forked from lijiext/lammps
486 lines
27 KiB
HTML
486 lines
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<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
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<HR>
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<H3>fix nvt/eff command
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</H3>
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<H3>fix npt/eff command
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</H3>
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<H3>fix nph/eff command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>fix ID group-ID style_name keyword value ...
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</PRE>
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<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
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<LI>style_name = <I>nvt/eff</I> or <I>npt/eff</I> or <I>nph/eff</I>
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<PRE>one or more keyword value pairs may be appended
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keyword = <I>temp</I> or <I>iso</I> or <I>aniso</I> or <I>tri</I> or <I>x</I> or <I>y</I> or <I>z</I> or <I>xy</I> or <I>yz</I> or <I>xz</I> or <I>couple</I> or <I>tchain</I> or <I>pchain</I> or <I>mtk</I> or <I>tloop</I> or <I>ploop</I> or <I>nreset</I> or <I>drag</I> or <I>dilate</I>
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<I>temp</I> values = Tstart Tstop Tdamp
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Tstart,Tstop = external temperature at start/end of run
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Tdamp = temperature damping parameter (time units)
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<I>iso</I> or <I>aniso</I> or <I>tri</I> values = Pstart Pstop Pdamp
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Pstart,Pstop = scalar external pressure at start/end of run (pressure units)
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Pdamp = pressure damping parameter (time units)
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<I>x</I> or <I>y</I> or <I>z</I> or <I>xy</I> or <I>yz</I> or <I>xz</I> values = Pstart Pstop Pdamp
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Pstart,Pstop = external stress tensor component at start/end of run (pressure units)
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Pdamp = stress damping parameter (time units)
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<I>couple</I> = <I>none</I> or <I>xyz</I> or <I>xy</I> or <I>yz</I> or <I>xz</I>
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<I>tchain</I> value = length of thermostat chain (1 = single thermostat)
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<I>pchain</I> values = length of thermostat chain on barostat (0 = no thermostat)
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<I>mtk</I> value = <I>yes</I> or <I>no</I> = add in MTK adjustment term or not
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<I>tloop</I> value = number of sub-cycles to perform on thermostat
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<I>ploop</I> value = number of sub-cycles to perform on barostat thermostat
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<I>nreset</I> value = reset reference cell every this many timesteps
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<I>drag</I> value = drag factor added to barostat/thermostat (0.0 = no drag)
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<I>dilate</I> value = <I>all</I> or <I>partial</I>
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</PRE>
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>fix 1 all nvt/eff temp 300.0 300.0 0.1
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fix 1 part npt/eff temp 300.0 300.0 0.1 iso 0.0 0.0 1.0
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fix 2 part npt/eff temp 300.0 300.0 0.1 tri 5.0 5.0 1.0
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fix 2 ice nph/eff x 1.0 1.0 0.5 y 2.0 2.0 0.5 z 3.0 3.0 0.5 yz 0.1 0.1 0.5 xz 0.2 0.2 0.5 xy 0.3 0.3 0.5 nreset 1000
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>These commands perform time integration on Nose-Hoover style
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non-Hamiltonian equations of motion which are designed to generate
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positions and velocities sampled from the canonical (nvt),
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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
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achieved by adding some dynamic variables which are coupled to the
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particle velocities (thermostatting) and simulation domain dimensions
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(barostatting). In addition to basic thermostatting and barostatting,
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these fixes can also create a chain of thermostats coupled to the
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particle thermostat, and another chain of thermostats coupled to the
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barostat variables. The barostat can be coupled to the overall box
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volume, or to individual dimensions, including the <I>xy</I>, <I>xz</I> and <I>yz</I>
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tilt dimensions. The external pressure of the barostat can be
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specified as either a scalar pressure (isobaric ensemble) or as
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components of a symmetric stress tensor (constant stress ensemble).
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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
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of the particles will match the target values specified by
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Tstart/Tstop and Pstart/Pstop.
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</P>
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<P>The equations of motion used are those of Shinoda et al. in
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<A HREF = "#Shinoda">(Shinoda)</A>, which combine the hydrostatic equations of
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Martyna, Tobias and Klein in <A HREF = "#Martyna">(Martyna)</A> with the strain
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energy proposed by Parrinello and Rahman in
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<A HREF = "#Parrinello">(Parrinello)</A>. The time integration schemes closely
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follow the time-reversible measure-preserving Verlet and
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rRESPA integrators derived by Tuckerman et al. in <A HREF = "#Tuckerman">(Tuckerman)</A>.
