lijiext
/
lammps
mirror of https://github.com/lammps/lammps.git
1
0
Fork 1
Code Issues Packages Projects Releases Wiki Activity

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14985 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2016-05-10 14:52:43 +00:00
parent df885d59ff
commit e8fe19dc71
29 changed files with 66 additions and 66 deletions

4
doc/html/_sources/angle_charmm.txt
View File

@ -39,7 +39,7 @@ with an additional Urey_Bradley term based on the distance *r* between
the 1st and 3rd atoms in the angle. K, theta0, Kub, and Rub are
coefficients defined for each angle type.
See :ref:`(MacKerell) <MacKerell>` for a description of the CHARMM force
See :ref:`(MacKerell) <angle-MacKerell>` for a description of the CHARMM force
field.
The following coefficients must be defined for each angle type via the
@ -100,7 +100,7 @@ Related commands
----------
.. _MacKerell:
.. _angle-MacKerell:

4
doc/html/_sources/angle_class2.txt
View File

@ -35,7 +35,7 @@ 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.
See :ref:`(Sun) <Sun>` for a description of the COMPASS class2 force field.
See :ref:`(Sun) <angle-Sun>` for a description of the COMPASS class2 force field.
Coefficients for the Ea, Ebb, and Eba formulas must be defined for
each angle type via the :doc:`angle_coeff <angle_coeff>` command as in
@ -127,7 +127,7 @@ Related commands
----------
.. _Sun:
.. _angle-Sun:

4
doc/html/_sources/angle_cosine_periodic.txt
View File

@ -35,7 +35,7 @@ trigonal center:
where C, B and n are coefficients defined for each angle type.
See :ref:`(Mayo) <Mayo>` for a description of the DREIDING force field
See :ref:`(Mayo) <cosine-Mayo>` for a description of the DREIDING force field
The following coefficients must be defined for each angle type via the
:doc:`angle_coeff <angle_coeff>` command as in the example above, or in
@ -96,7 +96,7 @@ Related commands
----------
.. _Mayo:
.. _cosine-Mayo:

4
doc/html/_sources/bond_class2.txt
View File

@ -31,7 +31,7 @@ The *class2* bond style uses the potential
where r0 is the equilibrium bond distance.
See :ref:`(Sun) <Sun>` for a description of the COMPASS class2 force field.
See :ref:`(Sun) <bond-Sun>` for a description of the COMPASS class2 force field.
The following coefficients must be defined for each bond type via the
:doc:`bond_coeff <bond_coeff>` command as in the example above, or in
@ -89,7 +89,7 @@ Related commands
----------
.. _Sun:
.. _bond-Sun:

4
doc/html/_sources/bond_fene_expand.txt
View File

@ -30,7 +30,7 @@ The *fene/expand* 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) <feneexpand-Kremer>`, used for bead-spring polymer models. The first
term is attractive, the 2nd Lennard-Jones term is repulsive.
The *fene/expand* bond style is similar to *fene* except that an extra
@ -99,7 +99,7 @@ Related commands
----------
.. _Kremer:
.. _feneexpand-Kremer:

4
doc/html/_sources/compute_saed.txt
View File

@ -51,7 +51,7 @@ Description
"""""""""""
Define a computation that calculates electron diffraction intensity as
described in :ref:`(Coleman) <Coleman>` on a mesh of reciprocal lattice nodes
described in :ref:`(Coleman) <saed-Coleman>` on a mesh of reciprocal lattice nodes
defined by the entire simulation domain (or manually) using simulated
radiation of wavelength lambda.
@ -184,7 +184,7 @@ The option defaults are Kmax = 1.70, Zone 1 0 0, c 1 1 1, dR_Ewald =
----------
.. _Coleman:
.. _saed-Coleman:

4
doc/html/_sources/dihedral_charmm.txt
View File

@ -35,7 +35,7 @@ The *charmm* dihedral style uses the potential
.. image:: Eqs/dihedral_charmm.jpg
:align: center
See :ref:`(MacKerell) <MacKerell>` for a description of the CHARMM force
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.
@ -128,7 +128,7 @@ Related commands
**(Cornell)** Cornell, Cieplak, Bayly, Gould, Merz, Ferguson,
Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).
.. _MacKerell:
.. _dihedral-MacKerell:

