dataesr/scientific-paragraphs-categorization huggingface dataset:
330 One of the software solutions for coupling of geophysical models is the OASIS coupler, which is widely used in the climate modeling community (see for example  Valcke (2013)  and  Maisonnave et al. (2013) ). Its latest fully parallelized version, OASIS3-MCT version 2. 0  (Valcke et al. , 2013) , proved its efficiency for high-resolution quasi-global models on top-end supercomputers  (Masson et al. , 2012).
The OASIS3-MCT coupling method OASIS3-MCT consists of a FORTRAN Application Programming Interface (API), whose subroutines have to be added in all coupled-system components. The part of the program in which the 340 OASIS3-MCT API routines are located is called component interface. There is no independent OA-SIS executable anymore, as was the case with OASIS3. With OASIS3-MCT every communication between the model components is directly executed via the Message Passing Interface (MPI) library. This significantly improves the performance over OASIS3, because the bottleneck due to the sequential separate coupler is entirely removed as shown e. g. in  Gasper et al. (2014).
Multiple usage of the MCT library occured in the CCLM+CLM coupled system implementation making some modifications of the OASIS3-MCT version 2. 0 necessary. Since the MCT library has no re-entrancy properties, a duplication of the MCT library and a renaming of the OASIS3-MCT calling instruction were necessary. This modification ensures the capability of coupling any other CESM component via OASIS3-MCT. The additional usage of the MCT library occured in the CESM framework of CLM version 4. 0. More precisely, the DATM model interface in the CESM module is using the CPL7 coupler including the MCT library for data exchange. Interpolation of 3D fields is necessary in an atmosphere-to-atmosphere coupling. The OASIS3-MCT library is used to provide 3D boundary conditions to the regional model and a 3D feedback to the global coarse-grid model.
CCLM+VEG3D and CCLM+CLM 650 The two-way coupling between COSMO-CLM and the land surface models VEG3D or CLM is similar to the other in several respects. First, the call to the LSM (OASIS send and receive; see Fig. 8 ) is placed at the same location in the code as the call to COSMO-CLM's native land surface scheme, TERRA_ML, which is switched off when either VEG3D or CLM is used. This ensures that the sequence of calls in COSMO-CLM remains the same regardless of whether TERRA_ML, VEG3D 655 or CLM is used. In the default configuration used here COSMO-CLM and CLM (or VEG3D) are executed sequentially, thus mimicking the "subroutine"-type of coupling used with TERRA_ML. Note that it is also possible to run COSMO-CLM and the LSM concurrently but this is not discussed here. Details of the time step organization of VEG3D and CLM are described in the appendix and shown in Fig.
Computational efficiency Optimising the performance of a coupled model system can save a substantial amount of resources 685 in terms of simulation time or costs. Sometimes, it is even a prerequisite for the applicability of a model system at higher resolutions or on climatological time scales. There are two main goals of a performance analysis: (1) To identify code patterns of inefficient behaviour in parallel applications for a given resources configuration by using sophisticated tools such as e. g. SCALASCA  (Geimer et al. , 2010)  and VampirTrace  (Müller et al. , 2008). (  2 ) To analyze the scalability of a coupled model 690 system and its components in order to obtain an optimum configuration of resources. The second is the subject of this chapter. For this purpose the Load-balancing Utility and Coupling Implementation Appraisel (LUCIA), developed at CERFACS, Toulouse, France  (Maisonnave and Caubel, 2014)  is used, which is available together with the OASIS3-MCT coupler.
Direct coupling costs The CCLM+MPI-ESM coupling is one of the most intensive couplings that has up to now been realized with OASIS3(-MCT) in terms of number of coupling fields and coupling time steps: 450 2D fields are exchanged every ECHAM coupling time step, that is, every ten minutes (see section 935 3. 2). Most of these 2D fields are levels of 3D atmopsheric fields. We show in this section that a conscious choice of coupling software and computing platform features can have a significant impact on simulation speed and costs. To make the CCLM+MPI-ESM coupling more efficient, all levels of a 3D variable are sent and received in one MPI message using the concept of pseudo-3D coupling as described in section 3. 1. 2, 940 reducing the number of sent and received fields (see Table  4 ). The change from 2D to pseudo-3D coupling lead to a decrease of the costs of the coupled system by 3.
