Changeset f75030 for molecuilder/src/molecules.cpp

Timestamp:

May 23, 2008, 9:17:19 AM (17 years ago)

Author:

Frederik Heber <heber@…>

Children:

6145aa7

Parents:

6c96f4

Message:

Lots of for loops now count in reverse order where it does not matter, some 3 -> NDIM

for(i=0;i<var;i++) is slower than for (i=var;i--;) if the order of the i's is not important (note: i-- is also a value and it stops when on i == 0 automatically)
in builder.cpp there were some remnant 3 actually meant to be NDIM

File:

• molecuilder/src/molecules.cpp (modified) (55 diffs)

molecuilder/src/molecules.cpp ¶

@@ -21 +21 @@
   int num = par->num;
 
-  for (int i=0;i<num;i++) {
-    for(int j=0;j<NDIM;j++)
+  for (int i=num;i--;) {
+    for(int j=NDIM;j--;)
       sum += (gsl_vector_get(x,j) - (vectors[i])->x[j])*(gsl_vector_get(x,j) - (vectors[i])->x[j]);
   }
@@ -57 +57 @@
   NumberOfBondsPerAtom = NULL;
   ElementCount = 0;
-  for(int i=0;i<MAX_ELEMENTS;i++)
+  for(int i=MAX_ELEMENTS;i--;)
     ElementsInMolecule[i] = 0;
   cell_size[0] = cell_size[2] = cell_size[5]= 20.;
@@ -69 +69 @@
 {
   if (ListOfBondsPerAtom != NULL)
-    for(int i=0;i<AtomCount;i++)
+    for(int i=AtomCount;i--;)
       Free((void **)&ListOfBondsPerAtom[i], "molecule::~molecule: ListOfBondsPerAtom[i]");
   Free((void **)&ListOfBondsPerAtom, "molecule::~molecule: ListOfBondsPerAtom");
@@ -200 +200 @@
 //    *out << endl;
     OrthoVector1.Zero();
-    for (int i=0;i<NDIM;i++) {
+    for (int i=NDIM;i--;) {
       l = TopReplacement->x.x[i] - TopOrigin->x.x[i];
       if (fabs(l) > BondDistance) { // is component greater than bond distance
@@ -312 +312 @@
       FirstOtherAtom->x.Zero();
       SecondOtherAtom->x.Zero();
-      for(i=0;i<NDIM;i++) { // rotate by half the bond angle in both directions (InBondVector is bondangle = 0 direction)
+      for(i=NDIM;i--;) { // rotate by half the bond angle in both directions (InBondVector is bondangle = 0 direction)
         FirstOtherAtom->x.x[i] = InBondVector.x[i] * cos(bondangle) + OrthoVector1.x[i] * (sin(bondangle));
         SecondOtherAtom->x.x[i] = InBondVector.x[i] * cos(bondangle) + OrthoVector1.x[i] * (-sin(bondangle));
@@ -319 +319 @@
       SecondOtherAtom->x.Scale(&BondRescale);
       //*out << Verbose(3) << "ReScaleCheck: " << FirstOtherAtom->x.Norm() << " and " << SecondOtherAtom->x.Norm() << "." << endl;
-      for(i=0;i<NDIM;i++) { // and make relative to origin atom
+      for(i=NDIM;i--;) { // and make relative to origin atom
         FirstOtherAtom->x.x[i] += TopOrigin->x.x[i]; 
         SecondOtherAtom->x.x[i] += TopOrigin->x.x[i];
@@ -471 +471 @@
       first->type = elemente->FindElement(1);
     }
-    for(j=0;j<NDIM;j++)
+    for(j=NDIM;j--;)
       first->x.x[j] = x[j];
      AddAtom(first);  // add to molecule
@@ -612 +612 @@
   ptr = start->next;  // start at first in list
   if (ptr != end) {   //list not empty?
-    for (int i=0;i<NDIM;i++) {
+    for (int i=NDIM;i--;) {
       max->x[i] = ptr->x.x[i];
       min->x[i] = ptr->x.x[i];
@@ -619 +619 @@
       ptr = ptr->next;
       //ptr->Output(1,1,out);
-      for (int i=0;i<NDIM;i++) {
+      for (int i=NDIM;i--;) {
         max->x[i] = (max->x[i] < ptr->x.x[i]) ? ptr->x.x[i] : max->x[i];
         min->x[i] = (min->x[i] > ptr->x.x[i]) ? ptr->x.x[i] : min->x[i];
@@ -626 +626 @@
   }
   // sanity check
-  for(int i=0;i<NDIM;i++) {
+  for(int i=NDIM;i--;) {
     if (max->x[i] - min->x[i] > BoxLengths->x[i])
       status = false;
@@ -637 +637 @@
     while (ptr->next != end) {
       ptr = ptr->next;
-      for (int i=0;i<NDIM;i++)
+      for (int i=NDIM;i--;)
         ptr->x.x[i] += -(max->x[i] + min->x[i])/2. + BoxLengths->x[i]/2.; // first term centers molecule at (0,0,0), second shifts to center of new box
     }
@@ -659 +659 @@
   atom *ptr = start->next;  // start at first in list
   if (ptr != end) {   //list not empty?
-    for (int i=0;i<NDIM;i++) {
+    for (int i=NDIM;i--;) {
       max->x[i] = ptr->x.x[i];
       min->x[i] = ptr->x.x[i];
@@ -666 +666 @@
       ptr = ptr->next;
       //ptr->Output(1,1,out);
-      for (int i=0;i<NDIM;i++) {
+      for (int i=NDIM;i--;) {
         max->x[i] = (max->x[i] < ptr->x.x[i]) ? ptr->x.x[i] : max->x[i];
         min->x[i] = (min->x[i] > ptr->x.x[i]) ? ptr->x.x[i] : min->x[i];
@@ -677 +677 @@
 //    *out << endl;
     
