Standard FORTRAN Research Articles

Predicting microRNA modulation in human prostate cancer using a simple String IDentifier (SID1.0)

To make faster and efficient the identification of mRNA targets common to more than one miRNA, and to identify new miRNAs modulated in specific pathways, a computer program identified as SID1.0 (simple String IDentifier) was developed and successfully applied in the identification of deregulated miRNAs in prostate cancer cells. This computationally inexpensive Fortran program is based on the strategy of exhaustive search and specifically designed to screen shared data (target genes, miRNAs and pathways) available from PicTar and DIANA-MicroT 3.0 databases. As far as we know this is the first software designed to filter data retrieved from available miRNA databases. SID1.0 takes advantage of the standard Fortran intrinsic functions for manipulating text strings and requires ASCII input files. In order to demonstrate SID1.0 applicability, some miRNAs expected from the literature to associate with cancerogenesis (miR-125b, miR-148a and miR-141), were randomly identified as main entries for SID1.0 to explore matching sequences of mRNA targets and also to explore KEGG pathways for the presence of ID codes of targeted genes. Besides genes and pathways already described in the literature, SID1.0 has proven to useful for predicting other genes involved in prostate carcinoma. These latter were used to identify new deregulated miRNAs: miR-141, miR-148a, miR-19a and miR-19b. Prediction data were preliminary confirmed by expression analysis of the identified miRNAs in androgen-dependent (LNCaP) and independent (PC3) prostate carcinoma cell lines and in normal prostatic epithelial cells (PrEC).

Electroweak radiative corrections to single top production

Radiative corrections to the single top s and t channel production processes are revisited. Complete one-loop electroweak corrections are calculated within the SANC system. New is a study of the regularisation of the top-legs associated infrared divergences with aid of the complex mass of the top quark. A comparison of these electroweak corrections with those computed by the conventional method is presented both for top production and decays. Standard FORM and FORTRAN SANC modules are created. These modules are compiled into a package sanc_cc_v1.40, which may be downloaded from SANC project homepages. Many numerical results are presented at the partonic level with the aim to demonstrate the correct working of modules. These modules are intended to be used in Monte Carlo generators for single top production at the LHC. Where possible, we compare our results with those existing in the literature; in particular, a comprehensive comparison with results of the CompHEP system is given.

HRMC_1.1: Hybrid Reverse Monte Carlo method with silicon and carbon potentials

The Hybrid Reverse Monte Carlo (HRMC) code models the atomic structure of materials via the use of a combination of constraints including experimental diffraction data and an empirical energy potential. This energy constraint is in the form of either the Environment Dependent Interatomic Potential (EDIP) for carbon and silicon and the original and modified Stillinger–Weber potentials applicable to silicon. In this version, an update is made to correct an error in the EDIP carbon energy calculation routine. New version program summary Program title: HRMC version 1.1 Catalogue identifier: AEAO_v1_1 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEAO_v1_1.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 36 991 No. of bytes in distributed program, including test data, etc.: 907 800 Distribution format: tar.gz Programming language: FORTRAN 77 Computer: Any computer capable of running executables produced by the g77 Fortran compiler. Operating system: Unix, Windows RAM: Depends on the type of empirical potential use, number of atoms and which constraints are employed. Classification: 7.7 Catalogue identifier of previous version: AEAO_v1_0 Journal reference of previous version: Comput. Phys. Comm. 178 (2008) 777 Does the new version supersede the previous version?: Yes Nature of problem: Atomic modelling using empirical potentials and experimental data. Solution method: Monte Carlo Reasons for new version: An error in a term associated with the calculation of energies using the EDIP carbon potential which results in incorrect energies. Summary of revisions: Fix to correct brackets in the two body part of the EDIP carbon potential routine. Additional comments: The code is not standard FORTRAN 77 but includes some additional features and therefore generates errors when compiled using the Nag95 compiler. It does compile successfully with the GNU g77 compiler ( http://www.gnu.org/software/fortran/fortran.html). Running time: Depends on the type of empirical potential use, number of atoms and which constraints are employed. The test included in the distribution took 37 minutes on a DEC Alpha PC.

