Merge branch 'master' of github.com:pandegroup/openmm into genpt

CMakeLists.txt

@@ -159,8 +159,8 @@ ENDIF (NOT CMAKE_CXX_FLAGS_RELEASE)
 # and make it available to the code so it can be built into the binaries.
 
 SET(OPENMM_LIBRARY_NAME OpenMM)
-SET(OPENMM_MAJOR_VERSION 6)
-SET(OPENMM_MINOR_VERSION 3)
+SET(OPENMM_MAJOR_VERSION 7)
+SET(OPENMM_MINOR_VERSION 0)
 SET(OPENMM_BUILD_VERSION 0)
 
 SET(OPENMM_COPYRIGHT_YEARS "2008-2015")
@@ -340,6 +340,7 @@ ELSE(DL_LIBRARY)
 ENDIF(DL_LIBRARY)
 
 IF(BUILD_TESTING)
+    INCLUDE_DIRECTORIES(${CMAKE_SOURCE_DIR}/tests)
     ADD_SUBDIRECTORY(platforms/reference/tests)
 ENDIF(BUILD_TESTING)
 

devtools/forcefield-scripts/processAmberForceField.py

@@ -405,8 +405,10 @@ for index, type in enumerate(types):
             sigma = (params[0]/params[1])**(1.0/6.0)
             epsilon = 4.184*params[1]*params[1]/(4*params[0])
     else:
-        sigma = 0
+        sigma = 1
         epsilon = 0
+    if sigma == 0 or epsilon == 0:
+        sigma, epsilon = 1, 0
     if q != 0 or epsilon != 0:
         print """  <Atom type="%d" charge="%s" sigma="%s" epsilon="%s"/>""" % (index, q, sigma, epsilon)
 print " </NonbondedForce>"

docs-source/usersguide/application.rst

@@ -675,11 +675,17 @@ Platforms
 
 When creating a :class:`Simulation`, you can optionally tell it what :class:`Platform` to use.
 OpenMM includes four platforms: :class:`Reference`, :class:`CPU`, :class:`CUDA`, and :class:`OpenCL`.  For a
-description of the differences between them, see Section :ref:`platforms`.  If you do not
-specify a :class:`Platform`, it will select one automatically.  Usually its choice will
-be reasonable, but you may want to change it.
+description of the differences between them, see Section :ref:`platforms`.  There are three ways in which
+the :class:`Platform` can be chosen:
 
-The following lines specify to use the :class:`CUDA` platform:
+1. By default, OpenMM will try to select the fastest available :class:`Platform`.  Usually its choice will
+be reasonable, but sometimes you may want to change it.
+
+2. Alternatively, you can set the :envvar:`OPENMM_DEFAULT_PLATFORM` environment variable to the name
+of the :class:`Platform` to use.  This overrides the default logic.
+
+3. Finally, you can explicitly specify a :class:`Platform` object in your script when you create the
+:class:`Simulation`.  The following lines specify to use the :class:`CUDA` platform:
 ::
 
     platform = Platform.getPlatformByName('CUDA')

examples/benchmark.py

@@ -52,7 +52,11 @@ def runOneTest(testName, options):
             cutoff = 2.0*unit.nanometers
             vdwCutoff = 1.2*unit.nanometers
             system = ff.createSystem(pdb.topology, nonbondedMethod=app.NoCutoff, constraints=constraints, mutualInducedTargetEpsilon=epsilon, polarization=polarization)
-        dt = 0.001*unit.picoseconds
+        for f in system.getForces():
+            if isinstance(f, mm.AmoebaMultipoleForce) or isinstance(f, mm.AmoebaVdwForce) or isinstance(f, mm.AmoebaGeneralizedKirkwoodForce) or isinstance(f, mm.AmoebaWcaDispersionForce):
+                f.setForceGroup(1)
+        dt = 0.002*unit.picoseconds
+        integ = mm.MTSIntegrator(dt, [(0,2), (1,1)])
     else:
         if explicit:
             ff = app.ForceField('amber99sb.xml', 'tip3p.xml')
@@ -77,6 +81,7 @@ def runOneTest(testName, options):
             constraints = app.HBonds
             hydrogenMass = None
         system = ff.createSystem(pdb.topology, nonbondedMethod=method, nonbondedCutoff=cutoff, constraints=constraints, hydrogenMass=hydrogenMass)
+        integ = mm.LangevinIntegrator(300*unit.kelvin, 91*(1/unit.picoseconds), dt)
     print('Step Size: %g fs' % dt.value_in_unit(unit.femtoseconds))
     properties = {}
     initialSteps = 5
@@ -95,7 +100,6 @@ def runOneTest(testName, options):
     
