From 69ffae65d0a7e85681e41f9d70e89f1ec89f919e Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Mon, 9 May 2016 21:12:06 +0000
Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14972
 f3b2605a-c512-4ea7-a41b-209d697bcdaa

---
 doc/html/Section_commands.html                   |  6 +++---
 doc/html/Section_howto.html                      | 12 ++++++------
 doc/html/Section_modify.html                     |  2 +-
 doc/html/angle_charmm.html                       |  2 +-
 doc/html/angle_class2.html                       |  2 +-
 doc/html/angle_cosine_periodic.html              |  2 +-
 doc/html/bond_class2.html                        |  2 +-
 doc/html/bond_fene.html                          |  2 +-
 doc/html/bond_fene_expand.html                   |  2 +-
 doc/html/change_box.html                         |  2 +-
 doc/html/compute_angle.html                      |  2 +-
 doc/html/compute_angle_local.html                |  2 +-
 doc/html/compute_angmom_chunk.html               |  2 +-
 doc/html/compute_body_local.html                 |  2 +-
 doc/html/compute_bond.html                       |  2 +-
 doc/html/compute_bond_local.html                 |  6 +++---
 doc/html/compute_chunk_atom.html                 |  2 +-
 doc/html/compute_com.html                        |  2 +-
 doc/html/compute_com_chunk.html                  |  2 +-
 doc/html/compute_dihedral.html                   |  2 +-
 doc/html/compute_dipole_chunk.html               |  2 +-
 doc/html/compute_displace_atom.html              |  2 +-
 doc/html/compute_dpd_atom.html                   |  2 +-
 doc/html/compute_erotate_asphere.html            |  2 +-
 doc/html/compute_erotate_rigid.html              |  2 +-
 doc/html/compute_erotate_sphere.html             |  2 +-
 doc/html/compute_erotate_sphere_atom.html        |  2 +-
 doc/html/compute_group_group.html                |  4 ++--
 doc/html/compute_improper.html                   |  2 +-
 doc/html/compute_inertia_chunk.html              |  2 +-
 doc/html/compute_ke.html                         |  2 +-
 doc/html/compute_ke_atom.html                    |  2 +-
 doc/html/compute_ke_atom_eff.html                |  2 +-
 doc/html/compute_ke_eff.html                     |  2 +-
 doc/html/compute_ke_rigid.html                   |  2 +-
 doc/html/compute_meso_e_atom.html                |  2 +-
 doc/html/compute_meso_rho_atom.html              |  2 +-
 doc/html/compute_meso_t_atom.html                |  2 +-
 doc/html/compute_msd.html                        |  2 +-
 doc/html/compute_msd_chunk.html                  |  2 +-
 doc/html/compute_omega_chunk.html                |  2 +-
 doc/html/compute_pair.html                       |  4 ++--
 doc/html/compute_pair_local.html                 | 12 ++++++------
 doc/html/compute_pe.html                         |  2 +-
 doc/html/compute_pe_atom.html                    |  2 +-
 doc/html/compute_property_atom.html              |  2 +-
 doc/html/compute_property_chunk.html             |  2 +-
 doc/html/compute_rdf.html                        |  2 +-
 doc/html/compute_reduce.html                     |  2 +-
 doc/html/compute_saed.html                       |  2 +-
 doc/html/compute_slice.html                      |  2 +-
 doc/html/compute_smd_contact_radius.html         |  2 +-
 doc/html/compute_smd_hourglass_error.html        |  2 +-
 doc/html/compute_smd_internal_energy.html        |  2 +-
 doc/html/compute_smd_plastic_strain.html         |  2 +-
 doc/html/compute_smd_plastic_strain_rate.html    |  2 +-
 doc/html/compute_smd_rho.html                    |  2 +-
 doc/html/compute_smd_tlsph_defgrad.html          |  2 +-
 doc/html/compute_smd_tlsph_dt.html               |  2 +-
 doc/html/compute_smd_tlsph_num_neighs.html       |  2 +-
 doc/html/compute_smd_tlsph_strain.html           |  2 +-
 doc/html/compute_smd_tlsph_strain_rate.html      |  2 +-
 doc/html/compute_smd_tlsph_stress.html           |  2 +-
 doc/html/compute_smd_triangle_mesh_vertices.html |  2 +-
 doc/html/compute_smd_ulsph_num_neighs.html       |  2 +-
 doc/html/compute_smd_ulsph_strain.html           |  2 +-
 doc/html/compute_smd_ulsph_strain_rate.html      |  2 +-
 doc/html/compute_smd_ulsph_stress.html           |  2 +-
 doc/html/compute_smd_vol.html                    |  2 +-
 doc/html/compute_temp.html                       |  4 ++--
 doc/html/compute_temp_asphere.html               |  4 ++--
 doc/html/compute_temp_body.html                  |  4 ++--
 doc/html/compute_temp_chunk.html                 |  8 ++++----
 doc/html/compute_temp_com.html                   |  4 ++--
 doc/html/compute_temp_cs.html                    |  4 ++--
 doc/html/compute_temp_deform.html                |  4 ++--
 doc/html/compute_temp_deform_eff.html            |  4 ++--
 doc/html/compute_temp_partial.html               |  4 ++--
 doc/html/compute_temp_profile.html               |  6 +++---
 doc/html/compute_temp_ramp.html                  |  6 +++---
 doc/html/compute_temp_region.html                |  4 ++--
 doc/html/compute_temp_region_eff.html            |  4 ++--
 doc/html/compute_temp_rotate.html                |  4 ++--
 doc/html/compute_temp_sphere.html                |  4 ++--
 doc/html/compute_ti.html                         |  2 +-
 doc/html/compute_torque_chunk.html               |  2 +-
 doc/html/compute_vacf.html                       |  2 +-
 doc/html/compute_vcm_chunk.html                  |  2 +-
 doc/html/compute_voronoi_atom.html               |  4 ++--
 doc/html/compute_xrd.html                        |  2 +-
 doc/html/dihedral_charmm.html                    |  4 ++--
 doc/html/dihedral_class2.html                    |  2 +-
 doc/html/displace_atoms.html                     |  2 +-
 doc/html/dump.html                               |  2 +-
 doc/html/dump_custom_vtk.html                    |  2 +-
 doc/html/dump_modify.html                        |  6 +++---
 doc/html/fix_append_atoms.html                   |  2 +-
 doc/html/fix_ave_chunk.html                      |  6 +++---
 doc/html/fix_ave_spatial.html                    |  4 ++--
 doc/html/fix_ave_spatial_sphere.html             |  4 ++--
 doc/html/fix_deform.html                         | 10 +++++-----
 doc/html/fix_deposit.html                        |  2 +-
 doc/html/fix_external.html                       |  2 +-
 doc/html/fix_gravity.html                        |  2 +-
 doc/html/fix_heat.html                           |  2 +-
 doc/html/fix_indent.html                         |  4 ++--
 doc/html/fix_langevin.html                       |  2 +-
 doc/html/fix_langevin_drude.html                 |  2 +-
 doc/html/fix_lb_fluid.html                       | 10 +++++-----
 doc/html/fix_move.html                           |  2 +-
 doc/html/fix_nh.html                             | 10 +++++-----
 doc/html/fix_nve_limit.html                      |  2 +-
 doc/html/fix_phonon.html                         |  2 +-
 doc/html/fix_pimd.html                           |  2 +-
 doc/html/fix_press_berendsen.html                |  6 +++---
 doc/html/fix_recenter.html                       |  2 +-
 doc/html/fix_rigid.html                          |  6 +++---
 doc/html/fix_temp_berendsen.html                 |  2 +-
 doc/html/fix_temp_csvr.html                      |  2 +-
 doc/html/fix_thermal_conductivity.html           |  2 +-
 doc/html/fix_viscous.html                        |  2 +-
 doc/html/fix_wall_piston.html                    |  2 +-
 doc/html/fix_wall_reflect.html                   |  2 +-
 doc/html/fix_wall_srd.html                       |  2 +-
 doc/html/improper_class2.html                    |  2 +-
 doc/html/improper_umbrella.html                  |  2 +-
 doc/html/lattice.html                            |  6 +++---
 doc/html/mass.html                               |  2 +-
 doc/html/min_modify.html                         |  2 +-
 doc/html/molecule.html                           |  2 +-
 doc/html/neighbor.html                           |  2 +-
 doc/html/package.html                            |  2 +-
 doc/html/pair_charmm.html                        |  2 +-
 doc/html/pair_class2.html                        |  2 +-
 doc/html/pair_hbond_dreiding.html                |  2 +-
 doc/html/pair_lcbop.html                         |  2 +-
 doc/html/pair_quip.html                          |  2 +-
 doc/html/pair_reax.html                          |  2 +-
 doc/html/pair_reax_c.html                        |  2 +-
 doc/html/read_data.html                          |  4 ++--
 doc/html/read_restart.html                       |  2 +-
 doc/html/region.html                             |  2 +-
 doc/html/searchindex.js                          |  2 +-
 doc/html/thermo_style.html                       |  6 +++---
 doc/html/timestep.html                           |  6 +++---
 doc/html/velocity.html                           |  4 ++--
 146 files changed, 214 insertions(+), 214 deletions(-)

diff --git a/doc/html/Section_commands.html b/doc/html/Section_commands.html
index 70187d7547..e92b48a4cf 100644
--- a/doc/html/Section_commands.html
+++ b/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>
diff --git a/doc/html/Section_howto.html b/doc/html/Section_howto.html
index fb994f4d9f..a4c652a14f 100644
--- a/doc/html/Section_howto.html
+++ b/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
-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
+<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="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
diff --git a/doc/html/Section_modify.html b/doc/html/Section_modify.html
index 2af9707e6d..88ab26a836 100644
--- a/doc/html/Section_modify.html
+++ b/doc/html/Section_modify.html
@@ -254,7 +254,7 @@ parallel.  E.g. don&#8217;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
diff --git a/doc/html/angle_charmm.html b/doc/html/angle_charmm.html
index 01aff21dc3..17487df462 100644
--- a/doc/html/angle_charmm.html
+++ b/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
diff --git a/doc/html/angle_class2.html b/doc/html/angle_class2.html
index 7ecdcae37a..9c5073c4b5 100644
--- a/doc/html/angle_class2.html
+++ b/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
diff --git a/doc/html/angle_cosine_periodic.html b/doc/html/angle_cosine_periodic.html
index d733a4a9e7..8fb86c916a 100644
--- a/doc/html/angle_cosine_periodic.html
+++ b/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>
diff --git a/doc/html/bond_class2.html b/doc/html/bond_class2.html
index dce4a2b06d..696c3d1c22 100644
--- a/doc/html/bond_class2.html
+++ b/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>
diff --git a/doc/html/bond_fene.html b/doc/html/bond_fene.html
index 5a18de630d..f136e86c5f 100644
--- a/doc/html/bond_fene.html
+++ b/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>
diff --git a/doc/html/bond_fene_expand.html b/doc/html/bond_fene_expand.html
index 9a0d3c81c5..d0d7bdcfd5 100644
--- a/doc/html/bond_fene_expand.html
+++ b/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
diff --git a/doc/html/change_box.html b/doc/html/change_box.html
index 67d959720c..d7aa07bbc1 100644
--- a/doc/html/change_box.html
+++ b/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>
diff --git a/doc/html/compute_angle.html b/doc/html/compute_angle.html
index 998f44a241..b29151ede2 100644
--- a/doc/html/compute_angle.html
+++ b/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>
diff --git a/doc/html/compute_angle_local.html b/doc/html/compute_angle_local.html
index 80d36a8df2..3cb8c9f1e7 100644
--- a/doc/html/compute_angle_local.html
+++ b/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>
diff --git a/doc/html/compute_angmom_chunk.html b/doc/html/compute_angmom_chunk.html
index 5e2921771e..a8722b532a 100644
--- a/doc/html/compute_angmom_chunk.html
+++ b/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>
diff --git a/doc/html/compute_body_local.html b/doc/html/compute_body_local.html
index af9e525674..33119b8b46 100644
--- a/doc/html/compute_body_local.html
+++ b/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>
diff --git a/doc/html/compute_bond.html b/doc/html/compute_bond.html
index 05dbb6b21a..615004f913 100644
--- a/doc/html/compute_bond.html
+++ b/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>
diff --git a/doc/html/compute_bond_local.html b/doc/html/compute_bond_local.html
index 1ece04f5b0..d1def02d18 100644
--- a/doc/html/compute_bond_local.html
+++ b/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
-output for <em>eng</em> will be in energy <span class="xref doc">units</span>.  The output for
-<em>force</em> will be in force <span class="xref doc">units</span>.</p>
+<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 <a class="reference internal" href="units.html"><span class="doc">units</span></a>.  The output for
+<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>
diff --git a/doc/html/compute_chunk_atom.html b/doc/html/compute_chunk_atom.html
index c40f622fef..8319769579 100644
--- a/doc/html/compute_chunk_atom.html
+++ b/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
diff --git a/doc/html/compute_com.html b/doc/html/compute_com.html
index c50edf375b..e7754ad7c7 100644
--- a/doc/html/compute_com.html
+++ b/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>
diff --git a/doc/html/compute_com_chunk.html b/doc/html/compute_com_chunk.html
index 12dd5d56ad..f18084b1b9 100644
--- a/doc/html/compute_com_chunk.html
+++ b/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>
diff --git a/doc/html/compute_dihedral.html b/doc/html/compute_dihedral.html
index 55916e86eb..ba623d5684 100644
--- a/doc/html/compute_dihedral.html
+++ b/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>
diff --git a/doc/html/compute_dipole_chunk.html b/doc/html/compute_dipole_chunk.html
index de0651b194..82317cf95d 100644
--- a/doc/html/compute_dipole_chunk.html
+++ b/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>
diff --git a/doc/html/compute_displace_atom.html b/doc/html/compute_displace_atom.html
index f24a84160a..14b3b05284 100644
--- a/doc/html/compute_displace_atom.html
+++ b/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>
diff --git a/doc/html/compute_dpd_atom.html b/doc/html/compute_dpd_atom.html
index b37d01442f..195981a949 100644
--- a/doc/html/compute_dpd_atom.html
+++ b/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>
diff --git a/doc/html/compute_erotate_asphere.html b/doc/html/compute_erotate_asphere.html
index c9e784b28a..4af35ae60a 100644
--- a/doc/html/compute_erotate_asphere.html
+++ b/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>
diff --git a/doc/html/compute_erotate_rigid.html b/doc/html/compute_erotate_rigid.html
index cc5c52525a..0e46c9e7fe 100644
--- a/doc/html/compute_erotate_rigid.html
+++ b/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>
diff --git a/doc/html/compute_erotate_sphere.html b/doc/html/compute_erotate_sphere.html
index 1a0559fdb7..4785bf0a12 100644
--- a/doc/html/compute_erotate_sphere.html
+++ b/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>
diff --git a/doc/html/compute_erotate_sphere_atom.html b/doc/html/compute_erotate_sphere_atom.html
index d33818079d..0ab254c224 100644
--- a/doc/html/compute_erotate_sphere_atom.html
+++ b/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>
diff --git a/doc/html/compute_group_group.html b/doc/html/compute_group_group.html
index bab284060f..a7a46a6236 100644
--- a/doc/html/compute_group_group.html
+++ b/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>.
-The vector values will be in force <span class="xref doc">units</span>.</p>
+&#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 <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>
diff --git a/doc/html/compute_improper.html b/doc/html/compute_improper.html
index b8a180f76e..5b1e51e336 100644
--- a/doc/html/compute_improper.html
+++ b/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>
diff --git a/doc/html/compute_inertia_chunk.html b/doc/html/compute_inertia_chunk.html
index 6472b84eed..ac29221054 100644
--- a/doc/html/compute_inertia_chunk.html
+++ b/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>
diff --git a/doc/html/compute_ke.html b/doc/html/compute_ke.html
index b3d25227a3..a3000f0f0d 100644
--- a/doc/html/compute_ke.html
+++ b/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>
diff --git a/doc/html/compute_ke_atom.html b/doc/html/compute_ke_atom.html
index 60e2752d10..ea8c40a8bb 100644
--- a/doc/html/compute_ke_atom.html
+++ b/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>
diff --git a/doc/html/compute_ke_atom_eff.html b/doc/html/compute_ke_atom_eff.html
index 0c5ec701d7..00b22b9256 100644
--- a/doc/html/compute_ke_atom_eff.html
+++ b/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>
diff --git a/doc/html/compute_ke_eff.html b/doc/html/compute_ke_eff.html
index 3f0d224ac6..b614a9d25b 100644
--- a/doc/html/compute_ke_eff.html
+++ b/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>
diff --git a/doc/html/compute_ke_rigid.html b/doc/html/compute_ke_rigid.html
index d8d1905549..27c5451b25 100644
--- a/doc/html/compute_ke_rigid.html
+++ b/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>
diff --git a/doc/html/compute_meso_e_atom.html b/doc/html/compute_meso_e_atom.html
index a88d739406..21b1e95553 100644
--- a/doc/html/compute_meso_e_atom.html
+++ b/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>
diff --git a/doc/html/compute_meso_rho_atom.html b/doc/html/compute_meso_rho_atom.html
index c4da0bc379..dd832b844d 100644
--- a/doc/html/compute_meso_rho_atom.html
+++ b/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>
diff --git a/doc/html/compute_meso_t_atom.html b/doc/html/compute_meso_t_atom.html
index ae8859ba9a..c6111acd65 100644
--- a/doc/html/compute_meso_t_atom.html
+++ b/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>
diff --git a/doc/html/compute_msd.html b/doc/html/compute_msd.html
index ff4d0ca8cf..71b3e59085 100644
--- a/doc/html/compute_msd.html
+++ b/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>
diff --git a/doc/html/compute_msd_chunk.html b/doc/html/compute_msd_chunk.html
index 9db300a8a1..0aba6d8d95 100644
--- a/doc/html/compute_msd_chunk.html
+++ b/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>
diff --git a/doc/html/compute_omega_chunk.html b/doc/html/compute_omega_chunk.html
index e2873b3b56..80f35b0737 100644
--- a/doc/html/compute_omega_chunk.html
+++ b/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>
diff --git a/doc/html/compute_pair.html b/doc/html/compute_pair.html
index a90747a5bb..a38d482dcb 100644
--- a/doc/html/compute_pair.html
+++ b/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
-values will typically also be in energy <span class="xref doc">units</span>, but see
+<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 <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">
diff --git a/doc/html/compute_pair_local.html b/doc/html/compute_pair_local.html
index 531e15cada..922b25d56a 100644
--- a/doc/html/compute_pair_local.html
+++ b/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
-<em>eng</em> will be in energy <span class="xref doc">units</span>.  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
+<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 <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 <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
-output for <em>eng</em> will be in energy <span class="xref doc">units</span>.  The output for
-<em>force</em> will be in force <span class="xref doc">units</span>.</p>
+<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 <a class="reference internal" href="units.html"><span class="doc">units</span></a>.  The output for
+<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>
diff --git a/doc/html/compute_pe.html b/doc/html/compute_pe.html
index aaaa9370ff..9c71a10b65 100644
--- a/doc/html/compute_pe.html
+++ b/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>
diff --git a/doc/html/compute_pe_atom.html b/doc/html/compute_pe_atom.html
index b5a74ff29b..2b95c153cf 100644
--- a/doc/html/compute_pe_atom.html
+++ b/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>
diff --git a/doc/html/compute_property_atom.html b/doc/html/compute_property_atom.html
index 66c8df0d2e..417c581ce8 100644
--- a/doc/html/compute_property_atom.html
+++ b/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>
diff --git a/doc/html/compute_property_chunk.html b/doc/html/compute_property_chunk.html
index d2cb052319..73abeb96ac 100644
--- a/doc/html/compute_property_chunk.html
+++ b/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
diff --git a/doc/html/compute_rdf.html b/doc/html/compute_rdf.html
index 90808a40ed..c8d486553f 100644
--- a/doc/html/compute_rdf.html
+++ b/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>
diff --git a/doc/html/compute_reduce.html b/doc/html/compute_reduce.html
index 001fd9b0ce..217f3fd4bf 100644
--- a/doc/html/compute_reduce.html
+++ b/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">
diff --git a/doc/html/compute_saed.html b/doc/html/compute_saed.html
index a42da1c77b..2f88ae8f11 100644
--- a/doc/html/compute_saed.html
+++ b/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
diff --git a/doc/html/compute_slice.html b/doc/html/compute_slice.html
index ffe52d1230..427f49ee77 100644
--- a/doc/html/compute_slice.html
+++ b/doc/html/compute_slice.html
@@ -220,7 +220,7 @@ array values calculated by this compute are &#8220;intensive&#8221;.  If there a
 multiple input vectors, and any value in them is extensive, then the
 array values calculated by this compute are &#8220;extensive&#8221;.  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">
diff --git a/doc/html/compute_smd_contact_radius.html b/doc/html/compute_smd_contact_radius.html
index 72a940008a..0e19b35fa0 100644
--- a/doc/html/compute_smd_contact_radius.html
+++ b/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>
diff --git a/doc/html/compute_smd_hourglass_error.html b/doc/html/compute_smd_hourglass_error.html
index 9c92105981..595c8b3498 100644
--- a/doc/html/compute_smd_hourglass_error.html
+++ b/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>
diff --git a/doc/html/compute_smd_internal_energy.html b/doc/html/compute_smd_internal_energy.html
index 5b084754cc..14290c8b0a 100644
--- a/doc/html/compute_smd_internal_energy.html
+++ b/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>
diff --git a/doc/html/compute_smd_plastic_strain.html b/doc/html/compute_smd_plastic_strain.html
index aab190912e..90dd34a979 100644
--- a/doc/html/compute_smd_plastic_strain.html
+++ b/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>
diff --git a/doc/html/compute_smd_plastic_strain_rate.html b/doc/html/compute_smd_plastic_strain_rate.html
index d97551d270..e0848e3f41 100644
--- a/doc/html/compute_smd_plastic_strain_rate.html
+++ b/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>
diff --git a/doc/html/compute_smd_rho.html b/doc/html/compute_smd_rho.html
index 3872b047f9..2d199a90cd 100644
--- a/doc/html/compute_smd_rho.html
+++ b/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>
diff --git a/doc/html/compute_smd_tlsph_defgrad.html b/doc/html/compute_smd_tlsph_defgrad.html
index dc3d4ba56a..8e23bd77f5 100644
--- a/doc/html/compute_smd_tlsph_defgrad.html
+++ b/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>
diff --git a/doc/html/compute_smd_tlsph_dt.html b/doc/html/compute_smd_tlsph_dt.html
index 78f5e83e4f..9bc9c23e81 100644
--- a/doc/html/compute_smd_tlsph_dt.html
+++ b/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>
diff --git a/doc/html/compute_smd_tlsph_num_neighs.html b/doc/html/compute_smd_tlsph_num_neighs.html
index 9b005a819c..926a1661c8 100644
--- a/doc/html/compute_smd_tlsph_num_neighs.html
+++ b/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>
diff --git a/doc/html/compute_smd_tlsph_strain.html b/doc/html/compute_smd_tlsph_strain.html
index 3dfc7b01b4..6b58d8c318 100644
--- a/doc/html/compute_smd_tlsph_strain.html
+++ b/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>
diff --git a/doc/html/compute_smd_tlsph_strain_rate.html b/doc/html/compute_smd_tlsph_strain_rate.html
index 06b2ca6984..e1b430b23f 100644
--- a/doc/html/compute_smd_tlsph_strain_rate.html
+++ b/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>
diff --git a/doc/html/compute_smd_tlsph_stress.html b/doc/html/compute_smd_tlsph_stress.html
index e8b2465097..d14538fad5 100644
--- a/doc/html/compute_smd_tlsph_stress.html
+++ b/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
diff --git a/doc/html/compute_smd_triangle_mesh_vertices.html b/doc/html/compute_smd_triangle_mesh_vertices.html
index b4b047eadd..2b4077d564 100644
--- a/doc/html/compute_smd_triangle_mesh_vertices.html
+++ b/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>
diff --git a/doc/html/compute_smd_ulsph_num_neighs.html b/doc/html/compute_smd_ulsph_num_neighs.html
index 865324dc9a..425c4b81e5 100644
--- a/doc/html/compute_smd_ulsph_num_neighs.html
+++ b/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>
diff --git a/doc/html/compute_smd_ulsph_strain.html b/doc/html/compute_smd_ulsph_strain.html
index 65c590ba28..86f90ceb6a 100644
--- a/doc/html/compute_smd_ulsph_strain.html
+++ b/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>
diff --git a/doc/html/compute_smd_ulsph_strain_rate.html b/doc/html/compute_smd_ulsph_strain_rate.html
index f899e66f21..0f60ae8efd 100644
--- a/doc/html/compute_smd_ulsph_strain_rate.html
+++ b/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>
diff --git a/doc/html/compute_smd_ulsph_stress.html b/doc/html/compute_smd_ulsph_stress.html
index dad5e3e8e2..51654a43e0 100644
--- a/doc/html/compute_smd_ulsph_stress.html
+++ b/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
diff --git a/doc/html/compute_smd_vol.html b/doc/html/compute_smd_vol.html
index 462bdec670..4029e0eb2f 100644
--- a/doc/html/compute_smd_vol.html
+++ b/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>
diff --git a/doc/html/compute_temp.html b/doc/html/compute_temp.html
index 865d29ee59..b11eee9e07 100644
--- a/doc/html/compute_temp.html
+++ b/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
-vector values will be in energy <span class="xref doc">units</span>.</p>
+<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 <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>
diff --git a/doc/html/compute_temp_asphere.html b/doc/html/compute_temp_asphere.html
index 164ab2a234..06c17edaa9 100644
--- a/doc/html/compute_temp_asphere.html
+++ b/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
-vector values will be in energy <span class="xref doc">units</span>.</p>
+<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 <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>
diff --git a/doc/html/compute_temp_body.html b/doc/html/compute_temp_body.html
index 6115c821b9..807216d419 100644
--- a/doc/html/compute_temp_body.html
+++ b/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
-vector values will be in energy <span class="xref doc">units</span>.</p>
+<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 <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>
diff --git a/doc/html/compute_temp_chunk.html b/doc/html/compute_temp_chunk.html
index 7c593e7a80..3d0d3eeb6d 100644
--- a/doc/html/compute_temp_chunk.html
+++ b/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
-vector values will be in energy <span class="xref doc">units</span>.  The array values
-will be in temperature <span class="xref doc">units</span> 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>
+<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 <a class="reference internal" href="units.html"><span class="doc">units</span></a>.  The array values
+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 <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>
diff --git a/doc/html/compute_temp_com.html b/doc/html/compute_temp_com.html
index 96cf303b8d..cd57a0da57 100644
--- a/doc/html/compute_temp_com.html
+++ b/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
-vector values will be in energy <span class="xref doc">units</span>.</p>
+<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 <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>
diff --git a/doc/html/compute_temp_cs.html b/doc/html/compute_temp_cs.html
index 8daa29344c..4751726a56 100644
--- a/doc/html/compute_temp_cs.html
+++ b/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
-vector values will be in energy <span class="xref doc">units</span>.</p>
+<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 <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>
diff --git a/doc/html/compute_temp_deform.html b/doc/html/compute_temp_deform.html
index c29816af3c..2922d5ce4a 100644
--- a/doc/html/compute_temp_deform.html
+++ b/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
-vector values will be in energy <span class="xref doc">units</span>.</p>
+<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 <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>
diff --git a/doc/html/compute_temp_deform_eff.html b/doc/html/compute_temp_deform_eff.html
index fbe48b1ac5..748ee79b41 100644
--- a/doc/html/compute_temp_deform_eff.html
+++ b/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
-vector values will be in energy <span class="xref doc">units</span>.</p>
+<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 <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>
diff --git a/doc/html/compute_temp_partial.html b/doc/html/compute_temp_partial.html
index 09178601b7..e20787b288 100644
--- a/doc/html/compute_temp_partial.html
+++ b/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
-vector values will be in energy <span class="xref doc">units</span>.</p>
+<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 <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>
diff --git a/doc/html/compute_temp_profile.html b/doc/html/compute_temp_profile.html
index fcff076551..849b471064 100644
--- a/doc/html/compute_temp_profile.html
+++ b/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
-vector values will be in energy <span class="xref doc">units</span>.  The first column
+<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 <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>
diff --git a/doc/html/compute_temp_ramp.html b/doc/html/compute_temp_ramp.html
index 46ecafd332..bb551f9957 100644
--- a/doc/html/compute_temp_ramp.html
+++ b/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
-vector values will be in energy <span class="xref doc">units</span>.</p>
+<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 <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>
diff --git a/doc/html/compute_temp_region.html b/doc/html/compute_temp_region.html
index 8c82ba5c23..028fae2b9a 100644
--- a/doc/html/compute_temp_region.html
+++ b/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
-vector values will be in energy <span class="xref doc">units</span>.</p>
+<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 <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>
diff --git a/doc/html/compute_temp_region_eff.html b/doc/html/compute_temp_region_eff.html
index e58cfd8664..25c158a78c 100644
--- a/doc/html/compute_temp_region_eff.html
+++ b/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
-vector values will be in energy <span class="xref doc">units</span>.</p>
+<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 <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>
diff --git a/doc/html/compute_temp_rotate.html b/doc/html/compute_temp_rotate.html
index a3d6dccafb..dd664c2735 100644
--- a/doc/html/compute_temp_rotate.html
+++ b/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
-vector values will be in energy <span class="xref doc">units</span>.</p>
+<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 <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>
diff --git a/doc/html/compute_temp_sphere.html b/doc/html/compute_temp_sphere.html
index 7ab79fd53d..0dec80de72 100644
--- a/doc/html/compute_temp_sphere.html
+++ b/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
-vector values will be in energy <span class="xref doc">units</span>.</p>
+<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 <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>
diff --git a/doc/html/compute_ti.html b/doc/html/compute_ti.html
index efb269d33a..5701aeee75 100644
--- a/doc/html/compute_ti.html
+++ b/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>
diff --git a/doc/html/compute_torque_chunk.html b/doc/html/compute_torque_chunk.html
index bb1e4de5c4..fb17297e21 100644
--- a/doc/html/compute_torque_chunk.html
+++ b/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>
diff --git a/doc/html/compute_vacf.html b/doc/html/compute_vacf.html
index 019154cb07..713789bce4 100644
--- a/doc/html/compute_vacf.html
+++ b/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>
diff --git a/doc/html/compute_vcm_chunk.html b/doc/html/compute_vcm_chunk.html
index 689e4d3d34..9672e1f90d 100644
--- a/doc/html/compute_vcm_chunk.html
+++ b/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>
diff --git a/doc/html/compute_voronoi_atom.html b/doc/html/compute_voronoi_atom.html
index c4ede1f7ec..5b05cb77a6 100644
--- a/doc/html/compute_voronoi_atom.html
+++ b/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.