Coarrays in the next Fortran standard

The WG5 committee, at its meeting in Delft, May 2005, decided to include co-arrays in the next Fortran Standard. A Fortran program containing co-arrays is interpreted as if it were replicated a fixed number of times and all copies were executed asynchronously. Each copy has its own set of data objects and is called an image. The array syntax of Fortran is extended with additional trailing subscripts in square brackets to give a clear and straightforward representation of access to data on other images. References without square brackets are to local data, so code that can run independently is uncluttered. Any occurrence of square brackets is a warning about communication between images. The additional syntax requires support in the compiler, but it has been designed to be easy to implement and to give the compiler scope both to apply its optimizations within each image and to optimize the communication between images. The extension includes execution control statements for synchronizing images and intrinsic procedures to return the number of images, to return the index of the current image, and to perform collective operations. The paper does not attempt to describe the full details of the feature as it now appears in the draft of the new standard. Instead, we describe a subset and demonstrate the use of this subset with examples.

Algorithm 892

A standard Fortran 95 module for printing scalars, vectors, and matrices to external files is provided. The module can display variables of default kind of all intrinsic types (integer, real, complex, logical, and character), and add-on modules are provided for data of the nondefault kind. The main module is self-contained and incorporating it only requires that it be compiled and linked with a program containing a “use dispmodule” statement. A generic interface and optional parameters are used, so that the same subroutine name, DISP, is used to display items of different data type and rank, irrespective of display options. The subroutine is quite versatile, and hopefully can improve Fortran's competitiveness against other array programming languages. The module also contains a function TOSTRING to convert numerical scalars and vectors to strings.

Statements and intrinsic procedures in consecutive Fortran standards

This paper contains the tables of statements and intrinsic procedures in consecutive Fortran standards: from Fortran 66 up to Fortran 2003.

General data analysis code for TDCR liquid scintillation counting

A non-radionuclide-specific computer code to analyze data, calculate detection efficiency and activity in a TDCR system is presented. The program was developed prioritizing flexibility in measuring conditions, parameters and calculation models. It is also intended to be well structured in order to easily replace subroutines which could eventually be improved by the user. It is written in standard FORTRAN language but a graphical interface is also available. Several tests were performed to check the ability of the code to deal with different decay schemes such as H-3, C-14, Fe-55, Mn-54 and Co-60.

HRMC: Hybrid Reverse Monte Carlo method with silicon and carbon potentials

Fortran 77 code is presented for a hybrid method of the Metropolis Monte Carlo (MMC) and Reverse Monte Carlo (RMC) for the simulation of amorphous silicon and carbon structures. In additional to the usual constraints of the pair correlation functions and average coordination, the code also incorporates an optional energy constraint. This energy constraint is in the form of either the Environment Dependent Interatomic Potential (applicable to silicon and carbon) and the original and modified Stillinger–Weber potentials (applicable to silicon). The code also allows porous systems to be modeled via a constraint on porosity and internal surface area using a novel restriction on the available simulation volume. Program summary Program title: HRMC version 1.0 Catalogue identifier: AEAO_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEAO_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 200 894 No. of bytes in distributed program, including test data, etc.: 907 557 Distribution format: tar.gz Programming language: FORTRAN 77 Computer: Any computer capable of running executables produced by the g77 Fortran compiler Operating system: Unix, Windows RAM: Depends on the type of empirical potential use, number of atoms and which constraints are employed Classification: 7.7 Nature of problem: Atomic modeling using empirical potentials and experimental data Solution method: Monte Carlo Additional comments: The code is not standard FORTRAN 77 but includes some additional features and therefore generates errors when compiled using the Nag95 compiler. It does compile successfully with the GNU g77 compiler ( http://www.gnu.org/software/fortran/fortran.html). Running time: Depends on the type of empirical potential use, number of atoms and which constraints are employed. The test included in the distribution took 37 minutes on a DEC Alpha PC.

