From 03111c1d358d540ba23ddc5adad8c47b44ca6018 Mon Sep 17 00:00:00 2001
From: mkirsz <s1351949@sms.ed.ac.uk>
Date: Sun, 22 Dec 2024 10:57:23 +0000
Subject: [PATCH] Descriptors to manage which atoms to calculate
---
include/tadah/models/descriptors/d2/d2_base.h | 1 +
include/tadah/models/descriptors/d3/d3_base.h | 62 +++++++++----------
include/tadah/models/descriptors/d_base.h | 5 +-
include/tadah/models/descriptors/dm/dm_base.h | 1 +
.../tadah/models/descriptors/dm/dm_mEAD.hpp | 2 +
src/d2_base.cpp | 7 +++
src/d2_blip.cpp | 3 +
src/d2_bp.cpp | 4 +-
src/d2_eam.cpp | 3 +
src/d2_lj.cpp | 3 +
src/d2_mie.cpp | 2 +
src/d2_zbl.cpp | 2 +
src/d3_base.cpp | 3 +
src/d_base.cpp | 23 +++++--
src/d_mjoin.cpp | 31 +++++++++-
src/dm_base.cpp | 7 +++
src/dm_blip.cpp | 2 +
src/dm_ead.cpp | 2 +
src/dm_eam.cpp | 2 +
19 files changed, 126 insertions(+), 39 deletions(-)
diff --git a/include/tadah/models/descriptors/d2/d2_base.h b/include/tadah/models/descriptors/d2/d2_base.h
index c70580c..8e7917c 100644
--- a/include/tadah/models/descriptors/d2/d2_base.h
+++ b/include/tadah/models/descriptors/d2/d2_base.h
@@ -22,6 +22,7 @@ public:
}
}
virtual ~D2_Base() {};
+ virtual std::vector<std::string> get_init_atoms(Config &c) override;
/** \brief Calculate \ref AED
*
diff --git a/include/tadah/models/descriptors/d3/d3_base.h b/include/tadah/models/descriptors/d3/d3_base.h
index ff4efec..c64a76b 100644
--- a/include/tadah/models/descriptors/d3/d3_base.h
+++ b/include/tadah/models/descriptors/d3/d3_base.h
@@ -4,37 +4,37 @@
#include <tadah/models/descriptors/d_base.h>
class D3_Base: public D_Base {
- public:
- virtual ~D3_Base() {};
+public:
+ virtual ~D3_Base() {};
- virtual void calc_aed(
- const size_t fidx,
- const double rij,
- const double rik,
- const double fc_ij,
- const double fc_ik,
- aed_type& aed)=0;
- virtual void calc_fd(
- const size_t fidx,
- const double rij,
- const double rik,
- const double fc_ij,
- const double fc_ik,
- const double fcp_ij,
- const double fcp_ik,
- fd_type &fd_ij)=0;
- virtual void calc_all(
- const size_t fidx,
- const double rij,
- const double rik,
- const double fc_ij,
- const double fc_ik,
- const double fcp_ij,
- const double fcp_ik,
- aed_type& aed,
- fd_type &fd_ij)=0;
- virtual size_t size()=0;
- virtual std::string label()=0;
+ virtual void calc_aed(
+ const size_t fidx,
+ const double rij,
+ const double rik,
+ const double fc_ij,
+ const double fc_ik,
+ aed_type& aed)=0;
+ virtual void calc_fd(
+ const size_t fidx,
+ const double rij,
+ const double rik,
+ const double fc_ij,
+ const double fc_ik,
+ const double fcp_ij,
+ const double fcp_ik,
+ fd_type &fd_ij)=0;
+ virtual void calc_all(
+ const size_t fidx,
+ const double rij,
+ const double rik,
+ const double fc_ij,
+ const double fc_ik,
+ const double fcp_ij,
+ const double fcp_ik,
+ aed_type& aed,
+ fd_type &fd_ij)=0;
+ virtual size_t size()override=0;
+ virtual std::string label()override=0;
+ virtual std::vector<std::string> get_init_atoms(Config &c) override;
};
-//template<> inline Registry<D3_Base,Config&>::Map Registry<D3_Base,Config&>::registry{};
#endif
