From 386524da388d1a293ce14929e9f34ff6fa5e1440 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Wed, 1 Sep 2010 20:40:15 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4654 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/fix_langevin_eff.html | 100 +-------- doc/fix_langevin_eff.txt | 100 +-------- doc/fix_nh_eff.html | 435 +++++-------------------------------- doc/fix_nh_eff.txt | 435 +++++-------------------------------- doc/fix_nve_eff.html | 13 +- doc/fix_nve_eff.txt | 13 +- doc/fix_nvt_sllod_eff.html | 98 ++------- doc/fix_nvt_sllod_eff.txt | 98 ++------- 8 files changed, 188 insertions(+), 1104 deletions(-) diff --git a/doc/fix_langevin_eff.html b/doc/fix_langevin_eff.html index d36c07b82a..895c8c47e9 100644 --- a/doc/fix_langevin_eff.html +++ b/doc/fix_langevin_eff.html @@ -45,10 +45,10 @@ fix 1 all langevin/eff 1.0 1.1 10.0 48279 scale 3 1.5

Description:

Apply a Langevin thermostat as described in (Schneider) -to a group of atoms which models an interaction with a background -implicit solvent. Used with fix nve/eff, this command -performs Brownian dynamics (BD), since the total force on each atom -will have the form: +to a group of nuclei and electrons in the electron force +field model. Used with fix nve/eff, +this command performs Brownian dynamics (BD), since the total force on +each atom will have the form: 

F = Fc + Ff + Fr
 Ff = - (m / damp) v
@@ -59,94 +59,10 @@ interactions (pair_style).
 

 
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
-particle's velocity (including the electronic radial degrees of
-freedom).  The proportionality constant for each atom is computed as
-m/damp, where m is the mass of the particle and damp is the damping
-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), 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 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 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 command.
-

-
See this howto section 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 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 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 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 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 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 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.
+
The operation of this fix is exactly like that described by the fix
+langevin command, except that the thermostatting
+is also applied to the radial electron velocity for electron
+particles.
 

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

diff --git a/doc/fix_langevin_eff.txt b/doc/fix_langevin_eff.txt
index 40cfd00c73..b48bb84772 100644
--- a/doc/fix_langevin_eff.txt
+++ b/doc/fix_langevin_eff.txt
@@ -35,10 +35,10 @@ fix 1 all langevin/eff 1.0 1.1 10.0 48279 scale 3 1.5 :pre
 [Description:]
 
 Apply a Langevin thermostat as described in "(Schneider)"_#Schneider
-to a group of atoms which models an interaction with a background
-implicit solvent.  Used with "fix nve/eff"_fix_nve_eff.html, this command
-performs Brownian dynamics (BD), since the total force on each atom
-will have the form:
+to a group of nuclei and electrons in the "electron force
+field"_pair_eff.html model.  Used with "fix nve/eff"_fix_nve_eff.html,
+this command performs Brownian dynamics (BD), since the total force on
+each atom will have the form:
 
 F = Fc + Ff + Fr
 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.
 
-Ff is a frictional drag or viscous damping term proportional to the
-particle's velocity (including the electronic radial degrees of
-freedom).  The proportionality constant for each atom is computed as
-m/damp, where m is the mass of the particle and damp is the damping
-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.
+The operation of this fix is exactly like that described by the "fix
+langevin"_fix_langevin.html command, except that the thermostatting
+is also applied to the radial electron velocity for electron
+particles.
 
 [Restart, fix_modify, output, run start/stop, minimize info:]
 
diff --git a/doc/fix_nh_eff.html b/doc/fix_nh_eff.html
index bc94601467..5677e960c8 100644
--- a/doc/fix_nh_eff.html
+++ b/doc/fix_nh_eff.html
@@ -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.
 
