diff --git a/src/RigidBodyController.cu b/src/RigidBodyController.cu
index 790ce71ab956c3fc8fb54757ee787f2af59e491f..43bb3bfb0314d519b7831d2f43dddabe677cb6ed 100644
--- a/src/RigidBodyController.cu
+++ b/src/RigidBodyController.cu
@@ -82,7 +82,7 @@ RigidBodyController::RigidBodyController(const Configuration& c, const char* pre
random = new RandomCPU(conf.seed + repID + 1); /* +1 to avoid using same seed as RandomCUDA */
- initializeForcePairs();
+ initializeForcePairs(); // Must run after construct_grids()
gpuErrchk(cudaDeviceSynchronize()); /* RBTODO: this should be extraneous */
//Boltzmann distribution
@@ -117,7 +117,7 @@ void RigidBodyController::construct_grids() {
// typedef std::tuple<String, float> GridKey;
// Build dictionary to reuse grids across all types, first finding scale factors
- std::vector<GridKey> all_keys;
+ std::vector<GridKey> all_files;
std::vector<GridKey>::iterator itr;
for (int t_idx = 0; t_idx < conf.numRigidTypes; ++t_idx)
@@ -129,10 +129,10 @@ void RigidBodyController::construct_grids() {
t.potential_grid_idx = new size_t[t.numPotGrids]; // TODO; don't allocate here
t.density_grid_idx = new size_t[t.numDenGrids]; // TODO; don't allocate here
t.pmf_grid_idx = new size_t[t.numPmfs]; // TODO; don't allocate here
- for (int i = 0; i < t.potentialGridKeys.size(); ++i)
+ for (int i = 0; i < t.potentialGridFiles.size(); ++i)
{
- String& name = t.potentialGridKeys[i];
+ String& name = t.potentialGridFiles[i];
float scale = 1.0f;
for (int j = 0; j < t.potentialGridScaleKeys.size(); ++j)
{
@@ -143,27 +143,27 @@ void RigidBodyController::construct_grids() {
GridKey key = GridKey(name, scale);
int key_idx = -1;
// Find key if it exists
- itr = std::find(all_keys.begin(), all_keys.end(), key);
- if (itr == all_keys.end())
+ itr = std::find(all_files.begin(), all_files.end(), key);
+ if (itr == all_files.end())
{
- key_idx = all_keys.size();
- all_keys.push_back( key );
+ key_idx = all_files.size();
+ all_files.push_back( key );
}
else
{
- key_idx = std::distance(all_keys.begin(), itr);
+ key_idx = std::distance(all_files.begin(), itr);
}
- // Assign index into all_keys to RigidBodyType
+ // Assign index into all_files to RigidBodyType
t.potential_grid_idx[i] = key_idx;
}
// Density
- for (int i = 0; i < t.densityGridKeys.size(); ++i)
+ for (int i = 0; i < t.densityGridFiles.size(); ++i)
{
- String& name = t.densityGridKeys[i];
+ String& name = t.densityGridFiles[i];
float scale = 1.0f;
for (int j = 0; j < t.densityGridScaleKeys.size(); ++j)
{
@@ -174,26 +174,26 @@ void RigidBodyController::construct_grids() {
GridKey key = GridKey(name, scale);
int key_idx = -1;
// Find key if it exists
- itr = std::find(all_keys.begin(), all_keys.end(), key);
- if (itr == all_keys.end())
+ itr = std::find(all_files.begin(), all_files.end(), key);
+ if (itr == all_files.end())
{
- key_idx = all_keys.size();
- all_keys.push_back( key );
+ key_idx = all_files.size();
+ all_files.push_back( key );
