Efficiency of linked cell algorithms
The linked cell algorithm is an essential part of molecular simulation software, both molecular dynamics and Monte Carlo. Though it scales linearly with the number of particles, there has been a constant interest in increasing its performance, because a large part of CPU time is spent to identify th...
Saved in:
| Published in | Computer physics communications Vol. 182; no. 3; pp. 611 - 615 |
|---|---|
| Main Authors | , |
| Format | Journal Article |
| Language | English |
| Published |
Elsevier B.V
01.03.2011
|
| Subjects | |
| Online Access | Get full text |
| ISSN | 0010-4655 1879-2944 |
| DOI | 10.1016/j.cpc.2010.11.002 |
Cover
| Abstract | The linked cell algorithm is an essential part of molecular simulation software, both molecular dynamics and Monte Carlo. Though it scales linearly with the number of particles, there has been a constant interest in increasing its performance, because a large part of CPU time is spent to identify the interacting particles. Several recent publications proposed improvements to the algorithm and investigated their efficiency by applying them to particular setups. Here we develop a general method to evaluate the efficiency of these algorithms which is mostly independent of the parameters of the simulation, and test it for a number of linked cell algorithms. We also propose a combination of linked cell reordering and interaction sorting that performs well for a broad range of simulation setups. |
|---|---|
| AbstractList | The linked cell algorithm is an essential part of molecular simulation software, both molecular dynamics and Monte Carlo. Though it scales linearly with the number of particles, there has been a constant interest in increasing its performance, because a large part of CPU time is spent to identify the interacting particles. Several recent publications proposed improvements to the algorithm and investigated their efficiency by applying them to particular setups. Here we develop a general method to evaluate the efficiency of these algorithms which is mostly independent of the parameters of the simulation, and test it for a number of linked cell algorithms. We also propose a combination of linked cell reordering and interaction sorting that performs well for a broad range of simulation setups. |
| Author | Welling, Ulrich Germano, Guido |
| Author_xml | – sequence: 1 givenname: Ulrich surname: Welling fullname: Welling, Ulrich email: ulrich.welling@staff.uni-marburg.de – sequence: 2 givenname: Guido surname: Germano fullname: Germano, Guido email: guido.germano@staff.uni-marburg.de |
| BookMark | eNp9kD1PwzAQhi1UJNrCD2DrgARLgs92Y1tMqCofUiUWmC3HuYBLGhc7Req_J6FMDJ1Op3ufu9MzIaM2tEjIJdAcKBS369xtXc7o0ENOKTshY1BSZ0wLMSJj2k8yUcznZ2SS0ppSKqXmY3K1rGvvPLZuPwv1rPHtJ1Yzh00zs817iL772KRzclrbJuHFX52St4fl6-IpW708Pi_uV5njBesyRM1R1BooE0LVUFqJipUOAZh01AJDVZXIREVRWl3WjJVWARfAGC-V5VNyfdi7jeFrh6kzG5-GX2yLYZeMKgTXilPWJ2-OJkFKyrnmc-ij8hB1MaQUsTbOd7bzoe2i9Y0BagaDZm16g2YwaAAM_T0C_8ht9Bsb90eZuwODvadvj9GkX7tY-YiuM1XwR-gfQ96JDA |
| CitedBy_id | crossref_primary_10_1093_mnras_stae1537 crossref_primary_10_1063_5_0246661 crossref_primary_10_1016_j_cpc_2017_09_017 crossref_primary_10_1021_acs_jpca_2c01918 crossref_primary_10_1140_epje_i2019_11883_x crossref_primary_10_1016_j_cpc_2012_03_008 crossref_primary_10_1080_08927022_2012_762097 crossref_primary_10_1002_jcc_21945 crossref_primary_10_1016_j_cpc_2022_108452 crossref_primary_10_1021_acs_jpcb_2c07997 crossref_primary_10_1093_gji_ggy231 crossref_primary_10_1016_j_cpc_2012_01_003 crossref_primary_10_1016_j_jcp_2011_08_022 crossref_primary_10_1016_j_jpdc_2019_03_008 