diff --git a/doc/src/compute_viscosity_cos.rst b/doc/src/compute_viscosity_cos.rst index 033a7f0956..7c0d130a7a 100644 --- a/doc/src/compute_viscosity_cos.rst +++ b/doc/src/compute_viscosity_cos.rst @@ -19,7 +19,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute cos all viscosity/cos variable V equal c_cos[7] @@ -39,7 +39,7 @@ e.g. :doc:`thermo_modify `, :doc:`fix npt `, etc. This command together with :doc:`fix_accelerate/cos` enables viscosity calculation with periodic perturbation method, -as described by :ref:`Hess`. +as described by :ref:`Hess`. An acceleration along the x-direction is applied to the simulation system by using :doc:`fix_accelerate/cos` command. The acceleration is a periodic function along the z-direction: @@ -112,10 +112,8 @@ See the :doc:`Howto thermostat ` doc page for a discussion of different ways to compute temperature and perform thermostatting. - ---------- - **Output info:** This compute calculates a global scalar (the temperature) and a global @@ -149,9 +147,8 @@ Default """"""" none - ---------- -.. _Hess: +.. _Hess1: -**(Hess)** Hess, B. The Journal of Chemical Physics 2002, 116 (1), 209–217. +**(Hess)** Hess, B. The Journal of Chemical Physics 2002, 116 (1), 209-217. diff --git a/doc/src/fix_accelerate_cos.rst b/doc/src/fix_accelerate_cos.rst index 60281d4acd..e1047dd455 100644 --- a/doc/src/fix_accelerate_cos.rst +++ b/doc/src/fix_accelerate_cos.rst @@ -20,14 +20,14 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS - fix 1 all accelerate/cos 0.02E-5 + fix 1 all accelerate/cos 0.02e-5 Description """"""""""" -Give each atom a acceleration in x-direciton based on its z coordinate. +Give each atom a acceleration in x-direction based on its z coordinate. The acceleration is a periodic function along the z-direction: .. math:: @@ -61,7 +61,7 @@ x-component velocity and z coordinate of a particle. The velocity amplitude :math:`V` can be calculated with :doc:`compute viscosity/cos `, which enables viscosity calculation with periodic perturbation method, -as described by :ref:`Hess`. +as described by :ref:`Hess`. Because the applied acceleration drives the system away from equilibration, the calculated shear viscosity is lower than the intrinsic viscosity due to the shear-thinning effect. @@ -72,11 +72,9 @@ the simulation time must be extended accordingly to get converged result. In order to get meaningful result, the group ID of this fix should be all. - ---------- - -**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. None of the fix_modify options are relevant to this fix. @@ -98,9 +96,8 @@ Default """"""" none - ---------- -.. _Hess: +.. _Hess2: -**(Hess)** Hess, B. The Journal of Chemical Physics 2002, 116 (1), 209–217. +**(Hess)** Hess, B. The Journal of Chemical Physics 2002, 116 (1), 209-217.