Additionally, there is the possibility to use COSMO-ART  (Vogel et al. , 2009) , which enables the calculation of transports of trace gases, aerosol and their interaction with atmospheric radiation and each other (atmospheric chemistry). Other regional processes in the climate system like ocean and ice sheet dynamics, plant responses, aerosol-cloud interaction, and the feedback to the GCM driving the RCM is made available by coupling COSMO-CLM via OASIS3-MCT with other models. The development of fully coupled COSMO-CLM is an ongoing research project within the CLM-Community. The COSMO-CLM model source code is freely available for scientific usage by members of the CLM-Community. The CLM-Community (www. clm-community. eu) is a network of scientists who accept the CLM-Community agreement. To become a member, please contact the CLM-Community coordination office at DWD, Germany (clm-coordination@dwd.
The time loop of TRIMNP covers a grid loop in which several grids on higher resolutions are potentially one-way nested for specific sub-regions with rather complex bathymetry, e. g. Katte-1160 gat of the North Sea. Note that for the coupling, only the first/main grid is applied. The grid loop begins with rcv_parent_data that sends data from the coarser grid to the nested grid. Then, do_update updates the forcing data passed from COSMO-CLM and CICE as well as the lateral boundary data are read from files. After updating, the physics and dynamics computations are mainly done in heat_flux, turbo_adv, turbo_gotm, do_constituent, do_explicit 1165 and do_implicit. At the end of the grid loop, the main grid sends data to the finer grid by calling snd_parent_data if necessary. At the end of each time step, output and restart data are written to files.
Eventually, stop_mpp is called at the end of the main program to de-allocate the memory of all variables and finalize the program. The time loop of CICE has two main parts. In the first part ice_step, physical, dynamical 1170 and thermo-dynamical processes of the time step t = t n are mainly computed in step_therm1, step_therm2, step_radiation, biogeochemistry and step_dynamics, followed by write_restart and final_restart for writing the output and restart files. Then, the time step is increased to a new time step t = t n+1 , followed by an update of forcing data from COSMO-CLM and TRIMNP via ice_receive_fld if necessary and a sending of fields to COSMO-1175 CLM and TRIMNP via ice_send_fld. At the end of the time loop, all file units are released in release_all_fileunits and oas_ice_finalize concludes the main program.
A6 CLM CLM is embedded within the CESM modelling system and its multiple components. In the case of land-only simulations, the active components are the driver/internal coupler (CPL7), CLM and a data atmosphere component. The later is substituted to the atmospheric component used in coupled mode 1195 and provides the atmospheric forcing usually read from a file. In the framework of the OASIS3-MCT coupling, however, the file reading is deactivated and replaced by the coupling fields received from OASIS3-MCT (receive_field_2cos). The send operation (send_field_2cos) is also positioned in the data atmosphere component in order to enforce the same sequence of calls as in CESM. The definition of coupling fields and grids for the OASIS3-MCT coupling is also done in.
1180 wards, the model setup is specified by reading the VEG3D namelist and by loading external landuse and soil datasets. The definition of the grid and the coupling fields is done in oas_veg3d_define. The main program includes two time loops. In the first time loop vegetation parameters are calculated for every simulated day. In the second loop (over the model time steps) the coupling fields from COSMO-CLM are received via OASIS3-MCT in receive_fld_2cos at every coupling 1185 34 Geosci. Model Dev. Discuss. , doi:10. 5194/gmd-2016-47, 2016 Manuscript under review for journal Geosci. Model Dev. Published: 20 April 2016 c Author(s) 2016. CC-BY 3. 0 License. time step. Using these updated fields the energy balance of the canopy for the current time level t n is solved iterativly and based on this the latent and sensible heat fluxes are calculated.
The Virtual Atomic and Molecular Data Centre (VAMDC) Consortium is a worldwide consortium which federates atomic and molecular databases through an e-science infrastructure and an organisation to support this activity. About 90% of the inter-connected databases handle data that are used for the interpretation of astronomical spectra and for modelling in many fields of astrophysics. Recently the VAMDC Consortium has connected databases from the radiation damage and the plasma communities, as well as promoting the publication of data from Indian institutes. This paper describes how the VAMDC Consortium is organised for the optimal distribution of atomic and molecular data for scientific research. It is noted that the VAMDC Consortium strongly advocates that authors of research papers using data cite the original experimental and theoretical papers as well as the relevant databases.
