CAVIAR: A simulation package for charged particles in environments surrounded by conductive boundaries
Source abstract
Abstract
We introduce CAVIAR, new scientific software that is developed for molecular simulation of ionic-liquids or charged colloids inside conductive boundaries. CAVIAR imports computer-aided-design geometries and uses them to simulate boundary walls. Then based on this geometry, a finite element mesh is generated and utilized for solving the Poisson equation. To avoid the complexity due to the singularity of point charges, we propose a new method, using the advantages of the superposition theorem of the linear partial differential equations. Within this paper, the CAVIAR structure, its features, and basic scientific algorithms are discussed.
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Research context
OpenAlex topics: Electrostatics and Colloid Interactions · Electrohydrodynamics and Fluid Dynamics · Aerosol Filtration and Electrostatic Precipitation
SciVX discovery tags are terminology-based. OpenAlex topics are source-provided classifications.
Affiliations
Department of Physics, Institute for Advanced Studies in Basic Sciences (IASBS) 1 , Zanjan 45137-66731, Iran
Research Center for Basic Sciences and Modern Technologies (RBST), Institute for Advanced Studies in Basic Sciences (IASBS) 2 , Zanjan 45137-66731, Iran
References (72)
Show source-provided references
1. 2007
2. Materials for electrochemical capacitors
3. Design of supercapacitor electrodes using molecular dynamics simulations10.1007/s40820-018-0188-2 ↗
4. A comparative study of room temperature ionic liquids and their organic solvent mixtures near charged electrodes10.1088/0953-8984/28/46/464002 ↗
5. Supercapacitors: Porous materials get energized10.1038/nmat4851 ↗
6. Theory of water desalination by porous electrodes with immobile chemical charge10.1016/j.colcom.2015.12.001 ↗
7. Review on the science and technology of water desalination by capacitive deionization10.1016/j.pmatsci.2013.03.005 ↗
8. Blue energy and desalination with nanoporous carbon electrodes: Capacitance from molecular simulations to continuous models10.1103/physrevx.8.021024 ↗
9. Fast parallel algorithms for short-range molecular dynamics10.1006/jcph.1995.1039 ↗
10. DL_POLY_2.0: A general-purpose parallel molecular dynamics simulation package10.1016/s0263-7855(96)00043-4 ↗
11. ESPResSo—An extensible simulation package for research on soft matter systems10.1016/j.cpc.2005.10.005 ↗
12. ESPResSo++: A modern multiscale simulation package for soft matter systems10.1016/j.cpc.2012.12.004 ↗
13. Die Berechnung optischer und elektrostatischer Gitterpotentiale10.1002/andp.19213690304 ↗
14. MMM1D: A method for calculating electrostatic interactions in one-dimensional periodic geometries10.1063/1.2052647 ↗
15. Comment on ‘MMM1D: A method for calculating electrostatic interactions in one-dimensional periodic geometries’ [J. Chem. Phys. 123, 144103 (2005)]10.1063/1.2346457 ↗
16. MMM2D: A fast and accurate summation method for electrostatic interactions in 2D slab geometries10.1016/s0010-4655(02)00586-6 ↗
17. A particle-particle, particle-density algorithm for the calculation of electrostatic interactions of particles with slablike geometry10.1063/1.2804382 ↗
18. How to mesh up ewald sums. I. A theoretical and numerical comparison of various particle mesh routines10.1063/1.477414 ↗
19. How to mesh up ewald sums. II. An accurate error estimate for the particle–particle–particle-mesh algorithm10.1063/1.477415 ↗
20. Electrostatics in periodic slab geometries. I10.1063/1.1491955 ↗
21. Electrostatics in periodic slab geometries. II10.1063/1.1491954 ↗
22. ICMMM2D: An accurate method to include planar dielectric interfaces via image charge summation10.1063/1.2790428 ↗
23. Electrostatic layer correction with image charges: A linear scaling method to treat slab 2D+ h systems with dielectric interfaces10.1063/1.3021064 ↗
24. An iterative, fast, linear-scaling method for computing induced charges on arbitrary dielectric boundaries10.1063/1.3376011 ↗
25. S. Kesselheim, M. Sega, and C. Holm, “The ICC* algorithm: A fast way to include dielectric boundary effects into molecular dynamics simulations,” arXiv:1003.1271 (2010).
