correct data in data file and pair_coeff changes are no longer needed
also re-create reference log files
This commit is contained in:
Axel Kohlmeyer
@ -15,12 +15,12 @@ Masses
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PairIJ Coeffs # dpd/coul/slater/long
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PairIJ Coeffs # dpd/coul/slater/long
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1 1 78 4.5 yes 1
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1 1 78 4.5 no 1
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1 2 78 4.5 yes 1
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1 2 78 4.5 no 1
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1 3 78 4.5 yes 1
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1 3 78 4.5 no 1
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2 2 78 4.5 no 1
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2 2 78 4.5 yes 1
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2 3 78 4.5 no 1
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2 3 78 4.5 yes 1
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3 3 78 4.5 no 1
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3 3 78 4.5 yes 1
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Atoms # full
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Atoms # full
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@ -33,13 +33,8 @@ pair_style dpd/coul/slater/long ${T} ${cut_DPD} ${seed} ${lambda} ${cut_coul}
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# Enable long range electrostatics solver
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# Enable long range electrostatics solver
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kspace_style pppm 1e-04
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kspace_style pppm 1e-04
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read_data data.dpd_coul_slater_long
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read_data data.dpd_coul_slater_long
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pair_coeff * * 78.0 4.5
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pair_coeff 2*3 2*3 78.0 4.5 yes
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# Construct neighbors every steps
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# Construct neighbors every steps
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neighbor 1.0 bin
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neighbor 1.0 bin
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neigh_modify every 1 delay 0 check yes
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neigh_modify every 1 delay 0 check yes
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@ -59,5 +54,3 @@ fix 1 all nve
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run 1000
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run 1000
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unfix 1
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@ -1,147 +0,0 @@
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LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-262-g0aff26705c-modified)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
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using 1 OpenMP thread(s) per MPI task
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# DPD Ionic Fluid
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variable T equal 1.0
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variable cut_DPD equal 1.0
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variable seed equal 165412
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variable lambda equal 0.25
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variable cut_coul equal 2.0
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#-------------------------------------------------------------------------------
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# Initialize LAMMPS run for 3-d periodic
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#-------------------------------------------------------------------------------
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units lj
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boundary p p p # periodic at all axes
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atom_style full
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dimension 3
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bond_style none
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angle_style none
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dihedral_style none
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improper_style none
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newton on
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comm_modify vel yes # store info of ghost atoms btw processors
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#-------------------------------------------------------------------------------
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# Box creation and configuration
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#-------------------------------------------------------------------------------
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# Define pair style and coefficients
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pair_style dpd/coul/slater/long ${T} ${cut_DPD} ${seed} ${lambda} ${cut_coul}
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pair_style dpd/coul/slater/long 1 ${cut_DPD} ${seed} ${lambda} ${cut_coul}
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pair_style dpd/coul/slater/long 1 1 ${seed} ${lambda} ${cut_coul}
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pair_style dpd/coul/slater/long 1 1 165412 ${lambda} ${cut_coul}
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pair_style dpd/coul/slater/long 1 1 165412 0.25 ${cut_coul}
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pair_style dpd/coul/slater/long 1 1 165412 0.25 2
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read_data data.dpd_coul_slater_long
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Reading data file ...
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orthogonal box = (0 0 0) to (5 5 5)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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375 atoms
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reading velocities ...
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375 velocities
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0 0 0
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special bond factors coul: 0 0 0
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0 = max # of 1-2 neighbors
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0 = max # of 1-3 neighbors
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0 = max # of 1-4 neighbors
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1 = max # of special neighbors
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special bonds CPU = 0.000 seconds
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read_data CPU = 0.003 seconds
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# Enable long range electrostatics solver
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kspace_style pppm 1e-04
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# Construct neighbors every steps
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neighbor 1.0 bin
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neigh_modify every 1 delay 0 check yes
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#-------------------------------------------------------------------------------
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# Run the simulation
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#-------------------------------------------------------------------------------
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thermo_style custom step temp press vol evdwl ecoul elong pe ke fnorm fmax
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thermo_modify norm no
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thermo 100
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timestep 0.01
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run_style verlet
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fix 1 all nve
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run 1000
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PPPM initialization ...
