From 40b996207e6c37b2f0919f53e3e32b626a513477 Mon Sep 17 00:00:00 2001
From: mkirsz <s1351949@sms.ed.ac.uk>
Date: Wed, 18 Dec 2024 12:25:52 +0000
Subject: [PATCH] rename aed
---
include/tadah/mlip/analytics/statistics.h | 2 +-
include/tadah/mlip/descriptors_calc.hpp | 10 +++++-----
include/tadah/mlip/models/basis.h | 4 ++--
include/tadah/mlip/models/m_blr.h | 12 ++++++------
include/tadah/mlip/models/m_krr.h | 12 ++++++------
include/tadah/mlip/models/m_tadah_base.h | 6 +++---
include/tadah/mlip/output/output.h | 2 +-
include/tadah/mlip/st_descriptors.h | 4 ++--
src/dm_bf_linear.cpp | 2 +-
src/dm_bf_polynomial2.cpp | 10 +++++-----
src/dm_kern_base.cpp | 8 ++++----
src/dm_kern_linear.cpp | 6 +++---
src/m_tadah_base.cpp | 12 ++++++------
src/st_descriptors.cpp | 4 ++--
14 files changed, 47 insertions(+), 47 deletions(-)
diff --git a/include/tadah/mlip/analytics/statistics.h b/include/tadah/mlip/analytics/statistics.h
index 0d86664..4bd75bf 100644
--- a/include/tadah/mlip/analytics/statistics.h
+++ b/include/tadah/mlip/analytics/statistics.h
@@ -5,7 +5,7 @@
/** Some basis statistical tools */
class Statistics {
- using vec = aed_type2;
+ using vec = aed_type;
public:
/** Residual sum of squares. */
static double res_sum_sq(const vec &obs, const vec &pred);
diff --git a/include/tadah/mlip/descriptors_calc.hpp b/include/tadah/mlip/descriptors_calc.hpp
index 10eb0bf..01ae99d 100644
--- a/include/tadah/mlip/descriptors_calc.hpp
+++ b/include/tadah/mlip/descriptors_calc.hpp
@@ -216,7 +216,7 @@ void DescriptorsCalc<D2,D3,DM,C2,C3,CM>::calc(const Structure &st, StDescriptors
// zero all aeds and set bias
for (size_t i=0; i<st.natoms(); ++i) {
- aed_type2 &aed = st_d.get_aed(i);
+ aed_type &aed = st_d.get_aed(i);
aed.set_zero();
aed(0)=static_cast<double>(bias); // set bias
}
@@ -226,7 +226,7 @@ void DescriptorsCalc<D2,D3,DM,C2,C3,CM>::calc(const Structure &st, StDescriptors
// can be calculated
if (initmb) {
for (size_t i=0; i<st.natoms(); ++i) {
- aed_type2 &aed = st_d.get_aed(i);
+ aed_type &aed = st_d.get_aed(i);
rho_type& rhoi = st_d.get_rho(i);
dm.calc_aed(rhoi,aed);
}
@@ -238,7 +238,7 @@ void DescriptorsCalc<D2,D3,DM,C2,C3,CM>::calc(const Structure &st, StDescriptors
Vec3d delij;
for (size_t i=0; i<st.natoms(); ++i) {
const Atom &a1 = st(i);
- aed_type2 &aed = st_d.get_aed(i);
+ aed_type &aed = st_d.get_aed(i);
for (size_t jj=0; jj<st.nn_size(i); ++jj) {
const Vec3d &a2pos = st.nn_pos(i,jj);
@@ -356,7 +356,7 @@ void DescriptorsCalc<D2,D3,DM,C2,C3,CM>::calc_dimer(const Structure &st, StDescr
// zero all aeds+rho and set bias
for (size_t i=0; i<4; ++i) {
- aed_type2 &aed = st_d.get_aed(i);
+ aed_type &aed = st_d.get_aed(i);
aed.set_zero();
aed(0)=static_cast<double>(bias); // set bias
}
@@ -401,7 +401,7 @@ void DescriptorsCalc<D2,D3,DM,C2,C3,CM>::calc_dimer(const Structure &st, StDescr