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</P>
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<HR>
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<P>The thermostat for fix styles <I>nvt</I> and <I>npt</I> is specified using the
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<I>temp</I> keyword. Other thermostat-related keywords are <I>tchain</I>,
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<I>tloop</I> and <I>drag</I>, which are discussed below.
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</P>
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<P>The thermostat is applied to the translational degrees of freedom
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for both nuclei and electrons, and for the radial electronic degrees of freedom. The translational degrees of freedom can also have
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a bias velocity removed before thermostatting takes place; see the
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description below. The desired temperature at each timestep is a
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ramped value during the run from <I>Tstart</I> to <I>Tstop</I>. The <I>Tdamp</I>
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parameter is specified in time units and determines how rapidly the
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temperature is relaxed. For example, using the default eFF (electron) units, a value of 1.0 means to relax
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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
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by the velocity/position update portion of the integration.
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</P>
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<HR>
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<P>The barostat for fix styles <I>npt/eff</I> and <I>nph/eff</I> is specified using one or
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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>,
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and <I>couple</I> keywords. These keywords give you the ability to specify
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all 6 components of an external stress tensor, and to couple various
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of these components together so that the dimensions they represent are
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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.
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</P>
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<P>Other barostat-related keywords are <I>pchain</I>, <I>mtk</I>, <I>ploop</I>,
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<I>nreset</I>, <I>drag</I>, and <I>dilate</I>, which are discussed below.
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</P>
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<P>Orthogonal simulation boxes have 3 adjustable dimensions (x,y,z).
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Triclinic (non-orthogonal) simulation boxes have 6 adjustable
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dimensions (x,y,z,xy,xz,yz). The <A HREF = "create_box.html">create_box</A>, <A HREF = "read_data.html">read
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data</A>, and <A HREF = "read_restart.html">read_restart</A> commands
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specify whether the simulation box is orthogonal or non-orthogonal
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(triclinic) and explain the meaning of the xy,xz,yz tilt factors.
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</P>
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<P>The target pressures for each of the 6 components of the stress tensor
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can be specified independently via the <I>x</I>, <I>y</I>, <I>z</I>, <I>xy</I>, <I>xz</I>, <I>yz</I>
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keywords, which correspond to the 6 simulation box dimensions. For
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each component, the external pressure or tensor component at each
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timestep is a ramped value during the run from <I>Pstart</I> to <I>Pstop</I>.
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If a target pressure is specified for a component, then the
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corresponding box dimension will change during a simulation. For
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example, if the <I>y</I> keyword is used, the y-box length will change. If
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the <I>xy</I> keyword is used, the xy tilt factor will change. A box
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dimension will not change if that component is not specified, although
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you have the option to change that dimension via the <A HREF = "fix_deform_eff.html">fix
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deform/eff</A> command.
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</P>
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<P>Note that in order to use the <I>xy</I>, <I>xz</I>, or <I>yz</I> keywords, the
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simulation box must be triclinic, even if its initial tilt factors are
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0.0.
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</P>
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<P>For all barostat keywords, the <I>Pdamp</I> parameter operates like the
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<I>Tdamp</I> parameter, determining the time scale on which pressure is
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relaxed. For example, a value of 1.0 means to relax the pressure
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in a timespan of (roughly) 1000 timesteps for the eFF default time unit (fmsec - see
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the <A HREF = "units.html">units</A> command), considering the default timestep is 0.001.
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</P>
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<P>Regardless of what atoms are in the fix group, a global pressure or
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stress tensor is computed for all atoms. Similarly, when the size of
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the simulation box is changed, all atoms are re-scaled to new
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positions, unless the keyword <I>dilate</I> is specified with a value of
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<I>partial</I>, in which case only the atoms in the fix group are
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re-scaled. The latter can be useful for leaving the coordinates of
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atoms in a solid substrate unchanged and controlling the pressure of a
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surrounding fluid.
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</P>
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<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).
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</P>
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<HR>
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<P>The <I>couple</I> keyword allows two or three of the diagonal components of
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the pressure tensor to be "coupled" together. The value specified
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with the keyword determines which are coupled. For example, <I>xz</I>
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means the <I>Pxx</I> and <I>Pzz</I> components of the stress tensor are coupled.
