Dealing with ATOMS and WATOMS

include/tadah/mlip/descriptors_calc.h

@@ -122,6 +122,7 @@ class DescriptorsCalc: public DC_Base {
         void calc(const Structure &st, StDescriptors &std);
         void calc_dimer(const Structure &st, StDescriptors &std);
         void common_constructor();
+        double weights[119];  // ignore zero index; w[1]->H
 
 };
 

include/tadah/mlip/structure_db.h

@@ -58,7 +58,7 @@ struct StructureDB {
      *      Required Config key: \ref DBFILE
      *
      */
-    void add(const Config &config);
+    void add(Config &config);
 
     /** Add all structures from a file */
     void add(const std::string fn);
@@ -137,6 +137,12 @@ struct StructureDB {
     /** Return unique elements for all Structures. */
     std::set<Element> get_unique_elements() const;
 
+    /** Find unique elements in provided Config file */
+    static std::set<Element> find_unique_elements(const Config &c);
+
+    /** Find unique elements in provided file */
+    static std::set<Element> find_unique_elements(const std::string &fn);
+
     /** Count number of structures and atoms in all datasets from the Config file. */
     static std::pair<int,int> count(const Config &c);
 
@@ -146,9 +152,9 @@ struct StructureDB {
     void clear_nn();
 
     /** Check consistency of the ATOMS key. */
-    void check_atoms_key(Config &config) const;
+    static void check_atoms_key(Config &config, std::set<Element> &unique_elements);
 
     /** Check consistency of the WATOMS key. Add if missing*/
-    void check_watoms_key(Config &config) const;
+    static void check_watoms_key(Config &config, std::set<Element> &unique_elements);
 };
 #endif

src/structure_db.cpp

 #include <tadah/mlip/structure_db.h>
+#include <tadah/core/periodic_table.h>
+#include <cstdio>
 
 StructureDB::StructureDB() {}
 StructureDB::StructureDB(Config &config) {
   add(config);
-  check_atoms_key(config);
-  check_watoms_key(config);
 }
 
 void StructureDB::add(const std::string fn) {
@@ -59,7 +59,7 @@ void StructureDB::remove(size_t i) {
   structures.erase(structures.begin()+i);
 }
 
-void StructureDB::add(const Config &config) {
+void StructureDB::add(Config &config) {
   for (const std::string &s : config("DBFILE")) {
     dbidx.push_back(size());
     add(s);
@@ -106,6 +106,50 @@ std::set<Element> StructureDB::get_unique_elements() const {
       st.unique_elements.begin(),st.unique_elements.end());
   return s;
 }
+std::set<Element> StructureDB::find_unique_elements(const std::string &fn) {
+  std::set<Element> s;
+  std::ifstream datafile(fn);
+  std::string line;
+
+  if (!datafile.is_open()) {
+    std::cerr << "Could not open the file." << std::endl;
+  }
+
+  char symbol[3];
+
+  // move to first non empty line
+  while (std::getline(datafile, line)) {
+    if (!line.empty()) {
+      break;
+    }
+  }
+  // skip 
+  for (int i = 0; i < 7; ++i) {
+    std::getline(datafile, line);
+  }
+  while (std::getline(datafile, line)) {
+    if(line.empty()) {
+      for (int i = 0; i < 8; ++i) {
+        if (!std::getline(datafile, line)) {
+          // Handle the case where there are not enough lines
+          break; // or handle the error
+        }
+      }
+      continue;
+    }
+    sscanf(line.c_str(), "%2s", symbol);
+    s.insert(PeriodicTable::find_by_symbol(symbol));
+  }
+  return s;
+}
+std::set<Element> StructureDB::find_unique_elements(const Config &c) {
+  std::set<Element> s;
+  for (const auto& fn: c("DBFILE")) {
+    std::set<Element> temp = find_unique_elements(fn);
+    s.insert(temp.begin(), temp.end());
+  }
+  return s;
+}
 
 template <typename T,typename U>                                                   
 std::pair<T,U> operator+(const std::pair<T,U>  &l,const std::pair<T,U>  &r) {   
@@ -140,8 +184,7 @@ std::pair<int,int> StructureDB::count(const std::string fn){
 void StructureDB::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();
+void StructureDB::check_atoms_key(Config &config, std::set<Element> &unique_elements) {
   bool error=false;
 
   if (config.exist("ATOMS")) {
@@ -153,7 +196,7 @@ void StructureDB::check_atoms_key(Config &config) const {
     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)  {
+      if (set_it->symbol != (*atoms_it))  {
         error=true;
       }
       ++set_it;
@@ -170,8 +213,7 @@ void StructureDB::check_atoms_key(Config &config) const {
     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();
+void StructureDB::check_watoms_key(Config &config, std::set<Element> &unique_elements) {
   bool error=false;
 
   if (config.exist("WATOMS")) {