toolbox.h

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/*
 * Copyright University of Reims Champagne-Ardenne
 * Authors and Contributors: Akilan RAJAMANI, Corentin LEFEBVRE, Johanna KLEIN,
 *                           Emmanuel PLUOT, Gaetan RUBEZ, Hassan KHARTABIL,
 *                           Jean-Charles BOISSON and Eric HENON
 * (24/07/2017)
 * jean-charles.boisson@univ-reims.fr, eric.henon@univ-reims.fr
 *
 * This software is a computer program whose purpose is to
 * detect and quantify interactions from electron density
 * obtained either internally from promolecular density or
 * calculated from an input wave function input file. It also
 * prepares for the visualization of isosurfaces representing
 * several descriptors (dg) coming from the IGM methodology.
 *
 * This software is governed by the CeCILL-C license under French law and
 * abiding by the rules of distribution of free software.  You can  use,
 * modify and/ or redistribute the software under the terms of the CeCILL-C
 * license as circulated by CEA, CNRS and INRIA at the following URL
 * "http://www.cecill.info".
 *
 * As a counterpart to the access to the source code and  rights to copy,
 * modify and redistribute granted by the license, users are provided only
 * with a limited warranty  and the software's author,  the holder of the
 * economic rights,  and the successive licensors  have only  limited
 * liability.
 *
 * In this respect, the user's attention is drawn to the risks associated
 * with loading,  using,  modifying and/or developing or reproducing the
 * software by the user in light of its specific status of free software,
 * that may mean  that it is complicated to manipulate,  and  that  also
 * therefore means  that it is reserved for developers  and  experienced
 * professionals having in-depth computer knowledge. Users are therefore
 * encouraged to load and test the software's suitability as regards their
 * requirements in conditions enabling the security of their systems and/or
 * data to be ensured and,  more generally, to use and operate it in the
 * same conditions as regards security.
 *
 * The fact that you are presently reading this means that you have had
 * knowledge of the CeCILL-C license and that you accept its terms.
 *
 * */

 
#ifndef _TOOLBOX_H_
#define _TOOLBOX_H_
 
 
// STL
// JC Move to general
//#include <set>
//#include <sstream>
//#include <iostream>
//#include <fstream>
//#include <iomanip>
//#include <fstream>
//#include <cstdlib>
//#include <vector>
 
// LOCAL
//#include <general.h>
#include <eig3.h>
//#include <reader.h> fait planter la compil ...
// donc, je redefinis les atomnames ici ...: pas propre ...
const std::string ATOM_NAMES_ERIC [] =
  {
    "H","He","Li","Be","B","C","N","O","F","Ne","Na","Mg","Al","Si","P","S","Cl","Ar","K","Ca","Sc","Ti","V","Cr","Mn","Fe","Co","Ni","Cu","Zn","Ga","Ge","As","Se","Br","Kr","Rb","Sr","Y","Zr","Nb","Mo","Tc", "Ru","Rh","Pd","Ag","Cd","In","Sn","Sb","Te","I","Xe","Cs","Ba","La","Ce","Pr","Nd","Pm","Sm","Eu","Gd","Tb","Dy","Ho","Er","Tm","Yb","Lu","Hf","Ta","W","Re","Os","Ir","Pt","Au","Hg","Tl","Pb","Bi","Po","At","Rn","Fr","Ra","Ac","Th","Pa","U","Np","Pu","Am","Cm","Bk","Cf","Es","Fm","Md","No","Lr"
  };
  

double getMaxFromPrec3DMatrix (double*** _3DMatrix, const unsigned int dimX, const unsigned int dimY, 
                               const unsigned int dimZ, double *** rho, const double lowerlimit, const double upperlimit);

double getMinFromPrec3DMatrix (double*** _3DMatrix, const unsigned int dimX, const unsigned int dimY,
                               const unsigned int dimZ, double *** rho, const double lowerlimit, const double upperlimit);
 

double getMaxFrom2Matrices(double*** cube1, double*** cube2,double threshold, const unsigned int dimX, const unsigned int dimY, const unsigned int dimZ);
// this method returns the maximum value found in cube1 for which cube2 >threshold
 

//double getMaxFromPrecVectorized3DMatrix (double* _Vectorized3DMatrix, double* cubeRho, const double threshold, const unsigned int dimX, const unsigned int dimY, const unsigned int dimZ);
double getMaxFromPrecVectorized3DMatrix (double* _Vectorized3DMatrix, double* cubeRho, const double lowerlimit, const double upperlimit,
                                         unsigned int dimX, const unsigned int dimY, const unsigned int dimZ);
 

std::string getCondensedInformationFromNumericSet(std::set<int> numericValues);

void space(size_t nbSpaces, size_t limit=100);

//void printCurrentState(bool start=true, bool end=false, unsigned int currentValue=0, unsigned int totalToReach=0);
void printCurrentState(unsigned int done, unsigned int total, time_t ellapsed);
 
 
void printDEBUG(std::string message);

double getScalarProduct( const double *vectorA, const double *vectorB );

double getCrossProductMagn(const double  *vectorA, const double  *vectorB);
 

double getNormOfVector( const double *vectorA);

/*double getNormOfVector(const double vectorA[3]);*/
 

void computeRotationMatrix(const double V[3], const double alpha, double rotMat[3][3]);

void fortranMatMul33Matrix3Vector(const double matrix[3][3], const double V[3], double VR[3]);

void print_3_3_matrix(const double matrix[3][3]);

std::string getAtomName(const unsigned int iatom);

bool isStringInt(const std::string s);

bool invSym33(double M[3][3], double MINV[3][3]);  

int modulo(int a, int b);
 

double distance(double a[3], double b[3]);
 

void getTransposed(double **M1, double M2[3][3]);

void getTransposed(double M1[3][3], double M2[3][3]);

bool isNumeric(std::string const &str);

double getSelfMaxRange(double*** cube,double*** cube2, double threshold,const unsigned int dimX, const unsigned int dimY, const unsigned int dimZ);

void merge(double* arr, double* temp, int left, int mid, int right);
 

void parallelMergeSort(double* arr, double* temp, int left, int right, int depth = 0);
 
 
 
#endif