git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4652 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/Section_intro.txt

@@ -135,6 +135,7 @@ commands)
   charged pairwise potentials: Coulombic, point-dipole
   manybody potentials: EAM, Finnis/Sinclair EAM, modified EAM (MEAM), \
     embedded ion method (EIM), Stillinger-Weber, Tersoff, AI-REBO, ReaxFF, COMB
+  electron force field (eFF)
   coarse-grained potentials: DPD, GayBerne, REsquared, colloidal, DLVO
   mesoscopic potentials: granular, Peridynamics
   bond potentials: harmonic, FENE, Morse, nonlinear, class 2, \

doc/compute_temp_deform_eff.txt

@@ -22,16 +22,17 @@ compute myTemp all temp/deform/eff :pre
 [Description:]
 
 Define a computation that calculates the temperature of a group of
-nuclei and electrons using the electron force field, after subtracting
-out a streaming velocity induced by the simulation box 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/eff"_fix_deform_eff.html command.  A compute of this style is
-created by the "fix nvt/sllod/eff"_fix_nvt_sllod_eff.html command to
-compute the thermal temperature of atoms for thermostatting purposes.
-A compute of this style can also be used by any command that computes
-a temperature, e.g. "thermo_modify"_thermo_modify.html, "fix
-npt/eff"_fix_nh.html, etc.
+nuclei and electrons in the "electron force field"_pair_eff.html
+model, after subtracting out a streaming velocity induced by the
+simulation box 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/eff"_fix_deform_eff.html command.  A
+compute of this style is created by the "fix
+nvt/sllod/eff"_fix_nvt_sllod_eff.html command to compute the thermal
+temperature of atoms for thermostatting purposes.  A compute of this
+style can also be used by any command that computes a temperature,
+e.g. "thermo_modify"_thermo_modify.html, "fix npt/eff"_fix_nh.html,
+etc.
 
 The calculation performed by this compute is exactly like that
 described by the "compute temp/deform"_compute_temp_deform.html

doc/compute_temp_region_eff.txt

@@ -23,9 +23,10 @@ compute mine flow temp/region/eff boundary :pre
 [Description:]
 
 Define a computation that calculates the temperature of a group of
-nuclei and electrons wihtin a geometric region using the electron
-force field.  A compute of this style can be used by commands that
-compute a temperature, e.g. "thermo_modify"_thermo_modify.html.
+nuclei and electrons in the "electron force field"_pair_eff.html
+model, within a geometric region using the electron force field.  A
+compute of this style can be used by commands that compute a
+temperature, e.g. "thermo_modify"_thermo_modify.html.
 
 The operation of this compute is exactly like that described by the
 "compute temp/region"_compute_temp_region.html command, where the

doc/fix_langevin_eff.html

@@ -60,7 +60,10 @@ interactions (<A HREF = "pair_style.html">pair_style</A>).
 <P>The Ff and Fr terms are added by this fix on a per-particle basis.
 </P>
 <P>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.
+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.
 </P>
 <P>Fr is a force due to solvent atoms at a temperature T randomly bumping
 into the particle.  As derived from the fluctuation/dissipation
@@ -73,15 +76,18 @@ the direction and magnitude of this force as described in
 a Gaussian random number) for speed.
 </P>
 <P>Note that the thermostat effect of this fix is applied to the
-translational and electronic radial degrees of freedom for the particles in a system.  The translational degrees of freedom can also have a bias
-velocity removed from them before thermostatting takes place; see the
-description below.
+translational and electronic radial degrees of freedom for the
+particles in a system.  The translational degrees of freedom can also
+have a bias velocity removed from them before thermostatting takes
+place; see the description below.
 </P>
 <P>IMPORTANT NOTE: Unlike the <A HREF = "fix_nh_eff.html">fix nvt/eff</A> command which
 performs Nose/Hoover thermostatting AND time integration, this fix
 does NOT perform time integration.  It only modifies forces to effect
 thermostatting.  Thus you must use a separate time integration fix,
-like <A HREF = "fix_nve_eff.html">fix nve/eff</A> to actually update the velocities (including electronic radial velocities) and positions of atoms (nuclei and electrons) using the modified forces.  Likewise, this fix
+like <A HREF = "fix_nve_eff.html">fix nve/eff</A> to actually update the velocities
+(including electronic radial velocities) and positions of atoms
+(nuclei and electrons) using the modified forces.  Likewise, this fix
 should not normally be used on atoms that also have their temperature
 controlled by another fix - e.g. by <A HREF = "fix_nh.html">fix nvt/eff</A> command.
 </P>
@@ -106,13 +112,14 @@ the remaining thermal degrees of freedom, and the bias is added back
 in.
 </P>
 <P>The <I>damp</I> parameter is specified in time units and determines how
-rapidly the temperature is relaxed.  For example, a value of 0.1
-means to relax the temperature in a timespan of 100 timesteps (for the default 0.001 timesteps and fmsec unit used in eFF - see the <A HREF = "units.html">units</A> command).
-The damp factor can be thought of as inversely related to the
-viscosity of the solvent.  I.e. a small relaxation time implies a
-hi-viscosity solvent and vice versa.  See the discussion about gamma
-and viscosity in the documentation for the <A HREF = "fix_viscous.html">fix
-viscous</A> command for more details.
+rapidly the temperature is relaxed.  For example, a value of 0.1 means
+to relax the temperature in a timespan of 100 timesteps (for the
+default 0.001 timesteps and fmsec unit used in eFF - see the
+<A HREF = "units.html">units</A> command).  The damp factor can be thought of as
+inversely related to the viscosity of the solvent.  I.e. a small
+relaxation time implies a hi-viscosity solvent and vice versa.  See
+the discussion about gamma and viscosity in the documentation for the
+<A HREF = "fix_viscous.html">fix viscous</A> command for more details.
 </P>
 <P>The random # <I>seed</I> must be a positive integer.  A Marsaglia random
 number generator is used.  Each processor uses the input seed to
@@ -182,7 +189,7 @@ LAMMPS</A> section for more info.
 </P>
 <P><B>Related commands:</B>
 </P>
-<P><A HREF = "fix_nh.html">fix nvt/eff</A>
+<P><A HREF = "fix_langevin.html">fix langevin</A>
 </P>
 <P><B>Default:</B>
 </P>

doc/pair_eff.html

@@ -15,10 +15,10 @@
 </P>
 <P>pair_style eff/cut cutoff eradius_limit_flag pressure_flag
 </P>
-<P>cutoff = global cutoff for Coulombic interactions
-eradius_limit_flag = 0 or 1 for whether electron size is restrained (optional)
-pressure_flag = 0 or 1 to define the type of pressure calculation (optional)
-</P>
+<UL><LI>cutoff = global cutoff for Coulombic interactions
+<LI>eradius_limit_flag = 0 or 1 for whether electron size is restrained (optional)
+<LI>pressure_flag = 0 or 1 to define the type of pressure calculation (optional) 
+</UL>
 <P><B>Examples:</B>
 </P>
 <PRE>pair_style eff/cut 39.7

doc/pair_eff.txt

@@ -14,7 +14,7 @@ pair_style eff/cut cutoff eradius_limit_flag pressure_flag
 
 cutoff = global cutoff for Coulombic interactions
 eradius_limit_flag = 0 or 1 for whether electron size is restrained (optional)
-pressure_flag = 0 or 1 to define the type of pressure calculation (optional)
+pressure_flag = 0 or 1 to define the type of pressure calculation (optional) :ul
 
 [Examples:]