XtalOpt version r7: An open-source evolutionary algorithm for crystal structure prediction

A new version of XtalOpt, a user-friendly GPL-licensed evolutionary algorithm for crystal structure prediction, is available for download from the CPC library or the XtalOpt website, http://xtalopt.openmolecules.net. The new version now supports four external geometry optimization codes (VASP, GULP, PWSCF, and CASTEP), as well as three queuing systems: PBS, SGE, SLURM, and “Local”. The local queuing system allows the geometry optimizations to be performed on the user?s workstation if an external computational cluster is unavailable. Support for the Windows operating system has been added, and a Windows installer is provided. Numerous bugfixes and feature enhancements have been made in the new release as well.

New version program summary

Program title:XtalOptCatalogue identifier: AEGX_v2_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGX_v2_0.htmlProgram obtainable from: CPC Program Library, Queen?s University, Belfast, N. IrelandLicensing provisions: GPL v2.1 or later [1]No. of lines in distributed program, including test data, etc.: 125 383No. of bytes in distributed program, including test data, etc.: 11 607 415Distribution format: tar.gzProgramming language: C++Computer: PCs, workstations, or clustersOperating system: Linux, MS WindowsClassification: 7.7External routines: Qt [2], Open Babel [3], Avogadro [4], and one of: VASP [5], PWSCF [6], GULP [7], CASTEP [8]Catalogue identifier of previous version: AEGX_v1_0Journal reference of previous version: Comput. Phys. Comm. 182 (2011) 372Does the new version supersede the previous version?: YesNature of problem: Predicting the crystal structure of a system from its stoichiometry alone remains a grand challenge in computational materials science, chemistry, and physics.Solution method: Evolutionary algorithms are stochastic search techniques which use concepts from biological evolution in order to locate the global minimum of a crystalline structure on its potential energy surface. Our evolutionary algorithm, XtalOpt, is freely available for use and collaboration under the GNU Public License. See the original publication on XtalOpt?s implementation [11] for more information on the method.Reasons for new version: Since XtalOpt?s initial release in June 2010, support for additional optimizers, queuing systems, and an operating system has been added. XtalOpt can now use VASP, GULP, PWSCF, or CASTEP to perform local geometry optimizations. The queue submission code has been rewritten, and now supports running any of the above codes on ssh-accessible computer clusters that use the Portable Batch System (PBS), Sun Grid Engine (SGE), or SLURM queuing systems for managing the optimization jobs. Alternatively, geometry optimizations may be performed on the user?s workstation using the new internal “Local” queuing system if high performance computing resources are unavailable. XtalOpt has been built and tested on the Microsoft Windows operating system (XP or later) in addition to Linux, and a Windows installer is provided. The installer includes a development version of Avogadro that contains expanded crystallography support [12] that is not available in the mainline Avogadro releases. Other notable new developments include:

• • 

  LIBSSH [10] is distributed with the XtalOpt sources and used for communication with the remote clusters, eliminating the previous requirement to set up public-key authentication;

• • 

  Plotting enthalpy (or energy) vs. structure number in the plot tab will trace out the history of the most stable structure as the search progresses A read-only mode has been added to allow inspection of previous searches through the user interface without connecting to a cluster or submitting new jobs;

• • 

  The tutorial [13] has been rewritten to reflect the changes to the interface and the newly supported codes. Expanded sections on optimizations schemes and save/resume have been added;

• • 

  The included version of SPGLIB has been updated. An option has been added to set the Cartesian tolerance of the space group detection. A new option has been added to the Progress table?s right-click menu that copies the selected structure?s POSCAR formatted representation to the clipboard;

• • 

  Numerous other small bugfixes/enhancements.

Summary of revisions: See “Reasons for new version” above.Running time: User dependent. The program runs until stopped by the user.References:

•  [1] 

  http://www.gnu.org/licenses/gpl.html.

•  [2] 

  http://www.trolltech.com/.

•  [3] 

  http://openbabel.org/.

•  [4] 

  http://avogadro.openmolecules.net.

•  [5] 

  http://cms.mpi.univie.ac.at/vasp.

•  [6] 

  http://www.quantum-espresso.org.

•  [7] 

  https://www.ivec.org/gulp.

•  [8] 

  http://www.castep.org.

•  [9] 

  http://spglib.sourceforge.net.

