big update
This commit is contained in:
tomswinburne
@ -27,6 +27,7 @@ group all type 1 4
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# oxDNA bond interactions - FENE backbone
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bond_style oxdna/fene
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bond_coeff * 2.0 0.25 0.7525
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special_bonds lj 0 1 1
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# oxDNA pair interactions
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pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
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@ -48,6 +49,7 @@ timestep 1e-5
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#comm_style tiled
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#fix 3 all balance 10000 1.1 rcb
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comm_modify cutoff 2.5
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#compute mol all chunk/atom molecule
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#compute mychunk all vcm/chunk mol
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1175
examples/USER/cgdna/examples/oxDNA/duplex1/log.30Jun20.duplex1.g++.1
Normal file
1175
examples/USER/cgdna/examples/oxDNA/duplex1/log.30Jun20.duplex1.g++.1
Normal file
File diff suppressed because it is too large
Load Diff
1175
examples/USER/cgdna/examples/oxDNA/duplex1/log.30Jun20.duplex1.g++.4
Normal file
1175
examples/USER/cgdna/examples/oxDNA/duplex1/log.30Jun20.duplex1.g++.4
Normal file
File diff suppressed because it is too large
Load Diff
@ -27,6 +27,7 @@ group all type 1 4
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# oxDNA bond interactions - FENE backbone
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bond_style oxdna/fene
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bond_coeff * 2.0 0.25 0.7525
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special_bonds lj 0 1 1
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# oxDNA pair interactions
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pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
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@ -48,6 +49,7 @@ timestep 1e-5
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#comm_style tiled
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#fix 3 all balance 10000 1.1 rcb
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comm_modify cutoff 2.5
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#compute mol all chunk/atom molecule
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#compute mychunk all vcm/chunk mol
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1176
examples/USER/cgdna/examples/oxDNA/duplex2/log.30Jun20.duplex2.g++.1
Normal file
1176
examples/USER/cgdna/examples/oxDNA/duplex2/log.30Jun20.duplex2.g++.1
Normal file
File diff suppressed because it is too large
Load Diff
1176
examples/USER/cgdna/examples/oxDNA/duplex2/log.30Jun20.duplex2.g++.4
Normal file
1176
examples/USER/cgdna/examples/oxDNA/duplex2/log.30Jun20.duplex2.g++.4
Normal file
File diff suppressed because it is too large
Load Diff
@ -27,6 +27,7 @@ group all type 1 4
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# oxDNA2 bond interactions - FENE backbone
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bond_style oxdna2/fene
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bond_coeff * 2.0 0.25 0.7564
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special_bonds lj 0 1 1
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# oxDNA2 pair interactions
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pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
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@ -49,6 +50,7 @@ timestep 1e-5
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#comm_style tiled
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#fix 3 all balance 10000 1.1 rcb
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comm_modify cutoff 2.5
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#compute mol all chunk/atom molecule
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#compute mychunk all vcm/chunk mol
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File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
@ -27,6 +27,7 @@ group all type 1 4
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# oxDNA2 bond interactions - FENE backbone
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bond_style oxdna2/fene
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bond_coeff * 2.0 0.25 0.7564
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special_bonds lj 0 1 1
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# oxDNA2 pair interactions
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pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
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@ -49,6 +50,7 @@ timestep 1e-5
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#comm_style tiled
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#fix 3 all balance 10000 1.1 rcb
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comm_modify cutoff 2.5
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#compute mol all chunk/atom molecule
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#compute mychunk all vcm/chunk mol
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File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
@ -27,6 +27,7 @@ group all type 1 4
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# oxDNA2 bond interactions - FENE backbone
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bond_style oxdna2/fene
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bond_coeff * 2.0 0.25 0.7564
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special_bonds lj 0 1 1
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# oxDNA2 pair interactions
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pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
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@ -49,6 +50,7 @@ timestep 1e-5
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#comm_style tiled
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#fix 3 all balance 10000 1.1 rcb
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comm_modify cutoff 2.5
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#compute mol all chunk/atom molecule
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#compute mychunk all vcm/chunk mol
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File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
@ -18,17 +18,19 @@ atom_style hybrid bond ellipsoid
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atom_modify sort 0 1.0
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# Pair interactions require lists of neighbours to be calculated
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neighbor 2.0 bin
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neighbor 1.0 bin
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neigh_modify every 10 delay 0 check yes
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read_data data.duplex4.4type
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mass * 3.1575
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mass * 3.1575 # sets per-type mass if not in data file
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set atom * mass 3.1575 # sets per-atom mass
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group all type 1 4
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# oxDNA bond interactions - FENE backbone
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bond_style oxdna2/fene
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bond_coeff * 2.0 0.25 0.7564
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special_bonds lj 0 1 1
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# oxDNA pair interactions
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pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
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@ -60,6 +62,7 @@ timestep 1e-4
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#comm_style tiled
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#fix 3 all balance 10000 1.1 rcb
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comm_modify cutoff 2.5
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#compute mol all chunk/atom molecule
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#compute mychunk all vcm/chunk mol
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@ -10,7 +10,7 @@ units lj
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dimension 3
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newton on
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newton off
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boundary p p p
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@ -22,13 +22,15 @@ neighbor 1.0 bin
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neigh_modify every 10 delay 0 check yes
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read_data data.duplex4.8type
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mass * 3.1575
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mass * 3.1575 # sets per-type mass if not in data file
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set atom * mass 3.1575 # sets per-atom mass
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group all type 1 8
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# oxDNA bond interactions - FENE backbone
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bond_style oxdna2/fene
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bond_coeff * 2.0 0.25 0.7564
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special_bonds lj 0 1 1
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# oxDNA pair interactions
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pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
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@ -60,6 +62,7 @@ timestep 1e-4
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#comm_style tiled
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#fix 3 all balance 10000 1.1 rcb
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comm_modify cutoff 2.5
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#compute mol all chunk/atom molecule
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#compute mychunk all vcm/chunk mol
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@ -0,0 +1,244 @@
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LAMMPS (30 Jun 2020)
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variable number equal 1
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variable ofreq equal 10000
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variable efreq equal 10000
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variable ntype equal 4
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variable T equal 0.1
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units lj
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dimension 3
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newton off
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boundary p p p
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atom_style hybrid bond ellipsoid
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WARNING: Atom_style hybrid defines both pertype and peratom masses - both must be set, only peratom masses will be used (../atom_vec_hybrid.cpp:156)
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atom_modify sort 0 1.0
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# Pair interactions require lists of neighbours to be calculated
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neighbor 1.0 bin
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neigh_modify every 10 delay 0 check yes
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read_data data.duplex4.4type
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orthogonal box = (-20 -20 -20) to (20 20 20)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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26 atoms
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reading velocities ...
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26 velocities
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26 ellipsoids
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scanning bonds ...
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2 = max bonds/atom
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reading bonds ...
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24 bonds
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2 = max # of 1-2 neighbors
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2 = max # of 1-3 neighbors
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4 = max # of 1-4 neighbors
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6 = max # of special neighbors
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special bonds CPU = 0.000 seconds
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read_data CPU = 0.003 seconds
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mass * 3.1575 # sets per-type mass if not in data file
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set atom * mass 3.1575 # sets per-atom mass
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26 settings made for mass
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group all type 1 4
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26 atoms in group all
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# oxDNA bond interactions - FENE backbone
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bond_style oxdna2/fene
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bond_coeff * 2.0 0.25 0.7564
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special_bonds lj 0 1 1
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2 = max # of 1-2 neighbors
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2 = max # of 1-3 neighbors
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4 = max # of 1-4 neighbors
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6 = max # of special neighbors
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special bonds CPU = 0.000 seconds
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# oxDNA pair interactions
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pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
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pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
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pair_coeff * * oxdna2/stk seqdep ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
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pair_coeff * * oxdna2/stk seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
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pair_coeff * * oxdna2/hbond seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
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label loop
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variable base loop ${ntype}
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variable base loop 4
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variable basemod equal ${base}%4
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variable basemod equal 1%4
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if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
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variable comp equal ${base}+3
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variable comp equal 1+3
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pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
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pair_coeff 1 ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
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pair_coeff 1 4 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
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if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
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next base
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jump in.duplex4.4type loop
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variable base loop ${ntype}
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variable base loop 4
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variable basemod equal ${base}%4
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variable basemod equal 2%4
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if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
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if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
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variable comp equal ${base}+1
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||||
variable comp equal 2+1
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||||
pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
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pair_coeff 2 3 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
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next base
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jump in.duplex4.4type loop
|
||||
variable base loop ${ntype}
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variable base loop 4
|
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variable basemod equal ${base}%4
|
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variable basemod equal 3%4
|
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if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
next base
|
||||
jump in.duplex4.4type loop
|
||||
variable base loop ${ntype}
|
||||
variable base loop 4
|
||||
variable basemod equal ${base}%4
|
||||
variable basemod equal 4%4
|
||||
if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
next base
|
||||
jump in.duplex4.4type loop
|
||||
|
||||
pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
|
||||
pair_coeff * * oxdna2/dh ${T} 0.2 0.815
|
||||
pair_coeff * * oxdna2/dh 0.1 0.2 0.815
|
||||
|
||||
# Langevin dynamics
|
||||
fix 1 all nve/asphere
|
||||
fix 2 all langevin ${T} ${T} 25.0 457145 angmom 10
|
||||
fix 2 all langevin 0.1 ${T} 25.0 457145 angmom 10
|
||||
fix 2 all langevin 0.1 0.1 25.0 457145 angmom 10
|
||||
|
||||
timestep 1e-4
|
||||
|
||||
#comm_style tiled
|
||||
#fix 3 all balance 10000 1.1 rcb
|
||||
comm_modify cutoff 2.5
|
||||
|
||||
#compute mol all chunk/atom molecule
|
||||
#compute mychunk all vcm/chunk mol
|
||||
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
|
||||
|
||||
#dump pos all xyz ${ofreq} traj.${number}.xyz
|
||||
|
||||
compute quat all property/atom quatw quati quatj quatk
|
||||
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
|
||||
#dump_modify quat sort id
|
||||
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
compute epot all pe
|
||||
variable erot equal c_erot
|
||||
variable ekin equal c_ekin
|
||||
variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
fix 5 all print 10000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
dump out all custom ${ofreq} out.${number}.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4] vx vy vz
|
||||
dump out all custom 10000 out.${number}.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4] vx vy vz
|
||||
dump out all custom 10000 out.1.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4] vx vy vz
|
||||
dump_modify out sort id
|
||||
dump_modify out format line "%d %d %d %13.6le %13.6le %13.6le %d %d %d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le "
|
||||
|
||||
#restart 10000 config0_restart config1_restart
|
||||
|
||||
run 100000
|
||||
Neighbor list info ...
|
||||
update every 10 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.6389877
|
||||
ghost atom cutoff = 4.6389877
|
||||
binsize = 2.3194939, bins = 18 18 18
|
||||
6 neighbor lists, perpetual/occasional/extra = 6 0 0
|
||||
(1) pair oxdna2/excv, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: half/bin/3d/newtoff
|
||||
bin: standard
|
||||
(2) pair oxdna2/stk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) pair oxdna2/hbond, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(4) pair oxdna2/xstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(5) pair oxdna2/coaxstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(6) pair oxdna2/dh, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
WARNING: Communication cutoff adjusted to 4.638987723814632 (../comm.cpp:690)
|
||||
0 ekin = 0 | erot = 0 | epot = -41.6285382417448 | etot = -41.6285382417448
|
||||
Per MPI rank memory allocation (min/avg/max) = 9.771 | 9.771 | 9.771 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -1.6384018 0.037304147 -1.6010976 6.7769766e-05
|
||||
10000 ekin = 0.876675896491307 | erot = 3.01631310953192 | epot = -43.6949424313443 | etot = -39.8019534253211
|
||||
20000 ekin = 1.02178060459022 | erot = 1.54107635735041 | epot = -40.2257383206528 | etot = -37.6628813587121
|
||||
30000 ekin = 1.77819697871127 | erot = 2.67180081099997 | epot = -40.9840548186678 | etot = -36.5340570289565
|
||||
40000 ekin = 2.55095642638533 | erot = 2.97955929579275 | epot = -40.0756048400153 | etot = -34.5450891178372
|
||||
50000 ekin = 2.43321388920862 | erot = 3.63137266285959 | epot = -39.3718897377946 | etot = -33.3073031857264
|
||||
60000 ekin = 2.51123200110303 | erot = 3.95693243683571 | epot = -38.8877878920178 | etot = -32.4196234540791
|
||||
70000 ekin = 3.33444097207872 | erot = 4.12593683683079 | epot = -38.7679893452499 | etot = -31.3076115363404
|
||||
80000 ekin = 3.41969296989344 | erot = 3.46589964095079 | epot = -37.5712487729465 | etot = -30.6856561621023
|
||||
90000 ekin = 3.53106755106414 | erot = 3.40955821292295 | epot = -35.9319384430368 | etot = -28.9913126790497
|
||||
100000 ekin = 3.47860763041501 | erot = 3.95117534418391 | epot = -37.6128506757402 | etot = -30.1830677011413
|
||||
100000 0.09276287 -1.4972391 0.050590991 -1.3128555 0.00017815014
|
||||
Loop time of 7.33046 on 1 procs for 100000 steps with 26 atoms
|
||||
|
||||
Performance: 117864.395 tau/day, 13641.712 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 6.4814 | 6.4814 | 6.4814 | 0.0 | 88.42
|
||||
Bond | 0.16262 | 0.16262 | 0.16262 | 0.0 | 2.22
|
||||
Neigh | 4.2e-05 | 4.2e-05 | 4.2e-05 | 0.0 | 0.00
|
||||
Comm | 0.019555 | 0.019555 | 0.019555 | 0.0 | 0.27
|
||||
Output | 0.00131 | 0.00131 | 0.00131 | 0.0 | 0.02
|
||||
Modify | 0.64596 | 0.64596 | 0.64596 | 0.0 | 8.81
|
||||
Other | | 0.01961 | | | 0.27
|
||||
|
||||
Nlocal: 26.0 ave 26.0 max 26.0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0.0 ave 0.0 max 0.0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 299.0 ave 299.0 max 299.0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 299
|
||||
Ave neighs/atom = 11.5
|
||||
Ave special neighs/atom = 5.076923076923077
|
||||
Neighbor list builds = 2
|
||||
Dangerous builds = 0
|
||||
|
||||
#write_restart config.${number}.*
|
||||
|
||||
|
||||
Total wall time: 0:00:07
|
||||
@ -0,0 +1,244 @@
|
||||
LAMMPS (30 Jun 2020)
|
||||
variable number equal 1
|
||||
variable ofreq equal 10000
|
||||
variable efreq equal 10000
|
||||
|
||||
variable ntype equal 4
|
||||
|
||||
variable T equal 0.1
|
||||
|
||||
units lj
|
||||
|
||||
dimension 3
|
||||
|
||||
newton off
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid
|
||||
WARNING: Atom_style hybrid defines both pertype and peratom masses - both must be set, only peratom masses will be used (../atom_vec_hybrid.cpp:156)
|
||||
atom_modify sort 0 1.0
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 10 delay 0 check yes
|
||||
|
||||
read_data data.duplex4.4type
|
||||
orthogonal box = (-20 -20 -20) to (20 20 20)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
26 atoms
|
||||
reading velocities ...
|
||||
26 velocities
|
||||
26 ellipsoids
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
reading bonds ...
|
||||
24 bonds
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
4 = max # of 1-4 neighbors
|
||||
6 = max # of special neighbors
|
||||
special bonds CPU = 0.001 seconds
|
||||
read_data CPU = 0.004 seconds
|
||||
mass * 3.1575 # sets per-type mass if not in data file
|
||||
set atom * mass 3.1575 # sets per-atom mass
|
||||
26 settings made for mass
|
||||
|
||||
group all type 1 4
|
||||
26 atoms in group all
|
||||
|
||||
# oxDNA bond interactions - FENE backbone
|
||||
bond_style oxdna2/fene
|
||||
bond_coeff * 2.0 0.25 0.7564
|
||||
special_bonds lj 0 1 1
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
4 = max # of 1-4 neighbors
|
||||
6 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
|
||||
# oxDNA pair interactions
|
||||
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
|
||||
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna2/stk seqdep ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/stk seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/hbond seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
|
||||
label loop
|
||||
variable base loop ${ntype}
|
||||
variable base loop 4
|
||||
variable basemod equal ${base}%4
|
||||
variable basemod equal 1%4
|
||||
if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
variable comp equal ${base}+3
|
||||
variable comp equal 1+3
|
||||
pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
next base
|
||||
jump in.duplex4.4type loop
|
||||
variable base loop ${ntype}
|
||||
variable base loop 4
|
||||
variable basemod equal ${base}%4
|
||||
variable basemod equal 2%4
|
||||
if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
variable comp equal ${base}+1
|
||||
variable comp equal 2+1
|
||||
pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
next base
|
||||
jump in.duplex4.4type loop
|
||||
variable base loop ${ntype}
|
||||
variable base loop 4
|
||||
variable basemod equal ${base}%4
|
||||
variable basemod equal 3%4
|
||||
if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
next base
|
||||
jump in.duplex4.4type loop
|
||||
variable base loop ${ntype}
|
||||
variable base loop 4
|
||||
variable basemod equal ${base}%4
|
||||
variable basemod equal 4%4
|
||||
if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
next base
|
||||
jump in.duplex4.4type loop
|
||||
|
||||
pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
|
||||
pair_coeff * * oxdna2/dh ${T} 0.2 0.815
|
||||
pair_coeff * * oxdna2/dh 0.1 0.2 0.815
|
||||
|
||||
# Langevin dynamics
|
||||
fix 1 all nve/asphere
|
||||
fix 2 all langevin ${T} ${T} 25.0 457145 angmom 10
|
||||
fix 2 all langevin 0.1 ${T} 25.0 457145 angmom 10
|
||||
fix 2 all langevin 0.1 0.1 25.0 457145 angmom 10
|
||||
|
||||
timestep 1e-4
|
||||
|
||||
#comm_style tiled
|
||||
#fix 3 all balance 10000 1.1 rcb
|
||||
comm_modify cutoff 2.5
|
||||
|
||||
#compute mol all chunk/atom molecule
|
||||
#compute mychunk all vcm/chunk mol
|
||||
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
|
||||
|
||||
#dump pos all xyz ${ofreq} traj.${number}.xyz
|
||||
|
||||
compute quat all property/atom quatw quati quatj quatk
|
||||
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
|
||||
#dump_modify quat sort id
|
||||
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
compute epot all pe
|
||||
variable erot equal c_erot
|
||||
variable ekin equal c_ekin
|
||||
variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
fix 5 all print 10000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
dump out all custom ${ofreq} out.${number}.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4] vx vy vz
|
||||
dump out all custom 10000 out.${number}.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4] vx vy vz
|
||||
dump out all custom 10000 out.1.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4] vx vy vz
|
||||
dump_modify out sort id
|
||||
dump_modify out format line "%d %d %d %13.6le %13.6le %13.6le %d %d %d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le "
|
||||
|
||||
#restart 10000 config0_restart config1_restart
|
||||
|
||||
run 100000
|
||||
Neighbor list info ...
|
||||
update every 10 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.6389877
|
||||
ghost atom cutoff = 4.6389877
|
||||
binsize = 2.3194939, bins = 18 18 18
|
||||
6 neighbor lists, perpetual/occasional/extra = 6 0 0
|
||||
(1) pair oxdna2/excv, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: half/bin/3d/newtoff
|
||||
bin: standard
|
||||
(2) pair oxdna2/stk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) pair oxdna2/hbond, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(4) pair oxdna2/xstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(5) pair oxdna2/coaxstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(6) pair oxdna2/dh, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
WARNING: Communication cutoff adjusted to 4.638987723814632 (../comm.cpp:690)
|
||||
0 ekin = 0 | erot = 0 | epot = -41.6285382417448 | etot = -41.6285382417448
|
||||
Per MPI rank memory allocation (min/avg/max) = 9.756 | 9.813 | 9.871 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -1.6384018 0.037304147 -1.6010976 6.7769766e-05
|
||||
10000 ekin = 0.705506935391957 | erot = 3.21864563172922 | epot = -44.0640899615318 | etot = -40.1399373944106
|
||||
20000 ekin = 1.16547426389222 | erot = 1.69259899672632 | epot = -41.827511978894 | etot = -38.9694387182755
|
||||
30000 ekin = 2.07592540045025 | erot = 2.81661265099434 | epot = -41.8258727293348 | etot = -36.9333346778902
|
||||
40000 ekin = 3.0352692177735 | erot = 2.43995587980307 | epot = -41.3155342467788 | etot = -35.8403091492022
|
||||
50000 ekin = 2.69044710203348 | erot = 2.86176633025683 | epot = -40.5544750556414 | etot = -35.0022616233511
|
||||
60000 ekin = 2.90956639769978 | erot = 2.84679944563592 | epot = -39.7474408128141 | etot = -33.9910749694784
|
||||
70000 ekin = 1.89941118514544 | erot = 3.71508585194422 | epot = -38.9575890625426 | etot = -33.3430920254529
|
||||
80000 ekin = 2.43472912058895 | erot = 3.11589280920166 | epot = -39.844809532279 | etot = -34.2941876024883
|
||||
90000 ekin = 2.3759389593227 | erot = 3.25835921096947 | epot = -38.913072246407 | etot = -33.2787740761149
|
||||
100000 ekin = 3.23901515322217 | erot = 3.3464944524431 | epot = -38.6302041314432 | etot = -32.044694525778
|
||||
100000 0.086373737 -1.5432369 0.057459797 -1.3611996 7.7958353e-05
|
||||
Loop time of 6.09292 on 4 procs for 100000 steps with 26 atoms
|
||||
|
||||
Performance: 141803.976 tau/day, 16412.497 timesteps/s
|
||||
99.7% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.047712 | 2.5625 | 5.2874 | 157.3 | 42.06
|
||||
Bond | 0.007398 | 0.053166 | 0.10097 | 19.8 | 0.87
|
||||
Neigh | 1.8e-05 | 1.8e-05 | 1.8e-05 | 0.0 | 0.00
|
||||
Comm | 0.29205 | 2.9624 | 5.4188 | 143.0 | 48.62
|
||||
Output | 0.000866 | 0.00099325 | 0.001303 | 0.0 | 0.02
|
||||
Modify | 0.016247 | 0.18354 | 0.37524 | 39.2 | 3.01
|
||||
Other | | 0.3303 | | | 5.42
|
||||
|
||||
Nlocal: 6.5 ave 14.0 max 0.0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
Nghost: 18.5 ave 24.0 max 12.0 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 0 2
|
||||
Neighs: 113.75 ave 239.0 max 0.0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 455
|
||||
Ave neighs/atom = 17.5
|
||||
Ave special neighs/atom = 5.076923076923077
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds = 0
|
||||
|
||||
#write_restart config.${number}.*
|
||||
|
||||
|
||||
Total wall time: 0:00:06
|
||||
@ -0,0 +1,286 @@
|
||||
LAMMPS (30 Jun 2020)
|
||||
variable number equal 1
|
||||
variable ofreq equal 10000
|
||||
variable efreq equal 10000
|
||||
|
||||
variable ntype equal 8
|
||||
|
||||
variable T equal 0.1
|
||||
|
||||
units lj
|
||||
|
||||
dimension 3
|
||||
|
||||
newton off
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid
|
||||
WARNING: Atom_style hybrid defines both pertype and peratom masses - both must be set, only peratom masses will be used (../atom_vec_hybrid.cpp:156)
|
||||
atom_modify sort 0 1.0
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 10 delay 0 check yes
|
||||
|
||||
read_data data.duplex4.8type
|
||||
orthogonal box = (-20 -20 -20) to (20 20 20)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
26 atoms
|
||||
reading velocities ...
|
||||
26 velocities
|
||||
26 ellipsoids
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
reading bonds ...
|
||||
24 bonds
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
4 = max # of 1-4 neighbors
|
||||
6 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.002 seconds
|
||||
mass * 3.1575 # sets per-type mass if not in data file
|
||||
set atom * mass 3.1575 # sets per-atom mass
|
||||
26 settings made for mass
|
||||
|
||||
group all type 1 8
|
||||
26 atoms in group all
|
||||
|
||||
# oxDNA bond interactions - FENE backbone
|
||||
bond_style oxdna2/fene
|
||||
bond_coeff * 2.0 0.25 0.7564
|
||||
special_bonds lj 0 1 1
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
4 = max # of 1-4 neighbors
|
||||
6 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
|
||||
# oxDNA pair interactions
|
||||
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
|
||||
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna2/stk seqdep ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/stk seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/hbond seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
|
||||
label loop
|
||||
variable base loop ${ntype}
|
||||
variable base loop 8
|
||||
variable basemod equal ${base}%4
|
||||
variable basemod equal 1%4
|
||||
if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
variable comp equal ${base}+3
|
||||
variable comp equal 1+3
|
||||
pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
next base
|
||||
jump in.duplex4.8type loop
|
||||
variable base loop ${ntype}
|
||||
variable base loop 8
|
||||
variable basemod equal ${base}%4
|
||||
variable basemod equal 2%4
|
||||
if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
variable comp equal ${base}+1
|
||||
variable comp equal 2+1
|
||||
pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
next base
|
||||
jump in.duplex4.8type loop
|
||||
variable base loop ${ntype}
|
||||
variable base loop 8
|
||||
variable basemod equal ${base}%4
|
||||
variable basemod equal 3%4
|
||||
if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
next base
|
||||
jump in.duplex4.8type loop
|
||||
variable base loop ${ntype}
|
||||
variable base loop 8
|
||||
variable basemod equal ${base}%4
|
||||
variable basemod equal 4%4
|
||||
if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
next base
|
||||
jump in.duplex4.8type loop
|
||||
variable base loop ${ntype}
|
||||
variable base loop 8
|
||||
variable basemod equal ${base}%4
|
||||
variable basemod equal 5%4
|
||||
if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
variable comp equal ${base}+3
|
||||
variable comp equal 5+3
|
||||
pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 5 ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 5 8 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
next base
|
||||
jump in.duplex4.8type loop
|
||||
variable base loop ${ntype}
|
||||
variable base loop 8
|
||||
variable basemod equal ${base}%4
|
||||
variable basemod equal 6%4
|
||||
if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
variable comp equal ${base}+1
|
||||
variable comp equal 6+1
|
||||
pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 6 ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 6 7 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
next base
|
||||
jump in.duplex4.8type loop
|
||||
variable base loop ${ntype}
|
||||
variable base loop 8
|
||||
variable basemod equal ${base}%4
|
||||
variable basemod equal 7%4
|
||||
if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
next base
|
||||
jump in.duplex4.8type loop
|
||||
variable base loop ${ntype}
|
||||
variable base loop 8
|
||||
variable basemod equal ${base}%4
|
||||
variable basemod equal 8%4
|
||||
if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
next base
|
||||
jump in.duplex4.8type loop
|
||||
|
||||
pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
|
||||
pair_coeff * * oxdna2/dh ${T} 0.2 0.815
|
||||
pair_coeff * * oxdna2/dh 0.1 0.2 0.815
|
||||
|
||||
# Langevin dynamics
|
||||
fix 1 all nve/asphere
|
||||
fix 2 all langevin ${T} ${T} 25.0 457145 angmom 10
|
||||
fix 2 all langevin 0.1 ${T} 25.0 457145 angmom 10
|
||||
fix 2 all langevin 0.1 0.1 25.0 457145 angmom 10
|
||||
|
||||
timestep 1e-4
|
||||
|
||||
#comm_style tiled
|
||||
#fix 3 all balance 10000 1.1 rcb
|
||||
comm_modify cutoff 2.5
|
||||
|
||||
#compute mol all chunk/atom molecule
|
||||
#compute mychunk all vcm/chunk mol
|
||||
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
|
||||
|
||||
#dump pos all xyz ${ofreq} traj.${number}.xyz
|
||||
|
||||
compute quat all property/atom quatw quati quatj quatk
|
||||
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
|
||||
#dump_modify quat sort id
|
||||
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
compute epot all pe
|
||||
variable erot equal c_erot
|
||||
variable ekin equal c_ekin
|
||||
variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
fix 5 all print 10000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
dump out all custom ${ofreq} out.${number}.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4] vx vy vz
|
||||
dump out all custom 10000 out.${number}.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4] vx vy vz
|
||||
dump out all custom 10000 out.1.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4] vx vy vz
|
||||
dump_modify out sort id
|
||||
dump_modify out format line "%d %d %d %13.6le %13.6le %13.6le %d %d %d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le "
|
||||
|
||||
#restart 10000 config0_restart config1_restart
|
||||
|
||||
run 100000
|
||||
Neighbor list info ...
|
||||
update every 10 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.6389877
|
||||
ghost atom cutoff = 4.6389877
|
||||
binsize = 2.3194939, bins = 18 18 18
|
||||
6 neighbor lists, perpetual/occasional/extra = 6 0 0
|
||||
(1) pair oxdna2/excv, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: half/bin/3d/newtoff
|
||||
bin: standard
|
||||
(2) pair oxdna2/stk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) pair oxdna2/hbond, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(4) pair oxdna2/xstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(5) pair oxdna2/coaxstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(6) pair oxdna2/dh, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
WARNING: Communication cutoff adjusted to 4.638987723814632 (../comm.cpp:690)
|
||||
0 ekin = 0 | erot = 0 | epot = -41.6285382417448 | etot = -41.6285382417448
|
||||
Per MPI rank memory allocation (min/avg/max) = 9.771 | 9.771 | 9.771 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -1.6384018 0.037304147 -1.6010976 6.7769766e-05
|
||||
10000 ekin = 0.876675896491307 | erot = 3.01631310953192 | epot = -43.6949424313443 | etot = -39.8019534253211
|
||||
20000 ekin = 1.02178060459022 | erot = 1.54107635735041 | epot = -40.2257383206528 | etot = -37.6628813587121
|
||||
30000 ekin = 1.77819697871127 | erot = 2.67180081099997 | epot = -40.9840548186678 | etot = -36.5340570289565
|
||||
40000 ekin = 2.55095642638533 | erot = 2.97955929579275 | epot = -40.0756048400153 | etot = -34.5450891178372
|
||||
50000 ekin = 2.43321388920862 | erot = 3.63137266285959 | epot = -39.3718897377946 | etot = -33.3073031857264
|
||||
60000 ekin = 2.51123200110303 | erot = 3.95693243683571 | epot = -38.8877878920178 | etot = -32.4196234540791
|
||||
70000 ekin = 3.33444097207872 | erot = 4.12593683683079 | epot = -38.7679893452499 | etot = -31.3076115363404
|
||||
80000 ekin = 3.41969296989344 | erot = 3.46589964095079 | epot = -37.5712487729465 | etot = -30.6856561621023
|
||||
90000 ekin = 3.53106755106414 | erot = 3.40955821292295 | epot = -35.9319384430368 | etot = -28.9913126790497
|
||||
100000 ekin = 3.47860763041501 | erot = 3.95117534418391 | epot = -37.6128506757402 | etot = -30.1830677011413
|
||||
100000 0.09276287 -1.4972391 0.050590991 -1.3128555 0.00017815014
|
||||
Loop time of 7.44606 on 1 procs for 100000 steps with 26 atoms
|
||||
|
||||
Performance: 116034.458 tau/day, 13429.914 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 | 6.5843 | 6.5843 | 6.5843 | 0.0 | 88.43
|
||||
Bond | 0.16149 | 0.16149 | 0.16149 | 0.0 | 2.17
|
||||
Neigh | 4.3e-05 | 4.3e-05 | 4.3e-05 | 0.0 | 0.00
|
||||
Comm | 0.022595 | 0.022595 | 0.022595 | 0.0 | 0.30
|
||||
Output | 0.001492 | 0.001492 | 0.001492 | 0.0 | 0.02
|
||||
Modify | 0.65313 | 0.65313 | 0.65313 | 0.0 | 8.77
|
||||
Other | | 0.02299 | | | 0.31
|
||||
|
||||
Nlocal: 26.0 ave 26.0 max 26.0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0.0 ave 0.0 max 0.0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 299.0 ave 299.0 max 299.0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 299
|
||||
Ave neighs/atom = 11.5
|
||||
Ave special neighs/atom = 5.076923076923077
|
||||
Neighbor list builds = 2
|
||||
Dangerous builds = 0
|
||||
|
||||
#write_restart config.${number}.*
|
||||
|
||||
|
||||
Total wall time: 0:00:07
|
||||
@ -0,0 +1,286 @@
|
||||
LAMMPS (30 Jun 2020)
|
||||
variable number equal 1
|
||||
variable ofreq equal 10000
|
||||
variable efreq equal 10000
|
||||
|
||||
variable ntype equal 8
|
||||
|
||||
variable T equal 0.1
|
||||
|
||||
units lj
|
||||
|
||||
dimension 3
|
||||
|
||||
newton off
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid
|
||||
WARNING: Atom_style hybrid defines both pertype and peratom masses - both must be set, only peratom masses will be used (../atom_vec_hybrid.cpp:156)
|
||||
atom_modify sort 0 1.0
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 10 delay 0 check yes
|
||||
|
||||
read_data data.duplex4.8type
|
||||
orthogonal box = (-20 -20 -20) to (20 20 20)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
26 atoms
|
||||
reading velocities ...
