Homec4science
Diffusion lammps (efficient_neuronet) Browse

lammps/doc/doc2/Section_modify.html
bfb019efa901efficient_neuronet

Last Change
Raw File

Section_modify.html
View Options

<HTML>
<CENTER> <A HREF = "Section_tools.html">Previous Section</A> - <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> -
<A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A> - <A HREF = "Section_python.html">Next
Section</A>
</CENTER>
<HR>
<H3>10. Modifying & extending LAMMPS
</H3>
<P>This section describes how to customize LAMMPS by modifying
and extending its source code.
</P>
10.1 <A HREF = "#mod_1">Atom styles</A><BR>
10.2 <A HREF = "#mod_2">Bond, angle, dihedral, improper potentials</A><BR>
10.3 <A HREF = "#mod_3">Compute styles</A><BR>
10.4 <A HREF = "#mod_4">Dump styles</A><BR>
10.5 <A HREF = "#mod_5">Dump custom output options</A><BR>
10.6 <A HREF = "#mod_6">Fix styles</A> which include integrators, temperature and pressure control, force constraints, boundary conditions, diagnostic output, etc<BR>
10.7 <A HREF = "mod_7">Input script commands</A><BR>
10.8 <A HREF = "#mod_8">Kspace computations</A><BR>
10.9 <A HREF = "#mod_9">Minimization styles</A><BR>
10.10 <A HREF = "#mod_10">Pairwise potentials</A><BR>
10.11 <A HREF = "#mod_11">Region styles</A><BR>
10.12 <A HREF = "#mod_12">Body styles</A><BR>
10.13 <A HREF = "#mod_13">Thermodynamic output options</A><BR>
10.14 <A HREF = "#mod_14">Variable options</A><BR>
10.15 <A HREF = "#mod_15">Submitting new features for inclusion in LAMMPS</A> <BR>
<P>LAMMPS is designed in a modular fashion so as to be easy to modify and
extend with new functionality. In fact, about 75% of its source code
is files added in this fashion.
</P>
<P>In this section, changes and additions users can make are listed along
with minimal instructions. If you add a new feature to LAMMPS and
think it will be of interest to general users, we encourage you to
submit it to the developers for inclusion in the released version of
LAMMPS. Information about how to do this is provided
<A HREF = "#mod_14">below</A>.
</P>
<P>The best way to add a new feature is to find a similar feature in
LAMMPS and look at the corresponding source and header files to figure
out what it does. You will need some knowledge of C++ to be able to
understand the hi-level structure of LAMMPS and its class
organization, but functions (class methods) that do actual
computations are written in vanilla C-style code and operate on simple
C-style data structures (vectors and arrays).
</P>
<P>Most of the new features described in this section require you to
write a new C++ derived class (except for exceptions described below,
where you can make small edits to existing files). Creating a new
class requires 2 files, a source code file (*.cpp) and a header file
(*.h). The derived class must provide certain methods to work as a
new option. Depending on how different your new feature is compared
to existing features, you can either derive from the base class
itself, or from a derived class that already exists. Enabling LAMMPS
to invoke the new class is as simple as putting the two source
files in the src dir and re-building LAMMPS.
</P>
<P>The advantage of C++ and its object-orientation is that all the code
and variables needed to define the new feature are in the 2 files you
write, and thus shouldn't make the rest of LAMMPS more complex or
cause side-effect bugs.
</P>
<P>Here is a concrete example. Suppose you write 2 files pair_foo.cpp
and pair_foo.h that define a new class PairFoo that computes pairwise
potentials described in the classic 1997 <A HREF = "#Foo">paper</A> by Foo, et al.
If you wish to invoke those potentials in a LAMMPS input script with a
command like
</P>
<PRE>pair_style foo 0.1 3.5
</PRE>
<P>then your pair_foo.h file should be structured as follows:
</P>
<PRE>#ifdef PAIR_CLASS
PairStyle(foo,PairFoo)
#else
...
(class definition for PairFoo)
...
#endif
</PRE>
<P>where "foo" is the style keyword in the pair_style command, and
PairFoo is the class name defined in your pair_foo.cpp and pair_foo.h
files.
</P>
<P>When you re-build LAMMPS, your new pairwise potential becomes part of
the executable and can be invoked with a pair_style command like the
example above. Arguments like 0.1 and 3.5 can be defined and
processed by your new class.
</P>
<P>As illustrated by this pairwise example, many kinds of options are
referred to in the LAMMPS documentation as the "style" of a particular
command.
</P>
<P>The instructions below give the header file for the base class that
these styles are derived from. Public variables in that file are ones
used and set by the derived classes which are also used by the base
class. Sometimes they are also used by the rest of LAMMPS. Virtual
functions in the base class header file which are set = 0 are ones you
must define in your new derived class to give it the functionality
LAMMPS expects. Virtual functions that are not set to 0 are functions
you can optionally define.
</P>
<P>Additionally, new output options can be added directly to the
thermo.cpp, dump_custom.cpp, and variable.cpp files as explained
below.
