From e8fe19dc71295cc9232d867580cfa53188d17573 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Tue, 10 May 2016 14:52:43 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14985 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/html/_sources/angle_charmm.txt | 4 ++-- doc/html/_sources/angle_class2.txt | 4 ++-- doc/html/_sources/angle_cosine_periodic.txt | 4 ++-- doc/html/_sources/bond_class2.txt | 4 ++-- doc/html/_sources/bond_fene_expand.txt | 4 ++-- doc/html/_sources/compute_saed.txt | 4 ++-- doc/html/_sources/dihedral_charmm.txt | 4 ++-- doc/html/_sources/dihedral_class2.txt | 4 ++-- doc/html/_sources/fix_lb_fluid.txt | 12 ++++++------ doc/html/_sources/fix_pimd.txt | 4 ++-- doc/html/_sources/improper_class2.txt | 4 ++-- doc/html/_sources/improper_umbrella.txt | 4 ++-- doc/html/_sources/pair_charmm.txt | 4 ++-- doc/html/_sources/pair_class2.txt | 4 ++-- doc/html/_sources/pair_hbond_dreiding.txt | 4 ++-- doc/html/angle_charmm.html | 4 ++-- doc/html/angle_class2.html | 4 ++-- doc/html/angle_cosine_periodic.html | 4 ++-- doc/html/bond_class2.html | 4 ++-- doc/html/bond_fene_expand.html | 4 ++-- doc/html/compute_saed.html | 4 ++-- doc/html/dihedral_charmm.html | 4 ++-- doc/html/dihedral_class2.html | 4 ++-- doc/html/fix_lb_fluid.html | 12 ++++++------ doc/html/improper_class2.html | 4 ++-- doc/html/improper_umbrella.html | 4 ++-- doc/html/pair_charmm.html | 4 ++-- doc/html/pair_class2.html | 4 ++-- doc/html/pair_hbond_dreiding.html | 4 ++-- 29 files changed, 66 insertions(+), 66 deletions(-) diff --git a/doc/html/_sources/angle_charmm.txt b/doc/html/_sources/angle_charmm.txt index 99228eda1b..ddfbd823e0 100644 --- a/doc/html/_sources/angle_charmm.txt +++ b/doc/html/_sources/angle_charmm.txt @@ -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) ` for a description of the CHARMM force +See :ref:`(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: diff --git a/doc/html/_sources/angle_class2.txt b/doc/html/_sources/angle_class2.txt index f1d1dd2ba0..78894f0597 100644 --- a/doc/html/_sources/angle_class2.txt +++ b/doc/html/_sources/angle_class2.txt @@ -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) ` for a description of the COMPASS class2 force field. +See :ref:`(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 ` command as in @@ -127,7 +127,7 @@ Related commands ---------- -.. _Sun: +.. _angle-Sun: diff --git a/doc/html/_sources/angle_cosine_periodic.txt b/doc/html/_sources/angle_cosine_periodic.txt index a35ffda20a..ac5637f8b1 100644 --- a/doc/html/_sources/angle_cosine_periodic.txt +++ b/doc/html/_sources/angle_cosine_periodic.txt @@ -35,7 +35,7 @@ trigonal center: where C, B and n are coefficients defined for each angle type. -See :ref:`(Mayo) ` for a description of the DREIDING force field +See :ref:`(Mayo) ` for a description of the DREIDING force field The following coefficients must be defined for each angle type via the :doc:`angle_coeff ` command as in the example above, or in @@ -96,7 +96,7 @@ Related commands ---------- -.. _Mayo: +.. _cosine-Mayo: diff --git a/doc/html/_sources/bond_class2.txt b/doc/html/_sources/bond_class2.txt index 839370434c..250b057f11 100644 --- a/doc/html/_sources/bond_class2.txt +++ b/doc/html/_sources/bond_class2.txt @@ -31,7 +31,7 @@ The *class2* bond style uses the potential where r0 is the equilibrium bond distance. -See :ref:`(Sun) ` for a description of the COMPASS class2 force field. +See :ref:`(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 ` command as in the example above, or in @@ -89,7 +89,7 @@ Related commands ---------- -.. _Sun: +.. _bond-Sun: diff --git a/doc/html/_sources/bond_fene_expand.txt b/doc/html/_sources/bond_fene_expand.txt index df8e6c6b34..e34fb71635 100644 --- a/doc/html/_sources/bond_fene_expand.txt +++ b/doc/html/_sources/bond_fene_expand.txt @@ -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) `, used for bead-spring polymer models. The first +:ref:`(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: diff --git a/doc/html/_sources/compute_saed.txt b/doc/html/_sources/compute_saed.txt index c0bd62d420..a0ceacbe62 100644 --- a/doc/html/_sources/compute_saed.txt +++ b/doc/html/_sources/compute_saed.txt @@ -51,7 +51,7 @@ Description """"""""""" Define a computation that calculates electron diffraction intensity as -described in :ref:`(Coleman) ` on a mesh of reciprocal lattice nodes +described in :ref:`(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: diff --git a/doc/html/_sources/dihedral_charmm.txt b/doc/html/_sources/dihedral_charmm.txt index 48049088eb..11cd781d93 100644 --- a/doc/html/_sources/dihedral_charmm.txt +++ b/doc/html/_sources/dihedral_charmm.txt @@ -35,7 +35,7 @@ The *charmm* dihedral style uses the potential .. image:: Eqs/dihedral_charmm.jpg :align: center -See :ref:`(MacKerell) ` for a description of the CHARMM force +See :ref:`(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) ` 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: diff --git a/doc/html/_sources/dihedral_class2.txt b/doc/html/_sources/dihedral_class2.txt index ae43594f11..ad8c5724f0 100644 --- a/doc/html/_sources/dihedral_class2.txt +++ b/doc/html/_sources/dihedral_class2.txt @@ -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) ` for a description of the COMPASS class2 force field. +See :ref:`(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: diff --git a/doc/html/_sources/fix_lb_fluid.txt b/doc/html/_sources/fix_lb_fluid.txt index ea8f4ab68e..5b1a899b25 100644 --- a/doc/html/_sources/fix_lb_fluid.txt +++ b/doc/html/_sources/fix_lb_fluid.txt @@ -109,7 +109,7 @@ functions, :align: center Full details of the lattice-Boltzmann algorithm used can be found in -:ref:`Mackay et al. `. +:ref:`Mackay et al. `. 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. ` for a +when modelling porous particles. See :ref:`Mackay et al. ` 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. `, the built-in LAMMPS integrators may prove to + :ref:`Mackay et al. `, the built-in LAMMPS integrators may prove to be unstable. Therefore, we have included our own integrators :doc:`fix lb/rigid/pc/sphere `, and :doc:`fix lb/pc `, to solve for the particle motion in these cases. These integrators should not be used with the :doc:`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. `. +interpolation methods are described in :ref:`Mackay et al. `. 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. `. Please include a citation to +test runs, see :ref:`Mackay et al. `. 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: diff --git a/doc/html/_sources/fix_pimd.txt b/doc/html/_sources/fix_pimd.txt index 4b3bc718bd..7bc5d4dde4 100644 --- a/doc/html/_sources/fix_pimd.txt +++ b/doc/html/_sources/fix_pimd.txt @@ -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) `. With the +chain thermostat is applied :ref:`(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: diff --git a/doc/html/_sources/improper_class2.txt b/doc/html/_sources/improper_class2.txt index d9f7b1b054..6f77d17fcf 100644 --- a/doc/html/_sources/improper_class2.txt +++ b/doc/html/_sources/improper_class2.txt @@ -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) ` for a description of the COMPASS class2 force field. +See :ref:`(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 ` command as @@ -132,7 +132,7 @@ Related commands ---------- -.. _Sun: +.. _improper-Sun: diff --git a/doc/html/_sources/improper_umbrella.txt b/doc/html/_sources/improper_umbrella.txt index 50d7cb87ec..51cb8b492a 100644 --- a/doc/html/_sources/improper_umbrella.txt +++ b/doc/html/_sources/improper_umbrella.txt @@ -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) ` for a description of the DREIDING force field. +See :ref:`(Mayo) ` for a description of the DREIDING force field. The following coefficients must be defined for each improper type via the :doc:`improper_coeff ` command as in the example @@ -97,7 +97,7 @@ Related commands ---------- -.. _Mayo: +.. _umbrella-Mayo: diff --git a/doc/html/_sources/pair_charmm.txt b/doc/html/_sources/pair_charmm.txt index 639776f1b0..294ec5038c 100644 --- a/doc/html/_sources/pair_charmm.txt +++ b/doc/html/_sources/pair_charmm.txt @@ -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 `_ MD code. -See :ref:`(MacKerell) ` for a description of the CHARMM force +See :ref:`(MacKerell) ` for a description of the CHARMM force field. .. image:: Eqs/pair_charmm.jpg @@ -239,7 +239,7 @@ Related commands ---------- -.. _MacKerell: +.. _pair-MacKerell: diff --git a/doc/html/_sources/pair_class2.txt b/doc/html/_sources/pair_class2.txt index a4b46ef415..f96ee59881 100644 --- a/doc/html/_sources/pair_class2.txt +++ b/doc/html/_sources/pair_class2.txt @@ -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 styles. -See :ref:`(Sun) ` for a description of the COMPASS class2 force field. +See :ref:`(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 ` command as in the examples @@ -211,7 +211,7 @@ Related commands ---------- -.. _Sun: +.. _pair-Sun: diff --git a/doc/html/_sources/pair_hbond_dreiding.txt b/doc/html/_sources/pair_hbond_dreiding.txt index 5197b71591..7758b480eb 100644 --- a/doc/html/_sources/pair_hbond_dreiding.txt +++ b/doc/html/_sources/pair_hbond_dreiding.txt @@ -69,7 +69,7 @@ hydrogen atoms for each donor/acceptor type pair are specified by the :doc:`pair_coeff ` command (see below). Style *hbond/dreiding/lj* is the original DREIDING potential of -:ref:`(Mayo) `. It uses a LJ 12/10 functional for the Donor-Acceptor +:ref:`(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: diff --git a/doc/html/angle_charmm.html b/doc/html/angle_charmm.html index 17487df462..b0ce5e4e43 100644 --- a/doc/html/angle_charmm.html +++ b/doc/html/angle_charmm.html @@ -155,7 +155,7 @@

