git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14972 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/html/Section_commands.html

@@ -335,7 +335,7 @@ commands need only be used if a non-default value is desired.</p>
 </ol>
 <p>Set parameters that need to be defined before atoms are created or
 read-in from a file.</p>
-<p>The relevant commands are <span class="xref doc">units</span>,
+<p>The relevant commands are <a class="reference internal" href="units.html"><span class="doc">units</span></a>,
 <a class="reference internal" href="dimension.html"><span class="doc">dimension</span></a>, <a class="reference internal" href="newton.html"><span class="doc">newton</span></a>,
 <a class="reference internal" href="processors.html"><span class="doc">processors</span></a>, <a class="reference internal" href="boundary.html"><span class="doc">boundary</span></a>,
 <a class="reference internal" href="atom_style.html"><span class="doc">atom_style</span></a>, <a class="reference internal" href="atom_modify.html"><span class="doc">atom_modify</span></a>.</p>
@@ -404,7 +404,7 @@ in the command&#8217;s documentation.</p>
 <p>Initialization:</p>
 <p><a class="reference internal" href="atom_modify.html"><span class="doc">atom_modify</span></a>, <a class="reference internal" href="atom_style.html"><span class="doc">atom_style</span></a>,
 <a class="reference internal" href="boundary.html"><span class="doc">boundary</span></a>, <a class="reference internal" href="dimension.html"><span class="doc">dimension</span></a>,
-<a class="reference internal" href="newton.html"><span class="doc">newton</span></a>, <a class="reference internal" href="processors.html"><span class="doc">processors</span></a>, <span class="xref doc">units</span></p>
+<a class="reference internal" href="newton.html"><span class="doc">newton</span></a>, <a class="reference internal" href="processors.html"><span class="doc">processors</span></a>, <a class="reference internal" href="units.html"><span class="doc">units</span></a></p>
 <p>Atom definition:</p>
 <p><a class="reference internal" href="create_atoms.html"><span class="doc">create_atoms</span></a>, <a class="reference internal" href="create_box.html"><span class="doc">create_box</span></a>,
 <a class="reference internal" href="lattice.html"><span class="doc">lattice</span></a>, <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a>,
@@ -575,7 +575,7 @@ in the command&#8217;s documentation.</p>
 <td><a class="reference internal" href="undump.html"><span class="doc">undump</span></a></td>
 <td><a class="reference internal" href="unfix.html"><span class="doc">unfix</span></a></td>
 </tr>
-<tr class="row-even"><td><span class="xref doc">units</span></td>
+<tr class="row-even"><td><a class="reference internal" href="units.html"><span class="doc">units</span></a></td>
 <td><a class="reference internal" href="variable.html"><span class="doc">variable</span></a></td>
 <td><a class="reference internal" href="velocity.html"><span class="doc">velocity</span></a></td>
 <td><a class="reference internal" href="write_coeff.html"><span class="doc">write_coeff</span></a></td>

doc/html/Section_howto.html

@@ -363,8 +363,8 @@ commands like <a class="reference internal" href="pair_coeff.html"><span class="
 <a class="reference internal" href="bond_coeff.html"><span class="doc">bond_coeff</span></a>.  See <a class="reference internal" href="Section_tools.html"><span class="doc">Section_tools</span></a>
 for additional tools that can use CHARMM or AMBER to assign force
 field coefficients and convert their output into LAMMPS input.</p>
-<p>See <a class="reference internal" href="pair_charmm.html#mackerell"><span class="std std-ref">(MacKerell)</span></a> for a description of the CHARMM force
+<p>See <a class="reference internal" href="special_bonds.html#mackerell"><span class="std std-ref">(MacKerell)</span></a> for a description of the CHARMM force
-field.  See <a class="reference internal" href="dihedral_charmm.html#cornell"><span class="std std-ref">(Cornell)</span></a> for a description of the AMBER force
+field.  See <a class="reference internal" href="special_bonds.html#cornell"><span class="std std-ref">(Cornell)</span></a> for a description of the AMBER force
 field.</p>
 <p>These style choices compute force field formulas that are consistent
 with common options in CHARMM or AMBER.  See each command&#8217;s
@@ -389,7 +389,7 @@ atoms involved in the bond, angle, or torsion terms. DREIDING has an
 <a class="reference internal" href="pair_hbond_dreiding.html"><span class="doc">explicit hydrogen bond term</span></a> to describe
 interactions involving a hydrogen atom on very electronegative atoms
 (N, O, F).</p>
-<p>See <a class="reference internal" href="pair_hbond_dreiding.html#mayo"><span class="std std-ref">(Mayo)</span></a> for a description of the DREIDING force field</p>
+<p>See <a class="reference internal" href="special_bonds.html#mayo"><span class="std std-ref">(Mayo)</span></a> for a description of the DREIDING force field</p>
 <p>These style choices compute force field formulas that are consistent
 with the DREIDING force field.  See each command&#8217;s
 documentation for the formula it computes.</p>
@@ -587,7 +587,7 @@ computations between frozen atoms by using this command:</p>
 <div class="section" id="tip3p-water-model">
 <span id="howto-7"></span><h2>6.7. TIP3P water model</h2>
 <p>The TIP3P water model as implemented in CHARMM
-<a class="reference internal" href="pair_charmm.html#mackerell"><span class="std std-ref">(MacKerell)</span></a> specifies a 3-site rigid water molecule with
+<a class="reference internal" href="special_bonds.html#mackerell"><span class="std std-ref">(MacKerell)</span></a> specifies a 3-site rigid water molecule with
 charges and Lennard-Jones parameters assigned to each of the 3 atoms.
 In LAMMPS the <a class="reference internal" href="fix_shake.html"><span class="doc">fix shake</span></a> command can be used to hold
 the two O-H bonds and the H-O-H angle rigid.  A bond style of
@@ -766,7 +766,7 @@ the partial charge assignemnts change:</p>
 <div class="line">H charge = 0.4238</div>
 <div class="line"><br /></div>
 </div>
-<p>See the <a class="reference internal" href="#berendsen"><span class="std std-ref">(Berendsen)</span></a> reference for more details on both
+<p>See the <a class="reference internal" href="fix_temp_berendsen.html#berendsen"><span class="std std-ref">(Berendsen)</span></a> reference for more details on both
 the SPC and SPC/E models.</p>
 <p>Wikipedia also has a nice article on <a class="reference external" href="http://en.wikipedia.org/wiki/Water_model">water models</a>.</p>
 <hr class="docutils" />
@@ -2731,7 +2731,7 @@ pairs as chunks.</p>
 model, representes induced dipoles by a pair of charges (the core atom
 and the Drude particle) connected by a harmonic spring. The Drude
 model has a number of features aimed at its use in molecular systems
-(<a class="reference internal" href="#lamoureux"><span class="std std-ref">Lamoureux and Roux</span></a>):</p>
+(<a class="reference internal" href="tutorial_drude.html#lamoureux"><span class="std std-ref">Lamoureux and Roux</span></a>):</p>
 <ul class="simple">
 <li>Thermostating of the additional degrees of freedom associated with the
 induced dipoles at very low temperature, in terms of the reduced

doc/html/Section_modify.html

@@ -254,7 +254,7 @@ parallel.  E.g. don’t accumulate a bunch of data on a single processor
 and analyze it.  You run the risk of seriously degrading the parallel
 efficiency.</li>
 <li>If your new feature reads arguments or writes output, make sure you
-follow the unit conventions discussed by the <span class="xref doc">units</span>
+follow the unit conventions discussed by the <a class="reference internal" href="units.html"><span class="doc">units</span></a>
 command.</li>
 <li>If you add something you think is truly useful and doesn&#8217;t impact
 LAMMPS performance when it isn&#8217;t used, send an email to the

doc/html/angle_charmm.html

@@ -155,7 +155,7 @@
 <p>with an additional Urey_Bradley term based on the distance <em>r</em> between
 the 1st and 3rd atoms in the angle.  K, theta0, Kub, and Rub are
 coefficients defined for each angle type.</p>
-<p>See <a class="reference internal" href="pair_charmm.html#mackerell"><span class="std std-ref">(MacKerell)</span></a> for a description of the CHARMM force
+<p>See <a class="reference internal" href="special_bonds.html#mackerell"><span class="std std-ref">(MacKerell)</span></a> for a description of the CHARMM force
 field.</p>
 <p>The following coefficients must be defined for each angle type via the
 <a class="reference internal" href="angle_coeff.html"><span class="doc">angle_coeff</span></a> command as in the example above, or in

