From 2c8227b10c9ddc58e6ebc570a88b04c849a26287 Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Tue, 10 May 2016 15:01:22 +0000
Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14987
 f3b2605a-c512-4ea7-a41b-209d697bcdaa

---
 doc/html/Section_howto.html           | 14 +++++++-------
 doc/html/_sources/Section_howto.txt   | 14 +++++++-------
 doc/html/_sources/bond_fene.txt       |  4 ++--
 doc/html/_sources/compute_xrd.txt     |  4 ++--
 doc/html/_sources/dihedral_charmm.txt | 11 ++++++-----
 doc/html/_sources/fix_nh.txt          | 20 ++++++++++----------
 doc/html/bond_fene.html               |  4 ++--
 doc/html/compute_xrd.html             |  4 ++--
 doc/html/dihedral_charmm.html         | 11 ++++++-----
 doc/html/fix_nh.html                  | 20 ++++++++++----------
 10 files changed, 54 insertions(+), 52 deletions(-)

diff --git a/doc/html/Section_howto.html b/doc/html/Section_howto.html
index a4c652a14f..ff7b7270e6 100644
--- a/doc/html/Section_howto.html
+++ b/doc/html/Section_howto.html
@@ -363,7 +363,7 @@ 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="special_bonds.html#mackerell"><span class="std std-ref">(MacKerell)</span></a> for a description of the CHARMM force
+<p>See <a class="reference internal" href="#howto-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
@@ -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="special_bonds.html#mackerell"><span class="std std-ref">(MacKerell)</span></a> specifies a 3-site rigid water molecule with
+<a class="reference internal" href="#howto-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="fix_temp_berendsen.html#berendsen"><span class="std std-ref">(Berendsen)</span></a> reference for more details on both
+<p>See the <a class="reference internal" href="#howto-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="tutorial_drude.html#lamoureux"><span class="std std-ref">Lamoureux and Roux</span></a>):</p>
+(<a class="reference internal" href="#howto-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
@@ -2776,7 +2776,7 @@ using Thole functions through the the <a class="reference internal" href="pair_t
 with a Coulomb pair style. It may be useful to use <em>coul/long/cs</em> or
 similar from the CORESHELL package if the core and Drude particle come
 too close, which can cause numerical issues.</p>
-<p id="berendsen"><strong>(Berendsen)</strong> Berendsen, Grigera, Straatsma, J Phys Chem, 91,
+<p id="howto-berendsen"><strong>(Berendsen)</strong> Berendsen, Grigera, Straatsma, J Phys Chem, 91,
 6269-6271 (1987).</p>
 <p id="cornell"><strong>(Cornell)</strong> Cornell, Cieplak, Bayly, Gould, Merz, Ferguson,
 Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).</p>
@@ -2784,7 +2784,7 @@ Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).</p>
 J Chem Phys, 120, 9665 (2004).</p>
 <p id="ikeshoji"><strong>(Ikeshoji)</strong> Ikeshoji and Hafskjold, Molecular Physics, 81, 251-261
 (1994).</p>
-<p id="mackerell"><strong>(MacKerell)</strong> MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
+<p id="howto-mackerell"><strong>(MacKerell)</strong> MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
 Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).</p>
 <p id="mayo"><strong>(Mayo)</strong> Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
 (1990).</p>
@@ -2794,7 +2794,7 @@ Phys, 79, 926 (1983).</p>
 <p id="shinoda"><strong>(Shinoda)</strong> Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).</p>
 <p id="mitchellfinchham"><strong>(Mitchell and Finchham)</strong> Mitchell, Finchham, J Phys Condensed Matter,
 5, 1031-1038 (1993).</p>
-<p id="lamoureux"><strong>(Lamoureux and Roux)</strong> G. Lamoureux, B. Roux, J. Chem. Phys 119, 3025 (2003)</p>
+<p id="howto-lamoureux"><strong>(Lamoureux and Roux)</strong> G. Lamoureux, B. Roux, J. Chem. Phys 119, 3025 (2003)</p>
 </div>
 </div>
 
diff --git a/doc/html/_sources/Section_howto.txt b/doc/html/_sources/Section_howto.txt
index 90584d156c..89fc18fadc 100644
--- a/doc/html/_sources/Section_howto.txt
+++ b/doc/html/_sources/Section_howto.txt
@@ -221,7 +221,7 @@ commands like :doc:`pair_coeff <pair_coeff>` or
 for additional tools that can use CHARMM or AMBER to assign force
 field coefficients and convert their output into LAMMPS input.
 
-See :ref:`(MacKerell) <MacKerell>` for a description of the CHARMM force
+See :ref:`(MacKerell) <howto-MacKerell>` for a description of the CHARMM force
 field.  See :ref:`(Cornell) <Cornell>` for a description of the AMBER force
 field.
 