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.  In addition to acting on the nuclear positions and velocities, they generate radius and radial velocities sampled for the electron wave packets in eFF.  This is
-achieved by adding some dynamic variables which are coupled to the
-particle velocities (thermostatting) and simulation domain dimensions
-(barostatting).  In addition to basic thermostatting and barostatting,
-these fixes can also create a chain of thermostats coupled to the
-particle thermostat, and another chain of thermostats coupled to the
-barostat variables. The barostat can be coupled to the overall box
-volume, or to individual dimensions, including the xy, xz and yz
-tilt dimensions. The external pressure of the barostat can be
-specified as either a scalar pressure (isobaric ensemble) or as
+non-Hamiltonian equations of motion for nuclei and electrons in the
+group for the electron force field model.  The fixes
+are designed to generate positions and velocities sampled from the
+canonical (nvt), isothermal-isobaric (npt), and isenthalpic (nph)
+ensembles.  This is achieved by adding some dynamic variables which
+are coupled to the particle velocities (thermostatting) and simulation
+domain dimensions (barostatting).  In addition to basic thermostatting
+and barostatting, these fixes can also create a chain of thermostats
+coupled to the particle thermostat, and another chain of thermostats
+coupled to the barostat variables. The barostat can be coupled to the
+overall box volume, or to individual dimensions, including the 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).
-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
 Tstart/Tstop and Pstart/Pstop.
 

-
The equations of motion used are those of Shinoda et al. in
-(Shinoda), which combine the hydrostatic equations of
-Martyna, Tobias and Klein in (Martyna) with the strain
-energy proposed by Parrinello and Rahman in
-(Parrinello).  The time integration schemes closely 
-follow the time-reversible measure-preserving Verlet and 
-rRESPA integrators derived by Tuckerman et al. in (Tuckerman). 
+
The operation of these fixes is exactly like that described by the
+fix nvt, npt, and nph commands, except that the radius
+and radial velocity of electrons are also updated.  Likewise the
+temperature and pressure calculated by the fix, using the computes it
+creates (as discussed in the fix nvt, npt, and nph
+doc page), are performed with computes that include the eFF contribution
+to the temperature or kinetic energy from the electron radial velocity.
 

-

-
-
The thermostat 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.
+
IMPORTANT NOTE: there are two different pressures that can be reported
+for eFF when defining the pair_style (see pair
+eff/cut 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 is applied to the translational degrees of freedom
-for both nuclei and electrons, and for the radial electronic degrees of freedom.  The translational degrees of freedom can also have
-a bias velocity removed before thermostatting takes place; see the
-description below.  The desired temperature at each timestep is a
-ramped value during the run from 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 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.
-

-

-
-
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, read
-data, and read_restart 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 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 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 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 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.
-

-

-
-
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 
-

-
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 
-

-
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 
-

-

-
-
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).  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).  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.
-

-

-
-
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 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 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 or fix temp/rescale
-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 command, so the the user must allow for these to equilibrate (i.e. evolve thermal partitioning) through integration.
-

-
See this howto section of the manual for a
-discussion of different ways to compute temperature and perform
-thermostatting and barostatting.
-

-

-
-
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 
-

-
compute fix-ID_temp all temp/eff
-compute fix-ID_press all pressure fix-ID_temp 
-

-
See the compute temp/eff and compute
-pressure 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 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 command or print this temperature
-or pressure during thermodynamic output via the thermo_style
-custom 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 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 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 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.
+
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
+command, so the the user must allow for these degrees of freedom to
+equilibrate (i.e. equi-partitioning of energy) through time
+integration.
 

 
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.  See the
-read_restart 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 temp and press options are
-supported by these fixes.  You can use them to assign a
-compute 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 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 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.
-

-
These fixes compute a global scalar and a global vector of quantities,
-which can be accessed by various output
-commands.  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:
-

-
-
These fixes can ramp their external temperature and pressure over
-multiple runs, using the start and stop keywords of the
-run command.  See the run command for details of
-how to do this.
-

-
These fixes are not invoked during energy
-minimization.
-

-
These fixes can be used with either the verlet or respa 
-integrators. 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):
-

-

-

-
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.
+
See the doc page for the fix nvt, npt, and nph commands
+for details.
 

