diff --git a/modules/mol/mm/pymod/export_topology.cc b/modules/mol/mm/pymod/export_topology.cc
index 1e90e1b969fab9d27d0c709c9ddf5fa9f17e74e4..fa5320904e0c4ae4fdcad34902ceea4bce7b955f 100644
--- a/modules/mol/mm/pymod/export_topology.cc
+++ b/modules/mol/mm/pymod/export_topology.cc
@@ -388,7 +388,6 @@ void export_Topology()
.def("AddExclusion",&ost::mol::mm::Topology::AddExclusion,(arg("idx_one"),arg("idx_two")))
.def("AddPositionConstraint",&ost::mol::mm::Topology::AddPositionConstraint,(arg("idx")))
.def("ResetPositionConstraints",&ost::mol::mm::Topology::ResetPositionConstraints)
- .def("SetDensity",&ost::mol::mm::Topology::SetDensity,(arg("density"),arg("resolution"),arg("scaling")=1.0))
.def("ResetExclusions",&ost::mol::mm::Topology::ResetExclusions)
.def("AddHarmonicPositionRestraint",&ost::mol::mm::Topology::AddHarmonicPositionRestraint,(arg("idx"),arg("ref_position"),arg("k"),arg("x_scale")=1.0,arg("y_scale")=1.0,arg("z_scale")=1.0))
.def("AddHarmonicDistanceRestraint",&ost::mol::mm::Topology::AddHarmonicDistanceRestraint,(arg("idx_one"),arg("idx_two"),arg("length"),arg("force_constant")))
@@ -439,9 +438,6 @@ void export_Topology()
.def("GetHarmonicDistanceRestraintParameters",&WrapGetHarmonicDistanceRestraintParam,(arg("interaction_idx")))
.def("GetFGMDHBondDonorParameters",&WrapGetFGMDHBondDonorParam,(arg("interaction_idx")))
.def("GetFGMDHBondAcceptorParameters",&WrapGetFGMDHBondAcceptorParam,(arg("interaction_idx")))
- .def("GetDensity",&ost::mol::mm::Topology::GetDensity)
- .def("GetDensityResolution",&ost::mol::mm::Topology::GetDensityResolution)
- .def("GetDensityScaling",&ost::mol::mm::Topology::GetDensityResolution)
//setter functions for interaction parameters
.def("SetHarmonicBondParameters",&ost::mol::mm::Topology::SetHarmonicBondParameters,(arg("interaction_idx"),arg("bond_length"),arg("force_constant")))
diff --git a/modules/mol/mm/src/CMakeLists.txt b/modules/mol/mm/src/CMakeLists.txt
index 3ebe98ba087cfc8cd22e891ccb0ee078c769f545..46f4d4cd576f47533c6661397f7428ae414a4820 100644
--- a/modules/mol/mm/src/CMakeLists.txt
+++ b/modules/mol/mm/src/CMakeLists.txt
@@ -16,11 +16,6 @@ set(OST_MOL_MM_HEADERS
index.hh
topology.hh
steep.hh
- openmm_plugins/density_plugin/openmmapi/density_force.hh
- openmm_plugins/density_plugin/openmmapi/density_kernels.hh
- openmm_plugins/density_plugin/openmmapi/density_force_impl.hh
- openmm_plugins/density_plugin/platforms/reference/reference_density_kernels.hh
- openmm_plugins/density_plugin/platforms/reference/reference_density_kernel_factory.hh
)
set(OST_MOL_MM_SOURCES
@@ -38,8 +33,6 @@ set(OST_MOL_MM_SOURCES
topology_creator.cc
topology.cc
steep.cc
- openmm_plugins/density_plugin/openmmapi/density_force.cc
- openmm_plugins/density_plugin/openmmapi/density_force_impl.cc
)
# create settings.hh as configurational header, needed to set the plugins path
@@ -69,37 +62,3 @@ copy_if_different("${CMAKE_CURRENT_SOURCE_DIR}" "${STAGE_DIR}/share/openstructur
"ost_mol_mm")
install(FILES "CHARMM27.dat" DESTINATION "share/openstructure/forcefields/")
-#The plugins that get loaded by OpenMM have to be built seperately
-
-##########################
-#build the density plugin#
-##########################
-
-#define the sources (headers are already handled above)
-SET(DENSITY_PLUGIN_REFERENCE_SOURCES
- openmm_plugins/density_plugin/platforms/reference/reference_density_kernel_factory.cc
- openmm_plugins/density_plugin/platforms/reference/reference_density_kernels.cc
-)
-
-# Set the library name
-SET(OPENMM_DENSITY_REFERENCE_LIBRARY_NAME density_plugin_reference)
-SET(SHARED_TARGET_DENSITY_PLUGIN ${OPENMM_DENSITY_REFERENCE_LIBRARY_NAME})
-
-ADD_LIBRARY(${SHARED_TARGET_DENSITY_PLUGIN} SHARED ${DENSITY_PLUGIN_REFERENCE_SOURCES})
-ADD_DEPENDENCIES(${SHARED_TARGET_DENSITY_PLUGIN} ost_mol_mm ost_img ost_mol_mm)
-
-SET_TARGET_PROPERTIES(${SHARED_TARGET_DENSITY_PLUGIN} PROPERTIES
- LIBRARY_OUTPUT_DIRECTORY ${STAGE_DIR}/share/openstructure/openmm_plugins/
- ARCHIVE_OUTPUT_DIRECTORY ${STAGE_DIR}/share/openstructure/openmm_plugins/
- RUNTIME_OUTPUT_DIRECTORY ${STAGE_DIR}/share/openstructure/openmm_plugins/)
-
-foreach(_DEPENDENCY ${_MOL_MM_DEPS})
- TARGET_LINK_LIBRARIES(${SHARED_TARGET_DENSITY_PLUGIN} ${_DEPENDENCY})
-endforeach()
-#also link against OpenMM and the mm module
-TARGET_LINK_LIBRARIES(${SHARED_TARGET_DENSITY_PLUGIN} ${OPEN_MM_LIBRARIES})
-TARGET_LINK_LIBRARIES(${SHARED_TARGET_DENSITY_PLUGIN} ost_mol_mm)
-
-file(MAKE_DIRECTORY ${STAGE_DIR}/share/openstructure/openmm_plugins/)
-INSTALL(TARGETS ${SHARED_TARGET_DENSITY_PLUGIN} LIBRARY
- DESTINATION "share/openstructure/openmm_plugins/")
diff --git a/modules/mol/mm/src/openmm_plugins/density_plugin/openmmapi/density_force.cc b/modules/mol/mm/src/openmm_plugins/density_plugin/openmmapi/density_force.cc
deleted file mode 100644
index 8ff809d9a768edb8efd64acbde96fe2e51bcae31..0000000000000000000000000000000000000000
--- a/modules/mol/mm/src/openmm_plugins/density_plugin/openmmapi/density_force.cc
+++ /dev/null
@@ -1,97 +0,0 @@
-/* -------------------------------------------------------------------------- *
- * OpenMM *
- * -------------------------------------------------------------------------- *
- * This is part of the OpenMM molecular simulation toolkit originating from *
- * Simbios, the NIH National Center for Physics-Based Simulation of *
- * Biological Structures at Stanford, funded under the NIH Roadmap for *
- * Medical Research, grant U54 GM072970. See https://simtk.org. *
- * *
- * Portions copyright (c) 2014 Stanford University and the Authors. *
