DVR3D: a program suite for the calculation of rotation-vibration spectra of triatomic molecules

The DVR3D program suite calculates energy levels, wavefunctions, and where appropriate dipole transition moments, for rotating and vibrating triatomic molecules. Potential energy and, where necessary, dipole surfaces must be provided. Expectation values of geometrically defined functions can be calculated, a feature which is particularly useful for fitting potential energy surfaces. The programs use an exact (within the Born-Oppenheimer approximation) Hamiltonian and offer a choice of Jacobi or Radau internal coordinates and several body-fixed axes. Rotationally excited states are treated using an efficient two-step algorithm. The programs uses a Discrete Variable Representation (DVR) based on Gauss-Jacobi and Gauss-Laguerre quadrature for all 3 internal coordinates and thus yields a fully point-wise representation of the wavefunctions. The vibrational step uses successive diagonalisation and truncation which is implemented for a number of possible coordinate orderings. The rotational, expectation value and transition dipole programs exploit the savings offered by performing integrals on a DVR grid. The new version has been rewritten in FORTRAN 90 to exploit the dynamic array allocations and the algorithm for dipole and spectra calculations have been substantially improved. New modules allow the z-axis to be embedded perpendicular to the plane of the molecule and for the calculation of expectation values.

Program summary

Title of the program: DVR3D suiteCatalogue number: ADTIProgram summary URL:http://cpc.cs.qub.ac.uk/summaries/ADTIProgram obtainable from: CPC Program Library, Queen's University of Belfast, N. IrelandProgramming language: Fortran 90No. of lines in distributed program, including test data, etc.: 61 574No. of bytes in distributed program, including test data, etc.: 972 404Distribution format: tar.gz

New version summary

Title of program: DVR3DRJZCatalogue number: ADTBProgram summary URL:http://cpc.cs.qub.ac.uk/summaries/ADTBProgram obtainable from: CPC Program Library, Queen's University of Belfast, N. IrelandReference in CPC to previous version: 86 (1995) 175Catalogue identifier of previous version: ADAKAuthors of previous version: J. Tennyson, J.R. Henderson and N.G. FultonDoes the new version supersede the original program?: DVR3DRJZ supersedes DVR3DRJComputer: PC running LinuxInstallation: desktopOther machines on which program tested: Compaq running True64 Unix; SGI Origin 2000, Sunfire V750 and V880 systems running SunOS, IBM p690 Regatta running AIXProgramming language used in the new version: Fortran 90Memory required to execute: case dependentNo. of lines in distributed program, including test data, etc.: 4203No. of bytes in distributed program, including test data, etc.: 30 087Has code been vectorised or parallelised?: The code has been extensively vectorised. A parallel version of the code, PDVR3D has been developed [1], contact the first author for detailsAdditional keywords: perpendicular embeddingDistribution format: gzNature of physical problem: DVR3DRJZ calculates the bound vibrational or Coriolis decoupled rotational-vibrational states of a triatomic system in body-fixed Jacobi (scattering) or Radau coordinates [2]Method of solution: All coordinates are treated in a discrete variable representation (DVR). The angular coordinate uses a DVR based on (associated) Legendre polynomials and the radial coordinates utilise a DVR based on either Morse oscillator-like or spherical oscillator functions. Intermediate diagonalisation and truncation is performed on the hierarchical expression of the Hamiltonian operator to yield the final secular problem. DVR3DRJ provides the vibrational wavefunctions necessary for ROTLEV3, ROLEV3B or ROTLEV3Z to calculate rotationally excited states, DIPOLE3 to calculate rotational-vibrational transition strengths and XPECT3 to compute expectation valuesRestrictions on the complexity of the problem: (1) The size of the final Hamiltonian matrix that can practically be diagonalised. (2) The order of integration in the radial coordinates that can be dealt with within the machine exponent range. Some adjustment in the code may be necessary when large order Gauss-Laguerre quadrature is usedTypical running time: Case dependent but usually dominated by the final (3D) matrix diagonalisation. The test runs take minutes on a fast PCUnusual features of the program: A user supplied subroutine containing the potential energy as an analytic function is a program requirementReferences:

[1]

H.Y. Mussa, J. Tennyson, Comput. Phys. Commun. 128 (2000) 434.

