diff --git a/src/Configuration.cpp b/src/Configuration.cpp
index 07b2796442586fb5431b0b71401f56f6412b3831..6a090d23b3579ecfbd58f5ccee00fac910848265 100644
--- a/src/Configuration.cpp
+++ b/src/Configuration.cpp
@@ -25,20 +25,20 @@ Configuration::Configuration(const char* config_file, int simNum, bool debug) :
readParameters(config_file);
// Get the number of particles
- printf("\nCounting particles specified in the ");
+ // printf("\nCounting particles specified in the ");
if (restartCoordinates.length() > 0) {
// Read them from the restart file.
- printf("restart file.\n");
+ // printf("restart file.\n");
num = countRestart(restartCoordinates.val());
} else {
if (readPartsFromFile) readAtoms();
if (numPartsFromFile > 0) {
// Determine number of particles from input file (PDB-style)
- printf("input file.\n");
+ // printf("input file.\n");
num = numPartsFromFile;
} else {
// Sum up all particles in config file
- printf("configuration file.\n");
+ // printf("configuration file.\n");
//int num0 = 0;
num = 0;
for (int i = 0; i < numParts; i++) num += part[i].num;
@@ -48,7 +48,7 @@ Configuration::Configuration(const char* config_file, int simNum, bool debug) :
// Set the number capacity
- printf("\nInitial particles: %d\n", num);
+ printf("\n%d particles\n", num);
if (numCap <= 0) numCap = numCapFactor*num; // max number of particles
if (numCap <= 0) numCap = 20;
@@ -152,7 +152,7 @@ Configuration::Configuration(const char* config_file, int simNum, bool debug) :
if (partGridFileScale[i] != 1.0f) part[i].pmf->scale(partGridFileScale[i]);
part[i].meanPmf = part[i].pmf->mean();
- printf("Loaded dx grid `%s'.\n", map.val());
+ printf("Loaded dx potential grid `%s'.\n", map.val());
printf("System size %s.\n", part[i].pmf->getExtent().toString().val());
} else if (len >= 4 && map[len-4]=='.' && map[len-3]=='d' && map[len-2]=='e' && map[len-1]=='f') {
// A system definition file.
@@ -429,7 +429,7 @@ Configuration::~Configuration() {
}
void Configuration::copyToCUDA() {
- printf("Copying to GPU %d\n", GPUManager::current());
+ printf("Copying particle data to GPU %d\n", GPUManager::current());
BrownianParticleType **part_addr = new BrownianParticleType*[numParts];
@@ -1400,7 +1400,7 @@ bool Configuration::readBondFile(const String& value, int currBond) {
bondTableFile[currBond] = tokenList[0];
- printf("Tabulated Bond Potential: %s\n", bondTableFile[currBond].val() );
+ // printf("Tabulated Bond Potential: %s\n", bondTableFile[currBond].val() );
return true;
}
@@ -1421,7 +1421,7 @@ bool Configuration::readAngleFile(const String& value, int currAngle) {
angleTableFile[currAngle] = tokenList[0];
- printf("Tabulated Angle Potential: %s\n", angleTableFile[currAngle].val() );
+ // printf("Tabulated Angle Potential: %s\n", angleTableFile[currAngle].val() );
return true;
}
@@ -1442,7 +1442,7 @@ bool Configuration::readDihedralFile(const String& value, int currDihedral) {
dihedralTableFile[currDihedral] = tokenList[0];
- printf("Tabulated Dihedral Potential: %s\n", dihedralTableFile[currDihedral].val() );
+ // printf("Tabulated Dihedral Potential: %s\n", dihedralTableFile[currDihedral].val() );
return true;
}
@@ -1622,8 +1622,8 @@ bool Configuration::readTableFile(const String& value, int currTab) {
partTableIndex1[currTab] = atoi(tokenList[1]);
partTableFile[currTab] = tokenList[2];
- printf("tabulatedPotential: %d %d %s\n", partTableIndex0[currTab],
- partTableIndex1[currTab], partTableFile[currTab].val() );
+ // printf("Tabulated Potential: %d %d %s\n", partTableIndex0[currTab],
+ // partTableIndex1[currTab], partTableFile[currTab].val() );
delete[] tokenList;
return true;
}
diff --git a/src/GrandBrownTown.cu b/src/GrandBrownTown.cu
index a5191dc45f175fbbd6b718b6a4a1ba3900eddb77..eedfdc18de72bf8c2f154e942a039306b3b50030 100644
--- a/src/GrandBrownTown.cu
+++ b/src/GrandBrownTown.cu
@@ -338,7 +338,7 @@ GrandBrownTown::~GrandBrownTown() {
// Run the Brownian Dynamics steps.
