[ViewVC] Diff of: group/trunk/OOPSE/libmdtools/SimSetup.cpp

Comparing:
branches/mmeineke/OOPSE/libmdtools/SimSetup.cpp (file contents), Revision 377 by mmeineke, Fri Mar 21 17:42:12 2003 UTC vs.
trunk/OOPSE/libmdtools/SimSetup.cpp (file contents), Revision 414 by mmeineke, Wed Mar 26 22:02:36 2003 UTC

+  if( simnfo->n_SRI ){
-<
+    the_sris = new SRI*[simnfo->n_SRI];
-<
+    the_excludes = new int[2 * simnfo->n_SRI];
->
+    Exclude::createArray(simnfo->n_SRI);
->
+    the_excludes = new Exclude*[simnfo->n_SRI];
+    simnfo->globalExcludes = new int;
+    simnfo->n_exclude = tot_SRI;
+  else{
-<
+    the_excludes = new int[2];
-<
+    the_excludes[0] = 0;
-<
+    the_excludes[1] = 0;
->
+    Exclude::createArray( 1 );
->
+    the_excludes = new Exclude*;
->
+    the_excludes[0] = new Exclude(0);
->
+    the_excludes[0]->setPair( 0,0 );
+    simnfo->globalExcludes = new int;
+    simnfo->globalExcludes[0] = 0;
-<
-<
+    simnfo->n_exclude = 1;
->
+    simnfo->n_exclude = 0;
+  // set the arrays into the SimInfo object
+  // get some of the tricky things that may still be in the globals
-–
+  if( simnfo->n_dipoles ){
-–
-–
+    if( !the_globals->haveRRF() ){
-–
+      sprintf( painCave.errMsg,
-–
+               "SimSetup Error, system has dipoles, but no rRF was set.\n");
-–
+      painCave.isFatal = 1;
-–
+      simError();
-–
+    }
-–
+    if( !the_globals->haveDielectric() ){
-–
+      sprintf( painCave.errMsg,
-–
+               "SimSetup Error, system has dipoles, but no"
-–
+               " dielectric was set.\n" );
-–
+      painCave.isFatal = 1;
-–
+      simError();
-–
+    }
-–
-–
+    simnfo->rRF        = the_globals->getRRF();
-–
+    simnfo->dielectric = the_globals->getDielectric();
-–
+  }
-–
-–
+#ifdef IS_MPI
-–
+  strcpy( checkPointMsg, "rRf and dielectric check out" );
-–
+  MPIcheckPoint();
-–
+#endif // is_mpi
+  if( the_globals->haveBox() ){
+    simnfo->box_x = the_globals->getBox();
-<
->
+  if (the_globals->getUseRF() ) {
->
+    simnfo->useReactionField = 1;
->
->
+    if( !the_globals->haveECR() ){
->
+      sprintf( painCave.errMsg,
->
+               "SimSetup Warning: using default value of 1/2 the smallest "
->
+               "box length for the electrostaticCutoffRadius.\n"
->
+               "I hope you have a very fast processor!\n");
->
+      painCave.isFatal = 0;
->
+      simError();
->
+      double smallest;
->
+      smallest = simnfo->box_x;
->
+      if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
->
+      if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
->
+      simnfo->ecr = 0.5 * smallest;
->
+    } else {
->
+      simnfo->ecr        = the_globals->getECR();
->
+    }
-+
+    if( !the_globals->haveEST() ){
-+
+      sprintf( painCave.errMsg,
-+
+               "SimSetup Warning: using default value of 0.05 * the "
-+
+               "electrostaticCutoffRadius for the electrostaticSkinThickness\n"
-+
+               );
-+
+      painCave.isFatal = 0;
-+
+      simError();
-+
+      simnfo->est = 0.05 * simnfo->ecr;
-+
+    } else {
-+
+      simnfo->est        = the_globals->getEST();
-+
+    }
-+
-+
+    if(!the_globals->haveDielectric() ){
-+
+      sprintf( painCave.errMsg,
-+
+               "SimSetup Error: You are trying to use Reaction Field without"
