From af2c80e437d3947dc16b772e8daac67b9653b417 Mon Sep 17 00:00:00 2001
From: Marcin Kirsz <mkirsz@ed.ac.uk>
Date: Thu, 27 Feb 2025 17:23:53 +0000
Subject: [PATCH] WiP
---
include/tadah/core/aed_type.h | 4 +
include/tadah/core/aeds_type.h | 4 +
include/tadah/core/config.h | 142 ++++++++++++++-----
include/tadah/core/core_types.h | 4 +
include/tadah/core/element.h | 7 +-
include/tadah/core/fd_type.h | 4 +
include/tadah/core/lapack.h | 4 +
include/tadah/core/maths.h | 4 +
include/tadah/core/normaliser_core.h | 5 +
include/tadah/core/periodic_table.h | 4 +
include/tadah/core/registry.h | 6 +-
include/tadah/core/utils.h | 4 +
include/tadah/core/vec3d.h | 5 +
include/tadah/core/vec3d_math_inl.h | 4 +
include/tadah/core/vec3d_soa_const_view.h | 5 +
include/tadah/core/vec3d_soa_view.h | 4 +
include/tadah/core/vec3d_soa_view_math_inl.h | 4 +
include/tadah/core/vec3dview.h | 4 +
include/tadah/core/vec3dview_math_inl.h | 4 +
src/aed_type.cpp | 5 +
src/aeds_type.cpp | 4 +
src/config.cpp | 5 +
src/element.cpp | 23 +--
src/fd_type.cpp | 4 +
src/lapack.cpp | 6 +
src/maths.cpp | 4 +
src/normaliser_core.cpp | 5 +
src/periodic_table.cpp | 5 +
src/utils.cpp | 5 +
29 files changed, 245 insertions(+), 43 deletions(-)
diff --git a/include/tadah/core/aed_type.h b/include/tadah/core/aed_type.h
index 9b05b7a..9b74a71 100644
--- a/include/tadah/core/aed_type.h
+++ b/include/tadah/core/aed_type.h
@@ -9,6 +9,9 @@
#include <iostream>
#include <chrono>
+namespace tadah {
+namespace core {
+
class aed_type {
double *data_ = nullptr;
size_t size_ = 0;
@@ -276,5 +279,6 @@ inline std::ostream& operator<<(std::ostream& os, const aed_type& v) {
// }
// };
+}}
#endif // AED_TYPE2_H
diff --git a/include/tadah/core/aeds_type.h b/include/tadah/core/aeds_type.h
index 37f5e99..ac22d3f 100644
--- a/include/tadah/core/aeds_type.h
+++ b/include/tadah/core/aeds_type.h
@@ -7,6 +7,9 @@
#include <cstring>
#include <iostream>
+namespace tadah {
+namespace core {
+
class aeds_type2 {
/* Column major order
*
@@ -69,4 +72,5 @@ public:
friend std::ostream& operator<<(std::ostream& os, const aeds_type2& v);
};
+}}
#endif // AEDS_TYPE2_H
diff --git a/include/tadah/core/config.h b/include/tadah/core/config.h
index 25eacc6..778689b 100644
--- a/include/tadah/core/config.h
+++ b/include/tadah/core/config.h
@@ -17,6 +17,10 @@
CMRC_DECLARE(CORE);
+namespace tadah {
+namespace core {
+
+
/** \brief A dictionary for key - value pairs.
*
* This dictionary object must be used in the workflow
@@ -66,37 +70,111 @@ public:
*/
const std::vector<std::string>& operator()(const std::string key) const;
- /** \brief Fill array with the values from the key.
- *
- * The array must be initialised to appropriate size.
- *
- * Usage example:
- *
- * \code{.cpp}
- * # Create new config object and read config file
- * Config config("config_file");
- *
- * # Fill array with config values of type double
- * std::vector<double> vd(10);
- * c.get<std::vector<double>>("RCUT2B", vd);
- * \endcode
- *
- * \tparam T indexable array
- */
- template <typename T>
- void get(const std::string key, T & value) const {
- if (c.count(to_upper(key))==0)
- throw std::runtime_error(knf+key);
- int i=0;
- try {
- for (auto v : c.at(to_upper(key))) {
- std::istringstream iss(v);
- iss >> value[i++];
- }
- } catch (...) {
- throw std::runtime_error("Config: Failed getting reading/writing to an array "+key);
+ /**
+ * @brief A C++11-friendly type trait to detect if T has a .size() method.
