Add helper code to set Drude temperatures, clean up common functionality

plugins/drude/openmmapi/include/openmm/DrudeIntegrator.h

@@ -120,10 +120,6 @@ protected:
      * cleanup.  It will also get called again if the application calls reinitialize() on the Context.
      */
     virtual void cleanup() override {};
-    /**
-     * When the user modifies the state, we need to mark that the forces need to be recalculated.
-     */
-    virtual void stateChanged(State::DataType changed) override {};
     /**
      * Get the names of all Kernels used by this Integrator.
      */

plugins/drude/openmmapi/include/openmm/DrudeLangevinIntegrator.h

@@ -32,7 +32,7 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
-#include "openmm/Integrator.h"
+#include "openmm/DrudeIntegrator.h"
 #include "openmm/Kernel.h"
 #include "openmm/internal/windowsExportDrude.h"
 
@@ -53,7 +53,7 @@ namespace OpenMM {
  * particles.
  */
 
-class OPENMM_EXPORT_DRUDE DrudeLangevinIntegrator : public Integrator {
+class OPENMM_EXPORT_DRUDE DrudeLangevinIntegrator : public DrudeIntegrator {
 public:
     /**
      * Create a DrudeLangevinIntegrator.
@@ -99,22 +99,6 @@ public:
     void setFriction(double coeff) {
         friction = coeff;
     }
-    /**
-     * Get the temperature of the heat bath applied to internal coordinates of Drude particles (in Kelvin).
-     *
-     * @return the temperature of the heat bath, measured in Kelvin
-     */
-    double getDrudeTemperature() const {
-        return drudeTemperature;
-    }
-    /**
-     * Set the temperature of the heat bath applied to internal coordinates of Drude particles (in Kelvin).
-     *
-     * @param temp    the temperature of the heat bath, measured in Kelvin
-     */
-    void setDrudeTemperature(double temp) {
-        drudeTemperature = temp;
-    }
     /**
      * Get the friction coefficient which determines how strongly the internal coordinates of Drude particles
      * are coupled to the heat bath (in inverse ps).
@@ -133,79 +117,34 @@ public:
     void setDrudeFriction(double coeff) {
         drudeFriction = coeff;
     }
-    /**
-     * Get the maximum distance a Drude particle can ever move from its parent particle, measured in nm.  This is implemented
-     * with a hard wall constraint.  If this distance is set to 0 (the default), the hard wall constraint is omitted.
-     */
-    double getMaxDrudeDistance() const;
-    /**
-     * Set the maximum distance a Drude particle can ever move from its parent particle, measured in nm.  This is implemented
-     * with a hard wall constraint.  If this distance is set to 0 (the default), the hard wall constraint is omitted.
-     */
-    void setMaxDrudeDistance(double distance);
-    /**
-     * Get the random number seed.  See setRandomNumberSeed() for details.
-     */
-    int getRandomNumberSeed() const {
-        return randomNumberSeed;
-    }
-    /**
-     * Set the random number seed.  The precise meaning of this parameter is undefined, and is left up
-     * to each Platform to interpret in an appropriate way.  It is guaranteed that if two simulations
-     * are run with different random number seeds, the sequence of random forces will be different.  On
-     * the other hand, no guarantees are made about the behavior of simulations that use the same seed.
-     * In particular, Platforms are permitted to use non-deterministic algorithms which produce different
-     * results on successive runs, even if those runs were initialized identically.
-     *
-     * If seed is set to 0 (which is the default value assigned), a unique seed is chosen when a Context
-     * is created from this Force. This is done to ensure that each Context receives unique random seeds
-     * without you needing to set them explicitly.
-     */
-    void setRandomNumberSeed(int seed) {
-        randomNumberSeed = seed;
-    }
     /**
      * Advance a simulation through time by taking a series of time steps.
      *
      * @param steps   the number of time steps to take
      */
-    void step(int steps);
+    void step(int steps) override;
 protected:
     /**
      * This will be called by the Context when it is created.  It informs the Integrator
      * of what context it will be integrating, and gives it a chance to do any necessary initialization.
      * It will also get called again if the application calls reinitialize() on the Context.
      */
-    void initialize(ContextImpl& context);
+    void initialize(ContextImpl& context) override;
     /**
      * This will be called by the Context when it is destroyed to let the Integrator do any necessary
      * cleanup.  It will also get called again if the application calls reinitialize() on the Context.
      */
-    void cleanup();
-    /**
-     * When the user modifies the state, we need to mark that the forces need to be recalculated.
-     */
-    void stateChanged(State::DataType changed);
+    void cleanup() override;
     /**
      * Get the names of all Kernels used by this Integrator.
      */
-    std::vector<std::string> getKernelNames();
+    std::vector<std::string> getKernelNames() override;
     /**
      * Compute the kinetic energy of the system at the current time.
      */
-    double computeKineticEnergy();
-    /**
-     * Return a list of velocities normally distributed around a target temperature, correctly
-     * handling center of mass velocities for the Drude pairs.
-     *
-     * @param system the system whose velocities are to be initialized.
-     * @param temperature the target temperature in Kelvin.
-     * @param randomSeed the random number seed to use when selecting velocities 
-     */
-    virtual std::vector<Vec3> getVelocitiesForTemperature(const System &system, double temperature, int randomSeed) const override;
+    double computeKineticEnergy() override;
 private:
-    double temperature, friction, drudeTemperature, drudeFriction, maxDrudeDistance;
-    int randomNumberSeed;
+    double temperature, friction, drudeFriction;
     Kernel kernel;
 };
 