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<I>Xyz</I> means all 3 diagonal components are coupled. Coupling means two
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things: the instantaneous stress will be computed as an average of the
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corresponding diagonal components, and the coupled box dimensions will
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be changed together in lockstep, meaning coupled dimensions will be
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dilated or contracted by the same percentage every timestep. The
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<I>Pstart</I>, <I>Pstop</I>, <I>Pdamp</I> parameters for any coupled dimensions must
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be identical. <I>Couple xyz</I> can be used for a 2d simulation; the <I>z</I>
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dimension is simply ignored.
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</P>
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<HR>
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<P>The <I>iso</I>, <I>aniso</I>, and <I>tri</I> keywords are simply shortcuts that are
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equivalent to specifying several other keywords together.
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</P>
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<P>The keyword <I>iso</I> means couple all 3 diagonal components together when
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pressure is computed (hydrostatic pressure), and dilate/contract the
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dimensions together. Using "iso Pstart Pstop Pdamp" is the same as
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specifying these 4 keywords:
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</P>
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<PRE>x Pstart Pstop Pdamp
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y Pstart Pstop Pdamp
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z Pstart Pstop Pdamp
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couple xyz
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</PRE>
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<P>The keyword <I>aniso</I> means <I>x</I>, <I>y</I>, and <I>z</I> dimensions are controlled
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independently using the <I>Pxx</I>, <I>Pyy</I>, and <I>Pzz</I> components of the
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stress tensor as the driving forces, and the specified scalar external
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pressure. Using "aniso Pstart Pstop Pdamp" is the same as specifying
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these 4 keywords:
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</P>
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<PRE>x Pstart Pstop Pdamp
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y Pstart Pstop Pdamp
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z Pstart Pstop Pdamp
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couple none
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</PRE>
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<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
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are controlled independently using their individual stress components
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as the driving forces, and the specified scalar pressure as the
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external normal stress. Using "tri Pstart Pstop Pdamp" is the same as
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specifying these 7 keywords:
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</P>
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<PRE>x Pstart Pstop Pdamp
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y Pstart Pstop Pdamp
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z Pstart Pstop Pdamp
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xy 0.0 0.0 Pdamp
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yz 0.0 0.0 Pdamp
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xz 0.0 0.0 Pdamp
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couple none
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</PRE>
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<HR>
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<P>In some cases (e.g. for solids) the pressure (volume) and/or
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temperature of the system can oscillate undesirably when a Nose/Hoover
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barostat and thermostat is applied. The optional <I>drag</I> keyword will
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damp these oscillations, although it alters the Nose/Hoover equations.
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A value of 0.0 (no drag) leaves the Nose/Hoover formalism unchanged.
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A non-zero value adds a drag term; the larger the value specified, the
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greater the damping effect. Performing a short run and monitoring the
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pressure and temperature is the best way to determine if the drag term
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is working. Typically a value between 0.2 to 2.0 is sufficient to
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damp oscillations after a few periods. Note that use of the drag
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keyword will interfere with energy conservation and will also change
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the distribution of positions and velocities so that they do not
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correspond to the nominal NVT, NPT, or NPH ensembles.
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</P>
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<P>An alternative way to control initial oscillations is to use chain
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thermostats. The keyword <I>tchain</I> determines the number of thermostats
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in the particle thermostat. A value of 1 corresponds to the original
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Nose-Hoover thermostat. The keyword <I>pchain</I> specifies the number of
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thermostats in the chain thermostatting the barostat degrees of
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freedom. A value of 0 corresponds to no thermostatting of the
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barostat variables.
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</P>
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<P>The <I>mtk</I> keyword controls whether or not the correction terms due to
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Martyna, Tuckerman, and Klein are included in the equations of motion
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<A HREF = "#Martyna">(Martyna)</A>. Specifying <I>no</I> reproduces the original
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Hoover barostat, whose volume probability distribution function
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differs from the true NPT and NPH ensembles by a factor of 1/V. Hence
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using <I>yes</I> is more correct, but in many cases the difference is
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negligible.
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</P>
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<P>The keyword <I>tloop</I> can be used to improve the accuracy of integration
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scheme at little extra cost. The initial and final updates of the
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thermostat variables are broken up into <I>tloop</I> substeps, each of
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length <I>dt</I>/<I>tloop</I>. This corresponds to using a first-order
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Suzuki-Yoshida scheme <A HREF = "#Tuckerman2006">(Tuckerman2006)</A>. The keyword
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<I>ploop</I> does the same thing for the barostat thermostat.
