Changeset 7f3b9d

Timestamp:

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

Author:

Frederik Heber <heber@…>

Branches:

Action_Thermostats, Add_AtomRandomPerturbation, Add_FitFragmentPartialChargesAction, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Added_ParseSaveFragmentResults, AddingActions_SaveParseParticleParameters, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_ParticleName_to_Atom, Adding_StructOpt_integration_tests, AtomFragments, Automaking_mpqc_open, AutomationFragmentation_failures, Candidate_v1.5.4, Candidate_v1.6.0, Candidate_v1.6.1, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, CombiningParticlePotentialParsing, Combining_Subpackages, Debian_Package_split, Debian_package_split_molecuildergui_only, Disabling_MemDebug, Docu_Python_wait, EmpiricalPotential_contain_HomologyGraph, EmpiricalPotential_contain_HomologyGraph_documentation, Enable_parallel_make_install, Enhance_userguide, Enhanced_StructuralOptimization, Enhanced_StructuralOptimization_continued, Example_ManyWaysToTranslateAtom, Exclude_Hydrogens_annealWithBondGraph, FitPartialCharges_GlobalError, Fix_BoundInBox_CenterInBox_MoleculeActions, Fix_ChargeSampling_PBC, Fix_ChronosMutex, Fix_FitPartialCharges, Fix_FitPotential_needs_atomicnumbers, Fix_ForceAnnealing, Fix_IndependentFragmentGrids, Fix_ParseParticles, Fix_ParseParticles_split_forward_backward_Actions, Fix_PopActions, Fix_QtFragmentList_sorted_selection, Fix_Restrictedkeyset_FragmentMolecule, Fix_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, Fix_fitting_potentials, Fixes, ForceAnnealing_goodresults, ForceAnnealing_oldresults, ForceAnnealing_tocheck, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, FragmentAction_writes_AtomFragments, FragmentMolecule_checks_bonddegrees, GeometryObjects, Gui_Fixes, Gui_displays_atomic_force_velocity, ImplicitCharges, IndependentFragmentGrids, IndependentFragmentGrids_IndividualZeroInstances, IndependentFragmentGrids_IntegrationTest, IndependentFragmentGrids_Sole_NN_Calculation, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, MoreRobust_FragmentAutomation, ODR_violation_mpqc_open, PartialCharges_OrthogonalSummation, PdbParser_setsAtomName, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, Rewrite_FitPartialCharges, RotateToPrincipalAxisSystem_UndoRedo, SaturateAtoms_findBestMatching, SaturateAtoms_singleDegree, StoppableMakroAction, Subpackage_CodePatterns, Subpackage_JobMarket, Subpackage_LinearAlgebra, Subpackage_levmar, Subpackage_mpqc_open, Subpackage_vmg, Switchable_LogView, ThirdParty_MPQC_rebuilt_buildsystem, TrajectoryDependenant_MaxOrder, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, TremoloParser_setsAtomName, Ubuntu_1604_changes, stable

Children:

040f93

Parents:

6097ea

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

Location:

src

Files:

• analyzer.cpp (modified) (2 diffs)
• builder.cpp (modified) (27 diffs)
• config.cpp (modified) (4 diffs)
• datacreator.cpp (modified) (15 diffs)
• helpers.cpp (modified) (3 diffs)
• helpers.hpp (modified) (1 diff)
• moleculelist.cpp (modified) (8 diffs)
• molecules.cpp (modified) (55 diffs)
• molecules.hpp (modified) (1 diff)
• parser.cpp (modified) (23 diffs)
• stackclass.hpp (modified) (1 diff)
• vector.cpp (modified) (24 diffs)
• verbose.cpp (modified) (1 diff)

src/analyzer.cpp

@@ -93 +93 @@
   output << endl << "Total Times" << endl << "===============" << endl << Time.Header << endl;
   Time.SetLastMatrix(0., 0);
-  for (int BondOrder=0;BondOrder<KeySet.Order;BondOrder++)
-    for(int i=0;i<KeySet.FragmentsPerOrder[BondOrder];i++)
-      for(int j=0;j<Time.RowCounter[Time.MatrixCounter];j++)
-        for(int k=0;k<Time.ColumnCounter;k++) {
+  for (int BondOrder=KeySet.Order;BondOrder--;)
+    for(int i=KeySet.FragmentsPerOrder[BondOrder];i--;)
+      for(int j=Time.RowCounter[Time.MatrixCounter];j--;)
+        for(int k=Time.ColumnCounter;k--;) {
           Time.Matrix[ Time.MatrixCounter ][j][k] += Time.Matrix[ KeySet.OrderSet[BondOrder][i] ][j][k];
         }
@@ -118 +118 @@
   output << "#Order\tFrag.No.\t" << Time.Header << endl;
   for (int BondOrder=0;BondOrder<KeySet.Order;BondOrder++) {
-    for(int i=0;i<KeySet.FragmentsPerOrder[BondOrder];i++)
-      for(int j=0;j<Time.RowCounter[Time.MatrixCounter];j++)
-        for(int k=0;k<Time.ColumnCounter;k++) {
+    for(int i=KeySet.FragmentsPerOrder[BondOrder];i--;)
+      for(int j=Time.RowCounter[Time.MatrixCounter];j--;)
+        for(int k=Time.ColumnCounter;k--;) {
           Time.Matrix[ Time.MatrixCounter ][j][k] += Time.Matrix[ KeySet.OrderSet[BondOrder][i] ][j][k];
         }