4
doc/html/_sources/dihedral_class2.txt
View File

@ -41,7 +41,7 @@ is an angle-angle-torsion term, and Ebb13 is a bond-bond-13 term.
Theta1 and theta2 are equilibrium angles and r1 r2 r3 are equilibrium
bond lengths.
See :ref:`(Sun) <Sun>` for a description of the COMPASS class2 force field.
See :ref:`(Sun) <dihedral-Sun>` for a description of the COMPASS class2 force field.
Coefficients for the Ed, Embt, Eebt, Eat, Eaat, and Ebb13 formulas
must be defined for each dihedral type via the
@ -186,7 +186,7 @@ Related commands
----------
.. _Sun:
.. _dihedral-Sun:

12
doc/html/_sources/fix_lb_fluid.txt
View File

@ -109,7 +109,7 @@ functions,
:align: center
Full details of the lattice-Boltzmann algorithm used can be found in
:ref:`Mackay et al. <Mackay>`.
:ref:`Mackay et al. <fluid-Mackay>`.
The fluid is coupled to the MD particles described by *group-ID*
through a velocity dependent force. The contribution to the fluid
@ -150,7 +150,7 @@ using the *setArea* keyword.
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 *setGamma* keyword. This may be useful
when modelling porous particles. See :ref:`Mackay et al. <Mackay>` for a
when modelling porous particles. See :ref:`Mackay et al. <fluid-Mackay>` for a
detailed description of the method by which the user can choose an
appropriate gamma value.
@ -165,7 +165,7 @@ appropriate gamma value.
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
:ref:`Mackay et al. <Mackay>`, the built-in LAMMPS integrators may prove to
:ref:`Mackay et al. <fluid-Mackay>`, the built-in LAMMPS integrators may prove to
be unstable. Therefore, we have included our own integrators :doc:`fix lb/rigid/pc/sphere <fix_lb_rigid_pc_sphere>`, and :doc:`fix lb/pc <fix_lb_pc>`, to solve for the particle motion in these
cases. These integrators should not be used with the
:doc:`lb/viscous <fix_lb_viscous>` fix, as they add hydrodynamic forces
@ -266,7 +266,7 @@ N timesteps.
If the keyword *trilinear* 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 :ref:`Mackay et al. <Mackay>`.
interpolation methods are described in :ref:`Mackay et al. <Mfluid-ackay>`.
If the keyword *D3Q19* is used, the 19 velocity (D3Q19) lattice is
used by the lattice-Boltzmann algorithm. By default, the 15 velocity
@ -306,7 +306,7 @@ screen every N timesteps.
For further details, as well as descriptions and results of several
test runs, see :ref:`Mackay et al. <Mackay>`. Please include a citation to
test runs, see :ref:`Mackay et al. <fluid-Mackay>`. Please include a citation to
this paper if the lb_fluid fix is used in work contributing to
published research.
@ -386,7 +386,7 @@ If walls are present, they are assumed to be stationary.
**(Ollila et al.)** Ollila, S.T.T., Denniston, C., Karttunen, M., and Ala-Nissila, T., Fluctuating lattice-Boltzmann model for complex fluids, J. Chem. Phys. 134 (2011) 064902.
.. _Mackay:
.. _fluid-Mackay:

4
doc/html/_sources/fix_pimd.txt
View File

@ -55,7 +55,7 @@ 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 :ref:`(Tuckerman) <Tuckerman>`. With the
chain thermostat is applied :ref:`(Tuckerman) <pimd-Tuckerman>`. With the
massive chain algorithm, a chain of NH thermostats is coupled to each
degree of freedom for each quasi-bead. The keyword *temp* sets the
target temperature for the system and the keyword *nhc* sets the
@ -184,7 +184,7 @@ and nhc = 2.
**(Feynman)** R. Feynman and A. Hibbs, Chapter 7, Quantum Mechanics and
Path Integrals, McGraw-Hill, New York (1965).
.. _Tuckerman:
.. _pimd-Tuckerman:

4
doc/html/_sources/improper_class2.txt
View File

@ -52,7 +52,7 @@ 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.
See :ref:`(Sun) <Sun>` for a description of the COMPASS class2 force field.
See :ref:`(Sun) <improper-Sun>` for a description of the COMPASS class2 force field.
Coefficients for the Ei and Eaa formulas must be defined for each
improper type via the :doc:`improper_coeff <improper_coeff>` command as
@ -132,7 +132,7 @@ Related commands
----------
.. _Sun:
.. _improper-Sun:

4
doc/html/_sources/improper_umbrella.txt
View File

@ -41,7 +41,7 @@ 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.
See :ref:`(Mayo) <Mayo>` for a description of the DREIDING force field.
See :ref:`(Mayo) <umbrella-Mayo>` for a description of the DREIDING force field.
The following coefficients must be defined for each improper type via
the :doc:`improper_coeff <improper_coeff>` command as in the example
@ -97,7 +97,7 @@ Related commands
----------
.. _Mayo:
.. _umbrella-Mayo:

4
doc/html/_sources/pair_charmm.txt
View File

@ -105,7 +105,7 @@ The *lj/charmm* styles compute LJ and Coulombic interactions with an
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 `CHARMM <http://www.scripps.edu/brooks>`_ MD code.
See :ref:`(MacKerell) <MacKerell>` for a description of the CHARMM force
See :ref:`(MacKerell) <pair-MacKerell>` for a description of the CHARMM force
field.
.. image:: Eqs/pair_charmm.jpg
@ -239,7 +239,7 @@ Related commands
----------
.. _MacKerell:
.. _pair-MacKerell:

4
doc/html/_sources/pair_class2.txt
View File

@ -100,7 +100,7 @@ Rc is the cutoff.
The *lj/class2/coul/cut* and *lj/class2/coul/long* styles add a
Coulombic term as described for the :doc:`lj/cut <pair_lj>` pair styles.
See :ref:`(Sun) <Sun>` for a description of the COMPASS class2 force field.
See :ref:`(Sun) <pair-Sun>` for a description of the COMPASS class2 force field.
The following coefficients must be defined for each pair of atoms
types via the :doc:`pair_coeff <pair_coeff>` command as in the examples
@ -211,7 +211,7 @@ Related commands
----------
.. _Sun:
.. _pair-Sun:

4
doc/html/_sources/pair_hbond_dreiding.txt
View File

@ -69,7 +69,7 @@ hydrogen atoms for each donor/acceptor type pair are specified by the
:doc:`pair_coeff <pair_coeff>` command (see below).
Style *hbond/dreiding/lj* is the original DREIDING potential of
:ref:`(Mayo) <Mayo>`. It uses a LJ 12/10 functional for the Donor-Acceptor
:ref:`(Mayo) <pair-Mayo>`. It uses a LJ 12/10 functional for the Donor-Acceptor
interactions. To match the results in the original paper, use n = 4.
Style *hbond/dreiding/morse* is an improved version using a Morse
@ -266,7 +266,7 @@ Related commands
----------
.. _Mayo:
.. _pair-Mayo:

4
doc/html/angle_charmm.html
View File

@ -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="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="#angle-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
@ -197,7 +197,7 @@ MOLECULE package (which it is by default). See the <a class="reference internal
<p><a class="reference internal" href="angle_coeff.html"><span class="doc">angle_coeff</span></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="mackerell"><strong>(MacKerell)</strong> MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
<p id="angle-mackerell"><strong>(MacKerell)</strong> MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).</p>
</div>
</div>

4
doc/html/angle_class2.html
View File

@ -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_modify.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="#angle-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
@ -222,7 +222,7 @@ for more info on packages.</p>
<p><a class="reference internal" href="angle_coeff.html"><span class="doc">angle_coeff</span></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="sun"><strong>(Sun)</strong> Sun, J Phys Chem B 102, 7338-7364 (1998).</p>
<p id="angle-sun"><strong>(Sun)</strong> Sun, J Phys Chem B 102, 7338-7364 (1998).</p>
</div>
</div>