plugins/drude/openmmapi/include/openmm/DrudeNoseHooverIntegrator.h

@@ -93,6 +93,18 @@ public:
      * Compute the kinetic energy of all (real and drude) particles at the current time.
      */
     double computeTotalKineticEnergy();
+    /**
+     * Return a list of velocities normally distributed around a target temperature, with the Drude
+     * temperatures assigned according to the Drude temperature assigned to the integrator.
+     *
+     * @param system the system whose velocities are to be initialized.
+     * @param temperature the target temperature in Kelvin.
+     * @param randomSeed the random number seed to use when selecting velocities 
+     */
+    virtual std::vector<Vec3> getVelocitiesForTemperature(const System &system, double temperature,
+                                                          int randomSeed) const override;
+protected:
+    double drudeTemperature;
 };
 
 } // namespace OpenMM

plugins/drude/openmmapi/include/openmm/DrudeSCFIntegrator.h

@@ -32,7 +32,7 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
-#include "openmm/Integrator.h"
+#include "openmm/DrudeIntegrator.h"
 #include "openmm/Kernel.h"
 #include "openmm/internal/windowsExportDrude.h"
 
@@ -47,7 +47,7 @@ namespace OpenMM {
  * particles.
  */
 
-class OPENMM_EXPORT_DRUDE DrudeSCFIntegrator : public Integrator {
+class OPENMM_EXPORT_DRUDE DrudeSCFIntegrator : public DrudeIntegrator {
 public:
     /**
      * Create a DrudeSCFIntegrator.
@@ -78,31 +78,27 @@ public:
      *
      * @param steps   the number of time steps to take
      */
-    void step(int steps);
+    void step(int steps) override;
 protected:
     /**
      * This will be called by the Context when it is created.  It informs the Integrator
      * of what context it will be integrating, and gives it a chance to do any necessary initialization.
      * It will also get called again if the application calls reinitialize() on the Context.
      */
-    void initialize(ContextImpl& context);
+    void initialize(ContextImpl& context) override;
     /**
      * This will be called by the Context when it is destroyed to let the Integrator do any necessary
      * cleanup.  It will also get called again if the application calls reinitialize() on the Context.
      */
-    void cleanup();
-    /**
-     * When the user modifies the state, we need to mark that the forces need to be recalculated.
-     */
-    void stateChanged(State::DataType changed);
+    void cleanup() override;
     /**
      * Get the names of all Kernels used by this Integrator.
      */
-    std::vector<std::string> getKernelNames();
+    std::vector<std::string> getKernelNames() override;
     /**
      * Compute the kinetic energy of the system at the current time.
      */
-    double computeKineticEnergy();
+    double computeKineticEnergy() override;
 private:
     double tolerance;
     Kernel kernel;

