gnu/packages/patches/avogadro-eigen3-update.patch

   1 From 43af3c117b0b3220b15c2fe2895b94bbd83d3a60 Mon Sep 17 00:00:00 2001
   2 From: Claudio Fernandes <claudiosf.claudio@gmail.com>
   3 Date: Sun, 15 Jan 2017 21:23:39 -0200
   4 Subject: [PATCH] Adapt Avogadro to Eigen 3.3
   5
   6 ---
   7  CMakeLists.txt                                     |  9 +------
   8  avogadro/src/mainwindow.cpp                        |  5 ++--
   9  libavogadro/src/camera.cpp                         | 10 ++++----
  10  libavogadro/src/camera.h                           | 14 +++++------
  11  libavogadro/src/engines/wireengine.cpp             |  4 ++--
  12  .../crystallography/crystallographyextension.cpp   |  2 +-
  13  .../crystallography/ui/ceviewoptionswidget.cpp     |  2 +-
  14  .../src/extensions/orca/orcaanalysedialog.cpp      |  1 -
  15  .../src/extensions/orca/orcainputdialog.cpp        |  1 -
  16  .../src/extensions/qtaim/qtaimmathutilities.cpp    |  1 +
  17  .../qtaim/qtaimwavefunctionevaluator.cpp           | 28 +++++++++++-----------
  18  .../extensions/surfaces/openqube/gamessukout.cpp   |  1 +
  19  .../src/extensions/surfaces/openqube/slaterset.cpp |  6 +++--
  20  libavogadro/src/glpainter_p.cpp                    | 14 +++++------
  21  libavogadro/src/glwidget.cpp                       |  4 ++--
  22  libavogadro/src/molecule.cpp                       | 26 ++++++++++++++++++--
  23  libavogadro/src/navigate.cpp                       |  2 +-
  24  libavogadro/src/tools/bondcentrictool.cpp          | 28 +++++++++++-----------
  25  libavogadro/src/tools/manipulatetool.cpp           | 17 +++++++------
  26  libavogadro/src/tools/navigatetool.cpp             |  3 ++-
  27  libavogadro/src/tools/skeletontree.cpp             |  7 +++---
  28  libavogadro/src/tools/skeletontree.h               |  2 +-
  29  22 files changed, 102 insertions(+), 85 deletions(-)
  30
  31 --- a/CMakeLists.txt
  32 +++ b/CMakeLists.txt
  33 @@ -231,14 +231,7 @@ if(NOT Linguist_FOUND)
  34    message(WARNING " Qt4 Linguist not found, please install it if you want Avogadro translations")
  35  endif()
  36
  37 -find_package(Eigen3) # find and setup Eigen3 if available
  38 -if(NOT EIGEN3_FOUND)
  39 -   message(STATUS "Cannot find Eigen3, trying Eigen2")
  40 -   find_package(Eigen2 REQUIRED) # Some version is required
  41 -else()
  42 -# Use Stage10 Eigen3 support
  43 -   set (EIGEN2_SUPPORT_STAGE10_FULL_EIGEN2_API TRUE)
  44 -endif()
  45 +find_package(Eigen3 REQUIRED) # find and setup Eigen3 if available
  46
  47  find_package(ZLIB REQUIRED)
  48  find_package(OpenBabel2 REQUIRED) # find and setup OpenBabel
  49 --- a/avogadro/src/mainwindow.cpp
  50 +++ b/avogadro/src/mainwindow.cpp
  51 @@ -115,7 +115,6 @@
  52  #include <QDebug>
  53
  54  #include <Eigen/Geometry>
  55 -#include <Eigen/Array>
  56  #define USEQUAT
  57  // This is a "hidden" exported Qt function on the Mac for Qt-4.x.