Introduction The Virtual Atomic and Molecular Data Centre (VAMDC) Consortium originates from two European funded projects: the VAMDC (http://www. vamdc-project. vamdc. eu/) Dubernet et al 2010 and the SUP@VAMDC (http:// www. sup-vamdc. vamdc. org/) (Zwölf et al 2014)  projects. The main scientific outcomes of these projects are: (1) An e-science infrastructure that interconnects about 30 databases (http://www. vamdc. eu/activities/research); (2) An overarching organisation: 'the VAMDC Consortium' that was launched 1 November 2014 and currently involves 35 groups, 19 of them having signed a memorandum of understanding (http://www. vamdc. org/structure/how-to-join-us/). Original content from this work may be used under the terms of the Creative Commons Attribution 3. 0 licence. Any further distribution of this work must maintain attribution to the author(s) and the title of the work, journal citation and DOI.
VAMDC Consortium activities cover four domains: research, which is the most developed domain, education and industry that are currently in their early development stage, and outreach activities. To facilitate its implementation VAMDC has developed protocols, data structures and query languages to allow disparate but complementary databases to be both interrogated simultaneously and to be utilised in a synchronised manner. This article describes the current status of the VAMDC including a description of the databases participating in this project. The data centre provides particularly comprehensive coverage of laboratory atomic and molecular physics data required for astrophysics studies. VAMDC therefore provides a unique access point for astronomers seeking the best atomic and molecular data for their studies.
Research services VAMDC offers a common entry point to all incorporated databases through the VAMDC portal(http://portal. vamdc. eu). This portal is flexibly designed offering the possibility of including new data and new databases within the VAMDC e-infrastructure, as well as providing software libraries and modules that can be included in the user's own programs, and providing stand-alone user-oriented software that retrieves and handles atomic and molecular data. Figure  1  depicts the structure of the VAMDC e-infrastructure.
XSAMS is an XML implementation of the VAMDC data model which is used to build the computer framework. The processes being represented by XSAMS are essentially quantum-mechanical in nature. XSAMS provides a standard approach to the description of atomic and molecular (A+M) physics in terms of physical processes connecting different quantum-states of atoms and molecules. The identification of the states is standardised by XSAMS to promote matching of corresponding states between databases. Several levels of detail are supported by XSAMS for the description of states and a range of coupling schemes may be specified. States of molecules are identified by tuples of the most-relevant quantum numbers, different tuples being specified in XSAMS for different classes of molecules. XSAMS describes both radiative and collisional transitions between states.
VAMDC connected databases Each database included in VAMDC may be interrogated individually by software via its own web-service, but these services conform strictly to the VAMDC standards and all use the same query protocol and language; thus, it is easy to send the same query to multiple databases. The query protocol is called VAMDC-TAP 44  , derived from the table Access Protocol of the International Virtual Observatory Alliance, and the query language is VAMDC SQL Sub-set 2 (VSS2) 45 , a limited form of structured query language tailored to suit the VAMDC data-model inherent in XSAMS. The combination of a service and a database is called a 'VAMDC data-node' and is achieved by building a small program, specific to the database and running inside a web server, to represent the database and to convert between internal and external representations of the data.
Such a program is called 'node software' and almost all the code for it is provided by VAMDC as a standard library; only minor customisation is needed for each database. Support is provided by VAMDC for building new data-nodes. The VAMDC nodes are distributed such that they are located at themembers' and partners' sites. At present most of the databases included in the VAMDC e-infrastructure are key databases used in astrophysics. Table  1  provides a summary of the databases currently accessible via VAMDC which are each discussed in turn below.
Database of species Many queries select by atomic and molecular species, and the names for species vary between scientific communities. VAMDC maintains a database of names, called the 'species database' from which community-specific terms may be refined into standard identifiers understood by all VAMDC nodes. VAMDC identifiers are based on InChIkeys  (Heller et al 2015). In most cases, the VAMDC identifier is just the standard InChIkey, but in special cases a suffix is added to distinguish molecular conformers. One copy of the species database is encapsulated in the web portal. Another copy is available for query by applications as a VAMDC data-node. We have designed software which updates the species database when a new species is introduced in any of the VAMDCconnected databases. Copies of the Species Database are distributed to user client software to allow the same query capability as the portal.
