git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@150 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/Section_commands.html

@@ -161,10 +161,10 @@ or restart file via the <A HREF = "read_data.html">read_data</A> or
 <A HREF = "read_restart.html">read_restart</A> commands.  These files can contain
 molecular topology information.  Or create atoms on a lattice (with no
 molecular topology), using these commands: <A HREF = "lattice.html">lattice</A>,
-<A HREF = "orient.html">orient</A>, <A HREF = "origin.html">origin</A>, <A HREF = "region.html">region</A>,
+<A HREF = "region.html">region</A>, <A HREF = "create_box.html">create_box</A>,
-<A HREF = "create_box.html">create_box</A>, <A HREF = "create_atoms.html">create_atoms</A>.  The
+<A HREF = "create_atoms.html">create_atoms</A>.  The entire set of atoms can be
-entire set of atoms can be duplicated to make a larger simulation
+duplicated to make a larger simulation using the
-using the <A HREF = "replicate.html">replicate</A> command.
+<A HREF = "replicate.html">replicate</A> command.
 </P>
 <P>(3) Settings
 </P>
@@ -222,9 +222,9 @@ in the command's documentation.
 <P>Atom definition:
 </P>
 <P><A HREF = "create_atoms.html">create_atoms</A>, <A HREF = "create_box.html">create_box</A>,
-<A HREF = "lattice.html">lattice</A>, <A HREF = "orient.html">orient</A>, <A HREF = "origin.html">origin</A>,
+<A HREF = "lattice.html">lattice</A>, <A HREF = "read_data.html">read_data</A>,
-<A HREF = "read_data.html">read_data</A>, <A HREF = "read_restart.html">read_restart</A>,
+<A HREF = "read_restart.html">read_restart</A>, <A HREF = "region.html">region</A>,
-<A HREF = "region.html">region</A>, <A HREF = "replicate.html">replicate</A>
+<A HREF = "replicate.html">replicate</A>
 </P>
 <P>Force fields:
 </P>
@@ -293,13 +293,12 @@ in the command's documentation.
 <TR ALIGN="center"><TD ><A HREF = "dump.html">dump</A></TD><TD ><A HREF = "dump_modify.html">dump_modify</A></TD><TD ><A HREF = "echo.html">echo</A></TD><TD ><A HREF = "fix.html">fix</A></TD><TD ><A HREF = "fix_modify.html">fix_modify</A></TD><TD ><A HREF = "group.html">group</A></TD></TR>
 <TR ALIGN="center"><TD ><A HREF = "improper_coeff.html">improper_coeff</A></TD><TD ><A HREF = "improper_style.html">improper_style</A></TD><TD ><A HREF = "include.html">include</A></TD><TD ><A HREF = "jump.html">jump</A></TD><TD ><A HREF = "kspace_modify.html">kspace_modify</A></TD><TD ><A HREF = "kspace_style.html">kspace_style</A></TD></TR>
 <TR ALIGN="center"><TD ><A HREF = "label.html">label</A></TD><TD ><A HREF = "lattice.html">lattice</A></TD><TD ><A HREF = "log.html">log</A></TD><TD ><A HREF = "mass.html">mass</A></TD><TD ><A HREF = "minimize.html">minimize</A></TD><TD ><A HREF = "min_modify.html">min_modify</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "min_style.html">min_style</A></TD><TD ><A HREF = "neigh_modify.html">neigh_modify</A></TD><TD ><A HREF = "neighbor.html">neighbor</A></TD><TD ><A HREF = "newton.html">newton</A></TD><TD ><A HREF = "next.html">next</A></TD><TD ><A HREF = "orient.html">orient</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "min_style.html">min_style</A></TD><TD ><A HREF = "neigh_modify.html">neigh_modify</A></TD><TD ><A HREF = "neighbor.html">neighbor</A></TD><TD ><A HREF = "newton.html">newton</A></TD><TD ><A HREF = "next.html">next</A></TD><TD ><A HREF = "pair_coeff.html">pair_coeff</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "origin.html">origin</A></TD><TD ><A HREF = "pair_coeff.html">pair_coeff</A></TD><TD ><A HREF = "pair_modify.html">pair_modify</A></TD><TD ><A HREF = "pair_style.html">pair_style</A></TD><TD ><A HREF = "pair_write.html">pair_write</A></TD><TD ><A HREF = "print.html">print</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "pair_modify.html">pair_modify</A></TD><TD ><A HREF = "pair_style.html">pair_style</A></TD><TD ><A HREF = "pair_write.html">pair_write</A></TD><TD ><A HREF = "print.html">print</A></TD><TD ><A HREF = "processors.html">processors</A></TD><TD ><A HREF = "read_data.html">read_data</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "processors.html">processors</A></TD><TD ><A HREF = "read_data.html">read_data</A></TD><TD ><A HREF = "read_restart.html">read_restart</A></TD><TD ><A HREF = "region.html">region</A></TD><TD ><A HREF = "replicate.html">replicate</A></TD><TD ><A HREF = "reset_timestep.html">reset_timestep</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "read_restart.html">read_restart</A></TD><TD ><A HREF = "region.html">region</A></TD><TD ><A HREF = "replicate.html">replicate</A></TD><TD ><A HREF = "reset_timestep.html">reset_timestep</A></TD><TD ><A HREF = "restart.html">restart</A></TD><TD ><A HREF = "run.html">run</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "restart.html">restart</A></TD><TD ><A HREF = "run.html">run</A></TD><TD ><A HREF = "run_style.html">run_style</A></TD><TD ><A HREF = "set.html">set</A></TD><TD ><A HREF = "shell.html">shell</A></TD><TD ><A HREF = "special_bonds.html">special_bonds</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "run_style.html">run_style</A></TD><TD ><A HREF = "set.html">set</A></TD><TD ><A HREF = "shell.html">shell</A></TD><TD ><A HREF = "special_bonds.html">special_bonds</A></TD><TD ><A HREF = "temp_modify.html">temp_modify</A></TD><TD ><A HREF = "temper.html">temper</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "temp_modify.html">temp_modify</A></TD><TD ><A HREF = "temper.html">temper</A></TD><TD ><A HREF = "temperature.html">temperature</A></TD><TD ><A HREF = "thermo.html">thermo</A></TD><TD ><A HREF = "thermo_modify.html">thermo_modify</A></TD><TD ><A HREF = "thermo_style.html">thermo_style</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "temperature.html">temperature</A></TD><TD ><A HREF = "thermo.html">thermo</A></TD><TD ><A HREF = "thermo_modify.html">thermo_modify</A></TD><TD ><A HREF = "thermo_style.html">thermo_style</A></TD><TD ><A HREF = "timestep.html">timestep</A></TD><TD ><A HREF = "undump.html">undump</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "timestep.html">timestep</A></TD><TD ><A HREF = "undump.html">undump</A></TD><TD ><A HREF = "unfix.html">unfix</A></TD><TD ><A HREF = "units.html">units</A></TD><TD ><A HREF = "variable.html">variable</A></TD><TD ><A HREF = "velocity.html">velocity</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "unfix.html">unfix</A></TD><TD ><A HREF = "units.html">units</A></TD><TD ><A HREF = "variable.html">variable</A></TD><TD ><A HREF = "velocity.html">velocity</A></TD><TD ><A HREF = "write_restart.html">write_restart</A> 
-<TR ALIGN="center"><TD ><A HREF = "write_restart.html">write_restart</A> 
 </TD></TR></TABLE></DIV>
 
