lammps 手册

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lammps 手册,学习lammps软件的初学者,非常实用。
LAMMPS USers manual Table of Contents USER-CG- CMM package……… 42 USER-CUDA package 42 LSER- EFF package.......….…..…..43 USER-EWALDN Package USER- OMP package.…………………, 44 USER-REAXC package 14 USER-SPH package .……14 5. Accelerating LAMMPS performance 46 5.1OPTpackage...,....47 5.2 USER-OMP package .47 5.3 GPU package...............…....49 5.4 USER-CUDA package.... 51 5.5 Comparison of GPU and USER-CUDA packages..........53 6. How-to discussions 6 6.1 Restarting a simulation………… …………56 6.2 2d simulations 8 6. 3 CHARMM, AMBER and dreidINg force fields 58 6.4 Running multiple simulations from one input script..............59 6.5 Multi-replica 6.6 Granular models 6.7 TIP3P water mode 62 6. 8 TIP4P water model ………………63 6.9 SPC water model 64 6. 10 Coupling laMMPs to other codes.................65 6.11visulizingLAMMPSsnapshots.......… 66 6. 12 Triclinic(non-orthogonal) simulation boxes. 6.13 NEMD Simulations 6 6. 14 Extended spherical and aspherical particles 69 6. 15 Output from LAMMPS(thermo, dumps, computes, fixes, variables)......72 6. 16 Thermostatting, barostatting, and computing temperature...........76 6.17 Walls 78 6. 18 Elastic 6.19 Library interface to LAMMPS….….…...80 6.20 Calculating thermal conductivity.............81 6.21 Calculating viscosity. 82 7. Example problems........ 85 8. Performance scalability ;a;垂。aa;。; eodebde04ddi 4; Iaboeboebde4;s; oede04e d“;s;a 87 9. Additic 88 amber2lmp binary2txt tooL 89 ch2lmp tool........... .89 chain tool 89 createatoms tool 89 data2xmovie tool .……90 eam database tool 音1 90 eam generate tool.….….….….….….….….….….….….….….….….90 eff tool emacs tool...……1, LAMMPS USers manual Table of Contents P Imp2arc tool.......... 9 lmp2 cfg tool...............1.....91 lmp2 vmd tool..….….….…..91 matlab tool micelle tool 9 msi2 Imp tool..........…… pymol_asphere tool python reax too 92 restart2data tool thermo extract tool vim tool ⅹ movie tool...,……………………………… 93 10. Modifying& extending lammPs..,……………………………94 10.1 Atom styl 95 10.2 Bond, angle, dihedral, improper potentials. 10.3 Compute styles.......…..…….97 10.4 Dump styles...…..….97 10.5 Dump custom output options. 98 10.6 Fix styles 98 10.7 Input script ce 10.8 Kspace computations 100 10.9 Minimization styles 100 10.10 Pairwise potentials .101 10.11 Region styles...,.,.,....101 10. 12 Thermodynamic output options 102 10.13 Variable options..........102 10.14 Submitting new features for inclusion in LAMMPS.………………………………103 11. Python interface to IlI Extending Python with a serial version of LAMMPS 106 11.2 Creating a shared MPI library..............................107 11.3 Extending Python with a parallel version of LAMMPS...........107 11.4 Extending Python with MPI 11.5 Testing the Python-LAMMPS interface 109 11.6 USing LAMMPS from Python. 10 11. 7 Example Python scripts that use LAMMPS 113 12. Errors 115 12.1 Common problems....,.,,.,…,.,,…….,15 12.2 Reporting bugs.…… 16 12. 3 Error warning messages …1116 Errors Warnings∷ 音音垂 179 13. Future and history.........,….……184 13. 1 Coming attractions................................... 184 13.2 Past versions............184 angle_style charmm command. ...................186 angle_ style charmm/ omp command……….….186 LAMMPS USers manual Table of Contents angle_style class2 command.……… ∴188 angle_style clas/ omp command-…… 188 angle_coeff command.…,.….….….,190 angle_style cosine command..…..…,.…,…,…,.,…,……,….,…,…,…,…….….….192 angle_ style cosine/ omp command.…… .192 angle_style cosine/ delta command.....,….….….….….….…….…….…………194 angle_ style cosine/delta/omp command 194 angle style cosine/periodic command 196 angle_ style cosine/ periodic/ omp command.…,…,…,….………….…….19 angle style cosine/shift command .198 angle style cosine/shift/omp command ········:·· 198 angle_style cosine/shift/exp command....... 200 angle_style cosine/shift/exp angle sty le cosine/squared command ……………202 angle style cosine 202 angle_style harmonic command.…….….….204 angle_style harmonic/ omp command...,.,..….….……204 angle style hybrid command …206 angle_ _style none command 208 angle_style sdk command 209 angle_style command. 210 angle style table command 212 angle style table/omp command 212 atom modify command 215 atom style command .217 bond_ style class2 command....….…….…..220 bond_style class2/omp command 220 bond coeff command. 222 bond_ style fene command………..224 bond style fene/omp command ....................224 bond_ style fene/ expand command.…….…,26 bond style fene/expand/omp command...........................226 bond style harmonic command 228 bond_style harmonic/omp command bond style harmonic/shift command 230 bond_style harmonic/shift/omp command....... 