git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14957 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/html/Section_accelerate.html

@@ -346,7 +346,7 @@ Lennard-Jones <a class="reference internal" href="pair_lj.html"><span class="doc
 <p>To see what accelerate styles are currently available, see
 <a class="reference internal" href="Section_commands.html#cmd-5"><span class="std std-ref">Section_commands 5</span></a> of the manual.  The
 doc pages for individual commands (e.g. <a class="reference internal" href="pair_lj.html"><span class="doc">pair lj/cut</span></a> or
-<a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>) also list any accelerated variants available
+<span class="xref doc">fix nve</span>) also list any accelerated variants available
 for that style.</p>
 <p>To use an accelerator package in LAMMPS, and one or more of the styles
 it provides, follow these general steps.  Details vary from package to

doc/html/Section_commands.html

@@ -679,7 +679,7 @@ g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.</p>
 <td><a class="reference internal" href="fix_npt_asphere.html"><span class="doc">npt/asphere (o)</span></a></td>
 <td><a class="reference internal" href="fix_npt_body.html"><span class="doc">npt/body</span></a></td>
 <td><a class="reference internal" href="fix_npt_sphere.html"><span class="doc">npt/sphere (o)</span></a></td>
-<td><a class="reference internal" href="fix_nve.html"><span class="doc">nve (ckio)</span></a></td>
+<td><span class="xref doc">nve (ckio)</span></td>
 <td><a class="reference internal" href="fix_nve_asphere.html"><span class="doc">nve/asphere (i)</span></a></td>
 </tr>
 <tr class="row-odd"><td><a class="reference internal" href="fix_nve_asphere_noforce.html"><span class="doc">nve/asphere/noforce</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" />
@@ -1749,7 +1749,7 @@ do NOT perform time integration updates.  Thus they should be used in
 conjunction with a constant NVE integration fix such as these:</p>
 </div>
 <ul class="simple">
-<li><a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a></li>
+<li><span class="xref doc">fix nve</span></li>
 <li><a class="reference internal" href="fix_nve_sphere.html"><span class="doc">fix nve/sphere</span></a></li>
 <li><a class="reference internal" href="fix_nve_asphere.html"><span class="doc">fix nve/asphere</span></a></li>
 </ul>
@@ -1816,7 +1816,7 @@ or read in via the <a class="reference internal" href="read_data.html"><span cla
 they do not move at all, move together as a group at constant velocity
 or in response to a net force acting on them, move in a prescribed
 fashion (e.g. rotate around a point), etc.  Note that if a time
-integration fix like <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> or <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a>
+integration fix like <span class="xref doc">fix nve</span> or <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a>
 is not used with the group that contains wall particles, their
 positions and velocities will not be updated.</p>
 <ul class="simple">
@@ -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_packages.html

@@ -2329,7 +2329,7 @@ classical limits in the simulation.</p>
 <p>See these two doc pages to get started:</p>
 <p><a class="reference internal" href="fix_qtb.html"><span class="doc">fix qtb</span></a> provides quantum nulcear correction through a
 colored thermostat and can be used with other time integration schemes
-like <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> or <a class="reference internal" href="fix_nh.html"><span class="doc">fix nph</span></a>.</p>
+like <span class="xref doc">fix nve</span> or <a class="reference internal" href="fix_nh.html"><span class="doc">fix nph</span></a>.</p>
 <p><a class="reference internal" href="fix_qbmsst.html"><span class="doc">fix qbmsst</span></a> enables quantum nuclear correction of a
 multi-scale shock technique simulation by coupling the quantum thermal
 bath with the shocked system.</p>

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/atom_modify.html

@@ -210,7 +210,7 @@ over the smaller set of atoms.  Otherwise the reordering required by
 this option will be a net slow-down.  The <a class="reference internal" href="neigh_modify.html"><span class="doc">neigh_modify include</span></a> and <a class="reference internal" href="comm_modify.html"><span class="doc">comm_modify group</span></a>
 commands are two examples of commands that require this setting to
 work efficiently.  Several <a class="reference internal" href="fix.html"><span class="doc">fixes</span></a>, most notably time
-integration fixes like <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>, also take advantage of
+integration fixes like <span class="xref doc">fix nve</span>, also take advantage of
 this setting if the group they operate on is the group specified by
 this command.  Note that specifying &#8220;all&#8221; as the group-ID effectively
 turns off the <em>first</em> option.</p>

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/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_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/fix.html

@@ -166,7 +166,7 @@ underscores.</p>
 <p class="last">The <a class="reference internal" href="unfix.html"><span class="doc">unfix</span></a> command is the only way to turn off a
 fix; simply specifying a new fix with a similar style will not turn
 off the first one.  This is especially important to realize for
-integration fixes.  For example, using a <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>
+integration fixes.  For example, using a <span class="xref doc">fix nve</span>
 command for a second run after using a <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a> command
 for the first run, will not cancel out the NVT time integration
 invoked by the &#8220;fix nvt&#8221; command.  Thus two time integrators would be
@@ -318,7 +318,7 @@ of <a class="reference internal" href="Section_commands.html#cmd-5"><span class=
 <li><a class="reference internal" href="fix_npt_asphere.html"><span class="doc">npt/asphere</span></a> - NPT for aspherical particles</li>
 <li><a class="reference internal" href="fix_nve_body.html"><span class="doc">npt/body</span></a> - NPT for body particles</li>
 <li><a class="reference internal" href="fix_npt_sphere.html"><span class="doc">npt/sphere</span></a> - NPT for spherical particles</li>
-<li><a class="reference internal" href="fix_nve.html"><span class="doc">nve</span></a> - constant NVE time integration</li>
+<li><span class="xref doc">nve</span> - constant NVE time integration</li>
 <li><a class="reference internal" href="fix_nve_asphere.html"><span class="doc">nve/asphere</span></a> - NVE for aspherical particles</li>
 <li><a class="reference internal" href="fix_nve_asphere_noforce.html"><span class="doc">nve/asphere/noforce</span></a> - NVE for aspherical particles without forces&#8221;</li>
 <li><a class="reference internal" href="fix_nve_body.html"><span class="doc">nve/body</span></a> - NVE for body particles</li>

doc/html/fix_drude_transform.html

@@ -208,7 +208,7 @@ atoms will simply not be transformed.</p>
 <hr class="docutils" />
 <p>This fix does NOT perform time integration. It only transform masses,
 coordinates, velocities and forces. Thus you must use separate time
-integration fixes, like <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> or <a class="reference internal" href="fix_nh.html"><span class="doc">fix npt</span></a> to actually update the velocities and positions of
+integration fixes, like <span class="xref doc">fix nve</span> or <a class="reference internal" href="fix_nh.html"><span class="doc">fix npt</span></a> to actually update the velocities and positions of
 atoms.  In order to thermalize the reduced degrees of freedom at
 different temperatures, two Nose-Hoover thermostats must be defined,
 acting on two distinct groups.</p>

