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Added special_bonds command to input files

This commit is contained in:
Oliver Henrich 2020-07-03 21:03:24 +01:00
parent 17e419e251
commit 8dae5d5fc7
31 changed files with 7517 additions and 7340 deletions
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2
examples/USER/cgdna/examples/oxDNA/duplex1/in.duplex1
View File

@ -27,6 +27,7 @@ group all type 1 4
# oxDNA bond interactions - FENE backbone
bond_style oxdna/fene
bond_coeff * 2.0 0.25 0.7525
special_bonds lj 0 1 1
# oxDNA pair interactions
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
@ -48,6 +49,7 @@ 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

55
examples/USER/cgdna/examples/oxDNA/duplex1/log.07Aug19.duplex1.g++.1 → examples/USER/cgdna/examples/oxDNA/duplex1/log.30Jun20.duplex1.g++.1
View File

@ -1,4 +1,4 @@
LAMMPS (7 Aug 2019)
LAMMPS (30 Jun 2020)
variable number equal 1
variable ofreq equal 1000
variable efreq equal 1000
@ -12,7 +12,10 @@ 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
@ -35,9 +38,8 @@ read_data data.duplex1
2 = max # of 1-3 neighbors
2 = max # of 1-4 neighbors
4 = max # of special neighbors
special bonds CPU = 9.5e-05 secs
read_data CPU = 0.001865 secs
special bonds CPU = 0.000 seconds
read_data CPU = 0.002 seconds
set atom * mass 3.1575
10 settings made for mass
@ -47,6 +49,12 @@ group all type 1 4
# oxDNA bond interactions - FENE backbone
bond_style oxdna/fene
bond_coeff * 2.0 0.25 0.7525
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
# oxDNA pair interactions
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
@ -69,6 +77,7 @@ 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
@ -99,9 +108,9 @@ 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 = 1.956
ghost atom cutoff = 1.956
binsize = 0.978, bins = 41 41 41
master list distance cutoff = 1.9560004
ghost atom cutoff = 2.5
binsize = 0.97800022, bins = 41 41 41
5 neighbor lists, perpetual/occasional/extra = 5 0 0
(1) pair oxdna/excv, perpetual
attributes: half, newton off
@ -128,8 +137,8 @@ Neighbor list info ...
pair build: copy
stencil: none
bin: none
WARNING: Communication cutoff 1.956 is shorter than a bond length based estimate of 2.12875. This may lead to errors. (../comm.cpp:685)
Per MPI rank memory allocation (min/avg/max) = 2.836 | 2.836 | 2.836 Mbytes
0 ekin = 0 | erot = 0 | epot = -14.6424332448164 | etot = -14.6424332448164
Per MPI rank memory allocation (min/avg/max) = 7.883 | 7.883 | 7.883 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -1.4711818 0.0069384985 -1.4642433 2.5836586e-06
1000 ekin = 0.00113448721737003 | erot = 0.00413455947734281 | epot = -14.6477022915193 | etot = -14.6424332448246
@ -1133,34 +1142,34 @@ Step Temp E_pair E_mol TotEng Press
999000 ekin = 0.188315843917336 | erot = 0.335221830001114 | epot = -15.1659709188676 | etot = -14.6424332449491
1000000 ekin = 0.1816243230724 | erot = 0.33096613964385 | epot = -15.155023707645 | etot = -14.6424332449287
1000000 0.013453654 -1.5270261 0.011523695 -1.4973399 -8.4815516e-05
Loop time of 17.1797 on 1 procs for 1000000 steps with 10 atoms
Loop time of 15.696 on 1 procs for 1000000 steps with 10 atoms
Performance: 50291.944 tau/day, 58208.268 timesteps/s
Performance: 55045.770 tau/day, 63710.382 timesteps/s
99.6% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 13.871 | 13.871 | 13.871 | 0.0 | 80.74
Bond | 0.52454 | 0.52454 | 0.52454 | 0.0 | 3.05
Pair | 11.973 | 11.973 | 11.973 | 0.0 | 76.28
Bond | 0.57492 | 0.57492 | 0.57492 | 0.0 | 3.66
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.14987 | 0.14987 | 0.14987 | 0.0 | 0.87
Output | 7e-06 | 7e-06 | 7e-06 | 0.0 | 0.00
Modify | 2.4075 | 2.4075 | 2.4075 | 0.0 | 14.01
Other | | 0.227 | | | 1.32
Comm | 0.18391 | 0.18391 | 0.18391 | 0.0 | 1.17
Output | 8e-06 | 8e-06 | 8e-06 | 0.0 | 0.00
Modify | 2.7068 | 2.7068 | 2.7068 | 0.0 | 17.25
Other | | 0.2573 | | | 1.64
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: 0:00:17
Total wall time: 0:00:15

