forked from lijiext/lammps
Added special_bonds command to input files
This commit is contained in:
parent
17e419e251
commit
8dae5d5fc7
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@ -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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@ -1,4 +1,4 @@
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LAMMPS (7 Aug 2019)
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LAMMPS (30 Jun 2020)
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variable number equal 1
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variable ofreq equal 1000
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variable efreq equal 1000
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@ -12,7 +12,10 @@ 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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@ -35,9 +38,8 @@ read_data data.duplex1
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2 = max # of 1-3 neighbors
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2 = max # of 1-4 neighbors
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4 = max # of special neighbors
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special bonds CPU = 9.5e-05 secs
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read_data CPU = 0.001865 secs
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special bonds CPU = 0.000 seconds
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read_data CPU = 0.002 seconds
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set atom * mass 3.1575
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10 settings made for mass
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@ -47,6 +49,12 @@ 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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2 = max # of 1-2 neighbors
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2 = max # of 1-3 neighbors
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2 = max # of 1-4 neighbors
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4 = 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 oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
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@ -69,6 +77,7 @@ 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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@ -99,9 +108,9 @@ run 1000000
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Neighbor list info ...
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update every 1 steps, delay 0 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 1.956
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ghost atom cutoff = 1.956
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binsize = 0.978, bins = 41 41 41
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master list distance cutoff = 1.9560004
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ghost atom cutoff = 2.5
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binsize = 0.97800022, bins = 41 41 41
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5 neighbor lists, perpetual/occasional/extra = 5 0 0
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(1) pair oxdna/excv, perpetual
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attributes: half, newton off
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@ -128,8 +137,8 @@ Neighbor list info ...
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pair build: copy
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stencil: none
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bin: none
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WARNING: Communication cutoff 1.956 is shorter than a bond length based estimate of 2.12875. This may lead to errors. (../comm.cpp:685)
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Per MPI rank memory allocation (min/avg/max) = 2.836 | 2.836 | 2.836 Mbytes
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0 ekin = 0 | erot = 0 | epot = -14.6424332448164 | etot = -14.6424332448164
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Per MPI rank memory allocation (min/avg/max) = 7.883 | 7.883 | 7.883 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 0 -1.4711818 0.0069384985 -1.4642433 2.5836586e-06
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1000 ekin = 0.00113448721737003 | erot = 0.00413455947734281 | epot = -14.6477022915193 | etot = -14.6424332448246
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@ -1133,34 +1142,34 @@ Step Temp E_pair E_mol TotEng Press
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999000 ekin = 0.188315843917336 | erot = 0.335221830001114 | epot = -15.1659709188676 | etot = -14.6424332449491
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1000000 ekin = 0.1816243230724 | erot = 0.33096613964385 | epot = -15.155023707645 | etot = -14.6424332449287
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1000000 0.013453654 -1.5270261 0.011523695 -1.4973399 -8.4815516e-05
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Loop time of 17.1797 on 1 procs for 1000000 steps with 10 atoms
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Loop time of 15.696 on 1 procs for 1000000 steps with 10 atoms
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Performance: 50291.944 tau/day, 58208.268 timesteps/s
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Performance: 55045.770 tau/day, 63710.382 timesteps/s
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99.6% CPU use with 1 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 13.871 | 13.871 | 13.871 | 0.0 | 80.74
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Bond | 0.52454 | 0.52454 | 0.52454 | 0.0 | 3.05
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Pair | 11.973 | 11.973 | 11.973 | 0.0 | 76.28
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Bond | 0.57492 | 0.57492 | 0.57492 | 0.0 | 3.66
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.14987 | 0.14987 | 0.14987 | 0.0 | 0.87
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Output | 7e-06 | 7e-06 | 7e-06 | 0.0 | 0.00
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Modify | 2.4075 | 2.4075 | 2.4075 | 0.0 | 14.01
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Other | | 0.227 | | | 1.32
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Comm | 0.18391 | 0.18391 | 0.18391 | 0.0 | 1.17
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Output | 8e-06 | 8e-06 | 8e-06 | 0.0 | 0.00
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Modify | 2.7068 | 2.7068 | 2.7068 | 0.0 | 17.25
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Other | | 0.2573 | | | 1.64
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Nlocal: 10 ave 10 max 10 min
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Nlocal: 10.0 ave 10.0 max 10.0 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 0 ave 0 max 0 min
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Nghost: 0.0 ave 0.0 max 0.0 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 45 ave 45 max 45 min
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Neighs: 37.0 ave 37.0 max 37.0 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 45
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Ave neighs/atom = 4.5
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Total # of neighbors = 37
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Ave neighs/atom = 3.7
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Ave special neighs/atom = 3.6
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Neighbor list builds = 0
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Dangerous builds = 0
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#write_restart config.${number}.*
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Total wall time: 0:00:17
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Total wall time: 0:00:15
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@ -1,4 +1,4 @@
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LAMMPS (7 Aug 2019)
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LAMMPS (30 Jun 2020)
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variable number equal 1
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variable ofreq equal 1000
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variable efreq equal 1000
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@ -12,7 +12,10 @@ 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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@ -35,9 +38,8 @@ read_data data.duplex1
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2 = max # of 1-3 neighbors
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2 = max # of 1-4 neighbors
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4 = max # of special neighbors
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special bonds CPU = 0.000216 secs
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read_data CPU = 0.003061 secs
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special bonds CPU = 0.001 seconds
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read_data CPU = 0.003 seconds
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set atom * mass 3.1575
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10 settings made for mass
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@ -47,6 +49,12 @@ 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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2 = max # of 1-2 neighbors
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2 = max # of 1-3 neighbors
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2 = max # of 1-4 neighbors
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4 = 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 oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
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@ -69,6 +77,7 @@ 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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@ -99,9 +108,9 @@ run 1000000
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Neighbor list info ...
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update every 1 steps, delay 0 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 1.956
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ghost atom cutoff = 1.956
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binsize = 0.978, bins = 41 41 41
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master list distance cutoff = 1.9560004
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ghost atom cutoff = 2.5
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binsize = 0.97800022, bins = 41 41 41
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5 neighbor lists, perpetual/occasional/extra = 5 0 0
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(1) pair oxdna/excv, perpetual
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attributes: half, newton off
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@ -128,8 +137,8 @@ Neighbor list info ...
