diff --git a/doc/src/Section_tools.txt b/doc/src/Section_tools.txt
index d95c4f0cd40555a18a1c0a315d54cff6f851e53d..9a1968762ab1d04994ccc041f8e14502fd11cdcc 100644
--- a/doc/src/Section_tools.txt
+++ b/doc/src/Section_tools.txt
@@ -48,6 +48,7 @@ own sub-directories with their own Makefiles and/or README files.
"chain"_#chain
"colvars"_#colvars
"createatoms"_#createatoms
+"doxygen"_#doxygen
"drude"_#drude
"eam database"_#eamdb
"eam generate"_#eamgn
@@ -172,6 +173,18 @@ The tool is authored by Xiaowang Zhou (Sandia), xzhou at sandia.gov.
:line
+doxygen tool :h4,link(doxygen)
+
+The tools/doxygen directory contains a shell script called
+doxygen.sh which can generate a call graph and API lists using
+the Doxygen_http://doxygen.org software.
+
+See the included README file for details.
+
+The tool is authored by Nandor Tamaskovics, numericalfreedom at googlemail.com.
+
+:line
+
drude tool :h4,link(drude)
The tools/drude directory contains a Python script called
diff --git a/tools/doxygen/Developer.dox.lammps b/tools/doxygen/Developer.dox.lammps
new file mode 100644
index 0000000000000000000000000000000000000000..04cde521b2c6f370712eed86fc49b740b25293e4
--- /dev/null
+++ b/tools/doxygen/Developer.dox.lammps
@@ -0,0 +1,459 @@
+/**
+
+@mainpage Lammps Developer Guide
+@tableofcontents
+
+<h1><center><a href=Manual/Manual.html>LAMMPS Documentation</a></center></h1>
+<h1><center>and</center></h1>
+<h1><center>LAMMPS Developer Guide</center></h1>
+<h2><center>LAMMPS_VERSION</center></h2>
+
+
+This document is a developer guide to the <a href=Manual/Manual.html><b>LAMMPS</b></a> molecular dynamics package, whose WWW site is at <a href=http://lammps.sandia.gov> lammps.sandia.gov</a>. It describes the internal structure and algorithms of the code. Sections will be added as we have time, and in response to requests from developers and users.
+
+
+@section SCT_Lammps_source_files LAMMPS source files
+
+<a href=Manual/Manual.html><b>LAMMPS</b></a> source files are in two directories of the distribution 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 directory itself. There are also dozens of "packages", which can be included or excluded when <a href=Manual/Manual.html><b>LAMMPS</b></a> is built. See the <a href=Manual/Section_start.html><b>doc/Section_start.html</b></a> section of the manual for more information about packages, or type "make" from within the src directory, which lists package-related commands, such as "make package-status". The 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 installed, copies of the package source files will also exist in the src directory itself. The src/STUBS sub-directory is not a package but contains a dummy version of the MPI library, used when building a serial version of the code.
+
+The lib directory also contains source code for external libraries, 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 such as Fortran. The files are compiled into libraries from within each sub-directory, e.g. performing a "make" in the lib/meam directory creates a libmeam.a file. These libraries are <b>statically</b> linked to during a <a href=Manual/Manual.html><b>LAMMPS</b></a> build, if the corresponding package is installed.
+
+<a href=Manual/Manual.html><b>LAMMPS</b></a> C++ source files almost always come in pairs, such as run.cpp and run.h. The pair of files defines a C++ class, the LAMMPS_NS::Run class in this case, which contains the code invoked by the <a href=Manual/run.html><b>run</b></a> command in a <a href=Manual/Manual.html><b>LAMMPS</b></a> input script. As this example illustrates, source file and class names often have a one-to-one correspondence with a command used in a <a href=Manual/Manual.html><b>LAMMPS</b></a> input script. Some source files and classes do not have a corresponding input script command, e.g. force.cpp and the LAMMPS_NS::Force class. They are discussed in the next section.
+
+
+@section SCT_Class_hierarchy_of_LAMMPS Class hierarchy of LAMMPS
+
+Though <a href=Manual/Manual.html><b>LAMMPS</b></a> has a lot of source files and classes, its class hierarchy is quite simple, as outlined in figure @ref classes. Each 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 class and its methods and data structures can be found by examining its *.h file.
+
+LAMMPS_NS::LAMMPS (src/lammps.cpp and src/lammps.h) is the top-level class for the entire code. It holds an "instance" of <a href=Manual/Manual.html><b>LAMMPS</b></a> and can be instantiated one or more times by a calling code. For example, the file src/main.cpp simply instantiates one instance of <a href=Manual/Manual.html><b>LAMMPS</b></a> and passes it the input script.
+
+The file src/library.cpp contains a C-style library interface to the LAMMPS_NS::LAMMPS class. See the lammps/couple and lammps/python directories for examples of simple programs that use <a href=Manual/Manual.html><b>LAMMPS</b></a> through its library interface. A driver program can instantiate the LAMMPS_NS::LAMMPS class multiple times, e.g. to embed several atomistic simulation regions within a mesoscale or continuum simulation domain.
+
+There are a dozen or so top-level classes within the LAMMPS_NS::LAMMPS class that are visible everywhere in the code. They are shaded blue in figure @ref classes. Thus any class can refer to the y-coordinate of local atom "i" as atom@f$\rightarrow@f$x[i][1]. This visibility is enabled by a bit of cleverness in the LAMMPS_NS::Pointers class (see src/pointers.h) which every class inherits from.
+
+There are a handful of virtual parent classes in <a href=Manual/Manual.html><b>LAMMPS</b></a> that define what <a href=Manual/Manual.html><b>LAMMPS</b></a> calls "styles". They are shaded red in figure @ref classes. Each of these are parents of a number of child classes that implement the interface defined by the parent class. For example, the "fix style" has around 100 child classes. They are the possible fixes that can be specified by the <a href=Manual/fix.html><b>fix</b></a> command in an input script, e.g. <a href=Manual/fix_nve.html><b>fix nve</b></a>, <a href=Manual/fix_shake.html><b>fix shake</b></a>, <a href=Manual/fix_ave_time.html><b>fix ave/time</b></a>, etc. The corresponding classes are LAMMPS_NS::Fix (for the parent class), LAMMPS_NS::FixNVE, LAMMPS_NS::FixShake, LAMMPS_NS::FixAveTime, etc. The source files for these classes are easy to identify in the src directory, since they begin with the word "fix", e,g, fix_nve.cpp, fix_shake.cpp, fix_ave_time.cpp, etc.
+
+The one exception is child class files for the "command" style. These implement specific commands in the input script that can be invoked before/after/between runs or which launch a simulation. Examples are the <a href=Manual/create_box.html><b>create_box</b></a>, <a href=Manual/minimize.html><b>minimize</b></a>, <a href=Manual/run.html><b>run</b></a>, and <a href=Manual/velocity.html><b>velocity</b></a> commands which encode the LAMMPS_NS::CreateBox, LAMMPS_NS::Minimize, LAMMPS_NS::Run, and LAMMPS_NS::Velocity classes. The corresponding files are create_box.cpp, minimize.cpp, run.cpp, and velocity.cpp.
+
+The list of command style files can be found by typing "grep COMMAND_CLASS *.h" from within the src directory, since that word in the header file identifies the class as an input script command. Similar words can be grepped to list files for the other <a href=Manual/Manual.html><b>LAMMPS</b></a> styles. E.g. ATOM_CLASS, PAIR_CLASS, BOND_CLASS, REGION_CLASS, FIX_CLASS, COMPUTE_CLASS, DUMP_CLASS, etc.
+
+<br>
+
+@anchor classes @image html classes.png "Class hierarchy within <a href=Manual/Manual.html><b>LAMMPS</b></a> source code"
+
+@anchor classes @image latex classes.eps "Class hierarchy within <a href=Manual/Manual.html><b>LAMMPS</b></a> source code"
+
+<br>
+
+More details on individual classes in figure @ref classes are as
+follows:
+
+- The LAMMPS_NS::Memory class handles allocation of all large vectors and arrays.
+
+- The LAMMPS_NS::Error class prints all error and warning messages.
+
+- The LAMMPS_NS::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 LAMMPS_NS::Input class reads an input script, stores variables, and invokes stand-alone commands that are child classes of the LAMMPS_NS::Command class.
+
+- As discussed above, the LAMMPS_NS::Command class is a parent class for certain input script commands that perform a one-time operation before/after/between simulations or which invoke a simulation. They are instantiated from within the LAMMPS_NS::Input class, invoked, then immediately destructed.
+
+- The LAMMPS_NS::Finish class is instantiated to print statistics to the screen after a simulation is performed, by commands like run and minimize.
+
+- The LAMMPS_NS::Special class walks the bond topology of a molecular system to find 1st, 2nd, 3rd neighbors of each atom. It is invoked by several commands, like <a href=Manual/read_data.html><b>read_data</b></a>, <a href=Manual/read_restart.html><b>read_restart</b></a>, and <a href=Manual/replicate.html><b>replicate</b></a>.
+
+- The LAMMPS_NS::Atom class stores all per-atom arrays. More precisely, they are allocated and stored by the LAMMPS_NS::AtomVec class, and the LAMMPS_NS::Atom class simply stores a pointer to them. The LAMMPS_NS::AtomVec class is a parent class for atom styles, defined by the <a href=Manual/atom_style.html><b>atom_style</b></a> command.
+
+- The LAMMPS_NS::Update class holds an integrator and a minimizer. The LAMMPS_NS::Integrate class is a parent style for the Verlet and rRESPA time integrators, as defined by the <a href=Manual/run_style.html><b>run_style</b></a> input command. The LAMMPS_NS::Min class is a parent style for various energy minimizers.
+
+- The LAMMPS_NS::Neighbor class builds and stores neighbor lists. The LAMMPS_NS::NeighList class stores a single list (for all atoms). The LAMMPS_NS::NeighRequest class is called by pair, fix, or compute styles when they need a particular kind of neighbor list.
+
+- The LAMMPS_NS::Comm class performs interprocessor 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. Sometimes the LAMMPS_NS::Irregular class is used, when atoms may migrate to arbitrary processors.
+
+- The LAMMPS_NS::Domain class stores the simulation box geometry, as well as the geometric LAMMPS_NS::Region and any user definition of a LAMMPS_NS::Lattice. The latter are defined by <a href=Manual/region.html><b>region</b></a> and <a href=Manual/lattice.html><b>lattice</b></a> commands in an input script.
+
+- The LAMMPS_NS::Force class computes various forces between atoms. The LAMMPS_NS::Pair parent class is for non-bonded or pair-wise forces, which in <a href=Manual/Manual.html><b>LAMMPS</b></a> lingo includes many-body forces such as the Tersoff 3-body potential. The LAMMPS_NS::Bond, LAMMPS_NS::Angle, LAMMPS_NS::Dihedral, LAMMPS_NS::Improper parent classes are styles for bonded interactions within a static molecular topology. The LAMMPS_NS::KSpace parent class is for computing long-range Coulombic interactions. One of its child classes, LAMMPS_NS::PPPM, uses the LAMMPS_NS::FFT3d and LAMMPS_NS::Remap classes to communicate grid-based information with neighboring processors.
+
+- The LAMMPS_NS::Modify class stores lists of LAMMPS_NS::Fix and LAMMPS_NS::Compute classes, both of which are parent styles.
+
+- The LAMMPS_NS::Group class manipulates groups that atoms are assigned to via the <a href=Manual/group.html><b>group</b></a> command. It also computes various attributes of groups of atoms.
+
+- The LAMMPS_NS::Output class is used to generate 3 kinds of output from a <a href=Manual/Manual.html><b>LAMMPS</b></a> simulation: thermodynamic information printed to the screen and log file, dump file snapshots, and restart files. These correspond to the LAMMPS_NS::Thermo, LAMMPS_NS::Dump, and LAMMPS_NS::WriteRestart classes respectively. The LAMMPS_NS::Dump class is a parent style.
+
+- The LAMMPS_NS::Timer class logs MPI timing information, output at the end of a run.
+
+
+@section SCT_How_a_timestep_works How a timestep works
+
+The first and most fundamental operation within <a href=Manual/Manual.html><b>LAMMPS</b></a> to understand is how a timestep is structured. Timestepping is performed by the LAMMPS_NS::Integrate class within the LAMMPS_NS::Update class. Since LAMMPS_NS::Integrate is a parent class, corresponding to the <a href=Manual/run_style.html><b>run_style</b></a> input script command, it has child classes. In this section, the timestep implemented by the LAMMPS_NS::Verlet child class is described. A similar timestep is implemented by the LAMMPS_NS::Respa child class, for the rRESPA hierarchical timestepping method. The LAMMPS_NS::Min parent 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 LAMMPS_NS::Verlet class is encoded in the src/verlet.cpp and verlet.h files. It implements the velocity-Verlet timestepping algorithm. The workhorse method is LAMMPS_NS::Verlet::run(), but first we highlight several other methods in the class.
+
+- The LAMMPS_NS::Verlet::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 LAMMPS_NS::Verlet::setup() or LAMMPS_NS::Verlet::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 LAMMPS_NS::Verlet::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 <a href=Manual/Manual.html><b>LAMMPS</b></a> runs are being invoked, interleaved by other commands, via the "pre no" and "every" options of the run command, the LAMMPS_NS::Verlet::setup_minimal() method is used.
+
+- The LAMMPS_NS::Verlet::force_clear() method initializes force and other arrays to zero before each timestep, so that forces (torques, etc) can be accumulated.
+
+Now for the LAMMPS_NS::Verlet::run() method. Its structure in hi-level pseudo code is shown in figure @ref Verlet. In the actual code in src/verlet.cpp some of these operations are conditionally invoked.
+
+
+@verbatim
+
+loop over N timesteps:
+ ev_set()
+
+ fix->initial_integrate()
+ fix->post_integrate()
+
+ nflag = neighbor->decide()
+ if nflag:
+ fix->pre_exchange()
+ domain->pbc()
+ domain->reset_box()
+ comm->setup()
+ neighbor->setup_bins()
+ comm->exchange()
+ comm->borders()
+ fix->pre_neighbor()
+ neighbor->build()
+ else
+ comm->forward_comm()
+
+ force_clear()
+ fix->pre_force()
+
+ pair->compute()
+ bond->compute()
+ angle->compute()
+ dihedral->compute()
+ improper->compute()
+ kspace->compute()
+
+ comm->reverse_comm()
+
+ fix->post_force()
+ fix->final_integrate()
+ fix->end_of_step()
+
+ if any output on this step: output->write()
+
+@endverbatim
+
+@anchor Verlet <center> **Pseudo-code for the Verlet::run() method** </center>
+
+
+The LAMMPS_NS::Integrate::ev_set() method (in the parent LAMMPS_NS::Integrate class), sets two flags LAMMPS_NS::Integrate::eflag and LAMMPS_NS::Integrate::vflag for energy and virial computation. Each flag encodes whether global and/or per-atom energy and virial should be calculated on this timestep, because some fix or variable or output will need it. These flags are passed to the various methods that compute particle interactions, so that they can skip the extra calculations if the energy and virial are not needed. See the comments with the LAMMPS_NS::Integrate::ev_set() method which document the flag values.
+
+At various points of the timestep, fixes are invoked, e.g. fix@f$\rightarrow@f$initial_integrate(). In the code, this is actually done via the LAMMPS_NS::Modify class which stores all the Fix objects and lists of which should be invoked at what point in the timestep. Fixes are the <a href=Manual/Manual.html><b>LAMMPS</b></a> mechanism for tailoring the operations of a timestep for a particular simulation. As described elsewhere (unwritten section), each fix has one or more methods, each of which is invoked at a specific stage of the timestep, as in figure @ref Verlet. All the fixes defined in an input script with an LAMMPS_NS::Fix::initial_integrate() method are invoked at the beginning of each timestep. The fix commands <a href=Manual/fix_nve.html><b>fix nve</b></a>, <a href=Manual/fix_nvt.html><b>fix nvt</b></a> and <a href=Manual/fix_npt.html><b>fix npt</b></a> are examples, since they perform the start-of-timestep velocity-Verlet integration to update velocities by a half-step, and coordinates by a full step. The LAMMPS_NS::Fix::post_integrate() method is next. Only a few fixes use this, e.g. to reflect particles off box boundaries in the LAMMPS_NS::FixWallReflect class.
+
+The LAMMPS_NS::Neighbor::decide() method in the Neighbor class determines whether neighbor lists need to be rebuilt on the current timestep. If not, coordinates of ghost atoms are acquired by each processor via the LAMMPS_NS::Comm::forward_comm() method of the LAMMPS_NS::Comm class. If neighbor lists need to be built, several operations within the inner if clause of figure @ref Verlet are first invoked. The LAMMPS_NS::Fix::pre_exchange() method of any defined fixes is invoked first. Typically this inserts or deletes particles from the system.
