Moved SFMT into libraries folder, and restructured it to allow multiple...

Moved SFMT into libraries folder, and restructured it to allow multiple independent random number generators

platforms/reference/tests/TestReferenceCustomHbondForce.cpp

@@ -42,7 +42,7 @@
 #include "openmm/PeriodicTorsionForce.h"
 #include "openmm/System.h"
 #include "openmm/VerletIntegrator.h"
-#include "../src/sfmt/SFMT.h"
+#include "sfmt/SFMT.h"
 #include <iostream>
 #include <vector>
 
@@ -105,7 +105,9 @@ void testHbond() {
 
     // Set the atoms in various positions, and verify that both systems give identical forces and energy.
 
-    init_gen_rand(0);
+    OpenMM_SFMT::SFMT sfmt;
+    init_gen_rand(0, sfmt);
+
     vector<Vec3> positions(5);
     VerletIntegrator integrator1(0.01);
     VerletIntegrator integrator2(0.01);
@@ -113,7 +115,7 @@ void testHbond() {
         Context c1(customSystem, integrator1, platform);
         Context c2(standardSystem, integrator2, platform);
         for (int j = 0; j < (int) positions.size(); j++)
-            positions[j] = Vec3(2.0*genrand_real2(), 2.0*genrand_real2(), 2.0*genrand_real2());
+            positions[j] = Vec3(2.0*genrand_real2(sfmt), 2.0*genrand_real2(sfmt), 2.0*genrand_real2(sfmt));
         c1.setPositions(positions);
         c2.setPositions(positions);
         State s1 = c1.getState(State::Forces | State::Energy);

platforms/reference/tests/TestReferenceCustomNonbondedForce.cpp

@@ -35,7 +35,7 @@
  */
 
 #include "../../../tests/AssertionUtilities.h"
-#include "../src/sfmt/SFMT.h"
+#include "sfmt/SFMT.h"
 #include "openmm/Context.h"
 #include "ReferencePlatform.h"
 #include "openmm/CustomNonbondedForce.h"
@@ -256,7 +256,9 @@ void testCoulombLennardJones() {
     customNonbonded->addPerParticleParameter("eps");
     vector<Vec3> positions(numParticles);
     vector<Vec3> velocities(numParticles);
-    init_gen_rand(0);
+    OpenMM_SFMT::SFMT sfmt;
+    init_gen_rand(0, sfmt);
+
     vector<double> params(3);
     for (int i = 0; i < numMolecules; i++) {
         if (i < numMolecules/2) {
@@ -281,10 +283,10 @@ void testCoulombLennardJones() {
             params[1] = 0.1;
             customNonbonded->addParticle(params);
         }
-        positions[2*i] = Vec3(boxSize*genrand_real2(), boxSize*genrand_real2(), boxSize*genrand_real2());
+        positions[2*i] = Vec3(boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt));
         positions[2*i+1] = Vec3(positions[2*i][0]+1.0, positions[2*i][1], positions[2*i][2]);
-        velocities[2*i] = Vec3(genrand_real2(), genrand_real2(), genrand_real2());
-        velocities[2*i+1] = Vec3(genrand_real2(), genrand_real2(), genrand_real2());
+        velocities[2*i] = Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt));
+        velocities[2*i+1] = Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt));
         standardNonbonded->addException(2*i, 2*i+1, 0.0, 1.0, 0.0);
         customNonbonded->addExclusion(2*i, 2*i+1);
     }

platforms/reference/tests/TestReferenceCustomTorsionForce.cpp

@@ -40,7 +40,7 @@
 #include "openmm/PeriodicTorsionForce.h"
 #include "openmm/System.h"
 #include "openmm/VerletIntegrator.h"
-#include "../src/sfmt/SFMT.h"
+#include "sfmt/SFMT.h"
 #include <iostream>
 #include <vector>
 
@@ -89,7 +89,9 @@ void testTorsions() {
 
     // Set the atoms in various positions, and verify that both systems give identical forces and energy.
 
-    init_gen_rand(0);
+    OpenMM_SFMT::SFMT sfmt;
+    init_gen_rand(0, sfmt);
+
     vector<Vec3> positions(5);
     VerletIntegrator integrator1(0.01);
     VerletIntegrator integrator2(0.01);
@@ -97,7 +99,7 @@ void testTorsions() {
         Context c1(customSystem, integrator1, platform);
         Context c2(harmonicSystem, integrator2, platform);
         for (int j = 0; j < (int) positions.size(); j++)
-            positions[j] = Vec3(5.0*genrand_real2(), 5.0*genrand_real2(), 5.0*genrand_real2());
+            positions[j] = Vec3(5.0*genrand_real2(sfmt), 5.0*genrand_real2(sfmt), 5.0*genrand_real2(sfmt));
         c1.setPositions(positions);
         c2.setPositions(positions);
         State s1 = c1.getState(State::Forces | State::Energy);