|
||||
26 velocities
|
||||
26 ellipsoids
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
reading bonds ...
|
||||
24 bonds
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
4 = max # of 1-4 neighbors
|
||||
6 = max # of special neighbors
|
||||
special bonds CPU = 0.001 seconds
|
||||
read_data CPU = 0.004 seconds
|
||||
mass * 3.1575 # sets per-type mass if not in data file
|
||||
set atom * mass 3.1575 # sets per-atom mass
|
||||
26 settings made for mass
|
||||
|
||||
group all type 1 8
|
||||
26 atoms in group all
|
||||
|
||||
# oxDNA bond interactions - FENE backbone
|
||||
bond_style oxdna2/fene
|
||||
bond_coeff * 2.0 0.25 0.7564
|
||||
special_bonds lj 0 1 1
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
4 = max # of 1-4 neighbors
|
||||
6 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
|
||||
# oxDNA pair interactions
|
||||
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
|
||||
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna2/stk seqdep ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/stk seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/hbond seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
|
||||
label loop
|
||||
variable base loop ${ntype}
|
||||
variable base loop 8
|
||||
variable basemod equal ${base}%4
|
||||
variable basemod equal 1%4
|
||||
if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
variable comp equal ${base}+3
|
||||
variable comp equal 1+3
|
||||
pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
next base
|
||||
jump in.duplex4.8type loop
|
||||
variable base loop ${ntype}
|
||||
variable base loop 8
|
||||
variable basemod equal ${base}%4
|
||||
variable basemod equal 2%4
|
||||
if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
variable comp equal ${base}+1
|
||||
variable comp equal 2+1
|
||||
pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
next base
|
||||
jump in.duplex4.8type loop
|
||||
variable base loop ${ntype}
|
||||
variable base loop 8
|
||||
variable basemod equal ${base}%4
|
||||
variable basemod equal 3%4
|
||||
if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
next base
|
||||
jump in.duplex4.8type loop
|
||||
variable base loop ${ntype}
|
||||
variable base loop 8
|
||||
variable basemod equal ${base}%4
|
||||
variable basemod equal 4%4
|
||||
if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
next base
|
||||
jump in.duplex4.8type loop
|
||||
variable base loop ${ntype}
|
||||
variable base loop 8
|
||||
variable basemod equal ${base}%4
|
||||
variable basemod equal 5%4
|
||||
if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
variable comp equal ${base}+3
|
||||
variable comp equal 5+3
|
||||
pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 5 ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 5 8 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
next base
|
||||
jump in.duplex4.8type loop
|
||||
variable base loop ${ntype}
|
||||
variable base loop 8
|
||||
variable basemod equal ${base}%4
|
||||
variable basemod equal 6%4
|
||||
if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
variable comp equal ${base}+1
|
||||
variable comp equal 6+1
|
||||
pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 6 ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 6 7 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
next base
|
||||
jump in.duplex4.8type loop
|
||||
variable base loop ${ntype}
|
||||
variable base loop 8
|
||||
variable basemod equal ${base}%4
|
||||
variable basemod equal 7%4
|
||||
if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
next base
|
||||
jump in.duplex4.8type loop
|
||||
variable base loop ${ntype}
|
||||
variable base loop 8
|
||||
variable basemod equal ${base}%4
|
||||
variable basemod equal 8%4
|
||||
if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
next base
|
||||
jump in.duplex4.8type loop
|
||||
|
||||
pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
|
||||
pair_coeff * * oxdna2/dh ${T} 0.2 0.815
|
||||
pair_coeff * * oxdna2/dh 0.1 0.2 0.815
|
||||
|
||||
# Langevin dynamics
|
||||
fix 1 all nve/asphere
|
||||
fix 2 all langevin ${T} ${T} 25.0 457145 angmom 10
|
||||
fix 2 all langevin 0.1 ${T} 25.0 457145 angmom 10
|
||||
fix 2 all langevin 0.1 0.1 25.0 457145 angmom 10
|
||||
|
||||
timestep 1e-4
|
||||
|
||||
#comm_style tiled
|
||||
#fix 3 all balance 10000 1.1 rcb
|
||||
comm_modify cutoff 2.5
|
||||
|
||||
#compute mol all chunk/atom molecule
|
||||
#compute mychunk all vcm/chunk mol
|
||||
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
|
||||
|
||||
#dump pos all xyz ${ofreq} traj.${number}.xyz
|
||||
|
||||
compute quat all property/atom quatw quati quatj quatk
|
||||
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
|
||||
#dump_modify quat sort id
|
||||
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
compute epot all pe
|
||||
variable erot equal c_erot
|
||||
variable ekin equal c_ekin
|
||||
variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
fix 5 all print 10000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
dump out all custom ${ofreq} out.${number}.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4] vx vy vz
|
||||
dump out all custom 10000 out.${number}.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4] vx vy vz
|
||||
dump out all custom 10000 out.1.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4] vx vy vz
|
||||
dump_modify out sort id
|
||||
dump_modify out format line "%d %d %d %13.6le %13.6le %13.6le %d %d %d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le "
|
||||
|
||||
#restart 10000 config0_restart config1_restart
|
||||
|
||||
run 100000
|
||||
Neighbor list info ...
|
||||
update every 10 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.6389877
|
||||
ghost atom cutoff = 4.6389877
|
||||
binsize = 2.3194939, bins = 18 18 18
|
||||
6 neighbor lists, perpetual/occasional/extra = 6 0 0
|
||||
(1) pair oxdna2/excv, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: half/bin/3d/newtoff
|
||||
bin: standard
|
||||
(2) pair oxdna2/stk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) pair oxdna2/hbond, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(4) pair oxdna2/xstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(5) pair oxdna2/coaxstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(6) pair oxdna2/dh, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
WARNING: Communication cutoff adjusted to 4.638987723814632 (../comm.cpp:690)
|
||||
0 ekin = 0 | erot = 0 | epot = -41.6285382417448 | etot = -41.6285382417448
|
||||
Per MPI rank memory allocation (min/avg/max) = 9.756 | 9.813 | 9.871 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -1.6384018 0.037304147 -1.6010976 6.7769766e-05
|
||||
10000 ekin = 0.705506935391957 | erot = 3.21864563172922 | epot = -44.0640899615318 | etot = -40.1399373944106
|
||||
20000 ekin = 1.16547426389222 | erot = 1.69259899672632 | epot = -41.827511978894 | etot = -38.9694387182755
|
||||
30000 ekin = 2.07592540045025 | erot = 2.81661265099434 | epot = -41.8258727293348 | etot = -36.9333346778902
|
||||
40000 ekin = 3.0352692177735 | erot = 2.43995587980307 | epot = -41.3155342467788 | etot = -35.8403091492022
|
||||
50000 ekin = 2.69044710203348 | erot = 2.86176633025683 | epot = -40.5544750556414 | etot = -35.0022616233511
|
||||
60000 ekin = 2.90956639769978 | erot = 2.84679944563592 | epot = -39.7474408128141 | etot = -33.9910749694784
|
||||
70000 ekin = 1.89941118514544 | erot = 3.71508585194422 | epot = -38.9575890625426 | etot = -33.3430920254529
|
||||
80000 ekin = 2.43472912058895 | erot = 3.11589280920166 | epot = -39.844809532279 | etot = -34.2941876024883
|
||||
90000 ekin = 2.3759389593227 | erot = 3.25835921096947 | epot = -38.913072246407 | etot = -33.2787740761149
|
||||
100000 ekin = 3.23901515322217 | erot = 3.3464944524431 | epot = -38.6302041314432 | etot = -32.044694525778
|
||||
100000 0.086373737 -1.5432369 0.057459797 -1.3611996 7.7958353e-05
|
||||
Loop time of 6.15993 on 4 procs for 100000 steps with 26 atoms
|
||||
|
||||
Performance: 140261.437 tau/day, 16233.963 timesteps/s
|
||||
99.7% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.049533 | 2.573 | 5.3124 | 157.6 | 41.77
|
||||
Bond | 0.007709 | 0.055244 | 0.10383 | 20.2 | 0.90
|
||||
Neigh | 1.8e-05 | 1.875e-05 | 1.9e-05 | 0.0 | 0.00
|
||||
Comm | 0.32774 | 3.0114 | 5.4815 | 142.5 | 48.89
|
||||
Output | 0.000925 | 0.0010595 | 0.00137 | 0.6 | 0.02
|
||||
Modify | 0.016369 | 0.18492 | 0.37491 | 39.3 | 3.00
|
||||
Other | | 0.3343 | | | 5.43
|
||||
|
||||
Nlocal: 6.5 ave 14.0 max 0.0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
Nghost: 18.5 ave 24.0 max 12.0 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 0 2
|
||||
Neighs: 113.75 ave 239.0 max 0.0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 455
|
||||
Ave neighs/atom = 17.5
|
||||
Ave special neighs/atom = 5.076923076923077
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds = 0
|
||||
|
||||
#write_restart config.${number}.*
|
||||
|
||||
|
||||
Total wall time: 0:00:06
|
||||
@ -27,6 +27,7 @@ group all type 1 4
|
||||
# oxRNA2 bond interactions - FENE backbone
|
||||
bond_style oxrna2/fene
|
||||
bond_coeff * 2.0 0.25 0.761070781051
|
||||
special_bonds lj 0 1 1
|
||||
|
||||
# oxRNA2 pair interactions
|
||||
pair_style hybrid/overlay oxrna2/excv oxrna2/stk oxrna2/hbond oxrna2/xstk oxrna2/coaxstk oxrna2/dh
|
||||
@ -50,6 +51,7 @@ timestep 1e-5
|
||||
|
||||
#comm_style tiled
|
||||
#fix 3 all balance 10000 1.1 rcb
|
||||
comm_modify cutoff 2.5
|
||||
|
||||
#compute mol all chunk/atom molecule
|
||||
#compute mychunk all vcm/chunk mol
|
||||
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
@ -1,5 +1,5 @@
|
||||
# Input File for DPD fluid under isothermal conditions using the VV-SSA integration scheme
|
||||
log log.dpd-shardlow
|
||||
|
||||
boundary p p p
|
||||
|
||||
units metal
|
||||
|
||||
@ -1,6 +1,5 @@
|
||||
# INPUT FILE FOR DPD_Fluid
|
||||
|
||||
log log.dpd-vv
|
||||
boundary p p p
|
||||
|
||||
units metal # ev, ps
|
||||
|
||||
@ -1,5 +1,5 @@
|
||||
# Input File for DPD fluid under isoenergetic conditions using the VV-SSA integration scheme
|
||||
log log.dpde-shardlow
|
||||
|
||||
boundary p p p
|
||||
|
||||
units metal # ev, ps
|
||||
|
||||
@ -1,6 +1,5 @@
|
||||
# INPUT FILE FOR DPD_Fluid
|
||||
|
||||
log log.dpde-vv
|
||||
boundary p p p
|
||||
|
||||
units metal # ev, ps
|
||||
|
||||
@ -1,5 +1,5 @@
|
||||
# Input File for DPD fluid under isoenthalpic conditions using the VV-SSA integration scheme
|
||||
log log.dpdh-shardlow
|
||||
|
||||
boundary p p p
|
||||
|
||||
units metal # ev, ps
|
||||
|
||||
@ -1,5 +1,5 @@
|
||||
# Input File for DPD fluid under isobaric conditions using the VV-SSA integration scheme
|
||||
log log.dpdp-shardlow
|
||||
|
||||
boundary p p p
|
||||
|
||||
units metal
|
||||
|
||||
@ -1,6 +1,5 @@
|
||||
# Example for running DPD-RX
|
||||
|
||||
log log.dpdrx-shardlow
|
||||
boundary p p p
|
||||
units metal # ev, ps
|
||||
atom_style dpd
|
||||
|
||||
@ -1,5 +1,5 @@
|
||||
# RDX coarse-grain model
|
||||
log log.multi-lucy
|
||||
|
||||
units metal # ev, ps
|
||||
atom_style dpd
|
||||
atom_modify map array
|
||||
|
||||
@ -1,5 +1,4 @@
|
||||
variable sname index adamantane_ionized
|
||||
log ${sname}.nve.log
|
||||
|
||||
units electron
|
||||
newton on
|
||||
|
||||
@ -1,5 +1,4 @@
|
||||
variable sname index Be-solid
|
||||
log ${sname}.spe.log
|
||||
|
||||
units electron
|
||||
newton on
|
||||
|
||||
@ -1,5 +1,4 @@
|
||||
variable sname index ch4
|
||||
log ${sname}.nve.log
|
||||
|
||||
units electron
|
||||
newton on
|
||||
|
||||
@ -1,5 +1,4 @@
|
||||
variable sname index ch4
|
||||
log ${sname}.nve.log
|
||||
|
||||
units electron
|
||||
newton on
|
||||
|
||||
@ -1,5 +1,4 @@
|
||||
variable sname index ch4_ionized
|
||||
log ${sname}.nvt.log
|
||||
|
||||
units electron
|
||||
newton on
|
||||
@ -15,6 +14,7 @@ pair_coeff * *
|
||||
comm_modify vel yes
|
||||
|
||||
# minimize
|
||||
|
||||
min_style cg
|
||||
min_modify line quadratic
|
||||
minimize 0 1.0e-6 10000 100000
|
||||
|
||||
@ -1,5 +1,4 @@
|
||||
variable sname index h_atom.ang
|
||||
log ${sname}.spe.log
|
||||
|
||||
units real
|
||||
newton on
|
||||
|
||||
@ -1,5 +1,4 @@
|
||||
variable sname index h_atom.bohr
|
||||
log ${sname}.spe.log
|
||||
|
||||
units electron
|
||||
newton on
|
||||
|
||||
@ -1,5 +1,4 @@
|
||||
variable sname index h2
|
||||
log ${sname}.spe.log
|
||||
|
||||
units electron
|
||||
newton on
|
||||
@ -47,4 +46,4 @@ unfix 3
|
||||
|
||||
#fix 1 all nve/eff
|
||||
|
||||
run 100000
|
||||
run 10000
|
||||
|
||||
@ -1,5 +1,4 @@
|
||||
variable sname index h2bulk
|
||||
log ${sname}.npt.log
|
||||
|
||||
units electron
|
||||
newton on
|
||||
@ -41,7 +40,8 @@ dump 2 all xyz 10000 ${sname}.npt.xyz
|
||||
compute 1 all property/atom spin eradius
|
||||
dump 3 all custom 10000 ${sname}.npt.lammpstrj id type x y z c_1[1] c_1[2]
|
||||
|
||||
run 10000000
|
||||
thermo 1
|
||||
run 10
|
||||
|
||||
unfix 1
|
||||
undump 2
|
||||
|
||||
@ -1,5 +1,4 @@
|
||||
variable sname index h2bulk
|
||||
log ${sname}.nve.log
|
||||
|
||||
units electron
|
||||
newton on
|
||||
@ -18,13 +17,13 @@ comm_modify vel yes
|
||||
|
||||
compute effTemp all temp/eff
|
||||
|
||||
thermo 1000
|
||||
thermo 10
|
||||
thermo_style custom step pe temp press
|
||||
thermo_modify temp effTemp
|
||||
|
||||
# structure minimization
|
||||
min_style cg
|
||||
minimize 0 1.0e-4 1000 10000
|
||||
minimize 0 1.0e-4 10 10
|
||||
|
||||
timestep 0.001
|
||||
|
||||
@ -41,7 +40,7 @@ dump 2 all xyz 1000 ${sname}.nve.xyz
|
||||
compute 1 all property/atom spin eradius
|
||||
dump 3 all custom 1000 ${sname}.nve.lammpstrj id type x y z c_1[1] c_1[2] c_peatom c_keatom
|
||||
|
||||
run 100000
|
||||
run 10
|
||||
|
||||
unfix 1
|
||||
#unfix 2
|
||||
|
||||
@ -1,5 +1,4 @@
|
||||
variable sname index h2bulk.ang
|
||||
log ${sname}.nve.log
|
||||
|
||||
units real
|
||||
newton on
|
||||
@ -29,13 +28,13 @@ variable epauli equal c_energies[2]
|
||||
variable ecoul equal c_energies[3]
|
||||
variable erres equal c_energies[4]
|
||||
|
||||
thermo 100
|
||||
thermo 10
|
||||
thermo_style custom step etotal pe ke v_eke v_epauli v_ecoul v_erres press v_press temp
|
||||
thermo_modify temp effTemp press effPress flush yes
|
||||
|
||||
# structure minimization
|
||||
min_style cg
|
||||
minimize 0 1.0e-4 1000 10000
|
||||
minimize 0 1.0e-4 10 10
|
||||
|
||||
timestep 0.001
|
||||
|
||||
@ -52,7 +51,7 @@ dump 2 all xyz 1000 ${sname}.nve.xyz
|
||||
compute 1 all property/atom spin eradius
|
||||
dump 3 all custom 1000 ${sname}.nve.lammpstrj id type x y z c_1[1] c_1[2] c_peatom c_keatom
|
||||
|
||||
run 100000
|
||||
run 10
|
||||
|
||||
unfix 1
|
||||
#unfix 2
|
||||
|
||||
@ -1,5 +1,4 @@
|
||||
variable sname index Li-dendritic
|
||||
log ${sname}.min.log
|
||||
|
||||
units electron
|
||||
newton on
|
||||
@ -7,8 +6,8 @@ boundary p p p
|
||||
|
||||
atom_style electron
|
||||
|
||||
#read_data data.${sname}
|
||||
read_restart ${sname}.min.restart2
|
||||
read_data data.${sname}
|
||||
#read_restart ${sname}.min.restart2
|
||||
|
||||
pair_style eff/cut 50.112
|
||||
pair_coeff * *
|
||||
|
||||
@ -1,5 +1,4 @@
|
||||
variable sname index Li-dendritic
|
||||
log ${sname}.min.log
|
||||
|
||||
units electron
|
||||
newton on
|
||||
@ -29,7 +28,7 @@ compute 1 all property/atom spin eradius
|
||||
#dump 1 all custom 100 ${sname}.min.lammpstrj id type x y z q c_1[1] c_1[2]
|
||||
#dump 2 all xyz 100 ${sname}.min.xyz
|
||||
min_modify line quadratic dmax 0.05
|
||||
minimize 0 1.0e-7 1000 2000
|
||||
minimize 0 1.0e-7 100 100
|
||||
|
||||
write_restart ${sname}.min.restart
|
||||
|
||||
@ -46,7 +45,7 @@ dump 1 all custom 100 ${sname}.nvt.lammpstrj id type x y z c_1[1] c_1
|
||||
dump 2 all xyz 100 ${sname}.nvt.xyz
|
||||
restart 100 ${sname}.nvt.restart1 ${sname}.nvt.restart2
|
||||
|
||||
run 10000
|
||||
run 100
|
||||
|
||||
undump 1
|
||||
undump 2
|
||||
|
||||
@ -1,5 +1,4 @@
|
||||
variable sname index Li.ang
|
||||
log ${sname}.spe.log
|
||||
|
||||
units real
|
||||
newton on
|
||||
@ -46,13 +45,13 @@ fix 0 all temp/rescale/eff 1 10.0 3000.0 0.05 1.0
|
||||
#fix 0 all langevin/eff 3000.0 3000.0 10.0 699483
|
||||
fix 1 all nve/eff
|
||||
|
||||
run 1000
|
||||
run 200
|
||||
unfix 0
|
||||
unfix 1
|
||||
|
||||
fix 1 all nvt/eff temp 3000.0 3000.0 100.0
|
||||
compute 1 all property/atom spin eradius ervel
|
||||
dump 1 all custom 1000 ${sname}.nvt.lammpstrj id type q c_1[1] c_1[2] x y z vx vy vz c_1[3]
|
||||
dump 1 all custom 500 ${sname}.nvt.lammpstrj id type q c_1[1] c_1[2] x y z vx vy vz c_1[3]
|
||||
|
||||
run 100000
|
||||
run 500
|
||||
|
||||
|
||||
@ -1,5 +1,4 @@
|
||||
variable sname index Li.bohr
|
||||
log ${sname}.spe.log
|
||||
|
||||
units electron
|
||||
newton off
|
||||
@ -35,15 +34,15 @@ thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain
|
||||
thermo_modify temp effTemp press effPress
|
||||
|
||||
min_style cg
|
||||
minimize 0 1e-6 100 2000
|
||||
minimize 0 1e-6 100 200
|
||||
|
||||
fix 0 all temp/rescale/eff 1 0.0 3000.0 0.02 0.5
|
||||
|
||||
fix 1 all npt/eff temp 3000.0 3000.0 0.1 iso 1e7 1e7 1.0
|
||||
|
||||
compute 1 all property/atom spin eradius
|
||||
dump 1 all custom 1 ${sname}.spe.lammpstrj &
|
||||
dump 1 all custom 100 ${sname}.spe.lammpstrj &
|
||||
id type q c_1[1] c_1[2] x y z
|
||||
|
||||
run 1000
|
||||
run 100
|
||||
|
||||
|
||||
1
examples/USER/mesont/C_10_10.mesocnt
Symbolic link
1
examples/USER/mesont/C_10_10.mesocnt
Symbolic link
@ -0,0 +1 @@
|
||||
../../../potentials/C_10_10.mesocnt
|
||||
19
examples/USER/mesont/README
Normal file
19
examples/USER/mesont/README
Normal file
@ -0,0 +1,19 @@
|
||||
=== USER-MESONT examples ===
|
||||
===============================
|
||||
|
||||
The files in this folder provide examples of using the CNT
|
||||
mesoscopic force field (USER-MESONT).
|
||||
|
||||
Contributing author: Maxim Shugaev (UVA), mvs9t@virginia.edu
|
||||
|
||||
"bundle" is an example with a single bundle composed of 7 nanotubes
|
||||
using the mesont/tpm pair style
|
||||
|
||||
"film" is an example with a film composed of 396 200-nm-long
|
||||
nanotubes (79596 nodes) using the mesont/tpm pair style
|
||||
|
||||
|
||||
Contributing author: Philipp Kloza (U Cambridge), pak37@cam.ac.uk
|
||||
|
||||
"cnt" is an example showing CNT aerogel formation
|
||||
using the mesocnt pair style
|
||||
1
examples/USER/mesont/TABTP_10_10.mesont
Symbolic link
1
examples/USER/mesont/TABTP_10_10.mesont
Symbolic link
@ -0,0 +1 @@
|
||||
../../../potentials/TABTP_10_10.mesont
|
||||
1521
examples/USER/mesont/cnt.data
Normal file
1521
examples/USER/mesont/cnt.data
Normal file
File diff suppressed because it is too large
Load Diff
93
examples/USER/mesont/data.bundle
Normal file
93
examples/USER/mesont/data.bundle
Normal file
@ -0,0 +1,93 @@
|
||||
|
||||
|
||||
77 atoms
|
||||
|
||||
1 atom types
|
||||
|
||||
-143.89 143.89 xlo xhi
|
||||
-143.89 143.89 ylo yhi
|
||||
0 220 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 1.0
|
||||
|
||||
Atoms
|
||||
|
||||
1 1 1 11 2 5860.43 6.785 20 0 0 0 0 0 0 0
|
||||
2 1 1 1 3 5860.43 6.785 20 0 0 0 20 0 0 0
|
||||
3 1 1 2 4 5860.43 6.785 20 0 0 0 40 0 0 0
|
||||
4 1 1 3 5 5860.43 6.785 20 0 0 0 60 0 0 0
|
||||
5 1 1 4 6 5860.43 6.785 20 0 0 0 80 0 0 0
|
||||
6 1 1 5 7 5860.43 6.785 20 0 0 0 100 0 0 0
|
||||
7 1 1 6 8 5860.43 6.785 20 0 0 0 120 0 0 0
|
||||
8 1 1 7 9 5860.43 6.785 20 0 0 0 140 0 0 0
|
||||
9 1 1 8 10 5860.43 6.785 20 0 0 0 160 0 0 0
|
||||
10 1 1 9 11 5860.43 6.785 20 0 0 0 180 0 0 0
|
||||
11 1 1 10 1 5860.43 6.785 20 0 0 0 200 0 0 0
|
||||
12 2 1 22 13 5860.43 6.785 20 0 16.6992 0 0 0 0 0
|
||||
13 2 1 12 14 5860.43 6.785 20 0 16.6992 0 20 0 0 0
|
||||
14 2 1 13 15 5860.43 6.785 20 0 16.6992 0 40 0 0 0
|
||||
15 2 1 14 16 5860.43 6.785 20 0 16.6992 0 60 0 0 0
|
||||
16 2 1 15 17 5860.43 6.785 20 0 16.6992 0 80 0 0 0
|
||||
17 2 1 16 18 5860.43 6.785 20 0 16.6992 0 100 0 0 0
|
||||
18 2 1 17 19 5860.43 6.785 20 0 16.6992 0 120 0 0 0
|
||||
19 2 1 18 20 5860.43 6.785 20 0 16.6992 0 140 0 0 0
|
||||
20 2 1 19 21 5860.43 6.785 20 0 16.6992 0 160 0 0 0
|
||||
21 2 1 20 22 5860.43 6.785 20 0 16.6992 0 180 0 0 0
|
||||
22 2 1 21 12 5860.43 6.785 20 0 16.6992 0 200 0 0 0
|
||||
23 3 1 33 24 5860.43 6.785 20 0 8.3496 14.4619 0 0 0 0
|
||||
24 3 1 23 25 5860.43 6.785 20 0 8.3496 14.4619 20 0 0 0
|
||||
25 3 1 24 26 5860.43 6.785 20 0 8.3496 14.4619 40 0 0 0
|
||||
26 3 1 25 27 5860.43 6.785 20 0 8.3496 14.4619 60 0 0 0
|
||||
27 3 1 26 28 5860.43 6.785 20 0 8.3496 14.4619 80 0 0 0
|
||||
28 3 1 27 29 5860.43 6.785 20 0 8.3496 14.4619 100 0 0 0
|
||||
29 3 1 28 30 5860.43 6.785 20 0 8.3496 14.4619 120 0 0 0
|
||||
30 3 1 29 31 5860.43 6.785 20 0 8.3496 14.4619 140 0 0 0
|
||||
31 3 1 30 32 5860.43 6.785 20 0 8.3496 14.4619 160 0 0 0
|
||||
32 3 1 31 33 5860.43 6.785 20 0 8.3496 14.4619 180 0 0 0
|
||||
33 3 1 32 23 5860.43 6.785 20 0 8.3496 14.4619 200 0 0 0
|
||||
34 4 1 44 35 5860.43 6.785 20 0 -8.3496 14.4619 0 0 0 0
|
||||
35 4 1 34 36 5860.43 6.785 20 0 -8.3496 14.4619 20 0 0 0
|
||||
36 4 1 35 37 5860.43 6.785 20 0 -8.3496 14.4619 40 0 0 0
|
||||
37 4 1 36 38 5860.43 6.785 20 0 -8.3496 14.4619 60 0 0 0
|
||||
38 4 1 37 39 5860.43 6.785 20 0 -8.3496 14.4619 80 0 0 0
|
||||
39 4 1 38 40 5860.43 6.785 20 0 -8.3496 14.4619 100 0 0 0
|
||||
40 4 1 39 41 5860.43 6.785 20 0 -8.3496 14.4619 120 0 0 0
|
||||
41 4 1 40 42 5860.43 6.785 20 0 -8.3496 14.4619 140 0 0 0
|
||||
42 4 1 41 43 5860.43 6.785 20 0 -8.3496 14.4619 160 0 0 0
|
||||
43 4 1 42 44 5860.43 6.785 20 0 -8.3496 14.4619 180 0 0 0
|
||||
44 4 1 43 34 5860.43 6.785 20 0 -8.3496 14.4619 200 0 0 0
|
||||
45 5 1 55 46 5860.43 6.785 20 0 -16.6992 0 0 0 0 0
|
||||
46 5 1 45 47 5860.43 6.785 20 0 -16.6992 0 20 0 0 0
|
||||
47 5 1 46 48 5860.43 6.785 20 0 -16.6992 0 40 0 0 0
|
||||
48 5 1 47 49 5860.43 6.785 20 0 -16.6992 0 60 0 0 0
|
||||
49 5 1 48 50 5860.43 6.785 20 0 -16.6992 0 80 0 0 0
|
||||
50 5 1 49 51 5860.43 6.785 20 0 -16.6992 0 100 0 0 0
|
||||
51 5 1 50 52 5860.43 6.785 20 0 -16.6992 0 120 0 0 0
|
||||
52 5 1 51 53 5860.43 6.785 20 0 -16.6992 0 140 0 0 0
|
||||
53 5 1 52 54 5860.43 6.785 20 0 -16.6992 0 160 0 0 0
|
||||
54 5 1 53 55 5860.43 6.785 20 0 -16.6992 0 180 0 0 0
|
||||
55 5 1 54 45 5860.43 6.785 20 0 -16.6992 0 200 0 0 0
|
||||
56 6 1 66 57 5860.43 6.785 20 0 -8.3496 -14.4619 0 0 0 0
|
||||
57 6 1 56 58 5860.43 6.785 20 0 -8.3496 -14.4619 20 0 0 0
|
||||
58 6 1 57 59 5860.43 6.785 20 0 -8.3496 -14.4619 40 0 0 0
|
||||
59 6 1 58 60 5860.43 6.785 20 0 -8.3496 -14.4619 60 0 0 0
|
||||
60 6 1 59 61 5860.43 6.785 20 0 -8.3496 -14.4619 80 0 0 0
|
||||
61 6 1 60 62 5860.43 6.785 20 0 -8.3496 -14.4619 100 0 0 0
|
||||
62 6 1 61 63 5860.43 6.785 20 0 -8.3496 -14.4619 120 0 0 0
|
||||
63 6 1 62 64 5860.43 6.785 20 0 -8.3496 -14.4619 140 0 0 0
|
||||
64 6 1 63 65 5860.43 6.785 20 0 -8.3496 -14.4619 160 0 0 0
|
||||
65 6 1 64 66 5860.43 6.785 20 0 -8.3496 -14.4619 180 0 0 0
|
||||
66 6 1 65 56 5860.43 6.785 20 0 -8.3496 -14.4619 200 0 0 0
|
||||
67 7 1 77 68 5860.43 6.785 20 0 8.3496 -14.4619 0 0 0 0
|
||||
68 7 1 67 69 5860.43 6.785 20 0 8.3496 -14.4619 20 0 0 0
|
||||
69 7 1 68 70 5860.43 6.785 20 0 8.3496 -14.4619 40 0 0 0
|
||||
70 7 1 69 71 5860.43 6.785 20 0 8.3496 -14.4619 60 0 0 0
|
||||
71 7 1 70 72 5860.43 6.785 20 0 8.3496 -14.4619 80 0 0 0
|
||||
72 7 1 71 73 5860.43 6.785 20 0 8.3496 -14.4619 100 0 0 0
|
||||
73 7 1 72 74 5860.43 6.785 20 0 8.3496 -14.4619 120 0 0 0
|
||||
74 7 1 73 75 5860.43 6.785 20 0 8.3496 -14.4619 140 0 0 0
|
||||
75 7 1 74 76 5860.43 6.785 20 0 8.3496 -14.4619 160 0 0 0
|
||||
76 7 1 75 77 5860.43 6.785 20 0 8.3496 -14.4619 180 0 0 0
|
||||
77 7 1 76 67 5860.43 6.785 20 0 8.3496 -14.4619 200 0 0 0
|
||||
79612
examples/USER/mesont/data.film
Normal file
79612
examples/USER/mesont/data.film
Normal file
File diff suppressed because it is too large
Load Diff
29
examples/USER/mesont/in.bundle
Normal file
29
examples/USER/mesont/in.bundle
Normal file
@ -0,0 +1,29 @@
|
||||
processors 1 1 *
|
||||
newton on
|
||||
units metal
|
||||
lattice sc 1.0
|
||||
boundary fs fs p
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 5 delay 0 check yes
|
||||
|
||||
atom_style mesont
|
||||
# cut, path, BendingMode, TPMType
|
||||
pair_style mesont/tpm 45.0 MESONT-TABTP_10_10.xrs 0 0
|
||||
read_data data.bundle
|
||||
pair_coeff * *
|
||||
|
||||
velocity all create 6000.0 2019
|
||||
timestep 0.005
|
||||
fix 1 all nve
|
||||
thermo 10
|
||||
reset_timestep 0
|
||||
|
||||
compute Es all mesont estretch
|
||||
compute Eb all mesont ebend
|
||||
compute Et all mesont etube
|
||||
compute B all property/atom buckling
|
||||
|
||||
thermo_style custom step time temp etotal ke pe c_Es c_Eb c_Et
|
||||
#dump out_dump all custom 50 dump.bundle id type x y z c_Es c_Eb c_Et c_B ix iy iz
|
||||
|
||||
run 100
|
||||
38
examples/USER/mesont/in.cnt
Normal file
38
examples/USER/mesont/in.cnt
Normal file
@ -0,0 +1,38 @@
|
||||
#Initialisation
|
||||
|
||||
units nano
|
||||
dimension 3
|
||||
boundary p p p
|
||||
atom_style full
|
||||
comm_modify cutoff 11.0
|
||||
neighbor 7.80 bin
|
||||
newton on
|
||||
|
||||
#Read data
|
||||
|
||||
read_data cnt.data
|
||||
replicate 1 2 2
|
||||
|
||||
#Force field
|
||||
|
||||
bond_style harmonic
|
||||
bond_coeff 1 268896.77 2.0
|
||||
|
||||
angle_style harmonic
|
||||
angle_coeff 1 46562.17 180.0
|
||||
|
||||
pair_style mesocnt
|
||||
pair_coeff * * C_10_10.mesocnt
|
||||
|
||||
#Output
|
||||
|
||||
thermo 1000
|
||||
dump xyz all xyz 1000 cnt.xyz
|
||||
|
||||
#Simulation setup
|
||||
|
||||
timestep 1.0e-05
|
||||
|
||||
#Nose-Hoover thermostat
|
||||
fix nvt all nvt temp 300 300 0.001
|
||||
run 10000
|
||||
28
examples/USER/mesont/in.film
Normal file
28
examples/USER/mesont/in.film
Normal file
@ -0,0 +1,28 @@
|
||||
newton on
|
||||
units metal
|
||||
lattice sc 1.0
|
||||
boundary p p fs
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 5 delay 0 check yes
|
||||
|
||||
atom_style mesont
|
||||
# cut, path, BendingMode, TPMType
|
||||
pair_style mesont/tpm 30.0 MESONT-TABTP_10_10.xrs 1 0
|
||||
read_data data.film
|
||||
pair_coeff * *
|
||||
|
||||
velocity all create 600.0 2019
|
||||
timestep 0.01
|
||||
fix 1 all nve
|
||||
thermo 10
|
||||
reset_timestep 0
|
||||
|
||||
compute Es all mesont estretch
|
||||
compute Eb all mesont ebend
|
||||
compute Et all mesont etube
|
||||
compute B all property/atom buckling
|
||||
|
||||
thermo_style custom step time temp etotal ke pe c_Es c_Eb c_Et
|
||||
#dump out_dump all custom 10 dump.film id type x y z c_Es c_Eb c_Et c_B ix iy iz
|
||||
|
||||
run 20
|
||||
90
examples/USER/mesont/log.2Jun2020.bundle.g++.1
Normal file
90
examples/USER/mesont/log.2Jun2020.bundle.g++.1
Normal file
@ -0,0 +1,90 @@
|
||||
LAMMPS (5 May 2020)
|
||||
processors 1 1 *
|
||||
newton on
|
||||
units metal
|
||||
lattice sc 1.0
|
||||
Lattice spacing in x,y,z = 1 1 1
|
||||
boundary fs fs p
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 5 delay 0 check yes
|
||||
|
||||
atom_style mesont
|
||||
# cut, path, BendingMode, TPMType
|
||||
pair_style mesont/tpm 45.0 MESONT-TABTP_10_10.xrs 0 0
|
||||
read_data data.bundle
|
||||
orthogonal box = (-143.89 -143.89 0) to (143.89 143.89 220)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
77 atoms
|
||||
read_data CPU = 0.000613213 secs
|
||||
pair_coeff * *
|
||||
|
||||
velocity all create 6000.0 2019
|
||||
timestep 0.005
|
||||
fix 1 all nve
|
||||
thermo 10
|
||||
reset_timestep 0
|
||||
|
||||
compute Es all mesont estretch
|
||||
compute Eb all mesont ebend
|
||||
compute Et all mesont etube
|
||||
compute B all property/atom buckling
|
||||
|
||||
thermo_style custom step time temp etotal ke pe c_Es c_Eb c_Et
|
||||
#dump out_dump all custom 50 dump.bundle id type x y z c_Es c_Eb c_Et c_B ix iy iz
|
||||
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 5 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 46
|
||||
ghost atom cutoff = 46
|
||||
binsize = 23, bins = 7 7 10
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair mesont/tpm, 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) = 4.675 | 4.675 | 4.675 Mbytes
|
||||
Step Time Temp TotEng KinEng PotEng c_Es c_Eb c_Et
|
||||
0 0 6000 -201.86935 58.942626 -260.81198 0 0 -260.81198
|
||||
10 0.05 5114.1875 -201.86234 50.240607 -252.10295 4.8334861 2.3998206 -259.33626
|
||||
20 0.1 3437.2958 -201.8522 33.767207 -235.61941 11.42384 8.3426957 -255.38594
|
||||
30 0.15 2430.6571 -201.85242 23.878219 -225.73064 10.346152 14.72688 -250.80367
|
||||
40 0.2 2154.4755 -201.85683 21.165074 -223.0219 6.8146112 18.325709 -248.16222
|
||||
50 0.25 2021.7899 -201.85503 19.861601 -221.71663 9.2972022 17.644143 -248.65798
|
||||
60 0.3 2234.553 -201.85193 21.951737 -223.80367 13.541921 13.673721 -251.01931
|
||||
70 0.35 3099.6503 -201.85721 30.450255 -232.30747 11.833679 9.0583807 -253.19953
|
||||
80 0.4 3849.9855 -201.8635 37.821376 -239.68487 7.9899173 6.4332848 -254.10807
|
||||
90 0.45 3618.1311 -201.85967 35.543692 -237.40336 9.2616931 7.0452637 -253.71032
|
||||
100 0.5 2866.2722 -201.85273 28.157602 -230.01033 12.204916 10.284525 -252.49977
|
||||
Loop time of 0.419735 on 1 procs for 100 steps with 77 atoms
|
||||
|
||||
Performance: 102.922 ns/day, 0.233 hours/ns, 238.245 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.41922 | 0.41922 | 0.41922 | 0.0 | 99.88
|
||||
Neigh | 5.8174e-05 | 5.8174e-05 | 5.8174e-05 | 0.0 | 0.01
|
||||
Comm | 7.0333e-05 | 7.0333e-05 | 7.0333e-05 | 0.0 | 0.02
|
||||
Output | 0.00017667 | 0.00017667 | 0.00017667 | 0.0 | 0.04
|
||||
Modify | 0.00011945 | 0.00011945 | 0.00011945 | 0.0 | 0.03
|
||||
Other | | 8.702e-05 | | | 0.02
|
||||
|
||||
Nlocal: 77 ave 77 max 77 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 35 ave 35 max 35 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: 2222 ave 2222 max 2222 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 2222
|
||||
Ave neighs/atom = 28.8571
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:01
|
||||
90
examples/USER/mesont/log.2Jun2020.bundle.g++.4
Normal file
90
examples/USER/mesont/log.2Jun2020.bundle.g++.4
Normal file
@ -0,0 +1,90 @@
|
||||
LAMMPS (5 May 2020)
|
||||
processors 1 1 *
|
||||
newton on
|
||||
units metal
|
||||
lattice sc 1.0
|
||||
Lattice spacing in x,y,z = 1 1 1
|
||||
boundary fs fs p
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 5 delay 0 check yes
|
||||
|
||||
atom_style mesont
|
||||
# cut, path, BendingMode, TPMType
|
||||
pair_style mesont/tpm 45.0 MESONT-TABTP_10_10.xrs 0 0
|
||||
read_data data.bundle
|
||||
orthogonal box = (-143.89 -143.89 0) to (143.89 143.89 220)
|
||||
1 by 1 by 4 MPI processor grid
|
||||
reading atoms ...
