Fix grammar and capitalization

doc/sphinx/advanced_methods.rst

@@ -1428,7 +1428,7 @@ it is possible to choose parameters for which the LB is more stable. The species
 
     ek.add_species(species)
 
-One can also add the species during the initialization step of the 
+One can also add the species during the initialization step of the
 :class:`espressomd.electrokinetics.Electrokinetics` by defining the list variable ``species``::
 
     ek = espressomd.electrokinetics.Electrokinetics(species=[species], ...)
@@ -1694,16 +1694,16 @@ bonded particles.
 Monte Carlo Methods
 -------------------
 
-.. note:: The whole Reaction Ensemble module uses Monte Carlo moves which require potential energies. Therefore the Reaction Ensemble requires support for energy calculations for all interactions which are used in the simulation. Please also note that the Monte Carlo methods may create and delete particles from the system. This process can invalidate particle ids.
+.. note:: The whole Reaction Ensemble module uses Monte Carlo moves which require potential energies. Therefore the Reaction Ensemble requires support for energy calculations for all interactions which are used in the simulation. Please also note that Monte Carlo methods may create and delete particles from the system. This process can invalidate particle ids.
 
 .. _Reaction Ensemble:
 
 Reaction Ensemble
 ~~~~~~~~~~~~~~~~~
 
 For a description of the available methods see :mod:`espressomd.reaction_ensemble`.
-Multiple reactions can be added to the same instance of the reaction ensemble. 
-An Example script can be found here:
+Multiple reactions can be added to the same instance of the reaction ensemble.
+An example script can be found here:
 
 * `Reaction ensemble / constant pH ensemble <https://github.com/espressomd/espresso/blob/python/samples/reaction_ensemble.py>`_
 
@@ -1793,7 +1793,7 @@ The parameter :math:`\Gamma` proportional to the reaction constant. It is define
 
 where :math:`\left<N_i\right>/V` is the average number density of particles of type :math:`i`.
 Note that the dimension of :math:`\Gamma` is :math:`V^{\bar\nu}`, therefore its
-units must be consistent with the units in which Espresso measures the box volume,
+units must be consistent with the units in which |es| measures the box volume,
 i.e. :math:`\sigma^3`.
 
 It is often convenient, and in some cases even necessary, that some particles
@@ -1807,16 +1807,16 @@ coefficients allow for it.  Corresponding means having the same position (index)
 the python lists of reactants and products which are used to set up the
 reaction.
 
-.. _Converting tabulated reaction constants to internal units in Espresso:
+.. _Converting tabulated reaction constants to internal units in ESPResSo:
 
-Converting tabulated reaction constants to internal units in Espresso
+Converting tabulated reaction constants to internal units in ESPResSo
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-The implementation in Espresso requires that the dimension of :math:`\Gamma`
-is consistent with the internal unit of volume, :math:`\sigma^3`. 
-The tabulated values of equilibrium constants for reactions in solution, :math:`K_c`, typically use
+The implementation in |es| requires that the dimension of :math:`\Gamma`
+is consistent with the internal unit of volume, :math:`\sigma^3`. The tabulated
+values of equilibrium constants for reactions in solution, :math:`K_c`, typically use
 :math:`c^{\ominus} = 1\,\mathrm{moldm^{-3}}` as the reference concentration,
-and have the dimension of :math:`(c^{\ominus})^{\bar\nu}`.  To be used with Espresso, the
+and have the dimension of :math:`(c^{\ominus})^{\bar\nu}`. To be used with |es|, the
 value of :math:`K_c` has to be converted as
 
 .. math::
@@ -1847,8 +1847,7 @@ An example script can be found here:
 * `Wang-Landau reaction ensemble <https://github.com/espressomd/espresso/blob/python/samples/wang_landau_reaction_ensemble.py>`__
 
 Combination of the Reaction Ensemble with the Wang-Landau algorithm
-:cite:`wang01a`
-allows for enhanced sampling of the reacting system, and
+:cite:`wang01a`. Allows for enhanced sampling of the reacting system
 and for the determination of the density of states with respect
 to the reaction coordinate or with respect to some other collective
 variable :cite:`landsgesell17a`. Here the 1/t Wang-Landau
@@ -1860,35 +1859,34 @@ Wang-Landau reaction ensemble.
 Multiple reactions and multiple collective variables can be set.
 For a description of the available methods see :mod:`espressomd.reaction_ensemble`:
 
-
-
 .. _Grand canonical ensemble simulation using the Reaction Ensemble:
 
-Grand canonical ensemble simulation 
+Grand canonical ensemble simulation
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 As a special case, all stoichiometric coefficients on one side of the chemical
