NERDSS Association Angle Explorer

ordinary COM–interface branch

WebGL · drag to orbit · wheel to zoom

reactant 1 / b₁ reactant 2 / b₂ sigma (I₂ → I₁) normal n₁ normal n₂

Geometry presets

Target angles

θ₁s₁ versus b₁constrained

θ₂s₂ versus b₂constrained

φ₁s₁ → n₁ about b₁constrained

φ₂s₂ → n₂ about b₂constrained

ωb₁ → b₂ about s₁constrained

Clear a checkbox to write nan for that angle. associate_box() then skips its rotation entirely, so the value is not a target of zero — it is left wherever diffusion put it.

Code-reported values

A highlighted value differs from its target. That happens where the source itself has nothing to measure — a projection of zero length, or an angle the parameter file left as nan.

Parameter file

Selected-angle trace

The normals are drawn in the lab frame

In the filenorm1 and norm2 are read in each molecule’s template frame — the frame of its .mol coordinates — not in the lab frame drawn above.
In the codedetermine_normal() recovers the molecule’s orientation from its own interface coordinates and rotates the template normal into the lab frame. Only then does calculate_phi() see it, so one norm1 gives a different arrow for every orientation the molecule takes.
What reaches φOnly the component of n across b. The component along b is invisible to φ — but it does reach ω on the θ = π branch, which is a degree of freedom these five sliders cannot set. This page pins n perpendicular to b; NERDSS does not require that.

When an angle does not apply

nanparse_input_array() maps nan to a quiet NaN and associate_box() skips that rotation entirely. It is not a target of zero — the angle is left wherever diffusion put it. Most sample inputs read [1.5707963, 1.5707963, nan, nan, M_PI].
M_PIThe parser accepts M_PI and pi, unsigned only. -M_PI is not a token it knows and aborts the run; write -3.141593. A dihedral is never reported as −π anyway, so prefer M_PI.
PointsA molecule with no interfaces has no normal: determine_normal() returns (0, 0, 0). When both reactants are points, associate_box() skips all five rotations.
RodsParsedRxn::isComplete() demands a non-zero norm only when the reactant is neither a rod nor a point. A rod’s φ is conventionally nan.
CollinearWith one interface, or all interfaces collinear, orient_crds_to_template() stops after the rotation that aligns interface 0, so the orientation it recovers ignores spin about that axis. φ is then pinned by the template rather than free.