26. ESPResSo 3.1: Molecular dynamics software for coarse-grained models
27. Computing induced charges in inhomogeneous dielectric media: Application in a Monte Carlo simulation of complex ionic systems10.1103/physreve.69.046702 ↗
28. The effect of finite pore length on ion structure and charging10.1063/1.4986346 ↗
29. Charge me slowly, I am in a hurry: Optimizing charge–discharge cycles in nanoporous supercapacitors10.1021/acsnano.8b04785 ↗
30. Electrochemical interface between an ionic liquid and a model metallic electrode10.1063/1.2464084 ↗
31. Influence of surface topology and electrostatic potential on water/electrode systems10.1063/1.469429 ↗
32. New coarse-grained models of imidazolium ionic liquids for bulk and interfacial molecular simulations10.1021/jp3008877 ↗
33. The electric double layer has a life of its own10.1021/jp503224w ↗
34. New perspectives on the charging mechanisms of supercapacitors10.1021/jacs.6b02115 ↗
35. A highly accurate and efficient algorithm for electrostatic interactions of charged particles confined by parallel metallic plates10.1063/1.4963667 ↗
36. 2007
37. Ewald summation for Coulomb interactions in a periodic supercell
38. 2005
39. 2004
40. A fast procedure for computing the distance between complex objects in three-dimensional space10.1109/56.2083 ↗
41. 2003
42. An improved version of rigid for discrete element simulation of particle flows with arbitrarily complex geometries10.1016/j.powtec.2013.12.009 ↗
43. An accurate and robust contact detection algorithm for particle-solid interaction in combined finite-discrete element analysis10.1002/nme.4913 ↗
44. An improved 3D DEM-FEM contact detection algorithm for the interaction simulations between particles and structures10.1016/j.powtec.2016.09.076 ↗
45. The point in polygon problem for arbitrary polygons10.1016/s0925-7721(01)00012-8 ↗
46. An algorithm for determining intersection segment-polygon in 3D10.1016/s0097-8493(98)00064-8 ↗
47. A Jordan surface theorem for three-dimensional digital spaces10.1007/bf02574681 ↗
48. What is object-oriented programming?10.1109/52.2020 ↗
49. 2013
50. 2010
51. deal. II—A general-purpose object-oriented finite element library10.1145/1268776.1268779 ↗
52. Algorithms and data structures for massively parallel generic adaptive finite element codes10.1145/2049673.2049678 ↗
53. Thermostat algorithms for molecular dynamics simulations
54. Molecular dynamics with coupling to an external bath10.1063/1.448118 ↗
55. A unified formulation of the constant temperature molecular dynamics methods10.1063/1.447334 ↗
56. Canonical dynamics: Equilibrium phase-space distributions10.1103/physreva.31.1695 ↗
57. Rattle: A “velocity” version of the shake algorithm for molecular dynamics calculations10.1016/0021-9991(83)90014-1 ↗
58. Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes10.1016/0021-9991(77)90098-5 ↗
59. A fast SHAKE algorithm to solve distance constraint equations for small molecules in molecular dynamics simulations10.1002/1096-987x(20010415)22:5<501::aid-jcc1021>3.0.co;2-v ↗
60. PETSc web page
61. S. Balay, S. Abhyankar, M. F. Adams, J. Brown, P. Brune, K. Buschelman, L. Dalcin, A. Dener, V. Eijkhout, W. D. Gropp, D. Karpeyev, D. Kaushik, M. G. Knepley, D. A. May, L. C. McInnes, R. T. Mills, T. Munson, K. Rupp, P. Sanan, B. F. Smith, S. Zampini, H. Zhang, and H. Zhang, “PETSc users manual,” Technical Report No. ANL-95/11, Revision 3.11, Argonne National Laboratory, 2019.
62. Efficient management of parallelism in object oriented numerical software libraries10.1007/978-1-4612-1986-6 ↗
63. S. Abhyankar, J. Brown, E. M. Constantinescu, D. Ghosh, B. F. Smith, and H. Zhang, “PETSc/TS: A modern scalable ODE/DAE solver library,” arXiv:1806.01437 (2018).
64. M. Heroux, R. Bartlett, V. H. R. Hoekstra, J. Hu, T. Kolda, R. Lehoucq, K. Long, R. Pawlowski, E. Phipps, A. Salinger, H. Thornquist, R. Tuminaro, J. Willenbring, and A. Williams, “An overview of trilinos,” Technical Report No. SAND2003-2927, Sandia National Laboratories, 2003.
65. M. A. Heroux, J. M. Willenbring, and R. Heaphy, “Trilinos developers guide,” Technical Report No. SAND2003-1898, Sandia National Laboratories, 2003.
66. M. A. Heroux, J. M. Willenbring, and R. Heaphy, “Trilinos developers guide Part II: ASCI software quality engineering practices version 1.0,” Technical Report No. SAND2003-1899, Sandia National Laboratories, 2003.
67. M. A. Heroux and J. M. Willenbring, “Trilinos users guide,” Technical Report No. SAND2003-2952, Sandia National Laboratories, 2003.10.2172/918334 ↗
68. An overview of the trilinos project10.1145/1089014.1089021 ↗
69. ESPResSo 4.0—An extensible software package for simulating soft matter systems10.1140/epjst/e2019-800186-9 ↗
70. Isogeometrical solution of Laplace equation
71. A fast isogeometric BEM for the three dimensional Laplace- and Helmholtz problems10.1016/j.cma.2017.10.020 ↗
72. 2009