CHIANTI CHIANTI (www. chiantidatabase. org), first released in 1996  (Dere et al 1997) , is a well-established atomic database for ions of astrophysical importance. Combined with spectroscopic diagnostic programs, it is used in the analysis of optically thin collisionally ionised plasmas. The CHIANTI database contains atomic structure data (experimental and calculated wavelengths and radiative data), and rates for electron and proton collisions, as well as for ionisation and recombination. The data are mostly obtained from published literature, and are regularly assessed and updated. The latest version 8 of CHIANTI (Del Zanna et al 2015), contains a large number of new atomic data for several isoelectronic sequences, calculated within the UK atomic processes in astrophysical plasmas (APAP) network (www.
apap-network. org). APAP/CHIANTI data are used world-wide by almost all atomic databases and modelling codes for astrophysical plasmas. For example, by the modelling codes for photoionised plasmas such as Cloudy  (Ferland et al 2013)  and MOCASSIN  (Ercolano et al 2008) ; by modelling codes for the x-rays such as PINTofALE  (Kashyap and Drake 2000)  and ISIS  (Houck and Denicola 2000) ; hydrodynamic codes such as HYDRAD  (Bradshaw and Mason 2003)  and RADYN  (Allred et al 2015) ; spectral modelling of supernovae such as TARDIS  (Kerzendorf and Sim 2014) ; and atomic databases such as XSTAR  (Bautista and Kallman 2001) , Stout  (Lykins et al 2015) , ATOMDB  (Smith et al 2001). The CHIANTI basic data is available via VAMDC, and version 8 is being added.
NIST atomic spectra database (NIST ASD) The NIST ASD athttp://www. nist. gov/pml/data/asd. cfm contains critically evaluated standard reference data on energy levels, spectral lines, and radiative transitions in atoms and ions of 110 elements from H to Ds. As of November 2015, ASD offers detailed information on more than 109 000 levels and 250 000 spectral lines, in particular, level identifications (configurations, terms, total angular momentum, etc) and radiative decay rates for almost 100 000 transitions. All data in ASD are carefully analysed and evaluated and proper uncertainties for numerical values are derived. ASD also offers several graphical data manipulation tools, e. g. , dynamic Grotrian diagrams and Saha-local thermodynamic equilibrium spectra, as well as spectroscopic diagnostic information for ions of several astrophysically abundant elements.
Spectr-W 3 The Spectr-W 3 project is the collaboration between the Russian Federal Nuclear Centre All-Russian Institute of Technical Physics (RFNC VNIITF) and the Joint Institute for High Temperatures of the Russian Academy of Sciences (JIHT RAS). The information accumulated in the Spectr-W 3 (Faenov et al 2002) atomic database contains over 450 000 records and includes experimental and theoretical data on ionisation potentials, energy levels, wavelengths, radiation transition probabilities, oscillator strengths, and (optionally) parameters providing analytical approximations for electroncollisional cross-sections and rates for atoms and ions. These  data were extracted from the scientific literature or provided directly by authors. The information is supplied with references to the original sources and comments, elucidating the details of experimental measurements or calculations, where necessary and available.
At the present time, Spectr-W 3 is the largest available database providing information on the spectral properties of multicharged ions. A new development of the Spectr-W 3 atomic database started in 2014 will create a new section containing information on x-ray emission spectrograms recorded at various plasma sources. Software for this section is currently being created and tested. The spectrograms, mostly obtained in the laser-produced-plasma experiments are also in preparation. Spectr-W 3 is hosted at http://spectr-w3. snz. ru/.