• [10] 

  http://www.libssh.org.

• [11] 

  D. Lonie, E. Zurek, Comp. Phys. Comm. 182 (2011) 372–387, doi:10.1016/j.cpc.2010.07.048.

• [12] 

  http://davidlonie.blogspot.com/2011/03/new-avogadro-crystallography-extension.html.

• [13] 

  http://xtalopt.openmolecules.net/globalsearch/docs/tut-xo.html.

     

XtalOpt: An open-source evolutionary algorithm for crystal structure prediction

The implementation and testing of XtalOpt, an evolutionary algorithm for crystal structure prediction, is outlined. We present our new periodic displacement (ripple) operator which is ideally suited to extended systems. It is demonstrated that hybrid operators, which combine two pure operators, reduce the number of duplicate structures in the search. This allows for better exploration of the potential energy surface of the system in question, while simultaneously zooming in on the most promising regions. A continuous workflow, which makes better use of computational resources as compared to traditional generation based algorithms, is employed. Various parameters in XtalOpt are optimized using a novel benchmarking scheme. XtalOpt is available under the GNU Public License, has been interfaced with various codes commonly used to study extended systems, and has an easy to use, intuitive graphical interface.

Program summary

Program title:XtalOptCatalogue identifier: AEGX_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGX_v1_0.htmlProgram obtainable from: CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions: GPL v2.1 or later [1]No. of lines in distributed program, including test data, etc.: 36 849No. of bytes in distributed program, including test data, etc.: 1 149 399Distribution format: tar.gzProgramming language: C++Computer: PCs, workstations, or clustersOperating system: LinuxClassification: 7.7External routines: QT [2], OpenBabel [3], AVOGADRO [4], SPGLIB [8] and one of: VASP [5], PWSCF [6], GULP [7].Nature of problem: Predicting the crystal structure of a system from its stoichiometry alone remains a grand challenge in computational materials science, chemistry, and physics.Solution method: Evolutionary algorithms are stochastic search techniques which use concepts from biological evolution in order to locate the global minimum on their potential energy surface. Our evolutionary algorithm, XtalOpt, is freely available to the scientific community for use and collaboration under the GNU Public License.Running time: User dependent. The program runs until stopped by the user.References:

• [1] 

  http://www.gnu.org/licenses/gpl.html.

• [2] 

  http://www.trolltech.com/.

• [3] 

  http://openbabel.org/.

• [4] 

  http://avogadro.openmolecules.net.

• [5] 

  http://cms.mpi.univie.ac.at/vasp.

• [6] 

  http://www.quantum-espresso.org.

• [7] 

  https://www.ivec.org/gulp.

• [8] 

  http://spglib.sourceforge.net.

     

Remotely sensed surface water extent as an indicator of short-term changes in ecohydrological processes in sub-Saharan Western Africa

The highly variable rainfall in the arid and semi-arid regions of sub-Saharan Western Africa drives both surface water availability and vegetation cover. Recent studies have established linkages between rainfall and vegetation cover at local to regional scales, but no study related yet remote sensing derived rainfall and vegetation cover to the available surface water. A new dataset based on SPOT VEGETATION (VGT) represents surface water bodies (SWB) in the arid and semi-arid regions of sub-Saharan Western Africa. Water bodies represent the integrated hydrological response of a catchment, and changes in their spatial extent involve complex interactions at the catchment scale. We analyzed time series of remotely sensed vegetation cover, rainfall and surface water extent for the period 1999–2008, and could detect and statistically demonstrate the links between these biophysical variables. Our findings for two regions in Mali and Burkina Faso suggest that vegetation cover is positively related to the amount of available surface water for those catchments that are mainly covered by annual plants. The observed relationships between remotely sensed variables allow developing ecological indicators that can indicate short-term changes in arid and semi-arid ecosystems at local to regional scales.     

Conjoint analysis to measure the perceived quality in volume rendering

Visualization algorithms can have a large number of parameters, making the space of possible rendering results rather high-dimensional. Only a systematic analysis of the perceived quality can truly reveal the optimal setting for each such parameter. However, an exhaustive search in which all possible parameter permutations are presented to each user within a study group would be infeasible to conduct. Additional complications may result from possible parameter co-dependencies. Here, we will introduce an efficient user study design and analysis strategy that is geared to cope with this problem. The user feedback is fast and easy to obtain and does not require exhaustive parameter testing. To enable such a framework we have modified a preference measuring methodology, conjoint analysis, that originated in psychology and is now also widely used in market research. We demonstrate our framework by a study that measures the perceived quality in volume rendering within the context of large parameter spaces.     