@@ -507,7 +507,7 @@ TIP3P water model
 -----------------
 
 The TIP3P water model as implemented in CHARMM
-:ref:`(MacKerell) <MacKerell>` specifies a 3-site rigid water molecule with
+:ref:`(MacKerell) <howto-MacKerell>` specifies a 3-site rigid water molecule with
 charges and Lennard-Jones parameters assigned to each of the 3 atoms.
 In LAMMPS the :doc:`fix shake <fix_shake>` command can be used to hold
 the two O-H bonds and the H-O-H angle rigid.  A bond style of
@@ -706,7 +706,7 @@ the partial charge assignemnts change:
 | H charge = 0.4238
 | 
 
-See the :ref:`(Berendsen) <Berendsen>` reference for more details on both
+See the :ref:`(Berendsen) <howto-Berendsen>` reference for more details on both
 the SPC and SPC/E models.
 
 Wikipedia also has a nice article on `water models <http://en.wikipedia.org/wiki/Water_model>`_.
@@ -2978,7 +2978,7 @@ The thermalized Drude model, similarly to the :ref:`core-shell <howto_26>`
 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
-(:ref:`Lamoureux and Roux <Lamoureux>`):
+(:ref:`Lamoureux and Roux <howto-Lamoureux>`):
 
 * Thermostating of the additional degrees of freedom associated with the
   induced dipoles at very low temperature, in terms of the reduced
@@ -3030,7 +3030,7 @@ too close, which can cause numerical issues.
 
 
 
-.. _Berendsen:
+.. _howto-Berendsen:
 
 
 
@@ -3058,7 +3058,7 @@ J Chem Phys, 120, 9665 (2004).
 **(Ikeshoji)** Ikeshoji and Hafskjold, Molecular Physics, 81, 251-261
 (1994).
 
-.. _MacKerell:
+.. _howto-MacKerell:
 
 
 
@@ -3098,7 +3098,7 @@ Phys, 79, 926 (1983).
 **(Mitchell and Finchham)** Mitchell, Finchham, J Phys Condensed Matter,
 5, 1031-1038 (1993).
 
-.. _Lamoureux:
+.. _howto-Lamoureux:
 
 
 
diff --git a/doc/html/_sources/bond_fene.txt b/doc/html/_sources/bond_fene.txt
index 380d712d20..8380d062cd 100644
--- a/doc/html/_sources/bond_fene.txt
+++ b/doc/html/_sources/bond_fene.txt
@@ -33,7 +33,7 @@ The *fene* bond style uses the potential
    :align: center
 
 to define a finite extensible nonlinear elastic (FENE) potential
-:ref:`(Kremer) <Kremer>`, used for bead-spring polymer models.  The first
+:ref:`(Kremer) <fene-Kremer>`, 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.
@@ -97,7 +97,7 @@ Related commands
 ----------
 
 
-.. _Kremer:
+.. _fene-Kremer:
 
 
 
diff --git a/doc/html/_sources/compute_xrd.txt b/doc/html/_sources/compute_xrd.txt
index 19473d2262..4702715ed0 100644
--- a/doc/html/_sources/compute_xrd.txt
+++ b/doc/html/_sources/compute_xrd.txt
@@ -52,7 +52,7 @@ Description
 """""""""""
 
 Define a computation that calculates x-ray diffraction intensity as described
-in :ref:`(Coleman) <Coleman>` on a mesh of reciprocal lattice nodes defined 
+in :ref:`(Coleman) <xrd-Coleman>` on a mesh of reciprocal lattice nodes defined 
 by the entire simulation domain (or manually) using a simulated radiation
 of wavelength lambda.
 
@@ -209,7 +209,7 @@ no manual flag, no echo flag.
 ----------
 
 
-.. _Coleman:
+.. _xrd-Coleman:
 
 
 
diff --git a/doc/html/_sources/dihedral_charmm.txt b/doc/html/_sources/dihedral_charmm.txt
index 11cd781d93..0754b6cbb6 100644
--- a/doc/html/_sources/dihedral_charmm.txt
+++ b/doc/html/_sources/dihedral_charmm.txt
@@ -35,10 +35,11 @@ The *charmm* dihedral style uses the potential
 .. image:: Eqs/dihedral_charmm.jpg
    :align: center
 
-See :ref:`(MacKerell) <dihedral-MacKerell>` 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 :ref:`(Cornell) <Cornell>`
-for a description of the AMBER force field.
+See :ref:`(MacKerell) <dihedral-MacKerell>` 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
+:ref:`(Cornell) <dihedral-Cornell>` for a description of the AMBER force
+field.
 