The STATFLUX code: a statistical method for calculation of flow and set of parameters, based on the Multiple-Compartment Biokinetical Model

The code STATFLUX, implementing a new and simple statistical procedure for the calculation of transfer coefficients in radionuclide transport to animals and plants, is proposed. The method is based on the general multiple-compartment model, which uses a system of linear equations involving geometrical volume considerations. Flow parameters were estimated by employing two different least-squares procedures: Derivative and Gauss–Marquardt methods, with the available experimental data of radionuclide concentrations as the input functions of time. The solution of the inverse problem, which relates a given set of flow parameter with the time evolution of concentration functions, is achieved via a Monte Carlo simulation procedure. Program summary Title of program:STATFLUX Catalogue identifier:ADYS_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/ADYS_v1_0 Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Licensing provisions: none Computer for which the program is designed and others on which it has been tested:Micro-computer with Intel Pentium III, 3.0 GHz Installation:Laboratory of Linear Accelerator, Department of Experimental Physics, University of São Paulo, Brazil Operating system:Windows 2000 and Windows XP Programming language used:Fortran-77 as implemented in Microsoft Fortran 4.0. NOTE: Microsoft Fortran includes non-standard features which are used in this program. Standard Fortran compilers such as, g77, f77, ifort and NAG95, are not able to compile the code and therefore it has not been possible for the CPC Program Library to test the program. Memory required to execute with typical data:8 Mbytes of RAM memory and 100 MB of Hard disk memory No. of bits in a word:16 No. of lines in distributed program, including test data, etc.:6912 No. of bytes in distributed program, including test data, etc.:229 541 Distribution format:tar.gz Nature of the physical problem:The investigation of transport mechanisms for radioactive substances, through environmental pathways, is very important for radiological protection of populations. One such pathway, associated with the food chain, is the grass–animal–man sequence. The distribution of trace elements in humans and laboratory animals has been intensively studied over the past 60 years [R.C. Pendlenton, C.W. Mays, R.D. Lloyd, A.L. Brooks, Differential accumulation of iodine-131 from local fallout in people and milk, Health Phys. 9 (1963) 1253–1262]. In addition, investigations on the incidence of cancer in humans, and a possible causal relationship to radioactive fallout, have been undertaken [E.S. Weiss, M.L. Rallison, W.T. London, W.T. Carlyle Thompson, Thyroid nodularity in southwestern Utah school children exposed to fallout radiation, Amer. J. Public Health 61 (1971) 241–249; M.L. Rallison, B.M. Dobyns, F.R. Keating, J.E. Rall, F.H. Tyler, Thyroid diseases in children, Amer. J. Med. 56 (1974) 457–463; J.L. Lyon, M.R. Klauber, J.W. Gardner, K.S. Udall, Childhood leukemia associated with fallout from nuclear testing, N. Engl. J. Med. 300 (1979) 397–402]. From the pathways of entry of radionuclides in the human (or animal) body, ingestion is the most important because it is closely related to life-long alimentary (or dietary) habits. Those radionuclides which are able to enter the living cells by either metabolic or other processes give rise to localized doses which can be very high. The evaluation of these internally localized doses is of paramount importance for the assessment of radiobiological risks and radiological protection. The time behavior of trace concentration in organs is the principal input for prediction of internal doses after acute or chronic exposure. The General Multiple-Compartment Model (GMCM) is the powerful and more accepted method for biokinetical studies, which allows the calculation of concentration of trace elements in organs as a function of time, when the flow parameters of the model are known. However, few biokinetics data exist in the literature, and the determination of flow and transfer parameters by statistical fitting for each system is an open problem. Restriction on the complexity of the problem:This version of the code works with the constant volume approximation, which is valid for many situations where the biological half-live of a trace is lower than the volume rise time. Another restriction is related to the central flux model. The model considered in the code assumes that exist one central compartment (e.g., blood) that connect the flow with all compartments, and the flow between other compartments is not included. Typical running time:Depends on the choice for calculations. Using the Derivative Method the time is very short (a few minutes) for any number of compartments considered. When the Gauss–Marquardt iterative method is used the calculation time can be approximately 5–6 hours when ∼15 compartments are considered.