</P>
<P>Here are additional guidelines for modifying LAMMPS and adding new
functionality:
</P>
<UL><LI>Think about whether what you want to do would be better as a pre- or
post-processing step. Many computations are more easily and more
quickly done that way.
<LI>Don't do anything within the timestepping of a run that isn't
parallel. E.g. don't accumulate a bunch of data on a single processor
and analyze it. You run the risk of seriously degrading the parallel
efficiency.
<LI>If your new feature reads arguments or writes output, make sure you
follow the unit conventions discussed by the <A HREF = "units.html">units</A>
command.
<LI>If you add something you think is truly useful and doesn't impact
LAMMPS performance when it isn't used, send an email to the
<A HREF = "http://lammps.sandia.gov/authors.html">developers</A>. We might be
interested in adding it to the LAMMPS distribution. See further
details on this at the bottom of this page.
</UL>
<HR>
<HR>
<A NAME = "mod_1"></A><H4>10.1 Atom styles
</H4>
<P>Classes that define an <A HREF = "atom_style.html">atom style</A> 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.
</P>
<P>Atom_vec_atomic.cpp is a simple example of an atom style.
</P>
<P>Here is a brief description of methods you define in your new derived
class. See atom_vec.h for details.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD >init</TD><TD > one time setup (optional)</TD></TR>
<TR><TD >grow</TD><TD > re-allocate atom arrays to longer lengths (required)</TD></TR>
<TR><TD >grow_reset</TD><TD > make array pointers in Atom and AtomVec classes consistent (required)</TD></TR>
<TR><TD >copy</TD><TD > copy info for one atom to another atom's array locations (required)</TD></TR>
<TR><TD >pack_comm</TD><TD > store an atom's info in a buffer communicated every timestep (required)</TD></TR>
<TR><TD >pack_comm_vel</TD><TD > add velocity info to communication buffer (required)</TD></TR>
<TR><TD >pack_comm_hybrid</TD><TD > store extra info unique to this atom style (optional)</TD></TR>
<TR><TD >unpack_comm</TD><TD > retrieve an atom's info from the buffer (required)</TD></TR>
<TR><TD >unpack_comm_vel</TD><TD > also retrieve velocity info (required)</TD></TR>
<TR><TD >unpack_comm_hybrid</TD><TD > retreive extra info unique to this atom style (optional)</TD></TR>
<TR><TD >pack_reverse</TD><TD > store an atom's info in a buffer communicating partial forces (required)</TD></TR>
<TR><TD >pack_reverse_hybrid</TD><TD > store extra info unique to this atom style (optional)</TD></TR>
<TR><TD >unpack_reverse</TD><TD > retrieve an atom's info from the buffer (required)</TD></TR>
<TR><TD >unpack_reverse_hybrid</TD><TD > retreive extra info unique to this atom style (optional)</TD></TR>
<TR><TD >pack_border</TD><TD > store an atom's info in a buffer communicated on neighbor re-builds (required)</TD></TR>
<TR><TD >pack_border_vel</TD><TD > add velocity info to buffer (required)</TD></TR>
<TR><TD >pack_border_hybrid</TD><TD > store extra info unique to this atom style (optional)</TD></TR>
<TR><TD >unpack_border</TD><TD > retrieve an atom's info from the buffer (required)</TD></TR>
<TR><TD >unpack_border_vel</TD><TD > also retrieve velocity info (required)</TD></TR>
<TR><TD >unpack_border_hybrid</TD><TD > retreive extra info unique to this atom style (optional)</TD></TR>
<TR><TD >pack_exchange</TD><TD > store all an atom's info to migrate to another processor (required)</TD></TR>
<TR><TD >unpack_exchange</TD><TD > retrieve an atom's info from the buffer (required)</TD></TR>
<TR><TD >size_restart</TD><TD > number of restart quantities associated with proc's atoms (required)</TD></TR>
<TR><TD >pack_restart</TD><TD > pack atom quantities into a buffer (required)</TD></TR>
<TR><TD >unpack_restart</TD><TD > unpack atom quantities from a buffer (required)</TD></TR>
<TR><TD >create_atom</TD><TD > create an individual atom of this style (required)</TD></TR>
<TR><TD >data_atom</TD><TD > parse an atom line from the data file (required)</TD></TR>
<TR><TD >data_atom_hybrid</TD><TD > parse additional atom info unique to this atom style (optional)</TD></TR>
<TR><TD >data_vel</TD><TD > parse one line of velocity information from data file (optional)</TD></TR>
<TR><TD >data_vel_hybrid</TD><TD > parse additional velocity data unique to this atom style (optional)</TD></TR>
<TR><TD >memory_usage</TD><TD > tally memory allocated by atom arrays (required)
</TD></TR></TABLE></DIV>
<P>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.
</P>
<P>IMPORTANT NOTE: It is possible to add some attributes, such as a
molecule ID, to atom styles that do not have them via the <A HREF = "fix_property_atom.html">fix
property/atom</A> command. This command also
allows new custom attributes consisting of extra integer or
floating-point values to be added to atoms. See the <A HREF = "fix_property_atom.html">fix
property/atom</A> doc page for examples of cases
where this is useful and details on how to initialize, access, and
output the custom values.
