mirror of https://github.com/lammps/lammps.git
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4654 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
cc0f92226a
commit
386524da38
|
|
@ -45,10 +45,10 @@ fix 1 all langevin/eff 1.0 1.1 10.0 48279 scale 3 1.5
|
||||||
<P><B>Description:</B>
|
<P><B>Description:</B>
|
||||||
</P>
|
</P>
|
||||||
<P>Apply a Langevin thermostat as described in <A HREF = "#Schneider">(Schneider)</A>
|
<P>Apply a Langevin thermostat as described in <A HREF = "#Schneider">(Schneider)</A>
|
||||||
to a group of atoms which models an interaction with a background
|
to a group of nuclei and electrons in the <A HREF = "pair_eff.html">electron force
|
||||||
implicit solvent. Used with <A HREF = "fix_nve_eff.html">fix nve/eff</A>, this command
|
field</A> model. Used with <A HREF = "fix_nve_eff.html">fix nve/eff</A>,
|
||||||
performs Brownian dynamics (BD), since the total force on each atom
|
this command performs Brownian dynamics (BD), since the total force on
|
||||||
will have the form:
|
each atom will have the form:
|
||||||
</P>
|
</P>
|
||||||
<PRE>F = Fc + Ff + Fr
|
<PRE>F = Fc + Ff + Fr
|
||||||
Ff = - (m / damp) v
|
Ff = - (m / damp) v
|
||||||
|
|
@ -59,94 +59,10 @@ interactions (<A HREF = "pair_style.html">pair_style</A>).
|
||||||
</P>
|
</P>
|
||||||
<P>The Ff and Fr terms are added by this fix on a per-particle basis.
|
<P>The Ff and Fr terms are added by this fix on a per-particle basis.
|
||||||
</P>
|
</P>
|
||||||
<P>Ff is a frictional drag or viscous damping term proportional to the
|
<P>The operation of this fix is exactly like that described by the <A HREF = "fix_langevin.html">fix
|
||||||
particle's velocity (including the electronic radial degrees of
|
langevin</A> command, except that the thermostatting
|
||||||
freedom). The proportionality constant for each atom is computed as
|
is also applied to the radial electron velocity for electron
|
||||||
m/damp, where m is the mass of the particle and damp is the damping
|
particles.
|
||||||
factor specified by the user.
|
|
||||||
</P>
|
|
||||||
<P>Fr is a force due to solvent atoms at a temperature T randomly bumping
|
|
||||||
into the particle. As derived from the fluctuation/dissipation
|
|
||||||
theorem, its magnitude as shown above is proportional to sqrt(Kb T m /
|
|
||||||
dt damp), where Kb is the Boltzmann constant, T is the desired
|
|
||||||
temperature, m is the mass of the particle, dt is the timestep size,
|
|
||||||
and damp is the damping factor. Random numbers are used to randomize
|
|
||||||
the direction and magnitude of this force as described in
|
|
||||||
<A HREF = "#Dunweg">(Dunweg)</A>, where a uniform random number is used (instead of
|
|
||||||
a Gaussian random number) for speed.
|
|
||||||
</P>
|
|
||||||
<P>Note that the thermostat effect of this fix is applied to the
|
|
||||||
translational and electronic radial degrees of freedom for the
|
|
||||||
particles in a system. The translational degrees of freedom can also
|
|
||||||
have a bias velocity removed from them before thermostatting takes
|
|
||||||
place; see the description below.
|
|
||||||
</P>
|
|
||||||
<P>IMPORTANT NOTE: Unlike the <A HREF = "fix_nh_eff.html">fix nvt/eff</A> command which
|
|
||||||
performs Nose/Hoover thermostatting AND time integration, this fix
|
|
||||||
does NOT perform time integration. It only modifies forces to effect
|
|
||||||
thermostatting. Thus you must use a separate time integration fix,
|
|
||||||
like <A HREF = "fix_nve_eff.html">fix nve/eff</A> to actually update the velocities
|
|
||||||
(including electronic radial velocities) and positions of atoms
|
|
||||||
(nuclei and electrons) using the modified forces. 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_nh.html">fix nvt/eff</A> command.
|
|
||||||
</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.
|
|
||||||
</P>
|
|
||||||
<P>The desired temperature at each timestep is a ramped value during the
|
|
||||||
run from <I>Tstart</I> to <I>Tstop</I>.
|
|
||||||
</P>
|
|
||||||
<P>Like other fixes that perform thermostatting, this fix can be used
|
|
||||||
with <A HREF = "compute.html">compute commands</A> that remove a "bias" from the
|
|
||||||
atom velocities. E.g. removing the center-of-mass velocity from a
|
|
||||||
group of atoms or removing the x-component of velocity from the
|
|
||||||
calculation. 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: 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>The <I>damp</I> parameter is specified in time units and determines how
|
|
||||||
rapidly the temperature is relaxed. For example, a value of 0.1 means
|
|
||||||
to relax the temperature in a timespan of 100 timesteps (for the
|
|
||||||
default 0.001 timesteps and fmsec unit used in eFF - see the
|
|
||||||
<A HREF = "units.html">units</A> command). The damp factor can be thought of as
|
|
||||||
inversely related to the viscosity of the solvent. I.e. a small
|
|
||||||
relaxation time implies a hi-viscosity solvent and vice versa. See
|
|
||||||
the discussion about gamma and viscosity in the documentation for the
|
|
||||||
<A HREF = "fix_viscous.html">fix viscous</A> command for more details.
|
|
||||||
</P>
|
|
||||||
<P>The random # <I>seed</I> must be a positive integer. A Marsaglia random
|
|
||||||
number generator is used. Each processor uses the input seed to
|
|
||||||
generate its own unique seed and its own stream of random numbers.
|
|
||||||
Thus the dynamics of the system will not be identical on two runs on
|
|
||||||
different numbers of processors.
|
|
||||||
</P>
|
|
||||||
<P>The keyword <I>scale</I> allows the damp factor to be scaled up or down by
|
|
||||||
the specified factor for atoms of that type. This can be useful when
|
|
||||||
different atom types have different sizes or masses. It can be used
|
|
||||||
multiple times to adjust damp for several atom types. Note that
|
|
||||||
specifying a ratio of 2 increases the relaxation time which is
|
|
||||||
equivalent to the solvent's viscosity acting on particles with 1/2 the
|
|
||||||
diameter. This is the opposite effect of scale factors used by the
|
|
||||||
<A HREF = "fix_viscous.html">fix viscous</A> command, since the damp factor in fix
|
|
||||||
<I>langevin</I> is inversely related to the gamma factor in fix <I>viscous</I>.
|
|
||||||
Also note that the damping factor in fix <I>langevin</I> includes the
|
|
||||||
particle mass in Ff, unlike fix <I>viscous</I>. Thus the mass and size of
|
|
||||||
different atom types should be accounted for in the choice of ratio
|
|
||||||
values.
