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* gnu/packages/chemistry.scm (avogadro): New variable. * gnu/packages/patches/avogadro-boost148.patch, gnu/packages/patches/avogadro-eigen3-update.patch, gnu/packages/patches/avogadro-python-eigen-lib.patch: New files. * gnu/local.mk (dist_patch_DATA): Add them.
603 lines
No EOL
26 KiB
Diff
603 lines
No EOL
26 KiB
Diff
From 43af3c117b0b3220b15c2fe2895b94bbd83d3a60 Mon Sep 17 00:00:00 2001
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From: Claudio Fernandes <claudiosf.claudio@gmail.com>
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Date: Sun, 15 Jan 2017 21:23:39 -0200
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Subject: [PATCH] Adapt Avogadro to Eigen 3.3
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---
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CMakeLists.txt | 9 +------
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avogadro/src/mainwindow.cpp | 5 ++--
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libavogadro/src/camera.cpp | 10 ++++----
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libavogadro/src/camera.h | 14 +++++------
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libavogadro/src/engines/wireengine.cpp | 4 ++--
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.../crystallography/crystallographyextension.cpp | 2 +-
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.../crystallography/ui/ceviewoptionswidget.cpp | 2 +-
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.../src/extensions/orca/orcaanalysedialog.cpp | 1 -
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.../src/extensions/orca/orcainputdialog.cpp | 1 -
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.../src/extensions/qtaim/qtaimmathutilities.cpp | 1 +
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.../qtaim/qtaimwavefunctionevaluator.cpp | 28 +++++++++++-----------
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.../extensions/surfaces/openqube/gamessukout.cpp | 1 +
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.../src/extensions/surfaces/openqube/slaterset.cpp | 6 +++--
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libavogadro/src/glpainter_p.cpp | 14 +++++------
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libavogadro/src/glwidget.cpp | 4 ++--
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libavogadro/src/molecule.cpp | 26 ++++++++++++++++++--
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libavogadro/src/navigate.cpp | 2 +-
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libavogadro/src/tools/bondcentrictool.cpp | 28 +++++++++++-----------
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libavogadro/src/tools/manipulatetool.cpp | 17 +++++++------
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libavogadro/src/tools/navigatetool.cpp | 3 ++-
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libavogadro/src/tools/skeletontree.cpp | 7 +++---
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libavogadro/src/tools/skeletontree.h | 2 +-
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22 files changed, 102 insertions(+), 85 deletions(-)
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--- a/CMakeLists.txt
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+++ b/CMakeLists.txt
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@@ -231,14 +231,7 @@ if(NOT Linguist_FOUND)
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message(WARNING " Qt4 Linguist not found, please install it if you want Avogadro translations")
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endif()
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-find_package(Eigen3) # find and setup Eigen3 if available
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-if(NOT EIGEN3_FOUND)
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- message(STATUS "Cannot find Eigen3, trying Eigen2")
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- find_package(Eigen2 REQUIRED) # Some version is required
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-else()
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-# Use Stage10 Eigen3 support
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- set (EIGEN2_SUPPORT_STAGE10_FULL_EIGEN2_API TRUE)
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-endif()
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+find_package(Eigen3 REQUIRED) # find and setup Eigen3 if available
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find_package(ZLIB REQUIRED)
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find_package(OpenBabel2 REQUIRED) # find and setup OpenBabel
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--- a/avogadro/src/mainwindow.cpp
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+++ b/avogadro/src/mainwindow.cpp
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@@ -115,7 +115,6 @@
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#include <QDebug>
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#include <Eigen/Geometry>
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-#include <Eigen/Array>
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#define USEQUAT
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// This is a "hidden" exported Qt function on the Mac for Qt-4.x.