crossref_primary_10_1103_PhysRevE_105_055305 crossref_primary_10_1080_08927022_2016_1267354 crossref_primary_10_1142_S0219720015400041 crossref_primary_10_1063_1_4973842 crossref_primary_10_1016_j_powtec_2018_09_034 crossref_primary_10_1002_adts_202400125 crossref_primary_10_1016_j_cpc_2013_06_003 crossref_primary_10_1016_j_pbiomolbio_2011_07_006 crossref_primary_10_1021_acs_jcim_3c00405 crossref_primary_10_1021_acs_jpcb_4c01441 crossref_primary_10_1016_j_jeurceramsoc_2023_11_026 crossref_primary_10_1063_5_0018516 crossref_primary_10_1088_1751_8121_ac852f crossref_primary_10_1038_s41598_017_07917_y crossref_primary_10_1063_5_0056515 |
| Cites_doi | 10.1063/1.475217 10.1016/0010-4655(90)90007-N 10.1016/j.jcp.2008.01.047 10.1007/s00778-005-0166-4 10.1002/(SICI)1096-987X(199703)18:4<478::AID-JCC3>3.0.CO;2-Q 10.1002/jcc.20071 10.1016/j.cpc.2007.05.009 10.1016/S0010-4655(98)00203-3 10.1063/1.463137 10.1016/j.cpc.2004.04.004 10.1002/jcc.10123 10.1063/1.2719690 10.1002/jcc.20267 10.1103/PhysRev.159.98 10.1016/S0010-4655(00)00050-3 10.1016/j.cpc.2005.03.110 10.1016/S0010-4655(98)00074-5 10.1021/j100303a004 10.1016/j.cpc.2008.05.008 10.1142/S0129183106010182 10.1016/0021-9991(73)90046-6 10.1063/1.442716 10.1016/j.molliq.2005.11.029 10.1016/0167-7977(88)90014-7 10.1016/j.cpc.2005.03.111 10.1006/jcph.1995.1039 10.1002/jcc.20563 |
| ContentType | Journal Article |
| Copyright | 2010 Elsevier B.V. |
| Copyright_xml | – notice: 2010 Elsevier B.V. |
| DBID | AAYXX CITATION 7SC 7U5 8FD H8D JQ2 L7M L~C L~D |
| DOI | 10.1016/j.cpc.2010.11.002 |
| DatabaseName | CrossRef Computer and Information Systems Abstracts Solid State and Superconductivity Abstracts Technology Research Database Aerospace Database ProQuest Computer Science Collection Advanced Technologies Database with Aerospace Computer and Information Systems Abstracts Academic Computer and Information Systems Abstracts Professional |
| DatabaseTitle | CrossRef Aerospace Database Technology Research Database Computer and Information Systems Abstracts – Academic ProQuest Computer Science Collection Computer and Information Systems Abstracts Solid State and Superconductivity Abstracts Advanced Technologies Database with Aerospace Computer and Information Systems Abstracts Professional |
| DatabaseTitleList | Technology Research Database Aerospace Database |
| DeliveryMethod | fulltext_linktorsrc |
| Discipline | Physics |
| EISSN | 1879-2944 |
| EndPage | 615 |
| ExternalDocumentID | 10_1016_j_cpc_2010_11_002 S0010465510004480 |
| GroupedDBID | --K --M -~X .DC .~1 0R~ 1B1 1RT 1~. 1~5 29F 4.4 457 4G. 5GY 5VS 7-5 71M 8P~ 9JN AACTN AAEDT AAEDW AAIAV AAIKJ AAKOC AALRI AAOAW AAQFI AAQXK AARLI AAXUO AAYFN ABBOA ABFNM ABMAC ABNEU ABQEM ABQYD ABXDB ABYKQ ACDAQ ACFVG ACGFS ACLVX ACNNM ACRLP ACSBN ACZNC ADBBV ADECG ADEZE ADJOM ADMUD AEBSH AEKER AENEX AFKWA AFTJW AFZHZ AGHFR AGUBO AGYEJ AHHHB AHZHX AI. AIALX AIEXJ AIKHN AITUG AIVDX AJBFU AJOXV AJSZI ALMA_UNASSIGNED_HOLDINGS AMFUW AMRAJ AOUOD ASPBG ATOGT AVWKF AXJTR AZFZN BBWZM BKOJK BLXMC CS3 DU5 EBS EFJIC EFLBG EJD EO8 EO9 EP2 EP3 F5P FDB FEDTE FGOYB FIRID FLBIZ FNPLU FYGXN G-2 G-Q GBLVA GBOLZ HLZ HME HMV HVGLF HZ~ IHE IMUCA J1W KOM LG9 LZ4 M38 M41 MO0 N9A NDZJH O-L O9- OAUVE OGIMB OZT P-8 P-9 P2P PC. Q38 R2- RIG ROL RPZ SBC SCB SDF SDG SES SEW SHN SPC SPCBC SPD SPG SSE SSK SSQ SSV SSZ T5K TN5 UPT VH1 WUQ ZMT ~02 ~G- AATTM AAXKI AAYWO AAYXX ABJNI ABWVN ACLOT ACRPL ACVFH ADCNI ADNMO AEIPS AEUPX AFJKZ AFPUW AGQPQ AIGII AIIUN AKBMS AKRWK AKYEP ANKPU APXCP CITATION EFKBS ~HD 7SC 7U5 8FD H8D JQ2 L7M L~C L~D |
| ID | FETCH-LOGICAL-c362t-ee93e4f9102448f1ba7e82bce1127c0a12e8dbe24d0e7a9bf22ba81341223b8a3 |