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pair build: copy
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stencil: none
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bin: none
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WARNING: Communication cutoff 1.956 is shorter than a bond length based estimate of 2.12875. This may lead to errors. (../comm.cpp:685)
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Per MPI rank memory allocation (min/avg/max) = 7.33 | 7.512 | 7.694 Mbytes
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0 ekin = 0 | erot = 0 | epot = -14.6424332448164 | etot = -14.6424332448164
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Per MPI rank memory allocation (min/avg/max) = 7.605 | 7.662 | 7.719 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 0 -1.4711818 0.0069384985 -1.4642433 2.5836586e-06
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1000 ekin = 0.00113448721737009 | erot = 0.0041345594773427 | epot = -14.6477022915193 | etot = -14.6424332448246
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@ -1133,34 +1142,34 @@ Step Temp E_pair E_mol TotEng Press
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999000 ekin = 0.18831584391307 | erot = 0.335221830005501 | epot = -15.1659709188615 | etot = -14.642433244943
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1000000 ekin = 0.181624323067755 | erot = 0.330966139649165 | epot = -15.1550237076395 | etot = -14.6424332449226
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1000000 0.013453654 -1.5270261 0.011523695 -1.4973399 -8.4815516e-05
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Loop time of 18.6281 on 4 procs for 1000000 steps with 10 atoms
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Loop time of 16.5005 on 4 procs for 1000000 steps with 10 atoms
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Performance: 46381.610 tau/day, 53682.419 timesteps/s
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Performance: 52362.058 tau/day, 60604.234 timesteps/s
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99.5% CPU use with 4 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.50691 | 7.0285 | 12.641 | 197.6 | 37.73
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Bond | 0.081876 | 0.27627 | 0.44175 | 28.5 | 1.48
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Pair | 0.51373 | 5.7702 | 10.408 | 174.5 | 34.97
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Bond | 0.084405 | 0.27056 | 0.44162 | 28.3 | 1.64
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 1.7692 | 2.0629 | 2.3468 | 17.0 | 11.07
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Output | 1.8e-05 | 2.625e-05 | 3e-05 | 0.0 | 0.00
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Modify | 0.17309 | 0.88362 | 1.5352 | 58.4 | 4.74
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Other | | 8.377 | | | 44.97
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Comm | 1.7403 | 2.0946 | 2.4247 | 18.8 | 12.69
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Output | 4e-05 | 6e-05 | 7.1e-05 | 0.0 | 0.00
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Modify | 0.17451 | 0.87938 | 1.53 | 58.2 | 5.33
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Other | | 7.486 | | | 45.37
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Nlocal: 2.5 ave 5 max 0 min
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Nlocal: 2.5 ave 5.0 max 0.0 min
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Histogram: 1 0 1 0 0 0 0 0 1 1
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Nghost: 7.5 ave 10 max 5 min
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Nghost: 7.5 ave 10.0 max 5.0 min
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Histogram: 1 0 1 0 0 0 0 0 1 1
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Neighs: 18.5 ave 35 max 0 min
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Neighs: 16.0 ave 30.0 max 0.0 min
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Histogram: 1 0 1 0 0 0 0 0 1 1
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Total # of neighbors = 74
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Ave neighs/atom = 7.4
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Total # of neighbors = 64
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Ave neighs/atom = 6.4
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Ave special neighs/atom = 3.6
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Neighbor list builds = 0
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Dangerous builds = 0
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#write_restart config.${number}.*
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Total wall time: 0:00:18
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Total wall time: 0:00:16
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@ -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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File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
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@ -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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@ -1,4 +1,4 @@
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LAMMPS (7 Aug 2019)
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LAMMPS (30 Jun 2020)
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variable number equal 1
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variable ofreq equal 1000
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variable efreq equal 1000
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@ -13,6 +13,7 @@ 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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@ -35,8 +36,8 @@ read_data data.duplex1
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2 = max # of 1-3 neighbors
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2 = max # of 1-4 neighbors
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4 = max # of special neighbors
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special bonds CPU = 0.000116 secs
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read_data CPU = 0.002026 secs
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special bonds CPU = 0.000 seconds
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read_data CPU = 0.003 seconds
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set atom * mass 3.1575
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10 settings made for mass
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@ -47,6 +48,12 @@ 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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2 = max # of 1-2 neighbors
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2 = max # of 1-3 neighbors
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2 = max # of 1-4 neighbors
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4 = max # of special neighbors
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special bonds CPU = 0.000 seconds
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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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@ -71,6 +78,7 @@ 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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@ -101,9 +109,9 @@ run 1000000
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Neighbor list info ...
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update every 1 steps, delay 0 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 2.6274
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ghost atom cutoff = 2.6274
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binsize = 1.3137, bins = 31 31 31
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master list distance cutoff = 2.6274048
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ghost atom cutoff = 2.6274048
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binsize = 1.3137024, bins = 31 31 31
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6 neighbor lists, perpetual/occasional/extra = 6 0 0
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(1) pair oxdna2/excv, perpetual
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attributes: half, newton off
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@ -135,7 +143,9 @@ Neighbor list info ...
