From 2b2454d6c28da845788e797c32612e7ffa79a93f Mon Sep 17 00:00:00 2001
From: Marcin Kirsz <mkirsz@ed.ac.uk>
Date: Wed, 30 Oct 2024 18:33:37 +0000
Subject: [PATCH] StructureDB to check ATOMS and WATOMS consistency and set
defaults if needed
---
include/tadah/mlip/structure.h | 4 +-
include/tadah/mlip/structure_db.h | 15 +++-
src/structure.cpp | 3 +-
src/structure_db.cpp | 136 +++++++++++++++++++++---------
4 files changed, 108 insertions(+), 50 deletions(-)
diff --git a/include/tadah/mlip/structure.h b/include/tadah/mlip/structure.h
index f42580e..47ef531 100644
--- a/include/tadah/mlip/structure.h
+++ b/include/tadah/mlip/structure.h
@@ -9,7 +9,7 @@
#include <fstream>
#include <iomanip>
#include <vector>
-#include <unordered_set>
+#include <set>
/**
* Container for a collection of Atom(s).
@@ -109,7 +109,7 @@ struct Structure {
double sweight=1.0;
/** List of chemical elements in this structure. */
- std::unordered_set<Element> unique_elements;
+ std::set<Element> unique_elements;
/** @return a reference to the i-th Atom.
*
diff --git a/include/tadah/mlip/structure_db.h b/include/tadah/mlip/structure_db.h
index 678a5e3..833c3cb 100644
--- a/include/tadah/mlip/structure_db.h
+++ b/include/tadah/mlip/structure_db.h
@@ -1,14 +1,15 @@
#ifndef STRUCTURE_DB_h
#define STRUCTURE_DB_h
-#include <tadah/mlip/structure.h>
+#include <tadah/core/element.h>
#include <tadah/core/config.h>
+#include <tadah/mlip/structure.h>
#include <string>
#include <iostream>
#include <fstream>
#include <vector>
-#include <unordered_set>
+#include <set>
/**
* Container for a collection of Structure(s).
@@ -49,7 +50,7 @@ struct StructureDB {
* \note
* Required Config key: \ref DBFILE
*/
- StructureDB(const Config &config);
+ StructureDB(Config &config);
/** Add structures listed in the config file
*
@@ -134,7 +135,7 @@ struct StructureDB {
size_t calc_natoms(size_t n) const;
/** Return unique elements for all Structures. */
- std::unordered_set<Element> get_unique_elements();
+ std::set<Element> get_unique_elements() const;
/** Count number of structures and atoms in all datasets from the Config file. */
static std::pair<int,int> count(const Config &c);
@@ -143,5 +144,11 @@ struct StructureDB {
static std::pair<int,int> count(const std::string fn);
void clear_nn();
+
+ /** Check consistency of the ATOMS key. */
+ void check_atoms_key(Config &config) const;
+
+ /** Check consistency of the WATOMS key. Add if missing*/
+ void check_watoms_key(Config &config) const;
};
#endif
diff --git a/src/structure.cpp b/src/structure.cpp
index d6e0b8d..acb4c1b 100644
--- a/src/structure.cpp
+++ b/src/structure.cpp
@@ -77,7 +77,6 @@ int Structure::read(std::ifstream &ifs) {
char symbol[3];
double px,py,pz,fx,fy,fz;
- PeriodicTable pd;
while(std::getline(ifs,line)) {
if(line.empty()) break;
//if(line == " ") break;
@@ -85,7 +84,7 @@ int Structure::read(std::ifstream &ifs) {
std::istringstream tmp(line);
tmp >> symbol >> px >> py >> pz >> fx >> fy >> fz;
- Element e = pd.find_by_symbol(symbol);
+ Element e = PeriodicTable::find_by_symbol(symbol);
unique_elements.insert(e);
atoms.push_back(Atom(e,px,py,pz,fx,fy,fz));
//Atom &a = atoms.back();
diff --git a/src/structure_db.cpp b/src/structure_db.cpp
index c6e9733..cdaf502 100644
--- a/src/structure_db.cpp
+++ b/src/structure_db.cpp
@@ -1,26 +1,28 @@
#include <tadah/mlip/structure_db.h>
StructureDB::StructureDB() {}
-StructureDB::StructureDB(const Config &config) {
- add(config);
+StructureDB::StructureDB(Config &config) {
+ add(config);
+ check_atoms_key(config);
+ check_watoms_key(config);
}
void StructureDB::add(const std::string fn) {
- std::ifstream ifs(fn);
- if (!ifs.is_open()) {
- throw std::runtime_error("DBFILE does not exist: "+fn);
- }
- while (true) {
- structures.push_back(Structure());
- int t = structures.back().read(ifs);
+ std::ifstream ifs(fn);
+ if (!ifs.is_open()) {
+ throw std::runtime_error("DBFILE does not exist: "+fn);
+ }
+ while (true) {
+ structures.push_back(Structure());
+ int t = structures.back().read(ifs);
- // did we read structure succesfully?
