129 lines
5.5 KiB
Plaintext
129 lines
5.5 KiB
Plaintext
LAMMPS (10 Feb 2021)
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# two LJ particles
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units real
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boundary p p p
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atom_style charge
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pair_style lj/cut/coul/long/soft 1.0 0.0 0.0 12.0 12.0
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region box block -15.0 15.0 -15.0 15.0 -15.0 15.0
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create_box 2 box
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Created orthogonal box = (-15.000000 -15.000000 -15.000000) to (15.000000 15.000000 15.000000)
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1 by 1 by 1 MPI processor grid
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# just two atoms...
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#create_atoms 1 single 0.0 0.0 0.0
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## create_atoms 2 single 3.36738 0.0 0.0
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#create_atoms 2 single 6.0 0.0 0.0
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# ...or a few on a lattice
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lattice bcc 5.0
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Lattice spacing in x,y,z = 5.0000000 5.0000000 5.0000000
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create_atoms 1 box basis 1 1 basis 2 2
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Created 432 atoms
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create_atoms CPU = 0.000 seconds
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mass 1 12.011
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mass 2 12.011
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pair_coeff 1 1 0.1 3.0 1.0
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pair_coeff 1 2 0.1 3.0 1.0
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pair_coeff 2 2 0.1 3.0 1.0
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set type 1 charge 0.1
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Setting atom values ...
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216 settings made for charge
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set type 2 charge -0.1
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Setting atom values ...
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216 settings made for charge
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kspace_style pppm 1.0e-5
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timestep 2.0
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velocity all create 300.0 12345
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fix INTEG all nvt temp 300.0 300.0 $(100.0*dt)
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fix INTEG all nvt temp 300.0 300.0 200
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variable lam equal ramp(1.0,0.0)
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variable q1 equal 0.1*v_lam
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variable q2 equal -0.1*v_lam
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fix ADAPT all adapt/fep 200 pair lj/cut/coul/long/soft lambda * * v_lam atom charge 1 v_q1 atom charge 2 v_q2
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thermo_style custom step etotal ke pe epair evdwl ecoul elong temp press v_lam v_q1 v_q2
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thermo 200
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#dump TRAJ all custom 20 dump.lammpstrj id type element xu yu zu
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#dump_modify TRAJ element C N
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run 2000
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PPPM initialization ...
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using 12-bit tables for long-range coulomb (src/lammps/src/kspace.cpp:339)
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G vector (1/distance) = 0.18385633
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grid = 8 8 8
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stencil order = 5
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estimated absolute RMS force accuracy = 0.0026371085
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estimated relative force accuracy = 7.9415739e-06
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using double precision FFTW3
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3d grid and FFT values/proc = 2197 512
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Neighbor list info ...
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update every 1 steps, delay 10 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 14
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ghost atom cutoff = 14
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binsize = 7, bins = 5 5 5
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cut/coul/long/soft, perpetual
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attributes: half, newton on
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pair build: half/bin/atomonly/newton
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stencil: half/bin/3d/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 3.832 | 3.832 | 3.832 Mbytes
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Step TotEng KinEng PotEng E_pair E_vdwl E_coul E_long Temp Press v_lam v_q1 v_q2
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0 -12.26816 385.41874 -397.6869 -397.6869 -104.94426 -143.9636 -148.77903 300 -85.376499 1 0.1 -0.1
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200 100.16354 367.45985 -267.29631 -267.29631 -81.614062 -73.094016 -112.58823 286.02127 773.38887 0.9 0.09 -0.09
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400 212.21213 408.60204 -196.38992 -196.38992 -61.139783 -47.980995 -87.269141 318.04529 999.04315 0.8 0.08 -0.08
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600 236.48535 384.11175 -147.6264 -147.6264 -50.471465 -30.008006 -67.146932 298.98267 991.19571 0.7 0.07 -0.07
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800 296.13924 393.67656 -97.537322 -97.537322 -35.286021 -14.501948 -47.749352 306.42767 1072.3208 0.6 0.06 -0.06
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1000 321.41212 388.66588 -67.253761 -67.253761 -27.633917 -7.5804948 -32.03935 302.52749 1042.921 0.5 0.05 -0.05
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1200 361.76959 401.68937 -39.919779 -39.919779 -18.818919 -2.1433883 -18.957472 312.66464 1024.5985 0.4 0.04 -0.04
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1400 378.95801 397.71207 -18.754062 -18.754062 -8.3450648 -0.50003204 -9.9089656 309.56881 1009.4706 0.3 0.03 -0.03
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1600 377.85273 381.94383 -4.0910985 -4.0910985 -0.39457825 -0.054299578 -3.6422206 297.29522 937.1911 0.2 0.02 -0.02
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1800 395.79855 387.74178 8.0567724 8.0567724 8.9308992 -0.0096463334 -0.8644804 301.8082 905.24994 0.1 0.01 -0.01
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WARNING: Using kspace solver on system with no charge (src/lammps/src/kspace.cpp:311)
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2000 395.41984 395.41984 0 0 0 0 0 307.7846 669.46448 0 0 -0
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Loop time of 2.57067 on 1 procs for 2000 steps with 432 atoms
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Performance: 134.439 ns/day, 0.179 hours/ns, 778.006 timesteps/s
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99.6% CPU use with 1 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 2.11 | 2.11 | 2.11 | 0.0 | 82.08
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Kspace | 0.34475 | 0.34475 | 0.34475 | 0.0 | 13.41
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Neigh | 0.074478 | 0.074478 | 0.074478 | 0.0 | 2.90
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Comm | 0.023527 | 0.023527 | 0.023527 | 0.0 | 0.92
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Output | 0.000318 | 0.000318 | 0.000318 | 0.0 | 0.01
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Modify | 0.012899 | 0.012899 | 0.012899 | 0.0 | 0.50
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Other | | 0.004675 | | | 0.18
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Nlocal: 432.000 ave 432 max 432 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 2702.00 ave 2702 max 2702 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 39560.0 ave 39560 max 39560 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 39560
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Ave neighs/atom = 91.574074
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Neighbor list builds = 66
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Dangerous builds = 0
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#write_data data.*.lmp
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Total wall time: 0:00:02
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