4
doc/html/angle_cosine_periodic.html
View File

@ -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="special_bonds.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="#cosine-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>
@ -193,7 +193,7 @@ MOLECULE package (which it is by default). See the <a class="reference internal
<p><a class="reference internal" href="angle_coeff.html"><span class="doc">angle_coeff</span></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="mayo"><strong>(Mayo)</strong> Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
<p id="cosine-mayo"><strong>(Mayo)</strong> Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
(1990).</p>
</div>
</div>

4
doc/html/bond_class2.html
View File

@ -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_modify.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="#bond-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>
@ -187,7 +187,7 @@ for more info on packages.</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="sun"><strong>(Sun)</strong> Sun, J Phys Chem B 102, 7338-7364 (1998).</p>
<p id="bond-sun"><strong>(Sun)</strong> Sun, J Phys Chem B 102, 7338-7364 (1998).</p>
</div>
</div>

4
doc/html/bond_fene_expand.html
View File

@ -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="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="#feneexpand-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
@ -196,7 +196,7 @@ 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="feneexpand-kremer"><strong>(Kremer)</strong> Kremer, Grest, J Chem Phys, 92, 5057 (1990).</p>
</div>
</div>

4
doc/html/compute_saed.html
View File

@ -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="fix_saed_vtk.html#coleman"><span class="std std-ref">(Coleman)</span></a> on a mesh of reciprocal lattice nodes
described in <a class="reference internal" href="#saed-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
@ -293,7 +293,7 @@ enabled if LAMMPS was built with that package. See the <a class="reference inte
<p>The option defaults are Kmax = 1.70, Zone 1 0 0, c 1 1 1, dR_Ewald =
0.01.</p>
<hr class="docutils" />
<p id="coleman"><strong>(Coleman)</strong> Coleman, Spearot, Capolungo, MSMSE, 21, 055020
<p id="saed-coleman"><strong>(Coleman)</strong> Coleman, Spearot, Capolungo, MSMSE, 21, 055020
(2013).</p>
<p id="brown"><strong>(Brown)</strong> Brown et al. International Tables for Crystallography
Volume C: Mathematical and Chemical Tables, 554-95 (2004).</p>

4
doc/html/dihedral_charmm.html
View File

@ -152,7 +152,7 @@
<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="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="#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>
@ -219,7 +219,7 @@ MOLECULE package (which it is by default). See the <a class="reference internal
<hr class="docutils" />
<p id="cornell"><strong>(Cornell)</strong> Cornell, Cieplak, Bayly, Gould, Merz, Ferguson,
Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).</p>
<p id="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>
</div>
</div>

4
doc/html/dihedral_class2.html
View File

@ -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_modify.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="#dihedral-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,
@ -280,7 +280,7 @@ section for more info on packages.</p>
<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="sun"><strong>(Sun)</strong> Sun, J Phys Chem B 102, 7338-7364 (1998).</p>
<p id="dihedral-sun"><strong>(Sun)</strong> Sun, J Phys Chem B 102, 7338-7364 (1998).</p>
</div>
</div>