+ *
+ * - Primary template: yields false if T does not have a .size() method.
+ * - Partial specialization: yields true if calling T::size() is valid.
+ */
+ template<typename, typename = void>
+ struct has_size : std::false_type {};
+
+ // This partial specialization is chosen if (void)std::declval<U>().size() is valid.
+ template<typename U>
+ struct has_size<U, typename std::enable_if<
+ std::is_same<
+ decltype(std::declval<U>().size()),
+ decltype(std::declval<U>().size())
+ >::value
+ >::type> : std::true_type {};
+
+ /**
+ * @brief Helper function that checks size at runtime (only if T has .size()).
+ *
+ * SFINAE: This overload is *only* compiled if T has a .size() method.
+ *
+ * @throw std::runtime_error if the container is too small.
+ */
+ template<typename T>
+ typename std::enable_if<has_size<T>::value, void>::type
+ check_size_if_applicable(const T &arr, std::size_t required, const std::string &key) const
+ {
+ if (arr.size() < required) {
+ throw std::runtime_error("Config array too small for key: " + key);
+ }
+ }
+
+ /**
+ * @brief Overload that does nothing if T *does not* have .size().
+ *
+ * SFINAE: This is only compiled for types that have no .size() method.
+ */
+ template<typename T>
+ typename std::enable_if<!has_size<T>::value, void>::type
+ check_size_if_applicable(const T&, std::size_t, const std::string&) const
+ {
+ // Do nothing: for types like raw pointers.
+ }
+
+ /**
+ * @brief Fill an existing array-like type @p arr with config values under @p key.
+ *
+ * - If @p arr has .size(), a check verifies @p arr can hold all config values.
+ * - If @p arr does not have .size() (e.g., raw pointer), no check is performed.
+ * - If parsing fails or key is missing, a runtime error is thrown.
+ *
+ * ### Usage example
+ * \code{.cpp}
+ * // Assume a config with a key "MyKey" of 4 numeric values.
+ * Config cfg("config_file");
+ *
+ * // 1) Use a container with .size(), e.g. std::vector<double>:
+ * std::vector<double> vec(5); // capacity 5
+ * cfg.get("MyKey", vec); // Will check vec.size() >= 4
+ *
+ * // 2) Use a raw pointer (no .size()):
+ * double arr[10];
+ * cfg.get("MyKey", arr); // No size check performed. Caller must ensure arr is big enough.
+ * \endcode
+ *
+ * @tparam T container or pointer type that supports operator[].
+ * @param key Name of the config key (case-insensitive).
+ * @param arr Destination where parsed values are stored.
+ * @throws std::runtime_error on key-not-found, array-too-small, or parse failure.
+ */
+ template <typename T>
+ void get(const std::string &key, T &arr) const {
+ // Convert to uppercase for case-insensitive retrieval.
+ const auto upperKey = to_upper(key);
+
+ // Check presence of the key in our config container.
+ const std::size_t numValues = c.count(upperKey);
+ if (numValues == 0) {
+ throw std::runtime_error(knf + key);
+ }
+
+ // If T has .size(), do a runtime size check. If not, do nothing.
+ check_size_if_applicable(arr, numValues, key);
+
+ try {
+ // For demonstration, assume c.at(...) returns a list of strings to be parsed.
+ const auto &values = c.at(upperKey);
+ for (std::size_t i = 0; i < values.size(); ++i) {
+ std::istringstream iss(values[i]);
+ iss >> arr[i]; // Works for both pointer indexing and container operator[]
+ if (iss.fail()) {
+ throw std::runtime_error(
+ "Config: Conversion failed for key: " + key +
+ " at value: '" + values[i] + "'"
+ );
+ }
+ }
+ } catch (...) {
+ throw std::runtime_error(
+ "Config: Failed reading/writing to an array [" + key + "]"
+ );
+ }
}
- }
/** \brief Return the first value for the key.