src/builder.cpp

@@ -59 +59 @@
  * \param *mol the molecule to add to
  */
-void AddAtoms(periodentafel *periode, molecule *mol)
+static void AddAtoms(periodentafel *periode, molecule *mol)
 {
   atom *first, *second, *third, *fourth;
@@ -113 +113 @@
           cout << Verbose(0) << "Enter relative coordinates." << endl;
           first->x.AskPosition(mol->cell_size, false);
-          for (int i=0;i<3;i++) {
+          for (int i=NDIM;i--;) {
             first->x.x[i] += second->x.x[i];
           }
@@ -227 +227 @@
         atoms = new (vector*[128]);
         valid = true;
-        for(int i=0;i<128;i++)
+        for(int i=128;i--;)
           atoms[i] = NULL;
         int i=0, j=0;
@@ -256 +256 @@
  * \param *mol the molecule with all the atoms
  */
-void CenterAtoms(molecule *mol)
+static void CenterAtoms(molecule *mol)
 {
   vector x, y;
@@ -285 +285 @@
     case 'c':
       cout << Verbose(0) << "Centering atoms in config file within given additional boundary." << endl;
-      for (int i=0;i<3;i++) {
+      for (int i=0;i<NDIM;i++) {
         cout << Verbose(0) << "Enter axis " << i << " boundary: ";
         cin >> y.x[i];
@@ -295 +295 @@
     case 'd':
       cout << Verbose(1) << "Centering atoms in config file within given simulation box." << endl;
-      for (int i=0;i<3;i++) {
+      for (int i=0;i<NDIM;i++) {
         cout << Verbose(0) << "Enter axis " << i << " boundary: ";
         cin >> x.x[i];
@@ -311 +311 @@
  * \param *mol the molecule with all the atoms
  */
-void AlignAtoms(periodentafel *periode, molecule *mol)
+static void AlignAtoms(periodentafel *periode, molecule *mol)
 {
   atom *first, *second, *third;
@@ -359 +359 @@
       cout << Verbose(0) << "Element is " << param.type->name << endl;
       mol->GetAlignVector(&param);
-      for (int i=0;i<3;i++) {
+      for (int i=NDIM;i--;) {
         x.x[i] = gsl_vector_get(param.x,i);
-        n.x[i] = gsl_vector_get(param.x,i+3);
+        n.x[i] = gsl_vector_get(param.x,i+NDIM);
       } 
       gsl_vector_free(param.x);
@@ -379 +379 @@
  * \param *mol the molecule with all the atoms
  */
-void MirrorAtoms(molecule *mol)
+static void MirrorAtoms(molecule *mol)
 {
   atom *first, *second, *third;
@@ -426 +426 @@
  * \param *mol the molecule with all the atoms
  */
-void RemoveAtoms(molecule *mol)
+static void RemoveAtoms(molecule *mol)
 {
   atom *first, *second;
@@ -484 +484 @@
  * \param *mol the molecule with all the atoms
  */
-void MeasureAtoms(periodentafel *periode, molecule *mol)
+static void MeasureAtoms(periodentafel *periode, molecule *mol)
 {
   atom *first, *second, *third;
@@ -507 +507 @@
     case 'a':
       first = mol->AskAtom("Enter first atom: ");
-      for (int i=0;i<256;i++)
+      for (int i=MAX_ELEMENTS;i--;)
         min[i] = 0.;
         
@@ -523 +523 @@
         //cout << Verbose(0) << "Bond length between Atom " << first->nr << " and " << second->nr << ": " << tmp1 << " a.u." << endl;         
       }
-      for (int i=0;i<256;i++)
+      for (int i=MAX_ELEMENTS;i--;)
         if (min[i] != 0.) cout << Verbose(0) << "Minimum Bond length between " << first->type->name << " Atom " << first->nr << " and next Ion of type " << (periode->FindElement(i))->name << ": " << min[i] << " a.u." << endl;
       break;
@@ -530 +530 @@
       first = mol->AskAtom("Enter first atom: ");
       second = mol->AskAtom("Enter second atom: ");
-      for (int i=0;i<NDIM;i++)
+      for (int i=NDIM;i--;)
         min[i] = 0.;
       x.CopyVector((const vector *)&first->x);
@@ -560 +560 @@
  * \param *configuration configuration structure for the to be written config files of all fragments
  */
-void FragmentAtoms(molecule *mol, config *configuration)
+static void FragmentAtoms(molecule *mol, config *configuration)
 {
   int Order1;
@@ -581 +581 @@
 /** Is called always as option 'T' in the menu.
  */
-void testroutine(molecule *mol)
+static void testroutine(molecule *mol)
 {
   // the current test routine checks the functionality of the KeySet&Graph concept:
@@ -654 +654 @@
  * \param *mol pointer to molecule structure with all the atoms and coordinates
  */
-void SaveConfig(char *ConfigFileName, config *configuration, periodentafel *periode, molecule *mol)
+static void SaveConfig(char *ConfigFileName, config *configuration, periodentafel *periode, molecule *mol)
 {
   char filename[MAXSTRINGSIZE];
@@ -709 +709 @@
  * \return exit code (0 - successful, all else - something's wrong)
  */
-int ParseCommandLineOptions(int argc, char **argv, molecule *&mol, periodentafel *&periode, config& configuration, char *&ConfigFileName, char *&ElementsFileName)
+static int ParseCommandLineOptions(int argc, char **argv, molecule *&mol, periodentafel *&periode, config& configuration, char *&ConfigFileName, char *&ElementsFileName)
 {
   element *finder;
@@ -846 +846 @@
               ExitFlag = 1;
               cout << Verbose(1) << "Translating all ions to new origin." << endl;
-              for (int i=0;i<3;i++)
+              for (int i=NDIM;i--;)
                 x.x[i] = atof(argv[argptr+i]);
               mol->Translate((const vector *)&x);
@@ -855 +855 @@
               cout << Verbose(1) << "Adding new atom." << endl;
               first = new atom;
-              for (int i=0;i<3;i++)
+              for (int i=NDIM;i--;)
                 first->x.x[i] = atof(argv[argptr+1+i]);
               finder = periode->start;
@@ -872 +872 @@
               j = -1;
               cout << Verbose(1) << "Scaling all ion positions by factor." << endl;
-              factor = (double *) Malloc(sizeof(double)*NDIM, "main: *factor");
+              factor = new double[NDIM];
               factor[0] = atof(argv[argptr]);
               if (argc > argptr+1)
@@ -881 +881 @@
               factor[2] = atof(argv[argptr]);
               mol->Scale(&factor);
-              for (int i=0;i<3;i++) {
+              for (int i=0;i<NDIM;i++) {
                 j += i+1;
-                x.x[i] = atof(argv[3+i]);
+                x.x[i] = atof(argv[NDIM+i]);
                 mol->cell_size[j]*=factor[i];
               }
-              Free((void **)&factor, "main: *factor");
+              delete[](factor);
               argptr+=1;
               break;
@@ -894 +894 @@
               cout << Verbose(1) << "Centering atoms in config file within given simulation box." << endl;
               j=-1;
-              for (int i=0;i<3;i++) {
+              for (int i=0;i<NDIM;i++) {
                 j += i+1;
                 x.x[i] = atof(argv[argptr++]);
@@ -914 +914 @@
               // translate each coordinate by boundary
               j=-1;
-              for (int i=0;i<3;i++) {
+              for (int i=0;i<NDIM;i++) {
                 j += i+1;
                 x.x[i] = atof(argv[argptr++]);
@@ -1056 +1056 @@
         second = mol->AskAtom("Enter second (shifting) atom: ");
         min_bond = 0.;
-        for (int i=0;i<3;i++)
+        for (int i=NDIM;i--;)
           min_bond += (first->x.x[i]-second->x.x[i])*(first->x.x[i] - second->x.x[i]);
         min_bond = sqrt(min_bond);
@@ -1062 +1062 @@
         cout << Verbose(0) << "Enter new bond length [a.u.]: ";
         cin >> bond;
-        for (int i=0;i<3;i++) {
+        for (int i=NDIM;i--;) {
           second->x.x[i] -= (second->x.x[i]-first->x.x[i])/min_bond*(min_bond-bond);
         }
@@ -1107 +1107 @@
           for (int i=1;i<faktor;i++) {  // then add this list with respective translation factor times
             x.AddVector(&y); // per factor one cell width further
-            for (int k=0;k<count;k++) { // go through every atom of the original cell
+            for (int k=count;k--;) { // go through every atom of the original cell
               first = new atom(); // create a new body
               first->x.CopyVector(Vectors[k]);  // use coordinate of original atom