}
else
{
- key_idx = std::distance(all_keys.begin(), itr);
+ key_idx = std::distance(all_files.begin(), itr);
}
- // Assign index into all_keys to RigidBodyType
+ // Assign index into all_files to RigidBodyType
t.density_grid_idx[i] = key_idx;
}
//PMF
- for (int i = 0; i < t.pmfKeys.size(); ++i)
+ for (int i = 0; i < t.pmfFiles.size(); ++i)
{
- String& name = t.pmfKeys[i];
+ String& name = t.pmfFiles[i];
float scale = 1.0f;
for (int j = 0; j < t.pmfScaleKeys.size(); ++j)
{
@@ -204,18 +204,18 @@ void RigidBodyController::construct_grids() {
GridKey key = GridKey(name, scale);
int key_idx = -1;
// Find key if it exists
- itr = std::find(all_keys.begin(), all_keys.end(), key);
- if (itr == all_keys.end())
+ itr = std::find(all_files.begin(), all_files.end(), key);
+ if (itr == all_files.end())
{
- key_idx = all_keys.size();
- all_keys.push_back( key );
+ key_idx = all_files.size();
+ all_files.push_back( key );
}
else
{
- key_idx = std::distance(all_keys.begin(), itr);
+ key_idx = std::distance(all_files.begin(), itr);
}
- // Assign index into all_keys to RigidBodyType
+ // Assign index into all_files to RigidBodyType
t.pmf_grid_idx[i] = key_idx;
}
@@ -232,27 +232,32 @@ void RigidBodyController::construct_grids() {
}
// Store grids
- grids = new BaseGrid[all_keys.size()];
- gpuErrchk(cudaMalloc( &grids_d, sizeof(RigidBodyGrid)*all_keys.size() ));
+ grids = new BaseGrid[all_files.size()];
+ gpuErrchk(cudaMalloc( &grids_d, sizeof(RigidBodyGrid)*all_files.size() ));
// Read and scale grids, then copy to GPU
- for (size_t i = 0; i < all_keys.size(); ++i)
+ for (size_t i = 0; i < all_files.size(); ++i)
{
- GridKey& key = all_keys[i];
- BaseGrid& g = grids[i];
- g = BaseGrid(key.name);
- g.scale(key.scale);
-
+ GridKey& key = all_files[i];
+ BaseGrid& g0 = grids[i];
+ g0 = BaseGrid(key.name);
+ g0.scale(key.scale);
+
+ RigidBodyGrid g = RigidBodyGrid();
+ g.nx = g0.nx;
+ g.ny = g0.ny;
+ g.nz = g0.nz;
+ g.size = g0.size;
+ g.val = g0.val;
+
// Copy to GPU, starting with grid data
- float* tmp1;
- float* tmp2;
+ float* tmp;
size_t sz = sizeof(float) * g.getSize();
- gpuErrchk(cudaMalloc( &tmp1, sz));
- gpuErrchk(cudaMemcpy( tmp1, g.val, sz, cudaMemcpyHostToDevice));
+ gpuErrchk(cudaMalloc( &tmp, sz));
+ gpuErrchk(cudaMemcpy( tmp, g.val, sz, cudaMemcpyHostToDevice));
// Set grid pointer to device
- tmp2 = g.val;
- g.val = tmp1;
+ g.val = tmp;
// Copy grid
sz = sizeof(RigidBodyGrid);
@@ -260,9 +265,8 @@ void RigidBodyController::construct_grids() {
gpuErrchk(cudaMemcpy(&grids_d[i], &g, sz, cudaMemcpyHostToDevice));
// Restore pointer
- g.val = tmp2;
- tmp1 = NULL;
- tmp2 = NULL; // probably unnecessary
+ g.val = NULL;
+ tmp = NULL;
}
}
@@ -372,8 +376,8 @@ void RigidBodyController::initializeForcePairs() {
// keys1[k1].printInline(); printf(":"); keys2[k2].print();
if ( keys1[k1] == keys2[k2] ) {
- gridKeyId1.push_back(k1);
- gridKeyId2.push_back(k2);
+ gridKeyId1.push_back( t1.density_grid_idx[k1] );
