From 5c92d3a7ac96e889a55c0e2cc1701d1244755da0 Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Wed, 17 Nov 2010 18:20:48 +0000
Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5248
 f3b2605a-c512-4ea7-a41b-209d697bcdaa

---
 doc/angle_class2.html    | 34 ++++++++++++-------
 doc/angle_class2.txt     | 30 ++++++++++++-----
 doc/dihedral_class2.html | 71 +++++++++++++++++++++++++++++-----------
 doc/dihedral_class2.txt  | 61 +++++++++++++++++++++++++---------
 doc/improper_class2.html | 24 ++++++++------
 doc/improper_class2.txt  | 22 ++++++++-----
 6 files changed, 168 insertions(+), 74 deletions(-)

diff --git a/doc/angle_class2.html b/doc/angle_class2.html
index 18f9024ce9..c50cfdb3c1 100644
--- a/doc/angle_class2.html
+++ b/doc/angle_class2.html
@@ -32,8 +32,13 @@ the equilibrium bond lengths.
 </P>
 <P>See <A HREF = "#Sun">(Sun)</A> for a description of the COMPASS class2 force field.
 </P>
-<P>For this style, coefficients for the Ea formula can be specified in
-the input script or data file.  These are the 4 coefficients:
+<P>Coefficients for the Ea, Ebb, and Eba formulas must be defined for
+each angle type via the <A HREF = "bond_coeff.html">bond_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>
+<P>These are the 4 coefficients for the Ea formula:
 </P>
 <UL><LI>theta0 (degrees)
 <LI>K2 (energy/radian^2)
@@ -43,20 +48,27 @@ the input script or data file.  These are the 4 coefficients:
 <P>Theta0 is specified in degrees, but LAMMPS converts it to radians
 internally; hence the units of the various K are in per-radian.
 </P>
-<P>Coefficients for the Ebb and Eba formulas can only be specified in the
-data file.
+<P>For the Ebb formula, each line in a <A HREF = "bond_coeff.html">bond_coeff</A>
+command in the input script lists 4 coefficients, the first of which
+is "bb" to indicate they are BondBond coefficients.  In a data file,
+these coefficients can be listed under a "BondBond Coeffs" heading and
+you must leave out the "bb", i.e. only list 3 coefficients after the
+angle type.
 </P>
-<P>For the Ebb formula, the coefficients are listed under a "BondBond
-Coeffs" heading and each line lists 3 coefficients:
-</P>
-<UL><LI>M (energy/distance^2)
+<UL><LI>bb
+<LI>M (energy/distance^2)
 <LI>r1 (distance)
 <LI>r2 (distance) 
 </UL>
-<P>For the Eba formula, the coefficients are listed under a "BondAngle
-Coeffs" heading and each line lists 4 coefficients:
+<P>For the Eba formula, each line in a <A HREF = "bond_coeff.html">bond_coeff</A>
+command in the input script lists 5 coefficients, the first of which
+is "ba" to indicate they are BondAngle coefficients.  In a data file,
+these coefficients can be listed under a "BondAngle Coeffs" heading
+and you must leave out the "ba", i.e. only list 4 coefficients after
+the angle type.
 </P>
-<UL><LI>N1 (energy/distance^2)
+<UL><LI>ba
+<LI>N1 (energy/distance^2)
 <LI>N2 (energy/distance^2)
 <LI>r1 (distance)
 <LI>r2 (distance) 
diff --git a/doc/angle_class2.txt b/doc/angle_class2.txt
index 3839723381..a1b2b8b8f8 100644
--- a/doc/angle_class2.txt
+++ b/doc/angle_class2.txt
@@ -29,8 +29,13 @@ the equilibrium bond lengths.
 
 See "(Sun)"_#Sun for a description of the COMPASS class2 force field.
 
