Loading doc/src/fix_eco_force.rst +58 −21 Changes for doc/src/fix_eco_force.rst: 58 added lines, 21 removed lines. Original line number Diff line number Diff line 1 fix eco/force command .. index:: fix eco/force fix eco/force command ===================== .. parsed-literal:: fix ID group-ID eco/force u0 eta rcut file • ID, group-ID are documented in fix command • u0 = energy added to each atom (energy units) • eta = cutoff value (usually 0.25) • rcut = cutoff radius for orientation parameter calculation • file = file that specifies orientation of each grain Examples: fix gb all eco/force 0.08 0.25 3.524 sigma5.ori * ID, group-ID are documented in fix command * u0 = energy added to each atom (energy units) * eta = cutoff value (usually 0.25) * rcut = cutoff radius for orientation parameter calculation * file = file that specifies orientation of each grain Examples """""""" .. code-block:: LAMMPS 1.1 Description: fix gb all eco/force 0.08 0.25 3.524 sigma5.ori Description """"""""""" The fix applies a synthetic driving force to a grain boundary which can be used for the investigation of grain boundary motion. The affiliation Loading @@ -28,6 +43,8 @@ described in (Ulomek), the implementation follows the efficient implementation from (Schratt & Mohles). The synthetic potential energy added to an atom j is given by the following formulas .. math:: \begin{eqnarray} w(|\vec{r}_{jk}|)=w_{jk}=\left\{\begin{array}{lc} \frac{|\vec{r}_{jk}|^{4}}{r_{\mathrm{cut}}^{4}}-2\frac{|\vec{r}_{jk}|^{2}}{r_{\mathrm{cut}}^{2}}+1, & |\vec{r}_{jk}|<r_{\mathrm{cut}} \\ Loading @@ -51,7 +68,8 @@ u(\chi_{j}) & = & \frac{u_{0}}{2}\left\{\begin{array}{lc} \label{eq:energy-mid} \end{eqnarray} which are fully explained in (Ulomek) and (Schratt & Mohles). which are fully explained in :ref: `(Ulomek) <Ulomek>` and `(Schratt & Mohles) <Schratt>`. 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 Loading Loading @@ -85,12 +103,13 @@ simulation. 1.2 Restart, fix_modify, output, run start/stop, minimize info: **Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to binary restart files. The fix_modify energy option is supported by this fix to add the potential energy of atominteractions with the grain boundary driving force to the system's poten- tial energy as part of thermodynamic output. No information about this fix is written to :doc: `binary restart files`. The :doc:`fix_modify <fix_modify>` *energy* option is supported by this fix to add the potential energy of atom interactions with the grain boundary driving force to the system's potential energy as part of thermodynamic output. The total sum of added synthetic potential energy is computed and can be accessed 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 Loading @@ -101,26 +120,43 @@ not invoked during energy minimization. 1.3 Restrictions: 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. 1.4 Related commands: Related commands """""""""""""""" :doc:`fix_modify <fix_modify>` fix_modify Default: none (Ulomek) Felix Ulomek et al. Modelling Simul. Mater. Sci. Eng. 23 (2015) 025007 (Schratt & Mohles) Adrian A. Schratt and Volker Mohles. Comp. Mat. Sci. 182 (2020) 109774 **Default:** none For illustration purposes, here is an example file that specifies a $\Sigma5\langle001\rangle$ tilt grain boundary. ---------- .. _Ulomek: **(Ulomek)** Ulomek, Brien, Foiles, Mohles, Modelling Simul. Mater. Sci. Eng. 23 (2015) 025007 .. _Schratt: **(Schratt)** Schratt, Mohles. Comp. Mat. Sci. 182 (2020) 109774 ---------- For illustration purposes, here is an example file that specifies a Sigma=5 <001> tilt grain boundary. This is for a lattice constant of 3.52 Angs. file: .. parsed-literal:: 1.5 File: 1.671685 0.557228 1.76212 0.557228 -1.671685 1.76212 2.228913 -1.114456 0.000000 Loading @@ -128,3 +164,4 @@ This is for a lattice constant of 3.52 Angs. 1.671685 -0.557228 1.76212 2.228913 1.114456 0.000000 Loading
