diff --git a/doc/html/Section_howto.html b/doc/html/Section_howto.html index a4c652a14f..ff7b7270e6 100644 --- a/doc/html/Section_howto.html +++ b/doc/html/Section_howto.html @@ -363,7 +363,7 @@ commands like bond_coeff. See Section_tools for additional tools that can use CHARMM or AMBER to assign force field coefficients and convert their output into LAMMPS input.
-See (MacKerell) for a description of the CHARMM force +
See (MacKerell) for a description of the CHARMM force field. See (Cornell) for a description of the AMBER force field.
These style choices compute force field formulas that are consistent @@ -587,7 +587,7 @@ computations between frozen atoms by using this command:
The TIP3P water model as implemented in CHARMM -(MacKerell) specifies a 3-site rigid water molecule with +(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 command can be used to hold the two O-H bonds and the H-O-H angle rigid. A bond style of @@ -766,7 +766,7 @@ the partial charge assignemnts change:
See the (Berendsen) reference for more details on both +
See the (Berendsen) reference for more details on both the SPC and SPC/E models.
Wikipedia also has a nice article on water models.
(Berendsen) Berendsen, Grigera, Straatsma, J Phys Chem, 91, 6269-6271 (1987).
(Cornell) Cornell, Cieplak, Bayly, Gould, Merz, Ferguson, Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).
@@ -2784,7 +2784,7 @@ Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995). J Chem Phys, 120, 9665 (2004).(Ikeshoji) Ikeshoji and Hafskjold, Molecular Physics, 81, 251-261 (1994).
-(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).
(Mayo) Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909 (1990).
@@ -2794,7 +2794,7 @@ Phys, 79, 926 (1983).(Shinoda) Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).
(Mitchell and Finchham) Mitchell, Finchham, J Phys Condensed Matter, 5, 1031-1038 (1993).
-(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)
diff --git a/doc/html/_sources/Section_howto.txt b/doc/html/_sources/Section_howto.txt index 90584d156c..89fc18fadc 100644 --- a/doc/html/_sources/Section_howto.txt +++ b/doc/html/_sources/Section_howto.txt @@ -221,7 +221,7 @@ commands like :doc:`pair_coeffThe fene bond style uses the potential
to define a finite extensible nonlinear elastic (FENE) potential -(Kremer), used for bead-spring polymer models. The first +(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.
@@ -195,7 +195,7 @@ style. LAMMPS will issue a warning it that’s not the case.Default: none
(Kremer) Kremer, Grest, J Chem Phys, 92, 5057 (1990).
+(Kremer) Kremer, Grest, J Chem Phys, 92, 5057 (1990).
diff --git a/doc/html/compute_xrd.html b/doc/html/compute_xrd.html index d594e6ce55..b16569ab91 100644 --- a/doc/html/compute_xrd.html +++ b/doc/html/compute_xrd.html @@ -167,7 +167,7 @@Define a computation that calculates x-ray diffraction intensity as described -in (Coleman) on a mesh of reciprocal lattice nodes defined +in (Coleman) on a mesh of reciprocal lattice nodes defined by the entire simulation domain (or manually) using a simulated radiation of wavelength lambda.
The x-ray diffraction intensity, I, at each reciprocal lattice point, k, @@ -318,7 +318,7 @@ enabled if LAMMPS was built with that package. See the -
(Coleman) Coleman, Spearot, Capolungo, MSMSE, 21, 055020 +
(Coleman) Coleman, Spearot, Capolungo, MSMSE, 21, 055020 (2013).
(Colliex) Colliex et al. International Tables for Crystallography Volume C: Mathematical and Chemical Tables, 249-429 (2004).
diff --git a/doc/html/dihedral_charmm.html b/doc/html/dihedral_charmm.html index ab802a304d..35e5af8c8d 100644 --- a/doc/html/dihedral_charmm.html +++ b/doc/html/dihedral_charmm.html @@ -152,10 +152,11 @@The charmm dihedral style uses the potential
-See (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) -for a description of the AMBER force field.
+See (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) for a description of the AMBER force +field.
The following coefficients must be defined for each dihedral type via the dihedral_coeff command as in the example above, or in the data file or restart files read by the read_data @@ -217,7 +218,7 @@ MOLECULE package (which it is by default). See the dihedral_coeff
Default: none
(Cornell) Cornell, Cieplak, Bayly, Gould, Merz, Ferguson, +
(Cornell) Cornell, Cieplak, Bayly, Gould, Merz, Ferguson, Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).
(MacKerell) MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field, Fischer, Gao, Guo, Ha, et al, J Phys Chem B, 102, 3586 (1998).
diff --git a/doc/html/fix_nh.html b/doc/html/fix_nh.html index f542b04a18..747e2cc8d0 100644 --- a/doc/html/fix_nh.html +++ b/doc/html/fix_nh.html @@ -239,12 +239,12 @@ correctly, the time-averaged temperature and stress tensor of the 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), which combine the hydrostatic equations of -Martyna, Tobias and Klein in (Martyna) with the strain +(Shinoda), which combine the hydrostatic equations of +Martyna, Tobias and Klein in (Martyna) with the strain energy proposed by Parrinello and Rahman in -(Parrinello). The time integration schemes closely +(Parrinello). The time integration schemes closely follow the time-reversible measure-preserving Verlet and rRESPA -integrators derived by Tuckerman et al in (Tuckerman).
+integrators derived by Tuckerman et al in (Tuckerman).The thermostat parameters for fix styles nvt and npt is specified using the temp keyword. Other thermostat-related keywords are @@ -402,7 +402,7 @@ freedom. A value of 0 corresponds to no thermostatting of the 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). Specifying no reproduces the original +(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 @@ -411,7 +411,7 @@ negligible.
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). The keyword ploop +Suzuki-Yoshida scheme (Tuckerman). The keyword ploop does the same thing for the barostat thermostat.The keyword nreset controls how often the reference dimensions used to define the strain energy are reset. If this keyword is not used, @@ -716,11 +716,11 @@ ploop = 1, nreset = 0, drag = 0.0, dilate = all, couple = none, scaleyz = scalexz = scalexy = yes if periodic in 2nd dimension and not coupled to barostat, otherwise no.
(Martyna) Martyna, Tobias and Klein, J Chem Phys, 101, 4177 (1994).
-(Parrinello) Parrinello and Rahman, J Appl Phys, 52, 7182 (1981).
-(Tuckerman) Tuckerman, Alejandre, Lopez-Rendon, Jochim, and +
(Martyna) Martyna, Tobias and Klein, J Chem Phys, 101, 4177 (1994).
+(Parrinello) Parrinello and Rahman, J Appl Phys, 52, 7182 (1981).
+(Tuckerman) Tuckerman, Alejandre, Lopez-Rendon, Jochim, and Martyna, J Phys A: Math Gen, 39, 5629 (2006).
-(Shinoda) Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).
+(Shinoda) Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).