// calculate many-body aed
if (initmb) {
for (size_t i=0; i<4; ++i) {
- aed_type2 &aed = st_d.get_aed(i);
+ aed_type &aed = st_d.get_aed(i);
rho_type& rhoi = st_d.get_rho(i);
dm.calc_aed(rhoi,aed);
}
diff --git a/include/tadah/mlip/models/basis.h b/include/tadah/mlip/models/basis.h
index 80f2bbe..f00caf0 100644
--- a/include/tadah/mlip/models/basis.h
+++ b/include/tadah/mlip/models/basis.h
@@ -56,7 +56,7 @@ larger than the amount of available AEDs\n");
for (size_t i=1; i<s; ++i) {
size_t st = std::get<0>(indices[i]);
size_t a = std::get<1>(indices[i]);
- const aed_type2 &aed = st_desc_db(st).get_aed(a);
+ const aed_type &aed = st_desc_db(st).get_aed(a);
for (size_t j=0; j<aed.size(); ++j) {
b(j,i)=aed[j];
}
@@ -97,7 +97,7 @@ larger than the amount of available AEDs\n");
const size_t st = indices[i];
T(i)=stdb(st).energy/st_desc_db(st).naed();
for( size_t a=0; a<st_desc_db(st).naed(); a++ ) {
- const aed_type2 &aed = st_desc_db(st).get_aed(a);
+ const aed_type &aed = st_desc_db(st).get_aed(a);
for (size_t j=0; j<aed.size(); ++j) {
b(j,i)+=aed[j]/st_desc_db(st).naed();
}
diff --git a/include/tadah/mlip/models/m_blr.h b/include/tadah/mlip/models/m_blr.h
index d687282..943a7fe 100644
--- a/include/tadah/mlip/models/m_blr.h
+++ b/include/tadah/mlip/models/m_blr.h
@@ -76,15 +76,15 @@ public:
norm = Normaliser(c);
}
- double epredict(const aed_type2 &aed) const{
+ double epredict(const aed_type &aed) const{
return bf.epredict(weights,aed);
};
- double fpredict(const fd_type &fdij, const aed_type2 &aedi, const size_t k) const{
+ double fpredict(const fd_type &fdij, const aed_type &aedi, const size_t k) const{
return bf.fpredict(weights,fdij,aedi,k);
}
- force_type fpredict(const fd_type &fdij, const aed_type2 &aedi) const{
+ force_type fpredict(const fd_type &fdij, const aed_type &aedi) const{
return bf.fpredict(weights,fdij,aedi);
}
@@ -167,7 +167,7 @@ public:
return c;
}
StructureDB predict(Config config_pred, StructureDB &stdb, DC_Base &dc,
- aed_type2 &predicted_error) {
+ aed_type &predicted_error) {
LinearRegressor::read_sigma(config_pred,Sigma);
DesignMatrix<BF> dm(bf,config_pred);
@@ -178,7 +178,7 @@ public:
double pmean = sqrt(predicted_error.mean());
// compute energy, forces and stresses
- aed_type2 Tpred = T_dgemv(dm.Phi, weights);
+ aed_type Tpred = T_dgemv(dm.Phi, weights);
// Construct StructureDB object with predicted values
StructureDB stdb_;
@@ -218,7 +218,7 @@ Hint: check different predict() methods.");
//std::cout << Phi.row(0) << std::endl;
// compute energy, forces and stresses
- aed_type2 Tpred = T_dgemv(Phi, weights);
+ aed_type Tpred = T_dgemv(Phi, weights);
double eweightglob=config.template get<double>("EWEIGHT");
double fweightglob=config.template get<double>("FWEIGHT");
diff --git a/include/tadah/mlip/models/m_krr.h b/include/tadah/mlip/models/m_krr.h