|
||||
77 atoms
|
||||
read_data CPU = 0.000590563 secs
|
||||
pair_coeff * *
|
||||
|
||||
velocity all create 6000.0 2019
|
||||
timestep 0.005
|
||||
fix 1 all nve
|
||||
thermo 10
|
||||
reset_timestep 0
|
||||
|
||||
compute Es all mesont estretch
|
||||
compute Eb all mesont ebend
|
||||
compute Et all mesont etube
|
||||
compute B all property/atom buckling
|
||||
|
||||
thermo_style custom step time temp etotal ke pe c_Es c_Eb c_Et
|
||||
#dump out_dump all custom 50 dump.bundle id type x y z c_Es c_Eb c_Et c_B ix iy iz
|
||||
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 5 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 46
|
||||
ghost atom cutoff = 46
|
||||
binsize = 23, bins = 7 7 10
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair mesont/tpm, 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) = 4.671 | 4.671 | 4.671 Mbytes
|
||||
Step Time Temp TotEng KinEng PotEng c_Es c_Eb c_Et
|
||||
0 0 6000 -201.86935 58.942626 -260.81198 0 0 -260.81198
|
||||
10 0.05 5114.1875 -201.86234 50.240607 -252.10295 4.8334861 2.3998206 -259.33626
|
||||
20 0.1 3437.2958 -201.8522 33.767207 -235.61941 11.42384 8.3426957 -255.38594
|
||||
30 0.15 2430.6571 -201.85242 23.878219 -225.73064 10.346152 14.72688 -250.80367
|
||||
40 0.2 2154.4755 -201.85683 21.165074 -223.0219 6.8146112 18.325709 -248.16222
|
||||
50 0.25 2021.7899 -201.85503 19.861601 -221.71663 9.2972022 17.644143 -248.65798
|
||||
60 0.3 2234.553 -201.85193 21.951737 -223.80367 13.541921 13.673721 -251.01931
|
||||
70 0.35 3099.6503 -201.85721 30.450255 -232.30747 11.833679 9.0583807 -253.19953
|
||||
80 0.4 3849.9855 -201.8635 37.821376 -239.68487 7.9899173 6.4332848 -254.10807
|
||||
90 0.45 3618.1311 -201.85967 35.543692 -237.40336 9.2616931 7.0452637 -253.71032
|
||||
100 0.5 2866.2722 -201.85273 28.157602 -230.01033 12.204916 10.284525 -252.49977
|
||||
Loop time of 0.145545 on 4 procs for 100 steps with 77 atoms
|
||||
|
||||
Performance: 296.815 ns/day, 0.081 hours/ns, 687.071 timesteps/s
|
||||
95.9% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.046723 | 0.097529 | 0.14388 | 11.0 | 67.01
|
||||
Neigh | 2.5511e-05 | 2.8729e-05 | 3.171e-05 | 0.0 | 0.02
|
||||
Comm | 0.00058556 | 0.045174 | 0.098462 | 16.5 | 31.04
|
||||
Output | 0.0001483 | 0.0010182 | 0.002851 | 3.5 | 0.70
|
||||
Modify | 3.8147e-05 | 4.065e-05 | 4.4107e-05 | 0.0 | 0.03
|
||||
Other | | 0.001755 | | | 1.21
|
||||
|
||||
Nlocal: 19.25 ave 21 max 16 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 0 2
|
||||
Nghost: 33.25 ave 40 max 28 min
|
||||
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 555.5 ave 606 max 460 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 0 2
|
||||
|
||||
Total # of neighbors = 2222
|
||||
Ave neighs/atom = 28.8571
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:01
|
||||
81
examples/USER/mesont/log.2Jun2020.film.g++.1
Normal file
81
examples/USER/mesont/log.2Jun2020.film.g++.1
Normal file
@ -0,0 +1,81 @@
|
||||
LAMMPS (5 May 2020)
|
||||
newton on
|
||||
units metal
|
||||
lattice sc 1.0
|
||||
Lattice spacing in x,y,z = 1 1 1
|
||||
boundary p p fs
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 5 delay 0 check yes
|
||||
|
||||
atom_style mesont
|
||||
# cut, path, BendingMode, TPMType
|
||||
pair_style mesont/tpm 30.0 MESONT-TABTP_10_10.xrs 1 0
|
||||
read_data data.film
|
||||
orthogonal box = (-2500 -2500 -300) to (2500 2500 402.42)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
79596 atoms
|
||||
read_data CPU = 0.0860629 secs
|
||||
pair_coeff * *
|
||||
|
||||
velocity all create 600.0 2019
|
||||
timestep 0.01
|
||||
fix 1 all nve
|
||||
thermo 10
|
||||
reset_timestep 0
|
||||
|
||||
compute Es all mesont estretch
|
||||
compute Eb all mesont ebend
|
||||
compute Et all mesont etube
|
||||
compute B all property/atom buckling
|
||||
|
||||
thermo_style custom step time temp etotal ke pe c_Es c_Eb c_Et
|
||||
#dump out_dump all custom 10 dump.film id type x y z c_Es c_Eb c_Et c_B ix iy iz
|
||||
|
||||
run 20
|
||||
Neighbor list info ...
|
||||
update every 5 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 31
|
||||
ghost atom cutoff = 31
|
||||
binsize = 15.5, bins = 323 323 26
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair mesont/tpm, 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) = 37.43 | 37.43 | 37.43 Mbytes
|
||||
Step Time Temp TotEng KinEng PotEng c_Es c_Eb c_Et
|
||||
0 0 600 1347.2158 6173.0767 -4825.8609 28.669574 21.29406 -4875.8245
|
||||
10 0.1 389.40755 1373.7864 4006.4045 -2632.6181 848.00267 1404.4323 -4885.053
|
||||
20 0.2 313.65714 1399.9427 3227.0494 -1827.1067 1201.1732 1882.1342 -4910.4141
|
||||
Loop time of 10.2438 on 1 procs for 20 steps with 79596 atoms
|
||||
|
||||
Performance: 1.687 ns/day, 14.228 hours/ns, 1.952 timesteps/s
|
||||
99.0% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 10.226 | 10.226 | 10.226 | 0.0 | 99.82
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00081086 | 0.00081086 | 0.00081086 | 0.0 | 0.01
|
||||
Output | 0.00046563 | 0.00046563 | 0.00046563 | 0.0 | 0.00
|
||||
Modify | 0.015165 | 0.015165 | 0.015165 | 0.0 | 0.15
|
||||
Other | | 0.001869 | | | 0.02
|
||||
|
||||
Nlocal: 79596 ave 79596 max 79596 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1879 ave 1879 max 1879 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: 642270 ave 642270 max 642270 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 642270
|
||||
Ave neighs/atom = 8.06912
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:11
|
||||
81
examples/USER/mesont/log.2Jun2020.film.g++.4
Normal file
81
examples/USER/mesont/log.2Jun2020.film.g++.4
Normal file
@ -0,0 +1,81 @@
|
||||
LAMMPS (5 May 2020)
|
||||
newton on
|
||||
units metal
|
||||
lattice sc 1.0
|
||||
Lattice spacing in x,y,z = 1 1 1
|
||||
boundary p p fs
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 5 delay 0 check yes
|
||||
|
||||
atom_style mesont
|
||||
# cut, path, BendingMode, TPMType
|
||||
pair_style mesont/tpm 30.0 MESONT-TABTP_10_10.xrs 1 0
|
||||
read_data data.film
|
||||
orthogonal box = (-2500 -2500 -300) to (2500 2500 402.42)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
79596 atoms
|
||||
read_data CPU = 0.0704217 secs
|
||||
pair_coeff * *
|
||||
|
||||
velocity all create 600.0 2019
|
||||
timestep 0.01
|
||||
fix 1 all nve
|
||||
thermo 10
|
||||
reset_timestep 0
|
||||
|
||||
compute Es all mesont estretch
|
||||
compute Eb all mesont ebend
|
||||
compute Et all mesont etube
|
||||
compute B all property/atom buckling
|
||||
|
||||
thermo_style custom step time temp etotal ke pe c_Es c_Eb c_Et
|
||||
#dump out_dump all custom 10 dump.film id type x y z c_Es c_Eb c_Et c_B ix iy iz
|
||||
|
||||
run 20
|
||||
Neighbor list info ...
|
||||
update every 5 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 31
|
||||
ghost atom cutoff = 31
|
||||
binsize = 15.5, bins = 323 323 26
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair mesont/tpm, 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) = 12.81 | 12.81 | 12.83 Mbytes
|
||||
Step Time Temp TotEng KinEng PotEng c_Es c_Eb c_Et
|
||||
0 0 600 1347.2158 6173.0767 -4825.8609 28.669574 21.29406 -4875.8245
|
||||
10 0.1 389.40755 1373.7864 4006.4045 -2632.6181 848.00267 1404.4323 -4885.053
|
||||
20 0.2 313.65714 1399.9427 3227.0494 -1827.1067 1201.1732 1882.1342 -4910.4141
|
||||
Loop time of 3.67186 on 4 procs for 20 steps with 79596 atoms
|
||||
|
||||
Performance: 4.706 ns/day, 5.100 hours/ns, 5.447 timesteps/s
|
||||
95.8% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.7317 | 3.1286 | 3.6556 | 18.8 | 85.20
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0036943 | 0.53094 | 0.92822 | 45.8 | 14.46
|
||||
Output | 0.00026512 | 0.00035298 | 0.00055647 | 0.0 | 0.01
|
||||
Modify | 0.010463 | 0.010884 | 0.011153 | 0.3 | 0.30
|
||||
Other | | 0.001109 | | | 0.03
|
||||
|
||||
Nlocal: 19899 ave 21951 max 18667 min
|
||||
Histogram: 1 1 0 1 0 0 0 0 0 1
|
||||
Nghost: 970.75 ave 1031 max 920 min
|
||||
Histogram: 1 0 0 1 1 0 0 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 160568 ave 181723 max 147382 min
|
||||
Histogram: 1 0 2 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 642270
|
||||
Ave neighs/atom = 8.06912
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:04
|
||||
126
examples/USER/mesont/log.9Jan20.cnt.g++.1
Normal file
126
examples/USER/mesont/log.9Jan20.cnt.g++.1
Normal file
@ -0,0 +1,126 @@
|
||||
LAMMPS (09 Jan 2020)
|
||||
#Initialisation
|
||||
|
||||
units nano
|
||||
dimension 3
|
||||
boundary p p p
|
||||
atom_style full
|
||||
comm_modify cutoff 11.0
|
||||
neighbor 7.80 bin
|
||||
newton on
|
||||
|
||||
#Read data
|
||||
|
||||
read_data cnt.data
|
||||
orthogonal box = (0 0 0) to (600 600 60)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
500 atoms
|
||||
scanning bonds ...
|
||||
1 = max bonds/atom
|
||||
scanning angles ...
|
||||
1 = max angles/atom
|
||||
reading bonds ...
|
||||
498 bonds
|
||||
reading angles ...
|
||||
496 angles
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
4 = max # of 1-4 neighbors
|
||||
6 = max # of special neighbors
|
||||
special bonds CPU = 0.000180006 secs
|
||||
read_data CPU = 0.00125766 secs
|
||||
replicate 1 2 2
|
||||
orthogonal box = (0 0 0) to (600 1200 120)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
2000 atoms
|
||||
1992 bonds
|
||||
1984 angles
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
4 = max # of 1-4 neighbors
|
||||
6 = max # of special neighbors
|
||||
special bonds CPU = 0.00054121 secs
|
||||
replicate CPU = 0.000902414 secs
|
||||
|
||||
#Force field
|
||||
|
||||
bond_style harmonic
|
||||
bond_coeff 1 268896.77 2.0
|
||||
|
||||
angle_style harmonic
|
||||
angle_coeff 1 46562.17 180.0
|
||||
|
||||
pair_style mesocnt
|
||||
pair_coeff * * 10_10.cnt
|
||||
Reading potential file 10_10.cnt with DATE: 2020-01-13
|
||||
|
||||
#Output
|
||||
|
||||
thermo 1000
|
||||
dump xyz all xyz 1000 cnt.xyz
|
||||
|
||||
#Simulation setup
|
||||
|
||||
timestep 1.0e-05
|
||||
|
||||
#Nose-Hoover thermostat
|
||||
fix nvt all nvt temp 300 300 0.001
|
||||
run 10000
|
||||
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (src/pair.cpp:226)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 10.177
|
||||
ghost atom cutoff = 11
|
||||
binsize = 5.0885, bins = 118 236 24
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair mesocnt, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 11.21 | 11.21 | 11.21 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -4632.0136 5.7939238e-17 -4632.0136 -0.00015032304
|
||||
1000 298.82235 -19950.274 13208.089 5628.7024 -0.0056205182
|
||||
2000 300.43933 -28320.212 11980.296 -3902.0877 -0.0045324757
|
||||
3000 300.4263 -36049.855 11338.405 -12274.161 -0.0018833539
|
||||
4000 299.13368 -43471.21 11926.882 -19160.553 -0.00043030866
|
||||
5000 293.77858 -50083.893 12334.927 -25586.884 -0.0015653738
|
||||
6000 296.4851 -56330.135 12325.63 -31730.376 -0.0012795986
|
||||
7000 298.20879 -62120.359 12582.297 -37192.574 -0.0013845796
|
||||
8000 299.45547 -67881.692 13058.926 -42425.669 -0.00021100885
|
||||
9000 301.82622 -73333.698 13598.257 -47240.197 -0.0006009197
|
||||
10000 307.16873 -78292.306 13818.929 -51756.96 -0.0005609903
|
||||
Loop time of 4.0316 on 1 procs for 10000 steps with 2000 atoms
|
||||
|
||||
Performance: 2143.072 ns/day, 0.011 hours/ns, 2480.408 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.5955 | 2.5955 | 2.5955 | 0.0 | 64.38
|
||||
Bond | 1.1516 | 1.1516 | 1.1516 | 0.0 | 28.57
|
||||
Neigh | 0.001163 | 0.001163 | 0.001163 | 0.0 | 0.03
|
||||
Comm | 0.0019577 | 0.0019577 | 0.0019577 | 0.0 | 0.05
|
||||
Output | 0.020854 | 0.020854 | 0.020854 | 0.0 | 0.52
|
||||
Modify | 0.21637 | 0.21637 | 0.21637 | 0.0 | 5.37
|
||||
Other | | 0.04409 | | | 1.09
|
||||
|
||||
Nlocal: 2000 ave 2000 max 2000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 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: 13320 ave 13320 max 13320 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 13320
|
||||
Ave neighs/atom = 6.66
|
||||
Ave special neighs/atom = 5.952
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:05
|
||||
126
examples/USER/mesont/log.9Jan20.cnt.g++.4
Normal file
126
examples/USER/mesont/log.9Jan20.cnt.g++.4
Normal file
@ -0,0 +1,126 @@
|
||||
LAMMPS (09 Jan 2020)
|
||||
#Initialisation
|
||||
|
||||
units nano
|
||||
dimension 3
|
||||
boundary p p p
|
||||
atom_style full
|
||||
comm_modify cutoff 11.0
|
||||
neighbor 7.80 bin
|
||||
newton on
|
||||
|
||||
#Read data
|
||||
|
||||
read_data cnt.data
|
||||
orthogonal box = (0 0 0) to (600 600 60)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
500 atoms
|
||||
scanning bonds ...
|
||||
1 = max bonds/atom
|
||||
scanning angles ...
|
||||
1 = max angles/atom
|
||||
reading bonds ...
|
||||
498 bonds
|
||||
reading angles ...
