diff --git a/doc/src/fix_rigid.txt b/doc/src/fix_rigid.txt index 63c7f8e9db4769a13cc0ff500e3954d9f481ecd5..ec7ed4f2b1e16374b0dd318a75cf31b3618711ce 100644 --- a/doc/src/fix_rigid.txt +++ b/doc/src/fix_rigid.txt @@ -118,8 +118,8 @@ Examples of large rigid bodies are a colloidal particle, or portions of a biomolecule such as a protein. Example of small rigid bodies are patchy nanoparticles, such as those -modeled in "this paper"_#Zhang3 by Sharon Glotzer's group, clumps of -granular particles, lipid molecules consiting of one or more point +modeled in "this paper"_#Zhang1 by Sharon Glotzer's group, clumps of +granular particles, lipid molecules consisting of one or more point dipoles connected to other spheroids or ellipsoids, irregular particles built from line segments (2d) or triangles (3d), and coarse-grain models of nano or colloidal particles consisting of a @@ -856,5 +856,5 @@ Martyna, Tuckerman, Tobias, Klein, Mol Phys, 87, 1117. [(Miller)] Miller, Eleftheriou, Pattnaik, Ndirango, and Newns, J Chem Phys, 116, 8649 (2002). -:link(Zhang3) +:link(Zhang1) [(Zhang)] Zhang, Glotzer, Nanoletters, 4, 1407-1413 (2004). diff --git a/doc/src/fix_thermal_conductivity.txt b/doc/src/fix_thermal_conductivity.txt index 17631ac7f50ca625d426b7368ac5415e4e5a1f34..0353c095b29d60e4be37a581968a70d06f778492 100644 --- a/doc/src/fix_thermal_conductivity.txt +++ b/doc/src/fix_thermal_conductivity.txt @@ -136,7 +136,7 @@ kinetic energy of atoms that are in constrained molecules, e.g. via "fix shake"_fix_shake.html or "fix rigid"_fix_rigid.html. This is because application of the constraints will alter the amount of transferred momentum. You should, however, be able to use flexible -molecules. See the "Zhang paper"_#Zhang1 for a discussion and results +molecules. See the "Zhang paper"_#Zhang2 for a discussion and results of this idea. When running a simulation with large, massive particles or molecules @@ -158,6 +158,6 @@ The option defaults are swap = 1. :link(Muller-Plathe1) [(Muller-Plathe)] Muller-Plathe, J Chem Phys, 106, 6082 (1997). -:link(Zhang1) +:link(Zhang2) [(Zhang)] Zhang, Lussetti, de Souza, Muller-Plathe, J Phys Chem B, 109, 15060-15067 (2005). diff --git a/doc/src/pair_gran.txt b/doc/src/pair_gran.txt index 93aab51e5c83943823da859056238e547006b112..d7e87af013f002a6e6472a4ae45e3f5c27fd3de5 100644 --- a/doc/src/pair_gran.txt +++ b/doc/src/pair_gran.txt @@ -45,7 +45,7 @@ pair_style gran/hooke 200000.0 70000.0 50.0 30.0 0.5 0 :pre The {gran} styles use the following formulas for the frictional force between two granular particles, as described in "(Brilliantov)"_#Brilliantov, "(Silbert)"_#Silbert, and -"(Zhang)"_#Zhang4, when the distance r between two particles of radii +"(Zhang)"_#Zhang3, when the distance r between two particles of radii Ri and Rj is less than their contact distance d = Ri + Rj. There is no force between the particles when r > d. @@ -115,7 +115,7 @@ gamma_t is in units of (1/(time*distance)). Note that in the Hookean case, Kn can be thought of as a linear spring constant with units of force/distance. In the Hertzian case, Kn is like a non-linear spring constant with units of force/area or -pressure, and as shown in the "(Zhang)"_#Zhang4 paper, Kn = 4G / +pressure, and as shown in the "(Zhang)"_#Zhang3 paper, Kn = 4G / (3(1-nu)) where nu = the Poisson ratio, G = shear modulus = E / (2(1+nu)), and E = Young's modulus. Similarly, Kt = 4G / (2-nu). (NOTE: in an earlier version of the manual, we incorrectly stated that @@ -267,5 +267,5 @@ p 5382-5392 (1996). [(Silbert)] Silbert, Ertas, Grest, Halsey, Levine, Plimpton, Phys Rev E, 64, p 051302 (2001). -:link(Zhang4) +:link(Zhang3) [(Zhang)] Zhang and Makse, Phys Rev E, 72, p 011301 (2005).