Changes in src/periodentafel.cpp [a67d19:4eb4fe]

File:

• src/periodentafel.cpp (modified) (13 diffs)

src/periodentafel.cpp

@@ -8 +8 @@
 
 #include <iomanip>
+#include <iostream>
 #include <fstream>
 #include <cstring>
 
+#include "Helpers/Assert.hpp"
 #include "element.hpp"
+#include "elements_db.hpp"
 #include "helpers.hpp"
 #include "lists.hpp"
@@ -18 +21 @@
 #include "verbose.hpp"
 
+using namespace std;
+
 /************************************* Functions for class periodentafel ***************************/
 
@@ -23 +28 @@
  * Initialises start and end of list and resets periodentafel::checkliste to false.
  */
-periodentafel::periodentafel() : start(new element), end(new element)
-{
-  start->previous = NULL;
-  start->next = end;
-  end->previous = start;
-  end->next = NULL;
+periodentafel::periodentafel()
+{
+  ASSERT(LoadElementsDatabase(new stringstream(elementsDB,ios_base::in)), "General element initialization failed");
+  ASSERT(LoadValenceDatabase(new stringstream(valenceDB,ios_base::in)), "Valence entry of element initialization failed");
+  ASSERT(LoadOrbitalsDatabase(new stringstream(orbitalsDB,ios_base::in)), "Orbitals entry of element initialization failed");
+  ASSERT(LoadHBondAngleDatabase(new stringstream(HbondangleDB,ios_base::in)), "HBond angle entry of element initialization failed");
+  ASSERT(LoadHBondLengthsDatabase(new stringstream(HbonddistanceDB,ios_base::in)), "HBond distance entry of element initialization failed");
 };
 
@@ -37 +43 @@
 {
   CleanupPeriodtable();
-  delete(end);
-  delete(start);
 };
 
 /** Adds element to period table list
  * \param *pointer element to be added
- * \return true - succeeded, false - does not occur
- */
-bool periodentafel::AddElement(element * const pointer)
-{
+ * \return iterator to added element
+ */
+periodentafel::iterator periodentafel::AddElement(element * const pointer)
+{
+  atomicNumber_t Z = pointer->getNumber();
+  ASSERT(!elements.count(Z), "Element is already present.");
   pointer->sort = &pointer->Z;
-  if (pointer->Z < 1 && pointer->Z >= MAX_ELEMENTS)
-    DoLog(0) && (Log() << Verbose(0) << "Invalid Z number!\n");
-  return add(pointer, end);
+  if (pointer->getNumber() < 1 && pointer->getNumber() >= MAX_ELEMENTS)
+    DoeLog(0) && (eLog() << Verbose(0) << "Invalid Z number!\n");
+  pair<iterator,bool> res = elements.insert(pair<atomicNumber_t,element*>(Z,pointer));
+  return res.first;
 };
 
 /** Removes element from list.
  * \param *pointer element to be removed
- * \return true - succeeded, false - element not found
- */
-bool periodentafel::RemoveElement(element * const pointer)
-{
-  return remove(pointer, start, end);
+ */
+void periodentafel::RemoveElement(element * const pointer)
+{
+  RemoveElement(pointer->getNumber());
+};
+
+/** Removes element from list.
+ * \param Z element to be removed
+ */
+void periodentafel::RemoveElement(atomicNumber_t Z)
+{
+  elements.erase(Z);
 };
 
 /** Removes every element from the period table.
- * \return true - succeeded, false - does not occur
- */
-bool periodentafel::CleanupPeriodtable()
-{
-  return cleanup(start,end);
+ */
+void periodentafel::CleanupPeriodtable()
+{
+  for(iterator iter=elements.begin();iter!=elements.end();++iter){
+    delete(*iter).second;
+  }
+  elements.clear();
 };
 
@@ -75 +91 @@
  * \return pointer to element or NULL if not found
  */
-element * const periodentafel::FindElement(const int Z) const
-{
-  element *walker = find(&Z, start,end);
-  return(walker);
+element * const periodentafel::FindElement(atomicNumber_t Z) const
+{
+  const_iterator res = elements.find(Z);
+  return res!=elements.end()?((*res).second):0;
 };
 
