IGMPlot 3.16
Optimized IGMplot version able to use wfn/wfx/xyz files
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output.cpp File Reference

Implementation of methods declared in output.h. More...

#include <output.h>
#include <string>
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Macros

#define INDEX   (k*data->getNbSteps(0)*data->getNbSteps(1)+j*data->getNbSteps(0)+i)
 The computation of the current index (using i, j, k)
 

Functions

void outCube (int cubeType, param_t *params, ProgData *data, double *cubeRho, double *cube)
 Writes down the given cube and some parameters to help interprete it.
 
void writeCube (param_t *params, ProgData *data, const char *cubeFileName, double ***rho, double ***cube, const bool usingRhoThreshold, const double lowerlimit, const double upperlimit, const double defaultValue)
 Writes down the given cube and some parameters to help interpreting it.
 
void outCubeRDG (param_t *params, ProgData *data, double *cube, double *rho, bool *shouldPrint)
 Writes down the given RDG cube and some parameters to help interpreting it.
 
void outCubeRho (param_t *params, ProgData *data, double *cube)
 Writes down the given Rho cube and some parameters to help interpreting it.
 
void outDat (param_t *params, ProgData *data, Results &results)
 Writes down the given Rho and RDG cubes.
 
void outPercent (param_t *params, Results &results, ProgData *data)
 Writes down the percentage participation for each atom to the INTER interactions.
 
void outPercentQM (param_t params, ProgData *data, double *dgInterAtSum, double dv, unsigned int nbAtoms)
 Writes down the percentage participation for each atom to the INTER interactions.
 
string getWorkPath ()
 returns a string with the current working path
 
void outVMD (param_t *params, ProgData *data, double max, double deltagIntraMaximumValue, double deltagInterMaximumValue, double dgAtWeakMaxValue)
 Writes down the VM script for visualisation.
 
void writeVMDfiles (param_t *params, ProgData *data, double deltagIntraMaximumValue, double deltagInterMaximumValue, double dgAtWeakMaxValue, std::vector< criticalpoint > cpList, double max, double selfmaxrange)
 Writes down the VM script for visualisation (quantum version)
 
void writeXYZ (param_t &params, ProgData *data, unsigned int nbAtoms, positions_t &atomCoordinates)
 write xyz atom coordinates using the xyz file format
 
void writeCPTXT (param_t &params, std::vector< criticalpoint > cpList)
 write the cp.txt output file after a critical point analysis
 
void writeAtomDOI (param_t params, ProgData *data, double *dgAtSum, double *dgAtSumW, double *dgAtSumW2, double dv, unsigned int nbAtoms)
 write Atom Degree of Interaction find within the atomi IGM framework
 
void writeSelfAtomDat (param_t params, ProgData *data, double *pauliAT, unsigned int nbAtoms)
 write Atom contributions to the Pauli repulsion between two fragments (SELF analysis)
 

Detailed Description

Implementation of methods declared in output.h.

Author
Gaetan & Emmanuel

Function Documentation

◆ getWorkPath()

string getWorkPath ( )

returns a string with the current working path

Returns
the current path of the execution

◆ outCube()

void outCube ( int cubeType,
param_t * params,
ProgData * data,
double * cubeRho,
double * cube )

Writes down the given cube and some parameters to help interprete it.

Parameters
cubeType: the type of the cube
params: the parameters read at the beginning of the program
data: the data received at the beginning of the program
cubeRho: the cubeRho processed during the program
cube: the cube itself
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◆ outCubeRDG()

void outCubeRDG ( param_t * params,
ProgData * data,
double * cube,
double * rho,
bool * shouldPrint )

Writes down the given RDG cube and some parameters to help interpreting it.

Parameters
paramsthe parameters read at the beginning of the program
datathe data received at the beginning of the program
cubethe cube itself
rhothe density values
shouldPrintTO DOCUMENT
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◆ outCubeRho()

void outCubeRho ( param_t * params,
ProgData * data,
double * cube )

Writes down the given Rho cube and some parameters to help interpreting it.

Parameters
paramsthe parameters read at the beginning of the program
datathe data received at the beginning of the program
cubethe cube itself
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◆ outDat()

void outDat ( param_t * params,
ProgData * data,
Results & results )

Writes down the given Rho and RDG cubes.

Parameters
paramsthe parameters read at the beginning of the program
datathe data received at the beginning of the program
resultsthe process results
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◆ outPercent()

void outPercent ( param_t * params,
Results & results,
ProgData * data )

Writes down the percentage participation for each atom to the INTER interactions.