diff --git a/include/tadah/models/descriptors/d_base.h b/include/tadah/models/descriptors/d_base.h
index 77f215b..8685b31 100644
--- a/include/tadah/models/descriptors/d_base.h
+++ b/include/tadah/models/descriptors/d_base.h
@@ -67,10 +67,13 @@ public:
virtual bool is_init_for_atom(int Z);
virtual bool is_init_for_atoms(int Zi, int Zj);
virtual void init_for_atom(int Zi);
+ virtual void init_for_atoms(const std::vector<std::string> &Zs);
virtual void uninit_for_atom(int Zi);
+ static std::vector<std::string> get_init_atoms(Config &c, std::string type);
+ virtual std::vector<std::string> get_init_atoms(Config &c)=0;
private:
bool manage_memory=false; // who owns fcut
- std::bitset<119> init_for_atoms;
+ std::bitset<119> init_for_atoms_map;
};
#endif
diff --git a/include/tadah/models/descriptors/dm/dm_base.h b/include/tadah/models/descriptors/dm/dm_base.h
index 03ca072..825a1c5 100644
--- a/include/tadah/models/descriptors/dm/dm_base.h
+++ b/include/tadah/models/descriptors/dm/dm_base.h
@@ -26,6 +26,7 @@ public:
}
}
virtual ~DM_Base() {};
+ virtual std::vector<std::string> get_init_atoms(Config &c) override;
/** \brief Calculate \ref AED
*
diff --git a/include/tadah/models/descriptors/dm/dm_mEAD.hpp b/include/tadah/models/descriptors/dm/dm_mEAD.hpp
index c28018a..b549362 100644
--- a/include/tadah/models/descriptors/dm/dm_mEAD.hpp
+++ b/include/tadah/models/descriptors/dm/dm_mEAD.hpp
@@ -48,6 +48,8 @@ DM_mEAD<F>::DM_mEAD(Config &config): DM_Base(config),
std::cout << std::endl;
std::cout << "rhoisize: " << rhoisize << std::endl;
}
+ auto init_atoms = get_init_atoms(config);
+ init_for_atoms(init_atoms);
}
template <typename F>
diff --git a/src/d2_base.cpp b/src/d2_base.cpp
index 00abcd0..aefca65 100644
--- a/src/d2_base.cpp
+++ b/src/d2_base.cpp
@@ -1 +1,8 @@
#include <tadah/models/descriptors/d2/d2_base.h>
+
+std::vector<std::string> D2_Base::get_init_atoms(Config &c) {
+ std::vector<std::string> init_atoms(c.size("TYPE2B"));
+ c.get("TYPE2B", init_atoms);
+ init_atoms.erase(init_atoms.begin(), init_atoms.begin() + nparams+1);
+ return init_atoms;
+}
diff --git a/src/d2_blip.cpp b/src/d2_blip.cpp
index 7cf352f..3c16d5b 100644
--- a/src/d2_blip.cpp
+++ b/src/d2_blip.cpp
@@ -41,6 +41,9 @@ D2_Blip::D2_Blip(Config &c): D2_Base(c)
}
s=mius.size();
+
+ auto init_atoms = get_init_atoms(c);
+ init_for_atoms(init_atoms);
}
void D2_Blip::calc_aed(
diff --git a/src/d2_bp.cpp b/src/d2_bp.cpp
index 383995c..2b564f7 100644
--- a/src/d2_bp.cpp
+++ b/src/d2_bp.cpp
@@ -37,7 +37,9 @@ D2_BP::D2_BP(Config &c): D2_Base(c) {
throw std::runtime_error("At least one of SGRID2B values is zero.\n");
}
- s=mius.size();
+ s = mius.size();
+ auto init_atoms = get_init_atoms(c);
+ init_for_atoms(init_atoms);
}
void D2_BP::calc_aed(
diff --git a/src/d2_eam.cpp b/src/d2_eam.cpp
index c168631..90b8b79 100644
--- a/src/d2_eam.cpp
+++ b/src/d2_eam.cpp
@@ -31,6 +31,9 @@ D2_EAM::D2_EAM(Config &c): D2_Base(c)
gen_splines(ef.nrho, ef.drho, ef.frho, frho_spline);
gen_splines(ef.nr, ef.dr, ef.rhor, rhor_spline);
gen_splines(ef.nr, ef.dr, ef.z2r, z2r_spline);
+