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pair build: copy
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stencil: none
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bin: none
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Per MPI rank memory allocation (min/avg/max) = 3.024 | 3.024 | 3.024 Mbytes
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WARNING: Communication cutoff adjusted to 2.627404783947349 (../comm.cpp:690)
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0 ekin = 0 | erot = 0 | epot = -14.6175140343334 | etot = -14.6175140343334
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Per MPI rank memory allocation (min/avg/max) = 8.021 | 8.021 | 8.021 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 0 -1.4712768 0.009525411 -1.4617514 4.663076e-06
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1000 ekin = 0.00113086229080528 | erot = 0.0043101016040658 | epot = -14.6229549982368 | etot = -14.617514034342
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@ -1139,34 +1149,34 @@ Step Temp E_pair E_mol TotEng Press
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999000 ekin = 0.190992053959174 | erot = 0.320462575795008 | epot = -15.1289686644104 | etot = -14.6175140346562
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1000000 ekin = 0.179708146665509 | erot = 0.311553394429298 | epot = -15.1087755756885 | etot = -14.6175140345937
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1000000 0.013311715 -1.5443684 0.033490821 -1.4929067 -3.7544839e-05
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Loop time of 18.4193 on 1 procs for 1000000 steps with 10 atoms
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Loop time of 17.0535 on 1 procs for 1000000 steps with 10 atoms
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Performance: 46907.305 tau/day, 54290.862 timesteps/s
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Performance: 50663.947 tau/day, 58638.827 timesteps/s
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99.5% CPU use with 1 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
|
||||
Pair | 14.935 | 14.935 | 14.935 | 0.0 | 81.08
|
||||
Bond | 0.55556 | 0.55556 | 0.55556 | 0.0 | 3.02
|
||||
Pair | 13.135 | 13.135 | 13.135 | 0.0 | 77.02
|
||||
Bond | 0.6362 | 0.6362 | 0.6362 | 0.0 | 3.73
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.16028 | 0.16028 | 0.16028 | 0.0 | 0.87
|
||||
Output | 7e-06 | 7e-06 | 7e-06 | 0.0 | 0.00
|
||||
Modify | 2.5402 | 2.5402 | 2.5402 | 0.0 | 13.79
|
||||
Other | | 0.2285 | | | 1.24
|
||||
Comm | 0.18919 | 0.18919 | 0.18919 | 0.0 | 1.11
|
||||
Output | 8e-06 | 8e-06 | 8e-06 | 0.0 | 0.00
|
||||
Modify | 2.8399 | 2.8399 | 2.8399 | 0.0 | 16.65
|
||||
Other | | 0.2536 | | | 1.49
|
||||
|
||||
Nlocal: 10 ave 10 max 10 min
|
||||
Nlocal: 10.0 ave 10.0 max 10.0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Nghost: 0.0 ave 0.0 max 0.0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 45 ave 45 max 45 min
|
||||
Neighs: 37.0 ave 37.0 max 37.0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 45
|
||||
Ave neighs/atom = 4.5
|
||||
Total # of neighbors = 37
|
||||
Ave neighs/atom = 3.7
|
||||
Ave special neighs/atom = 3.6
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
#write_restart config.${number}.*
|
||||
Total wall time: 0:00:18
|
||||
Total wall time: 0:00:17
|
|
@ -1,4 +1,4 @@
|
|||
LAMMPS (7 Aug 2019)
|
||||
LAMMPS (30 Jun 2020)
|
||||
variable number equal 1
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
|
@ -13,6 +13,7 @@ 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
|
||||
|
@ -35,8 +36,8 @@ read_data data.duplex1
|
|||
2 = max # of 1-3 neighbors
|
||||
2 = max # of 1-4 neighbors
|
||||
4 = max # of special neighbors
|
||||
special bonds CPU = 0.000198 secs
|
||||
read_data CPU = 0.004522 secs
|
||||
special bonds CPU = 0.001 seconds
|
||||
read_data CPU = 0.004 seconds
|
||||
|
||||
set atom * mass 3.1575
|
||||
10 settings made for mass
|
||||
|
@ -47,6 +48,12 @@ group all type 1 4
|
|||
# oxDNA2 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
|
||||
2 = max # of 1-4 neighbors
|
||||
4 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
|
||||
# oxDNA2 pair interactions
|
||||
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
|
||||
|
@ -71,6 +78,7 @@ 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
|
||||
|
@ -101,9 +109,9 @@ run 1000000
|
|||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.6274
|
||||
ghost atom cutoff = 2.6274
|
||||
binsize = 1.3137, bins = 31 31 31
|
||||
master list distance cutoff = 2.6274048
|
||||
ghost atom cutoff = 2.6274048
|
||||
binsize = 1.3137024, bins = 31 31 31
|
||||
6 neighbor lists, perpetual/occasional/extra = 6 0 0
|
||||
(1) pair oxdna2/excv, perpetual
|
||||
attributes: half, newton off
|
||||
|
@ -135,7 +143,9 @@ Neighbor list info ...
|
|||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.653 | 7.835 | 8.018 Mbytes
|
||||
WARNING: Communication cutoff adjusted to 2.627404783947349 (../comm.cpp:690)
|
||||
0 ekin = 0 | erot = 0 | epot = -14.6175140343334 | etot = -14.6175140343334
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.903 | 7.96 | 8.018 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -1.4712768 0.009525411 -1.4617514 4.663076e-06
|
||||
1000 ekin = 0.00113086229080478 | erot = 0.00431010160406708 | epot = -14.6229549982368 | etot = -14.617514034342
|
||||
|
@ -1139,34 +1149,34 @@ Step Temp E_pair E_mol TotEng Press
|
|||
999000 ekin = 0.190992053959209 | erot = 0.320462575794744 | epot = -15.1289686644103 | etot = -14.6175140346563
|
||||
1000000 ekin = 0.179708146665587 | erot = 0.311553394428757 | epot = -15.1087755756882 | etot = -14.6175140345938
|
||||
1000000 0.013311715 -1.5443684 0.033490821 -1.4929067 -3.7544839e-05
|
||||
Loop time of 20.7945 on 4 procs for 1000000 steps with 10 atoms
|
||||
Loop time of 17.7119 on 4 procs for 1000000 steps with 10 atoms
|
||||
|
||||
Performance: 41549.361 tau/day, 48089.538 timesteps/s
|
||||
99.6% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
Performance: 48780.802 tau/day, 56459.261 timesteps/s
|
||||
99.5% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.66725 | 7.9254 | 14.304 | 209.9 | 38.11
|
||||
Bond | 0.095496 | 0.30973 | 0.49863 | 30.5 | 1.49
|
||||
Pair | 0.59564 | 6.28 | 11.307 | 181.3 | 35.46
|
||||
Bond | 0.083757 | 0.28777 | 0.47668 | 30.6 | 1.62
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 1.8943 | 2.1825 | 2.4604 | 15.6 | 10.50
|
||||
Output | 2e-05 | 2.9e-05 | 3.2e-05 | 0.0 | 0.00
|
||||
Modify | 0.18231 | 0.95644 | 1.673 | 62.4 | 4.60
|
||||
Other | | 9.421 | | | 45.30
|
||||
Comm | 1.8539 | 2.1875 | 2.4877 | 17.3 | 12.35
|
||||
Output | 2.1e-05 | 3.85e-05 | 4.5e-05 | 0.0 | 0.00
|
||||
Modify | 0.18254 | 0.92719 | 1.638 | 61.5 | 5.23
|
||||
Other | | 8.029 | | | 45.33
|
||||
|
||||
Nlocal: 2.5 ave 5 max 0 min