-For this style, coefficients for the Ea formula can be specified in
-the input script or data file.  These are the 4 coefficients:
+Coefficients for the Ea, Ebb, and Eba formulas must be defined for
+each angle type via the "bond_coeff"_bond_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.
+
+These are the 4 coefficients for the Ea formula:
 
 theta0 (degrees)
 K2 (energy/radian^2)
@@ -40,19 +45,26 @@ K4 (energy/radian^4) :ul
 Theta0 is specified in degrees, but LAMMPS converts it to radians
 internally; hence the units of the various K are in per-radian.
 
-Coefficients for the Ebb and Eba formulas can only be specified in the
-data file.
-
-For the Ebb formula, the coefficients are listed under a "BondBond
-Coeffs" heading and each line lists 3 coefficients:
+For the Ebb formula, each line in a "bond_coeff"_bond_coeff.html
+command in the input script lists 4 coefficients, the first of which
+is "bb" to indicate they are BondBond coefficients.  In a data file,
+these coefficients can be listed under a "BondBond Coeffs" heading and
+you must leave out the "bb", i.e. only list 3 coefficients after the
+angle type.
 
+bb
 M (energy/distance^2)
 r1 (distance)
 r2 (distance) :ul
 
-For the Eba formula, the coefficients are listed under a "BondAngle
-Coeffs" heading and each line lists 4 coefficients:
+For the Eba formula, each line in a "bond_coeff"_bond_coeff.html
+command in the input script lists 5 coefficients, the first of which
+is "ba" to indicate they are BondAngle coefficients.  In a data file,
+these coefficients can be listed under a "BondAngle Coeffs" heading
+and you must leave out the "ba", i.e. only list 4 coefficients after
+the angle type.
 
+ba
 N1 (energy/distance^2)
 N2 (energy/distance^2)
 r1 (distance)
diff --git a/doc/dihedral_class2.html b/doc/dihedral_class2.html
index f5a7bace10..92418d6f2b 100644
--- a/doc/dihedral_class2.html
+++ b/doc/dihedral_class2.html
@@ -35,8 +35,14 @@ bond lengths.
 </P>
 <P>See <A HREF = "#Sun">(Sun)</A> for a description of the COMPASS class2 force field.
 </P>
-<P>For this style, coefficients for the Ed formula can be specified in
-either the input script or data file.  These are the 6 coefficients:
+<P>Coefficients for the Ed, Embt, Eebt, Eat, Eaat, and Ebb13 formulas
+must be defined for each dihedral type via the
+<A HREF = "dihedral_coeff.html">dihedral_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>
+<P>These are the 6 coefficients for the Ed formula:
 </P>
 <UL><LI>K1 (energy)
 <LI>phi1 (degrees)
@@ -45,21 +51,30 @@ either the input script or data file.  These are the 6 coefficients:
 <LI>K3 (energy)
 <LI>phi3 (degrees) 
 </UL>
-<P>Coefficients for all the other formulas can only be specified in the
-data file.
+<P>For the Embt formula, each line in a
+<A HREF = "dihedral_coeff.html">dihedral_coeff</A> command in the input script lists
+5 coefficients, the first of which is "mbt" to indicate they are
+MiddleBondTorsion coefficients.  In a data file, these coefficients
+should be listed under a "MiddleBondTorsion Coeffs" heading and you
+must leave out the "mbt", i.e. only list 4 coefficients after the
+dihedral type.
 </P>
-<P>For the Embt formula, the coefficients are listed under a
-"MiddleBondTorsion Coeffs" heading and each line lists 4 coefficients:
-</P>
-<UL><LI>A1 (energy/distance)
+<UL><LI>mbt
+<LI>A1 (energy/distance)
 <LI>A2 (energy/distance)
 <LI>A3 (energy/distance)
 <LI>r2 (distance) 
 </UL>
-<P>For the Eebt formula, the coefficients are listed under a
-"EndBondTorsion Coeffs" heading and each line lists 8 coefficients:
+<P>For the Eebt formula, each line in a
+<A HREF = "dihedral_coeff.html">dihedral_coeff</A> command in the input script lists
+9 coefficients, the first of which is "ebt" to indicate they are
+EndBondTorsion coefficients.  In a data file, these coefficients
+should be listed under a "EndBondTorsion Coeffs" heading and you must
+leave out the "ebt", i.e. only list 8 coefficients after the dihedral
+type.
 </P>
-<UL><LI>B1 (energy/distance)
+<UL><LI>ebt
+<LI>B1 (energy/distance)
 <LI>B2 (energy/distance)
 <LI>B3 (energy/distance)
 <LI>C1 (energy/distance)
@@ -68,10 +83,15 @@ data file.
 <LI>r1 (distance)
 <LI>r3 (distance) 
 </UL>
-<P>For the Eat formula, the coefficients are listed under a "AngleTorsion
-Coeffs" heading and each line lists 8 coefficients:
+<P>For the Eat formula, each line in a
+<A HREF = "dihedral_coeff.html">dihedral_coeff</A> command in the input script lists
+9 coefficients, the first of which is "at" to indicate they are
+AngleTorsion coefficients.  In a data file, these coefficients should
+be listed under a "AngleTorsion Coeffs" heading and you must leave out
+the "at", i.e. only list 8 coefficients after the dihedral type.
 </P>
-<UL><LI>D1 (energy/radian)
+<UL><LI>at
+<LI>D1 (energy/radian)
 <LI>D2 (energy/radian)
 <LI>D3 (energy/radian)
 <LI>E1 (energy/radian)
@@ -84,20 +104,31 @@ Coeffs" heading and each line lists 8 coefficients:
 to radians internally; hence the units of D and E are in
 energy/radian.
 </P>
-<P>For the Eaat formula, the coefficients are listed under a
-"AngleAngleTorsion Coeffs" heading and each line lists 3 coefficients:
+<P>For the Eaat formula, each line in a
+<A HREF = "dihedral_coeff.html">dihedral_coeff</A> command in the input script lists
+4 coefficients, the first of which is "aat" to indicate they are
+AngleAngleTorsion coefficients.  In a data file, these coefficients
+should be listed under a "AngleAngleTorsion Coeffs" heading and you
+must leave out the "aat", i.e. only list 3 coefficients after the
+dihedral type.
 </P>
-<UL><LI>M (energy/radian^2)
+<UL><LI>aat
+<LI>M (energy/radian^2)
 <LI>theta1 (degrees)
 <LI>theta2 (degrees) 
 </UL>
 <P>Theta1 and theta2 are specified in degrees, but LAMMPS converts them
 to radians internally; hence the units of M are in energy/radian^2.
 </P>
-<P>For the Ebb13 formula, the coefficients are listed under a "BondBond13
-Coeffs" heading and each line lists 3 coefficients:
+<P>For the Ebb13 formula, each line in a
+<A HREF = "dihedral_coeff.html">dihedral_coeff</A> command in the input script lists
+4 coefficients, the first of which is "bb13" to indicate they are
+BondBond13 coefficients.  In a data file, these coefficients should be
+listed under a "BondBond13 Coeffs" heading and you must leave out the
+"bb13", i.e. only list 3 coefficients after the dihedral type.
 </P>
-<UL><LI>N (energy/distance^2)
+<UL><LI>bb13
+<LI>N (energy/distance^2)
 <LI>r1 (distance)
 <LI>r3 (distance) 
 </UL>
diff --git a/doc/dihedral_class2.txt b/doc/dihedral_class2.txt
index 002896a3bd..4f83ce6c58 100644
--- a/doc/dihedral_class2.txt
+++ b/doc/dihedral_class2.txt
@@ -32,8 +32,14 @@ bond lengths.
 
 See "(Sun)"_#Sun for a description of the COMPASS class2 force field.
 
