File avogadro-port-to-eigen3.patch of Package avogadro-qt4
From 43af3c117b0b3220b15c2fe2895b94bbd83d3a60 Mon Sep 17 00:00:00 2001
From: Claudio Fernandes <claudiosf.claudio@gmail.com>
Date: Sun, 15 Jan 2017 21:23:39 -0200
Subject: [PATCH] Adapt Avogadro to Eigen 3.3
---
CMakeLists.txt | 9 +-----
avogadro/src/mainwindow.cpp | 5 ++--
libavogadro/src/camera.cpp | 10 +++----
libavogadro/src/camera.h | 14 +++++-----
libavogadro/src/engines/wireengine.cpp | 4 +--
.../crystallographyextension.cpp | 2 +-
.../ui/ceviewoptionswidget.cpp | 2 +-
.../src/extensions/orca/orcaanalysedialog.cpp | 1 -
.../src/extensions/orca/orcainputdialog.cpp | 1 -
.../extensions/qtaim/qtaimmathutilities.cpp | 1 +
.../qtaim/qtaimwavefunctionevaluator.cpp | 28 +++++++++----------
.../surfaces/openqube/gamessukout.cpp | 1 +
.../surfaces/openqube/slaterset.cpp | 6 ++--
libavogadro/src/glpainter_p.cpp | 14 +++++-----
libavogadro/src/glwidget.cpp | 4 +--
libavogadro/src/molecule.cpp | 26 +++++++++++++++--
libavogadro/src/navigate.cpp | 2 +-
libavogadro/src/tools/bondcentrictool.cpp | 28 +++++++++----------
libavogadro/src/tools/manipulatetool.cpp | 17 ++++++-----
libavogadro/src/tools/navigatetool.cpp | 3 +-
libavogadro/src/tools/skeletontree.cpp | 7 +++--
libavogadro/src/tools/skeletontree.h | 2 +-
22 files changed, 102 insertions(+), 85 deletions(-)
Index: avogadro-1.2.0/CMakeLists.txt
===================================================================
--- avogadro-1.2.0.orig/CMakeLists.txt
+++ avogadro-1.2.0/CMakeLists.txt
@@ -231,14 +231,7 @@ if(NOT Linguist_FOUND)
message(WARNING " Qt4 Linguist not found, please install it if you want Avogadro translations")
endif()
-find_package(Eigen3) # find and setup Eigen3 if available
-if(NOT EIGEN3_FOUND)
- message(STATUS "Cannot find Eigen3, trying Eigen2")
- find_package(Eigen2 REQUIRED) # Some version is required
-else()
-# Use Stage10 Eigen3 support
- set (EIGEN2_SUPPORT_STAGE10_FULL_EIGEN2_API TRUE)
-endif()
+find_package(Eigen3 REQUIRED) # find and setup Eigen3 if available
find_package(ZLIB REQUIRED)
find_package(OpenBabel2 REQUIRED) # find and setup OpenBabel
Index: avogadro-1.2.0/avogadro/src/mainwindow.cpp
===================================================================
--- avogadro-1.2.0.orig/avogadro/src/mainwindow.cpp
+++ avogadro-1.2.0/avogadro/src/mainwindow.cpp
@@ -115,7 +115,6 @@
#include <QDebug>
#include <Eigen/Geometry>
-#include <Eigen/Array>
#define USEQUAT
// This is a "hidden" exported Qt function on the Mac for Qt-4.x.
#ifdef Q_WS_MAC
@@ -2775,7 +2774,7 @@ protected:
linearGoal.row(1) = linearGoal.row(2).cross(linearGoal.row(0));
// calculate the translation matrix
- Transform3d goal(linearGoal);
+ Projective3d goal(linearGoal);
goal.pretranslate(- 3.0 * (d->glWidget->radius() + CAMERA_NEAR_DISTANCE) * Vector3d::UnitZ());
@@ -2840,7 +2839,7 @@ protected:
Matrix3d linearGoal = Matrix3d::Identity();
// calculate the translation matrix
- Transform3d goal(linearGoal);
+ Projective3d goal(linearGoal);
goal.pretranslate(- 3.0 * (d->glWidget->radius() + CAMERA_NEAR_DISTANCE) * Vector3d::UnitZ());
Index: avogadro-1.2.0/libavogadro/src/camera.cpp
===================================================================
--- avogadro-1.2.0.orig/libavogadro/src/camera.cpp
+++ avogadro-1.2.0/libavogadro/src/camera.cpp
@@ -47,7 +47,7 @@ namespace Avogadro
CameraPrivate() {};
- Eigen::Transform3d modelview, projection;
+ Eigen::Projective3d modelview, projection;
const GLWidget *parent;
double angleOfViewY;
double orthoScale;
@@ -169,20 +169,20 @@ namespace Avogadro
double Camera::distance(const Eigen::Vector3d & point) const
{
- return ( d->modelview * point ).norm();
+ return ( d->modelview * point.homogeneous() ).head<3>().norm();
}
- void Camera::setModelview(const Eigen::Transform3d &matrix)
+ void Camera::setModelview(const Eigen::Projective3d &matrix)
{
d->modelview = matrix;
}
- const Eigen::Transform3d & Camera::modelview() const
+ const Eigen::Projective3d & Camera::modelview() const
{
return d->modelview;
}
- Eigen::Transform3d & Camera::modelview()
+ Eigen::Projective3d & Camera::modelview()
{
return d->modelview;
}
Index: avogadro-1.2.0/libavogadro/src/camera.h
===================================================================
--- avogadro-1.2.0.orig/libavogadro/src/camera.h
+++ avogadro-1.2.0/libavogadro/src/camera.h
@@ -101,16 +101,16 @@ namespace Avogadro {
double angleOfViewY() const;
/** Sets 4x4 "modelview" matrix representing the camera orientation and position.
