Merge branch 'clean-master2' of github.com:julient31/lammps into pppm_spin
Conflicts: src/SPIN/fix_nve_spin.h
This commit is contained in:
julient31
13
examples/SPIN/gneb/README
Normal file
13
examples/SPIN/gneb/README
Normal file
@ -0,0 +1,13 @@
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Perform geodesic NEB calculations for spin configurations.
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The two examples are:
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- the magnetic switching of an iron nanoisland
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- the collapse of a magnetic skyrmion
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Run those examples as:
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mpirun -np 3 lmp_mpi -in in.gneb.iron -partition 3x1
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You should be able to use any number of replicas >= 3.
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In the interpolate/ directory, a c routine is provided to
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interpolate the MEP.
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68
examples/SPIN/gneb/iron/final.iron_spin
Normal file
68
examples/SPIN/gneb/iron/final.iron_spin
Normal file
@ -0,0 +1,68 @@
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32
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||||
1 2.2000000000000002e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
2 2.2000000000000002e+00 1.4332499999999999e+00 1.4332499999999999e+00 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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||||
3 2.2000000000000002e+00 2.8664999999999998e+00 0.0000000000000000e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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||||
4 2.2000000000000002e+00 4.2997499999999995e+00 1.4332499999999999e+00 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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||||
5 2.2000000000000002e+00 5.7329999999999997e+00 0.0000000000000000e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
6 2.2000000000000002e+00 7.1662499999999998e+00 1.4332499999999999e+00 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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||||
7 2.2000000000000002e+00 8.5994999999999990e+00 0.0000000000000000e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
8 2.2000000000000002e+00 1.0032750000000000e+01 1.4332499999999999e+00 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
9 2.2000000000000002e+00 0.0000000000000000e+00 2.8664999999999998e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
10 2.2000000000000002e+00 2.8664999999999998e+00 2.8664999999999998e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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||||
11 2.2000000000000002e+00 5.7329999999999997e+00 2.8664999999999998e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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12 2.2000000000000002e+00 8.5994999999999990e+00 2.8664999999999998e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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||||
13 2.2000000000000002e+00 1.4332499999999999e+00 4.2997499999999995e+00 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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14 2.2000000000000002e+00 4.2997499999999995e+00 4.2997499999999995e+00 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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15 2.2000000000000002e+00 7.1662499999999998e+00 4.2997499999999995e+00 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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||||
16 2.2000000000000002e+00 1.0032750000000000e+01 4.2997499999999995e+00 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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17 2.2000000000000002e+00 0.0000000000000000e+00 5.7329999999999997e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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||||
18 2.2000000000000002e+00 1.4332499999999999e+00 7.1662499999999998e+00 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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19 2.2000000000000002e+00 2.8664999999999998e+00 5.7329999999999997e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
20 2.2000000000000002e+00 4.2997499999999995e+00 7.1662499999999998e+00 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
21 2.2000000000000002e+00 5.7329999999999997e+00 5.7329999999999997e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
22 2.2000000000000002e+00 7.1662499999999998e+00 7.1662499999999998e+00 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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||||
23 2.2000000000000002e+00 8.5994999999999990e+00 5.7329999999999997e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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24 2.2000000000000002e+00 1.0032750000000000e+01 7.1662499999999998e+00 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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25 2.2000000000000002e+00 0.0000000000000000e+00 8.5994999999999990e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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26 2.2000000000000002e+00 2.8664999999999998e+00 8.5994999999999990e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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27 2.2000000000000002e+00 5.7329999999999997e+00 8.5994999999999990e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
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28 2.2000000000000002e+00 8.5994999999999990e+00 8.5994999999999990e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
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29 2.2000000000000002e+00 1.4332499999999999e+00 1.0032750000000000e+01 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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30 2.2000000000000002e+00 4.2997499999999995e+00 1.0032750000000000e+01 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
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31 2.2000000000000002e+00 7.1662499999999998e+00 1.0032750000000000e+01 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
32 2.2000000000000002e+00 1.0032750000000000e+01 1.0032750000000000e+01 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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|
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|
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50
examples/SPIN/gneb/iron/in.gneb.iron
Normal file
50
examples/SPIN/gneb/iron/in.gneb.iron
Normal file
@ -0,0 +1,50 @@
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units metal
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dimension 3
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boundary p p f
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atom_style spin
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# necessary for the serial algorithm (sametag)
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atom_modify map array
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# setting mass, mag. moments, and interactions for bcc iron
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# (mass not necessary for fixed lattice calculation)
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read_data initial.iron_spin
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mass 1 55.845
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pair_style spin/exchange 3.5
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pair_coeff * * exchange 3.4 0.02726 0.2171 1.841
|
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neighbor 0.1 bin
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||||
neigh_modify every 10 check yes delay 20
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fix 1 all precession/spin zeeman 0.1 0.0 0.0 1.0 anisotropy 0.0001 1.0 0.0 0.0
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fix_modify 1 energy yes
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fix 3 all neb/spin 1.0
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timestep 0.0001
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thermo 100
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compute out_mag all spin
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compute out_pe all pe
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compute out_ke all ke
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compute out_temp all temp
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variable magx equal c_out_mag[1]
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variable magy equal c_out_mag[2]
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variable magz equal c_out_mag[3]
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variable magnorm equal c_out_mag[4]
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variable emag equal c_out_mag[5]
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thermo 100
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thermo_style custom step time v_magx v_magz v_magnorm etotal
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thermo_modify format float %20.15g
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compute outsp all property/atom spx spy spz sp fmx fmy fmz
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variable u universe 1 2 3 4
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dump 1 all custom 200 dump.$u type x y z c_outsp[1] c_outsp[2] c_outsp[3]
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min_style spin
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min_modify alpha_damp 1.0 discrete_factor 10.0
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neb/spin 1.0e-12 1.0e-12 200000 100000 1000 final final.iron_spin verbose
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82
examples/SPIN/gneb/iron/initial.iron_spin
Normal file
82
examples/SPIN/gneb/iron/initial.iron_spin
Normal file
@ -0,0 +1,82 @@
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LAMMPS data file via write_data, version 4 Jan 2019, timestep = 0
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32 atoms
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1 atom types
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||||
0.0000000000000000e+00 1.1465999999999999e+01 xlo xhi
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||||
0.0000000000000000e+00 1.1465999999999999e+01 ylo yhi
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||||
0.0000000000000000e+00 2.8664999999999998e+00 zlo zhi
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Masses
|
||||
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||||
1 55.845
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||||
|
||||
Atoms # spin
|
||||
|
||||
1 1 2.2000000000000002e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
|
||||
2 1 2.2000000000000002e+00 1.4332499999999999e+00 1.4332499999999999e+00 1.4332499999999999e+00 1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
|
||||
3 1 2.2000000000000002e+00 2.8664999999999998e+00 0.0000000000000000e+00 0.0000000000000000e+00 1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
|
||||
4 1 2.2000000000000002e+00 4.2997499999999995e+00 1.4332499999999999e+00 1.4332499999999999e+00 1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
|
||||
5 1 2.2000000000000002e+00 5.7329999999999997e+00 0.0000000000000000e+00 0.0000000000000000e+00 1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
|
||||
6 1 2.2000000000000002e+00 7.1662499999999998e+00 1.4332499999999999e+00 1.4332499999999999e+00 1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
|
||||
7 1 2.2000000000000002e+00 8.5994999999999990e+00 0.0000000000000000e+00 0.0000000000000000e+00 1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
|
||||
8 1 2.2000000000000002e+00 1.0032750000000000e+01 1.4332499999999999e+00 1.4332499999999999e+00 1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
|
||||
9 1 2.2000000000000002e+00 0.0000000000000000e+00 2.8664999999999998e+00 0.0000000000000000e+00 1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
|
||||
11 1 2.2000000000000002e+00 2.8664999999999998e+00 2.8664999999999998e+00 0.0000000000000000e+00 1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
|
||||
13 1 2.2000000000000002e+00 5.7329999999999997e+00 2.8664999999999998e+00 0.0000000000000000e+00 1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
|
||||
15 1 2.2000000000000002e+00 8.5994999999999990e+00 2.8664999999999998e+00 0.0000000000000000e+00 1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
|
||||
10 1 2.2000000000000002e+00 1.4332499999999999e+00 4.2997499999999995e+00 1.4332499999999999e+00 1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
|
||||
12 1 2.2000000000000002e+00 4.2997499999999995e+00 4.2997499999999995e+00 1.4332499999999999e+00 1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
|
||||
14 1 2.2000000000000002e+00 7.1662499999999998e+00 4.2997499999999995e+00 1.4332499999999999e+00 1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
|
||||
16 1 2.2000000000000002e+00 1.0032750000000000e+01 4.2997499999999995e+00 1.4332499999999999e+00 1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
|
||||
17 1 2.2000000000000002e+00 0.0000000000000000e+00 5.7329999999999997e+00 0.0000000000000000e+00 1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
|
||||
18 1 2.2000000000000002e+00 1.4332499999999999e+00 7.1662499999999998e+00 1.4332499999999999e+00 1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
|
||||
19 1 2.2000000000000002e+00 2.8664999999999998e+00 5.7329999999999997e+00 0.0000000000000000e+00 1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
|
||||
20 1 2.2000000000000002e+00 4.2997499999999995e+00 7.1662499999999998e+00 1.4332499999999999e+00 1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
|
||||
21 1 2.2000000000000002e+00 5.7329999999999997e+00 5.7329999999999997e+00 0.0000000000000000e+00 1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
|
||||
22 1 2.2000000000000002e+00 7.1662499999999998e+00 7.1662499999999998e+00 1.4332499999999999e+00 1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
|
||||
23 1 2.2000000000000002e+00 8.5994999999999990e+00 5.7329999999999997e+00 0.0000000000000000e+00 1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
|
||||
24 1 2.2000000000000002e+00 1.0032750000000000e+01 7.1662499999999998e+00 1.4332499999999999e+00 1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
|
||||
25 1 2.2000000000000002e+00 0.0000000000000000e+00 8.5994999999999990e+00 0.0000000000000000e+00 1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
|
||||
27 1 2.2000000000000002e+00 2.8664999999999998e+00 8.5994999999999990e+00 0.0000000000000000e+00 1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
|
||||
29 1 2.2000000000000002e+00 5.7329999999999997e+00 8.5994999999999990e+00 0.0000000000000000e+00 1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
|
||||
31 1 2.2000000000000002e+00 8.5994999999999990e+00 8.5994999999999990e+00 0.0000000000000000e+00 1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
|
||||
26 1 2.2000000000000002e+00 1.4332499999999999e+00 1.0032750000000000e+01 1.4332499999999999e+00 1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
|
||||
28 1 2.2000000000000002e+00 4.2997499999999995e+00 1.0032750000000000e+01 1.4332499999999999e+00 1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
|
||||
30 1 2.2000000000000002e+00 7.1662499999999998e+00 1.0032750000000000e+01 1.4332499999999999e+00 1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
|
||||
32 1 2.2000000000000002e+00 1.0032750000000000e+01 1.0032750000000000e+01 1.4332499999999999e+00 1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
|
||||
|
||||
Velocities
|
||||
|
||||
1 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
2 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
3 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
4 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
5 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
6 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
7 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
8 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
9 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
11 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
13 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
15 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
10 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
12 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
14 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
16 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
17 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
18 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
19 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
20 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
21 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
22 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
23 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
24 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
25 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
27 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
29 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
31 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
26 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
28 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
30 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
32 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
401
examples/SPIN/gneb/skyrmion/final.skyrmion
Normal file
401
examples/SPIN/gneb/skyrmion/final.skyrmion
Normal file
@ -0,0 +1,401 @@
|
||||
400
|
||||
1 2.5 0.0 0.0 0.0 0.0 0.0 1.0
|
||||
2 2.5 0.0 3.0 0.0 0.0 0.0 1.0
|
||||
3 2.5 0.0 6.0 0.0 0.0 0.0 1.0
|
||||
4 2.5 0.0 9.0 0.0 0.0 0.0 1.0
|
||||
5 2.5 0.0 12.0 0.0 0.0 0.0 1.0
|
||||
6 2.5 0.0 15.0 0.0 0.0 0.0 1.0
|
||||
7 2.5 0.0 18.0 0.0 0.0 0.0 1.0
|
||||
8 2.5 0.0 21.0 0.0 0.0 0.0 1.0
|
||||
9 2.5 0.0 24.0 0.0 0.0 0.0 1.0
|
||||
10 2.5 0.0 27.0 0.0 0.0 0.0 1.0
|
||||
11 2.5 0.0 30.0 0.0 0.0 0.0 1.0
|
||||
12 2.5 0.0 33.0 0.0 0.0 0.0 1.0
|
||||
13 2.5 0.0 36.0 0.0 0.0 0.0 1.0
|
||||
14 2.5 0.0 39.0 0.0 0.0 0.0 1.0
|
||||
15 2.5 0.0 42.0 0.0 0.0 0.0 1.0
|
||||
16 2.5 0.0 45.0 0.0 0.0 0.0 1.0
|
||||
17 2.5 0.0 48.0 0.0 0.0 0.0 1.0
|
||||
18 2.5 0.0 51.0 0.0 0.0 0.0 1.0
|
||||
19 2.5 0.0 54.0 0.0 0.0 0.0 1.0
|
||||
20 2.5 0.0 57.0 0.0 0.0 0.0 1.0
|
||||
21 2.5 3.0 0.0 0.0 0.0 0.0 1.0
|
||||
22 2.5 3.0 3.0 0.0 0.0 0.0 1.0
|
||||
23 2.5 3.0 6.0 0.0 0.0 0.0 1.0
|
||||
24 2.5 3.0 9.0 0.0 0.0 0.0 1.0
|
||||
25 2.5 3.0 12.0 0.0 0.0 0.0 1.0
|
||||
26 2.5 3.0 15.0 0.0 0.0 0.0 1.0
|
||||
27 2.5 3.0 18.0 0.0 0.0 0.0 1.0
|
||||
28 2.5 3.0 21.0 0.0 0.0 0.0 1.0
|
||||
29 2.5 3.0 24.0 0.0 0.0 0.0 1.0
|
||||
30 2.5 3.0 27.0 0.0 0.0 0.0 1.0
|
||||
31 2.5 3.0 30.0 0.0 0.0 0.0 1.0
|
||||
32 2.5 3.0 33.0 0.0 0.0 0.0 1.0
|
||||
33 2.5 3.0 36.0 0.0 0.0 0.0 1.0
|
||||
34 2.5 3.0 39.0 0.0 0.0 0.0 1.0
|
||||
35 2.5 3.0 42.0 0.0 0.0 0.0 1.0
|
||||
36 2.5 3.0 45.0 0.0 0.0 0.0 1.0
|
||||
37 2.5 3.0 48.0 0.0 0.0 0.0 1.0
|
||||
38 2.5 3.0 51.0 0.0 0.0 0.0 1.0
|
||||
39 2.5 3.0 54.0 0.0 0.0 0.0 1.0
|
||||
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303 2.5 45.0 6.0 0.0 0.0 0.0 1.0
|
||||
304 2.5 45.0 9.0 0.0 0.0 0.0 1.0
|
||||
305 2.5 45.0 12.0 0.0 0.0 0.0 1.0
|
||||
306 2.5 45.0 15.0 0.0 0.0 0.0 1.0
|
||||
307 2.5 45.0 18.0 0.0 0.0 0.0 1.0
|
||||
308 2.5 45.0 21.0 0.0 0.0 0.0 1.0
|
||||
309 2.5 45.0 24.0 0.0 0.0 0.0 1.0
|
||||
310 2.5 45.0 27.0 0.0 0.0 0.0 1.0
|
||||
311 2.5 45.0 30.0 0.0 0.0 0.0 1.0
|
||||
312 2.5 45.0 33.0 0.0 0.0 0.0 1.0
|
||||
313 2.5 45.0 36.0 0.0 0.0 0.0 1.0
|
||||
314 2.5 45.0 39.0 0.0 0.0 0.0 1.0
|
||||
315 2.5 45.0 42.0 0.0 0.0 0.0 1.0
|
||||
316 2.5 45.0 45.0 0.0 0.0 0.0 1.0
|
||||
317 2.5 45.0 48.0 0.0 0.0 0.0 1.0
|
||||
318 2.5 45.0 51.0 0.0 0.0 0.0 1.0
|
||||
319 2.5 45.0 54.0 0.0 0.0 0.0 1.0
|
||||
320 2.5 45.0 57.0 0.0 0.0 0.0 1.0
|
||||
321 2.5 48.0 0.0 0.0 0.0 0.0 1.0
|
||||
322 2.5 48.0 3.0 0.0 0.0 0.0 1.0
|
||||
323 2.5 48.0 6.0 0.0 0.0 0.0 1.0
|
||||
324 2.5 48.0 9.0 0.0 0.0 0.0 1.0
|
||||
325 2.5 48.0 12.0 0.0 0.0 0.0 1.0
|
||||
326 2.5 48.0 15.0 0.0 0.0 0.0 1.0
|
||||
327 2.5 48.0 18.0 0.0 0.0 0.0 1.0
|
||||
328 2.5 48.0 21.0 0.0 0.0 0.0 1.0
|
||||
329 2.5 48.0 24.0 0.0 0.0 0.0 1.0
|
||||
330 2.5 48.0 27.0 0.0 0.0 0.0 1.0
|
||||
331 2.5 48.0 30.0 0.0 0.0 0.0 1.0
|
||||
332 2.5 48.0 33.0 0.0 0.0 0.0 1.0
|
||||
333 2.5 48.0 36.0 0.0 0.0 0.0 1.0
|
||||
334 2.5 48.0 39.0 0.0 0.0 0.0 1.0
|
||||
335 2.5 48.0 42.0 0.0 0.0 0.0 1.0
|
||||
336 2.5 48.0 45.0 0.0 0.0 0.0 1.0
|
||||
337 2.5 48.0 48.0 0.0 0.0 0.0 1.0
|
||||
338 2.5 48.0 51.0 0.0 0.0 0.0 1.0
|
||||
339 2.5 48.0 54.0 0.0 0.0 0.0 1.0
|
||||
340 2.5 48.0 57.0 0.0 0.0 0.0 1.0
|
||||
341 2.5 51.0 0.0 0.0 0.0 0.0 1.0
|
||||
342 2.5 51.0 3.0 0.0 0.0 0.0 1.0
|
||||
343 2.5 51.0 6.0 0.0 0.0 0.0 1.0
|
||||
344 2.5 51.0 9.0 0.0 0.0 0.0 1.0
|
||||
345 2.5 51.0 12.0 0.0 0.0 0.0 1.0
|
||||
346 2.5 51.0 15.0 0.0 0.0 0.0 1.0
|
||||
347 2.5 51.0 18.0 0.0 0.0 0.0 1.0
|
||||
348 2.5 51.0 21.0 0.0 0.0 0.0 1.0
|
||||
349 2.5 51.0 24.0 0.0 0.0 0.0 1.0
|
||||
350 2.5 51.0 27.0 0.0 0.0 0.0 1.0
|
||||
351 2.5 51.0 30.0 0.0 0.0 0.0 1.0
|
||||
352 2.5 51.0 33.0 0.0 0.0 0.0 1.0
|
||||
353 2.5 51.0 36.0 0.0 0.0 0.0 1.0
|
||||
354 2.5 51.0 39.0 0.0 0.0 0.0 1.0
|
||||
355 2.5 51.0 42.0 0.0 0.0 0.0 1.0
|
||||
356 2.5 51.0 45.0 0.0 0.0 0.0 1.0
|
||||
357 2.5 51.0 48.0 0.0 0.0 0.0 1.0
|
||||
358 2.5 51.0 51.0 0.0 0.0 0.0 1.0
|
||||
359 2.5 51.0 54.0 0.0 0.0 0.0 1.0
|
||||
360 2.5 51.0 57.0 0.0 0.0 0.0 1.0
|
||||
361 2.5 54.0 0.0 0.0 0.0 0.0 1.0
|
||||
362 2.5 54.0 3.0 0.0 0.0 0.0 1.0
|
||||
363 2.5 54.0 6.0 0.0 0.0 0.0 1.0
|
||||
364 2.5 54.0 9.0 0.0 0.0 0.0 1.0
|
||||
365 2.5 54.0 12.0 0.0 0.0 0.0 1.0
|
||||
366 2.5 54.0 15.0 0.0 0.0 0.0 1.0
|
||||
367 2.5 54.0 18.0 0.0 0.0 0.0 1.0
|
||||
368 2.5 54.0 21.0 0.0 0.0 0.0 1.0
|
||||
369 2.5 54.0 24.0 0.0 0.0 0.0 1.0
|
||||
370 2.5 54.0 27.0 0.0 0.0 0.0 1.0
|
||||
371 2.5 54.0 30.0 0.0 0.0 0.0 1.0
|
||||
372 2.5 54.0 33.0 0.0 0.0 0.0 1.0
|
||||
373 2.5 54.0 36.0 0.0 0.0 0.0 1.0
|
||||
374 2.5 54.0 39.0 0.0 0.0 0.0 1.0
|
||||
375 2.5 54.0 42.0 0.0 0.0 0.0 1.0
|
||||
376 2.5 54.0 45.0 0.0 0.0 0.0 1.0
|
||||
377 2.5 54.0 48.0 0.0 0.0 0.0 1.0
|
||||
378 2.5 54.0 51.0 0.0 0.0 0.0 1.0
|
||||
379 2.5 54.0 54.0 0.0 0.0 0.0 1.0
|
||||
380 2.5 54.0 57.0 0.0 0.0 0.0 1.0
|
||||
381 2.5 57.0 0.0 0.0 0.0 0.0 1.0
|
||||
382 2.5 57.0 3.0 0.0 0.0 0.0 1.0
|
||||
383 2.5 57.0 6.0 0.0 0.0 0.0 1.0
|
||||
384 2.5 57.0 9.0 0.0 0.0 0.0 1.0
|
||||
385 2.5 57.0 12.0 0.0 0.0 0.0 1.0
|
||||
386 2.5 57.0 15.0 0.0 0.0 0.0 1.0
|
||||
387 2.5 57.0 18.0 0.0 0.0 0.0 1.0
|
||||
388 2.5 57.0 21.0 0.0 0.0 0.0 1.0
|
||||
389 2.5 57.0 24.0 0.0 0.0 0.0 1.0
|
||||
390 2.5 57.0 27.0 0.0 0.0 0.0 1.0
|
||||
391 2.5 57.0 30.0 0.0 0.0 0.0 1.0
|
||||
392 2.5 57.0 33.0 0.0 0.0 0.0 1.0
|
||||
393 2.5 57.0 36.0 0.0 0.0 0.0 1.0
|
||||
394 2.5 57.0 39.0 0.0 0.0 0.0 1.0
|
||||
395 2.5 57.0 42.0 0.0 0.0 0.0 1.0
|
||||
396 2.5 57.0 45.0 0.0 0.0 0.0 1.0
|
||||
397 2.5 57.0 48.0 0.0 0.0 0.0 1.0
|
||||
398 2.5 57.0 51.0 0.0 0.0 0.0 1.0
|
||||
399 2.5 57.0 54.0 0.0 0.0 0.0 1.0
|
||||
400 2.5 57.0 57.0 0.0 0.0 0.0 1.0
|
||||
47
examples/SPIN/gneb/skyrmion/in.gneb.skyrmion
Normal file
47
examples/SPIN/gneb/skyrmion/in.gneb.skyrmion
Normal file
@ -0,0 +1,47 @@
|
||||
|
||||
units metal
|
||||
dimension 3
|
||||
boundary p p f
|
||||
atom_style spin
|
||||
|
||||
# necessary for the serial algorithm (sametag)
|
||||
atom_modify map array
|
||||
|
||||
# setting mass, mag. moments, and interactions for bcc iron
|
||||
# (mass not necessary for fixed lattice calculation)
|
||||
|
||||
read_data initial.skyrmion
|
||||
mass 1 55.845
|
||||
|
||||
pair_style hybrid/overlay spin/exchange 3.1 spin/dmi 3.1
|
||||
pair_coeff * * spin/exchange exchange 3.1 0.01593 0.06626915552 1.211
|
||||
pair_coeff * * spin/dmi dmi 3.1 0.12e-03 0.0 0.0 1.0
|
||||
|
||||
neighbor 0.1 bin
|
||||
neigh_modify every 10 check yes delay 20
|
||||
|
||||
fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 anisotropy 5e-05 0.0 0.0 1.0
|
||||
fix_modify 1 energy yes
|
||||
fix 2 all langevin/spin 0.0 0.0 21
|
||||
fix 3 all neb/spin 1.0
|
||||
|
||||
timestep 0.0001
|
||||
|
||||
compute out_mag all spin
|
||||
variable magx equal c_out_mag[1]
|
||||
variable magy equal c_out_mag[2]
|
||||
variable magz equal c_out_mag[3]
|
||||
variable magnorm equal c_out_mag[4]
|
||||
variable emag equal c_out_mag[5]
|
||||
|
||||
thermo 100
|
||||
thermo_style custom step time v_magx v_magz v_magnorm etotal
|
||||
thermo_modify format float %20.15g
|
||||
|
||||
compute outsp all property/atom spx spy spz sp fmx fmy fmz
|
||||
variable u universe 1 2 3 4
|
||||
dump 1 all custom 1 dump.$u type x y z c_outsp[1] c_outsp[2] c_outsp[3]
|
||||
|
||||
min_style spin
|
||||
min_modify alpha_damp 1.0 discrete_factor 10.0
|
||||
neb/spin 1.0e-9 1.0e-9 10000 10000 10 final final.skyrmion
|
||||
818
examples/SPIN/gneb/skyrmion/initial.skyrmion
Normal file
818
examples/SPIN/gneb/skyrmion/initial.skyrmion
Normal file
@ -0,0 +1,818 @@
|
||||
LAMMPS data file via write_data, version 28 Feb 2019, timestep = 6
|
||||
|
||||
400 atoms
|
||||
1 atom types
|
||||
|
||||
0.0000000000000000e+00 6.0000000000000000e+01 xlo xhi
|
||||
0.0000000000000000e+00 6.0000000000000000e+01 ylo yhi
|
||||
0.0000000000000000e+00 3.0000000000000000e+00 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 55.845
|
||||
|
||||
Atoms # spin
|
||||
|
||||
1 1 2.5000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 -3.9693242391277868e-03 -3.9693242391277929e-03 9.9998424434096433e-01 0 0 0
|
||||
21 1 2.5000000000000000e+00 3.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 -1.1868011343002482e-02 -4.8145058779812530e-03 9.9991798205648519e-01 0 0 0
|
||||
41 1 2.5000000000000000e+00 6.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 -1.9561861499557517e-02 -6.5828744882500201e-03 9.9978697697966845e-01 0 0 0
|
||||
61 1 2.5000000000000000e+00 9.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 -2.6644762521588476e-02 -9.3989438861432541e-03 9.9960077855311480e-01 0 0 0
|
||||
81 1 2.5000000000000000e+00 1.2000000000000000e+01 0.0000000000000000e+00 0.0000000000000000e+00 -3.2364838887478299e-02 -1.3362272507461704e-02 9.9938679542868891e-01 0 0 0
|
||||
101 1 2.5000000000000000e+00 1.5000000000000000e+01 0.0000000000000000e+00 0.0000000000000000e+00 -3.5634992015801843e-02 -1.8429703183501425e-02 9.9919492261750509e-01 0 0 0
|
||||
121 1 2.5000000000000000e+00 1.8000000000000000e+01 0.0000000000000000e+00 0.0000000000000000e+00 -3.5235119566844247e-02 -2.4270277420221115e-02 9.9908430073895971e-01 0 0 0
|
||||
141 1 2.5000000000000000e+00 2.1000000000000000e+01 0.0000000000000000e+00 0.0000000000000000e+00 -3.0237916900163156e-02 -3.0163850736159143e-02 9.9908748890690546e-01 0 0 0
|
||||
161 1 2.5000000000000000e+00 2.4000000000000000e+01 0.0000000000000000e+00 0.0000000000000000e+00 -2.0551704657275890e-02 -3.5058787503171429e-02 9.9917391321755789e-01 0 0 0
|
||||
181 1 2.5000000000000000e+00 2.7000000000000000e+01 0.0000000000000000e+00 0.0000000000000000e+00 -7.2971667669136115e-03 -3.7860607272964066e-02 9.9925638640646097e-01 0 0 0
|
||||
201 1 2.5000000000000000e+00 3.0000000000000000e+01 0.0000000000000000e+00 0.0000000000000000e+00 7.2971667669136028e-03 -3.7860607272964066e-02 9.9925638640646086e-01 0 0 0
|
||||
221 1 2.5000000000000000e+00 3.3000000000000000e+01 0.0000000000000000e+00 0.0000000000000000e+00 2.0551704657275901e-02 -3.5058787503171443e-02 9.9917391321755789e-01 0 0 0
|
||||
241 1 2.5000000000000000e+00 3.6000000000000000e+01 0.0000000000000000e+00 0.0000000000000000e+00 3.0237916900163156e-02 -3.0163850736159153e-02 9.9908748890690535e-01 0 0 0
|
||||
261 1 2.5000000000000000e+00 3.9000000000000000e+01 0.0000000000000000e+00 0.0000000000000000e+00 3.5235119566844234e-02 -2.4270277420221108e-02 9.9908430073895960e-01 0 0 0
|
||||
281 1 2.5000000000000000e+00 4.2000000000000000e+01 0.0000000000000000e+00 0.0000000000000000e+00 3.5634992015801829e-02 -1.8429703183501414e-02 9.9919492261750498e-01 0 0 0
|
||||
301 1 2.5000000000000000e+00 4.5000000000000000e+01 0.0000000000000000e+00 0.0000000000000000e+00 3.2364838887478306e-02 -1.3362272507461704e-02 9.9938679542868891e-01 0 0 0
|
||||
321 1 2.5000000000000000e+00 4.8000000000000000e+01 0.0000000000000000e+00 0.0000000000000000e+00 2.6644762521588494e-02 -9.3989438861432611e-03 9.9960077855311491e-01 0 0 0
|
||||
341 1 2.5000000000000000e+00 5.1000000000000000e+01 0.0000000000000000e+00 0.0000000000000000e+00 1.9561861499557517e-02 -6.5828744882500201e-03 9.9978697697966856e-01 0 0 0
|
||||
361 1 2.5000000000000000e+00 5.4000000000000000e+01 0.0000000000000000e+00 0.0000000000000000e+00 1.1868011343002482e-02 -4.8145058779812547e-03 9.9991798205648508e-01 0 0 0
|
||||
381 1 2.5000000000000000e+00 5.7000000000000000e+01 0.0000000000000000e+00 0.0000000000000000e+00 3.9693242391277929e-03 -3.9693242391277937e-03 9.9998424434096445e-01 0 0 0
|
||||
2 1 2.5000000000000000e+00 0.0000000000000000e+00 3.0000000000000000e+00 0.0000000000000000e+00 -4.8145058779812512e-03 -1.1868011343002475e-02 9.9991798205648519e-01 0 0 0
|
||||
22 1 2.5000000000000000e+00 3.0000000000000000e+00 3.0000000000000000e+00 0.0000000000000000e+00 -1.4489047587394138e-02 -1.4489047587394138e-02 9.9979004545955574e-01 0 0 0
|
||||
42 1 2.5000000000000000e+00 6.0000000000000000e+00 3.0000000000000000e+00 0.0000000000000000e+00 -2.4184841732588187e-02 -2.0009637034407928e-02 9.9950723251816487e-01 0 0 0
|
||||
62 1 2.5000000000000000e+00 9.0000000000000000e+00 3.0000000000000000e+00 0.0000000000000000e+00 -3.3534698701154796e-02 -2.8894018478272422e-02 9.9901979944303421e-01 0 0 0
|
||||
82 1 2.5000000000000000e+00 1.2000000000000000e+01 3.0000000000000000e+00 0.0000000000000000e+00 -4.1631298256624205e-02 -4.1569375222726884e-02 9.9826791095830603e-01 0 0 0
|
||||
102 1 2.5000000000000000e+00 1.5000000000000000e+01 3.0000000000000000e+00 0.0000000000000000e+00 -4.6947676140268457e-02 -5.8031121465001792e-02 9.9721026100143129e-01 0 0 0
|
||||
122 1 2.5000000000000000e+00 1.8000000000000000e+01 3.0000000000000000e+00 0.0000000000000000e+00 -4.7535409319668050e-02 -7.7312985281705895e-02 9.9587302763336383e-01 0 0 0
|
||||
142 1 2.5000000000000000e+00 2.1000000000000000e+01 3.0000000000000000e+00 0.0000000000000000e+00 -4.1653952417990837e-02 -9.7059251840902777e-02 9.9440658177630958e-01 0 0 0
|
||||
162 1 2.5000000000000000e+00 2.4000000000000000e+01 3.0000000000000000e+00 0.0000000000000000e+00 -2.8752729368399305e-02 -1.1365104497068100e-01 9.9310458690459180e-01 0 0 0
|
||||
182 1 2.5000000000000000e+00 2.7000000000000000e+01 3.0000000000000000e+00 0.0000000000000000e+00 -1.0293413501576094e-02 -1.2321728304286263e-01 9.9232633079951105e-01 0 0 0
|
||||
202 1 2.5000000000000000e+00 3.0000000000000000e+01 3.0000000000000000e+00 0.0000000000000000e+00 1.0293413501576086e-02 -1.2321728304286261e-01 9.9232633079951116e-01 0 0 0
|
||||
222 1 2.5000000000000000e+00 3.3000000000000000e+01 3.0000000000000000e+00 0.0000000000000000e+00 2.8752729368399291e-02 -1.1365104497068100e-01 9.9310458690459180e-01 0 0 0
|
||||
242 1 2.5000000000000000e+00 3.6000000000000000e+01 3.0000000000000000e+00 0.0000000000000000e+00 4.1653952417990824e-02 -9.7059251840902777e-02 9.9440658177630958e-01 0 0 0
|
||||
262 1 2.5000000000000000e+00 3.9000000000000000e+01 3.0000000000000000e+00 0.0000000000000000e+00 4.7535409319668057e-02 -7.7312985281705895e-02 9.9587302763336383e-01 0 0 0
|
||||
282 1 2.5000000000000000e+00 4.2000000000000000e+01 3.0000000000000000e+00 0.0000000000000000e+00 4.6947676140268443e-02 -5.8031121465001792e-02 9.9721026100143140e-01 0 0 0
|
||||
302 1 2.5000000000000000e+00 4.5000000000000000e+01 3.0000000000000000e+00 0.0000000000000000e+00 4.1631298256624191e-02 -4.1569375222726877e-02 9.9826791095830592e-01 0 0 0
|
||||
322 1 2.5000000000000000e+00 4.8000000000000000e+01 3.0000000000000000e+00 0.0000000000000000e+00 3.3534698701154809e-02 -2.8894018478272433e-02 9.9901979944303410e-01 0 0 0
|
||||
342 1 2.5000000000000000e+00 5.1000000000000000e+01 3.0000000000000000e+00 0.0000000000000000e+00 2.4184841732588204e-02 -2.0009637034407945e-02 9.9950723251816487e-01 0 0 0
|
||||
362 1 2.5000000000000000e+00 5.4000000000000000e+01 3.0000000000000000e+00 0.0000000000000000e+00 1.4489047587394149e-02 -1.4489047587394138e-02 9.9979004545955585e-01 0 0 0
|
||||
382 1 2.5000000000000000e+00 5.7000000000000000e+01 3.0000000000000000e+00 0.0000000000000000e+00 4.8145058779812547e-03 -1.1868011343002482e-02 9.9991798205648519e-01 0 0 0
|
||||
3 1 2.5000000000000000e+00 0.0000000000000000e+00 6.0000000000000000e+00 0.0000000000000000e+00 -6.5828744882500158e-03 -1.9561861499557527e-02 9.9978697697966856e-01 0 0 0
|
||||
23 1 2.5000000000000000e+00 3.0000000000000000e+00 6.0000000000000000e+00 0.0000000000000000e+00 -2.0009637034407932e-02 -2.4184841732588200e-02 9.9950723251816498e-01 0 0 0
|
||||
43 1 2.5000000000000000e+00 6.0000000000000000e+00 6.0000000000000000e+00 0.0000000000000000e+00 -3.4047077037887570e-02 -3.4047077037887577e-02 9.9884012388887977e-01 0 0 0
|
||||
63 1 2.5000000000000000e+00 9.0000000000000000e+00 6.0000000000000000e+00 0.0000000000000000e+00 -4.8498220596720307e-02 -5.0241530269051260e-02 9.9755887607457838e-01 0 0 0
|
||||
83 1 2.5000000000000000e+00 1.2000000000000000e+01 6.0000000000000000e+00 0.0000000000000000e+00 -6.2196104012276265e-02 -7.3954811425103587e-02 9.9532021506285684e-01 0 0 0
|
||||
103 1 2.5000000000000000e+00 1.5000000000000000e+01 6.0000000000000000e+00 0.0000000000000000e+00 -7.2649992877525826e-02 -1.0567933713226435e-01 9.9174283775491956e-01 0 0 0
|
||||
123 1 2.5000000000000000e+00 1.8000000000000000e+01 6.0000000000000000e+00 0.0000000000000000e+00 -7.6126593015943808e-02 -1.4398087111736477e-01 9.8664798717073865e-01 0 0 0
|
||||
143 1 2.5000000000000000e+00 2.1000000000000000e+01 6.0000000000000000e+00 0.0000000000000000e+00 -6.8709104650143085e-02 -1.8428174194944069e-01 9.8046891767268973e-01 0 0 0
|
||||
163 1 2.5000000000000000e+00 2.4000000000000000e+01 6.0000000000000000e+00 0.0000000000000000e+00 -4.8457456104349643e-02 -2.1884669159068457e-01 9.7455528346405618e-01 0 0 0
|
||||
183 1 2.5000000000000000e+00 2.7000000000000000e+01 6.0000000000000000e+00 0.0000000000000000e+00 -1.7543173966404597e-02 -2.3902270727461428e-01 9.7085548999544657e-01 0 0 0
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93 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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113 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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133 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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153 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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173 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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193 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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213 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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233 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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253 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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273 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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293 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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313 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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333 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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353 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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373 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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393 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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54 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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74 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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94 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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114 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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134 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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154 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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174 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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194 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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214 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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234 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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254 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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274 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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294 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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314 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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334 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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354 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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374 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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394 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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15 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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55 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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115 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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135 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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155 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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175 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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195 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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215 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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235 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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255 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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275 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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295 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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315 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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335 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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355 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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375 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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395 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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36 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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56 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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76 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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96 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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116 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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136 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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156 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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176 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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196 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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216 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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236 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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256 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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276 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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296 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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316 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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336 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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356 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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376 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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396 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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117 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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137 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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157 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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177 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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197 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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217 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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237 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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257 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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277 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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297 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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317 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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337 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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357 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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377 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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397 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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18 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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38 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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58 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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78 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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98 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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118 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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138 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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158 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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178 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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198 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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218 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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238 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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258 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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278 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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298 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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318 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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338 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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358 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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378 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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398 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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19 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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39 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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59 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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79 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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99 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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119 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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139 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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159 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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179 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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199 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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219 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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239 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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259 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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279 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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299 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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319 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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339 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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359 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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379 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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399 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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20 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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40 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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60 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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80 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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100 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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120 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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140 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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160 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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180 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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200 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
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220 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
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240 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
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260 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
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280 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
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300 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
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320 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
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340 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
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360 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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380 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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400 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
60
examples/SPIN/iron/in.spin.iron_cubic
Normal file
60
examples/SPIN/iron/in.spin.iron_cubic
Normal file
@ -0,0 +1,60 @@
|
||||
# bcc iron in a 3d periodic box
|
||||
|
||||
clear
|
||||
units metal
|
||||
atom_style spin
|
||||
|
||||
dimension 3
|
||||
boundary p p p
|
||||
|
||||
# necessary for the serial algorithm (sametag)
|
||||
atom_modify map array
|
||||
|
||||
lattice bcc 2.8665
|
||||
region box block 0.0 5.0 0.0 5.0 0.0 5.0
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
|
||||
# setting mass, mag. moments, and interactions for bcc iron
|
||||
|
||||
mass 1 55.845
|
||||
set group all spin 2.2 -1.0 0.0 0.0
|
||||
velocity all create 100 4928459 rot yes dist gaussian
|
||||
|
||||
pair_style hybrid/overlay eam/alloy spin/exchange 3.5
|
||||
pair_coeff * * eam/alloy Fe_Mishin2006.eam.alloy Fe
|
||||
pair_coeff * * spin/exchange exchange 3.4 0.02726 0.2171 1.841
|
||||
neighbor 0.1 bin
|
||||
neigh_modify every 10 check yes delay 20
|
||||
|
||||
fix 1 all precession/spin cubic 0.001 0.0005 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0
|
||||
fix_modify 1 energy yes
|
||||
fix 2 all langevin/spin 0.0 0.0 21
|
||||
|
||||
fix 3 all nve/spin lattice yes
|
||||
timestep 0.0001
|
||||
|
||||
# compute and output options
|
||||
|
||||
compute out_mag all spin
|
||||
compute out_pe all pe
|
||||
compute out_ke all ke
|
||||
compute out_temp all temp
|
||||
|
||||
variable magx equal c_out_mag[1]
|
||||
variable magy equal c_out_mag[2]
|
||||
variable magz equal c_out_mag[3]
|
||||
variable magnorm equal c_out_mag[4]
|
||||
variable emag equal c_out_mag[5]
|
||||
variable tmag equal c_out_mag[6]
|
||||
|
||||
thermo_style custom step time v_magx v_magy v_magz v_magnorm v_tmag v_emag pe etotal
|
||||
thermo 50
|
||||
|
||||
compute outsp all property/atom spx spy spz sp fmx fmy fmz
|
||||
dump 100 all custom 1 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
|
||||
|
||||
run 2000
|
||||
# min_style spin
|
||||
# min_modify alpha_damp 1.0 discrete_factor 10
|
||||
# minimize 1.0e-16 1.0e-16 10000 10000
|
||||
60
examples/SPIN/nickel/in.spin.nickel_cubic
Normal file
60
examples/SPIN/nickel/in.spin.nickel_cubic
Normal file
@ -0,0 +1,60 @@
|
||||
# fcc nickel in a 3d periodic box
|
||||
|
||||
clear
|
||||
units metal
|
||||
atom_style spin
|
||||
|
||||
dimension 3
|
||||
boundary p p p
|
||||
|
||||
# necessary for the serial algorithm (sametag)
|
||||
atom_modify map array
|
||||
|
||||
lattice fcc 3.524
|
||||
region box block 0.0 5.0 0.0 5.0 0.0 5.0
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
|
||||
# setting mass, mag. moments, and interactions for cobalt
|
||||
|
||||
mass 1 58.69
|
||||
|
||||
set group all spin/random 31 0.63
|
||||
#set group all spin 0.63 0.0 0.0 1.0
|
||||
velocity all create 100 4928459 rot yes dist gaussian
|
||||
|
||||
pair_style hybrid/overlay eam/alloy spin/exchange 4.0
|
||||
pair_coeff * * eam/alloy Ni99.eam.alloy Ni
|
||||
pair_coeff * * spin/exchange exchange 4.0 0.50 0.2280246862 1.229983475
|
||||
|
||||
neighbor 0.1 bin
|
||||
neigh_modify every 10 check yes delay 20
|
||||
|
||||
fix 1 all precession/spin cubic -0.0001 0.0 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0 &
|
||||
zeeman 0.0 0.0 0.0 1.0
|
||||
fix_modify 1 energy yes
|
||||
fix 2 all langevin/spin 0.0 0.0 21
|
||||
|
||||
fix 3 all nve/spin lattice yes
|
||||
timestep 0.0001
|
||||
|
||||
# compute and output options
|
||||
|
||||
compute out_mag all spin
|
||||
compute out_pe all pe
|
||||
compute out_ke all ke
|
||||
compute out_temp all temp
|
||||
|
||||
variable magz equal c_out_mag[3]
|
||||
variable magnorm equal c_out_mag[4]
|
||||
variable emag equal c_out_mag[5]
|
||||
variable tmag equal c_out_mag[6]
|
||||
|
||||
thermo_style custom step time v_magnorm v_emag temp v_tmag etotal
|
||||
thermo 50
|
||||
|
||||
compute outsp all property/atom spx spy spz sp fmx fmy fmz
|
||||
dump 50 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
|
||||
|
||||
run 2000
|
||||
|
||||
@ -40,6 +40,6 @@ thermo_style custom step time v_magnorm v_emag v_tmag temp etotal
|
||||
thermo_modify format float %20.15g
|
||||
|
||||
compute outsp all property/atom spx spy spz sp fmx fmy fmz
|
||||
dump 10 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
|
||||
dump 1 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
|
||||
|
||||
run 100
|
||||
|
||||
59
examples/SPIN/setforce_spin/in.spinmin.setforce
Normal file
59
examples/SPIN/setforce_spin/in.spinmin.setforce
Normal file
@ -0,0 +1,59 @@
|
||||
|
||||
units metal
|
||||
dimension 3
|
||||
boundary f f f
|
||||
atom_style spin
|
||||
|
||||
# necessary for the serial algorithm (sametag)
|
||||
atom_modify map array
|
||||
|
||||
lattice sc 3.0
|
||||
region box block 0.0 10.0 0.0 10.0 0.0 1.0
|
||||
create_box 2 box
|
||||
region reg1 block 0.0 10.0 0.0 5.0 0.0 1.0
|
||||
region reg2 block 0.0 10.0 6.0 10.0 0.0 1.0
|
||||
create_atoms 1 region reg1
|
||||
create_atoms 2 region reg2
|
||||
|
||||
# setting mass, mag. moments, and interactions for bcc iron
|
||||
|
||||
mass 1 55.845
|
||||
mass 2 55.845
|
||||
set region reg1 spin 2.2 0.0 0.0 1.0
|
||||
set region reg2 spin/random 31 2.2
|
||||
|
||||
group fixed_spin region reg1
|
||||
|
||||
pair_style hybrid/overlay spin/exchange 3.1 spin/dmi 3.1
|
||||
pair_coeff * * spin/exchange exchange 3.1 -0.01593 0.06626915552 1.211
|
||||
pair_coeff * * spin/dmi dmi 3.1 0.12e-03 0.0 0.0 1.0
|
||||
|
||||
neighbor 0.1 bin
|
||||
neigh_modify every 10 check yes delay 20
|
||||
|
||||
fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 anisotropy 5e-05 0.0 0.0 1.0
|
||||
fix_modify 1 energy yes
|
||||
fix 2 fixed_spin setforce/spin 0.0 0.0 0.0
|
||||
fix 3 all langevin/spin 0.0 0.1 21
|
||||
fix 4 all nve/spin lattice no
|
||||
|
||||
timestep 0.0001
|
||||
|
||||
compute out_mag all spin
|
||||
variable magx equal c_out_mag[1]
|
||||
variable magy equal c_out_mag[2]
|
||||
variable magz equal c_out_mag[3]
|
||||
variable magnorm equal c_out_mag[4]
|
||||
variable emag equal c_out_mag[5]
|
||||
variable tmag equal c_out_mag[6]
|
||||
|
||||
thermo 1000
|
||||
thermo_style custom step time v_magx v_magz v_magnorm v_tmag etotal
|
||||
thermo_modify format float %20.15g
|
||||
|
||||
compute outsp all property/atom spx spy spz sp fmx fmy fmz
|
||||
dump 1 all custom 1000 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[5] c_outsp[6] c_outsp[7]
|
||||
|
||||
min_style spin
|
||||
min_modify alpha_damp 1.0 discrete_factor 20.0
|
||||
minimize 1.0e-16 1.0e-16 50000 1000
|
||||
6
examples/USER/e3b/README
Normal file
6
examples/USER/e3b/README
Normal file
@ -0,0 +1,6 @@
|
||||
The input script in.lammps simulates bulk water using the 2015 E3B potential.
|
||||
|
||||
This script also demonstrates the use of compute pair to calculate the
|
||||
potential energy contribution of the e3b pair style. These potential energy
|
||||
contributions can be found in the output file e3b.txt. See the LAMMPS
|
||||
documentation for more details.
|
||||
1973
examples/USER/e3b/e3b_box.data
Normal file
1973
examples/USER/e3b/e3b_box.data
Normal file
File diff suppressed because it is too large
Load Diff
95
examples/USER/e3b/in.e3b-tip4p2005
Normal file
95
examples/USER/e3b/in.e3b-tip4p2005
Normal file
@ -0,0 +1,95 @@
|
||||
#LAMMPS input file
|
||||
#to simulate bulk E3B3 water model
|
||||
|
||||
#####################################################################
|
||||
|
||||
variable samp_rate equal 10
|
||||
variable thermo_rate equal 10
|
||||
variable Wlat equal 3.10744 #for water density 0.997g/mL
|
||||
variable L equal 3 #(L*2)^3 = Nmolec, L=3 -> N=216
|
||||
|
||||
variable equil equal 100
|
||||
variable run equal 100
|
||||
|
||||
variable ts equal 2.0
|
||||
variable Tdamp equal 100*${ts}
|
||||
variable Pdamp equal 1000*${ts}
|
||||
variable myT equal 298.0
|
||||
variable myP equal 1.0
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
dimension 3
|
||||
|
||||
boundary p p p
|
||||
|
||||
#############################################################################
|
||||
#setup box
|
||||
read_data e3b_box.data
|
||||
|
||||
#############################################################################
|
||||
#set up potential
|
||||
|
||||
pair_style hybrid/overlay e3b 1 lj/cut/tip4p/long 1 2 1 1 0.1546 8.5
|
||||
pair_modify table 0 table/disp 0 shift yes
|
||||
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
|
||||
kspace_style pppm/tip4p 1.0e-6
|
||||
|
||||
pair_coeff * * lj/cut/tip4p/long 0.0 0.0
|
||||
pair_coeff 1 1 lj/cut/tip4p/long 0.1852 3.1589
|
||||
pair_coeff * * e3b preset 2015
|
||||
|
||||
#potential coeffs aren't too important since will be rigid anyways
|
||||
bond_coeff 1 554.13 0.9572
|
||||
angle_coeff 1 45.769 104.52
|
||||
|
||||
#############################################################################
|
||||
#setup for run
|
||||
thermo ${thermo_rate}
|
||||
thermo_style custom step vol temp epair pe etotal press density
|
||||
|
||||
timestep ${ts}
|
||||
run_style verlet
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify every 1 delay 3 check yes
|
||||
|
||||
#############################################################################
|
||||
|
||||
#dump positions only in first batch run
|
||||
#dump 7 all custom ${samp_rate} dump.lammpstrj id x y z
|
||||
#dump_modify 7 sort id
|
||||
|
||||
#############################################################################
|
||||
#initialize velocity and rigid constraint
|
||||
|
||||
fix rigid all shake 1.0e-8 100 0 b 1 a 1 t 1 2
|
||||
velocity all create ${myT} 15856 dist gaussian rot yes mom yes
|
||||
|
||||
#scale velocity
|
||||
run 0
|
||||
velocity all scale ${myT}
|
||||
|
||||
compute e3b all pair e3b
|
||||
fix e3b all ave/time 1 1 ${thermo_rate} c_e3b c_e3b[*] &
|
||||
file e3b.txt title2 "step pe_e3b pe_e2 pe_ea pe_eb pe_ec"
|
||||
|
||||
#############################################################################
|
||||
#equilibrate bulk water at NVT
|
||||
|
||||
fix 1 all nvt temp ${myT} ${myT} ${Tdamp}
|
||||
run ${equil}
|
||||
|
||||
#############################################################################
|
||||
#run at NVT
|
||||
|
||||
#dump 1 all custom ${samp_rate} dump.lammpstrj id x y z type
|
||||
#dump_modify 1 sort id
|
||||
|
||||
run ${run}
|
||||
|
||||
# write_restart lammps.restart
|
||||
332
examples/USER/e3b/log.29Mar2019.e3b-tip4p2005.g++.1
Normal file
332
examples/USER/e3b/log.29Mar2019.e3b-tip4p2005.g++.1
Normal file
@ -0,0 +1,332 @@
|
||||
LAMMPS (29 Mar 2019)
|
||||
#LAMMPS input file
|
||||
#to simulate bulk E3B3 water model
|
||||
|
||||
#####################################################################
|
||||
|
||||
variable samp_rate equal 10
|
||||
variable thermo_rate equal 10
|
||||
variable Wlat equal 3.10744 #for water density 0.997g/mL
|
||||
variable L equal 3 #(L*2)^3 = Nmolec, L=3 -> N=216
|
||||
|
||||
variable equil equal 100
|
||||
variable run equal 100
|
||||
|
||||
variable ts equal 2.0
|
||||
variable Tdamp equal 100*${ts}
|
||||
variable Tdamp equal 100*2
|
||||
variable Pdamp equal 1000*${ts}
|
||||
variable Pdamp equal 1000*2
|
||||
variable myT equal 298.0
|
||||
variable myP equal 1.0
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
dimension 3
|
||||
|
||||
boundary p p p
|
||||
|
||||
#############################################################################
|
||||
#setup box
|
||||
read_data e3b_box.data
|
||||
orthogonal box = (-9.32232 -9.32232 -9.32232) to (9.32232 9.32232 9.32232)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
648 atoms
|
||||
reading velocities ...
|
||||
648 velocities
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
scanning angles ...
|
||||
1 = max angles/atom
|
||||
reading bonds ...
|
||||
432 bonds
|
||||
reading angles ...
|
||||
216 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 = 0.000257254 secs
|
||||
read_data CPU = 0.00286555 secs
|
||||
|
||||
#############################################################################
|
||||
#set up potential
|
||||
|
||||
pair_style hybrid/overlay e3b 1 lj/cut/tip4p/long 1 2 1 1 0.1546 8.5
|
||||
pair_modify table 0 table/disp 0 shift yes
|
||||
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
|
||||
kspace_style pppm/tip4p 1.0e-6
|
||||
|
||||
pair_coeff * * lj/cut/tip4p/long 0.0 0.0
|
||||
pair_coeff 1 1 lj/cut/tip4p/long 0.1852 3.1589
|
||||
pair_coeff * * e3b preset 2015
|
||||
|
||||
#potential coeffs aren't too important since will be rigid anyways
|
||||
bond_coeff 1 554.13 0.9572
|
||||
angle_coeff 1 45.769 104.52
|
||||
|
||||
#############################################################################
|
||||
#setup for run
|
||||
thermo ${thermo_rate}
|
||||
thermo 10
|
||||
thermo_style custom step vol temp epair pe etotal press density
|
||||
|
||||
timestep ${ts}
|
||||
timestep 2
|
||||
run_style verlet
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify every 1 delay 3 check yes
|
||||
|
||||
#############################################################################
|
||||
|
||||
#dump positions only in first batch run
|
||||
#dump 7 all custom ${samp_rate} dump.lammpstrj id x y z
|
||||
#dump_modify 7 sort id
|
||||
|
||||
#############################################################################
|
||||
#initialize velocity and rigid constraint
|
||||
|
||||
fix rigid all shake 1.0e-8 100 0 b 1 a 1 t 1 2
|
||||
0 = # of size 2 clusters
|
||||
0 = # of size 3 clusters
|
||||
0 = # of size 4 clusters
|
||||
216 = # of frozen angles
|
||||
find clusters CPU = 0.000185728 secs
|
||||
velocity all create ${myT} 15856 dist gaussian rot yes mom yes
|
||||
velocity all create 298 15856 dist gaussian rot yes mom yes
|
||||
|
||||
#scale velocity
|
||||
run 0
|
||||
PPPM initialization ...
|
||||
extracting TIP4P info from pair style
|
||||
using polynomial approximation for long-range coulomb (../kspace.cpp:319)
|
||||
G vector (1/distance) = 0.409658
|
||||
grid = 36 36 36
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.000341883
|
||||
estimated relative force accuracy = 1.02957e-06
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 91125 46656
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 3 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 10.8092
|
||||
ghost atom cutoff = 10.8092
|
||||
binsize = 5.4046, bins = 4 4 4
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair e3b, perpetual, skip from (2)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair lj/cut/tip4p/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) = 16.4 | 16.4 | 16.4 Mbytes
|
||||
Step Volume Temp E_pair PotEng TotEng Press Density
|
||||
0 6481.2982 298 -512.62432 -512.62432 -129.77504 14088.322 0.99697602
|
||||
Loop time of 1.19209e-06 on 1 procs for 0 steps with 648 atoms
|
||||
|
||||
251.7% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Bond | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Kspace | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 1.192e-06 | | |100.00
|
||||
|
||||
Nlocal: 648 ave 648 max 648 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 5943 ave 5943 max 5943 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 18984 ave 18984 max 18984 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 18984
|
||||
Ave neighs/atom = 29.2963
|
||||
Ave special neighs/atom = 2
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
velocity all scale ${myT}
|
||||
velocity all scale 298
|
||||
|
||||
compute e3b all pe/e3b
|
||||
fix e3b all ave/time 1 1 ${thermo_rate} c_e3b c_e3b[*] file e3b.txt title2 "step pe_e3b pe_ea pe_eb pe_ec pe_e2"
|
||||
fix e3b all ave/time 1 1 10 c_e3b c_e3b[*] file e3b.txt title2 "step pe_e3b pe_ea pe_eb pe_ec pe_e2"
|
||||
|
||||
#############################################################################
|
||||
#equilibrate bulk water at NVT
|
||||
|
||||
fix 1 all nvt temp ${myT} ${myT} ${Tdamp}
|
||||
fix 1 all nvt temp 298 ${myT} ${Tdamp}
|
||||
fix 1 all nvt temp 298 298 ${Tdamp}
|
||||
fix 1 all nvt temp 298 298 200
|
||||
run ${equil}
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
extracting TIP4P info from pair style
|
||||
using polynomial approximation for long-range coulomb (../kspace.cpp:319)
|
||||
G vector (1/distance) = 0.409658
|
||||
grid = 36 36 36
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.000341883
|
||||
estimated relative force accuracy = 1.02957e-06
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 91125 46656
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 3 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 10.8092
|
||||
ghost atom cutoff = 10.8092
|
||||
binsize = 5.4046, bins = 4 4 4
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair e3b, perpetual, skip from (2)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair lj/cut/tip4p/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) = 16.88 | 16.88 | 16.88 Mbytes
|
||||
Step Volume Temp E_pair PotEng TotEng Press Density
|
||||
0 6481.2982 298 -512.33264 -512.33264 -129.48336 14091.383 0.99697602
|
||||
10 6481.2982 905.58028 -1442.0378 -1442.0378 -278.61245 -798.38952 0.99697602
|
||||
20 6481.2982 816.39844 -1363.5999 -1363.5999 -314.74903 3023.9064 0.99697602
|
||||
30 6481.2982 783.3897 -1370.6594 -1370.6594 -364.21587 7095.4765 0.99697602
|
||||
40 6481.2982 793.12519 -1425.8404 -1425.8404 -406.88933 7030.242 0.99697602
|
||||
50 6481.2982 810.90264 -1495.4822 -1495.4822 -453.69195 6944.2325 0.99697602
|
||||
60 6481.2982 766.64937 -1491.2317 -1491.2317 -506.29493 9062.0151 0.99697602
|
||||
70 6481.2982 761.77292 -1538.7368 -1538.7368 -560.06492 7693.2197 0.99697602
|
||||
80 6481.2982 730.44938 -1554.1818 -1554.1818 -615.75215 7345.9601 0.99697602
|
||||
90 6481.2982 695.46244 -1563.9869 -1563.9869 -670.50605 7809.0685 0.99697602
|
||||
100 6481.2982 691.5674 -1613.2754 -1613.2754 -724.79866 7143.062 0.99697602
|
||||
Loop time of 1.94577 on 1 procs for 100 steps with 648 atoms
|
||||
|
||||
Performance: 8.881 ns/day, 2.702 hours/ns, 51.393 timesteps/s
|
||||
99.7% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.91572 | 0.91572 | 0.91572 | 0.0 | 47.06
|
||||
Bond | 6.7234e-05 | 6.7234e-05 | 6.7234e-05 | 0.0 | 0.00
|
||||
Kspace | 0.92654 | 0.92654 | 0.92654 | 0.0 | 47.62
|
||||
Neigh | 0.087331 | 0.087331 | 0.087331 | 0.0 | 4.49
|
||||
Comm | 0.0054724 | 0.0054724 | 0.0054724 | 0.0 | 0.28
|
||||
Output | 0.0003047 | 0.0003047 | 0.0003047 | 0.0 | 0.02
|
||||
Modify | 0.0093319 | 0.0093319 | 0.0093319 | 0.0 | 0.48
|
||||
Other | | 0.001007 | | | 0.05
|
||||
|
||||
Nlocal: 648 ave 648 max 648 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 5911 ave 5911 max 5911 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 19136 ave 19136 max 19136 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 19136
|
||||
Ave neighs/atom = 29.5309
|
||||
Ave special neighs/atom = 2
|
||||
Neighbor list builds = 15
|
||||
Dangerous builds = 0
|
||||
|
||||
#############################################################################
|
||||
#run at NVT
|
||||
|
||||
#dump 1 all custom ${samp_rate} dump.lammpstrj id x y z type
|
||||
#dump_modify 1 sort id
|
||||
|
||||
run ${run}
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
extracting TIP4P info from pair style
|
||||
using polynomial approximation for long-range coulomb (../kspace.cpp:319)
|
||||
G vector (1/distance) = 0.409658
|
||||
grid = 36 36 36
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.000341883
|
||||
estimated relative force accuracy = 1.02957e-06
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 91125 46656
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 3 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 10.8092
|
||||
ghost atom cutoff = 10.8092
|
||||
binsize = 5.4046, bins = 4 4 4
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair e3b, perpetual, skip from (2)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair lj/cut/tip4p/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) = 16.88 | 16.88 | 16.88 Mbytes
|
||||
Step Volume Temp E_pair PotEng TotEng Press Density
|
||||
100 6481.2982 691.5674 -1613.2754 -1613.2754 -724.79866 7131.3961 0.99697602
|
||||
110 6481.2982 668.27004 -1635.5867 -1635.5867 -777.04068 6965.8705 0.99697602
|
||||
120 6481.2982 646.18686 -1659.5025 -1659.5025 -829.32738 6196.7432 0.99697602
|
||||
130 6481.2982 650.7802 -1716.9557 -1716.9557 -880.87943 5626.5466 0.99697602
|
||||
140 6481.2982 586.262 -1681.8052 -1681.8052 -928.61728 6103.747 0.99697602
|
||||
150 6481.2982 615.88299 -1767.8614 -1767.8614 -976.61859 3897.648 0.99697602
|
||||
160 6481.2982 585.23516 -1773.2038 -1773.2038 -1021.3352 4821.7742 0.99697602
|
||||
170 6481.2982 558.77885 -1782.2817 -1782.2817 -1064.4022 5092.7248 0.99697602
|
||||
180 6481.2982 564.01576 -1830.0301 -1830.0301 -1105.4226 4316.1636 0.99697602
|
||||
190 6481.2982 526.53776 -1821.3122 -1821.3122 -1144.8538 4529.5062 0.99697602
|
||||
200 6481.2982 537.81273 -1873.6662 -1873.6662 -1182.7226 4244.313 0.99697602
|
||||
Loop time of 1.9157 on 1 procs for 100 steps with 648 atoms
|
||||
|
||||
Performance: 9.020 ns/day, 2.661 hours/ns, 52.200 timesteps/s
|
||||
99.6% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.90464 | 0.90464 | 0.90464 | 0.0 | 47.22
|
||||
Bond | 6.9141e-05 | 6.9141e-05 | 6.9141e-05 | 0.0 | 0.00
|
||||
Kspace | 0.92769 | 0.92769 | 0.92769 | 0.0 | 48.43
|
||||
Neigh | 0.067551 | 0.067551 | 0.067551 | 0.0 | 3.53
|
||||
Comm | 0.0051386 | 0.0051386 | 0.0051386 | 0.0 | 0.27
|
||||
Output | 0.00029993 | 0.00029993 | 0.00029993 | 0.0 | 0.02
|
||||
Modify | 0.0092504 | 0.0092504 | 0.0092504 | 0.0 | 0.48
|
||||
Other | | 0.001062 | | | 0.06
|
||||
|
||||
Nlocal: 648 ave 648 max 648 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 5901 ave 5901 max 5901 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 18971 ave 18971 max 18971 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 18971
|
||||
Ave neighs/atom = 29.2762
|
||||
Ave special neighs/atom = 2
|
||||
Neighbor list builds = 12
|
||||
Dangerous builds = 0
|
||||
|
||||
# write_restart lammps.restart
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:03
|
||||
332
examples/USER/e3b/log.29Mar2019.e3b-tip4p2005.g++.4
Normal file
332
examples/USER/e3b/log.29Mar2019.e3b-tip4p2005.g++.4
Normal file
@ -0,0 +1,332 @@
|
||||
LAMMPS (29 Mar 2019)
|
||||
#LAMMPS input file
|
||||
#to simulate bulk E3B3 water model
|
||||
|
||||
#####################################################################
|
||||
|
||||
variable samp_rate equal 10
|
||||
variable thermo_rate equal 10
|
||||
variable Wlat equal 3.10744 #for water density 0.997g/mL
|
||||
variable L equal 3 #(L*2)^3 = Nmolec, L=3 -> N=216
|
||||
|
||||
variable equil equal 100
|
||||
variable run equal 100
|
||||
|
||||
variable ts equal 2.0
|
||||
variable Tdamp equal 100*${ts}
|
||||
variable Tdamp equal 100*2
|
||||
variable Pdamp equal 1000*${ts}
|
||||
variable Pdamp equal 1000*2
|
||||
variable myT equal 298.0
|
||||
variable myP equal 1.0
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
dimension 3
|
||||
|
||||
boundary p p p
|
||||
|
||||
#############################################################################
|
||||
#setup box
|
||||
read_data e3b_box.data
|
||||
orthogonal box = (-9.32232 -9.32232 -9.32232) to (9.32232 9.32232 9.32232)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
648 atoms
|
||||
reading velocities ...
|
||||
648 velocities
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
scanning angles ...
|
||||
1 = max angles/atom
|
||||
reading bonds ...
|
||||
432 bonds
|
||||
reading angles ...
|
||||
216 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 = 0.00029397 secs
|
||||
read_data CPU = 0.00397325 secs
|
||||
|
||||
#############################################################################
|
||||
#set up potential
|
||||
|
||||
pair_style hybrid/overlay e3b 1 lj/cut/tip4p/long 1 2 1 1 0.1546 8.5
|
||||
pair_modify table 0 table/disp 0 shift yes
|
||||
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
|
||||
kspace_style pppm/tip4p 1.0e-6
|
||||
|
||||
pair_coeff * * lj/cut/tip4p/long 0.0 0.0
|
||||
pair_coeff 1 1 lj/cut/tip4p/long 0.1852 3.1589
|
||||
pair_coeff * * e3b preset 2015
|
||||
|
||||
#potential coeffs aren't too important since will be rigid anyways
|
||||
bond_coeff 1 554.13 0.9572
|
||||
angle_coeff 1 45.769 104.52
|
||||
|
||||
#############################################################################
|
||||
#setup for run
|
||||
thermo ${thermo_rate}
|
||||
thermo 10
|
||||
thermo_style custom step vol temp epair pe etotal press density
|
||||
|
||||
timestep ${ts}
|
||||
timestep 2
|
||||
run_style verlet
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify every 1 delay 3 check yes
|
||||
|
||||
#############################################################################
|
||||
|
||||
#dump positions only in first batch run
|
||||
#dump 7 all custom ${samp_rate} dump.lammpstrj id x y z
|
||||
#dump_modify 7 sort id
|
||||
|
||||
#############################################################################
|
||||
#initialize velocity and rigid constraint
|
||||
|
||||
fix rigid all shake 1.0e-8 100 0 b 1 a 1 t 1 2
|
||||
0 = # of size 2 clusters
|
||||
0 = # of size 3 clusters
|
||||
0 = # of size 4 clusters
|
||||
216 = # of frozen angles
|
||||
find clusters CPU = 0.000289917 secs
|
||||
velocity all create ${myT} 15856 dist gaussian rot yes mom yes
|
||||
velocity all create 298 15856 dist gaussian rot yes mom yes
|
||||
|
||||
#scale velocity
|
||||
run 0
|
||||
PPPM initialization ...
|
||||
extracting TIP4P info from pair style
|
||||
using polynomial approximation for long-range coulomb (../kspace.cpp:319)
|
||||
G vector (1/distance) = 0.409658
|
||||
grid = 36 36 36
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.000341883
|
||||
estimated relative force accuracy = 1.02957e-06
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 32805 11664
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 3 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 10.8092
|
||||
ghost atom cutoff = 10.8092
|
||||
binsize = 5.4046, bins = 4 4 4
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair e3b, perpetual, skip from (2)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair lj/cut/tip4p/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) = 10.69 | 10.69 | 10.69 Mbytes
|
||||
Step Volume Temp E_pair PotEng TotEng Press Density
|
||||
0 6481.2982 298 -512.62432 -512.62432 -129.77504 14088.322 0.99697602
|
||||
Loop time of 3.30806e-05 on 4 procs for 0 steps with 648 atoms
|
||||
|
||||
77.1% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Bond | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Kspace | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 3.308e-05 | | |100.00
|
||||
|
||||
Nlocal: 162 ave 168 max 157 min
|
||||
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||
Nghost: 3738 ave 3743 max 3732 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 0 2
|
||||
Neighs: 4746 ave 5380 max 4318 min
|
||||
Histogram: 1 1 0 0 1 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 18984
|
||||
Ave neighs/atom = 29.2963
|
||||
Ave special neighs/atom = 2
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
velocity all scale ${myT}
|
||||
velocity all scale 298
|
||||
|
||||
compute e3b all pe/e3b
|
||||
fix e3b all ave/time 1 1 ${thermo_rate} c_e3b c_e3b[*] file e3b.txt title2 "step pe_e3b pe_ea pe_eb pe_ec pe_e2"
|
||||
fix e3b all ave/time 1 1 10 c_e3b c_e3b[*] file e3b.txt title2 "step pe_e3b pe_ea pe_eb pe_ec pe_e2"
|
||||
|
||||
#############################################################################
|
||||
#equilibrate bulk water at NVT
|
||||
|
||||
fix 1 all nvt temp ${myT} ${myT} ${Tdamp}
|
||||
fix 1 all nvt temp 298 ${myT} ${Tdamp}
|
||||
fix 1 all nvt temp 298 298 ${Tdamp}
|
||||
fix 1 all nvt temp 298 298 200
|
||||
run ${equil}
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
extracting TIP4P info from pair style
|
||||
using polynomial approximation for long-range coulomb (../kspace.cpp:319)
|
||||
G vector (1/distance) = 0.409658
|
||||
grid = 36 36 36
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.000341883
|
||||
estimated relative force accuracy = 1.02957e-06
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 32805 11664
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 3 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 10.8092
|
||||
ghost atom cutoff = 10.8092
|
||||
binsize = 5.4046, bins = 4 4 4
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair e3b, perpetual, skip from (2)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair lj/cut/tip4p/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) = 11.18 | 11.18 | 11.18 Mbytes
|
||||
Step Volume Temp E_pair PotEng TotEng Press Density
|
||||
0 6481.2982 298 -512.33264 -512.33264 -129.48336 14091.383 0.99697602
|
||||
10 6481.2982 905.58028 -1442.0378 -1442.0378 -278.61245 -798.38952 0.99697602
|
||||
20 6481.2982 816.39844 -1363.5999 -1363.5999 -314.74903 3023.9064 0.99697602
|
||||
30 6481.2982 783.3897 -1370.6594 -1370.6594 -364.21587 7095.4765 0.99697602
|
||||
40 6481.2982 793.12519 -1425.8404 -1425.8404 -406.88933 7030.242 0.99697602
|
||||
50 6481.2982 810.90264 -1495.4822 -1495.4822 -453.69195 6944.2325 0.99697602
|
||||
60 6481.2982 766.64937 -1491.2317 -1491.2317 -506.29493 9062.0151 0.99697602
|
||||
70 6481.2982 761.77292 -1538.7368 -1538.7368 -560.06492 7693.2197 0.99697602
|
||||
80 6481.2982 730.44938 -1554.1818 -1554.1818 -615.75215 7345.9601 0.99697602
|
||||
90 6481.2982 695.46244 -1563.9869 -1563.9869 -670.50605 7809.0685 0.99697602
|
||||
100 6481.2982 691.5674 -1613.2754 -1613.2754 -724.79866 7143.062 0.99697602
|
||||
Loop time of 1.20724 on 4 procs for 100 steps with 648 atoms
|
||||
|
||||
Performance: 14.314 ns/day, 1.677 hours/ns, 82.834 timesteps/s
|
||||
97.6% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.37421 | 0.39416 | 0.42739 | 3.2 | 32.65
|
||||
Bond | 5.8651e-05 | 7.1406e-05 | 8.2016e-05 | 0.0 | 0.01
|
||||
Kspace | 0.67929 | 0.71762 | 0.74038 | 2.8 | 59.44
|
||||
Neigh | 0.042206 | 0.042236 | 0.042263 | 0.0 | 3.50
|
||||
Comm | 0.0248 | 0.031467 | 0.035969 | 2.7 | 2.61
|
||||
Output | 0.00064564 | 0.0008018 | 0.0012648 | 0.0 | 0.07
|
||||
Modify | 0.018263 | 0.01869 | 0.019076 | 0.2 | 1.55
|
||||
Other | | 0.002194 | | | 0.18
|
||||
|
||||
Nlocal: 162 ave 170 max 151 min
|
||||
Histogram: 1 0 0 0 0 1 0 1 0 1
|
||||
Nghost: 3726.75 ave 3737 max 3720 min
|
||||
Histogram: 1 0 1 1 0 0 0 0 0 1
|
||||
Neighs: 4784 ave 5474 max 4389 min
|
||||
Histogram: 1 1 1 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 19136
|
||||
Ave neighs/atom = 29.5309
|
||||
Ave special neighs/atom = 2
|
||||
Neighbor list builds = 15
|
||||
Dangerous builds = 0
|
||||
|
||||
#############################################################################
|
||||
#run at NVT
|
||||
|
||||
#dump 1 all custom ${samp_rate} dump.lammpstrj id x y z type
|
||||
#dump_modify 1 sort id
|
||||
|
||||
run ${run}
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
extracting TIP4P info from pair style
|
||||
using polynomial approximation for long-range coulomb (../kspace.cpp:319)
|
||||
G vector (1/distance) = 0.409658
|
||||
grid = 36 36 36
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.000341883
|
||||
estimated relative force accuracy = 1.02957e-06
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 32805 11664
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 3 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 10.8092
|
||||
ghost atom cutoff = 10.8092
|
||||
binsize = 5.4046, bins = 4 4 4
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair e3b, perpetual, skip from (2)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair lj/cut/tip4p/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) = 11.18 | 11.18 | 11.18 Mbytes
|
||||
Step Volume Temp E_pair PotEng TotEng Press Density
|
||||
100 6481.2982 691.5674 -1613.2754 -1613.2754 -724.79866 7131.3961 0.99697602
|
||||
110 6481.2982 668.27004 -1635.5867 -1635.5867 -777.04068 6965.8705 0.99697602
|
||||
120 6481.2982 646.18686 -1659.5025 -1659.5025 -829.32738 6196.7432 0.99697602
|
||||
130 6481.2982 650.7802 -1716.9557 -1716.9557 -880.87943 5626.5466 0.99697602
|
||||
140 6481.2982 586.262 -1681.8052 -1681.8052 -928.61728 6103.747 0.99697602
|
||||
150 6481.2982 615.88299 -1767.8614 -1767.8614 -976.61859 3897.648 0.99697602
|
||||
160 6481.2982 585.23516 -1773.2038 -1773.2038 -1021.3352 4821.7742 0.99697602
|
||||
170 6481.2982 558.77885 -1782.2817 -1782.2817 -1064.4022 5092.7248 0.99697602
|
||||
180 6481.2982 564.01576 -1830.0301 -1830.0301 -1105.4226 4316.1636 0.99697602
|
||||
190 6481.2982 526.53776 -1821.3122 -1821.3122 -1144.8538 4529.5062 0.99697602
|
||||
200 6481.2982 537.81273 -1873.6662 -1873.6662 -1182.7226 4244.313 0.99697602
|
||||
Loop time of 1.21286 on 4 procs for 100 steps with 648 atoms
|
||||
|
||||
Performance: 14.247 ns/day, 1.685 hours/ns, 82.450 timesteps/s
|
||||
97.6% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.37664 | 0.39663 | 0.4367 | 3.8 | 32.70
|
||||
Bond | 6.175e-05 | 6.7353e-05 | 7.4148e-05 | 0.0 | 0.01
|
||||
Kspace | 0.6969 | 0.73237 | 0.75103 | 2.5 | 60.38
|
||||
Neigh | 0.033138 | 0.03317 | 0.033202 | 0.0 | 2.73
|
||||
Comm | 0.022651 | 0.02763 | 0.034947 | 3.0 | 2.28
|
||||
Output | 0.00065303 | 0.00096697 | 0.0018971 | 0.0 | 0.08
|
||||
Modify | 0.017379 | 0.018252 | 0.018955 | 0.4 | 1.50
|
||||
Other | | 0.003775 | | | 0.31
|
||||
|
||||
Nlocal: 162 ave 175 max 156 min
|
||||
Histogram: 1 2 0 0 0 0 0 0 0 1
|
||||
Nghost: 3689.5 ave 3721 max 3651 min
|
||||
Histogram: 1 0 0 0 0 1 1 0 0 1
|
||||
Neighs: 4742.75 ave 5159 max 4485 min
|
||||
Histogram: 2 0 0 0 1 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 18971
|
||||
Ave neighs/atom = 29.2762
|
||||
Ave special neighs/atom = 2
|
||||
Neighbor list builds = 12
|
||||
Dangerous builds = 0
|
||||
|
||||
# write_restart lammps.restart
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:02
|
||||
1
examples/USER/misc/drip/C.drip
Symbolic link
1
examples/USER/misc/drip/C.drip
Symbolic link
@ -0,0 +1 @@
|
||||
../../../../potentials/C.drip
|
||||
1
examples/USER/misc/drip/CH.rebo
Symbolic link
1
examples/USER/misc/drip/CH.rebo
Symbolic link
@ -0,0 +1 @@
|
||||
../../../../potentials/CH.rebo
|
||||
6
examples/USER/misc/drip/README.txt
Normal file
6
examples/USER/misc/drip/README.txt
Normal file
@ -0,0 +1,6 @@
|
||||
in.C_drip:
|
||||
Use DRIP and REBO to relax a bilayer graphene.
|
||||
|
||||
in.CH_drip:
|
||||
Use DRIP and REBO to relax a bilayer graphene with additional hydrogen atoms
|
||||
on top of it.
|
||||
416
examples/USER/misc/drip/data.C
Normal file
416
examples/USER/misc/drip/data.C
Normal file
@ -0,0 +1,416 @@
|
||||
LAMMPS data file
|
||||
|
||||
400 atoms
|
||||
1 atom types
|
||||
|
||||
0.0 2.465000000000000e+01 xlo xhi
|
||||
0.0 2.134752620328641e+01 ylo yhi
|
||||
0.0 3.000000000000000e+01 zlo zhi
|
||||
1.232500000000000e+01 0.000000000000000e+00 0.000000000000000e+00 xy xz yz
|
||||
|
||||
Masses
|
||||
|
||||
1 12.011
|
||||
|
||||
Atoms # molecular
|
||||
|
||||
1 1 1 0.000000000000000e+00 0.000000000000000e+00 1.498097531971289e+01
|
||||
2 1 1 9.859999999999999e+00 1.707802096262913e+01 1.489139792549795e+01
|
||||
3 1 1 2.588250000000000e+01 6.404257860985923e+00 1.495586615731768e+01
|
||||
4 1 1 2.711500000000000e+01 7.115842067762138e+00 1.501795235919980e+01
|
||||
5 1 1 4.930000000000000e+00 8.539010481314564e+00 1.492827527515956e+01
|
||||
6 1 1 6.162499999999999e+00 9.250594688090777e+00 1.500678649580791e+01
|
||||
7 1 1 3.204499999999999e+01 1.565485254907670e+01 1.511662064028576e+01
|
||||
8 1 1 3.081250000000000e+01 1.494326834230049e+01 1.505500683988625e+01
|
||||
9 1 1 7.395000000000000e+00 8.539010481314564e+00 1.504923694256975e+01
|
||||
10 1 1 8.627500000000000e+00 9.250594688090777e+00 1.503332570633445e+01
|
||||
11 1 1 9.859999999999999e+00 8.539010481314564e+00 1.508137430939768e+01
|
||||
12 1 1 1.109250000000000e+01 9.250594688090777e+00 1.510475862694483e+01
|
||||
13 1 1 1.109250000000000e+01 1.778960516940534e+01 1.494613902888088e+01
|
||||
14 1 1 2.958000000000000e+01 1.565485254907670e+01 1.516279958068751e+01
|
||||
15 1 1 1.232500000000000e+01 8.539010481314564e+00 1.511276583208523e+01
|
||||
16 1 1 1.355750000000000e+01 9.250594688090777e+00 1.495632206546155e+01
|
||||
17 1 1 1.479000000000000e+01 8.539010481314564e+00 1.498291715828213e+01
|
||||
18 1 1 1.602250000000000e+01 9.250594688090777e+00 1.509801558902469e+01
|
||||
19 1 1 2.711499999999999e+01 1.565485254907670e+01 1.500089766276763e+01
|
||||
20 1 1 2.588250000000000e+01 1.494326834230049e+01 1.505114888970355e+01
|
||||
21 1 1 1.725500000000000e+01 8.539010481314564e+00 1.504495103103041e+01
|
||||
22 1 1 1.848750000000000e+01 9.250594688090777e+00 1.513527732850389e+01
|
||||
23 1 1 1.972000000000000e+01 8.539010481314564e+00 1.502400693288890e+01
|
||||
24 1 1 2.095250000000000e+01 9.250594688090777e+00 1.490419939433632e+01
|
||||
25 1 1 2.465000000000000e+01 1.565485254907670e+01 1.492998117758711e+01
|
||||
26 1 1 2.834750000000000e+01 1.494326834230049e+01 1.496091474579883e+01
|
||||
27 1 1 2.465000000000000e+01 7.115842067762138e+00 1.497394355694102e+01
|
||||
28 1 1 2.341750000000000e+01 6.404257860985923e+00 1.500235588455933e+01
|
||||
29 1 1 2.218500000000000e+01 7.115842067762138e+00 1.503766448268803e+01
|
||||
30 1 1 2.465000000000000e+01 4.269505240657282e+00 1.488340764495658e+01
|
||||
31 1 1 2.588250000000000e+01 4.981089447433495e+00 1.490587231994899e+01
|
||||
32 1 1 3.697500000000000e+00 6.404257860985923e+00 1.500462204163887e+01
|
||||
33 1 1 4.930000000000000e+00 7.115842067762138e+00 1.507823175629797e+01
|
||||
34 1 1 2.095250000000000e+01 1.778960516940534e+01 1.485635836857104e+01
|
||||
35 1 1 1.972000000000000e+01 1.707802096262913e+01 1.508733405608850e+01
|
||||
36 1 1 6.162500000000000e+00 6.404257860985923e+00 1.495657175139946e+01
|
||||
37 1 1 7.395000000000000e+00 7.115842067762138e+00 1.505630699893542e+01
|
||||
38 1 1 8.627500000000000e+00 6.404257860985923e+00 1.493710859708546e+01
|
||||
39 1 1 9.859999999999999e+00 7.115842067762138e+00 1.498031036104573e+01
|
||||
40 1 1 1.848750000000000e+01 1.778960516940534e+01 1.492663969598082e+01
|
||||
41 1 1 1.725500000000000e+01 1.707802096262913e+01 1.487928391741343e+01
|
||||
42 1 1 2.218500000000000e+01 1.280851572197185e+01 1.493339893560164e+01
|
||||
43 1 1 1.232500000000000e+01 7.115842067762138e+00 1.507943978677017e+01
|
||||
44 1 1 1.355750000000000e+01 6.404257860985923e+00 1.484914917113341e+01
|
||||
45 1 1 1.479000000000000e+01 7.115842067762138e+00 1.516663648122805e+01
|
||||
46 1 1 1.602250000000000e+01 1.778960516940534e+01 1.494170266401908e+01
|
||||
47 1 1 1.479000000000000e+01 1.707802096262913e+01 1.489834582180523e+01
|
||||
48 1 1 1.602250000000000e+01 6.404257860985923e+00 1.502658138746657e+01
|
||||
49 1 1 1.725500000000000e+01 7.115842067762138e+00 1.498697322036154e+01
|
||||
50 1 1 1.848750000000000e+01 6.404257860985923e+00 1.504573856434245e+01
|
||||
51 1 1 1.972000000000000e+01 7.115842067762138e+00 1.498510668772038e+01
|
||||
52 1 1 1.355750000000000e+01 1.778960516940534e+01 1.503160986637731e+01
|
||||
53 1 1 1.232500000000000e+01 1.707802096262913e+01 1.482446479934924e+01
|
||||
54 1 1 2.095250000000000e+01 6.404257860985923e+00 1.510811524523195e+01
|
||||
55 1 1 2.341750000000000e+01 1.494326834230049e+01 1.505440697642049e+01
|
||||
56 1 1 2.218500000000000e+01 1.707802096262913e+01 1.489480063588714e+01
|
||||
57 1 1 2.218500000000000e+01 8.539010481314564e+00 1.495045959051609e+01
|
||||
58 1 1 2.465000000000000e+01 8.539010481314564e+00 1.512601015985335e+01
|
||||
59 1 1 2.588250000000000e+01 1.067376310164321e+01 1.495691790117351e+01
|
||||
60 1 1 2.711500000000000e+01 1.138534730841942e+01 1.496195578420333e+01
|
||||
61 1 1 9.859999999999999e+00 1.565485254907670e+01 1.488138963237187e+01
|
||||
62 1 1 8.627500000000000e+00 1.494326834230049e+01 1.498700505084123e+01
|
||||
63 1 1 2.834750000000000e+01 1.067376310164321e+01 1.504459111637339e+01
|
||||
64 1 1 2.958000000000000e+01 1.138534730841942e+01 1.495098625433358e+01
|
||||
65 1 1 7.395000000000000e+00 1.280851572197185e+01 1.505608046573023e+01
|
||||
66 1 1 8.627500000000000e+00 1.352009992874806e+01 1.484199719552881e+01
|
||||
67 1 1 3.081250000000000e+01 1.352009992874806e+01 1.483451056838223e+01
|
||||
68 1 1 2.958000000000000e+01 1.280851572197185e+01 1.502332948089694e+01
|
||||
69 1 1 9.859999999999999e+00 1.280851572197185e+01 1.506286085730730e+01
|
||||
70 1 1 2.465000000000000e+01 1.138534730841942e+01 1.506305034228861e+01
|
||||
71 1 1 1.109250000000000e+01 1.352009992874806e+01 1.491918072685150e+01
|
||||
72 1 1 1.355750000000000e+01 1.352009992874806e+01 1.494644661191470e+01
|
||||
73 1 1 2.834750000000000e+01 1.352009992874806e+01 1.496099714517733e+01
|
||||
74 1 1 2.711500000000000e+01 1.280851572197185e+01 1.498298656405413e+01
|
||||
75 1 1 1.479000000000000e+01 1.280851572197185e+01 1.511808602386498e+01
|
||||
76 1 1 1.602250000000000e+01 1.352009992874806e+01 1.509196186449678e+01
|
||||
77 1 1 1.725500000000000e+01 1.280851572197185e+01 1.494017769280163e+01
|
||||
78 1 1 1.848750000000000e+01 1.352009992874806e+01 1.486540173862453e+01
|
||||
79 1 1 2.588250000000000e+01 1.352009992874806e+01 1.502414429870090e+01
|
||||
80 1 1 2.465000000000000e+01 1.280851572197185e+01 1.491189258035136e+01
|
||||
81 1 1 1.972000000000000e+01 1.280851572197185e+01 1.503451993485524e+01
|
||||
82 1 1 2.095250000000000e+01 1.352009992874806e+01 1.503423133885440e+01
|
||||
83 1 1 1.232500000000000e+01 1.280851572197185e+01 1.492432047742539e+01
|
||||
84 1 1 2.341750000000000e+01 1.067376310164321e+01 1.500488865182437e+01
|
||||
85 1 1 1.109250000000000e+01 1.494326834230049e+01 1.509530225402135e+01
|
||||
86 1 1 1.232500000000000e+01 1.565485254907670e+01 1.500246060086581e+01
|
||||
87 1 1 2.588250000000000e+01 9.250594688090777e+00 1.498734533172262e+01
|
||||
88 1 1 2.218500000000000e+01 1.565485254907670e+01 1.504729297899704e+01
|
||||
89 1 1 2.095250000000000e+01 1.494326834230049e+01 1.486622917148261e+01
|
||||
90 1 1 2.711500000000000e+01 8.539010481314564e+00 1.494373650471835e+01
|
||||
91 1 1 2.834750000000000e+01 9.250594688090777e+00 1.488792788684821e+01
|
||||
92 1 1 6.162500000000000e+00 1.067376310164321e+01 1.486731884367082e+01
|
||||
93 1 1 7.395000000000000e+00 1.138534730841942e+01 1.509646856144050e+01
|
||||
94 1 1 1.972000000000000e+01 1.565485254907670e+01 1.488798024124609e+01
|
||||
95 1 1 1.848750000000000e+01 1.494326834230049e+01 1.489558509878004e+01
|
||||
96 1 1 8.627500000000000e+00 1.067376310164321e+01 1.497336164791434e+01
|
||||
97 1 1 9.859999999999999e+00 1.138534730841942e+01 1.496081048392299e+01
|
||||
98 1 1 1.109250000000000e+01 1.067376310164321e+01 1.494580009249847e+01
|
||||
99 1 1 1.232500000000000e+01 1.138534730841942e+01 1.510396759497348e+01
|
||||
100 1 1 1.725500000000000e+01 1.565485254907670e+01 1.499338417222946e+01
|
||||
101 1 1 1.602250000000000e+01 1.494326834230049e+01 1.511840116374763e+01
|
||||
102 1 1 1.355750000000000e+01 1.067376310164321e+01 1.503281161003896e+01
|
||||
103 1 1 1.479000000000000e+01 1.138534730841942e+01 1.499843298302028e+01
|
||||
104 1 1 1.602250000000000e+01 1.067376310164321e+01 1.491311607132768e+01
|
||||
105 1 1 1.725500000000000e+01 1.138534730841942e+01 1.504030511972019e+01
|
||||
106 1 1 1.479000000000000e+01 1.565485254907670e+01 1.486944422096690e+01
|
||||
107 1 1 1.355750000000000e+01 1.494326834230049e+01 1.476511580670247e+01
|
||||
108 1 1 1.848750000000000e+01 1.067376310164321e+01 1.483733215135541e+01
|
||||
109 1 1 1.972000000000000e+01 1.138534730841942e+01 1.483307878319485e+01
|
||||
110 1 1 2.095250000000000e+01 1.067376310164321e+01 1.472377202887134e+01
|
||||
111 1 1 2.218500000000000e+01 1.138534730841942e+01 1.494032335018560e+01
|
||||
112 1 1 2.341750000000000e+01 9.250594688090777e+00 1.511930030385710e+01
|
||||
113 1 1 2.341750000000000e+01 1.778960516940534e+01 1.506163255648677e+01
|
||||
114 1 1 1.109250000000000e+01 6.404257860985923e+00 1.507183137955260e+01
|
||||
115 1 1 2.218500000000000e+01 4.269505240657282e+00 1.492921198534790e+01
|
||||
116 1 1 2.341750000000000e+01 7.115842067762137e-01 1.506491820629175e+01
|
||||
117 1 1 1.232500000000000e+00 2.134752620328641e+00 1.507012124249483e+01
|
||||
118 1 1 2.465000000000000e+00 2.846336827104855e+00 1.503655403336380e+01
|
||||
119 1 1 2.218500000000000e+01 1.992435778973398e+01 1.505948767536701e+01
|
||||
120 1 1 2.095250000000000e+01 1.921277358295777e+01 1.514330257618634e+01
|
||||
121 1 1 3.697500000000000e+00 2.134752620328641e+00 1.502497496406354e+01
|
||||
122 1 1 4.930000000000000e+00 2.846336827104855e+00 1.507374298221752e+01
|
||||
123 1 1 6.162500000000000e+00 2.134752620328641e+00 1.493733326297393e+01
|
||||
124 1 1 7.395000000000000e+00 2.846336827104855e+00 1.487495201368372e+01
|
||||
125 1 1 1.972000000000000e+01 1.992435778973398e+01 1.505808760634221e+01
|
||||
126 1 1 1.848750000000000e+01 1.921277358295777e+01 1.493872889432326e+01
|
||||
127 1 1 2.218500000000000e+01 0.000000000000000e+00 1.501312853963581e+01
|
||||
128 1 1 8.627500000000000e+00 2.134752620328641e+00 1.505205628279858e+01
|
||||
129 1 1 2.341750000000000e+01 4.981089447433495e+00 1.507571160792217e+01
|
||||
130 1 1 1.109250000000000e+01 2.134752620328641e+00 1.489358054803088e+01
|
||||
131 1 1 1.232500000000000e+01 2.846336827104855e+00 1.499912561242418e+01
|
||||
132 1 1 1.725500000000000e+01 1.992435778973398e+01 1.497577189332382e+01
|
||||
133 1 1 1.602250000000000e+01 1.921277358295777e+01 1.499040615876794e+01
|
||||
134 1 1 1.355750000000000e+01 2.134752620328641e+00 1.516072772863512e+01
|
||||
135 1 1 1.479000000000000e+01 2.846336827104855e+00 1.507211585538748e+01
|
||||
136 1 1 1.602250000000000e+01 2.134752620328641e+00 1.504045728176403e+01
|
||||
137 1 1 1.725500000000000e+01 2.846336827104855e+00 1.504684394670705e+01
|
||||
138 1 1 1.479000000000000e+01 1.992435778973398e+01 1.510384904069957e+01
|
||||
139 1 1 1.355750000000000e+01 1.921277358295777e+01 1.511446984282775e+01
|
||||
140 1 1 9.859999999999999e+00 2.846336827104855e+00 1.502182693962230e+01
|
||||
141 1 1 1.848750000000000e+01 2.134752620328641e+00 1.492115016417242e+01
|
||||
142 1 1 2.341750000000000e+01 1.921277358295777e+01 1.511940999724034e+01
|
||||
143 1 1 2.095250000000000e+01 7.115842067762137e-01 1.499411067303495e+01
|
||||
144 1 1 1.232500000000000e+00 7.115842067762137e-01 1.506494802778743e+01
|
||||
145 1 1 3.451000000000000e+01 1.992435778973398e+01 1.504957420337895e+01
|
||||
146 1 1 3.327750000000000e+01 1.921277358295777e+01 1.511072511003059e+01
|
||||
147 1 1 2.465000000000000e+00 0.000000000000000e+00 1.500837434607164e+01
|
||||
148 1 1 3.697500000000000e+00 7.115842067762137e-01 1.499541651074234e+01
|
||||
149 1 1 4.930000000000000e+00 0.000000000000000e+00 1.509518604163723e+01
|
||||
150 1 1 6.162500000000000e+00 7.115842067762137e-01 1.497074687620619e+01
|
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|
||||
337 2 1 9.859999999999999e+00 1.138534730841942e+01 1.829413303647114e+01
|
||||
338 2 1 1.109250000000000e+01 1.209693151519563e+01 1.856999584032139e+01
|
||||
339 2 1 1.232500000000000e+01 1.138534730841942e+01 1.851349651735582e+01
|
||||
340 2 1 1.355750000000000e+01 1.209693151519563e+01 1.831123823696192e+01
|
||||
341 2 1 1.479000000000000e+01 1.138534730841942e+01 1.843448433334394e+01
|
||||
342 2 1 1.602250000000000e+01 1.209693151519563e+01 1.839428881565063e+01
|
||||
343 2 1 1.725500000000000e+01 1.138534730841942e+01 1.849178099784848e+01
|
||||
344 2 1 1.848750000000000e+01 1.209693151519563e+01 1.824975358434335e+01
|
||||
345 2 1 1.972000000000000e+01 1.138534730841942e+01 1.839694145030204e+01
|
||||
346 2 1 2.095250000000000e+01 1.209693151519563e+01 1.829096787226717e+01
|
||||
347 2 1 2.218500000000000e+01 1.138534730841942e+01 1.840263887228008e+01
|
||||
348 2 1 2.341750000000000e+01 1.209693151519563e+01 1.837666030509410e+01
|
||||
349 2 1 2.465000000000000e+01 1.138534730841942e+01 1.835828025909527e+01
|
||||
350 2 1 2.588250000000000e+01 1.209693151519563e+01 1.833582168089864e+01
|
||||
351 2 1 2.711500000000000e+01 1.138534730841942e+01 1.836353031742933e+01
|
||||
352 2 1 2.834750000000000e+01 1.209693151519563e+01 1.845852602484125e+01
|
||||
353 2 1 2.958000000000000e+01 1.138534730841942e+01 1.853888136458308e+01
|
||||
354 2 1 3.081250000000000e+01 1.209693151519563e+01 1.831036168742244e+01
|
||||
355 2 1 8.627500000000000e+00 1.352009992874806e+01 1.835261188649090e+01
|
||||
356 2 1 9.859999999999999e+00 1.423168413552428e+01 1.821705864207346e+01
|
||||
357 2 1 1.109250000000000e+01 1.352009992874806e+01 1.831524712388831e+01
|
||||
358 2 1 1.232500000000000e+01 1.423168413552428e+01 1.852378179475058e+01
|
||||
359 2 1 1.355750000000000e+01 1.352009992874806e+01 1.852309441840510e+01
|
||||
360 2 1 1.479000000000000e+01 1.423168413552428e+01 1.836621027472939e+01
|
||||
361 2 1 1.602250000000000e+01 1.352009992874806e+01 1.849039311610116e+01
|
||||
362 2 1 1.725500000000000e+01 1.423168413552428e+01 1.842269825087092e+01
|
||||
363 2 1 1.848750000000000e+01 1.352009992874806e+01 1.825468998789840e+01
|
||||
364 2 1 1.972000000000000e+01 1.423168413552428e+01 1.849561590548242e+01
|
||||
365 2 1 7.395000000000000e+00 1.138534730841942e+01 1.859813014678126e+01
|
||||
366 2 1 3.451000000000000e+01 1.992435778973398e+01 1.813501916227946e+01
|
||||
367 2 1 2.834750000000000e+01 9.250594688090777e+00 1.847653992697568e+01
|
||||
368 2 1 2.711499999999999e+01 9.962178894866991e+00 1.849053529347614e+01
|
||||
369 2 1 1.355750000000000e+01 7.827426274538350e+00 1.835096749618396e+01
|
||||
370 2 1 1.479000000000000e+01 7.115842067762138e+00 1.844059942495262e+01
|
||||
371 2 1 1.602250000000000e+01 7.827426274538350e+00 1.844461353068087e+01
|
||||
372 2 1 1.725500000000000e+01 7.115842067762138e+00 1.836290600804645e+01
|
||||
373 2 1 1.848750000000000e+01 7.827426274538350e+00 1.825818280452995e+01
|
||||
374 2 1 1.972000000000000e+01 7.115842067762138e+00 1.837997086460227e+01
|
||||
375 2 1 2.095250000000000e+01 7.827426274538350e+00 1.826491847987811e+01
|
||||
376 2 1 2.218500000000000e+01 7.115842067762138e+00 1.841142851923555e+01
|
||||
377 2 1 2.341750000000000e+01 7.827426274538350e+00 1.826594520665525e+01
|
||||
378 2 1 2.465000000000000e+01 7.115842067762138e+00 1.838708488224049e+01
|
||||
379 2 1 2.588250000000000e+01 7.827426274538350e+00 1.830434555380351e+01
|
||||
380 2 1 2.711500000000000e+01 7.115842067762138e+00 1.859652575977937e+01
|
||||
381 2 1 2.834750000000000e+01 7.827426274538350e+00 1.844094595194482e+01
|
||||
382 2 1 6.162499999999999e+00 9.250594688090777e+00 1.856484810097502e+01
|
||||
383 2 1 1.109250000000000e+01 7.827426274538350e+00 1.847502232204046e+01
|
||||
384 2 1 7.395000000000000e+00 9.962178894866991e+00 1.854741705791729e+01
|
||||
385 2 1 9.859999999999999e+00 9.962178894866991e+00 1.837074522628645e+01
|
||||
386 2 1 1.109250000000000e+01 9.250594688090777e+00 1.846206781979952e+01
|
||||
387 2 1 1.232500000000000e+01 9.962178894866991e+00 1.823251181425658e+01
|
||||
388 2 1 1.355750000000000e+01 9.250594688090777e+00 1.834993099844037e+01
|
||||
389 2 1 1.479000000000000e+01 9.962178894866991e+00 1.843248036437880e+01
|
||||
390 2 1 1.602250000000000e+01 9.250594688090777e+00 1.855142577781635e+01
|
||||
391 2 1 1.725500000000000e+01 9.962178894866991e+00 1.847587547064991e+01
|
||||
392 2 1 1.848750000000000e+01 9.250594688090777e+00 1.850249139638135e+01
|
||||
393 2 1 1.972000000000000e+01 9.962178894866991e+00 1.841266132895000e+01
|
||||
394 2 1 2.095250000000000e+01 9.250594688090777e+00 1.837466808881276e+01
|
||||
395 2 1 2.218500000000000e+01 9.962178894866991e+00 1.834587370280250e+01
|
||||
396 2 1 2.341750000000000e+01 9.250594688090777e+00 1.846590574952954e+01
|
||||
397 2 1 2.465000000000000e+01 9.962178894866991e+00 1.835650105398410e+01
|
||||
398 2 1 2.588250000000000e+01 9.250594688090777e+00 1.838143174570202e+01
|
||||
399 2 1 8.627500000000000e+00 9.250594688090777e+00 1.843904853716322e+01
|
||||
400 2 1 3.574249999999999e+01 2.063594199651019e+01 1.839864514570517e+01
|
||||
562
examples/USER/misc/drip/data.CH
Normal file
562
examples/USER/misc/drip/data.CH
Normal file
@ -0,0 +1,562 @@
|
||||
LAMMPS data file
|
||||
|
||||
545 atoms
|
||||
2 atom types
|
||||
|
||||
0.0 2.465000000000000e+01 xlo xhi
|
||||
0.0 2.134752620328641e+01 ylo yhi
|
||||
0.0 3.000000000000000e+01 zlo zhi
|
||||
1.232500000000000e+01 0.000000000000000e+00 0.000000000000000e+00 xy xz yz
|
||||
|
||||
Masses
|
||||
|
||||
1 12.011
|
||||
2 1.0
|
||||
|
||||
Atoms # molecular
|
||||
|
||||
1 1 1 0.000000000000000e+00 0.000000000000000e+00 1.498097531971289e+01
|
||||
2 1 1 9.859999999999999e+00 1.707802096262913e+01 1.489139792549795e+01
|
||||
3 1 1 2.588250000000000e+01 6.404257860985923e+00 1.495586615731768e+01
|
||||
4 1 1 2.711500000000000e+01 7.115842067762138e+00 1.501795235919980e+01
|
||||
5 1 1 4.930000000000000e+00 8.539010481314564e+00 1.492827527515956e+01
|
||||
6 1 1 6.162499999999999e+00 9.250594688090777e+00 1.500678649580791e+01
|
||||
7 1 1 3.204499999999999e+01 1.565485254907670e+01 1.511662064028576e+01
|
||||
8 1 1 3.081250000000000e+01 1.494326834230049e+01 1.505500683988625e+01
|
||||
9 1 1 7.395000000000000e+00 8.539010481314564e+00 1.504923694256975e+01
|
||||
10 1 1 8.627500000000000e+00 9.250594688090777e+00 1.503332570633445e+01
|
||||
11 1 1 9.859999999999999e+00 8.539010481314564e+00 1.508137430939768e+01
|
||||
12 1 1 1.109250000000000e+01 9.250594688090777e+00 1.510475862694483e+01
|
||||
13 1 1 1.109250000000000e+01 1.778960516940534e+01 1.494613902888088e+01
|
||||
14 1 1 2.958000000000000e+01 1.565485254907670e+01 1.516279958068751e+01
|
||||
15 1 1 1.232500000000000e+01 8.539010481314564e+00 1.511276583208523e+01
|
||||
16 1 1 1.355750000000000e+01 9.250594688090777e+00 1.495632206546155e+01
|
||||
17 1 1 1.479000000000000e+01 8.539010481314564e+00 1.498291715828213e+01
|
||||
18 1 1 1.602250000000000e+01 9.250594688090777e+00 1.509801558902469e+01
|
||||
19 1 1 2.711499999999999e+01 1.565485254907670e+01 1.500089766276763e+01
|
||||
20 1 1 2.588250000000000e+01 1.494326834230049e+01 1.505114888970355e+01
|
||||
21 1 1 1.725500000000000e+01 8.539010481314564e+00 1.504495103103041e+01
|
||||
22 1 1 1.848750000000000e+01 9.250594688090777e+00 1.513527732850389e+01
|
||||
23 1 1 1.972000000000000e+01 8.539010481314564e+00 1.502400693288890e+01
|
||||
24 1 1 2.095250000000000e+01 9.250594688090777e+00 1.490419939433632e+01
|
||||
25 1 1 2.465000000000000e+01 1.565485254907670e+01 1.492998117758711e+01
|
||||
26 1 1 2.834750000000000e+01 1.494326834230049e+01 1.496091474579883e+01
|
||||
27 1 1 2.465000000000000e+01 7.115842067762138e+00 1.497394355694102e+01
|
||||
28 1 1 2.341750000000000e+01 6.404257860985923e+00 1.500235588455933e+01
|
||||
29 1 1 2.218500000000000e+01 7.115842067762138e+00 1.503766448268803e+01
|
||||
30 1 1 2.465000000000000e+01 4.269505240657282e+00 1.488340764495658e+01
|
||||
31 1 1 2.588250000000000e+01 4.981089447433495e+00 1.490587231994899e+01
|
||||
32 1 1 3.697500000000000e+00 6.404257860985923e+00 1.500462204163887e+01
|
||||
33 1 1 4.930000000000000e+00 7.115842067762138e+00 1.507823175629797e+01
|
||||
34 1 1 2.095250000000000e+01 1.778960516940534e+01 1.485635836857104e+01
|
||||
35 1 1 1.972000000000000e+01 1.707802096262913e+01 1.508733405608850e+01
|
||||
36 1 1 6.162500000000000e+00 6.404257860985923e+00 1.495657175139946e+01
|
||||
37 1 1 7.395000000000000e+00 7.115842067762138e+00 1.505630699893542e+01
|
||||
38 1 1 8.627500000000000e+00 6.404257860985923e+00 1.493710859708546e+01
|
||||
39 1 1 9.859999999999999e+00 7.115842067762138e+00 1.498031036104573e+01
|
||||
40 1 1 1.848750000000000e+01 1.778960516940534e+01 1.492663969598082e+01
|
||||
41 1 1 1.725500000000000e+01 1.707802096262913e+01 1.487928391741343e+01
|
||||
42 1 1 2.218500000000000e+01 1.280851572197185e+01 1.493339893560164e+01
|
||||
43 1 1 1.232500000000000e+01 7.115842067762138e+00 1.507943978677017e+01
|
||||
44 1 1 1.355750000000000e+01 6.404257860985923e+00 1.484914917113341e+01
|
||||
45 1 1 1.479000000000000e+01 7.115842067762138e+00 1.516663648122805e+01
|
||||
46 1 1 1.602250000000000e+01 1.778960516940534e+01 1.494170266401908e+01
|
||||
47 1 1 1.479000000000000e+01 1.707802096262913e+01 1.489834582180523e+01
|
||||
48 1 1 1.602250000000000e+01 6.404257860985923e+00 1.502658138746657e+01
|
||||
49 1 1 1.725500000000000e+01 7.115842067762138e+00 1.498697322036154e+01
|
||||
50 1 1 1.848750000000000e+01 6.404257860985923e+00 1.504573856434245e+01
|
||||
51 1 1 1.972000000000000e+01 7.115842067762138e+00 1.498510668772038e+01
|
||||
52 1 1 1.355750000000000e+01 1.778960516940534e+01 1.503160986637731e+01
|
||||
53 1 1 1.232500000000000e+01 1.707802096262913e+01 1.482446479934924e+01
|
||||
54 1 1 2.095250000000000e+01 6.404257860985923e+00 1.510811524523195e+01
|
||||
55 1 1 2.341750000000000e+01 1.494326834230049e+01 1.505440697642049e+01
|
||||
56 1 1 2.218500000000000e+01 1.707802096262913e+01 1.489480063588714e+01
|
||||
57 1 1 2.218500000000000e+01 8.539010481314564e+00 1.495045959051609e+01
|
||||
58 1 1 2.465000000000000e+01 8.539010481314564e+00 1.512601015985335e+01
|
||||
59 1 1 2.588250000000000e+01 1.067376310164321e+01 1.495691790117351e+01
|
||||
60 1 1 2.711500000000000e+01 1.138534730841942e+01 1.496195578420333e+01
|
||||
61 1 1 9.859999999999999e+00 1.565485254907670e+01 1.488138963237187e+01
|
||||
62 1 1 8.627500000000000e+00 1.494326834230049e+01 1.498700505084123e+01
|
||||
63 1 1 2.834750000000000e+01 1.067376310164321e+01 1.504459111637339e+01
|
||||
64 1 1 2.958000000000000e+01 1.138534730841942e+01 1.495098625433358e+01
|
||||
65 1 1 7.395000000000000e+00 1.280851572197185e+01 1.505608046573023e+01
|
||||
66 1 1 8.627500000000000e+00 1.352009992874806e+01 1.484199719552881e+01
|
||||
67 1 1 3.081250000000000e+01 1.352009992874806e+01 1.483451056838223e+01
|
||||
68 1 1 2.958000000000000e+01 1.280851572197185e+01 1.502332948089694e+01
|
||||
69 1 1 9.859999999999999e+00 1.280851572197185e+01 1.506286085730730e+01
|
||||
70 1 1 2.465000000000000e+01 1.138534730841942e+01 1.506305034228861e+01
|
||||
71 1 1 1.109250000000000e+01 1.352009992874806e+01 1.491918072685150e+01
|
||||
72 1 1 1.355750000000000e+01 1.352009992874806e+01 1.494644661191470e+01
|
||||
73 1 1 2.834750000000000e+01 1.352009992874806e+01 1.496099714517733e+01
|
||||
74 1 1 2.711500000000000e+01 1.280851572197185e+01 1.498298656405413e+01
|
||||
75 1 1 1.479000000000000e+01 1.280851572197185e+01 1.511808602386498e+01
|
||||
76 1 1 1.602250000000000e+01 1.352009992874806e+01 1.509196186449678e+01
|
||||
77 1 1 1.725500000000000e+01 1.280851572197185e+01 1.494017769280163e+01
|
||||
78 1 1 1.848750000000000e+01 1.352009992874806e+01 1.486540173862453e+01
|
||||
79 1 1 2.588250000000000e+01 1.352009992874806e+01 1.502414429870090e+01
|
||||
80 1 1 2.465000000000000e+01 1.280851572197185e+01 1.491189258035136e+01
|
||||
81 1 1 1.972000000000000e+01 1.280851572197185e+01 1.503451993485524e+01
|
||||
82 1 1 2.095250000000000e+01 1.352009992874806e+01 1.503423133885440e+01
|
||||
83 1 1 1.232500000000000e+01 1.280851572197185e+01 1.492432047742539e+01
|
||||
84 1 1 2.341750000000000e+01 1.067376310164321e+01 1.500488865182437e+01
|
||||
85 1 1 1.109250000000000e+01 1.494326834230049e+01 1.509530225402135e+01
|
||||
86 1 1 1.232500000000000e+01 1.565485254907670e+01 1.500246060086581e+01
|
||||
87 1 1 2.588250000000000e+01 9.250594688090777e+00 1.498734533172262e+01
|
||||
88 1 1 2.218500000000000e+01 1.565485254907670e+01 1.504729297899704e+01
|
||||
89 1 1 2.095250000000000e+01 1.494326834230049e+01 1.486622917148261e+01
|
||||
90 1 1 2.711500000000000e+01 8.539010481314564e+00 1.494373650471835e+01
|
||||
91 1 1 2.834750000000000e+01 9.250594688090777e+00 1.488792788684821e+01
|
||||
92 1 1 6.162500000000000e+00 1.067376310164321e+01 1.486731884367082e+01
|
||||
93 1 1 7.395000000000000e+00 1.138534730841942e+01 1.509646856144050e+01
|
||||
94 1 1 1.972000000000000e+01 1.565485254907670e+01 1.488798024124609e+01
|
||||
95 1 1 1.848750000000000e+01 1.494326834230049e+01 1.489558509878004e+01
|
||||
96 1 1 8.627500000000000e+00 1.067376310164321e+01 1.497336164791434e+01
|
||||
97 1 1 9.859999999999999e+00 1.138534730841942e+01 1.496081048392299e+01
|
||||
98 1 1 1.109250000000000e+01 1.067376310164321e+01 1.494580009249847e+01
|
||||
99 1 1 1.232500000000000e+01 1.138534730841942e+01 1.510396759497348e+01
|
||||
100 1 1 1.725500000000000e+01 1.565485254907670e+01 1.499338417222946e+01
|
||||
101 1 1 1.602250000000000e+01 1.494326834230049e+01 1.511840116374763e+01
|
||||
102 1 1 1.355750000000000e+01 1.067376310164321e+01 1.503281161003896e+01
|
||||
103 1 1 1.479000000000000e+01 1.138534730841942e+01 1.499843298302028e+01
|
||||
104 1 1 1.602250000000000e+01 1.067376310164321e+01 1.491311607132768e+01
|
||||
105 1 1 1.725500000000000e+01 1.138534730841942e+01 1.504030511972019e+01
|
||||
106 1 1 1.479000000000000e+01 1.565485254907670e+01 1.486944422096690e+01
|
||||
107 1 1 1.355750000000000e+01 1.494326834230049e+01 1.476511580670247e+01
|
||||
108 1 1 1.848750000000000e+01 1.067376310164321e+01 1.483733215135541e+01
|
||||
109 1 1 1.972000000000000e+01 1.138534730841942e+01 1.483307878319485e+01
|
||||
110 1 1 2.095250000000000e+01 1.067376310164321e+01 1.472377202887134e+01
|
||||
111 1 1 2.218500000000000e+01 1.138534730841942e+01 1.494032335018560e+01
|
||||
112 1 1 2.341750000000000e+01 9.250594688090777e+00 1.511930030385710e+01
|
||||
113 1 1 2.341750000000000e+01 1.778960516940534e+01 1.506163255648677e+01
|
||||
114 1 1 1.109250000000000e+01 6.404257860985923e+00 1.507183137955260e+01
|
||||
115 1 1 2.218500000000000e+01 4.269505240657282e+00 1.492921198534790e+01
|
||||
116 1 1 2.341750000000000e+01 7.115842067762137e-01 1.506491820629175e+01
|
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498 2 2 1.109250000000000e+01 1.209693151519563e+01 2.000000000000000e+01
|
||||
499 2 2 1.232500000000000e+01 1.138534730841942e+01 2.000000000000000e+01
|
||||
500 2 2 1.355750000000000e+01 1.209693151519563e+01 2.000000000000000e+01
|
||||
501 2 2 1.479000000000000e+01 1.138534730841942e+01 2.000000000000000e+01
|
||||
502 2 2 1.602250000000000e+01 1.209693151519563e+01 2.000000000000000e+01
|
||||
503 2 2 2.095250000000000e+01 1.209693151519563e+01 2.000000000000000e+01
|
||||
504 2 2 2.218500000000000e+01 1.138534730841942e+01 2.000000000000000e+01
|
||||
505 2 2 2.341750000000000e+01 1.209693151519563e+01 2.000000000000000e+01
|
||||
506 2 2 2.465000000000000e+01 1.138534730841942e+01 2.000000000000000e+01
|
||||
507 2 2 2.588250000000000e+01 1.209693151519563e+01 2.000000000000000e+01
|
||||
508 2 2 2.711500000000000e+01 1.138534730841942e+01 2.000000000000000e+01
|
||||
509 2 2 2.834750000000000e+01 1.209693151519563e+01 2.000000000000000e+01
|
||||
510 2 2 2.958000000000000e+01 1.138534730841942e+01 2.000000000000000e+01
|
||||
511 2 2 3.081250000000000e+01 1.209693151519563e+01 2.000000000000000e+01
|
||||
512 2 2 8.627500000000000e+00 1.352009992874806e+01 2.000000000000000e+01
|
||||
513 2 2 9.859999999999999e+00 1.423168413552428e+01 2.000000000000000e+01
|
||||
514 2 2 1.109250000000000e+01 1.352009992874806e+01 2.000000000000000e+01
|
||||
515 2 2 1.602250000000000e+01 1.352009992874806e+01 2.000000000000000e+01
|
||||
516 2 2 1.725500000000000e+01 1.423168413552428e+01 2.000000000000000e+01
|
||||
517 2 2 1.848750000000000e+01 1.352009992874806e+01 2.000000000000000e+01
|
||||
518 2 2 1.972000000000000e+01 1.423168413552428e+01 2.000000000000000e+01
|
||||
519 2 2 7.395000000000000e+00 1.138534730841942e+01 2.000000000000000e+01
|
||||
520 2 2 3.451000000000000e+01 1.992435778973398e+01 2.000000000000000e+01
|
||||
521 2 2 2.834750000000000e+01 9.250594688090777e+00 2.000000000000000e+01
|
||||
522 2 2 2.711499999999999e+01 9.962178894866991e+00 2.000000000000000e+01
|
||||
523 2 2 1.355750000000000e+01 7.827426274538350e+00 2.000000000000000e+01
|
||||
524 2 2 1.479000000000000e+01 7.115842067762138e+00 2.000000000000000e+01
|
||||
525 2 2 1.972000000000000e+01 7.115842067762138e+00 2.000000000000000e+01
|
||||
526 2 2 2.095250000000000e+01 7.827426274538350e+00 2.000000000000000e+01
|
||||
527 2 2 2.218500000000000e+01 7.115842067762138e+00 2.000000000000000e+01
|
||||
528 2 2 2.341750000000000e+01 7.827426274538350e+00 2.000000000000000e+01
|
||||
529 2 2 2.465000000000000e+01 7.115842067762138e+00 2.000000000000000e+01
|
||||
530 2 2 2.588250000000000e+01 7.827426274538350e+00 2.000000000000000e+01
|
||||
531 2 2 2.711500000000000e+01 7.115842067762138e+00 2.000000000000000e+01
|
||||
532 2 2 2.834750000000000e+01 7.827426274538350e+00 2.000000000000000e+01
|
||||
533 2 2 6.162499999999999e+00 9.250594688090777e+00 2.000000000000000e+01
|
||||
534 2 2 1.109250000000000e+01 7.827426274538350e+00 2.000000000000000e+01
|
||||
535 2 2 1.232500000000000e+01 9.962178894866991e+00 2.000000000000000e+01
|
||||
536 2 2 1.355750000000000e+01 9.250594688090777e+00 2.000000000000000e+01
|
||||
537 2 2 1.479000000000000e+01 9.962178894866991e+00 2.000000000000000e+01
|
||||
538 2 2 1.602250000000000e+01 9.250594688090777e+00 2.000000000000000e+01
|
||||
539 2 2 1.725500000000000e+01 9.962178894866991e+00 2.000000000000000e+01
|
||||
540 2 2 1.848750000000000e+01 9.250594688090777e+00 2.000000000000000e+01
|
||||
541 2 2 2.341750000000000e+01 9.250594688090777e+00 2.000000000000000e+01
|
||||
542 2 2 2.465000000000000e+01 9.962178894866991e+00 2.000000000000000e+01
|
||||
543 2 2 2.588250000000000e+01 9.250594688090777e+00 2.000000000000000e+01
|
||||
544 2 2 8.627500000000000e+00 9.250594688090777e+00 2.000000000000000e+01
|
||||
545 2 2 3.574249999999999e+01 2.063594199651019e+01 2.000000000000000e+01
|
||||
30
examples/USER/misc/drip/in.CH_drip
Normal file
30
examples/USER/misc/drip/in.CH_drip
Normal file
@ -0,0 +1,30 @@
|
||||
# Define unit set and class of atomic model
|
||||
units metal
|
||||
atom_style molecular
|
||||
|
||||
# BC
|
||||
boundary p p s
|
||||
|
||||
# read config
|
||||
read_data data.CH
|
||||
|
||||
|
||||
# potential
|
||||
pair_style hybrid/overlay drip rebo
|
||||
pair_coeff * * drip C.drip C NULL # only applies to species 1, i.e. C
|
||||
pair_coeff * * rebo CH.rebo C H # species 1 is C and species 2 is H
|
||||
|
||||
|
||||
compute peratom all pe/atom
|
||||
|
||||
# set what thermodynamic information to print to log
|
||||
thermo 10 # print every 1 timestep
|
||||
|
||||
# set what information to write to dump file
|
||||
dump id all custom 1 lammps.dump id type x y z fx fy fz c_peratom
|
||||
dump_modify id every 10 format line "%d %d %13.5e %13.5e %13.5e %13.5e %13.5e %13.5e %13.5e"
|
||||
dump_modify id sort id
|
||||
|
||||
# minimize energy
|
||||
minimize 1.0e-15 1.0e-15 100 100
|
||||
|
||||
29
examples/USER/misc/drip/in.C_drip
Normal file
29
examples/USER/misc/drip/in.C_drip
Normal file
@ -0,0 +1,29 @@
|
||||
# Define unit set and class of atomic model
|
||||
units metal
|
||||
atom_style molecular
|
||||
|
||||
# BC
|
||||
boundary p p s
|
||||
|
||||
# read config
|
||||
read_data data.C
|
||||
|
||||
|
||||
# potential
|
||||
pair_style hybrid/overlay drip rebo
|
||||
pair_coeff * * drip C.drip C
|
||||
pair_coeff * * rebo CH.rebo C
|
||||
|
||||
compute peratom all pe/atom
|
||||
|
||||
# set what thermodynamic information to print to log
|
||||
thermo 10 # print every 1 timestep
|
||||
|
||||
# set what information to write to dump file
|
||||
dump id all custom 1 lammps.dump id type x y z fx fy fz c_peratom
|
||||
dump_modify id every 10 format line "%d %d %13.5e %13.5e %13.5e %13.5e %13.5e %13.5e %13.5e"
|
||||
dump_modify id sort id
|
||||
|
||||
# minimize energy
|
||||
minimize 1.0e-15 1.0e-15 100 100
|
||||
|
||||
111
examples/USER/misc/drip/log.30Apr19.CH_drip.g++.1
Normal file
111
examples/USER/misc/drip/log.30Apr19.CH_drip.g++.1
Normal file
@ -0,0 +1,111 @@
|
||||
LAMMPS (30 Apr 2019)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Define unit set and class of atomic model
|
||||
units metal
|
||||
atom_style molecular
|
||||
|
||||
# BC
|
||||
boundary p p s
|
||||
|
||||
# read config
|
||||
read_data data.CH
|
||||
triclinic box = (0 0 0) to (24.65 21.3475 30) with tilt (12.325 0 0)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
545 atoms
|
||||
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 = 0.000152826 secs
|
||||
read_data CPU = 0.000973701 secs
|
||||
|
||||
|
||||
# potential
|
||||
pair_style hybrid/overlay drip rebo
|
||||
pair_coeff * * drip C.drip C NULL # only applies to species 1, i.e. C
|
||||
Reading potential file C.drip with DATE: 2019-04-19
|
||||
pair_coeff * * rebo CH.rebo C H # species 1 is C and species 2 is H
|
||||
Reading potential file CH.rebo with DATE: 2018-7-3
|
||||
|
||||
|
||||
compute peratom all pe/atom
|
||||
|
||||
# set what thermodynamic information to print to log
|
||||
thermo 10 # print every 1 timestep
|
||||
|
||||
# set what information to write to dump file
|
||||
dump id all custom 1 lammps.dump id type x y z fx fy fz c_peratom
|
||||
dump_modify id every 10 format line "%d %d %13.5e %13.5e %13.5e %13.5e %13.5e %13.5e %13.5e"
|
||||
dump_modify id sort id
|
||||
|
||||
# minimize energy
|
||||
minimize 1.0e-15 1.0e-15 100 100
|
||||
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 17.7
|
||||
ghost atom cutoff = 17.7
|
||||
binsize = 8.85, bins = 5 3 1
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair drip, perpetual, skip from (2)
|
||||
attributes: full, newton on, ghost
|
||||
pair build: skip/ghost
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair rebo, perpetual
|
||||
attributes: full, newton on, ghost
|
||||
pair build: full/bin/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 12.92 | 12.92 | 12.92 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 0 -2884.3731 0 -2884.3731 366196.9 2779.5956
|
||||
10 0 -3240.4807 0 -3240.4807 -20237.368 2779.5956
|
||||
20 0 -3281.0671 0 -3281.0671 -13303.696 2779.5956
|
||||
30 0 -3282.2176 0 -3282.2176 -19187.215 2779.5956
|
||||
40 0 -3282.4004 0 -3282.4004 -21740.059 2779.5956
|
||||
50 0 -3282.4755 0 -3282.4755 -22659.554 2779.5956
|
||||
57 0 -3282.5011 0 -3282.5011 -23313.198 2779.5956
|
||||
Loop time of 3.04218 on 1 procs for 57 steps with 545 atoms
|
||||
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = max force evaluations
|
||||
Energy initial, next-to-last, final =
|
||||
-2884.37307546 -3282.49993222 -3282.5010627
|
||||
Force two-norm initial, final = 115.342 0.193154
|
||||
Force max component initial, final = 12.0934 0.03617
|
||||
Final line search alpha, max atom move = 1 0.03617
|
||||
Iterations, force evaluations = 57 100
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 3.0291 | 3.0291 | 3.0291 | 0.0 | 99.57
|
||||
Bond | 1.8835e-05 | 1.8835e-05 | 1.8835e-05 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0016081 | 0.0016081 | 0.0016081 | 0.0 | 0.05
|
||||
Output | 0.0079796 | 0.0079796 | 0.0079796 | 0.0 | 0.26
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 0.003517 | | | 0.12
|
||||
|
||||
Nlocal: 545 ave 545 max 545 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 3175 ave 3175 max 3175 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 294122 ave 294122 max 294122 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 294122
|
||||
Ave neighs/atom = 539.673
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:03
|
||||
111
examples/USER/misc/drip/log.30Apr19.CH_drip.g++.4
Normal file
111
examples/USER/misc/drip/log.30Apr19.CH_drip.g++.4
Normal file
@ -0,0 +1,111 @@
|
||||
LAMMPS (30 Apr 2019)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Define unit set and class of atomic model
|
||||
units metal
|
||||
atom_style molecular
|
||||
|
||||
# BC
|
||||
boundary p p s
|
||||
|
||||
# read config
|
||||
read_data data.CH
|
||||
triclinic box = (0 0 0) to (24.65 21.3475 30) with tilt (12.325 0 0)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
545 atoms
|
||||
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 = 0.000135422 secs
|
||||
read_data CPU = 0.00368595 secs
|
||||
|
||||
|
||||
# potential
|
||||
pair_style hybrid/overlay drip rebo
|
||||
pair_coeff * * drip C.drip C NULL # only applies to species 1, i.e. C
|
||||
Reading potential file C.drip with DATE: 2019-04-19
|
||||
pair_coeff * * rebo CH.rebo C H # species 1 is C and species 2 is H
|
||||
Reading potential file CH.rebo with DATE: 2018-7-3
|
||||
|
||||
|
||||
compute peratom all pe/atom
|
||||
|
||||
# set what thermodynamic information to print to log
|
||||
thermo 10 # print every 1 timestep
|
||||
|
||||
# set what information to write to dump file
|
||||
dump id all custom 1 lammps.dump id type x y z fx fy fz c_peratom
|
||||
dump_modify id every 10 format line "%d %d %13.5e %13.5e %13.5e %13.5e %13.5e %13.5e %13.5e"
|
||||
dump_modify id sort id
|
||||
|
||||
# minimize energy
|
||||
minimize 1.0e-15 1.0e-15 100 100
|
||||
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 17.7
|
||||
ghost atom cutoff = 17.7
|
||||
binsize = 8.85, bins = 5 3 1
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair drip, perpetual, skip from (2)
|
||||
attributes: full, newton on, ghost
|
||||
pair build: skip/ghost
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair rebo, perpetual
|
||||
attributes: full, newton on, ghost
|
||||
pair build: full/bin/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 11.03 | 11.1 | 11.16 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 0 -2884.3731 0 -2884.3731 366196.9 2779.5956
|
||||
10 0 -3240.4807 0 -3240.4807 -20237.368 2779.5956
|
||||
20 0 -3281.0671 0 -3281.0671 -13303.696 2779.5956
|
||||
30 0 -3282.2176 0 -3282.2176 -19187.216 2779.5956
|
||||
40 0 -3282.4004 0 -3282.4004 -21740.027 2779.5956
|
||||
50 0 -3282.4753 0 -3282.4753 -22682.604 2779.5956
|
||||
57 0 -3282.5023 0 -3282.5023 -23355.081 2779.5956
|
||||
Loop time of 1.66218 on 4 procs for 57 steps with 545 atoms
|
||||
|
||||
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = max force evaluations
|
||||
Energy initial, next-to-last, final =
|
||||
-2884.37307546 -3282.50070864 -3282.50227121
|
||||
Force two-norm initial, final = 115.342 0.228488
|
||||
Force max component initial, final = 12.0934 0.03365
|
||||
Final line search alpha, max atom move = 1 0.03365
|
||||
Iterations, force evaluations = 57 100
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.5571 | 1.5945 | 1.6314 | 2.3 | 95.93
|
||||
Bond | 2.265e-05 | 2.9087e-05 | 3.4571e-05 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.020248 | 0.05608 | 0.092328 | 11.8 | 3.37
|
||||
Output | 0.0053282 | 0.0054213 | 0.0056982 | 0.2 | 0.33
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 0.006172 | | | 0.37
|
||||
|
||||
Nlocal: 136.25 ave 177 max 100 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
Nghost: 2874.75 ave 2912 max 2835 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 73530.5 ave 73544 max 73517 min
|
||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||
|
||||
Total # of neighbors = 294122
|
||||
Ave neighs/atom = 539.673
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:01
|
||||
110
examples/USER/misc/drip/log.30Apr19.C_drip.g++.1
Normal file
110
examples/USER/misc/drip/log.30Apr19.C_drip.g++.1
Normal file
@ -0,0 +1,110 @@
|
||||
LAMMPS (30 Apr 2019)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Define unit set and class of atomic model
|
||||
units metal
|
||||
atom_style molecular
|
||||
|
||||
# BC
|
||||
boundary p p s
|
||||
|
||||
# read config
|
||||
read_data data.C
|
||||
triclinic box = (0 0 0) to (24.65 21.3475 30) with tilt (12.325 0 0)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
400 atoms
|
||||
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 = 0.000912905 secs
|
||||
read_data CPU = 0.00252986 secs
|
||||
|
||||
|
||||
# potential
|
||||
pair_style hybrid/overlay drip rebo
|
||||
pair_coeff * * drip C.drip C
|
||||
Reading potential file C.drip with DATE: 2019-04-19
|
||||
pair_coeff * * rebo CH.rebo C
|
||||
Reading potential file CH.rebo with DATE: 2018-7-3
|
||||
|
||||
compute peratom all pe/atom
|
||||
|
||||
# set what thermodynamic information to print to log
|
||||
thermo 10 # print every 1 timestep
|
||||
|
||||
# set what information to write to dump file
|
||||
dump id all custom 1 lammps.dump id type x y z fx fy fz c_peratom
|
||||
dump_modify id every 10 format line "%d %d %13.5e %13.5e %13.5e %13.5e %13.5e %13.5e %13.5e"
|
||||
dump_modify id sort id
|
||||
|
||||
# minimize energy
|
||||
minimize 1.0e-15 1.0e-15 100 100
|
||||
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 17.7
|
||||
ghost atom cutoff = 17.7
|
||||
binsize = 8.85, bins = 5 3 1
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair drip, perpetual
|
||||
attributes: full, newton on, ghost
|
||||
pair build: full/bin/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) pair rebo, perpetual, copy from (1)
|
||||
attributes: full, newton on, ghost
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 12.21 | 12.21 | 12.21 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 0 -2941.0549 0 -2941.0549 -52204.715 2052.0534
|
||||
10 0 -2966.9787 0 -2966.9787 -29717.01 2052.0534
|
||||
20 0 -2967.0695 0 -2967.0695 -29614.636 2052.0534
|
||||
30 0 -2967.0859 0 -2967.0859 -29867.385 2052.0534
|
||||
40 0 -2967.0888 0 -2967.0888 -29997.486 2052.0534
|
||||
50 0 -2967.0896 0 -2967.0896 -30072.387 2052.0534
|
||||
51 0 -2967.0896 0 -2967.0896 -30076.548 2052.0534
|
||||
Loop time of 2.93337 on 1 procs for 51 steps with 400 atoms
|
||||
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = max force evaluations
|
||||
Energy initial, next-to-last, final =
|
||||
-2941.05486197 -2967.08958376 -2967.08962073
|
||||
Force two-norm initial, final = 35.5666 0.0471918
|
||||
Force max component initial, final = 6.23617 0.0050012
|
||||
Final line search alpha, max atom move = 1 0.0050012
|
||||
Iterations, force evaluations = 51 101
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.9239 | 2.9239 | 2.9239 | 0.0 | 99.68
|
||||
Bond | 1.2398e-05 | 1.2398e-05 | 1.2398e-05 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0010808 | 0.0010808 | 0.0010808 | 0.0 | 0.04
|
||||
Output | 0.0059283 | 0.0059283 | 0.0059283 | 0.0 | 0.20
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 0.002466 | | | 0.08
|
||||
|
||||
Nlocal: 400 ave 400 max 400 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 2357 ave 2357 max 2357 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 294122 ave 294122 max 294122 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 294122
|
||||
Ave neighs/atom = 735.305
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:03
|
||||
111
examples/USER/misc/drip/log.30Apr19.C_drip.g++.4
Normal file
111
examples/USER/misc/drip/log.30Apr19.C_drip.g++.4
Normal file
@ -0,0 +1,111 @@
|
||||
LAMMPS (30 Apr 2019)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Define unit set and class of atomic model
|
||||
units metal
|
||||
atom_style molecular
|
||||
|
||||
# BC
|
||||
boundary p p s
|
||||
|
||||
# read config
|
||||
read_data data.C
|
||||
triclinic box = (0 0 0) to (24.65 21.3475 30) with tilt (12.325 0 0)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
400 atoms
|
||||
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 = 0.0003407 secs
|
||||
read_data CPU = 0.00411105 secs
|
||||
|
||||
|
||||
# potential
|
||||
pair_style hybrid/overlay drip rebo
|
||||
pair_coeff * * drip C.drip C
|
||||
Reading potential file C.drip with DATE: 2019-04-19
|
||||
pair_coeff * * rebo CH.rebo C
|
||||
Reading potential file CH.rebo with DATE: 2018-7-3
|
||||
|
||||
compute peratom all pe/atom
|
||||
|
||||
# set what thermodynamic information to print to log
|
||||
thermo 10 # print every 1 timestep
|
||||
|
||||
# set what information to write to dump file
|
||||
dump id all custom 1 lammps.dump id type x y z fx fy fz c_peratom
|
||||
dump_modify id every 10 format line "%d %d %13.5e %13.5e %13.5e %13.5e %13.5e %13.5e %13.5e"
|
||||
dump_modify id sort id
|
||||
|
||||
# minimize energy
|
||||
minimize 1.0e-15 1.0e-15 100 100
|
||||
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 17.7
|
||||
ghost atom cutoff = 17.7
|
||||
binsize = 8.85, bins = 5 3 1
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair drip, perpetual
|
||||
attributes: full, newton on, ghost
|
||||
pair build: full/bin/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) pair rebo, perpetual, copy from (1)
|
||||
attributes: full, newton on, ghost
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:934)
|
||||
Per MPI rank memory allocation (min/avg/max) = 10.7 | 10.77 | 10.83 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 0 -2941.0549 0 -2941.0549 -52204.715 2052.0534
|
||||
10 0 -2966.9787 0 -2966.9787 -29717.01 2052.0534
|
||||
20 0 -2967.0695 0 -2967.0695 -29614.636 2052.0534
|
||||
30 0 -2967.0859 0 -2967.0859 -29867.385 2052.0534
|
||||
40 0 -2967.0888 0 -2967.0888 -29997.486 2052.0534
|
||||
50 0 -2967.0896 0 -2967.0896 -30072.387 2052.0534
|
||||
51 0 -2967.0896 0 -2967.0896 -30076.548 2052.0534
|
||||
Loop time of 1.47901 on 4 procs for 51 steps with 400 atoms
|
||||
|
||||
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = max force evaluations
|
||||
Energy initial, next-to-last, final =
|
||||
-2941.05486197 -2967.08958376 -2967.08962073
|
||||
Force two-norm initial, final = 35.5666 0.0471918
|
||||
Force max component initial, final = 6.23617 0.0050012
|
||||
Final line search alpha, max atom move = 1 0.0050012
|
||||
Iterations, force evaluations = 51 101
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.4314 | 1.4405 | 1.4548 | 0.8 | 97.40
|
||||
Bond | 1.955e-05 | 2.265e-05 | 2.4796e-05 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.014506 | 0.029363 | 0.038964 | 5.5 | 1.99
|
||||
Output | 0.00424 | 0.0043345 | 0.0046172 | 0.2 | 0.29
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 0.004772 | | | 0.32
|
||||
|
||||
Nlocal: 100 ave 100 max 100 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 2132 ave 2132 max 2132 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 73530.5 ave 73544 max 73517 min
|
||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||
|
||||
Total # of neighbors = 294122
|
||||
Ave neighs/atom = 735.305
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:01
|
||||
@ -1 +0,0 @@
|
||||
../../../../potentials/CH.airebo
|
||||
1
examples/USER/misc/kolmogorov_crespi_z/CH.rebo
Symbolic link
1
examples/USER/misc/kolmogorov_crespi_z/CH.rebo
Symbolic link
@ -0,0 +1 @@
|
||||
../../../../potentials/CH.rebo
|
||||
@ -22,7 +22,7 @@ group adsorbant type 2
|
||||
######################## Potential defition ########################
|
||||
pair_style hybrid/overlay rebo kolmogorov/crespi/z 14.0
|
||||
####################################################################
|
||||
pair_coeff * * rebo CH.airebo C C # chemical
|
||||
pair_coeff * * rebo CH.rebo C C # chemical
|
||||
pair_coeff 1 2 kolmogorov/crespi/z CC.KC C C # long-range
|
||||
####################################################################
|
||||
|
||||
|
||||
@ -1,208 +0,0 @@
|
||||
LAMMPS (8 Mar 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Initialization
|
||||
units metal
|
||||
boundary p p p
|
||||
atom_style atomic
|
||||
processors * * 1 # domain decomposition over x and y
|
||||
|
||||
# System and atom definition
|
||||
# we use 2 atom types so that inter- and intra-layer
|
||||
# interactions can be specified separately
|
||||
read_data data.bilayer-graphene # read lammps data file
|
||||
orthogonal box = (0 0 -20) to (17.04 19.6761 40)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
256 atoms
|
||||
mass 1 12.0107 # carbon mass (g/mole) | membrane
|
||||
mass 2 12.0107 # carbon mass (g/mole) | adsorbate
|
||||
# Neighbor update settings
|
||||
neighbor 2.0 bin
|
||||
neigh_modify every 1
|
||||
neigh_modify delay 0
|
||||
neigh_modify check yes
|
||||
# Separate atom groups
|
||||
group membrane type 1
|
||||
128 atoms in group membrane
|
||||
group adsorbant type 2
|
||||
128 atoms in group adsorbant
|
||||
|
||||
######################## Potential defition ########################
|
||||
pair_style hybrid/overlay rebo kolmogorov/crespi/z 14.0
|
||||
####################################################################
|
||||
pair_coeff * * rebo CH.airebo C C # chemical
|
||||
Reading potential file CH.airebo with DATE: 2011-10-25
|
||||
pair_coeff 1 2 kolmogorov/crespi/z CC.KC C C # long-range
|
||||
####################################################################
|
||||
|
||||
#### Simulation settings ####
|
||||
timestep 0.0001
|
||||
velocity all create 300.0 12345
|
||||
fix thermostat all nve
|
||||
compute COM1 membrane com
|
||||
compute COM2 adsorbant com
|
||||
############################
|
||||
|
||||
# Output
|
||||
#dump 1 all xyz 100 trajec.xyz
|
||||
#dump_modify 1 format line "%s %12.6f %12.6f %12.6f" element "C" "C"
|
||||
thermo 10
|
||||
thermo_style custom step time etotal pe temp c_COM1[3] c_COM2[3] # spcpu
|
||||
thermo_modify line one format float %14.8f
|
||||
|
||||
###### Run molecular dynamics ######
|
||||
run 1000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 16
|
||||
ghost atom cutoff = 16
|
||||
binsize = 8, bins = 3 3 8
|
||||
3 neighbor lists, perpetual/occasional/extra = 3 0 0
|
||||
(1) pair rebo, perpetual
|
||||
attributes: full, newton on, ghost
|
||||
pair build: full/bin/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) pair kolmogorov/crespi/z, perpetual, skip from (3)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) neighbor class addition, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.998 | 4.998 | 4.998 Mbytes
|
||||
Step Time TotEng PotEng Temp c_COM1[3] c_COM2[3]
|
||||
0 0.00000000 -1888.67041214 -1898.55881323 300.00000000 0.00000000 3.30000000
|
||||
10 0.00100000 -1888.67037221 -1898.21029897 289.42778520 -0.00020126 3.30020126
|
||||
20 0.00200000 -1888.67021541 -1897.22943612 259.67456089 -0.00041357 3.30041357
|
||||
30 0.00300000 -1888.66999308 -1895.86681311 218.34126559 -0.00063673 3.30063673
|
||||
40 0.00400000 -1888.66978354 -1894.47163830 176.02000692 -0.00087055 3.30087055
|
||||
50 0.00500000 -1888.66966068 -1893.37123377 142.63902862 -0.00111486 3.30111486
|
||||
60 0.00600000 -1888.66966132 -1892.75822749 124.04127205 -0.00136952 3.30136952
|
||||
70 0.00700000 -1888.66976974 -1892.63445751 120.28297808 -0.00163441 3.30163441
|
||||
80 0.00800000 -1888.66992867 -1892.83467462 126.35245792 -0.00190946 3.30190946
|
||||
90 0.00900000 -1888.67006868 -1893.11387069 134.81862145 -0.00219458 3.30219458
|
||||
100 0.01000000 -1888.67013621 -1893.25481851 139.09272853 -0.00248973 3.30248973
|
||||
110 0.01100000 -1888.67011201 -1893.15155790 135.96068294 -0.00279489 3.30279489
|
||||
120 0.01200000 -1888.67001496 -1892.84002960 126.51230266 -0.00311004 3.30311004
|
||||
130 0.01300000 -1888.66988997 -1892.47004238 115.29120968 -0.00343519 3.30343519
|
||||
140 0.01400000 -1888.66979230 -1892.23503116 108.16426723 -0.00377038 3.30377038
|
||||
150 0.01500000 -1888.66976478 -1892.28630583 109.72070257 -0.00411562 3.30411562
|
||||
160 0.01600000 -1888.66982054 -1892.66640611 121.25071190 -0.00447099 3.30447099
|
||||
170 0.01700000 -1888.66993790 -1893.28862637 140.12442721 -0.00483654 3.30483654
|
||||
180 0.01800000 -1888.67007017 -1893.97029258 160.80119589 -0.00521235 3.30521235
|
||||
190 0.01900000 -1888.67016712 -1894.50458787 177.00801243 -0.00559851 3.30559851
|
||||
200 0.02000000 -1888.67019459 -1894.73890106 184.11590729 -0.00599512 3.30599512
|
||||
210 0.02100000 -1888.67014420 -1894.62906014 180.78501932 -0.00640230 3.30640230
|
||||
220 0.02200000 -1888.67003680 -1894.25249103 169.36370738 -0.00682016 3.30682016
|
||||
230 0.02300000 -1888.66991386 -1893.77601613 154.91186767 -0.00724883 3.30724883
|
||||
240 0.02400000 -1888.66982525 -1893.38995084 143.20188490 -0.00768845 3.30768845
|
||||
250 0.02500000 -1888.66980630 -1893.23138936 138.39193056 -0.00813913 3.30813913
|
||||
260 0.02600000 -1888.66986130 -1893.32993923 141.38012476 -0.00860097 3.30860097
|
||||
270 0.02700000 -1888.66996305 -1893.60070606 149.59171763 -0.00907408 3.30907408
|
||||
280 0.02800000 -1888.67006686 -1893.88587226 158.24010433 -0.00955849 3.30955849
|
||||
290 0.02900000 -1888.67012981 -1894.02402669 162.42960292 -0.01005424 3.31005424
|
||||
300 0.03000000 -1888.67012722 -1893.91715234 159.18726627 -0.01056129 3.31056129
|
||||
310 0.03100000 -1888.67005731 -1893.57037242 148.66857852 -0.01107957 3.31107957
|
||||
320 0.03200000 -1888.66994573 -1893.09358619 134.20694883 -0.01160898 3.31160898
|
||||
330 0.03300000 -1888.66983589 -1892.66132663 121.09614207 -0.01214935 3.31214935
|
||||
340 0.03400000 -1888.66977410 -1892.44446345 114.51869676 -0.01270046 3.31270046
|
||||
350 0.03500000 -1888.66978826 -1892.53901235 117.38674604 -0.01326207 3.31326207
|
||||
360 0.03600000 -1888.66987439 -1892.92337288 129.04508371 -0.01383390 3.31383390
|
||||
370 0.03700000 -1888.66999800 -1893.46445570 145.45701555 -0.01441561 3.31441561
|
||||
380 0.03800000 -1888.67010960 -1893.97065516 160.81100020 -0.01500688 3.31500688
|
||||
390 0.03900000 -1888.67016540 -1894.26835818 169.84119247 -0.01560734 3.31560734
|
||||
400 0.04000000 -1888.67014667 -1894.26967975 169.88185546 -0.01621664 3.31621664
|
||||
410 0.04100000 -1888.67006166 -1894.00321069 161.80014280 -0.01683442 3.31683442
|
||||
420 0.04200000 -1888.66994367 -1893.60086324 149.59707418 -0.01746033 3.31746033
|
||||
430 0.04300000 -1888.66984058 -1893.24559841 138.82197275 -0.01809405 3.31809405
|
||||
440 0.04400000 -1888.66979399 -1893.09727874 134.32357877 -0.01873527 3.31873527
|
||||
450 0.04500000 -1888.66982139 -1893.22837442 138.30000378 -0.01938373 3.31938373
|
||||
460 0.04600000 -1888.66990972 -1893.59670383 149.47191354 -0.02003918 3.32003918
|
||||
470 0.04700000 -1888.67002173 -1894.06542598 163.68887743 -0.02070143 3.32070143
|
||||
480 0.04800000 -1888.67011389 -1894.46010842 175.66018439 -0.02137030 3.32137030
|
||||
490 0.04900000 -1888.67015175 -1894.63688098 181.02206322 -0.02204565 3.32204565
|
||||
500 0.05000000 -1888.67012158 -1894.53632221 177.97216882 -0.02272740 3.32272740
|
||||
510 0.05100000 -1888.67003762 -1894.20444731 167.90610436 -0.02341547 3.32341547
|
||||
520 0.05200000 -1888.66993151 -1893.77231066 154.79891353 -0.02410981 3.32410981
|
||||
530 0.05300000 -1888.66984505 -1893.40525927 143.66572038 -0.02481040 3.32481040
|
||||
540 0.05400000 -1888.66981408 -1893.23762083 138.58074854 -0.02551724 3.32551724
|
||||
550 0.05500000 -1888.66985005 -1893.31793594 141.01630317 -0.02623032 3.32623032
|
||||
560 0.05600000 -1888.66993737 -1893.59069013 149.28862751 -0.02694963 3.32694963
|
||||
570 0.05700000 -1888.67003852 -1893.92089571 159.30352588 -0.02767517 3.32767517
|
||||
580 0.05800000 -1888.67011322 -1894.15124753 166.28980524 -0.02840691 3.32840691
|
||||
590 0.05900000 -1888.67013192 -1894.16548041 166.72104345 -0.02914478 3.32914478
|
||||
600 0.06000000 -1888.67008713 -1893.93443318 159.71275856 -0.02988871 3.32988871
|
||||
610 0.06100000 -1888.66999438 -1893.52841656 147.39760646 -0.03063856 3.33063856
|
||||
620 0.06200000 -1888.66988809 -1893.09235021 134.17119963 -0.03139416 3.33139416
|
||||
630 0.06300000 -1888.66980996 -1892.79172016 125.05288240 -0.03215531 3.33215531
|
||||
640 0.06400000 -1888.66979261 -1892.74755390 123.71346730 -0.03292176 3.33292176
|
||||
650 0.06500000 -1888.66984332 -1892.98665459 130.96590324 -0.03369323 3.33369323
|
||||
660 0.06600000 -1888.66994245 -1893.42999868 144.41332389 -0.03446937 3.33446937
|
||||
670 0.06700000 -1888.67005233 -1893.92310681 159.37018806 -0.03524986 3.33524986
|
||||
680 0.06800000 -1888.67013309 -1894.29451581 170.63575808 -0.03603430 3.33603430
|
||||
690 0.06900000 -1888.67015452 -1894.41878117 174.40514192 -0.03682229 3.33682229
|
||||
700 0.07000000 -1888.67010897 -1894.26288036 169.67671530 -0.03761343 3.33761343
|
||||
710 0.07100000 -1888.67001367 -1893.89812904 158.61357114 -0.03840729 3.33840729
|
||||
720 0.07200000 -1888.66990378 -1893.47348746 145.73388454 -0.03920344 3.33920344
|
||||
730 0.07300000 -1888.66982212 -1893.15984839 136.22099960 -0.04000148 3.34000148
|
||||
740 0.07400000 -1888.66980109 -1893.08373746 133.91254029 -0.04080098 3.34080098
|
||||
750 0.07500000 -1888.66984794 -1893.27755511 139.79127024 -0.04160156 3.34160156
|
||||
760 0.07600000 -1888.66994215 -1893.66837365 151.64528967 -0.04240282 3.34240282
|
||||
770 0.07700000 -1888.67004554 -1894.10941206 165.02263027 -0.04320441 3.34320441
|
||||
780 0.07800000 -1888.67011702 -1894.43947545 175.03411436 -0.04400599 3.34400599
|
||||
790 0.07900000 -1888.67013297 -1894.54590471 178.26254255 -0.04480726 3.34480726
|
||||
800 0.08000000 -1888.67008751 -1894.40384142 173.95392406 -0.04560792 3.34560792
|
||||
810 0.08100000 -1888.66999923 -1894.08389003 164.24973321 -0.04640773 3.34640773
|
||||
820 0.08200000 -1888.66990447 -1893.72313979 153.30795965 -0.04720647 3.34720647
|
||||
830 0.08300000 -1888.66984367 -1893.46839190 145.58111626 -0.04800393 3.34800393
|
||||
840 0.08400000 -1888.66984156 -1893.41412536 143.93481093 -0.04879995 3.34879995
|
||||
850 0.08500000 -1888.66989670 -1893.56426154 148.48805553 -0.04959439 3.34959439
|
||||
860 0.08600000 -1888.66998222 -1893.83463719 156.68827294 -0.05038713 3.35038713
|
||||
870 0.08700000 -1888.67006171 -1894.09325045 164.53181920 -0.05117805 3.35117805
|
||||
880 0.08800000 -1888.67010273 -1894.21712661 168.28880100 -0.05196706 3.35196706
|
||||
890 0.08900000 -1888.67008993 -1894.14263950 166.02935656 -0.05275408 3.35275408
|
||||
900 0.09000000 -1888.67002891 -1893.89014571 158.37090587 -0.05353904 3.35353904
|
||||
910 0.09100000 -1888.66994326 -1893.55535709 148.21649469 -0.05432186 3.35432186
|
||||
920 0.09200000 -1888.66986526 -1893.27257949 139.63979178 -0.05510247 3.35510247
|
||||
930 0.09300000 -1888.66982730 -1893.16330891 136.32582949 -0.05588078 3.35588078
|
||||
940 0.09400000 -1888.66984631 -1893.28643285 140.06065785 -0.05665670 3.35665670
|
||||
950 0.09500000 -1888.66991503 -1893.61245342 149.94957268 -0.05743015 3.35743015
|
||||
960 0.09600000 -1888.67000691 -1894.03423922 162.74316516 -0.05820101 3.35820101
|
||||
970 0.09700000 -1888.67008649 -1894.40848025 174.09469037 -0.05896915 3.35896915
|
||||
980 0.09800000 -1888.67012436 -1894.61056767 180.22458605 -0.05973444 3.35973444
|
||||
990 0.09900000 -1888.67010608 -1894.58107659 179.33042338 -0.06049672 3.36049672
|
||||
1000 0.10000000 -1888.67003981 -1894.34773305 172.25312330 -0.06125581 3.36125581
|
||||
Loop time of 3.90147 on 1 procs for 1000 steps with 256 atoms
|
||||
|
||||
Performance: 2.215 ns/day, 10.837 hours/ns, 256.314 timesteps/s
|
||||
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 3.8786 | 3.8786 | 3.8786 | 0.0 | 99.41
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.010816 | 0.010816 | 0.010816 | 0.0 | 0.28
|
||||
Output | 0.002461 | 0.002461 | 0.002461 | 0.0 | 0.06
|
||||
Modify | 0.0051703 | 0.0051703 | 0.0051703 | 0.0 | 0.13
|
||||
Other | | 0.004447 | | | 0.11
|
||||
|
||||
Nlocal: 256 ave 256 max 256 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1721 ave 1721 max 1721 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 37312 ave 37312 max 37312 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 94592 ave 94592 max 94592 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 94592
|
||||
Ave neighs/atom = 369.5
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:03
|
||||
@ -1,208 +0,0 @@
|
||||
LAMMPS (8 Mar 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Initialization
|
||||
units metal
|
||||
boundary p p p
|
||||
atom_style atomic
|
||||
processors * * 1 # domain decomposition over x and y
|
||||
|
||||
# System and atom definition
|
||||
# we use 2 atom types so that inter- and intra-layer
|
||||
# interactions can be specified separately
|
||||
read_data data.bilayer-graphene # read lammps data file
|
||||
orthogonal box = (0 0 -20) to (17.04 19.6761 40)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
256 atoms
|
||||
mass 1 12.0107 # carbon mass (g/mole) | membrane
|
||||
mass 2 12.0107 # carbon mass (g/mole) | adsorbate
|
||||
# Neighbor update settings
|
||||
neighbor 2.0 bin
|
||||
neigh_modify every 1
|
||||
neigh_modify delay 0
|
||||
neigh_modify check yes
|
||||
# Separate atom groups
|
||||
group membrane type 1
|
||||
128 atoms in group membrane
|
||||
group adsorbant type 2
|
||||
128 atoms in group adsorbant
|
||||
|
||||
######################## Potential defition ########################
|
||||
pair_style hybrid/overlay rebo kolmogorov/crespi/z 14.0
|
||||
####################################################################
|
||||
pair_coeff * * rebo CH.airebo C C # chemical
|
||||
Reading potential file CH.airebo with DATE: 2011-10-25
|
||||
pair_coeff 1 2 kolmogorov/crespi/z CC.KC C C # long-range
|
||||
####################################################################
|
||||
|
||||
#### Simulation settings ####
|
||||
timestep 0.0001
|
||||
velocity all create 300.0 12345
|
||||
fix thermostat all nve
|
||||
compute COM1 membrane com
|
||||
compute COM2 adsorbant com
|
||||
############################
|
||||
|
||||
# Output
|
||||
#dump 1 all xyz 100 trajec.xyz
|
||||
#dump_modify 1 format line "%s %12.6f %12.6f %12.6f" element "C" "C"
|
||||
thermo 10
|
||||
thermo_style custom step time etotal pe temp c_COM1[3] c_COM2[3] # spcpu
|
||||
thermo_modify line one format float %14.8f
|
||||
|
||||
###### Run molecular dynamics ######
|
||||
run 1000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 16
|
||||
ghost atom cutoff = 16
|
||||
binsize = 8, bins = 3 3 8
|
||||
3 neighbor lists, perpetual/occasional/extra = 3 0 0
|
||||
(1) pair rebo, perpetual
|
||||
attributes: full, newton on, ghost
|
||||
pair build: full/bin/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) pair kolmogorov/crespi/z, perpetual, skip from (3)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) neighbor class addition, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.572 | 4.572 | 4.572 Mbytes
|
||||
Step Time TotEng PotEng Temp c_COM1[3] c_COM2[3]
|
||||
0 0.00000000 -1888.67041214 -1898.55881323 300.00000000 0.00000000 3.30000000
|
||||
10 0.00100000 -1888.67037221 -1898.21029897 289.42778520 -0.00020126 3.30020126
|
||||
20 0.00200000 -1888.67021541 -1897.22943612 259.67456089 -0.00041357 3.30041357
|
||||
30 0.00300000 -1888.66999308 -1895.86681311 218.34126559 -0.00063673 3.30063673
|
||||
40 0.00400000 -1888.66978354 -1894.47163830 176.02000692 -0.00087055 3.30087055
|
||||
50 0.00500000 -1888.66966068 -1893.37123377 142.63902862 -0.00111486 3.30111486
|
||||
60 0.00600000 -1888.66966132 -1892.75822749 124.04127205 -0.00136952 3.30136952
|
||||
70 0.00700000 -1888.66976974 -1892.63445751 120.28297808 -0.00163441 3.30163441
|
||||
80 0.00800000 -1888.66992867 -1892.83467462 126.35245792 -0.00190946 3.30190946
|
||||
90 0.00900000 -1888.67006868 -1893.11387069 134.81862145 -0.00219458 3.30219458
|
||||
100 0.01000000 -1888.67013621 -1893.25481851 139.09272853 -0.00248973 3.30248973
|
||||
110 0.01100000 -1888.67011201 -1893.15155790 135.96068294 -0.00279489 3.30279489
|
||||
120 0.01200000 -1888.67001496 -1892.84002960 126.51230266 -0.00311004 3.30311004
|
||||
130 0.01300000 -1888.66988997 -1892.47004238 115.29120968 -0.00343519 3.30343519
|
||||
140 0.01400000 -1888.66979230 -1892.23503116 108.16426723 -0.00377038 3.30377038
|
||||
150 0.01500000 -1888.66976478 -1892.28630583 109.72070257 -0.00411562 3.30411562
|
||||
160 0.01600000 -1888.66982054 -1892.66640611 121.25071190 -0.00447099 3.30447099
|
||||
170 0.01700000 -1888.66993790 -1893.28862637 140.12442721 -0.00483654 3.30483654
|
||||
180 0.01800000 -1888.67007017 -1893.97029258 160.80119589 -0.00521235 3.30521235
|
||||
190 0.01900000 -1888.67016712 -1894.50458787 177.00801243 -0.00559851 3.30559851
|
||||
200 0.02000000 -1888.67019459 -1894.73890106 184.11590729 -0.00599512 3.30599512
|
||||
210 0.02100000 -1888.67014420 -1894.62906014 180.78501932 -0.00640230 3.30640230
|
||||
220 0.02200000 -1888.67003680 -1894.25249103 169.36370738 -0.00682016 3.30682016
|
||||
230 0.02300000 -1888.66991386 -1893.77601613 154.91186767 -0.00724883 3.30724883
|
||||
240 0.02400000 -1888.66982525 -1893.38995084 143.20188490 -0.00768845 3.30768845
|
||||
250 0.02500000 -1888.66980630 -1893.23138936 138.39193056 -0.00813913 3.30813913
|
||||
260 0.02600000 -1888.66986130 -1893.32993923 141.38012476 -0.00860097 3.30860097
|
||||
270 0.02700000 -1888.66996305 -1893.60070606 149.59171763 -0.00907408 3.30907408
|
||||
280 0.02800000 -1888.67006686 -1893.88587226 158.24010433 -0.00955849 3.30955849
|
||||
290 0.02900000 -1888.67012981 -1894.02402669 162.42960292 -0.01005424 3.31005424
|
||||
300 0.03000000 -1888.67012722 -1893.91715234 159.18726627 -0.01056129 3.31056129
|
||||
310 0.03100000 -1888.67005731 -1893.57037242 148.66857852 -0.01107957 3.31107957
|
||||
320 0.03200000 -1888.66994573 -1893.09358619 134.20694883 -0.01160898 3.31160898
|
||||
330 0.03300000 -1888.66983589 -1892.66132663 121.09614207 -0.01214935 3.31214935
|
||||
340 0.03400000 -1888.66977410 -1892.44446345 114.51869676 -0.01270046 3.31270046
|
||||
350 0.03500000 -1888.66978826 -1892.53901235 117.38674604 -0.01326207 3.31326207
|
||||
360 0.03600000 -1888.66987439 -1892.92337288 129.04508371 -0.01383390 3.31383390
|
||||
370 0.03700000 -1888.66999800 -1893.46445570 145.45701555 -0.01441561 3.31441561
|
||||
380 0.03800000 -1888.67010960 -1893.97065516 160.81100020 -0.01500688 3.31500688
|
||||
390 0.03900000 -1888.67016540 -1894.26835818 169.84119247 -0.01560734 3.31560734
|
||||
400 0.04000000 -1888.67014667 -1894.26967975 169.88185546 -0.01621664 3.31621664
|
||||
410 0.04100000 -1888.67006166 -1894.00321069 161.80014280 -0.01683442 3.31683442
|
||||
420 0.04200000 -1888.66994367 -1893.60086324 149.59707418 -0.01746033 3.31746033
|
||||
430 0.04300000 -1888.66984058 -1893.24559841 138.82197275 -0.01809405 3.31809405
|
||||
440 0.04400000 -1888.66979399 -1893.09727874 134.32357877 -0.01873527 3.31873527
|
||||
450 0.04500000 -1888.66982139 -1893.22837442 138.30000378 -0.01938373 3.31938373
|
||||
460 0.04600000 -1888.66990972 -1893.59670383 149.47191354 -0.02003918 3.32003918
|
||||
470 0.04700000 -1888.67002173 -1894.06542598 163.68887743 -0.02070143 3.32070143
|
||||
480 0.04800000 -1888.67011389 -1894.46010842 175.66018439 -0.02137030 3.32137030
|
||||
490 0.04900000 -1888.67015175 -1894.63688098 181.02206322 -0.02204565 3.32204565
|
||||
500 0.05000000 -1888.67012158 -1894.53632221 177.97216882 -0.02272740 3.32272740
|
||||
510 0.05100000 -1888.67003762 -1894.20444731 167.90610436 -0.02341547 3.32341547
|
||||
520 0.05200000 -1888.66993151 -1893.77231066 154.79891353 -0.02410981 3.32410981
|
||||
530 0.05300000 -1888.66984505 -1893.40525927 143.66572038 -0.02481040 3.32481040
|
||||
540 0.05400000 -1888.66981408 -1893.23762083 138.58074854 -0.02551724 3.32551724
|
||||
550 0.05500000 -1888.66985005 -1893.31793594 141.01630317 -0.02623032 3.32623032
|
||||
560 0.05600000 -1888.66993737 -1893.59069013 149.28862751 -0.02694963 3.32694963
|
||||
570 0.05700000 -1888.67003852 -1893.92089571 159.30352588 -0.02767517 3.32767517
|
||||
580 0.05800000 -1888.67011322 -1894.15124753 166.28980524 -0.02840691 3.32840691
|
||||
590 0.05900000 -1888.67013192 -1894.16548041 166.72104345 -0.02914478 3.32914478
|
||||
600 0.06000000 -1888.67008713 -1893.93443318 159.71275856 -0.02988871 3.32988871
|
||||
610 0.06100000 -1888.66999438 -1893.52841656 147.39760646 -0.03063856 3.33063856
|
||||
620 0.06200000 -1888.66988809 -1893.09235021 134.17119963 -0.03139416 3.33139416
|
||||
630 0.06300000 -1888.66980996 -1892.79172016 125.05288240 -0.03215531 3.33215531
|
||||
640 0.06400000 -1888.66979261 -1892.74755390 123.71346730 -0.03292176 3.33292176
|
||||
650 0.06500000 -1888.66984332 -1892.98665459 130.96590324 -0.03369323 3.33369323
|
||||
660 0.06600000 -1888.66994245 -1893.42999868 144.41332389 -0.03446937 3.33446937
|
||||
670 0.06700000 -1888.67005233 -1893.92310681 159.37018806 -0.03524986 3.33524986
|
||||
680 0.06800000 -1888.67013309 -1894.29451581 170.63575808 -0.03603430 3.33603430
|
||||
690 0.06900000 -1888.67015452 -1894.41878117 174.40514192 -0.03682229 3.33682229
|
||||
700 0.07000000 -1888.67010897 -1894.26288036 169.67671530 -0.03761343 3.33761343
|
||||
710 0.07100000 -1888.67001367 -1893.89812904 158.61357114 -0.03840729 3.33840729
|
||||
720 0.07200000 -1888.66990378 -1893.47348746 145.73388454 -0.03920344 3.33920344
|
||||
730 0.07300000 -1888.66982212 -1893.15984839 136.22099960 -0.04000148 3.34000148
|
||||
740 0.07400000 -1888.66980109 -1893.08373746 133.91254029 -0.04080098 3.34080098
|
||||
750 0.07500000 -1888.66984794 -1893.27755511 139.79127024 -0.04160156 3.34160156
|
||||
760 0.07600000 -1888.66994215 -1893.66837365 151.64528967 -0.04240282 3.34240282
|
||||
770 0.07700000 -1888.67004554 -1894.10941206 165.02263027 -0.04320441 3.34320441
|
||||
780 0.07800000 -1888.67011702 -1894.43947545 175.03411436 -0.04400599 3.34400599
|
||||
790 0.07900000 -1888.67013297 -1894.54590471 178.26254255 -0.04480726 3.34480726
|
||||
800 0.08000000 -1888.67008751 -1894.40384142 173.95392406 -0.04560792 3.34560792
|
||||
810 0.08100000 -1888.66999923 -1894.08389003 164.24973321 -0.04640773 3.34640773
|
||||
820 0.08200000 -1888.66990447 -1893.72313979 153.30795965 -0.04720647 3.34720647
|
||||
830 0.08300000 -1888.66984367 -1893.46839190 145.58111626 -0.04800393 3.34800393
|
||||
840 0.08400000 -1888.66984156 -1893.41412536 143.93481093 -0.04879995 3.34879995
|
||||
850 0.08500000 -1888.66989670 -1893.56426154 148.48805553 -0.04959439 3.34959439
|
||||
860 0.08600000 -1888.66998222 -1893.83463719 156.68827294 -0.05038713 3.35038713
|
||||
870 0.08700000 -1888.67006171 -1894.09325045 164.53181920 -0.05117805 3.35117805
|
||||
880 0.08800000 -1888.67010273 -1894.21712661 168.28880100 -0.05196706 3.35196706
|
||||
890 0.08900000 -1888.67008993 -1894.14263950 166.02935656 -0.05275408 3.35275408
|
||||
900 0.09000000 -1888.67002891 -1893.89014571 158.37090587 -0.05353904 3.35353904
|
||||
910 0.09100000 -1888.66994326 -1893.55535709 148.21649469 -0.05432186 3.35432186
|
||||
920 0.09200000 -1888.66986526 -1893.27257949 139.63979178 -0.05510247 3.35510247
|
||||
930 0.09300000 -1888.66982730 -1893.16330891 136.32582949 -0.05588078 3.35588078
|
||||
940 0.09400000 -1888.66984631 -1893.28643285 140.06065785 -0.05665670 3.35665670
|
||||
950 0.09500000 -1888.66991503 -1893.61245342 149.94957268 -0.05743015 3.35743015
|
||||
960 0.09600000 -1888.67000691 -1894.03423922 162.74316516 -0.05820101 3.35820101
|
||||
970 0.09700000 -1888.67008649 -1894.40848025 174.09469037 -0.05896915 3.35896915
|
||||
980 0.09800000 -1888.67012436 -1894.61056767 180.22458605 -0.05973444 3.35973444
|
||||
990 0.09900000 -1888.67010608 -1894.58107659 179.33042338 -0.06049672 3.36049672
|
||||
1000 0.10000000 -1888.67003981 -1894.34773305 172.25312330 -0.06125581 3.36125581
|
||||
Loop time of 1.32192 on 4 procs for 1000 steps with 256 atoms
|
||||
|
||||
Performance: 6.536 ns/day, 3.672 hours/ns, 756.476 timesteps/s
|
||||
98.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.1157 | 1.172 | 1.2369 | 4.0 | 88.66
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.071678 | 0.13667 | 0.19304 | 11.8 | 10.34
|
||||
Output | 0.0029244 | 0.0031272 | 0.0035112 | 0.4 | 0.24
|
||||
Modify | 0.0016961 | 0.0017477 | 0.0017846 | 0.1 | 0.13
|
||||
Other | | 0.008334 | | | 0.63
|
||||
|
||||
Nlocal: 64 ave 64 max 64 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1265 ave 1265 max 1265 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 9328 ave 9328 max 9328 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 23648 ave 23648 max 23648 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 94592
|
||||
Ave neighs/atom = 369.5
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:01
|
||||
@ -0,0 +1,210 @@
|
||||
LAMMPS (30 Apr 2019)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Initialization
|
||||
units metal
|
||||
boundary p p p
|
||||
atom_style atomic
|
||||
processors * * 1 # domain decomposition over x and y
|
||||
|
||||
# System and atom definition
|
||||
# we use 2 atom types so that inter- and intra-layer
|
||||
# interactions can be specified separately
|
||||
read_data data.bilayer-graphene # read lammps data file
|
||||
orthogonal box = (0 0 -20) to (17.04 19.6761 40)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
256 atoms
|
||||
read_data CPU = 0.000291348 secs
|
||||
mass 1 12.0107 # carbon mass (g/mole) | membrane
|
||||
mass 2 12.0107 # carbon mass (g/mole) | adsorbate
|
||||
# Neighbor update settings
|
||||
neighbor 2.0 bin
|
||||
neigh_modify every 1
|
||||
neigh_modify delay 0
|
||||
neigh_modify check yes
|
||||
# Separate atom groups
|
||||
group membrane type 1
|
||||
128 atoms in group membrane
|
||||
group adsorbant type 2
|
||||
128 atoms in group adsorbant
|
||||
|
||||
######################## Potential defition ########################
|
||||
pair_style hybrid/overlay rebo kolmogorov/crespi/z 14.0
|
||||
####################################################################
|
||||
pair_coeff * * rebo CH.rebo C C # chemical
|
||||
Reading potential file CH.rebo with DATE: 2018-7-3
|
||||
pair_coeff 1 2 kolmogorov/crespi/z CC.KC C C # long-range
|
||||
####################################################################
|
||||
|
||||
#### Simulation settings ####
|
||||
timestep 0.0001
|
||||
velocity all create 300.0 12345
|
||||
fix thermostat all nve
|
||||
compute COM1 membrane com
|
||||
compute COM2 adsorbant com
|
||||
############################
|
||||
|
||||
# Output
|
||||
#dump 1 all xyz 100 trajec.xyz
|
||||
#dump_modify 1 format line "%s %12.6f %12.6f %12.6f" element "C" "C"
|
||||
thermo 10
|
||||
thermo_style custom step time etotal pe temp c_COM1[3] c_COM2[3] # spcpu
|
||||
thermo_modify line one format float %14.8f
|
||||
|
||||
###### Run molecular dynamics ######
|
||||
run 1000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 16
|
||||
ghost atom cutoff = 16
|
||||
binsize = 8, bins = 3 3 8
|
||||
3 neighbor lists, perpetual/occasional/extra = 3 0 0
|
||||
(1) pair rebo, perpetual
|
||||
attributes: full, newton on, ghost
|
||||
pair build: full/bin/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) pair kolmogorov/crespi/z, perpetual, skip from (3)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) neighbor class addition, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.998 | 4.998 | 4.998 Mbytes
|
||||
Step Time TotEng PotEng Temp c_COM1[3] c_COM2[3]
|
||||
0 0.00000000 -1888.67041233 -1898.55881343 300.00000000 0.00000000 3.30000000
|
||||
10 0.00100000 -1888.67037240 -1898.21029916 289.42778520 -0.00020126 3.30020126
|
||||
20 0.00200000 -1888.67021561 -1897.22943631 259.67456089 -0.00041357 3.30041357
|
||||
30 0.00300000 -1888.66999327 -1895.86681330 218.34126559 -0.00063673 3.30063673
|
||||
40 0.00400000 -1888.66978373 -1894.47163849 176.02000692 -0.00087055 3.30087055
|
||||
50 0.00500000 -1888.66966087 -1893.37123396 142.63902861 -0.00111486 3.30111486
|
||||
60 0.00600000 -1888.66966151 -1892.75822768 124.04127204 -0.00136952 3.30136952
|
||||
70 0.00700000 -1888.66976993 -1892.63445770 120.28297806 -0.00163441 3.30163441
|
||||
80 0.00800000 -1888.66992887 -1892.83467481 126.35245790 -0.00190946 3.30190946
|
||||
90 0.00900000 -1888.67006887 -1893.11387088 134.81862143 -0.00219458 3.30219458
|
||||
100 0.01000000 -1888.67013641 -1893.25481870 139.09272852 -0.00248973 3.30248973
|
||||
110 0.01100000 -1888.67011221 -1893.15155809 135.96068294 -0.00279489 3.30279489
|
||||
120 0.01200000 -1888.67001516 -1892.84002980 126.51230266 -0.00311004 3.30311004
|
||||
130 0.01300000 -1888.66989017 -1892.47004258 115.29120969 -0.00343519 3.30343519
|
||||
140 0.01400000 -1888.66979250 -1892.23503136 108.16426724 -0.00377038 3.30377038
|
||||
150 0.01500000 -1888.66976498 -1892.28630603 109.72070258 -0.00411562 3.30411562
|
||||
160 0.01600000 -1888.66982073 -1892.66640631 121.25071190 -0.00447099 3.30447099
|
||||
170 0.01700000 -1888.66993810 -1893.28862656 140.12442720 -0.00483654 3.30483654
|
||||
180 0.01800000 -1888.67007037 -1893.97029277 160.80119589 -0.00521235 3.30521235
|
||||
190 0.01900000 -1888.67016732 -1894.50458806 177.00801243 -0.00559851 3.30559851
|
||||
200 0.02000000 -1888.67019479 -1894.73890125 184.11590729 -0.00599512 3.30599512
|
||||
210 0.02100000 -1888.67014440 -1894.62906034 180.78501933 -0.00640230 3.30640230
|
||||
220 0.02200000 -1888.67003699 -1894.25249122 169.36370739 -0.00682016 3.30682016
|
||||
230 0.02300000 -1888.66991405 -1893.77601632 154.91186768 -0.00724883 3.30724883
|
||||
240 0.02400000 -1888.66982545 -1893.38995103 143.20188490 -0.00768845 3.30768845
|
||||
250 0.02500000 -1888.66980650 -1893.23138955 138.39193054 -0.00813913 3.30813913
|
||||
260 0.02600000 -1888.66986149 -1893.32993943 141.38012473 -0.00860097 3.30860097
|
||||
270 0.02700000 -1888.66996324 -1893.60070625 149.59171759 -0.00907408 3.30907408
|
||||
280 0.02800000 -1888.67006705 -1893.88587245 158.24010430 -0.00955849 3.30955849
|
||||
290 0.02900000 -1888.67013001 -1894.02402688 162.42960290 -0.01005424 3.31005424
|
||||
300 0.03000000 -1888.67012741 -1893.91715254 159.18726627 -0.01056129 3.31056129
|
||||
310 0.03100000 -1888.67005750 -1893.57037262 148.66857854 -0.01107957 3.31107957
|
||||
320 0.03200000 -1888.66994592 -1893.09358639 134.20694885 -0.01160898 3.31160898
|
||||
330 0.03300000 -1888.66983608 -1892.66132683 121.09614209 -0.01214935 3.31214935
|
||||
340 0.03400000 -1888.66977429 -1892.44446364 114.51869677 -0.01270046 3.31270046
|
||||
350 0.03500000 -1888.66978845 -1892.53901254 117.38674604 -0.01326207 3.31326207
|
||||
360 0.03600000 -1888.66987459 -1892.92337308 129.04508370 -0.01383390 3.31383390
|
||||
370 0.03700000 -1888.66999819 -1893.46445589 145.45701553 -0.01441561 3.31441561
|
||||
380 0.03800000 -1888.67010979 -1893.97065536 160.81100019 -0.01500688 3.31500688
|
||||
390 0.03900000 -1888.67016559 -1894.26835837 169.84119248 -0.01560734 3.31560734
|
||||
400 0.04000000 -1888.67014686 -1894.26967995 169.88185548 -0.01621664 3.31621664
|
||||
410 0.04100000 -1888.67006186 -1894.00321089 161.80014284 -0.01683442 3.31683442
|
||||
420 0.04200000 -1888.66994386 -1893.60086344 149.59707422 -0.01746033 3.31746033
|
||||
430 0.04300000 -1888.66984078 -1893.24559860 138.82197278 -0.01809405 3.31809405
|
||||
440 0.04400000 -1888.66979419 -1893.09727893 134.32357877 -0.01873527 3.31873527
|
||||
450 0.04500000 -1888.66982159 -1893.22837461 138.30000376 -0.01938373 3.31938373
|
||||
460 0.04600000 -1888.66990991 -1893.59670402 149.47191350 -0.02003918 3.32003918
|
||||
470 0.04700000 -1888.67002193 -1894.06542618 163.68887740 -0.02070143 3.32070143
|
||||
480 0.04800000 -1888.67011408 -1894.46010861 175.66018436 -0.02137030 3.32137030
|
||||
490 0.04900000 -1888.67015195 -1894.63688117 181.02206322 -0.02204565 3.32204565
|
||||
500 0.05000000 -1888.67012178 -1894.53632241 177.97216884 -0.02272740 3.32272740
|
||||
510 0.05100000 -1888.67003782 -1894.20444750 167.90610440 -0.02341547 3.32341547
|
||||
520 0.05200000 -1888.66993171 -1893.77231086 154.79891357 -0.02410981 3.32410981
|
||||
530 0.05300000 -1888.66984524 -1893.40525947 143.66572040 -0.02481040 3.32481040
|
||||
540 0.05400000 -1888.66981428 -1893.23762103 138.58074854 -0.02551724 3.32551724
|
||||
550 0.05500000 -1888.66985024 -1893.31793613 141.01630314 -0.02623032 3.32623032
|
||||
560 0.05600000 -1888.66993756 -1893.59069032 149.28862746 -0.02694963 3.32694963
|
||||
570 0.05700000 -1888.67003871 -1893.92089591 159.30352583 -0.02767517 3.32767517
|
||||
580 0.05800000 -1888.67011342 -1894.15124772 166.28980520 -0.02840691 3.32840691
|
||||
590 0.05900000 -1888.67013211 -1894.16548061 166.72104344 -0.02914478 3.32914478
|
||||
600 0.06000000 -1888.67008732 -1893.93443338 159.71275857 -0.02988871 3.32988871
|
||||
610 0.06100000 -1888.66999458 -1893.52841675 147.39760649 -0.03063856 3.33063856
|
||||
620 0.06200000 -1888.66988829 -1893.09235041 134.17119966 -0.03139416 3.33139416
|
||||
630 0.06300000 -1888.66981016 -1892.79172036 125.05288241 -0.03215531 3.33215531
|
||||
640 0.06400000 -1888.66979281 -1892.74755409 123.71346729 -0.03292176 3.33292176
|
||||
650 0.06500000 -1888.66984352 -1892.98665478 130.96590321 -0.03369323 3.33369323
|
||||
660 0.06600000 -1888.66994264 -1893.42999887 144.41332385 -0.03446937 3.33446937
|
||||
670 0.06700000 -1888.67005253 -1893.92310700 159.37018803 -0.03524986 3.33524986
|
||||
680 0.06800000 -1888.67013328 -1894.29451600 170.63575807 -0.03603430 3.33603430
|
||||
690 0.06900000 -1888.67015472 -1894.41878137 174.40514195 -0.03682229 3.33682229
|
||||
700 0.07000000 -1888.67010916 -1894.26288055 169.67671536 -0.03761343 3.33761343
|
||||
710 0.07100000 -1888.67001386 -1893.89812923 158.61357122 -0.03840729 3.33840729
|
||||
720 0.07200000 -1888.66990397 -1893.47348765 145.73388461 -0.03920344 3.33920344
|
||||
730 0.07300000 -1888.66982231 -1893.15984859 136.22099965 -0.04000148 3.34000148
|
||||
740 0.07400000 -1888.66980129 -1893.08373765 133.91254030 -0.04080098 3.34080098
|
||||
750 0.07500000 -1888.66984814 -1893.27755530 139.79127022 -0.04160156 3.34160156
|
||||
760 0.07600000 -1888.66994235 -1893.66837384 151.64528962 -0.04240282 3.34240282
|
||||
770 0.07700000 -1888.67004573 -1894.10941225 165.02263022 -0.04320441 3.34320441
|
||||
780 0.07800000 -1888.67011722 -1894.43947564 175.03411433 -0.04400599 3.34400599
|
||||
790 0.07900000 -1888.67013317 -1894.54590490 178.26254255 -0.04480726 3.34480726
|
||||
800 0.08000000 -1888.67008771 -1894.40384162 173.95392409 -0.04560792 3.34560792
|
||||
810 0.08100000 -1888.66999942 -1894.08389023 164.24973325 -0.04640773 3.34640773
|
||||
820 0.08200000 -1888.66990467 -1893.72313999 153.30795968 -0.04720647 3.34720647
|
||||
830 0.08300000 -1888.66984387 -1893.46839210 145.58111627 -0.04800393 3.34800393
|
||||
840 0.08400000 -1888.66984175 -1893.41412556 143.93481091 -0.04879995 3.34879995
|
||||
850 0.08500000 -1888.66989690 -1893.56426173 148.48805548 -0.04959439 3.34959439
|
||||
860 0.08600000 -1888.66998242 -1893.83463738 156.68827289 -0.05038713 3.35038713
|
||||
870 0.08700000 -1888.67006191 -1894.09325064 164.53181916 -0.05117805 3.35117805
|
||||
880 0.08800000 -1888.67010292 -1894.21712680 168.28880099 -0.05196706 3.35196706
|
||||
890 0.08900000 -1888.67009013 -1894.14263970 166.02935659 -0.05275408 3.35275408
|
||||
900 0.09000000 -1888.67002911 -1893.89014590 158.37090593 -0.05353904 3.35353904
|
||||
910 0.09100000 -1888.66994346 -1893.55535729 148.21649476 -0.05432186 3.35432186
|
||||
920 0.09200000 -1888.66986545 -1893.27257968 139.63979183 -0.05510247 3.35510247
|
||||
930 0.09300000 -1888.66982750 -1893.16330910 136.32582951 -0.05588078 3.35588078
|
||||
940 0.09400000 -1888.66984650 -1893.28643304 140.06065783 -0.05665670 3.35665670
|
||||
950 0.09500000 -1888.66991522 -1893.61245361 149.94957262 -0.05743015 3.35743015
|
||||
960 0.09600000 -1888.67000710 -1894.03423941 162.74316510 -0.05820101 3.35820101
|
||||
970 0.09700000 -1888.67008668 -1894.40848044 174.09469033 -0.05896915 3.35896915
|
||||
980 0.09800000 -1888.67012456 -1894.61056787 180.22458605 -0.05973444 3.35973444
|
||||
990 0.09900000 -1888.67010627 -1894.58107679 179.33042341 -0.06049672 3.36049672
|
||||
1000 0.10000000 -1888.67004000 -1894.34773324 172.25312335 -0.06125581 3.36125581
|
||||
Loop time of 2.60456 on 1 procs for 1000 steps with 256 atoms
|
||||
|
||||
Performance: 3.317 ns/day, 7.235 hours/ns, 383.942 timesteps/s
|
||||
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.5864 | 2.5864 | 2.5864 | 0.0 | 99.30
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0079134 | 0.0079134 | 0.0079134 | 0.0 | 0.30
|
||||
Output | 0.0027175 | 0.0027175 | 0.0027175 | 0.0 | 0.10
|
||||
Modify | 0.00419 | 0.00419 | 0.00419 | 0.0 | 0.16
|
||||
Other | | 0.00331 | | | 0.13
|
||||
|
||||
Nlocal: 256 ave 256 max 256 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1721 ave 1721 max 1721 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 37312 ave 37312 max 37312 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 94592 ave 94592 max 94592 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 94592
|
||||
Ave neighs/atom = 369.5
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:02
|
||||
@ -0,0 +1,210 @@
|
||||
LAMMPS (30 Apr 2019)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Initialization
|
||||
units metal
|
||||
boundary p p p
|
||||
atom_style atomic
|
||||
processors * * 1 # domain decomposition over x and y
|
||||
|
||||
# System and atom definition
|
||||
# we use 2 atom types so that inter- and intra-layer
|
||||
# interactions can be specified separately
|
||||
read_data data.bilayer-graphene # read lammps data file
|
||||
orthogonal box = (0 0 -20) to (17.04 19.6761 40)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
256 atoms
|
||||
read_data CPU = 0.0488505 secs
|
||||
mass 1 12.0107 # carbon mass (g/mole) | membrane
|
||||
mass 2 12.0107 # carbon mass (g/mole) | adsorbate
|
||||
# Neighbor update settings
|
||||
neighbor 2.0 bin
|
||||
neigh_modify every 1
|
||||
neigh_modify delay 0
|
||||
neigh_modify check yes
|
||||
# Separate atom groups
|
||||
group membrane type 1
|
||||
128 atoms in group membrane
|
||||
group adsorbant type 2
|
||||
128 atoms in group adsorbant
|
||||
|
||||
######################## Potential defition ########################
|
||||
pair_style hybrid/overlay rebo kolmogorov/crespi/z 14.0
|
||||
####################################################################
|
||||
pair_coeff * * rebo CH.rebo C C # chemical
|
||||
Reading potential file CH.rebo with DATE: 2018-7-3
|
||||
pair_coeff 1 2 kolmogorov/crespi/z CC.KC C C # long-range
|
||||
####################################################################
|
||||
|
||||
#### Simulation settings ####
|
||||
timestep 0.0001
|
||||
velocity all create 300.0 12345
|
||||
fix thermostat all nve
|
||||
compute COM1 membrane com
|
||||
compute COM2 adsorbant com
|
||||
############################
|
||||
|
||||
# Output
|
||||
#dump 1 all xyz 100 trajec.xyz
|
||||
#dump_modify 1 format line "%s %12.6f %12.6f %12.6f" element "C" "C"
|
||||
thermo 10
|
||||
thermo_style custom step time etotal pe temp c_COM1[3] c_COM2[3] # spcpu
|
||||
thermo_modify line one format float %14.8f
|
||||
|
||||
###### Run molecular dynamics ######
|
||||
run 1000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 16
|
||||
ghost atom cutoff = 16
|
||||
binsize = 8, bins = 3 3 8
|
||||
3 neighbor lists, perpetual/occasional/extra = 3 0 0
|
||||
(1) pair rebo, perpetual
|
||||
attributes: full, newton on, ghost
|
||||
pair build: full/bin/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) pair kolmogorov/crespi/z, perpetual, skip from (3)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) neighbor class addition, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.572 | 4.572 | 4.572 Mbytes
|
||||
Step Time TotEng PotEng Temp c_COM1[3] c_COM2[3]
|
||||
0 0.00000000 -1888.67041233 -1898.55881343 300.00000000 0.00000000 3.30000000
|
||||
10 0.00100000 -1888.67037240 -1898.21029916 289.42778520 -0.00020126 3.30020126
|
||||
20 0.00200000 -1888.67021561 -1897.22943631 259.67456089 -0.00041357 3.30041357
|
||||
30 0.00300000 -1888.66999327 -1895.86681330 218.34126559 -0.00063673 3.30063673
|
||||
40 0.00400000 -1888.66978373 -1894.47163849 176.02000692 -0.00087055 3.30087055
|
||||
50 0.00500000 -1888.66966087 -1893.37123396 142.63902861 -0.00111486 3.30111486
|
||||
60 0.00600000 -1888.66966151 -1892.75822768 124.04127204 -0.00136952 3.30136952
|
||||
70 0.00700000 -1888.66976993 -1892.63445770 120.28297806 -0.00163441 3.30163441
|
||||
80 0.00800000 -1888.66992887 -1892.83467481 126.35245790 -0.00190946 3.30190946
|
||||
90 0.00900000 -1888.67006887 -1893.11387088 134.81862143 -0.00219458 3.30219458
|
||||
100 0.01000000 -1888.67013641 -1893.25481870 139.09272852 -0.00248973 3.30248973
|
||||
110 0.01100000 -1888.67011221 -1893.15155809 135.96068294 -0.00279489 3.30279489
|
||||
120 0.01200000 -1888.67001516 -1892.84002980 126.51230266 -0.00311004 3.30311004
|
||||
130 0.01300000 -1888.66989017 -1892.47004258 115.29120969 -0.00343519 3.30343519
|
||||
140 0.01400000 -1888.66979250 -1892.23503136 108.16426724 -0.00377038 3.30377038
|
||||
150 0.01500000 -1888.66976498 -1892.28630603 109.72070258 -0.00411562 3.30411562
|
||||
160 0.01600000 -1888.66982073 -1892.66640631 121.25071190 -0.00447099 3.30447099
|
||||
170 0.01700000 -1888.66993810 -1893.28862656 140.12442720 -0.00483654 3.30483654
|
||||
180 0.01800000 -1888.67007037 -1893.97029277 160.80119589 -0.00521235 3.30521235
|
||||
190 0.01900000 -1888.67016732 -1894.50458806 177.00801243 -0.00559851 3.30559851
|
||||
200 0.02000000 -1888.67019479 -1894.73890125 184.11590729 -0.00599512 3.30599512
|
||||
210 0.02100000 -1888.67014440 -1894.62906034 180.78501933 -0.00640230 3.30640230
|
||||
220 0.02200000 -1888.67003699 -1894.25249122 169.36370739 -0.00682016 3.30682016
|
||||
230 0.02300000 -1888.66991405 -1893.77601632 154.91186768 -0.00724883 3.30724883
|
||||
240 0.02400000 -1888.66982545 -1893.38995103 143.20188490 -0.00768845 3.30768845
|
||||
250 0.02500000 -1888.66980650 -1893.23138955 138.39193054 -0.00813913 3.30813913
|
||||
260 0.02600000 -1888.66986149 -1893.32993943 141.38012473 -0.00860097 3.30860097
|
||||
270 0.02700000 -1888.66996324 -1893.60070625 149.59171759 -0.00907408 3.30907408
|
||||
280 0.02800000 -1888.67006705 -1893.88587245 158.24010430 -0.00955849 3.30955849
|
||||
290 0.02900000 -1888.67013001 -1894.02402688 162.42960290 -0.01005424 3.31005424
|
||||
300 0.03000000 -1888.67012741 -1893.91715254 159.18726627 -0.01056129 3.31056129
|
||||
310 0.03100000 -1888.67005750 -1893.57037262 148.66857854 -0.01107957 3.31107957
|
||||
320 0.03200000 -1888.66994592 -1893.09358639 134.20694885 -0.01160898 3.31160898
|
||||
330 0.03300000 -1888.66983608 -1892.66132683 121.09614209 -0.01214935 3.31214935
|
||||
340 0.03400000 -1888.66977429 -1892.44446364 114.51869677 -0.01270046 3.31270046
|
||||
350 0.03500000 -1888.66978845 -1892.53901254 117.38674604 -0.01326207 3.31326207
|
||||
360 0.03600000 -1888.66987459 -1892.92337308 129.04508370 -0.01383390 3.31383390
|
||||
370 0.03700000 -1888.66999819 -1893.46445589 145.45701553 -0.01441561 3.31441561
|
||||
380 0.03800000 -1888.67010979 -1893.97065536 160.81100019 -0.01500688 3.31500688
|
||||
390 0.03900000 -1888.67016559 -1894.26835837 169.84119248 -0.01560734 3.31560734
|
||||
400 0.04000000 -1888.67014686 -1894.26967995 169.88185548 -0.01621664 3.31621664
|
||||
410 0.04100000 -1888.67006186 -1894.00321089 161.80014284 -0.01683442 3.31683442
|
||||
420 0.04200000 -1888.66994386 -1893.60086344 149.59707422 -0.01746033 3.31746033
|
||||
430 0.04300000 -1888.66984078 -1893.24559860 138.82197278 -0.01809405 3.31809405
|
||||
440 0.04400000 -1888.66979419 -1893.09727893 134.32357877 -0.01873527 3.31873527
|
||||
450 0.04500000 -1888.66982159 -1893.22837461 138.30000376 -0.01938373 3.31938373
|
||||
460 0.04600000 -1888.66990991 -1893.59670402 149.47191350 -0.02003918 3.32003918
|
||||
470 0.04700000 -1888.67002193 -1894.06542618 163.68887740 -0.02070143 3.32070143
|
||||
480 0.04800000 -1888.67011408 -1894.46010861 175.66018436 -0.02137030 3.32137030
|
||||
490 0.04900000 -1888.67015195 -1894.63688117 181.02206322 -0.02204565 3.32204565
|
||||
500 0.05000000 -1888.67012178 -1894.53632241 177.97216884 -0.02272740 3.32272740
|
||||
510 0.05100000 -1888.67003782 -1894.20444750 167.90610440 -0.02341547 3.32341547
|
||||
520 0.05200000 -1888.66993171 -1893.77231086 154.79891357 -0.02410981 3.32410981
|
||||
530 0.05300000 -1888.66984524 -1893.40525947 143.66572040 -0.02481040 3.32481040
|
||||
540 0.05400000 -1888.66981428 -1893.23762103 138.58074854 -0.02551724 3.32551724
|
||||
550 0.05500000 -1888.66985024 -1893.31793613 141.01630314 -0.02623032 3.32623032
|
||||
560 0.05600000 -1888.66993756 -1893.59069032 149.28862746 -0.02694963 3.32694963
|
||||
570 0.05700000 -1888.67003871 -1893.92089591 159.30352583 -0.02767517 3.32767517
|
||||
580 0.05800000 -1888.67011342 -1894.15124772 166.28980520 -0.02840691 3.32840691
|
||||
590 0.05900000 -1888.67013211 -1894.16548061 166.72104344 -0.02914478 3.32914478
|
||||
600 0.06000000 -1888.67008732 -1893.93443338 159.71275857 -0.02988871 3.32988871
|
||||
610 0.06100000 -1888.66999458 -1893.52841675 147.39760649 -0.03063856 3.33063856
|
||||
620 0.06200000 -1888.66988829 -1893.09235041 134.17119966 -0.03139416 3.33139416
|
||||
630 0.06300000 -1888.66981016 -1892.79172036 125.05288241 -0.03215531 3.33215531
|
||||
640 0.06400000 -1888.66979281 -1892.74755409 123.71346729 -0.03292176 3.33292176
|
||||
650 0.06500000 -1888.66984352 -1892.98665478 130.96590321 -0.03369323 3.33369323
|
||||
660 0.06600000 -1888.66994264 -1893.42999887 144.41332385 -0.03446937 3.33446937
|
||||
670 0.06700000 -1888.67005253 -1893.92310700 159.37018803 -0.03524986 3.33524986
|
||||
680 0.06800000 -1888.67013328 -1894.29451600 170.63575807 -0.03603430 3.33603430
|
||||
690 0.06900000 -1888.67015472 -1894.41878137 174.40514195 -0.03682229 3.33682229
|
||||
700 0.07000000 -1888.67010916 -1894.26288055 169.67671536 -0.03761343 3.33761343
|
||||
710 0.07100000 -1888.67001386 -1893.89812923 158.61357122 -0.03840729 3.33840729
|
||||
720 0.07200000 -1888.66990397 -1893.47348765 145.73388461 -0.03920344 3.33920344
|
||||
730 0.07300000 -1888.66982231 -1893.15984859 136.22099965 -0.04000148 3.34000148
|
||||
740 0.07400000 -1888.66980129 -1893.08373765 133.91254030 -0.04080098 3.34080098
|
||||
750 0.07500000 -1888.66984814 -1893.27755530 139.79127022 -0.04160156 3.34160156
|
||||
760 0.07600000 -1888.66994235 -1893.66837384 151.64528962 -0.04240282 3.34240282
|
||||
770 0.07700000 -1888.67004573 -1894.10941225 165.02263022 -0.04320441 3.34320441
|
||||
780 0.07800000 -1888.67011722 -1894.43947564 175.03411433 -0.04400599 3.34400599
|
||||
790 0.07900000 -1888.67013317 -1894.54590490 178.26254255 -0.04480726 3.34480726
|
||||
800 0.08000000 -1888.67008771 -1894.40384162 173.95392409 -0.04560792 3.34560792
|
||||
810 0.08100000 -1888.66999942 -1894.08389023 164.24973325 -0.04640773 3.34640773
|
||||
820 0.08200000 -1888.66990467 -1893.72313999 153.30795968 -0.04720647 3.34720647
|
||||
830 0.08300000 -1888.66984387 -1893.46839210 145.58111627 -0.04800393 3.34800393
|
||||
840 0.08400000 -1888.66984175 -1893.41412556 143.93481091 -0.04879995 3.34879995
|
||||
850 0.08500000 -1888.66989690 -1893.56426173 148.48805548 -0.04959439 3.34959439
|
||||
860 0.08600000 -1888.66998242 -1893.83463738 156.68827289 -0.05038713 3.35038713
|
||||
870 0.08700000 -1888.67006191 -1894.09325064 164.53181916 -0.05117805 3.35117805
|
||||
880 0.08800000 -1888.67010292 -1894.21712680 168.28880099 -0.05196706 3.35196706
|
||||
890 0.08900000 -1888.67009013 -1894.14263970 166.02935659 -0.05275408 3.35275408
|
||||
900 0.09000000 -1888.67002911 -1893.89014590 158.37090593 -0.05353904 3.35353904
|
||||
910 0.09100000 -1888.66994346 -1893.55535729 148.21649476 -0.05432186 3.35432186
|
||||
920 0.09200000 -1888.66986545 -1893.27257968 139.63979183 -0.05510247 3.35510247
|
||||
930 0.09300000 -1888.66982750 -1893.16330910 136.32582951 -0.05588078 3.35588078
|
||||
940 0.09400000 -1888.66984650 -1893.28643304 140.06065783 -0.05665670 3.35665670
|
||||
950 0.09500000 -1888.66991522 -1893.61245361 149.94957262 -0.05743015 3.35743015
|
||||
960 0.09600000 -1888.67000710 -1894.03423941 162.74316510 -0.05820101 3.35820101
|
||||
970 0.09700000 -1888.67008668 -1894.40848044 174.09469033 -0.05896915 3.35896915
|
||||
980 0.09800000 -1888.67012456 -1894.61056787 180.22458605 -0.05973444 3.35973444
|
||||
990 0.09900000 -1888.67010627 -1894.58107679 179.33042341 -0.06049672 3.36049672
|
||||
1000 0.10000000 -1888.67004000 -1894.34773324 172.25312335 -0.06125581 3.36125581
|
||||
Loop time of 1.55992 on 4 procs for 1000 steps with 256 atoms
|
||||
|
||||
Performance: 5.539 ns/day, 4.333 hours/ns, 641.059 timesteps/s
|
||||
96.5% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.3161 | 1.3724 | 1.4128 | 3.0 | 87.98
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.11734 | 0.16017 | 0.21617 | 8.9 | 10.27
|
||||
Output | 0.0032182 | 0.0051764 | 0.010916 | 4.6 | 0.33
|
||||
Modify | 0.0020187 | 0.0022321 | 0.0026002 | 0.5 | 0.14
|
||||
Other | | 0.0199 | | | 1.28
|
||||
|
||||
Nlocal: 64 ave 64 max 64 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1265 ave 1265 max 1265 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 9328 ave 9328 max 9328 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 23648 ave 23648 max 23648 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 94592
|
||||
Ave neighs/atom = 369.5
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:01
|
||||
1
examples/airebo/CH.rebo
Symbolic link
1
examples/airebo/CH.rebo
Symbolic link
@ -0,0 +1 @@
|
||||
../../potentials/CH.rebo
|
||||
22
examples/airebo/in.airebo-0-0
Normal file
22
examples/airebo/in.airebo-0-0
Normal file
@ -0,0 +1,22 @@
|
||||
# AIREBO polyethelene benchmark
|
||||
|
||||
units metal
|
||||
atom_style atomic
|
||||
|
||||
read_data data.airebo
|
||||
|
||||
replicate 17 16 2
|
||||
|
||||
neighbor 0.5 bin
|
||||
neigh_modify delay 5 every 1
|
||||
|
||||
pair_style airebo 3.0 0 0
|
||||
pair_coeff * * CH.airebo C H
|
||||
|
||||
velocity all create 300.0 761341
|
||||
|
||||
fix 1 all nve
|
||||
timestep 0.0005
|
||||
|
||||
thermo 10
|
||||
run 100
|
||||
22
examples/airebo/in.rebo2
Normal file
22
examples/airebo/in.rebo2
Normal file
@ -0,0 +1,22 @@
|
||||
# REBO polyethelene benchmark
|
||||
|
||||
units metal
|
||||
atom_style atomic
|
||||
|
||||
read_data data.airebo
|
||||
|
||||
replicate 17 16 2
|
||||
|
||||
neighbor 0.5 bin
|
||||
neigh_modify delay 5 every 1
|
||||
|
||||
pair_style rebo
|
||||
pair_coeff * * CH.rebo C H
|
||||
|
||||
velocity all create 300.0 761341
|
||||
|
||||
fix 1 all nve
|
||||
timestep 0.0005
|
||||
|
||||
thermo 10
|
||||
run 100
|
||||
89
examples/airebo/log.30Apr2019.airebo-0-0.g++.1
Normal file
89
examples/airebo/log.30Apr2019.airebo-0-0.g++.1
Normal file
@ -0,0 +1,89 @@
|
||||
LAMMPS (30 Apr 2019)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# AIREBO polyethelene benchmark
|
||||
|
||||
units metal
|
||||
atom_style atomic
|
||||
|
||||
read_data data.airebo
|
||||
orthogonal box = (-2.1 -2.1 0) to (2.1 2.1 25.579)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
60 atoms
|
||||
read_data CPU = 0.000232458 secs
|
||||
|
||||
replicate 17 16 2
|
||||
orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
32640 atoms
|
||||
replicate CPU = 0.00206327 secs
|
||||
|
||||
neighbor 0.5 bin
|
||||
neigh_modify delay 5 every 1
|
||||
|
||||
pair_style airebo 3.0 0 0
|
||||
pair_coeff * * CH.airebo C H
|
||||
Reading potential file CH.airebo with DATE: 2011-10-25
|
||||
|
||||
velocity all create 300.0 761341
|
||||
|
||||
fix 1 all nve
|
||||
timestep 0.0005
|
||||
|
||||
thermo 10
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 6.5
|
||||
ghost atom cutoff = 6.5
|
||||
binsize = 3.25, bins = 22 21 16
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair airebo, perpetual
|
||||
attributes: full, newton on, ghost
|
||||
pair build: full/bin/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 34.21 | 34.21 | 34.21 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 300 -138442.83 0 -137177.16 2463.0755
|
||||
10 179.38448 -137931.29 0 -137174.48 15656.69
|
||||
20 206.89283 -138047.06 0 -137174.19 -24047.407
|
||||
30 150.81289 -137807.48 0 -137171.21 -16524.191
|
||||
40 173.24289 -137902.32 0 -137171.42 -5721.7187
|
||||
50 151.80722 -137812.37 0 -137171.91 3489.8954
|
||||
60 199.06038 -138013.7 0 -137173.88 17887.025
|
||||
70 217.84848 -138093.82 0 -137174.73 -12266.16
|
||||
80 202.34667 -138029.28 0 -137175.59 -7623.6634
|
||||
90 194.92367 -137997.12 0 -137174.75 -32277.173
|
||||
100 185.2078 -137954.64 0 -137173.26 -6888.5104
|
||||
Loop time of 9.70367 on 1 procs for 100 steps with 32640 atoms
|
||||
|
||||
Performance: 0.445 ns/day, 53.909 hours/ns, 10.305 timesteps/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 | 7.2508 | 7.2508 | 7.2508 | 0.0 | 74.72
|
||||
Neigh | 2.3573 | 2.3573 | 2.3573 | 0.0 | 24.29
|
||||
Comm | 0.03116 | 0.03116 | 0.03116 | 0.0 | 0.32
|
||||
Output | 0.0014739 | 0.0014739 | 0.0014739 | 0.0 | 0.02
|
||||
Modify | 0.0447 | 0.0447 | 0.0447 | 0.0 | 0.46
|
||||
Other | | 0.01819 | | | 0.19
|
||||
|
||||
Nlocal: 32640 ave 32640 max 32640 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 26460 ave 26460 max 26460 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 4.90213e+06 ave 4.90213e+06 max 4.90213e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 4902134
|
||||
Ave neighs/atom = 150.188
|
||||
Neighbor list builds = 9
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:10
|
||||
89
examples/airebo/log.30Apr2019.airebo-0-0.g++.4
Normal file
89
examples/airebo/log.30Apr2019.airebo-0-0.g++.4
Normal file
@ -0,0 +1,89 @@
|
||||
LAMMPS (30 Apr 2019)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# AIREBO polyethelene benchmark
|
||||
|
||||
units metal
|
||||
atom_style atomic
|
||||
|
||||
read_data data.airebo
|
||||
orthogonal box = (-2.1 -2.1 0) to (2.1 2.1 25.579)
|
||||
1 by 1 by 4 MPI processor grid
|
||||
reading atoms ...
|
||||
60 atoms
|
||||
read_data CPU = 0.000363827 secs
|
||||
|
||||
replicate 17 16 2
|
||||
orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
32640 atoms
|
||||
replicate CPU = 0.00244427 secs
|
||||
|
||||
neighbor 0.5 bin
|
||||
neigh_modify delay 5 every 1
|
||||
|
||||
pair_style airebo 3.0 0 0
|
||||
pair_coeff * * CH.airebo C H
|
||||
Reading potential file CH.airebo with DATE: 2011-10-25
|
||||
|
||||
velocity all create 300.0 761341
|
||||
|
||||
fix 1 all nve
|
||||
timestep 0.0005
|
||||
|
||||
thermo 10
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 6.5
|
||||
ghost atom cutoff = 6.5
|
||||
binsize = 3.25, bins = 22 21 16
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair airebo, perpetual
|
||||
attributes: full, newton on, ghost
|
||||
pair build: full/bin/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 11.75 | 11.94 | 12.13 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 300 -138442.83 0 -137177.16 2463.0755
|
||||
10 179.38448 -137931.29 0 -137174.48 15656.69
|
||||
20 206.89283 -138047.06 0 -137174.19 -24047.407
|
||||
30 150.81289 -137807.48 0 -137171.21 -16524.191
|
||||
40 173.24289 -137902.32 0 -137171.42 -5721.7187
|
||||
50 151.80722 -137812.37 0 -137171.91 3489.8954
|
||||
60 199.06038 -138013.7 0 -137173.88 17887.025
|
||||
70 217.84848 -138093.82 0 -137174.73 -12266.16
|
||||
80 202.34667 -138029.28 0 -137175.59 -7623.6634
|
||||
90 194.92367 -137997.12 0 -137174.75 -32277.173
|
||||
100 185.2078 -137954.64 0 -137173.26 -6888.5104
|
||||
Loop time of 6.71962 on 4 procs for 100 steps with 32640 atoms
|
||||
|
||||
Performance: 0.643 ns/day, 37.331 hours/ns, 14.882 timesteps/s
|
||||
96.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 4.4598 | 4.6375 | 4.7708 | 5.5 | 69.01
|
||||
Neigh | 1.5903 | 1.6452 | 1.7207 | 3.8 | 24.48
|
||||
Comm | 0.16708 | 0.37041 | 0.56709 | 25.1 | 5.51
|
||||
Output | 0.001061 | 0.0059808 | 0.0090635 | 4.3 | 0.09
|
||||
Modify | 0.030086 | 0.03154 | 0.032522 | 0.5 | 0.47
|
||||
Other | | 0.02897 | | | 0.43
|
||||
|
||||
Nlocal: 8160 ave 8163 max 8157 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 1 1
|
||||
Nghost: 11605.8 ave 11615 max 11593 min
|
||||
Histogram: 1 0 0 0 0 0 2 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 1.22553e+06 ave 1.22734e+06 max 1.22455e+06 min
|
||||
Histogram: 2 0 0 1 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 4902134
|
||||
Ave neighs/atom = 150.188
|
||||
Neighbor list builds = 9
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:07
|
||||
@ -1,36 +1,38 @@
|
||||
LAMMPS (27 Nov 2018)
|
||||
LAMMPS (30 Apr 2019)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# AIREBO polyethelene benchmark
|
||||
|
||||
units metal
|
||||
atom_style atomic
|
||||
units metal
|
||||
atom_style atomic
|
||||
|
||||
read_data data.airebo
|
||||
read_data data.airebo
|
||||
orthogonal box = (-2.1 -2.1 0) to (2.1 2.1 25.579)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
60 atoms
|
||||
read_data CPU = 0.000225067 secs
|
||||
|
||||
replicate 17 16 2
|
||||
replicate 17 16 2
|
||||
orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
32640 atoms
|
||||
Time spent = 0.00141144 secs
|
||||
replicate CPU = 0.00226521 secs
|
||||
|
||||
neighbor 0.5 bin
|
||||
neigh_modify delay 5 every 1
|
||||
neighbor 0.5 bin
|
||||
neigh_modify delay 5 every 1
|
||||
|
||||
pair_style airebo/morse 3.0 1 1
|
||||
pair_coeff * * ../../potentials/CH.airebo-m C H
|
||||
Reading potential file ../../potentials/CH.airebo-m with DATE: 2016-03-15
|
||||
pair_style airebo/morse 3.0 1 1
|
||||
pair_coeff * * CH.airebo-m C H
|
||||
Reading potential file CH.airebo-m with DATE: 2016-03-15
|
||||
|
||||
velocity all create 300.0 761341
|
||||
velocity all create 300.0 761341
|
||||
|
||||
fix 1 all nve
|
||||
timestep 0.0005
|
||||
fix 1 all nve
|
||||
timestep 0.0005
|
||||
|
||||
thermo 10
|
||||
run 100
|
||||
thermo 10
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
@ -45,7 +47,7 @@ Neighbor list info ...
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 106.4 | 106.4 | 106.4 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 300 -139283.82 0 -138018.14 152.25271
|
||||
0 300 -139283.82 0 -138018.14 152.25266
|
||||
10 166.76148 -138718.75 0 -138015.19 17412.343
|
||||
20 207.7293 -138891.79 0 -138015.4 -19395.339
|
||||
30 138.54469 -138596.42 0 -138011.92 -11909.248
|
||||
@ -55,21 +57,21 @@ Step Temp E_pair E_mol TotEng Press
|
||||
70 185.72779 -138799.18 0 -138015.61 -10803.744
|
||||
80 164.28396 -138709.5 0 -138016.4 -1524.7353
|
||||
90 180.26403 -138776.42 0 -138015.9 -27143.467
|
||||
100 164.05694 -138706.58 0 -138014.44 5157.5516
|
||||
Loop time of 64.6107 on 1 procs for 100 steps with 32640 atoms
|
||||
100 164.05694 -138706.58 0 -138014.44 5157.5517
|
||||
Loop time of 111.537 on 1 procs for 100 steps with 32640 atoms
|
||||
|
||||
Performance: 0.067 ns/day, 358.948 hours/ns, 1.548 timesteps/s
|
||||
Performance: 0.039 ns/day, 619.650 hours/ns, 0.897 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 59.916 | 59.916 | 59.916 | 0.0 | 92.73
|
||||
Neigh | 4.6347 | 4.6347 | 4.6347 | 0.0 | 7.17
|
||||
Comm | 0.025572 | 0.025572 | 0.025572 | 0.0 | 0.04
|
||||
Output | 0.00098896 | 0.00098896 | 0.00098896 | 0.0 | 0.00
|
||||
Modify | 0.022327 | 0.022327 | 0.022327 | 0.0 | 0.03
|
||||
Other | | 0.01076 | | | 0.02
|
||||
Pair | 103.58 | 103.58 | 103.58 | 0.0 | 92.87
|
||||
Neigh | 7.8371 | 7.8371 | 7.8371 | 0.0 | 7.03
|
||||
Comm | 0.046259 | 0.046259 | 0.046259 | 0.0 | 0.04
|
||||
Output | 0.001497 | 0.001497 | 0.001497 | 0.0 | 0.00
|
||||
Modify | 0.047151 | 0.047151 | 0.047151 | 0.0 | 0.04
|
||||
Other | | 0.02204 | | | 0.02
|
||||
|
||||
Nlocal: 32640 ave 32640 max 32640 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
@ -84,4 +86,4 @@ Total # of neighbors = 22210922
|
||||
Ave neighs/atom = 680.482
|
||||
Neighbor list builds = 8
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:01:05
|
||||
Total wall time: 0:01:53
|
||||
@ -1,36 +1,38 @@
|
||||
LAMMPS (27 Nov 2018)
|
||||
LAMMPS (30 Apr 2019)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# AIREBO polyethelene benchmark
|
||||
|
||||
units metal
|
||||
atom_style atomic
|
||||
units metal
|
||||
atom_style atomic
|
||||
|
||||
read_data data.airebo
|
||||
read_data data.airebo
|
||||
orthogonal box = (-2.1 -2.1 0) to (2.1 2.1 25.579)
|
||||
1 by 1 by 4 MPI processor grid
|
||||
reading atoms ...
|
||||
60 atoms
|
||||
read_data CPU = 0.000880957 secs
|
||||
|
||||
replicate 17 16 2
|
||||
replicate 17 16 2
|
||||
orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
32640 atoms
|
||||
Time spent = 0.000637531 secs
|
||||
replicate CPU = 0.00271702 secs
|
||||
|
||||
neighbor 0.5 bin
|
||||
neigh_modify delay 5 every 1
|
||||
neighbor 0.5 bin
|
||||
neigh_modify delay 5 every 1
|
||||
|
||||
pair_style airebo/morse 3.0 1 1
|
||||
pair_coeff * * ../../potentials/CH.airebo-m C H
|
||||
Reading potential file ../../potentials/CH.airebo-m with DATE: 2016-03-15
|
||||
pair_style airebo/morse 3.0 1 1
|
||||
pair_coeff * * CH.airebo-m C H
|
||||
Reading potential file CH.airebo-m with DATE: 2016-03-15
|
||||
|
||||
velocity all create 300.0 761341
|
||||
velocity all create 300.0 761341
|
||||
|
||||
fix 1 all nve
|
||||
timestep 0.0005
|
||||
fix 1 all nve
|
||||
timestep 0.0005
|
||||
|
||||
thermo 10
|
||||
run 100
|
||||
thermo 10
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
@ -45,7 +47,7 @@ Neighbor list info ...
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 29.37 | 29.75 | 30.13 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 300 -139283.82 0 -138018.14 152.25271
|
||||
0 300 -139283.82 0 -138018.14 152.25266
|
||||
10 166.76148 -138718.75 0 -138015.19 17412.343
|
||||
20 207.7293 -138891.79 0 -138015.4 -19395.339
|
||||
30 138.54469 -138596.42 0 -138011.92 -11909.248
|
||||
@ -55,21 +57,21 @@ Step Temp E_pair E_mol TotEng Press
|
||||
70 185.72779 -138799.18 0 -138015.61 -10803.744
|
||||
80 164.28396 -138709.5 0 -138016.4 -1524.7353
|
||||
90 180.26403 -138776.42 0 -138015.9 -27143.467
|
||||
100 164.05694 -138706.58 0 -138014.44 5157.5516
|
||||
Loop time of 18.1922 on 4 procs for 100 steps with 32640 atoms
|
||||
100 164.05694 -138706.58 0 -138014.44 5157.5517
|
||||
Loop time of 68.9923 on 4 procs for 100 steps with 32640 atoms
|
||||
|
||||
Performance: 0.237 ns/day, 101.068 hours/ns, 5.497 timesteps/s
|
||||
98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
Performance: 0.063 ns/day, 383.290 hours/ns, 1.449 timesteps/s
|
||||
96.8% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 15.968 | 16.084 | 16.308 | 3.4 | 88.41
|
||||
Neigh | 1.6017 | 1.6334 | 1.7006 | 3.1 | 8.98
|
||||
Comm | 0.1603 | 0.45122 | 0.59951 | 26.0 | 2.48
|
||||
Output | 0.00042605 | 0.00073195 | 0.0016003 | 0.0 | 0.00
|
||||
Modify | 0.0092106 | 0.010544 | 0.014411 | 2.2 | 0.06
|
||||
Other | | 0.01193 | | | 0.07
|
||||
Pair | 60.09 | 60.276 | 60.515 | 2.1 | 87.37
|
||||
Neigh | 6.7521 | 6.8996 | 7.0678 | 4.3 | 10.00
|
||||
Comm | 1.5441 | 1.7514 | 2.0838 | 16.9 | 2.54
|
||||
Output | 0.0010803 | 0.001972 | 0.0043106 | 3.0 | 0.00
|
||||
Modify | 0.031365 | 0.032539 | 0.034404 | 0.7 | 0.05
|
||||
Other | | 0.03104 | | | 0.04
|
||||
|
||||
Nlocal: 8160 ave 8167 max 8153 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
@ -84,4 +86,4 @@ Total # of neighbors = 22210922
|
||||
Ave neighs/atom = 680.482
|
||||
Neighbor list builds = 8
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:18
|
||||
Total wall time: 0:01:10
|
||||
@ -1,36 +1,38 @@
|
||||
LAMMPS (27 Nov 2018)
|
||||
LAMMPS (30 Apr 2019)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# AIREBO polyethelene benchmark
|
||||
|
||||
units metal
|
||||
atom_style atomic
|
||||
units metal
|
||||
atom_style atomic
|
||||
|
||||
read_data data.airebo
|
||||
read_data data.airebo
|
||||
orthogonal box = (-2.1 -2.1 0) to (2.1 2.1 25.579)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
60 atoms
|
||||
read_data CPU = 0.000217438 secs
|
||||
|
||||
replicate 17 16 2
|
||||
replicate 17 16 2
|
||||
orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
32640 atoms
|
||||
Time spent = 0.00144172 secs
|
||||
replicate CPU = 0.00204968 secs
|
||||
|
||||
neighbor 0.5 bin
|
||||
neigh_modify delay 5 every 1
|
||||
neighbor 0.5 bin
|
||||
neigh_modify delay 5 every 1
|
||||
|
||||
pair_style airebo 3.0 1 1
|
||||
pair_coeff * * ../../potentials/CH.airebo C H
|
||||
Reading potential file ../../potentials/CH.airebo with DATE: 2011-10-25
|
||||
pair_style airebo 3.0 1 1
|
||||
pair_coeff * * CH.airebo C H
|
||||
Reading potential file CH.airebo with DATE: 2011-10-25
|
||||
|
||||
velocity all create 300.0 761341
|
||||
velocity all create 300.0 761341
|
||||
|
||||
fix 1 all nve
|
||||
timestep 0.0005
|
||||
fix 1 all nve
|
||||
timestep 0.0005
|
||||
|
||||
thermo 10
|
||||
run 100
|
||||
thermo 10
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
@ -45,31 +47,31 @@ Neighbor list info ...
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 106.4 | 106.4 | 106.4 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 300 -139300.72 0 -138035.04 7988.6647
|
||||
0 300 -139300.72 0 -138035.04 7988.6646
|
||||
10 161.34683 -138712.9 0 -138032.19 33228.921
|
||||
20 208.59504 -138912.79 0 -138032.74 -3211.8806
|
||||
30 139.7513 -138618.85 0 -138029.25 10878.143
|
||||
40 142.14562 -138629.02 0 -138029.32 14601.302
|
||||
50 114.23401 -138510.95 0 -138029 24691.125
|
||||
50 114.23401 -138510.95 0 -138029 24691.124
|
||||
60 164.92002 -138726 0 -138030.21 35125.541
|
||||
70 162.15256 -138715.9 0 -138031.79 5658.7946
|
||||
80 157.16184 -138695.77 0 -138032.72 19824.698
|
||||
90 196.15907 -138860.65 0 -138033.07 -7950.8462
|
||||
90 196.15907 -138860.65 0 -138033.07 -7950.8463
|
||||
100 178.31875 -138784.89 0 -138032.57 30997.671
|
||||
Loop time of 57.9914 on 1 procs for 100 steps with 32640 atoms
|
||||
Loop time of 98.1502 on 1 procs for 100 steps with 32640 atoms
|
||||
|
||||
Performance: 0.074 ns/day, 322.174 hours/ns, 1.724 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
Performance: 0.044 ns/day, 545.279 hours/ns, 1.019 timesteps/s
|
||||
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 53.275 | 53.275 | 53.275 | 0.0 | 91.87
|
||||
Neigh | 4.6548 | 4.6548 | 4.6548 | 0.0 | 8.03
|
||||
Comm | 0.026622 | 0.026622 | 0.026622 | 0.0 | 0.05
|
||||
Output | 0.00097251 | 0.00097251 | 0.00097251 | 0.0 | 0.00
|
||||
Modify | 0.022773 | 0.022773 | 0.022773 | 0.0 | 0.04
|
||||
Other | | 0.01089 | | | 0.02
|
||||
Pair | 90.237 | 90.237 | 90.237 | 0.0 | 91.94
|
||||
Neigh | 7.796 | 7.796 | 7.796 | 0.0 | 7.94
|
||||
Comm | 0.048884 | 0.048884 | 0.048884 | 0.0 | 0.05
|
||||
Output | 0.0016053 | 0.0016053 | 0.0016053 | 0.0 | 0.00
|
||||
Modify | 0.045511 | 0.045511 | 0.045511 | 0.0 | 0.05
|
||||
Other | | 0.0217 | | | 0.02
|
||||
|
||||
Nlocal: 32640 ave 32640 max 32640 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
@ -84,4 +86,4 @@ Total # of neighbors = 22217840
|
||||
Ave neighs/atom = 680.694
|
||||
Neighbor list builds = 8
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:59
|
||||
Total wall time: 0:01:39
|
||||
@ -1,36 +1,38 @@
|
||||
LAMMPS (27 Nov 2018)
|
||||
LAMMPS (30 Apr 2019)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# AIREBO polyethelene benchmark
|
||||
|
||||
units metal
|
||||
atom_style atomic
|
||||
units metal
|
||||
atom_style atomic
|
||||
|
||||
read_data data.airebo
|
||||
read_data data.airebo
|
||||
orthogonal box = (-2.1 -2.1 0) to (2.1 2.1 25.579)
|
||||
1 by 1 by 4 MPI processor grid
|
||||
reading atoms ...
|
||||
60 atoms
|
||||
read_data CPU = 0.000266314 secs
|
||||
|
||||
replicate 17 16 2
|
||||
replicate 17 16 2
|
||||
orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
32640 atoms
|
||||
Time spent = 0.00262594 secs
|
||||
replicate CPU = 0.00146151 secs
|
||||
|
||||
neighbor 0.5 bin
|
||||
neigh_modify delay 5 every 1
|
||||
neighbor 0.5 bin
|
||||
neigh_modify delay 5 every 1
|
||||
|
||||
pair_style airebo 3.0 1 1
|
||||
pair_coeff * * ../../potentials/CH.airebo C H
|
||||
Reading potential file ../../potentials/CH.airebo with DATE: 2011-10-25
|
||||
pair_style airebo 3.0 1 1
|
||||
pair_coeff * * CH.airebo C H
|
||||
Reading potential file CH.airebo with DATE: 2011-10-25
|
||||
|
||||
velocity all create 300.0 761341
|
||||
velocity all create 300.0 761341
|
||||
|
||||
fix 1 all nve
|
||||
timestep 0.0005
|
||||
fix 1 all nve
|
||||
timestep 0.0005
|
||||
|
||||
thermo 10
|
||||
run 100
|
||||
thermo 10
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
@ -45,31 +47,31 @@ Neighbor list info ...
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 29.37 | 29.75 | 30.13 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 300 -139300.72 0 -138035.04 7988.6647
|
||||
0 300 -139300.72 0 -138035.04 7988.6646
|
||||
10 161.34683 -138712.9 0 -138032.19 33228.921
|
||||
20 208.59504 -138912.79 0 -138032.74 -3211.8806
|
||||
30 139.7513 -138618.85 0 -138029.25 10878.143
|
||||
40 142.14562 -138629.02 0 -138029.32 14601.302
|
||||
50 114.23401 -138510.95 0 -138029 24691.125
|
||||
50 114.23401 -138510.95 0 -138029 24691.124
|
||||
60 164.92002 -138726 0 -138030.21 35125.541
|
||||
70 162.15256 -138715.9 0 -138031.79 5658.7946
|
||||
80 157.16184 -138695.77 0 -138032.72 19824.698
|
||||
90 196.15907 -138860.65 0 -138033.07 -7950.8462
|
||||
90 196.15907 -138860.65 0 -138033.07 -7950.8463
|
||||
100 178.31875 -138784.89 0 -138032.57 30997.671
|
||||
Loop time of 16.4395 on 4 procs for 100 steps with 32640 atoms
|
||||
Loop time of 60.4943 on 4 procs for 100 steps with 32640 atoms
|
||||
|
||||
Performance: 0.263 ns/day, 91.331 hours/ns, 6.083 timesteps/s
|
||||
98.5% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
Performance: 0.071 ns/day, 336.080 hours/ns, 1.653 timesteps/s
|
||||
97.7% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 14.263 | 14.349 | 14.483 | 2.3 | 87.28
|
||||
Neigh | 1.6071 | 1.6283 | 1.6636 | 1.7 | 9.90
|
||||
Comm | 0.26261 | 0.43435 | 0.52323 | 16.1 | 2.64
|
||||
Output | 0.00042105 | 0.0007121 | 0.001538 | 0.0 | 0.00
|
||||
Modify | 0.00898 | 0.009112 | 0.0093675 | 0.2 | 0.06
|
||||
Other | | 0.0184 | | | 0.11
|
||||
Pair | 51.737 | 52.46 | 52.86 | 6.2 | 86.72
|
||||
Neigh | 6.5823 | 6.6605 | 6.726 | 2.0 | 11.01
|
||||
Comm | 0.92426 | 1.3125 | 2.0111 | 37.0 | 2.17
|
||||
Output | 0.0010669 | 0.0019811 | 0.0043974 | 3.1 | 0.00
|
||||
Modify | 0.030364 | 0.031523 | 0.032495 | 0.5 | 0.05
|
||||
Other | | 0.028 | | | 0.05
|
||||
|
||||
Nlocal: 8160 ave 8174 max 8146 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
@ -84,4 +86,4 @@ Total # of neighbors = 22217840
|
||||
Ave neighs/atom = 680.694
|
||||
Neighbor list builds = 8
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:16
|
||||
Total wall time: 0:01:01
|
||||
89
examples/airebo/log.30Apr2019.rebo2.g++.1
Normal file
89
examples/airebo/log.30Apr2019.rebo2.g++.1
Normal file
@ -0,0 +1,89 @@
|
||||
LAMMPS (30 Apr 2019)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# REBO polyethelene benchmark
|
||||
|
||||
units metal
|
||||
atom_style atomic
|
||||
|
||||
read_data data.airebo
|
||||
orthogonal box = (-2.1 -2.1 0) to (2.1 2.1 25.579)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
60 atoms
|
||||
read_data CPU = 0.000190735 secs
|
||||
|
||||
replicate 17 16 2
|
||||
orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
32640 atoms
|
||||
replicate CPU = 0.00197148 secs
|
||||
|
||||
neighbor 0.5 bin
|
||||
neigh_modify delay 5 every 1
|
||||
|
||||
pair_style rebo
|
||||
pair_coeff * * CH.rebo C H
|
||||
Reading potential file CH.rebo with DATE: 2018-7-3
|
||||
|
||||
velocity all create 300.0 761341
|
||||
|
||||
fix 1 all nve
|
||||
timestep 0.0005
|
||||
|
||||
thermo 10
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 6.5
|
||||
ghost atom cutoff = 6.5
|
||||
binsize = 3.25, bins = 22 21 16
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair rebo, perpetual
|
||||
attributes: full, newton on, ghost
|
||||
pair build: full/bin/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 34.21 | 34.21 | 34.21 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 300 -138442.83 0 -137177.16 2463.0748
|
||||
10 179.37985 -137931.27 0 -137174.48 15655.936
|
||||
20 206.87654 -138046.99 0 -137174.19 -24042.627
|
||||
30 150.80122 -137807.43 0 -137171.21 -16524.118
|
||||
40 173.24945 -137902.35 0 -137171.42 -5716.9119
|
||||
50 151.80455 -137812.36 0 -137171.91 3480.4584
|
||||
60 199.08777 -138013.82 0 -137173.88 17881.372
|
||||
70 217.85748 -138093.86 0 -137174.73 -12270.999
|
||||
80 202.37482 -138029.39 0 -137175.59 -7622.7319
|
||||
90 194.90628 -137997.05 0 -137174.75 -32267.471
|
||||
100 185.17818 -137954.51 0 -137173.26 -6901.7499
|
||||
Loop time of 9.44819 on 1 procs for 100 steps with 32640 atoms
|
||||
|
||||
Performance: 0.457 ns/day, 52.490 hours/ns, 10.584 timesteps/s
|
||||
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 7.037 | 7.037 | 7.037 | 0.0 | 74.48
|
||||
Neigh | 2.3182 | 2.3182 | 2.3182 | 0.0 | 24.54
|
||||
Comm | 0.029898 | 0.029898 | 0.029898 | 0.0 | 0.32
|
||||
Output | 0.0014331 | 0.0014331 | 0.0014331 | 0.0 | 0.02
|
||||
Modify | 0.043851 | 0.043851 | 0.043851 | 0.0 | 0.46
|
||||
Other | | 0.01774 | | | 0.19
|
||||
|
||||
Nlocal: 32640 ave 32640 max 32640 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 26460 ave 26460 max 26460 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 4.90213e+06 ave 4.90213e+06 max 4.90213e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 4902134
|
||||
Ave neighs/atom = 150.188
|
||||
Neighbor list builds = 9
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:09
|
||||
89
examples/airebo/log.30Apr2019.rebo2.g++.4
Normal file
89
examples/airebo/log.30Apr2019.rebo2.g++.4
Normal file
@ -0,0 +1,89 @@
|
||||
LAMMPS (30 Apr 2019)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# REBO polyethelene benchmark
|
||||
|
||||
units metal
|
||||
atom_style atomic
|
||||
|
||||
read_data data.airebo
|
||||
orthogonal box = (-2.1 -2.1 0) to (2.1 2.1 25.579)
|
||||
1 by 1 by 4 MPI processor grid
|
||||
reading atoms ...
|
||||
60 atoms
|
||||
read_data CPU = 0.000682831 secs
|
||||
|
||||
replicate 17 16 2
|
||||
orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
32640 atoms
|
||||
replicate CPU = 0.00221777 secs
|
||||
|
||||
neighbor 0.5 bin
|
||||
neigh_modify delay 5 every 1
|
||||
|
||||
pair_style rebo
|
||||
pair_coeff * * CH.rebo C H
|
||||
Reading potential file CH.rebo with DATE: 2018-7-3
|
||||
|
||||
velocity all create 300.0 761341
|
||||
|
||||
fix 1 all nve
|
||||
timestep 0.0005
|
||||
|
||||
thermo 10
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 6.5
|
||||
ghost atom cutoff = 6.5
|
||||
binsize = 3.25, bins = 22 21 16
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair rebo, perpetual
|
||||
attributes: full, newton on, ghost
|
||||
pair build: full/bin/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 11.75 | 11.94 | 12.13 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 300 -138442.83 0 -137177.16 2463.0748
|
||||
10 179.37985 -137931.27 0 -137174.48 15655.936
|
||||
20 206.87654 -138046.99 0 -137174.19 -24042.627
|
||||
30 150.80122 -137807.43 0 -137171.21 -16524.118
|
||||
40 173.24945 -137902.35 0 -137171.42 -5716.9119
|
||||
50 151.80455 -137812.36 0 -137171.91 3480.4584
|
||||
60 199.08777 -138013.82 0 -137173.88 17881.372
|
||||
70 217.85748 -138093.86 0 -137174.73 -12270.999
|
||||
80 202.37482 -138029.39 0 -137175.59 -7622.7319
|
||||
90 194.90628 -137997.05 0 -137174.75 -32267.471
|
||||
100 185.17818 -137954.51 0 -137173.26 -6901.7499
|
||||
Loop time of 6.35645 on 4 procs for 100 steps with 32640 atoms
|
||||
|
||||
Performance: 0.680 ns/day, 35.314 hours/ns, 15.732 timesteps/s
|
||||
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 4.4335 | 4.5041 | 4.56 | 2.1 | 70.86
|
||||
Neigh | 1.5332 | 1.5919 | 1.6466 | 3.6 | 25.04
|
||||
Comm | 0.098299 | 0.20854 | 0.26277 | 14.2 | 3.28
|
||||
Output | 0.0011072 | 0.0018047 | 0.0037503 | 2.6 | 0.03
|
||||
Modify | 0.028811 | 0.030358 | 0.031516 | 0.6 | 0.48
|
||||
Other | | 0.01977 | | | 0.31
|
||||
|
||||
Nlocal: 8160 ave 8163 max 8157 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 1 1
|
||||
Nghost: 11605.8 ave 11615 max 11593 min
|
||||
Histogram: 1 0 0 0 0 0 2 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 1.22553e+06 ave 1.22735e+06 max 1.22455e+06 min
|
||||
Histogram: 2 0 0 1 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 4902134
|
||||
Ave neighs/atom = 150.188
|
||||
Neighbor list builds = 9
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:06
|
||||
98
examples/granular/in.pour.drum
Normal file
98
examples/granular/in.pour.drum
Normal file
@ -0,0 +1,98 @@
|
||||
# pour two types of particles (cohesive and non-cohesive) into cylinder
|
||||
# 'turn' cylinder by changing direction of gravity, then rotate it.
|
||||
# This simulates a rotating drum powder characterization experiment.
|
||||
|
||||
variable name string rotating_drum_two_types
|
||||
|
||||
atom_style sphere
|
||||
units lj
|
||||
|
||||
###############################################
|
||||
# Geometry-related parameters
|
||||
###############################################
|
||||
|
||||
variable boxx equal 30
|
||||
variable boxy equal 30
|
||||
variable boxz equal 50
|
||||
|
||||
variable drum_rad equal ${boxx}*0.5
|
||||
variable drum_height equal 20
|
||||
|
||||
variable xc equal 0.5*${boxx}
|
||||
variable yc equal 0.5*${boxx}
|
||||
variable zc equal 0.5*${boxz}
|
||||
|
||||
###############################################
|
||||
# Particle-related parameters
|
||||
###############################################
|
||||
variable rlo equal 0.25
|
||||
variable rhi equal 0.5
|
||||
variable dlo equal 2.0*${rlo}
|
||||
variable dhi equal 2.0*${rhi}
|
||||
|
||||
variable cyl_rad_inner equal ${drum_rad}-1.1*${rhi}
|
||||
|
||||
variable dens equal 1.0
|
||||
|
||||
variable skin equal 0.4*${rhi}
|
||||
|
||||
#############
|
||||
processors * * 1
|
||||
region boxreg block 0 ${boxx} 0 ${boxy} 0 ${boxz}
|
||||
create_box 2 boxreg
|
||||
change_box all boundary p p f
|
||||
comm_modify vel yes
|
||||
|
||||
variable theta equal 0
|
||||
|
||||
region curved_wall cylinder z ${xc} ${yc} ${drum_rad} 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
|
||||
region bottom_wall plane ${xc} ${yc} 0 0 0 1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
|
||||
|
||||
region insreg cylinder z ${xc} ${yc} ${cyl_rad_inner} ${drum_height} ${boxz}
|
||||
|
||||
fix 0 all balance 100 1.0 shift xy 5 1.1
|
||||
fix 1 all nve/sphere
|
||||
fix grav all gravity 10 vector 0 0 -1
|
||||
fix ins1 all pour 2000 1 1234 region insreg diam range ${dlo} ${dhi} dens ${dens} ${dens}
|
||||
fix ins2 all pour 2000 2 1234 region insreg diam range ${dlo} ${dhi} dens ${dens} ${dens}
|
||||
|
||||
comm_modify vel yes
|
||||
|
||||
neighbor ${skin} bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
pair_style granular
|
||||
pair_coeff 1 * hertz/material 1e5 0.2 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji
|
||||
pair_coeff 2 2 jkr 1e5 0.1 0.3 50 tangential mindlin NULL 1.0 0.5 rolling sds 1e3 1e3 0.1 twisting marshall damping tsuji
|
||||
|
||||
fix 3 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region curved_wall
|
||||
fix 4 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region bottom_wall
|
||||
|
||||
thermo_style custom step atoms ke v_theta
|
||||
thermo_modify lost warn
|
||||
thermo 100
|
||||
|
||||
timestep 0.001
|
||||
|
||||
#dump 1 all custom 100 ${name}.dump id type radius mass x y z
|
||||
|
||||
#For removal later
|
||||
compute 1 all property/atom radius
|
||||
variable zmax atom z+c_1>0.5*${drum_height}
|
||||
group delgroup dynamic all var zmax every 10000
|
||||
|
||||
run 2000
|
||||
|
||||
#Remove any particles that are above z > 0.5*drum_height
|
||||
delete_atoms group delgroup
|
||||
|
||||
#Add top lid
|
||||
region top_wall plane ${xc} ${yc} ${drum_height} 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
|
||||
fix 5 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region top_wall
|
||||
|
||||
# 'Turn' drum by switching the direction of gravity
|
||||
unfix grav
|
||||
fix grav all gravity 10 vector 0 -1 0
|
||||
|
||||
variable theta equal 2*PI*elapsed/20000.0
|
||||
run 3000
|
||||
67
examples/granular/in.pour.flatwall
Normal file
67
examples/granular/in.pour.flatwall
Normal file
@ -0,0 +1,67 @@
|
||||
# pour two types of particles (cohesive and non-cohesive) on flat wall
|
||||
|
||||
variable name string pour_two_types
|
||||
|
||||
atom_style sphere
|
||||
units lj
|
||||
|
||||
###############################################
|
||||
# Geometry-related parameters
|
||||
###############################################
|
||||
|
||||
variable boxx equal 20
|
||||
variable boxy equal 20
|
||||
variable boxz equal 30
|
||||
|
||||
variable xc1 equal 0.3*${boxx}
|
||||
variable xc2 equal 0.7*${boxx}
|
||||
variable yc equal 0.5*${boxy}
|
||||
|
||||
###############################################
|
||||
# Particle-related parameters
|
||||
###############################################
|
||||
variable rlo equal 0.25
|
||||
variable rhi equal 0.5
|
||||
variable dlo equal 2.0*${rlo}
|
||||
variable dhi equal 2.0*${rhi}
|
||||
|
||||
variable dens equal 1.0
|
||||
|
||||
variable skin equal 0.3*${rhi}
|
||||
|
||||
#############
|
||||
processors * * 1
|
||||
region boxreg block 0 ${boxx} 0 ${boxy} 0 ${boxz}
|
||||
create_box 2 boxreg
|
||||
change_box all boundary p p f
|
||||
|
||||
comm_modify vel yes
|
||||
|
||||
region insreg1 cylinder z ${xc1} ${yc} 5 15 ${boxz}
|
||||
region insreg2 cylinder z ${xc2} ${yc} 5 15 ${boxz}
|
||||
|
||||
fix 1 all nve/sphere
|
||||
fix grav all gravity 10.0 vector 0 0 -1
|
||||
fix ins1 all pour 1500 1 3123 region insreg1 diam range ${dlo} ${dhi} dens ${dens} ${dens}
|
||||
fix ins2 all pour 1500 2 3123 region insreg2 diam range ${dlo} ${dhi} dens ${dens} ${dens}
|
||||
|
||||
comm_modify vel yes
|
||||
|
||||
neighbor ${skin} bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
pair_style granular
|
||||
pair_coeff 1 * jkr 1000.0 50.0 0.3 10 tangential mindlin 800.0 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall
|
||||
pair_coeff 2 2 hertz 200.0 20.0 tangential linear_history 300.0 1.0 0.1 rolling sds 200.0 100.0 0.1 twisting marshall
|
||||
|
||||
fix 3 all wall/gran granular hertz/material 1e5 1e3 0.3 tangential mindlin NULL 1.0 0.5 zplane 0 NULL
|
||||
|
||||
thermo_style custom step cpu atoms ke
|
||||
thermo_modify lost warn
|
||||
thermo 100
|
||||
|
||||
timestep 0.001
|
||||
|
||||
#dump 1 all custom 100 ${name}.dump id type radius mass x y z
|
||||
|
||||
run 5000
|
||||
271
examples/granular/log.29Mar19.pour.drum.g++.1
Normal file
271
examples/granular/log.29Mar19.pour.drum.g++.1
Normal file
@ -0,0 +1,271 @@
|
||||
LAMMPS (29 Mar 2019)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:88)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# pour two types of particles (cohesive and non-cohesive) into cylinder
|
||||
# 'turn' cylinder by changing direction of gravity, then rotate it.
|
||||
# This simulates a rotating drum powder characterization experiment.
|
||||
|
||||
variable name string rotating_drum_two_types
|
||||
|
||||
atom_style sphere
|
||||
units lj
|
||||
|
||||
###############################################
|
||||
# Geometry-related parameters
|
||||
###############################################
|
||||
|
||||
variable boxx equal 30
|
||||
variable boxy equal 30
|
||||
variable boxz equal 50
|
||||
|
||||
variable drum_rad equal ${boxx}*0.5
|
||||
variable drum_rad equal 30*0.5
|
||||
variable drum_height equal 20
|
||||
|
||||
variable xc equal 0.5*${boxx}
|
||||
variable xc equal 0.5*30
|
||||
variable yc equal 0.5*${boxx}
|
||||
variable yc equal 0.5*30
|
||||
variable zc equal 0.5*${boxz}
|
||||
variable zc equal 0.5*50
|
||||
|
||||
###############################################
|
||||
# Particle-related parameters
|
||||
###############################################
|
||||
variable rlo equal 0.25
|
||||
variable rhi equal 0.5
|
||||
variable dlo equal 2.0*${rlo}
|
||||
variable dlo equal 2.0*0.25
|
||||
variable dhi equal 2.0*${rhi}
|
||||
variable dhi equal 2.0*0.5
|
||||
|
||||
variable cyl_rad_inner equal ${drum_rad}-1.1*${rhi}
|
||||
variable cyl_rad_inner equal 15-1.1*${rhi}
|
||||
variable cyl_rad_inner equal 15-1.1*0.5
|
||||
|
||||
variable dens equal 1.0
|
||||
|
||||
variable skin equal 0.4*${rhi}
|
||||
variable skin equal 0.4*0.5
|
||||
|
||||
#############
|
||||
processors * * 1
|
||||
region boxreg block 0 ${boxx} 0 ${boxy} 0 ${boxz}
|
||||
region boxreg block 0 30 0 ${boxy} 0 ${boxz}
|
||||
region boxreg block 0 30 0 30 0 ${boxz}
|
||||
region boxreg block 0 30 0 30 0 50
|
||||
create_box 2 boxreg
|
||||
Created orthogonal box = (0 0 0) to (30 30 50)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
change_box all boundary p p f
|
||||
comm_modify vel yes
|
||||
|
||||
variable theta equal 0
|
||||
|
||||
region curved_wall cylinder z ${xc} ${yc} ${drum_rad} 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
|
||||
region curved_wall cylinder z 15 ${yc} ${drum_rad} 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
|
||||
region curved_wall cylinder z 15 15 ${drum_rad} 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
|
||||
region curved_wall cylinder z 15 15 15 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
|
||||
region curved_wall cylinder z 15 15 15 0 20 side in rotate v_theta ${xc} ${yc} 0 0 0 1
|
||||
region curved_wall cylinder z 15 15 15 0 20 side in rotate v_theta 15 ${yc} 0 0 0 1
|
||||
region curved_wall cylinder z 15 15 15 0 20 side in rotate v_theta 15 15 0 0 0 1
|
||||
region bottom_wall plane ${xc} ${yc} 0 0 0 1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
|
||||
region bottom_wall plane 15 ${yc} 0 0 0 1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
|
||||
region bottom_wall plane 15 15 0 0 0 1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
|
||||
region bottom_wall plane 15 15 0 0 0 1 side in rotate v_theta 15 ${yc} 0 0 0 1
|
||||
region bottom_wall plane 15 15 0 0 0 1 side in rotate v_theta 15 15 0 0 0 1
|
||||
|
||||
region insreg cylinder z ${xc} ${yc} ${cyl_rad_inner} ${drum_height} ${boxz}
|
||||
region insreg cylinder z 15 ${yc} ${cyl_rad_inner} ${drum_height} ${boxz}
|
||||
region insreg cylinder z 15 15 ${cyl_rad_inner} ${drum_height} ${boxz}
|
||||
region insreg cylinder z 15 15 14.45 ${drum_height} ${boxz}
|
||||
region insreg cylinder z 15 15 14.45 20 ${boxz}
|
||||
region insreg cylinder z 15 15 14.45 20 50
|
||||
|
||||
fix 0 all balance 100 1.0 shift xy 5 1.1
|
||||
fix 1 all nve/sphere
|
||||
fix grav all gravity 10 vector 0 0 -1
|
||||
fix ins1 all pour 2000 1 1234 region insreg diam range ${dlo} ${dhi} dens ${dens} ${dens}
|
||||
fix ins1 all pour 2000 1 1234 region insreg diam range 0.5 ${dhi} dens ${dens} ${dens}
|
||||
fix ins1 all pour 2000 1 1234 region insreg diam range 0.5 1 dens ${dens} ${dens}
|
||||
fix ins1 all pour 2000 1 1234 region insreg diam range 0.5 1 dens 1 ${dens}
|
||||
fix ins1 all pour 2000 1 1234 region insreg diam range 0.5 1 dens 1 1
|
||||
Particle insertion: 9396 every 490 steps, 2000 by step 1
|
||||
fix ins2 all pour 2000 2 1234 region insreg diam range ${dlo} ${dhi} dens ${dens} ${dens}
|
||||
fix ins2 all pour 2000 2 1234 region insreg diam range 0.5 ${dhi} dens ${dens} ${dens}
|
||||
fix ins2 all pour 2000 2 1234 region insreg diam range 0.5 1 dens ${dens} ${dens}
|
||||
fix ins2 all pour 2000 2 1234 region insreg diam range 0.5 1 dens 1 ${dens}
|
||||
fix ins2 all pour 2000 2 1234 region insreg diam range 0.5 1 dens 1 1
|
||||
Particle insertion: 9396 every 490 steps, 2000 by step 1
|
||||
|
||||
comm_modify vel yes
|
||||
|
||||
neighbor ${skin} bin
|
||||
neighbor 0.2 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
pair_style granular
|
||||
pair_coeff 1 * hertz/material 1e5 0.2 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji
|
||||
pair_coeff 2 2 jkr 1e5 0.1 0.3 50 tangential mindlin NULL 1.0 0.5 rolling sds 1e3 1e3 0.1 twisting marshall damping tsuji
|
||||
|
||||
fix 3 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region curved_wall
|
||||
fix 4 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region bottom_wall
|
||||
|
||||
thermo_style custom step atoms ke v_theta
|
||||
thermo_modify lost warn
|
||||
thermo 100
|
||||
|
||||
timestep 0.001
|
||||
|
||||
dump 1 all custom 100 ${name}.dump id type radius mass x y z
|
||||
dump 1 all custom 100 rotating_drum_two_types.dump id type radius mass x y z
|
||||
|
||||
#For removal later
|
||||
compute 1 all property/atom radius
|
||||
variable zmax atom z+c_1>0.5*${drum_height}
|
||||
variable zmax atom z+c_1>0.5*20
|
||||
group delgroup dynamic all var zmax every 10000
|
||||
dynamic group delgroup defined
|
||||
|
||||
run 2000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.2
|
||||
ghost atom cutoff = 1.2
|
||||
binsize = 0.6, bins = 50 50 84
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair granular, perpetual
|
||||
attributes: half, newton on, size, history
|
||||
pair build: half/size/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 13.02 | 13.02 | 13.02 Mbytes
|
||||
Step Atoms KinEng v_theta
|
||||
0 0 -0 0
|
||||
100 4000 -0 0
|
||||
200 4000 -0 0
|
||||
300 4000 -0 0
|
||||
400 4000 -0 0
|
||||
500 4000 -0 0
|
||||
600 4000 -0 0
|
||||
700 4000 -0 0
|
||||
800 4000 -0 0
|
||||
900 4000 -0 0
|
||||
1000 4000 -0 0
|
||||
1100 4000 -0 0
|
||||
1200 4000 -0 0
|
||||
1300 4000 -0 0
|
||||
1400 4000 -0 0
|
||||
1500 4000 -0 0
|
||||
1600 4000 -0 0
|
||||
1700 4000 -0 0
|
||||
1800 4000 -0 0
|
||||
1900 4000 -0 0
|
||||
2000 4000 -0 0
|
||||
Loop time of 3.54461 on 1 procs for 2000 steps with 4000 atoms
|
||||
|
||||
Performance: 48750.057 tau/day, 564.237 timesteps/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 | 0.61949 | 0.61949 | 0.61949 | 0.0 | 17.48
|
||||
Neigh | 1.2492 | 1.2492 | 1.2492 | 0.0 | 35.24
|
||||
Comm | 0.046404 | 0.046404 | 0.046404 | 0.0 | 1.31
|
||||
Output | 0.15901 | 0.15901 | 0.15901 | 0.0 | 4.49
|
||||
Modify | 1.4165 | 1.4165 | 1.4165 | 0.0 | 39.96
|
||||
Other | | 0.05391 | | | 1.52
|
||||
|
||||
Nlocal: 4000 ave 4000 max 4000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 166 ave 166 max 166 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 8195 ave 8195 max 8195 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 8195
|
||||
Ave neighs/atom = 2.04875
|
||||
Neighbor list builds = 1004
|
||||
Dangerous builds = 3
|
||||
|
||||
#Remove any particles that are above z > 0.5*drum_height
|
||||
delete_atoms group delgroup
|
||||
Deleted 0 atoms, new total = 4000
|
||||
|
||||
#Add top lid
|
||||
region top_wall plane ${xc} ${yc} ${drum_height} 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
|
||||
region top_wall plane 15 ${yc} ${drum_height} 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
|
||||
region top_wall plane 15 15 ${drum_height} 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
|
||||
region top_wall plane 15 15 20 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
|
||||
region top_wall plane 15 15 20 0 0 -1 side in rotate v_theta 15 ${yc} 0 0 0 1
|
||||
region top_wall plane 15 15 20 0 0 -1 side in rotate v_theta 15 15 0 0 0 1
|
||||
fix 5 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region top_wall
|
||||
|
||||
# 'Turn' drum by switching the direction of gravity
|
||||
unfix grav
|
||||
fix grav all gravity 10 vector 0 -1 0
|
||||
|
||||
variable theta equal 2*PI*elapsed/20000.0
|
||||
run 3000
|
||||
Per MPI rank memory allocation (min/avg/max) = 24.81 | 24.81 | 24.81 Mbytes
|
||||
Step Atoms KinEng v_theta
|
||||
2000 4000 64.333531 0
|
||||
2100 4000 106.69182 0.031415927
|
||||
2200 4000 121.8461 0.062831853
|
||||
2300 4000 88.767952 0.09424778
|
||||
2400 4000 82.850721 0.12566371
|
||||
2500 4000 91.683284 0.15707963
|
||||
2600 4000 31.56344 0.18849556
|
||||
2700 4000 4.5697672 0.21991149
|
||||
2800 4000 3.9879051 0.25132741
|
||||
2900 4000 4.4394235 0.28274334
|
||||
3000 4000 5.1212931 0.31415927
|
||||
3100 4000 5.8608892 0.34557519
|
||||
3200 4000 6.600714 0.37699112
|
||||
3300 4000 7.3497851 0.40840704
|
||||
3400 4000 8.0490988 0.43982297
|
||||
3500 4000 8.6712396 0.4712389
|
||||
3600 4000 9.1328667 0.50265482
|
||||
3700 4000 9.4683561 0.53407075
|
||||
3800 4000 9.5878145 0.56548668
|
||||
3900 4000 9.387745 0.5969026
|
||||
4000 4000 8.9117631 0.62831853
|
||||
4100 4000 8.2344368 0.65973446
|
||||
4200 4000 7.5335088 0.69115038
|
||||
4300 4000 6.8426179 0.72256631
|
||||
4400 4000 6.0567247 0.75398224
|
||||
4500 4000 5.4166132 0.78539816
|
||||
4600 4000 4.6012409 0.81681409
|
||||
4700 4000 3.8314982 0.84823002
|
||||
4800 4000 3.1916415 0.87964594
|
||||
4900 4000 2.7833964 0.91106187
|
||||
5000 4000 2.5051362 0.9424778
|
||||
Loop time of 11.9545 on 1 procs for 3000 steps with 4000 atoms
|
||||
|
||||
Performance: 21682.142 tau/day, 250.951 timesteps/s
|
||||
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 4.8291 | 4.8291 | 4.8291 | 0.0 | 40.40
|
||||
Neigh | 2.7489 | 2.7489 | 2.7489 | 0.0 | 22.99
|
||||
Comm | 0.071249 | 0.071249 | 0.071249 | 0.0 | 0.60
|
||||
Output | 0.20547 | 0.20547 | 0.20547 | 0.0 | 1.72
|
||||
Modify | 4.0179 | 4.0179 | 4.0179 | 0.0 | 33.61
|
||||
Other | | 0.0819 | | | 0.69
|
||||
|
||||
Nlocal: 4000 ave 4000 max 4000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 322 ave 322 max 322 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 14849 ave 14849 max 14849 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 14849
|
||||
Ave neighs/atom = 3.71225
|
||||
Neighbor list builds = 1290
|
||||
Dangerous builds = 672
|
||||
Total wall time: 0:00:15
|
||||
271
examples/granular/log.29Mar19.pour.drum.g++.4
Normal file
271
examples/granular/log.29Mar19.pour.drum.g++.4
Normal file
@ -0,0 +1,271 @@
|
||||
LAMMPS (29 Mar 2019)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:88)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# pour two types of particles (cohesive and non-cohesive) into cylinder
|
||||
# 'turn' cylinder by changing direction of gravity, then rotate it.
|
||||
# This simulates a rotating drum powder characterization experiment.
|
||||
|
||||
variable name string rotating_drum_two_types
|
||||
|
||||
atom_style sphere
|
||||
units lj
|
||||
|
||||
###############################################
|
||||
# Geometry-related parameters
|
||||
###############################################
|
||||
|
||||
variable boxx equal 30
|
||||
variable boxy equal 30
|
||||
variable boxz equal 50
|
||||
|
||||
variable drum_rad equal ${boxx}*0.5
|
||||
variable drum_rad equal 30*0.5
|
||||
variable drum_height equal 20
|
||||
|
||||
variable xc equal 0.5*${boxx}
|
||||
variable xc equal 0.5*30
|
||||
variable yc equal 0.5*${boxx}
|
||||
variable yc equal 0.5*30
|
||||
variable zc equal 0.5*${boxz}
|
||||
variable zc equal 0.5*50
|
||||
|
||||
###############################################
|
||||
# Particle-related parameters
|
||||
###############################################
|
||||
variable rlo equal 0.25
|
||||
variable rhi equal 0.5
|
||||
variable dlo equal 2.0*${rlo}
|
||||
variable dlo equal 2.0*0.25
|
||||
variable dhi equal 2.0*${rhi}
|
||||
variable dhi equal 2.0*0.5
|
||||
|
||||
variable cyl_rad_inner equal ${drum_rad}-1.1*${rhi}
|
||||
variable cyl_rad_inner equal 15-1.1*${rhi}
|
||||
variable cyl_rad_inner equal 15-1.1*0.5
|
||||
|
||||
variable dens equal 1.0
|
||||
|
||||
variable skin equal 0.4*${rhi}
|
||||
variable skin equal 0.4*0.5
|
||||
|
||||
#############
|
||||
processors * * 1
|
||||
region boxreg block 0 ${boxx} 0 ${boxy} 0 ${boxz}
|
||||
region boxreg block 0 30 0 ${boxy} 0 ${boxz}
|
||||
region boxreg block 0 30 0 30 0 ${boxz}
|
||||
region boxreg block 0 30 0 30 0 50
|
||||
create_box 2 boxreg
|
||||
Created orthogonal box = (0 0 0) to (30 30 50)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
change_box all boundary p p f
|
||||
comm_modify vel yes
|
||||
|
||||
variable theta equal 0
|
||||
|
||||
region curved_wall cylinder z ${xc} ${yc} ${drum_rad} 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
|
||||
region curved_wall cylinder z 15 ${yc} ${drum_rad} 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
|
||||
region curved_wall cylinder z 15 15 ${drum_rad} 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
|
||||
region curved_wall cylinder z 15 15 15 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
|
||||
region curved_wall cylinder z 15 15 15 0 20 side in rotate v_theta ${xc} ${yc} 0 0 0 1
|
||||
region curved_wall cylinder z 15 15 15 0 20 side in rotate v_theta 15 ${yc} 0 0 0 1
|
||||
region curved_wall cylinder z 15 15 15 0 20 side in rotate v_theta 15 15 0 0 0 1
|
||||
region bottom_wall plane ${xc} ${yc} 0 0 0 1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
|
||||
region bottom_wall plane 15 ${yc} 0 0 0 1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
|
||||
region bottom_wall plane 15 15 0 0 0 1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
|
||||
region bottom_wall plane 15 15 0 0 0 1 side in rotate v_theta 15 ${yc} 0 0 0 1
|
||||
region bottom_wall plane 15 15 0 0 0 1 side in rotate v_theta 15 15 0 0 0 1
|
||||
|
||||
region insreg cylinder z ${xc} ${yc} ${cyl_rad_inner} ${drum_height} ${boxz}
|
||||
region insreg cylinder z 15 ${yc} ${cyl_rad_inner} ${drum_height} ${boxz}
|
||||
region insreg cylinder z 15 15 ${cyl_rad_inner} ${drum_height} ${boxz}
|
||||
region insreg cylinder z 15 15 14.45 ${drum_height} ${boxz}
|
||||
region insreg cylinder z 15 15 14.45 20 ${boxz}
|
||||
region insreg cylinder z 15 15 14.45 20 50
|
||||
|
||||
fix 0 all balance 100 1.0 shift xy 5 1.1
|
||||
fix 1 all nve/sphere
|
||||
fix grav all gravity 10 vector 0 0 -1
|
||||
fix ins1 all pour 2000 1 1234 region insreg diam range ${dlo} ${dhi} dens ${dens} ${dens}
|
||||
fix ins1 all pour 2000 1 1234 region insreg diam range 0.5 ${dhi} dens ${dens} ${dens}
|
||||
fix ins1 all pour 2000 1 1234 region insreg diam range 0.5 1 dens ${dens} ${dens}
|
||||
fix ins1 all pour 2000 1 1234 region insreg diam range 0.5 1 dens 1 ${dens}
|
||||
fix ins1 all pour 2000 1 1234 region insreg diam range 0.5 1 dens 1 1
|
||||
Particle insertion: 9396 every 490 steps, 2000 by step 1
|
||||
fix ins2 all pour 2000 2 1234 region insreg diam range ${dlo} ${dhi} dens ${dens} ${dens}
|
||||
fix ins2 all pour 2000 2 1234 region insreg diam range 0.5 ${dhi} dens ${dens} ${dens}
|
||||
fix ins2 all pour 2000 2 1234 region insreg diam range 0.5 1 dens ${dens} ${dens}
|
||||
fix ins2 all pour 2000 2 1234 region insreg diam range 0.5 1 dens 1 ${dens}
|
||||
fix ins2 all pour 2000 2 1234 region insreg diam range 0.5 1 dens 1 1
|
||||
Particle insertion: 9396 every 490 steps, 2000 by step 1
|
||||
|
||||
comm_modify vel yes
|
||||
|
||||
neighbor ${skin} bin
|
||||
neighbor 0.2 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
pair_style granular
|
||||
pair_coeff 1 * hertz/material 1e5 0.2 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji
|
||||
pair_coeff 2 2 jkr 1e5 0.1 0.3 50 tangential mindlin NULL 1.0 0.5 rolling sds 1e3 1e3 0.1 twisting marshall damping tsuji
|
||||
|
||||
fix 3 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region curved_wall
|
||||
fix 4 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region bottom_wall
|
||||
|
||||
thermo_style custom step atoms ke v_theta
|
||||
thermo_modify lost warn
|
||||
thermo 100
|
||||
|
||||
timestep 0.001
|
||||
|
||||
dump 1 all custom 100 ${name}.dump id type radius mass x y z
|
||||
dump 1 all custom 100 rotating_drum_two_types.dump id type radius mass x y z
|
||||
|
||||
#For removal later
|
||||
compute 1 all property/atom radius
|
||||
variable zmax atom z+c_1>0.5*${drum_height}
|
||||
variable zmax atom z+c_1>0.5*20
|
||||
group delgroup dynamic all var zmax every 10000
|
||||
dynamic group delgroup defined
|
||||
|
||||
run 2000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.2
|
||||
ghost atom cutoff = 1.2
|
||||
binsize = 0.6, bins = 50 50 84
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair granular, perpetual
|
||||
attributes: half, newton on, size, history
|
||||
pair build: half/size/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 12.25 | 12.25 | 12.25 Mbytes
|
||||
Step Atoms KinEng v_theta
|
||||
0 0 -0 0
|
||||
100 4000 -0 0
|
||||
200 4000 -0 0
|
||||
300 4000 -0 0
|
||||
400 4000 -0 0
|
||||
500 4000 -0 0
|
||||
600 4000 -0 0
|
||||
700 4000 -0 0
|
||||
800 4000 -0 0
|
||||
900 4000 -0 0
|
||||
1000 4000 -0 0
|
||||
1100 4000 -0 0
|
||||
1200 4000 -0 0
|
||||
1300 4000 -0 0
|
||||
1400 4000 -0 0
|
||||
1500 4000 -0 0
|
||||
1600 4000 -0 0
|
||||
1700 4000 -0 0
|
||||
1800 4000 -0 0
|
||||
1900 4000 -0 0
|
||||
2000 4000 -0 0
|
||||
Loop time of 2.0709 on 4 procs for 2000 steps with 4000 atoms
|
||||
|
||||
Performance: 83442.024 tau/day, 965.764 timesteps/s
|
||||
97.7% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.24679 | 0.26336 | 0.28853 | 3.0 | 12.72
|
||||
Neigh | 0.52279 | 0.5332 | 0.53858 | 0.9 | 25.75
|
||||
Comm | 0.17418 | 0.20253 | 0.23266 | 4.7 | 9.78
|
||||
Output | 0.092897 | 0.093531 | 0.09515 | 0.3 | 4.52
|
||||
Modify | 0.88151 | 0.89571 | 0.90582 | 0.9 | 43.25
|
||||
Other | | 0.08257 | | | 3.99
|
||||
|
||||
Nlocal: 1000 ave 1001 max 999 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Nghost: 267.75 ave 276 max 262 min
|
||||
Histogram: 1 0 1 0 1 0 0 0 0 1
|
||||
Neighs: 2031.5 ave 2091 max 1958 min
|
||||
Histogram: 1 0 0 0 1 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 8126
|
||||
Ave neighs/atom = 2.0315
|
||||
Neighbor list builds = 1004
|
||||
Dangerous builds = 3
|
||||
|
||||
#Remove any particles that are above z > 0.5*drum_height
|
||||
delete_atoms group delgroup
|
||||
Deleted 0 atoms, new total = 4000
|
||||
|
||||
#Add top lid
|
||||
region top_wall plane ${xc} ${yc} ${drum_height} 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
|
||||
region top_wall plane 15 ${yc} ${drum_height} 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
|
||||
region top_wall plane 15 15 ${drum_height} 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
|
||||
region top_wall plane 15 15 20 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
|
||||
region top_wall plane 15 15 20 0 0 -1 side in rotate v_theta 15 ${yc} 0 0 0 1
|
||||
region top_wall plane 15 15 20 0 0 -1 side in rotate v_theta 15 15 0 0 0 1
|
||||
fix 5 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region top_wall
|
||||
|
||||
# 'Turn' drum by switching the direction of gravity
|
||||
unfix grav
|
||||
fix grav all gravity 10 vector 0 -1 0
|
||||
|
||||
variable theta equal 2*PI*elapsed/20000.0
|
||||
run 3000
|
||||
Per MPI rank memory allocation (min/avg/max) = 21.6 | 22.6 | 23.82 Mbytes
|
||||
Step Atoms KinEng v_theta
|
||||
2000 4000 64.255821 0
|
||||
2100 4000 106.47082 0.031415927
|
||||
2200 4000 121.52634 0.062831853
|
||||
2300 4000 87.748818 0.09424778
|
||||
2400 4000 82.712784 0.12566371
|
||||
2500 4000 90.618713 0.15707963
|
||||
2600 4000 30.096031 0.18849556
|
||||
2700 4000 4.0838611 0.21991149
|
||||
2800 4000 3.7485959 0.25132741
|
||||
2900 4000 4.2159774 0.28274334
|
||||
3000 4000 4.8730048 0.31415927
|
||||
3100 4000 5.6109465 0.34557519
|
||||
3200 4000 6.4290528 0.37699112
|
||||
3300 4000 7.2699677 0.40840704
|
||||
3400 4000 8.0895944 0.43982297
|
||||
3500 4000 8.7222781 0.4712389
|
||||
3600 4000 9.133205 0.50265482
|
||||
3700 4000 9.3404584 0.53407075
|
||||
3800 4000 9.3359844 0.56548668
|
||||
3900 4000 9.0916854 0.5969026
|
||||
4000 4000 8.5596424 0.62831853
|
||||
4100 4000 7.9734883 0.65973446
|
||||
4200 4000 7.2154383 0.69115038
|
||||
4300 4000 6.7039232 0.72256631
|
||||
4400 4000 6.1542738 0.75398224
|
||||
4500 4000 5.4049454 0.78539816
|
||||
4600 4000 4.4603192 0.81681409
|
||||
4700 4000 3.6197985 0.84823002
|
||||
4800 4000 2.9895571 0.87964594
|
||||
4900 4000 2.5314553 0.91106187
|
||||
5000 4000 2.2645533 0.9424778
|
||||
Loop time of 6.64209 on 4 procs for 3000 steps with 4000 atoms
|
||||
|
||||
Performance: 39023.861 tau/day, 451.665 timesteps/s
|
||||
96.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.8376 | 2.126 | 2.3131 | 12.6 | 32.01
|
||||
Neigh | 0.97762 | 1.0518 | 1.1337 | 5.4 | 15.84
|
||||
Comm | 0.53699 | 0.84265 | 1.2325 | 27.6 | 12.69
|
||||
Output | 0.13922 | 0.14159 | 0.14388 | 0.4 | 2.13
|
||||
Modify | 1.8815 | 2.1026 | 2.3368 | 11.2 | 31.66
|
||||
Other | | 0.3774 | | | 5.68
|
||||
|
||||
Nlocal: 1000 ave 1256 max 744 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Nghost: 579.5 ave 789 max 498 min
|
||||
Histogram: 2 1 0 0 0 0 0 0 0 1
|
||||
Neighs: 3696.25 ave 4853 max 2590 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 14785
|
||||
Ave neighs/atom = 3.69625
|
||||
Neighbor list builds = 1230
|
||||
Dangerous builds = 676
|
||||
Total wall time: 0:00:08
|
||||
134
examples/granular/log.29Mar19.pour.flatwall.g++.1
Normal file
134
examples/granular/log.29Mar19.pour.flatwall.g++.1
Normal file
@ -0,0 +1,134 @@
|
||||
LAMMPS (29 Mar 2019)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:88)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# pour two types of particles (cohesive and non-cohesive) on flat wall
|
||||
|
||||
variable name string pour_two_types
|
||||
|
||||
atom_style sphere
|
||||
units lj
|
||||
|
||||
###############################################
|
||||
# Geometry-related parameters
|
||||
###############################################
|
||||
|
||||
variable boxx equal 20
|
||||
variable boxy equal 20
|
||||
variable boxz equal 30
|
||||
|
||||
variable xc1 equal 0.3*${boxx}
|
||||
variable xc1 equal 0.3*20
|
||||
variable xc2 equal 0.7*${boxx}
|
||||
variable xc2 equal 0.7*20
|
||||
variable yc equal 0.5*${boxy}
|
||||
variable yc equal 0.5*20
|
||||
|
||||
###############################################
|
||||
# Particle-related parameters
|
||||
###############################################
|
||||
variable rlo equal 0.25
|
||||
variable rhi equal 0.5
|
||||
variable dlo equal 2.0*${rlo}
|
||||
variable dlo equal 2.0*0.25
|
||||
variable dhi equal 2.0*${rhi}
|
||||
variable dhi equal 2.0*0.5
|
||||
|
||||
variable dens equal 1.0
|
||||
|
||||
variable skin equal 0.3*${rhi}
|
||||
variable skin equal 0.3*0.5
|
||||
|
||||
#############
|
||||
processors * * 1
|
||||
region boxreg block 0 ${boxx} 0 ${boxy} 0 ${boxz}
|
||||
region boxreg block 0 20 0 ${boxy} 0 ${boxz}
|
||||
region boxreg block 0 20 0 20 0 ${boxz}
|
||||
region boxreg block 0 20 0 20 0 30
|
||||
create_box 2 boxreg
|
||||
Created orthogonal box = (0 0 0) to (20 20 30)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
change_box all boundary p p f
|
||||
|
||||
comm_modify vel yes
|
||||
|
||||
region insreg1 cylinder z ${xc1} ${yc} 5 15 ${boxz}
|
||||
region insreg1 cylinder z 6 ${yc} 5 15 ${boxz}
|
||||
region insreg1 cylinder z 6 10 5 15 ${boxz}
|
||||
region insreg1 cylinder z 6 10 5 15 30
|
||||
region insreg2 cylinder z ${xc2} ${yc} 5 15 ${boxz}
|
||||
region insreg2 cylinder z 14 ${yc} 5 15 ${boxz}
|
||||
region insreg2 cylinder z 14 10 5 15 ${boxz}
|
||||
region insreg2 cylinder z 14 10 5 15 30
|
||||
|
||||
fix 1 all nve/sphere
|
||||
fix grav all gravity 10.0 vector 0 0 -1
|
||||
fix ins1 all pour 1500 1 3123 region insreg1 diam range ${dlo} ${dhi} dens ${dens} ${dens}
|
||||
fix ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 ${dhi} dens ${dens} ${dens}
|
||||
fix ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 1 dens ${dens} ${dens}
|
||||
fix ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 1 dens 1 ${dens}
|
||||
fix ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 1 dens 1 1
|
||||
Particle insertion: 562 every 346 steps, 1500 by step 693
|
||||
fix ins2 all pour 1500 2 3123 region insreg2 diam range ${dlo} ${dhi} dens ${dens} ${dens}
|
||||
fix ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 ${dhi} dens ${dens} ${dens}
|
||||
fix ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 1 dens ${dens} ${dens}
|
||||
fix ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 1 dens 1 ${dens}
|
||||
fix ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 1 dens 1 1
|
||||
Particle insertion: 562 every 346 steps, 1500 by step 693
|
||||
|
||||
comm_modify vel yes
|
||||
|
||||
neighbor ${skin} bin
|
||||
neighbor 0.15 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
pair_style granular
|
||||
pair_coeff 1 * jkr 1000.0 50.0 0.3 10 tangential mindlin 800.0 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall
|
||||
pair_coeff 2 2 hertz 200.0 20.0 tangential linear_history 300.0 1.0 0.1 rolling sds 200.0 100.0 0.1 twisting marshall
|
||||
|
||||
fix 3 all wall/gran granular hertz/material 1e5 1e3 0.3 tangential mindlin NULL 1.0 0.5 zplane 0 NULL
|
||||
|
||||
thermo_style custom step cpu atoms ke
|
||||
thermo_modify lost warn
|
||||
thermo 100
|
||||
|
||||
timestep 0.001
|
||||
|
||||
#dump 1 all custom 100 ${name}.dump id type radius mass x y z
|
||||
|
||||
run 5000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.15
|
||||
ghost atom cutoff = 1.15
|
||||
binsize = 0.575, bins = 35 35 53
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair granular, perpetual
|
||||
attributes: half, newton on, size, history
|
||||
pair build: half/size/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 12.22 | 12.22 | 12.22 Mbytes
|
||||
Step CPU Atoms KinEng
|
||||
0 0 0 -0
|
||||
100 3.8153191 855 -0
|
||||
200 4.195287 855 -0
|
||||
300 4.5890362 855 -0
|
||||
400 10.636087 1500 -0
|
||||
500 11.306909 1500 -0
|
||||
600 11.968198 1500 -0
|
||||
700 22.631892 2288 -0
|
||||
800 23.711387 2288 -0
|
||||
900 24.754344 2288 -0
|
||||
1000 25.811778 2288 -0
|
||||
1100 35.368869 2845 -0
|
||||
1200 37.149843 2845 -0
|
||||
1300 39.026458 2845 -0
|
||||
1400 41.757583 3000 -0
|
||||
1500 45.155503 3000 -0
|
||||
1600 48.570241 3000 -0
|
||||
1700 52.839322 3000 -0
|
||||
1800 59.772697 3000 -0
|
||||
1900 69.493305 3000 -0
|
||||
2000 114.61886 3000 -0
|
||||
2100 152.89232 3000 -0
|
||||
191
examples/granular/log.29Mar19.pour.flatwall.g++.4
Normal file
191
examples/granular/log.29Mar19.pour.flatwall.g++.4
Normal file
@ -0,0 +1,191 @@
|
||||
LAMMPS (29 Mar 2019)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:88)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# pour two types of particles (cohesive and non-cohesive) on flat wall
|
||||
|
||||
variable name string pour_two_types
|
||||
|
||||
atom_style sphere
|
||||
units lj
|
||||
|
||||
###############################################
|
||||
# Geometry-related parameters
|
||||
###############################################
|
||||
|
||||
variable boxx equal 20
|
||||
variable boxy equal 20
|
||||
variable boxz equal 30
|
||||
|
||||
variable xc1 equal 0.3*${boxx}
|
||||
variable xc1 equal 0.3*20
|
||||
variable xc2 equal 0.7*${boxx}
|
||||
variable xc2 equal 0.7*20
|
||||
variable yc equal 0.5*${boxy}
|
||||
variable yc equal 0.5*20
|
||||
|
||||
###############################################
|
||||
# Particle-related parameters
|
||||
###############################################
|
||||
variable rlo equal 0.25
|
||||
variable rhi equal 0.5
|
||||
variable dlo equal 2.0*${rlo}
|
||||
variable dlo equal 2.0*0.25
|
||||
variable dhi equal 2.0*${rhi}
|
||||
variable dhi equal 2.0*0.5
|
||||
|
||||
variable dens equal 1.0
|
||||
|
||||
variable skin equal 0.3*${rhi}
|
||||
variable skin equal 0.3*0.5
|
||||
|
||||
#############
|
||||
processors * * 1
|
||||
region boxreg block 0 ${boxx} 0 ${boxy} 0 ${boxz}
|
||||
region boxreg block 0 20 0 ${boxy} 0 ${boxz}
|
||||
region boxreg block 0 20 0 20 0 ${boxz}
|
||||
region boxreg block 0 20 0 20 0 30
|
||||
create_box 2 boxreg
|
||||
Created orthogonal box = (0 0 0) to (20 20 30)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
change_box all boundary p p f
|
||||
|
||||
comm_modify vel yes
|
||||
|
||||
region insreg1 cylinder z ${xc1} ${yc} 5 15 ${boxz}
|
||||
region insreg1 cylinder z 6 ${yc} 5 15 ${boxz}
|
||||
region insreg1 cylinder z 6 10 5 15 ${boxz}
|
||||
region insreg1 cylinder z 6 10 5 15 30
|
||||
region insreg2 cylinder z ${xc2} ${yc} 5 15 ${boxz}
|
||||
region insreg2 cylinder z 14 ${yc} 5 15 ${boxz}
|
||||
region insreg2 cylinder z 14 10 5 15 ${boxz}
|
||||
region insreg2 cylinder z 14 10 5 15 30
|
||||
|
||||
fix 1 all nve/sphere
|
||||
fix grav all gravity 10.0 vector 0 0 -1
|
||||
fix ins1 all pour 1500 1 3123 region insreg1 diam range ${dlo} ${dhi} dens ${dens} ${dens}
|
||||
fix ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 ${dhi} dens ${dens} ${dens}
|
||||
fix ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 1 dens ${dens} ${dens}
|
||||
fix ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 1 dens 1 ${dens}
|
||||
fix ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 1 dens 1 1
|
||||
Particle insertion: 562 every 346 steps, 1500 by step 693
|
||||
fix ins2 all pour 1500 2 3123 region insreg2 diam range ${dlo} ${dhi} dens ${dens} ${dens}
|
||||
fix ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 ${dhi} dens ${dens} ${dens}
|
||||
fix ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 1 dens ${dens} ${dens}
|
||||
fix ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 1 dens 1 ${dens}
|
||||
fix ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 1 dens 1 1
|
||||
Particle insertion: 562 every 346 steps, 1500 by step 693
|
||||
|
||||
comm_modify vel yes
|
||||
|
||||
neighbor ${skin} bin
|
||||
neighbor 0.15 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
pair_style granular
|
||||
pair_coeff 1 * jkr 1000.0 50.0 0.3 10 tangential mindlin 800.0 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall
|
||||
pair_coeff 2 2 hertz 200.0 20.0 tangential linear_history 300.0 1.0 0.1 rolling sds 200.0 100.0 0.1 twisting marshall
|
||||
|
||||
fix 3 all wall/gran granular hertz/material 1e5 1e3 0.3 tangential mindlin NULL 1.0 0.5 zplane 0 NULL
|
||||
|
||||
thermo_style custom step cpu atoms ke
|
||||
thermo_modify lost warn
|
||||
thermo 100
|
||||
|
||||
timestep 0.001
|
||||
|
||||
dump 1 all custom 100 ${name}.dump id type radius mass x y z
|
||||
dump 1 all custom 100 pour_two_types.dump id type radius mass x y z
|
||||
|
||||
run 5000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.15
|
||||
ghost atom cutoff = 1.15
|
||||
binsize = 0.575, bins = 35 35 53
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair granular, perpetual
|
||||
attributes: half, newton on, size, history
|
||||
pair build: half/size/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 11.98 | 11.98 | 11.98 Mbytes
|
||||
Step CPU Atoms KinEng
|
||||
0 0 0 -0
|
||||
100 0.11584234 855 -0
|
||||
200 0.12743592 855 -0
|
||||
300 0.13925815 855 -0
|
||||
400 0.35203671 1500 -0
|
||||
500 0.37055922 1500 -0
|
||||
600 0.38671875 1500 -0
|
||||
700 0.71736908 2288 -0
|
||||
800 0.74506783 2288 -0
|
||||
900 0.77112222 2288 -0
|
||||
1000 0.79632139 2288 -0
|
||||
1100 1.0384252 2845 -0
|
||||
1200 1.08093 2845 -0
|
||||
1300 1.1224561 2845 -0
|
||||
1400 1.1811485 3000 -0
|
||||
1500 1.2414908 3000 -0
|
||||
1600 1.3105879 3000 -0
|
||||
1700 1.390928 3000 -0
|
||||
1800 1.4869275 3000 -0
|
||||
1900 1.5958266 3000 -0
|
||||
2000 1.7172487 3000 -0
|
||||
2100 1.851155 3000 -0
|
||||
2200 1.9957182 3000 -0
|
||||
2300 2.1593764 3000 -0
|
||||
2400 2.3433132 3000 -0
|
||||
2500 2.532742 3000 -0
|
||||
2600 2.7376895 3000 -0
|
||||
2700 2.9463468 3000 -0
|
||||
2800 3.1645725 3000 -0
|
||||
2900 3.3879526 3000 -0
|
||||
3000 3.6152103 3000 -0
|
||||
3100 3.8467371 3000 -0
|
||||
3200 4.0787683 3000 -0
|
||||
3300 4.3097105 3000 -0
|
||||
3400 4.5423617 3000 -0
|
||||
3500 4.7773693 3000 -0
|
||||
3600 5.0127218 3000 -0
|
||||
3700 5.2519271 3000 -0
|
||||
3800 5.4951298 3000 -0
|
||||
3900 5.7210469 3000 -0
|
||||
4000 5.9432652 3000 -0
|
||||
4100 6.1687591 3000 -0
|
||||
4200 6.3942792 3000 -0
|
||||
4300 6.6331475 3000 -0
|
||||
4400 6.8632154 3000 -0
|
||||
4500 7.0979366 3000 -0
|
||||
4600 7.3305347 3000 -0
|
||||
4700 7.5670528 3000 -0
|
||||
4800 7.8086057 3000 -0
|
||||
4900 8.0407174 3000 -0
|
||||
5000 8.2765219 3000 -0
|
||||
Loop time of 8.27669 on 4 procs for 5000 steps with 3000 atoms
|
||||
|
||||
Performance: 52194.788 tau/day, 604.106 timesteps/s
|
||||
97.7% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.6106 | 3.4073 | 5.4191 | 95.7 | 41.17
|
||||
Neigh | 0.51456 | 0.64572 | 0.81542 | 16.6 | 7.80
|
||||
Comm | 0.2808 | 2.5222 | 4.4998 | 121.9 | 30.47
|
||||
Output | 0.15695 | 0.15919 | 0.16502 | 0.8 | 1.92
|
||||
Modify | 1.3517 | 1.4192 | 1.4904 | 4.9 | 17.15
|
||||
Other | | 0.123 | | | 1.49
|
||||
|
||||
Nlocal: 750 ave 1036 max 482 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
Nghost: 429.75 ave 475 max 386 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Neighs: 4051.75 ave 6274 max 2057 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 16207
|
||||
Ave neighs/atom = 5.40233
|
||||
Neighbor list builds = 1165
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:08
|
||||
Reference in New Issue
Block a user