diff --git a/doc/src/Section_howto.txt b/doc/src/Section_howto.txt index 6774e4a4f6..2d0844fb72 100644 --- a/doc/src/Section_howto.txt +++ b/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) diff --git a/doc/src/bond_fene.txt b/doc/src/bond_fene.txt index 46b38214e4..2e25fd90ff 100644 --- a/doc/src/bond_fene.txt +++ b/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). diff --git a/doc/src/compute_xrd.txt b/doc/src/compute_xrd.txt index 61b86c557f..826970ffd9 100644 --- a/doc/src/compute_xrd.txt +++ b/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). - - diff --git a/doc/src/dihedral_charmm.txt b/doc/src/dihedral_charmm.txt index 581dfd1df2..0420c55ce9 100644 --- a/doc/src/dihedral_charmm.txt +++ b/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). diff --git a/doc/src/fix_nh.txt b/doc/src/fix_nh.txt index 4131940d4c..0537bba3b2 100644 --- a/doc/src/fix_nh.txt +++ b/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).