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using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
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G vector (1/distance) = 1.4828454
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grid = 20 20 20
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stencil order = 5
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estimated absolute RMS force accuracy = 7.7240141e-05
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estimated relative force accuracy = 7.7240141e-05
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using double precision FFTW3
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3d grid and FFT values/proc = 24389 8000
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Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
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Neighbor list info ...
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update: every = 1 steps, delay = 0 steps, check = yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 3
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ghost atom cutoff = 3
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binsize = 1.5, bins = 4 4 4
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair dpd/coul/slater/long, perpetual
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attributes: half, newton on
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pair build: half/bin/newton
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stencil: half/bin/3d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 8.359 | 8.359 | 8.359 Mbytes
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Step Temp Press Volume E_vdwl E_coul E_long PotEng KinEng Fnorm Fmax
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0 0.9849949 69.271905 125 4673.0443 0 -30.365103 4642.6792 552.58214 646.76798 65.851035
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100 1.0614027 69.794624 125 4659.0139 0 -31.906319 4627.1075 595.44692 612.94396 60.338653
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200 0.9422517 68.721098 125 4687.8862 0 -33.81531 4654.0709 528.6032 620.25627 62.726994
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300 0.8956649 69.323482 125 4721.0824 0 -33.854275 4687.2281 502.46801 670.22699 73.087908
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400 0.99584547 69.670416 125 4713.9086 0 -30.783633 4683.125 558.66931 607.65881 59.224652
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500 1.0565931 69.497816 125 4701.2584 0 -26.80545 4674.4529 592.74873 646.18907 71.398122
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600 1.0071523 70.26222 125 4659.2061 0 -29.98909 4629.217 565.01243 630.00244 58.264115
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700 1.0507355 67.920078 125 4695.255 0 -32.649209 4662.6058 589.46259 651.80459 70.573524
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800 0.98561942 68.279591 125 4745.7603 0 -28.98491 4716.7754 552.9325 627.14371 67.196483
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900 0.96470105 70.742864 125 4706.3605 0 -30.271633 4676.0889 541.19729 644.43036 79.474998
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1000 1.0204819 70.164419 125 4654.6077 0 -27.797433 4626.8103 572.49035 624.19728 71.825307
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Loop time of 2.10153 on 1 procs for 1000 steps with 375 atoms
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Performance: 411128.483 tau/day, 475.843 timesteps/s, 178.441 katom-step/s
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99.7% CPU use with 1 MPI tasks x 1 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 | 1.1779 | 1.1779 | 1.1779 | 0.0 | 56.05
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Bond | 6.507e-05 | 6.507e-05 | 6.507e-05 | 0.0 | 0.00
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Kspace | 0.74636 | 0.74636 | 0.74636 | 0.0 | 35.51
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Neigh | 0.12903 | 0.12903 | 0.12903 | 0.0 | 6.14
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Comm | 0.039726 | 0.039726 | 0.039726 | 0.0 | 1.89
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Output | 0.00027587 | 0.00027587 | 0.00027587 | 0.0 | 0.01
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Modify | 0.0037596 | 0.0037596 | 0.0037596 | 0.0 | 0.18
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Other | | 0.004451 | | | 0.21
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Nlocal: 375 ave 375 max 375 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 3613 ave 3613 max 3613 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 62354 ave 62354 max 62354 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 62354
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Ave neighs/atom = 166.27733
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Ave special neighs/atom = 0
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Neighbor list builds = 65
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Dangerous builds = 0
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unfix 1
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Total wall time: 0:00:02
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@ -1,147 +0,0 @@
