共查询到20条相似文献，搜索用时 15 毫秒
1.
Feldmann MT Cummings JC Kent DR Muller RP Goddard WA 《Journal of computational chemistry》2008,29(1):8-16
A manager-worker-based parallelization algorithm for Quantum Monte Carlo (QMC-MW) is presented and compared with the pure iterative parallelization algorithm, which is in common use. The new manager-worker algorithm performs automatic load balancing, allowing it to perform near the theoretical maximal speed even on heterogeneous parallel computers. Furthermore, the new algorithm performs as well as the pure iterative algorithm on homogeneous parallel computers. When combined with the dynamic distributable decorrelation algorithm (DDDA) [Feldmann et al., J Comput Chem 28, 2309 (2007)], the new manager-worker algorithm allows QMC calculations to be terminated at a prespecified level of convergence rather than upon a prespecified number of steps (the common practice). This allows a guaranteed level of precision at the least cost. Additionally, we show (by both analytic derivation and experimental verification) that standard QMC implementations are not \"perfectly parallel\" as is often claimed. 相似文献
2.
We present a method of parallelizing flat histogram Monte Carlo simulations, which give the free energy of a molecular system as an output. In the serial version, a constant probability distribution, as a function of any system parameter, is calculated by updating an external potential that is added to the system Hamiltonian. This external potential is related to the free energy. In the parallel implementation, the simulation is distributed on to different processors. With regular intervals the modifying potential is summed over all processors and distributed back to every processor, thus spreading the information of which parts of parameter space have been explored. This implementation is shown to decrease the execution time linearly with added number of processors. 相似文献
3.
Kent DR Muller RP Anderson AG Goddard WA Feldmann MT 《Journal of computational chemistry》2007,28(14):2309-2316
We describe the Dynamic Distributable Decorrelation Algorithm (DDDA) which efficiently calculates the true statistical error of an expectation value obtained from serially correlated data \"on-the-fly,\" as the calculation progresses. DDDA is an improvement on the Flyvbjerg-Petersen renormalization group blocking method (Flyvberg and Peterson, J Chem Phys 1989, 91, 461). This \"on-the-fly\" determination of statistical quantities allows dynamic termination of Monte Carlo calculations once a specified level of convergence is attained. This is highly desirable when the required precision might take days or months to compute, but cannot be accurately estimated prior to the calculation. Furthermore, DDDA allows for a parallel implementation which requires very low communication, O(log(2)N), and can also evaluate the variance of a calculation efficiently \"on-the-fly.\" Quantum Monte Carlo calculations are presented to illustrate \"on-the-fly\" variance calculations for serial and massively parallel Monte Carlo calculations. 相似文献
4.
Daniel Beuve&#x;Mery Mehdi Rahman Philippe Ducarme Robert Brasseur 《Journal of computational chemistry》2001,22(2):172-177
We have built clusters of PC using up to 320 processors in parallel. The first cluster was built in 1996 from 64 computers. The parallel architectures are named RAMSES. In this article, we share our experience and discuss our choices. The architecture is composed of Pentium processors connected by a 100 Mbits/s Ethernet network. Because RAMSES are built of independent computers, the system is easily maintained, and can be modified by adding or removing machines. Two programs, which are dedicated to molecular modeling and were previously developed on single machines (OSIRIS and IMPALA), have been adapted. IMPALA models peptide and protein interaction with membranes, OSIRIS simulates an ab initio folding of globular proteins. After parallelization, each program consists of two parts: one is the human/RAMSES interface, and the second is the simulation per se. The parallel architecture is transparent for the users. Tests of the IMPALA and OSIRIS efficiencies are shown and discussed. © 2000 John Wiley & Sons, Inc. J Comput Chem 22: 172–177, 2001 相似文献
5.