-    for (int i=0;i<NDIM;i++) {
+    for (int i=NDIM;i--;) {
       min->x[i] *= -1.;
       max->x[i] += min->x[i];
@@ -696 +696 @@
   atom *ptr = start->next;  // start at first in list
  
-  for(int i=0;i<NDIM;i++) // zero center vector
+  for(int i=NDIM;i--;) // zero center vector
     center->x[i] = 0.;
     
@@ -720 +720 @@
   vector tmp;
   
-  for(int i=0;i<NDIM;i++) // zero center vector
+  for(int i=NDIM;i--;) // zero center vector
     center->x[i] = 0.;
     
@@ -957 +957 @@
   bool result = true;
   int j =-1;
-  for (int i=0;i<3;i++) {
+  for (int i=0;i<NDIM;i++) {
     j += i+1;
     result = result && ((x->x[i] >= 0) && (x->x[i] < cell_size[j]));
@@ -1207 +1207 @@
 {
         int i = 0;
-  for(i=0;i<MAX_ELEMENTS;i++)
+  for(i=MAX_ELEMENTS;i--;)
         ElementsInMolecule[i] = 0;
         ElementCount = 0;
@@ -1217 +1217 @@
     i++;
   }
-  for(i=0;i<MAX_ELEMENTS;i++)
+  for(i=MAX_ELEMENTS;i--;)
         ElementCount += (ElementsInMolecule[i] != 0 ? 1 : 0);
 };
@@ -1282 +1282 @@
 {
   configuration.MaxPsiDouble = configuration.PsiMaxNoDown = configuration.PsiMaxNoUp = configuration.PsiType = 0;
-  for(int i=0;i<MAX_ELEMENTS;i++) {
+  for(int i=MAX_ELEMENTS;i--;) {
     if (ElementsInMolecule[i] != 0) {
       //cout << "CalculateOrbitals: " << elemente->FindElement(i)->name << " has a valence of " << (int)elemente->FindElement(i)->Valence << " and there are " << ElementsInMolecule[i] << " of it." << endl;
@@ -1352 +1352 @@
     *out << Verbose(1) << "Allocating " << NumberCells << " cells." << endl;
     CellList = (molecule **) Malloc(sizeof(molecule *)*NumberCells, "molecule::CreateAdjacencyList - ** CellList");
-    for (int i=0;i<NumberCells;i++)
+    for (int i=NumberCells;i--;)
       CellList[i] = NULL;
   
@@ -1382 +1382 @@
       
     // 3a. go through every cell
-    for (N[0]=0;N[0]<divisor[0];N[0]++)
-      for (N[1]=0;N[1]<divisor[1];N[1]++)
-        for (N[2]=0;N[2]<divisor[2];N[2]++) {
+    for (N[0]=divisor[0];N[0]--;)
+      for (N[1]=divisor[1];N[1]--;)
+        for (N[2]=divisor[2];N[2]--;) {
           Index = N[2] + (N[1] + N[0] * divisor[1]) * divisor[2];
           if (CellList[Index] != NULL) { // if there atoms in this cell
@@ -1424 +1424 @@
         }
     // 4. free the cell again
-    for (int i=0;i<NumberCells;i++)
+    for (int i=NumberCells;i--;)
       if (CellList[i] != NULL) {
         delete(CellList[i]);
@@ -1696 +1696 @@
 