-The Voronoi face area will be in distance <span class="xref doc">units</span> squared.</p>
+<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 <a class="reference internal" href="units.html"><span class="doc">units</span></a> squared.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>
diff --git a/doc/html/compute_xrd.html b/doc/html/compute_xrd.html
index 278301034a..d594e6ce55 100644
--- a/doc/html/compute_xrd.html
+++ b/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,
diff --git a/doc/html/dihedral_charmm.html b/doc/html/dihedral_charmm.html
index 7e484d1e67..629d2161b3 100644
--- a/doc/html/dihedral_charmm.html
+++ b/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
diff --git a/doc/html/dihedral_class2.html b/doc/html/dihedral_class2.html
index a796fdfb4e..931013ddec 100644
--- a/doc/html/dihedral_class2.html
+++ b/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,
diff --git a/doc/html/displace_atoms.html b/doc/html/displace_atoms.html
index 21efabec21..241ed70662 100644
--- a/doc/html/displace_atoms.html
+++ b/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>
diff --git a/doc/html/dump.html b/doc/html/dump.html
index 16ab8c594f..9a927a1fa5 100644
--- a/doc/html/dump.html
+++ b/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
diff --git a/doc/html/dump_custom_vtk.html b/doc/html/dump_custom_vtk.html
index 425fc7dec2..d23a7c09f7 100644
--- a/doc/html/dump_custom_vtk.html
+++ b/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
diff --git a/doc/html/dump_modify.html b/doc/html/dump_modify.html
index 40e325766e..455724908b 100644
--- a/doc/html/dump_modify.html
+++ b/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
diff --git a/doc/html/fix_append_atoms.html b/doc/html/fix_append_atoms.html
index 8f394db17e..d53243c00f 100644
--- a/doc/html/fix_append_atoms.html
+++ b/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>
diff --git a/doc/html/fix_ave_chunk.html b/doc/html/fix_ave_chunk.html
index c5895fe148..b636808101 100644
--- a/doc/html/fix_ave_chunk.html
+++ b/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">
diff --git a/doc/html/fix_ave_spatial.html b/doc/html/fix_ave_spatial.html
index e8eb9f1a64..a435667770 100644
--- a/doc/html/fix_ave_spatial.html
+++ b/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
diff --git a/doc/html/fix_ave_spatial_sphere.html b/doc/html/fix_ave_spatial_sphere.html
index 07c8229dac..109f9aa98d 100644
--- a/doc/html/fix_ave_spatial_sphere.html
+++ b/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>
diff --git a/doc/html/fix_deform.html b/doc/html/fix_deform.html
index 8192f41e59..82306671d2 100644
--- a/doc/html/fix_deform.html
+++ b/doc/html/fix_deform.html
@@ -266,7 +266,7 @@ after 10 psec, the box length will have doubled.  After 20 psec, it
 will have tripled.</p>
 <p>The <em>erate</em> style changes a dimension of the the box at a &#8220;constant
 engineering strain rate&#8221;.  The units of the specified strain rate are
-1/time.  See the <span class="xref doc">units</span> command for the time units
+1/time.  See the <a class="reference internal" href="units.html"><span class="doc">units</span></a> command for the time units
 associated with different choices of simulation units,
 e.g. picoseconds for &#8220;metal&#8221; units).  Tensile strain is unitless and
 is defined as delta/L0, where L0 is the original box length and delta
@@ -289,7 +289,7 @@ strain rate&#8221;.  Note that this is not an &#8220;engineering strain rate&#82
 the other styles are.  Rather, for a &#8220;true&#8221; rate, the rate of change
 is constant, which means the box dimension changes non-linearly with
 time from its initial to final value.  The units of the specified
-strain rate are 1/time.  See the <span class="xref doc">units</span> command for the
+strain rate are 1/time.  See the <a class="reference internal" href="units.html"><span class="doc">units</span></a> command for the
 time units associated with different choices of simulation units,
 e.g. picoseconds for &#8220;metal&#8221; units).  Tensile strain is unitless and
 is defined as delta/L0, where L0 is the original box length and delta
@@ -405,7 +405,7 @@ tilt factor will be 15 Angstroms.  After 2 psec, it will be 25
 Angstroms.</p>
 <p>The <em>erate</em> style changes a tilt factor at a &#8220;constant engineering
 shear strain rate&#8221;.  The units of the specified shear strain rate are
-1/time.  See the <span class="xref doc">units</span> command for the time units
+1/time.  See the <a class="reference internal" href="units.html"><span class="doc">units</span></a> command for the time units
 associated with different choices of simulation units,
 e.g. picoseconds for &#8220;metal&#8221; units).  Shear strain is unitless and is
 defined as offset/length, where length is the box length perpendicular
@@ -433,7 +433,7 @@ rate&#8221;, as the other styles are.  Rather, for a &#8220;true&#8221; rate, th
 of change is constant, which means the tilt factor changes
 non-linearly with time from its initial to final value.  The units of
 the specified shear strain rate are 1/time.  See the
-<span class="xref doc">units</span> command for the time units associated with
+<a class="reference internal" href="units.html"><span class="doc">units</span></a> command for the time units associated with
 different choices of simulation units, e.g. picoseconds for &#8220;metal&#8221;
 units).  Shear strain is unitless and is defined as offset/length,
 where length is the box length perpendicular to the shear direction
@@ -608,7 +608,7 @@ irregular-shaped sub-domain.  For extreme values of tilt, LAMMPS may
 also lose atoms and generate an error.</p>
 <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.  Note that the
diff --git a/doc/html/fix_deposit.html b/doc/html/fix_deposit.html
index d74fda40ee..278f20266c 100644
--- a/doc/html/fix_deposit.html
+++ b/doc/html/fix_deposit.html
@@ -334,7 +334,7 @@ particles will be consecutive even if particles leave the system over
 time.</p>
 <p>The <em>units</em> keyword determines the meaning of the distance units used
 for the other deposition parameters.  A <em>box</em> value selects standard
-distance units as defined by the <span class="xref doc">units</span> command,
+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.  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.
diff --git a/doc/html/fix_external.html b/doc/html/fix_external.html
index 1005484ea5..d2a176da50 100644
--- a/doc/html/fix_external.html
+++ b/doc/html/fix_external.html
@@ -217,7 +217,7 @@ method of the FixExternal class:</p>
 </div>
 <p>where eng is the potential energy.  Eng is an extensive quantity,
 meaning it should be the sum over per-atom energies of all affected
-atoms.  It should also be provided in <span class="xref doc">energy units</span>
+atoms.  It should also be provided in <a class="reference internal" href="units.html"><span class="doc">energy units</span></a>
 consistent with the simulation.  See the details below for how to
 insure this energy setting is used appropriately in a minimization.</p>
 </div>
diff --git a/doc/html/fix_gravity.html b/doc/html/fix_gravity.html
index 6d6aac1460..006dcb0889 100644
--- a/doc/html/fix_gravity.html
+++ b/doc/html/fix_gravity.html
@@ -179,7 +179,7 @@ adds the same force to each atom, independent of its mass.  This
 command imparts the same acceleration to each atom (force/mass).</p>
 <p>The <em>magnitude</em> of the acceleration is specified in force/mass units.
 For granular systems (LJ units) this is typically 1.0.  See the
-<span class="xref doc">units</span> command for details.</p>
+<a class="reference internal" href="units.html"><span class="doc">units</span></a> command for details.</p>
 <p>Style <em>chute</em> is typically used for simulations of chute flow where
 the specified <em>angle</em> is the chute angle, with flow occurring in the +x
 direction.  For 3d systems, the tilt is away from the z axis; for 2d
diff --git a/doc/html/fix_heat.html b/doc/html/fix_heat.html
index ecf031e9cf..701cdc1be4 100644
--- a/doc/html/fix_heat.html
+++ b/doc/html/fix_heat.html
@@ -170,7 +170,7 @@ parameter can be specified as a numeric constant or as a variable (see
 below).  If it is a numeric constant or equal-style variable which
 evaluates to a scalar value, then the <em>eflux</em> determines the change in
 aggregate energy of the entire group of atoms per unit time, e.g. in
-eV/psec for <span class="xref doc">metal units</span>.  In this case it is an
+eV/psec for <a class="reference internal" href="units.html"><span class="doc">metal units</span></a>.  In this case it is an
 &#8220;extensive&#8221; quantity, meaning its magnitude should be scaled with the
 number of atoms in the group.  Note that since <em>eflux</em> has per-time
 units (i.e. it is a flux), this means that a larger value of N will
diff --git a/doc/html/fix_indent.html b/doc/html/fix_indent.html
index 7fc26b7806..c8a8ce8bb9 100644
--- a/doc/html/fix_indent.html
+++ b/doc/html/fix_indent.html
@@ -253,7 +253,7 @@ is now a containing wall that traps the particles inside it.  If the
 radius shrinks over time, it will squeeze the particles.</p>
 <p>The <em>units</em> keyword determines the meaning of the distance units used
 to define the indenter geometry.  A <em>box</em> value selects standard
-distance units as defined by the <span class="xref doc">units</span> command,
+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.  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.
@@ -267,7 +267,7 @@ the <a class="reference internal" href="thermo_style.html"><span class="doc">the
 lattice spacings in a variable formula.</p>
 <p>The force constant <em>K</em> is not affected by the <em>units</em> keyword.  It is
 always in force/distance^2 units where force and distance are defined
-by the <span class="xref doc">units</span> command.  If you wish K to be scaled by the
+by the <a class="reference internal" href="units.html"><span class="doc">units</span></a> command.  If you wish K to be scaled by the
 lattice spacing, you can define K with a variable whose formula
 contains <em>xlat</em>, <em>ylat</em>, <em>zlat</em> keywords of the
 <a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style</span></a> command, e.g.</p>
diff --git a/doc/html/fix_langevin.html b/doc/html/fix_langevin.html
index 1df0b59dbb..edf3efa19a 100644
--- a/doc/html/fix_langevin.html
+++ b/doc/html/fix_langevin.html
@@ -257,7 +257,7 @@ in.</p>
 <p>The <em>damp</em> parameter is specified in time units and determines how
 rapidly the temperature is relaxed.  For example, a value of 100.0
 means to relax the temperature in a timespan of (roughly) 100 time
-units (tau or fmsec or psec - see the <span class="xref doc">units</span> command).
+units (tau or fmsec or psec - see the <a class="reference internal" href="units.html"><span class="doc">units</span></a> command).
 The damp factor can be thought of as inversely related to the
 viscosity of the solvent.  I.e. a small relaxation time implies a
 hi-viscosity solvent and vice versa.  See the discussion about gamma
diff --git a/doc/html/fix_langevin_drude.html b/doc/html/fix_langevin_drude.html
index 188354f331..f01d0bd451 100644
--- a/doc/html/fix_langevin_drude.html
+++ b/doc/html/fix_langevin_drude.html
@@ -273,7 +273,7 @@ particles.</p>
 <p><em>damp_com</em> is the characteristic time for reaching thermal equilibrium
 of the centers of mass.  For example, a value of 100.0 means to relax
 the temperature of the centers of mass in a timespan of (roughly) 100
-time units (tau or fmsec or psec - see the <span class="xref doc">units</span>
+time units (tau or fmsec or psec - see the <a class="reference internal" href="units.html"><span class="doc">units</span></a>
 command).  <em>damp_drude</em> is the characteristic time for reaching
 thermal equilibrium of the dipoles. It is typically a few timesteps.</p>
 <p>The number <em>seed_com</em> and <em>seed_drude</em> are positive integers. They set
diff --git a/doc/html/fix_lb_fluid.html b/doc/html/fix_lb_fluid.html
index 201785ea67..5f779c9a19 100644
--- a/doc/html/fix_lb_fluid.html
+++ b/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>
diff --git a/doc/html/fix_move.html b/doc/html/fix_move.html
index d1f6c72c2f..66cf61d80e 100644
--- a/doc/html/fix_move.html
+++ b/doc/html/fix_move.html
@@ -294,7 +294,7 @@ velocity.</p>
 <p>The <em>units</em> keyword determines the meaning of the distance units used
 to define the <em>linear</em> velocity and <em>wiggle</em> amplitude and <em>rotate</em>
 origin.  This setting is ignored for the <em>variable</em> style.  A <em>box</em>
-value selects standard units as defined by the <span class="xref doc">units</span>
+value selects standard units as defined by the <a class="reference internal" href="units.html"><span class="doc">units</span></a>
 command, e.g. velocity in Angstroms/fmsec and amplitude and position
 in Angstroms for units = real.  A <em>lattice</em> value means the velocity
 units are in lattice spacings per time and the amplitude and position
diff --git a/doc/html/fix_nh.html b/doc/html/fix_nh.html
index bdf5b051b7..f542b04a18 100644
--- a/doc/html/fix_nh.html
+++ b/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
@@ -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,
diff --git a/doc/html/fix_nve_limit.html b/doc/html/fix_nve_limit.html
index 0167dbee46..ede833982c 100644
--- a/doc/html/fix_nve_limit.html
+++ b/doc/html/fix_nve_limit.html
@@ -156,7 +156,7 @@ be computable (which typically means 2 atoms must have a separation
 distance &gt; 0.0).  But large velocities generated by large forces are
 reset to a value that corresponds to a displacement of length <em>xmax</em>
 in a single timestep.  <em>Xmax</em> is specified in distance units; see the
-<span class="xref doc">units</span> command for details.  The value of <em>xmax</em> should be
+<a class="reference internal" href="units.html"><span class="doc">units</span></a> command for details.  The value of <em>xmax</em> should be
 consistent with the neighbor skin distance and the frequency of
 neighbor list re-building, so that pairwise interactions are not
 missed on successive timesteps as atoms move.  See the
diff --git a/doc/html/fix_phonon.html b/doc/html/fix_phonon.html
index 74398f2dd0..0eed3acb9e 100644
--- a/doc/html/fix_phonon.html
+++ b/doc/html/fix_phonon.html
@@ -236,7 +236,7 @@ dynamical matrix at only the gamma-point will/can be evaluated. Please keep in
 mind that fix-phonon is designed for cyrstals, it will be inefficient and
 even degrade the performance of lammps in case the unit cell is too large.</p>
 <p>The calculated dynamical matrix elements are written out in
-<span class="xref doc">energy/distance^2/mass</span> units.  The coordinates for <em>q</em>
+<a class="reference internal" href="units.html"><span class="doc">energy/distance^2/mass</span></a> units.  The coordinates for <em>q</em>
 points in the log file is in the units of the basis vectors of the
 corresponding reciprocal lattice.</p>
 </div>
diff --git a/doc/html/fix_pimd.html b/doc/html/fix_pimd.html
index 6d835d4fc4..9fd1a77fa6 100644
--- a/doc/html/fix_pimd.html
+++ b/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
diff --git a/doc/html/fix_press_berendsen.html b/doc/html/fix_press_berendsen.html
index 5480fb3db8..ffd58394b6 100644
--- a/doc/html/fix_press_berendsen.html
+++ b/doc/html/fix_press_berendsen.html
@@ -205,7 +205,7 @@ although you have the option to change that dimension via the <a class="referenc
 <p>For all barostat keywords, the <em>Pdamp</em> parameter determines the time
 scale on which pressure is relaxed.  For example, a value of 10.0
 means to relax the pressure in a timespan of (roughly) 10 time units
-(tau or fmsec or psec - see the <span class="xref doc">units</span> command).</p>
+(tau or fmsec or psec - see the <a class="reference internal" href="units.html"><span class="doc">units</span></a> command).</p>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
 <p class="last">A Berendsen barostat will not work well for arbitrary values of
@@ -214,7 +214,7 @@ fluctuate wildly; if it is too large, the pressure will take a very
 long time to equilibrate.  A good choice for many models is a <em>Pdamp</em>
 of around 1000 timesteps.  However, note that <em>Pdamp</em> is specified in
 time units, and that timesteps are NOT the same as time units for most
-<span class="xref doc">units</span> settings.</p>
+<a class="reference internal" href="units.html"><span class="doc">units</span></a> settings.</p>
 </div>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
@@ -322,7 +322,7 @@ various <a class="reference internal" href="Section_howto.html#howto-15"><span c
 <div class="section" id="default">
 <h2>Default</h2>
 <p>The keyword defaults are dilate = all, modulus = 10.0 in units of
-pressure for whatever <span class="xref doc">units</span> are defined.</p>
+pressure for whatever <a class="reference internal" href="units.html"><span class="doc">units</span></a> are defined.</p>
 <hr class="docutils" />
 <p id="berendsen"><strong>(Berendsen)</strong> Berendsen, Postma, van Gunsteren, DiNola, Haak, J Chem
 Phys, 81, 3684 (1984).</p>
diff --git a/doc/html/fix_recenter.html b/doc/html/fix_recenter.html
index ae3ced35a4..4f1bdc2285 100644
--- a/doc/html/fix_recenter.html
+++ b/doc/html/fix_recenter.html
@@ -176,7 +176,7 @@ example, the COM could be computed on a protein to keep it in the
 center of the simulation box.  But the entire system (protein + water)
 could be shifted.</p>
 <p>If the <em>units</em> keyword is set to <em>box</em>, then the distance units of
-x,y,z are defined by the <span class="xref doc">units</span> command - e.g. Angstroms
+x,y,z are defined by the <a class="reference internal" href="units.html"><span class="doc">units</span></a> command - e.g. Angstroms
 for <em>real</em> units.  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>fraction</em> value
diff --git a/doc/html/fix_rigid.html b/doc/html/fix_rigid.html
index 357919f88a..d543973b84 100644
--- a/doc/html/fix_rigid.html
+++ b/doc/html/fix_rigid.html
@@ -467,7 +467,7 @@ that dimension via the <a class="reference internal" href="fix_deform.html"><spa
 <em>Tdamp</em> parameter, determining the time scale on which pressure is
 relaxed.  For example, a value of 10.0 means to relax the pressure in
 a timespan of (roughly) 10 time units (e.g. tau or fmsec or psec - see
-the <span class="xref doc">units</span> command).</p>
+the <a class="reference internal" href="units.html"><span class="doc">units</span></a> command).</p>
 <p>Regardless of what atoms are in the fix group (the only atoms which
 are time integrated), a global pressure or stress tensor is computed
 for all atoms.  Similarly, when the size of the simulation box is
@@ -532,7 +532,7 @@ run from <em>Tstart</em> to <em>Tstop</em>.  The <em>Tdamp</em> parameter is spe
 time units and determines how rapidly the temperature is relaxed.  For
 example, a value of 100.0 means to relax the temperature in a timespan
 of (roughly) 100 time units (tau or fmsec or psec - see the
-<span class="xref doc">units</span> command).  The random # <em>seed</em> must be a positive
+<a class="reference internal" href="units.html"><span class="doc">units</span></a> command).  The random # <em>seed</em> must be a positive
 integer.</p>
 <p>The way that Langevin thermostatting operates is explained on the <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a> doc page.  If you wish to simply viscously
 damp the rotational motion without thermostatting, you can set
@@ -555,7 +555,7 @@ from <em>Tstart</em> to <em>Tstop</em>.  The <em>Tdamp</em> parameter is specifi
 units and determines how rapidly the temperature is relaxed.  For
 example, a value of 100.0 means to relax the temperature in a timespan
 of (roughly) 100 time units (tau or fmsec or psec - see the
-<span class="xref doc">units</span> command).</p>
+<a class="reference internal" href="units.html"><span class="doc">units</span></a> command).</p>
 <p>Nose/Hoover chains are used in conjunction with this thermostat.  The
 <em>tparam</em> keyword can optionally be used to change the chain settings
 used.  <em>Tchain</em> is the number of thermostats in the Nose Hoover chain.
diff --git a/doc/html/fix_temp_berendsen.html b/doc/html/fix_temp_berendsen.html
index 3f4a5f9a88..ebbb13626c 100644
--- a/doc/html/fix_temp_berendsen.html
+++ b/doc/html/fix_temp_berendsen.html
@@ -168,7 +168,7 @@ run from <em>Tstart</em> to <em>Tstop</em>.  The <em>Tdamp</em> parameter is spe
 time units and determines how rapidly the temperature is relaxed.  For
 example, a value of 100.0 means to relax the temperature in a timespan
 of (roughly) 100 time units (tau or fmsec or psec - see the
-<span class="xref doc">units</span> command).</p>
+<a class="reference internal" href="units.html"><span class="doc">units</span></a> command).</p>
 <p><em>Tstart</em> can be specified as an equal-style <a class="reference internal" href="variable.html"><span class="doc">variable</span></a>.
 In this case, the <em>Tstop</em> setting is ignored.  If the value is a
 variable, it should be specified as v_name, where name is the variable
diff --git a/doc/html/fix_temp_csvr.html b/doc/html/fix_temp_csvr.html
index f157f77c32..0d3874ecdd 100644
--- a/doc/html/fix_temp_csvr.html
+++ b/doc/html/fix_temp_csvr.html
@@ -183,7 +183,7 @@ run from <em>Tstart</em> to <em>Tstop</em>.  The <em>Tdamp</em> parameter is spe
 time units and determines how rapidly the temperature is relaxed.  For
 example, a value of 100.0 means to relax the temperature in a timespan
 of (roughly) 100 time units (tau or fmsec or psec - see the
-<span class="xref doc">units</span> command).</p>
+<a class="reference internal" href="units.html"><span class="doc">units</span></a> command).</p>
 <p><em>Tstart</em> can be specified as an equal-style <a class="reference internal" href="variable.html"><span class="doc">variable</span></a>.
 In this case, the <em>Tstop</em> setting is ignored.  If the value is a
 variable, it should be specified as v_name, where name is the variable
diff --git a/doc/html/fix_thermal_conductivity.html b/doc/html/fix_thermal_conductivity.html
index 071608653d..2d0426f6fe 100644
--- a/doc/html/fix_thermal_conductivity.html
+++ b/doc/html/fix_thermal_conductivity.html
@@ -232,7 +232,7 @@ cummulative kinetic energy transferred between the bottom and middle
 of the simulation box (in the <em>edim</em> direction) is stored as a scalar
 quantity by this fix.  This quantity is zeroed when the fix is defined
 and accumlates thereafter, once every N steps.  The units of the
-quantity are energy; see the <span class="xref doc">units</span> command for details.
+quantity are energy; see the <a class="reference internal" href="units.html"><span class="doc">units</span></a> command for details.
 The scalar value calculated by this fix is &#8220;intensive&#8221;.</p>
 <p>No parameter of this fix can be used with the <em>start/stop</em> keywords of
 the <a class="reference internal" href="run.html"><span class="doc">run</span></a> command.  This fix is not invoked during <a class="reference internal" href="minimize.html"><span class="doc">energy minimization</span></a>.</p>
diff --git a/doc/html/fix_viscous.html b/doc/html/fix_viscous.html
index 00e6da04ee..af89e65c1d 100644
--- a/doc/html/fix_viscous.html
+++ b/doc/html/fix_viscous.html
@@ -174,7 +174,7 @@ times to adjust gamma for several atom types.</p>
 <p class="first admonition-title">Note</p>
 <p class="last">You should specify gamma in force/velocity units.  This is not
 the same as mass/time units, at least for some of the LAMMPS
-<span class="xref doc">units</span> options like &#8220;real&#8221; or &#8220;metal&#8221; that are not
+<a class="reference internal" href="units.html"><span class="doc">units</span></a> options like &#8220;real&#8221; or &#8220;metal&#8221; that are not
 self-consistent.</p>
 </div>
 <p>In a Brownian dynamics context, gamma = Kb T / D, where Kb =
diff --git a/doc/html/fix_wall_piston.html b/doc/html/fix_wall_piston.html
index 7146d85180..8ebde444af 100644
--- a/doc/html/fix_wall_piston.html
+++ b/doc/html/fix_wall_piston.html
@@ -195,7 +195,7 @@ wall/piston.</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.</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 spacings.</p>
diff --git a/doc/html/fix_wall_reflect.html b/doc/html/fix_wall_reflect.html
index b74be31273..c103099fae 100644
--- a/doc/html/fix_wall_reflect.html
+++ b/doc/html/fix_wall_reflect.html
@@ -207,7 +207,7 @@ variable is used.  It is not relevant when EDGE is used to specify a
 face position.  In the variable case, the variable is assumed to
 produce a value compatible with the <em>units</em> setting you specify.</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 spacings.</p>
diff --git a/doc/html/fix_wall_srd.html b/doc/html/fix_wall_srd.html
index db9ceab4fa..c72f90b6bb 100644
--- a/doc/html/fix_wall_srd.html
+++ b/doc/html/fix_wall_srd.html
@@ -241,7 +241,7 @@ to define a wall position, but only when a numeric constant is used.
 It is not relevant when EDGE or a variable is used to specify a face
 position.</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 spacings.</p>
diff --git a/doc/html/improper_class2.html b/doc/html/improper_class2.html
index 495228c950..0d190caf4c 100644
--- a/doc/html/improper_class2.html
+++ b/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
diff --git a/doc/html/improper_umbrella.html b/doc/html/improper_umbrella.html
index 278f2db6d2..716c7c95c2 100644
--- a/doc/html/improper_umbrella.html
+++ b/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
diff --git a/doc/html/lattice.html b/doc/html/lattice.html
index c86217a804..636cba7437 100644
--- a/doc/html/lattice.html
+++ b/doc/html/lattice.html
@@ -214,7 +214,7 @@ be used by other commands as distance units.  No additional
 keyword/value pairs can be specified for the <em>none</em> style.  By
 default, a &#8220;lattice none 1.0&#8221; is defined, which means the lattice
 spacing is the same as one distance unit, as defined by the
-<span class="xref doc">units</span> command.</p>
+<a class="reference internal" href="units.html"><span class="doc">units</span></a> command.</p>
 <p>Lattices of style <em>sc</em>, <em>fcc</em>, <em>bcc</em>, and <em>diamond</em> are 3d lattices
 that define a cubic unit cell with edge length = 1.0.  This means a1 =
 1 0 0, a2 = 0 1 0, and a3 = 0 0 1.  Style <em>hcp</em> has a1 = 1 0 0, a2 = 0
@@ -252,7 +252,7 @@ simulation box.</p>
 scaled when mapping it into the simulation box.  I.e. it determines a
 multiplicative factor to apply to the unit cell, to convert it to a
 lattice of the desired size and distance units in the simulation box.
-The meaning of the <em>scale</em> argument depends on the <span class="xref doc">units</span>
+The meaning of the <em>scale</em> argument depends on the <a class="reference internal" href="units.html"><span class="doc">units</span></a>
 being used in your simulation.</p>
 <p>For all unit styles except <em>lj</em>, the scale argument is specified in
 the distance units defined by the unit style.  For example, in <em>real</em>
@@ -303,7 +303,7 @@ E.g. the <a class="reference internal" href="region.html"><span class="doc">regi
 <p class="first admonition-title">Note</p>
 <p class="last">Though they are called lattice spacings, all the commands that
 have a &#8220;units lattice&#8221; option, simply use the 3 values as scale
-factors on the distance units defined by the <span class="xref doc">units</span>
+factors on the distance units defined by the <a class="reference internal" href="units.html"><span class="doc">units</span></a>
 command.  Thus if you do not like the lattice spacings computed by
 LAMMPS (e.g. for a non-orthogonal or rotated unit cell), you can
 define the 3 values to be whatever you wish, via the <em>spacing</em> option.</p>
diff --git a/doc/html/mass.html b/doc/html/mass.html
index 4a114e414e..b52482445a 100644
--- a/doc/html/mass.html
+++ b/doc/html/mass.html
@@ -148,7 +148,7 @@
 <h2>Description</h2>
 <p>Set the mass for all atoms of one or more atom types.  Per-type mass
 values can also be set in the <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> data file
-using the &#8220;Masses&#8221; keyword.  See the <span class="xref doc">units</span> command for
+using the &#8220;Masses&#8221; keyword.  See the <a class="reference internal" href="units.html"><span class="doc">units</span></a> command for
 what mass units to use.</p>
 <p>The I index can be specified in one of two ways.  An explicit numeric
 value can be used, as in the 1st example above.  Or a wild-card
diff --git a/doc/html/min_modify.html b/doc/html/min_modify.html
index b611c15acb..5434586014 100644
--- a/doc/html/min_modify.html
+++ b/doc/html/min_modify.html
@@ -161,7 +161,7 @@ a particular search direction.  The <em>dmax</em> parameter is how far any
 atom can move in a single line search in any dimension (x, y, or z).
 For the <em>quickmin</em> and <em>fire</em> minimization styles, the <em>dmax</em> setting
 is how far any atom can move in a single iteration (timestep).  Thus a
-value of 0.1 in real <span class="xref doc">units</span> means no atom will move
+value of 0.1 in real <a class="reference internal" href="units.html"><span class="doc">units</span></a> means no atom will move
 further than 0.1 Angstroms in a single outer iteration.  This prevents
 highly overlapped atoms from being moved long distances (e.g. through
 another atom) due to large forces.</p>
diff --git a/doc/html/molecule.html b/doc/html/molecule.html
index ad70071851..5c395f38e7 100644
--- a/doc/html/molecule.html
+++ b/doc/html/molecule.html
@@ -359,7 +359,7 @@ support per-atom mass, as opposed to per-type mass.  See the
 <a class="reference internal" href="mass.html"><span class="doc">mass</span></a> command for details.  If this section is not
 included, the default mass for each atom is derived from its volume
 (see Diameters section) and a default density of 1.0, in
-<span class="xref doc">units</span> of mass/volume.</p>
+<a class="reference internal" href="units.html"><span class="doc">units</span></a> of mass/volume.</p>
 <hr class="docutils" />
 <p><em>Bonds</em> section:</p>
 <ul class="simple">
diff --git a/doc/html/neighbor.html b/doc/html/neighbor.html
index bd83c40781..d1c2630e8b 100644
--- a/doc/html/neighbor.html
+++ b/doc/html/neighbor.html
@@ -191,7 +191,7 @@ are printed to the screen and log file.  See <a class="reference internal" href=
 </div>
 <div class="section" id="related-commands">
 <h2>Related commands</h2>
-<p><a class="reference internal" href="neigh_modify.html"><span class="doc">neigh_modify</span></a>, <span class="xref doc">units</span>,
+<p><a class="reference internal" href="neigh_modify.html"><span class="doc">neigh_modify</span></a>, <a class="reference internal" href="units.html"><span class="doc">units</span></a>,
 <span class="xref doc">comm_modify</span></p>
 </div>
 <div class="section" id="default">
diff --git a/doc/html/package.html b/doc/html/package.html
index c736f2a56e..5f676a479c 100644
--- a/doc/html/package.html
+++ b/doc/html/package.html
@@ -366,7 +366,7 @@ cutoff, e.g. to allow for a smaller fraction of KSpace work with a
 <a class="reference internal" href="kspace_style.html"><span class="doc">long-range Coulombic solver</span></a> because the GPU is
 faster at performing pairwise interactions, then it may be optimal to
 make the <em>binsize</em> smaller than the default.  For example, with a
-cutoff of 20*sigma in LJ <span class="xref doc">units</span> and a neighbor skin
+cutoff of 20*sigma in LJ <a class="reference internal" href="units.html"><span class="doc">units</span></a> and a neighbor skin
 distance of sigma, a <em>binsize</em> = 5.25*sigma can be more efficient than
 the default.</p>
 <p>The <em>split</em> keyword can be used for load balancing force calculations
diff --git a/doc/html/pair_charmm.html b/doc/html/pair_charmm.html
index aa95dafcfd..61434f9e63 100644
--- a/doc/html/pair_charmm.html
+++ b/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.