+
+Periodic boundary conditions are then applied by the LAMMPS_NS::Domain class via its LAMMPS_NS::Domain::pbc() method to remap particles that have moved outside the simulation box back into the box. Note that this is not done every timestep. but only when neighbor lists are rebuilt. This is so that each processor’s sub-domain will have consistent (nearby) atom coordinates for its owned and ghost atoms. It is also why dumped atom coordinates can be slightly outside the simulation box.
+
+The box boundaries are then reset (if needed) via the LAMMPS_NS::Domain::reset_box() method of the Domain class, e.g. if box boundaries are shrink-wrapped to current particle coordinates. A change in the box size or shape requires internal information for communicating ghost atoms (LAMMPS_NS::Comm class) and neighbor list bins (LAMMPS_NS::Neighbor class) be updated. The LAMMPS_NS::Comm::setup() method of the LAMMPS_NS::Comm class and LAMMPS_NS::Neighbor::setup_bins() method of the LAMMPS_NS::Neighbor class perform the update.
+
+The code is now ready to migrate atoms that have left a processor’s geometric sub-domain to new processors. The LAMMPS_NS::Comm::exchange() method of the LAMMPS_NS::Comm class performs this operation. The LAMMPS_NS::Comm::borders() method of the LAMMPS_NS::Comm class then identifies ghost atoms surrounding each processor’s sub-domain and communicates ghost atom information to neighboring processors. It does this by looping over all the atoms owned by a processor to make lists of those to send to each neighbor processor. On subsequent timesteps, the lists are used by the LAMMPS_NS::Comm::forward_comm() method.
+
+Fixes with a LAMMPS_NS::Fix::pre_neighbor() method are then called. These typically re-build some data structure stored by the fix that depends on the current atoms owned by each processor.
+
+Now that each processor has a current list of its owned and ghost atoms, <a href=Manual/Manual.html><b>LAMMPS</b></a> is ready to rebuild neighbor lists via the LAMMPS_NS::Neighbor::build() method of the LAMMPS_NS::Neighbor class. This is typically done by binning all owned and ghost atoms, and scanning a stencil of bins around each owned atom’s bin to make a Verlet list of neighboring atoms within the force cutoff plus neighbor skin distance.
+
+In the next portion of the timestep, all interaction forces between particles are computed, after zeroing the per-atom force vector via the LAMMPS_NS::Verlet::force_clear() method. If the newton flag is set to "on" by the <a href=Manual/newton.html><b>newton</b></a> command, forces on both owned and ghost atoms are calculated.
+
+Pairwise forces are calculated first, which enables the global virial (if requested) to be calculated cheaply (at the end of the LAMMPS_NS::Pair::compute() method), by a dot product of atom coordinates and forces. By including owned and ghost atoms in the dot product, the effect of periodic boundary conditions is correctly accounted for. Molecular topology interactions (bonds, angles, dihedrals, impropers) are calculated next. The final contribution is from long-range Coulombic interactions, invoked by the LAMMPS_NS::KSpace class.
+
+If the newton flag is on, forces on ghost atoms are communicated and summed back to their corresponding owned atoms. The LAMMPS_NS::Comm::reverse_comm() method of the LAMMPS_NS::Comm class performs this operation, which is essentially the inverse operation of sending copies of owned atom coordinates to other processor’s ghost atoms.
+
+At this point in the timestep, the total force on each atom is known. Additional force constraints (external forces, SHAKE, etc) are applied by Fixes that have a LAMMPS_NS::Fix::post_force() method. The second half of the velocity-Verlet integration is then performed (another half-step update of the velocities) via fixes like <a href=Manual/fix_nve.html><b>fix nve</b></a>, <a href=Manual/fix_nvt.html><b>fix nvt</b></a> and <a href=Manual/fix_npt.html><b>fix npt</b></a>.
+
+At the end of the timestep, fixes that define an LAMMPS_NS::Fix::end_of_step() method are invoked. These typically perform a diagnostic calculation, e.g. the <a href=Manual/fix_ave_time.html><b>fix ave/time</b></a> and <a href=Manual/fix_ave_time.html><b>fix ave/spatial</b></a> fixes.
+
+The final operation of the timestep is to perform any requested output, via the LAMMPS_NS::Output::write() method of the LAMMPS_NS::Output class. There are 3 kinds of <a href=Manual/Manual.html><b>LAMMPS</b></a> output:
+
+- thermodynamic output to the screen and log file,
+- snapshots of atom data to a dump file, and
+- restart files.
+
+See the <a href=Manual/thermo_style.html><b>thermo_style</b></a>, <a href=Manual/dump.html><b>dump</b></a>, and <a href=Manual/restart.html><b>restart</b></a> commands for more details.
+
+The iteration performed by an energy minimization is similar to the dynamics timestep of figure @ref Verlet. Forces are computed, neighbor lists are built as needed, atoms migrate to new processors, and atom coordinates and forces are communicated to neighboring processors. The only difference is what LAMMPS_NS::Fix class operations are invoked when. Only a subset of <a href=Manual/Manual.html><b>LAMMPS</b></a> fixes are useful during energy minimization, as explained in their individual doc pages. The relevant LAMMPS_NS::Fix class methods are LAMMPS_NS::Fix::min_pre_exchange(), LAMMPS_NS::Fix::min_pre_force(), and LAMMPS_NS::Fix::min_post_force(). Each is invoked at the appropriate place within the minimization iteration. For example, the LAMMPS_NS::Fix::min_post_force() method is analogous to the LAMMPS_NS::Fix::post_force() method for dynamics; it is used to alter or constrain forces on each atom, which affects the minimization procedure.
+
+
+@section SCT_Extending_LAMMPS Extending LAMMPS
+
+The <a href=Manual/Section_modify.html><b>Section_modify.html</b></a> file in the doc directory of the LAMMPS distribution gives an overview of how <a href=Manual/Manual.html><b>LAMMPS</b></a> can be extended by writing new classes that derive from existing parent classes in LAMMPS.
+
+
+@subsection SST_New_fixes New fixes
+
+(this section has been provided by Kirill Lykov)
+
+Here, some specific coding details are provided for writing a new fix.
+
+Writing fixes is a flexible way of extending LAMMPS. Users can implement many things using fixes:
+
+- changing particles attributes (positions, velocities, forces, etc.). Example: LAMMPS_NS::FixFreeze.
+
+- reading/writing data. Example: LAMMPS_NS::FixReadRestart.
+
+- implementing boundary conditions. Example: LAMMPS_NS::FixWall.
+
+- saving information about particles for future use (previous positions, for instance). Example: LAMMPS_NS::FixStoreState.
+
+All fixes are derived from class LAMMPS_NS::Fix and must have constructor with the signature:
+
+@verbatim
+
+`FixMine(class LAMMPS *, int, char **)`
+
+@endverbatim
+
+Every fix must be registered in <a href=Manual/Manual.html><b>LAMMPS</b></a> by writing the following lines of code in the header before include guards:
+
+@verbatim
+
+#ifdef FIX_CLASS
+FixStyle(your/fix/name,FixMine)
+#else
+
+@endverbatim
+
+Where `your/fix/name` is a name of your fix in the script and FixMine is the name of the class. This code allows <a href=Manual/Manual.html><b>LAMMPS</b></a> to find your fix when it parses input script. In addition, your fix header must be included in the file style_fix.h. In case if you use <a href=Manual/Manual.html><b>LAMMPS</b></a> make, this file is generated automatically - all files starting with prefix `fix_` are included, so call your header the same way. Otherwise, don’t forget to add your include into style_fix.h.
+
+Let’s write a simple fix which will print average velocity at the end of each timestep. First of all, implement a constructor:
+
+@verbatim
+
+FixPrintVel::FixPrintVel(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
+{
+
+ if (narg < 4)
+ error->all(FLERR,"Illegal fix print command");
+
+ nevery = atoi(arg[3]);
+
+ if (nevery <= 0)
+ error->all(FLERR,"Illegal fix print command");
+}
+
+@endverbatim
+
+In the constructor you should parse your fix arguments which are specified in the script. All fixes have pretty the same syntax:
+
+@verbatim
+
+fix [fix_identifier] [group_name] [fix_name] [fix_arguments].
+
+@endverbatim
+
+The first 3 parameters are parsed by Fix class constructor, while `[fix_arguments]` should be parsed by you. In our case, we need to specify how often we want to print an average velocity. For instance, once in 50 timesteps: `fix 1 print/vel 50`. There is a special variable in Fix class called nevery which specifies how often the method `end_of_step()` is called. Thus all we need to do is just set it up.
+
+The next method we need to implement is `setmask()`:
+
+@verbatim
+
+int FixPrintVel::setmask()
+{
+ int mask = 0;
+ mask |= FixConst::END_OF_STEP;
+ return mask;
+}
+
+@endverbatim
+
+Here user specifies which methods of your fix should be called during the execution. For instance, `END_OF_STEP` corresponds to the LAMMPS_NS::Fix::end_of_step() method. Overall, there are 8 most important methods that are called in predefined order during the execution of the Verlet algorithm as was mentioned in Section 3:
+
+- LAMMPS_NS::Fix::initial_integrate()
+
+- LAMMPS_NS::Fix::post_integrate()
+
+- LAMMPS_NS::Fix::pre_exchange()
+
+- LAMMPS_NS::Fix::pre_neighbor()
+
+- LAMMPS_NS::Fix::pre_force()
+
+- LAMMPS_NS::Fix::post_force()
+
+- LAMMPS_NS::Fix::final_integrate()
+
+- LAMMPS_NS::Fix::end_of_step()
+
+The fix developer must understand when he wants to execute his code. In case if we want to write `FixPrintVel`, we need only LAMMPS_NS::Fix::end_of_step():
+
+@verbatim
+
+void FixPrintVel::end_of_step()
+{
+ // for add3, scale3
+ using namespace MathExtra;
+
+ double** v = atom->v;
+ int nlocal = atom->nlocal;
+ double localAvgVel[4]; // 4th element for particles count
+ memset(localAvgVel, 0, 4 * sizeof(double));
+ for (int particleInd = 0; particleInd < nlocal; ++particleInd) {
+ add3(localAvgVel, v[particleInd], localAvgVel);
+ }
+ localAvgVel[3] = nlocal;
+ double globalAvgVel[4];
+ memset(globalAvgVel, 0, 4 * sizeof(double));
+ MPI_Allreduce(localAvgVel, globalAvgVel, 4, MPI_DOUBLE, MPI_SUM, world);
+ scale3(1.0 / globalAvgVel[3], globalAvgVel);
+ if (comm->me == 0) {
+ printf("%e, %e, %e\n",
+ globalAvgVel[0], globalAvgVel[1], globalAvgVel[2]);
+ }
+}
+
+@endverbatim
+
+
+In the code above, we use MathExtra routines defined in math_extra.h. There are bunch of math functions to work with arrays of doubles as with math vectors.
+
+In this code we use an instance of LAMMPS_NS::Atom class. This object is stored in the LAMMPS_NS::Pointers class (see pointers.h). This object contains all global information about the simulation system. Data from LAMMPS_NS::Pointers class available to all classes inherited from it using protected inheritance. Hence when you write you own class, which is going to use <a href=Manual/Manual.html><b>LAMMPS</b></a> data, don’t forget to inherit from the class LAMMPS_NS::Pointers. When writing fixes we inherit from class LAMMPS_NS::Fix which is inherited from LAMMPS_NS::Pointers so there is no need to inherit from it directly.
+
+The code above computes average velocity for all particles in the simulation. Yet you have one unused parameter in fix call from the script - `[group_name]`. This parameter specifies the group of atoms used in the fix. So we should compute average for all particles in the simulation if `group_name == all`, but it can be any group. The group information is specified by groupbit which is defined in class LAMMPS_NS::Fix:
+
+@verbatim
+
+for (int particleInd = 0; particleInd < nlocal; ++particleInd) {
+ if (atom->mask[particleInd] & groupbit) {
+ //Do all job here
+ }
+ }
+
+@endverbatim
+
+Class LAMMPS_NS::Atom encapsulates atoms positions, velocities, forces, etc. The user can access them using particle index. Note, that particle indexes are usually changed every timestep because of sorting.
+
+Lets consider another LAMMPS_NS::Fix example. We want to have a fix which stores atoms position from previous time step in your fix. The local atoms indexes will not be valid on the next iteration. In order to handle this situation there are several methods which should be implemented:
+
+- LAMMPS_NS::Fix::memory_usage() `/double memory_usage/` - return how much memory fix uses
+
+- LAMMPS_NS::Fix::grow_arrays() `/void grow_arrays(int)/` - do reallocation of the per particle arrays in your fix
+
+- LAMMPS_NS::Fix::copy_arrays() `/void copy_arrays(int i, int j)/` - copy i-th per-particle information to j-th. Used when atoms sorting is performed
+
+- LAMMPS_NS::Fix::set_arrays() `/void set_arrays(int i)/` - sets i-th particle related information to zero
+
+Note, that if your class implements these methods, it must call add calls of LAMMPS_NS::Atom::add_callback and LAMMPS_NS::Atom::delete_callback to constructor and destructor:
+
+@verbatim
+
+FixSavePos::FixSavePos(LAMMPS *lmp, int narg, char **arg)
+{
+ //...
+ atom->add_callback(0);
+}
+
+FixSavePos::~FixSavePos()
+{
+ atom->delete_callback(id, 0);
+}
+
+@endverbatim
+
+Since we want to store positions of atoms from previous timestep, we
+need to add `double** x` to the header file. Than add allocation code to
+constructor:
+
+@verbatim
+
+memory->create(this->x, atom->nmax, 3, "FixSavePos:x"); .
+
+@endverbatim
+
+Free memory at destructor:
+
+@verbatim
+
+memory->destroy(x);
+
+@endverbatim
+
+Finally, implement mentioned methods:
+
+@verbatim
+
+double FixSavePos::memory_usage()
+{
+ int nmax = atom->nmax;
+ double bytes = 0.0;
+ bytes += nmax * 3 * sizeof(double);
+ return bytes;
+}
+
+void FixSavePos::grow_arrays(int nmax)
+{
+ memory->grow(this->x, nmax, 3, "FixSavePos:x");
+}
+
+void FixSavePos::copy_arrays(int i, int j)
+{
+ memcpy(this->x[j], this->x[i], sizeof(double) * 3);
+}
+
+void FixSavePos::set_arrays(int i)
+{
+ memset(this->x[i], 0, sizeof(double) * 3);
+}
+
+int FixSavePos::pack_exchange(int i, double *buf)
+{
+ int m = 0;
+ buf[m++] = x[i][0];
+ buf[m++] = x[i][1];
+ buf[m++] = x[i][2];
+
+ return m;
+}
+
+int FixSavePos::unpack_exchange(int nlocal, double *buf)
+{
+ int m = 0;
+ x[nlocal][0] = buf[m++];
+ x[nlocal][1] = buf[m++];
+ x[nlocal][2] = buf[m++];
+
+ return m;
+}
+
+@endverbatim
+
+Now, a little bit about memory allocation. We used LAMMPS_NS::Memory class which 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.
+
+Finally, if you need to write or read some global information used in your fix to of from a restart file, you might do it by setting flag
+
+@verbatim
+
+restart_global = 1
+
+@endverbatim
+
+in the constructor and implementing methods LAMMPS_NS::Fix::write_restart() `/void write_restart(FILE *fp)/` and LAMMPS_NS::Fix::restart() `/void restart(char *buf)/`.
+
+
+@subsection SST_New_commands New commands
+
+New commands can be added to <a href=Manual/Manual.html><b>LAMMPS</b></a> input scripts by adding new classes that have a “command†method. For example, the <a href=Manual/create_atoms.html><b>create_atoms</b></a>, <a href=Manual/read_data.html><b>read_data</b></a>, <a href=Manual/velocity.html><b>velocity</b></a> and <a href=Manual/run.html><b>run</b></a> commands are all implemented in this fashion. When such a command is encountered in the <a href=Manual/Manual.html><b>LAMMPS</b></a> 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 <a href=Manual/Manual.html><b>LAMMPS</b></a> data structures.
+
+
+@subsection SST_New_computes New computes
+
+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 LAMMPS_NS::Compute class. New styles can be created to add new calculations to <a href=Manual/Manual.html><b>LAMMPS</b></a>. Compute_temp.cpp is a simple example of computing a scalar temperature.
+
+
+@subsection SST_New_pair_styles New pair styles
+
+Classes that compute pairwise interactions are derived from the LAMMPS_NS::Pair class. In <a href=Manual/Manual.html><b>LAMMPS</b></a>, 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 <a href=Manual/Manual.html><b>LAMMPS</b></a>.
