Merge remote-tracking branch 'upstream/master'

.travis.yml

@@ -11,11 +11,11 @@ before_install:
 
 script:
   - cmake -DCMAKE_INSTALL_PREFIX=$HOME/OpenMM .
-  - make
-  - make install
+  - make -j2
+  - make -j2 install
   - sudo make PythonInstall
   - # run all of the tests
-  - ctest -V
+  - ctest -j2 -V
   - # get a list of all of the failed tests into this stupid ctest format
   - python -c 'fn = "Testing/Temporary/LastTestsFailed.log"; import os; os.path.exists(fn) or exit(0); l = [line.split(":")[0] for line in open(fn)]; triplets = zip(l, l, [","]*len(l)); print "".join(",".join(t) for t in triplets)' > FailedTests.log
   - # rerun all of the failed tests

CMakeLists.txt

@@ -273,7 +273,8 @@ ENDIF(WIN32)
 SET(OPENMM_BUILD_STATIC_LIB OFF CACHE BOOL "Whether to build static OpenMM libraries")
 IF(OPENMM_BUILD_STATIC_LIB)
     ADD_LIBRARY(${STATIC_TARGET} STATIC ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_ABS_INCLUDE_FILES})
-    SET_TARGET_PROPERTIES(${STATIC_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_USE_STATIC_LIBRARIES -DOPENMM_BUILDING_STATIC_LIBRARY -DLEPTON_USE_STATIC_LIBRARIES -DLEPTON_BUILDING_STATIC_LIBRARY -DOPENMMM_VALIDATE_BUILDING_STATIC_LIBRARY -DOPENMM_VALIDATE_BUILDING_STATIC_LIBRARY")
+    SET(EXTRA_COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_USE_STATIC_LIBRARIES -DLEPTON_USE_STATIC_LIBRARIES -DPTW32_STATIC_LIB")
+    SET_TARGET_PROPERTIES(${STATIC_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_BUILDING_STATIC_LIBRARY -DLEPTON_BUILDING_STATIC_LIBRARY -DOPENMMM_VALIDATE_BUILDING_STATIC_LIBRARY -DOPENMM_VALIDATE_BUILDING_STATIC_LIBRARY")
 ENDIF(OPENMM_BUILD_STATIC_LIB)
 
 IF(OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS)

docs/usersguide/application.rst

@@ -660,7 +660,9 @@ amber99sbildn.xml  AMBER99SB plus improved side chain torsions\ :cite:`Lindorff-
 amber99sbnmr.xml   AMBER99SB with modifications to fit NMR data\ :cite:`Li2010`
 amber03.xml        AMBER03\ :cite:`Duan2003`
 amber10.xml        AMBER10
-amoeba2009.xml     AMOEBA\ :cite:`Ren2002`                                                       
+amoeba2009.xml     AMOEBA 2009\ :cite:`Ren2002`.  This force field is deprecated.  It is 
+                   recommended to use AMOEBA 2013 instead.
+amoeba2013.xml     AMOEBA 2013\ :cite:`Shi2013`
 =================  ================================================================================
 
 
@@ -675,7 +677,9 @@ files:
 File         Water Model                                 
 ===========  ============================================
 tip3p.xml    TIP3P water model\ :cite:`Jorgensen1983`  
+tip3pfb.xml  TIP3P-FB water model\ :cite:`Wang2014`    
 tip4pew.xml  TIP4P-Ew water model\ :cite:`Horn2004`    
+tip4pfb.xml  TIP4P-FB water model\ :cite:`Wang2014`    
 tip5p.xml    TIP5P water model\ :cite:`Mahoney2000`    
 spce.xml     SPC/E water model\ :cite:`Berendsen1987`  
 swm4ndp.xml  SWM4-NDP water model\ :cite:`Lamoureux2006`
@@ -692,15 +696,16 @@ the following files:
 
 .. tabularcolumns:: |l|L|
 
-=================  ==============================================================================================
+=================  =================================================================================================
 File               Implicit Solvation Model                                                                      
-=================  ==============================================================================================
+=================  =================================================================================================
 amber96_obc.xml    GBSA-OBC solvation model\ :cite:`Onufriev2004` for use with AMBER96 force field
 amber99_obc.xml    GBSA-OBC solvation model for use with AMBER99 force fields
 amber03_obc.xml    GBSA-OBC solvation model for use with AMBER03 force field
 amber10_obc.xml    GBSA-OBC solvation model for use with AMBER10 force field
-amoeba2009_gk.xml  Generalized Kirkwood solvation model\ :cite:`Schnieders2007` for use with AMOEBA force field
-=================  ==============================================================================================
+amoeba2009_gk.xml  Generalized Kirkwood solvation model\ :cite:`Schnieders2007` for use with AMOEBA 2009 force field
+amoeba2013_gk.xml  Generalized Kirkwood solvation model for use with AMOEBA 2013 force field
+=================  =================================================================================================
 