* @param matrix the matrix to copy from
- * @sa Eigen::Transform3d & modelview(), applyModelview() */
- void setModelview(const Eigen::Transform3d &matrix);
+ * @sa Eigen::Projective3d & modelview(), applyModelview() */
+ void setModelview(const Eigen::Projective3d &matrix);
/** @return a constant reference to the 4x4 "modelview" matrix representing
* the camera orientation and position
- * @sa setModelview(), Eigen::Transform3d & modelview() */
- const Eigen::Transform3d & modelview() const;
+ * @sa setModelview(), Eigen::Projective3d & modelview() */
+ const Eigen::Projective3d & modelview() const;
/** @return a non-constant reference to the 4x4 "modelview" matrix representing
* the camera orientation and position
- * @sa setModelview(), const Eigen::Transform3d & modelview() const */
- Eigen::Transform3d & modelview();
+ * @sa setModelview(), const Eigen::Projective3d & modelview() const */
+ Eigen::Projective3d & modelview();
/** Calls gluPerspective() or glOrtho() with parameters automatically chosen
* for rendering the GLWidget's molecule with this camera. Should be called
* only in GL_PROJECTION matrix mode. Example code is given
@@ -342,7 +342,7 @@ namespace Avogadro {
* @return {x/w, y/w, z/w} vector
*/
Eigen::Vector3d V4toV3DivW(const Eigen::Vector4d & v4) {
- return v4.start<3>()/v4.w();
+ return v4.head<3>()/v4.w();
}
};
Index: avogadro-1.2.0/libavogadro/src/engines/wireengine.cpp
===================================================================
--- avogadro-1.2.0.orig/libavogadro/src/engines/wireengine.cpp
+++ avogadro-1.2.0/libavogadro/src/engines/wireengine.cpp
@@ -109,7 +109,7 @@ namespace Avogadro {
const Camera *camera = pd->camera();
// perform a rough form of frustum culling
- Eigen::Vector3d transformedPos = pd->camera()->modelview() * v;
+ Eigen::Vector3d transformedPos = (pd->camera()->modelview() * v.homogeneous()).head<3>();
double dot = transformedPos.z() / transformedPos.norm();
if(dot > -0.8)
return true;
@@ -167,7 +167,7 @@ namespace Avogadro {
map = pd->colorMap(); // fall back to global color map
// perform a rough form of frustum culling
- Eigen::Vector3d transformedEnd1 = pd->camera()->modelview() * v1;
+ Eigen::Vector3d transformedEnd1 = (pd->camera()->modelview() * v1.homogeneous()).head<3>();
double dot = transformedEnd1.z() / transformedEnd1.norm();
if(dot > -0.8)
return true; // i.e., don't bother rendering
Index: avogadro-1.2.0/libavogadro/src/extensions/crystallography/crystallographyextension.cpp
===================================================================
--- avogadro-1.2.0.orig/libavogadro/src/extensions/crystallography/crystallographyextension.cpp
+++ avogadro-1.2.0/libavogadro/src/extensions/crystallography/crystallographyextension.cpp
@@ -1989,7 +1989,7 @@ namespace Avogadro
// fix coordinates
// Apply COB matrix:
Eigen::Matrix3d invCob;
- cob.computeInverse(&invCob);
+ invCob = cob.inverse();
for (QList<Eigen::Vector3d>::iterator
it = fcoords.begin(),
it_end = fcoords.end();
Index: avogadro-1.2.0/libavogadro/src/extensions/crystallography/ui/ceviewoptionswidget.cpp
===================================================================
--- avogadro-1.2.0.orig/libavogadro/src/extensions/crystallography/ui/ceviewoptionswidget.cpp
+++ avogadro-1.2.0/libavogadro/src/extensions/crystallography/ui/ceviewoptionswidget.cpp
@@ -139,7 +139,7 @@ namespace Avogadro
{
// View into a Miller plane
Camera *camera = m_glWidget->camera();
- Eigen::Transform3d modelView;
+ Eigen::Projective3d modelView;
modelView.setIdentity();
// OK, so we want to rotate to look along the normal at the plane
Index: avogadro-1.2.0/libavogadro/src/extensions/orca/orcaanalysedialog.cpp
===================================================================