- * Authors: Peter Eastman *
- * Contributors: *
- * *
- * Permission is hereby granted, free of charge, to any person obtaining a *
- * copy of this software and associated documentation files (the "Software"), *
- * to deal in the Software without restriction, including without limitation *
- * the rights to use, copy, modify, merge, publish, distribute, sublicense, *
- * and/or sell copies of the Software, and to permit persons to whom the *
- * Software is furnished to do so, subject to the following conditions: *
- * *
- * The above copyright notice and this permission notice shall be included in *
- * all copies or substantial portions of the Software. *
- * *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
- * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
- * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
- * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
- * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
- * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
- * USE OR OTHER DEALINGS IN THE SOFTWARE. *
- * -------------------------------------------------------------------------- */
-
-#include <ost/mol/mm/density_force.hh>
-#include <ost/mol/mm/density_force_impl.hh>
-#include <openmm/OpenMMException.h>
-#include <openmm/internal/AssertionUtilities.h>
-#include <string.h>
-
-namespace ost{ namespace mol{ namespace mm{
-
-OpenMM::ForceImpl* DensityForce::createImpl() const {
- return new DensityForceImpl(*this);
-}
-
-void DensityForce::updateParametersInContext(OpenMM::Context& context) {
- dynamic_cast<DensityForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
-}
-
-void DensityForce::addParticle(Real mass){
- masses_.push_back(mass);
- in_body_.push_back(false);
-}
-
-Real DensityForce::getParticleMass(int idx) const{
- if(idx >= this->getNumParticles() || idx < 0){
- throw OpenMM::OpenMMException("Invalid index provided!");
- }
- return masses_[idx];
-}
-
-bool DensityForce::isInBody(int idx) const{
- if(idx >= this->getNumParticles() || idx < 0){
- throw OpenMM::OpenMMException("Invalid index provided!");
- }
- return in_body_[idx];
-}
-
-void DensityForce::defineBody(const std::vector<int>& indices){
- //first check, whether any of the indices is invalid or already part of a body
- int num_particles = this->getNumParticles();
- for(std::vector<int>::const_iterator i = indices.begin();
- i != indices.end(); ++i){
- if(*i >= num_particles || *i < 0){
- throw OpenMM::OpenMMException("Invalid index provided!");
- }
- if(in_body_[*i]){
- throw OpenMM::OpenMMException("Particle can be part of only one body!");
- }
- }
-
- //let's change the state of the according particles
- for(std::vector<int>::const_iterator i = indices.begin();
- i != indices.end(); ++i){
- in_body_[*i] = true;
- }
-
- //and finally define the body
- bodies_.push_back(indices);
-}
-
-const std::vector<int>& DensityForce::getBody(int idx) const{
- if(idx >= this->getNumBodies() || idx < 0){
- throw OpenMM::OpenMMException("Invalid index provided!");
- }
- return bodies_[idx];
-}
-
-}}} //ns
diff --git a/modules/mol/mm/src/openmm_plugins/density_plugin/openmmapi/density_force.hh b/modules/mol/mm/src/openmm_plugins/density_plugin/openmmapi/density_force.hh
deleted file mode 100644
index f932ff797b978cd54ebe8be72c03935f587f73af..0000000000000000000000000000000000000000
--- a/modules/mol/mm/src/openmm_plugins/density_plugin/openmmapi/density_force.hh
+++ /dev/null
@@ -1,94 +0,0 @@
-#ifndef OPENMM_DENSITYFORCE_H_
-#define OPENMM_DENSITYFORCE_H_
-
-/* -------------------------------------------------------------------------- *
- * OpenMM *
- * -------------------------------------------------------------------------- *
- * This is part of the OpenMM molecular simulation toolkit originating from *
- * Simbios, the NIH National Center for Physics-Based Simulation of *
- * Biological Structures at Stanford, funded under the NIH Roadmap for *
- * Medical Research, grant U54 GM072970. See https://simtk.org. *
- * *
- * Portions copyright (c) 2014 Stanford University and the Authors. *
- * Authors: Peter Eastman *
- * Contributors: *
- * *
- * Permission is hereby granted, free of charge, to any person obtaining a *
- * copy of this software and associated documentation files (the "Software"), *
- * to deal in the Software without restriction, including without limitation *
- * the rights to use, copy, modify, merge, publish, distribute, sublicense, *
- * and/or sell copies of the Software, and to permit persons to whom the *
- * Software is furnished to do so, subject to the following conditions: *
- * *
- * The above copyright notice and this permission notice shall be included in *
- * all copies or substantial portions of the Software. *
- * *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
- * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
- * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
- * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
- * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
- * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
- * USE OR OTHER DEALINGS IN THE SOFTWARE. *
- * -------------------------------------------------------------------------- */
-
-#include <openmm/Context.h>
-#include <openmm/Force.h>
-#include <ost/img/image.hh>
-
-namespace ost { namespace mol{ namespace mm{
-
-
-class DensityForce : public OpenMM::Force {
-public:
- /**
- * Create an DensityForce. The density force only makes sense for simulation boxes
- * with orthogonal base vectors.