 
 For example, to use the GBSA-OBC solvation model with the Amber99SB force field,
@@ -1297,8 +1302,9 @@ water models:
 
     modeller.addSolvent(forcefield, model='tip5p')
 
-Allowed values for the :code:`model` option are 'tip3p', 'spce', 'tip4pew',
-and 'tip5p'.  Be sure to include the single quotes around the value.
+Allowed values for the :code:`model` option are 'tip3p', 'tip3pfb', 'spce', 
+'tip4pew', 'tip4pfb', and 'tip5p'.  Be sure to include the single quotes 
+around the value.
 
 Another option is to add extra ion pairs to give a desired total ionic strength.
 For example:
@@ -2180,6 +2186,49 @@ second atom has class OS and the third has class P:
 
     <Proper class1="" class2="OS" class3="P" class4="" per="3" phase="0.0" k="0.66944"/>
 
+<CustomNonbondedForce>
+===============
+
+To add a CustomNonbondedForce to the System, include a tag that looks like this:
+
+.. code-block:: xml
+
+    <CustomNonbondedForce energy="scale*epsilon1*epsilon2*((sigma1+sigma2)/r)^12" bondCutoff="3">
+     <GlobalParameter name="scale" defaultValue="1"/>
+     <PerParticleParameter name="sigma"/>
+     <PerParticleParameter name="epsilon"/>
+     <Atom type="0" sigma="0.3249" epsilon="0.7112"/>
+     <Atom type="1" sigma="0.1069" epsilon="0.0656"/>
+     <Atom type="2" sigma="0.3399" epsilon="0.4577"/>
+     ...
+    </CustomNonbondedForce>
+
+The energy expression for the CustomNonbondedForce is specified by the
+:code:`energy` attribute.  This is a mathematical expression that gives the
+energy of each pairwise interaction as a function of the distance *r*\ .  It
+also may depend on an arbitrary list of global or per-particle parameters.  Use
+a :code:`<GlobalParameter>` tag to define a global parameter, and a
+:code:`<PerParticleParameter>` tag to define a per-particle parameter.
+
+Exclusions are created automatically based on the :code:`bondCutoff` attribute.
+After setting the nonbonded parameters for all atoms, the force field calls
+:code:`createExclusionsFromBonds()` on the CustomNonbondedForce, passing in this
+value as its argument.  To avoid creating exclusions, set :code:`bondCutoff` to 0.
+
+Each :code:`<Atom>` tag specifies the parameters for one atom type
+(specified with the :code:`type` attribute) or atom class (specified with
+the :code:`class` attribute).  It is fine to mix these two methods, having
+some tags specify a type and others specify a class.  However you do it, you
+must make sure that a unique set of parameters is defined for every atom type.
+The remaining attributes are the values to use for the per-atom parameters. All
+per-atom parameters must be specified for every :code:`<Atom>` tag, and the
+attribute name must match the name of the parameter.  For instance, if there is
+a per-atom parameter with the name “radius”, then every :code:`<Atom>` tag
+must include an attribute called :code:`radius`\ .
+
+CustomNonbondedForce also allows you to define tabulated functions.  See section
+:ref:`tabulated-functions` for details.
+
 <CustomGBForce>
 ===============
 
@@ -2237,30 +2286,8 @@ attribute name must match the name of the parameter.  For instance, if there is
 a per-atom parameter with the name “radius”, then every :code:`<Atom>` tag
 must include an attribute called :code:`radius`\ .
 