--- avogadro-1.2.0.orig/libavogadro/src/extensions/orca/orcaanalysedialog.cpp
+++ avogadro-1.2.0/libavogadro/src/extensions/orca/orcaanalysedialog.cpp
@@ -41,7 +41,6 @@
#include <openbabel/mol.h>
#include <Eigen/Geometry>
-#include <Eigen/LeastSquares>
#include <vector>
Index: avogadro-1.2.0/libavogadro/src/extensions/orca/orcainputdialog.cpp
===================================================================
--- avogadro-1.2.0.orig/libavogadro/src/extensions/orca/orcainputdialog.cpp
+++ avogadro-1.2.0/libavogadro/src/extensions/orca/orcainputdialog.cpp
@@ -33,7 +33,6 @@
#include <openbabel/mol.h>
#include <Eigen/Geometry>
-#include <Eigen/LeastSquares>
#include <vector>
Index: avogadro-1.2.0/libavogadro/src/extensions/qtaim/qtaimmathutilities.cpp
===================================================================
--- avogadro-1.2.0.orig/libavogadro/src/extensions/qtaim/qtaimmathutilities.cpp
+++ avogadro-1.2.0/libavogadro/src/extensions/qtaim/qtaimmathutilities.cpp
@@ -28,6 +28,7 @@
#include <cmath>
#include <Eigen/QR>
+#include <Eigen/Eigenvalues>
namespace Avogadro {
namespace QTAIMMathUtilities {
Index: avogadro-1.2.0/libavogadro/src/extensions/qtaim/qtaimwavefunctionevaluator.cpp
===================================================================
--- avogadro-1.2.0.orig/libavogadro/src/extensions/qtaim/qtaimwavefunctionevaluator.cpp
+++ avogadro-1.2.0/libavogadro/src/extensions/qtaim/qtaimwavefunctionevaluator.cpp
@@ -35,21 +35,21 @@ namespace Avogadro
m_nprim=wfn.numberOfGaussianPrimitives();
m_nnuc=wfn.numberOfNuclei();
- m_nucxcoord=Map<Matrix<qreal,Dynamic,1> >(wfn.xNuclearCoordinates(),m_nnuc);
- m_nucycoord=Map<Matrix<qreal,Dynamic,1> >(wfn.yNuclearCoordinates(),m_nnuc);
- m_nuczcoord=Map<Matrix<qreal,Dynamic,1> >(wfn.zNuclearCoordinates(),m_nnuc);
- m_nucz=Map<Matrix<qint64,Dynamic,1> >(wfn.nuclearCharges(),m_nnuc);
- m_X0=Map<Matrix<qreal,Dynamic,1> >(wfn.xGaussianPrimitiveCenterCoordinates(),m_nprim,1);
- m_Y0=Map<Matrix<qreal,Dynamic,1> >(wfn.yGaussianPrimitiveCenterCoordinates(),m_nprim,1);
- m_Z0=Map<Matrix<qreal,Dynamic,1> >(wfn.zGaussianPrimitiveCenterCoordinates(),m_nprim,1);
- m_xamom=Map<Matrix<qint64,Dynamic,1> >(wfn.xGaussianPrimitiveAngularMomenta(),m_nprim,1);
- m_yamom=Map<Matrix<qint64,Dynamic,1> >(wfn.yGaussianPrimitiveAngularMomenta(),m_nprim,1);
- m_zamom=Map<Matrix<qint64,Dynamic,1> >(wfn.zGaussianPrimitiveAngularMomenta(),m_nprim,1);
- m_alpha=Map<Matrix<qreal,Dynamic,1> >(wfn.gaussianPrimitiveExponentCoefficients(),m_nprim,1);
+ m_nucxcoord=Map<Matrix<qreal,Dynamic,1> >(const_cast<qreal*>(wfn.xNuclearCoordinates()),m_nnuc);
+ m_nucycoord=Map<Matrix<qreal,Dynamic,1> >(const_cast<qreal*>(wfn.yNuclearCoordinates()),m_nnuc);
+ m_nuczcoord=Map<Matrix<qreal,Dynamic,1> >(const_cast<qreal*>(wfn.zNuclearCoordinates()),m_nnuc);
+ m_nucz=Map<Matrix<qint64,Dynamic,1> >(const_cast<qint64*>(wfn.nuclearCharges()),m_nnuc);
+ m_X0=Map<Matrix<qreal,Dynamic,1> >(const_cast<qreal*>(wfn.xGaussianPrimitiveCenterCoordinates()),m_nprim,1);
+ m_Y0=Map<Matrix<qreal,Dynamic,1> >(const_cast<qreal*>(wfn.yGaussianPrimitiveCenterCoordinates()),m_nprim,1);
+ m_Z0=Map<Matrix<qreal,Dynamic,1> >(const_cast<qreal*>(wfn.zGaussianPrimitiveCenterCoordinates()),m_nprim,1);
+ m_xamom=Map<Matrix<qint64,Dynamic,1> >(const_cast<qint64*>(wfn.xGaussianPrimitiveAngularMomenta()),m_nprim,1);
+ m_yamom=Map<Matrix<qint64,Dynamic,1> >(const_cast<qint64*>(wfn.yGaussianPrimitiveAngularMomenta()),m_nprim,1);
+ m_zamom=Map<Matrix<qint64,Dynamic,1> >(const_cast<qint64*>(wfn.zGaussianPrimitiveAngularMomenta()),m_nprim,1);
+ m_alpha=Map<Matrix<qreal,Dynamic,1> >(const_cast<qreal*>(wfn.gaussianPrimitiveExponentCoefficients()),m_nprim,1);
// TODO Implement screening for unoccupied molecular orbitals.