 
Restrictions:
 

@@ -439,24 +114,22 @@ space measure of the underlying non-Hamiltonian equations of motion.
 LAMMPS was built with that package.  See the Making
 LAMMPS section for more info.
 

-
Non-periodic dimensions cannot be barostatted.  Z, xz, and yz,
-cannot be barostatted 2D simulations.  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.  The
-create_box, read data, and
-read_restart commands specify whether the
-simulation box is orthogonal or non-orthogonal (triclinic) and explain
-the meaning of the xy,xz,yz tilt factors.
+
Other restriction discussed on the doc page for the fix nvt, npt, and
+nph commands also apply.
 

-
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.
-

-
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.  
+
IMPORTANT NOTE: The temperature for systems (regions or groups) with
+only electrons and no nuclei is 0.0 (i.e. 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.
 

 
Related commands:
 

-
fix nve/eff, fix_modify, run_style
+
fix nvt, fix nph, fix npt,
+fix_modify, run_style
 

 
Default:
 

diff --git a/doc/fix_nh_eff.txt b/doc/fix_nh_eff.txt
index e0aa4aeebb..3d7a261e77 100644
--- a/doc/fix_nh_eff.txt
+++ b/doc/fix_nh_eff.txt
@@ -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:]
 
 These commands perform time integration on Nose-Hoover style
-non-Hamiltonian equations of motion which are designed to generate
-positions and velocities sampled from the canonical (nvt),
-isothermal-isobaric (npt), and isenthalpic (nph) ensembles.  In addition to acting on the nuclear positions and velocities, they generate radius and radial velocities sampled for the electron wave packets in eFF.  This is
-achieved by adding some dynamic variables which are coupled to the
-particle velocities (thermostatting) and simulation domain dimensions
-(barostatting).  In addition to basic thermostatting and barostatting,
-these fixes can also create a chain of thermostats coupled to the
-particle thermostat, and another chain of thermostats coupled to the
-barostat variables. The barostat can be coupled to the overall box
-volume, or to individual dimensions, including the {xy}, {xz} and {yz}
-tilt dimensions. The external pressure of the barostat can be
-specified as either a scalar pressure (isobaric ensemble) or as
+non-Hamiltonian equations of motion for nuclei and electrons in the
+group for the "electron force field"_pair_eff.html model.  The fixes
+are designed to generate positions and velocities sampled from the
+canonical (nvt), isothermal-isobaric (npt), and isenthalpic (nph)
+ensembles.  This is achieved by adding some dynamic variables which
+are coupled to the particle velocities (thermostatting) and simulation
+domain dimensions (barostatting).  In addition to basic thermostatting
+and barostatting, these fixes can also create a chain of thermostats
+coupled to the particle thermostat, and another chain of thermostats
+coupled to the barostat variables. The barostat can be coupled to the
+overall box volume, or to individual dimensions, including the {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).
-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
 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. 
+The operation of these fixes is exactly like that described by the
+"fix nvt, npt, and nph"_fix_nh.html commands, except that the radius
+and radial velocity of electrons are also updated.  Likewise the
+temperature and pressure calculated by the fix, using the computes it
+creates (as discussed in the "fix nvt, npt, and nph"_fix_nh.html
+doc page), are performed with computes that include the eFF contribution
+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
-{temp} keyword.  Other thermostat-related keywords are {tchain},
-{tloop} and {drag}, which are discussed below.
-
-The thermostat is applied to the translational degrees of freedom
-for both nuclei and electrons, and for the radial electronic degrees of freedom.  The translational degrees of freedom can also have
-a bias velocity removed before thermostatting takes place; see the
-description below.  The desired temperature at each timestep is a
-ramped value during the run from {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.
+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 degrees of freedom to
+equilibrate (i.e. equi-partitioning of energy) through time
+integration.
 
 [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.
-
-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.
+See the doc page for the "fix nvt, npt, and nph"_fix_nh.html commands
+for details.
 
