Unverified Commit d1b5b0a1 authored by Axel Kohlmeyer's avatar Axel Kohlmeyer Committed by GitHub
Browse files

Merge pull request #2210 from ohenrich/user-cgdna 

Update of example input and log files
parents d768069c 8dae5d5f

examples/USER/cgdna/examples/oxDNA/duplex1/in.duplex1

+2 −0
Original line number Diff line number Diff line
@@ -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

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

+32 −23
Original line number Diff line number Diff line 
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

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

+32 −23
Original line number Diff line number Diff line 
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

examples/USER/cgdna/examples/oxDNA/duplex2/in.duplex2

+2 −0
Original line number Diff line number Diff line
@@ -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

examples/USER/cgdna/examples/oxDNA/duplex2/log.07Aug19.duplex2.g++.1

deleted100644 → 0
+0 −1168

File deleted.

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