doc/html/fix_gld.html

@@ -173,7 +173,7 @@ to be a Prony series.</p>
 <p class="last">While this fix bears many similarities to <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a>, it has one significant
 difference. Namely, <a class="reference internal" href="#"><span class="doc">fix gld</span></a> performs time integration,
 whereas <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a> does NOT. To this end, the
-specification of another fix to perform time integration, such as <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>, is NOT necessary.</p>
+specification of another fix to perform time integration, such as <span class="xref doc">fix nve</span>, is NOT necessary.</p>
 </div>
 <p>With this fix active, the force on the <em>j</em>th atom is given as</p>
 <img alt="_images/fix_gld1.jpg" class="align-center" src="_images/fix_gld1.jpg" />

doc/html/fix_gle.html

@@ -164,7 +164,7 @@ vibrational modes in the system to inexpensive (approximate)
 modelling of nuclear quantum effects. Contrary to
 <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a>, this fix performs both
 thermostatting and evolution of the Hamiltonian equations of motion, so it
-should not be used together with <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> &#8211; at least not
+should not be used together with <span class="xref doc">fix nve</span> &#8211; at least not
 on the same atom groups.</p>
 <p>Each degree of freedom in the thermostatted group is supplemented
 with Ns additional degrees of freedom s, and the equations of motion

doc/html/fix_heat.html

@@ -209,7 +209,7 @@ energy change is 0.0 or use <a class="reference internal" href="fix_viscous.html
 energy from the system.</p>
 <p>This fix does not change the coordinates of its atoms; it only scales
 their velocities.  Thus you must still use an integration fix
-(e.g. <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>) on the affected atoms.  This fix should
+(e.g. <span class="xref doc">fix nve</span>) on the affected atoms.  This fix should
 not normally be used on atoms that have their temperature controlled
 by another fix - e.g. <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a> or <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a> fix.</p>
 </div>

doc/html/fix_ipi.html

@@ -193,7 +193,7 @@ environment.</p>
 </div>
 <div class="section" id="related-commands">
 <h2>Related commands</h2>
-<p><a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a></p>
+<p><span class="xref doc">fix nve</span></p>
 <hr class="docutils" />
 <p id="ipicpc"><strong>(IPI-CPC)</strong> Ceriotti, More and Manolopoulos, Comp Phys Comm, 185,
 1019-1026 (2014).</p>

doc/html/fix_langevin.html

@@ -177,7 +177,7 @@
 <h2>Description</h2>
 <p>Apply a Langevin thermostat as described in <a class="reference internal" href="fix_langevin_eff.html#schneider"><span class="std std-ref">(Schneider)</span></a>
 to a group of atoms which models an interaction with a background
-implicit solvent.  Used with <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>, this command
+implicit solvent.  Used with <span class="xref doc">fix nve</span>, this command
 performs Brownian dynamics (BD), since the total force on each atom
 will have the form:</p>
 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">F</span> <span class="o">=</span> <span class="n">Fc</span> <span class="o">+</span> <span class="n">Ff</span> <span class="o">+</span> <span class="n">Fr</span>
@@ -218,7 +218,7 @@ thermostatting takes place; see the description below.</p>
 Nose/Hoover thermostatting AND time integration, this fix does NOT
 perform time integration.  It only modifies forces to effect
 thermostatting.  Thus you must use a separate time integration fix,
-like <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> to actually update the velocities and
+like <span class="xref doc">fix nve</span> to actually update the velocities and
 positions of atoms using the modified forces.  Likewise, this fix
 should not normally be used on atoms that also have their temperature
 controlled by another fix - e.g. by <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a> or <a class="reference internal" href="fix_temp_rescale.html"><span class="doc">fix temp/rescale</span></a> commands.</p>

doc/html/fix_langevin_drude.html

@@ -209,7 +209,7 @@ from them before thermostating takes place; see the description below.</p>
 <p class="last">Like the <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a> command, this fix does
 NOT perform time integration. It only modifies forces to effect
 thermostating. Thus you must use a separate time integration fix, like
-<a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> or <a class="reference internal" href="fix_nh.html"><span class="doc">fix nph</span></a> to actually update the
+<span class="xref doc">fix nve</span> or <a class="reference internal" href="fix_nh.html"><span class="doc">fix nph</span></a> to actually update the
 velocities and positions of atoms using the modified forces.
 Likewise, this fix should not normally be used on atoms that also have
 their temperature controlled by another fix - e.g. by <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a> or <a class="reference internal" href="fix_temp_rescale.html"><span class="doc">fix temp/rescale</span></a> commands.</p>

doc/html/fix_lb_fluid.html

@@ -210,7 +210,7 @@ finite difference LB integrator is used.  If <em>LBtype</em> is set equal to
 functions,</p>
 <img alt="_images/fix_lb_fluid_properties.jpg" class="align-center" src="_images/fix_lb_fluid_properties.jpg" />
 <p>Full details of the lattice-Boltzmann algorithm used can be found in
-<a class="reference internal" href="#mackay"><span class="std std-ref">Mackay et al.</span></a>.</p>
+<a class="reference internal" href="fix_lb_viscous.html#mackay"><span class="std std-ref">Mackay et al.</span></a>.</p>
 <p>The fluid is coupled to the MD particles described by <em>group-ID</em>
 through a velocity dependent force.  The contribution to the fluid
 force on a given lattice mesh site j due to MD particle alpha is
@@ -242,7 +242,7 @@ using the <em>setArea</em> keyword.</p>
 <p>The user also has the option of specifying their own value for the
 force coupling constant, for all the MD particles associated with the
 fix, through the use of the <em>setGamma</em> keyword.  This may be useful
-when modelling porous particles.  See <a class="reference internal" href="#mackay"><span class="std std-ref">Mackay et al.</span></a> for a
+when modelling porous particles.  See <a class="reference internal" href="fix_lb_viscous.html#mackay"><span class="std std-ref">Mackay et al.</span></a> for a
 detailed description of the method by which the user can choose an
 appropriate gamma value.</p>
 <div class="admonition note">
@@ -256,7 +256,7 @@ This fix adds the hydrodynamic force to the total force acting on the
 particles, after which any of the built-in LAMMPS integrators can be
 used to integrate the particle motion.  However, if the user specifies
 their own value for the force coupling constant, as mentioned in
-<a class="reference internal" href="#mackay"><span class="std std-ref">Mackay et al.</span></a>, the built-in LAMMPS integrators may prove to
+<a class="reference internal" href="fix_lb_viscous.html#mackay"><span class="std std-ref">Mackay et al.</span></a>, the built-in LAMMPS integrators may prove to
 be unstable.  Therefore, we have included our own integrators <a class="reference internal" href="fix_lb_rigid_pc_sphere.html"><span class="doc">fix lb/rigid/pc/sphere</span></a>, and <a class="reference internal" href="fix_lb_pc.html"><span class="doc">fix lb/pc</span></a>, to solve for the particle motion in these
 cases.  These integrators should not be used with the
 <a class="reference internal" href="fix_lb_viscous.html"><span class="doc">lb/viscous</span></a> fix, as they add hydrodynamic forces
@@ -341,7 +341,7 @@ N timesteps.</p>
 <p>If the keyword <em>trilinear</em> is used, the trilinear stencil is used to
 interpolate the particle nodes onto the fluid mesh.  By default, the
 immersed boundary method, Peskin stencil is used.  Both of these
-interpolation methods are described in <a class="reference internal" href="#mackay"><span class="std std-ref">Mackay et al.</span></a>.</p>
+interpolation methods are described in <a class="reference internal" href="fix_lb_viscous.html#mackay"><span class="std std-ref">Mackay et al.</span></a>.</p>
 <p>If the keyword <em>D3Q19</em> is used, the 19 velocity (D3Q19) lattice is
 used by the lattice-Boltzmann algorithm.  By default, the 15 velocity
 (D3Q15) lattice is used.</p>
@@ -371,7 +371,7 @@ the fluid densities and velocities at each lattice site are printed to the
 screen every N timesteps.</p>
 <hr class="docutils" />
 <p>For further details, as well as descriptions and results of several
-test runs, see <a class="reference internal" href="#mackay"><span class="std std-ref">Mackay et al.</span></a>.  Please include a citation to
+test runs, see <a class="reference internal" href="fix_lb_viscous.html#mackay"><span class="std std-ref">Mackay et al.</span></a>.  Please include a citation to
 this paper if the lb_fluid fix is used in work contributing to
 published research.</p>
 </div>

