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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1627 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp 2008-03-18 22:21:46 +00:00
parent e280d54724
commit cd92c5fb0c
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7
doc/Section_commands.html
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@ -321,9 +321,10 @@ of each style or click on the style itself for a full description:
<TR ALIGN="center"><TD ><A HREF = "fix_deposit.html">deposit</A></TD><TD ><A HREF = "fix_drag.html">drag</A></TD><TD ><A HREF = "fix_dt_reset.html">dt/reset</A></TD><TD ><A HREF = "fix_efield.html">efield</A></TD><TD ><A HREF = "fix_enforce2d.html">enforce2d</A></TD><TD ><A HREF = "fix_freeze.html">freeze</A></TD><TD ><A HREF = "fix_gravity.html">gravity</A></TD><TD ><A HREF = "fix_gyration.html">gyration</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_heat.html">heat</A></TD><TD ><A HREF = "fix_indent.html">indent</A></TD><TD ><A HREF = "fix_langevin.html">langevin</A></TD><TD ><A HREF = "fix_lineforce.html">lineforce</A></TD><TD ><A HREF = "fix_msd.html">msd</A></TD><TD ><A HREF = "fix_momentum.html">momentum</A></TD><TD ><A HREF = "fix_nph.html">nph</A></TD><TD ><A HREF = "fix_npt.html">npt</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_npt_asphere.html">npt/asphere</A></TD><TD ><A HREF = "fix_nve.html">nve</A></TD><TD ><A HREF = "fix_nve_asphere.html">nve/asphere</A></TD><TD ><A HREF = "fix_nve_limit.html">nve/limit</A></TD><TD ><A HREF = "fix_nve_noforce.html">nve/noforce</A></TD><TD ><A HREF = "fix_nve_sphere.html">nve/sphere</A></TD><TD ><A HREF = "fix_nvt.html">nvt</A></TD><TD ><A HREF = "fix_nvt_asphere.html">nvt/asphere</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_nvt_sllod.html">nvt/sllod</A></TD><TD ><A HREF = "fix_orient_fcc.html">orient/fcc</A></TD><TD ><A HREF = "fix_planeforce.html">planeforce</A></TD><TD ><A HREF = "fix_poems.html">poems</A></TD><TD ><A HREF = "fix_pour.html">pour</A></TD><TD ><A HREF = "fix_print.html">print</A></TD><TD ><A HREF = "fix_rdf.html">rdf</A></TD><TD ><A HREF = "fix_recenter.html">recenter</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_rigid.html">rigid</A></TD><TD ><A HREF = "fix_setforce.html">setforce</A></TD><TD ><A HREF = "fix_shake.html">shake</A></TD><TD ><A HREF = "fix_spring.html">spring</A></TD><TD ><A HREF = "fix_spring_rg.html">spring/rg</A></TD><TD ><A HREF = "fix_spring_self.html">spring/self</A></TD><TD ><A HREF = "fix_temp_berendsen.html">temp/berendsen</A></TD><TD ><A HREF = "fix_temp_rescale.html">temp/rescale</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_tmd.html">tmd</A></TD><TD ><A HREF = "fix_viscosity.html">viscosity</A></TD><TD ><A HREF = "fix_viscous.html">viscous</A></TD><TD ><A HREF = "fix_wall_gran.html">wall/gran</A></TD><TD ><A HREF = "fix_wall_lj126.html">wall/lj126</A></TD><TD ><A HREF = "fix_wall_lj93.html">wall/lj93</A></TD><TD ><A HREF = "fix_wall_reflect.html">wall/reflect</A></TD><TD ><A HREF = "fix_wiggle.html">wiggle</A>
<TR ALIGN="center"><TD ><A HREF = "fix_nvt_sllod.html">nvt/sllod</A></TD><TD ><A HREF = "fix_orient_fcc.html">orient/fcc</A></TD><TD ><A HREF = "fix_planeforce.html">planeforce</A></TD><TD ><A HREF = "fix_poems.html">poems</A></TD><TD ><A HREF = "fix_pour.html">pour</A></TD><TD ><A HREF = "fix_press_berendsen.html">press/berendsen</A></TD><TD ><A HREF = "fix_print.html">print</A></TD><TD ><A HREF = "fix_rdf.html">rdf</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_recenter.html">recenter</A></TD><TD ><A HREF = "fix_rigid.html">rigid</A></TD><TD ><A HREF = "fix_setforce.html">setforce</A></TD><TD ><A HREF = "fix_shake.html">shake</A></TD><TD ><A HREF = "fix_spring.html">spring</A></TD><TD ><A HREF = "fix_spring_rg.html">spring/rg</A></TD><TD ><A HREF = "fix_spring_self.html">spring/self</A></TD><TD ><A HREF = "fix_temp_berendsen.html">temp/berendsen</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_temp_rescale.html">temp/rescale</A></TD><TD ><A HREF = "fix_tmd.html">tmd</A></TD><TD ><A HREF = "fix_viscosity.html">viscosity</A></TD><TD ><A HREF = "fix_viscous.html">viscous</A></TD><TD ><A HREF = "fix_wall_gran.html">wall/gran</A></TD><TD ><A HREF = "fix_wall_lj126.html">wall/lj126</A></TD><TD ><A HREF = "fix_wall_lj93.html">wall/lj93</A></TD><TD ><A HREF = "fix_wall_reflect.html">wall/reflect</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_wiggle.html">wiggle</A>
</TD></TR></TABLE></DIV>
<HR>