- // if not remove last object from the list
- if (t==1) structures.pop_back();
+ // did we read structure succesfully?
+ // if not remove last object from the list
+ if (t==1) structures.pop_back();
- if (ifs.eof()) break;
- }
- ifs.close();
+ if (ifs.eof()) break;
+ }
+ ifs.close();
}
int StructureDB::add(const std::string fn, int first, int N) {
std::ifstream ifs(fn);
@@ -50,59 +52,59 @@ int StructureDB::add(const std::string fn, int first, int N) {
}
void StructureDB::add(const Structure &s) {
- structures.push_back(s);
+ structures.push_back(s);
}
void StructureDB::remove(size_t i) {
- structures.erase(structures.begin()+i);
+ structures.erase(structures.begin()+i);
}
void StructureDB::add(const Config &config) {
- for (const std::string &s : config("DBFILE")) {
- dbidx.push_back(size());
- add(s);
- }
+ for (const std::string &s : config("DBFILE")) {
dbidx.push_back(size());
+ add(s);
+ }
+ dbidx.push_back(size());
}
size_t StructureDB::size() const {
- return structures.size();
+ return structures.size();
}
size_t StructureDB::size(size_t n) const {
- return dbidx[n+1]-dbidx[n];
+ return dbidx[n+1]-dbidx[n];
}
Structure &StructureDB::operator()(size_t s) {
- return structures[s];
+ return structures[s];
}
const Structure &StructureDB::operator()(size_t s) const {
- return structures[s];
+ return structures[s];
}
Atom &StructureDB::operator()(size_t s, size_t a) {
- return structures[s].atoms[a];
+ return structures[s].atoms[a];
}
size_t StructureDB::calc_natoms() const {
- size_t natoms=0;
- for (auto struc: structures) natoms += struc.natoms();
- return natoms;
+ size_t natoms=0;
+ for (auto struc: structures) natoms += struc.natoms();
+ return natoms;
}
size_t StructureDB::calc_natoms(size_t n) const {
- size_t start = dbidx[n];
- size_t stop = dbidx[n+1];
- size_t natoms=0;
- for (size_t i=start; i<stop; ++i) {
- natoms += (*this)(i).natoms();
- }
- return natoms;
+ size_t start = dbidx[n];
+ size_t stop = dbidx[n+1];
+ size_t natoms=0;
+ for (size_t i=start; i<stop; ++i) {
+ natoms += (*this)(i).natoms();
+ }
+ return natoms;
}
-std::unordered_set<Element> StructureDB::get_unique_elements() {
- std::unordered_set<Element> s;
- for (const auto & st: structures) s.insert(
- st.unique_elements.begin(),st.unique_elements.end());
- return s;
+std::set<Element> StructureDB::get_unique_elements() const {
+ std::set<Element> s;
+ for (const auto & st: structures) s.insert(
+ st.unique_elements.begin(),st.unique_elements.end());
+ return s;
}
template <typename T,typename U>
@@ -136,5 +138,55 @@ std::pair<int,int> StructureDB::count(const std::string fn){
return res;
}
void StructureDB::clear_nn() {
- for (auto &struc: structures) struc.clear_nn();
+ for (auto &struc: structures) struc.clear_nn();
+}
+void StructureDB::check_atoms_key(Config &config) const {
+ std::set<Element> unique_elements = get_unique_elements();
+ bool error=false;
+
+ if (config.exist("ATOMS")) {
+ // user set this key so here we check does it correspond to unique_elements
+ if (unique_elements.size()!=config.size("ATOMS")) {
+ error=true;
+ }
+
+ auto set_it = unique_elements.begin();
+ auto atoms_it = config("ATOMS").begin();
+ while (set_it != unique_elements.end() && atoms_it != config("ATOMS").end()) {
+ if (set_it->symbol != *atoms_it) {
+ error=true;
+ }
+ ++set_it;
+ ++atoms_it;
+ }
+ if (error) {
+ throw std::runtime_error("\n"
+ "Mismatch between elements in datasets and ATOMS in the config file.\n"
+ "Please either update the ATOMS in the config file or remove ATOMS\n"
+ "key completely. Tadah! will automatically configure this key.\n"
+ );
+ }
+ } else {
+ for (const auto &s : unique_elements) config.add("ATOMS", s.symbol);
+ }
+}
+void StructureDB::check_watoms_key(Config &config) const {
+ std::set<Element> unique_elements = get_unique_elements();
+ bool error=false;
+
+ if (config.exist("WATOMS")) {
+ // user set this key so here we check does it correspond to unique_elements
+ if (unique_elements.size()!=config.size("WATOMS")) {
+ error=true;
+ }
+ if (error) {
+ throw std::runtime_error("\n"
+ "Mismatch between elements in datasets and WATOMS in the config file.\n"
+ "Please either update the WATOMS in the config file or remove WATOMS\n"
+ "key completely. In the latter case Tadah! will use default values.\n"
+ );
+ }
+ } else {
+ for (const auto &s : unique_elements) config.add("WATOMS", s.Z);
+ }
}
--
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