55
examples/USER/cgdna/examples/oxDNA/duplex1/log.07Aug19.duplex1.g++.4 → examples/USER/cgdna/examples/oxDNA/duplex1/log.30Jun20.duplex1.g++.4
View File

@ -1,4 +1,4 @@
LAMMPS (7 Aug 2019)
LAMMPS (30 Jun 2020)
variable number equal 1
variable ofreq equal 1000
variable efreq equal 1000
@ -12,7 +12,10 @@ 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
@ -35,9 +38,8 @@ read_data data.duplex1
2 = max # of 1-3 neighbors
2 = max # of 1-4 neighbors
4 = max # of special neighbors
special bonds CPU = 0.000216 secs
read_data CPU = 0.003061 secs
special bonds CPU = 0.001 seconds
read_data CPU = 0.003 seconds
set atom * mass 3.1575
10 settings made for mass
@ -47,6 +49,12 @@ group all type 1 4
# oxDNA bond interactions - FENE backbone
bond_style oxdna/fene
bond_coeff * 2.0 0.25 0.7525
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
# oxDNA pair interactions
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
@ -69,6 +77,7 @@ 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
@ -99,9 +108,9 @@ 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 = 1.956
ghost atom cutoff = 1.956
binsize = 0.978, bins = 41 41 41
master list distance cutoff = 1.9560004
ghost atom cutoff = 2.5
binsize = 0.97800022, bins = 41 41 41
5 neighbor lists, perpetual/occasional/extra = 5 0 0
(1) pair oxdna/excv, perpetual
attributes: half, newton off
@ -128,8 +137,8 @@ Neighbor list info ...
pair build: copy
stencil: none
bin: none
WARNING: Communication cutoff 1.956 is shorter than a bond length based estimate of 2.12875. This may lead to errors. (../comm.cpp:685)
Per MPI rank memory allocation (min/avg/max) = 7.33 | 7.512 | 7.694 Mbytes
0 ekin = 0 | erot = 0 | epot = -14.6424332448164 | etot = -14.6424332448164
Per MPI rank memory allocation (min/avg/max) = 7.605 | 7.662 | 7.719 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -1.4711818 0.0069384985 -1.4642433 2.5836586e-06
1000 ekin = 0.00113448721737009 | erot = 0.0041345594773427 | epot = -14.6477022915193 | etot = -14.6424332448246
@ -1133,34 +1142,34 @@ Step Temp E_pair E_mol TotEng Press
999000 ekin = 0.18831584391307 | erot = 0.335221830005501 | epot = -15.1659709188615 | etot = -14.642433244943
1000000 ekin = 0.181624323067755 | erot = 0.330966139649165 | epot = -15.1550237076395 | etot = -14.6424332449226
1000000 0.013453654 -1.5270261 0.011523695 -1.4973399 -8.4815516e-05
Loop time of 18.6281 on 4 procs for 1000000 steps with 10 atoms
Loop time of 16.5005 on 4 procs for 1000000 steps with 10 atoms
Performance: 46381.610 tau/day, 53682.419 timesteps/s
Performance: 52362.058 tau/day, 60604.234 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 | 0.50691 | 7.0285 | 12.641 | 197.6 | 37.73
Bond | 0.081876 | 0.27627 | 0.44175 | 28.5 | 1.48
Pair | 0.51373 | 5.7702 | 10.408 | 174.5 | 34.97
Bond | 0.084405 | 0.27056 | 0.44162 | 28.3 | 1.64
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 1.7692 | 2.0629 | 2.3468 | 17.0 | 11.07
Output | 1.8e-05 | 2.625e-05 | 3e-05 | 0.0 | 0.00
Modify | 0.17309 | 0.88362 | 1.5352 | 58.4 | 4.74
Other | | 8.377 | | | 44.97
Comm | 1.7403 | 2.0946 | 2.4247 | 18.8 | 12.69
Output | 4e-05 | 6e-05 | 7.1e-05 | 0.0 | 0.00
Modify | 0.17451 | 0.87938 | 1.53 | 58.2 | 5.33
Other | | 7.486 | | | 45.37
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: 0:00:18
Total wall time: 0:00:16

2
examples/USER/cgdna/examples/oxDNA/duplex2/in.duplex2
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@ -27,6 +27,7 @@ group all type 1 4
# oxDNA bond interactions - FENE backbone
bond_style oxdna/fene
bond_coeff * 2.0 0.25 0.7525
special_bonds lj 0 1 1
# oxDNA pair interactions
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
@ -48,6 +49,7 @@ 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