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LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-262-g0aff26705c-modified)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
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using 1 OpenMP thread(s) per MPI task
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# DPD Ionic Fluid
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variable T equal 1.0
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variable cut_DPD equal 1.0
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variable seed equal 165412
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variable lambda equal 0.25
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variable cut_coul equal 2.0
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#-------------------------------------------------------------------------------
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# Initialize LAMMPS run for 3-d periodic
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#-------------------------------------------------------------------------------
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units lj
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boundary p p p # periodic at all axes
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atom_style full
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dimension 3
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bond_style none
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angle_style none
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dihedral_style none
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improper_style none
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newton on
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comm_modify vel yes # store info of ghost atoms btw processors
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#-------------------------------------------------------------------------------
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# Box creation and configuration
|
|
||||||
#-------------------------------------------------------------------------------
|
|
||||||
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|
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# Define pair style and coefficients
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pair_style dpd/coul/slater/long ${T} ${cut_DPD} ${seed} ${lambda} ${cut_coul}
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|
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pair_style dpd/coul/slater/long 1 ${cut_DPD} ${seed} ${lambda} ${cut_coul}
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pair_style dpd/coul/slater/long 1 1 ${seed} ${lambda} ${cut_coul}
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pair_style dpd/coul/slater/long 1 1 165412 ${lambda} ${cut_coul}
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pair_style dpd/coul/slater/long 1 1 165412 0.25 ${cut_coul}
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pair_style dpd/coul/slater/long 1 1 165412 0.25 2
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read_data data.dpd_coul_slater_long
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|
||||||
Reading data file ...
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|
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orthogonal box = (0 0 0) to (5 5 5)
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|
||||||
1 by 2 by 2 MPI processor grid
|
|
||||||
reading atoms ...
|
|
||||||
375 atoms
|
|
||||||
reading velocities ...
|
|
||||||
375 velocities
|
|
||||||
Finding 1-2 1-3 1-4 neighbors ...
|
|
||||||
special bond factors lj: 0 0 0
|
|
||||||
special bond factors coul: 0 0 0
|
|
||||||
0 = max # of 1-2 neighbors
|
|
||||||
0 = max # of 1-3 neighbors
|
|
||||||
0 = max # of 1-4 neighbors
|
|
||||||
1 = max # of special neighbors
|
|
||||||
special bonds CPU = 0.000 seconds
|
|
||||||
read_data CPU = 0.003 seconds
|
|
||||||
|
|
||||||
# Enable long range electrostatics solver
|
|
||||||
kspace_style pppm 1e-04
|
|
||||||
|
|
||||||
# Construct neighbors every steps
|
|
||||||
neighbor 1.0 bin
|
|
||||||
neigh_modify every 1 delay 0 check yes
|
|
||||||
|
|
||||||
#-------------------------------------------------------------------------------
|
|
||||||
# Run the simulation
|
|
||||||
#-------------------------------------------------------------------------------
|
|
||||||
|
|
||||||
thermo_style custom step temp press vol evdwl ecoul elong pe ke fnorm fmax
|
|
||||||
thermo_modify norm no
|
|
||||||
thermo 100
|
|
||||||
|
|
||||||
timestep 0.01
|
|
||||||
run_style verlet
|
|
||||||
|
|
||||||
fix 1 all nve
|
|
||||||
|
|
||||||
run 1000
|
|
||||||
PPPM initialization ...
|
|
||||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
|
||||||
G vector (1/distance) = 1.4828454
|
|
||||||
grid = 20 20 20
|
|
||||||
stencil order = 5
|
|
||||||
estimated absolute RMS force accuracy = 7.7240141e-05
|
|
||||||
estimated relative force accuracy = 7.7240141e-05
|
|
||||||
using double precision FFTW3
|
|
||||||
3d grid and FFT values/proc = 10469 2000
|
|
||||||
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
|
|
||||||
Neighbor list info ...
