[ViewVC] Diff of: group/branches/new_design/OOPSE-3.0/src/brains/SimCreator.cpp

Comparing branches/new_design/OOPSE-3.0/src/brains/SimCreator.cpp (file contents):
Revision 1703 by tim, Wed Nov 3 19:56:02 2004 UTC vs.
Revision 1725 by tim, Wed Nov 10 22:01:06 2004 UTC

+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
+ */
-–
-–
+ /**
-–
+  * @file SimCreator.cpp
-–
+  * @author tlin
-–
+  * @date 11/03/2004
-–
+  * @time 13:51am
-–
+  * @version 1.0
-–
+  */
-<
+#include "brains/SimCreator.hpp"
->
+/**
->
+ * @file SimCreator.cpp
->
+ * @author tlin
->
+ * @date 11/03/2004
->
+ * @time 13:51am
->
+ * @version 1.0
->
+ */
->
->
+#include "brains/SimCreator.hpp"
+namespace oopse {
-–
+void SimCreator::parseFile(const string & mdfile) {
-+
+void SimSetup::parseFile(char* mdfile,  MakeStamps* stamps, Globals* globals){
-+
+#ifdef IS_MPI
-+
+  if (worldRank == 0){
-+
+#endif // is_mpi
-+
-+
-+
+    globals->initalize();
-+
+    set_interface_stamps(stamps, globals);
-+
-+
+#ifdef IS_MPI
-+
+    mpiEventInit();
-+
+#endif
-+
-+
+    yacc_BASS(mdfile);
-+
-+
+#ifdef IS_MPI
-+
+    throwMPIEvent(NULL);
-+
+  }
-+
+  else{
-+
+  set_interface_stamps(stamps, globals);
-+
+  mpiEventInit();
-+
+  MPIcheckPoint();
-+
+  mpiEventLoop();
-+
+  }
-+
+#endif
-+
-+
-+
+SimInfo* SimCreator::createSim(const std::string& mdfile) {
-+
+    MakeStamps* stamps = new MakeStamps();
-+
-+
+    Globals* globals = new Globals();
-+
-+
+    //parse meta-data file
-+
+    parseFile(mdfile, stamps, globals);
-+
-+
+    //create the force field
-+
+    ForceFiled* ff = ForceFieldFactory::getInstance()->createObject(globals->getForceField());
-+
-+
+    //create SimInfo
-+
+    SimInfo* info = new SimInfo();
-+
+    info->setGlobals(globals);
-+
+    info->setForceField(ff);
-+
-+
+    //extract the molecule stamps and add them into SimInfo
-+
+    compList(stamps, info);
-+
-+
+    //gather parameters (SimCreator only retrieves the parameters which will be used to create
-+
+    // the simulation)
-+
+    gatherParameters(info);
-+
-+
+    //divide the molecules and determine the global index of molecules
-+
-+
+    //create the molecules
-+
+    createMolecules(info);
-+
-+
+    //set the global index of atoms, rigidbodies and cutoffgroups (only need to be set once, the
-+
+    //global index will never change again). Local indices of atoms and rigidbodies are already set by
-+
+    //MoleculeCreator class which actually delegates the responsibility to LocalIndexManager.
-+
+    setGlobalIndices(info);
-+
-+
+    //allocate memory for DataStorage(circular reference, need to break it)
-+
+    info->setSnapshotManager(new SimSnapshotManager(info);
-+
-+
+    //load initial coordinates, some extra information are pushed into SimInfo's property map ( such as
-+
+    //eta, chi for NPT integrator)
-+
+    DumpReader reader(info->getInitFilename());
-+
+    int nframes = reader->getNframes();
-+
-+
+    if (nframes > 0) {
-+
+        reader.readFrame(info, nframes - 1);
-+
+    } else {
-+
+        //invalid initial coordinate file
-+
-+
+    }
-+
-+
-+
+    //initialize fortran
-+
-+
+    return info;
-+
+}
-+
-+
+void SimCreator::gatherParameters(SimInfo* info) {
-+
+    //model->addProperty(new StringGenericData("Ensemble", globals->getForceFiled()));
-+
+    //model->addProperty(new DoubleGenericData("dt"), globals->getDt());
-+
-+
+    //setup seed for random number generator
-+
+    int seedValue;
-+
+    Globals* globals = info->getGlobals();
-+
-+
+    if (globals->haveSeed()){
-+
+        seedValue = globals->getSeed();
-+
-+
+        if(seedValue / 1000000000 == 0){
-+
+            sprintf(painCave.errMsg,
-+
+            "Seed for sprng library should contain at least 9 digits\n"
