-
Notifications
You must be signed in to change notification settings - Fork 12
Home
RMG is a DFT-based electronic structure code developed at North Carolina State University. The original version was written in 1993-1994 and it has been updated and expanded continuously since that time. It uses real-space meshes to represent the wavefunctions, the charge density, and the ionic pseudopotentials. The real-space formulation is advantageous for parallelization, because each processor can be assigned a region of space, and for convergence acceleration, since multiple length scales can be dealt with separately. Both norm-conserving and ultrasoft pseudopotentials (UPPs) are allowed.
The parallelization strategy for the main RMG routines employs a mixed programming model that utilizes MPI, OpenMP and Posix threads. Domain decomposition is used to assign different regions of space to different cores, and a domain may span an entire node, consisting of, e.g., 16 cores on a Cray XK6. This greatly reduces the required communications and makes the communication latency more uniform. The orbitals are processed in blocks and do local synchronization within nodes at specific points of the SCF cycle, greatly reducing the need for global synchronization. The RMG code scales nearly linearly up to 100k processor cores and 20k GPUs on Cray XK6. It is expected to also scale well on large parallel clusters that include low-latency, high speed switches, such as InfiniBand.
RMG can be used through a Graphical User Interface (GUI) or text input. Both accept atomic coordinate files in several formats. RMG also has GUI and text-based interfaces for coupling it with the BerkeleyGW code for computing band gap corrections and exciton binding energies. RMG has been tested on a large number of systems, including big supercells of bulk materials containing various impurities, surfaces and interfaces and bulk transition metals, as well as molecular dynamics of liquid water and of breakage of carbon nanotubes. In all cases, the results agree very well with plane-wave calculations and experiment.
The RMG code suite consists of several modules. The current distribution contains the code needed to perform DFT calculations for a large number of atoms. Other modules, planned to be released in the future will: (i) perform quantum transport calculations for nanoscale devices using an optimized localized basis, and (ii) execute hybrid DFT calculations that embed a full density-functional region (e.g., containing a biomolecule and its first solvation shell) into a larger "solvent" region treated by the much simpler orbital-free DFT method, which works well for closed shell molecules (e.g., water).
The main RMG code is licensed under the GPL v2 while RmgLib is covered by the modified BSD license.
RMG was originally written in C with small portions in Fortran 77. Over time as features were added, this led to some issues with ease of maintenance so the decision was made to improve the modularity of the code and rewrite significant portions in C++. The C++11 std was targeted since it has native cross platform support for threading which is necessary for a hybrid MPI/threads implementation. This process is not entirely complete but as of November 2014 large portions of the code have been rewritten in C++. Additionally a separate library has been created that encapsulates much of the basic functionality needed to implement massively parallel solvers for certain types of differential equations.
Another development focus has been GPU integration. Currently RMG makes effective use of Nvidia GPU's to accelerate a number of computational tasks. Future work will provide support for AMD and Intel accelerators as well as extending the areas where GPU's are used in the code base.
The RMG source includes Spglib for working with crystal symmetries and the libxc library of exchange correlation functionals.
"2x4 GaP(100) surface: atomic structure and optical anisotropy", A. M. Frisch, W. G. Schmidt, J. Bernholc, M. Pristovsek, N. Esser and W. Richter, Phys. Rev. B 60, 2488 (1999).
"Mechanical Properties and Electronic Transport in Carbon Nanotubes", J. Bernholc, M. Buongiorno Nardelli, J.-L. Fattebert, D. Orlikowski, R. Roland and Q. Zhao, in "Nanotubes," edited by D. Tomanek and R. J. Enbody, Kluwer Academic Publishing (2000).
"GaP(001) and InP(001): Reflectance anisotropy and surface geometry", N. Esser, W. G. Schmidt, J. Bernholc, A. M. Frisch, P. Vogt, M. Zorn, M. Pristovsek, W. Richter, F. Bechstedt, Th. Hannappel and S. Visbeck, J. Vac. Sci. Techn. B 17, 1691 (1999).
"(001) surfaces of GaP and InP: Structural motifs, electronic states and optical signatures", W. G. Schmidt, J. Bernholc and F. Bechstedt, Appl. Surf. Sci. 166, 179 (2000).
"Self-energy effects in the optical anisotropy of GaP(001)", W.G. Schmidt, J. L. Fattebert, J. Bernholc and F. Bechstedt, Surf. Rev. Lett. 6, 1159 (1999).
"Angle resolved photoemission spectroscopy of the InP(001) surface", A. M. Frisch, P. Vogt, S. Visbeck, Th. Hannappel, F. Willig, W. Braun, W. Richter, J. Bernholc, W. G. Schmidt and N. Esser Appl. Surf. Sci. 166, 224 (2000).