</P>
<P>New <A HREF = "pair_style.html">pair styles</A>, <A HREF = "fix.html">fixes</A>, or
<A HREF = "compute.html">computes</A> 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:
</P>
<PRE>int index = atom->find_custom(char *name, int &flag);
</PRE>
<P>The "name" of a custom attribute, as specified in the <A HREF = "fix_property_atom.html">fix
property/atom</A> 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
</P>
<PRE>int *ivector = atom->ivector[index];
double *dvector = atom->dvector[index];
</PRE>
<P>Ivector or dvector are vectors of length Nlocal = # of owned atoms,
which store the attributes of individual atoms.
</P>
<HR>
<A NAME = "mod_2"></A><H4>10.2 Bond, angle, dihedral, improper potentials
</H4>
<P>Classes that compute molecular interactions are derived from the Bond,
Angle, Dihedral, and Improper classes. New styles can be created to
add new potentials to LAMMPS.
</P>
<P>Bond_harmonic.cpp is the simplest example of a bond style. Ditto for
the harmonic forms of the angle, dihedral, and improper style
commands.
</P>
<P>Here is a brief description of common methods you define in your
new derived class. See bond.h, angle.h, dihedral.h, and improper.h
for details and specific additional methods.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD >init</TD><TD > check if all coefficients are set, calls <I>init_style</I> (optional)</TD></TR>
<TR><TD >init_style</TD><TD > check if style specific conditions are met (optional)</TD></TR>
<TR><TD >compute</TD><TD > compute the molecular interactions (required)</TD></TR>
<TR><TD >settings</TD><TD > apply global settings for all types (optional)</TD></TR>
<TR><TD >coeff</TD><TD > set coefficients for one type (required)</TD></TR>
<TR><TD >equilibrium_distance</TD><TD > length of bond, used by SHAKE (required, bond only)</TD></TR>
<TR><TD >equilibrium_angle</TD><TD > opening of angle, used by SHAKE (required, angle only)</TD></TR>
<TR><TD >write & read_restart</TD><TD > writes/reads coeffs to restart files (required)</TD></TR>
<TR><TD >single</TD><TD > force and energy of a single bond or angle (required, bond or angle only)</TD></TR>
<TR><TD >memory_usage</TD><TD > tally memory allocated by the style (optional)
</TD></TR></TABLE></DIV>
<HR>
<A NAME = "mod_3"></A><H4>10.3 Compute styles
</H4>
<P>Classes that compute scalar and vector quantities like temperature
and the pressure tensor, as well as classes that compute per-atom
quantities like kinetic energy and the centro-symmetry parameter
are derived from the Compute class. New styles can be created
to add new calculations to LAMMPS.
</P>
<P>Compute_temp.cpp is a simple example of computing a scalar
temperature. Compute_ke_atom.cpp is a simple example of computing
per-atom kinetic energy.
</P>
<P>Here is a brief description of methods you define in your new derived
class. See compute.h for details.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD >init</TD><TD > perform one time setup (required)</TD></TR>
<TR><TD >init_list</TD><TD > neighbor list setup, if needed (optional)</TD></TR>
<TR><TD >compute_scalar</TD><TD > compute a scalar quantity (optional)</TD></TR>
<TR><TD >compute_vector</TD><TD > compute a vector of quantities (optional)</TD></TR>
<TR><TD >compute_peratom</TD><TD > compute one or more quantities per atom (optional)</TD></TR>
<TR><TD >compute_local</TD><TD > compute one or more quantities per processor (optional)</TD></TR>
<TR><TD >pack_comm</TD><TD > pack a buffer with items to communicate (optional)</TD></TR>
<TR><TD >unpack_comm</TD><TD > unpack the buffer (optional)</TD></TR>
<TR><TD >pack_reverse</TD><TD > pack a buffer with items to reverse communicate (optional)</TD></TR>
<TR><TD >unpack_reverse</TD><TD > unpack the buffer (optional)</TD></TR>
<TR><TD >remove_bias</TD><TD > remove velocity bias from one atom (optional)</TD></TR>
<TR><TD >remove_bias_all</TD><TD > remove velocity bias from all atoms in group (optional)</TD></TR>
<TR><TD >restore_bias</TD><TD > restore velocity bias for one atom after remove_bias (optional)</TD></TR>
<TR><TD >restore_bias_all</TD><TD > same as before, but for all atoms in group (optional)</TD></TR>
<TR><TD >pair_tally_callback</TD><TD > callback function for <I>tally</I>-style computes (optional).</TD></TR>
<TR><TD >memory_usage</TD><TD > tally memory usage (optional)
</TD></TR></TABLE></DIV>
<P>Tally-style computes are a special case, as their computation is done
in two stages: the callback function is registered with the pair style
and then called from the Pair::ev_tally() function, which is called for
each pair after force and energy has been computed for this pair. Then
the tallied values are retrieved with the standard compute_scalar or
compute_vector or compute_peratom methods. The USER-TALLY package
provides <I>examples</I>_compute_tally.html for utilizing this mechanism.
