[ase-users] Lammps Pt test fails due to unknown eam potential
Ask Hjorth Larsen
asklarsen at gmail.com
Wed Sep 26 02:45:37 CEST 2018
Hi Leon,
Am Di., 25. Sep. 2018 um 14:51 Uhr schrieb laavakyan via ase-users
<ase-users at listserv.fysik.dtu.dk>:
>
> Hello, Ask,
>
> may be compilation should be performed with extensions?
> Try
> make yes-MANYBODY
> or
> make yes-USER-MEAMC
> and recompile
Thank you very much. Indeed the yes-MANYBODY did the trick.
Best regards
Ask
>
> Thanks for the care for lammpsrun calculator,
> Best regards,
> Leon
>
> On 25.09.2018 13:00, ase-users-request at listserv.fysik.dtu.dk wrote:
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> > 1. Lammps Pt test fails due to unknown eam potential
> > (Ask Hjorth Larsen)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Mon, 24 Sep 2018 17:42:25 +0200
> > From: Ask Hjorth Larsen <asklarsen at gmail.com>
> > To: ase-users <ase-users at listserv.fysik.dtu.dk>
> > Subject: [ase-users] Lammps Pt test fails due to unknown eam potential
> > Message-ID:
> > <CACu53wkkrJ3hy_AoP6M+5-0LcHz=AzzN4K4GoYgv1P75hqcpyw at mail.gmail.com>
> > Content-Type: text/plain; charset="UTF-8"
> >
> > Hello,
> >
> > I was trying to compile a recent LAMMPS (22 Aug 2018)
> > and run the lammpsrun/Pt_md_constraints_multistep.py test:
> >
> > ase test /home/askhl/src/ase/ase/test/lammpsrun/Pt_md_constraints_multistep.py
> > --calculators=lammpsrun
> >
> > However I get this error:
> >
> > ### interactions
> > pair_style eam
> > ERROR: Unknown pair style eam (../force.cpp:262)
> > Last command: pair_style eam
> >
> > I have not compiled or used Lammps before, so I may simply be doing
> > something wrong. However the test passes when I use the lammps
> > provided with debian, which is called 0~20161109.git9806da6-7. Might
> > it be that the most recent Lammps does not have that kind of
> > potential, or did I mess up the compilation (used cmake with basically
> > no extra configuration).
> >
> > More info obtained by setting tmp_dir and looking at things below.
> >
> > Any help would be appreciated.
> >
> > Best regards
> > Ask
> >
> > Input file generated by ASE:
> > --------------------
> > $ cat in_lammps000001w8rfw53_
> > # (written by ASE)
> > clear
> > variable dump_file string
> > "/home/aimsuser/testlammps/out/trj_lammps000001n6v3qle_"
> > variable data_file string
> > "/home/aimsuser/testlammps/out/data_lammps000001i4lcno3c"
> > units metal
> > boundary p p s
> > atom_modify sort 0 0.0
> >
> > read_data /home/aimsuser/testlammps/out/data_lammps000001i4lcno3c
> >
> > ### interactions
> > pair_style eam
> > pair_coeff 1 1 Pt_u3.eam
> >
> > ### run
> > fix fix_nve all nve
> > dump dump_all all custom 1
> > /home/aimsuser/testlammps/out/trj_lammps000001n6v3qle_ id type x y z
> > vx vy vz fx fy fz
> > thermo_style custom step temp press cpu pxx pyy pzz pxy pxz pyz ke pe
> > etotal vol lx ly lz atoms
> > thermo_modify flush yes
> > thermo 1
> > run 0
> > print "__end_of_ase_invoked_calculation__"
> > log /dev/stdout
> >
> >
> > Output of calculation using lammps from debian:
> > ----------------------------------------------
> > $ lammps < in_lammps000001w8rfw53_
> > LAMMPS (9 Nov 2016)
> > OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
> > using 1 OpenMP thread(s) per MPI task
> > OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
> > using 1 OpenMP thread(s) per MPI task
> > Reading data file ...
> > triclinic box = (0 0 0) to (27.7186 24.005 69.0529) with tilt (-13.8593 0 0)
> > 1 by 1 by 1 MPI processor grid
> > reading atoms ...
> > 500 atoms
> > Reading potential file Pt_u3.eam with DATE: 2007-06-11
> > Neighbor list info ...
> > 1 neighbor list requests
> > update every 1 steps, delay 10 steps, check yes
> > max neighbors/atom: 2000, page size: 100000
> > master list distance cutoff = 7.3
> > ghost atom cutoff = 7.3
> > binsize = 3.65, bins = 12 7 3
> > Setting up Verlet run ...
> > Unit style : metal
> > Current step : 0
> > Time step : 0.001
> > Memory usage per processor = 3.9235 Mbytes
> > Step Temp Press CPU Pxx Pyy Pzz Pxy Pxz Pyz KinEng PotEng TotEng
> > Volume Lx Ly Lz Atoms
> > 0 0 -99591.425 0 -114534.53
> > -114534.53 -69705.222 -1.2231988e-05 -5.6701194e-06 -9.254435e-06
> > 0 -2758.6375 -2758.6375 6032.8181 27.718586
> > 24.004999 9.0666628 500
> > Loop time of 3.27732e-06 on 1 procs for 0 steps with 500 atoms
> >
> > 0.0% CPU use with 1 MPI tasks x 1 OpenMP threads
> >
> > MPI task timing breakdown:
> > Section | min time | avg time | max time |%varavg| %total
> > ---------------------------------------------------------------
> > Pair | 0 | 0 | 0 | 0.0 | 0.00
> > Neigh | 0 | 0 | 0 | 0.0 | 0.00
> > Comm | 0 | 0 | 0 | 0.0 | 0.00
> > Output | 0 | 0 | 0 | 0.0 | 0.00
> > Modify | 0 | 0 | 0 | 0.0 | 0.00
> > Other | | 3.277e-06 | | |100.00
> >
> > Nlocal: 500 ave 500 max 500 min
> > Histogram: 1 0 0 0 0 0 0 0 0 0
> > Nghost: 846 ave 846 max 846 min
> > Histogram: 1 0 0 0 0 0 0 0 0 0
> > Neighs: 16700 ave 16700 max 16700 min
> > Histogram: 1 0 0 0 0 0 0 0 0 0
> >
> > Total # of neighbors = 16700
> > Ave neighs/atom = 33.4
> > Neighbor list builds = 0
> > Dangerous builds = 0
> > __end_of_ase_invoked_calculation__
> > Total wall time: 0:00:00
> > Total wall time: 0:00:00
> >
> > Output of calculation using newly compiled lammps:
> > ----------------------------------------------------------------------
> > $ lmp_serial < in_lammps000001w8rfw53_
> > LAMMPS (22 Aug 2018)
> > Reading data file ...
> > triclinic box = (0 0 0) to (27.7186 24.005 69.0529) with tilt (-13.8593 0 0)
> > 1 by 1 by 1 MPI processor grid
> > reading atoms ...
> > 500 atoms
> > ERROR: Unknown pair style eam (../force.cpp:262)
> > Last command: pair_style eam
> >
> >
> > ------------------------------
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