doc/html/angle_class2.html

@@ -151,7 +151,7 @@
 <p>where Ea is the angle term, Ebb is a bond-bond term, and Eba is a
 bond-angle term.  Theta0 is the equilibrium angle and r1 and r2 are
 the equilibrium bond lengths.</p>
-<p>See <a class="reference internal" href="pair_class2.html#sun"><span class="std std-ref">(Sun)</span></a> for a description of the COMPASS class2 force field.</p>
+<p>See <a class="reference internal" href="pair_modify.html#sun"><span class="std std-ref">(Sun)</span></a> for a description of the COMPASS class2 force field.</p>
 <p>Coefficients for the Ea, Ebb, and Eba formulas must be defined for
 each angle type via the <a class="reference internal" href="angle_coeff.html"><span class="doc">angle_coeff</span></a> command as in
 the example above, or in the data file or restart files read by the

doc/html/angle_cosine_periodic.html

@@ -151,7 +151,7 @@ used for an octahedral complex and <em>n</em> = 3 might be used for a
 trigonal center:</p>
 <img alt="_images/angle_cosine_periodic.jpg" class="align-center" src="_images/angle_cosine_periodic.jpg" />
 <p>where C, B and n are coefficients defined for each angle type.</p>
-<p>See <a class="reference internal" href="pair_hbond_dreiding.html#mayo"><span class="std std-ref">(Mayo)</span></a> for a description of the DREIDING force field</p>
+<p>See <a class="reference internal" href="special_bonds.html#mayo"><span class="std std-ref">(Mayo)</span></a> for a description of the DREIDING force field</p>
 <p>The following coefficients must be defined for each angle type via the
 <a class="reference internal" href="angle_coeff.html"><span class="doc">angle_coeff</span></a> command as in the example above, or in
 the data file or restart files read by the <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a>

doc/html/bond_class2.html

@@ -147,7 +147,7 @@
 <p>The <em>class2</em> bond style uses the potential</p>
 <img alt="_images/bond_class2.jpg" class="align-center" src="_images/bond_class2.jpg" />
 <p>where r0 is the equilibrium bond distance.</p>
-<p>See <a class="reference internal" href="pair_class2.html#sun"><span class="std std-ref">(Sun)</span></a> for a description of the COMPASS class2 force field.</p>
+<p>See <a class="reference internal" href="pair_modify.html#sun"><span class="std std-ref">(Sun)</span></a> for a description of the COMPASS class2 force field.</p>
 <p>The following coefficients must be defined for each bond type via the
 <a class="reference internal" href="bond_coeff.html"><span class="doc">bond_coeff</span></a> command as in the example above, or in
 the data file or restart files read by the <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a>

doc/html/bond_fene.html

@@ -150,7 +150,7 @@
 <p>The <em>fene</em> bond style uses the potential</p>
 <img alt="_images/bond_fene.jpg" class="align-center" src="_images/bond_fene.jpg" />
 <p>to define a finite extensible nonlinear elastic (FENE) potential
-<a class="reference internal" href="bond_fene_expand.html#kremer"><span class="std std-ref">(Kremer)</span></a>, used for bead-spring polymer models.  The first
+<a class="reference internal" href="special_bonds.html#kremer"><span class="std std-ref">(Kremer)</span></a>, used for bead-spring polymer models.  The first
 term is attractive, the 2nd Lennard-Jones term is repulsive.  The
 first term extends to R0, the maximum extent of the bond.  The 2nd
 term is cutoff at 2^(1/6) sigma, the minimum of the LJ potential.</p>

doc/html/bond_fene_expand.html

@@ -147,7 +147,7 @@
 <p>The <em>fene/expand</em> bond style uses the potential</p>
 <img alt="_images/bond_fene_expand.jpg" class="align-center" src="_images/bond_fene_expand.jpg" />
 <p>to define a finite extensible nonlinear elastic (FENE) potential
-<a class="reference internal" href="#kremer"><span class="std std-ref">(Kremer)</span></a>, used for bead-spring polymer models.  The first
+<a class="reference internal" href="special_bonds.html#kremer"><span class="std std-ref">(Kremer)</span></a>, used for bead-spring polymer models.  The first
 term is attractive, the 2nd Lennard-Jones term is repulsive.</p>
 <p>The <em>fene/expand</em> bond style is similar to <em>fene</em> except that an extra
 shift factor of delta (positive or negative) is added to <em>r</em> to

doc/html/change_box.html

@@ -409,7 +409,7 @@ including this one, have been processed.</p>
 <hr class="docutils" />
 <p>The <em>units</em> keyword determines the meaning of the distance units used
 to define various arguments.  A <em>box</em> value selects standard distance
-units as defined by the <span class="xref doc">units</span> command, e.g. Angstroms for
+units as defined by the <a class="reference internal" href="units.html"><span class="doc">units</span></a> command, e.g. Angstroms for
 units = real or metal.  A <em>lattice</em> value means the distance units are
 in lattice spacings.  The <a class="reference internal" href="lattice.html"><span class="doc">lattice</span></a> command must have
 been previously used to define the lattice spacing.</p>

doc/html/compute_angle.html

@@ -158,7 +158,7 @@ number of sub_styles defined by the <a class="reference internal" href="angle_st
 or vector values from a compute as input.  See <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">this section</span></a> for an overview of LAMMPS output
 options.</p>
 <p>The vector values are &#8220;extensive&#8221; and will be in energy
-<span class="xref doc">units</span>.</p>
+<a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>

doc/html/compute_angle_local.html

@@ -181,7 +181,7 @@ keywords.  The vector or array can be accessed by any command that
 uses local values from a compute as input.  See <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">this section</span></a> for an overview of LAMMPS output
 options.</p>
 <p>The output for <em>theta</em> will be in degrees.  The output for <em>eng</em> will
-be in energy <span class="xref doc">units</span>.</p>
+be in energy <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>

doc/html/compute_angmom_chunk.html

@@ -191,7 +191,7 @@ These values can be accessed by any command that uses global array
 values from a compute as input.  See <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">Section_howto 15</span></a> for an overview of LAMMPS output
 options.</p>
 <p>The array values are &#8220;intensive&#8221;.  The array values will be in
-mass-velocity-distance <span class="xref doc">units</span>.</p>
+mass-velocity-distance <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>

doc/html/compute_body_local.html

@@ -196,7 +196,7 @@ specified, a local array is produced where the number of columns = the
 number of keywords.  The vector or array can be accessed by any
 command that uses local values from a compute as input.  See <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">this section</span></a> for an overview of LAMMPS output
 options.</p>
-<p>The <span class="xref doc">units</span> for output values depend on the body style.</p>
+<p>The <a class="reference internal" href="units.html"><span class="doc">units</span></a> for output values depend on the body style.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>

doc/html/compute_bond.html

@@ -158,7 +158,7 @@ These values can be used by any command that uses global scalar or
 vector values from a compute as input.  See <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">this section</span></a> for an overview of LAMMPS output
 options.</p>
 <p>The vector values are &#8220;extensive&#8221; and will be in energy
-<span class="xref doc">units</span>.</p>
+<a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>

doc/html/compute_bond_local.html

@@ -187,9 +187,9 @@ local array is produced where the number of columns = the number of
 keywords.  The vector or array can be accessed by any command that
 uses local values from a compute as input.  See <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">this section</span></a> for an overview of LAMMPS output
 options.</p>
-<p>The output for <em>dist</em> will be in distance <span class="xref doc">units</span>.  The
+<p>The output for <em>dist</em> will be in distance <a class="reference internal" href="units.html"><span class="doc">units</span></a>.  The
-output for <em>eng</em> will be in energy <span class="xref doc">units</span>.  The output for
+output for <em>eng</em> will be in energy <a class="reference internal" href="units.html"><span class="doc">units</span></a>.  The output for
-<em>force</em> will be in force <span class="xref doc">units</span>.</p>
+<em>force</em> will be in force <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>

doc/html/compute_chunk_atom.html

@@ -644,7 +644,7 @@ and <em>crmax</em>.</p>
 be used.  For non-orthogonal (triclinic) simulation boxes, only the
 <em>reduced</em> option may be used.</p>
 <p>A <em>box</em> value selects standard distance units as defined by the
-<span class="xref doc">units</span> command, e.g. Angstroms for units = real or metal.
+<a class="reference internal" href="units.html"><span class="doc">units</span></a> command, e.g. Angstroms for units = real or metal.
 A <em>lattice</em> value means the distance units are in lattice spacings.
 The <a class="reference internal" href="lattice.html"><span class="doc">lattice</span></a> command must have been previously used to
 define the lattice spacing.  A <em>reduced</em> value means normalized

doc/html/compute_com.html

@@ -165,7 +165,7 @@ accessed by indices 1-3 by any command that uses global vector values
 from a compute as input.  See <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">this section</span></a> for an overview of LAMMPS output
 options.</p>
 <p>The vector values are &#8220;intensive&#8221;.  The vector values will be in
-distance <span class="xref doc">units</span>.</p>
+distance <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>