doc/html/fix_move.html

@@ -175,14 +175,14 @@ whose movement can influence nearby atoms.</p>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
 <p class="last">The atoms affected by this fix should not normally be time
-integrated by other fixes (e.g. <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>, <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a>), since that will change their positions and
+integrated by other fixes (e.g. <span class="xref doc">fix nve</span>, <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a>), since that will change their positions and
 velocities twice.</p>
 </div>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
 <p class="last">As atoms move due to this fix, they will pass thru periodic
 boundaries and be remapped to the other side of the simulation box,
-just as they would during normal time integration (e.g. via the <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> command).  It is up to you to decide whether
+just as they would during normal time integration (e.g. via the <span class="xref doc">fix nve</span> command).  It is up to you to decide whether
 periodic boundaries are appropriate with the kind of atom motion you
 are prescribing with this fix.</p>
 </div>
@@ -211,7 +211,7 @@ specified, <em>V</em> is the specified velocity vector with components
 specified.  This style also sets the velocity of each atom to V =
 (Vx,Vy,Vz).  If any of the velocity components is specified as NULL,
 then the position and velocity of that component is time integrated
-the same as the <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> command would perform, using
+the same as the <span class="xref doc">fix nve</span> command would perform, using
 the corresponding force component on the atom.</p>
 <p>Note that the <em>linear</em> style is identical to using the <em>variable</em>
 style with an <a class="reference internal" href="variable.html"><span class="doc">equal-style variable</span></a> that uses the
@@ -234,7 +234,7 @@ elapsed since the fix was specified.  This style also sets the
 velocity of each atom to the time derivative of this expression.  If
 any of the amplitude components is specified as NULL, then the
 position and velocity of that component is time integrated the same as
-the <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> command would perform, using the
+the <span class="xref doc">fix nve</span> command would perform, using the
 corresponding force component on the atom.</p>
 <p>Note that the <em>wiggle</em> style is identical to using the <em>variable</em>
 style with <a class="reference internal" href="variable.html"><span class="doc">equal-style variables</span></a> that use the
@@ -282,7 +282,7 @@ atom.</p>
 <p>Any of the 6 variables can be specified as NULL.  If both the
 displacement and velocity variables for a particular x,y,z component
 are specified as NULL, then the position and velocity of that
-component is time integrated the same as the <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>
+component is time integrated the same as the <span class="xref doc">fix nve</span>
 command would perform, using the corresponding force component on the
 atom.  If only the velocity variable for a component is specified as
 NULL, then the displacement variable will be used to set the position
@@ -337,7 +337,7 @@ position and velocity of atoms on the outermost rRESPA level.</p>
 </div>
 <div class="section" id="related-commands">
 <h2>Related commands</h2>
-<p><a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>, <a class="reference internal" href="displace_atoms.html"><span class="doc">displace_atoms</span></a></p>
+<p><span class="xref doc">fix nve</span>, <a class="reference internal" href="displace_atoms.html"><span class="doc">displace_atoms</span></a></p>
 <p><strong>Default:</strong> none</p>
 <p>The option default is units = lattice.</p>
 </div>

