From f311c16c7efe81d1232a097a382b75f92ad27946 Mon Sep 17 00:00:00 2001
From: mkirsz <s1351949@sms.ed.ac.uk>
Date: Wed, 31 Jan 2024 17:47:50 +0000
Subject: [PATCH] Getting rid of Eigen aeds.
---
descriptors/d2/d2_base.cpp | 4 ++--
descriptors/d2/d2_base.h | 8 ++++----
descriptors/d2/d2_blip.cpp | 4 ++--
descriptors/d2/d2_blip.h | 4 ++--
descriptors/d2/d2_bp.cpp | 4 ++--
descriptors/d2/d2_bp.h | 4 ++--
descriptors/d2/d2_dummy.cpp | 4 ++--
descriptors/d2/d2_dummy.h | 4 ++--
descriptors/d2/d2_eam.cpp | 4 ++--
descriptors/d2/d2_eam.h | 4 ++--
descriptors/d2/d2_lj.cpp | 4 ++--
descriptors/d2/d2_lj.h | 4 ++--
descriptors/d2/d2_mie.cpp | 4 ++--
descriptors/d2/d2_mie.h | 4 ++--
descriptors/d3/d3_base.h | 4 ++--
descriptors/d3/d3_dummy.cpp | 4 ++--
descriptors/d3/d3_dummy.h | 4 ++--
descriptors/dm/dm_base.h | 2 +-
descriptors/dm/dm_blip.cpp | 2 +-
descriptors/dm/dm_blip.h | 2 +-
descriptors/dm/dm_dummy.cpp | 2 +-
descriptors/dm/dm_dummy.h | 2 +-
descriptors/dm/dm_ead.cpp | 2 +-
descriptors/dm/dm_ead.h | 2 +-
descriptors/dm/dm_eam.cpp | 2 +-
descriptors/dm/dm_eam.h | 2 +-
descriptors/dm/dm_mEAD.cpp | 2 +-
descriptors/dm/dm_mEAD.h | 2 +-
ekm.h | 4 ++--
functions/basis_functions/bf_base.h | 6 +++---
functions/basis_functions/bf_linear.cpp | 6 +++---
functions/basis_functions/bf_linear.h | 6 +++---
functions/basis_functions/bf_polynomial2.cpp | 10 +++++-----
functions/basis_functions/bf_polynomial2.h | 6 +++---
functions/function_base.h | 16 ++++++++--------
functions/kernels/kern_base.cpp | 14 +++++++-------
functions/kernels/kern_base.h | 18 +++++++++---------
functions/kernels/kern_linear.cpp | 12 ++++++------
functions/kernels/kern_linear.h | 14 +++++++-------
functions/kernels/kern_lq.cpp | 6 +++---
functions/kernels/kern_lq.h | 6 +++---
functions/kernels/kern_polynomial.cpp | 10 +++++-----
functions/kernels/kern_polynomial.h | 6 +++---
functions/kernels/kern_quadratic.cpp | 6 +++---
functions/kernels/kern_quadratic.h | 6 +++---
functions/kernels/kern_rbf.cpp | 10 +++++-----
functions/kernels/kern_rbf.h | 6 +++---
functions/kernels/kern_sigmoid.cpp | 8 ++++----
functions/kernels/kern_sigmoid.h | 6 +++---
m_core.h | 6 +++---
m_krr_core.h | 6 +++---
51 files changed, 144 insertions(+), 144 deletions(-)
diff --git a/descriptors/d2/d2_base.cpp b/descriptors/d2/d2_base.cpp
index 017b0ce..c1b6561 100644
--- a/descriptors/d2/d2_base.cpp
+++ b/descriptors/d2/d2_base.cpp
@@ -4,8 +4,8 @@ void D2_Base::calc_fd_approx(
const double ,
const double ,
const double ,
- aed_rtype aedp,
- aed_rtype aedn,
+ aed_type2& aedp,
+ aed_type2& aedn,
fd_type &fd_ij,
const double h) {
diff --git a/descriptors/d2/d2_base.h b/descriptors/d2/d2_base.h
index 6ff85db..2ca5df4 100644
--- a/descriptors/d2/d2_base.h
+++ b/descriptors/d2/d2_base.h
@@ -20,7 +20,7 @@ class D2_Base: public D_Base {
const double rij,
const double rij_sq,
const double fc_ij,
- aed_rtype aed)=0;
+ aed_type2& aed)=0;
/** \brief Calculate \ref FD
*
@@ -49,8 +49,8 @@ class D2_Base: public D_Base {
const double rij,
const double fcijp,
const double fcijn,
- aed_rtype aedp,
- aed_rtype aedn,
+ aed_type2& aedp,
+ aed_type2& aedn,
fd_type &fd_ij,
const double h);
@@ -60,7 +60,7 @@ class D2_Base: public D_Base {
const double rij_sq,
const double fc_ij,
const double fcp_ij,
- aed_rtype aed,
+ aed_type2& aed,
fd_type &fd_ij)=0;
virtual std::string label()=0;
};
diff --git a/descriptors/d2/d2_blip.cpp b/descriptors/d2/d2_blip.cpp
index 35640da..d8571b1 100644
--- a/descriptors/d2/d2_blip.cpp
+++ b/descriptors/d2/d2_blip.cpp
@@ -35,7 +35,7 @@ void D2_Blip::calc_aed(
const double rij,
const double ,
const double fc_ij,
- aed_rtype aed)
+ aed_type2 &aed)
{
size_t i=fidx;
@@ -62,7 +62,7 @@ void D2_Blip::calc_all(
const double ,
const double fc_ij,
const double fcp_ij,
- aed_rtype aed,
+ aed_type2 &aed,
fd_type &fd_ij)
{
diff --git a/descriptors/d2/d2_blip.h b/descriptors/d2/d2_blip.h
index beb7d76..50a4454 100644
--- a/descriptors/d2/d2_blip.h
+++ b/descriptors/d2/d2_blip.h
@@ -57,7 +57,7 @@ class D2_Blip : public D2_Base {
const double rij,
const double rij_sq,
const double fc_ij,
- aed_rtype aed);
+ aed_type2 &aed);
void calc_dXijdri(
const double rij,
const double rij_sq,
@@ -69,7 +69,7 @@ class D2_Blip : public D2_Base {
const double rij_sq,
const double fc_ij,
const double fcp_ij,
- aed_rtype aed,
+ aed_type2 &aed,
fd_type &fd_ij);
size_t size();
std::string label();
diff --git a/descriptors/d2/d2_bp.cpp b/descriptors/d2/d2_bp.cpp
index abdce9d..9ab3863 100644
--- a/descriptors/d2/d2_bp.cpp
+++ b/descriptors/d2/d2_bp.cpp
@@ -34,7 +34,7 @@ void D2_BP::calc_aed(
const double rij,
const double ,
const double fc_ij,
- aed_rtype aed)
+ aed_type2 &aed)
{
size_t i=fidx;
@@ -60,7 +60,7 @@ void D2_BP::calc_all(
