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avogadro
avogadro-port-to-eigen3.patch
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File avogadro-port-to-eigen3.patch of Package avogadro
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();
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