Merge branch 'master' into qc

openmmapi/include/openmm/internal/AssertionUtilities.h

@@ -50,6 +50,8 @@ void OPENMM_EXPORT throwException(const char* file, int line, const std::string&
 
 #define ASSERT_EQUAL(expected, found) {if (!((expected) == (found))) {std::stringstream details; details << "Expected "<<(expected)<<", found "<<(found); throwException(__FILE__, __LINE__, details.str());}};
 
+#define ASSERT_EQUAL_CONTAINERS(expected, found) {if (!((expected) == (found))) {std::stringstream details; details << "Containers not equal"; throwException(__FILE__, __LINE__, details.str());}};
+ 
 #define ASSERT_EQUAL_TOL(expected, found, tol) {double _scale_ = std::abs(expected) > 1.0 ? std::abs(expected) : 1.0; if (!(std::abs((expected)-(found))/_scale_ <= (tol))) {std::stringstream details; details << "Expected "<<(expected)<<", found "<<(found); throwException(__FILE__, __LINE__, details.str());}};
 
 #define ASSERT_EQUAL_VEC(expected, found, tol) {double _norm_ = std::sqrt((expected).dot(expected)); double _scale_ = _norm_ > 1.0 ? _norm_ : 1.0; if ((std::abs(((expected)[0])-((found)[0]))/_scale_ > (tol)) || (std::abs(((expected)[1])-((found)[1]))/_scale_ > (tol)) || (std::abs(((expected)[2])-((found)[2]))/_scale_ > (tol))) {std::stringstream details; details << " Expected "<<(expected)<<", found "<<(found); throwException(__FILE__, __LINE__, details.str());}};

openmmapi/include/openmm/internal/MSVC_erfc.h

@@ -9,7 +9,9 @@
  */
 
 #if defined(_MSC_VER) 
+#ifndef M_PI
 #define M_PI 3.14159265358979323846264338327950288
+#endif
 
 #if _MSC_VER <= 1700 // 1700 is VC11, 1800 is VC12 
 /***************************

openmmapi/src/Context.cpp

@@ -278,3 +278,7 @@ void Context::loadCheckpoint(istream& stream) {
 ContextImpl& Context::getImpl() {
     return *impl;
 }
+
+const vector<vector<int> >& Context::getMolecules() const {
+    return impl->getMolecules();
+}

openmmapi/src/ContextImpl.cpp

@@ -44,9 +44,12 @@
 #include <map>
 #include <utility>
 #include <vector>
+#include <string.h>
 
 using namespace OpenMM;
 using namespace std;
+const static char CHECKPOINT_MAGIC_BYTES[] = "OpenMM Binary Checkpoint\n";
+
 
 ContextImpl::ContextImpl(Context& owner, const System& system, Integrator& integrator, Platform* platform, const map<string, string>& properties) :
         owner(owner), system(system), integrator(integrator), hasInitializedForces(false), hasSetPositions(false), integratorIsDeleted(false),
@@ -398,6 +401,7 @@ static string readString(istream& stream) {
 }
 
 void ContextImpl::createCheckpoint(ostream& stream) {
+    stream.write(CHECKPOINT_MAGIC_BYTES, sizeof(CHECKPOINT_MAGIC_BYTES)/sizeof(CHECKPOINT_MAGIC_BYTES[0]));
     writeString(stream, getPlatform().getName());
     int numParticles = getSystem().getNumParticles();
     stream.write((char*) &numParticles, sizeof(int));
@@ -412,6 +416,12 @@ void ContextImpl::createCheckpoint(ostream& stream) {
 }
 
 void ContextImpl::loadCheckpoint(istream& stream) {
+    static const int magiclength = sizeof(CHECKPOINT_MAGIC_BYTES)/sizeof(CHECKPOINT_MAGIC_BYTES[0]);
+    char magicbytes[magiclength];
+    stream.read(magicbytes, magiclength);
+    if (memcmp(magicbytes, CHECKPOINT_MAGIC_BYTES, magiclength) != 0)
+        throw OpenMMException("loadCheckpoint: Checkpoint header was not correct");
+
     string platformName = readString(stream);
     if (platformName != getPlatform().getName())
         throw OpenMMException("loadCheckpoint: Checkpoint was created with a different Platform: "+platformName);

openmmapi/src/CustomNonbondedForceImpl.cpp

@@ -43,6 +43,7 @@
 #include <cmath>
 #include <sstream>
 #include <utility>
+#include <algorithm>
 
 using namespace OpenMM;
 using namespace std;

openmmapi/src/MonteCarloAnisotropicBarostatImpl.cpp

@@ -35,6 +35,7 @@
 #include "openmm/kernels.h"
 #include <cmath>
 #include <vector>
+#include <algorithm>
 
 using namespace OpenMM;
 using namespace OpenMM_SFMT;

openmmapi/src/MonteCarloBarostatImpl.cpp

@@ -35,6 +35,7 @@
 #include "openmm/kernels.h"
 #include <cmath>
 #include <vector>
+#include <algorithm>
 
 using namespace OpenMM;
 using namespace OpenMM_SFMT;

openmmapi/src/NonbondedForceImpl.cpp

@@ -39,6 +39,7 @@
 #include <cmath>
 #include <map>
 #include <sstream>
+#include <algorithm>
 
 using namespace OpenMM;
 using namespace std;