"Understanding reflectance anisotropy: Surface-state signatures and bulk-related features in the optical spectrum of InP(001)(2x4)", W. G. Schmidt, N. Esser, A. M. Frisch, P. Vogt, J. Bernholc, F. Bechstedt, M. Zorn, Th. Hannappel, S. Visbeck, F. Willig, W. Richter, Phys. Rev. B 61, R16335 (2000).
"Towards grid-based O(N) DFT methods: optimized non-orthogonal orbitals and multigrid acceleration", J.-L. Fattebert and J. Bernholc, Phys. Rev. B 62, 1713 (2000).
"Step-induced optical anisotropy of Si(111):H surfaces", W. G. Schmidt and J. Bernholc, Phys. Rev. B, 61, 7604 (2000).
"Understanding reflectance anisotropy: Surface-state signatures and bulk-related features", W. G. Schmidt, F. Bechstedt, and J. Bernholc, J. Vac. Sci. Tech. B 18, 2215 (2000).
"Terrace and step contributions to the surface optical anisotropy of Si(001)", W.G. Schmidt, F. Bechstedt and J. Bernholc, Phys. Rev. B 63, 45322 (2001).
"Terrace and step contributions to the surface optical anisotropy of Si(001)", W.G. Schmidt, F. Bechstedt and J. Bernholc, Proc. 25th Intern. Conf. Phys. Semicond., Springer-Verlag, Berlin, 299 (2001).
"Optical anisotropy of the SiC(001) (3x2) surface: evidence for the two-adlayer asymmetric-dimer model", W. Lu, W. G. Schmidt, E. L. Briggs, and J. Bernholc, Phys. Rev. Lett. 85, 4381 (2000).
"An O(N) real-space method for ab initio quantum transport calculations: application to carbon nanotube-metal contacts", M. Buongiorno Nardelli, J.-L. Fattebert, and J. Bernholc, Phys. Rev. B 64, 245423 (2001).
"Ultimate strength of carbon nanotubes: a theoretical study", Q. Zhao, M. Buongiorno Nardelli and J. Bernholc, Phys. Rev. B 65, 144105 (2002).
"GaAs(001) Surface Reconstructions: Geometries, Chemical Bonding and Optical Properties", W.G. Schmidt, F. Bechstedt, and J. Bernholc, Appl. Surf. Sci. 190, 264 (2002).
"GaAs(001): Surface structure and optical properties", W. G. Schmidt, F. Bechstedt, K. Fleischer, C. Cobet, N. Esser, W. Richter, J. Bernholc, and G. Onida, Phys. Stat. Sol. 188, 1401 (2001).
"Quantum Transport in Nanotube-Based Structures", M. Buongiorno Nardelli, J.-L. Fattebert, and J. Bernholc, Proc. Mat. Res. Soc. 706, Z8.2 (2002).
"Structure and Energetics of Ga-rich GaAs(001) Surfaces", K. Seino, W. G. Schmidt, F. Bechstedt, and J. Bernholc, Surf. Sci. 507-510, 406 (2002).
"Ab initio investigations of lithium diffusion in carbon nanotube systems", V. Meunier, C. Roland, J. Bernholc, Phys. Rev. Lett. 88, 075506 (2002).
"Cycloaddition reaction vs dimer cleavage at the Si(001): C5H8 interface", W. Lu, W. G. Schmidt and J. Bernholc, Phys. Rev. B 68, 115327 (2003).
"Spontaneous polarization and piezoelectricity in boron nitride nanotubes", S. M. Nakhmanson, V. Meunier, J. Bernholc, M. Buongiorno Nardelli, Phys. Rev. B 67, 235406 (2003).
"Interplay of surface reconstruction and surface electric fields in the optical spectroscopy of GaAs(001)", W. G. Schmidt, F. Bechstedt, W. Lu and J. Bernholc, Phys. Rev. B 66, 085334 (2002).
"Nanowire-induced optical anisotropy of the Si(111)-In surface", S. Wang, W. Lu, W. G. Schmidt and J. Bernholc, Phys. Rev. B 68, 035329 (2003).
"Calculation of surface optical properties: From qualitative understanding to quantitative predictions", W. G. Schmidt, K. Seino, P. H. Hahn, F. Bechstedt, W. Lu, S. Wang, and J. Bernholc, Thin Solid Films 455/456, 764 (2004).
