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Axel Kohlmeyer
2018-10-23 09:17:00 -04:00
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doc/src/Developer/developer.tex
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@ -22,10 +22,10 @@ users.
LAMMPS source files are in two directories of the distribution LAMMPS source files are in two directories of the distribution
tarball. The src directory has the majority of them, all of which are tarball. The src directory has the majority of them, all of which are
C++ files (*.cpp and *.h). Many of these files are in the src C++ files (*.cpp and *.h). Many of these files are in the src
directory itself. There are also dozens of "packages", which can be directory itself. There are also dozens of ``packages'', which can be
included or excluded when LAMMPS is built. See the included or excluded when LAMMPS is built. See the
doc/Section\_build.html section of the manual for more information doc/Section\_build.html section of the manual for more information
about packages, or type "make" from within the src directory, which about packages, or type ``make'' from within the src directory, which
lists package-related commands, such as ``make package-status''. The lists package-related commands, such as ``make package-status''. The
source files for each package are in an all-uppercase sub-directory of source files for each package are in an all-uppercase sub-directory of
src, like src/MOLECULE or src/USER-CUDA. If the package is currently src, like src/MOLECULE or src/USER-CUDA. If the package is currently
@ -38,17 +38,17 @@ The lib directory also contains source code for external libraries,
used by a few of the packages. Each sub-directory, like meam or gpu, used by a few of the packages. Each sub-directory, like meam or gpu,
contains the source files, some of which are in different languages contains the source files, some of which are in different languages
such as Fortran. The files are compiled into libraries from within such as Fortran. The files are compiled into libraries from within
each sub-directory, e.g. performing a "make" in the lib/meam directory each sub-directory, e.g. performing a ``make'' in the lib/meam directory
creates a libmeam.a file. These libraries are linked to during a creates a libmeam.a file. These libraries are linked to during a
LAMMPS build, if the corresponding package is installed. LAMMPS build, if the corresponding package is installed.
LAMMPS C++ source files almost always come in pairs, such as run.cpp LAMMPS C++ source files almost always come in pairs, such as run.cpp
and run.h. The pair of files defines a C++ class, the Run class in and run.h. The pair of files defines a C++ class, the Run class in
this case, which contains the code invoked by the "run" command in a this case, which contains the code invoked by the ``run'' command in a
LAMMPS input script. As this example illustrates, source file and LAMMPS input script. As this example illustrates, source file and
class names often have a one-to-one correspondence with a command used class names often have a one-to-one correspondence with a command used
in a LAMMPS input script. Some source files and classes do not have a in a LAMMPS input script. Some source files and classes do not have a
corresponding input script command, e.g. force.cpp and the Force corresponding input script command, e.g. ``force.cpp'' and the Force
class. They are discussed in the next section. class. They are discussed in the next section.
\pagebreak \pagebreak
@ -57,12 +57,12 @@ class. They are discussed in the next section.
Though LAMMPS has a lot of source files and classes, its class Though LAMMPS has a lot of source files and classes, its class
hierarchy is quite simple, as outlined in Fig \ref{fig:classes}. Each hierarchy is quite simple, as outlined in Fig \ref{fig:classes}. Each
boxed name refers to a class and has a pair of associated source files boxed name refers to a class and has a pair of associated source files
in lammps/src, e.g. memory.cpp and memory.h. More details on the in lammps/src, e.g. ``memory.cpp'' and ``memory.h''. More details on the
class and its methods and data structures can be found by examining class and its methods and data structures can be found by examining
its *.h file. its *.h file.
LAMMPS (lammps.cpp/h) is the top-level class for the entire code. It LAMMPS (lammps.cpp/h) is the top-level class for the entire code. It
holds an "instance" of LAMMPS and can be instantiated one or more holds an ``instance'' of LAMMPS and can be instantiated one or more
times by a calling code. For example, the file src/main.cpp simply times by a calling code. For example, the file src/main.cpp simply
instantiates one instance of LAMMPS and passes it the input script. instantiates one instance of LAMMPS and passes it the input script.
@ -81,7 +81,7 @@ enabled by a bit of cleverness in the Pointers class (see
src/pointers.h) which every class inherits from. src/pointers.h) which every class inherits from.