A package of Linux scripts for the parallelization of Monte Carlo simulations

Despite the fact that fast computers are nowadays available at low cost, there are many situations where obtaining a reasonably low statistical uncertainty in a Monte Carlo (MC) simulation involves a prohibitively large amount of time. This limitation can be overcome by having recourse to parallel computing. Most tools designed to facilitate this approach require modification of the source code and the installation of additional software, which may be inconvenient for some users. We present a set of tools, named clonEasy, that implement a parallelization scheme of a MC simulation that is free from these drawbacks. In clonEasy, which is designed to run under Linux, a set of “clone” CPUs is governed by a “master” computer by taking advantage of the capabilities of the Secure Shell (ssh) protocol. Any Linux computer on the Internet that can be ssh-accessed by the user can be used as a clone. A key ingredient for the parallel calculation to be reliable is the availability of an independent string of random numbers for each CPU. Many generators—such as RANLUX, RANECU or the Mersenne Twister—can readily produce these strings by initializing them appropriately and, hence, they are suitable to be used with clonEasy. This work was primarily motivated by the need to find a straightforward way to parallelize PENELOPE, a code for MC simulation of radiation transport that (in its current 2005 version) employs the generator RANECU, which uses a combination of two multiplicative linear congruential generators (MLCGs). Thus, this paper is focused on this class of generators and, in particular, we briefly present an extension of RANECU that increases its period up to ∼ 5 × 10 27 and we introduce seedsMLCG, a tool that provides the information necessary to initialize disjoint sequences of an MLCG to feed different CPUs. This program, in combination with clonEasy, allows to run PENELOPE in parallel easily, without requiring specific libraries or significant alterations of the sequential code. Program summary 1

Revised and extended Utilities for the Ratip package

Revised and extended Utilities for the Ratip package

Stream input/output in Fortran

Traditionally, and indeed until the advent of Fortran2003, Standard Fortran I/O has been entirely record-based. This is fine if you are reading or writing a file of records such as a text file, where each line is a record, since it means that you don't need to be concerned about the record terminators (which, depending on the platform, may be line-feeds, or carriage-returns, or both). It can, however, be a serious handicap when you want to use Fortran to read a file generated by some instrument, or produced by a package such as a spreadsheet or database system. Often these files do not have records that Fortran can recognise, or they have a more complex structure than a simple linear sequence of records, but Standard Fortran has not previously provided any means of accessing them simply as a stream of bytes or characters. Another problem is that sometimes one wants to access the records in some random order, rather than in a strict sequence. One can do this in Fortran using direct-access files, but these are restricted to files where all records have the same length. Stream I/O provides solutions to all these problems.