</P>
<HR>
<A NAME = "mod_4"></A><H4>10.4 Dump styles
</H4>
<A NAME = "mod_5"></A><H4>10.5 Dump custom output options
</H4>
<P>Classes that dump per-atom info to files are derived from the Dump
class. To dump new quantities or in a new format, a new derived dump
class can be added, but it is typically simpler to modify the
DumpCustom class contained in the dump_custom.cpp file.
</P>
<P>Dump_atom.cpp is a simple example of a derived dump class.
</P>
<P>Here is a brief description of methods you define in your new derived
class. See dump.h for details.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD >write_header</TD><TD > write the header section of a snapshot of atoms</TD></TR>
<TR><TD >count</TD><TD > count the number of lines a processor will output</TD></TR>
<TR><TD >pack</TD><TD > pack a proc's output data into a buffer</TD></TR>
<TR><TD >write_data</TD><TD > write a proc's data to a file
</TD></TR></TABLE></DIV>
<P>See the <A HREF = "dump.html">dump</A> command and its <I>custom</I> style for a list of
keywords for atom information that can already be dumped by
DumpCustom. It includes options to dump per-atom info from Compute
classes, so adding a new derived Compute class is one way to calculate
new quantities to dump.
</P>
<P>Alternatively, you can add new keywords to the dump custom command.
Search for the word "customize" in dump_custom.cpp to see the
half-dozen or so locations where code will need to be added.
</P>
<HR>
<A NAME = "mod_6"></A><H4>10.6 Fix styles
</H4>
<P>In LAMMPS, a "fix" is any operation that is computed during
timestepping that alters some property of the system. Essentially
everything that happens during a simulation besides force computation,
neighbor list construction, and output, is a "fix". This includes
time integration (update of coordinates and velocities), force
constraints or boundary conditions (SHAKE or walls), and diagnostics
(compute a diffusion coefficient). New styles can be created to add
new options to LAMMPS.
</P>
<P>Fix_setforce.cpp is a simple example of setting forces on atoms to
prescribed values. There are dozens of fix options already in LAMMPS;
choose one as a template that is similar to what you want to
implement.
</P>
<P>Here is a brief description of methods you can define in your new
derived class. See fix.h for details.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD >setmask</TD><TD > determines when the fix is called during the timestep (required)</TD></TR>
<TR><TD >init</TD><TD > initialization before a run (optional)</TD></TR>
<TR><TD >setup_pre_exchange</TD><TD > called before atom exchange in setup (optional)</TD></TR>
<TR><TD >setup_pre_force</TD><TD > called before force computation in setup (optional)</TD></TR>
<TR><TD >setup</TD><TD > called immediately before the 1st timestep and after forces are computed (optional)</TD></TR>
<TR><TD >min_setup_pre_force</TD><TD > like setup_pre_force, but for minimizations instead of MD runs (optional)</TD></TR>
<TR><TD >min_setup</TD><TD > like setup, but for minimizations instead of MD runs (optional)</TD></TR>
<TR><TD >initial_integrate</TD><TD > called at very beginning of each timestep (optional)</TD></TR>
<TR><TD >pre_exchange</TD><TD > called before atom exchange on re-neighboring steps (optional)</TD></TR>
<TR><TD >pre_neighbor</TD><TD > called before neighbor list build (optional)</TD></TR>
<TR><TD >pre_force</TD><TD > called before pair & molecular forces are computed (optional)</TD></TR>
<TR><TD >post_force</TD><TD > called after pair & molecular forces are computed and communicated (optional)</TD></TR>
<TR><TD >final_integrate</TD><TD > called at end of each timestep (optional)</TD></TR>
<TR><TD >end_of_step</TD><TD > called at very end of timestep (optional)</TD></TR>
<TR><TD >write_restart</TD><TD > dumps fix info to restart file (optional)</TD></TR>
<TR><TD >restart</TD><TD > uses info from restart file to re-initialize the fix (optional)</TD></TR>
<TR><TD >grow_arrays</TD><TD > allocate memory for atom-based arrays used by fix (optional)</TD></TR>
<TR><TD >copy_arrays</TD><TD > copy atom info when an atom migrates to a new processor (optional)</TD></TR>
<TR><TD >pack_exchange</TD><TD > store atom's data in a buffer (optional)</TD></TR>
<TR><TD >unpack_exchange</TD><TD > retrieve atom's data from a buffer (optional)</TD></TR>
<TR><TD >pack_restart</TD><TD > store atom's data for writing to restart file (optional)</TD></TR>
<TR><TD >unpack_restart</TD><TD > retrieve atom's data from a restart file buffer (optional)</TD></TR>
<TR><TD >size_restart</TD><TD > size of atom's data (optional)</TD></TR>
<TR><TD >maxsize_restart</TD><TD > max size of atom's data (optional)</TD></TR>
<TR><TD >setup_pre_force_respa</TD><TD > same as setup_pre_force, but for rRESPA (optional)</TD></TR>
<TR><TD >initial_integrate_respa</TD><TD > same as initial_integrate, but for rRESPA (optional)</TD></TR>
<TR><TD >post_integrate_respa</TD><TD > called after the first half integration step is done in rRESPA (optional)</TD></TR>
<TR><TD >pre_force_respa</TD><TD > same as pre_force, but for rRESPA (optional)</TD></TR>
