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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
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@ -19,7 +19,7 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute cos all viscosity/cos compute cos all viscosity/cos
variable V equal c_cos[7] 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>` This command together with :doc:`fix_accelerate/cos<fix_accelerate_cos>`
enables viscosity calculation with periodic perturbation method, 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 An acceleration along the x-direction is applied to the simulation system
by using :doc:`fix_accelerate/cos<fix_accelerate_cos>` command. by using :doc:`fix_accelerate/cos<fix_accelerate_cos>` command.
The acceleration is a periodic function along the z-direction: 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 discussion of different ways to compute temperature and perform
thermostatting. thermostatting.
---------- ----------
**Output info:** **Output info:**
This compute calculates a global scalar (the temperature) and a global This compute calculates a global scalar (the temperature) and a global
@ -149,9 +147,8 @@ Default
""""""" """""""
none 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
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@ -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 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: The acceleration is a periodic function along the z-direction:
.. math:: .. 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>`, The velocity amplitude :math:`V` can be calculated with :doc:`compute viscosity/cos <compute_viscosity_cos>`,
which enables viscosity calculation with periodic perturbation method, 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, Because the applied acceleration drives the system away from equilibration,
the calculated shear viscosity is lower than the intrinsic viscosity the calculated shear viscosity is lower than the intrinsic viscosity
due to the shear-thinning effect. 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. 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. No information about this fix is written to binary restart files.
None of the fix_modify options are relevant to this fix. None of the fix_modify options are relevant to this fix.
@ -98,9 +96,8 @@ Default
""""""" """""""
none 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.