reader.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 _READER_H_
#define _READER_H_
 
// LOCAL
//#include <ProgData.h>
#include <Results.h>
#include <WFreader.h>
 
// JC IBSI
// Already included by Results.h
//#include <vector>

typedef enum ATOM_TYPES
  {
    HYDROGEN, HELIUM, LITHIUM, BERYLLIUM, BORON, CARBON, NITROGEN, OXYGEN, FLUORINE, NEON, SODIUM, MAGNESIUM, ALUMINIUM, SILICON, PHOSPHORUS, SULFUR, CHLORINE, ARGON, POTASSIUM, CALCIUM, SCANDIUM,
    TITANIUM, VANADIUM, CHROMIUM, MANGANESE, IRON, COBALT, NICKEL, COPPER, ZINC, GALLIUM, GERMANIUM, ARSENIC, SELENIUM, BROMINE, KRYPTON, RUBIDIUM, STRONTIUM, YTTRIUM, ZIRCONIUM, NIOBIUM, MOLYBDENUM,
    TECHNETIUM, RUTHENIUM, RHODIUM, PALLADIUM, SILVER, CADMIUM, INDIUM, TIN, ANTIMONY, TELLURIUM, IODINE, XENON, CESIUM, BARIUM, LANTHANUM, CERIUM, PRASEODYMIUM, NEODYMIUM, PROMETHIUM, SAMARIUM, EUROPIUM, GADOLINIUM, TERBIUM, DYSPROSIUM, HOLMIUM, ERBIUM, THULIUM, YTTERBIUM, LUTETIUM, 
    HAFNIUM, TANTALUM, TUNGSTEN, RHENIUM, OSMIUM, IRIDIUM, PLATINIUM, GOLD, MERCURY, THALLIUM, LEAD, BISMUTH, POLONIUM, ASTATINE, RADON, FRANCIUM, RADIUM,
ACTINIUM, THORIUM, PROTACTINIUM, URANIUM, NEPTUNIUM, PLUTONIUM, AMERICIUM, CURIUM, BERKELIUM, CALIFORNIUM, EINSTEINIUM, FERMIUM, MENDELEVIUM, NOVELIUM, LAWRENCIUM, SIZE_ATOM
  }atom_types_t;

// modif Eric : 20/04/2019: atom name list in the range [0:SIZE_ATOM-1]
const std::string ATOM_NAMES [] =
  {
    "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"
  };

// modif Eric : 04/04/2021:
const unsigned int ATOM_COREORB [] =
  {
     0 , 0  , 1  , 1  , 1 , 1 , 1 , 1 , 1 , 1  , 5  , 5  , 5  , 5  , 5 , 5  , 5  , 5 , 9 , 9  , 9  , 9  , 9 , 9  , 9  , 9  , 9  , 9  , 9  , 9  , 14 , 14 , 14 , 14 , 14 , 14 , 18 , 18 , 18 , 18 , 18 , 18 , 18 ,  18 , 18 , 18 , 18 , 18 , 23 , 23 , 23 , 23 , 23 , 23 ,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE
  };

const unsigned int ATOM_ELECTRONS [] =
  {
     1 , 2  , 3  , 4  , 5 , 6 , 7 , 8 , 9 , 10 , 11 , 12 , 13 , 14 , 15, 16 , 17 , 18, 19, 20 , 21 , 22 , 23, 24 , 25 , 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 , 39 , 40 , 41 , 42 , 43 ,  44 , 45 , 46 , 47 , 48 , 49 , 50 , 51 , 52 , 53 , 54 ,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE,MAXCORE
  };

void setFrag(const std::string definition, const param_types_t FRAG, const int nbAtoms);
 

bool isANumber(const std::string &s);

int conversionAtom(std::string& tmp);

int conversionParam(std::string& param);

void readParam(const char* parameterFileName, param_t* params);

ProgData* readxyzMinMax(param_t * params);

bool isWFmodeActivated();

bool isWFXmodeActivated();
 

bool isWFNmodeActivated();

bool isRKFmodeActivated();

std::string getMoleculeAatomDefinition();
 

std::string getMoleculeBatomDefinition();
 
 

unsigned int wfn_getMoleculeAnbAtoms();

unsigned int wfn_getMoleculeBnbAtoms();

void analyseSetFRAG1FRAG2(const std::string definition1, const std::string definition2, const int nbAtoms, param_t *params);

bool isInMoleculeA(unsigned int atomNaturalIndex);

bool isInMoleculeB(unsigned int atomNaturalIndex);
 

std::string getCondensedDescriptionOfMoleculeA();

std::string getCondensedDescriptionOfMoleculeB();

void howUsingIGMplot();

bool isIBSImodeActivated();

bool isELFmodeActivated();
 

bool isIGMmodeActivated();

bool isfullAOAccActivated();

bool isHirshmodeActivated();

bool isCriticmodeActivated();
 

bool isParseRKF();
// the RKF binary file will be parsed no grid calculation
// useful to read the content of an RKF binary file

bool isPauli();

bool isPauliAtomic();
 

bool isPROSELF();

bool isTOPELF();
 
 
 

bool isdgSCALED();
 

bool isCriticMEDIUMmodeActivated();

bool isCriticFINEmodeActivated();

bool isCriticULTRAFINEmodeActivated();

bool isCriticAddSeedsmodeActivated();
 

bool isPeakFocusIntraActivated();

bool isPeakFocusInterActivated();

bool atomBondsHaveBeenRegistered();

std::vector< std::pair< unsigned int,  unsigned int > > & getChosenBonds();

void checkKeywords(param_t *params);
 
#endif