   // initialise each vertex as white with no predecessor, empty queue, color Root lightgray
-  for (int i=0;i<AtomCount;i++) {
+  for (int i=AtomCount;i--;) {
     PredecessorList[i] = NULL;
     ShortestPathList[i] = -1;
@@ -1702 +1702 @@
   }
   MinimumRingSize = new int[AtomCount];
-  for(int i=0;i<AtomCount;i++)
+  for(int i=AtomCount;i--;)
     MinimumRingSize[i] = AtomCount;
 
@@ -1891 +1891 @@
       Free((void **)&Walker->ComponentNr, "molecule::InitComponentNumbers: **Walker->ComponentNr");
     Walker->ComponentNr = (int *) Malloc(sizeof(int)*NumberOfBondsPerAtom[Walker->nr], "molecule::InitComponentNumbers: *Walker->ComponentNr");
-    for (int i=0;i<NumberOfBondsPerAtom[Walker->nr];i++)
+    for (int i=NumberOfBondsPerAtom[Walker->nr];i--;)
       Walker->ComponentNr[i] = -1;
   }
@@ -2261 +2261 @@
 
   // initialize mask list
-  for(int i=0;i<AtomCount;i++)
+  for(int i=AtomCount;i--;)
     AtomMask[i] = false;
   
@@ -2414 +2414 @@
   }
   SortIndex = (int *) Malloc(sizeof(int)*AtomCount, "molecule::FragmentMolecule: *SortIndex");
-  for(int i=0;i<AtomCount;i++)
+  for(int i=AtomCount;i--;)
     SortIndex[i] = -1;
   while (runner->next != elemente->end) { // go through every element
@@ -2533 +2533 @@
   
   // free the index lookup list
-  for (int i=0;i<FragmentCounter;i++)
+  for (int i=FragmentCounter;i--;)
     Free((void **)&ListOfLocalAtoms[i], "molecule::FragmentMolecule - *ListOfLocalAtoms[]");
   Free((void **)&ListOfLocalAtoms, "molecule::FragmentMolecule - **ListOfLocalAtoms");
@@ -2649 +2649 @@
 
   *out << Verbose(1) << "Begin of ParseOrderAtSiteFromFile" << endl;
-  for(int i=0;i<AtomCount;i++)
+  for(int i=AtomCount;i--;)
     OrderArray[i] = 0;
   line << path << "/" << FRAGMENTPREFIX << ORDERATSITEFILE;
   file.open(line.str().c_str());
   if (file != NULL) {
-    for (int i=0;i<AtomCount;i++) // initialise with 0
+    for (int i=AtomCount;i--;) // initialise with 0
       OrderArray[i] = 0;
     while (!file.eof()) { // parse from file
@@ -2697 +2697 @@
   *out << Verbose(2) << "(Re-)Allocating memory." << endl;
   if (ListOfBondsPerAtom != NULL) {
-    for(int i=0;i<AtomCount;i++)
+    for(int i=AtomCount;i--;)
       Free((void **)&ListOfBondsPerAtom[i], "molecule::CreateListOfBondsPerAtom: ListOfBondsPerAtom[i]");
     Free((void **)&ListOfBondsPerAtom, "molecule::CreateListOfBondsPerAtom: ListOfBondsPerAtom");
@@ -2707 +2707 @@
 
   // reset bond counts per atom
-  for(int i=0;i<AtomCount;i++)
+  for(int i=AtomCount;i--;)
     NumberOfBondsPerAtom[i] = 0;
   // count bonds per atom
@@ -2716 +2716 @@
     NumberOfBondsPerAtom[Binder->rightatom->nr]++;
   }
-  // allocate list of bonds per atom
-  for(int i=0;i<AtomCount;i++)
+  for(int i=AtomCount;i--;) {
+    // allocate list of bonds per atom
     ListOfBondsPerAtom[i] = (bond **) Malloc(sizeof(bond *)*NumberOfBondsPerAtom[i], "molecule::CreateListOfBondsPerAtom: **ListOfBondsPerAtom[]");
-  // clear the list again, now each NumberOfBondsPerAtom marks current free field
-  for(int i=0;i<AtomCount;i++)
+    // clear the list again, now each NumberOfBondsPerAtom marks current free field
     NumberOfBondsPerAtom[i] = 0;
+  }
   // fill the list
   Binder = first;
@@ -2774 +2774 @@
 
