Lammps

  • Script de soumission (à adapter suivant vos besoins sur la version du code notamment) : run_lammps.pbs
  • Les binaires sont disponibles sous /sw/codes/lammps.
    [homer@thor ]$ ls /sw/codes/lammps/
    2013  2016 2017 2018 2021
    
  • les modules permettent de charger l'environnement de compilation dédié à la version choisi :
  • charger l'environnement mpt au préalable
    [homer@thor ]$ module av codes/lammps
    
    -------------------------------------- /sw/Modules/modulefiles --------------------------------------
    codes/lammps/2013 codes/lammps/2016 codes/lammps/2017 codes/lammps/2018 codes/lammps/2021
    

Version 2021

  • Configuration compilée :

- utilisation des compilateurs intel icpc version 18 (module intel-compilers-18 intel-cmkl-18),
- interface fft (thread) mkl ;
- plusieurs packages additionnels
- une compilation en mode d'optimisation Release sous /sw/codes/lammps/2021/mpt_thread/bin
- une seconde compilation en mode optimisation Release et interface fft/mkl sequential sous /sw/codes/lammps/2021/mpt/bin
- emplacement des binaires chargés par le module :

[homer@thor mpt_build]$ ls -lhrt /sw/codes/lammps/2021/mpt_thread/bin/*
total 772K
-rwxr-xr-x 1 homer pprime 247K Jun  9 17:54 msi2lmp
-rwxr-xr-x 1 homer pprime  30K Jun  9 17:55 binary2txt
-rwxr-xr-x 1 homer pprime  28K Jun  9 17:55 chain.x
-rwxr-xr-x 1 homer pprime 455K Jun 10 09:28 lmp
lrwxrwxrwx 1 root     root     33 Jun 10 09:48 lammps -> /sw/codes/lammps/2021/mpt_thread/bin/lmp

Usage

  1. charger le module codes/lammps/2021
  2. utiliser mpiexec_mpt dans les scripts de lancement
[homer@thor lammps]$ module add codes/lammps/2021
[homer@thor lammps]$ module li
Currently Loaded Modulefiles:
  1) intel-cc-18/18.2.199          4) intel-cmkl-18/18.2.199        7) codes/lammps/2021
  2) intel-fc-18/18.2.199          5) mpt/2.12
  3) intel-compilers-18/18.2.199   6) gnu-compilers/7.5.0

[homer@thor lammps]$ mpirun -n 1 lammps -h

Large-scale Atomic/Molecular Massively Parallel Simulator - 27 May 2021

Usage example: lammps -var t 300 -echo screen -in in.alloy

List of command line options supported by this LAMMPS executable:

-echo none/screen/log/both  : echoing of input script (-e)
-help                       : print this help message (-h)
-in none/filename           : read input from file or stdin (default) (-i)
-kokkos on/off ...          : turn KOKKOS mode on or off (-k)
-log none/filename          : where to send log output (-l)
-mdi '<mdi flags>'          : pass flags to the MolSSI Driver Interface
-mpicolor color             : which exe in a multi-exe mpirun cmd (-m)
-cite                       : select citation reminder style (-c)
-nocite                     : disable citation reminder (-nc)
-package style ...          : invoke package command (-pk)
-partition size1 size2 ...  : assign partition sizes (-p)
-plog basename              : basename for partition logs (-pl)
-pscreen basename           : basename for partition screens (-ps)
-restart2data rfile dfile ... : convert restart to data file (-r2data)
-restart2dump rfile dgroup dstyle dfile ...
                            : convert restart to dump file (-r2dump)
-reorder topology-specs     : processor reordering (-r)
-screen none/filename       : where to send screen output (-sc)
-suffix gpu/intel/opt/omp   : style suffix to apply (-sf)
-var varname value          : set index style variable (-v)

OS: Linux 2.6.32-431.17.1.el6.x86_64 on x86_64

Compiler: Intel Classic C++ 18.00.2 / Intel(R) C++ g++ 7.5 mode with OpenMP 5.0 preview 1
C++ standard: C++11
MPI v3.0: SGI MPT 2.12  04/01/15 02:12:06

Accelerator configuration:

GPU present: no

Active compile time flags:

-DLAMMPS_GZIP
-DLAMMPS_PNG
-DLAMMPS_JPEG
-DLAMMPS_SMALLBIG
sizeof(smallint): 32-bit
sizeof(imageint): 32-bit
sizeof(tagint):   32-bit
sizeof(bigint):   64-bit

Installed packages:

ASPHERE BODY COLLOID COMPRESS DIPOLE GRANULAR KSPACE MANYBODY MC MISC MOLECULE
MPIIO PERI REPLICA RIGID SHOCK SPIN SRD USER-BROWNIAN USER-DIFFRACTION
USER-MEAMC VORONOI

