diff --git a/Configuration.cpp b/Configuration.cpp
index 258ce8170aadd486d702fe7ff01ac721cb0fcb97..c74fac5c527d1fb3c397606def72c684be41e2a4 100644
--- a/Configuration.cpp
+++ b/Configuration.cpp
@@ -777,7 +777,17 @@ int Configuration::readParameters(const char * config_file) {
rigidBody[currRB].addDensityGrid(value);
else if (param == String("potentialGrid"))
rigidBody[currRB].addPotentialGrid(value);
-
+ else if (param == String("densityGridScale"))
+ rigidBody[currRB].scaleDensityGrid(value);
+ else if (param == String("potentialGridScale"))
+ rigidBody[currRB].scalePotentialGrid(value);
+ else if (param == String("pmfScale"))
+ rigidBody[currRB].scalePMF(value);
+ else if (param == String("position"))
+ rigidBody[currRB].initPos = stringToVector3( value );
+ else if (param == String("orientation"))
+ rigidBody[currRB].initRot = stringToMatrix3( value );
+
// COMMON
else if (param == String("num")) {
if (currPartClass == partClassPart)
@@ -817,6 +827,26 @@ Vector3 Configuration::stringToVector3(String s) {
(float) strtod(token[2], NULL) );
return v;
}
+Matrix3 Configuration::stringToMatrix3(String s) {
+ // tokenize and return
+ int numTokens = s.tokenCount();
+ if (numTokens != 9) {
+ printf("ERROR: could not convert input to Matrix3.\n"); // TODO improve this message
+ exit(1);
+ }
+ String* token = new String[numTokens];
+ s.tokenize(token);
+ Matrix3 m( (float) strtod(token[0], NULL),
+ (float) strtod(token[1], NULL),
+ (float) strtod(token[2], NULL),
+ (float) strtod(token[3], NULL),
+ (float) strtod(token[4], NULL),
+ (float) strtod(token[5], NULL),
+ (float) strtod(token[6], NULL),
+ (float) strtod(token[7], NULL),
+ (float) strtod(token[8], NULL) );
+ return m;
+}
void Configuration::readAtoms() {
// Open the file
diff --git a/Configuration.h b/Configuration.h
index cb255b12fd4b9dd0a785f7c963b3db02c494f50f..b9143b7eceb4ee7160c3ad39acf1b7423ba226c4 100644
--- a/Configuration.h
+++ b/Configuration.h
@@ -44,7 +44,7 @@ class Configuration {
void setDefaults();
Vector3 stringToVector3(String s);
-
+ Matrix3 stringToMatrix3(String s);
int readParameters(const char* config_file);
void readAngles();
diff --git a/RigidBody.cu b/RigidBody.cu
index 2a6347876e12c5b7e735f6773ab6f940b8740e4d..0477a2771521de361b764433068770dd78bd8b99 100644
--- a/RigidBody.cu
+++ b/RigidBody.cu
@@ -19,10 +19,10 @@ RigidBody::RigidBody(const Configuration& cref, RigidBodyType& tref)
Temp = 295;
// tempgrid = c->temperatureGrid;
- position = Vector3();
+ position = t->initPos; // Vector3();
// Orientation matrix that brings vector from the RB frame to the lab frame
- orientation = Matrix3(1.0f);
+ orientation = t->initRot; //Matrix3(1.0f);
momentum = Vector3() * t->mass; // lab frame
/* DebugM(4, "velocity " << rbParams->velocity << "\n" << endi); */
diff --git a/RigidBodyType.cu b/RigidBodyType.cu
index bf0f416793c8f7b9c9e1aa33eafd37220a26607e..88720bb77679655e89a3e7b119f408f14b459e68 100644
--- a/RigidBodyType.cu
+++ b/RigidBodyType.cu
@@ -94,25 +94,29 @@ void RigidBodyType::setDampingCoeffs(float timestep) { /* MUST ONLY BE CALLED ON
transDamping = 2.3900574 * transDamping;
rotDamping = 2.3900574 * rotDamping;
-
-}
-void RigidBodyType::addPotentialGrid(String s) {
- // tokenize and return
- int numTokens = s.tokenCount();
- if (numTokens != 2) {
- printf("ERROR: could not add Grid.\n"); // TODO improve this message
- exit(1);
+ // Also apply scale factors
+ applyScaleFactors();
+}
+void RigidBodyType::applyScaleFactors() { /* currently this is called before raw is updated */
+ applyScaleFactor(potentialGridScaleKeys, potentialGridScale, potentialGridKeys, potentialGrids);
+ applyScaleFactor(densityGridScaleKeys, densityGridScale, densityGridKeys, densityGrids);
+ applyScaleFactor(pmfScaleKeys, pmfScale, pmfKeys, pmfs);
+}
+void RigidBodyType::applyScaleFactor(
+ const std::vector<String> &scaleKeys, const std::vector<float> &scaleFactors,
+ const std::vector<String> &gridKeys, std::vector<BaseGrid> &grids) {
+ for (int i = 0; i < scaleKeys.size(); i++) {
+ const String &k1 = scaleKeys[i];
+ for (int j = 0; j < gridKeys.size(); j++) {
+ const String &k2 = gridKeys[j];
+ if ( k1 == k2 )
