From 02b505005e36e79fc520f1b455fc1ce942913b7e Mon Sep 17 00:00:00 2001
From: Niklaus Johner <nij2003@med.cornell.edu>
Date: Wed, 21 Mar 2012 14:55:38 -0400
Subject: [PATCH] Added functions to calculate the minimal distance between the
points In two Vec3List, with and without periodic boundary conditions
---
modules/geom/pymod/export_vecmat3_op.cc | 6 +++++-
modules/geom/src/vecmat3_op.cc | 21 +++++++++++++++++++++
modules/geom/src/vecmat3_op.hh | 20 +++++++++++++++++++-
3 files changed, 45 insertions(+), 2 deletions(-)
diff --git a/modules/geom/pymod/export_vecmat3_op.cc b/modules/geom/pymod/export_vecmat3_op.cc
index 75787dd53..9e49c8686 100644
--- a/modules/geom/pymod/export_vecmat3_op.cc
+++ b/modules/geom/pymod/export_vecmat3_op.cc
@@ -38,7 +38,8 @@ Real (*Mat3Comp)(const Mat3& m, unsigned int i, unsigned int j) = &Comp;
Real (*Mat3Minor)(const Mat3& m, unsigned int i, unsigned int j) = &Minor;
Vec3 (*Vec3Min)(const Vec3&, const Vec3&) = &Min;
Vec3 (*Vec3Max)(const Vec3&, const Vec3&) = &Max;
-
+Real (*Vec3Distance2WithPBC)(const Vec3&, const Vec3&, const Vec3&) = &Distance2WithPBC;
+Real (*Vec3DistanceWithPBC)(const Vec3&, const Vec3&, const Vec3&) = &DistanceWithPBC;
void export_VecMat3_op()
{
@@ -64,5 +65,8 @@ void export_VecMat3_op()
def("OrthogonalVector",OrthogonalVector);
def("Min",Vec3Min);
def("Max",Vec3Max);
+ def("Distance2WithPBC",Vec3Distance2WithPBC);
+ def("DistanceWithPBC",Vec3DistanceWithPBC);
def("MinDistance",MinDistance);
+ def("MinDistanceWithPBC",MinDistanceWithPBC);
}
diff --git a/modules/geom/src/vecmat3_op.cc b/modules/geom/src/vecmat3_op.cc
index 8dd8eb11b..ca7497b8c 100644
--- a/modules/geom/src/vecmat3_op.cc
+++ b/modules/geom/src/vecmat3_op.cc
@@ -192,6 +192,7 @@ Real DihedralAngle(const Vec3& p1, const Vec3& p2, const Vec3& p3,
Dot(r12cross, r23cross));
}
+
Real MinDistance(const Vec3List& l1, const Vec3List& l2)
{
// returns the minimal distance between two sets of points (Vec3List)
@@ -207,4 +208,24 @@ Real MinDistance(const Vec3List& l1, const Vec3List& l2)
return std::sqrt(min);
}
+Real MinDistanceWithPBC(const Vec3List& l1, const Vec3List& l2, Vec3& basis_vec)
+{
+ // returns the minimal distance between two sets of points (Vec3List)
+ // given the periodic boundary condition along x,y,z given in the basis_vec
+ if (l1.size()==0 || l2.size()==0){throw std::runtime_error("cannot calculate minimal distance: empty Vec3List");}
+ Real min=Length2(*l1.begin()-*l2.begin());
+ Real d;
+ Vec3 v;
+ for (int i=0; i<3; i++) {
+ basis_vec[i]=std::fabs(basis_vec[i]);
+ }
+ for (Vec3List::const_iterator p1=l1.begin(),e1=l1.end(); p1!=e1; p1++) {
+ for (Vec3List::const_iterator p2=l2.begin(),e2=l2.end(); p2!=e2; p2++) {
+ d=Distance2WithPBC(*p1, *p2, basis_vec);
+ if (d<min) min=d;
+ }
+ }
+ return std::sqrt(min);
+}
+
} // ns
diff --git a/modules/geom/src/vecmat3_op.hh b/modules/geom/src/vecmat3_op.hh
index 373b9561b..53918c2e5 100644
--- a/modules/geom/src/vecmat3_op.hh
+++ b/modules/geom/src/vecmat3_op.hh
@@ -194,9 +194,27 @@ inline Real Distance(const Vec3& p1, const Vec3& p2)
return Length(p1-p2);
}
+
+//! return the squared distance between two points with periodic boundaries in x,y,z given in basis_vec
+inline Real Distance2WithPBC(const Vec3& v1, const Vec3& v2, const Vec3& basis_vec){
+ Vec3 v;
+ v=v1-v2;
+ for (int i=0; i<3; i++) {
+ if (std::fabs(v[i])>basis_vec[i]/2.){
+ v[i]=std::fabs(v[i])-basis_vec[i]*int(std::fabs(v[i])/basis_vec[i]+0.5);
+ }
+ }
+ return Length2(v);
+}
+//! return the distance between two points with periodic boundaries in x,y,z given in basis_vec
+inline Real DistanceWithPBC(const Vec3& v1, const Vec3& v2, const Vec3& basis_vec){
+ return sqrt(Distance2WithPBC(v1, v2, basis_vec));
+}
//! returns the minimal distance between the points in two Vec3List
Real MinDistance(const Vec3List& l1, const Vec3List& l2);
-
+//! returns the minimal distance between the points in two Vec3List
+// with periodic boundaries in x,y,z given in basis_vec
+Real MinDistanceWithPBC(const Vec3List& l1, const Vec3List& l2, Vec3& basis_vec);
} // ns
#endif
--
GitLab