|
||||
Nlocal: 2.5 ave 5.0 max 0.0 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||
Nghost: 7.5 ave 10 max 5 min
|
||||
Nghost: 7.5 ave 10.0 max 5.0 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||
Neighs: 18.5 ave 35 max 0 min
|
||||
Neighs: 16.0 ave 30.0 max 0.0 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 74
|
||||
Ave neighs/atom = 7.4
|
||||
Total # of neighbors = 64
|
||||
Ave neighs/atom = 6.4
|
||||
Ave special neighs/atom = 3.6
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
#write_restart config.${number}.*
|
||||
Total wall time: 0:00:20
|
||||
Total wall time: 0:00:17
|
|
@ -27,6 +27,7 @@ group all type 1 4
|
|||
# oxDNA2 bond interactions - FENE backbone
|
||||
bond_style oxdna2/fene
|
||||
bond_coeff * 2.0 0.25 0.7564
|
||||
special_bonds lj 0 1 1
|
||||
|
||||
# oxDNA2 pair interactions
|
||||
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
|
||||
|
@ -49,6 +50,7 @@ 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
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
|
|||
# oxDNA2 bond interactions - FENE backbone
|
||||
bond_style oxdna2/fene
|
||||
bond_coeff * 2.0 0.25 0.7564
|
||||
special_bonds lj 0 1 1
|
||||
|
||||
# oxDNA2 pair interactions
|
||||
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
|
||||
|
@ -49,6 +50,7 @@ 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
|
||||
|
|
|
@ -1,4 +1,4 @@
|
|||
LAMMPS (7 Aug 2019)
|
||||
LAMMPS (30 Jun 2020)
|
||||
variable number equal 3
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
|
@ -13,6 +13,7 @@ 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
|
||||
|
@ -35,8 +36,8 @@ read_data data.duplex3
|
|||
2 = max # of 1-3 neighbors
|
||||
2 = max # of 1-4 neighbors
|
||||
4 = max # of special neighbors
|
||||
special bonds CPU = 0.000145 secs
|
||||
read_data CPU = 0.001965 secs
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.002 seconds
|
||||
|
||||
set atom * mass 1.0
|
||||
10 settings made for mass
|
||||
|
@ -47,6 +48,12 @@ group all type 1 4
|
|||
# oxDNA2 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
|
||||
2 = max # of 1-4 neighbors
|
||||
4 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
|
||||
# oxDNA2 pair interactions
|
||||
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
|
||||
|
@ -71,6 +78,7 @@ 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
|
||||
|
@ -101,9 +109,9 @@ run 1000000
|
|||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.6274
|
||||
ghost atom cutoff = 2.6274
|
||||
binsize = 1.3137, bins = 31 31 31
|
||||
master list distance cutoff = 2.6274048
|
||||
ghost atom cutoff = 2.6274048
|
||||
binsize = 1.3137024, bins = 31 31 31
|
||||
6 neighbor lists, perpetual/occasional/extra = 6 0 0
|
||||
(1) pair oxdna2/excv, perpetual
|
||||
attributes: half, newton off
|
||||
|
@ -135,7 +143,9 @@ Neighbor list info ...
|
|||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.024 | 3.024 | 3.024 Mbytes
|
||||
WARNING: Communication cutoff adjusted to 2.627404783947349 (../comm.cpp:690)
|
||||
0 ekin = 0 | erot = 0 | epot = -14.6249037416652 | etot = -14.6249037416652
|
||||
Per MPI rank memory allocation (min/avg/max) = 8.021 | 8.021 | 8.021 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -1.4720158 0.009525411 -1.4624904 3.1370518e-06
|
||||
1000 ekin = 0.00366431201929618 | erot = 0.00193726360267488 | epot = -14.630505317301 | etot = -14.624903741679
|
||||
|
@ -1139,34 +1149,34 @@ Step Temp E_pair E_mol TotEng Press
|
|||
999000 ekin = 0.330110494517114 | erot = 0.658973630822449 | epot = -15.6139878677246 | etot = -14.624903742385
|
||||
1000000 ekin = 0.345190458650495 | erot = 0.661138339466907 | epot = -15.6312325406154 | etot = -14.624903742498
|
||||
1000000 0.025569664 -1.5839232 0.020799898 -1.5286042 -3.5789082e-06
|
||||
Loop time of 25.9663 on 1 procs for 1000000 steps with 10 atoms
|
||||
Loop time of 16.5683 on 1 procs for 1000000 steps with 10 atoms
|
||||
|
||||
Performance: 33273.840 tau/day, 38511.388 timesteps/s
|
||||
99.6% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
Performance: 52147.644 tau/day, 60356.069 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 | 21.428 | 21.428 | 21.428 | 0.0 | 82.52
|
||||
Bond | 0.76981 | 0.76981 | 0.76981 | 0.0 | 2.96
|
||||
Pair | 12.734 | 12.734 | 12.734 | 0.0 | 76.86
|
||||
Bond | 0.62259 | 0.62259 | 0.62259 | 0.0 | 3.76
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.25709 | 0.25709 | 0.25709 | 0.0 | 0.99
|
||||
Output | 9e-06 | 9e-06 | 9e-06 | 0.0 | 0.00
|
||||
Modify | 3.1584 | 3.1584 | 3.1584 | 0.0 | 12.16
|
||||
Other | | 0.3534 | | | 1.36
|
||||
Comm | 0.18386 | 0.18386 | 0.18386 | 0.0 | 1.11
|
||||
Output | 7e-06 | 7e-06 | 7e-06 | 0.0 | 0.00
|
||||
Modify | 2.7788 | 2.7788 | 2.7788 | 0.0 | 16.77
|
||||
Other | | 0.2491 | | | 1.50
|
||||
|
||||
Nlocal: 10 ave 10 max 10 min
|
||||
Nlocal: 10.0 ave 10.0 max 10.0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Nghost: 0.0 ave 0.0 max 0.0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 45 ave 45 max 45 min
|
||||
Neighs: 37.0 ave 37.0 max 37.0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 45
|
||||
Ave neighs/atom = 4.5
|
||||
Total # of neighbors = 37
|
||||
Ave neighs/atom = 3.7
|
||||
Ave special neighs/atom = 3.6
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
#write_restart config.${number}.*
|
||||
Total wall time: 0:00:25
|
||||
Total wall time: 0:00:16
|
|
@ -1,4 +1,4 @@
|
|||
LAMMPS (7 Aug 2019)
|
||||
LAMMPS (30 Jun 2020)
|
||||
variable number equal 3
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
|
@ -13,6 +13,7 @@ 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
|
||||
|
@ -35,8 +36,8 @@ read_data data.duplex3
|
|||
2 = max # of 1-3 neighbors
|
||||
2 = max # of 1-4 neighbors
|
||||
4 = max # of special neighbors
|
||||
special bonds CPU = 0.000188 secs
|
||||
read_data CPU = 0.002791 secs
|
||||
special bonds CPU = 0.001 seconds
|
||||
read_data CPU = 0.004 seconds
|
||||
|
||||
set atom * mass 1.0
|
||||
10 settings made for mass
|
||||
|
@ -47,6 +48,12 @@ group all type 1 4
|
|||
# oxDNA2 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
|
||||
2 = max # of 1-4 neighbors
|
||||
4 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
|
||||
# oxDNA2 pair interactions
|
||||
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
|
||||
|
@ -71,6 +78,7 @@ 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
|
||||
|
@ -101,9 +109,9 @@ run 1000000
|
|||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.6274
|
||||
ghost atom cutoff = 2.6274
|
||||
binsize = 1.3137, bins = 31 31 31
|
||||
master list distance cutoff = 2.6274048
|
||||
ghost atom cutoff = 2.6274048
|
||||
binsize = 1.3137024, bins = 31 31 31
|
||||
6 neighbor lists, perpetual/occasional/extra = 6 0 0
|
||||
(1) pair oxdna2/excv, perpetual
|
||||
attributes: half, newton off
|
||||
|
@ -135,7 +143,9 @@ Neighbor list info ...
|
|||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.653 | 7.835 | 8.018 Mbytes
|
||||
WARNING: Communication cutoff adjusted to 2.627404783947349 (../comm.cpp:690)
|
||||
0 ekin = 0 | erot = 0 | epot = -14.6249037416652 | etot = -14.6249037416652
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.903 | 7.96 | 8.018 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -1.4720158 0.009525411 -1.4624904 3.1370518e-06
|
||||
1000 ekin = 0.00366431201929595 | erot = 0.00193726360268106 | epot = -14.630505317301 | etot = -14.624903741679
|
||||
|
@ -1139,34 +1149,34 @@ Step Temp E_pair E_mol TotEng Press
|
|||
999000 ekin = 0.330110494517446 | erot = 0.658973630822486 | epot = -15.613987867725 | etot = -14.6249037423851
|
||||
1000000 ekin = 0.345190458651126 | erot = 0.66113833946702 | epot = -15.6312325406162 | etot = -14.624903742498
|
||||
1000000 0.025569664 -1.5839232 0.020799898 -1.5286042 -3.5789082e-06
|
||||
Loop time of 20.0167 on 4 procs for 1000000 steps with 10 atoms
|
||||
Loop time of 17.6535 on 4 procs for 1000000 steps with 10 atoms
|
||||
|
||||
Performance: 43164.007 tau/day, 49958.342 timesteps/s
|
||||
Performance: 48942.073 tau/day, 56645.918 timesteps/s
|
||||
99.5% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.59089 | 7.5652 | 13.908 | 205.5 | 37.79
|
||||
Bond | 0.090803 | 0.29363 | 0.47758 | 29.6 | 1.47
|
||||
Pair | 0.58208 | 6.2309 | 11.391 | 182.5 | 35.30
|
||||
Bond | 0.087981 | 0.28429 | 0.45668 | 28.3 | 1.61
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 1.7298 | 2.0312 | 2.2983 | 16.6 | 10.15
|
||||
Output | 1.4e-05 | 2.075e-05 | 2.3e-05 | 0.0 | 0.00
|
||||
Modify | 0.17638 | 0.90613 | 1.5893 | 60.1 | 4.53
|
||||
Other | | 9.22 | | | 46.06
|
||||
Comm | 1.8415 | 2.1564 | 2.4456 | 17.3 | 12.21
|
||||
Output | 1.5e-05 | 2.275e-05 | 2.6e-05 | 0.0 | 0.00
|
||||
Modify | 0.1751 | 0.91094 | 1.6034 | 60.5 | 5.16
|
||||
Other | | 8.071 | | | 45.72
|
||||
|
||||
Nlocal: 2.5 ave 5 max 0 min
|
||||
Nlocal: 2.5 ave 5.0 max 0.0 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||
Nghost: 7.5 ave 10 max 5 min
|
||||
Nghost: 7.5 ave 10.0 max 5.0 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||
Neighs: 18.5 ave 35 max 0 min
|
||||
Neighs: 16.0 ave 30.0 max 0.0 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 74
|
||||
Ave neighs/atom = 7.4
|
||||
Total # of neighbors = 64
|
||||
Ave neighs/atom = 6.4
|
||||
Ave special neighs/atom = 3.6
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
#write_restart config.${number}.*
|
||||
Total wall time: 0:00:20
|
||||
Total wall time: 0:00:17
|
|
@ -18,17 +18,19 @@ atom_style hybrid bond ellipsoid
|
|||
atom_modify sort 0 1.0
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 2.0 bin
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 10 delay 0 check yes
|
||||
|
||||
read_data data.duplex4.4type
|
||||
mass * 3.1575
|
||||
mass * 3.1575 # sets per-type mass if not in data file
|
||||
set atom * mass 3.1575 # sets per-atom mass
|
||||
|
||||
group all type 1 4
|
||||
|
||||
# oxDNA bond interactions - FENE backbone
|
||||
bond_style oxdna2/fene
|
||||
bond_coeff * 2.0 0.25 0.7564
|
||||
special_bonds lj 0 1 1
|
||||
|
||||
# oxDNA pair interactions
|
||||
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
|
||||
|
@ -60,6 +62,7 @@ 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
|
||||
|
|
|
@ -10,7 +10,7 @@ units lj
|
|||
|
||||
dimension 3
|
||||
|
||||
newton on
|
||||
newton off
|
||||
|
||||
boundary p p p
|
||||
|
||||
|
@ -22,13 +22,15 @@ neighbor 1.0 bin
|
|||
neigh_modify every 10 delay 0 check yes
|
||||
|
||||
read_data data.duplex4.8type
|
||||
mass * 3.1575
|
||||
mass * 3.1575 # sets per-type mass if not in data file
|
||||
set atom * mass 3.1575 # sets per-atom mass
|
||||
|
||||
group all type 1 8
|
||||
|
||||
# oxDNA bond interactions - FENE backbone
|
||||
bond_style oxdna2/fene
|
||||
bond_coeff * 2.0 0.25 0.7564
|
||||
special_bonds lj 0 1 1
|
||||
|
||||
# oxDNA pair interactions
|
||||
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
|
||||
|
@ -60,6 +62,7 @@ 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
|
||||
|
|
|
@ -1,4 +1,4 @@
|
|||
LAMMPS (7 Aug 2019)
|
||||
LAMMPS (30 Jun 2020)
|
||||
variable number equal 1
|
||||
variable ofreq equal 10000
|
||||
variable efreq equal 10000
|
||||
|
@ -16,10 +16,11 @@ 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 2.0 bin
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 10 delay 0 check yes
|
||||
|
||||
read_data data.duplex4.4type
|
