Replaced some tabs with spaces

openmmapi/src/Context.cpp

@@ -53,7 +53,7 @@ Context::Context(const System& system, Integrator& integrator, Platform& platfor
 }
 
 Context::~Context() {
-	delete impl;
+    delete impl;
 }
 
 const System& Context::getSystem() const {

openmmapi/src/MonteCarloBarostatImpl.cpp

@@ -64,13 +64,13 @@ void MonteCarloBarostatImpl::updateContextState(ContextImpl& context) {
     if (++step < owner.getFrequency() || owner.getFrequency() == 0)
         return;
     step = 0;
-
+    
     // Compute the current potential energy.
-
+    
     double initialEnergy = context.getOwner().getState(State::Energy).getPotentialEnergy();
-
+    
     // Modify the periodic box size.
-
+    
     Vec3 box[3];
     context.getPeriodicBoxVectors(box[0], box[1], box[2]);
     double volume = box[0][0]*box[1][1]*box[2][2];
@@ -79,7 +79,7 @@ void MonteCarloBarostatImpl::updateContextState(ContextImpl& context) {
     double lengthScale = std::pow(newVolume/volume, 1.0/3.0);
     kernel.getAs<ApplyMonteCarloBarostatKernel>().scaleCoordinates(context, lengthScale, lengthScale, lengthScale);
     context.getOwner().setPeriodicBoxVectors(box[0]*lengthScale, box[1]*lengthScale, box[2]*lengthScale);
-
+    
     // Compute the energy of the modified system.
     
     double finalEnergy = context.getOwner().getState(State::Energy).getPotentialEnergy();
@@ -88,7 +88,7 @@ void MonteCarloBarostatImpl::updateContextState(ContextImpl& context) {
     double w = finalEnergy-initialEnergy + pressure*deltaVolume - context.getMolecules().size()*kT*std::log(newVolume/volume);
     if (w > 0 && genrand_real2(random) > std::exp(-w/kT)) {
         // Reject the step.
-
+        
         kernel.getAs<ApplyMonteCarloBarostatKernel>().restoreCoordinates(context);
         context.getOwner().setPeriodicBoxVectors(box[0], box[1], box[2]);
         volume = newVolume;
@@ -145,33 +145,33 @@ void MonteCarloAnisotropicBarostatImpl::updateContextState(ContextImpl& context)
     if (owner.getScaleX() == 0 && owner.getScaleY() == 0 && owner.getScaleZ() == 0)
         return;
     step = 0;
-
+    
     // Compute the current potential energy.
-
+    
     double initialEnergy = context.getOwner().getState(State::Energy).getPotentialEnergy();
     double pressure;
-
+    
     // Choose which axis to modify at random.
     double rnd = genrand_real2(random)*3.0;
     int axis;
     while (1) {
         if (rnd < 1.0 && owner.getScaleX()) {
             axis = 0;
-	    pressure = context.getParameter(MonteCarloAnisotropicBarostat::PressureX())*(AVOGADRO*1e-25);
+            pressure = context.getParameter(MonteCarloAnisotropicBarostat::PressureX())*(AVOGADRO*1e-25);
             break;
         } else if (rnd < 2.0 && owner.getScaleY()) {
             axis = 1;
-	    pressure = context.getParameter(MonteCarloAnisotropicBarostat::PressureY())*(AVOGADRO*1e-25);
+            pressure = context.getParameter(MonteCarloAnisotropicBarostat::PressureY())*(AVOGADRO*1e-25);
             break;
         } else if (owner.getScaleZ()) {
             axis = 2;
-	    pressure = context.getParameter(MonteCarloAnisotropicBarostat::PressureZ())*(AVOGADRO*1e-25);
+            pressure = context.getParameter(MonteCarloAnisotropicBarostat::PressureZ())*(AVOGADRO*1e-25);
             break;
         }
     }
-
+    
     // Modify the periodic box size.
-
+    
     Vec3 box[3];
     context.getPeriodicBoxVectors(box[0], box[1], box[2]);
     double volume = box[0][0]*box[1][1]*box[2][2];
@@ -179,11 +179,11 @@ void MonteCarloAnisotropicBarostatImpl::updateContextState(ContextImpl& context)
     double newVolume = volume+deltaVolume;
     Vec3 lengthScale;
     for (int i=0; i<3; i++)
-      lengthScale[i] = 1.0;
+        lengthScale[i] = 1.0;
     lengthScale[axis] = newVolume/volume;
     kernel.getAs<ApplyMonteCarloAnisotropicBarostatKernel>().scaleCoordinates(context, lengthScale[0], lengthScale[1], lengthScale[2]);
     context.getOwner().setPeriodicBoxVectors(box[0]*lengthScale[0], box[1]*lengthScale[1], box[2]*lengthScale[2]);
-
+    
     // Compute the energy of the modified system.
     
