From dfa76e78c6a6289f0c6811c7c44e1745aa8e5f9a Mon Sep 17 00:00:00 2001
From: mkirsz <s1351949@sms.ed.ac.uk>
Date: Fri, 22 Nov 2024 23:55:23 +0000
Subject: [PATCH] Update to random_shuffle
---
include/tadah/mlip/models/basis.h | 153 +++++++++++++++---------------
1 file changed, 79 insertions(+), 74 deletions(-)
diff --git a/include/tadah/mlip/models/basis.h b/include/tadah/mlip/models/basis.h
index 74a4071..80f2bbe 100644
--- a/include/tadah/mlip/models/basis.h
+++ b/include/tadah/mlip/models/basis.h
@@ -6,98 +6,103 @@
#include <tadah/core/core_types.h>
#include <tadah/core/config.h>
+#include <algorithm>
#include <numeric>
#include <stdexcept>
#include <vector>
template <typename K>
class Basis {
- private:
- Config &config;
- int verbose;
- public:
- Matrix b;
- t_type T; // Vectors corresponding to basis vectors
- Basis(Config &c):
- config(c),
- verbose(c.get<int>("VERBOSE"))
+private:
+ Config &config;
+ int verbose;
+public:
+ Matrix b;
+ t_type T; // Vectors corresponding to basis vectors
+ Basis(Config &c):
+ config(c),
+ verbose(c.get<int>("VERBOSE"))
- {}
+ {}
- void set_basis(Matrix &b_) {
- b=b_;
- }
- void build_random_basis(size_t s, StDescriptorsDB &st_desc_db) {
+ void set_basis(Matrix &b_) {
+ b=b_;
+ }
+ void build_random_basis(size_t s, StDescriptorsDB &st_desc_db) {
- // generate indices
- std::vector<std::tuple<size_t,size_t>> indices;
- size_t counter=0;
- for( size_t st = 0; st < st_desc_db.size(); st++ ) {
- for( size_t a = 0; a < st_desc_db(st).naed() ; a++ ) {
- indices.push_back(std::tuple<size_t,size_t>(st,a));
- counter++;
- }
- }
+ // generate indices
+ std::vector<std::tuple<size_t,size_t>> indices;
+ size_t counter=0;
+ for( size_t st = 0; st < st_desc_db.size(); st++ ) {
+ for( size_t a = 0; a < st_desc_db(st).naed() ; a++ ) {
+ indices.push_back(std::tuple<size_t,size_t>(st,a));
+ counter++;
+ }
+ }
- if (counter < s) {
- throw std::runtime_error("The number of requestd basis vectors is\n \
- larger than the amount of available AEDs\n");
- }
+ if (counter < s) {
+ throw std::runtime_error("The number of requestd basis vectors is\n \
+larger than the amount of available AEDs\n");
+ }
- std::random_shuffle(indices.begin(), indices.end());
+ std::random_device rd;
+ std::default_random_engine rng(rd()); // Initialize random engine
+ std::shuffle(indices.begin(), indices.end(),rng);
- b.resize(st_desc_db(0).dim(),s);
- b.set_zero();
- // set first basis function as "bias vector"
- b(0,0)=1;
- 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);
- for (size_t j=0; j<aed.size(); ++j) {
- b(j,i)=aed[j];
- }
- }
- }
- void prep_basis_for_krr(StDescriptorsDB &st_desc_db,
- StructureDB &stdb) {
+ b.resize(st_desc_db(0).dim(),s);
+ b.set_zero();
+ // set first basis function as "bias vector"
+ b(0,0)=1;
+ 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);
+ for (size_t j=0; j<aed.size(); ++j) {
+ b(j,i)=aed[j];
+ }
+ }
+ }
+ void prep_basis_for_krr(StDescriptorsDB &st_desc_db,
+ StructureDB &stdb) {
- size_t s = config.get<size_t>("SBASIS");
+ size_t s = config.get<size_t>("SBASIS");
- if (stdb.size() != st_desc_db.size()) {
- throw std::runtime_error("The size of StructureDB is different \n \
- from StDescriptorsDB. This is likely to be a bug.\n");
- }
+ if (stdb.size() != st_desc_db.size()) {
+ throw std::runtime_error("The size of StructureDB is different \n \
+from StDescriptorsDB. This is likely to be a bug.\n");
+ }
- // generate indices
- std::vector<size_t> indices;
- for( size_t st = 0; st < stdb.size(); st++ ) {
- indices.push_back(st);
- }
+ // generate indices
+ std::vector<size_t> indices;
+ for( size_t st = 0; st < stdb.size(); st++ ) {
+ indices.push_back(st);
+ }
- if (indices.size() < s) {
- throw std::runtime_error("The number of requestd basis vectors is\n \
- larger than the amount of available AEDs\n");
- }
+ if (indices.size() < s) {
+ throw std::runtime_error("The number of requestd basis vectors is\n \
+larger than the amount of available AEDs\n");
+ }
- std::random_shuffle(indices.begin(), indices.end());
+ std::random_device rd;
+ std::default_random_engine rng(rd()); // Initialize random engine
+ std::shuffle(indices.begin(), indices.end(),rng);
- b.resize(st_desc_db(0).dim(),s);
- T.resize(s);
- b.set_zero();
- b(0,0)=1;
- // Here we add all atomic energy descriptors into single
- // descriptor which represents total energy of this configuration
- for (size_t i=1; i<s; ++i) {
- 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);
- for (size_t j=0; j<aed.size(); ++j) {
- b(j,i)+=aed[j]/st_desc_db(st).naed();
- }
- }
- }
+ b.resize(st_desc_db(0).dim(),s);
+ T.resize(s);
+ b.set_zero();
+ b(0,0)=1;
+ // Here we add all atomic energy descriptors into single
+ // descriptor which represents total energy of this configuration
+ for (size_t i=1; i<s; ++i) {
+ 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);
+ for (size_t j=0; j<aed.size(); ++j) {
+ b(j,i)+=aed[j]/st_desc_db(st).naed();
}
+ }
+ }
+ }
};
#endif
--
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