.. index:: pair: namespace; site
.. _doxid-namespacesite:

namespace site
==============

.. toctree::
	:hidden:

	enum_site_Family.rst
	enum_site_IonState.rst
	enum_site_Kind.rst
	struct_site_DensityZ.rst
	struct_site_GuestOccupancy.rst
	struct_site_IonEnvironment.rst
	struct_site_Table.rst

Overview
~~~~~~~~




.. ref-code-block:: cpp
	:class: doxyrest-overview-code-block

	
	namespace site {

	// enums

	enum :ref:`Family<doxid-namespacesite_1aa3661d15289b4b8576f48217ed337ca3>`;
	enum :ref:`IonState<doxid-namespacesite_1a7cdb003964d40a8454361db4b34b4791>`;
	enum :ref:`Kind<doxid-namespacesite_1adda3a91ca98e5b5e1ffb889ae6440c90>`;

	// structs

	struct :ref:`DensityZ<doxid-structsite_1_1_density_z>`;
	struct :ref:`GuestOccupancy<doxid-structsite_1_1_guest_occupancy>`;
	struct :ref:`IonEnvironment<doxid-structsite_1_1_ion_environment>`;
	struct :ref:`Table<doxid-structsite_1_1_table>`;

	// global functions

	:ref:`DensityZ<doxid-structsite_1_1_density_z>` :ref:`densityZ<doxid-namespacesite_1a75c8588cd72dda60fecb01240009ca6c>`(const :ref:`molSys::PointCloud<doxid-structmol_sys_1_1_point_cloud>`<:ref:`molSys::Point<doxid-structmol_sys_1_1_point>`<double>, double>& yCloud, int typeI, int nbin, int axis);
	:ref:`DensityZ<doxid-structsite_1_1_density_z>` :ref:`densityZ<doxid-namespacesite_1a0e086c58b6a8de67c895bd1e034f58e6>`(const :ref:`molSys::PointCloud<doxid-structmol_sys_1_1_point_cloud>`<:ref:`molSys::Point<doxid-structmol_sys_1_1_point>`<double>, double>& yCloud, const :ref:`Table<doxid-structsite_1_1_table>`& table, :ref:`Kind<doxid-namespacesite_1adda3a91ca98e5b5e1ffb889ae6440c90>` kind, int nbin, int axis);
	bool :target:`iceScoreAllowed<doxid-namespacesite_1a05342583b5b8258d5347b3f18983d4b2>`(:ref:`Family<doxid-namespacesite_1aa3661d15289b4b8576f48217ed337ca3>` f);
	const char* :target:`refuseIceScore<doxid-namespacesite_1a3043411870d52f19774d045fa21dfc09>`(:ref:`Family<doxid-namespacesite_1aa3661d15289b4b8576f48217ed337ca3>` f);
	const char* :target:`familyName<doxid-namespacesite_1a1dacaa43f0631e0bc75cc37531b89ce7>`(:ref:`Family<doxid-namespacesite_1aa3661d15289b4b8576f48217ed337ca3>` f);
	:ref:`Family<doxid-namespacesite_1aa3661d15289b4b8576f48217ed337ca3>` :target:`parseFamily<doxid-namespacesite_1a44e7fbcc66c892d4e98d896e5041cf4c>`(std::string_view name);
	std::vector<int> :target:`indicesOf<doxid-namespacesite_1a651f87e7aaca786cffd536a4d2b286c4>`(const :ref:`molSys::PointCloud<doxid-structmol_sys_1_1_point_cloud>`<:ref:`molSys::Point<doxid-structmol_sys_1_1_point>`<double>, double>& yCloud, const :ref:`Table<doxid-structsite_1_1_table>`& table, :ref:`Kind<doxid-namespacesite_1adda3a91ca98e5b5e1ffb889ae6440c90>` kind);
	int :target:`lammpsTypeOfKind<doxid-namespacesite_1a1dd96ee4ccc36bc86f348ec029859b53>`(const :ref:`Table<doxid-structsite_1_1_table>`& table, :ref:`Kind<doxid-namespacesite_1adda3a91ca98e5b5e1ffb889ae6440c90>` kind);
	:ref:`molSys::PointCloud<doxid-structmol_sys_1_1_point_cloud>`<:ref:`molSys::Point<doxid-structmol_sys_1_1_point>`<double>, double> :target:`ionCloud<doxid-namespacesite_1a55a0dd31fcceddabfa6cda601eeb807c>`(const :ref:`molSys::PointCloud<doxid-structmol_sys_1_1_point_cloud>`<:ref:`molSys::Point<doxid-structmol_sys_1_1_point>`<double>, double>& src, const :ref:`Table<doxid-structsite_1_1_table>`& table);
	:ref:`Table<doxid-structsite_1_1_table>` :target:`parseSiteSpec<doxid-namespacesite_1ab556d24c5f6d7d7be9ba2e4d975259be>`(std::string_view spec);
	:ref:`IonEnvironment<doxid-structsite_1_1_ion_environment>` :ref:`ionEnvironment<doxid-namespacesite_1a59c0f056c026caebb259d8c8e0d032e1>`(const :ref:`molSys::PointCloud<doxid-structmol_sys_1_1_point_cloud>`<:ref:`molSys::Point<doxid-structmol_sys_1_1_point>`<double>, double>& yCloud, const std::vector<bool>& iceFlag, const std::vector<int>& ionIndices, int waterType, double cutoff);
	std::vector<int> :ref:`shellRingCensus<doxid-namespacesite_1a3327b0f82b57a80d113b241dec0eb711>`(const std::vector<std::vector<int>>& rings, const std::vector<int>& shell, int maxRingSize);
	:ref:`GuestOccupancy<doxid-structsite_1_1_guest_occupancy>` :ref:`guestOccupancy<doxid-namespacesite_1adf97b42407e86bc9d067855b19397ac8>`(const :ref:`molSys::PointCloud<doxid-structmol_sys_1_1_point_cloud>`<:ref:`molSys::Point<doxid-structmol_sys_1_1_point>`<double>, double>& yCloud, const std::vector<std::vector<int>>& cages, const std::vector<int>& guestIndices, double radius);
	std::array<double, 3> :ref:`periodicCentroid<doxid-namespacesite_1a208c6e1f8e6106530d6c75bb16dccaad>`(const :ref:`molSys::PointCloud<doxid-structmol_sys_1_1_point_cloud>`<:ref:`molSys::Point<doxid-structmol_sys_1_1_point>`<double>, double>& yCloud, const std::vector<int>& atoms);

	} // namespace site
.. _details-namespacesite:

Detailed Documentation
~~~~~~~~~~~~~~~~~~~~~~



