{"id":3171,"date":"2022-02-10T11:05:24","date_gmt":"2022-02-10T02:05:24","guid":{"rendered":"https:\/\/mdcl.issp.u-tokyo.ac.jp\/scc\/?page_id=3171"},"modified":"2025-01-17T13:10:42","modified_gmt":"2025-01-17T04:10:42","slug":"lammps_guide","status":"publish","type":"page","link":"https:\/\/mdcl.issp.u-tokyo.ac.jp\/scc\/system\/lammps_guide","title":{"rendered":"LAMMPS"},"content":{"rendered":"

LAMMPS<\/span><\/h2>\r\n

\u30aa\u30fc\u30d7\u30f3\u30bd\u30fc\u30b9\u306e\u6c4e\u7528\u53e4\u5178\u5206\u5b50\u52d5\u529b\u5b66\u30a2\u30d7\u30ea\u30b1\u30fc\u30b7\u30e7\u30f3\u3002\u30bd\u30d5\u30c8\u30de\u30bf\u30fc\u3001\u56fa\u4f53\u3001\u30e1\u30bd\u30b9\u30b3\u30d4\u30c3\u30af\u7cfb\u306a\u3069\u306e\u591a\u304f\u306e\u7cfb\u3067\u52d5\u529b\u5b66\u8a08\u7b97\u3092\u884c\u3046\u3053\u3068\u304c\u3067\u304d\u308b\u3002\u539f\u5b50\u306e\u52d5\u529b\u5b66\u8a08\u7b97\u3084\u4e00\u822c\u7684\u306a\u7c92\u5b50\u306e\u30b7\u30df\u30e5\u30ec\u30fc\u30bf\u30fc\u3068\u3057\u3066\u3082\u5229\u7528\u53ef\u80fd\u3067\u3001\u7a7a\u9593\u5206\u5272\u3092\u7528\u3044\u305f\u4e26\u884c\u8a08\u7b97\u306b\u3082\u5bfe\u5fdc\u3059\u308b\u3002GPL\u30e9\u30a4\u30bb\u30f3\u30b9\u3092\u63a1\u7528\u3057\u3001\u30b3\u30fc\u30c9\u306f\u5909\u66f4\u3084\u62e1\u5f35\u304c\u5bb9\u6613\u3068\u306a\u308b\u3088\u3046\u306b\u30c7\u30b6\u30a4\u30f3\u3055\u308c\u3066\u3044\u308b\u3002<\/span><\/p>\r\n

\u53c2\u8003\u6587\u732e<\/span><\/h3>\r\n

Official home Page:\u00a0<\/span>http:\/\/lammps.sandia.gov\/<\/a>
\r\nOfficial Document:\u00a0<\/span>http:\/\/lammps.sandia.gov\/doc\/Manual.html<\/a>
\r\nLAMMPS on MateriApps:\u00a0<\/span>https:\/\/ma.issp.u-tokyo.ac.jp\/app\/596<\/a><\/p>\r\n

\u63d0\u4f9b\u30d0\u30fc\u30b8\u30e7\u30f3 (2025-01-17)<\/span><\/h3>\r\n

LAMMPS \u672c\u4f53<\/span>
\r\n20240829_update1<\/span><\/p>\r\n

\u7269\u6027\u7814\u30b9\u30d1\u30b3\u30f3\u3067\u306e\u5229\u7528\u65b9\u6cd5<\/span><\/h3>\r\n

\u4ee5\u4e0b\u3001 $MA_ROOT<\/code> \u306f\u6b21\u306e\u30c7\u30a3\u30ec\u30af\u30c8\u30ea\u306b\u7f6e\u304d\u63db\u3048\u3066\u304f\u3060\u3055\u3044\u3002<\/p>\r\n

System B: \/home\/issp\/materiapps\/oneapi_compiler_classic-2023.0.0--openmpi-4.1.5<\/code>
\r\nSystem C (CPU): \/home\/issp\/materiapps\/PrgEnv-intel_8.3.3<\/code>
\r\nSystem C (GPU): \/home\/issp\/materiapps\/nvhpc-nompi_24.7__openmpi_nvhpc_4.1.2<\/code><\/p>\r\n