   // initialise each vertex as white with no predecessor, empty queue, color Root lightgray
-  for (int i=0;i<AtomCount;i++) {
+  for (int i=AtomCount;i--;) {
     PredecessorList[i] = NULL;
     ShortestPathList[i] = -1;
@@ -2890 +2890 @@
   // reset parent list
   *out << Verbose(3) << "Resetting ParentList." << endl;
-  for (int i=0;i<Father->AtomCount;i++)
+  for (int i=Father->AtomCount;i--;)
     ParentList[i] = NULL;
   
@@ -2972 +2972 @@
   
   Leaf->BondDistance = BondDistance;
-  for(int i=0;i<NDIM*2;i++)
+  for(int i=NDIM*2;i--;)
     Leaf->cell_size[i] = cell_size[i]; 
 
   // initialise SonList (indicates when we need to replace a bond with hydrogen instead)
-  for(int i=0;i<AtomCount;i++)
+  for(int i=AtomCount;i--;)
     SonList[i] = NULL;
 
@@ -3298 +3298 @@
   // initialised touched list (stores added atoms on this level) 
   *out << Verbose(1+verbosity) << "Clearing touched list." << endl;
-  for (TouchedIndex=0;TouchedIndex<=SubOrder;TouchedIndex++)  // empty touched list
+  for (TouchedIndex=SubOrder+1;TouchedIndex--;)  // empty touched list
     TouchedList[TouchedIndex] = -1;
   TouchedIndex = 0;
@@ -3307 +3307 @@
     // count the set bit of i
     bits = 0;
-    for (int j=0;j<SetDimension;j++)
+    for (int j=SetDimension;j--;)
       bits += (i & (1 << j)) >> j;
       
@@ -3339 +3339 @@
         while (Binder->next != FragmentSearch->BondsPerSPList[2*SP+1]) {                // compare to end node of this level
           Binder = Binder->next;
-          for (int k=0;k<TouchedIndex;k++) {
+          for (int k=TouchedIndex;k--;) {
             if (Binder->Contains(TouchedList[k]))   // if we added this very endpiece
               SubSetDimension++;
@@ -3419 +3419 @@
   int Counter = FragmentSearch.FragmentCounter;
 
-  for (int i=0;i<AtomCount;i++) {
+  for (int i=AtomCount;i--;) {
     PredecessorList[i] = NULL;
   }
@@ -3431 +3431 @@
   FragmentSearch.ShortestPathList[RootKeyNr] = 0;
   // prepare the atom stack counters (number of atoms with certain SP on stack)
-  for (int i=0;i<Order;i++)
+  for (int i=Order;i--;)
     NumberOfAtomsSPLevel[i] = 0;
   NumberOfAtomsSPLevel[0] = 1;  // for root
@@ -3528 +3528 @@
   }
   
