--- trunk/src/io/RestReader.cpp 2005/03/10 15:10:24 417
+++ trunk/src/io/RestReader.cpp 2006/05/17 21:51:42 963
@@ -60,7 +60,6 @@
#ifdef IS_MPI
#include <mpi.h>
-#include "brains/mpiSimulation.hpp"
#define TAKE_THIS_TAG_CHAR 0
#define TAKE_THIS_TAG_INT 1
#define TAKE_THIS_TAG_DOUBLE 2
@@ -69,7 +68,7 @@ namespace oopse {
namespace oopse {
RestReader::RestReader( SimInfo* info ) : info_(info){
-
+
idealName = "idealCrystal.in";
isScanned = false;
@@ -93,6 +92,7 @@ namespace oopse {
"File \"idealCrystal.in\" opened successfully for reading." );
MPIcheckPoint();
#endif
+
return;
}
@@ -220,13 +220,13 @@ namespace oopse {
int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
MPI_Status istatus;
- int localIndex;
int nCurObj;
int nitems;
-
- nTotObjs = info_->getTotIntegrableObjects();
+ int haveError;
+
+ nTotObjs = info_->getNGlobalIntegrableObjects();
haveError = 0;
-
+
if (worldRank == masterNode) {
eof_test = fgets(read_buffer, sizeof(read_buffer), inIdealFile);
if( eof_test == NULL ){
@@ -259,19 +259,19 @@ namespace oopse {
painCave.isFatal = 1;
simError();
}
-
+
for (i=0 ; i < info_->getNGlobalMolecules(); i++) {
int which_node = info_->getMolToProc(i);
if(which_node == masterNode){
//molecules belong to master node
- localIndex = info_->getMoleculeByGlobalIndex(i);
+ mol = info_->getMoleculeByGlobalIndex(i);
- if(localIndex == NULL) {
- strcpy(painCave.errMsg,
- "RestReader Error: Molecule not found on node %d!",
- worldRank);
+ if(mol == NULL) {
+ sprintf(painCave.errMsg,
+ "RestReader Error: Molecule not found on node %d!\n",
+ worldRank);
painCave.isFatal = 1;
simError();
}
@@ -291,8 +291,9 @@ namespace oopse {
painCave.isFatal = 1;
simError();
}
-
- parseIdealLine(read_buffer, integrableObjects[j]);
+
+ parseIdealLine(read_buffer, integrableObject);
+
}
} else {
//molecule belongs to slave nodes
@@ -313,9 +314,7 @@ namespace oopse {
simError();
}
- if(haveError) nodeZeroError();
-
- MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
+ MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
}
}
@@ -328,9 +327,9 @@ namespace oopse {
if(which_node == worldRank){
//molecule with global index i belongs to this processor
- localIndex = info_->getMoleculeByGlobalIndex(i);
+ mol = info_->getMoleculeByGlobalIndex(i);
- if(localIndex == NULL) {
+ if(mol == NULL) {
sprintf(painCave.errMsg,
"RestReader Error: molecule not found on node %d\n",
worldRank);
@@ -338,7 +337,7 @@ namespace oopse {
simError();
}
- nCurObj = localIndex->getNIntegrableObjects();
+ nCurObj = mol->getNIntegrableObjects();
MPI_Send(&nCurObj, 1, MPI_INT, masterNode,
TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
@@ -367,17 +366,17 @@ namespace oopse {
char *foo; // the pointer to the current string token
- double pos[3]; // position place holders
- double q[4]; // the quaternions
- double RfromQ[3][3]; // the rotation matrix
- double normalize; // to normalize the reference unit vector
- double uX, uY, uZ; // reference unit vector place holders
- double uselessToken;
+ RealType pos[3]; // position place holders
+ RealType q[4]; // the quaternions
+ RealType RfromQ[3][3]; // the rotation matrix
+ RealType normalize; // to normalize the reference unit vector
+ RealType uX, uY, uZ; // reference unit vector place holders
+ RealType uselessToken;
StringTokenizer tokenizer(readLine);
int nTokens;
nTokens = tokenizer.countTokens();
-
+
if (nTokens < 14) {
sprintf(painCave.errMsg,
"RestReader Error: Not enough Tokens.\n");