Salvatore Cardamone Jonathan R. R. Kimmitt Hugh G. A. Burton Timothy J. Todman Shurui Li Wayne Luk Alex J. W. Thom 《International journal of quantum chemistry》2019,119(12):e25853
Massively parallel architectures offer the potential to significantly accelerate an application relative to their serial counterparts. However, not all applications exhibit an adequate level of data and/or task parallelism to exploit such platforms. Furthermore, the power consumption associated with these forms of computation renders “scaling out” for exascale levels of performance incompatible with modern sustainable energy policies. In this work, we investigate the potential for field-programmable gate arrays (FPGAs) to feature in future exascale platforms, and their capacity to improve performance per unit power measurements for the purposes of scientific computing. We have focused our efforts on variational Monte Carlo, and report on the benefits of coprocessing with a FPGA relative to a purely multicore system. 相似文献
6.
Sarah Wolf Emanuele Curotto Massimo Mella 《International journal of quantum chemistry》2014,114(10):611-625
The torsional ground state for ethane, the torsional, rotational, and mixed torsional and rotational ground state of propane are computed with a version of diffusion Monte Carlo adapted to handle the geometric complexity of curved spaces such as the Ramachandra space. The quantum NVT ensemble average for the mixed torsional and rotational degrees of freedom of propane is computed, using a version of Monte Carlo path integral, also adapted to handle curved spaces. These three problems are selected to demonstrate the generality and the applicability of the approaches described. The spaces of coordinates can be best constructed from the parameters of continuous Lie groups, and alternative methods based on vector spaces, where extended Lagrangian terms would be too cumbersome to implement. We note that the geometric coupling between the torsions and the rotations of propane produces a substantial effect on the ground state energy of propane, and that the quantum effects on the energy of propane are quite large even well above room temperature. © 2014 Wiley Periodicals, Inc. 相似文献
7.
We report calculations of the ground state energy and binding curve of the chromium dimer using the variational and diffusion quantum Monte Carlo (VMC and DMC) methods. We examined various single‐determinant and multideterminant wavefunctions multiplied by a Jastrow factor as a trial/guiding wavefunction for VMC/DMC. The molecular orbitals in the single determinants were calculated using restricted or unrestricted Hartree–Fock or density functional theory (DFT) calculations where five commonly used local (SVWN5), semilocal (PW91 and BLYP), and hybrid (B1LYP and B3LYP) functionals were examined. The multideterminant expansions were obtained from the generalized valence bond and (truncated) unrestricted configuration interaction with single and double excitations (UCISD) methods. We also examined a UCISD wavefunction in which UCISD expansions were added to the UB3LYP single‐determinant reference, and their coefficients were optimized at the VMC level. In addition to the wavefunction dependence, the effects of pseudopotentials and backflow transformation were also investigated. The UB3LYP single‐determinant and multideterminant wavefunctions were found to give the variationally best DMC energies within the framework of single‐determinant and multideterminants, respectively, though both the DMC energies were higher than twice the DMC atomic energy. Some of the VMC binding curves show a flat or quite shallow well bottom, which gets recovered deeper by DMC. All the DMC binding curves have a minimum indicating a bound state, but the unrestricted ones overestimate the equilibrium bond length. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012 相似文献
8.
Aspuru-Guzik A Salomón-Ferrer R Austin B Lester WA 《Journal of computational chemistry》2005,26(7):708-715
A new algorithm is presented for the sparse representation and evaluation of Slater determinants in the quantum Monte Carlo (QMC) method. The approach, combined with the use of localized orbitals in a Slater-type orbital basis set, significantly extends the size molecule that can be treated with the QMC method. Application of the algorithm to systems containing up to 390 electrons confirms that the cost of evaluating the Slater determinant scales linearly with system size. 相似文献
9.