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#ifdef Q_WS_MAC
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@@ -2775,7 +2774,7 @@ protected:
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linearGoal.row(1) = linearGoal.row(2).cross(linearGoal.row(0));
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// calculate the translation matrix
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- Transform3d goal(linearGoal);
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+ Projective3d goal(linearGoal);
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goal.pretranslate(- 3.0 * (d->glWidget->radius() + CAMERA_NEAR_DISTANCE) * Vector3d::UnitZ());
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@@ -2840,7 +2839,7 @@ protected:
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Matrix3d linearGoal = Matrix3d::Identity();
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// calculate the translation matrix
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- Transform3d goal(linearGoal);
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+ Projective3d goal(linearGoal);
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goal.pretranslate(- 3.0 * (d->glWidget->radius() + CAMERA_NEAR_DISTANCE) * Vector3d::UnitZ());
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--- a/libavogadro/src/camera.cpp
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+++ b/libavogadro/src/camera.cpp
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@@ -47,7 +47,7 @@ namespace Avogadro
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CameraPrivate() {};
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- Eigen::Transform3d modelview, projection;
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+ Eigen::Projective3d modelview, projection;
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const GLWidget *parent;
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double angleOfViewY;
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double orthoScale;
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@@ -169,20 +169,20 @@ namespace Avogadro
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double Camera::distance(const Eigen::Vector3d & point) const
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{
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- return ( d->modelview * point ).norm();
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+ return ( d->modelview * point.homogeneous() ).head<3>().norm();
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}
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- void Camera::setModelview(const Eigen::Transform3d &matrix)
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+ void Camera::setModelview(const Eigen::Projective3d &matrix)
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{
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d->modelview = matrix;
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}
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- const Eigen::Transform3d & Camera::modelview() const
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+ const Eigen::Projective3d & Camera::modelview() const
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{
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return d->modelview;
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}
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- Eigen::Transform3d & Camera::modelview()
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+ Eigen::Projective3d & Camera::modelview()
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{
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return d->modelview;
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}
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--- a/libavogadro/src/camera.h
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+++ b/libavogadro/src/camera.h
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@@ -101,16 +101,16 @@ namespace Avogadro {
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double angleOfViewY() const;
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/** Sets 4x4 "modelview" matrix representing the camera orientation and position.
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* @param matrix the matrix to copy from
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- * @sa Eigen::Transform3d & modelview(), applyModelview() */
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- void setModelview(const Eigen::Transform3d &matrix);
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+ * @sa Eigen::Projective3d & modelview(), applyModelview() */
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+ void setModelview(const Eigen::Projective3d &matrix);
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/** @return a constant reference to the 4x4 "modelview" matrix representing
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* the camera orientation and position
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- * @sa setModelview(), Eigen::Transform3d & modelview() */
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- const Eigen::Transform3d & modelview() const;
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+ * @sa setModelview(), Eigen::Projective3d & modelview() */
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+ const Eigen::Projective3d & modelview() const;
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/** @return a non-constant reference to the 4x4 "modelview" matrix representing
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* the camera orientation and position
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- * @sa setModelview(), const Eigen::Transform3d & modelview() const */
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- Eigen::Transform3d & modelview();
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+ * @sa setModelview(), const Eigen::Projective3d & modelview() const */
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+ Eigen::Projective3d & modelview();
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/** Calls gluPerspective() or glOrtho() with parameters automatically chosen
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* for rendering the GLWidget's molecule with this camera. Should be called
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* only in GL_PROJECTION matrix mode. Example code is given
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@@ -342,7 +342,7 @@ namespace Avogadro {
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* @return {x/w, y/w, z/w} vector
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*/
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Eigen::Vector3d V4toV3DivW(const Eigen::Vector4d & v4) {
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- return v4.start<3>()/v4.w();
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+ return v4.head<3>()/v4.w();
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}