List of individual style options included in this LAMMPS executable

* Atom styles:

angle           atomic          body            bond            charge
dipole          ellipsoid       full            hybrid          line
molecular       peri            sphere          spin            template
tri

* Integrate styles:

respa           verlet          verlet/split

* Minimize styles:

cg              fire            fire/old        hftn            quickmin
sd              spin            spin/cg         spin/lbfgs

* Pair styles:

adp             airebo          airebo/morse    atm             beck
body/nparticle  body/rounded/polygon            body/rounded/polyhedron
bop             born            born/coul/dsf   born/coul/long  born/coul/msm
born/coul/wolf  brownian        brownian/poly   buck            buck/coul/cut
buck/coul/long  buck/coul/msm   buck/long/coul/long             colloid
comb            comb3           coul/cut        coul/cut/global coul/debye
coul/dsf        coul/long       coul/msm        coul/streitz    coul/wolf
reax            dpd             dpd/tstat       dsmc            eam
eam/alloy       eam/cd          eam/cd/old      eam/fs          eam/he
eim             gauss           gayberne        gran/hertz/history
gran/hooke      gran/hooke/history              granular        gw
gw/zbl          hbond/dreiding/lj               hbond/dreiding/morse
hybrid          hybrid/overlay  hybrid/scaled   lcbop           line/lj
lj96/cut        lj/charmm/coul/charmm           lj/charmm/coul/charmm/implicit
lj/charmm/coul/long             lj/charmm/coul/msm
lj/charmmfsw/coul/charmmfsh     lj/charmmfsw/coul/long          lj/cubic
lj/cut          lj/cut/coul/cut lj/cut/coul/debye               lj/cut/coul/dsf
lj/cut/coul/long                lj/cut/coul/msm lj/cut/coul/wolf
lj/cut/dipole/cut               lj/cut/dipole/long              lj/cut/tip4p/cut
lj/cut/tip4p/long               lj/expand       lj/gromacs
lj/gromacs/coul/gromacs         lj/long/coul/long
lj/long/dipole/long             lj/long/tip4p/long              lj/relres
lj/smooth       lj/smooth/linear                lj/sf           lubricate
lubricateU      lubricateU/poly lubricate/poly  meam/c          meam
mie/cut         morse           nb3b/harmonic   nm/cut          nm/cut/coul/cut
nm/cut/coul/long                peri/eps        peri/lps        peri/pmb
peri/ves        polymorphic     rebo            resquared       soft
spin/dipole/cut spin/dipole/long                spin/dmi        spin/exchange
spin/exchange/biquadratic       spin/magelec    spin/neel       sw
table           tersoff         tersoff/mod     tersoff/mod/c   tersoff/zbl
tip4p/cut       tip4p/long      tri/lj          ufm             vashishta
vashishta/table yukawa          yukawa/colloid  zbl             zero

* Bond styles:

fene            fene/expand     gromos          harmonic        hybrid
morse           nonlinear       quartic         table           zero

* Angle styles:

charmm          cosine          cosine/delta    cosine/periodic cosine/squared
harmonic        hybrid          table           zero

* Dihedral styles:

charmm          charmmfsw       harmonic        helix           hybrid
multi/harmonic  opls            zero

* Improper styles:

cvff            harmonic        hybrid          umbrella        zero

* KSpace styles:

ewald           ewald/dipole    ewald/dipole/spin               ewald/disp
msm             msm/cg          pppm            pppm/cg         pppm/dipole
pppm/dipole/spin                pppm/disp       pppm/disp/tip4p pppm/stagger
pppm/tip4p

* Fix styles

adapt           addforce        append/atoms    atom/swap       ave/atom
ave/chunk       ave/correlate   ave/histo       ave/histo/weight
ave/time        aveforce        balance         bond/break      bond/create
bond/create/angle               bond/swap       box/relax       brownian
brownian/asphere                brownian/sphere charge/regulation
cmap            controller      deform          deposit         ave/spatial
ave/spatial/sphere              drag            dt/reset        efield
ehex            enforce2d       evaporate       external        freeze
gcmc            gld             gravity         halt            heat
hyper/global    hyper/local     indent          langevin        langevin/spin
lineforce       momentum        move            msst            neb
neb/spin        nph             nph/asphere     nph/body        nph/sphere
nphug           npt             npt/asphere     npt/body        npt/sphere
numdiff         nve             nve/asphere     nve/asphere/noforce
nve/body        nve/limit       nve/line        nve/noforce     nve/sphere
nve/spin        nve/tri         nvt             nvt/asphere     nvt/body
nvt/sllod       nvt/sphere      oneway          orient/bcc      orient/fcc
planeforce      pour            precession/spin press/berendsen print
propel/self     property/atom   qeq/comb        rattle          recenter
restrain        rigid           rigid/nph       rigid/nph/small rigid/npt
rigid/npt/small rigid/nve       rigid/nve/small rigid/nvt       rigid/nvt/small
rigid/small     saed/vtk        setforce        setforce/spin   shake
spring          spring/chunk    spring/rg       spring/self     srd
store/force     store/state     temp/berendsen  temp/csld       temp/csvr
temp/rescale    tfmc            thermal/conductivity            tmd
ttm             tune/kspace     vector          viscosity       viscous
wall/body/polygon               wall/body/polyhedron            wall/colloid
wall/gran       wall/gran/region                wall/harmonic   wall/lj1043
wall/lj126      wall/lj93       wall/morse      wall/piston     wall/reflect
wall/region     wall/srd        widom