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</P>
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<P>The keyword <I>nreset</I> controls how often the reference dimensions used
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to define the strain energy are reset. If this keyword is not used,
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or is given a value of zero, then the reference dimensions are set to
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those of the initial simulation domain and are never changed. If the
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simulation domain changes significantly during the simulation, then
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the final average pressure tensor will differ significantly from the
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specified values of the external stress tensor. A value of <I>nstep</I>
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means that every <I>nstep</I> timesteps, the reference dimensions are set
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to those of the current simulation domain.
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</P>
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<HR>
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<P>IMPORTANT NOTE: Using a barostat coupled to tilt dimensions <I>xy</I>,
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<I>xz</I>, <I>yz</I> can sometimes result in arbitrarily large values of the
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tilt dimensions, i.e. a dramatically deformed simulation box. LAMMPS
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imposes reasonable limits on how large the tilt values can be, and
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exits with an error if these are exceeded. This error typically
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indicates that there is something badly wrong with how the simulation
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was constructed. The three most common sources of this error are
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using keyword <I>tri</I> on a liquid system, specifying an external shear
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stress tensor that exceeds the yield stress of the solid, and
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specifying values of <I>Pstart</I> that are too far from the current stress
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value. In other words, triclinic barostatting should be used with
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|
|
care. This also is true for other barostat styles, although they tend
|
||
|
|
to be more forgiving of insults.
|
||
|
|
</P>
|
||
|
|
<P>IMPORTANT NOTE: Unlike the <A HREF = "fix_temp_berendsen.html">fix
|
||
|
|
temp/berendsen</A> command which performs
|
||
|
|
thermostatting but NO time integration, these fixes perform
|
||
|
|
thermostatting/barostatting AND time integration. Thus you should not
|
||
|
|
use any other time integration fix, such as <A HREF = "fix_nve_eff.html">fix nve/eff</A> on
|
||
|
|
atoms to which this fix is applied. Likewise, the <I>temp</I> options for
|
||
|
|
fix nvt/eff and fix npt/eff should not normally be used on atoms that also
|
||
|
|
have their temperature controlled by another fix - e.g. by <A HREF = "fix_nh.html">fix
|
||
|
|
langevin/eff</A> or <A HREF = "fix_temp_rescale.html">fix temp/rescale</A>
|
||
|
|
commands.
|
||
|
|
</P>
|
||
|
|
<P>IMPORTANT NOTE: currently, there is no available option for the user to set or create temperature distributions that include the radial electronic degrees of freedom with the <A HREF = "velocity.html">velocity</A> command, so the the user must allow for these to equilibrate (i.e. evolve thermal partitioning) through integration.
|
||
|
|
</P>
|
||
|
|
<P>See <A HREF = "Section_howto.html#4_16">this howto section</A> of the manual for a
|
||
|
|
discussion of different ways to compute temperature and perform
|
||
|
|
thermostatting and barostatting.
|
||
|
|
</P>
|
||
|
|
<HR>
|
||
|
|
|
||
|
|
<P>These fixes compute a temperature and pressure each timestep. To do
|
||
|
|
this, the fix creates its own computes of style "temp" and "pressure",
|
||
|
|
as if one of these two sets of commands had been issued:
|
||
|
|
</P>
|
||
|
|
<PRE>compute fix-ID_temp group-ID temp/eff
|
||
|
|
compute fix-ID_press group-ID pressure fix-ID_temp
|
||
|
|
</PRE>
|
||
|
|
<PRE>compute fix-ID_temp all temp/eff
|
||
|
|
compute fix-ID_press all pressure fix-ID_temp
|
||
|
|
</PRE>
|
||
|
|
<P>See the <A HREF = "compute_temp_eff.html">compute temp/eff</A> and <A HREF = "compute_pressure.html">compute
|
||
|
|
pressure</A> commands for details. Note that the
|
||
|
|
IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID
|
||
|
|
+ underscore + "press". For fix nvt/eff, the group for the new computes
|
||
|
|
is the same as the fix group. For fix nph/eff and fix npt/eff, the group for
|
||
|
|
the new computes is "all" since pressure is computed for the entire
|
||
|
|
system.
