Homec4science
Diffusion lammps (efficient_neuronet) Browse

lammps/doc/fix_nh_eff.html
73573bf2372eefficient_neuronet

Last Change
Raw File

fix_nh_eff.html
View Options

<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 nvt/eff command
</H3>
<H3>fix npt/eff command
</H3>
<H3>fix nph/eff command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID style_name keyword value ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>style_name = <I>nvt/eff</I> or <I>npt/eff</I> or <I>nph/eff</I>
<PRE>one or more keyword value pairs may be appended
keyword = <I>temp</I> or <I>iso</I> or <I>aniso</I> or <I>tri</I> or <I>x</I> or <I>y</I> or <I>z</I> or <I>xy</I> or <I>yz</I> or <I>xz</I> or <I>couple</I> or <I>tchain</I> or <I>pchain</I> or <I>mtk</I> or <I>tloop</I> or <I>ploop</I> or <I>nreset</I> or <I>drag</I> or <I>dilate</I>
<I>temp</I> values = Tstart Tstop Tdamp
Tstart,Tstop = external temperature at start/end of run
Tdamp = temperature damping parameter (time units)
<I>iso</I> or <I>aniso</I> or <I>tri</I> values = Pstart Pstop Pdamp
Pstart,Pstop = scalar external pressure at start/end of run (pressure units)
Pdamp = pressure damping parameter (time units)
<I>x</I> or <I>y</I> or <I>z</I> or <I>xy</I> or <I>yz</I> or <I>xz</I> values = Pstart Pstop Pdamp
Pstart,Pstop = external stress tensor component at start/end of run (pressure units)
Pdamp = stress damping parameter (time units)
<I>couple</I> = <I>none</I> or <I>xyz</I> or <I>xy</I> or <I>yz</I> or <I>xz</I>
<I>tchain</I> value = length of thermostat chain (1 = single thermostat)
<I>pchain</I> values = length of thermostat chain on barostat (0 = no thermostat)
<I>mtk</I> value = <I>yes</I> or <I>no</I> = add in MTK adjustment term or not
<I>tloop</I> value = number of sub-cycles to perform on thermostat
<I>ploop</I> value = number of sub-cycles to perform on barostat thermostat
<I>nreset</I> value = reset reference cell every this many timesteps
<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 nvt/eff temp 300.0 300.0 0.1
fix 1 part npt/eff temp 300.0 300.0 0.1 iso 0.0 0.0 1.0
fix 2 part npt/eff temp 300.0 300.0 0.1 tri 5.0 5.0 1.0
fix 2 ice nph/eff x 1.0 1.0 0.5 y 2.0 2.0 0.5 z 3.0 3.0 0.5 yz 0.1 0.1 0.5 xz 0.2 0.2 0.5 xy 0.3 0.3 0.5 nreset 1000
</PRE>
<P><B>Description:</B>
</P>
<P>These commands perform time integration on Nose-Hoover style
non-Hamiltonian equations of motion which are designed to generate
positions and velocities sampled from the canonical (nvt),
isothermal-isobaric (npt), and isenthalpic (nph) ensembles. In addition to acting on the nuclear positions and velocities, they generate radius and radial velocities sampled for the electron wave packets in eFF. This is
achieved by adding some dynamic variables which are coupled to the
particle velocities (thermostatting) and simulation domain dimensions
(barostatting). In addition to basic thermostatting and barostatting,
these fixes can also create a chain of thermostats coupled to the
particle thermostat, and another chain of thermostats coupled to the
barostat variables. The barostat can be coupled to the overall box
volume, or to individual dimensions, including the <I>xy</I>, <I>xz</I> and <I>yz</I>
tilt dimensions. The external pressure of the barostat can be
specified as either a scalar pressure (isobaric ensemble) or as
components of a symmetric stress tensor (constant stress ensemble).
The user must be cautious when using very high anisotropic pressures, since the spherical Gaussians that represent the electrons in eFF will not deform anisotropically. When used correctly, the time-averaged temperature and stress tensor
of the particles will match the target values specified by
Tstart/Tstop and Pstart/Pstop.
</P>
<P>The equations of motion used are those of Shinoda et al. in
<A HREF = "#Shinoda">(Shinoda)</A>, which combine the hydrostatic equations of
Martyna, Tobias and Klein in <A HREF = "#Martyna">(Martyna)</A> with the strain
energy proposed by Parrinello and Rahman in
<A HREF = "#Parrinello">(Parrinello)</A>. The time integration schemes closely
follow the time-reversible measure-preserving Verlet and
rRESPA integrators derived by Tuckerman et al. in <A HREF = "#Tuckerman">(Tuckerman)</A>.