     # Run the simulation.
     
-    integ = mm.LangevinIntegrator(300*unit.kelvin, 91*(1/unit.picoseconds), dt)
     integ.setConstraintTolerance(1e-5)
     if len(properties) > 0:
         context = mm.Context(system, integ, platform, properties)

libraries/sfmt/src/SFMT.cpp

@@ -124,11 +124,13 @@ public:
 };
 
 void SFMT::createCheckpoint(std::ostream& stream) {
+    stream.write((char*) &data->baseData, sizeof(data->baseData));
     stream.write((char*) &data->sfmt, sizeof(data->sfmt));
     stream.write((char*) &data->idx, sizeof(data->idx));
 }
 
 void SFMT::loadCheckpoint(std::istream& stream) {
+    stream.read((char*) &data->baseData, sizeof(data->baseData));
     stream.read((char*) &data->sfmt, sizeof(data->sfmt));
     stream.read((char*) &data->idx, sizeof(data->idx));
 }

openmmapi/include/openmm/CustomAngleForce.h

@@ -171,7 +171,7 @@ public:
      * @param parameters    the list of parameters for the new angle
      * @return the index of the angle that was added
      */
-    int addAngle(int particle1, int particle2, int particle3, const std::vector<double>& parameters);
+    int addAngle(int particle1, int particle2, int particle3, const std::vector<double>& parameters=std::vector<double>());
     /**
      * Get the force field parameters for an angle term.
      *
@@ -191,7 +191,7 @@ public:
      * @param particle3     the index of the third particle connected by the angle
      * @param parameters    the list of parameters for the angle
      */
-    void setAngleParameters(int index, int particle1, int particle2, int particle3, const std::vector<double>& parameters);
+    void setAngleParameters(int index, int particle1, int particle2, int particle3, const std::vector<double>& parameters=std::vector<double>());
     /**
      * Update the per-angle parameters in a Context to match those stored in this Force object.  This method provides
      * an efficient method to update certain parameters in an existing Context without needing to reinitialize it.

openmmapi/include/openmm/CustomBondForce.h

@@ -170,7 +170,7 @@ public:
      * @param parameters    the list of parameters for the new bond
      * @return the index of the bond that was added
      */
-    int addBond(int particle1, int particle2, const std::vector<double>& parameters);
+    int addBond(int particle1, int particle2, const std::vector<double>& parameters=std::vector<double>());
     /**
      * Get the force field parameters for a bond term.
      *
@@ -188,7 +188,7 @@ public:
      * @param particle2     the index of the second particle connected by the bond
      * @param parameters    the list of parameters for the bond
      */
-    void setBondParameters(int index, int particle1, int particle2, const std::vector<double>& parameters);
+    void setBondParameters(int index, int particle1, int particle2, const std::vector<double>& parameters=std::vector<double>());
     /**
      * Update the per-bond parameters in a Context to match those stored in this Force object.  This method provides
      * an efficient method to update certain parameters in an existing Context without needing to reinitialize it.

openmmapi/include/openmm/CustomCentroidBondForce.h

@@ -237,7 +237,7 @@ public:
      *                    If this is omitted, then particle masses will be used as weights.
      * @return the index of the group that was added
      */
-    int addGroup(const std::vector<int>& particles, const std::vector<double>& weights = std::vector<double>());
+    int addGroup(const std::vector<int>& particles, const std::vector<double>& weights=std::vector<double>());
     /**
      * Get the properties of a group.
      *
@@ -256,7 +256,7 @@ public:
      * @param weights     the weight to use for each particle when computing the center position.
      *                    If this is omitted, then particle masses will be used as weights.
      */
-    void setGroupParameters(int index, const std::vector<int>& particles, const std::vector<double>& weights = std::vector<double>());
+    void setGroupParameters(int index, const std::vector<int>& particles, const std::vector<double>& weights=std::vector<double>());
     /**
      * Add a bond to the force
      *
@@ -264,7 +264,7 @@ public:
      * @param parameters  the list of per-bond parameter values for the new bond
      * @return the index of the bond that was added
      */
-    int addBond(const std::vector<int>& groups, const std::vector<double>& parameters);
+    int addBond(const std::vector<int>& groups, const std::vector<double>& parameters=std::vector<double>());
     /**
      * Get the properties of a bond.
      *
@@ -280,7 +280,7 @@ public:
      * @param groups      the indices of the groups in the bond
      * @param parameters  the list of per-bond parameter values for the bond
      */
-    void setBondParameters(int index, const std::vector<int>& groups, const std::vector<double>& parameters);
+    void setBondParameters(int index, const std::vector<int>& groups, const std::vector<double>& parameters=std::vector<double>());
     /**
      * Add a tabulated function that may appear in the energy expression.
      *

