Orca 5.0.3 Citation
Jesper Sahu
ORCA is a general-purpose quantum chemistry program package that features virtually all modern electronic structure methods (density functional theory, many-body perturbation and coupled cluster theories, and multireference and semiempirical methods). It is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules. It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- and multireference correlated ab initio methods. It can also treat environmental and relativistic effects.
ORCA uses standard Gaussian basis functions and is fully parallelized. Due to the user-friendly style, ORCA is considered to be a helpful tool not only for computational chemists, but also for chemists, physicists and biologists that are interested in developing the full information content of their experimental data with help of calculations.
ORCA is able to carry out geometry optimizations and to predict a large number of spectroscopic parameters at different levels of theory. Besides the use of Hartee Fock theory, density functional theory (DFT) and semiempirical methods, high level ab initio quantum chemical methods, based on the configuration interaction and coupled cluster methods, are included into ORCA to an increasing degree.
ORCA is released as precompiled binaries at no cost for academic research use. User should read and agree the license terms on ORCA End Users License Agreement and is expected to register with the ORCA developers in the official forum.
Parallel version of ORCA is installed in our HPC cluster system. It can be run in either single-core or parallel (MPI) mode. ORCA requires MPI even for communication between cores on a single node. Single core operations do not require any specifics. For MPI mode, you should give the number of processes in the ORCA input file:
The efficiency is such that for RI-DFT perhaps up to 20 processors are a good idea while for hybrid DFT and Hartree-Fock a few more processors are appropriate. Above this, the overhead becomes signicant and the parallelization loses efficiency. Coupled cluster calculations usually scale well up to at least 8 processors but probably it is also worthwhile to try 20. For Numerical Frequencies or Gradient runs it makes sense to use as many processors as 3*Number of Atoms.
To allow easy use of ORCA, we have prepared sample SLURM command file and ORCA input files for your reference. Explanation is embedded in these files. These sample files could be obtained at /share1/orca/sample/.
OrcaArtworkModelTWWTWWTWWHDRaceHylianGenderMale[1]Main appearance(s)The Wind WakerEra(s)Era of the Great SeaFamily
- Sturgeon (brother)[citation needed]
- Sue-Belle (grand-niece)[citation needed]
Orca lives on Outset Island on the ground floor of a house he shares with his older brother Sturgeon and great-niece Sue-Belle.[6] Orca does not get along well with his older brother, who considers Orca a "hooligan" for preferring martial arts to book study.[6][7] Orca has a calm disposition and thinks his brother is high-strung.[8]
At the beginning of The Wind Waker, Orca offers to teach Link basic sword techniques using the Hero's Sword. However, he refuses to give Link a sword for fear of upsetting Link's Grandma.[9] He refuses no matter how many times Link completes the tutorial and continues to insist Link must practice more.[10] Orca is unaware of Tetra's fall into the Fairy Woods when Link returns for practice, but the swordsman senses a change that prompts him to give Link the Hero's Sword.[11]
Upon Link's return to Outset Island later in the game, Orca remarks that he has changed.[12] Orca asks Link to show him how much his skills have improved.[13] If Link accepts, a mini-game begins in which Link must strike Orca as many times as he can before Orca strikes him three times.[14] Before starting, Orca taunts Link, stating that his skill level is only that of a page.[15]
If Link hits Orca 100 times before being hit three, Orca declares him to be a knight,[16] and gives him a Purple Rupee. 300 hits convinces Orca to give Link an Orange Rupee and increase his rank to "swordsman".[17] For 500 hits, he gives Link a Piece of Heart.
At 1000 hits, Orca loses count and ends the battle. He gives the young hero a Silver Rupee and calls him Master Link from then on.[18] He remarks that his arm feels numb, and asks Link if his left index finger is numb too.[19] This is a fourth-wall-breaking reference to the prolonged holding of the L-Target that is required if the Targeting Mode is left to the default "Hold".