230 bond style harmonic/shift/cut command...............................232 bond style harmonic/shift/cut/omp command 232 bond- style hybrid command....….….….….….….…..…...234 bond style morse command. .236 bond style morse/omp command …236 bond style none command 238 bond_ style nonlinear command. ...................239 bond style nonlinear/omp command ..……………………………239 bond- style quartic command 音1 ………241 bond_style quartic./ omp command.……………1241 bond style command 243 bond_ style table command…….….….….…...1245 LAMMPS USers manual Table of contents bond_ style table/ omp command…… 245 boundary command. 248 change box command clear command 250 communicate command 251 compute command................................253 compute ackland/atom command. …………………………257 compute angle/local command. 259 compute atom/molecule command 261 compute bond/local command .263 compute centro/atom compute cluster/atom command 267 compute cna/atom command. ....................................268 compute com command ……………270 compute com/molecule compute coord/ atom command.….…..273 compute damage/atom command. 4 compute dihedral/local command........................275 compute displace./ atom command...........…..…….………..276 compute rotate/asphere command 278 compute rotate/sphere command..........279 compute event/displace command............................280 compute group/group command 28 compute gyration command.………,… 282 compute gyration/molecule command 283 compute heat/flux command..........285 compute improper/local command. 289 compute ke command 290 compute ke/ atom command.….….….….….….….….….291 compute ke/atom/eff command........292 compute ke/ eff command.….….….…….…..294 compute meso e/atom command ·.·:··;·;·······;············:····· 296 compute meso_rho/ yatom command…….….….….….….….297 compute meso_t/atom command...........................298 compute_modify command. .299 compute msd command 300 compute msd/molecule command. .302 compute pair command 304 compute pair/local command 306 compute pe command..... 308 compute pe/cuda command. compute pe/atom command. 310 compute pressure command..,..,…,………………312 compute pressure/cuda command 312 compute property/atom command. compute property/ Mlocal command.…….…….….………316 compute property/ molecule command.............……….318 compute rdf command…….….………319 LAMMPS USers manual Table of Contents compute reduce command 321 compute reduce/region command.…… 321 compute slice command............................324 compute stress/atom command 4垂垂音垂 …1326 compute temp command 328 compute temp/cuda command 328 compute temp/ asphere command.…….….….….….… compute temp/com command compute temp/deform command …………………………………………………… compute temp/deform/eff command 337 compute temp/eff command. compute temp/ partial command…… .340 compute temp/partial compute temp/ profile command.……… ∴342 compute temp/ ramp command...............…………44 compute temp/ region command.…….…..346 compute temp/region/eff command …348 computetemp/rotatecommand...................,349 compute temp/sphere command. compute ti command 53 create atoms command..w..w.w..w.35. create box command. ...................................................................,.....................................................358 delete atoms command 1360 delete bonds command dielectric command .364 dihedral style charmm command 365 dihedral_style charmm/omp command 365 dihedral_ style class2 command 367 dihedral_ style class2/ omp command.……….367 dihedral coeff command dihedral_style cosine/shift/exp command............373 dihedral_style cosine/shift/exp/omp command. 73 dihedral_style harmonic command.............375 dihedral_style harmonic/omp command ……375 dihedral_style helix command ∴37 dihedral_style helix/omp command 377 dihedral style hybrid command................................379 dihedral_style multi/harmonic command. 381 dihedral style multi/harmonic/omp command .·········· 381 dihedral style none command. 383 dihedral_ style opls command…...………………………………384 dihedral_style opls/omp command 384 dihedral_ style command . 386 dimension command. ..........................................................................................................................388 displace_atoms command.........389 displace_ box command.….….….….…….….…..….…..….….……31 dump command...,..….….….….…….394 dump image command…….….…….394 LAMMPS USers manual Table of contents dump image command.… 401 dump_modify command...... .408 echo command..…..……416 丘 ix command…… 417 fix adapt command.…….……. 