 [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"_Section_start.html#2_3 section for more info.
 
-Non-periodic dimensions cannot be barostatted.  {Z}, {xz}, and {yz},
-cannot be barostatted 2D simulations.  {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.  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.
+Other restriction discussed on the doc page for the "fix nvt, npt, and
+nph"_fix_nh.html commands also apply.
 
-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.
-
-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.  
+IMPORTANT NOTE: The temperature for systems (regions or groups) with
+only electrons and no nuclei is 0.0 (i.e. 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.
 
 [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:]
 
diff --git a/doc/fix_nve_eff.html b/doc/fix_nve_eff.html
index 8652ee5e54..28a9a32018 100644
--- a/doc/fix_nve_eff.html
+++ b/doc/fix_nve_eff.html
@@ -25,9 +25,13 @@
 
Description:
 

 
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
-creates a system trajectory consistent with the microcanonical
-ensemble.
+nuclei and electrons in the group for the electron force
+field model.  V is volume; E is energy.  This creates a
+system trajectory consistent with the microcanonical ensemble.
+

+
The operation of this fix is exactly like that described by the fix
+nve command, except that the radius and radial velocity
+of electrons are also updated.
 

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

@@ -47,7 +51,8 @@ LAMMPS section for more info.
 

 
Related commands:
 

-
fix nvt/eff, fix npt/eff
+
fix nve, fix nvt/eff, fix
+npt/eff
 

 
Default: none
 

diff --git a/doc/fix_nve_eff.txt b/doc/fix_nve_eff.txt
index 4775908a26..33f257c985 100644
--- a/doc/fix_nve_eff.txt
+++ b/doc/fix_nve_eff.txt
@@ -22,9 +22,13 @@ fix 1 all nve/eff :pre
 [Description:]
 
 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
-creates a system trajectory consistent with the microcanonical
-ensemble.
+nuclei and electrons in the group for the "electron force
+field"_pair_eff.html model.  V is volume; E is energy.  This creates a
+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:]
 
@@ -44,6 +48,7 @@ LAMMPS"_Section_start.html#2_3 section for more info.
 
 [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
diff --git a/doc/fix_nvt_sllod_eff.html b/doc/fix_nvt_sllod_eff.html
index ba4b7368f8..e1fdf0c048 100644
--- a/doc/fix_nvt_sllod_eff.html
+++ b/doc/fix_nvt_sllod_eff.html
@@ -27,77 +27,20 @@ fix 1 all nvt/sllod/eff temp 300.0 300.0 0.1 drag 0.2
 
Description:
 

 
Perform constant NVT integration to update positions and velocities
-each timestep for atoms in the group using a Nose/Hoover temperature
-thermostat.  In eFF, this will include the radius and radial velocity of the electrons.
-V is volume; T is temperature.  This creates a system
-trajectory consistent with the canonical ensemble. 
+each timestep for nuclei and electrons in the group for the electron
+force field model, using a Nose/Hoover temperature
+thermostat.  V is volume; T is temperature.  This creates a system
+trajectory consistent with the canonical ensemble.
 

-
This thermostat is used for a simulation box that is changing size
-and/or shape, for example in a non-equilibrium MD (NEMD) simulation.
-The size/shape change is induced by use of the fix
-deform command, so each point in the simulation box
-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
-actual velocity to yield a thermal velocity which is used for
-temperature computation and thermostatting.  The thermal velocity is computed over all degrees of freedom, including the electronic ones.  For example, if the box
-is being sheared in x, relative to y, then points at the bottom of the
-box (low y) have a small x velocity, while points at the top of the
-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 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) (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
-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 
-

-
See the compute temp/deform/eff 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 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 command or print this temperature
-during thermodynamic output via the thermo_style
-custom 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 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 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 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.
+
The operation of this fix is exactly like that described by the fix
+nvt/sllod command, except that the radius and
+radial velocity of electrons are also updated and thermostatted.
+Likewise the temperature calculated by the fix, using the compute it
+creates (as discussed in the fix nvt, npt, and nph doc
+page), is performed with a compute
+temp/deform/eff commmand that includes
+the eFF contribution to the temperature from the electron radial
+velocity.
 

