move over doxygen comments for a few LAMMPS classes
This commit is contained in:
Axel Kohlmeyer
178
src/atom.cpp
178
src/atom.cpp
@ -47,6 +47,33 @@ using namespace MathConst;
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/* ---------------------------------------------------------------------- */
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/** \class LAMMPS_NS::Atom
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* \brief Class to provide access to atom data
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\verbatim embed:rst
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The Atom class provides access to atom style related global settings and
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per-atom data that is stored with atoms and migrates with them from
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sub-domain to sub-domain as atoms move around. This includes topology
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data, which is stored with either one specific atom or all atoms involved
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depending on the settings of the :doc:`newton command <newton>`.
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The actual per-atom data is allocated and managed by one of the various
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classes derived from the AtomVec class as determined by
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the :doc:`atom_style command <atom_style>`. The pointers in the Atom class
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are updated by the AtomVec class as needed.
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\endverbatim
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*/
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/** Atom class constructor
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*
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* This resets and initialized all kinds of settings,
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* parameters, and pointer variables for per-atom arrays.
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* This also initializes the factory for creating
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* instances of classes derived from the AtomVec base
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* class, which correspond to the selected atom style.
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*
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* \param lmp pointer to the base LAMMPS class */
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Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
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{
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natoms = 0;
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@ -688,7 +715,6 @@ AtomVec *Atom::avec_creator(LAMMPS *lmp)
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return new T(lmp);
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}
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/* ---------------------------------------------------------------------- */
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void Atom::init()
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@ -2301,12 +2327,17 @@ int Atom::find_custom(const char *name, int &flag)
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return -1;
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}
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/* ----------------------------------------------------------------------
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add a custom variable with name of type flag = 0/1 for int/double
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assumes name does not already exist
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return index in ivector or dvector of its location
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------------------------------------------------------------------------- */
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/** \brief Add a custom per-atom property with the given name and type
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\verbatim embed:rst
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This function will add a custom per-atom property with the name "name"
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as either list of int or double to the list of custom properties. This
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function is called, e.g. from :doc:`fix property/atom <fix_property_atom>`.
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\endverbatim
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* \param name Name of the property (w/o a "d_" or "i_" prefix)
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* \param flag Data type of property: 0 for int, 1 for double
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* \return Index of property in the respective list of properties
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*/
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int Atom::add_custom(const char *name, int flag)
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{
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int index;
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@ -2338,12 +2369,19 @@ int Atom::add_custom(const char *name, int flag)
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return index;
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}
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/* ----------------------------------------------------------------------
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remove a custom variable of type flag = 0/1 for int/double at index
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free memory for vector and name and set ptrs to NULL
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ivector/dvector and iname/dname lists never shrink
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------------------------------------------------------------------------- */
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/*! \brief Remove a custom per-atom property of a given type
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*
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\verbatim embed:rst
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This will remove a property that was requested e.g. by the
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:doc:`fix property/atom <fix_property_atom>` command. It frees the
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allocated memory and sets the pointer to ``NULL`` to the entry in
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the list can be reused. The lists of those pointers will never be
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compacted or never shrink, so that index to name mappings remain valid.
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\endverbatim
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*
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* \param flag whether the property is integer (=0) or double (=1)
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* \param index of that property in the respective list.
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*/
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void Atom::remove_custom(int flag, int index)
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{
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if (flag == 0) {
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@ -2359,16 +2397,123 @@ void Atom::remove_custom(int flag, int index)
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}
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}
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/* ----------------------------------------------------------------------
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return a pointer to a named internal variable
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if don't recognize name, return NULL
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------------------------------------------------------------------------- */
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/** Provide access to internal data of the Atom class by keyword
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*
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\verbatim embed:rst
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This function is a way to access internal per-atom data. This data is
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distributed across MPI ranks and thus only the data for "local" atoms
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are expected to be available. Whether also data for "ghost" atoms is
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stored and up-to-date depends on various simulation settings.
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This table lists a large part of the supported names, their data types,
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length of the data area, and a short description.
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.. list-table::
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:header-rows: 1
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:widths: auto
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* - Name
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- Type
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- Items per atom
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- Description
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* - mass
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- double
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- 1
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- per-type mass. This array is **NOT** a per-atom array
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but of length ``ntypes+1``, element 0 is ignored.
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* - id
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- tagint
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- 1
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- atom ID of the particles
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* - type
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- int
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- 1
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- atom type of the particles
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* - mask
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- int
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- 1
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- bitmask for mapping to groups. Individual bits are set
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to 0 or 1 for each group.
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* - image
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- imageint
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- 1
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- 3 image flags encoded into a single integer.
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See :cpp:func:`lammps_encode_image_flags`.
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* - x
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- double
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- 3
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- x-, y-, and z-coordinate of the particles
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* - v
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- double
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- 3
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- x-, y-, and z-component of the velocity of the particles
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* - f
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- double
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- 3
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- x-, y-, and z-component of the force on the particles
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* - molecule
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- int
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- 1
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- molecule ID of the particles
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* - q
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- double
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- 1
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- charge of the particles
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* - mu
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- double
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- 3
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- dipole moment of the particles
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* - omega
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- double
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- 3
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- x-, y-, and z-component of rotational velocity of the particles
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* - angmom
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- double
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- 3
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- x-, y-, and z-component of angular momentum of the particles
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* - torque
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- double
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- 3
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- x-, y-, and z-component of the torque on the particles
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* - radius
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- double
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- 1
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- radius of the (extended) particles
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* - rmass
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- double
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- 1
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- per-atom mass of the particles. ``NULL`` if per-type masses are
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used. See the :cpp:func:`rmass_flag<lammps_extract_setting>` setting.
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* - ellipsoid
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- int
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- 1
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- 1 if the particle is an ellipsoidal particle, 0 if not
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* - line
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- int
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- 1
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- 1 if the particle is a line particle, 0 if not
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* - tri
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- int
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- 1
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- 1 if the particle is a triangulated particle, 0 if not
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* - body
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- int
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- 1
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- 1 if the particle is a body particle, 0 if not
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\endverbatim
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*
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* \param name string with the keyword of the desired property.
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Typically the name of the pointer variable returned
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* \return pointer to the requested data cast to ``void *`` or NULL */
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void *Atom::extract(char *name)
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{
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// --------------------------------------------------------------------
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// 4th customization section: customize by adding new variable name
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/* NOTE: this array is only of length ntypes+1 */
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if (strcmp(name,"mass") == 0) return (void *) mass;
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if (strcmp(name,"id") == 0) return (void *) tag;
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@ -2389,6 +2534,7 @@ void *Atom::extract(char *name)
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if (strcmp(name,"ellipsoid") == 0) return (void *) ellipsoid;
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if (strcmp(name,"line") == 0) return (void *) line;
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if (strcmp(name,"tri") == 0) return (void *) tri;
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if (strcmp(name,"body") == 0) return (void *) body;
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if (strcmp(name,"vfrac") == 0) return (void *) vfrac;
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if (strcmp(name,"s0") == 0) return (void *) s0;
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