core: virtual_sites: Removed default argument from virtual function and non-functional virtual COM feature

doc/sphinx/installation.rst

@@ -421,14 +421,6 @@ General features
 -  ``BOND_CONSTRAINT`` Turns on the RATTLE integrator which allows for fixed lengths bonds
    between particles.
 
--  ``VIRTUAL_SITES_COM`` Virtual sites are particles, the position and velocity of which is
-   not obtained by integrating equations of motion. Rather, they are
-   placed using the position (and orientation) of other particles. The
-   feature allows to place a virtual particle into the center of mass of
-   a set of other particles.
-
-   .. seealso:: :ref:`Virtual sites`
-
 -  ``VIRTUAL_SITES_RELATIVE`` Virtual sites are particles, the position and velocity of which is
    not obtained by integrating equations of motion. Rather, they are
    placed using the position (and orientation) of other particles. The

doc/sphinx/particles.rst

@@ -436,79 +436,6 @@ For correct results, the LB thermostat has to be deactivated for virtual sites::
 Please note that the velocity attribute of the virtual particles does not carry valid information for this virtual sites scheme.
 
 
-..
-    .. _Virtual sites in the center of mass of a molecule:
-
-    Virtual sites in the center of mass of a molecule
-    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-    .. todo:: This is not implemented in Python, yet
-
-    To activate this implementation, enable the feature ``VIRTUAL_SITES_COM`` in :file:`myconfig.hpp`. Virtual sites are then placed in the center of mass of
-    a set of particles (as defined below). Their velocity will also be that
-    of the center of mass. Forces accumulating on the virtual sites are
-    distributed back to the particles which form the molecule. To place a
-    virtual site at the center of a molecule, perform the following steps in
-    that order
-
-    #. Create a particle of the desired type for each molecule. It should be
-       placed at least roughly in the center of the molecule to make sure,
-       its on the same node as the other particles forming the molecule, in
-       a simulation with more than one CPU.
-
-    #. Make it a virtual site using
-
-       part virtual 1
-
-    #. Declare the list of molecules and the particles they consist of:
-
-       analyze set { ...} ...
-
-       The lists of particles in a molecule comprise the non-virtual
-       particles as well as the virtual site. The id of this molecule is its
-       index in this list. For example,
-
-       analyze set {0 1 2 3 4} {0 5 6 7 8} {1 9 10 11}
-
-       declares three molecules, of which the first two consist of three
-       particles and a virtual site each (particles 14 and 58,
-       respectively). The third molecule has type 1 and consists of two
-       particles and a virtual site. The virtual sites were determined
-       before by setting the flag. You can choose freely one out of each
-       molecule, for example particles 1, 5, and 9.
-
-    #. Assign to all particles that belong to the same molecule the
-       molecules id
-
-       part mol
-
-       The molid is the index of the particle in the above list, so you
-       would assign 0 to particles 1-4, 1 to particles 5-8 and 2 to
-       particles 9-11. Alternatively, you can call
-
-       analyze set topo_part_sync
-
-       to set the s from the molecule declarations.
-
-    #. Update the position of all virtual particles (optional)
-
-       integrate 0
-
-    The type of the molecule you can choose freely, it is only used in
-    certain analysis functions, namely ``energy_kinetic_mol``,
-    ``pressure_mol`` and ``dipmom_mol``, which compute kinetic energy,
-    pressure and dipole moment per molecule type, respectively.
-
-    .. _Additional features:
-
-    Additional features
-    ~~~~~~~~~~~~~~~~~~~
-
-    The behavior of virtual sites can be fine-tuned with the following
-    switches in :file:`myconfig.hpp`.
-
-    - ``THERMOSTAT_IGNORE_NON_VIRTUAL`` specifies that the thermostat does not act on non-virtual particles
-
 .. _Particle number counting feature:
 
 Particle number counting feature

src/core/CMakeLists.txt

@@ -125,11 +125,10 @@ set(EspressoCore_SRC
   observables/LBVelocityProfile.cpp
   virtual_sites/lb_inertialess_tracers.cpp
   virtual_sites/lb_inertialess_tracers_cuda_interface.cpp
-  virtual_sites/virtual_sites_com.cpp
   virtual_sites/VirtualSitesInertialessTracers.cpp
   virtual_sites/VirtualSitesRelative.cpp
   accumulators/TimeSeries.cpp
-        observables/PidObservable.cpp)
+  observables/PidObservable.cpp)
 
 if(CUDA)
   set(EspressoCuda_SRC

src/core/event.cpp

@@ -466,7 +466,7 @@ void on_ghost_flags_change() {
 
 void update_dependent_particles() {
 #ifdef VIRTUAL_SITES
-  virtual_sites()->update();
+  virtual_sites()->update(true);
 #endif
   cells_update_ghosts();
 

src/core/integrate.cpp

@@ -189,7 +189,7 @@ void integrate_vv(int n_steps, int reuse_forces) {
     lb_lbcoupling_deactivate();
 
 #ifdef VIRTUAL_SITES
-    virtual_sites()->update();
+    virtual_sites()->update(true);
 #endif
 
     // Communication step: distribute ghost positions
@@ -248,7 +248,7 @@ void integrate_vv(int n_steps, int reuse_forces) {
 
 // VIRTUAL_SITES pos (and vel for DPD) update for security reason !!!
 #ifdef VIRTUAL_SITES
-    virtual_sites()->update();
+    virtual_sites()->update(true);
 #endif
 
     // Communication step: distribute ghost positions

src/core/virtual_sites/VirtualSites.hpp

@@ -43,7 +43,7 @@ class VirtualSites {
    *  Velocities are only updated if get_have_velocity() returns true.
    *  @param recalc_positions  Skip the recalculation of positions if false.
    */
-  virtual void update(bool recalc_positions = true) const = 0;
+  virtual void update(bool recalc_positions) const = 0;
   /** Back-transfer forces (and torques) to non-virtual particles. */
   virtual void back_transfer_forces_and_torques() const = 0;
   /** @brief Called after force calculation (and before rattle/shake) */