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};
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--- a/libavogadro/src/engines/wireengine.cpp
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+++ b/libavogadro/src/engines/wireengine.cpp
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@@ -109,7 +109,7 @@ namespace Avogadro {
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const Camera *camera = pd->camera();
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// perform a rough form of frustum culling
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- Eigen::Vector3d transformedPos = pd->camera()->modelview() * v;
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+ Eigen::Vector3d transformedPos = (pd->camera()->modelview() * v.homogeneous()).head<3>();
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double dot = transformedPos.z() / transformedPos.norm();
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if(dot > -0.8)
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return true;
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@@ -167,7 +167,7 @@ namespace Avogadro {
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map = pd->colorMap(); // fall back to global color map
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// perform a rough form of frustum culling
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- Eigen::Vector3d transformedEnd1 = pd->camera()->modelview() * v1;
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+ Eigen::Vector3d transformedEnd1 = (pd->camera()->modelview() * v1.homogeneous()).head<3>();
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double dot = transformedEnd1.z() / transformedEnd1.norm();
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if(dot > -0.8)
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return true; // i.e., don't bother rendering
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--- a/libavogadro/src/extensions/crystallography/crystallographyextension.cpp
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+++ b/libavogadro/src/extensions/crystallography/crystallographyextension.cpp
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@@ -1989,7 +1989,7 @@ namespace Avogadro
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// fix coordinates
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// Apply COB matrix:
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Eigen::Matrix3d invCob;
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- cob.computeInverse(&invCob);
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+ invCob = cob.inverse();
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for (QList<Eigen::Vector3d>::iterator
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it = fcoords.begin(),
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it_end = fcoords.end();
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--- a/libavogadro/src/extensions/crystallography/ui/ceviewoptionswidget.cpp
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+++ b/libavogadro/src/extensions/crystallography/ui/ceviewoptionswidget.cpp
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@@ -139,7 +139,7 @@ namespace Avogadro
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{
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// View into a Miller plane
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Camera *camera = m_glWidget->camera();
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- Eigen::Transform3d modelView;
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+ Eigen::Projective3d modelView;
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modelView.setIdentity();
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// OK, so we want to rotate to look along the normal at the plane
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--- a/libavogadro/src/extensions/orca/orcaanalysedialog.cpp
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+++ b/libavogadro/src/extensions/orca/orcaanalysedialog.cpp
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@@ -41,7 +41,6 @@
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#include <openbabel/mol.h>
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#include <Eigen/Geometry>
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-#include <Eigen/LeastSquares>
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#include <vector>
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--- a/libavogadro/src/extensions/orca/orcainputdialog.cpp
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+++ b/libavogadro/src/extensions/orca/orcainputdialog.cpp
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@@ -33,7 +33,6 @@
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#include <openbabel/mol.h>
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#include <Eigen/Geometry>
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-#include <Eigen/LeastSquares>
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#include <vector>
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--- a/libavogadro/src/extensions/qtaim/qtaimmathutilities.cpp
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+++ b/libavogadro/src/extensions/qtaim/qtaimmathutilities.cpp
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@@ -28,6 +28,7 @@
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#include <cmath>
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#include <Eigen/QR>
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+#include <Eigen/Eigenvalues>
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namespace Avogadro {
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namespace QTAIMMathUtilities {
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--- a/libavogadro/src/extensions/qtaim/qtaimwavefunctionevaluator.cpp
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+++ b/libavogadro/src/extensions/qtaim/qtaimwavefunctionevaluator.cpp
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@@ -35,21 +35,21 @@ namespace Avogadro
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m_nprim=wfn.numberOfGaussianPrimitives();
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m_nnuc=wfn.numberOfNuclei();
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- m_nucxcoord=Map<Matrix<qreal,Dynamic,1> >(wfn.xNuclearCoordinates(),m_nnuc);
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- m_nucycoord=Map<Matrix<qreal,Dynamic,1> >(wfn.yNuclearCoordinates(),m_nnuc);
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- m_nuczcoord=Map<Matrix<qreal,Dynamic,1> >(wfn.zNuclearCoordinates(),m_nnuc);
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- m_nucz=Map<Matrix<qint64,Dynamic,1> >(wfn.nuclearCharges(),m_nnuc);
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- m_X0=Map<Matrix<qreal,Dynamic,1> >(wfn.xGaussianPrimitiveCenterCoordinates(),m_nprim,1);
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- m_Y0=Map<Matrix<qreal,Dynamic,1> >(wfn.yGaussianPrimitiveCenterCoordinates(),m_nprim,1);