src/config.cpp

@@ -282 +282 @@
         case 'j': // BoxLength
           cout << Verbose(0) << "enter lower triadiagonalo form of basis matrix" << endl << endl;
-          for (int i=0;i<6;i++) {
+          for (int i=6;i--;) {
             cout << Verbose(0) << "Cell size" << i << ": ";
             cin >> mol->cell_size[i];
@@ -408 +408 @@
 
 /** Retrieves the path in the given config file name.
- * \param *filename config file string
+ * \param filename config file string
  */
-void config::RetrieveConfigPathAndName(char *filename)
+void config::RetrieveConfigPathAndName(string filename)
 {
   char *ptr = NULL;
+  char *buffer = new char[MAXSTRINGSIZE];
+  strncpy(buffer, filename.c_str(), MAXSTRINGSIZE);
   int last = -1;
-  for(int i=0;i<MAXSTRINGSIZE;i++) {
-    if (filename[i] == '/')
-      last = i;
-    if (filename[i] == '\0')
+  for(last=MAXSTRINGSIZE;last--;) {
+    if (buffer[last] == '/')
       break;
   }
-  if (last == -1) { // no path in front, set to local directory.
+  if (last == 0) { // no path in front, set to local directory.
     strcpy(configpath, "./");
-    ptr = filename;
+    ptr = buffer;
   } else {
-    strncpy(configpath, filename, last+1);
-    ptr = &filename[last+1];
+    strncpy(configpath, buffer, last+1);
+    ptr = &buffer[last+1];
     if (last < 254)
       configpath[last+1]='\0';
@@ -431 +431 @@
   strcpy(configname, ptr);
   cout << "Found configpath: " << configpath << ", dir slash was found at " << last << ", config name is " << configname << "." << endl;
+  delete[](buffer);
 };
 
@@ -824 +825 @@
   
   
-  for (i=0;i<128;i++) elementhash[i] = NULL;
+  for (i=MAX_ELEMENTS;i--;) 
+    elementhash[i] = NULL;
   cout << Verbose(0) << "Parsing Ions ..." << endl;
   No=0;