|
||||
496 angles
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
4 = max # of 1-4 neighbors
|
||||
6 = max # of special neighbors
|
||||
special bonds CPU = 0.000354767 secs
|
||||
read_data CPU = 0.00286365 secs
|
||||
replicate 1 2 2
|
||||
orthogonal box = (0 0 0) to (600 1200 120)
|
||||
1 by 4 by 1 MPI processor grid
|
||||
2000 atoms
|
||||
1992 bonds
|
||||
1984 angles
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
4 = max # of 1-4 neighbors
|
||||
6 = max # of special neighbors
|
||||
special bonds CPU = 0.00019598 secs
|
||||
replicate CPU = 0.00055337 secs
|
||||
|
||||
#Force field
|
||||
|
||||
bond_style harmonic
|
||||
bond_coeff 1 268896.77 2.0
|
||||
|
||||
angle_style harmonic
|
||||
angle_coeff 1 46562.17 180.0
|
||||
|
||||
pair_style mesocnt
|
||||
pair_coeff * * 10_10.cnt
|
||||
Reading potential file 10_10.cnt with DATE: 2020-01-13
|
||||
|
||||
#Output
|
||||
|
||||
thermo 1000
|
||||
dump xyz all xyz 1000 cnt.xyz
|
||||
|
||||
#Simulation setup
|
||||
|
||||
timestep 1.0e-05
|
||||
|
||||
#Nose-Hoover thermostat
|
||||
fix nvt all nvt temp 300 300 0.001
|
||||
run 10000
|
||||
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (src/pair.cpp:226)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 10.177
|
||||
ghost atom cutoff = 11
|
||||
binsize = 5.0885, bins = 118 236 24
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair mesocnt, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.725 | 2.725 | 2.725 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -4632.0136 5.7939238e-17 -4632.0136 -0.00015032304
|
||||
1000 298.82235 -19950.274 13208.089 5628.7024 -0.0056205182
|
||||
2000 300.43861 -28320.205 11980.287 -3902.1202 -0.0045324738
|
||||
3000 300.41076 -36049.308 11339.149 -12273.513 -0.0018848513
|
||||
4000 299.13326 -43471.424 11927.668 -19159.998 -0.00042845101
|
||||
5000 293.78857 -50083.216 12333.969 -25586.752 -0.0015664633
|
||||
6000 296.45482 -56329.621 12326.419 -31730.328 -0.0012773686
|
||||
7000 298.19097 -62119.086 12581.4 -37192.937 -0.0013862831
|
||||
8000 299.46424 -67880.989 13057.62 -42425.908 -0.00020874264
|
||||
9000 301.80677 -73332.208 13597.237 -47240.532 -0.00060074773
|
||||
10000 307.17104 -78292.912 13818.889 -51757.51 -0.00056148282
|
||||
Loop time of 1.23665 on 4 procs for 10000 steps with 2000 atoms
|
||||
|
||||
Performance: 6986.607 ns/day, 0.003 hours/ns, 8086.351 timesteps/s
|
||||
96.1% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.66321 | 0.68439 | 0.71413 | 2.5 | 55.34
|
||||
Bond | 0.28561 | 0.29434 | 0.30976 | 1.7 | 23.80
|
||||
Neigh | 0.00043321 | 0.00043637 | 0.00043917 | 0.0 | 0.04
|
||||
Comm | 0.026656 | 0.05346 | 0.097228 | 12.7 | 4.32
|
||||
Output | 0.0070224 | 0.0073031 | 0.0081415 | 0.6 | 0.59
|
||||
Modify | 0.12769 | 0.15394 | 0.18743 | 6.5 | 12.45
|
||||
Other | | 0.04279 | | | 3.46
|
||||
|
||||
Nlocal: 500 ave 504 max 496 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Nghost: 22 ave 24 max 20 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: 3330 ave 3368 max 3292 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 13320
|
||||
Ave neighs/atom = 6.66
|
||||
Ave special neighs/atom = 5.952
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:02
|
||||
171
examples/USER/misc/cauchy/log.2Jun2020.cauchystat.g++.1
Normal file
171
examples/USER/misc/cauchy/log.2Jun2020.cauchystat.g++.1
Normal file
@ -0,0 +1,171 @@
|
||||
LAMMPS (2 Jun 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
units metal
|
||||
atom_style atomic
|
||||
atom_modify map array
|
||||
|
||||
# Box and atom positions:
|
||||
boundary p p p
|
||||
|
||||
# Defining lattice and creating simulation
|
||||
# box with atoms inside
|
||||
lattice fcc 4.05
|
||||
Lattice spacing in x,y,z = 4.05 4.05 4.05
|
||||
region simbox prism 0 5 0 5 0 5 0 0 0 units lattice
|
||||
create_box 2 simbox
|
||||
Created triclinic box = (0.0 0.0 0.0) to (20.25 20.25 20.25) with tilt (0.0 0.0 0.0)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 2 box
|
||||
Created 500 atoms
|
||||
create_atoms CPU = 0.000 seconds
|
||||
|
||||
# Atomic mass:
|
||||
mass 1 58.69
|
||||
mass 2 26.98154
|
||||
|
||||
# Potential, Al fcc crystal
|
||||
pair_style eam/alloy
|
||||
pair_coeff * * NiAlH_jea.eam.alloy Ni Al
|
||||
Reading potential file NiAlH_jea.eam.alloy with DATE: 2007-11-30
|
||||
neigh_modify delay 5
|
||||
|
||||
thermo 100
|
||||
thermo_style custom step temp pxx pyy pzz pxy pxz pyz
|
||||
compute cna all cna/atom 2.8
|
||||
|
||||
fix 1 all npt/cauchy temp 600.0 600.0 1.0 x 0.0 0.0 0.1 y 0.0 0.0 0.1 z 0.0 0.0 0.1 couple none alpha 0.001 continue no
|
||||
Using fix npt/cauchy with alpha=0.001000
|
||||
this is NOT a continuation run
|
||||
|
||||
# dump 1 all cfg 1000 test*.cfg mass type xs ys zs type c_cna
|
||||
|
||||
timestep 0.002
|
||||
|
||||
variable px equal pxx
|
||||
variable py equal pyy
|
||||
variable pz equal pzz
|
||||
variable sxy equal pxy
|
||||
variable sxz equal pxz
|
||||
variable syz equal pyz
|
||||
variable t equal temp
|
||||
|
||||
fix avg all ave/time 1 100 100 v_t v_px v_py v_pz v_sxy v_sxz v_syz file avg.txt
|
||||
|
||||
variable lx equal lx
|
||||
variable ly equal ly
|
||||
variable lz equal ly
|
||||
variable xy equal xy
|
||||
variable xz equal xz
|
||||
variable yz equal yz
|
||||
|
||||
fix box all ave/time 1 100 100 v_lx v_ly v_lz v_xy v_xz v_yz file box.txt
|
||||
|
||||
velocity all create 1200 4928459 rot yes dist gaussian
|
||||
|
||||
run 1000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 7.65
|
||||
ghost atom cutoff = 7.65
|
||||
binsize = 3.825, bins = 6 6 6
|
||||
2 neighbor lists, perpetual/occasional/extra = 1 1 0
|
||||
(1) pair eam/alloy, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton/tri
|
||||
stencil: half/bin/3d/newton/tri
|
||||
bin: standard
|
||||
(2) compute cna/atom, occasional
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.04 | 4.04 | 4.04 Mbytes
|
||||
Step Temp Pxx Pyy Pzz Pxy Pxz Pyz
|
||||
0 1200 9859.2374 9729.7389 10279.526 -110.10907 -391.60768 295.10918
|
||||
100 461.95579 11262.405 9918.4702 7373.1896 1389.9833 -165.54737 -128.04989
|
||||
200 452.7497 4758.0631 6285.2022 9593.9725 389.15901 835.71435 -1853.9679
|
||||
300 451.50974 7980.6036 7524.3514 9584.5276 297.33672 -154.88768 -1927.573
|
||||
400 461.52812 5074.9544 4877.0864 2689.9029 389.66084 224.44814 563.12739
|
||||
500 458.17416 7672.6668 5358.5073 4670.0236 -1251.047 1175.8268 -373.96822
|
||||
600 461.28593 3629.8562 7265.1611 6970.1746 523.3139 1295.8252 -121.17116
|
||||
700 466.86592 5224.2421 4121.434 4368.4226 230.85768 -65.765274 -1271.8354
|
||||
800 491.38828 -233.79818 2799.6028 5023.998 919.08469 -411.66796 422.33219
|
||||
900 473.16465 6486.5426 4028.6955 2503.9771 451.96928 1309.8322 -557.83472
|
||||
1000 472.85932 4303.6923 4674.969 5268.2263 94.551283 1425.2222 -1352.0883
|
||||
Loop time of 0.667831 on 1 procs for 1000 steps with 500 atoms
|
||||
|
||||
Performance: 258.748 ns/day, 0.093 hours/ns, 1497.385 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 | 0.60535 | 0.60535 | 0.60535 | 0.0 | 90.64
|
||||
Neigh | 0.031207 | 0.031207 | 0.031207 | 0.0 | 4.67
|
||||
Comm | 0.0072828 | 0.0072828 | 0.0072828 | 0.0 | 1.09
|
||||
Output | 0.00013593 | 0.00013593 | 0.00013593 | 0.0 | 0.02
|
||||
Modify | 0.021677 | 0.021677 | 0.021677 | 0.0 | 3.25
|
||||
Other | | 0.002176 | | | 0.33
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 2017 ave 2017 max 2017 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 24689 ave 24689 max 24689 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 24689
|
||||
Ave neighs/atom = 49.378
|
||||
Neighbor list builds = 34
|
||||
Dangerous builds = 0
|
||||
|
||||
fix 1 all npt/cauchy temp 600.0 600.0 1.0 x 0.0 0.0 0.1 y 0.0 0.0 0.1 z 0.0 0.0 0.1 xy -10000.0 -10000.0 0.1 couple none alpha 0.001 continue yes
|
||||
Using fix npt/cauchy with alpha=0.001000
|
||||
this is a continuation run
|
||||
|
||||
run 1000
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.056 | 4.056 | 4.056 Mbytes
|
||||
Step Temp Pxx Pyy Pzz Pxy Pxz Pyz
|
||||
1000 472.85932 4303.6923 4674.969 5268.2263 94.551283 1425.2222 -1352.0883
|
||||
1100 471.04772 5593.1614 5874.9866 3608.9922 -1861.938 459.86813 -813.36883
|
||||
1200 473.34727 2337.4765 2050.4694 4330.2198 -3590.2197 -1285.2197 748.05138
|
||||
1300 465.46146 4909.5722 2880.9183 4995.0092 -2860.6934 -895.40937 -382.07529
|
||||
1400 508.53262 92.575576 3722.114 557.50955 -3121.7616 349.61453 194.50883
|
||||
1500 498.3458 -5755.2341 -3798.1481 -1445.2041 -3218.0889 1733.9101 -555.96313
|
||||
1600 546.45888 -257.8015 407.74313 -39.808565 -3578.1152 1438.3545 -1710.3112
|
||||
1700 570.72803 -2951.9777 -622.89115 1138.4111 -4573.8049 -984.65144 2906.3201
|
||||
1800 650.7567 6086.093 1111.3418 1726.5919 -3504.6481 1140.9639 414.77939
|
||||
1900 690.31291 2762.9298 -609.22637 289.53512 -3788.5686 -1307.3139 759.83909
|
||||
2000 724.0376 -676.49959 522.5367 -468.29812 -6602.9226 -1712.1389 46.769914
|
||||
Loop time of 0.665662 on 1 procs for 1000 steps with 500 atoms
|
||||
|
||||
Performance: 259.591 ns/day, 0.092 hours/ns, 1502.265 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 | 0.56182 | 0.56182 | 0.56182 | 0.0 | 84.40
|
||||
Neigh | 0.069662 | 0.069662 | 0.069662 | 0.0 | 10.47
|
||||
Comm | 0.0090612 | 0.0090612 | 0.0090612 | 0.0 | 1.36
|
||||
Output | 0.00015483 | 0.00015483 | 0.00015483 | 0.0 | 0.02
|
||||
Modify | 0.02264 | 0.02264 | 0.02264 | 0.0 | 3.40
|
||||
Other | | 0.00232 | | | 0.35
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 2044 ave 2044 max 2044 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 23800 ave 23800 max 23800 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 23800
|
||||
Ave neighs/atom = 47.6
|
||||
Neighbor list builds = 77
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:01
|
||||
1
examples/USER/misc/orient_eco/Ni_u3.eam
Symbolic link
1
examples/USER/misc/orient_eco/Ni_u3.eam
Symbolic link
@ -0,0 +1 @@
|
||||
../../../../potentials/Ni_u3.eam
|
||||
25615
examples/USER/misc/orient_eco/data.sigma5
Normal file
25615
examples/USER/misc/orient_eco/data.sigma5
Normal file
File diff suppressed because it is too large
Load Diff
20
examples/USER/misc/orient_eco/in.orient_eco
Normal file
20
examples/USER/misc/orient_eco/in.orient_eco
Normal file
@ -0,0 +1,20 @@
|
||||
|
||||
units metal
|
||||
atom_style atomic
|
||||
read_data data.sigma5
|
||||
|
||||
pair_style eam
|
||||
pair_coeff * * Ni_u3.eam
|
||||
timestep 0.001
|
||||
|
||||
fix integrator all npt temp 750 750 0.1 iso 0 0 0.1
|
||||
fix eco all orient/eco 0.08 0.25 3.6 sigma5.ori
|
||||
|
||||
thermo 100
|
||||
thermo_style custom step temp etotal press vol f_eco
|
||||
velocity all create 750 18527782
|
||||
|
||||
#dump save all custom 100 orient_eco.dump xs ys zs f_eco[1] f_eco[2]
|
||||
#dump_modify save sort id
|
||||
|
||||
run 1000
|
||||
91
examples/USER/misc/orient_eco/log.2Jun2020.orent_eco.g++.1
Normal file
91
examples/USER/misc/orient_eco/log.2Jun2020.orent_eco.g++.1
Normal file
@ -0,0 +1,91 @@
|
||||
LAMMPS (2 Jun 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
|
||||
units metal
|
||||
atom_style atomic
|
||||
read_data data.sigma5
|
||||
orthogonal box = (-90.27200752837744 -4.427188724235731e-07 0.0) to (90.27200752837744 88.54377448471462 17.5)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
25600 atoms
|
||||
read_data CPU = 0.020 secs
|
||||
|
||||
pair_style eam
|
||||
pair_coeff * * Ni_u3.eam
|
||||
Reading potential file Ni_u3.eam with DATE: 2007-06-11
|
||||
timestep 0.001
|
||||
|
||||
fix integrator all npt temp 750 750 0.1 iso 0 0 0.1
|
||||
fix eco all orient/eco 0.08 0.25 3.6 sigma5.ori
|
||||
|
||||
thermo 100
|
||||
thermo_style custom step temp etotal press vol f_eco
|
||||
velocity all create 750 18527782
|
||||
|
||||
#dump save all custom 100 orient_eco.dump xs ys zs f_eco[1] f_eco[2]
|
||||
#dump_modify save sort id
|
||||
|
||||
run 1000
|
||||
fix orient/eco: cutoff=3.6 norm_fac=30.012843706295556 neighbors=18
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 6.8
|
||||
ghost atom cutoff = 6.8
|
||||
binsize = 3.4, bins = 54 27 6
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair eam, perpetual, half/full from (2)
|
||||
attributes: half, newton on
|
||||
pair build: halffull/newton
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) fix orient/eco, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 42.15 | 42.15 | 42.15 Mbytes
|
||||
Step Temp TotEng Press Volume f_eco
|
||||
0 750 -111027.95 15148.458 279755.85 8.7507522e-10
|
||||
100 422.2475 -110928.85 214.27204 285332.91 -1.0089186
|
||||
200 388.79514 -110721.02 -481.9574 286443.13 -0.78446905
|
||||
300 441.87285 -110478.56 -174.88288 286640.75 -1.1348357
|
||||
400 486.71094 -110211.6 65.075638 287023.56 -1.495318
|
||||
500 531.12815 -109923.33 97.309245 287552.73 -2.9498072
|
||||
600 569.82126 -109622.61 -85.73157 288229.35 -4.2855812
|
||||
700 615.84724 -109317.16 -52.508824 288799.86 -6.5214427
|
||||
800 666.09015 -109018.62 38.120383 289305.37 -8.4745641
|
||||
900 705.03939 -108738.66 263.39673 289867.87 -12.4514
|
||||
1000 735.59866 -108500.52 242.46405 290353.65 -15.427653
|
||||
Loop time of 109.966 on 1 procs for 1000 steps with 25600 atoms
|
||||
|
||||
Performance: 0.786 ns/day, 30.546 hours/ns, 9.094 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 27.002 | 27.002 | 27.002 | 0.0 | 24.55
|
||||
Neigh | 0.83228 | 0.83228 | 0.83228 | 0.0 | 0.76
|
||||
Comm | 0.12623 | 0.12623 | 0.12623 | 0.0 | 0.11
|
||||
Output | 0.00080323 | 0.00080323 | 0.00080323 | 0.0 | 0.00
|
||||
Modify | 81.917 | 81.917 | 81.917 | 0.0 | 74.49
|
||||
Other | | 0.08839 | | | 0.08
|
||||
|
||||
Nlocal: 25600 ave 25600 max 25600 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 28259 ave 28259 max 28259 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 1.59326e+06 ave 1.59326e+06 max 1.59326e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 3.18651e+06 ave 3.18651e+06 max 3.18651e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 3186510
|
||||
Ave neighs/atom = 124.473
|
||||
Neighbor list builds = 10
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:01:50
|
||||
91
examples/USER/misc/orient_eco/log.2Jun2020.orent_eco.g++.4
Normal file
91
examples/USER/misc/orient_eco/log.2Jun2020.orent_eco.g++.4
Normal file
@ -0,0 +1,91 @@
|
||||
LAMMPS (2 Jun 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
|
||||
units metal
|
||||
atom_style atomic
|
||||
read_data data.sigma5
|
||||
orthogonal box = (-90.27200752837744 -4.427188724235731e-07 0.0) to (90.27200752837744 88.54377448471462 17.5)
|
||||
4 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
25600 atoms
|
||||
read_data CPU = 0.025 secs
|
||||
|
||||
pair_style eam
|
||||
pair_coeff * * Ni_u3.eam
|
||||
Reading potential file Ni_u3.eam with DATE: 2007-06-11
|
||||
timestep 0.001
|
||||
|
||||
fix integrator all npt temp 750 750 0.1 iso 0 0 0.1
|
||||
fix eco all orient/eco 0.08 0.25 3.6 sigma5.ori
|
||||
|
||||
thermo 100
|
||||
thermo_style custom step temp etotal press vol f_eco
|
||||
velocity all create 750 18527782
|
||||
|
||||
#dump save all custom 100 orient_eco.dump xs ys zs f_eco[1] f_eco[2]
|
||||
#dump_modify save sort id
|
||||
|
||||
run 1000
|
||||
fix orient/eco: cutoff=3.6 norm_fac=30.012843706295556 neighbors=18
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 6.8
|
||||
ghost atom cutoff = 6.8
|
||||
binsize = 3.4, bins = 54 27 6
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair eam, perpetual, half/full from (2)
|
||||
attributes: half, newton on
|
||||
pair build: halffull/newton
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) fix orient/eco, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 11.69 | 11.7 | 11.72 Mbytes
|
||||
Step Temp TotEng Press Volume f_eco
|
||||
0 750 -111027.95 15148.458 279755.85 8.749339e-10
|
||||
100 422.2475 -110928.85 214.27204 285332.91 -1.0089186
|
||||
200 388.79514 -110721.02 -481.9574 286443.13 -0.78446905
|
||||
300 441.87285 -110478.56 -174.88288 286640.75 -1.1348357
|
||||
400 486.71094 -110211.6 65.075638 287023.56 -1.495318
|
||||
500 531.12815 -109923.33 97.309245 287552.73 -2.9498072
|
||||
600 569.82126 -109622.61 -85.73157 288229.35 -4.2855812
|
||||
700 615.84724 -109317.16 -52.508824 288799.86 -6.5214427
|
||||
800 666.09015 -109018.62 38.120383 289305.37 -8.4745641
|
||||
900 705.03939 -108738.66 263.39673 289867.87 -12.4514
|
||||
1000 735.59866 -108500.52 242.46405 290353.65 -15.427653
|
||||
Loop time of 29.6634 on 4 procs for 1000 steps with 25600 atoms
|
||||
|
||||
Performance: 2.913 ns/day, 8.240 hours/ns, 33.712 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 | 7.0794 | 7.1053 | 7.1325 | 0.7 | 23.95
|
||||
Neigh | 0.20947 | 0.21088 | 0.21231 | 0.2 | 0.71
|
||||
Comm | 0.15708 | 0.18471 | 0.22338 | 6.7 | 0.62
|
||||
Output | 0.00032616 | 0.00064683 | 0.0015936 | 0.0 | 0.00
|
||||
Modify | 22.105 | 22.118 | 22.139 | 0.3 | 74.56
|
||||
Other | | 0.0437 | | | 0.15
|
||||
|
||||
Nlocal: 6400 ave 6421 max 6384 min
|
||||
Histogram: 1 1 0 0 0 1 0 0 0 1
|
||||
Nghost: 9872.5 ave 9892 max 9855 min
|
||||
Histogram: 1 0 0 1 0 1 0 0 0 1
|
||||
Neighs: 398314 ave 400737 max 395743 min
|
||||
Histogram: 1 0 0 1 0 0 0 1 0 1
|
||||
FullNghs: 796628 ave 801194 max 792566 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 3186510
|
||||
Ave neighs/atom = 124.473
|
||||
Neighbor list builds = 10
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:29
|
||||
6
examples/USER/misc/orient_eco/sigma5.ori
Normal file
6
examples/USER/misc/orient_eco/sigma5.ori
Normal file
@ -0,0 +1,6 @@
|
||||
1.671685 0.557228 1.76212
|
||||
0.557228 -1.671685 1.76212
|
||||
2.228913 -1.114456 0.000000
|
||||
0.557228 1.671685 1.76212
|
||||
1.671685 -0.557228 1.76212
|
||||
2.228913 1.114456 0.000000
|
||||
@ -0,0 +1 @@
|
||||
../../../../../potentials/SiCGe.tersoff
|
||||
@ -16,4 +16,4 @@ mass ${Si} 28.08550
|
||||
###########################
|
||||
|
||||
pair_style tersoff
|
||||
pair_coeff * * Si.opt.tersoff Si(D)
|
||||
pair_coeff * * SiCGe.tersoff Si(D)
|
||||
|
||||
@ -1,192 +1,192 @@
|
||||
5409.83472486 3.05075234 0.00000214
|
||||
-1277.48270695 -863.24917964 -862.95613831
|
||||
-193.14095266 0.11071645 0.00000015
|
||||
-1277.48270619 -863.24917934 862.95613793
|
||||
-193.17613831 0.34066975 -0.00000031
|
||||
-1276.01088244 861.54715125 -861.62537402
|
||||
83.46959051 -0.09801326 0.00000000
|
||||
-1276.01088167 861.54715064 861.62537387
|
||||
3.05073556 5409.83419867 0.00000137
|
||||
-863.13224993 -1277.34160622 -862.92133430
|
||||
0.12865796 -193.14095472 -0.00000023
|
||||
-863.13224825 -1277.34160485 862.92133392
|
||||
-0.23661028 83.46934214 -0.00000046
|
||||
861.66402909 -1276.15172701 861.66024333
|
||||
-0.00634065 -193.17585981 -0.00000015
|
||||
861.66402909 -1276.15172686 -861.66024394
|
||||
0.00000031 0.00000031 5410.11037330
|
||||
-862.89766079 -862.97973912 -1277.71823542
|
||||
0.00000000 -0.00000008 83.84059083
|
||||
862.89766018 862.97973851 -1277.71823557
|
||||
0.00000015 0.00000015 -193.17558390
|
||||
-861.60900269 861.52691291 -1276.08157137
|
||||
-0.00000015 -0.00000031 -193.17573821
|
||||
861.60900330 -861.52691284 -1276.08157236
|
||||
-1277.48271824 -863.13225435 -862.89768596
|
||||
5409.83567916 3.04882502 2.82007861
|
||||
-1277.34161080 -863.24919475 862.97975804
|
||||
-193.14089260 0.11950100 0.11994134
|
||||
-1277.52243157 863.24943259 -863.11331046
|
||||
-193.17597070 0.16713301 -0.02106496
|
||||
-1274.64156872 859.96385388 860.17328202
|
||||
83.46945758 -0.16730525 -0.06100253
|
||||
-863.24919444 -1277.34161103 -862.97975804
|
||||
3.04882666 5409.83567944 -2.82007731
|
||||
-863.13225496 -1277.48271916 862.89768688
|
||||
0.11950094 -193.14089255 -0.11994043
|
||||
863.24943320 -1277.52243118 863.11331076
|
||||
-0.16730522 83.46945778 0.06100314
|
||||
859.96385365 -1274.64156819 -860.17328225
|
||||
0.16713979 -193.17596607 0.02106008
|
||||
-862.95611199 -862.92132598 -1277.71824411
|
||||
2.82004085 -2.82004013 5410.11000835
|
||||
862.92132743 862.95611344 -1277.71824587
|
||||
-0.11994722 0.11994786 83.84083834
|
||||
-862.88110757 862.88110699 -1277.34764097
|
||||
0.02099713 0.06108924 -193.17561785
|
||||
860.25587487 -860.25587502 -1274.81548840
|
||||
-0.06108897 -0.02099687 -193.17561808
|
||||
-193.14095465 0.12865765 0.00000015
|
||||
-1277.34160508 -863.13224794 862.92133361
|
||||
5409.83419867 3.05073968 0.00000092
|
||||
-1277.34160584 -863.13224924 -862.92133483
|
||||
83.46934214 -0.23660998 -0.00000076
|
||||
-1276.15172724 861.66402917 861.66024325
|
||||
-193.17585988 -0.00634042 -0.00000031
|
||||
-1276.15172694 861.66402940 -861.66024325
|
||||
0.11071645 -193.14095243 0.00000046
|
||||
-863.24917949 -1277.48270718 862.95613831
|
||||
3.05075524 5409.83472478 -0.00000046
|
||||
-863.24918117 -1277.48270825 -862.95613923
|
||||
0.34066922 -193.17613823 0.00000046
|
||||
861.54715094 -1276.01088228 -861.62537295
|
||||
-0.09801303 83.46959035 0.00000015
|
||||
861.54713538 -1276.01088145 861.62537387
|
||||
-0.00000046 -0.00000023 83.84059068
|
||||
862.97973867 862.89766010 -1277.71823633
|
||||
-0.00000214 -0.00000053 5410.11037574
|
||||
-862.97973943 -862.89766079 -1277.71823633
|
||||
0.00000015 0.00000008 -193.17558374
|
||||
861.52691291 -861.60900269 -1276.08157198
|
||||
-0.00000015 -0.00000015 -193.17573814
|
||||
-861.52691368 861.60900261 -1276.08157243
|
||||
-1277.48271855 -863.13225405 -862.89768612
|
||||
-193.14095469 0.12865732 0.00000061
|
||||
-1277.48271786 -863.13225450 862.89768520
|
||||
-193.14089232 0.11950085 -0.11994115
|
||||
-1277.34161255 -863.24919673 -862.97975957
|
||||
5409.83568051 3.04882517 -2.82007644
|
||||
-1277.52243110 863.24943259 863.11330990
|
||||
83.46945732 -0.16730494 0.06100319
|
||||
-1274.64156796 859.96385342 -860.17328103
|
||||
-193.17597041 0.16713331 0.02106477
|
||||
-863.24919482 -1277.34161057 862.97975774
|
||||
0.11950077 -193.14089270 0.11994160
|
||||
-863.13225473 -1277.48271839 -862.89768673
|
||||
3.04882502 5409.83568081 2.82007903
|
||||
863.24943084 -1277.52242966 -863.11330868
|
||||
0.16713324 -193.17597064 -0.02106522
|
||||
859.96385510 -1274.64156926 860.17328255
|
||||
-0.16730411 83.46945641 -0.06100350
|
||||
862.95611161 862.92132537 -1277.71824365
|
||||
0.11994725 -0.11994740 83.84083859
|
||||
-862.92132606 -862.95611207 -1277.71824548
|
||||
-2.82003936 2.82004013 5410.11000806
|
||||
862.88110509 -862.88110547 -1277.34764015
|
||||
0.06108893 0.02099703 -193.17561792
|
||||
-860.25587388 860.25587441 -1274.81548916
|
||||
-0.02099726 -0.06108878 -193.17561777
|
||||
-193.17613465 -0.23660693 0.00000015
|
||||
-1277.52241409 863.24943328 -862.88111478
|
||||
83.46934549 0.34066334 -0.00000015
|
||||
-1277.52241425 863.24943335 862.88111508
|
||||
5404.58897235 -9.71806749 0.00000015
|
||||
-1273.31333522 -858.38273960 -858.96245956
|
||||
-193.21062369 -0.11938368 0.00000000
|
||||
-1273.31333598 -858.38273967 858.96245926
|
||||
0.34066342 83.46934572 0.00000015
|
||||
863.24943335 -1277.52241402 862.88111478
|
||||
-0.23660723 -193.17613480 -0.00000046
|
||||
863.24943320 -1277.52241425 -862.88111432
|
||||
-9.71806582 5404.58897135 -0.00000183
|
||||
-858.38273891 -1273.31333552 -858.96245926
|
||||
-0.11938338 -193.21062369 0.00000000
|
||||
-858.38273937 -1273.31333598 858.96245987
|
||||
-0.00000031 -0.00000008 -193.17559595
|
||||
-863.11328229 863.11328297 -1277.34763999
|
||||
0.00000000 -0.00000015 -193.17559595
|
||||
863.11328305 -863.11328282 -1277.34763984
|
||||
0.00000122 -0.00000259 5404.30470550
|
||||
-858.80486827 -858.80486866 -1273.17865241
|
||||
-0.00000031 0.00000000 83.09905870
|
||||
858.80486827 858.80486812 -1273.17865272
|
||||
-193.17613450 -0.23660702 0.00000031
|
||||
-1276.01089136 861.66402482 -861.60900483
|
||||
-193.17596134 -0.16730494 0.02099535
|
||||
-1276.15175745 861.54714988 861.52691337
|
||||
83.46947097 0.16714109 0.06108436
|
||||
-1273.31334651 -858.38273311 -858.80488185
|
||||
5404.58493608 -3.04507687 -2.81778617
|
||||
-1276.19187193 -861.66399965 861.74280750
|
||||
-193.21058304 -0.11920641 -0.12012575
|
||||
861.54714972 -1276.15175730 861.52691337
|
||||
0.16714140 83.46947120 0.06108451
|
||||
861.66402345 -1276.01089022 -861.60900330
|
||||
-0.16730487 -193.17596164 0.02099489
|
||||
-858.38273281 -1273.31334681 -858.80488063
|
||||
-3.04507603 5404.58493554 -2.81778617
|
||||
-861.66400079 -1276.19187270 861.74280887
|
||||
-0.11920511 -193.21058281 -0.12012498
|
||||
-861.62536929 861.66025668 -1276.08157121
|
||||
-0.02106026 0.06099877 -193.17561197
|
||||
861.66025752 -861.62537051 -1276.08157274
|
||||
0.06099923 -0.02106049 -193.17561227
|
||||
-858.96244980 -858.96244965 -1273.17866523
|
||||
-2.81780608 -2.81780615 5404.30474272
|
||||
861.58531232 861.58531248 -1275.71087663
|
||||
0.12013467 0.12013460 83.09915619
|
||||
83.46958166 -0.00634218 -0.00000023
|
||||
-1274.64157002 859.96383191 860.25587098
|
||||
-193.17585332 -0.09802844 0.00000023
|
||||
-1274.64157155 859.96383290 -860.25587243
|
||||
-193.21062064 -0.11939070 -0.00000008
|
||||
-1276.19189573 -861.66398638 861.58531118
|
||||
5404.58377546 3.62403097 0.00000015
|
||||
-1276.19189558 -861.66398615 -861.58531103
|
||||
-0.09802859 -193.17585355 -0.00000015
|
||||
859.96383206 -1274.64156979 -860.25587113
|
||||
-0.00634187 83.46958204 -0.00000008
|
||||
859.96383282 -1274.64157132 860.25587212
|
||||
-0.11939055 -193.21062041 0.00000000
|
||||
-861.66398576 -1276.19189528 861.58531087
|
||||
3.62402982 5404.58377698 -0.00000076
|
||||
-861.66398927 -1276.19189772 -861.58531331
|
||||
0.00000000 0.00000000 -193.17573654
|
||||
860.17327676 -860.17327637 -1274.81551212
|
||||
0.00000031 0.00000023 -193.17573676
|
||||
-860.17327615 860.17327645 -1274.81551258
|
||||
0.00000000 0.00000015 83.09907327
|
||||
861.74281299 861.74281299 -1275.71086763
|
||||
-0.00000046 -0.00000015 5404.30514861
|
||||
-861.74281406 -861.74281421 -1275.71086938
|
||||
83.46958227 -0.00634221 -0.00000026
|
||||
-1276.01088968 861.66402284 861.60900330
|
||||
83.46947136 0.16714109 -0.06108436
|
||||
-1276.15175722 861.54714957 -861.52691391
|
||||
-193.17596141 -0.16730510 -0.02099527
|
||||
-1273.31334666 -858.38273281 858.80488124
|
||||
-193.21058304 -0.11920641 0.12012636
|
||||
-1276.19187285 -861.66400087 -861.74280773
|
||||
5404.58493638 -3.04507565 2.81778602
|
||||
3.05073556 5409.83419867 0.00000137
|
||||
-863.24919414 -1277.34161118 -862.97975804
|
||||
0.11071644 -193.14095221 0.00000015
|
||||
-863.24919482 -1277.34161057 862.97975774
|
||||
0.34066372 83.46934579 0.00000015
|
||||
861.54714972 -1276.15175730 861.52691337
|
||||
-0.09802844 -193.17585342 -0.00000005
|
||||
861.54715133 -1276.15175913 -861.52691490
|
||||
-0.16730502 -193.17596118 -0.02099497
|
||||
861.66402314 -1276.01088976 861.60900383
|
||||
0.16714125 83.46947151 -0.06108497
|
||||
-858.38273296 -1273.31334681 858.80488139
|
||||
-0.11920686 -193.21058311 0.12012605
|
||||
-861.66400079 -1276.19187255 -861.74280811
|
||||
-3.04506703 5404.58493432 2.81779319
|
||||
0.00000031 0.00000031 5410.11037330
|
||||
-862.95611222 -862.92132598 -1277.71824426
|
||||
-0.00000027 -0.00000023 83.84059068
|
||||
862.95611161 862.92132537 -1277.71824365
|
||||
-0.00000015 0.00000006 -193.17559671
|
||||
-861.62536929 861.66025668 -1276.08157121
|
||||
0.00000031 -0.00000000 -193.17573662
|
||||
861.62536952 -861.66025637 -1276.08157175
|
||||
-1277.48270695 -863.24917964 -862.95613831
|
||||
5409.83567791 3.04882503 2.82007909
|
||||
-1277.34160500 -863.13224794 862.92133361
|
||||
-193.14089232 0.11950085 -0.11994115
|
||||
-1277.52241409 863.24943335 -862.88111478
|
||||
-193.17596134 -0.16730494 0.02099535
|
||||
-1274.64156987 859.96383191 860.25587098
|
||||
83.46947136 0.16714109 -0.06108436
|
||||
-863.13224993 -1277.34160622 -862.92133430
|
||||
3.04882664 5409.83567981 -2.82007772
|
||||
-863.24917934 -1277.48270718 862.95613862
|
||||
0.11950077 -193.14089270 0.11994160
|
||||
863.24943366 -1277.52241409 862.88111478
|
||||
0.16714140 83.46947120 0.06108451
|
||||
859.96383191 -1274.64156979 -860.25587113
|
||||
-0.16730502 -193.17596118 -0.02099497
|
||||
-862.89766079 -862.97973912 -1277.71823542
|
||||
2.82004053 -2.82003977 5410.11000766
|
||||
862.97973867 862.89766003 -1277.71823633
|
||||
0.11994725 -0.11994740 83.84083859
|
||||
-863.11328229 863.11328297 -1277.34763999
|
||||
-0.02106026 0.06099877 -193.17561197
|
||||
860.17327676 -860.17327637 -1274.81551212
|
||||
-0.06099938 0.02106080 -193.17561235
|
||||
-861.66025645 861.62536929 -1276.08157213
|
||||
0.02106049 -0.06099862 -193.17561189
|
||||
858.96245049 858.96245041 -1273.17866553
|
||||
-0.12013444 -0.12013475 83.09915550
|
||||
-193.14095266 0.11071661 0.00000023
|
||||
-1277.34161164 -863.24919490 862.97975758
|
||||
5409.83419895 3.05073908 0.00000031
|
||||
-1277.34161248 -863.24919704 -862.97976018
|
||||
83.46934641 0.34066377 0.00000031
|
||||
-1276.15175798 861.54714988 861.52691307
|
||||
-193.17585317 -0.09802854 0.00000018
|
||||
-1276.15175745 861.54714957 -861.52691314
|
||||
0.12865765 -193.14095472 0.00000000
|
||||
-863.13225527 -1277.48271931 862.89768673
|
||||
3.05075511 5409.83472469 -0.00000046
|
||||
-863.13225489 -1277.48271839 -862.89768612
|
||||
-0.23660723 -193.17613471 0.00000061
|
||||
861.66402345 -1276.01089068 -861.60900391
|
||||
-0.00634202 83.46958197 0.00000012
|
||||
861.66402314 -1276.01088961 861.60900353
|
||||
-0.00000015 -0.00000015 83.84059098
|
||||
862.92132797 862.95611360 -1277.71824533
|
||||
-0.00000145 -0.00000137 5410.11037498
|
||||
-862.92132598 -862.95611222 -1277.71824426
|
||||
-0.00000031 -0.00000009 -193.17559671
|
||||
861.66025660 -861.62536929 -1276.08157182
|
||||
0.00000015 0.00000014 -193.17573668
|
||||
-861.66025615 861.62536929 -1276.08157190
|
||||
-1277.48270619 -863.24917934 862.95613793
|
||||
-193.14089264 0.11950070 0.11994149
|
||||
-1277.34160589 -863.13224892 -862.92133438
|
||||
5409.83568112 3.04882502 -2.82007598
|
||||
-1277.52241409 863.24943313 862.88111386
|
||||
83.46947128 0.16714155 0.06108420
|
||||
-1274.64157216 859.96383297 -860.25587243
|
||||
-193.17596164 -0.16730510 -0.02099535
|
||||
-863.13224825 -1277.34160470 862.92133392
|
||||
0.11950069 -193.14089248 -0.11994088
|
||||
-863.24918118 -1277.48270824 -862.95613907
|
||||
3.04882479 5409.83568081 2.82007857
|
||||
863.24943366 -1277.52241409 -862.88111386
|
||||
-0.16730494 -193.17596164 0.02099504
|
||||
859.96383191 -1274.64157155 860.25587228
|
||||
0.16714109 83.46947120 -0.06108481
|
||||
862.89766018 862.97973836 -1277.71823542
|
||||
-0.11994717 0.11994762 83.84083846
|
||||
-862.97973940 -862.89766100 -1277.71823603
|
||||
-2.82004089 2.82004165 5410.11001111
|
||||
863.11328534 -863.11328473 -1277.34764213
|
||||
0.06099900 -0.02106019 -193.17561197
|
||||
-860.17327706 860.17327752 -1274.81551319
|
||||
0.02106049 -0.06099877 -193.17561212
|
||||
-193.17613831 0.34066975 0.00000000
|
||||
-1277.52243217 863.24943252 -863.11331043
|
||||
83.46934255 -0.23660983 0.00000046
|
||||
-1277.52243126 863.24943229 863.11330975
|
||||
5404.58897296 -9.71806756 0.00000046
|
||||
-1273.31334689 -858.38273326 -858.80488185
|
||||
-193.21062125 -0.11939087 -0.00000018
|
||||
-1273.31334666 -858.38273265 858.80488124
|
||||
-0.23661028 83.46934221 -0.00000038
|
||||
863.24943259 -1277.52243133 863.11331043
|
||||
0.34066924 -193.17613846 -0.00000015
|
||||
863.24943168 -1277.52243072 -863.11330883
|
||||
-9.71806704 5404.58897205 -0.00000107
|
||||
-858.38273265 -1273.31334697 -858.80488063
|
||||
-0.11939101 -193.21062043 0.00000006
|
||||
-858.38273296 -1273.31334681 858.80488139
|
||||
0.00000015 0.00000000 -193.17558413
|
||||
-862.88110730 862.88110699 -1277.34764060
|
||||
-0.00000001 -0.00000001 -193.17558374
|
||||
862.88110539 -862.88110516 -1277.34764030
|
||||
0.00000122 -0.00000264 5404.30470473
|
||||
-858.96244965 -858.96244934 -1273.17866523
|
||||
-0.00000046 0.00000006 83.09907322
|
||||
858.96245026 858.96245041 -1273.17866553
|
||||
-1276.01088335 861.54715186 -861.62537494
|
||||
-193.17596632 0.16713991 -0.02106865
|
||||
-1276.15172701 861.66401376 861.66024356
|
||||
83.46945641 -0.16730418 0.06100182
|
||||
-1273.31333507 -858.38273911 -858.96245926
|
||||
5404.58493280 -3.04507046 -2.81778113
|
||||
-1276.19189558 -861.66398654 861.58531085
|
||||
-193.21058250 -0.11920503 0.12012704
|
||||
861.66401292 -1276.15172617 861.66024257
|
||||
-0.16730418 83.46945627 0.06100192
|
||||
861.54715110 -1276.01088167 -861.62537387
|
||||
0.16713972 -193.17596591 -0.02106965
|
||||
-858.38273891 -1273.31333542 -858.96245910
|
||||
-3.04506741 5404.58493142 -2.81778205
|
||||
-861.66398683 -1276.19189578 861.58531200
|
||||
-0.11920541 -193.21058250 0.12012674
|
||||
-861.60900269 861.52691291 -1276.08157152
|
||||
0.02099737 0.06108917 -193.17561785
|
||||
861.52691246 -861.60900299 -1276.08157243
|
||||
0.06108909 0.02099718 -193.17561746
|
||||
-858.80486827 -858.80486867 -1273.17865256
|
||||
-2.81780745 -2.81780722 5404.30474364
|
||||
861.74281375 861.74281365 -1275.71086885
|
||||
-0.12013460 -0.12013475 83.09915550
|
||||
83.46959035 -0.09801326 0.00000000
|
||||
-1274.64156874 859.96385402 860.17328225
|
||||
-193.17585994 -0.00634034 0.00000031
|
||||
-1274.64156789 859.96385357 -860.17328072
|
||||
-193.21062369 -0.11938345 0.00000015
|
||||
-1276.19187300 -861.66400056 861.74280857
|
||||
5404.58377637 3.62403189 -0.00000071
|
||||
-1276.19187285 -861.66400087 -861.74280780
|
||||
-0.00634065 -193.17585981 -0.00000015
|
||||
859.96385345 -1274.64156845 -860.17328227
|
||||
-0.09801307 83.46959066 0.00000092
|
||||
859.96385342 -1274.64156728 860.17328103
|
||||
-0.11938399 -193.21062370 0.00000031
|
||||
-861.66399988 -1276.19187163 861.74280780
|
||||
3.62403013 5404.58377402 0.00000142
|
||||
-861.66400079 -1276.19187255 -861.74280803
|
||||
-0.00000031 -0.00000038 -193.17573821
|
||||
860.25587448 -860.25587441 -1274.81548871
|
||||
0.00000000 -0.00000026 -193.17573875
|
||||
-860.25587388 860.25587456 -1274.81548916
|
||||
0.00000015 -0.00000009 83.09905855
|
||||
861.58531164 861.58531156 -1275.71087571
|
||||
0.00000046 0.00000089 5404.30514766
|
||||
-861.58531232 -861.58531217 -1275.71087655
|
||||
2.81780737 2.81780753 5404.30474547
|
||||
-1276.01088198 861.54713523 861.62537356
|
||||
83.46945674 -0.16730402 -0.06100344
|
||||
-1276.15172688 861.66402939 -861.66024402
|
||||
-193.17596584 0.16713972 0.02106034
|
||||
-1273.31333552 -858.38273940 858.96245956
|
||||
-193.21058227 -0.11920503 -0.12012498
|
||||
-1276.19189573 -861.66398605 -861.58531085
|
||||
5404.58493188 -3.04506924 2.81779059
|
||||
861.66402925 -1276.15172686 -861.66024394
|
||||
0.16713982 -193.17596610 0.02106041
|
||||
861.54713537 -1276.01088130 861.62537448
|
||||
-0.16730426 83.46945625 -0.06100350
|
||||
-858.38273967 -1273.31333570 858.96245987
|
||||
-0.11920511 -193.21058281 -0.12012514
|
||||
-861.66398958 -1276.19189780 -861.58531314
|
||||
-3.04506687 5404.58493417 2.81779303
|
||||
861.60900299 -861.52691253 -1276.08157236
|
||||
-0.06108885 -0.02099714 -193.17561830
|
||||
-861.52691343 861.60900260 -1276.08157198
|
||||
-0.02099726 -0.06108848 -193.17561792
|
||||
858.80486782 858.80486829 -1273.17865256
|
||||
0.12013467 0.12013460 83.09915604
|
||||
-861.74281406 -861.74281426 -1275.71086942
|
||||
2.81780737 2.81780737 5404.30474524
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
LAMMPS (16 Jul 2018)
|
||||
LAMMPS (15 Jun 2020)
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (5.431 5.431 5.431)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
orthogonal box = (0.0 0.0 0.0) to (5.431 5.431 5.431)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
8 atoms
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
@ -11,6 +11,9 @@ Finding 1-2 1-3 1-4 neighbors ...