platforms/reference/tests/TestReferenceEwald.cpp

@@ -40,7 +40,7 @@
 #include "openmm/System.h"
 #include "openmm/VerletIntegrator.h"
 #include "../src/SimTKUtilities/SimTKOpenMMRealType.h"
-#include "../src/sfmt/SFMT.h"
+#include "sfmt/SFMT.h"
 #include "openmm/HarmonicBondForce.h"
 #include <iostream>
 #include <vector>
@@ -312,11 +312,13 @@ void testErrorTolerance(NonbondedForce::NonbondedMethod method) {
     NonbondedForce* force = new NonbondedForce();
     system.addForce(force);
     vector<Vec3> positions(numParticles);
-    init_gen_rand(0);
+    OpenMM_SFMT::SFMT sfmt;
+    init_gen_rand(0, sfmt);
+
     for (int i = 0; i < numParticles; i++) {
         system.addParticle(1.0);
         force->addParticle(-1.0+i*2.0/(numParticles-1), 1.0, 0.0);
-        positions[i] = Vec3(boxWidth*genrand_real2(), boxWidth*genrand_real2(), boxWidth*genrand_real2());
+        positions[i] = Vec3(boxWidth*genrand_real2(sfmt), boxWidth*genrand_real2(sfmt), boxWidth*genrand_real2(sfmt));
     }
     force->setNonbondedMethod(method);
     ReferencePlatform platform;

platforms/reference/tests/TestReferenceGBSAOBCForce.cpp

@@ -41,7 +41,7 @@
 #include "openmm/LangevinIntegrator.h"
 #include "openmm/NonbondedForce.h"
 #include "../src/SimTKUtilities/SimTKOpenMMRealType.h"
-#include "../src/sfmt/SFMT.h"
+#include "sfmt/SFMT.h"
 #include <iostream>
 #include <vector>
 
@@ -144,9 +144,11 @@ void testForce() {
     // Set random positions for all the particles.
     
     vector<Vec3> positions(numParticles);
-    init_gen_rand(0);
+    OpenMM_SFMT::SFMT sfmt;
+    init_gen_rand(0, sfmt);
+
     for (int i = 0; i < numParticles; ++i)
-        positions[i] = Vec3(5.0*genrand_real2(), 5.0*genrand_real2(), 5.0*genrand_real2());
+        positions[i] = Vec3(5.0*genrand_real2(sfmt), 5.0*genrand_real2(sfmt), 5.0*genrand_real2(sfmt));
     context.setPositions(positions);
     State state = context.getState(State::Forces | State::Energy);
     

platforms/reference/tests/TestReferenceGBVIForce.cpp

@@ -43,7 +43,7 @@
 #include "openmm/LangevinIntegrator.h"
 #include "openmm/NonbondedForce.h"
 #include "../src/SimTKUtilities/SimTKOpenMMRealType.h"
-#include "../src/sfmt/SFMT.h"
+#include "sfmt/SFMT.h"
 #include <iostream>
 #include <vector>
 

platforms/reference/tests/TestReferenceLangevinIntegrator.cpp

@@ -41,7 +41,7 @@
 #include "openmm/System.h"
 #include "openmm/LangevinIntegrator.h"
 #include "../src/SimTKUtilities/SimTKOpenMMRealType.h"
-#include "../src/sfmt/SFMT.h"
+#include "sfmt/SFMT.h"
 #include <iostream>
 #include <vector>
 
@@ -147,10 +147,12 @@ void testConstraints() {
     Context context(system, integrator, platform);
     vector<Vec3> positions(numParticles);
     vector<Vec3> velocities(numParticles);
-    init_gen_rand(0);
+    OpenMM_SFMT::SFMT sfmt;
+    init_gen_rand(0, sfmt);
+
     for (int i = 0; i < numParticles; ++i) {
         positions[i] = Vec3(i/2, (i+1)/2, 0);
-        velocities[i] = Vec3(genrand_real2()-0.5, genrand_real2()-0.5, genrand_real2()-0.5);
+        velocities[i] = Vec3(genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5);
     }
     context.setPositions(positions);
     context.setVelocities(velocities);

platforms/reference/tests/TestReferenceNeighborList.cpp

@@ -31,7 +31,7 @@
 
 #include "../../../tests/AssertionUtilities.h"
 #include "../src/SimTKReference/ReferenceNeighborList.h"
-#include "../src/sfmt/SFMT.h"
+#include "sfmt/SFMT.h"
 #include <cassert>
 #include <iostream>
 
@@ -103,12 +103,14 @@ void testPeriodic() {
     const double cutoff = 3.0;
     const RealOpenMM periodicBoxSize[3] = {20.0, 15.0, 22.0};
     RealOpenMM* particleList[numParticles];
-    init_gen_rand(0);
+    OpenMM_SFMT::SFMT sfmt;
+    init_gen_rand(0, sfmt);
+
     for (int i = 0; i <numParticles; i++) {
         particleList[i] = new RealOpenMM[3];
-        particleList[i][0] = (RealOpenMM) (genrand_real2()*periodicBoxSize[0]*3);
-        particleList[i][1] = (RealOpenMM) (genrand_real2()*periodicBoxSize[1]*3);
-        particleList[i][2] = (RealOpenMM) (genrand_real2()*periodicBoxSize[2]*3);
+        particleList[i][0] = (RealOpenMM) (genrand_real2(sfmt)*periodicBoxSize[0]*3);
+        particleList[i][1] = (RealOpenMM) (genrand_real2(sfmt)*periodicBoxSize[1]*3);
+        particleList[i][2] = (RealOpenMM) (genrand_real2(sfmt)*periodicBoxSize[2]*3);
     }
     vector<set<int> > exclusions(numParticles);
     NeighborList neighborList;