* Compute styles:

adf             aggregate/atom  angle           angle/local     angmom/chunk
body/local      bond            bond/local      centro/atom
centroid/stress/atom            chunk/atom      chunk/spread/atom
cluster/atom    cna/atom        com             com/chunk       contact/atom
coord/atom      damage/atom     dihedral        dihedral/local  dilatation/atom
dipole/chunk    displace/atom   erotate/asphere erotate/rigid   erotate/sphere
erotate/sphere/atom             event/displace  fragment/atom   global/atom
group/group     gyration        gyration/chunk  heat/flux       hexorder/atom
improper        improper/local  inertia/chunk   ke              ke/atom
ke/rigid        msd             msd/chunk       msd/nongauss    omega/chunk
orientorder/atom                pair            pair/local      pe
pe/atom         plasticity/atom pressure        property/atom   property/chunk
property/local  rdf             reduce          reduce/chunk    reduce/region
rigid/local     saed            slice           spin            stress/atom
temp            temp/asphere    temp/body       temp/chunk      temp/com
temp/deform     temp/partial    temp/profile    temp/ramp       temp/region
temp/sphere     ti              torque/chunk    vacf            vcm/chunk
voronoi/atom    xrd

* Region styles:

block           cone            cylinder        intersect       plane
prism           sphere          union

* Dump styles:

atom            atom/gz         atom/mpiio      cfg             cfg/gz
cfg/mpiio       custom          custom/gz       custom/mpiio    dcd
image           local           local/gz        movie           xtc
xyz             xyz/gz          xyz/mpiio

* Command styles

balance         change_box      create_atoms    create_bonds    create_box
delete_atoms    delete_bonds    reset_ids       kim_init        kim_interactions
kim_param       kim_property    kim_query       displace_atoms  hyper
info            minimize        neb             neb/spin        prd
read_data       read_dump       read_restart    replicate       rerun
reset_atom_ids  reset_mol_ids   run             set             tad
temper          velocity        write_coeff     write_data      write_dump
write_restart

Version 2018

  • Configuration actuelle :

- utilisation des compilateurs intel icpc version 16 (module intel-compilers-16 intel-cmkl-16),
- interface fftw3/mkl (disponible à /opt/intel/impi/5.1/compilers_and_libraries_2016.1.150/linux/mkl/lib/intel64/libfftw2xc_double_intel.a)
- plusieurs packages additionnels
- une compilation en mode d'optimisation Release, et une seconde en mode RelWithDebInfo disponible sous /sw/codes/lammps/2018/mpt/bin
- emplacement des binaires :

[homer@thor mpt_build]$ ls -lhrt /sw/codes/lammps/2018/mpt/bin/*
-rwxr-xr-x 1 root root  21M Apr  6 12:34 /sw/codes/lammps/2018/mpt/bin/lmp_sgi_O3avx_ompintel
lrwxrwxrwx 1 root root   52 Apr  6 12:41 /sw/codes/lammps/2018/mpt/bin/lmp -> /sw/codes/lammps/2018/mpt/bin/lmp_sgi_O3avx_ompintel
lrwxrwxrwx 1 root root   52 Apr  6 12:41 /sw/codes/lammps/2018/mpt/bin/lammps -> /sw/codes/lammps/2018/mpt/bin/lmp_sgi_O3avx_ompintel
-rwxr-xr-x 1 root root 685K Apr  6 12:44 /sw/codes/lammps/2018/mpt/bin/voro++
-rwxr-xr-x 1 root root  58M Apr  8 14:03 /sw/codes/lammps/2018/mpt/bin/lmp_sgi_O2avx_ompintel
  • Utilisation du module codes/lammps/2018
    [homer@thor mpt_build]$ module show codes/lammps/2018
    -------------------------------------------------------------------
    /sw/Modules/modulefiles/codes/lammps/2018:
    
    conflict     intel-cmkl-14 intel-cmkl-15
    conflict     intel-compilers-14 intel-compilers-15
    conflict     intel-mpi-4 intel-mpi-5 openmpi
    module-whatis     loads the LAMMPS code environment
    prepend-path     PATH /sw/codes/lammps/2018/mpt/bin
    prepend-path     MANPATH /sw/codes/lammps/2018/mpt/share/man/man1
    system         bash /sw/codes/lammps/2018/mpt/etc/profile.d/lammps.sh
    prepend-path     LD_LIBRARY_PATH /opt/intel/impi/5.1/compilers_and_libraries_2016.1.150/linux/tbb/lib/intel64/gcc4.4
    -------------------------------------------------------------------
    