[2]

J. Tennyson, B.T. Sutcliffe, Internat. J. Quantum Chem. 42 (1992) 941.

New version summary

Title of program: ROTLEV3Catalogue number: ADTCProgram summary URL:http://cpc.cs.qub.ac.uk/summaries/ADTCProgram obtainable from: CPC Program Library, Queen's University of Belfast, N. IrelandReference in CPC to previous version: 86 (1995) 175Catalogue identifier of previous version: ADALAuthors of previous version: J. Tennyson, J.R. Henderson and N.G. FultonDoes the new version supersede the original program?: YesComputer: PC running LinuxInstallation: desktopOther machines on which program tested: Compaq running True64 Unix; SGI Origin 2000, Sunfire V750 and V880 systems running SunOSProgramming language used: Fortran 90High speed storage required: case dependentNo. of lines in distributed program, including test data, etc.: 1514No. of bytes in distributed program, including test data, etc.: 12 652Has code been vectorised or parallelised?: The code has been extensively vectorised. A parallel version of the code, PROTLEV3 has been developed [1], contact the first author for detailsDistribution format: gzNature of physical problem: ROTLEV3 performs the second step in a two-step variational calculation for the bound rotational-vibrational levels of a triatomic system represented in either Jacobi or unsymmetrised Radau coordinatesMethod of solution: A basis is constructed from the solutions of the Coriolis decoupled problem provided by DVR3DRJZ. The angular coordinate is transformed back to a basis set representation. The sparse Hamiltonian matrix can be diagonalised iteratively or in coreRestrictions on the complexity of the problem: The size of matrix that can practically be diagonalisedTypical running time: Case dependent. The sample data takes less than a minute on a fast PCUnusual features of the program: Most data is read directly from DVR3DRJZ. ROTLEV3 can provide data to drive DIPOLE3 and/or XPECT3References: [1] H.Y. Mussa, J. Tennyson, Comput. Phys. Commun. 128 (2000) 434.

New version summary

Title of program: ROTLEV3BCatalogue number: ADTDProgram summary URL:http://cpc.cs.qub.ac.uk/summaries/ADTDProgram obtainable from: CPC Program Library, Queen's University of Belfast, N. IrelandReference in CPC to previous version: 86 (1995) 175Catalogue identifier of previous version: ADAMAuthors of previous version: J. Tennyson, J.R. Henderson and N.G. FultonDoes the new version supersede the original program?: YesComputer: PC running LinuxInstallation: desktopOther machines on which program tested: Compaq running True64 Unix, Sunfire V750 and V880 systems running SunOSProgramming language used: Fortran 90High speed storage required: case dependentNo. of lines in distributed program, including test data, etc.: 2215No. of bytes in distributed program, including test data, etc.: 16 595Has code been vectorised or parallelised?: The code has been extensively vectorised. A parallel version of the code, PROTLEV3B has been developed [1], contact the first author for detailsDistribution format: gzNature of physical problem: ROTLEV3B performs the second step in a two-step variational calculation for the bound rotational-vibrational levels of a triatomic system represented by symmetrised Radau coordinates using a bisector embedding [2]Method of solution: A basis is constructed from the solutions of the Coriolis decoupled problem provided by DVR3DRJZ. The problem is constructed entirely within the DVR. The Hamiltonian matrix can be diagonalised iteratively or in coreRestrictions on the complexity of the problem: The size of matrix that can practically be diagonalisedTypical running time: Case dependent. The sample data takes a few minutes on a fast PCUnusual features of the program: Most data is read directly from DVR3DRJZ. ROTLEV3B can provide data to drive DIPOLE3 and/or XPECT3References:

[1]

H.Y. Mussa, J. Tennyson, Comput. Phys. Commun. 128 (2000) 434.