-CustomGBForce also allows you to define tabulated functions.  To define a
-function, include a :code:`<Function>` tag inside the
-:code:`<CustomGBForce>` tag:
-
-.. code-block:: xml
-
-    <Function name="myfn" min="-5" max="5">
-    0.983674857694 -0.980096396266 -0.975743130031 -0.970451936613 -0.964027580076
-    -0.956237458128 -0.946806012846 -0.935409070603 -0.921668554406 -0.905148253645
-    -0.885351648202 -0.861723159313 -0.833654607012 -0.800499021761 -0.761594155956
-    -0.716297870199 -0.664036770268 -0.604367777117 -0.537049566998 -0.46211715726
-    -0.379948962255 -0.291312612452 -0.197375320225 -0.099667994625 0.0
-    0.099667994625 0.197375320225 0.291312612452 0.379948962255 0.46211715726
-    0.537049566998 0.604367777117 0.664036770268 0.716297870199 0.761594155956
-    0.800499021761 0.833654607012 0.861723159313 0.885351648202 0.905148253645
-    0.921668554406 0.935409070603 0.946806012846 0.956237458128 0.964027580076
-    0.970451936613 0.975743130031 0.980096396266 0.983674857694 0.986614298151
-    0.989027402201
-    </Function>
-
-The tag’s attributes define the name of the function and the range of values for
-which it is defined.  The tabulated values are listed inside the body of the
-tag, with successive values separated by white space.  Again, see the API
-documentation for more details.
+CustomGBForce also allows you to define tabulated functions.  See section
+:ref:`tabulated-functions` for details.
 
 Writing Custom Expressions
 ==========================
@@ -2297,6 +2324,55 @@ is exactly equivalent to
 The definition of an intermediate value may itself involve other intermediate
 values.  All uses of a value must appear *before* that value’s definition.
 
+.. _tabulated-functions:
+
+TabulatedFunctions
+==================
+
+Some forces, such as CustomNonbondedForce and CustomGBForce, allow you to define
+tabulated functions.  To define a function, include a :code:`<Function>` tag inside the
+:code:`<CustomNonbondedForce>` or :code:`<CustomGBForce>` tag:
+
+.. code-block:: xml
+
+    <Function name="myfn" type="Continuous1D" min="-5" max="5">
+    0.983674857694 -0.980096396266 -0.975743130031 -0.970451936613 -0.964027580076
+    -0.956237458128 -0.946806012846 -0.935409070603 -0.921668554406 -0.905148253645
+    -0.885351648202 -0.861723159313 -0.833654607012 -0.800499021761 -0.761594155956
+    -0.716297870199 -0.664036770268 -0.604367777117 -0.537049566998 -0.46211715726
+    -0.379948962255 -0.291312612452 -0.197375320225 -0.099667994625 0.0
+    0.099667994625 0.197375320225 0.291312612452 0.379948962255 0.46211715726
+    0.537049566998 0.604367777117 0.664036770268 0.716297870199 0.761594155956
+    0.800499021761 0.833654607012 0.861723159313 0.885351648202 0.905148253645
+    0.921668554406 0.935409070603 0.946806012846 0.956237458128 0.964027580076
+    0.970451936613 0.975743130031 0.980096396266 0.983674857694 0.986614298151
+    0.989027402201
+    </Function>
+
+The tag’s attributes define the name of the function, the type of function, and
+the range of values for which it is defined.  The required set of attributed
+depends on the function type:
+
+.. tabularcolumns:: |l|L|
+
+============  =======================================================
+Type          Required Attributes
+============  =======================================================
+Continuous1D  min, max
+Continuous2D  xmin, ymin, xmax, ymax, xsize, ysize
+Continuous3D  xmin, ymin, zmin, xmax, ymax, zmax, xsize, ysize, zsize
+Discrete1D
+Discrete2D    xsize, ysize
+Discrete3D    xsize, ysize, zsize
+============  =======================================================
+
+
+The "min" and "max" attributes define the range of the independent variables for
+a continuous function.  The "size" attributes define the size of the table along
+each axis.  The tabulated values are listed inside the body of the tag, with
+successive values separated by white space.  See the API documentation for more
+details.
+
 
 Using Multiple Files
 ********************

docs/usersguide/references.bib

@@ -336,10 +336,20 @@
    type = {Journal Article}
 }
 
+@article{Shi2013
+   author = {Shi, Yue and Xia, Zhen and Zhang, Jiajing and Best, Robert and Wu, Chuanjie and Ponder, Jay W. and Ren, Pengyu},
+   title = {Polarizable Atomic Multipole-Based AMOEBA Force Field for Proteins},
+   journal = {Journal of Chemical Theory and Computation},
+   volume = {9},
+   number = {9},
+   pages = {4046-4063},
+   year = {2013},
+   type = {Journal Article}
+}
+
 @article{Shirts2007
    author = {Shirts, Michael R. and Mobley, David L. and Chodera, John D. and Pande, Vijay S.},
-   title = {Accurate and Efficient Corrections for Missing Dispersion Interactions in Molecular
-Simulations},
+   title = {Accurate and Efficient Corrections for Missing Dispersion Interactions in Molecular Simulations},
    journal = {Journal of Physical Chemistry B},
    volume = {111},
    pages = {13052-13063},
@@ -399,3 +409,12 @@ Simulations},
    type = {Journal Article}
 }
 