plugins/drude/openmmapi/src/DrudeHelpers.cpp

+/* -------------------------------------------------------------------------- *
+ *                                   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) 2008-2015 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 "sfmt/SFMT.h"
+#include "SimTKOpenMMRealType.h"
+#include "openmm/DrudeForce.h"
+#include "openmm/DrudeLangevinIntegrator.h"
+#include "openmm/Context.h"
+#include "openmm/System.h"
+#include "openmm/OpenMMException.h"
+
+#include <set>
+
+namespace OpenMM {
+
+std::vector<Vec3> assignDrudeVelocities(const System &system, double temperature, double drudeTemperature, int randomSeed) {
+    // Find the underlying Drude force object
+    const DrudeForce* drudeForce = NULL;
+    for (int i = 0; i < system.getNumForces(); i++)
+        if (dynamic_cast<const DrudeForce*>(&system.getForce(i)) != NULL) {
+            if (drudeForce == NULL)
+                drudeForce = dynamic_cast<const DrudeForce*>(&system.getForce(i));
+            else
+                throw OpenMMException("The System contains multiple DrudeForces");
+        }
+    if (drudeForce == NULL)
+        throw OpenMMException("The System does not contain a DrudeForce");
+
+    // Figure out which particles are individual and which are Drude pairs
+    std::set<int> particles;
+    std::vector<std::pair<int, int>> pairParticles;
+    for (int i = 0; i < system.getNumParticles(); i++) {
+        particles.insert(i);
+    }
+    for (int i = 0; i < drudeForce->getNumParticles(); i++) {
+        int p, p1, p2, p3, p4;
+        double charge, polarizability, aniso12, aniso34;
+        drudeForce->getParticleParameters(i, p, p1, p2, p3, p4, charge, polarizability, aniso12, aniso34);
+        particles.erase(p);
+        particles.erase(p1);
+        pairParticles.emplace_back(p, p1);
+    }
+    std::vector<int> normalParticles(particles.begin(), particles.end());
+
+    // Generate the list of Gaussian random numbers.
+    OpenMM_SFMT::SFMT sfmt;
+    init_gen_rand(randomSeed, sfmt);
+    std::vector<double> randoms;
+    while (randoms.size() < system.getNumParticles()*3) {
+        double x, y, r2;
+        do {
+            x = 2.0*genrand_real2(sfmt)-1.0;
+            y = 2.0*genrand_real2(sfmt)-1.0;
+            r2 = x*x + y*y;
+        } while (r2 >= 1.0 || r2 == 0.0);
+        double multiplier = sqrt((-2.0*std::log(r2))/r2);
+        randoms.push_back(x*multiplier);
+        randoms.push_back(y*multiplier);
+    }
+
+    // Assign the velocities.
+    std::vector<Vec3> velocities(system.getNumParticles(), Vec3());
+    int nextRandom = 0;
+    // First the indivitual atoms
+    for (const auto &atom : normalParticles ) {
+        double mass = system.getParticleMass(atom);
+        if (mass != 0) {
+            double velocityScale = sqrt(BOLTZ*temperature/mass);
+            velocities[atom] = Vec3(randoms[nextRandom++], randoms[nextRandom++], randoms[nextRandom++])*velocityScale;
+        }
+    }
+    // Now the particle-Drude pairs
+    for (const auto &pair : pairParticles ) {
+        const auto atom1 = pair.first;
+        const auto atom2 = pair.second;
+        double mass1 = system.getParticleMass(atom1);
+        double mass2 = system.getParticleMass(atom2);
+        if (mass1 != 0 && mass2 != 0) {
+            double invMass = 1.0 / (mass1 + mass2);
+            double redMass = mass1 * mass2 * invMass;
+            double fracM1 = mass1 * invMass;
+            double fracM2 = mass2 * invMass;
+            Vec3 comVelocity = Vec3(randoms[nextRandom++], randoms[nextRandom++], randoms[nextRandom++])*sqrt(BOLTZ*temperature*invMass);
+            Vec3 relVelocity = Vec3(randoms[nextRandom++], randoms[nextRandom++], randoms[nextRandom++])*sqrt(BOLTZ*drudeTemperature/redMass);
+            velocities[atom1] = comVelocity - fracM2 * relVelocity;
+            velocities[atom2] = comVelocity + fracM1 * relVelocity;
+        }
+    }
+    return velocities;
+}
+
+}

plugins/drude/openmmapi/src/DrudeIntegrator.cpp

@@ -29,7 +29,6 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
-#include "sfmt/SFMT.h"
 #include "SimTKOpenMMRealType.h"
 #include "openmm/DrudeForce.h"
 #include "openmm/DrudeIntegrator.h"
@@ -40,80 +39,12 @@
 
 using namespace OpenMM;
 
