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guix/gnu/packages/patches/avogadro-eigen3-update.patch
Kei Kebreau 7d01ee66d4
gnu: Add avogadro. 
* 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.
2018-08-25 17:05:30 -04:00

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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
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