diff options
| -rw-r--r-- | gnu/local.mk | 3 | ||||
| -rw-r--r-- | gnu/packages/chemistry.scm | 85 | ||||
| -rw-r--r-- | gnu/packages/patches/avogadro-boost148.patch | 69 | ||||
| -rw-r--r-- | gnu/packages/patches/avogadro-eigen3-update.patch | 603 | ||||
| -rw-r--r-- | gnu/packages/patches/avogadro-python-eigen-lib.patch | 161 |
5 files changed, 0 insertions, 921 deletions
diff --git a/gnu/local.mk b/gnu/local.mk index ee57d6fe51..4ca5d60937 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -823,9 +823,6 @@ dist_patch_DATA = \ %D%/packages/patches/audiofile-function-signature.patch \ %D%/packages/patches/automake-skip-amhello-tests.patch \ %D%/packages/patches/avahi-localstatedir.patch \ - %D%/packages/patches/avogadro-boost148.patch \ - %D%/packages/patches/avogadro-eigen3-update.patch \ - %D%/packages/patches/avogadro-python-eigen-lib.patch \ %D%/packages/patches/avidemux-install-to-lib.patch \ %D%/packages/patches/awesome-reproducible-png.patch \ %D%/packages/patches/aws-c-event-stream-cmake-prefix.patch \ diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm index 5351ea596b..e7b061515b 100644 --- a/gnu/packages/chemistry.scm +++ b/gnu/packages/chemistry.scm @@ -52,91 +52,6 @@ #:use-module (guix build-system gnu) #:use-module (guix build-system python)) -(define-public avogadro - (package - (name "avogadro") - (version "1.2.0") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/cryos/avogadro") - (commit version))) - (sha256 - (base32 "0258py3lkba85qhs5ynancinyym61vlp0zaq9yrfs3hhnhpzv9n2")) - (file-name (git-file-name name version)) - (patches - (search-patches "avogadro-eigen3-update.patch" - "avogadro-python-eigen-lib.patch" - "avogadro-boost148.patch")))) - (build-system cmake-build-system) - (arguments - `(#:tests? #f - #:configure-flags - (list "-DENABLE_GLSL=ON" - (string-append "-DPYTHON_LIBRARIES=" - (assoc-ref %build-inputs "python") - "/lib") - (string-append "-DPYTHON_INCLUDE_DIRS=" - (assoc-ref %build-inputs "python") - "/include/python" - ,(version-major+minor - (package-version python)))) - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'patch-python-lib-path - (lambda* (#:key outputs #:allow-other-keys) - ;; This is necessary to install the Python module in the correct - ;; directory. - (substitute* "libavogadro/src/python/CMakeLists.txt" - (("^EXECUTE_PROCESS.*$") "") - (("^.*from sys import stdout.*$") "") - (("^.*OUTPUT_VARIABLE.*") - (string-append "set(PYTHON_LIB_PATH \"" - (assoc-ref outputs "out") - "/lib/python" - ,(version-major+minor - (package-version python)) - "/site-packages\")"))) - #t)) - (add-after 'install 'wrap-program - (lambda* (#:key inputs outputs #:allow-other-keys) - ;; Make sure 'avogadro' runs with the correct PYTHONPATH. - (let* ((out (assoc-ref outputs "out"))) - (setenv "PYTHONPATH" - (string-append - (assoc-ref outputs "out") - "/lib/python" - ,(version-major+minor - (package-version python)) - "/site-packages:" - (getenv "PYTHONPATH"))) - (wrap-program (string-append out "/bin/avogadro") - `("PYTHONPATH" ":" prefix (,(getenv "PYTHONPATH"))))) - #t))))) - (native-inputs - `(("doxygen" ,doxygen) - ("pkg-config" ,pkg-config))) - (inputs - `(("boost" ,boost) - ("eigen" ,eigen) - ("glew" ,glew) - ("openbabel" ,openbabel) - ("python" ,python-2) - ("python-numpy" ,python2-numpy) - ("python-pyqt" ,python2-pyqt-4) - ("python-sip" ,python2-sip) - ("qt" ,qt-4) - ("zlib" ,zlib))) - (home-page "https://avogadro.cc") - (synopsis "Advanced molecule editor") - (description - "Avogadro is an advanced molecule editor and visualizer designed for use -in computational chemistry, molecular modeling, bioinformatics, materials -science, and related areas. It offers flexible high quality rendering and a -powerful plugin architecture.") - (license license:gpl2+))) - (define-public avogadrolibs (package (name "avogadrolibs") diff --git a/gnu/packages/patches/avogadro-boost148.patch b/gnu/packages/patches/avogadro-boost148.patch deleted file mode 100644 index f244f14674..0000000000 --- a/gnu/packages/patches/avogadro-boost148.patch +++ /dev/null @@ -1,69 +0,0 @@ -Index: avogadro-1.2.0/libavogadro/src/pythonengine_p.h -=================================================================== ---- avogadro-1.2.0.orig/libavogadro/src/pythonengine_p.h -+++ avogadro-1.2.0/libavogadro/src/pythonengine_p.h -@@ -31,7 +31,9 @@ - - #include <avogadro/global.h> - #include <avogadro/engine.h> -+#ifndef Q_MOC_RUN - #include <boost/python.hpp> -+#endif - - namespace Avogadro { - -Index: avogadro-1.2.0/libavogadro/src/pythonextension_p.h -=================================================================== ---- avogadro-1.2.0.orig/libavogadro/src/pythonextension_p.h -+++ avogadro-1.2.0/libavogadro/src/pythonextension_p.h -@@ -33,7 +33,9 @@ - #include <avogadro/extension.h> - #include <avogadro/primitive.h> - #include <avogadro/glwidget.h> -+#ifndef Q_MOC_RUN - #include <boost/python.hpp> -+#endif - - #include <QWidget> - #include <QList> -Index: avogadro-1.2.0/libavogadro/src/pythontool_p.h -=================================================================== ---- avogadro-1.2.0.orig/libavogadro/src/pythontool_p.h -+++ avogadro-1.2.0/libavogadro/src/pythontool_p.h -@@ -31,7 +31,9 @@ - - #include <avogadro/global.h> - #include <avogadro/tool.h> -+#ifndef Q_MOC_RUN - #include <boost/python.hpp> -+#endif - - #include <QObject> - #include <QAction> -Index: avogadro-1.2.0/libavogadro/src/pythoninterpreter.h -=================================================================== ---- avogadro-1.2.0.orig/libavogadro/src/pythoninterpreter.h -+++ avogadro-1.2.0/libavogadro/src/pythoninterpreter.h -@@ -26,7 +26,9 @@ - #define PYTHONINTERPRETER_H - - #include <avogadro/global.h> -+#ifndef Q_MOC_RUN - #include <boost/python.hpp> -+#endif - #include <avogadro/primitive.h> - #include <QString> - -Index: avogadro-1.2.0/libavogadro/src/pythonscript.h -=================================================================== ---- avogadro-1.2.0.orig/libavogadro/src/pythonscript.h -+++ avogadro-1.2.0/libavogadro/src/pythonscript.h -@@ -27,6 +27,8 @@ - #define PYTHONSCRIPT_H - - #include <avogadro/global.h> -+#ifndef Q_MOC_RUN - #include <boost/python.hpp> -+#endif - - #include "pythonerror.h" diff --git a/gnu/packages/patches/avogadro-eigen3-update.patch b/gnu/packages/patches/avogadro-eigen3-update.patch deleted file mode 100644 index a5f669292f..0000000000 --- a/gnu/packages/patches/avogadro-eigen3-update.patch +++ /dev/null @@ -1,603 +0,0 @@ -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 ++-- - .../crystallography/crystallographyextension.cpp | 2 +- - .../crystallography/ui/ceviewoptionswidget.cpp | 2 +- - .../src/extensions/orca/orcaanalysedialog.cpp | 1 - - .../src/extensions/orca/orcainputdialog.cpp | 1 - - .../src/extensions/qtaim/qtaimmathutilities.cpp | 1 + - .../qtaim/qtaimwavefunctionevaluator.cpp | 28 +++++++++++----------- - .../extensions/surfaces/openqube/gamessukout.cpp | 1 + - .../src/extensions/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(-) - ---- a/CMakeLists.txt -+++ b/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 ---- a/avogadro/src/mainwindow.cpp -+++ b/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()); - ---- a/libavogadro/src/camera.cpp -+++ b/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; - } ---- a/libavogadro/src/camera.h -+++ b/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(); - } - }; - ---- a/libavogadro/src/engines/wireengine.cpp -+++ b/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 ---- a/libavogadro/src/extensions/crystallography/crystallographyextension.cpp -+++ b/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(); ---- a/libavogadro/src/extensions/crystallography/ui/ceviewoptionswidget.cpp -+++ b/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 ---- a/libavogadro/src/extensions/orca/orcaanalysedialog.cpp -+++ b/libavogadro/src/extensions/orca/orcaanalysedialog.cpp -@@ -41,7 +41,6 @@ - #include <openbabel/mol.h> - - #include <Eigen/Geometry> --#include <Eigen/LeastSquares> - - #include <vector> - ---- a/libavogadro/src/extensions/orca/orcainputdialog.cpp -+++ b/libavogadro/src/extensions/orca/orcainputdialog.cpp -@@ -33,7 +33,6 @@ - #include <openbabel/mol.h> - - #include <Eigen/Geometry> --#include <Eigen/LeastSquares> - - #include <vector> - ---- a/libavogadro/src/extensions/qtaim/qtaimmathutilities.cpp -+++ b/libavogadro/src/extensions/qtaim/qtaimmathutilities.cpp -@@ -28,6 +28,7 @@ - - #include <cmath> - #include <Eigen/QR> -+#include <Eigen/Eigenvalues> - - namespace Avogadro { - namespace QTAIMMathUtilities { ---- a/libavogadro/src/extensions/qtaim/qtaimwavefunctionevaluator.cpp -+++ b/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(); - ---- a/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp -+++ b/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp -@@ -19,6 +19,7 @@ - using Eigen::Vector3d; - using std::vector; - -+#include <iostream> - #include <fstream> - - namespace OpenQube ---- a/libavogadro/src/extensions/surfaces/openqube/slaterset.cpp -+++ b/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()) ---- a/libavogadro/src/glpainter_p.cpp -+++ b/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(); ---- a/libavogadro/src/glwidget.cpp -+++ b/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, ' ') ---- a/libavogadro/src/molecule.cpp -+++ b/libavogadro/src/molecule.cpp -@@ -38,7 +38,7 @@ - #include "zmatrix.h" - - #include <Eigen/Geometry> --#include <Eigen/LeastSquares> -+#include <Eigen/Eigenvalues> - - #include <vector> - -@@ -1907,7 +1907,29 @@ 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(); - } ---- a/libavogadro/src/navigate.cpp -+++ b/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; ---- a/libavogadro/src/tools/bondcentrictool.cpp -+++ b/libavogadro/src/tools/bondcentrictool.cpp -@@ -578,8 +578,8 @@ namespace Avogadro { - - Vector3d clicked = *m_clickedAtom->pos(); - -- Vector3d axis = Vector3d(0, 0, ((widget->camera()->modelview() * other).z() >= -- (widget->camera()->modelview() * center).z() ? -1 : 1)); -+ Vector3d axis = Vector3d(0, 0, ((widget->camera()->modelview() * other.homogeneous()).z() >= -+ (widget->camera()->modelview() * center.homogeneous()).z() ? -1 : 1)); - - Vector3d centerProj = widget->camera()->project(center); - centerProj -= Vector3d(0,0,centerProj.z()); -@@ -673,8 +673,8 @@ namespace Avogadro { - - Vector3d clicked = *m_clickedAtom->pos(); - -- Vector3d axis = Vector3d(0, 0, ((widget->camera()->modelview() * other).z() >= -- (widget->camera()->modelview() * center).z() ? -1 : 1)); -+ Vector3d axis = Vector3d(0, 0, ((widget->camera()->modelview() * other.homogeneous()).z() >= -+ (widget->camera()->modelview() * center.homogeneous()).z() ? -1 : 1)); - - Vector3d centerProj = widget->camera()->project(center); - centerProj -= Vector3d(0,0,centerProj.z()); -@@ -1362,10 +1362,10 @@ 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 +1444,10 @@ 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 +1506,12 @@ 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 ########## ---- a/libavogadro/src/tools/manipulatetool.cpp -+++ b/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(); - } - ---- a/libavogadro/src/tools/navigatetool.cpp -+++ b/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)); ---- a/libavogadro/src/tools/skeletontree.cpp -+++ b/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 ---- a/libavogadro/src/tools/skeletontree.h -+++ b/libavogadro/src/tools/skeletontree.h -@@ -230,6 +230,6 @@ namespace Avogadro { - * @param centerVector Center location to rotate around. - */ - void recursiveRotate(Node* n, -- const Eigen::Transform3d &rotationMatrix); -+ const Eigen::Projective3d &rotationMatrix); - - }; - } // End namespace Avogadro \ No newline at end of file diff --git a/gnu/packages/patches/avogadro-python-eigen-lib.patch b/gnu/packages/patches/avogadro-python-eigen-lib.patch deleted file mode 100644 index ac9f2e30af..0000000000 --- a/gnu/packages/patches/avogadro-python-eigen-lib.patch +++ /dev/null @@ -1,161 +0,0 @@ -From 2d4be7ede177a8df7340fe3b209698d591ee8a04 Mon Sep 17 00:00:00 2001 -From: Claudio Fernandes <claudiosf.claudio@gmail.com> -Date: Mon, 16 Jan 2017 19:48:23 -0200 -Subject: [PATCH] Adapt libavogadro/python to Eigen 3.3 - ---- - libavogadro/src/python/camera.cpp | 2 +- - libavogadro/src/python/eigen.cpp | 60 +++++++++++++++++++-------------------- - 2 files changed, 31 insertions(+), 31 deletions(-) - -diff --git a/libavogadro/src/python/camera.cpp b/libavogadro/src/python/camera.cpp -index 69ca87bf8..30b32af7d 100644 ---- a/libavogadro/src/python/camera.cpp -+++ b/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; -diff --git a/libavogadro/src/python/eigen.cpp b/libavogadro/src/python/eigen.cpp -index c1faedbcc..20b4e719d 100644 ---- a/libavogadro/src/python/eigen.cpp -+++ b/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 -@@ -529,6 +529,6 @@ 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(); |