src/datacreator.cpp

@@ -48 +48 @@
   output << "#Order\tFrag.No.\t" << Energy.Header << endl;
   for (int BondOrder=0;BondOrder<KeySet.Order;BondOrder++) {
-    for(int i=0;i<KeySet.FragmentsPerOrder[BondOrder];i++) {
-      for(int j=0;j<Energy.RowCounter[ KeySet.OrderSet[BondOrder][i] ];j++)
-        for(int k=0;k<Energy.ColumnCounter;k++)
+    for(int i=KeySet.FragmentsPerOrder[BondOrder];i--;) {
+      for(int j=Energy.RowCounter[ KeySet.OrderSet[BondOrder][i] ];j--;)
+        for(int k=Energy.ColumnCounter;k--;)
           Energy.Matrix[Energy.MatrixCounter][j][k] -= EnergyFragments.Matrix[ KeySet.OrderSet[BondOrder][i] ][j][k];
     }
@@ -89 +89 @@
         }
         if (j != -1)
-          for(int k=0;k<Force.ColumnCounter;k++) {
+          for(int k=Force.ColumnCounter;k--;) {
             Force.Matrix[Force.MatrixCounter][j][k] += ForceFragments.Matrix[ KeySet.OrderSet[BondOrder][i] ][l][k];
           }
@@ -136 +136 @@
 void CreateMaxFragmentOrder(class MatrixContainer &Fragments, class KeySetsContainer &KeySet, int BondOrder)
 {
-  for(int j=0;j<Fragments.RowCounter[ Fragments.MatrixCounter ];j++) {
-    for(int i=0;i<KeySet.FragmentsPerOrder[BondOrder];i++) {
+  for(int j=Fragments.RowCounter[ Fragments.MatrixCounter ];j--;) {
+    for(int i=KeySet.FragmentsPerOrder[BondOrder];i--;) {
       if (fabs(Fragments.Matrix[ Fragments.MatrixCounter ][j][1]) < fabs(Fragments.Matrix[ KeySet.OrderSet[BondOrder][i] ][j][1])) {
-        for (int k=0;k<Fragments.ColumnCounter;k++)
+        for (int k=Fragments.ColumnCounter;k--;)
           Fragments.Matrix[ Fragments.MatrixCounter ][j][k] = Fragments.Matrix[ KeySet.OrderSet[BondOrder][i] ][j][k];
       }
@@ -156 +156 @@
     int i=0;
     do {  // first get a minimum value unequal to 0
-      for (int k=0;k<Fragments.ColumnCounter;k++)
+      for (int k=Fragments.ColumnCounter;k--;)
         Fragments.Matrix[ Fragments.MatrixCounter ][j][k] = Fragments.Matrix[ KeySet.OrderSet[BondOrder][i] ][j][k];
       i++;
@@ -162 +162 @@
     for(;i<KeySet.FragmentsPerOrder[BondOrder];i++) { // then find lowest
       if (fabs(Fragments.Matrix[ Fragments.MatrixCounter ][j][1]) > fabs(Fragments.Matrix[ KeySet.OrderSet[BondOrder][i] ][j][1])) {
-        for (int k=0;k<Fragments.ColumnCounter;k++)
+        for (int k=Fragments.ColumnCounter;k--;)
           Fragments.Matrix[ Fragments.MatrixCounter ][j][k] = Fragments.Matrix[ KeySet.OrderSet[BondOrder][i] ][j][k];
       }
@@ -211 +211 @@
 void CreateMinimumForce(class MatrixContainer &Force, int MatrixNumber)
 {
-  for (int l=0;l<Force.ColumnCounter;l++)
+  for (int l=Force.ColumnCounter;l--;)
     Force.Matrix[MatrixNumber][ Force.RowCounter[MatrixNumber] ][l] = 0.;
   for (int l=5;l<Force.ColumnCounter;l+=3) {
@@ -217 +217 @@
     int k=0;
     do {
-      for (int m=0;m<3;m++) {
+      for (int m=NDIM;m--;) {
         stored += Force.Matrix[MatrixNumber][ k ][l+m] 
               * Force.Matrix[MatrixNumber][ k ][l+m];
@@ -226 +226 @@
     for (;k<Force.RowCounter[MatrixNumber];k++) {
       double tmp = 0;
-      for (int m=0;m<3;m++)
+      for (int m=NDIM;m--;)
         tmp += Force.Matrix[MatrixNumber][ k ][l+m] 
               * Force.Matrix[MatrixNumber][ k ][l+m];
       if ((fabs(tmp) > MYEPSILON) && (tmp < stored)) {  // current force is greater than stored
-        for (int m=0;m<3;m++)
+        for (int m=NDIM;m--;)
           Force.Matrix[MatrixNumber][ Force.RowCounter[MatrixNumber] ][l+m]  = Force.Matrix[MatrixNumber][ k ][l+m]; 
         stored = tmp;
@@ -246 +246 @@
 {
   int divisor = 0;
-  for (int l=0;l<Force.ColumnCounter;l++)
+  for (int l=Force.ColumnCounter;l--;)
     Force.Matrix[MatrixNumber][ Force.RowCounter[MatrixNumber] ][l] = 0.;
   for (int l=5;l<Force.ColumnCounter;l+=3) {
     double tmp = 0;
-    for (int k=0;k<Force.RowCounter[MatrixNumber];k++) {
+    for (int k=Force.RowCounter[MatrixNumber];k--;) {
       double norm = 0.;
-      for (int m=0;m<3;m++)
+      for (int m=NDIM;m--;)
         norm += Force.Matrix[MatrixNumber][ k ][l+m] 
               * Force.Matrix[MatrixNumber][ k ][l+m];
@@ -272 +272 @@
   for (int l=5;l<Force.ColumnCounter;l+=3) {
     double stored = 0;
-    for (int k=0;k<Force.RowCounter[MatrixNumber];k++) {
+    for (int k=Force.RowCounter[MatrixNumber];k--;) {
       double tmp = 0;
-      for (int m=0;m<3;m++)
+      for (int m=NDIM;m--;)
         tmp += Force.Matrix[MatrixNumber][ k ][l+m] 
               * Force.Matrix[MatrixNumber][ k ][l+m];
       if (tmp > stored) {  // current force is greater than stored
-        for (int m=0;m<3;m++)
+        for (int m=NDIM;m--;)
           Force.Matrix[MatrixNumber][ Force.RowCounter[MatrixNumber] ][l+m]  = Force.Matrix[MatrixNumber][ k ][l+m]; 
         stored = tmp;
@@ -293 +293 @@
 void CreateVectorSumForce(class MatrixContainer &Force, int MatrixNumber)
 {
-  for (int l=0;l<Force.ColumnCounter;l++)
+  for (int l=Force.ColumnCounter;l--;)
     Force.Matrix[MatrixNumber][ Force.RowCounter[MatrixNumber] ][l] = 0.;
   for (int l=5;l<Force.ColumnCounter;l++) {
-    for (int k=0;k<Force.RowCounter[MatrixNumber];k++)
+    for (int k=Force.RowCounter[MatrixNumber];k--;)
       Force.Matrix[MatrixNumber][ Force.RowCounter[MatrixNumber] ][l] += Force.Matrix[MatrixNumber][k][l];
   }
@@ -423 +423 @@
   line >> item;
   line >> item;
-  for (int i=7; i< Force.ColumnCounter;i+=3) {
+  for (int i=7; i< Force.ColumnCounter;i+=NDIM) {
     line >> item;
     item[strlen(item)-1] = '\0';  // kill residual index char (the '0')
@@ -452 +452 @@
   line >> item;
   line >> item;
-  for (int i=7; i< Force.ColumnCounter;i+=3) {
+  for (int i=7; i< Force.ColumnCounter;i+=NDIM) {
     line >> item;
     item[strlen(item)-1] = '\0';  // kill residual index char (the '0')
@@ -482 +482 @@
   line >> item;
   line >> item;
-  for (int i=7; i< Force.ColumnCounter;i+=3) {
+  for (int i=7; i< Force.ColumnCounter;i+=NDIM) {
     line >> item;
     item[strlen(item)-1] = '\0';  // kill residual index char (the '0')
@@ -512 +512 @@
   line >> item;
   line >> item;
-  for (int i=7; i< Force.ColumnCounter;i+=3) {
+  for (int i=7; i< Force.ColumnCounter;i+=NDIM) {
     line >> item;
     item[strlen(item)-1] = '\0';  // kill residual index char (the '0')