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
special bonds CPU = 4.2e-05 secs
|
||||
read_data CPU = 0.002 secs
|
||||
Reading potential file ../../../../../potentials/SiCGe.tersoff with DATE: 2009-03-18
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
@ -23,36 +26,40 @@ Neighbor list info ...
|
||||
pair build: full/bin
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Calculating Dynamical Matrix...
|
||||
Dynamical Matrix calculation took 0.001183 seconds
|
||||
Calculating Dynamical Matrix ...
|
||||
Total # of atoms = 8
|
||||
Atoms in group = 8
|
||||
Total dynamical matrix elements = 576
|
||||
10% 20% 30% 50% 60% 70% 80%
|
||||
Finished Calculating Dynamical Matrix
|
||||
Loop time of 1.22396e+06 on 4 procs for 0 steps with 8 atoms
|
||||
Loop time of 0.000775099 on 1 procs for 48 steps with 8 atoms
|
||||
|
||||
0.0% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
Performance: 5350.544 ns/day, 0.004 hours/ns, 61927.589 timesteps/s
|
||||
91.3% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.00016781 | 0.00041345 | 0.00051464 | 0.0 | 0.00
|
||||
Bond | 1.9255e-06 | 2.1775e-06 | 2.4787e-06 | 0.0 | 0.00
|
||||
Pair | 0.00074148 | 0.00074148 | 0.00074148 | 0.0 | 95.66
|
||||
Bond | 3.8147e-06 | 3.8147e-06 | 3.8147e-06 | 0.0 | 0.49
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00056143 | 0.00066602 | 0.00090865 | 0.0 | 0.00
|
||||
Comm | 7.8678e-06 | 7.8678e-06 | 7.8678e-06 | 0.0 | 1.02
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 1.224e+06 | | |100.00
|
||||
Modify | 9.5367e-07 | 9.5367e-07 | 9.5367e-07 | 0.0 | 0.12
|
||||
Other | | 2.098e-05 | | | 2.71
|
||||
|
||||
Nlocal: 2 ave 3 max 1 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
Nghost: 56 ave 57 max 55 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
Nlocal: 8 ave 8 max 8 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 86 ave 86 max 86 min
|
||||
Histogram: 1 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: 32 ave 48 max 16 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 128 ave 128 max 128 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 128
|
||||
Ave neighs/atom = 16
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
|
||||
@ -0,0 +1 @@
|
||||
../../../../../potentials/SiCGe.tersoff
|
||||
@ -38,5 +38,5 @@ dynmat = dynmat.reshape((dynlen, dynlen))
|
||||
eigvals, eigvecs = np.linalg.eig(dynmat)
|
||||
|
||||
# frequencies in THz
|
||||
omegas = np.sqrt(np.abs(eigvals))
|
||||
omegas = np.sqrt(np.abs(eigvals))/2/np.pi
|
||||
print(omegas)
|
||||
|
||||
@ -0,0 +1 @@
|
||||
../Silicon/ff-silicon.lmp
|
||||
@ -0,0 +1,192 @@
|
||||
5409.83472486 3.05075234 0.00000214
|
||||
-1277.48271855 -863.13225405 -862.89768612
|
||||
-193.14095469 0.12865732 0.00000061
|
||||
-1277.48271786 -863.13225450 862.89768520
|
||||
-193.17613450 -0.23660702 0.00000031
|
||||
-1276.01089136 861.66402482 -861.60900483
|
||||
83.46958227 -0.00634221 -0.00000026
|
||||
-1276.01088968 861.66402284 861.60900330
|
||||
3.05073556 5409.83419867 0.00000137
|
||||
-863.24919414 -1277.34161118 -862.97975804
|
||||
0.11071644 -193.14095221 0.00000015
|
||||
-863.24919482 -1277.34161057 862.97975774
|
||||
0.34066372 83.46934579 0.00000015
|
||||
861.54714972 -1276.15175730 861.52691337
|
||||
-0.09802844 -193.17585342 -0.00000005
|
||||
861.54715133 -1276.15175913 -861.52691490
|
||||
0.00000031 0.00000031 5410.11037330
|
||||
-862.95611222 -862.92132598 -1277.71824426
|
||||
-0.00000027 -0.00000023 83.84059068
|
||||
862.95611161 862.92132537 -1277.71824365
|
||||
-0.00000015 0.00000006 -193.17559671
|
||||
-861.62536929 861.66025668 -1276.08157121
|
||||
0.00000031 -0.00000000 -193.17573662
|
||||
861.62536952 -861.66025637 -1276.08157175
|
||||
-1277.48270695 -863.24917964 -862.95613831
|
||||
5409.83567791 3.04882503 2.82007909
|
||||
-1277.34160500 -863.13224794 862.92133361
|
||||
-193.14089232 0.11950085 -0.11994115
|
||||
-1277.52241409 863.24943335 -862.88111478
|
||||
-193.17596134 -0.16730494 0.02099535
|
||||
-1274.64156987 859.96383191 860.25587098
|
||||
83.46947136 0.16714109 -0.06108436
|
||||
-863.13224993 -1277.34160622 -862.92133430
|
||||
3.04882664 5409.83567981 -2.82007772
|
||||
-863.24917934 -1277.48270718 862.95613862
|
||||
0.11950077 -193.14089270 0.11994160
|
||||
863.24943366 -1277.52241409 862.88111478
|
||||
0.16714140 83.46947120 0.06108451
|
||||
859.96383191 -1274.64156979 -860.25587113
|
||||
-0.16730502 -193.17596118 -0.02099497
|
||||
-862.89766079 -862.97973912 -1277.71823542
|
||||
2.82004053 -2.82003977 5410.11000766
|
||||
862.97973867 862.89766003 -1277.71823633
|
||||
0.11994725 -0.11994740 83.84083859
|
||||
-863.11328229 863.11328297 -1277.34763999
|
||||
-0.02106026 0.06099877 -193.17561197
|
||||
860.17327676 -860.17327637 -1274.81551212
|
||||
-0.06099938 0.02106080 -193.17561235
|
||||
-193.14095266 0.11071661 0.00000023
|
||||
-1277.34161164 -863.24919490 862.97975758
|
||||
5409.83419895 3.05073908 0.00000031
|
||||
-1277.34161248 -863.24919704 -862.97976018
|
||||
83.46934641 0.34066377 0.00000031
|
||||
-1276.15175798 861.54714988 861.52691307
|
||||
-193.17585317 -0.09802854 0.00000018
|
||||
-1276.15175745 861.54714957 -861.52691314
|
||||
0.12865765 -193.14095472 0.00000000
|
||||
-863.13225527 -1277.48271931 862.89768673
|
||||
3.05075511 5409.83472469 -0.00000046
|
||||
-863.13225489 -1277.48271839 -862.89768612
|
||||
-0.23660723 -193.17613471 0.00000061
|
||||
861.66402345 -1276.01089068 -861.60900391
|
||||
-0.00634202 83.46958197 0.00000012
|
||||
861.66402314 -1276.01088961 861.60900353
|
||||
-0.00000015 -0.00000015 83.84059098
|
||||
862.92132797 862.95611360 -1277.71824533
|
||||
-0.00000145 -0.00000137 5410.11037498
|
||||
-862.92132598 -862.95611222 -1277.71824426
|
||||
-0.00000031 -0.00000009 -193.17559671
|
||||
861.66025660 -861.62536929 -1276.08157182
|
||||
0.00000015 0.00000014 -193.17573668
|
||||
-861.66025615 861.62536929 -1276.08157190
|
||||
-1277.48270619 -863.24917934 862.95613793
|
||||
-193.14089264 0.11950070 0.11994149
|
||||
-1277.34160589 -863.13224892 -862.92133438
|
||||
5409.83568112 3.04882502 -2.82007598
|
||||
-1277.52241409 863.24943313 862.88111386
|
||||
83.46947128 0.16714155 0.06108420
|
||||
-1274.64157216 859.96383297 -860.25587243
|
||||
-193.17596164 -0.16730510 -0.02099535
|
||||
-863.13224825 -1277.34160470 862.92133392
|
||||
0.11950069 -193.14089248 -0.11994088
|
||||
-863.24918118 -1277.48270824 -862.95613907
|
||||
3.04882479 5409.83568081 2.82007857
|
||||
863.24943366 -1277.52241409 -862.88111386
|
||||
-0.16730494 -193.17596164 0.02099504
|
||||
859.96383191 -1274.64157155 860.25587228
|
||||
0.16714109 83.46947120 -0.06108481
|
||||
862.89766018 862.97973836 -1277.71823542
|
||||
-0.11994717 0.11994762 83.84083846
|
||||
-862.97973940 -862.89766100 -1277.71823603
|
||||
-2.82004089 2.82004165 5410.11001111
|
||||
863.11328534 -863.11328473 -1277.34764213
|
||||
0.06099900 -0.02106019 -193.17561197
|
||||
-860.17327706 860.17327752 -1274.81551319
|
||||
0.02106049 -0.06099877 -193.17561212
|
||||
-193.17613831 0.34066975 0.00000000
|
||||
-1277.52243217 863.24943252 -863.11331043
|
||||
83.46934255 -0.23660983 0.00000046
|
||||
-1277.52243126 863.24943229 863.11330975
|
||||
5404.58897296 -9.71806756 0.00000046
|
||||
-1273.31334689 -858.38273326 -858.80488185
|
||||
-193.21062125 -0.11939087 -0.00000018
|
||||
-1273.31334666 -858.38273265 858.80488124
|
||||
-0.23661028 83.46934221 -0.00000038
|
||||
863.24943259 -1277.52243133 863.11331043
|
||||
0.34066924 -193.17613846 -0.00000015
|
||||
863.24943168 -1277.52243072 -863.11330883
|
||||
-9.71806704 5404.58897205 -0.00000107
|
||||
-858.38273265 -1273.31334697 -858.80488063
|
||||
-0.11939101 -193.21062043 0.00000006
|
||||
-858.38273296 -1273.31334681 858.80488139
|
||||
0.00000015 0.00000000 -193.17558413
|
||||
-862.88110730 862.88110699 -1277.34764060
|
||||
-0.00000001 -0.00000001 -193.17558374
|
||||
862.88110539 -862.88110516 -1277.34764030
|
||||
0.00000122 -0.00000264 5404.30470473
|
||||
-858.96244965 -858.96244934 -1273.17866523
|
||||
-0.00000046 0.00000006 83.09907322
|
||||
858.96245026 858.96245041 -1273.17866553
|
||||
-1276.01088335 861.54715186 -861.62537494
|
||||
-193.17596632 0.16713991 -0.02106865
|
||||
-1276.15172701 861.66401376 861.66024356
|
||||
83.46945641 -0.16730418 0.06100182
|
||||
-1273.31333507 -858.38273911 -858.96245926
|
||||
5404.58493280 -3.04507046 -2.81778113
|
||||
-1276.19189558 -861.66398654 861.58531085
|
||||
-193.21058250 -0.11920503 0.12012704
|
||||
861.66401292 -1276.15172617 861.66024257
|
||||
-0.16730418 83.46945627 0.06100192
|
||||
861.54715110 -1276.01088167 -861.62537387
|
||||
0.16713972 -193.17596591 -0.02106965
|
||||
-858.38273891 -1273.31333542 -858.96245910
|
||||
-3.04506741 5404.58493142 -2.81778205
|
||||
-861.66398683 -1276.19189578 861.58531200
|
||||
-0.11920541 -193.21058250 0.12012674
|
||||
-861.60900269 861.52691291 -1276.08157152
|
||||
0.02099737 0.06108917 -193.17561785
|
||||
861.52691246 -861.60900299 -1276.08157243
|
||||
0.06108909 0.02099718 -193.17561746
|
||||
-858.80486827 -858.80486867 -1273.17865256
|
||||
-2.81780745 -2.81780722 5404.30474364
|
||||
861.74281375 861.74281365 -1275.71086885
|
||||
-0.12013460 -0.12013475 83.09915550
|
||||
83.46959035 -0.09801326 0.00000000
|
||||
-1274.64156874 859.96385402 860.17328225
|
||||
-193.17585994 -0.00634034 0.00000031
|
||||
-1274.64156789 859.96385357 -860.17328072
|
||||
-193.21062369 -0.11938345 0.00000015
|
||||
-1276.19187300 -861.66400056 861.74280857
|
||||
5404.58377637 3.62403189 -0.00000071
|
||||
-1276.19187285 -861.66400087 -861.74280780
|
||||
-0.00634065 -193.17585981 -0.00000015
|
||||
859.96385345 -1274.64156845 -860.17328227
|
||||
-0.09801307 83.46959066 0.00000092
|
||||
859.96385342 -1274.64156728 860.17328103
|
||||
-0.11938399 -193.21062370 0.00000031
|
||||
-861.66399988 -1276.19187163 861.74280780
|
||||
3.62403013 5404.58377402 0.00000142
|
||||
-861.66400079 -1276.19187255 -861.74280803
|
||||
-0.00000031 -0.00000038 -193.17573821
|
||||
860.25587448 -860.25587441 -1274.81548871
|
||||
0.00000000 -0.00000026 -193.17573875
|
||||
-860.25587388 860.25587456 -1274.81548916
|
||||
0.00000015 -0.00000009 83.09905855
|
||||
861.58531164 861.58531156 -1275.71087571
|
||||
0.00000046 0.00000089 5404.30514766
|
||||
-861.58531232 -861.58531217 -1275.71087655
|
||||
-1276.01088198 861.54713523 861.62537356
|
||||
83.46945674 -0.16730402 -0.06100344
|
||||
-1276.15172688 861.66402939 -861.66024402
|
||||
-193.17596584 0.16713972 0.02106034
|
||||
-1273.31333552 -858.38273940 858.96245956
|
||||
-193.21058227 -0.11920503 -0.12012498
|
||||
-1276.19189573 -861.66398605 -861.58531085
|
||||
5404.58493188 -3.04506924 2.81779059
|
||||
861.66402925 -1276.15172686 -861.66024394
|
||||
0.16713982 -193.17596610 0.02106041
|
||||
861.54713537 -1276.01088130 861.62537448
|
||||
-0.16730426 83.46945625 -0.06100350
|
||||
-858.38273967 -1273.31333570 858.96245987
|
||||
-0.11920511 -193.21058281 -0.12012514
|
||||
-861.66398958 -1276.19189780 -861.58531314
|
||||
-3.04506687 5404.58493417 2.81779303
|
||||
861.60900299 -861.52691253 -1276.08157236
|
||||
-0.06108885 -0.02099714 -193.17561830
|
||||
-861.52691343 861.60900260 -1276.08157198
|
||||
-0.02099726 -0.06108848 -193.17561792
|
||||
858.80486782 858.80486829 -1273.17865256
|
||||
0.12013467 0.12013460 83.09915604
|
||||
-861.74281406 -861.74281426 -1275.71086942
|
||||
2.81780737 2.81780737 5404.30474524
|
||||
@ -0,0 +1,71 @@
|
||||
LAMMPS (15 Jun 2020)
|
||||
Reading data file ...
|
||||
orthogonal box = (0.0 0.0 0.0) to (5.431 5.431 5.431)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
8 atoms
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
special bonds CPU = 4.2e-05 secs
|
||||
read_data CPU = 0.001 secs
|
||||
Reading potential file ../../../../../potentials/SiCGe.tersoff with DATE: 2009-03-18
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4
|
||||
ghost atom cutoff = 4
|
||||
binsize = 2, bins = 3 3 3
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair tersoff, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Calculating Dynamical Matrix ...
|
||||
Total # of atoms = 8
|
||||
Atoms in group = 8
|
||||
Total dynamical matrix elements = 576
|
||||
10% 20% 30% 50% 60% 70% 80%[3.34264870e-05 6.09176101e-05 1.72068597e-04 1.60807822e+01
|
||||
1.60807027e+01 1.60806903e+01 1.48964054e+01 1.49012648e+01
|
||||
1.49129598e+01 1.49081641e+01 1.48999471e+01 1.49095175e+01
|
||||
1.21983946e+01 1.21957091e+01 1.22010862e+01 1.22037817e+01
|
||||
1.22037910e+01 1.22037868e+01 6.89648276e+00 6.89524412e+00
|
||||
6.89619622e+00 6.89553366e+00 6.89615471e+00 6.89557491e+00]
|
||||
|
||||
Finished Calculating Dynamical Matrix
|
||||
Loop time of 0.000677109 on 1 procs for 48 steps with 8 atoms
|
||||
|
||||
Performance: 6124.865 ns/day, 0.004 hours/ns, 70889.645 timesteps/s
|
||||
91.3% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.00064349 | 0.00064349 | 0.00064349 | 0.0 | 95.04
|
||||
Bond | 9.5367e-07 | 9.5367e-07 | 9.5367e-07 | 0.0 | 0.14
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 1.1683e-05 | 1.1683e-05 | 1.1683e-05 | 0.0 | 1.73
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 9.5367e-07 | 9.5367e-07 | 9.5367e-07 | 0.0 | 0.14
|
||||
Other | | 2.003e-05 | | | 2.96
|
||||
|
||||
Nlocal: 8 ave 8 max 8 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 86 ave 86 max 86 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: 128 ave 128 max 128 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 128
|
||||
Ave neighs/atom = 16
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
@ -0,0 +1 @@
|
||||
../Silicon/silicon_input_file.lmp
|
||||
@ -1,15 +1,15 @@
|
||||
#This script implements the BKS pair potential for various silicon dioxide compounds. Inner part is fixed with a harmonic potential. Long range Coulomb interactions are evaluated with the pppm method.
|
||||
|
||||
#Pair Potentials
|
||||
pair_style hybrid/overlay buck/coul/long ${cut_off} table linear 39901
|
||||
pair_coeff 1 1 buck/coul/long 0.0 1.0 0.0 #No interactions between Si atoms
|
||||
pair_coeff 1 2 buck/coul/long 18003.757200 0.205205 133.538100
|
||||
pair_coeff 2 2 buck/coul/long 1388.773000 0.362319 175.000000 #BKS interaction in PRL 64 1955 (1990)
|
||||
pair_modify shift yes
|
||||
pair_coeff 1 2 table potential_SiO2.TPF Si-O ${cut_off}
|
||||
pair_coeff 2 2 table potential_SiO2.TPF O-O ${cut_off} #See the potential file for more information
|
||||
kspace_style pppm 1.0e-4
|
||||
pair_style hybrid/overlay buck/coul/long ${cut_off} table linear 39901
|
||||
pair_coeff 1 1 buck/coul/long 0.0 1.0 0.0 #No interactions between Si atoms
|
||||
pair_coeff 1 2 buck/coul/long 18003.757200 0.205205 133.538100
|
||||
pair_coeff 2 2 buck/coul/long 1388.773000 0.362319 175.000000 #BKS interaction in PRL 64 1955 (1990)
|
||||
pair_modify shift yes
|
||||
pair_coeff 1 2 table potential_SiO2.TPF Si-O ${cut_off}
|
||||
pair_coeff 2 2 table potential_SiO2.TPF O-O ${cut_off} #See the potential file for more information
|
||||
kspace_style pppm 1.0e-4
|
||||
|
||||
#Neighbor style
|
||||
neighbor 2.0 bin
|
||||
neigh_modify check yes every 1 delay 0 page 100000 one 2000
|
||||
neighbor 2.0 bin
|
||||
neigh_modify check yes every 1 delay 0 page 100000 one 2000
|
||||
|
||||
@ -3,60 +3,60 @@
|
||||
|
||||
## This part defines units, alpha-quartz crystal, and atomic information
|
||||
#General
|
||||
units metal
|
||||
dimension 3
|
||||
boundary p p p
|
||||
atom_style charge
|
||||
units metal
|
||||
dimension 3
|
||||
boundary p p p
|
||||
atom_style charge
|
||||
|
||||
#Lattice
|
||||
lattice custom 1.0 &
|
||||
a1 4.916000 0.000000 0.000000 &
|
||||
a2 -2.45800 4.257381 0.000000 &
|
||||
a3 0.000000 0.000000 5.405400 &
|
||||
&
|
||||
basis 0.469700 0.000000 0.000000 &
|
||||
basis 0.000000 0.469700 0.666667 &
|
||||
basis 0.530300 0.530300 0.333333 &
|
||||
&
|
||||
basis 0.413500 0.266900 0.119100 &
|
||||
basis 0.266900 0.413500 0.547567 &
|
||||
basis 0.733100 0.146600 0.785767 &
|
||||
basis 0.586500 0.853400 0.214233 &
|
||||
basis 0.853400 0.586500 0.452433 &
|
||||
basis 0.146600 0.733100 0.880900 #American Mineralogist 65 920 1980 (Space Group 154)
|
||||
lattice custom 1.0 &
|
||||
a1 4.916000 0.000000 0.000000 &
|
||||
a2 -2.45800 4.257381 0.000000 &
|
||||
a3 0.000000 0.000000 5.405400 &
|
||||
&
|
||||
basis 0.469700 0.000000 0.000000 &
|
||||
basis 0.000000 0.469700 0.666667 &
|
||||
basis 0.530300 0.530300 0.333333 &
|
||||
&
|
||||
basis 0.413500 0.266900 0.119100 &
|
||||
basis 0.266900 0.413500 0.547567 &
|
||||
basis 0.733100 0.146600 0.785767 &
|
||||
basis 0.586500 0.853400 0.214233 &
|
||||
basis 0.853400 0.586500 0.452433 &
|
||||
basis 0.146600 0.733100 0.880900 #American Mineralogist 65 920 1980 (Space Group 154)
|
||||
|
||||
#Computational Cell
|
||||
region orthorhombic_unit_cell block 0 4.916000 0 8.514762 0 5.405400 units box
|
||||
create_box 2 orthorhombic_unit_cell
|
||||
create_atoms 1 box &
|
||||
basis 1 1 &
|
||||
basis 2 1 &
|
||||
basis 3 1 &
|
||||
basis 4 2 &
|
||||
basis 5 2 &
|
||||
basis 6 2 &
|
||||
basis 7 2 &
|
||||
basis 8 2 &
|
||||
basis 9 2
|
||||
replicate ${x_rep} ${y_rep} ${z_rep}
|
||||
region orthorhombic_unit_cell block 0 4.916000 0 8.514762 0 5.405400 units box
|
||||
create_box 2 orthorhombic_unit_cell
|
||||
create_atoms 1 box &
|
||||
basis 1 1 &
|
||||
basis 2 1 &
|
||||
basis 3 1 &
|
||||
basis 4 2 &
|
||||
basis 5 2 &
|
||||
basis 6 2 &
|
||||
basis 7 2 &
|
||||
basis 8 2 &
|
||||
basis 9 2
|
||||
replicate ${x_rep} ${y_rep} ${z_rep}
|
||||
|
||||
#Atomic Information
|
||||
mass 1 28.085500
|
||||
mass 2 15.999400
|
||||
set type 1 charge +2.4
|
||||
set type 2 charge -1.2
|
||||
mass 1 28.085500
|
||||
mass 2 15.999400
|
||||
set type 1 charge +2.4
|
||||
set type 2 charge -1.2
|
||||
|
||||
|
||||
## This part implements the BKS pair potential with a cut-off distance for the Buckingham term. Long range Coulomb interactions are evaluated with the pppm method.
|
||||
include alpha_quartz_potential.mod
|
||||
include alpha_quartz_potential.mod
|
||||
|
||||
|
||||
## This part equilibrates your crystal to a pressure of ${pressure}(unit pressure) and a temperature of ${temperature}(unit temperatureture) with quantum nuclear effects
|
||||
variable p_damp equal ${delta_t}*1000 #Recommended pressure damping parameter in fix nph
|
||||
fix scapegoat_qtb all nph iso ${pressure} ${pressure} ${p_damp} #NPH does the time integration
|
||||
fix quartz_qtb all qtb temp ${temperature} damp ${damp_qtb} seed 35082 f_max 120.00 N_f 100 #Change f_max (THz) if your Debye frequency is higher
|
||||
thermo_style custom step temp press etotal vol lx ly lz pxx pyy pzz pxy pyz pxz
|
||||
thermo 100
|
||||
run 2000 # 2 ps
|
||||
unfix quartz_qtb
|
||||
unfix scapegoat_qtb
|
||||
variable p_damp equal ${delta_t}*1000 #Recommended pressure damping parameter in fix nph
|
||||
fix scapegoat_qtb all nph iso ${pressure} ${pressure} ${p_damp} ptemp ${temperature} #NPH does the time integration
|
||||
fix quartz_qtb all qtb temp ${temperature} damp ${damp_qtb} seed 35082 f_max 120.00 N_f 100 #Change f_max (THz) if your Debye frequency is higher
|
||||
thermo_style custom step temp press etotal vol lx ly lz pxx pyy pzz pxy pyz pxz
|
||||
thermo 200
|
||||
run 2000 # 2 ps
|
||||
unfix quartz_qtb
|
||||
unfix scapegoat_qtb
|
||||
|
||||
55
examples/USER/qtb/alpha_quartz_qbmsst/in.alpha_quartz_qbmsst
Normal file
55
examples/USER/qtb/alpha_quartz_qbmsst/in.alpha_quartz_qbmsst
Normal file
@ -0,0 +1,55 @@
|
||||
## This script first uses fix qtb to equilibrate alpha quartz structure to an initial state with quantum nuclear correction and then simulate shock induced phase transition through the quantum thermal bath multi-scale shock technique
|
||||
variable x_rep equal 2 #plot is made with x_rep = 8 #x-direction replication number
|
||||
variable y_rep equal 1 #plot is made with y_rep = 5 #y-direction replication number
|
||||
variable z_rep equal 4 #plot is made with z_rep = 15 #z-direction replication number
|
||||
variable cut_off equal 10.0 #Cut-off distance for the Buckingham term (Angstrom in metal units)
|
||||
variable pressure equal 1.03125 #Initial state pressure (bar in metal units)
|
||||
variable temperature equal 300.0 #Initial state quantum temperature (K in metal units)
|
||||
variable delta_t equal 1.0e-3 #MD timestep length (ps in metal units)
|
||||
variable damp_qtb equal 1 #1/gamma where gamma is the friction coefficient in quantum thermal bath (ps in metal units)
|
||||
variable v_msst equal 78.0 #Shock velocity (Angstrom/ps in metal units)
|
||||
variable q_msst equal 40.0 #Box mass-like parameter in the MSST (mass^2/length^4, where mass=grams/mole and length=Angstrom in metal units)
|
||||
variable tscale_msst equal 0.05 #Temperature reduction parameter in the MSST (unitless)
|
||||
variable eta_qbmsst equal 1.0 #Coupling constant between the shock and the quantum thermal bath (unitless constant)
|
||||
|
||||
|
||||
## This part uses fix qtb to prepare alpha-quartz with quantum nuclear correction of the initial state
|
||||
include alpha_quartz_qtb.mod
|
||||
|
||||
|
||||
## This part demonstrates how to retart fix qbmsst during any stage of the shock simulation.
|
||||
## PPPM may break down when compression ratio becomes extremely large. One can always use this restart technique to resume the shock simulation.
|
||||
#Compression restart 1
|
||||
reset_timestep 0
|
||||
#Beta is the number of time steps between each update of the quantum bath temperature. Setting a larger beta can reduce thermal flactuations.