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- m_Z0=Map<Matrix<qreal,Dynamic,1> >(wfn.zGaussianPrimitiveCenterCoordinates(),m_nprim,1);
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- m_xamom=Map<Matrix<qint64,Dynamic,1> >(wfn.xGaussianPrimitiveAngularMomenta(),m_nprim,1);
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- m_yamom=Map<Matrix<qint64,Dynamic,1> >(wfn.yGaussianPrimitiveAngularMomenta(),m_nprim,1);
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- m_zamom=Map<Matrix<qint64,Dynamic,1> >(wfn.zGaussianPrimitiveAngularMomenta(),m_nprim,1);
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- m_alpha=Map<Matrix<qreal,Dynamic,1> >(wfn.gaussianPrimitiveExponentCoefficients(),m_nprim,1);
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+ m_nucxcoord=Map<Matrix<qreal,Dynamic,1> >(const_cast<qreal*>(wfn.xNuclearCoordinates()),m_nnuc);
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+ m_nucycoord=Map<Matrix<qreal,Dynamic,1> >(const_cast<qreal*>(wfn.yNuclearCoordinates()),m_nnuc);
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+ m_nuczcoord=Map<Matrix<qreal,Dynamic,1> >(const_cast<qreal*>(wfn.zNuclearCoordinates()),m_nnuc);
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+ m_nucz=Map<Matrix<qint64,Dynamic,1> >(const_cast<qint64*>(wfn.nuclearCharges()),m_nnuc);
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+ m_X0=Map<Matrix<qreal,Dynamic,1> >(const_cast<qreal*>(wfn.xGaussianPrimitiveCenterCoordinates()),m_nprim,1);
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+ m_Y0=Map<Matrix<qreal,Dynamic,1> >(const_cast<qreal*>(wfn.yGaussianPrimitiveCenterCoordinates()),m_nprim,1);
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+ m_Z0=Map<Matrix<qreal,Dynamic,1> >(const_cast<qreal*>(wfn.zGaussianPrimitiveCenterCoordinates()),m_nprim,1);
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+ m_xamom=Map<Matrix<qint64,Dynamic,1> >(const_cast<qint64*>(wfn.xGaussianPrimitiveAngularMomenta()),m_nprim,1);
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+ m_yamom=Map<Matrix<qint64,Dynamic,1> >(const_cast<qint64*>(wfn.yGaussianPrimitiveAngularMomenta()),m_nprim,1);
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+ m_zamom=Map<Matrix<qint64,Dynamic,1> >(const_cast<qint64*>(wfn.zGaussianPrimitiveAngularMomenta()),m_nprim,1);
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+ m_alpha=Map<Matrix<qreal,Dynamic,1> >(const_cast<qreal*>(wfn.gaussianPrimitiveExponentCoefficients()),m_nprim,1);
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// TODO Implement screening for unoccupied molecular orbitals.
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- m_occno=Map<Matrix<qreal,Dynamic,1> >(wfn.molecularOrbitalOccupationNumbers(),m_nmo,1);
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- m_orbe=Map<Matrix<qreal,Dynamic,1> >(wfn.molecularOrbitalEigenvalues(),m_nmo,1);
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- m_coef=Map<Matrix<qreal,Dynamic,Dynamic,RowMajor> >(wfn.molecularOrbitalCoefficients(),m_nmo,m_nprim);
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+ m_occno=Map<Matrix<qreal,Dynamic,1> >(const_cast<qreal*>(wfn.molecularOrbitalOccupationNumbers()),m_nmo,1);
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+ m_orbe=Map<Matrix<qreal,Dynamic,1> >(const_cast<qreal*>(wfn.molecularOrbitalEigenvalues()),m_nmo,1);
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+ m_coef=Map<Matrix<qreal,Dynamic,Dynamic,RowMajor> >(const_cast<qreal*>(wfn.molecularOrbitalCoefficients()),m_nmo,m_nprim);
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m_totalEnergy=wfn.totalEnergy();
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m_virialRatio=wfn.virialRatio();
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--- a/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp
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+++ b/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp
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@@ -19,6 +19,7 @@
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using Eigen::Vector3d;
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using std::vector;
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+#include <iostream>
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#include <fstream>
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namespace OpenQube
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--- a/libavogadro/src/extensions/surfaces/openqube/slaterset.cpp
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+++ b/libavogadro/src/extensions/surfaces/openqube/slaterset.cpp
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@@ -25,9 +25,9 @@
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#include "cube.h"
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-#include <Eigen/Array>
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#include <Eigen/LU>
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#include <Eigen/QR>
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+#include <Eigen/Eigenvalues>
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#include <cmath>
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@@ -250,7 +250,9 @@ bool SlaterSet::initialize()
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SelfAdjointEigenSolver<MatrixXd> s(m_overlap);
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MatrixXd p = s.eigenvectors();
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- MatrixXd m = p * s.eigenvalues().cwise().inverse().cwise().sqrt().asDiagonal() * p.inverse();
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+ // TODO check if this is correct
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+ MatrixXd m1 = (s.eigenvalues().array().inverse().sqrt());
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+ MatrixXd m = p.array()*(m1.diagonal().array())*p.inverse().array();
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m_normalized = m * m_eigenVectors;
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if (!(m_overlap*m*m).isIdentity())
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--- a/libavogadro/src/glpainter_p.cpp
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+++ b/libavogadro/src/glpainter_p.cpp
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@@ -789,13 +789,13 @@ namespace Avogadro
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} else {
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points[theta-1] = Eigen::AngleAxisd(theta * (M_PI / 180.0) / 2, n) * u;
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}
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- points[theta-1] = d->widget->camera()->modelview() * (origin + points[theta-1]);
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+ points[theta-1] = (d->widget->camera()->modelview() * (origin + points[theta-1]).homogeneous()).head<3>();
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}
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// Get vectors representing the points' positions in terms of the model view.
