lammps/doc/fix_npt_asphere.txt

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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 cummulative 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:]

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 atoms store torque and angular momentum and a
quaternion to represent their orientation, as defined by the
"atom_style"_atom_style.html.  It also require they store a per-type
"shape"_shape.html.  The particles cannot store a per-particle
diameter or per-particle mass.

All particles in the group must be finite-size.  They cannot be point
particles, but they can be aspherical or spherical.

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.