git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7257 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/Section_packages.html

@@ -211,28 +211,38 @@ have questions.
 
 <H4>USER-CG-CMM package 
 </H4>
-<P>This package implements 4 commands which can be used in a LAMMPS input
+<P>This package implements 3 commands which can be used in a LAMMPS input
 script:
 </P>
-<UL><LI>pair_style cg/cmm
+<UL><LI>pair_style lj/sdk
-<LI>pair_style cg/cmm/coul/cut
+<LI>pair_style lj/sdk/coul/long
-<LI>pair_style cg/cmm/coul/long
+<LI>angle_style sdk 
-<LI>angle_style cg/cmm 
 </UL>
 <P>These styles allow coarse grained MD simulations with the
 parametrization of Shinoda, DeVane, Klein, Mol Sim, 33, 27 (2007)
-(cg/cmm), with extensions to simulate ionic liquids, electrolytes,
+(SDK), with extensions to simulate ionic liquids, electrolytes,
-lipids and charged amino acids (to be published soon).
+lipids and charged amino acids.
 </P>
 <P>See the doc pages for these commands for details.
 </P>
 <P>There are example scripts for using this package in
 examples/USER/cg-cmm.
 </P>
+<P>This is the second generation implementation reducing the the clutter
+of the previous version. For many systems with long range
+electrostatics, it will be faster to use pair_style hybrid/overlay
+with lj/sdk and coul/long instead of the combined lj/sdk/coul/long
+style, since the number of charged atom types is usually small.  To
+exploit this property, the use of the kspace_style pppm/cg is
+recommended over regular pppm. For all new styles, input file backward
+compatibility is provided.  The old implementation is still available
+through appending the /old suffix. These will be discontinued and
+removed after the new implementation has been fully validated.
+</P>
 <P>The current version of this package should be considered beta
-quality. The CG potentials work correctly and well, but there will be
+quality. The CG potentials work correctly for "normal" situations, but
-optimizations, cleanups and additional tools to aid in setting up and
+have not been testing with all kinds of potential parameters and
-analyzing simulations with this package added in the next months.
+simuation systems.
 </P>
 <P>The person who created this package is Axel Kohlmeyer at Temple U
 (akohlmey at gmail.com).  Contact him directly if you have questions.

doc/Section_packages.txt

@@ -199,28 +199,38 @@ have questions.
 
 USER-CG-CMM package :h4
 
-This package implements 4 commands which can be used in a LAMMPS input
+This package implements 3 commands which can be used in a LAMMPS input
 script:
 
-pair_style cg/cmm
+pair_style lj/sdk
-pair_style cg/cmm/coul/cut
+pair_style lj/sdk/coul/long
-pair_style cg/cmm/coul/long
+angle_style sdk :ul
-angle_style cg/cmm :ul
 
 These styles allow coarse grained MD simulations with the
 parametrization of Shinoda, DeVane, Klein, Mol Sim, 33, 27 (2007)
-(cg/cmm), with extensions to simulate ionic liquids, electrolytes,
+(SDK), with extensions to simulate ionic liquids, electrolytes,
-lipids and charged amino acids (to be published soon).
+lipids and charged amino acids.
 
 See the doc pages for these commands for details.
 
 There are example scripts for using this package in
 examples/USER/cg-cmm.
 
+This is the second generation implementation reducing the the clutter
+of the previous version. For many systems with long range
+electrostatics, it will be faster to use pair_style hybrid/overlay
+with lj/sdk and coul/long instead of the combined lj/sdk/coul/long
+style, since the number of charged atom types is usually small.  To
+exploit this property, the use of the kspace_style pppm/cg is
+recommended over regular pppm. For all new styles, input file backward
+compatibility is provided.  The old implementation is still available
+through appending the /old suffix. These will be discontinued and
+removed after the new implementation has been fully validated.
+
 The current version of this package should be considered beta
-quality. The CG potentials work correctly and well, but there will be
+quality. The CG potentials work correctly for "normal" situations, but
-optimizations, cleanups and additional tools to aid in setting up and
+have not been testing with all kinds of potential parameters and
-analyzing simulations with this package added in the next months.
+simuation systems.
 