 <P>Fix styles.  See the <A HREF = "fix.html">fix</A> command for one-line descriptions
@@ -312,8 +311,8 @@ or click on the command itself for a full description:
 <TR ALIGN="center"><TD ><A HREF = "fix_nve.html">fix nve</A></TD><TD ><A HREF = "fix_nve_gran.html">fix nve/gran</A></TD><TD ><A HREF = "fix_nvt.html">fix nvt</A></TD><TD ><A HREF = "fix_orient_fcc.html">fix orient/fcc</A></TD><TD ><A HREF = "fix_planeforce.html">fix planeforce</A></TD><TD ><A HREF = "fix_poems.html">fix poems</A></TD></TR>
 <TR ALIGN="center"><TD ><A HREF = "fix_print.html">fix print</A></TD><TD ><A HREF = "fix_rdf.html">fix rdf</A></TD><TD ><A HREF = "fix_recenter.html">fix recenter</A></TD><TD ><A HREF = "fix_rigid.html">fix rigid</A></TD><TD ><A HREF = "fix_setforce.html">fix setforce</A></TD><TD ><A HREF = "fix_shake.html">fix shake</A></TD></TR>
 <TR ALIGN="center"><TD ><A HREF = "fix_spring.html">fix spring</A></TD><TD ><A HREF = "fix_spring_rg.html">fix spring/rg</A></TD><TD ><A HREF = "fix_spring_self.html">fix spring/self</A></TD><TD ><A HREF = "fix_temp_rescale.html">fix temp/rescale</A></TD><TD ><A HREF = "fix_tmd.html">fix tmd</A></TD><TD ><A HREF = "fix_uniaxial.html">fix uniaxial</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "fix_vcm.html">fix vcm</A></TD><TD ><A HREF = "fix_viscous.html">fix viscous</A></TD><TD ><A HREF = "fix_volume_rescale.html">fix volume/rescale</A></TD><TD ><A HREF = "fix_wall_gran.html">fix wall/gran</A></TD><TD ><A HREF = "fix_wall_lj93.html">fix wall/lj93</A></TD><TD ><A HREF = "fix_wall_reflect.html">fix wall/reflect</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "fix_vcm.html">fix vcm</A></TD><TD ><A HREF = "fix_viscous.html">fix viscous</A></TD><TD ><A HREF = "fix_volume_rescale.html">fix volume/rescale</A></TD><TD ><A HREF = "fix_wall_gran.html">fix wall/gran</A></TD><TD ><A HREF = "fix_wall_lj93.html">fix wall/lj93</A></TD><TD ><A HREF = "fix_wall_lj126.html">fix wall/lj126</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "fix_wiggle.html">fix wiggle</A> 
+<TR ALIGN="center"><TD ><A HREF = "fix_wall_reflect.html">fix wall/reflect</A></TD><TD ><A HREF = "fix_wiggle.html">fix wiggle</A> 
 </TD></TR></TABLE></DIV>
 
 <P>Pair styles.  See the <A HREF = "pair_style.html">pair_style</A> command for an

doc/Section_commands.txt

@@ -158,10 +158,10 @@ or restart file via the "read_data"_read_data.html or
 "read_restart"_read_restart.html commands.  These files can contain
 molecular topology information.  Or create atoms on a lattice (with no
 molecular topology), using these commands: "lattice"_lattice.html,
-"orient"_orient.html, "origin"_origin.html, "region"_region.html,
+"region"_region.html, "create_box"_create_box.html,
-"create_box"_create_box.html, "create_atoms"_create_atoms.html.  The
+"create_atoms"_create_atoms.html.  The entire set of atoms can be
-entire set of atoms can be duplicated to make a larger simulation
+duplicated to make a larger simulation using the
-using the "replicate"_replicate.html command.
+"replicate"_replicate.html command.
 
 (3) Settings
 
@@ -219,9 +219,9 @@ Initialization:
 Atom definition:
 
 "create_atoms"_create_atoms.html, "create_box"_create_box.html,
-"lattice"_lattice.html, "orient"_orient.html, "origin"_origin.html,
+"lattice"_lattice.html, "read_data"_read_data.html,
-"read_data"_read_data.html, "read_restart"_read_restart.html,
+"read_restart"_read_restart.html, "region"_region.html,
-"region"_region.html, "replicate"_replicate.html
+"replicate"_replicate.html
 
 Force fields:
 
@@ -324,8 +324,6 @@ in the command's documentation.
 "neighbor"_neighbor.html,
 "newton"_newton.html,
 "next"_next.html,
-"orient"_orient.html,
-"origin"_origin.html,
 "pair_coeff"_pair_coeff.html,
 "pair_modify"_pair_modify.html,
 "pair_style"_pair_style.html,
@@ -401,6 +399,7 @@ or click on the command itself for a full description:
 "fix volume/rescale"_fix_volume_rescale.html,
 "fix wall/gran"_fix_wall_gran.html,
 "fix wall/lj93"_fix_wall_lj93.html,
+"fix wall/lj126"_fix_wall_lj126.html,
 "fix wall/reflect"_fix_wall_reflect.html,
 "fix wiggle"_fix_wiggle.html :tb(c=6,ea=c)
 