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 (MacKerell) for a description of the CHARMM force +

See (MacKerell) for a description of the CHARMM force field.

The following coefficients must be defined for each angle type via the angle_coeff command as in the example above, or in @@ -197,7 +197,7 @@ MOLECULE package (which it is by default). See the angle_coeff

Default: none

-

(MacKerell) MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field, +

(MacKerell) MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field, Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).

diff --git a/doc/html/angle_class2.html b/doc/html/angle_class2.html index 9c5073c4b5..2fdf1a1e11 100644 --- a/doc/html/angle_class2.html +++ b/doc/html/angle_class2.html @@ -151,7 +151,7 @@

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 (Sun) for a description of the COMPASS class2 force field.

+

See (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 angle_coeff 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.

angle_coeff

Default: none

-

(Sun) Sun, J Phys Chem B 102, 7338-7364 (1998).

+

(Sun) Sun, J Phys Chem B 102, 7338-7364 (1998).

diff --git a/doc/html/angle_cosine_periodic.html b/doc/html/angle_cosine_periodic.html index 8fb86c916a..bf2cfe324b 100644 --- a/doc/html/angle_cosine_periodic.html +++ b/doc/html/angle_cosine_periodic.html @@ -151,7 +151,7 @@ used for an octahedral complex and n = 3 might be used for a trigonal center:

_images/angle_cosine_periodic.jpg

where C, B and n are coefficients defined for each angle type.

-

See (Mayo) for a description of the DREIDING force field

+

See (Mayo) for a description of the DREIDING force field

The following coefficients must be defined for each angle type via the angle_coeff command as in the example above, or in the data file or restart files read by the read_data @@ -193,7 +193,7 @@ MOLECULE package (which it is by default). See the angle_coeff

Default: none

-

(Mayo) Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909 +

(Mayo) Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909 (1990).

diff --git a/doc/html/bond_class2.html b/doc/html/bond_class2.html index 696c3d1c22..73540afcde 100644 --- a/doc/html/bond_class2.html +++ b/doc/html/bond_class2.html @@ -147,7 +147,7 @@

The class2 bond style uses the potential

_images/bond_class2.jpg

where r0 is the equilibrium bond distance.

-

See (Sun) for a description of the COMPASS class2 force field.

+

See (Sun) for a description of the COMPASS class2 force field.

The following coefficients must be defined for each bond type via the bond_coeff command as in the example above, or in the data file or restart files read by the read_data @@ -187,7 +187,7 @@ for more info on packages.

bond_coeff, delete_bonds

Default: none

-

(Sun) Sun, J Phys Chem B 102, 7338-7364 (1998).