"Atomic Indium nanowires on Si(111): The (4x1)-(8x2)-phase transition studied with Reflectance Anisotropy Spectroscopy", K. Fleischer, S. Chandola, N. Esser, W. Richter, J. F. McGilp, F. Bechstedt, S. Wang, W. Lu, W.G. Schmidt, J. Bernholc, Appl. Surf. Sci. 234, 302 (2004).
"Gallium-rich reconstructions on GaAs(001)", M. Pristovsek, S. Tsukamoto, A. Ohtake, N. Koguchi, B. G. Orr, W. G. Schmidt, and J. Bernholc, Phys. Stat. Sol. (b) 240, 91-98 (2003).
"Ab initio studies of polarization and piezoelectricity in vinylidene fluoride and BN-based polymers", S. M. Nakhmanson, M. Buongiorno Nardelli and J. Bernholc, Phys. Rev. Lett. 92, 115504 (2004).
"Oxidation- and organic-molecule-induced changes of the Si surface optical anisotropy: ab initio predictions", W. G. Schmidt, F. Fuchs, A. Hermann, K. Seino, F. Bechstedt, R. Passmann, M.Wahl, M. Gensch, K. Hinrichs, N. Esser, S. Wang, W. Lu and J. Bernholc, J. Phys.: Condens. Matter 16, S4323 (2004).
"Optical Absorption of Water: Coulomb Effects versus Hydrogen Bonding", P. H. Hahn, W. G. Schmidt, K. Seino, M. Preuss, F. Bechstedt, and J. Bernholc, Phys. Rev. Lett. 94, 037404 (2005), listed also in Virtual Journal of Biological Physics Research, February 1 (2005).
"Carbon nanotube-metal cluster composites: a new road to chemical sensors?", Q. Zhao, M. Buongiorno Nardelli, W. Lu and J. Bernholc, Nano Letters 5, 847 (2005).
"Non-equilibrium quantum transport properties of organic molecules on silicon", W. Lu, V. Meunier, and J. Bernholc, Phys. Rev. Lett. 95, 206805 (2005).
"Electron transport in molecular systems", V. Meunier, W. Lu, J. Bernholc, and B. G. Sumpter, Journal of Physics: Conference Series 16, 283 (2005).
"Collective polarization effects in beta-polyvinylidene fluoride and its copolymers with tri- and tetrafluoroethylene", S. M. Nakhmanson, M. Buongiorno Nardelli and J. Bernholc, Phys. Rev. B 72, 115210 (2005).
"Density Functional Theory Studies of Quantum Transport in Molecular Systems", V. Meunier, W. Lu, B. G. Sumpter, J. Bernholc, Intern. J. Quantum Chem. 106, 3334 (2006).
"Atomic Scale Design of Nanostructures", J. Bernholc, W. Lu, S. M. Nakhmanson, P. H. Hahn, V. Meunier, M. Buongiorno Nardelli, and W. G. Schmidt, Molecular Physics, 105, 147 (2007).
"Resonant Coupling and Negative Differential Resistance in Metal/Ferrocenyl-Alkanethiolate/STM structures", S. Wang, W. Lu, Q. Zhao, and J. Bernholc, Phys. Rev. B 74, 195430 (2006). listed also in Virtual Journal of Nanoscale Science & Technology, December 4 (2006).
"Implementation of ultrasoft pseudopotentials in large-scale, grid-based electronic structure calculations", M. Hodak, S. Wang, W. Lu, and J. Bernholc, Phys. Rev. B, 76, 085108 (2007).
"Hybrid ab initio Kohn-Sham DFT/frozen-density orbital-free DFT simulation method suitable for biological systems", M. Hodak, W. Lu, and J. Bernholc, J. Chem. Phys. 128, 014101 (2008).
"Effects of end group functionalization and level alignment on electron transport in molecular devices", G. Kim, S. Wang, W. Lu, M. Buongiorno Nardelli, and J. Bernholc, J. Chem. Phys. 128, 024708 (2008).
"Doping-dependent negative differential resistance in hybrid organic/inorganic Si-porphyrin-Si junctions", F. J. Ribeiro, W. Lu, and J. Bernholc, ACS Nano 2, 1517 (2008).
"Recent developments and applications of the real-space multigrid method", J. Bernholc, M. Hodak, and W. Lu, J. Phys. Condens. Matter 20, 294205 (2008).
"Functional implications of multistage copper binding to the prion protein", M. Hodak, R. Chisnell, W. Lu, and J. Bernholc, Proc. Nat. Acad. Sci. 106, 11576 (2009).
"Performance evaluation for petascale quantum simulation tools", S. Tomov, W. Lu, J. Bernholc, S. Moore, and J. Dongarra, Proceedings of Cray User Group 2009 (CUG09): Compute the Future (2009).
