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Introducing k-point parallelism into VASP

Asimina Maniopoulou, Erlend R.M. Davidson, Ricardo Grau-Crespo, Aron Walsh, Ian J. Bush, C. Richard A. Catlow, Scott M. Woodley
2012 Computer Physics Communications  
We report here an improved parallelisation strategy that also distributes the k-point sampling workload over different processors, allowing much better scalability for massively parallel computers.  ...  As a result, some difficult problems requiring large k-point sampling become tractable in current computing facilities.  ...  Kresse and the VASP team for helpful input and for making the code available to us.  ... 
doi:10.1016/j.cpc.2012.03.009 fatcat:szrq2kd3cbcvxmckxeiipyejfu

Deep Variational Autoencoder with Shallow Parallel Path for Top-N Recommendation (VASP) [article]

Vojtěch Vančura, Pavel Kordík
2021 arXiv   pre-print
We show how to learn FLVAE in parallel with Neural EASE and achieve the state of the art performance on the MovieLens 20M dataset and competitive results on the Netflix Prize dataset.  ...  Recently introduced EASE algorithm presents a simple and elegant way, how to solve the top-N recommendation task.  ...  As a demonstration, we build the VASP, a Variational Autoencoder with a Shallow parallel Path.  ... 
arXiv:2102.05774v1 fatcat:ooytegm2l5hw7jprqrefedsi6q

Precise parallel volumetric comparison of molecular surfaces and electrostatic isopotentials

Georgi D. Georgiev, Kevin F. Dodd, Brian Y. Chen
2020 Algorithms for Molecular Biology  
Earlier methods have generally used parallelism to enhance computational throughput, pClay is the first algorithm to use parallelism to make arbitrarily high precision comparisons practical.  ...  Our results also demonstrate the parallel performance of pClay on both workstation CPUs and a 61-core Xeon Phi.  ...  Next, we use VASP-E to analyze the field and generate an isopotential surface at a given threshold k.  ... 
doi:10.1186/s13015-020-00168-z pmid:32489400 pmcid:PMC7247173 fatcat:sjvfruvrtbfnhlbembq2x447z4

Helium under high pressure: A comparative study of all-electron and pseudopotential methods within density functional theory [article]

W. Xiao, Z. X. Tian, W. T. Geng
2012 arXiv   pre-print
[Ref. 13] k points level volume = 8 a.u. 3 Volume = 120 a.u. 3 VASP Wien2k VASP Wien2k  (0, 0, 0) 1 0 0 0 0 2-4 37.52 37.50 1.01 1.01 X (0, 0.5, 0.5) 1-4 23.27 23.26 0.77  ...  DISCUSSION To get more insight into subtle difference between VASP and Wien2k, we have examined carefully the eigenvalues of He.  ... 
arXiv:1201.1598v1 fatcat:lggtfgajm5gpdpjziviqof7kxe

All-Electron APW+lo calculation of magnetic molecules with the SIRIUS domain-specific package [article]

Long Zhang, Anton Kozhevnikov, Thomas Schulthess, S. B. Trickey, Hai-Ping Cheng
2022 arXiv   pre-print
Compared to other packages the additional APW and FLAPW task and data parallelism and the additional eigensystem solver provided by the SIRIUS package can be exploited for performance gains in in the ground  ...  If one performs single k-point calculation for an isolated system, the lack of band parallelism within a k-point makes it run with one MPI task only.  ...  Like the Mn-taa, this calculation also benefits from the band parallelization within a single k-point and the distributed storage of the G-vector related arrays.  ... 
arXiv:2105.07363v2 fatcat:i6zht2ojnbh2jcss3247ui57ou

Spectral signatures of thermal spin disorder and excess Mn in half-metallic NiMnSb

K. D. Belashchenko, Jeevaka Weerasinghe, Sai Mu, B. S. Pujari
2015 Physical Review B  
Temperature-dependent spin disorder, introduced within the vector disordered local moment model, causes the valence band at the Γ point to broaden and shift upwards, crossing the Fermi level and thereby  ...  The Γ point is antibonding for these bands.  ...  The spin moment of Mn E varies from 0.84 to 3.04 µ B between the points closest to 0 and π in good agreement with VASP calculations. PDOS at θ = 0, π, and SD state are shown in Fig. 6 .  ... 
doi:10.1103/physrevb.91.180408 fatcat:pftgptsxzjhwnloehpbew5i2bi

Reusability in Science: From Initial User Engagement to Dissemination of Results [article]

Ketan Maheshwari, David Kelly, Scott J. Krieder, Justin M. Wozniak, Daniel S. Katz, Mei Zhi-Gang, Mainak Mookherjee
2013 arXiv   pre-print
Effective use of parallel and distributed computing in science depends upon multiple interdependent entities and activities that form an ecosystem.  ...  k-points for a constant cut-off energy. 1 string dirs[] = [ "300", "400", "500", ... ]; 2 file out[]<simple_mapper; 3 location="stdouts", 4 prefix="vasp", suffix=".out">; 5 foreach dir, i in dirs {  ...  $subdirname 14 cp CONTCAR output/vasp-contcar-$dirname.$subdirname Reusable shell script to launch parallel VASP under Swift 1 #!  ... 
arXiv:1309.1813v1 fatcat:lmgr5yf2mvbyllpuko2cm3g75i

VASP on a GPU: Application to exact-exchange calculations of the stability of elemental boron

M. Hutchinson, M. Widom
2012 Computer Physics Communications  
Porting the widely used electronic density functional code VASP to run on a GPU results in a 5-20 fold performance boost of exact-exchange compared with a traditional CPU.  ...  Table 2 Table 2 of k-mesh convergence. k-point meshes are Monkhorst-Pack. Units are meV/atom.  ...  The port operates within the existing parallelism in VASP, distributing data across processors with MPI.  ... 
doi:10.1016/j.cpc.2012.02.017 fatcat:irkbbm5h7vba5mto76vuxy6laa