|
|
||||||
update: every = 1 steps, delay = 0 steps, check = yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 3
|
|
||||||
ghost atom cutoff = 3
|
|
||||||
binsize = 1.5, bins = 4 4 4
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair dpd/coul/slater/long, perpetual
|
|
||||||
attributes: half, newton on
|
|
||||||
pair build: half/bin/newton
|
|
||||||
stencil: half/bin/3d
|
|
||||||
bin: standard
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 7.208 | 7.208 | 7.209 Mbytes
|
|
||||||
Step Temp Press Volume E_vdwl E_coul E_long PotEng KinEng Fnorm Fmax
|
|
||||||
0 0.9849949 69.076433 125 4673.0443 0 -30.365103 4642.6792 552.58214 613.18374 70.700582
|
|
||||||
100 0.95374867 69.110009 125 4681.1097 0 -31.260804 4649.8489 535.053 629.95109 62.05418
|
|
||||||
200 1.0076152 69.824904 125 4670.7458 0 -28.382203 4642.3636 565.27213 656.8501 72.049813
|
|
||||||
300 1.0014752 69.666331 125 4696.454 0 -26.943577 4669.5105 561.8276 631.49861 74.737274
|
|
||||||
400 0.98863876 69.731774 125 4700.7552 0 -23.816077 4676.9391 554.62634 637.74742 68.928573
|
|
||||||
500 0.95782852 68.588075 125 4698.588 0 -29.249543 4669.3385 537.3418 646.31897 68.800569
|
|
||||||
600 0.97443232 70.864079 125 4674.8821 0 -26.415644 4648.4664 546.65653 606.50755 78.664429
|
|
||||||
700 0.98783988 68.908299 125 4692.5536 0 -28.092022 4664.4616 554.17817 638.98401 69.691814
|
|
||||||
800 0.98000145 69.83977 125 4706.6365 0 -29.648365 4676.9881 549.78082 626.84362 73.133934
|
|
||||||
900 1.0526251 69.466078 125 4671.9648 0 -30.941117 4641.0237 590.52269 618.1049 62.333546
|
|
||||||
1000 0.98340746 69.527121 125 4728.2894 0 -31.869907 4696.4195 551.69159 630.14208 61.392611
|
|
||||||
Loop time of 0.928543 on 4 procs for 1000 steps with 375 atoms
|
|
||||||
|
|
||||||
Performance: 930490.137 tau/day, 1076.956 timesteps/s, 403.859 katom-step/s
|
|
||||||
98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 0.30761 | 0.34974 | 0.38864 | 4.9 | 37.67
|
|
||||||
Bond | 8.4633e-05 | 9.0539e-05 | 9.9184e-05 | 0.0 | 0.01
|
|
||||||
Kspace | 0.39038 | 0.42976 | 0.47215 | 4.4 | 46.28
|
|
||||||
Neigh | 0.033986 | 0.035576 | 0.036791 | 0.5 | 3.83
|
|
||||||
Comm | 0.10247 | 0.10324 | 0.10481 | 0.3 | 11.12
|
|
||||||
Output | 0.00024145 | 0.00027404 | 0.00036867 | 0.0 | 0.03
|
|
||||||
Modify | 0.0022402 | 0.0025068 | 0.0026343 | 0.3 | 0.27
|
|
||||||
Other | | 0.007356 | | | 0.79
|
|
||||||
|
|
||||||
Nlocal: 93.75 ave 96 max 93 min
|
|
||||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
|
||||||
Nghost: 2289.75 ave 2317 max 2271 min
|
|
||||||
Histogram: 1 1 0 0 1 0 0 0 0 1
|
|
||||||
Neighs: 15590.2 ave 16765 max 14540 min
|
|
||||||
Histogram: 1 0 1 0 0 1 0 0 0 1
|
|
||||||
|
|
||||||
Total # of neighbors = 62361
|
|
||||||
Ave neighs/atom = 166.296
|
|
||||||
Ave special neighs/atom = 0
|
|
||||||
Neighbor list builds = 64
|
|
||||||
Dangerous builds = 0
|
|
||||||
|
|
||||||
unfix 1
|
|
||||||
|
|
||||||
Total wall time: 0:00:00
|
|
||||||
@ -0,0 +1,145 @@
|
|||||||
|
LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-468-gd830412228-modified)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
# DPD Ionic Fluid
|
||||||
|
|
||||||
|
variable T equal 1.0
|
||||||
|
variable cut_DPD equal 1.0
|
||||||
|
variable seed equal 165412
|
||||||
|
variable lambda equal 0.25
|
||||||
|
variable cut_coul equal 2.0
|
||||||
|
|
||||||
|
#-------------------------------------------------------------------------------
|
||||||
|
# Initialize LAMMPS run for 3-d periodic
|
||||||
|
#-------------------------------------------------------------------------------
|
||||||
|
|
||||||
|
units lj
|
||||||
|
boundary p p p # periodic at all axes
|
||||||
|
atom_style full
|
||||||
|
dimension 3
|
||||||
|
|
||||||
|
bond_style none
|
||||||
|
angle_style none
|
||||||
|
dihedral_style none
|
||||||
|
improper_style none
|
||||||
|
|
||||||
|
newton on
|
||||||
|
comm_modify vel yes # store info of ghost atoms btw processors
|
||||||
|
|
||||||
|
#-------------------------------------------------------------------------------
|
||||||
|
# Box creation and configuration
|
||||||
|
#-------------------------------------------------------------------------------
|
||||||
|
|
||||||
|
# Define pair style and coefficients
|
||||||
|
pair_style dpd/coul/slater/long ${T} ${cut_DPD} ${seed} ${lambda} ${cut_coul}
|
||||||
|
pair_style dpd/coul/slater/long 1 ${cut_DPD} ${seed} ${lambda} ${cut_coul}
|
||||||
|
pair_style dpd/coul/slater/long 1 1 ${seed} ${lambda} ${cut_coul}
|
||||||
|
pair_style dpd/coul/slater/long 1 1 165412 ${lambda} ${cut_coul}
|
||||||
|
pair_style dpd/coul/slater/long 1 1 165412 0.25 ${cut_coul}
|
||||||
|
pair_style dpd/coul/slater/long 1 1 165412 0.25 2
|
||||||
|
|
||||||
|
# Enable long range electrostatics solver
|
||||||
|
kspace_style pppm 1e-04
|
||||||
|
|
||||||
|
read_data data.dpd_coul_slater_long
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (5 5 5)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
375 atoms
|
||||||
|
reading velocities ...
|
||||||
|
375 velocities
|
||||||
|
Finding 1-2 1-3 1-4 neighbors ...
|
||||||
|
special bond factors lj: 0 0 0
|
||||||
|
special bond factors coul: 0 0 0
|
||||||
|
0 = max # of 1-2 neighbors
|
||||||
|
0 = max # of 1-3 neighbors
|
||||||
|
0 = max # of 1-4 neighbors
|
||||||
|
1 = max # of special neighbors
|
||||||
|
special bonds CPU = 0.001 seconds
|
||||||
|
read_data CPU = 0.004 seconds
|
||||||
|
|
||||||
|
# Construct neighbors every steps
|
||||||
|
neighbor 1.0 bin
|
||||||
|
neigh_modify every 1 delay 0 check yes
|
||||||
|
|
||||||
|
#-------------------------------------------------------------------------------
|
||||||
|
# Run the simulation
|
||||||
|
#-------------------------------------------------------------------------------
|
||||||
|
|
||||||
|
thermo_style custom step temp press vol evdwl ecoul elong pe ke fnorm fmax
|
||||||
|
thermo_modify norm no
|
||||||
|
thermo 100
|
||||||
|
|
||||||
|
timestep 0.01
|
||||||
|
run_style verlet
|
||||||
|
|
||||||
|
fix 1 all nve
|
||||||
|
|
||||||
|
run 1000
|
||||||
|
PPPM initialization ...
