136 lines
5.1 KiB
Plaintext
136 lines
5.1 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 dlam equal -0.1
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variable dq equal -0.01
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variable mdq equal -v_dq
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compute FEP all fep 300.0 pair lj/cut/coul/long/soft lambda * * v_dlam atom charge 1 v_dq atom charge 2 v_mdq
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variable diff equal "0.1*evdwl + (1.0-0.9^3)*ecoul + (1.0-0.9^2)*elong + c_FEP[1]"
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thermo_style custom step etotal epair evdwl ecoul elong temp press c_FEP[1] v_diff
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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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FEP settings ...
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temperature = 300.000000
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tail no
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lj/cut/coul/long/soft lambda 1-2 1-2
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1-1 charge
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2-2 charge
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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 E_pair E_vdwl E_coul E_long Temp Press c_FEP[1] v_diff
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0 -12.26816 -397.6869 -104.94426 -143.9636 -148.77903 300 -85.376499 77.776579 1.8999913e-11
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200 37.48027 -329.94625 -90.682292 -100.26614 -138.99782 285.99532 753.55244 62.649939 -3.2116532e-12
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400 90.468672 -316.02846 -73.92701 -103.34631 -138.75514 316.40687 1029.3728 61.763027 -2.3732127e-12
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600 51.256072 -323.62945 -73.949374 -108.09188 -141.5882 291.80122 1016.7465 63.589594 -2.4300562e-12
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800 81.04264 -324.43236 -81.254005 -105.21556 -137.9628 315.61128 993.70961 62.851749 -2.4016344e-12
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1000 49.737002 -317.2545 -83.027749 -96.415828 -137.81092 285.65671 868.03876 60.615539 -3.3111291e-12
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1200 75.239535 -312.294 -70.8241 -102.021 -139.4489 301.6461 1070.4194 61.225392 -3.0198066e-12
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1400 66.48368 -328.58216 -82.267016 -106.59484 -139.72031 307.50906 929.51913 63.660761 -2.4300562e-12
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1600 44.171107 -313.98549 -64.634967 -109.51577 -139.83476 278.77985 1072.9026 62.710873 -2.9558578e-12
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1800 75.795844 -307.72311 -70.578314 -98.507621 -138.63717 298.52125 1093.0178 60.094459 -3.3395509e-12
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2000 66.677947 -312.73751 -69.196548 -104.10753 -139.43342 295.3272 1084.1493 61.625147 -1.5489832e-12
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Loop time of 2.63335 on 1 procs for 2000 steps with 432 atoms
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Performance: 131.240 ns/day, 0.183 hours/ns, 759.488 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 | 2.1575 | 2.1575 | 2.1575 | 0.0 | 81.93
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Kspace | 0.35767 | 0.35767 | 0.35767 | 0.0 | 13.58
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Neigh | 0.076131 | 0.076131 | 0.076131 | 0.0 | 2.89
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Comm | 0.023625 | 0.023625 | 0.023625 | 0.0 | 0.90
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Output | 0.000348 | 0.000348 | 0.000348 | 0.0 | 0.01
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Modify | 0.012821 | 0.012821 | 0.012821 | 0.0 | 0.49
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Other | | 0.005206 | | | 0.20
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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: 2673.00 ave 2673 max 2673 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 39631.0 ave 39631 max 39631 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 39631
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Ave neighs/atom = 91.738426
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Neighbor list builds = 68
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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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