diff --git a/doc/html/pair_class2.html b/doc/html/pair_class2.html
index 0d814a4666..811c54043a 100644
--- a/doc/html/pair_class2.html
+++ b/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
diff --git a/doc/html/pair_hbond_dreiding.html b/doc/html/pair_hbond_dreiding.html
index 3ccb65b0d9..d8a9bd8c31 100644
--- a/doc/html/pair_hbond_dreiding.html
+++ b/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
diff --git a/doc/html/pair_lcbop.html b/doc/html/pair_lcbop.html
index fdfff24b22..7e2e82ff4a 100644
--- a/doc/html/pair_lcbop.html
+++ b/doc/html/pair_lcbop.html
@@ -189,7 +189,7 @@ the <a class="reference internal" href="Section_start.html#start-3"><span class=
 <p>This pair potential requires the <a class="reference internal" href="newton.html"><span class="doc">newton</span></a> setting to be
 &#8220;on&#8221; for pair interactions.</p>
 <p>The C.lcbop potential file provided with LAMMPS (see the potentials
-directory) is parameterized for metal <span class="xref doc">units</span>.  You can use
+directory) is parameterized for metal <a class="reference internal" href="units.html"><span class="doc">units</span></a>.  You can use
 the LCBOP potential with any LAMMPS units, but you would need to
 create your own LCBOP potential file with coefficients listed in the
 appropriate units if your simulation doesn&#8217;t use &#8220;metal&#8221; units.</p>
diff --git a/doc/html/pair_quip.html b/doc/html/pair_quip.html
index 809b7af472..e2bae6d90b 100644
--- a/doc/html/pair_quip.html
+++ b/doc/html/pair_quip.html
@@ -188,7 +188,7 @@ script that reads a restart file.</p>
 <p>This pair style is part of the USER-QUIP package.  It is only enabled
 if LAMMPS was built with that package.  See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
 <p>QUIP potentials are parametrized in electron-volts and Angstroms and
-therefore should be used with LAMMPS metal <span class="xref doc">units</span>.</p>
+therefore should be used with LAMMPS metal <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
 </div>
 <div class="section" id="related-commands">
 <h2>Related commands</h2>
diff --git a/doc/html/pair_reax.html b/doc/html/pair_reax.html
index 441498d8bc..3093a0b62b 100644
--- a/doc/html/pair_reax.html
+++ b/doc/html/pair_reax.html
@@ -303,7 +303,7 @@ script that reads a restart file.</p>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>
 <p>The ReaxFF potential files provided with LAMMPS in the potentials
-directory are parameterized for real <span class="xref doc">units</span>.  You can use
+directory are parameterized for real <a class="reference internal" href="units.html"><span class="doc">units</span></a>.  You can use
 the ReaxFF potential with any LAMMPS units, but you would need to
 create your own potential file with coefficients listed in the
 appropriate units if your simulation doesn&#8217;t use &#8220;real&#8221; units.</p>
diff --git a/doc/html/pair_reax_c.html b/doc/html/pair_reax_c.html
index 28ec735904..2019b8ecd1 100644
--- a/doc/html/pair_reax_c.html
+++ b/doc/html/pair_reax_c.html
@@ -367,7 +367,7 @@ script that reads a restart file.</p>
 <p>This pair style is part of the USER-REAXC package.  It is only enabled
 if LAMMPS was built with that package.  See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
 <p>The ReaxFF potential files provided with LAMMPS in the potentials
-directory are parameterized for real <span class="xref doc">units</span>.  You can use
+directory are parameterized for real <a class="reference internal" href="units.html"><span class="doc">units</span></a>.  You can use
 the ReaxFF potential with any LAMMPS units, but you would need to
 create your own potential file with coefficients listed in the
 appropriate units if your simulation doesn&#8217;t use &#8220;real&#8221; units.</p>
diff --git a/doc/html/read_data.html b/doc/html/read_data.html
index 0df3ff5d6b..6a15a6f1a2 100644
--- a/doc/html/read_data.html
+++ b/doc/html/read_data.html
@@ -711,7 +711,7 @@ of analysis.</p>
 <li>x,y,z = coordinates of atom (distance units)</li>
 </ul>
 <p>The units for these quantities depend on the unit style; see the
-<span class="xref doc">units</span> command for details.</p>
+<a class="reference internal" href="units.html"><span class="doc">units</span></a> command for details.</p>
 <p>For 2d simulations specify z as 0.0, or a value within the <em>zlo zhi</em>
 setting in the data file header.</p>
 <p>The atom-ID is used to identify the atom throughout the simulation and
@@ -1249,7 +1249,7 @@ ervel = electron radial velocity (0 for fixed-core):ul</p>
 used after an <em>Atoms</em> section.  This is because the <em>Atoms</em> section
 must have assigned a unique atom ID to each atom so that velocities
 can be assigned to them.</p>
-<p>Vx, vy, vz, and ervel are in <span class="xref doc">units</span> of velocity.  Lx, ly,
+<p>Vx, vy, vz, and ervel are in <a class="reference internal" href="units.html"><span class="doc">units</span></a> of velocity.  Lx, ly,
 lz are in units of angular momentum (distance-velocity-mass).  Wx, Wy,
 Wz are in units of angular velocity (radians/time).</p>
 <p>For atom_style hybrid, following the 4 initial values (ID,vx,vy,vz),
diff --git a/doc/html/read_restart.html b/doc/html/read_restart.html
index c69218b4a7..c42c14766e 100644
--- a/doc/html/read_restart.html
+++ b/doc/html/read_restart.html
@@ -248,7 +248,7 @@ means these quantities do not need to be re-specified in the input
 script that reads the restart file, though you can redefine many of
 these settings after the restart file is read.</p>
 <ul class="simple">
-<li><span class="xref doc">units</span></li>
+<li><a class="reference internal" href="units.html"><span class="doc">units</span></a></li>
 <li><a class="reference internal" href="atom_style.html"><span class="doc">atom style</span></a> and <a class="reference internal" href="atom_modify.html"><span class="doc">atom_modify</span></a> settings id, map, sort</li>
 <li><a class="reference internal" href="comm_style.html"><span class="doc">comm style</span></a> and <a class="reference external" href="comm_modify">comm_modify</a> settings mode, cutoff, vel</li>
 <li><a class="reference internal" href="timestep.html"><span class="doc">timestep</span></a></li>
diff --git a/doc/html/region.html b/doc/html/region.html
index 1429773e67..de04067047 100644
--- a/doc/html/region.html
+++ b/doc/html/region.html
@@ -330,7 +330,7 @@ with the <em>vel</em> keyword, the amplitude vector specified with the
 <em>wiggle</em> keyword, and the rotation point specified with the <em>rotate</em>
 keyword, since they each involve a distance metric.</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 spacings which are used as follows:</p>
diff --git a/doc/html/searchindex.js b/doc/html/searchindex.js
index 06757bb775..25c3902bf4 100644
--- a/doc/html/searchindex.js
+++ b/doc/html/searchindex.js
@@ -1 +1 @@
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,250,392,482,493],advantag:[1,6,8,11,14,18,40,41,42,226,386,411,496,501],advect:[3,6,329],advertis:8,advis:[381,448],afer:3,affect:[1,6,10,14,15,16,17,41,63,64,76,97,129,153,162,176,182,205,206,211,218,219,221,222,223,224,227,228,229,230,232,233,243,249,251,253,259,266,270,271,272,273,275,276,277,283,288,289,290,292,313,314,327,341,351,364,371,377,378,379,381,382,383,386,412,433,434,441,484,485,487,489,490,492,495,497],affin:[16,17,18,232,386,401],afil:247,aforement:18,afresh:[301,495,513],afshar:406,after:[],afterrun:495,afterward:3,afterword:42,ag1:177,ag2:177,again:[6,11,12,16,17,65,152,158,164,172,202,206,232,249,299,355,370,381,433,434,482,484,485,487,489,494,501,503,513,516],against:[11,12,13,67,233,381,449,450],aggreg:[6,12,69,72,74,85,103,120,127,249,265,311,313,327,482,514],aggress:[249,501],agilio:[9,13],agre:[3,8,198,379,388,421,450],agreement:[5,7],ahd:418,ahead:348,aidan:[0,5,7,9,13,374],aij:13,aim:6,airebo:[],ajaramil:[7,9,13],aka:205,akohlmei:[7,9,13,207,250],aktulga:[7,9,306,450],al2o3:457,al2o3_001:[130,314],al3:177,ala:[256,457],alain:9,alat:[294,436],alb:[447,470,472],albeit:312,albert:9,alchem:[96,172],alcohol:344,alcu:[387,392],alcu_eam:447,alderton:405,alejandr:[269,270],alessandro:13,algebra:439,algorithm:[0,1,6,7,8,9,42,64,206,215,226,229,232,256,258,259,283,296,304,313,316,317,336,337,341,344,349,377,378,379,383,386,408,412,434,439,454,456,482,484,501],alia:[9,16],alias:[1,372],aliceblu:206,align:[6,9,12,29,42,76,180,198,222,226,251,374,487,490,508],alkali:412,all:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,22,33,37,39,40,41,42,43,45,51,55,56,58,59,60,62,63,64,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,166,171,172,173,174,175,176,177,178,179,180,181,182,184,186,191,197,198,199,202,203,204,205,206,207,209,210,211,212,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,235,236,237,238,239,240,241,242,243,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,262,264,265,267,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,286,287,288,289,290,291,292,293,294,295,296,298,299,300,301,302,303,304,305,306,308,309,310,311,312,313,314,315,316,317,318,319,320,321,325,326,328,329,330,331,332,333,336,337,338,339,340,341,342,343,344,346,347,348,349,350,351,352,353,354,355,356,360,365,367,369,370,371,372,373,374,376,379,380,381,382,383,385,386,387,388,389,391,392,393,395,396,397,398,399,401,402,405,406,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,428,432,433,434,435,436,437,438,439,440,441,442,443,444,446,447,448,449,450,451,452,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,478,479,480,481,482,484,485,486,487,488,489,490,491,492,494,495,496,497,498,499,500,501,502,504,505,506,508,509,513,514,516,517,518],allen:[29,96,405,415],allentildeslei:96,allign:3,allindex:353,alloc:[3,5,6,8,9,11,12,63,243,343,380,382,386,445,450,487,495],allocat:3,alloi:[],allosw:76,allow:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,22,37,39,40,41,42,56,58,59,60,61,62,64,65,66,82,101,118,120,154,156,157,158,171,176,177,178,180,186,197,198,199,202,203,205,206,207,209,210,212,214,215,216,218,219,220,221,222,223,224,226,228,229,230,231,232,233,237,238,243,245,246,247,248,250,253,256,259,260,264,266,269,270,294,298,299,300,301,302,303,307,313,314,316,318,320,321,325,329,336,337,338,339,341,342,343,344,345,346,352,354,356,365,367,371,372,374,379,380,381,382,385,386,388,389,392,393,394,395,396,397,402,410,412,416,417,418,419,424,428,433,434,439,441,447,450,451,454,456,457,466,473,476,478,480,482,485,487,489,490,491,492,493,494,497,499,500,501,504,505,509,513,514],almost:[2,3,12,63,251,303,341,372,383,386,466],alo:402,alon:[6,7,229,309,449,450,485],alond:13,along:[6,8,12,29,41,76,96,130,176,177,178,201,202,205,218,229,251,256,257,261,266,268,303,313,316,318,322,326,327,336,340,341,347,350,352,374,377,378,379,381,402,405,416,419,422,424,428,436,449,450,469,487,490,497,498,513],alonso:[437,438],alpha:[6,12,52,210,256,303,304,308,379,387,390,393,402,406,408,410,411,413,418,423,424,436,442,446,471,473,505,508],alpha_c:432,alpha_i:458,alpha_lj:432,alphabet:[2,3,22,37,45,56,66,186,197,209,356,365,380,399,467,487],alphanumer:[3,66,209,302,310,354,380,513],alreadi:[3,7,8,9,12,16,17,18,43,58,178,179,181,204,214,218,222,223,226,228,232,260,301,303,329,352,353,380,381,406,417,419,426,434,466,476,479,483,487,488,492,497,513],also:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,22,29,36,37,38,40,41,42,43,45,55,56,57,61,62,64,66,70,76,77,78,80,82,87,88,96,98,99,101,104,114,115,116,117,118,119,124,126,128,129,131,152,153,154,155,156,157,158,159,160,161,162,164,165,166,167,168,170,171,172,173,174,175,178,179,180,181,182,184,186,19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201,294,304,306,367,413,415,514],chiefli:448,child:8,chip:[7,9,17,18,386,500],chipot:231,chiral:364,chmod:[11,12],cho:436,chocol:[7,206],choic:[3,6,9,12,15,16,18,41,42,55,96,153,156,157,171,182,198,218,222,223,226,229,232,233,247,253,256,267,269,296,300,304,313,336,365,372,377,378,381,383,386,419,432,441,445,487,496,497,500,501,507,508],choos:[1,3,6,7,8,9,12,16,17,18,29,40,55,96,129,168,169,205,227,228,229,230,233,242,253,256,267,269,271,272,273,274,275,276,277,299,300,317,329,333,347,371,372,378,476,482,484,496,502],chose:[470,472],chosen:[2,3,6,12,17,152,178,181,190,198,205,211,216,230,233,242,245,246,254,256,267,269,274,296,299,310,329,333,336,337,342,344,345,351,372,373,378,386,407,408,412,416,423,426,452,470,482,496,501,502,508],chri:176,christian:[7,9,14,17],christoph:7,chunk:[],chunkid:[70,80,87,99,104,115,117,126,158,173,175,218],chute:[4,9,10,248],ciccotti:316,cieplak:[6,184,499],cii:219,cij:219,ciko:2,circl:[43,76,325],circular:[3,6,156,200],circumst:18,circumv:[101,118,308],citat:[],cite:[3,7,8,12,253,457],civ:9,ckio:2,cko:2,cl1:177,clarendon:[29,405],clarifi:[7,470,472],clariti:354,clark:444,class2:[],classic:[0,3,5,6,7,8,9,243,296,303,308,341,366,412],classifi:[467,475],claus:485,clean:[6,12,14,15,17,495],cleanli:[486,517],clear:[],clearli:7,clebsch:152,clermont:[9,13],clever:491,click:[2,11,22,37,45,56,178,186,197,205,250,356,365,381,399,467,509],client:[250,252],climb:[268,381,501],clinic:[7,13],clo:[167,201,514],clock:[12,482,501],clockwis:347,clone:509,close:[3,6,11,12,13,40,42,71,76,153,181,202,228,229,230,247,254,256,269,290,313,316,347,350,370,372,375,377,378,381,386,388,392,402,403,422,436,441,449,453,455,469,472,491,497,508,509,511],closer:[3,10,42,128,176,201,202,226,230,234,338,381],closest:[228,294,313,344,415,451,466,476],cloud:[457,508],clovertown:18,clsuter:77,clump1:[298,313],clump2:[298,313],clump3:[298,313],clump:313,cluster:[],clutter:3,cmap:487,cmatrix:247,cmax:436,cmd:[11,12,296,498],cmdarg:11,cmin:436,cmm:[],cmoput:145,cn1:219,cn2:219,cna:[],cnn:219,cnr:[9,13],cnt:[419,491],co2:[41,177,316,380],coars:[7,9,10,29,36,41,55,190,298,313,329,417,452,496,499],coarser:[372,513],coarsest:152,code:[],coeff:[3,7,8,12,21,22,33,45,51,184,185,186,191,355,356,362,399,419,423,441,454,456,459,487,515],coeffcient:487,coeffici:[],coefficienct:406,coefficient0:410,coefficient1:410,coeffieci:[6,390,422],coeffincientn:410,coexist:[245,412],cohes:[6,413,436],coincid:[134,350,397,433,434,482],colberg:204,cold:[6,163,245,249,382,508],coldest:337,coleman8:9,coleman:[9,130,177,314],colin:9,collabor:[7,8,15],collect:[3,6,7,8,9,13,41,43,70,80,87,92,99,104,109,115,117,126,158,166,173,175,178,202,203,206,218,231,259,265,298,308,311,313,352,371,380,382,400,487,494,500,506,518],collid:[237,329,351],colliex:177,collinear:[3,298],collis:[3,256,329,347,351,409,416,479],colllis:329,colloid:[],colombo:40,colon:[207,352,488],color1:206,color2:206,color:[3,9,42,202,205,206,226,246,303,308],column:[3,6,9,12,13,43,66,69,70,71,72,74,76,80,82,85,87,88,90,99,101,103,104,115,117,118,120,122,125,126,127,128,129,131,152,153,158,166,173,175,176,177,198,202,203,206,209,217,218,219,221,222,223,224,259,266,267,303,313,330,331,341,351,414,418,449,450,488,502,504,513],columnar:176,colvar:[],colvarmodul:12,com:[],comamnd:232,comand:229,comannd:386,comb3:[],comb:[],comb_1:305,comb_2:305,combiant:403,combin:[3,6,7,9,11,13,36,41,66,69,74,85,96,103,114,120,127,156,157,171,202,205,215,221,250,259,269,296,302,317,333,342,350,353,355,371,372,374,378,386,400,402,403,408,412,413,419,431,432,458,468,470,472,473,475,478,490,495,500,508,513,515],come:[],comfort:[12,13],comit:509,comm:[0,3,11,12,64,78,204,250,252,253,372,381,386,406,441,446,469,489],comm_modifi:[],comm_modift:64,comm_styl:[],comm_world:11,command:[],comment:[2,4,7,11,12,38,57,184,198,202,241,254,313,341,380,381,387,410,411,413,423,436,443,450,457,458,468,469,470,471,472,475,484,485,487,508,509,513],commerci:7,commit:[9,509],commmand:[3,6,12,62,119,291,422,481,482,484,501,517],common:[],commonli:[3,6,9,12,17,25,60,62,116,118,180,202,205,207,366,417,426,458,470,472,487,490,499],commun:[1,3,6,7,8,9,10,11,12,14,15,16,18,41,42,61,64,65,76,176,181,182,205,206,226,227,228,230,231,232,250,252,256,258,259,260,269,295,302,304,305,306,313,317,329,341,352,369,371,382,383,384,386,408,409,445,480,484,485,496,497,513,516,518],communc:371,comp:[7,204,252,253,316,372,381,412,441,446,451,465,469,471],compact:[66,209,399,467],compani:[5,7],compar:[1,3,4,6,8,12,17,40,95,122,130,161,177,186,197,206,236,304,352,354,371,372,379,381,436,457,482,501,502,508],comparison:[],comparison_of_nvidia_graphics_processing_unit:14,compass:[7,9,21,22,37,44,45,56,185,186,197,355,356,365,398,467],compat:[3,5,7,8,9,11,12,13,17,18,42,76,129,131,189,202,207,211,217,218,219,221,222,223,224,226,295,307,333,336,343,346,349,371,386,420,439,441,469,484,485,513],compens:[6,227,228,311,382,412],compet:340,competit:372,compil:[3,7,8,9,12,13,14,15,16,17,18,19,176,202,204,205,207,250,340,372,386,439,487,488,492,513],compl:17,complain:[11,12,17],complement:436,complementari:[7,402,424],complet:[3,6,9,11,12,15,42,62,76,206,222,226,231,259,296,299,302,329,340,342,353,354,370,381,386,413,454,456,474,482,487,492,495,499,501,504,508,513],complex:[4,6,8,11,12,13,25,41,43,65,101,118,152,154,166,178,179,256,325,350,369,381,412,439,469,485,487,490,513],compli:[336,340],complic:[6,7,9,12,13,216,245,485],complier:12,compon:[3,6,8,12,64,66,70,71,78,87,88,97,98,99,100,101,104,105,108,113,115,116,117,118,119,120,121,122,124,125,129,139,142,143,144,145,148,149,150,152,153,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,173,174,175,201,202,203,205,206,212,213,217,218,219,220,221,222,223,224,225,229,230,232,233,238,243,248,252,253,256,259,261,265,266,268,269,270,274,275,276,277,288,289,290,292,293,295,296,297,300,311,313,315,316,318,322,323,326,329,332,333,334,336,343,344,349,350,351,371,374,378,379,380,381,386,406,412,416,433,434,454,456,457,458,487,488,497,505,513,514],componenet:6,composit:[6,216,256,410],compound:[401,412,413,475],compres:[76,126,218],compress:[],compris:[41,350,451,474],compton:[130,177],comptu:3,compuat:372,comput:[],computation:[3,6,227,228,341,392],computational:508,compute_arrai:8,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[130,314],compute_scalar:8,compute_temp:8,compute_vector:8,compute_xrd:177,concaten:[2,3,517],concav:350,concentr:[76,410],concept:[6,158,168,218,496],conceptu:[3,6,76,166,230,232,381,402,419,436,492],concern:[6,78,96,204,246],concetr:76,concis:[11,340],conclud:12,concret:8,concurr:[16,372,513],conden:[341,470,472],condens:[6,160,341,388,404,410,424,475],condit:[],conducit:6,conduct:[],cone:490,confer:439,confid:[3,501],config:[12,202,484],configfil:231,configur:[1,2,6,12,15,17,38,62,134,180,198,201,202,205,209,230,231,232,233,237,245,252,253,283,296,304,340,369,379,381,388,392,411,436,439,468,470,472,475,482,487,489,490,501,509],confin:[487,501],conflict:[3,12,41,203,441,485,509],conform:[3,6,13,62,229,230,268,312,318,340,364,381,412,499],confus:[3,475],conjuct:[9,406],conjug:[7,8,253,378,412,449,450],conjunct:[6,7,76,95,96,126,161,166,172,178,182,206,210,211,253,256,260,283,299,300,304,305,306,308,313,317,329,337,344,349,371,372,381,393,395,399,402,406,412,418,424,441,444,452,473,487,490,494,508,518],connect:[3,6,9,96,163,181,229,250,298,313,316,326,381,403,416,449,450,466,472,484,485,487,491,508],conner:388,connor:388,conput:3,consecut:[3,11,12,40,76,178,206,210,211,233,250,251,402,424,428,482,488,490],consequ:[1,6,216,341,423,501],conserv:[],consid:[6,75,76,83,96,127,160,163,164,181,202,203,206,210,211,217,219,222,226,228,229,233,257,270,295,313,336,337,340,341,344,372,399,412,419,450,451,457,466,482,483,485,488,489,490,492,495,497,505,508,513],consider:[6,8,253,254,332,333,334,386,496],consist:[3,6,8,9,11,12,41,43,69,74,85,103,115,120,123,124,127,158,161,163,178,190,201,207,212,213,218,232,233,236,238,243,246,253,254,255,266,269,271,272,273,274,275,276,277,278,279,281,282,283,284,286,287,288,289,290,291,292,300,303,308,310,312,313,332,333,334,335,345,371,372,374,380,381,386,388,392,394,400,402,412,415,419,422,433,434,436,439,441,451,454,456,457,469,476,485,487,488,489,490,491,492,499,508,513],consistent_fe_initi:215,consit:313,constant:[],constitu:[3,6,259,313,346,350,400,451],constitut:[454,456],constrain:[3,6,8,155,156,157,158,159,161,164,165,166,167,168,170,171,209,218,233,245,246,251,259,263,298,299,311,313,316,327,337,344,379,380,412,492,499,508],constraint:[],construct:[6,8,12,14,38,55,57,64,67,71,75,77,78,82,101,118,130,152,177,230,269,295,312,350,382,386,405,439,441,466,468,469,490,491,506,513],constructor:[8,11],consult:450,consum:[1,308,445,513],consumpt:369,contact:[],contact_stiff:[453,455],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,41,42,57,66,96,100,128,130,152,154,158,166,176,177,178,180,184,186,197,198,202,203,205,206,207,209,210,211,215,217,218,219,221,222,223,224,226,231,233,238,241,247,251,252,253,256,267,283,294,295,298,299,301,302,303,306,310,313,314,319,329,336,340,341,350,351,354,370,372,380,381,384,385,387,388,389,392,401,402,405,410,411,412,419,420,436,439,443,447,448,449,450,458,468,469,470,471,472,473,475,482,483,484,485,487,488,489,490,492,494,496,499,501,502,504,505,508,509,513,516,518],content:[4,8,9,12,18,450,503,505],context:[3,6,8,12,17,128,129,206,227,228,233,298,310,345,378,478,487,494,503,513,514],contibut:75,contigu:484,contin:16,continu:[0,2,3,5,6,9,12,13,14,42,76,88,114,115,174,206,209,210,211,216,218,219,220,221,222,223,224,226,229,230,231,232,233,245,246,247,249,250,251,253,254,255,261,266,267,269,271,272,273,274,275,276,277,288,289,290,291,292,297,299,302,303,313,314,318,328,329,331,338,339,341,347,350,354,370,385,386,392,406,409,426,429,449,450,451,454,456,471,482,485,487,489,490,495,501,502,504,505,513,516],continuum:[6,7,9,215,341,454,456],contour_integr:215,contract:[62,230,232,269,300,313],contradictori:3,contrain:316,contraint:283,contrari:[247,254],contrast:[1,6,43,56,67,160,163,203,232,352,454,456,478,517],contrib:341,contribut:[3,4,5,6,7,8,9,12,13,17,66,68,70,72,73,75,76,79,80,82,84,86,87,93,96,97,98,99,100,102,104,113,115,117,119,120,121,122,124,126,129,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,211,216,217,218,219,221,222,223,224,230,245,253,256,259,260,264,270,290,291,298,299,307,310,313,314,316,343,371,379,381,389,406,409,410,412,419,433,434,439,441,449,450,457,499,505,508,509],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,42,96,100,134,152,187,202,203,205,209,215,216,226,230,231,232,249,250,253,254,269,271,272,273,274,275,276,277,300,305,313,320,321,332,333,334,341,345,369,371,383,412,415,439,449,450,453,455,468,472,482,484,496,502,503],control_typ:215,controlfil:450,convect:100,conveni:[6,12,29,202,207,224,314,374,458,473,509,513],convent:[3,8,29,189,196,197,203,206,312,326,353,410,412,513],converg:[3,6,42,97,202,203,205,207,212,226,229,230,238,243,274,303,305,308,312,316,377,378,379,381,401,402,424,457,482,494,501],convers:[3,8,152,205,206,216,219,300,371,402,403,404,412,424,428,432,444,485,501],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,62,66,76,100,178,185,202,205,206,219,224,267,299,302,352,355,357,361,364,374,381,387,410,439,470,472,479,485,487,488,489,494,504,508,513,516,518],convex:[43,350],convinc:[7,12],cook:9,cooki:7,cool:[7,168,249,311],cooordin:[202,203],cooper:[5,7],coord123:126,coord1:[3,126,218,222,223],coord2:[3,126,218,222,223],coord3:[3,126,218,222,223],coord:[],coordb:457,coordbb:457,coordiat:379,coordin:[1,3,4,6,7,8,11,13,14,15,17,41,42,43,62,64,65,66,70,72,76,79,80,82,87,88,96,98,99,104,114,115,117,125,126,128,146,152,161,167,173,175,176,178,182,201,202,203,204,205,206,207,209,212,217,218,221,222,223,226,227,228,229,230,231,232,233,236,238,239,243,245,248,249,250,251,252,253,254,266,268,269,271,272,273,275,276,277,290,293,294,295,298,299,300,310,311,313,315,316,318,323,326,327,328,329,331,339,340,341,348,349,351,352,374,379,380,381,386,387,388,391,411,457,482,487,488,489,490,492,495,497,501,508,513,514],coordn:[126,218],copi:[0,3,4,8,9,11,12,15,17,41,131,205,341,381,399,449,485,509],copper:479,coproccesor:16,coprocessor:[1,7,9,16,17,386,500],coproprocessor:17,copy_arrai:8,copyright:[7,8,298],coral:206,core:[],core_shel:160,coreshel:[],cornel:[6,184,499],corner123i:125,corner123x:125,corner123z:125,corner1i:125,corner1x:125,corner1z:125,corner2i:125,corner2x:125,corner2z:125,corner3i:125,corner3x:125,corner3z:125,corner:[3,6,41,125,205,350,351,374,474,487,509],cornflowerblu:206,cornsilk:206,corp:9,corpor:16,corr:401,correct:[3,6,9,11,12,16,17,62,87,96,97,113,114,119,122,128,160,165,172,203,205,232,245,247,253,269,270,290,298,300,303,340,346,350,371,381,387,388,389,390,391,392,393,394,395,396,397,398,400,401,402,403,404,405,406,409,410,411,412,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,444,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,474,475,477,478,479,480,487,502,505,508,509],correction_max_iter:215,correctli:[3,8,11,17,76,88,113,114,115,155,156,157,159,161,163,164,165,166,167,170,171,174,202,206,212,233,238,243,254,263,269,270,306,313,316,326,328,347,350,381,382,386,404,434,439,484,485,487,497,509,514],correl:[],correpond:241,correspond:[1,2,4,6,8,9,10,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,41,43,44,45,46,47,48,49,50,52,54,55,57,75,76,96,107,108,121,124,125,126,127,130,131,139,142,143,144,145,146,148,149,150,152,155,156,165,172,176,177,184,185,186,187,188,189,190,192,193,195,196,198,201,202,203,205,206,210,211,212,218,220,221,222,223,225,228,230,232,239,243,244,248,253,256,257,265,266,267,269,271,272,273,274,275,276,277,278,279,283,286,288,289,290,292,295,296,300,305,313,315,316,332,334,336,345,346,347,349,350,351,353,355,356,357,358,360,361,364,366,372,376,378,380,381,387,388,390,393,394,395,396,397,398,399,400,401,402,405,406,410,411,412,413,414,415,416,417,418,419,422,424,425,426,427,428,429,430,431,432,433,436,437,439,441,442,443,444,446,447,449,450,451,452,457,458,459,468,469,470,471,472,473,475,477,478,479,482,484,485,487,488,490,500,501,502,504,505,508,513],correspondingli:[433,434,496],corrupt:3,cosin:[],cosineshift:27,cosmo:[247,252],cossq:[],cost:[1,6,10,11,12,17,40,42,76,121,130,153,177,205,206,218,222,223,226,227,228,242,269,305,341,371,372,384,402,424,428,439,441,468,484,496],costheta0:[468,470,472,475],costheta:447,costli:[11,97,247,382],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,42,51,62,70,76,80,87,96,99,104,115,117,121,124,126,158,168,173,175,191,202,203,205,206,210,211,218,219,222,226,232,243,252,302,303,304,308,311,313,315,329,330,336,340,341,342,346,350,352,354,362,368,370,377,379,382,386,389,414,418,419,422,449,450,483,484,485,487,489,491,494,495,502,503,508,513,514],coulomb:[3,5,6,7,8,9,10,12,14,15,18,77,97,119,120,128,153,179,183,304,306,342,371,372,379,386,393,395,396,397,398,401,402,403,404,405,412,416,417,419,424,428,432,435,441,444,449,450,452,457,467,472,473,475,478,492,499,505,508],coulommb:6,cound:3,count:[1,3,6,8,11,12,16,42,66,72,82,100,126,128,129,166,176,182,212,213,216,218,221,222,223,225,226,233,238,242,245,251,269,283,299,316,332,333,350,372,379,380,381,383,386,414,418,441,505,513],counter:[3,347,482,493,495,501],counteract:245,counterbal:249,counterbalanc:29,counterpart:[202,313,482],counterproduct:18,coupl:[],courant:319,cours:[3,8,138,140,172,202,210,211,246,312,326,340,346,348,349,351,352,372,433,459,484,487,500,508,513,516],courtesi:374,cov:457,coval:[6,9,29,412,436,457,508],covari:247,cover:[6,12,76,198,206,215,256,412,474],coverag:[76,222],cpc:252,cpp:[1,3,6,8,9,11,12,13,96,202,210,211,243,316],cpu:[1,3,9,10,12,14,15,16,17,18,66,76,206,220,236,254,342,369,372,386,399,467,482,500,501,504,505,506,513],cpuremain:505,cr2:177,cr3:177,crack:[4,382],crada:[5,7],crai:[5,7,13,18,202],crash:[3,12,382,508],craympi:386,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:215,create_faceset:215,create_group:204,create_nodeset:215,createatom:[],creation:[],crimson:206,critchlei:298,criteria:[3,128,179,205,206,227,228,229,264,379,446,474,489,492,513],criterion:[12,42,133,178,181,216,226,229,245,283,305,319,347,352,379,381,401,412,416,457,492,501,502],criterioni:501,critic:[6,49,50,267,336,341,379],crmax:76,crmin:76,cross:[3,12,22,76,98,156,176,186,202,203,205,217,222,228,232,266,268,290,313,322,326,328,337,344,356,374,381,397,406,409,410,417,418,419,424,426,428,447,452,454,456,470,472,479,487,491,497,516],crossov:1,crossterm:487,crozier:[0,7,13],crucial:303,crystal:[3,4,6,13,78,118,294,295,339,374,382,487,491,505,508],crystallin:[6,114,295,374,471,508],crystallis:336,crystallogr:[130,177],crystallograph:[374,505],crystallographi:[130,177,374],cs1:177,cs_chunk:6,cs_im:[41,487],cs_re:[41,487],csanyi:[152,448,458],cscl:436,csequ:6,csh:[11,12,399],cshrc:[11,12],csic:[411,468,470,472,475],csinfo:6,csisi:[411,468,470,472,475],csld:[],cst:410,cstherm:6,cstyle:484