1168
examples/USER/cgdna/examples/oxDNA/duplex2/log.07Aug19.duplex2.g++.1
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examples/USER/cgdna/examples/oxDNA/duplex2/log.07Aug19.duplex2.g++.4
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examples/USER/cgdna/examples/oxDNA/duplex2/log.30Jun20.duplex2.g++.1 Normal file
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examples/USER/cgdna/examples/oxDNA/duplex2/log.30Jun20.duplex2.g++.4 Normal file
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2
examples/USER/cgdna/examples/oxDNA2/duplex1/in.duplex1
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@ -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

52
examples/USER/cgdna/examples/oxDNA2/duplex1/log.07Aug19.duplex1.g++.1 → examples/USER/cgdna/examples/oxDNA2/duplex1/log.30Jun20.duplex1.g++.1
View File

@ -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 = 0.000116 secs
read_data CPU = 0.002026 secs
special bonds CPU = 0.000 seconds
read_data CPU = 0.003 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) = 3.024 | 3.024 | 3.024 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) = 8.021 | 8.021 | 8.021 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -1.4712768 0.009525411 -1.4617514 4.663076e-06
1000 ekin = 0.00113086229080528 | erot = 0.0043101016040658 | epot = -14.6229549982368 | etot = -14.617514034342
@ -1139,34 +1149,34 @@ Step Temp E_pair E_mol TotEng Press
999000 ekin = 0.190992053959174 | erot = 0.320462575795008 | epot = -15.1289686644104 | etot = -14.6175140346562
1000000 ekin = 0.179708146665509 | erot = 0.311553394429298 | epot = -15.1087755756885 | etot = -14.6175140345937
1000000 0.013311715 -1.5443684 0.033490821 -1.4929067 -3.7544839e-05
Loop time of 18.4193 on 1 procs for 1000000 steps with 10 atoms
Loop time of 17.0535 on 1 procs for 1000000 steps with 10 atoms
Performance: 46907.305 tau/day, 54290.862 timesteps/s
Performance: 50663.947 tau/day, 58638.827 timesteps/s
99.5% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
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

54
examples/USER/cgdna/examples/oxDNA2/duplex1/log.07Aug19.duplex1.g++.4 → examples/USER/cgdna/examples/oxDNA2/duplex1/log.30Jun20.duplex1.g++.4
View File

@ -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

2
examples/USER/cgdna/examples/oxDNA2/duplex2/in.duplex2
View File

@ -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

1174
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2
examples/USER/cgdna/examples/oxDNA2/duplex3/in.duplex3
View File

@ -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

54
examples/USER/cgdna/examples/oxDNA2/duplex3/log.07Aug19.duplex3.g++.1 → examples/USER/cgdna/examples/oxDNA2/duplex3/log.30Jun20.duplex3.g++.1
View File

@ -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

52
examples/USER/cgdna/examples/oxDNA2/duplex3/log.07Aug19.duplex3.g++.4 → examples/USER/cgdna/examples/oxDNA2/duplex3/log.30Jun20.duplex3.g++.4
View File

@ -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

7
examples/USER/cgdna/examples/oxDNA2/unique_bp/in.duplex4.4type
View File

@ -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

7
examples/USER/cgdna/examples/oxDNA2/unique_bp/in.duplex4.8type
View File

@ -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

84
examples/USER/cgdna/examples/oxDNA2/unique_bp/log.07Aug19.duplex4.4type.g++1 → examples/USER/cgdna/examples/oxDNA2/unique_bp/log.30Jun20.duplex4.4type.g++1
View File

@ -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}.*

88
examples/USER/cgdna/examples/oxDNA2/unique_bp/log.07Aug19.duplex4.4type.g++4 → examples/USER/cgdna/examples/oxDNA2/unique_bp/log.30Jun20.duplex4.4type.g++4
View File

@ -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

104
examples/USER/cgdna/examples/oxDNA2/unique_bp/log.07Aug19.duplex4.8type.g++1 → examples/USER/cgdna/examples/oxDNA2/unique_bp/log.30Jun20.duplex4.8type.g++1
View File

@ -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}.*

110
examples/USER/cgdna/examples/oxDNA2/unique_bp/log.07Aug19.duplex4.8type.g++4 → examples/USER/cgdna/examples/oxDNA2/unique_bp/log.30Jun20.duplex4.8type.g++4
View File

@ -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

2
examples/USER/cgdna/examples/oxRNA2/duplex4/in.duplex4
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@ -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

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5
src/USER-CGDNA/bond_oxdna_fene.cpp
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@ -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");
}
/* ---------------------------------------------------------------------- */