+

(Sun) Sun, J Phys Chem B 102, 7338-7364 (1998).

diff --git a/doc/html/bond_fene_expand.html b/doc/html/bond_fene_expand.html index d0d7bdcfd5..c634b02940 100644 --- a/doc/html/bond_fene_expand.html +++ b/doc/html/bond_fene_expand.html @@ -147,7 +147,7 @@

The fene/expand bond style uses the potential

_images/bond_fene_expand.jpg

to define a finite extensible nonlinear elastic (FENE) potential -(Kremer), used for bead-spring polymer models. The first +(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 shift factor of delta (positive or negative) is added to r to @@ -196,7 +196,7 @@ style. LAMMPS will issue a warning it that’s not the case.

bond_coeff, delete_bonds

Default: none

-

(Kremer) Kremer, Grest, J Chem Phys, 92, 5057 (1990).

+

(Kremer) Kremer, Grest, J Chem Phys, 92, 5057 (1990).

diff --git a/doc/html/compute_saed.html b/doc/html/compute_saed.html index 2f88ae8f11..5a40350a0d 100644 --- a/doc/html/compute_saed.html +++ b/doc/html/compute_saed.html @@ -169,7 +169,7 @@

Description

Define a computation that calculates electron diffraction intensity as -described in (Coleman) on a mesh of reciprocal lattice nodes +described in (Coleman) on a mesh of reciprocal lattice nodes defined by the entire simulation domain (or manually) using simulated radiation of wavelength lambda.

The electron diffraction intensity I at each reciprocal lattice point @@ -293,7 +293,7 @@ enabled if LAMMPS was built with that package. See the -

(Coleman) Coleman, Spearot, Capolungo, MSMSE, 21, 055020 +

(Coleman) Coleman, Spearot, Capolungo, MSMSE, 21, 055020 (2013).

(Brown) Brown et al. International Tables for Crystallography Volume C: Mathematical and Chemical Tables, 554-95 (2004).

diff --git a/doc/html/dihedral_charmm.html b/doc/html/dihedral_charmm.html index 629d2161b3..ab802a304d 100644 --- a/doc/html/dihedral_charmm.html +++ b/doc/html/dihedral_charmm.html @@ -152,7 +152,7 @@

Description

The charmm dihedral style uses the potential

_images/dihedral_charmm.jpg -

See (MacKerell) for a description of the CHARMM force +

See (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 (Cornell) for a description of the AMBER force field.

@@ -219,7 +219,7 @@ MOLECULE package (which it is by default). See the

(Cornell) Cornell, Cieplak, Bayly, Gould, Merz, Ferguson, Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).

-

(MacKerell) MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field, +

(MacKerell) MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field, Fischer, Gao, Guo, Ha, et al, J Phys Chem B, 102, 3586 (1998).

diff --git a/doc/html/dihedral_class2.html b/doc/html/dihedral_class2.html index 931013ddec..6a4bd55c5c 100644 --- a/doc/html/dihedral_class2.html +++ b/doc/html/dihedral_class2.html @@ -156,7 +156,7 @@ Eebt is an end-bond-torsion term, Eat is an angle-torsion term, Eaat is an angle-angle-torsion term, and Ebb13 is a bond-bond-13 term.

Theta1 and theta2 are equilibrium angles and r1 r2 r3 are equilibrium bond lengths.

-

See (Sun) for a description of the COMPASS class2 force field.

+

See (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 dihedral_coeff command as in the example above, @@ -280,7 +280,7 @@ section for more info on packages.

dihedral_coeff

Default: none

-

(Sun) Sun, J Phys Chem B 102, 7338-7364 (1998).

+

(Sun) Sun, J Phys Chem B 102, 7338-7364 (1998).

diff --git a/doc/html/fix_lb_fluid.html b/doc/html/fix_lb_fluid.html index 5f779c9a19..03cc2f6720 100644 --- a/doc/html/fix_lb_fluid.html +++ b/doc/html/fix_lb_fluid.html @@ -210,7 +210,7 @@ finite difference LB integrator is used. If LBtype is set equal to functions,

_images/fix_lb_fluid_properties.jpg

Full details of the lattice-Boltzmann algorithm used can be found in -Mackay et al..

+Mackay et al..

The fluid is coupled to the MD particles described by group-ID 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 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 Mackay et al. for a +when modelling porous particles. See Mackay et al. for a detailed description of the method by which the user can choose an appropriate gamma value.

@@ -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 -Mackay et al., the built-in LAMMPS integrators may prove to +Mackay et al., the built-in LAMMPS integrators may prove to be unstable. Therefore, we have included our own integrators fix lb/rigid/pc/sphere, and fix lb/pc, to solve for the particle motion in these cases. These integrators should not be used with the lb/viscous fix, as they add hydrodynamic forces @@ -341,7 +341,7 @@ 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 Mackay et al..

+interpolation methods are described in Mackay et al..