,csvr:[],ctcm:[387,410],ctemp_cor:236,cterm:318,ctr:9,ctype:11,cu1:177,cu2:177,cu3au:436,cube:[6,42,176,181,226,236,350,374,508],cubic:[],cuda:[],cuda_arch:[9,15],cuda_get:15,cuda_hom:[9,15],cuda_prec:[9,15],cufft:14,cuh:392,cummul:[3,6,224,227,228,229,231,242,247,253,255,329,332,333,334,335,337,344,418,505],cumul:[6,216,218,221,222,223,237,245,253,267,269,274,283,313,314,381],curli:2,current:[0,1,3,5,6,7,8,9,10,11,12,13,15,16,17,18,41,42,43,58,62,64,66,76,78,88,96,113,114,120,128,129,142,153,158,166,168,174,176,179,182,201,202,203,204,205,206,207,210,211,215,218,222,223,224,226,227,228,229,230,231,232,233,237,238,243,245,247,250,251,253,259,266,269,270,275,276,277,283,288,289,290,292,298,299,304,305,307,310,311,312,313,316,317,318,319,320,321,322,323,325,327,328,329,332,333,334,340,341,344,345,346,347,348,349,351,352,354,369,370,371,372,375,376,378,379,380,381,386,392,399,401,405,410,412,413,416,419,420,423,433,434,436,437,438,441,447,449,450,453,454,455,456,459,470,472,473,476,482,483,484,485,487,488,489,490,491,493,494,495,497,499,501,502,504,505,509,513,514,515,516,517,518],curv:[6,178,245,295],curvatur:[415,451,479],custom:[],cut0:485,cut1:496,cut2:496,cut:[],cuthi:[294,306],cutinn:[394,433,434],cutlo:[294,306],cutmax:447,cutoff1:[398,405,424,428,432,435,444,452],cutoff2:[393,395,396,398,404,405,424,428,432,435,444,452,473],cutoff:[3,6,8,10,16,18,40,46,47,55,56,64,75,77,78,82,96,101,118,120,127,128,152,176,179,181,182,228,229,234,241,294,303,304,306,308,310,313,317,329,342,346,350,352,369,371,372,379,382,383,384,386,387,388,389,390,391,392,393,394,395,396,397,398,400,402,403,404,405,406,407,408,409,410,411,412,413,414,415,417,418,419,420,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,449,450,451,452,457,458,459,460,461,462,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,485,489,492,496,508,513],cutoffa:411,cutoffc:411,cuu3:410,cval:177,cvd:336,cvel:318,cvff:[],cwiggl:[3,266,346,349,351,513],cyan:[2,205,206],cycl:[3,245,267,269,270,274],cyclic:[3,198],cygwin:12,cylind:[3,4,76,205,218,251,299,347,350,490],cylindr:[6,251,326,347],cypress:386,cyrot:392,cyrstal:295,d3q15:256,d3q19:256,d_double_doubl:15,d_e:341,d_flag2:302,d_flag:302,d_name:[125,202,302,331,497],d_single_doubl:15,d_single_singl:15,d_sx:302,d_sy:302,d_sz:302,daan:339,dai:12,daili:12,daivi:290,damag:[],dammak:308,damp:[3,6,209,214,253,254,255,260,269,270,274,300,303,304,308,313,332,333,345,347,348,378,379,381,393,395,397,402,405,412,416,424,432,444,452,467,473,501,508],damp_com:254,damp_drud:254,dampen:[313,508],dampflag:[347,416],dan:17,danger:[3,12,245,352,406,505],dangl:181,daniel:9,darden:[372,405],darkblu:206,darkcyan:206,darken:205,darkgoldenrod:206,darkgrai:206,darkgreen:206,darkkhaki:206,darkmagenta:206,darkolivegreen:206,darkorang:206,darkorchid:206,darkr:206,darksalmon:206,darkseagreen:206,darkslateblu:206,darkslategrai:206,darkturquois:206,darkviolet:206,dasgupta:304,dash:[416,504],dat:[6,100,198,215,483],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,314],dataset:314,datatyp:3,date:[0,4,6,12,13,201,449,450,513],datom1:127,datom2:127,datom3:127,datom4:127,datum:[3,6,43,69,72,74,85,103,120,127,202,219],davenport:435,davi:346,david:[9,19,371,372,470,472],daw:[410,447],dbg:14,dcd:[3,6,7,202,204,205,206,207,296,488,492],ddim:201,deactiv:432,dealt:252,debug:[6,7,11,12,13,14,17,58,130,134,177,178,296,301,369,371,386,420,441,476,485,486,494,497,504,513],deby:[],decai:[101,402,479],decid:[3,6,12,16,76,266,302,313,342,502,509],decipher:374,deck:302,declar:204,declin:329,decod:205,decompos:[96,458],decomposit:[3,5,7,18,65,215,296,317],decoupl:[6,508],decreas:[3,202,203,212,213,220,229,232,238,243,245,253,340,371],decrement:318,deepli:368,deeppink:206,deepskyblu:206,def:[12,13,485],defaul:64,defect:[6,75,176,439],defgrad:[],defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,52,54,55,56,57,58,59,60,61,62,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,184,185,186,187,188,189,190,192,193,195,196,197,198,199,200,201,202,203,204,205,206,209,210,211,212,213,214,215,216,217,218,219,221,222,223,224,225,226,227,228,229,230,232,233,236,237,238,240,243,244,245,248,251,252,253,254,255,256,264,266,268,269,270,271,272,273,274,275,276,277,279,280,281,284,286,287,288,289,290,291,292,294,295,296,298,299,300,302,304,306,311,313,314,315,316,319,323,327,329,331,332,333,334,335,337,338,339,341,343,344,346,347,348,349,350,351,352,354,355,356,357,358,359,360,361,364,365,366,367,369,371,372,374,376,378,379,380,381,382,383,384,385,386,388,389,390,391,393,394,395,396,397,398,399,400,402,403,405,406,407,408,409,411,412,414,415,416,417,418,419,420,422,424,425,426,427,428,429,430,431,432,433,434,435,439,440,441,442,443,444,446,447,449,450,451,452,453,454,455,456,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,484,485,487,488,490,491,492,493,496,497,498,499,501,502,504,505,508,510,511,512,513,514,515],definit:[2,3,6,8,12,13,83,86,128,152,206,218,219,220,221,222,223,224,232,240,251,274,314,331,343,346,349,351,353,365,369,380,389,392,400,407,408,412,422,447,454,456,458,474,485,487,489,496,498,513],defint:505,deform:[],deg2theta:177,deg:508,degener:[3,298],degrad:[8,18,295,372,496],degre:[3,6,8,20,21,24,28,29,32,35,36,38,69,85,101,103,105,107,108,110,112,113,118,124,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,177,178,184,185,188,189,196,198,201,205,218,229,236,245,247,248,253,254,259,269,270,274,275,276,277,288,289,290,292,296,298,312,313,316,332,333,334,339,355,357,361,364,366,379,405,410,418,497,505,508,514],degress:[158,218],del:501,delai:[3,6,12,382,409,505],deleg:419,delet:[2,3,7,8,12,55,60,63,66,176,181,182,209,218,219,221,222,223,224,227,229,242,245,269,314,332,333,352,354,370,380,382,385,441,466,487,488,489,490,498,499,504,509,510,512,513,514],delete_atom:[],delete_bond:[],delete_el:215,deli:201,delimit:[485,513],deloc:[270,412,457],delr:436,delt_lo:501,delta:[],delta_1:392,delta_3:392,delta_7:392,delta_conf:3,delta_ij:[436,447],delta_pi:392,delta_r:447,delta_sigma:392,delx:201,delz:201,demand:308,demo:11,demon:293,demonstr:[303,436],den:299,dendrim:418,denniston:[9,256,258,259,260,295],denomin:[7,183],denot:[130,236,254,295,306,308,402,417,419,450,454,456],dens:[76,229,412],densiti:[3,6,7,9,18,41,42,62,111,128,138,152,164,176,178,210,211,215,218,222,223,226,232,243,256,259,262,263,295,299,300,302,304,341,346,374,376,380,387,388,392,410,436,437,438,447,451,457,461,463,464,465,487,496,497,505],density_continu:456,density_summ:456,depart:[0,7],departur:[267,303],deped:8,depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,41,42,44,45,46,47,48,49,50,52,54,55,57,64,66,69,72,74,75,76,85,101,103,114,120,121,124,125,126,127,131,152,154,155,161,165,166,172,178,179,184,185,186,187,188,189,190,192,193,195,196,197,198,201,202,203,205,206,209,210,211,212,213,216,218,220,221,222,224,225,226,228,230,232,238,239,244,247,248,249,251,253,254,256,258,259,266,269,271,272,273,274,275,276,277,278,279,286,288,289,290,292,294,305,308,310,313,315,316,317,323,329,332,333,334,336,338,340,341,343,345,346,349,350,351,352,354,355,356,357,358,360,361,364,366,372,374,379,380,382,383,384,386,387,388,390,391,392,393,394,395,396,397,398,399,400,401,402,403,405,406,410,411,412,413,414,415,416,417,418,419,424,425,426,427,428,429,430,431,432,433,436,437,439,440,442,443,444,446,447,449,450,451,452,457,458,459,467,468,469,470,471,472,473,475,477,478,479,482,484,487,489,490,493,497,499,501,504,505,507,513,514],dependend:6,depflag:12,dephas:[482,501],depos:233,deposit:[],deprec:[3,304,449],depth:[52,156,205,341,415,451],dequidt:9,der:[96,119,400,401,432,449,450,478,508],deriv:[6,7,8,9,38,57,66,96,152,172,198,219,230,232,245,253,266,269,271,272,273,274,275,276,277,294,300,304,308,338,339,341,346,347,350,378,380,388,392,400,405,412,413,417,426,430,431,436,439,449,450,467,469,478,508],derjagin:478,derlet:294,descend:206,descent:[7,378],descib:[41,205,304],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,40,41,42,43,57,65,66,72,75,76,78,97,122,125,128,130,142,152,153,156,157,158,162,163,166,169,171,172,176,177,178,180,181,190,195,198,202,203,204,209,210,211,218,219,220,221,222,223,224,226,229,230,231,232,233,235,236,241,246,247,250,251,252,253,254,255,256,258,259,260,264,268,269,270,274,282,291,294,296,301,302,303,304,305,306,313,318,326,329,330,331,332,333,334,335,336,337,338,339,344,346,347,349,354,371,372,374,377,378,379,380,381,385,388,389,391,393,394,395,397,398,399,400,401,402,405,410,412,413,415,416,417,419,422,424,425,426,427,428,429,430,431,432,433,434,435,436,439,440,446,447,448,449,450,451,452,457,458,459,466,467,468,469,470,471,472,473,475,477,478,479,480,482,484,485,487,488,489,490,491,497,500,501,504,509,513,514,516],descript:[],descriptor:[152,202,420],deserno:372,design:[0,3,6,7,8,11,13,14,15,17,130,160,163,177,215,229,235,236,269,270,294,295,314,336,341,389,390,391,394,397,402,404,412,432,433,434,437,438,447,450,469],desir:[2,3,6,7,9,11,12,14,15,16,33,41,51,62,76,97,100,124,129,153,160,178,191,201,218,224,230,232,243,245,246,253,254,255,259,269,290,298,299,300,301,304,308,313,316,329,332,333,334,335,340,347,362,368,371,372,374,377,379,380,381,406,410,418,433,434,468,470,472,483,484,485,487,491,496,501,502,504,505,513,514,516],desk:7,desktop:[4,6,7,10,12,205],despit:508,destabil:392,destre:364,destroi:[9,11,40,227,228],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,22,37,41,42,43,56,66,70,71,72,76,80,83,87,99,100,104,113,115,117,119,121,123,124,126,129,131,152,153,155,156,157,158,161,171,172,173,175,178,179,182,183,186,197,201,202,203,205,206,209,210,211,215,218,219,220,221,222,224,226,228,229,230,231,232,233,243,245,246,247,248,250,251,253,255,256,260,266,267,268,269,270,271,272,273,274,275,276,277,281,283,288,289,290,291,292,295,298,299,300,302,303,305,306,307,313,316,317,329,332,333,334,335,336,337,339,340,341,342,343,344,345,352,354,356,365,371,372,375,379,380,382,383,386,387,388,389,391,392,394,396,397,398,399,400,401,402,405,406,412,413,415,416,417,418,419,424,425,426,427,428,429,430,431,432,433,434,435,436,440,441,446,449,450,451,457,458,459,467,474,477,478,480,485,487,488,489,490,492,493,496,497,499,502,505,506,509,513,514,518],detect:[2,3,12,43,64,66,95,101,244,299,340,381,401,418,423,482,484,487,498,501,513],determ:386,determin:[1,3,6,8,9,12,15,40,41,43,52,60,61,62,64,65,72,76,96,113,119,121,124,130,131,139,153,166,167,176,177,178,201,202,203,205,206,207,208,212,213,214,217,218,219,220,221,222,223,224,225,226,230,232,233,236,238,245,248,249,251,253,254,259,264,266,267,269,275,276,277,288,289,290,292,294,296,299,300,303,310,311,312,313,314,315,319,321,323,329,332,333,334,336,342,343,346,347,348,349,350,351,352,365,371,372,374,380,382,383,386,388,389,396,401,405,409,410,414,416,419,420,428,436,439,441,450,451,457,466,469,473,478,484,487,488,490,492,494,497,501,503,504,506,513,514],determinist:317,detil:120,devan:[9,452],devanathan:472,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,43,250,274,298,303,304,307,388,392,412,438,439,457,475,489],devemi:9,deviat:[267,274,294,414],deviator:9,devic:[1,3,12,15,17,250,386],device_typ:386,devin:[305,401],devis:438,dfactor:205,dff:508,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_singl:[3,12,372],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,307,439],dhi:[62,201,232,299],dhug:[267,303],dhugoniot:[267,303],dia:436,diagnost:[],diagon:[3,6,92,152,153,154,230,269,300,313,344,454,456],diagonalstyl:458,diagram:[42,130,177,197,226,296],diallo:418,diam:[205,206,299,380],diamet:[3,6,41,43,125,178,202,203,205,206,210,211,253,299,302,313,329,331,345,347,380,400,415,416,426,451,474,478,487,488,497],diamond:[374,412,436],diamter:[41,299],dick:6,dicsuss:266,dictat:[216,267],did:[3,12,379,406,409,410,416,441,470,472,495],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,174,343,371],differ:[1,2,3,4,6,7,8,9,11,12,14,15,16,17,18,22,37,38,40,42,43,55,56,57,64,67,72,75,76,96,101,105,107,108,132,152,154,155,156,157,158,159,161,164,165,166,167,168,170,171,172,178,179,181,186,197,198,201,202,205,206,209,211,214,216,218,221,226,227,228,229,230,231,232,236,241,244,245,246,247,248,249,250,253,254,256,266,269,270,271,272,273,275,276,277,279,281,284,286,287,288,289,292,294,296,298,300,303,304,305,308,311,313,316,318,326,327,329,332,333,334,337,338,339,341,344,345,346,347,350,354,355,365,368,370,371,372,374,375,377,378,380,381,383,384,385,386,387,388,392,396,397,399,400,401,406,407,408,410,412,415,416,4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87,509],donadio:333,done:[1,3,6,7,8,12,14,15,16,17,18,38,40,42,57,62,65,76,172,175,178,181,198,202,205,206,215,216,218,220,221,222,223,224,226,227,228,229,230,232,233,241,243,245,250,251,253,254,261,269,275,276,277,288,289,290,292,293,295,296,297,299,302,310,313,314,316,329,332,333,334,336,338,339,352,354,370,371,372,379,381,382,385,386,388,396,410,419,420,421,428,434,435,436,441,449,466,469,474,482,483,484,485,488,491,492,495,505,506,508,509,513,514],donor:418,dot:[153,174,212,238,248,268],doti:[392,447],doubl:[1,2,3,6,8,9,11,12,14,15,16,17,40,96,232,243,301,350,354,370,372,385,386,392,413,417,439,449,450,483,487,491,495,500,513,514],dover:215,down:[3,6,7,8,11,40,76,230,245,253,329,345,386,412,441,457,486,506],downhil:[377,378],download:[5,7,8,9,11,12,13,17,250,420,448],downsid:6,downward:310,dozen:[8,9,12,119,209,449,450],dpack_arrai:12,dpack_memcpi:12,dpack_point:12,dpd:[],dpde:262,dpdtheta:[41,89,90,408],dpdtheta_i:[240,241],dproduct:389,dr_ewald:[130,314],drag:[],dragforc:256,drai:[267,303],drain:[249,345,379],dramat:[9,62,201,227,228,229,230,232,269,329,332,333,372,386,441,457,484],drautz:392,draw:205,drawback:302,drawn:[43,202,205,206,246,482],drayleigh:[267,303],dreid:[],drfourth:116,drho:[125,387,410],drift:[6,114,116,246,247,253,254,265,311,329,496,504,508],drive:[11,12,213,230,232,248,269,294,300,313,348,381],driven:[6,190],driver:[6,12,14,15,209,243,250],drop:[3,206,406],droplet:419,drsquar:116,drude:[],dry:242,dsecriptor:420,dsf:[],dsmc:[],dstyle:299,dt_collis:256,dt_lb:256,dt_md:256,dt_srd:329,dtilt:[62,232],dtneb:501,dtqm:303,dtype:[127,228],dual:[16,17,329,386],dudarev:177,due:[1,3,6,9,12,16,17,19,41,55,58,60,61,64,70,75,76,79,80,87,88,95,97,98,99,104,113,114,115,116,117,122,128,130,138,152,153,155,156,157,159,161,164,165,166,167,168,170,171,173,177,178,181,182,202,203,205,209,212,213,221,225,227,228,229,230,231,232,233,238,239,242,243,246,247,250,251,253,254,255,256,259,260,261,265,266,267,268,269,274,283,294,297,299,311,312,313,315,326,328,329,330,332,333,334,335,336,338,339,341,345,346,348,349,350,352,372,377,379,381,382,383,403,406,407,408,410,414,415,419,433,434,441,447,449,451,452,466,469,470,472,476,478,479,482,484,487,488,489,496,501,504,505,506,508,513,514],duffi:341,duin:[9,304,309,449,450],duke:372,dummi:[12,29,471],dump0:203,dump10000:203,dump1:492,dump20000:203,dump2:492,dump2vtk_tri:146,dump:[],dump_0:203,dump_1:203,dump_atom:8,dump_custom:8,dump_h5md:204,dump_modifi:[],dump_p:203,dumpcustom:8,dumptimestep:492,dunbrack:[6,20,184,397,499],dunweg:[253,255],duplic:[2,3,14,15,17,42,43,179,203,226,247,294,487],dupont:[5,7,13],durat:[37,56,155,156,157,159,160,161,163,164,165,166,167,170,171,197,206,218,245,308,341,365,416,467],dure:[2,3,6,8,9,12,16,17,38,40,42,57,76,96,138,140,154,160,179,182,198,202,203,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,232,233,234,237,238,239,241,242,243,244,245,246,247,248,249,250,251,253,254,255,256,257,258,259,260,261,262,263,265,266,268,269,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,318,322,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,372,379,381,385,386,406,432,439,441,450,469,482,483,485,487,490,492,494,495,497,499,501,502,505,506,513,517,518],dvector:8,dvlo:478,dvx:6,dx_lb:256,dy3:177,dyamic:12,dyanam:6,dyanmic:501,dynam:[],dynamo:[5,387,410,436],dyne:[],dyre:429,dysam:490,e28637:29,e_1:392,e_2:392,e_b:413,e_data:203,e_e:412,e_hbond:418,e_i:[6,392,413],e_j:[6,392],e_k:[392,412],e_kl:6,e_lj:[388,405],e_n:[392,412],e_nn:412,e_pr:412,e_rebo:388,e_tors:388,e_tot:439,e_vol:439,eaa:355,eaat:185,each:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,40,41,42,43,44,46,47,48,49,50,51,52,54,55,56,57,58,60,62,64,65,66,67,68,70,71,72,73,75,76,77,78,79,80,81,82,83,84,86,87,88,90,92,94,96,98,99,101,102,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,121,122,123,124,125,126,127,128,129,130,131,132,146,152,153,154,156,157,158,159,160,161,162,165,166,167,168,170,171,172,173,174,175,176,177,178,181,182,184,185,186,187,188,189,190,191,192,193,195,196,197,198,201,202,203,204,205,206,207,208,209,210,211,212,213,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,241,242,243,245,246,247,248,249,250,251,252,253,254,255,256,257,259,260,261,262,263,265,266,267,268,269,271,272,273,274,275,276,277,278,279,280,281,283,284,285,286,287,288,289,290,291,292,294,295,296,297,298,299,300,301,302,304,305,306,308,310,313,314,315,316,317,318,322,323,325,326,327,328,329,330,331,332,333,334,336,339,340,341,342,343,344,345,346,347,349,350,351,352,354,355,357,358,359,360,361,362,364,365,366,370,371,372,374,378,379,380,381,382,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,412,413,4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5,494,518],equilater:497,equilibr:[3,4,5,6,7,9,62,100,178,209,216,219,229,230,245,267,269,270,290,291,300,303,304,305,306,337,338,339,344,401,402,449,450,483,497],equilibria:344,equilibribum:[227,228],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,39,44,48,49,50,52,54,57,59,62,161,162,185,187,230,232,245,246,247,254,256,269,274,290,303,304,308,312,316,318,326,329,336,337,339,344,355,357,361,364,401,436,443,457,508],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:215,equival:[6,12,13,29,62,64,136,137,145,150,176,180,206,221,224,230,232,245,253,269,290,300,312,313,349,388,406,412,457,470,472,473,487,490,495,496,505,508],equlibrium:6,equliibr:[304,306],er3:177,eradiu:[41,125,203,412,487],eras:[315,338],erat:[232,434],erc:402,erfc:[402,424,441],erforc:[125,203],erg:[],erhart:[216,410,470,472],ermscal:389,ernst:9,eror:3,eros:436,erose_form:436,erot:[],errata:[470,472],erratum:346,erron:3,error:[],erta:416,ervel:[125,203,487],escap:[233,508],especi:[8,16,166,178,209,216,226,245,303,308,311,312,386,484],espresso:[9,307],essenti:[8,11,12,27,97,140,159,160,161,164,165,166,167,168,170,187,219,274,295,345,372,388,402,424,472,492,505],essex:29,establish:[96,249],estim:[1,3,6,10,12,38,42,57,100,153,215,226,237,267,329,336,371,372,377,441,450,469,501,505],esu:[],esub:436,eta:[6,256,269,303,304,306,345,411,413,415,447,471,475],eta_dot:269,eta_ij:447,eta_ji:413,etag:[41,487],etail:505,etap:269,etap_dot:269,etc:[1,2,3,4,6,7,8,9,10,11,12,13,15,16,40,41,43,55,64,72,98,99,100,105,121,122,125,127,153,155,158,159,160,161,162,164,165,166,167,168,170,172,178,180,181,182,191,202,203,205,206,209,210,215,216,217,218,221,222,223,224,227,228,232,233,243,245,246,253,269,299,310,314,341,342,350,354,370,371,379,380,381,382,384,410,411,419,432,434,439,445,449,450,468,470,472,475,482,485,487,488,489,494,496,497,501,502,503,504,505,506,508,513,516,518],ethernet:18,etol:[379,381,482,501],etot0:303,etot:[6,105,107,108,122,153,164,206,236,254,267,303,504,505],eu2:177,eu3:177,euler:[379,381],eulerian:215,euqat:460,europhi:256,ev_tal:8,evalu:[2,3,9,11,12,38,57,76,96,97,100,119,129,131,152,154,158,168,176,178,201,202,203,205,206,210,211,212,213,215,217,218,219,220,221,222,223,224,225,232,238,246,248,249,251,252,253,254,295,301,304,315,319,323,332,333,334,343,346,349,351,352,354,371,372,377,379,386,439,441,447,453,455,457,469,482,483,485,489,490,492,494,495,496,497,501,503,505,513,514],evalut:[354,485],evan:[166,290],evanseck:[6,20,184,397,499],evapor:[],evaul:[8,379],evdwl:[119,154,449,450,505],even:[3,6,8,12,15,17,18,34,40,42,53,58,60,62,64,66,75,76,97,119,131,176,179,180,194,198,202,203,206,209,210,211,216,217,218,221,222,223,224,226,227,228,230,232,233,236,251,254,267,269,270,295,299,308,310,313,314,325,329,337,341,344,346,350,352,363,371,377,379,381,386,391,412,413,416,419,422,441,451,475,476,480,487,488,490,492,493,494,496,497,499,502,504,505,506,508,518],evenli:[3,42,58,153,198,226,256,422,476],event:[],eventu:[3,6,12,15,180,304,501],ever:[9,55,57,252,329],evera:[400,415,451,467],everi:[0,1,2,3,6,8,9,11,12,15,16,40,42,76,77,100,125,131,140,166,181,202,203,204,205,206,207,209,210,211,212,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,232,233,237,242,243,245,247,249,250,251,256,257,265,269,270,274,293,294,295,299,300,301,302,303,304,305,306,308,310,311,313,314,316,318,329,331,332,333,334,335,336,337,340,341,342,343,344,352,354,370,372,381,382,383,386,406,409,419,432,449,450,457,463,481,482,483,487,489,491,492,494,495,496,501,502,503,505,509,513,518],everyth:[8,119,509],everywher:[128,426],eviri:412,evolut:[247,256,296,482],evolv:[256,296,342],ewald:[2,3,5,6,7,8,9,12,97,122,130,153,342,371,372,379,393,395,396,402,405,412,424,428,444,452,467,469,473],ewald_disp:405,ewalddisp:3,exact:[22,42,45,76,134,172,181,186,226,229,246,247,253,254,255,299,308,309,329,341,356,371,399,489,494,501,513,516,518],exactli:[3,6,12,14,17,38,42,43,57,62,76,77,100,128,156,162,169,178,198,210,211,221,226,232,237,241,246,253,254,255,270,282,283,291,295,302,303,329,334,335,348,386,399,406,410,416,419,433,441,469,489,490,497,501,513],exager:508,examin:[6,8,17,229,295],examp:[485,513],exampl:[],exce:[3,6,16,17,18,42,61,76,180,217,218,221,222,223,224,226,230,232,237,242,269,295,310,314,320,321,329,379,386,487,513],exceed:[3,42,62,226,232,269,329,495],excel:412,except:[1,2,5,6,8,10,11,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,41,42,44,45,46,47,48,49,50,52,54,55,56,57,62,63,66,76,98,99,120,121,124,129,153,155,156,157,158,159,160,161,162,164,165,166,167,168,169,170,171,178,182,184,185,186,187,188,189,190,192,193,195,196,197,198,201,202,203,206,209,212,218,219,221,225,226,230,232,239,244,245,248,251,253,255,269,270,271,272,273,274,275,276,277,278,279,282,283,286,288,289,290,291,292,296,305,306,313,315,316,326,329,332,334,335,341,345,349,352,353,354,355,356,357,358,360,361,364,365,366,371,372,374,376,380,381,382,384,385,386,387,388,390,393,394,395,396,397,398,399,400,401,402,404,405,406,410,411,412,413,414,415,416,417,418,419,424,425,426,427,428,429,430,431,432,433,434,437,442,443,444,446,449,450,451,452,459,467,468,469,470,471,472,473,475,477,478,479,482,484,485,487,489,490,492,495,496,497,498,499,501,505,508,513,514,517],excess:[220,412],exchang:[2,3,6,8,64,65,209,215,216,245,253,305,313,337,341,344,371,386,412,502],exchange:371,excit:412,exclud:[3,6,9,12,16,17,66,76,113,124,152,158,165,166,182,202,218,222,227,228,257,265,298,311,313,336,347,352,379,380,382,394,416,419,422,433,434,441,466,499],exclus:[1,3,12,16,96,386,401,439,441,496,506],excurs:[269,482],exectubl:12,execut:[1,2,3,4,6,8,9,11,12,17,63,179,205,250,307,354,370,373,385,483,485,495,498,501,513],exempl:457,exemplari:246,exemplifi:412,exert:[6,251,254,308,348,349,350,372],exhaust:[215,385,513],exhibit:[101,269,378,412,496],exist:[3,6,7,8,11,12,13,16,37,56,58,62,72,75,134,178,179,197,204,205,206,209,214,225,228,230,233,245,298,299,301,302,352,353,355,357,358,359,361,365,375,380,386,407,408,419,449,466,476,483,485,487,488,489,498,499,500,509,513,514,516],exit:[2,3,11,12,42,60,202,226,241,370,385,485,486,495,504,513],exlanatori:3,exp:[],expand:[],expans:[12,152,202,498,513],expect:[1,3,8,12,13,14,15,16,17,18,19,42,43,76,113,159,170,176,198,226,238,245,247,266,294,300,302,303,308,313,352,372,382,399,436,439,441,482,485,487,489,492,496,501,513],expens:[6,76,206,294,298,313,341,352,371,372,382,386,485],experi:[6,13,15,17,225,233,250,259,268,300,312,313,377,381,406,441,496,501],experienc:[6,12,258,259],experiment:[245,371,386,501],expert:12,expertis:7,explain:[1,3,6,8,9,11,12,16,18,42,62,66,69,72,74,76,77,78,81,82,85,95,103,158,166,198,202,203,205,206,209,218,219,224,226,228,230,232,269,294,302,313,326,352,354,370,371,374,380,381,385,391,410,422,457,459,474,485,488,489,492,494,497,508,509,513,518],explan:[3,6,62,125,152,202,203,218,268,294,419,481,484,485,487,496],explanatori:[3,8,129,202,203,217,218,221,222,223,313,380,484,513],explantori:[3,309],explic:440,explicit:[6,9,11,22,45,82,96,125,128,172,186,210,211,232,320,321,356,376,388,389,392,397,399,410,412,423,433,473,481,484,488,491,509],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,44,46,47,48,49,50,52,54,55,57,76,121,124,155,165,168,176,178,184,185,187,188,189,190,192,193,195,196,198,202,203,206,212,222,225,232,239,244,246,248,253,269,271,272,273,274,275,276,277,278,279,286,288,289,290,292,302,303,305,313,315,316,332,334,335,341,345,349,355,357,358,360,361,364,366,380,386,387,388,390,393,394,395,396,397,398,399,400,401,402,403,405,406,409,410,411,413,414,415,416,417,418,419,423,424,425,426,427,428,429,430,431,432,433,437,439,441,442,443,444,446,451,452,459,460,461,462,463,464,465,467,468,469,470,471,472,473,475,477,478,479,487,489,490,496,497,499,500,506,508,509],explictli:[16,500],exploit:[15,17,296],explor:[130,177],expon:[3,304,306,410,415,418,432,440,452],exponenti:[96,447,468,475,479,501,513],expos:11,exposit:[215,406,409],express:[6,152,164,178,210,211,230,266,294,304,341,347,354,392,410,412,426,436,457,458,467,513],expressiont:392,extend:[],extens:[3,6,9,17,45,46,47,54,56,66,68,73,84,91,92,93,96,97,100,102,105,108,109,119,121,129,131,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,203,209,212,213,216,224,225,231,234,238,243,244,245,247,248,249,251,253,255,267,269,274,283,294,295,311,312,313,315,318,323,326,328,332,333,334,335,336,338,339,341,343,346,350,351,415,436,439,450,451,458,504,505],extent:[1,3,42,43,46,60,76,176,180,202,214,222,226,251,348,351,371,374,388,453,455,469,484,487,490],exterior:[3,6,176,350],extern:[],extra:[3,6,8,11,12,16,17,41,42,47,64,76,113,121,122,124,130,153,155,156,157,159,161,164,165,166,167,168,170,171,177,178,179,180,184,206,221,226,228,269,301,302,303,313,329,379,380,383,384,405,416,419,422,436,441,484,485,487,490,499,508,513],extract:[3,6,11,13,36,66,68,73,84,96,102,119,127,129,131,210,211,306,381,402,413,436,458,485,492,504],extract_atom:11,extract_comput:[11,485],extract_fix:11,extract_glob:11,extract_vari:11,extramak:[12,15],extrapol:1,extrem:[1,3,6,17,61,205,220,230,232,269,339,412,471,508],extrema:432,extrins:215,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[174,343],f_a:[470,471,472],f_ave:129,f_c:471,f_f:472,f_fix_id:303,f_foo:513,f_harm:339,f_i:[29,447],f_id:[6,76,129,131,202,203,209,217,218,219,220,221,222,223,224,264,331,343,505,513],f_ij:447,f_indent:224,f_int:338,f_j:29,f_jj:100,f_k:447,f_langevin:341,f_max:[303,308],f_msst:267,f_r:[254,470,471,472],f_sigma:392,f_solid:339,f_ss:6,face:[3,6,60,62,76,166,176,180,214,222,223,346,348,349,350,351,374,415,436,451,487,490],face_threshold:176,facet:176,facil:[0,12],facilit:[6,13,43],fact:[6,8,16,247,299,329,339,416,449,457,499],factor:[1,3,6,12,18,24,28,32,35,36,40,42,47,48,60,61,62,77,96,100,113,120,127,128,130,152,172,177,180,184,195,201,202,205,206,210,211,219,226,230,232,233,245,250,253,255,256,267,269,270,274,296,300,304,312,316,319,321,329,333,337,344,345,346,350,361,372,374,380,386,388,389,392,393,395,397,402,403,404,406,407,408,412,416,419,423,424,436,439,441,443,444,450,452,459,468,473,484,487,490,491,496,499,501,502,505,508,513],factori:[3,485],factoriz:371,fail:[3,9,11,12,62,182,230,233,371,379,381,404,450,485],failur:[133,454,486,513],fairli:[11,441,496,501,509],faken:78,falcon:250,fall:[3,6,206,221,299,485,513],fals:[95,352,354,457,513],fame:8,famili:[475,484],familiar:[0,11,509],fan:447,far:[3,6,12,17,60,62,64,95,202,203,206,207,226,227,228,230,233,269,294,312,313,329,346,357,361,377,381,382,474,485,487,492,505],farago:253,farrel:[470,472],farther:202,fashion:[6,8,42,76,178,206,209,210,211,216,222,226,228,233,245,247,251,266,267,269,271,272,273,274,275,276,277,285,288,289,290,291,292,302,303,305,313,318,322,328,331,339,341,345,346,347,349,351,381,419,433,490,499,513,517],fasolino:421,fast:[6,7,9,12,13,17,40,202,203,280,303,342,371,372,394,433,434,439,467,469,489,494,496,505,514,518],faster:[1,6,9,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,42,44,46,47,48,49,50,52,54,55,57,64,66,116,121,124,155,165,184,185,187,188,189,190,192,193,195,196,198,202,203,206,212,225,226,232,239,244,248,252,253,269,271,272,273,274,275,276,277,278,279,286,288,289,290,292,300,304,305,313,315,316,329,332,334,336,338,341,345,349,355,357,358,360,361,364,366,371,372,383,384,386,387,388,390,392,393,394,395,396,397,398,399,400,401,402,405,406,410,411,413,414,415,416,417,418,419,424,425,426,427,428,429,430,431,432,433,437,442,443,444,