<TR><TD >post_force_respa</TD><TD > same as post_force, but for rRESPA (optional)</TD></TR>
<TR><TD >final_integrate_respa</TD><TD > same as final_integrate, but for rRESPA (optional)</TD></TR>
<TR><TD >min_pre_force</TD><TD > called after pair & molecular forces are computed in minimizer (optional)</TD></TR>
<TR><TD >min_post_force</TD><TD > called after pair & molecular forces are computed and communicated in minmizer (optional)</TD></TR>
<TR><TD >min_store</TD><TD > store extra data for linesearch based minimization on a LIFO stack (optional)</TD></TR>
<TR><TD >min_pushstore</TD><TD > push the minimization LIFO stack one element down (optional)</TD></TR>
<TR><TD >min_popstore</TD><TD > pop the minimization LIFO stack one element up (optional)</TD></TR>
<TR><TD >min_clearstore</TD><TD > clear minimization LIFO stack (optional)</TD></TR>
<TR><TD >min_step</TD><TD > reset or move forward on line search minimization (optional)</TD></TR>
<TR><TD >min_dof</TD><TD > report number of degrees of freedom <I>added</I> by this fix in minimization (optional)</TD></TR>
<TR><TD >max_alpha</TD><TD > report maximum allowed step size during linesearch minimization (optional)</TD></TR>
<TR><TD >pack_comm</TD><TD > pack a buffer to communicate a per-atom quantity (optional)</TD></TR>
<TR><TD >unpack_comm</TD><TD > unpack a buffer to communicate a per-atom quantity (optional)</TD></TR>
<TR><TD >pack_reverse_comm</TD><TD > pack a buffer to reverse communicate a per-atom quantity (optional)</TD></TR>
<TR><TD >unpack_reverse_comm</TD><TD > unpack a buffer to reverse communicate a per-atom quantity (optional)</TD></TR>
<TR><TD >dof</TD><TD > report number of degrees of freedom <I>removed</I> by this fix during MD (optional)</TD></TR>
<TR><TD >compute_scalar</TD><TD > return a global scalar property that the fix computes (optional)</TD></TR>
<TR><TD >compute_vector</TD><TD > return a component of a vector property that the fix computes (optional)</TD></TR>
<TR><TD >compute_array</TD><TD > return a component of an array property that the fix computes (optional)</TD></TR>
<TR><TD >deform</TD><TD > called when the box size is changed (optional)</TD></TR>
<TR><TD >reset_target</TD><TD > called when a change of the target temperature is requested during a run (optional)</TD></TR>
<TR><TD >reset_dt</TD><TD > is called when a change of the time step is requested during a run (optional)</TD></TR>
<TR><TD >modify_param</TD><TD > called when a fix_modify request is executed (optional)</TD></TR>
<TR><TD >memory_usage</TD><TD > report memory used by fix (optional)</TD></TR>
<TR><TD >thermo</TD><TD > compute quantities for thermodynamic output (optional)
</TD></TR></TABLE></DIV>
<P>Typically, only a small fraction of these methods are defined for a
particular fix. Setmask is mandatory, as it determines when the fix
will be invoked during the timestep. Fixes that perform time
integration (<I>nve</I>, <I>nvt</I>, <I>npt</I>) implement initial_integrate() and
final_integrate() to perform velocity Verlet updates. Fixes that
constrain forces implement post_force().
</P>
<P>Fixes that perform diagnostics typically implement end_of_step(). For
an end_of_step fix, one of your fix arguments must be the variable
"nevery" which is used to determine when to call the fix and you must
set this variable in the constructor of your fix. By convention, this
is the first argument the fix defines (after the ID, group-ID, style).
</P>
<P>If the fix needs to store information for each atom that persists from
timestep to timestep, it can manage that memory and migrate the info
with the atoms as they move from processors to processor by
implementing the grow_arrays, copy_arrays, pack_exchange, and
unpack_exchange methods. Similarly, the pack_restart and
unpack_restart methods can be implemented to store information about
the fix in restart files. If you wish an integrator or force
constraint fix to work with rRESPA (see the <A HREF = "run_style.html">run_style</A>
command), the initial_integrate, post_force_integrate, and
final_integrate_respa methods can be implemented. The thermo method
enables a fix to contribute values to thermodynamic output, as printed
quantities and/or to be summed to the potential energy of the system.
</P>
<HR>
<A NAME = "mod_7"></A><H4>10.7 Input script commands
</H4>
<P>New commands can be added to LAMMPS input scripts by adding new
classes that have a "command" method. For example, the create_atoms,
read_data, velocity, and run commands are all implemented in this
fashion. When such a command is encountered in the LAMMPS input
script, LAMMPS simply creates a class with the corresponding name,
invokes the "command" method of the class, and passes it the arguments
from the input script. The command method can perform whatever
operations it wishes on LAMMPS data structures.
</P>
<P>The single method your new class must define is as follows:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD >command</TD><TD > operations performed by the new command
</TD></TR></TABLE></DIV>
<P>Of course, the new class can define other methods and variables as
needed.
