diff --git a/doc/src/fix_eco_force.rst b/doc/src/fix_eco_force.rst index fdaa119b5b..94a96cb784 100644 --- a/doc/src/fix_eco_force.rst +++ b/doc/src/fix_eco_force.rst @@ -30,7 +30,7 @@ The fix applies a synthetic driving force to a grain boundary which can be used for the investigation of grain boundary motion. The affiliation of atoms to either of the two grains forming the grain boundary is determined from an orientation-dependent order parameter as described -in (Ulomek). The potential energy of atoms is either increased by an amount +in :ref:`(Ulomek) `. The potential energy of atoms is either increased by an amount of 0.5*u0 or -0.5*u0 according to the orientation of the surrounding crystal. This creates a potential energy gradient which pushes atoms near the grain boundary to orient according to the energetically favorable @@ -39,8 +39,8 @@ with one grain boundary and open ends, or two opposite grain boundaries in a periodic system. In either case, the entire system can experience a displacement during the simulation which needs to be accounted for in the evaluation of the grain boundary velocity. While the basic method is -described in (Ulomek), the implementation follows the efficient -implementation from (Schratt & Mohles). The synthetic potential energy added to an +described in :ref:`(Ulomek) `, the implementation follows the efficient +implementation from :ref:`(Schratt & Mohles) `. The synthetic potential energy added to an atom j is given by the following formulas .. math:: @@ -68,8 +68,8 @@ u(\chi_{j}) & = & \frac{u_{0}}{2}\left\{\begin{array}{lc} \label{eq:energy-mid} \end{eqnarray} -which are fully explained in :ref: `(Ulomek) ` -and `(Schratt & Mohles) `. +which are fully explained in :ref:`(Ulomek) ` +and :ref:`(Schratt & Mohles) `. The force on each atom is the negative gradient of the synthetic potential energy. It depends on the surrounding of this atom. An atom far from the grain boundary does not @@ -94,7 +94,7 @@ the 6 oriented crystal basis vectors is specified. Each line of the input file contains the three components of a primitive lattice vector oriented according to the grain orientation in the simulation box. The first (last) three lines correspond to the primitive lattice vectors of the first (second) grain. An example for -a Σ5⟨001⟩ misorientation is given at the end. +a :math:`\Sigma\langle001\rangle` misorientation is given at the end. If no synthetic energy difference between the grains is created, u0=0, the force computation is omitted. In this case, the order parameter of the @@ -114,8 +114,8 @@ The total sum of added synthetic potential energy is computed and can be accesse by various output options. The order parameter as well as the thermally masked output parameter are stored in per-atom arrays and can also be accessed by various output commands. -No parameter of this fix -can be used with the start/stop keywords of the run command. This fix is + +No parameter of this fix can be used with the start/stop keywords of the run command. This fix is not invoked during energy minimization. @@ -124,7 +124,7 @@ Restrictions """""""""""" This fix is part of the MISC package. It is only enabled if LAMMPS was -built with that package. See the Making LAMMPS section for more info. +built with that package. See the :doc:`Build package ` doc page for more info. @@ -143,7 +143,7 @@ Related commands .. _Schratt: -**(Schratt)** Schratt, Mohles. Comp. Mat. Sci. 182 (2020) 109774 +**(Schratt & Mohles)** Schratt, Mohles. Comp. Mat. Sci. 182 (2020) 109774 ---------- @@ -153,7 +153,7 @@ Sigma=5 <001> tilt grain boundary. This is for a lattice constant of 3.52 Angs. -file: +sigma5.ori: .. parsed-literal::