-For this style, coefficients for the Ed formula can be specified in
-either the input script or data file.  These are the 6 coefficients:
+Coefficients for the Ed, Embt, Eebt, Eat, Eaat, and Ebb13 formulas
+must be defined for each dihedral type via the
+"dihedral_coeff"_dihedral_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.
+
+These are the 6 coefficients for the Ed formula:
 
 K1 (energy)
 phi1 (degrees)
@@ -42,20 +48,29 @@ phi2 (degrees)
 K3 (energy)
 phi3 (degrees) :ul
 
-Coefficients for all the other formulas can only be specified in the
-data file.
-
-For the Embt formula, the coefficients are listed under a
-"MiddleBondTorsion Coeffs" heading and each line lists 4 coefficients:
+For the Embt formula, each line in a
+"dihedral_coeff"_dihedral_coeff.html command in the input script lists
+5 coefficients, the first of which is "mbt" to indicate they are
+MiddleBondTorsion coefficients.  In a data file, these coefficients
+should be listed under a "MiddleBondTorsion Coeffs" heading and you
+must leave out the "mbt", i.e. only list 4 coefficients after the
+dihedral type.
 
+mbt
 A1 (energy/distance)
 A2 (energy/distance)
 A3 (energy/distance)
 r2 (distance) :ul
 
-For the Eebt formula, the coefficients are listed under a
-"EndBondTorsion Coeffs" heading and each line lists 8 coefficients:
+For the Eebt formula, each line in a
+"dihedral_coeff"_dihedral_coeff.html command in the input script lists
+9 coefficients, the first of which is "ebt" to indicate they are
+EndBondTorsion coefficients.  In a data file, these coefficients
+should be listed under a "EndBondTorsion Coeffs" heading and you must
+leave out the "ebt", i.e. only list 8 coefficients after the dihedral
+type.
 
+ebt
 B1 (energy/distance)
 B2 (energy/distance)
 B3 (energy/distance)
@@ -65,9 +80,14 @@ C3 (energy/distance)
 r1 (distance)
 r3 (distance) :ul
 
-For the Eat formula, the coefficients are listed under a "AngleTorsion
-Coeffs" heading and each line lists 8 coefficients:
+For the Eat formula, each line in a
+"dihedral_coeff"_dihedral_coeff.html command in the input script lists
+9 coefficients, the first of which is "at" to indicate they are
+AngleTorsion coefficients.  In a data file, these coefficients should
+be listed under a "AngleTorsion Coeffs" heading and you must leave out
+the "at", i.e. only list 8 coefficients after the dihedral type.
 
+at
 D1 (energy/radian)
 D2 (energy/radian)
 D3 (energy/radian)
@@ -81,9 +101,15 @@ Theta1 and theta2 are specified in degrees, but LAMMPS converts them
 to radians internally; hence the units of D and E are in
 energy/radian.
 
-For the Eaat formula, the coefficients are listed under a
-"AngleAngleTorsion Coeffs" heading and each line lists 3 coefficients:
+For the Eaat formula, each line in a
+"dihedral_coeff"_dihedral_coeff.html command in the input script lists
+4 coefficients, the first of which is "aat" to indicate they are
+AngleAngleTorsion coefficients.  In a data file, these coefficients
+should be listed under a "AngleAngleTorsion Coeffs" heading and you
+must leave out the "aat", i.e. only list 3 coefficients after the
+dihedral type.
 
+aat
 M (energy/radian^2)
 theta1 (degrees)
 theta2 (degrees) :ul
@@ -91,9 +117,14 @@ theta2 (degrees) :ul
 Theta1 and theta2 are specified in degrees, but LAMMPS converts them
 to radians internally; hence the units of M are in energy/radian^2.
 
-For the Ebb13 formula, the coefficients are listed under a "BondBond13
-Coeffs" heading and each line lists 3 coefficients:
+For the Ebb13 formula, each line in a
+"dihedral_coeff"_dihedral_coeff.html command in the input script lists
+4 coefficients, the first of which is "bb13" to indicate they are
+BondBond13 coefficients.  In a data file, these coefficients should be
+listed under a "BondBond13 Coeffs" heading and you must leave out the
+"bb13", i.e. only list 3 coefficients after the dihedral type.
 
+bb13
 N (energy/distance^2)
 r1 (distance)
 r3 (distance) :ul
diff --git a/doc/improper_class2.html b/doc/improper_class2.html
index ccd5f828da..dd3e2cdb11 100644
--- a/doc/improper_class2.html
+++ b/doc/improper_class2.html
@@ -50,13 +50,13 @@ this is not required.
 </P>
 <P>See <A HREF = "#Sun">(Sun)</A> for a description of the COMPASS class2 force field.
 </P>
-<P>The following coefficients must be defined for each improper type via the
-<A HREF = "improper_coeff.html">improper_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>Coefficients for the Ei and Eaa formulas must be defined for each
+improper type via the <A HREF = "improper_coeff.html">improper_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>
-<P>For this style, coefficients for the Ei formula can be specified in
-either the input script or data file.  These are the 2 coefficients:
+<P>These are the 2 coefficients for the Ei formula:
 </P>
 <UL><LI>K (energy/radian^2)
 <LI>X0 (degrees) 
@@ -64,11 +64,15 @@ either the input script or data file.  These are the 2 coefficients:
 <P>X0 is specified in degrees, but LAMMPS converts it to radians
 internally; hence the units of K are in energy/radian^2.
 </P>
-<P>Coefficients for the Eaa formula can only be specified in the data
-file.  For the Eaa formula, the coefficients are listed under a
-"AngleAngle Coeffs" heading and each line lists 6 coefficients:
+<P>For the Eaa formula, each line in a
+<A HREF = "improper_coeff.html">improper_coeff</A> command in the input script lists
+7 coefficients, the first of which is "aa" to indicate they are
+AngleAngle coefficients.  In a data file, these coefficients should be
+listed under a "AngleAngle Coeffs" heading and you must leave out the
+"aa", i.e. only list 6 coefficients after the improper type.
 </P>
-<UL><LI>M1 (energy/distance)
+<UL><LI>aa
+<LI>M1 (energy/distance)
 <LI>M2 (energy/distance)
 <LI>M3 (energy/distance)
 <LI>theta1 (degrees)
diff --git a/doc/improper_class2.txt b/doc/improper_class2.txt
index 634075f217..c38cf6750f 100644
--- a/doc/improper_class2.txt
+++ b/doc/improper_class2.txt
@@ -47,13 +47,13 @@ this is not required.
 
 See "(Sun)"_#Sun for a description of the COMPASS class2 force field.
 
-The following coefficients must be defined for each improper type via the
-"improper_coeff"_improper_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:
+Coefficients for the Ei and Eaa formulas must be defined for each
+improper type via the "improper_coeff"_improper_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.
 
-For this style, coefficients for the Ei formula can be specified in
-either the input script or data file.  These are the 2 coefficients:
+These are the 2 coefficients for the Ei formula:
 
 K (energy/radian^2)
 X0 (degrees) :ul
@@ -61,10 +61,14 @@ X0 (degrees) :ul
 X0 is specified in degrees, but LAMMPS converts it to radians
 internally; hence the units of K are in energy/radian^2.
 
-Coefficients for the Eaa formula can only be specified in the data
-file.  For the Eaa formula, the coefficients are listed under a
-"AngleAngle Coeffs" heading and each line lists 6 coefficients:
+For the Eaa formula, each line in a
+"improper_coeff"_improper_coeff.html command in the input script lists
+7 coefficients, the first of which is "aa" to indicate they are
+AngleAngle coefficients.  In a data file, these coefficients should be
+listed under a "AngleAngle Coeffs" heading and you must leave out the
+"aa", i.e. only list 6 coefficients after the improper type.
 
+aa
 M1 (energy/distance)
 M2 (energy/distance)
 M3 (energy/distance)