fix(ml/mm): do ONIOM

docs/reference-manual/special/metatomic.rst

@@ -0,0 +1,53 @@
+.. _metatomic:
+
+Metatomic potentials
+====================
+
+The Metatomic interface evaluates an exported atomistic model through the
+applied-forces framework. The selected atoms are provided to the model as a
+Metatomic ``System`` with positions, cell, periodic boundary conditions, atom
+types, and engine-built neighbor lists.
+
+By default, the Metatomic contribution is added on top of the unmodified
+molecular-mechanics topology. This additive mode is useful as a control
+calculation and for models that augment, rather than replace, force-field terms.
+
+For embedded subsystem simulations where the Metatomic model replaces the
+molecular-mechanics description of the selected atoms, :mdp:`metatomic-oniom`
+enables the ONIOM-style subtractive scheme:
+
+.. math::
+
+   E = E_\mathrm{MM}(\mathrm{full}) + E_\mathrm{ML}(\mathrm{embedded})
+       - E_\mathrm{MM}(\mathrm{embedded})
+
+The subtractive term is applied through embedded-system topology preprocessing:
+bonded and non-bonded molecular-mechanics terms represented by the model are
+removed from the classical force-field contribution, while the model energy is
+added through the Metatomic force provider. Boundary bonded terms involving
+both Metatomic and MM atoms remain in the molecular-mechanics topology.
+
+Boundary link atoms
+-------------------
+
+The :mdp:`metatomic-link-atoms` option enables hydrogen caps at bonds that cross
+the Metatomic/MM boundary and requires :mdp:`metatomic-oniom`. Direct MM
+neighbors bonded to selected Metatomic atoms are included in the embedded atom
+set so the bonded terms at the boundary are handled consistently. During model
+evaluation, these boundary atoms are represented as hydrogen link atoms placed
+along the corresponding boundary bond. The link-atom position is part of the
+automatic differentiation graph, so forces are propagated back to the real atoms
+connected by the boundary bond.
+
+This option requires a model trained for link-atom-capped boundary chemistry.
+If the same boundary MM atom is bonded to multiple selected Metatomic atoms,
+each cut bond is represented by a distinct hydrogen cap in the model input.
+
+Model-requested charges
+-----------------------
+
+Metatomic models can declare additional inputs through their
+``requested_inputs`` metadata. When a model requests ``charges`` or a
+``charges/<variant>`` input, |Gromacs| provides a per-atom Metatomic
+``TensorMap`` with ``quantity = charge`` and ``unit = e``. Charge inputs are
+model-controlled; no :ref:`mdp` option enables or disables them.

docs/reference-manual/special/special.rst

@@ -28,6 +28,6 @@ the use of |Gromacs| for specific scientific problems.
    colvars
    plumed
    nnpot
+   metatomic
    fmm
 
-

docs/user-guide/mdp-options.rst

@@ -3798,6 +3798,34 @@ interface implementation follow :ref:`nnpot`.
    (0.1) [nm] Distance between link atom and the bonded MM atom.
 
 
+.. _mdp-metatomic:
+
+Metatomic simulations
+^^^^^^^^^^^^^^^^^^^^^
+
+The Metatomic interface evaluates exported atomistic models through the
+applied-forces framework. Further details are described in :ref:`metatomic`.
+
+.. mdp:: metatomic-oniom
+
+   (false) Enable the subtractive ONIOM topology preprocessing for the selected
+   Metatomic input group. When enabled, bonded and non-bonded
+   molecular-mechanics terms represented by the model are removed from the
+   classical force-field contribution and the Metatomic model contribution is
+   added through the applied-forces framework. When disabled, the Metatomic
+   contribution is added on top of the unmodified molecular-mechanics topology.
+
+.. mdp:: metatomic-link-atoms
+
+   (false) Enable hydrogen link atoms at bonds crossing the Metatomic/MM
+   boundary. Direct MM neighbors bonded to selected Metatomic atoms are included
+   in the embedded atom set and represented as hydrogen caps during model
+   evaluation. This requires :mdp:`metatomic-oniom` and a model trained for
+   link-atom-capped boundary chemistry. If a boundary MM atom is bonded to
+   multiple selected Metatomic atoms, each cut bond is represented by a distinct
+   hydrogen cap in the model input.
+
+
 .. _mdp-fmm:
 
 Fast Multipole Method (FMM) Interface

src/external/thread_mpi/test/notmpi.cpp

@@ -167,19 +167,25 @@ int main(int argc, char *argv[])
 #elif defined(THREAD_WINDOWS)
     /* Windows threads here */
     {
-        DWORD *th;
-
-        th = (DWORD*)malloc(sizeof(DWORD)*n);
+        std::vector<HANDLE> threads(n);
+        std::vector<DWORD>  threadIds(n);
 
         for (i = 1; i < n; i++)
         {
-            CreateThread(NULL, 0, thread_starter, (void*)(id_array+i), 0, th+i);
+            threads[i] =
+                    CreateThread(NULL, 0, thread_starter, (void*)(id_array+i), 0, &threadIds[i]);
+            if (threads[i] == NULL)
+            {
+                fprintf(stderr, "CreateThread failed with error %lu\n", GetLastError());
+                exit(1);
+            }
         }
         thread_fn(id_array+0);
 
         for (i = 1; i < n; i++)
         {
-            WaitForSingleObject(th+i, INFINITE);
+            WaitForSingleObject(threads[i], INFINITE);
+            CloseHandle(threads[i]);
         }
     }
 #endif