Loading examples/USER/viscosity/log.1000SPCE.lammps 0 → 100644 +160 −0 Original line number Diff line number Diff line LAMMPS (3 Mar 2020) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) using 1 OpenMP thread(s) per MPI task # DFF generated Lammps input file units real atom_style full boundary p p p pair_style lj/cut/coul/long 10.0 pair_modify mix arithmetic pair_modify tail yes kspace_style pppm 1.0e-4 dielectric 1.0 special_bonds amber bond_style harmonic angle_style harmonic dihedral_style none improper_style none read_data data.1000SPCE.lmp orthogonal box = (0 0 0) to (31.043 31.043 31.043) 2 by 2 by 2 MPI processor grid reading atoms ... 3000 atoms scanning bonds ... 2 = max bonds/atom scanning angles ... 1 = max angles/atom reading bonds ... 2000 bonds reading angles ... 1000 angles 2 = max # of 1-2 neighbors 1 = max # of 1-3 neighbors 1 = max # of 1-4 neighbors 2 = max # of special neighbors special bonds CPU = 0.00114917 secs read_data CPU = 0.00953543 secs variable T equal 300 variable P equal 1.0 velocity all create ${T} 12345 mom yes rot yes dist gaussian velocity all create 300 12345 mom yes rot yes dist gaussian timestep 1.0 # Constraint ################################## fix com all momentum 100 linear 1 1 1 fix rigid all shake 1e-4 20 0 b 1 a 1 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 1000 = # of frozen angles find clusters CPU = 0.000442737 secs # Viscosity ################################## variable A equal 0.02e-5 # angstrom/fs^2 fix cos all accelerate/cos ${A} fix cos all accelerate/cos 2e-07 compute cos all viscosity/cos variable density equal density variable lz equal lz variable vMax equal c_cos[7] # velocity of atoms at z=0 variable invVis equal v_vMax/${A}/v_density*39.4784/v_lz/v_lz*100 # reciprocal of viscosity 1/Pa/s variable invVis equal v_vMax/2e-07/v_density*39.4784/v_lz/v_lz*100 fix npt all npt temp ${T} ${T} 100 iso ${P} ${P} 1000 fix npt all npt temp 300 ${T} 100 iso ${P} ${P} 1000 fix npt all npt temp 300 300 100 iso ${P} ${P} 1000 fix npt all npt temp 300 300 100 iso 1 ${P} 1000 fix npt all npt temp 300 300 100 iso 1 1 1000 fix_modify npt temp cos thermo_style custom step cpu temp press pe density v_vMax v_invVis thermo_modify temp cos thermo 100 ################################################ dump 1 all custom 10000 dump.lammpstrj id mol type element q xu yu zu dump_modify 1 sort id element O H run 2000 PPPM initialization ... using 12-bit tables for long-range coulomb (src/kspace.cpp:332) G vector (1/distance) = 0.263539 grid = 16 16 16 stencil order = 5 estimated absolute RMS force accuracy = 0.0325342 estimated relative force accuracy = 9.79757e-05 using double precision MKL FFT 3d grid and FFT values/proc = 3375 512 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 6 6 6 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/cut/coul/long, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 10.14 | 10.14 | 10.14 Mbytes Step CPU Temp Press PotEng Density v_vMax v_invVis 0 0 450.04468 9838.6886 -7651.736 0.99999331 0.0001293705 2649.9663 100 0.33736925 497.65155 2024.4827 -8342.2499 0.98595028 0.00019602427 4034.2452 200 0.67116638 446.48518 27.075082 -8908.9684 0.9652009 0.00027615455 5723.7907 300 0.99760895 401.79875 -776.99871 -9381.8986 0.95205822 0.00019626685 4086.6103 400 1.3239019 369.65373 -510.5336 -9803.6463 0.94817309 0.00022998514 4795.2142 500 1.6488092 343.35807 -936.31982 -10146.023 0.94840581 0.0001434423 2990.5423 600 1.9826063 319.86131 -1381.3302 -10405.812 0.95459202 6.6411532e-05 1381.5767 700 2.3172637 307.74606 -98.775733 -10643.5 0.96669652 0.00010446317 2164.0664 800 2.6562841 305.14214 -540.57804 -10865.742 0.97808367 5.4381233e-05 1122.1765 900 2.9938415 288.01316 639.00486 -10925.39 0.98686357 0.00010878474 2238.1355 1000 3.327893 295.07773 -226.06503 -11033.826 0.99128496 0.00011935058 2451.8608 1100 3.6618862 299.21578 306.34231 -11049.152 0.99552203 8.9538943e-05 1836.8166 1200 3.9984287 301.82462 85.804646 -11013.564 0.99713434 0.00015912276 3262.51 1300 4.3320735 308.6009 268.08897 -11009.836 0.99695358 0.00026212596 5374.72 1400 4.668875 298.36903 -258.75495 -10962.299 0.99503447 0.00033087355 6788.7027 1500 5.0003694 299.96073 99.512082 -10980.551 0.99315631 0.00033996557 6979.6425 1600 5.3367337 304.18018 -500.65441 -11002.054 0.9914558 0.00039075642 8026.9849 1700 5.6780828 301.63978 -499.07458 -10992.88 0.99234354 0.00038101175 7824.4738 1800 6.0140638 303.25858 640.03432 -11053.335 0.99553958 0.00041336203 8479.7267 1900 6.3532521 301.40882 208.28331 -11119.481 0.99534534 0.00032474734 6662.3144 2000 6.6938104 298.0462 -236.47954 -11162.212 0.99421846 0.00023869721 4898.8129 Loop time of 6.69387 on 8 procs for 2000 steps with 3000 atoms Performance: 25.815 ns/day, 0.930 hours/ns, 298.781 timesteps/s 99.7% CPU use with 8 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.36 | 4.4981 | 4.6781 | 5.1 | 67.20 Bond | 0.00074545 | 0.00088463 | 0.0012464 | 0.0 | 0.01 Kspace | 0.86696 | 1.0476 | 1.1863 | 10.5 | 15.65 Neigh | 0.37733 | 0.37785 | 0.3784 | 0.1 | 5.64 Comm | 0.19874 | 0.20168 | 0.20729 | 0.6 | 3.01 Output | 0.0015529 | 0.0015803 | 0.0017546 | 0.2 | 0.02 Modify | 0.54083 | 0.55143 | 0.55445 | 0.6 | 8.24 Other | | 0.01483 | | | 0.22 Nlocal: 375 ave 385 max 361 min Histogram: 1 1 0 0 1 0 2 0 1 2 Nghost: 5772.25 ave 5789 max 5757 min Histogram: 1 1 2 0 0 0 2 0 0 2 Neighs: 135285 ave 144189 max 127550 min Histogram: 1 2 1 1 0 0 0 0 1 2 Total # of neighbors = 1082280 Ave neighs/atom = 360.76 Ave special neighs/atom = 2 Neighbor list builds = 101 Dangerous builds = 1 Total wall time: 0:00:06 Loading
examples/USER/viscosity/log.1000SPCE.lammps 0 → 100644 +160 −0 Original line number Diff line number Diff line LAMMPS (3 Mar 2020) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) using 1 OpenMP thread(s) per MPI task # DFF generated Lammps input file units real atom_style full boundary p p p pair_style lj/cut/coul/long 10.0 pair_modify mix arithmetic pair_modify tail yes kspace_style pppm 1.0e-4 dielectric 1.0 special_bonds amber bond_style harmonic angle_style harmonic dihedral_style none improper_style none read_data data.1000SPCE.lmp orthogonal box = (0 0 0) to (31.043 31.043 31.043) 2 by 2 by 2 MPI processor grid reading atoms ... 3000 atoms scanning bonds ... 2 = max bonds/atom scanning angles ... 1 = max angles/atom reading bonds ... 2000 bonds reading angles ... 1000 angles 2 = max # of 1-2 neighbors 1 = max # of 1-3 neighbors 1 = max # of 1-4 neighbors 2 = max # of special neighbors special bonds CPU = 0.00114917 secs read_data CPU = 0.00953543 secs variable T equal 300 variable P equal 1.0 velocity all create ${T} 12345 mom yes rot yes dist gaussian velocity all create 300 12345 mom yes rot yes dist gaussian timestep 1.0 # Constraint ################################## fix com all momentum 100 linear 1 1 1 fix rigid all shake 1e-4 20 0 b 1 a 1 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 1000 = # of frozen angles find clusters CPU = 0.000442737 secs # Viscosity ################################## variable A equal 0.02e-5 # angstrom/fs^2 fix cos all accelerate/cos ${A} fix cos all accelerate/cos 2e-07 compute cos all viscosity/cos variable density equal density variable lz equal lz variable vMax equal c_cos[7] # velocity of atoms at z=0 variable invVis equal v_vMax/${A}/v_density*39.4784/v_lz/v_lz*100 # reciprocal of viscosity 1/Pa/s variable invVis equal v_vMax/2e-07/v_density*39.4784/v_lz/v_lz*100 fix