No global scalar or vector or per-atom quantities are stored by this
fix for access by various "output commands"_Section_howto.html#4_15.
This fix can ramp its target pressure over multiple runs, using the
{start} and {stop} keywords of the "run"_run.html command. See the
"run"_run.html command for details of how to do this.
This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
Any dimension being adjusted by this fix must be periodic. A
dimension whose target pressures are specified as NULL can be
non-periodic or periodic.
[Related commands:]
"fix nve"_fix_nve.html, "fix nph"_fix_nph.html, "fix
npt"_fix_npt.html, "fix temp/berendsen"_fix_temp_berendsen.html,
"fix_modify"_fix_modify.html
[Default:]
The keyword defaults are dilate = all, modulus = 10.0 in units of
pressure for whatever "units"_units.html are defined.
:line
:link(Berendsen)
[(Berendsen)] Berendsen, Postma, van Gunsteren, DiNola, Haak, J Chem
Phys, 81, 3684 (1984).