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update format from enumerate to itemize and start next subsection

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Axel Kohlmeyer
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@ -149,95 +149,152 @@ statements including all headers of all styles of a given type that
are currently active (or "installed).
More details on individual classes in :ref:`class-topology` are as
More details on individual classes in the :ref:`class-topology` are as
follows:
#. The Memory class handles allocation of all large vectors and arrays.
- The Memory class handles allocation of all large vectors and arrays.
#. The Error class prints all error and warning messages.
- The Error class prints all error and warning messages.
#. The Universe class sets up partitions of processors so that multiple
simulations can be run, each on a subset of the processors allocated
for a run, e.g. by the mpirun command.
- The Universe class sets up partitions of processors so that multiple
simulations can be run, each on a subset of the processors allocated
for a run, e.g. by the mpirun command.
#. The Input class reads and processes input input strings and files,
stores variables, and invokes :doc:`commands <Commands_all>`.
- The Input class reads and processes input input strings and files,
stores variables, and invokes :doc:`commands <Commands_all>`.
#. As discussed above, command style classes are directly derived from
the Pointers class. They provide input script commands that perform
one-time operations before/after/between simulations or which invoke
a simulation. They are instantiated from within the Input class,
invoked, then immediately destructed.
- As discussed above, command style classes are directly derived from
the Pointers class. They provide input script commands that perform
one-time operations before/after/between simulations or which invoke a
simulation. They are instantiated from within the Input class,
invoked, then immediately destructed.
#. The Finish class is instantiated to print statistics to the
screen after a simulation is performed, by commands like run and
minimize.
- The Finish class is instantiated to print statistics to the screen
after a simulation is performed, by commands like run and minimize.
#. The Special class walks the bond topology of a molecular system
to find first, second, third neighbors of each atom. It is invoked by
several commands, like :doc:`read_data <read_data>`,
:doc:`read_restart <read_restart>`, or :doc:`replicate <replicate>`.
- The Special class walks the bond topology of a molecular system to
find first, second, third neighbors of each atom. It is invoked by
several commands, like :doc:`read_data <read_data>`,
:doc:`read_restart <read_restart>`, or :doc:`replicate <replicate>`.
#. The Atom class stores per-atom properties associated with atom
styles. More precisely, they are allocated and managed by a class
derived from the AtomVec class, and the Atom class simply stores
pointers to them. The classes derived from AtomVec represent the
different atom styles and they are instantiated through the
:doc:`atom_style <atom_style>` command.
- The Atom class stores per-atom properties associated with atom styles.
More precisely, they are allocated and managed by a class derived from
the AtomVec class, and the Atom class simply stores pointers to them.
The classes derived from AtomVec represent the different atom styles
and they are instantiated through the :doc:`atom_style <atom_style>`
command.
#. The Update class holds instances of an integrator and a minimizer
class. The Integrate class is a parent style for the Verlet and
r-RESPA time integrators, as defined by the :doc:`run_style
<run_style>` command. The Min class is a parent style for various
energy minimizers.
- The Update class holds instances of an integrator and a minimizer
class. The Integrate class is a parent style for the Verlet and
r-RESPA time integrators, as defined by the :doc:`run_style
<run_style>` command. The Min class is a parent style for various
energy minimizers.
#. The Neighbor class builds and stores neighbor lists. The NeighList
class stores a single list (for all atoms). A NeighRequest class
instance is created by pair, fix, or compute styles when they need a
particular kind of neighbor list and use the NeighRequest properties
to select the neighbor list settings for the given request. There can
be multiple instances of the NeighRequest class and the Neighbor
class will try to optimize how they are computed by creating copies
or sub-lists where possible.
- The Neighbor class builds and stores neighbor lists. The NeighList
class stores a single list (for all atoms). A NeighRequest class
instance is created by pair, fix, or compute styles when they need a
particular kind of neighbor list and use the NeighRequest properties
to select the neighbor list settings for the given request. There can
be multiple instances of the NeighRequest class and the Neighbor class
will try to optimize how they are computed by creating copies or
sub-lists where possible.
#. The Comm class performs inter-processor communication, typically of
ghost atom information. This usually involves MPI message exchanges
with 6 neighboring processors in the 3d logical grid of processors
mapped to the simulation box. There are two :doc:`communication
styles <comm_style>` enabling different ways to do the domain
decomposition. Sometimes the Irregular class is used, when atoms may
migrate to arbitrary processors.
- The Comm class performs inter-processor communication, typically of
ghost atom information. This usually involves MPI message exchanges
with 6 neighboring processors in the 3d logical grid of processors
mapped to the simulation box. There are two :doc:`communication styles
<comm_style>` enabling different ways to do the domain decomposition.
Sometimes the Irregular class is used, when atoms may migrate to
arbitrary processors.
#. The Domain class stores the simulation box geometry, as well as
geometric Regions and any user definition of a Lattice. The latter
are defined by the :doc:`region <region>` and :doc:`lattice <lattice>`
commands in an input script.