@@ -88 +104 @@
 element * const periodentafel::FindElement(const char * const shorthand) const
 {
-  element *walker =  periodentafel::start;
-  while (walker->next != periodentafel::end) {
-    walker = walker->next;
-    if (strncmp(walker->symbol, shorthand, 3) == 0)
-      return(walker);
+  element *res = 0;
+  for(const_iterator iter=elements.begin();iter!=elements.end();++iter) {
+    if((*iter).second->getSymbol() == shorthand){
+      res = (*iter).second;
+      break;
+    }
   }
-  return (NULL);
+  return res;
 };
 
 /** Asks for element number and returns pointer to element
+ * \return desired element or NULL
  */
 element * const periodentafel::AskElement() const
 {
-  element *walker = NULL;
+  element * walker = NULL;
   int Z;
   do {
@@ -116 +134 @@
 element * const periodentafel::EnterElement()
 {
-  element *walker = NULL;
-  int Z = -1;
+  atomicNumber_t Z = 0;
   DoLog(0) && (Log() << Verbose(0) << "Atomic number: " << Z << endl);
   cin >> Z;
-  walker = FindElement(Z);
-  if (walker == NULL) {
+  element * const res = FindElement(Z);
+  if (!res) {
+    // TODO: make this using the constructor
     DoLog(0) && (Log() << Verbose(0) << "Element not found in database, please enter." << endl);
-    walker = new element;
-    walker->Z = Z;
+    element *tmp = new element;
+    tmp->Z = Z;
     DoLog(0) && (Log() << Verbose(0) << "Mass: " << endl);
-    cin >> walker->mass;
+    cin >> tmp->mass;
     DoLog(0) && (Log() << Verbose(0) << "Name [max 64 chars]: " << endl);
-    cin >> walker->name;
+    cin >> tmp->name;
     DoLog(0) && (Log() << Verbose(0) << "Short form [max 3 chars]: " << endl);
-    cin >> walker->symbol;
-    periodentafel::AddElement(walker);
+    cin >> tmp->symbol;
+    AddElement(tmp);
+    return tmp;
   }
-  return(walker);
-};
+  return res;
+};
+
+
+/******************** Access to iterators ****************************/
+periodentafel::const_iterator periodentafel::begin(){
+  return elements.begin();
+}
+
+periodentafel::const_iterator periodentafel::end(){
+  return elements.end();
+}
+
+periodentafel::reverse_iterator periodentafel::rbegin(){
+  return reverse_iterator(elements.end());
+}
+
+periodentafel::reverse_iterator periodentafel::rend(){
+  return reverse_iterator(elements.begin());
+}
 