| IEDL.DBID | .~1 |
| ISSN | 0010-4655 |
| IngestDate | Thu Oct 02 10:46:23 EDT 2025 Sat Sep 27 20:27:29 EDT 2025 Wed Oct 01 04:08:34 EDT 2025 Thu Apr 24 23:08:23 EDT 2025 Fri Feb 23 02:30:56 EST 2024 |
| IsPeerReviewed | true |
| IsScholarly | true |
| Issue | 3 |
| Keywords | Molecular simulation Linked cell list Monte Carlo Neighbour list Molecular dynamics Linked cell reordering Interaction sorting |
| Language | English |
| License | https://www.elsevier.com/tdm/userlicense/1.0 |
| LinkModel | DirectLink |
| MergedId | FETCHMERGED-LOGICAL-c362t-ee93e4f9102448f1ba7e82bce1127c0a12e8dbe24d0e7a9bf22ba81341223b8a3 |
| Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 ObjectType-Article-2 ObjectType-Feature-1 |
| PQID | 1770339351 |
| PQPubID | 23500 |
| PageCount | 5 |
| ParticipantIDs | proquest_miscellaneous_864398302 proquest_miscellaneous_1770339351 crossref_citationtrail_10_1016_j_cpc_2010_11_002 crossref_primary_10_1016_j_cpc_2010_11_002 elsevier_sciencedirect_doi_10_1016_j_cpc_2010_11_002 |
| ProviderPackageCode | CITATION AAYXX |
| PublicationCentury | 2000 |
| PublicationDate | 2011-03-01 |
| PublicationDateYYYYMMDD | 2011-03-01 |
| PublicationDate_xml | – month: 03 year: 2011 text: 2011-03-01 day: 01 |
| PublicationDecade | 2010 |
| PublicationTitle | Computer physics communications |
| PublicationYear | 2011 |
| Publisher | Elsevier B.V |
| Publisher_xml | – name: Elsevier B.V |
| References | Swope, Andersen, Berens (br0310) 1982; 76 Kadau, Germann, Lomdahl (br0170) 2006; 17 Allen, Tildesley (br0010) 1989 Quentrec, Brot (br0040) 1973; 13 Chialvo, Debenedetti (br0030) 1983; 60 Gonnet (br0150) 2007; 28 Heinz, Hünenberger (br0220) 2004; 25 Pütz, Kolb (br0210) 1998; 113 Benetis, Jensen, Karčiauskas, Šaltenis (br0120) 2006; 15 Frenkel, Smit (br0080) 2002 Mattson, Rice (br0070) 1999; 119 Hockney, Eastwood (br0050) 1981 Knuth (br0290) 1973 Petrella, Andricioael, Brooks, Karplus (br0090) 2003; 24 Verlet (br0020) 1967; 159 Mason (br0140) 2005; 170 Wilson, Allen, Warren, Sauron, Smith (br0250) 1997; 18 Krämer, Seeger (br0130) 2009; 34 Mecke, Winkelmann, Fischer (br0300) 1997; 107 Yao, Wang, Liu, Cheng (br0100) 2004; 161 Liu, Schmidt, Voss, Mueller-Wittig (br0200) 2008; 179 Wu, Hsu, Lee (br0280) 2005; 170 Heffelfinger (br0260) 2000; 128 Anderson, Lorenz, Travesset (br0190) 2008; 227 Tuckerman, Berne, Martyna (br0320) 1992; 97 Meloni, Rosati, Colombo (br0180) 2007; 126 Auerbach, Paul, Lutz, Bakker, Rudge, Abraham (br0060) 1987; 91 Wang, Hsiao, Chuang, Lee (br0110) 2007; 177 Plimpton (br0240) 1995; 117 Shaw (br0270) 2005; 26 Sutmann, Stegailov (br0160) 2006; 125 Rapaport (br0230) 1988; 9 Verlet (10.1016/j.cpc.2010.11.002_br0020) 1967; 159 Pütz (10.1016/j.cpc.2010.11.002_br0210) 1998; 113 Petrella (10.1016/j.cpc.2010.11.002_br0090) 2003; 24 Swope (10.1016/j.cpc.2010.11.002_br0310) 1982; 76 Shaw (10.1016/j.cpc.2010.11.002_br0270) 2005; 26 Liu (10.1016/j.cpc.2010.11.002_br0200) 2008; 179 Auerbach (10.1016/j.cpc.2010.11.002_br0060) 1987; 91 Wilson (10.1016/j.cpc.2010.11.002_br0250) 1997; 18 Kadau (10.1016/j.cpc.2010.11.002_br0170) 2006; 17 Heinz (10.1016/j.cpc.2010.11.002_br0220) 2004; 25 Frenkel (10.1016/j.cpc.2010.11.002_br0080) 2002 Wang (10.1016/j.cpc.2010.11.002_br0110) 2007; 177 Knuth (10.1016/j.cpc.2010.11.002_br0290) 1973 Benetis (10.1016/j.cpc.2010.11.002_br0120) 2006; 15 Heffelfinger (10.1016/j.cpc.2010.11.002_br0260) 2000; 128 Rapaport (10.1016/j.cpc.2010.11.002_br0230) 1988; 9 Chialvo (10.1016/j.cpc.2010.11.002_br0030) 1983; 60 Anderson (10.1016/j.cpc.2010.11.002_br0190) 2008; 227 Plimpton (10.1016/j.cpc.2010.11.002_br0240) 1995; 117 