  • Usage
    [homer@thor mpt_build]$ module purge 
    [homer@thor mpt_build]$ module add codes/lammps/2018
    [homer@thor mpt_build]$ module li
    Currently Loaded Modulefiles:
      1) intel-cc-16/16.0.1          3) intel-compilers-16/16.0.1   5) mpt/2.12                    7) utils/cmake-3.8.2
      2) intel-fc-16/16.0.1          4) intel-cmkl-16/16.0.1        6) codes/lammps/2018
    [homer@thor mpt_build]$ which lammps
    /sw/codes/lammps/2018/mpt/bin/lammps
    [homer@thor mpt_build]$ mpirun -n 1 lammps -h
    LAMMPS (12 Dec 2018)
    OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
      using 1 OpenMP thread(s) per MPI task
    
    Large-scale Atomic/Molecular Massively Parallel Simulator - 12 Dec 2018
    
    Usage example: lammps -var t 300 -echo screen -in in.alloy
    
    List of command line options supported by this LAMMPS executable:
    
    -echo none/screen/log/both  : echoing of input script (-e)
    -help                       : print this help message (-h)
    -in filename                : read input from file, not stdin (-i)
    -kokkos on/off ...          : turn KOKKOS mode on or off (-k)
    -log none/filename          : where to send log output (-l)
    -mpicolor color             : which exe in a multi-exe mpirun cmd (-m)
    -nocite                     : disable writing log.cite file (-nc)
    -package style ...          : invoke package command (-pk)
    -partition size1 size2 ...  : assign partition sizes (-p)
    -plog basename              : basename for partition logs (-pl)
    -pscreen basename           : basename for partition screens (-ps)
    -restart2data rfile dfile ... : convert restart to data file (-r2data)
    -restart2dump rfile dgroup dstyle dfile ...
                                : convert restart to dump file (-r2dump)
    -reorder topology-specs     : processor reordering (-r)
    -screen none/filename       : where to send screen output (-sc)
    -suffix gpu/intel/opt/omp   : style suffix to apply (-sf)
    -var varname value          : set index style variable (-v)
    
    Active compile time flags:
    
    -DLAMMPS_GZIP
    -DLAMMPS_PNG
    -DLAMMPS_JPEG
    
    Installed packages:
    
    ASPHERE BODY COLLOID COMPRESS CORESHELL DIPOLE GRANULAR KSPACE MANYBODY MC
    MEAM MISC MOLECULE MPIIO OPT PERI POEMS REAX REPLICA RIGID SHOCK SNAP SPIN SRD
    USER-DIFFRACTION USER-INTEL USER-MEAMC USER-OMP VORONOI
    
    List of individual style options included in this LAMMPS executable
    
    * Atom styles:
    
    angle           atomic          body            bond            charge
    dipole          ellipsoid       full            hybrid          line
    molecular       peri            sphere          spin            template
    tri
    
    * Integrate styles:
    
    respa           respa/omp       verlet          verlet/split
    
    * Minimize styles:
    
    cg              fire            hftn            quickmin        sd
    
    * Pair styles:
    
