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14
doc/html/Section_howto.html
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@ -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> <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 for additional tools that can use CHARMM or AMBER to assign force
field coefficients and convert their output into LAMMPS input.</p> 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. 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> field.</p>
<p>These style choices compute force field formulas that are consistent <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"> <div class="section" id="tip3p-water-model">
<span id="howto-7"></span><h2>6.7. TIP3P water model</h2> <span id="howto-7"></span><h2>6.7. TIP3P water model</h2>
<p>The TIP3P water model as implemented in CHARMM <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. 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 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 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">H charge = 0.4238</div>
<div class="line"><br /></div> <div class="line"><br /></div>
</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> 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> <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" /> <hr class="docutils" />
@ -2731,7 +2731,7 @@ pairs as chunks.</p>
model, representes induced dipoles by a pair of charges (the core atom model, representes induced dipoles by a pair of charges (the core atom
and the Drude particle) connected by a harmonic spring. The Drude and the Drude particle) connected by a harmonic spring. The Drude
model has a number of features aimed at its use in molecular systems 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"> <ul class="simple">
<li>Thermostating of the additional degrees of freedom associated with the <li>Thermostating of the additional degrees of freedom associated with the
induced dipoles at very low temperature, in terms of the reduced 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 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 similar from the CORESHELL package if the core and Drude particle come
too close, which can cause numerical issues.</p> 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> 6269-6271 (1987).</p>
<p id="cornell"><strong>(Cornell)</strong> Cornell, Cieplak, Bayly, Gould, Merz, Ferguson, <p id="cornell"><strong>(Cornell)</strong> Cornell, Cieplak, Bayly, Gould, Merz, Ferguson,
Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).</p> 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> J Chem Phys, 120, 9665 (2004).</p>
<p id="ikeshoji"><strong>(Ikeshoji)</strong> Ikeshoji and Hafskjold, Molecular Physics, 81, 251-261 <p id="ikeshoji"><strong>(Ikeshoji)</strong> Ikeshoji and Hafskjold, Molecular Physics, 81, 251-261
(1994).</p> (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> 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 <p id="mayo"><strong>(Mayo)</strong> Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
(1990).</p> (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="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, <p id="mitchellfinchham"><strong>(Mitchell and Finchham)</strong> Mitchell, Finchham, J Phys Condensed Matter,
5, 1031-1038 (1993).</p> 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>
</div> </div>

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@ -221,7 +221,7 @@ commands like :doc:`pair_coeff <pair_coeff>` or
for additional tools that can use CHARMM or AMBER to assign force for additional tools that can use CHARMM or AMBER to assign force
field coefficients and convert their output into LAMMPS input. 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. See :ref:`(Cornell) <Cornell>` for a description of the AMBER force
field. field.
@ -507,7 +507,7 @@ TIP3P water model
----------------- -----------------
The TIP3P water model as implemented in CHARMM 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. 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 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 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 | 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. the SPC and SPC/E models.
Wikipedia also has a nice article on `water models <http://en.wikipedia.org/wiki/Water_model>`_. 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 model, representes induced dipoles by a pair of charges (the core atom
and the Drude particle) connected by a harmonic spring. The Drude and the Drude particle) connected by a harmonic spring. The Drude
model has a number of features aimed at its use in molecular systems 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 * Thermostating of the additional degrees of freedom associated with the
induced dipoles at very low temperature, in terms of the reduced 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 **(Ikeshoji)** Ikeshoji and Hafskjold, Molecular Physics, 81, 251-261
(1994). (1994).
.. _MacKerell: .. _howto-MacKerell:
@ -3098,7 +3098,7 @@ Phys, 79, 926 (1983).
**(Mitchell and Finchham)** Mitchell, Finchham, J Phys Condensed Matter, **(Mitchell and Finchham)** Mitchell, Finchham, J Phys Condensed Matter,
5, 1031-1038 (1993). 5, 1031-1038 (1993).
.. _Lamoureux: .. _howto-Lamoureux:

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@ -33,7 +33,7 @@ The *fene* bond style uses the potential
:align: center :align: center
to define a finite extensible nonlinear elastic (FENE) potential 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 term is attractive, the 2nd Lennard-Jones term is repulsive. The
first term extends to R0, the maximum extent of the bond. The 2nd 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. term is cutoff at 2^(1/6) sigma, the minimum of the LJ potential.
@ -97,7 +97,7 @@ Related commands
---------- ----------
.. _Kremer: .. _fene-Kremer:

4
doc/html/_sources/compute_xrd.txt
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@ -52,7 +52,7 @@ Description
""""""""""" """""""""""
Define a computation that calculates x-ray diffraction intensity as described 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 by the entire simulation domain (or manually) using a simulated radiation
of wavelength lambda. of wavelength lambda.
@ -209,7 +209,7 @@ no manual flag, no echo flag.
---------- ----------
.. _Coleman: .. _xrd-Coleman:

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doc/html/_sources/dihedral_charmm.txt
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@ -35,10 +35,11 @@ The *charmm* dihedral style uses the potential
.. image:: Eqs/dihedral_charmm.jpg .. image:: Eqs/dihedral_charmm.jpg
:align: center :align: center
See :ref:`(MacKerell) <dihedral-MacKerell>` for a description of the CHARMM force See :ref:`(MacKerell) <dihedral-MacKerell>` for a description of the CHARMM
field. This dihedral style can also be used for the AMBER force field force field. This dihedral style can also be used for the AMBER force
(see comment on weighting factors below). See :ref:`(Cornell) <Cornell>` field (see comment on weighting factors below). See
for a description of the AMBER force field. :ref:`(Cornell) <dihedral-Cornell>` for a description of the AMBER force
field.
The following coefficients must be defined for each dihedral type via the 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 :doc:`dihedral_coeff <dihedral_coeff>` command as in the example above, or in
@ -121,7 +122,7 @@ Related commands
---------- ----------
.. _Cornell: .. _dihedral-Cornell:

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@ -122,12 +122,12 @@ particles will match the target values specified by Tstart/Tstop and
Pstart/Pstop. Pstart/Pstop.
The equations of motion used are those of Shinoda et al in The equations of motion used are those of Shinoda et al in
:ref:`(Shinoda) <Shinoda>`, which combine the hydrostatic equations of :ref:`(Shinoda) <nh-Shinoda>`, which combine the hydrostatic equations of
Martyna, Tobias and Klein in :ref:`(Martyna) <Martyna>` with the strain Martyna, Tobias and Klein in :ref:`(Martyna) <nh-Martyna>` with the strain
energy proposed by Parrinello and Rahman in 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 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 The *mtk* keyword controls whether or not the correction terms due to
Martyna, Tuckerman, and Klein are included in the equations of motion 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 Hoover barostat, whose volume probability distribution function
differs from the true NPT and NPH ensembles by a factor of 1/V. Hence 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 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 scheme at little extra cost. The initial and final updates of the
thermostat variables are broken up into *tloop* substeps, each of thermostat variables are broken up into *tloop* substeps, each of
length *dt*\ /\ *tloop*\ . This corresponds to using a first-order 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. does the same thing for the barostat thermostat.
The keyword *nreset* controls how often the reference dimensions used 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). **(Martyna)** Martyna, Tobias and Klein, J Chem Phys, 101, 4177 (1994).
.. _Parrinello: .. _nh-Parrinello:
**(Parrinello)** Parrinello and Rahman, J Appl Phys, 52, 7182 (1981). **(Parrinello)** Parrinello and Rahman, J Appl Phys, 52, 7182 (1981).
.. _Tuckerman: .. _nh-Tuckerman:
**(Tuckerman)** Tuckerman, Alejandre, Lopez-Rendon, Jochim, and **(Tuckerman)** Tuckerman, Alejandre, Lopez-Rendon, Jochim, and
Martyna, J Phys A: Math Gen, 39, 5629 (2006). Martyna, J Phys A: Math Gen, 39, 5629 (2006).
.. _Shinoda: .. _nh-Shinoda:

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@ -150,7 +150,7 @@
<p>The <em>fene</em> bond style uses the potential</p> <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" /> <img alt="_images/bond_fene.jpg" class="align-center" src="_images/bond_fene.jpg" />
<p>to define a finite extensible nonlinear elastic (FENE) potential <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 term is attractive, the 2nd Lennard-Jones term is repulsive. The
first term extends to R0, the maximum extent of the bond. The 2nd 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> 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><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> <p><strong>Default:</strong> none</p>
<hr class="docutils" /> <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>
</div> </div>

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@ -167,7 +167,7 @@
<div class="section" id="description"> <div class="section" id="description">
<h2>Description</h2> <h2>Description</h2>
<p>Define a computation that calculates x-ray diffraction intensity as described <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 by the entire simulation domain (or manually) using a simulated radiation
of wavelength lambda.</p> of wavelength lambda.</p>
<p>The x-ray diffraction intensity, I, at each reciprocal lattice point, k, <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, <p>The option defaults are 2Theta = 1 179 (degrees), c = 1 1 1, LP = 1,
no manual flag, no echo flag.</p> no manual flag, no echo flag.</p>
<hr class="docutils" /> <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> (2013).</p>
<p id="colliex"><strong>(Colliex)</strong> Colliex et al. International Tables for Crystallography <p id="colliex"><strong>(Colliex)</strong> Colliex et al. International Tables for Crystallography
Volume C: Mathematical and Chemical Tables, 249-429 (2004).</p> Volume C: Mathematical and Chemical Tables, 249-429 (2004).</p>

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@ -152,10 +152,11 @@
<h2>Description</h2> <h2>Description</h2>
<p>The <em>charmm</em> dihedral style uses the potential</p> <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" /> <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 <p>See <a class="reference internal" href="#dihedral-mackerell"><span class="std std-ref">(MacKerell)</span></a> for a description of the CHARMM
field. This dihedral style can also be used for the AMBER force field force field. This dihedral style can also be used for the AMBER force
(see comment on weighting factors below). See <a class="reference internal" href="special_bonds.html#cornell"><span class="std std-ref">(Cornell)</span></a> field (see comment on weighting factors below). See
for a description of the AMBER force field.</p> <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 <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 <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> 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><a class="reference internal" href="dihedral_coeff.html"><span class="doc">dihedral_coeff</span></a></p>
<p><strong>Default:</strong> none</p> <p><strong>Default:</strong> none</p>
<hr class="docutils" /> <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> Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).</p>
<p id="dihedral-mackerell"><strong>(MacKerell)</strong> MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field, <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> Fischer, Gao, Guo, Ha, et al, J Phys Chem B, 102, 3586 (1998).</p>

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@ -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 particles will match the target values specified by Tstart/Tstop and
Pstart/Pstop.</p> Pstart/Pstop.</p>
<p>The equations of motion used are those of Shinoda et al in <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 <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="fix_rigid.html#martyna"><span class="std std-ref">(Martyna)</span></a> with the strain 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 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 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" /> <hr class="docutils" />
<p>The thermostat parameters for fix styles <em>nvt</em> and <em>npt</em> is specified <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 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> barostat variables.</p>
<p>The <em>mtk</em> keyword controls whether or not the correction terms due to <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 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 Hoover barostat, whose volume probability distribution function
differs from the true NPT and NPH ensembles by a factor of 1/V. Hence 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 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 scheme at little extra cost. The initial and final updates of the
thermostat variables are broken up into <em>tloop</em> substeps, each of 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 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> does the same thing for the barostat thermostat.</p>
<p>The keyword <em>nreset</em> controls how often the reference dimensions used <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, 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 scaleyz = scalexz = scalexy = yes if periodic in 2nd dimension and
not coupled to barostat, otherwise no.</p> not coupled to barostat, otherwise no.</p>
<hr class="docutils" /> <hr class="docutils" />
<p id="martyna"><strong>(Martyna)</strong> Martyna, Tobias and Klein, J Chem Phys, 101, 4177 (1994).</p> <p id="nh-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="nh-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-tuckerman"><strong>(Tuckerman)</strong> Tuckerman, Alejandre, Lopez-Rendon, Jochim, and
Martyna, J Phys A: Math Gen, 39, 5629 (2006).</p> 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> <p id="nh-shinoda"><strong>(Shinoda)</strong> Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).</p>
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