Commit 6d5ab3da authored by Axel Kohlmeyer's avatar Axel Kohlmeyer
Browse files

Merge branch 'github-rebo-bugfix' of https://github.com/CF17/lammps into test-rebo 

# Conflicts:
#	examples/airebo/log.23Jun17.airebo-m.g++.1
#	examples/airebo/log.23Jun17.airebo-m.g++.4
#	examples/airebo/log.23Jun17.airebo.g++.1
#	examples/airebo/log.23Jun17.airebo.g++.4
#	examples/airebo/log.27Nov18.airebo-m.g++.1
#	examples/airebo/log.27Nov18.airebo-m.g++.4
#	examples/airebo/log.27Nov18.airebo.g++.1
#	examples/airebo/log.27Nov18.airebo.g++.4
#	examples/airebo/log.29Jun18.airebo-m.g++.1
#	examples/airebo/log.29Jun18.airebo-m.g++.4
#	examples/airebo/log.29Jun18.airebo.g++.1
#	examples/airebo/log.29Jun18.airebo.g++.4
parents 444dcca4 e51720a2

doc/src/pair_airebo.txt

+9 −8
Original line number Diff line number Diff line
@@ -36,7 +36,7 @@ pair_style airebo/morse 3.0 
pair_coeff * * ../potentials/CH.airebo-m H C :pre



pair_style rebo

pair_coeff * * ../potentials/CH.airebo H C :pre

pair_coeff * * ../potentials/CH.rebo H C :pre



[Description:]
@@ -57,7 +57,8 @@ The {rebo} pair style computes the Reactive Empirical Bond Order (REBO) 
Potential of "(Brenner)"_#Brenner. Note that this is the so-called

2nd generation REBO from 2002, not the original REBO from 1990.

As discussed below, 2nd generation REBO is closely related to the

initial AIREBO; it is just a subset of the potential energy terms.

initial AIREBO; it is just a subset of the potential energy terms

with a few slightly different parameters



The AIREBO potential consists of three terms:
@@ -113,12 +114,12 @@ various dihedral angle preferences in hydrocarbon configurations. 
:line



Only a single pair_coeff command is used with the {airebo}, {airebo}

or {rebo} style which specifies an AIREBO or AIREBO-M potential file

with parameters for C and H.  Note that the {rebo} style in LAMMPS

uses the same AIREBO-formatted potential file.  These are mapped to

LAMMPS atom types by specifying N additional arguments after the

filename in the pair_coeff command, where N is the number of LAMMPS

atom types:

or {rebo} style which specifies an AIREBO, REBO, or AIREBO-M potential

file with parameters for C and H.  Note that as of LAMMPS version

15 November 2018 the {rebo} style in LAMMPS uses its own potential

file (CH.rebo).  These are mapped to LAMMPS atom types by specifying

N additional arguments after the filename in the pair_coeff command,

where N is the number of LAMMPS atom types:



filename

N element names = mapping of AIREBO elements to atom types :ul

examples/airebo/in.airebo-0-0

0 → 100644
+22 −0
Original line number Diff line number Diff line 
# AIREBO polyethelene benchmark



units		    metal

atom_style	    atomic



read_data	    data.airebo



replicate	    17 16 2



neighbor	    0.5 bin

neigh_modify	    delay 5 every 1



pair_style	    airebo 3.0 0 0

pair_coeff	    * * ../../potentials/CH.airebo C H



velocity	    all create 300.0 761341



fix		    1 all nve

timestep	    0.0005



thermo		    10

run		    100

examples/airebo/in.rebo2

0 → 100644
+22 −0
Original line number Diff line number Diff line 
# AIREBO polyethelene benchmark



units		    metal

atom_style	    atomic



read_data	    data.airebo



replicate	    17 16 2



neighbor	    0.5 bin

neigh_modify	    delay 5 every 1



pair_style	    rebo

pair_coeff	    * * ../../potentials/CH.rebo C H



velocity	    all create 300.0 761341



fix		    1 all nve

timestep	    0.0005



thermo		    10

run		    100

examples/airebo/log.29Jun18.airebo-0-0.g++.1

0 → 100644
+88 −0
Original line number Diff line number Diff line 
LAMMPS (29 Jun 2018)

OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)

  using 1 OpenMP thread(s) per MPI task

# AIREBO polyethelene benchmark



units		    metal

atom_style	    atomic



read_data	    data.airebo

  orthogonal box = (-2.1 -2.1 0) to (2.1 2.1 25.579)

  1 by 1 by 1 MPI processor grid

  reading atoms ...

