From d419feee38196407beb007f33ea63f71631f11aa Mon Sep 17 00:00:00 2001
From: Niklaus Johner <nij2003@med.cornell.edu>
Date: Tue, 22 Oct 2013 11:15:45 -0400
Subject: [PATCH] Added function to retrieve unit cell vectors from CoordFrame.
The function to calculate the unit cell vectors was added to geom
---
modules/geom/src/vecmat3_op.cc | 17 +++++++++++++++++
modules/geom/src/vecmat3_op.hh | 3 ++-
modules/mol/base/pymod/export_coord_frame.cc | 1 +
modules/mol/base/src/coord_frame.cc | 5 +++++
modules/mol/base/src/coord_frame.hh | 4 +++-
5 files changed, 28 insertions(+), 2 deletions(-)
diff --git a/modules/geom/src/vecmat3_op.cc b/modules/geom/src/vecmat3_op.cc
index 2653a081f..dfa969cd4 100644
--- a/modules/geom/src/vecmat3_op.cc
+++ b/modules/geom/src/vecmat3_op.cc
@@ -250,6 +250,23 @@ std::vector<unsigned int> MinDistanceIndices(const Vec3List& l1, const Vec3List&
}
return il;
}
+
+Vec3List CalculateUnitCellVectors(const Vec3& ucell_size, const Vec3& ucell_angles){
+ // Calculates the unit cell vectors from their sizes and angles.
+ // The angles are given as Vec3(gamma,beta,alpha)
+ geom::Vec3List ucell_vec;
+ geom::Vec3 ucell_vec1,ucell_vec2,ucell_vec3;
+ Real cosa=cos(ucell_angles[2]),cosb=cos(ucell_angles[1]);
+ Real cosg=cos(ucell_angles[0]),sing=sin(ucell_angles[0]);
+ ucell_vec1=geom::Vec3(ucell_size[0],0,0);
+ ucell_vec2=ucell_size[1]*geom::Vec3(cosg,sing,0);
+ ucell_vec3=ucell_size[2]*geom::Vec3(cosb,(cosa-cosb*cosg)/sing,\
+ pow(1-(cosa*cosa+cosb*cosb-2.*cosa*cosb*cosg)/(sing*sing),0.5));
+ ucell_vec.push_back(ucell_vec1);
+ ucell_vec.push_back(ucell_vec2);
+ ucell_vec.push_back(ucell_vec3);
+ return ucell_vec;
+}
Vec3 WrapVec3(const Vec3& v1,const Vec3& box_center,const Vec3& basis_vec){
Vec3 v;
diff --git a/modules/geom/src/vecmat3_op.hh b/modules/geom/src/vecmat3_op.hh
index b4a18d3cb..1c4ef40bb 100644
--- a/modules/geom/src/vecmat3_op.hh
+++ b/modules/geom/src/vecmat3_op.hh
@@ -218,7 +218,8 @@ Real DLLEXPORT_OST_GEOM MinDistanceWithPBC(const Vec3List& l1, const Vec3List& l
//! returns the indices index1, index2 corresponding to the points in
//! the Vec3List l1 and l2 having the minimal distance.
std::vector<unsigned int> DLLEXPORT_OST_GEOM MinDistanceIndices(const Vec3List& l1, const Vec3List& l2);
-
+//! Calculates the Unit Cell Vectors from their sizes and angles (given as Vec3(gamma,beta,alpha)).
+Vec3List DLLEXPORT_OST_GEOM CalculateUnitCellVectors(const Vec3& ucell_size, const Vec3& ucell_angles);
//!wraps a vector in a box with periodic boundaries
Vec3 DLLEXPORT_OST_GEOM WrapVec3(const Vec3& v1,const Vec3& box_center,const Vec3& basis_vec);
//!wraps all the verctors in a Vec3List in a box with periodic boundaries
diff --git a/modules/mol/base/pymod/export_coord_frame.cc b/modules/mol/base/pymod/export_coord_frame.cc
index e3e269e7d..7ea3c2f3a 100644
--- a/modules/mol/base/pymod/export_coord_frame.cc
+++ b/modules/mol/base/pymod/export_coord_frame.cc
@@ -69,6 +69,7 @@ void export_CoordFrame()
.def("SetCellAngles",&CoordFrame::SetCellAngles)
.def("GetCellAngles",&CoordFrame::GetCellAngles)
.add_property("cell_angles",&CoordFrame::GetCellAngles,&CoordFrame::SetCellAngles)
+ .def("GetCellVectors",&CoordFrame::GetCellVectors)
.def("GetAtomPos", get_atom_pos)
.def("GetDistanceBetwAtoms", get_dist_atom)
.def("GetAngle", get_angle)
diff --git a/modules/mol/base/src/coord_frame.cc b/modules/mol/base/src/coord_frame.cc
index 8ba796305..ff04e00d8 100644
--- a/modules/mol/base/src/coord_frame.cc
+++ b/modules/mol/base/src/coord_frame.cc
@@ -48,6 +48,11 @@ namespace ost { namespace mol {
}
}
+ geom::Vec3List CoordFrame::GetCellVectors() const
+ {
+ return geom::CalculateUnitCellVectors(ucell_size_,ucell_angles_);
+ }
+
geom::Vec3 CoordFrame::GetAtomPos(const AtomHandle& atom) const
{
return this->GetAtomPos(atom.GetIndex());
diff --git a/modules/mol/base/src/coord_frame.hh b/modules/mol/base/src/coord_frame.hh
index e624ebf87..f319e1a3b 100644
--- a/modules/mol/base/src/coord_frame.hh
+++ b/modules/mol/base/src/coord_frame.hh
@@ -77,7 +77,9 @@ public:
geom::Vec3 GetCellAngles() const {
return this->ucell_angles_;
}
-
+
+ geom::Vec3List GetCellVectors() const;
+
geom::Vec3 GetAtomPos(const AtomHandle& atom) const;
geom::Vec3 GetAtomPos(int atom_index) const;
Real GetDistanceBetwAtoms(const AtomHandle& a1, const AtomHandle& a2) const;
--
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