From 00fe58b57bdc3375651e8912dfbca43667749edd Mon Sep 17 00:00:00 2001
From: mkirsz <s1351949@sms.ed.ac.uk>
Date: Mon, 25 Nov 2024 18:09:14 +0000
Subject: [PATCH] Helper methods for comparison
---
include/tadah/mlip/atom.h | 6 ++++++
include/tadah/mlip/structure.h | 15 +++++++++++++-
src/atom.cpp | 36 ++++++++++++++++++++--------------
src/structure.cpp | 17 ++++++++++++++++
4 files changed, 58 insertions(+), 16 deletions(-)
diff --git a/include/tadah/mlip/atom.h b/include/tadah/mlip/atom.h
index 4a6fd87..04d82a4 100644
--- a/include/tadah/mlip/atom.h
+++ b/include/tadah/mlip/atom.h
@@ -79,5 +79,11 @@ struct Atom: public Element {
*/
bool operator==(const Atom &) const;
+ /** Return true if both atoms have the same position and type.
+ *
+ * This method compares chemical type and position only
+ */
+ bool is_the_same(const Atom &, double thr=1e-6) const;
+
};
#endif
diff --git a/include/tadah/mlip/structure.h b/include/tadah/mlip/structure.h
index 1fa835b..9648e65 100644
--- a/include/tadah/mlip/structure.h
+++ b/include/tadah/mlip/structure.h
@@ -251,10 +251,23 @@ struct Structure {
* This operator compares cell, stress tensor, number of atoms,
* eweight, fweight and sweight, all atom positions and forces.
*
- * It does NOT compare labels/
+ * Assumes atoms have the same order.
+ *
+ * It does NOT compare labels.
*/
bool operator==(const Structure& st) const;
+ /** Return true if both structures are the same.
+ *
+ * This method compares cell vectors, number of atoms,
+ * species and atomic coordinates
+ *
+ * Order ot atoms does not matter.
+ *
+ * It does NOT compare energies, stresses, forces and labels.
+ */
+ bool is_the_same(const Structure& st, double thr=1e-6) const;
+
// move iterator forward to the next structure
// return number of atoms in the structure
// return 0 if there is no more structures
diff --git a/src/atom.cpp b/src/atom.cpp
index a84be1e..164a6c4 100644
--- a/src/atom.cpp
+++ b/src/atom.cpp
@@ -5,25 +5,31 @@
Atom::Atom() {}
Atom::Atom(const Element &element,
- const double px, const double py, const double pz,
- const double fx, const double fy, const double fz):
- Element(element),
- position(px,py,pz),
- force(fx,fy,fz)
+ const double px, const double py, const double pz,
+ const double fx, const double fy, const double fz):
+ Element(element),
+ position(px,py,pz),
+ force(fx,fy,fz)
{}
std::ostream& operator<<(std::ostream& os, const Atom& atom)
{
- os << (Element&)atom;
- os << "Coordinates: " << std::left << atom.position << std::endl;
- os << "Force: " << std::left << atom.force << std::endl;
- return os;
+ os << (Element&)atom;
+ os << "Coordinates: " << std::left << atom.position << std::endl;
+ os << "Force: " << std::left << atom.force << std::endl;
+ return os;
}
bool Atom::operator==(const Atom &a) const {
- double EPSILON = std::numeric_limits<double>::epsilon();
- return
- position.isApprox(a.position, EPSILON)
- && force.isApprox(a.force, EPSILON)
- && Element::operator==(a)
- ;
+ double EPSILON = std::numeric_limits<double>::epsilon();
+ return
+ position.isApprox(a.position, EPSILON)
+ && force.isApprox(a.force, EPSILON)
+ && Element::operator==(a)
+ ;
+}
+bool Atom::is_the_same(const Atom &a, double thr) const {
+ return
+ position.isApprox(a.position, thr)
+ && Element::operator==(a)
+ ;
}
diff --git a/src/structure.cpp b/src/structure.cpp
index 4aa0675..f5c6748 100644
--- a/src/structure.cpp
+++ b/src/structure.cpp
@@ -192,6 +192,23 @@ bool Structure::operator==(const Structure& st) const
}
return result;
}
+bool Structure::is_the_same(const Structure& st, double thr) const
+{
+ bool result =
+ cell.isApprox(st.cell, thr)
+ && natoms()==st.natoms();
+ if (!result) return result;
+
+ size_t count=0;;
+ for (size_t i=0;i<natoms();++i) {
+ for (size_t j=i;j<natoms();++j) {
+ result = atoms[i].is_the_same(st.atoms[j], thr);
+ if (result) count++;
+ }
+ }
+
+ return count==natoms() ? true : false;
+}
int Structure::next_structure(std::ifstream &ifs) {
std::string line;
std::getline(ifs,line);
--
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