From e3470528b306251a9cdf46be9111db3c96755278 Mon Sep 17 00:00:00 2001
From: mkirsz <s1351949@sms.ed.ac.uk>
Date: Tue, 17 Dec 2024 13:07:35 +0000
Subject: [PATCH] Fix and cleanup of inheritance
---
.../functions/basis_functions/bf_base.h | 15 +++--
.../functions/basis_functions/bf_linear.h | 8 +--
.../basis_functions/bf_polynomial2.h | 8 +--
.../tadah/models/functions/function_base.h | 56 +++++++++----------
.../models/functions/kernels/kern_base.h | 28 +++++-----
.../models/functions/kernels/kern_linear.h | 16 +++---
.../tadah/models/functions/kernels/kern_lq.h | 8 +--
.../functions/kernels/kern_polynomial.h | 8 +--
.../models/functions/kernels/kern_quadratic.h | 8 +--
.../tadah/models/functions/kernels/kern_rbf.h | 8 +--
.../models/functions/kernels/kern_sigmoid.h | 8 +--
src/bf_base.cpp | 2 +
src/bf_linear.cpp | 2 +-
src/bf_polynomial2.cpp | 3 +-
src/function_base.cpp | 15 +++++
src/kern_base.cpp | 2 +
src/kern_linear.cpp | 2 +-
src/kern_lq.cpp | 2 +-
src/kern_polynomial.cpp | 2 +-
src/kern_quadratic.cpp | 2 +-
src/kern_rbf.cpp | 2 +-
src/kern_sigmoid.cpp | 2 +-
22 files changed, 113 insertions(+), 94 deletions(-)
diff --git a/include/tadah/models/functions/basis_functions/bf_base.h b/include/tadah/models/functions/basis_functions/bf_base.h
index c68da21..19f76fb 100644
--- a/include/tadah/models/functions/basis_functions/bf_base.h
+++ b/include/tadah/models/functions/basis_functions/bf_base.h
@@ -8,11 +8,14 @@
/** \brief Base class to be used by all basis functions */
struct BF_Base: public virtual Function_Base {
- virtual ~BF_Base();
- virtual double epredict(const t_type &, const aed_type2& ) const=0;
- virtual double fpredict(const t_type &, const fd_type &,
- const aed_type2& , const size_t ) const=0;
- virtual force_type fpredict(const t_type &, const fd_type &,
- const aed_type2& ) const=0;
+ BF_Base();
+ BF_Base(const Config &c);
+ virtual ~BF_Base();
+
+ // virtual double epredict(const t_type &, const aed_type2& ) const=0;
+ // virtual double fpredict(const t_type &, const fd_type &,
+ // const aed_type2& , const size_t ) const=0;
+ // virtual force_type fpredict(const t_type &, const fd_type &,
+ // const aed_type2& ) const=0;
};
#endif
diff --git a/include/tadah/models/functions/basis_functions/bf_linear.h b/include/tadah/models/functions/basis_functions/bf_linear.h
index ca36097..4595199 100644
--- a/include/tadah/models/functions/basis_functions/bf_linear.h
+++ b/include/tadah/models/functions/basis_functions/bf_linear.h
@@ -24,7 +24,7 @@ struct BF_Linear : public virtual BF_Base {
* @brief Retrieve the label of the basis function.
* @return String label of the basis function.
*/
- std::string get_label() const;
+ std::string get_label() const override;
std::string label = "BF_Linear"; ///< Label identifying the basis function.
@@ -34,7 +34,7 @@ struct BF_Linear : public virtual BF_Base {
* @param aed Atomic descriptors.
* @return Predicted energy.
*/
- double epredict(const t_type &weights, const aed_type2 &aed) const;
+ double epredict(const t_type &weights, const aed_type2 &aed) const override;
/**
* @brief Predicts force for a specific dimension using the linear basis function.
@@ -45,7 +45,7 @@ struct BF_Linear : public virtual BF_Base {
* @return Predicted force component.