doc/create_atoms.html

@@ -13,41 +13,62 @@
 </H3>
 <P><B>Syntax:</B>
 </P>
-<PRE>create_atoms type region-ID 
+<PRE>create_atoms type keyword values ... 
 </PRE>
 <UL><LI>type = atom type (1-N) of atoms to create on a lattice 
-<LI>region-ID = ID of region each atom will belong to (optional) 
+
+<LI>zero or more keyword/value pairs may be appended 
+
+<LI>keyword = <I>region</I> or <I>basis</I> 
+
+<PRE>  <I>region</I> value = region-ID
+    region-ID = atoms will only be created if contained in the region
+  <I>basis</I> values = M itype
+    M = which basis atom
+    itype = atom type (1-N) to assign to the basis atom 
+</PRE>
+
 </UL>
 <P><B>Examples:</B>
 </P>
-<PRE>create_atoms 1 regsphere
+<PRE>create_atoms 1
-create_atoms 3 
+create_atoms 3 region regsphere
+create_atoms 1 basis 2 5 
 </PRE>
 <P><B>Description:</B>
 </P>
 <P>This command creates atoms on a lattice as an alternative to reading
 in their coordinates via a <A HREF = "read_data.html">read_data</A> or
 <A HREF = "read_restart.html">read_restart</A> command.  A simulation box must
-already exist, which is created with the <A HREF = "create_box.html">create_box</A>
+already exist, which is typically created via the
-command.
+<A HREF = "create_box.html">create_box</A> command.
 </P>
 <P>Before using this command, a lattice must be defined using the
 <A HREF = "lattice.html">lattice</A> command.  If a region is not specified, the
 create_atoms command fills the entire simulation box with atoms on the
-lattice.  If a region is specified, then the geometric volume is
+lattice.  If a region is specified (see the <A HREF = "region.html">region</A>
-filled that is inside the simulation box and is also consistent with
+command), then the geometric volume is filled that is inside the
-the region volume.
+simulation box and is also consistent with the region volume.  Note
+that a region can be specified so that its "volume" is either inside
+or outside a geometric boundary.
 </P>
-<P>The <I>create_atoms</I> command can be used multiple times with different
+<P>The <A HREF = "lattice.html">lattice</A> command specifies one or more basis atoms
-lattice orientations to create grain boundaries.  Used in conjunction
+in each unit cell.  By default, when created, all basis atoms are
-with the <A HREF = "delete_atoms.html">delete_atoms</A> command, reasonably complex
+assigned the argument <I>type</I> as their atom type.  The keyword <I>basis</I>
-geometries can be created.  The <I>create_atoms</I> command can also be
+can be used to override the default for one or more basis atoms and
-used to add atoms to a system previously read in from a data or
+assign them a different atom type.
-restart file.  In all these cases, care should be taken to insure that
-new atoms do not overlap existing atoms inappropriately.
 </P>
-<P>Created atoms are assigned the specified atom type and a velocity of
+<P>By using the create_atoms command multiple times (interleaved with
-0.0.
+<A HREF = "lattice.html">lattice</A> commands specifying different orientations),
+grain boundaries can be created.  Using the create_atoms command in
+conjunction with the <A HREF = "delete_atoms.html">delete_atoms</A> command,
+reasonably complex geometries can be created.  The create_atoms
+command can also be used to add atoms to a system previously read in
+from a data or restart file.  In all these cases, care should be taken
+to insure that new atoms do not overlap existing atoms
+inappropriately.
+</P>
+<P>Created atoms are assigned a velocity of 0.0.
 </P>
 <P><B>Restrictions:</B>
 </P>
@@ -56,8 +77,7 @@ previously defined to use this command.
 </P>
 <P><B>Related commands:</B>
 </P>
-<P><A HREF = "lattice.html">lattice</A>, <A HREF = "orient.html">orient</A>, <A HREF = "origin.html">origin</A>,
+<P><A HREF = "lattice.html">lattice</A>, <A HREF = "region.html">region</A>, <A HREF = "create_box.html">create_box</A>,
-<A HREF = "region.html">region</A>, <A HREF = "create_box.html">create_box</A>,
 <A HREF = "read_data.html">read_data</A>, <A HREF = "read_restart.html">read_restart</A>
 </P>
 <P><B>Default:</B> none

doc/create_atoms.txt

@@ -10,41 +10,58 @@ create_atoms command :h3
 
 [Syntax:]
 
-create_atoms type region-ID :pre
+create_atoms type keyword values ... :pre
 
-type = atom type (1-N) of atoms to create on a lattice
+type = atom type (1-N) of atoms to create on a lattice :ulb,l
-region-ID = ID of region each atom will belong to (optional) :ul
+zero or more keyword/value pairs may be appended :l
+keyword = {region} or {basis} :l
+  {region} value = region-ID
+    region-ID = atoms will only be created if contained in the region
+  {basis} values = M itype
+    M = which basis atom
+    itype = atom type (1-N) to assign to the basis atom :pre
+:ule
 
 [Examples:]
 
-create_atoms 1 regsphere
+create_atoms 1
-create_atoms 3 :pre
+create_atoms 3 region regsphere
+create_atoms 1 basis 2 5 :pre
 
 [Description:]
 
 This command creates atoms on a lattice as an alternative to reading
 in their coordinates via a "read_data"_read_data.html or
 "read_restart"_read_restart.html command.  A simulation box must
-already exist, which is created with the "create_box"_create_box.html
+already exist, which is typically created via the
-command.
+"create_box"_create_box.html command.
 
 Before using this command, a lattice must be defined using the
 "lattice"_lattice.html command.  If a region is not specified, the
 create_atoms command fills the entire simulation box with atoms on the
-lattice.  If a region is specified, then the geometric volume is
+lattice.  If a region is specified (see the "region"_region.html
-filled that is inside the simulation box and is also consistent with
+command), then the geometric volume is filled that is inside the
-the region volume.
+simulation box and is also consistent with the region volume.  Note
+that a region can be specified so that its "volume" is either inside
+or outside a geometric boundary.
 
-The {create_atoms} command can be used multiple times with different
+The "lattice"_lattice.html command specifies one or more basis atoms
-lattice orientations to create grain boundaries.  Used in conjunction
+in each unit cell.  By default, when created, all basis atoms are
-with the "delete_atoms"_delete_atoms.html command, reasonably complex
+assigned the argument {type} as their atom type.  The keyword {basis}
-geometries can be created.  The {create_atoms} command can also be
+can be used to override the default for one or more basis atoms and
-used to add atoms to a system previously read in from a data or
+assign them a different atom type.
-restart file.  In all these cases, care should be taken to insure that
-new atoms do not overlap existing atoms inappropriately.
 
-Created atoms are assigned the specified atom type and a velocity of
+By using the create_atoms command multiple times (interleaved with
-0.0.
+"lattice"_lattice.html commands specifying different orientations),
+grain boundaries can be created.  Using the create_atoms command in
+conjunction with the "delete_atoms"_delete_atoms.html command,
+reasonably complex geometries can be created.  The create_atoms
+command can also be used to add atoms to a system previously read in
+from a data or restart file.  In all these cases, care should be taken
+to insure that new atoms do not overlap existing atoms
+inappropriately.
+
+Created atoms are assigned a velocity of 0.0.
 
 [Restrictions:]
 
@@ -53,8 +70,7 @@ previously defined to use this command.
 
