diff options
| -rw-r--r-- | gnu/local.mk | 3 | ||||
| -rw-r--r-- | gnu/packages/chemistry.scm | 80 | ||||
| -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, 916 insertions, 0 deletions
diff --git a/gnu/local.mk b/gnu/local.mk index 60db25a60c..b1bd1c089c 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -584,6 +584,9 @@ dist_patch_DATA = \ %D%/packages/patches/audacity-build-with-system-portaudio.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/azr3.patch \ diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm index 2d7cb7aad1..03120aaeee 100644 --- a/gnu/packages/chemistry.scm +++ b/gnu/packages/chemistry.scm @@ -23,16 +23,96 @@ #:use-module (guix download) #:use-module (gnu packages) #:use-module (gnu packages algebra) + #:use-module (gnu packages boost) #:use-module (gnu packages compression) + #:use-module (gnu packages documentation) + #:use-module (gnu packages gl) #:use-module (gnu packages gv) #:use-module (gnu packages maths) #:use-module (gnu packages pkg-config) #:use-module (gnu packages python) + #:use-module (gnu packages qt) #:use-module (gnu packages xml) #:use-module (guix build-system cmake) #: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 url-fetch) + (uri (string-append "https://github.com/cryos/avogadro/archive/" + version ".tar.gz")) + (sha256 + (base32 + "02v4h6hi1m7ilv0apdf74a8l1cm6dxnxyqp0rdaidrp3i9pf6lv4")) + (file-name (string-append name "-" version ".tar.gz")) + (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/python2.7")) + #: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/python2.7/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/python2.7/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 domainfinder (package (name "domainfinder") diff --git a/gnu/packages/patches/avogadro-boost148.patch b/gnu/packages/patches/avogadro-boost148.patch new file mode 100644 index 0000000000..f244f14674 --- /dev/null +++ b/gnu/packages/patches/avogadro-boost148.patch @@ -0,0 +1,69 @@ +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 new file mode 100644 index 0000000000..a5f669292f --- /dev/null +++ b/gnu/packages/patches/avogadro-eigen3-update.patch @@ -0,0 +1,603 @@ +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 new file mode 100644 index 0000000000..ac9f2e30af --- /dev/null +++ b/gnu/packages/patches/avogadro-python-eigen-lib.patch @@ -0,0 +1,161 @@ +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(); |