git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14986 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/src/Section_howto.txt

@@ -184,7 +184,7 @@ commands like "pair_coeff"_pair_coeff.html or
 for additional tools that can use CHARMM or AMBER to assign force
 field coefficients and convert their output into LAMMPS input.
 
-See "(MacKerell)"_#MacKerell for a description of the CHARMM force
+See "(MacKerell)"_#howto-MacKerell for a description of the CHARMM force
 field.  See "(Cornell)"_#Cornell for a description of the AMBER force
 field.
 
@@ -439,7 +439,7 @@ computations between frozen atoms by using this command:
 6.7 TIP3P water model :link(howto_7),h4
 
 The TIP3P water model as implemented in CHARMM
-"(MacKerell)"_#MacKerell specifies a 3-site rigid water molecule with
+"(MacKerell)"_#howto-MacKerell specifies a 3-site rigid water molecule with
 charges and Lennard-Jones parameters assigned to each of the 3 atoms.
 In LAMMPS the "fix shake"_fix_shake.html command can be used to hold
 the two O-H bonds and the H-O-H angle rigid.  A bond style of
@@ -623,7 +623,7 @@ the partial charge assignemnts change:
 O charge = -0.8476
 H charge = 0.4238 :all(b),p
 
-See the "(Berendsen)"_#Berendsen reference for more details on both
+See the "(Berendsen)"_#howto-Berendsen reference for more details on both
 the SPC and SPC/E models.
 
 Wikipedia also has a nice article on "water
@@ -2715,7 +2715,7 @@ The thermalized Drude model, similarly to the "core-shell"_#howto_26
 model, representes induced dipoles by a pair of charges (the core atom
 and the Drude particle) connected by a harmonic spring. The Drude
 model has a number of features aimed at its use in molecular systems
-("Lamoureux and Roux"_#Lamoureux):
+("Lamoureux and Roux"_#howto-Lamoureux):
 
 Thermostating of the additional degrees of freedom associated with the
 induced dipoles at very low temperature, in terms of the reduced
@@ -2774,7 +2774,7 @@ too close, which can cause numerical issues.
 :line
 :line
 
-:link(Berendsen)
+:link(howto-Berendsen)
 [(Berendsen)] Berendsen, Grigera, Straatsma, J Phys Chem, 91,
 6269-6271 (1987).
 
@@ -2790,7 +2790,7 @@ J Chem Phys, 120, 9665 (2004).
 [(Ikeshoji)] Ikeshoji and Hafskjold, Molecular Physics, 81, 251-261
 (1994).
 
-:link(MacKerell)
+:link(howto-MacKerell)
 [(MacKerell)] MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
 Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
 
@@ -2812,5 +2812,5 @@ Phys, 79, 926 (1983).
 [(Mitchell and Finchham)] Mitchell, Finchham, J Phys Condensed Matter,
 5, 1031-1038 (1993).
 
-:link(Lamoureux)
+:link(howto-Lamoureux)
 [(Lamoureux and Roux)] G. Lamoureux, B. Roux, J. Chem. Phys 119, 3025 (2003)

doc/src/bond_fene.txt

@@ -26,7 +26,7 @@ The {fene} bond style uses the potential
 :c,image(Eqs/bond_fene.jpg)
 
 to define a finite extensible nonlinear elastic (FENE) potential
-"(Kremer)"_#Kremer, used for bead-spring polymer models.  The first
+"(Kremer)"_#fene-Kremer, used for bead-spring polymer models.  The first
 term is attractive, the 2nd Lennard-Jones term is repulsive.  The
 first term extends to R0, the maximum extent of the bond.  The 2nd
 term is cutoff at 2^(1/6) sigma, the minimum of the LJ potential.
@@ -84,5 +84,5 @@ style.  LAMMPS will issue a warning it that's not the case.
 
 :line
 
-:link(Kremer)
+:link(fene-Kremer)
 [(Kremer)] Kremer, Grest, J Chem Phys, 92, 5057 (1990).

doc/src/compute_xrd.txt

@@ -45,7 +45,7 @@ fix 2 all ave/histo/weight 1 1 1 10 100 250 c_2\[1\] c_2\[2\] mode vector file D
 [Description:]
 
 Define a computation that calculates x-ray diffraction intensity as described
-in "(Coleman)"_#Coleman on a mesh of reciprocal lattice nodes defined 
+in "(Coleman)"_#xrd-Coleman on a mesh of reciprocal lattice nodes defined 
 by the entire simulation domain (or manually) using a simulated radiation
 of wavelength lambda. 
 
