Changeset f75030 for molecuilder/src/builder.cpp

Timestamp:

May 23, 2008, 9:17:19 AM (18 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/builder.cpp (modified) (27 diffs)

molecuilder/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