[2]

J. Tennyson, B.T. Sutcliffe, Internat. J. Quantum Chem. 42 (1992) 941.

Program summary

Title of program: ROTLEV3ZCatalogue number: ADTEProgram summary URL:http://cpc.cs.qub.ac.uk/summaries/ADTEProgram obtainable from: CPC Program Library, Queen's University of Belfast, N. IrelandComputer: PC running LinuxInstallation: desktopOther machines on which program tested: Compaq running True64 Unix, Sunfire V750 and V880 systems running SunOSProgramming language used: Fortran 90High speed storage required: case dependentNo. of lines in distributed program, including test data, etc.: 2919No. of bytes in distributed program, including test data, etc.: 17 241Keywords: rotationally excited state, Coriolis coupling, secondary variational method, sparse matrix, vectorised, perpendicular embedding, Radau coordinatesHas code been vectorised or parallelised?: The code has been extensively vectorisedDistribution format: gzNature of physical problem: ROTLEV3Z performs the second step in a two-step variational calculation for the bound rotational-vibrational levels of a triatomic system represented by symmetrised Radau coordinates using a perpendicular embedding [1]Method of solution: A basis is constructed from the solutions of the Coriolis decoupled problem provided by DVR3DRJZ. The problem is constructed entirely within the DVR. The Hamiltonian matrix is diagonalised in coreRestrictions on the complexity of the problem: The size of matrix that can practically be diagonalisedTypical running time: Case dependent. The sample data takes a few minutes on a fast PCUnusual features of the program: Most data is read directly from DVR3DRJZReferences: [1] M.A. Kostin, O.L. Polyansky, J.Tennyson, J. Chem. Phys. 116 (2002) 7564.

New version summary

Title of program: DIPOLE3Catalogue number: ADTFProgram summary URL:http://cpc.cs.qub.ac.uk/summaries/ADTFProgram obtainable from: CPC Program Library, Queen's University of Belfast, N. IrelandReference in CPC to previous version: 86 (1995) 175Catalogue identifier of previous version: ADANAuthors of previous version: J. Tennyson, J.R. Henderson and N.G. FultonDoes the new version supersede the original program?: YesComputer: PC running LinuxInstallation: desktopOther machines on which program tested: Compaq running True64 Unix; SGI Origin 2000; sunfire V750 and V880 systemsProgramming language used: Fortran 90High speed storage required: case dependentNo. of lines in distributed program, including test data, etc.: 1921No. of bytes in distributed program, including test data, etc.: 15 685Has code been vectorised or parallelised?: The code has been extensively vectorised. Commands to parallelise the code using OpenMP are included in the sourceDistribution format: gzNature of physical problem: DIPOLE3 calculates dipole transition intensities between previously calculated wavefunction for both rotational and rotational-vibrational transitionsMethod of solution: Integrals over dipole surfaces are constructed using a DVR in all three coordinates, this requires a transformation of the angular wavefunctions. Wavefunctions generated by DVR3DRJZ and ROTLEV3 or ROTLEV3B are then used to give transition intensities for individual pairs of statesRestrictions on the complexity of the problem: The complexity of the problem that can be solved by DVR3DRJZ, ROTLEV3 or ROTLEV3BTypical running time: Case dependent. The test data takes a few seconds on a fast PCUnusual features of the program: Most data is read directly from DVR3DRJZ and ROTLEV3 or ROTLEV3B. DIPOLE provides data to drive SPECTRA