446,451,452,459,467,468,469,470,471,472,473,475,477,478,479,482,490,496,500,508],fastest:[1,6,14,17,166,222,341,342,386,484],fatal:[3,504],fault:[75,450],faulti:12,fava:415,favor:229,favorit:7,fbmc:336,fcc:[],fcm:[285,513],fdirect:236,fdotr:420,fdt:[],fdti:96,fe2:177,fe3:177,fe_md_boundari:215,featu:8,featur:[],fecr:410,feedback:[7,250],feel:[7,250,251,259,294,350,352,381,441],felling:438,felt:350,femtosecond:[],fene:[],fennel:[402,424],fep:[],ferguson:[6,184,499],fermi:[1,9,10,12,15,164,386,472],fermion:412,fernando:435,ferrand:[9,13],few:[1,3,4,5,6,7,9,10,11,12,13,14,18,40,66,207,217,218,219,221,222,223,224,254,269,299,302,304,316,343,371,379,380,381,388,457,484,487,492,496,498,506,516],fewer:[1,3,11,15,16,64,259,496],fewest:3,fextern:243,feynman:296,fff:485,ffield:[401,413,449,450,457],ffmpeg:[3,12,205],ffplai:205,fft:[1,3,7,9,11,12,14,15,97,121,122,153,295,371,372,496],fft_inc:[12,372],fft_lib:12,fft_path:12,fftbench:[371,506],fftw2:12,fftw3:12,fftw:[9,12],fhg:[7,9],ficiti:466,fictiti:[6,212,213,238,243,247,296,312,402,424,428,466],field1:[488,492],field2:488,field:[],fifth:[6,326,443],figur:[1,3,8,12,303,484,485,509],fij:405,file0:294,file1:[11,13,294,340,354,380,492,494,498],file2:[11,13,340,354,380,492,494,498],file:[],file_from:204,filen:380,filenam:[3,12,13,38,42,57,198,202,203,205,206,207,215,218,219,220,221,222,223,224,226,231,241,294,298,301,304,305,306,309,310,313,314,340,341,368,369,370,380,381,387,388,392,402,410,411,413,421,436,437,438,443,447,448,449,450,457,458,468,469,470,471,472,475,483,484,485,488,489,494,498,505,513,516,517,518],filennam:494,filep:[3,202,203,206,489,494,518],filepo:310,fill:[7,9,178,205,299,341,374,382,392,439,450,490,509],filter:[206,215],final_integr:8,final_integrate_respa:8,finchham:[6,160,404],find:[0,3,4,6,7,8,9,11,12,13,14,16,38,40,57,64,76,78,96,129,181,198,207,216,229,230,241,242,245,268,294,299,300,308,312,377,379,381,382,402,419,424,428,436,457,467,469,508,509,513],find_custom:8,fine:[16,17,182,212,238,339,382,386,509,513],finer:[152,178,513],finest:371,finger:[178,201,266,490],finish:[6,11,42,226,354,368,370,371,383,385,386,474,492,513,514],finit:[],finni:[7,410,467],finvers:236,fiorin:[9,231],fire:[],firebrick:206,first:[0,1,2,3,5,6,8,9,10,11,12,14,15,16,17,21,38,40,42,43,46,47,55,57,60,62,64,65,76,88,97,100,114,115,116,118,124,128,129,139,142,145,146,150,153,163,166,172,174,176,177,179,180,181,185,198,202,203,204,205,206,207,209,210,218,219,221,222,223,224,226,229,232,241,245,246,251,256,266,267,268,269,294,296,301,302,303,305,310,313,316,318,326,327,329,330,331,338,339,340,341,343,347,352,354,355,362,374,379,380,381,382,385,386,387,388,391,392,393,395,397,399,401,402,410,412,413,416,417,419,420,421,422,423,424,428,433,434,436,438,439,441,443,447,449,450,457,458,466,468,469,470,471,472,475,479,482,483,484,485,487,488,489,492,494,496,499,500,501,504,505,508,509,513,514,515,516,518],fischer:[6,9,19,20,184,397,499],fit:[3,6,9,12,38,57,198,241,312,329,388,392,421,436,441,462,469,471,495,509,513],five:[78,164,303,380,392,437,487,501],fix:[],fix_deposit:3,fix_flux:215,fix_id:[3,230,267,269,271,272,273,274,275,276,277,300,303],fix_manifoldforc:509,fix_modifi:[],fix_nh:8,fix_nv:509,fix_poem:3,fix_pour:3,fix_qeq:3,fix_rattl:316,fix_reax_bond:449,fix_saed_vtk:314,fix_setforc:8,fix_shak:316,fix_srd:3,fixedpoint:[230,269],fixextern:243,fixid:215,fji:405,flag1:[235,384],flag2:[235,384],flag:[3,8,9,11,12,14,15,16,17,39,41,59,70,79,80,87,88,95,98,99,104,114,115,117,130,173,177,181,199,202,203,205,206,207,224,229,231,235,250,253,257,259,265,266,295,302,313,326,328,329,336,340,349,352,367,369,372,380,384,385,386,388,418,423,436,439,466,480,482,484,485,487,488,489,491,492,493,497,509,513],flag_buck:396,flag_coul:[396,405,428],flag_lj:[405,428],flagfld:[394,433,434],flaghi:[3,394,433,434],flaglog:[394,433,434],flagn:235,flagvf:[394,433,434],flat:[6,341,346,347,351],flavor:[2,7,12],fld:[346,433,434],flen:389,flex_press:389,flexibl:[3,6,8,179,205,218,222,231,247,270,337,344,412,471,505],flip:[3,6,232,269,348,349],floor:513,flop:12,floralwhit:206,flow:[],fluctuat:[6,67,96,230,245,246,253,256,269,274,294,295,300,317,339,341,364,408],fluid:[],fluid_veloc:260,flush:[3,206,504],flux:[],flv:205,fly:[7,9,12,42,205,209,215,220,233,236,313,316,342,392,439,505,508],fmackai:9,fmag:234,fmass:296,fmax:[379,505],fmomentum:236,fmsec:[2,206,253,254,266,269,300,313,332,333,496,507,514],fname:370,fno:[9,16],fnorm:[379,505],fnpt:236,fnvt:236,foce:419,fock:389,focu:316,fogarti:[9,306,450],foil:[152,294,458],fold:[327,496],folk:7,follow:[0,1,2,3,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,41,42,43,44,46,47,48,49,50,52,54,55,57,62,66,67,75,76,78,89,100,101,107,108,118,125,128,129,131,152,153,156,157,158,164,166,171,174,176,178,179,184,187,188,189,190,192,193,195,196,198,202,204,205,206,209,215,216,217,218,219,220,221,222,223,224,226,231,232,233,236,237,240,241,243,245,246,247,250,252,253,254,256,259,267,269,274,275,276,277,288,289,290,292,295,296,298,301,302,303,304,306,308,310,312,313,314,316,331,332,333,334,337,338,339,340,341,343,344,352,353,357,358,359,360,361,364,366,369,374,376,379,380,381,386,387,388,389,390,391,392,393,394,395,396,397,398,400,401,402,403,404,405,406,407,408,409,410,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,440,441,442,443,444,446,447,448,449,450,451,452,454,456,457,458,459,460,461,462,463,464,465,466,468,469,470,471,472,473,474,475,477,478,479,480,482,484,485,487,488,490,492,494,495,496,499,501,502,503,508,509,513,514,517],foo:[4,8,11,12,202,205,243,485,498,513],foot:6,footprint:[12,386],fopenmp:[9,16,18],forc:[],force_uvm:17,forceatom:259,forcefield:[312,418],forcegroup:256,forcezero:377,ford:405,forestgreen:206,forev:76,forget:[254,508],forgiv:269,fork:[],form:[2,3,6,8,12,19,22,45,55,58,66,70,79,80,82,87,88,96,98,99,101,104,114,115,117,128,152,153,172,173,182,186,206,209,210,211,228,246,247,253,255,259,266,290,295,306,308,312,313,341,346,350,355,356,359,364,376,378,380,381,388,389,392,399,407,408,410,412,414,418,419,423,435,436,438,439,443,444,447,449,450,451,457,458,459,467,469,470,471,472,478,481,484,485,487,492,497,504,508,513],formal:[6,83,86,100,246,247,253,269,296,329,337,457],format:[2,3,6,7,8,9,12,13,22,38,42,45,57,58,72,82,186,198,202,203,204,205,206,207,218,221,222,223,224,226,228,241,295,298,302,304,306,309,313,314,325,340,341,352,353,356,376,380,381,387,388,392,399,410,413,423,436,438,448,449,450,452,458,469,475,476,484,485,487,488,489,492,503,504,505,513,515,516],former:[6,12,16,40,42,206,226,341,345,392,394,493,499,513],formerli:[7,13],formul:[1,6,9,41,67,153,212,238,253,269,290,304,306,312,316,340,371,388,392,410,412,415,436,446],formula:[2,3,6,7,13,21,22,37,45,55,56,75,78,96,98,99,100,105,107,108,117,124,130,131,153,155,156,157,158,159,160,161,162,164,165,166,167,168,169,170,171,177,178,183,185,186,197,201,202,210,211,212,213,218,219,220,221,224,225,232,238,248,249,251,253,254,266,294,295,301,310,315,323,327,329,332,333,334,343,346,349,351,352,354,355,356,358,365,374,380,388,389,391,392,397,398,399,400,405,406,410,411,415,416,417,418,420,423,424,426,427,428,430,431,433,434,436,440,441,442,451,452,459,467,468,469,470,471,472,475,477,478,483,487,490,497,504,505,513,514],forth:[1,6,11,12,13,14,15,385,485,490,494],fortran:[3,6,9,11,12,13,243,410,419,436,449,450],fortun:8,forward:[3,8,96,370,381,386],foster:[392,446,447],foul:181,found:[3,6,9,12,78,172,202,229,231,245,250,256,295,336,342,354,370,382,399,402,405,482,488,489,504],four:[6,11,55,88,114,115,152,174,267,341,364,380,381,439,482],fourier:[],fourth:[6,116,312,326,336,397,443,457],fox:[6,130,184,465,499],fphi:[38,57,469],fpic:12,fplo:[38,57,469],fprime:469,fqdn:252,fqq:405,fraction:[1,3,6,8,12,16,40,42,86,121,153,181,201,205,206,216,227,228,229,230,267,299,303,310,311,329,334,335,374,381,386,392,394,416,433,434,492,497],fragment:[43,250,310],fraig:43,frame:[92,152,206,215,267,303,348,415],framer:[205,206],framework:[5,247,387,458],franc:9,fraunhof:9,free:[5,6,7,9,13,29,63,66,75,96,172,210,211,294,329,338,339,340,341,378,381,389,412,432,439,447,478,484],freedom:[3,6,8,105,107,108,110,112,113,124,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,218,229,236,245,247,253,254,259,269,270,274,275,276,277,288,289,290,292,296,298,313,316,332,333,334,339,379,405,505,508,514],freeli:[0,6,7,12,156,157,171,176,205],freez:[],frenkel:[245,339],freq:214,frequenc:[3,6,16,40,114,206,220,283,295,296,303,308,369,406,412,450,457,482,496,501,513,517],frequent:[3,67,71,75,77,78,82,97,101,118,152,206,227,228,242,337,344,441,473,494],fri:[267,303],friction:[4,5,6,9,1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],yate:439,yb2:177,yb3:177,ybox:232,ycm:313,year:[5,7],yeh:371,yellow:[205,206],yellowgreen:206,yet:[3,7,17,40,43,205,210,310,346,372,378,379,386,398,400,401,412,478,485,487,488,509,513,515,516,517],yflag:[165,166,257,259,265,313,336],yhi:[6,62,180,202,232,340,346,349,351,487,490,505],yhi_bound:[6,202],yield:[6,100,122,129,153,161,166,206,219,230,236,269,290,304,337,343,344,347,352,371,391,406,416,441,446,505,513],yip:338,ylat:[178,232,251,505],ylo:[6,62,180,202,232,340,346,349,351,487,490,505],ylo_bound:[6,202],ymax:[214,513],ymin:513,yorig:76,york:[296,372],yoshida:[269,313],you:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,33,35,38,40,41,42,43,44,46,47,48,49,50,51,52,54,55,57,60,61,62,64,66,68,70,72,73,76,77,78,79,80,82,84,87,88,89,90,96,97,98,99,100,101,102,104,113,114,115,117,118,119,121,122,124,126,128,129,152,153,155,156,157,158,161,165,166,171,172,173,174,175,176,178,179,180,181,182,184,185,186,187,188,189,190,191,192,193,195,196,197,198,201,202,203,205,206,207,209,210,211,212,213,216,217,218,219,221,222,223,224,225,226,227,228,229,230,232,233,236,238,239,241,242,243,244,245,246,247,248,249,250,251,253,254,255,264,266,269,271,272,273,274,275,276,277,278,279,283,285,286,288,289,290,291,292,295,296,298,299,300,302,304,305,308,311,312,313,315,316,318,326,328,329,330,332,333,334,335,337,338,339,340,341,343,344,345,346,347,349,350,351,352,354,355,357,358,360,361,362,364,366,370,371,372,374,376,378,379,380,381,382,385,386,387,388,390,392,393,394,395,396,397,398,399,400,401,402,405,406,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,436,437,438,439,441,442,443,444,445,446,447,448,449,450,451,452,457,458,459,460,461,462,463,464,465,466,468,469,470,471,472,473,475,477,478,479,481,482,483,484,485,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,504,505,506,508,509,513,514,515,516,518],young:[416,453,455],your:[],yourself:[6,8,12,13,230,380,509],yplane:347,ypo:178,ysu:[3,202,203,331,488],yuan:9,yukawa:[],yukawa_1_1:476,yxz:484,yzx:484,z_i:[412,472,479],z_j:[472,479],z_meam:436,zachari:13,zannoni:415,zbl:[],zblcut:472,zblcutinn:458,zblcutout:458,zblexpscal:472,zblz:458,zcm:313,zcylind:347,zepeda:216,zero:[],zeta:[3,256,304,413],zfactor:205,zflag:[165,166,257,259,265,313,336],zhang:[313,337,416],zhi:[3,6,180,202,214,340,346,349,351,487,490,505],zhi_bound:[6,202],zhou:[13,392,413,447,470,472],zhu:465,ziegenhain:13,ziegler:[298,436,467,472,479],zimmerman2004:215,zimmerman2010:215,zimmerman:[9,75,215,392],zlat:[232,251,505],zlib:[9,202],zlim:457,zlo:[3,6,180,202,214,340,346,348,349,351,487,490,505],zlo_bound:[6,202],zmax:[214,256,513],zmin:[256,513],zn2:177,zone:[130,314],zoom:[3,202,205,206],zorig:76,zplane:347,zr4:177,zrest:328,zsu:[3,202,203,331,488],zwall:346,zwall_veloc:256,zxy:484,zybin:450,zyx:484},titles:["LAMMPS Documentation","5. Accelerating LAMMPS performance","3. Commands","12. Errors","7. Example problems","13. Future and history","6. How-to discussions","1. Introduction","10. Modifying &amp; extending LAMMPS","4. Packages","8. Performance &amp; scalability","11. Python interface to LAMMPS","2. Getting Started","9. Additional tools","5.USER-CUDA package","5.GPU package","5.USER-INTEL package","5.KOKKOS package","5.USER-OMP package","5.OPT package","angle_style charmm command","angle_style class2 command","angle_coeff command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style hybrid command","angle_style none command","angle_style quartic command","angle_style sdk command","angle_style command","angle_style table command","angle_style zero command","atom_modify command","atom_style command","balance command","Body particles","bond_style class2 command","bond_coeff command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style hybrid command","bond_style morse command","bond_style none command","bond_style nonlinear command","bond_style quartic command","bond_style command","bond_style table command","bond_write command","bond_style zero command","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local command","compute bond command","compute bond/local command","compute centro/atom command","compute chunk/atom command","compute cluster/atom command","compute cna/atom command","compute com command","compute com/chunk command","compute contact/atom command","compute coord/atom command","compute damage/atom command","compute dihedral command","compute dihedral/local command","compute dilatation/atom command","compute dipole/chunk command","compute displace/atom command","compute dpd command","compute dpd/atom command","compute erotate/asphere command","compute erotate/rigid command","compute erotate/sphere command","compute erotate/sphere/atom command","compute event/displace command","compute fep command","compute group/group command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute hexorder/atom command","compute improper command","compute improper/local command","compute inertia/chunk command","compute ke command","compute ke/atom command","compute ke/atom/eff command","compute ke/eff command","compute ke/rigid command","compute meso/e/atom command","compute meso/rho/atom command","compute meso/t/atom command","compute_modify command","compute msd command","compute msd/chunk command","compute msd/nongauss command","compute omega/chunk command","compute orientorder/atom command","compute pair command","compute pair/local command","compute pe command","compute pe/atom command","compute plasticity/atom command","compute pressure command","compute property/atom command","compute property/chunk command","compute property/local command","compute rdf command","compute reduce command","compute saed command","compute slice command","compute smd/contact/radius command","compute smd/damage command","compute smd/hourglass/error command","compute smd/internal/energy command","compute smd/plastic/strain command","compute smd/plastic/strain/rate command","compute smd/rho command","compute smd/tlsph/defgrad command","compute smd/tlsph/dt command","compute smd/tlsph/num/neighs command","compute smd/tlsph/shape command","compute smd/tlsph/strain command","compute smd/tlsph/strain/rate command","compute smd/tlsph/stress command","compute smd/triangle/mesh/vertices","compute smd/ulsph/num/neighs command","compute smd/ulsph/strain command","compute smd/ulsph/strain/rate command","compute smd/ulsph/stress command","compute smd/vol command","compute sna/atom command","compute stress/atom command","compute force/tally command","compute temp command","compute temp/asphere command","compute temp/body command","compute temp/chunk command","compute temp/com command","compute temp/cs command","compute temp/deform command","compute temp/deform/eff command","compute temp/drude command","compute temp/eff command","compute temp/partial command","compute temp/profile command","compute temp/ramp command","compute temp/region command","compute temp/region/eff command","compute temp/rotate command","compute temp/sphere command","compute ti command","compute torque/chunk command","compute vacf command","compute vcm/chunk command","compute voronoi/atom command","compute xrd command","create_atoms command","create_bonds command","create_box command","delete_atoms command","delete_bonds command","dielectric command","dihedral_style charmm command","dihedral_style class2 command","dihedral_coeff command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style hybrid command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style none command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style command","dihedral_style table command","dihedral_style zero command","dimension command","displace_atoms command","dump command","dump custom/vtk command","dump h5md command","dump image command","dump_modify command","dump molfile command","echo command","fix command","fix adapt command","fix adapt/fep command","fix addforce command","fix addtorque command","fix append/atoms command","fix atc command","fix atom/swap command","fix ave/atom command","fix ave/chunk command","fix ave/correlate command","fix ave/correlate/long command","fix ave/histo command","fix ave/spatial command","fix ave/spatial/sphere command","fix ave/time command","fix aveforce command","fix balance command","fix bond/break command","fix bond/create command","fix bond/swap command","fix box/relax command","fix colvars command","fix deform command","fix deposit command","fix drag command","fix drude command","fix drude/transform/direct command","fix dt/reset command","fix efield command","fix enforce2d command","fix eos/cv command","fix eos/table command","fix evaporate command","fix external command","fix freeze command","fix gcmc command","fix gld command","fix gle command","fix gravity command","fix heat command","fix imd command","fix indent command","fix ipi command","fix langevin command","fix langevin/drude command","fix langevin/eff command","fix lb/fluid command","fix lb/momentum command","fix lb/pc command","fix lb/rigid/pc/sphere command","fix lb/viscous command","fix lineforce command","fix meso command","fix meso/stationary command","fix_modify command","fix momentum command","fix move command","fix msst command","fix neb command","fix nvt command","fix nvt/eff command","fix nph/asphere command","fix nph/body command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/body command","fix npt/sphere command","fix nve command","fix nve/asphere command","fix nve/asphere/noforce command","fix nve/body command","fix nve/eff command","fix nve/limit command","fix nve/line command","fix nve/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/body command","fix nvt/sllod command","fix nvt/sllod/eff command","fix nvt/sphere command","fix oneway command","fix orient/fcc command","fix phonon command","fix pimd command","fix planeforce command","fix poems","fix pour command","fix press/berendsen command","fix print command","fix property/atom command","fix qbmsst command","fix qeq/point command","fix qeq/comb command","fix qeq/reax command","fix qmmm command","fix qtb command","fix reax/bonds command","fix reax/c/species command","fix recenter command","fix restrain command","fix rigid command","fix saed/vtk command","fix setforce command","fix shake command","fix shardlow command","fix smd command","fix smd/adjust_dt command","fix smd/integrate_tlsph command","fix smd/integrate_ulsph command","fix smd/move_tri_surf command","fix smd/setvel command","&lt;no title&gt;","fix smd/wall_surface command","fix spring command","fix spring/rg command","fix spring/self command","fix srd command","fix store/force command","fix store/state command","fix temp/berendsen command","fix temp/csvr command","fix temp/rescale command","fix temp/rescale/eff command","fix tfmc command","fix thermal/conductivity command","fix ti/rs command","fix ti/spring command","fix tmd command","fix ttm command","fix tune/kspace command","fix vector command","fix viscosity command","fix viscous command","fix wall/lj93 command","fix wall/gran command","fix wall/piston command","fix wall/reflect command","fix wall/region command","fix wall/srd command","group command","group2ndx command","if command","improper_style class2 command","improper_coeff command","improper_style cossq command","improper_style cvff command","improper_style distance command","improper_style fourier command","improper_style harmonic command","improper_style hybrid command","improper_style none command","improper_style ring command","improper_style command","improper_style umbrella command","improper_style zero command","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","mass command","min_modify command","min_style command","minimize command","molecule command","neb command","neigh_modify command","neighbor command","newton command","next command","package command","pair_style adp command","pair_style airebo command","pair_style awpmd/cut command","pair_style beck command","pair_style body command","pair_style bop command","pair_style born command","pair_style brownian command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_coeff command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dpd/conservative command","pair_style dpd/fdt command","pair_style dsmc command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style hybrid command","pair_style kim command","pair_style lcbop command","pair_style line/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style lj/mdf command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mgpt command","pair_style mie/cut command","pair_modify command","pair_style morse command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style none command","pair_style peri/pmb command","pair_style polymorphic command","pair_style quip command","pair_style reax command","pair_style reax/c command","pair_style resquared command","pair_style lj/sdk command","pair_style smd/hertz command","pair_style smd/tlsph command","pair_style smd/tri_surface command","pair_style smd/ulsph command","pair_style smtbq command","pair_style snap command","pair_style soft command","pair_style sph/heatconduction command","pair_style sph/idealgas command","pair_style sph/lj command","pair_style sph/rhosum command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style command","pair_style sw command","pair_style table command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style thole command","pair_style tri/lj command","pair_style vashishta command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","pair_style zero command","partition command","prd command","print command","processors command","python command","quit command","read_data command","read_dump command","read_restart command","region command","replicate command","rerun command","reset_timestep command","restart command","run command","run_style command","set command","shell command","special_bonds command","suffix command","tad command","temper command","thermo command","thermo_modify command","thermo_style command","timer command","timestep command","&lt;no title&gt;","LAMMPS GitHub tutorial","uncompute command","undump command","unfix command","variable command","velocity command","write_coeff command","write_data command","write_dump command","write_restart command"],titleterms:{"break":227,"default":[37,40,41,56,60,61,62,64,65,76,96,97,101,113,114,116,118,119,130,134,135,152,158,166,167,171,177,178,181,183,197,200,201,202,203,205,206,207,208,210,211,212,214,215,216,218,222,223,224,227,228,230,231,232,233,237,242,245,246,251,253,254,255,256,257,259,264,267,269,270,274,290,291,295,296,299,300,301,302,303,305,308,310,311,313,314,329,331,336,337,338,339,342,344,346,348,352,365,369,371,372,374,375,377,378,380,382,383,384,386,389,392,394,412,433,434,439,441,449,450,466,467,482,483,484,487,488,490,492,494,495,496,499,501,503,504,505,506,507,514,516,517],"function":513,"long":[220,393,395,396,397,398,402,404,405,424,428,432,444,452,473],"new":8,"static":12,acceler:1,account:509,ackland:67,acknowledg:7,adapt:[210,211],addforc:212,addit:[12,13,509],addtorqu:213,adiabat:6,adjust_dt:319,adp:387,after:509,airebo:388,alloi:410,amber2lmp:13,amber:6,angl:[8,68,69],angle_coeff:22,angle_styl:[2,20,21,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39],angmom:70,append:214,arrai:6,aspher:[6,9,91,156,271,275,279,280,288],atc:[9,215],atom:[6,7,8,67,71,75,76,77,78,81,82,83,86,88,90,94,101,106,107,110,111,112,118,122,123,125,152,153,176,214,216,217,302,513],atom_modifi:40,atom_styl:41,attract:5,aveforc:225,awpmd:[9,389],balanc:[42,226],barostat:6,basal:71,beck:390,berendsen:[300,332],between:6,binary2txt:13,bodi:[6,8,9,43,72,157,272,276,281,289,391],bond:[8,13,73,74,227,228,229,309],bond_coeff:45,bond_styl:[2,44,46,47,48,49,50,51,52,53,54,55,56,57,59],bond_writ:58,bop:392,born:[393,404],boundari:[7,60],box:[6,61,230],branch:509,brownian:394,buck:[395,396,404,435],bug:3,build:[11,12],calcul:6,call:12,categori:2,centro:75,ch2lmp:13,chain:13,chang:509,change_box:62,charmm:[6,20,184,397,432],chunk:[6,70,76,80,87,99,104,115,117,126,158,173,175,218],citat:7,class2:[9,21,44,185,355,398],clear:63,cluster:77,cmm:9,cna:78,code:6,coeffici:6,colloid:[9,346,400,478],colvar:[9,13,231],com:[79,80,159],comb3:401,comb:[305,401],come:5,comm_modifi:64,comm_styl:65,command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,510,511,512,513,514,515,516,517,518],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,513],compute_modifi:113,condit:7,conduct:[6,337],conserv:407,constant:[6,513],constraint:7,contact:[81,132],coord:82,core:6,coreshel:9,correl:[219,220],cosin:[23,24,25,26,27,28,187],cossq:357,coul:[393,395,396,397,398,402,403,404,417,424,428,432,444,452],coupl:6,creat:228,create_atom:178,create_bond:179,create_box:180,createatom:13,creation:7,csld:333,csvr:333,cubic:426,cuda:[9,14,121,124,155,165,212,225,239,244,248,269,278,315,316,332,334,345,393,395,397,398,410,416,417,424,425,427,430,442,468,470],custom:[8,202,203],cut:[50,389,395,398,402,405,412,414,424,425,432,440,444,473],cvff:358,damag:[83,133],data2xmovi:13,data:6,databas:13,deby:[402,424],defgrad:139,deform:[161,162,232],delete_atom:181,delete_bond:182,delta:24,deposit:233,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,510,511,512,513,514,515,516,517,518],diagnost:7,diel:403,dielectr:183,diffract:9,diffus:6,dihedr:[8,84,85],dihedral_coeff:186,dihedral_styl:[2,184,185,187,188,189,190,191,192,193,194,195,196,197,198,199],dilat:86,dimens:200,dipol:[6,9,29,87,405],direct:236,directori:4,discuss:6,disp:6,displac:[88,95],displace_atom:201,distanc:359,distribut:[7,12],document:0,dpd:[9,89,90,406,407,408],drag:234,dreid:[6,418],drude:[6,9,163,235,236,254],dsf:[402,424],dsmc:409,dump:[6,8,202,203,204,205,207],dump_modifi:206,dynam:304,eam:[13,410],echo:208,edip:411,eff:[9,13,107,108,162,164,169,255,270,282,291,335,412],efield:238,eim:413,elast:6,emac:13,energi:[135,408],enforce2d:239,ensembl:7,erot:[91,92,93,94],error:[3,134],evapor:242,event:95,exampl:[1,4,6,11,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,325,326,327,328,329,330,331,332,333,334,335,336,337,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,500,501,502,503,504,505,506,507,510,511,512,513,514,515,516,517,518],exp:[27,187],expand:[47,427],extend:[8,11],extern:243,fcc:294,fdt:408,featur:[7,8,509,513],fene:[46,47],fep:[9,13,96,211],field:[6,7],file:6,finit:6,fire:304,fix:[2,6,8,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256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adust:172,advanc:[3,250,392,482,493],advantag:[1,6,8,11,14,18,40,41,42,226,386,411,496,501],advect:[3,6,329],advertis:8,advis:[381,448],afer:3,affect:[1,6,10,14,15,16,17,41,63,64,76,97,129,153,162,176,182,205,206,211,218,219,221,222,223,224,227,228,229,230,232,233,243,249,251,253,259,266,270,271,272,273,275,276,277,283,288,289,290,292,313,314,327,341,351,364,371,377,378,379,381,382,383,386,412,433,434,441,484,485,487,489,490,492,495,497],affin:[16,17,18,232,386,401],afil:247,aforement:18,afresh:[301,495,514],afshar:406,after:[],afterrun:495,afterward:3,afterword:42,ag1:177,ag2:177,again:[6,11,12,16,17,65,152,158,164,172,202,206,232,249,299,355,370,381,433,434,482,484,485,487,489,494,501,503,514,517],against:[11,12,13,67,233,381,449,450],aggreg:[6,12,69,72,74,85,103,120,127,249,265,311,313,327,482,515],aggress:[249,501],agilio:[9,13],agre:[3,8,198,379,388,421,450],agreement:[5,7],ahd:418,ahead:348,aidan:[0,5,7,9,13,374],aij:13,aim:6,airebo:[],ajaramil:[7,9,13],aka:205,akohlmei:[7,9,13,207,250],aktulga:[7,9,306,450],al2o3:457,al2o3_001:[130,314],al3:177,ala:[256,457],alain:9,alat:[294,436],alb:[447,470,472],albeit:312,albert:9,alchem:[96,172],alcohol:344,alcu:[387,392],alcu_eam:447,alderton:405,alejandr:[269,270],alessandro:13,algebra:439,algorithm:[0,1,6,7,8,9,42,64,206,215,226,229,232,256,258,259,283,296,304,313,316,317,336,337,341,344,349,377,378,379,383,386,408