\u74b0\u5883\u8a2d\u5b9a<\/span><\/h4>\r\n

LAMMPS \u306f<\/p>\r\n

\r\n
$MA_ROOT\/lammps\/<\/code><\/pre>\r\n<\/div>\r\n
\u4ee5\u4e0b\u306b\u30d0\u30fc\u30b8\u30e7\u30f3\u3054\u3068\u306b\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3057\u3066\u3042\u308a\u307e\u3059\u3002<\/p>\r\n
\r\n
$ source $MA_ROOT\/lammps\/lammpsvars.sh<\/span><\/code><\/pre>\r\n<\/div>\r\n
\u3068\u3057\u3066\u8a2d\u5b9a\u30d5\u30a1\u30a4\u30eb\u3092\u8aad\u307f\u8fbc\u3080\u3068\u3001\u6700\u65b0\u306e\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u6e08\u307f\u30d0\u30fc\u30b8\u30e7\u30f3\u306e\u30c7\u30a3\u30ec\u30af\u30c8\u30ea\u304c\u74b0\u5883\u5909\u6570 LAMMPS_ROOT<\/code> \u306b\u8a2d\u5b9a\u3055\u308c\u3001 \u5b9f\u884c\u30d0\u30a4\u30ca\u30ea\u306e\u3042\u308b\u30c7\u30a3\u30ec\u30af\u30c8\u30ea $LAMMPS_ROOT\/bin<\/code> \u304cPATH \u306b\u8ffd\u52a0\u3055\u308c\u3001 \u5fc5\u8981\u306a\u30e9\u30a4\u30d6\u30e9\u30ea\u306e\u5834\u6240\u304c LD_LIBRARY_PATH \u306b\u8ffd\u52a0\u3055\u308c\u307e\u3059\u3002 \u544a\u77e5\u306a\u304f\u30d0\u30fc\u30b8\u30e7\u30f3\u304c\u66f4\u65b0\u3055\u308c\u308b\u3053\u3068\u304c\u3042\u308a\u307e\u3059\u3002 \u30d0\u30fc\u30b8\u30e7\u30f3\u3092\u56fa\u5b9a\u3057\u305f\u3044\u5834\u5408\u306f\u3001\u305d\u308c\u305e\u308c\u306e\u30d0\u30fc\u30b8\u30e7\u30f3\u540d\u306e\u3064\u3044\u305f\u8a2d\u5b9a\u30d5\u30a1\u30a4\u30eb\u3092source<\/code>\u3057\u3066\u304f\u3060\u3055\u3044\u3002<\/span><\/p>\r\n
\u5b9f\u884c\u30d0\u30a4\u30ca\u30ea<\/span><\/h4>\r\n
\u5b9f\u884c\u30d0\u30a4\u30ca\u30ea\u540d\u306f lammps<\/code> \u3067\u3059\u3002 \u5b9f\u884c\u306b\u306f\u305f\u3068\u30481\u30d7\u30ed\u30bb\u30b9\u3067\u3042\u3063\u3066\u3082 srun<\/code> (ohtaka) \u304a\u3088\u3073 mpiexec<\/code> (kugui) \u304c\u5fc5\u8981\u3068\u306a\u308a\u307e\u3059\u3002<\/span><\/p>\r\n
\u30d1\u30c3\u30b1\u30fc\u30b8<\/h4>\r\n
Lammps\u306e\u30d1\u30c3\u30b1\u30fc\u30b8 (https:\/\/docs.lammps.org\/Packages_list.html<\/a>) \u306e\u3046\u3061\u3001\u8ffd\u52a0\u306e\u30e9\u30a4\u30d6\u30e9\u30ea\u304c\u5fc5\u8981\u306b\u306a\u308b\u3082\u306e\u4ee5\u5916<\/strong>\u3001\u5177\u4f53\u7684\u306b\u306f\u4ee5\u4e0b\u306e\u3082\u306e\u304c\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3055\u308c\u3066\u3044\u307e\u3059\u3002<\/p>\r\n
AMOEBA ASPHERE BOCS BODY BPM BROWNIAN CG-DNA CG-SPICA CLASS2 COLLOID COLVARS CORESHELL DIELECTRIC DIFFRACTION DIPOLE DPD-BASIC DPD-MESO DPD-REACT DPD-SMOOTH DRUDE EFF EXTRA-COMMAND EXTRA-COMPUTE EXTRA-DUMP EXTRA-FIX EXTRA-MOLECULE EXTRA-PAIR FEP GRANULAR INTEL INTERLAYER KSPACE MANIFOLD MANYBODY MC MEAM MESONT MGPT MISC ML-IAP ML-POD ML-RANN ML-SNAP ML-UF3 MOFFF MOLECULE OPENMP OPT ORIENT PERI PHONON PLUGIN POEMS PTM QEQ QTB REACTION REAXFF REPLICA RHEO RIGID SHOCK SMTBQ SPH SPIN SRD TALLY UEF YAFF<\/p>\r\n
\u6280\u8853\u7684\u306b\u306f\u3001all_on.cmake<\/code>\u3068nolib.cmake<\/code>\u3092\u7528\u3044\u3066\u30d3\u30eb\u30c9\u3055\u308c\u3066\u3044\u307e\u3059\u3002<\/p>\r\n
\u30b5\u30f3\u30d7\u30eb\u30b9\u30af\u30ea\u30d7\u30c8\u3068\u5165\u529b\u30d5\u30a1\u30a4\u30eb\u306e\u5834\u6240<\/span><\/h4>\r\n
\r\n
$LAMMPS_ROOT\/share\/lammps\/examples<\/span><\/code><\/pre>\r\n<\/div>\r\n
