{"id":"https://openalex.org/W2160779294","doi":null,"title":"The development and expansion of HOOMD-blue through six years of GPU proliferation","display_name":"The development and expansion of HOOMD-blue through six years of GPU proliferation","publication_year":2013,"publication_date":"2013-08-26","ids":{"openalex":"https://openalex.org/W2160779294","mag":"2160779294"},"language":"en","primary_location":{"id":"mag:2160779294","doi":null,"is_oa":true,"landing_page_url":"https://arxiv.org/pdf/1308.5587.pdf","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"arXiv (Cornell University)","raw_type":null},"volume":null,"type":"preprint","is_traditional":true,"indexed_in":[],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/1308.5587.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5111685523","display_name":"Joshua A. Anderson","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Joshua A. Anderson","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5045900230","display_name":"Sharon C. Glotzer","orcid":"https://orcid.org/0000-0002-7197-0085","observed_orcids":["https://orcid.org/0000-0002-7197-0085"]},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sharon C. Glotzer","raw_affiliation_strings":["\u2020University of Michigan"],"raw_orcid":"https://orcid.org/0000-0002-7197-0085","affiliations":[{"raw_affiliation_string":"\u2020University of Michigan","institution_ids":["https://openalex.org/I27837315"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":19,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10054","display_name":"Parallel Computing and Optimization Techniques","score":0.9872999787330627,"subfield":{"id":"https://openalex.org/subfields/1708","display_name":"Hardware and Architecture"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10054","display_name":"Parallel Computing and Optimization Techniques","score":0.9872999787330627,"subfield":{"id":"https://openalex.org/subfields/1708","display_name":"Hardware and Architecture"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10481","display_name":"Computer Graphics and Visualization Techniques","score":0.005200000014156103,"subfield":{"id":"https://openalex.org/subfields/1704","display_name":"Computer Graphics and Computer-Aided Design"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.002300000051036477,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/hoomd-blue","display_name":"HOOMD-blue","score":1.0},{"id":"https://openalex.org/keywords/gpu-acceleration","display_name":"GPU acceleration","score":0.906000018119812},{"id":"https://openalex.org/keywords/molecular-dynamics-simulation","display_name":"molecular dynamics simulation","score":0.6370000243186951},{"id":"https://openalex.org/keywords/soft-matter","display_name":"soft matter","score":0.7250000238418579},{"id":"https://openalex.org/keywords/force-fields","display_name":"force fields","score":0.7839999794960022},{"id":"https://openalex.org/keywords/integrator","display_name":"integrator","score":0.7580000162124634},{"id":"https://openalex.org/keywords/open-source-software","display_name":"open source software","score":0.6039999723434448},{"id":"https://openalex.org/keywords/python-scripting","display_name":"Python scripting","score":0.6190000176429749},{"id":"https://openalex.org/keywords/object-oriented-design","display_name":"object-oriented design","score":0.7390000224113464},{"id":"https://openalex.org/keywords/performance-optimization","display_name":"performance optimization","score":0.6430000066757202},{"id":"https://openalex.org/keywords/simulation-kernel","display_name":"simulation kernel","score":0.41499999165534973},{"id":"https://openalex.org/keywords/software-history","display_name":"software development history","score":0.4959999918937683}],"concepts":[{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.8833334445953369},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7369896173477173},{"id":"https://openalex.org/C61423126","wikidata":"https://www.wikidata.org/wiki/Q187432","display_name":"Scripting language","level":2,"score":0.7120122313499451},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.5056314468383789},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.5001699924468994},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.490567147731781},{"id":"https://openalex.org/C50630238","wikidata":"https://www.wikidata.org/wiki/Q971505","display_name":"General-purpose computing on graphics processing units","level":3,"score":0.4802701473236084},{"id":"https://openalex.org/C169590947","wikidata":"https://www.wikidata.org/wiki/Q47506","display_name":"Compiler","level":2,"score":0.42428433895111084},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.3443586230278015},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.32582634687423706},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.3254087567329407},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.31114286184310913},{"id":"https://openalex.org/C21442007","wikidata":"https://www.wikidata.org/wiki/Q1027879","display_name":"Graphics","level":2,"score":0.0867963433265686},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"mag:2160779294","doi":null,"is_oa":true,"landing_page_url":"https://arxiv.org/pdf/1308.5587.pdf","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"arXiv (Cornell University)","raw_type":null}],"best_oa_location":{"id":"mag:2160779294","doi":null,"is_oa":true,"landing_page_url":"https://arxiv.org/pdf/1308.5587.pdf","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"arXiv (Cornell University)","raw_type":null},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":69,"referenced_works":["https://openalex.org/W1566375238","https://openalex.org/W1593902291","https://openalex.org/W1919509928","https://openalex.org/W1963753250","https://openalex.org/W1967101381","https://openalex.org/W1968611891","https://openalex.org/W1972758026","https://openalex.org/W1982852233","https://openalex.org/W1984096850","https://openalex.org/W1986677755","https://openalex.org/W1988054515","https://openalex.org/W1989619262","https://openalex.org/W1990499321","https://openalex.org/W1990848505","https://openalex.org/W1995010320","https://openalex.org/W1995081305","https://openalex.org/W1996528487","https://openalex.org/W2000370753","https://openalex.org/W2001510804","https://openalex.org/W2004822259","https://openalex.org/W2006071024","https://openalex.org/W2010594128","https://openalex.org/W2010727979","https://openalex.org/W2019465613","https://openalex.org/W2022047513","https://openalex.org/W2030307856","https://openalex.org/W2034699949","https://openalex.org/W2035720425","https://openalex.org/W2036277048","https://openalex.org/W2041658612","https://openalex.org/W2044028691","https://openalex.org/W2046855636","https://openalex.org/W2048621586","https://openalex.org/W2049599954","https://openalex.org/W2050624723","https://openalex.org/W2056896797","https://openalex.org/W2057573569","https://openalex.org/W2062797706","https://openalex.org/W2063446784","https://openalex.org/W2064742217","https://openalex.org/W2070532360","https://openalex.org/W2076876335","https://openalex.org/W2077139454","https://openalex.org/W2078391824","https://openalex.org/W2078713630","https://openalex.org/W2079411557","https://openalex.org/W2082516877","https://openalex.org/W2087902004","https://openalex.org/W2091848301","https://openalex.org/W2094250408","https://openalex.org/W2097650833","https://openalex.org/W2100597169","https://openalex.org/W2114239896","https://openalex.org/W2118438578","https://openalex.org/W2130162426","https://openalex.org/W2144574395","https://openalex.org/W2150981663","https://openalex.org/W2153185479","https://openalex.org/W2153284517","https://openalex.org/W2159497832","https://openalex.org/W2168363974","https://openalex.org/W2170711116","https://openalex.org/W2314014312","https://openalex.org/W2320546585","https://openalex.org/W2323723186","https://openalex.org/W2327303067","https://openalex.org/W2327377041","https://openalex.org/W2329066917","https://openalex.org/W3022298626"],"related_works":["https://openalex.org/W2980609865","https://openalex.org/W2048621586","https://openalex.org/W1660043925","https://openalex.org/W3046057334","https://openalex.org/W3045908301","https://openalex.org/W2783659808","https://openalex.org/W2138531335","https://openalex.org/W3155528695","https://openalex.org/W2079411557","https://openalex.org/W4403464187"],"abstract_inverted_index":{"HOOMD-blue":[0,65,133],"is":[1,58,92,118],"the":[2,10,53,59,68,80,93,124],"first":[3,60],"general":[4],"purpose":[5],"MD":[6],"code":[7,117],"built":[8],"from":[9],"ground":[11],"up":[12],"for":[13,123],"GPU":[14,86],"acceleration,":[15],"and":[16,31,104,126],"has":[17],"been":[18],"actively":[19],"developed":[20],"since":[21],"March":[22],"2007.":[23],"It":[24],"supports":[25],"a":[26],"variety":[27],"of":[28,90],"force":[29],"fields":[30],"int":[32],"egrators":[33],"targeted":[34],"at":[35],"soft-matter":[36],"simulations.":[37,107],"As":[38],"an":[39],"open":[40],"so":[41],"urce":[42],"project,":[43],"numerous":[44],"developers":[45],"have":[46,71],"contributed":[47],"useful":[48],"feature":[49],"additions":[50],"back":[51],"to":[52,78,101,120],"main":[54],"code.":[55],"High":[56],"performance":[57,83],"desig":[61],"n":[62],"priority":[63],"in":[64],"development.":[66],"Over":[67],"years,":[69],"we":[70],"rewritten":[72],"core":[73],"computation":[74],"kernels":[75],"several":[76],"times":[77],"obtain":[79],"best":[81],"possible":[82],"on":[84],"each":[85],"hardware":[87],"generation.":[88],"Ease":[89],"use":[91],"second":[94],"priority.":[95],"Python":[96],"job":[97],"scripts":[98],"allow":[99],"users":[100,125],"easily":[102],"configure":[103],"control":[105],"their":[106],"Good":[108],"object-orien":[109],"ted":[110],"software":[111],"engineering":[112],"practices":[113],"ensure":[114],"that":[115,132],"HOOMD-blue\u2019s":[116],"easy":[119],"extend,":[121],"both":[122],"developers.":[127],"Extensive":[128],"validation":[129],"tests":[130],"show":[131],"produces":[134],"correct":[135],"results.":[136]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":4},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":3}],"updated_date":"2026-10-16T09:59:22.235173","created_date":"2016-06-24T00:00:00"}