-reaction can be set to zero.  Such reaction creates particles *ex nihilo*, and
-is equivalent to exchange with a reservoir. Then the simulation in the reaction ensemble becomes equivalent with the
-grandcanonical simulation. Formally, this can be expressed by the reaction
+reaction can be set to zero. Such a reaction creates particles *ex nihilo*, and
+is equivalent to exchanging particles with a reservoir. Then the simulation
+in the reaction ensemble becomes equivalent to the grand canonical simulation.
+Formally, this can be expressed by the reaction
 
 .. math::
 
     \mathrm{\emptyset \rightleftharpoons\ \nu_A A  }  \,,
 
 where, if :math:`\nu_A=1`, the reaction constant :math:`\Gamma` defines the chemical potential of species A.
 However, if :math:`\nu_A\neq 1`, the statistics of the reaction ensemble becomes
-equivalent to the grandcanonical only in the limit of large average number of species A in the box.
+equivalent to the grand canonical only in the limit of large average number of species A in the box.
 If the reaction contains more than one product, then the reaction constant
 :math:`\Gamma` defines only the sum of their chemical potentials but not the
 chemical potential of each product alone.
 
 Since the Reaction Ensemble acceptance transition probability can be
-derived from the grand canonical acceptance transition probability we
+derived from the grand canonical acceptance transition probability, we
 can use the reaction ensemble to implement grand canonical simulation
-moves. This is done via adding reactions that only have reactants (for the
+moves. This is done by adding reactions that only have reactants (for the
 deletion of particles) or only have products (for the creation of
-particles). There exists a one to one mapping of the expressions in the
+particles). There exists a one-to-one mapping of the expressions in the
 grand canonical transition probabilities and the expressions in the
 reaction ensemble transition probabilities.
 
@@ -1912,7 +1910,7 @@ As before in the Reaction Ensemble one can define multiple reactions (e.g. for a
     cpH.add_reaction(gamma=1/(10**-14/K_diss), reactant_types=[3], reactant_coefficients=[1], product_types=[0, 2], product_coefficients=[1, 1], default_charges={0:0, 2:1, 3:1} )
 
 
-An Example script can be found here:
+An example script can be found here:
 
 * `Reaction ensemble / constant pH ensemble <https://github.com/espressomd/espresso/blob/python/samples/reaction_ensemble.py>`_
 
@@ -1943,7 +1941,7 @@ For a description of the available methods see :mod:`espressomd.reaction_ensembl
 Widom Insertion (for homogeneous systems)
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-The Widom insertion method measures the change in excess free energy , i.e. the excess chemical potential due to the insertion of a new particle, or a group of particles:
+The Widom insertion method measures the change in excess free energy, i.e. the excess chemical potential due to the insertion of a new particle, or a group of particles:
 
 .. math::
 
@@ -1964,9 +1962,9 @@ For this one has to provide the following reaction to the Widom method:
 
 
 The call of ``add_reaction`` define the insertion :math:`\mathrm{\emptyset \to type_B}` (which is the 0th defined reaction).
-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 isertion is defined, then the excess chemical potential for this insertion can be measured by calling ``widom.measure_excess_chemical_potential(1)``. 
+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 isertion 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.
 
 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.:
@@ -1976,7 +1974,7 @@ The implementation can also deal with the simultaneous insertion of multiple par
    \mu^\mathrm{ex, pair}&:=\Delta F^\mathrm{ex, pair}:= F^\mathrm{ex}(N_1+1, N_2+1,V,T)-F^\mathrm{ex}(N_1, N_2 ,V,T)\\
    &=-kT \ln \left(\frac{1}{V^2} \int_V \int_V d^3r_{N_1+1} d^3 r_{N_2+1} \langle \exp(-\beta \Delta E_\mathrm{pot}) \rangle_{N_1, N_2} \right)
 
-Note that the measurement involves three averages: the canonical ensemble average :math:`\langle \cdot \rangle_{N_1, N_2}` and the two averages over the position of particles :math:`N_1+1` and :math:`N_2+1`. 
+Note that the measurement involves three averages: the canonical ensemble average :math:`\langle \cdot \rangle_{N_1, N_2}` and the two averages over the position of particles :math:`N_1+1` and :math:`N_2+1`.
 Since the averages over the position of the inserted particles are obtained via brute force sampling of the insertion positions it can be beneficial to have multiple insertion tries on the same configuration of the other particles.
 
 One can measure the change in excess free energy due to the simultaneous insertions of particles of type 1 and 2 and the simultaneous removal of a particle of type 3:
@@ -1994,9 +1992,9 @@ For this one has to provide the following reaction to the Widom method:
     product_coefficients=[1,1], default_charges={1: 0})
     widom.measure_excess_chemical_potential(0)
 
-Be aware that in the current implementation for MC moves which add and remove particles, the insertion of the new particle always takes place at the position where the last particle was removed. Be sure that this is the behaviour you want to have. Otherwise implement a new function ``WidomInsertion::make_reaction_attempt`` in the core. 
+Be aware that in the current implementation, for MC moves which add and remove particles, the insertion of the new particle always takes place at the position where the last particle was removed. Be sure that this is the behaviour you want to have. Otherwise implement a new function ``WidomInsertion::make_reaction_attempt`` in the core.
 
-An example script which demonstrates the useage for measuring the pair excess chemical potential for inserting an ion pair into a salt solution can be found here:
+An example script which demonstrates the usage for measuring the pair excess chemical potential for inserting an ion pair into a salt solution can be found here:
 
 * `Widom Insertion <https://github.com/espressomd/espresso/blob/python/samples/widom_insertion.py>`_
 

doc/sphinx/electrostatics.rst

@@ -455,24 +455,24 @@ one.
 For details on the MMM family of algorithms, refer to appendix :ref:`The MMM family of algorithms`.
 
 
-.. _Scafacos Electrostatics:
+.. _ScaFaCoS Electrostatics:
 
-Scafacos Electrostatics
+ScaFaCoS Electrostatics
 -----------------------
 
-Espresso can use the electrostatics methods from the SCAFACOS *Scalable
+|es| can use the electrostatics methods from the ScaFaCoS *Scalable
 fast Coulomb solvers* library. The specific methods available depend on the compile-time options of the library, and can be queried using :meth:`espressomd.scafacos.available_methods`
 
-To use SCAFACOS, create an instance of :class:`espressomd.electrostatics.Scafacos` and add it to the list of active actors. Three parameters have to be specified:
+To use ScaFaCoS, create an instance of :class:`espressomd.electrostatics.Scafacos` and add it to the list of active actors. Three parameters have to be specified:
 
-* ``method_name``: name of the SCAFACOS method being used.
+* ``method_name``: name of the ScaFaCoS method being used.
 * ``method_params``: dictionary containing the method-specific parameters
 * ``prefactor``: Coulomb prefactor as defined in :eq:`coulomb_prefactor`.
 
-The method-specific parameters are described in the SCAFACOS manual.
-Additionally, methods supporting tuning have the parameter ``tolerance_field`` which sets the desired root mean square accuracy for the electric field
+The method-specific parameters are described in the ScaFaCoS manual.
+In addition, methods supporting tuning have a parameter ``tolerance_field`` which sets the desired root mean square accuracy for the electric field.
 
-To use the, e.g.,  ``ewald`` solver from SCAFACOS as electrostatics solver for your system, set its
+To use the, e.g., ``ewald`` solver from ScaFaCoS as electrostatics solver for your system, set its
 cutoff to :math:`1.5` and tune the other parameters for an accuracy of
 :math:`10^{-3}`, use::
 
@@ -483,5 +483,5 @@ cutoff to :math:`1.5` and tune the other parameters for an accuracy of
 
 
 For details of the various methods and their parameters please refer to
-the SCAFACOS manual. To use this feature, SCAFACOS has to be built as a shared library. SCAFACOS can be used only once, either for Coulomb or for dipolar interactions.
+the ScaFaCoS manual. To use this feature, ScaFaCoS has to be built as a shared library. ScaFaCoS can be used only once, either for Coulomb or for dipolar interactions.
 

doc/sphinx/installation.rst

@@ -240,7 +240,7 @@ lines below (optional steps which modify the build process are commented out):
     #cp myconfig-default.hpp myconfig.hpp # use the default configuration as template
     #nano myconfig.hpp                    # edit to add/remove features as desired
     cmake ..
-    #ccmake . // in order to add/remove features like SCAFACOS or CUDA
+    #ccmake . // in order to add/remove features like ScaFaCoS or CUDA
     make
 
 This will build |es| with a default feature set, namely

doc/sphinx/io.rst

@@ -98,7 +98,7 @@ Be aware of the following limitations:
 
   * Checkpointing makes use of the ``pickle`` python package. Objects will only be restored as far as they support pickling. This is the case for Python's basic data types, ``numpy`` arrays and many other objects. Still, pickling support cannot be taken for granted.
 
-  * Pickling support of the Espresso system instance and contained objects such as bonded and non-bonded interactions and electrostatics methods. However, there are many more combinations of active interactions and algorithms then can be tested.