- m_occno=Map<Matrix<qreal,Dynamic,1> >(wfn.molecularOrbitalOccupationNumbers(),m_nmo,1);
- m_orbe=Map<Matrix<qreal,Dynamic,1> >(wfn.molecularOrbitalEigenvalues(),m_nmo,1);
- m_coef=Map<Matrix<qreal,Dynamic,Dynamic,RowMajor> >(wfn.molecularOrbitalCoefficients(),m_nmo,m_nprim);
+ m_occno=Map<Matrix<qreal,Dynamic,1> >(const_cast<qreal*>(wfn.molecularOrbitalOccupationNumbers()),m_nmo,1);
+ m_orbe=Map<Matrix<qreal,Dynamic,1> >(const_cast<qreal*>(wfn.molecularOrbitalEigenvalues()),m_nmo,1);
+ m_coef=Map<Matrix<qreal,Dynamic,Dynamic,RowMajor> >(const_cast<qreal*>(wfn.molecularOrbitalCoefficients()),m_nmo,m_nprim);
m_totalEnergy=wfn.totalEnergy();
m_virialRatio=wfn.virialRatio();
Index: avogadro-1.2.0/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp
===================================================================
--- avogadro-1.2.0.orig/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp
+++ avogadro-1.2.0/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp
@@ -19,6 +19,7 @@
using Eigen::Vector3d;
using std::vector;
+#include <iostream>
#include <fstream>
namespace OpenQube
Index: avogadro-1.2.0/libavogadro/src/extensions/surfaces/openqube/slaterset.cpp
===================================================================
--- avogadro-1.2.0.orig/libavogadro/src/extensions/surfaces/openqube/slaterset.cpp
+++ avogadro-1.2.0/libavogadro/src/extensions/surfaces/openqube/slaterset.cpp
@@ -25,9 +25,9 @@
#include "cube.h"
-#include <Eigen/Array>
#include <Eigen/LU>
#include <Eigen/QR>
+#include <Eigen/Eigenvalues>
#include <cmath>
@@ -250,7 +250,9 @@ bool SlaterSet::initialize()
SelfAdjointEigenSolver<MatrixXd> s(m_overlap);
MatrixXd p = s.eigenvectors();
- MatrixXd m = p * s.eigenvalues().cwise().inverse().cwise().sqrt().asDiagonal() * p.inverse();
+ // TODO check if this is correct
+ MatrixXd m1 = (s.eigenvalues().array().inverse().sqrt());
+ MatrixXd m = p.array()*(m1.diagonal().array())*p.inverse().array();
m_normalized = m * m_eigenVectors;
if (!(m_overlap*m*m).isIdentity())
Index: avogadro-1.2.0/libavogadro/src/glpainter_p.cpp
===================================================================
--- avogadro-1.2.0.orig/libavogadro/src/glpainter_p.cpp
+++ avogadro-1.2.0/libavogadro/src/glpainter_p.cpp
@@ -789,13 +789,13 @@ namespace Avogadro
} else {
points[theta-1] = Eigen::AngleAxisd(theta * (M_PI / 180.0) / 2, n) * u;
}
- points[theta-1] = d->widget->camera()->modelview() * (origin + points[theta-1]);
+ points[theta-1] = (d->widget->camera()->modelview() * (origin + points[theta-1]).homogeneous()).head<3>();
}
// Get vectors representing the points' positions in terms of the model view.
- Eigen::Vector3d _origin = d->widget->camera()->modelview() * origin;
- Eigen::Vector3d _direction1 = d->widget->camera()->modelview() * (origin+u);
- Eigen::Vector3d _direction2 = d->widget->camera()->modelview() * (origin+v);
+ Eigen::Vector3d _origin = (d->widget->camera()->modelview() * origin.homogeneous()).head<3>();
+ Eigen::Vector3d _direction1 = (d->widget->camera()->modelview() * (origin+u).homogeneous()).head<3>();
+ Eigen::Vector3d _direction2 = (d->widget->camera()->modelview() * (origin+v).homogeneous()).head<3>();
glPushAttrib(GL_ALL_ATTRIB_BITS);
glPushMatrix();
@@ -880,12 +880,12 @@ namespace Avogadro
} else {
points[theta-1] = Eigen::AngleAxisd(theta * (M_PI / 180.0) / 2, n) * u;
}
- points[theta-1] = d->widget->camera()->modelview() * (origin + points[theta-1]);
+ points[theta-1] = (d->widget->camera()->modelview() * (origin + points[theta-1]).homogeneous()).head<3>();
}
// Get vectors representing the points' positions in terms of the model view.