+
+
+@subsection SST_New_bonds_angles_dihedrals_impropers New bonds, angles, dihedrals and impropers
+
+Classes that compute molecular interactions are derived from the LAMMPS_NS::Bond, LAMMPS_NS::Angle, LAMMPS_NS::Dihedral, and LAMMPS_NS::Improper classes. New styles can be created to add new potentials to <a href=Manual/Manual.html><b>LAMMPS</b></a>.
+
+*/
diff --git a/tools/doxygen/Doxyfile.lammps b/tools/doxygen/Doxyfile.lammps
new file mode 100644
index 0000000000000000000000000000000000000000..f872541857c2df63a7a7881ae35ce4ca0f044f8a
--- /dev/null
+++ b/tools/doxygen/Doxyfile.lammps
@@ -0,0 +1,2557 @@
+# Doxyfile 1.8.15
+
+# This file describes the settings to be used by the documentation system
+# doxygen (www.doxygen.org) for a project.
+#
+# All text after a double hash (##) is considered a comment and is placed in
+# front of the TAG it is preceding.
+#
+# All text after a single hash (#) is considered a comment and will be ignored.
+# The format is:
+# TAG = value [value, ...]
+# For lists, items can also be appended using:
+# TAG += value [value, ...]
+# Values that contain spaces should be placed between quotes (\" \").
+
+#---------------------------------------------------------------------------
+# Project related configuration options
+#---------------------------------------------------------------------------
+
+# This tag specifies the encoding used for all characters in the config file
+# that follow. The default is UTF-8 which is also the encoding used for all text
+# before the first occurrence of this tag. Doxygen uses libiconv (or the iconv
+# built into libc) for the transcoding. See
+# https://www.gnu.org/software/libiconv/ for the list of possible encodings.
+# The default value is: UTF-8.
+
+DOXYFILE_ENCODING = UTF-8
+
+# The PROJECT_NAME tag is a single word (or a sequence of words surrounded by
+# double-quotes, unless you are using Doxywizard) that should identify the
+# project for which the documentation is generated. This name is used in the
+# title of most generated pages and in a few other places.
+# The default value is: My Project.
+
+PROJECT_NAME = "LAMMPS - Large Atomic and Molecular Massive Parallel Simulator"
+
+# The PROJECT_NUMBER tag can be used to enter a project or revision number. This
+# could be handy for archiving the generated documentation or if some version
+# control system is used.
+
+PROJECT_NUMBER =
+
+# Using the PROJECT_BRIEF tag one can provide an optional one line description
+# for a project that appears at the top of each page and should give viewer a
+# quick idea about the purpose of the project. Keep the description short.
+
+PROJECT_BRIEF = "LAMMPS - Developer Guide - LAMMPS_VERSION"
+
+# With the PROJECT_LOGO tag one can specify a logo or an icon that is included
+# in the documentation. The maximum height of the logo should not exceed 55
+# pixels and the maximum width should not exceed 200 pixels. Doxygen will copy
+# the logo to the output directory.
+
+PROJECT_LOGO =
+
+# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) path
+# into which the generated documentation will be written. If a relative path is
+# entered, it will be relative to the location where doxygen was started. If
+# left blank the current directory will be used.
+
+OUTPUT_DIRECTORY = tools/doxygen/doc
+
+# If the CREATE_SUBDIRS tag is set to YES then doxygen will create 4096 sub-
+# directories (in 2 levels) under the output directory of each output format and
+# will distribute the generated files over these directories. Enabling this
+# option can be useful when feeding doxygen a huge amount of source files, where
+# putting all generated files in the same directory would otherwise causes
+# performance problems for the file system.
+# The default value is: NO.
+
+CREATE_SUBDIRS = NO
+
+# If the ALLOW_UNICODE_NAMES tag is set to YES, doxygen will allow non-ASCII
+# characters to appear in the names of generated files. If set to NO, non-ASCII
+# characters will be escaped, for example _xE3_x81_x84 will be used for Unicode
+# U+3044.
+# The default value is: NO.
+
+ALLOW_UNICODE_NAMES = NO
+
+# The OUTPUT_LANGUAGE tag is used to specify the language in which all
+# documentation generated by doxygen is written. Doxygen will use this
+# information to generate all constant output in the proper language.
+# Possible values are: Afrikaans, Arabic, Armenian, Brazilian, Catalan, Chinese,
+# Chinese-Traditional, Croatian, Czech, Danish, Dutch, English (United States),
+# Esperanto, Farsi (Persian), Finnish, French, German, Greek, Hungarian,
+# Indonesian, Italian, Japanese, Japanese-en (Japanese with English messages),
+# Korean, Korean-en (Korean with English messages), Latvian, Lithuanian,
+# Macedonian, Norwegian, Persian (Farsi), Polish, Portuguese, Romanian, Russian,
+# Serbian, Serbian-Cyrillic, Slovak, Slovene, Spanish, Swedish, Turkish,
+# Ukrainian and Vietnamese.
+# The default value is: English.
+
+OUTPUT_LANGUAGE = English
+
+# The OUTPUT_TEXT_DIRECTION tag is used to specify the direction in which all
+# documentation generated by doxygen is written. Doxygen will use this
+# information to generate all generated output in the proper direction.
+# Possible values are: None, LTR, RTL and Context.
+# The default value is: None.
+
+OUTPUT_TEXT_DIRECTION = None
+
+# If the BRIEF_MEMBER_DESC tag is set to YES, doxygen will include brief member
+# descriptions after the members that are listed in the file and class
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+BRIEF_MEMBER_DESC = YES
+
+# If the REPEAT_BRIEF tag is set to YES, doxygen will prepend the brief
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+# The default value is: YES.
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+REPEAT_BRIEF = YES
+
+# This tag implements a quasi-intelligent brief description abbreviator that is
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+# following values are used ($name is automatically replaced with the name of
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+# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then
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+# The default value is: NO.
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+ALWAYS_DETAILED_SEC = NO
+
+# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all
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+
+INLINE_INHERITED_MEMB = NO
+
+# If the FULL_PATH_NAMES tag is set to YES, doxygen will prepend the full path
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+FULL_PATH_NAMES = YES
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+# The STRIP_FROM_PATH tag can be used to strip a user-defined part of the path.
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+#
+# Note that you can specify absolute paths here, but also relative paths, which
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+# This tag requires that the tag FULL_PATH_NAMES is set to YES.
+
+STRIP_FROM_PATH =
+
+# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of the
+# path mentioned in the documentation of a class, which tells the reader which
+# header file to include in order to use a class. If left blank only the name of
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+# specify the list of include paths that are normally passed to the compiler
+# using the -I flag.
+
+STRIP_FROM_INC_PATH =
+
+# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter (but
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+SHORT_NAMES = NO
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+# If the JAVADOC_AUTOBRIEF tag is set to YES then doxygen will interpret the
+# first line (until the first dot) of a Javadoc-style comment as the brief
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+# description.)
+# The default value is: NO.
+
+JAVADOC_AUTOBRIEF = NO
+
+# If the QT_AUTOBRIEF tag is set to YES then doxygen will interpret the first
+# line (until the first dot) of a Qt-style comment as the brief description. If
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+# The default value is: NO.
+
+QT_AUTOBRIEF = NO
+
+# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make doxygen treat a
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+# tag to YES if you prefer the old behavior instead.
+#
+# Note that setting this tag to YES also means that rational rose comments are
+# not recognized any more.
+# The default value is: NO.
+
+MULTILINE_CPP_IS_BRIEF = NO
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+# If the INHERIT_DOCS tag is set to YES then an undocumented member inherits the
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+INHERIT_DOCS = YES
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+# If the SEPARATE_MEMBER_PAGES tag is set to YES then doxygen will produce a new
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+SEPARATE_MEMBER_PAGES = NO
+
+# The TAB_SIZE tag can be used to set the number of spaces in a tab. Doxygen
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+# For example adding
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+# will allow you to put the command \sideeffect (or @sideeffect) in the
+# documentation, which will result in a user-defined paragraph with heading
+# "Side Effects:". You can put \n's in the value part of an alias to insert
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+
+ALIASES =
+
+# This tag can be used to specify a number of word-keyword mappings (TCL only).
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+TCL_SUBST =
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+# members will be omitted, etc.
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+OPTIMIZE_OUTPUT_JAVA = NO
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+OPTIMIZE_OUTPUT_VHDL = NO
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+
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+CPP_CLI_SUPPORT = NO
+
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+# should set this option to NO.
+# The default value is: YES.
+
+IDL_PROPERTY_SUPPORT = YES
+
+# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC
+# tag is set to YES then doxygen will reuse the documentation of the first
+# member in the group (if any) for the other members of the group. By default
+# all members of a group must be documented explicitly.
+# The default value is: NO.
+
+DISTRIBUTE_GROUP_DOC = NO
+
+# If one adds a struct or class to a group and this option is enabled, then also
+# any nested class or struct is added to the same group. By default this option
+# is disabled and one has to add nested compounds explicitly via \ingroup.
+# The default value is: NO.
+
+GROUP_NESTED_COMPOUNDS = NO
+
+# Set the SUBGROUPING tag to YES to allow class member groups of the same type
+# (for instance a group of public functions) to be put as a subgroup of that
+# type (e.g. under the Public Functions section). Set it to NO to prevent
+# subgrouping. Alternatively, this can be done per class using the
+# \nosubgrouping command.
+# The default value is: YES.
+
+SUBGROUPING = YES
+
+# When the INLINE_GROUPED_CLASSES tag is set to YES, classes, structs and unions
+# are shown inside the group in which they are included (e.g. using \ingroup)
+# instead of on a separate page (for HTML and Man pages) or section (for LaTeX
+# and RTF).
+#
+# Note that this feature does not work in combination with
+# SEPARATE_MEMBER_PAGES.
+# The default value is: NO.
+
+INLINE_GROUPED_CLASSES = NO
+
+# When the INLINE_SIMPLE_STRUCTS tag is set to YES, structs, classes, and unions
+# with only public data fields or simple typedef fields will be shown inline in
+# the documentation of the scope in which they are defined (i.e. file,
+# namespace, or group documentation), provided this scope is documented. If set
+# to NO, structs, classes, and unions are shown on a separate page (for HTML and
+# Man pages) or section (for LaTeX and RTF).
+# The default value is: NO.
+
+INLINE_SIMPLE_STRUCTS = NO
+
+# When TYPEDEF_HIDES_STRUCT tag is enabled, a typedef of a struct, union, or
+# enum is documented as struct, union, or enum with the name of the typedef. So
+# typedef struct TypeS {} TypeT, will appear in the documentation as a struct
+# with name TypeT. When disabled the typedef will appear as a member of a file,
+# namespace, or class. And the struct will be named TypeS. This can typically be
+# useful for C code in case the coding convention dictates that all compound
+# types are typedef'ed and only the typedef is referenced, never the tag name.
+# The default value is: NO.
+
+TYPEDEF_HIDES_STRUCT = NO
+
+# The size of the symbol lookup cache can be set using LOOKUP_CACHE_SIZE. This
+# cache is used to resolve symbols given their name and scope. Since this can be
+# an expensive process and often the same symbol appears multiple times in the
+# code, doxygen keeps a cache of pre-resolved symbols. If the cache is too small
+# doxygen will become slower. If the cache is too large, memory is wasted. The
+# cache size is given by this formula: 2^(16+LOOKUP_CACHE_SIZE). The valid range
+# is 0..9, the default is 0, corresponding to a cache size of 2^16=65536
+# symbols. At the end of a run doxygen will report the cache usage and suggest
+# the optimal cache size from a speed point of view.
+# Minimum value: 0, maximum value: 9, default value: 0.
+
+LOOKUP_CACHE_SIZE = 0
+
+#---------------------------------------------------------------------------
+# Build related configuration options
+#---------------------------------------------------------------------------
+
+# If the EXTRACT_ALL tag is set to YES, doxygen will assume all entities in
+# documentation are documented, even if no documentation was available. Private
+# class members and static file members will be hidden unless the
+# EXTRACT_PRIVATE respectively EXTRACT_STATIC tags are set to YES.
+# Note: This will also disable the warnings about undocumented members that are
+# normally produced when WARNINGS is set to YES.
+# The default value is: NO.
+
+EXTRACT_ALL = YES
+
+# If the EXTRACT_PRIVATE tag is set to YES, all private members of a class will
+# be included in the documentation.
+# The default value is: NO.
+
+EXTRACT_PRIVATE = YES
+
+# If the EXTRACT_PACKAGE tag is set to YES, all members with package or internal
+# scope will be included in the documentation.
+# The default value is: NO.
+
+EXTRACT_PACKAGE = YES
+
+# If the EXTRACT_STATIC tag is set to YES, all static members of a file will be
+# included in the documentation.
+# The default value is: NO.
+
+EXTRACT_STATIC = YES
+
+# If the EXTRACT_LOCAL_CLASSES tag is set to YES, classes (and structs) defined
+# locally in source files will be included in the documentation. If set to NO,
+# only classes defined in header files are included. Does not have any effect
+# for Java sources.
+# The default value is: YES.
+
+EXTRACT_LOCAL_CLASSES = YES
+
+# This flag is only useful for Objective-C code. If set to YES, local methods,
+# which are defined in the implementation section but not in the interface are
+# included in the documentation. If set to NO, only methods in the interface are
+# included.
+# The default value is: NO.
+
+EXTRACT_LOCAL_METHODS = YES
+
+# If this flag is set to YES, the members of anonymous namespaces will be
+# extracted and appear in the documentation as a namespace called
+# 'anonymous_namespace{file}', where file will be replaced with the base name of
+# the file that contains the anonymous namespace. By default anonymous namespace
+# are hidden.
+# The default value is: NO.
+
+EXTRACT_ANON_NSPACES = YES
+
+# If the HIDE_UNDOC_MEMBERS tag is set to YES, doxygen will hide all
+# undocumented members inside documented classes or files. If set to NO these
+# members will be included in the various overviews, but no documentation
+# section is generated. This option has no effect if EXTRACT_ALL is enabled.
+# The default value is: NO.
+
+HIDE_UNDOC_MEMBERS = NO
+
+# If the HIDE_UNDOC_CLASSES tag is set to YES, doxygen will hide all
+# undocumented classes that are normally visible in the class hierarchy. If set
+# to NO, these classes will be included in the various overviews. This option
+# has no effect if EXTRACT_ALL is enabled.
+# The default value is: NO.
+
+HIDE_UNDOC_CLASSES = NO
+
+# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, doxygen will hide all friend
+# (class|struct|union) declarations. If set to NO, these declarations will be
+# included in the documentation.
+# The default value is: NO.
+
+HIDE_FRIEND_COMPOUNDS = NO
+
+# If the HIDE_IN_BODY_DOCS tag is set to YES, doxygen will hide any
+# documentation blocks found inside the body of a function. If set to NO, these
+# blocks will be appended to the function's detailed documentation block.
+# The default value is: NO.
+
+HIDE_IN_BODY_DOCS = NO
+
+# The INTERNAL_DOCS tag determines if documentation that is typed after a
+# \internal command is included. If the tag is set to NO then the documentation
+# will be excluded. Set it to YES to include the internal documentation.
+# The default value is: NO.
+
+INTERNAL_DOCS = NO
+
+# If the CASE_SENSE_NAMES tag is set to NO then doxygen will only generate file
+# names in lower-case letters. If set to YES, upper-case letters are also
+# allowed. This is useful if you have classes or files whose names only differ
+# in case and if your file system supports case sensitive file names. Windows
+# and Mac users are advised to set this option to NO.
+# The default value is: system dependent.
+
+CASE_SENSE_NAMES = YES
+
+# If the HIDE_SCOPE_NAMES tag is set to NO then doxygen will show members with
+# their full class and namespace scopes in the documentation. If set to YES, the
+# scope will be hidden.
+# The default value is: NO.
+
+HIDE_SCOPE_NAMES = NO
+
+# If the HIDE_COMPOUND_REFERENCE tag is set to NO (default) then doxygen will
+# append additional text to a page's title, such as Class Reference. If set to
+# YES the compound reference will be hidden.
+# The default value is: NO.
+
+HIDE_COMPOUND_REFERENCE= NO
+
+# If the SHOW_INCLUDE_FILES tag is set to YES then doxygen will put a list of
+# the files that are included by a file in the documentation of that file.
+# The default value is: YES.
+
+SHOW_INCLUDE_FILES = YES
+
+# If the SHOW_GROUPED_MEMB_INC tag is set to YES then Doxygen will add for each
+# grouped member an include statement to the documentation, telling the reader
+# which file to include in order to use the member.
+# The default value is: NO.
+
+SHOW_GROUPED_MEMB_INC = NO
+
+# If the FORCE_LOCAL_INCLUDES tag is set to YES then doxygen will list include
+# files with double quotes in the documentation rather than with sharp brackets.