*
@@ -316,6 +394,6 @@ private:
const static std::string knf;//="Key not found: ";
};
-
-
+}
+}
#endif
diff --git a/include/tadah/core/core_types.h b/include/tadah/core/core_types.h
index a98a2d2..25061f0 100644
--- a/include/tadah/core/core_types.h
+++ b/include/tadah/core/core_types.h
@@ -8,6 +8,9 @@
#include <vector>
+namespace tadah {
+namespace core {
+
typedef Vec3d force_type;
typedef aed_type t_type;
typedef aed_type rho_type;
@@ -35,4 +38,5 @@ class mat {
#endif
/////////////////////////////////////////
+}}
#endif
diff --git a/include/tadah/core/element.h b/include/tadah/core/element.h
index cc37c4e..f1e910e 100644
--- a/include/tadah/core/element.h
+++ b/include/tadah/core/element.h
@@ -5,6 +5,9 @@
#include <functional>
#include <string>
+namespace tadah {
+namespace core {
+
struct Element {
private:
void check(const std::string &symbol, const int Z);
@@ -29,9 +32,11 @@ struct Element {
static int toAtomicNumber(const std::string &symbol);
static std::string toSymbol(int Z);
};
+}}
+
namespace std {
template <>
- struct hash<Element>;
+ struct hash<tadah::core::Element>;
}
#endif
diff --git a/include/tadah/core/fd_type.h b/include/tadah/core/fd_type.h
index 4b665d6..5211cf2 100644
--- a/include/tadah/core/fd_type.h
+++ b/include/tadah/core/fd_type.h
@@ -12,6 +12,9 @@
#include <cstring>
#include <limits>
+namespace tadah {
+namespace core {
+
class fd_type {
size_t rows_ = 0;
double* data_ = nullptr;
@@ -84,4 +87,5 @@ public:
bool operator==(const fd_type& v1) const;
};
+}}
#endif // FD_TYPE_H
diff --git a/include/tadah/core/lapack.h b/include/tadah/core/lapack.h
index 3a92dea..99945b8 100644
--- a/include/tadah/core/lapack.h
+++ b/include/tadah/core/lapack.h
@@ -3,6 +3,9 @@
#include <tadah/core/maths.h>
+namespace tadah {
+namespace core {
+
extern "C" {
/**
@@ -213,4 +216,5 @@ double norm_X(Matrix &A, char norm='1');
aed_type solve_posv(Matrix &A, aed_type /*&*/T, char uplo='U');
double condition_number(Matrix &A, char uplo='U');
+}}
#endif
diff --git a/include/tadah/core/maths.h b/include/tadah/core/maths.h
index eec93ed..b890c0a 100644
--- a/include/tadah/core/maths.h
+++ b/include/tadah/core/maths.h
@@ -17,6 +17,9 @@
#include <array>
+namespace tadah {
+namespace core {
+
template <typename D>
class Matrix_Base {
// column-major order
@@ -440,4 +443,5 @@ public:
typedef Matrix3d_T<> Matrix3d;
+}}
#endif
diff --git a/include/tadah/core/normaliser_core.h b/include/tadah/core/normaliser_core.h
index 621a26c..5232ab5 100644
--- a/include/tadah/core/normaliser_core.h
+++ b/include/tadah/core/normaliser_core.h
@@ -4,6 +4,9 @@
#include <tadah/core/config.h>
#include <tadah/core/core_types.h>
+namespace tadah {
+namespace core {
+
// We do calculate and store st. dev. and mean
// for the first column of Phi matrix
// for linear kernel, first column are 1s
@@ -26,4 +29,6 @@ class Normaliser_Core {
void normalise(fd_type &fd);
void normalise(fd_type &fd, size_t k);
};
+
+}}
#endif
diff --git a/include/tadah/core/periodic_table.h b/include/tadah/core/periodic_table.h
index acc199b..672d386 100644
--- a/include/tadah/core/periodic_table.h
+++ b/include/tadah/core/periodic_table.h
@@ -5,6 +5,9 @@
#include <map>
#include <tadah/core/element.h>