-std::vector<Vec3> DrudeIntegrator::getVelocitiesForTemperature(const System &system, double temperature, int randomSeedIn) const {
-    // Find the underlying Drude force object
-    const DrudeForce* drudeForce = NULL;
-    for (int i = 0; i < system.getNumForces(); i++)
-        if (dynamic_cast<const DrudeForce*>(&system.getForce(i)) != NULL) {
-            if (drudeForce == NULL)
-                drudeForce = dynamic_cast<const DrudeForce*>(&system.getForce(i));
-            else
-                throw OpenMMException("The System contains multiple DrudeForces");
-        }
-    if (drudeForce == NULL)
-        throw OpenMMException("The System does not contain a DrudeForce");
-
-    // Figure out which particles are individual and which are Drude pairs
-    std::set<int> particles;
-    std::vector<std::pair<int, int>> pairParticles;
-    for (int i = 0; i < system.getNumParticles(); i++) {
-        particles.insert(i);
-    }
-    for (int i = 0; i < drudeForce->getNumParticles(); i++) {
-        int p, p1, p2, p3, p4;
-        double charge, polarizability, aniso12, aniso34;
-        drudeForce->getParticleParameters(i, p, p1, p2, p3, p4, charge, polarizability, aniso12, aniso34);
-        particles.erase(p);
-        particles.erase(p1);
-        pairParticles.emplace_back(p, p1);
-    }
-    std::vector<int> normalParticles(particles.begin(), particles.end());
-
-    // Generate the list of Gaussian random numbers.
-    OpenMM_SFMT::SFMT sfmt;
-    init_gen_rand(randomSeedIn, sfmt);
-    std::vector<double> randoms;
-    while (randoms.size() < system.getNumParticles()*3) {
-        double x, y, r2;
-        do {
-            x = 2.0*genrand_real2(sfmt)-1.0;
-            y = 2.0*genrand_real2(sfmt)-1.0;
-            r2 = x*x + y*y;
-        } while (r2 >= 1.0 || r2 == 0.0);
-        double multiplier = sqrt((-2.0*std::log(r2))/r2);
-        randoms.push_back(x*multiplier);
-        randoms.push_back(y*multiplier);
-    }
+namespace OpenMM {
+    extern std::vector<Vec3> assignDrudeVelocities(const System &system, double temperature, double drudeTemperature, int randomSeed);
+}
 
-    // Assign the velocities.
-    std::vector<Vec3> velocities(system.getNumParticles(), Vec3());
-    int nextRandom = 0;
-    // First the indivitual atoms
-    for (const auto &atom : normalParticles ) {
-        double mass = system.getParticleMass(atom);
-        if (mass != 0) {
-            double velocityScale = sqrt(BOLTZ*temperature/mass);
-            velocities[atom] = Vec3(randoms[nextRandom++], randoms[nextRandom++], randoms[nextRandom++])*velocityScale;
-        }
-    }
-    // Now the particle-Drude pairs
-    for (const auto &pair : pairParticles ) {
-        const auto atom1 = pair.first;
-        const auto atom2 = pair.second;
-        double mass1 = system.getParticleMass(atom1);
-        double mass2 = system.getParticleMass(atom2);
-        if (mass1 != 0 && mass2 != 0) {
-            double invMass = 1.0 / (mass1 + mass2);
-            double redMass = mass1 * mass2 * invMass;
-            double fracM1 = mass1 * invMass;
-            double fracM2 = mass2 * invMass;
-            Vec3 comVelocity = Vec3(randoms[nextRandom++], randoms[nextRandom++], randoms[nextRandom++])*sqrt(BOLTZ*temperature*invMass);
-            Vec3 relVelocity = Vec3(randoms[nextRandom++], randoms[nextRandom++], randoms[nextRandom++])*sqrt(BOLTZ*drudeTemperature/redMass);
-            velocities[atom1] = comVelocity - fracM2 * relVelocity;
-            velocities[atom2] = comVelocity + fracM1 * relVelocity;
-        }
-    }
-    return velocities;
+std::vector<Vec3> DrudeIntegrator::getVelocitiesForTemperature(const System &system, double temperature, int randomSeedIn) const {
+    return assignDrudeVelocities(system, temperature, drudeTemperature, randomSeedIn);
 }
 
 double DrudeIntegrator::getMaxDrudeDistance() const {

plugins/drude/openmmapi/src/DrudeLangevinIntegrator.cpp

@@ -29,8 +29,6 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
-#include "sfmt/SFMT.h"
-#include "SimTKOpenMMRealType.h"
 #include "openmm/DrudeLangevinIntegrator.h"
 #include "openmm/Context.h"
 #include "openmm/OpenMMException.h"
@@ -45,7 +43,7 @@ using namespace OpenMM;
 using std::string;
 using std::vector;
 