|
|
||||||
</P>
|
|
||||||
<P>The keyword <I>tally</I> enables the calculation of the cummulative energy
|
|
||||||
added/subtracted to the atoms as they are thermostatted. Effectively
|
|
||||||
it is the energy exchanged between the infinite thermal reservoir and
|
|
||||||
the particles. As described below, this energy can then be printed
|
|
||||||
out or added to the potential energy of the system to monitor energy
|
|
||||||
conservation.
|
|
||||||
</P>
|
</P>
|
||||||
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
|
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
|
||||||
</P>
|
</P>
|
||||||
|
|
|
||||||
|
|
@ -35,10 +35,10 @@ fix 1 all langevin/eff 1.0 1.1 10.0 48279 scale 3 1.5 :pre
|
||||||
[Description:]
|
[Description:]
|
||||||
|
|
||||||
Apply a Langevin thermostat as described in "(Schneider)"_#Schneider
|
Apply a Langevin thermostat as described in "(Schneider)"_#Schneider
|
||||||
to a group of atoms which models an interaction with a background
|
to a group of nuclei and electrons in the "electron force
|
||||||
implicit solvent. Used with "fix nve/eff"_fix_nve_eff.html, this command
|
field"_pair_eff.html model. Used with "fix nve/eff"_fix_nve_eff.html,
|
||||||
performs Brownian dynamics (BD), since the total force on each atom
|
this command performs Brownian dynamics (BD), since the total force on
|
||||||
will have the form:
|
each atom will have the form:
|
||||||
|
|
||||||
F = Fc + Ff + Fr
|
F = Fc + Ff + Fr
|
||||||
Ff = - (m / damp) v
|
Ff = - (m / damp) v
|
||||||
|
|
@ -49,94 +49,10 @@ interactions ("pair_style"_pair_style.html).
|
||||||
|
|
||||||
The Ff and Fr terms are added by this fix on a per-particle basis.
|
The Ff and Fr terms are added by this fix on a per-particle basis.
|
||||||
|
|
||||||
Ff is a frictional drag or viscous damping term proportional to the
|
The operation of this fix is exactly like that described by the "fix
|
||||||
particle's velocity (including the electronic radial degrees of
|
langevin"_fix_langevin.html command, except that the thermostatting
|
||||||
freedom). The proportionality constant for each atom is computed as
|
is also applied to the radial electron velocity for electron
|
||||||
m/damp, where m is the mass of the particle and damp is the damping
|
particles.
|
||||||
factor specified by the user.
|
|
||||||
|
|
||||||
Fr is a force due to solvent atoms at a temperature T randomly bumping
|
|
||||||
into the particle. As derived from the fluctuation/dissipation
|
|
||||||
theorem, its magnitude as shown above is proportional to sqrt(Kb T m /
|
|
||||||
dt damp), where Kb is the Boltzmann constant, T is the desired
|
|
||||||
temperature, m is the mass of the particle, dt is the timestep size,
|
|
||||||
and damp is the damping factor. Random numbers are used to randomize
|
|
||||||
the direction and magnitude of this force as described in
|
|
||||||
"(Dunweg)"_#Dunweg, where a uniform random number is used (instead of
|
|
||||||
a Gaussian random number) for speed.
|
|
||||||
|
|
||||||
Note that the thermostat effect of this fix is applied to the
|
|
||||||
translational and electronic radial degrees of freedom for the
|
|
||||||
particles in a system. The translational degrees of freedom can also
|
|
||||||
have a bias velocity removed from them before thermostatting takes
|
|
||||||
place; see the description below.
|
|
||||||
|
|
||||||
IMPORTANT NOTE: Unlike the "fix nvt/eff"_fix_nh_eff.html command which
|
|
||||||
performs Nose/Hoover thermostatting AND time integration, this fix
|
|
||||||
does NOT perform time integration. It only modifies forces to effect
|
|
||||||
thermostatting. Thus you must use a separate time integration fix,
|
|
||||||
like "fix nve/eff"_fix_nve_eff.html to actually update the velocities
|
|
||||||
(including electronic radial velocities) and positions of atoms
|
|
||||||
(nuclei and electrons) using the modified forces. Likewise, this fix
|
|
||||||
should not normally be used on atoms that also have their temperature
|
|
||||||
controlled by another fix - e.g. by "fix nvt/eff"_fix_nh.html command.
|
|
||||||
|
|
||||||
See "this howto section"_Section_howto.html#4_16 of the manual for a
|
|
||||||
discussion of different ways to compute temperature and perform
|
|
||||||
thermostatting.
|
|
||||||
|
|
||||||
The desired temperature at each timestep is a ramped value during the
|
|
||||||
run from {Tstart} to {Tstop}.
|
|
||||||
|
|
||||||
Like other fixes that perform thermostatting, this fix can be used
|
|
||||||
with "compute commands"_compute.html that remove a "bias" from the
|
|
||||||
atom velocities. E.g. removing the center-of-mass velocity from a
|
|
||||||
group of atoms or removing the x-component of velocity from the
|
|
||||||
calculation. 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: bias is removed from each atom, thermostatting is performed on
|
|
||||||
the remaining thermal degrees of freedom, and the bias is added back
|
|
||||||
in.
|
|
||||||
|
|
||||||
The {damp} parameter is specified in time units and determines how
|
|
||||||
rapidly the temperature is relaxed. For example, a value of 0.1 means
|
|
||||||
to relax the temperature in a timespan of 100 timesteps (for the
|
|
||||||
default 0.001 timesteps and fmsec unit used in eFF - see the
|
|
||||||
"units"_units.html command). The damp factor can be thought of as
|
|
||||||
inversely related to the viscosity of the solvent. I.e. a small
|
|
||||||
relaxation time implies a hi-viscosity solvent and vice versa. See
|
|
||||||
the discussion about gamma and viscosity in the documentation for the
|
|
||||||
"fix viscous"_fix_viscous.html command for more details.
|
|
||||||
|
|
||||||
The random # {seed} must be a positive integer. A Marsaglia random
|
|
||||||
number generator is used. Each processor uses the input seed to
|
|
||||||
generate its own unique seed and its own stream of random numbers.
|
|
||||||
Thus the dynamics of the system will not be identical on two runs on
|
|
||||||
different numbers of processors.
|
|
||||||
|
|
||||||
The keyword {scale} allows the damp factor to be scaled up or down by
|
|
||||||
the specified factor for atoms of that type. This can be useful when
|
|
||||||
different atom types have different sizes or masses. It can be used
|
|
||||||
multiple times to adjust damp for several atom types. Note that
|
|
||||||
specifying a ratio of 2 increases the relaxation time which is
|
|
||||||
equivalent to the solvent's viscosity acting on particles with 1/2 the
|
|
||||||
diameter. This is the opposite effect of scale factors used by the
|
|
||||||
"fix viscous"_fix_viscous.html command, since the damp factor in fix
|
|
||||||
{langevin} is inversely related to the gamma factor in fix {viscous}.
|
|
||||||
Also note that the damping factor in fix {langevin} includes the
|
|
||||||
particle mass in Ff, unlike fix {viscous}. Thus the mass and size of
|
|
||||||
different atom types should be accounted for in the choice of ratio
|
|
||||||
values.