- */
-
- //since the density is scaled in Angstrom, the resolution is also in Angstrom
- DensityForce(const ost::img::ImageHandle& d, Real r, Real s): density_(d),
- resolution_(r),
- scaling_(s) { }
-
- void addParticle(Real mass);
-
- int getNumParticles() const { return masses_.size(); }
-
- int getNumBodies() const { return bodies_.size(); }
-
- Real getParticleMass(int idx) const;
-
- bool isInBody(int idx) const;
-
- void defineBody(const std::vector<int>& indices);
-
- const std::vector<int>& getBody(int idx) const;
-
- void setScaling(Real scaling) { scaling_ = scaling; }
-
- Real getScaling() const { return scaling_; }
-
- ost::img::ImageHandle getDensity() const { return density_; }
-
- Real getResolution() const { return resolution_; }
-
- void updateParametersInContext(OpenMM::Context& context);
-
- bool usesPeriodicBoundaryConditions() const { return false; }
-
-protected:
- OpenMM::ForceImpl* createImpl() const;
-private:
-
- ost::img::ImageHandle density_;
- std::vector<Real> masses_;
- std::vector<bool> in_body_;
- std::vector<std::vector<int> > bodies_;
- Real resolution_;
- Real scaling_;
-};
-
-}}} // ns
-
-#endif /*OPENMM_DENSITYFORCE_H_*/
diff --git a/modules/mol/mm/src/openmm_plugins/density_plugin/openmmapi/density_force_impl.cc b/modules/mol/mm/src/openmm_plugins/density_plugin/openmmapi/density_force_impl.cc
deleted file mode 100644
index 1d2b859a0eb006fe13c389a9818d2958bc69a801..0000000000000000000000000000000000000000
--- a/modules/mol/mm/src/openmm_plugins/density_plugin/openmmapi/density_force_impl.cc
+++ /dev/null
@@ -1,71 +0,0 @@
-/* -------------------------------------------------------------------------- *
- * OpenMM *
- * -------------------------------------------------------------------------- *
- * This is part of the OpenMM molecular simulation toolkit originating from *
- * Simbios, the NIH National Center for Physics-Based Simulation of *
- * Biological Structures at Stanford, funded under the NIH Roadmap for *
- * Medical Research, grant U54 GM072970. See https://simtk.org. *
- * *
- * Portions copyright (c) 2014 Stanford University and the Authors. *
- * Authors: Peter Eastman *
- * Contributors: *
- * *
- * Permission is hereby granted, free of charge, to any person obtaining a *
- * copy of this software and associated documentation files (the "Software"), *
- * to deal in the Software without restriction, including without limitation *
- * the rights to use, copy, modify, merge, publish, distribute, sublicense, *
- * and/or sell copies of the Software, and to permit persons to whom the *
- * Software is furnished to do so, subject to the following conditions: *
- * *
- * The above copyright notice and this permission notice shall be included in *
- * all copies or substantial portions of the Software. *
- * *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
- * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
- * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
- * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
- * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
- * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
- * USE OR OTHER DEALINGS IN THE SOFTWARE. *
- * -------------------------------------------------------------------------- */
-
-#include <ost/mol/mm/density_force_impl.hh>
-#include <ost/mol/mm/density_kernels.hh>
-#include <openmm/OpenMMException.h>
-#include <openmm/internal/ContextImpl.h>
-#include <cmath>
-#include <map>
-#include <set>
-#include <sstream>
-
-namespace ost{ namespace mol{ namespace mm{
-
-DensityForceImpl::DensityForceImpl(const DensityForce& owner) : owner(owner) {
-}
-
-DensityForceImpl::~DensityForceImpl() {
-}
-
-void DensityForceImpl::initialize(OpenMM::ContextImpl& context) {
- kernel = context.getPlatform().createKernel(CalcDensityForceKernel::Name(), context);
- kernel.getAs<CalcDensityForceKernel>().initialize(context.getSystem(), owner);
-}
-
-double DensityForceImpl::calcForcesAndEnergy(OpenMM::ContextImpl& context, bool includeForces, bool includeEnergy, int groups) {
- if ((groups&(1<<owner.getForceGroup())) != 0)
- return kernel.getAs<CalcDensityForceKernel>().execute(context, includeForces, includeEnergy);
- return 0.0;
-}
-
-std::vector<std::string> DensityForceImpl::getKernelNames() {
- std::vector<std::string> names;
- names.push_back(CalcDensityForceKernel::Name());
- return names;
-}
-
-void DensityForceImpl::updateParametersInContext(OpenMM::ContextImpl& context) {
- kernel.getAs<CalcDensityForceKernel>().copyParametersToContext(context, owner);
-}
-
-}}} //ns
-
diff --git a/modules/mol/mm/src/openmm_plugins/density_plugin/openmmapi/density_force_impl.hh b/modules/mol/mm/src/openmm_plugins/density_plugin/openmmapi/density_force_impl.hh
deleted file mode 100644
index 850b2c5c23a33b48773bcc29b5001f1ad904353b..0000000000000000000000000000000000000000
--- a/modules/mol/mm/src/openmm_plugins/density_plugin/openmmapi/density_force_impl.hh
+++ /dev/null
@@ -1,74 +0,0 @@
-#ifndef OPENMM_DENSITYFORCEIMPL_H_
-#define OPENMM_DENSITYFORCEIMPL_H_
-
-/* -------------------------------------------------------------------------- *
- * OpenMM *
- * -------------------------------------------------------------------------- *
- * This is part of the OpenMM molecular simulation toolkit originating from *
- * Simbios, the NIH National Center for Physics-Based Simulation of *
- * Biological Structures at Stanford, funded under the NIH Roadmap for *
- * Medical Research, grant U54 GM072970. See https://simtk.org. *
- * *
- * Portions copyright (c) 2014 Stanford University and the Authors. *
- * Authors: Peter Eastman *
- * Contributors: *
- * *
- * Permission is hereby granted, free of charge, to any person obtaining a *
- * copy of this software and associated documentation files (the "Software"), *
- * to deal in the Software without restriction, including without limitation *
- * the rights to use, copy, modify, merge, publish, distribute, sublicense, *
- * and/or sell copies of the Software, and to permit persons to whom the *
- * Software is furnished to do so, subject to the following conditions: *
- * *
- * The above copyright notice and this permission notice shall be included in *
- * all copies or substantial portions of the Software. *
- * *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
- * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
- * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
- * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
- * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
- * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
- * USE OR OTHER DEALINGS IN THE SOFTWARE. *
- * -------------------------------------------------------------------------- */
-
-#include <ost/mol/mm/density_force.hh>
-#include <openmm/internal/ForceImpl.h>
-#include <openmm/Kernel.h>
-#include <utility>
-#include <set>
-#include <string>
-
-namespace ost{ namespace mol{ namespace mm{
-
-/**
- * This is the internal implementation of DensityForce.
- */
-
-class DensityForceImpl : public OpenMM::ForceImpl {
-public:
- DensityForceImpl(const DensityForce& owner);
- ~DensityForceImpl();
- void initialize(OpenMM::ContextImpl& context);
- const DensityForce& getOwner() const {
- return owner;
- }
- void updateContextState(OpenMM::ContextImpl& context) {
- // This force field doesn't update the state directly.
- }
- double calcForcesAndEnergy(OpenMM::ContextImpl& context, bool includeForces, bool includeEnergy, int groups);
- std::map<std::string, double> getDefaultParameters() {
- return std::map<std::string, double>(); // This force field doesn't define any parameters.
