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Merged
merged 14 commits into from
Aug 13, 2025
Merged

refactoring: Create class for coordination number calculation #43

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5f035a2
refactor: move charge models to new multicharge namespace and create …
Thomas3R Jun 6, 2025
7fec355
refactor: create class for coordination number calculation
Thomas3R Jun 12, 2025
b85b2c7
Update comment in dftd_ncoord.cpp
Thomas3R Jun 13, 2025
6886aa7
Move cn and dcndr allocation into ncoord and dncoord functions.
Thomas3R Jun 18, 2025
c65dc27
NCoordBase constructor initializer list and code cleanup
Thomas3R Jun 18, 2025
b2a6fc0
rename functions for consistency
Thomas3R Jun 18, 2025
fc8baed
Leave deletion of arrays to object destructor
Thomas3R Jun 18, 2025
5b22339
Clean up NCoordBase member variables in destructor
Thomas3R Jul 18, 2025
2afd44e
NCoord refactor and bug fixes
Thomas3R Jul 22, 2025
3c7eed9
Update src/dftd_ncoord.cpp
Thomas3R Aug 13, 2025
f6a37e7
Address PR review comments
Thomas3R Aug 13, 2025
e3aa2d6
Merge branch 'dftd4:main' into ncoord
Thomas3R Aug 13, 2025
27096bd
Merge branch 'ncoord' of github.com:Thomas3R/cpp-d4 into ncoord
Thomas3R Aug 13, 2025
3f8cb39
remove reduntant charge model intance from numerical gradient test
Thomas3R Aug 13, 2025
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6 changes: 4 additions & 2 deletions include/dftd_cblas.h
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -35,8 +35,8 @@ inline int BLAS_Add_Mat_x_Vec(
bool Transpose,
double alpha
) {
if (A.rows == C.N && A.cols == V.N) {
if (Transpose) {
if (A.cols == C.N && A.rows == V.N) {
cblas_dgemv(
CblasRowMajor,
CblasTrans,
Expand All @@ -52,7 +52,9 @@ inline int BLAS_Add_Mat_x_Vec(
1
);
return EXIT_SUCCESS;
} else {
};
} else {
if (A.rows == C.N && A.cols == V.N) {
cblas_dgemv(
CblasRowMajor,
CblasNoTrans,
Expand Down
338 changes: 137 additions & 201 deletions include/dftd_ncoord.h
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Original file line number Diff line number Diff line change
Expand Up @@ -28,6 +28,143 @@

namespace dftd4 {


class NCoordBase
{
public:
TVector<double> cn;
TMatrix<double> dcndr;
static const double rad[];
double kcn; // Steepness of counting function
double norm_exp;
double cutoff;
/**
* Wrapper for coordination number calculation.
*
* @param mol Molecule object.
* @param dist Distance matrix.
* @param cutoff Real-space cutoff (default: @see {dftd_cutoff.h}).
* @param lgrad Flag for gradient computation.
* @return Exit status.
*/
int get_ncoord( // with ghost atoms
const TMolecule &mol,
const TMatrix<double> &dist,
const double cutoff,
bool lgrad);
/**
* Wrapper for coordination number calculation.
*
* @param mol Molecule object.
* @param realIdx List for real atoms excluding ghost/non atoms.
* @param dist Distance matrix.
* @param cutoff Real-space cutoff (default: @see {dftd_cutoff.h}).
* @param cn Vector of coordination numbers.
* @return Exit status.
*/
int get_ncoord( // without ghost atoms
const TMolecule &mol,
const TIVector &realIdx,
const TMatrix<double> &dist,
bool lgrad);
/**
* Calculate the coordination number.
*
* @param mol Molecule object.
* @param realIdx List for real atoms excluding ghost/non atoms.
* @param dist Distance matrix.
* @return Exit status.
*/
int ncoord_base(
const TMolecule &mol,
const TIVector &realIdx,
const TMatrix<double> &dist);
/**
* Calculate error function coordination number and derivative
* w.r.t. nuclear coordinates.
*
* @param mol Molecule object.
* @param realIdx List for real atoms excluding ghost/non atoms.
* @param dist Distance matrix.
* @return Exit status.
*/
int dncoord_base(
const TMolecule &mol,
const TIVector &realIdx,
const TMatrix<double> &dist);
/**
* Electronegativity factor.
*
* @param i atom index
* @param j atom index
* @return Value of the electronegativity factor.
*/
virtual double get_en_factor(int i, int j) const;
/**
* base class function for coordination number contributions.
*
* @param rr atomic distance over covalent radii
* @return Value of the counting function.
*/
virtual double count_fct(double rr) const = 0;
/**
* Derivative of the counting function w.r.t. the distance.
*
* @param rr atomic distance over covalent radii
* @return Derivative of the counting function.
*/
virtual double dcount_fct(double rr) const = 0;
/**
* TCutoff function for large coordination numbers
*
* @param cn_max Maximum CN (not strictly obeyed).
* @param cn On input coordination number, on output modified CN.
* @param dcndr On input derivative of CN w.r.t. cartesian coordinates,
* on output derivative of modified CN.
* @param lgrad Flag for gradient calculation.
*/
virtual int cut_coordination_number(const double cn_max, TVector<double> &cn, TMatrix<double> &dcndr, bool lgrad) = 0;
// Constructor
NCoordBase(double optional_kcn = 7.5, double optional_norm_exp = 1.0, double optional_cutoff = 25.0);
// Virtual destructor
virtual ~NCoordBase() {
cn.DelVec();
dcndr.DelMat();
}
};

