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4
doc/src/angle_charmm.txt
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@ -30,7 +30,7 @@ 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)"_#MacKerell for a description of the CHARMM force
See "(MacKerell)"_#angle-MacKerell for a description of the CHARMM force
field.
The following coefficients must be defined for each angle type via the
@ -85,6 +85,6 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
:line
:link(MacKerell)
:link(angle-MacKerell)
[(MacKerell)] MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).

4
doc/src/angle_class2.txt
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@ -30,7 +30,7 @@ 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)"_#Sun for a description of the COMPASS class2 force field.
See "(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 "angle_coeff"_angle_coeff.html command as in
@ -115,5 +115,5 @@ for more info on packages.
:line
:link(Sun)
:link(angle-Sun)
[(Sun)] Sun, J Phys Chem B 102, 7338-7364 (1998).

4
doc/src/angle_cosine_periodic.txt
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@ -30,7 +30,7 @@ trigonal center:
where C, B and n are coefficients defined for each angle type.
See "(Mayo)"_#Mayo for a description of the DREIDING force field
See "(Mayo)"_#cosine-Mayo for a description of the DREIDING force field
The following coefficients must be defined for each angle type via the
"angle_coeff"_angle_coeff.html command as in the example above, or in
@ -85,6 +85,6 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
:line
:link(Mayo)
:link(cosine-Mayo)
[(Mayo)] Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
(1990).

4
doc/src/bond_class2.txt
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@ -26,7 +26,7 @@ The {class2} bond style uses the potential
where r0 is the equilibrium bond distance.
See "(Sun)"_#Sun for a description of the COMPASS class2 force field.
See "(Sun)"_#bond-Sun for a description of the COMPASS class2 force field.
The following coefficients must be defined for each bond type via the
"bond_coeff"_bond_coeff.html command as in the example above, or in
@ -77,5 +77,5 @@ for more info on packages.
:line
:link(Sun)
:link(bond-Sun)
[(Sun)] Sun, J Phys Chem B 102, 7338-7364 (1998).

4
doc/src/bond_fene_expand.txt
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@ -25,7 +25,7 @@ The {fene/expand} bond style uses the potential
:c,image(Eqs/bond_fene_expand.jpg)
to define a finite extensible nonlinear elastic (FENE) potential
"(Kremer)"_#Kremer, used for bead-spring polymer models. The first
"(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
@ -88,5 +88,5 @@ style. LAMMPS will issue a warning it that's not the case.
:line
:link(Kremer)
:link(feneexpand-Kremer)
[(Kremer)] Kremer, Grest, J Chem Phys, 92, 5057 (1990).

4
doc/src/compute_saed.txt
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@ -45,7 +45,7 @@ fix saed/vtk 1 1 1 c_2 file Ni_000.saed :pre
[Description:]
Define a computation that calculates electron diffraction intensity as
described in "(Coleman)"_#Coleman on a mesh of reciprocal lattice nodes
described in "(Coleman)"_#saed-Coleman on a mesh of reciprocal lattice nodes
defined by the entire simulation domain (or manually) using simulated
radiation of wavelength lambda.
@ -169,7 +169,7 @@ The option defaults are Kmax = 1.70, Zone 1 0 0, c 1 1 1, dR_Ewald =
:line
:link(Coleman)
:link(saed-Coleman)
[(Coleman)] Coleman, Spearot, Capolungo, MSMSE, 21, 055020
(2013).

4
doc/src/dihedral_charmm.txt
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@ -26,7 +26,7 @@ The {charmm} dihedral style uses the potential
:c,image(Eqs/dihedral_charmm.jpg)
See "(MacKerell)"_#MacKerell for a description of the CHARMM force
See "(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 "(Cornell)"_#Cornell
for a description of the AMBER force field.
@ -110,6 +110,6 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
[(Cornell)] Cornell, Cieplak, Bayly, Gould, Merz, Ferguson,
Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).
:link(MacKerell)
:link(dihedral-MacKerell)
[(MacKerell)] MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
Fischer, Gao, Guo, Ha, et al, J Phys Chem B, 102, 3586 (1998).

4
doc/src/dihedral_class2.txt
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@ -36,7 +36,7 @@ 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 "(Sun)"_#Sun for a description of the COMPASS class2 force field.
See "(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
@ -174,5 +174,5 @@ section for more info on packages.
:line
:link(Sun)
:link(dihedral-Sun)
[(Sun)] Sun, J Phys Chem B 102, 7338-7364 (1998).