- }
- std::vector<std::string> getKernelNames();
-
- void updateParametersInContext(OpenMM::ContextImpl& context);
-private:
- const DensityForce& owner;
- OpenMM::Kernel kernel;
-};
-
-}}} //ns
-
-#endif /*OPENMM_DENSITYFORCEIMPL_H_*/
-
diff --git a/modules/mol/mm/src/openmm_plugins/density_plugin/openmmapi/density_kernels.hh b/modules/mol/mm/src/openmm_plugins/density_plugin/openmmapi/density_kernels.hh
deleted file mode 100644
index 78e16cfa795519c82252b7edce168329ea404e97..0000000000000000000000000000000000000000
--- a/modules/mol/mm/src/openmm_plugins/density_plugin/openmmapi/density_kernels.hh
+++ /dev/null
@@ -1,80 +0,0 @@
-#ifndef DENSITY_KERNELS_H_
-#define DENSITY_KERNELS_H_
-
-/* -------------------------------------------------------------------------- *
- * OpenMM *
- * -------------------------------------------------------------------------- *
- * This is part of the OpenMM molecular simulation toolkit originating from *
- * Simbios, the NIH National Center for Physics-Based Simulation of *
- * Biological Structures at Stanford, funded under the NIH Roadmap for *
- * Medical Research, grant U54 GM072970. See https://simtk.org. *
- * *
- * Portions copyright (c) 2014 Stanford University and the Authors. *
- * Authors: Peter Eastman *
- * Contributors: *
- * *
- * Permission is hereby granted, free of charge, to any person obtaining a *
- * copy of this software and associated documentation files (the "Software"), *
- * to deal in the Software without restriction, including without limitation *
- * the rights to use, copy, modify, merge, publish, distribute, sublicense, *
- * and/or sell copies of the Software, and to permit persons to whom the *
- * Software is furnished to do so, subject to the following conditions: *
- * *
- * The above copyright notice and this permission notice shall be included in *
- * all copies or substantial portions of the Software. *
- * *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
- * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
- * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
- * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
- * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
- * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
- * USE OR OTHER DEALINGS IN THE SOFTWARE. *
- * -------------------------------------------------------------------------- */
-
-#include <ost/mol/mm/density_force.hh>
-#include <openmm/KernelImpl.h>
-#include <openmm/Platform.h>
-#include <openmm/System.h>
-#include <string>
-
-namespace ost{ namespace mol{ namespace mm{
-
-/**
- * This kernel is invoked by DensityForce to calculate the forces acting on the system and the energy of the system.
- */
-class CalcDensityForceKernel : public OpenMM::KernelImpl {
-public:
- static std::string Name() {
- return "CalcDensityForce";
- }
- CalcDensityForceKernel(std::string name, const OpenMM::Platform& platform) : OpenMM::KernelImpl(name, platform) {
- }
- /**
- * Initialize the kernel.
- *
- * @param system the System this kernel will be applied to
- * @param force the DensityForce this kernel will be used for
- */
- virtual void initialize(const OpenMM::System& system, const DensityForce& force) = 0;
- /**
- * Execute the kernel to calculate the forces and/or energy.
- *
- * @param context the context in which to execute this kernel
- * @param includeForces true if forces should be calculated
- * @param includeEnergy true if the energy should be calculated
- * @return the potential energy due to the force
- */
- virtual double execute(OpenMM::ContextImpl& context, bool includeForces, bool includeEnergy) = 0;
- /**
- * Copy changed parameters over to a context.
- *
- * @param context the context to copy parameters to
- * @param force the DensityForce to copy the parameters from
- */
- virtual void copyParametersToContext(OpenMM::ContextImpl& context, const DensityForce& force) = 0;
-};
-
-}}} //ns
-
-#endif /*DENSITY_KERNELS_H_*/
diff --git a/modules/mol/mm/src/openmm_plugins/density_plugin/platforms/reference/reference_density_kernel_factory.cc b/modules/mol/mm/src/openmm_plugins/density_plugin/platforms/reference/reference_density_kernel_factory.cc
deleted file mode 100644
index 8df88868d90895b7b48b89e436799fd3bde97956..0000000000000000000000000000000000000000
--- a/modules/mol/mm/src/openmm_plugins/density_plugin/platforms/reference/reference_density_kernel_factory.cc
+++ /dev/null
@@ -1,62 +0,0 @@
-/* -------------------------------------------------------------------------- *
- * OpenMMExample *
- * -------------------------------------------------------------------------- *
- * This is part of the OpenMM molecular simulation toolkit originating from *
- * Simbios, the NIH National Center for Physics-Based Simulation of *
- * Biological Structures at Stanford, funded under the NIH Roadmap for *
- * Medical Research, grant U54 GM072970. See https://simtk.org. *
- * *
- * Portions copyright (c) 2014 Stanford University and the Authors. *
- * Authors: Peter Eastman *
- * Contributors: *
- * *
- * Permission is hereby granted, free of charge, to any person obtaining a *
- * copy of this software and associated documentation files (the "Software"), *
- * to deal in the Software without restriction, including without limitation *
- * the rights to use, copy, modify, merge, publish, distribute, sublicense, *
- * and/or sell copies of the Software, and to permit persons to whom the *
- * Software is furnished to do so, subject to the following conditions: *
- * *
- * The above copyright notice and this permission notice shall be included in *
- * all copies or substantial portions of the Software. *
- * *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
- * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
- * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
- * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
- * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
- * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
- * USE OR OTHER DEALINGS IN THE SOFTWARE. *
- * -------------------------------------------------------------------------- */
-
-#include <ost/mol/mm/reference_density_kernel_factory.hh>
-#include <ost/mol/mm/reference_density_kernels.hh>
-#include <openmm/reference/ReferencePlatform.h>
-#include <openmm/internal/ContextImpl.h>
-#include <openmm/OpenMMException.h>
-
-using namespace ost::mol::mm;
-
-extern "C" void registerPlatforms() {
-}
-
-extern "C" void registerKernelFactories() {
- for (int i = 0; i < OpenMM::Platform::getNumPlatforms(); i++) {
- OpenMM::Platform& platform = OpenMM::Platform::getPlatform(i);
- if (dynamic_cast<OpenMM::ReferencePlatform*>(&platform) != NULL) {
- ReferenceDensityKernelFactory* factory = new ReferenceDensityKernelFactory();
- platform.registerKernelFactory(CalcDensityForceKernel::Name(), factory);
- }
- }
-}
-
-extern "C" void registerDensityReferenceKernelFactories() {
- registerKernelFactories();
-}
-
-OpenMM::KernelImpl* ReferenceDensityKernelFactory::createKernelImpl(std::string name, const OpenMM::Platform& platform, OpenMM::ContextImpl& context) const {
- OpenMM::ReferencePlatform::PlatformData& data = *static_cast<OpenMM::ReferencePlatform::PlatformData*>(context.getPlatformData());
- if (name == CalcDensityForceKernel::Name())
- return new ReferenceCalcDensityForceKernel(name, platform);
- throw OpenMM::OpenMMException((std::string("Tried to create kernel with illegal kernel name '")+name+"'").c_str());
-}
diff --git a/modules/mol/mm/src/openmm_plugins/density_plugin/platforms/reference/reference_density_kernel_factory.hh b/modules/mol/mm/src/openmm_plugins/density_plugin/platforms/reference/reference_density_kernel_factory.hh
deleted file mode 100644
index 14dfdf44c23060f65f12c3939815b8bd27664608..0000000000000000000000000000000000000000
--- a/modules/mol/mm/src/openmm_plugins/density_plugin/platforms/reference/reference_density_kernel_factory.hh
+++ /dev/null
@@ -1,53 +0,0 @@
-#ifndef OPENMM_REFERENCEDensityKERNELFACTORY_H_
-#define OPENMM_REFERENCEDensityKERNELFACTORY_H_
-
-/* -------------------------------------------------------------------------- *
- * OpenMM *
- * -------------------------------------------------------------------------- *
- * This is part of the OpenMM molecular simulation toolkit originating from *
- * Simbios, the NIH National Center for Physics-Based Simulation of *
- * Biological Structures at Stanford, funded under the NIH Roadmap for *
- * Medical Research, grant U54 GM072970. See https://simtk.org. *
- * *
- * Portions copyright (c) 2014 Stanford University and the Authors. *
- * Authors: Peter Eastman *
- * Contributors: *
- * *
- * Permission is hereby granted, free of charge, to any person obtaining a *
- * copy of this software and associated documentation files (the "Software"), *
- * to deal in the Software without restriction, including without limitation *
- * the rights to use, copy, modify, merge, publish, distribute, sublicense, *
- * and/or sell copies of the Software, and to permit persons to whom the *
- * Software is furnished to do so, subject to the following conditions: *
- * *
- * The above copyright notice and this permission notice shall be included in *
- * all copies or substantial portions of the Software. *
- * *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
- * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
- * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
- * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
- * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
- * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
- * USE OR OTHER DEALINGS IN THE SOFTWARE. *
- * -------------------------------------------------------------------------- */
-
-#include <openmm/KernelFactory.h>
-
-/**
- * This KernelFactory creates kernels for the reference implementation of the Density plugin.