Anthony Scemama Michel Caffarel Emmanuel Oseret William Jalby 《Journal of computational chemistry》2013,34(11):938-951
Various strategies to implement efficiently quantum Monte Carlo (QMC) simulations for large chemical systems are presented. These include: (i) the introduction of an efficient algorithm to calculate the computationally expensive Slater matrices. This novel scheme is based on the use of the highly localized character of atomic Gaussian basis functions (not the molecular orbitals as usually done), (ii) the possibility of keeping the memory footprint minimal, (iii) the important enhancement of single‐core performance when efficient optimization tools are used, and (iv) the definition of a universal, dynamic, fault‐tolerant, and load‐balanced framework adapted to all kinds of computational platforms (massively parallel machines, clusters, or distributed grids). These strategies have been implemented in the QMC=Chem code developed at Toulouse and illustrated with numerical applications on small peptides of increasing sizes (158, 434, 1056, and 1731 electrons). Using 10–80 k computing cores of the Curie machine (GENCI‐TGCC‐CEA, France), QMC=Chem has been shown to be capable of running at the petascale level, thus demonstrating that for this machine a large part of the peak performance can be achieved. Implementation of large‐scale QMC simulations for future exascale platforms with a comparable level of efficiency is expected to be feasible. © 2013 Wiley Periodicals, Inc. 相似文献
10.
Aspuru-Guzik A Salomón-Ferrer R Austin B Perusquía-Flores R Griffin MA Oliva RA Skinner D Domin D Lester WA 《Journal of computational chemistry》2005,26(8):856-862
The Zori 1.0 package for electronic structure computations is described. Zori performs variational and diffusion Monte Carlo computations as well as correlated wave function optimization. This article presents an overview of the implemented methods and code capabilities. 相似文献
11.
12.
Ellen T. Swann Michelle L. Coote Amanda S. Barnard Manolo C. Per 《International journal of quantum chemistry》2017,117(9)
Accurate calculation of hydrogen abstraction reaction barriers is a challenging problem, often requiring high level quantum chemistry methods that scale poorly with system size. Quantum Monte Carlo (QMC) methods provide an alternative approach that exhibit much better scaling, but these methods are still computationally expensive. We describe approaches that can significantly reduce the cost of QMC calculations of barrier heights, using the hydrogen abstraction of methanol by a hydrogen atom as an illustrative example. By analysing the combined influence of trial wavefunctions and pseudopotential quadrature settings on the barrier heights, variance, and time‐step errors, we devise a simple protocol that minimizes the cost of the QMC calculations while retaining accuracy comparable to large‐basis coupled cluster theory. We demonstrate that this protocol is transferable to other hydrogen abstraction reactions. 相似文献
13.
Jinzu Weng Xi Chen Zhen Yao Lorenz T. Biegler 《Macromolecular theory and simulations》2015,24(5):521-536
14.
Hong Zhang Xin‐Lu Cheng Simone Chiesa 《International journal of quantum chemistry》2011,111(15):4452-4456
Bond dissociation energies (BDEs) for some nitro or amino contained prototypical molecules in energetic materials are computed by fixed‐node diffusion quantum Monte Carlo method. The nodes are determined from a Slater determinant calculated within density functional theory at the B3LYP/6‐311G** level. The possible errors, the nodal error, and the cancellation of nodal errors in calculating BDE are discussed, and the accuracy is compared with other available ab initio computations and experimental results. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2010 相似文献
15.
Anthony Scemama Thomas Applencourt Emmanuel Giner Michel Caffarel 《Journal of computational chemistry》2016,37(20):1866-1875
An algorithm to compute efficiently the first two derivatives of (very) large multideterminant wavefunctions for quantum Monte Carlo calculations is presented. The calculation of determinants and their derivatives is performed using the Sherman–Morrison formula for updating the inverse Slater matrix. An improved implementation based on the reduction of the number of column substitutions and on a very efficient implementation of the calculation of the scalar products involved is presented. It is emphasized that multideterminant expansions contain in general a large number of identical spin‐specific determinants: for typical configuration interaction‐type wavefunctions the number of unique spin‐specific determinants ( ) with a non‐negligible weight in the expansion is of order . We show that a careful implementation of the calculation of the Ndet ‐dependent contributions can make this step negligible enough so that in practice the algorithm scales as the total number of unique spin‐specific determinants, , over a wide range of total number of determinants (here, Ndet up to about one million), thus greatly reducing the total computational cost. Finally, a new truncation scheme for the multideterminant expansion is proposed so that larger expansions can be considered without increasing the computational time. The algorithm is illustrated with all‐electron fixed‐node diffusion Monte Carlo calculations of the total energy of the chlorine atom. Calculations using a trial wavefunction including about 750,000 determinants with a computational increase of ～400 compared to a single‐determinant calculation are shown to be feasible. © 2016 Wiley Periodicals, Inc. 相似文献
16.