+ auto init_atoms = get_init_atoms(c);
+ init_for_atoms(init_atoms);
}
void D2_EAM::calc_aed(
diff --git a/src/d2_lj.cpp b/src/d2_lj.cpp
index 64f33a3..3d41583 100644
--- a/src/d2_lj.cpp
+++ b/src/d2_lj.cpp
@@ -9,6 +9,9 @@ D2_LJ::D2_LJ(Config &c): D2_Base(c)
if (!c.get<bool>("INIT2B")) return;
init();
s=2;
+
+ auto init_atoms = get_init_atoms(c);
+ init_for_atoms(init_atoms);
}
void D2_LJ::calc_aed(
diff --git a/src/d2_mie.cpp b/src/d2_mie.cpp
index 2d35258..450c2d9 100644
--- a/src/d2_mie.cpp
+++ b/src/d2_mie.cpp
@@ -14,6 +14,8 @@ D2_MIE::D2_MIE(Config &c): D2_Base(c)
if (n<0 || m<0) {
throw std::runtime_error("Both Mie exponents must by positive\n");
}
+ auto init_atoms = get_init_atoms(c);
+ init_for_atoms(init_atoms);
}
void D2_MIE::calc_aed(
diff --git a/src/d2_zbl.cpp b/src/d2_zbl.cpp
index e158b5e..90542c7 100644
--- a/src/d2_zbl.cpp
+++ b/src/d2_zbl.cpp
@@ -37,6 +37,8 @@ D2_ZBL::D2_ZBL(Config &c): D2_Base(c)
a[i][j] = screening_length(Zi,Zj);
}
}
+ auto init_atoms = get_init_atoms(c);
+ init_for_atoms(init_atoms);
}
D2_ZBL::~D2_ZBL() {
if (a) {
diff --git a/src/d3_base.cpp b/src/d3_base.cpp
index bf59bc8..fe5fa69 100644
--- a/src/d3_base.cpp
+++ b/src/d3_base.cpp
@@ -1,3 +1,6 @@
#include <tadah/models/descriptors/d3/d3_base.h>
//template struct Registry<D3_Base, Config &>;
+std::vector<std::string> D3_Base::get_init_atoms(Config &c) {
+ return {};
+}
diff --git a/src/d_base.cpp b/src/d_base.cpp
index 3999fb4..2443396 100644
--- a/src/d_base.cpp
+++ b/src/d_base.cpp
@@ -79,7 +79,6 @@ D_Base::D_Base(Config &c):
double wi = c.get<double>("WATOMS",i);
int Z = PeriodicTable::find_by_symbol(symbol).Z;
weights[Z]=wi;
- init_for_atom(Z);
}
}
}
@@ -104,14 +103,28 @@ double D_Base::get_rcut() {
return fcut->get_rcut();
}
bool D_Base::is_init_for_atom(int Z) {
- return init_for_atoms[Z];
+ return init_for_atoms_map[Z];
}
bool D_Base::is_init_for_atoms(int Zi, int Zj) {
- return init_for_atoms[Zi] && init_for_atoms[Zj];
+ return init_for_atoms_map[Zi] && init_for_atoms_map[Zj];
}
void D_Base::init_for_atom(int Z) {
- init_for_atoms.set(Z);
+ init_for_atoms_map.set(Z);
+}
+void D_Base::init_for_atoms(const std::vector<std::string> &Zs) {
+ for (const auto &Z_str : Zs){
+ int Z = PeriodicTable::find_by_symbol(Z_str).Z;
+ init_for_atom(Z);
+ }
}
void D_Base::uninit_for_atom(int Z) {
- init_for_atoms.reset(Z);
+ init_for_atoms_map.reset(Z);
+}
+std::vector<std::string> D_Base::get_init_atoms(Config &c, std::string type) {
+ std::vector<std::string> init_atoms(c.size(type));
+ c.get(type, init_atoms);
+ std::unique_ptr<D_Base> d(CONFIG::factory<D_Base>(init_atoms[0]));
+ size_t nparams = d->nparams;
+ init_atoms.erase(init_atoms.begin(), init_atoms.begin() + nparams);
+ return init_atoms;
}
diff --git a/src/d_mjoin.cpp b/src/d_mjoin.cpp
index 1e67b93..9c1e368 100644
--- a/src/d_mjoin.cpp
+++ b/src/d_mjoin.cpp
@@ -147,11 +147,40 @@ std::vector<Config> D_mJoin::parse_config(Config &c, std::string type_str) {
for (const auto& k : d->keys) {
int n = std::stoi(*it++);
+ c1.add(type_str,n);
for (int j = 0; j < n; ++j) {
- c1.add(k,*(data_map[k]++)); /// Problem?