|
||||
fix shock all qbmsst z ${v_msst} q ${q_msst} tscale ${tscale_msst} damp ${damp_qtb} f_max 120 N_f 100 seed 35082 eta ${eta_qbmsst} beta 5 T_init ${temperature}
|
||||
fix_modify shock energy yes
|
||||
variable dhug equal f_shock[1]
|
||||
variable dray equal f_shock[2]
|
||||
variable lgr_vel equal f_shock[3]
|
||||
variable lgr_pos equal f_shock[4]
|
||||
variable T_qm equal f_shock[5] #Temperature with quantum nuclear correction
|
||||
thermo_style custom step v_T_qm press etotal vol lx ly lz pzz v_dhug v_dray v_lgr_vel v_lgr_pos
|
||||
thermo 200
|
||||
timestep ${delta_t}
|
||||
run 1000
|
||||
write_restart restart.1000
|
||||
|
||||
#Compression restart 2
|
||||
#Read restart file and load potential again
|
||||
clear
|
||||
read_restart restart.1000
|
||||
include alpha_quartz_potential.mod
|
||||
#Use the same fix id and add no tscale if the system is already compressed
|
||||
fix shock all qbmsst z ${v_msst} q ${q_msst} tscale 0.0 damp ${damp_qtb} f_max 120 N_f 100 seed 35082 eta ${eta_qbmsst} beta 5 T_init ${temperature}
|
||||
fix_modify shock energy yes
|
||||
variable dhug equal f_shock[1]
|
||||
variable dray equal f_shock[2]
|
||||
variable lgr_vel equal f_shock[3]
|
||||
variable lgr_pos equal f_shock[4]
|
||||
variable T_qm equal f_shock[5] #Temperature with quantum nuclear correction
|
||||
thermo_style custom step v_T_qm press etotal vol lx ly lz pzz v_dhug v_dray v_lgr_vel v_lgr_pos
|
||||
thermo 500
|
||||
timestep ${delta_t}
|
||||
restart 1000 restart
|
||||
run 10000 #10 ps
|
||||
@ -0,0 +1,430 @@
|
||||
LAMMPS (15 Jun 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
## This script first uses fix qtb to equilibrate alpha quartz structure to an initial state with quantum nuclear correction and then simulate shock induced phase transition through the quantum thermal bath multi-scale shock technique
|
||||
variable x_rep equal 2 #plot is made with x_rep = 8 #x-direction replication number
|
||||
variable y_rep equal 1 #plot is made with y_rep = 5 #y-direction replication number
|
||||
variable z_rep equal 4 #plot is made with z_rep = 15 #z-direction replication number
|
||||
variable cut_off equal 10.0 #Cut-off distance for the Buckingham term (Angstrom in metal units)
|
||||
variable pressure equal 1.03125 #Initial state pressure (bar in metal units)
|
||||
variable temperature equal 300.0 #Initial state quantum temperature (K in metal units)
|
||||
variable delta_t equal 1.0e-3 #MD timestep length (ps in metal units)
|
||||
variable damp_qtb equal 1 #1/gamma where gamma is the friction coefficient in quantum thermal bath (ps in metal units)
|
||||
variable v_msst equal 78.0 #Shock velocity (Angstrom/ps in metal units)
|
||||
variable q_msst equal 40.0 #Box mass-like parameter in the MSST (mass^2/length^4, where mass=grams/mole and length=Angstrom in metal units)
|
||||
variable tscale_msst equal 0.05 #Temperature reduction parameter in the MSST (unitless)
|
||||
variable eta_qbmsst equal 1.0 #Coupling constant between the shock and the quantum thermal bath (unitless constant)
|
||||
|
||||
|
||||
## This part uses fix qtb to prepare alpha-quartz with quantum nuclear correction of the initial state
|
||||
include alpha_quartz_qtb.mod
|
||||
## This script first constructs an alpha quartz structure of a given size. It then uses fix qtb to equilibrate the computational cell to the specified temperature and pressure.
|
||||
|
||||
|
||||
## This part defines units, alpha-quartz crystal, and atomic information
|
||||
#General
|
||||
units metal
|
||||
dimension 3
|
||||
boundary p p p
|
||||
atom_style charge
|
||||
|
||||
#Lattice
|
||||
lattice custom 1.0 a1 4.916000 0.000000 0.000000 a2 -2.45800 4.257381 0.000000 a3 0.000000 0.000000 5.405400 basis 0.469700 0.000000 0.000000 basis 0.000000 0.469700 0.666667 basis 0.530300 0.530300 0.333333 basis 0.413500 0.266900 0.119100 basis 0.266900 0.413500 0.547567 basis 0.733100 0.146600 0.785767 basis 0.586500 0.853400 0.214233 basis 0.853400 0.586500 0.452433 basis 0.146600 0.733100 0.880900 #American Mineralogist 65 920 1980 (Space Group 154)
|
||||
Lattice spacing in x,y,z = 7.374 4.25738 5.4054
|
||||
|
||||
#Computational Cell
|
||||
region orthorhombic_unit_cell block 0 4.916000 0 8.514762 0 5.405400 units box
|
||||
create_box 2 orthorhombic_unit_cell
|
||||
Created orthogonal box = (0.0 0.0 0.0) to (4.916 8.514762 5.4054)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box basis 1 1 basis 2 1 basis 3 1 basis 4 2 basis 5 2 basis 6 2 basis 7 2 basis 8 2 basis 9 2
|
||||
Created 18 atoms
|
||||
create_atoms CPU = 0.000 seconds
|
||||
replicate ${x_rep} ${y_rep} ${z_rep}
|
||||
replicate 2 ${y_rep} ${z_rep}
|
||||
replicate 2 1 ${z_rep}
|
||||
replicate 2 1 4
|
||||
orthogonal box = (0.0 0.0 0.0) to (9.832 8.514762 21.6216)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
144 atoms
|
||||
replicate CPU = 0.000271082 secs
|
||||
|
||||
#Atomic Information
|
||||
mass 1 28.085500
|
||||
mass 2 15.999400
|
||||
set type 1 charge +2.4
|
||||
48 settings made for charge
|
||||
set type 2 charge -1.2
|
||||
96 settings made for charge
|
||||
|
||||
|
||||
## This part implements the BKS pair potential with a cut-off distance for the Buckingham term. Long range Coulomb interactions are evaluated with the pppm method.
|
||||
include alpha_quartz_potential.mod
|
||||
#This script implements the BKS pair potential for various silicon dioxide compounds. Inner part is fixed with a harmonic potential. Long range Coulomb interactions are evaluated with the pppm method.
|
||||
|
||||
#Pair Potentials
|
||||
pair_style hybrid/overlay buck/coul/long ${cut_off} table linear 39901
|
||||
pair_style hybrid/overlay buck/coul/long 10 table linear 39901
|
||||
pair_coeff 1 1 buck/coul/long 0.0 1.0 0.0 #No interactions between Si atoms
|
||||
pair_coeff 1 2 buck/coul/long 18003.757200 0.205205 133.538100
|
||||
pair_coeff 2 2 buck/coul/long 1388.773000 0.362319 175.000000 #BKS interaction in PRL 64 1955 (1990)
|
||||
pair_modify shift yes
|
||||
pair_coeff 1 2 table potential_SiO2.TPF Si-O ${cut_off}
|
||||
pair_coeff 1 2 table potential_SiO2.TPF Si-O 10
|
||||
pair_coeff 2 2 table potential_SiO2.TPF O-O ${cut_off} #See the potential file for more information
|
||||
pair_coeff 2 2 table potential_SiO2.TPF O-O 10
|
||||
WARNING: 1 of 39901 force values in table are inconsistent with -dE/dr.
|
||||
Should only be flagged at inflection points (src/pair_table.cpp:471)
|
||||
kspace_style pppm 1.0e-4
|
||||
|
||||
#Neighbor style
|
||||
neighbor 2.0 bin
|
||||
neigh_modify check yes every 1 delay 0 page 100000 one 2000
|
||||
|
||||
|
||||
## This part equilibrates your crystal to a pressure of ${pressure}(unit pressure) and a temperature of ${temperature}(unit temperatureture) with quantum nuclear effects
|
||||
variable p_damp equal ${delta_t}*1000 #Recommended pressure damping parameter in fix nph
|
||||
variable p_damp equal 0.001*1000
|
||||
fix scapegoat_qtb all nph iso ${pressure} ${pressure} ${p_damp} ptemp ${temperature} #NPH does the time integration
|
||||
fix scapegoat_qtb all nph iso 1.03125 ${pressure} ${p_damp} ptemp ${temperature}
|
||||
fix scapegoat_qtb all nph iso 1.03125 1.03125 ${p_damp} ptemp ${temperature}
|
||||
fix scapegoat_qtb all nph iso 1.03125 1.03125 1 ptemp ${temperature}
|
||||
fix scapegoat_qtb all nph iso 1.03125 1.03125 1 ptemp 300
|
||||
fix quartz_qtb all qtb temp ${temperature} damp ${damp_qtb} seed 35082 f_max 120.00 N_f 100 #Change f_max (THz) if your Debye frequency is higher
|
||||
fix quartz_qtb all qtb temp 300 damp ${damp_qtb} seed 35082 f_max 120.00 N_f 100
|
||||
fix quartz_qtb all qtb temp 300 damp 1 seed 35082 f_max 120.00 N_f 100
|
||||
thermo_style custom step temp press etotal vol lx ly lz pxx pyy pzz pxy pyz pxz
|
||||
thermo 200
|
||||
run 2000 # 2 ps
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:332)
|
||||
G vector (1/distance) = 0.301598
|
||||
grid = 9 8 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.00117056
|
||||
estimated relative force accuracy = 8.12908e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 5280 1080
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 2 2 4
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair buck/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
(2) pair table, perpetual, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 80.09 | 80.09 | 80.09 Mbytes
|
||||
Step Temp Press TotEng Volume Lx Ly Lz Pxx Pyy Pzz Pxy Pyz Pxz
|
||||
0 0 -34026.791 -2793.6042 1810.0985 9.832 8.514762 21.6216 -37470.578 -37470.432 -27139.363 -6.4345368e-12 0.94245783 4.2212262e-10
|
||||
200 170.7381 43248.332 -2790.8398 1879.164 9.9554912 8.6217086 21.89317 39337.624 42979.126 47428.246 324.91326 454.85872 -2034.6053
|
||||
400 258.09921 -28257.8 -2788.3487 1856.1432 9.9146707 8.5863569 21.803402 -19478.873 -29571.375 -35723.152 4633.9026 8487.8103 -626.12005
|
||||
600 277.77032 -22751.351 -2786.2715 1866.9783 9.9339253 8.6030319 21.845744 -21727.335 -29200.027 -17326.692 -4327.8571 -8218.4965 252.30681
|
||||
800 349.8665 30508.003 -2784.2204 1873.4953 9.9454706 8.6130304 21.871134 29929.055 33562.672 28032.281 -3188.5605 12329.482 7558.5678
|
||||
1000 373.67651 -18839.569 -2783.2178 1855.5937 9.9136922 8.5855095 21.80125 -18063.486 -22288.321 -16166.902 -416.09547 -10368.975 9030.4208
|
||||
1200 423.3474 6846.9905 -2781.9271 1896.2131 9.9855083 8.6477041 21.959181 2147.3938 11765.857 6627.7202 -7627.6782 -1297.6517 -4758.4746
|
||||
1400 418.54527 -6416.7506 -2781.4358 1834.2719 9.8755745 8.5524986 21.717425 5693.0543 -19487.901 -5455.405 827.66513 -523.1508 -3890.9919
|
||||
1600 429.42796 3939.8836 -2780.5861 1895.8859 9.984934 8.6472068 21.957918 3755.6959 -1326.4343 9390.3893 1948.1153 4489.8629 1466.0914
|
||||
1800 447.7623 -8344.6306 -2780.1071 1858.4925 9.9188518 8.5899779 21.812596 -17549.498 3336.8135 -10821.208 1643.4226 -644.56065 -8935.9666
|
||||
2000 438.1306 -6691.4691 -2780.7407 1871.3547 9.9416812 8.6097487 21.862801 -6959.2196 -8486.8466 -4628.341 -1019.9006 443.03694 -2751.917
|
||||
Loop time of 2.46815 on 1 procs for 2000 steps with 144 atoms
|
||||
|
||||
Performance: 70.012 ns/day, 0.343 hours/ns, 810.323 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 | 2.0003 | 2.0003 | 2.0003 | 0.0 | 81.04
|
||||
Kspace | 0.20006 | 0.20006 | 0.20006 | 0.0 | 8.11
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.023753 | 0.023753 | 0.023753 | 0.0 | 0.96
|
||||
Output | 0.0001986 | 0.0001986 | 0.0001986 | 0.0 | 0.01
|
||||
Modify | 0.23896 | 0.23896 | 0.23896 | 0.0 | 9.68
|
||||
Other | | 0.004907 | | | 0.20
|
||||
|
||||
Nlocal: 144 ave 144 max 144 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 3943 ave 3943 max 3943 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 41952 ave 41952 max 41952 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 41952
|
||||
Ave neighs/atom = 291.333
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
unfix quartz_qtb
|
||||
unfix scapegoat_qtb
|
||||
|
||||
|
||||
## This part demonstrates how to retart fix qbmsst during any stage of the shock simulation.
|
||||
## PPPM may break down when compression ratio becomes extremely large. One can always use this restart technique to resume the shock simulation.
|
||||
#Compression restart 1
|
||||
reset_timestep 0
|
||||
#Beta is the number of time steps between each update of the quantum bath temperature. Setting a larger beta can reduce thermal flactuations.
|
||||
fix shock all qbmsst z ${v_msst} q ${q_msst} tscale ${tscale_msst} damp ${damp_qtb} f_max 120 N_f 100 seed 35082 eta ${eta_qbmsst} beta 5 T_init ${temperature}
|
||||
fix shock all qbmsst z 78 q ${q_msst} tscale ${tscale_msst} damp ${damp_qtb} f_max 120 N_f 100 seed 35082 eta ${eta_qbmsst} beta 5 T_init ${temperature}
|
||||
fix shock all qbmsst z 78 q 40 tscale ${tscale_msst} damp ${damp_qtb} f_max 120 N_f 100 seed 35082 eta ${eta_qbmsst} beta 5 T_init ${temperature}
|
||||
fix shock all qbmsst z 78 q 40 tscale 0.05 damp ${damp_qtb} f_max 120 N_f 100 seed 35082 eta ${eta_qbmsst} beta 5 T_init ${temperature}
|
||||
fix shock all qbmsst z 78 q 40 tscale 0.05 damp 1 f_max 120 N_f 100 seed 35082 eta ${eta_qbmsst} beta 5 T_init ${temperature}
|
||||
fix shock all qbmsst z 78 q 40 tscale 0.05 damp 1 f_max 120 N_f 100 seed 35082 eta 1 beta 5 T_init ${temperature}
|
||||
fix shock all qbmsst z 78 q 40 tscale 0.05 damp 1 f_max 120 N_f 100 seed 35082 eta 1 beta 5 T_init 300
|
||||
QBMSST parameters:
|
||||
Shock in z direction
|
||||
Cell mass-like parameter qmass (units of mass^2/length^4) = 4.00000e+01
|
||||
Shock velocity = 7.80000e+01
|
||||
Artificial viscosity (units of mass/length/time) = 0.00000e+00
|
||||
Initial pressure calculated on first step
|
||||
Initial volume calculated on first step
|
||||
Initial energy calculated on first step
|
||||
fix_modify shock energy yes
|
||||
variable dhug equal f_shock[1]
|
||||
variable dray equal f_shock[2]
|
||||
variable lgr_vel equal f_shock[3]
|
||||
variable lgr_pos equal f_shock[4]
|
||||
variable T_qm equal f_shock[5] #Temperature with quantum nuclear correction
|
||||
thermo_style custom step v_T_qm press etotal vol lx ly lz pzz v_dhug v_dray v_lgr_vel v_lgr_pos
|
||||
thermo 200
|
||||
timestep ${delta_t}
|
||||
timestep 0.001
|
||||
run 1000
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:332)
|
||||
G vector (1/distance) = 0.303132
|
||||
grid = 9 8 16
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.00104699
|
||||
estimated relative force accuracy = 7.27093e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 5520 1152
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 2 2 4
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair buck/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
(2) pair table, perpetual, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
Fix QBMSST v0 = 1.87135e+03
|
||||
Fix QBMSST p0 = -4.62948e+03
|
||||
Fix QBMSST e0 = to be -2.78074e+03
|
||||
Fix QBMSST initial strain rate of -4.01096e-01 established by reducing temperature by factor of 5.00000e-02
|
||||
Per MPI rank memory allocation (min/avg/max) = 80.1 | 80.1 | 80.1 Mbytes
|
||||
Step v_T_qm Press TotEng Volume Lx Ly Lz Pzz v_dhug v_dray v_lgr_vel v_lgr_pos
|
||||
0 300 -6922.9433 -2780.7394 1871.3547 9.9416812 8.6097487 21.862801 -4819.9907 10.953265 -190.51273 0 0
|
||||
200 294.95797 54876.416 -2779.2988 1723.7621 9.9416812 8.6097487 20.138495 108897.19 -29.773973 -9271.7281 6.1518102 -15.057867
|
||||
400 288.3711 139521.03 -2778.7321 1628.5574 9.9416812 8.6097487 19.026231 222107.71 8.0682073 24727.575 10.120041 -28.714693
|
||||
600 280.56521 98070.281 -2779.8934 1687.2434 9.9416812 8.6097487 19.711852 164558.51 2.6076928 16005.656 7.6739491 -42.705007
|
||||
800 274.94701 106060.26 -2779.2916 1651.0723 9.9416812 8.6097487 19.289269 176842.6 -39.645354 -1804.9466 9.1815975 -56.628078
|
||||
1000 268.47106 189695.34 -2779.4951 1492.6355 9.9416812 8.6097487 17.438272 277351.5 -84.834482 -33116.996 15.785409 -69.870519
|
||||
Loop time of 2.05219 on 1 procs for 1000 steps with 144 atoms
|
||||
|
||||
Performance: 42.101 ns/day, 0.570 hours/ns, 487.284 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 | 1.6815 | 1.6815 | 1.6815 | 0.0 | 81.94
|
||||
Kspace | 0.10373 | 0.10373 | 0.10373 | 0.0 | 5.05
|
||||
Neigh | 0.0061183 | 0.0061183 | 0.0061183 | 0.0 | 0.30
|
||||
Comm | 0.012444 | 0.012444 | 0.012444 | 0.0 | 0.61
|
||||
Output | 0.00014687 | 0.00014687 | 0.00014687 | 0.0 | 0.01
|
||||
Modify | 0.24529 | 0.24529 | 0.24529 | 0.0 | 11.95
|
||||
Other | | 0.002948 | | | 0.14
|
||||
|
||||
Nlocal: 144 ave 144 max 144 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 4243 ave 4243 max 4243 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 48210 ave 48210 max 48210 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 48210
|
||||
Ave neighs/atom = 334.792
|
||||
Neighbor list builds = 8
|
||||
Dangerous builds = 0
|
||||
write_restart restart.1000
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:332)
|
||||
G vector (1/distance) = 0.306435
|
||||
grid = 9 8 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.000955688
|
||||
estimated relative force accuracy = 6.63689e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 5280 1080
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 2 2 3
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair buck/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
(2) pair table, perpetual, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
|
||||
#Compression restart 2
|
||||
#Read restart file and load potential again
|
||||
clear
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.1000
|
||||
restoring atom style charge from restart
|
||||
orthogonal box = (-0.05484062286382799 -0.04749337384227555 2.0916641327653274) to (9.886840622863804 8.562255373842252 19.52993586723476)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
restoring pair style hybrid/overlay from restart
|
||||
144 atoms
|
||||
read_restart CPU = 0.0002563 secs
|
||||
include alpha_quartz_potential.mod
|
||||
#This script implements the BKS pair potential for various silicon dioxide compounds. Inner part is fixed with a harmonic potential. Long range Coulomb interactions are evaluated with the pppm method.
|
||||
|
||||
#Pair Potentials
|
||||
pair_style hybrid/overlay buck/coul/long ${cut_off} table linear 39901
|
||||
pair_style hybrid/overlay buck/coul/long 10 table linear 39901
|
||||
pair_coeff 1 1 buck/coul/long 0.0 1.0 0.0 #No interactions between Si atoms
|
||||
pair_coeff 1 2 buck/coul/long 18003.757200 0.205205 133.538100
|
||||
pair_coeff 2 2 buck/coul/long 1388.773000 0.362319 175.000000 #BKS interaction in PRL 64 1955 (1990)
|
||||
pair_modify shift yes
|
||||
pair_coeff 1 2 table potential_SiO2.TPF Si-O ${cut_off}
|
||||
pair_coeff 1 2 table potential_SiO2.TPF Si-O 10
|
||||
pair_coeff 2 2 table potential_SiO2.TPF O-O ${cut_off} #See the potential file for more information
|
||||
pair_coeff 2 2 table potential_SiO2.TPF O-O 10
|
||||
WARNING: 1 of 39901 force values in table are inconsistent with -dE/dr.
|
||||
Should only be flagged at inflection points (src/pair_table.cpp:471)
|
||||
kspace_style pppm 1.0e-4
|
||||
|
||||
#Neighbor style
|
||||
neighbor 2.0 bin
|
||||
neigh_modify check yes every 1 delay 0 page 100000 one 2000
|
||||
#Use the same fix id and add no tscale if the system is already compressed
|
||||
fix shock all qbmsst z ${v_msst} q ${q_msst} tscale 0.0 damp ${damp_qtb} f_max 120 N_f 100 seed 35082 eta ${eta_qbmsst} beta 5 T_init ${temperature}
|
||||
fix shock all qbmsst z 78 q ${q_msst} tscale 0.0 damp ${damp_qtb} f_max 120 N_f 100 seed 35082 eta ${eta_qbmsst} beta 5 T_init ${temperature}
|
||||
fix shock all qbmsst z 78 q 40 tscale 0.0 damp ${damp_qtb} f_max 120 N_f 100 seed 35082 eta ${eta_qbmsst} beta 5 T_init ${temperature}
|
||||
fix shock all qbmsst z 78 q 40 tscale 0.0 damp 1 f_max 120 N_f 100 seed 35082 eta ${eta_qbmsst} beta 5 T_init ${temperature}
|
||||
fix shock all qbmsst z 78 q 40 tscale 0.0 damp 1 f_max 120 N_f 100 seed 35082 eta 1 beta 5 T_init ${temperature}
|
||||
fix shock all qbmsst z 78 q 40 tscale 0.0 damp 1 f_max 120 N_f 100 seed 35082 eta 1 beta 5 T_init 300
|
||||
QBMSST parameters:
|
||||
Shock in z direction
|
||||
Cell mass-like parameter qmass (units of mass^2/length^4) = 4.00000e+01
|
||||
Shock velocity = 7.80000e+01
|
||||
Artificial viscosity (units of mass/length/time) = 0.00000e+00
|
||||
Initial pressure calculated on first step
|
||||
Initial volume calculated on first step
|
||||
Initial energy calculated on first step
|
||||
Resetting global fix info from restart file:
|
||||
fix style: qbmsst, fix ID: shock
|
||||
fix_modify shock energy yes
|
||||
variable dhug equal f_shock[1]
|
||||
variable dray equal f_shock[2]
|
||||
variable lgr_vel equal f_shock[3]
|
||||
variable lgr_pos equal f_shock[4]
|
||||
variable T_qm equal f_shock[5] #Temperature with quantum nuclear correction
|
||||
thermo_style custom step v_T_qm press etotal vol lx ly lz pzz v_dhug v_dray v_lgr_vel v_lgr_pos
|
||||
thermo 500
|
||||
timestep ${delta_t}
|
||||
timestep 0.001
|
||||
restart 1000 restart
|
||||
run 10000 #10 ps
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:332)
|
||||
G vector (1/distance) = 0.306435
|
||||
grid = 9 8 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.000955688
|
||||
estimated relative force accuracy = 6.63689e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 5280 1080
|
||||
All restart file global fix info was re-assigned
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 2 2 3
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair buck/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
(2) pair table, perpetual, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 80.12 | 80.12 | 80.12 Mbytes
|
||||
Step v_T_qm Press TotEng Volume Lx Ly Lz Pzz v_dhug v_dray v_lgr_vel v_lgr_pos
|
||||
1000 268.47106 189686.77 -2781.5194 1492.6355 9.9416812 8.6097487 17.438272 277378.37 -84.692548 -33090.129 15.785409 0
|
||||
1500 362.13476 692245.96 -2800.9352 1011.2037 9.9416812 8.6097487 11.813766 661095.53 188.71833 -49928.712 35.851981 -24.11484
|
||||
2000 860.78914 714816.8 -2830.893 997.64749 9.9416812 8.6097487 11.65539 653537.64 852.68158 -68765.537 36.41702 -44.978484
|
||||
2500 1620.8281 709511.19 -2840.8217 1000.3425 9.9416812 8.6097487 11.686875 660030.01 1184.3105 -60030.892 36.304689 -65.69966
|
||||
3000 2395.6824 649526.84 -2832.6859 995.56591 9.9416812 8.6097487 11.631071 660984.37 939.07209 -63050.693 36.503782 -86.383242
|
||||
3500 3034.6774 715794.56 -2822.6098 995.8622 9.9416812 8.6097487 11.634532 712849.74 1055.7295 -10938.816 36.491433 -106.99315
|
||||
4000 3487.9039 736791.25 -2804.1216 994.13867 9.9416812 8.6097487 11.614397 765817.85 943.15747 40595.305 36.563271 -127.76315
|
||||
4500 3718.6279 813775.8 -2788.1942 995.82514 9.9416812 8.6097487 11.634099 881961.06 1370.5559 158141.68 36.492977 -148.68649
|
||||
5000 3691.4947 750146.58 -2770.5541 1018.4785 9.9416812 8.6097487 11.898756 770500.36 196.2793 65528.786 35.548762 -169.8589
|
||||
5500 3585.8602 831522.51 -2766.0198 1005.6834 9.9416812 8.6097487 11.749273 916093.67 1088.1987 200476.48 36.082073 -190.89436
|
||||
6000 3431.6405 749891.94 -2771.6404 1011.9077 9.9416812 8.6097487 11.82199 781321.11 268.24344 70882.55 35.82264 -212.20913
|
||||
6500 3350.2876 666113.16 -2780.4124 1028.8353 9.9416812 8.6097487 12.019753 749294.32 371.38231 52939.676 35.117081 -233.59556
|
||||
7000 3339.2397 675783.2 -2782.7559 1022.6541 9.9416812 8.6097487 11.947539 690109.39 -26.949124 -11388.054 35.374719 -254.95868
|
||||
7500 3395.582 726601.74 -2784.7652 1018.1439 9.9416812 8.6097487 11.894846 759167.86 506.5811 53917.852 35.56271 -276.24361
|
||||
8000 3393.2372 625141.93 -2771.6398 1035.4915 9.9416812 8.6097487 12.097517 598674.46 -895.80046 -92142.112 34.839641 -297.61681
|
||||
8500 3272.9752 659367.77 -2776.608 1031.8188 9.9416812 8.6097487 12.054609 688358.42 -142.30814 -5513.8593 34.992722 -318.94541
|
||||
9000 3277.8848 724828.76 -2777.6502 1017.6314 9.9416812 8.6097487 11.888859 724452.11 58.574942 18775.738 35.58407 -340.1718
|
||||
9500 3273.7854 620652.38 -2780.0794 1023.5922 9.9416812 8.6097487 11.958499 747175.42 317.3826 46458.505 35.335617 -361.41643
|
||||
10000 3329.1766 668606.38 -2786.3493 1022.9534 9.9416812 8.6097487 11.951035 703351.81 168.14538 2103.38 35.362244 -382.64609
|
||||
10500 3398.9956 642919.16 -2784.2833 1016.2587 9.9416812 8.6097487 11.872822 661298.16 -230.03577 -45520.34 35.641287 -403.78721
|
||||
11000 3418.7053 675754.06 -2782.6318 1005.7483 9.9416812 8.6097487 11.75003 689789.84 -136.97148 -25773.422 36.079372 -424.97556
|
||||
Loop time of 32.4277 on 1 procs for 10000 steps with 144 atoms
|
||||
|
||||
Performance: 26.644 ns/day, 0.901 hours/ns, 308.378 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 | 28.397 | 28.397 | 28.397 | 0.0 | 87.57
|
||||
Kspace | 1.0225 | 1.0225 | 1.0225 | 0.0 | 3.15
|
||||
Neigh | 0.27594 | 0.27594 | 0.27594 | 0.0 | 0.85
|
||||
Comm | 0.1797 | 0.1797 | 0.1797 | 0.0 | 0.55
|
||||
Output | 0.10409 | 0.10409 | 0.10409 | 0.0 | 0.32
|
||||
Modify | 2.4112 | 2.4112 | 2.4112 | 0.0 | 7.44
|
||||
Other | | 0.03707 | | | 0.11
|
||||
|
||||
Nlocal: 144 ave 144 max 144 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 5541 ave 5541 max 5541 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 74662 ave 74662 max 74662 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 74662
|
||||
Ave neighs/atom = 518.486
|
||||
Neighbor list builds = 207
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:37
|
||||
@ -0,0 +1,430 @@
|
||||
LAMMPS (15 Jun 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
## This script first uses fix qtb to equilibrate alpha quartz structure to an initial state with quantum nuclear correction and then simulate shock induced phase transition through the quantum thermal bath multi-scale shock technique
|
||||
variable x_rep equal 2 #plot is made with x_rep = 8 #x-direction replication number
|
||||
variable y_rep equal 1 #plot is made with y_rep = 5 #y-direction replication number
|
||||
variable z_rep equal 4 #plot is made with z_rep = 15 #z-direction replication number
|
||||
variable cut_off equal 10.0 #Cut-off distance for the Buckingham term (Angstrom in metal units)
|
||||
variable pressure equal 1.03125 #Initial state pressure (bar in metal units)
|
||||
variable temperature equal 300.0 #Initial state quantum temperature (K in metal units)
|
||||
variable delta_t equal 1.0e-3 #MD timestep length (ps in metal units)
|
||||
variable damp_qtb equal 1 #1/gamma where gamma is the friction coefficient in quantum thermal bath (ps in metal units)
|
||||
variable v_msst equal 78.0 #Shock velocity (Angstrom/ps in metal units)
|
||||
variable q_msst equal 40.0 #Box mass-like parameter in the MSST (mass^2/length^4, where mass=grams/mole and length=Angstrom in metal units)
|
||||
variable tscale_msst equal 0.05 #Temperature reduction parameter in the MSST (unitless)
|
||||
variable eta_qbmsst equal 1.0 #Coupling constant between the shock and the quantum thermal bath (unitless constant)
|
||||
|
||||
|
||||
## This part uses fix qtb to prepare alpha-quartz with quantum nuclear correction of the initial state
|
||||
include alpha_quartz_qtb.mod
|
||||
## This script first constructs an alpha quartz structure of a given size. It then uses fix qtb to equilibrate the computational cell to the specified temperature and pressure.
|
||||
|
||||
|
||||
## This part defines units, alpha-quartz crystal, and atomic information
|
||||
#General
|
||||
units metal
|
||||
dimension 3
|
||||
boundary p p p
|
||||
atom_style charge
|
||||
|
||||
#Lattice
|
||||
lattice custom 1.0 a1 4.916000 0.000000 0.000000 a2 -2.45800 4.257381 0.000000 a3 0.000000 0.000000 5.405400 basis 0.469700 0.000000 0.000000 basis 0.000000 0.469700 0.666667 basis 0.530300 0.530300 0.333333 basis 0.413500 0.266900 0.119100 basis 0.266900 0.413500 0.547567 basis 0.733100 0.146600 0.785767 basis 0.586500 0.853400 0.214233 basis 0.853400 0.586500 0.452433 basis 0.146600 0.733100 0.880900 #American Mineralogist 65 920 1980 (Space Group 154)
|
||||
Lattice spacing in x,y,z = 7.374 4.25738 5.4054
|
||||
|
||||
#Computational Cell
|
||||
region orthorhombic_unit_cell block 0 4.916000 0 8.514762 0 5.405400 units box
|
||||
create_box 2 orthorhombic_unit_cell
|
||||
Created orthogonal box = (0.0 0.0 0.0) to (4.916 8.514762 5.4054)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box basis 1 1 basis 2 1 basis 3 1 basis 4 2 basis 5 2 basis 6 2 basis 7 2 basis 8 2 basis 9 2
|
||||
Created 18 atoms
|
||||
create_atoms CPU = 0.000 seconds
|
||||
replicate ${x_rep} ${y_rep} ${z_rep}
|
||||
replicate 2 ${y_rep} ${z_rep}
|
||||
replicate 2 1 ${z_rep}
|
||||
replicate 2 1 4
|
||||
orthogonal box = (0.0 0.0 0.0) to (9.832 8.514762 21.6216)
|
||||
1 by 1 by 4 MPI processor grid
|
||||
144 atoms
|
||||
replicate CPU = 0.000225782 secs
|
||||
|
||||
#Atomic Information
|
||||
mass 1 28.085500
|
||||
mass 2 15.999400
|
||||
set type 1 charge +2.4
|
||||
48 settings made for charge
|
||||
set type 2 charge -1.2
|
||||
96 settings made for charge
|
||||
|
||||
|
||||
## This part implements the BKS pair potential with a cut-off distance for the Buckingham term. Long range Coulomb interactions are evaluated with the pppm method.
