Merge pull request #1793 from glotzerlab/mesh_helfrich_energy

Mesh helfrich energy
glotzerlab · Oct 16, 2024 · 5cd89bf · 5cd89bf
2 parents 614e405 + 36f306f
commit 5cd89bf
Show file tree

Hide file tree

Showing 14 changed files with 1,729 additions and 26 deletions.
diff --git a/hoomd/error.py b/hoomd/error.py
@@ -51,6 +51,11 @@ def __init__(self, *args, **kwargs):
             "This build of HOOMD-blue does not support GPUs.")
 
 
+class MPINotAvailableError(NotImplementedError):
+    """Error for when a feature is not implemented for MPI."""
+    pass
+
+
 class IncompleteSpecificationError(ValueError):
     """Error when a value is missing."""
     pass

diff --git a/hoomd/md/BendingRigidityMeshForceCompute.cc b/hoomd/md/BendingRigidityMeshForceCompute.cc
@@ -55,7 +55,7 @@ void BendingRigidityMeshForceCompute::setParams(unsigned int type, Scalar K)
 void BendingRigidityMeshForceCompute::setParamsPython(std::string type, pybind11::dict params)
     {
     auto typ = m_mesh_data->getMeshBondData()->getTypeByName(type);
-    auto _params = rigidity_params(params);
+    auto _params = bending_params(params);
     setParams(typ, _params.k);
     }
 

diff --git a/hoomd/md/BendingRigidityMeshForceCompute.h b/hoomd/md/BendingRigidityMeshForceCompute.h
@@ -23,37 +23,36 @@ namespace hoomd
     {
 namespace md
     {
-
-//! Computes rigidity energy forces on the mesh
-/*! BendingRigidity energy forces are computed on every particle in a mesh.
-
-    \ingroup computes
-*/
-class PYBIND11_EXPORT BendingRigidityMeshForceCompute : public ForceCompute
+struct bending_params
     {
-    struct rigidity_params
-        {
-        Scalar k;
+    Scalar k;
 
 #ifndef __HIPCC__
-        rigidity_params() : k(0) { }
+    bending_params() : k(0) { }
 
-        rigidity_params(pybind11::dict params) : k(params["k"].cast<Scalar>()) { }
+    bending_params(pybind11::dict params) : k(params["k"].cast<Scalar>()) { }
 
-        pybind11::dict asDict()
-            {
-            pybind11::dict v;
-            v["k"] = k;
-            return v;
-            }
-#endif
+    pybind11::dict asDict()
+        {
+        pybind11::dict v;
+        v["k"] = k;
+        return v;
         }
+#endif
+    }
 #if HOOMD_LONGREAL_SIZE == 32
-        __attribute__((aligned(4)));
+    __attribute__((aligned(4)));
 #else
-        __attribute__((aligned(8)));
+    __attribute__((aligned(8)));
 #endif
 
+//! Computes rigidity energy forces on the mesh
+/*! BendingRigidity energy forces are computed on every particle in a mesh.
+
+    \ingroup computes
+*/
+class PYBIND11_EXPORT BendingRigidityMeshForceCompute : public ForceCompute
+    {
     public:
     //! Constructs the compute
     BendingRigidityMeshForceCompute(std::shared_ptr<SystemDefinition> sysdef,

diff --git a/hoomd/md/CMakeLists.txt b/hoomd/md/CMakeLists.txt
@@ -25,6 +25,7 @@ set(_md_sources module-md.cc
                    HarmonicAngleForceCompute.cc
                    HarmonicDihedralForceCompute.cc
                    HarmonicImproperForceCompute.cc
+                   HelfrichMeshForceCompute.cc
                    IntegrationMethodTwoStep.cc
                    IntegratorTwoStep.cc
                    ManifoldZCylinder.cc
@@ -133,6 +134,8 @@ set(_md_headers ActiveForceComputeGPU.h
                 HarmonicDihedralForceCompute.h
                 HarmonicImproperForceComputeGPU.h
                 HarmonicImproperForceCompute.h
+		HelfrichMeshForceComputeGPU.h
+		HelfrichMeshForceCompute.h
                 IntegrationMethodTwoStep.h
                 IntegratorTwoStep.h
                 ManifoldZCylinder.h
@@ -225,6 +228,7 @@ list(APPEND _md_sources ActiveForceComputeGPU.cc
                            HarmonicAngleForceComputeGPU.cc
                            HarmonicDihedralForceComputeGPU.cc
                            HarmonicImproperForceComputeGPU.cc
+			   HelfrichMeshForceComputeGPU.cc
                            MolecularForceCompute.cu
                            NeighborListGPU.cc
                            NeighborListGPUBinned.cc
@@ -261,6 +265,7 @@ set(_md_cu_sources ActiveForceComputeGPU.cu
                       HarmonicAngleForceGPU.cu
                       HarmonicDihedralForceGPU.cu
                       HarmonicImproperForceGPU.cu
+		      HelfrichMeshForceComputeGPU.cu
                       MolecularForceCompute.cu
                       NeighborListGPUBinned.cu
                       NeighborListGPU.cu