index 610c1fc..92aee1d 100644
--- a/include/tadah/mlip/models/m_krr.h
+++ b/include/tadah/mlip/models/m_krr.h
@@ -79,15 +79,15 @@ public:
norm = Normaliser(c);
}
- double epredict(const aed_type2 &aed) const {
+ double epredict(const aed_type &aed) const {
return kernel.epredict(weights,aed);
};
- double fpredict(const fd_type &fdij, const aed_type2 &aedi, const size_t k) const {
+ double fpredict(const fd_type &fdij, const aed_type &aedi, const size_t k) const {
return kernel.fpredict(weights,fdij,aedi,k);
}
- force_type fpredict(const fd_type &fdij, const aed_type2 &aedi) const {
+ force_type fpredict(const fd_type &fdij, const aed_type &aedi) const {
return kernel.fpredict(weights,fdij,aedi);
}
@@ -237,7 +237,7 @@ public:
return c;
}
StructureDB predict(Config config_pred, StructureDB &stdb, DC_Base &dc,
- aed_type2 &predicted_error) {
+ aed_type &predicted_error) {
LinearRegressor::read_sigma(config_pred,Sigma);
DesignMatrix<K> dm(kernel,config_pred);
@@ -249,7 +249,7 @@ public:
double pmean = sqrt(predicted_error.mean());
// compute energy, forces and stresses
- aed_type2 Tpred = T_dgemv(dm.Phi, weights);
+ aed_type Tpred = T_dgemv(dm.Phi, weights);
// Construct StructureDB object with predicted values
StructureDB stdb_;
@@ -288,7 +288,7 @@ Hint: check different predict() methods.");
phi_type &Phi = desmat.Phi;
// compute energy, forces and stresses
- aed_type2 Tpred = T_dgemv(Phi, weights);
+ aed_type Tpred = T_dgemv(Phi, weights);
double eweightglob=config.template get<double>("EWEIGHT");
double fweightglob=config.template get<double>("FWEIGHT");
diff --git a/include/tadah/mlip/models/m_tadah_base.h b/include/tadah/mlip/models/m_tadah_base.h
index c98e4e6..d719829 100644
--- a/include/tadah/mlip/models/m_tadah_base.h
+++ b/include/tadah/mlip/models/m_tadah_base.h
@@ -29,11 +29,11 @@ public:
double epredict(const StDescriptors &std);
///** \brief Predict force between a pair of atoms in a k-direction. */
- //virtual double fpredict(const fd_type &fdij, const aed_type2 &aedi, size_t k)=0;
+ //virtual double fpredict(const fd_type &fdij, const aed_type &aedi, size_t k)=0;
///** \brief Predict force between a pair of atoms. */
//virtual force_type fpredict(const fd_type &fdij,
- // const aed_type2 &aedi)=0;
+ // const aed_type &aedi)=0;
/** \brief Predict total force on an atom a. */
virtual void fpredict(const size_t a, force_type &v,
@@ -96,7 +96,7 @@ public:
virtual void train(StDescriptorsDB &, const StructureDB &) {};
virtual StructureDB predict(Config config_pred, StructureDB &stdb, DC_Base &dc,
- aed_type2 &predicted_error)=0;
+ aed_type &predicted_error)=0;
virtual StructureDB predict(StructureDB &stdb)=0;
diff --git a/include/tadah/mlip/output/output.h b/include/tadah/mlip/output/output.h
index 0f0a7a3..1a08850 100644