+@article{Wang2014
+   author = {Wang, Lee-Ping and Martinez, Todd J. and Pande, Vijay S.},
+   title = {Building force fields: an automatic, systematic, and reproducible approach},
+   journal = {Journal of Physical Chemistry Letters},
+   volume = {5},
+   pages = {1885-1891},
+   year = {2014},
+   type = {Journal Article}
+}

libraries/lepton/src/ParsedExpression.cpp

@@ -269,7 +269,15 @@ ExpressionTreeNode ParsedExpression::substituteSimplerExpression(const Expressio
                 return ExpressionTreeNode(new Operation::Constant(dynamic_cast<const Operation::MultiplyConstant*>(&node.getOperation())->getValue()*getConstantValue(children[0])));
             if (children[0].getOperation().getId() == Operation::NEGATE) // Combine a multiply and a negate into a single multiply
                 return ExpressionTreeNode(new Operation::MultiplyConstant(-dynamic_cast<const Operation::MultiplyConstant*>(&node.getOperation())->getValue()), children[0].getChildren()[0]);
+            break;
         }
+        default:
+        {
+            // If operation ID is not one of the above,
+            // we don't substitute a simpler expression.
+            break;
+        }
+
     }
     return ExpressionTreeNode(node.getOperation().clone(), children);
 }

openmmapi/include/openmm/Context.h

@@ -35,12 +35,12 @@
 #include "Integrator.h"
 #include "State.h"
 #include "System.h"
-#include <ctime>
 #include <iosfwd>
 #include <map>
 #include <string>
 #include <vector>
 #include "internal/windowsExport.h"
+#include "internal/OSRngSeed.h"
 
 namespace OpenMM {
 
@@ -164,7 +164,7 @@ public:
      * @param temperature    the temperature for which to select the velocities (measured in Kelvin)
      * @param randomSeed     the random number seed to use when selecting velocities
      */
-    void setVelocitiesToTemperature(double temperature, int randomSeed=time(NULL));
+    void setVelocitiesToTemperature(double temperature, int randomSeed=osrngseed());
     /**
      * Get the value of an adjustable parameter defined by a Force object in the System.
      * 

openmmapi/include/openmm/CustomNonbondedForce.h

@@ -344,6 +344,8 @@ public:
     /**
      * Add a particle pair to the list of interactions that should be excluded.
      * 
+     * In many cases, you can use createExclusionsFromBonds() rather than adding each exclusion explicitly.
+     *
      * @param particle1  the index of the first particle in the pair
      * @param particle2  the index of the second particle in the pair
      * @return the index of the exclusion that was added
@@ -365,6 +367,15 @@ public:
      * @param particle2  the index of the second particle in the pair
      */
     void setExclusionParticles(int index, int particle1, int particle2);
+    /**
+     * Identify exclusions based on the molecular topology.  Particles which are separated by up to a specified number of
+     * bonds are added as exclusions.
+     *
+     * @param bonds       the set of bonds based on which to construct exclusions.  Each element specifies the indices of
+     *                    two particles that are bonded to each other.
+     * @param bondCutoff  pairs of particles that are separated by this many bonds or fewer are added to the list of exclusions
+     */
+    void createExclusionsFromBonds(const std::vector<std::pair<int, int> >& bonds, int bondCutoff);
     /**
      * Add a tabulated function that may appear in the energy expression.
      *

openmmapi/include/openmm/internal/OSRngSeed.h

+#ifndef OPENMM_OSRNGSEED_H_
+#define OPENMM_OSRNGSEED_H_
+
+
+/* -------------------------------------------------------------------------- *
+ *                                   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) 2013 Stanford University and the Authors.           *
+ * Authors: Robert T. McGibbon                                                *
+ * 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.                                     *
+ * -------------------------------------------------------------------------- */
+
+
+
+/**
+ * Return an integer int for use as a seed for a random number generator.
+ * 
+ * The behavior of this function is platform dependent. On Windows machines,
+ * this uses CryptGenRandom from the CryptoAPI to get a single int. On other
+ * platforms (*nix, apple), we read from /dev/urandom
+ */
+int osrngseed(void);
+
+#endif /* OPENMM_OSRNGSEED_H_ */
\ No newline at end of file