*/
double fpredict(const t_type &weights, const fd_type &fdij,
- const aed_type2 &aedi, const size_t k) const;
+ const aed_type2 &aedi, const size_t k) const override;
/**
* @brief Predicts forces using the linear basis function.
@@ -55,6 +55,6 @@ struct BF_Linear : public virtual BF_Base {
* @return Predicted forces.
*/
force_type fpredict(const t_type &weights, const fd_type &fdij,
- const aed_type2 &aedi) const;
+ const aed_type2 &aedi) const override;
};
#endif
diff --git a/include/tadah/models/functions/basis_functions/bf_polynomial2.h b/include/tadah/models/functions/basis_functions/bf_polynomial2.h
index f8dcd9f..59400d5 100644
--- a/include/tadah/models/functions/basis_functions/bf_polynomial2.h
+++ b/include/tadah/models/functions/basis_functions/bf_polynomial2.h
@@ -26,7 +26,7 @@ struct BF_Polynomial2 : public virtual BF_Base {
* @brief Retrieve the label of the basis function.
* @return String label of the basis function.
*/
- std::string get_label() const;
+ std::string get_label() const override;
/**
* @brief Predicts energy using the polynomial basis function.
@@ -34,7 +34,7 @@ struct BF_Polynomial2 : public virtual BF_Base {
* @param aed Atomic descriptors.
* @return Predicted energy.
*/
- double epredict(const t_type &weights, const aed_type2 &aed) const;
+ double epredict(const t_type &weights, const aed_type2 &aed) const override;
/**
* @brief Predicts force for a specific dimension using the polynomial basis function.
@@ -45,7 +45,7 @@ struct BF_Polynomial2 : public virtual BF_Base {
* @return Predicted force component.
*/
double fpredict(const t_type &weights, const fd_type &fdij,
- const aed_type2 &aedi, const size_t k) const;
+ const aed_type2 &aedi, const size_t k) const override;
/**
* @brief Predicts forces using the polynomial basis function.
@@ -55,6 +55,6 @@ struct BF_Polynomial2 : public virtual BF_Base {
* @return Predicted forces.
*/
force_type fpredict(const t_type &weights, const fd_type &fdij,
- const aed_type2 &aedi) const;
+ const aed_type2 &aedi) const override;
};
#endif
diff --git a/include/tadah/models/functions/function_base.h b/include/tadah/models/functions/function_base.h
index 01d73b7..d9486c8 100644
--- a/include/tadah/models/functions/function_base.h
+++ b/include/tadah/models/functions/function_base.h
@@ -8,35 +8,31 @@
/** Base class for Kernels and Basis Functions */
struct Function_Base {
- private:
- int verbose;
-
- public:
- Function_Base() {
- verbose=0;
- }
- Function_Base(const Config &c) {
- verbose = c.get<int>("VERBOSE");
- }
- void set_verbose(int v) { verbose=v; }
- int get_verbose() { return verbose; }
-
- // Derived classes must implement Derived() and Derived(Config)
- virtual ~Function_Base() {};
-
- // For Kernels
- virtual double operator() (const aed_type2& , const aed_type2& ) { return 0.0; };
- virtual aed_type2 derivative(const aed_type2& , const aed_type2& ) { return aed_type2(); };
- virtual double prime(const aed_type2& , const aed_type2& ,
- const aed_type2& ) { return 0.0; }
- virtual void set_basis(const Matrix ) {};
-
- /** \brief Return label of this object */
- virtual std::string get_label() const=0;
- virtual double epredict(const t_type &, const aed_type2& ) const=0;
- virtual double fpredict(const t_type &, const fd_type &,