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

@@ -132,15 +75,20 @@ quantities as does the fix nvt/eff command.
 LAMMPS was built with that package.  See the Making
 LAMMPS section for more info.
 

-
This fix works best without Nose-Hoover chain thermostats i.e. using tchain = 1.
-Setting tchain to larger values can result in poor equilibration.
+
This fix works best without Nose-Hoover chain thermostats, i.e. using
+tchain = 1.  Setting tchain to larger values can result in poor
+equilibration.
 

 
Related commands:
 

-
fix nve/eff, fix nvt/eff, fix langevin/eff,
-fix_modify, compute temp/deform/eff
+
fix nve/eff, fix nvt/eff, fix
+langevin/eff, fix
+nvt/sllod, fix_modify, compute
+temp/deform/eff
 

-
Default: Same as fix nvt/eff, except tchain = 1.
+
Default:
+

+
Same as fix nvt/eff, except tchain = 1.
 

 

 
diff --git a/doc/fix_nvt_sllod_eff.txt b/doc/fix_nvt_sllod_eff.txt
index d3414c4782..697640a5be 100644
--- a/doc/fix_nvt_sllod_eff.txt
+++ b/doc/fix_nvt_sllod_eff.txt
@@ -24,77 +24,20 @@ fix 1 all nvt/sllod/eff temp 300.0 300.0 0.1 drag 0.2 :pre
 [Description:]
 
 Perform constant NVT integration to update positions and velocities
-each timestep for atoms in the group using a Nose/Hoover temperature
-thermostat.  In eFF, this will include the radius and radial velocity of the electrons.
-V is volume; T is temperature.  This creates a system
-trajectory consistent with the canonical ensemble. 
+each timestep for nuclei and electrons in the group for the "electron
+force field"_pair_eff.html model, using a Nose/Hoover temperature
+thermostat.  V is volume; T is temperature.  This creates a system
+trajectory consistent with the canonical ensemble.
 
-This thermostat is used for a simulation box that is changing size
-and/or shape, for example in a non-equilibrium MD (NEMD) simulation.
-The size/shape change is induced by use of the "fix
-deform"_fix_deform.html command, so each point in the simulation box
-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
-actual velocity to yield a thermal velocity which is used for
-temperature computation and thermostatting.  The thermal velocity is computed over all degrees of freedom, including the electronic ones.  For example, if the box
-is being sheared in x, relative to y, then points at the bottom of the
-box (low y) have a small x velocity, while points at the top of the
-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.
+The operation of this fix is exactly like that described by the "fix
+nvt/sllod"_fix_nvt_sllod.html command, except that the radius and
+radial velocity of electrons are also updated and thermostatted.
+Likewise the temperature calculated by the fix, using the compute it
+creates (as discussed in the "fix nvt, npt, and nph"_fix_nh.html doc
+page), is performed with a "compute
+temp/deform/eff"_compute_temp_deform_eff.html commmand that includes
+the eFF contribution to the temperature from the electron radial
+velocity.
 
 [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"_Section_start.html#2_3 section for more info.
 
-This fix works best without Nose-Hoover chain thermostats i.e. using tchain = 1.
-Setting tchain to larger values can result in poor equilibration.
+This fix works best without Nose-Hoover chain thermostats, i.e. using
+tchain = 1.  Setting tchain to larger values can result in poor
+equilibration.
 
 [Related commands:]
 
-"fix nve/eff"_fix_nve_eff.html, "fix nvt/eff"_fix_nh_eff.html, "fix langevin/eff"_fix_langevin_eff.html,
-"fix_modify"_fix_modify.html, "compute temp/deform/eff"_compute_temp_deform_eff.html
+"fix nve/eff"_fix_nve_eff.html, "fix nvt/eff"_fix_nh_eff.html, "fix
+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