+ gridKeyId2.push_back( t2.potential_grid_idx[k2] );
paired = true;
}
}
@@ -415,9 +419,9 @@ void RigidBodyController::initializeForcePairs() {
for(int k1 = 0; k1 < keys1.size(); k1++) {
for(int k2 = 0; k2 < keys2.size(); k2++) {
if ( keys1[k1] == keys2[k2] ) {
- gridKeyId1.push_back(k1);
- gridKeyId2.push_back(k2);
- paired = true;
+ gridKeyId1.push_back( t1.density_grid_idx[k1] );
+ gridKeyId2.push_back( t1.pmf_grid_idx[k2] );
+ paired = true;
}
}
}
diff --git a/src/RigidBodyType.cu b/src/RigidBodyType.cu
index 6d74c46eb235177fab3ee23d95eceeb9e0664e3f..170369161feb76ffa7c95fb6a337ed9dbd673761 100644
--- a/src/RigidBodyType.cu
+++ b/src/RigidBodyType.cu
@@ -79,7 +79,7 @@ void RigidBodyType::setDampingCoeffs(float timestep) { /* MUST ONLY BE CALLED ON
}
-void RigidBodyType::addGrid(String s, std::vector<String> &keys) {
+void RigidBodyType::addGrid(String s, std::vector<String> &keys, std::vector<String> &files) {
// tokenize and return
int numTokens = s.tokenCount();
if (numTokens != 2) {
@@ -88,17 +88,18 @@ void RigidBodyType::addGrid(String s, std::vector<String> &keys) {
}
String* token = new String[numTokens];
s.tokenize(token);
- String key = token[0];
- keys.push_back( key );
+ keys.push_back( String(token[0]) );
+ files.push_back( String(token[1]) );
+ delete[] token;
}
void RigidBodyType::addPotentialGrid(String s) {
- addGrid(s, potentialGridKeys);
+ addGrid(s, potentialGridKeys, potentialGridFiles);
}
void RigidBodyType::addDensityGrid(String s) {
- addGrid(s, densityGridKeys);
+ addGrid(s, densityGridKeys, potentialGridFiles);
}
void RigidBodyType::addPMF(String s) {
- addGrid(s, pmfKeys);
+ addGrid(s, pmfKeys, potentialGridFiles);
}
void RigidBodyType::addScaleFactor(String s, std::vector<String> &keys, std::vector<float> &vals) {
@@ -114,6 +115,7 @@ void RigidBodyType::addScaleFactor(String s, std::vector<String> &keys, std::vec
float v = (float) strtod(token[1], NULL);
keys.push_back( key );
vals.push_back( v );
+ delete[] token;
}
void RigidBodyType::scalePotentialGrid(String s) {
addScaleFactor(s, potentialGridScaleKeys, potentialGridScale);
diff --git a/src/RigidBodyType.h b/src/RigidBodyType.h
index ef42d226c4a2af2e35422128177cd922a6d6076f..575a31348eb24dd305e913bbf46bf0b095bb8649 100644
--- a/src/RigidBodyType.h
+++ b/src/RigidBodyType.h
@@ -32,7 +32,7 @@ private:
void clear();
// void copy(const RigidBodyType& src);
- void addGrid(String s, std::vector<String> &keys);
+ void addGrid(String s, std::vector<String> &keys, std::vector<String> &files);
void addScaleFactor(String s, std::vector<String> &keys, std::vector<float> &vals);
public:
@@ -75,6 +75,10 @@ public:
std::vector<String> densityGridKeys;
std::vector<String> pmfKeys;
+ std::vector<String> potentialGridFiles;
+ std::vector<String> densityGridFiles;
+ std::vector<String> pmfFiles;
+
std::vector<String> potentialGridScaleKeys;
std::vector<String> densityGridScaleKeys;
std::vector<String> pmfScaleKeys;