Conjugate gradient relaxation of random finite cluster of Si atoms v003

Jump to: Models | Files | Wiki

ClusterEnergyAndForces_5atom_Si__TE_700998615333_003

Title A single sentence description.	Conjugate gradient relaxation of random finite cluster of Si atoms v003
Description	Computes the potential energy and forces of a random cluster of Si atoms and performs a conjugate gradient relaxation of the positions. The positions of the atoms in this Test were obtained by first randomly initializing a set of Si atoms in a cubic box of side length 6.2 Angstroms (fixed, reflective boundary conditions). Dynamics were then performed in LAMMPS (http://lammps.sandia.gov) under a Tersoff (T2) potential by heating the system to ~4100K under a Langevin thermostat for 190 timesteps (each timestep = 0.001ps). Finally, the atomic positions were extracted and are used as the initial positions for the relaxation.
Species The supported atomic species.	Si
Disclaimer A statement of applicability provided by the contributor, informing users of the intended use of this KIM Item.	See test driver source (ClusterEnergyAndForces__TD_000043093022_003) for required formatting of xyz file. This kimspec file was generated automatically using the openkim-pipeline `testgenie` utility along with the template files in the test driver directory.

Contributor	Daniel S. Karls
Maintainer	Daniel S. Karls
Published on KIM	2019
How to Cite	This Test is archived in OpenKIM [1-4]. [1] Karls DS. Conjugate gradient relaxation of random finite cluster of Si atoms v003 [Internet]. OpenKIM; 2019. Available from: https://openkim.org/cite/TE_700998615333_003 [2] Karls DS. Conjugate gradient relaxation of atomic cluster v003. OpenKIM; 2019. doi:10.25950/b47dd4c4 [3] Tadmor EB, Elliott RS, Sethna JP, Miller RE, Becker CA. The potential of atomistic simulations and the Knowledgebase of Interatomic Models. JOM. 2011;63(7):17. doi:10.1007/s11837-011-0102-6 [4] Elliott RS, Tadmor EB. Knowledgebase of Interatomic Models (KIM) Application Programming Interface (API). OpenKIM; 2011. doi:10.25950/ff8f563a Click here to download the above citation in BibTeX format.
Funding	Not available

Short KIM ID The unique KIM identifier code.	TE_700998615333_003
Extended KIM ID The long form of the KIM ID including a human readable prefix (100 characters max), two underscores, and the Short KIM ID. Extended KIM IDs can only contain alpha-numeric characters (letters and digits) and underscores and must begin with a letter.	ClusterEnergyAndForces_5atom_Si__TE_700998615333_003
Citable Link	https://openkim.org/cite/TE_700998615333_003
KIM Item Type	Test
Driver	ClusterEnergyAndForces__TD_000043093022_003
Properties Properties as defined in kimspec.edn. These properties are inhereted from the Test Driver.	tag:staff@noreply.openkim.org,2014-04-15:property/configuration-cluster-relaxed
KIM API Version	2.0
Simulator Name The name of the simulator as defined in kimspec.edn. This Simulator Name is inhereted from the Test Driver.	LAMMPS
Programming Language(s) The programming languages used in the code and the percentage of the code written in each one.	100.00% Python

Previous Version	ClusterEnergyAndForces_5atom_Si__TE_700998615333_002

Models

EDIP_LAMMPS__MD_783584031339_000

Model	Link to Test Results page	Benchmark time Usertime multiplied by the Whetstone Benchmark. This number can be used (approximately) to compare the performance of different models independently of the architecture on which the test was run. Measured in Millions of Whetstone Instructions (MWI)
EDIP_LAMMPS_JiangMorganSzlufarska_2012_SiC__MO_667792548433_000	view	1565
EDIP_LAMMPS_JustoBazantKaxiras_1998_Si__MO_315965276297_000	view	4317
EDIP_LAMMPS_LucasBertolusPizzagalli_2009_SiC__MO_634310164305_000	view	3441

EDIP__MD_506186535567_002

Model	Test Results	Link to Test Results page	Benchmark time Usertime multiplied by the Whetstone Benchmark. This number can be used (approximately) to compare the performance of different models independently of the architecture on which the test was run. Measured in Millions of Whetstone Instructions (MWI)
EDIP_JustoBazantKaxiras_1998_Si__MO_958932894036_002		view	1408

