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

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"
@@ -21 +18 @@
 #include "verbose.hpp"
 
-using namespace std;
-
 /************************************* Functions for class periodentafel ***************************/
 
@@ -28 +23 @@
  * Initialises start and end of list and resets periodentafel::checkliste to false.
  */
-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");
+periodentafel::periodentafel() : start(new element), end(new element)
+{
+  start->previous = NULL;
+  start->next = end;
+  end->previous = start;
+  end->next = NULL;
 };
 
@@ -43 +37 @@
 {
   CleanupPeriodtable();
+  delete(end);
+  delete(start);
 };
 
 /** Adds element to period table list
  * \param *pointer element to be added
- * \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.");
+ * \return true - succeeded, false - does not occur
+ */
+bool periodentafel::AddElement(element * const pointer)
+{
   pointer->sort = &pointer->Z;
-  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;
+  if (pointer->Z < 1 && pointer->Z >= MAX_ELEMENTS)
+    DoLog(0) && (Log() << Verbose(0) << "Invalid Z number!\n");
+  return add(pointer, end);
 };
 
 /** Removes element from list.
  * \param *pointer element to be removed
- */
-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);
+ * \return true - succeeded, false - element not found
+ */
+bool periodentafel::RemoveElement(element * const pointer)
+{
+  return remove(pointer, start, end);
 };
 
 /** Removes every element from the period table.
- */
-void periodentafel::CleanupPeriodtable()
-{
-  for(iterator iter=elements.begin();iter!=elements.end();++iter){
-    delete(*iter).second;
-  }
-  elements.clear();
+ * \return true - succeeded, false - does not occur
+ */
+bool periodentafel::CleanupPeriodtable()
+{
+  return cleanup(start,end);
 };
 
@@ -91 +75 @@
  * \return pointer to element or NULL if not found
  */
-element * const periodentafel::FindElement(atomicNumber_t Z) const
-{
-  const_iterator res = elements.find(Z);
-  return res!=elements.end()?((*res).second):0;
+element * const periodentafel::FindElement(const int Z) const
+{
+  element *walker = find(&Z, start,end);
+  return(walker);
 };
 
@@ -104 +88 @@
 element * const periodentafel::FindElement(const char * const shorthand) const
 {
-  element *res = 0;
-  for(const_iterator iter=elements.begin();iter!=elements.end();++iter) {
-    if((*iter).second->getSymbol() == shorthand){
-      res = (*iter).second;
-      break;
-    }
+  element *walker =  periodentafel::start;
+  while (walker->next != periodentafel::end) {
+    walker = walker->next;
+    if (strncmp(walker->symbol, shorthand, 3) == 0)
+      return(walker);
   }
-  return res;
+  return (NULL);
 };
 
 /** 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 {
@@ -134 +116 @@
 element * const periodentafel::EnterElement()
 {
-  atomicNumber_t Z = 0;
+  element *walker = NULL;
+  int Z = -1;
   DoLog(0) && (Log() << Verbose(0) << "Atomic number: " << Z << endl);
   cin >> Z;
-  element * const res = FindElement(Z);
-  if (!res) {
-    // TODO: make this using the constructor
+  walker = FindElement(Z);
+  if (walker == NULL) {
     DoLog(0) && (Log() << Verbose(0) << "Element not found in database, please enter." << endl);
-    element *tmp = new element;
-    tmp->Z = Z;
+    walker = new element;
+    walker->Z = Z;
     DoLog(0) && (Log() << Verbose(0) << "Mass: " << endl);
-    cin >> tmp->mass;
+    cin >> walker->mass;
     DoLog(0) && (Log() << Verbose(0) << "Name [max 64 chars]: " << endl);
-    cin >> tmp->name;
+    cin >> walker->name;
     DoLog(0) && (Log() << Verbose(0) << "Short form [max 3 chars]: " << endl);
-    cin >> tmp->symbol;
-    AddElement(tmp);
-    return tmp;
+    cin >> walker->symbol;
+    periodentafel::AddElement(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());
-}
+  return(walker);
+};
 
 /** Prints period table to given stream.
  * \param output stream
  */
-bool periodentafel::Output(ostream * const output) const
+bool periodentafel::Output(ofstream * const output) const
 {
   bool result = true;
+  element *walker = start;
   if (output != NULL) {
-    for(const_iterator iter=elements.begin(); iter !=elements.end();++iter){
-      result = result && (*iter).second->Output(output);
+    while (walker->next != end) {
+      walker = walker->next;
+      result = result && walker->Output(output);
     }
     return result;
@@ -192 +157 @@
  * \param *checkliste elements table for this molecule
  */
-bool periodentafel::Checkout(ostream * const output, const int * const checkliste) const
-{
+bool periodentafel::Checkout(ofstream * const output, const int * const checkliste) const
+{
+  element *walker = start;
   bool result = true;
   int No = 1;
@@ -200 +166 @@
     *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;
-    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]);
+    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]);
       }
     }
@@ -216 +183 @@
 bool periodentafel::LoadPeriodentafel(const char *path)
 {
-  ifstream input;
+  ifstream infile;
+  double tmp;
+  element *ptr;
   bool status = true;
   bool otherstatus = true;
@@ -225 +194 @@
   strncat(filename, "/", MAXSTRINGSIZE-strlen(filename));
   strncat(filename, STANDARDELEMENTSDB, MAXSTRINGSIZE-strlen(filename));
-  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
+  infile.open(filename);
+  if (infile != NULL) {
+    infile.getline(header1, MAXSTRINGSIZE);
+    infile.getline(header2, MAXSTRINGSIZE); // skip first two header lines
     DoLog(0) && (Log() << Verbose(0) <<  "Parsed elements:");
-    while (!(*input).eof()) {
+    while (!infile.eof()) {
       element *neues = new element;
-      (*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;
+      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;
       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))
-        elements[neues->getNumber()] = neues;
+        periodentafel::AddElement(neues);
       else {
         DoLog(0) && (Log() << Verbose(0) << "Could not parse element: ");
@@ -311 +231 @@
     }
     DoLog(0) && (Log() << Verbose(0) << endl);
-    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;
+    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;
       //Log() << Verbose(3) << "Element " << (int)tmp << " has " << FindElement((int)tmp)->Valence << " valence electrons." << endl;
     }
-    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;
+    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;
       //Log() << Verbose(3) << "Element " << (int)tmp << " has " << FindElement((int)tmp)->NoValenceOrbitals << " number of singly occupied valence orbitals." << endl;
     }
-    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;
+    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;
+      //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;
     }
-    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;
-    }
-    return true;
-  } else
-                return false;
-}
+    infile.close();
+  } else
+    otherstatus = false;
+
+  if (!otherstatus)
+    DoeLog(2) && (eLog()<< Verbose(2) << "Something went wrong while parsing the other databases!" << endl);
+
+  return status;
+};
 
 /** Stores element list to file.
@@ -427 +334 @@
     f << header1 << endl;
     f << header2 << endl;
-    for(const_iterator iter=elements.begin();iter!=elements.end();++iter){
-         result = result && (*iter).second->Output(&f);
+    element *walker = periodentafel::start;
+    while (walker->next != periodentafel::end) {
+      walker = walker->next;
+      result = result && walker->Output(&f);
     }
     f.close();
-    return true;
-  } else
-    return result;
-};
+  } else
+    result = false;
+  return result;
+};