 The following coefficients must be defined for each dihedral type via the
 :doc:`dihedral_coeff <dihedral_coeff>` command as in the example above, or in
@@ -121,7 +122,7 @@ Related commands
 ----------
 
 
-.. _Cornell:
+.. _dihedral-Cornell:
 
 
 
diff --git a/doc/html/_sources/fix_nh.txt b/doc/html/_sources/fix_nh.txt
index 2036335a56..517d86d209 100644
--- a/doc/html/_sources/fix_nh.txt
+++ b/doc/html/_sources/fix_nh.txt
@@ -122,12 +122,12 @@ particles will match the target values specified by Tstart/Tstop and
 Pstart/Pstop.
 
 The equations of motion used are those of Shinoda et al in
-:ref:`(Shinoda) <Shinoda>`, which combine the hydrostatic equations of
-Martyna, Tobias and Klein in :ref:`(Martyna) <Martyna>` with the strain
+:ref:`(Shinoda) <nh-Shinoda>`, which combine the hydrostatic equations of
+Martyna, Tobias and Klein in :ref:`(Martyna) <nh-Martyna>` with the strain
 energy proposed by Parrinello and Rahman in
-:ref:`(Parrinello) <Parrinello>`.  The time integration schemes closely
+:ref:`(Parrinello) <nh-Parrinello>`.  The time integration schemes closely
 follow the time-reversible measure-preserving Verlet and rRESPA
-integrators derived by Tuckerman et al in :ref:`(Tuckerman) <Tuckerman>`.
+integrators derived by Tuckerman et al in :ref:`(Tuckerman) <nh-Tuckerman>`.
 
 
 ----------
@@ -320,7 +320,7 @@ barostat variables.
 
 The *mtk* keyword controls whether or not the correction terms due to
 Martyna, Tuckerman, and Klein are included in the equations of motion
-:ref:`(Martyna) <Martyna>`.  Specifying *no* reproduces the original
+:ref:`(Martyna) <nh-Martyna>`.  Specifying *no* 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 *yes* is more correct, but in many cases the difference is
@@ -330,7 +330,7 @@ The keyword *tloop* can be used to improve the accuracy of integration
 scheme at little extra cost.  The initial and final updates of the
 thermostat variables are broken up into *tloop* substeps, each of
 length *dt*\ /\ *tloop*\ . This corresponds to using a first-order
-Suzuki-Yoshida scheme :ref:`(Tuckerman) <Tuckerman>`.  The keyword *ploop*
+Suzuki-Yoshida scheme :ref:`(Tuckerman) <nh-Tuckerman>`.  The keyword *ploop*
 does the same thing for the barostat thermostat.
 
 The keyword *nreset* controls how often the reference dimensions used
@@ -698,26 +698,26 @@ not coupled to barostat, otherwise no.
 ----------
 
 
-.. _Martyna:
+.. _nh-Martyna:
 
 
 
 **(Martyna)** Martyna, Tobias and Klein, J Chem Phys, 101, 4177 (1994).
 
-.. _Parrinello:
+.. _nh-Parrinello:
 
 
 
 **(Parrinello)** Parrinello and Rahman, J Appl Phys, 52, 7182 (1981).
 
-.. _Tuckerman:
+.. _nh-Tuckerman:
 
 
 
 **(Tuckerman)** Tuckerman, Alejandre, Lopez-Rendon, Jochim, and
 Martyna, J Phys A: Math Gen, 39, 5629 (2006).
 
-.. _Shinoda:
+.. _nh-Shinoda:
 
 
 
diff --git a/doc/html/bond_fene.html b/doc/html/bond_fene.html
index f136e86c5f..f67f75ac61 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="special_bonds.html#kremer"><span class="std std-ref">(Kremer)</span></a>, used for bead-spring polymer models.  The first
+<a class="reference internal" href="#fene-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>
@@ -195,7 +195,7 @@ style.  LAMMPS will issue a warning it that&#8217;s not the case.</p>
 <p><a class="reference internal" href="bond_coeff.html"><span class="doc">bond_coeff</span></a>, <a class="reference internal" href="delete_bonds.html"><span class="doc">delete_bonds</span></a></p>
 <p><strong>Default:</strong> none</p>
 <hr class="docutils" />
-<p id="kremer"><strong>(Kremer)</strong> Kremer, Grest, J Chem Phys, 92, 5057 (1990).</p>
+<p id="fene-kremer"><strong>(Kremer)</strong> Kremer, Grest, J Chem Phys, 92, 5057 (1990).</p>
 </div>
 </div>
 