-  // creating fragments with the found edge sets
+  // creating fragments with the found edge sets  (may be done in reverse order, faster)
   SP = 0;
-  for(int i=0;i<Order;i++) { // sum up all found edges
+  for(int i=Order;i--;) { // sum up all found edges
     Binder = FragmentSearch.BondsPerSPList[2*i];
     while (Binder->next != FragmentSearch.BondsPerSPList[2*i+1]) {
@@ -3576 +3576 @@
   // free'ing the bonds lists
   *out << Verbose(0) << "Free'ing all found lists. and resetting index lists" << endl;
-  for(int i=0;i<Order;i++) {
+  for(int i=Order;i--;) {
     *out << Verbose(1) << "Current SP level is " << i << ": ";
     Binder = FragmentSearch.BondsPerSPList[2*i];
@@ -3625 +3625 @@
   while (flag) {
     // remove bonds that are beyond bonddistance
-    for(int i=0;i<NDIM;i++)
+    for(int i=NDIM;i--;)
       TranslationVector.x[i] = 0.; 
     // scan all bonds
@@ -3632 +3632 @@
     while ((!flag) && (Binder->next != last)) {
       Binder = Binder->next;
-      for (int i=0;i<NDIM;i++) {
+      for (int i=NDIM;i--;) {
         tmp = fabs(Binder->leftatom->x.x[i] - Binder->rightatom->x.x[i]);
         //*out << Verbose(3) << "Checking " << i << "th distance of " << *Binder->leftatom << " to " << *Binder->rightatom << ": " << tmp << "." << endl;
@@ -3646 +3646 @@
     if (flag) {
       // create translation vector from their periodically modified distance
-      for (int i=0;i<NDIM;i++) {
+      for (int i=NDIM;i--;) {
         tmp = Binder->leftatom->x.x[i] - Binder->rightatom->x.x[i];
         if (fabs(tmp) > BondDistance)
@@ -3656 +3656 @@
       //*out << endl;
       // apply to all atoms of first component via BFS
-      for (int i=0;i<AtomCount;i++)
+      for (int i=AtomCount;i--;)
         ColorList[i] = white;
       AtomStack->Push(Binder->leftatom);
@@ -3832 +3832 @@
   FragmentSearch.FragmentSet = new KeySet;
   FragmentSearch.Root = FindAtom(RootKeyNr);
-  for (int i=0;i<AtomCount;i++) {
+  for (int i=AtomCount;i--;) {
     FragmentSearch.Labels[i] = -1;
     FragmentSearch.ShortestPathList[i] = -1;
@@ -3865 +3865 @@
       FragmentSearch.BondsPerSPList = (bond **) Malloc(sizeof(bond *)*Order*2, "molecule::PowerSetGenerator: ***BondsPerSPList");
       FragmentSearch.BondsPerSPCount = (int *) Malloc(sizeof(int)*Order, "molecule::PowerSetGenerator: *BondsPerSPCount");
-      for (int i=0;i<Order;i++) {
+      for (int i=Order;i--;) {
         FragmentSearch.BondsPerSPList[2*i] = new bond();    // start node
         FragmentSearch.BondsPerSPList[2*i+1] = new bond();  // end node
@@ -3933 +3933 @@
       // free Order-dependent entries of UniqueFragments structure for next loop cycle
       Free((void **)&FragmentSearch.BondsPerSPCount, "molecule::PowerSetGenerator: *BondsPerSPCount");
-      for (int i=0;i<Order;i++) {
+      for (int i=Order;i--;) {
         delete(FragmentSearch.BondsPerSPList[2*i]);
         delete(FragmentSearch.BondsPerSPList[2*i+1]);
@@ -3989 +3989 @@
  * \return <0, \a *a less than \a *b, ==0 if equal, >0 \a *a greater than \a *b
  */
-int CompareDoubles (const void * a, const void * b)
+inline int CompareDoubles (const void * a, const void * b)
 {
   if (*(double *)a > *(double *)b)
@@ -4040 +4040 @@
   /// -# ElementsInMolecule
   if (result) {
-    for (flag=0;flag<MAX_ELEMENTS;flag++) {
+    for (flag=MAX_ELEMENTS;flag--;) {
       //*out << Verbose(5) << "Element " <<  flag << ": " << ElementsInMolecule[flag] << " <-> " << OtherMolecule->ElementsInMolecule[flag] << "." << endl;
       if (ElementsInMolecule[flag] != OtherMolecule->ElementsInMolecule[flag])
@@ -4074 +4074 @@
     while (Walker->next != end) {
       Walker = Walker->next;
-    //for (i=0;i<AtomCount;i++) {
       Distances[Walker->nr] = CenterOfGravity.Distance(&Walker->x);
     }
@@ -4091 +4090 @@
     PermutationMap = (int *) Malloc(sizeof(int)*AtomCount, "molecule::IsEqualToWithinThreshold: *PermutationMap");
     *out << Verbose(5) << "Combining Permutation Maps" << endl;
-    for(int i=0;i<AtomCount;i++)
+    for(int i=AtomCount;i--;)
       PermutationMap[PermMap[i]] = (int) OtherPermMap[i];
     
@@ -4136 +4135 @@
   *out << Verbose(3) << "Begin of GetFatherAtomicMap." << endl;
   int *AtomicMap = (int *) Malloc(sizeof(int)*AtomCount, "molecule::GetAtomicMap: *AtomicMap");  //Calloc
-  for (int i=0;i<AtomCount;i++)
+  for (int i=AtomCount;i--;)
     AtomicMap[i] = -1;
   if (OtherMolecule == this) {  // same molecule
-    for (int i=0;i<AtomCount;i++) // no need as -1 means already that there is trivial correspondence
+    for (int i=AtomCount;i--;) // no need as -1 means already that there is trivial correspondence
       AtomicMap[i] = i;
     *out << Verbose(4) << "Map is trivial." << endl;