New version summary

Title of program: SPECTRACatalogue number: ADTGProgram summary URL:http://cpc.cs.qub.ac.uk/summaries/ADTGProgram obtainable from: CPC Program Library, Queen's University of Belfast, N. IrelandComputer: PC running LinuxInstallation: desktopOther machines on which program tested: Compaq running True64 UnixReference in CPC to previous version: 75 (1993) 339Catalogue identifier of previous version: ACNBAuthors of previous version: J. Tennyson, S. Miller and C.R. Le SueurDoes the new version supersede the original program?: YesProgramming language used: Fortran 90High speed storage required: case dependentNo. of lines in distributed program, including test data, etc.: 1037No. of bytes in distributed program, including test data, etc.: 9159Has code been vectorised or parallelised?: As execution times are very short this is usually not importantDistribution format: gzNature of physical problem: SPECTRA generates synthetic, frequency ordered spectra as a function of temperature. Absolute intensities can be calculated if the necessary data to calculate the partition function is suppliedMethod of solution: Transitions are sorted by frequency and weighted using Boltzmann statisticsRestrictions on the complexity of the problem: The complexity of problem that can be solved by other programs in the suiteTypical running time: Case dependent, but very small for sample dataUnusual features of the program: Most data is read directly from DIPOLE3. Some data from DVR3DRJZ and ROTLEV3 or ROTLEV3B may also be required

Program summary

Title of program: XPECT3Catalogue number: ADTHProgram summary URL:http://cpc.cs.qub.ac.uk/summaries/ADTHProgram obtainable from: CPC Program Library, Queen's University of Belfast, N. IrelandComputer: PC running LinuxInstallation: desktopOther machines on which program tested: Compaq running True64 UnixProgramming language used: Fortran 90High speed storage required: case dependentNo. of lines in distributed program, including test data, etc.: 1214No. of bytes in distributed program, including test data, etc.: 9361Distribution format: gzKeywords: Expectation values, Hellmann-Feynman theorem, potential fittingHas code been vectorised or parallelised?: The code has been extensively vectorisedNature of physical problem: XPECT3 calculates expectation of geometrically defined operators using previously calculated wavefunctionsMethod of solution: Integrals over the user defined surfaces are constructed using a DVR in all three coordinates. Wavefunctions generated by DVR3DRJZ and ROTLEV3 or ROTLEV3B are then used to give expectation values for each stateRestrictions on the complexity of the problem: The complexity of problem that can be solved by DVR3DRJZ, ROTLEV3 or ROTLEV3BTypical running time: Case dependent. The test data takes a few seconds on a fast PCUnusual features of the program: Most data is read directly from DVR3DRJZ and ROTLEV3 or ROTLEV3B.     

Functional un|unparsing

Danvy??s functional unparsing problem (Danvy in J. Funct. Program. 8(6), 621?C625, 1998) is to implement a type-safe ??printf?? function, which converts a sequence of heterogeneous arguments to a string according to a given format. The dual problem is to implement a type-safe ??scanf?? function, which extracts a sequence of heterogeneous arguments from a string by interpreting (Friedman and Wand in LFP, pp. 348?C355, 1984 and in Essentials of Programming Languages, MIT Press, 2008) the same format as an equally heterogeneous sequence of patterns that binds zero or more variables. We derive multiple solutions to both problems (Wand in J. ACM 27(1), 164?C180, 1980) from their formal specifications (Wand in Theor. Comput. Sci. 20(1), 3?C32, 1982). On one hand, our solutions show how the Hindley-Milner type system, unextended, permits accessing heterogeneous sequences with the static assurance of type safety. On the other hand, our solutions demonstrate the use of control operators (Felleisen et al. in Proceedings of the 1988 ACM Conference on Lisp and Functional Programming, pp. 52?C62, ACM Press, New York, 1988; Wand in POPL 85: Conference Record of the Annual ACM Symposium on Principles of Programming Languages, vol. 16, ACM Press, New York, 1985; Meyer and Wand in Logics of Programs, Lecture Notes in Computer Science, vol. 193, pp. 219?C224, Springer, Berlin, 1985) to communicate with formats as coroutines (Wand in Proceedings of the 1980 ACM Conference on Lisp and Functional Programming, vol. 12, pp. 285?C299, ACM Press, New York, 1980 and Haynes et al. in LFP, pp. 293?C298, 1984).     