 [Related commands:]
 
-"lattice"_lattice.html, "orient"_orient.html, "origin"_origin.html,
+"lattice"_lattice.html, "region"_region.html, "create_box"_create_box.html,
-"region"_region.html, "create_box"_create_box.html,
 "read_data"_read_data.html, "read_restart"_read_restart.html
 
 [Default:] none

doc/displace_atoms.html

@@ -58,9 +58,9 @@ those bounds will be moved the minimum (0.0) or maximum (5.0) amount.
 <P>Distance units for the displacement are determined by the setting of
 <I>box</I> or <I>lattice</I> for the <I>units</I> keyword.  <I>Box</I> means distance
 units as defined by the <A HREF = "units.html">units</A> command - e.g. Angstroms
-for <I>real</I> units.  <I>Lattice</I> means to use lattice spacings as defined
+for <I>real</I> units.  <I>Lattice</I> means distance units are in lattice
-by the <A HREF = "lattice.html">lattice</A> command.  The default is to use lattice
+spacings.  The <A HREF = "lattice.html">lattice</A> command must have been
-units.
+previously used to define the lattice spacing.
 </P>
 <P>Care should be taken not to move atoms on top of other atoms.  After
 the move, atoms are remapped to the periodic simulation box.  In
@@ -76,7 +76,9 @@ once they have been displaced.  This means that your system must be
 ready to perform a simulation before using this command (force fields
 setup, atom masses set, etc).
 </P>
-<P><B>Related commands:</B> none
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "lattice.html">lattice</A>
 </P>
 <P><B>Default:</B>
 </P>

doc/displace_atoms.txt

@@ -50,9 +50,9 @@ those bounds will be moved the minimum (0.0) or maximum (5.0) amount.
 Distance units for the displacement are determined by the setting of
 {box} or {lattice} for the {units} keyword.  {Box} means distance
 units as defined by the "units"_units.html command - e.g. Angstroms
-for {real} units.  {Lattice} means to use lattice spacings as defined
+for {real} units.  {Lattice} means distance units are in lattice
-by the "lattice"_lattice.html command.  The default is to use lattice
+spacings.  The "lattice"_lattice.html command must have been
-units.
+previously used to define the lattice spacing.
 
 Care should be taken not to move atoms on top of other atoms.  After
 the move, atoms are remapped to the periodic simulation box.  In
@@ -68,7 +68,9 @@ once they have been displaced.  This means that your system must be
 ready to perform a simulation before using this command (force fields
 setup, atom masses set, etc).
 
-[Related commands:] none
+[Related commands:]
+
+"lattice"_lattice.html
 
 [Default:]
 

doc/fix_indent.html

@@ -94,10 +94,11 @@ each run.
 to define the indenter.  A <I>box</I> value selects standard distance units
 as defined by the <A HREF = "units.html">units</A> command, e.g. Angstroms for units
 = real or metal.  A <I>lattice</I> value means the distance units are in
-cubic lattice spacings.  The <A HREF = "lattice.html">lattice</A> command must first
+lattice spacings.  The <A HREF = "lattice.html">lattice</A> command must have been
-be used to define a lattice.  Note that the units choice affects not
+previously used to define the lattice spacing.  Note that the units
-only the indenter's physical geometry, but also its velocity and force
+choice affects not only the indenter's physical geometry, but also its
-constant since they are defined in terms of distance as well.
+velocity and force constant since they are defined in terms of
+distance as well.
 </P>
 <P>This fix supports the <A HREF = "fix_modify.html">fix_modify</A> options for
 <I>thermo</I> and <I>energy</I>.  The former will print the contribution the fix

doc/fix_indent.txt

@@ -85,10 +85,11 @@ The {units} keyword determines the meaning of the distance units used
 to define the indenter.  A {box} value selects standard distance units
 as defined by the "units"_units.html command, e.g. Angstroms for units
 = real or metal.  A {lattice} value means the distance units are in
-cubic lattice spacings.  The "lattice"_lattice.html command must first
+lattice spacings.  The "lattice"_lattice.html command must have been
-be used to define a lattice.  Note that the units choice affects not
+previously used to define the lattice spacing.  Note that the units
-only the indenter's physical geometry, but also its velocity and force
+choice affects not only the indenter's physical geometry, but also its
-constant since they are defined in terms of distance as well.
+velocity and force constant since they are defined in terms of
+distance as well.
 
 This fix supports the "fix_modify"_fix_modify.html options for
 {thermo} and {energy}.  The former will print the contribution the fix

doc/fix_recenter.html

@@ -65,10 +65,11 @@ could be shifted.
 </P>
 <P>If the <I>units</I> keyword is set to <I>box</I>, then the distance units of
 x,y,z are defined by the <A HREF = "units.html">units</A> command - e.g. Angstroms
-for <I>real</I> units.  <I>Lattice</I> means to use lattice spacings as defined
+for <I>real</I> units.  A <I>lattice</I> value means the distance units are in
-by the <A HREF = "lattice.html">lattice</A> command.  <I>Fraction</I> means a fractional
+lattice spacings.  The <A HREF = "lattice.html">lattice</A> command must have been
-distance between the lo/hi box boundaries, e.g. 0.5 = middle of the
+previously used to define the lattice spacing.  A <I>fraction</I> value
-box.  The default is to use lattice units.
+means a fractional distance between the lo/hi box boundaries, e.g. 0.5
+= middle of the box.  The default is to use lattice units.
 </P>
 <P>Note that the <A HREF = "velocity.html">velocity</A> command can be used to create
 velocities with zero aggregate linear and/or angular momentum.

doc/fix_recenter.txt

@@ -57,10 +57,11 @@ could be shifted.
 
 If the {units} keyword is set to {box}, then the distance units of
 x,y,z are defined by the "units"_units.html command - e.g. Angstroms
-for {real} units.  {Lattice} means to use lattice spacings as defined
+for {real} units.  A {lattice} value means the distance units are in
-by the "lattice"_lattice.html command.  {Fraction} means a fractional
+lattice spacings.  The "lattice"_lattice.html command must have been
-distance between the lo/hi box boundaries, e.g. 0.5 = middle of the
+previously used to define the lattice spacing.  A {fraction} value
-box.  The default is to use lattice units.
+means a fractional distance between the lo/hi box boundaries, e.g. 0.5
+= middle of the box.  The default is to use lattice units.
 