doc/src/fix_eco_force.rst +58 −21 Changes for doc/src/fix_eco_force.rst: 58 added lines, 21 removed lines. Original line number Diff line number Diff line 1 fix eco/force command .. index:: fix eco/force fix eco/force command ===================== .. parsed-literal:: fix ID group-ID eco/force u0 eta rcut file • ID, group-ID are documented in fix command • u0 = energy added to each atom (energy units) • eta = cutoff value (usually 0.25) • rcut = cutoff radius for orientation parameter calculation • file = file that specifies orientation of each grain Examples: fix gb all eco/force 0.08 0.25 3.524 sigma5.ori * ID, group-ID are documented in fix command * u0 = energy added to each atom (energy units) * eta = cutoff value (usually 0.25) * rcut = cutoff radius for orientation parameter calculation * file = file that specifies orientation of each grain Examples """""""" .. code-block:: LAMMPS 1.1 Description: fix gb all eco/force 0.08 0.25 3.524 sigma5.ori Description """"""""""" The fix applies a synthetic driving force to a grain boundary which can be used for the investigation of grain boundary motion. The affiliation Loading @@ -28,6 +43,8 @@ described in (Ulomek), the implementation follows the efficient implementation from (Schratt & Mohles). The synthetic potential energy added to an atom j is given by the following formulas .. math:: \begin{eqnarray} w(|\vec{r}_{jk}|)=w_{jk}=\left\{\begin{array}{lc} \frac{|\vec{r}_{jk}|^{4}}{r_{\mathrm{cut}}^{4}}-2\frac{|\vec{r}_{jk}|^{2}}{r_{\mathrm{cut}}^{2}}+1, & |\vec{r}_{jk}|<r_{\mathrm{cut}} \\ Loading @@ -51,7 +68,8 @@ u(\chi_{j}) & = & \frac{u_{0}}{2}\left\{\begin{array}{lc} \label{eq:energy-mid} \end{eqnarray} which are fully explained in (Ulomek) and (Schratt & Mohles). which are fully explained in :ref: `(Ulomek) <Ulomek>` and `(Schratt & Mohles) <Schratt>`. 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 Loading Loading @@ -85,12 +103,13 @@ simulation. 1.2 Restart, fix_modify, output, run start/stop, minimize info: **Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to binary restart files. The fix_modify energy option is supported by this fix to add the potential energy of atominteractions with the grain boundary driving force to the system's poten- tial energy as part of thermodynamic output. No information about this fix is written to :doc: `binary restart files`. The :doc:`fix_modify <fix_modify>` *energy* option is supported by this fix to add the potential energy of atom interactions with the grain boundary driving force to the system's potential energy as part of thermodynamic output. The total sum of added synthetic potential energy is computed and can be accessed 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 Loading @@ -101,26 +120,43 @@ not invoked during energy minimization. 1.3 Restrictions: 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. 1.4 Related commands: Related commands """""""""""""""" :doc:`fix_modify <fix_modify>` fix_modify Default: none (Ulomek) Felix Ulomek et al. Modelling Simul. Mater. Sci. Eng. 23 (2015) 025007 (Schratt & Mohles) Adrian A. Schratt and Volker Mohles. Comp. Mat. Sci. 182 (2020) 109774 **Default:** none For illustration purposes, here is an example file that specifies a $\Sigma5\langle001\rangle$ tilt grain boundary. ---------- .. _Ulomek: **(Ulomek)** Ulomek, Brien, Foiles, Mohles, Modelling Simul. Mater. Sci. Eng. 23 (2015) 025007 .. _Schratt: **(Schratt)** Schratt, Mohles. Comp. Mat. Sci. 182 (2020) 109774 ---------- For illustration purposes, here is an example file that specifies a Sigma=5 <001> tilt grain boundary. This is for a lattice constant of 3.52 Angs. file: .. parsed-literal:: 1.5 File: 1.671685 0.557228 1.76212 0.557228 -1.671685 1.76212 2.228913 -1.114456 0.000000 Loading @@ -128,3 +164,4 @@ This is for a lattice constant of 3.52 Angs. 1.671685 -0.557228 1.76212 2.228913 1.114456 0.000000