doc/html/fix_nh.html

@@ -240,11 +240,11 @@ particles will match the target values specified by Tstart/Tstop and
 Pstart/Pstop.</p>
 <p>The equations of motion used are those of Shinoda et al in
 <a class="reference internal" href="pair_sdk.html#shinoda"><span class="std std-ref">(Shinoda)</span></a>, which combine the hydrostatic equations of
-Martyna, Tobias and Klein in <a class="reference internal" href="#martyna"><span class="std std-ref">(Martyna)</span></a> with the strain
+Martyna, Tobias and Klein in <a class="reference internal" href="fix_rigid.html#martyna"><span class="std std-ref">(Martyna)</span></a> with the strain
 energy proposed by Parrinello and Rahman in
-<a class="reference internal" href="#parrinello"><span class="std std-ref">(Parrinello)</span></a>.  The time integration schemes closely
+<a class="reference internal" href="fix_nh_eff.html#parrinello"><span class="std std-ref">(Parrinello)</span></a>.  The time integration schemes closely
 follow the time-reversible measure-preserving Verlet and rRESPA
-integrators derived by Tuckerman et al in <a class="reference internal" href="fix_pimd.html#tuckerman"><span class="std std-ref">(Tuckerman)</span></a>.</p>
+integrators derived by Tuckerman et al in <a class="reference internal" href="run_style.html#tuckerman"><span class="std std-ref">(Tuckerman)</span></a>.</p>
 <hr class="docutils" />
 <p>The thermostat parameters for fix styles <em>nvt</em> and <em>npt</em> is specified
 using the <em>temp</em> keyword.  Other thermostat-related keywords are
@@ -325,7 +325,7 @@ be used with care, since it can be unphysical to dilate some atoms and
 not others, because it can introduce large, instantaneous
 displacements between a pair of atoms (one dilated, one not) that are
 far from the dilation origin.  Also note that for atoms not in the fix
-group, a separate time integration fix like <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> or
+group, a separate time integration fix like <span class="xref doc">fix nve</span> or
 <a class="reference internal" href="#"><span class="doc">fix nvt</span></a> can be used on them, independent of whether they
 are dilated or not.</p>
 <hr class="docutils" />
@@ -402,7 +402,7 @@ freedom. A value of 0 corresponds to no thermostatting of the
 barostat variables.</p>
 <p>The <em>mtk</em> keyword controls whether or not the correction terms due to
 Martyna, Tuckerman, and Klein are included in the equations of motion
-<a class="reference internal" href="#martyna"><span class="std std-ref">(Martyna)</span></a>.  Specifying <em>no</em> reproduces the original
+<a class="reference internal" href="fix_rigid.html#martyna"><span class="std std-ref">(Martyna)</span></a>.  Specifying <em>no</em> reproduces the original
 Hoover barostat, whose volume probability distribution function
 differs from the true NPT and NPH ensembles by a factor of 1/V.  Hence
 using <em>yes</em> is more correct, but in many cases the difference is
@@ -411,7 +411,7 @@ negligible.</p>
 scheme at little extra cost.  The initial and final updates of the
 thermostat variables are broken up into <em>tloop</em> substeps, each of
 length <em>dt</em>/<em>tloop</em>. This corresponds to using a first-order
-Suzuki-Yoshida scheme <a class="reference internal" href="fix_pimd.html#tuckerman"><span class="std std-ref">(Tuckerman)</span></a>.  The keyword <em>ploop</em>
+Suzuki-Yoshida scheme <a class="reference internal" href="run_style.html#tuckerman"><span class="std std-ref">(Tuckerman)</span></a>.  The keyword <em>ploop</em>
 does the same thing for the barostat thermostat.</p>
 <p>The keyword <em>nreset</em> controls how often the reference dimensions used
 to define the strain energy are reset.  If this keyword is not used,
@@ -494,7 +494,7 @@ become inefficient due to the highly skewed simulation box.</p>
 <p class="last">Unlike the <a class="reference internal" href="fix_temp_berendsen.html"><span class="doc">fix temp/berendsen</span></a> command
 which performs thermostatting but NO time integration, these fixes
 perform thermostatting/barostatting AND time integration.  Thus you
-should not use any other time integration fix, such as <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> on atoms to which this fix is applied.  Likewise,
+should not use any other time integration fix, such as <span class="xref doc">fix nve</span> on atoms to which this fix is applied.  Likewise,
 fix nvt and fix npt should not normally be used on atoms that also
 have their temperature controlled by another fix - e.g. by <a class="reference internal" href="#"><span class="doc">fix langevin</span></a> or <a class="reference internal" href="fix_temp_rescale.html"><span class="doc">fix temp/rescale</span></a>
 commands.</p>
@@ -706,7 +706,7 @@ over time or the atom count becomes very small.</p>
 </div>
 <div class="section" id="related-commands">
 <h2>Related commands</h2>
-<p><a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>, <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a>,
+<p><span class="xref doc">fix nve</span>, <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a>,
 <a class="reference internal" href="run_style.html"><span class="doc">run_style</span></a></p>
 </div>
 <div class="section" id="default">

doc/html/fix_nphug.html

@@ -221,7 +221,7 @@ the simulation. These can be overridden using the fix_modify keywords <em>e0</em
 <p class="last">Unlike the <a class="reference internal" href="fix_temp_berendsen.html"><span class="doc">fix temp/berendsen</span></a> command
 which performs thermostatting but NO time integration, this fix
 performs thermostatting/barostatting AND time integration.  Thus you
-should not use any other time integration fix, such as <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> on atoms to which this fix is applied.  Likewise,
+should not use any other time integration fix, such as <span class="xref doc">fix nve</span> on atoms to which this fix is applied.  Likewise,
 this fix should not be used on atoms that have their temperature
 controlled by another fix - e.g. by <a class="reference internal" href="fix_nh.html"><span class="doc">fix langevin</span></a> or <a class="reference internal" href="fix_temp_rescale.html"><span class="doc">fix temp/rescale</span></a> commands.</p>
 </div>

doc/html/fix_nve_asphere.html

@@ -151,7 +151,7 @@
 orientation, and angular velocity for aspherical particles in the
 group each timestep.  V is volume; E is energy.  This creates a system
 trajectory consistent with the microcanonical ensemble.</p>
-<p>This fix differs from the <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> command, which
+<p>This fix differs from the <span class="xref doc">fix nve</span> command, which
 assumes point particles and only updates their position and velocity.</p>
 </div>
 <div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
@@ -192,7 +192,7 @@ shape attribute.</p>
 </div>
 <div class="section" id="related-commands">
 <h2>Related commands</h2>
-<p><a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>, <a class="reference internal" href="fix_nve_sphere.html"><span class="doc">fix nve/sphere</span></a></p>
+<p><span class="xref doc">fix nve</span>, <a class="reference internal" href="fix_nve_sphere.html"><span class="doc">fix nve/sphere</span></a></p>
 <p><strong>Default:</strong> none</p>
 </div>
 </div>

doc/html/fix_nve_body.html

@@ -149,7 +149,7 @@ orientation, and angular velocity for body particles in the group each
 timestep.  V is volume; E is energy.  This creates a system trajectory
 consistent with the microcanonical ensemble.  See <a class="reference internal" href="Section_howto.html#howto-14"><span class="std std-ref">Section_howto 14</span></a> of the manual and the <a class="reference internal" href="body.html"><span class="doc">body</span></a>
 doc page for more details on using body particles.</p>
-<p>This fix differs from the <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> command, which
+<p>This fix differs from the <span class="xref doc">fix nve</span> command, which
 assumes point particles and only updates their position and velocity.</p>
 </div>
 <div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
@@ -172,7 +172,7 @@ point particles.</p>
 </div>
 <div class="section" id="related-commands">
 <h2>Related commands</h2>
-<p><a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>, <a class="reference internal" href="fix_nve_sphere.html"><span class="doc">fix nve/sphere</span></a>, <a class="reference internal" href="fix_nve_asphere.html"><span class="doc">fix nve/asphere</span></a></p>
+<p><span class="xref doc">fix nve</span>, <a class="reference internal" href="fix_nve_sphere.html"><span class="doc">fix nve/sphere</span></a>, <a class="reference internal" href="fix_nve_asphere.html"><span class="doc">fix nve/asphere</span></a></p>
 <p><strong>Default:</strong> none</p>
 </div>
 </div>