+# The default value is: NO.
+
+FORCE_LOCAL_INCLUDES = NO
+
+# If the INLINE_INFO tag is set to YES then a tag [inline] is inserted in the
+# documentation for inline members.
+# The default value is: YES.
+
+INLINE_INFO = YES
+
+# If the SORT_MEMBER_DOCS tag is set to YES then doxygen will sort the
+# (detailed) documentation of file and class members alphabetically by member
+# name. If set to NO, the members will appear in declaration order.
+# The default value is: YES.
+
+SORT_MEMBER_DOCS = YES
+
+# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the brief
+# descriptions of file, namespace and class members alphabetically by member
+# name. If set to NO, the members will appear in declaration order. Note that
+# this will also influence the order of the classes in the class list.
+# The default value is: NO.
+
+SORT_BRIEF_DOCS = NO
+
+# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen will sort the
+# (brief and detailed) documentation of class members so that constructors and
+# destructors are listed first. If set to NO the constructors will appear in the
+# respective orders defined by SORT_BRIEF_DOCS and SORT_MEMBER_DOCS.
+# Note: If SORT_BRIEF_DOCS is set to NO this option is ignored for sorting brief
+# member documentation.
+# Note: If SORT_MEMBER_DOCS is set to NO this option is ignored for sorting
+# detailed member documentation.
+# The default value is: NO.
+
+SORT_MEMBERS_CTORS_1ST = NO
+
+# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the hierarchy
+# of group names into alphabetical order. If set to NO the group names will
+# appear in their defined order.
+# The default value is: NO.
+
+SORT_GROUP_NAMES = YES
+
+# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be sorted by
+# fully-qualified names, including namespaces. If set to NO, the class list will
+# be sorted only by class name, not including the namespace part.
+# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES.
+# Note: This option applies only to the class list, not to the alphabetical
+# list.
+# The default value is: NO.
+
+SORT_BY_SCOPE_NAME = YES
+
+# If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to do proper
+# type resolution of all parameters of a function it will reject a match between
+# the prototype and the implementation of a member function even if there is
+# only one candidate or it is obvious which candidate to choose by doing a
+# simple string match. By disabling STRICT_PROTO_MATCHING doxygen will still
+# accept a match between prototype and implementation in such cases.
+# The default value is: NO.
+
+STRICT_PROTO_MATCHING = NO
+
+# The GENERATE_TODOLIST tag can be used to enable (YES) or disable (NO) the todo
+# list. This list is created by putting \todo commands in the documentation.
+# The default value is: YES.
+
+GENERATE_TODOLIST = YES
+
+# The GENERATE_TESTLIST tag can be used to enable (YES) or disable (NO) the test
+# list. This list is created by putting \test commands in the documentation.
+# The default value is: YES.
+
+GENERATE_TESTLIST = YES
+
+# The GENERATE_BUGLIST tag can be used to enable (YES) or disable (NO) the bug
+# list. This list is created by putting \bug commands in the documentation.
+# The default value is: YES.
+
+GENERATE_BUGLIST = YES
+
+# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or disable (NO)
+# the deprecated list. This list is created by putting \deprecated commands in
+# the documentation.
+# The default value is: YES.
+
+GENERATE_DEPRECATEDLIST= YES
+
+# The ENABLED_SECTIONS tag can be used to enable conditional documentation
+# sections, marked by \if <section_label> ... \endif and \cond <section_label>
+# ... \endcond blocks.
+
+ENABLED_SECTIONS =
+
+# The MAX_INITIALIZER_LINES tag determines the maximum number of lines that the
+# initial value of a variable or macro / define can have for it to appear in the
+# documentation. If the initializer consists of more lines than specified here
+# it will be hidden. Use a value of 0 to hide initializers completely. The
+# appearance of the value of individual variables and macros / defines can be
+# controlled using \showinitializer or \hideinitializer command in the
+# documentation regardless of this setting.
+# Minimum value: 0, maximum value: 10000, default value: 30.
+
+MAX_INITIALIZER_LINES = 30
+
+# Set the SHOW_USED_FILES tag to NO to disable the list of files generated at
+# the bottom of the documentation of classes and structs. If set to YES, the
+# list will mention the files that were used to generate the documentation.
+# The default value is: YES.
+
+SHOW_USED_FILES = YES
+
+# Set the SHOW_FILES tag to NO to disable the generation of the Files page. This
+# will remove the Files entry from the Quick Index and from the Folder Tree View
+# (if specified).
+# The default value is: YES.
+
+SHOW_FILES = YES
+
+# Set the SHOW_NAMESPACES tag to NO to disable the generation of the Namespaces
+# page. This will remove the Namespaces entry from the Quick Index and from the
+# Folder Tree View (if specified).
+# The default value is: YES.
+
+SHOW_NAMESPACES = YES
+
+# The FILE_VERSION_FILTER tag can be used to specify a program or script that
+# doxygen should invoke to get the current version for each file (typically from
+# the version control system). Doxygen will invoke the program by executing (via
+# popen()) the command command input-file, where command is the value of the
+# FILE_VERSION_FILTER tag, and input-file is the name of an input file provided
+# by doxygen. Whatever the program writes to standard output is used as the file
+# version. For an example see the documentation.
+
+FILE_VERSION_FILTER =
+
+# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed
+# by doxygen. The layout file controls the global structure of the generated
+# output files in an output format independent way. To create the layout file
+# that represents doxygen's defaults, run doxygen with the -l option. You can
+# optionally specify a file name after the option, if omitted DoxygenLayout.xml
+# will be used as the name of the layout file.
+#
+# Note that if you run doxygen from a directory containing a file called
+# DoxygenLayout.xml, doxygen will parse it automatically even if the LAYOUT_FILE
+# tag is left empty.
+
+LAYOUT_FILE =
+
+# The CITE_BIB_FILES tag can be used to specify one or more bib files containing
+# the reference definitions. This must be a list of .bib files. The .bib
+# extension is automatically appended if omitted. This requires the bibtex tool
+# to be installed. See also https://en.wikipedia.org/wiki/BibTeX for more info.
+# For LaTeX the style of the bibliography can be controlled using
+# LATEX_BIB_STYLE. To use this feature you need bibtex and perl available in the
+# search path. See also \cite for info how to create references.
+
+CITE_BIB_FILES =
+
+#---------------------------------------------------------------------------
+# Configuration options related to warning and progress messages
+#---------------------------------------------------------------------------
+
+# The QUIET tag can be used to turn on/off the messages that are generated to
+# standard output by doxygen. If QUIET is set to YES this implies that the
+# messages are off.
+# The default value is: NO.
+
+QUIET = NO
+
+# The WARNINGS tag can be used to turn on/off the warning messages that are
+# generated to standard error (stderr) by doxygen. If WARNINGS is set to YES
+# this implies that the warnings are on.
+#
+# Tip: Turn warnings on while writing the documentation.
+# The default value is: YES.
+
+WARNINGS = YES
+
+# If the WARN_IF_UNDOCUMENTED tag is set to YES then doxygen will generate
+# warnings for undocumented members. If EXTRACT_ALL is set to YES then this flag
+# will automatically be disabled.
+# The default value is: YES.
+
+WARN_IF_UNDOCUMENTED = YES
+
+# If the WARN_IF_DOC_ERROR tag is set to YES, doxygen will generate warnings for
+# potential errors in the documentation, such as not documenting some parameters
+# in a documented function, or documenting parameters that don't exist or using
+# markup commands wrongly.
+# The default value is: YES.
+
+WARN_IF_DOC_ERROR = YES
+
+# This WARN_NO_PARAMDOC option can be enabled to get warnings for functions that
+# are documented, but have no documentation for their parameters or return
+# value. If set to NO, doxygen will only warn about wrong or incomplete
+# parameter documentation, but not about the absence of documentation.
+# The default value is: NO.
+
+WARN_NO_PARAMDOC = NO
+
+# If the WARN_AS_ERROR tag is set to YES then doxygen will immediately stop when
+# a warning is encountered.
+# The default value is: NO.
+
+WARN_AS_ERROR = NO
+
+# The WARN_FORMAT tag determines the format of the warning messages that doxygen
+# can produce. The string should contain the $file, $line, and $text tags, which
+# will be replaced by the file and line number from which the warning originated
+# and the warning text. Optionally the format may contain $version, which will
+# be replaced by the version of the file (if it could be obtained via
+# FILE_VERSION_FILTER)
+# The default value is: $file:$line: $text.
+
+WARN_FORMAT = "$file:$line: $text"
+
+# The WARN_LOGFILE tag can be used to specify a file to which warning and error
+# messages should be written. If left blank the output is written to standard
+# error (stderr).
+
+WARN_LOGFILE =
+
+#---------------------------------------------------------------------------
+# Configuration options related to the input files
+#---------------------------------------------------------------------------
+
+# The INPUT tag is used to specify the files and/or directories that contain
+# documented source files. You may enter file names like myfile.cpp or
+# directories like /usr/src/myproject. Separate the files or directories with
+# spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
+# Note: If this tag is empty the current directory is searched.
+
+INPUT = tools/doxygen/Developer.dox \
+ src/ \
+ src/ASPHERE \
+ src/BODY \
+ src/CLASS2 \
+ src/COLLOID \
+ src/COMPRESS \
+ src/CORESHELL \
+ src/DEPEND \
+ src/DIPOLE \
+ src/GPU \
+ src/GRANULAR \
+ src/KIM \
+ src/KOKKOS \
+ src/KSPACE \
+ src/LATTE \
+ src/MAKE \
+ src/MANYBODY \
+ src/MC \
+ src/MEAM \
+ src/MISC \
+ src/MOLECULE \
+ src/MPIIO \
+ src/MSCG \
+ src/OPT \
+ src/PERI \
+ src/POEMS \
+ src/PYTHON \
+ src/QEQ \
+ src/REAX \
+ src/REPLICA \
+ src/RIGID \
+ src/SHOCK \
+ src/SNAP \
+ src/SRD \
+ src/VORONOI \
+ src/USER-AWPMD \
+ src/USER-CGDNA \
+ src/USER-CGSDK \
+ src/USER-COLVARS \
+ src/USER-DIFFRACTION \
+ src/USER-DPD \
+ src/USER-DRUDE \
+ src/USER-EFF \
+ src/USER-FEP \
+ src/USER-H5MD \
+ src/USER-INTEL \
+ src/USER-LB \
+ src/USER-MANIFOLD \
+ src/USER-MEAMC \
+ src/USER-MESO \
+ src/USER-MGPT \
+ src/USER-MISC \
+ src/USER-MOLFILE \
+ src/USER-NETCDF \
+ src/USER-OMP \
+ src/USER-PHONON \
+ src/USER-QMMM \
+ src/USER-QTB \
+ src/USER-QUIP \
+ src/USER-REAXC \
+ src/USER-SMD \
+ src/USER-SMTBQ \
+ src/USER-SPH \
+ src/USER-TALLY \
+ src/USER-UEF \
+ src/USER-VTK \
+ src/STUBS
+
+# This tag can be used to specify the character encoding of the source files
+# that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
+# libiconv (or the iconv built into libc) for the transcoding. See the libiconv
+# documentation (see: https://www.gnu.org/software/libiconv/) for the list of
+# possible encodings.
+# The default value is: UTF-8.
+
+INPUT_ENCODING = UTF-8
+
+# If the value of the INPUT tag contains directories, you can use the
+# FILE_PATTERNS tag to specify one or more wildcard patterns (like *.cpp and
+# *.h) to filter out the source-files in the directories.
+#
+# Note that for custom extensions or not directly supported extensions you also
+# need to set EXTENSION_MAPPING for the extension otherwise the files are not
+# read by doxygen.
+#
+# If left blank the following patterns are tested:*.c, *.cc, *.cxx, *.cpp,
+# *.c++, *.java, *.ii, *.ixx, *.ipp, *.i++, *.inl, *.idl, *.ddl, *.odl, *.h,
+# *.hh, *.hxx, *.hpp, *.h++, *.cs, *.d, *.php, *.php4, *.php5, *.phtml, *.inc,
+# *.m, *.markdown, *.md, *.mm, *.dox, *.py, *.pyw, *.f90, *.f95, *.f03, *.f08,
+# *.f, *.for, *.tcl, *.vhd, *.vhdl, *.ucf and *.qsf.
+
+FILE_PATTERNS = *.c \
+ *.cc \
+ *.cxx \
+ *.cpp \
+ *.c++ \
+ *.java \
+ *.ii \
+ *.ixx \
+ *.ipp \
+ *.i++ \
+ *.inl \
+ *.idl \
+ *.ddl \
+ *.odl \
+ *.h \
+ *.hh \
+ *.hxx \
+ *.hpp \
+ *.h++ \
+ *.cs \
+ *.d \
+ *.php \
+ *.php4 \
+ *.php5 \
+ *.phtml \
+ *.inc \
+ *.m \
+ *.markdown \
+ *.md \
+ *.mm \
+ *.dox \
+ *.py \
+ *.pyw \
+ *.f90 \
+ *.f95 \
+ *.f03 \
+ *.f08 \
+ *.f \
+ *.for \
+ *.tcl \
+ *.vhd \
+ *.vhdl \
+ *.ucf \
+ *.qsf
+
+# The RECURSIVE tag can be used to specify whether or not subdirectories should
+# be searched for input files as well.
+# The default value is: NO.
+
+RECURSIVE = NO
+
+# The EXCLUDE tag can be used to specify files and/or directories that should be
+# excluded from the INPUT source files. This way you can easily exclude a
+# subdirectory from a directory tree whose root is specified with the INPUT tag.
+#
+# Note that relative paths are relative to the directory from which doxygen is
+# run.
+
+EXCLUDE =
+
+# The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
+# directories that are symbolic links (a Unix file system feature) are excluded
+# from the input.
+# The default value is: NO.
+
+EXCLUDE_SYMLINKS = NO
+
+# If the value of the INPUT tag contains directories, you can use the
+# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude
+# certain files from those directories.
+#
+# Note that the wildcards are matched against the file with absolute path, so to
+# exclude all test directories for example use the pattern */test/*
+
+EXCLUDE_PATTERNS =
+
+# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
+# (namespaces, classes, functions, etc.) that should be excluded from the
+# output. The symbol name can be a fully qualified name, a word, or if the
+# wildcard * is used, a substring. Examples: ANamespace, AClass,
+# AClass::ANamespace, ANamespace::*Test
+#
+# Note that the wildcards are matched against the file with absolute path, so to
+# exclude all test directories use the pattern */test/*
+
+EXCLUDE_SYMBOLS =
+
+# The EXAMPLE_PATH tag can be used to specify one or more files or directories
+# that contain example code fragments that are included (see the \include
+# command).
+
+EXAMPLE_PATH = examples
+
+# If the value of the EXAMPLE_PATH tag contains directories, you can use the
+# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp and
+# *.h) to filter out the source-files in the directories. If left blank all
+# files are included.
+
+EXAMPLE_PATTERNS = in.*
+
+# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be
+# searched for input files to be used with the \include or \dontinclude commands
+# irrespective of the value of the RECURSIVE tag.
+# The default value is: NO.
+
+EXAMPLE_RECURSIVE = NO
+
+# The IMAGE_PATH tag can be used to specify one or more files or directories
+# that contain images that are to be included in the documentation (see the
+# \image command).
+
+IMAGE_PATH = tools/doxygen
+
+# The INPUT_FILTER tag can be used to specify a program that doxygen should
+# invoke to filter for each input file. Doxygen will invoke the filter program
+# by executing (via popen()) the command:
+#
+# <filter> <input-file>
+#
+# where <filter> is the value of the INPUT_FILTER tag, and <input-file> is the
+# name of an input file. Doxygen will then use the output that the filter
+# program writes to standard output. If FILTER_PATTERNS is specified, this tag
+# will be ignored.
+#
+# Note that the filter must not add or remove lines; it is applied before the
+# code is scanned, but not when the output code is generated. If lines are added
+# or removed, the anchors will not be placed correctly.
+#
+# Note that for custom extensions or not directly supported extensions you also
+# need to set EXTENSION_MAPPING for the extension otherwise the files are not
+# properly processed by doxygen.
+
+INPUT_FILTER =
+
+# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern
+# basis. Doxygen will compare the file name with each pattern and apply the
+# filter if there is a match. The filters are a list of the form: pattern=filter
+# (like *.cpp=my_cpp_filter). See INPUT_FILTER for further information on how
+# filters are used. If the FILTER_PATTERNS tag is empty or if none of the
+# patterns match the file name, INPUT_FILTER is applied.
+#
+# Note that for custom extensions or not directly supported extensions you also
+# need to set EXTENSION_MAPPING for the extension otherwise the files are not
+# properly processed by doxygen.