Three-dimensional space-vector modulation algorithm for four-leg multilevel converters using abc coordinates

In this paper, a novel three-dimensional (3-D) space-vector algorithm for four-leg multilevel converters is presented. It can be applied to active power filters or neutral-current compensator applications for mitigating harmonics and zero-sequence components using abc coordinates (referred from now on this paper as natural coordinates). This technique greatly simplifies the selection of the 3-D region where a given voltage vector is supposed to be found. Compared to a three-level modulation algorithm for three-leg multilevel converters, this algorithm does not increase its complexity and the calculations of the active vectors with the corresponding switching time that generate the reference voltage vector. In addition, the low-computational cost of the proposed algorithm is always the same and it is independent of the number of levels of the converter.     

Mothers' Affect in the Homework Context: The Importance of Staying Positive.

This research investigated mothers' affect in the context of children's homework. Mothers (N=109) of children 8 to 12 years old were interviewed daily about their affect while interacting with children, their assistance with children's homework, and children's behavior while completing homework. At this time and 6 months later, children's motivational and emotional functioning was assessed. Although mothers' negative affect was lower than their positive affect, it was elevated on days their assistance with homework was high. This was accounted for by mothers' perceptions of children as helpless on days they provided heightened assistance. Mothers' positive affect in the homework context buffered children's motivational and emotional functioning against mothers' negative affect as well as children's helplessness. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Developing an Automated Enzyme Immunoassay for High-Throughput Screening of Bovine Serum Antibodies to Neospora Caninum

An enzyme-linked immunosorbent assay (ELISA) for Neospora caninum antibodies was automated with a robotic workstation, the Beckman Coulter Biomek 2000, to screen 200 bovine sera. Comparing these results with manually run ELISA data, a 95.92% agreement (K = 0.9592) between the two assays was obtained. The automated assay was specific and sensitive with excellent positive and negative predictive values. The results were repeatable and reproducible. The automation flexibility was high and the operation complexity was minimal. High-throughput screening (HTS) for bovine antibodies to Neospora caninum was achieved. The assay was developed according to the internationally recognized ISO17025 standard requirements.     

Feedback passivity of nonlinear discrete-time systems with direct input-output link

This paper is devoted to the study of the feedback passivity property in nonlinear discrete-time systems. The relative degree and zero dynamics of the non-passive system are related to the feedback passivity of the system. Two main results are presented. First, some relative degree-related properties of passive systems in general form are stated. Second, sufficient conditions in order to render a multiple-input multiple-output (MIMO) system passive by means of a static state feedback control law are obtained.     

Lightweight Bytecode Verification

In this paper, we provide a theoretical foundation for and improvements to the existing bytecode verification technology, a critical component of the Java security model, for mobile code used with the Java “micro edition” (J2ME), which is intended for embedded computing devices. In Java, remotely loaded “bytecode” class files are required to be bytecode verified before execution, that is, to undergo a static type analysis that protects the platform's Java run-time system from so-called type confusion attacks such as pointer manipulation. The data flow analysis that performs the verification, however, is beyond the capacity of most embedded devices because of the memory requirements that the typical algorithm will need. We propose to take a proof-carrying code approach to data flow analysis in defining an alternative technique called “lightweight analysis” that uses the notion of a “certificate” to reanalyze a previously analyzed data flow problem, even on poorly resourced platforms. We formally prove that the technique provides the same guarantees as standard bytecode safety verification analysis, in particular that it is “tamper proof” in the sense that the guarantees provided by the analysis cannot be broken by crafting a “false” certificate or by altering the analyzed code. We show how the Java bytecode verifier fits into this framework for an important subset of the Java Virtual Machine; we also show how the resulting “lightweight bytecode verification” technique generalizes and simulates the J2ME verifier (to be expected as Sun's J2ME “K-Virtual machine” verifier was directly based on an early version of this work), as well as Leroy's “on-card bytecode verifier,” which is specifically targeted for Java Cards.