- Eigen::Vector3d _direction1 = d->widget->camera()->modelview() * (origin + u);
- Eigen::Vector3d _direction2 = d->widget->camera()->modelview() * (origin + v);
+ Eigen::Vector3d _direction1 = (d->widget->camera()->modelview() * (origin + u).homogeneous()).head<3>();
+ Eigen::Vector3d _direction2 = (d->widget->camera()->modelview() * (origin + v).homogeneous()).head<3>();
glPushAttrib(GL_ALL_ATTRIB_BITS);
glPushMatrix();
Index: avogadro-1.2.0/libavogadro/src/glwidget.cpp
===================================================================
--- avogadro-1.2.0.orig/libavogadro/src/glwidget.cpp
+++ avogadro-1.2.0/libavogadro/src/glwidget.cpp
@@ -765,7 +765,7 @@ namespace Avogadro {
GLfloat fogColor[4]= {static_cast<GLfloat>(d->background.redF()), static_cast<GLfloat>(d->background.greenF()),
static_cast<GLfloat>(d->background.blueF()), static_cast<GLfloat>(d->background.alphaF())};
glFogfv(GL_FOG_COLOR, fogColor);
- Vector3d distance = camera()->modelview() * d->center;
+ Vector3d distance = (camera()->modelview() * d->center.homogeneous()).head<3>();
double distanceToCenter = distance.norm();
glFogf(GL_FOG_DENSITY, 1.0);
glHint(GL_FOG_HINT, GL_NICEST);
@@ -1711,7 +1711,7 @@ namespace Avogadro {
if (d->renderModelViewDebug) {
// Model view matrix:
- const Eigen::Transform3d &modelview = d->camera->modelview();
+ const Eigen::Projective3d &modelview = d->camera->modelview();
y += d->pd->painter()->drawText
(x, y, tr("ModelView row 1: %L1 %L2 %L3 %L4")
.arg(modelview(0, 0), 6, 'f', 2, ' ')
Index: avogadro-1.2.0/libavogadro/src/molecule.cpp
===================================================================
--- avogadro-1.2.0.orig/libavogadro/src/molecule.cpp
+++ avogadro-1.2.0/libavogadro/src/molecule.cpp
@@ -38,7 +38,7 @@
#include "zmatrix.h"
#include <Eigen/Geometry>
-#include <Eigen/LeastSquares>
+#include <Eigen/Eigenvalues>
#include <vector>
@@ -1908,7 +1908,29 @@ namespace Avogadro{
}
d->center /= static_cast<double>(nAtoms);
Eigen::Hyperplane<double, 3> planeCoeffs;
- Eigen::fitHyperplane(numAtoms(), atomPositions, &planeCoeffs);
+ //Eigen::fitHyperplane(numAtoms(), atomPositions, &planeCoeffs);
+
+ // TODO check if this is OK
+ /************************/
+ typedef Eigen::Matrix<double,3,3> CovMatrixType;
+ typedef Eigen::Vector3d VectorType;
+
+ VectorType mean = d->center;
+ int size=3;
+ int numPoints=numAtoms();
+ VectorType ** points=atomPositions;
+ CovMatrixType covMat = CovMatrixType::Zero(size, size);
+ VectorType remean = VectorType::Zero(size);
+ for(int i = 0; i < numPoints; ++i)
+ {
+ VectorType diff = (*(points[i]) - mean).conjugate();
+ covMat += diff * diff.adjoint();
+ }
+ Eigen::SelfAdjointEigenSolver<CovMatrixType> eig(covMat);
+ planeCoeffs.normal() = eig.eigenvectors().col(0);
+ /************************/
+
+
delete[] atomPositions;
d->normalVector = planeCoeffs.normal();
}
Index: avogadro-1.2.0/libavogadro/src/navigate.cpp
===================================================================
--- avogadro-1.2.0.orig/libavogadro/src/navigate.cpp
+++ avogadro-1.2.0/libavogadro/src/navigate.cpp
@@ -40,7 +40,7 @@ namespace Avogadro {
void Navigate::zoom(GLWidget *widget, const Eigen::Vector3d &goal,
double delta)
{
- Vector3d transformedGoal = widget->camera()->modelview() * goal;
+ Vector3d transformedGoal = (widget->camera()->modelview() * goal.homogeneous()).head<3>();
double distanceToGoal = transformedGoal.norm();
double t = ZOOM_SPEED * delta;
Index: avogadro-1.2.0/libavogadro/src/tools/bondcentrictool.cpp
===================================================================
--- avogadro-1.2.0.orig/libavogadro/src/tools/bondcentrictool.cpp
+++ avogadro-1.2.0/libavogadro/src/tools/bondcentrictool.cpp
@@ -578,8 +578,13 @@ namespace Avogadro {
Vector3d clicked = *m_clickedAtom->pos();
- Vector3d axis = Vector3d(0, 0, ((widget->camera()->modelview() * other).z() >=
- (widget->camera()->modelview() * center).z() ? -1 : 1));
+ Eigen::Vector4d otherTransformedHomog = widget->camera()->modelview() * other.homogeneous();
+ Vector3d otherTransformed = otherTransformedHomog.hnormalized();
+ Eigen::Vector4d centerTransformedHomog = (widget->camera()->modelview() * center.homogeneous());
+ Vector3d centerTransformed = centerTransformedHomog.hnormalized();
+
+ Vector3d axis = Vector3d(0, 0, (otherTransformed.z() >=
+ centerTransformed.z() ? -1 : 1));
Vector3d centerProj = widget->camera()->project(center);
centerProj -= Vector3d(0,0,centerProj.z());
@@ -673,8 +678,13 @@ namespace Avogadro {
Vector3d clicked = *m_clickedAtom->pos();
- Vector3d axis = Vector3d(0, 0, ((widget->camera()->modelview() * other).z() >=
- (widget->camera()->modelview() * center).z() ? -1 : 1));
+ Eigen::Vector4d otherTransformedHomog = (widget->camera()->modelview() * other.homogeneous());
