From unknown Tue Jun 17 01:43:51 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#32219] [PATCH] gnu: Add avogadro. Resent-From: Kei Kebreau Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 20 Jul 2018 05:11:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 32219 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 32219@debbugs.gnu.org Cc: Kei Kebreau X-Debbugs-Original-To: guix-patches@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.1532063460897 (code B ref -1); Fri, 20 Jul 2018 05:11:02 +0000 Received: (at submit) by debbugs.gnu.org; 20 Jul 2018 05:11:00 +0000 Received: from localhost ([127.0.0.1]:48710 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fgNgu-0000EK-C0 for submit@debbugs.gnu.org; Fri, 20 Jul 2018 01:11:00 -0400 Received: from eggs.gnu.org ([208.118.235.92]:46588) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fgNgr-0000E5-LG for submit@debbugs.gnu.org; Fri, 20 Jul 2018 01:10:55 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1fgNgh-00085P-N4 for submit@debbugs.gnu.org; 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Fri, 20 Jul 2018 01:10:34 -0400 Received: from submission (posteo.de [89.146.220.130]) by mout02.posteo.de (Postfix) with ESMTPS id 4E01721132 for ; Fri, 20 Jul 2018 07:10:31 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1532063431; bh=Q3TQNen4S4htQcAofodnDZb1Z5e6syNfvP/cZo9hnXo=; h=From:To:Cc:Subject:Date:From; b=GmcOTW+23u/MqXHDqXyF1d8ZakYymCxCsZFa0NVAtN8hPxJWDB6yTs6jmh6aLMBeb 0SHfD2b2ZyofWa6PLhDJJ228OGfKRgdlwdeCRbIdBwJz4Z4M260o6AHvhj2r945Sqh prO5BHHLTXK/SCsT8aUCb9tmB9kggdosaofC7i9lS6Wt/Sx8V3v39fan9B0Ah4bGqF Vucj6XOCZs+EhQdEj4bj+yAfHB8BArKk6GqIVMNhCIWFZch08F4o5Ms3iR+8j/QJtp EAT25uefCNBu8ZTNCOBAcynqi5KhScrM61mHVkretInWRGQFhH7JK35/0J+fudvdf4 YB/x3YRCJmfKg== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 41WzVF48fBz9rxG; Fri, 20 Jul 2018 07:10:29 +0200 (CEST) From: Kei Kebreau Date: Fri, 20 Jul 2018 01:10:26 -0400 Message-Id: <20180720051026.28287-1-kkebreau@posteo.net> X-Mailer: git-send-email 2.18.0 X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] [fuzzy] X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.6.x X-Received-From: 2001:4830:134:3::11 X-Spam-Score: -4.0 (----) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -5.0 (-----) * gnu/packages/chemistry.scm (avogadro): New variable. * gnu/packages/patches/avogadro-boost148.patch, gnu/packages/patches/avogadro-eigen3-update.patch, gnu/packages/patches/avogadro-python-eigen-lib.patch: New files. * gnu/local.mk (dist_patch_DATA): Add them. --- gnu/local.mk | 3 + gnu/packages/chemistry.scm | 81 +++ gnu/packages/patches/avogadro-boost148.patch | 70 ++ .../patches/avogadro-eigen3-update.patch | 603 ++++++++++++++++++ .../patches/avogadro-python-eigen-lib.patch | 162 +++++ 5 files changed, 919 insertions(+) create mode 100644 gnu/packages/patches/avogadro-boost148.patch create mode 100644 gnu/packages/patches/avogadro-eigen3-update.patch create mode 100644 gnu/packages/patches/avogadro-python-eigen-lib.patch diff --git a/gnu/local.mk b/gnu/local.mk index e55c2bf3b..923257ff6 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -579,6 +579,9 @@ 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 a81c14b43..9aa1b5e4f 100644 --- a/gnu/packages/chemistry.scm +++ b/gnu/packages/chemistry.scm @@ -21,17 +21,98 @@ #:use-module (guix packages) #:use-module ((guix licenses) #:prefix license:) #: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 000000000..a2e570d8b --- /dev/null +++ b/gnu/packages/patches/avogadro-boost148.patch @@ -0,0 +1,70 @@ +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 + #include ++#ifndef Q_MOC_RUN + #include ++#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 + #include + #include ++#ifndef Q_MOC_RUN + #include ++#endif + + #include + #include +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 + #include ++#ifndef Q_MOC_RUN + #include ++#endif + + #include + #include +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 ++#ifndef Q_MOC_RUN + #include ++#endif + #include + #include + +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 +@@ -27,7 +27,9 @@ + #define PYTHONSCRIPT_H + + #include ++#ifndef Q_MOC_RUN + #include ++#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 000000000..2269b0a14 --- /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 +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 + + #include +-#include + #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::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 + + #include +-#include + + #include + +--- a/libavogadro/src/extensions/orca/orcainputdialog.cpp ++++ b/libavogadro/src/extensions/orca/orcainputdialog.cpp +@@ -33,7 +33,6 @@ + #include + + #include +-#include + + #include + +--- a/libavogadro/src/extensions/qtaim/qtaimmathutilities.cpp ++++ b/libavogadro/src/extensions/qtaim/qtaimmathutilities.cpp +@@ -28,6 +28,7 @@ + + #include + #include ++#include + + 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 >(wfn.xNuclearCoordinates(),m_nnuc); +- m_nucycoord=Map >(wfn.yNuclearCoordinates(),m_nnuc); +- m_nuczcoord=Map >(wfn.zNuclearCoordinates(),m_nnuc); +- m_nucz=Map >(wfn.nuclearCharges(),m_nnuc); +- m_X0=Map >(wfn.xGaussianPrimitiveCenterCoordinates(),m_nprim,1); +- m_Y0=Map >(wfn.yGaussianPrimitiveCenterCoordinates(),m_nprim,1); +- m_Z0=Map >(wfn.zGaussianPrimitiveCenterCoordinates(),m_nprim,1); +- m_xamom=Map >(wfn.xGaussianPrimitiveAngularMomenta(),m_nprim,1); +- m_yamom=Map >(wfn.yGaussianPrimitiveAngularMomenta(),m_nprim,1); +- m_zamom=Map >(wfn.zGaussianPrimitiveAngularMomenta(),m_nprim,1); +- m_alpha=Map >(wfn.gaussianPrimitiveExponentCoefficients(),m_nprim,1); ++ m_nucxcoord=Map >(const_cast(wfn.xNuclearCoordinates()),m_nnuc); ++ m_nucycoord=Map >(const_cast(wfn.yNuclearCoordinates()),m_nnuc); ++ m_nuczcoord=Map >(const_cast(wfn.zNuclearCoordinates()),m_nnuc); ++ m_nucz=Map >(const_cast(wfn.nuclearCharges()),m_nnuc); ++ m_X0=Map >(const_cast(wfn.xGaussianPrimitiveCenterCoordinates()),m_nprim,1); ++ m_Y0=Map >(const_cast(wfn.yGaussianPrimitiveCenterCoordinates()),m_nprim,1); ++ m_Z0=Map >(const_cast(wfn.zGaussianPrimitiveCenterCoordinates()),m_nprim,1); ++ m_xamom=Map >(const_cast(wfn.xGaussianPrimitiveAngularMomenta()),m_nprim,1); ++ m_yamom=Map >(const_cast(wfn.yGaussianPrimitiveAngularMomenta()),m_nprim,1); ++ m_zamom=Map >(const_cast(wfn.zGaussianPrimitiveAngularMomenta()),m_nprim,1); ++ m_alpha=Map >(const_cast(wfn.gaussianPrimitiveExponentCoefficients()),m_nprim,1); + // TODO Implement screening for unoccupied molecular orbitals. +- m_occno=Map >(wfn.molecularOrbitalOccupationNumbers(),m_nmo,1); +- m_orbe=Map >(wfn.molecularOrbitalEigenvalues(),m_nmo,1); +- m_coef=Map >(wfn.molecularOrbitalCoefficients(),m_nmo,m_nprim); ++ m_occno=Map >(const_cast(wfn.molecularOrbitalOccupationNumbers()),m_nmo,1); ++ m_orbe=Map >(const_cast(wfn.molecularOrbitalEigenvalues()),m_nmo,1); ++ m_coef=Map >(const_cast(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 + #include + + 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 + #include + #include ++#include + + #include + +@@ -250,7 +250,9 @@ bool SlaterSet::initialize() + + SelfAdjointEigenSolver 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(d->background.redF()), static_cast(d->background.greenF()), + static_cast(d->background.blueF()), static_cast(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 +-#include ++#include + + #include + +@@ -1907,7 +1907,29 @@ namespace Avogadro{ + } + d->center /= static_cast(nAtoms); + Eigen::Hyperplane planeCoeffs; +- Eigen::fitHyperplane(numAtoms(), atomPositions, &planeCoeffs); ++ //Eigen::fitHyperplane(numAtoms(), atomPositions, &planeCoeffs); ++ ++ // TODO check if this is OK ++ /************************/ ++ typedef Eigen::Matrix 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 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 + + 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(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(p)->setPos(fragmentRotation * *static_cast(p)->pos()); ++ static_cast(p)->setPos((fragmentRotation * static_cast(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(p)->setPos(fragmentRotation * *static_cast(p)->pos()); ++ static_cast(p)->setPos((fragmentRotation * static_cast(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 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 + #include + #include ++#include + + 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 +@@ -230,7 +230,7 @@ namespace Avogadro { + * @param centerVector Center location to rotate around. + */ + void recursiveRotate(Node* n, +- const Eigen::Transform3d &rotationMatrix); ++ const Eigen::Projective3d &rotationMatrix); + + }; + } // End namespace Avogadro 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 000000000..405a9d82d --- /dev/null +++ b/gnu/packages/patches/avogadro-python-eigen-lib.patch @@ -0,0 +1,162 @@ +From 2d4be7ede177a8df7340fe3b209698d591ee8a04 Mon Sep 17 00:00:00 2001 +From: Claudio Fernandes +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 + 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 + 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 + 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 + Transform3d_to_python_array() + { + #ifndef WIN32 +- to_python_converter(); ++ to_python_converter(); + #endif +- to_python_converter(); +- to_python_converter(); ++ to_python_converter(); ++ to_python_converter(); + } + + }; +@@ -373,17 +373,17 @@ template <> struct ScalarTraits + // 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() ); ++ converter::registry::push_back( &convertible, &construct, type_id() ); + +- converter::registry::insert( &convert, type_id() ); ++ converter::registry::insert( &convert, type_id() ); + } + + static void* convert(PyObject *obj_ptr) +@@ -401,7 +401,7 @@ template <> struct ScalarTraits + throw_error_already_set(); // the 1D array does not have exactly 3 elements + + double *values = reinterpret_cast(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 + // 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(array->data); +- Eigen::Transform3d *storage = new Eigen::Transform3d(); ++ Eigen::Projective3d *storage = new Eigen::Projective3d(); + double *dataPtr = storage->data(); + + for (int i = 0; i < 16; ++i) +@@ -467,21 +467,21 @@ class EigenUnitTestHelper + void set_vector3d_ptr(Eigen::Vector3d* vec) { m_vector3d = *vec; } + void set_const_vector3d_ptr(const Eigen::Vector3d* const vec) { m_vector3d = *vec; } + +- //Eigen::Transform3d transform3d() { return m_transform3d; } +- //Eigen::Transform3d& transform3d_ref() { return m_transform3d; } +- const Eigen::Transform3d& const_transform3d_ref() { return m_transform3d; } +- Eigen::Transform3d* transform3d_ptr() { return &m_transform3d; } +- const Eigen::Transform3d* const_transform3d_ptr() { return &m_transform3d; } +- +- //void set_transform3d(Eigen::Transform3d vec) { m_transform3d = vec; } +- //void set_transform3d_ref(Eigen::Transform3d& vec) { m_transform3d = vec; } +- void set_const_transform3d_ref(const Eigen::Transform3d& vec) { m_transform3d = vec; } +- void set_transform3d_ptr(Eigen::Transform3d* vec) { m_transform3d = *vec; } +- void set_const_transform3d_ptr(const Eigen::Transform3d* const vec) { m_transform3d = *vec; } ++ //Eigen::Projective3d transform3d() { return m_transform3d; } ++ //Eigen::Projective3d& transform3d_ref() { return m_transform3d; } ++ const Eigen::Projective3d& const_transform3d_ref() { return m_transform3d; } ++ Eigen::Projective3d* transform3d_ptr() { return &m_transform3d; } ++ const Eigen::Projective3d* const_transform3d_ptr() { return &m_transform3d; } ++ ++ //void set_transform3d(Eigen::Projective3d vec) { m_transform3d = vec; } ++ //void set_transform3d_ref(Eigen::Projective3d& vec) { m_transform3d = vec; } ++ void set_const_transform3d_ref(const Eigen::Projective3d& vec) { m_transform3d = vec; } ++ void set_transform3d_ptr(Eigen::Projective3d* vec) { m_transform3d = *vec; } ++ void set_const_transform3d_ptr(const Eigen::Projective3d* const vec) { m_transform3d = *vec; } + + private: + Eigen::Vector3d m_vector3d; +- Eigen::Transform3d m_transform3d; ++ Eigen::Projective3d m_transform3d; + + }; + #endif +@@ -529,7 +529,7 @@ void export_Eigen() + Vector3x_to_python_array(); + Vector3x_from_python_array(); + +- // Eigen::Transform3d ++ // Eigen::Projective3d + Transform3d_to_python_array(); + Transform3d_from_python_array(); + -- 2.18.0 From unknown Tue Jun 17 01:43:51 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#32219] [PATCH] gnu: Add avogadro. Resent-From: ludo@gnu.org (Ludovic =?UTF-8?Q?Court=C3=A8s?=) Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 21 Aug 2018 21:26:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 32219 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Kei Kebreau Cc: 32219@debbugs.gnu.org Received: via spool by 32219-submit@debbugs.gnu.org id=B32219.153488675013981 (code B ref 32219); Tue, 21 Aug 2018 21:26:01 +0000 Received: (at 32219) by debbugs.gnu.org; 21 Aug 2018 21:25:50 +0000 Received: from localhost ([127.0.0.1]:57092 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fsE9t-0003dQ-UM for submit@debbugs.gnu.org; Tue, 21 Aug 2018 17:25:50 -0400 Received: from eggs.gnu.org ([208.118.235.92]:58159) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fsE9s-0003dC-0P for 32219@debbugs.gnu.org; Tue, 21 Aug 2018 17:25:48 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1fsE9l-0001Ze-W0 for 32219@debbugs.gnu.org; Tue, 21 Aug 2018 17:25:42 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=-1.9 required=5.0 tests=BAYES_00 autolearn=disabled version=3.3.2 Received: from fencepost.gnu.org ([2001:4830:134:3::e]:44542) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1fsE9l-0001ZW-Ri; Tue, 21 Aug 2018 17:25:41 -0400 Received: from [2a01:e0a:1d:7270:af76:b9b:ca24:c465] (port=55040 helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1fsE9l-0001yo-JX; Tue, 21 Aug 2018 17:25:41 -0400 From: ludo@gnu.org (Ludovic =?UTF-8?Q?Court=C3=A8s?=) In-Reply-To: <20180720051026.28287-1-kkebreau@posteo.net> (Kei Kebreau's message of "Fri, 20 Jul 2018 01:10:26 -0400") References: <20180720051026.28287-1-kkebreau@posteo.net> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/26.1 (gnu/linux) Date: Tue, 21 Aug 2018 23:25:40 +0200 Message-ID: <874lfnmmy3.fsf@gnu.org> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 2001:4830:134:3::e X-Spam-Score: -5.0 (-----) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -6.0 (------) Hello Kei, Kei Kebreau skribis: > * gnu/packages/chemistry.scm (avogadro): New variable. > * gnu/packages/patches/avogadro-boost148.patch, > gnu/packages/patches/avogadro-eigen3-update.patch, > gnu/packages/patches/avogadro-python-eigen-lib.patch: New files. > * gnu/local.mk (dist_patch_DATA): Add them. This patch apparently fell through the cracks but I see no reason not to apply it. Thank you! Ludo=E2=80=99. From unknown Tue Jun 17 01:43:51 2025 MIME-Version: 1.0 X-Mailer: MIME-tools 5.505 (Entity 5.505) X-Loop: help-debbugs@gnu.org From: help-debbugs@gnu.org (GNU bug Tracking System) To: Kei Kebreau Subject: bug#32219: closed (Re: [bug#32219] [PATCH] gnu: Add avogadro.) Message-ID: References: <87efemggdb.fsf@posteo.net> <20180720051026.28287-1-kkebreau@posteo.net> X-Gnu-PR-Message: they-closed 32219 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 32219@debbugs.gnu.org Date: Sat, 25 Aug 2018 23:46:02 +0000 Content-Type: multipart/mixed; boundary="----------=_1535240762-7000-1" This is a multi-part message in MIME format... ------------=_1535240762-7000-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #32219: [PATCH] gnu: Add avogadro. which was filed against the guix-patches package, has been closed. The explanation is attached below, along with your original report. If you require more details, please reply to 32219@debbugs.gnu.org. --=20 32219: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D32219 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1535240762-7000-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 32219-done) by debbugs.gnu.org; 25 Aug 2018 23:45:47 +0000 Received: from localhost ([127.0.0.1]:60842 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ftiFX-0001oS-KJ for submit@debbugs.gnu.org; Sat, 25 Aug 2018 19:45:47 -0400 Received: from mout01.posteo.de ([185.67.36.65]:53674) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ftiFV-0001oD-A9 for 32219-done@debbugs.gnu.org; Sat, 25 Aug 2018 19:45:45 -0400 Received: from submission (posteo.de [89.146.220.130]) by mout01.posteo.de (Postfix) with ESMTPS id 38CA32104D for <32219-done@debbugs.gnu.org>; Sun, 26 Aug 2018 01:45:39 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1535240739; bh=PeireCWIhYMY0Ak/EryDAOTSoyDp70sOh4ahgQNj3mQ=; h=From:To:Cc:Subject:Date:From; b=GQdFvCBAu8KdtU9z8EEZv8raahYksfcDOOHIkjlddmmkxckpgjB2X6tAkJmxDTS72 saInunbfKsgULggAvS18Lf5Wg9vs9rflrXQfRbdFZ/69viDkV6PNJXPkcaiFCUf0Jg EuZa2TqUlGOHnTjuviy17ehWUU2riLzl7Ardh94fSyssgRPqQun5+lRmtZ6KpDLOl2 6Vk/K0Kh5NAMK30aVEvsEuQPGO3+w35yDetlPWjAwMIErLKLr51KT4di0Ok+ncWZxC wVKqUKg2lA/KLee3Xm7DeAICywUpOOqRyeC3NcSgajbqA9SISZAW0ZQz5pxK9IQdmV VhsCpTXu/moLA== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 41yZXK6RWhz6tm5; Sun, 26 Aug 2018 01:45:37 +0200 (CEST) From: Kei Kebreau To: ludo@gnu.org (Ludovic =?utf-8?Q?Court=C3=A8s?=) Subject: Re: [bug#32219] [PATCH] gnu: Add avogadro. References: <20180720051026.28287-1-kkebreau@posteo.net> <874lfnmmy3.fsf@gnu.org> Date: Sat, 25 Aug 2018 19:45:36 -0400 In-Reply-To: <874lfnmmy3.fsf@gnu.org> ("Ludovic \=\?utf-8\?Q\?Court\=C3\=A8s\=22'\?\= \=\?utf-8\?Q\?s\?\= message of "Tue, 21 Aug 2018 23:25:40 +0200") Message-ID: <87efemggdb.fsf@posteo.net> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/26.1 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 32219-done Cc: 32219-done@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -3.3 (---) ludo@gnu.org (Ludovic Court=C3=A8s) writes: > Hello Kei, > > Kei Kebreau skribis: > >> * gnu/packages/chemistry.scm (avogadro): New variable. >> * gnu/packages/patches/avogadro-boost148.patch, >> gnu/packages/patches/avogadro-eigen3-update.patch, >> gnu/packages/patches/avogadro-python-eigen-lib.patch: New files. >> * gnu/local.mk (dist_patch_DATA): Add them. > > This patch apparently fell through the cracks but I see no reason not to > apply it. > > Thank you! > > Ludo=E2=80=99. Thank you for reviewing! I've pushed this to master. ------------=_1535240762-7000-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 20 Jul 2018 05:11:00 +0000 Received: from localhost ([127.0.0.1]:48710 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fgNgu-0000EK-C0 for submit@debbugs.gnu.org; Fri, 20 Jul 2018 01:11:00 -0400 Received: from eggs.gnu.org ([208.118.235.92]:46588) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fgNgr-0000E5-LG for submit@debbugs.gnu.org; Fri, 20 Jul 2018 01:10:55 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1fgNgh-00085P-N4 for submit@debbugs.gnu.org; Fri, 20 Jul 2018 01:10:48 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=0.8 required=5.0 tests=BAYES_50,T_DKIM_INVALID autolearn=disabled version=3.3.2 Received: from lists.gnu.org ([2001:4830:134:3::11]:38017) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1fgNgh-00085H-JK for submit@debbugs.gnu.org; Fri, 20 Jul 2018 01:10:43 -0400 Received: from eggs.gnu.org ([2001:4830:134:3::10]:37530) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1fgNgd-0004ap-AZ for guix-patches@gnu.org; Fri, 20 Jul 2018 01:10:43 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1fgNgY-00081w-U7 for guix-patches@gnu.org; Fri, 20 Jul 2018 01:10:39 -0400 Received: from mout02.posteo.de ([185.67.36.66]:52111) by eggs.gnu.org with esmtps (TLS1.0:DHE_RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1fgNgY-0007zv-0b for guix-patches@gnu.org; Fri, 20 Jul 2018 01:10:34 -0400 Received: from submission (posteo.de [89.146.220.130]) by mout02.posteo.de (Postfix) with ESMTPS id 4E01721132 for ; Fri, 20 Jul 2018 07:10:31 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1532063431; bh=Q3TQNen4S4htQcAofodnDZb1Z5e6syNfvP/cZo9hnXo=; h=From:To:Cc:Subject:Date:From; b=GmcOTW+23u/MqXHDqXyF1d8ZakYymCxCsZFa0NVAtN8hPxJWDB6yTs6jmh6aLMBeb 0SHfD2b2ZyofWa6PLhDJJ228OGfKRgdlwdeCRbIdBwJz4Z4M260o6AHvhj2r945Sqh prO5BHHLTXK/SCsT8aUCb9tmB9kggdosaofC7i9lS6Wt/Sx8V3v39fan9B0Ah4bGqF Vucj6XOCZs+EhQdEj4bj+yAfHB8BArKk6GqIVMNhCIWFZch08F4o5Ms3iR+8j/QJtp EAT25uefCNBu8ZTNCOBAcynqi5KhScrM61mHVkretInWRGQFhH7JK35/0J+fudvdf4 YB/x3YRCJmfKg== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 41WzVF48fBz9rxG; Fri, 20 Jul 2018 07:10:29 +0200 (CEST) From: Kei Kebreau To: guix-patches@gnu.org Subject: [PATCH] gnu: Add avogadro. Date: Fri, 20 Jul 2018 01:10:26 -0400 Message-Id: <20180720051026.28287-1-kkebreau@posteo.net> X-Mailer: git-send-email 2.18.0 X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] [fuzzy] X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.6.x X-Received-From: 2001:4830:134:3::11 X-Spam-Score: -4.0 (----) X-Debbugs-Envelope-To: submit Cc: Kei Kebreau X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -5.0 (-----) * gnu/packages/chemistry.scm (avogadro): New variable. * gnu/packages/patches/avogadro-boost148.patch, gnu/packages/patches/avogadro-eigen3-update.patch, gnu/packages/patches/avogadro-python-eigen-lib.patch: New files. * gnu/local.mk (dist_patch_DATA): Add them. --- gnu/local.mk | 3 + gnu/packages/chemistry.scm | 81 +++ gnu/packages/patches/avogadro-boost148.patch | 70 ++ .../patches/avogadro-eigen3-update.patch | 603 ++++++++++++++++++ .../patches/avogadro-python-eigen-lib.patch | 162 +++++ 5 files changed, 919 insertions(+) create mode 100644 gnu/packages/patches/avogadro-boost148.patch create mode 100644 gnu/packages/patches/avogadro-eigen3-update.patch create mode 100644 gnu/packages/patches/avogadro-python-eigen-lib.patch diff --git a/gnu/local.mk b/gnu/local.mk index e55c2bf3b..923257ff6 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -579,6 +579,9 @@ 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 a81c14b43..9aa1b5e4f 100644 --- a/gnu/packages/chemistry.scm +++ b/gnu/packages/chemistry.scm @@ -21,17 +21,98 @@ #:use-module (guix packages) #:use-module ((guix licenses) #:prefix license:) #: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 000000000..a2e570d8b --- /dev/null +++ b/gnu/packages/patches/avogadro-boost148.patch @@ -0,0 +1,70 @@ +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 + #include ++#ifndef Q_MOC_RUN + #include ++#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 + #include + #include ++#ifndef Q_MOC_RUN + #include ++#endif + + #include + #include +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 + #include ++#ifndef Q_MOC_RUN + #include ++#endif + + #include + #include +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 ++#ifndef Q_MOC_RUN + #include ++#endif + #include + #include + +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 +@@ -27,7 +27,9 @@ + #define PYTHONSCRIPT_H + + #include ++#ifndef Q_MOC_RUN + #include ++#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 000000000..2269b0a14 --- /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 +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 + + #include +-#include + #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::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 + + #include +-#include + + #include + +--- a/libavogadro/src/extensions/orca/orcainputdialog.cpp ++++ b/libavogadro/src/extensions/orca/orcainputdialog.cpp +@@ -33,7 +33,6 @@ + #include + + #include +-#include + + #include + +--- a/libavogadro/src/extensions/qtaim/qtaimmathutilities.cpp ++++ b/libavogadro/src/extensions/qtaim/qtaimmathutilities.cpp +@@ -28,6 +28,7 @@ + + #include + #include ++#include + + 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 >(wfn.xNuclearCoordinates(),m_nnuc); +- m_nucycoord=Map >(wfn.yNuclearCoordinates(),m_nnuc); +- m_nuczcoord=Map >(wfn.zNuclearCoordinates(),m_nnuc); +- m_nucz=Map >(wfn.nuclearCharges(),m_nnuc); +- m_X0=Map >(wfn.xGaussianPrimitiveCenterCoordinates(),m_nprim,1); +- m_Y0=Map >(wfn.yGaussianPrimitiveCenterCoordinates(),m_nprim,1); +- m_Z0=Map >(wfn.zGaussianPrimitiveCenterCoordinates(),m_nprim,1); +- m_xamom=Map >(wfn.xGaussianPrimitiveAngularMomenta(),m_nprim,1); +- m_yamom=Map >(wfn.yGaussianPrimitiveAngularMomenta(),m_nprim,1); +- m_zamom=Map >(wfn.zGaussianPrimitiveAngularMomenta(),m_nprim,1); +- m_alpha=Map >(wfn.gaussianPrimitiveExponentCoefficients(),m_nprim,1); ++ m_nucxcoord=Map >(const_cast(wfn.xNuclearCoordinates()),m_nnuc); ++ m_nucycoord=Map >(const_cast(wfn.yNuclearCoordinates()),m_nnuc); ++ m_nuczcoord=Map >(const_cast(wfn.zNuclearCoordinates()),m_nnuc); ++ m_nucz=Map >(const_cast(wfn.nuclearCharges()),m_nnuc); ++ m_X0=Map >(const_cast(wfn.xGaussianPrimitiveCenterCoordinates()),m_nprim,1); ++ m_Y0=Map >(const_cast(wfn.yGaussianPrimitiveCenterCoordinates()),m_nprim,1); ++ m_Z0=Map >(const_cast(wfn.zGaussianPrimitiveCenterCoordinates()),m_nprim,1); ++ m_xamom=Map >(const_cast(wfn.xGaussianPrimitiveAngularMomenta()),m_nprim,1); ++ m_yamom=Map >(const_cast(wfn.yGaussianPrimitiveAngularMomenta()),m_nprim,1); ++ m_zamom=Map >(const_cast(wfn.zGaussianPrimitiveAngularMomenta()),m_nprim,1); ++ m_alpha=Map >(const_cast(wfn.gaussianPrimitiveExponentCoefficients()),m_nprim,1); + // TODO Implement screening for unoccupied molecular orbitals. +- m_occno=Map >(wfn.molecularOrbitalOccupationNumbers(),m_nmo,1); +- m_orbe=Map >(wfn.molecularOrbitalEigenvalues(),m_nmo,1); +- m_coef=Map >(wfn.molecularOrbitalCoefficients(),m_nmo,m_nprim); ++ m_occno=Map >(const_cast(wfn.molecularOrbitalOccupationNumbers()),m_nmo,1); ++ m_orbe=Map >(const_cast(wfn.molecularOrbitalEigenvalues()),m_nmo,1); ++ m_coef=Map >(const_cast(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 + #include + + 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 + #include + #include ++#include + + #include + +@@ -250,7 +250,9 @@ bool SlaterSet::initialize() + + SelfAdjointEigenSolver 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(d->background.redF()), static_cast(d->background.greenF()), + static_cast(d->background.blueF()), static_cast(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 +-#include ++#include + + #include + +@@ -1907,7 +1907,29 @@ namespace Avogadro{ + } + d->center /= static_cast(nAtoms); + Eigen::Hyperplane planeCoeffs; +- Eigen::fitHyperplane(numAtoms(), atomPositions, &planeCoeffs); ++ //Eigen::fitHyperplane(numAtoms(), atomPositions, &planeCoeffs); ++ ++ // TODO check if this is OK ++ /************************/ ++ typedef Eigen::Matrix 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 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 + + 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(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(p)->setPos(fragmentRotation * *static_cast(p)->pos()); ++ static_cast(p)->setPos((fragmentRotation * static_cast(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(p)->setPos(fragmentRotation * *static_cast(p)->pos()); ++ static_cast(p)->setPos((fragmentRotation * static_cast(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 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 + #include + #include ++#include + + 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 +@@ -230,7 +230,7 @@ namespace Avogadro { + * @param centerVector Center location to rotate around. + */ + void recursiveRotate(Node* n, +- const Eigen::Transform3d &rotationMatrix); ++ const Eigen::Projective3d &rotationMatrix); + + }; + } // End namespace Avogadro 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 000000000..405a9d82d --- /dev/null +++ b/gnu/packages/patches/avogadro-python-eigen-lib.patch @@ -0,0 +1,162 @@ +From 2d4be7ede177a8df7340fe3b209698d591ee8a04 Mon Sep 17 00:00:00 2001 +From: Claudio Fernandes +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 + 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 + 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 + 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 + Transform3d_to_python_array() + { + #ifndef WIN32 +- to_python_converter(); ++ to_python_converter(); + #endif +- to_python_converter(); +- to_python_converter(); ++ to_python_converter(); ++ to_python_converter(); + } + + }; +@@ -373,17 +373,17 @@ template <> struct ScalarTraits + // 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() ); ++ converter::registry::push_back( &convertible, &construct, type_id() ); + +- converter::registry::insert( &convert, type_id() ); ++ converter::registry::insert( &convert, type_id() ); + } + + static void* convert(PyObject *obj_ptr) +@@ -401,7 +401,7 @@ template <> struct ScalarTraits + throw_error_already_set(); // the 1D array does not have exactly 3 elements + + double *values = reinterpret_cast(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 + // 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(array->data); +- Eigen::Transform3d *storage = new Eigen::Transform3d(); ++ Eigen::Projective3d *storage = new Eigen::Projective3d(); + double *dataPtr = storage->data(); + + for (int i = 0; i < 16; ++i) +@@ -467,21 +467,21 @@ class EigenUnitTestHelper + void set_vector3d_ptr(Eigen::Vector3d* vec) { m_vector3d = *vec; } + void set_const_vector3d_ptr(const Eigen::Vector3d* const vec) { m_vector3d = *vec; } + +- //Eigen::Transform3d transform3d() { return m_transform3d; } +- //Eigen::Transform3d& transform3d_ref() { return m_transform3d; } +- const Eigen::Transform3d& const_transform3d_ref() { return m_transform3d; } +- Eigen::Transform3d* transform3d_ptr() { return &m_transform3d; } +- const Eigen::Transform3d* const_transform3d_ptr() { return &m_transform3d; } +- +- //void set_transform3d(Eigen::Transform3d vec) { m_transform3d = vec; } +- //void set_transform3d_ref(Eigen::Transform3d& vec) { m_transform3d = vec; } +- void set_const_transform3d_ref(const Eigen::Transform3d& vec) { m_transform3d = vec; } +- void set_transform3d_ptr(Eigen::Transform3d* vec) { m_transform3d = *vec; } +- void set_const_transform3d_ptr(const Eigen::Transform3d* const vec) { m_transform3d = *vec; } ++ //Eigen::Projective3d transform3d() { return m_transform3d; } ++ //Eigen::Projective3d& transform3d_ref() { return m_transform3d; } ++ const Eigen::Projective3d& const_transform3d_ref() { return m_transform3d; } ++ Eigen::Projective3d* transform3d_ptr() { return &m_transform3d; } ++ const Eigen::Projective3d* const_transform3d_ptr() { return &m_transform3d; } ++ ++ //void set_transform3d(Eigen::Projective3d vec) { m_transform3d = vec; } ++ //void set_transform3d_ref(Eigen::Projective3d& vec) { m_transform3d = vec; } ++ void set_const_transform3d_ref(const Eigen::Projective3d& vec) { m_transform3d = vec; } ++ void set_transform3d_ptr(Eigen::Projective3d* vec) { m_transform3d = *vec; } ++ void set_const_transform3d_ptr(const Eigen::Projective3d* const vec) { m_transform3d = *vec; } + + private: + Eigen::Vector3d m_vector3d; +- Eigen::Transform3d m_transform3d; ++ Eigen::Projective3d m_transform3d; + + }; + #endif +@@ -529,7 +529,7 @@ void export_Eigen() + Vector3x_to_python_array(); + Vector3x_from_python_array(); + +- // Eigen::Transform3d ++ // Eigen::Projective3d + Transform3d_to_python_array(); + Transform3d_from_python_array(); + -- 2.18.0 ------------=_1535240762-7000-1--