|
||
|
|
</P>
|
||
|
|
<P>Note that these are NOT the computes used by thermodynamic output (see
|
||
|
|
the <A HREF = "thermo_style.html">thermo_style</A> command) with ID = <I>thermo_temp</I>
|
||
|
|
and <I>thermo_press</I>. This means you can change the attributes of this
|
||
|
|
fix's temperature or pressure via the
|
||
|
|
<A HREF = "compute_modify.html">compute_modify</A> command or print this temperature
|
||
|
|
or pressure during thermodynamic output via the <A HREF = "thermo_style.html">thermo_style
|
||
|
|
custom</A> command using the appropriate compute-ID.
|
||
|
|
It also means that changing attributes of <I>thermo_temp</I> or
|
||
|
|
<I>thermo_press</I> will have no effect on this fix.
|
||
|
|
</P>
|
||
|
|
<P>Like other fixes that perform thermostatting, fix nvt/eff and fix npt/eff can
|
||
|
|
be used with <A HREF = "compute.html">compute commands</A> that calculate a
|
||
|
|
temperature after removing a "bias" from the atom velocities.
|
||
|
|
E.g. removing the center-of-mass velocity from a group of atoms or
|
||
|
|
only calculating temperature on the x-component of velocity or only
|
||
|
|
calculating temperature for atoms in a geometric region. This is not
|
||
|
|
done by default, but only if the <A HREF = "fix_modify.html">fix_modify</A> command
|
||
|
|
is used to assign a temperature compute to this fix that includes such
|
||
|
|
a bias term. See the doc pages for individual <A HREF = "compute.html">compute
|
||
|
|
commands</A> to determine which ones include a bias. In
|
||
|
|
this case, the thermostat works in the following manner: the current
|
||
|
|
temperature is calculated taking the bias into account, bias is
|
||
|
|
removed from each atom, thermostatting is performed on the remaining
|
||
|
|
thermal degrees of freedom, and the bias is added back in.
|
||
|
|
</P>
|
||
|
|
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
|
||
|
|
</P>
|
||
|
|
<P>These fixes writes the state of all the thermostat and barostat
|
||
|
|
variables to <A HREF = "restart.html">binary restart files</A>. See the
|
||
|
|
<A HREF = "read_restart.html">read_restart</A> command for info on how to re-specify
|
||
|
|
a fix in an input script that reads a restart file, so that the
|
||
|
|
operation of the fix continues in an uninterrupted fashion.
|
||
|
|
</P>
|
||
|
|
<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>temp</I> and <I>press</I> options are
|
||
|
|
supported by these fixes. You can use them to assign a
|
||
|
|
<A HREF = "compute.html">compute</A> you have defined to this fix which will be used
|
||
|
|
in its thermostatting or barostatting procedure, as described above.
|
||
|
|
If you do this, note that the kinetic energy derived from the compute
|
||
|
|
temperature should be consistent with the virial term computed using
|
||
|
|
all atoms for the pressure. LAMMPS will warn you if you choose to
|
||
|
|
compute temperature on a subset of atoms.
|
||
|
|
</P>
|
||
|
|
<P>IMPORTANT NOTE:
|
||
|
|
</P>
|
||
|
|
<P>IMPORTANT NOTE: If both the <I>temp</I> and <I>press</I> keywords are used in a
|
||
|
|
single thermo_modify command (or in two separate commands), then the
|
||
|
|
order in which the keywords are specified is important. Note that a
|
||
|
|
<A HREF = "compute_pressure.html">pressure compute</A> defines its own temperature
|
||
|
|
compute as an argument when it is specified. The <I>temp</I> keyword will
|
||
|
|
override this (for the pressure compute being used by fix npt/eff), but
|
||
|
|
only if the <I>temp</I> keyword comes after the <I>press</I> keyword. If the
|
||
|
|
<I>temp</I> keyword comes before the <I>press</I> keyword, then the new pressure
|
||
|
|
compute specified by the <I>press</I> keyword will be unaffected by the
|
||
|
|
<I>temp</I> setting.
|
||
|
|
</P>
|
||
|
|
<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by these
|
||
|
|
fixes to add the energy change induced by Nose/Hoover thermostatting
|
||
|
|
and barostatting to the system's potential energy as part of
|
||
|
|
<A HREF = "thermo_style.html">thermodynamic output</A>.