+  * Pickling support of the :class:`espressomd.system.System` instance and contained objects such as bonded and non-bonded interactions and electrostatics methods. However, there are many more combinations of active interactions and algorithms then can be tested.
 
   * The active actors, i.e., the content of ``system.actors``, are checkpointed. For lattice-Boltzmann fluids, this only includes the parameters such as the lattice constant (``agrid``). The actual flow field has to be saved separately with the lattice-Boltzmann specific methods 
     :meth:`espressomd.lb.HydrodynamicInteraction.save_checkpoint`

doc/sphinx/lb.rst

@@ -259,7 +259,7 @@ Choosing between the GPU and CPU implementations
 
 .. note:: Feature ``CUDA`` required
 
-Espresso contains an implementation of the LBM for NVIDIA
+|es| contains an implementation of the LBM for NVIDIA
 GPUs using the CUDA framework. On CUDA-supporting machines this can be
 activated by compiling with the feature ``CUDA``. Within the
 Python script, the :class:`~espressomd.lb.LBFluid` object can be substituted with the :class:`~espressomd.lb.LBFluidGPU` object to switch from CPU based to GPU based execution. For further

doc/sphinx/magnetostatics.rst

@@ -163,28 +163,28 @@ To use the method, create an instance of :class:`~espressomd.magnetostatics.Dipo
   bh = DipolarBarnesHutGpu(prefactor=pf_dds_gpu, epssq=200.0, itolsq=8.0)
   system.actors.add(bh)
 
-.. _Scafacos Magnetostatics:
+.. _ScaFaCoS Magnetostatics:
 
-Scafacos Magnetostatics
+ScaFaCoS Magnetostatics
 -----------------------
 
-Espresso can use the methods from the Scafacos *Scalable fast Coulomb solvers*
+|es| can use the methods from the ScaFaCoS *Scalable fast Coulomb solvers*
 library for dipoles, if the methods support dipolar calculations. The feature
 ``SCAFACOS_DIPOLES`` has to be added to :file:`myconfig.hpp` to activate this
 feature. Dipolar calculations are only included in the ``dipolar`` branch of
-the Scafacos code.
+the ScaFaCoS code.
 
-To use SCAFACOS, create an instance of :class:`~espressomd.magnetostatics.Scafacos`
+To use ScaFaCoS, create an instance of :class:`~espressomd.magnetostatics.Scafacos`
 and add it to the list of active actors. Three parameters have to be specified:
 
-* ``method_name``: name of the SCAFACOS method being used.
+* ``method_name``: name of the ScaFaCoS method being used.
 * ``method_params``: dictionary containing the method-specific parameters
 * ``prefactor``
 
-The method-specific parameters are described in the SCAFACOS manual.
-Additionally, methods supporting tuning have the parameter ``tolerance_field`` which sets the desired root mean square accuracy for the electric field
+The method-specific parameters are described in the ScaFaCoS manual.
+In addition, methods supporting tuning have a parameter ``tolerance_field`` which sets the desired root mean square accuracy for the electric field
 
 For details of the various methods and their parameters please refer to
-the SCAFACOS manual. To use this feature, SCAFACOS has to be built as a shared library. SCAFACOS can be used only once, either for Coulomb or for dipolar interactions.
+the ScaFaCoS manual. To use this feature, ScaFaCoS has to be built as a shared library. ScaFaCoS can be used only once, either for Coulomb or for dipolar interactions.
 
 

doc/tutorials/01-lennard_jones/01-lennard_jones.ipynb

@@ -86,7 +86,7 @@
    "source": [
     "## Units\n",
     "\n",
-    "Novice users must understand that Espresso has no fixed unit system. The unit \n",
+    "Novice users must understand that ESPResSo has no fixed unit system. The unit \n",
     "system is set by the user. Conventionally, reduced units are employed, in other \n",
     "words LJ units."
    ]

doc/tutorials/11-ferrofluid/11-ferrofluid_part1.ipynb

@@ -221,7 +221,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "We start with checking for the presence of Espresso features and importing all necessary packages."
+    "We start with checking for the presence of ESPResSo features and importing all necessary packages."
    ]
   },
   {

doc/tutorials/11-ferrofluid/11-ferrofluid_part2.ipynb

@@ -41,7 +41,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "We import all necessary packages and check for the required Espresso features"
+    "We import all necessary packages and check for the required ESPResSo features"
    ]
   },
   {

doc/tutorials/11-ferrofluid/11-ferrofluid_part3.ipynb

@@ -112,7 +112,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "First we import all necessary packages and check for the required Espresso features"
+    "First we import all necessary packages and check for the required ESPResSo features"
    ]
   },
   {