const double ,
const double fc_ij,
const double fcp_ij,
- aed_rtype aed,
+ aed_type2 &aed,
fd_type &fd_ij)
{
diff --git a/descriptors/d2/d2_bp.h b/descriptors/d2/d2_bp.h
index d73e873..26ea63e 100644
--- a/descriptors/d2/d2_bp.h
+++ b/descriptors/d2/d2_bp.h
@@ -38,7 +38,7 @@ class D2_BP : public D2_Base {
const double rij,
const double ,
const double fc_ij,
- aed_rtype aed);
+ aed_type2 &aed);
void calc_dXijdri(
const double rij,
const double ,
@@ -50,7 +50,7 @@ class D2_BP : public D2_Base {
const double ,
const double fc_ij,
const double fcp_ij,
- aed_rtype aed,
+ aed_type2 &aed,
fd_type &fd_ij);
size_t size();
std::string label();
diff --git a/descriptors/d2/d2_dummy.cpp b/descriptors/d2/d2_dummy.cpp
index 4ea73ba..7c0383a 100644
--- a/descriptors/d2/d2_dummy.cpp
+++ b/descriptors/d2/d2_dummy.cpp
@@ -11,7 +11,7 @@ void D2_Dummy::calc_aed(
const double,
const double,
const double,
- aed_rtype ) {}
+ aed_type2 & ) {}
void D2_Dummy::calc_dXijdri(
const double,
const double,
@@ -23,7 +23,7 @@ void D2_Dummy::calc_all(
const double,
const double,
const double,
- aed_rtype ,
+ aed_type2 & ,
fd_type &) {}
size_t D2_Dummy::size() { return s; }
std::string D2_Dummy::label() { return lab; }
diff --git a/descriptors/d2/d2_dummy.h b/descriptors/d2/d2_dummy.h
index 87a73fd..df4e145 100644
--- a/descriptors/d2/d2_dummy.h
+++ b/descriptors/d2/d2_dummy.h
@@ -21,7 +21,7 @@ class D2_Dummy : public D2_Base {
const double,
const double,
const double,
- aed_rtype aed);
+ aed_type2 &aed);
void calc_dXijdri(
const double,
const double,
@@ -33,7 +33,7 @@ class D2_Dummy : public D2_Base {
const double,
const double,
const double,
- aed_rtype aed,
+ aed_type2 &aed,
fd_type &fd_ij);
size_t size();
std::string label();
diff --git a/descriptors/d2/d2_eam.cpp b/descriptors/d2/d2_eam.cpp
index 99bcbf1..47be89a 100644
--- a/descriptors/d2/d2_eam.cpp
+++ b/descriptors/d2/d2_eam.cpp
@@ -40,7 +40,7 @@ void D2_EAM::calc_aed(
const double rij,
const double,
const double,
- aed_rtype aed)
+ aed_type2 &aed)
{
double r = rij;
@@ -83,7 +83,7 @@ void D2_EAM::calc_all(
const double,
const double,
const double,
- aed_rtype aed,
+ aed_type2 &aed,
fd_type &fd_ij)
{
double r = rij;
diff --git a/descriptors/d2/d2_eam.h b/descriptors/d2/d2_eam.h
index 6a8545d..35f9fe1 100644
--- a/descriptors/d2/d2_eam.h
+++ b/descriptors/d2/d2_eam.h
@@ -59,7 +59,7 @@ class D2_EAM : public D2_Base {
double rij,
const double rij_sq,
const double,
- aed_rtype aed);
+ aed_type2 &aed);
void calc_dXijdri(
double rij,
const double rij_sq,
@@ -71,7 +71,7 @@ class D2_EAM : public D2_Base {
const double rij_sq,
const double,
const double,
- aed_rtype aed,
+ aed_type2 &aed,
fd_type &fd_ij);
size_t size();
std::string label();
diff --git a/descriptors/d2/d2_lj.cpp b/descriptors/d2/d2_lj.cpp
index b052348..05eedd6 100644
--- a/descriptors/d2/d2_lj.cpp
+++ b/descriptors/d2/d2_lj.cpp
@@ -14,7 +14,7 @@ void D2_LJ::calc_aed(
const double,
const double rij_sq,
const double fc_ij,
- aed_rtype aed)
+ aed_type2 &aed)
{
double r2_inv = 1.0/rij_sq;
double r6_inv = r2_inv*r2_inv*r2_inv;
@@ -41,7 +41,7 @@ void D2_LJ::calc_all(
const double rij_sq,
const double fc_ij,
const double fcp_ij,
- aed_rtype aed,
+ aed_type2 &aed,
fd_type &fd_ij)
{
double r2_inv = 1.0/rij_sq;
diff --git a/descriptors/d2/d2_lj.h b/descriptors/d2/d2_lj.h
index a1a3f8d..93bce92 100644
--- a/descriptors/d2/d2_lj.h
+++ b/descriptors/d2/d2_lj.h
@@ -39,7 +39,7 @@ class D2_LJ : public D2_Base {
const double,
const double rij_sq,
const double fc_ij,
- aed_rtype aed);
+ aed_type2 &aed);
void calc_dXijdri(
const double rij,
const double rij_sq,
@@ -51,7 +51,7 @@ class D2_LJ : public D2_Base {
const double rij_sq,
const double fc_ij,
const double fcp_ij,
- aed_rtype aed,
+ aed_type2 &aed,
fd_type &fd_ij);
size_t size();
std::string label();
diff --git a/descriptors/d2/d2_mie.cpp b/descriptors/d2/d2_mie.cpp
index d173664..cf43d9f 100644
--- a/descriptors/d2/d2_mie.cpp
+++ b/descriptors/d2/d2_mie.cpp
@@ -25,7 +25,7 @@ void D2_MIE::calc_aed(
const double rij,
const double,
const double fc_ij,
- aed_rtype aed)
+ aed_type2 &aed)
{
double rn_inv = 1.0/pow(rij,n);
double rm_inv = 1.0/pow(rij,m);
@@ -50,7 +50,7 @@ void D2_MIE::calc_all(
const double,
const double fc_ij,
const double fcp_ij,
- aed_rtype aed,
+ aed_type2 &aed,
fd_type &fd_ij)
{
diff --git a/descriptors/d2/d2_mie.h b/descriptors/d2/d2_mie.h
index 054fb22..073e2d7 100644
--- a/descriptors/d2/d2_mie.h
+++ b/descriptors/d2/d2_mie.h
@@ -34,7 +34,7 @@ class D2_MIE : public D2_Base {
const double,
const double rij_sq,
const double fc_ij,
- aed_rtype aed);
+ aed_type2 &aed);
void calc_dXijdri(
const double rij,
const double rij_sq,
@@ -46,7 +46,7 @@ class D2_MIE : public D2_Base {
const double rij_sq,
