Merge branch 'master' into polymorphic-update

src/USER-CGDNA/*      @ohenrich

src/USER-CGSDK/*      @akohlmey

src/USER-COLVARS/*    @giacomofiorin

src/USER-DPD/*        @timattox

src/USER-INTEL/*      @wmbrownintel

src/USER-MANIFOLD/*   @Pakketeretet2

src/USER-MEAMC/*      @martok

# cmake

cmake/*               @junghans @rbberger

cmake/Modules/Packages/USER-COLVARS.cmake @junghans @rbberger @giacomofiorin

# python

python/*              @rbberger

  if(NOT BUILD_SHARED_LIBS)

    install(TARGETS lepton EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})

  endif()

  # Change the define below to LEPTON_BUILDING_SHARED_LIBRARY when linking Lepton as a DLL with MSVC

  target_compile_definitions(lepton PRIVATE -DLEPTON_BUILDING_STATIC_LIBRARY)

  set_target_properties(lepton PROPERTIES OUTPUT_NAME lammps_lepton${LAMMPS_MACHINE})

  target_include_directories(lepton PRIVATE ${LEPTON_DIR}/include)

endif()

if(COLVARS_LEPTON)

  target_link_libraries(lammps PRIVATE lepton)

  target_compile_options(colvars PRIVATE -DLEPTON)

  target_compile_definitions(colvars PRIVATE -DLEPTON)

  # Disable the line below when linking Lepton as a DLL with MSVC

  target_compile_definitions(colvars PRIVATE -DLEPTON_USE_STATIC_LIBRARIES)

  target_include_directories(colvars PUBLIC ${LEPTON_DIR}/include)

endif()

.TH LAMMPS "19 March 2020" "2020-03-19"

.TH LAMMPS "15 April 2020" "2020-04-15"

.SH NAME

.B LAMMPS

\- Molecular Dynamics Simulator.

.. note::

   The simulation box size/shape can be changed by arbitrarily

   large amounts by this command.  This is not a problem, except that the

   The simulation box size/shape can be changed by arbitrarily large

   amounts by this command.  This is not a problem, except that the

   mapping of processors to the simulation box is not changed from its

   initial 3d configuration; see the :doc:`processors <processors>`

   command.  Thus, if the box size/shape changes dramatically, the

   mapping of processors to the simulation box may not end up as optimal

   as the initial mapping attempted to be.

   mapping of processors to the simulation box may not end up as

   optimal as the initial mapping attempted to be.  You may wish to

   re-balance the atoms by using the :doc:`balance <balance>` command

   if that is the case.

.. note::

   Because the keywords used in this command are applied one at a

   time to the simulation box and the atoms in it, care must be taken

   with triclinic cells to avoid exceeding the limits on skew after each

   transformation in the sequence.  If skew is exceeded before the final

   transformation this can be avoided by changing the order of the

   sequence, or breaking the transformation into two or more smaller

   transformations.  For more information on the allowed limits for box

   skew see the discussion on triclinic boxes on :doc:`Howto triclinic <Howto_triclinic>` doc page.

   You cannot use this command after reading a restart file (and

   before a run is performed) if the restart file stored per-atom

   information from a fix and any of the specified keywords change the

   box size or shape or boundary conditions.  This is because atoms

   may be moved to new processors and the restart info will not

   migrate with them.  LAMMPS will generate an error if this could

   happen.  Only the *ortho* and *triclinic* keywords do not trigger

   this error.  One solution is to perform a "run 0" command before

   using the change_box command.  This clears the per-atom restart

   data, whether it has been re-assigned to a new fix or not.

.. note::

   Because the keywords used in this command are applied one at a time

   to the simulation box and the atoms in it, care must be taken with

   triclinic cells to avoid exceeding the limits on skew after each

   transformation in the sequence.  If skew is exceeded before the

   final transformation this can be avoided by changing the order of

   the sequence, or breaking the transformation into two or more

   smaller transformations.  For more information on the allowed

   limits for box skew see the discussion on triclinic boxes on

   :doc:`Howto triclinic <Howto_triclinic>` doc page.

----------

  .. parsed-literal::

       *bond* args = atom1 atom2 Kstart Kstop r0

       *bond* args = atom1 atom2 Kstart Kstop r0start (r0stop)

         atom1,atom2 = IDs of 2 atoms in bond

         Kstart,Kstop = restraint coefficients at start/end of run (energy units)

         r0 = equilibrium bond distance (distance units)

         r0start = equilibrium bond distance at start of run (distance units)

         r0stop = equilibrium bond distance at end of run (optional) (distance units). If not

           specified it is assumed to be equal to r0start

       *lbond* args = atom1 atom2 Kstart Kstop r0start (r0stop)

         atom1,atom2 = IDs of 2 atoms in bond

         Kstart,Kstop = restraint coefficients at start/end of run (energy units)

         r0start = equilibrium bond distance at start of run (distance units)

         r0stop = equilibrium bond distance at end of run (optional) (distance units). If not

           specified it is assumed to be equal to r0start

       *angle* args = atom1 atom2 atom3 Kstart Kstop theta0

         atom1,atom2,atom3 = IDs of 3 atoms in angle, atom2 = middle atom

         Kstart,Kstop = restraint coefficients at start/end of run (energy units)

.. code-block:: LAMMPS

   fix holdem all restrain bond 45 48 2000.0 2000.0 2.75

   fix holdem all restrain lbond 45 48 2000.0 2000.0 2.75

   fix holdem all restrain dihedral 1 2 3 4 2000.0 2000.0 120.0

   fix holdem all restrain bond 45 48 2000.0 2000.0 2.75 dihedral 1 2 3 4 2000.0 2000.0 120.0

   fix texas_holdem all restrain dihedral 1 2 3 4 0.0 2000.0 120.0 dihedral 1 2 3 5 0.0 2000.0 -120.0 dihedral 1 2 3 6 0.0 2000.0 0.0

----------

The *lbond* keyword applies a lower bound bond restraint to the specified atoms

using the same functional form used by the :doc:`bond_style harmonic <bond_harmonic>` command if the distance between

the atoms is smaller than the equilibrium bond distance and 0 otherwise. The potential associated with

the restraint is

.. math::

   E = K (r - r_0)^2 ,if\;r < r_0

.. math::

   E = 0 \qquad\quad\quad ,if\;r \ge r_0

with the following coefficients:

* :math:`K` (energy/distance\^2)

* :math:`r_0` (distance)

:math:`K` and :math:`r_0` are specified with the fix.  Note that the usual 1/2 factor

is included in :math:`K`.

----------

The *angle* keyword applies an angle restraint to the specified atoms

using the same functional form used by the :doc:`angle_style harmonic <angle_harmonic>` command.  The potential associated with

the restraint is