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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>
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>

14
doc/html/_sources/Section_howto.txt
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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
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:

4
doc/html/_sources/bond_fene.txt
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@ -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:

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
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:

11
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
: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:

20
doc/html/_sources/fix_nh.txt
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@ -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:

4
doc/html/bond_fene.html
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@ -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>

4
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@ -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>

11
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@ -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>

20
doc/html/fix_nh.html
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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
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>
<p id="nh-shinoda"><strong>(Shinoda)</strong> Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).</p>
</div>
</div>