|
||||||
|
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||||
|
G vector (1/distance) = 1.4828454
|
||||||
|
grid = 20 20 20
|
||||||
|
stencil order = 5
|
||||||
|
estimated absolute RMS force accuracy = 7.7240141e-05
|
||||||
|
estimated relative force accuracy = 7.7240141e-05
|
||||||
|
using double precision KISS FFT
|
||||||
|
3d grid and FFT values/proc = 24389 8000
|
||||||
|
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update: every = 1 steps, delay = 0 steps, check = yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 3
|
||||||
|
ghost atom cutoff = 3
|
||||||
|
binsize = 1.5, bins = 4 4 4
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair dpd/coul/slater/long, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 8.359 | 8.359 | 8.359 Mbytes
|
||||||
|
Step Temp Press Volume E_vdwl E_coul E_long PotEng KinEng Fnorm Fmax
|
||||||
|
0 0.9849949 69.242343 125 4673.0443 -3.2653869 -30.365103 4639.4138 552.58214 646.89929 65.851035
|
||||||
|
100 1.023885 69.716134 125 4676.9465 -4.9878506 -34.092864 4637.8658 574.39949 663.35845 94.350026
|
||||||
|
200 1.0286646 69.674249 125 4636.201 -4.6314926 -33.406897 4598.1626 577.08087 614.52805 62.295431
|
||||||
|
300 0.9745797 69.689534 125 4679.9157 -4.3964184 -30.560567 4644.9588 546.73921 603.46282 60.56253
|
||||||
|
400 0.99487931 69.17085 125 4678.0362 -4.9518269 -34.446596 4638.6378 558.12729 656.99738 88.090014
|
||||||
|
500 0.97732377 69.551562 125 4684.3709 -5.0851581 -33.863212 4645.4226 548.27864 647.12533 75.851935
|
||||||
|
600 0.95396337 68.358297 125 4706.824 -4.269168 -33.634096 4668.9207 535.17345 604.31276 63.41042
|
||||||
|
700 0.99397324 68.365109 125 4669.1062 -4.700146 -35.014001 4629.3921 557.61899 633.29262 74.300913
|
||||||
|
800 1.0157864 69.263686 125 4664.1398 -4.0142381 -34.372669 4625.7529 569.85616 595.81462 67.046561
|
||||||
|
900 0.9925779 70.008922 125 4652.3023 -2.7845751 -33.095293 4616.4224 556.8362 620.13154 82.785317
|
||||||
|
1000 0.97336501 68.973657 125 4688.8002 -5.5239266 -36.42345 4646.8529 546.05777 625.66451 64.948859
|
||||||
|
Loop time of 0.755094 on 1 procs for 1000 steps with 375 atoms
|
||||||
|
|
||||||
|
Performance: 1144228.093 tau/day, 1324.338 timesteps/s, 496.627 katom-step/s
|
||||||
|
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.14421 | 0.14421 | 0.14421 | 0.0 | 19.10
|
||||||
|
Bond | 3.8885e-05 | 3.8885e-05 | 3.8885e-05 | 0.0 | 0.01
|
||||||
|
Kspace | 0.53292 | 0.53292 | 0.53292 | 0.0 | 70.58
|
||||||
|
Neigh | 0.056741 | 0.056741 | 0.056741 | 0.0 | 7.51
|
||||||
|
Comm | 0.017676 | 0.017676 | 0.017676 | 0.0 | 2.34
|
||||||
|
Output | 0.00024925 | 0.00024925 | 0.00024925 | 0.0 | 0.03
|
||||||
|
Modify | 0.0016688 | 0.0016688 | 0.0016688 | 0.0 | 0.22
|
||||||
|
Other | | 0.001588 | | | 0.21
|
||||||
|
|
||||||
|
Nlocal: 375 ave 375 max 375 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 3570 ave 3570 max 3570 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 19729 ave 19729 max 19729 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 19729
|
||||||
|
Ave neighs/atom = 52.610667
|
||||||
|
Ave special neighs/atom = 0
|
||||||
|
Neighbor list builds = 66