|
|
||||||
|
|
||||||
The keyword {tally} enables the calculation of the cummulative energy
|
|
||||||
added/subtracted to the atoms as they are thermostatted. Effectively
|
|
||||||
it is the energy exchanged between the infinite thermal reservoir and
|
|
||||||
the particles. As described below, this energy can then be printed
|
|
||||||
out or added to the potential energy of the system to monitor energy
|
|
||||||
conservation.
|
|
||||||
|
|
||||||
[Restart, fix_modify, output, run start/stop, minimize info:]
|
[Restart, fix_modify, output, run start/stop, minimize info:]
|
||||||
|
|
||||||
|
|
|
||||||
|
|
@ -56,382 +56,57 @@ 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.
|
||||||
<P><B>Description:</B>
|
<P><B>Description:</B>
|
||||||
</P>
|
</P>
|
||||||
<P>These commands perform time integration on Nose-Hoover style
|
<P>These commands perform time integration on Nose-Hoover style
|
||||||
non-Hamiltonian equations of motion which are designed to generate
|
non-Hamiltonian equations of motion for nuclei and electrons in the
|
||||||
positions and velocities sampled from the canonical (nvt),
|
group for the <A HREF = "pair_eff.html">electron force field</A> model. The fixes
|
||||||
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
|
are designed to generate positions and velocities sampled from the
|
||||||
achieved by adding some dynamic variables which are coupled to the
|
canonical (nvt), isothermal-isobaric (npt), and isenthalpic (nph)
|
||||||
particle velocities (thermostatting) and simulation domain dimensions
|
ensembles. This is achieved by adding some dynamic variables which
|
||||||
(barostatting). In addition to basic thermostatting and barostatting,
|
are coupled to the particle velocities (thermostatting) and simulation
|
||||||
these fixes can also create a chain of thermostats coupled to the
|
domain dimensions (barostatting). In addition to basic thermostatting
|
||||||
particle thermostat, and another chain of thermostats coupled to the
|
and barostatting, these fixes can also create a chain of thermostats
|
||||||
barostat variables. The barostat can be coupled to the overall box
|
coupled to the particle thermostat, and another chain of thermostats
|
||||||
volume, or to individual dimensions, including the <I>xy</I>, <I>xz</I> and <I>yz</I>
|
coupled to the barostat variables. The barostat can be coupled to the
|
||||||
tilt dimensions. The external pressure of the barostat can be
|
overall box volume, or to individual dimensions, including the <I>xy</I>,
|
||||||
specified as either a scalar pressure (isobaric ensemble) or as
|
<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).
|
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
|
When used correctly, the time-averaged temperature and stress tensor
|
||||||
of the particles will match the target values specified by
|
of the particles will match the target values specified by
|
||||||
Tstart/Tstop and Pstart/Pstop.
|
Tstart/Tstop and Pstart/Pstop.
|
||||||
</P>
|
</P>
|
||||||
<P>The equations of motion used are those of Shinoda et al. in
|
<P>The operation of these fixes is exactly like that described by the
|
||||||
<A HREF = "#Shinoda">(Shinoda)</A>, which combine the hydrostatic equations of
|
<A HREF = "fix_nh.html">fix nvt, npt, and nph</A> commands, except that the radius
|
||||||
Martyna, Tobias and Klein in <A HREF = "#Martyna">(Martyna)</A> with the strain
|
and radial velocity of electrons are also updated. Likewise the
|
||||||
energy proposed by Parrinello and Rahman in
|
temperature and pressure calculated by the fix, using the computes it
|
||||||
<A HREF = "#Parrinello">(Parrinello)</A>. The time integration schemes closely
|
creates (as discussed in the <A HREF = "fix_nh.html">fix nvt, npt, and nph</A>
|
||||||
follow the time-reversible measure-preserving Verlet and
|
doc page), are performed with computes that include the eFF contribution
|
||||||
rRESPA integrators derived by Tuckerman et al. in <A HREF = "#Tuckerman">(Tuckerman)</A>.
|
to the temperature or kinetic energy from the electron radial velocity.
|
||||||
</P>
|
</P>
|
||||||
<HR>
|
<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
|
||||||
<P>The thermostat for fix styles <I>nvt</I> and <I>npt</I> is specified using the
|
eff/cut</A> to understand these settings), one
|
||||||
<I>temp</I> keyword. Other thermostat-related keywords are <I>tchain</I>,
|
(default) that considers electrons do not contribute radial virial
|
||||||
<I>tloop</I> and <I>drag</I>, which are discussed below.
|
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>
|
</P>
|
||||||
<P>The thermostat is applied to the translational degrees of freedom
|
<P>IMPORTANT NOTE: currently, there is no available option for the user
|
||||||
for both nuclei and electrons, and for the radial electronic degrees of freedom. The translational degrees of freedom can also have
|
to set or create temperature distributions that include the radial
|
||||||
a bias velocity removed before thermostatting takes place; see the
|
electronic degrees of freedom with the <A HREF = "velocity.html">velocity</A>
|
||||||
description below. The desired temperature at each timestep is a
|
command, so the the user must allow for these degrees of freedom to
|
||||||
ramped value during the run from <I>Tstart</I> to <I>Tstop</I>. The <I>Tdamp</I>
|
equilibrate (i.e. equi-partitioning of energy) through time
|
||||||
parameter is specified in time units and determines how rapidly the
|
integration.
|
||||||
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>
|
||||||
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
|
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
|
||||||
</P>
|
</P>
|
||||||
<P>These fixes writes the state of all the thermostat and barostat
|
<P>See the doc page for the <A HREF = "fix_nh.html">fix nvt, npt, and nph</A> commands
|
||||||
variables to <A HREF = "restart.html">binary restart files</A>. See the
|
for details.
|
||||||
<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>
|
||||||
<P><B>Restrictions:</B>
|
<P><B>Restrictions:</B>
|
||||||
</P>
|
</P>
|
||||||
|
|
@ -439,24 +114,22 @@ space measure of the underlying non-Hamiltonian equations of motion.
|
||||||
LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
|
LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
|
||||||
LAMMPS</A> section for more info.
|
LAMMPS</A> section for more info.
|
||||||
</P>
|
</P>
|
||||||
<P>Non-periodic dimensions cannot be barostatted. <I>Z</I>, <I>xz</I>, and <I>yz</I>,
|
<P>Other restriction discussed on the doc page for the <A HREF = "fix_nh.html">fix nvt, npt, and
|
||||||
cannot be barostatted 2D simulations. <I>Xy</I>, <I>xz</I>, and <I>yz</I> can only
|
nph</A> commands also apply.
|
||||||
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>
|
||||||
<P>For the <I>temp</I> keyword, the final Tstop cannot be 0.0 since it would
|
<P>IMPORTANT NOTE: The temperature for systems (regions or groups) with
|
||||||
make the external T = 0.0 at some timestep during the simulation which
|
only electrons and no nuclei is 0.0 (i.e. not defined) in the current
|
||||||
is not allowed in the Nose/Hoover formulation.