- const aed_type2&, const size_t ) const=0;
- virtual force_type fpredict(const t_type &, const fd_type &,
- const aed_type2& ) const=0;
+private:
+ int verbose;
+
+public:
+ Function_Base();
+ Function_Base(const Config &c);
+ void set_verbose(int v);
+ int get_verbose();
+
+ // Derived classes must implement Derived() and Derived(Config)
+ virtual ~Function_Base();
+
+ // For Kernels
+ virtual double operator() (const aed_type2& , const aed_type2& ) const;
+ virtual aed_type2 derivative(const aed_type2& , const aed_type2& ) const;
+ virtual double prime(const aed_type2& , const aed_type2& ,
+ const aed_type2& ) const;
+ virtual void set_basis(const Matrix );
+
+ /** \brief Return label of this object */
+ virtual std::string get_label() const=0;
+ virtual double epredict(const t_type &, const aed_type2& ) const=0;
+ virtual double fpredict(const t_type &, const fd_type &,
+ const aed_type2&, const size_t ) const=0;
+ virtual force_type fpredict(const t_type &, const fd_type &,
+ const aed_type2& ) const=0;
};
#endif
diff --git a/include/tadah/models/functions/kernels/kern_base.h b/include/tadah/models/functions/kernels/kern_base.h
index 41da02e..aac4d94 100644
--- a/include/tadah/models/functions/kernels/kern_base.h
+++ b/include/tadah/models/functions/kernels/kern_base.h
@@ -16,22 +16,24 @@
class Kern_Base: public virtual Function_Base {
public:
Matrix basis;
+ Kern_Base();
+ Kern_Base(const Config &c);
virtual ~Kern_Base();
- /**
- * Calculate kernel value given two vectors
- *
- * - b = basis vector
- * - af = atomic energy descriptor
- */
+ // /**
+ // * Calculate kernel value given two vectors
+ // *
+ // * - b = basis vector
+ // * - af = atomic energy descriptor
+ // */
virtual double operator() (const aed_type2 &b, const aed_type2 &af) const=0;
-
- /**
- * Calculate the kernel derivative wrt to the second argument
- *
- * - b = basis vector
- * - af = atomic energy descriptor
- */
+ //
+ // /**
+ // * Calculate the kernel derivative wrt to the second argument
+ // *
+ // * - b = basis vector
+ // * - af = atomic energy descriptor
+ // */
virtual aed_type2 derivative(const aed_type2 &b, const aed_type2 &af) const=0;
/**
diff --git a/include/tadah/models/functions/kernels/kern_linear.h b/include/tadah/models/functions/kernels/kern_linear.h
index 697d85f..83090cb 100644
--- a/include/tadah/models/functions/kernels/kern_linear.h
+++ b/include/tadah/models/functions/kernels/kern_linear.h
@@ -18,21 +18,21 @@ class Kern_Linear : public virtual Kern_Base {
public:
Kern_Linear ();
Kern_Linear (const Config &c);
- std::string get_label() const;
+ std::string get_label() const override;
/**
* Label used for this class
*/
std::string label = "Kern_Linear";
- double operator() (const aed_type2& b, const aed_type2& af) const;
- aed_type2 derivative(const aed_type2& b, const aed_type2& ) const;
- double prime(const aed_type2& b, const aed_type2& af, const aed_type2& ff) const;
- void set_basis(const Matrix ) {}
+ double operator() (const aed_type2& b, const aed_type2& af) const override;
+ aed_type2 derivative(const aed_type2& b, const aed_type2& ) const override;
+ double prime(const aed_type2& b, const aed_type2& af, const aed_type2& ff) const override;
+ void set_basis(const Matrix ) override {}
- double epredict(const t_type &weights, const aed_type2& aed) const;