Krämer (10.1016/j.cpc.2010.11.002_br0130) 2009; 34 Wu (10.1016/j.cpc.2010.11.002_br0280) 2005; 170 Allen (10.1016/j.cpc.2010.11.002_br0010) 1989 Mattson (10.1016/j.cpc.2010.11.002_br0070) 1999; 119 Mecke (10.1016/j.cpc.2010.11.002_br0300) 1997; 107 Quentrec (10.1016/j.cpc.2010.11.002_br0040) 1973; 13 Gonnet (10.1016/j.cpc.2010.11.002_br0150) 2007; 28 Yao (10.1016/j.cpc.2010.11.002_br0100) 2004; 161 Mason (10.1016/j.cpc.2010.11.002_br0140) 2005; 170 Tuckerman (10.1016/j.cpc.2010.11.002_br0320) 1992; 97 Hockney (10.1016/j.cpc.2010.11.002_br0050) 1981 Meloni (10.1016/j.cpc.2010.11.002_br0180) 2007; 126 Sutmann (10.1016/j.cpc.2010.11.002_br0160) 2006; 125 |
| References_xml | – year: 1989 ident: br0010 article-title: Computer Simulation of Liquids – volume: 107 start-page: 9264 year: 1997 end-page: 9270 ident: br0300 article-title: Molecular dynamics simulation of the liquid-vapor interface: the Lennard-Jones fluid publication-title: J. Chem. Phys. – volume: 15 start-page: 229 year: 2006 end-page: 250 ident: br0120 article-title: Nearest and reverse nearest neighbor queries for moving objects publication-title: VLDB J. – volume: 34 start-page: 4 year: 2009 ident: br0130 article-title: Semantics and implementation of continuous sliding window queries over data streams publication-title: ACM T. Database Syst. – volume: 18 start-page: 478 year: 1997 end-page: 488 ident: br0250 article-title: Replicated data and domain decomposition molecular dynamics techniques for simulation of anisotropic potentials publication-title: J. Comput. Chem. – volume: 119 start-page: 135 year: 1999 end-page: 148 ident: br0070 article-title: Near-neighbor calculations using a modified cell-linked list method publication-title: Comput. Phys. Commun. – volume: 170 start-page: 31 year: 2005 end-page: 41 ident: br0140 article-title: Faster neighbour list generation using a novel lattice vector representation publication-title: Comput. Phys. Commun. – volume: 117 start-page: 1 year: 1995 end-page: 19 ident: br0240 article-title: Fast parallel algorithms for short-range molecular dynamics publication-title: J. Comput. Phys. – volume: 177 start-page: 551 year: 2007 end-page: 559 ident: br0110 article-title: Algorithm optimization in molecular dynamics simulation publication-title: Comput. Phys. Commun. – volume: 97 start-page: 1990 year: 1992 end-page: 2001 ident: br0320 article-title: Reversible multiple time scale molecular dynamics publication-title: J. Chem. Phys. – volume: 128 start-page: 219 year: 2000 end-page: 237 ident: br0260 article-title: Parallel atomistic simulation publication-title: Comput. Phys. Commun. – year: 1981 ident: br0050 article-title: Computer Simulations Using Particles – volume: 126 start-page: 121102 year: 2007 ident: br0180 article-title: Efficient particle labeling in atomistic simulations publication-title: J. Chem. Phys. – volume: 159 start-page: 98 year: 1967 end-page: 103 ident: br0020 article-title: Computer experiments on classical fluids publication-title: Phys. Rev. – volume: 227 start-page: 5342 year: 2008 end-page: 5359 ident: br0190 article-title: General purpose molecular dynamics simulations fully implemented on graphics processing units publication-title: J. Comput. Phys. – volume: 179 start-page: 634 year: 2008 end-page: 641 ident: br0200 article-title: Accelerating molecular dynamics simulations using graphics processing units with CUDA publication-title: Comput. Phys. Commun. – volume: 60 start-page: 215 year: 1983 end-page: 224 ident: br0030 article-title: On the use of the Verlet neighbor list in molecular dynamics publication-title: Comput. Phys. Commun. – volume: 