 The person who created this package is Axel Kohlmeyer at Temple U
 (akohlmey at gmail.com).  Contact him directly if you have questions.

doc/pair_gauss.html

@@ -13,9 +13,14 @@
 </H3>
 <H3>pair_style gauss/omp command 
 </H3>
+<H3>pair_style gauss/cut command 
+</H3>
+<H3>pair_style gauss/cut/omp command 
+</H3>
 <P><B>Syntax:</B> 
 </P>
-<PRE>pair_style gauss cutoff 
+<PRE>pair_style gauss cutoff
+pair_style gauss/cut cutoff 
 </PRE>
 <UL><LI>cutoff = global cutoff for Gauss interactions (distance units) 
 </UL>
@@ -25,6 +30,9 @@
 pair_coeff * * 1.0 0.9
 pair_coeff 1 4 1.0 0.9 10.0 
 </PRE>
+<PRE>pair_style gauss/cut 3.5
+pair_coeff 1 4 0.2805 1.45 0.112 
+</PRE>
 <P><B>Description:</B> 
 </P>
 <P>Style <I>gauss</I> computes a tethering potential of the form
@@ -47,12 +55,38 @@ commands:
 <P>The last coefficient is optional. If not specified, the global cutoff
 is used.
 </P>
+<P>Style <I>gauss/cut</I> computes a generalized Gaussian interaction potential 
+between pairs of particles:
+</P>
+<CENTER><IMG SRC = "Eqs/pair_gauss_cut.jpg">
+</CENTER>
+<P>where H determines together with the standard deviation sigma_h the
+peak height of the Gaussian function, and r_mh the peak position.
+Examples of the use of the Gaussian potentials include implicit
+solvent simulations of salt ions <A HREF = "#Lenart">(Lenart)</A> and of surfactants
+<A HREF = "#Jusufi">(Jusufi)</A>.  In these instances the Gaussian potential mimics
+the hydration barrier between a pair of particles. The hydration
+barrier is located at r_mh and has a width of sigma_h. The prefactor
+determines the hight of the potential barrier.
+</P>
+<P>The following coefficients must be defined for each pair of atom types
+via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the example above,
+or in the data file or restart files read by the
+<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
+commands:
+</P>
+<UL><LI>H (energy * distance units)
+<LI>r_mh (distance units)
+<LI>sigma_h (distance units) 
+</UL>
+<P>The global cutoff (r_c) specified in the pair_style command is used.
+</P>
 <HR>
 
-<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>omp</I>, or <I>opt</I> suffix are functionally 
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>omp</I>, or <I>opt</I> suffix are functionally
-the same as the corresponding style without the suffix.  They have 
+the same as the corresponding style without the suffix.  They have
-been optimized to run faster, depending on your available hardware, 
+been optimized to run faster, depending on your available hardware, as
-as discussed in <A HREF = "Section_accelerate.html">this section</A> of the manual.
+discussed in <A HREF = "Section_accelerate.html">this section</A> of the manual.
 The accelerated styles take the same arguments and should produce the
 same results, except for round-off and precision issues.
 </P>
@@ -73,13 +107,17 @@ instructions on how to use the accelerated styles effectively.
 
 <P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
 </P>
-<P>This pair style does not support mixing.  Thus, coefficients for all
+<P>These pair style do not support mixing.  Thus, coefficients for all
 I,J pairs must be specified explicitly.
 </P>
-<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
+<P>The <I>gauss</I> style does not support the <A HREF = "pair_modify.html">pair_modify</A>
 shift option. There is no effect due to the Gaussian well beyond the
 cutoff; hence reasonable cutoffs need to be specified.
 </P>
+<P>The <I>gauss/cut</I> style supports the <A HREF = "pair_modify.html">pair_modify</A> shift
+option for the energy of the Gauss-potential portion of the pair
+interaction.
+</P>
 <P>The <A HREF = "pair_modify.html">pair_modify</A> table and tail options are not
 relevant for this pair style.
 </P>
@@ -95,7 +133,7 @@ to be specified in an input script that reads a restart file.
 <A HREF = "run_style.html">run_style respa</A> command.  It does not support the
 <I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
 </P>
-<P>This pair style tallies an "occupancy" count of how many Gaussian-well
+<P>Thes <I>gauss</I> pair style tallies an "occupancy" count of how many Gaussian-well
 sites have an atom within the distance at which the force is a maximum
 = sqrt(0.5/b).  This quantity can be accessed via the <A HREF = "compute_pair.html">compute
 pair</A> command as a vector of values of length 1.
@@ -109,11 +147,16 @@ thermo_style custom step temp epair v_occ
 </PRE>
 <HR>
 
-<P><B>Restrictions:</B> none
+<P><B>Restrictions:</B>
+</P>
+<P>The <I>gauss/cut</I> style is part of the "user-misc" package. It is only enabled
+if LAMMPS is build with that package. See the <A HREF = "Section_start.html#3">Making of LAMMPS</A>
+section for more info.
 </P>
 <P><B>Related commands:</B>
 </P>
-<P><A HREF = "pair_coeff.html">pair_coeff</A>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>, 
+<A HREF = "pair_coul_diel.html">pair_style coul/diel</A>
 </P>
 <P><B>Default:</B> none
 </P>

doc/pair_gauss.txt

@@ -8,10 +8,13 @@
 
 pair_style gauss command :h3
 pair_style gauss/omp command :h3
+pair_style gauss/cut command :h3
+pair_style gauss/cut/omp command :h3
 