doc/html/fix_nve_eff.html

@@ -147,7 +147,7 @@
 <p>Perform constant NVE integration to update position and velocity for
 nuclei and electrons in the group for the <a class="reference internal" href="pair_eff.html"><span class="doc">electron force field</span></a> model.  V is volume; E is energy.  This creates a
 system trajectory consistent with the microcanonical ensemble.</p>
-<p>The operation of this fix is exactly like that described by the <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> command, except that the radius and radial velocity
+<p>The operation of this fix is exactly like that described by the <span class="xref doc">fix nve</span> command, except that the radius and radial velocity
 of electrons are also updated.</p>
 </div>
 <div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
@@ -165,7 +165,7 @@ LAMMPS was built with that package.  See the <a class="reference internal" href=
 </div>
 <div class="section" id="related-commands">
 <h2>Related commands</h2>
-<p><a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>, <a class="reference internal" href="fix_nh_eff.html"><span class="doc">fix nvt/eff</span></a>, <a class="reference internal" href="fix_nh_eff.html"><span class="doc">fix npt/eff</span></a></p>
+<p><span class="xref doc">fix nve</span>, <a class="reference internal" href="fix_nh_eff.html"><span class="doc">fix nvt/eff</span></a>, <a class="reference internal" href="fix_nh_eff.html"><span class="doc">fix npt/eff</span></a></p>
 <p><strong>Default:</strong> none</p>
 </div>
 </div>

doc/html/fix_nve_limit.html

@@ -164,7 +164,7 @@ missed on successive timesteps as atoms move.  See the
 for details.</p>
 <p>Note that if a velocity reset occurs the integrator will not conserve
 energy.  On steps where no velocity resets occur, this integrator is
-exactly like the <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> command.  Since forces are
+exactly like the <span class="xref doc">fix nve</span> command.  Since forces are
 unaltered, pressures computed by thermodynamic output will still be
 very large for overlapped configurations.</p>
 <div class="admonition note">
@@ -202,7 +202,7 @@ the <a class="reference internal" href="run.html"><span class="doc">run</span></
 </div>
 <div class="section" id="related-commands">
 <h2>Related commands</h2>
-<p><a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>, <a class="reference internal" href="fix_nve_noforce.html"><span class="doc">fix nve/noforce</span></a>,
+<p><span class="xref doc">fix nve</span>, <a class="reference internal" href="fix_nve_noforce.html"><span class="doc">fix nve/noforce</span></a>,
 <a class="reference internal" href="pair_soft.html"><span class="doc">pair_style soft</span></a></p>
 <p><strong>Default:</strong> none</p>
 </div>

doc/html/fix_nve_line.html

@@ -150,7 +150,7 @@ group each timestep.  V is volume; E is energy.  This creates a system
 trajectory consistent with the microcanonical ensemble.  See
 <a class="reference internal" href="Section_howto.html"><span class="doc">Section_howto 14</span></a> of the manual for an overview of
 using line segment particles.</p>
-<p>This fix differs from the <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> command, which
+<p>This fix differs from the <span class="xref doc">fix nve</span> command, which
 assumes point particles and only updates their position and velocity.</p>
 </div>
 <div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
@@ -170,7 +170,7 @@ was built with that package.  See the <a class="reference internal" href="Sectio
 </div>
 <div class="section" id="related-commands">
 <h2>Related commands</h2>
-<p><a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>, <a class="reference internal" href="fix_nve_asphere.html"><span class="doc">fix nve/asphere</span></a></p>
+<p><span class="xref doc">fix nve</span>, <a class="reference internal" href="fix_nve_asphere.html"><span class="doc">fix nve/asphere</span></a></p>
 <p><strong>Default:</strong> none</p>
 </div>
 </div>

doc/html/fix_nve_noforce.html

@@ -171,7 +171,7 @@ This fix is not invoked during <a class="reference internal" href="minimize.html
 </div>
 <div class="section" id="related-commands">
 <h2>Related commands</h2>
-<p><a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a></p>
+<p><span class="xref doc">fix nve</span></p>
 <p><strong>Default:</strong> none</p>
 </div>
 </div>

doc/html/fix_nve_sphere.html

@@ -158,7 +158,7 @@
 angular velocity for finite-size spherical particles in the group each
 timestep.  V is volume; E is energy.  This creates a system trajectory
 consistent with the microcanonical ensemble.</p>
-<p>This fix differs from the <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> command, which
+<p>This fix differs from the <span class="xref doc">fix nve</span> command, which
 assumes point particles and only updates their position and velocity.</p>
 <p>If the <em>update</em> keyword is used with the <em>dipole</em> value, then the
 orientation of the dipole moment of each particle is also updated
@@ -203,7 +203,7 @@ be point particles.</p>
 </div>
 <div class="section" id="related-commands">
 <h2>Related commands</h2>
-<p><a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>, <a class="reference internal" href="fix_nve_asphere.html"><span class="doc">fix nve/asphere</span></a></p>
+<p><span class="xref doc">fix nve</span>, <a class="reference internal" href="fix_nve_asphere.html"><span class="doc">fix nve/asphere</span></a></p>
 <p><strong>Default:</strong> none</p>
 </div>
 </div>

doc/html/fix_nve_tri.html

@@ -150,7 +150,7 @@ group each timestep.  V is volume; E is energy.  This creates a system
 trajectory consistent with the microcanonical ensemble.  See
 <a class="reference internal" href="Section_howto.html"><span class="doc">Section_howto 14</span></a> of the manual for an overview of
 using triangular particles.</p>
-<p>This fix differs from the <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> command, which
+<p>This fix differs from the <span class="xref doc">fix nve</span> command, which
 assumes point particles and only updates their position and velocity.</p>
 </div>
 <div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
@@ -170,7 +170,7 @@ was built with that package.  See the <a class="reference internal" href="Sectio
 </div>
 <div class="section" id="related-commands">
 <h2>Related commands</h2>
-<p><a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>, <a class="reference internal" href="fix_nve_asphere.html"><span class="doc">fix nve/asphere</span></a></p>
+<p><span class="xref doc">fix nve</span>, <a class="reference internal" href="fix_nve_asphere.html"><span class="doc">fix nve/asphere</span></a></p>
 <p><strong>Default:</strong> none</p>
 </div>
 </div>

doc/html/fix_nvt_sllod.html

@@ -267,7 +267,7 @@ equilibration.</p>
 </div>
 <div class="section" id="related-commands">
 <h2>Related commands</h2>
-<p><a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>, <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a>, <a class="reference internal" href="fix_temp_rescale.html"><span class="doc">fix temp/rescale</span></a>, <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a>,
+<p><span class="xref doc">fix nve</span>, <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a>, <a class="reference internal" href="fix_temp_rescale.html"><span class="doc">fix temp/rescale</span></a>, <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a>,
 <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a>, <a class="reference internal" href="compute_temp_deform.html"><span class="doc">compute temp/deform</span></a></p>
 </div>
 <div class="section" id="default">

doc/html/fix_pimd.html

@@ -171,7 +171,7 @@ index (the second term in the effective potential above).  The
 quasi-beads also interact with the two neighboring quasi-beads through
 the spring potential in imaginary-time space (first term in effective
 potential).  To sample the canonical ensemble, a Nose-Hoover massive
-chain thermostat is applied <a class="reference internal" href="#tuckerman"><span class="std std-ref">(Tuckerman)</span></a>.  With the
+chain thermostat is applied <a class="reference internal" href="run_style.html#tuckerman"><span class="std std-ref">(Tuckerman)</span></a>.  With the
 massive chain algorithm, a chain of NH thermostats is coupled to each
 degree of freedom for each quasi-bead.  The keyword <em>temp</em> sets the
 target temperature for the system and the keyword <em>nhc</em> sets the

doc/html/fix_press_berendsen.html

@@ -175,7 +175,7 @@ unchanged and controlling the pressure of a surrounding fluid.</p>
 commands which perform Nose/Hoover barostatting AND time integration,
 this fix does NOT perform time integration.  It only modifies the box
 size and atom coordinates to effect barostatting.  Thus you must use a
-separate time integration fix, like <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> or <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a> to actually update the positions and velocities of
+separate time integration fix, like <span class="xref doc">fix nve</span> or <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a> to actually update the positions and velocities of
 atoms.  This fix can be used in conjunction with thermostatting fixes
 to control the temperature, such as <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a> or <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a> or <a class="reference internal" href="fix_temp_berendsen.html"><span class="doc">fix temp/berendsen</span></a>.</p>
 </div>
@@ -316,7 +316,7 @@ various <a class="reference internal" href="Section_howto.html#howto-15"><span c
 </div>
 <div class="section" id="related-commands">
 <h2>Related commands</h2>
-<p><a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>, <a class="reference internal" href="fix_nh.html"><span class="doc">fix nph</span></a>, <a class="reference internal" href="fix_nh.html"><span class="doc">fix npt</span></a>, <a class="reference internal" href="fix_temp_berendsen.html"><span class="doc">fix temp/berendsen</span></a>,
+<p><span class="xref doc">fix nve</span>, <a class="reference internal" href="fix_nh.html"><span class="doc">fix nph</span></a>, <a class="reference internal" href="fix_nh.html"><span class="doc">fix npt</span></a>, <a class="reference internal" href="fix_temp_berendsen.html"><span class="doc">fix temp/berendsen</span></a>,
 <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a></p>
 </div>
 <div class="section" id="default">

doc/html/fix_qtb.html

@@ -158,7 +158,7 @@
 <h2>Description</h2>
 <p>This command performs the quantum thermal bath scheme proposed by
 <a class="reference internal" href="#dammak"><span class="std std-ref">(Dammak)</span></a> to include self-consistent quantum nuclear effects,
-when used in conjunction with the <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> or <a class="reference internal" href="fix_nh.html"><span class="doc">fix nph</span></a> commands.</p>
+when used in conjunction with the <span class="xref doc">fix nve</span> or <a class="reference internal" href="fix_nh.html"><span class="doc">fix nph</span></a> commands.</p>
 <p>Classical molecular dynamics simulation does not include any quantum
 nuclear effect. Quantum treatment of the vibrational modes will
 introduce zero point energy into the system, alter the energy power
@@ -241,7 +241,7 @@ Mbytes.</p>
 Nose/Hoover thermostatting AND time integration, this fix does NOT
 perform time integration. It only modifies forces to a colored
 thermostat. Thus you must use a separate time integration fix, like
-<a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> or <a class="reference internal" href="fix_nh.html"><span class="doc">fix nph</span></a> to actually update the
+<span class="xref doc">fix nve</span> or <a class="reference internal" href="fix_nh.html"><span class="doc">fix nph</span></a> to actually update the
 velocities and positions of atoms (as shown in the
 examples). Likewise, this fix should not normally be used with other
 fixes or commands that also specify system temperatures , e.g. <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a> and <a class="reference internal" href="fix_temp_rescale.html"><span class="doc">fix temp/rescale</span></a>.</p>
@@ -263,7 +263,7 @@ LAMMPS was built with that package. See the <a class="reference internal" href="
 <hr class="docutils" />
 <div class="section" id="related-commands">
 <h2>Related commands</h2>
-<p><a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>, <a class="reference internal" href="fix_nh.html"><span class="doc">fix nph</span></a>, <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a>, <a class="reference internal" href="fix_qbmsst.html"><span class="doc">fix qbmsst</span></a></p>
+<p><span class="xref doc">fix nve</span>, <a class="reference internal" href="fix_nh.html"><span class="doc">fix nph</span></a>, <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a>, <a class="reference internal" href="fix_qbmsst.html"><span class="doc">fix qbmsst</span></a></p>
 </div>
 <hr class="docutils" />
 <div class="section" id="default">

doc/html/fix_recenter.html

@@ -187,7 +187,7 @@ velocities with zero aggregate linear and/or angular momentum.</p>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
 <p class="last">This fix performs its operations at the same point in the
-timestep as other time integration fixes, such as <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>, <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a>, or <a class="reference internal" href="fix_nh.html"><span class="doc">fix npt</span></a>.
+timestep as other time integration fixes, such as <span class="xref doc">fix nve</span>, <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a>, or <a class="reference internal" href="fix_nh.html"><span class="doc">fix npt</span></a>.
 Thus fix recenter should normally be the last such fix specified in
 the input script, since the adjustments it makes to atom coordinates
 should come after the changes made by time integration.  LAMMPS will

