Initial serialization proxies for Amoeba

plugins/amoeba/serialization/tests/TestSerializeAmoebaOutOfPlaneBendForce.cpp

+/* -------------------------------------------------------------------------- *
+ *                                OpenMMAmoeba                                *
+ * -------------------------------------------------------------------------- *
+ * 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) 2010 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 "../../../tests/AssertionUtilities.h"
+#include "openmm/AmoebaOutOfPlaneBendForce.h"
+#include "openmm/serialization/XmlSerializer.h"
+#include <iostream>
+#include <sstream>
+
+using namespace OpenMM;
+using namespace std;
+
+void testSerialization() {
+    // Create a Force.
+
+    AmoebaOutOfPlaneBendForce force;
+    force.setAmoebaGlobalOutOfPlaneBendCubic( 12.3 );
+    force.setAmoebaGlobalOutOfPlaneBendQuartic( 98.7 );
+    force.setAmoebaGlobalOutOfPlaneBendPentic( 91.7 );
+    force.setAmoebaGlobalOutOfPlaneBendSextic( 93.7 );
+    force.addOutOfPlaneBend(0, 1, 3, 4, 2.0);
+    force.addOutOfPlaneBend(0, 2, 3, 5, 2.1);
+    force.addOutOfPlaneBend(2, 3, 5, 6, 2.2);
+    force.addOutOfPlaneBend(5, 1, 8, 8, 2.3);
+
+    // Serialize and then deserialize it.
+
+    stringstream buffer;
+    XmlSerializer::serialize<AmoebaOutOfPlaneBendForce>(&force, "Force", buffer);
+    AmoebaOutOfPlaneBendForce* copy = XmlSerializer::deserialize<AmoebaOutOfPlaneBendForce>(buffer);
+
+    // Compare the two forces to see if they are identical.  
+    AmoebaOutOfPlaneBendForce& force2 = *copy;
+    ASSERT_EQUAL(force.getAmoebaGlobalOutOfPlaneBendCubic(), force2.getAmoebaGlobalOutOfPlaneBendCubic());
+    ASSERT_EQUAL(force.getAmoebaGlobalOutOfPlaneBendQuartic(), force2.getAmoebaGlobalOutOfPlaneBendQuartic());
+    ASSERT_EQUAL(force.getAmoebaGlobalOutOfPlaneBendPentic(), force2.getAmoebaGlobalOutOfPlaneBendPentic());
+    ASSERT_EQUAL(force.getAmoebaGlobalOutOfPlaneBendSextic(), force2.getAmoebaGlobalOutOfPlaneBendSextic());
+    ASSERT_EQUAL(force.getNumOutOfPlaneBends(), force2.getNumOutOfPlaneBends());
+    for (int i = 0; i < force.getNumOutOfPlaneBends(); i++) {
+        int a1, a2, a3, a4, b1, b2, b3, b4;
+        double ka, kb;
+        force.getOutOfPlaneBendParameters(i, a1, a2, a3, a4, ka);
+        force2.getOutOfPlaneBendParameters(i, b1, b2, b3, b4, kb);
+        ASSERT_EQUAL(a1, b1);
+        ASSERT_EQUAL(a2, b2);
+        ASSERT_EQUAL(a3, b3);
+        ASSERT_EQUAL(a4, b4);
+        ASSERT_EQUAL(ka, kb);
+    }
+}
+
+int main() {
+    try {
+        testSerialization();
+    }
+    catch(const exception& e) {
+        cout << "exception: " << e.what() << endl;
+        return 1;
+    }
+    cout << "Done" << endl;
+    return 0;
+}
+

plugins/amoeba/serialization/tests/TestSerializeAmoebaPiTorsionForce.cpp

+/* -------------------------------------------------------------------------- *
+ *                                OpenMMAmoeba                                *
+ * -------------------------------------------------------------------------- *
+ * 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) 2010 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 "../../../tests/AssertionUtilities.h"
+#include "openmm/AmoebaPiTorsionForce.h"
+#include "openmm/serialization/XmlSerializer.h"
+#include <iostream>
+#include <sstream>
+
+using namespace OpenMM;
+using namespace std;
+
+void testSerialization() {
+    // Create a Force.
+
+    AmoebaPiTorsionForce force;
+    force.addPiTorsion(0, 1, 3, 4, 5, 6, 2.0);
+    force.addPiTorsion(0, 2, 3, 5, 12, 13, 2.1);
+    force.addPiTorsion(2, 3, 5, 6, 81, 91, 2.2);
+    force.addPiTorsion(5, 1, 8, 8, 101, 102, 2.3);
+
+    // Serialize and then deserialize it.
+
+    stringstream buffer;
+    XmlSerializer::serialize<AmoebaPiTorsionForce>(&force, "Force", buffer);
+    AmoebaPiTorsionForce* copy = XmlSerializer::deserialize<AmoebaPiTorsionForce>(buffer);
+
+    // Compare the two forces to see if they are identical.  
+    AmoebaPiTorsionForce& force2 = *copy;
+    ASSERT_EQUAL(force.getNumPiTorsions(), force2.getNumPiTorsions());
+    for (int i = 0; i < force.getNumPiTorsions(); i++) {
+        int a1, a2, a3, a4, a5, a6, b1, b2, b3, b4, b5, b6;
+        double ka, kb;
+        force.getPiTorsionParameters( i, a1, a2, a3, a4, a5, a6, ka);
+        force2.getPiTorsionParameters(i, b1, b2, b3, b4, b5, b6, kb);
+        ASSERT_EQUAL(a1, b1);
+        ASSERT_EQUAL(a2, b2);
+        ASSERT_EQUAL(a3, b3);
+        ASSERT_EQUAL(a4, b4);
+        ASSERT_EQUAL(a5, b5);
+        ASSERT_EQUAL(a6, b6);
+        ASSERT_EQUAL(ka, kb);
+    }
+}
+
+int main() {
+    try {
+        testSerialization();
+    }
+    catch(const exception& e) {
+        cout << "exception: " << e.what() << endl;
+        return 1;
+    }
+    cout << "Done" << endl;
+    return 0;
+}
+