|
||||
include alpha_quartz_potential.mod
|
||||
#This script implements the BKS pair potential for various silicon dioxide compounds. Inner part is fixed with a harmonic potential. Long range Coulomb interactions are evaluated with the pppm method.
|
||||
|
||||
#Pair Potentials
|
||||
pair_style hybrid/overlay buck/coul/long ${cut_off} table linear 39901
|
||||
pair_style hybrid/overlay buck/coul/long 10 table linear 39901
|
||||
pair_coeff 1 1 buck/coul/long 0.0 1.0 0.0 #No interactions between Si atoms
|
||||
pair_coeff 1 2 buck/coul/long 18003.757200 0.205205 133.538100
|
||||
pair_coeff 2 2 buck/coul/long 1388.773000 0.362319 175.000000 #BKS interaction in PRL 64 1955 (1990)
|
||||
pair_modify shift yes
|
||||
pair_coeff 1 2 table potential_SiO2.TPF Si-O ${cut_off}
|
||||
pair_coeff 1 2 table potential_SiO2.TPF Si-O 10
|
||||
pair_coeff 2 2 table potential_SiO2.TPF O-O ${cut_off} #See the potential file for more information
|
||||
pair_coeff 2 2 table potential_SiO2.TPF O-O 10
|
||||
WARNING: 1 of 39901 force values in table are inconsistent with -dE/dr.
|
||||
Should only be flagged at inflection points (src/pair_table.cpp:471)
|
||||
kspace_style pppm 1.0e-4
|
||||
|
||||
#Neighbor style
|
||||
neighbor 2.0 bin
|
||||
neigh_modify check yes every 1 delay 0 page 100000 one 2000
|
||||
|
||||
|
||||
## This part equilibrates your crystal to a pressure of ${pressure}(unit pressure) and a temperature of ${temperature}(unit temperatureture) with quantum nuclear effects
|
||||
variable p_damp equal ${delta_t}*1000 #Recommended pressure damping parameter in fix nph
|
||||
variable p_damp equal 0.001*1000
|
||||
fix scapegoat_qtb all nph iso ${pressure} ${pressure} ${p_damp} ptemp ${temperature} #NPH does the time integration
|
||||
fix scapegoat_qtb all nph iso 1.03125 ${pressure} ${p_damp} ptemp ${temperature}
|
||||
fix scapegoat_qtb all nph iso 1.03125 1.03125 ${p_damp} ptemp ${temperature}
|
||||
fix scapegoat_qtb all nph iso 1.03125 1.03125 1 ptemp ${temperature}
|
||||
fix scapegoat_qtb all nph iso 1.03125 1.03125 1 ptemp 300
|
||||
fix quartz_qtb all qtb temp ${temperature} damp ${damp_qtb} seed 35082 f_max 120.00 N_f 100 #Change f_max (THz) if your Debye frequency is higher
|
||||
fix quartz_qtb all qtb temp 300 damp ${damp_qtb} seed 35082 f_max 120.00 N_f 100
|
||||
fix quartz_qtb all qtb temp 300 damp 1 seed 35082 f_max 120.00 N_f 100
|
||||
thermo_style custom step temp press etotal vol lx ly lz pxx pyy pzz pxy pyz pxz
|
||||
thermo 200
|
||||
run 2000 # 2 ps
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:332)
|
||||
G vector (1/distance) = 0.301598
|
||||
grid = 9 8 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.00117056
|
||||
estimated relative force accuracy = 8.12908e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 2400 288
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 2 2 4
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair buck/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
(2) pair table, perpetual, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 79.7 | 79.7 | 79.7 Mbytes
|
||||
Step Temp Press TotEng Volume Lx Ly Lz Pxx Pyy Pzz Pxy Pyz Pxz
|
||||
0 0 -34026.791 -2793.6042 1810.0985 9.832 8.514762 21.6216 -37470.578 -37470.432 -27139.363 1.0530512e-10 0.94245783 4.0087238e-10
|
||||
200 153.57631 45538.205 -2790.8177 1873.0866 9.9447472 8.612404 21.869543 41721.016 44095.248 50798.351 -3961.4596 1223.325 2871.656
|
||||
400 234.74785 -34404.175 -2789.0189 1850.2127 9.9041 8.5772024 21.780156 -28329.333 -39376.313 -35506.88 -1154.5043 -5411.1071 2246.6749
|
||||
600 265.24833 -20905.145 -2786.2727 1874.9981 9.948129 8.6153326 21.87698 -22753.886 -21091.083 -18870.468 -4645.5548 2968.2945 1415.0311
|
||||
800 297.79035 32990.58 -2784.8247 1853.6946 9.910309 8.5825796 21.79381 30061.364 35359.18 33551.195 -3092.2971 1525.52 -6461.0249
|
||||
1000 367.71884 -27539.239 -2783.0102 1864.7161 9.9299114 8.5995557 21.836917 -20273.387 -38720.429 -23623.901 7639.0334 -866.35665 543.52723
|
||||
1200 399.77109 3807.7814 -2781.511 1893.4978 9.9807399 8.6435745 21.948695 1625.8226 7441.2236 2356.298 -4057.1674 3814.9305 1528.4567
|
||||
1400 466.57962 -4148.235 -2780.1546 1851.5925 9.9065614 8.5793341 21.785568 -10883.19 1816.768 -3378.2828 896.25296 -7208.541 -42.253127
|
||||
1600 497.86539 14505.31 -2778.9409 1882.2616 9.9609584 8.6264432 21.905193 8268.1103 20614.738 14633.082 -2690.5669 6807.3187 11995.878
|
||||
1800 557.31182 -108.04462 -2778.1875 1875.514 9.9490413 8.6161228 21.878986 948.68308 -1929.7575 656.94053 -1628.2172 -6594.5909 -4423.4368
|
||||
2000 480.39449 -8852.2243 -2778.4963 1862.9552 9.9267847 8.596848 21.830042 -18274.307 3038.8369 -11321.203 -5002.1016 12023.282 6845.2769
|
||||
Loop time of 1.42181 on 4 procs for 2000 steps with 144 atoms
|
||||
|
||||
Performance: 121.535 ns/day, 0.197 hours/ns, 1406.656 timesteps/s
|
||||
87.5% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.72578 | 0.80093 | 0.87518 | 6.1 | 56.33
|
||||
Kspace | 0.33737 | 0.41245 | 0.48642 | 8.4 | 29.01
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.066098 | 0.071334 | 0.076039 | 1.6 | 5.02
|
||||
Output | 0.00021172 | 0.00039291 | 0.00093484 | 0.0 | 0.03
|
||||
Modify | 0.090105 | 0.1077 | 0.11384 | 3.1 | 7.58
|
||||
Other | | 0.029 | | | 2.04
|
||||
|
||||
Nlocal: 36 ave 36 max 36 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 2614 ave 2614 max 2614 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 10488 ave 11326 max 9404 min
|
||||
Histogram: 1 0 0 0 0 0 2 0 0 1
|
||||
|
||||
Total # of neighbors = 41952
|
||||
Ave neighs/atom = 291.333
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
unfix quartz_qtb
|
||||
unfix scapegoat_qtb
|
||||
|
||||
|
||||
## This part demonstrates how to retart fix qbmsst during any stage of the shock simulation.
|
||||
## PPPM may break down when compression ratio becomes extremely large. One can always use this restart technique to resume the shock simulation.
|
||||
#Compression restart 1
|
||||
reset_timestep 0
|
||||
#Beta is the number of time steps between each update of the quantum bath temperature. Setting a larger beta can reduce thermal flactuations.
|
||||
fix shock all qbmsst z ${v_msst} q ${q_msst} tscale ${tscale_msst} damp ${damp_qtb} f_max 120 N_f 100 seed 35082 eta ${eta_qbmsst} beta 5 T_init ${temperature}
|
||||
fix shock all qbmsst z 78 q ${q_msst} tscale ${tscale_msst} damp ${damp_qtb} f_max 120 N_f 100 seed 35082 eta ${eta_qbmsst} beta 5 T_init ${temperature}
|
||||
fix shock all qbmsst z 78 q 40 tscale ${tscale_msst} damp ${damp_qtb} f_max 120 N_f 100 seed 35082 eta ${eta_qbmsst} beta 5 T_init ${temperature}
|
||||
fix shock all qbmsst z 78 q 40 tscale 0.05 damp ${damp_qtb} f_max 120 N_f 100 seed 35082 eta ${eta_qbmsst} beta 5 T_init ${temperature}
|
||||
fix shock all qbmsst z 78 q 40 tscale 0.05 damp 1 f_max 120 N_f 100 seed 35082 eta ${eta_qbmsst} beta 5 T_init ${temperature}
|
||||
fix shock all qbmsst z 78 q 40 tscale 0.05 damp 1 f_max 120 N_f 100 seed 35082 eta 1 beta 5 T_init ${temperature}
|
||||
fix shock all qbmsst z 78 q 40 tscale 0.05 damp 1 f_max 120 N_f 100 seed 35082 eta 1 beta 5 T_init 300
|
||||
QBMSST parameters:
|
||||
Shock in z direction
|
||||
Cell mass-like parameter qmass (units of mass^2/length^4) = 4.00000e+01
|
||||
Shock velocity = 7.80000e+01
|
||||
Artificial viscosity (units of mass/length/time) = 0.00000e+00
|
||||
Initial pressure calculated on first step
|
||||
Initial volume calculated on first step
|
||||
Initial energy calculated on first step
|
||||
fix_modify shock energy yes
|
||||
variable dhug equal f_shock[1]
|
||||
variable dray equal f_shock[2]
|
||||
variable lgr_vel equal f_shock[3]
|
||||
variable lgr_pos equal f_shock[4]
|
||||
variable T_qm equal f_shock[5] #Temperature with quantum nuclear correction
|
||||
thermo_style custom step v_T_qm press etotal vol lx ly lz pzz v_dhug v_dray v_lgr_vel v_lgr_pos
|
||||
thermo 200
|
||||
timestep ${delta_t}
|
||||
timestep 0.001
|
||||
run 1000
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:332)
|
||||
G vector (1/distance) = 0.30088
|
||||
grid = 9 8 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.00120534
|
||||
estimated relative force accuracy = 8.37062e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 2400 288
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 2 2 4
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair buck/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
(2) pair table, perpetual, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
Fix QBMSST v0 = 1.86296e+03
|
||||
Fix QBMSST p0 = -1.13219e+04
|
||||
Fix QBMSST e0 = to be -2.77850e+03
|
||||
Fix QBMSST initial strain rate of -4.21890e-01 established by reducing temperature by factor of 5.00000e-02
|
||||
Per MPI rank memory allocation (min/avg/max) = 79.7 | 79.7 | 79.7 Mbytes
|
||||
Step v_T_qm Press TotEng Volume Lx Ly Lz Pzz v_dhug v_dray v_lgr_vel v_lgr_pos
|
||||
0 300 -9106.318 -2778.4963 1862.9552 9.9267847 8.596848 21.830042 -11562.002 12.009862 -240.0699 0 0
|
||||
200 296.47213 25984.111 -2777.5178 1770.2164 9.9267847 8.596848 20.743332 64970.204 -25.305765 -1564.7673 3.8828772 -15.16768
|
||||
400 291.06707 69977.517 -2777.6325 1684.893 9.9267847 8.596848 19.743515 144833.82 -12.184734 6667.384 7.4552796 -29.607028
|
||||
600 287.21118 39706.699 -2778.0322 1716.9533 9.9267847 8.596848 20.119196 87971.152 -38.593844 -23279.741 6.1129484 -43.751298
|
||||
800 284.33611 18833.281 -2778.1637 1792.7576 9.9267847 8.596848 21.007468 43725.433 -8.1267799 -3885.5802 2.9391022 -58.454556
|
||||
1000 281.98328 -6030.6935 -2778.3314 1881.8369 9.9267847 8.596848 22.051297 -14118.602 1.3183874 13055.078 -0.79055793 -73.780965
|
||||
Loop time of 1.25215 on 4 procs for 1000 steps with 144 atoms
|
||||
|
||||
Performance: 69.001 ns/day, 0.348 hours/ns, 798.628 timesteps/s
|
||||
90.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.67979 | 0.73665 | 0.8091 | 5.4 | 58.83
|
||||
Kspace | 0.18687 | 0.25893 | 0.31544 | 9.1 | 20.68
|
||||
Neigh | 0.0011306 | 0.0012404 | 0.0013735 | 0.3 | 0.10
|
||||
Comm | 0.040339 | 0.041345 | 0.042296 | 0.4 | 3.30
|
||||
Output | 0.00020051 | 0.00035506 | 0.00081801 | 0.0 | 0.03
|
||||
Modify | 0.19595 | 0.2007 | 0.20253 | 0.6 | 16.03
|
||||
Other | | 0.01292 | | | 1.03
|
||||
|
||||
Nlocal: 36 ave 38 max 34 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
Nghost: 2527.75 ave 2547 max 2518 min
|
||||
Histogram: 2 0 0 1 0 0 0 0 0 1
|
||||
Neighs: 10194.8 ave 11177 max 9437 min
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 40779
|
||||
Ave neighs/atom = 283.188
|
||||
Neighbor list builds = 6
|
||||
Dangerous builds = 0
|
||||
write_restart restart.1000
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:332)
|
||||
G vector (1/distance) = 0.302953
|
||||
grid = 9 8 16
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.00105569
|
||||
estimated relative force accuracy = 7.33134e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 2640 288
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 2 2 4
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair buck/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
(2) pair table, perpetual, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
|
||||
#Compression restart 2
|
||||
#Read restart file and load potential again
|
||||
clear
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.1000
|
||||
restoring atom style charge from restart
|
||||
orthogonal box = (-0.04739235907204603 -0.041042988010289584 -0.21484841641189512) to (9.879392359072014 8.555804988010294 21.83644841641206)
|
||||
1 by 1 by 4 MPI processor grid
|
||||
restoring pair style hybrid/overlay from restart
|
||||
144 atoms
|
||||
read_restart CPU = 0.000472307 secs
|
||||
include alpha_quartz_potential.mod
|
||||
#This script implements the BKS pair potential for various silicon dioxide compounds. Inner part is fixed with a harmonic potential. Long range Coulomb interactions are evaluated with the pppm method.
|
||||
|
||||
#Pair Potentials
|
||||
pair_style hybrid/overlay buck/coul/long ${cut_off} table linear 39901
|
||||
pair_style hybrid/overlay buck/coul/long 10 table linear 39901
|
||||
pair_coeff 1 1 buck/coul/long 0.0 1.0 0.0 #No interactions between Si atoms
|
||||
pair_coeff 1 2 buck/coul/long 18003.757200 0.205205 133.538100
|
||||
pair_coeff 2 2 buck/coul/long 1388.773000 0.362319 175.000000 #BKS interaction in PRL 64 1955 (1990)
|
||||
pair_modify shift yes
|
||||
pair_coeff 1 2 table potential_SiO2.TPF Si-O ${cut_off}
|
||||
pair_coeff 1 2 table potential_SiO2.TPF Si-O 10
|
||||
pair_coeff 2 2 table potential_SiO2.TPF O-O ${cut_off} #See the potential file for more information
|
||||
pair_coeff 2 2 table potential_SiO2.TPF O-O 10
|
||||
WARNING: 1 of 39901 force values in table are inconsistent with -dE/dr.
|
||||
Should only be flagged at inflection points (src/pair_table.cpp:471)
|
||||
kspace_style pppm 1.0e-4
|
||||
|
||||
#Neighbor style
|
||||
neighbor 2.0 bin
|
||||
neigh_modify check yes every 1 delay 0 page 100000 one 2000
|
||||
#Use the same fix id and add no tscale if the system is already compressed
|
||||
fix shock all qbmsst z ${v_msst} q ${q_msst} tscale 0.0 damp ${damp_qtb} f_max 120 N_f 100 seed 35082 eta ${eta_qbmsst} beta 5 T_init ${temperature}
|
||||
fix shock all qbmsst z 78 q ${q_msst} tscale 0.0 damp ${damp_qtb} f_max 120 N_f 100 seed 35082 eta ${eta_qbmsst} beta 5 T_init ${temperature}
|
||||
fix shock all qbmsst z 78 q 40 tscale 0.0 damp ${damp_qtb} f_max 120 N_f 100 seed 35082 eta ${eta_qbmsst} beta 5 T_init ${temperature}
|
||||
fix shock all qbmsst z 78 q 40 tscale 0.0 damp 1 f_max 120 N_f 100 seed 35082 eta ${eta_qbmsst} beta 5 T_init ${temperature}
|
||||
fix shock all qbmsst z 78 q 40 tscale 0.0 damp 1 f_max 120 N_f 100 seed 35082 eta 1 beta 5 T_init ${temperature}
|
||||
fix shock all qbmsst z 78 q 40 tscale 0.0 damp 1 f_max 120 N_f 100 seed 35082 eta 1 beta 5 T_init 300
|
||||
QBMSST parameters:
|
||||
Shock in z direction
|
||||
Cell mass-like parameter qmass (units of mass^2/length^4) = 4.00000e+01
|
||||
Shock velocity = 7.80000e+01
|
||||
Artificial viscosity (units of mass/length/time) = 0.00000e+00
|
||||
Initial pressure calculated on first step
|
||||
Initial volume calculated on first step
|
||||
Initial energy calculated on first step
|
||||
Resetting global fix info from restart file:
|
||||
fix style: qbmsst, fix ID: shock
|
||||
fix_modify shock energy yes
|
||||
variable dhug equal f_shock[1]
|
||||
variable dray equal f_shock[2]
|
||||
variable lgr_vel equal f_shock[3]
|
||||
variable lgr_pos equal f_shock[4]
|
||||
variable T_qm equal f_shock[5] #Temperature with quantum nuclear correction
|
||||
thermo_style custom step v_T_qm press etotal vol lx ly lz pzz v_dhug v_dray v_lgr_vel v_lgr_pos
|
||||
thermo 500
|
||||
timestep ${delta_t}
|
||||
timestep 0.001
|
||||
restart 1000 restart
|
||||
run 10000 #10 ps
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:332)
|
||||
G vector (1/distance) = 0.302953
|
||||
grid = 9 8 16
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.00105569
|
||||
estimated relative force accuracy = 7.33134e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 2640 288
|
||||
All restart file global fix info was re-assigned
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 2 2 4
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair buck/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
(2) pair table, perpetual, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 79.71 | 79.71 | 79.71 Mbytes
|
||||
Step v_T_qm Press TotEng Volume Lx Ly Lz Pzz v_dhug v_dray v_lgr_vel v_lgr_pos
|
||||
1000 281.98328 -6031.2395 -2778.6227 1881.8369 9.9267847 8.596848 22.051297 -14113.621 1.3373278 13060.059 -0.79055793 0
|
||||
1500 266.12746 44405.573 -2777.9815 1739.6543 9.9267847 8.596848 20.385206 92590.239 -12.06041 397.47049 5.1624821 -37.823748
|
||||
2000 255.79411 17620.408 -2777.9685 1785.7619 9.9267847 8.596848 20.925494 48670.364 -16.082827 -4813.6764 3.2320016 -73.974437
|
||||
2500 256.8887 40153.833 -2778.4337 1752.9461 9.9267847 8.596848 20.540959 79665.002 7.7413878 -1368.8927 4.6059671 -112.35254
|
||||
3000 261.55251 5315.4799 -2779.0755 1834.3375 9.9267847 8.596848 21.4947 15896.368 22.588205 3192.882 1.1981949 -148.36068
|
||||
3500 261.57101 57911.809 -2778.1223 1713.3956 9.9267847 8.596848 20.077507 110996.8 -9.4471543 -3240.9018 6.2619064 -186.41261
|
||||
4000 254.88665 13952.95 -2778.4816 1818.2782 9.9267847 8.596848 21.306518 26833.588 2.2818412 647.88057 1.8705799 -222.72504
|
||||
4500 240.08908 73322.997 -2776.7382 1668.6666 9.9267847 8.596848 19.553375 151978.11 -43.917346 189.1572 8.1346613 -260.52885
|
||||
5000 214.49084 1925.2557 -2777.0657 1890.0985 9.9267847 8.596848 22.148106 -5218.7292 -44.5537 28890.787 -1.1364617 -297.26329
|
||||
5500 194.6515 71804.842 -2777.3417 1669.7297 9.9267847 8.596848 19.565832 146911.42 -34.911593 -3985.0635 8.0901523 -334.1879
|
||||
6000 186.23814 10196.007 -2777.1394 1837.3793 9.9267847 8.596848 21.530344 23550.907 -18.381207 13401.096 1.0708382 -371.9208
|
||||
6500 172.53603 5474.3725 -2777.4502 1818.0038 9.9267847 8.596848 21.303303 18389.825 -22.65951 -8026.2088 1.8820667 -407.83084
|
||||
7000 160.91186 107908.64 -2777.6746 1621.7378 9.9267847 8.596848 19.003464 196841.27 -8.6606903 5654.1938 10.099523 -444.9925
|
||||
7500 146.01905 147030.69 -2777.2543 1539.7536 9.9267847 8.596848 18.042777 253089.02 -43.928324 -6926.1018 13.532114 -478.63113
|
||||
8000 207.17758 837859.1 -2796.8957 989.32874 9.9267847 8.596848 11.592918 811765.11 1172.3778 89652.363 36.577833 -503.41923
|
||||
8500 725.15657 853732.89 -2832.3144 974.18299 9.9267847 8.596848 11.415441 773926.64 1749.5702 39098.598 37.21197 -524.17835
|
||||
9000 1554.6089 807867.74 -2843.0063 990.10922 9.9267847 8.596848 11.602064 749697.22 1959.0322 28239.71 36.545155 -544.77354
|
||||
9500 2440.1194 748145.05 -2839.2364 992.38871 9.9267847 8.596848 11.628775 691503.58 1437.0708 -28040.223 36.449715 -565.41198
|
||||
10000 3112.1817 823862.43 -2820.0495 982.35471 9.9267847 8.596848 11.511197 754954.89 1330.6807 26987.244 36.869828 -586.12357
|
||||
10500 3550.0273 868916.79 -2803.7678 983.70386 9.9267847 8.596848 11.527006 867368.45 1727.9058 140533.46 36.813341 -607.00946
|
||||
11000 3839.7527 830581.55 -2795.3804 995.31485 9.9267847 8.596848 11.663063 811740 1150.0462 94652.768 36.327201 -628.02229
|
||||
Loop time of 15.1476 on 4 procs for 10000 steps with 144 atoms
|
||||
|
||||
Performance: 57.039 ns/day, 0.421 hours/ns, 660.171 timesteps/s
|
||||
91.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 7.7228 | 9.085 | 10.626 | 36.0 | 59.98
|
||||
Kspace | 1.6343 | 3.1795 | 4.5467 | 61.0 | 20.99
|
||||
Neigh | 0.02063 | 0.027076 | 0.034395 | 3.1 | 0.18
|
||||
Comm | 0.54719 | 0.57781 | 0.60468 | 2.8 | 3.81
|
||||
Output | 0.10128 | 0.1019 | 0.10373 | 0.3 | 0.67
|
||||
Modify | 2.0819 | 2.1159 | 2.1495 | 1.8 | 13.97
|
||||
Other | | 0.06035 | | | 0.40
|
||||
|
||||
Nlocal: 36 ave 38 max 33 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 1 1
|
||||
Nghost: 4267 ave 4304 max 4239 min
|
||||
Histogram: 1 0 1 0 1 0 0 0 0 1
|
||||
Neighs: 18859.2 ave 25108 max 12333 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 75437
|
||||
Ave neighs/atom = 523.868
|
||||
Neighbor list builds = 95
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:17
|
||||
@ -1,4 +1,4 @@
|
||||
#Potential between O,Si atoms. r ranges from 0.1 to 20.0. This file+BKS(with no shift)=alpha*(r-rs)^2(0.1<r<rs);BKS(20.0>r>rs). alpha=100, rsOO=1.43869, rsSiO=1.19362. All with metal units.
|
||||
#Potential between O,Si atoms. UNITS: metal r ranges from 0.1 to 20.0. This file+BKS(with no shift)=alpha*(r-rs)^2(0.1<r<rs);BKS(20.0>r>rs). alpha=100, rsOO=1.43869, rsSiO=1.19362. All with metal units.
|
||||
|
||||
Si-O
|
||||
N 39901
|
||||
|
||||
79
examples/USER/qtb/alpha_quartz_qtb/in.alpha_quartz_qtb
Normal file
79
examples/USER/qtb/alpha_quartz_qtb/in.alpha_quartz_qtb
Normal file
@ -0,0 +1,79 @@
|
||||
## This script first constructs an alpha quartz structure of a given size. It then uses fix qtb to equilibrate the computational cell to the specified temperature and pressure.
|
||||
variable x_rep equal 2 #x-direction replication number
|
||||
variable y_rep equal 2 #y-direction replication number
|
||||
variable z_rep equal 2 #z-direction replication number
|
||||
variable cut_off equal 10.0 #Cut-off distance for the Buckingham term (Angstrom in metal units)
|
||||
variable pressure equal 1.03125 #Initial state pressure (bar in metal units)
|
||||
variable temperature equal 300.0 #Initial state quantum temperature (K in metal units)
|
||||
variable delta_t equal 1.0e-3 #MD timestep length (ps in metal units)
|
||||
variable damp_qtb equal 1 #1/gamma where gamma is the friction coefficient in quantum thermal bath (ps in metal units)
|
||||
|
||||
## This part defines units, alpha-quartz crystal, and atomic information
|
||||
#General
|
||||
units metal
|
||||
dimension 3
|
||||
boundary p p p
|
||||
atom_style charge
|
||||
|
||||
#Lattice
|
||||
lattice custom 1.0 &
|
||||
a1 4.916000 0.000000 0.000000 &
|
||||
a2 -2.45800 4.257381 0.000000 &
|
||||
a3 0.000000 0.000000 5.405400 &
|
||||
&
|
||||
basis 0.469700 0.000000 0.000000 &
|
||||
basis 0.000000 0.469700 0.666667 &
|
||||
basis 0.530300 0.530300 0.333333 &
|
||||
&
|
||||
basis 0.413500 0.266900 0.119100 &
|
||||
basis 0.266900 0.413500 0.547567 &
|
||||
basis 0.733100 0.146600 0.785767 &
|
||||
basis 0.586500 0.853400 0.214233 &
|
||||
basis 0.853400 0.586500 0.452433 &
|
||||
basis 0.146600 0.733100 0.880900 #American Mineralogist 65 920 1980 (Space Group 154)
|
||||
|
||||
#Computational Cell
|
||||
region orthorhombic_unit_cell block 0 4.916000 0 8.514762 0 5.405400 units box
|
||||
create_box 2 orthorhombic_unit_cell
|
||||
create_atoms 1 box &
|
||||
basis 1 1 &
|
||||
basis 2 1 &
|
||||
basis 3 1 &
|
||||
basis 4 2 &
|
||||
basis 5 2 &
|
||||
basis 6 2 &
|
||||
basis 7 2 &
|
||||
basis 8 2 &
|
||||
basis 9 2
|
||||
replicate ${x_rep} ${y_rep} ${z_rep}
|
||||
|
||||
#Atomic Information
|
||||
mass 1 28.085500
|
||||
mass 2 15.999400
|
||||
set type 1 charge +2.4
|
||||
set type 2 charge -1.2
|
||||
|
||||
|
||||
## This part implements the BKS pair potential with a cut-off distance for the Buckingham term. Long range Coulomb interactions are evaluated with the pppm method.
|
||||
#Pair Potentials
|
||||
pair_style buck/coul/long ${cut_off} #BKS interaction, PRL 64 1955 (1990)
|
||||
pair_coeff 1 1 0.0 1.0 0.0
|
||||
pair_coeff 1 2 18003.757200 0.205205 133.538100
|
||||
pair_coeff 2 2 1388.773000 0.362319 175.000000
|
||||
pair_modify shift yes
|
||||
kspace_style pppm 1.0e-4
|
||||
|
||||
#Neighbor style
|
||||
neighbor 2.0 bin
|
||||
neigh_modify check yes every 1 delay 0 page 100000 one 2000
|
||||
|
||||
|
||||
## This part equilibrates your crystal to a pressure of ${pressure}(unit pressure) and a temperature of ${temperature}(unit temperatureture) with quantum nuclear effects
|
||||
variable p_damp equal ${delta_t}*1000 #Recommended pressure damping parameter in fix nph
|
||||
fix scapegoat_qtb all nph iso ${pressure} ${pressure} ${p_damp} ptemp ${temperature} #NPH does the time integration
|
||||
fix quartz_qtb all qtb temp ${temperature} damp ${damp_qtb} seed 35082 f_max 120.00 N_f 100 #Change f_max (THz) if your Debye frequency is higher
|
||||
thermo_style custom step temp press etotal vol lx ly lz pxx pyy pzz pxy pyz pxz
|
||||
thermo 500
|
||||
run 10000 # 20 ps
|
||||
unfix quartz_qtb
|
||||
unfix scapegoat_qtb
|
||||
@ -0,0 +1,152 @@
|
||||
LAMMPS (15 Jun 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
## This script first constructs an alpha quartz structure of a given size. It then uses fix qtb to equilibrate the computational cell to the specified temperature and pressure.
|
||||
variable x_rep equal 2 #x-direction replication number
|
||||
variable y_rep equal 2 #y-direction replication number
|
||||
variable z_rep equal 2 #z-direction replication number
|
||||
variable cut_off equal 10.0 #Cut-off distance for the Buckingham term (Angstrom in metal units)
|
||||
variable pressure equal 1.03125 #Initial state pressure (bar in metal units)
|
||||
variable temperature equal 300.0 #Initial state quantum temperature (K in metal units)
|
||||
variable delta_t equal 1.0e-3 #MD timestep length (ps in metal units)
|
||||
variable damp_qtb equal 1 #1/gamma where gamma is the friction coefficient in quantum thermal bath (ps in metal units)
|
||||
|
||||
## This part defines units, alpha-quartz crystal, and atomic information
|
||||
#General
|
||||
units metal
|
||||
dimension 3
|
||||
boundary p p p
|
||||
atom_style charge
|
||||
|
||||
#Lattice
|
||||
lattice custom 1.0 a1 4.916000 0.000000 0.000000 a2 -2.45800 4.257381 0.000000 a3 0.000000 0.000000 5.405400 basis 0.469700 0.000000 0.000000 basis 0.000000 0.469700 0.666667 basis 0.530300 0.530300 0.333333 basis 0.413500 0.266900 0.119100 basis 0.266900 0.413500 0.547567 basis 0.733100 0.146600 0.785767 basis 0.586500 0.853400 0.214233 basis 0.853400 0.586500 0.452433 basis 0.146600 0.733100 0.880900 #American Mineralogist 65 920 1980 (Space Group 154)
|
||||
Lattice spacing in x,y,z = 7.374 4.25738 5.4054
|
||||
|
||||
#Computational Cell
|
||||
region orthorhombic_unit_cell block 0 4.916000 0 8.514762 0 5.405400 units box
|
||||
create_box 2 orthorhombic_unit_cell
|
||||
Created orthogonal box = (0.0 0.0 0.0) to (4.916 8.514762 5.4054)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box basis 1 1 basis 2 1 basis 3 1 basis 4 2 basis 5 2 basis 6 2 basis 7 2 basis 8 2 basis 9 2
|
||||
Created 18 atoms
|
||||
create_atoms CPU = 0.000 seconds
|
||||
replicate ${x_rep} ${y_rep} ${z_rep}
|
||||
replicate 2 ${y_rep} ${z_rep}
|
||||
replicate 2 2 ${z_rep}
|
||||
replicate 2 2 2
|
||||
orthogonal box = (0.0 0.0 0.0) to (9.832 17.029524 10.8108)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
144 atoms
|
||||
replicate CPU = 0.000219584 secs
|
||||
|
||||
#Atomic Information
|
||||
mass 1 28.085500
|
||||
mass 2 15.999400
|
||||
set type 1 charge +2.4
|
||||
48 settings made for charge
|
||||
set type 2 charge -1.2
|
||||
96 settings made for charge
|
||||
|
||||
|
||||
## This part implements the BKS pair potential with a cut-off distance for the Buckingham term. Long range Coulomb interactions are evaluated with the pppm method.