125 start-page: 197 year: 2006 end-page: 203 ident: br0160 article-title: Optimization of neighbor list techniques in liquid matter simulations publication-title: J. Mol. Liq. – year: 2002 ident: br0080 article-title: Understanding Molecular Simulation – volume: 161 start-page: 27 year: 2004 end-page: 36 ident: br0100 article-title: Improved neighbor list algorithm in molecular simulations using cell decomposition and data sorting method publication-title: Comput. Phys. Commun. – volume: 113 start-page: 145 year: 1998 end-page: 167 ident: br0210 article-title: Optimization techniques for parallel molecular dynamics using domain decomposition publication-title: Comput. Phys. Commun. – volume: 25 start-page: 1474 year: 2004 end-page: 1486 ident: br0220 article-title: A fast pairlist-construction algorithm for molecular simulations under periodic boundary conditions publication-title: J. Comput. Chem. – volume: 13 start-page: 430 year: 1973 end-page: 432 ident: br0040 article-title: New method for searching for neighbors in molecular dynamics computations publication-title: J. Comput. Phys. – volume: 24 start-page: 222 year: 2003 end-page: 231 ident: br0090 article-title: An improved method for nonbonded list generation: rapid determination of near-neighbor pairs publication-title: J. Comput. Chem. – volume: 91 start-page: 4881 year: 1987 end-page: 4890 ident: br0060 article-title: A special purpose computer for molecular dynamics: motivation, design, implementation, and application publication-title: J. Phys. Chem. – volume: 28 start-page: 570 year: 2007 end-page: 573 ident: br0150 article-title: A simple algorithm to accelerate the computation of non-bonded interactions in cell-based molecular dynamics simulations publication-title: J. Comput. Chem. – year: 1973 ident: br0290 article-title: The Art of Computer Programming, Vol. 3 – volume: 9 start-page: 1 year: 1988 end-page: 53 ident: br0230 article-title: Large-scale molecular dynamics simulation using vector and parallel computers publication-title: Comput. Phys. Rep. – volume: 76 start-page: 637 year: 1982 end-page: 649 ident: br0310 article-title: Computer-simulation method for the calculation of equilibrium-constants for the formation of physical clusters of molecules — application to small water clusters publication-title: J. Chem. Phys. – volume: 26 start-page: 1318 year: 2005 end-page: 1328 ident: br0270 article-title: A fast, scalable method for the parallel evaluation of distance-limited pairwise particle interactions publication-title: J. Comput. Chem. – volume: 17 start-page: 1755 year: 2006 end-page: 1761 ident: br0170 article-title: Molecular dynamics comes of age: 320 billion atom simulation on BlueGene/L publication-title: Int. J. Mod. Phys. C – volume: 170 start-page: 175 year: 2005 end-page: 185 ident: br0280 article-title: Parallel implementation of molecular dynamics simulation for short-ranged interaction publication-title: Comput. Phys. Commun. – volume: 107 start-page: 9264 year: 1997 ident: 10.1016/j.cpc.2010.11.002_br0300 article-title: Molecular dynamics simulation of the liquid-vapor interface: the Lennard-Jones fluid publication-title: J. Chem. Phys. doi: 10.1063/1.475217 – volume: 60 start-page: 215 year: 1983 ident: 10.1016/j.cpc.2010.11.002_br0030 article-title: On the use of the Verlet neighbor list in molecular dynamics publication-title: Comput. Phys. Commun. doi: 10.1016/0010-4655(90)90007-N – volume: 227 start-page: 5342 year: 2008 ident: 10.1016/j.cpc.2010.11.002_br0190 article-title: General purpose molecular dynamics simulations fully implemented on graphics