-+
+               "setting a dielectric constant!\n"
-+
+               );
-+
+      painCave.isFatal = 1;
-+
+      simError();
-+
+    }
-+
+    simnfo->dielectric = the_globals->getDielectric();
-+
+  } else {
-+
+    if (simnfo->n_dipoles) {
-+
-+
+      if( !the_globals->haveECR() ){
-+
+        sprintf( painCave.errMsg,
-+
+                 "SimSetup Warning: using default value of 1/2 the smallest"
-+
+                 "box length for the electrostaticCutoffRadius.\n"
-+
+                 "I hope you have a very fast processor!\n");
-+
+        painCave.isFatal = 0;
-+
+        simError();
-+
+        double smallest;
-+
+        smallest = simnfo->box_x;
-+
+        if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
-+
+        if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
-+
+        simnfo->ecr = 0.5 * smallest;
-+
+      } else {
-+
+        simnfo->ecr        = the_globals->getECR();
-+
+      }
-+
-+
+      if( !the_globals->haveEST() ){
-+
+        sprintf( painCave.errMsg,
-+
+                 "SimSetup Warning: using default value of 5% of the"
-+
+                 "electrostaticCutoffRadius for the "
-+
+                 "electrostaticSkinThickness\n"
-+
+                 );
-+
+        painCave.isFatal = 0;
-+
+        simError();
-+
+        simnfo->est = 0.05 * simnfo->ecr;
-+
+      } else {
-+
+        simnfo->est        = the_globals->getEST();
-+
+      }
-+
+    }
-+
+  }
-+
+#ifdef IS_MPI
-+
+  strcpy( checkPointMsg, "electrostatic parameters check out" );
-+
+  MPIcheckPoint();
-+
+#endif // is_mpi
+ if( the_globals->haveInitialConfig() ){
+  strcpy( checkPointMsg,
+          "Successfully intialized the mixingRule for Fortran." );
+  MPIcheckPoint();
-+
+#endif // is_mpi
-+
+}
-+
-+
-+
+void SimSetup::makeMolecules( void ){
-+
-+
+  int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
-+
+  molInit info;
-+
+  DirectionalAtom* dAtom;
-+
+  LinkedAssign* extras;
-+
+  LinkedAssign* current_extra;
-+
+  AtomStamp* currentAtom;
-+
+  BondStamp* currentBond;
-+
+  BendStamp* currentBend;
-+
+  TorsionStamp* currentTorsion;
-+
-+
+  //init the forceField paramters
-+
-+
+  the_ff->readParams();
-+
-+
-+
+  // init the molecules
-+
-+
+  atomOffset = 0;
-+
+  excludeOffset = 0;
-+
+  for(i=0; i<simnfo->n_mol; i++){
-+
-+
+    stampID = the_molecules[i].getStampID();
-+
-+
+    info.nAtoms    = comp_stamps[stampID]->getNAtoms();
-+
+    info.nBonds    = comp_stamps[stampID]->getNBonds();
-+
+    info.nBends    = comp_stamps[stampID]->getNBends();
-+
+    info.nTorsions = comp_stamps[stampID]->getNTorsions();
-+
+    info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
-+
-+
+    info.myAtoms = &the_atoms[atomOffset];
-+
+    info.myExcludes = &the_excludes[excludeOffset];
-+
+    info.myBonds = new Bond*[info.nBonds];
-+
+    info.myBends = new Bend*[info.nBends];
-+
+    info.myTorsions = new Torsions*[info.nTorsions];
-+
-+
+    theBonds = new bond_pair[info.nBonds];
-+
+    theBends = new bend_set[info.nBends];
-+
+    theTorsions = new torsion_set[info.nTorsions];
-+
-+
+    // make the Atoms
-+
-+
+    for(j=0; j<info.nAtoms; j++){
-+
-+
+      currentAtom = theComponents[stampID]->getAtom( j );
-+
+      if( currentAtom->haveOrientation() ){
-+
-+