const double fc_ij,
const double fcp_ij,
- aed_rtype aed,
+ aed_type2 &aed,
fd_type &fd_ij);
size_t size();
std::string label();
diff --git a/descriptors/d3/d3_base.h b/descriptors/d3/d3_base.h
index 281932a..837b247 100644
--- a/descriptors/d3/d3_base.h
+++ b/descriptors/d3/d3_base.h
@@ -13,7 +13,7 @@ class D3_Base: public D_Base {
const double rik,
const double fc_ij,
const double fc_ik,
- aed_rtype aed)=0;
+ aed_type2& aed)=0;
virtual void calc_fd(
const size_t fidx,
const double rij,
@@ -31,7 +31,7 @@ class D3_Base: public D_Base {
const double fc_ik,
const double fcp_ij,
const double fcp_ik,
- aed_rtype aed,
+ aed_type2& aed,
fd_type &fd_ij)=0;
virtual size_t size()=0;
virtual std::string label()=0;
diff --git a/descriptors/d3/d3_dummy.cpp b/descriptors/d3/d3_dummy.cpp
index c145bfd..12d0074 100644
--- a/descriptors/d3/d3_dummy.cpp
+++ b/descriptors/d3/d3_dummy.cpp
@@ -11,7 +11,7 @@ void D3_Dummy::calc_aed(
const double,
const double,
const double,
- aed_rtype ) {}
+ aed_type2& ) {}
void D3_Dummy::calc_fd(
const size_t,
const double,
@@ -29,7 +29,7 @@ void D3_Dummy::calc_all(
const double,
const double,
const double,
- aed_rtype ,
+ aed_type2& ,
fd_type &) {}
size_t D3_Dummy::size() { return s;}
std::string D3_Dummy::label() {return lab;}
diff --git a/descriptors/d3/d3_dummy.h b/descriptors/d3/d3_dummy.h
index 616b08a..d4d4925 100644
--- a/descriptors/d3/d3_dummy.h
+++ b/descriptors/d3/d3_dummy.h
@@ -14,7 +14,7 @@ class D3_Dummy: public D3_Base {
const double rik,
const double fc_ij,
const double fc_ik,
- aed_rtype aed);
+ aed_type2& aed);
void calc_fd(
const size_t fidx,
const double rij,
@@ -32,7 +32,7 @@ class D3_Dummy: public D3_Base {
const double fc_ik,
const double fcp_ij,
const double fcp_ik,
- aed_rtype aed,
+ aed_type2& aed,
fd_type &fd_ij);
size_t size();
std::string label();
diff --git a/descriptors/dm/dm_base.h b/descriptors/dm/dm_base.h
index 5062a7b..89ac3b6 100644
--- a/descriptors/dm/dm_base.h
+++ b/descriptors/dm/dm_base.h
@@ -19,7 +19,7 @@ class DM_Base: public D_Base {
*/
virtual void calc_aed(
rho_rtype rho,
- aed_rtype aed)=0;
+ aed_type2 &aed)=0;
/** \brief Calculate \ref FD
*
diff --git a/descriptors/dm/dm_blip.cpp b/descriptors/dm/dm_blip.cpp
index abd287e..68b1adb 100644
--- a/descriptors/dm/dm_blip.cpp
+++ b/descriptors/dm/dm_blip.cpp
@@ -39,7 +39,7 @@ DM_Blip::DM_Blip(Config &c):
void DM_Blip::calc_aed(
rho_rtype rhoi,
- aed_rtype aed)
+ aed_type2 &aed)
{
size_t Lshift = 0;
size_t ii=0;
diff --git a/descriptors/dm/dm_blip.h b/descriptors/dm/dm_blip.h
index 9f6eab4..a95c510 100644
--- a/descriptors/dm/dm_blip.h
+++ b/descriptors/dm/dm_blip.h
@@ -55,7 +55,7 @@ class DM_Blip: public DM_Base {
DM_Blip(Config&);
void calc_aed(
rho_rtype rho,
- aed_rtype aed);
+ aed_type2 &aed);
int calc_dXijdri_dXjidri(
const double rij,
const double rij_sq,
diff --git a/descriptors/dm/dm_dummy.cpp b/descriptors/dm/dm_dummy.cpp
index e104902..8ff4852 100644
--- a/descriptors/dm/dm_dummy.cpp
+++ b/descriptors/dm/dm_dummy.cpp
@@ -6,7 +6,7 @@ DM_Dummy::DM_Dummy() {}
DM_Dummy::DM_Dummy(Config&) {}
void DM_Dummy::calc_aed(
rho_rtype,
- aed_rtype ) {}
+ aed_type2 & ) {}
int DM_Dummy::calc_dXijdri_dXjidri(
const double,
const double,
diff --git a/descriptors/dm/dm_dummy.h b/descriptors/dm/dm_dummy.h
index dab6979..3d69926 100644
--- a/descriptors/dm/dm_dummy.h
+++ b/descriptors/dm/dm_dummy.h
@@ -18,7 +18,7 @@ class DM_Dummy: public DM_Base {
DM_Dummy(Config&);
void calc_aed(
rho_rtype rho,
- aed_rtype aed);
+ aed_type2 &aed);
int calc_dXijdri_dXjidri(
const double rij,
const double rij_sq,
diff --git a/descriptors/dm/dm_ead.cpp b/descriptors/dm/dm_ead.cpp
index 0ad4862..7b4d1d2 100644
--- a/descriptors/dm/dm_ead.cpp
+++ b/descriptors/dm/dm_ead.cpp
@@ -43,7 +43,7 @@ DM_EAD::DM_EAD(Config &config):
void DM_EAD::calc_aed(
rho_rtype rhoi,
- aed_rtype aed)
+ aed_type2 &aed)
{
size_t Lshift = 0;
size_t ii=0;
diff --git a/descriptors/dm/dm_ead.h b/descriptors/dm/dm_ead.h
index bc93bc9..508ab7d 100644
--- a/descriptors/dm/dm_ead.h
+++ b/descriptors/dm/dm_ead.h
@@ -54,7 +54,7 @@ class DM_EAD: public DM_Base {
DM_EAD(Config&);
void calc_aed(
rho_rtype rho,
- aed_rtype aed);
+ aed_type2 &aed);
int calc_dXijdri_dXjidri(
const double rij,
const double rij_sq,
diff --git a/descriptors/dm/dm_eam.cpp b/descriptors/dm/dm_eam.cpp
index b2ea2ff..98b681f 100644
--- a/descriptors/dm/dm_eam.cpp
+++ b/descriptors/dm/dm_eam.cpp
@@ -37,7 +37,7 @@ DM_EAM::DM_EAM(Config &c):
void DM_EAM::calc_aed(
rho_rtype rho,
- aed_rtype aed)
+ aed_type2 &aed)
{
//std::cout << "rho[i]: " << rho(0) << std::endl;
double p = rho(0)*ef.rdrho + 1.0;
diff --git a/descriptors/dm/dm_eam.h b/descriptors/dm/dm_eam.h
index 62c3c29..9d92f01 100644
--- a/descriptors/dm/dm_eam.h