processing units publication-title: J. Comput. Phys. doi: 10.1016/j.jcp.2008.01.047 – volume: 15 start-page: 229 year: 2006 ident: 10.1016/j.cpc.2010.11.002_br0120 article-title: Nearest and reverse nearest neighbor queries for moving objects publication-title: VLDB J. doi: 10.1007/s00778-005-0166-4 – volume: 18 start-page: 478 year: 1997 ident: 10.1016/j.cpc.2010.11.002_br0250 article-title: Replicated data and domain decomposition molecular dynamics techniques for simulation of anisotropic potentials publication-title: J. Comput. Chem. doi: 10.1002/(SICI)1096-987X(199703)18:4<478::AID-JCC3>3.0.CO;2-Q – volume: 25 start-page: 1474 year: 2004 ident: 10.1016/j.cpc.2010.11.002_br0220 article-title: A fast pairlist-construction algorithm for molecular simulations under periodic boundary conditions publication-title: J. Comput. Chem. doi: 10.1002/jcc.20071 – volume: 177 start-page: 551 year: 2007 ident: 10.1016/j.cpc.2010.11.002_br0110 article-title: Algorithm optimization in molecular dynamics simulation publication-title: Comput. Phys. Commun. doi: 10.1016/j.cpc.2007.05.009 – volume: 119 start-page: 135 year: 1999 ident: 10.1016/j.cpc.2010.11.002_br0070 article-title: Near-neighbor calculations using a modified cell-linked list method publication-title: Comput. Phys. Commun. doi: 10.1016/S0010-4655(98)00203-3 – volume: 97 start-page: 1990 year: 1992 ident: 10.1016/j.cpc.2010.11.002_br0320 article-title: Reversible multiple time scale molecular dynamics publication-title: J. Chem. Phys. doi: 10.1063/1.463137 – volume: 161 start-page: 27 year: 2004 ident: 10.1016/j.cpc.2010.11.002_br0100 article-title: Improved neighbor list algorithm in molecular simulations using cell decomposition and data sorting method publication-title: Comput. Phys. Commun. doi: 10.1016/j.cpc.2004.04.004 – volume: 24 start-page: 222 year: 2003 ident: 10.1016/j.cpc.2010.11.002_br0090 article-title: An improved method for nonbonded list generation: rapid determination of near-neighbor pairs publication-title: J. Comput. Chem. doi: 10.1002/jcc.10123 – volume: 126 start-page: 121102 year: 2007 ident: 10.1016/j.cpc.2010.11.002_br0180 article-title: Efficient particle labeling in atomistic simulations publication-title: J. Chem. Phys. doi: 10.1063/1.2719690 – volume: 26 start-page: 1318 year: 2005 ident: 10.1016/j.cpc.2010.11.002_br0270 article-title: A fast, scalable method for the parallel evaluation of distance-limited pairwise particle interactions publication-title: J. Comput. Chem. doi: 10.1002/jcc.20267 – volume: 159 start-page: 98 year: 1967 ident: 10.1016/j.cpc.2010.11.002_br0020 article-title: Computer experiments on classical fluids publication-title: Phys. Rev. doi: 10.1103/PhysRev.159.98 – volume: 128 start-page: 219 year: 2000 ident: 10.1016/j.cpc.2010.11.002_br0260 article-title: Parallel atomistic simulation publication-title: Comput. Phys. Commun. doi: 10.1016/S0010-4655(00)00050-3 – volume: 170 start-page: 175 year: 2005 ident: 10.1016/j.cpc.2010.11.002_br0280 article-title: Parallel implementation of molecular dynamics simulation for short-ranged interaction publication-title: Comput. Phys. Commun. doi: 10.1016/j.cpc.2005.03.110 – volume: 113 start-page: 145 year: 1998 ident: 10.1016/j.cpc.2010.11.002_br0210 article-title: Optimization techniques for parallel molecular dynamics using domain decomposition publication-title: Comput. Phys. Commun. doi: 10.1016/S0010-4655(98)00074-5 – volume: 91 start-page: 4881 year: 1987 ident: 10.1016/j.cpc.2010.11.002_br0060 article-title: A special purpose computer for molecular dynamics: motivation, design, implementation, and application