11.3. Atom styles
Classes that define an atom style are derived from the AtomVec class and managed by the Atom class. The atom style determines what attributes are associated with an atom. A new atom style can be created if one of the existing atom styles does not define all the attributes you need to store and communicate with atoms.
Atom_vec_atomic.cpp is a simple example of an atom style.
Here is a brief description of methods you define in your new derived class. See atom_vec.h for details.
|init||one time setup (optional)|
|grow||re-allocate atom arrays to longer lengths (required)|
|grow_reset||make array pointers in Atom and AtomVec classes consistent (required)|
|copy||copy info for one atom to another atom’s array locations (required)|
|pack_comm||store an atom’s info in a buffer communicated every timestep (required)|
|pack_comm_vel||add velocity info to communication buffer (required)|
|pack_comm_hybrid||store extra info unique to this atom style (optional)|
|unpack_comm||retrieve an atom’s info from the buffer (required)|
|unpack_comm_vel||also retrieve velocity info (required)|
|unpack_comm_hybrid||retrieve extra info unique to this atom style (optional)|
|pack_reverse||store an atom’s info in a buffer communicating partial forces (required)|
|pack_reverse_hybrid||store extra info unique to this atom style (optional)|
|unpack_reverse||retrieve an atom’s info from the buffer (required)|
|unpack_reverse_hybrid||retrieve extra info unique to this atom style (optional)|
|pack_border||store an atom’s info in a buffer communicated on neighbor re-builds (required)|
|pack_border_vel||add velocity info to buffer (required)|
|pack_border_hybrid||store extra info unique to this atom style (optional)|
|unpack_border||retrieve an atom’s info from the buffer (required)|
|unpack_border_vel||also retrieve velocity info (required)|
|unpack_border_hybrid||retrieve extra info unique to this atom style (optional)|
|pack_exchange||store all an atom’s info to migrate to another processor (required)|
|unpack_exchange||retrieve an atom’s info from the buffer (required)|
|size_restart||number of restart quantities associated with proc’s atoms (required)|
|pack_restart||pack atom quantities into a buffer (required)|
|unpack_restart||unpack atom quantities from a buffer (required)|
|create_atom||create an individual atom of this style (required)|
|data_atom||parse an atom line from the data file (required)|
|data_atom_hybrid||parse additional atom info unique to this atom style (optional)|
|data_vel||parse one line of velocity information from data file (optional)|
|data_vel_hybrid||parse additional velocity data unique to this atom style (optional)|
|memory_usage||tally memory allocated by atom arrays (required)|
The constructor of the derived class sets values for several variables that you must set when defining a new atom style, which are documented in atom_vec.h. New atom arrays are defined in atom.cpp. Search for the word “customize” and you will find locations you will need to modify.
It is possible to add some attributes, such as a molecule ID, to atom styles that do not have them via the fix property/atom command. This command also allows new custom attributes consisting of extra integer or floating-point values to be added to atoms. See the fix property/atom doc page for examples of cases where this is useful and details on how to initialize, access, and output the custom values.
New pair styles, fixes, or computes can be added to LAMMPS, as discussed below. The code for these classes can use the per-atom properties defined by fix property/atom. The Atom class has a find_custom() method that is useful in this context:
int index = atom->find_custom(char *name, int &flag);
The “name” of a custom attribute, as specified in the fix property/atom command, is checked to verify that it exists and its index is returned. The method also sets flag = 0/1 depending on whether it is an integer or floating-point attribute. The vector of values associated with the attribute can then be accessed using the returned index as
int *ivector = atom->ivector[index]; double *dvector = atom->dvector[index];
Ivector or dvector are vectors of length Nlocal = # of owned atoms, which store the attributes of individual atoms.