+ c1.add(k,*(data_map[k]++));
}
}
+ // read init atoms
+ size_t found_init_atoms=0;
+ while (it != types.end()) {
+ if (it->find(prefix) == 0) {
+ break;
+ }
+ c1.add(type_str,*it++);
+ found_init_atoms++;
+ }
+ // if (it != types.end() && it != types.begin()) {
+ // --it;
+ // }
+ if (!found_init_atoms) {
+ throw std::runtime_error(
+ "Error: No element types specified. "
+ "Please provide element types for this calculator. "
+ "For example: '"+token+" Ti Ti Ti Nb' sets the calculator to compute Ti-Ti and Ti-Nb interactions. "
+ "Token: " + token);
+ }
+
+ if (found_init_atoms % 2 != 0) {
+ throw std::runtime_error(
+ "Error: Element types must be provided in pairs. "
+ "Ensure each element is paired correctly. "
+ "For instance, '" + token + " Ti * Nb Zr' means that interactions of Ti with any atom, as well as Nb-Zr, will be computed. "
+ "Token: " + token);
+ }
+
configs.push_back(c1);
delete d;
}
diff --git a/src/dm_base.cpp b/src/dm_base.cpp
index 7fe63ac..c6247e5 100644
--- a/src/dm_base.cpp
+++ b/src/dm_base.cpp
@@ -1,3 +1,10 @@
#include <tadah/models/descriptors/dm/dm_base.h>
void DM_Base::set_rfidx(size_t rfidx_) { rfidx=rfidx_; }
size_t DM_Base::get_rfidx() { return rfidx; }
+
+std::vector<std::string> DM_Base::get_init_atoms(Config &c) {
+ std::vector<std::string> init_atoms(c.size("TYPEMB"));
+ c.get("TYPEMB", init_atoms);
+ init_atoms.erase(init_atoms.begin(), init_atoms.begin() + nparams+1);
+ return init_atoms;
+}
diff --git a/src/dm_blip.cpp b/src/dm_blip.cpp
index c68b8ec..48408d2 100644
--- a/src/dm_blip.cpp
+++ b/src/dm_blip.cpp
@@ -40,6 +40,8 @@ DM_Blip::DM_Blip(Config &c): DM_Base(c),
std::cout << std::endl;
std::cout << "rhoisize: " << rhoisize << std::endl;
}
+ auto init_atoms = get_init_atoms(c);
+ init_for_atoms(init_atoms);
}
void DM_Blip::calc_aed(
diff --git a/src/dm_ead.cpp b/src/dm_ead.cpp
index b7419b3..8cb83aa 100644
--- a/src/dm_ead.cpp
+++ b/src/dm_ead.cpp
@@ -47,6 +47,8 @@ DM_EAD::DM_EAD(Config &config): DM_Base(config),
std::cout << std::endl;
std::cout << "rhoisize: " << rhoisize << std::endl;
}
+ auto init_atoms = get_init_atoms(config);
+ init_for_atoms(init_atoms);
}
void DM_EAD::calc_aed(
diff --git a/src/dm_eam.cpp b/src/dm_eam.cpp
index 8450987..3408b29 100644
--- a/src/dm_eam.cpp
+++ b/src/dm_eam.cpp
@@ -32,6 +32,8 @@ DM_EAM::DM_EAM(Config &c): DM_Base(c)
gen_splines(ef.nr, ef.dr, ef.z2r, z2r_spline);
rhoisize = 1;
+ auto init_atoms = get_init_atoms(c);
+ init_for_atoms(init_atoms);
}
void DM_EAM::calc_aed(
--
GitLab