fix_nh.txt
490401bd6a57lammm-devel

fix_nh.txt
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			"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c

			:link(lws,http://lammps.sandia.gov)
			:link(ld,Manual.html)
			:link(lc,Section_commands.html#comm)

			:line

			fix nvt command :h3
			fix nvt/cuda command :h3
			fix nvt/kk command :h3
			fix nvt/omp command :h3
			fix npt command :h3
			fix npt/cuda command :h3
			fix npt/intel command :h3
			fix npt/kk command :h3
			fix npt/omp command :h3
			fix nph command :h3
			fix nph/kk command :h3
			fix nph/omp command :h3

			[Syntax:]

			fix ID group-ID style_name keyword value ... :pre

			ID, group-ID are documented in "fix"_fix.html command :ulb,l
			style_name = {nvt} or {npt} or {nph} :l
			one or more keyword/value pairs may be appended :l
			keyword = {temp} or {iso} or {aniso} or {tri} or {x} or {y} or {z} or {xy} or {yz} or {xz} or {couple} or {tchain} or {pchain} or {mtk} or {tloop} or {ploop} or {nreset} or {drag} or {dilate} or {scalexy} or {scaleyz} or {scalexz} or {flip} or {fixedpoint}
			{temp} values = Tstart Tstop Tdamp
			Tstart,Tstop = external temperature at start/end of run
			Tdamp = temperature damping parameter (time units)
			{iso} or {aniso} or {tri} values = Pstart Pstop Pdamp
			Pstart,Pstop = scalar external pressure at start/end of run (pressure units)
			Pdamp = pressure damping parameter (time units)
			{x} or {y} or {z} or {xy} or {yz} or {xz} values = Pstart Pstop Pdamp
			Pstart,Pstop = external stress tensor component at start/end of run (pressure units)
			Pdamp = stress damping parameter (time units)
			{couple} = {none} or {xyz} or {xy} or {yz} or {xz}
			{tchain} value = N
			N = length of thermostat chain (1 = single thermostat)
			{pchain} values = N
			N length of thermostat chain on barostat (0 = no thermostat)
			{mtk} value = {yes} or {no} = add in MTK adjustment term or not
			{tloop} value = M
			M = number of sub-cycles to perform on thermostat
			{ploop} value = M
			M = number of sub-cycles to perform on barostat thermostat
			{nreset} value = reset reference cell every this many timesteps
			{drag} value = Df
			Df = drag factor added to barostat/thermostat (0.0 = no drag)
			{dilate} value = dilate-group-ID
			dilate-group-ID = only dilate atoms in this group due to barostat volume changes
			{scalexy} value = {yes} or {no} = scale xy with ly
			{scaleyz} value = {yes} or {no} = scale yz with lz
			{scalexz} value = {yes} or {no} = scale xz with lz
			{flip} value = {yes} or {no} = allow or disallow box flips when it becomes highly skewed
			{fixedpoint} values = x y z
			x,y,z = perform barostat dilation/contraction around this point (distance units) :pre

			:ule

			[Examples:]

			fix 1 all nvt temp 300.0 300.0 100.0
			fix 1 water npt temp 300.0 300.0 100.0 iso 0.0 0.0 1000.0
			fix 2 jello npt temp 300.0 300.0 100.0 tri 5.0 5.0 1000.0
			fix 2 ice nph x 1.0 1.0 0.5 y 2.0 2.0 0.5 z 3.0 3.0 0.5 yz 0.1 0.1 0.5 xz 0.2 0.2 0.5 xy 0.3 0.3 0.5 nreset 1000 :pre

			[Description:]

			These commands perform time integration on Nose-Hoover style
			non-Hamiltonian equations of motion which are designed to generate
			positions and velocities sampled from the canonical (nvt),
			isothermal-isobaric (npt), and isenthalpic (nph) ensembles. This
			updates the position and velocity for atoms in the group each
			timestep.