- */
-
-namespace ost{ namespace mol{ namespace mm{
-
-class ReferenceDensityKernelFactory : public OpenMM::KernelFactory {
-public:
- OpenMM::KernelImpl* createKernelImpl(std::string name,
- const OpenMM::Platform& platform,
- OpenMM::ContextImpl& context) const;
-};
-
-
-}}} //ns
-
-#endif /*OPENMM_REFERENCEDENSITYKERNELFACTORY_H_*/
diff --git a/modules/mol/mm/src/openmm_plugins/density_plugin/platforms/reference/reference_density_kernels.cc b/modules/mol/mm/src/openmm_plugins/density_plugin/platforms/reference/reference_density_kernels.cc
deleted file mode 100644
index 77edcd5524b5a5eb3df997727f36a25104a0876a..0000000000000000000000000000000000000000
--- a/modules/mol/mm/src/openmm_plugins/density_plugin/platforms/reference/reference_density_kernels.cc
+++ /dev/null
@@ -1,342 +0,0 @@
-/* -------------------------------------------------------------------------- *
- * OpenMM *
- * -------------------------------------------------------------------------- *
- * This is part of the OpenMM molecular simulation toolkit originating from *
- * Simbios, the NIH National Center for Physics-Based Simulation of *
- * Biological Structures at Stanford, funded under the NIH Roadmap for *
- * Medical Research, grant U54 GM072970. See https://simtk.org. *
- * *
- * Portions copyright (c) 2014 Stanford University and the Authors. *
- * Authors: Peter Eastman *
- * Contributors: *
- * *
- * Permission is hereby granted, free of charge, to any person obtaining a *
- * copy of this software and associated documentation files (the "Software"), *
- * to deal in the Software without restriction, including without limitation *
- * the rights to use, copy, modify, merge, publish, distribute, sublicense, *
- * and/or sell copies of the Software, and to permit persons to whom the *
- * Software is furnished to do so, subject to the following conditions: *
- * *
- * The above copyright notice and this permission notice shall be included in *
- * all copies or substantial portions of the Software. *
- * *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
- * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
- * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
- * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
- * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
- * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
- * USE OR OTHER DEALINGS IN THE SOFTWARE. *
- * -------------------------------------------------------------------------- */
-
-#include <ost/mol/mm/reference_density_kernels.hh>
-#include <ost/mol/mm/density_force.hh>
-#include <openmm/OpenMMException.h>
-#include <openmm/internal/ContextImpl.h>
-#include <openmm/reference/RealVec.h>
-#include <openmm/reference/ReferencePlatform.h>
-
-using namespace OpenMM;
-using namespace std;
-
-namespace{
-
-static vector<RealVec>& extractPositions(ContextImpl& context) {
- ReferencePlatform::PlatformData* data =
- reinterpret_cast<ReferencePlatform::PlatformData*>(context.getPlatformData());
- return *((vector<RealVec>*) data->positions);
-}
-
-static vector<RealVec>& extractForces(ContextImpl& context) {
- ReferencePlatform::PlatformData* data =
- reinterpret_cast<ReferencePlatform::PlatformData*>(context.getPlatformData());
- return *((vector<RealVec>*) data->forces);
-}
-
-} //anon ns
-
-
-namespace ost{ namespace mol { namespace mm{
-
-ReferenceCalcDensityForceKernel::~ReferenceCalcDensityForceKernel(){
- if(data_ != NULL) delete [] data_;
-}
-
-void ReferenceCalcDensityForceKernel::initialize(const System& system, const DensityForce& force) {
-
- if(system.getNumParticles() != force.getNumParticles()){
- std::string err = "DensityForce must contain same number of";
- err += " particles as system!";
- throw OpenMM::OpenMMException(err);
- }
-
- if(data_ != NULL) delete [] data_;
-
- ost::img::ImageHandle density = force.getDensity();
-
- x_sampling_ = density.GetSpatialSampling()[0] * 0.1;
- y_sampling_ = density.GetSpatialSampling()[1] * 0.1;
- z_sampling_ = density.GetSpatialSampling()[2] * 0.1;
- one_over_x_sampling_ = Real(1.0) / x_sampling_;
- one_over_y_sampling_ = Real(1.0) / y_sampling_;
- one_over_z_sampling_ = Real(1.0) / z_sampling_;
- half_x_sampling_ = Real(0.5) * x_sampling_;
- half_y_sampling_ = Real(0.5) * y_sampling_;
- half_z_sampling_ = Real(0.5) * z_sampling_;
- x_origin_ = density.GetAbsoluteOrigin()[0] * 0.1;
- y_origin_ = density.GetAbsoluteOrigin()[1] * 0.1;
- z_origin_ = density.GetAbsoluteOrigin()[2] * 0.1;
- x_extent_ = density.GetSize()[0];
- y_extent_ = density.GetSize()[1];
- z_extent_ = density.GetSize()[2];
-
- data_ = new Real[x_extent_ * y_extent_ * z_extent_];
- int current_idx = 0;
- for(int i = 0; i < x_extent_; ++i){
- for(int j = 0; j < y_extent_; ++j){
- for(int k = 0; k < z_extent_; ++k){
- data_[current_idx] = density.GetReal(ost::img::Point(i,j,k));
- ++current_idx;
- }
- }
- }
-
- idx_helper_one_ = y_extent_ * z_extent_;
- idx_helper_two_ = z_extent_;
-
- //sigma for gaussian like representations of the atoms
- resolution_ = force.getResolution() * 0.1;
- s_ = resolution_ * 0.425;
- one_s_ = Real(1.0) / s_;
- square_one_s_ = Real(1.0) / (s_ * s_);
- one_sqrt_2_pi_s_ = Real(1.0) / std::sqrt(Real(2.0) * Real(M_PI) * s_);
- padding_dist_ = s_ * Real(3.0);
- scaling_ = 10000 * force.getScaling();
-
- //let's get body and particle info...