1
doc/Section_commands.txt
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@ -412,6 +412,7 @@ of each style or click on the style itself for a full description:
"planeforce"_fix_planeforce.html,
"poems"_fix_poems.html,
"pour"_fix_pour.html,
"press/berendsen"_fix_press_berendsen.html,
"print"_fix_print.html,
"rdf"_fix_rdf.html,
"recenter"_fix_recenter.html,

1
doc/fix.html
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@ -140,6 +140,7 @@ list of fix styles available in LAMMPS:
<LI><A HREF = "fix_planeforce.html">planeforce</A> - constrain atoms to move in a plane
<LI><A HREF = "fix_poems.html">poems</A> - constrain clusters of atoms to move as coupled rigid bodies
<LI><A HREF = "fix_pour.html">pour</A> - pour new atoms into a granular simulation domain
<LI><A HREF = "fix_press_berendsen.html">press/berendsen</A> - pressure control by Berendsen barostat
<LI><A HREF = "fix_print.html">print</A> - print text and variables during a simulation
<LI><A HREF = "fix_rdf.html">rdf</A> - compute radial distribution functions
<LI><A HREF = "fix_recenter.html">recenter</A> - constrain the center-of-mass position of a group of atoms

2
doc/fix.txt
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@ -140,6 +140,8 @@ list of fix styles available in LAMMPS:
"poems"_fix_poems.html - constrain clusters of atoms to move \
as coupled rigid bodies
"pour"_fix_pour.html - pour new atoms into a granular simulation domain
"press/berendsen"_fix_press_berendsen.html - pressure control by \
Berendsen barostat
"print"_fix_print.html - print text and variables during a simulation
"rdf"_fix_rdf.html - compute radial distribution functions
"recenter"_fix_recenter.html - constrain the center-of-mass position \

30
doc/fix_nph.html
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@ -56,8 +56,8 @@ 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 HREF = "fix_langevin.html">fix
langevin</A> or <A HREF = "fix_temp_rescale.html">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
@ -72,6 +72,15 @@ 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>
<HR>
<P>The pressure can be controlled in one of several styles, as specified
@ -112,14 +121,13 @@ 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
implemented in LAMMPS.
shape. Parinello-Rahman boundary conditions (tilted box) for this fix
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>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>
@ -187,10 +195,6 @@ the simulation.
dimension whose target pressures are specified as NULL can be
non-periodic or periodic.
</P>
<P>You should not use <A HREF = "fix_nvt.html">fix nvt</A> with this fix. Instead, use
<A HREF = "fix_npt.html">fix npt</A> if you want to control both temperature and
pressure via Nose/Hoover.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_nve.html">fix nve</A>, <A HREF = "fix_npt.html">fix npt</A>,

30
doc/fix_nph.txt
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@ -47,8 +47,8 @@ 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 ""fix
langevin"_fix_langevin.html or "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
@ -63,6 +63,15 @@ 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.
:line
The pressure can be controlled in one of several styles, as specified
@ -103,14 +112,13 @@ 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
implemented in LAMMPS.
shape. Parinello-Rahman boundary conditions (tilted box) for this fix
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).
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
@ -177,10 +185,6 @@ 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.
You should not use "fix nvt"_fix_nvt.html with this fix. Instead, use
"fix npt"_fix_npt.html if you want to control both temperature and
pressure via Nose/Hoover.
[Related commands:]
"fix nve"_fix_nve.html, "fix npt"_fix_npt.html,

22
doc/fix_npt.html
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@ -77,15 +77,15 @@ 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_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>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>
<HR>
@ -127,8 +127,8 @@ 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.
shape. Parinello-Rahman boundary conditions (tilted box) for this fix
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.

22
doc/fix_npt.txt
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@ -66,15 +66,15 @@ 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_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.
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.
:line
@ -116,8 +116,8 @@ 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.
shape. Parinello-Rahman boundary conditions (tilted box) for this fix
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.

195
doc/fix_press_berendsen.html Normal file
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@ -0,0 +1,195 @@
<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>
<PRE> <I>dilate</I> value = <I>all</I> or <I>partial</I>
</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>
<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>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 conditions (tilted box) for this fix
are not yet implemented in LAMMPS.
</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>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.
</P>
<HR>
<A NAME = "Berendsen"></A>
<P><B>(Berendsen)</B> Berendsen, Postma, van Gunsteren, DiNola, Haak, J Chem
Phys, 81, 3684 (1984).
</P>
</HTML>

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"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} :l
{dilate} value = {all} or {partial} :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.
: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}.
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 conditions (tilted box) for this fix
are not yet implemented in LAMMPS.
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:]
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.
:line
:link(Berendsen)
[(Berendsen)] Berendsen, Postma, van Gunsteren, DiNola, Haak, J Chem
Phys, 81, 3684 (1984).