Parameters
paramsthe parameters read at the beginning of the program
resultsthe results' values, including delta values
theprogram's data
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◆ outPercentQM()

void outPercentQM ( param_t params,
ProgData * data,
double * dgInterAtSum,
double dv,
unsigned int nbAtoms )

Writes down the percentage participation for each atom to the INTER interactions.

Parameters
paramsthe parameters read at the beginning of the program
datato get atom names
dgInterAtSumthe atomic contribution values
dvthe elementary volume in the grid
datams the number of atoms in the system
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◆ outVMD()

void outVMD ( param_t * params,
ProgData * data,
double max,
double deltagIntraMaximumValue,
double deltagInterMaximumValue,
double dgAtWeakMaxValue )

Writes down the VM script for visualisation.

Parameters
paramsthe parameters read at the beginning of the program
datathe program's data
maxthe maximum percent found
deltagIntraMaximumValueThe maximum value found in deltagIntra interaction (useful for VMD files)
deltagInterMaximumValueThe maximum value found in deltagInter interaction (useful for VMD files)
dgAtWeakMaxValueThe maximum value of the set of atomic contributions to weak interactions
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◆ writeAtomDOI()

void writeAtomDOI ( param_t params,
ProgData * data,
double * dgAtSum,
double * dgAtSumW,
double * dgAtSumW2,
double dv,
unsigned int nbAtoms )

write Atom Degree of Interaction find within the atomi IGM framework

Parameters
params: input --> to retrieve the output filename
data: pointer to a structure containing data like getNbSteps0 ...
dgAtSum,dgAtSumW,dgAtSumW2: input --> atomic scorings
dvinput --> elementary integration volume
nbAtomsthe number of atoms in the system
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◆ writeCPTXT()

void writeCPTXT ( param_t & params,
std::vector< criticalpoint > cpList )

write the cp.txt output file after a critical point analysis


Parameters
params: input --> to retrieve the output filename
cpList: input --> structure containing all information about found critical points
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◆ writeCube()

void writeCube ( param_t * params,
ProgData * data,
const char * cubeFileName,
double *** rho,
double *** cube,
const bool usingThreshold = false,
const double lowerlimit = 0.0,
const double upperlimit = 0.0,
const double defaultValue = 0.0 )

Writes down the given cube and some parameters to help interpreting it.

Parameters
paramsthe parameters read at the beginning of the program
datathe data received at the beginning of the program
cubeFileNameSpecific part of the file name that will contain the cube values (to identify it ). Convention is : params->outputName + "-" + cubeFileName + ".cube"
rhothe rho values processed during the program
cubethe cube to write itself
usingThresholdif no need of using threshold, everything is written
lowerlimitthe lower limit of the ED range that allows (or not) writing the cube information
upperlimitthe upper limit of the ED range that allows (or not) writing the cube information
defaultValuethe value if the ED value is out of the [lowerlimit:upperlimit] range
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◆ writeSelfAtomDat()

void writeSelfAtomDat ( param_t params,
ProgData * data,
double * pauliAT,
unsigned int nbAtoms )

write Atom contributions to the Pauli repulsion between two fragments (SELF analysis)

Parameters
params: input --> to retrieve the output filename
data: pointer to a structure containing data like getNbSteps0 ...
pauliAT: input --> atomic scorings
nbAtomsthe number of atoms in the system
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◆ writeVMDfiles()

void writeVMDfiles ( param_t * params,
ProgData * data,
double deltagIntraMaximumValue = 0.08,
double deltagInterMaximumValue = 0.01,
double dgAtWeakMaxValue,
std::vector< criticalpoint > cpList,
double max,
double selfmaxrange )

Writes down the VM script for visualisation (quantum version)

Warning
only use for Quantum computation but will be generic at the end
Parameters
paramsthe parameters read at the beginning of the program
datathe program's data
deltagIntraMaximumValueThe maximum value found in deltagIntra interaction (useful for VMD files)
deltagInterMaximumValueThe maximum value found in deltagInter interaction (useful for VMD files)
dgAtWeakMaxValueThe maximum value of the set of atomic contributions to weak interactions
cpListThe list of found critical points
maxthe maximum value within the atomic contrib to the INTER interactions
selfmaxrangethe maximum SELF value to color dg/rho with SELF
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◆ writeXYZ()

void writeXYZ ( param_t & params,
ProgData * data,
unsigned int nbAtoms,
positions_t & atomCoordinates )

write xyz atom coordinates using the xyz file format

Parameters
params: input --> to retrieve the output filename
data: pointer to a structure containing data like getNbSteps0 ...
nbAtoms: input --> number of atom of the system to be printed
atomCoordinates: input --> structure containing information about positions of the atoms (xyz)
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