+ double epredict(const t_type &weights, const aed_type2& aed) const override;
double fpredict(const t_type &weights, const fd_type &fdij,
- const aed_type2& aedi, const size_t k) const;
+ const aed_type2& aedi, const size_t k) const override;
force_type fpredict(const t_type &weights, const fd_type &fdij,
- const aed_type2& aedi) const;
+ const aed_type2& aedi) const override;
};
#endif
diff --git a/include/tadah/models/functions/kernels/kern_lq.h b/include/tadah/models/functions/kernels/kern_lq.h
index 7dbfb7e..126da98 100644
--- a/include/tadah/models/functions/kernels/kern_lq.h
+++ b/include/tadah/models/functions/kernels/kern_lq.h
@@ -24,10 +24,10 @@ class Kern_LQ : public virtual Kern_Base {
* Label used for this class
*/
std::string label = "Kern_LQ";
- double operator() (const aed_type2& b, const aed_type2& af) const;
- aed_type2 derivative(const aed_type2& b, const aed_type2& af) const;
- double prime(const aed_type2& b, const aed_type2& af, const aed_type2& ff) const;
- std::string get_label() const;
+ double operator() (const aed_type2& b, const aed_type2& af) const override;
+ aed_type2 derivative(const aed_type2& b, const aed_type2& af) const override;
+ double prime(const aed_type2& b, const aed_type2& af, const aed_type2& ff) const override;
+ std::string get_label() const override;
};
#endif
diff --git a/include/tadah/models/functions/kernels/kern_polynomial.h b/include/tadah/models/functions/kernels/kern_polynomial.h
index 2467249..cc105ab 100644
--- a/include/tadah/models/functions/kernels/kern_polynomial.h
+++ b/include/tadah/models/functions/kernels/kern_polynomial.h
@@ -27,10 +27,10 @@ class Kern_Polynomial : public virtual Kern_Base {
* Label used for this class
*/
std::string label = "Kern_Polynomial";
- std::string get_label() const;
- double operator() (const aed_type2& b, const aed_type2& af) const;
- aed_type2 derivative(const aed_type2& b, const aed_type2& af) const;
- double prime(const aed_type2& b, const aed_type2& af, const aed_type2& ff) const;
+ std::string get_label() const override;
+ double operator() (const aed_type2& b, const aed_type2& af) const override;
+ aed_type2 derivative(const aed_type2& b, const aed_type2& af) const override;
+ double prime(const aed_type2& b, const aed_type2& af, const aed_type2& ff) const override;
};
#endif
diff --git a/include/tadah/models/functions/kernels/kern_quadratic.h b/include/tadah/models/functions/kernels/kern_quadratic.h
index 187c3e8..150efa1 100644
--- a/include/tadah/models/functions/kernels/kern_quadratic.h
+++ b/include/tadah/models/functions/kernels/kern_quadratic.h
@@ -23,10 +23,10 @@ class Kern_Quadratic : public virtual Kern_Base {
* Label used for this class
*/
std::string label = "Kern_Quadratic";
- double operator() (const aed_type2& b, const aed_type2& af) const;
- aed_type2 derivative(const aed_type2& b, const aed_type2& af) const;
- double prime(const aed_type2& b, const aed_type2& af, const aed_type2& ff) const;
- std::string get_label() const;
+ double operator() (const aed_type2& b, const aed_type2& af) const override;
+ aed_type2 derivative(const aed_type2& b, const aed_type2& af) const override;
+ double prime(const aed_type2& b, const aed_type2& af, const aed_type2& ff) const override;
+ std::string get_label() const override;