If struck outside a training context, Orca automatically blocks the strike with his spear. He expresses annoyance when Link strikes him three times,[20] and again more pointedly after five times.[21] On the sixth strike, he yells at Link to stop and knocks him down.[22]
In their youth, Orca and Sturgeon longed to learn the Hurricane Spin. They spent several years collecting the requisite Knight's Crests, but grew old before they could gather the ten needed to learn the secret technique.[23][24]
After Link departs from Outset Island,[when?] Orca sends him a Letter with instructions to bring back Knight's Crests.[25] When Link presents 10 Knight Crests to Orca, he teaches Link the Hurricane Spin technique that he and Sturgeon were never able to master. Orca drops his spear and cries tears of joy at having his long-held dream come true.[26] Orca will then say that there is no longer anything left for him to teach Link,[27] and expresses his certainty that Link will be successful in his quest to save Aryll and bring her home to Outset Island.[28]
The first time Link shows Orca Knight's Crests, Orca drops his spear. If Link has less than 10, he is then able to attack Orca while he is without his spear. Orca will still block the attack, defending himself with only his hands and legs.
Managing endangered species often involves evaluating the relative impacts of multiple anthropogenic and ecological pressures. This challenge is particularly formidable for cetaceans, which spend the majority of their time underwater. Noninvasive physiological approaches can be especially informative in this regard. We used a combination of fecal thyroid (T3) and glucocorticoid (GC) hormone measures to assess two threats influencing the endangered southern resident killer whales (SRKW; Orcinus orca) that frequent the inland waters of British Columbia, Canada and Washington, U.S.A. Glucocorticoids increase in response to nutritional and psychological stress, whereas thyroid hormone declines in response to nutritional stress but is unaffected by psychological stress. The inadequate prey hypothesis argues that the killer whales have become prey limited due to reductions of their dominant prey, Chinook salmon (Oncorhynchus tshawytscha). The vessel impact hypothesis argues that high numbers of vessels in close proximity to the whales cause disturbance via psychological stress and/or impaired foraging ability. The GC and T3 measures supported the inadequate prey hypothesis. In particular, GC concentrations were negatively correlated with short-term changes in prey availability. Whereas, T3 concentrations varied by date and year in a manner that corresponded with more long-term prey availability. Physiological correlations with prey overshadowed any impacts of vessels since GCs were lowest during the peak in vessel abundance, which also coincided with the peak in salmon availability. Our results suggest that identification and recovery of strategic salmon populations in the SRKW diet are important to effectively promote SRKW recovery.
This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.
Funding: This work has been funded by the National Oceanic and Atmospheric Administration-Northwest Fisheries Science Center, the Joint Institute for the Study of the Atmosphere and Ocean, Washington Sea Grant No. NA10OAR417005, the Canadian Consulate General, Northwest Science Association, University of Washington Department of Biology, Lynn Riddiford and Jim Truman, Elizabeth Welch and the Center for Conservation Biology. M.J. Ford, M.B. Hanson, J. Hempelmann, and C. Emmons are employees of Northwest Fisheries Science Center. All authors were involved in the preparation of the manuscript. M.B. Hanson, J. Hempelmann, and C. Emmons were involved in data collection and analysis. K.L. Ayres, R.K. Booth are employees with the Center for Conservation Biology, a nonprofit directed by S.K. Wasser. K.L. Ayres and S.K. Wasser designed the study, applied for funding, collected data and did most of the analysis, decision to publish and preparation of the manuscript. R.K. Booth was involved in study design/methods and data analysis. The other funding agencies had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing interests: Authors Michael J. Ford and M. Bradley Hanson were partially responsible for funding decisions from Northwest Fisheries Science Center. Washington SeaGrant is also administered by NOAA, however the NOAA employees that are authors on this paper were not directly involved with SeaGrant funding decisions. Funding from this agency was a major part of funding this research. Authors Katherine Ayres, Rebecca Booth and Samuel Wasser work for the Center for Conservation Biology, which also partially funded this work. Author Kari Koski is an employee for the Soundwatch Boater Education program that provided the vessel traffic data for this research. Soundwatch is a boater education program that often consults on vessel regulations decisions based on their monitoring research. This does not alter the authors' adherence to all the PLoS ONE policies on sharing data and materials.
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