From c8ea97951347dd0a4e8bffa53eb6e20df574e8cc Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Tue, 17 Dec 2013 15:12:58 +0000
Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11122
 f3b2605a-c512-4ea7-a41b-209d697bcdaa

---
 doc/create_box.html | 50 +++++++++++++++++++++++++++++++++++++++++----
 doc/create_box.txt  | 47 +++++++++++++++++++++++++++++++++++++-----
 doc/read_data.html  | 11 +++++++---
 doc/read_data.txt   | 11 +++++++---
 4 files changed, 104 insertions(+), 15 deletions(-)

diff --git a/doc/create_box.html b/doc/create_box.html
index 235e2bc3ff..eaa8f42a2f 100644
--- a/doc/create_box.html
+++ b/doc/create_box.html
@@ -13,14 +13,31 @@
 </H3>
 <P><B>Syntax:</B>
 </P>
-<PRE>create_box N region-ID 
+<PRE>create_box N region-ID keyword value ... 
 </PRE>
-<UL><LI>N = # of atom types to use in this simulation
+<UL><LI>N = # of atom types to use in this simulation 
+
 <LI>region-ID = ID of region to use as simulation domain 
+
+<LI>zero or more keyword/value pairs may be appended 
+
+<LI>keyword = <I>bond types</I> or <I>angle types</I> or <I>dihedral types</I> or <I>improper types</I> or <I>extra bond per atom</I> or <I>extra angle per atom</I> or <I>extra dihedral per atom</I> or <I>extra improper per atom</I> 
+
+<PRE>  <I>bond types</I> value = # of bond types
+  <I>angle types</I> value = # of angle types
+  <I>dihedral types</I> value = # of dihedral types
+  <I>improper types</I> value = # of improper types
+  <I>extra bond per atom</I> value = # of bonds per atom
+  <I>extra angle per atom</I> value = # of angles per atom
+  <I>extra dihedral per atom</I> value = # of dihedrals per atom
+  <I>extra improper per atom</I> value = # of impropers per atom 
+</PRE>
+
 </UL>
 <P><B>Examples:</B>
 </P>
-<PRE>create_box 2 mybox 
+<PRE>create_box 2 mybox
+create_box 2 mybox "bond types" 2 "extra bond per atom" 1 
 </PRE>
 <P><B>Description:</B>
 </P>
@@ -84,6 +101,30 @@ boundary conditions (see the <A HREF = "boundary.html">boundary</A> command), a
 (mostly empty) box may cause a parallel simulation to lose atoms the
 first time that LAMMPS shrink-wraps the box around the atoms.
 </P>
+<HR>
+
+<P>The optional keywords can be used to create a system that allows for
+bond (angle, dihedral, improper) interactions to be added later,
+similar to the way they would be specified in a data file.  Note that
+if these keywords are not used, then the create_box command creates an
+atomic (non-molecular) simulation that does not allow bonds between
+pairs of atoms to be defined or a <A HREF = "bond_style.html">bond potential</A> to
+be specified.
+</P>
+<P>As an example, see the examples/deposit/in.deposit.mol script, which
+deposits molecules onto a substrate.  Initially there are no molecules
+in the system, but they are added later by the <A HREF = "fix_deposit.html">fix
+deposit</A> command.  The create_box command is used in
+the script with the "bond types" and "extra bond per atom" keywords to
+allow molecules with bonds to be later added to the system.
+</P>
+<P>The keywords that can be specified are listed above.  Note that each
+is a multi-word keyword which must be specified as a single argument.
+This means the keyword must be enclosed in quotes, as in the example
+above.
+</P>
+<HR>
+
 <P><B>Restrictions:</B>
 </P>
 <P>An <A HREF = "atom_style.html">atom_style</A> and <A HREF = "region.html">region</A> must have
@@ -91,7 +132,8 @@ been previously defined to use this command.
 </P>
 <P><B>Related commands:</B>
 </P>
-<P><A HREF = "create_atoms.html">create_atoms</A>, <A HREF = "region.html">region</A>
+<P><A HREF = "read_data.html">read_data</A>, <A HREF = "create_atoms.html">create_atoms</A>,
+<A HREF = "region.html">region</A>
 </P>
 <P><B>Default:</B> none
 </P>
diff --git a/doc/create_box.txt b/doc/create_box.txt
index 08fce9e6b0..365df94f62 100644
--- a/doc/create_box.txt
+++ b/doc/create_box.txt
@@ -10,14 +10,26 @@ create_box command :h3
 
 [Syntax:]
 
-create_box N region-ID :pre
+create_box N region-ID keyword value ... :pre
 
-N = # of atom types to use in this simulation
-region-ID = ID of region to use as simulation domain :ul
+N = # of atom types to use in this simulation :ulb,l
+region-ID = ID of region to use as simulation domain :l
+zero or more keyword/value pairs may be appended :l
+keyword = {bond types} or {angle types} or {dihedral types} or {improper types} or {extra bond per atom} or {extra angle per atom} or {extra dihedral per atom} or {extra improper per atom} :l
+  {bond types} value = # of bond types
+  {angle types} value = # of angle types
+  {dihedral types} value = # of dihedral types
+  {improper types} value = # of improper types
+  {extra bond per atom} value = # of bonds per atom
+  {extra angle per atom} value = # of angles per atom
+  {extra dihedral per atom} value = # of dihedrals per atom
+  {extra improper per atom} value = # of impropers per atom :pre
+:ule
 
 [Examples:]
 
-create_box 2 mybox :pre
+create_box 2 mybox
+create_box 2 mybox "bond types" 2 "extra bond per atom" 1 :pre
 
 [Description:]
 
@@ -81,6 +93,30 @@ boundary conditions (see the "boundary"_boundary.html command), a huge
 (mostly empty) box may cause a parallel simulation to lose atoms the
 first time that LAMMPS shrink-wraps the box around the atoms.
 
+:line
+
+The optional keywords can be used to create a system that allows for
+bond (angle, dihedral, improper) interactions to be added later,
+similar to the way they would be specified in a data file.  Note that
+if these keywords are not used, then the create_box command creates an
+atomic (non-molecular) simulation that does not allow bonds between
+pairs of atoms to be defined or a "bond potential"_bond_style.html to
+be specified.
+
+As an example, see the examples/deposit/in.deposit.mol script, which
+deposits molecules onto a substrate.  Initially there are no molecules
+in the system, but they are added later by the "fix
+deposit"_fix_deposit.html command.  The create_box command is used in
+the script with the "bond types" and "extra bond per atom" keywords to
+allow molecules with bonds to be later added to the system.
+
+The keywords that can be specified are listed above.  Note that each
+is a multi-word keyword which must be specified as a single argument.
+This means the keyword must be enclosed in quotes, as in the example
+above.
+
+:line
+
 [Restrictions:]
 
 An "atom_style"_atom_style.html and "region"_region.html must have
@@ -88,6 +124,7 @@ been previously defined to use this command.
 
 [Related commands:]
 
-"create_atoms"_create_atoms.html, "region"_region.html
+"read_data"_read_data.html, "create_atoms"_create_atoms.html,
+"region"_region.html
 
 [Default:] none
diff --git a/doc/read_data.html b/doc/read_data.html
index 36685b4ab1..e2ed8ef618 100644
--- a/doc/read_data.html
+++ b/doc/read_data.html
@@ -103,6 +103,9 @@ is different than the default.
 <LI><I>dihedral types</I> = # of dihedral types in system
 <LI><I>improper types</I> = # of improper types in system
 <LI><I>extra bond per atom</I> = leave space for this many new bonds per atom
+<LI><I>extra angle per atom</I> = leave space for this many new angles per atom
+<LI><I>extra dihedral per atom</I> = leave space for this many new dihedrals per atom
+<LI><I>extra improper per atom</I> = leave space for this many new impropers per atom
 <LI><I>ellipsoids</I> = # of ellipsoids in system
 <LI><I>lines</I> = # of line segments in system
 <LI><I>triangles</I> = # of triangles in system
@@ -178,10 +181,12 @@ command).  When using "shrink-wrap" boundary conditions (see the
 a parallel simulation to lose atoms the first time that LAMMPS
 shrink-wraps the box around the atoms.
 </P>
-<P>The "extra bond per atom" setting should be used if new bonds will be
-added to the system when a simulation runs, e.g. by using the <A HREF = "fix_bond_create.html">fix
+<P>The "extra bond per atom" setting (angle, dihedral, improper) should
+be used if new bonds (angles, dihedrals, impropers) will be added to
+the system when a simulation runs, e.g. by using the <A HREF = "fix_bond_create.html">fix
 bond/create</A> command.  This will pre-allocate
-space in LAMMPS data structures for storing the new bonds.
+space in LAMMPS data structures for storing the new bonds (angles,
+dihedrals, impropers).
 </P>
 <P>The "ellipsoids" and "lines" and "triangles" and "bodies" settings are
 only used with <A HREF = "atom_style.html">atom_style ellipsoid or line or tri or
diff --git a/doc/read_data.txt b/doc/read_data.txt
index e56a62c68c..68f60f0289 100644
--- a/doc/read_data.txt
+++ b/doc/read_data.txt
@@ -97,6 +97,9 @@ is different than the default.
 {dihedral types} = # of dihedral types in system
 {improper types} = # of improper types in system
 {extra bond per atom} = leave space for this many new bonds per atom
+{extra angle per atom} = leave space for this many new angles per atom
+{extra dihedral per atom} = leave space for this many new dihedrals per atom
+{extra improper per atom} = leave space for this many new impropers per atom
 {ellipsoids} = # of ellipsoids in system
 {lines} = # of line segments in system
 {triangles} = # of triangles in system
@@ -172,10 +175,12 @@ command).  When using "shrink-wrap" boundary conditions (see the
 a parallel simulation to lose atoms the first time that LAMMPS
 shrink-wraps the box around the atoms.
 
-The "extra bond per atom" setting should be used if new bonds will be
-added to the system when a simulation runs, e.g. by using the "fix
+The "extra bond per atom" setting (angle, dihedral, improper) should
+be used if new bonds (angles, dihedrals, impropers) will be added to
+the system when a simulation runs, e.g. by using the "fix
 bond/create"_fix_bond_create.html command.  This will pre-allocate
-space in LAMMPS data structures for storing the new bonds.
+space in LAMMPS data structures for storing the new bonds (angles,
+dihedrals, impropers).
 
 The "ellipsoids" and "lines" and "triangles" and "bodies" settings are
 only used with "atom_style ellipsoid or line or tri or