src/helpers.cpp

@@ -106 +106 @@
   if (buffer == NULL)
     cout << Verbose(0) << output << endl;
-  for (i=0;i<size;i++)  // reset
+  for (i=size;i--;)  // reset
     buffer[i] = i % 2 == 0 ? 'p': 'c';
   buffer[size] = '\0'; // and set length marker on its end
@@ -147 +147 @@
   int res = 1;
   int j;
-  for (j=0;j<n;j++)
+  for (j=n;j--;)
     res *= base;
   return res;
@@ -172 +172 @@
   returnstring[order] = '\0';
   number = digits;
-  for (int i=order-1;i>=0;i--){
+  for (int i=order-1;i--;){
     returnstring[i] = '0' + (char)(number % 10);
     number = (int)floor(((double)number / 10.));

src/helpers.hpp

@@ -266 +266 @@
   int i;
   if (ptr != NULL) {
-    for(i=0;i<dim;i++)
+    for(i=dim;i--;)
       if (ptr[i] != NULL)
         free(ptr[i]);

src/moleculelist.cpp

@@ -22 +22 @@
 {
   ListOfMolecules = (molecule **) Malloc(sizeof(molecule *)*NumMolecules, "MoleculeListClass:MoleculeListClass: **ListOfMolecules");
-  for (int i=0;i<NumMolecules;i++)
+  for (int i=NumMolecules;i--;)
     ListOfMolecules[i] = NULL;
   NumberOfMolecules = NumMolecules;
@@ -34 +34 @@
 {
   cout << Verbose(3) << this << ": Freeing ListOfMolcules." << endl;
-  for (int i=0;i<NumberOfMolecules;i++) {
+  for (int i=NumberOfMolecules;i--;) {
     if (ListOfMolecules[i] != NULL) { // if NULL don't free
       cout << Verbose(4) << "ListOfMolecules: Freeing " << ListOfMolecules[i] << "." << endl;
@@ -66 +66 @@
     else {
       Count = (**(molecule **)a).AtomCount;
-      aList = (int *) Malloc(sizeof(int)*Count, "MolCompare: *aList");
-      bList = (int *) Malloc(sizeof(int)*Count, "MolCompare: *bList");
+      aList = new int[Count];
+      bList = new int[Count];
   
       // fill the lists
@@ -114 +114 @@
         }
       }
-      Free((void **)&aList, "MolCompare: *aList");
-      Free((void **)&bList, "MolCompare: *bList");
+      delete[](aList);
+      delete[](bList);
       return flag;
     }
@@ -244 +244 @@
     ListOfMolecules[i]->SetBoxDimension(&BoxDimension);  // update Box of atoms by boundary
     int j = -1;
-    for (int k=0;k<3;k++) {
+    for (int k=0;k<NDIM;k++) {
       j += k+1;
       BoxDimension.x[k] = 5.;
@@ -268 +268 @@
     outputFragment.close();
     outputFragment.clear();
-    Free((void **)&FragmentNumber, "MoleculeListClass::OutputConfigForListOfFragments: *FragmentNumber");
+    delete(FragmentNumber);
+    //Free((void **)&FragmentNumber, "MoleculeListClass::OutputConfigForListOfFragments: *FragmentNumber");
   }
   cout << " done." << endl;
@@ -461 +462 @@
     ListOfLocalAtoms = (atom ***) Malloc(sizeof(atom **)*Counter, "MoleculeLeafClass::FillBondStructureFromReference - ***ListOfLocalAtoms");
     if (ListOfLocalAtoms != NULL) {
-      for (int i=0;i<Counter;i++)
+      for (int i=Counter;i--;)
         ListOfLocalAtoms[i] = NULL;
       FreeList = FreeList && true;
@@ -501 +502 @@
     KeySetCounter = Count();
     FragmentList = (Graph **) Malloc(sizeof(Graph *)*KeySetCounter, "MoleculeLeafClass::AssignKeySetsToFragment - **FragmentList");
-    for(int i=0;i<KeySetCounter;i++)
+    for(int i=KeySetCounter;i--;)
       FragmentList[i] = NULL;
     KeySetCounter = 0;

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;

src/molecules.hpp

@@ -457 +457 @@
   void Load(char *filename, periodentafel *periode, molecule *mol);
   void LoadOld(char *filename, periodentafel *periode, molecule *mol);
-  void RetrieveConfigPathAndName(char * filename);
+  void RetrieveConfigPathAndName(string filename);
   bool Save(ofstream *file, periodentafel *periode, molecule *mol) const;
   void Edit(molecule *mol);