-
- num_particles_ = system.getNumParticles();
- num_bodies_ = force.getNumBodies();
-
- particle_masses_.resize(num_particles_);
-
- for(int i = 0; i < num_particles_; ++i){
- particle_masses_[i] = force.getParticleMass(i);
- }
-
- bodies_.clear();
- //let's set every particle not belonging to a body to its own body
- for(int i = 0; i < num_particles_; ++i){
- if(force.isInBody(i)) continue;
- std::vector<int> body(1,i);
- bodies_.push_back(body);
- }
-
- //let's fill the defined bodies!
- for(int i = 0; i < num_bodies_; ++i){
- const std::vector<int>& current_body = force.getBody(i);
- bodies_.push_back(current_body);
- }
-
- //let's update the num_bodies_ !!!
- num_bodies_ = bodies_.size();
-}
-
-double ReferenceCalcDensityForceKernel::execute(ContextImpl& context,
- bool includeForces,
- bool includeEnergy) {
-
-
-
- vector<RealVec>& pos = extractPositions(context);
- vector<RealVec>& force = extractForces(context);
-
- //distance of a density position towards a particle
- Real x_d;
- Real y_d;
- Real z_d;
-
- //derivative of a full body
- Real body_dx;
- Real body_dy;
- Real body_dz;
-
- //return value for the full energy, will be updated when iterating over
- //all bodies
- Real overall_energy = 0.0;
-
- //some helper variables
- Real dd;
- Real e_term;
- Real density;
- Real p_density;
- std::vector<Real> p_dx;
- std::vector<Real> p_dy;
- std::vector<Real> p_dz;
- std::vector<Real> p_m;
- Real denominator;
- Real nominator;
- Real a, b;
- Real temp_one, temp_two;
- Real prefac;
- Real min_x_pos, max_x_pos;
- Real min_y_pos, max_y_pos;
- Real min_z_pos, max_z_pos;
- Real body_x_origin, body_y_origin, body_z_origin;
- int body_x_extent, body_y_extent, body_z_extent;
- int num_voxels;
-
- for(int body_idx = 0; body_idx < num_bodies_; ++body_idx){
-
- int body_size = bodies_[body_idx].size();
-
- //set derivatives for every particle in each direction to zero
- //and extract the required masses
- p_dx.assign(body_size,0.0);
- p_dy.assign(body_size,0.0);
- p_dz.assign(body_size,0.0);
- p_m.resize(body_size);
-
- for(int p_idx = 0; p_idx < body_size; ++p_idx){
- p_m[p_idx] = particle_masses_[bodies_[body_idx][p_idx]];
- }
-
- min_x_pos = std::numeric_limits<Real>::max();
- max_x_pos = -std::numeric_limits<Real>::max();
- min_y_pos = std::numeric_limits<Real>::max();
- max_y_pos = -std::numeric_limits<Real>::max();
- min_z_pos = std::numeric_limits<Real>::max();
- max_z_pos = -std::numeric_limits<Real>::max();
-
- //let's find out how big this thing is...
- for(int p_idx = 0; p_idx < body_size; ++p_idx){
- RealVec& p = pos[bodies_[body_idx][p_idx]];
- min_x_pos = (p[0] < min_x_pos) ? p[0]: min_x_pos;
- max_x_pos = (p[0] > max_x_pos) ? p[0]: max_x_pos;
- min_y_pos = (p[1] < min_y_pos) ? p[1]: min_y_pos;
- max_y_pos = (p[1] > max_y_pos) ? p[1]: max_y_pos;
- min_z_pos = (p[2] < min_z_pos) ? p[2]: min_z_pos;
- max_z_pos = (p[2] > max_z_pos) ? p[2]: max_z_pos;
- }
-
- //we add some padding
- min_x_pos -= padding_dist_;
- max_x_pos += padding_dist_;
- min_y_pos -= padding_dist_;
- max_y_pos += padding_dist_;
- min_z_pos -= padding_dist_;
- max_z_pos += padding_dist_;
-
- body_x_extent = std::max(3,
- static_cast<int>(std::ceil((max_x_pos - min_x_pos)*one_over_x_sampling_)));
- body_y_extent = std::max(3,
- static_cast<int>(std::ceil((max_y_pos - min_y_pos)*one_over_y_sampling_)));
- body_z_extent = std::max(3,
- static_cast<int>(std::ceil((max_z_pos - min_z_pos)*one_over_z_sampling_)));
- num_voxels = body_x_extent * body_y_extent * body_z_extent;
-
- Real overlap = min_x_pos + body_x_extent * x_sampling_ - max_x_pos;
- body_x_origin = min_x_pos - 0.5 * overlap;
- overlap = min_y_pos + body_y_extent * y_sampling_ - max_y_pos;
- body_y_origin = min_y_pos - 0.5 * overlap;
- overlap = min_z_pos + body_z_extent * z_sampling_ - max_z_pos;
- body_z_origin = min_z_pos - 0.5 * overlap;
-
-
- density_values_.resize(num_voxels);
- body_values_.assign(num_voxels,0.0);
-
- //let's fill the density values
- int current_idx = 0;
- for(int i = 0; i < body_x_extent; ++i){
- for(int j = 0; j < body_y_extent; ++j){
- for(int k = 0; k < body_z_extent; ++k){
- density_values_[current_idx] =
- this->GetIntpolValue(body_x_origin + i * x_sampling_ + half_x_sampling_,
- body_y_origin + j * y_sampling_ + half_y_sampling_,
- body_z_origin + k * z_sampling_ + half_z_sampling_);
- ++current_idx;
- }
- }
- }
-
- for(int p_idx = 0; p_idx < body_size; ++p_idx){
-
- //the actual position of the particle
- RealVec& p = pos[bodies_[body_idx][p_idx]];
- current_idx = 0;
-
- for(int i = 0; i < body_x_extent; ++i){
-
- x_d = p[0] - (body_x_origin + i * x_sampling_ + half_x_sampling_);
-
- for(int j = 0; j < body_y_extent; ++j){
-
- y_d = p[1] - (body_y_origin + j * y_sampling_ + half_y_sampling_);
-
- for(int k = 0; k < body_z_extent; ++k){
-
- z_d = p[2] - (body_z_origin + k * z_sampling_ + half_z_sampling_);
-
- dd = x_d * x_d + y_d * y_d + z_d * z_d;
-
- e_term = std::exp(Real(-0.5) * dd * square_one_s_);
- density = density_values_[current_idx];
- p_dx[p_idx] += (density * (x_d * one_s_) * e_term);
- p_dy[p_idx] += (density * (y_d * one_s_) * e_term);
- p_dz[p_idx] += (density * (z_d * one_s_) * e_term);
- p_density = p_m[p_idx] * one_sqrt_2_pi_s_ * e_term;
- body_values_[current_idx] += p_density;
- ++current_idx;
-
- }
- }
- }
- }
-
- nominator = 0.0;
- denominator = 0.0;
- temp_one = 0.0;
- temp_two = 0.0;
-
- for(int i = 0; i < num_voxels; ++i){
- a = density_values_[i];
- b = body_values_[i];
- nominator += (a * b);
- temp_one += (a * a);
- temp_two += (b * b);
- }
-
- if(temp_one == 0.0 || temp_two == 0.0) continue;
-
- denominator = std::sqrt(temp_one * temp_two);
- prefac = scaling_ / denominator * one_sqrt_2_pi_s_;
-
- body_dx = 0.0;
- body_dy = 0.0;
- body_dz = 0.0;
-
- for(int p_idx = 0; p_idx < body_size; ++p_idx){
- body_dx -= prefac * p_m[p_idx] * p_dx[p_idx];