There are a handful of virtual parent classes in LAMMPS that define There are a handful of virtual parent classes in LAMMPS that define
what LAMMPS calls "styles". They are shaded red in Fig what LAMMPS calls ``styles''. They are shaded red in Fig
\ref{fig:classes}. Each of these are parents of a number of child \ref{fig:classes}. Each of these are parents of a number of child
classes that implement the interface defined by the parent class. For classes that implement the interface defined by the parent class. For
example, the fix style has around 100 child classes. They are the example, the fix style has around 100 child classes. They are the
@ -89,17 +89,17 @@ possible fixes that can be specified by the fix command in an input
script, e.g. fix nve, fix shake, fix ave/time, etc. The corresponding script, e.g. fix nve, fix shake, fix ave/time, etc. The corresponding
classes are Fix (for the parent class), FixNVE, FixShake, FixAveTime, classes are Fix (for the parent class), FixNVE, FixShake, FixAveTime,
etc. The source files for these classes are easy to identify in the etc. The source files for these classes are easy to identify in the
src directory, since they begin with the word "fix", e,g, src directory, since they begin with the word ``fix'', e,g,
fix\_nve.cpp, fix\_shake,cpp, fix\_ave\_time.cpp, etc. fix\_nve.cpp, fix\_shake,cpp, fix\_ave\_time.cpp, etc.
The one exception is child class files for the "command" style. These The one exception is child class files for the ``command'' style. These
implement specific commands in the input script that can be invoked implement specific commands in the input script that can be invoked
before/after/between runs or which launch a simulation. Examples are before/after/between runs or which launch a simulation. Examples are
the create\_box, minimize, run, and velocity commands which encode the the create\_box, minimize, run, and velocity commands which encode the
CreateBox, Minimize, Run, and Velocity classes. The corresponding CreateBox, Minimize, Run, and Velocity classes. The corresponding
files are create\_box,cpp, minimize.cpp, run.cpp, and velocity.cpp. files are create\_box,cpp, minimize.cpp, run.cpp, and velocity.cpp.
The list of command style files can be found by typing "grep The list of command style files can be found by typing ``grep
COMMAND\_CLASS *.h" from within the src directory, since that word in COMMAND\_CLASS *.h'' from within the src directory, since that word in
the header file identifies the class as an input script command. the header file identifies the class as an input script command.
Similar words can be grepped to list files for the other LAMMPS Similar words can be grepped to list files for the other LAMMPS
styles. E.g. ATOM\_CLASS, PAIR\_CLASS, BOND\_CLASS, REGION\_CLASS, styles. E.g. ATOM\_CLASS, PAIR\_CLASS, BOND\_CLASS, REGION\_CLASS,
@ -471,13 +471,13 @@ FixStyle(your/fix/name,FixMine)
\end{verbatim} \end{verbatim}
\end{center} \end{center}
Where "your/fix/name" is a name of your fix in the script and FixMine Where ``your/fix/name'' is a name of your fix in the script and FixMine
is the name of the class. This code allows LAMMPS to find your fix is the name of the class. This code allows LAMMPS to find your fix
when it parses input script. In addition, your fix header must be when it parses input script. In addition, your fix header must be
included in the file "style\_fix.h". In case if you use LAMMPS make, included in the file ``style\_fix.h''. In case if you use LAMMPS make,
this file is generated automatically - all files starting with prefix this file is generated automatically - all files starting with prefix
fix\_ are included, so call your header the same way. Otherwise, don't fix\_ are included, so call your header the same way. Otherwise, don't
forget to add your include into "style\_fix.h". forget to add your include into ``style\_fix.h''.
Let's write a simple fix which will print average velocity at the end Let's write a simple fix which will print average velocity at the end
of each timestep. First of all, implement a constructor: of each timestep. First of all, implement a constructor:
@ -567,11 +567,11 @@ void FixPrintVel::end_of_step()
\end{center} \end{center}
In the code above, we use MathExtra routines defined in In the code above, we use MathExtra routines defined in
"math\_extra.h". There are bunch of math functions to work with ``math\_extra.h''. There are bunch of math functions to work with
arrays of doubles as with math vectors. arrays of doubles as with math vectors.
In this code we use an instance of Atom class. This object is stored In this code we use an instance of Atom class. This object is stored
in the Pointers class (see "pointers.h"). This object contains all in the Pointers class (see ``pointers.h''). This object contains all
global information about the simulation system. Data from Pointers global information about the simulation system. Data from Pointers
class available to all classes inherited from it using protected class available to all classes inherited from it using protected
inheritance. Hence when you write you own class, which is going to use inheritance. Hence when you write you own class, which is going to use
@ -689,7 +689,7 @@ int FixSavePos::unpack_exchange(int nlocal, double *buf)
Now, a little bit about memory allocation. We used Memory class which Now, a little bit about memory allocation. We used Memory class which
is just a bunch of template functions for allocating 1D and 2D is just a bunch of template functions for allocating 1D and 2D
arrays. So you need to add include "memory.h" to have access to them. arrays. So you need to add include ``memory.h'' to have access to them.
Finally, if you need to write/read some global information used in Finally, if you need to write/read some global information used in
your fix to the restart file, you might do it by setting flag your fix to the restart file, you might do it by setting flag