publication-title: J. Phys. Chem. doi: 10.1021/j100303a004 – volume: 179 start-page: 634 year: 2008 ident: 10.1016/j.cpc.2010.11.002_br0200 article-title: Accelerating molecular dynamics simulations using graphics processing units with CUDA publication-title: Comput. Phys. Commun. doi: 10.1016/j.cpc.2008.05.008 – year: 1989 ident: 10.1016/j.cpc.2010.11.002_br0010 – volume: 17 start-page: 1755 year: 2006 ident: 10.1016/j.cpc.2010.11.002_br0170 article-title: Molecular dynamics comes of age: 320 billion atom simulation on BlueGene/L publication-title: Int. J. Mod. Phys. C doi: 10.1142/S0129183106010182 – volume: 34 start-page: 4 year: 2009 ident: 10.1016/j.cpc.2010.11.002_br0130 article-title: Semantics and implementation of continuous sliding window queries over data streams publication-title: ACM T. Database Syst. – volume: 13 start-page: 430 year: 1973 ident: 10.1016/j.cpc.2010.11.002_br0040 article-title: New method for searching for neighbors in molecular dynamics computations publication-title: J. Comput. Phys. doi: 10.1016/0021-9991(73)90046-6 – volume: 76 start-page: 637 year: 1982 ident: 10.1016/j.cpc.2010.11.002_br0310 article-title: Computer-simulation method for the calculation of equilibrium-constants for the formation of physical clusters of molecules — application to small water clusters publication-title: J. Chem. Phys. doi: 10.1063/1.442716 – volume: 125 start-page: 197 year: 2006 ident: 10.1016/j.cpc.2010.11.002_br0160 article-title: Optimization of neighbor list techniques in liquid matter simulations publication-title: J. Mol. Liq. doi: 10.1016/j.molliq.2005.11.029 – volume: 9 start-page: 1 year: 1988 ident: 10.1016/j.cpc.2010.11.002_br0230 article-title: Large-scale molecular dynamics simulation using vector and parallel computers publication-title: Comput. Phys. Rep. doi: 10.1016/0167-7977(88)90014-7 – volume: 170 start-page: 31 year: 2005 ident: 10.1016/j.cpc.2010.11.002_br0140 article-title: Faster neighbour list generation using a novel lattice vector representation publication-title: Comput. Phys. Commun. doi: 10.1016/j.cpc.2005.03.111 – volume: 117 start-page: 1 year: 1995 ident: 10.1016/j.cpc.2010.11.002_br0240 article-title: Fast parallel algorithms for short-range molecular dynamics publication-title: J. Comput. Phys. doi: 10.1006/jcph.1995.1039 – year: 1973 ident: 10.1016/j.cpc.2010.11.002_br0290 – year: 1981 ident: 10.1016/j.cpc.2010.11.002_br0050 – volume: 28 start-page: 570 year: 2007 ident: 10.1016/j.cpc.2010.11.002_br0150 article-title: A simple algorithm to accelerate the computation of non-bonded interactions in cell-based molecular dynamics simulations publication-title: J. Comput. Chem. doi: 10.1002/jcc.20563 – year: 2002 ident: 10.1016/j.cpc.2010.11.002_br0080 |
| SSID | ssj0007793 |
| Score | 2.1989665 |
| Snippet | The linked cell algorithm is an essential part of molecular simulation software, both molecular dynamics and Monte Carlo. Though it scales linearly with the... |
| SourceID | proquest crossref elsevier |
| SourceType | Aggregation Database Enrichment Source Index Database Publisher |
| StartPage | 611 |
| SubjectTerms | Algorithms Central processing units Computer programs Computer simulation Interaction sorting Linked cell list Linked cell reordering Mathematical models Molecular dynamics Molecular simulation Monte Carlo Monte Carlo methods Neighbour list Software |
| Title | Efficiency of linked cell algorithms |
| URI | https://dx.doi.org/10.1016/j.cpc.2010.11.002 https://www.proquest.com/docview/1770339351 https://www.proquest.com/docview/864398302 |
| Volume | 182 |
| hasFullText | 1 |
| inHoldings | 1 |
| isFullTextHit | |