openmmapi/src/AndersenThermostat.cpp

@@ -31,13 +31,13 @@
 
 #include "openmm/AndersenThermostat.h"
 #include "openmm/internal/AndersenThermostatImpl.h"
-#include <ctime>
+#include "openmm/internal/OSRngSeed.h"
 
 using namespace OpenMM;
 
 AndersenThermostat::AndersenThermostat(double defaultTemperature, double defaultCollisionFrequency) :
         defaultTemp(defaultTemperature), defaultFreq(defaultCollisionFrequency) {
-    setRandomNumberSeed((int) time(NULL));
+    setRandomNumberSeed(osrngseed());
 }
 
 ForceImpl* AndersenThermostat::createImpl() const {

openmmapi/src/BrownianIntegrator.cpp

@@ -33,8 +33,8 @@
 #include "openmm/Context.h"
 #include "openmm/OpenMMException.h"
 #include "openmm/internal/ContextImpl.h"
+#include "openmm/internal/OSRngSeed.h"
 #include "openmm/kernels.h"
-#include <ctime>
 #include <string>
 
 using namespace OpenMM;
@@ -46,7 +46,7 @@ BrownianIntegrator::BrownianIntegrator(double temperature, double frictionCoeff,
     setFriction(frictionCoeff);
     setStepSize(stepSize);
     setConstraintTolerance(1e-5);
-    setRandomNumberSeed((int) time(NULL));
+    setRandomNumberSeed(osrngseed());
 }
 
 void BrownianIntegrator::initialize(ContextImpl& contextRef) {

openmmapi/src/CustomIntegrator.cpp

@@ -34,8 +34,8 @@
 #include "openmm/OpenMMException.h"
 #include "openmm/internal/AssertionUtilities.h"
 #include "openmm/internal/ContextImpl.h"
+#include "openmm/internal/OSRngSeed.h"
 #include "openmm/kernels.h"
-#include <ctime>
 #include <string>
 
 using namespace OpenMM;
@@ -45,7 +45,7 @@ using std::vector;
 CustomIntegrator::CustomIntegrator(double stepSize) : globalsAreCurrent(true), forcesAreValid(false) {
     setStepSize(stepSize);
     setConstraintTolerance(1e-5);
-    setRandomNumberSeed((int) time(NULL));
+    setRandomNumberSeed(osrngseed());
     kineticEnergy = "m*v*v/2";
 }
 

openmmapi/src/CustomNonbondedForce.cpp

@@ -174,6 +174,33 @@ void CustomNonbondedForce::setExclusionParticles(int index, int particle1, int p
     exclusions[index].particle1 = particle1;
     exclusions[index].particle2 = particle2;
 }
+
+void CustomNonbondedForce::createExclusionsFromBonds(const vector<pair<int, int> >& bonds, int bondCutoff) {
+    if (bondCutoff < 1)
+        return;
+    vector<set<int> > exclusions(particles.size());
+    vector<set<int> > bonded12(exclusions.size());
+    for (int i = 0; i < (int) bonds.size(); ++i) {
+        int p1 = bonds[i].first;
+        int p2 = bonds[i].second;
+        exclusions[p1].insert(p2);
+        exclusions[p2].insert(p1);
+        bonded12[p1].insert(p2);
+        bonded12[p2].insert(p1);
+    }
+    for (int level = 0; level < bondCutoff-1; level++) {
+        vector<set<int> > currentExclusions = exclusions;
+        for (int i = 0; i < (int) particles.size(); i++) {
+            for (set<int>::const_iterator iter = currentExclusions[i].begin(); iter != currentExclusions[i].end(); ++iter)
+                exclusions[*iter].insert(bonded12[i].begin(), bonded12[i].end());
+        }
+    }
+    for (int i = 0; i < (int) exclusions.size(); ++i)
+        for (set<int>::const_iterator iter = exclusions[i].begin(); iter != exclusions[i].end(); ++iter)
+            if (*iter < i)
+                addExclusion(*iter, i);
+}
+
 int CustomNonbondedForce::addTabulatedFunction(const std::string& name, TabulatedFunction* function) {
     functions.push_back(FunctionInfo(name, function));
     return functions.size()-1;

