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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11122 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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50
doc/create_box.html
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@ -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>

47
doc/create_box.txt
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@ -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

11
doc/read_data.html
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@ -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

11
doc/read_data.txt
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@ -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