			The thermostatting and barostatting is achieved by adding some dynamic
			variables which are coupled to the particle velocities
			(thermostatting) and simulation domain dimensions (barostatting). In
			addition to basic thermostatting and barostatting, these fixes can
			also create a chain of thermostats coupled to the particle thermostat,
			and another chain of thermostats coupled to the barostat
			variables. The barostat can be coupled to the overall box volume, or
			to individual dimensions, including the {xy}, {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). When used
			correctly, the time-averaged temperature and stress tensor of the
			particles will match the target values specified by Tstart/Tstop and
			Pstart/Pstop.

			The equations of motion used are those of Shinoda et al in
			"(Shinoda)"_#Shinoda, which combine the hydrostatic equations of
			Martyna, Tobias and Klein in "(Martyna)"_#Martyna with the strain
			energy proposed by Parrinello and Rahman in
			"(Parrinello)"_#Parrinello. The time integration schemes closely
			follow the time-reversible measure-preserving Verlet and rRESPA
			integrators derived by Tuckerman et al in "(Tuckerman)"_#Tuckerman.

			:line

			The thermostat parameters for fix styles {nvt} and {npt} is specified
			using the {temp} keyword. Other thermostat-related keywords are
			{tchain}, {tloop} and {drag}, which are discussed below.

			The thermostat is applied to only the translational degrees of freedom
			for the particles. The translational degrees of freedom can also have
			a bias velocity removed before thermostatting takes place; see the
			description below. The desired temperature at each timestep is a
			ramped value during the run from {Tstart} to {Tstop}. The {Tdamp}
			parameter is specified in time units and determines how rapidly the
			temperature is relaxed. For example, a value of 10.0 means to relax
			the temperature in a timespan of (roughly) 10 time units (e.g. tau or
			fmsec or psec - see the "units"_units.html command). The atoms in the
			fix group are the only ones whose velocities and positions are updated
			by the velocity/position update portion of the integration.

			NOTE: A Nose-Hoover thermostat will not work well for arbitrary values
			of {Tdamp}. If {Tdamp} is too small, the temperature can fluctuate
			wildly; if it is too large, the temperature will take a very long time
			to equilibrate. A good choice for many models is a {Tdamp} of around
			100 timesteps. Note that this is NOT the same as 100 time units for
			most "units"_units.html settings.

			:line

			The barostat parameters for fix styles {npt} and {nph} 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.

			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"_fix_deform.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 10.0 means to relax the pressure in
			a timespan of (roughly) 10 time units (e.g. tau or fmsec or psec - see
			the "units"_units.html command).

			NOTE: A Nose-Hoover barostat will not work well for arbitrary values
			of {Pdamp}. If {Pdamp} is too small, the pressure and volume can
			fluctuate wildly; if it is too large, the pressure will take a very
			long time to equilibrate. A good choice for many models is a {Pdamp}
			of around 1000 timesteps. Note that this is NOT the same as 1000 time
			units for most "units"_units.html settings.

			Regardless of what atoms are in the fix group (the only atoms which
			are time integrated), 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 {dilate-group-ID} for a group that
			represents a subset of the atoms. This can be useful, for example, to
			leave the coordinates of atoms in a solid substrate unchanged and
			controlling the pressure of a surrounding fluid. This option should
			be used with care, since it can be unphysical to dilate some atoms and
			not others, because it can introduce large, instantaneous
			displacements between a pair of atoms (one dilated, one not) that are
			far from the dilation origin. Also note that for atoms not in the fix
			group, a separate time integration fix like "fix nve"_fix_nve.html or
			"fix nvt"_fix_nh.html can be used on them, independent of whether they
			are dilated or not.

			: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 "(Tuckerman)"_#Tuckerman. 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.

			The {scaleyz}, {scalexz}, and {scalexy} keywords control whether or
			not the corresponding tilt factors are scaled with the associated box
			dimensions when barostatting triclinic periodic cells. The default
			values {yes} will turn on scaling, which corresponds to adjusting the
			linear dimensions of the cell while preserving its shape. Choosing
			{no} ensures that the tilt factors are not scaled with the box
			dimensions. See below for restrictions and default values in different
			situations. In older versions of LAMMPS, scaling of tilt factors was
			not performed. The old behavior can be recovered by setting all three
			scale keywords to {no}.

			The {flip} keyword allows the tilt factors for a triclinic box to
			exceed half the distance of the parallel box length, as discussed
			below. If the {flip} value is set to {yes}, the bound is enforced by
			flipping the box when it is exceeded. If the {flip} value is set to
			{no}, the tilt will continue to change without flipping. Note that if
			applied stress induces large deformations (e.g. in a liquid), this
			means the box shape can tilt dramatically and LAMMPS will run less
			efficiently, due to the large volume of communication needed to
			acquire ghost atoms around a processor's irregular-shaped sub-domain.
			For extreme values of tilt, LAMMPS may also lose atoms and generate an
			error.

			The {fixedpoint} keyword specifies the fixed point for barostat volume
			changes. By default, it is the center of the box. Whatever point is
			chosen will not move during the simulation. For example, if the lower
			periodic boundaries pass through (0,0,0), and this point is provided
			to {fixedpoint}, then the lower periodic boundaries will remain at
			(0,0,0), while the upper periodic boundaries will move twice as
			far. In all cases, the particle trajectories are unaffected by the
			chosen value, except for a time-dependent constant translation of
			positions.

			:line

			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 allows the tilt
			factors to grow a small amount beyond the normal limit of half the box
			length (0.6 times the box length), and then performs a box "flip" to
			an equivalent periodic cell. See the discussion of the {flip} keyword
			above, to allow this bound to be exceeded, if desired.

			The flip operation is described in more detail in the doc page for
			"fix deform"_fix_deform.html. Both the barostat dynamics and the atom
			trajectories are unaffected by this operation. However, if a tilt
			factor is incremented by a large amount (1.5 times the box length) on
			a single timestep, LAMMPS can not accomodate this event and will
			terminate the simulation with an error. This error typically indicates
			that there is something badly wrong with how the simulation was
			constructed, such as specifying values of {Pstart} that are too far
			from the current stress value, or specifying a timestep that is too
			large. Triclinic barostatting should be used with care. This also is
			true for other barostat styles, although they tend to be more
			forgiving of insults. In particular, it is important to recognize that
			equilibrium liquids can not support a shear stress and that
			equilibrium solids can not support shear stresses that exceed the
			yield stress.

			One exception to this rule is if the 1st dimension in the tilt factor
			(x for xy) is non-periodic. In that case, the limits on the tilt
			factor are not enforced, since flipping the box in that dimension does
			not change the atom positions due to non-periodicity. In this mode,
			if you tilt the system to extreme angles, the simulation will simply
			become inefficient due to the highly skewed simulation box.

			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"_fix_nve.html on atoms to which this fix is applied. Likewise,
			fix nvt and fix npt should not normally be used on atoms that also
			have their temperature controlled by another fix - e.g. by "fix
			langevin"_fix_nh.html or "fix temp/rescale"_fix_temp_rescale.html
			commands.

			See "this howto section"_Section_howto.html#howto_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
			compute fix-ID_press group-ID pressure fix-ID_temp :pre

			compute fix-ID_temp all temp
			compute fix-ID_press all pressure fix-ID_temp :pre

			See the "compute temp"_compute_temp.html and "compute
			pressure"_compute_pressure.html commands for details. Note that the
			IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID
			+ underscore + "press". For fix nvt, the group for the new computes
			is the same as the fix group. For fix nph and fix npt, 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 and fix npt 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.

			:line

			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.

			:line

			The fix npt and fix nph commands can be used with rigid bodies or
			mixtures of rigid bodies and non-rigid particles (e.g. solvent). But
			there are also "fix rigid/npt"_fix_rigid.html and "fix
			rigid/nph"_fix_rigid.html commands, which are typically a more natural
			choice. See the doc page for those commands for more discussion of
			the various ways to do this.

			:line

			Styles with a {cuda}, {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
			functionally the same as the corresponding style without the suffix.
			They have been optimized to run faster, depending on your available
			hardware, as discussed in "Section_accelerate"_Section_accelerate.html
			of the manual. The accelerated styles take the same arguments and
			should produce the same results, except for round-off and precision
			issues.

			These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
			KOKKOS, USER-OMP and OPT packages, respectively. They are only
			enabled if LAMMPS was built with those packages. See the "Making
			LAMMPS"_Section_start.html#start_3 section for more info.