</P>
<HR>
<P>The thermostat for fix styles <I>nvt</I> and <I>npt</I> is specified using the
<I>temp</I> keyword. Other thermostat-related keywords are <I>tchain</I>,
<I>tloop</I> and <I>drag</I>, which are discussed below.
</P>
<P>The thermostat is applied to the translational degrees of freedom
for both nuclei and electrons, and for the radial electronic degrees of freedom. The translational degrees of freedom can also have
a bias velocity removed before thermostatting takes place; see the
description below. 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, using the default eFF (electron) units, a value of 1.0 means to relax
the temperature in a timespan of (roughly) 100 time steps. This is because the default time unit in eFF is fmsec, while the default timestep is set to 0.001 fmsec (see the <A HREF = "units.html">units</A> command). The atoms in the fix group are the only ones whose velocities (including the radial electronic velocities) and positions are updated
by the velocity/position update portion of the integration.
</P>
<HR>
<P>The barostat for fix styles <I>npt/eff</I> and <I>nph/eff</I> is specified using one or
more of the <I>iso</I>, <I>aniso</I>, <I>tri</I>, <I>x</I>, <I>y</I>, <I>z</I>, <I>xy</I>, <I>xz</I>, <I>yz</I>,
and <I>couple</I> keywords. These keywords give you the ability to specify
all 6 components of an external stress tensor, and to couple various
of these components together so that the dimensions they represent are
varied together during a constant-pressure simulation. Again, results with stress tensors containing large anisotropic character should be read with caution in the current eFF formulation.
</P>
<P>Other barostat-related keywords are <I>pchain</I>, <I>mtk</I>, <I>ploop</I>,
<I>nreset</I>, <I>drag</I>, and <I>dilate</I>, which are discussed below.
</P>
<P>Orthogonal simulation boxes have 3 adjustable dimensions (x,y,z).
Triclinic (non-orthogonal) simulation boxes have 6 adjustable
dimensions (x,y,z,xy,xz,yz). The <A HREF = "create_box.html">create_box</A>, <A HREF = "read_data.html">read
data</A>, and <A HREF = "read_restart.html">read_restart</A> commands
specify whether the simulation box is orthogonal or non-orthogonal
(triclinic) and explain the meaning of the xy,xz,yz tilt factors.
</P>
<P>The target pressures for each of the 6 components of the stress tensor
can be specified independently via the <I>x</I>, <I>y</I>, <I>z</I>, <I>xy</I>, <I>xz</I>, <I>yz</I>
keywords, which correspond to the 6 simulation box dimensions. For
each component, the external pressure or tensor component at each
timestep is a ramped value during the run from <I>Pstart</I> to <I>Pstop</I>.
If a target pressure is specified for a component, then the
corresponding box dimension will change during a simulation. For
example, if the <I>y</I> keyword is used, the y-box length will change. If
the <I>xy</I> keyword is used, the xy tilt factor will change. A box
dimension will not change if that component is not specified, although
you have the option to change that dimension via the <A HREF = "fix_deform_eff.html">fix
deform/eff</A> command.
</P>
<P>Note that in order to use the <I>xy</I>, <I>xz</I>, or <I>yz</I> keywords, the
simulation box must be triclinic, even if its initial tilt factors are
0.0.
</P>
<P>For all barostat keywords, 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 1.0 means to relax the pressure
in a timespan of (roughly) 1000 timesteps for the eFF default time unit (fmsec - see
the <A HREF = "units.html">units</A> command), considering the default timestep is 0.001.
</P>
<P>Regardless of what atoms are in the fix group, a global pressure or
stress tensor 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: there are two different pressures that can be reported for eFF when defining the pair_style (see <A HREF = "pair_eff_cut.html">pair eff/cut</A> to understand these settings), one (default) that considers electrons do not contribute radial virial components (i.e. electrons treated as incompressible 'rigid' spheres) and one that does. The radial electronic contributions to the virials are only tallied if the flexible pressure option is set, and this will affect both global and per-atom quantities. In principle, the true pressure of a system is somewhere in between the rigid and the flexible eFF pressures, but, for most cases, the difference between these two pressures will not be significant over long-term averaged runs (i.e. even though the energy partitioning changes, the total energy remains similar).