||||
|
@ -38,9 +39,11 @@ read_data data.duplex4.4type
|
|||
2 = max # of 1-3 neighbors
|
||||
4 = max # of 1-4 neighbors
|
||||
6 = max # of special neighbors
|
||||
special bonds CPU = 6.2e-05 secs
|
||||
read_data CPU = 0.001124 secs
|
||||
mass * 3.1575
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.003 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
|
||||
|
@ -48,6 +51,12 @@ group all type 1 4
|
|||
# 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
|
||||
|
@ -115,6 +124,7 @@ 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
|
||||
|
@ -149,9 +159,9 @@ 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 = 5.63899
|
||||
ghost atom cutoff = 5.63899
|
||||
binsize = 2.81949, bins = 15 15 15
|
||||
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
|
||||
|
@ -183,47 +193,49 @@ Neighbor list info ...
|
|||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.89 | 3.89 | 3.89 Mbytes
|
||||
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 = 1.01296379553452 | erot = 1.38476360245491 | epot = -41.9785360036035 | etot = -39.5808086056141
|
||||
20000 ekin = 1.75607695499755 | erot = 1.86620102096623 | epot = -41.9558496477913 | etot = -38.3335716718275
|
||||
30000 ekin = 2.25878673688255 | erot = 2.60035907744906 | epot = -41.2869827431736 | etot = -36.427836928842
|
||||
40000 ekin = 2.11105717434601 | erot = 3.16611217122795 | epot = -40.2762731426449 | etot = -34.999103797071
|
||||
50000 ekin = 3.05379083545185 | erot = 2.45050275456902 | epot = -40.3032957287999 | etot = -34.799002138779
|
||||
60000 ekin = 3.05154113920288 | erot = 2.52539576708931 | epot = -39.6800099891302 | etot = -34.103073082838
|
||||
70000 ekin = 3.23212209366503 | erot = 3.28914763888578 | epot = -40.1240667487288 | etot = -33.602797016178
|
||||
80000 ekin = 2.82623224207568 | erot = 2.91292948677805 | epot = -39.0983962904507 | etot = -33.3592345615969
|
||||
90000 ekin = 3.05995314905566 | erot = 3.5429982411034 | epot = -39.1646070343971 | etot = -32.561655644238
|
||||
100000 ekin = 3.46139546969836 | erot = 4.11704803295073 | epot = -38.5124679837256 | etot = -30.9340244810765
|
||||
100000 0.092303879 -1.5243833 0.043134544 -1.3481182 6.862374e-06
|
||||
Loop time of 7.99505 on 1 procs for 100000 steps with 26 atoms
|
||||
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: 108066.893 tau/day, 12507.742 timesteps/s
|
||||
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 | 7.2072 | 7.2072 | 7.2072 | 0.0 | 90.15
|
||||
Bond | 0.14292 | 0.14292 | 0.14292 | 0.0 | 1.79
|
||||
Neigh | 1.9e-05 | 1.9e-05 | 1.9e-05 | 0.0 | 0.00
|
||||
Comm | 0.015676 | 0.015676 | 0.015676 | 0.0 | 0.20
|
||||
Output | 0.001372 | 0.001372 | 0.001372 | 0.0 | 0.02
|
||||
Modify | 0.61071 | 0.61071 | 0.61071 | 0.0 | 7.64
|
||||
Other | | 0.01714 | | | 0.21
|
||||
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 ave 26 max 26 min
|
||||
Nlocal: 26.0 ave 26.0 max 26.0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Nghost: 0.0 ave 0.0 max 0.0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 325 ave 325 max 325 min
|
||||
Neighs: 299.0 ave 299.0 max 299.0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 325
|
||||
Ave neighs/atom = 12.5
|
||||
Ave special neighs/atom = 5.07692
|
||||
Neighbor list builds = 1
|
||||
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}.*
|
|
@ -1,4 +1,4 @@
|
|||
LAMMPS (7 Aug 2019)
|
||||
LAMMPS (30 Jun 2020)
|
||||
variable number equal 1
|
||||
variable ofreq equal 10000
|
||||
variable efreq equal 10000
|
||||
|
@ -16,10 +16,11 @@ 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 2.0 bin
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 10 delay 0 check yes
|
||||
|
||||
read_data data.duplex4.4type
|
||||
|
@ -38,9 +39,11 @@ read_data data.duplex4.4type
|
|||
2 = max # of 1-3 neighbors
|
||||
4 = max # of 1-4 neighbors
|
||||
6 = max # of special neighbors
|
||||
special bonds CPU = 0.000173 secs
|
||||
read_data CPU = 0.00242 secs
|
||||
mass * 3.1575
|
||||
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
|
||||
|
@ -48,6 +51,12 @@ group all type 1 4
|
|||
# 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
|
||||
|
@ -115,6 +124,7 @@ 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
|
||||
|
@ -149,9 +159,9 @@ 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 = 5.63899
|
||||
ghost atom cutoff = 5.63899
|
||||
binsize = 2.81949, bins = 15 15 15
|
||||
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
|
||||
|
@ -183,50 +193,52 @@ Neighbor list info ...