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- Eigen::Vector3d _origin = d->widget->camera()->modelview() * origin;
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- Eigen::Vector3d _direction1 = d->widget->camera()->modelview() * (origin+u);
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- Eigen::Vector3d _direction2 = d->widget->camera()->modelview() * (origin+v);
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+ Eigen::Vector3d _origin = (d->widget->camera()->modelview() * origin.homogeneous()).head<3>();
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+ Eigen::Vector3d _direction1 = (d->widget->camera()->modelview() * (origin+u).homogeneous()).head<3>();
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+ Eigen::Vector3d _direction2 = (d->widget->camera()->modelview() * (origin+v).homogeneous()).head<3>();
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glPushAttrib(GL_ALL_ATTRIB_BITS);
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glPushMatrix();
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@@ -880,12 +880,12 @@ namespace Avogadro
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} else {
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points[theta-1] = Eigen::AngleAxisd(theta * (M_PI / 180.0) / 2, n) * u;
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}
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- points[theta-1] = d->widget->camera()->modelview() * (origin + points[theta-1]);
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+ points[theta-1] = (d->widget->camera()->modelview() * (origin + points[theta-1]).homogeneous()).head<3>();
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}
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// Get vectors representing the points' positions in terms of the model view.
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- Eigen::Vector3d _direction1 = d->widget->camera()->modelview() * (origin + u);
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- Eigen::Vector3d _direction2 = d->widget->camera()->modelview() * (origin + v);
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+ Eigen::Vector3d _direction1 = (d->widget->camera()->modelview() * (origin + u).homogeneous()).head<3>();
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+ Eigen::Vector3d _direction2 = (d->widget->camera()->modelview() * (origin + v).homogeneous()).head<3>();
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glPushAttrib(GL_ALL_ATTRIB_BITS);
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glPushMatrix();
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--- a/libavogadro/src/glwidget.cpp
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+++ b/libavogadro/src/glwidget.cpp
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@@ -765,7 +765,7 @@ namespace Avogadro {
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GLfloat fogColor[4]= {static_cast<GLfloat>(d->background.redF()), static_cast<GLfloat>(d->background.greenF()),
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static_cast<GLfloat>(d->background.blueF()), static_cast<GLfloat>(d->background.alphaF())};
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glFogfv(GL_FOG_COLOR, fogColor);
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- Vector3d distance = camera()->modelview() * d->center;
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+ Vector3d distance = (camera()->modelview() * d->center.homogeneous()).head<3>();
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double distanceToCenter = distance.norm();
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glFogf(GL_FOG_DENSITY, 1.0);
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glHint(GL_FOG_HINT, GL_NICEST);
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@@ -1711,7 +1711,7 @@ namespace Avogadro {
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if (d->renderModelViewDebug) {
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// Model view matrix:
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- const Eigen::Transform3d &modelview = d->camera->modelview();
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+ const Eigen::Projective3d &modelview = d->camera->modelview();
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y += d->pd->painter()->drawText
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(x, y, tr("ModelView row 1: %L1 %L2 %L3 %L4")
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.arg(modelview(0, 0), 6, 'f', 2, ' ')
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--- a/libavogadro/src/molecule.cpp
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+++ b/libavogadro/src/molecule.cpp
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@@ -38,7 +38,7 @@
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#include "zmatrix.h"
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#include <Eigen/Geometry>
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-#include <Eigen/LeastSquares>
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+#include <Eigen/Eigenvalues>
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#include <vector>
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@@ -1907,7 +1907,29 @@ namespace Avogadro{
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}
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d->center /= static_cast<double>(nAtoms);
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Eigen::Hyperplane<double, 3> planeCoeffs;
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- Eigen::fitHyperplane(numAtoms(), atomPositions, &planeCoeffs);
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+ //Eigen::fitHyperplane(numAtoms(), atomPositions, &planeCoeffs);
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+
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+ // TODO check if this is OK
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+ /************************/
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+ typedef Eigen::Matrix<double,3,3> CovMatrixType;
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+ typedef Eigen::Vector3d VectorType;
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+
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+ VectorType mean = d->center;
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+ int size=3;
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+ int numPoints=numAtoms();