-DrudeLangevinIntegrator::DrudeLangevinIntegrator(double temperature, double frictionCoeff, double drudeTemperature, double drudeFrictionCoeff, double stepSize) {
+DrudeLangevinIntegrator::DrudeLangevinIntegrator(double temperature, double frictionCoeff, double drudeTemperature, double drudeFrictionCoeff, double stepSize) : DrudeIntegrator(stepSize) {
     setTemperature(temperature);
     setFriction(frictionCoeff);
     setDrudeTemperature(drudeTemperature);
@@ -56,16 +54,6 @@ DrudeLangevinIntegrator::DrudeLangevinIntegrator(double temperature, double fric
     setRandomNumberSeed(0);
 }
 
-double DrudeLangevinIntegrator::getMaxDrudeDistance() const {
-    return maxDrudeDistance;
-}
-
-void DrudeLangevinIntegrator::setMaxDrudeDistance(double distance) {
-    if (distance < 0)
-        throw OpenMMException("setMaxDrudeDistance: Distance cannot be negative");
-    maxDrudeDistance = distance;
-}
-
 void DrudeLangevinIntegrator::initialize(ContextImpl& contextRef) {
     if (owner != NULL && &contextRef.getOwner() != owner)
         throw OpenMMException("This Integrator is already bound to a context");
@@ -90,9 +78,6 @@ void DrudeLangevinIntegrator::cleanup() {
     kernel = Kernel();
 }
 
-void DrudeLangevinIntegrator::stateChanged(State::DataType changed) {
-}
-
 vector<string> DrudeLangevinIntegrator::getKernelNames() {
     std::vector<std::string> names;
     names.push_back(IntegrateDrudeLangevinStepKernel::Name());
@@ -103,82 +88,6 @@ double DrudeLangevinIntegrator::computeKineticEnergy() {
     return kernel.getAs<IntegrateDrudeLangevinStepKernel>().computeKineticEnergy(*context, *this);
 }
 
-std::vector<Vec3> DrudeLangevinIntegrator::getVelocitiesForTemperature(const System &system, double temperature, int randomSeed) const {
-    // Find the underlying Drude force object
-    const DrudeForce* drudeForce = NULL;
-    for (int i = 0; i < system.getNumForces(); i++)
-        if (dynamic_cast<const DrudeForce*>(&system.getForce(i)) != NULL) {
-            if (drudeForce == NULL)
-                drudeForce = dynamic_cast<const DrudeForce*>(&system.getForce(i));
-            else
-                throw OpenMMException("The System contains multiple DrudeForces");
-        }
-    if (drudeForce == NULL)
-        throw OpenMMException("The System does not contain a DrudeForce");
-
-    // Figure out which particles are individual and which are Drude pairs
-    std::set<int> particles;
-    std::vector<std::pair<int, int>> pairParticles;
-    for (int i = 0; i < system.getNumParticles(); i++) {
-        particles.insert(i);
-    }
-    for (int i = 0; i < drudeForce->getNumParticles(); i++) {
-        int p, p1, p2, p3, p4;
-        double charge, polarizability, aniso12, aniso34;
-        drudeForce->getParticleParameters(i, p, p1, p2, p3, p4, charge, polarizability, aniso12, aniso34);
-        particles.erase(p);
-        particles.erase(p1);
-        pairParticles.emplace_back(p, p1);
-    }
-    std::vector<int> normalParticles(particles.begin(), particles.end());
-
-    // Generate the list of Gaussian random numbers.
-    OpenMM_SFMT::SFMT sfmt;
-    init_gen_rand(randomSeed, sfmt);
-    std::vector<double> randoms;
-    while (randoms.size() < system.getNumParticles()*3) {
-        double x, y, r2;
-        do {
-            x = 2.0*genrand_real2(sfmt)-1.0;
-            y = 2.0*genrand_real2(sfmt)-1.0;
-            r2 = x*x + y*y;
-        } while (r2 >= 1.0 || r2 == 0.0);
-        double multiplier = sqrt((-2.0*std::log(r2))/r2);
-        randoms.push_back(x*multiplier);
-        randoms.push_back(y*multiplier);
-    }
-
-    // Assign the velocities.
-    std::vector<Vec3> velocities(system.getNumParticles(), Vec3());
-    int nextRandom = 0;
-    // First the indivitual atoms
-    for (const auto &atom : normalParticles ) {
-        double mass = system.getParticleMass(atom);
-        if (mass != 0) {
-            double velocityScale = sqrt(BOLTZ*temperature/mass);
-            velocities[atom] = Vec3(randoms[nextRandom++], randoms[nextRandom++], randoms[nextRandom++])*velocityScale;
-        }
-    }
-    // Now the particle-Drude pairs
-    for (const auto &pair : pairParticles ) {
-        const auto atom1 = pair.first;
-        const auto atom2 = pair.second;
-        double mass1 = system.getParticleMass(atom1);
-        double mass2 = system.getParticleMass(atom2);
-        if (mass1 != 0 && mass2 != 0) {
-            double invMass = 1.0 / (mass1 + mass2);
-            double redMass = mass1 * mass2 * invMass;
-            double fracM1 = mass1 * invMass;
-            double fracM2 = mass2 * invMass;
-            Vec3 comVelocity = Vec3(randoms[nextRandom++], randoms[nextRandom++], randoms[nextRandom++])*sqrt(BOLTZ*temperature*invMass);
-            Vec3 relVelocity = Vec3(randoms[nextRandom++], randoms[nextRandom++], randoms[nextRandom++])*sqrt(BOLTZ*drudeTemperature/redMass);
-            velocities[atom1] = comVelocity - fracM2 * relVelocity;
-            velocities[atom2] = comVelocity + fracM1 * relVelocity;
-        }
-    }
-    return velocities;
-}
-
 void DrudeLangevinIntegrator::step(int steps) {
     if (context == NULL)
         throw OpenMMException("This Integrator is not bound to a context!");    

