Documentation V1

doc/src/fix_integration_spin.txt

@@ -40,8 +40,8 @@ the equations of motion of the spin lattice system, following the scheme:
 according to the implementation reported in "(Omelyan)"_#Omelyan1.
 
 A sectoring enables this scheme for parallel calculations. 
-The implementation of this sectoring algorithm is reported in
-"(Tranchida)"_#Tranchida1. 
+The implementation of this sectoring algorithm is reported 
+in "(Tranchida)"_#Tranchida1.
 
 :line
 
@@ -51,7 +51,6 @@ This fix style can only be used if LAMMPS was built with the
 SPIN package. See the "Making LAMMPS"_Section_start.html#start_3
 section for more info on packages.
 
-
 [Related commands:]
 
 "atom_style spin"_atom_style.html, "fix nve"_fix_nve.html
@@ -61,9 +60,8 @@ section for more info on packages.
 :line
 
 :link(Omelyan1)
-[(Omelyan)] I.P. Omelyan, I.M. Mryglod, R. Folk. Phys. Rev. Lett. 
-86(5), 898. (2001)
+[(Omelyan)] Omelyan, Mryglod, and Folk. Phys. Rev. Lett. 
+86(5), 898. (2001).
 
 :link(Tranchida1)
-[(Tranchida)] J. Tranchida, S.J. Plimpton, P. Thibaudeau, A.P. Thompson. 
-arXiv preprint arXiv:1801.10233. (2018)
+[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson.

doc/src/fix_langevin_spin.txt

@@ -42,7 +42,7 @@ The components of eta are drawn from a Gaussian probability law. Their amplitude
 is defined as a proportion of the temperature of the external thermostat T (in K 
 in metal units).
 
-More details about this implementation are reported in "(Tranchida)"_#Tranchida1.
+More details about this implementation are reported in "(Tranchida)"_#Tranchida2.
 
 Note: due to the form of the sLLG equation, this fix has to be the last defined 
 magnetic fix before the integration/spin fix. As an example:
@@ -97,6 +97,5 @@ This fix has to be the last defined magnetic fix before the integration fix
 :link(Mayergoyz1)
 [(Mayergoyz)] I.D. Mayergoyz, G. Bertotti, C. Serpico (2009). Elsevier (2009)
 
-:link(Tranchida1)
-[(Tranchida)] J. Tranchida, S.J. Plimpton, P. Thibaudeau, A.P. Thompson. 
-arXiv preprint arXiv:1801.10233. (2018)
+:link(Tranchida2)
+[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson. 

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"_#Zhang1 by Sharon Glotzer's group, clumps of
-granular particles, lipid molecules consisting of one or more point
+modeled in "this paper"_#Zhang3 by Sharon Glotzer's group, clumps of
+granular particles, lipid molecules consiting 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
@@ -851,5 +851,5 @@ Martyna, Tuckerman, Tobias, Klein, Mol Phys, 87, 1117.
 [(Miller)] Miller, Eleftheriou, Pattnaik, Ndirango, and Newns,
 J Chem Phys, 116, 8649 (2002).
 
-:link(Zhang1)
+:link(Zhang3)
 [(Zhang)] Zhang, Glotzer, Nanoletters, 4, 1407-1413 (2004).

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"_#Zhang2 for a discussion and results
+molecules.  See the "Zhang paper"_#Zhang1 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(Zhang2)
+:link(Zhang1)
 [(Zhang)] Zhang, Lussetti, de Souza, Muller-Plathe, J Phys Chem B,
 109, 15060-15067 (2005).

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)"_#Zhang3, when the distance r between two particles of radii
+"(Zhang)"_#Zhang4, 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)"_#Zhang3 paper, Kn = 4G /
+pressure, and as shown in the "(Zhang)"_#Zhang4 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(Zhang3)
+:link(Zhang4)
 [(Zhang)] Zhang and Makse, Phys Rev E, 72, p 011301 (2005).

doc/src/pair_meam_spline.txt

@@ -164,5 +164,9 @@ for more info.
 Kress, Modelling Simulation Materials Science Engineering, 8, 825
 (2000).
 