12
doc/src/fix_lb_fluid.txt
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@ -100,7 +100,7 @@ functions,
:c,image(Eqs/fix_lb_fluid_properties.jpg)
Full details of the lattice-Boltzmann algorithm used can be found in
"Mackay et al."_#Mackay.
"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
@ -140,7 +140,7 @@ 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."_#Mackay for a
when modelling porous particles. See "Mackay et al."_#fluid-Mackay for a
detailed description of the method by which the user can choose an
appropriate gamma value.
@ -153,7 +153,7 @@ 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."_#Mackay, the built-in LAMMPS integrators may prove to
"Mackay et al."_#fluid-Mackay, the built-in LAMMPS integrators may prove to
be unstable. Therefore, we have included our own integrators "fix
lb/rigid/pc/sphere"_fix_lb_rigid_pc_sphere.html, and "fix
lb/pc"_fix_lb_pc.html, to solve for the particle motion in these
@ -248,7 +248,7 @@ 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."_#Mackay.
interpolation methods are described in "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
@ -284,7 +284,7 @@ screen every N timesteps.
:line
For further details, as well as descriptions and results of several
test runs, see "Mackay et al."_#Mackay. Please include a citation to
test runs, see "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.
@ -360,7 +360,7 @@ If walls are present, they are assumed to be stationary.
:link(Ollila)
[(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.
:link(Mackay)
:link(fluid-Mackay)
[(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.
:link(Mackay2)

4
doc/src/fix_pimd.txt
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@ -49,7 +49,7 @@ 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 "(Tuckerman)"_#Tuckerman. With the
chain thermostat is applied "(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
@ -161,7 +161,7 @@ and nhc = 2.
[(Feynman)] R. Feynman and A. Hibbs, Chapter 7, Quantum Mechanics and
Path Integrals, McGraw-Hill, New York (1965).
:link(Tuckerman)
:link(pimd-Tuckerman)
[(Tuckerman)] M. Tuckerman and B. Berne, J Chem Phys, 99, 2796 (1993).
:link(Cao1)

4
doc/src/improper_class2.txt
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@ -47,7 +47,7 @@ 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 "(Sun)"_#Sun for a description of the COMPASS class2 force field.
See "(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 "improper_coeff"_improper_coeff.html command as
@ -120,5 +120,5 @@ section for more info on packages.
:line
:link(Sun)
:link(improper-Sun)
[(Sun)] Sun, J Phys Chem B 102, 7338-7364 (1998).

4
doc/src/improper_umbrella.txt
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@ -35,7 +35,7 @@ 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 "(Mayo)"_#Mayo for a description of the DREIDING force field.
See "(Mayo)"_#umbrella-Mayo for a description of the DREIDING force field.
The following coefficients must be defined for each improper type via
the "improper_coeff"_improper_coeff.html command as in the example
@ -85,6 +85,6 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
:line
:link(Mayo)
:link(umbrella-Mayo)
[(Mayo)] Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
(1990),

4
doc/src/pair_charmm.txt
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@ -68,7 +68,7 @@ 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 "(MacKerell)"_#MacKerell for a description of the CHARMM force
See "(MacKerell)"_#pair-MacKerell for a description of the CHARMM force
field.
:c,image(Eqs/pair_charmm.jpg)
@ -194,6 +194,6 @@ the MOLECULE and KSPACE packages are installed by default.
:line
:link(MacKerell)
:link(pair-MacKerell)
[(MacKerell)] MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).

4
doc/src/pair_class2.txt
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@ -64,7 +64,7 @@ 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_lj.html pair styles.
See "(Sun)"_#Sun for a description of the COMPASS class2 force field.
See "(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 "pair_coeff"_pair_coeff.html command as in the examples
@ -169,5 +169,5 @@ LAMMPS"_Section_start.html#start_3 section for more info.
:line
:link(Sun)
:link(pair-Sun)
[(Sun)] Sun, J Phys Chem B 102, 7338-7364 (1998).

4
doc/src/pair_hbond_dreiding.txt
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@ -57,7 +57,7 @@ hydrogen atoms for each donor/acceptor type pair are specified by the
"pair_coeff"_pair_coeff.html command (see below).
Style {hbond/dreiding/lj} is the original DREIDING potential of
"(Mayo)"_#Mayo. It uses a LJ 12/10 functional for the Donor-Acceptor
"(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
@ -234,7 +234,7 @@ thermo_style custom step temp epair v_E_hbond :pre
:line
:link(Mayo)
:link(pair-Mayo)
[(Mayo)] Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
(1990).