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Energy conserving, linear scaling Born-Oppenheimer molecular dynamics
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10.1063/1.4755991
/content/aip/journal/jcp/137/13/10.1063/1.4755991
http://aip.metastore.ingenta.com/content/aip/journal/jcp/137/13/10.1063/1.4755991

Figures

Image of FIG. 1.
FIG. 1.

Total energy versus time for an extended Lagrangian Born-Oppenheimer MD (XL BOMD) trajectory of liquid methane with 1 SCF cycle per 0.25 fs time step and regular Born-Oppenheimer MD trajectories with 1, 2, 4, and 10 SCF cycles per time step that employ the partial charges computed at each time step as a starting guess for the SCF procedure in the next.

Image of FIG. 2.
FIG. 2.

Time per density matrix calculation as a function of the number of orbitals for (a) liquid methane, and (b) polyethylene. Diagonalization and the dense matrix SP2 computations were performed using the Intel MKL DSYEV and DGEMM, respectively on 12 cores of a dual X5660 Xeon node. The sparse matrix SP2 computations were performed on one core of the same node.

Image of FIG. 3.
FIG. 3.

Per-atom error in the potential energy, ΔU, for liquid methane and polyethylene as a function of the number of atoms and the size of the threshold on matrix elements, ɛ, in the scheme.

Image of FIG. 4.
FIG. 4.

Per-atom error in the interatomic forces, ΔF, for liquid methane (open symbols) and polyethylene (filled symbols). The diamond, circle, and square symbols correspond to thresholds on matrix elements in the scheme of ɛ = 10−5, 10−6, and 10−7, respectively.

Image of FIG. 5.
FIG. 5.

Total energy versus time for extended Lagrangian Born-Oppenheimer MD trajectories with dissipation for liquid methane. (a) Exact forces, (b) sparse matrix SP2 with ɛ = 10−5.

Image of FIG. 6.
FIG. 6.

Standard deviation of the total energy about its mean value as a function of the size of the MD time step for MD trajectories computed with exact forces and forces obtained from the scheme with thresholds ɛ = 10−5, 10−6, and 10−7. The time step of 0.25 fs used throughout this work is marked with an arrow.

Image of FIG. 7.
FIG. 7.

Total energy as a function of simulation time for MD simulations of a C100H202 polyethylene molecule in the gas phase with exact forces computed with the SP2 algorithm using dense matrix algebra and sparse matrix algebra with ɛ = 10−5. The systematic drift in the calculation is less than 0.05 μeV atom−1 ps−1.

Image of FIG. 8.
FIG. 8.

Time average pair distribution functions for gas phase C100H202 computed from MD trajectories with exact forces and those from calculations with ɛ = 10−5. The plots have been offset for clarity.

Image of FIG. 9.
FIG. 9.

Time average radial distribution functions for liquid methane computed from MD trajectories with exact forces and those from calculations with ɛ = 10−5. The plots have been offset for clarity.

Tables

Generic image for table
Table I.

Levels of sparsity as measured using the fraction of non-zero elements in the self-consistent density matrices for liquid methane and C166H332 computed using dense matrix algebra and sparse matrix algebra with ɛ = 10−5, 10−6, and 10−7.

Generic image for table
Table II.

Average measures of the error in the self-consistent density matrices for polyethylene and liquid methane computed with the SP2 algorithm using sparse matrix algebra with a numerical threshold on matrix elements, ɛ, and with dense matrix algebra.

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2012-10-03
2014-04-20
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Energy conserving, linear scaling Born-Oppenheimer molecular dynamics
http://aip.metastore.ingenta.com/content/aip/journal/jcp/137/13/10.1063/1.4755991
10.1063/1.4755991
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