  58  #ifdef Q_WS_MAC
  59 @@ -2775,7 +2774,7 @@ protected:
  60      linearGoal.row(1) = linearGoal.row(2).cross(linearGoal.row(0));
  61
  62      // calculate the translation matrix
  63 -    Transform3d goal(linearGoal);
  64 +    Projective3d goal(linearGoal);
  65
  66      goal.pretranslate(- 3.0 * (d->glWidget->radius() + CAMERA_NEAR_DISTANCE) * Vector3d::UnitZ());
  67
  68 @@ -2840,7 +2839,7 @@ protected:
  69      Matrix3d linearGoal = Matrix3d::Identity();
  70
  71      // calculate the translation matrix
  72 -    Transform3d goal(linearGoal);
  73 +    Projective3d goal(linearGoal);
  74
  75      goal.pretranslate(- 3.0 * (d->glWidget->radius() + CAMERA_NEAR_DISTANCE) * Vector3d::UnitZ());
  76
  77 --- a/libavogadro/src/camera.cpp
  78 +++ b/libavogadro/src/camera.cpp
  79 @@ -47,7 +47,7 @@ namespace Avogadro
  80
  81        CameraPrivate() {};
  82
  83 -      Eigen::Transform3d modelview, projection;
  84 +      Eigen::Projective3d modelview, projection;
  85        const GLWidget *parent;
  86        double angleOfViewY;
  87        double orthoScale;
  88 @@ -169,20 +169,20 @@ namespace Avogadro
  89
  90    double Camera::distance(const Eigen::Vector3d & point) const
  91    {
  92 -    return ( d->modelview * point ).norm();
  93 +    return ( d->modelview * point.homogeneous() ).head<3>().norm();
  94    }
  95
  96 -  void Camera::setModelview(const Eigen::Transform3d &matrix)
  97 +  void Camera::setModelview(const Eigen::Projective3d &matrix)
  98    {
  99      d->modelview = matrix;
 100    }
 101
 102 -  const Eigen::Transform3d & Camera::modelview() const
 103 +  const Eigen::Projective3d & Camera::modelview() const
 104    {
 105      return d->modelview;
 106    }
 107
 108 -  Eigen::Transform3d & Camera::modelview()
 109 +  Eigen::Projective3d & Camera::modelview()
 110    {
 111      return d->modelview;
 112    }
 113 --- a/libavogadro/src/camera.h
 114 +++ b/libavogadro/src/camera.h
 115 @@ -101,16 +101,16 @@ namespace Avogadro {
 116        double angleOfViewY() const;
 117        /** Sets 4x4 "modelview" matrix representing the camera orientation and position.
 118          * @param matrix the matrix to copy from
 119 -        * @sa Eigen::Transform3d & modelview(), applyModelview() */
 120 -      void setModelview(const Eigen::Transform3d &matrix);
 121 +        * @sa Eigen::Projective3d & modelview(), applyModelview() */
 122 +      void setModelview(const Eigen::Projective3d &matrix);
 123        /** @return a constant reference to the 4x4 "modelview" matrix representing
 124          *         the camera orientation and position
 125 -        * @sa setModelview(), Eigen::Transform3d & modelview() */
 126 -      const Eigen::Transform3d & modelview() const;
 127 +        * @sa setModelview(), Eigen::Projective3d & modelview() */
 128 +      const Eigen::Projective3d & modelview() const;
 129        /** @return a non-constant reference to the 4x4 "modelview" matrix representing
 130          *         the camera orientation and position
 131 -        * @sa setModelview(), const Eigen::Transform3d & modelview() const */
 132 -      Eigen::Transform3d & modelview();
 133 +        * @sa setModelview(), const Eigen::Projective3d & modelview() const */
 134 +      Eigen::Projective3d & modelview();
 135        /** Calls gluPerspective() or glOrtho() with parameters automatically chosen
 136          * for rendering the GLWidget's molecule with this camera. Should be called
 137          * only in GL_PROJECTION matrix mode. Example code is given
 138 @@ -342,7 +342,7 @@ namespace Avogadro {
 139         * @return {x/w, y/w, z/w} vector
 140         */
 141        Eigen::Vector3d V4toV3DivW(const Eigen::Vector4d & v4) {
 142 -        return v4.start<3>()/v4.w();
 143 +        return v4.head<3>()/v4.w();
 144        }
 145    };
 146
 147 --- a/libavogadro/src/engines/wireengine.cpp
 148 +++ b/libavogadro/src/engines/wireengine.cpp
 149 @@ -109,7 +109,7 @@ namespace Avogadro {