</P>
<HR>
<P>The <I>couple</I> keyword allows two or three of the diagonal components of
the pressure tensor to be "coupled" together. The value specified
with the keyword determines which are coupled. For example, <I>xz</I>
means the <I>Pxx</I> and <I>Pzz</I> components of the stress tensor are coupled.
<I>Xyz</I> means all 3 diagonal components are coupled. Coupling means two
things: the instantaneous stress will be computed as an average of the
corresponding diagonal components, and the coupled box dimensions will
be changed together in lockstep, meaning coupled dimensions will be
dilated or contracted by the same percentage every timestep. The
<I>Pstart</I>, <I>Pstop</I>, <I>Pdamp</I> parameters for any coupled dimensions must
be identical. <I>Couple xyz</I> can be used for a 2d simulation; the <I>z</I>
dimension is simply ignored.
</P>
<HR>
<P>The <I>iso</I>, <I>aniso</I>, and <I>tri</I> keywords are simply shortcuts that are
equivalent to specifying several other keywords together.
</P>
<P>The keyword <I>iso</I> means couple all 3 diagonal components together when
pressure is computed (hydrostatic pressure), and dilate/contract the
dimensions together. Using "iso Pstart Pstop Pdamp" is the same as
specifying these 4 keywords:
</P>
<PRE>x Pstart Pstop Pdamp
y Pstart Pstop Pdamp
z Pstart Pstop Pdamp
couple xyz
</PRE>
<P>The keyword <I>aniso</I> means <I>x</I>, <I>y</I>, and <I>z</I> dimensions are controlled
independently using the <I>Pxx</I>, <I>Pyy</I>, and <I>Pzz</I> components of the
stress tensor as the driving forces, and the specified scalar external
pressure. Using "aniso Pstart Pstop Pdamp" is the same as specifying
these 4 keywords:
</P>
<PRE>x Pstart Pstop Pdamp
y Pstart Pstop Pdamp
z Pstart Pstop Pdamp
couple none
</PRE>
<P>The keyword <I>tri</I> means <I>x</I>, <I>y</I>, <I>z</I>, <I>xy</I>, <I>xz</I>, and <I>yz</I> dimensions
are controlled independently using their individual stress components
as the driving forces, and the specified scalar pressure as the
external normal stress. Using "tri Pstart Pstop Pdamp" is the same as
specifying these 7 keywords:
</P>
<PRE>x Pstart Pstop Pdamp
y Pstart Pstop Pdamp
z Pstart Pstop Pdamp
xy 0.0 0.0 Pdamp
yz 0.0 0.0 Pdamp
xz 0.0 0.0 Pdamp
couple none
</PRE>
<HR>
<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. Note that use of the drag
keyword will interfere with energy conservation and will also change
the distribution of positions and velocities so that they do not
correspond to the nominal NVT, NPT, or NPH ensembles.
</P>
<P>An alternative way to control initial oscillations is to use chain
thermostats. The keyword <I>tchain</I> determines the number of thermostats
in the particle thermostat. A value of 1 corresponds to the original
Nose-Hoover thermostat. The keyword <I>pchain</I> specifies the number of
thermostats in the chain thermostatting the barostat degrees of
freedom. A value of 0 corresponds to no thermostatting of the
barostat variables.
</P>
<P>The <I>mtk</I> keyword controls whether or not the correction terms due to
Martyna, Tuckerman, and Klein are included in the equations of motion
<A HREF = "#Martyna">(Martyna)</A>. Specifying <I>no</I> reproduces the original
Hoover barostat, whose volume probability distribution function
differs from the true NPT and NPH ensembles by a factor of 1/V. Hence
using <I>yes</I> is more correct, but in many cases the difference is
negligible.
</P>
<P>The keyword <I>tloop</I> can be used to improve the accuracy of integration
scheme at little extra cost. The initial and final updates of the
thermostat variables are broken up into <I>tloop</I> substeps, each of
length <I>dt</I>/<I>tloop</I>. This corresponds to using a first-order
Suzuki-Yoshida scheme <A HREF = "#Tuckerman2006">(Tuckerman2006)</A>. The keyword
<I>ploop</I> does the same thing for the barostat thermostat.
</P>
<P>The keyword <I>nreset</I> controls how often the reference dimensions used
to define the strain energy are reset. If this keyword is not used,
or is given a value of zero, then the reference dimensions are set to
those of the initial simulation domain and are never changed. If the
simulation domain changes significantly during the simulation, then
the final average pressure tensor will differ significantly from the
specified values of the external stress tensor. A value of <I>nstep</I>
means that every <I>nstep</I> timesteps, the reference dimensions are set
to those of the current simulation domain.