+ Vector3d otherTransformed = otherTransformedHomog.hnormalized();
+ Eigen::Vector4d centerTransformedHomog = (widget->camera()->modelview() * center.homogeneous());
+ Vector3d centerTransformed = centerTransformedHomog.hnormalized();
+
+ Vector3d axis = Vector3d(0, 0, (otherTransformed.z() >=
+ centerTransformed.z() ? -1 : 1));
Vector3d centerProj = widget->camera()->project(center);
centerProj -= Vector3d(0,0,centerProj.z());
@@ -1362,10 +1372,10 @@ namespace Avogadro {
planeVec = length * (planeVec / planeVec.norm());
- Vector3d topLeft = widget->camera()->modelview() * (left + planeVec);
- Vector3d topRight = widget->camera()->modelview() * (right + planeVec);
- Vector3d botRight = widget->camera()->modelview() * (right - planeVec);
- Vector3d botLeft = widget->camera()->modelview() * (left - planeVec);
+ Vector3d topLeft = (widget->camera()->modelview() * (left + planeVec).homogeneous()).head<3>();
+ Vector3d topRight = (widget->camera()->modelview() * (right + planeVec).homogeneous()).head<3>();
+ Vector3d botRight = (widget->camera()->modelview() * (right - planeVec).homogeneous()).head<3>();
+ Vector3d botLeft = (widget->camera()->modelview() * (left - planeVec).homogeneous()).head<3>();
float alpha = 0.4;
double lineWidth = 1.5;
@@ -1444,10 +1454,10 @@ namespace Avogadro {
C = D + ((C-D).normalized() * minWidth);
}
- Vector3d topLeft = widget->camera()->modelview() * D;
- Vector3d topRight = widget->camera()->modelview() * C;
- Vector3d botRight = widget->camera()->modelview() * B;
- Vector3d botLeft = widget->camera()->modelview() * A;
+ Vector3d topLeft = (widget->camera()->modelview() * D.homogeneous()).head<3>();
+ Vector3d topRight = (widget->camera()->modelview() * C.homogeneous()).head<3>();
+ Vector3d botRight = (widget->camera()->modelview() * B.homogeneous()).head<3>();
+ Vector3d botLeft = (widget->camera()->modelview() * A.homogeneous()).head<3>();
float alpha = 0.4;
double lineWidth = 1.5;
@@ -1506,12 +1516,12 @@ namespace Avogadro {
Vector3d positionVector)
{
//Rotate skeleton around a particular axis and center point
- Eigen::Transform3d rotation;
+ Eigen::Projective3d rotation;
rotation = Eigen::AngleAxisd(angle, rotationVector);
rotation.pretranslate(centerVector);
rotation.translate(-centerVector);
- return rotation*positionVector;
+ return (rotation*positionVector.homogeneous()).head<3>();
}
// ########## showAnglesChanged ##########
Index: avogadro-1.2.0/libavogadro/src/tools/manipulatetool.cpp
===================================================================
--- avogadro-1.2.0.orig/libavogadro/src/tools/manipulatetool.cpp
+++ avogadro-1.2.0/libavogadro/src/tools/manipulatetool.cpp
@@ -40,7 +40,6 @@
#include <QAbstractButton>
using Eigen::Vector3d;
-using Eigen::Transform3d;
using Eigen::AngleAxisd;
namespace Avogadro {
@@ -138,7 +137,7 @@ namespace Avogadro {
double yRotate = m_settingsWidget->yRotateSpinBox->value() * DEG_TO_RAD;
double zRotate = m_settingsWidget->zRotateSpinBox->value() * DEG_TO_RAD;
- Eigen::Transform3d rotation;
+ Eigen::Projective3d rotation;
rotation.matrix().setIdentity();
rotation.translation() = center;
rotation.rotate(AngleAxisd(xRotate, Vector3d::UnitX())
@@ -152,12 +151,12 @@ namespace Avogadro {
if (p->type() == Primitive::AtomType) {
Atom *atom = static_cast<Atom*>(p);
tempPos = translate + *(atom->pos());
- atom->setPos(rotation * tempPos);
+ atom->setPos((rotation * tempPos.homogeneous()).head<3>());
}
} else {
foreach(Atom *atom, widget->molecule()->atoms()) {
tempPos = translate + *(atom->pos());
- atom->setPos(rotation * tempPos);
+ atom->setPos((rotation * tempPos.homogeneous()).head<3>());
}
}
@@ -199,7 +198,7 @@ namespace Avogadro {
widget->setCursor(Qt::SizeVerCursor);
// Move the selected atom(s) in to or out of the screen
- Vector3d transformedGoal = widget->camera()->modelview() * *goal;
+ Vector3d transformedGoal = (widget->camera()->modelview() * goal->homogeneous()).head<3>();
double distanceToGoal = transformedGoal.norm();
double t = ZOOM_SPEED * delta;
@@ -255,7 +254,7 @@ namespace Avogadro {
// Rotate the selected atoms about the center
// rotate only selected primitives
- Transform3d fragmentRotation;
+ Eigen::Projective3d fragmentRotation;
fragmentRotation.matrix().setIdentity();
fragmentRotation.translation() = *center;
fragmentRotation.rotate(
@@ -266,7 +265,7 @@ namespace Avogadro {
foreach(Primitive *p, widget->selectedPrimitives())
if (p->type() == Primitive::AtomType)
- static_cast<Atom *>(p)->setPos(fragmentRotation * *static_cast<Atom *>(p)->pos());
+ static_cast<Atom *>(p)->setPos((fragmentRotation * static_cast<Atom *>(p)->pos()->homogeneous()).head<3>());
widget->molecule()->update();
}
@@ -274,7 +273,7 @@ namespace Avogadro {
double delta) const
{
// Tilt the selected atoms about the center
