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1
doc/Section_intro.html
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@ -138,6 +138,7 @@ commands)
<UL><LI> pairwise potentials: Lennard-Jones, Buckingham, Morse, Yukawa, soft, class 2 (COMPASS), tabulated
<LI> charged pairwise potentials: Coulombic, point-dipole
<LI> manybody potentials: EAM, Finnis/Sinclair EAM, modified EAM (MEAM), embedded ion method (EIM), Stillinger-Weber, Tersoff, AI-REBO, ReaxFF, COMB
<LI> electron force field (eFF)
<LI> coarse-grained potentials: DPD, GayBerne, REsquared, colloidal, DLVO
<LI> mesoscopic potentials: granular, Peridynamics
<LI> bond potentials: harmonic, FENE, Morse, nonlinear, class 2, quartic (breakable)

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doc/compute_temp_deform_eff.html
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@ -25,16 +25,17 @@
<P><B>Description:</B>
</P>
<P>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 <A HREF = "fix_deform_eff.html">fix
deform/eff</A> command. A compute of this style is
created by the <A HREF = "fix_nvt_sllod_eff.html">fix nvt/sllod/eff</A> 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. <A HREF = "thermo_modify.html">thermo_modify</A>, <A HREF = "fix_nh.html">fix
npt/eff</A>, etc.
nuclei and electrons in the <A HREF = "pair_eff.html">electron force field</A>
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 <A HREF = "fix_deform_eff.html">fix deform/eff</A> command. A
compute of this style is created by the <A HREF = "fix_nvt_sllod_eff.html">fix
nvt/sllod/eff</A> 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. <A HREF = "thermo_modify.html">thermo_modify</A>, <A HREF = "fix_nh.html">fix npt/eff</A>,
etc.
</P>
<P>The calculation performed by this compute is exactly like that
described by the <A HREF = "compute_temp_deform.html">compute temp/deform</A>

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doc/compute_temp_region_eff.html
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@ -26,9 +26,10 @@
<P><B>Description:</B>
</P>
<P>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. <A HREF = "thermo_modify.html">thermo_modify</A>.
nuclei and electrons in the <A HREF = "pair_eff.html">electron force field</A>
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. <A HREF = "thermo_modify.html">thermo_modify</A>.
</P>
<P>The operation of this compute is exactly like that described by the
<A HREF = "compute_temp_region.html">compute temp/region</A> command, where the