</P>
<HR>
<P>IMPORTANT NOTE: Using a barostat coupled to tilt dimensions <I>xy</I>,
<I>xz</I>, <I>yz</I> can sometimes result in arbitrarily large values of the
tilt dimensions, i.e. a dramatically deformed simulation box. LAMMPS
imposes reasonable limits on how large the tilt values can be, and
exits with an error if these are exceeded. This error typically
indicates that there is something badly wrong with how the simulation
was constructed. The three most common sources of this error are
using keyword <I>tri</I> on a liquid system, specifying an external shear
stress tensor that exceeds the yield stress of the solid, and
specifying values of <I>Pstart</I> that are too far from the current stress
value. In other words, triclinic barostatting should be used with
care. This also is true for other barostat styles, although they tend
to be more forgiving of insults.
</P>
<P>IMPORTANT NOTE: Unlike the <A HREF = "fix_temp_berendsen.html">fix
temp/berendsen</A> command which performs
thermostatting but NO time integration, these fixes perform
thermostatting/barostatting AND time integration. Thus you should not
use any other time integration fix, such as <A HREF = "fix_nve_eff.html">fix nve/eff</A> on
atoms to which this fix is applied. Likewise, the <I>temp</I> options for
fix nvt/eff and fix npt/eff should not normally be used on atoms that also
have their temperature controlled by another fix - e.g. by <A HREF = "fix_nh.html">fix
langevin/eff</A> or <A HREF = "fix_temp_rescale.html">fix temp/rescale</A>
commands.
</P>
<P>IMPORTANT NOTE: currently, there is no available option for the user to set or create temperature distributions that include the radial electronic degrees of freedom with the <A HREF = "velocity.html">velocity</A> command, so the the user must allow for these to equilibrate (i.e. evolve thermal partitioning) through integration.
</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>These fixes compute a temperature and pressure each timestep. To do
this, the fix creates its own computes of style "temp" and "pressure",
as if one of these two sets of commands had been issued:
</P>
<PRE>compute fix-ID_temp group-ID temp/eff
compute fix-ID_press group-ID pressure fix-ID_temp
</PRE>
<PRE>compute fix-ID_temp all temp/eff
compute fix-ID_press all pressure fix-ID_temp
</PRE>
<P>See the <A HREF = "compute_temp_eff.html">compute temp/eff</A> and <A HREF = "compute_pressure.html">compute
pressure</A> commands for details. Note that the
IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID
+ underscore + "press". For fix nvt/eff, the group for the new computes
is the same as the fix group. For fix nph/eff and fix npt/eff, the group for
the new computes is "all" since pressure is computed for the entire
system.
</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, fix nvt/eff and fix npt/eff 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>These fixes writes the state of all the thermostat and barostat
variables 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 these fixes. 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:
</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/eff), 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 these
fixes 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>These fixes compute a global scalar and a global vector of quantities,
which can be accessed by various <A HREF = "Section_howto.html#4_15">output
commands</A>. The scalar values calculated by
this fix are "extensive"; the vector values are "intensive".
</P>
<P>The scalar is the cumulative energy change due to the fix.
</P>
<P>The vector stores internal Nose/Hoover thermostat and barostat
variables. The number and meaning of the vector values depends on
which fix is used and the settings for keywords <I>tchain</I> and <I>pchain</I>,
which specify the number of Nose/Hoover chains for the thermostat and
barostat. If no thermostatting is done, then <I>tchain</I> is 0. If no
barostatting is done, then <I>pchain</I> is 0. In the following list,
"ndof" is 0, 1, 3, or 6, and is the number of degrees of freedom in
the barostat. Its value is 0 if no barostat is used, else its value
is 6 if any off-diagonal stress tensor component is barostatted, else
its value is 1 if <I>couple xyz</I> is used or <I>couple xy</I> for a 2d
simulation, otherwise its value is 3.