 150      const Camera *camera = pd->camera();
 151
 152      // perform a rough form of frustum culling
 153 -    Eigen::Vector3d transformedPos = pd->camera()->modelview() * v;
 154 +    Eigen::Vector3d transformedPos = (pd->camera()->modelview() * v.homogeneous()).head<3>();
 155      double dot = transformedPos.z() / transformedPos.norm();
 156      if(dot > -0.8)
 157        return true;
 158 @@ -167,7 +167,7 @@ namespace Avogadro {
 159        map = pd->colorMap(); // fall back to global color map
 160
 161      // perform a rough form of frustum culling
 162 -    Eigen::Vector3d transformedEnd1 = pd->camera()->modelview() * v1;
 163 +    Eigen::Vector3d transformedEnd1 = (pd->camera()->modelview() * v1.homogeneous()).head<3>();
 164      double dot = transformedEnd1.z() / transformedEnd1.norm();
 165      if(dot > -0.8)
 166        return true; // i.e., don't bother rendering
 167 --- a/libavogadro/src/extensions/crystallography/crystallographyextension.cpp
 168 +++ b/libavogadro/src/extensions/crystallography/crystallographyextension.cpp
 169 @@ -1989,7 +1989,7 @@ namespace Avogadro
 170      // fix coordinates
 171      // Apply COB matrix:
 172      Eigen::Matrix3d invCob;
 173 -    cob.computeInverse(&invCob);
 174 +    invCob = cob.inverse();
 175      for (QList<Eigen::Vector3d>::iterator
 176             it = fcoords.begin(),
 177             it_end = fcoords.end();
 178 --- a/libavogadro/src/extensions/crystallography/ui/ceviewoptionswidget.cpp
 179 +++ b/libavogadro/src/extensions/crystallography/ui/ceviewoptionswidget.cpp
 180 @@ -139,7 +139,7 @@ namespace Avogadro
 181    {
 182      // View into a Miller plane
 183      Camera *camera = m_glWidget->camera();
 184 -    Eigen::Transform3d modelView;
 185 +    Eigen::Projective3d modelView;
 186      modelView.setIdentity();
 187
 188      // OK, so we want to rotate to look along the normal at the plane
 189 --- a/libavogadro/src/extensions/orca/orcaanalysedialog.cpp
 190 +++ b/libavogadro/src/extensions/orca/orcaanalysedialog.cpp
 191 @@ -41,7 +41,6 @@
 192  #include <openbabel/mol.h>
 193
 194  #include <Eigen/Geometry>
 195 -#include <Eigen/LeastSquares>
 196
 197  #include <vector>
 198
 199 --- a/libavogadro/src/extensions/orca/orcainputdialog.cpp
 200 +++ b/libavogadro/src/extensions/orca/orcainputdialog.cpp
 201 @@ -33,7 +33,6 @@
 202  #include <openbabel/mol.h>
 203
 204  #include <Eigen/Geometry>
 205 -#include <Eigen/LeastSquares>
 206
 207  #include <vector>
 208
 209 --- a/libavogadro/src/extensions/qtaim/qtaimmathutilities.cpp
 210 +++ b/libavogadro/src/extensions/qtaim/qtaimmathutilities.cpp
 211 @@ -28,6 +28,7 @@
 212
 213  #include <cmath>
 214  #include <Eigen/QR>
 215 +#include <Eigen/Eigenvalues>
 216
 217  namespace Avogadro {
 218    namespace QTAIMMathUtilities {
 219 --- a/libavogadro/src/extensions/qtaim/qtaimwavefunctionevaluator.cpp
 220 +++ b/libavogadro/src/extensions/qtaim/qtaimwavefunctionevaluator.cpp
 221 @@ -35,21 +35,21 @@ namespace Avogadro
 222      m_nprim=wfn.numberOfGaussianPrimitives();
 223      m_nnuc=wfn.numberOfNuclei();
 224
 225 -    m_nucxcoord=Map<Matrix<qreal,Dynamic,1> >(wfn.xNuclearCoordinates(),m_nnuc);
 226 -    m_nucycoord=Map<Matrix<qreal,Dynamic,1> >(wfn.yNuclearCoordinates(),m_nnuc);
 227 -    m_nuczcoord=Map<Matrix<qreal,Dynamic,1> >(wfn.zNuclearCoordinates(),m_nnuc);
 228 -    m_nucz=Map<Matrix<qint64,Dynamic,1> >(wfn.nuclearCharges(),m_nnuc);
 229 -    m_X0=Map<Matrix<qreal,Dynamic,1> >(wfn.xGaussianPrimitiveCenterCoordinates(),m_nprim,1);
 230 -    m_Y0=Map<Matrix<qreal,Dynamic,1> >(wfn.yGaussianPrimitiveCenterCoordinates(),m_nprim,1);
 231 -    m_Z0=Map<Matrix<qreal,Dynamic,1> >(wfn.zGaussianPrimitiveCenterCoordinates(),m_nprim,1);
 232 -    m_xamom=Map<Matrix<qint64,Dynamic,1> >(wfn.xGaussianPrimitiveAngularMomenta(),m_nprim,1);
 233 -    m_yamom=Map<Matrix<qint64,Dynamic,1> >(wfn.yGaussianPrimitiveAngularMomenta(),m_nprim,1);
 234 -    m_zamom=Map<Matrix<qint64,Dynamic,1> >(wfn.zGaussianPrimitiveAngularMomenta(),m_nprim,1);