     double finalEnergy = context.getOwner().getState(State::Energy).getPotentialEnergy();
@@ -191,7 +191,7 @@ void MonteCarloAnisotropicBarostatImpl::updateContextState(ContextImpl& context)
     double w = finalEnergy-initialEnergy + pressure*deltaVolume - context.getMolecules().size()*kT*std::log(newVolume/volume);
     if (w > 0 && genrand_real2(random) > std::exp(-w/kT)) {
         // Reject the step.
-
+        
         kernel.getAs<ApplyMonteCarloAnisotropicBarostatKernel>().restoreCoordinates(context);
         context.getOwner().setPeriodicBoxVectors(box[0], box[1], box[2]);
         volume = newVolume;

platforms/cuda/tests/TestCudaMonteCarloBarostat.cpp

@@ -98,9 +98,9 @@ void testIdealGas(int aniso) {
     const double temp[] = {300.0, 600.0, 1000.0};
     const double initialVolume = numParticles*BOLTZ*temp[1]/pressureInMD;
     const double initialLength = std::pow(initialVolume, 1.0/3.0);
-
+    
     // Create a gas of noninteracting particles.
-
+    
     System system;
     system.setDefaultPeriodicBoxVectors(Vec3(initialLength, 0, 0), Vec3(0, 0.5*initialLength, 0), Vec3(0, 0, 2*initialLength));
     vector<Vec3> positions(numParticles);
@@ -112,32 +112,32 @@ void testIdealGas(int aniso) {
     }
     MonteCarloBarostat* barostat = new MonteCarloBarostat(pressure, temp[0], frequency);
     if (aniso)
-      MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(Vec3(pressure, pressure, pressure), temp[0], frequency);
+        MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(Vec3(pressure, pressure, pressure), temp[0], frequency);
     system.addForce(barostat);
-
+    
     // Test it for three different temperatures.
-
+    
     for (int i = 0; i < 3; i++) {
         barostat->setTemperature(temp[i]);
         LangevinIntegrator integrator(temp[i], 0.1, 0.01);
         Context context(system, integrator, platform);
         context.setPositions(positions);
-
+        
         // Let it equilibrate.
-
+        
         integrator.step(10000);
-
+        
         // Now run it for a while and see if the volume is correct.
-
+        
         double volume = 0.0;
         for (int j = 0; j < steps; ++j) {
             Vec3 box[3];
             context.getState(0).getPeriodicBoxVectors(box[0], box[1], box[2]);
             volume += box[0][0]*box[1][1]*box[2][2];
-	    if (!aniso) {
-	      ASSERT_EQUAL_TOL(0.5*box[0][0], box[1][1], 1e-5);
-	      ASSERT_EQUAL_TOL(2*box[0][0], box[2][2], 1e-5);
-	    }
+            if (!aniso) {
+                ASSERT_EQUAL_TOL(0.5*box[0][0], box[1][1], 1e-5);
+                ASSERT_EQUAL_TOL(2*box[0][0], box[2][2], 1e-5);
+            }
             integrator.step(frequency);
         }
         volume /= steps;
@@ -168,9 +168,9 @@ void testRandomSeed() {
         positions[i] = Vec3((i%2 == 0 ? 2 : -2), (i%4 < 2 ? 2 : -2), (i < 4 ? 2 : -2));
         velocities[i] = Vec3(0, 0, 0);
     }
-
+    
     // Try twice with the same random seed.
-
+    
     barostat->setRandomNumberSeed(5);
     Context context(system, integrator, platform);
     context.setPositions(positions);
@@ -182,9 +182,9 @@ void testRandomSeed() {
     context.setVelocities(velocities);
     integrator.step(10);
     State state2 = context.getState(State::Positions);
-
+    
     // Try twice with a different random seed.
-
+    
     barostat->setRandomNumberSeed(10);
     context.reinitialize();
     context.setPositions(positions);
@@ -196,9 +196,9 @@ void testRandomSeed() {
     context.setVelocities(velocities);
     integrator.step(10);
     State state4 = context.getState(State::Positions);
-
+    
     // Compare the results.
-
+    
     for (int i = 0; i < numParticles; i++) {
         for (int j = 0; j < 3; j++) {
             ASSERT(state1.getPositions()[i][j] == state2.getPositions()[i][j]);
@@ -219,9 +219,9 @@ void testWater(int aniso) {
     const double angle = 109.47*M_PI/180;
     const double dOH = 0.1;
     const double dHH = dOH*2*std::sin(0.5*angle);
-
+    
     // Create a box of SPC water molecules.
-
+    
     System system;
     system.setDefaultPeriodicBoxVectors(Vec3(gridSize*spacing, 0, 0), Vec3(0, gridSize*spacing, 0), Vec3(0, 0, gridSize*spacing));
     NonbondedForce* nonbonded = new NonbondedForce();
@@ -256,11 +256,11 @@ void testWater(int aniso) {
     system.addForce(nonbonded);
     MonteCarloBarostat* barostat = new MonteCarloBarostat(pressure, temp, frequency);
     if (aniso)
-      MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(Vec3(pressure, pressure, pressure), temp, frequency);
+        MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(Vec3(pressure, pressure, pressure), temp, frequency);
     system.addForce(barostat);
-
+    
     // Simulate it and see if the density matches the expected value (1 g/mL).
-
+    
     LangevinIntegrator integrator(temp, 1.0, 0.002);
     Context context(system, integrator, platform);
     context.setPositions(positions);