BOT3P: Bologna Radiation Transport Analysis Pre-Post-Processors Version 4.0

BOT3P consists of a set of standard FORTRAN-77 language programs developed at the ENEA-Bologna Nuclear Data Centre. BOT3P Version 1.0 was originally conceived to give the users of the DORT and TORT deterministic transport codes some useful diagnostic tools to prepare and check their input data files. BOT3P Version 3.0 introduced some important additions in the input geometrical model description and extended the possibility to produce the geometrical, material distribution, and fixed neutron source data to the deterministic transport codes TWODANT, THREEDANT, and PARTISN, and in the case of X-Y-Z mesh grids, a geometrical input to the MCNP Monte Carlo transport code, starting from the same input to BOT3P.BOT3P Version 4.0 extends the modeling capabilities of previous BOT3P versions, reduces CPU times, and facilitates the debugging of the computer code input. Version 4.0 also produces the geometrical entries for the sensitivity code SUSD3D, for both Cartesian and cylindrical geometries, and stores the fine-mesh arrays and the material zone map in a binary file, the contents of which can be visualized by the graphics modules of BOT3P. This new feature makes interfacing to any deterministic and Monte Carlo transport code easy and might open new promising application fields to this package.BOT3P was developed on a DIGITAL UNIX ALPHA 500/333 workstation and successfully used in some complex neutron shielding and criticality benchmarks. It was also tested on Red Hat Linux 7.1 and is designed to run on most UNIX platforms. All BOT3P versions are publicly available from the Organization for Economic Cooperation and Development/Nuclear Energy Agency Data Bank.

Software for computing eigenvalue bounds for iterative subspace matrix methods

This paper describes software for computing eigenvalue bounds to the standard and generalized hermitian eigenvalue problem as described in [Y. Zhou, R. Shepard, M. Minkoff, Computing eigenvalue bounds for iterative subspace matrix methods, Comput. Phys. Comm. 167 (2005) 90–102]. The software discussed in this manuscript applies to any subspace method, including Lanczos, Davidson, SPAM, Generalized Davidson Inverse Iteration, Jacobi–Davidson, and the Generalized Jacobi–Davidson methods, and it is applicable to either outer or inner eigenvalues. This software can be applied during the subspace iterations in order to truncate the iterative process and to avoid unnecessary effort when converging specific eigenvalues to a required target accuracy, and it can be applied to the final set of Ritz values to assess the accuracy of the converged results. Program summary Title of program: SUBROUTINE BOUNDS_OPT Catalogue identifier: ADVE Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Program summary URL: http://cpc.cs.qub.ac.uk/summaries/ADVE Computers: any computer that supports a Fortran 90 compiler Operating systems: any computer that supports a Fortran 90 compiler Programming language: Standard Fortran 90 High speed storage required: 5 m + 5 working-precision and 2 m + 7 integer for m Ritz values No. of bits in a word: The floating point working precision is parameterized with the symbolic constant WP No. of lines in distributed program, including test data, etc.: 2452 No. of bytes in distributed program, including test data, etc.: 281 543 Distribution format: tar.gz Nature of physical problem: The computational solution of eigenvalue problems using iterative subspace methods has widespread applications in the physical sciences and engineering as well as other areas of mathematical modeling (economics, social sciences, etc.). The accuracy of the solution of such problems and the utility of those errors is a fundamental problem that is of importance in order to provide the modeler with information of the reliability of the computational results. Such applications include using these bounds to terminate the iterative procedure at specified accuracy limits. Method of solution: The Ritz values and their residual norms are computed and used as input for the procedure. While knowledge of the exact eigenvalues is not required, we require that the Ritz values are isolated from the exact eigenvalues outside of the Ritz spectrum and that there are no skipped eigenvalues within the Ritz spectrum. Using a multipass refinement approach, upper and lower bounds are computed for each Ritz value. Typical running time: While typical applications would deal with m < 20 , for m = 100 000 , the running time is 0.12 s on an Apple PowerBook.

Finite element resistivity modelling for three-dimensional structures with arbitrary anisotropy

We present a three-dimensional finite element algorithm for direct current resistivity modelling. The standard Fortran code allows for nearly arbitrary conductivity structures including general anisotropy. The problem is formulated in terms of secondary potentials where mixed boundary conditions are incorporated. Also in case of anisotropy, this type of boundary condition is superior to the Dirichlet type. We have verified the finite element method using an anisotropic two-layered earth, whose analytical solutions are available. For this simple model, the algorithm achieves high accuracy. The relative deviation between numerical and analytical solution is less than 1.2%. Due to the lack of further analytical references, the responses of three representative model types serve as a cross-check for plausibility and prove the operativeness of the code.