--- a/include/tadah/mlip/output/output.h
+++ b/include/tadah/mlip/output/output.h
@@ -45,7 +45,7 @@ class Output {
out_unc.close();
}
- void print_predict_all(StructureDB &stdb, StructureDB &stpred, aed_type2 & predicted_error) {
+ void print_predict_all(StructureDB &stdb, StructureDB &stpred, aed_type & predicted_error) {
std::ofstream out_error("error.pred");
std::ofstream out_energy("energy.pred");
std::ofstream out_force("forces.pred");
diff --git a/include/tadah/mlip/st_descriptors.h b/include/tadah/mlip/st_descriptors.h
index 56618d5..f5cf2ad 100644
--- a/include/tadah/mlip/st_descriptors.h
+++ b/include/tadah/mlip/st_descriptors.h
@@ -69,8 +69,8 @@ struct StDescriptors {
rhos_type rhos;
- aed_type2 & get_aed(const size_t i);
- const aed_type2 &get_aed(const size_t i) const;
+ aed_type & get_aed(const size_t i);
+ const aed_type &get_aed(const size_t i) const;
rho_type& get_rho(const size_t i);
size_t naed() const;
diff --git a/src/dm_bf_linear.cpp b/src/dm_bf_linear.cpp
index 3aea01b..4f5dac2 100644
--- a/src/dm_bf_linear.cpp
+++ b/src/dm_bf_linear.cpp
@@ -18,7 +18,7 @@ void DM_BF_Linear::calc_phi_energy_row(phi_type &Phi, size_t &row,
const double fac, const Structure &, const StDescriptors &st_d)
{
for (size_t i=0; i<st_d.naed(); ++i) {
- const aed_type2 &aed = st_d.get_aed(i);
+ const aed_type &aed = st_d.get_aed(i);
for (size_t j=0; j<aed.size(); ++j) {
Phi(row,j)+=aed[j]*fac;
}
diff --git a/src/dm_bf_polynomial2.cpp b/src/dm_bf_polynomial2.cpp
index 9c48624..c7fb188 100644
--- a/src/dm_bf_polynomial2.cpp
+++ b/src/dm_bf_polynomial2.cpp
@@ -23,7 +23,7 @@ void DM_BF_Polynomial2::calc_phi_energy_row(phi_type &Phi,
const StDescriptors &st_d)
{
for (size_t a=0; a<st_d.naed();++a) {
- const aed_type2& aed = st_d.get_aed(a);
+ const aed_type& aed = st_d.get_aed(a);
size_t b=0;
for (size_t i=0; i<st_d.dim(); ++i) {
for (size_t ii=i; ii<st_d.dim(); ++ii) {
@@ -40,13 +40,13 @@ void DM_BF_Polynomial2::calc_phi_force_rows(phi_type &Phi,
const StDescriptors &st_d)
{
for (size_t a=0; a<st.natoms(); ++a) {
- const aed_type2& aedi = st_d.get_aed(a);
+ const aed_type& aedi = st_d.get_aed(a);
for (size_t jj=0; jj<st_d.fd[a].size(); ++jj) {
const size_t j=st.near_neigh_idx[a][jj];
size_t aa = st.get_nn_iindex(a,j,jj);
const fd_type &fdji = st_d.fd[j][aa];
const fd_type &fdij = st_d.fd[a][jj];
- const aed_type2& aedj = st_d.get_aed(j);
+ const aed_type& aedj = st_d.get_aed(j);
for (size_t k=0; k<3; ++k) {
size_t b=0;
@@ -72,14 +72,14 @@ void DM_BF_Polynomial2::calc_phi_stress_rows(phi_type &Phi,
double V_inv = 1/st.get_volume();
for (size_t a=0; a<st.natoms(); ++a) {
const Vec3d &ri = st(a).position;
- const aed_type2& aedi = st_d.get_aed(a);
+ const aed_type& aedi = st_d.get_aed(a);
for (size_t jj=0; jj<st_d.fd[a].size(); ++jj) {
const size_t j=st.near_neigh_idx[a][jj];