+namespace tadah {
+namespace core {
+
struct PeriodicTable {
static std::map<std::string, Element> symbol;
static std::map<std::string, Element> name;
@@ -29,4 +32,5 @@ struct PeriodicTable {
static void init_masses();
};
+}}
#endif
diff --git a/include/tadah/core/registry.h b/include/tadah/core/registry.h
index a39e9d3..f0afb3c 100644
--- a/include/tadah/core/registry.h
+++ b/include/tadah/core/registry.h
@@ -8,10 +8,12 @@
#include <sstream>
#include <iostream>
+namespace tadah {
+namespace core {
+
template<typename T, typename... Args>
using Factory = std::function<T*(Args&...)>;
-namespace CONFIG {
template<typename Base, typename... Args>
struct Registry {
@@ -41,6 +43,6 @@ Base* factory(const std::string& type, Args&... args) {
throw std::runtime_error(oss.str());
}
-}
+}}
#endif
diff --git a/include/tadah/core/utils.h b/include/tadah/core/utils.h
index 2516067..213a363 100644
--- a/include/tadah/core/utils.h
+++ b/include/tadah/core/utils.h
@@ -12,6 +12,8 @@
#include <tuple>
#include <cstddef>
+namespace tadah {
+namespace core {
/** Vector printing to streams */
template <typename T>
@@ -314,4 +316,6 @@ std::vector<histogram_bin> generate_2d_histogram(
const std::vector<std::pair<double,double>>& data_2d,
int x_bins,
int y_bins);
+
+}}
#endif
diff --git a/include/tadah/core/vec3d.h b/include/tadah/core/vec3d.h
index 0a7a0a7..2e38a4c 100644
--- a/include/tadah/core/vec3d.h
+++ b/include/tadah/core/vec3d.h
@@ -7,6 +7,9 @@
#include <string>
#include <limits>
+namespace tadah {
+namespace core {
+
class Vec3d {
public:
double v[3] = { };
@@ -138,4 +141,6 @@ public:
// We'll declare multiply by Matrix3d in separate file "vec3d_math_inl.h"
};
+
+}}
#endif
diff --git a/include/tadah/core/vec3d_math_inl.h b/include/tadah/core/vec3d_math_inl.h
index b0e70c0..66a91ae 100644
--- a/include/tadah/core/vec3d_math_inl.h
+++ b/include/tadah/core/vec3d_math_inl.h
@@ -5,6 +5,9 @@
#include <tadah/core/vec3d.h>
#include <tadah/core/maths.h>
+namespace tadah {
+namespace core {
+
/**
* @brief Inline method: multiply in-place by a 3x3 matrix => x = M*x
*
@@ -24,5 +27,6 @@ inline Vec3d& transformBy(Vec3d &v, const Matrix3d &M)
return v;
}
+}}
#endif // VEC3D_MATH_INL_H
diff --git a/include/tadah/core/vec3d_soa_const_view.h b/include/tadah/core/vec3d_soa_const_view.h
index bb3fe2b..a55d1a6 100644
--- a/include/tadah/core/vec3d_soa_const_view.h
+++ b/include/tadah/core/vec3d_soa_const_view.h
@@ -8,6 +8,9 @@
#include <iostream>
#include <tadah/core/vec3d.h> // for returning Vec3d in operations (e.g. cross, etc.)
+namespace tadah {
+namespace core {
+
/**
* @class Vec3dSoAConstView
* @brief A read-only "view" into SoA data for x,y,z.
@@ -148,5 +151,7 @@ public:
}
};
+}}
+
#endif // VEC3D_SOA_CONST_VIEW_H
diff --git a/include/tadah/core/vec3d_soa_view.h b/include/tadah/core/vec3d_soa_view.h
index b8f530b..4c25f6b 100644
--- a/include/tadah/core/vec3d_soa_view.h
+++ b/include/tadah/core/vec3d_soa_view.h
@@ -8,6 +8,9 @@
#include <iostream>
#include <tadah/core/vec3d.h> // so we can return Vec3d in operations (e.g. operator+, cross, etc.)
+namespace tadah {
+namespace core {
+
/**
* @class Vec3dSoAView
* @brief A non-owning "view" into SoA data for x,y,z.