</P>
<HR>
<A NAME = "mod_8"></A><H4>10.8 Kspace computations
</H4>
<P>Classes that compute long-range Coulombic interactions via K-space
representations (Ewald, PPPM) are derived from the KSpace class. New
styles can be created to add new K-space options to LAMMPS.
</P>
<P>Ewald.cpp is an example of computing K-space interactions.
</P>
<P>Here is a brief description of methods you define in your new derived
class. See kspace.h for details.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD >init</TD><TD > initialize the calculation before a run</TD></TR>
<TR><TD >setup</TD><TD > computation before the 1st timestep of a run</TD></TR>
<TR><TD >compute</TD><TD > every-timestep computation</TD></TR>
<TR><TD >memory_usage</TD><TD > tally of memory usage
</TD></TR></TABLE></DIV>
<HR>
<A NAME = "mod_9"></A><H4>10.9 Minimization styles
</H4>
<P>Classes that perform energy minimization derived from the Min class.
New styles can be created to add new minimization algorithms to
LAMMPS.
</P>
<P>Min_cg.cpp is an example of conjugate gradient minimization.
</P>
<P>Here is a brief description of methods you define in your new derived
class. See min.h for details.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD >init</TD><TD > initialize the minimization before a run</TD></TR>
<TR><TD >run</TD><TD > perform the minimization</TD></TR>
<TR><TD >memory_usage</TD><TD > tally of memory usage
</TD></TR></TABLE></DIV>
<HR>
<A NAME = "mod_10"></A><H4>10.10 Pairwise potentials
</H4>
<P>Classes that compute pairwise interactions are derived from the Pair
class. In LAMMPS, pairwise calculation include manybody potentials
such as EAM or Tersoff where particles interact without a static bond
topology. New styles can be created to add new pair potentials to
LAMMPS.
</P>
<P>Pair_lj_cut.cpp is a simple example of a Pair class, though it
includes some optional methods to enable its use with rRESPA.
</P>
<P>Here is a brief description of the class methods in pair.h:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD >compute</TD><TD > workhorse routine that computes pairwise interactions</TD></TR>
<TR><TD >settings</TD><TD > reads the input script line with arguments you define</TD></TR>
<TR><TD >coeff</TD><TD > set coefficients for one i,j type pair</TD></TR>
<TR><TD >init_one</TD><TD > perform initialization for one i,j type pair</TD></TR>
<TR><TD >init_style</TD><TD > initialization specific to this pair style</TD></TR>
<TR><TD >write & read_restart</TD><TD > write/read i,j pair coeffs to restart files</TD></TR>
<TR><TD >write & read_restart_settings</TD><TD > write/read global settings to restart files</TD></TR>
<TR><TD >single</TD><TD > force and energy of a single pairwise interaction between 2 atoms</TD></TR>
<TR><TD >compute_inner/middle/outer</TD><TD > versions of compute used by rRESPA
</TD></TR></TABLE></DIV>
<P>The inner/middle/outer routines are optional.
</P>
<HR>
<A NAME = "mod_11"></A><H4>10.11 Region styles
</H4>
<P>Classes that define geometric regions are derived from the Region
class. Regions are used elsewhere in LAMMPS to group atoms, delete
atoms to create a void, insert atoms in a specified region, etc. New
styles can be created to add new region shapes to LAMMPS.
</P>
<P>Region_sphere.cpp is an example of a spherical region.
</P>
<P>Here is a brief description of methods you define in your new derived
class. See region.h for details.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD >match</TD><TD > determine whether a point is in the region
</TD></TR></TABLE></DIV>
<HR>
<A NAME = "mod_12"></A><H4>10.11 Body styles
</H4>
<P>Classes that define body particles are derived from the Body class.
Body particles can represent complex entities, such as surface meshes
of discrete points, collections of sub-particles, deformable objects,
etc.
</P>
<P>See <A HREF = "Section_howto.html#howto_14">Section_howto 14</A> of the manual for
an overview of using body particles and the <A HREF = "body.html">body</A> doc page
for details on the various body styles LAMMPS supports. New styles
can be created to add new kinds of body particles to LAMMPS.
</P>
<P>Body_nparticle.cpp is an example of a body particle that is treated as
a rigid body containing N sub-particles.
</P>
<P>Here is a brief description of methods you define in your new derived
class. See body.h for details.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD >data_body</TD><TD > process a line from the Bodies section of a data file</TD></TR>
<TR><TD >noutrow</TD><TD > number of sub-particles output is generated for</TD></TR>
<TR><TD >noutcol</TD><TD > number of values per-sub-particle output is generated for</TD></TR>
<TR><TD >output</TD><TD > output values for the Mth sub-particle</TD></TR>
<TR><TD >pack_comm_body</TD><TD > body attributes to communicate every timestep</TD></TR>
<TR><TD >unpack_comm_body</TD><TD > unpacking of those attributes</TD></TR>
<TR><TD >pack_border_body</TD><TD > body attributes to communicate when reneighboring is done</TD></TR>
<TR><TD >unpack_border_body</TD><TD > unpacking of those attributes
</TD></TR></TABLE></DIV>
<HR>
<A NAME = "mod_13"></A><H4>10.13 Thermodynamic output options
</H4>
<P>There is one class that computes and prints thermodynamic information
to the screen and log file; see the file thermo.cpp.