Global Functions
----------------

.. index:: pair: function; densityZ
.. _doxid-namespacesite_1a75c8588cd72dda60fecb01240009ca6c:

.. ref-code-block:: cpp
	:class: doxyrest-title-code-block

	:ref:`DensityZ<doxid-structsite_1_1_density_z>` densityZ(const :ref:`molSys::PointCloud<doxid-structmol_sys_1_1_point_cloud>`<:ref:`molSys::Point<doxid-structmol_sys_1_1_point>`<double>, double>& yCloud, int typeI, int nbin, int axis)

Histogram Point::{x,y,z} for typeI (0 = every atom). axis is 0, 1, or 2.

.. index:: pair: function; densityZ
.. _doxid-namespacesite_1a0e086c58b6a8de67c895bd1e034f58e6:

.. ref-code-block:: cpp
	:class: doxyrest-title-code-block

	:ref:`DensityZ<doxid-structsite_1_1_density_z>` densityZ(const :ref:`molSys::PointCloud<doxid-structmol_sys_1_1_point_cloud>`<:ref:`molSys::Point<doxid-structmol_sys_1_1_point>`<double>, double>& yCloud, const :ref:`Table<doxid-structsite_1_1_table>`& table, :ref:`Kind<doxid-namespacesite_1adda3a91ca98e5b5e1ffb889ae6440c90>` kind, int nbin, int axis)

Same histogram, restricted to atoms whose :ref:`Table <doxid-structsite_1_1_table>` kind matches.

.. index:: pair: function; ionEnvironment
.. _doxid-namespacesite_1a59c0f056c026caebb259d8c8e0d032e1:

.. ref-code-block:: cpp
	:class: doxyrest-title-code-block

	:ref:`IonEnvironment<doxid-structsite_1_1_ion_environment>` ionEnvironment(const :ref:`molSys::PointCloud<doxid-structmol_sys_1_1_point_cloud>`<:ref:`molSys::Point<doxid-structmol_sys_1_1_point>`<double>, double>& yCloud, const std::vector<bool>& iceFlag, const std::vector<int>& ionIndices, int waterType, double cutoff)

``iceFlag`` is indexed like ``yCloud.pts``; ``waterType`` selects the water oxygens (0 accepts every atom that is not an ion); ``cutoff`` is the first shell radius in the cloud's length unit.

.. index:: pair: function; shellRingCensus
.. _doxid-namespacesite_1a3327b0f82b57a80d113b241dec0eb711:

.. ref-code-block:: cpp
	:class: doxyrest-title-code-block

	std::vector<int> shellRingCensus(const std::vector<std::vector<int>>& rings, const std::vector<int>& shell, int maxRingSize)

Rings of the water network that pass through a first shell: the census by size of every ring with at least one vertex in ``shell``.

An ion is not a vertex of the network, so the rings it would have closed are gone and the rings its shell still carries measure how far the network survives around it (the hydration-shell ring census of a brine or an ionic solution). ``census[s]`` counts rings of size s up to ``maxRingSize``.

.. index:: pair: function; guestOccupancy
.. _doxid-namespacesite_1adf97b42407e86bc9d067855b19397ac8:

.. ref-code-block:: cpp
	:class: doxyrest-title-code-block

	:ref:`GuestOccupancy<doxid-structsite_1_1_guest_occupancy>` guestOccupancy(const :ref:`molSys::PointCloud<doxid-structmol_sys_1_1_point_cloud>`<:ref:`molSys::Point<doxid-structmol_sys_1_1_point>`<double>, double>& yCloud, const std::vector<std::vector<int>>& cages, const std::vector<int>& guestIndices, double radius)

``cages`` are vertex index lists into ``yCloud.pts``; ``radius`` in the cloud's length unit (half the cage diameter, about 4 A for a 5^12 cage).

.. index:: pair: function; periodicCentroid
.. _doxid-namespacesite_1a208c6e1f8e6106530d6c75bb16dccaad:

.. ref-code-block:: cpp
	:class: doxyrest-title-code-block

	std::array<double, 3> periodicCentroid(const :ref:`molSys::PointCloud<doxid-structmol_sys_1_1_point_cloud>`<:ref:`molSys::Point<doxid-structmol_sys_1_1_point>`<double>, double>& yCloud, const std::vector<int>& atoms)

Periodic centroid of a set of atoms: every atom is unwrapped to its minimum image about the first, and the mean is taken there.