+++ b/descriptors/dm/dm_eam.h
@@ -58,7 +58,7 @@ class DM_EAM: public DM_Base {
DM_EAM(Config&);
void calc_aed(
rho_rtype rho,
- aed_rtype aed);
+ aed_type2 &aed);
int calc_dXijdri_dXjidri(
const double rij,
const double rij_sq,
diff --git a/descriptors/dm/dm_mEAD.cpp b/descriptors/dm/dm_mEAD.cpp
index 74ba53a..a6e3e51 100644
--- a/descriptors/dm/dm_mEAD.cpp
+++ b/descriptors/dm/dm_mEAD.cpp
@@ -47,7 +47,7 @@ DM_mEAD<F>::DM_mEAD(Config &config):
template <typename F>
void DM_mEAD<F>::calc_aed(
rho_rtype rhoi,
- aed_rtype aed)
+ aed_type2 &aed)
{
size_t Lshift = 0;
size_t ii=0;
diff --git a/descriptors/dm/dm_mEAD.h b/descriptors/dm/dm_mEAD.h
index 45224e9..0ccdd23 100644
--- a/descriptors/dm/dm_mEAD.h
+++ b/descriptors/dm/dm_mEAD.h
@@ -111,7 +111,7 @@ class DM_mEAD: public DM_Base, public F {
DM_mEAD(Config&);
void calc_aed(
rho_rtype rho,
- aed_rtype aed);
+ aed_type2 &aed);
int calc_dXijdri_dXjidri(
const double rij,
const double rij_sq,
diff --git a/ekm.h b/ekm.h
index 5f60bc4..562c0f5 100644
--- a/ekm.h
+++ b/ekm.h
@@ -14,7 +14,7 @@ class EKM {
EKM(T &t):
kernel(t)
{}
- void configure(aeds_type &basis) {
+ void configure(aeds_type2 &basis) {
// KK is temp matrix
KK = Eigen::MatrixXd(basis.size(), basis.size());
@@ -39,7 +39,7 @@ class EKM {
Phi.row(i)= KK*Phi.row(i).transpose();
}
}
- aed_type project(aed_rtype aed, aeds_type &basis) {
+ aed_type project(aed_type2 &aed, aeds_type2 &basis) {
aed_type temp(basis.size());
for (long int b=0; b<basis.cols(); b++) {
temp(b) = kernel(aed,basis[b]);
diff --git a/functions/basis_functions/bf_base.h b/functions/basis_functions/bf_base.h
index d76cd71..533cf63 100644
--- a/functions/basis_functions/bf_base.h
+++ b/functions/basis_functions/bf_base.h
@@ -9,10 +9,10 @@
/** \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_rctype& )=0;
+ virtual double epredict(const t_type &, const aed_type2& )=0;
virtual double fpredict(const t_type &, const fd_type &,
- const aed_rctype& , const size_t )=0;
+ const aed_type2& , const size_t )=0;
virtual force_type fpredict(const t_type &, const fd_type &,
- const aed_rctype& )=0;
+ const aed_type2& )=0;
};
#endif
diff --git a/functions/basis_functions/bf_linear.cpp b/functions/basis_functions/bf_linear.cpp
index 1b427b1..6daabe0 100644
--- a/functions/basis_functions/bf_linear.cpp
+++ b/functions/basis_functions/bf_linear.cpp
@@ -9,17 +9,17 @@ BF_Linear::BF_Linear(const Config &c): Function_Base(c) {}
std::string BF_Linear::get_label() {
return label;
}
-double BF_Linear::epredict(const t_type &weights, const aed_rctype& aed)
+double BF_Linear::epredict(const t_type &weights, const aed_type2& aed)
{
return weights.transpose()*aed;
}
double BF_Linear::fpredict(const t_type &weights, const fd_type &fdij,
- const aed_rctype& , const size_t k)
+ const aed_type2& , const size_t k)
{
return -fdij.col(k).transpose() * weights;
}
force_type BF_Linear::fpredict(const t_type &weights, const fd_type &fdij,
- const aed_rctype& )
+ const aed_type2& )
{
return -Vec3d(fdij.transpose() * weights);
}
diff --git a/functions/basis_functions/bf_linear.h b/functions/basis_functions/bf_linear.h
index 6355fbb..7548c38 100644
--- a/functions/basis_functions/bf_linear.h
+++ b/functions/basis_functions/bf_linear.h
@@ -9,10 +9,10 @@ struct BF_Linear: public virtual BF_Base
BF_Linear(const Config &c);
std::string get_label();
std::string label = "BF_Linear";
- double epredict(const t_type &weights, const aed_rctype& aed);
+ double epredict(const t_type &weights, const aed_type2& aed);
double fpredict(const t_type &weights, const fd_type &fdij,
- const aed_rctype& aedi, const size_t k);
+ const aed_type2& aedi, const size_t k);
force_type fpredict(const t_type &weights, const fd_type &fdij,
- const aed_rctype& aedi);
+ const aed_type2& aedi);
};
#endif
diff --git a/functions/basis_functions/bf_polynomial2.cpp b/functions/basis_functions/bf_polynomial2.cpp
index 107b4c2..d30e522 100644
--- a/functions/basis_functions/bf_polynomial2.cpp
+++ b/functions/basis_functions/bf_polynomial2.cpp
@@ -10,19 +10,19 @@ std::string BF_Polynomial2::get_label()
{
return label;
}
-double BF_Polynomial2::epredict(const t_type &weights, const aed_rctype& aed)
+double BF_Polynomial2::epredict(const t_type &weights, const aed_type2& aed)
{
size_t b=0;
double res=0.0;
- for (long int i=0; i<aed.size(); ++i) {
- for (long int ii=i; ii<aed.size(); ++ii) {
+ for (size_t i=0; i<aed.size(); ++i) {
+ for (size_t ii=i; ii<aed.size(); ++ii) {
res+= weights(b++)*aed(i)*aed(ii);
}
}
return res;
}
double BF_Polynomial2::fpredict(const t_type &weights, const fd_type &fdij,
- const aed_rctype& aedi, const size_t k)
+ const aed_type2& aedi, const size_t k)
{
double res=0.0;
size_t b=0;