    adp             adp/omp         airebo          airebo/morse    airebo/morse/omp
    airebo/omp      atm             beck            beck/omp        body/nparticle
    body/rounded/polygon            body/rounded/polyhedron         bop
    born            born/coul/dsf   born/coul/dsf/cs                born/coul/long
    born/coul/long/cs               born/coul/long/omp              born/coul/msm
    born/coul/msm/omp               born/coul/wolf  born/coul/wolf/cs
    born/coul/wolf/omp              born/omp        brownian        brownian/omp
    brownian/poly   brownian/poly/omp               buck            buck/coul/cut
    buck/coul/cut/omp               buck/coul/long  buck/coul/long/cs
    buck/coul/long/omp              buck/coul/msm   buck/coul/msm/omp
    buck/long/coul/long             buck/long/coul/long/omp         buck/omp
    colloid         colloid/omp     comb            comb3           comb/omp
    coul/cut        coul/cut/omp    coul/debye      coul/debye/omp  coul/dsf
    coul/dsf/omp    coul/long       coul/long/cs    coul/long/omp   coul/msm
    coul/msm/omp    coul/streitz    coul/wolf       coul/wolf/cs    coul/wolf/omp
    dpd             dpd/omp         dpd/tstat       dpd/tstat/omp   dsmc
    eam             eam/alloy       eam/alloy/omp   eam/alloy/opt   eam/cd
    eam/cd/old      eam/cd/omp      eam/cd/old/omp  eam/fs          eam/fs/omp
    eam/fs/opt      eam/omp         eam/opt         eim             eim/omp
    gauss           gauss/omp       gayberne        gayberne/omp
    gran/hertz/history              gran/hertz/history/omp          gran/hooke
    gran/hooke/history              gran/hooke/history/omp          gran/hooke/omp
    gw              gw/zbl          hbond/dreiding/lj
    hbond/dreiding/lj/omp           hbond/dreiding/morse
    hbond/dreiding/morse/omp        hybrid          hybrid/overlay  lcbop
    line/lj         lj96/cut        lj96/cut/omp    lj/charmm/coul/charmm
    lj/charmm/coul/charmm/implicit  lj/charmm/coul/charmm/implicit/omp
    lj/charmm/coul/charmm/omp       lj/charmm/coul/long
    lj/charmm/coul/long/omp         lj/charmm/coul/long/opt
    lj/charmm/coul/msm              lj/charmm/coul/msm/omp
    lj/charmmfsw/coul/charmmfsh     lj/charmmfsw/coul/long          lj/cubic
    lj/cubic/omp    lj/cut          lj/cut/coul/cut lj/cut/coul/cut/omp
    lj/cut/coul/debye               lj/cut/coul/debye/omp           lj/cut/coul/dsf
    lj/cut/coul/dsf/omp             lj/cut/coul/long
    lj/cut/coul/long/cs             lj/cut/coul/long/omp
    lj/cut/coul/long/opt            lj/cut/coul/msm lj/cut/coul/msm/omp
    lj/cut/coul/wolf                lj/cut/coul/wolf/omp
    lj/cut/dipole/cut               lj/cut/dipole/cut/omp
    lj/cut/dipole/long              lj/cut/omp      lj/cut/opt      lj/cut/tip4p/cut
    lj/cut/tip4p/cut/omp            lj/cut/tip4p/long
    lj/cut/tip4p/long/omp           lj/cut/tip4p/long/opt           lj/expand
    lj/expand/omp   lj/gromacs      lj/gromacs/coul/gromacs
    lj/gromacs/coul/gromacs/omp     lj/gromacs/omp  lj/long/coul/long
    lj/long/coul/long/omp           lj/long/coul/long/opt
    lj/long/dipole/long             lj/long/tip4p/long
    lj/long/tip4p/long/omp          lj/smooth       lj/smooth/linear
    lj/sf           lj/smooth/linear/omp            lj/sf/omp       lj/smooth/omp
    lubricate       lubricateU      lubricateU/poly lubricate/omp   lubricate/poly
    lubricate/poly/omp              meam            meam/c          mie/cut
    morse           morse/omp       morse/opt       nb3b/harmonic   nm/cut
    nm/cut/coul/cut nm/cut/coul/cut/omp             nm/cut/coul/long
    nm/cut/coul/long/omp            nm/cut/omp      peri/eps        peri/lps
    peri/lps/omp    peri/pmb        peri/pmb/omp    peri/ves        polymorphic
    reax            rebo            rebo/omp        resquared       resquared/omp
    snap            soft            soft/omp        spin/dmi        spin/exchange
    spin/magelec    spin/neel       sw              sw/omp          table
    table/omp       tersoff         tersoff/mod     tersoff/mod/c
    tersoff/mod/c/omp               tersoff/mod/omp tersoff/omp     tersoff/zbl
    tersoff/zbl/omp tip4p/cut       tip4p/cut/omp   tip4p/long      tip4p/long/omp
    tri/lj          ufm             ufm/omp         ufm/opt         vashishta
    vashishta/omp   vashishta/table vashishta/table/omp             yukawa
    yukawa/colloid  yukawa/colloid/omp              yukawa/omp      zbl
    zbl/omp         zero
    
    

Version 2017

Compilation

  • Compilé avec compilateur intel (v15), mpt, et wrapper fftw/intel et optimisé O3
  • Packages installés (http://lammps.sandia.gov/doc/Section_packages.html#)
    [homer@thor src]$ make ps | grep YES
    Installed YES: package ASPHERE
    Installed YES: package BODY
    Installed YES: package CLASS2
    Installed YES: package COLLOID
    Installed YES: package COMPRESS
    Installed YES: package CORESHELL
    Installed YES: package DIPOLE
    Installed YES: package GRANULAR
    Installed YES: package KSPACE
    Installed YES: package MANYBODY
    Installed YES: package MC
    Installed YES: package MEAM
    Installed YES: package MISC
    Installed YES: package MOLECULE
    Installed YES: package MPIIO
    Installed YES: package OPT
    Installed YES: package PERI
    Installed YES: package POEMS
    Installed YES: package QEQ
    Installed YES: package REAX
    Installed YES: package REPLICA
    Installed YES: package RIGID
    Installed YES: package SHOCK
    Installed YES: package SNAP
    Installed YES: package SRD
    Installed YES: package VORONOI
    Installed YES: package USER-MEAMC
    Installed YES: package USER-SPH
    