 235 -    m_alpha=Map<Matrix<qreal,Dynamic,1> >(wfn.gaussianPrimitiveExponentCoefficients(),m_nprim,1);
 236 +    m_nucxcoord=Map<Matrix<qreal,Dynamic,1> >(const_cast<qreal*>(wfn.xNuclearCoordinates()),m_nnuc);
 237 +    m_nucycoord=Map<Matrix<qreal,Dynamic,1> >(const_cast<qreal*>(wfn.yNuclearCoordinates()),m_nnuc);
 238 +    m_nuczcoord=Map<Matrix<qreal,Dynamic,1> >(const_cast<qreal*>(wfn.zNuclearCoordinates()),m_nnuc);
 239 +    m_nucz=Map<Matrix<qint64,Dynamic,1> >(const_cast<qint64*>(wfn.nuclearCharges()),m_nnuc);
 240 +    m_X0=Map<Matrix<qreal,Dynamic,1> >(const_cast<qreal*>(wfn.xGaussianPrimitiveCenterCoordinates()),m_nprim,1);
 241 +    m_Y0=Map<Matrix<qreal,Dynamic,1> >(const_cast<qreal*>(wfn.yGaussianPrimitiveCenterCoordinates()),m_nprim,1);
 242 +    m_Z0=Map<Matrix<qreal,Dynamic,1> >(const_cast<qreal*>(wfn.zGaussianPrimitiveCenterCoordinates()),m_nprim,1);
 243 +    m_xamom=Map<Matrix<qint64,Dynamic,1> >(const_cast<qint64*>(wfn.xGaussianPrimitiveAngularMomenta()),m_nprim,1);
 244 +    m_yamom=Map<Matrix<qint64,Dynamic,1> >(const_cast<qint64*>(wfn.yGaussianPrimitiveAngularMomenta()),m_nprim,1);
 245 +    m_zamom=Map<Matrix<qint64,Dynamic,1> >(const_cast<qint64*>(wfn.zGaussianPrimitiveAngularMomenta()),m_nprim,1);
 246 +    m_alpha=Map<Matrix<qreal,Dynamic,1> >(const_cast<qreal*>(wfn.gaussianPrimitiveExponentCoefficients()),m_nprim,1);
 247      // TODO Implement screening for unoccupied molecular orbitals.
 248 -    m_occno=Map<Matrix<qreal,Dynamic,1> >(wfn.molecularOrbitalOccupationNumbers(),m_nmo,1);
 249 -    m_orbe=Map<Matrix<qreal,Dynamic,1> >(wfn.molecularOrbitalEigenvalues(),m_nmo,1);
 250 -    m_coef=Map<Matrix<qreal,Dynamic,Dynamic,RowMajor> >(wfn.molecularOrbitalCoefficients(),m_nmo,m_nprim);
 251 +    m_occno=Map<Matrix<qreal,Dynamic,1> >(const_cast<qreal*>(wfn.molecularOrbitalOccupationNumbers()),m_nmo,1);
 252 +    m_orbe=Map<Matrix<qreal,Dynamic,1> >(const_cast<qreal*>(wfn.molecularOrbitalEigenvalues()),m_nmo,1);
 253 +    m_coef=Map<Matrix<qreal,Dynamic,Dynamic,RowMajor> >(const_cast<qreal*>(wfn.molecularOrbitalCoefficients()),m_nmo,m_nprim);
 254      m_totalEnergy=wfn.totalEnergy();
 255      m_virialRatio=wfn.virialRatio();
 256
 257 --- a/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp
 258 +++ b/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp
 259 @@ -19,6 +19,7 @@
 260  using Eigen::Vector3d;
 261  using std::vector;
 262
 263 +#include <iostream>
 264  #include <fstream>
 265
 266  namespace OpenQube
 267 --- a/libavogadro/src/extensions/surfaces/openqube/slaterset.cpp
 268 +++ b/libavogadro/src/extensions/surfaces/openqube/slaterset.cpp
 269 @@ -25,9 +25,9 @@
 270
 271  #include "cube.h"
 272
 273 -#include <Eigen/Array>
 274  #include <Eigen/LU>
 275  #include <Eigen/QR>
 276 +#include <Eigen/Eigenvalues>
 277
 278  #include <cmath>
 279
 280 @@ -250,7 +250,9 @@ bool SlaterSet::initialize()
 281
 282    SelfAdjointEigenSolver<MatrixXd> s(m_overlap);
 283    MatrixXd p = s.eigenvectors();
 284 -  MatrixXd m = p * s.eigenvalues().cwise().inverse().cwise().sqrt().asDiagonal() * p.inverse();
 285 +  // TODO check if this is correct
 286 +  MatrixXd m1 = (s.eigenvalues().array().inverse().sqrt());
 287 +  MatrixXd m = p.array()*(m1.diagonal().array())*p.inverse().array();
 288    m_normalized = m * m_eigenVectors;
 289
 290    if (!(m_overlap*m*m).isIdentity())
 291 --- a/libavogadro/src/glpainter_p.cpp
 292 +++ b/libavogadro/src/glpainter_p.cpp
 293 @@ -789,13 +789,13 @@ namespace Avogadro
 294          } else {
 295            points[theta-1] = Eigen::AngleAxisd(theta * (M_PI / 180.0) / 2, n) * u;
 296          }
 297 -        points[theta-1] = d->widget->camera()->modelview() * (origin + points[theta-1]);
 298 +        points[theta-1] = (d->widget->camera()->modelview() * (origin + points[theta-1]).homogeneous()).head<3>();
 299        }
 300
 301      // Get vectors representing the points' positions in terms of the model view.
 302 -    Eigen::Vector3d _origin = d->widget->camera()->modelview() * origin;
 303 -    Eigen::Vector3d _direction1 = d->widget->camera()->modelview() * (origin+u);
 304 -    Eigen::Vector3d _direction2 = d->widget->camera()->modelview() * (origin+v);
 305 +    Eigen::Vector3d _origin = (d->widget->camera()->modelview() * origin.homogeneous()).head<3>();
 306 +    Eigen::Vector3d _direction1 = (d->widget->camera()->modelview() * (origin+u).homogeneous()).head<3>();
 307 +    Eigen::Vector3d _direction2 = (d->widget->camera()->modelview() * (origin+v).homogeneous()).head<3>();
 308
 309      glPushAttrib(GL_ALL_ATTRIB_BITS);
 310      glPushMatrix();
 311 @@ -880,12 +880,12 @@ namespace Avogadro
 312          } else {
 313            points[theta-1] = Eigen::AngleAxisd(theta * (M_PI / 180.0) / 2, n) * u;
 314          }
 315 -        points[theta-1] = d->widget->camera()->modelview() * (origin + points[theta-1]);
 316 +        points[theta-1] = (d->widget->camera()->modelview() * (origin + points[theta-1]).homogeneous()).head<3>();
 317        }
 318
 319      // Get vectors representing the points' positions in terms of the model view.
 320 -    Eigen::Vector3d _direction1 = d->widget->camera()->modelview() * (origin + u);
 321 -    Eigen::Vector3d _direction2 = d->widget->camera()->modelview() * (origin + v);
 322 +    Eigen::Vector3d _direction1 = (d->widget->camera()->modelview() * (origin + u).homogeneous()).head<3>();
 323 +    Eigen::Vector3d _direction2 = (d->widget->camera()->modelview() * (origin + v).homogeneous()).head<3>();
 324
 325      glPushAttrib(GL_ALL_ATTRIB_BITS);
 326      glPushMatrix();
 327 --- a/libavogadro/src/glwidget.cpp
 328 +++ b/libavogadro/src/glwidget.cpp
 329 @@ -765,7 +765,7 @@ namespace Avogadro {
 330        GLfloat fogColor[4]= {static_cast<GLfloat>(d->background.redF()), static_cast<GLfloat>(d->background.greenF()),
 331                              static_cast<GLfloat>(d->background.blueF()), static_cast<GLfloat>(d->background.alphaF())};
 332        glFogfv(GL_FOG_COLOR, fogColor);
 333 -      Vector3d distance = camera()->modelview() * d->center;
 334 +      Vector3d distance = (camera()->modelview() * d->center.homogeneous()).head<3>();
 335        double distanceToCenter = distance.norm();
 336        glFogf(GL_FOG_DENSITY, 1.0);
 337        glHint(GL_FOG_HINT, GL_NICEST);
 338 @@ -1711,7 +1711,7 @@ namespace Avogadro {
 339
 340        if (d->renderModelViewDebug) {
 341          // Model view matrix:
 342 -        const Eigen::Transform3d &modelview = d->camera->modelview();
 343 +        const Eigen::Projective3d &modelview = d->camera->modelview();
 344          y += d->pd->painter()->drawText
 345              (x, y, tr("ModelView row 1: %L1 %L2 %L3 %L4")
 346               .arg(modelview(0, 0), 6, 'f', 2, ' ')
 347 --- a/libavogadro/src/molecule.cpp
 348 +++ b/libavogadro/src/molecule.cpp
 349 @@ -38,7 +38,7 @@
 350  #include "zmatrix.h"
 351
 352  #include <Eigen/Geometry>
 353 -#include <Eigen/LeastSquares>
 354 +#include <Eigen/Eigenvalues>
 355
 356  #include <vector>
 357
 358 @@ -1907,7 +1907,29 @@ namespace Avogadro{
 359          }
 360          d->center /= static_cast<double>(nAtoms);
 361          Eigen::Hyperplane<double, 3> planeCoeffs;
 362 -        Eigen::fitHyperplane(numAtoms(), atomPositions, &planeCoeffs);
 363 +        //Eigen::fitHyperplane(numAtoms(), atomPositions, &planeCoeffs);
 364 +
 365 +        // TODO check if this is OK
 366 +        /************************/
 367 +        typedef Eigen::Matrix<double,3,3> CovMatrixType;
 368 +        typedef Eigen::Vector3d VectorType;
 369 +
 370 +        VectorType mean = d->center;
 371 +        int size=3;
 372 +        int numPoints=numAtoms();
 373 +        VectorType ** points=atomPositions;
 374 +        CovMatrixType covMat = CovMatrixType::Zero(size, size);
 375 +        VectorType remean = VectorType::Zero(size);
 376 +        for(int i = 0; i < numPoints; ++i)
 377 +        {
 378 +          VectorType diff = (*(points[i]) - mean).conjugate();
 379 +          covMat += diff * diff.adjoint();
 380 +        }
 381 +        Eigen::SelfAdjointEigenSolver<CovMatrixType> eig(covMat);
 382 +        planeCoeffs.normal() = eig.eigenvectors().col(0);
 383 +        /************************/
 384 +
 385 +
 386          delete[] atomPositions;
 387          d->normalVector = planeCoeffs.normal();
 388        }
 389 --- a/libavogadro/src/navigate.cpp
 390 +++ b/libavogadro/src/navigate.cpp
 391 @@ -40,7 +40,7 @@ namespace Avogadro {
 392    void Navigate::zoom(GLWidget *widget, const Eigen::Vector3d &goal,
 393                        double delta)
 394    {
 395 -    Vector3d transformedGoal = widget->camera()->modelview() * goal;
 396 +    Vector3d transformedGoal = (widget->camera()->modelview() * goal.homogeneous()).head<3>();
 397      double distanceToGoal = transformedGoal.norm();
 398
 399      double t = ZOOM_SPEED * delta;
 400 --- a/libavogadro/src/tools/bondcentrictool.cpp
 401 +++ b/libavogadro/src/tools/bondcentrictool.cpp
 402 @@ -578,8 +578,8 @@ namespace Avogadro {
 403
 404            Vector3d clicked = *m_clickedAtom->pos();
 405
 406 -          Vector3d axis = Vector3d(0, 0, ((widget->camera()->modelview() * other).z() >=
 407 -                (widget->camera()->modelview() * center).z() ? -1 : 1));
 408 +          Vector3d axis = Vector3d(0, 0, ((widget->camera()->modelview() * other.homogeneous()).z() >=
 409 +                (widget->camera()->modelview() * center.homogeneous()).z() ? -1 : 1));
 410
 411            Vector3d centerProj = widget->camera()->project(center);
 412            centerProj -= Vector3d(0,0,centerProj.z());
 413 @@ -673,8 +673,8 @@ namespace Avogadro {
 414
 415            Vector3d clicked = *m_clickedAtom->pos();
 416
 417 -          Vector3d axis = Vector3d(0, 0, ((widget->camera()->modelview() * other).z() >=
 418 -                (widget->camera()->modelview() * center).z() ? -1 : 1));
 419 +          Vector3d axis = Vector3d(0, 0, ((widget->camera()->modelview() * other.homogeneous()).z() >=
 420 +                (widget->camera()->modelview() * center.homogeneous()).z() ? -1 : 1));
 421
 422            Vector3d centerProj = widget->camera()->project(center);
 423            centerProj -= Vector3d(0,0,centerProj.z());
 424 @@ -1362,10 +1362,10 @@ namespace Avogadro {
 425
 426      planeVec = length * (planeVec / planeVec.norm());
 427
 428 -    Vector3d topLeft = widget->camera()->modelview() * (left + planeVec);
 429 -    Vector3d topRight = widget->camera()->modelview() * (right + planeVec);
 430 -    Vector3d botRight = widget->camera()->modelview() * (right - planeVec);
 431 -    Vector3d botLeft = widget->camera()->modelview() * (left - planeVec);
 432 +    Vector3d topLeft = (widget->camera()->modelview() * (left + planeVec).homogeneous()).head<3>();
 433 +    Vector3d topRight = (widget->camera()->modelview() * (right + planeVec).homogeneous()).head<3>();
 434 +    Vector3d botRight = (widget->camera()->modelview() * (right - planeVec).homogeneous()).head<3>();
 435 +    Vector3d botLeft = (widget->camera()->modelview() * (left - planeVec).homogeneous()).head<3>();
 436
 437      float alpha = 0.4;
 438      double lineWidth = 1.5;
 439 @@ -1444,10 +1444,10 @@ namespace Avogadro {
 440        C = D + ((C-D).normalized() * minWidth);
 441      }
 442
 443 -    Vector3d topLeft = widget->camera()->modelview() * D;
 444 -    Vector3d topRight = widget->camera()->modelview() * C;
 445 -    Vector3d botRight = widget->camera()->modelview() * B;
 446 -    Vector3d botLeft = widget->camera()->modelview() * A;
 447 +    Vector3d topLeft = (widget->camera()->modelview() * D.homogeneous()).head<3>();
 448 +    Vector3d topRight = (widget->camera()->modelview() * C.homogeneous()).head<3>();
 449 +    Vector3d botRight = (widget->camera()->modelview() * B.homogeneous()).head<3>();
 450 +    Vector3d botLeft = (widget->camera()->modelview() * A.homogeneous()).head<3>();
 451
 452      float alpha = 0.4;
 453      double lineWidth = 1.5;
 454 @@ -1506,12 +1506,12 @@ namespace Avogadro {
 455        Vector3d positionVector)
 456    {
 457      //Rotate skeleton around a particular axis and center point
 458 -    Eigen::Transform3d rotation;
 459 +    Eigen::Projective3d rotation;
 460      rotation = Eigen::AngleAxisd(angle, rotationVector);
 461      rotation.pretranslate(centerVector);
 462      rotation.translate(-centerVector);
 463
 464 -    return rotation*positionVector;
 465 +    return (rotation*positionVector.homogeneous()).head<3>();
 466    }
 467
 468    // ##########  showAnglesChanged  ##########
 469 --- a/libavogadro/src/tools/manipulatetool.cpp
 470 +++ b/libavogadro/src/tools/manipulatetool.cpp
 471 @@ -40,7 +40,6 @@
 472  #include <QAbstractButton>
 473
 474  using Eigen::Vector3d;
 475 -using Eigen::Transform3d;
 476  using Eigen::AngleAxisd;
 477
 478  namespace Avogadro {
 479 @@ -138,7 +137,7 @@ namespace Avogadro {
 480      double yRotate = m_settingsWidget->yRotateSpinBox->value() * DEG_TO_RAD;
 481      double zRotate = m_settingsWidget->zRotateSpinBox->value() * DEG_TO_RAD;
 482
 483 -    Eigen::Transform3d rotation;
 484 +    Eigen::Projective3d rotation;
 485      rotation.matrix().setIdentity();
 486      rotation.translation() = center;
 487      rotation.rotate(AngleAxisd(xRotate, Vector3d::UnitX())
 488 @@ -152,12 +151,12 @@ namespace Avogadro {
 489          if (p->type() == Primitive::AtomType) {
 490            Atom *atom = static_cast<Atom*>(p);
 491            tempPos = translate + *(atom->pos());
 492 -          atom->setPos(rotation * tempPos);
 493 +          atom->setPos((rotation * tempPos.homogeneous()).head<3>());
 494          }
 495      } else {
 496        foreach(Atom *atom, widget->molecule()->atoms()) {
 497          tempPos = translate + *(atom->pos());
 498 -        atom->setPos(rotation * tempPos);
 499 +        atom->setPos((rotation * tempPos.homogeneous()).head<3>());
 500        }
 501      }
 502
 503 @@ -199,7 +198,7 @@ namespace Avogadro {
 504      widget->setCursor(Qt::SizeVerCursor);
 505
 506      // Move the selected atom(s) in to or out of the screen
 507 -    Vector3d transformedGoal = widget->camera()->modelview() * *goal;
 508 +    Vector3d transformedGoal = (widget->camera()->modelview() * goal->homogeneous()).head<3>();
 509      double distanceToGoal = transformedGoal.norm();
 510
 511      double t = ZOOM_SPEED * delta;
 512 @@ -255,7 +254,7 @@ namespace Avogadro {
 513
 514      // Rotate the selected atoms about the center
 515      // rotate only selected primitives
 516 -    Transform3d fragmentRotation;
 517 +    Eigen::Projective3d fragmentRotation;
 518      fragmentRotation.matrix().setIdentity();
 519      fragmentRotation.translation() = *center;
 520      fragmentRotation.rotate(
 521 @@ -266,7 +265,7 @@ namespace Avogadro {
 522
 523      foreach(Primitive *p, widget->selectedPrimitives())
 524        if (p->type() == Primitive::AtomType)
 525 -        static_cast<Atom *>(p)->setPos(fragmentRotation * *static_cast<Atom *>(p)->pos());
 526 +        static_cast<Atom *>(p)->setPos((fragmentRotation * static_cast<Atom *>(p)->pos()->homogeneous()).head<3>());
 527      widget->molecule()->update();
 528    }
 529
 530 @@ -274,7 +273,7 @@ namespace Avogadro {
 531                              double delta) const
 532    {
 533      // Tilt the selected atoms about the center
 534 -    Transform3d fragmentRotation;
 535 +    Eigen::Projective3d fragmentRotation;
 536      fragmentRotation.matrix().setIdentity();
 537      fragmentRotation.translation() = *center;
 538      fragmentRotation.rotate(AngleAxisd(delta * ROTATION_SPEED, widget->camera()->backTransformedZAxis()));
 539 @@ -282,7 +281,7 @@ namespace Avogadro {
 540
 541      foreach(Primitive *p, widget->selectedPrimitives())
 542        if (p->type() == Primitive::AtomType)
 543 -        static_cast<Atom *>(p)->setPos(fragmentRotation * *static_cast<Atom *>(p)->pos());
 544 +        static_cast<Atom *>(p)->setPos((fragmentRotation * static_cast<Atom *>(p)->pos()->homogeneous()).head<3>());
 545      widget->molecule()->update();
 546    }
 547
 548 --- a/libavogadro/src/tools/navigatetool.cpp
 549 +++ b/libavogadro/src/tools/navigatetool.cpp
 550 @@ -92,7 +92,8 @@ namespace Avogadro {
 551        double sumOfWeights = 0.;
 552        QList<Atom*> atoms = widget->molecule()->atoms();
 553        foreach (Atom *atom, atoms) {
 554 -        Vector3d transformedAtomPos = widget->camera()->modelview() * *atom->pos();
 555 +        Vector3d transformedAtomPos = (widget->camera()->modelview() *
 556 +                                       atom->pos()->homogeneous()).head<3>();
 557          double atomDistance = transformedAtomPos.norm();
 558          double dot = transformedAtomPos.z() / atomDistance;
 559          double weight = exp(-30. * (1. + dot));
 560 --- a/libavogadro/src/tools/skeletontree.cpp
 561 +++ b/libavogadro/src/tools/skeletontree.cpp
 562 @@ -29,6 +29,7 @@
 563  #include <avogadro/atom.h>
 564  #include <avogadro/bond.h>
 565  #include <avogadro/molecule.h>
 566 +#include <iostream>
 567
 568  using namespace Eigen;
 569  using namespace std;
 570 @@ -221,7 +222,7 @@ namespace Avogadro {
 571    {
 572      if (m_rootNode) {
 573        //Rotate skeleton around a particular axis and center point
 574 -      Eigen::Transform3d rotation;
 575 +      Eigen::Projective3d rotation;
 576        rotation = Eigen::AngleAxisd(angle, rotationAxis);
 577        rotation.pretranslate(centerVector);
 578        rotation.translate(-centerVector);
 579 @@ -248,11 +249,11 @@ namespace Avogadro {
 580    // ##########  recursiveRotate  ##########
 581
 582    void SkeletonTree::recursiveRotate(Node* n,
 583 -                                     const Eigen::Transform3d &rotationMatrix)
 584 +                                     const Eigen::Projective3d &rotationMatrix)
 585    {
 586      // Update the root node with the new position
 587      Atom* a = n->atom();
 588 -    a->setPos(rotationMatrix * (*a->pos()));
 589 +    a->setPos((rotationMatrix * (*a->pos()).homogeneous()).head<3>());
 590      a->update();
 591
 592      // Now update the children
 593 --- a/libavogadro/src/tools/skeletontree.h
 594 +++ b/libavogadro/src/tools/skeletontree.h
 595 @@ -230,6 +230,6 @@ namespace Avogadro {
 596         * @param centerVector Center location to rotate around.
 597         */
 598        void recursiveRotate(Node* n,
 599 -                           const Eigen::Transform3d &rotationMatrix);
 600 +                           const Eigen::Projective3d &rotationMatrix);
 601
 602    };
 603  } // End namespace Avogadro