platforms/opencl/src/kernels/monteCarloBarostat.cl

@@ -22,7 +22,7 @@ __kernel void scalePositions(float scaleX, float scaleY, float scaleZ, int numMo
         int ycell = (int) floor(center.y*invPeriodicBoxSize.y);
         int zcell = (int) floor(center.z*invPeriodicBoxSize.z);
         real4 delta = (real4) (xcell*periodicBoxSize.x, ycell*periodicBoxSize.y, zcell*periodicBoxSize.z, 0);
-	real4 scaleXYZ = (real4) (scaleX, scaleY, scaleZ, 1);
+        real4 scaleXYZ = (real4) (scaleX, scaleY, scaleZ, 1);
         center -= delta;
 
         // Now scale the position of the molecule center.

platforms/reference/tests/TestReferenceMonteCarloBarostat.cpp

@@ -97,9 +97,9 @@ void testIdealGas(int aniso) {
     const double temp[] = {300.0, 600.0, 1000.0};
     const double initialVolume = numParticles*BOLTZ*temp[1]/pressureInMD;
     const double initialLength = std::pow(initialVolume, 1.0/3.0);
-
+    
     // Create a gas of noninteracting particles.
-
+    
     ReferencePlatform platform;
     System system;
     system.setDefaultPeriodicBoxVectors(Vec3(initialLength, 0, 0), Vec3(0, 0.5*initialLength, 0), Vec3(0, 0, 2*initialLength));
@@ -112,32 +112,32 @@ void testIdealGas(int aniso) {
     }
     MonteCarloBarostat* barostat = new MonteCarloBarostat(pressure, temp[0], frequency);
     if (aniso)
-      MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(Vec3(pressure, pressure, pressure), temp[0], frequency);
+        MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(Vec3(pressure, pressure, pressure), temp[0], frequency);
     system.addForce(barostat);
-
+    
     // Test it for three different temperatures.
-
+    
     for (int i = 0; i < 3; i++) {
         barostat->setTemperature(temp[i]);
         LangevinIntegrator integrator(temp[i], 0.1, 0.01);
         Context context(system, integrator, platform);
         context.setPositions(positions);
-
+        
         // Let it equilibrate.
-
+        
         integrator.step(10000);
-
+        
         // Now run it for a while and see if the volume is correct.
-
+        
         double volume = 0.0;
         for (int j = 0; j < steps; ++j) {
             Vec3 box[3];
             context.getState(0).getPeriodicBoxVectors(box[0], box[1], box[2]);
             volume += box[0][0]*box[1][1]*box[2][2];
-	    if (!aniso) {
-	      ASSERT_EQUAL_TOL(0.5*box[0][0], box[1][1], 1e-5);
-	      ASSERT_EQUAL_TOL(2*box[0][0], box[2][2], 1e-5);
-	    }
+            if (!aniso) {
+                ASSERT_EQUAL_TOL(0.5*box[0][0], box[1][1], 1e-5);
+                ASSERT_EQUAL_TOL(2*box[0][0], box[2][2], 1e-5);
+            }
             integrator.step(frequency);
         }
         volume /= steps;
@@ -169,9 +169,9 @@ void testRandomSeed() {
         positions[i] = Vec3((i%2 == 0 ? 2 : -2), (i%4 < 2 ? 2 : -2), (i < 4 ? 2 : -2));
         velocities[i] = Vec3(0, 0, 0);
     }
-
+    
     // Try twice with the same random seed.
-
+    
     barostat->setRandomNumberSeed(5);
     Context context(system, integrator, platform);
     context.setPositions(positions);
@@ -183,9 +183,9 @@ void testRandomSeed() {
     context.setVelocities(velocities);
     integrator.step(10);
     State state2 = context.getState(State::Positions);
-
+    
     // Try twice with a different random seed.
-
+    
     barostat->setRandomNumberSeed(10);
     context.reinitialize();
     context.setPositions(positions);
@@ -197,9 +197,9 @@ void testRandomSeed() {
     context.setVelocities(velocities);
     integrator.step(10);
     State state4 = context.getState(State::Positions);
-
+    
     // Compare the results.
-
+    
     for (int i = 0; i < numParticles; i++) {
         for (int j = 0; j < 3; j++) {
             ASSERT(state1.getPositions()[i][j] == state2.getPositions()[i][j]);