[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 407 by mmeineke, Wed Mar 26 20:22:02 2003 UTC

+  // 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() ){
+#endif // is_mpi
-+
-+
+void SimSetup::makeMolecules( void ){
-+
-+
+  int i, j, exI, exJ, tempEx, stampID, atomOffset;
-+
+  molInit info;
-+
+  DirectionalAtom* dAtom;
-+
+  AtomStamp* currentAtom;
-+
+  BondStamp* currentBond;
-+
+  BendStamp* currentBend;
-+
+  TorsionStamp* currentTorsion;
-+
-+
+  //init the forceField paramters
-+
-+
+  the_ff->readParams();
-+
-+
-+
+  // init the molecules
-+
-+
+  atomOffset = 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.myAtoms = &the_atoms[atomOffset];
-+
+    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<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
-+
-+
+      the_excludes[index*2] =
-+
+        the_atoms[exI]->getGlobalIndex() + 1;
-+
+      the_excludes[index*2 + 1] =
-+
+        the_atoms[exJ]->getGlobalIndex() + 1;
-+
-+
+#else  // isn't MPI
-+
-+
+      the_excludes[index*2] =     exI + 1;
-+
+      the_excludes[index*2 + 1] = exJ + 1;
-+
+      // fortran index from 1 (hence the +1 in the indexing)
-+
-+
+#endif  //is_mpi
-+
-+
+  }
-+
-+
-+
-+
-+
-+
-+
-+
-+
-+
-+
-+
-+
-+
-+
+void SimSetup::makeAtoms( void ){
+  int i, j, k, index;

Diff Legend

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+Removed lines
-+
+Added lines
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+Changed lines
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+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 407 by mmeineke, Wed Mar 26 20:22:02 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 407 by mmeineke, Wed Mar 26 20:22:02 2003 UTC