Arne Lüchow 《Journal of computational chemistry》2014,35(11):854-864
The maxima of squared electronic wave functions are analyzed for a number of small molecules. They are in principle observables and show considerable chemical insight from first principles. The maxima contain substantial information about the relative electron positions in a molecule, such as the pairing of opposite spin electrons and the Pauli repulsion which are lost in the electron density. Single bond and double bond as well as polar bond pairs and lone pairs are obtained from the maximum analysis. In many cases, we find a correspondence to the electron arrangements in molecules as assumed by Lewis in 1916. © 2014 Wiley Periodicals, Inc. 相似文献
17.
HongXinHUANG 《中国化学快报》2004,15(4):501-504
In this paper we proposed a novel exact fixed-node quantum Monte Carlo (EFNQMC)algorithm,which is a self-optimizing and self-improving procedure,In contrast to the previous EFNQMC method,the trial function is optimized synchronistically in the diffusion procedure,but not before the beginning of EFNQMC computation.In order to optimize the trial function,the improved steepest descent technique is used,in which the step size is automatically adjustable.The procedure is quasi-Newton and converges super linearly.We also use a novel trial function,which has correct electron-electron and electron-nucleus cusp conditions.The novel EFNQMC algorithm and the novel trial function are employed to calculate the energies of 1^1A1 state of CH2,^1Ag state of C8 and the ground-states of H2,LiH,Li2,H2O,respectively.The test results show that both the novel algorithm and the trial function proposed in the present paper are very excellent. 相似文献
18.
量子ＭｏｎｔｅＣａｒｌｏ固定节面法试探函数研究黄宏新曹泽星（湖南师范大学化学系长沙４１００８１）关键词量子ＭｏｎｔｅＣａｒｌｏ方法试探函数奇点条件固定节面量子ＭｏｎｔｅＣａｒｌｏ（ＦＮＱＭＣ）方法是ＱＭＣ方法中使用最多的一种，它的试探函数一般是这样组... 相似文献
19.
Luca Bertini Dario Bressanini Massimo Mella Gabriele Morosi 《International journal of quantum chemistry》1999,74(1):23-33
The relative performance of trial wave functions expressed as linear combination of correlated exponentials has been tested on a variety of systems. The results are compared against other correlated functions commonly used in the literature to assess the capabilities of the proposed ansatz. A possible departure from the simple exponential functional form used in previous works is discussed, along with its advantages and drawbacks. We also discuss how to implement an efficient optimization procedure for this correlated basis set. ©1999 John Wiley & Sons, Inc. Int J Quant Chem 74: 23–33, 1999 相似文献
20.
Florent Calvo 《International journal of quantum chemistry》2010,110(13):2347-2354
Nested Markov chain Monte Carlo is a rigorous way to enhance sampling of a given energy landscape using an auxiliary, approximate potential energy surface. Its practical efficiency mainly depends on how cheap and how different are the auxiliary potential with respect to the reference system. In this article, a combined efficiency index is proposed and assessed for two important families of energy surfaces. As illustrated for water clusters, many‐body polarizable potentials can be approximated by simplifying the polarization contribution and keeping only the two‐body terms. In small systems, neglecting polarization entirely is also acceptable. When the reference potential energy is obtained from diagonalization of a quantum mechanical Hamiltonian, a first‐order perturbation scheme can be used to estimate the energy difference occuring on a Monte Carlo move. Our results indicate that this perturbation approximation performs well provided that the number of steps between successive diagonalization is adjusted beforehand. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem 110:2342–2346, 2010 相似文献