@@ -35,7 +35,7 @@ double BF_Polynomial2::fpredict(const t_type &weights, const fd_type &fdij,
return res;
}
force_type BF_Polynomial2::fpredict(const t_type &weights, const fd_type &fdij,
- const aed_rctype& aedi)
+ const aed_type2& aedi)
{
force_type v;
v.setZero();
diff --git a/functions/basis_functions/bf_polynomial2.h b/functions/basis_functions/bf_polynomial2.h
index 65f4212..9508423 100644
--- a/functions/basis_functions/bf_polynomial2.h
+++ b/functions/basis_functions/bf_polynomial2.h
@@ -9,10 +9,10 @@ struct BF_Polynomial2: public virtual BF_Base
BF_Polynomial2(const Config &c);
std::string label = "BF_Polynomial2";
std::string get_label();
- double epredict(const t_type &weights, const aed_rctype& aed);
+ double epredict(const t_type &weights, const aed_type2& aed);
double fpredict(const t_type &weights, const fd_type &fdij,
- const aed_rctype& aedi, const size_t k);
+ const aed_type2& aedi, const size_t k);
force_type fpredict(const t_type &weights, const fd_type &fdij,
- const aed_rctype& aedi);
+ const aed_type2& aedi);
};
#endif
diff --git a/functions/function_base.h b/functions/function_base.h
index 66d5823..e1f6c5b 100644
--- a/functions/function_base.h
+++ b/functions/function_base.h
@@ -30,19 +30,19 @@ struct Function_Base {
virtual ~Function_Base() {};
// For Kernels
- virtual double operator() (const aed_rctype& , const aed_rctype& ) { return 0.0; };
- virtual aed_type derivative(const aed_rctype& , const aed_rctype& ) { return aed_type(); };
- virtual double prime(const aed_rctype& , const aed_rctype& ,
- const aed_rctype& ) { return 0.0; }
- virtual void set_basis(const aeds_type ) {};
+ 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 aeds_type2 ) {};
/** \brief Return label of this object */
virtual std::string get_label()=0;
- virtual double epredict(const t_type &, const aed_rctype& )=0;
+ virtual double epredict(const t_type &, const aed_type2& )=0;
virtual double fpredict(const t_type &, const fd_type &,
- const aed_rctype&, const size_t )=0;
+ const aed_type2&, const size_t )=0;
virtual force_type fpredict(const t_type &, const fd_type &,
- const aed_rctype& )=0;
+ const aed_type2& )=0;
};
template<> inline Registry<Function_Base>::Map Registry<Function_Base>::registry{};
template<> inline Registry<Function_Base,Config&>::Map Registry<Function_Base,Config&>::registry{};
diff --git a/functions/kernels/kern_base.cpp b/functions/kernels/kern_base.cpp
index 171af0c..6e132db 100644
--- a/functions/kernels/kern_base.cpp
+++ b/functions/kernels/kern_base.cpp
@@ -1,33 +1,33 @@
#include "kern_base.h"
Kern_Base::~Kern_Base() {}
-void Kern_Base::set_basis(const aeds_type b)
+void Kern_Base::set_basis(const aeds_type2 b)
{
basis = b;
}
-double Kern_Base::epredict(const t_type &kweights, const aed_rctype &aed)
+double Kern_Base::epredict(const t_type &kweights, const aed_type2 &aed)
{
double energy=0;
- for (long int b=0; b<basis.cols(); ++b) {
+ for (size_t b=0; b<basis.cols(); ++b) {
energy += kweights[b]*(*this)(basis.col(b),aed);
}
return energy;
}
double Kern_Base::fpredict(const t_type &kweights, const fd_type &fdij,
- const aed_rctype &aedi, const size_t k)
+ const aed_type2 &aedi, const size_t k)
{
double res=0.0;
- for (long int b=0; b<basis.cols(); ++b) {
+ for (size_t b=0; b<basis.cols(); ++b) {
res -= kweights[b]*(*this).prime(basis.col(b),aedi,fdij.col(k));
}
return res;
}
force_type Kern_Base::fpredict(const t_type &kweights, const fd_type &fdij,
- const aed_rctype &aedi)
+ const aed_type2 &aedi)
{
force_type v;
v.setZero();
- for (long int b=0; b<basis.cols(); ++b) {
+ for (size_t b=0; b<basis.cols(); ++b) {
for (size_t k=0; k<3; ++k) {
v(k) -= kweights[b]*(*this).prime(basis.col(b),aedi,fdij.col(k));
}
diff --git a/functions/kernels/kern_base.h b/functions/kernels/kern_base.h
index 4a62048..fc94fba 100644
--- a/functions/kernels/kern_base.h
+++ b/functions/kernels/kern_base.h
@@ -15,7 +15,7 @@
*/
class Kern_Base: public virtual Function_Base {
public:
- aeds_type basis;
+ aeds_type2 basis;
virtual ~Kern_Base();
/**
@@ -24,7 +24,7 @@ class Kern_Base: public virtual Function_Base {
* - b = basis vector
* - af = atomic energy descriptor
*/
- virtual double operator() (const aed_rctype &b, const aed_rctype &af)=0;
+ virtual double operator() (const aed_type2 &b, const aed_type2 &af)=0;
/**
* Calculate the kernel derivative wrt to the second argument
@@ -32,7 +32,7 @@ class Kern_Base: public virtual Function_Base {
* - b = basis vector
* - af = atomic energy descriptor
*/
- virtual aed_type derivative(const aed_rctype &b, const aed_rctype &af)=0;
+ virtual aed_type2 derivative(const aed_type2 &b, const aed_type2 &af)=0;
/**
* Calculate inner product of the kernel derivative
@@ -43,16 +43,16 @@ class Kern_Base: public virtual Function_Base {