LJ__MD_414112407348_003

Model	Test Results	Link to Test Results page	Benchmark time Usertime multiplied by the Whetstone Benchmark. This number can be used (approximately) to compare the performance of different models independently of the architecture on which the test was run. Measured in Millions of Whetstone Instructions (MWI)
LJ_ElliottAkerson_2015_Universal__MO_959249795837_003 This Model has a disclaimer This model was automatically fit using Lorentz-Berthelot mixing rules. It reproduces the dimer equilibrium separation (covalent radii) and the bond dissociation energies. It has not been fitted to other physical properties and its ability to model structures other than dimers is unknown.		view	1503

MEAM_LAMMPS__MD_249792265679_002

Model	Link to Test Results page	Benchmark time Usertime multiplied by the Whetstone Benchmark. This number can be used (approximately) to compare the performance of different models independently of the architecture on which the test was run. Measured in Millions of Whetstone Instructions (MWI)
MEAM_LAMMPS_AslamBaskesDickel_2019_FeMnSiC__MO_427873955970_002	view	3166
MEAM_LAMMPS_CuiGaoCui_2012_LiSi__MO_557492625287_002	view	5227
MEAM_LAMMPS_DuLenoskyHennig_2011_Si__MO_883726743759_002	view	2209
MEAM_LAMMPS_HuangDongLiu_2018_Si__MO_050147023220_002	view	3561
MEAM_LAMMPS_JelinekGrohHorstemeyer_2012_AlSiMgCuFe__MO_262519520678_002	view	3902
MEAM_LAMMPS_KangEunJun_2014_SiC__MO_477506997611_002	view	4196
MEAM_LAMMPS_Lee_2007_Si__MO_774917820956_001	view	3680
MEAM_LAMMPS_LenoskySadighAlonso_2000_Si__MO_533426548156_002	view	3680
MEAM_LAMMPS_Wagner_2007_SiC__MO_430846853065_002	view	3650

MFF__MD_514777050453_001

Model	Test Results	Link to Test Results page	Benchmark time Usertime multiplied by the Whetstone Benchmark. This number can be used (approximately) to compare the performance of different models independently of the architecture on which the test was run. Measured in Millions of Whetstone Instructions (MWI)
MFF_MistriotisFlytzanisFarantos_1989_Si__MO_080526771943_001		view	1503

SNAP__MD_536750310735_000

Model	Test Results	Link to Test Results page	Benchmark time Usertime multiplied by the Whetstone Benchmark. This number can be used (approximately) to compare the performance of different models independently of the architecture on which the test was run. Measured in Millions of Whetstone Instructions (MWI)
SNAP_ZuoChenLi_2019_Si__MO_869330304805_000 This Model has a disclaimer This potential is designed for Si diamond systems. It is not appropriate for other elements. The potential was trained using LAMMPS version 12Dec2018. Newer LAMMPS may see energy differences, but the relative values should remain to be the same.		view	1003
SNAP_ZuoChenLi_2019quadratic_Si__MO_721469752060_000 This Model has a disclaimer This potential is designed for Si diamond systems. It is not appropriate for other elements. The potential was trained using LAMMPS version 12Dec2018. Newer LAMMPS may see energy differences, but the relative values should remain to be the same.		view	877

SW__MD_335816936951_005

Model	Link to Test Results page	Benchmark time Usertime multiplied by the Whetstone Benchmark. This number can be used (approximately) to compare the performance of different models independently of the architecture on which the test was run. Measured in Millions of Whetstone Instructions (MWI)
SW_BalamaneHaliciogluTiller_1992_Si__MO_113686039439_005	view	1222
SW_BalamaneHauchShi_2017Brittle_Si__MO_381114941873_003	view	1002
SW_HauchHollandMarder_1999Brittle_Si__MO_119167353542_005	view	1190
SW_LeeHwang_2012GGA_Si__MO_040570764911_001	view	1096
SW_LeeHwang_2012LDA_Si__MO_517338295712_001	view	1128
SW_StillingerWeber_1985_Si__MO_405512056662_006	view	1096
SW_ZhangXieHu_2014OptimizedSW1_Si__MO_800412945727_005	view	1190
SW_ZhangXieHu_2014OptimizedSW2_Si__MO_475612090600_005	view	1159