- Transform3d fragmentRotation;
+ Eigen::Projective3d fragmentRotation;
fragmentRotation.matrix().setIdentity();
fragmentRotation.translation() = *center;
fragmentRotation.rotate(AngleAxisd(delta * ROTATION_SPEED, widget->camera()->backTransformedZAxis()));
@@ -282,7 +281,7 @@ namespace Avogadro {
foreach(Primitive *p, widget->selectedPrimitives())
if (p->type() == Primitive::AtomType)
- static_cast<Atom *>(p)->setPos(fragmentRotation * *static_cast<Atom *>(p)->pos());
+ static_cast<Atom *>(p)->setPos((fragmentRotation * static_cast<Atom *>(p)->pos()->homogeneous()).head<3>());
widget->molecule()->update();
}
Index: avogadro-1.2.0/libavogadro/src/tools/navigatetool.cpp
===================================================================
--- avogadro-1.2.0.orig/libavogadro/src/tools/navigatetool.cpp
+++ avogadro-1.2.0/libavogadro/src/tools/navigatetool.cpp
@@ -92,7 +92,8 @@ namespace Avogadro {
double sumOfWeights = 0.;
QList<Atom*> atoms = widget->molecule()->atoms();
foreach (Atom *atom, atoms) {
- Vector3d transformedAtomPos = widget->camera()->modelview() * *atom->pos();
+ Vector3d transformedAtomPos = (widget->camera()->modelview() *
+ atom->pos()->homogeneous()).head<3>();
double atomDistance = transformedAtomPos.norm();
double dot = transformedAtomPos.z() / atomDistance;
double weight = exp(-30. * (1. + dot));
Index: avogadro-1.2.0/libavogadro/src/tools/skeletontree.cpp
===================================================================
--- avogadro-1.2.0.orig/libavogadro/src/tools/skeletontree.cpp
+++ avogadro-1.2.0/libavogadro/src/tools/skeletontree.cpp
@@ -29,6 +29,7 @@
#include <avogadro/atom.h>
#include <avogadro/bond.h>
#include <avogadro/molecule.h>
+#include <iostream>
using namespace Eigen;
using namespace std;
@@ -221,7 +222,7 @@ namespace Avogadro {
{
if (m_rootNode) {
//Rotate skeleton around a particular axis and center point
- Eigen::Transform3d rotation;
+ Eigen::Projective3d rotation;
rotation = Eigen::AngleAxisd(angle, rotationAxis);
rotation.pretranslate(centerVector);
rotation.translate(-centerVector);
@@ -248,11 +249,11 @@ namespace Avogadro {
// ########## recursiveRotate ##########
void SkeletonTree::recursiveRotate(Node* n,
- const Eigen::Transform3d &rotationMatrix)
+ const Eigen::Projective3d &rotationMatrix)
{
// Update the root node with the new position
Atom* a = n->atom();
- a->setPos(rotationMatrix * (*a->pos()));
+ a->setPos((rotationMatrix * (*a->pos()).homogeneous()).head<3>());
a->update();
// Now update the children
Index: avogadro-1.2.0/libavogadro/src/tools/skeletontree.h
===================================================================
--- avogadro-1.2.0.orig/libavogadro/src/tools/skeletontree.h
+++ avogadro-1.2.0/libavogadro/src/tools/skeletontree.h
@@ -230,7 +230,7 @@ namespace Avogadro {
* @param centerVector Center location to rotate around.
*/
void recursiveRotate(Node* n,
- const Eigen::Transform3d &rotationMatrix);
+ const Eigen::Projective3d &rotationMatrix);
};
} // End namespace Avogadro
Index: avogadro-1.2.0/libavogadro/src/python/camera.cpp
===================================================================
--- avogadro-1.2.0.orig/libavogadro/src/python/camera.cpp
+++ avogadro-1.2.0/libavogadro/src/python/camera.cpp
@@ -10,7 +10,7 @@ using namespace Avogadro;
void export_Camera()
{
- const Eigen::Transform3d& (Camera::*modelview_ptr)() const = &Camera::modelview;
+ const Eigen::Projective3d& (Camera::*modelview_ptr)() const = &Camera::modelview;
Eigen::Vector3d (Camera::*unProject_ptr1)(const Eigen::Vector3d&) const = &Camera::unProject;
Eigen::Vector3d (Camera::*unProject_ptr2)(const QPoint&, const Eigen::Vector3d&) const = &Camera::unProject;
Eigen::Vector3d (Camera::*unProject_ptr3)(const QPoint&) const = &Camera::unProject;
Index: avogadro-1.2.0/libavogadro/src/python/eigen.cpp
===================================================================
--- avogadro-1.2.0.orig/libavogadro/src/python/eigen.cpp
+++ avogadro-1.2.0/libavogadro/src/python/eigen.cpp
@@ -305,9 +305,9 @@ template <> struct ScalarTraits<double>
struct innerclass
{
//
- // Eigen::Transform3d --> python array (4x4)
+ // Eigen::Projective3d --> python array (4x4)
//
- static PyObject* convert(Eigen::Transform3d const &trans)
+ static PyObject* convert(Eigen::Projective3d const &trans)
{
npy_intp dims[2] = { 4, 4 };
PyObject *result = PyArray_SimpleNew(2, dims, PyArray_DOUBLE);
@@ -321,9 +321,9 @@ template <> struct ScalarTraits<double>
return incref(result);
}
//
- // Eigen::Transform3d* --> python array (4x4)
+ // Eigen::Projective3d* --> python array (4x4)
//
- static PyObject* convert(Eigen::Transform3d *trans)
+ static PyObject* convert(Eigen::Projective3d *trans)
{
npy_intp dims[2] = { 4, 4 };
PyObject *result = PyArray_SimpleNew(2, dims, PyArray_DOUBLE);
