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 2022
- les modules permettent de charger l'environnement de compilation dédié à la version choisi :
- charger l'environnement
mptau 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 codes/lammps/2022
Version 2022¶
- Configuration compilée :
- utilisation des compilateurs intel
icpcversion 18 (module intel-compilers-18 intel-cmkl-18),
- interface fft (thread)mkl;
- plusieurs packages additionnels
- une compilation en mode d'optimisationReleasesous/sw/codes/lammps/2022/mpt/bin
- emplacement des binaires chargés par le module :
[homer@thor mpt_build]$ ls -lhrt /sw/codes/lammps/2022/mpt/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/2022/mpt/bin/lmp
Usage¶
- charger le module
codes/lammps/2022 - utiliser
mpiexec_mptdans les scripts de lancement
[homer@thor lammps]$ module add codes/lammps/2022
[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/2022
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 - 23 Jun 2022 - Update 1
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)
-skiprun : skip loops in run and minimize (-sr)
-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 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:
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
Available compression formats:
Extension: .gz Command: gzip
Extension: .bz2 Command: bzip2
Extension: .xz Command: xz
Extension: .lzma Command: xz
Installed packages:
ASPHERE BODY BROWNIAN COLLOID COMPRESS CORESHELL DIFFRACTION DIPOLE
EXTRA-MOLECULE GRANULAR KSPACE MANYBODY MC MEAM MISC MOLECULE MPIIO PERI
REPLICA RIGID SHOCK SPIN SRD
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 agni airebo airebo/morse atm
body/nparticle body/rounded/polygon body/rounded/polyhedron
bop born born/coul/long born/coul/long/cs
born/coul/msm brownian brownian/poly buck buck/coul/cut
buck/coul/long buck/coul/long/cs buck/coul/msm
buck/long/coul/long colloid comb comb3
coul/cut coul/debye coul/dsf coul/long coul/long/cs
coul/msm coul/streitz coul/wolf coul/wolf/cs reax
dsmc eam eam/alloy eam/cd eam/cd/old
eam/fs eam/he edip edip/multi eim
extep 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 list
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/cut
lj/cut/coul/cut lj/cut/coul/long lj/cut/coul/long/cs
lj/cut/coul/msm lj/cut/dipole/cut lj/cut/dipole/long
lj/cut/tip4p/cut lj/cut/tip4p/long lj/expand
lj/long/coul/long lj/long/dipole/long
lj/long/tip4p/long lj/sf/dipole/sf local/density lubricate
lubricateU lubricateU/poly lubricate/poly meam meam/c
meam/spline meam/sw/spline morse nb3b/harmonic 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 srp sw sw/angle/table sw/mod
table tersoff tersoff/mod tersoff/mod/c tersoff/table
tersoff/zbl threebody/table tip4p/cut tip4p/long tracker
tri/lj vashishta vashishta/table yukawa yukawa/colloid
zbl zero
* Bond styles:
fene fene/expand fene/nm gaussian gromos
harmonic harmonic/shift harmonic/shift/cut hybrid
morse nonlinear quartic special table
zero
* Angle styles:
charmm cosine cosine/delta cosine/periodic cosine/shift
cosine/shift/exp cosine/squared dipole fourier
fourier/simple gaussian harmonic hybrid quartic
table zero
* Dihedral styles:
charmm charmmfsw cosine/shift/exp fourier
harmonic helix hybrid multi/harmonic nharmonic
opls quadratic spherical table table/cut
zero
* Improper styles:
cossq cvff distance fourier harmonic
hybrid ring umbrella zero
* KSpace styles:
ewald ewald/dipole ewald/dipole/spin ewald/disp
ewald/disp/dipole msm msm/cg pppm
pppm/cg pppm/dipole pppm/dipole/spin pppm/disp
pppm/disp/tip4p pppm/stagger pppm/tip4p
* Fix styles
accelerate/cos 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 damping/cundall deform deposit ave/spatial
ave/spatial/sphere lb/pc lb/rigid/pc/sphere
client/md dt/reset efield ehex enforce2d
evaporate external freeze gcmc gravity
grem halt heat hyper/global hyper/local
imd indent ipi langevin langevin/spin
lineforce mol/swap momentum move msst
neb neb/spin nph nph/asphere nph/body
nph/sphere nphug npt npt/asphere npt/body
npt/sphere 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 pimd 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/self srd store/force store/state temp/berendsen
temp/rescale tfmc thermal/conductivity tune/kspace
vector 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:
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 dipole/chunk
displace/atom erotate/asphere erotate/rigid erotate/sphere
erotate/sphere/atom event/displace fabric fragment/atom
global/atom group/group gyration gyration/chunk heat/flux
improper improper/local inertia/chunk ke ke/atom
ke/rigid msd msd/chunk 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/cs temp/deform
temp/partial temp/profile temp/ramp temp/region temp/sphere
torque/chunk vacf vcm/chunk viscosity/cos xrd
* Region styles:
block cone cylinder ellipsoid intersect
plane prism sphere union
* Dump styles:
atom atom/gz atom/mpiio cfg cfg/gz
cfg/mpiio custom custom/gz custom/mpiio image
local local/gz movie 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 message server
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 temper/grem temper/npt
velocity write_coeff write_data write_dump write_restart
Version 2021¶
- Configuration compilée :
- utilisation des compilateurs intel
icpcversion 18 (module intel-compilers-18 intel-cmkl-18),
- interface fft (thread)mkl;
- plusieurs packages additionnels
- une compilation en mode d'optimisationReleasesous/sw/codes/lammps/2021/mpt_thread/bin
- une seconde compilation en mode optimisationReleaseet 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¶
- charger le module
codes/lammps/2021 - utiliser
mpiexec_mptdans 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
icpcversion 16 (module intel-compilers-16 intel-cmkl-16),
- interfacefftw3/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'optimisationRelease, et une seconde en modeRelWithDebInfodisponible 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 binairelmp_sgi_O3avx_ompintel(voir http://lammps.sandia.gov/doc/Section_packages.html#user-intel-package) - Une 3è version avec une optimisation
O2est aussi disponible (avec les packages d'optimisationUSER-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