* - ff = force descriptor (TODO i-th dir component of it)
* TODO consider calculating all 3-directions at once
*/
- virtual double prime(const aed_rctype &b, const aed_rctype &af,
- const aed_rctype &ff)=0;
+ virtual double prime(const aed_type2 &b, const aed_type2 &af,
+ const aed_type2 &ff)=0;
/** \brief Set basis for calculations */
- virtual void set_basis(const aeds_type b);
+ virtual void set_basis(const aeds_type2 b);
- virtual double epredict(const t_type &kweights, const aed_rctype &aed);
+ virtual double epredict(const t_type &kweights, const aed_type2 &aed);
virtual double fpredict(const t_type &kweights, const fd_type &fdij,
- const aed_rctype &aedi, const size_t k);
+ const aed_type2 &aedi, const size_t k);
virtual force_type fpredict(const t_type &kweights, const fd_type &fdij,
- const aed_rctype &aedi);
+ const aed_type2 &aedi);
};
#endif
diff --git a/functions/kernels/kern_linear.cpp b/functions/kernels/kern_linear.cpp
index 3c80fb7..201cc34 100644
--- a/functions/kernels/kern_linear.cpp
+++ b/functions/kernels/kern_linear.cpp
@@ -7,15 +7,15 @@ Kern_Linear::Kern_Linear() {}
Kern_Linear::Kern_Linear (const Config &c):
Function_Base(c)
{}
-double Kern_Linear::operator() (const aed_rctype& b, const aed_rctype& af)
+double Kern_Linear::operator() (const aed_type2& b, const aed_type2& af)
{
return b.transpose()*af;;
}
-aed_type Kern_Linear::derivative(const aed_rctype& b, const aed_rctype&)
+aed_type2 Kern_Linear::derivative(const aed_type2& b, const aed_type2&)
{
return b;
}
-double Kern_Linear::prime(const aed_rctype& b, const aed_rctype& , const aed_rctype& ff)
+double Kern_Linear::prime(const aed_type2& b, const aed_type2& , const aed_type2& ff)
{
// return derivative(b,af).transpose() * ff;
return b.transpose() * ff;
@@ -24,17 +24,17 @@ std::string Kern_Linear::get_label()
{
return label;
}
-double Kern_Linear::epredict(const t_type &weights, const aed_rctype& aed)
+double Kern_Linear::epredict(const t_type &weights, const aed_type2& aed)
{
return weights.transpose()*aed;
}
double Kern_Linear::fpredict(const t_type &weights, const fd_type &fdij,
- const aed_rctype& , const size_t k)
+ const aed_type2& , const size_t k)
{
return -fdij.col(k).transpose() * weights;
}
force_type Kern_Linear::fpredict(const t_type &weights, const fd_type &fdij,
- const aed_rctype& )
+ const aed_type2& )
{
return -fdij.transpose() * weights;
}
diff --git a/functions/kernels/kern_linear.h b/functions/kernels/kern_linear.h
index cbad9db..aa90767 100644
--- a/functions/kernels/kern_linear.h
+++ b/functions/kernels/kern_linear.h
@@ -22,15 +22,15 @@ class Kern_Linear : public virtual Kern_Base {
* Label used for this class
*/
std::string label = "Kern_Linear";
- double operator() (const aed_rctype& b, const aed_rctype& af);
- aed_type derivative(const aed_rctype& b, const aed_rctype& );
- double prime(const aed_rctype& b, const aed_rctype& af, const aed_rctype& ff);
- void set_basis(const aeds_type ) {}
+ double operator() (const aed_type2& b, const aed_type2& af);
+ aed_type2 derivative(const aed_type2& b, const aed_type2& );
+ double prime(const aed_type2& b, const aed_type2& af, const aed_type2& ff);
+ void set_basis(const aeds_type2 ) {}
- double epredict(const t_type &weights, const aed_rctype& aed);
+ double epredict(const t_type &weights, const aed_type2& aed);
double fpredict(const t_type &weights, const fd_type &fdij,
- const aed_rctype& aedi, const size_t k);
+ const aed_type2& aedi, const size_t k);
force_type fpredict(const t_type &weights, const fd_type &fdij,
- const aed_rctype& aedi);
+ const aed_type2& aedi);
};
#endif
diff --git a/functions/kernels/kern_lq.cpp b/functions/kernels/kern_lq.cpp
index 82b3db7..3b2f7ef 100644
--- a/functions/kernels/kern_lq.cpp
+++ b/functions/kernels/kern_lq.cpp
@@ -9,17 +9,17 @@ Kern_LQ::Kern_LQ (const Config &c):
{
if (get_verbose()) std::cout << std::endl << label << std::endl;
}
-double Kern_LQ::operator() (const aed_rctype& b, const aed_rctype& af)
+double Kern_LQ::operator() (const aed_type2& b, const aed_type2& af)
{
double x = b.transpose()*af;
return x*x + x;
}
-aed_type Kern_LQ::derivative(const aed_rctype& b, const aed_rctype& af)
+aed_type2 Kern_LQ::derivative(const aed_type2& b, const aed_type2& af)
{
double temp = 2.0 * b.transpose()*af;
return temp*b + b;
}
-double Kern_LQ::prime(const aed_rctype& b, const aed_rctype& af, const aed_rctype& ff)
+double Kern_LQ::prime(const aed_type2& b, const aed_type2& af, const aed_type2& ff)
{
return derivative(b, af).transpose()*ff;
}
diff --git a/functions/kernels/kern_lq.h b/functions/kernels/kern_lq.h
index 9d5bd19..62f582d 100644
--- a/functions/kernels/kern_lq.h
+++ b/functions/kernels/kern_lq.h
@@ -23,9 +23,9 @@ class Kern_LQ : public virtual Kern_Base {