npt all npt temp ${T} ${T} 100 iso ${P} ${P} 1000 fix npt all npt temp 300 ${T} 100 iso ${P} ${P} 1000 fix npt all npt temp 300 300 100 iso ${P} ${P} 1000 fix npt all npt temp 300 300 100 iso 1 ${P} 1000 fix npt all npt temp 300 300 100 iso 1 1 1000 fix_modify npt temp cos thermo_style custom step cpu temp press pe density v_vMax v_invVis thermo_modify temp cos thermo 100 ################################################ dump 1 all custom 10000 dump.lammpstrj id mol type element q xu yu zu dump_modify 1 sort id element O H run 2000 PPPM initialization ... using 12-bit tables for long-range coulomb (src/kspace.cpp:332) G vector (1/distance) = 0.263539 grid = 16 16 16 stencil order = 5 estimated absolute RMS force accuracy = 0.0325342 estimated relative force accuracy = 9.79757e-05 using double precision MKL FFT 3d grid and FFT values/proc = 3375 512 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 6 6 6 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/cut/coul/long, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 10.14 | 10.14 | 10.14 Mbytes Step CPU Temp Press PotEng Density v_vMax v_invVis 0 0 450.04468 9838.6886 -7651.736 0.99999331 0.0001293705 2649.9663 100 0.33736925 497.65155 2024.4827 -8342.2499 0.98595028 0.00019602427 4034.2452 200 0.67116638 446.48518 27.075082 -8908.9684 0.9652009 0.00027615455 5723.7907 300 0.99760895 401.79875 -776.99871 -9381.8986 0.95205822 0.00019626685 4086.6103 400 1.3239019 369.65373 -510.5336 -9803.6463 0.94817309 0.00022998514 4795.2142 500 1.6488092 343.35807 -936.31982 -10146.023 0.94840581 0.0001434423 2990.5423 600 1.9826063 319.86131 -1381.3302 -10405.812 0.95459202 6.6411532e-05 1381.5767 700 2.3172637 307.74606 -98.775733 -10643.5 0.96669652 0.00010446317 2164.0664 800 2.6562841 305.14214 -540.57804 -10865.742 0.97808367 5.4381233e-05 1122.1765 900 2.9938415 288.01316 639.00486 -10925.39 0.98686357 0.00010878474 2238.1355 1000 3.327893 295.07773 -226.06503 -11033.826 0.99128496 0.00011935058 2451.8608 1100 3.6618862 299.21578 306.34231 -11049.152 0.99552203 8.9538943e-05 1836.8166 1200 3.9984287 301.82462 85.804646 -11013.564 0.99713434 0.00015912276 3262.51 1300 4.3320735 308.6009 268.08897 -11009.836 0.99695358 0.00026212596 5374.72 1400 4.668875 298.36903 -258.75495 -10962.299 0.99503447 0.00033087355 6788.7027 1500 5.0003694 299.96073 99.512082 -10980.551 0.99315631 0.00033996557 6979.6425 1600 5.3367337 304.18018 -500.65441 -11002.054 0.9914558 0.00039075642 8026.9849 1700 5.6780828 301.63978 -499.07458 -10992.88 0.99234354 0.00038101175 7824.4738 1800 6.0140638 303.25858 640.03432 -11053.335 0.99553958 0.00041336203 8479.7267 1900 6.3532521 301.40882 208.28331 -11119.481 0.99534534 0.00032474734 6662.3144 2000 6.6938104 298.0462 -236.47954 -11162.212 0.99421846 0.00023869721 4898.8129 Loop time of 6.69387 on 8 procs for 2000 steps with 3000 atoms Performance: 25.815 ns/day, 0.930 hours/ns, 298.781 timesteps/s 99.7% CPU use with 8 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.36 | 4.4981 | 4.6781 | 5.1 | 67.20 Bond | 0.00074545 | 0.00088463 | 0.0012464 | 0.0 | 0.01 Kspace | 0.86696 | 1.0476 | 1.1863 | 10.5 | 15.65 Neigh | 0.37733 | 0.37785 | 0.3784 | 0.1 | 5.64 Comm | 0.19874 | 0.20168 | 0.20729 | 0.6 | 3.01 Output | 0.0015529 | 0.0015803 | 0.0017546 | 0.2 | 0.02 Modify | 0.54083 | 0.55143 | 0.55445 | 0.6 | 8.24 Other | | 0.01483 | | | 0.22 Nlocal: 375 ave 385 max 361 min Histogram: 1 1 0 0 1 0 2 0 1 2 Nghost: 5772.25 ave 5789 max 5757 min Histogram: 1 1 2 0 0 0 2 0 0 2 Neighs: 135285 ave 144189 max 127550 min Histogram: 1 2 1 1 0 0 0 0 1 2 Total # of neighbors = 1082280 Ave neighs/atom = 360.76 Ave special neighs/atom = 2 Neighbor list builds = 101 Dangerous builds = 1 Total wall time: 0:00:06