</P>
<P>There are two styles defined in thermo.cpp: "one" and "multi". There
is also a flexible "custom" style which allows the user to explicitly
list keywords for quantities to print when thermodynamic info is
output. See the <A HREF = "thermo_style.html">thermo_style</A> command for a list
of defined quantities.
</P>
<P>The thermo styles (one, multi, etc) are simply lists of keywords.
Adding a new style thus only requires defining a new list of keywords.
Search for the word "customize" with references to "thermo style" in
thermo.cpp to see the two locations where code will need to be added.
</P>
<P>New keywords can also be added to thermo.cpp to compute new quantities
for output. Search for the word "customize" with references to
"keyword" in thermo.cpp to see the several locations where code will
need to be added.
</P>
<P>Note that the <A HREF = "thermo.html">thermo_style custom</A> command already allows
for thermo output of quantities calculated by <A HREF = "fix.html">fixes</A>,
<A HREF = "compute.html">computes</A>, and <A HREF = "variable.html">variables</A>. Thus, it may
be simpler to compute what you wish via one of those constructs, than
by adding a new keyword to the thermo command.
</P>
<HR>
<A NAME = "mod_14"></A><H4>10.14 Variable options
</H4>
<P>There is one class that computes and stores <A HREF = "variable.html">variable</A>
information in LAMMPS; see the file variable.cpp. The value
associated with a variable can be periodically printed to the screen
via the <A HREF = "print.html">print</A>, <A HREF = "fix_print.html">fix print</A>, or
<A HREF = "thermo_style.html">thermo_style custom</A> commands. Variables of style
"equal" can compute complex equations that involve the following types
of arguments:
</P>
<PRE>thermo keywords = ke, vol, atoms, ...
other variables = v_a, v_myvar, ...
math functions = div(x,y), mult(x,y), add(x,y), ...
group functions = mass(group), xcm(group,x), ...
atom values = x[123], y[3], vx[34], ...
compute values = c_mytemp[0], c_thermo_press[3], ...
</PRE>
<P>Adding keywords for the <A HREF = "thermo_style.html">thermo_style custom</A> command
(which can then be accessed by variables) was discussed
<A HREF = "Section_modify.html#thermo">here</A> on this page.
</P>
<P>Adding a new math function of one or two arguments can be done by
editing one section of the Variable::evaulate() method. Search for
the word "customize" to find the appropriate location.
</P>
<P>Adding a new group function can be done by editing one section of the
Variable::evaulate() method. Search for the word "customize" to find
the appropriate location. You may need to add a new method to the
Group class as well (see the group.cpp file).
</P>
<P>Accessing a new atom-based vector can be done by editing one section
of the Variable::evaulate() method. Search for the word "customize"
to find the appropriate location.
</P>
<P>Adding new <A HREF = "compute.html">compute styles</A> (whose calculated values can
then be accessed by variables) was discussed
<A HREF = "Section_modify.html#compute">here</A> on this page.
</P>
<HR>
<HR>
<A NAME = "mod_15"></A><H4>10.15 Submitting new features for inclusion in LAMMPS
</H4>
<P>We encourage users to submit new features to <A HREF = "http://lammps.sandia.gov/authors.html">the
developers</A> that they add to
LAMMPS, especially if you think they will be of interest to other
users. If they are broadly useful we may add them as core files to
LAMMPS or as part of a <A HREF = "Section_start.html#start_3">standard package</A>.
Else we will add them as a user-contributed file or package. Examples
of user packages are in src sub-directories that start with USER. The
USER-MISC package is simply a collection of (mostly) unrelated single
files, which is the simplest way to have your contribution quickly
added to the LAMMPS distribution. You can see a list of the both
standard and user packages by typing "make package" in the LAMMPS src
directory.
</P>
<P>Note that by providing us the files to release, you are agreeing to
make them open-source, i.e. we can release them under the terms of the
GPL, used as a license for the rest of LAMMPS. See <A HREF = "Section_intro.html#intro_4">Section
1.4</A> for details.
</P>
<P>With user packages and files, all we are really providing (aside from
the fame and fortune that accompanies having your name in the source
code and on the <A HREF = "http://lammps.sandia.gov/authors.html">Authors page</A>
of the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW site</A>), is a means for you to distribute your
work to the LAMMPS user community, and a mechanism for others to
easily try out your new feature. This may help you find bugs or make
contact with new collaborators. Note that you're also implicitly
agreeing to support your code which means answer questions, fix bugs,
and maintain it if LAMMPS changes in some way that breaks it (an
unusual event).
</P>
<P>NOTE: If you prefer to actively develop and support your add-on
feature yourself, then you may wish to make it available for download
from your own website, as a user package that LAMMPS users can add to
their copy of LAMMPS. See the <A HREF = "http://lammps.sandia.gov/offsite.html">Offsite LAMMPS packages and
tools</A> page of the LAMMPS web
site for examples of groups that do this. We are happy to advertise
your package and web site from that page. Simply email the
<A HREF = "http://lammps.sandia.gov/authors.html">developers</A> with info about
your package and we will post it there.