doc/html/compute_com_chunk.html

@@ -189,7 +189,7 @@ values can be accessed by any command that uses global array values
 from a compute as input.  See <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">Section_howto 15</span></a> for an overview of LAMMPS output
 options.</p>
 <p>The array values are &#8220;intensive&#8221;.  The array values will be in
-distance <span class="xref doc">units</span>.</p>
+distance <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>

doc/html/compute_dihedral.html

@@ -157,7 +157,7 @@ number of sub_styles defined by the <a class="reference internal" href="dihedral
 or vector values from a compute as input.  See <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">this section</span></a> for an overview of LAMMPS output
 options.</p>
 <p>The vector values are &#8220;extensive&#8221; and will be in energy
-<span class="xref doc">units</span>.</p>
+<a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>

doc/html/compute_dipole_chunk.html

@@ -194,7 +194,7 @@ chunk. These values can be accessed by any command that uses global
 array values from a compute as input.  See <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">Section_howto 15</span></a> for an overview of LAMMPS output
 options.</p>
 <p>The array values are &#8220;intensive&#8221;.  The array values will be in
-dipole units, i.e. charge units times distance <span class="xref doc">units</span>.</p>
+dipole units, i.e. charge units times distance <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>

doc/html/compute_displace_atom.html

@@ -177,7 +177,7 @@ correctly with time=0 atom coordinates from the restart file.</p>
 accessed by indices 1-4 by any command that uses per-atom values from
 a compute as input.  See <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">Section_howto 15</span></a> for an overview of LAMMPS output
 options.</p>
-<p>The per-atom array values will be in distance <span class="xref doc">units</span>.</p>
+<p>The per-atom array values will be in distance <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>

doc/html/compute_dpd_atom.html

@@ -156,7 +156,7 @@ that uses per-particle values from a compute as input.  See
 <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">Section_howto15</span></a> for an overview of
 LAMMPS output options.</p>
 <p>The per-particle array values will be in energy (u_cond, u_mech) and
-temperature (dpdTheta) <span class="xref doc">units</span>.</p>
+temperature (dpdTheta) <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>

doc/html/compute_erotate_asphere.html

@@ -165,7 +165,7 @@ used by any command that uses a global scalar value from a compute as
 input.  See <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">Section_howto 15</span></a> for an
 overview of LAMMPS output options.</p>
 <p>The scalar value calculated by this compute is &#8220;extensive&#8221;.  The
-scalar value will be in energy <span class="xref doc">units</span>.</p>
+scalar value will be in energy <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>

doc/html/compute_erotate_rigid.html

@@ -163,7 +163,7 @@ uses a global scalar value from a compute as input.  See
 <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">Section_howto 15</span></a> for an overview of
 LAMMPS output options.</p>
 <p>The scalar value calculated by this compute is &#8220;extensive&#8221;.  The
-scalar value will be in energy <span class="xref doc">units</span>.</p>
+scalar value will be in energy <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>

doc/html/compute_erotate_sphere.html

@@ -160,7 +160,7 @@ used by any command that uses a global scalar value from a compute as
 input.  See <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">Section_howto 15</span></a> for an
 overview of LAMMPS output options.</p>
 <p>The scalar value calculated by this compute is &#8220;extensive&#8221;.  The
-scalar value will be in energy <span class="xref doc">units</span>.</p>
+scalar value will be in energy <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>

doc/html/compute_erotate_sphere_atom.html

@@ -162,7 +162,7 @@ in the specified compute group or for point particles with a radius =
 any command that uses per-atom values from a compute as input.  See
 <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">Section_howto 15</span></a> for an overview of
 LAMMPS output options.</p>
-<p>The per-atom vector values will be in energy <span class="xref doc">units</span>.</p>
+<p>The per-atom vector values will be in energy <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>

doc/html/compute_group_group.html

@@ -213,8 +213,8 @@ These values can be used by any command that uses global scalar or
 vector values from a compute as input.  See <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">this section</span></a> for an overview of LAMMPS output
 options.</p>
 <p>Both the scalar and vector values calculated by this compute are
-&#8220;extensive&#8221;.  The scalar value will be in energy <span class="xref doc">units</span>.
+&#8220;extensive&#8221;.  The scalar value will be in energy <a class="reference internal" href="units.html"><span class="doc">units</span></a>.
-The vector values will be in force <span class="xref doc">units</span>.</p>
+The vector values will be in force <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>

doc/html/compute_improper.html

@@ -157,7 +157,7 @@ number of sub_styles defined by the <a class="reference internal" href="improper
 or vector values from a compute as input.  See <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">this section</span></a> for an overview of LAMMPS output
 options.</p>
 <p>The vector values are &#8220;extensive&#8221; and will be in energy
-<span class="xref doc">units</span>.</p>
+<a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>

doc/html/compute_inertia_chunk.html

@@ -190,7 +190,7 @@ as listed above.  These values can be accessed by any command that
 uses global array values from a compute as input.  See <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">Section_howto 15</span></a> for an overview of LAMMPS output
 options.</p>
 <p>The array values are &#8220;intensive&#8221;.  The array values will be in
-mass*distance^2 <span class="xref doc">units</span>.</p>
+mass*distance^2 <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>

doc/html/compute_ke.html

@@ -166,7 +166,7 @@ can be used by any command that uses a global scalar value from a
 compute as input.  See <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">Section_howto 15</span></a>
 for an overview of LAMMPS output options.</p>
 <p>The scalar value calculated by this compute is &#8220;extensive&#8221;.  The
-scalar value will be in energy <span class="xref doc">units</span>.</p>
+scalar value will be in energy <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>

doc/html/compute_ke_atom.html

@@ -155,7 +155,7 @@ specified compute group.</p>
 any command that uses per-atom values from a compute as input.  See
 <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">Section_howto 15</span></a> for an overview of
 LAMMPS output options.</p>
-<p>The per-atom vector values will be in energy <span class="xref doc">units</span>.</p>
+<p>The per-atom vector values will be in energy <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>

doc/html/compute_ke_atom_eff.html

@@ -180,7 +180,7 @@ electrons) not in the specified compute group.</p>
 accessed by any command that uses per-atom computes as input.  See
 <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">Section_howto 15</span></a> for an overview of
 LAMMPS output options.</p>
-<p>The per-atom vector values will be in energy <span class="xref doc">units</span>.</p>
+<p>The per-atom vector values will be in energy <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>

doc/html/compute_ke_eff.html

@@ -181,7 +181,7 @@ used by any command that uses a global scalar value from a compute as
 input.  See <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">Section_howto 15</span></a> for an
 overview of LAMMPS output options.</p>
 <p>The scalar value calculated by this compute is &#8220;extensive&#8221;.  The
-scalar value will be in energy <span class="xref doc">units</span>.</p>
+scalar value will be in energy <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>

doc/html/compute_ke_rigid.html

@@ -161,7 +161,7 @@ rigid bodies).  This value can be used by any command that uses a
 global scalar value from a compute as input.  See <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">Section_howto 15</span></a> for an overview of LAMMPS output
 options.</p>
 <p>The scalar value calculated by this compute is &#8220;extensive&#8221;.  The
-scalar value will be in energy <span class="xref doc">units</span>.</p>
+scalar value will be in energy <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>

doc/html/compute_meso_e_atom.html

@@ -158,7 +158,7 @@ specified compute group.</p>
 any command that uses per-atom values from a compute as input.  See
 <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">Section_howto 15</span></a> for an overview of
 LAMMPS output options.</p>
-<p>The per-atom vector values will be in energy <span class="xref doc">units</span>.</p>
+<p>The per-atom vector values will be in energy <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>

doc/html/compute_meso_rho_atom.html

@@ -158,7 +158,7 @@ specified compute group.</p>
 any command that uses per-atom values from a compute as input.  See
 <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">Section_howto 15</span></a> for an overview of
 LAMMPS output options.</p>
-<p>The per-atom vector values will be in mass/volume <span class="xref doc">units</span>.</p>
+<p>The per-atom vector values will be in mass/volume <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>

doc/html/compute_meso_t_atom.html

@@ -159,7 +159,7 @@ specified compute group.</p>
 any command that uses per-atom values from a compute as input.  See
 <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">Section_howto 15</span></a> for an overview of
 LAMMPS output options.</p>
-<p>The per-atom vector values will be in temperature <span class="xref doc">units</span>.</p>
+<p>The per-atom vector values will be in temperature <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>

doc/html/compute_msd.html

@@ -215,7 +215,7 @@ accessed by indices 1-4 by any command that uses global vector values
 from a compute as input.  See <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">this section</span></a> for an overview of LAMMPS output
 options.</p>
 <p>The vector values are &#8220;intensive&#8221;.  The vector values will be in
-distance^2 <span class="xref doc">units</span>.</p>
+distance^2 <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>