- body_dy -= prefac * p_m[p_idx] * p_dy[p_idx];
- body_dz -= prefac * p_m[p_idx] * p_dz[p_idx];
- }
-
- //finally update the forces accordingly
- for(int p_idx = 0; p_idx < body_size; ++p_idx){
- force[bodies_[body_idx][p_idx]][0] += body_dx;
- force[bodies_[body_idx][p_idx]][1] += body_dy;
- force[bodies_[body_idx][p_idx]][2] += body_dz;
- }
-
- overall_energy -= (scaling_ * nominator/denominator);
- }
-
- return overall_energy;
-}
-
-void ReferenceCalcDensityForceKernel::copyParametersToContext(ContextImpl& context, const DensityForce& force) {
- //ToDo
-}
-
-}}} //ns
diff --git a/modules/mol/mm/src/openmm_plugins/density_plugin/platforms/reference/reference_density_kernels.hh b/modules/mol/mm/src/openmm_plugins/density_plugin/platforms/reference/reference_density_kernels.hh
deleted file mode 100644
index 7a06088ee572d7d91e606601d2fe9eb0b41725a2..0000000000000000000000000000000000000000
--- a/modules/mol/mm/src/openmm_plugins/density_plugin/platforms/reference/reference_density_kernels.hh
+++ /dev/null
@@ -1,164 +0,0 @@
-#ifndef REFERENCE_DENSITY_KERNELS_H_
-#define REFERENCE_DENSITY_KERNELS_H_
-
-/* -------------------------------------------------------------------------- *
- * OpenMM *
- * -------------------------------------------------------------------------- *
- * This is part of the OpenMM molecular simulation toolkit originating from *
- * Simbios, the NIH National Center for Physics-Based Simulation of *
- * Biological Structures at Stanford, funded under the NIH Roadmap for *
- * Medical Research, grant U54 GM072970. See https://simtk.org. *
- * *
- * Portions copyright (c) 2014 Stanford University and the Authors. *
- * Authors: Peter Eastman *
- * Contributors: *
- * *
- * Permission is hereby granted, free of charge, to any person obtaining a *
- * copy of this software and associated documentation files (the "Software"), *
- * to deal in the Software without restriction, including without limitation *
- * the rights to use, copy, modify, merge, publish, distribute, sublicense, *
- * and/or sell copies of the Software, and to permit persons to whom the *
- * Software is furnished to do so, subject to the following conditions: *
- * *
- * The above copyright notice and this permission notice shall be included in *
- * all copies or substantial portions of the Software. *
- * *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
- * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
- * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
- * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
- * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
- * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
- * USE OR OTHER DEALINGS IN THE SOFTWARE. *
- * -------------------------------------------------------------------------- */
-
-#include <ost/mol/mm/density_kernels.hh>
-#include <openmm/Platform.h>
-#include <vector>
-#include <set>
-#include <limits>
-
-namespace ost{ namespace mol{ namespace mm{
-
-/**
- * This kernel is invoked by DensityForce to calculate the forces acting on the system and the energy of the system.
- */
-class ReferenceCalcDensityForceKernel : public CalcDensityForceKernel {
-public:
- ReferenceCalcDensityForceKernel(std::string name, const OpenMM::Platform& platform) : CalcDensityForceKernel(name, platform), data_(NULL) {
- }
-
- ~ReferenceCalcDensityForceKernel();
-
- /**
- * Initialize the kernel.
- *
- * @param system the System this kernel will be applied to
- * @param force the DensityForce this kernel will be used for
- */
- void initialize(const OpenMM::System& system, const DensityForce& force);
- /**
- * Execute the kernel to calculate the forces and/or energy.
- *
- * @param context the context in which to execute this kernel
- * @param includeForces true if forces should be calculated
- * @param includeEnergy true if the energy should be calculated
- * @return the potential energy due to the force
- */
- double execute(OpenMM::ContextImpl& context, bool includeForces, bool includeEnergy);
- /**
- * Copy changed parameters over to a context.
- *
- * @param context the context to copy parameters to
- * @param force the DensityForce to copy the parameters from
- */
- void copyParametersToContext(OpenMM::ContextImpl& context, const DensityForce& force);
-private:
-
- inline Real GetValue(int a, int b, int c){
- return data_[a * idx_helper_one_ + b * idx_helper_two_ + c];
- }
-
- inline Real GetIntpolValue(Real x, Real y, Real z){
-
- //distances to origin
- Real dx = x - x_origin_;
- Real dy = y - y_origin_;
- Real dz = z - z_origin_;
-
- int x_bin = std::floor(dx * one_over_x_sampling_);
- int y_bin = std::floor(dy * one_over_y_sampling_);
- int z_bin = std::floor(dz * one_over_z_sampling_);
-
- if(x_bin < 0 || x_bin >= (x_extent_-1) ||
- y_bin < 0 || y_bin >= (y_extent_-1) ||
- z_bin < 0 || z_bin >= (z_extent_-1)) return 0.0;
-
- //distances in fraction of bin towards base bin
- dx = (dx - x_bin * x_sampling_) * one_over_x_sampling_;
- dy = (dy - y_bin * y_sampling_) * one_over_y_sampling_;
- dz = (dz - z_bin * z_sampling_) * one_over_z_sampling_;
-
- intpol_values_[0] = this->GetValue(x_bin,y_bin,z_bin);
- intpol_values_[1] = this->GetValue(x_bin+1,y_bin,z_bin);
- intpol_values_[2] = this->GetValue(x_bin,y_bin+1,z_bin);
- intpol_values_[3] = this->GetValue(x_bin+1,y_bin+1,z_bin);
- intpol_values_[4] = this->GetValue(x_bin,y_bin,z_bin+1);
- intpol_values_[5] = this->GetValue(x_bin+1,y_bin,z_bin+1);
- intpol_values_[6] = this->GetValue(x_bin,y_bin+1,z_bin+1);
- intpol_values_[7] = this->GetValue(x_bin+1,y_bin+1,z_bin+1);
-
- //do first bilinear interpolation
- Real f11 = (1.0 - dx) * intpol_values_[0] + dx * intpol_values_[1];
- Real f12 = (1.0 - dx) * intpol_values_[2] + dx * intpol_values_[3];
- Real f21 = (1.0 - dx) * intpol_values_[4] + dx * intpol_values_[5];
