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14
doc/src/Section_howto.txt
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@ -184,7 +184,7 @@ commands like "pair_coeff"_pair_coeff.html or
for additional tools that can use CHARMM or AMBER to assign force for additional tools that can use CHARMM or AMBER to assign force
field coefficients and convert their output into LAMMPS input. 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. See "(Cornell)"_#Cornell for a description of the AMBER force
field. field.
@ -439,7 +439,7 @@ computations between frozen atoms by using this command:
6.7 TIP3P water model :link(howto_7),h4 6.7 TIP3P water model :link(howto_7),h4
The TIP3P water model as implemented in CHARMM 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. 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 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 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 O charge = -0.8476
H charge = 0.4238 :all(b),p 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. the SPC and SPC/E models.
Wikipedia also has a nice article on "water 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 model, representes induced dipoles by a pair of charges (the core atom
and the Drude particle) connected by a harmonic spring. The Drude and the Drude particle) connected by a harmonic spring. The Drude
model has a number of features aimed at its use in molecular systems 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 Thermostating of the additional degrees of freedom associated with the
induced dipoles at very low temperature, in terms of the reduced induced dipoles at very low temperature, in terms of the reduced
@ -2774,7 +2774,7 @@ too close, which can cause numerical issues.
:line :line
:line :line
:link(Berendsen) :link(howto-Berendsen)
[(Berendsen)] Berendsen, Grigera, Straatsma, J Phys Chem, 91, [(Berendsen)] Berendsen, Grigera, Straatsma, J Phys Chem, 91,
6269-6271 (1987). 6269-6271 (1987).
@ -2790,7 +2790,7 @@ J Chem Phys, 120, 9665 (2004).
[(Ikeshoji)] Ikeshoji and Hafskjold, Molecular Physics, 81, 251-261 [(Ikeshoji)] Ikeshoji and Hafskjold, Molecular Physics, 81, 251-261
(1994). (1994).
:link(MacKerell) :link(howto-MacKerell)
[(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). 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, [(Mitchell and Finchham)] Mitchell, Finchham, J Phys Condensed Matter,
5, 1031-1038 (1993). 5, 1031-1038 (1993).
:link(Lamoureux) :link(howto-Lamoureux)
[(Lamoureux and Roux)] G. Lamoureux, B. Roux, J. Chem. Phys 119, 3025 (2003) [(Lamoureux and Roux)] G. Lamoureux, B. Roux, J. Chem. Phys 119, 3025 (2003)

4
doc/src/bond_fene.txt
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@ -26,7 +26,7 @@ The {fene} bond style uses the potential
:c,image(Eqs/bond_fene.jpg) :c,image(Eqs/bond_fene.jpg)
to define a finite extensible nonlinear elastic (FENE) potential 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 term is attractive, the 2nd Lennard-Jones term is repulsive. The
first term extends to R0, the maximum extent of the bond. The 2nd 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. 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 :line
:link(Kremer) :link(fene-Kremer)
[(Kremer)] Kremer, Grest, J Chem Phys, 92, 5057 (1990). [(Kremer)] Kremer, Grest, J Chem Phys, 92, 5057 (1990).

6
doc/src/compute_xrd.txt
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@ -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:] [Description:]
Define a computation that calculates x-ray diffraction intensity as described 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 by the entire simulation domain (or manually) using a simulated radiation
of wavelength lambda. of wavelength lambda.
@ -189,7 +189,7 @@ no manual flag, no echo flag.
:line :line
:link(Coleman) :link(xrd-Coleman)
[(Coleman)] Coleman, Spearot, Capolungo, MSMSE, 21, 055020 [(Coleman)] Coleman, Spearot, Capolungo, MSMSE, 21, 055020
(2013). (2013).
@ -200,5 +200,3 @@ Volume C: Mathematical and Chemical Tables, 249-429 (2004).
:link(Peng) :link(Peng)
[(Peng)] Peng, Ren, Dudarev, Whelan, Acta Crystallogr. A, 52, 257-76 [(Peng)] Peng, Ren, Dudarev, Whelan, Acta Crystallogr. A, 52, 257-76
(1996). (1996).

11
doc/src/dihedral_charmm.txt
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@ -26,10 +26,11 @@ The {charmm} dihedral style uses the potential
:c,image(Eqs/dihedral_charmm.jpg) :c,image(Eqs/dihedral_charmm.jpg)
See "(MacKerell)"_#dihedral-MacKerell for a description of the CHARMM force See "(MacKerell)"_#dihedral-MacKerell for a description of the CHARMM
field. This dihedral style can also be used for the AMBER force field force field. This dihedral style can also be used for the AMBER force
(see comment on weighting factors below). See "(Cornell)"_#Cornell field (see comment on weighting factors below). See
for a description of the AMBER force field. "(Cornell)"_#dihedral-Cornell for a description of the AMBER force
field.
The following coefficients must be defined for each dihedral type via the 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 "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 :line
:link(Cornell) :link(dihedral-Cornell)
[(Cornell)] Cornell, Cieplak, Bayly, Gould, Merz, Ferguson, [(Cornell)] Cornell, Cieplak, Bayly, Gould, Merz, Ferguson,
Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995). Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).

20
doc/src/fix_nh.txt
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@ -94,12 +94,12 @@ particles will match the target values specified by Tstart/Tstop and
Pstart/Pstop. Pstart/Pstop.
The equations of motion used are those of Shinoda et al in The equations of motion used are those of Shinoda et al in
"(Shinoda)"_#Shinoda, which combine the hydrostatic equations of "(Shinoda)"_#nh-Shinoda, which combine the hydrostatic equations of
Martyna, Tobias and Klein in "(Martyna)"_#Martyna with the strain Martyna, Tobias and Klein in "(Martyna)"_#nh-Martyna with the strain
energy proposed by Parrinello and Rahman in 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 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 :line
@ -274,7 +274,7 @@ barostat variables.
The {mtk} keyword controls whether or not the correction terms due to The {mtk} keyword controls whether or not the correction terms due to
Martyna, Tuckerman, and Klein are included in the equations of motion 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 Hoover barostat, whose volume probability distribution function
differs from the true NPT and NPH ensembles by a factor of 1/V. Hence 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 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 scheme at little extra cost. The initial and final updates of the
thermostat variables are broken up into {tloop} substeps, each of thermostat variables are broken up into {tloop} substeps, each of
length {dt}/{tloop}. This corresponds to using a first-order 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. does the same thing for the barostat thermostat.
The keyword {nreset} controls how often the reference dimensions used The keyword {nreset} controls how often the reference dimensions used
@ -628,15 +628,15 @@ not coupled to barostat, otherwise no.
:line :line
:link(Martyna) :link(nh-Martyna)
[(Martyna)] Martyna, Tobias and Klein, J Chem Phys, 101, 4177 (1994). [(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). [(Parrinello)] Parrinello and Rahman, J Appl Phys, 52, 7182 (1981).
:link(Tuckerman) :link(nh-Tuckerman)
[(Tuckerman)] Tuckerman, Alejandre, Lopez-Rendon, Jochim, and [(Tuckerman)] Tuckerman, Alejandre, Lopez-Rendon, Jochim, and
Martyna, J Phys A: Math Gen, 39, 5629 (2006). 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). [(Shinoda)] Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).