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
Total wall time: 0:00:00
|
||||||
@ -0,0 +1,145 @@
|
|||||||
|
LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-468-gd830412228-modified)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
# DPD Ionic Fluid
|
||||||
|
|
||||||
|
variable T equal 1.0
|
||||||
|
variable cut_DPD equal 1.0
|
||||||
|
variable seed equal 165412
|
||||||
|
variable lambda equal 0.25
|
||||||
|
variable cut_coul equal 2.0
|
||||||
|
|
||||||
|
#-------------------------------------------------------------------------------
|
||||||
|
# Initialize LAMMPS run for 3-d periodic
|
||||||
|
#-------------------------------------------------------------------------------
|
||||||
|
|
||||||
|
units lj
|
||||||
|
boundary p p p # periodic at all axes
|
||||||
|
atom_style full
|
||||||
|
dimension 3
|
||||||
|
|
||||||
|
bond_style none
|
||||||
|
angle_style none
|
||||||
|
dihedral_style none
|
||||||
|
improper_style none
|
||||||
|
|
||||||
|
newton on
|
||||||
|
comm_modify vel yes # store info of ghost atoms btw processors
|
||||||
|
|
||||||
|
#-------------------------------------------------------------------------------
|
||||||
|
# Box creation and configuration
|
||||||
|
#-------------------------------------------------------------------------------
|
||||||
|
|
||||||
|
# Define pair style and coefficients
|
||||||
|
pair_style dpd/coul/slater/long ${T} ${cut_DPD} ${seed} ${lambda} ${cut_coul}
|
||||||
|
pair_style dpd/coul/slater/long 1 ${cut_DPD} ${seed} ${lambda} ${cut_coul}
|
||||||
|
pair_style dpd/coul/slater/long 1 1 ${seed} ${lambda} ${cut_coul}
|
||||||
|
pair_style dpd/coul/slater/long 1 1 165412 ${lambda} ${cut_coul}
|
||||||
|
pair_style dpd/coul/slater/long 1 1 165412 0.25 ${cut_coul}
|
||||||
|
pair_style dpd/coul/slater/long 1 1 165412 0.25 2
|
||||||
|
|
||||||
|
# Enable long range electrostatics solver
|
||||||
|
kspace_style pppm 1e-04
|
||||||
|
|
||||||
|
read_data data.dpd_coul_slater_long
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (5 5 5)
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
375 atoms
|
||||||
|
reading velocities ...
|
||||||
|
375 velocities
|
||||||
|
Finding 1-2 1-3 1-4 neighbors ...
|
||||||
|
special bond factors lj: 0 0 0
|
||||||
|
special bond factors coul: 0 0 0
|
||||||
|
0 = max # of 1-2 neighbors
|
||||||
|
0 = max # of 1-3 neighbors
|
||||||
|
0 = max # of 1-4 neighbors
|
||||||
|
1 = max # of special neighbors
|
||||||
|
special bonds CPU = 0.000 seconds
|
||||||
|
read_data CPU = 0.004 seconds
|
||||||
|
|
||||||
|
# Construct neighbors every steps
|
||||||
|
neighbor 1.0 bin
|
||||||
|
neigh_modify every 1 delay 0 check yes
|
||||||
|
|
||||||
|
#-------------------------------------------------------------------------------
|
||||||
|
# Run the simulation
|
||||||
|
#-------------------------------------------------------------------------------
|
||||||
|
|
||||||
|
thermo_style custom step temp press vol evdwl ecoul elong pe ke fnorm fmax
|
||||||
|
thermo_modify norm no
|
||||||
|
thermo 100
|
||||||
|
|
||||||
|
timestep 0.01
|
||||||
|
run_style verlet
|
||||||
|
|
||||||
|
fix 1 all nve
|
||||||
|
|
||||||
|
run 1000
|
||||||
|
PPPM initialization ...