Identifying representative users in matrix factorization-based recommender systems: application to solving the content-less new item cold-start problem

Matrix factorization has proven to be one of the most accurate recommendation approaches. However, it faces one major shortcoming: the latent features that result from the factorization are not directly interpretable. Providing interpretation for these features is important not only to help explain the recommendations presented to users, but also to understand the underlying relations between the users and the items. This paper consists of 2 contributions. First, we propose to automatically interpret features as users, referred to as representative users. This interpretation relies on the study of the matrices that result from the factorization and on their link with the original rating matrix. Such an interpretation is not only performed automatically, as it does not require any human expertise, but it also helps to explain the recommendations. The second proposition of this paper is to exploit this interpretation to alleviate the content-less new item cold-start problem. The experiments conducted on several benchmark datasets confirm that the features discovered by a Non-Negative Matrix Factorization can be interpreted as users and that representative users are a reliable source of information that allows to accurately estimate ratings on new items. They are thus a promising way to solve the new item cold-start problem.     

Influence of Data Clouds Fusion From 3D Real-Time Vision System on Robotic Group Dead Reckoning in Unknown Terrain

This paper proposes the solution of tasks set required for autonomous robotic group behavior optimization during the mission on a distributed area in a cluttered hazardous terrain.The navigation scheme uses the benefits of the original real-time technical vision system(TVS)based on a dynamic triangulation principle.The method uses TVS output data with fuzzy logic rules processing for resolution stabilization.Based on previous researches,the dynamic communication network model is modified to implement the propagation of information with a feedback method for more stable data exchange inside the robotic group.According to the comparative analysis of approximation methods,in this paper authors are proposing to use two-steps post-processing path planning aiming to get a smooth and energy-saving trajectory.The article provides a wide range of studies and computational experiment results for different scenarios for evaluation of common cloud point influence on robotic motion planning.     

Helicoseir as Shape of a Rotating String (I): 2D Theory and Simulation Using ANCF

A physically simple but mathematically cumbersome problem of rotating heavy string with one fixed top point was studied. A nonlinear equation of its two-dimensional shapes of relative equilibrium was obtained and solved numerically. A linear case of small displacements was analyzed in terms of Bessel functions. The qualitative and quantitative behavior of the problem is discussed with the help of a bifurcation diagram. Dynamics of the two-dimensional model near the equilibrium positions were studied with the help of a simulation using the absolute nodal coordinate formulation (ANCF); the equilibriums were found to be instable. The reason for instability is explained using a variational principle. The outlines for further full three-dimensional analysis are briefly proposed in this paper, and the full derivation will be explained in the next paper.     

Profile miniaturization and performance improvement of a rectangular patch antenna using magnetic metamaterial substrates

The idea of profile miniaturization and performance improvement of a rectangular patch antenna using a metamaterial substrate with large values in the real part of effective relative permeability is proposed in microwave frequency range. The volume profile of the antenna is minimized by tuning the effective relative permeability and thickness of the substrate material. The specific type of metamaterial which can be used as substrate material for the antenna miniaturization purpose is suggested. The proposed idea is validated through finite‐difference time‐domain (FDTD) simulations for sample rectangular patch antennas with metamaterial substrates at the frequency about 10 GHz. Improvement of the power directivity is found for the metamaterial substrate with large value in the real part of effective permeability. © 2016 Wiley Periodicals, Inc. Int J RF and Microwave CAE 26:254–261, 2016.     