plugins/drude/openmmapi/src/DrudeNoseHooverIntegrator.cpp

@@ -46,11 +46,16 @@ using namespace OpenMM;
 using std::string;
 using std::vector;
 
+namespace OpenMM {
+    extern std::vector<Vec3> assignDrudeVelocities(const System &system, double temperature, double drudeTemperature, int randomSeed);
+}
+
 DrudeNoseHooverIntegrator::DrudeNoseHooverIntegrator(double temperature, double collisionFrequency, 
                                                      double drudeTemperature, double drudeCollisionFrequency,
                                                      double stepSize, int chainLength, int numMTS, int numYoshidaSuzuki) :
-    NoseHooverIntegrator(stepSize) {
-
+    NoseHooverIntegrator(stepSize),
+    drudeTemperature(drudeTemperature)
+{
     setMaxDrudeDistance(0);
     hasSubsystemThermostats_ = false;
     addSubsystemThermostat(std::vector<int>(), std::vector<std::pair<int, int>>(), temperature,
@@ -143,3 +148,8 @@ double DrudeNoseHooverIntegrator::computeTotalKineticEnergy() {
     return vvKernel.getAs<IntegrateVelocityVerletStepKernel>().computeKineticEnergy(*context, *this);
 }
 
+std::vector<Vec3> DrudeNoseHooverIntegrator::getVelocitiesForTemperature(const System &system, double temperature,
+                                                                         int randomSeedIn) const {
+    return assignDrudeVelocities(system, temperature, drudeTemperature, randomSeedIn);
+}
+

plugins/drude/openmmapi/src/DrudeSCFIntegrator.cpp

@@ -42,7 +42,9 @@ using namespace OpenMM;
 using std::string;
 using std::vector;
 
-DrudeSCFIntegrator::DrudeSCFIntegrator(double stepSize) {
+DrudeSCFIntegrator::DrudeSCFIntegrator(double stepSize) : DrudeIntegrator(stepSize)
+{
+    setDrudeTemperature(0.0);  // This is only used to initialize velocities for this integrator
     setStepSize(stepSize);
     setMinimizationErrorTolerance(0.1);
     setConstraintTolerance(1e-5);
@@ -72,9 +74,6 @@ void DrudeSCFIntegrator::cleanup() {
     kernel = Kernel();
 }
 
-void DrudeSCFIntegrator::stateChanged(State::DataType changed) {
-}
-
 vector<string> DrudeSCFIntegrator::getKernelNames() {
     std::vector<std::string> names;
     names.push_back(IntegrateDrudeSCFStepKernel::Name());