+ grids[j].scale( scaleFactors[i] );
+ }
}
- String* token = new String[numTokens];
- s.tokenize(token);
- String key = token[0];
- BaseGrid g(token[1]);
-
- potentialGrids.push_back( g );
- potentialGridKeys.push_back( key );
}
-void RigidBodyType::addDensityGrid(String s) {
+
+void RigidBodyType::addGrid(String s, std::vector<String> &keys, std::vector<BaseGrid> &grids) {
// tokenize and return
int numTokens = s.tokenCount();
if (numTokens != 2) {
@@ -123,12 +127,21 @@ void RigidBodyType::addDensityGrid(String s) {
s.tokenize(token);
String key = token[0];
BaseGrid g(token[1]);
-
- densityGrids.push_back( g );
- densityGridKeys.push_back( key );
+ keys.push_back( key );
+ grids.push_back( g );
+}
+void RigidBodyType::addPotentialGrid(String s) {
+ addGrid(s, potentialGridKeys, potentialGrids);
+}
+void RigidBodyType::addDensityGrid(String s) {
+ addGrid(s, densityGridKeys, densityGrids);
}
void RigidBodyType::addPMF(String s) {
+ addGrid(s, pmfKeys, pmfs);
+}
+
+void RigidBodyType::addScaleFactor(String s, std::vector<String> &keys, std::vector<float> &vals) {
// tokenize and return
int numTokens = s.tokenCount();
if (numTokens != 2) {
@@ -138,10 +151,18 @@ void RigidBodyType::addPMF(String s) {
String* token = new String[numTokens];
s.tokenize(token);
String key = token[0];
- BaseGrid g(token[1]);
-
- pmfs.push_back( g );
- pmfKeys.push_back( key );
+ float v = (float) strtod(token[1], NULL);
+ keys.push_back( key );
+ vals.push_back( v );
+}
+void RigidBodyType::scalePotentialGrid(String s) {
+ addScaleFactor(s, potentialGridScaleKeys, potentialGridScale);
+}
+void RigidBodyType::scaleDensityGrid(String s) {
+ addScaleFactor(s, densityGridScaleKeys, densityGridScale);
+}
+void RigidBodyType::scalePMF(String s) {
+ addScaleFactor(s, pmfScaleKeys, pmfScale);
}
void RigidBodyType::updateRaw() {
@@ -176,7 +197,6 @@ void RigidBodyType::updateRaw() {
rawDensityOrigins[i] = densityGrids[i].getOrigin();
}
for (int i=0; i < numPmfs; i++)
- rawPmfs[i] = pmfs[i];
-
+ rawPmfs[i] = pmfs[i];
}
diff --git a/RigidBodyType.h b/RigidBodyType.h
index c9e32586aa84b09b9c45c8ebaa2544182df0d708..389d27cf6ffe4adc99879bcc107e3b57aa020b5a 100644
--- a/RigidBodyType.h
+++ b/RigidBodyType.h
@@ -18,6 +18,13 @@ private:
void clear();
// void copy(const RigidBodyType& src);
+ void addGrid(String s, std::vector<String> &keys, std::vector<BaseGrid> &grids);
+ void addScaleFactor(String s, std::vector<String> &keys, std::vector<float> &vals);
+ void applyScaleFactors();
+ void applyScaleFactor(
+ const std::vector<String> &scaleKeys, const std::vector<float> &scaleFactors,
+ const std::vector<String> &gridKeys, std::vector<BaseGrid> &grids);
+
public:
/* RigidBodyType(const String& name = "") : */
/* name(name), num(0), */
@@ -27,8 +34,9 @@ public:
RigidBodyType(const String& name = "") :
name(name), num(0),
- reservoir(NULL), mass(1.0f), inertia(), transDamping(),
- rotDamping(), numPotGrids(0), numDenGrids(0), numPmfs(0) { }
+ reservoir(NULL), mass(1.0f), inertia(), transDamping(),
+ rotDamping(), numPotGrids(0), numDenGrids(0), numPmfs(0),
+ initPos(), initRot(Matrix3(1.0f)) { }
/* RigidBodyType(const RigidBodyType& src) { copy(src); } */
~RigidBodyType() { clear(); }
@@ -38,6 +46,10 @@ RigidBodyType(const String& name = "") :
void addPotentialGrid(String s);
void addDensityGrid(String s);
void addPMF(String s);
+ void scalePotentialGrid(String s);
+ void scaleDensityGrid(String s);
+ void scalePMF(String s);
+
void updateRaw();
void setDampingCoeffs(float timestep);
@@ -56,6 +68,9 @@ public:
Vector3 transForceCoeff;
Vector3 rotTorqueCoeff;
+ Vector3 initPos;
+ Matrix3 initRot;
+
std::vector<String> potentialGridKeys;
std::vector<String> densityGridKeys;
std::vector<String> pmfKeys;
@@ -64,6 +79,15 @@ public:
std::vector<BaseGrid> densityGrids;
std::vector<BaseGrid> pmfs;
+ std::vector<String> potentialGridScaleKeys;
+ std::vector<String> densityGridScaleKeys;
+ std::vector<String> pmfScaleKeys;
+
+ std::vector<float> potentialGridScale;
+ std::vector<float> densityGridScale;
+ std::vector<float> pmfScale;
+
+
// RBTODO: clear std::vectors after initialization
// duplicates of std::vector grids for device
int numPotGrids;