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+ VectorType ** points=atomPositions;
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+ CovMatrixType covMat = CovMatrixType::Zero(size, size);
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+ VectorType remean = VectorType::Zero(size);
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+ for(int i = 0; i < numPoints; ++i)
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+ {
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+ VectorType diff = (*(points[i]) - mean).conjugate();
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+ covMat += diff * diff.adjoint();
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+ }
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+ Eigen::SelfAdjointEigenSolver<CovMatrixType> eig(covMat);
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+ planeCoeffs.normal() = eig.eigenvectors().col(0);
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+ /************************/
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+
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+
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delete[] atomPositions;
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d->normalVector = planeCoeffs.normal();
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}
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--- a/libavogadro/src/navigate.cpp
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+++ b/libavogadro/src/navigate.cpp
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@@ -40,7 +40,7 @@ namespace Avogadro {
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void Navigate::zoom(GLWidget *widget, const Eigen::Vector3d &goal,
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double delta)
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{
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- Vector3d transformedGoal = widget->camera()->modelview() * goal;
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+ Vector3d transformedGoal = (widget->camera()->modelview() * goal.homogeneous()).head<3>();
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double distanceToGoal = transformedGoal.norm();
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double t = ZOOM_SPEED * delta;
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--- a/libavogadro/src/tools/bondcentrictool.cpp
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+++ b/libavogadro/src/tools/bondcentrictool.cpp
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@@ -578,8 +578,8 @@ namespace Avogadro {
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Vector3d clicked = *m_clickedAtom->pos();
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- Vector3d axis = Vector3d(0, 0, ((widget->camera()->modelview() * other).z() >=
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- (widget->camera()->modelview() * center).z() ? -1 : 1));
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+ Vector3d axis = Vector3d(0, 0, ((widget->camera()->modelview() * other.homogeneous()).z() >=
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+ (widget->camera()->modelview() * center.homogeneous()).z() ? -1 : 1));
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Vector3d centerProj = widget->camera()->project(center);
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centerProj -= Vector3d(0,0,centerProj.z());
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@@ -673,8 +673,8 @@ namespace Avogadro {
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Vector3d clicked = *m_clickedAtom->pos();
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- Vector3d axis = Vector3d(0, 0, ((widget->camera()->modelview() * other).z() >=
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- (widget->camera()->modelview() * center).z() ? -1 : 1));
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+ Vector3d axis = Vector3d(0, 0, ((widget->camera()->modelview() * other.homogeneous()).z() >=
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+ (widget->camera()->modelview() * center.homogeneous()).z() ? -1 : 1));
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Vector3d centerProj = widget->camera()->project(center);
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centerProj -= Vector3d(0,0,centerProj.z());
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@@ -1362,10 +1362,10 @@ namespace Avogadro {
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planeVec = length * (planeVec / planeVec.norm());
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- Vector3d topLeft = widget->camera()->modelview() * (left + planeVec);
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- Vector3d topRight = widget->camera()->modelview() * (right + planeVec);
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- Vector3d botRight = widget->camera()->modelview() * (right - planeVec);
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- Vector3d botLeft = widget->camera()->modelview() * (left - planeVec);
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+ Vector3d topLeft = (widget->camera()->modelview() * (left + planeVec).homogeneous()).head<3>();
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+ Vector3d topRight = (widget->camera()->modelview() * (right + planeVec).homogeneous()).head<3>();
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+ Vector3d botRight = (widget->camera()->modelview() * (right - planeVec).homogeneous()).head<3>();
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+ Vector3d botLeft = (widget->camera()->modelview() * (left - planeVec).homogeneous()).head<3>();
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float alpha = 0.4;
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double lineWidth = 1.5;
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@@ -1444,10 +1444,10 @@ namespace Avogadro {
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C = D + ((C-D).normalized() * minWidth);
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}
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- Vector3d topLeft = widget->camera()->modelview() * D;
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- Vector3d topRight = widget->camera()->modelview() * C;
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- Vector3d botRight = widget->camera()->modelview() * B;
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- Vector3d botLeft = widget->camera()->modelview() * A;