Mie scattering by ensembles of particles with very large size parameters

We present a computer program for the simulation of Mie scattering in case of arbitrarily large size parameters. The elements of the scattering matrix, efficiency factors as well as the corresponding cross-sections, the albedo and the scattering asymmetry parameter are calculated. Single particles as well as particle ensembles consisting of several components and particle size distributions can be considered. Program summary Title of program: miex Catalogue identifier: ADUD Program summary URL: http://cpc.cs.qub.ac.uk/summaries/ADUD Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Computer for which the program is designed and others on which it has been tested: Computers: Any machine running standard FORTRAN 90; miex has been tested on an Intel Celeron processor (Redhat Linux 9.0, Intel Fortran Compiler 7.1), an Intel XEON processor (SuSE Linux 9.0, Intel Fortran Compiler 8.0), and a Sun-Blade-1000 (OS 8.5, Sun Workshop Compiler Fortran 90 2.0). Installations: standard Operating systems or monitors under which the program has been tested: Redhat Linux 9.0, SuSE Linux 9.0, Sun OS 8.5 Programming language used: Fortran 90 Memory required to execute with typical data: 1 MByte – several 100 MByte (see Appendix A for examples) No. of bits in a word: 8 No. of processors used: 1 Has the code been vectorized or parallelized?: No No. of lines in distributed program, including test data, etc.: 78 238 No. of bytes in distributed program, including test data, etc.: 1 015 805 Distributed format: tar.gz Nature of the physical problem: Among a variety of applications, Mie scattering is of essential importance for the continuum radiative transfer in cosmic dust configurations. In this particular case, Mie theory describes the interaction of electromagnetic radiation with spherical dust grains on the basis of their complex refractive index and size parameter. Both, broad grain size distributions (radii a: nanometers–millimeters) and a very wide wavelength range ( λ≈10 −10– 10 −2 m ) of the interacting radiation are considered. Previous numerical solutions to the Mie scattering problem are not appropriate to consider size parameters x=2 πa/ λ>10 4–10 5. In contrast to this, the presented code allows to consider arbitrary size parameters. It will be useful not only for applications in astrophysics but also in other fields of science (atmospheric and ocean optics, biophysics, etc.) and industry (particle sizing, ecology control measurements, etc.). Method of solution: Calculations of Mie scattering coefficients and efficiency factors as outlined by Voshchinnikov (2004), combined with standard solutions of the scattering amplitude functions. Single scattering by particle ensembles is calculated by proper averaging of the respective parameters. Restrictions on the complexity of the problem: Single scattering Typical running time: Seconds to minutes Unusual features of the program: None

BOT3P—Bologna Transport Analysis Pre-Post-Processors Version 3.0

BOT3P is a set of standard FORTRAN 77 language programs developed at the ENEA-Bologna Nuclear Data Centre. BOT3P Version 1.0 was originally conceived to give the users of the DORT and TORT deterministic transport codes some useful diagnostic tools to prepare and to check their input data files. BOT3P Version 3.0 contains some important additions in the input geometrical model description, such as “rod” and “hexagonal” geometrical objects, respecting the exact cross-sectional area value and very suitable to describe a reactor lattice in detail. Moreover, it has extended the possibility to produce the geometrical, material distribution, and fixed neutron source data for the deterministic transport codes TWODANT and THREEDANT of the DANTSYS system and for the PARTISN code too, starting from the same input to BOT3P. When users require X-Y-Z TORT/THREEDANT/PARTISN mesh grids to be generated, BOT3P Version 3.0 produces a geometrical input for the MCNP Monte Carlo transport code also, where the MCNP cells correspond to the X-Y-Z bodies created for TORT.BOT3P Version 3.0 lets users specify areas/volumes of the model where the zone/material distribution can be defined not only by a combinatorial geometry but also by an external source, such as one originated from computerized tomography scan data (only for three-dimensional applications) and from one or more external DORT/TORT input files. BOT3P was developed on a DIGITAL UNIX ALPHA 500/333 workstation and successfully used in some complex neutron shielding and criticality benchmarks. It was also tested on Red Hat Linux 7.1 and is designed to run on most UNIX platforms. All BOT3P versions are publicly available from the Organisation for Economic Co-operation and Development/Nuclear Energy Agency Data Bank (NEA-1627, NEA-1678).