|
||
|
|
</P>
|
||
|
|
<P>These fixes compute a global scalar and a global vector of quantities,
|
||
|
|
which can be accessed by various <A HREF = "Section_howto.html#4_15">output
|
||
|
|
commands</A>. The scalar values calculated by
|
||
|
|
this fix are "extensive"; the vector values are "intensive".
|
||
|
|
</P>
|
||
|
|
<P>The scalar is the cumulative energy change due to the fix.
|
||
|
|
</P>
|
||
|
|
<P>The vector stores internal Nose/Hoover thermostat and barostat
|
||
|
|
variables. The number and meaning of the vector values depends on
|
||
|
|
which fix is used and the settings for keywords <I>tchain</I> and <I>pchain</I>,
|
||
|
|
which specify the number of Nose/Hoover chains for the thermostat and
|
||
|
|
barostat. If no thermostatting is done, then <I>tchain</I> is 0. If no
|
||
|
|
barostatting is done, then <I>pchain</I> is 0. In the following list,
|
||
|
|
"ndof" is 0, 1, 3, or 6, and is the number of degrees of freedom in
|
||
|
|
the barostat. Its value is 0 if no barostat is used, else its value
|
||
|
|
is 6 if any off-diagonal stress tensor component is barostatted, else
|
||
|
|
its value is 1 if <I>couple xyz</I> is used or <I>couple xy</I> for a 2d
|
||
|
|
simulation, otherwise its value is 3.
|
||
|
|
</P>
|
||
|
|
<P>The order of values in the global vector and their meaning is as
|
||
|
|
follows. The notation means there are tchain values for eta, followed
|
||
|
|
by tchain for eta_dot, followed by ndof for omega, etc:
|
||
|
|
</P>
|
||
|
|
<UL><LI>eta[tchain] = particle thermostat displacements
|
||
|
|
<LI>eta_dot[tchain] = particle thermostat velocities
|
||
|
|
<LI>omega[ndof] = barostat displacements
|
||
|
|
<LI>omega_dot[ndof] = barostat velocities
|
||
|
|
<LI>etap[pchain] = barostat thermostat displacements
|
||
|
|
<LI>etap_dot[pchain] = barostat thermostat velocities
|
||
|
|
<LI>PE_eta[tchain] = potential energy of each particle thermostat displacement
|
||
|
|
<LI>KE_eta_dot[tchain] = kinetic energy of each particle thermostat velocity
|
||
|
|
<LI>PE_omega[ndof] = potential energy of each barostat displacement
|
||
|
|
<LI>KE_omega_dot[ndof] = kinetic energy of each barostat velocity
|
||
|
|
<LI>PE_etap[pchain] = potential energy of each barostat thermostat displacement
|
||
|
|
<LI>KE_etap_dot[pchain] = kinetic energy of each barostat thermostat velocity
|
||
|
|
<LI>PE_strain[1] = scalar strain energy
|
||
|
|
</UL>
|
||
|
|
<P>These fixes can ramp their external temperature and pressure over
|
||
|
|
multiple runs, using the <I>start</I> and <I>stop</I> keywords of the
|
||
|
|
<A HREF = "run.html">run</A> command. See the <A HREF = "run.html">run</A> command for details of
|
||
|
|
how to do this.
|
||
|
|
</P>
|
||
|
|
<P>These fixes are not invoked during <A HREF = "minimize.html">energy
|
||
|
|
minimization</A>.
|
||
|
|
</P>
|
||
|
|
<P>These fixes can be used with either the <I>verlet</I> or <I>respa</I>
|
||
|
|
<A HREF = "run_style.html">integrators</A>. When using one of the barostat fixes
|
||
|
|
with <I>respa</I>, LAMMPS uses an integrator constructed
|
||
|
|
according to the following factorization of the Liouville propagator
|
||
|
|
(for two rRESPA levels):
|
||
|
|
</P>
|
||
|
|
<CENTER><IMG SRC = "Eqs/fix_nh1.jpg">
|
||
|
|
</CENTER>
|
||
|
|
<P>This factorization differs somewhat from that of Tuckerman et al., in that
|
||
|
|
the barostat is only updated at the outermost rRESPA level, whereas
|
||
|
|
Tuckerman's factorization requires splitting the pressure into pieces
|
||
|
|
corresponding to the forces computed at each rRESPA level. In theory, the
|
||
|
|
latter method will exhibit better numerical stability. In practice,
|
||
|
|
because Pdamp is normally chosen to be a large multiple of the
|
||
|
|
outermost rRESPA timestep, the barostat dynamics are not the
|
||
|
|
limiting factor for numerical stability. Both
|
||
|
|
factorizations are time-reversible and can be shown to preserve the phase
|
||
|
|
space measure of the underlying non-Hamiltonian equations of motion.