doc/html/compute_msd_chunk.html

@@ -226,7 +226,7 @@ accessed by any command that uses global array values from a compute
 as input.  See <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">this section</span></a> for an
 overview of LAMMPS output options.</p>
 <p>The array values are &#8220;intensive&#8221;.  The array values will be in
-distance^2 <span class="xref doc">units</span>.</p>
+distance^2 <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>

doc/html/compute_omega_chunk.html

@@ -191,7 +191,7 @@ These values can be accessed by any command that uses global array
 values from a compute as input.  See <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">Section_howto 15</span></a> for an overview of LAMMPS output
 options.</p>
 <p>The array values are &#8220;intensive&#8221;.  The array values will be in
-velocity/distance <span class="xref doc">units</span>.</p>
+velocity/distance <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>

doc/html/compute_pair.html

@@ -185,8 +185,8 @@ from a compute as input.  See <a class="reference internal" href="Section_howto.
 options.</p>
 <p>The scalar and vector values calculated by this compute are
 &#8220;extensive&#8221;.</p>
-<p>The scalar value will be in energy <span class="xref doc">units</span>.  The vector
+<p>The scalar value will be in energy <a class="reference internal" href="units.html"><span class="doc">units</span></a>.  The vector
-values will typically also be in energy <span class="xref doc">units</span>, but see
+values will typically also be in energy <a class="reference internal" href="units.html"><span class="doc">units</span></a>, but see
 the doc page for the pair style for details.</p>
 </div>
 <div class="section" id="restrictions">

doc/html/compute_pair_local.html

@@ -179,9 +179,9 @@ example of ones that do are the <a class="reference internal" href="pair_gran.ht
 which calculate the tangential force between two particles and return
 its components and magnitude acting on atom I for N = 1,2,3,4.  See
 individual pair styles for detils.</p>
-<p>The output <em>dist</em> will be in distance <span class="xref doc">units</span>.  The output
+<p>The output <em>dist</em> will be in distance <a class="reference internal" href="units.html"><span class="doc">units</span></a>.  The output
-<em>eng</em> will be in energy <span class="xref doc">units</span>.  The outputs <em>force</em>,
+<em>eng</em> will be in energy <a class="reference internal" href="units.html"><span class="doc">units</span></a>.  The outputs <em>force</em>,
-<em>fx</em>, <em>fy</em>, and <em>fz</em> will be in force <span class="xref doc">units</span>.  The output
+<em>fx</em>, <em>fy</em>, and <em>fz</em> will be in force <a class="reference internal" href="units.html"><span class="doc">units</span></a>.  The output
 <em>pN</em> will be in whatever units the pair style defines.</p>
 <p>Note that as atoms migrate from processor to processor, there will be
 no consistent ordering of the entries within the local vector or array
@@ -217,9 +217,9 @@ local array is produced where the number of columns = the number of
 keywords.  The vector or array can be accessed by any command that
 uses local values from a compute as input.  See <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">this section</span></a> for an overview of LAMMPS output
 options.</p>
-<p>The output for <em>dist</em> will be in distance <span class="xref doc">units</span>.  The
+<p>The output for <em>dist</em> will be in distance <a class="reference internal" href="units.html"><span class="doc">units</span></a>.  The
-output for <em>eng</em> will be in energy <span class="xref doc">units</span>.  The output for
+output for <em>eng</em> will be in energy <a class="reference internal" href="units.html"><span class="doc">units</span></a>.  The output for
-<em>force</em> will be in force <span class="xref doc">units</span>.</p>
+<em>force</em> will be in force <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>

doc/html/compute_pe.html

@@ -200,7 +200,7 @@ value can be used by any command that uses a global scalar value from
 a compute as input.  See <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">Section_howto 15</span></a> for an overview of LAMMPS output
 options.</p>
 <p>The scalar value calculated by this compute is &#8220;extensive&#8221;.  The
-scalar value will be in energy <span class="xref doc">units</span>.</p>
+scalar value will be in energy <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>

doc/html/compute_pe_atom.html

@@ -191,7 +191,7 @@ those are global contributions to the system energy.</p>
 any command that uses per-atom values from a compute as input.  See
 <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">Section_howto 15</span></a> for an overview of
 LAMMPS output options.</p>
-<p>The per-atom vector values will be in energy <span class="xref doc">units</span>.</p>
+<p>The per-atom vector values will be in energy <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>

doc/html/compute_property_atom.html

@@ -262,7 +262,7 @@ per-atom array is produced where the number of columns = the number of
 inputs.  The vector or array can be accessed by any command that uses
 per-atom values from a compute as input.  See <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">this section</span></a> for an overview of LAMMPS output
 options.</p>
-<p>The vector or array values will be in whatever <span class="xref doc">units</span> the
+<p>The vector or array values will be in whatever <a class="reference internal" href="units.html"><span class="doc">units</span></a> the
 corresponding attribute is in, e.g. velocity units for vx, charge
 units for q, etc.</p>
 </div>

doc/html/compute_property_chunk.html

@@ -186,7 +186,7 @@ is the center point of the bin in the corresponding dimension.  Style
 <em>bin/1d</em> only defines a <em>coord1</em> attribute.  Style <em>bin/2d</em> adds a
 <em>coord2</em> attribute.  Style <em>bin/3d</em> adds a <em>coord3</em> attribute.</p>
 <p>Note that if the value of the <em>units</em> keyword used in the <a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom command</span></a> is <em>box</em> or <em>lattice</em>, the
-<em>coordN</em> attributes will be in distance <span class="xref doc">units</span>.  If the
+<em>coordN</em> attributes will be in distance <a class="reference internal" href="units.html"><span class="doc">units</span></a>.  If the
 value of the <em>units</em> keyword is <em>reduced</em>, the <em>coordN</em> attributes
 will be in unitless reduced units (0-1).</p>
 <p>The simplest way to output the results of the compute property/chunk

doc/html/compute_rdf.html

@@ -242,7 +242,7 @@ by any command that uses a global values from a compute as input.  See
 LAMMPS output options.</p>
 <p>The array values calculated by this compute are all &#8220;intensive&#8221;.</p>
 <p>The first column of array values will be in distance
-<span class="xref doc">units</span>.  The g(r) columns of array values are normalized
+<a class="reference internal" href="units.html"><span class="doc">units</span></a>.  The g(r) columns of array values are normalized
 numbers &gt;= 0.0.  The coordination number columns of array values are
 also numbers &gt;= 0.0.</p>
 </div>

doc/html/compute_reduce.html

@@ -281,7 +281,7 @@ for an overview of LAMMPS output options.</p>
 &#8220;intensive&#8221;, except when the <em>sum</em> or <em>sumsq</em> modes are used on
 per-atom or local vectors, in which case the calculated values are
 &#8220;extensive&#8221;.</p>
-<p>The scalar or vector values will be in whatever <span class="xref doc">units</span> the
+<p>The scalar or vector values will be in whatever <a class="reference internal" href="units.html"><span class="doc">units</span></a> the
 quantities being reduced are in.</p>
 </div>
 <div class="section" id="restrictions">

doc/html/compute_saed.html

@@ -169,7 +169,7 @@
 <div class="section" id="description">
 <h2>Description</h2>
 <p>Define a computation that calculates electron diffraction intensity as
-described in <a class="reference internal" href="compute_xrd.html#coleman"><span class="std std-ref">(Coleman)</span></a> on a mesh of reciprocal lattice nodes
+described in <a class="reference internal" href="fix_saed_vtk.html#coleman"><span class="std std-ref">(Coleman)</span></a> on a mesh of reciprocal lattice nodes
 defined by the entire simulation domain (or manually) using simulated
 radiation of wavelength lambda.</p>
 <p>The electron diffraction intensity I at each reciprocal lattice point

doc/html/compute_slice.html

@@ -220,7 +220,7 @@ array values calculated by this compute are “intensive”.  If there a
 multiple input vectors, and any value in them is extensive, then the
 array values calculated by this compute are “extensive”.  Values
 produced by a variable are treated as intensive.</p>
-<p>The vector or array values will be in whatever <span class="xref doc">units</span> the
+<p>The vector or array values will be in whatever <a class="reference internal" href="units.html"><span class="doc">units</span></a> the
 input quantities are in.</p>
 </div>
 <div class="section" id="restrictions">

doc/html/compute_smd_contact_radius.html

@@ -158,7 +158,7 @@ specified compute group.</p>
 any command that uses per-particle values from a compute as input.  See
 <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">Section_howto 15</span></a> for an overview of
 LAMMPS output options.</p>
-<p>The per-particle vector values will be in distance <span class="xref doc">units</span>.</p>
+<p>The per-particle vector values will be in distance <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>