@@ -386,7 +385,7 @@ namespace oopse {
}
std::string name = tokenizer.nextToken();
-
+
if (name != sd->getType()) {
sprintf(painCave.errMsg,
@@ -401,13 +400,13 @@ namespace oopse {
pos[0] = tokenizer.nextTokenAsDouble();
pos[1] = tokenizer.nextTokenAsDouble();
pos[2] = tokenizer.nextTokenAsDouble();
-
+
// store the positions in the stuntdouble as generic data doubles
DoubleGenericData* refPosX = new DoubleGenericData();
refPosX->setID("refPosX");
refPosX->setData(pos[0]);
sd->addProperty(refPosX);
-
+
DoubleGenericData* refPosY = new DoubleGenericData();
refPosY->setID("refPosY");
refPosY->setData(pos[1]);
@@ -417,7 +416,7 @@ namespace oopse {
refPosZ->setID("refPosZ");
refPosZ->setData(pos[2]);
sd->addProperty(refPosZ);
-
+
// we don't need the velocities
uselessToken = tokenizer.nextTokenAsDouble();
uselessToken = tokenizer.nextTokenAsDouble();
@@ -493,7 +492,7 @@ namespace oopse {
char *parseErr;
std::vector<StuntDouble*> vecParticles;
- std::vector<double> tempZangs;
+ std::vector<RealType> tempZangs;
inAngFileName = info_->getRestFileName();
@@ -594,18 +593,19 @@ namespace oopse {
// first thing first, suspend fatalities.
painCave.isEventLoop = 1;
-
+
+ int masterNode = 0;
int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
- int haveError, index;
-
- int *MolToProcMap = mpiSim->getMolToProcMap();
- int localIndex;
+ int haveError;
+ int index;
+
int nCurObj;
- double angleTranfer;
+ RealType angleTranfer;
- nTotObjs = info_->getTotIntegrableObjects();
+ nTotObjs = info_->getNGlobalIntegrableObjects();
haveError = 0;
- if (worldRank == 0) {
+
+ if (worldRank == masterNode) {
eof_test = fgets(read_buffer, sizeof(read_buffer), inAngFile);
if( eof_test == NULL ){
@@ -636,69 +636,82 @@ namespace oopse {
simError();
}
- }
- // At this point, node 0 has a tempZangs vector completed, and
- // everyone else has nada
- index = 0;
-
- for (i=0 ; i < mpiSim->getNMolGlobal(); i++) {
- // Get the Node number which has this atom
- which_node = MolToProcMap[i];
+ // At this point, node 0 has a tempZangs vector completed, and
+ // everyone else has nada
+ index = 0;
- if (worldRank == 0) {
- if (which_node == 0) {
- localIndex = mpiSim->getGlobalToLocalMol(i);
-
- if(localIndex == -1) {
- strcpy(painCave.errMsg, "Molecule not found on node 0!");
- haveError = 1;
+ for (i=0 ; i < info_->getNGlobalMolecules(); i++) {
+ // Get the Node number which has this atom
+ which_node = info_->getMolToProc(i);
+
+ if (worldRank == masterNode) {
+ mol = info_->getMoleculeByGlobalIndex(i);
+
+ if(mol == NULL) {
+ strcpy(painCave.errMsg, "Molecule not found on node 0!");
+ haveError = 1;
+ simError();
+ }
+
+ for (integrableObject = mol->beginIntegrableObject(ii);
+ integrableObject != NULL;
+ integrableObject = mol->nextIntegrableObject(ii)){
+
+ integrableObject->setZangle(tempZangs[index]);
+ index++;
+ }
+
+ } else {
+ // I am MASTER OF THE UNIVERSE, but I don't own this molecule
+
+ MPI_Recv(&nCurObj, 1, MPI_INT, which_node,
+ TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
+
+ for(j=0; j < nCurObj; j++){
+ angleTransfer = tempZangs[index];
+ MPI_Send(&angleTransfer, 1, MPI_REALTYPE, which_node,
+ TAKE_THIS_TAG_DOUBLE, MPI_COMM_WORLD);
+ index++;
+ }
+
+ }
+ }
+ } else {
+ // I am SLAVE TO THE MASTER
+ for (i=0 ; i < info_->getNGlobalMolecules(); i++) {
+ int which_node = info_->getMolToProc(i);
+
+ if (which_node == worldRank) {
+
+ // BUT I OWN THIS MOLECULE!!!