  • Une 2nde version disposant de fonctionnalité d'optimisation (USER-INTEL, USER-OMP) supplémentaire pour certains potentiels est disponible avec le binaire lmp_sgi_O3avx_ompintel (voir http://lammps.sandia.gov/doc/Section_packages.html#user-intel-package)
  • Une 3è version avec une optimisation O2 est aussi disponible (avec les packages d'optimisation USER-INTEL, USER-OMP, linké avec thread building block d'intel) avec le binaire : lmp_sgi_O2avx_ompintel.

Utilisation

[homer@thor ~]$ module purge
[homer@thor ~]$ module add codes/lammps/2017
[homer@thor ~]$ mpirun -np 1 lammps -h
LAMMPS (11 Aug 2017)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
  using 1 OpenMP thread(s) per MPI task

Large-scale Atomic/Molecular Massively Parallel Simulator - 11 Aug 2017

Version 2016

Compilation

  • Packages installés
[homer@thor src]$ make ps | grep YES
Installed YES: package ASPHERE
Installed YES: package BODY
Installed YES: package CLASS2
Installed YES: package COLLOID
Installed YES: package COMPRESS
Installed YES: package CORESHELL
Installed YES: package DIPOLE
Installed YES: package GRANULAR
Installed YES: package KSPACE
Installed YES: package MANYBODY
Installed YES: package MC
Installed YES: package MEAM
Installed YES: package MISC
Installed YES: package MOLECULE
Installed YES: package MPIIO
Installed YES: package OPT
Installed YES: package PERI
Installed YES: package POEMS
Installed YES: package QEQ
Installed YES: package REAX
Installed YES: package REPLICA
Installed YES: package RIGID
Installed YES: package SHOCK
Installed YES: package SNAP
Installed YES: package SRD
Installed YES: package VORONOI

Utilisation

[homer@thor src]$ module purge
[homer@thor src]$ module add codes/lammps/2016
[homer@thor src]$ mpirun -n  1 lammps -h
LAMMPS (14 May 2016)
WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:90)
  using 1 OpenMP thread(s) per MPI task

Command line options:

-cuda on/off                : turn CUDA mode on or off (-c)
-echo none/screen/log/both  : echoing of input script (-e)
-help                       : print this help message (-h)
-in filename                : read input from file, not stdin (-i)
-kokkos on/off ...          : turn KOKKOS mode on or off (-k)
-log none/filename          : where to send log output (-l)
-nocite                     : disable writing log.cite file (-nc)
-package style ...          : invoke package command (-pk)
-partition size1 size2 ...  : assign partition sizes (-p)
-plog basename              : basename for partition logs (-pl)
-pscreen basename           : basename for partition screens (-ps)
-restart rfile dfile ...    : convert restart to data file (-r)
-reorder topology-specs     : processor reordering (-r)
-screen none/filename       : where to send screen output (-sc)
-suffix cuda/gpu/opt/omp    : style suffix to apply (-sf)
-var varname value          : set index style variable (-v)

Style options compiled with this executable

* Atom styles:

angle           atomic          body            bond            charge
dipole          ellipsoid       full            hybrid          line
molecular       peri            sphere          template        tri

* Integrate styles:

respa           verlet          verlet/split

* Minimize styles:

cg              fire            hftn            quickmin        sd

* Pair styles:

adp             airebo          airebo/morse    beck            body
bop             born/coul/long/cs               born/coul/long  born/coul/msm
born/coul/wolf  born            brownian        brownian/poly   buck/coul/cut
buck/coul/long/cs               buck/coul/long  buck/coul/msm   buck
buck/long/coul/long             colloid         comb3           comb
coul/cut        coul/debye      coul/dsf        coul/long/cs    coul/long
coul/msm        coul/streitz    coul/wolf       dpd             dpd/tstat
dsmc            eam/alloy       eam/fs          eam             eim
gauss           gayberne        gran/hertz/history              gran/hooke
gran/hooke/history              hbond/dreiding/lj
hbond/dreiding/morse            hybrid          hybrid/overlay  lcbop
line/lj         lj96/cut        lj/charmm/coul/charmm
lj/charmm/coul/charmm/implicit  lj/charmm/coul/long
lj/charmm/coul/msm              lj/class2/coul/cut
lj/class2/coul/long             lj/class2       lj/cubic        lj/cut/coul/cut
lj/cut/coul/debye               lj/cut/coul/dsf lj/cut/coul/long/cs
lj/cut/coul/long                lj/cut/coul/msm lj/cut/dipole/cut
lj/cut/dipole/long              lj/cut          lj/cut/tip4p/cut
lj/cut/tip4p/long               lj/expand       lj/gromacs/coul/gromacs
lj/gromacs      lj/long/coul/long               lj/long/dipole/long
lj/long/tip4p/long              lj/smooth       lj/smooth/linear
lubricate       lubricate/poly  lubricateU      lubricateU/poly mie/cut
morse           nb3b/harmonic   nm/cut/coul/cut nm/cut/coul/long
nm/cut          peri/eps        peri/lps        peri/pmb        peri/ves
polymorphic     rebo            resquared       snap            soft
sw              table           tersoff         tersoff/mod     tersoff/zbl
tip4p/cut       tip4p/long      tri/lj          vashishta       yukawa/colloid
yukawa          zbl             zero