Tersoff_LAMMPS__MD_077075034781_005

Model	Link to Test Results page	Benchmark time Usertime multiplied by the Whetstone Benchmark. This number can be used (approximately) to compare the performance of different models independently of the architecture on which the test was run. Measured in Millions of Whetstone Instructions (MWI)
Tersoff_LAMMPS_ErhartAlbe_2005_SiC__MO_903987585848_005	view	1565
Tersoff_LAMMPS_MunetohMotookaMoriguchi_2007_SiO__MO_501246546792_000	view	3869
Tersoff_LAMMPS_PlummerTucker_2019_TiSiC__MO_751442731010_000	view	2087
Tersoff_LAMMPS_Tersoff_1988T2_Si__MO_245095684871_004	view	1305
Tersoff_LAMMPS_Tersoff_1988T3_Si__MO_186459956893_004	view	3690
Tersoff_LAMMPS_Tersoff_1989_SiC__MO_171585019474_004	view	1454
Tersoff_LAMMPS_Tersoff_1989_SiGe__MO_350526375143_004	view	1454
Tersoff_LAMMPS_Tersoff_1990_SiC__MO_444207127575_000	view	1565
Tersoff_LAMMPS_Tersoff_1994_SiC__MO_794973922560_000	view	4048

ThreeBodyBondOrder_KDS__MD_697985444380_000

Model	Test Results	Link to Test Results page	Benchmark time Usertime multiplied by the Whetstone Benchmark. This number can be used (approximately) to compare the performance of different models independently of the architecture on which the test was run. Measured in Millions of Whetstone Instructions (MWI)
ThreeBodyBondOrder_KDS_KhorDasSarma_1988_Si__MO_722489435928_000		view	1663

ThreeBodyBondOrder_PPM__MD_184422512875_000

Model	Test Results	Link to Test Results page	Benchmark time Usertime multiplied by the Whetstone Benchmark. This number can be used (approximately) to compare the performance of different models independently of the architecture on which the test was run. Measured in Millions of Whetstone Instructions (MWI)
ThreeBodyBondOrder_PPM_PurjaPunMishin_2017_Si__MO_566683736730_000		view	1376

ThreeBodyBondOrder_WR__MD_817691861922_000

Model	Test Results	Link to Test Results page	Benchmark time Usertime multiplied by the Whetstone Benchmark. This number can be used (approximately) to compare the performance of different models independently of the architecture on which the test was run. Measured in Millions of Whetstone Instructions (MWI)
ThreeBodyBondOrder_WR_WangRockett_1991_Si__MO_081872846741_000		view	1376

ThreeBodyCluster_BH__MD_043141570610_000

Model	Test Results	Link to Test Results page	Benchmark time Usertime multiplied by the Whetstone Benchmark. This number can be used (approximately) to compare the performance of different models independently of the architecture on which the test was run. Measured in Millions of Whetstone Instructions (MWI)
ThreeBodyCluster_BH_BiswasHamann_1987_Si__MO_019616213550_000		view	1599

ThreeBodyCluster_Gong__MD_065419309200_000

Model	Test Results	Link to Test Results page	Benchmark time Usertime multiplied by the Whetstone Benchmark. This number can be used (approximately) to compare the performance of different models independently of the architecture on which the test was run. Measured in Millions of Whetstone Instructions (MWI)
ThreeBodyCluster_Gong_Gong_1993_Si__MO_407755720412_000		view	1312

ThreeBodyCluster_KP__MD_527786671773_000

Model	Test Results	Link to Test Results page	Benchmark time Usertime multiplied by the Whetstone Benchmark. This number can be used (approximately) to compare the performance of different models independently of the architecture on which the test was run. Measured in Millions of Whetstone Instructions (MWI)
ThreeBodyCluster_KP_KaxirasPandey_1988_Si__MO_072486242437_000		view	1663

ThreeBodyCluster_SRS__MD_814842199451_000

Model	Test Results	Link to Test Results page	Benchmark time Usertime multiplied by the Whetstone Benchmark. This number can be used (approximately) to compare the performance of different models independently of the architecture on which the test was run. Measured in Millions of Whetstone Instructions (MWI)
ThreeBodyCluster_SRS_StephensonRadnySmith_1996_Si__MO_604248666067_000		view	1344