|
temperature calculations, a practical example would be a uniform
|
||||||
</P>
|
electron gas or a very hot plasma, where electrons remain delocalized
|
||||||
<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.
|
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>
|
||||||
<P><B>Related commands:</B>
|
<P><B>Related commands:</B>
|
||||||
</P>
|
</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><A HREF = "fix_nh.html">fix nvt</A>, <A HREF = "fix_nh.html">fix nph</A>, <A HREF = "fix_nh.html">fix npt</A>,
|
||||||
|
<A HREF = "fix_modify.html">fix_modify</A>, <A HREF = "run_style.html">run_style</A>
|
||||||
</P>
|
</P>
|
||||||
<P><B>Default:</B>
|
<P><B>Default:</B>
|
||||||
</P>
|
</P>
|
||||||
|
|
|
||||||
|
|
@ -48,382 +48,57 @@ 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.
|
||||||
[Description:]
|
[Description:]
|
||||||
|
|
||||||
These commands perform time integration on Nose-Hoover style
|
These commands perform time integration on Nose-Hoover style
|
||||||
non-Hamiltonian equations of motion which are designed to generate
|
non-Hamiltonian equations of motion for nuclei and electrons in the
|
||||||
positions and velocities sampled from the canonical (nvt),
|
group for the "electron force field"_pair_eff.html model. The fixes
|
||||||
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
|
are designed to generate positions and velocities sampled from the
|
||||||
achieved by adding some dynamic variables which are coupled to the
|
canonical (nvt), isothermal-isobaric (npt), and isenthalpic (nph)
|
||||||
particle velocities (thermostatting) and simulation domain dimensions
|
ensembles. This is achieved by adding some dynamic variables which
|
||||||
(barostatting). In addition to basic thermostatting and barostatting,
|
are coupled to the particle velocities (thermostatting) and simulation
|
||||||
these fixes can also create a chain of thermostats coupled to the
|
domain dimensions (barostatting). In addition to basic thermostatting
|
||||||
particle thermostat, and another chain of thermostats coupled to the
|
and barostatting, these fixes can also create a chain of thermostats
|
||||||
barostat variables. The barostat can be coupled to the overall box
|
coupled to the particle thermostat, and another chain of thermostats
|
||||||
volume, or to individual dimensions, including the {xy}, {xz} and {yz}
|
coupled to the barostat variables. The barostat can be coupled to the
|
||||||
tilt dimensions. The external pressure of the barostat can be
|
overall box volume, or to individual dimensions, including the {xy},
|
||||||
specified as either a scalar pressure (isobaric ensemble) or as
|
{xz} and {yz} 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).
|
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
|
When used correctly, the time-averaged temperature and stress tensor
|
||||||
of the particles will match the target values specified by
|
of the particles will match the target values specified by
|
||||||
Tstart/Tstop and Pstart/Pstop.
|
Tstart/Tstop and Pstart/Pstop.
|
||||||
|
|
||||||
The equations of motion used are those of Shinoda et al. in
|
The operation of these fixes is exactly like that described by the
|
||||||
"(Shinoda)"_#Shinoda, which combine the hydrostatic equations of
|
"fix nvt, npt, and nph"_fix_nh.html commands, except that the radius
|
||||||
Martyna, Tobias and Klein in "(Martyna)"_#Martyna with the strain
|
and radial velocity of electrons are also updated. Likewise the
|
||||||
energy proposed by Parrinello and Rahman in
|
temperature and pressure calculated by the fix, using the computes it
|
||||||
"(Parrinello)"_#Parrinello. The time integration schemes closely
|
creates (as discussed in the "fix nvt, npt, and nph"_fix_nh.html
|
||||||
follow the time-reversible measure-preserving Verlet and
|
doc page), are performed with computes that include the eFF contribution
|
||||||
rRESPA integrators derived by Tuckerman et al. in "(Tuckerman)"_#Tuckerman.
|
to the temperature or kinetic energy from the electron radial velocity.
|
||||||
|
|
||||||
:line
|
IMPORTANT NOTE: there are two different pressures that can be reported
|
||||||
|
for eFF when defining the pair_style (see "pair
|
||||||
|
eff/cut"_pair_eff_cut.html 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).
|
||||||
|
|
||||||
The thermostat for fix styles {nvt} and {npt} is specified using the
|
IMPORTANT NOTE: currently, there is no available option for the user
|
||||||
{temp} keyword. Other thermostat-related keywords are {tchain},
|
to set or create temperature distributions that include the radial
|
||||||
{tloop} and {drag}, which are discussed below.
|
electronic degrees of freedom with the "velocity"_velocity.html
|
||||||
|
command, so the the user must allow for these degrees of freedom to
|
||||||
The thermostat is applied to the translational degrees of freedom
|
equilibrate (i.e. equi-partitioning of energy) through time
|
||||||
for both nuclei and electrons, and for the radial electronic degrees of freedom. The translational degrees of freedom can also have
|
integration.
|
||||||
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 {Tstart} to {Tstop}. The {Tdamp}
|
|
||||||
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 "units"_units.html 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.
|
|
||||||
|
|
||||||
:line
|
|
||||||
|
|
||||||
The barostat for fix styles {npt/eff} and {nph/eff} is specified using one or
|
|
||||||
more of the {iso}, {aniso}, {tri}, {x}, {y}, {z}, {xy}, {xz}, {yz},
|
|
||||||
and {couple} 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.
|
|
||||||
|
|
||||||
Other barostat-related keywords are {pchain}, {mtk}, {ploop},
|
|
||||||
{nreset}, {drag}, and {dilate}, which are discussed below.
|
|
||||||
|
|
||||||
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 "create_box"_create_box.html, "read
|
|
||||||
data"_read_data.html, and "read_restart"_read_restart.html commands
|
|
||||||
specify whether the simulation box is orthogonal or non-orthogonal
|
|
||||||
(triclinic) and explain the meaning of the xy,xz,yz tilt factors.
|
|
||||||
|
|
||||||
The target pressures for each of the 6 components of the stress tensor
|
|
||||||
can be specified independently via the {x}, {y}, {z}, {xy}, {xz}, {yz}
|
|
||||||
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 {Pstart} to {Pstop}.
|
|
||||||
If a target pressure is specified for a component, then the
|
|
||||||
corresponding box dimension will change during a simulation. For
|
|
||||||
example, if the {y} keyword is used, the y-box length will change. If
|
|
||||||
the {xy} 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 "fix
|
|
||||||
deform/eff"_fix_deform_eff.html command.
|
|
||||||
|
|
||||||
Note that in order to use the {xy}, {xz}, or {yz} keywords, the
|
|
||||||
simulation box must be triclinic, even if its initial tilt factors are
|
|
||||||
0.0.
|
|
||||||
|
|
||||||
For all barostat keywords, the {Pdamp} parameter operates like the
|
|
||||||
{Tdamp} 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 "units"_units.html command), considering the default timestep is 0.001.
|
|
||||||
|
|
||||||
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 {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: there are two different pressures that can be reported for eFF when defining the pair_style (see "pair eff/cut"_pair_eff_cut.html 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).