@@ -179,5 +182,6 @@ public:
}
};
+}}
#endif // VEC3D_SOA_VIEW_H
diff --git a/include/tadah/core/vec3d_soa_view_math_inl.h b/include/tadah/core/vec3d_soa_view_math_inl.h
index f010117..7f1ced5 100644
--- a/include/tadah/core/vec3d_soa_view_math_inl.h
+++ b/include/tadah/core/vec3d_soa_view_math_inl.h
@@ -5,6 +5,9 @@
#include <tadah/core/vec3d_soa_view.h>
#include <tadah/core/maths.h>
+namespace tadah {
+namespace core {
+
/**
* @brief Inline function to multiply Vec3dSoAView by a 3x3 matrix in place:
* x => M*x
@@ -26,5 +29,6 @@ inline Vec3dSoAView& transformBy(Vec3dSoAView &view, const Matrix3d &M)
return view;
}
+}}
#endif // VEC3D_SOA_VIEW_MATH_INL_H
diff --git a/include/tadah/core/vec3dview.h b/include/tadah/core/vec3dview.h
index 50b2c54..fa057a8 100644
--- a/include/tadah/core/vec3dview.h
+++ b/include/tadah/core/vec3dview.h
@@ -8,6 +8,9 @@
#include <tadah/core/vec3d.h> // so we can return Vec3d from some operations
+namespace tadah {
+namespace core {
+
/**
* @class Vec3dView
* @brief A non-owning "view" of 3 doubles in memory, providing
@@ -194,5 +197,6 @@ public:
}
};
+}}
#endif // VEC3DVIEW_H
diff --git a/include/tadah/core/vec3dview_math_inl.h b/include/tadah/core/vec3dview_math_inl.h
index 4e5fe19..e817e29 100644
--- a/include/tadah/core/vec3dview_math_inl.h
+++ b/include/tadah/core/vec3dview_math_inl.h
@@ -5,6 +5,9 @@
#include <tadah/core/vec3dview.h>
#include <tadah/core/maths.h>
+namespace tadah {
+namespace core {
+
/**
* @brief Inline multiply: x = M*x for a pointer-based Vec3dView
*/
@@ -21,5 +24,6 @@ inline Vec3dView& transformBy(Vec3dView &v, const Matrix3d &M)
return v;
}
+}}
#endif // VEC3DVIEW_MATH_INL_H
diff --git a/src/aed_type.cpp b/src/aed_type.cpp
index 7bf86d7..fb843d0 100644
--- a/src/aed_type.cpp
+++ b/src/aed_type.cpp
@@ -1,5 +1,8 @@
#include <tadah/core/aed_type.h>
+namespace tadah {
+namespace core {
+
aed_type& aed_type::operator=(const aed_type& other) {
if (this != &other) {
if (allocated_) {
@@ -89,3 +92,5 @@ void aed_type::random(int seed, double lower, double upper) {
(*this)[i] = unif(engine);
}
}
+
+}}
diff --git a/src/aeds_type.cpp b/src/aeds_type.cpp
index 70b91c4..6ea8c6f 100644
--- a/src/aeds_type.cpp
+++ b/src/aeds_type.cpp
@@ -1,6 +1,9 @@
#include <tadah/core/aeds_type.h>
#include <tadah/core/aed_type.h>
+namespace tadah {
+namespace core {
+
aeds_type2::aeds_type2() {}
aeds_type2::aeds_type2(size_t dim, size_t natoms)
@@ -115,4 +118,5 @@ std::ostream& operator<<(std::ostream& os, const aeds_type2& v) {
}
return os;
}
+}}
diff --git a/src/config.cpp b/src/config.cpp
index 345e741..560e1c7 100644
--- a/src/config.cpp
+++ b/src/config.cpp
@@ -1,6 +1,9 @@
#include <tadah/core/config.h>
#include <sstream>
+namespace tadah {
+namespace core {
+
Config::Config()
{
read_tadah_configuration();
@@ -343,3 +346,5 @@ void Config::deserialize(const std::vector<char>& buffer) {
}
+}
+}
diff --git a/src/element.cpp b/src/element.cpp
index 4742236..1c6e90d 100644
--- a/src/element.cpp
+++ b/src/element.cpp
@@ -1,6 +1,9 @@
#include <tadah/core/element.h>
#include <tadah/core/periodic_table.h>
+namespace tadah {
+namespace core {
+
void Element::check(const std::string &symbol, const int Z) {
if (symbol.size() > 2)
throw std::runtime_error("Wrong symbol: "+symbol);
@@ -34,18 +37,22 @@ bool Element::operator<(const Element& other) const {