};
#endif
diff --git a/include/tadah/models/functions/kernels/kern_rbf.h b/include/tadah/models/functions/kernels/kern_rbf.h
index 340d457..b746bd3 100644
--- a/include/tadah/models/functions/kernels/kern_rbf.h
+++ b/include/tadah/models/functions/kernels/kern_rbf.h
@@ -25,10 +25,10 @@ class Kern_RBF : public virtual Kern_Base {
Kern_RBF ();
Kern_RBF (const Config &c);
std::string label = "Kern_RBF";
- double operator() (const aed_type2& b, const aed_type2& af) const;
- aed_type2 derivative(const aed_type2& b, const aed_type2& af) const;
- double prime(const aed_type2& b, const aed_type2& af, const aed_type2& ff) const;
- std::string get_label() const;
+ double operator() (const aed_type2& b, const aed_type2& af) const override;
+ aed_type2 derivative(const aed_type2& b, const aed_type2& af) const override;
+ double prime(const aed_type2& b, const aed_type2& af, const aed_type2& ff) const override;
+ std::string get_label() const override;
private:
double gamma;
diff --git a/include/tadah/models/functions/kernels/kern_sigmoid.h b/include/tadah/models/functions/kernels/kern_sigmoid.h
index 7f9c0f6..072f208 100644
--- a/include/tadah/models/functions/kernels/kern_sigmoid.h
+++ b/include/tadah/models/functions/kernels/kern_sigmoid.h
@@ -26,10 +26,10 @@ class Kern_Sigmoid : public virtual Kern_Base {
Kern_Sigmoid ();
Kern_Sigmoid (const Config &c);
std::string label = "Kern_Sigmoid";
- double operator() (const aed_type2& b, const aed_type2& af) const;
- aed_type2 derivative(const aed_type2& b, const aed_type2& af) const;
- double prime(const aed_type2& b, const aed_type2& af, const aed_type2& ff) const;
- std::string get_label() const;
+ double operator() (const aed_type2& b, const aed_type2& af) const override;
+ aed_type2 derivative(const aed_type2& b, const aed_type2& af) const override;
+ double prime(const aed_type2& b, const aed_type2& af, const aed_type2& ff) const override;
+ std::string get_label() const override;
};
#endif
diff --git a/src/bf_base.cpp b/src/bf_base.cpp
index 043999f..67b6d57 100644
--- a/src/bf_base.cpp
+++ b/src/bf_base.cpp
@@ -1,2 +1,4 @@
#include <tadah/models/functions/basis_functions/bf_base.h>
+BF_Base::BF_Base(const Config &c): Function_Base(c) {}
+BF_Base::BF_Base() {}
BF_Base::~BF_Base() {}
diff --git a/src/bf_linear.cpp b/src/bf_linear.cpp
index 50a612b..b9e73ce 100644
--- a/src/bf_linear.cpp
+++ b/src/bf_linear.cpp
@@ -1,7 +1,7 @@
#include <tadah/models/functions/basis_functions/bf_linear.h>
BF_Linear::BF_Linear() {}
-BF_Linear::BF_Linear(const Config &c): Function_Base(c) {}
+BF_Linear::BF_Linear(const Config &c): BF_Base(c) {}
std::string BF_Linear::get_label() const {
return label;
}
diff --git a/src/bf_polynomial2.cpp b/src/bf_polynomial2.cpp
index 8d6e6fc..387e3f1 100644
--- a/src/bf_polynomial2.cpp
+++ b/src/bf_polynomial2.cpp
@@ -1,8 +1,7 @@
#include <tadah/models/functions/basis_functions/bf_polynomial2.h>
-
BF_Polynomial2::BF_Polynomial2() {}
-BF_Polynomial2::BF_Polynomial2(const Config &c): Function_Base(c)
+BF_Polynomial2::BF_Polynomial2(const Config &c): BF_Base(c)
{}
std::string BF_Polynomial2::get_label() const
{
diff --git a/src/function_base.cpp b/src/function_base.cpp
index 8e80b84..748af71 100644
--- a/src/function_base.cpp
+++ b/src/function_base.cpp
@@ -1,2 +1,17 @@
