SpeciesSet.h

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//////////////////////////////////////////////////////////////////////////////////////
// This file is distributed under the University of Illinois/NCSA Open Source License.
// See LICENSE file in top directory for details.
//
// Copyright (c) 2016 Jeongnim Kim and QMCPACK developers.
//
// File developed by: Jeremy McMinnis, jmcminis@gmail.com, University of Illinois at Urbana-Champaign
//                    Jeongnim Kim, jeongnim.kim@gmail.com, University of Illinois at Urbana-Champaign
//                    Raymond Clay III, j.k.rofling@gmail.com, Lawrence Livermore National Laboratory
//
// File created by: Jeongnim Kim, jeongnim.kim@gmail.com, University of Illinois at Urbana-Champaign
//////////////////////////////////////////////////////////////////////////////////////


#ifndef QMCPLUSPLUS_SPECIES_SET_H
#define QMCPLUSPLUS_SPECIES_SET_H

#include <string>
#include <vector>

namespace qmcplusplus
{
/** \class SpeciesSet
 *  \brief Custom container for set of attributes for a set of species.
 *
 *  A confusingly equivalent of std::map<std::string, <std::map<std::string, Scalar>>
 *  implemented as two sets of key vectors and a single vector of Scalars. It leaks its implementation
 *  details i.e. the indexing to the vectors. Reduces readability and increases semantic load.
 *  Looks like premature optimization.
 *
 *  \todo prove this helps overall performance, if not remove it. Else document it and it's use
*/
class SpeciesSet
{
public:
  using Scalar_t        = double;
  using SpeciesAttrib_t = std::vector<Scalar_t>;
  using AttribList_t    = std::vector<SpeciesAttrib_t>;

  //! The number of species
  unsigned TotalNum = 0;

  //! Species name list
  std::vector<std::string> speciesName;

  //! attribute name list
  std::vector<std::string> attribName;

  //! List of species attributes
  AttribList_t d_attrib;

  ///return the number of species
  inline int size() const { return TotalNum; }
  ///return the number of species
  inline int getTotalNum() const { return TotalNum; }
  ///set the number of species
  inline void setTotalNum(const unsigned n) { TotalNum = n; }
  //! return the number of attributes in our list
  inline int numAttributes() const { return d_attrib.size(); }

  /**
   * @param aname Unique name of the species be added.
   * @return the index of the species
   * @brief When a name species does not exist, add a new species
   */
  int addSpecies(const std::string& aname);

  /** for a new attribute, allocate the data, !More often used to get the index of a species
   * @param aname a unique name of an attribute
   * @return the index of a new attribute
   */
  int addAttribute(const std::string& aname);

  /**
   * @param aname Unique name of the species to be looked up.
   * @return the index of the species
   * @brief When a name species does not exist, return attribute.size()
   */
  int getAttribute(const std::string& aname) const;

  /** Check for attribute presence
   *  This replaces code that gets numAttributes then tries to addAttribute for
   *  a particular name and compares the numAttributes and index of the new Attribute
   * @param aname Unique name of the species to be looked up.
   * @return is an attribute of that name present
   */
  bool hasAttribute(const std::string& aname) const;

  /**
   * @param i attribute index
   * @param j species index
   * @return the value of i-th attribute for the j-th species
   */
  inline double operator()(int i, int j) const { return d_attrib[i][j]; }

  /**
   * assignment operator
   * @param i attribute index
   * @param j species index
   * @return the value of i-th attribute for the j-th species
   */
  inline double& operator()(int i, int j) { return d_attrib[i][j]; }

  /**
   * @param m the number of species to be added
   */
  void create(unsigned m);

  /**
   * @param name a name of species
   * @return an ID for the species with name.
   * @brief if the input species is not found, add a new species
   */
  inline int findSpecies(const std::string& name) const
  {
    int i = 0;
    while (i < speciesName.size())
    {
      if (speciesName[i] == name)
        return i;
      i++;
    }
    return i;
  }

  /** almost all code ignores this and just uses addAttribute for the same purpose.
   */
  inline int findAttribute(const std::string& name) const { return findIndex(name, attribName); }

  inline int findIndex(const std::string& name, const std::vector<std::string>& alist) const
  {
    int i = 0;
    while (i < alist.size())
    {
      if (alist[i] == name)
        return i;
      i++;
    }
    return -1;
  }

  inline const std::string& getSpeciesName(int index) const { return speciesName[index]; }
};
} // namespace qmcplusplus
#endif