bool Element::operator>(const Element& other) const {
return this->Z > other.Z;
}
+int Element::toAtomicNumber(const std::string &symbol) {
+ return PeriodicTable::find_by_symbol(symbol).Z;
+}
+std::string Element::toSymbol(int Z) {
+ return PeriodicTable::find_by_Z(Z).symbol;
+}
+
+}}
+
namespace std {
template <>
- struct hash<Element> {
- size_t operator()(const Element &e) const {
+ struct hash<tadah::core::Element> {
+ size_t operator()(const tadah::core::Element &e) const {
return hash<int>()(e.Z);
}
};
}
-int Element::toAtomicNumber(const std::string &symbol) {
- return PeriodicTable::find_by_symbol(symbol).Z;
-}
-std::string Element::toSymbol(int Z) {
- return PeriodicTable::find_by_Z(Z).symbol;
-}
+
diff --git a/src/fd_type.cpp b/src/fd_type.cpp
index 892ee88..a478261 100644
--- a/src/fd_type.cpp
+++ b/src/fd_type.cpp
@@ -1,6 +1,9 @@
#include <tadah/core/fd_type.h>
#include <tadah/core/aed_type.h>
+namespace tadah {
+namespace core {
+
fd_type::fd_type(const fd_type& other) : rows_(other.rows_) {
data_ = static_cast<double*>(malloc(3 * rows_ * sizeof(double)));
@@ -127,3 +130,4 @@ bool fd_type::operator==(const fd_type& v1) const {
return isApprox(v1, EPS);
}
+}}
diff --git a/src/lapack.cpp b/src/lapack.cpp
index 916256e..0ad89dc 100644
--- a/src/lapack.cpp
+++ b/src/lapack.cpp
@@ -1,4 +1,8 @@
#include <tadah/core/lapack.h>
+
+namespace tadah {
+namespace core {
+
// Some usefull operations on vectors and matrices
aed_type T_dgemv(Matrix &mat, aed_type &vec, char trans) {
int m = mat.rows();
@@ -75,3 +79,5 @@ double condition_number(Matrix &A, char uplo) {
return 1/rcond;
}
+
+}}
diff --git a/src/maths.cpp b/src/maths.cpp
index 8026e45..0f7681e 100644
--- a/src/maths.cpp
+++ b/src/maths.cpp
@@ -1 +1,5 @@
#include <tadah/core/maths.h>
+
+namespace tadah {
+namespace core {
+}}
diff --git a/src/normaliser_core.cpp b/src/normaliser_core.cpp
index f3f9b0c..824d54c 100644
--- a/src/normaliser_core.cpp
+++ b/src/normaliser_core.cpp
@@ -1,5 +1,8 @@
#include <tadah/core/normaliser_core.h>
+namespace tadah {
+namespace core {
+
Normaliser_Core::Normaliser_Core () {}
Normaliser_Core::Normaliser_Core (Config &c):
bias(c.get<bool>("BIAS")),
@@ -65,3 +68,5 @@ void Normaliser_Core::normalise(fd_type &fd, size_t k) {
}
}
}
+
+}}
diff --git a/src/periodic_table.cpp b/src/periodic_table.cpp
index 0488631..40a8f00 100644
--- a/src/periodic_table.cpp
+++ b/src/periodic_table.cpp
@@ -1,5 +1,8 @@
#include <tadah/core/periodic_table.h>
+namespace tadah {
+namespace core {
+
// Definition of static members
std::map<std::string, Element> PeriodicTable::symbol;
std::map<std::string, Element> PeriodicTable::name;
@@ -351,3 +354,5 @@ void PeriodicTable::init_masses() {
masses[117] = 294.000; // Tennessine
masses[118] = 294.000; // Oganesson
}
+
+}}
diff --git a/src/utils.cpp b/src/utils.cpp
index 7714325..c306192 100644
--- a/src/utils.cpp
+++ b/src/utils.cpp
@@ -8,6 +8,9 @@
#include <cmath>
#include <limits>
+namespace tadah {
+namespace core {
+
v_type logspace(double start, double stop, int num, double base) {
if (start==0) {
throw std::runtime_error("log series cannot start at 0\n");
@@ -306,3 +309,5 @@ std::vector<histogram_bin> generate_2d_histogram(
return histogram_bins;
}
+
+}}
--
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