|
|
||||||
|
|
||||||
:line
|
|
||||||
|
|
||||||
The {couple} 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, {xz}
|
|
||||||
means the {Pxx} and {Pzz} components of the stress tensor are coupled.
|
|
||||||
{Xyz} 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
|
|
||||||
{Pstart}, {Pstop}, {Pdamp} parameters for any coupled dimensions must
|
|
||||||
be identical. {Couple xyz} can be used for a 2d simulation; the {z}
|
|
||||||
dimension is simply ignored.
|
|
||||||
|
|
||||||
:line
|
|
||||||
|
|
||||||
The {iso}, {aniso}, and {tri} keywords are simply shortcuts that are
|
|
||||||
equivalent to specifying several other keywords together.
|
|
||||||
|
|
||||||
The keyword {iso} 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:
|
|
||||||
|
|
||||||
x Pstart Pstop Pdamp
|
|
||||||
y Pstart Pstop Pdamp
|
|
||||||
z Pstart Pstop Pdamp
|
|
||||||
couple xyz :pre
|
|
||||||
|
|
||||||
The keyword {aniso} means {x}, {y}, and {z} dimensions are controlled
|
|
||||||
independently using the {Pxx}, {Pyy}, and {Pzz} 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:
|
|
||||||
|
|
||||||
x Pstart Pstop Pdamp
|
|
||||||
y Pstart Pstop Pdamp
|
|
||||||
z Pstart Pstop Pdamp
|
|
||||||
couple none :pre
|
|
||||||
|
|
||||||
The keyword {tri} means {x}, {y}, {z}, {xy}, {xz}, and {yz} 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:
|
|
||||||
|
|
||||||
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
|
|
||||||
|
|
||||||
:line
|
|
||||||
|
|
||||||
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. 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.
|
|
||||||
|
|
||||||
An alternative way to control initial oscillations is to use chain
|
|
||||||
thermostats. The keyword {tchain} determines the number of thermostats
|
|
||||||
in the particle thermostat. A value of 1 corresponds to the original
|
|
||||||
Nose-Hoover thermostat. The keyword {pchain} 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.
|
|
||||||
|
|
||||||
The {mtk} keyword controls whether or not the correction terms due to
|
|
||||||
Martyna, Tuckerman, and Klein are included in the equations of motion
|
|
||||||
"(Martyna)"_#Martyna. Specifying {no} 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 {yes} is more correct, but in many cases the difference is
|
|
||||||
negligible.
|
|
||||||
|
|
||||||
The keyword {tloop} 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 {tloop} substeps, each of
|
|
||||||
length {dt}/{tloop}. This corresponds to using a first-order
|
|
||||||
Suzuki-Yoshida scheme "(Tuckerman2006)"_#Tuckerman2006. The keyword
|
|
||||||
{ploop} does the same thing for the barostat thermostat.
|
|
||||||
|
|
||||||
The keyword {nreset} 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 {nstep}
|
|
||||||
means that every {nstep} timesteps, the reference dimensions are set
|
|
||||||
to those of the current simulation domain.
|
|
||||||
|
|
||||||
:line
|
|
||||||
|
|
||||||
IMPORTANT NOTE: Using a barostat coupled to tilt dimensions {xy},
|
|
||||||
{xz}, {yz} 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 {tri} on a liquid system, specifying an external shear
|
|
||||||
stress tensor that exceeds the yield stress of the solid, and
|
|
||||||
specifying values of {Pstart} 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.
|
|
||||||
|
|
||||||
IMPORTANT NOTE: Unlike the "fix
|
|
||||||
temp/berendsen"_fix_temp_berendsen.html 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 "fix nve/eff"_fix_nve_eff.html on
|
|
||||||
atoms to which this fix is applied. Likewise, the {temp} 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 "fix
|
|
||||||
langevin/eff"_fix_nh.html or "fix temp/rescale"_fix_temp_rescale.html
|
|
||||||
commands.
|
|
||||||
|
|
||||||
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 "velocity"_velocity.html command, so the the user must allow for these to equilibrate (i.e. evolve thermal partitioning) through integration.
|
|
||||||
|
|
||||||
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
|
|
||||||
|
|
||||||
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:
|
|
||||||
|
|
||||||
compute fix-ID_temp group-ID temp/eff
|
|
||||||
compute fix-ID_press group-ID pressure fix-ID_temp :pre
|
|
||||||
|
|
||||||
compute fix-ID_temp all temp/eff
|
|
||||||
compute fix-ID_press all pressure fix-ID_temp :pre
|
|
||||||
|
|
||||||
See the "compute temp/eff"_compute_temp_eff.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". 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.
|
|
||||||
|
|
||||||
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, fix nvt/eff and fix npt/eff 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:]
|
[Restart, fix_modify, output, run start/stop, minimize info:]
|
||||||
|
|
||||||
These fixes writes the state of all the thermostat and barostat
|
See the doc page for the "fix nvt, npt, and nph"_fix_nh.html commands
|
||||||
variables to "binary restart files"_restart.html. See the
|
for details.
|
||||||
"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 these fixes. 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:
|
|
||||||
|
|
||||||
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/eff), 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 these
|
|
||||||
fixes 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.
|
|
||||||
|
|
||||||
These fixes compute a global scalar and a global vector of quantities,
|
|
||||||
which can be accessed by various "output
|
|
||||||
commands"_Section_howto.html#4_15. The scalar values calculated by
|
|
||||||
this fix are "extensive"; the vector values are "intensive".
|
|
||||||
|
|
||||||
The scalar is the cumulative energy change due to the fix.
|
|
||||||
|
|
||||||
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 {tchain} and {pchain},
|
|
||||||
which specify the number of Nose/Hoover chains for the thermostat and
|
|
||||||
barostat. If no thermostatting is done, then {tchain} is 0. If no
|
|
||||||
barostatting is done, then {pchain} 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 {couple xyz} is used or {couple xy} for a 2d
|
|
||||||
simulation, otherwise its value is 3.
|
|
||||||
|
|
||||||
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:
|
|
||||||
|
|
||||||
eta\[tchain\] = particle thermostat displacements
|
|
||||||
eta_dot\[tchain\] = particle thermostat velocities
|
|
||||||
omega\[ndof\] = barostat displacements
|
|
||||||
omega_dot\[ndof\] = barostat velocities
|
|
||||||
etap\[pchain\] = barostat thermostat displacements
|
|
||||||
etap_dot\[pchain\] = barostat thermostat velocities
|
|
||||||
PE_eta\[tchain\] = potential energy of each particle thermostat displacement
|
|
||||||
KE_eta_dot\[tchain\] = kinetic energy of each particle thermostat velocity
|
|
||||||
PE_omega\[ndof\] = potential energy of each barostat displacement
|
|
||||||
KE_omega_dot\[ndof\] = kinetic energy of each barostat velocity
|
|
||||||
PE_etap\[pchain\] = potential energy of each barostat thermostat displacement
|
|
||||||
KE_etap_dot\[pchain\] = kinetic energy of each barostat thermostat velocity
|
|
||||||
PE_strain\[1\] = scalar strain energy :ul
|
|
||||||
|
|
||||||
These fixes can ramp their external 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.