 /** Prints period table to given stream.
  * \param output stream
  */
-bool periodentafel::Output(ofstream * const output) const
+bool periodentafel::Output(ostream * const output) const
 {
   bool result = true;
-  element *walker = start;
   if (output != NULL) {
-    while (walker->next != end) {
-      walker = walker->next;
-      result = result && walker->Output(output);
+    for(const_iterator iter=elements.begin(); iter !=elements.end();++iter){
+      result = result && (*iter).second->Output(output);
     }
     return result;
@@ -157 +192 @@
  * \param *checkliste elements table for this molecule
  */
-bool periodentafel::Checkout(ofstream * const output, const int * const checkliste) const
-{
-  element *walker = start;
+bool periodentafel::Checkout(ostream * const output, const int * const checkliste) const
+{
   bool result = true;
   int No = 1;
@@ -166 +200 @@
     *output << "# Ion type data (PP = PseudoPotential, Z = atomic number)" << endl;
     *output << "#Ion_TypeNr.\tAmount\tZ\tRGauss\tL_Max(PP)L_Loc(PP)IonMass\t# chemical name, symbol" << endl;
-    while (walker->next != end) {
-      walker = walker->next;
-      if ((walker != NULL) && (walker->Z > 0) && (walker->Z < MAX_ELEMENTS) && (checkliste[walker->Z])) {
-        walker->No = No;
-        result = result && walker->Checkout(output, No++, checkliste[walker->Z]);
+    for(const_iterator iter=elements.begin(); iter!=elements.end();++iter){
+      if (((*iter).first < MAX_ELEMENTS) && (checkliste[(*iter).first])) {
+        (*iter).second->No = No;
+        result = result && (*iter).second->Checkout(output, No++, checkliste[(*iter).first]);
       }
     }
@@ -183 +216 @@
 bool periodentafel::LoadPeriodentafel(const char *path)
 {
-  ifstream infile;
-  double tmp;
-  element *ptr;
+  ifstream input;
   bool status = true;
   bool otherstatus = true;
@@ -194 +225 @@
   strncat(filename, "/", MAXSTRINGSIZE-strlen(filename));
   strncat(filename, STANDARDELEMENTSDB, MAXSTRINGSIZE-strlen(filename));
-  infile.open(filename);
-  if (infile != NULL) {
-    infile.getline(header1, MAXSTRINGSIZE);
-    infile.getline(header2, MAXSTRINGSIZE); // skip first two header lines
+  input.open(filename);
+  status = status && LoadElementsDatabase(&input);
+
+  // fill valence DB per element
+  strncpy(filename, path, MAXSTRINGSIZE);
+  strncat(filename, "/", MAXSTRINGSIZE-strlen(filename));
+  strncat(filename, STANDARDVALENCEDB, MAXSTRINGSIZE-strlen(filename));
+  input.open(filename);
+  otherstatus = otherstatus && LoadValenceDatabase(&input);
+
+  // fill orbitals DB per element
+  strncpy(filename, path, MAXSTRINGSIZE);
+  strncat(filename, "/", MAXSTRINGSIZE-strlen(filename));
+  strncat(filename, STANDARDORBITALDB, MAXSTRINGSIZE-strlen(filename));
+  input.open(filename);
+  otherstatus = otherstatus && LoadOrbitalsDatabase(&input);
+
+  // fill H-BondAngle DB per element
+  strncpy(filename, path, MAXSTRINGSIZE);
+  strncat(filename, "/", MAXSTRINGSIZE-strlen(filename));
+  strncat(filename, STANDARDHBONDANGLEDB, MAXSTRINGSIZE-strlen(filename));
+  input.open(filename);
+  otherstatus = otherstatus && LoadHBondAngleDatabase(&input);
+
+  // fill H-BondDistance DB per element
+  strncpy(filename, path, MAXSTRINGSIZE);
+  strncat(filename, "/", MAXSTRINGSIZE-strlen(filename));
+  strncat(filename, STANDARDHBONDDISTANCEDB, MAXSTRINGSIZE-strlen(filename));
+  input.open(filename);
+  otherstatus = otherstatus && LoadHBondLengthsDatabase(&input);
+
+  if (!otherstatus){
+    DoeLog(2) && (eLog()<< Verbose(2) << "Something went wrong while parsing the other databases!" << endl);
+  }
+
+  return status;
+};
+
+/** load the element info.
+ * \param *input stream to parse from
+ * \return true - parsing successful, false - something went wrong
+ */
+bool periodentafel::LoadElementsDatabase(istream *input)
+{
+  if ((*input) != NULL) {
+    (*input).getline(header1, MAXSTRINGSIZE);
+    (*input).getline(header2, MAXSTRINGSIZE); // skip first two header lines
     DoLog(0) && (Log() << Verbose(0) <<  "Parsed elements:");
-    while (!infile.eof()) {
+    while (!(*input).eof()) {
       element *neues = new element;
-      infile >> neues->name;