			You can specify the accelerated styles explicitly in your input script
			by including their suffix, or you can use the "-suffix command-line
			switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
			use the "suffix"_suffix.html command in your input script.

			See "Section_accelerate"_Section_accelerate.html of the manual for
			more instructions on how to use the accelerated styles effectively.

			:line

			[Restart, fix_modify, output, run start/stop, minimize info:]

			These fixes writes the state of all the thermostat and barostat
			variables to "binary restart files"_restart.html. See the
			"read_restart"_read_restart.html command for info on how to re-specify
			a fix in an input script that reads a restart file, so that the
			operation of the fix continues in an uninterrupted fashion.

			The "fix_modify"_fix_modify.html {temp} and {press} options are
			supported by 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.

			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), 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#howto_15. The scalar value calculated by
			these fixes is "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 (unitless)
			eta_dot\[tchain\] = particle thermostat velocities (1/time units)
			omega\[ndof\] = barostat displacements (unitless)
			omega_dot\[ndof\] = barostat velocities (1/time units)
			etap\[pchain\] = barostat thermostat displacements (unitless)
			etap_dot\[pchain\] = barostat thermostat velocities (1/time units)
			PE_eta\[tchain\] = potential energy of each particle thermostat displacement (energy units)
			KE_eta_dot\[tchain\] = kinetic energy of each particle thermostat velocity (energy units)
			PE_omega\[ndof\] = potential energy of each barostat displacement (energy units)
			KE_omega_dot\[ndof\] = kinetic energy of each barostat velocity (energy units)
			PE_etap\[pchain\] = potential energy of each barostat thermostat displacement (energy units)
			KE_etap_dot\[pchain\] = kinetic energy of each barostat thermostat velocity (energy units)
			PE_strain\[1\] = scalar strain energy (energy units) :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.

			:line

			[Restrictions:]

			{X}, {y}, {z} cannot be barostatted if the associated dimension is not
			periodic. {Xy}, {xz}, and {yz} can only be barostatted if the
			simulation domain is triclinic and the 2nd dimension in the keyword
			({y} dimension in {xy}) is periodic. {Z}, {xz}, and {yz}, cannot be
			barostatted for 2D simulations. 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
			make the external T = 0.0 at some timestep during the simulation which
			is not allowed in the Nose/Hoover formulation.

			The {scaleyz yes} and {scalexz yes} keyword/value pairs can not be used
			for 2D simulations. {scaleyz yes}, {scalexz yes}, and {scalexy yes} options
			can only be used if the 2nd dimension in the keyword is periodic,
			and if the tilt factor is not coupled to the barostat via keywords
			{tri}, {yz}, {xz}, and {xy}.

			These fixes can be used with dynamic groups as defined by the
			"group"_group.html command. Likewise they can be used with groups to
			which atoms are added or deleted over time, e.g. a deposition
			simulation. However, the conservation properties of the thermostat
			and barostat are defined for systems with a static set of atoms. You
			may observe odd behavior if the atoms in a group vary dramatically
			over time or the atom count becomes very small.

			[Related commands:]

			"fix nve"_fix_nve.html, "fix_modify"_fix_modify.html,
			"run_style"_run_style.html

			[Default:]

			The keyword defaults are tchain = 3, pchain = 3, mtk = yes, tloop =
			ploop = 1, nreset = 0, drag = 0.0, dilate = all, couple = none,
			scaleyz = scalexz = scalexy = yes if periodic in 2nd dimension and
			not coupled to barostat, otherwise no.

			:line

			:link(Martyna)
			[(Martyna)] Martyna, Tobias and Klein, J Chem Phys, 101, 4177 (1994).

			:link(Parrinello)
			[(Parrinello)] Parrinello and Rahman, J Appl Phys, 52, 7182 (1981).

			:link(Tuckerman)
			[(Tuckerman)] Tuckerman, Alejandre, Lopez-Rendon, Jochim, and
			Martyna, J Phys A: Math Gen, 39, 5629 (2006).

			:link(Shinoda)
			[(Shinoda)] Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).

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