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+ Vector3d topLeft = (widget->camera()->modelview() * D.homogeneous()).head<3>();
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+ Vector3d topRight = (widget->camera()->modelview() * C.homogeneous()).head<3>();
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+ Vector3d botRight = (widget->camera()->modelview() * B.homogeneous()).head<3>();
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+ Vector3d botLeft = (widget->camera()->modelview() * A.homogeneous()).head<3>();
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float alpha = 0.4;
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double lineWidth = 1.5;
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@@ -1506,12 +1506,12 @@ namespace Avogadro {
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Vector3d positionVector)
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{
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//Rotate skeleton around a particular axis and center point
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- Eigen::Transform3d rotation;
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+ Eigen::Projective3d rotation;
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rotation = Eigen::AngleAxisd(angle, rotationVector);
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rotation.pretranslate(centerVector);
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rotation.translate(-centerVector);
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- return rotation*positionVector;
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+ return (rotation*positionVector.homogeneous()).head<3>();
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}
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// ########## showAnglesChanged ##########
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--- a/libavogadro/src/tools/manipulatetool.cpp
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+++ b/libavogadro/src/tools/manipulatetool.cpp
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@@ -40,7 +40,6 @@
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#include <QAbstractButton>
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using Eigen::Vector3d;
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-using Eigen::Transform3d;
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using Eigen::AngleAxisd;
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namespace Avogadro {
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@@ -138,7 +137,7 @@ namespace Avogadro {
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double yRotate = m_settingsWidget->yRotateSpinBox->value() * DEG_TO_RAD;
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double zRotate = m_settingsWidget->zRotateSpinBox->value() * DEG_TO_RAD;
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- Eigen::Transform3d rotation;
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+ Eigen::Projective3d rotation;
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rotation.matrix().setIdentity();
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rotation.translation() = center;
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rotation.rotate(AngleAxisd(xRotate, Vector3d::UnitX())
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@@ -152,12 +151,12 @@ namespace Avogadro {
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if (p->type() == Primitive::AtomType) {
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Atom *atom = static_cast<Atom*>(p);
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tempPos = translate + *(atom->pos());
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- atom->setPos(rotation * tempPos);
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+ atom->setPos((rotation * tempPos.homogeneous()).head<3>());
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}
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} else {
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foreach(Atom *atom, widget->molecule()->atoms()) {
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tempPos = translate + *(atom->pos());
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- atom->setPos(rotation * tempPos);
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+ atom->setPos((rotation * tempPos.homogeneous()).head<3>());
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}
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}
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@@ -199,7 +198,7 @@ namespace Avogadro {
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widget->setCursor(Qt::SizeVerCursor);
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// Move the selected atom(s) in to or out of the screen
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- Vector3d transformedGoal = widget->camera()->modelview() * *goal;
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+ Vector3d transformedGoal = (widget->camera()->modelview() * goal->homogeneous()).head<3>();
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double distanceToGoal = transformedGoal.norm();
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double t = ZOOM_SPEED * delta;
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@@ -255,7 +254,7 @@ namespace Avogadro {
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// Rotate the selected atoms about the center
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// rotate only selected primitives
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- Transform3d fragmentRotation;
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+ Eigen::Projective3d fragmentRotation;
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fragmentRotation.matrix().setIdentity();
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fragmentRotation.translation() = *center;
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fragmentRotation.rotate(
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@@ -266,7 +265,7 @@ namespace Avogadro {
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foreach(Primitive *p, widget->selectedPrimitives())
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if (p->type() == Primitive::AtomType)
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- static_cast<Atom *>(p)->setPos(fragmentRotation * *static_cast<Atom *>(p)->pos());
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+ static_cast<Atom *>(p)->setPos((fragmentRotation * static_cast<Atom *>(p)->pos()->homogeneous()).head<3>());