- The Domain class stores the simulation box geometry, as well as
geometric Regions and any user definition of a Lattice. The latter
are defined by the :doc:`region <region>` and :doc:`lattice <lattice>`
commands in an input script.
#. The Force class computes various forces between atoms. The Pair
parent class is for non-bonded or pair-wise forces, which in LAMMPS
also includes many-body forces such as the Tersoff 3-body potential
if those are computed by walking pairwise neighbor lists. The Bond,
Angle, Dihedral, Improper parent classes are styles for bonded
interactions within a static molecular topology. The KSpace parent
class is for computing long-range Coulombic interactions. One of its
child classes, PPPM, uses the FFT3D and Remap classes to redistribute
and communicate grid-based information across the parallel
processors.
- The Force class computes various forces between atoms. The Pair
parent class is for non-bonded or pair-wise forces, which in LAMMPS
also includes many-body forces such as the Tersoff 3-body potential if
those are computed by walking pairwise neighbor lists. The Bond,
Angle, Dihedral, Improper parent classes are styles for bonded
interactions within a static molecular topology. The KSpace parent
class is for computing long-range Coulombic interactions. One of its
child classes, PPPM, uses the FFT3D and Remap classes to redistribute
and communicate grid-based information across the parallel processors.
#. The Modify class stores lists of class instances derived from the
:doc:`Fix <fix>` and :doc:`Compute <compute>` base classes.
- The Modify class stores lists of class instances derived from the
:doc:`Fix <fix>` and :doc:`Compute <compute>` base classes.
#. The Group class manipulates groups that atoms are assigned to
via the :doc:`group <group>` command. It also has functions to
compute various attributes of groups of atoms.
- The Group class manipulates groups that atoms are assigned to via the
:doc:`group <group>` command. It also has functions to compute
various attributes of groups of atoms.
#. The Output class is used to generate 3 kinds of output from a
LAMMPS simulation: thermodynamic information printed to the screen
and log file, dump file snapshots, and restart files. These
correspond to the Thermo, Dump, and WriteRestart classes
respectively. The Dump class is a base class with several
derived classes implementing dump style variants.
- The Output class is used to generate 3 kinds of output from a LAMMPS
simulation: thermodynamic information printed to the screen and log
file, dump file snapshots, and restart files. These correspond to the
:doc:`Thermo <thermo_style>`, :doc:`Dump <dump>`, and
:doc:`WriteRestart <write_restart>` classes respectively. The Dump
class is a base class with several derived classes implementing
various dump style variants.
#. The Timer class logs timing information, output at the end
of a run.
- The Timer class logs timing information, output at the end
of a run.
.. TODO section on "Spatial decomposition and parallel operations"
.. diagram of 3d processor grid, brick vs. tiled. local vs. ghost
.. atoms, 6-way communication with pack/unpack functions,
.. PBC as part of the communication
.. TODO section on "Fixes, Computes, and Variables"
.. how and when data is computed and provided and how it is
.. referenced. flags in Fix/Compute/Variable classes tell
.. style and amount of available data.
How a timestep works
====================
The first and most fundamental operation within LAMMPS to understand is
how a timestep is structured. Timestepping is performed by calling
methods of the Integrate class instance within the Update class. Since
Integrate is a base class, it will point to an instance of a derived
class corresponding to what is selected by the :doc:`run_style
<run_style>` input script command.
In this section, the timestep implemented by the Verlet class is
described. A similar timestep protocol is implemented by the Respa
class, for the r-RESPA hierarchical timestepping method.
The Min base class performs energy minimization, so does not perform a
literal timestep. But it has logic similar to what is described here,
to compute forces and invoke fixes at each iteration of a minimization.
Differences between time integration and minimization are highlighted at
the end of this section.
The Verlet class is encoded in the ``src/verlet.cpp`` and ``verlet.h``
files. It implements the velocity-Verlet timestepping algorithm. The
workhorse method is ``Verlet::run()``, but first we highlight several
other methods in the class.
- The ``init()`` method is called at the beginning of each dynamics
run. It simply sets some internal flags, based on user settings in
other parts of the code.
- The ``setup()`` or ``setup_minimal()`` methods are also called before
each run. The velocity-Verlet method requires current forces be
calculated before the first timestep, so these routines compute
forces due to all atomic interactions, using the same logic that
appears in the timestepping described next. A few fixes are also
invoked, using the mechanism described in the next section. Various
counters are also initialized before the run begins. The
``setup_minimal()`` method is a variant that has a flag for performing
less setup. This is used when runs are continued and information
from the previous run is still valid. For example, if repeated
short LAMMPS runs are being invoked, interleaved by other commands,
via the *pre no* and *every* options of the run command, the
``setup_minimal()`` method is used.
- The ``force_clear()`` method initializes force and other arrays to
zero before each timestep, so that forces (torques, etc) can be
accumulated.