TIPbase-TOPbase Atomic data calculated within the framework of the international opacity project (OP) and iron project (IP) are available in TOPbase (the OP database for radiative processes)  (Seaton 1987 , Cunto and Mendoza 1992 , Cunto et al 1993)  and TIPbase (the IP database, for collisional and radiative processes)  (Hummer et al 1993). Included are energy levels/ terms, radiative transitions probabilities, photoionisation cross sections and collision strengths for a large selection of ions in the range H to Ni. These theoretical data have been calculated using state-of-the-art computer programs such as various versions of the R-matrix suite of codes  (Berrington et al 1995, Berrington and Ballance 2002) , superstructure  (Eissner et al 1974)  and autostructure  (Badnell 2011)  or CIV3  (Hibbert 1975 , Hibbert et al 1991).
Stark-B The Stark-B (Sahal-Bréchot et al 2015) database is a collaborative project between the Laboratoire d'Etude du Rayonnement et de la matire en Astrophysique and the Astronomical Observatory of Belgrade. The database contains calculated widths and shifts of isolated lines of atoms and ions due to electron and ion collisions (Stark broadening parameters), calculated in a series of papers by Dimitrijevi'c, Sahal-Br'echot and their co-workers, using the semiclassical-perturbation approach developed by  Sahal-Bréchot (1969a , 1969b , 1974)  supplemented by  Fleurier et al (1977) , and updated by  Dimitrijević and Sahal-Bréchot (1984)  and in subsequent papers (see  Dimitrijević and Sahal-Bréchot 2014). The database's principal purpose is to provide the Stark broadening data needed for the modelling and spectroscopic diagnostics of stellar atmospheres and envelopes but it is also useful for laboratory plasmas, as well as for laser produced, fusion and technological plasmas.
Cologne database for molecular spectroscopy (CDMS) The CDMS  (Mueller et al 2005)  provides transition frequencies of atoms and molecules mostly for radio astronomical observations. The included species have been or may be observed in the interstellar medium (ISM), in the circumstellar envelopes (CSEs) of very young and very old stars, or in planetary atmospheres. As of October 2015, 789 species are available which refer not only to the main isotopic species and the ground vibrational state, but also to minor isotopic species and excited vibrational states as far as these may be of interest for radio astronomers. The catalogue is similar to that of the Jet Propulsion Laboratory (Pickett et al 1998 and while duplication is avoided, nevertheless, some overlap exists. CDMS welcomes outside contributions after critical evaluation.
HITRAN The HITRAN database (Rothman et al 2013) is a longstanding compilation of molecular spectroscopic parameters that are required for radiative-transfer codes. This latest edition of HITRAN has a traditional line-by-line high resolution section that contains essential spectral parameters for 47 molecules along with their significant isotopologues appropriate for the terrestrial atmospheric and diverse room temperature applications. There is a section that contains highresolution experimental cross-sections for so-called heavy molecules, including, for example, the chlorofluorocarbons and halocarbons, that are not amenable to full quantummechanical description as in the traditional part of HITRAN. There is also a section of the compilation that provides collision-induced absorption cross-sections.
Spectroscopy and molecular properties of ozone (SMPO) SMPO is an information system  (Babikov et al 2014)   O. The line parameters (line position, line intensity, energy of lower state, air-broadening coefficient, self pressure-induced broadening coefficient and exponent of temperature dependence of air broadening coefficients) have calculated values. The CDSD-296 databank covers the 5. 9-12784. 1 cm -1 spectral range and contains more than 419600 lines. This line list was generated using an intensity cutoff of 10 -30 cm/molecule at a reference temperature of 296 K. Recently the CDSD-296 databank  (Tashkun et al 2015)  has been extended to include all 12 stable carbon dioxide isotopologues, and the full database will be available through the VAMDC portal in 2016. The CDSD-1000 databank  (Tashkun et al 2003)  covers the spectral range 257-9648 cm -1 and contains more than 3950 500 lines.
ExoCross The ExoMol project  (Tennyson and Yurchenko 2012)  provides computed line lists for molecules likely to be of importance in hot atmospheres such as those of extrasolar planets and cold stars. Because of the elevated temperatures in these environments, a very large number of transitions must be included in spectral simulations: up to 10 11 lines in some cases. To ease the computational burden involved in the calculation of opacities (which in many practical cases are not required at high resolution), ExoMol provides pre-calculated absorption cross sections  (Hill et al 2013)  at a range of temperatures through a service on the project website (http:// www. exomol. com/xsecs/). The ExoMol database has just undergone a comprehensive upgrade to its data structures  (Tennyson et al 2016).