-      //infile >> ws;
-      infile >> neues->symbol;
-      //infile >> ws;
-      infile >> neues->period;
-      //infile >> ws;
-      infile >> neues->group;
-      //infile >> ws;
-      infile >> neues->block;
-      //infile >> ws;
-      infile >> neues->Z;
-      //infile >> ws;
-      infile >> neues->mass;
-      //infile >> ws;
-      infile >> neues->CovalentRadius;
-      //infile >> ws;
-      infile >> neues->VanDerWaalsRadius;
-      //infile >> ws;
-      infile >> ws;
+      (*input) >> neues->name;
+      //(*input) >> ws;
+      (*input) >> neues->symbol;
+      //(*input) >> ws;
+      (*input) >> neues->period;
+      //(*input) >> ws;
+      (*input) >> neues->group;
+      //(*input) >> ws;
+      (*input) >> neues->block;
+      //(*input) >> ws;
+      (*input) >> neues->Z;
+      //(*input) >> ws;
+      (*input) >> neues->mass;
+      //(*input) >> ws;
+      (*input) >> neues->CovalentRadius;
+      //(*input) >> ws;
+      (*input) >> neues->VanDerWaalsRadius;
+      //(*input) >> ws;
+      (*input) >> ws;
       DoLog(0) && (Log() << Verbose(0) << " " << neues->symbol);
+      if (elements.count(neues->Z)) {// if element already present, remove and delete it
+        element * const Elemental = FindElement(neues->Z);
+        ASSERT(Elemental != NULL, "element should be present but is not??");
+        RemoveElement(Elemental);
+        delete(Elemental);
+      }
       //neues->Output((ofstream *)&cout);
       if ((neues->Z > 0) && (neues->Z < MAX_ELEMENTS))
-        periodentafel::AddElement(neues);
+        elements[neues->getNumber()] = neues;
       else {
         DoLog(0) && (Log() << Verbose(0) << "Could not parse element: ");
@@ -231 +311 @@
     }
     DoLog(0) && (Log() << Verbose(0) << endl);
-    infile.close();
-    infile.clear();
-  } else
-    status = false;
-
-  // fill valence DB per element
-  strncpy(filename, path, MAXSTRINGSIZE);
-  strncat(filename, "/", MAXSTRINGSIZE-strlen(filename));
-  strncat(filename, STANDARDVALENCEDB, MAXSTRINGSIZE-strlen(filename));
-  infile.open(filename);
-  if (infile != NULL) {
-    while (!infile.eof()) {
-      infile >> tmp;
-      infile >> ws;
-      infile >> FindElement((int)tmp)->Valence;
-      infile >> ws;
+    return true;
+  } else
+    return false;
+}
+
+/** load the valence info.
+ * \param *input stream to parse from
+ * \return true - parsing successful, false - something went wrong
+ */
+bool periodentafel::LoadValenceDatabase(istream *input)
+{
+  char dummy[MAXSTRINGSIZE];
+  if ((*input) != NULL) {
+    (*input).getline(dummy, MAXSTRINGSIZE);
+    while (!(*input).eof()) {
+      atomicNumber_t Z;
+      (*input) >> Z;
+      ASSERT(elements.count(Z), "Element not present");
+      (*input) >> ws;
+      (*input) >> elements[Z]->Valence;
+      (*input) >> ws;
       //Log() << Verbose(3) << "Element " << (int)tmp << " has " << FindElement((int)tmp)->Valence << " valence electrons." << endl;
     }
-    infile.close();
-    infile.clear();
-  } else
-    otherstatus = false;
-
-  // fill valence DB per element
-  strncpy(filename, path, MAXSTRINGSIZE);
-  strncat(filename, "/", MAXSTRINGSIZE-strlen(filename));
-  strncat(filename, STANDARDORBITALDB, MAXSTRINGSIZE-strlen(filename));
-  infile.open(filename);
-  if (infile != NULL) {
-    while (!infile.eof()) {
-      infile >> tmp;
-      infile >> ws;
-      infile >> FindElement((int)tmp)->NoValenceOrbitals;
-      infile >> ws;
+    return true;
+  } else
+                return false;
+}
+
+/** load the orbitals info.
+ * \param *input stream to parse from
+ * \return true - parsing successful, false - something went wrong
+ */
+bool periodentafel::LoadOrbitalsDatabase(istream *input)
+{
+  char dummy[MAXSTRINGSIZE];
+  if ((*input) != NULL) {
+    (*input).getline(dummy, MAXSTRINGSIZE);
+    while (!(*input).eof()) {
+      atomicNumber_t Z;
+      (*input) >> Z;
+      ASSERT(elements.count(Z), "Element not present");
+      (*input) >> ws;
+      (*input) >> elements[Z]->NoValenceOrbitals;
+      (*input) >> ws;
       //Log() << Verbose(3) << "Element " << (int)tmp << " has " << FindElement((int)tmp)->NoValenceOrbitals << " number of singly occupied valence orbitals." << endl;