 Note that the "velocity"_velocity.html command can be used to create
 velocities with zero aggregate linear and/or angular momentum.

doc/lattice.html

@@ -13,14 +13,31 @@
 </H3>
 <P><B>Syntax:</B>
 </P>
-<PRE>lattice style value 
+<PRE>lattice style scale keyword values ... 
 </PRE>
-<UL><LI>style = <I>none</I> or <I>sc</I> or <I>bcc</I> or <I>fcc</I> or <I>sq</I> or <I>sq2</I> or <I>hex</I> or <I>diamond</I> 
+<UL><LI>style = <I>none</I> or <I>sc</I> or <I>bcc</I> or <I>fcc</I> or <I>diamond</I> or         <I>sq</I> or <I>sq2</I> or <I>hex</I> or <I>user</I> 
 
-<PRE>  <I>none</I> value = none
+<LI>scale = scale factor between lattice and simulation box 
+
+<PRE>  for style <I>none</I>:
+    scale is not specified (nor any optional args)
   for all other styles:
-    value = reduced density (for LJ units)
+    scale = reduced density rho* (for LJ units)
-    value = cubic lattice constant in Angstroms (for real or metal units) 
+    scale = lattice constant in Angstroms (for real or metal units) 
+</PRE>
+<LI>zero or more keyword/value pairs may be appended 
+
+<LI>keyword = <I>origin</I> or <I>orient</I> or <I>a1</I> or <I>a2</I> or <I>a3</I> or <I>basis</I> 
+
+<PRE>  <I>origin</I> values = x y z
+    x,y,z = fractions of a unit cell (0 <= x,y,z < 1)
+  <I>orient</I> values = dim i j k
+    dim = <I>x</I> or <I>y</I> or <I>z</I>
+    i,j,k = integer lattice directions
+  <I>a1</I>,<I>a2</I>,<I>a3</I> values = x y z
+    x,y,z = primitive vector components that define unit cell
+  <I>basis</I> values = x y z
+    x,y,z = fractional coords of a basis atom (0 <= x,y,z < 1) 
 </PRE>
 