src/parser.cpp

@@ -64 +64 @@
 MatrixContainer::~MatrixContainer() {
   if (Matrix != NULL) {
-    for(int i=0;i<MatrixCounter;i++) {
+    for(int i=MatrixCounter;i--;) {
       if (RowCounter != NULL) {
-          for(int j=0;j<=RowCounter[i];j++)
+          for(int j=RowCounter[i]+1;j--;)
             Free((void **)&Matrix[i][j], "MatrixContainer::~MatrixContainer: *Matrix[][]");
         Free((void **)&Matrix[i], "MatrixContainer::~MatrixContainer: **Matrix[]");
@@ -72 +72 @@
     }
     if ((RowCounter != NULL) && (Matrix[MatrixCounter] != NULL))
-      for(int j=0;j<=RowCounter[MatrixCounter];j++)
+      for(int j=RowCounter[MatrixCounter]+1;j--;)
         Free((void **)&Matrix[MatrixCounter][j], "MatrixContainer::~MatrixContainer: *Matrix[MatrixCounter][]");
     if (MatrixCounter != 0)
@@ -79 +79 @@
   }
   if (Indices != NULL)
-    for(int i=0;i<=MatrixCounter;i++) {
+    for(int i=MatrixCounter+1;i--;) {
       Free((void **)&Indices[i], "MatrixContainer::~MatrixContainer: *Indices[]");
     }
@@ -123 +123 @@
   Matrix = (double ***) Malloc(sizeof(double **)*(MatrixCounter+1), "MatrixContainer::ParseMatrix: ***Matrix"); // one more each for the total molecule
   RowCounter = (int *) Malloc(sizeof(int)*(MatrixCounter+1), "MatrixContainer::ParseMatrix: *RowCounter");
-  for(int i=0;i<=MatrixCounter;i++) {
+  for(int i=MatrixCounter+1;i--;) {
     Matrix[i] = NULL;
     RowCounter[i] = -1;
   }
-  for(int i=0;i<=MatrixCounter;i++) {
+  for(int i=MatrixCounter+1;i--;) {
     // open matrix file
     stringstream line;
@@ -143 +143 @@
     }
     // skip some initial lines
-    for (int m=0;m<=skiplines;m++)
+    for (int m=skiplines+1;m--;)
       input.getline(Header, 1023);
     // scan header for number of columns
     line.str(Header);
-    for(int k=0;k<skipcolumns;k++)
+    for(int k=skipcolumns;k--;)
       line >> Header;
     //cout << line.str() << endl;
@@ -173 +173 @@
     input.clear();
     input.seekg(ios::beg);
-    for (int m=0;m<=skiplines;m++)
+    for (int m=skiplines+1;m--;)
       input.getline(Header, 1023);    // skip header
     line.str(Header);
-    for(int k=0;k<skipcolumns;k++)  // skip columns in header too
+    for(int k=skipcolumns;k--;)  // skip columns in header too
       line >> filename;
     strncpy(Header, line.str().c_str(), 1023);  
@@ -184 +184 @@
       stringstream line(filename);
       //cout << "Matrix at level " << j << ":";// << filename << endl;
-      for(int k=0;k<skipcolumns;k++)
+      for(int k=skipcolumns;k--;)
         line >> filename;
       for(int k=0;(k<ColumnCounter) && (!line.eof());k++) {
@@ -193 +193 @@
     }
     Matrix[i][ RowCounter[i] ] = (double *) Malloc(sizeof(double)*ColumnCounter, "MatrixContainer::ParseMatrix: *Matrix[RowCounter[i]][]");
-    for(int j=0;j<ColumnCounter;j++)
+    for(int j=ColumnCounter;j--;)
       Matrix[i][ RowCounter[i] ][j] = 0.;
     input.close();
@@ -216 +216 @@
   Matrix = (double ***) Malloc(sizeof(double **)*(MatrixCounter+1), "MatrixContainer::ParseMatrix: ***Matrix"); // one more each for the total molecule
   RowCounter = (int *) Malloc(sizeof(int)*(MatrixCounter+1), "MatrixContainer::ParseMatrix: *RowCounter");
-  for(int i=0;i<=MatrixCounter;i++) {
+  for(int i=MatrixCounter+1;i--;) {
     RowCounter[i] = RCounter[i];
     Matrix[i] = (double **) Malloc(sizeof(double *)*(RowCounter[i]+1), "MatrixContainer::ParseMatrix: **Matrix[]");  
-    for(int j=0;j<=RowCounter[i];j++) {
+    for(int j=RowCounter[i]+1;j--;) {
       Matrix[i][j] = (double *) Malloc(sizeof(double)*ColumnCounter, "MatrixContainer::ParseMatrix: *Matrix[][]");
-      for(int k=0;k<ColumnCounter;k++)
+      for(int k=ColumnCounter;k--;)
         Matrix[i][j][k] = 0.;
     }
@@ -233 +233 @@
 bool MatrixContainer::ResetMatrix()
 {
-  for(int i=0;i<=MatrixCounter;i++)
-    for(int j=0;j<=RowCounter[i];j++)
-      for(int k=0;k<ColumnCounter;k++)
+  for(int i=MatrixCounter+1;i--;)
+    for(int j=RowCounter[i]+1;j--;)
+      for(int k=ColumnCounter;k--;)
         Matrix[i][j][k] = 0.;
    return true;
@@ -247 +247 @@
 bool MatrixContainer::SetLastMatrix(double value, int skipcolumns)
 {
-  for(int j=0;j<=RowCounter[MatrixCounter];j++)
+  for(int j=RowCounter[MatrixCounter]+1;j--;)
     for(int k=skipcolumns;k<ColumnCounter;k++)
       Matrix[MatrixCounter][j][k] = value;
@@ -260 +260 @@
 bool MatrixContainer::SetLastMatrix(double **values, int skipcolumns)
 {
-  for(int j=0;j<=RowCounter[MatrixCounter];j++)
+  for(int j=RowCounter[MatrixCounter]+1;j--;)
     for(int k=skipcolumns;k<ColumnCounter;k++)
       Matrix[MatrixCounter][j][k] = values[j][k];
@@ -301 +301 @@
               }
               if (Order == SubOrder) { // equal order is always copy from Energies
-                for(int l=0;l<ColumnCounter;l++) // then adds/subtract each column 