openmmapi/src/LangevinIntegrator.cpp

@@ -33,8 +33,8 @@
 #include "openmm/Context.h"
 #include "openmm/OpenMMException.h"
 #include "openmm/internal/ContextImpl.h"
+#include "openmm/internal/OSRngSeed.h"
 #include "openmm/kernels.h"
-#include <ctime>
 #include <string>
 
 using namespace OpenMM;
@@ -46,7 +46,7 @@ LangevinIntegrator::LangevinIntegrator(double temperature, double frictionCoeff,
     setFriction(frictionCoeff);
     setStepSize(stepSize);
     setConstraintTolerance(1e-5);
-    setRandomNumberSeed((int) time(NULL));
+    setRandomNumberSeed(osrngseed());
 }
 
 void LangevinIntegrator::initialize(ContextImpl& contextRef) {

openmmapi/src/MonteCarloAnisotropicBarostat.cpp

@@ -31,13 +31,13 @@
 
 #include "openmm/MonteCarloAnisotropicBarostat.h"
 #include "openmm/internal/MonteCarloAnisotropicBarostatImpl.h"
-#include <ctime>
+#include "openmm/internal/OSRngSeed.h"
 
 using namespace OpenMM;
 
 MonteCarloAnisotropicBarostat::MonteCarloAnisotropicBarostat(const Vec3& defaultPressure, double temperature, bool scaleX, bool scaleY, bool scaleZ, int frequency) :
         defaultPressure(defaultPressure), temperature(temperature), scaleX(scaleX), scaleY(scaleY), scaleZ(scaleZ), frequency(frequency) {
-    setRandomNumberSeed((int) time(NULL));
+    setRandomNumberSeed(osrngseed());
 }
 
 ForceImpl* MonteCarloAnisotropicBarostat::createImpl() const {

openmmapi/src/MonteCarloBarostat.cpp

@@ -31,13 +31,13 @@
 
 #include "openmm/MonteCarloBarostat.h"
 #include "openmm/internal/MonteCarloBarostatImpl.h"
-#include <ctime>
+#include "openmm/internal/OSRngSeed.h"
 
 using namespace OpenMM;
 
 MonteCarloBarostat::MonteCarloBarostat(double defaultPressure, double temperature, int frequency) :
         defaultPressure(defaultPressure), temperature(temperature), frequency(frequency) {
-    setRandomNumberSeed((int) time(NULL));
+    setRandomNumberSeed(osrngseed());
 }
 
 ForceImpl* MonteCarloBarostat::createImpl() const {

openmmapi/src/OSRngSeed.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) 2013 Stanford University and the Authors.           *
+ * Authors: Robert T. McGibbon                                                *
+ * 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 <stdexcept>
+#if defined(_WIN32) || defined(__CYGWIN__)
+#include <windows.h>
+static HCRYPTPROV hCryptProv = 0;
+#pragma comment(lib, "advapi32.lib")
+#else
+#include <fcntl.h>
+#include <unistd.h>
+#endif
+#include "openmm/internal/OSRngSeed.h"
+
+int osrngseed(void) {
+    int value;
+#if defined(_WIN32) || defined(__CYGWIN__)
+    if (!::CryptAcquireContextW(&hCryptProv, 0, 0, PROV_RSA_FULL, CRYPT_VERIFYCONTEXT | CRYPT_SILENT)) {
+        throw std::runtime_error("Failed to initialize Windows random API (CryptoGen)");
+    }
+    if (!CryptGenRandom(hCryptProv, sizeof(int), (BYTE*) &value)) {
+        ::CryptReleaseContext(hCryptProv, 0);
+        throw std::runtime_error("Failed to get random numbers");
+    }
+    if (!::CryptReleaseContext(hCryptProv, 0)) {
+        throw std::runtime_error("Failed to release Windows random API context");
+    }
+#else
+    int m_fd = open("/dev/urandom", O_RDONLY);
+    if (m_fd == -1) {
+        throw std::runtime_error("Failed to open /dev/urandom");
+    }
+    if (read(m_fd, &value, sizeof(int)) != sizeof(int)) {
+        throw std::runtime_error("Failed to read bytes from /dev/urandom");
+    }
+    close(m_fd);
+#endif
+    return value;
+}
\ No newline at end of file