-+
+            "OOPSE will generate a seed for user\n");
-+
+            painCave.isFatal = 0;
-+
+            simError();
-+
-+
+    //using seed generated by system instead of invalid seed set by user
-+
+#ifndef IS_MPI
-+
+            seedValue = make_sprng_seed();
-+
+#else
-+
+            if (worldRank == 0){
-+
+                seedValue = make_sprng_seed();
-+
+            }
-+
+            MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
-+
+#endif
-+
+        } //end if (seedValue /1000000000 == 0)
-+
+    } else{
-+
-+
+#ifndef IS_MPI
-+
+        seedValue = make_sprng_seed();
-+
+#else
-+
+        if (worldRank == 0){
-+
+            seedValue = make_sprng_seed();
-+
+        }
-+
+        MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
-+
+#endif
-+
+    }//end of globals->haveSeed()
-+
+    info->setSeed(seedValue);
-+
-+
+    //
-+
+    std::string prefix;
-+
+#ifdef IS_MPI
-+
+    if (worldRank == 0){
-+
+#endif // is_mpi
-+
-+
+        if(globals->haveFinalConfig()) {
-+
+            prefix = getPrefix(globals->getFinalConfig());
-+
+        } else {
-+
+            prefix = getPrefix(mdfile_);
-+
+        }
-+
-+
+        info->setFinalConfFileName(prefix + ".eor");
-+
+        info->setDumpFileName(prefix + ".dump");
-+
+        info->setStatFileName(prefix + ".stat");
-+
-+
+#ifdef IS_MPI
-+
+    }
-+
+#endif
-+
-+
-+
-+
+}
-+
-+
+#ifdef IS_MPI
-+
+void SimCreator::mpiMolDivide(){
-+
-+
+    mpiSim = new mpiSimulation(info);
-+
-+
+    mpiSim->divideLabor();
-+
-+
+}
-+
+#endif
-+
-+
+Molecule* SimCreator::createMolecules(SimInfo* info) {
-+
+    MoleculeCreator molCreator;
-+
+    int stampId;
-+
-+
-+
+    for (int i = 0; i < info->getNGlobalMolecules(); i++){
-+
+        if (info->getMolToProc(i) == worldRank){
-+
-+
+            stampId = info->getMoleculeStampId(i);
-+
+            Molecule* mol = molCreator.createMolecule(info->getForceField(),
-+
+                                                                                info->getMoleculeStamp(stampId), stampId, i);
-+
-+
+            info->addMolecule(mol);
-+
+        }
-+
+    }
-+
-+
+}
-+
-+
-+
+void SimSetup::compList(MakeStamps* stamps,SimInfo* info) {
-+
+    int i;
-+
+    char* id;
-+
+    MoleculeStamp* currentStamp;
-+
+    Component* the_components = info->getGlobals()->getComponents();
-+
+    int n_components = info->getGlobals()->getNComponents();
-+
-+
+    if (!globals->haveNMol()){
-+
+        // we don't have the total number of molecules, so we assume it is
-+
+        // given in each component
-+
-+
+        for (i = 0; i < n_components; i++){
-+
+            if (!the_components[i]->haveNMol()){
-+
+                // we have a problem
-+
+                sprintf(painCave.errMsg,
-+
+                    "SimSetup Error. No global NMol or component NMol given.\n"
-+
+                    "\tCannot calculate the number of atoms.\n");
-+
+                painCave.isFatal = 1;
-+
+                simError();
-+
+            }
-+
-+
+            id = the_components[i]->getType();
-+
+            currentStamp = stamps->extractMolStamp(id);
-+
+            if (currentStamp == NULL){
-+
+                sprintf(painCave.errMsg,
-+
+                    "SimSetup error: Component \"%s\" was not found in the "
-+
+                    "list of declared molecules\n",
-+
+                    id);
-+
+                painCave.isFatal = 1;
-+
+                simError();
-+
+            }
-+
-+
+            info->addMoleculeStamp(currentStamp, the_components[i]->getNMol);
-+
-+
+        } //end for (i = 0; i < n_components; i++)
-+
-+
+    } else{
-+
+        sprintf(painCave.errMsg,
-+
+                "SimSetup error.\n"
-+