class NCoordErf : public NCoordBase {
public:
// erf() based counting function
double count_fct(double) const override;
// derivative of the erf() based counting function
double dcount_fct(double) const override;
// Soft maximum/cutoff for coordination number
int cut_coordination_number(const double, TVector<double>&, TMatrix<double>&, bool) override;
// Constructor
NCoordErf(double optional_kcn = 7.5, double optional_norm_exp = 1.0, double optional_cutoff = 25.0)
: NCoordBase(optional_kcn, optional_norm_exp, optional_cutoff){}
// Use default destructor; base class handles cleanup
~NCoordErf() override = default;
};

class NCoordErfD4 : public NCoordBase {
public:
// erf() based counting function
double count_fct(double) const override;
// derivative of the erf() based counting function
double dcount_fct(double) const override;
// coordination number scaling factor based on electronegativity difference
double get_en_factor(int, int) const override;
// Soft maximum/cutoff for coordination number
int cut_coordination_number(const double, TVector<double>&, TMatrix<double>&, bool) override;
// Constructor
NCoordErfD4(double optional_kcn = 7.5, double optional_norm_exp = 1.0, double optional_cutoff = 25.0)
: NCoordBase(optional_kcn, optional_norm_exp, optional_cutoff){}
// Use default destructor; base class handles cleanup
~NCoordErfD4() override = default;
};

/**
* Calculate all distance pairs and store in matrix.
*
Expand All @@ -51,207 +188,6 @@ extern int calc_distances(
*/
extern void initializeRealIdx(int nat, TVector<int> &realIdx);

///////////////////////////////////////////////////////////////////////////////
///////////////////////////////////////////////////////////////////////////////

/**
* Wrapper for error function coordination number.
*
* @param mol Molecule object.
* @param realIdx List for real atoms excluding ghost/non atoms.
* @param dist Distance matrix.
* @param cn Vector of coordination numbers.
* @param cutoff Real-space cutoff (default: @see {dftd_cutoff.h}).
* @param dcndr Derivative of coordination number.
* @param lgrad Flag for gradient computation.
* @return Exit status.
*/
extern int get_ncoord_erf(
const TMolecule &mol,
const TIVector &realIdx,
const TMatrix<double> &dist,
double cutoff,
TVector<double> &cn,
TMatrix<double> &dcndr,
bool lgrad = false
);

/**
* Wrapper for error function coordination number.
*
* @param mol Molecule object.
* @param dist Distance matrix.
* @param cn Vector of coordination numbers.
* @param cutoff Real-space cutoff (default: @see {dftd_cutoff.h}).
* @param dcndr Derivative of coordination number.
* @param lgrad Flag for gradient computation.
* @return Exit status.
*/
extern int get_ncoord_erf(
const TMolecule &mol,
const TMatrix<double> &dist,
double cutoff,
TVector<double> &cn,
TMatrix<double> &dcndr,
bool lgrad = false
);

/**
* Calculate error function coordination number.
*
* @param mol Molecule object.
* @param realIdx List for real atoms excluding ghost/non atoms.
* @param dist Distance matrix.
* @param cutoff Real-space cutoff (default: @see {dftd_cutoff.h}).
* @param cn Vector of coordination numbers.
* @return Exit status.
*/
extern int ncoord_erf(
const TMolecule &mol,
const TIVector &realIdx,
const TMatrix<double> &dist,
double cutoff,
TVector<double> &cn
);