+<<<<<<< HEAD
 :link(Zhang4)
+=======
+:link(Zhang2)
+>>>>>>> Documentation V1
 [(Zhang)] Zhang and Trinkle, Computational Materials Science, 124, 204-210 (2016).

doc/src/pair_spin_exchange.txt

@@ -45,7 +45,7 @@ The coefficients a, b, and d need to be fitted so that the function above matche
 the value of the exchange interaction for the N neighbor shells taken into account.
 
 Examples and more explanations about this function and its parametrization are reported 
-in "(Tranchida)"_#Tranchida1.
+in "(Tranchida)"_#Tranchida3.
 
 From this exchange interaction, each spin i will be submitted 
 to a magnetic torque omega, and its associated atom can be submitted to a
@@ -57,7 +57,7 @@ force F for spin-lattice calculations (see
 with h the Planck constant (in metal units).
 
 More details about the derivation of these torques/forces are reported in
-"(Tranchida)"_#Tranchida1.
+"(Tranchida)"_#Tranchida3.
 
 :line
 
@@ -77,6 +77,5 @@ See the "Making LAMMPS"_Section_start.html#start_3 section for more info.
 
 :line
 
-:link(Tranchida1)
-[(Tranchida)]https://arxiv.org/abs/1801.10233
-
+:link(Tranchida3)
+[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson.

doc/src/pair_spin_me.txt

@@ -45,7 +45,7 @@ force F for spin-lattice calculations (see
 with h the Planck constant (in metal units).
 
 More details about the derivation of these torques/forces are reported in
-"(Tranchida)"_#Tranchida1.
+"(Tranchida)"_#Tranchida4.
 
 :line
 
@@ -68,6 +68,5 @@ See the "Making LAMMPS"_Section_start.html#start_3 section for more info.
 :link(Katsura1)
 [(Katsura)] H. Katsura, N. Nagaosa, A.V. Balatsky. Phys. Rev. Lett., 95(5), 057205. (2005)
 
-:link(Tranchida1)
-[(Tranchida)] J. Tranchida, S.J. Plimpton, P. Thibaudeau, A.P. Thompson. 
-arXiv preprint arXiv:1801.10233. (2018)
+:link(Tranchida4)
+[(Tranchida)] Tranchida, Plimpton, Thibaudeau, and Thompson. 

doc/src/pair_spin_soc_dmi.txt

@@ -49,7 +49,7 @@ the value of the DM interaction for the N neighbor shells taken
 into account.
 
 Examples and more explanations about this function and its parametrization are reported 
-in "(Tranchida)"_#Tranchida1.
+in "(Tranchida)"_#Tranchida5.
 
 From this DM interaction, each spin i will be submitted to a magnetic torque
 omega and its associated atom to a force F (for spin-lattice calculations only), 
@@ -60,7 +60,7 @@ such as:
 with h the Planck constant (in metal units).
 
 More details about the derivation of these torques/forces are reported in
-"(Tranchida)"_#Tranchida1.
+"(Tranchida)"_#Tranchida5.
 
 :line
 
@@ -80,6 +80,5 @@ See the "Making LAMMPS"_Section_start.html#start_3 section for more info.
 
 :line
 
-:link(Tranchida1)
-[(Tranchida)]https://arxiv.org/abs/1801.10233
-
+:link(Tranchida5)
+[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson.

doc/src/pair_spin_soc_neel.txt

@@ -49,7 +49,7 @@ the value of the DM interaction for the N neighbor shells taken
 into account.
 
 Examples and more explanations about this function and its parametrization are reported 
-in "(Tranchida)"_#Tranchida1.
+in "(Tranchida)"_#Tranchida6.
 
 From this DM interaction, each spin i will be submitted to a magnetic torque
 omega and its associated atom to a force F (for spin-lattice calculations only), 
@@ -60,7 +60,7 @@ such as:
 with h the Planck constant (in metal units).
 
 More details about the derivation of these torques/forces are reported in
-"(Tranchida)"_#Tranchida1.
+"(Tranchida)"_#Tranchida6.
 
 :line
 
@@ -80,6 +80,6 @@ See the "Making LAMMPS"_Section_start.html#start_3 section for more info.
 
 :line
 
-:link(Tranchida1)
-[(Tranchida)]https://arxiv.org/abs/1801.10233
+:link(Tranchida6)
+[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson.