Fix the example according to the convention
This commit is contained in:
Vsevak
1
examples/TIP4P/gpu_dump/data.spce
Symbolic link
1
examples/TIP4P/gpu_dump/data.spce
Symbolic link
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../../rdf-adf/data.spce
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9018
examples/TIP4P/gpu_dump/dump.force_cpu.19Dec19.tip4p.g++.1
Normal file
9018
examples/TIP4P/gpu_dump/dump.force_cpu.19Dec19.tip4p.g++.1
Normal file
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
49
examples/TIP4P/gpu_dump/in.tip4p
Normal file
49
examples/TIP4P/gpu_dump/in.tip4p
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# sample script to compare and debug GPU accelerated tip4p water
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# use '-sf gpu' to enables the GPU accelerated pair style
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# without it the original lj/cut/tip4p/long from module KSPACE will be used
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units real
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boundary p p p
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atom_style full
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bond_style harmonic
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angle_style harmonic
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atom_modify map array
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pair_style lj/cut/tip4p/long 1 2 1 1 0.1546 9.0 9.0
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pair_modify table 0
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#long-range solver for TIP4P from module KSPACE works on CPU
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suffix off
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newton on
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kspace_style pppm/tip4p 1.0e-5
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suffix on
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read_data data.spce
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pair_coeff * * 0.0 0.0
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pair_coeff 1 1 0.1852 3.1589
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bond_coeff 1 0.0 0.9572
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angle_coeff 1 0.0 104.52
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group water type 1 2
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#maintain the water molecule rigid
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fix 1 water shake 1.0e-4 200 0 b 1 a 1
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fix 2 water nve
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thermo 100
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thermo_style custom step etotal ke pe temp evdwl ecoul elong press
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thermo_modify format float "%.15g"
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velocity water create 300 123
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if $(is_active(package,gpu)) &
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then "dump 11 all custom 1 dump.force_gpu id type x y z fx fy fz"&
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else "dump 11 all custom 1 dump.force_cpu id type x y z fx fy fz"
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dump_modify 11 sort id
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timestep 1
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run 1
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127
examples/TIP4P/gpu_dump/log.19Dec19.tip4p.g++.1
Normal file
127
examples/TIP4P/gpu_dump/log.19Dec19.tip4p.g++.1
Normal file
@ -0,0 +1,127 @@
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LAMMPS (30 Oct 2019)
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#
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units real
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boundary p p p
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atom_style full
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bond_style harmonic
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angle_style harmonic
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atom_modify map array
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pair_style lj/cut/tip4p/long 1 2 1 1 0.1546 9.0 9.0
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pair_modify table 0
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#long-range solver for TIP4P from module KSPACE works on CPU
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suffix off
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newton on
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kspace_style pppm/tip4p 1.0e-5
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suffix on
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read_data data.spce
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orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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4500 atoms
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scanning bonds ...
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2 = max bonds/atom
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scanning angles ...
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1 = max angles/atom
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reading bonds ...
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3000 bonds
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reading angles ...
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1500 angles
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2 = max # of 1-2 neighbors
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1 = max # of 1-3 neighbors
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1 = max # of 1-4 neighbors
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2 = max # of special neighbors
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special bonds CPU = 0.00143709 secs
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read_data CPU = 0.0185545 secs
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pair_coeff * * 0.0 0.0
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pair_coeff 1 1 0.1852 3.1589
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bond_coeff 1 0.0 0.9572
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angle_coeff 1 0.0 104.52
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group water type 1 2
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4500 atoms in group water
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#maintain the water molecule rigid
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fix 1 water shake 1.0e-4 200 0 b 1 a 1
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0 = # of size 2 clusters
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0 = # of size 3 clusters
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0 = # of size 4 clusters
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1500 = # of frozen angles
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fix 2 water nve
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thermo 100
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thermo_style custom step etotal ke pe temp evdwl ecoul elong press
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thermo_modify format float "%.15g"
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velocity water create 300 123
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if $(is_active(package,gpu)) then "dump 11 all custom 1 dump.force_gpu id type x y z fx fy fz" else "dump 11 all custom 1 dump.force_cpu id type x y z fx fy fz"
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if 0 then "dump 11 all custom 1 dump.force_gpu id type x y z fx fy fz" else "dump 11 all custom 1 dump.force_cpu id type x y z fx fy fz"
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dump 11 all custom 1 dump.force_cpu id type x y z fx fy fz
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dump_modify 11 sort id
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timestep 1
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run 1
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PPPM initialization ...
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extracting TIP4P info from pair style
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using polynomial approximation for long-range coulomb (../kspace.cpp:323)
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G vector (1/distance) = 0.342797
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grid = 36 36 36
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stencil order = 5
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estimated absolute RMS force accuracy = 0.00261362
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estimated relative force accuracy = 7.87083e-06
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using double precision KISS FFT
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3d grid and FFT values/proc = 79507 46656
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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 = 11.3092
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ghost atom cutoff = 11.3092
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binsize = 5.6546, bins = 7 7 7
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cut/tip4p/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/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 30.18 | 30.18 | 30.18 Mbytes
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Step TotEng KinEng PotEng Temp E_vdwl E_coul E_long Press
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0 -6581.1098053463 2681.834801985 -9262.9446073313 300 3652.16918734499 90723.8782743546 -103638.992069031 20828.2770003273
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1 -6293.09711304554 1787.55263217222 -8080.64974521776 199.96227554909 3652.66537554581 91910.2042281151 -103643.519348879 20986.2037813061
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Loop time of 0.0943946 on 1 procs for 1 steps with 4500 atoms
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Performance: 0.915 ns/day, 26.221 hours/ns, 10.594 timesteps/s
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101.7% 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 | 0.071838 | 0.071838 | 0.071838 | 0.0 | 76.10
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Bond | 1.974e-06 | 1.974e-06 | 1.974e-06 | 0.0 | 0.00
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Kspace | 0.012686 | 0.012686 | 0.012686 | 0.0 | 13.44
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.00012462 | 0.00012462 | 0.00012462 | 0.0 | 0.13
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Output | 0.0093175 | 0.0093175 | 0.0093175 | 0.0 | 9.87
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Modify | 0.00038138 | 0.00038138 | 0.00038138 | 0.0 | 0.40
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Other | | 4.484e-05 | | | 0.05
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Nlocal: 4500 ave 4500 max 4500 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 15219 ave 15219 max 15219 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 1.37151e+06 ave 1.37151e+06 max 1.37151e+06 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 1371514
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Ave neighs/atom = 304.781
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Ave special neighs/atom = 2
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Neighbor list builds = 0
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Dangerous builds = 0
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Total wall time: 0:00:00
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120
examples/TIP4P/gpu_dump/log.19Dec19.tip4p.g++.1.gtx1070.dp
Normal file
120
examples/TIP4P/gpu_dump/log.19Dec19.tip4p.g++.1.gtx1070.dp
Normal file
@ -0,0 +1,120 @@
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LAMMPS (30 Oct 2019)
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package gpu 1
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#
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units real
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boundary p p p
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||||||
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|
||||||
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atom_style full
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||||||
|
bond_style harmonic
|
||||||
|
angle_style harmonic
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||||||
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atom_modify map array
|
||||||
|
|
||||||
|
pair_style lj/cut/tip4p/long 1 2 1 1 0.1546 9.0 9.0
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||||||
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pair_modify table 0
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||||||
|
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||||||
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#long-range solver for TIP4P from module KSPACE works on CPU
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||||||
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suffix off
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||||||
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newton on
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||||||
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kspace_style pppm/tip4p 1.0e-5
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||||||
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suffix on
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||||||
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read_data data.spce
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orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736)
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1 by 1 by 1 MPI processor grid
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||||||
|
reading atoms ...
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||||||
|
4500 atoms
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||||||
|
scanning bonds ...
|
||||||
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2 = max bonds/atom
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||||||
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scanning angles ...
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||||||
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1 = max angles/atom
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||||||
|
reading bonds ...
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||||||
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3000 bonds
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||||||
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reading angles ...
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||||||
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1500 angles
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||||||
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2 = max # of 1-2 neighbors
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1 = max # of 1-3 neighbors
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1 = max # of 1-4 neighbors
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2 = max # of special neighbors
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special bonds CPU = 0.000921346 secs
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read_data CPU = 0.0115216 secs
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pair_coeff * * 0.0 0.0
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pair_coeff 1 1 0.1852 3.1589
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bond_coeff 1 0.0 0.9572
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angle_coeff 1 0.0 104.52
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group water type 1 2
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4500 atoms in group water
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#maintain the water molecule rigid
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||||||
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fix 1 water shake 1.0e-4 200 0 b 1 a 1
|
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0 = # of size 2 clusters
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||||||
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0 = # of size 3 clusters
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||||||
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0 = # of size 4 clusters
|
||||||
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1500 = # of frozen angles
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|
fix 2 water nve
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||||||
|
|
||||||
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thermo 100
|
||||||
|
thermo_style custom step etotal ke pe temp evdwl ecoul elong press
|
||||||
|
thermo_modify format float "%.15g"
|
||||||
|
|
||||||
|
velocity water create 300 123
|
||||||
|
|
||||||
|
if $(is_active(package,gpu)) then "dump 11 all custom 1 dump.force_gpu id type x y z fx fy fz" else "dump 11 all custom 1 dump.force_cpu id type x y z fx fy fz"
|
||||||
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if 1 then "dump 11 all custom 1 dump.force_gpu id type x y z fx fy fz" else "dump 11 all custom 1 dump.force_cpu id type x y z fx fy fz"
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||||||
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dump 11 all custom 1 dump.force_gpu id type x y z fx fy fz
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||||||
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dump_modify 11 sort id
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||||||
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|
||||||
|
timestep 1
|
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|
||||||
|
run 1
|
||||||
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PPPM initialization ...
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||||||
|
extracting TIP4P info from pair style
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||||||
|
using polynomial approximation for long-range coulomb (../kspace.cpp:323)
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G vector (1/distance) = 0.342797
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grid = 36 36 36
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stencil order = 5
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estimated absolute RMS force accuracy = 0.00261362
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||||||
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estimated relative force accuracy = 7.87083e-06
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using double precision KISS FFT
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3d grid and FFT values/proc = 79507 46656
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WARNING: Increasing communication cutoff for TIP4P GPU style (../pair_lj_cut_tip4p_long_gpu.cpp:220)
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Per MPI rank memory allocation (min/avg/max) = 25.12 | 25.12 | 25.12 Mbytes
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Step TotEng KinEng PotEng Temp E_vdwl E_coul E_long Press
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||||||
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0 -6581.10980534572 2681.834801985 -9262.94460733072 300 3652.169187345 90723.8782743551 -103638.992069031 20828.2770003278
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1 -6293.09711304691 1787.55263217221 -8080.64974521913 199.96227554909 3652.6653755458 91910.2042281137 -103643.519348879 20986.203781307
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Loop time of 0.0230916 on 1 procs for 1 steps with 4500 atoms
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||||||
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Performance: 3.742 ns/day, 6.414 hours/ns, 43.306 timesteps/s
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103.9% CPU use with 1 MPI tasks x no OpenMP threads
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||||||
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|
||||||
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MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.000606 | 0.000606 | 0.000606 | 0.0 | 2.62
|
||||||
|
Bond | 1.682e-06 | 1.682e-06 | 1.682e-06 | 0.0 | 0.01
|
||||||
|
Kspace | 0.012588 | 0.012588 | 0.012588 | 0.0 | 54.51
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0.00015025 | 0.00015025 | 0.00015025 | 0.0 | 0.65
|
||||||
|
Output | 0.0093124 | 0.0093124 | 0.0093124 | 0.0 | 40.33
|
||||||
|
Modify | 0.00039674 | 0.00039674 | 0.00039674 | 0.0 | 1.72
|
||||||
|
Other | | 3.623e-05 | | | 0.16
|
||||||
|
|
||||||
|
Nlocal: 4500 ave 4500 max 4500 min
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||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
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||||||
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Nghost: 16834 ave 16834 max 16834 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
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||||||
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Neighs: 0 ave 0 max 0 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 0
|
||||||
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Ave neighs/atom = 0
|
||||||
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Ave special neighs/atom = 2
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||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
Please see the log.cite file for references relevant to this simulation
|
||||||
|
|
||||||
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Total wall time: 0:00:00
|
||||||
File diff suppressed because it is too large
Load Diff
@ -1,19 +0,0 @@
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# data
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|
||||||
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||||||
3 atoms
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|
||||||
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||||||
1 atom types
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|
||||||
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|
||||||
-10 10 xlo xhi
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||||||
-10 10 ylo yhi
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|
||||||
-10 10 zlo zhi
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||||||
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||||||
Masses
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||||||
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||||||
1 1.00794
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||||||
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||||||
Atoms
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||||||
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||||||
1 1 0 0 0
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||||||
2 1 1.5 0 0
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||||||
3 1 0 1.5 0
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||||||
@ -1,80 +0,0 @@
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|||||||
#LAMMPS input file
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|
||||||
#All informations can be find on http://lammps.sandia.gov/
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|
||||||
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|
||||||
#choose the system of unit (real, metal, SI...)
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|
||||||
units real
|
|
||||||
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|
||||||
#define the boundary conditions, periodic here
|
|
||||||
boundary p p p
|
|
||||||
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|
||||||
#define the atom style, bond style and angle style
|
|
||||||
atom_style full
|
|
||||||
bond_style harmonic
|
|
||||||
angle_style harmonic
|
|
||||||
atom_modify map array
|
|
||||||
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|
||||||
#comm_modify cutoff 15
|
|
||||||
#atom_modify first water
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|
||||||
#neigh_modify cluster yes
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|
||||||
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|
||||||
#choose the interaction between water molecules:
|
|
||||||
pair_style lj/cut/tip4p/long 1 2 1 1 0.1546 9.0 9.0
|
|
||||||
pair_modify table 0
|
|
||||||
#water model is TIP4P/2005
|
|
||||||
#water molecules less than 1nm from each other interact via a cut lennard jones potential
|
|
||||||
#water molecules interact via coulomb interactions calculated in real or conjugate space depending on the distance separating molecules
|
|
||||||
|
|
||||||
#define the long-range solver (here for long range coulombic interaction)
|
|
||||||
suffix off
|
|
||||||
newton on
|
|
||||||
kspace_style pppm/tip4p 1.0e-5
|
|
||||||
suffix on
|
|
||||||
|
|
||||||
#neighbor 5.0 bin
|
|
||||||
#neigh_modify every 1 check yes
|
|
||||||
|
|
||||||
#import the initial position of atoms, the coordinates of the box, etc
|
|
||||||
read_data data.spce
|
|
||||||
replicate 2 2 2
|
|
||||||
|
|
||||||
#define the pair coeff for LJ interaction
|
|
||||||
pair_coeff * * 0.0 0.0
|
|
||||||
pair_coeff 1 1 0.1852 3.1589
|
|
||||||
|
|
||||||
#define the coef for water molecule (distances between O-H and angle between H-O-H atoms)
|
|
||||||
bond_coeff 1 0.0 0.9572
|
|
||||||
angle_coeff 1 0.0 104.52
|
|
||||||
|
|
||||||
#define groups
|
|
||||||
group water type 1 2
|
|
||||||
|
|
||||||
#maintain the water molecule rigid
|
|
||||||
fix 1 water shake 1.0e-4 200 0 b 1 a 1
|
|
||||||
|
|
||||||
#udate position and velocity each timesteps using constant NVE integration
|
|
||||||
fix 2 water nve
|
|
||||||
|
|
||||||
#apply Langevin thermostat on water molecules
|
|
||||||
#fix 3 water langevin 300.0 300.0 100.0 123
|
|
||||||
|
|
||||||
#choose how often you want thermodynamic info to be print during the computation
|
|
||||||
thermo 1000
|
|
||||||
thermo_modify flush yes
|
|
||||||
thermo_style custom step etotal ke pe temp evdwl ecoul elong press
|
|
||||||
#thermo_modify format float "%.15g"
|
|
||||||
#give an initial random velocity to water molecule (corresponding to a temperature equal to 300K)
|
|
||||||
velocity water create 300 123
|
|
||||||
|
|
||||||
#print the position of atoms to visualise it with VMD for example
|
|
||||||
#dump 4 all atom 1 dump.lammpstrj
|
|
||||||
#dump_modify 4 flush yes
|
|
||||||
|
|
||||||
#if $(is_active(package,gpu)) &
|
|
||||||
# then "dump 11 all custom 1 dump.force_gpu id type x y z fx fy fz"&
|
|
||||||
# else "dump 11 all custom 1 dump.force_cpu id type x y z fx fy fz"
|
|
||||||
|
|
||||||
#choose the timestep, 2fs is a common choice
|
|
||||||
timestep 1
|
|
||||||
|
|
||||||
#run during 50000 timestep (0.1 ns)
|
|
||||||
run 50000
|
|
||||||
Reference in New Issue
Block a user