|
|
||||||
|
|
||||||
These fixes are not invoked during "energy
|
|
||||||
minimization"_minimize.html.
|
|
||||||
|
|
||||||
These fixes can be used with either the {verlet} or {respa}
|
|
||||||
"integrators"_run_style.html. When using one of the barostat fixes
|
|
||||||
with {respa}, LAMMPS uses an integrator constructed
|
|
||||||
according to the following factorization of the Liouville propagator
|
|
||||||
(for two rRESPA levels):
|
|
||||||
|
|
||||||
:c,image(Eqs/fix_nh1.jpg)
|
|
||||||
|
|
||||||
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.
|
|
||||||
|
|
||||||
IMPORTANT NOTE: using the {respa} integrator may be useful for the simulations that sample the electronic motions at a faster pace than the nuclear motions.
|
|
||||||
|
|
||||||
[Restrictions:]
|
[Restrictions:]
|
||||||
|
|
||||||
|
|
@ -431,24 +106,22 @@ This fix is part of the "user-eff" package. It is only enabled if
|
||||||
LAMMPS was built with that package. See the "Making
|
LAMMPS was built with that package. See the "Making
|
||||||
LAMMPS"_Section_start.html#2_3 section for more info.
|
LAMMPS"_Section_start.html#2_3 section for more info.
|
||||||
|
|
||||||
Non-periodic dimensions cannot be barostatted. {Z}, {xz}, and {yz},
|
Other restriction discussed on the doc page for the "fix nvt, npt, and
|
||||||
cannot be barostatted 2D simulations. {Xy}, {xz}, and {yz} can only
|
nph"_fix_nh.html commands also apply.
|
||||||
be barostatted if the simulation domain is triclinic and the 2nd
|
|
||||||
dimension in the keyword ({y} dimension in {xy}) is periodic. The
|
|
||||||
"create_box"_create_box.html, "read data"_read_data.html, and
|
|
||||||
"read_restart"_read_restart.html commands specify whether the
|
|
||||||
simulation box is orthogonal or non-orthogonal (triclinic) and explain
|
|
||||||
the meaning of the xy,xz,yz tilt factors.
|
|
||||||
|
|
||||||
For the {temp} keyword, the final Tstop cannot be 0.0 since it would
|
IMPORTANT NOTE: The temperature for systems (regions or groups) with
|
||||||
make the external T = 0.0 at some timestep during the simulation which
|
only electrons and no nuclei is 0.0 (i.e. not defined) in the current
|
||||||
is not allowed in the Nose/Hoover formulation.
|
temperature calculations, a practical example would be a uniform
|
||||||
|
electron gas or a very hot plasma, where electrons remain delocalized
|
||||||
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.
|
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.
|
||||||
|
|
||||||
[Related commands:]
|
[Related commands:]
|
||||||
|
|
||||||
"fix nve/eff"_fix_nve_eff.html, "fix_modify"_fix_modify.html, "run_style"_run_style.html
|
"fix nvt"_fix_nh.html, "fix nph"_fix_nh.html, "fix npt"_fix_nh.html,
|
||||||
|
"fix_modify"_fix_modify.html, "run_style"_run_style.html
|
||||||
|
|
||||||
[Default:]
|
[Default:]
|
||||||
|
|
||||||
|
|
|
||||||
|
|
@ -25,9 +25,13 @@
|
||||||
<P><B>Description:</B>
|
<P><B>Description:</B>
|
||||||
</P>
|
</P>
|
||||||
<P>Perform constant NVE integration to update position and velocity for
|
<P>Perform constant NVE integration to update position and velocity for
|
||||||
atoms in the group each timestep, including the translational and radial electron motions. V is volume; E is energy. This
|
nuclei and electrons in the group for the <A HREF = "pair_eff.html">electron force
|
||||||
creates a system trajectory consistent with the microcanonical
|
field</A> model. V is volume; E is energy. This creates a
|
||||||
ensemble.
|
system trajectory consistent with the microcanonical ensemble.
|
||||||
|
</P>
|
||||||
|
<P>The operation of this fix is exactly like that described by the <A HREF = "fix_nve.html">fix
|
||||||
|
nve</A> command, except that the radius and radial velocity
|
||||||
|
of electrons are also updated.
|
||||||
</P>
|
</P>
|
||||||
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
|
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
|
||||||
</P>
|
</P>
|
||||||
|
|
@ -47,7 +51,8 @@ LAMMPS</A> section for more info.
|
||||||
</P>
|
</P>
|
||||||
<P><B>Related commands:</B>
|
<P><B>Related commands:</B>
|
||||||
</P>
|
</P>
|
||||||
<P><A HREF = "fix_nh.html">fix nvt/eff</A>, <A HREF = "fix_nh.html">fix npt/eff</A>
|
<P><A HREF = "fix_nve.html">fix nve</A>, <A HREF = "fix_nh_eff.html">fix nvt/eff</A>, <A HREF = "fix_nh_eff.html">fix
|
||||||
|
npt/eff</A>
|
||||||
</P>
|
</P>
|
||||||
<P><B>Default:</B> none
|
<P><B>Default:</B> none
|
||||||
</P>
|
</P>
|
||||||
|
|
|
||||||
|
|
@ -22,9 +22,13 @@ fix 1 all nve/eff :pre
|
||||||
[Description:]
|
[Description:]
|
||||||
|
|
||||||
Perform constant NVE integration to update position and velocity for
|
Perform constant NVE integration to update position and velocity for
|
||||||
atoms in the group each timestep, including the translational and radial electron motions. V is volume; E is energy. This
|
nuclei and electrons in the group for the "electron force
|
||||||
creates a system trajectory consistent with the microcanonical
|
field"_pair_eff.html model. V is volume; E is energy. This creates a
|
||||||
ensemble.
|
system trajectory consistent with the microcanonical ensemble.
|
||||||
|
|
||||||
|
The operation of this fix is exactly like that described by the "fix
|
||||||
|
nve"_fix_nve.html command, except that the radius and radial velocity
|
||||||
|
of electrons are also updated.
|
||||||
|
|
||||||
[Restart, fix_modify, output, run start/stop, minimize info:]
|
[Restart, fix_modify, output, run start/stop, minimize info:]
|
||||||
|
|
||||||
|
|
@ -44,6 +48,7 @@ LAMMPS"_Section_start.html#2_3 section for more info.
|
||||||
|
|
||||||
[Related commands:]
|
[Related commands:]
|
||||||
|
|
||||||
"fix nvt/eff"_fix_nh.html, "fix npt/eff"_fix_nh.html
|
"fix nve"_fix_nve.html, "fix nvt/eff"_fix_nh_eff.html, "fix
|
||||||
|
npt/eff"_fix_nh_eff.html
|
||||||
|
|
||||||
[Default:] none
|
[Default:] none
|
||||||
|
|
|
||||||
|
|
@ -27,77 +27,20 @@ fix 1 all nvt/sllod/eff temp 300.0 300.0 0.1 drag 0.2
|
||||||
<P><B>Description:</B>
|
<P><B>Description:</B>
|
||||||
</P>
|
</P>
|
||||||
<P>Perform constant NVT integration to update positions and velocities
|
<P>Perform constant NVT integration to update positions and velocities
|
||||||
each timestep for atoms in the group using a Nose/Hoover temperature
|
each timestep for nuclei and electrons in the group for the <A HREF = "pair_eff.html">electron
|
||||||
thermostat. In eFF, this will include the radius and radial velocity of the electrons.