DensityTool: A post-processing tool for space- and spin-resolved density of states from VASP [article]

Lucas Lodeiro, Tomáš Rauch
2021 arXiv   pre-print
DensityTool can be applied to manipulate, visualize, and understand the local electronic structure of any system calculated with VASP.  ...  Here, we present a simple tool which takes the partial charge density and the energy eigenvalues calculated by VASP as input and constructs local charge and spin densities.  ...  For this case, the partial charge density written by VASP is the starting point. Only its average in the plane parallel to the slab surface is needed and it is calculated with the PCA routine.  ... 
arXiv:2112.11050v1 fatcat:erl54h3prbaf5hty2ce7d62qii

Tests on the Accuracy and Scalability of the Full-Potential DFT Method Based on Multiple Scattering Theory

Peiyu Cao, Jun Fang, Xingyu Gao, Fuyang Tian, Haifeng Song
2020 Frontiers in Chemistry  
It is shown that the calculated lattice parameters, bulk moduli, and elastic constants agree with those obtained from the VASP, WIEN2k, EMTO, and Elk codes.  ...  The Monkhorst-Pack k-point mesh was set to be 21×21×21 in all the KKR tests.  ...  This is due to the two-level parallelism over atoms and energy points implemented in MuST package.  ... 
doi:10.3389/fchem.2020.590047 pmid:33344416 pmcid:PMC7746799 fatcat:or5xh4c3qbetxcnz6bmsk34lom

VASP mediated actin dynamics activate and recruit a filopodia myosin [article]

Ashley L Arthur, Amy Crawford, Anne Houdusse, Margaret A Titus
2021 bioRxiv   pre-print
The actin regulator locally produces a cortical actin network, that activates the MF myosin and together they shape the actin network to promote extension of parallel bundles during filopodia formation  ...  Analysis of VASP mutants and treatment of cells with anti-actin drugs shows that myosin recruitment and activation in Dictyostelium requires localized VASP-dependent actin polymerization.  ...  Jan Faix (U Hannover) for providing the dDia2 nulls and VASP antibody and Dr Brad Nolen (U. Oregon) for supplying the CK666.  ... 
doi:10.1101/2021.03.16.435667 fatcat:rfcs5wtisjdctlszqpjuvmkiby

FINETUNA: Fine-tuning Accelerated Molecular Simulations [article]

Joseph Musielewicz, Xiaoxiao Wang, Tian Tian, Zachary Ulissi
2022 arXiv   pre-print
This allows VASP to work in tandem with our framework while requiring 75% fewer self-consistent cycles than conventional single point calculations.  ...  Finally, we demonstrate a technique for leveraging the interactive functionality built in to VASP to efficiently compute single point calculations within our online active learning framework without the  ...  i) Standard ASE VASP (M1): cold-start VASP process on each single point ii) ASE VASP with wavefunction cache (M2): use local file (WAVECAR) to store and pass wavefunction between single points.  ... 
arXiv:2205.01223v2 fatcat:4pgzloplpffv5fjzgqcn5go4ae

Highly Efficient Free Energy Calculations of the Fe Equation of State Using Temperature-Dependent Effective Potential Method

Igor Mosyagin, Olle Hellman, Weine Olovsson, Sergei I. Simak, Igor A. Abrikosov
2016 Journal of Physical Chemistry A  
We show that for a model system considered in this work, hcp Fe, the obtained thermal equation of state at 2000 K is in excellent agreement with the results of standard calculations within the quasiharmonic  ...  The same number of Brillouin zone integration points was used in VASP and Wien2k: it was carried out with the Γ-point.  ...  to carry out highly parallel molecular dynamics simulation.  ... 
doi:10.1021/acs.jpca.6b08633 pmid:27700093 pmcid:PMC5199118 fatcat:j4lykcxml5chbopqkwfuzvaogi

VASP mediated actin dynamics activate and recruit a filopodia myosin

Ashley L Arthur, Amy Crawford, Anne Houdusse, Margaret A Titus
2021 eLife  
The actin regulator locally produces a cortical actin network that activates myosin and together they shape the actin network to promote extension of parallel bundles of actin during filopodia formation  ...  Analysis of VASP mutants and treatment of cells with anti-actin drugs shows that myosin recruitment and activation in Dictyostelium requires localized VASP-dependent actin polymerization.  ...  Jan Faix (U Hannover) for providing the dDia2 nulls and VASP antibody and Dr Brad Nolen (U. Oregon) for supplying the CK666, Dr. Günther Gerisch (Max Planck) for the GFP-tubulin plasmid, Dr. G.W.  ... 
doi:10.7554/elife.68082 pmid:34042588 pmcid:PMC8352590 fatcat:fvnu34inobfhplzyfawps2rk4u

Fast Approximate Evaluation of Parallel Overhead from a Minimal Set of Measured Execution Times

Siegfried Höfinger, Thomas Ruh, Ernst Haunschmid
2018 Parallel Processing Letters  
The focus here is on an analytic solution that takes into account as many data points as there are unknowns, i.e. model parameters.  ...  Here we continue the development of our recently proposed technique that uses plain execution times to predict the extent of parallel overhead.  ...  square deviation (RMSD) from the measured execution times, RM SD = 1 k k n [t n (exp) − t n (app)] 2 (8) where t n (exp) are the k experimentally observed data points and t n (app) their corresponding  ... 
doi:10.1142/s0129626418500032 fatcat:xmze4tko6vhgjiqvviyfmtiaby
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