Hi all,
I've made some modifications to the ball and stick engine to draw correctly
bonds that cross periodic boundaries. However, I cannot push the commit
because gerrit rejects my ssh connection.
I created a gerrit account and generated an ssh public key. Yet, I get the
error
$ git gerrit-push
Permission denied (publickey).
fatal: The remote end hung up unexpectedly
The public key I pasted to my gerrit account matches my id_rsa.pub file for
sure. I went through all the troubleshooting instructions to no avail.
I don't know how to solve this problem. Therefore I'm sending the patch here
as an attachment.
Best,
Tuukka Verho
diff --git a/libavogadro/src/engines/bsdyengine.cpp b/libavogadro/src/engines/bsdyengine.cpp
index d485c86..a409755 100644
--- a/libavogadro/src/engines/bsdyengine.cpp
+++ b/libavogadro/src/engines/bsdyengine.cpp
@@ -151,9 +151,9 @@ namespace Avogadro
Vector3d v1(*atom1->pos());
Vector3d v2(*atom2->pos());
- Vector3d d = v2 - v1;
- d.normalize();
- Vector3d v3((v1 + v2 + d*(radius(atom1) - radius(atom2))) / 2);
+ Vector3d d = distanceVector(v1, v2, pd);
+
+ double centerAdjust = (radius(atom1) - radius(atom2)) / d.norm();
double shift = 0.15;
int order = 1;
@@ -164,14 +164,14 @@ namespace Avogadro
pd->painter()->setColor( map );
else
pd->painter()->setColor(atom1->customColorName());
- pd->painter()->drawMultiCylinder( v1, v3, m_bondRadius, order, shift );
+ pd->painter()->drawMultiCylinder( v1, v1 + d*(1+centerAdjust)/2, m_bondRadius, order, shift );
map->setFromPrimitive(atom2);
if (atom2->customColorName().isEmpty())
pd->painter()->setColor( map );
else
pd->painter()->setColor(atom2->customColorName());
- pd->painter()->drawMultiCylinder( v3, v2, m_bondRadius, order, shift );
+ pd->painter()->drawMultiCylinder( v2, v2 - d*(1-centerAdjust)/2, m_bondRadius, order, shift );
}
glDisable( GL_NORMALIZE );
@@ -237,9 +237,9 @@ namespace Avogadro
Vector3d v1(*atom1->pos());
Vector3d v2(*atom2->pos());
- Vector3d d = v2 - v1;
- d.normalize();
- Vector3d v3((v1 + v2 + d*(radius(atom1) - radius(atom2))) / 2);
+ Vector3d d = distanceVector(v1, v2, pd);
+
+ double centerAdjust = (radius(atom1) - radius(atom2)) / d.norm();
double shift = 0.15;
int order = 1;
@@ -250,19 +250,22 @@ namespace Avogadro
map->setFromPrimitive(atom1);
map->setAlpha(m_alpha);
pd->painter()->setColor( map );
- pd->painter()->drawMultiCylinder( v1, v3, m_bondRadius, order, shift );
+ pd->painter()->drawMultiCylinder( v1, v1 + d*(1+centerAdjust)/2, m_bondRadius, order, shift );
map->setFromPrimitive(atom2);
map->setAlpha(m_alpha);
pd->painter()->setColor( map );
- pd->painter()->drawMultiCylinder( v3, v2, m_bondRadius, order, shift );
+ pd->painter()->drawMultiCylinder( v2, v2 - d*(1-centerAdjust)/2, m_bondRadius, order, shift );
}
// Render the selected bond.