@@ -337,9 +337,9 @@ template <> struct ScalarTraits<double>
return incref(result);
}
//
- // const Eigen::Transform3d* --> python array (4x4)
+ // const Eigen::Projective3d* --> python array (4x4)
//
- static PyObject* convert(const Eigen::Transform3d *trans)
+ static PyObject* convert(const Eigen::Projective3d *trans)
{
npy_intp dims[2] = { 4, 4 };
PyObject *result = PyArray_SimpleNew(2, dims, PyArray_DOUBLE);
@@ -358,10 +358,10 @@ template <> struct ScalarTraits<double>
Transform3d_to_python_array()
{
#ifndef WIN32
- to_python_converter<Eigen::Transform3d, innerclass>();
+ to_python_converter<Eigen::Projective3d, innerclass>();
#endif
- to_python_converter<Eigen::Transform3d*, innerclass>();
- to_python_converter<const Eigen::Transform3d*, innerclass>();
+ to_python_converter<Eigen::Projective3d*, innerclass>();
+ to_python_converter<const Eigen::Projective3d*, innerclass>();
}
};
@@ -373,17 +373,17 @@ template <> struct ScalarTraits<double>
// Insert an rvalue from_python converter at the tail of the
// chain. Used for implicit conversions
//
- // python array --> Eigen::Transform3d
+ // python array --> Eigen::Projective3d
//
// used for:
//
- // void function(Eigen::Transform3d vec)
- // void function(Eigen::Transform3d & vec)
- // void function(const Eigen::Transform3d & vec)
+ // void function(Eigen::Projective3d vec)
+ // void function(Eigen::Projective3d & vec)
+ // void function(const Eigen::Projective3d & vec)
//
- converter::registry::push_back( &convertible, &construct, type_id<Eigen::Transform3d>() );
+ converter::registry::push_back( &convertible, &construct, type_id<Eigen::Projective3d>() );
- converter::registry::insert( &convert, type_id<Eigen::Transform3d>() );
+ converter::registry::insert( &convert, type_id<Eigen::Projective3d>() );
}
static void* convert(PyObject *obj_ptr)
@@ -401,7 +401,7 @@ template <> struct ScalarTraits<double>
throw_error_already_set(); // the 1D array does not have exactly 3 elements
double *values = reinterpret_cast<double*>(array->data);
- Eigen::Transform3d *c_obj = new Eigen::Transform3d();
+ Eigen::Projective3d *c_obj = new Eigen::Projective3d();
double *dataPtr = c_obj->data();
for (int i = 0; i < 16; ++i)
@@ -432,7 +432,7 @@ template <> struct ScalarTraits<double>
// I think this is a better way to get at the double array, where is this
// deleted though? Does Boost::Python do it?
double *values = reinterpret_cast<double*>(array->data);
- Eigen::Transform3d *storage = new Eigen::Transform3d();
+ Eigen::Projective3d *storage = new Eigen::Projective3d();
double *dataPtr = storage->data();
for (int i = 0; i < 16; ++i)
@@ -467,21 +467,21 @@ class EigenUnitTestHelper
void set_vector3d_ptr(Eigen::Vector3d* vec) { m_vector3d = *vec; }
void set_const_vector3d_ptr(const Eigen::Vector3d* const vec) { m_vector3d = *vec; }
- //Eigen::Transform3d transform3d() { return m_transform3d; }
- //Eigen::Transform3d& transform3d_ref() { return m_transform3d; }
- const Eigen::Transform3d& const_transform3d_ref() { return m_transform3d; }
- Eigen::Transform3d* transform3d_ptr() { return &m_transform3d; }
- const Eigen::Transform3d* const_transform3d_ptr() { return &m_transform3d; }
-
- //void set_transform3d(Eigen::Transform3d vec) { m_transform3d = vec; }
- //void set_transform3d_ref(Eigen::Transform3d& vec) { m_transform3d = vec; }
- void set_const_transform3d_ref(const Eigen::Transform3d& vec) { m_transform3d = vec; }
- void set_transform3d_ptr(Eigen::Transform3d* vec) { m_transform3d = *vec; }
- void set_const_transform3d_ptr(const Eigen::Transform3d* const vec) { m_transform3d = *vec; }
+ //Eigen::Projective3d transform3d() { return m_transform3d; }
+ //Eigen::Projective3d& transform3d_ref() { return m_transform3d; }
+ const Eigen::Projective3d& const_transform3d_ref() { return m_transform3d; }
+ Eigen::Projective3d* transform3d_ptr() { return &m_transform3d; }
+ const Eigen::Projective3d* const_transform3d_ptr() { return &m_transform3d; }
+
+ //void set_transform3d(Eigen::Projective3d vec) { m_transform3d = vec; }
+ //void set_transform3d_ref(Eigen::Projective3d& vec) { m_transform3d = vec; }
+ void set_const_transform3d_ref(const Eigen::Projective3d& vec) { m_transform3d = vec; }
+ void set_transform3d_ptr(Eigen::Projective3d* vec) { m_transform3d = *vec; }
+ void set_const_transform3d_ptr(const Eigen::Projective3d* const vec) { m_transform3d = *vec; }
private:
Eigen::Vector3d m_vector3d;
- Eigen::Transform3d m_transform3d;
+ Eigen::Projective3d m_transform3d;
};
#endif
@@ -529,7 +529,7 @@ void export_Eigen()
Vector3x_to_python_array<Eigen::Vector3i>();
Vector3x_from_python_array<Eigen::Vector3i>();
- // Eigen::Transform3d
+ // Eigen::Projective3d
Transform3d_to_python_array();
Transform3d_from_python_array();