+
+FILTER_PATTERNS =
+
+# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using
+# INPUT_FILTER) will also be used to filter the input files that are used for
+# producing the source files to browse (i.e. when SOURCE_BROWSER is set to YES).
+# The default value is: NO.
+
+FILTER_SOURCE_FILES = NO
+
+# The FILTER_SOURCE_PATTERNS tag can be used to specify source filters per file
+# pattern. A pattern will override the setting for FILTER_PATTERN (if any) and
+# it is also possible to disable source filtering for a specific pattern using
+# *.ext= (so without naming a filter).
+# This tag requires that the tag FILTER_SOURCE_FILES is set to YES.
+
+FILTER_SOURCE_PATTERNS =
+
+# If the USE_MDFILE_AS_MAINPAGE tag refers to the name of a markdown file that
+# is part of the input, its contents will be placed on the main page
+# (index.html). This can be useful if you have a project on for instance GitHub
+# and want to reuse the introduction page also for the doxygen output.
+
+USE_MDFILE_AS_MAINPAGE =
+
+#---------------------------------------------------------------------------
+# Configuration options related to source browsing
+#---------------------------------------------------------------------------
+
+# If the SOURCE_BROWSER tag is set to YES then a list of source files will be
+# generated. Documented entities will be cross-referenced with these sources.
+#
+# Note: To get rid of all source code in the generated output, make sure that
+# also VERBATIM_HEADERS is set to NO.
+# The default value is: NO.
+
+SOURCE_BROWSER = YES
+
+# Setting the INLINE_SOURCES tag to YES will include the body of functions,
+# classes and enums directly into the documentation.
+# The default value is: NO.
+
+INLINE_SOURCES = YES
+
+# Setting the STRIP_CODE_COMMENTS tag to YES will instruct doxygen to hide any
+# special comment blocks from generated source code fragments. Normal C, C++ and
+# Fortran comments will always remain visible.
+# The default value is: YES.
+
+STRIP_CODE_COMMENTS = YES
+
+# If the REFERENCED_BY_RELATION tag is set to YES then for each documented
+# function all documented functions referencing it will be listed.
+# The default value is: NO.
+
+REFERENCED_BY_RELATION = NO
+
+# If the REFERENCES_RELATION tag is set to YES then for each documented function
+# all documented entities called/used by that function will be listed.
+# The default value is: NO.
+
+REFERENCES_RELATION = NO
+
+# If the REFERENCES_LINK_SOURCE tag is set to YES and SOURCE_BROWSER tag is set
+# to YES then the hyperlinks from functions in REFERENCES_RELATION and
+# REFERENCED_BY_RELATION lists will link to the source code. Otherwise they will
+# link to the documentation.
+# The default value is: YES.
+
+REFERENCES_LINK_SOURCE = YES
+
+# If SOURCE_TOOLTIPS is enabled (the default) then hovering a hyperlink in the
+# source code will show a tooltip with additional information such as prototype,
+# brief description and links to the definition and documentation. Since this
+# will make the HTML file larger and loading of large files a bit slower, you
+# can opt to disable this feature.
+# The default value is: YES.
+# This tag requires that the tag SOURCE_BROWSER is set to YES.
+
+SOURCE_TOOLTIPS = YES
+
+# If the USE_HTAGS tag is set to YES then the references to source code will
+# point to the HTML generated by the htags(1) tool instead of doxygen built-in
+# source browser. The htags tool is part of GNU's global source tagging system
+# (see https://www.gnu.org/software/global/global.html). You will need version
+# 4.8.6 or higher.
+#
+# To use it do the following:
+# - Install the latest version of global
+# - Enable SOURCE_BROWSER and USE_HTAGS in the config file
+# - Make sure the INPUT points to the root of the source tree
+# - Run doxygen as normal
+#
+# Doxygen will invoke htags (and that will in turn invoke gtags), so these
+# tools must be available from the command line (i.e. in the search path).
+#
+# The result: instead of the source browser generated by doxygen, the links to
+# source code will now point to the output of htags.
+# The default value is: NO.
+# This tag requires that the tag SOURCE_BROWSER is set to YES.
+
+USE_HTAGS = NO
+
+# If the VERBATIM_HEADERS tag is set the YES then doxygen will generate a
+# verbatim copy of the header file for each class for which an include is
+# specified. Set to NO to disable this.
+# See also: Section \class.
+# The default value is: YES.
+
+VERBATIM_HEADERS = YES
+
+#---------------------------------------------------------------------------
+# Configuration options related to the alphabetical class index
+#---------------------------------------------------------------------------
+
+# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index of all
+# compounds will be generated. Enable this if the project contains a lot of
+# classes, structs, unions or interfaces.
+# The default value is: YES.
+
+ALPHABETICAL_INDEX = YES
+
+# The COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns in
+# which the alphabetical index list will be split.
+# Minimum value: 1, maximum value: 20, default value: 5.
+# This tag requires that the tag ALPHABETICAL_INDEX is set to YES.
+
+COLS_IN_ALPHA_INDEX = 5
+
+# In case all classes in a project start with a common prefix, all classes will
+# be put under the same header in the alphabetical index. The IGNORE_PREFIX tag
+# can be used to specify a prefix (or a list of prefixes) that should be ignored
+# while generating the index headers.
+# This tag requires that the tag ALPHABETICAL_INDEX is set to YES.
+
+IGNORE_PREFIX =
+
+#---------------------------------------------------------------------------
+# Configuration options related to the HTML output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_HTML tag is set to YES, doxygen will generate HTML output
+# The default value is: YES.
+
+GENERATE_HTML = YES
+
+# The HTML_OUTPUT tag is used to specify where the HTML docs will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it.
+# The default directory is: html.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_OUTPUT = html
+
+# The HTML_FILE_EXTENSION tag can be used to specify the file extension for each
+# generated HTML page (for example: .htm, .php, .asp).
+# The default value is: .html.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_FILE_EXTENSION = .html
+
+# The HTML_HEADER tag can be used to specify a user-defined HTML header file for
+# each generated HTML page. If the tag is left blank doxygen will generate a
+# standard header.
+#
+# To get valid HTML the header file that includes any scripts and style sheets
+# that doxygen needs, which is dependent on the configuration options used (e.g.
+# the setting GENERATE_TREEVIEW). It is highly recommended to start with a
+# default header using
+# doxygen -w html new_header.html new_footer.html new_stylesheet.css
+# YourConfigFile
+# and then modify the file new_header.html. See also section "Doxygen usage"
+# for information on how to generate the default header that doxygen normally
+# uses.
+# Note: The header is subject to change so you typically have to regenerate the
+# default header when upgrading to a newer version of doxygen. For a description
+# of the possible markers and block names see the documentation.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_HEADER =
+
+# The HTML_FOOTER tag can be used to specify a user-defined HTML footer for each
+# generated HTML page. If the tag is left blank doxygen will generate a standard
+# footer. See HTML_HEADER for more information on how to generate a default
+# footer and what special commands can be used inside the footer. See also
+# section "Doxygen usage" for information on how to generate the default footer
+# that doxygen normally uses.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_FOOTER =
+
+# The HTML_STYLESHEET tag can be used to specify a user-defined cascading style
+# sheet that is used by each HTML page. It can be used to fine-tune the look of
+# the HTML output. If left blank doxygen will generate a default style sheet.
+# See also section "Doxygen usage" for information on how to generate the style
+# sheet that doxygen normally uses.
+# Note: It is recommended to use HTML_EXTRA_STYLESHEET instead of this tag, as
+# it is more robust and this tag (HTML_STYLESHEET) will in the future become
+# obsolete.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_STYLESHEET =
+
+# The HTML_EXTRA_STYLESHEET tag can be used to specify additional user-defined
+# cascading style sheets that are included after the standard style sheets
+# created by doxygen. Using this option one can overrule certain style aspects.
+# This is preferred over using HTML_STYLESHEET since it does not replace the
+# standard style sheet and is therefore more robust against future updates.
+# Doxygen will copy the style sheet files to the output directory.
+# Note: The order of the extra style sheet files is of importance (e.g. the last
+# style sheet in the list overrules the setting of the previous ones in the
+# list). For an example see the documentation.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_EXTRA_STYLESHEET =
+
+# The HTML_EXTRA_FILES tag can be used to specify one or more extra images or
+# other source files which should be copied to the HTML output directory. Note
+# that these files will be copied to the base HTML output directory. Use the
+# $relpath^ marker in the HTML_HEADER and/or HTML_FOOTER files to load these
+# files. In the HTML_STYLESHEET file, use the file name only. Also note that the
+# files will be copied as-is; there are no commands or markers available.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_EXTRA_FILES =
+
+# The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. Doxygen
+# will adjust the colors in the style sheet and background images according to
+# this color. Hue is specified as an angle on a colorwheel, see
+# https://en.wikipedia.org/wiki/Hue for more information. For instance the value
+# 0 represents red, 60 is yellow, 120 is green, 180 is cyan, 240 is blue, 300
+# purple, and 360 is red again.
+# Minimum value: 0, maximum value: 359, default value: 220.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_COLORSTYLE_HUE = 220
+
+# The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of the colors
+# in the HTML output. For a value of 0 the output will use grayscales only. A
+# value of 255 will produce the most vivid colors.
+# Minimum value: 0, maximum value: 255, default value: 100.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_COLORSTYLE_SAT = 100
+
+# The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to the
+# luminance component of the colors in the HTML output. Values below 100
+# gradually make the output lighter, whereas values above 100 make the output
+# darker. The value divided by 100 is the actual gamma applied, so 80 represents
+# a gamma of 0.8, The value 220 represents a gamma of 2.2, and 100 does not
+# change the gamma.
+# Minimum value: 40, maximum value: 240, default value: 80.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_COLORSTYLE_GAMMA = 80
+
+# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML
+# page will contain the date and time when the page was generated. Setting this
+# to YES can help to show when doxygen was last run and thus if the
+# documentation is up to date.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_TIMESTAMP = NO
+
+# If the HTML_DYNAMIC_MENUS tag is set to YES then the generated HTML
+# documentation will contain a main index with vertical navigation menus that
+# are dynamically created via Javascript. If disabled, the navigation index will
+# consists of multiple levels of tabs that are statically embedded in every HTML
+# page. Disable this option to support browsers that do not have Javascript,
+# like the Qt help browser.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_DYNAMIC_MENUS = YES
+
+# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
+# documentation will contain sections that can be hidden and shown after the
+# page has loaded.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_DYNAMIC_SECTIONS = NO
+
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of entries
+# shown in the various tree structured indices initially; the user can expand
+# and collapse entries dynamically later on. Doxygen will expand the tree to
+# such a level that at most the specified number of entries are visible (unless
+# a fully collapsed tree already exceeds this amount). So setting the number of
+# entries 1 will produce a full collapsed tree by default. 0 is a special value
+# representing an infinite number of entries and will result in a full expanded
+# tree by default.
+# Minimum value: 0, maximum value: 9999, default value: 100.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
+# If the GENERATE_DOCSET tag is set to YES, additional index files will be
+# generated that can be used as input for Apple's Xcode 3 integrated development
+# environment (see: https://developer.apple.com/tools/xcode/), introduced with
+# OSX 10.5 (Leopard). To create a documentation set, doxygen will generate a
+# Makefile in the HTML output directory. Running make will produce the docset in
+# that directory and running make install will install the docset in
+# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find it at
+# startup. See https://developer.apple.com/tools/creatingdocsetswithdoxygen.html
+# for more information.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+GENERATE_DOCSET = NO
+
+# This tag determines the name of the docset feed. A documentation feed provides
+# an umbrella under which multiple documentation sets from a single provider
+# (such as a company or product suite) can be grouped.
+# The default value is: Doxygen generated docs.
+# This tag requires that the tag GENERATE_DOCSET is set to YES.
+
+DOCSET_FEEDNAME = "Doxygen generated docs"
+
+# This tag specifies a string that should uniquely identify the documentation
+# set bundle. This should be a reverse domain-name style string, e.g.
+# com.mycompany.MyDocSet. Doxygen will append .docset to the name.
+# The default value is: org.doxygen.Project.
+# This tag requires that the tag GENERATE_DOCSET is set to YES.
+
+DOCSET_BUNDLE_ID = org.doxygen.Project
+
+# The DOCSET_PUBLISHER_ID tag specifies a string that should uniquely identify
+# the documentation publisher. This should be a reverse domain-name style
+# string, e.g. com.mycompany.MyDocSet.documentation.
+# The default value is: org.doxygen.Publisher.
+# This tag requires that the tag GENERATE_DOCSET is set to YES.
+
+DOCSET_PUBLISHER_ID = org.doxygen.Publisher
+
+# The DOCSET_PUBLISHER_NAME tag identifies the documentation publisher.
+# The default value is: Publisher.
+# This tag requires that the tag GENERATE_DOCSET is set to YES.
+
+DOCSET_PUBLISHER_NAME = Publisher
+
+# If the GENERATE_HTMLHELP tag is set to YES then doxygen generates three
+# additional HTML index files: index.hhp, index.hhc, and index.hhk. The
+# index.hhp is a project file that can be read by Microsoft's HTML Help Workshop
+# (see: http://www.microsoft.com/en-us/download/details.aspx?id=21138) on
+# Windows.
+#
+# The HTML Help Workshop contains a compiler that can convert all HTML output
+# generated by doxygen into a single compiled HTML file (.chm). Compiled HTML
+# files are now used as the Windows 98 help format, and will replace the old
+# Windows help format (.hlp) on all Windows platforms in the future. Compressed
+# HTML files also contain an index, a table of contents, and you can search for
+# words in the documentation. The HTML workshop also contains a viewer for
+# compressed HTML files.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+GENERATE_HTMLHELP = NO
+
+# The CHM_FILE tag can be used to specify the file name of the resulting .chm
+# file. You can add a path in front of the file if the result should not be
+# written to the html output directory.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
+CHM_FILE =
+
+# The HHC_LOCATION tag can be used to specify the location (absolute path
+# including file name) of the HTML help compiler (hhc.exe). If non-empty,
+# doxygen will try to run the HTML help compiler on the generated index.hhp.
+# The file has to be specified with full path.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
+HHC_LOCATION =
+
+# The GENERATE_CHI flag controls if a separate .chi index file is generated
+# (YES) or that it should be included in the master .chm file (NO).
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
+GENERATE_CHI = NO
+
+# The CHM_INDEX_ENCODING is used to encode HtmlHelp index (hhk), content (hhc)
+# and project file content.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
+CHM_INDEX_ENCODING =
+
+# The BINARY_TOC flag controls whether a binary table of contents is generated
+# (YES) or a normal table of contents (NO) in the .chm file. Furthermore it
+# enables the Previous and Next buttons.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
+BINARY_TOC = NO
+
+# The TOC_EXPAND flag can be set to YES to add extra items for group members to
+# the table of contents of the HTML help documentation and to the tree view.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
+TOC_EXPAND = NO
+
+# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and
+# QHP_VIRTUAL_FOLDER are set, an additional index file will be generated that
+# can be used as input for Qt's qhelpgenerator to generate a Qt Compressed Help
+# (.qch) of the generated HTML documentation.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+GENERATE_QHP = NO
+
+# If the QHG_LOCATION tag is specified, the QCH_FILE tag can be used to specify
+# the file name of the resulting .qch file. The path specified is relative to
+# the HTML output folder.
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QCH_FILE =
+
+# The QHP_NAMESPACE tag specifies the namespace to use when generating Qt Help
+# Project output. For more information please see Qt Help Project / Namespace
+# (see: http://doc.qt.io/qt-4.8/qthelpproject.html#namespace).
+# The default value is: org.doxygen.Project.
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHP_NAMESPACE = org.doxygen.Project
+
+# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating Qt
+# Help Project output. For more information please see Qt Help Project / Virtual
+# Folders (see: http://doc.qt.io/qt-4.8/qthelpproject.html#virtual-folders).
+# The default value is: doc.
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHP_VIRTUAL_FOLDER = doc
+
+# If the QHP_CUST_FILTER_NAME tag is set, it specifies the name of a custom
+# filter to add. For more information please see Qt Help Project / Custom
+# Filters (see: http://doc.qt.io/qt-4.8/qthelpproject.html#custom-filters).
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHP_CUST_FILTER_NAME =
+
+# The QHP_CUST_FILTER_ATTRS tag specifies the list of the attributes of the
+# custom filter to add. For more information please see Qt Help Project / Custom
+# Filters (see: http://doc.qt.io/qt-4.8/qthelpproject.html#custom-filters).
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHP_CUST_FILTER_ATTRS =
+
+# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this
+# project's filter section matches. Qt Help Project / Filter Attributes (see:
+# http://doc.qt.io/qt-4.8/qthelpproject.html#filter-attributes).