doc/html/compute_smd_hourglass_error.html

@@ -162,7 +162,7 @@ any command that uses per-particle values from a compute as input.  See
 <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">How-to discussions, section 6.15</span></a>
 for an overview of LAMMPS output options.</p>
 <p>The per-particle vector values will are dimensionless. See
-<span class="xref doc">units</span>.</p>
+<a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>

doc/html/compute_smd_internal_energy.html

@@ -153,7 +153,7 @@ Mach Dynamics in LAMMPS.</p>
 by any command that uses per-particle values from a compute as input.
 See <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">How-to discussions, section 6.15</span></a> for
 an overview of LAMMPS output options.</p>
-<p>The per-particle vector values will be given in <span class="xref doc">units</span> of energy.</p>
+<p>The per-particle vector values will be given in <a class="reference internal" href="units.html"><span class="doc">units</span></a> of energy.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>

doc/html/compute_smd_plastic_strain.html

@@ -154,7 +154,7 @@ Mach Dynamics in LAMMPS.</p>
 by any command that uses per-particle values from a compute as input.
 See <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">How-to discussions, section 6.15</span></a> for
 an overview of LAMMPS output options.</p>
-<p>The per-particle values will be given dimensionless. See <span class="xref doc">units</span>.</p>
+<p>The per-particle values will be given dimensionless. See <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>

doc/html/compute_smd_plastic_strain_rate.html

@@ -154,7 +154,7 @@ Mach Dynamics in LAMMPS.</p>
 by any command that uses per-particle values from a compute as input.
 See <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">How-to discussions, section 6.15</span></a> for
 an overview of LAMMPS output options.</p>
-<p>The per-particle values will be given in <span class="xref doc">units</span> of one over time.</p>
+<p>The per-particle values will be given in <a class="reference internal" href="units.html"><span class="doc">units</span></a> of one over time.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>

doc/html/compute_smd_rho.html

@@ -155,7 +155,7 @@ Mach Dynamics in LAMMPS.</p>
 by any command that uses per-particle values from a compute as input.
 See <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">How-to discussions, section 6.15</span></a> for
 an overview of LAMMPS output options.</p>
-<p>The per-particle values will be in <span class="xref doc">units</span> of mass over volume.</p>
+<p>The per-particle values will be in <a class="reference internal" href="units.html"><span class="doc">units</span></a> of mass over volume.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>

doc/html/compute_smd_tlsph_defgrad.html

@@ -155,7 +155,7 @@ which can be accessed by any command that uses per-particle values
 from a compute as input. See <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">How-to discussions, section 6.15</span></a> for an overview of LAMMPS output
 options.</p>
 <p>The per-particle vector values will be given dimensionless. See
-<span class="xref doc">units</span>.  The per-particle vector has 10 entries. The first
+<a class="reference internal" href="units.html"><span class="doc">units</span></a>.  The per-particle vector has 10 entries. The first
 nine entries correspond to the xx, xy, xz, yx, yy, yz, zx, zy, zz
 components of the asymmetric deformation gradient tensor. The tenth
 entry is the determinant of the deformation gradient.</p>

doc/html/compute_smd_tlsph_dt.html

@@ -159,7 +159,7 @@ Mach Dynamics in LAMMPS.</p>
 by any command that uses per-particle values from a compute as input.
 See <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">How-to discussions, section 6.15</span></a> for
 an overview of LAMMPS output options.</p>
-<p>The per-particle values will be given in <span class="xref doc">units</span> of time.</p>
+<p>The per-particle values will be given in <a class="reference internal" href="units.html"><span class="doc">units</span></a> of time.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>

doc/html/compute_smd_tlsph_num_neighs.html

@@ -154,7 +154,7 @@ Mach Dynamics in LAMMPS.</p>
 by any command that uses per-particle values from a compute as input.
 See <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">How-to discussions, section 6.15</span></a> for
 an overview of LAMMPS output options.</p>
-<p>The per-particle values are dimensionless. See <span class="xref doc">units</span>.</p>
+<p>The per-particle values are dimensionless. See <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>

doc/html/compute_smd_tlsph_strain.html

@@ -154,7 +154,7 @@ which can be accessed by any command that uses per-particle values
 from a compute as input.  See <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">How-to discussions, section 6.15</span></a> for an overview of LAMMPS output
 options.</p>
 <p>The per-particle tensor values will be given dimensionless. See
-<span class="xref doc">units</span>.</p>
+<a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
 <p>The per-particle vector has 6 entries, corresponding to the xx, yy,
 zz, xy, xz, yz components of the symmetric strain tensor.</p>
 </div>

doc/html/compute_smd_tlsph_strain_rate.html

@@ -153,7 +153,7 @@ Mach Dynamics in LAMMPS.</p>
 which can be accessed by any command that uses per-particle values
 from a compute as input. See <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">How-to discussions, section 6.15</span></a> for an overview of LAMMPS output
 options.</p>
-<p>The values will be given in <span class="xref doc">units</span> of one over time.</p>
+<p>The values will be given in <a class="reference internal" href="units.html"><span class="doc">units</span></a> of one over time.</p>
 <p>The per-particle vector has 6 entries, corresponding to the xx, yy,
 zz, xy, xz, yz components of the symmetric strain rate tensor.</p>
 </div>

doc/html/compute_smd_tlsph_stress.html

@@ -154,7 +154,7 @@ accessed by any command that uses per-particle values from a compute
 as input. See
 <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">How-to discussions, section 6.15</span></a>
 for an overview of LAMMPS output options.</p>
-<p>The values will be given in <span class="xref doc">units</span> of pressure.</p>
+<p>The values will be given in <a class="reference internal" href="units.html"><span class="doc">units</span></a> of pressure.</p>
 <p>The per-particle vector has 7 entries. The first six entries
 correspond to the xx, yy, zz, xy, xz and yz components of the
 symmetric Cauchy stress tensor. The seventh entry is the second

doc/html/compute_smd_triangle_mesh_vertices.html

@@ -161,7 +161,7 @@ which is created via the <a href="#id6"><span class="problematic" id="id7">`fix
 <p>The output of this compute can be used with the dump2vtk_tris tool to
 generate a VTK representation of the smd/wall_surace mesh for
 visualization purposes.</p>
-<p>The values will be given in <span class="xref doc">units</span> of distance.</p>
+<p>The values will be given in <a class="reference internal" href="units.html"><span class="doc">units</span></a> of distance.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>

doc/html/compute_smd_ulsph_num_neighs.html

@@ -154,7 +154,7 @@ Mach Dynamics in LAMMPS.</p>
 any command that uses per-particle values from a compute as input.
 See <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">Section_howto 15</span></a> for an overview of
 LAMMPS output options.</p>
-<p>The per-particle values will be given dimentionless, see <span class="xref doc">units</span>.</p>
+<p>The per-particle values will be given dimentionless, see <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>

doc/html/compute_smd_ulsph_strain.html

@@ -156,7 +156,7 @@ LAMMPS output options.</p>
 <p>The per-particle vector has 6 entries, corresponding to the xx, yy,
 zz, xy, xz, yz components of the symmetric strain rate tensor.</p>
 <p>The per-particle tensor values will be given dimensionless, see
-<span class="xref doc">units</span>.</p>
+<a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>

doc/html/compute_smd_ulsph_strain_rate.html

@@ -154,7 +154,7 @@ Mach Dynamics in LAMMPS.</p>
 which can be accessed by any command that uses per-particle values
 from a compute as input. See <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">Section_howto 15</span></a> for an overview of LAMMPS output
 options.</p>
-<p>The values will be given in <span class="xref doc">units</span> of one over time.</p>
+<p>The values will be given in <a class="reference internal" href="units.html"><span class="doc">units</span></a> of one over time.</p>
 <p>The per-particle vector has 6 entries, corresponding to the xx, yy,
 zz, xy, xz, yz components of the symmetric strain rate tensor.</p>
 </div>

doc/html/compute_smd_ulsph_stress.html

@@ -152,7 +152,7 @@ Mach Dynamics in LAMMPS.</p>
 which can be accessed by any command that uses per-particle values
 from a compute as input. See <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">Section_howto 15</span></a> for an overview of LAMMPS output
 options.</p>
-<p>The values will be given in <span class="xref doc">units</span> of pressure.</p>
+<p>The values will be given in <a class="reference internal" href="units.html"><span class="doc">units</span></a> of pressure.</p>
 <p>The per-particle vector has 7 entries. The first six entries
 correspond to the xx, yy, zz, xy, xz, yz components of the symmetric
 Cauchy stress tensor. The seventh entry is the second invariant of the