@@ -189,7 +189,7 @@ no manual flag, no echo flag.
 
 :line
 
-:link(Coleman)
+:link(xrd-Coleman)
 [(Coleman)] Coleman, Spearot, Capolungo, MSMSE, 21, 055020
 (2013).
 
@@ -200,5 +200,3 @@ Volume C: Mathematical and Chemical Tables, 249-429 (2004).
 :link(Peng)
 [(Peng)] Peng, Ren, Dudarev, Whelan, Acta Crystallogr. A, 52, 257-76
 (1996).
-
-

doc/src/dihedral_charmm.txt

@@ -26,10 +26,11 @@ The {charmm} dihedral style uses the potential
 
 :c,image(Eqs/dihedral_charmm.jpg)
 
-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.
+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)"_#dihedral-Cornell for a description of the AMBER force
+field.
 
 The following coefficients must be defined for each dihedral type via the
 "dihedral_coeff"_dihedral_coeff.html command as in the example above, or in
@@ -106,7 +107,7 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
 
 :line
 
-:link(Cornell)
+:link(dihedral-Cornell)
 [(Cornell)] Cornell, Cieplak, Bayly, Gould, Merz, Ferguson,
 Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).
 

doc/src/fix_nh.txt

@@ -94,12 +94,12 @@ particles will match the target values specified by Tstart/Tstop and
 Pstart/Pstop.
 
 The equations of motion used are those of Shinoda et al in
-"(Shinoda)"_#Shinoda, which combine the hydrostatic equations of
-Martyna, Tobias and Klein in "(Martyna)"_#Martyna with the strain
+"(Shinoda)"_#nh-Shinoda, which combine the hydrostatic equations of
+Martyna, Tobias and Klein in "(Martyna)"_#nh-Martyna with the strain
 energy proposed by Parrinello and Rahman in
-"(Parrinello)"_#Parrinello.  The time integration schemes closely
+"(Parrinello)"_#nh-Parrinello.  The time integration schemes closely
 follow the time-reversible measure-preserving Verlet and rRESPA
-integrators derived by Tuckerman et al in "(Tuckerman)"_#Tuckerman.
+integrators derived by Tuckerman et al in "(Tuckerman)"_#nh-Tuckerman.
 
 :line
 
@@ -274,7 +274,7 @@ barostat variables.
 
 The {mtk} keyword controls whether or not the correction terms due to
 Martyna, Tuckerman, and Klein are included in the equations of motion
-"(Martyna)"_#Martyna.  Specifying {no} reproduces the original
+"(Martyna)"_#nh-Martyna.  Specifying {no} reproduces the original
 Hoover barostat, whose volume probability distribution function
 differs from the true NPT and NPH ensembles by a factor of 1/V.  Hence
 using {yes} is more correct, but in many cases the difference is
@@ -284,7 +284,7 @@ The keyword {tloop} can be used to improve the accuracy of integration
 scheme at little extra cost.  The initial and final updates of the
 thermostat variables are broken up into {tloop} substeps, each of
 length {dt}/{tloop}. This corresponds to using a first-order
-Suzuki-Yoshida scheme "(Tuckerman)"_#Tuckerman.  The keyword {ploop}
+Suzuki-Yoshida scheme "(Tuckerman)"_#nh-Tuckerman.  The keyword {ploop}
 does the same thing for the barostat thermostat.
 
 The keyword {nreset} controls how often the reference dimensions used
@@ -628,15 +628,15 @@ not coupled to barostat, otherwise no.
 
 :line
 
-:link(Martyna)
+:link(nh-Martyna)
 [(Martyna)] Martyna, Tobias and Klein, J Chem Phys, 101, 4177 (1994).
 
-:link(Parrinello)
+:link(nh-Parrinello)
 [(Parrinello)] Parrinello and Rahman, J Appl Phys, 52, 7182 (1981).
 
-:link(Tuckerman)
+:link(nh-Tuckerman)
 [(Tuckerman)] Tuckerman, Alejandre, Lopez-Rendon, Jochim, and
 Martyna, J Phys A: Math Gen, 39, 5629 (2006).
 
-:link(Shinoda)
+:link(nh-Shinoda)
 [(Shinoda)] Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).