|
force field</A> model, using a Nose/Hoover temperature
|
||||||
V is volume; T is temperature. This creates a system
|
thermostat. V is volume; T is temperature. This creates a system
|
||||||
trajectory consistent with the canonical ensemble.
|
trajectory consistent with the canonical ensemble.
|
||||||
</P>
|
</P>
|
||||||
<P>This thermostat is used for a simulation box that is changing size
|
<P>The operation of this fix is exactly like that described by the <A HREF = "fix_nvt_sllod.html">fix
|
||||||
and/or shape, for example in a non-equilibrium MD (NEMD) simulation.
|
nvt/sllod</A> command, except that the radius and
|
||||||
The size/shape change is induced by use of the <A HREF = "fix_deform.html">fix
|
radial velocity of electrons are also updated and thermostatted.
|
||||||
deform</A> command, so each point in the simulation box
|
Likewise the temperature calculated by the fix, using the compute it
|
||||||
can be thought of as having a "streaming" velocity. The streaming velocity will only affect the translational degrees of freedom in eFF. This position-dependent streaming velocity is subtracted from each atom's
|
creates (as discussed in the <A HREF = "fix_nh.html">fix nvt, npt, and nph</A> doc
|
||||||
actual velocity to yield a thermal velocity which is used for
|
page), is performed with a <A HREF = "compute_temp_deform_eff.html">compute
|
||||||
temperature computation and thermostatting. The thermal velocity is computed over all degrees of freedom, including the electronic ones. For example, if the box
|
temp/deform/eff</A> commmand that includes
|
||||||
is being sheared in x, relative to y, then points at the bottom of the
|
the eFF contribution to the temperature from the electron radial
|
||||||
box (low y) have a small x velocity, while points at the top of the
|
velocity.
|
||||||
box (hi y) have a large x velocity. These velocities do not
|
|
||||||
contribute to the thermal "temperature" of the atom, hence the use of this command.
|
|
||||||
</P>
|
|
||||||
<P>IMPORTANT NOTE: <A HREF = "fix_deform.html">Fix deform</A> has an option for
|
|
||||||
remapping either atom coordinates or velocities to the changing
|
|
||||||
simulation box. To use fix nvt/sllod, fix deform should NOT remap
|
|
||||||
atom positions, because fix nvt/sllod adjusts the atom positions and
|
|
||||||
velocities to create a velocity profile that matches the changing box
|
|
||||||
size/shape. Fix deform SHOULD remap atom velocities when atoms cross
|
|
||||||
periodic boundaries since that is consistent with maintaining the
|
|
||||||
velocity profile created by fix nvt/sllod. LAMMPS will give an
|
|
||||||
error if this setting is not consistent.
|
|
||||||
</P>
|
|
||||||
<P>The SLLOD equations of motion coupled to a Nose/Hoover thermostat are
|
|
||||||
discussed in <A HREF = "#Tuckerman">(Tuckerman)</A> (eqs 4 and 5), which is what is
|
|
||||||
implemented in LAMMPS in a velocity Verlet formulation.
|
|
||||||
</P>
|
|
||||||
<P>Additional parameters affecting the thermostat are specified by
|
|
||||||
keywords and values documented with the <A HREF = "fix_nh_eff.html">fix nvt/eff</A>
|
|
||||||
command. See, for example, discussion of the <I>temp</I> and <I>drag</I>
|
|
||||||
keywords.
|
|
||||||
</P>
|
|
||||||
<P>This fix computes a temperature each timestep. To do this, the fix
|
|
||||||
creates its own compute of style "temp/deform/eff", as if this command had
|
|
||||||
been issued:
|
|
||||||
</P>
|
|
||||||
<PRE>compute fix-ID_temp group-ID temp/deform/eff
|
|
||||||
</PRE>
|
|
||||||
<P>See the <A HREF = "compute_temp_deform_eff.html">compute temp/deform/eff</A> command for
|
|
||||||
details. Note that the ID of the new compute is the fix-ID +
|
|
||||||
underscore + "temp", and the group for the new compute is the same as
|
|
||||||
the fix group.
|
|
||||||
</P>
|
|
||||||
<P>Note that this is NOT the compute used by thermodynamic output (see
|
|
||||||
the <A HREF = "thermo_style.html">thermo_style</A> command) with ID = <I>thermo_temp</I>.
|
|
||||||
This means you can change the attributes of this fix's temperature
|
|
||||||
(e.g. its degrees-of-freedom) via the
|
|
||||||
<A HREF = "compute_modify.html">compute_modify</A> command or print this temperature
|
|
||||||
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> 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>
|
||||||
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
|
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
|
||||||
</P>
|
</P>
|
||||||
|
|
@ -132,15 +75,20 @@ quantities as does the <A HREF = "fix_nh_eff.html">fix nvt/eff</A> command.
|
||||||
LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
|
LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
|
||||||
LAMMPS</A> section for more info.
|
LAMMPS</A> section for more info.
|
||||||
</P>
|
</P>
|
||||||
<P>This fix works best without Nose-Hoover chain thermostats i.e. using tchain = 1.
|
<P>This fix works best without Nose-Hoover chain thermostats, i.e. using
|
||||||
Setting tchain to larger values can result in poor equilibration.
|
tchain = 1. Setting tchain to larger values can result in poor
|
||||||
|
equilibration.
|
||||||
</P>
|
</P>
|
||||||
<P><B>Related commands:</B>
|
<P><B>Related commands:</B>
|
||||||
</P>
|
</P>
|
||||||
<P><A HREF = "fix_nve_eff.html">fix nve/eff</A>, <A HREF = "fix_nh_eff.html">fix nvt/eff</A>, <A HREF = "fix_langevin_eff.html">fix langevin/eff</A>,
|
<P><A HREF = "fix_nve_eff.html">fix nve/eff</A>, <A HREF = "fix_nh_eff.html">fix nvt/eff</A>, <A HREF = "fix_langevin_eff.html">fix
|
||||||
<A HREF = "fix_modify.html">fix_modify</A>, <A HREF = "compute_temp_deform_eff.html">compute temp/deform/eff</A>
|
langevin/eff</A>, <A HREF = "fix_nvt_sllod.html">fix
|
||||||
|
nvt/sllod</A>, <A HREF = "fix_modify.html">fix_modify</A>, <A HREF = "compute_temp_deform_eff.html">compute
|
||||||
|
temp/deform/eff</A>
|
||||||
</P>
|
</P>
|
||||||
<P><B>Default:</B> Same as <A HREF = "fix_nh_eff.html">fix nvt/eff</A>, except tchain = 1.