void GrandBrownTown::run() {
- printf("\n");
+ printf("\n\n");
Vector3 runningNetForce(0.0f);
// Open the files for recording ionic currents
@@ -671,7 +671,7 @@ void GrandBrownTown::run() {
setlocale(LC_NUMERIC, "");
// Do the output
- printf("Step %ld [%.2f%% complete | %.3f ms/step | %.3f ns/day]\n",
+ printf("\rStep %ld [%.2f%% complete | %.3f ms/step | %.3f ns/day]",
s, percent, msPerStep, nsPerDay);
/* printf("T: %.5g ns | E: %.5g | F: %.5g %.5g %.5g\n",
t, energy, force0.x, force0.y, force0.z);
@@ -705,19 +705,19 @@ void GrandBrownTown::run() {
int length;
switch (imd_recv_header(clientsock, &length)) {
case IMD_DISCONNECT:
- printf("[IMD] Disconnecting...\n");
+ printf("\n[IMD] Disconnecting...\n");
imd_disconnect(clientsock);
clientsock = NULL;
sleep(5);
break;
case IMD_KILL:
- printf("[IMD] Killing...\n");
+ printf("\n[IMD] Killing...\n");
imd_disconnect(clientsock);
clientsock = NULL;
sleep(5);
break;
default:
- printf("[IMD] Something weird happened. Disconnecting..\n");
+ printf("\n[IMD] Something weird happened. Disconnecting..\n");
break;
}
}
@@ -732,7 +732,7 @@ void GrandBrownTown::run() {
int tot_min = (int) std::fmod(elapsed / 60.0f, 60.0f);
float tot_sec = std::fmod(elapsed, 60.0f);
- printf("Final Step: %d\n", (int) steps);
+ printf("\nFinal Step: %d\n", (int) steps);
printf("Total Run Time: ");
if (tot_hrs > 0) printf("%dh%dm%.1fs\n", tot_hrs, tot_min, tot_sec);
diff --git a/src/Random.h b/src/Random.h
index 4dcd2317bdca607fffed159898ffe6197c6afab8..7abdaecfb99d94826d2254d44075fcfe86b50e80 100644
--- a/src/Random.h
+++ b/src/Random.h
@@ -74,7 +74,7 @@ public:
rand48_seed |= RAND48_SEED & INT64_LITERAL(0x0000ffff);
rand48_mult = RAND48_MULT;
rand48_add = RAND48_ADD;
- print("INIT\n");
+ // print("INIT\n");
}
HOST DEVICE inline void print(char* string)
diff --git a/src/RandomCPU.h b/src/RandomCPU.h
index 7c9876fe901c46d220927d2a1c9c0e32565801bb..db77245dcec85a26345fc157e452df93206c8467 100644
--- a/src/RandomCPU.h
+++ b/src/RandomCPU.h
@@ -80,7 +80,6 @@ public:
rand48_seed |= RAND48_SEED & INT64_LITERAL(0x0000ffff);
rand48_mult = RAND48_MULT;
rand48_add = RAND48_ADD;
- print("INIT\n");
}
HOST DEVICE inline void print(const char* string)
diff --git a/src/RigidBodyController.cu b/src/RigidBodyController.cu
index 1fc9a6a01c6d8115a5b21e073340d90680ff9083..dd2a5e6600bc66bed2b232f98976769665d2a6ad 100644
--- a/src/RigidBodyController.cu
+++ b/src/RigidBodyController.cu
@@ -15,7 +15,7 @@
#define gpuErrchk(ans) { gpuAssert((ans), __FILE__, __LINE__); }
inline void gpuAssert(cudaError_t code, String file, int line, bool abort=true) {
if (code != cudaSuccess) {
- fprintf(stderr,"CUDA Error: %s %s %d\n", cudaGetErrorString(code), __FILE__, line);
+ fprintf(stderr,"CUDA Error: %s %s %d\n", cudaGetErrorString(code), __FILE__, line);
if (abort) exit(code);
}
}
@@ -133,7 +133,7 @@ void RigidBodyController::initializeForcePairs() {
// Loop over all pairs of rigid body types
// the references here make the code more readable, but they may incur a performance loss
RigidBodyForcePair::createStreams();
- printf("Initializing force pairs\n");
+ // printf("Initializing force pairs\n");
for (int ti = 0; ti < conf.numRigidTypes; ti++) {
RigidBodyType& t1 = conf.rigidBody[ti];
for (int tj = ti; tj < conf.numRigidTypes; tj++) {