 [Syntax:] 
 
-pair_style gauss cutoff :pre
+pair_style gauss cutoff
+pair_style gauss/cut cutoff :pre
 
 cutoff = global cutoff for Gauss interactions (distance units) :ul
 
@@ -21,6 +24,10 @@ pair_style gauss 12.0
 pair_coeff * * 1.0 0.9
 pair_coeff 1 4 1.0 0.9 10.0 :pre
 
+pair_style gauss/cut 3.5
+pair_coeff 1 4 0.2805 1.45 0.112 :pre
+
+
 [Description:] 
 
 Style {gauss} computes a tethering potential of the form
@@ -43,12 +50,38 @@ cutoff (distance units) :ul
 The last coefficient is optional. If not specified, the global cutoff
 is used.
 
+Style {gauss/cut} computes a generalized Gaussian interaction potential 
+between pairs of particles:
+
+:c,image(Eqs/pair_gauss_cut.jpg)
+
+where H determines together with the standard deviation sigma_h the
+peak height of the Gaussian function, and r_mh the peak position.
+Examples of the use of the Gaussian potentials include implicit
+solvent simulations of salt ions "(Lenart)"_#Lenart and of surfactants
+"(Jusufi)"_#Jusufi.  In these instances the Gaussian potential mimics
+the hydration barrier between a pair of particles. The hydration
+barrier is located at r_mh and has a width of sigma_h. The prefactor
+determines the hight of the potential barrier.
+
+The following coefficients must be defined for each pair of atom types
+via the "pair_coeff"_pair_coeff.html command as in the example above,
+or in the data file or restart files read by the
+"read_data"_read_data.html or "read_restart"_read_restart.html
+commands:
+
+H (energy * distance units)
+r_mh (distance units)
+sigma_h (distance units) :ul
+
+The global cutoff (r_c) specified in the pair_style command is used.
+
 :line
 
-Styles with a {cuda}, {gpu}, {omp}, or {opt} suffix are functionally 
+Styles with a {cuda}, {gpu}, {omp}, or {opt} suffix are functionally
-the same as the corresponding style without the suffix.  They have 
+the same as the corresponding style without the suffix.  They have
-been optimized to run faster, depending on your available hardware, 
+been optimized to run faster, depending on your available hardware, as
-as discussed in "this section"_Section_accelerate.html of the manual.
+discussed in "this section"_Section_accelerate.html of the manual.
 The accelerated styles take the same arguments and should produce the
 same results, except for round-off and precision issues.
 
@@ -69,13 +102,17 @@ instructions on how to use the accelerated styles effectively.
 
 [Mixing, shift, table, tail correction, restart, rRESPA info]:
 
-This pair style does not support mixing.  Thus, coefficients for all
+These pair style do not support mixing.  Thus, coefficients for all
 I,J pairs must be specified explicitly.
 
-This pair style does not support the "pair_modify"_pair_modify.html
+The {gauss} style does not support the "pair_modify"_pair_modify.html
 shift option. There is no effect due to the Gaussian well beyond the
 cutoff; hence reasonable cutoffs need to be specified.
 
+The {gauss/cut} style supports the "pair_modify"_pair_modify.html shift
+option for the energy of the Gauss-potential portion of the pair
+interaction.
+
 The "pair_modify"_pair_modify.html table and tail options are not
 relevant for this pair style.
 
@@ -91,7 +128,7 @@ This pair style can only be used via the {pair} keyword of the
 "run_style respa"_run_style.html command.  It does not support the
 {inner}, {middle}, {outer} keywords.
 
-This pair style tallies an "occupancy" count of how many Gaussian-well
+Thes {gauss} pair style tallies an "occupancy" count of how many Gaussian-well
 sites have an atom within the distance at which the force is a maximum
 = sqrt(0.5/b).  This quantity can be accessed via the "compute
 pair"_compute_pair.html command as a vector of values of length 1.
@@ -105,10 +142,15 @@ thermo_style custom step temp epair v_occ :pre
 
 :line
 
-[Restrictions:] none
+[Restrictions:]
+
+The {gauss/cut} style is part of the "user-misc" package. It is only enabled
+if LAMMPS is build with that package. See the "Making of LAMMPS"_Section_start.html#3
+section for more info.
 