 </UL>
@@ -28,47 +45,176 @@
 </P>
 <PRE>lattice fcc 3.52
 lattice hex 0.85
+lattice sq 0.8 origin 0.0 0.5 0.0 orient x 1 1 0 orient y -1 1 0
+lattice user 3.52 a1 1.0 0.0 0.0 a2 0.5 1.0 0.0 a3 0.0 0.0 0.5 &
+                  basis 0.0 0.0 0.0 basis 0.5 0.5 0.5
 lattice none 
 </PRE>
 <P><B>Description:</B>
 </P>
-<P>Define a lattice type and lattice constant.  This is required before
+<P>Define a lattice for use by other commands.  In LAMMPS, a lattice is
-using a commands that (optionally) use the lattice, such as
+simply a set of points in space, determined by a unit cell with basis
-<A HREF = "create_atoms.html">create_atoms</A> or <A HREF = "region.html">region</A>.  The lattice
+atoms, that is replicated infinitely in all dimensions.  The arguments
-type must be consistent with the dimension of the simulation - see the
+of the lattice command can be used to define a wide variety of
-<A HREF = "dimension.html">dimension</A> command.  Styles <I>sc</I> or <I>bcc</I> or <I>fcc</I> or
+crystallographic lattices.
-<I>diamond</I> are for 3d problems.  Styles <I>sq</I> or <I>sq2</I> or <I>hex</I> are for
-2d problems.  Lattices of style <I>fcc</I>, <I>bcc</I>, <I>hex</I>, or <I>diamond</I> are
-described in any solid-state physics text.  A <I>sc</I> lattice is simple
-cubic, with atoms at the corners of a cube.  A <I>sq</I> lattice is square
-with atoms at the corners of a square.  A <I>sq2</I> lattice is a <I>sq</I>
-lattice with an additional atom at the center of the square.
 </P>
-<P>For unit style <I>real</I> or <I>metal</I>, the specified value is the cubic
+<P>A lattice is used by LAMMPS in two ways.  First, the
-lattice constant in Angstroms.  For unit style <I>lj</I>, the value is the
+<A HREF = "create_atoms.hmtl">create_atoms</A> command creates atoms on the lattice
-reduced density (rho*) which LAMMPS converts into a cubic lattice
+points inside the simulation box.  Note that the
-constant.  For 3d problems, the relationship "rho* = rho sigma^3" is
+<A HREF = "create_atoms.html">create_atoms</A> command allows different atom types
-used for the conversion, where rho = N/V with V = the volume of the
+to be assigned to different basis atoms of the lattice.  Second, the
-cubic cell and N = 4 for <I>fcc</I>, 2 for <I>bcc</I>, 1 for <I>sc</I>, and 8 for
+lattice spacing in the x,y,z dimensions implied by the lattice, can be
-<I>diamond</I> lattices.  For 2d problems, the relationship "rho* = rho
+used by other commands as distance units (e.g. <A HREF = "region.html">region</A>
-sigma^2" is used for the conversion, where N = 2 for <I>sq2</I> or <I>hex</I>
+and <A HREF = "velocity.html">velocity</A>), which are often convenient when the
-and 1 for <I>sq</I>.  In the hex case, the unit cell is actually
+underlying problem geometry is atoms on a lattice.
-rectangular; it is extended by a factor of sqrt(3) in the y-dimension.
 </P>
-<P>The command "lattice none" can be used to turn off the lattice
+<P>The lattice style must be consistent with the dimension of the
-setting.  Any command that attempts to use a lattice constant will
+simulation - see the <A HREF = "dimension.html">dimension</A> command.  Styles <I>sc</I>
-then generate an error.
+or <I>bcc</I> or <I>fcc</I> or <I>diamond</I> are for 3d problems.  Styles <I>sq</I> or
+<I>sq2</I> or <I>hex</I> are for 2d problems.  Style <I>user</I> can be used for
+either 2d or 3d problems.
 </P>
-<P><B>Restrictions:</B> none
+<P>A lattice consists of a unit cell, a set of basis atoms within that
+cell, and a set of transformation parameters (scale, origin, orient)
+that map the unit cell into the simulation box.  The vectors a1,a2,a3
+are the edge vectors of the unit cell.  This is the nomenclature for
+"primitive" vectors in solid-state crytallography, but in LAMMPS the
+unit cell they determine does not have to be a "primitive cell" of
+minimum volume.
+</P>
+<HR>
+
+<P>Lattices of style <I>sc</I>, <I>fcc</I>, <I>bcc</I>, and <I>diamond</I> are 3d lattices
+that define a cubic unit cell with edge length = 1.0.  This means a1 =
+1.0 0.0 0.0, a2 = 0.0 1.0 0.0, and a3 = 0.0 0.0 1.0.  The placement of
+the basis atoms within the unit cell are described in any solid-state
+physics text.  A <I>sc</I> lattice has 1 basis atom at the
+lower-left-bottom corner of the cube.  A <I>bcc</I> lattice has 2 basis
+atoms, one at the corner and one at the center of the cube.  A <I>fcc</I>
+lattice has 4 basis atoms, one at the corner and 3 at the cube face
+centers.  A <I>diamond</I> lattice has 8 basis atoms.
+</P>
+<P>Lattices of style <I>sq</I> and <I>sq2</I> are 2d lattices that define a square
+unit cell with edge length = 1.0.  This means a1 = 1.0 0.0 0.0 and a2
+= 0.0 1.0 0.0.  A <I>sq</I> lattice has 1 basis atom at the lower-left
+corner of the square.  A <I>sq2</I> lattice has 2 basis atoms, one at the
+corner and one at the center of the square.  A <I>hex</I> style is also a
+2d lattice, but the unit cell is rectangular, with a1 = 1.0 0.0 0.0
+and a2 = 0.0 sqrt(3.0) 0.0.  It has 2 basis atoms, one at the corner
+and one at the center of the rectangle.
+</P>
+<P>A lattice of style <I>user</I> allows you to specify a1, a2, a3, and a list
+of basis atoms to put in the unit cell.  By default, a1,a2,a3 are 3
+orthogonal unit vectors (edges of a unit cube).  But you can specify
+them to be of any length and non-orthogonal to each other, so that
+they describe a tilted parallelepiped.  Via the <I>basis</I> keyword you
+add atoms, one at a time, to the unit cell.  Its arguments are
+fractional coordinates (0.0 <= x,y,z < 1.0), so that a value of 0.5
+means a position half-way across the unit cell in that dimension.
+</P>
+<HR>
+
+<P>This sub-section discusses the arguments that determine how the
+idealized unit cell is transformed into a lattice of points within the
+simulation box with desired spacings.
+</P>
+<P>The <I>scale</I> argument determines how the size of the unit cell will be
+scaled when mapping it into the simulation box.  I.e. it determines a
+multiplicative factor to apply to the unit cell, to convert it to a
+lattice of the desired size and distance units in the simulation box.
+The meaning of the <I>scale</I> argument depends on the <A HREF = "unit.html">units</A>
+being used in your simulation.
+</P>
+<P>For unit style <I>real</I> or <I>metal</I>, the scale argument is in Angstroms.
+For example, if the unit cell is a unit cube with edge length 1.0,
+setting scale = 3.52 would create a cubic lattice with a spacing of
+3.52 Angstroms.
+</P>
+<P>For unit style <I>lj</I>, the scale argument is the Lennard-Jones reduced
+density, typically written as rho*.  LAMMPS converts this value into
+the multiplicative factor via the formula "factor^dim = rho/rho*",
+where rho = N/V with V = the volume of the lattice unit cell and N =
+the number of basis atoms in the unit cell (described below), and dim
+= 2 or 3 for the dimensionality of the simulation.  Effectively, this
+means that if LJ particles of size sigma = 1.0 are used in the
+simulation, the lattice of particles will be at the desired reduced
+density.
+</P>
+<P>The <I>origin</I> option specifies how the unit cell will be shifted or
+translated when mapping it into the simulation box.  The x,y,z values
+are fractional values (0.0 <= x,y,z < 1.0) meaning shift the lattice
+by a fraction of the lattice spacing in each dimension.  The meaning
+of "lattice spacing" is discussed below.
+</P>
+<P>The <I>orient</I> option specifies how the unit cell will be rotated when
+mapping it into the simulation box.  The <I>dim</I> argument is one of the
+3 coordinate axes in the simulation box.  The other 3 arguments are
+the crystallographic direction in the lattice that you want to orient
+along that axis, specified as integers.  E.g. "orient x 2 1 0" means
+the x-axis in the simulation box will be the [210] lattice
+direction.  The 3 lattice directions you specify must be mutually
+orthogonal and obey the right-hand rule, i.e. (X cross Y) points in
+the Z direction.
+</P>
+<HR>
+
+<P>Several LAMMPS commands have the option to use distance units that are
+inferred from "lattice spacings" in the x,y,z directions.  E.g. the
+<A HREF = "region.html">region</A> command can create a block of size 10x20x20,
+where 10 means 10 lattice spacings in the x direction.
+</P>
+<P>These lattice spacings are computed by LAMMPS in the following way.  A
+unit cell of the lattice is mapped into the simulation box (scaled,
+shifted, rotated), so that it now has (perhaps) a modified shape and
+orientation.  The lattice spacing in X is defined as the difference
+between the min/max extent of the x coordinates of the 8 corner points
+of the modified unit cell.  Similarly, the Y and Z lattice spacings
+are defined as the min/max of the y and z coordinates.
+</P>
+<P>Note that if the unit cell has axis-aligned edges (a1,a2,a3) and is
+not rotated (via the <I>orient</I> keyword), then the lattice spacings in
+each dimension are simply the scale factor (descibed above) multiplied
+by the length of a1,a2,a3.  Thus a <I>hex</I> style lattice with a scale
+factor of 3.0 Angstroms, would have a lattice spacing of 3.0 in x and
+3*sqrt(3.0) in y.
+</P>
+<P>For unit cells with a more general shape or when a rotation is
+applied, the lattice spacing is less intuitive.  But regardless, the
+values of the computed lattice spacings are printed by LAMMPS, so
+their effect in commands that use the spacings should be decipherable.
+</P>
+<HR>
+
+<P>The command "lattice none" can be used to turn off a previous lattice
+definition.  Any command that attempts to use the lattice directly
+(<A HREF = "create_atoms.html">create_atoms</A>) or associated lattice spacings will
+then generate an error.  No additional arguments need be used with
+"lattice none".
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>The <I>a1,a2,a3,basis</I> keywords can only be used with style <I>user</I>.
+</P>
+<P>For lattices oriented at an angle or with a non-orthognal unit cell,
+care must be taken when using the <A HREF = "region.html">region</A> and
+<A HREF = "create_atoms.html">create_atoms</A> commands to create a periodic system.
+If the box size is not chosen appropriately, the system may not
+actually be periodic, and atoms may overlap incorretly at the faces of
+the simulation box.
 </P>
 <P><B>Related commands:</B>
 </P>
-<P><A HREF = "dimension.html">dimension</A>, <A HREF = "orient.html">orient</A>,
+<P><A HREF = "dimension.html">dimension</A>, <A HREF = "create_atoms.html">create_atoms</A>,
-<A HREF = "origin.html">origin</A>, <A HREF = "create_atoms.html">create_atoms</A>,
 <A HREF = "region.html">region</A>
 </P>
 <P><B>Default:</B>
 </P>
 <PRE>lattice none 
 </PRE>
+<P>For other lattice styles, the option defaults are origin = 0.0 0.0
+0.0, orient = x 1 0 0, orient = y 0 1 0, orient = z 0 0 1, a1 = 1.0
+0.0 0.0, a2 = 0.0 1.0 0.0, and a3 = 0.0 0.0 1.0.
+</P>
 </HTML>

doc/lattice.txt

@@ -10,58 +10,201 @@ lattice command :h3
 
 [Syntax:]
 