doc/html/compute_smd_vol.html

@@ -153,7 +153,7 @@ Mach Dynamics in LAMMPS.</p>
 by any command that uses per-particle values from a compute as input.
 See <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">How-to discussions, section 6.15</span></a> for
 an overview of LAMMPS output options.</p>
-<p>The per-particle vector values will be given in <span class="xref doc">units</span> of
+<p>The per-particle vector values will be given in <a class="reference internal" href="units.html"><span class="doc">units</span></a> of
 volume.</p>
 <p>Additionally, the compute returns a scalar, which is the sum of the
 per-particle volumes of the group for which the fix is defined.</p>

doc/html/compute_temp.html

@@ -207,8 +207,8 @@ vector values from a compute as input.  See <a class="reference internal" href="
 options.</p>
 <p>The scalar value calculated by this compute is &#8220;intensive&#8221;.  The
 vector values are &#8220;extensive&#8221;.</p>
-<p>The scalar value will be in temperature <span class="xref doc">units</span>.  The
+<p>The scalar value will be in temperature <a class="reference internal" href="units.html"><span class="doc">units</span></a>.  The
-vector values will be in energy <span class="xref doc">units</span>.</p>
+vector values will be in energy <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>

doc/html/compute_temp_asphere.html

@@ -238,8 +238,8 @@ vector values from a compute as input.  See <a class="reference internal" href="
 options.</p>
 <p>The scalar value calculated by this compute is &#8220;intensive&#8221;.  The
 vector values are &#8220;extensive&#8221;.</p>
-<p>The scalar value will be in temperature <span class="xref doc">units</span>.  The
+<p>The scalar value will be in temperature <a class="reference internal" href="units.html"><span class="doc">units</span></a>.  The
-vector values will be in energy <span class="xref doc">units</span>.</p>
+vector values will be in energy <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>

doc/html/compute_temp_body.html

@@ -219,8 +219,8 @@ vector values from a compute as input.  See <a class="reference internal" href="
 options.</p>
 <p>The scalar value calculated by this compute is &#8220;intensive&#8221;.  The
 vector values are &#8220;extensive&#8221;.</p>
-<p>The scalar value will be in temperature <span class="xref doc">units</span>.  The
+<p>The scalar value will be in temperature <a class="reference internal" href="units.html"><span class="doc">units</span></a>.  The
-vector values will be in energy <span class="xref doc">units</span>.</p>
+vector values will be in energy <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>

doc/html/compute_temp_chunk.html

@@ -312,10 +312,10 @@ compute as input.  Again, see <a class="reference internal" href="Section_howto.
 options.</p>
 <p>The scalar value calculated by this compute is &#8220;intensive&#8221;.  The
 vector values are &#8220;extensive&#8221;.  The array values are &#8220;intensive&#8221;.</p>
-<p>The scalar value will be in temperature <span class="xref doc">units</span>.  The
+<p>The scalar value will be in temperature <a class="reference internal" href="units.html"><span class="doc">units</span></a>.  The
-vector values will be in energy <span class="xref doc">units</span>.  The array values
+vector values will be in energy <a class="reference internal" href="units.html"><span class="doc">units</span></a>.  The array values
-will be in temperature <span class="xref doc">units</span> for the <em>temp</em> value, and in
+will be in temperature <a class="reference internal" href="units.html"><span class="doc">units</span></a> for the <em>temp</em> value, and in
-energy <span class="xref doc">units</span> for the <em>kecom</em> and <em>internal</em> values.</p>
+energy <a class="reference internal" href="units.html"><span class="doc">units</span></a> for the <em>kecom</em> and <em>internal</em> values.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>

doc/html/compute_temp_com.html

@@ -189,8 +189,8 @@ vector values from a compute as input.  See <a class="reference internal" href="
 options.</p>
 <p>The scalar value calculated by this compute is &#8220;intensive&#8221;.  The
 vector values are &#8220;extensive&#8221;.</p>
-<p>The scalar value will be in temperature <span class="xref doc">units</span>.  The
+<p>The scalar value will be in temperature <a class="reference internal" href="units.html"><span class="doc">units</span></a>.  The
-vector values will be in energy <span class="xref doc">units</span>.</p>
+vector values will be in energy <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>

doc/html/compute_temp_cs.html

@@ -204,8 +204,8 @@ These values can be used by any command that uses global scalar or
 vector values from a compute as input.</p>
 <p>The scalar value calculated by this compute is &#8220;intensive&#8221;.  The
 vector values are &#8220;extensive&#8221;.</p>
-<p>The scalar value will be in temperature <span class="xref doc">units</span>.  The
+<p>The scalar value will be in temperature <a class="reference internal" href="units.html"><span class="doc">units</span></a>.  The
-vector values will be in energy <span class="xref doc">units</span>.</p>
+vector values will be in energy <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>

doc/html/compute_temp_deform.html

@@ -229,8 +229,8 @@ vector values from a compute as input.  See <a class="reference internal" href="
 options.</p>
 <p>The scalar value calculated by this compute is &#8220;intensive&#8221;.  The
 vector values are &#8220;extensive&#8221;.</p>
-<p>The scalar value will be in temperature <span class="xref doc">units</span>.  The
+<p>The scalar value will be in temperature <a class="reference internal" href="units.html"><span class="doc">units</span></a>.  The
-vector values will be in energy <span class="xref doc">units</span>.</p>
+vector values will be in energy <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>

doc/html/compute_temp_deform_eff.html

@@ -170,8 +170,8 @@ vector values from a compute as input.  See <a class="reference internal" href="
 options.</p>
 <p>The scalar value calculated by this compute is &#8220;intensive&#8221;.  The
 vector values are &#8220;extensive&#8221;.</p>
-<p>The scalar value will be in temperature <span class="xref doc">units</span>.  The
+<p>The scalar value will be in temperature <a class="reference internal" href="units.html"><span class="doc">units</span></a>.  The
-vector values will be in energy <span class="xref doc">units</span>.</p>
+vector values will be in energy <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>

doc/html/compute_temp_partial.html

@@ -209,8 +209,8 @@ vector values from a compute as input.  See <a class="reference internal" href="
 options.</p>
 <p>The scalar value calculated by this compute is &#8220;intensive&#8221;.  The
 vector values are &#8220;extensive&#8221;.</p>
-<p>The scalar value will be in temperature <span class="xref doc">units</span>.  The
+<p>The scalar value will be in temperature <a class="reference internal" href="units.html"><span class="doc">units</span></a>.  The
-vector values will be in energy <span class="xref doc">units</span>.</p>
+vector values will be in energy <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>

doc/html/compute_temp_profile.html

@@ -262,10 +262,10 @@ vector or array values from a compute as input.  See <a class="reference interna
 options.</p>
 <p>The scalar value calculated by this compute is &#8220;intensive&#8221;.  The
 vector values are &#8220;extensive&#8221;.  The array values are &#8220;intensive&#8221;.</p>
-<p>The scalar value will be in temperature <span class="xref doc">units</span>.  The
+<p>The scalar value will be in temperature <a class="reference internal" href="units.html"><span class="doc">units</span></a>.  The
-vector values will be in energy <span class="xref doc">units</span>.  The first column
+vector values will be in energy <a class="reference internal" href="units.html"><span class="doc">units</span></a>.  The first column
 of array values are counts; the values in the second column will be in
-temperature <span class="xref doc">units</span>.</p>
+temperature <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>

doc/html/compute_temp_ramp.html

@@ -169,7 +169,7 @@ simulation, N = number of atoms in the group, k = Boltzmann constant,
 and T = temperature.</p>
 <p>The <em>units</em> keyword determines the meaning of the distance units used
 for coordinates (c1,c2) and velocities (vlo,vhi).  A <em>box</em> value
-selects standard distance units as defined by the <span class="xref doc">units</span>
+selects standard distance units as defined by the <a class="reference internal" href="units.html"><span class="doc">units</span></a>
 command, e.g. Angstroms for units = real or metal.  A <em>lattice</em> value
 means the distance units are in lattice spacings; e.g. velocity =
 lattice spacings / tau.  The <a class="reference internal" href="lattice.html"><span class="doc">lattice</span></a> command must have
@@ -207,8 +207,8 @@ vector values from a compute as input.  See <a class="reference internal" href="
 options.</p>
 <p>The scalar value calculated by this compute is &#8220;intensive&#8221;.  The
 vector values are &#8220;extensive&#8221;.</p>
-<p>The scalar value will be in temperature <span class="xref doc">units</span>.  The
+<p>The scalar value will be in temperature <a class="reference internal" href="units.html"><span class="doc">units</span></a>.  The
-vector values will be in energy <span class="xref doc">units</span>.</p>
+vector values will be in energy <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>