,412,434,439,454,456,482,484,501],alia:[9,16],alias:[1,372],aliceblu:206,align:[6,9,12,29,42,76,180,198,222,226,251,374,487,490,508],alkali:412,all:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,22,33,37,39,40,41,42,43,45,51,55,56,58,59,60,62,63,64,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,166,171,172,173,174,175,176,177,178,179,180,181,182,184,186,191,197,198,199,202,203,204,205,206,207,209,210,211,212,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,235,236,237,238,239,240,241,242,243,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,262,264,265,267,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,286,287,288,289,290,291,292,293,294,295,296,298,299,300,301,302,303,304,305,306,308,309,310,311,312,313,314,315,316,317,318,319,320,321,325,326,328,329,330,331,332,333,336,337,338,339,340,341,342,343,344,346,347,348,349,350,351,352,353,354,355,356,360,365,367,369,370,371,372,373,374,376,379,380,381,382,383,385,386,387,388,389,391,392,393,395,396,397,398,399,401,402,405,406,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,428,432,433,434,435,436,437,438,439,440,441,442,443,444,446,447,448,449,450,451,452,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,478,479,480,481,482,484,485,486,487,488,489,490,491,492,494,495,496,497,498,499,500,501,502,504,505,506,508,509,513,514,515,517,518,519],allen:[29,96,405,415],allentildeslei:96,allign:3,allindex:353,alloc:[3,5,6,8,9,11,12,63,243,343,380,382,386,445,450,487,495],allocat:3,alloi:[],allosw:76,allow:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,22,37,39,40,41,42,56,58,59,60,61,62,64,65,66,82,101,118,120,154,156,157,158,171,176,177,178,180,186,197,198,199,202,203,205,206,207,209,210,212,214,215,216,218,219,220,221,222,223,224,226,228,229,230,231,232,233,237,238,243,245,246,247,248,250,253,256,259,260,264,266,269,270,294,298,299,300,301,302,303,307,313,314,316,318,320,321,325,329,336,337,338,339,341,342,343,344,345,346,352,354,356,365,367,371,372,374,379,380,381,382,385,386,388,389,392,393,394,395,396,397,402,410,412,416,417,418,419,424,428,433,434,439,441,447,450,451,454,456,457,466,473,476,478,480,482,485,487,489,490,491,492,493,494,497,499,500,501,504,505,509,514,515],almost:[2,3,12,63,251,303,341,372,383,386,466],alo:402,alon:[6,7,229,309,449,450,485],alond:13,along:[6,8,12,29,41,76,96,130,176,177,178,201,202,205,218,229,251,256,257,261,266,268,303,313,316,318,322,326,327,336,340,341,347,350,352,374,377,378,379,381,402,405,416,419,422,424,428,436,449,450,469,487,490,497,498,514],alonso:[437,438],alpha:[6,12,52,210,256,303,304,308,379,387,390,393,402,406,408,410,411,413,418,423,424,436,442,446,471,473,505,508],alpha_c:432,alpha_i:458,alpha_lj:432,alphabet:[2,3,22,37,45,56,66,186,197,209,356,365,380,399,467,487],alphanumer:[3,66,209,302,310,354,380,514],alreadi:[3,7,8,9,12,16,17,18,43,58,178,179,181,204,214,218,222,223,226,228,232,260,301,303,329,352,353,380,381,406,417,419,426,434,466,476,479,483,487,488,492,497,513,514],also:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,22,29,36,37,38,40,41,42,43,45,55,56,57,61,62,64,66,70,76,77,78,80,82,87,88,96,98,99,101,104,114,115,116,117,118,119,124,126,128,129,131,152,153,154,155,156,157,158,159,160,161,162,164,165,166,167,168,170,171,172,173,174,175,178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2,449,450],chen:341,cheng:401,chenoweth:[449,450],chenoweth_2008:[449,450],chi:[103,167,201,294,304,306,367,413,415,515],chiefli:448,child:8,chip:[7,9,17,18,386,500],chipot:231,chiral:364,chmod:[11,12],cho:436,chocol:[7,206],choic:[3,6,9,12,15,16,18,41,42,55,96,153,156,157,171,182,198,218,222,223,226,229,232,233,247,253,256,267,269,296,300,304,313,336,365,372,377,378,381,383,386,419,432,441,445,487,496,497,500,501,507,508,513],choos:[1,3,6,7,8,9,12,16,17,18,29,40,55,96,129,168,169,205,227,228,229,230,233,242,253,256,267,269,271,272,273,274,275,276,277,299,300,317,329,333,347,371,372,378,476,482,484,496,502],chose:[470,472],chosen:[2,3,6,12,17,152,178,181,190,198,205,211,216,230,233,242,245,246,254,256,267,269,274,296,299,310,329,333,336,337,342,344,345,351,372,373,378,386,407,408,412,416,423,426,452,470,482,496,501,502,508],chri:176,christian:[7,9,14,17],christoph:7,chunk:[],chunkid:[70,80,87,99,104,115,117,126,158,173,175,218],chute:[4,9,10,248],ciccotti:316,cieplak:[6,184,499],cii:219,cij:219,ciko:2,circl:[43,76,325],circular:[3,6,156,200],circumst:18,circumv:[101,118,308],citat:[],cite:[3,7,8,12,253,457],civ:9,ckio:2,cko:2,cl1:177,clarendon:[29,405],clarifi:[7,470,472],clariti:354,clark:444,class2:[],classic:[0,3,5,6,7,8,9,243,296,303,308,341,366,412],classifi:[467,475],claus:485,clean:[6,12,14,15,17,495],cleanli:[486,518],clear:[],clearli:7,clebsch:152,clermont:[9,13],clever:491,click:[2,11,22,37,45,56,178,186,197,205,250,356,365,381,399,467,509],client:[250,252],climb:[268,381,501],clinic:[7,13],clo:[167,201,515],clock:[12,482,501],clockwis:347,clone:509,close:[3,6,11,12,13,40,42,71,76,153,181,202,228,229,230,247,254,256,269,290,313,316,347,350,370,372,375,377,378,381,386,388,392,402,403,422,436,441,449,453,455,469,472,491,497,508,509,511],closer:[3,10,42,128,176,201,202,226,230,234,338,381],closest:[228,294,313,344,415,451,466,476],cloud:[457,508],clovertown:18,clsuter:77,clump1:[298,313],clump2:[298,313],clump3:[298,313],clump:313,cluster:[],clutter:3,cmap:487,cmatrix:247,cmax:436,cmd:[11,12,296,498],cmdarg:11,cmin:436,cmm:[],cmoput:145,cn1:219,cn2:219,cna:[],cnn:219,cnr:[9,13],cnt:[419,491],co2:[41,177,316,380],coars:[7,9,10,29,36,41,55,190,298,313,329,417,452,496,499],coarser:[372,514],coarsest:152,code:[],coeff:[3,7,8,12,21,22,33,45,51,184,185,186,191,355,356,362,399,419,423,441,454,456,459,487,516],coeffcient:487,coeffici:[],coefficienct:406,coefficient0:410,coefficient1:410,coeffieci:[6,390,422],coeffincientn:410,coexist:[245,412],cohes:[6,413,436],coincid:[134,350,397,433,434,482],colberg:204,cold:[6,163,245,249,382,508],coldest:337,coleman8:9,coleman:[9,130,177,314],colin:9,collabor:[7,8,15],collect:[3,6,7,8,9,13,41,43,70,80,87,92,99,104,109,115,117,126,158,166,173,175,178,202,203,206,218,231,259,265,298,308,311,313,352,371,380,382,400,487,494,500,506,519],collid:[237,329,351],colliex:177,collinear:[3,298],collis:[3,256,329,347,351,409,416,479],colllis:329,colloid:[],colombo:40,colon:[207,352,488],color1:206,color2:206,color:[3,9,42,202,205,206,226,246,303,308],column:[3,6,9,12,13,43,66,69,70,71,72,74,76,80,82,85,87,88,90,99,101,103,104,115,117,118,120,122,125,126,127,128,129,131,152,153,158,166,173,175,176,177,198,202,203,206,209,217,218,219,221,222,223,224,259,266,267,303,313,330,331,341,351,414,418,449,450,488,502,504,514],columnar:176,colvar:[],colvarmodul:12,com:[],comamnd:232,comand:229,comannd:386,comb3:[],comb:[],comb_1:305,comb_2:305,combiant:403,combin:[3,6,7,9,11,13,36,41,66,69,74,85,96,103,114,120,127,156,157,171,202,205,215,221,250,259,269,296,302,317,333,342,350,353,355,371,372,374,378,386,400,402,403,408,412,413,419,431,432,458,468,470,472,473,475,478,490,495,500,508,514,516],come:[],comfort:[12,13],comit:509,comm:[0,3,11,12,64,78,204,250,252,253,372,381,386,406,441,446,469,489],comm_modifi:[],comm_modift:64,comm_styl:[],comm_world:11,command:[],comment:[2,4,7,11,12,38,57,184,198,202,241,254,313,341,380,381,387,410,411,413,423,436,443,450,457,458,468,469,470,471,472,475,484,485,487,508,509,514],commerci:7,commit:[9,509],commmand:[3,6,12,62,119,291,422,481,482,484,501,518],common:[],commonli:[3,6,9,12,17,25,60,62,116,118,180,202,205,207,366,417,426,458,470,472,487,490,499],commun:[1,3,6,7,8,9,10,11,12,14,15,16,18,41,42,61,64,65,76,176,181,182,205,206,226,227,228,230,231,232,250,252,256,258,259,260,269,295,302,304,305,306,313,317,329,341,352,369,371,382,383,384,386,408,409,445,480,484,485,496,497,514,517,519],communc:371,comp:[7,204,252,253,316,372,381,412,441,446,451,465,469,471],compact:[66,209,399,467],compani:[5,7],compar:[1,3,4,6,8,12,17,40,95,122,130,161,177,186,197,206,236,304,352,354,371,372,379,381,436,457,482,501,502,508,513],comparison:[],comparison_of_nvidia_graphics_processing_unit:14,compass:[7,9,21,22,37,44,45,56,185,186,197,355,356,365,398,467],compat:[3,5,7,8,9,11,12,13,17,18,42,76,129,131,189,202,207,211,217,218,219,221,222,223,224,226,295,307,333,336,343,346,349,371,386,420,439,441,469,484,485,514],compens:[6,227,228,311,382,412],compet:340,competit:372,compil:[3,7,8,9,12,13,14,15,16,17,18,19,176,202,204,205,207,250,340,372,386,439,487,488,492,514],compl:17,complain:[11,12,17],complement:436,complementari:[7,402,424],complet:[3,6,9,11,12,15,42,62,76,206,222,226,231,259,296,299,302,329,340,342,353,354,370,381,386,413,454,456,474,482,487,492,495,499,501,504,508,514],complex:[4,6,8,11,12,13,25,41,43,65,101,118,152,154,166,178,179,256,325,350,369,381,412,439,469,485,487,490,514],compli:[336,340],complic:[6,7,9,12,13,216,245,485],complier:12,compon:[3,6,8,12,64,66,70,71,78,87,88,97,98,99,100,101,104,105,108,113,115,116,117,118,119,120,121,122,124,125,129,139,142,143,144,145,148,149,150,152,153,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,173,174,175,201,202,203,205,206,212,213,217,218,219,220,221,222,223,224,225,229,230,232,233,238,243,248,252,253,256,259,261,265,266,268,269,270,274,275,276,277,288,289,290,292,293,295,296,297,300,311,313,315,316,318,322,323,326,329,332,333,334,336,343,344,349,350,351,371,374,378,379,380,381,386,406,412,416,433,434,454,456,457,458,487,488,497,505,514,515],componenet:6,composit:[6,216,256,410],compound:[401,412,413,475],compres:[76,126,218],compress:[],compris:[41,350,451,474],compton:[130,177],comptu:3,compuat:372,comput:[],computation:[3,6,227,228,341,392],computational:508,compute_arrai:8,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[130,314],compute_scalar:8,compute_temp:8,compute_vector:8,compute_xrd:177,concaten:[2,3,518],concav:350,concentr:[76,410],concept:[6,158,168,218,496],conceptu:[3,6,76,166,230,232,381,402,419,436,492],concern:[6,78,96,204,246],concetr:76,concis:[11,340],conclud:12,concret:8,concurr:[16,372,514],conden:[341,470,472],condens:[6,160,341,388,404,410,424,475],condit:[],conducit:6,conduct:[],cone:490,confer:439,confid:[3,501],config:[12,202,484],configfil:231,configur:[1,2,6,12,15,17,38,62,134,180,198,201,202,205,209,230,231,232,233,237,245,252,253,283,296,304,340,369,379,381,388,392,411,436,439,468,470,472,475,482,487,489,490,501,509],confin:[487,501],conflict:[3,12,41,203,441,485,509],conform:[3,6,13,62,229,230,268,312,318,340,364,381,412,499],confus:[3,475],conjuct:[9,406],conjug:[7,8,253,378,412,449,450],conjunct:[6,7,76,95,96,126,161,166,172,178,182,206,210,211,253,256,260,283,299,300,304,305,306,308,313,317,329,337,344,349,371,372,381,393,395,399,402,406,412,418,424,441,444,452,473,487,490,494,508,519],connect:[3,6,9,96,163,181,229,250,298,313,316,326,381,403,416,449,450,466,472,484,485,487,491,508],conner:388,connor:388,conput:3,consecut:[3,11,12,40,76,178,206,210,211,233,250,251,402,424,428,482,488,490],consequ:[1,6,216,341,423,501],conserv:[],consid:[6,75,76,83,96,127,160,163,164,181,202,203,206,210,211,217,219,222,226,228,229,233,257,270,295,313,336,337,340,341,344,372,399,412,419,450,451,457,466,482,483,485,488,489,490,492,495,497,505,508,514],consider:[6,8,253,254,332,333,334,386,496],consist:[3,6,8,9,11,12,41,43,69,74,85,103,115,120,123,124,127,158,161,163,178,190,201,207,212,213,218,232,233,236,238,243,246,253,254,255,266,269,271,272,273,274,275,276,277,278,279,281,282,283,284,286,287,288,289,290,291,292,300,303,308,310,312,313,332,333,334,335,345,371,372,374,380,381,386,388,392,394,400,402,412,415,419,422,433,434,436,439,441,451,454,456,457,469,476,485,487,488,489,490,491,492,499,508,514],consistent_fe_initi:215,consit:313,constant:[],constitu:[3,6,259,313,346,350,400,451],constitut:[454,456],constrain:[3,6,8,155,156,157,158,159,161,164,165,166,167,168,170,171,209,218,233,245,246,251,259,263,298,299,311,313,316,327,337,344,379,380,412,492,499,508],constraint:[],construct:[6,8,12,14,38,55,57,64,67,71,75,77,78,82,101,118,130,152,177,230,269,295,312,350,382,386,405,439,441,466,468,469,490,491,506,514],constructor:[8,11],consult:450,consum:[1,308,445,514],consumpt:369,contact:[],contact_stiff:[453,455],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,41,42,57,66,96,100,128,130,152,154,158,166,176,177,178,180,184,186,197,198,202,203,205,206,207,209,210,211,215,217,218,219,221,222,223,224,226,231,233,238,241,247,251,252,253,256,267,283,294,295,298,299,301,302,303,306,310,313,314,319,329,336,340,341,350,351,354,370,372,380,381,384,385,387,388,389,392,401,402,405,410,411,412,419,420,436,439,443,447,448,449,450,458,468,469,470,471,472,473,475,482,483,484,485,487,488,489,490,492,494,496,499,501,502,504,505,508,509,514,517,519],content:[4,8,9,12,18,450,503,505],context:[3,6,8,12,17,128,129,206,227,228,233,298,310,345,378,478,487,494,503,513,514,515],contibut:75,contigu:484,contin:16,continu:[0,2,3,5,6,9,12,13,14,42,76,88,114,115,174,206,209,210,211,216,218,219,220,221,222,223,224,226,229,230,231,232,233,245,246,247,249,250,251,253,254,255,261,266,267,269,271,272,273,274,275,276,277,288,289,290,291,292,297,299,302,303,313,314,318,328,329,331,338,339,341,347,350,354,370,385,386,392,406,409,426,429,449,450,451,454,456,471,482,485,487,489,490,495,501,502,504,505,514,517],continuum:[6,7,9,215,341,454,456],contour_integr:215,contract:[62,230,232,269,300,313],contradictori:3,contrain:316,contraint:283,contrari:[247,254],contrast:[1,6,43,56,67,160,163,203,232,352,454,456,478,518],contrib:341,contribut:[3,4,5,6,7,8,9,12,13,17,66,68,70,72,73,75,76,79,80,82,84,86,87,93,96,97,98,99,100,102,104,113,115,117,119,120,121,122,124,126,129,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,211,216,217,218,219,221,222,223,224,230,245,253,256,259,260,264,270,290,291,298,299,307,310,313,314,316,343,371,379,381,389,406,409,410,412,419,433,434,439,441,449,450,457,499,505,508,509],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,42,96,100,134,152,187,202,203,205,209,215,216,226,230,231,232,249,250,253,254,269,271,272,273,274,275,276,277,300,305,313,320,321,332,333,334,341,345,369,371,383,412,415,439,449,450,453,455,468,472,482,484,496,502,503],control_typ:215,controlfil:450,convect:100,conveni:[6,12,29,202,207,224,314,374,458,473,509,514],convent:[3,8,29,189,196,197,203,206,312,326,353,410,412,514],converg:[3,6,42,97,202,203,205,207,212,226,229,230,238,243,274,303,305,308,312,316,377,378,379,381,401,402,424,457,482,494,501],convers:[3,8,152,205,206,216,219,300,371,402,403,404,412,424,428,432,444,485,501,513],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,62,66,76,100,178,185,202,205,206,219,224,267,299,302,352,355,357,361,364,374,381,387,410,439,470,472,479,485,487,488,489,494,504,508,513,514,517,519],convex:[43,350],convinc:[7,12],cook:9,cooki:7,cool:[7,168,249,311],cooordin:[202,203],cooper:[5,7],coord123:126,coord1:[3,126,218,222,223],coord2:[3,126,218,222,223],coord3:[3,126,218,222,223],coord:[],coordb:457,coordbb:457,coordiat:379,coordin:[1,3,4,6,7,8,11,13,14,15,17,41,42,43,62,64,65,66,70,72,76,79,80,82,87,88,96,98,99,104,114,115,117,125,126,128,146,152,161,167,173,175,176,178,182,201,202,203,204,205,206,207,209,212,217,218,221,222,223,226,227,228,229,230,231,232,233,236,238,239,243,245,248,249,250,251,252,253,254,266,268,269,271,272,273,275,276,277,290,293,294,295,298,299,300,310,311,313,315,316,318,323,326,327,328,329,331,339,340,341,348,349,351,352,374,379,380,381,386,387,388,391,411,457,482,487,488,489,490,492,495,497,501,508,514,515],coordn:[126,218],copi:[0,3,4,8,9,11,12,15,17,41,131,205,341,381,399,449,485,509],copper:479,coproccesor:16,coprocessor:[1,7,9,16,17,386,500],coproprocessor:17,copy_arrai:8,copyright:[7,8,298],coral:206,core:[],core_shel:160,coreshel:[],cornel:[6,184,499],corner123i:125,corner123x:125,corner123z:125,corner1i:125,corner1x:125,corner1z:125,corner2i:125,corner2x:125,corner2z:125,corner3i:125,corner3x:125,corner3z:125,corner:[3,6,41,125,205,350,351,374,474,487,509],cornflowerblu:206,cornsilk:206,corp:9,corpor:16,corr:401,correct:[3,6,9,11,12,16,17,62,87,96,97,113,114,119,122,128,160,165,172,203,205,232,245,247,253,269,270,290,298,300,303,340,346,350,371,381,387,388,389,390,391,392,393,394,395,396,397,398,400,401,402,403,404,405,406,409,410,411,412,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,444,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,474,475,477,478,479,480,487,502,505,508,509],correction_max_iter:215,correctli:[3,8,11,17,76,88,113,114,115,155,156,157,159,161,163,164,165,166,167,170,171,174,202,206,212,233,238,243,254,263,269,270,306,313,316,326,328,347,350,381,382,386,404,434,439,484,485,487,497,509,513,515],correl:[],correpond:241,correspond:[1,2,4,6,8,9,10,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,41,43,44,45,46,47,48,49,50,52,54,55,57,75,76,96,107,108,121,124,125,126,127,130,131,139,142,143,144,145,146,148,149,150,152,155,156,165,172,176,177,184,185,186,187,188,189,190,192,193,195,196,198,201,202,203,205,206,210,211,212,218,220,221,222,223,225,228,230,232,239,243,244,248,253,256,257,265,266,267,269,271,272,273,274,275,276,277,278,279,283,286,288,289,290,292,295,296,300,305,313,315,316,332,334,336,345,346,347,349,350,351,353,355,356,357,358,360,361,364,366,372,376,378,380,381,387,388,390,393,394,395,396,397,398,399,400,401,402,405,406,410,411,412,413,414,415,416,417,418,419,422,424,425,426,427,428,429,430,431,432,433,436,437,439,441,442,443,444,446,447,449,450,451,452,457,458,459,468,469,470,471,472,473,475,477,478,479,482,484,485,487,488,490,500,501,502,504,505,508,514],correspondingli:[433,434,496],corrupt:3,cosin:[],cosineshift:27,cosmo:[247,252],cossq:[],cost:[1,6,10,11,12,17,40,42,76,121,130,153,177,205,206,218,222,223,226,227,228,242,269,305,341,371,372,384,402,424,428,439,441,468,484,496],costheta0:[468,470,472,475],costheta:447,costli:[11,97,247,382],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,42,51,62,70,76,80,87,96,99,104,115,117,121,124,126,158,168,173,175,191,202,203,205,206,210,211,218,219,222,226,232,243,252,302,303,304,308,311,313,315,329,330,336,340,341,342,346,350,352,354,362,368,370,377,379,382,386,389,414,418,419,422,449,450,483,484,485,487,489,491,494,495,502,503,508,514,515],coulomb:[3,5,6,7,8,9,10,12,14,15,18,77,97,119,120,128,153,179,183,304,306,342,371,372,379,386,393,395,396,397,398,401,402,403,404,405,412,416,417,419,424,428,432,435,441,444,449,450,452,457,467,472,473,475,478,492,499,505,508,513],coulommb:6,cound:3,count:[1,3,6,8,11,12,16,42,66,72,82,100,126,128,129,166,176,182,212,213,216,218,221,222,223,225,226,233,238,242,245,251,269,283,299,316,332,333,350,372,379,380,381,383,386,414,418,441,505,514],counter:[3,347,482,493,495,501],counteract:245,counterbal:249,counterbalanc:29,counterpart:[202,313,482],counterproduct:18,coupl:[],courant:319,cours:[3,8,138,140,172,202,210,211,246,312,326,340,346,348,349,351,352,372,433,459,484,487,500,508,514,517],courtesi:374,cov:457,coval:[6,9,29,412,436,457,508],covari:247,cover:[6,12,76,198,206,215,256,412,474],coverag:[76,222],cpc:252,cpp:[1,3,6,8,9,11,12,13,96,202,210,211,243,316],cpu:[1,3,9,10,12,14,15,16,17,18,66,76,206,220,236,254,342,369,372,386,399,467,482,500,501,504,505,506,514],cpuremain:505,cr2:177,cr3:177,crack:[4,382],crada:[5,7],crai:[5,7,13,18,202],crash:[3,12,382,508],craympi:386,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:215,create_faceset:215,create_group:204,create_nodeset:215,createatom:[],creation:[],crimson:206,critchlei:298,criteria:[3,128,179,205,206,227,228,229,264,379,446,474,489,492,514],criterion:[12,42,133,178,181,216,226,229,245,283,305,319,347,352,379,381,401,412,416,457,492,501,502],criterioni:501,critic:[6,49,50,267,336,341,379],crmax:76,crmin:76,cross:[3,12,22,76,98,156,176,186,202,203,205,217,222,228,232,266,268,290,313,322,326,328,337,344,356,374,381,397,406,409,410,417,418,419,424,426,428,447,452,454,456,470,472,479,487,491,497,517],crossov:1,crossterm:487,crozier:[0,7,13],crucial:303,crystal:[3,4,6,13,78,118,294,295,339,374,382,487,491,505,508],crystallin:[6,114,295,374,471,508],crystallis:336,crystallogr:[130,177],crystallograph:[374,505],crystallographi:[130,177,374],cs1:177,cs_chunk:6,cs_im:[41,487],cs_re:[41,487],csanyi:[152,448,458],cscl:436,csequ:6,csh:[11,12,399],cshrc:[11,12],csic:[411,468,470,472,475],csinfo:6,csisi:[411,468,470,472,475],csld:[],cst:410,cstherm:6,cstyle:484,csvr:[],ctcm:[387,410],ctemp_cor:236,cterm:318,ctr:9,ctype:11,cu1:177,cu2:177,cu3au:436,cube:[6,42,176,181,226,236,350,374,508],cubic:[],cuda:[],cuda_arch:[9,15],cuda_get:15,cuda_hom:[9,15],cuda_prec:[9,15],cufft:14,cuh:392,cummul:[3,6,224,227,228,229,231,242,247,253,255,329,332,333,334,335,337,344,418,505],cumul:[6,216,218,221,222,223,237,245,253,267,269,274,283,313,314,381],curli:2,current:[0,1,3,5,6,7,8,9,10,11,12,13,15,16,17,18,41,42,43,58,62,64,66,76,78,88,96,113,114,120,128,129,142,153,158,166,168,174,176,179,182,201,202,203,204,205,206,207,210,211,215,218,222,223,224,226,227,228,229,230,231,232,233,237,238,243,245,247,250,251,253,259,266,269,270,275,276,277,283,288,289,290,292,298,299,304,305,307,310,311,312,313,316,317,318,319,320,321,322,323,325,327,328,329,332,333,334,340,341,344,345,346,347,348,349,351,352,354,369,370,371,372,375,376,378,379,380,381,386,392,399,401,405,410,412,413,416,419,420,423,433,434,436,437,438,441,447,449,450,453,454,455,456,459,470,472,473,476,482,483,484,485,487,488,489,490,491,493,494,495,497,499,501,502,504,505,509,514,515,516,517,518,519],curv:[6,178,245,295],curvatur:[415,451,479],custom:[],cut0:485,cut1:496,cut2:496,cut:[],cuthi:[294,306],cutinn:[394,433,434],cutlo:[294,306],cutmax:447,cutoff1:[398,405,424,428,432,435,444,452],cutoff2:[393,395,396,398,404,405,424,428,432,435,444,452,473],cutoff:[3,6,8,10,16,18,40,46,47,55,56,64,75,77,78,82,96,101,118,120,127,128,152,176,179,181,182,228,229,234,241,294,303,304,306,308,310,313,317,329,342,346,350,352,369,371,372,379,382,383,384,386,387,388,389,390,391,392,393,394,395,396,397,398,400,402,403,404,405,406,407,408,409,410,411,412,413,414,415,417,418,419,420,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,449,450,451,452,457,458,459,460,461,462,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,485,489,492,496,508,514],cutoffa:411,cutoffc:411,cuu3:410,cval:177,cvd:336,cvel:318,cvff:[],cwiggl:[3,266,346,349,351,514],cyan:[2,205,206],cycl:[3,245,267,269,270,274],cyclic:[3,198],cygwin:12,cylind:[3,4,76,205,218,251,299,347,350,490],cylindr:[6,251,326,347],cypress:386,cyrot:392,cyrstal:295,d3q15:256,d3q19:256,d_double_doubl:15,d_e:341,d_flag2:302,d_flag:302,d_name:[125,202,302,331,497],d_single_doubl:15,d_single_singl:15,d_sx:302,d_sy:302,d_sz:302,daan:339,dai:12,daili:12,daivi:290,damag:[],dammak:308,damp:[3,6,209,214,253,254,255,260,269,270,274,300,303,304,308,313,332,333,345,347,348,378,379,381,393,395,397,402,405,412,416,424,432,444,452,467,473,501,508],damp_com:254,damp_drud:254,dampen:[313,508],dampflag:[347,416],dan:17,danger:[3,12,245,352,406,505],dangl:181,daniel:9,darden:[372,405],darkblu:206,darkcyan:206,darken:205,darkgoldenrod:206,darkgrai:206,darkgreen:206,darkkhaki:206,darkmagenta:206,darkolivegreen:206,darkorang:206,darkorchid:206,darkr:206,darksalmon:206,darkseagreen:206,darkslateblu:206,darkslategrai:206,darkturquois:206,darkviolet:206,dasgupta:304,dash:[416,504],dat:[6,100,198,215,483],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,314],dataset:314,datatyp:3,date:[0,4,6,12,13,201,449,450,514],datom1:127,datom2:127,datom3:127,datom4:127,datum:[3,6,43,69,72,74,85,103,120,127,202,219],davenport:435,davi:346,david:[9,19,371,372,470,472],daw:[410,447],dbg:14,dcd:[3,6,7,202,204,205,206,207,296,488,492],ddim:201,deactiv:432,dealt:252,debug:[6,7,11,12,13,14,17,58,130,134,177,178,296,301,369,371,386,420,441,476,485,486,494,497,504,514],deby:[],decai:[101,402,479],decid:[3,6,12,16,76,266,302,313,342,502,509],decipher:374,deck:302,declar:204,declin:329,decod:205,decompos:[96,458],decomposit:[3,5,7,18,65,215,296,317],decoupl:[6,508],decreas:[3,202,203,212,213,220,229,232,238,243,245,253,340,371],decrement:318,deepli:368,deeppink:206,deepskyblu:206,def:[12,13,485],defaul:64,defect:[6,75,176,439],defgrad:[],defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,52,54,55,56,57,58,59,60,61,62,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,184,185,186,187,188,189,190,192,193,195,196,197,198,199,200,201,202,203,204,205,206,209,210,211,212,213,214,215,216,217,218,219,221,222,223,224,225,226,227,228,229,230,232,233,236,237,238,240,243,244,245,248,251,252,253,254,255,256,264,266,268,269,270,271,272,273,274,275,276,277,279,280,281,284,286,287,288,289,290,291,292,294,295,296,298,299,300,302,304,306,311,313,314,315,316,319,323,327,329,331,332,333,334,335,337,338,339,341,343,344,346,347,348,349,350,351,352,354,355,356,357,358,359,360,361,364,365,366,367,369,371,372,374,376,378,379,380,381,382,383,384,385,386,388,389,390,391,393,394,395,396,397,398,399,400,402,403,405,406,407,408,409,411,412,414,415,416,417,418,419,420,422,424,425,426,427,428,429,430,431,432,433,434,435,439,440,441,442,443,444,446,447,449,450,451,452,453,454,455,456,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,484,485,487,488,490,491,492,493,496,497,498,499,501,502,504,505,508,510,511,512,513,514,515,516],definit:[2,3,6,8,12,13,83,86,128,152,206,218,219,220,221,222,223,224,232,240,251,274,314,331,343,346,349,351,353,365,369,380,389,392,400,407,408,412,422,447,454,456,458,474,485,487,489,496,498,513,514],defint:505,deform:[],deg2theta:177,deg:508,degener:[3,298],degrad:[8,18,295,372,496],degre:[3,6,8,20,21,24,28,29,32,35,36,38,69,85,101,103,105,107,108,110,112,113,118,124,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,177,178,184,185,188,189,196,198,201,205,218,229,236,245,247,248,253,254,259,269,270,274,275,276,277,288,289,290,292,296,298,312,313,316,332,333,334,339,355,357,361,364,366,379,405,410,418,497,505,508,515],degress:[158,218],del:501,delai:[3,6,12,382,409,505],deleg:419,delet:[2,3,7,8,12,55,60,63,66,176,181,182,209,218,219,221,222,223,224,227,229,242,245,269,314,332,333,352,354,370,380,382,385,441,466,487,488,489,490,498,499,504,509,510,512,514,515],delete_atom:[],delete_bond:[],delete_el:215,deli:201,delimit:[485,514],deloc:[270,412,457],delr:436,delt_lo:501,delta:[],delta_1:392,delta_3:392,delta_7:392,delta_conf:3,delta_ij:[436,447],delta_pi:392,delta_r:447,delta_sigma:392,delx:201,delz:201,demand:308,demo:11,demon:293,demonstr:[303,436],den:299,dendrim:418,denniston:[9,256,258,259,260,295],denomin:[7,183],denot:[130,236,254,295,306,308,402,417,419,450,454,456],dens:[76,229,412],densiti:[3,6,7,9,18,41,42,62,111,128,138,152,164,176,178,210,211,215,218,222,223,226,232,243,256,259,262,263,295,299,300,302,304,341,346,374,376,380,387,388,392,410,436,437,438,447,451,457,461,463,464,465,487,496,497,505,513],density_continu:456,density_summ:456,depart:[0,7],departur:[267,303],deped:8,depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,41,42,44,45,46,47,48,49,50,52,54,55,57,64,66,69,72,74,75,76,85,101,103,114,120,121,124,125,126,127,131,152,154,155,161,165,166,172,178,179,184,185,186,187,188,189,190,192,193,195,196,197,198,201,202,203,205,206,209,210,211,212,213,216,218,220,221,222,224,225,226,228,230,232,238,239,244,247,248,249,251,253,254,256,258,259,266,269,271,272,273,274,275,276,277,278,279,286,288,289,290,292,294,305,308,310,313,315,316,317,323,329,332,333,334,336,338,340,341,343,345,346,349,350,351,352,354,355,356,357,358,360,361,364,366,372,374,379,380,382,383,384,386,387,388,390,391,392,393,394,395,396,397,398,399,400,401,402,403,405,406,410,411,412,413,414,415,416,417,418,419,424,425,426,427,428,429,430,431,432,433,436,437,439,440,442,443,444,446,447,449,450,451,452,457,458,459,467,468,469,470,471,472,473,475,477,478,479,482,484,487,489,490,493,497,499,501,504,505,507,514,515],dependend:6,depflag:12,dephas:[482,501],depos:233,deposit:[],deprec:[3,304,449],depth:[52,156,205,341,415,451],dequidt:9,der:[96,119,400,401,432,449,450,478,508],deriv:[6,7,8,9,38,57,66,96,152,172,198,219,230,232,245,253,266,269,271,272,273,274,275,276,277,294,300,304,308,338,339,341,346,347,350,378,380,388,392,400,405,412,413,417,426,430,431,436,439,449,450,467,469,478,508],derjagin:478,derlet:294,descend:206,descent:[7,378],descib:[41,205,304],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,40,41,42,43,57,65,66,72,75,76,78,97,122,125,128,130,142,152,153,156,157,158,162,163,166,169,171,172,176,177,178,180,181,190,195,198,202,203,204,209,210,211,218,219,220,221,222,223,224,226,229,230,231,232,233,235,236,241,246,247,250,251,252,253,254,255,256,258,259,260,264,268,269,270