* Bond styles:

class2          fene/expand     fene            harmonic        hybrid
morse           nonlinear       quartic         table           zero

* Angle styles:

charmm          class2          cosine/delta    cosine          cosine/periodic
cosine/squared  harmonic        hybrid          table           zero

* Dihedral styles:

charmm          class2          harmonic        helix           hybrid
multi/harmonic  opls            zero

* Improper styles:

class2          cvff            harmonic        hybrid          umbrella
zero

* KSpace styles:

ewald/disp      ewald           msm/cg          msm             pppm/cg
pppm/disp       pppm/disp/tip4p pppm            pppm/stagger    pppm/tip4p

* Fix styles

adapt           addforce        append/atoms    atom/swap       ave/atom
ave/chunk       ave/correlate   aveforce        ave/histo       ave/histo/weight
ave/spatial     ave/time        balance         bond/break      bond/create
bond/swap       box/relax       deform          deposit         drag
dt/reset        efield          enforce2d       evaporate       external
freeze          gcmc            gld             gravity         heat
indent          langevin        lineforce       momentum        move
msst            neb             nph/asphere     nph/body        nph
nph/sphere      nphug           npt/asphere     npt/body        npt
npt/sphere      nve/asphere     nve/asphere/noforce             nve/body
nve             nve/limit       nve/line        nve/noforce     nve/sphere
nve/tri         nvt/asphere     nvt/body        nvt             nvt/sllod
nvt/sphere      oneway          orient/fcc      planeforce      pour
press/berendsen print           property/atom   qeq/comb        qeq/dynamic
qeq/fire        qeq/point       qeq/shielded    qeq/slater      rattle
recenter        restrain        rigid           rigid/nph       rigid/nph/small
rigid/npt       rigid/npt/small rigid/nve       rigid/nve/small rigid/nvt
rigid/nvt/small rigid/small     setforce        shake           spring
spring/rg       spring/self     srd             store/force     store/state
temp/berendsen  temp/csld       temp/csvr       temp/rescale    tfmc
thermal/conductivity            tmd             ttm             tune/kspace
vector          viscosity       viscous         wall/colloid    wall/gran
wall/harmonic   wall/lj1043     wall/lj126      wall/lj93       wall/piston
wall/reflect    wall/region     wall/srd

* Compute styles:

angle           angle/local     angmom/chunk    body/local      bond
bond/local      centro/atom     chunk/atom      cluster/atom    cna/atom
com/chunk       com             contact/atom    coord/atom      damage/atom
dihedral        dihedral/local  dilatation/atom dipole/chunk    displace/atom
erotate/asphere erotate/rigid   erotate/sphere/atom             erotate/sphere
event/displace  group/group     gyration/chunk  gyration        heat/flux
hexorder/atom   improper        improper/local  inertia/chunk   ke/atom
ke              ke/rigid        msd/chunk       msd             msd/nongauss
omega/chunk     orientorder/atom                pair            pair/local
pe/atom         pe              plasticity/atom pressure        property/atom
property/chunk  property/local  rdf             reduce          reduce/region
slice           sna/atom        snad/atom       snav/atom       stress/atom
temp/asphere    temp/body       temp/chunk      temp/com        temp/cs
temp/deform     temp            temp/partial    temp/profile    temp/ramp
temp/region     temp/sphere     ti              torque/chunk    vacf
vcm/chunk

* Region styles:

block           cone            cylinder        intersect       plane
prism           sphere          union

* Dump styles:

atom            atom/mpiio      cfg             cfg/mpiio       custom
custom/mpiio    dcd             image           local           movie
xtc             xyz             xyz/mpiio

* Command styles

balance         change_box      create_atoms    create_bonds    create_box
delete_atoms    delete_bonds    displace_atoms  info            minimize
neb             prd             read_data       read_dump       read_restart
replicate       rerun           run             set             tad
temper          velocity        write_coeff     write_data      write_dump
write_restart