/**
* Calculate error function coordination number and derivative
* w.r.t. nuclear coordinates.
*
* @param mol Molecule object.
* @param realIdx List for real atoms excluding ghost/non atoms.
* @param dist Distance matrix.
* @param cutoff Real-space cutoff (default: @see {dftd_cutoff.h}).
* @param cn Vector of coordination numbers.
* @param dcndr Derivative of coordination number.
* @return Exit status.
*/
extern int dncoord_erf(
const TMolecule &mol,
const TIVector &realIdx,
const TMatrix<double> &dist,
double cutoff,
TVector<double> &cn,
TMatrix<double> &dcndr
);

///////////////////////////////////////////////////////////////////////////////
///////////////////////////////////////////////////////////////////////////////

/**
* Wrapper for error function coordination number for DFT-D4.
*
* @param mol Molecule object.
* @param realIdx List for real atoms excluding ghost/non atoms.
* @param dist Distance matrix.
* @param cutoff Real-space cutoff (default: @see {dftd_cutoff.h}).
* @param cn Vector of coordination numbers.
* @return Exit status.
*/
extern int get_ncoord_d4(
const TMolecule &mol,
const TIVector &realIdx,
const TMatrix<double> &dist,
double cutoff,
TVector<double> &cn,
TMatrix<double> &dcndr,
bool lgrad = false
);

/**
* Wrapper for error function coordination number for DFT-D4.
*
* @param mol Molecule object.
* @param dist Distance matrix.
* @param cutoff Real-space cutoff (default: @see {dftd_cutoff.h}).
* @param cn Vector of coordination numbers.
* @return Exit status.
*/
extern int get_ncoord_d4(
const TMolecule &mol,
const TMatrix<double> &dist,
double cutoff,
TVector<double> &cn,
TMatrix<double> &dcndr,
bool lgrad = false
);

/**
* Calculate covalent coordination number for DFT-D4.
*
* @param mol Molecule object.
* @param realIdx List for real atoms excluding ghost/non atoms.
* @param dist Distance matrix.
* @param cutoff Real-space cutoff (default: @see {dftd_cutoff.h}).
* @param cn Vector of coordination numbers.
* @return Exit status.
*/
extern int ncoord_d4(
const TMolecule &mol,
const TIVector &realIdx,
const TMatrix<double> &dist,
double cutoff,
TVector<double> &cn
);

/**
* Calculate covalent coordination number and derivative
* w.r.t. nuclear coordinates
*
* @param mol Molecule object.
* @param realIdx List for real atoms excluding ghost/non atoms.
* @param dist Distance matrix.
* @param cutoff Real-space cutoff (default: @see {dftd_cutoff.h}).
* @param cn Vector of coordination numbers.
* @param dcndr Derivative of coordination number.
* @return Exit status.
*/
extern int dncoord_d4(
const TMolecule &mol,
const TIVector &realIdx,
const TMatrix<double> &dist,
double cutoff,
TVector<double> &cn,
TMatrix<double> &dcndr
);

///////////////////////////////////////////////////////////////////////////////
///////////////////////////////////////////////////////////////////////////////

/**
* Error function counting function for coordination number contributions.
*
* @param k Steepness of the counting function.
* @param rr Current distance over cutoff radius.
* @return Value of the counting function.
*/
extern double erf_count(double k, double rr);

/**
* Derivative of the counting function w.r.t. the distance.
*
* @param k Steepness of the counting function.
* @param rr TCutoff radius.
* @return Derivative of the counting function.
*/
extern double derf_count(double k, double rr);

/**
* TCutoff function for large coordination numbers
*
* @param cn_max Maximum CN (not strictly obeyed).
* @param cn On input coordination number, on output modified CN.
* @param dcndr On input derivative of CN w.r.t. cartesian coordinates,
* on output derivative of modified CN.
* @param lgrad Flag for gradient.
*/
extern int cut_coordination_number(
double cn_max,
TVector<double> &cn,
TMatrix<double> &dcndr,
bool lgrad
);

extern inline double log_cn_cut(double cn_max, double cn);

extern inline double dlog_cn_cut(double cn_max, double cn);
Expand Down
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