     }
-    infile.close();
-    infile.clear();
-  } else
-    otherstatus = false;
-
-  // fill H-BondDistance DB per element
-  strncpy(filename, path, MAXSTRINGSIZE);
-  strncat(filename, "/", MAXSTRINGSIZE-strlen(filename));
-  strncat(filename, STANDARDHBONDDISTANCEDB, MAXSTRINGSIZE-strlen(filename));
-  infile.open(filename);
-  if (infile != NULL) {
-    while (!infile.eof()) {
-      infile >> tmp;
-      ptr = FindElement((int)tmp);
-      infile >> ws;
-      infile >> ptr->HBondDistance[0];
-      infile >> ptr->HBondDistance[1];
-      infile >> ptr->HBondDistance[2];
-      infile >> ws;
+    return true;
+  } else
+    return false;
+}
+
+/** load the hbond angles info.
+ * \param *input stream to parse from
+ * \return true - parsing successful, false - something went wrong
+ */
+bool periodentafel::LoadHBondAngleDatabase(istream *input)
+{
+  char dummy[MAXSTRINGSIZE];
+  if ((*input) != NULL) {
+    (*input).getline(dummy, MAXSTRINGSIZE);
+    while (!(*input).eof()) {
+      atomicNumber_t Z;
+      (*input) >> Z;
+      ASSERT(elements.count(Z), "Element not present");
+      (*input) >> ws;
+      (*input) >> elements[Z]->HBondAngle[0];
+      (*input) >> elements[Z]->HBondAngle[1];
+      (*input) >> elements[Z]->HBondAngle[2];
+      (*input) >> ws;
+      //Log() << Verbose(3) << "Element " << (int)tmp << " has " << FindElement((int)tmp)->HBondAngle[0] << ", " << FindElement((int)tmp)->HBondAngle[1] << ", " << FindElement((int)tmp)->HBondAngle[2] << " degrees bond angle for one, two, three connected hydrogens." << endl;
+    }
+    return true;
+  } else
+                return false;
+}
+
+/** load the hbond lengths info.
+ * \param *input stream to parse from
+ * \return true - parsing successful, false - something went wrong
+ */
+bool periodentafel::LoadHBondLengthsDatabase(istream *input)
+{
+  char dummy[MAXSTRINGSIZE];
+  if ((*input) != NULL) {
+    (*input).getline(dummy, MAXSTRINGSIZE);
+    while (!(*input).eof()) {
+      atomicNumber_t Z;
+      (*input) >> Z;
+      ASSERT(elements.count(Z), "Element not present");
+      (*input) >> ws;
+      (*input) >> elements[Z]->HBondDistance[0];
+      (*input) >> elements[Z]->HBondDistance[1];
+      (*input) >> elements[Z]->HBondDistance[2];
+      (*input) >> ws;
       //Log() << Verbose(3) << "Element " << (int)tmp << " has " << FindElement((int)tmp)->HBondDistance[0] << " Angstrom typical distance to hydrogen." << endl;
     }
-    infile.close();
-    infile.clear();
-  } else
-    otherstatus = false;
-
-  // fill H-BondAngle DB per element
-  strncpy(filename, path, MAXSTRINGSIZE);
-  strncat(filename, "/", MAXSTRINGSIZE-strlen(filename));
-  strncat(filename, STANDARDHBONDANGLEDB, MAXSTRINGSIZE-strlen(filename));
-  infile.open(filename);
-  if (infile != NULL) {
-    while (!infile.eof()) {
-      infile >> tmp;
-      ptr = FindElement((int)tmp);
-      infile >> ws;
-      infile >> ptr->HBondAngle[0];
-      infile >> ptr->HBondAngle[1];
-      infile >> ptr->HBondAngle[2];
-      infile >> ws;
-      //Log() << Verbose(3) << "Element " << (int)tmp << " has " << FindElement((int)tmp)->HBondAngle[0] << ", " << FindElement((int)tmp)->HBondAngle[1] << ", " << FindElement((int)tmp)->HBondAngle[2] << " degrees bond angle for one, two, three connected hydrogens." << endl;
-    }
-    infile.close();
-  } else
-    otherstatus = false;
-
-  if (!otherstatus)
-    DoeLog(2) && (eLog()<< Verbose(2) << "Something went wrong while parsing the other databases!" << endl);
-
-  return status;
-};
+    return true;
+  } else
+                return false;
+}
 
 /** Stores element list to file.
@@ -334 +427 @@
     f << header1 << endl;
     f << header2 << endl;
-    element *walker = periodentafel::start;
-    while (walker->next != periodentafel::end) {
-      walker = walker->next;
-      result = result && walker->Output(&f);
+    for(const_iterator iter=elements.begin();iter!=elements.end();++iter){
+         result = result && (*iter).second->Output(&f);
     }
     f.close();
-  } else
-    result = false;
-  return result;
-};
+    return true;
+  } else
+    return result;
+};