git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5711 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/pair_eff.html

@@ -182,8 +182,24 @@ the method in <A HREF = "#Jaramillo-Botero">(Jaramillo-Botero)</A>.
 <P>Work is underway to extend the eFF to higher Z elements with
 increasingly non-spherical electrons (p-block and d-block), to provide
 explicit terms for electron correlation/exchange, and to improve its
-computational efficiency for atoms with a large number of core
-electrons using core approximating pseudo-potentials.
+computational efficiency via atom models with fixed 2 s core electrons
+and atom models represented as pseudo-cores plus valence electrons.
+</P>
+<P>The current version adds support for models with fixed-core and
+effective pseudo-core (i.e. effective core pseudopotentials, ECP)
+definitions.  to enable larger timesteps (i.e. by avoiding the high
+frequency vibrational modes -translational and radial- of the 2 s
+electrons), and in the ECP case to reduce the p-character effects in
+higher Z elements (e.g. Silicon).  A fixed-core should be defined with
+a mass that includes the corresponding nuclear mass plus the 2 s
+electrons in atomic mass units (2x5.4857990943e-4), and a radius
+equivalent to that of minimized 1s electrons (see examples under
+/examples/USER/eff/fixed-core).  An pseudo-core should be described
+with a mass that includes the corresponding nuclear mass, plus all the
+core electrons (i.e no outer shell electrons), and a radius equivalent
+to that of a corresponding minimized full-electron system.  The charge
+for a pseudo-core atom should be given by the number of outer shell
+electrons.
 </P>
 <P>In general, eFF excels at computing the properties of materials in
 extreme conditions and tracing the system dynamics over multi-picosend
@@ -266,9 +282,9 @@ Dense Matter, Phys Rev Lett, 99:185003 (2007).
 </P>
 <A NAME = "Jaramillo-Botero"></A>
 
-<P><B>(Jaramillo-Botero_2010)</B> Jaramillo-Botero, Su, Qi, Goddard,
-Large-scale, Long-term Non-adiabatic Electron Molecular Dynamics for
-Describing Material Properties and Phenomena in Extreme Environments,
-to appear in J Comp Chem (2010).
+<P><B>(Jaramillo-Botero)</B> Jaramillo-Botero, Su, Qi, Goddard, Large-scale,
+Long-term Non-adiabatic Electron Molecular Dynamics for Describing
+Material Properties and Phenomena in Extreme Environments, J Comp
+Chem, 32, 497-512 (2011).
 </P>
 </HTML>

doc/pair_eff.txt

@@ -179,8 +179,24 @@ the method in "(Jaramillo-Botero)"_#Jaramillo-Botero.
 Work is underway to extend the eFF to higher Z elements with
 increasingly non-spherical electrons (p-block and d-block), to provide
 explicit terms for electron correlation/exchange, and to improve its
-computational efficiency for atoms with a large number of core
-electrons using core approximating pseudo-potentials.
+computational efficiency via atom models with fixed 2 s core electrons
+and atom models represented as pseudo-cores plus valence electrons.
+
+The current version adds support for models with fixed-core and
+effective pseudo-core (i.e. effective core pseudopotentials, ECP)
+definitions.  to enable larger timesteps (i.e. by avoiding the high
+frequency vibrational modes -translational and radial- of the 2 s
+electrons), and in the ECP case to reduce the p-character effects in
+higher Z elements (e.g. Silicon).  A fixed-core should be defined with
+a mass that includes the corresponding nuclear mass plus the 2 s
+electrons in atomic mass units (2x5.4857990943e-4), and a radius
+equivalent to that of minimized 1s electrons (see examples under
+/examples/USER/eff/fixed-core).  An pseudo-core should be described
+with a mass that includes the corresponding nuclear mass, plus all the
+core electrons (i.e no outer shell electrons), and a radius equivalent
+to that of a corresponding minimized full-electron system.  The charge
+for a pseudo-core atom should be given by the number of outer shell
+electrons.
 
 In general, eFF excels at computing the properties of materials in
 extreme conditions and tracing the system dynamics over multi-picosend
@@ -257,12 +273,11 @@ If not specified, eradius_limit_flag = 0 and pressure_flag = 0.
 :line
 
 :link(Su)
-
 [(Su)] Su and Goddard, Excited Electron Dynamics Modeling of Warm
 Dense Matter, Phys Rev Lett, 99:185003 (2007).
 
 :link(Jaramillo-Botero)
-[(Jaramillo-Botero_2010)] Jaramillo-Botero, Su, Qi, Goddard,
-Large-scale, Long-term Non-adiabatic Electron Molecular Dynamics for
-Describing Material Properties and Phenomena in Extreme Environments,
-to appear in J Comp Chem (2010).
+[(Jaramillo-Botero)] Jaramillo-Botero, Su, Qi, Goddard, Large-scale,
+Long-term Non-adiabatic Electron Molecular Dynamics for Describing
+Material Properties and Phenomena in Extreme Environments, J Comp
+Chem, 32, 497-512 (2011).

doc/read_data.html

@@ -303,8 +303,8 @@ of analysis.
 <LI>x,y,z = coordinates of atom
 <LI>mux,muy,muz = direction of dipole moment of atom
 <LI>quatw,quati,quatj,quatk = quaternion components for orientation of atom
-<LI>spin = electron spin (+1/-1), 0 for nuclei
-<LI>eradius = electron radius 
+<LI>spin = electron spin (+1/-1), 0 = nuclei, 2 = fixed-core, 3 = pseudo-cores (i.e. ECP)
+<LI>eradius = electron radius (or fixed-core radius) 
 </UL>
 <P>The units for these quantities depend on the unit style; see the
 <A HREF = "units.html">units</A> command for details.
@@ -704,11 +704,11 @@ style dipole or ellipsoid.
 
 <P>where the keywords have these meanings:
 </P>
-<UL><LI>vx,vy,vz = translational velocity of atom
-<LI>lx,ly,lz = angular momentum of aspherical atom
-<LI>wx,wy,wz = angular velocity of granular atom
-<LI>evel = electron radial velocity 
-</UL>
+<P>vx,vy,vz = translational velocity of atom
+lx,ly,lz = angular momentum of aspherical atom
+wx,wy,wz = angular velocity of granular atom
+evel = electron radial velocity (0 for fixed-core):ul
+</P>
 <P>The velocity lines can appear in any order.  This section can only be
 used after an <I>Atoms</I> section.  This is because the <I>Atoms</I> section
 must have assigned a unique atom ID to each atom so that velocities

doc/read_data.txt

@@ -282,8 +282,8 @@ volume = volume of atom (distance^3 units)
 x,y,z = coordinates of atom
 mux,muy,muz = direction of dipole moment of atom
 quatw,quati,quatj,quatk = quaternion components for orientation of atom
-spin = electron spin (+1/-1), 0 for nuclei
-eradius = electron radius :ul
+spin = electron spin (+1/-1), 0 = nuclei, 2 = fixed-core, 3 = pseudo-cores (i.e. ECP)
+eradius = electron radius (or fixed-core radius) :ul
 
 The units for these quantities depend on the unit style; see the
 "units"_units.html command for details.
@@ -619,7 +619,7 @@ where the keywords have these meanings:
 vx,vy,vz = translational velocity of atom
 lx,ly,lz = angular momentum of aspherical atom
 wx,wy,wz = angular velocity of granular atom
-evel = electron radial velocity :ul
+evel = electron radial velocity (0 for fixed-core):ul
 
 The velocity lines can appear in any order.  This section can only be
 used after an {Atoms} section.  This is because the {Atoms} section