+        dAtom = new DirectionalAtom(j + atomOffset);
-+
+        simnfo->n_oriented++;
-+
+        info.myAtoms[j] = dAtom;
-+
-+
+        ux = currentAtom->getOrntX();
-+
+        uy = currentAtom->getOrntY();
-+
+        uz = currentAtom->getOrntZ();
-+
-+
+        uSqr = (ux * ux) + (uy * uy) + (uz * uz);
-+
-+
+        u = sqrt( uSqr );
-+
+        ux = ux / u;
-+
+        uy = uy / u;
-+
+        uz = uz / u;
-+
-+
+        dAtom->setSUx( ux );
-+
+        dAtom->setSUy( uy );
-+
+        dAtom->setSUz( uz );
-+
+      }
-+
+      else{
-+
+        info.myAtoms[j] = new GeneralAtom(j + atomOffset);
-+
+      }
-+
+      info.myAtoms[j]->setType( currentAtom->getType() );
-+
-+
+#ifdef IS_MPI
-+
-+
+      info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
-+
+#endif // is_mpi
-+
+    }
-+
-+
+    // make the bonds
-+
+    for(j=0; j<info.nBonds; j++){
-+
-+
+      currentBond = comp_stamps[stampID]->getBond( j );
-+
+      theBonds[j].a = currentBond->getA() + atomOffset;
-+
+      theBonds[j].b = currentBond->getB() + atomOffset;
-+
-+
+      exI = theBonds[i].a;
-+
+      exJ = theBonds[i].b;
-+
-+
+      // exclude_I must always be the smaller of the pair
-+
+      if( exI > exJ ){
-+
+        tempEx = exI;
-+
+        exI = exJ;
-+
+        exJ = tempEx;
-+
+      }
-+
+#ifdef IS_MPI
-+
+      tempEx = exI;
-+
+      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
-+
+      tempEx = exJ;
-+
+      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
-+
-+
+      the_excludes[j+excludeOffset]->setPair( exI, exJ );
-+
+#else  // isn't MPI
-+
+      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
-+
+#endif  //is_mpi
-+
+    }
-+
+    excludeOffset += info.nBonds;
-+
-+
+    //make the bends
-+
+    for(j=0; j<info.nBends; j++){
-+
-+
+      currentBend = comp_stamps[stampID]->getBend( j );
-+
+      theBends[j].a = currentBend->getA() + atomOffset;
-+
+      theBends[j].b = currentBend->getB() + atomOffset;
-+
+      theBends[j].c = currentBend->getC() + atomOffset;
-+
-+
+      if( currentBend->haveExtras() ){
-+
-+
+        extras = current_bend->getExtras();
-+
+        current_extra = extras;
-+
-+
+        while( current_extra != NULL ){
-+
+          if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
-+
-+
+            switch( current_extra->getType() ){
-+
-+
+            case 0:
-+
+              theBends[j].ghost =
-+
+                current_extra->getInt() + atomOffset;
-+
+              theBends[j].isGhost = 1;
-+
+              break;
-+
-+
+            case 1:
-+
+              theBends[j].ghost =
-+
+                (int)current_extra->getDouble() + atomOffset;
-+
+              theBends[j].isGhost = 1;
-+
+              break;
-+
-+
+            default:
-+
+              sprintf( painCave.errMsg,
-+
+                       "SimSetup Error: ghostVectorSource was neiter a "
-+
+                       "double nor an int.\n"
-+
+                       "-->Bend[%d] in %s\n",
-+
+                       j, comp_stamps[stampID]->getID() );
-+
+              painCave.isFatal = 1;
-+
+              simError();
-+
+            }
-+
+          }
-+
-+
+          else{
-+
-+
+            sprintf( painCave.errMsg,
-+
+                     "SimSetup Error: unhandled bend assignment:\n"
-+