openmmapi/include/openmm/CustomCompoundBondForce.h

@@ -219,7 +219,7 @@ public:
      * @param parameters  the list of per-bond parameter values for the new bond
      * @return the index of the bond that was added
      */
-    int addBond(const std::vector<int>& particles, const std::vector<double>& parameters);
+    int addBond(const std::vector<int>& particles, const std::vector<double>& parameters=std::vector<double>());
     /**
      * Get the properties of a bond.
      *
@@ -235,7 +235,7 @@ public:
      * @param particles   the indices of the particles in the bond
      * @param parameters  the list of per-bond parameter values for the bond
      */
-    void setBondParameters(int index, const std::vector<int>& particles, const std::vector<double>& parameters);
+    void setBondParameters(int index, const std::vector<int>& particles, const std::vector<double>& parameters=std::vector<double>());
     /**
      * Add a tabulated function that may appear in the energy expression.
      *

openmmapi/include/openmm/CustomExternalForce.h

@@ -67,6 +67,14 @@ namespace OpenMM {
  * force->addPerParticleParameter("z0");
  * </pre></tt>
  *
+ * Special care is needed in systems that use periodic boundary conditions.  In that case, each particle really represents
+ * an infinite set of particles repeating through space.  The variables x, y, and z contain the coordinates of one of those
+ * periodic copies, but there is no guarantee about which.  It might even change from one time step to the next.  You can handle
+ * this situation by using the function periodicdistance(x1, y1, z1, x2, y2, z2), which returns the minimum distance between
+ * periodic copies of the points (x1, y1, z1) and (x2, y2, z2).  For example, the force given above would be rewritten as
+ *
+ * <tt>CustomExternalForce* force = new CustomExternalForce("k*periodicdistance(x, y, z, x0, y0, z0)^2");</tt>
+ *
  * Expressions may involve the operators + (add), - (subtract), * (multiply), / (divide), and ^ (power), and the following
  * functions: sqrt, exp, log, sin, cos, sec, csc, tan, cot, asin, acos, atan, sinh, cosh, tanh, erf, erfc, min, max, abs, floor, ceil, step, delta, select.  All trigonometric functions
  * are defined in radians, and log is the natural logarithm.  step(x) = 0 if x is less than 0, 1 otherwise.  delta(x) = 1 if x is 0, 0 otherwise.
@@ -172,7 +180,7 @@ public:
      * @param parameters   the list of parameters for the new force term
      * @return the index of the particle term that was added
      */
-    int addParticle(int particle, const std::vector<double>& parameters);
+    int addParticle(int particle, const std::vector<double>& parameters=std::vector<double>());
     /**
      * Get the force field parameters for a force field term.
      *
@@ -188,7 +196,7 @@ public:
      * @param particle      the index of the particle this term is applied to
      * @param parameters    the list of parameters for the force field term
      */
-    void setParticleParameters(int index, int particle, const std::vector<double>& parameters);
+    void setParticleParameters(int index, int particle, const std::vector<double>& parameters=std::vector<double>());
     /**
      * Update the per-particle parameters in a Context to match those stored in this Force object.  This method provides
      * an efficient method to update certain parameters in an existing Context without needing to reinitialize it.
@@ -206,9 +214,7 @@ public:
      *
      * @returns false
      */
-    bool usesPeriodicBoundaryConditions() const {
-        return false;
-    }
+    bool usesPeriodicBoundaryConditions() const;
 protected:
     ForceImpl* createImpl() const;
 private:

openmmapi/include/openmm/CustomGBForce.h

@@ -319,7 +319,7 @@ public:
      * @param parameters    the list of parameters for the new particle
      * @return the index of the particle that was added
      */
-    int addParticle(const std::vector<double>& parameters);
+    int addParticle(const std::vector<double>& parameters=std::vector<double>());
     /**
      * Get the nonbonded force parameters for a particle.
      *

openmmapi/include/openmm/CustomHbondForce.h

@@ -296,7 +296,7 @@ public:
      * @param parameters  the list of per-donor parameter values for the new donor
      * @return the index of the donor that was added
      */
-    int addDonor(int d1, int d2, int d3, const std::vector<double>& parameters);
+    int addDonor(int d1, int d2, int d3, const std::vector<double>& parameters=std::vector<double>());
     /**
      * Get the properties of a donor group.
      *
@@ -320,7 +320,7 @@ public:
      *                    less than three particles, this must be -1.
      * @param parameters  the list of per-donor parameter values for the donor
      */
-    void setDonorParameters(int index, int d1, int d2, int d3, const std::vector<double>& parameters);
+    void setDonorParameters(int index, int d1, int d2, int d3, const std::vector<double>& parameters=std::vector<double>());
     /**
      * Add an acceptor group to the force
      *
@@ -332,7 +332,7 @@ public:
      * @param parameters  the list of per-acceptor parameter values for the new acceptor
      * @return the index of the acceptor that was added
      */
-    int addAcceptor(int a1, int a2, int a3, const std::vector<double>& parameters);
+    int addAcceptor(int a1, int a2, int a3, const std::vector<double>& parameters=std::vector<double>());
     /**
      * Get the properties of an acceptor group.
      *
@@ -356,7 +356,7 @@ public:
      *                    less than three particles, this must be -1.
      * @param parameters  the list of per-acceptor parameter values for the acceptor
      */
-    void setAcceptorParameters(int index, int a1, int a2, int a3, const std::vector<double>& parameters);
+    void setAcceptorParameters(int index, int a1, int a2, int a3, const std::vector<double>& parameters=std::vector<double>());
     /**
      * Add a donor-acceptor pair to the list of interactions that should be excluded.
      *

openmmapi/include/openmm/CustomManyParticleForce.h

@@ -348,7 +348,7 @@ public:
      * @param type          the type of the new particle
      * @return the index of the particle that was added
      */
-    int addParticle(const std::vector<double>& parameters, int type=0);
+    int addParticle(const std::vector<double>& parameters=std::vector<double>(), int type=0);
     /**
      * Get the nonbonded force parameters for a particle.
      *

openmmapi/include/openmm/CustomNonbondedForce.h

@@ -328,7 +328,7 @@ public:
      * @param parameters    the list of parameters for the new particle
      * @return the index of the particle that was added
      */
-    int addParticle(const std::vector<double>& parameters);
+    int addParticle(const std::vector<double>& parameters=std::vector<double>());
     /**
      * Get the nonbonded force parameters for a particle.
      *

openmmapi/include/openmm/CustomTorsionForce.h

@@ -172,7 +172,7 @@ public:
      * @param parameters    the list of parameters for the new torsion
      * @return the index of the torsion that was added
      */
-    int addTorsion(int particle1, int particle2, int particle3, int particle4, const std::vector<double>& parameters);
+    int addTorsion(int particle1, int particle2, int particle3, int particle4, const std::vector<double>& parameters=std::vector<double>());
     /**
      * Get the force field parameters for a torsion term.
      *
@@ -194,7 +194,7 @@ public:
      * @param particle4     the index of the fourth particle connected by the torsion
      * @param parameters    the list of parameters for the torsion
      */
-    void setTorsionParameters(int index, int particle1, int particle2, int particle3, int particle4, const std::vector<double>& parameters);
+    void setTorsionParameters(int index, int particle1, int particle2, int particle3, int particle4, const std::vector<double>& parameters=std::vector<double>());
     /**
      * Update the per-torsion parameters in a Context to match those stored in this Force object.  This method provides
      * an efficient method to update certain parameters in an existing Context without needing to reinitialize it.