421 fix addforce command 425 fix addforce/cuda fix addtorque command 428 fix append_atoms fix atc command .432 fix ave/atom command.w..w..w.m. 436 fix ave/correlate command. 438 fix ave/histo fix ave/spatial command 448 fix ave/time command. …………453 fix aveforce command. 458 fix aveforce/ uda command..……458 fix bond/break command fix bond/create command. .463 fix bond/swap command …1466 fix box/relax command 469 fix deform command. fix deposit command 480 fix drag command..........,.,,,.,.,,..4.83 fix dt/reset command .484 fix efield command …1486 fix enforced command 487 fix enforced/cuda command 487 fix evaporate command.….….….….….….….…...4.8 fix external command. fix freeze command. 40 0 fix freeze/ uda command.......………1492 fix gcmc command.......,.,….,….,….,….….4.94 fix gravity command 面音面4垂 497 fix gravity/cuda command 497 fix gravity/omp command 497 fix heat command ·:··········:·:·········;···:·· 499 fix imd command 501 fix indent command fix langevin command 507 fix langevin/eff command 511 fix lineforce command 513 fix meso command........................... 514 fix meso/stationary command …515 fix modify command 音1 …516 fix momentum command fix move command. 519 fix msst command LAMMPS USers manual Table of Contents fix neb command. 525 fix nvt command 527 fix nvt/ cuda command........…..…….…….………….27 fix npt command 527 fix npt/cuda command.………… 527 fix nph command.…. 527 fix nvt/eff command .….…535 fix npt/eff command 535 fix nph/eff command.........535 fix nph/asphere command .538 fix nph/ sphere command.........…..…..….…….…...540 fix nphug command .542 fixnpaspherecommand.....................545 fix npt/sphere command 548 fix nve command..…… 550 fix nve/cuda command. .......................................................................................................550 fixnve/asplherecommand..................151 fix nve/asphere/noforce command.................................................552 fix nveleff command 553 fix nve/limit command 554 fix nve/line command. …56 fix nve/ fix nve/sphere command 558 fix nve/sphere/omp command.......................558 fix nve/tri command .560 fix nvt/asphere command 561 fix nvt/sllod command 563 fix nvt/sllod/eff command 565 fix nvt/sphere command.…………..67 fix orient/fcc command 4·:·.····· .569 fix planeforce command………… 573 fix poems 574 fix pour command..................,.,.,….,…,.576 fix press/berendsen command 番b音面看4 fix print command.……… 581 fix geg/comb command. 583 fix qeq/comb/ omp command......….….….……..…..983 fix geg/reax command 585 fix reax/ fix reax/c/bonds command 587 fix recenter command. …588 fix restrain command 590 fix rigid command fix rigid/nve command 592 fix rigid/nvt command. 音1 592 fix setforce command.............................................................598 fix setforce/ cuda command.....……598 fix shake command 600 LAMMPS USers manual Table of contents fix shake/cuda command 600 fix smd command 602 fix spring command.….….….….….….….….….….….….….….….….….….….….…..605 fix spring/rg command...…….……….607 fix spring/ self command………… 609 fix srd command 611 fix store/force command …………616 fix store/state command 617 fix temp/ berendsen command...........….….….619 fix temp/berendsen/cuda command 619 fix temp/rescale command 622 fix temp/rescale/cuda command 622 fix temp/rescale/limit/cuda command. fix temp/rescaleeff command. 625 fix thermal/conductivity command...............627 fix tmd command.…,…………….630 fix ttm command...…………1632 fix viscosity command........................,….635 fix viscous command 638 fix viscous/cuda command. 638 fix wall/j93 command .640 fix wal/jl26 command.....….….….….….….….….….….…..…....640 fix wall/colloid command 640 fix wall/harmonic command 640 fix wall/gran command 644 fix wall/piston command.........647 fix wall/reflect command 649 fix wall/region command 652 fix wall! srd command.……………655 group command........... 658 if command 660 improper_style class2 command.........................663 Improper_ style class2/ omp command.……….63 improper_coeff command...............................666 improper__ style cvff command............668 improper_style cvff/omp command....... 668 improper style harmonic command improper_style harmonic/omp command .670 improper_style hybrid command.………….….….….…………………….672 improper_ style none command 673 ·· improper style command. 674 improper_ style umbrella command 676 improper_ style umbrella,/ omp command..……………………………,676 include command..………………………………….678 jump command...........……679 kspace_ modify command…….….681 kspace_style command....,.….…….….683 label command ……………………….686

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