@@ -143,20 +143,20 @@ void RigidBodyController::initializeForcePairs() {
const std::vector<String>& keys1 = t1.densityGridKeys;
const std::vector<String>& keys2 = t2.potentialGridKeys;
- printf(" Working on type pair ");
- t1.name.printInline(); printf(":"); t2.name.print();
+ // printf(" Working on type pair ");
+ // t1.name.printInline(); printf(":"); t2.name.print();
// Loop over all pairs of grid keys (e.g. "Elec")
std::vector<int> gridKeyId1;
std::vector<int> gridKeyId2;
- printf(" Grid keys %d:%d\n",keys1.size(),keys2.size());
+ // printf(" Grid keys %d:%d\n",keys1.size(),keys2.size());
bool paired = false;
for(int k1 = 0; k1 < keys1.size(); k1++) {
for(int k2 = 0; k2 < keys2.size(); k2++) {
- printf(" checking grid keys ");
- keys1[k1].printInline(); printf(":"); keys2[k2].print();
+ // printf(" checking grid keys ");
+ // keys1[k1].printInline(); printf(":"); keys2[k2].print();
if ( keys1[k1] == keys2[k2] ) {
gridKeyId1.push_back(k1);
@@ -177,11 +177,11 @@ void RigidBodyController::initializeForcePairs() {
RigidBody* rb1 = &(rbs1[i]);
RigidBody* rb2 = &(rbs2[j]);
- printf(" pushing RB force pair for %d:%d\n",i,j);
+ // printf(" pushing RB force pair for %d:%d\n",i,j);
RigidBodyForcePair fp = RigidBodyForcePair(&(t1),&(t2),rb1,rb2,gridKeyId1,gridKeyId2, false, conf.rigidBodyGridGridPeriod );
gpuErrchk(cudaDeviceSynchronize()); /* RBTODO: this should be extraneous */
forcePairs.push_back( fp );
- printf(" done pushing RB force pair for %d:%d\n",i,j);
+ // printf(" done pushing RB force pair for %d:%d\n",i,j);
}
}
}
@@ -510,7 +510,7 @@ void RigidBodyController::print(int step) {
if ( step % conf.outputPeriod == 0 ) {
if ( ! trajFile.rdbuf()->is_open() ) {
// open file
- printf("OPENING RIGID BODY TRAJECTORY FILE\n");
+ // printf("OPENING RIGID BODY TRAJECTORY FILE\n");
// RBTODO: backup_file(simParams->rigidBodyTrajectoryFile);
char fname[140];
@@ -533,7 +533,7 @@ void RigidBodyController::print(int step) {
trajFile << "# RigidBody trajectory file" << std::endl;
printLegend(trajFile);
}
- printf("WRITING RIGID BODY COORDINATES AT STEP %d\n",step);
+ // printf("WRITING RIGID BODY COORDINATES AT STEP %d\n",step);
printData(step,trajFile);
trajFile.flush();
}
@@ -543,7 +543,7 @@ void RigidBodyController::print(int step) {
/* ((step % simParams->restartFrequency) == 0) && */
/* (step != simParams->firstTimestep) ) { */
if ( step % conf.outputPeriod == 0 && step != 0 ){
- printf("RIGID BODY: WRITING RESTART FILE AT STEP %d\n", step);
+ // printf("RIGID BODY: WRITING RESTART FILE AT STEP %d\n", step);
char fname[140];
strcpy(fname,outArg);
strcat(fname, ".rigid");
@@ -603,7 +603,7 @@ void RigidBodyController::printData(int step,std::ofstream &file) {
}
int RigidBodyForcePair::initialize() {
- printf(" Initializing (streams for) RB force pair...\n");
+ // printf(" Initializing (streams for) RB force pair...\n");
const int numGrids = gridKeyId1.size();
// RBTODO assert gridKeysIds are same size
@@ -653,7 +653,7 @@ void RigidBodyForcePair::swap(RigidBodyForcePair& a, RigidBodyForcePair& b) {
RigidBodyForcePair::~RigidBodyForcePair() {
- printf(" Destructing RB force pair\n");
+ //printf(" Destructing RB force pair\n");
const int numGrids = gridKeyId1.size();
// printf(" numGrids = %d\n",numGrids);