12
doc/html/fix_lb_fluid.html
View File

@ -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="fix_lb_viscous.html#mackay"><span class="std std-ref">Mackay et al.</span></a>.</p>
<a class="reference internal" href="#fluid-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="fix_lb_viscous.html#mackay"><span class="std std-ref">Mackay et al.</span></a> for a
when modelling porous particles. See <a class="reference internal" href="#fluid-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="fix_lb_viscous.html#mackay"><span class="std std-ref">Mackay et al.</span></a>, the built-in LAMMPS integrators may prove to
<a class="reference internal" href="#fluid-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="fix_lb_viscous.html#mackay"><span class="std std-ref">Mackay et al.</span></a>.</p>
interpolation methods are described in <span class="xref std std-ref">Mackay et al.</span>.</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="fix_lb_viscous.html#mackay"><span class="std std-ref">Mackay et al.</span></a>. Please include a citation to
test runs, see <a class="reference internal" href="#fluid-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>
@ -426,7 +426,7 @@ The D3Q15 lattice is used for the lattice-Boltzmann algorithm.
If walls are present, they are assumed to be stationary.</p>
<hr class="docutils" />
<p id="ollila"><strong>(Ollila et al.)</strong> Ollila, S.T.T., Denniston, C., Karttunen, M., and Ala-Nissila, T., Fluctuating lattice-Boltzmann model for complex fluids, J. Chem. Phys. 134 (2011) 064902.</p>
<p id="mackay"><strong>(Mackay et al.)</strong> Mackay, F. E., Ollila, S.T.T., and Denniston, C., Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid, Computer Physics Communications 184 (2013) 2021-2031.</p>
<p id="fluid-mackay"><strong>(Mackay et al.)</strong> Mackay, F. E., Ollila, S.T.T., and Denniston, C., Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid, Computer Physics Communications 184 (2013) 2021-2031.</p>
<p id="mackay2"><strong>(Mackay and Denniston)</strong> Mackay, F. E., and Denniston, C., Coupling MD particles to a lattice-Boltzmann fluid through the use of conservative forces, J. Comput. Phys. 237 (2013) 289-298.</p>
<p id="adhikari"><strong>(Adhikari et al.)</strong> Adhikari, R., Stratford, K., Cates, M. E., and Wagner, A. J., Fluctuating lattice Boltzmann, Europhys. Lett. 71 (2005) 473-479.</p>
</div>

4
doc/html/improper_class2.html
View File

@ -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_modify.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="#improper-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
@ -224,7 +224,7 @@ section for more info on packages.</p>
<p><a class="reference internal" href="improper_coeff.html"><span class="doc">improper_coeff</span></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="sun"><strong>(Sun)</strong> Sun, J Phys Chem B 102, 7338-7364 (1998).</p>
<p id="improper-sun"><strong>(Sun)</strong> Sun, J Phys Chem B 102, 7338-7364 (1998).</p>
</div>
</div>

4
doc/html/improper_umbrella.html
View File

@ -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="special_bonds.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="#umbrella-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
@ -192,7 +192,7 @@ MOLECULE package (which it is by default). See the <a class="reference internal
<p><a class="reference internal" href="improper_coeff.html"><span class="doc">improper_coeff</span></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="mayo"><strong>(Mayo)</strong> Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
<p id="umbrella-mayo"><strong>(Mayo)</strong> Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
(1990),</p>
</div>
</div>

4
doc/html/pair_charmm.html
View File

@ -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="special_bonds.html#mackerell"><span class="std std-ref">(MacKerell)</span></a> for a description of the CHARMM force
See <a class="reference internal" href="#pair-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.
@ -321,7 +321,7 @@ the MOLECULE and KSPACE packages are installed by default.</p>
<p><a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="mackerell"><strong>(MacKerell)</strong> MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
<p id="pair-mackerell"><strong>(MacKerell)</strong> MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).</p>
</div>
</div>

4
doc/html/pair_class2.html
View File

@ -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="pair_modify.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-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
@ -293,7 +293,7 @@ LAMMPS was built with that package. See the <a class="reference internal" href=
<p><a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="sun"><strong>(Sun)</strong> Sun, J Phys Chem B 102, 7338-7364 (1998).</p>
<p id="pair-sun"><strong>(Sun)</strong> Sun, J Phys Chem B 102, 7338-7364 (1998).</p>
</div>
</div>

4
doc/html/pair_hbond_dreiding.html
View File

@ -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="special_bonds.html#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="#pair-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
@ -339,7 +339,7 @@ heading) the following commands could be included in an input script:</p>
<p><a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="mayo"><strong>(Mayo)</strong> Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
<p id="pair-mayo"><strong>(Mayo)</strong> Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
(1990).</p>
<p id="liu"><strong>(Liu)</strong> Liu, Bryantsev, Diallo, Goddard III, J. Am. Chem. Soc 131 (8)
2798 (2009)</p>