Merge pull request #825 from peastman/remove

Added removeForce() and removeConstraint() to System

openmmapi/include/openmm/System.h

@@ -168,6 +168,12 @@ public:
      * @param distance  the required distance between the two particles, measured in nm
      */
     void setConstraintParameters(int index, int particle1, int particle2, double distance);
+    /**
+     * Remove a constraint from the System.
+     * 
+     * @param index    the index of the constraint to remove
+     */
+    void removeConstraint(int index);
     /**
      * Add a Force to the System.  The Force should have been created on the heap with the
      * "new" operator.  The System takes over ownership of it, and deletes the Force when the
@@ -198,6 +204,13 @@ public:
      * @param index  the index of the Force to get
      */
     Force& getForce(int index);
+    /**
+     * Remove a Force from the System.  The memory associated with the removed Force
+     * object is deleted.
+     *
+     * @param index   the index of the Force to remove
+     */
+    void removeForce(int index);
     /**
      * Get the default values of the vectors defining the axes of the periodic box (measured in nm).  Any newly
      * created Context will have its box vectors set to these.  They will affect

openmmapi/src/System.cpp

@@ -61,10 +61,11 @@ void System::setParticleMass(int index, double mass) {
     masses[index] = mass;
 }
 
-
 void System::setVirtualSite(int index, VirtualSite* virtualSite) {
     if (index >= (int) virtualSites.size())
         virtualSites.resize(getNumParticles(), NULL);
+    if (virtualSites[index] != NULL)
+        delete virtualSites[index];
     virtualSites[index] = virtualSite;
 }
 
@@ -93,6 +94,11 @@ void System::setConstraintParameters(int index, int particle1, int particle2, do
     constraints[index].distance = distance;
 }
 
+void System::removeConstraint(int index) {
+    ASSERT_VALID_INDEX(index, constraints);
+    constraints.erase(constraints.begin()+index);
+}
+
 const Force& System::getForce(int index) const {
     ASSERT_VALID_INDEX(index, forces);
     return *forces[index];
@@ -103,6 +109,12 @@ Force& System::getForce(int index) {
     return *forces[index];
 }
 
+void System::removeForce(int index) {
+    ASSERT_VALID_INDEX(index, forces);
+    delete forces[index];
+    forces.erase(forces.begin()+index);
+}
+
 void System::getDefaultPeriodicBoxVectors(Vec3& a, Vec3& b, Vec3& c) const {
     a = periodicBoxVectors[0];
     b = periodicBoxVectors[1];

tests/TestSystem.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) 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 "openmm/internal/AssertionUtilities.h"
+#include "openmm/HarmonicAngleForce.h"
+#include "openmm/HarmonicBondForce.h"
+#include "openmm/System.h"
+#include "openmm/VirtualSite.h"
+#include <iostream>
+
+using namespace OpenMM;
+using namespace std;
+
+/**
+ * Test the methods for manipulating System objects.
+ */
+void testCreateSystem() {
+    int numParticles = 10;
+    System system;
+    
+    // Test adding and modifying particles.
+    
+    for (int i = 0; i < numParticles; i++)
+        system.addParticle(1.0+0.1*i);
+    system.setParticleMass(5, 100.0);
+    ASSERT_EQUAL(numParticles, system.getNumParticles());
+    for (int i = 0; i < numParticles; i++) {
+        double mass = (i == 5 ? 100.0 : 1.0+0.1*i);
+        ASSERT_EQUAL(mass, system.getParticleMass(i));
+    }
+    
+    // Test adding, removing, and modifying constraints.
+    
+    for (int i = 0; i < numParticles-1; i++)
+        system.addConstraint(i, i+1, 0.2*i);
+    system.removeConstraint(5);
+    system.setConstraintParameters(3, 0, 5, 99.0);
+    ASSERT_EQUAL(numParticles-2, system.getNumConstraints());
+    for (int i = 0; i < numParticles-2; i++) {
+        int p1, p2;
+        double dist;
+        system.getConstraintParameters(i, p1, p2, dist);
+        if (i == 3) {
+            ASSERT_EQUAL(0, p1);
+            ASSERT_EQUAL(5, p2);
+            ASSERT_EQUAL(99.0, dist);
+        }
+        else {
+            int j = (i < 5 ? i : i+1);
+            ASSERT_EQUAL(j, p1);
+            ASSERT_EQUAL(j+1, p2);
+            ASSERT_EQUAL(0.2*j, dist);
+        }
+    }
+    
+    // Test adding and removing forces.
+    
+    HarmonicBondForce* bonds = new HarmonicBondForce();
+    system.addForce(bonds);
+    HarmonicAngleForce* angles = new HarmonicAngleForce();
+    system.addForce(angles);
+    ASSERT_EQUAL(2, system.getNumForces());
+    ASSERT_EQUAL(bonds, &system.getForce(0));
+    ASSERT_EQUAL(angles, &system.getForce(1));
+    system.removeForce(0);
+    ASSERT_EQUAL(1, system.getNumForces());
+    ASSERT_EQUAL(angles, &system.getForce(0));
+    
+    // Test adding and removing virtual sites.
+    
+    for (int i = 0; i < numParticles; i++) {
+        ASSERT_EQUAL(false, system.isVirtualSite(i));
+    }
+    TwoParticleAverageSite* site = new TwoParticleAverageSite(2, 3, 0.4, 0.6);
+    system.setVirtualSite(4, site);
+    for (int i = 0; i < numParticles; i++) {
+        ASSERT_EQUAL(i == 4, system.isVirtualSite(i));
+    }
+    ASSERT_EQUAL(site, &system.getVirtualSite(4));
+    system.setVirtualSite(4, NULL);
+    for (int i = 0; i < numParticles; i++) {
+        ASSERT_EQUAL(false, system.isVirtualSite(i));
+    }
+}
+
+int main() {
+    try {
+        testCreateSystem();
+    }
+    catch(const exception& e) {
+        cout << "exception: " << e.what() << endl;
+        return 1;
+    }
+    cout << "Done" << endl;
+    return 0;
+}