+                "\tSorry, the ability to specify total"
-+
+                " nMols and then give molfractions in the components\n"
-+
+                "\tis not currently supported."
-+
+                " Please give nMol in the components.\n");
-+
+        painCave.isFatal = 1;
-+
+        simError();
-+
+    }
-+
-+
+#ifdef IS_MPI
-+
+  strcpy(checkPointMsg, "Component stamps successfully extracted\n");
-+
+  MPIcheckPoint();
-+
+#endif // is_mpi
-+
+}
-+
-+
+void SimCreator::setGlobalIndices(SimInfo* info) {
-+
+    typename SimInfo::MoleculeIterator mi;
-+
+    typename Molecule::AtomIterator ai;
-+
+    typename Molecule::RigidBodyIterator ri;
-+
+    typename Molecule::CutoffGroupIterator ci;
-+
+    Molecule* mol;
-+
+    Atom* atom;
-+
+    RigidBody* rb;
-+
+    CutoffGroup* cg;
-+
+    int beginAtomIndex;
-+
+    int beginRigidBodyIndex;
-+
+    int beginCutoffGroupIndex;
-+
-+
+#ifdef IS_MPI
-+
+    beginAtomIndex = 0;
-+
+    beginRigidBodyIndex = 0;
-+
+    beginCutoffGroupIndex = 0;
-+
+#else
-+
+    int nproc;
-+
+    int myNode;
-+
-+
+    myNode = worldRank;
-+
+    MPI_Comm_size(MPI_COMM_WORLD, &nproc);
-+
-+
+    std::vector<int> tmpAtomsInProc(nproc, 0);
-+
+    std::vector<int> tmpRigidBodiesInProc(nproc, 0);
-+
+    std::vector<int> tmpCutoffGroupsInProc(nproc, 0);
-+
+    std::vector<int> NumAtomsInProc(nproc, 0);
-+
+    std::vector<int> NumRigidBodiesInProc(nproc, 0);
-+
+    std::vector<int> NumCutoffGroupsInProc(nproc, 0);
-+
-+
+    tmpAtomInProc[myNode] = info->getNAtoms();
-+
+    tmpRigidBodiesInProc[myNode] = info->getNRigidBodiess();
-+
+    tmpCutoffGroupsInProc[myNode] = info->getNCutoffGroupss();
-+
-+
+    //do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups
-+
+    MPI_Allreduce(&tmpAtomsInProc[0], &NumAtomsInProc[0], nproc, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
-+
+    MPI_Allreduce(&tmpRigidBodiesInProc[0], &NumRigidBodiesInProc[0], nproc, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
-+
+    MPI_Allreduce(&tmpCutoffGroupsInProc[0], &NumCutoffGroupsInProc[0], nproc, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
-+
-+
+    beginAtomIndex = 0;
-+
+    beginRigidBodyIndex = 0;
-+
+    beginCutoffGroupIndex = 0;
-+
-+
+    for (int i = 0; i < nproc; i++) {
-+
+        beginAtomIndex += NumAtomsInProc[i];
-+
+        beginRigidBodyIndex += NumRigidBodiesInProc[i];
-+
+        beginCutoffGroupIndex += NumCutoffGroupsInProc[i];
-+
+    }
-+
-+
+#endif
-+
-+
+    for (mol = info->beginMolecule(mi); mol != NULL; mol  = info->nextMolecule(mi)) {
-+
-+
+        //local index(index in DataStorge) of atom is important
-+
+        for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
-+
+            atom->setGlobalIndex(beginAtomIndex++);
-+
+        }
-+
-+
+        for (rb = mol->beginRigidBody(ri); rb != NULL; rb = mol->nextRigidBody(ri)) {
-+
+            rb->setGlobalIndex(beginRigidBodyIndex++);
-+
+        }
-+
-+
+        //local index of cutoff group is trivial, it only depends on the order of travesing
-+
+        for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
-+
+            cg->setGlobalIndex(beginCutoffGroupIndex++);
-+
+        }
-+
-+
+    }
-+
+}
-+
+} //end namespace oopse

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+Removed lines
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Comparing branches/new_design/OOPSE-3.0/src/brains/SimCreator.cpp (file contents): Revision 1703 by tim, Wed Nov 3 19:56:02 2004 UTC vs. Revision 1725 by tim, Wed Nov 10 22:01:06 2004 UTC

Diff Legend

Comparing branches/new_design/OOPSE-3.0/src/brains/SimCreator.cpp (file contents):
Revision 1703 by tim, Wed Nov 3 19:56:02 2004 UTC vs.
Revision 1725 by tim, Wed Nov 10 22:01:06 2004 UTC