if (pd->isSelected(b)) {
pd->painter()->setColor(&selectionMap);
- pd->painter()->drawMultiCylinder( v1, v2,
- SEL_BOND_EXTRA_RADIUS + m_bondRadius, order, shift );
+ pd->painter()->drawMultiCylinder(v1, v1 + d*(1+centerAdjust)/2, SEL_BOND_EXTRA_RADIUS +
+ m_bondRadius, order, shift);
+ pd->painter()->drawMultiCylinder(v2, v2 - d*(1-centerAdjust)/2, SEL_BOND_EXTRA_RADIUS +
+ m_bondRadius, order, shift);
+
}
}
return true;
@@ -281,9 +284,7 @@ namespace Avogadro
Atom* atom2 = pd->molecule()->atomById(b->endAtomId());
Vector3d v1(*atom1->pos());
Vector3d v2(*atom2->pos());
- Vector3d d = v2 - v1;
- d.normalize();
- Vector3d v3((v1 + v2 + d*(radius(atom1)-radius(atom2))) / 2);
+ Vector3d d = distanceVector(v1, v2, pd);
double shift = 0.15;
int order = 1;
@@ -291,17 +292,19 @@ namespace Avogadro
if (pd->isSelected(b)) {
pd->painter()->setColor(&cSel);
- pd->painter()->drawMultiCylinder(v1, v2, SEL_BOND_EXTRA_RADIUS +
+ pd->painter()->drawMultiCylinder(v1, v1 + d/2, SEL_BOND_EXTRA_RADIUS +
+ m_bondRadius, order, shift);
+ pd->painter()->drawMultiCylinder(v2, v2 - d/2, SEL_BOND_EXTRA_RADIUS +
m_bondRadius, order, shift);
}
else {
map->setFromPrimitive(atom1);
pd->painter()->setColor(map);
- pd->painter()->drawMultiCylinder(v1, v3, m_bondRadius, order, shift);
+ pd->painter()->drawMultiCylinder(v1, v1 + d/2, m_bondRadius, order, shift);
map->setFromPrimitive( atom2 );
pd->painter()->setColor(map);
- pd->painter()->drawMultiCylinder(v3, v2, m_bondRadius, order, shift);
+ pd->painter()->drawMultiCylinder(v2 , v2 - d/2, m_bondRadius, order, shift);
}
}
@@ -330,11 +333,18 @@ namespace Avogadro
bool BSDYEngine::renderPick(PainterDevice *pd)
{
// Render the bonds
- foreach(Bond *b, bonds()) {
- pd->painter()->setName(b);
+ foreach(Bond *b, bonds()) {
+ Vector3d v1(*b->beginPos());
+ Vector3d v2(*b->endPos());
+ Vector3d d = distanceVector(v1, v2, pd);
+
// Add a slight slop factor to make it easier to pick
// (e.g., for bond-centric tool)
- pd->painter()->drawCylinder(*b->beginPos(), *b->endPos(), m_bondRadius+0.05);
+
+ pd->painter()->setName(b);
+ pd->painter()->drawCylinder(v1, v1 + d/2, m_bondRadius+0.05);
+ pd->painter()->setName(b);
+ pd->painter()->drawCylinder(v2, v2 - d/2, m_bondRadius+0.05);
}
// Render the atoms
@@ -361,6 +371,31 @@ namespace Avogadro
}
return m_atomRadiusPercentage;
}
+
+ // Get the shortest vector from v1 to v2 taking into account possible
+ // periodic boundary conditions
+ Vector3d BSDYEngine::distanceVector(const Vector3d& v1, const Vector3d& v2, PainterDevice* pd)
+ {
+ Vector3d d = v2 - v1;
+ OpenBabel::OBUnitCell* unitCell = pd->molecule()->OBUnitCell();
+ if (unitCell) {
+ std::vector<OpenBabel::vector3> cv = unitCell->GetCellVectors();
+ Vector3d a = Vector3d(cv[0].x(), cv[0].y(), cv[0].z());
+ Vector3d b = Vector3d(cv[1].x(), cv[1].y(), cv[1].z());
+ Vector3d c = Vector3d(cv[2].x(), cv[2].y(), cv[2].z());
+ for (int i=-1; i<2; i++) {
+ for (int j=-1; j<2; j++) {
+ for (int k=-1; k<2; k++) {
+ Vector3d v2_ = v2 + i*a + j*b + k*c;
+ Vector3d d_ = v2_ - v1;
+ if (d_.norm() < d.norm())
+ d = d_;
+ }
+ }
+ }
+ }
+ return d;
+ }
void BSDYEngine::setAtomRadiusPercentage(int value)
{
diff --git a/libavogadro/src/engines/bsdyengine.h b/libavogadro/src/engines/bsdyengine.h
index 30917f5..ac23d53 100644
--- a/libavogadro/src/engines/bsdyengine.h
+++ b/libavogadro/src/engines/bsdyengine.h
@@ -34,7 +34,7 @@ namespace Avogadro {
//! Ball and Stick Engine class.
class Atom;
- class BSDYSettingsWidget;
+ class BSDYSettingsWidget;
class BSDYEngine : public Engine
{
Q_OBJECT
@@ -80,6 +80,7 @@ namespace Avogadro {
private:
double radius(const Atom *atom) const;
+ Eigen::Vector3d distanceVector(const Eigen::Vector3d& v1, const Eigen::Vector3d& v2, PainterDevice* pd);
BSDYSettingsWidget *m_settingsWidget;
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