 [Related commands:]
 
-"pair_coeff"_pair_coeff.html
+"pair_coeff"_pair_coeff.html, 
+"pair_style coul/diel"_pair_coul_diel.html
 
 [Default:] none

doc/pair_tersoff.html

@@ -11,20 +11,29 @@
 
 <H3>pair_style tersoff command 
 </H3>
+<H3>pair_style tersoff/table command 
+</H3>
+<H3>pair_style tersoff/cuda 
+</H3>
+<H3>pair_style tersoff/omp 
+</H3>
+<H3>pair_style tersoff/table/omp command 
+</H3>
 <P><B>Syntax:</B>
 </P>
-<PRE>pair_style tersoff 
+<PRE>pair_style style 
-</PRE>
-<PRE>pair_style tersoff/cuda 
-</PRE>
-<PRE>pair_style tersoff/omp 
 </PRE>
+<P>style = <I>tersoff</I> or <I>tersoff/table</I> or <I>tersoff/cuda</I> or <I>tersoff/omp</I> or <I>tersoff/table/omp</I>
+</P>
 <P><B>Examples:</B>
 </P>
 <PRE>pair_style tersoff
 pair_coeff * * Si.tersoff Si
 pair_coeff * * SiC.tersoff Si C Si 
 </PRE>
+<PRE>pair_style tersoff/table
+pair_coeff * * SiCGe.tersoff Si(D) 
+</PRE>
 <P><B>Description:</B>
 </P>
 <P>The <I>tersoff</I> style computes a 3-body Tersoff potential
@@ -36,6 +45,12 @@ pair_coeff * * SiC.tersoff Si C Si
 The summations in the formula are over all neighbors J and K of atom I
 within a cutoff distance = R + D. 
 </P>
+<P>The <I>tersoff/table</I> style uses tabulated forms for the two-body, 
+environment and angular functions. Linear interpolation is performed
+between adjacent table entries. The table length is chosen to be
+accurate within 10^-6 with respect to the <I>tersoff</I> style energy.
+The <I>tersoff/table</I> should give better performance in terms of speed.
+</P>
 <P>Only a single pair_coeff command is used with the <I>tersoff</I> style
 which specifies a Tersoff potential file with parameters for all
 needed elements.  These are mapped to LAMMPS atom types by specifying
@@ -132,7 +147,8 @@ it reduces to the form of <A HREF = "#Albe">Albe et al.</A> when beta = 1 and m
 Note that in the current Tersoff implementation in LAMMPS, m must be
 specified as either 3 or 1.  Tersoff used a slightly different but
 equivalent form for alloys, which we will refer to as Tersoff_2
-potential <A HREF = "#Tersoff_2">(Tersoff_2)</A>.
+potential <A HREF = "#Tersoff_2">(Tersoff_2)</A>. The <I>tersoff/table</I> style implements
+Teroff_2 parameterization only.
 </P>
 <P>LAMMPS parameter values for Tersoff_2 can be obtained as follows:
 gamma_ijk = omega_ik, lambda3 = 0 and the value of

doc/pair_tersoff.txt

@@ -7,12 +7,16 @@
 :line
 
 pair_style tersoff command :h3
+pair_style tersoff/table command :h3
+pair_style tersoff/cuda :h3
+pair_style tersoff/omp :h3
+pair_style tersoff/table/omp command :h3
 
 [Syntax:]
 
-pair_style tersoff :pre
+pair_style style :pre
-pair_style tersoff/cuda :pre
+
-pair_style tersoff/omp :pre
+style = {tersoff} or {tersoff/table} or {tersoff/cuda} or {tersoff/omp} or {tersoff/table/omp}
 
 [Examples:]
 
@@ -20,6 +24,9 @@ pair_style tersoff
 pair_coeff * * Si.tersoff Si
 pair_coeff * * SiC.tersoff Si C Si :pre
 
+pair_style tersoff/table
+pair_coeff * * SiCGe.tersoff Si(D) :pre
+
 [Description:]
 
 The {tersoff} style computes a 3-body Tersoff potential
@@ -31,6 +38,12 @@ where f_R is a two-body term and f_A includes three-body interactions.
 The summations in the formula are over all neighbors J and K of atom I
 within a cutoff distance = R + D. 
 
+The {tersoff/table} style uses tabulated forms for the two-body, 
+environment and angular functions. Linear interpolation is performed
+between adjacent table entries. The table length is chosen to be
+accurate within 10^-6 with respect to the {tersoff} style energy.
+The {tersoff/table} should give better performance in terms of speed.
+
 Only a single pair_coeff command is used with the {tersoff} style
 which specifies a Tersoff potential file with parameters for all
 needed elements.  These are mapped to LAMMPS atom types by specifying
@@ -127,7 +140,8 @@ it reduces to the form of "Albe et al."_#Albe when beta = 1 and m = 1.
 Note that in the current Tersoff implementation in LAMMPS, m must be
 specified as either 3 or 1.  Tersoff used a slightly different but
 equivalent form for alloys, which we will refer to as Tersoff_2
-potential "(Tersoff_2)"_#Tersoff_2.
+potential "(Tersoff_2)"_#Tersoff_2. The {tersoff/table} style implements
+Teroff_2 parameterization only.
 
 LAMMPS parameter values for Tersoff_2 can be obtained as follows:
 gamma_ijk = omega_ik, lambda3 = 0 and the value of