</P>
<P>The previous sections of this doc page describe how to add new "style"
files of various kinds to LAMMPS. Packages are simply collections of
one or more new class files which are invoked as a new style within a
LAMMPS input script. If designed correctly, these additions typically
do not require changes to the main core of LAMMPS; they are simply
add-on files. If you think your new feature requires non-trivial
changes in core LAMMPS files, you'll need to <A HREF = "http://lammps.sandia.gov/authors.html">communicate with the
developers</A>, since we may or may
not want to make those changes. An example of a trivial change is
making a parent-class method "virtual" when you derive a new child
class from it.
</P>
<P>Here are the steps you need to follow to submit a single file or user
package for our consideration. Following these steps will save both
you and us time. See existing files in packages in the src dir for
examples.
</P>
<UL><LI>All source files you provide must compile with the most current
version of LAMMPS.
<LI>If you want your file(s) to be added to main LAMMPS or one of its
standard packages, then it needs to be written in a style compatible
with other LAMMPS source files. This is so the developers can
understand it and hopefully maintain it. This basically means that
the code accesses data structures, performs its operations, and is
formatted similar to other LAMMPS source files, including the use of
the error class for error and warning messages.
<LI>If you want your contribution to be added as a user-contributed
feature, and it's a single file (actually a *.cpp and *.h file) it can
rapidly be added to the USER-MISC directory. Send us the one-line
entry to add to the USER-MISC/README file in that dir, along with the
2 source files. You can do this multiple times if you wish to
contribute several individual features.
<LI>If you want your contribution to be added as a user-contribution and
it is several related featues, it is probably best to make it a user
package directory with a name like USER-FOO. In addition to your new
files, the directory should contain a README text file. The README
should contain your name and contact information and a brief
description of what your new package does. If your files depend on
other LAMMPS style files also being installed (e.g. because your file
is a derived class from the other LAMMPS class), then an Install.sh
file is also needed to check for those dependencies. See other README
and Install.sh files in other USER directories as examples. Send us a
tarball of this USER-FOO directory.
<LI>Your new source files need to have the LAMMPS copyright, GPL notice,
and your name and email address at the top, like other
user-contributed LAMMPS source files. They need to create a class
that is inside the LAMMPS namespace. If the file is for one of the
USER packages, including USER-MISC, then we are not as picky about the
coding style (see above). I.e. the files do not need to be in the
same stylistic format and syntax as other LAMMPS files, though that
would be nice for developers as well as users who try to read your
code.
<LI>You must also create a documentation file for each new command or
style you are adding to LAMMPS. This will be one file for a
single-file feature. For a package, it might be several files. These
are simple text files which we auto-convert to HTML. Thus they must
be in the same format as other *.txt files in the lammps/doc directory
for similar commands and styles; use one or more of them as a starting
point. As appropriate, the text files can include links to equations
(see doc/Eqs/*.tex for examples, we auto-create the associated JPG
files), or figures (see doc/JPG for examples), or even additional PDF
files with further details (see doc/PDF for examples). The doc page
should also include literature citations as appropriate; see the
bottom of doc/fix_nh.txt for examples and the earlier part of the same
file for how to format the cite itself. The "Restrictions" section of
the doc page should indicate that your command is only available if
LAMMPS is built with the appropriate USER-MISC or USER-FOO package.
See other user package doc files for examples of how to do this. The
txt2html tool we use to convert to HTML can be downloaded from <A HREF = "http://www.sandia.gov/~sjplimp/download.html">this
site</A>, so you can perform
the HTML conversion yourself to proofread your doc page.
<LI>For a new package (or even a single command) you can include one or
more example scripts. These should run in no more than 1 minute, even
on a single processor, and not require large data files as input. See
directories under examples/USER for examples of input scripts other
users provided for their packages.
<LI>If there is a paper of yours describing your feature (either the
algorithm/science behind the feature itself, or its initial usage, or
its implementation in LAMMPS), you can add the citation to the *.cpp
source file. See src/USER-EFF/atom_vec_electron.cpp for an example.
A LaTeX citation is stored in a variable at the top of the file and a
single line of code that references the variable is added to the
constructor of the class. Whenever a user invokes your feature from
their input script, this will cause LAMMPS to output the citation to a
log.cite file and prompt the user to examine the file. Note that you
should only use this for a paper you or your group authored.
E.g. adding a cite in the code for a paper by Nose and Hoover if you
write a fix that implements their integrator is not the intended
usage. That kind of citation should just be in the doc page you
provide.
</UL>
<P>Finally, as a general rule-of-thumb, the more clear and
self-explanatory you make your doc and README files, and the easier
you make it for people to get started, e.g. by providing example
scripts, the more likely it is that users will try out your new
feature.
</P>
<HR>
<HR>
<A NAME = "Foo"></A>
<P><B>(Foo)</B> Foo, Morefoo, and Maxfoo, J of Classic Potentials, 75, 345 (1997).
</P>
</HTML>
c4science · Help