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Analyzing Complex FTMS Simulations: a Case Study in High-Level Visualization of Ion Motions. Wojciech Burakiewicz Robert van Liere. Centrum voor Wiskunde en Informatica Amsterdam, The Netherlands. CWI. Create new tools Clarify images Show physical phenomena. Data properties:
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Analyzing Complex FTMS Simulations:a Case Study in High-Level Visualization of Ion Motions Wojciech Burakiewicz Robert van Liere Centrum voor Wiskunde en Informatica Amsterdam, The Netherlands CWI
Create new tools Clarify images Show physical phenomena Data properties: Large datasets Complex phenomena Visualization tools available: Point clouds Trajectories/Animation Motivation Study the dynamics of complex phenomena in particle simulations
Outline • Study subject: Fourier Transform Mass Spectrometry • Mass spectrometry • Simulations • Visualization • Standard techniques • Our visualization tools • Evaluation • Conclusions
Fourier Transform Mass Spectrometry Mass Spectrometry: • Determine chemical composition of substances at very low concentrations • Investigate chemical properties of molecules • Computer simulations: • Understand physical phenomena • Increase resolution and accuracy
B D ~ 1 in vacuum Fourier Transform Mass Spectrometry • Investigated substance: • Ionized • Trapped in electromagnetic field • Oscillation frequency ~ mass • Signal induced by oscillating ions measured on the detection plates. • By studying the signal we discover the substance composition T E E T D
FTMS Datasets • Simulations: • Up to 10^6 ions simulated over 10^5 time steps • Experimental timescale: 100ms – 1s • Output: • Detected signal – similar to the real experiment • Ion positions for each time step: • File size: in Giga Bytes
Investigated Phenomena • Ion cloud structure • Different ion motions • Trapping motion • Inside cloud motion • Cloud-cloud interactions • Frequency shifts • Phase locking
Investigated Phenomena • Ion cloud structure • Different ion motions • Trapping motion • Inside cloud motion • Cloud-cloud interactions • Frequency shifts • Phase locking • Ion density • m/z distribution • Cloud dephasing
Investigated Phenomena • Ion cloud structure • Different ion motions • Cyclotron motion • Inside cloud motion • Cloud-cloud interactions • Frequency shifts • Phase locking
Investigated Phenomena • Ion cloud structure • Different ion motions • Trapping motion • Inside cloud motion • Cloud-cloud interactions • Frequency shifts • Phase locking Interaction
Investigated Phenomena • Ion cloud structure • Different ion motions • Trapping motion • Inside cloud motion • Cloud-cloud interactions • Frequency shifts • Phase locking • Frqtheo≠ Frqmeasured • Clusters oscillate together
Visualization: Standard tools • 2D or 3D point clouds, • Dynamics: Trajectories/Animation • Problems • Image cluttering • Phenomena difficult to discern
Visualization: Standard tools • 2D or 3D point clouds, • Dynamics: Trajectories/Animation • Problems • Image cluttering • Phenomena difficult to discern
Our visualization tools • Comet icon • Ion cloud structure • Camera control • Ion and cloud motions • Frequency icons • Cloud frequency perturbations
Comet icon • Partition the ion group along the center of gravity trajectory • Count ions in each partition • Choose partition size according to number of ions
m/z of ions in the group - color ion density in the comet - shape + saturation dephase state of the comet - shape detailed m/z distribution in the comet - color bar Comet Icon
Comet Icon • Cloud evolution
Camera Control • We postion the camera according to data properties in each frame: • find cluster's center of gravity trajectory • obtain local coordinate frame by computing the Frenet frame for this trajectory • position the camera in this local coordinate frame
Camera Control • Adjust camera in local coordinates: • Camera positioned in the XY plane • Camera viewing along the Z axis • Camera placed arbitrarily • Trapping motion of the ions
Camera Control • Adjust camera in local coordinates: • Camera positioned in the XY plane • Camera viewing along the Z axis • Camera placed arbitrarily • Relative cloud motions
Camera Control • Adjust camera in local coordinates: • Camera positioned in the XY plane • Camera viewing along the Z axis • Camera placed arbitrarily • Relative ion motions inside the cloud
Camera Control • Adjust camera in local coordinates: • Camera positioned in the XY plane • Camera viewing along the Z axis • Camera placed arbitrarily • Relative ion motions inside the cloud
Frequency Icons • Ion dynamics in frequency/phase terms • frequency icon: actual oscillation frequencies of ion clusters relative to theoretical frequencies • dephase icon: dephasing of each ion cluster • Frequency shifts • Phase locking
Frequency Icons • Ion dynamics in frequency/phase terms • frequency icon: actual oscillation frequencies of ion clusters relative to theoretical frequencies • dephase icon • Dephasing of ion clusters
Frequency Icons • Ion dynamics in frequency/phase terms • frequency icon: actual oscillation frequencies of ion clusters relative to theoretical frequencies • dephase icon
Ion cloud structure Different ion motions Trapping motion Inside cloud motion Cloud-cloud interactions Frequency shifts Phase locking Dephasing Comet icon Camera control Frequency icons Resume
Clarity of image Visibility of physical phenomena Evaluation (1)
Clarity of image Visibility of physical phenomena Evaluation (1)
Evaluation (2) • Our tool has been used by physicists: • FOM Institute for Atomic and Molecular Physics, Amsterdam • The Institute for Energy Problems of Chemical Physics, Moscow • With our tool a number of discoveries were made: • Dephasing and phase-locking are strongly influenced by the density of the ions in the trap • Excitation profile has great influence on the instrument detection accuracy and resolution
Conclusions • The standard visualization tools do not suffice: • Image cluttering • Phenomena difficult to discern • Our visualization tools explicitly show important phenomena • Users apply this tool to do science