- Real f22 = (1.0 - dx) * intpol_values_[6] + dx * intpol_values_[7];
-
- Real f1 = (1.0 - dy) * f11 + dy * f12;
- Real f2 = (1.0 - dy) * f21 + dy * f22;
-
- return (1.0 - dz) * f1 + dz * f2;
- }
-
- //this stuff is required to store and extract the internal density values
- Real* data_;
- Real intpol_values_[8];
- int idx_helper_one_;
- int idx_helper_two_;
- Real x_sampling_;
- Real y_sampling_;
- Real z_sampling_;
- Real one_over_x_sampling_;
- Real one_over_y_sampling_;
- Real one_over_z_sampling_;
- Real half_x_sampling_;
- Real half_y_sampling_;
- Real half_z_sampling_;
- Real x_origin_;
- Real y_origin_;
- Real z_origin_;
- int x_extent_;
- int y_extent_;
- int z_extent_;
-
- //this is stuff used in the actual force calculation
- Real resolution_;
- Real s_;
- Real one_s_;
- Real square_one_s_;
- Real one_sqrt_2_pi_s_;
- Real padding_dist_;
- Real scaling_;
- std::vector<Real> density_values_;
- std::vector<Real> body_values_;
-
- //this is stuff containing information of the simulated system
- int num_bodies_;
- int num_particles_;
- std::vector<float> particle_masses_;
- std::vector<std::vector<int> > bodies_;
-};
-
-}}} // ns
-
-#endif /*REFERENCE_DENSITY_KERNELS_H_*/
diff --git a/modules/mol/mm/src/system_creator.cc b/modules/mol/mm/src/system_creator.cc
index aa365ee2926740ee5d99c853da708ebcfe254722..7d51c905eb8d2d7f019c121b35c435dc217ead11 100644
--- a/modules/mol/mm/src/system_creator.cc
+++ b/modules/mol/mm/src/system_creator.cc
@@ -18,7 +18,6 @@
//------------------------------------------------------------------------------
#include <ost/mol/mm/system_creator.hh>
-#include <ost/mol/mm/density_force.hh>
#include <OpenMM.h>
namespace ost{ namespace mol{ namespace mm{
@@ -443,26 +442,6 @@ SystemPtr SystemCreator::Create(const TopologyPtr top,
sys->addForce(&barostat);
}
- //add density if valid
- ost::img::ImageHandle density = top->GetDensity();
- if(density.IsValid()){
- Real r = top->GetDensityResolution();
- Real s = top->GetDensityScaling();
- DensityForce* density_force_ptr = new DensityForce(density,r,s);
- for(std::vector<Real>::iterator i = masses.begin();
- i != masses.end(); ++i){
- density_force_ptr->addParticle(*i);
- }
- const std::vector<std::vector<int> >& density_bodies = top->GetDensityBodies();
- for(std::vector<std::vector<int> >::const_iterator i = density_bodies.begin();
- i != density_bodies.end(); ++i){
- density_force_ptr->defineBody(*i);
- }
- sys->addForce(density_force_ptr);
- }
-
-
-
return sys;
}
}}} //ns
diff --git a/modules/mol/mm/src/topology.cc b/modules/mol/mm/src/topology.cc
index 58a72827d7d5f81dd3b8013a88223fafc352eb9c..d9810ce34ff1eef869b206658a54be8e9abf530f 100644
--- a/modules/mol/mm/src/topology.cc
+++ b/modules/mol/mm/src/topology.cc
@@ -255,41 +255,6 @@ void Topology::AddPositionConstraint(uint index){
position_constraints_.push_back(index);
}
-void Topology::SetDensity(const ost::img::ImageHandle& d, Real r, Real s){
- density_ = d;
- density_resolution_ = r;
- density_scaling_ = s;
- in_density_body_.assign(num_particles_,false);
- density_bodies_.clear();
-}
-
-void Topology::DefineDensityBody(const std::vector<int>& indices){
-
- if(!density_.IsValid()){
- throw ost::Error("Must set valid density before you can define density bodies");
- }
-
- //first check, whether any of the indices is invalid or already part of a body
- for(std::vector<int>::const_iterator i = indices.begin();
- i != indices.end(); ++i){
- if(*i >= static_cast<int>(num_particles_) || *i < 0){
- throw ost::Error("Invalid index provided!");
- }
- if(in_density_body_[*i]){
- throw ost::Error("Particle can be part of only one body!");
- }
- }
-
- //let's change the state of the according particles
- for(std::vector<int>::const_iterator i = indices.begin();
- i != indices.end(); ++i){
- in_density_body_[*i] = true;
- }
-
- //and finally define the body
- density_bodies_.push_back(indices);
-}
-
uint Topology::AddHarmonicPositionRestraint(uint ind, const geom::Vec3& ref_position, Real k,
Real x_scale, Real y_scale, Real z_scale){
if(ind >= num_particles_){
diff --git a/modules/mol/mm/src/topology.hh b/modules/mol/mm/src/topology.hh
index 486accf1eb55c6ba1fe0db5fea040a445d6bb182..501d4e90102622cde79e8ef07828bd2a297cc8ac 100644
--- a/modules/mol/mm/src/topology.hh
+++ b/modules/mol/mm/src/topology.hh
@@ -128,12 +128,6 @@ public:
void AddPositionConstraint(uint index);
- void SetDensity(const ost::img::ImageHandle& d, Real r, Real s = 1.0);
-
- void DefineDensityBody(const std::vector<int>& indices);
-
- int GetNumDensityBodies() const { return density_bodies_.size(); }
-
void ResetPositionConstraints() { position_constraints_.clear(); }
void ResetExclusions() { exclusions_.clear(); }
@@ -219,12 +213,6 @@ public:
void GetFGMDHBondAcceptorParameters(uint index, uint& index_one, uint& index_two) const;
- ost::img::ImageHandle GetDensity() { return density_; }
-
- Real GetDensityResolution() { return density_resolution_; }
-
- Real GetDensityScaling() { return density_scaling_; }
-
void SetHarmonicBondParameters(uint index, const Real bond_length, const Real force_constant);
void SetHarmonicAngleParameters(uint index, const Real angle, const Real force_constant);
@@ -285,8 +273,6 @@ public:
const std::vector<Index<2> >& GetFGMDHBondAcceptors() const { return fgmd_hbond_acceptors_; }
- const std::vector<std::vector<int> >& GetDensityBodies() const { return density_bodies_; }
-
std::vector<Real> GetSigmas() const { return sigmas_; }
@@ -811,13 +797,6 @@ private:
std::set<Index<2> > added_lj_pairs_;
std::set<Index<2> > added_distance_constraints_;
std::set<Index<2> > added_exclusions_;
-
- //density map
- ost::img::ImageHandle density_;
- Real density_resolution_;
- Real density_scaling_;
- std::vector<std::vector<int> > density_bodies_;
- std::vector<bool> in_density_body_;
};