</P>
<P>The order of values in the global vector and their meaning is as
follows. The notation means there are tchain values for eta, followed
by tchain for eta_dot, followed by ndof for omega, etc:
</P>
<UL><LI>eta[tchain] = particle thermostat displacements
<LI>eta_dot[tchain] = particle thermostat velocities
<LI>omega[ndof] = barostat displacements
<LI>omega_dot[ndof] = barostat velocities
<LI>etap[pchain] = barostat thermostat displacements
<LI>etap_dot[pchain] = barostat thermostat velocities
<LI>PE_eta[tchain] = potential energy of each particle thermostat displacement
<LI>KE_eta_dot[tchain] = kinetic energy of each particle thermostat velocity
<LI>PE_omega[ndof] = potential energy of each barostat displacement
<LI>KE_omega_dot[ndof] = kinetic energy of each barostat velocity
<LI>PE_etap[pchain] = potential energy of each barostat thermostat displacement
<LI>KE_etap_dot[pchain] = kinetic energy of each barostat thermostat velocity
<LI>PE_strain[1] = scalar strain energy
</UL>
<P>These fixes can ramp their external 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>These fixes are not invoked during <A HREF = "minimize.html">energy
minimization</A>.
</P>
<P>These fixes can be used with either the <I>verlet</I> or <I>respa</I>
<A HREF = "run_style.html">integrators</A>. When using one of the barostat fixes
with <I>respa</I>, LAMMPS uses an integrator constructed
according to the following factorization of the Liouville propagator
(for two rRESPA levels):
</P>
<CENTER><IMG SRC = "Eqs/fix_nh1.jpg">
</CENTER>
<P>This factorization differs somewhat from that of Tuckerman et al., in that
the barostat is only updated at the outermost rRESPA level, whereas
Tuckerman's factorization requires splitting the pressure into pieces
corresponding to the forces computed at each rRESPA level. In theory, the
latter method will exhibit better numerical stability. In practice,
because Pdamp is normally chosen to be a large multiple of the
outermost rRESPA timestep, the barostat dynamics are not the
limiting factor for numerical stability. Both
factorizations are time-reversible and can be shown to preserve the phase
space measure of the underlying non-Hamiltonian equations of motion.
</P>
<P>IMPORTANT NOTE: using the <I>respa</I> integrator may be useful for the simulations that sample the electronic motions at a faster pace than the nuclear motions.
</P>
<P><B>Restrictions:</B>
</P>
<P>This fix is part of the "user-eff" 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>Non-periodic dimensions cannot be barostatted. <I>Z</I>, <I>xz</I>, and <I>yz</I>,
cannot be barostatted 2D simulations. <I>Xy</I>, <I>xz</I>, and <I>yz</I> can only
be barostatted if the simulation domain is triclinic and the 2nd
dimension in the keyword (<I>y</I> dimension in <I>xy</I>) is periodic. The
<A HREF = "create_box.html">create_box</A>, <A HREF = "read_data.html">read data</A>, and
<A HREF = "read_restart.html">read_restart</A> commands specify whether the
simulation box is orthogonal or non-orthogonal (triclinic) and explain
the meaning of the xy,xz,yz tilt factors.
</P>
<P>For the <I>temp</I> keyword, the final Tstop cannot be 0.0 since it would
make the external T = 0.0 at some timestep during the simulation which
is not allowed in the Nose/Hoover formulation.
</P>
<P>IMPORTANT NOTE: The temperature for systems (regions or groups) with only electrons is not defined in the current temperature calculations, a practical example would be a uniform electron gas or a very hot plasma, where electrons remain delocalized from the nuclei. This is because, even though electron virials are included in the temperature calculation, these are averaged over the nuclear degrees of freedom only. In such cases a corrective term must be added to the pressure to get the correct kinetic contribution.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_nve_eff.html">fix nve/eff</A>, <A HREF = "fix_modify.html">fix_modify</A>, <A HREF = "run_style.html">run_style</A>
</P>
<P><B>Default:</B>
</P>
<P>The keyword defaults are tchain = 3, pchain = 3, mtk = yes, tloop =
ploop = 1, nreset = 0, drag = 0.0, dilate = all, and couple = none.
</P>
<HR>
<A NAME = "Martyna"></A>
<P><B>(Martyna)</B> Martyna, Tobias and Klein, J Chem Phys, 101, 4177 (1994).
</P>
<A NAME = "Parrinello"></A>
<P><B>(Parrinello)</B> Parrinello and Rahman, J Appl Phys, 52, 7182 (1981).
</P>
<A NAME = "Tuckerman"></A>
<P><B>(Tuckerman)</B> Tuckerman, Alejandre, Lopez-Rendon, Jochim, and
Martyna, J Phys A: Math Gen, 39, 5629 (2006).
</P>
<A NAME = "Shinoda"></A>
<P><B>(Shinoda)</B> Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).
</P>
</HTML>
c4science · Help