| isPrint | |
| journalDatabaseRights | – providerCode: PRVESC databaseName: Baden-Württemberg Complete Freedom Collection (Elsevier) customDbUrl: eissn: 1879-2944 dateEnd: 99991231 omitProxy: true ssIdentifier: ssj0007793 issn: 0010-4655 databaseCode: GBLVA dateStart: 20110101 isFulltext: true titleUrlDefault: https://www.sciencedirect.com providerName: Elsevier – providerCode: PRVESC databaseName: Elsevier ScienceDirect Freedom Collection customDbUrl: eissn: 1879-2944 dateEnd: 99991231 omitProxy: true ssIdentifier: ssj0007793 issn: 0010-4655 databaseCode: AIKHN dateStart: 19950101 isFulltext: true titleUrlDefault: https://www.sciencedirect.com providerName: Elsevier – providerCode: PRVESC databaseName: Elsevier SD Complete Freedom Collection [SCCMFC] customDbUrl: eissn: 1879-2944 dateEnd: 99991231 omitProxy: true ssIdentifier: ssj0007793 issn: 0010-4655 databaseCode: ACRLP dateStart: 19950101 isFulltext: true titleUrlDefault: https://www.sciencedirect.com providerName: Elsevier – providerCode: PRVESC databaseName: Elsevier SD Freedom Collection customDbUrl: eissn: 1879-2944 dateEnd: 99991231 omitProxy: true ssIdentifier: ssj0007793 issn: 0010-4655 databaseCode: .~1 dateStart: 19950101 isFulltext: true titleUrlDefault: https://www.sciencedirect.com providerName: Elsevier – providerCode: PRVLSH databaseName: Elsevier Journals customDbUrl: mediaType: online eissn: 1879-2944 dateEnd: 99991231 omitProxy: true ssIdentifier: ssj0007793 issn: 0010-4655 databaseCode: AKRWK dateStart: 19690701 isFulltext: true providerName: Library Specific Holdings |
| link | http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwnV1LS8NAEF5KRfAiPrE-SoSehNg8NtnkWEpLtdiDWOxt2d1stFKbYturv92ZzUZRtAfJIRB2SfIlzDez880sIS2VAccJCUFOyoRLpREBqNhNdaQUxCNxnmHt8N0oHozp7SSa1Ei3qoVBWaW1_aVNN9baXmlbNNuL6RRrfDE_CYxvspIJxu2UMtzF4Pr9S-bBmG28C_YGR1eZTaPxUgtVqruwkaddWfmFm35YaUM9_T2ya31Gp1M-1j6p6fkB2TbaTbU8JK2eaQOBNZROkTuYktWZgyvyjpg9FRD9P78uj8i433voDly7-YGrgFNWrtZpqGkObA4EnOS-FEwngVQaHCSmPOEHOsmkDmjmaSZSmQeBFAm2ZwPCl4kIj0l9Xsz1CXFYnkYikikckoZYzKq9yIuzRLMsYmHeIF712lzZzuC4QcWMVxKwFw5IcUQKIgYOSDXI1eeURdkWY9NgWmHJv31bDmZ707TLCncO_zzCJua6WC-5z8BOYU2x3yDOH2MSdLWwudnp_-5-RnbK5WOUm52T-uptrS_A_1jJpvnBmmSrczMcjPA8vH8cfgDSrtjh |
| linkProvider | Elsevier |
| linkToHtml | http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwnV1LS8NAEF6KInoRn1ifEXoSYtO8dnOU0lK17amF3pbdzUYrNSm2vfrbndlsFEV7kNzCLkm-LPPN7HwzS0hDpcBxQkKQk1DhhtKIAFTsJjpSCuKROEuxdngwjHvj8GESTWqkXdXCoKzS2v7Sphtrbe80LZrN-XSKNb6YnwTGN1lJBnH7Zhj5FCOw2_cvnQeltvMuGBwcXqU2jchLzVUp78JOnnZr5Rdy-mGmDfd098iudRqdu_K99klN5wdky4g31eKQNDqmDwQWUTpF5mBOVqcObsk7YvZUQPj__Lo4IuNuZ9Tuufb0A1cBqSxdrZNAhxnQOTAwy1pSUM18qTR4SFR5ouVrlkrth6mnqUhk5vtSMOzPBowvmQiOyUZe5PqEODRLIhHJBC4ZBljNqr3Ii1OmaRrRIKsTr_psrmxrcDyhYsYrDdgLB6Q4IgUhAwek6uTmc8q87IuxbnBYYcm__VwOdnvdtOsKdw6LHmETuS5WC96iYKiwqLhVJ84fYxj6Wtjd7PR_T78i273RoM_798PHM7JT7iWj9uycbCzfVvoCnJGlvDSL7QM139jT |
| openUrl | ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fsummon.serialssolutions.com&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Efficiency+of+linked+cell+algorithms&rft.jtitle=Computer+physics+communications&rft.au=Welling%2C+Ulrich&rft.au=Germano%2C+Guido&rft.date=2011-03-01&rft.issn=0010-4655&rft.volume=182&rft.issue=3&rft.spage=611&rft.epage=615&rft_id=info:doi/10.1016%2Fj.cpc.2010.11.002&rft.externalDBID=NO_FULL_TEXT |
| thumbnail_l | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=0010-4655&client=summon |
| thumbnail_m | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=0010-4655&client=summon |
| thumbnail_s | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=0010-4655&client=summon |