doc/html/compute_temp_region.html

@@ -202,8 +202,8 @@ vector values from a compute as input.  See <a class="reference internal" href="
 options.</p>
 <p>The scalar value calculated by this compute is &#8220;intensive&#8221;.  The
 vector values are &#8220;extensive&#8221;.</p>
-<p>The scalar value will be in temperature <span class="xref doc">units</span>.  The
+<p>The scalar value will be in temperature <a class="reference internal" href="units.html"><span class="doc">units</span></a>.  The
-vector values will be in energy <span class="xref doc">units</span>.</p>
+vector values will be in energy <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>

doc/html/compute_temp_region_eff.html

@@ -162,8 +162,8 @@ vector values from a compute as input.  See <a class="reference internal" href="
 options.</p>
 <p>The scalar value calculated by this compute is &#8220;intensive&#8221;.  The
 vector values are &#8220;extensive&#8221;.</p>
-<p>The scalar value will be in temperature <span class="xref doc">units</span>.  The
+<p>The scalar value will be in temperature <a class="reference internal" href="units.html"><span class="doc">units</span></a>.  The
-vector values will be in energy <span class="xref doc">units</span>.</p>
+vector values will be in energy <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>

doc/html/compute_temp_rotate.html

@@ -188,8 +188,8 @@ vector values from a compute as input.  See <a class="reference internal" href="
 options.</p>
 <p>The scalar value calculated by this compute is &#8220;intensive&#8221;.  The
 vector values are &#8220;extensive&#8221;.</p>
-<p>The scalar value will be in temperature <span class="xref doc">units</span>.  The
+<p>The scalar value will be in temperature <a class="reference internal" href="units.html"><span class="doc">units</span></a>.  The
-vector values will be in energy <span class="xref doc">units</span>.</p>
+vector values will be in energy <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>

doc/html/compute_temp_sphere.html

@@ -226,8 +226,8 @@ vector values from a compute as input.  See <a class="reference internal" href="
 options.</p>
 <p>The scalar value calculated by this compute is &#8220;intensive&#8221;.  The
 vector values are &#8220;extensive&#8221;.</p>
-<p>The scalar value will be in temperature <span class="xref doc">units</span>.  The
+<p>The scalar value will be in temperature <a class="reference internal" href="units.html"><span class="doc">units</span></a>.  The
-vector values will be in energy <span class="xref doc">units</span>.</p>
+vector values will be in energy <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>

doc/html/compute_ti.html

@@ -226,7 +226,7 @@ value can be used by any command that uses a global scalar value from
 a compute as input.  See <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">Section_howto 15</span></a> for an overview of LAMMPS output
 options.</p>
 <p>The scalar value calculated by this compute is &#8220;extensive&#8221;.</p>
-<p>The scalar value will be in energy <span class="xref doc">units</span>.</p>
+<p>The scalar value will be in energy <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>

doc/html/compute_torque_chunk.html

@@ -190,7 +190,7 @@ can be accessed by any command that uses global array values from a
 compute as input.  See <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">Section_howto 15</span></a>
 for an overview of LAMMPS output options.</p>
 <p>The array values are &#8220;intensive&#8221;.  The array values will be in
-force-distance <span class="xref doc">units</span>.</p>
+force-distance <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>

doc/html/compute_vacf.html

@@ -180,7 +180,7 @@ accessed by indices 1-4 by any command that uses global vector values
 from a compute as input.  See <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">this section</span></a> for an overview of LAMMPS output
 options.</p>
 <p>The vector values are &#8220;intensive&#8221;.  The vector values will be in
-velocity^2 <span class="xref doc">units</span>.</p>
+velocity^2 <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>

doc/html/compute_vcm_chunk.html

@@ -180,7 +180,7 @@ These values can be accessed by any command that uses global array
 values from a compute as input.  See <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">Section_howto 15</span></a> for an overview of LAMMPS output
 options.</p>
 <p>The array values are &#8220;intensive&#8221;.  The array values will be in
-velocity <span class="xref doc">units</span>.</p>
+velocity <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>

doc/html/compute_voronoi_atom.html

@@ -317,8 +317,8 @@ keyword to turn off the production of the per-atom quantities.  For
 the default value <em>yes</em> both quantities are produced.  For the value
 <em>no</em>, only the local array is produced.</p>
 </div>
-<p>The Voronoi cell volume will be in distance <span class="xref doc">units</span> cubed.
+<p>The Voronoi cell volume will be in distance <a class="reference internal" href="units.html"><span class="doc">units</span></a> cubed.
-The Voronoi face area will be in distance <span class="xref doc">units</span> squared.</p>
+The Voronoi face area will be in distance <a class="reference internal" href="units.html"><span class="doc">units</span></a> squared.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>

doc/html/compute_xrd.html

@@ -167,7 +167,7 @@
 <div class="section" id="description">
 <h2>Description</h2>
 <p>Define a computation that calculates x-ray diffraction intensity as described
-in <a class="reference internal" href="#coleman"><span class="std std-ref">(Coleman)</span></a> on a mesh of reciprocal lattice nodes defined
+in <a class="reference internal" href="fix_saed_vtk.html#coleman"><span class="std std-ref">(Coleman)</span></a> on a mesh of reciprocal lattice nodes defined
 by the entire simulation domain (or manually) using a simulated radiation
 of wavelength lambda.</p>
 <p>The x-ray diffraction intensity, I, at each reciprocal lattice point, k,

doc/html/dihedral_charmm.html

@@ -152,9 +152,9 @@
 <h2>Description</h2>
 <p>The <em>charmm</em> dihedral style uses the potential</p>
 <img alt="_images/dihedral_charmm.jpg" class="align-center" src="_images/dihedral_charmm.jpg" />
-<p>See <a class="reference internal" href="pair_charmm.html#mackerell"><span class="std std-ref">(MacKerell)</span></a> for a description of the CHARMM force
+<p>See <a class="reference internal" href="special_bonds.html#mackerell"><span class="std std-ref">(MacKerell)</span></a> for a description of the CHARMM force
 field.  This dihedral style can also be used for the AMBER force field
-(see comment on weighting factors below).  See <a class="reference internal" href="#cornell"><span class="std std-ref">(Cornell)</span></a>
+(see comment on weighting factors below).  See <a class="reference internal" href="special_bonds.html#cornell"><span class="std std-ref">(Cornell)</span></a>
 for a description of the AMBER force field.</p>
 <p>The following coefficients must be defined for each dihedral type via the
 <a class="reference internal" href="dihedral_coeff.html"><span class="doc">dihedral_coeff</span></a> command as in the example above, or in

doc/html/dihedral_class2.html

@@ -156,7 +156,7 @@ Eebt is an end-bond-torsion term, Eat is an angle-torsion term, Eaat
 is an angle-angle-torsion term, and Ebb13 is a bond-bond-13 term.</p>
 <p>Theta1 and theta2 are equilibrium angles and r1 r2 r3 are equilibrium
 bond lengths.</p>
-<p>See <a class="reference internal" href="pair_class2.html#sun"><span class="std std-ref">(Sun)</span></a> for a description of the COMPASS class2 force field.</p>
+<p>See <a class="reference internal" href="pair_modify.html#sun"><span class="std std-ref">(Sun)</span></a> for a description of the COMPASS class2 force field.</p>
 <p>Coefficients for the Ed, Embt, Eebt, Eat, Eaat, and Ebb13 formulas
 must be defined for each dihedral type via the
 <a class="reference internal" href="dihedral_coeff.html"><span class="doc">dihedral_coeff</span></a> command as in the example above,

doc/html/displace_atoms.html

@@ -217,7 +217,7 @@ atom&#8217;s rotation.</p>
 <p>Distance units for displacements and the origin point of the <em>rotate</em>
 style are determined by the setting of <em>box</em> or <em>lattice</em> for the
 <em>units</em> keyword.  <em>Box</em> means distance units as defined by the
-<span class="xref doc">units</span> command - e.g. Angstroms for <em>real</em> units.
+<a class="reference internal" href="units.html"><span class="doc">units</span></a> command - e.g. Angstroms for <em>real</em> units.
 <em>Lattice</em> means distance units are in lattice spacings.  The
 <a class="reference internal" href="lattice.html"><span class="doc">lattice</span></a> command must have been previously used to
 define the lattice spacing.</p>

doc/html/dump.html

@@ -587,7 +587,7 @@ mass.  <em>Vx</em>, <em>vy</em>, <em>vz</em>, <em>fx</em>, <em>fy</em>, <em>fz</
 atom velocity and force and atomic charge.</p>
 <p>There are several options for outputting atom coordinates.  The <em>x</em>,
 <em>y</em>, <em>z</em> attributes write atom coordinates &#8220;unscaled&#8221;, in the
-appropriate distance <span class="xref doc">units</span> (Angstroms, sigma, etc).  Use
+appropriate distance <a class="reference internal" href="units.html"><span class="doc">units</span></a> (Angstroms, sigma, etc).  Use
 <em>xs</em>, <em>ys</em>, <em>zs</em> if you want the coordinates &#8220;scaled&#8221; to the box size,
 so that each value is 0.0 to 1.0.  If the simulation box is triclinic
 (tilted), then all atom coords will still be between 0.0 and 1.0.  Use