+                     "    -->%s in Bend[%d] in %s\n",
-+
+                     current_extra->getlhs(),
-+
+                     j, comp_stamps[stampID]->getID() );
-+
+            painCave.isFatal = 1;
-+
+            simError();
-+
+          }
-+
-+
+          current_extra = current_extra->getNext();
-+
+        }
-+
+      }
-+
-+
+      if( !theBends[j].isGhost ){
-+
-+
+        exI = theBends[j].a;
-+
+        exJ = theBends[j].c;
-+
+      }
-+
+      else{
-+
-+
+        exI = theBends[j].a;
-+
+        exJ = theBends[j].b;
-+
+      }
-+
-+
+      // exclude_I must always be the smaller of the pair
-+
+      if( exI > exJ ){
-+
+        tempEx = exI;
-+
+        exI = exJ;
-+
+        exJ = tempEx;
-+
+      }
-+
+#ifdef IS_MPI
-+
+      tempEx = exI;
-+
+      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
-+
+      tempEx = exJ;
-+
+      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
-+
-+
+      the_excludes[j+excludeOffset]->setPair( exI, exJ );
-+
+#else  // isn't MPI
-+
+      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
-+
+#endif  //is_mpi
-+
+    }
-+
+    excludeOffset += info.nBends;
-+
-+
+    for(j=0; j<info.nTorsions; j++){
-+
-+
+      currentTorsion = comp_stamps[stampID]->getTorsion( j );
-+
+      theTorsions[j].a = currentTorsion->getA() + atomOffset;
-+
+      theTorsions[j].b = currentTorsion->getB() + atomOffset;
-+
+      theTorsions[j].c = currentTorsion->getC() + atomOffset;
-+
+      theTorsions[j].d = currentTorsion->getD() + atomOffset;
-+
-+
+      exI = theTorsions[j].a;
-+
+      exJ = theTorsions[j].d;
-+
-+
+      // exclude_I must always be the smaller of the pair
-+
+      if( exI > exJ ){
-+
+        tempEx = exI;
-+
+        exI = exJ;
-+
+        exJ = tempEx;
-+
+      }
-+
+#ifdef IS_MPI
-+
+      tempEx = exI;
-+
+      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
-+
+      tempEx = exJ;
-+
+      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
-+
-+
+      the_excludes[j+excludeOffset]->setPair( exI, exJ );
-+
+#else  // isn't MPI
-+
+      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
-+
+#endif  //is_mpi
-+
+    }
-+
+    excludeOffset += info.nTorsions;
-+
-+
-+
+    // send the arrays off to the forceField for init.
-+
-+
+    the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
-+
+    the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
-+
+    the_ff->initializeBends( info.nBends, info.myBends, theBends );
-+
+    the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
-+
-+
-+
+    the_molecules[i].initialize( info );
-+
+    atomOffset += info.nAtoms;
-+
+  }
-+
-+
+  // clean up the forcefield
-+
-+
+  the_ff->cleanMe();
-+
-+
+void SimSetup::makeAtoms( void ){

Diff Legend

-–
+Removed lines
-+
+Added lines
-<
+Changed lines
->
+Changed lines

Comparing: branches/mmeineke/OOPSE/libmdtools/SimSetup.cpp (file contents), Revision 377 by mmeineke, Fri Mar 21 17:42:12 2003 UTC vs. trunk/OOPSE/libmdtools/SimSetup.cpp (file contents), Revision 414 by mmeineke, Wed Mar 26 22:02:36 2003 UTC

Diff Legend

Comparing:
branches/mmeineke/OOPSE/libmdtools/SimSetup.cpp (file contents), Revision 377 by mmeineke, Fri Mar 21 17:42:12 2003 UTC vs.
trunk/OOPSE/libmdtools/SimSetup.cpp (file contents), Revision 414 by mmeineke, Wed Mar 26 22:02:36 2003 UTC