If the keyword D3Q19 is used, the 19 velocity (D3Q19) lattice is used by the lattice-Boltzmann algorithm. By default, the 15 velocity (D3Q15) lattice is used.

@@ -371,7 +371,7 @@ the fluid densities and velocities at each lattice site are printed to the screen every N timesteps.

For further details, as well as descriptions and results of several -test runs, see Mackay et al.. Please include a citation to +test runs, see Mackay et al.. Please include a citation to this paper if the lb_fluid fix is used in work contributing to published research.

@@ -426,7 +426,7 @@ The D3Q15 lattice is used for the lattice-Boltzmann algorithm. 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 et al.) 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.

+

(Mackay et al.) 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.

(Mackay and Denniston) 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.

(Adhikari et al.) Adhikari, R., Stratford, K., Cates, M. E., and Wagner, A. J., Fluctuating lattice Boltzmann, Europhys. Lett. 71 (2005) 473-479.

diff --git a/doc/html/improper_class2.html b/doc/html/improper_class2.html index 0d190caf4c..f3fb9e5f0c 100644 --- a/doc/html/improper_class2.html +++ b/doc/html/improper_class2.html @@ -165,7 +165,7 @@ theta angles, since it is always the center atom.

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 (Sun) for a description of the COMPASS class2 force field.

+

See (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 improper_coeff 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.

improper_coeff

Default: none

-

(Sun) Sun, J Phys Chem B 102, 7338-7364 (1998).

+

(Sun) Sun, J Phys Chem B 102, 7338-7364 (1998).

diff --git a/doc/html/improper_umbrella.html b/doc/html/improper_umbrella.html index 716c7c95c2..41f7eeac34 100644 --- a/doc/html/improper_umbrella.html +++ b/doc/html/improper_umbrella.html @@ -154,7 +154,7 @@ axis and the IJK plane:

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 (Mayo) for a description of the DREIDING force field.

+

See (Mayo) for a description of the DREIDING force field.

The following coefficients must be defined for each improper type via the improper_coeff 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 improper_coeff

Default: none

-

(Mayo) Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909 +

(Mayo) Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909 (1990),

diff --git a/doc/html/pair_charmm.html b/doc/html/pair_charmm.html index 61434f9e63..f7311633d1 100644 --- a/doc/html/pair_charmm.html +++ b/doc/html/pair_charmm.html @@ -222,7 +222,7 @@ additional switching function S(r) that ramps the energy and force smoothly to zero between an inner and outer cutoff. It is a widely used potential in the CHARMM MD code. -See (MacKerell) for a description of the CHARMM force +See (MacKerell) for a description of the CHARMM force field.

_images/pair_charmm.jpg

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.

pair_coeff

Default: none

-

(MacKerell) MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field, +

(MacKerell) MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field, Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).

diff --git a/doc/html/pair_class2.html b/doc/html/pair_class2.html index 811c54043a..d1f5e991eb 100644 --- a/doc/html/pair_class2.html +++ b/doc/html/pair_class2.html @@ -213,7 +213,7 @@

Rc is the cutoff.

The lj/class2/coul/cut and lj/class2/coul/long styles add a Coulombic term as described for the lj/cut pair styles.

-

See (Sun) for a description of the COMPASS class2 force field.

+

See (Sun) for a description of the COMPASS class2 force field.

The following coefficients must be defined for each pair of atoms types via the pair_coeff 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 pair_coeff

Default: none

-

(Sun) Sun, J Phys Chem B 102, 7338-7364 (1998).

+

(Sun) Sun, J Phys Chem B 102, 7338-7364 (1998).

diff --git a/doc/html/pair_hbond_dreiding.html b/doc/html/pair_hbond_dreiding.html index d8a9bd8c31..090f404892 100644 --- a/doc/html/pair_hbond_dreiding.html +++ b/doc/html/pair_hbond_dreiding.html @@ -181,7 +181,7 @@ the donor atom, e.g. in a bond list read in from a data file via the hydrogen atoms for each donor/acceptor type pair are specified by the pair_coeff command (see below).

Style hbond/dreiding/lj is the original DREIDING potential of -(Mayo). It uses a LJ 12/10 functional for the Donor-Acceptor +(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 potential for the Donor-Acceptor interactions. (Liu) showed @@ -339,7 +339,7 @@ heading) the following commands could be included in an input script:

pair_coeff

Default: none

-

(Mayo) Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909 +

(Mayo) Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909 (1990).

(Liu) Liu, Bryantsev, Diallo, Goddard III, J. Am. Chem. Soc 131 (8) 2798 (2009)