doc/html/dump_custom_vtk.html

@@ -312,7 +312,7 @@ atom type.  <em>mass</em> is the atom mass.  <em>vx</em>, <em>vy</em>, <em>vz</e
 charge.</p>
 <p>There are several options for outputting atom coordinates.  The <em>x</em>,
 <em>y</em>, <em>z</em> attributes are used to write atom coordinates &#8220;unscaled&#8221;, in
-the appropriate distance <span class="xref doc">units</span> (Angstroms, sigma, etc).
+the appropriate distance <a class="reference internal" href="units.html"><span class="doc">units</span></a> (Angstroms, sigma, etc).
 Additionaly, you can use <em>xs</em>, <em>ys</em>, <em>zs</em> if you want to also save the
 coordinates &#8220;scaled&#8221; to the box size, so that each value is 0.0 to
 1.0.  If the simulation box is triclinic (tilted), then all atom

doc/html/dump_modify.html

@@ -444,7 +444,7 @@ nanometer accuracy, e.g. for N = 1000, the coordinates are written to
 <p>The <em>sfactor</em> and <em>tfactor</em> keywords only apply to the dump <em>xtc</em>
 style.  They allow customization of the unit conversion factors used
 when writing to XTC files.  By default they are initialized for
-whatever <span class="xref doc">units</span> style is being used, to write out
+whatever <a class="reference internal" href="units.html"><span class="doc">units</span></a> style is being used, to write out
 coordinates in nanometers and time in picoseconds.  I.e. for <em>real</em>
 units, LAMMPS defines <em>sfactor</em> = 0.1 and <em>tfactor</em> = 0.001, since the
 Angstroms and fmsec used by <em>real</em> units are 0.1 nm and 0.001 psec
@@ -542,7 +542,7 @@ that atoms of each type will be drawn in the image.  The specified
 <em>type</em> should be an integer from 1 to Ntypes.  As with the <em>acolor</em>
 keyword, a wildcard asterisk can be used as part of the <em>type</em>
 argument to specify a range of atomt types.  The specified <em>diam</em> is
-the size in whatever distance <span class="xref doc">units</span> the input script is
+the size in whatever distance <a class="reference internal" href="units.html"><span class="doc">units</span></a> the input script is
 using, e.g. Angstroms.</p>
 <hr class="docutils" />
 <p>The <em>amap</em> keyword can be used with the <a class="reference internal" href="dump_image.html"><span class="doc">dump image</span></a>
@@ -687,7 +687,7 @@ set the diameter that bonds of each type will be drawn in the image.
 The specified <em>type</em> should be an integer from 1 to Nbondtypes.  As
 with the <em>bcolor</em> keyword, a wildcard asterisk can be used as part of
 the <em>type</em> argument to specify a range of bond types.  The specified
-<em>diam</em> is the size in whatever distance <span class="xref doc">units</span> you are
+<em>diam</em> is the size in whatever distance <a class="reference internal" href="units.html"><span class="doc">units</span></a> you are
 using, e.g. Angstroms.</p>
 <hr class="docutils" />
 <p>The <em>bitrate</em> keyword can be used with the <a class="reference internal" href="dump_image.html"><span class="doc">dump movie</span></a> command to define the size of the resulting

doc/html/fix_append_atoms.html

@@ -193,7 +193,7 @@ measured from zhi and is set with the <em>extent</em> argument.</p>
 <p>The <em>units</em> keyword determines the meaning of the distance units used
 to define a wall position, but only when a numeric constant is used.
 A <em>box</em> value selects standard distance units as defined by the
-<span class="xref doc">units</span> command, e.g. Angstroms for units = real or metal.
+<a class="reference internal" href="units.html"><span class="doc">units</span></a> command, e.g. Angstroms for units = real or metal.
 A <em>lattice</em> value means the distance units are in lattice spacings.
 The <a class="reference internal" href="lattice.html"><span class="doc">lattice</span></a> command must have been previously used to
 define the lattice spacings.</p>

doc/html/fix_ave_chunk.html

@@ -293,7 +293,7 @@ an input value from that compute.</p>
 each chunk, i.e. number/volume.  The <em>density/mass</em> value means the
 mass density is computed for each chunk, i.e. total-mass/volume.  The
 output values are in units of 1/volume or density (mass/volume).  See
-the <span class="xref doc">units</span> command doc page for the definition of density
+the <a class="reference internal" href="units.html"><span class="doc">units</span></a> command doc page for the definition of density
 for each choice of units, e.g. gram/cm^3.  If the chunks defined by
 the <a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom</span></a> command are spatial
 bins, the volume is the bin volume.  Otherwise it is the volume of the
@@ -475,11 +475,11 @@ coordinate.  For <em>bin/cylinder</em>, Coord1 and Coord2 are used.  Coord1
 is the radial coordinate (away from the cylinder axis), and coord2 is
 the coordinate along the cylinder axis.</p>
 <p>Note that if the value of the <em>units</em> keyword used in the <a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom command</span></a> is <em>box</em> or <em>lattice</em>, the
-coordinate values will be in distance <span class="xref doc">units</span>.  If the
+coordinate values will be in distance <a class="reference internal" href="units.html"><span class="doc">units</span></a>.  If the
 value of the <em>units</em> keyword is <em>reduced</em>, the coordinate values will
 be in unitless reduced units (0-1).  This is not true for the Coord1 value
 of style <em>bin/sphere</em> or <em>bin/cylinder</em> which both represent radial
-dimensions.  Those values are always in distance <span class="xref doc">units</span>.</p>
+dimensions.  Those values are always in distance <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
 </div>
 <hr class="docutils" />
 <div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">

doc/html/fix_ave_spatial.html

@@ -345,7 +345,7 @@ each bin, i.e. a weighting of 1 for each atom.  The <em>density/mass</em>
 value means the mass density is computed in each bind, i.e. each atom
 is weighted by its mass.  The resulting density is normalized by the
 volume of the bin so that units of number/volume or density are
-output.  See the <span class="xref doc">units</span> command doc page for the
+output.  See the <a class="reference internal" href="units.html"><span class="doc">units</span></a> command doc page for the
 definition of density for each choice of units, e.g. gram/cm^3.</p>
 <p>If a value begins with &#8220;<a href="#id1"><span class="problematic" id="id2">c_</span></a>&#8221;, a compute ID must follow which has been
 previously defined in the input script.  If no bracketed integer is
@@ -409,7 +409,7 @@ are coordinate value.  For orthogonal simulation boxes, any of the 3
 options may be used.  For non-orthogonal (triclinic) simulation boxes,
 only the <em>reduced</em> option may be used.</p>
 <p>A <em>box</em> value selects standard distance units as defined by the
-<span class="xref doc">units</span> command, e.g. Angstroms for units = real or metal.
+<a class="reference internal" href="units.html"><span class="doc">units</span></a> command, e.g. Angstroms for units = real or metal.
 A <em>lattice</em> value means the distance units are in lattice spacings.
 The <a class="reference internal" href="lattice.html"><span class="doc">lattice</span></a> command must have been previously used to
 define the lattice spacing.  A <em>reduced</em> value means normalized

doc/html/fix_ave_spatial_sphere.html

@@ -257,7 +257,7 @@ each bin, i.e. a weighting of 1 for each atom.  The <em>density/mass</em>
 value means the mass density is computed in each bin, i.e. each atom
 is weighted by its mass.  The resulting density is normalized by the
 volume of the bin so that units of number/volume or density are
-output.  See the <span class="xref doc">units</span> command doc page for the
+output.  See the <a class="reference internal" href="units.html"><span class="doc">units</span></a> command doc page for the
 definition of density for each choice of units, e.g. gram/cm^3.
 The bin volume will always be calculated in box units, independent
 of the use of the <em>units</em> keyword in this command.</p>
@@ -323,7 +323,7 @@ simulation boxes, any of the 3 options may be used.  For
 non-orthogonal (triclinic) simulation boxes, only the <em>reduced</em> option
 may be used.</p>
 <p>A <em>box</em> value selects standard distance units as defined by the
-<span class="xref doc">units</span> command, e.g. Angstroms for units = real or metal.
+<a class="reference internal" href="units.html"><span class="doc">units</span></a> command, e.g. Angstroms for units = real or metal.
 A <em>lattice</em> value means the distance units are in lattice spacings.
 The <a class="reference internal" href="lattice.html"><span class="doc">lattice</span></a> command must have been previously used to
 define the lattice spacing.</p>