diff --git a/doc/html/compute_xrd.html b/doc/html/compute_xrd.html
index d594e6ce55..b16569ab91 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="fix_saed_vtk.html#coleman"><span class="std std-ref">(Coleman)</span></a> on a mesh of reciprocal lattice nodes defined
+in <a class="reference internal" href="#xrd-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,
@@ -318,7 +318,7 @@ enabled if LAMMPS was built with that package.  See the <a class="reference inte
 <p>The option defaults are 2Theta = 1 179 (degrees), c = 1 1 1, LP = 1,
 no manual flag, no echo flag.</p>
 <hr class="docutils" />
-<p id="coleman"><strong>(Coleman)</strong> Coleman, Spearot, Capolungo, MSMSE, 21, 055020
+<p id="xrd-coleman"><strong>(Coleman)</strong> Coleman, Spearot, Capolungo, MSMSE, 21, 055020
 (2013).</p>
 <p id="colliex"><strong>(Colliex)</strong> Colliex et al. International Tables for Crystallography
 Volume C: Mathematical and Chemical Tables, 249-429 (2004).</p>
diff --git a/doc/html/dihedral_charmm.html b/doc/html/dihedral_charmm.html
index ab802a304d..35e5af8c8d 100644
--- a/doc/html/dihedral_charmm.html
+++ b/doc/html/dihedral_charmm.html
@@ -152,10 +152,11 @@
 <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="#dihedral-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="special_bonds.html#cornell"><span class="std std-ref">(Cornell)</span></a>
-for a description of the AMBER force field.</p>
+<p>See <a class="reference internal" href="#dihedral-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="#dihedral-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
 the data file or restart files read by the <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a>
@@ -217,7 +218,7 @@ MOLECULE package (which it is by default).  See the <a class="reference internal
 <p><a class="reference internal" href="dihedral_coeff.html"><span class="doc">dihedral_coeff</span></a></p>
 <p><strong>Default:</strong> none</p>
 <hr class="docutils" />
-<p id="cornell"><strong>(Cornell)</strong> Cornell, Cieplak, Bayly, Gould, Merz, Ferguson,
+<p id="dihedral-cornell"><strong>(Cornell)</strong> Cornell, Cieplak, Bayly, Gould, Merz, Ferguson,
 Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).</p>
 <p id="dihedral-mackerell"><strong>(MacKerell)</strong> MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
 Fischer, Gao, Guo, Ha, et al, J Phys Chem B, 102, 3586 (1998).</p>
diff --git a/doc/html/fix_nh.html b/doc/html/fix_nh.html
index f542b04a18..747e2cc8d0 100644
--- a/doc/html/fix_nh.html
+++ b/doc/html/fix_nh.html
@@ -239,12 +239,12 @@ correctly, the time-averaged temperature and stress tensor of the
 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="fix_rigid.html#martyna"><span class="std std-ref">(Martyna)</span></a> with the strain
+<a class="reference internal" href="#nh-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="#nh-martyna"><span class="std std-ref">(Martyna)</span></a> with the strain
 energy proposed by Parrinello and Rahman in
-<a class="reference internal" href="fix_nh_eff.html#parrinello"><span class="std std-ref">(Parrinello)</span></a>.  The time integration schemes closely
+<a class="reference internal" href="#nh-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="run_style.html#tuckerman"><span class="std std-ref">(Tuckerman)</span></a>.</p>
+integrators derived by Tuckerman et al in <a class="reference internal" href="#nh-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="fix_rigid.html#martyna"><span class="std std-ref">(Martyna)</span></a>.  Specifying <em>no</em> reproduces the original
+<a class="reference internal" href="#nh-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="run_style.html#tuckerman"><span class="std std-ref">(Tuckerman)</span></a>.  The keyword <em>ploop</em>
+Suzuki-Yoshida scheme <a class="reference internal" href="#nh-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,
@@ -716,11 +716,11 @@ ploop = 1, nreset = 0, drag = 0.0, dilate = all, couple = none,
 scaleyz = scalexz = scalexy = yes if periodic in 2nd dimension and
 not coupled to barostat, otherwise no.</p>
 <hr class="docutils" />
-<p id="martyna"><strong>(Martyna)</strong> Martyna, Tobias and Klein, J Chem Phys, 101, 4177 (1994).</p>
-<p id="parrinello"><strong>(Parrinello)</strong> Parrinello and Rahman, J Appl Phys, 52, 7182 (1981).</p>
-<p id="tuckerman"><strong>(Tuckerman)</strong> Tuckerman, Alejandre, Lopez-Rendon, Jochim, and
+<p id="nh-martyna"><strong>(Martyna)</strong> Martyna, Tobias and Klein, J Chem Phys, 101, 4177 (1994).</p>
+<p id="nh-parrinello"><strong>(Parrinello)</strong> Parrinello and Rahman, J Appl Phys, 52, 7182 (1981).</p>
+<p id="nh-tuckerman"><strong>(Tuckerman)</strong> Tuckerman, Alejandre, Lopez-Rendon, Jochim, and
 Martyna, J Phys A: Math Gen, 39, 5629 (2006).</p>
-<p id="shinoda"><strong>(Shinoda)</strong> Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).</p>
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