* Label used for this class
*/
std::string label = "Kern_LQ";
- double operator() (const aed_rctype& b, const aed_rctype& af);
- aed_type derivative(const aed_rctype& b, const aed_rctype& af);
- double prime(const aed_rctype& b, const aed_rctype& af, const aed_rctype& ff);
+ double operator() (const aed_type2& b, const aed_type2& af);
+ aed_type2 derivative(const aed_type2& b, const aed_type2& af);
+ double prime(const aed_type2& b, const aed_type2& af, const aed_type2& ff);
std::string get_label();
};
diff --git a/functions/kernels/kern_polynomial.cpp b/functions/kernels/kern_polynomial.cpp
index 01dcf5e..4b2f5d1 100644
--- a/functions/kernels/kern_polynomial.cpp
+++ b/functions/kernels/kern_polynomial.cpp
@@ -13,15 +13,15 @@ Kern_Polynomial::Kern_Polynomial (const Config &c):
if (get_verbose()) std::cout << std::endl << label << " | degree: " << d
<<" | gamma: " << gamma << " | c: " << c << std::endl;
}
-double Kern_Polynomial::operator() (const aed_rctype& b, const aed_rctype& af)
+double Kern_Polynomial::operator() (const aed_type2& b, const aed_type2& af)
{
- return std::pow(gamma*(b.dot(af))+c,d);
+ return std::pow(gamma*(b*af)+c,d);
}
-aed_type Kern_Polynomial::derivative(const aed_rctype& b, const aed_rctype& af)
+aed_type2 Kern_Polynomial::derivative(const aed_type2& b, const aed_type2& af)
{
- return d*gamma*std::pow(gamma*(b.dot(af))+c,d-1)*b;
+ return d*gamma*std::pow(gamma*(b*af)+c,d-1)*b;
}
-double Kern_Polynomial::prime(const aed_rctype& b, const aed_rctype& af, const aed_rctype& ff)
+double Kern_Polynomial::prime(const aed_type2& b, const aed_type2& af, const aed_type2& ff)
{
return derivative(b, af).transpose()*ff;
}
diff --git a/functions/kernels/kern_polynomial.h b/functions/kernels/kern_polynomial.h
index 02bf262..4d281ce 100644
--- a/functions/kernels/kern_polynomial.h
+++ b/functions/kernels/kern_polynomial.h
@@ -26,9 +26,9 @@ class Kern_Polynomial : public virtual Kern_Base {
*/
std::string label = "Kern_Polynomial";
std::string get_label();
- double operator() (const aed_rctype& b, const aed_rctype& af);
- aed_type derivative(const aed_rctype& b, const aed_rctype& af);
- double prime(const aed_rctype& b, const aed_rctype& af, const aed_rctype& ff);
+ double operator() (const aed_type2& b, const aed_type2& af);
+ aed_type2 derivative(const aed_type2& b, const aed_type2& af);
+ double prime(const aed_type2& b, const aed_type2& af, const aed_type2& ff);
};
#endif
diff --git a/functions/kernels/kern_quadratic.cpp b/functions/kernels/kern_quadratic.cpp
index 0d61f73..60ba58c 100644
--- a/functions/kernels/kern_quadratic.cpp
+++ b/functions/kernels/kern_quadratic.cpp
@@ -9,17 +9,17 @@ Kern_Quadratic::Kern_Quadratic (const Config &c):
{
if (get_verbose()) std::cout << std::endl << label << std::endl;
}
-double Kern_Quadratic::operator() (const aed_rctype& b, const aed_rctype& af)
+double Kern_Quadratic::operator() (const aed_type2& b, const aed_type2& af)
{
double x = b.transpose()*af;
return x*x;
}
-aed_type Kern_Quadratic::derivative(const aed_rctype& b, const aed_rctype& af)
+aed_type2 Kern_Quadratic::derivative(const aed_type2& b, const aed_type2& af)
{
double temp = 2.0 * b.transpose()*af;
return b*temp;;
}
-double Kern_Quadratic::prime(const aed_rctype& b, const aed_rctype& af, const aed_rctype& ff)
+double Kern_Quadratic::prime(const aed_type2& b, const aed_type2& af, const aed_type2& ff)
{
//return dot(derivative(b, af), ff);
// it is faster this way
diff --git a/functions/kernels/kern_quadratic.h b/functions/kernels/kern_quadratic.h
index d9e886b..fef8b5b 100644
--- a/functions/kernels/kern_quadratic.h
+++ b/functions/kernels/kern_quadratic.h
@@ -21,9 +21,9 @@ class Kern_Quadratic : public virtual Kern_Base {
* Label used for this class
*/
std::string label = "Kern_Quadratic";
- double operator() (const aed_rctype& b, const aed_rctype& af);
- aed_type derivative(const aed_rctype& b, const aed_rctype& af);
- double prime(const aed_rctype& b, const aed_rctype& af, const aed_rctype& ff);
+ double operator() (const aed_type2& b, const aed_type2& af);
+ aed_type2 derivative(const aed_type2& b, const aed_type2& af);
+ double prime(const aed_type2& b, const aed_type2& af, const aed_type2& ff);
std::string get_label();
};
diff --git a/functions/kernels/kern_rbf.cpp b/functions/kernels/kern_rbf.cpp
index a96a935..b26dfe5 100644
--- a/functions/kernels/kern_rbf.cpp
+++ b/functions/kernels/kern_rbf.cpp
@@ -12,16 +12,16 @@ Kern_RBF::Kern_RBF (const Config &c):
if (get_verbose()) std::cout << std::endl << label << " | sigma: " << sigma
<< " | gamma: " << gamma << std::endl;
}
-double Kern_RBF::operator() (const aed_rctype& b, const aed_rctype& af)
+double Kern_RBF::operator() (const aed_type2& b, const aed_type2& af)
