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correct minor formatting and markup issues

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This commit is contained in:
Axel Kohlmeyer
2020-04-28 17:23:16 -04:00
parent 681878aa24
commit 846146c9d4
2 changed files with 11 additions and 17 deletions
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11
doc/src/compute_viscosity_cos.rst
View File

@ -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 <thermo_modify>`, :doc:`fix npt <fix_nh>`, etc.
This command together with :doc:`fix_accelerate/cos<fix_accelerate_cos>`
enables viscosity calculation with periodic perturbation method,
as described by :ref:`Hess<Hess>`.
as described by :ref:`Hess<Hess1>`.
An acceleration along the x-direction is applied to the simulation system
by using :doc:`fix_accelerate/cos<fix_accelerate_cos>` command.
The acceleration is a periodic function along the z-direction:
@ -112,10 +112,8 @@ See the :doc:`Howto thermostat <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.

17
doc/src/fix_accelerate_cos.rst
View File

@ -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 <compute_viscosity_cos>`,
which enables viscosity calculation with periodic perturbation method,
as described by :ref:`Hess<Hess>`.
as described by :ref:`Hess<Hess2>`.
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.