Incite 1: Visualization of EPLF (Electron Pair Localization Function)

Table of Contents

Introduction

In this article, we show how the NERSC Visualization Group has worked closely with the Quantum Monte Carlo Study of Photoprotection via Carotenoids in Photosynthetic Centers Project at NERSC to visualize the Electron Pair Localization Function of Spheroidene. [1].

First Light: test with small molecules

We implemented the algorithm described in [1] and we tested it in small molecules, CH3, F2, and N2. We visualized the results with AVS/Express.

First light: isosurfaces of EPLF for N2 VMC,
403 grid, mean value of each bin.

3D Visualization

Results for N2

5200 walkers, 14 electrons, 7 up and 7 down.

EPLF N2 DMC,
1003 grid, median3.
EPLF N2 DMC,
1003 grid, median5.
EPLF N2 DMC,
1003 grid, median5.
EPLF N2 DMC,
1003 grid, median5.
EPLF for N2 VMC, 1003 grid, median5. EPLF for N2 VMC, 1003 grid, median5


Results for F2

5200 walkers, 18 electrons, 9 up and 9 down.

F2 DMC EPLF,
1003 grid, median3.
F2 DMC EPLF,
1003 grid, median3.
F2 DMC EPLF,
1003 grid, median5.
F2 DMC EPLF,
1003 grid, median5.
Results for CH3

5200 walkers, 9 electrons, 5 up and 4 down.

CH3 DMC EPLF,
1003 grid, median5.
CH3 DMC EPLF,
1003 grid, median5.
CH3 DMC EPLF,
1003 grid, median3.
Results for Spheroidene

Spheroidene Triplet, 5324 walkers, 314 electrons, 158 up and 156 down.

Spheroidene Triplet EPLF,
2003 grid, median5.
Spheroidene Triplet EPLF,
3003 grid, median5.
Spheroidene Triplet EPLF,
2003 grid, median5.
Spheroidene Triplet EPLF,
2003 grid, median5.
Spheroidene Triplet EPLF,
3003 grid, median5.
Spheroidene Triplet EPLF,
3003 grid, median5.


Spheroidene Singlet, 5324 walkers, 314 electrons, 157 up and 157 down.

Spheroidene Singlet EPLF,
2003 grid, median5.
Spheroidene Singlet EPLF,
2003 grid, median5.


Comparison of Spheroidene Triplet and Singlet

Spheroidene Singlet EPLF,
2003 grid, median5.
Spheroidene Triplet EPLF,
2003 grid, median5.
Spheroidene Singlet EPLF,
2003 grid, median5.
Spheroidene Triplet EPLF,
2003 grid, median5.
Spheroidene, Triplet - Singlet Spin Up density differences,
2003 grid, median5.
Spheroidene, Triplet - Singlet Spin Down density differences,
2003 grid, median5.
Spheroidene, Triplet - Singlet Spin Up density differences,
2003 grid, median5.
Spheroidene, Triplet - Singlet Spin Down density differences,
2003 grid, median5.

Results for BChlorophyll

BChlorophyll Triplet EPLF, 5120 walkers, 304 electrons, 153 up and 151 down. BChlorophyll Singlet EPLF, 5120 walkers, 304 electrons, 152 up and 152 down.

BChlorophyll EPLF, Triplet,
2003 grid, median5.
BChlorophyll EPLF, Triplet,
2003 grid, median5.
BChlorophyll EPLF, Triplet,
2003 grid, median5.
BChlorophyll EPLF, Singlet,
2003 grid, median5.
BChlorophyll Triplet - Singlet Spin Up density differences,
2003 grid, median5.
BChlorophyll Triplet - Singlet Spin Down density differences,
2003 grid, median5.

Discussion and Next Steps

Images of spheroidene and chlorophyll:
Spheroidene isosurfaces tarball
BChloroplyll isosurfaces tarball

References

[1] Electron pair localization function: A practical tool to visualize electron localization in molecules from quantum Monte Carlo data, Anthony Scemama, Patrick Chaquin, and Michel Caffarel, Journal of Chemical Physics, Vol 121, Number 4, 22 July 2004.