platforms/reference/tests/TestReferenceVariableLangevinIntegrator.cpp

@@ -41,7 +41,7 @@
 #include "openmm/System.h"
 #include "openmm/VariableLangevinIntegrator.h"
 #include "../src/SimTKUtilities/SimTKOpenMMRealType.h"
-#include "../src/sfmt/SFMT.h"
+#include "sfmt/SFMT.h"
 #include <iostream>
 #include <vector>
 
@@ -148,10 +148,12 @@ void testConstraints() {
     Context context(system, integrator, platform);
     vector<Vec3> positions(numParticles);
     vector<Vec3> velocities(numParticles);
-    init_gen_rand(0);
+    OpenMM_SFMT::SFMT sfmt;
+    init_gen_rand(0, sfmt);
+
     for (int i = 0; i < numParticles; ++i) {
         positions[i] = Vec3(i/2, (i+1)/2, 0);
-        velocities[i] = Vec3(genrand_real2()-0.5, genrand_real2()-0.5, genrand_real2()-0.5);
+        velocities[i] = Vec3(genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5);
     }
     context.setPositions(positions);
     context.setVelocities(velocities);

platforms/reference/tests/TestReferenceVariableVerletIntegrator.cpp

@@ -41,7 +41,7 @@
 #include "openmm/System.h"
 #include "openmm/VariableVerletIntegrator.h"
 #include "../src/SimTKUtilities/SimTKOpenMMRealType.h"
-#include "../src/sfmt/SFMT.h"
+#include "sfmt/SFMT.h"
 #include <iostream>
 #include <vector>
 
@@ -104,10 +104,12 @@ void testConstraints() {
     Context context(system, integrator, platform);
     vector<Vec3> positions(numParticles);
     vector<Vec3> velocities(numParticles);
-    init_gen_rand(0);
+    OpenMM_SFMT::SFMT sfmt;
+    init_gen_rand(0, sfmt);
+
     for (int i = 0; i < numParticles; ++i) {
         positions[i] = Vec3(i/2, (i+1)/2, 0);
-        velocities[i] = Vec3(genrand_real2()-0.5, genrand_real2()-0.5, genrand_real2()-0.5);
+        velocities[i] = Vec3(genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5);
     }
     context.setPositions(positions);
     context.setVelocities(velocities);
@@ -176,9 +178,11 @@ void testConstrainedClusters() {
     positions[5] = Vec3(2, 0, 0);
     positions[6] = Vec3(1, 1, 0);
     vector<Vec3> velocities(numParticles);
-    init_gen_rand(0);
+    OpenMM_SFMT::SFMT sfmt;
+    init_gen_rand(0, sfmt);
+
     for (int i = 0; i < numParticles; ++i)
-        velocities[i] = Vec3(genrand_real2()-0.5, genrand_real2()-0.5, genrand_real2()-0.5);
+        velocities[i] = Vec3(genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5);
     context.setPositions(positions);
     context.setVelocities(velocities);
 

platforms/reference/tests/TestReferenceVerletIntegrator.cpp

@@ -41,7 +41,7 @@
 #include "openmm/System.h"
 #include "openmm/VerletIntegrator.h"
 #include "../src/SimTKUtilities/SimTKOpenMMRealType.h"
-#include "../src/sfmt/SFMT.h"
+#include "sfmt/SFMT.h"
 #include <iostream>
 #include <vector>
 
@@ -103,10 +103,12 @@ void testConstraints() {
     Context context(system, integrator, platform);
     vector<Vec3> positions(numParticles);
     vector<Vec3> velocities(numParticles);
-    init_gen_rand(0);
+    OpenMM_SFMT::SFMT sfmt;
+    init_gen_rand(0, sfmt);
+
     for (int i = 0; i < numParticles; ++i) {
         positions[i] = Vec3(i/2, (i+1)/2, 0);
-        velocities[i] = Vec3(genrand_real2()-0.5, genrand_real2()-0.5, genrand_real2()-0.5);
+        velocities[i] = Vec3(genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5);
     }
     context.setPositions(positions);
     context.setVelocities(velocities);
@@ -167,9 +169,11 @@ void testConstrainedClusters() {
     positions[5] = Vec3(2, 0, 0);
     positions[6] = Vec3(1, 1, 0);
     vector<Vec3> velocities(numParticles);
-    init_gen_rand(0);
+    OpenMM_SFMT::SFMT sfmt;
+    init_gen_rand(0, sfmt);
+
     for (int i = 0; i < numParticles; ++i)
-        velocities[i] = Vec3(genrand_real2()-0.5, genrand_real2()-0.5, genrand_real2()-0.5);
+        velocities[i] = Vec3(genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5);
     context.setPositions(positions);
     context.setVelocities(velocities);