+
+ mol = info_->getMoleculeByGlobalIndex(i);
+
+ if(mol == NULL) {
+ sprintf(painCave.errMsg,
+ "RestReader Error: molecule not found on node %d\n",
+ worldRank);
+ painCave.isFatal = 1;
simError();
}
-
- vecParticles = (info_->molecules[localIndex]).getIntegrableObjects();
- for(j = 0; j < vecParticles.size(); j++){
- vecParticles[j]->setZangle(tempZangs[index]);
- index++;
- }
-
- } else {
- // I am MASTER OF THE UNIVERSE, but I don't own this molecule
-
- MPI_Recv(&nCurObj, 1, MPI_INT, which_node,
- TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
-
- for(j=0; j < nCurObj; j++){
- angleTransfer = tempZangs[index];
- MPI_Send(&angleTransfer, 1, MPI_DOUBLE, which_node,
- TAKE_THIS_TAG_DOUBLE, MPI_COMM_WORLD);
- index++;
- }
-
- }
-
- } else {
- // I am SLAVE TO THE MASTER
-
- if (which_node == worldRank) {
-
- // BUT I OWN THIS MOLECULE!!!
-
- localIndex = mpiSim->getGlobalToLocalMol(i);
- vecParticles = (info_->molecules[localIndex]).getIntegrableObjects();
- nCurObj = vecParticles.size();
-
- MPI_Send(&nCurObj, 1, MPI_INT, 0,
- TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
-
- for(j = 0; j < vecParticles.size(); j++){
-
- MPI_Recv(&angleTransfer, 1, MPI_DOUBLE, 0,
- TAKE_THIS_TAG_DOUBLE, MPI_COMM_WORLD, &istatus);
- vecParticles[j]->setZangle(angleTransfer);
- }
- }
+
+ nCurObj = mol->getNIntegrableObjects();
+
+ MPI_Send(&nCurObj, 1, MPI_INT, 0,
+ TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
+
+ for (integrableObject = mol->beginIntegrableObject(ii);
+ integrableObject != NULL;
+ integrableObject = mol->nextIntegrableObject(ii)){
+
+ MPI_Recv(&angleTransfer, 1, MPI_REALTYPE, 0,
+ TAKE_THIS_TAG_DOUBLE, MPI_COMM_WORLD, &istatus);
+
+ integrableObject->setZangle(angleTransfer);
+ }
+ }
}
- }
+ }
#endif
}
@@ -732,69 +745,84 @@ namespace oopse {
// first thing first, suspend fatalities.