"First-principles methodology for quantum transport in multiterminal junctions", K. K. Saha, W. Lu, J. Bernholc, V. Meunier, J. Chem. Phys. 131, 164105 (2009).
"Insights into prion protein function from atomistic simulations", M. Hodak and J. Bernholc, Prion 4, 13 (2010).
"Electron transport in multiterminal molecular devices: A density functional theory study", K. K. Saha, W. Lu, J. Bernholc, V. Meunier, Phys. Rev. B 81, 125420 (2010).
"Negative Differential Resistance in C60-Based Electronic Devices", X. Zheng, W. Lu, T. A. Abtew, V. Meunier, and J. Bernholc, ACS Nano 4, 7205 (2010).
"Quantum-Interference-Controlled Three-Terminal Molecular Transistors Based on a Single Ring-Shaped Molecule Connected to Graphene Nanoribbon Electrodes", K. K. Saha, B. K. Nikolic, V. Meunier, W. Lu, and J. Bernholc, Phys. Rev. Lett. 105, 236803 (2010).
"Mechanism of copper(II)-induced misfolding of Parkinson's disease protein", F. Rose, M. Hodak, and J. Bernholc, Nature Scientific Reports 1, 11 (2011).
"Hybrid quantum simulations of biomolecules: the role of copper in neurodegenerative diseases", J. Bernholc, M. Hodak, W. Lu, and F. Rose, Proceedings of the 2010 Scientific Discovery through Advanced Computing (SciDAC) Conference, pp. 12-22 (2011).
"Scaling the RMG Quantum Mechanics Code", S. Moore, E. Briggs, M. Hodak, W. Lu, J. Bernholc, C. W. Lee, Proc. Extreme Scaling Workshop (BW-XSEDE '12). University of Illinois at Urbana-Champaign, Champaign, IL, USA, , Article 8 , 6 pages.#
“Enzymatic Mechanism of Copper-Containing Nitrite Reductase,” Y. Li, M. Hodak, and J. Bernholc, ACS Biochemistry, 54, 1233 (2015), http://dx.doi.org/10.1021/bi5007767.
“Charge Transport in DNA Nanowires,” B. Tan, M. Hodak, W. Lu, and J. Bernholc, Phys. Rev. B 92, 075429 (2015), http://link.aps.org/doi/10.1103/PhysRevB.92.075429
“Mechanisms of NH3 and NO2 detection in carbon-nanotube-based sensors: An ab initio investigation,” Y. Li, M. Hodak, W. Lu, and J. Bernholc, Carbon 101, 177 (2016). http://dx.doi.org/10.1016/j.carbon.2016.01.092
“Selective sensing of ethylene and glucose using carbon-nanotube-based sensors: An ab initio investigation,” Y. Li, M. Hodak, W. Lu, and J. Bernholc, Nanoscale 9, 1687-1698 (2017) http://dx.doi.org/10.1039/C6NR07371A
“Controllable conversion of quasi-freestanding polymer chains to graphene nanoribbons,” C. Ma, Z. Xiao, H. Zhang, L. Liang, J. Huang, W. Lu, K. Hong, J. Bernholc, A.-P. Li, Nature Communications 8, 14815 (2017) http://dx.doi.org/10.1038/ncomms14815
“Binding of Copper and Cisplatin to Atox1 Is Mediated by Glutathione through the Formation of Metal−Sulfur Clusters,” N. V. Dolgova, C. Yu, J. P. Cvitkovic, M. Hodak,K. H. Nienaber, K. L. Summers, J. J. H. Cotelesage, J. Bernholc, G. A. Kaminski, I. J. Pickering, G. N. George, and O. Y. Dmitriev. Biochemistry, 56, 3129 (2017), http://dx.doi.org/10.1021/acs.biochem.7b00293
“Design of Atomically Precise Nanoscale Negative Differential Resistance Devices,“ Z. Xiao, C. Ma, J. Huang, L. Liang, W. Lu, K. Hong, B. G. Sumpter, A.-P. Li, J. Bernholc, Adv. Theory Simul. 2, 1800172 (2019), https://onlinelibrary.wiley.com/doi/epdf/10.1002/adts.201800172.
“Direct writing of heterostructures in single atomically precise graphene nanoribbons,” C. Ma, Z. Xiao, J. Huang, L. Liang, W. Lu, K. Hong, B. G. Sumpter, J. Bernholc, A.-P. Li, Phys. Rev. Materials 3, 016001 (2019), https://journals.aps.org/prmaterials/abstract/10.1103/PhysRevMaterials.3.016001.