doc/html/fix_rigid.html

@@ -288,10 +288,10 @@ differences may accumulate to produce divergent trajectories.</p>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
 <p class="last">You should not update the atoms in rigid bodies via other
-time-integration fixes (e.g. <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>, <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a>, <a class="reference internal" href="fix_nh.html"><span class="doc">fix npt</span></a>), or you will be integrating
+time-integration fixes (e.g. <span class="xref doc">fix nve</span>, <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a>, <a class="reference internal" href="fix_nh.html"><span class="doc">fix npt</span></a>), or you will be integrating
 their motion more than once each timestep.  When performing a hybrid
 simulation with some atoms in rigid bodies, and some not, a separate
-time integration fix like <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> or <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a> should be used for the non-rigid particles.</p>
+time integration fix like <span class="xref doc">fix nve</span> or <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a> should be used for the non-rigid particles.</p>
 </div>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
@@ -303,7 +303,7 @@ your time integration fix.  E.g. use &#8220;fix 1 mobile nve&#8221; instead of
 move.  You can move atoms with a constant velocity by assigning them
 an initial velocity (via the <a class="reference internal" href="velocity.html"><span class="doc">velocity</span></a> command),
 setting the force on them to 0.0 (via the <a class="reference internal" href="fix_setforce.html"><span class="doc">fix setforce</span></a> command), and integrating them as usual
-(e.g. via the <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> command).</p>
+(e.g. via the <span class="xref doc">fix nve</span> command).</p>
 </div>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
@@ -685,10 +685,10 @@ also accounted for by this fix.</p>
 <hr class="docutils" />
 <p>If your simlulation is a hybrid model with a mixture of rigid bodies
 and non-rigid particles (e.g. solvent) there are several ways these
-rigid fixes can be used in tandem with <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>, <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a>, <a class="reference internal" href="fix_nh.html"><span class="doc">fix npt</span></a>, and <a class="reference internal" href="fix_nh.html"><span class="doc">fix nph</span></a>.</p>
+rigid fixes can be used in tandem with <span class="xref doc">fix nve</span>, <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a>, <a class="reference internal" href="fix_nh.html"><span class="doc">fix npt</span></a>, and <a class="reference internal" href="fix_nh.html"><span class="doc">fix nph</span></a>.</p>
 <p>If you wish to perform NVE dynamics (no thermostatting or
 barostatting), use fix rigid or fix rigid/nve to integrate the rigid
-bodies, and <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> to integrate the non-rigid
+bodies, and <span class="xref doc">fix nve</span> to integrate the non-rigid
 particles.</p>
 <p>If you wish to perform NVT dynamics (thermostatting, but no
 barostatting), you can use fix rigid/nvt for the rigid bodies, and any

doc/html/fix_shardlow.html

@@ -148,7 +148,7 @@
 integrate the DPD equations of motion.  The SSA splits the integration
 into a stochastic and deterministic integration step.  The fix
 <em>shardlow</em> performs the stochastic integration step and must be used
-in conjunction with a deterministic integrator (e.g. <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> or <span class="xref doc">fix nph</span>).  The stochastic
+in conjunction with a deterministic integrator (e.g. <span class="xref doc">fix nve</span> or <span class="xref doc">fix nph</span>).  The stochastic
 integration of the dissipative and random forces is performed prior to
 the deterministic integration of the conservative force. Further
 details regarding the method are provided in <a class="reference internal" href="pair_dpd_fdt.html#lisal"><span class="std std-ref">(Lisal)</span></a> and
@@ -176,7 +176,7 @@ for more info.</p>
 <p>This fix is currently limited to orthogonal simulation cell
 geometries.</p>
 <p>This fix must be used with an additional fix that specifies time
-integration, e.g. <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> or <a class="reference internal" href="fix_nh.html"><span class="doc">fix nph</span></a>.</p>
+integration, e.g. <span class="xref doc">fix nve</span> or <a class="reference internal" href="fix_nh.html"><span class="doc">fix nph</span></a>.</p>
 <p>The Shardlow splitting algorithm requires the sizes of the sub-domain
 lengths to be larger than twice the cutoff+skin.  Generally, the
 domain decomposition is dependant on the number of processors

doc/html/fix_temp_berendsen.html

@@ -184,7 +184,7 @@ time.  Thus it is easy to specify a time-dependent temperature.</p>
 Nose/Hoover thermostatting AND time integration, this fix does NOT
 perform time integration.  It only modifies velocities to effect
 thermostatting.  Thus you must use a separate time integration fix,
-like <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> to actually update the positions of atoms
+like <span class="xref doc">fix nve</span> to actually update the positions of atoms
 using the modified velocities.  Likewise, this fix should not normally
 be used on atoms that also have their temperature controlled by
 another fix - e.g. by <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a> or <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a> commands.</p>
@@ -270,7 +270,7 @@ over time or the atom count becomes very small.</p>
 </div>
 <div class="section" id="related-commands">
 <h2>Related commands</h2>
-<p><a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>, <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a>, <a class="reference internal" href="fix_temp_rescale.html"><span class="doc">fix temp/rescale</span></a>, <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a>,
+<p><span class="xref doc">fix nve</span>, <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a>, <a class="reference internal" href="fix_temp_rescale.html"><span class="doc">fix temp/rescale</span></a>, <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a>,
 <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a>, <a class="reference internal" href="compute_temp.html"><span class="doc">compute temp</span></a>,
 <a class="reference internal" href="fix_press_berendsen.html"><span class="doc">fix press/berendsen</span></a></p>
 <p><strong>Default:</strong> none</p>

doc/html/fix_temp_csvr.html

@@ -199,7 +199,7 @@ time.  Thus it is easy to specify a time-dependent temperature.</p>
 Nose/Hoover thermostatting AND time integration, these fixes do NOT
 perform time integration. They only modify velocities to effect
 thermostatting.  Thus you must use a separate time integration fix,
-like <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> to actually update the positions of atoms
+like <span class="xref doc">fix nve</span> to actually update the positions of atoms
 using the modified velocities.  Likewise, these fixes should not
 normally be used on atoms that also have their temperature controlled
 by another fix - e.g. by <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a> or <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a> commands.</p>
@@ -269,7 +269,7 @@ over time or the atom count becomes very small.</p>
 </div>
 <div class="section" id="related-commands">
 <h2>Related commands</h2>
-<p><a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>, <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a>, <a class="reference internal" href="fix_temp_rescale.html"><span class="doc">fix temp/rescale</span></a>, <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a>,
+<p><span class="xref doc">fix nve</span>, <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a>, <a class="reference internal" href="fix_temp_rescale.html"><span class="doc">fix temp/rescale</span></a>, <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a>,
 <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a>, <a class="reference internal" href="compute_temp.html"><span class="doc">compute temp</span></a>,
 <a class="reference internal" href="fix_temp_berendsen.html"><span class="doc">fix temp/berendsen</span></a></p>
 <p><strong>Default:</strong> none</p>

doc/html/fix_temp_rescale.html

@@ -193,7 +193,7 @@ value.</p>
 Nose/Hoover thermostatting AND time integration, this fix does NOT
 perform time integration.  It only modifies velocities to effect
 thermostatting.  Thus you must use a separate time integration fix,
-like <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> to actually update the positions of atoms
+like <span class="xref doc">fix nve</span> to actually update the positions of atoms
 using the modified velocities.  Likewise, this fix should not normally
 be used on atoms that also have their temperature controlled by
 another fix - e.g. by <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a> or <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a> commands.</p>

doc/html/fix_tfmc.html

@@ -192,7 +192,7 @@ Carlo algorithm and thus strictly speaking does not perform time
 integration, it is similar in the sense that it uses the forces on all
 atoms in order to update their positions. Therefore, it is implemented
 as a time integration fix, and no other fixes of this type (such as
-<a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>) should be used at the same time. Because
+<span class="xref doc">fix nve</span>) should be used at the same time. Because
 velocities do not play a role in this kind of Monte Carlo simulations,
 instantaneous temperatures as calculated by <a class="reference internal" href="compute_temp.html"><span class="doc">temperature computes</span></a> or <a class="reference internal" href="thermo_style.html"><span class="doc">thermodynamic output</span></a> have no meaning: the only relevant
 temperature is the sampling temperature <em>Temp</em>.  Similarly, performing