Spectroscopic LSJ notation for atomic levels obtained from relativistic calculations

Today, relativistic calculations are known to provide a very successful means in the study of open-shell atoms and ions. But although accurate atomic data are obtained from these computations, they are traditionally carried out in jj-coupling and, hence, do often not allow for a simple LSJ classification of the atomic levels as needed by experiment. In fact, this lack of providing a proper spectroscopic notation from relativistic structure calculations has recently hampered not only the spectroscopy of medium and heavy elements, but also the interpretation and analysis of inner-shell processes, for which the occurrence of additional vacancies usually leads to a very detailed fine structure. Therefore, in order to facilitate the classification of atomic levels from such computations, here we present a program (within the Ratip environment) which help transform the atomic wave functions from jj-coupled multiconfiguration Dirac–Fock computations into a LS-coupled representation. Beside of a proper LSJ assignment to the atomic levels, the program also supports the full transformation of the wave functions if required for (nonrelativistic) computations. Program summary Title of program: Lsj Catalogue number: ADTL Program summary URL: http://cpc.cs.qub.ac.uk/summaries/ADTL Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Licensing provisions: None Computer for which the new version has been tested: IBM RS 6000, PC Pentium III Installations: University of Kassel (Germany) Operating systems: IBM AIX 4.1.2+, Linux 7.1.+ Program language used in the new version: ANSI standard Fortran 90/95 Memory required to execute with typical data: Memory requirements depend on the shell structure and the size of the wave function expansion which is used to represent the atomic levels No. of bits in a word: All real variables are parametrized by a selected kind parameter and, thus, can easily be adapted to any required precision as supported by the compiler. Presently, the kind parameter is set to double precision (two 32-bit words) in the module rabs_constant No. of lines in distributed program, including test data, etc.: 225 242 No. of bytes in distributed program, including test data, etc.: 3 646 630 CPU time required to execute test data: 5 s on a 1 GHz Pentium III processor Distribution format: tar gzip file Keywords: Atomic, LSJ spectroscopic notation, LS− jj transformation, multiconfiguration Dirac–Fock, recoupling of angular momenta, relativistic Nature of the physical problem: The spectroscopic LSJ notation is determined for atomic levels which were calculated previously in the framework of the jj-coupled multiconfiguration Dirac–Fock (MCDF) model. This notation is based on a complete jj− LS transformation of the leading jj-coupled configuration state functions (CSF) in the wave function representation of the selected levels. Restrictions onto the complexity of the problem: The jj→ LS transformation of the ( jj-coupled) CSF is supported for all shell structures including open s-, p-, d-, and f-shells. For shells with l>3 (i.e. beyond the f-subshells), however, a proper transformation of the antisymmetrized subshell states can be carried out only for the case of one or two equivalent electrons. This restriction also applies for the transformation of the g 7/2 and g 9/2 subshell states which are otherwise supported by the Ratip package [Fritzsche, J. Elec. Spec. Rel. Phen. 114–116 (2001) 1155]. The jj↔ LS transformation matrices, which are applied internally by the program, are consistent with the definition of the (reduced) coefficients of fractional parentage [Gaigalas et al., At. Data Nucl. Data Tables 70 (1998) 1; Gaigalas et al., At. Data Nucl. Data Tables 76 (2000) 235] as published previously. Unusual features of the program: The Lsj program is designed as a part of the Ratip package [Fritzsche, Elec. Spec. Rel. Phen. 114–116 (2001) 1155] for the computation of (relativistic) atomic transition and ionization properties. This (new) component therefore supports the transformation of all atomic states which are generated either with Ratip or by means of the Grasp92 code [Parpia et al., Comput. Phys. Comm. 94 (1996) 249]. Moreover, the normalization of the transformed states is tested within the LSJ-coupled basis.