size_t aa = st.get_nn_iindex(a,j,jj);
const fd_type &fdji = st_d.fd[j][aa];
const fd_type &fdij = st_d.fd[a][jj];
const Vec3d &rj = st.nn_pos(a,jj);
- const aed_type2& aedj = st_d.get_aed(j);
+ const aed_type& aedj = st_d.get_aed(j);
size_t mn=0;
for (size_t x=0; x<3; ++x) {
for (size_t y=x; y<3; ++y) {
diff --git a/src/dm_kern_base.cpp b/src/dm_kern_base.cpp
index 9e569e0..f78c71e 100644
--- a/src/dm_kern_base.cpp
+++ b/src/dm_kern_base.cpp
@@ -27,13 +27,13 @@ void DM_Kern_Base::calc_phi_energy_row(phi_type &Phi, size_t &row, const double
void DM_Kern_Base::calc_phi_force_rows(phi_type &Phi, size_t &row, const double fac,
const Structure &st, const StDescriptors &st_d) {
for (size_t i=0; i<st.natoms(); ++i) {
- const aed_type2& aedi = st_d.get_aed(i);
+ const aed_type& aedi = st_d.get_aed(i);
for (size_t jj=0; jj<st_d.fd[i].size(); ++jj) {
size_t j=st.near_neigh_idx[i][jj];
size_t ii = st.get_nn_iindex(i,j,jj);
const fd_type &fdji = st_d.fd[j][ii];
const fd_type &fdij = st_d.fd[i][jj];
- const aed_type2& aedj = st_d.get_aed(j);
+ const aed_type& aedj = st_d.get_aed(j);
for (size_t b=0; b<basis.cols(); ++b) {
for (size_t k=0; k<3; ++k) {
Phi(row+k,b) -= fac*((*this).prime(basis.col(b), aedi,fdij(k)) -
@@ -50,13 +50,13 @@ void DM_Kern_Base::calc_phi_stress_rows(phi_type &Phi, size_t &row, const doubl
double V_inv = 1/st.get_volume();
for (size_t i=0; i<st.natoms(); ++i) {
const Vec3d &ri = st(i).position;
- const aed_type2& aedi = st_d.get_aed(i);
+ const aed_type& aedi = st_d.get_aed(i);
for (size_t jj=0; jj<st_d.fd[i].size(); ++jj) {
size_t j=st.near_neigh_idx[i][jj];
size_t ii = st.get_nn_iindex(i,j,jj);
const fd_type &fdji = st_d.fd[j][ii];
const fd_type &fdij = st_d.fd[i][jj];
- const aed_type2& aedj = st_d.get_aed(j);
+ const aed_type& aedj = st_d.get_aed(j);
const Vec3d &rj = st.nn_pos(i,jj);
size_t mn=0;
for (size_t x=0; x<3; ++x) {
diff --git a/src/dm_kern_linear.cpp b/src/dm_kern_linear.cpp
index df6126a..84c484b 100644
--- a/src/dm_kern_linear.cpp
+++ b/src/dm_kern_linear.cpp
@@ -19,7 +19,7 @@ void DM_Kern_Linear::calc_phi_energy_row(phi_type &Phi, size_t &row,
const double fac, const Structure &, const StDescriptors &st_d)
{
for (size_t a=0; a<st_d.naed();++a) {
- const aed_type2 &aed = st_d.get_aed(a); // TODO
+ const aed_type &aed = st_d.get_aed(a); // TODO
for (size_t j=0; j<aed.size(); ++j) {
Phi(row,j)+=aed[j]*fac;
}
@@ -34,7 +34,7 @@ void DM_Kern_Linear::calc_phi_force_rows(phi_type &Phi, size_t &row,
const size_t j=st.near_neigh_idx[a][jj];
const size_t aa = st.get_nn_iindex(a,j,jj);
for (size_t k=0; k<3; ++k) {
- aed_type2 temp = (st_d.fd[a][jj](k)-
+ aed_type temp = (st_d.fd[a][jj](k)-
st_d.fd[j][aa](k))*fac;
for (size_t d=0; d<temp.size(); ++d) {
Phi(row+k,d) -= temp[d];
@@ -60,7 +60,7 @@ void DM_Kern_Linear::calc_phi_stress_rows(phi_type &Phi, size_t &row,
