source: molecuilder/src/periodentafel.cpp@ 732da7

/** \file periodentafel.cpp
 *
 * Function implementations for the class periodentafel.
 *
 */

using namespace std;

#include <iomanip>
#include <fstream>
#include <cstring>

#include "element.hpp"
#include "helpers.hpp"
#include "lists.hpp"
#include "log.hpp"
#include "periodentafel.hpp"
#include "verbose.hpp"

/************************************* Functions for class periodentafel ***************************/

/** constructor for class periodentafel
 * 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;
};

/** destructor for class periodentafel
 * Removes every element and afterwards deletes start and end of list.
 */
periodentafel::~periodentafel()
{
  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)
{
  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);
};

/** 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);
};

/** Removes every element from the period table.
 * \return true - succeeded, false - does not occur
 */
bool periodentafel::CleanupPeriodtable()
{
  return cleanup(start,end);
};

/** Finds an element by its atomic number.
 * If element is not yet in list, returns NULL.
 * \param Z atomic number
 * \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);
};

/** Finds an element by its atomic number.
 * If element is not yet in list, datas are asked and stored in database.
 * \param shorthand chemical symbol of the element, e.g. H for hydrogene
 * \return pointer to element
 */
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);
  }
  return (NULL);
};

/** Asks for element number and returns pointer to element
 */
element * const periodentafel::AskElement() const
{
  element *walker = NULL;
  int Z;
  do {
    DoLog(0) && (Log() << Verbose(0) << "Atomic number Z: ");
    cin >> Z;
    walker = this->FindElement(Z);  // give type
  } while (walker == NULL);
  return walker;
};

/** Asks for element and if not found, presents mask to enter info.
 * \return pointer to either present or newly created element
 */
element * const periodentafel::EnterElement()
{
  element *walker = NULL;
  int Z = -1;
  DoLog(0) && (Log() << Verbose(0) << "Atomic number: " << Z << endl);
  cin >> Z;
  walker = FindElement(Z);
  if (walker == NULL) {
    DoLog(0) && (Log() << Verbose(0) << "Element not found in database, please enter." << endl);
    walker = new element;
    walker->Z = Z;
    DoLog(0) && (Log() << Verbose(0) << "Mass: " << endl);
    cin >> walker->mass;
    DoLog(0) && (Log() << Verbose(0) << "Name [max 64 chars]: " << endl);
    cin >> walker->name;
    DoLog(0) && (Log() << Verbose(0) << "Short form [max 3 chars]: " << endl);
    cin >> walker->symbol;
    periodentafel::AddElement(walker);
  }
  return(walker);
};

/** Prints period table to given stream.
 * \param output stream
 */
bool periodentafel::Output(ofstream * const output) const
{
  bool result = true;
  element *walker = start;
  if (output != NULL) {
    while (walker->next != end) {
      walker = walker->next;
      result = result && walker->Output(output);
    }
    return result;
  } else
    return false;
};

/** Prints period table to given stream.
 * \param *output output stream
 * \param *checkliste elements table for this molecule
 */
bool periodentafel::Checkout(ofstream * const output, const int * const checkliste) const
{
  element *walker = start;
  bool result = true;
  int No = 1;

  if (output != NULL) {
    *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]);
      }
    }
    return result;
  } else
    return false;
};

/** Loads element list from file.
 * \param *path to to standard file names
 */
bool periodentafel::LoadPeriodentafel(const char *path)
{
  ifstream infile;
  double tmp;
  element *ptr;
  bool status = true;
  bool otherstatus = true;
  char filename[255];

  // fill elements DB
  strncpy(filename, path, MAXSTRINGSIZE);
  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
    DoLog(0) && (Log() << Verbose(0) <<  "Parsed elements:");
    while (!infile.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;
      DoLog(0) && (Log() << Verbose(0) << " " << neues->symbol);
      //neues->Output((ofstream *)&cout);
      if ((neues->Z > 0) && (neues->Z < MAX_ELEMENTS))
        periodentafel::AddElement(neues);
      else {
        DoLog(0) && (Log() << Verbose(0) << "Could not parse element: ");
        neues->Output((ofstream *)&cout);
        delete(neues);
      }
    }
    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;
      //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;
      //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;
      //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;
};

/** Stores element list to file.
 */
bool periodentafel::StorePeriodentafel(const char *path) const
{
  bool result = true;
  ofstream f;
  char filename[MAXSTRINGSIZE];

  strncpy(filename, path, MAXSTRINGSIZE);
  strncat(filename, "/", MAXSTRINGSIZE-strlen(filename));
  strncat(filename, STANDARDELEMENTSDB, MAXSTRINGSIZE-strlen(filename));
  f.open(filename);
  if (f != NULL) {
    f << header1 << endl;
    f << header2 << endl;
    element *walker = periodentafel::start;
    while (walker->next != periodentafel::end) {
      walker = walker->next;
      result = result && walker->Output(&f);
    }
    f.close();
  } else
    result = false;
  return result;
};