TorchML__MD_173118614730_000

Model	Test Results	Link to Test Results page	Benchmark time Usertime multiplied by the Whetstone Benchmark. This number can be used (approximately) to compare the performance of different models independently of the architecture on which the test was run. Measured in Millions of Whetstone Instructions (MWI)
TorchML_MACE_GuptaTadmorMartiniani_2024_Si__MO_781946209112_000		view	73621
TorchML_NequIP_GuptaTadmorMartiniani_2024_Si__MO_196181738937_000		view	102480

No Driver

Model	Link to Test Results page	Benchmark time Usertime multiplied by the Whetstone Benchmark. This number can be used (approximately) to compare the performance of different models independently of the architecture on which the test was run. Measured in Millions of Whetstone Instructions (MWI)
Sim_LAMMPS_ADP_StarikovGordeevLysogorskiy_2020_SiAuAl__SM_113843830602_000	view	1137
Sim_LAMMPS_ADP_StarikovLopanitsynaSmirnova_2018_SiAu__SM_985135773293_000	view	2431
Sim_LAMMPS_EDIP_JiangMorganSzlufarska_2012_SiC__SM_435704953434_000	view	2495
Sim_LAMMPS_GW_GaoWeber_2002_SiC__SM_606253546840_000	view	2111
Sim_LAMMPS_GWZBL_Samolyuk_2016_SiC__SM_720598599889_000	view	1951
Sim_LAMMPS_MEAM_CuiGaoCui_2012_LiSi__SM_562938628131_000	view	1193
Sim_LAMMPS_MEAM_DuLenoskyHennig_2011_Si__SM_662785656123_000	view	2399
Sim_LAMMPS_MEAM_JelinekGrohHorstemeyer_2012_AlSiMgCuFe__SM_656517352485_000	view	3263
Sim_LAMMPS_MEAM_LenoskySadighAlonso_2000_Si__SM_622320990752_000	view	2495
Sim_LAMMPS_MEAM_Wagner_2007_SiC__SM_264944083668_000	view	2879
Sim_LAMMPS_ModifiedTersoff_KumagaiIzumiHara_2007_Si__SM_773333226968_000	view	2815
Sim_LAMMPS_ModifiedTersoff_PurjaPunMishin_2017_Si__SM_184524061456_000	view	2495
Sim_LAMMPS_ReaxFF_BrugnoliMiyataniAkaji_SiCeNaClHO_2023__SM_282799919035_000	view	6547
Sim_LAMMPS_ReaxFF_ManzanoMoeiniMarinelli_2012_CaSiOH__SM_714124634215_000	view	1711
Sim_LAMMPS_TersoffZBL_DevanathanDiazdelaRubiaWeber_1998_SiC__SM_578912636995_000	view	2239
Sim_LAMMPS_Vashishta_BroughtonMeliVashishta_1997_SiO__SM_422553794879_000	view	2591
Sim_LAMMPS_Vashishta_NakanoKaliaVashishta_1994_SiO__SM_503555646986_000	view	2527
Sim_LAMMPS_Vashishta_VashishtaKaliaNakano_2007_SiC__SM_196548226654_000	view	2079
Sim_LAMMPS_Vashishta_VashishtaKaliaRino_1990_SiO__SM_887826436433_000	view	2463
Tersoff_LAMMPS_ErhartAlbe_2005SiII_SiC__MO_408791041969_004	view	3690

Errors

No Driver

Model	Error Categories	Link to Error page
Sim_LAMMPS_Buckingham_CarreHorbachIspas_2008_SiO__SM_886641404623_000	other	view
Sim_LAMMPS_Buckingham_FreitasSantosColaco_2015_SiCaOAl__SM_154093256665_000	other	view

Files

LICENSE.CDDL
Makefile
README.txt
cluster.xyz
kimprovenance.edn
kimspec.edn
pipeline.stdin.tpl
runner

Download

ClusterEnergyAndForces_5atom_Si__TE_700998615333_003.txz	Tar+XZ	Linux and OS X archive
ClusterEnergyAndForces_5atom_Si__TE_700998615333_003.zip	Zip	Windows archive

Download Dependency

This Test requires a Test Driver. Archives for the Test Driver ClusterEnergyAndForces__TD_000043093022_003 appear below.

ClusterEnergyAndForces__TD_000043093022_003.txz	Tar+XZ	Linux and OS X archive
ClusterEnergyAndForces__TD_000043093022_003.zip	Zip	Windows archive

Wiki

Wiki is ready to accept new content.