From df885d59ff661de8fdfa85508a45e7b2084908b9 Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Tue, 10 May 2016 14:49:23 +0000
Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14984
 f3b2605a-c512-4ea7-a41b-209d697bcdaa

---
 doc/src/angle_charmm.txt          |  4 ++--
 doc/src/angle_class2.txt          |  4 ++--
 doc/src/angle_cosine_periodic.txt |  4 ++--
 doc/src/bond_class2.txt           |  4 ++--
 doc/src/bond_fene_expand.txt      |  4 ++--
 doc/src/compute_saed.txt          |  4 ++--
 doc/src/dihedral_charmm.txt       |  4 ++--
 doc/src/dihedral_class2.txt       |  4 ++--
 doc/src/fix_lb_fluid.txt          | 12 ++++++------
 doc/src/fix_pimd.txt              |  4 ++--
 doc/src/improper_class2.txt       |  4 ++--
 doc/src/improper_umbrella.txt     |  4 ++--
 doc/src/pair_charmm.txt           |  4 ++--
 doc/src/pair_class2.txt           |  4 ++--
 doc/src/pair_hbond_dreiding.txt   |  4 ++--
 15 files changed, 34 insertions(+), 34 deletions(-)

diff --git a/doc/src/angle_charmm.txt b/doc/src/angle_charmm.txt
index 5cc66e508e..5d734bada4 100644
--- a/doc/src/angle_charmm.txt
+++ b/doc/src/angle_charmm.txt
@@ -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).
diff --git a/doc/src/angle_class2.txt b/doc/src/angle_class2.txt
index 1bf4f05f5a..0bee802650 100644
--- a/doc/src/angle_class2.txt
+++ b/doc/src/angle_class2.txt
@@ -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).
diff --git a/doc/src/angle_cosine_periodic.txt b/doc/src/angle_cosine_periodic.txt
index 16df251eef..7abc6beaf9 100644
--- a/doc/src/angle_cosine_periodic.txt
+++ b/doc/src/angle_cosine_periodic.txt
@@ -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).
diff --git a/doc/src/bond_class2.txt b/doc/src/bond_class2.txt
index 198b88ba59..4784809f67 100644
--- a/doc/src/bond_class2.txt
+++ b/doc/src/bond_class2.txt
@@ -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).
diff --git a/doc/src/bond_fene_expand.txt b/doc/src/bond_fene_expand.txt
index 8d6a0f97b2..5025304ce5 100644
--- a/doc/src/bond_fene_expand.txt
+++ b/doc/src/bond_fene_expand.txt
@@ -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).
diff --git a/doc/src/compute_saed.txt b/doc/src/compute_saed.txt
index 45b7df3f31..11be0177dc 100644
--- a/doc/src/compute_saed.txt
+++ b/doc/src/compute_saed.txt
@@ -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).
 
diff --git a/doc/src/dihedral_charmm.txt b/doc/src/dihedral_charmm.txt
index 5024a74e99..581dfd1df2 100644
--- a/doc/src/dihedral_charmm.txt
+++ b/doc/src/dihedral_charmm.txt
@@ -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).
diff --git a/doc/src/dihedral_class2.txt b/doc/src/dihedral_class2.txt
index 2d9381006e..6f91881126 100644
--- a/doc/src/dihedral_class2.txt
+++ b/doc/src/dihedral_class2.txt
@@ -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).
diff --git a/doc/src/fix_lb_fluid.txt b/doc/src/fix_lb_fluid.txt
index ebd26a3b76..968762ff18 100755
--- a/doc/src/fix_lb_fluid.txt
+++ b/doc/src/fix_lb_fluid.txt
@@ -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)
diff --git a/doc/src/fix_pimd.txt b/doc/src/fix_pimd.txt
index 4763fb25a3..c9e882bcb8 100644
--- a/doc/src/fix_pimd.txt
+++ b/doc/src/fix_pimd.txt
@@ -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) 
diff --git a/doc/src/improper_class2.txt b/doc/src/improper_class2.txt
index 19063e8875..890e15f04a 100644
--- a/doc/src/improper_class2.txt
+++ b/doc/src/improper_class2.txt
@@ -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).
diff --git a/doc/src/improper_umbrella.txt b/doc/src/improper_umbrella.txt
index 2bbfd97519..f54c24482a 100644
--- a/doc/src/improper_umbrella.txt
+++ b/doc/src/improper_umbrella.txt
@@ -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),
diff --git a/doc/src/pair_charmm.txt b/doc/src/pair_charmm.txt
index d07681edc3..3c0cc94bcc 100644
--- a/doc/src/pair_charmm.txt
+++ b/doc/src/pair_charmm.txt
@@ -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).
diff --git a/doc/src/pair_class2.txt b/doc/src/pair_class2.txt
index 66ba2b7f30..457d34f658 100644
--- a/doc/src/pair_class2.txt
+++ b/doc/src/pair_class2.txt
@@ -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).
diff --git a/doc/src/pair_hbond_dreiding.txt b/doc/src/pair_hbond_dreiding.txt
index e7395aeba3..f14d68d36e 100644
--- a/doc/src/pair_hbond_dreiding.txt
+++ b/doc/src/pair_hbond_dreiding.txt
@@ -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).