High-performance linear algebra algorithms using new generalized data structures for matrices

We present a novel way to produce dense linear algebra factorization algorithms. The current state-of-the-art (SOA) dense linear algebra algorithms have a performance inefficiency, and thus they give suboptimal performance for most LAPACK factorizations. We show that using standard Fortran and C two-dimensional arrays is the main source of this inefficiency. For the other standard format (packed one-dimensional arrays for symmetric and/or triangular matrices), the situation is much worse. We show how to correct these performance inefficiencies by using new data structures (NDS) along with so-called kernel routines. The NDS generalize the current storage layouts for both standard formats. We use the concept of Equivalence and Elementary Matrices along with coordinate (linear) transformations to prove that our method works for an entire class of dense linear algebra algorithms. Also, we use the Algorithms and Architecture approach to explain why our new method gives higher efficiency. The simplest forms of the new factorization algorithms are a direct generalization of the commonly used LINPACK algorithms. On IBM platforms they can be generated from simple, textbook-type codes by the XLF Fortran compiler. On the IBM POWER3 processor, our implementation of Cholesky factorization achieves 92% of peak performance, whereas conventional SOA full-format LAPACK DPOTRF achieves 77% of peak performance. All programming for our NDS can be accomplished in standard Fortran through the use of three- and four-dimensional arrays. Thus, no new compiler support is necessary. Finally, we describe block hybrid formats (BHF). BHF allow one to use no additional storage over conventional (full and packed) matrix storage. This means that new algorithms based on BHF can be used as a backward-compatible replacement for LAPACK or LINPACK algorithms.

PII: S0045-7825(02)00548-0

PHAST is a software package written in standard Fortran, with MPI and CUDA extensions, able to efficiently perform parallel multicanonical Monte Carlo simulations of single or multiple heteropolymeric chains, as coarse-grained models for proteins. The outcome data can be straightforwardly analyzed within its microcanonical Statistical Thermodynamics module, which allows for computing the entropy, caloric curve, specific heat and free energies. As a case study, we investigate the aggregation of heteropolymers bioinspired on Aβ25−33 fragments and their cross-seeding with IAPP20−29 isoforms. Excellent parallel scaling is observed, even under numerically difficult first-order like phase transitions, which are properly described by the built-in fully reconfigurable force fields. Still, the package is free and open source, this shall motivate users to readily adapt it to specific purposes.Program summaryProgram Title: PHASTProgram Files doi: http://dx.doi.org/10.17632/ggds2grzw9.1 Licensing provisions: GNU GPL version 3Programming language: FORTRAN 90, MPICH 3.0.4, CUDA 8.0Nature of the problem: Nowadays powerful multicore processors (CPUs) and Graphical Processing Units (GPUs) became much popular and cost-effective, so enabling thermostatistical studies of complex molecular systems to be performed even in personal computers. PHAST provides not only an easily-reconfigurable parallel program for Monte Carlo simulations of linear heteropolymers, as coarse-grained models of proteins, but also permits the automatized microcanonical thermodynamic analysis of those systems.Solution method: PHAST has three main modules for complementary tasks as: to map any .pdb file-sequence to its inner lexicon by using a configurable hydrophobic scale, while the main simulational module performs parallel Monte Carlo simulations in the multicanonical (MUCA) ensemble and, the analysis module which extracts microcanonical observables from MUCA weights.External routines/libraries: cuRAND (CUDA), Grace-5.1.22 or higher.