-lattice style value :pre
+lattice style scale keyword values ... :pre
 
-style = {none} or {sc} or {bcc} or {fcc} or {sq} or {sq2} or {hex} or {diamond} :ulb,l
+style = {none} or {sc} or {bcc} or {fcc} or {diamond} or \
-  {none} value = none
+        {sq} or {sq2} or {hex} or {user} :ulb,l
+scale = scale factor between lattice and simulation box :l
+  for style {none}:
+    scale is not specified (nor any optional args)
   for all other styles:
-    value = reduced density (for LJ units)
+    scale = reduced density rho* (for LJ units)
-    value = cubic lattice constant in Angstroms (for real or metal units) :pre
+    scale = lattice constant in Angstroms (for real or metal units) :pre
+zero or more keyword/value pairs may be appended :l
+keyword = {origin} or {orient} or {a1} or {a2} or {a3} or {basis} :l
+  {origin} values = x y z
+    x,y,z = fractions of a unit cell (0 <= x,y,z < 1)
+  {orient} values = dim i j k
+    dim = {x} or {y} or {z}
+    i,j,k = integer lattice directions
+  {a1},{a2},{a3} values = x y z
+    x,y,z = primitive vector components that define unit cell
+  {basis} values = x y z
+    x,y,z = fractional coords of a basis atom (0 <= x,y,z < 1) :pre
 :ule
 
 [Examples:]
 
 lattice fcc 3.52
 lattice hex 0.85
+lattice sq 0.8 origin 0.0 0.5 0.0 orient x 1 1 0 orient y -1 1 0
+lattice user 3.52 a1 1.0 0.0 0.0 a2 0.5 1.0 0.0 a3 0.0 0.0 0.5 &
+                  basis 0.0 0.0 0.0 basis 0.5 0.5 0.5
 lattice none :pre
 
 [Description:]
 
-Define a lattice type and lattice constant.  This is required before
+Define a lattice for use by other commands.  In LAMMPS, a lattice is
-using a commands that (optionally) use the lattice, such as
+simply a set of points in space, determined by a unit cell with basis
-"create_atoms"_create_atoms.html or "region"_region.html.  The lattice
+atoms, that is replicated infinitely in all dimensions.  The arguments
-type must be consistent with the dimension of the simulation - see the
+of the lattice command can be used to define a wide variety of
-"dimension"_dimension.html command.  Styles {sc} or {bcc} or {fcc} or
+crystallographic lattices.
-{diamond} are for 3d problems.  Styles {sq} or {sq2} or {hex} are for
-2d problems.  Lattices of style {fcc}, {bcc}, {hex}, or {diamond} are
-described in any solid-state physics text.  A {sc} lattice is simple
-cubic, with atoms at the corners of a cube.  A {sq} lattice is square
-with atoms at the corners of a square.  A {sq2} lattice is a {sq}
-lattice with an additional atom at the center of the square.
 
-For unit style {real} or {metal}, the specified value is the cubic
+A lattice is used by LAMMPS in two ways.  First, the
-lattice constant in Angstroms.  For unit style {lj}, the value is the
+"create_atoms"_create_atoms.hmtl command creates atoms on the lattice
-reduced density (rho*) which LAMMPS converts into a cubic lattice
+points inside the simulation box.  Note that the
-constant.  For 3d problems, the relationship "rho* = rho sigma^3" is
+"create_atoms"_create_atoms.html command allows different atom types
-used for the conversion, where rho = N/V with V = the volume of the
+to be assigned to different basis atoms of the lattice.  Second, the
-cubic cell and N = 4 for {fcc}, 2 for {bcc}, 1 for {sc}, and 8 for
+lattice spacing in the x,y,z dimensions implied by the lattice, can be
-{diamond} lattices.  For 2d problems, the relationship "rho* = rho
+used by other commands as distance units (e.g. "region"_region.html
-sigma^2" is used for the conversion, where N = 2 for {sq2} or {hex}
+and "velocity"_velocity.html), which are often convenient when the
-and 1 for {sq}.  In the hex case, the unit cell is actually
+underlying problem geometry is atoms on a lattice.
-rectangular; it is extended by a factor of sqrt(3) in the y-dimension.
 
-The command "lattice none" can be used to turn off the lattice
+The lattice style must be consistent with the dimension of the
-setting.  Any command that attempts to use a lattice constant will
+simulation - see the "dimension"_dimension.html command.  Styles {sc}
-then generate an error.
+or {bcc} or {fcc} or {diamond} are for 3d problems.  Styles {sq} or
+{sq2} or {hex} are for 2d problems.  Style {user} can be used for
+either 2d or 3d problems.
 
