forked from lijiext/lammps
199 lines
7.9 KiB
Plaintext
199 lines
7.9 KiB
Plaintext
"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 ""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.
|
|
|
|
: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) are not
|
|
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" 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 with underscore + "temp" or
|
|
"press" appended 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_pressure}. 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 thermodyanmic 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_pressure} 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.
|
|
|
|
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.
|
|
|
|
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,
|
|
"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).
|