|
<P><B>Default:</B>
|
||||||
|
</P>
|
||||||
|
<P>Same as <A HREF = "fix_nh_eff.html">fix nvt/eff</A>, except tchain = 1.
|
||||||
</P>
|
</P>
|
||||||
<HR>
|
<HR>
|
||||||
|
|
||||||
|
|
|
||||||
|
|
@ -24,77 +24,20 @@ fix 1 all nvt/sllod/eff temp 300.0 300.0 0.1 drag 0.2 :pre
|
||||||
[Description:]
|
[Description:]
|
||||||
|
|
||||||
Perform constant NVT integration to update positions and velocities
|
Perform constant NVT integration to update positions and velocities
|
||||||
each timestep for atoms in the group using a Nose/Hoover temperature
|
each timestep for nuclei and electrons in the group for the "electron
|
||||||
thermostat. In eFF, this will include the radius and radial velocity of the electrons.
|
force field"_pair_eff.html model, using a Nose/Hoover temperature
|
||||||
V is volume; T is temperature. This creates a system
|
thermostat. V is volume; T is temperature. This creates a system
|
||||||
trajectory consistent with the canonical ensemble.
|
trajectory consistent with the canonical ensemble.
|
||||||
|
|
||||||
This thermostat is used for a simulation box that is changing size
|
The operation of this fix is exactly like that described by the "fix
|
||||||
and/or shape, for example in a non-equilibrium MD (NEMD) simulation.
|
nvt/sllod"_fix_nvt_sllod.html command, except that the radius and
|
||||||
The size/shape change is induced by use of the "fix
|
radial velocity of electrons are also updated and thermostatted.
|
||||||
deform"_fix_deform.html command, so each point in the simulation box
|
Likewise the temperature calculated by the fix, using the compute it
|
||||||
can be thought of as having a "streaming" velocity. The streaming velocity will only affect the translational degrees of freedom in eFF. This position-dependent streaming velocity is subtracted from each atom's
|
creates (as discussed in the "fix nvt, npt, and nph"_fix_nh.html doc
|
||||||
actual velocity to yield a thermal velocity which is used for
|
page), is performed with a "compute
|
||||||
temperature computation and thermostatting. The thermal velocity is computed over all degrees of freedom, including the electronic ones. For example, if the box
|
temp/deform/eff"_compute_temp_deform_eff.html commmand that includes
|
||||||
is being sheared in x, relative to y, then points at the bottom of the
|
the eFF contribution to the temperature from the electron radial
|
||||||
box (low y) have a small x velocity, while points at the top of the
|
velocity.
|
||||||
box (hi y) have a large x velocity. These velocities do not
|
|
||||||
contribute to the thermal "temperature" of the atom, hence the use of this command.
|
|
||||||
|
|
||||||
IMPORTANT NOTE: "Fix deform"_fix_deform.html has an option for
|
|
||||||
remapping either atom coordinates or velocities to the changing
|
|
||||||
simulation box. To use fix nvt/sllod, fix deform should NOT remap
|
|
||||||
atom positions, because fix nvt/sllod adjusts the atom positions and
|
|
||||||
velocities to create a velocity profile that matches the changing box
|
|
||||||
size/shape. Fix deform SHOULD remap atom velocities when atoms cross
|
|
||||||
periodic boundaries since that is consistent with maintaining the
|
|
||||||
velocity profile created by fix nvt/sllod. LAMMPS will give an
|
|
||||||
error if this setting is not consistent.
|
|
||||||
|
|
||||||
The SLLOD equations of motion coupled to a Nose/Hoover thermostat are
|
|
||||||
discussed in "(Tuckerman)"_#Tuckerman (eqs 4 and 5), which is what is
|
|
||||||
implemented in LAMMPS in a velocity Verlet formulation.
|
|
||||||
|
|
||||||
Additional parameters affecting the thermostat are specified by
|
|
||||||
keywords and values documented with the "fix nvt/eff"_fix_nh_eff.html
|
|
||||||
command. See, for example, discussion of the {temp} and {drag}
|
|
||||||
keywords.
|
|
||||||
|
|
||||||
This fix computes a temperature each timestep. To do this, the fix
|
|
||||||
creates its own compute of style "temp/deform/eff", as if this command had
|
|
||||||
been issued:
|
|
||||||
|
|
||||||
compute fix-ID_temp group-ID temp/deform/eff :pre
|
|
||||||
|
|
||||||
See the "compute temp/deform/eff"_compute_temp_deform_eff.html command for
|
|
||||||
details. Note that the ID of the new compute is the fix-ID +
|
|
||||||
underscore + "temp", and the group for the new compute is the same as
|
|
||||||
the fix group.
|
|
||||||
|
|
||||||
Note that this is NOT the compute used by thermodynamic output (see
|
|
||||||
the "thermo_style"_thermo_style.html command) with ID = {thermo_temp}.
|
|
||||||
This means you can change the attributes of this fix's temperature
|
|
||||||
(e.g. its degrees-of-freedom) via the
|
|
||||||
"compute_modify"_compute_modify.html command or print this temperature
|
|
||||||
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} 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:]
|
[Restart, fix_modify, output, run start/stop, minimize info:]
|
||||||
|
|
||||||
|
|
@ -129,15 +72,20 @@ This fix is part of the "user-eff" package. It is only enabled if
|
||||||
LAMMPS was built with that package. See the "Making
|
LAMMPS was built with that package. See the "Making
|
||||||
LAMMPS"_Section_start.html#2_3 section for more info.
|
LAMMPS"_Section_start.html#2_3 section for more info.
|
||||||
|
|
||||||
This fix works best without Nose-Hoover chain thermostats i.e. using tchain = 1.
|
This fix works best without Nose-Hoover chain thermostats, i.e. using
|
||||||
Setting tchain to larger values can result in poor equilibration.
|
tchain = 1. Setting tchain to larger values can result in poor
|
||||||
|
equilibration.
|
||||||
|
|
||||||
[Related commands:]
|
[Related commands:]
|
||||||
|
|
||||||
"fix nve/eff"_fix_nve_eff.html, "fix nvt/eff"_fix_nh_eff.html, "fix langevin/eff"_fix_langevin_eff.html,
|
"fix nve/eff"_fix_nve_eff.html, "fix nvt/eff"_fix_nh_eff.html, "fix
|
||||||
"fix_modify"_fix_modify.html, "compute temp/deform/eff"_compute_temp_deform_eff.html
|
langevin/eff"_fix_langevin_eff.html, "fix
|
||||||
|
nvt/sllod"_fix_nvt_sllod.html, "fix_modify"_fix_modify.html, "compute
|
||||||
|
temp/deform/eff"_compute_temp_deform_eff.html
|
||||||
|
|
||||||
[Default:] Same as "fix nvt/eff"_fix_nh_eff.html, except tchain = 1.
|
[Default:]
|
||||||
|
|
||||||
|
Same as "fix nvt/eff"_fix_nh_eff.html, except tchain = 1.
|
||||||
|
|
||||||
:line
|
:line
|
||||||
|
|
||||||
|
|
|
||||||
Loading…
Reference in New Issue