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Central chapter for thermostats and integrators #4080

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Jan 4, 2021
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Central chapter for thermostats and integrators #4080

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b0055bf
docs: Fix thermostat/integrator/cellsystem names
jngrad Dec 31, 2020
7e9d2c0
docs: Restructure chapter on integrators
jngrad Dec 31, 2020
4ceb80c
docs: Re-arrange integrators and thermostats
jngrad Dec 31, 2020
c49cc64
docs: Move thermostats into integrators chapter
jngrad Jan 1, 2021
36bd7ed
docs: Add section on Brownian Dynamics
jngrad Jan 1, 2021
c51a3f6
docs: Update link in Jupyter notebook
jngrad Jan 1, 2021
c8042b2
docs: Clarify Brownian text
jngrad Jan 4, 2021
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2 changes: 1 addition & 1 deletion doc/sphinx/advanced_methods.rst
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Expand Up @@ -1894,7 +1894,7 @@ The call of ``add_reaction`` define the insertion :math:`\mathrm{\emptyset \to t
Multiple reactions for the insertions of different types can be added to the same ``WidomInsertion`` instance.
Measuring the excess chemical potential using the insertion method is done via calling ``widom.measure_excess_chemical_potential(0)``.
If another particle insertion is defined, then the excess chemical potential for this insertion can be measured by calling ``widom.measure_excess_chemical_potential(1)``.
Be aware that the implemented method only works for the canonical ensemble. If the numbers of particles fluctuate (i.e. in a semi grand canonical simulation) one has to adapt the formulas from which the excess chemical potential is calculated! This is not implemented. Also in a isobaric-isothermal simulation (NPT) the corresponding formulas for the excess chemical potentials need to be adapted. This is not implemented.
Be aware that the implemented method only works for the canonical ensemble. If the numbers of particles fluctuate (i.e. in a semi grand canonical simulation) one has to adapt the formulas from which the excess chemical potential is calculated! This is not implemented. Also in a isobaric-isothermal simulation (NpT) the corresponding formulas for the excess chemical potentials need to be adapted. This is not implemented.

The implementation can also deal with the simultaneous insertion of multiple particles and can therefore measure the change of excess free energy of multiple particles like e.g.:

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4 changes: 2 additions & 2 deletions doc/sphinx/electrostatics.rst
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Expand Up @@ -318,7 +318,7 @@ MMM1D is used with::

where the prefactor :math:`C` is defined in Eqn. :eq:`coulomb_prefactor`.
MMM1D Coulomb method for systems with periodicity (0 0 1). Needs the
nsquared cell system (see section :ref:`Cellsystems`). The first form sets parameters
N-squared cell system (see section :ref:`Cellsystems`). The first form sets parameters
manually. The switch radius determines at which xy-distance the force
calculation switches from the near to the far formula. The Bessel cutoff
does not need to be specified as it is automatically determined from the
Expand All @@ -336,7 +336,7 @@ MMM1D on GPU
:class:`espressomd.electrostatics.MMM1DGPU`

MMM1D is also available in a GPU implementation. Unlike its CPU
counterpart, it does not need the nsquared cell system.
counterpart, it does not need the N-squared cell system.

::

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4 changes: 2 additions & 2 deletions doc/sphinx/installation.rst
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Expand Up @@ -355,9 +355,9 @@ General features
In addition, there are switches that enable additional features in the
integrator or thermostat:

- ``NPT`` Enables an on-the-fly NPT integration scheme.
- ``NPT`` Enables an on-the-fly NpT integration scheme.

.. seealso:: :ref:`Isotropic NPT thermostat`
.. seealso:: :ref:`Isotropic NpT thermostat`

- ``ENGINE``

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2 changes: 1 addition & 1 deletion doc/sphinx/introduction.rst
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Expand Up @@ -448,7 +448,7 @@ report so to the developers using the instructions in :ref:`Contributing`.
+--------------------------------+------------------------+------------------+------------+
| Langevin Thermostat | Core | Core | Yes |
+--------------------------------+------------------------+------------------+------------+
| Isotropic NPT | Experimental | None | Yes |
| Isotropic NpT | Experimental | None | Yes |
+--------------------------------+------------------------+------------------+------------+
| Quaternion Integrator | Core | Good | Yes |
+--------------------------------+------------------------+------------------+------------+
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