-[Restrictions:] none
+A lattice consists of a unit cell, a set of basis atoms within that
+cell, and a set of transformation parameters (scale, origin, orient)
+that map the unit cell into the simulation box.  The vectors a1,a2,a3
+are the edge vectors of the unit cell.  This is the nomenclature for
+"primitive" vectors in solid-state crytallography, but in LAMMPS the
+unit cell they determine does not have to be a "primitive cell" of
+minimum volume.
+
+:line
+
+Lattices of style {sc}, {fcc}, {bcc}, and {diamond} are 3d lattices
+that define a cubic unit cell with edge length = 1.0.  This means a1 =
+1.0 0.0 0.0, a2 = 0.0 1.0 0.0, and a3 = 0.0 0.0 1.0.  The placement of
+the basis atoms within the unit cell are described in any solid-state
+physics text.  A {sc} lattice has 1 basis atom at the
+lower-left-bottom corner of the cube.  A {bcc} lattice has 2 basis
+atoms, one at the corner and one at the center of the cube.  A {fcc}
+lattice has 4 basis atoms, one at the corner and 3 at the cube face
+centers.  A {diamond} lattice has 8 basis atoms.
+
+Lattices of style {sq} and {sq2} are 2d lattices that define a square
+unit cell with edge length = 1.0.  This means a1 = 1.0 0.0 0.0 and a2
+= 0.0 1.0 0.0.  A {sq} lattice has 1 basis atom at the lower-left
+corner of the square.  A {sq2} lattice has 2 basis atoms, one at the
+corner and one at the center of the square.  A {hex} style is also a
+2d lattice, but the unit cell is rectangular, with a1 = 1.0 0.0 0.0
+and a2 = 0.0 sqrt(3.0) 0.0.  It has 2 basis atoms, one at the corner
+and one at the center of the rectangle.
+
+A lattice of style {user} allows you to specify a1, a2, a3, and a list
+of basis atoms to put in the unit cell.  By default, a1,a2,a3 are 3
+orthogonal unit vectors (edges of a unit cube).  But you can specify
+them to be of any length and non-orthogonal to each other, so that
+they describe a tilted parallelepiped.  Via the {basis} keyword you
+add atoms, one at a time, to the unit cell.  Its arguments are
+fractional coordinates (0.0 <= x,y,z < 1.0), so that a value of 0.5
+means a position half-way across the unit cell in that dimension.
+
+:line
+
+This sub-section discusses the arguments that determine how the
+idealized unit cell is transformed into a lattice of points within the
+simulation box with desired spacings.
+
+The {scale} argument determines how the size of the unit cell will be
+scaled when mapping it into the simulation box.  I.e. it determines a
+multiplicative factor to apply to the unit cell, to convert it to a
+lattice of the desired size and distance units in the simulation box.
+The meaning of the {scale} argument depends on the "units"_unit.html
+being used in your simulation.
+
+For unit style {real} or {metal}, the scale argument is in Angstroms.
+For example, if the unit cell is a unit cube with edge length 1.0,
+setting scale = 3.52 would create a cubic lattice with a spacing of
+3.52 Angstroms.
+
+For unit style {lj}, the scale argument is the Lennard-Jones reduced
+density, typically written as rho*.  LAMMPS converts this value into
+the multiplicative factor via the formula "factor^dim = rho/rho*",
+where rho = N/V with V = the volume of the lattice unit cell and N =
+the number of basis atoms in the unit cell (described below), and dim
+= 2 or 3 for the dimensionality of the simulation.  Effectively, this
+means that if LJ particles of size sigma = 1.0 are used in the
+simulation, the lattice of particles will be at the desired reduced
+density.
+
+The {origin} option specifies how the unit cell will be shifted or
+translated when mapping it into the simulation box.  The x,y,z values
+are fractional values (0.0 <= x,y,z < 1.0) meaning shift the lattice
+by a fraction of the lattice spacing in each dimension.  The meaning
+of "lattice spacing" is discussed below.
+
+The {orient} option specifies how the unit cell will be rotated when
+mapping it into the simulation box.  The {dim} argument is one of the
+3 coordinate axes in the simulation box.  The other 3 arguments are
+the crystallographic direction in the lattice that you want to orient
+along that axis, specified as integers.  E.g. "orient x 2 1 0" means
+the x-axis in the simulation box will be the \[210\] lattice
+direction.  The 3 lattice directions you specify must be mutually
+orthogonal and obey the right-hand rule, i.e. (X cross Y) points in
+the Z direction.
+
+:line
+
+Several LAMMPS commands have the option to use distance units that are
+inferred from "lattice spacings" in the x,y,z directions.  E.g. the
+"region"_region.html command can create a block of size 10x20x20,
+where 10 means 10 lattice spacings in the x direction.
+
+These lattice spacings are computed by LAMMPS in the following way.  A
+unit cell of the lattice is mapped into the simulation box (scaled,
+shifted, rotated), so that it now has (perhaps) a modified shape and
+orientation.  The lattice spacing in X is defined as the difference
+between the min/max extent of the x coordinates of the 8 corner points
+of the modified unit cell.  Similarly, the Y and Z lattice spacings
+are defined as the min/max of the y and z coordinates.
+
+Note that if the unit cell has axis-aligned edges (a1,a2,a3) and is
+not rotated (via the {orient} keyword), then the lattice spacings in
+each dimension are simply the scale factor (descibed above) multiplied
+by the length of a1,a2,a3.  Thus a {hex} style lattice with a scale
+factor of 3.0 Angstroms, would have a lattice spacing of 3.0 in x and
+3*sqrt(3.0) in y.
+
+For unit cells with a more general shape or when a rotation is
+applied, the lattice spacing is less intuitive.  But regardless, the
+values of the computed lattice spacings are printed by LAMMPS, so
+their effect in commands that use the spacings should be decipherable.
+
+:line
+
+The command "lattice none" can be used to turn off a previous lattice
+definition.  Any command that attempts to use the lattice directly
+("create_atoms"_create_atoms.html) or associated lattice spacings will
+then generate an error.  No additional arguments need be used with
+"lattice none".
+
+:line
+
+[Restrictions:]
+
+The {a1,a2,a3,basis} keywords can only be used with style {user}.
+
+For lattices oriented at an angle or with a non-orthognal unit cell,
+care must be taken when using the "region"_region.html and
+"create_atoms"_create_atoms.html commands to create a periodic system.
+If the box size is not chosen appropriately, the system may not
+actually be periodic, and atoms may overlap incorretly at the faces of
+the simulation box.
 
 [Related commands:]
 
-"dimension"_dimension.html, "orient"_orient.html,
+"dimension"_dimension.html, "create_atoms"_create_atoms.html,
-"origin"_origin.html, "create_atoms"_create_atoms.html,
 "region"_region.html
 
 [Default:]
 
 lattice none :pre
+
+For other lattice styles, the option defaults are origin = 0.0 0.0
+0.0, orient = x 1 0 0, orient = y 0 1 0, orient = z 0 0 1, a1 = 1.0
+0.0 0.0, a2 = 0.0 1.0 0.0, and a3 = 0.0 0.0 1.0.

doc/temperature.html

@@ -97,8 +97,9 @@ for coordinates (c1,c2) and velocities (vlo,vhi) defined for the
 <I>ramp</I> style.  A <I>box</I> value selects standard distance units as
 defined by the <A HREF = "units.html">units</A> command, e.g. Angstroms for units =
 real or metal.  A <I>lattice</I> value means the distance units are in
-cubic lattice spacings; e.g. lattice spacings / tau.  The
+lattice spacings; e.g. velocity = lattice spacings / tau.  The
-<A HREF = "lattice.html">lattice</A> command must first be used to define a lattice.
+<A HREF = "lattice.html">lattice</A> command must have been previously used to
+define the lattice spacing.
 </P>
 <P>LAMMPS defines a temperature with ID = <I>default</I> which computes a
 <I>full</I> style on the <I>all</I> group of atoms.  This is the temperature

doc/temperature.txt

@@ -87,8 +87,9 @@ for coordinates (c1,c2) and velocities (vlo,vhi) defined for the
 {ramp} style.  A {box} value selects standard distance units as
 defined by the "units"_units.html command, e.g. Angstroms for units =
 real or metal.  A {lattice} value means the distance units are in
-cubic lattice spacings; e.g. lattice spacings / tau.  The
+lattice spacings; e.g. velocity = lattice spacings / tau.  The
-"lattice"_lattice.html command must first be used to define a lattice.
+"lattice"_lattice.html command must have been previously used to
+define the lattice spacing.
 
 LAMMPS defines a temperature with ID = {default} which computes a
 {full} style on the {all} group of atoms.  This is the temperature