painCave.isEventLoop = 1;
+ int masterNode = 0;
int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
- int haveError, index;
+ int haveError;
int which_node;
MPI_Status istatus;
- int *MolToProcMap = mpiSim->getMolToProcMap();
- int localIndex;
+
int nCurObj;
- double angleTranfer;
+ RealType angleTranfer;
- nTotObjs = info_->getTotIntegrableObjects();
+ nTotObjs = info_->getNGlobalIntegrableObjects();
haveError = 0;
-
- for (i=0 ; i < mpiSim->getNMolGlobal(); i++) {
- // Get the Node number which has this atom
- which_node = MolToProcMap[i];
-
- // let's let node 0 pass out constant values to all the processors
- if (worldRank == 0) {
- if (which_node == 0) {
- localIndex = mpiSim->getGlobalToLocalMol(i);
-
- if(localIndex == -1) {
- strcpy(painCave.errMsg, "Molecule not found on node 0!");
- haveError = 1;
- simError();
- }
-
- vecParticles = (info_->molecules[localIndex]).getIntegrableObjects();
- for(j = 0; j < vecParticles.size(); j++){
- vecParticles[j]->setZangle( 0.0 );
- }
-
- } else {
- // I am MASTER OF THE UNIVERSE, but I don't own this molecule
-
- MPI_Recv(&nCurObj, 1, MPI_INT, which_node,
- TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
-
- for(j=0; j < nCurObj; j++){
- angleTransfer = 0.0;
- MPI_Send(&angleTransfer, 1, MPI_DOUBLE, which_node,
- TAKE_THIS_TAG_DOUBLE, MPI_COMM_WORLD);
- index++;
- }
- }
- } else {
- // I am SLAVE TO THE MASTER
-
- if (which_node == worldRank) {
-
- // BUT I OWN THIS MOLECULE!!!
-
- localIndex = mpiSim->getGlobalToLocalMol(i);
- vecParticles = (info_->molecules[localIndex]).getIntegrableObjects();
- nCurObj = vecParticles.size();
-
- MPI_Send(&nCurObj, 1, MPI_INT, 0,
- TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
-
- for(j = 0; j < vecParticles.size(); j++){
-
- MPI_Recv(&angleTransfer, 1, MPI_DOUBLE, 0,
+ if (worldRank == masterNode) {
+
+ for (i=0 ; i < info_->getNGlobalMolecules(); i++) {
+ // Get the Node number which has this atom
+ which_node = info_->getMolToProc(i);
+
+ // let's let node 0 pass out constant values to all the processors
+ if (worldRank == masterNode) {
+ mol = info_->getMoleculeByGlobalIndex(i);
+
+ if(mol == NULL) {
+ strcpy(painCave.errMsg, "Molecule not found on node 0!");
+ haveError = 1;
+ simError();
+ }
+
+ for (integrableObject = mol->beginIntegrableObject(ii);
+ integrableObject != NULL;
+ integrableObject = mol->nextIntegrableObject(ii)){
+
+ integrableObject->setZangle( 0.0 );
+
+ }
+
+ } else {
+ // I am MASTER OF THE UNIVERSE, but I don't own this molecule
+
+ MPI_Recv(&nCurObj, 1, MPI_INT, which_node,
+ TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
+
+ for(j=0; j < nCurObj; j++){
+ angleTransfer = 0.0;
+ MPI_Send(&angleTransfer, 1, MPI_REALTYPE, which_node,
+ TAKE_THIS_TAG_DOUBLE, MPI_COMM_WORLD);
+
+ }
+ }
+ }
+ } else {
+ // I am SLAVE TO THE MASTER
+ for (i=0 ; i < info_->getNGlobalMolecules(); i++) {
+ int which_node = info_->getMolToProc(i);
+
+ if (which_node == worldRank) {
+
+ // BUT I OWN THIS MOLECULE!!!
+ mol = info_->getMoleculeByGlobalIndex(i);
+
+ if(mol == NULL) {
+ sprintf(painCave.errMsg,
+ "RestReader Error: molecule not found on node %d\n",
+ worldRank);
+ painCave.isFatal = 1;
+ simError();
+ }
+
+ nCurObj = mol->getNIntegrableObjects();
+
+ MPI_Send(&nCurObj, 1, MPI_INT, 0,
+ TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
+
+ for (integrableObject = mol->beginIntegrableObject(ii);
+ integrableObject != NULL;
+ integrableObject = mol->nextIntegrableObject(ii)){
+
+ MPI_Recv(&angleTransfer, 1, MPI_REALTYPE, 0,
TAKE_THIS_TAG_DOUBLE, MPI_COMM_WORLD, &istatus);
vecParticles[j]->setZangle(angleTransfer);
}