openmmapi/src/VariableLangevinIntegrator.cpp

@@ -33,10 +33,11 @@
 #include "openmm/Context.h"
 #include "openmm/OpenMMException.h"
 #include "openmm/internal/ContextImpl.h"
+#include "openmm/internal/OSRngSeed.h"
 #include "openmm/kernels.h"
 #include <limits>
 #include <string>
-#include <ctime>
+
 
 using namespace OpenMM;
 using std::string;
@@ -47,7 +48,7 @@ VariableLangevinIntegrator::VariableLangevinIntegrator(double temperature, doubl
     setFriction(frictionCoeff);
     setErrorTolerance(errorTol);
     setConstraintTolerance(1e-5);
-    setRandomNumberSeed((int) time(NULL));
+    setRandomNumberSeed(osrngseed());
 }
 
 void VariableLangevinIntegrator::initialize(ContextImpl& contextRef) {

platforms/cuda/src/CudaKernels.cpp

@@ -1520,7 +1520,7 @@ void CudaCalcNonbondedForceKernel::initialize(const System& system, const Nonbon
     else
         dispersionCoefficient = 0.0;
     alpha = 0;
-    if (force.getNonbondedMethod() == NonbondedForce::Ewald && cu.getContextIndex() == 0) {
+    if (force.getNonbondedMethod() == NonbondedForce::Ewald) {
         // Compute the Ewald parameters.
 
         int kmaxx, kmaxy, kmaxz;
@@ -1528,6 +1528,7 @@ void CudaCalcNonbondedForceKernel::initialize(const System& system, const Nonbon
         defines["EWALD_ALPHA"] = cu.doubleToString(alpha);
         defines["TWO_OVER_SQRT_PI"] = cu.doubleToString(2.0/sqrt(M_PI));
         defines["USE_EWALD"] = "1";
+        if (cu.getContextIndex() == 0) {
             ewaldSelfEnergy = -ONE_4PI_EPS0*alpha*sumSquaredCharges/sqrt(M_PI);
 
             // Create the reciprocal space kernels.
@@ -1547,7 +1548,8 @@ void CudaCalcNonbondedForceKernel::initialize(const System& system, const Nonbon
             int elementSize = (cu.getUseDoublePrecision() ? sizeof(double2) : sizeof(float2));
             cosSinSums = new CudaArray(cu, (2*kmaxx-1)*(2*kmaxy-1)*(2*kmaxz-1), elementSize, "cosSinSums");
         }
-    else if (force.getNonbondedMethod() == NonbondedForce::PME && cu.getContextIndex() == 0) {
+    }
+    else if (force.getNonbondedMethod() == NonbondedForce::PME) {
         // Compute the PME parameters.
 
         int gridSizeX, gridSizeY, gridSizeZ;
@@ -1560,6 +1562,7 @@ void CudaCalcNonbondedForceKernel::initialize(const System& system, const Nonbon
         defines["EWALD_ALPHA"] = cu.doubleToString(alpha);
         defines["TWO_OVER_SQRT_PI"] = cu.doubleToString(2.0/sqrt(M_PI));
         defines["USE_EWALD"] = "1";
+        if (cu.getContextIndex() == 0) {
             ewaldSelfEnergy = -ONE_4PI_EPS0*alpha*sumSquaredCharges/sqrt(M_PI);
             pmeDefines["PME_ORDER"] = cu.intToString(PmeOrder);
             pmeDefines["NUM_ATOMS"] = cu.intToString(numParticles);
@@ -1698,6 +1701,7 @@ void CudaCalcNonbondedForceKernel::initialize(const System& system, const Nonbon
                 }
             }
         }
+    }
     else
         ewaldSelfEnergy = 0.0;
 

platforms/cuda/tests/TestCudaLocalEnergyMinimizer.cpp

@@ -7,7 +7,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010-2012 Stanford University and the Authors.      *
+ * Portions copyright (c) 2010-2014 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -170,6 +170,7 @@ void testVirtualSites() {
     VerletIntegrator integrator(0.01);
     Context context(system, integrator, platform);
     context.setPositions(positions);
+    context.applyConstraints(1e-5);
     State initialState = context.getState(State::Forces | State::Energy);
     LocalEnergyMinimizer::minimize(context, tolerance);
     State finalState = context.getState(State::Forces | State::Energy | State::Positions);