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Register a new userPushing the limit of molecular dynamics with ab initio accuracy to 100 million atoms with machine learning
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For 35 years, {it ab initio} molecular dynamics (AIMD) has been the method of choice for modeling complex atomistic phenomena from first principles. However, most AIMD applications are limited by computational cost to systems with thousands of atoms at most. We report that a machine learning-based simulation protocol (Deep Potential Molecular Dynamics), while retaining {it ab initio} accuracy, can simulate more than 1 nanosecond-long trajectory of over 100 million atoms per day, using a highly optimized code (GPU DeePMD-kit) on the Summit supercomputer. Our code can efficiently scale up to the entire Summit supercomputer, attaining $91$ PFLOPS in double precision ($45.5%$ of the peak) and {$162$/$275$ PFLOPS in mixed-single/half precision}. The great accomplishment of this work is that it opens the door to simulating unprecedented size and time scales with {it ab initio} accuracy. It also poses new challenges to the next-generation supercomputer for a better integration of machine learning and physical modeling.
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We present the GPU version of DeePMD-kit, which, upon training a deep neural network model using ab initio data, can drive extremely large-scale molecular dynamics (MD) simulation with ab initio accuracy. Our tests show that the GPU version is 7 times faster than the CPU version with the same power consumption. The code can scale up to the entire Summit supercomputer. For a copper system of 113, 246, 208 atoms, the code can perform one nanosecond MD simulation per day, reaching a peak performance of 86 PFLOPS (43% of the peak). Such unprecedented ability to perform MD simulation with ab initio accuracy opens up the possibility of studying many important issues in materials and molecules, such as heterogeneous catalysis, electrochemical cells, irradiation damage, crack propagation, and biochemical reactions.
The capabilities of CP2K, a density-functional theory package and OMEN, a nano-device simulator, are combined to study transport phenomena from first-principles in unprecedentedly large nanostructures. Based on the Hamiltonian and overlap matrices generated by CP2K for a given system, OMEN solves the Schroedinger equation with open boundary conditions (OBCs) for all possible electron momenta and energies. To accelerate this core operation a robust algorithm called SplitSolve has been developed. It allows to simultaneously treat the OBCs on CPUs and the Schroedinger equation on GPUs, taking advantage of hybrid nodes. Our key achievements on the Cray-XK7 Titan are (i) a reduction in time-to-solution by more than one order of magnitude as compared to standard methods, enabling the simulation of structures with more than 50000 atoms, (ii) a parallel efficiency of 97% when scaling from 756 up to 18564 nodes, and (iii) a sustained performance of 15 DP-PFlop/s.
Recent developments in path integral methodology have significantly reduced the computational expense of including quantum mechanical effects in the nuclear motion in ab initio molecular dynamics simulations. However, the implementation of these developments requires a considerable programming effort, which has hindered their adoption. Here we describe i-PI, an interface written in Python that has been designed to minimise the effort required to bring state-of-the-art path integral techniques to an electronic structure program. While it is best suited to first principles calculations and path integral molecular dynamics, i-PI can also be used to perform classical molecular dynamics simulations, and can just as easily be interfaced with an empirical forcefield code. To give just one example of the many potential applications of the interface, we use it in conjunction with the CP2K electronic structure package to showcase the importance of nuclear quantum effects in high pressure water.
The electronic structure in matter under extreme conditions is a challenging complex system prevalent in astrophysical objects and highly relevant for technological applications. We show how machine-learning surrogates in terms of neural networks have a profound impact on the efficient modeling of matter under extreme conditions. We demonstrate the utility of a surrogate model that is trained on emph{ab initio} quantum Monte Carlo data for various applications in the emerging field of warm dense matter research.
Ab initio molecular dynamics (AIMD) is a valuable technique for studying molecules and materials at finite temperatures where the nuclei evolve on potential energy surfaces obtained from accurate electronic structure calculations. In this work, a quantum computer-based AIMD method is presented. The electronic energies are calculated on a quantum computer using the variational quantum eigensolver (VQE) method. We compute the energy gradients numerically using the Hellmann-Feynman theorem, finite differences, and a correlated sampling technique. Our method only requires additional classical calculations of electron integrals for each degree of freedom, without any additional computations on a quantum computer beyond the initial VQE run. To achieve comparable accuracy, our gradient calculation method requires three to five orders of magnitude fewer measurements than other brute force methods without correlated sampling. As a proof of concept, AIMD dynamics simulations are demonstrated for the H2 molecule on IBM quantum devices. To the best of our knowledge, it is the first successful attempt to run AIMD on quantum devices for a chemical system. In addition, we demonstrate the validity of the method for larger molecules using full configuration interaction (FCI) wave functions. As quantum hardware and noise mitigation techniques continue to improve, the method can be utilized for studying larger molecular and material systems.
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