+                for(int l=ColumnCounter;l--;) // then adds/subtract each column 
                   Matrix[ KeySet.OrderSet[Order][CurrentFragment] ][m][l] += MatrixValues.Matrix[ KeySet.OrderSet[SubOrder][j] ][k][l];
               } else {
-                for(int l=0;l<ColumnCounter;l++)
+                for(int l=ColumnCounter;l--;)
                   Matrix[ KeySet.OrderSet[Order][CurrentFragment] ][m][l] -= Matrix[ KeySet.OrderSet[SubOrder][j] ][k][l];
               }
@@ -392 +392 @@
   cout << "Parsing energy indices." << endl;
   Indices = (int **) Malloc(sizeof(int *)*(MatrixCounter+1), "EnergyMatrix::ParseIndices: **Indices");
-  for(int i=0;i<=MatrixCounter;i++) {
+  for(int i=MatrixCounter+1;i--;) {
     Indices[i] = (int *) Malloc(sizeof(int)*RowCounter[i], "EnergyMatrix::ParseIndices: *Indices[]");
-    for(int j=0;j<RowCounter[i];j++)
+    for(int j=RowCounter[i];j--;)
       Indices[i][j] = j;
   } 
@@ -410 +410 @@
 {
   // sum energy
-  for(int i=0;i<KeySet.FragmentsPerOrder[Order];i++)
-    for(int j=0;j<RowCounter[ KeySet.OrderSet[Order][i] ];j++)
-      for(int k=0;k<ColumnCounter;k++)
+  for(int i=KeySet.FragmentsPerOrder[Order];i--;)
+    for(int j=RowCounter[ KeySet.OrderSet[Order][i] ];j--;)
+      for(int k=ColumnCounter;k--;)
         Matrix[MatrixCounter][j][k] += Fragments.Matrix[ KeySet.OrderSet[Order][i] ][j][k];
   return true;
@@ -455 +455 @@
   }
   Indices[MatrixCounter] = (int *) Malloc(sizeof(int)*RowCounter[MatrixCounter], "ForceMatrix::ParseIndices: *Indices[]");
-  for(int j=0;j<RowCounter[MatrixCounter];j++) {
+  for(int j=RowCounter[MatrixCounter];j--;) {
     Indices[MatrixCounter][j] = j;
   }
@@ -503 +503 @@
  */
 KeySetsContainer::~KeySetsContainer() {
-  for(int i=0;i<FragmentCounter;i++)
+  for(int i=FragmentCounter;i--;)
     Free((void **)&KeySets[i], "KeySetsContainer::~KeySetsContainer: *KeySets[]");
-  for(int i=0;i<Order;i++)
+  for(int i=Order;i--;)
     Free((void **)&OrderSet[i], "KeySetsContainer::~KeySetsContainer: *OrderSet[]");
   Free((void **)&KeySets, "KeySetsContainer::~KeySetsContainer: **KeySets");
@@ -528 +528 @@
   cout << "Parsing key sets." << endl;
   KeySets = (int **) Malloc(sizeof(int *)*FragmentCounter, "KeySetsContainer::ParseKeySets: **KeySets");
-  for(int i=0;i<FragmentCounter;i++)
+  for(int i=FragmentCounter;i--;)
     KeySets[i] = NULL;
   line << name << FRAGMENTPREFIX << KEYSETFILE;
@@ -543 +543 @@
     // parse the values
     KeySets[i] = (int *) Malloc(sizeof(int)*AtomCounter[i], "KeySetsContainer::ParseKeySets: *KeySets[]");
-    for(int j=0;j<AtomCounter[i];j++)
+    for(int j=AtomCounter[i];j--;)
       KeySets[i][j] = -1;
     FragmentNumber = FixedDigitNumber(FragmentCounter, i);
@@ -570 +570 @@
   // scan through all to determine order
   Order=0;
-  for(int i=0;i<FragmentCounter;i++) {
+  for(int i=FragmentCounter;i--;) {
     Counter=0;
-    for(int j=0;j<AtomCounter[i];j++)
+    for(int j=AtomCounter[i];j--;)
       if (KeySets[i][j] != -1)
         Counter++;
@@ -582 +582 @@
   // scan through all to determine fragments per order
   FragmentsPerOrder = (int *) Malloc(sizeof(int)*Order, "KeySetsContainer::ParseManyBodyTerms: *FragmentsPerOrder");
-  for(int i=0;i<Order;i++)
+  for(int i=Order;i--;)
     FragmentsPerOrder[i] = 0;
-  for(int i=0;i<FragmentCounter;i++) {
+  for(int i=FragmentCounter;i--;) {
     Counter=0;
-    for(int j=0;j<AtomCounter[i];j++)
+    for(int j=AtomCounter[i];j--;)
       if (KeySets[i][j] != -1)
         Counter++;
@@ -596 +596 @@
   // scan through all to gather indices to each order set
   OrderSet = (int **) Malloc(sizeof(int *)*Order, "KeySetsContainer::ParseManyBodyTerms: **OrderSet");
-  for(int i=0;i<Order;i++)
+  for(int i=Order;i--;)
     OrderSet[i] = (int *) Malloc(sizeof(int)*FragmentsPerOrder[i], "KeySetsContainer::ParseManyBodyTermsKeySetsContainer::ParseManyBodyTerms: *OrderSet[]");
-  for(int i=0;i<Order;i++)
+  for(int i=Order;i--;)
     FragmentsPerOrder[i] = 0;
-  for(int i=0;i<FragmentCounter;i++) {
+  for(int i=FragmentCounter;i--;) {
     Counter=0;
-    for(int j=0;j<AtomCounter[i];j++)
+    for(int j=AtomCounter[i];j--;)
       if (KeySets[i][j] != -1)
         Counter++;
@@ -632 +632 @@
   if ((GreaterSet < 0) || (SmallerSet < 0) || (GreaterSet > FragmentCounter) || (SmallerSet > FragmentCounter)) // index out of bounds
     return false;
-  for(int i=0;i<AtomCounter[SmallerSet];i++) {
+  for(int i=AtomCounter[SmallerSet];i--;) {
     intermediate = false;
-    for (int j=0;j<AtomCounter[GreaterSet];j++)
+    for (int j=AtomCounter[GreaterSet];j--;)
       intermediate = (intermediate || ((KeySets[SmallerSet][i] == KeySets[GreaterSet][j]) || (KeySets[SmallerSet][i] == -1)));
     result = result && intermediate;