,274,282,291,294,296,301,302,303,304,305,306,313,318,326,329,330,331,332,333,334,335,336,337,338,339,344,346,347,349,354,371,372,374,377,378,379,380,381,385,388,389,391,393,394,395,397,398,399,400,401,402,405,410,412,413,415,416,417,419,422,424,425,426,427,428,429,430,431,432,433,434,435,436,439,440,446,447,448,449,450,451,452,457,458,459,466,467,468,469,470,471,472,473,475,477,478,479,480,482,484,485,487,488,489,490,491,497,500,501,504,509,514,515,517],descript:[],descriptor:[152,202,420],deserno:372,design:[0,3,6,7,8,11,13,14,15,17,130,160,163,177,215,229,235,236,269,270,294,295,314,336,341,389,390,391,394,397,402,404,412,432,433,434,437,438,447,450,469],desir:[2,3,6,7,9,11,12,14,15,16,33,41,51,62,76,97,100,124,129,153,160,178,191,201,218,224,230,232,243,245,246,253,254,255,259,269,290,298,299,300,301,304,308,313,316,329,332,333,334,335,340,347,362,368,371,372,374,377,379,380,381,406,410,418,433,434,468,470,472,483,484,485,487,491,496,501,502,504,505,514,515,517],desk:7,desktop:[4,6,7,10,12,205],despit:508,destabil:392,destre:364,destroi:[9,11,40,227,228],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,22,37,41,42,43,56,66,70,71,72,76,80,83,87,99,100,104,113,115,117,119,121,123,124,126,129,131,152,153,155,156,157,158,161,171,172,173,175,178,179,182,183,186,197,201,202,203,205,206,209,210,211,215,218,219,220,221,222,224,226,228,229,230,231,232,233,243,245,246,247,248,250,251,253,255,256,260,266,267,268,269,270,271,272,273,274,275,276,277,281,283,288,289,290,291,292,295,298,299,300,302,303,305,306,307,313,316,317,329,332,333,334,335,336,337,339,340,341,342,343,344,345,352,354,356,365,371,372,375,379,380,382,383,386,387,388,389,391,392,394,396,397,398,399,400,401,402,405,406,412,413,415,416,417,418,419,424,425,426,427,428,429,430,431,432,433,434,435,436,440,441,446,449,450,451,457,458,459,467,474,477,478,480,485,487,488,489,490,492,493,496,497,499,502,505,506,509,514,515,519],detect:[2,3,12,43,64,66,95,101,244,299,340,381,401,418,423,482,484,487,498,501,514],determ:386,determin:[1,3,6,8,9,12,15,40,41,43,52,60,61,62,64,65,72,76,96,113,119,121,124,130,131,139,153,166,167,176,177,178,201,202,203,205,206,207,208,212,213,214,217,218,219,220,221,222,223,224,225,226,230,232,233,236,238,245,248,249,251,253,254,259,264,266,267,269,275,276,277,288,289,290,292,294,296,299,300,303,310,311,312,313,314,315,319,321,323,329,332,333,334,336,342,343,346,347,348,349,350,351,352,365,371,372,374,380,382,383,386,388,389,396,401,405,409,410,414,416,419,420,428,436,439,441,450,451,457,466,469,473,478,484,487,488,490,492,494,497,501,503,504,506,513,514,515],determinist:317,detil:120,devan:[9,452],devanathan:472,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,43,250,274,298,303,304,307,388,392,412,438,439,457,475,489],devemi:9,deviat:[267,274,294,414],deviator:9,devic:[1,3,12,15,17,250,386],device_typ:386,devin:[305,401],devis:438,dfactor:205,dff:508,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_singl:[3,12,372],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,307,439],dhi:[62,201,232,299],dhug:[267,303],dhugoniot:[267,303],dia:436,diagnost:[],diagon:[3,6,92,152,153,154,230,269,300,313,344,454,456],diagonalstyl:458,diagram:[42,130,177,197,226,296],diallo:418,diam:[205,206,299,380],diamet:[3,6,41,43,125,178,202,203,205,206,210,211,253,299,302,313,329,331,345,347,380,400,415,416,426,451,474,478,487,488,497],diamond:[374,412,436],diamter:[41,299],dick:6,dicsuss:266,dictat:[216,267],did:[3,12,379,406,409,410,416,441,470,472,495],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,174,343,371],differ:[1,2,3,4,6,7,8,9,11,12,14,15,16,17,18,22,37,38,40,42,43,55,56,57,64,67,72,75,76,96,101,105,107,108,132,152,154,155,156,157,158,159,161,164,165,166,167,168,170,171,172,178,179,181,186,197,198,201,202,205,206,209,211,214,216,218,221,226,227,228,229,230,231,232,236,241,244,245,246,247,248,249,250,253,254,256,266,269,270,271,272,273,275,276,277,279,281,284,286,287,288,289,292,294,296,298,300,303,304,305,308,311,313,316,318,326,327,329,332,333,334,337,338,339,341,344,345,346,347,350,354,355,365,368,370,371,372,374,375,377,378,380,381,383,384,385,386,387,388,392,396,397,399,400,401,406,407,408,410,412,415,416,417,419,422,424,425,427,428,435,436,437,438,440,441,443,447,449,450,451,452,453,454,456,457,458,459,467,468,469,470,472,474,475,478,481,482,484,485,487,489,490,491,492,495,496,497,499,501,502,504,505,506,508,513,514,515,517],differenti:[1,3,6,29,198,371,402,447,471],difficult:[230,296,386,418,496],difficulti:[101,118,316,449],diffract:[],diffus:[],digit:[2,3,206,354,439,514],dih_table1:198,dih_table2:198,dihedr:[],dihedral_coeff:[],dihedral_cosineshift:27,dihedral_styl:[],dihedralcoeff:[3,199],dihedraltyp:228,dihydrid:412,dij:316,dilat:[],dim1:3,dim2:3,dim:[3,62,76,155,159,160,161,164,165,166,167,168,170,178,201,222,232,251,347,374,436,490,513,514,515],dimdim:514,dimems:295,dimens:[],dimensinon:76,dimension:[3,40,101,124,130,152,155,158,159,160,161,164,165,166,167,168,170,177,200,218,222,268,295,341,374,377,381,447,487,497],dimensionless:[116,133,134,136,139,141,143,148,152,341,372,458,478],diment:3,dimentionless:147,dimer:[6,313,436],dimgrai:206,dimstr:[42,226],dinola:[300,332],dintel_offload_noaffin:16,dipol:[],dipolar:[4,29,41,202,203,331,508],dir1:498,dir2:498,dir:[1,3,4,8,10,11,12,267,294,303,328,447,449,450,485,498,514],dirac:152,direc:447,direct:[],directli:[3,6,8,9,11,12,96,125,152,154,202,203,204,205,212,238,247,251,256,295,314,333,345,347,348,349,350,374,378,386,387,388,393,395,396,402,405,410,412,424,428,441,444,452,466,485,497,498,499,505,514],directoi:14,directori:[],disabl:[3,12,16,341,423,485,500,514],disadvantag:[6,226],disallow:[202,232,269],disappear:489,discard:[2,3,42,76,220,222,226,342,350,484,489,490],discontinu:[198,379,430],discourag:436,discov:[13,342],discret:[6,8,41,43,205,206,253,256],discuss:[],disk:[6,93,94,101,171,200,233,245,299,485],disloc:[75,439],disord:[40,75,439],disp:[],dispar:451,disperion:[405,428],dispers:[3,6,7,9,176,295,371,372,396,405,428,433,441,450,469,475],displac:[],displace_atom:[],displace_box:62,displacemet:490,displai:[11,13,22,37,45,56,186,197,202,205,356,365,399,467],dispters:3,disregard:439,dissip:[6,9,41,89,90,240,246,253,295,317,338,339,394,406,407,408,416,433,434,467],dissolut:227,dist:[6,74,100,120,129,202,296,312,409,466,482,515],distanc:[],distinct:[6,236,310,371,451],distinguish:[6,95,152,259,412,486,514],distort:[176,387],distrbut:387,distribut:[],distro:[123,399,446,447],ditto:[8,12,14,15,16,17,18,43,127,228,479,485],div:8,divd:129,diverg:[3,12,40,313,339,388,489,508,517],divid:[3,6,16,42,100,124,129,138,140,153,175,176,186,197,206,218,219,221,226,232,294,337,344,349,371,379,381,413,450,457,475,496,504,514],divis:[6,256,392,422,432,484,505,514],dl_poli:[6,7],dlambda:172,dlammps_async_imd:250,dlammps_bigbig:[12,40],dlammps_ffmpeg:[3,12,205],dlammps_gzip:[3,12,202,205,340,487,488,492],dlammps_jpeg:[3,12,205],dlammps_longlong_to_long:12,dlammps_memalign:[9,12,16],dlammps_png:[3,12,205],dlammps_smallbig:12,dlammps_smallsmal:12,dlammps_xdr:[12,202],dlen:497,dlmp_intel_offload:[9,16],dlo:[62,201,232,299],dlopen:6,dlvo:[7,400,478],dm_lb:256,dmax:[329,377],dmpvtk:203,dmpvtp:203,dna:7,doc:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,22,37,41,43,56,60,62,66,70,72,80,87,96,99,104,113,115,116,117,119,121,123,124,126,129,131,153,156,157,158,171,173,175,178,179,180,186,197,201,202,203,204,205,206,207,209,210,211,216,217,218,219,220,221,222,223,224,233,245,253,254,264,269,270,275,276,277,281,288,289,290,291,292,299,302,313,326,329,332,333,334,343,347,350,352,354,356,365,370,379,380,381,386,387,388,391,399,401,402,410,411,413,418,419,421,422,436,437,438,441,443,446,447,448,458,467,468,470,472,474,475,485,487,488,489,490,492,495,496,497,504,505,509,514,515,517,518],docuement:451,dodd:43,dodgerblu:206,doe:[0,1,2,3,5,6,7,8,9,11,12,14,15,16,17,18,33,38,40,42,43,51,55,57,62,65,66,71,75,76,77,96,97,100,115,119,122,128,129,130,154,156,158,160,161,166,168,172,177,178,179,180,182,184,186,191,197,198,201,202,203,204,205,206,209,215,216,218,222,225,226,228,229,230,232,236,238,241,242,245,246,249,251,253,254,256,259,265,269,270,271,272,273,275,276,277,288,289,290,291,292,300,301,302,306,308,311,313,329,332,334,336,337,341,344,345,346,349,350,351,352,357,358,359,361,362,364,370,371,372,373,374,380,381,382,387,388,389,390,391,392,394,396,397,398,400,401,402,403,405,406,409,410,411,412,414,415,416,417,419,420,421,422,423,426,427,429,430,431,433,434,436,437,438,439,441,447,448,449,450,451,453,454,455,456,457,458,459,460,461,462,463,464,465,466,468,469,470,471,472,473,474,475,477,478,479,480,482,483,484,485,487,488,489,490,491,494,495,497,498,499,500,501,504,505,508,509,514,519],doegenomestolif:7,doesn:[3,7,8,12,178,202,203,216,222,223,326,380,382,386,388,401,411,421,449,450,468,470,471,472,475,487,489],dof:[3,8,124,156,157,158,171,218,313,515],dof_per_atom:[158,218],dof_per_chunk:[158,218],doff:[380,487],dog:[],doi:[6,231],domain:[3,6,7,12,13,18,40,42,43,61,64,65,76,130,167,177,180,201,204,205,206,209,216,226,230,232,233,249,252,256,269,270,296,3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505,514],elt:436,emac:[],email:[0,3,5,7,8,9,11,413],emb:[3,9,350],emb_lin_neg:436,embed:[3,4,5,7,9,11,12,13,29,97,154,176,341,387,410,413,432,436,437,438,447,467,476,485],embt:185,emi:[7,9],emil:9,emol:[449,450,505],emphas:416,empir:[9,215,333,388,412],emploi:[295,304,308,471],empti:[3,60,76,176,180,313,371,382,423,487,498,499,514],enabl:[3,6,8,9,11,12,13,14,15,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,33,35,37,38,40,41,44,46,47,48,49,50,51,52,54,55,56,57,63,64,65,67,71,83,86,92,96,97,107,108,109,110,111,112,116,119,121,123,124,130,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,154,155,156,157,160,162,164,165,169,170,172,176,177,184,185,187,188,189,190,191,192,193,195,196,197,198,202,203,204,206,207,209,210,211,212,213,214,216,220,223,225,227,228,229,231,232,233,238,239,242,243,244,245,246,247,248,250,251,252,253,254,255,256,257,258,259,260,262,263,265,267,269,270,271,272,273,274,275,276,277,278,279,280,281,282,284,286,287,288,289,290,291,292,294,295,296,298,299,303,304,305,306,307,308,309,310,312,313,315,316,318,319,320,321,322,323,325,326,328,329,332,334,335,336,337,338,339,341,342,344,345,346,347,348,349,350,353,355,357,358,360,361,362,364,365,366,372,379,381,385,386,387,388,390,391,392,393,394,395,396,397,398,400,401,402,403,404,405,406,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,436,437,438,439,441,442,443,444,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,477,478,479,485,488,489,490,494,496,506,514,519],enclos:[2,6,12,180,202,301,354,436,457,483,485,495,514],encod:[13,40,43,202,205,206,302,419],encompass:[3,6,41,43,60,62,128,179,325,343,467,490],encount:[3,8,12,62,118,221,385,492,514],encourag:[7,8,307,327],end12i:125,end12x:125,end12z:125,end1i:125,end1x:125,end1z:125,end2i:125,end2x:125,end2z:125,end:[1,2,3,5,6,8,11,12,15,16,17,18,19,38,41,42,43,58,60,62,76,125,181,182,185,201,202,203,205,206,207,210,211,219,221,223,224,229,232,246,251,253,255,268,269,270,283,300,312,313,318,329,332,333,334,335,337,340,341,344,348,351,352,370,371,380,381,385,386,406,410,415,422,435,439,451,454,456,458,459,476,482,485,487,488,489,490,492,494,495,499,503,505,508,514,519],end_of_step:8,endbondtors:[3,185,191,487],endif:8,energet:[229,388,450],energi:[],energy_compon:457,energy_update_freq:450,enforc:[6,9,60,61,115,201,202,203,204,205,207,209,216,229,232,269,293,295,305,313,316,354,371,424,484,514,515],enforce2d:[],eng:[11,69,74,120,202,243,352,354,401,438],eng_previ:354,engil:9,engilitycorp:9,engin:[215,232,298,318,338,410,437],enhanc:[211,215,482],enlarg:[62,205],enough:[3,41,64,95,178,179,181,182,226,254,299,303,308,313,342,346,347,350,382,386,402,445,487,491,492],enpub:410,ensembl:[],ensight:6,ensur:[3,6,152,202,203,216,220,230,245,246,269,319,340,372,392,409,432,468,475],enter:[60,168,413,439,475,501],enthalpi:[135,271,272,273,410,504,505,514],entir:[0,2,3,6,11,14,15,42,43,66,89,90,97,121,122,124,128,130,153,158,177,178,206,209,210,211,218,222,223,226,229,231,242,245,246,249,253,254,265,269,271,272,273,274,275,276,277,294,296,298,311,313,327,341,343,354,386,405,428,441,469,487,495,496],entireti:474,entiti:[6,8,41,43,202,313],entri:[3,8,12,38,43,57,69,74,85,103,120,127,130,139,142,143,144,145,146,148,149,150,176,198,203,206,210,221,222,223,231,241,303,352,380,392,411,436,443,450,458,468,469,470,471,472,475,514],entropi:501,entry1:[38,57,206,399,469],entry2:206,entryn:206,enumer:[179,202,480],enumuer:6,env:386,environ:[1,3,6,11,12,16,17,18,205,247,252,294,386,387,392,399,401,411,412,447,470,484,498,514],epair:[119,206,414,418,449,450,505],epen:[449,450],epfl:[247,252],epp:405,epq:405,eps0:478,eps14:432,epsilon0:472,epsilon:[3,6,36,46,47,51,54,55,96,184,210,211,245,313,329,346,350,377,379,391,397,398,400,402,403,404,405,415,417,418,419,422,423,424,425,426,427,428,429,430,431,432,435,440,444,451,452,462,468,473,474,477,478,496,508,513],epsilon_0:479,epsilon_14:397,epsilon_:451,epsilon_d:403,epsilon_i:[415,441,451],epsilon_i_:451,epsilon_i_a:[415,451],epsilon_i_b:[415,451],epsilon_i_c:[415,451],epsilon_ij:441,epsilon_j:[415,441,451],epsilon_j_:451,epsilon_j_a:[415,451],epsilon_j_b:[415,451],epsilon_j_c:[415,451],epsilon_lj:451,epton:446,eqch:173,eqeq:[449,450],eqp:405,eqq:405,equal:[2,3,6,8,11,12,17,40,42,55,66,69,72,74,76,81,85,95,96,100,103,120,122,127,129,131,153,156,172,174,176,178,201,205,206,209,210,211,212,213,216,219,220,221,224,225,226,230,232,233,238,245,246,248,249,251,253,254,256,259,260,266,267,274,285,294,296,299,301,303,304,305,308,310,312,313,315,318,323,325,332,333,334,337,338,339,341,343,344,346,349,351,352,354,370,374,379,381,382,383,385,386,401,406,408,414,415,418,422,433,439,440,447,449,450,451,453,454,455,457,458,459,469,474,475,479,483,484,485,487,489,490,494,495,498,501,503,505,514,515],equat:[3,6,7,8,9,100,118,124,130,177,186,197,209,230,236,237,240,241,247,253,254,256,259,267,268,269,270,274,290,294,296,303,304,308,316,317,329,337,341,344,346,347,349,351,364,371,372,400,405,406,408,412,413,416,421,433,434,436,441,451,454,456,461,462,464,465,479,508],equi:270,equidist:268,equil:[3,304,375,494,519],equilater:497,equilibr:[3,4,5,6,7,9,62,100,178,209,216,219,229,230,245,267,269,270,290,291,300,303,304,305,306,337,338,339,344,401,402,449,450,483,497],equilibria:344,equilibribum:[227,228],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,39,44,48,49,50,52,54,57,59,62,161,162,185,187,230,232,245,246,247,254,256,269,274,290,303,304,308,312,316,318,326,329,336,337,339,344,355,357,361,364,401,436,443,457,508],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:215,equival:[6,12,13,29,62,64,136,137,145,150,176,180,206,221,224,230,232,245,253,269,290,300,312,313,349,388,406,412,457,470,472,473,487,490,495,496,505,508],equlibrium:6,equliibr:[304,306],er3:177,eradiu:[41,125,203,412,487],eras:[315,338],erat:[232,434],erc:402,erfc:[402,424,441],erforc:[125,203],erg:513,erhart:[216,410,470,472],ermscal:389,ernst:9,eror:3,eros:436,erose_form:436,erot:[],errata:[470,472],erratum:346,erron:3,error:[],erta:416,ervel:[125,203,487],escap:[233,508],especi:[8,16,166,178,209,216,226,245,303,308,311,312,386,484],espresso:[9,307],essenti:[8,11,12,27,97,140,159,160,161,164,165,166,167,168,170,187,219,274,295,345,372,388,402,424,472,492,505],essex:29,establish:[96,249],estim:[1,3,6,10,12,38,42,57,100,153,215,226,237,267,329,336,371,372,377,441,450,469,501,505],esu:513,esub:436,eta:[6,256,269,303,304,306,345,411,413,415,447,471,475,513],eta_dot:269,eta_ij:447,eta_ji:413,etag:[41,487],etail:505,etap:269,etap_dot:269,etc:[1,2,3,4,6,7,8,9,10,11,12,13,15,16,40,41,43,55,64,72,98,99,100,105,121,122,125,127,153,155,158,159,160,161,162,164,165,166,167,168,170,172,178,180,181,182,191,202,203,205,206,209,210,215,216,217,218,221,222,223,224,227,228,232,233,243,245,246,253,269,299,310,314,341,342,350,354,370,371,379,380,381,382,384,410,411,419,432,434,439,445,449,450,468,470,472,475,482,485,487,488,489,494,496,497,501,502,503,504,505,506,508,513,514,517,519],ethernet:18,etol:[379,381,482,501],etot0:303,etot:[6,105,107,108,122,153,164,206,236,254,267,303,504,505],eu2:177,eu3:177,euler:[379,381],eulerian:215,euqat:460,europhi:256,ev_tal:8,evalu:[2,3,9,11,12,38,57,76,96,97,100,119,129,131,152,154,158,168,176,178,201,202,203,205,206,210,211,212,213,215,217,218,219,220,221,222,223,224,225,232,238,246,248,249,251,252,253,254,295,301,304,315,319,323,332,333,334,343,346,349,351,352,354,371,372,377,379,386,439,441,447,453,455,457,469,482,483,485,489,490,492,494,495,496,497,501,503,505,514,515],evalut:[354,485],evan:[166,290],evanseck:[6,20,184,397,499],evapor:[],evaul:[8,379],evdwl:[119,154,449,450,505],even:[3,6,8,12,15,17,18,34,40,42,53,58,60,62,64,66,75,76,97,119,131,176,179,180,194,198,202,203,206,209,210,211,216,217,218,221,222,223,224,226,227,228,230,232,233,236,251,254,267,269,270,295,299,308,310,313,314,325,329,337,341,344,346,350,352,363,371,377,379,381,386,391,412,413,416,419,422,441,451,475,476,480,487,488,490,492,493,494,496,497,499,502,504,505,506,508,519],evenli:[3,42,58,153,198,226,256,422,476],event:[],eventu:[3,6,12,15,180,304,501],ever:[9,55,57,252,329],evera:[400,415,451,467],everi:[0,1,2,3,6,8,9,11,12,15,16,40,42,76,77,100,125,131,140,166,181,202,203,204,205,206,207,209,210,211,212,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,232,233,237,242,243,245,247,249,250,251,256,257,265,269,270,274,293,294,295,299,300,301,302,303,304,305,306,308,310,311,313,314,316,318,329,331,332,333,334,335,336,337,340,341,342,343,344,352,354,370,372,381,382,383,386,406,409,419,432,449,450,457,463,481,482,483,487,489,491,492,494,495,496,501,502,503,505,509,514,519],everyth:[8,119,509],everywher:[128,426],eviri:412,evolut:[247,256,296,482],evolv:[256,296,342],ewald:[2,3,5,6,7,8,9,12,97,122,130,153,342,371,372,379,393,395,396,402,405,412,424,428,444,452,467,469,473],ewald_disp:405,ewalddisp:3,exact:[22,42,45,76,134,172,181,186,226,229,246,247,253,254,255,299,308,309,329,341,356,371,399,489,494,501,514,517,519],exactli:[3,6,12,14,17,38,42,43,57,62,76,77,100,128,156,162,169,178,198,210,211,221,226,232,237,241,246,253,254,255,270,282,283,291,295,302,303,329,334,335,348,386,399,406,410,416,419,433,441,469,489,490,497,501,514],exager:508,examin:[6,8,17,229,295],examp:[485,514],exampl:[],exce:[3,6,16,17,18,42,61,76,180,217,218,221,222,223,224,226,230,232,237,242,269,295,310,314,320,321,329,379,386,487,514],exceed:[3,42,62,226,232,269,329,495],excel:412,except:[1,2,5,6,8,10,11,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,41,42,44,45,46,47,48,49,50,52,54,55,56,57,62,63,66,76,98,99,120,121,124,129,153,155,156,157,158,159,160,161,162,164,165,166,167,168,169,170,171,178,182,184,185,186,187,188,189,190,192,193,195,196,197,198,201,202,203,206,209,212,218,219,221,225,226,230,232,239,244,245,248,251,253,255,269,270,271,272,273,274,275,276,277,278,279,282,283,286,288,289,290,291,292,296,305,306,313,315,316,326,329,332,334,335,341,345,349,352,353,354,355,356,357,358,360,361,364,365,366,371,372,374,376,380,381,382,384,385,386,387,388,390,393,394,395,396,397,398,399,400,401,402,404,405,406,410,411,412,413,414,415,416,417,418,419,424,425,426,427,428,429,430,431,432,433,434,437,442,443,444,446,449,450,451,452,459,467,468,469,470,471,472,473,475,477,478,479,482,484,485,487,489,490,492,495,496,497,498,499,501,505,508,513,514,515,518],excess:[220,412],exchang:[2,3,6,8,64,65,209,215,216,245,253,305,313,337,341,344,371,386,412,502],exchange:371,excit:412,exclud:[3,6,9,12,16,17,66,76,113,124,152,158,165,166,182,202,218,222,227,228,257,265,298,311,313,336,347,352,379,380,382,394,416,419,422,433,434,441,466,499],exclus:[1,3,12,16,96,386,401,439,441,496,506],excurs:[269,482],exectubl:12,execut:[1,2,3,4,6,8,9,11,12,17,63,179,205,250,307,354,370,373,385,483,485,495,498,501,514],exempl:457,exemplari:246,exemplifi:412,exert:[6,251,254,308,348,349,350,372],exhaust:[215,385,514],exhibit:[101,269,378,412,496],exist:[3,6,7,8,11,12,13,16,37,56,58,62,72,75,134,178,179,197,204,205,206,209,214,225,228,230,233,245,298,299,301,302,352,353,355,357,358,359,361,365,375,380,386,407,408,419,449,466,476,483,485,487,488,489,498,499,500,509,514,515,517],exit:[2,3,11,12,42,60,202,226,241,370,385,485,486,495,504,514],exlanatori:3,exp:[],expand:[],expans:[12,152,202,498,514],expect:[1,3,8,12,13,14,15,16,17,18,19,42,43,76,113,159,170,176,198,226,238,245,247,266,294,300,302,303,308,313,352,372,382,399,436,439,441,482,485,487,489,492,496,501,514],expens:[6,76,206,294,298,313,341,352,371,372,382,386,485],experi:[6,13,15,17,225,233,250,259,268,300,312,313,377,381,406,441,496,501],experienc:[6,12,258,259],experiment:[245,371,386,501],expert:12,expertis:7,explain:[1,3,6,8,9,11,12,16,18,42,62,66,69,72,74,76,77,78,81,82,85,95,103,158,166,198,202,203,205,206,209,218,219,224,226,228,230,232,269,294,302,313,326,352,354,370,371,374,380,381,385,391,410,422,457,459,474,485,488,489,492,494,497,508,509,514,519],explan:[3,6,62,125,152,202,203,218,268,294,419,481,484,485,487,496],explanatori:[3,8,129,202,203,217,218,221,222,223,313,380,484,514],explantori:[3,309],explic:440,explicit:[6,9,11,22,45,82,96,125,128,172,186,210,211,232,320,321,356,376,388,389,392,397,399,410,412,423,433,473,481,484,488,491,509],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,44,46,47,48,49,50,52,54,55,57,76,121,124,155,165,168,176,178,184,185,187,188,189,190,192,193,195,196,198,202,203,206,212,222,225,232,239,244,246,248,253,269,271,272,273,274,275,276,277,278,279,286,288,289,290,292,302,303,305,313,315,316,332,334,335,341,345,349,355,357,358,360,361,364,366,380,386,387,388,390,393,394,395,396,397,398,399,400,401,402,403,405,406,409,410,411,413,414,415,416,417,418,419,423,424,425,426,427,428,429,430,431,432,433,437,439,441,442,443,444,446,451,452,459,460,461,462,463,464,465,467,468,469,470,471,472,473,475,477,478,479,487,489,490,496,497,499,500,506,508,509],explictli:[16,500],exploit:[15,17,296],explor:[130,177],expon:[3,304,306,410,415,418,432,440,452],exponenti:[96,447,468,475,479,501,514],expos:11,exposit:[215,406,409],express:[6,152,164,178,210,211,230,266,294,304,341,347,354,392,410,412,426,436,457,458,467,514],expressiont:392,extend:[],extens:[3,6,9,17,45,46,47,54,56,66,68,73,84,91,92,93,96,97,100,102,105,108,109,119,121,129,131,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,203,209,212,213,216,224,225,231,234,238,243,244,245,247,248,249,251,253,255,267,269,274,283,294,295,311,312,313,315,318,323,326,328,332,333,334,335,336,338,339,341,343,346,350,351,415,436,439,450,451,458,504,505,513],extent:[1,3,42,43,46,60,76,176,180,202,214,222,226,251,348,351,371,374,388,453,455,469,484,487,490],exterior:[3,6,176,350],extern:[],extra:[3,6,8,11,12,16,17,41,42,47,64,76,113,121,122,124,130,153,155,156,157,159,161,164,165,166,167,168,170,171,177,178,179,180,184,206,221,226,228,269,301,302,303,313,329,379,380,383,384,405,416,419,422,436,441,484,485,487,490,499,508,514],extract:[3,6,11,13,36,66,68,73,84,96,102,119,127,129,131,210,211,306,381,402,413,436,458,485,492,504],extract_atom:11,extract_comput:[11,485],extract_fix:11,extract_glob:11,extract_vari:11,extramak:[12,15],extrapol:1,extrem:[1,3,6,17,61,205,220,230,232,269,339,412,471,508],extrema:432,extrins:215,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[174,343],f_a:[470,471,472],f_ave:129,f_c:471,f_f:472,f_fix_id:303,f_foo:514,f_harm:339,f_i:[29,447],f_id:[6,76,129,131,202,203,209,217,218,219,220,221,222,223,224,264,331,343,505,514],f_ij:447,f_indent:224,f_int:338,f_j:29,f_jj:100,f_k:447,f_langevin:341,f_max:[303,308],f_msst:267,f_r:[254,470,471,472],f_sigma:392,f_solid:339,f_ss:6,face:[3,6,60,62,76,166,176,180,214,222,223,346,348,349,350,351,374,415,436,451,487,490],face_threshold:176,facet:176,facil:[0,12],facilit:[6,13,43],fact:[6,8,16,247,299,329,339,416,449,457,499],factor:[1,3,6,12,18,24,28,32,35,36,40,42,47,48,60,61,62,77,96,100,113,120,127,128,130,152,172,177,180,184,195,201,202,205,206,210,211,219,226,230,232,233,245,250,253,255,256,267,269,270,274,296,300,304,312,316,319,321,329,333,337,344,345,346,350,361,372,374,380,386,388,389,392,393,395,397,402,403,404,406,407,408,412,416,419,423,424,436,439,441,443,444,450,452,459,468,473,484,487,490,491,496,499,501,502,505,508,513,514],factori:[3,485],factoriz:371,fail:[3,9,11,12,62,182,230,233,371,379,381,404,450,485],failur:[133,454,486,514],fairli:[11,441,496,501,509],faken:78,falcon:250,fall:[3,6,206,221,299,485,514],fals:[95,352,354,457,514],fame:8,famili:[475,484],familiar:[0,11,509],fan:447,far:[3,6,12,17,60,62,64,95,202,203,206,207,226,227,228,230,233,269,294,312,313,329,346,357,361,377,381,382,474,485,487,492,505],farago:253,farrel:[470,472],farther:202,fashion:[6,8,42,76,178,206,209,210,211,216,222,226,228,233,245,247,251,266,267,269,271,272,273,274,275,276,277,285,288,289,290,291,292,302,303,305,313,318,322,328,331,339,341,345,346,347,349,351,381,419,433,490,499,514,518],fasolino:421,fast:[6,7,9,12,13,17,40,202,203,280,303,342,371,372,394,433,434,439,467,469,489,494,496,505,515,519],faster:[1,6,9,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,42,44,46,47,48,49,50,52,54,55,57,64,66,116,121,124,155,165,184,185,187,188,189,190,192,193,195,196,198,202,203,206,212,225,226,232,239,244,248,252,253,269,271,272,273,274,275,276,277,278,279,286,288,289,290,292,300,304,305,313,315,316,329,332,334,336,338,341,345,349,355,357,358,360,361,364,366,371,372,383,384,386,387,388,390,392,393,394,395,396,397,398,399,400,401,402,405,406,410,411,413,414,415,416,417,418,419,424,425,426,427,428,429,430,431,432,433,437,442,443,444,446,451,452,459,467,468,469,470,471,472,473,475,477,478,479,482,490,496,500,508],fastest:[1,6,14,17,166,222,341,342,386,484],fatal:[3,504],fault:[75,450],faulti:12,fava:415,favor:229,favorit:7,fbmc:336,fcc:[],fcm:[285,514],fdirect:236,fdotr:420,fdt:[],fdti:96,fe2:177,fe3:177,fe_md_boundari:215,featu:8,featur:[],fecr:410,feedback:[7,250],feel:[7,250,251,259,294,350,352,381,441],felling:438,felt:350,femtosecond:513,fene:[],fennel:[402,424],fep:[],ferguson:[6,184,499],fermi:[1,9,10,12,15,164,386,472],fermion:412,fernando:435,ferrand:[9,13],few:[1,3,4,5,6,7,9,10,11,12,13,14,18,40,66,207,217,218,219,221,222,223,224,254,269,299,302,304,316,343,371,379,380,381,388,457,484,487,492,496,498,506,517],fewer:[1,3,11,15,16,64,259,496],fewest:3,fextern:243,feynman:296,fff:485,ffield:[401,413,449,450,457],ffmpeg:[3,12,205],ffplai:205,fft:[1,3,7,9,11,12,14,15,97,121,122,153,295,371,372,496],fft_inc:[12,372],fft_lib:12,fft_path:12,fftbench:[371,506],fftw2:12,fftw3:12,fftw:[9,12],fhg:[7,9],ficiti:466,fictiti:[6,212,213,238,243,247,296,312,402,424,428,466],field1:[488,492],field2:488,field:[],fifth:[6,326,443],figur:[1,3,8,12,303,484,485,509],fij:405,file0:294,file1:[11,13,294,340,354,380,492,494,498],file2:[11,13,340,354,380,492,494,498],file:[],file_from:204,filen:380,filenam:[3,12,13,38,42,57,198,202,203,205,206,207,215,218,219,220,221,222,223,224,226,231,241,294,298,301,304,305,306,309,310,313,314,340,341,368,369,370,380,381,387,388,392,402,410,411,413,421,436,437,438,443,447,448,449,450,457,458,468,469,470,471,472,475,483,484,485,488,489,494,498,505,514,517,518,519],filennam:494,filep:[3,202,203,206,489,494,519],filepo:310,fill:[7,9,178,205,299,341,374,382,392,439,450,490,509],filter:[206,215],final_integr:8,final_integrate_respa:8,finchham:[6,160,404],find:[0,3,4,6,7,8,9,11,12,13,14,16,38,40,57,64,76,78,96,129,181,198,207,216,229,230,241,242,245,268,294,299,300,308,312,377,379,381,382,402,419,424,428,436,457,467,469,508,509,514],find_custom:8,fine:[16,17,182,212,238,339,382,386,509,514],finer:[152,178,514],finest:371,finger:[178,201,266,490],finish:[6,11,42,226,354,368,370,371,383,385,386,474,492,514,515],finit:[],finni:[7,410,467],finvers:236,fiorin:[9,231],fire:[],firebrick:206,first:[0,1,2,3,5,6,8,9,10,11,12,14,15,16,17,21,38,40,42,43,46,47,55,57,60,62,64,65,76,88,97,100,114,115,116,118,124,128,129,139,142,145,146,150,153,163,166,172,174,176,177,179,180,181,185,198,202,203,204,205,206,207,209,210,218,219,221,222,223,224,226,229,232,241,245,246,251,256,266,267,268,269,294,296,301,302,303,305,310,313,316,318,326,327,329,330,331,338,339,340,341,343,347,352,354,355,362,374,379,380,381,382,385,386,387,388,391,392,393,395,397,399,401,402,410,412,413,416,417,419,420,421,422,423,424,428,433,434,436,438,439,441,443,447,449,450,457,458,466,468,469,470,471,472,475,479,482,483,484,485,487,488,489,492,494,496,499,500,501,504,505,508,509,514,515,516,517,519],fischer:[6,9,19,20,184,397,499],fit:[3,6,9,12,38,57,198,241,312