|
|||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 9.499 | 9.682 | 9.864 Mbytes
|
||||
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 = 1.20524984175817 | erot = 1.2679122962101 | epot = -41.9183873815797 | etot = -39.4452252436114
|
||||
20000 ekin = 1.60856540355485 | erot = 2.64140880508964 | epot = -41.0106168994545 | etot = -36.76064269081
|
||||
30000 ekin = 2.821101638199 | erot = 3.06373823252434 | epot = -40.9348041675027 | etot = -35.0499642967793
|
||||
40000 ekin = 2.36296917392486 | erot = 3.53353555114673 | epot = -39.5591676362755 | etot = -33.6626629112039
|
||||
50000 ekin = 2.93383938780818 | erot = 3.39920211088179 | epot = -40.3602175538497 | etot = -34.0271760551597
|
||||
60000 ekin = 2.42811021532829 | erot = 2.75130045540831 | epot = -39.3178531324554 | etot = -34.1384424617188
|
||||
70000 ekin = 2.7282200818863 | erot = 3.76502037022117 | epot = -40.5673105068195 | etot = -34.074070054712
|
||||
80000 ekin = 2.90877851656705 | erot = 2.43617899356904 | epot = -38.4099618426175 | etot = -33.0650043324814
|
||||
90000 ekin = 3.89203816080263 | erot = 2.67194811393274 | epot = -39.1880466354802 | etot = -32.6240603607448
|
||||
100000 ekin = 3.98445325397832 | erot = 2.77079124049636 | epot = -39.2805505658488 | etot = -32.5253060713741
|
||||
100000 0.10625209 -1.5603519 0.049561514 -1.3575422 -1.7755557e-05
|
||||
Loop time of 7.14827 on 4 procs for 100000 steps with 26 atoms
|
||||
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: 120868.376 tau/day, 13989.395 timesteps/s
|
||||
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 | 0.047776 | 3.0726 | 6.3143 | 172.8 | 42.98
|
||||
Bond | 0.00736 | 0.056846 | 0.10864 | 20.7 | 0.80
|
||||
Neigh | 1.9e-05 | 1.9e-05 | 1.9e-05 | 0.0 | 0.00
|
||||
Comm | 0.30925 | 3.451 | 6.3739 | 157.5 | 48.28
|
||||
Output | 0.000896 | 0.0010197 | 0.001301 | 0.5 | 0.01
|
||||
Modify | 0.015512 | 0.18417 | 0.37845 | 39.4 | 2.58
|
||||
Other | | 0.3826 | | | 5.35
|
||||
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 13 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Nghost: 19.5 ave 26 max 13 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Neighs: 123.5 ave 247 max 0 min
|
||||
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 = 494
|
||||
Ave neighs/atom = 19
|
||||
Ave special neighs/atom = 5.07692
|
||||
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: 0:00:07
|
||||
Total wall time: 0:00:06
|
|
@ -1,4 +1,4 @@
|
|||
LAMMPS (7 Aug 2019)
|
||||
LAMMPS (30 Jun 2020)
|
||||
variable number equal 1
|
||||
variable ofreq equal 10000
|
||||
variable efreq equal 10000
|
||||
|
@ -11,11 +11,12 @@ units lj
|
|||
|
||||
dimension 3
|
||||
|
||||
newton on
|
||||
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
|
||||
|
@ -31,16 +32,18 @@ read_data data.duplex4.8type
|
|||
26 velocities
|
||||
26 ellipsoids
|
||||
scanning bonds ...
|
||||
1 = max bonds/atom
|
||||
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 = 6.5e-05 secs
|
||||
read_data CPU = 0.001139 secs
|
||||
mass * 3.1575
|
||||
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
|
||||
|
@ -48,6 +51,12 @@ group all type 1 8
|
|||
# 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
|
||||
|
@ -157,6 +166,7 @@ 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
|
||||
|
@ -191,81 +201,83 @@ 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 = 4.63899
|
||||
ghost atom cutoff = 4.63899
|
||||
binsize = 2.31949, bins = 18 18 18
|
||||
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 on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
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 on
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) pair oxdna2/hbond, perpetual, copy from (1)
|
||||
attributes: half, newton on
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(4) pair oxdna2/xstk, perpetual, copy from (1)
|
||||
attributes: half, newton on
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(5) pair oxdna2/coaxstk, perpetual, copy from (1)
|
||||
attributes: half, newton on
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(6) pair oxdna2/dh, perpetual, copy from (1)
|
||||
attributes: half, newton on
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.905 | 3.905 | 3.905 Mbytes
|
||||
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 = 1.0129637955345 | erot = 1.38476360245492 | epot = -41.9785360036034 | etot = -39.580808605614
|
||||
20000 ekin = 1.75607695499755 | erot = 1.86620102096618 | epot = -41.9558496477911 | etot = -38.3335716718274
|
||||
30000 ekin = 2.25878673688259 | erot = 2.60035907744898 | epot = -41.2869827431736 | etot = -36.427836928842
|
||||
40000 ekin = 2.11105717434584 | erot = 3.16611217122799 | epot = -40.2762731426449 | etot = -34.9991037970711
|
||||
50000 ekin = 3.05379083545187 | erot = 2.45050275456888 | epot = -40.3032957287998 | etot = -34.7990021387791
|
||||
60000 ekin = 3.05154113920291 | erot = 2.5253957670889 | epot = -39.6800099891299 | etot = -34.1030730828381
|
||||
70000 ekin = 3.23212209366464 | erot = 3.28914763888543 | epot = -40.1240667487278 | etot = -33.6027970161777
|
||||
80000 ekin = 2.82623224207591 | erot = 2.91292948677732 | epot = -39.0983962904496 | etot = -33.3592345615963
|
||||
90000 ekin = 3.05995314905694 | erot = 3.54299824110274 | epot = -39.164607034397 | etot = -32.5616556442373
|
||||
100000 ekin = 3.46139546969892 | erot = 4.11704803295143 | epot = -38.512467983727 | etot = -30.9340244810767
|
||||
100000 0.092303879 -1.5243833 0.043134544 -1.3481182 6.862374e-06
|
||||
Loop time of 7.94086 on 1 procs for 100000 steps with 26 atoms
|
||||
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: 108804.336 tau/day, 12593.094 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
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 | 7.1507 | 7.1507 | 7.1507 | 0.0 | 90.05
|
||||
Bond | 0.14487 | 0.14487 | 0.14487 | 0.0 | 1.82
|
||||
Neigh | 6.4e-05 | 6.4e-05 | 6.4e-05 | 0.0 | 0.00
|
||||
Comm | 0.032259 | 0.032259 | 0.032259 | 0.0 | 0.41
|
||||
Output | 0.003484 | 0.003484 | 0.003484 | 0.0 | 0.04
|
||||
Modify | 0.59013 | 0.59013 | 0.59013 | 0.0 | 7.43
|
||||
Other | | 0.01934 | | | 0.24
|
||||
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 ave 26 max 26 min
|
||||
Nlocal: 26.0 ave 26.0 max 26.0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Nghost: 0.0 ave 0.0 max 0.0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 323 ave 323 max 323 min
|
||||
Neighs: 299.0 ave 299.0 max 299.0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 323
|
||||
Ave neighs/atom = 12.4231
|
||||
Ave special neighs/atom = 5.07692
|
||||
Neighbor list builds = 4
|
||||
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}.*
|
|
@ -1,4 +1,4 @@
|
|||
LAMMPS (7 Aug 2019)
|
||||
LAMMPS (30 Jun 2020)
|
||||
variable number equal 1
|
||||
variable ofreq equal 10000
|
||||
variable efreq equal 10000
|
||||
|
@ -11,11 +11,12 @@ units lj
|
|||
|
||||
dimension 3
|
||||
|
||||
newton on
|
||||
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
|
||||
|
@ -31,16 +32,18 @@ read_data data.duplex4.8type
|
|||
26 velocities
|
||||
26 ellipsoids
|
||||
scanning bonds ...