openmmapi/include/openmm/internal/CustomCentroidBondForceImpl.h

@@ -41,6 +41,7 @@
 #include "lepton/ParsedExpression.h"
 #include <utility>
 #include <map>
+#include <set>
 #include <string>
 
 namespace OpenMM {
@@ -93,7 +94,7 @@ private:
     class FunctionPlaceholder;
     static Lepton::ExpressionTreeNode replaceFunctions(const Lepton::ExpressionTreeNode& node, std::map<std::string, int> atoms,
             std::map<std::string, std::vector<int> >& distances, std::map<std::string, std::vector<int> >& angles,
-            std::map<std::string, std::vector<int> >& dihedrals);
+            std::map<std::string, std::vector<int> >& dihedrals, std::set<std::string>& variables);
     void addBondsBetweenGroups(int group1, int group2, std::vector<std::pair<int, int> >& bonds) const;
     const CustomCentroidBondForce& owner;
     Kernel kernel;

openmmapi/include/openmm/internal/CustomCompoundBondForceImpl.h

@@ -40,6 +40,7 @@
 #include "lepton/ParsedExpression.h"
 #include <utility>
 #include <map>
+#include <set>
 #include <string>
 
 namespace OpenMM {
@@ -83,7 +84,7 @@ private:
     class FunctionPlaceholder;
     static Lepton::ExpressionTreeNode replaceFunctions(const Lepton::ExpressionTreeNode& node, std::map<std::string, int> atoms,
             std::map<std::string, std::vector<int> >& distances, std::map<std::string, std::vector<int> >& angles,
-            std::map<std::string, std::vector<int> >& dihedrals);
+            std::map<std::string, std::vector<int> >& dihedrals, std::set<std::string>& variables);
     const CustomCompoundBondForce& owner;
     Kernel kernel;
 };

openmmapi/include/openmm/internal/CustomHbondForceImpl.h

@@ -9,7 +9,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008-2010 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2015 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -40,6 +40,7 @@
 #include "lepton/ParsedExpression.h"
 #include <utility>
 #include <map>
+#include <set>
 #include <string>
 
 namespace OpenMM {
@@ -84,7 +85,7 @@ private:
     class FunctionPlaceholder;
     static Lepton::ExpressionTreeNode replaceFunctions(const Lepton::ExpressionTreeNode& node, std::map<std::string, int> atoms,
             std::map<std::string, std::vector<int> >& distances, std::map<std::string, std::vector<int> >& angles,
-            std::map<std::string, std::vector<int> >& dihedrals);
+            std::map<std::string, std::vector<int> >& dihedrals, std::set<std::string>& variables);
     const CustomHbondForce& owner;
     Kernel kernel;
 };

openmmapi/include/openmm/internal/CustomManyParticleForceImpl.h

@@ -40,6 +40,7 @@
 #include "lepton/ParsedExpression.h"
 #include <utility>
 #include <map>
+#include <set>
 #include <string>
 
 namespace OpenMM {
@@ -98,7 +99,7 @@ private:
     class FunctionPlaceholder;
     static Lepton::ExpressionTreeNode replaceFunctions(const Lepton::ExpressionTreeNode& node, std::map<std::string, int> atoms,
             std::map<std::string, std::vector<int> >& distances, std::map<std::string, std::vector<int> >& angles,
-            std::map<std::string, std::vector<int> >& dihedrals);
+            std::map<std::string, std::vector<int> >& dihedrals, std::set<std::string>& variables);
     static void generatePermutations(std::vector<int>& values, int numFixed, std::vector<std::vector<int> >& result);
     const CustomManyParticleForce& owner;
     Kernel kernel;

openmmapi/src/ContextImpl.cpp

@@ -41,6 +41,7 @@
 #include "openmm/Context.h"
 #include <algorithm>
 #include <cmath>
+#include <cstdlib>
 #include <iostream>
 #include <map>
 #include <utility>
@@ -115,6 +116,11 @@ ContextImpl::ContextImpl(Context& owner, const System& system, Integrator& integ
     // Select a platform to use.
     
     vector<pair<double, Platform*> > candidatePlatforms;
+    if (platform == NULL) {
+        char* defaultPlatform = getenv("OPENMM_DEFAULT_PLATFORM");
+        if (defaultPlatform != NULL)
+            platform = &Platform::getPlatformByName(string(defaultPlatform));
+    }
     if (platform == NULL) {
         for (int i = 0; i < Platform::getNumPlatforms(); i++) {
             Platform& p = Platform::getPlatform(i);