,329,388,392,421,436,441,462,469,471,495,509,514],five:[78,164,303,380,392,437,487,501],fix:[],fix_deposit:3,fix_flux:215,fix_id:[3,230,267,269,271,272,273,274,275,276,277,300,303],fix_manifoldforc:509,fix_modifi:[],fix_nh:8,fix_nv:509,fix_poem:3,fix_pour:3,fix_qeq:3,fix_rattl:316,fix_reax_bond:449,fix_saed_vtk:314,fix_setforc:8,fix_shak:316,fix_srd:3,fixedpoint:[230,269],fixextern:243,fixid:215,fji:405,flag1:[235,384],flag2:[235,384],flag:[3,8,9,11,12,14,15,16,17,39,41,59,70,79,80,87,88,95,98,99,104,114,115,117,130,173,177,181,199,202,203,205,206,207,224,229,231,235,250,253,257,259,265,266,295,302,313,326,328,329,336,340,349,352,367,369,372,380,384,385,386,388,418,423,436,439,466,480,482,484,485,487,488,489,491,492,493,497,509,514],flag_buck:396,flag_coul:[396,405,428],flag_lj:[405,428],flagfld:[394,433,434],flaghi:[3,394,433,434],flaglog:[394,433,434],flagn:235,flagvf:[394,433,434],flat:[6,341,346,347,351],flavor:[2,7,12],fld:[346,433,434],flen:389,flex_press:389,flexibl:[3,6,8,179,205,218,222,231,247,270,337,344,412,471,505],flip:[3,6,232,269,348,349],floor:514,flop:12,floralwhit:206,flow:[],fluctuat:[6,67,96,230,245,246,253,256,269,274,294,295,300,317,339,341,364,408],fluid:[],fluid_veloc:260,flush:[3,206,504],flux:[],flv:205,fly:[7,9,12,42,205,209,215,220,233,236,313,316,342,392,439,505,508],fmackai:9,fmag:234,fmass:296,fmax:[379,505],fmomentum:236,fmsec:[2,206,253,254,266,269,300,313,332,333,496,507,513,515],fname:370,fno:[9,16],fnorm:[379,505],fnpt:236,fnvt:236,foce:419,fock:389,focu:316,fogarti:[9,306,450],foil:[152,294,458],fold:[327,496],folk:7,follow:[0,1,2,3,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,41,42,43,44,46,47,48,49,50,52,54,55,57,62,66,67,75,76,78,89,100,101,107,108,118,125,128,129,131,152,153,156,157,158,164,166,171,174,176,178,179,184,187,188,189,190,192,193,195,196,198,202,204,205,206,209,215,216,217,218,219,220,221,222,223,224,226,231,232,233,236,237,240,241,243,245,246,247,250,252,253,254,256,259,267,269,274,275,276,277,288,289,290,292,295,296,298,301,302,303,304,306,308,310,312,313,314,316,331,332,333,334,337,338,339,340,341,343,344,352,353,357,358,359,360,361,364,366,369,374,376,379,380,381,386,387,388,389,390,391,392,393,394,395,396,397,398,400,401,402,403,404,405,406,407,408,409,410,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,440,441,442,443,444,446,447,448,449,450,451,452,454,456,457,458,459,460,461,462,463,464,465,466,468,469,470,471,472,473,474,475,477,478,479,480,482,484,485,487,488,490,492,494,495,496,499,501,502,503,508,509,514,515,518],foo:[4,8,11,12,202,205,243,485,498,514],foot:6,footprint:[12,386],fopenmp:[9,16,18],forc:[],force_uvm:17,forceatom:259,forcefield:[312,418],forcegroup:256,forcezero:377,ford:405,forestgreen:206,forev:76,forget:[254,508],forgiv:269,fork:[],form:[2,3,6,8,12,19,22,45,55,58,66,70,79,80,82,87,88,96,98,99,101,104,114,115,117,128,152,153,172,173,182,186,206,209,210,211,228,246,247,253,255,259,266,290,295,306,308,312,313,341,346,350,355,356,359,364,376,378,380,381,388,389,392,399,407,408,410,412,414,418,419,423,435,436,438,439,443,444,447,449,450,451,457,458,459,467,469,470,471,472,478,481,484,485,487,492,497,504,508,514],formal:[6,83,86,100,246,247,253,269,296,329,337,457],format:[2,3,6,7,8,9,12,13,22,38,42,45,57,58,72,82,186,198,202,203,204,205,206,207,218,221,222,223,224,226,228,241,295,298,302,304,306,309,313,314,325,340,341,352,353,356,376,380,381,387,388,392,399,410,413,423,436,438,448,449,450,452,458,469,475,476,484,485,487,488,489,492,503,504,505,514,516,517],former:[6,12,16,40,42,206,226,341,345,392,394,493,499,514],formerli:[7,13],formul:[1,6,9,41,67,153,212,238,253,269,290,304,306,312,316,340,371,388,392,410,412,415,436,446],formula:[2,3,6,7,13,21,22,37,45,55,56,75,78,96,98,99,100,105,107,108,117,124,130,131,153,155,156,157,158,159,160,161,162,164,165,166,167,168,169,170,171,177,178,183,185,186,197,201,202,210,211,212,213,218,219,220,221,224,225,232,238,248,249,251,253,254,266,294,295,301,310,315,323,327,329,332,333,334,343,346,349,351,352,354,355,356,358,365,374,380,388,389,391,392,397,398,399,400,405,406,410,411,415,416,417,418,420,423,424,426,427,428,430,431,433,434,436,440,441,442,451,452,459,467,468,469,470,471,472,475,477,478,483,487,490,497,504,505,513,514,515],forth:[1,6,11,12,13,14,15,385,485,490,494],fortran:[3,6,9,11,12,13,243,410,419,436,449,450],fortun:8,forward:[3,8,96,370,381,386],foster:[392,446,447],foul:181,found:[3,6,9,12,78,172,202,229,231,245,250,256,295,336,342,354,370,382,399,402,405,482,488,489,504],four:[6,11,55,88,114,115,152,174,267,341,364,380,381,439,482],fourier:[],fourth:[6,116,312,326,336,397,443,457],fox:[6,130,184,465,499],fphi:[38,57,469],fpic:12,fplo:[38,57,469],fprime:469,fqdn:252,fqq:405,fraction:[1,3,6,8,12,16,40,42,86,121,153,181,201,205,206,216,227,228,229,230,267,299,303,310,311,329,334,335,374,381,386,392,394,416,433,434,492,497],fragment:[43,250,310],fraig:43,frame:[92,152,206,215,267,303,348,415],framer:[205,206],framework:[5,247,387,458],franc:9,fraunhof:9,free:[5,6,7,9,13,29,63,66,75,96,172,210,211,294,329,338,339,340,341,378,381,389,412,432,439,447,478,484],freedom:[3,6,8,105,107,108,110,112,113,124,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,218,229,236,245,247,253,254,259,269,270,274,275,276,277,288,289,290,292,296,298,313,316,332,333,334,339,379,405,505,508,515],freeli:[0,6,7,12,156,157,171,176,205],freez:[],frenkel:[245,339],freq:214,frequenc:[3,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ermophys:441,thermost:[6,160,214,231,236,254,348,508],thermostat:[],thermostatequ:6,thesi:[371,372,433,448],thess:393,theta0:[20,21,24,26,27,28,32,33,35,36,152,187,312,364],theta0max:152,theta10:392,theta1:[185,355,392],theta2:[185,355,392],theta3:[355,392],theta4:392,theta5:392,theta6:392,theta7:392,theta8:392,theta9:392,theta:[3,6,26,27,37,38,39,66,69,86,101,118,152,177,178,187,199,201,205,248,308,312,341,355,364,418,447,471,487,490,497],theta_0:443,theta_:[364,392],theta_c:418,theta_ijk:392,theta_ijl:355,theta_jik:[437,438],theta_pi:392,theta_sigma:392,thex:304,thi:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,436,437,438,439,440,441,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,508,509,510,511,512,513,514,515,516,517,518,519],thick:[76,130,205,222,490],thie:122,thijss:336,thin:[128,205],thing:[3,6,11,12,55,72,76,230,269,300,313,329,484,485,489,509,514],think:[3,6,7,8,11,13,206,313,352,357,361,374,379,419,449,450,469,485,489,492,514],third:[6,9,12,29,100,146,152,153,176,218,219,221,222,223,224,246,310,326,327,341,401,413,436,443,473,475,482,483,485,487,490],thirumalai:190,thistl:206,tho:411,thole:[],thompson:[0,5,7,9,13,124,152,153,304,374,458],those:[1,2,3,5,6,7,8,9,10,12,13,17,18,20,21,23,24,25,26,27,28,29,30,31,32,33,35,38,40,41,43,44,46,47,48,49,50,51,52,54,55,57,64,76,77,82,96,100,101,118,120,121,122,124,128,152,153,155,158,165,168,176,178,182,184,185,187,188,189,190,191,192,193,195,196,198,201,202,203,205,206,216,217,218,219,222,223,224,230,232,233,242,248,250,251,252,253,259,266,268,269,271,272,273,274,275,276,277,278,279,286,288,289,290,292,299,302,305,313,331,338,339,343,347,348,349,352,353,355,357,358,360,361,362,364,366,371,372,379,381,382,386,387,388,390,393,394,395,396,397,398,399,400,401,402,405,406,410,411,413,414,415,416,417,418,419,424,425,426,427,428,429,430,431,432,433,436,437,441,442,443,444,446,449,450,451,452,458,459,467,468,469,470,471,472,473,475,477,478,479,482,484,485,487,489,490,491,492,494,496,497,499,501,504,505,506,508,509,514,518,519],though:[6,8,12,40,41,66,76,100,115,178,199,202,206,216,222,227,228,230,232,237,270,311,313,315,325,337,344,354,367,371,374,381,406,409,410,412,413,415,416,432,433,441,475,482,487,489,490,495,499,506,514],thought:[161,253,290,313,345,346,378,416,423,508],thread:[1,3,9,12,16,17,18,250,342,369,386,500,506],threads_per_atom:3,three:[1,3,6,55,66,79,96,100,101,116,129,130,142,152,156,177,178,190,209,229,230,235,257,269,274,295,300,304,313,329,336,338,341,359,360,364,371,372,380,386,387,388,392,410,411,413,415,416,420,423,436,437,438,439,443,447,450,451,457,458,468,470,471,472,475,485,487,490,514],threebodi:468,thresh:[42,202,203,205,206,226,485],threshhold:[3,42,205,226,352,485],threshold:[3,42,95,176,206,226,294,382,450,482,501],thrid:485,through:[3,6,7,9,11,12,66,178,182,202,203,207,230,243,245,250,251,256,258,259,260,269,270,296,304,322,336,341,346,350,370,377,388,408,411,412,416,422,424,439,452,457,459,466,473,482,485,488,498,504,508],throughout:[6,16,128,130,342,386,439,487],thru:[3,6,7,11,12,70,79,80,87,88,98,99,104,114,115,116,117,173,201,202,206,221,266,329,349,354,370,379,385,490],thrust:1,thu:[1,2,3,6,8,11,12,18,33,38,40,42,43,51,62,64,66,67,70,71,75,76,77,78,80,82,87,88,97,99,100,101,104,114,115,117,118,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Documentation","5. Accelerating LAMMPS performance","3. Commands","12. Errors","7. Example problems","13. Future and history","6. How-to discussions","1. Introduction","10. Modifying &amp; extending LAMMPS","4. Packages","8. Performance &amp; scalability","11. Python interface to LAMMPS","2. Getting Started","9. Additional tools","5.USER-CUDA package","5.GPU package","5.USER-INTEL package","5.KOKKOS package","5.USER-OMP package","5.OPT package","angle_style charmm command","angle_style class2 command","angle_coeff command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style hybrid command","angle_style none command","angle_style quartic command","angle_style sdk command","angle_style command","angle_style table command","angle_style zero command","atom_modify command","atom_style command","balance command","Body particles","bond_style class2 command","bond_coeff command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style hybrid command","bond_style morse command","bond_style none command","bond_style nonlinear command","bond_style quartic command","bond_style command","bond_style table command","bond_write command","bond_style zero command","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local command","compute bond command","compute bond/local command","compute centro/atom command","compute chunk/atom command","compute cluster/atom command","compute cna/atom command","compute com command","compute com/chunk command","compute contact/atom command","compute coord/atom command","compute damage/atom command","compute dihedral command","compute dihedral/local command","compute dilatation/atom command","compute dipole/chunk command","compute displace/atom command","compute dpd command","compute dpd/atom command","compute erotate/asphere command","compute erotate/rigid command","compute erotate/sphere command","compute erotate/sphere/atom command","compute event/displace command","compute fep command","compute group/group command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute hexorder/atom command","compute improper command","compute improper/local command","compute inertia/chunk command","compute ke command","compute ke/atom command","compute ke/atom/eff command","compute ke/eff command","compute ke/rigid command","compute meso/e/atom command","compute meso/rho/atom command","compute meso/t/atom command","compute_modify command","compute msd command","compute msd/chunk command","compute msd/nongauss command","compute omega/chunk command","compute orientorder/atom command","compute pair command","compute pair/local command","compute pe command","compute pe/atom command","compute plasticity/atom command","compute pressure command","compute property/atom command","compute property/chunk command","compute property/local command","compute rdf command","compute reduce command","compute saed command","compute slice command","compute smd/contact/radius command","compute smd/damage command","compute smd/hourglass/error command","compute smd/internal/energy command","compute smd/plastic/strain command","compute smd/plastic/strain/rate command","compute smd/rho command","compute smd/tlsph/defgrad command","compute smd/tlsph/dt command","compute smd/tlsph/num/neighs command","compute smd/tlsph/shape command","compute smd/tlsph/strain command","compute smd/tlsph/strain/rate command","compute smd/tlsph/stress command","compute smd/triangle/mesh/vertices","compute smd/ulsph/num/neighs command","compute smd/ulsph/strain command","compute smd/ulsph/strain/rate command","compute smd/ulsph/stress command","compute smd/vol command","compute sna/atom command","compute stress/atom command","compute force/tally command","compute temp command","compute temp/asphere command","compute temp/body command","compute temp/chunk command","compute temp/com command","compute temp/cs command","compute temp/deform command","compute temp/deform/eff command","compute temp/drude command","compute temp/eff command","compute temp/partial command","compute temp/profile command","compute temp/ramp command","compute temp/region command","compute temp/region/eff command","compute temp/rotate command","compute temp/sphere command","compute ti command","compute torque/chunk command","compute vacf command","compute vcm/chunk command","compute voronoi/atom command","compute xrd command","create_atoms command","create_bonds command","create_box command","delete_atoms command","delete_bonds command","dielectric command","dihedral_style charmm command","dihedral_style class2 command","dihedral_coeff command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style hybrid command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style none command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style command","dihedral_style table command","dihedral_style zero command","dimension command","displace_atoms command","dump command","dump custom/vtk command","dump h5md command","dump image command","dump_modify command","dump molfile command","echo command","fix command","fix adapt command","fix adapt/fep command","fix addforce command","fix addtorque command","fix append/atoms command","fix atc command","fix atom/swap command","fix ave/atom command","fix ave/chunk command","fix ave/correlate command","fix ave/correlate/long command","fix ave/histo command","fix ave/spatial command","fix ave/spatial/sphere command","fix ave/time command","fix aveforce command","fix balance command","fix bond/break command","fix bond/create command","fix bond/swap command","fix box/relax command","fix colvars command","fix deform command","fix deposit command","fix drag command","fix drude command","fix drude/transform/direct command","fix dt/reset command","fix efield command","fix enforce2d command","fix eos/cv command","fix eos/table command","fix evaporate command","fix external command","fix freeze command","fix gcmc command","fix gld command","fix gle command","fix gravity command","fix heat command","fix imd command","fix indent command","fix ipi command","fix langevin command","fix langevin/drude command","fix langevin/eff command","fix lb/fluid command","fix lb/momentum command","fix lb/pc command","fix lb/rigid/pc/sphere command","fix lb/viscous command","fix lineforce command","fix meso command","fix meso/stationary command","fix_modify command","fix momentum command","fix move command","fix msst command","fix neb command","fix nvt command","fix nvt/eff command","fix nph/asphere command","fix nph/body command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/body command","fix npt/sphere command","fix nve command","fix nve/asphere command","fix nve/asphere/noforce command","fix nve/body command","fix nve/eff command","fix nve/limit command","fix nve/line command","fix nve/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/body command","fix nvt/sllod command","fix nvt/sllod/eff command","fix nvt/sphere command","fix oneway command","fix orient/fcc command","fix phonon command","fix pimd command","fix planeforce command","fix poems","fix pour command","fix press/berendsen command","fix print command","fix property/atom command","fix qbmsst command","fix qeq/point command","fix qeq/comb command","fix qeq/reax command","fix qmmm command","fix qtb command","fix reax/bonds command","fix reax/c/species command","fix recenter command","fix restrain command","fix rigid command","fix saed/vtk command","fix setforce command","fix shake command","fix shardlow command","fix smd command","fix smd/adjust_dt command","fix smd/integrate_tlsph command","fix smd/integrate_ulsph command","fix smd/move_tri_surf command","fix smd/setvel command","&lt;no title&gt;","fix smd/wall_surface command","fix spring command","fix spring/rg command","fix spring/self command","fix srd command","fix store/force command","fix store/state command","fix temp/berendsen command","fix temp/csvr command","fix temp/rescale command","fix temp/rescale/eff command","fix tfmc command","fix thermal/conductivity command","fix ti/rs command","fix ti/spring command","fix tmd command","fix ttm command","fix tune/kspace command","fix vector command","fix viscosity command","fix viscous command","fix wall/lj93 command","fix wall/gran command","fix wall/piston command","fix wall/reflect command","fix wall/region command","fix wall/srd command","group command","group2ndx command","if command","improper_style class2 command","improper_coeff command","improper_style cossq command","improper_style cvff command","improper_style distance command","improper_style fourier command","improper_style harmonic command","improper_style hybrid command","improper_style none command","improper_style ring command","improper_style command","improper_style umbrella command","improper_style zero command","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","mass command","min_modify command","min_style command","minimize command","molecule command","neb command","neigh_modify command","neighbor command","newton command","next command","package command","pair_style adp command","pair_style airebo command","pair_style awpmd/cut command","pair_style beck command","pair_style body command","pair_style bop command","pair_style born command","pair_style brownian command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_coeff command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dpd/conservative command","pair_style dpd/fdt command","pair_style dsmc command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style hybrid command","pair_style kim command","pair_style lcbop command","pair_style line/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style lj/mdf command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mgpt command","pair_style mie/cut command","pair_modify command","pair_style morse command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style none command","pair_style peri/pmb command","pair_style polymorphic command","pair_style quip command","pair_style reax command","pair_style reax/c command","pair_style resquared command","pair_style lj/sdk command","pair_style smd/hertz command","pair_style smd/tlsph command","pair_style smd/tri_surface command","pair_style smd/ulsph command","pair_style smtbq command","pair_style snap command","pair_style soft command","pair_style sph/heatconduction command","pair_style sph/idealgas command","pair_style sph/lj command","pair_style sph/rhosum command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style command","pair_style sw command","pair_style table command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style thole command","pair_style tri/lj command","pair_style vashishta command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","pair_style zero command","partition command","prd command","print command","processors command","python command","quit command","read_data command","read_dump command","read_restart command","region command","replicate command","rerun command","reset_timestep command","restart command","run command","run_style command","set command","shell command","special_bonds command","suffix command","tad command","temper command","thermo command","thermo_modify command","thermo_style command","timer command","timestep command","&lt;no title&gt;","LAMMPS GitHub tutorial","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_coeff command","write_data command","write_dump command","write_restart command"],titleterms:{"break":227,"default":[37,40,41,56,60,61,62,64,65,76,96,97,101,113,114,116,118,119,130,134,135,152,158,166,167,171,177,178,181,183,197,200,201,202,203,205,206,207,208,210,211,212,214,215,216,218,222,223,224,227,228,230,231,232,233,237,242,245,246,251,253,254,255,256,257,259,264,267,269,270,274,290,291,295,296,299,300,301,302,303,305,308,310,311,313,314,329,331,336,337,338,339,342,344,346,348,352,365,369,371,372,374,375,377,378,380,382,383,384,386,389,392,394,412,433,434,439,441,449,450,466,467,482,483,484,487,488,490,492,494,495,496,499,501,503,504,505,506,507,513,515,517,518],"function":514,"long":[220,393,395,396,397,398,402,404,405,424,428,432,444,452,473],"new":8,"static":12,acceler:1,account:509,ackland:67,acknowledg:7,adapt:[210,211],addforc:212,addit:[12,13,509],addtorqu:213,adiabat:6,adjust_dt:319,adp:387,after:509,airebo:388,alloi:410,amber2lmp:13,amber:6,angl:[8,68,69],angle_coeff:22,angle_styl:[2,20,21,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39],angmom:70,append:214,arrai:6,aspher:[6,9,91,156,271,275,279,280,288],atc:[9,215],atom:[6,7,8,67,71,75,76,77,78,81,82,83,86,88,90,94,101,106,107,110,111,112,118,122,123,125,152,153,176,214,216,217,302,514],atom_modifi:40,atom_styl:41,attract:5,aveforc:225,awpmd:[9,389],balanc:[42,226],barostat:6,basal:71,beck:390,berendsen:[300,332],between:6,binary2txt:13,bodi:[6,8,9,43,72,157,272,276,281,289,391],bond:[8,13,73,74,227,228,229,309],bond_coeff:45,bond_styl:[2,44,46,47,48,49,50,51,52,53,54,55,56,57,59],bond_writ:58,bop:392,born:[393,404],boundari:[7,60],box:[6,61,230],branch:509,brownian:394,buck:[395,396,404,435],bug:3,build:[11,12],calcul:6,call:12,categori:2,centro:75,ch2lmp:13,chain:13,chang:509,change_box:62,charmm:[6,20,184,397,432],chunk:[6,70,76,80,87,99,104,115,117,126,158,173,175,218],citat:7,class2:[9,21,44,185,355,398],clear:63,cluster:77,cmm:9,cna:78,code:6,coeffici:6,colloid:[9,346,400,478],colvar:[9,13,231],com:[79,80,159],comb3:401,comb:[305,401],come:5,comm_modifi:64,comm_styl:65,command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,510,511,512,513,514,515,516,517,518,519],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,514],compute_modifi:113,condit:7,conduct:[6,337],conserv:407,constant:[6,514],constraint:7,contact:[81,132],coord:82,core:6,coreshel:9,correl:[219,220],cosin:[23,24,25,26,27,28,187],cossq:357,coul:[393,395,396,397,398,402,403,404,417,424,428,432,444,452],coupl:6,creat:228,create_atom:178,create_bond:179,create_box:180,createatom:13,creation:7,csld:333,csvr:333,cubic:426,cuda:[9,14,121,124,155,165,212,225,239,244,248,269,278,315,316,332,334,345,393,395,397,398,410,416,417,424,425,427,430,442,468,470],custom:[8,202,203],cut:[50,389,395,398,402,405,412,414,424,425,432,440,444,473],cvff:358,damag: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\ No newline at end of file
diff --git a/doc/html/thermo_style.html b/doc/html/thermo_style.html
index 6b7762882e..f3c15b1f9d 100644
--- a/doc/html/thermo_style.html
+++ b/doc/html/thermo_style.html
@@ -325,8 +325,8 @@ keywords for the <a class="reference internal" href="run.html"><span class="doc"
 runs that keep track of an initial starting time.  If these keywords
 are not used, then <em>elapsed</em> and <em>elaplong</em> are the same value.</p>
 <p>The <em>dt</em> keyword is the current timestep size in time
-<span class="xref doc">units</span>.  The <em>time</em> keyword is the current elapsed
-simulation time, also in time <span class="xref doc">units</span>, which is simply
+<a class="reference internal" href="units.html"><span class="doc">units</span></a>.  The <em>time</em> keyword is the current elapsed
+simulation time, also in time <a class="reference internal" href="units.html"><span class="doc">units</span></a>, which is simply
 (step*dt) if the timestep size has not changed and the timestep has
 not been reset.  If the timestep has changed (e.g. via <a class="reference internal" href="fix_dt_reset.html"><span class="doc">fix dt/reset</span></a>) or the timestep has been reset (e.g. via
 the &#8220;reset_timestep&#8221; command), then the simulation time is effectively
@@ -335,7 +335,7 @@ a cummulative value up to the current point.</p>
 run.  The <em>tpcpu</em> and <em>spcpu</em> keywords are measures of how fast your
 simulation is currently running.  The <em>tpcpu</em> keyword is simulation
 time per CPU second, where simulation time is in time
-<span class="xref doc">units</span>.  E.g. for metal units, the <em>tpcpu</em> value would be
+<a class="reference internal" href="units.html"><span class="doc">units</span></a>.  E.g. for metal units, the <em>tpcpu</em> value would be
 picoseconds per CPU second.  The <em>spcpu</em> keyword is the number of
 timesteps per CPU second.  Both quantities are on-the-fly metrics,
 measured relative to the last time they were invoked.  Thus if you are
diff --git a/doc/html/timestep.html b/doc/html/timestep.html
index fdd732fda4..259788b107 100644
--- a/doc/html/timestep.html
+++ b/doc/html/timestep.html
@@ -145,7 +145,7 @@
 <div class="section" id="description">
 <h2>Description</h2>
 <p>Set the timestep size for subsequent molecular dynamics simulations.
-See the <span class="xref doc">units</span> command for the time units associated with
+See the <a class="reference internal" href="units.html"><span class="doc">units</span></a> command for the time units associated with
 each choice of units that LAMMPS supports.</p>
 <p>The default value for the timestep size also depends on the choice of
 units for the simulation; see the default values below.</p>
@@ -160,7 +160,7 @@ the outer loop (largest) timestep.</p>
 <div class="section" id="related-commands">
 <h2>Related commands</h2>
 <p><a class="reference internal" href="fix_dt_reset.html"><span class="doc">fix dt/reset</span></a>, <a class="reference internal" href="run.html"><span class="doc">run</span></a>,
-<a class="reference internal" href="run_style.html"><span class="doc">run_style</span></a> respa, <span class="xref doc">units</span></p>
+<a class="reference internal" href="run_style.html"><span class="doc">run_style</span></a> respa, <a class="reference internal" href="units.html"><span class="doc">units</span></a></p>
 </div>
 <div class="section" id="default">
 <h2>Default</h2>
@@ -171,7 +171,7 @@ the outer loop (largest) timestep.</p>
 <col width="34%" />
 </colgroup>
 <tbody valign="top">
-<tr class="row-odd"><td>choice of <span class="xref doc">units</span></td>
+<tr class="row-odd"><td>choice of <a class="reference internal" href="units.html"><span class="doc">units</span></a></td>
 <td>time units</td>
 <td>default timestep size</td>
 </tr>
diff --git a/doc/html/velocity.html b/doc/html/velocity.html
index 2c80e15638..06accf9593 100644
--- a/doc/html/velocity.html
+++ b/doc/html/velocity.html
@@ -225,7 +225,7 @@ angular will set the angular momentum of each rigid body to zero.
 This is done by adjusting the velocities of the atoms in each rigid
 body.</p>
 <p>All temperatures specified in the velocity command are in temperature
-units; see the <span class="xref doc">units</span> command.  The units of velocities and
+units; see the <a class="reference internal" href="units.html"><span class="doc">units</span></a> command.  The units of velocities and
 coordinates depend on whether the <em>units</em> keyword is set to <em>box</em> or
 <em>lattice</em>, as discussed below.</p>
 <p>For all styles, no atoms are assigned z-component velocities if the
@@ -316,7 +316,7 @@ zeroing of linear or angular momentum is then performed for each rigid
 body defined by the fix, as described above.</p>
 <p>The <em>units</em> keyword is used by <em>set</em> and <em>ramp</em>.  If units = box,
 the velocities and coordinates specified in the velocity command are
-in the standard units described by the <span class="xref doc">units</span> command
+in the standard units described by the <a class="reference internal" href="units.html"><span class="doc">units</span></a> command
 (e.g. Angstroms/fmsec for real units).  If units = lattice, velocities
 are in units of lattice spacings per time (e.g. spacings/fmsec) and
 coordinates are in lattice spacings.  The <a class="reference internal" href="lattice.html"><span class="doc">lattice</span></a>