src/stackclass.hpp

@@ -251 +251 @@
 template <typename T> void StackClass<T>::ClearStack()
 {
-  for(int i=0;i<EntryCount; i++)
+  for(int i=EntryCount; i--;)
     StackList[i] = NULL;
   CurrentFirstEntry = 0;

src/vector.cpp

@@ -25 +25 @@
 {
   double res = 0.;
-  for (int i=0;i<NDIM;i++)
+  for (int i=NDIM;i--;)
     res += (x[i]-y->x[i])*(x[i]-y->x[i]);
   return (res);  
@@ -55 +55 @@
         // create the translation vector
         TranslationVector.Zero();
-        for (int i=0;i<NDIM;i++)
+        for (int i=NDIM;i--;)
           TranslationVector.x[i] = (double)N[i];
         TranslationVector.MatrixMultiplication(matrix);
@@ -84 +84 @@
   TestVector.CopyVector(this);
   TestVector.InverseMatrixMultiplication(matrix);
-  for(int i=0;i<NDIM;i++) { // correct periodically
+  for(int i=NDIM;i--;) { // correct periodically
     if (TestVector.x[i] < 0) {  // get every coefficient into the interval [0,1)
       TestVector.x[i] += ceil(TestVector.x[i]);
@@ -106 +106 @@
 {
   double res = 0.;
-  for (int i=0;i<NDIM;i++)
+  for (int i=NDIM;i--;)
     res += x[i]*y->x[i];
   return (res);  
@@ -126 +126 @@
 {
   double res = 0.;
-  for (int i=0;i<NDIM;i++)
+  for (int i=NDIM;i--;)
     res += this->x[i]*this->x[i];
   return (sqrt(res));  
@@ -136 +136 @@
 {
   double res = 0.;
-  for (int i=0;i<NDIM;i++)
+  for (int i=NDIM;i--;)
     res += this->x[i]*this->x[i];
   res = 1./sqrt(res);
@@ -146 +146 @@
 void vector::Zero()
 {
-  for (int i=0;i<NDIM;i++)
+  for (int i=NDIM;i--;)
     this->x[i] = 0.;
 };
@@ -259 +259 @@
 void vector::Scale(double **factor)
 {
-  for (int i=0;i<NDIM;i++)
+  for (int i=NDIM;i--;)
     x[i] *= (*factor)[i];
 };
@@ -265 +265 @@
 void vector::Scale(double *factor)
 {
-  for (int i=0;i<NDIM;i++)
+  for (int i=NDIM;i--;)
     x[i] *= *factor;
 };
@@ -271 +271 @@
 void vector::Scale(double factor)
 {
-  for (int i=0;i<NDIM;i++)
+  for (int i=NDIM;i--;)
     x[i] *= factor;
 };
@@ -280 +280 @@
 void vector::Translate(const vector *trans)
 {
-  for (int i=0;i<NDIM;i++)
+  for (int i=NDIM;i--;)
     x[i] += trans->x[i];
 }; 
@@ -295 +295 @@
   C.x[2] = M[2]*x[0]+M[5]*x[1]+M[8]*x[2];
   // transfer the result into this
-  for (int i=0;i<NDIM;i++)
+  for (int i=NDIM;i--;)
     x[i] = C.x[i];
 };
@@ -327 +327 @@
     C.x[2] = B[2]*x[0]+B[5]*x[1]+B[8]*x[2];
     // transfer the result into this
-    for (int i=0;i<NDIM;i++)
+    for (int i=NDIM;i--;)
       x[i] = C.x[i];
   } else {
@@ -344 +344 @@
 void vector::LinearCombinationOfVectors(const vector *x1, const vector *x2, const vector *x3, double *factors)
 {
-  for(int i=0;i<NDIM;i++)
+  for(int i=NDIM;i--;)
     x[i] = factors[0]*x1->x[i] + factors[1]*x2->x[i] + factors[2]*x3->x[i]; 
 };
@@ -359 +359 @@
   Output((ofstream *)&cout);
   cout << "\t";
-  for (int i=0;i<NDIM;i++)
+  for (int i=NDIM;i--;)
     x[i] -= 2.*projection*n->x[i];
   cout << "Projected vector: ";
@@ -446 +446 @@
   x1.Scale(x1.Projection(this));
   SubtractVector(&x1);
-  for (int i=0;i<NDIM;i++)
+  for (int i=NDIM;i--;)
           result = result || (fabs(x[i]) > MYEPSILON);
 
@@ -468 +468 @@
   vector->Output((ofstream *)&cout);
   cout << endl;
-  for (j=0;j<NDIM;j++)
+  for (j=NDIM;j--;)
     Components[j] = -1;
   // find two components != 0
@@ -537 +537 @@
          par.num = num;
         
-         for (i=0;i<NDIM;i++)
+         for (i=NDIM;i--;)
                 gsl_vector_set(x, i, (vectors[0]->x[i] - vectors[1]->x[i])/2.); 
          
@@ -573 +573 @@
    while (status == GSL_CONTINUE && iter < 100);
  
-  for (i=0;i<(size_t)np;i++)
+  for (i=(size_t)np;i--;)
     this->x[i] = gsl_vector_get(s->x, i);
    gsl_vector_free(x);
@@ -587 +587 @@
 void vector::AddVector(const vector *y)
 {
-  for (int i=0;i<NDIM;i++)
+  for (int i=NDIM;i--;)
     this->x[i] += y->x[i];
 }
@@ -596 +596 @@
 void vector::SubtractVector(const vector *y)
 {
-  for (int i=0;i<NDIM;i++)
+  for (int i=NDIM;i--;)
     this->x[i] -= y->x[i];
 }
@@ -605 +605 @@
 void vector::CopyVector(const vector *y)
 {
-  for (int i=0;i<NDIM;i++)
+  for (int i=NDIM;i--;)
     this->x[i] = y->x[i];
 }
@@ -783 +783 @@
     cout << Verbose(2) << i << ": sign matrix is " << sign[0] << "\t" << sign[1] << "\t" << sign[2] << "\n";
     // apply sign matrix 
-    for (j=0;j<NDIM;j++)
+    for (j=NDIM;j--;)
       x[j] *= sign[j];
     // calculate angle and check
@@ -792 +792 @@
     }
     // unapply sign matrix (is its own inverse)
-    for (j=0;j<NDIM;j++)
+    for (j=NDIM;j--;)
       x[j] *= sign[j];
   }

src/verbose.cpp

@@ -7 +7 @@
 ostream& Verbose::print (ostream &ost) const
 {
-  for (int i=0;i<Verbosity;i++)
+  for (int i=Verbosity;i--;)
     ost.put('\t');
   //cout << "Verbose(.) called." << endl;