|
||||||
|
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||||
|
G vector (1/distance) = 1.4828454
|
||||||
|
grid = 20 20 20
|
||||||
|
stencil order = 5
|
||||||
|
estimated absolute RMS force accuracy = 7.7240141e-05
|
||||||
|
estimated relative force accuracy = 7.7240141e-05
|
||||||
|
using double precision KISS FFT
|
||||||
|
3d grid and FFT values/proc = 10469 2000
|
||||||
|
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update: every = 1 steps, delay = 0 steps, check = yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 3
|
||||||
|
ghost atom cutoff = 3
|
||||||
|
binsize = 1.5, bins = 4 4 4
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair dpd/coul/slater/long, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 7.208 | 7.208 | 7.209 Mbytes
|
||||||
|
Step Temp Press Volume E_vdwl E_coul E_long PotEng KinEng Fnorm Fmax
|
||||||
|
0 0.9849949 69.04687 125 4673.0443 -3.2653869 -30.365103 4639.4138 552.58214 613.14254 70.700582
|
||||||
|
100 1.0206537 69.308834 125 4676.3153 -4.5693306 -33.647673 4638.0983 572.58672 630.70953 76.020236
|
||||||
|
200 0.99990746 68.572978 125 4707.1556 -3.4977853 -33.275671 4670.3821 560.94809 633.00167 77.040049
|
||||||
|
300 0.91055241 69.390592 125 4685.5268 -2.9764038 -29.986737 4652.5637 510.8199 614.61006 62.799933
|
||||||
|
400 1.0080135 69.442971 125 4677.3078 -4.8740989 -32.908722 4639.525 565.49557 649.20121 61.033612
|
||||||
|
500 0.99500653 68.275189 125 4718.6774 -4.2475783 -35.206868 4679.223 558.19867 657.3073 74.738502
|
||||||
|
600 1.052925 70.601712 125 4703.6749 -2.8511316 -34.085418 4666.7383 590.69094 641.70441 59.043346
|
||||||
|
700 0.96467445 69.502018 125 4720.4257 -4.3345734 -34.310005 4681.7811 541.18237 656.24965 72.433637
|
||||||
|
800 1.0657358 70.960958 125 4685.5637 -5.8903418 -35.207202 4644.4661 597.87781 595.54446 61.462159
|
||||||
|
900 1.0273388 68.735518 125 4693.5106 -2.4175829 -28.602387 4662.4906 576.33707 598.80294 71.747886
|
||||||
|
1000 0.9702835 69.885576 125 4701.4385 -3.6513555 -29.487331 4668.2999 544.32904 666.55262 73.231425
|
||||||
|
Loop time of 0.270344 on 4 procs for 1000 steps with 375 atoms
|
||||||
|
|
||||||
|
Performance: 3195929.791 tau/day, 3698.993 timesteps/s, 1.387 Matom-step/s
|
||||||
|
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.031268 | 0.035485 | 0.039491 | 1.6 | 13.13
|
||||||
|
Bond | 3.3378e-05 | 3.4848e-05 | 3.5667e-05 | 0.0 | 0.01
|
||||||
|
Kspace | 0.18632 | 0.19083 | 0.19556 | 0.8 | 70.59
|
||||||
|
Neigh | 0.012413 | 0.012991 | 0.013598 | 0.4 | 4.81
|
||||||
|
Comm | 0.028195 | 0.028407 | 0.028626 | 0.1 | 10.51
|
||||||
|
Output | 0.00013369 | 0.00015738 | 0.00022498 | 0.0 | 0.06
|
||||||
|
Modify | 0.00055373 | 0.00059062 | 0.00068807 | 0.0 | 0.22
|
||||||
|
Other | | 0.001846 | | | 0.68
|
||||||
|
|
||||||
|
Nlocal: 93.75 ave 95 max 92 min
|
||||||
|
Histogram: 1 0 0 0 0 0 2 0 0 1
|
||||||
|
Nghost: 2286 ave 2307 max 2269 min
|
||||||
|
Histogram: 1 0 1 0 0 1 0 0 0 1
|
||||||
|
Neighs: 4945 ave 5443 max 4513 min
|
||||||
|
Histogram: 1 0 1 0 0 1 0 0 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 19780
|
||||||
|
Ave neighs/atom = 52.746667
|
||||||
|
Ave special neighs/atom = 0
|
||||||
|
Neighbor list builds = 66
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
Total wall time: 0:00:00
|
||||||
Reference in New Issue
Block a user