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widget->molecule()->update();
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}
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@@ -274,7 +273,7 @@ namespace Avogadro {
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double delta) const
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{
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// Tilt the selected atoms about the center
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- Transform3d fragmentRotation;
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+ Eigen::Projective3d fragmentRotation;
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fragmentRotation.matrix().setIdentity();
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fragmentRotation.translation() = *center;
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fragmentRotation.rotate(AngleAxisd(delta * ROTATION_SPEED, widget->camera()->backTransformedZAxis()));
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@@ -282,7 +281,7 @@ namespace Avogadro {
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foreach(Primitive *p, widget->selectedPrimitives())
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if (p->type() == Primitive::AtomType)
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- static_cast<Atom *>(p)->setPos(fragmentRotation * *static_cast<Atom *>(p)->pos());
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+ static_cast<Atom *>(p)->setPos((fragmentRotation * static_cast<Atom *>(p)->pos()->homogeneous()).head<3>());
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widget->molecule()->update();
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}
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--- a/libavogadro/src/tools/navigatetool.cpp
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+++ b/libavogadro/src/tools/navigatetool.cpp
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@@ -92,7 +92,8 @@ namespace Avogadro {
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double sumOfWeights = 0.;
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QList<Atom*> atoms = widget->molecule()->atoms();
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foreach (Atom *atom, atoms) {
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- Vector3d transformedAtomPos = widget->camera()->modelview() * *atom->pos();
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+ Vector3d transformedAtomPos = (widget->camera()->modelview() *
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+ atom->pos()->homogeneous()).head<3>();
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double atomDistance = transformedAtomPos.norm();
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double dot = transformedAtomPos.z() / atomDistance;
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double weight = exp(-30. * (1. + dot));
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--- a/libavogadro/src/tools/skeletontree.cpp
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+++ b/libavogadro/src/tools/skeletontree.cpp
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@@ -29,6 +29,7 @@
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#include <avogadro/atom.h>
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#include <avogadro/bond.h>
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#include <avogadro/molecule.h>
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+#include <iostream>
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using namespace Eigen;
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using namespace std;
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@@ -221,7 +222,7 @@ namespace Avogadro {
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{
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if (m_rootNode) {
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//Rotate skeleton around a particular axis and center point
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- Eigen::Transform3d rotation;
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+ Eigen::Projective3d rotation;
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rotation = Eigen::AngleAxisd(angle, rotationAxis);
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rotation.pretranslate(centerVector);
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rotation.translate(-centerVector);
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@@ -248,11 +249,11 @@ namespace Avogadro {
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// ########## recursiveRotate ##########
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void SkeletonTree::recursiveRotate(Node* n,
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- const Eigen::Transform3d &rotationMatrix)
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+ const Eigen::Projective3d &rotationMatrix)
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{
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// Update the root node with the new position
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Atom* a = n->atom();
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- a->setPos(rotationMatrix * (*a->pos()));
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+ a->setPos((rotationMatrix * (*a->pos()).homogeneous()).head<3>());
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a->update();
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// Now update the children
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--- a/libavogadro/src/tools/skeletontree.h
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+++ b/libavogadro/src/tools/skeletontree.h
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@@ -230,6 +230,6 @@ namespace Avogadro {
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* @param centerVector Center location to rotate around.
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*/
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void recursiveRotate(Node* n,
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- const Eigen::Transform3d &rotationMatrix);
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+ const Eigen::Projective3d &rotationMatrix);
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};
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} // End namespace Avogadro
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