scholarly journals SPARC: Simulation Package for Ab-initio Real-space Calculations

SoftwareX ◽  
2021 ◽  
Vol 15 ◽  
pp. 100709
Author(s):  
Qimen Xu ◽  
Abhiraj Sharma ◽  
Benjamin Comer ◽  
Hua Huang ◽  
Edmond Chow ◽  
...  
SoftwareX ◽  
2020 ◽  
Vol 11 ◽  
pp. 100423
Author(s):  
Qimen Xu ◽  
Abhiraj Sharma ◽  
Phanish Suryanarayana

Author(s):  
K. Chowdhury ◽  
S. Ghosh ◽  
M. Mukherjee

AbstractThe direct method program SAYTAN has been applied successfully to redetermine the structure of cytochrome c


1995 ◽  
Vol 408 ◽  
Author(s):  
D. J. Sullivan ◽  
E. L. Briggs ◽  
C. J. Brabec ◽  
J. Bernholc

AbstractWe have developed a set of techniques for performing large scale ab initio calculations using multigrid accelerations and a real-space grid as a basis. The multigrid methods permit efficient calculations on ill-conditioned systems with long length scales or high energy cutoffs. We discuss the design of pseudopotentials for real-space grids, and the computation of ionic forces. The technique has been applied to several systems, including an isolated C60 molecule, the wurtzite phase of GaN, a 64-atom cell of GaN with the Ga d-states in valence, and a 443-atom protein. The method has been implemented on both vector and parallel architectures. We also discuss ongoing work on O(N) implementations and solvated biomolecules.


2007 ◽  
Vol 2007.20 (0) ◽  
pp. 261-262
Author(s):  
Nobuyuki ISHIZAKI ◽  
Yoshinori SHIIHARA ◽  
Osamu KUWAZURU ◽  
Nobuhiro YOSHIKAWA

2018 ◽  
Author(s):  
Carlos Outeiral Rubiera ◽  
Mark Vincent ◽  
Ángel Martín Pendás ◽  
Paul L. A. Popelier

Ab initio quantum chemistry is an independent source of information supplying an ever widening group of experimental chemists. However, bridging the gap between these ab initio data and chemical insight remains a challenge. In particular, there is a need for a bond order index that characterizes novel bonding patterns in a reliable manner, while recovering the familiar effects occurring in well-known bonds. In this article, through a large body of calculations, we show how the delocalization index derived from Quantum Chemical Topology (QCT) serves as such a bond order. This index is defined in a parameter-free, intuitive and consistent manner, and with little qualitative dependency on the level of theory used. The delocalization index is also able to detect the subtler bonding effects that underpin most practical organic and inorganic chemistry. We explore and connect the properties of this index and open the door for its extensive usage in the understanding and discovery of novel chemistry.


2018 ◽  
Author(s):  
Carlos Outeiral Rubiera ◽  
Mark Vincent ◽  
Ángel Martín Pendás ◽  
Paul L. A. Popelier

Ab initio quantum chemistry is an independent source of information supplying an ever widening group of experimental chemists. However, bridging the gap between these ab initio data and chemical insight remains a challenge. In particular, there is a need for a bond order index that characterizes novel bonding patterns in a reliable manner, while recovering the familiar effects occurring in well-known bonds. In this article, through a large body of calculations, we show how the delocalization index derived from Quantum Chemical Topology (QCT) serves as such a bond order. This index is defined in a parameter-free, intuitive and consistent manner, and with little qualitative dependency on the level of theory used. The delocalization index is also able to detect the subtler bonding effects that underpin most practical organic and inorganic chemistry. We explore and connect the properties of this index and open the door for its extensive usage in the understanding and discovery of novel chemistry.


2016 ◽  
Vol 72 (4) ◽  
pp. 480-488
Author(s):  
Gábor Oszlányi ◽  
András Sütő

Alternating-projection-type dual-space algorithms have a clear construction, but are susceptible to stagnation and, thus, inefficient for solving the phase problemab initio. To improve this behaviour new omit maps are introduced, which are real-space perturbations applied periodically during the iteration process. The omit maps are calledvolumic, because they delete some predetermined subvolume of the unit cell without searching for atomic regions or analysing the electron density in any other way. The basic algorithms of positivity, histogram matching and low-density elimination are tested by their solution statistics. It is concluded that, while all these algorithms based on weak constraints are practically useless in their pure forms, appropriate volumic omit maps can transform them to practically useful methods. In addition, the efficiency of the already useful reflector-type charge-flipping algorithm can be further improved. It is important that these results are obtained by using non-sharpened structure factors and without any weighting scheme or reciprocal-space perturbation. The mathematical background of volumic omit maps and their expected applications are also discussed.


2015 ◽  
Vol 71 (6) ◽  
pp. 592-598 ◽  
Author(s):  
Rick P. Millane ◽  
Romain D. Arnal

Uniqueness of the phase problem in macromolecular crystallography, and its relationship to the case of single particle imaging, is considered. The crystallographic problem is characterized by a constraint ratio that depends only on the size and symmetry of the molecule and the unit cell. The results are used to evaluate the effect of various real-space constraints. The case of an unknown molecular envelope is considered in detail. The results indicate the quite wide circumstances under whichab initiophasing should be possible.


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