|
||||
#Pair Potentials
|
||||
pair_style buck/coul/long ${cut_off} #BKS interaction, PRL 64 1955 (1990)
|
||||
pair_style buck/coul/long 10
|
||||
pair_coeff 1 1 0.0 1.0 0.0
|
||||
pair_coeff 1 2 18003.757200 0.205205 133.538100
|
||||
pair_coeff 2 2 1388.773000 0.362319 175.000000
|
||||
pair_modify shift yes
|
||||
kspace_style pppm 1.0e-4
|
||||
|
||||
#Neighbor style
|
||||
neighbor 2.0 bin
|
||||
neigh_modify check yes every 1 delay 0 page 100000 one 2000
|
||||
|
||||
|
||||
## This part equilibrates your crystal to a pressure of ${pressure}(unit pressure) and a temperature of ${temperature}(unit temperatureture) with quantum nuclear effects
|
||||
variable p_damp equal ${delta_t}*1000 #Recommended pressure damping parameter in fix nph
|
||||
variable p_damp equal 0.001*1000
|
||||
fix scapegoat_qtb all nph iso ${pressure} ${pressure} ${p_damp} ptemp ${temperature} #NPH does the time integration
|
||||
fix scapegoat_qtb all nph iso 1.03125 ${pressure} ${p_damp} ptemp ${temperature}
|
||||
fix scapegoat_qtb all nph iso 1.03125 1.03125 ${p_damp} ptemp ${temperature}
|
||||
fix scapegoat_qtb all nph iso 1.03125 1.03125 1 ptemp ${temperature}
|
||||
fix scapegoat_qtb all nph iso 1.03125 1.03125 1 ptemp 300
|
||||
fix quartz_qtb all qtb temp ${temperature} damp ${damp_qtb} seed 35082 f_max 120.00 N_f 100 #Change f_max (THz) if your Debye frequency is higher
|
||||
fix quartz_qtb all qtb temp 300 damp ${damp_qtb} seed 35082 f_max 120.00 N_f 100
|
||||
fix quartz_qtb all qtb temp 300 damp 1 seed 35082 f_max 120.00 N_f 100
|
||||
thermo_style custom step temp press etotal vol lx ly lz pxx pyy pzz pxy pyz pxz
|
||||
thermo 500
|
||||
run 10000 # 20 ps
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:332)
|
||||
G vector (1/distance) = 0.307414
|
||||
grid = 9 15 10
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.000822922
|
||||
estimated relative force accuracy = 5.71487e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 5984 1350
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 2 3 2
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair buck/coul/long, 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) = 79.54 | 79.54 | 79.54 Mbytes
|
||||
Step Temp Press TotEng Volume Lx Ly Lz Pxx Pyy Pzz Pxy Pyz Pxz
|
||||
0 0 -34025.794 -2793.6041 1810.0985 9.832 17.029524 10.8108 -37478.502 -37477.413 -27121.466 -1.3649088e-10 1.3388978 5.8209479e-10
|
||||
500 281.29079 -40385.348 -2786.6755 1844.5575 9.893999 17.136909 10.878971 -44649.574 -45631.516 -30874.953 -5970.3691 3630.1324 5208.8966
|
||||
1000 405.39848 -15491.657 -2783.3315 1874.0851 9.9465141 17.227868 10.936714 -7770.4561 -21469.887 -17234.627 -4706.5632 -8313.9522 -5109.7918
|
||||
1500 428.98568 -12118.951 -2781.3232 1874.1627 9.9466513 17.228106 10.936865 -11239.135 -11740.052 -13377.666 -3778.9317 -6220.1431 12775.412
|
||||
2000 522.11905 -6687.482 -2779.2181 1855.9626 9.914349 17.172157 10.901347 -8016.0133 -10737.23 -1309.2028 -4980.3805 5270.2674 5848.5479
|
||||
2500 496.74376 4264.2623 -2778.9979 1849.3244 9.9025147 17.151659 10.888335 -477.1374 3487.19 9782.7343 -4961.2016 2380.6522 4736.0758
|
||||
3000 456.49628 2320.781 -2779.3844 1853.2925 9.9095923 17.163918 10.896117 5479.6232 -2954.3023 4437.022 3719.9287 4445.0723 -3278.5058
|
||||
3500 485.20722 -7480.1789 -2778.6062 1859.6305 9.920876 17.183462 10.908524 -9340.6334 -6129.8494 -6970.0541 -7379.3507 1772.8159 334.33057
|
||||
4000 527.61216 -13499.73 -2777.3433 1889.9405 9.9744857 17.276316 10.96747 -16483.038 -7465.2297 -16550.923 -2517.02 -1863.063 3314.927
|
||||
4500 519.94117 721.60614 -2777.8506 1879.6562 9.9563603 17.244922 10.947541 -913.2791 -1765.7541 4843.8516 4466.5704 -14141.087 -6439.5669
|
||||
5000 505.27757 -6278.3805 -2777.3641 1881.2931 9.9592497 17.249927 10.950718 -14254.233 -2653.6233 -1927.2858 1838.1568 5767.9267 597.47761
|
||||
5500 500.70903 11303.821 -2777.8881 1871.0076 9.9410666 17.218433 10.930724 -6452.7947 24876.967 15487.29 522.01171 10473.257 9780.893
|
||||
6000 526.65329 7991.2419 -2777.172 1856.9227 9.9160583 17.175117 10.903227 -68.823156 11005.468 13037.081 1253.9214 10039.559 1053.0486
|
||||
6500 485.30026 12811.546 -2777.5866 1845.31 9.8953442 17.139239 10.88045 10063.921 20215.037 8155.6798 -3886.954 2249.2807 4855.0011
|
||||
7000 507.85472 2649.7919 -2777.3359 1861.2877 9.923822 17.188564 10.911763 -4214.7779 6995.1472 5169.0064 -2188.489 6157.0955 533.65478
|
||||
7500 528.5729 3161.4629 -2779.0851 1855.7946 9.9140499 17.171639 10.901018 2935.365 -2873.1363 9422.1601 771.1885 -4360.9131 4939.8209
|
||||
8000 533.77283 4534.849 -2777.6538 1858.4772 9.9188246 17.179909 10.906268 -1187.9433 15739.396 -946.90551 -5187.8588 2446.5059 8079.2032
|
||||
8500 518.71765 1108.9877 -2777.7019 1866.6125 9.9332765 17.20494 10.922159 8720.4976 -8234.9325 2841.3979 5148.5004 -2125.3524 -4127.7468
|
||||
9000 536.71495 -496.88283 -2778.0262 1877.7099 9.9529227 17.238968 10.943761 -3481.5874 -4611.6246 6602.5634 -2788.5111 -13323.148 4338.813
|
||||
9500 527.06773 -236.09043 -2778.1125 1895.9227 9.9849986 17.294525 10.97903 -12233.409 7578.0514 3947.0863 -6399.0254 995.22838 8590.7109
|
||||
10000 526.77335 -4480.6866 -2777.7171 1886.8998 9.9691335 17.267046 10.961585 -3139.961 1336.993 -11639.092 13496.371 -11543.676 -6180.9262
|
||||
Loop time of 8.86837 on 1 procs for 10000 steps with 144 atoms
|
||||
|
||||
Performance: 97.425 ns/day, 0.246 hours/ns, 1127.603 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 | 6.1503 | 6.1503 | 6.1503 | 0.0 | 69.35
|
||||
Kspace | 1.1522 | 1.1522 | 1.1522 | 0.0 | 12.99
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.11705 | 0.11705 | 0.11705 | 0.0 | 1.32
|
||||
Output | 0.00035834 | 0.00035834 | 0.00035834 | 0.0 | 0.00
|
||||
Modify | 1.4245 | 1.4245 | 1.4245 | 0.0 | 16.06
|
||||
Other | | 0.02397 | | | 0.27
|
||||
|
||||
Nlocal: 144 ave 144 max 144 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 3804 ave 3804 max 3804 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 41952 ave 41952 max 41952 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 41952
|
||||
Ave neighs/atom = 291.333
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
unfix quartz_qtb
|
||||
unfix scapegoat_qtb
|
||||
Total wall time: 0:00:08
|
||||
@ -0,0 +1,152 @@
|
||||
LAMMPS (15 Jun 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
## This script first constructs an alpha quartz structure of a given size. It then uses fix qtb to equilibrate the computational cell to the specified temperature and pressure.
|
||||
variable x_rep equal 2 #x-direction replication number
|
||||
variable y_rep equal 2 #y-direction replication number
|
||||
variable z_rep equal 2 #z-direction replication number
|
||||
variable cut_off equal 10.0 #Cut-off distance for the Buckingham term (Angstrom in metal units)
|
||||
variable pressure equal 1.03125 #Initial state pressure (bar in metal units)
|
||||
variable temperature equal 300.0 #Initial state quantum temperature (K in metal units)
|
||||
variable delta_t equal 1.0e-3 #MD timestep length (ps in metal units)
|
||||
variable damp_qtb equal 1 #1/gamma where gamma is the friction coefficient in quantum thermal bath (ps in metal units)
|
||||
|
||||
## This part defines units, alpha-quartz crystal, and atomic information
|
||||
#General
|
||||
units metal
|
||||
dimension 3
|
||||
boundary p p p
|
||||
atom_style charge
|
||||
|
||||
#Lattice
|
||||
lattice custom 1.0 a1 4.916000 0.000000 0.000000 a2 -2.45800 4.257381 0.000000 a3 0.000000 0.000000 5.405400 basis 0.469700 0.000000 0.000000 basis 0.000000 0.469700 0.666667 basis 0.530300 0.530300 0.333333 basis 0.413500 0.266900 0.119100 basis 0.266900 0.413500 0.547567 basis 0.733100 0.146600 0.785767 basis 0.586500 0.853400 0.214233 basis 0.853400 0.586500 0.452433 basis 0.146600 0.733100 0.880900 #American Mineralogist 65 920 1980 (Space Group 154)
|
||||
Lattice spacing in x,y,z = 7.374 4.25738 5.4054
|
||||
|
||||
#Computational Cell
|
||||
region orthorhombic_unit_cell block 0 4.916000 0 8.514762 0 5.405400 units box
|
||||
create_box 2 orthorhombic_unit_cell
|
||||
Created orthogonal box = (0.0 0.0 0.0) to (4.916 8.514762 5.4054)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box basis 1 1 basis 2 1 basis 3 1 basis 4 2 basis 5 2 basis 6 2 basis 7 2 basis 8 2 basis 9 2
|
||||
Created 18 atoms
|
||||
create_atoms CPU = 0.000 seconds
|
||||
replicate ${x_rep} ${y_rep} ${z_rep}
|
||||
replicate 2 ${y_rep} ${z_rep}
|
||||
replicate 2 2 ${z_rep}
|
||||
replicate 2 2 2
|
||||
orthogonal box = (0.0 0.0 0.0) to (9.832 17.029524 10.8108)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
144 atoms
|
||||
replicate CPU = 0.000231981 secs
|
||||
|
||||
#Atomic Information
|
||||
mass 1 28.085500
|
||||
mass 2 15.999400
|
||||
set type 1 charge +2.4
|
||||
48 settings made for charge
|
||||
set type 2 charge -1.2
|
||||
96 settings made for charge
|
||||
|
||||
|
||||
## This part implements the BKS pair potential with a cut-off distance for the Buckingham term. Long range Coulomb interactions are evaluated with the pppm method.
|
||||
#Pair Potentials
|
||||
pair_style buck/coul/long ${cut_off} #BKS interaction, PRL 64 1955 (1990)
|
||||
pair_style buck/coul/long 10
|
||||
pair_coeff 1 1 0.0 1.0 0.0
|
||||
pair_coeff 1 2 18003.757200 0.205205 133.538100
|
||||
pair_coeff 2 2 1388.773000 0.362319 175.000000
|
||||
pair_modify shift yes
|
||||
kspace_style pppm 1.0e-4
|
||||
|
||||
#Neighbor style
|
||||
neighbor 2.0 bin
|
||||
neigh_modify check yes every 1 delay 0 page 100000 one 2000
|
||||
|
||||
|
||||
## This part equilibrates your crystal to a pressure of ${pressure}(unit pressure) and a temperature of ${temperature}(unit temperatureture) with quantum nuclear effects
|
||||
variable p_damp equal ${delta_t}*1000 #Recommended pressure damping parameter in fix nph
|
||||
variable p_damp equal 0.001*1000
|
||||
fix scapegoat_qtb all nph iso ${pressure} ${pressure} ${p_damp} ptemp ${temperature} #NPH does the time integration
|
||||
fix scapegoat_qtb all nph iso 1.03125 ${pressure} ${p_damp} ptemp ${temperature}
|
||||
fix scapegoat_qtb all nph iso 1.03125 1.03125 ${p_damp} ptemp ${temperature}
|
||||
fix scapegoat_qtb all nph iso 1.03125 1.03125 1 ptemp ${temperature}
|
||||
fix scapegoat_qtb all nph iso 1.03125 1.03125 1 ptemp 300
|
||||
fix quartz_qtb all qtb temp ${temperature} damp ${damp_qtb} seed 35082 f_max 120.00 N_f 100 #Change f_max (THz) if your Debye frequency is higher
|
||||
fix quartz_qtb all qtb temp 300 damp ${damp_qtb} seed 35082 f_max 120.00 N_f 100
|
||||
fix quartz_qtb all qtb temp 300 damp 1 seed 35082 f_max 120.00 N_f 100
|
||||
thermo_style custom step temp press etotal vol lx ly lz pxx pyy pzz pxy pyz pxz
|
||||
thermo 500
|
||||
run 10000 # 20 ps
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:332)
|
||||
G vector (1/distance) = 0.307414
|
||||
grid = 9 15 10
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.000822922
|
||||
estimated relative force accuracy = 5.71487e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 2688 405
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 2 3 2
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair buck/coul/long, 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) = 79.08 | 79.08 | 79.09 Mbytes
|
||||
Step Temp Press TotEng Volume Lx Ly Lz Pxx Pyy Pzz Pxy Pyz Pxz
|
||||
0 0 -34025.794 -2793.6041 1810.0985 9.832 17.029524 10.8108 -37478.502 -37477.413 -27121.466 -5.9958847e-10 1.3388978 7.2750373e-10
|
||||
500 222.04947 -50221.579 -2787.6677 1851.5661 9.9065143 17.158586 10.892732 -61493.697 -53512.432 -35658.61 4973.9976 7095.5481 -2041.6341
|
||||
1000 361.92367 -14345.85 -2783.1509 1861.0579 9.9234137 17.187857 10.911314 -4145.4149 -28701.195 -10190.939 7896.3934 -3901.2874 -490.57107
|
||||
1500 457.97039 -4934.8727 -2779.8321 1860.2254 9.9219337 17.185294 10.909687 -3680.7192 -3045.0707 -8078.8283 456.70383 -4705.3346 -2175.8144
|
||||
2000 523.52684 -9516.755 -2778.5181 1866.3577 9.9328244 17.204157 10.921662 -11042.489 -7777.5634 -9730.2127 -2016.3336 6027.001 -4150.3656
|
||||
2500 489.58881 -4968.5157 -2777.3948 1864.0745 9.9287723 17.197139 10.917206 -13652.344 -2823.514 1570.3111 -7481.9537 -1150.3548 10502.368
|
||||
3000 559.52782 -2882.7076 -2777.5527 1883.2223 9.9626528 17.255821 10.95446 3061.1755 -10570.656 -1138.642 -12045.354 -856.20951 16292.443
|
||||
3500 521.67929 9974.5929 -2776.7752 1880.5936 9.9580152 17.247789 10.94936 15358.559 7855.8683 6709.3509 7292.9372 -9848.9204 -523.61056
|
||||
4000 497.90872 -2012.9259 -2776.5554 1862.1703 9.9253904 17.191281 10.913488 -1154.5123 4270.0275 -9154.2927 971.94826 -10157.618 4694.0509
|
||||
4500 533.64016 -7218.9278 -2775.8789 1883.3041 9.962797 17.256071 10.954618 -18299.547 -5497.566 2140.3296 -1335.6063 -10353.21 5703.7506
|
||||
5000 551.61416 1590.9702 -2777.6093 1866.2047 9.9325531 17.203687 10.921363 -4600.02 6535.3 2837.6306 3412.3383 9492.18 1017.5742
|
||||
5500 499.36075 188.82067 -2777.9872 1863.2925 9.9273838 17.194734 10.91568 -3238.914 1143.013 2662.363 4193.7623 -11565.423 2575.9361
|
||||
6000 478.563 4064.8319 -2778.946 1867.7185 9.935238 17.208337 10.924316 1947.7246 3346.7411 6900.0301 -6339.9554 4133.6942 -4555.406
|
||||
6500 512.63865 10227.461 -2778.8476 1855.5323 9.9135828 17.17083 10.900505 7423.8967 7558.2024 15700.285 -621.4585 -2620.4837 -3256.7524
|
||||
7000 489.9889 13037.303 -2778.8793 1856.2469 9.9148553 17.173034 10.901904 10690.345 16770.786 11650.779 -4056.5527 -5023.8847 469.21909
|
||||
7500 495.52187 1320.5068 -2778.1189 1871.7467 9.9423755 17.2207 10.932164 1978.2905 738.78041 1244.4496 1826.0923 -7829.3563 1873.2713
|
||||
8000 474.60945 -4203.2068 -2778.8915 1866.5966 9.9332482 17.204891 10.922128 -1480.6896 -12516.261 1387.3306 2731.4462 -1292.9741 10743.939
|
||||
8500 473.16225 -6266.1992 -2778.594 1872.9075 9.9444304 17.224259 10.934423 -12680.492 -2832.6603 -3285.4455 7226.9632 3762.6841 -5834.9064
|
||||
9000 486.6579 2843.7947 -2778.0388 1877.3735 9.9523282 17.237939 10.943107 805.23659 6213.7247 1512.4228 2685.2063 -3517.5266 -17054.035
|
||||
9500 549.35112 -1028.3899 -2776.8124 1880.7965 9.9583733 17.248409 10.949754 -1817.8413 2754.8459 -4022.1743 -3101.1463 8397.2345 -8608.1342
|
||||
10000 562.27081 12885.53 -2775.7435 1850.2864 9.9042316 17.154633 10.890222 15758.218 9989.5121 12908.859 -25.724137 -16691.374 267.85371
|
||||
Loop time of 3.80648 on 4 procs for 10000 steps with 144 atoms
|
||||
|
||||
Performance: 226.981 ns/day, 0.106 hours/ns, 2627.100 timesteps/s
|
||||
94.8% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.3526 | 1.6581 | 1.9634 | 21.3 | 43.56
|
||||
Kspace | 0.92143 | 1.2222 | 1.5232 | 24.7 | 32.11
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.31886 | 0.32256 | 0.32604 | 0.5 | 8.47
|
||||
Output | 0.0003643 | 0.00083923 | 0.0022533 | 0.0 | 0.02
|
||||
Modify | 0.39166 | 0.45985 | 0.52607 | 8.9 | 12.08
|
||||
Other | | 0.143 | | | 3.76
|
||||
|
||||
Nlocal: 36 ave 36 max 36 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 2614 ave 2614 max 2614 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 10488 ave 12570 max 8406 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 41952
|
||||
Ave neighs/atom = 291.333
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
unfix quartz_qtb
|
||||
unfix scapegoat_qtb
|
||||
Total wall time: 0:00:03
|
||||
@ -1,6 +1,6 @@
|
||||
dimension 2
|
||||
units si
|
||||
atom_style meso
|
||||
atom_style sph
|
||||
|
||||
# create simulation box
|
||||
region box block -0.050e-3 1.044e-3 -0.05e-3 1.044e-3 -1.0e-6 1.0e-6 units box
|
||||
@ -28,7 +28,7 @@ group integrate_full union fluid driver
|
||||
mass 3 2.0e-7
|
||||
mass 2 2.0e-7
|
||||
mass 1 4.0e-7
|
||||
set group all meso/rho 1000.0
|
||||
set group all sph/rho 1000.0
|
||||
|
||||
# use Tait's EOS in combination with Morris' laminar viscosity.
|
||||
# We set rho_0 = 1000 kg/m^3, c = 0.1 m/s, h = 6.5e-5 m.
|
||||
@ -37,8 +37,8 @@ pair_style hybrid sph/taitwater/morris
|
||||
pair_coeff * * sph/taitwater/morris 1000 0.1 1.0e-3 6.5e-5
|
||||
pair_coeff 2 3 none # exclude interaction between walls and shear driver
|
||||
|
||||
compute rho_peratom all meso/rho/atom
|
||||
compute e_peratom all meso/e/atom
|
||||
compute rho_peratom all sph/rho/atom
|
||||
compute e_peratom all sph/e/atom
|
||||
compute ke_peratom all ke/atom
|
||||
compute esph all reduce sum c_e_peratom
|
||||
compute ke all ke
|
||||
@ -49,8 +49,8 @@ velocity driver set 0.001 0.0 0.0 units box
|
||||
fix freeze_fix driver setforce 0.0 0.0 0.0
|
||||
|
||||
# do full time integration for shear driver and fluid, but keep walls stationary
|
||||
fix integrate_fix_full integrate_full meso
|
||||
fix integrate_fix_stationary walls meso/stationary
|
||||
fix integrate_fix_full integrate_full sph
|
||||
fix integrate_fix_stationary walls sph/stationary
|
||||
|
||||
dump dump_id all custom 100 dump.lammpstrj id type xs ys zs vx vy c_rho_peratom c_e_peratom
|
||||
dump_modify dump_id first yes
|
||||
|
||||
@ -1,4 +1,4 @@
|
||||
# mesoscopic heat conduction
|
||||
# SPH heat conduction
|
||||
# heat flow from hot right region to cold left region
|
||||
# compare the temperature profile at the end opf the simulation,
|
||||
# contained in file dump.last, to analytic solution.
|
||||
@ -6,7 +6,7 @@
|
||||
#
|
||||
dimension 2
|
||||
units si
|
||||
atom_style meso
|
||||
atom_style sph
|
||||
boundary f p p
|
||||
|
||||
lattice sq 0.01
|
||||
@ -17,23 +17,23 @@ mass 1 1.0e-5
|
||||
|
||||
region left block EDGE 49.9 EDGE EDGE EDGE EDGE
|
||||
region right block 50 EDGE EDGE EDGE EDGE EDGE
|
||||
set region left meso/e 1.0 # internal energies
|
||||
set region right meso/e 2.0
|
||||
set group all meso/rho 0.1 # mesoscopic density is also needed for this pair style
|
||||
set region left sph/e 1.0 # internal energies
|
||||
set region right sph/e 2.0
|
||||
set group all sph/rho 0.1 # SPH density is also needed for this pair style
|
||||
# For correct temperature profiles, mescoscopic density and mass * number density must coincide!
|
||||
|
||||
pair_style sph/heatconduction
|
||||
# i j diffusion coeff. cutoff
|
||||
pair_coeff 1 1 1.0e-4 2.0e-2
|
||||
|
||||
compute ie_atom all meso/e/atom
|
||||
compute ie_atom all sph/e/atom
|
||||
compute ie all reduce sum c_ie_atom
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step temp c_ie
|
||||
timestep 0.25e-1
|
||||
neighbor 0.2e-2 bin
|
||||
fix integrate_fix all meso/stationary
|
||||
fix integrate_fix all sph/stationary
|
||||
|
||||
dump dump_fix all custom 10 dump.heat id type x y z c_ie_atom
|
||||
dump_modify dump_fix first yes
|
||||
|
||||
@ -1,11 +1,11 @@
|
||||
# mesoscopic heat conduction
|
||||
# SPH heat conduction
|
||||
# heat flow from hot right region to cold left region
|
||||
# compare the temperature profile at the end opf the simulation,
|
||||
# contained in file dump.last, to analytic solution.
|
||||
#
|
||||
#
|
||||
units si
|
||||
atom_style meso
|
||||
atom_style sph
|
||||
newton on
|
||||
boundary f p p
|
||||
|
||||
@ -17,9 +17,9 @@ mass 1 1.0e-5
|
||||
|
||||
region left block EDGE 49.9 EDGE EDGE EDGE EDGE
|
||||
region right block 50 EDGE EDGE EDGE EDGE EDGE
|
||||
set region left meso/e 1.0 # internal energies
|
||||
set region right meso/e 2.0
|
||||
set group all meso/rho 10.0 # mesoscopic density is also needed for this pair style
|
||||
set region left sph/e 1.0 # internal energies
|
||||
set region right sph/e 2.0
|
||||
set group all sph/rho 10.0 # SPH density is also needed for this pair style
|
||||
# For correct temperature profiles, mescoscopic density and mass * number density must coincide!
|
||||
|
||||
pair_style sph/heatconduction
|
||||
@ -28,13 +28,13 @@ pair_coeff 1 1 1.0e-4 2.0e-2
|
||||
neighbor 0.2e-2 bin
|
||||
neigh_modify every 20 delay 0 check no
|
||||
|
||||
compute ie_atom all meso/e/atom
|
||||
compute ie_atom all sph/e/atom
|
||||
compute ie all reduce sum c_ie_atom
|
||||
|
||||
thermo_style custom step temp c_ie
|
||||
thermo_modify norm no
|
||||
|
||||
fix integrate_fix all meso/stationary
|
||||
fix integrate_fix all sph/stationary
|
||||
|
||||
thermo 10
|
||||
timestep 0.25e-1
|
||||
|
||||
@ -1,4 +1,4 @@
|
||||
atom_style meso
|
||||
atom_style sph
|
||||
dimension 2
|
||||
boundary s p p
|
||||
|
||||
@ -13,20 +13,20 @@ set region right type 2
|
||||
|
||||
mass 1 1
|
||||
mass 2 0.25
|
||||
set type 1 meso/e 2.5 # internal energy corresponding to p=1, rho=1
|
||||
set type 2 meso/e 0.625 # internal energy corresponding to p=0.25, rho=0.25
|
||||
set type 1 meso/rho 1.0
|
||||
set type 2 meso/rho 0.25
|
||||
set type 1 sph/e 2.5 # internal energy corresponding to p=1, rho=1
|
||||
set type 2 sph/e 0.625 # internal energy corresponding to p=0.25, rho=0.25
|
||||
set type 1 sph/rho 1.0
|
||||
set type 2 sph/rho 0.25
|
||||
|
||||
pair_style hybrid/overlay sph/rhosum 1 sph/idealgas
|
||||
pair_coeff * * sph/rhosum 4.0
|
||||
pair_coeff * * sph/idealgas 0.75 4.0
|
||||
|
||||
compute rhoatom all meso/rho/atom
|
||||
compute ieatom all meso/e/atom
|
||||
compute emeso all reduce sum c_ieatom # total internal energy
|
||||
compute rhoatom all shp/rho/atom
|
||||
compute ieatom all sph/e/atom
|
||||
compute esph all reduce sum c_ieatom # total internal energy
|
||||
compute ke all ke
|
||||
variable etot equal c_ke+c_emeso # total energy
|
||||
variable etot equal c_ke+c_esph # total energy
|
||||
|
||||
# dump positions and local density
|
||||
dump dump_id all custom 100 dump.2d id type x z y c_rhoatom
|
||||
@ -35,10 +35,10 @@ dump_modify dump_id first yes
|
||||
neighbor 0.5 bin
|
||||
neigh_modify every 5 delay 0 check yes
|
||||
thermo 10
|
||||
thermo_style custom step c_ke c_emeso v_etot
|
||||
thermo_style custom step c_ke c_esph v_etot
|
||||
thermo_modify norm no
|
||||
|
||||
fix integration_fix all meso
|
||||
fix integration_fix all sph
|
||||
fix 1 all setforce NULL 0.0 0.0 # treat as a quasi 1d problem
|
||||
timestep 0.05
|
||||
log log.2d
|
||||
|
||||
@ -1,4 +1,4 @@
|
||||
atom_style meso
|
||||
atom_style sph
|
||||
boundary s p p
|
||||
|
||||
region box block -100 150 -4 4 -4 4 units box
|
||||
@ -12,20 +12,20 @@ set region right type 2
|
||||
|
||||
mass 1 1
|
||||
mass 2 0.25
|
||||
set type 1 meso/e 2.5 # internal energy corresponding to p=1, rho=1
|
||||
set type 2 meso/e 0.625 # internal energy corresponding to p=0.25, rho=0.25
|
||||
set type 1 meso/rho 1.0
|
||||
set type 2 meso/rho 0.25
|
||||
set type 1 sph/e 2.5 # internal energy corresponding to p=1, rho=1
|
||||
set type 2 sph/e 0.625 # internal energy corresponding to p=0.25, rho=0.25
|
||||
set type 1 sph/rho 1.0
|
||||
set type 2 sph/rho 0.25
|
||||
|
||||
pair_style hybrid/overlay sph/rhosum 1 sph/idealgas
|
||||
pair_coeff * * sph/rhosum 4.0
|
||||
pair_coeff * * sph/idealgas 0.75 4.0
|
||||
|
||||
compute rhoatom all meso/rho/atom
|
||||
compute ieatom all meso/e/atom
|
||||
compute emeso all reduce sum c_ieatom # total internal energy
|
||||
compute rhoatom all sph/rho/atom
|
||||
compute ieatom all sph/e/atom
|
||||
compute esph all reduce sum c_ieatom # total internal energy
|
||||
compute ke all ke
|
||||
variable etot equal c_ke+c_emeso # total energy
|
||||
variable etot equal c_ke+c_esph # total energy
|
||||
|
||||
# dump positions and local density
|
||||
dump dump_id all custom 100 dump.3d id type x z y c_rhoatom
|
||||
@ -34,10 +34,10 @@ dump_modify dump_id first yes
|
||||
neighbor 0.5 bin
|
||||
neigh_modify every 5 delay 0 check yes
|
||||
thermo 10
|
||||
thermo_style custom step c_ke c_emeso v_etot
|
||||
thermo_style custom step c_ke c_esph v_etot
|
||||
thermo_modify norm no
|
||||
|
||||
fix integration_fix all meso
|
||||
fix integration_fix all sph
|
||||
fix 1 all setforce NULL 0.0 0.0 # treat as a quasi 1d problem
|
||||
timestep 0.05
|
||||
log log.3d
|
||||
|
||||
@ -1,5 +1,5 @@
|
||||
processors * 1 1 # manually assign processors to spatial regions
|
||||
atom_style meso
|
||||
atom_style sph
|
||||
dimension 2
|
||||
newton on
|
||||
boundary f f p
|
||||
@ -22,8 +22,8 @@ pair_coeff 1 1 sph/rhosum ${h}
|
||||
fix gfix water gravity -9.81 vector 0 1 0 # add gravity. This fix also computes potential energy of mass in gravity field.
|
||||
fix 2d_fix all enforce2d
|
||||
|
||||
compute rho_peratom all meso/rho/atom
|
||||
compute e_peratom all meso/e/atom
|
||||
compute rho_peratom all sph/rho/atom
|
||||
compute e_peratom all sph/e/atom
|
||||
compute esph all reduce sum c_e_peratom
|
||||
compute ke all ke
|
||||
variable etot equal c_esph+c_ke+f_gfix
|
||||
@ -32,10 +32,10 @@ variable etot equal c_esph+c_ke+f_gfix
|
||||
fix dtfix all dt/reset 1 NULL ${dt} 0.0005 units box # use a variable timestep
|
||||
|
||||
# time-integrate position, velocities, internal energy and density of water particles
|
||||
fix integrate_water_fix water meso
|
||||
fix integrate_water_fix water sph
|
||||
|
||||
# time-integrate only internal energy and density of boundary particles
|
||||
fix integrate_bc_fix bc meso/stationary
|
||||
fix integrate_bc_fix bc sph/stationary
|
||||
dump dump_id all custom 100 dump.lammpstrj id type xs ys zs c_rho_peratom c_e_peratom fx fy
|
||||
dump_modify dump_id first yes
|
||||
thermo 10
|
||||
|
||||
Reference in New Issue
Block a user