Optical monitoring of characteristics of the stratospheric aerosol layer and total ozone content at the Siberian Lidar Station (Tomsk: 56° 30′ N; 85° E)

We consider the results of long-term remote optical monitoring obtained at the Siberian Lidar Station of Institute of Atmospheric Optics, Siberian Branch, Russian Academy of Sciences, Tomsk (56° 30′ N, 85° E). The scattering characteristics of stratospheric aerosol layer, obtained according to data of lidar measurements recorded since 1986, are presented. We analyse the trends of changes in the total ozone (TO) content over Tomsk for the period 1996–2013 according to data of spectrophotometric measurements employing Total Ozone Mapping Spectrometer (TOMS) data for the period 1979–1994. We determined the periods of elevated content of stratospheric aerosol over Tomsk after a series of explosive eruptions of volcanoes in the Pacific Ring of Fire and Iceland in 2006–2011. Since the second half of the 1990s we have recorded an increasing TO trend, equalling 0.65 DU/year for the period 1996–2013.     

Cooperative linear cargo transport with molecular spiders

Molecular spiders are nanoscale walkers made with DNA enzyme legs attached to a common body. They move over a surface of DNA substrates, cleaving them and leaving behind product DNA strands, which they are able to revisit. Simple one-dimensional models of spider motion show significant superdiffusive motion when the leg-substrate bindings are longer-lived than the leg-product bindings. This gives the spiders potential as a faster-than-diffusion transport mechanism. However, analysis shows that single-spider motion eventually decays into an ordinary diffusive motion, owing to the ever increasing size of the region of cleaved products. Inspired by cooperative behavior of natural molecular walkers, we propose a symmetric exclusion process model for multiple walkers interacting as they move over a one-dimensional lattice. We show that when walkers are sequentially released from the origin, the collective effect is to prevent the leading walkers from moving too far backwards. Hence, there is an effective outward pressure on the leading walkers that keeps them moving superdiffusively for longer times, despite the growth of the product region. Multi-spider systems move faster and farther than single spiders or systems with multiple simple random walkers.     

Java-MaC: A Run-Time Assurance Approach for Java Programs

We describe Java-MaC, a prototype implementation of the Monitoring and Checking (MaC) architecture for Java programs. The MaC architecture provides assurance that the target program is running correctly with respect to a formal requirements specification by monitoring and checking the execution of the target program at run-time. MaC bridges the gap between formal verification, which ensures the correctness of a design rather than an implementation, and testing, which does not provide formal guarantees about the correctness of the system.Use of formal requirement specifications in run-time monitoring and checking is the salient aspect of the MaC architecture. MaC is a lightweight formal method solution which works as a viable complement to the current heavyweight formal methods. In addition, analysis processes of the architecture including instrumentation of the target program, monitoring, and checking are performed fully automatically without human direction, which increases the accuracy of the analysis. Another important feature of the architecture is the clear separation between monitoring implementation-dependent low-level behaviors and checking high-level behaviors, which allows the reuse of a high-level requirement specification even when the target program implementation changes. Furthermore, this separation makes the architecture modular and allows the flexibility of incorporating third party tools into the architecture. The paper presents an overview of the MaC architecture and a prototype implementation Java-MaC.     

Novel hydrogen gas sensor based on single ZnO nanorod

For extensive use in an industrialized process of individual ZnO nano/microrods as building nanoblock in novel hydrogen sensors, a simple, inexpensive, and bio-safe synthesis process and nanofabrication route is required. Here, we report a cost-effective and fast synthesis route for ZnO one-dimensional nanorod using an aqueous-based approach in a reactor. Our synthesis technique permits nano/microrods to be easily transferred to other substrates and to be distributed on the surface. This flexibility of substrate choice opens the possibility of using focused ion beam (FIB/SEM) system for handling and fabricating nanosensors. The main advantage of this procedure is a quick verification/testing of concept and is compatible with micro/nanoelectronic devices. The described nanofabrication steps permitted us to obtain a 90% success rate for building single nanorod sensor. A sensitivity of ∼4% was obtained for a single ZnO nanorod hydrogen sensor at 200 ppm H₂ in the air at room temperature. The nanosensor has a high selectivity for H₂, since its sensitivity for O₂, CH₄, CO, ethanol or LPG are less than 0.25%.