doc/html/fix_ttm.html

@@ -273,7 +273,7 @@ the electronic subsystem.  The ordering of the Nx*Ny*Nz columns is
 with the z index varing fastest, y the next fastest, and x the
 slowest.</p>
 <p>These fixes do not change the coordinates of their atoms; they only
-scales their velocities.  Thus a time integration fix (e.g. <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>) should still be used to time integrate the affected
+scales their velocities.  Thus a time integration fix (e.g. <span class="xref doc">fix nve</span>) should still be used to time integrate the affected
 atoms.  The fixes should not normally be used on atoms that have their
 temperature controlled by another fix - e.g. <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a> or
 <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a>.</p>

doc/html/fix_wall_piston.html

@@ -169,7 +169,7 @@ specified group and drive the system with an effective infinite-mass
 piston capable of driving shock waves.</p>
 <p>A momentum mirror technique is used, which means that if an atom (or
 the wall) moves such that an atom is outside the wall on a timestep by
-a distance delta (e.g. due to <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>), then it is put
+a distance delta (e.g. due to <span class="xref doc">fix nve</span>), then it is put
 back inside the face by the same delta, and the velocity relative to
 the moving wall is flipped in z.  For instance, a stationary particle
 hit with a piston wall with velocity vz, will end the timestep with a

doc/html/fix_wall_reflect.html

@@ -173,10 +173,10 @@
 <p>Bound the simulation with one or more walls which reflect particles
 in the specified group when they attempt to move thru them.</p>
 <p>Reflection means that if an atom moves outside the wall on a timestep
-by a distance delta (e.g. due to <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>), then it is
+by a distance delta (e.g. due to <span class="xref doc">fix nve</span>), then it is
 put back inside the face by the same delta, and the sign of the
 corresponding component of its velocity is flipped.</p>
-<p>When used in conjunction with <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> and <a class="reference internal" href="run_style.html"><span class="doc">run_style verlet</span></a>, the resultant time-integration algorithm is
+<p>When used in conjunction with <span class="xref doc">fix nve</span> and <a class="reference internal" href="run_style.html"><span class="doc">run_style verlet</span></a>, the resultant time-integration algorithm is
 equivalent to the primitive splitting algorithm (PSA) described by
 <a class="reference internal" href="#bond"><span class="std std-ref">Bond</span></a>.  Because each reflection event divides
 the corresponding timestep asymmetrically, energy conservation is only

doc/html/genindex.html

@@ -1206,10 +1206,6 @@
   </dt>
 
       
-  <dt><a href="fix_nve.html#index-0">fix nve</a>
-  </dt>
-
-      
   <dt><a href="fix_nve_asphere.html#index-0">fix nve/asphere</a>
   </dt>
 

doc/html/improper_class2.html

@@ -165,7 +165,7 @@ theta angles, since it is always the center atom.</p>
 <p>Since atom J is the atom of symmetry, normally the bonds J-I, J-K, J-L
 would exist for an improper to be defined between the 4 atoms, but
 this is not required.</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 Ei and Eaa formulas must be defined for each
 improper type via the <a class="reference internal" href="improper_coeff.html"><span class="doc">improper_coeff</span></a> command as
 in the example above, or in the data file or restart files read by the

doc/html/improper_umbrella.html

@@ -154,7 +154,7 @@ axis and the IJK plane:</p>
 <p>If omega0 = 0 the potential term has a minimum for the planar
 structure.  Otherwise it has two minima at +/- omega0, with a barrier
 in between.</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 improper type via
 the <a class="reference internal" href="improper_coeff.html"><span class="doc">improper_coeff</span></a> command as in the example
 above, or in the data file or restart files read by the

doc/html/pair_charmm.html

@@ -222,7 +222,7 @@
 additional switching function S(r) that ramps the energy and force
 smoothly to zero between an inner and outer cutoff.  It is a widely
 used potential in the <a class="reference external" href="http://www.scripps.edu/brooks">CHARMM</a> MD code.
-See <a class="reference internal" href="#mackerell"><span class="std std-ref">(MacKerell)</span></a> for a description of the CHARMM force
+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>
 <img alt="_images/pair_charmm.jpg" class="align-center" src="_images/pair_charmm.jpg" />
 <p>Both the LJ and Coulombic terms require an inner and outer cutoff.

doc/html/pair_class2.html

@@ -213,7 +213,7 @@
 <p>Rc is the cutoff.</p>
 <p>The <em>lj/class2/coul/cut</em> and <em>lj/class2/coul/long</em> styles add a
 Coulombic term as described for the <a class="reference internal" href="pair_lj.html"><span class="doc">lj/cut</span></a> pair styles.</p>
-<p>See <a class="reference internal" href="#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 pair of atoms
 types via the <a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a> command as in the examples
 above, or in the data file or restart files read by the

doc/html/pair_hbond_dreiding.html

@@ -181,7 +181,7 @@ the donor atom, e.g. in a bond list read in from a data file via the
 hydrogen atoms for each donor/acceptor type pair are specified by the
 <a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a> command (see below).</p>
 <p>Style <em>hbond/dreiding/lj</em> is the original DREIDING potential of
-<a class="reference internal" href="#mayo"><span class="std std-ref">(Mayo)</span></a>.  It uses a LJ 12/10 functional for the Donor-Acceptor
+<a class="reference internal" href="special_bonds.html#mayo"><span class="std std-ref">(Mayo)</span></a>.  It uses a LJ 12/10 functional for the Donor-Acceptor
 interactions. To match the results in the original paper, use n = 4.</p>
 <p>Style <em>hbond/dreiding/morse</em> is an improved version using a Morse
 potential for the Donor-Acceptor interactions. <a class="reference internal" href="#liu"><span class="std std-ref">(Liu)</span></a> showed

doc/html/rerun.html

@@ -250,7 +250,7 @@ simulation.</p>
 include and perform all the usual operations of an input script that
 uses the <a class="reference internal" href="run.html"><span class="doc">run</span></a> command.  There are a few exceptions and
 points to consider, as discussed here.</p>
-<p>Fixes that perform time integration, such as <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> or
+<p>Fixes that perform time integration, such as <span class="xref doc">fix nve</span> or
 <a class="reference internal" href="fix_nh.html"><span class="doc">fix npt</span></a> are not invoked, since no time integration is
 performed.  Fixes that perturb or constrain the forces on atoms will
 be invoked, just as they would during a normal run.  Examples are <a class="reference internal" href="fix_indent.html"><span class="doc">fix indent</span></a> and <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a>.  So you