Version 2013

Utilisation

module purge
module load codes/lammps/2013
mpirun -np 1 lammps_mpt -h
LAMMPS (31 Dec 2013)
WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:100)
using 1 OpenMP thread(s) per MPI task

Command line options:

-cuda on/off : turn CUDA mode on or off (-c)
-echo none/screen/log/both : echoing of input script (-e)
-in filename : read input from file, not stdin (-i)
-help : print this help message (-h)
-log none/filename : where to send log output (-l)
-nocite : disable writing log.cite file (-nc)
-partition size1 size2 ... : assign partition sizes (-p)
-plog basename : basename for partition logs (-pl)
-pscreen basename : basename for partition screens (-ps)
-reorder topology-specs : processor reordering (-r)
-screen none/filename : where to send screen output (-sc)
-suffix cuda/gpu/opt/omp : style suffix to apply (-sf)
-var varname value : set index style variable (-v)

Style options compiled with this executable

* Atom styles:

angle atomic body bond charge
ellipsoid full hybrid line molecular
sphere tri

* Integrate styles:

respa verlet

* Minimize styles:

cg fire hftn quickmin sd

* Pair styles:

adp airebo beck bop born/coul/long
born/coul/msm born/coul/wolf born buck/coul/cut buck/coul/long
buck/coul/msm buck buck/long/coul/long comb3
comb coul/cut coul/debye coul/dsf coul/long
coul/msm coul/wolf dpd dpd/tstat eam/alloy
eam/alloy/opt eam/fs eam/fs/opt eam eam/opt
eim gauss gayberne gran/hertz/history
gran/hooke gran/hooke/history hbond/dreiding/lj
hbond/dreiding/morse hybrid hybrid/overlay lcbop
line/lj lj96/cut lj/charmm/coul/charmm
lj/charmm/coul/charmm/implicit lj/charmm/coul/long
lj/charmm/coul/long/opt lj/charmm/coul/msm lj/cubic
lj/cut/coul/cut lj/cut/coul/debye lj/cut/coul/dsf lj/cut/coul/long
lj/cut/coul/long/opt lj/cut/coul/msm lj/cut lj/cut/opt
lj/cut/tip4p/cut lj/cut/tip4p/long
lj/cut/tip4p/long/opt lj/expand lj/gromacs/coul/gromacs
lj/gromacs lj/long/coul/long lj/long/coul/long/opt
lj/long/tip4p/long lj/smooth lj/smooth/linear
meam mie/cut morse morse/opt nb3b/harmonic
rebo resquared soft sw table
tersoff tersoff/mod tersoff/zbl tip4p/cut tip4p/long
tri/lj yukawa zbl

* Bond styles:

fene/expand fene harmonic hybrid morse
nonlinear quartic table

* Angle styles:

charmm cosine/delta cosine cosine/periodic cosine/squared
harmonic hybrid table

* Dihedral styles:

charmm harmonic helix hybrid multi/harmonic
opls

* Improper styles:

cvff harmonic hybrid umbrella

* KSpace styles:

ewald/disp ewald msm/cg msm pppm/cg
pppm/disp pppm/disp/tip4p pppm pppm/old pppm/stagger
pppm/tip4p

* Fix styles

adapt addforce ave/atom ave/correlate aveforce
ave/histo ave/spatial ave/time balance box/relax
deform drag dt/reset enforce2d external
freeze gravity heat indent langevin
lineforce momentum move nph/asphere nph
nph/sphere npt/asphere npt npt/sphere nve/asphere
nve/asphere/noforce nve nve/limit nve/line
nve/noforce nve/sphere nve/tri nvt/asphere nvt
nvt/sllod nvt/sphere planeforce pour press/berendsen
print property/atom qeq/comb recenter restrain
setforce spring spring/rg spring/self store/force
store/state temp/berendsen temp/rescale tmd tune/kspace
viscous wall/gran wall/harmonic wall/lj1043 wall/lj126
wall/lj93 wall/reflect wall/region

* Compute styles:

angle/local atom/molecule bond/local centro/atom cluster/atom
cna/atom com com/molecule contact/atom coord/atom
dihedral/local displace/atom erotate/asphere erotate/sphere/atom
erotate/sphere group/group gyration gyration/molecule
heat/flux improper/local inertia/molecule ke/atom
ke msd msd/molecule pair pair/local
pe/atom pe pressure property/atom property/local
property/molecule rdf reduce reduce/region
slice stress/atom temp/asphere temp/com temp/deform
temp temp/partial temp/profile temp/ramp temp/region
temp/sphere vacf

* Region styles:

block cone cylinder intersect plane
prism sphere union

* Dump styles:

atom cfg custom dcd image
local movie xyz

* Command styles

balance change_box create_atoms create_box delete_atoms
delete_bonds displace_atoms minimize read_data read_dump
read_restart replicate rerun run set
velocity write_data write_dump write_restart