|
||
|
|
</P>
|
||
|
|
<P>IMPORTANT NOTE: using the <I>respa</I> integrator may be useful for the simulations that sample the electronic motions at a faster pace than the nuclear motions.
|
||
|
|
</P>
|
||
|
|
<P><B>Restrictions:</B>
|
||
|
|
</P>
|
||
|
|
<P>This fix is part of the "user-eff" package. It is only enabled if
|
||
|
|
LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
|
||
|
|
LAMMPS</A> section for more info.
|
||
|
|
</P>
|
||
|
|
<P>Non-periodic dimensions cannot be barostatted. <I>Z</I>, <I>xz</I>, and <I>yz</I>,
|
||
|
|
cannot be barostatted 2D simulations. <I>Xy</I>, <I>xz</I>, and <I>yz</I> can only
|
||
|
|
be barostatted if the simulation domain is triclinic and the 2nd
|
||
|
|
dimension in the keyword (<I>y</I> dimension in <I>xy</I>) is periodic. The
|
||
|
|
<A HREF = "create_box.html">create_box</A>, <A HREF = "read_data.html">read data</A>, and
|
||
|
|
<A HREF = "read_restart.html">read_restart</A> commands specify whether the
|
||
|
|
simulation box is orthogonal or non-orthogonal (triclinic) and explain
|
||
|
|
the meaning of the xy,xz,yz tilt factors.
|
||
|
|
</P>
|
||
|
|
<P>For the <I>temp</I> keyword, the final Tstop cannot be 0.0 since it would
|
||
|
|
make the external T = 0.0 at some timestep during the simulation which
|
||
|
|
is not allowed in the Nose/Hoover formulation.
|
||
|
|
</P>
|
||
|
|
<P>IMPORTANT NOTE: The temperature for systems (regions or groups) with only electrons is not defined in the current temperature calculations, a practical example would be a uniform electron gas or a very hot plasma, where electrons remain delocalized from the nuclei. This is because, even though electron virials are included in the temperature calculation, these are averaged over the nuclear degrees of freedom only. In such cases a corrective term must be added to the pressure to get the correct kinetic contribution.
|
||
|
|
</P>
|
||
|
|
<P><B>Related commands:</B>
|
||
|
|
</P>
|
||
|
|
<P><A HREF = "fix_nve_eff.html">fix nve/eff</A>, <A HREF = "fix_modify.html">fix_modify</A>, <A HREF = "run_style.html">run_style</A>
|
||
|
|
</P>
|
||
|
|
<P><B>Default:</B>
|
||
|
|
</P>
|
||
|
|
<P>The keyword defaults are tchain = 3, pchain = 3, mtk = yes, tloop =
|
||
|
|
ploop = 1, nreset = 0, drag = 0.0, dilate = all, and couple = none.
|
||
|
|
</P>
|
||
|
|
<HR>
|
||
|
|
|
||
|
|
<A NAME = "Martyna"></A>
|
||
|
|
|
||
|
|
<P><B>(Martyna)</B> Martyna, Tobias and Klein, J Chem Phys, 101, 4177 (1994).
|
||
|
|
</P>
|
||
|
|
<A NAME = "Parrinello"></A>
|
||
|
|
|
||
|
|
<P><B>(Parrinello)</B> Parrinello and Rahman, J Appl Phys, 52, 7182 (1981).
|
||
|
|
</P>
|
||
|
|
<A NAME = "Tuckerman"></A>
|
||
|
|
|
||
|
|
<P><B>(Tuckerman)</B> Tuckerman, Alejandre, Lopez-Rendon, Jochim, and
|
||
|
|
Martyna, J Phys A: Math Gen, 39, 5629 (2006).
|
||
|
|
</P>
|
||
|
|
<A NAME = "Shinoda"></A>
|
||
|
|
|
||
|
|
<P><B>(Shinoda)</B> Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).
|
||
|
|
</P>
|
||
|
|
</HTML>
|