size_t mn=0;
for (size_t x=0; x<3; ++x) {
for (size_t y=x; y<3; ++y) {
- aed_type2 temp = V_inv*(fdij(y)-fdji(y))*0.5*fac[mn]*(ri(x)-rj(x));
+ aed_type temp = V_inv*(fdij(y)-fdji(y))*0.5*fac[mn]*(ri(x)-rj(x));
for (size_t d=0; d<temp.size(); ++d) {
Phi(row+mn,d) += temp[d];
}
diff --git a/src/m_tadah_base.cpp b/src/m_tadah_base.cpp
index ca18ccb..2efa8f1 100644
--- a/src/m_tadah_base.cpp
+++ b/src/m_tadah_base.cpp
@@ -9,8 +9,8 @@ fpredict(const size_t a, force_type &v,
const size_t aa = st.get_nn_iindex(a,j,jj);
const fd_type &fdji = std.fd[j][aa];
const fd_type &fdij = std.fd[a][jj];
- const aed_type2 &aedi = std.get_aed(a);
- const aed_type2 &aedj = std.get_aed(j);
+ const aed_type &aedi = std.get_aed(a);
+ const aed_type &aedj = std.get_aed(j);
v += fpredict(fdij,aedi);
v -= fpredict(fdji,aedj);
}
@@ -111,14 +111,14 @@ spredict(const size_t a, stress_type &s,
{
double V_inv = 1/st.get_volume();
const Vec3d &ri = st.atoms[a].position;
- const aed_type2 &aedi = std.get_aed(a);
+ const aed_type &aedi = std.get_aed(a);
for (size_t jj=0; jj<st.nn_size(a); ++jj) {
size_t j=st.near_neigh_idx[a][jj];
const size_t aa = st.get_nn_iindex(a,j,jj);
const Vec3d &rj = st.nn_pos(a,jj);
const fd_type &fdij = std.fd[a][jj];
const fd_type &fdji = std.fd[j][aa];
- const aed_type2 &aedj = std.get_aed(j);
+ const aed_type &aedj = std.get_aed(j);
const force_type fij = fpredict(fdij,aedi);
const force_type fji = fpredict(fdji,aedj);
@@ -142,14 +142,14 @@ stress_force_predict(const StDescriptors &std, Structure &st_)
for (size_t a=0; a<st_.natoms(); ++a) {
force_type v;
const Vec3d &ri = st_.atoms[a].position;
- const aed_type2 &aedi = std.get_aed(a);
+ const aed_type &aedi = std.get_aed(a);
for (size_t jj=0; jj<st_.nn_size(a); ++jj) {
size_t j=st_.near_neigh_idx[a][jj];
const size_t aa = st_.get_nn_iindex(a,j,jj);
const Vec3d &rj = st_.nn_pos(a,jj);
const fd_type &fdij = std.fd[a][jj];
const fd_type &fdji = std.fd[j][aa];
- const aed_type2 &aedj = std.get_aed(j);
+ const aed_type &aedj = std.get_aed(j);
const force_type fij = fpredict(fdij,aedi);
const force_type fji = fpredict(fdji,aedj);
diff --git a/src/st_descriptors.cpp b/src/st_descriptors.cpp
index e7a2840..a0407e8 100644
--- a/src/st_descriptors.cpp
+++ b/src/st_descriptors.cpp
@@ -31,11 +31,11 @@ StDescriptors::StDescriptors(const Structure &s, const Config &c):
}
StDescriptors::StDescriptors() {}
-aed_type2 & StDescriptors::get_aed(const size_t i) {
+aed_type & StDescriptors::get_aed(const size_t i) {
return aeds.col(i);
}
-const aed_type2 &StDescriptors::get_aed(const size_t i) const {
+const aed_type &StDescriptors::get_aed(const size_t i) const {
return aeds.col(i);
}
rho_type& StDescriptors::get_rho(const size_t i) {
--
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