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHP_SECT_FILTER_ATTRS =
+
+# The QHG_LOCATION tag can be used to specify the location of Qt's
+# qhelpgenerator. If non-empty doxygen will try to run qhelpgenerator on the
+# generated .qhp file.
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHG_LOCATION =
+
+# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files will be
+# generated, together with the HTML files, they form an Eclipse help plugin. To
+# install this plugin and make it available under the help contents menu in
+# Eclipse, the contents of the directory containing the HTML and XML files needs
+# to be copied into the plugins directory of eclipse. The name of the directory
+# within the plugins directory should be the same as the ECLIPSE_DOC_ID value.
+# After copying Eclipse needs to be restarted before the help appears.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+GENERATE_ECLIPSEHELP = NO
+
+# A unique identifier for the Eclipse help plugin. When installing the plugin
+# the directory name containing the HTML and XML files should also have this
+# name. Each documentation set should have its own identifier.
+# The default value is: org.doxygen.Project.
+# This tag requires that the tag GENERATE_ECLIPSEHELP is set to YES.
+
+ECLIPSE_DOC_ID = org.doxygen.Project
+
+# If you want full control over the layout of the generated HTML pages it might
+# be necessary to disable the index and replace it with your own. The
+# DISABLE_INDEX tag can be used to turn on/off the condensed index (tabs) at top
+# of each HTML page. A value of NO enables the index and the value YES disables
+# it. Since the tabs in the index contain the same information as the navigation
+# tree, you can set this option to YES if you also set GENERATE_TREEVIEW to YES.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+DISABLE_INDEX = NO
+
+# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
+# structure should be generated to display hierarchical information. If the tag
+# value is set to YES, a side panel will be generated containing a tree-like
+# index structure (just like the one that is generated for HTML Help). For this
+# to work a browser that supports JavaScript, DHTML, CSS and frames is required
+# (i.e. any modern browser). Windows users are probably better off using the
+# HTML help feature. Via custom style sheets (see HTML_EXTRA_STYLESHEET) one can
+# further fine-tune the look of the index. As an example, the default style
+# sheet generated by doxygen has an example that shows how to put an image at
+# the root of the tree instead of the PROJECT_NAME. Since the tree basically has
+# the same information as the tab index, you could consider setting
+# DISABLE_INDEX to YES when enabling this option.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+GENERATE_TREEVIEW = YES
+
+# The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values that
+# doxygen will group on one line in the generated HTML documentation.
+#
+# Note that a value of 0 will completely suppress the enum values from appearing
+# in the overview section.
+# Minimum value: 0, maximum value: 20, default value: 4.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+ENUM_VALUES_PER_LINE = 4
+
+# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be used
+# to set the initial width (in pixels) of the frame in which the tree is shown.
+# Minimum value: 0, maximum value: 1500, default value: 250.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+TREEVIEW_WIDTH = 250
+
+# If the EXT_LINKS_IN_WINDOW option is set to YES, doxygen will open links to
+# external symbols imported via tag files in a separate window.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+EXT_LINKS_IN_WINDOW = NO
+
+# Use this tag to change the font size of LaTeX formulas included as images in
+# the HTML documentation. When you change the font size after a successful
+# doxygen run you need to manually remove any form_*.png images from the HTML
+# output directory to force them to be regenerated.
+# Minimum value: 8, maximum value: 50, default value: 10.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+FORMULA_FONTSIZE = 10
+
+# Use the FORMULA_TRANSPARENT tag to determine whether or not the images
+# generated for formulas are transparent PNGs. Transparent PNGs are not
+# supported properly for IE 6.0, but are supported on all modern browsers.
+#
+# Note that when changing this option you need to delete any form_*.png files in
+# the HTML output directory before the changes have effect.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+FORMULA_TRANSPARENT = YES
+
+# Enable the USE_MATHJAX option to render LaTeX formulas using MathJax (see
+# https://www.mathjax.org) which uses client side Javascript for the rendering
+# instead of using pre-rendered bitmaps. Use this if you do not have LaTeX
+# installed or if you want to formulas look prettier in the HTML output. When
+# enabled you may also need to install MathJax separately and configure the path
+# to it using the MATHJAX_RELPATH option.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+USE_MATHJAX = NO
+
+# When MathJax is enabled you can set the default output format to be used for
+# the MathJax output. See the MathJax site (see:
+# http://docs.mathjax.org/en/latest/output.html) for more details.
+# Possible values are: HTML-CSS (which is slower, but has the best
+# compatibility), NativeMML (i.e. MathML) and SVG.
+# The default value is: HTML-CSS.
+# This tag requires that the tag USE_MATHJAX is set to YES.
+
+MATHJAX_FORMAT = HTML-CSS
+
+# When MathJax is enabled you need to specify the location relative to the HTML
+# output directory using the MATHJAX_RELPATH option. The destination directory
+# should contain the MathJax.js script. For instance, if the mathjax directory
+# is located at the same level as the HTML output directory, then
+# MATHJAX_RELPATH should be ../mathjax. The default value points to the MathJax
+# Content Delivery Network so you can quickly see the result without installing
+# MathJax. However, it is strongly recommended to install a local copy of
+# MathJax from https://www.mathjax.org before deployment.
+# The default value is: https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.2/.
+# This tag requires that the tag USE_MATHJAX is set to YES.
+
+MATHJAX_RELPATH = http://cdn.mathjax.org/mathjax/latest
+
+# The MATHJAX_EXTENSIONS tag can be used to specify one or more MathJax
+# extension names that should be enabled during MathJax rendering. For example
+# MATHJAX_EXTENSIONS = TeX/AMSmath TeX/AMSsymbols
+# This tag requires that the tag USE_MATHJAX is set to YES.
+
+MATHJAX_EXTENSIONS =
+
+# The MATHJAX_CODEFILE tag can be used to specify a file with javascript pieces
+# of code that will be used on startup of the MathJax code. See the MathJax site
+# (see: http://docs.mathjax.org/en/latest/output.html) for more details. For an
+# example see the documentation.
+# This tag requires that the tag USE_MATHJAX is set to YES.
+
+MATHJAX_CODEFILE =
+
+# When the SEARCHENGINE tag is enabled doxygen will generate a search box for
+# the HTML output. The underlying search engine uses javascript and DHTML and
+# should work on any modern browser. Note that when using HTML help
+# (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets (GENERATE_DOCSET)
+# there is already a search function so this one should typically be disabled.
+# For large projects the javascript based search engine can be slow, then
+# enabling SERVER_BASED_SEARCH may provide a better solution. It is possible to
+# search using the keyboard; to jump to the search box use <access key> + S
+# (what the <access key> is depends on the OS and browser, but it is typically
+# <CTRL>, <ALT>/<option>, or both). Inside the search box use the <cursor down
+# key> to jump into the search results window, the results can be navigated
+# using the <cursor keys>. Press <Enter> to select an item or <escape> to cancel
+# the search. The filter options can be selected when the cursor is inside the
+# search box by pressing <Shift>+<cursor down>. Also here use the <cursor keys>
+# to select a filter and <Enter> or <escape> to activate or cancel the filter
+# option.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+SEARCHENGINE = YES
+
+# When the SERVER_BASED_SEARCH tag is enabled the search engine will be
+# implemented using a web server instead of a web client using Javascript. There
+# are two flavors of web server based searching depending on the EXTERNAL_SEARCH
+# setting. When disabled, doxygen will generate a PHP script for searching and
+# an index file used by the script. When EXTERNAL_SEARCH is enabled the indexing
+# and searching needs to be provided by external tools. See the section
+# "External Indexing and Searching" for details.
+# The default value is: NO.
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+SERVER_BASED_SEARCH = NO
+
+# When EXTERNAL_SEARCH tag is enabled doxygen will no longer generate the PHP
+# script for searching. Instead the search results are written to an XML file
+# which needs to be processed by an external indexer. Doxygen will invoke an
+# external search engine pointed to by the SEARCHENGINE_URL option to obtain the
+# search results.
+#
+# Doxygen ships with an example indexer (doxyindexer) and search engine
+# (doxysearch.cgi) which are based on the open source search engine library
+# Xapian (see: https://xapian.org/).
+#
+# See the section "External Indexing and Searching" for details.
+# The default value is: NO.
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+EXTERNAL_SEARCH = NO
+
+# The SEARCHENGINE_URL should point to a search engine hosted by a web server
+# which will return the search results when EXTERNAL_SEARCH is enabled.
+#
+# Doxygen ships with an example indexer (doxyindexer) and search engine
+# (doxysearch.cgi) which are based on the open source search engine library
+# Xapian (see: https://xapian.org/). See the section "External Indexing and
+# Searching" for details.
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+SEARCHENGINE_URL =
+
+# When SERVER_BASED_SEARCH and EXTERNAL_SEARCH are both enabled the unindexed
+# search data is written to a file for indexing by an external tool. With the
+# SEARCHDATA_FILE tag the name of this file can be specified.
+# The default file is: searchdata.xml.
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+SEARCHDATA_FILE = searchdata.xml
+
+# When SERVER_BASED_SEARCH and EXTERNAL_SEARCH are both enabled the
+# EXTERNAL_SEARCH_ID tag can be used as an identifier for the project. This is
+# useful in combination with EXTRA_SEARCH_MAPPINGS to search through multiple
+# projects and redirect the results back to the right project.
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+EXTERNAL_SEARCH_ID =
+
+# The EXTRA_SEARCH_MAPPINGS tag can be used to enable searching through doxygen
+# projects other than the one defined by this configuration file, but that are
+# all added to the same external search index. Each project needs to have a
+# unique id set via EXTERNAL_SEARCH_ID. The search mapping then maps the id of
+# to a relative location where the documentation can be found. The format is:
+# EXTRA_SEARCH_MAPPINGS = tagname1=loc1 tagname2=loc2 ...
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+EXTRA_SEARCH_MAPPINGS =
+
+#---------------------------------------------------------------------------
+# Configuration options related to the LaTeX output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_LATEX tag is set to YES, doxygen will generate LaTeX output.
+# The default value is: YES.
+
+GENERATE_LATEX = NO
+
+# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it.
+# The default directory is: latex.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_OUTPUT = latex
+
+# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be
+# invoked.
+#
+# Note that when enabling USE_PDFLATEX this option is only used for generating
+# bitmaps for formulas in the HTML output, but not in the Makefile that is
+# written to the output directory.
+# The default file is: latex.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_CMD_NAME = latex
+
+# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to generate
+# index for LaTeX.
+# The default file is: makeindex.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+MAKEINDEX_CMD_NAME = makeindex
+
+# If the COMPACT_LATEX tag is set to YES, doxygen generates more compact LaTeX
+# documents. This may be useful for small projects and may help to save some
+# trees in general.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+COMPACT_LATEX = NO
+
+# The PAPER_TYPE tag can be used to set the paper type that is used by the
+# printer.
+# Possible values are: a4 (210 x 297 mm), letter (8.5 x 11 inches), legal (8.5 x
+# 14 inches) and executive (7.25 x 10.5 inches).
+# The default value is: a4.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+PAPER_TYPE = a4
+
+# The EXTRA_PACKAGES tag can be used to specify one or more LaTeX package names
+# that should be included in the LaTeX output. The package can be specified just
+# by its name or with the correct syntax as to be used with the LaTeX
+# \usepackage command. To get the times font for instance you can specify :
+# EXTRA_PACKAGES=times or EXTRA_PACKAGES={times}
+# To use the option intlimits with the amsmath package you can specify:
+# EXTRA_PACKAGES=[intlimits]{amsmath}
+# If left blank no extra packages will be included.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+EXTRA_PACKAGES =
+
+# The LATEX_HEADER tag can be used to specify a personal LaTeX header for the
+# generated LaTeX document. The header should contain everything until the first
+# chapter. If it is left blank doxygen will generate a standard header. See
+# section "Doxygen usage" for information on how to let doxygen write the
+# default header to a separate file.
+#
+# Note: Only use a user-defined header if you know what you are doing! The
+# following commands have a special meaning inside the header: $title,
+# $datetime, $date, $doxygenversion, $projectname, $projectnumber,
+# $projectbrief, $projectlogo. Doxygen will replace $title with the empty
+# string, for the replacement values of the other commands the user is referred
+# to HTML_HEADER.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_HEADER =
+
+# The LATEX_FOOTER tag can be used to specify a personal LaTeX footer for the
+# generated LaTeX document. The footer should contain everything after the last
+# chapter. If it is left blank doxygen will generate a standard footer. See
+# LATEX_HEADER for more information on how to generate a default footer and what
+# special commands can be used inside the footer.
+#
+# Note: Only use a user-defined footer if you know what you are doing!
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_FOOTER =
+
+# The LATEX_EXTRA_STYLESHEET tag can be used to specify additional user-defined
+# LaTeX style sheets that are included after the standard style sheets created
+# by doxygen. Using this option one can overrule certain style aspects. Doxygen
+# will copy the style sheet files to the output directory.
+# Note: The order of the extra style sheet files is of importance (e.g. the last
+# style sheet in the list overrules the setting of the previous ones in the
+# list).
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_EXTRA_STYLESHEET =
+
+# The LATEX_EXTRA_FILES tag can be used to specify one or more extra images or
+# other source files which should be copied to the LATEX_OUTPUT output
+# directory. Note that the files will be copied as-is; there are no commands or
+# markers available.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_EXTRA_FILES =
+
+# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated is
+# prepared for conversion to PDF (using ps2pdf or pdflatex). The PDF file will
+# contain links (just like the HTML output) instead of page references. This
+# makes the output suitable for online browsing using a PDF viewer.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+PDF_HYPERLINKS = YES
+
+# If the USE_PDFLATEX tag is set to YES, doxygen will use pdflatex to generate
+# the PDF file directly from the LaTeX files. Set this option to YES, to get a
+# higher quality PDF documentation.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+USE_PDFLATEX = YES
+
+# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \batchmode
+# command to the generated LaTeX files. This will instruct LaTeX to keep running
+# if errors occur, instead of asking the user for help. This option is also used
+# when generating formulas in HTML.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_BATCHMODE = NO
+
+# If the LATEX_HIDE_INDICES tag is set to YES then doxygen will not include the
+# index chapters (such as File Index, Compound Index, etc.) in the output.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_HIDE_INDICES = NO
+
+# If the LATEX_SOURCE_CODE tag is set to YES then doxygen will include source
+# code with syntax highlighting in the LaTeX output.
+#
+# Note that which sources are shown also depends on other settings such as
+# SOURCE_BROWSER.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_SOURCE_CODE = NO
+
+# The LATEX_BIB_STYLE tag can be used to specify the style to use for the
+# bibliography, e.g. plainnat, or ieeetr. See
+# https://en.wikipedia.org/wiki/BibTeX and \cite for more info.
+# The default value is: plain.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_BIB_STYLE = plain
+
+# If the LATEX_TIMESTAMP tag is set to YES then the footer of each generated
+# page will contain the date and time when the page was generated. Setting this
+# to NO can help when comparing the output of multiple runs.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_TIMESTAMP = NO
+
+#---------------------------------------------------------------------------
+# Configuration options related to the RTF output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_RTF tag is set to YES, doxygen will generate RTF output. The
+# RTF output is optimized for Word 97 and may not look too pretty with other RTF
+# readers/editors.
+# The default value is: NO.
+
+GENERATE_RTF = NO
+
+# The RTF_OUTPUT tag is used to specify where the RTF docs will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it.
+# The default directory is: rtf.
+# This tag requires that the tag GENERATE_RTF is set to YES.
+
+RTF_OUTPUT = rtf
+
+# If the COMPACT_RTF tag is set to YES, doxygen generates more compact RTF
+# documents. This may be useful for small projects and may help to save some
+# trees in general.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_RTF is set to YES.
+
+COMPACT_RTF = NO
+
+# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated will
+# contain hyperlink fields. The RTF file will contain links (just like the HTML
+# output) instead of page references. This makes the output suitable for online
+# browsing using Word or some other Word compatible readers that support those
+# fields.
+#
+# Note: WordPad (write) and others do not support links.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_RTF is set to YES.
+
+RTF_HYPERLINKS = NO
+
+# Load stylesheet definitions from file. Syntax is similar to doxygen's config
+# file, i.e. a series of assignments. You only have to provide replacements,
+# missing definitions are set to their default value.
+#
+# See also section "Doxygen usage" for information on how to generate the
+# default style sheet that doxygen normally uses.
+# This tag requires that the tag GENERATE_RTF is set to YES.
+
+RTF_STYLESHEET_FILE =
+
+# Set optional variables used in the generation of an RTF document. Syntax is
+# similar to doxygen's config file. A template extensions file can be generated
+# using doxygen -e rtf extensionFile.