{
- const aed_type v = af-b;
- return exp(-gamma*(v.dot(v)));
+ const aed_type2 v = af-b;
+ return exp(-gamma*(v*v));
}
-aed_type Kern_RBF::derivative(const aed_rctype& b, const aed_rctype& af)
+aed_type2 Kern_RBF::derivative(const aed_type2& b, const aed_type2& af)
{
return -2.0*gamma*(af-b)*(*this)(af,b);
}
-double Kern_RBF::prime(const aed_rctype& b, const aed_rctype& af, const aed_rctype& ff)
+double Kern_RBF::prime(const aed_type2& b, const aed_type2& af, const aed_type2& ff)
{
return derivative(b, af).transpose()*ff;
}
diff --git a/functions/kernels/kern_rbf.h b/functions/kernels/kern_rbf.h
index d91c493..6b76845 100644
--- a/functions/kernels/kern_rbf.h
+++ b/functions/kernels/kern_rbf.h
@@ -23,9 +23,9 @@ class Kern_RBF : public virtual Kern_Base {
Kern_RBF ();
Kern_RBF (const Config &c);
std::string label = "Kern_RBF";
- double operator() (const aed_rctype& b, const aed_rctype& af);
- aed_type derivative(const aed_rctype& b, const aed_rctype& af);
- double prime(const aed_rctype& b, const aed_rctype& af, const aed_rctype& ff);
+ double operator() (const aed_type2& b, const aed_type2& af);
+ aed_type2 derivative(const aed_type2& b, const aed_type2& af);
+ double prime(const aed_type2& b, const aed_type2& af, const aed_type2& ff);
std::string get_label();
private:
diff --git a/functions/kernels/kern_sigmoid.cpp b/functions/kernels/kern_sigmoid.cpp
index 6f0c947..8ce2e83 100644
--- a/functions/kernels/kern_sigmoid.cpp
+++ b/functions/kernels/kern_sigmoid.cpp
@@ -12,15 +12,15 @@ Kern_Sigmoid::Kern_Sigmoid (const Config &c):
if (get_verbose()) std::cout << std::endl << label << " | gamma: " << gamma
<< " | c: " << c << std::endl;
}
-double Kern_Sigmoid::operator() (const aed_rctype& b, const aed_rctype& af)
+double Kern_Sigmoid::operator() (const aed_type2& b, const aed_type2& af)
{
- return std::tanh(gamma*(b.dot(af))+c);
+ return std::tanh(gamma*(b*af)+c);
}
-aed_type Kern_Sigmoid::derivative(const aed_rctype& b, const aed_rctype& af)
+aed_type2 Kern_Sigmoid::derivative(const aed_type2& b, const aed_type2& af)
{
return gamma*(1.0-std::pow((*this)(af,b),2))*b;
}
-double Kern_Sigmoid::prime(const aed_rctype& b, const aed_rctype& af, const aed_rctype& ff)
+double Kern_Sigmoid::prime(const aed_type2& b, const aed_type2& af, const aed_type2& ff)
{
return derivative(b, af).transpose()*ff;
}
diff --git a/functions/kernels/kern_sigmoid.h b/functions/kernels/kern_sigmoid.h
index 600251a..e94c79a 100644
--- a/functions/kernels/kern_sigmoid.h
+++ b/functions/kernels/kern_sigmoid.h
@@ -24,9 +24,9 @@ class Kern_Sigmoid : public virtual Kern_Base {
Kern_Sigmoid ();
Kern_Sigmoid (const Config &c);
std::string label = "Kern_Sigmoid";
- double operator() (const aed_rctype& b, const aed_rctype& af);
- aed_type derivative(const aed_rctype& b, const aed_rctype& af);
- double prime(const aed_rctype& b, const aed_rctype& af, const aed_rctype& ff);
+ double operator() (const aed_type2& b, const aed_type2& af);
+ aed_type2 derivative(const aed_type2& b, const aed_type2& af);
+ double prime(const aed_type2& b, const aed_type2& af, const aed_type2& ff);
std::string get_label();
};
diff --git a/m_core.h b/m_core.h
index c2783bd..0d9c042 100644
--- a/m_core.h
+++ b/m_core.h
@@ -38,14 +38,14 @@ class M_Predict {
* If aed contains sum over all nearest neighbours than the result is
* a local atomic energy \f$ E_i \f$.
* */
- virtual double epredict(const aed_rctype &aed)=0;
+ virtual double epredict(const aed_type2 &aed)=0;
/** \brief Predict force between a pair of atoms in a k-direction. */
- virtual double fpredict(const fd_type &fdij, const aed_rctype &aedi, size_t k)=0;
+ virtual double fpredict(const fd_type &fdij, const aed_type2 &aedi, size_t k)=0;
/** \brief Predict force between a pair of atoms. */
virtual force_type fpredict(const fd_type &fdij,
- const aed_rctype &aedi)=0;
+ const aed_type2 &aedi)=0;
};
class M_Train {
public:
diff --git a/m_krr_core.h b/m_krr_core.h
index ff7b370..e228141 100644
--- a/m_krr_core.h
+++ b/m_krr_core.h
@@ -83,15 +83,15 @@ class M_KRR_Core:
// M_KRR_Core<K>(kernel, c)
// {}
//
-// double epredict(const aed_rctype &aed) {
+// double epredict(const aed_type2 &aed) {
// return kernel.epredict(weights,aed);
// };
//
-// double fpredict(const fd_type &fdij, const aed_rctype &aedi, const size_t k) {
+// double fpredict(const fd_type &fdij, const aed_type2 &aedi, const size_t k) {
// return kernel.fpredict(weights,fdij,aedi,k);
// }
//
-// force_type fpredict(const fd_type &fdij, const aed_rctype &aedi) {
+// force_type fpredict(const fd_type &fdij, const aed_type2 &aedi) {
// return kernel.fpredict(weights,fdij,aedi).array();
// }
//
--
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