\u306bLAMMPS\u516c\u5f0f\u306e\u30b5\u30f3\u30d7\u30eb\u96c6\u304c\u3042\u308a\u307e\u3059\u3002\u3054\u81ea\u8eab\u306e\u30c7\u30a3\u30ec\u30af\u30c8\u30ea\u306b\u30b3\u30d4\u30fc\u3057\u3066\u304a\u4f7f\u3044\u304f\u3060\u3055\u3044\u3002<\/span><\/p>\r\n
\r\n
$ cp -r $LAMMPS_ROOT\/share\/lammps\/examples .<\/span><\/code><\/pre>\r\n<\/div>\r\n
\u30b8\u30e7\u30d6\u306e\u5b9f\u884c\u65b9\u6cd5<\/span><\/h4>\r\n
\r\n
$MA_ROOT\/lammps\/sample_jobscript\/<\/code><\/pre>\r\n<\/div>\r\n
\u306b\u30b9\u30af\u30ea\u30d7\u30c8\u306e\u30b5\u30f3\u30d7\u30eb lammps.sh<\/code> \u304c\u7528\u610f\u3055\u308c\u3066\u3044\u308b\u306e\u3067\u3001\u30ab\u30ec\u30f3\u30c8\u30d5\u30a9\u30eb\u30c0\u306b\u30b3\u30d4\u30fc\u3057\u307e\u3059\u3002 lammps.sh<\/code> \u3067\u5b9f\u884c\u90e8\u5206\u306b\u8a18\u8f09\u3055\u308c\u3066\u3044\u308b\u5165\u529b\u30d5\u30a1\u30a4\u30eb\u540d in.param<\/code> \u3092\u9069\u5207\u306a\u3082\u306e\u306b\u5909\u66f4\u3057\u305f\u4e0a\u3067\u30b8\u30e7\u30d6\u3092\u6295\u5165\u3057\u307e\u3059\u3002<\/span><\/p>\r\n
\r\n
$ cp $MA_ROOT\/lammps\/sample_jobscript\/lammps.sh .\r\n\r\n# System B\r\n$ sbatch lammps.sh\r\n# System C\r\n$ qsub lammps.sh<\/code><\/pre>\r\n<\/div>","protected":false},"excerpt":{"rendered":"LAMMPS \u30aa\u30fc\u30d7\u30f3\u30bd\u30fc\u30b9\u306e\u6c4e\u7528\u53e4\u5178\u5206\u5b50\u52d5\u529b\u5b66\u30a2\u30d7\u30ea\u30b1\u30fc\u30b7\u30e7\u30f3\u3002\u30bd\u30d5\u30c8\u30de\u30bf\u30fc\u3001\u56fa\u4f53\u3001\u30e1\u30bd\u30b9\u30b3\u30d4\u30c3\u30af\u7cfb\u306a\u3069\u306e\u591a\u304f\u306e\u7cfb\u3067\u52d5\u529b\u5b66\u8a08\u7b97\u3092\u884c\u3046\u3053\u3068\u304c\u3067\u304d\u308b\u3002\u539f\u5b50\u306e\u52d5\u529b\u5b66\u8a08\u7b97\u3084\u4e00\u822c\u7684\u306a\u7c92\u5b50\u306e\u30b7\u30df\u30e5\u30ec\u30fc\u30bf\u30fc\u3068\u3057\u3066\u3082\u5229\u7528\u53ef\u80fd\u3067\u3001\u7a7a\u9593\u5206 […]","protected":false},"author":1,"featured_media":0,"parent":12,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"_locale":"ja","_original_post":"https:\/\/mdcl.issp.u-tokyo.ac.jp\/scc\/?page_id=3171","footnotes":""},"class_list":["post-3171","page","type-page","status-publish","hentry","ja"],"acf":[],"_links":{"self":[{"href":"https:\/\/mdcl.issp.u-tokyo.ac.jp\/scc\/wp-json\/wp\/v2\/pages\/3171","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/mdcl.issp.u-tokyo.ac.jp\/scc\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/mdcl.issp.u-tokyo.ac.jp\/scc\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/mdcl.issp.u-tokyo.ac.jp\/scc\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/mdcl.issp.u-tokyo.ac.jp\/scc\/wp-json\/wp\/v2\/comments?post=3171"}],"version-history":[{"count":11,"href":"https:\/\/mdcl.issp.u-tokyo.ac.jp\/scc\/wp-json\/wp\/v2\/pages\/3171\/revisions"}],"predecessor-version":[{"id":6661,"href":"https:\/\/mdcl.issp.u-tokyo.ac.jp\/scc\/wp-json\/wp\/v2\/pages\/3171\/revisions\/6661"}],"up":[{"embeddable":true,"href":"https:\/\/mdcl.issp.u-tokyo.ac.jp\/scc\/wp-json\/wp\/v2\/pages\/12"}],"wp:attachment":[{"href":"https:\/\/mdcl.issp.u-tokyo.ac.jp\/scc\/wp-json\/wp\/v2\/media?parent=3171"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}