+# This tag requires that the tag GENERATE_RTF is set to YES.
+
+RTF_EXTENSIONS_FILE =
+
+# If the RTF_SOURCE_CODE tag is set to YES then doxygen will include source code
+# with syntax highlighting in the RTF output.
+#
+# Note that which sources are shown also depends on other settings such as
+# SOURCE_BROWSER.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_RTF is set to YES.
+
+RTF_SOURCE_CODE = NO
+
+#---------------------------------------------------------------------------
+# Configuration options related to the man page output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_MAN tag is set to YES, doxygen will generate man pages for
+# classes and files.
+# The default value is: NO.
+
+GENERATE_MAN = NO
+
+# The MAN_OUTPUT tag is used to specify where the man pages will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it. A directory man3 will be created inside the directory specified by
+# MAN_OUTPUT.
+# The default directory is: man.
+# This tag requires that the tag GENERATE_MAN is set to YES.
+
+MAN_OUTPUT = man
+
+# The MAN_EXTENSION tag determines the extension that is added to the generated
+# man pages. In case the manual section does not start with a number, the number
+# 3 is prepended. The dot (.) at the beginning of the MAN_EXTENSION tag is
+# optional.
+# The default value is: .3.
+# This tag requires that the tag GENERATE_MAN is set to YES.
+
+MAN_EXTENSION = .3
+
+# The MAN_SUBDIR tag determines the name of the directory created within
+# MAN_OUTPUT in which the man pages are placed. If defaults to man followed by
+# MAN_EXTENSION with the initial . removed.
+# This tag requires that the tag GENERATE_MAN is set to YES.
+
+MAN_SUBDIR =
+
+# If the MAN_LINKS tag is set to YES and doxygen generates man output, then it
+# will generate one additional man file for each entity documented in the real
+# man page(s). These additional files only source the real man page, but without
+# them the man command would be unable to find the correct page.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_MAN is set to YES.
+
+MAN_LINKS = NO
+
+#---------------------------------------------------------------------------
+# Configuration options related to the XML output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_XML tag is set to YES, doxygen will generate an XML file that
+# captures the structure of the code including all documentation.
+# The default value is: NO.
+
+GENERATE_XML = NO
+
+# The XML_OUTPUT tag is used to specify where the XML pages will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it.
+# The default directory is: xml.
+# This tag requires that the tag GENERATE_XML is set to YES.
+
+XML_OUTPUT = xml
+
+# If the XML_PROGRAMLISTING tag is set to YES, doxygen will dump the program
+# listings (including syntax highlighting and cross-referencing information) to
+# the XML output. Note that enabling this will significantly increase the size
+# of the XML output.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_XML is set to YES.
+
+XML_PROGRAMLISTING = YES
+
+#---------------------------------------------------------------------------
+# Configuration options related to the DOCBOOK output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_DOCBOOK tag is set to YES, doxygen will generate Docbook files
+# that can be used to generate PDF.
+# The default value is: NO.
+
+GENERATE_DOCBOOK = NO
+
+# The DOCBOOK_OUTPUT tag is used to specify where the Docbook pages will be put.
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be put in
+# front of it.
+# The default directory is: docbook.
+# This tag requires that the tag GENERATE_DOCBOOK is set to YES.
+
+DOCBOOK_OUTPUT = docbook
+
+# If the DOCBOOK_PROGRAMLISTING tag is set to YES, doxygen will include the
+# program listings (including syntax highlighting and cross-referencing
+# information) to the DOCBOOK output. Note that enabling this will significantly
+# increase the size of the DOCBOOK output.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_DOCBOOK is set to YES.
+
+DOCBOOK_PROGRAMLISTING = NO
+
+#---------------------------------------------------------------------------
+# Configuration options for the AutoGen Definitions output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_AUTOGEN_DEF tag is set to YES, doxygen will generate an
+# AutoGen Definitions (see http://autogen.sourceforge.net/) file that captures
+# the structure of the code including all documentation. Note that this feature
+# is still experimental and incomplete at the moment.
+# The default value is: NO.
+
+GENERATE_AUTOGEN_DEF = NO
+
+#---------------------------------------------------------------------------
+# Configuration options related to the Perl module output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_PERLMOD tag is set to YES, doxygen will generate a Perl module
+# file that captures the structure of the code including all documentation.
+#
+# Note that this feature is still experimental and incomplete at the moment.
+# The default value is: NO.
+
+GENERATE_PERLMOD = NO
+
+# If the PERLMOD_LATEX tag is set to YES, doxygen will generate the necessary
+# Makefile rules, Perl scripts and LaTeX code to be able to generate PDF and DVI
+# output from the Perl module output.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_PERLMOD is set to YES.
+
+PERLMOD_LATEX = NO
+
+# If the PERLMOD_PRETTY tag is set to YES, the Perl module output will be nicely
+# formatted so it can be parsed by a human reader. This is useful if you want to
+# understand what is going on. On the other hand, if this tag is set to NO, the
+# size of the Perl module output will be much smaller and Perl will parse it
+# just the same.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_PERLMOD is set to YES.
+
+PERLMOD_PRETTY = YES
+
+# The names of the make variables in the generated doxyrules.make file are
+# prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX. This is useful
+# so different doxyrules.make files included by the same Makefile don't
+# overwrite each other's variables.
+# This tag requires that the tag GENERATE_PERLMOD is set to YES.
+
+PERLMOD_MAKEVAR_PREFIX =
+
+#---------------------------------------------------------------------------
+# Configuration options related to the preprocessor
+#---------------------------------------------------------------------------
+
+# If the ENABLE_PREPROCESSING tag is set to YES, doxygen will evaluate all
+# C-preprocessor directives found in the sources and include files.
+# The default value is: YES.
+
+ENABLE_PREPROCESSING = YES
+
+# If the MACRO_EXPANSION tag is set to YES, doxygen will expand all macro names
+# in the source code. If set to NO, only conditional compilation will be
+# performed. Macro expansion can be done in a controlled way by setting
+# EXPAND_ONLY_PREDEF to YES.
+# The default value is: NO.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+MACRO_EXPANSION = NO
+
+# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES then
+# the macro expansion is limited to the macros specified with the PREDEFINED and
+# EXPAND_AS_DEFINED tags.
+# The default value is: NO.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+EXPAND_ONLY_PREDEF = NO
+
+# If the SEARCH_INCLUDES tag is set to YES, the include files in the
+# INCLUDE_PATH will be searched if a #include is found.
+# The default value is: YES.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+SEARCH_INCLUDES = YES
+
+# The INCLUDE_PATH tag can be used to specify one or more directories that
+# contain include files that are not input files but should be processed by the
+# preprocessor.
+# This tag requires that the tag SEARCH_INCLUDES is set to YES.
+
+INCLUDE_PATH =
+
+# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard
+# patterns (like *.h and *.hpp) to filter out the header-files in the
+# directories. If left blank, the patterns specified with FILE_PATTERNS will be
+# used.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+INCLUDE_FILE_PATTERNS =
+
+# The PREDEFINED tag can be used to specify one or more macro names that are
+# defined before the preprocessor is started (similar to the -D option of e.g.
+# gcc). The argument of the tag is a list of macros of the form: name or
+# name=definition (no spaces). If the definition and the "=" are omitted, "=1"
+# is assumed. To prevent a macro definition from being undefined via #undef or
+# recursively expanded use the := operator instead of the = operator.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+PREDEFINED =
+
+# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then this
+# tag can be used to specify a list of macro names that should be expanded. The
+# macro definition that is found in the sources will be used. Use the PREDEFINED
+# tag if you want to use a different macro definition that overrules the
+# definition found in the source code.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+EXPAND_AS_DEFINED =
+
+# If the SKIP_FUNCTION_MACROS tag is set to YES then doxygen's preprocessor will
+# remove all references to function-like macros that are alone on a line, have
+# an all uppercase name, and do not end with a semicolon. Such function macros
+# are typically used for boiler-plate code, and will confuse the parser if not
+# removed.
+# The default value is: YES.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+SKIP_FUNCTION_MACROS = YES
+
+#---------------------------------------------------------------------------
+# Configuration options related to external references
+#---------------------------------------------------------------------------
+
+# The TAGFILES tag can be used to specify one or more tag files. For each tag
+# file the location of the external documentation should be added. The format of
+# a tag file without this location is as follows:
+# TAGFILES = file1 file2 ...
+# Adding location for the tag files is done as follows:
+# TAGFILES = file1=loc1 "file2 = loc2" ...
+# where loc1 and loc2 can be relative or absolute paths or URLs. See the
+# section "Linking to external documentation" for more information about the use
+# of tag files.
+# Note: Each tag file must have a unique name (where the name does NOT include
+# the path). If a tag file is not located in the directory in which doxygen is
+# run, you must also specify the path to the tagfile here.
+
+TAGFILES =
+
+# When a file name is specified after GENERATE_TAGFILE, doxygen will create a
+# tag file that is based on the input files it reads. See section "Linking to
+# external documentation" for more information about the usage of tag files.
+
+GENERATE_TAGFILE =
+
+# If the ALLEXTERNALS tag is set to YES, all external class will be listed in
+# the class index. If set to NO, only the inherited external classes will be
+# listed.
+# The default value is: NO.
+
+ALLEXTERNALS = NO
+
+# If the EXTERNAL_GROUPS tag is set to YES, all external groups will be listed
+# in the modules index. If set to NO, only the current project's groups will be
+# listed.
+# The default value is: YES.
+
+EXTERNAL_GROUPS = YES
+
+# If the EXTERNAL_PAGES tag is set to YES, all external pages will be listed in
+# the related pages index. If set to NO, only the current project's pages will
+# be listed.
+# The default value is: YES.
+
+EXTERNAL_PAGES = YES
+
+# The PERL_PATH should be the absolute path and name of the perl script
+# interpreter (i.e. the result of 'which perl').
+# The default file (with absolute path) is: /usr/bin/perl.
+
+PERL_PATH = /usr/bin/perl
+
+#---------------------------------------------------------------------------
+# Configuration options related to the dot tool
+#---------------------------------------------------------------------------
+
+# If the CLASS_DIAGRAMS tag is set to YES, doxygen will generate a class diagram
+# (in HTML and LaTeX) for classes with base or super classes. Setting the tag to
+# NO turns the diagrams off. Note that this option also works with HAVE_DOT
+# disabled, but it is recommended to install and use dot, since it yields more
+# powerful graphs.
+# The default value is: YES.
+
+CLASS_DIAGRAMS = YES
+
+# You can define message sequence charts within doxygen comments using the \msc
+# command. Doxygen will then run the mscgen tool (see:
+# http://www.mcternan.me.uk/mscgen/)) to produce the chart and insert it in the
+# documentation. The MSCGEN_PATH tag allows you to specify the directory where
+# the mscgen tool resides. If left empty the tool is assumed to be found in the
+# default search path.
+
+MSCGEN_PATH =
+
+# You can include diagrams made with dia in doxygen documentation. Doxygen will
+# then run dia to produce the diagram and insert it in the documentation. The
+# DIA_PATH tag allows you to specify the directory where the dia binary resides.
+# If left empty dia is assumed to be found in the default search path.
+
+DIA_PATH =
+
+# If set to YES the inheritance and collaboration graphs will hide inheritance
+# and usage relations if the target is undocumented or is not a class.
+# The default value is: YES.
+
+HIDE_UNDOC_RELATIONS = YES
+
+# If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is
+# available from the path. This tool is part of Graphviz (see:
+# http://www.graphviz.org/), a graph visualization toolkit from AT&T and Lucent
+# Bell Labs. The other options in this section have no effect if this option is
+# set to NO
+# The default value is: NO.
+
+HAVE_DOT = NO
+
+# The DOT_NUM_THREADS specifies the number of dot invocations doxygen is allowed
+# to run in parallel. When set to 0 doxygen will base this on the number of
+# processors available in the system. You can set it explicitly to a value
+# larger than 0 to get control over the balance between CPU load and processing
+# speed.
+# Minimum value: 0, maximum value: 32, default value: 0.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOT_NUM_THREADS = 0
+
+# When you want a differently looking font in the dot files that doxygen
+# generates you can specify the font name using DOT_FONTNAME. You need to make
+# sure dot is able to find the font, which can be done by putting it in a
+# standard location or by setting the DOTFONTPATH environment variable or by
+# setting DOT_FONTPATH to the directory containing the font.
+# The default value is: Helvetica.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOT_FONTNAME = Helvetica
+
+# The DOT_FONTSIZE tag can be used to set the size (in points) of the font of
+# dot graphs.
+# Minimum value: 4, maximum value: 24, default value: 10.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOT_FONTSIZE = 10
+
+# By default doxygen will tell dot to use the default font as specified with
+# DOT_FONTNAME. If you specify a different font using DOT_FONTNAME you can set
+# the path where dot can find it using this tag.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOT_FONTPATH =
+
+# If the CLASS_GRAPH tag is set to YES then doxygen will generate a graph for
+# each documented class showing the direct and indirect inheritance relations.
+# Setting this tag to YES will force the CLASS_DIAGRAMS tag to NO.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+CLASS_GRAPH = YES
+
+# If the COLLABORATION_GRAPH tag is set to YES then doxygen will generate a
+# graph for each documented class showing the direct and indirect implementation
+# dependencies (inheritance, containment, and class references variables) of the
+# class with other documented classes.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+COLLABORATION_GRAPH = YES
+
+# If the GROUP_GRAPHS tag is set to YES then doxygen will generate a graph for
+# groups, showing the direct groups dependencies.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+GROUP_GRAPHS = YES
+
+# If the UML_LOOK tag is set to YES, doxygen will generate inheritance and
+# collaboration diagrams in a style similar to the OMG's Unified Modeling
+# Language.
+# The default value is: NO.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+UML_LOOK = NO
+
+# If the UML_LOOK tag is enabled, the fields and methods are shown inside the
+# class node. If there are many fields or methods and many nodes the graph may
+# become too big to be useful. The UML_LIMIT_NUM_FIELDS threshold limits the
+# number of items for each type to make the size more manageable. Set this to 0
+# for no limit. Note that the threshold may be exceeded by 50% before the limit
+# is enforced. So when you set the threshold to 10, up to 15 fields may appear,
+# but if the number exceeds 15, the total amount of fields shown is limited to
+# 10.
+# Minimum value: 0, maximum value: 100, default value: 10.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+UML_LIMIT_NUM_FIELDS = 10
+
+# If the TEMPLATE_RELATIONS tag is set to YES then the inheritance and
+# collaboration graphs will show the relations between templates and their
+# instances.
+# The default value is: NO.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+TEMPLATE_RELATIONS = NO
+
+# If the INCLUDE_GRAPH, ENABLE_PREPROCESSING and SEARCH_INCLUDES tags are set to
+# YES then doxygen will generate a graph for each documented file showing the
+# direct and indirect include dependencies of the file with other documented
+# files.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+INCLUDE_GRAPH = YES
+
+# If the INCLUDED_BY_GRAPH, ENABLE_PREPROCESSING and SEARCH_INCLUDES tags are
+# set to YES then doxygen will generate a graph for each documented file showing
+# the direct and indirect include dependencies of the file with other documented
+# files.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+INCLUDED_BY_GRAPH = YES
+
+# If the CALL_GRAPH tag is set to YES then doxygen will generate a call
+# dependency graph for every global function or class method.
+#
+# Note that enabling this option will significantly increase the time of a run.
+# So in most cases it will be better to enable call graphs for selected
+# functions only using the \callgraph command. Disabling a call graph can be
+# accomplished by means of the command \hidecallgraph.
+# The default value is: NO.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+CALL_GRAPH = NO
+
+# If the CALLER_GRAPH tag is set to YES then doxygen will generate a caller
+# dependency graph for every global function or class method.
+#
+# Note that enabling this option will significantly increase the time of a run.
+# So in most cases it will be better to enable caller graphs for selected
+# functions only using the \callergraph command. Disabling a caller graph can be
+# accomplished by means of the command \hidecallergraph.
+# The default value is: NO.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+CALLER_GRAPH = NO
+
+# If the GRAPHICAL_HIERARCHY tag is set to YES then doxygen will graphical
+# hierarchy of all classes instead of a textual one.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+GRAPHICAL_HIERARCHY = YES
+
+# If the DIRECTORY_GRAPH tag is set to YES then doxygen will show the
+# dependencies a directory has on other directories in a graphical way. The
+# dependency relations are determined by the #include relations between the
+# files in the directories.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DIRECTORY_GRAPH = YES
+
+# The DOT_IMAGE_FORMAT tag can be used to set the image format of the images
+# generated by dot. For an explanation of the image formats see the section
+# output formats in the documentation of the dot tool (Graphviz (see:
+# http://www.graphviz.org/)).