#include <tadah/models/functions/function_base.h>
+Function_Base::Function_Base(): verbose(0) {
+}
+Function_Base::Function_Base(const Config &c) {
+ verbose = (c.exist("VERBOSE")) ? c.get<int>("VERBOSE") : 0;
+}
+void Function_Base::set_verbose(int v) { verbose=v; }
+int Function_Base::get_verbose() { return verbose; }
+
+Function_Base::~Function_Base() {};
+
+double Function_Base::operator() (const aed_type2& , const aed_type2& ) const {std::cout << "FB" <<std::endl; return 0.0; };
+aed_type2 Function_Base::derivative(const aed_type2& , const aed_type2& ) const { return aed_type2(); };
+double Function_Base::prime(const aed_type2& , const aed_type2& ,
+ const aed_type2& ) const { return 0.0; }
+void Function_Base::set_basis(const Matrix ) {};
diff --git a/src/kern_base.cpp b/src/kern_base.cpp
index 557cfd1..105de45 100644
--- a/src/kern_base.cpp
+++ b/src/kern_base.cpp
@@ -1,5 +1,7 @@
#include <tadah/models/functions/kernels/kern_base.h>
+Kern_Base::Kern_Base() {}
+Kern_Base::Kern_Base(const Config &c): Function_Base(c) {}
Kern_Base::~Kern_Base() {}
void Kern_Base::set_basis(const Matrix b)
{
diff --git a/src/kern_linear.cpp b/src/kern_linear.cpp
index 52e6ee0..ef72038 100644
--- a/src/kern_linear.cpp
+++ b/src/kern_linear.cpp
@@ -2,7 +2,7 @@
Kern_Linear::Kern_Linear() {}
Kern_Linear::Kern_Linear (const Config &c):
- Function_Base(c)
+ Kern_Base(c)
{}
double Kern_Linear::operator() (const aed_type2& b, const aed_type2& af) const
{
diff --git a/src/kern_lq.cpp b/src/kern_lq.cpp
index 4a4733d..7bb370a 100644
--- a/src/kern_lq.cpp
+++ b/src/kern_lq.cpp
@@ -2,7 +2,7 @@
Kern_LQ::Kern_LQ () {}
Kern_LQ::Kern_LQ (const Config &c):
- Function_Base(c)
+ Kern_Base(c)
{
if (get_verbose()) std::cout << std::endl << label << std::endl;
read_basis_from_config(c,basis);
diff --git a/src/kern_polynomial.cpp b/src/kern_polynomial.cpp
index cdc3a62..84a615b 100644
--- a/src/kern_polynomial.cpp
+++ b/src/kern_polynomial.cpp
@@ -2,7 +2,7 @@
Kern_Polynomial::Kern_Polynomial () {}
Kern_Polynomial::Kern_Polynomial (const Config &config):
- Function_Base(config),
+ Kern_Base(config),
d(config.get<int>("MPARAMS",0)),
gamma(config.get<double>("MPARAMS",1)),
c(config.get<double>("MPARAMS",2))
diff --git a/src/kern_quadratic.cpp b/src/kern_quadratic.cpp
index 1f19615..3852a96 100644
--- a/src/kern_quadratic.cpp
+++ b/src/kern_quadratic.cpp
@@ -2,7 +2,7 @@
Kern_Quadratic::Kern_Quadratic () {}
Kern_Quadratic::Kern_Quadratic (const Config &c):
- Function_Base(c)
+ Kern_Base(c)
{
if (get_verbose()) std::cout << std::endl << label << std::endl;
diff --git a/src/kern_rbf.cpp b/src/kern_rbf.cpp
index f8fb513..9a374ac 100644
--- a/src/kern_rbf.cpp
+++ b/src/kern_rbf.cpp
@@ -2,7 +2,7 @@
Kern_RBF::Kern_RBF () {}
Kern_RBF::Kern_RBF (const Config &c):
- Function_Base(c),
+ Kern_Base(c),
sigma(c.get<double>("MPARAMS")),
gamma(1.0/(2.0*sigma*sigma))
{
diff --git a/src/kern_sigmoid.cpp b/src/kern_sigmoid.cpp
index b3fbd49..1586030 100644
--- a/src/kern_sigmoid.cpp
+++ b/src/kern_sigmoid.cpp
@@ -2,7 +2,7 @@
Kern_Sigmoid::Kern_Sigmoid () {}
Kern_Sigmoid::Kern_Sigmoid (const Config &config):
- Function_Base(config),
+ Kern_Base(config),
gamma(config.get<double>("MPARAMS",0)),
c(config.get<double>("MPARAMS",1))
{
--
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