|
||||
1 = max bonds/atom
|
||||
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 = 0.000232 secs
|
||||
read_data CPU = 0.002447 secs
|
||||
mass * 3.1575
|
||||
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
|
||||
|
@ -48,6 +51,12 @@ group all type 1 8
|
|||
# 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
|
||||
|
@ -157,6 +166,7 @@ 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
|
||||
|
@ -191,84 +201,86 @@ 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 = 4.63899
|
||||
ghost atom cutoff = 4.63899
|
||||
binsize = 2.31949, bins = 18 18 18
|
||||
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 on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
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 on
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) pair oxdna2/hbond, perpetual, copy from (1)
|
||||
attributes: half, newton on
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(4) pair oxdna2/xstk, perpetual, copy from (1)
|
||||
attributes: half, newton on
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(5) pair oxdna2/coaxstk, perpetual, copy from (1)
|
||||
attributes: half, newton on
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(6) pair oxdna2/dh, perpetual, copy from (1)
|
||||
attributes: half, newton on
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 9.381 | 9.563 | 9.746 Mbytes
|
||||
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 = 1.20524984175816 | erot = 1.26791229621008 | epot = -41.9183873815797 | etot = -39.4452252436115
|
||||
20000 ekin = 1.6085654035548 | erot = 2.6414088050897 | epot = -41.0106168994546 | etot = -36.7606426908101
|
||||
30000 ekin = 2.82110163819891 | erot = 3.06373823252419 | epot = -40.9348041675026 | etot = -35.0499642967795
|
||||
40000 ekin = 2.35553603700794 | erot = 3.60405945883761 | epot = -39.5418687902286 | etot = -33.5822732943831
|
||||
50000 ekin = 3.06061403125833 | erot = 3.35548669087246 | epot = -40.3236585928169 | etot = -33.9075578706861
|
||||
60000 ekin = 2.7347216991605 | erot = 4.23926242244084 | epot = -39.5379959923263 | etot = -32.564011870725
|
||||
70000 ekin = 3.46562604991873 | erot = 2.8521307045909 | epot = -38.7237000550356 | etot = -32.4059433005259
|
||||
80000 ekin = 3.17815543267806 | erot = 3.11078099027451 | epot = -39.7525036398366 | etot = -33.463567216884
|
||||
90000 ekin = 3.51635117668857 | erot = 2.58384069017333 | epot = -39.4762533092413 | etot = -33.3760614423795
|
||||
100000 ekin = 3.64218174280962 | erot = 2.88607181210736 | epot = -37.6002449519119 | etot = -31.0719913969949
|
||||
100000 0.097124846 -1.5164679 0.070304678 -1.3060794 -2.9111933e-05
|
||||
Loop time of 5.64462 on 4 procs for 100000 steps with 26 atoms
|
||||
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: 153066.031 tau/day, 17715.976 timesteps/s
|
||||
99.0% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
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 | 0.069668 | 2.1601 | 4.2189 | 138.7 | 38.27
|
||||
Bond | 0.008542 | 0.052544 | 0.095929 | 18.7 | 0.93
|
||||
Neigh | 4.8e-05 | 5.6e-05 | 6.4e-05 | 0.0 | 0.00
|
||||
Comm | 0.90402 | 3.1443 | 5.4155 | 124.9 | 55.70
|
||||
Output | 0.001003 | 0.0011317 | 0.001468 | 0.6 | 0.02
|
||||
Modify | 0.021098 | 0.20024 | 0.38154 | 39.2 | 3.55
|
||||
Other | | 0.0863 | | | 1.53
|
||||
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 13 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Nghost: 17.5 ave 22 max 13 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Neighs: 80.25 ave 167 max 0 min
|
||||
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 = 321
|
||||
Ave neighs/atom = 12.3462
|
||||
Ave special neighs/atom = 5.07692
|
||||
Neighbor list builds = 3
|
||||
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: 0:00:05
|
||||
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
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
|
@ -328,9 +328,8 @@ void BondOxdnaFene::coeff(int narg, char **arg)
|
|||
|
||||
void BondOxdnaFene::init_style()
|
||||
{
|
||||
if (force->special_lj[1] != 0.0 || force->special_lj[2] != 1.0 || force->special_lj[3] != 1.0 ||
|
||||
force->special_coul[1] != 1.0 || force->special_coul[2] != 1.0 || force->special_coul[3] != 1.0)
|
||||
error->all(FLERR,"Must use 'special_bonds lj 0 1 1 coul 1 1 1' with bond style oxdna/fene");
|
||||
if (force->special_lj[1] != 0.0 || force->special_lj[2] != 1.0 || force->special_lj[3] != 1.0)
|
||||
error->all(FLERR,"Must use 'special_bonds lj 0 1 1' with bond style oxdna/fene, oxdna2/fene or oxrna2/fene");
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
|
Loading…
Reference in New Issue