+# Note: If you choose svg you need to set HTML_FILE_EXTENSION to xhtml in order
+# to make the SVG files visible in IE 9+ (other browsers do not have this
+# requirement).
+# Possible values are: png, jpg, gif, svg, png:gd, png:gd:gd, png:cairo,
+# png:cairo:gd, png:cairo:cairo, png:cairo:gdiplus, png:gdiplus and
+# png:gdiplus:gdiplus.
+# The default value is: png.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOT_IMAGE_FORMAT = png
+
+# If DOT_IMAGE_FORMAT is set to svg, then this option can be set to YES to
+# enable generation of interactive SVG images that allow zooming and panning.
+#
+# Note that this requires a modern browser other than Internet Explorer. Tested
+# and working are Firefox, Chrome, Safari, and Opera.
+# Note: For IE 9+ you need to set HTML_FILE_EXTENSION to xhtml in order to make
+# the SVG files visible. Older versions of IE do not have SVG support.
+# The default value is: NO.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+INTERACTIVE_SVG = NO
+
+# The DOT_PATH tag can be used to specify the path where the dot tool can be
+# found. If left blank, it is assumed the dot tool can be found in the path.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOT_PATH =
+
+# The DOTFILE_DIRS tag can be used to specify one or more directories that
+# contain dot files that are included in the documentation (see the \dotfile
+# command).
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOTFILE_DIRS =
+
+# The MSCFILE_DIRS tag can be used to specify one or more directories that
+# contain msc files that are included in the documentation (see the \mscfile
+# command).
+
+MSCFILE_DIRS =
+
+# The DIAFILE_DIRS tag can be used to specify one or more directories that
+# contain dia files that are included in the documentation (see the \diafile
+# command).
+
+DIAFILE_DIRS =
+
+# When using plantuml, the PLANTUML_JAR_PATH tag should be used to specify the
+# path where java can find the plantuml.jar file. If left blank, it is assumed
+# PlantUML is not used or called during a preprocessing step. Doxygen will
+# generate a warning when it encounters a \startuml command in this case and
+# will not generate output for the diagram.
+
+PLANTUML_JAR_PATH =
+
+# When using plantuml, the PLANTUML_CFG_FILE tag can be used to specify a
+# configuration file for plantuml.
+
+PLANTUML_CFG_FILE =
+
+# When using plantuml, the specified paths are searched for files specified by
+# the !include statement in a plantuml block.
+
+PLANTUML_INCLUDE_PATH =
+
+# The DOT_GRAPH_MAX_NODES tag can be used to set the maximum number of nodes
+# that will be shown in the graph. If the number of nodes in a graph becomes
+# larger than this value, doxygen will truncate the graph, which is visualized
+# by representing a node as a red box. Note that doxygen if the number of direct
+# children of the root node in a graph is already larger than
+# DOT_GRAPH_MAX_NODES then the graph will not be shown at all. Also note that
+# the size of a graph can be further restricted by MAX_DOT_GRAPH_DEPTH.
+# Minimum value: 0, maximum value: 10000, default value: 50.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOT_GRAPH_MAX_NODES = 50
+
+# The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the graphs
+# generated by dot. A depth value of 3 means that only nodes reachable from the
+# root by following a path via at most 3 edges will be shown. Nodes that lay
+# further from the root node will be omitted. Note that setting this option to 1
+# or 2 may greatly reduce the computation time needed for large code bases. Also
+# note that the size of a graph can be further restricted by
+# DOT_GRAPH_MAX_NODES. Using a depth of 0 means no depth restriction.
+# Minimum value: 0, maximum value: 1000, default value: 0.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+MAX_DOT_GRAPH_DEPTH = 0
+
+# Set the DOT_TRANSPARENT tag to YES to generate images with a transparent
+# background. This is disabled by default, because dot on Windows does not seem
+# to support this out of the box.
+#
+# Warning: Depending on the platform used, enabling this option may lead to
+# badly anti-aliased labels on the edges of a graph (i.e. they become hard to
+# read).
+# The default value is: NO.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOT_TRANSPARENT = NO
+
+# Set the DOT_MULTI_TARGETS tag to YES to allow dot to generate multiple output
+# files in one run (i.e. multiple -o and -T options on the command line). This
+# makes dot run faster, but since only newer versions of dot (>1.8.10) support
+# this, this feature is disabled by default.
+# The default value is: NO.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOT_MULTI_TARGETS = NO
+
+# If the GENERATE_LEGEND tag is set to YES doxygen will generate a legend page
+# explaining the meaning of the various boxes and arrows in the dot generated
+# graphs.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+GENERATE_LEGEND = YES
+
+# If the DOT_CLEANUP tag is set to YES, doxygen will remove the intermediate dot
+# files that are used to generate the various graphs.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOT_CLEANUP = YES
diff --git a/tools/doxygen/README b/tools/doxygen/README
new file mode 100644
index 0000000000000000000000000000000000000000..c6a6229995e28bd4b09b6e0f8b146e87f1a2c8ff
--- /dev/null
+++ b/tools/doxygen/README
@@ -0,0 +1,158 @@
+==========================
+doxygen documentation tool
+==========================
+
+The tools/doxygen directory contains additional tools that assist development oriented users in creating source code documentation of LAMMPS with the "doxygen" documentation generation platform in a user defined format flavor.
+
+
+==================
+Directory contents
+==================
+
+The tools/doxygen directory comprises the following files:
+
+ - "doxygen.sh" = Bash shell script for creating the LAMMPS documentation with
+ the "doxygen" documentation platform
+
+ - "Doxyfile.lammps" = Flavor definition for documentation of LAMMPS with the
+ "doxygen" documentation platform. During processing, a new file named
+ "Doxyfile" is produced that should not be edited.
+
+ - "Developer.dox.lammps" = Transcripted version of the developer documentation
+ in "doxygen" (markdown markup language) format in order to help understanding
+ the code working principles within the "doxygen" documentation context.
+ During processing, a new file named "Developer.dox" is produced that should
+ not be edited.
+
+
+=====================
+Building instructions
+=====================
+
+The "doxygen" documentation is generated by executing the "doxygen.sh" bash
+script from the lammps root directory.
+
+ user@host:/.../lammps-root> bash tools/doxygen/doxygen.sh
+
+The "doxygen.sh" script has no user executable rights and must be launched
+with explicit activation of a "bash" shell.
+
+Before the "doxygen" documentation can be generated, all pre-selected LAMMPS
+packages are deselected in order to avoid duplicates in the source code.
+For this, the "doxygen.sh" bash script implicitly includes the command
+
+ user@host:/.../lammps-root/src> make no-all
+
+This could disturb an already configured production environment.
+For this reason, the generation of the "doxygen" documentation for LAMMPS
+is best recommended on a freshly cloned copy of the git repository and
+selecting the desired development branch:
+
+ user@host:/.../anypath> git clone https://github.com/lammps/lammps.git
+ user@host:/.../anypath> cd lammps
+ user@host:/.../anypath/lammps> git checkout your-desired-branch
+ user@host:/.../anypath/lammps> tools/doxygen/doxygen.sh
+
+The generated "doxygen" documentation {does not include the additional packages}
+in the "lib" directory, as many of these packages themselves are at least partially
+documented in doxygen format and their adverse documentation instructions
+could disturb the building process. For this reason, the directory "src/USER-ATC"
+must also be excluded. However, the "USER-ATC" package itself is already profoundly
+documented with the "doxygen" platform.
+
+The files "Doxyfile" and "Developer.dox" are automatically generated in the
+tools/doxygen directory during the build process.
+
+To the conversion of images the "fig2dev" package must be available on the
+development system.
+
+
+=======
+Results
+=======
+
+The doxygen documentation for LAMMPS is created in the following directories:
+
+ "tools/doxygen/doc" = LAMMPS documetation in "doxygen" html format.
+ In order to read the html documentation, start with loading the "index.html"
+ file into an internet browser of choice from this directory. The generation
+ of other formats (pdf, docbook, rtf or man) is disabled by default but can be
+ activated if needed. In order to get the desired formatting results, some
+ adjustments in the configuration file "Doxyfile.lammps" may be required.
+
+ "tools/doxygen/doc/Manual" = an image copy of the the vintage LAMMPS
+ documentation for quick reference browsing. In order to read the vintage
+ LAMMPS documentation, start with loading the "Manual.html" file into an
+ internet browser of choice from this directory. The doxygen documentation
+ integrates the vintage LAMMPS documentation with appropriate links.
+
+
+===============
+Important notes
+===============
+
+The "doxygen.sh" bash script builds the vintage LAMMPS documentation and makes
+an image copy of it into the directory "tools/doxygen/doc/Manual". The generation
+of the vintage LAMMPS documentation must perfectly work for the "html" format.
+In order to fulfill this requirement, additional development packages may have
+to be available on the build platform.
+
+
+======================
+Latest doxygen version
+======================
+
+The "Doxyfile.lammps" configuration file is using the "doxygen" version 1.8.15.
+If the latest features of the "doxygen" documentation platform are desired,
+it can be downloaded and built with the following steps:
+
+ user@host:/.../anypath> git clone https://github.com/doxygen/doxygen.git
+ user@host:/.../anypath> cd doxygen
+ user@host:/.../anypath/doxygen> mkdir build
+ user@host:/.../anypath/doxygen/build> cd build
+ user@host:/.../anypath/doxygen/build> cmake -G "Unix Makefiles" -Dbuild_doc=ON -DCMAKE_INSTALL_PREFIX=/.../installpath ../
+ user@host:/.../anypath/doxygen/build> make -j 8
+ user@host:/.../anypath/doxygen/build> make docs
+ user@host:/.../anypath/doxygen/build> make install
+
+The compilation of the "doxygen" documentation platform uses the "cmake" build system.
+
+After a successful build process, the "doxygen" executable can be found under the path
+
+user@host:/.../installpath/bin/doxygen
+
+With this steps, the most up-to-date version of the "doxygen" documentation system
+can be obtained. Please note that in order to define different compilation flavors,
+many other build options are available than mentioned above. With appropriate
+adjustments in the "Doxyfile.lammps" configuration file, different documentation
+flavors and representations can be created. The use of an up-do-date "doxygen"
+version is highly recommended for including the latest formatting and compatibility
+features.
+
+To the generation of the "doxygen" documentation in the "make docs" step above,
+additional development packages and numerous latex packages may have to be available
+on the build platform.
+
+Depending on the selected installation path, in the "make install" step root rights
+could be required for successful installation.
+
+The maintenance of the "doxygen" documentation platform continuously includes new
+features, bugfixes and adjustments to advanced coding standards or changing operating
+system platform requirements. The maintenance can be carried out with the outlined
+build procedure after merging the latest commits from the official "doxygen" git
+repository into its local copy (git fetch and git merge or git pull).
+
+
+========================
+Authoring and maintainer
+========================
+
+
+The tool is authored by Nandor Tamaskovics, numericalfreedom at googlemail.com.
+
+
+===============
+Acknowledgement
+===============
+
+The effort for the development of the "doxygen" documentation platform is greatly acknowledged to Dimitri van Heesch (see also http://doxygen.org).
diff --git a/tools/doxygen/doxygen.sh b/tools/doxygen/doxygen.sh
new file mode 100644
index 0000000000000000000000000000000000000000..29c7ea68b5747f943648572cf7fc73dd5148e75e
--- /dev/null
+++ b/tools/doxygen/doxygen.sh
@@ -0,0 +1,107 @@
+#!/bin/bash
+
+LAMMPSBASE=${PWD} ;
+LAMMPSSRC="${LAMMPSBASE}/src" ;
+LAMMPSDOC="${LAMMPSBASE}/doc" ;
+LAMMPSDOCHTML="${LAMMPSDOC}/html" ;
+LAMMPSDEVELOPERDOC="${LAMMPSBASE}/doc/src/Developer" ;
+LAMMPSDOCTMP="/tmp/lammps-docs-*" ;
+LAMMPSDOCMAKE="${LAMMPSDOC}/Makefile" ;
+LAMMPSDOXYGEN="${LAMMPSBASE}/tools/doxygen" ;
+LAMMPSDOXYGENDOC="${LAMMPSDOXYGEN}/doc" ;
+LAMMPSDOXYGENDOCMANUAL="${LAMMPSDOXYGEN}/doc/html/Manual" ;
+
+LAMMPSDOXYFILE=${LAMMPSDOXYGEN}/Doxyfile.lammps ;
+DOXYFILE=${LAMMPSDOXYGEN}/Doxyfile ;
+
+LAMMPSDEVELOPERDOXFILE=${LAMMPSDOXYGEN}/Developer.dox.lammps ;
+DEVELOPERDOXFILE=${LAMMPSDOXYGEN}/Developer.dox ;
+
+FIG2DEV=`which fig2dev` ;
+DOXYGEN=`which doxygen` ;
+
+
+if [[ -d ${LAMMPSSRC} && -d ${LAMMPSDEVELOPERDOC} && -d ${LAMMPSDOC} && -f ${LAMMPSDOCMAKE} && -d ${LAMMPSDOXYGEN} && -f ${LAMMPSDOXYFILE} ]] ;
+ then
+ cd ${LAMMPSSRC} ;
+ make no-all ;
+ cd ${LAMMPSBASE} ;
+ else
+ echo "Cannot configure LAMMPS sources - Please run doxygen.sh from the LAMMPS root directory." >&2 ;
+ exit 1 ;
+ fi ;
+
+
+if [ ! -x ${FIG2DEV} ] ;
+ then
+ echo "${FIG2DEV} not found - Please install ${FIG2DEV} for Your operating system." >&2 ;
+ exit 1 ;
+ fi ;
+
+
+if [ -d ${LAMMPSDEVELOPERDOC} ] ;
+ then
+ ${FIG2DEV} -L png ${LAMMPSDEVELOPERDOC}/classes.fig > tools/doxygen/classes.png ;
+ ${FIG2DEV} -L eps ${LAMMPSDEVELOPERDOC}/classes.fig > tools/doxygen/classes.eps ;
+ else
+ echo "LAMMPS developer documentation not found - Please control Your LAMMPS installation." >&2 ;
+ exit 1 ;
+ fi ;
+
+
+if [ ! -x ${DOXYGEN} ] ;
+ then
+ echo "doxygen not found - Please install doxygen for Your operating system." >&2 ;
+ exit 1 ;
+ fi ;
+
+
+if [[ -d ${LAMMPSSRC} && -f ${LAMMPSDOXYFILE} && -f ${LAMMPSDEVELOPERDOXFILE} ]] ;
+ then
+ ICS=' ';
+ read -r -a array < ${LAMMPSSRC}/version.h ;
+ version=`echo ${array[2]} ${array[3]} ${array[4]} | sed s/\"//g`;
+ cp -av ${LAMMPSDOXYFILE} ${DOXYFILE} ;
+ sed -i "s/LAMMPS_VERSION/${version}/g" ${DOXYFILE} ;
+ cp -av ${LAMMPSDEVELOPERDOXFILE} ${DEVELOPERDOXFILE} ;
+ sed -i "s/LAMMPS_VERSION/${version}/g" ${DEVELOPERDOXFILE} ;
+ ${DOXYGEN} ${DOXYFILE} ;
+ else
+ echo "Doxyfile prototype not found - Please control Your LAMMPS installation." >&2 ;
+ exit 1 ;
+ fi ;
+
+
+if [[ -d ${LAMMPSDOC} && -f ${LAMMPSDOCMAKE} ]] ;
+ then
+ cd ${LAMMPSDOC} ;
+ for d in ${LAMMPSDOCTMP} ;
+ do
+ rm -vrf $d;
+ done ;
+ make clean ;
+ make html ;
+ make pdf ;
+ cd ${LAMMPSBASE} ;
+ echo "${LAMMPSDOC} exists." ;
+ else
+ echo "Cannot build LAMMPS native documentation - Please run doxygen.sh from the LAMMPS root directory."i >&2 ;
+ exit 1 ;
+ fi ;
+
+
+if [ -d ${LAMMPSDOCHTML} ] ;
+ then
+ if [ -d ${LAMMPSDOXYGENDOCMANUAL} ] ;
+ then
+ rm -vrf ${LAMMPSDOXYGENDOCMANUAL} ;
+ echo "${LAMMPSDOXYGENDOCMANUAL} removed." ;
+ fi ;
+ cp -av ${LAMMPSDOCHTML} ${LAMMPSDOXYGENDOCMANUAL} ;
+ cp -av ${LAMMPSDOC}/*.pdf ${LAMMPSDOXYGENDOCMANUAL} ;
+ echo "${LAMMPSDOXYGENDOCMANUAL} copied." ;
+ else
+ echo "Cannot include LAMMPS native documentation into the doxygen documentation - Please run doxygen.sh from the LAMMPS root directory." >&2 ;
+ exit 1 ;
+ fi ;
+