  60 atoms



replicate	    17 16 2

  orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158)

  1 by 1 by 1 MPI processor grid

  32640 atoms

  Time spent = 0.00136042 secs



neighbor	    0.5 bin

neigh_modify	    delay 5 every 1



pair_style	    airebo 3.0 0 0

pair_coeff	    * * ../../potentials/CH.airebo C H

Reading potential file ../../potentials/CH.airebo with DATE: 2011-10-25



velocity	    all create 300.0 761341



fix		    1 all nve

timestep	    0.0005



thermo		    10

run		    100

Neighbor list info ...

  update every 1 steps, delay 5 steps, check yes

  max neighbors/atom: 2000, page size: 100000

  master list distance cutoff = 6.5

  ghost atom cutoff = 6.5

  binsize = 3.25, bins = 22 21 16

  1 neighbor lists, perpetual/occasional/extra = 1 0 0

  (1) pair airebo, perpetual

      attributes: full, newton on, ghost

      pair build: full/bin/ghost

      stencil: full/ghost/bin/3d

      bin: standard

Per MPI rank memory allocation (min/avg/max) = 34.21 | 34.21 | 34.21 Mbytes

Step Temp E_pair E_mol TotEng Press 

       0          300   -138442.83            0   -137177.16    2463.0756 

      10    179.38448   -137931.29            0   -137174.48    15656.689 

      20    206.89283   -138047.05            0   -137174.19   -24047.407 

      30    150.81289   -137807.48            0   -137171.21   -16524.191 

      40    173.24289   -137902.32            0   -137171.42   -5721.7187 

      50    151.80722   -137812.37            0   -137171.91    3489.8954 

      60    199.06038    -138013.7            0   -137173.88    17887.024 

      70    217.84848   -138093.82            0   -137174.73    -12266.16 

      80    202.34667   -138029.28            0   -137175.59   -7623.6635 

      90    194.92367   -137997.12            0   -137174.75   -32277.173 

     100     185.2078   -137954.64            0   -137173.26   -6888.5104 

Loop time of 5.00753 on 1 procs for 100 steps with 32640 atoms



Performance: 0.863 ns/day, 27.820 hours/ns, 19.970 timesteps/s

99.8% CPU use with 1 MPI tasks x 1 OpenMP threads



MPI task timing breakdown:

Section |  min time  |  avg time  |  max time  |%varavg| %total

---------------------------------------------------------------

Pair    | 3.4898     | 3.4898     | 3.4898     |   0.0 | 69.69

Neigh   | 1.4697     | 1.4697     | 1.4697     |   0.0 | 29.35

Comm    | 0.015885   | 0.015885   | 0.015885   |   0.0 |  0.32

Output  | 0.00096607 | 0.00096607 | 0.00096607 |   0.0 |  0.02

Modify  | 0.021901   | 0.021901   | 0.021901   |   0.0 |  0.44

Other   |            | 0.009297   |            |       |  0.19



Nlocal:    32640 ave 32640 max 32640 min

Histogram: 1 0 0 0 0 0 0 0 0 0

Nghost:    26460 ave 26460 max 26460 min

Histogram: 1 0 0 0 0 0 0 0 0 0

Neighs:    0 ave 0 max 0 min

Histogram: 1 0 0 0 0 0 0 0 0 0

FullNghs:  4.90213e+06 ave 4.90213e+06 max 4.90213e+06 min

Histogram: 1 0 0 0 0 0 0 0 0 0



Total # of neighbors = 4902134

Ave neighs/atom = 150.188

Neighbor list builds = 9

Dangerous builds = 0

Total wall time: 0:00:05

examples/airebo/log.29Jun18.airebo-0-0.g++.4

0 → 100644
+88 −0
Original line number Diff line number Diff line 
LAMMPS (29 Jun 2018)

OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)

  using 1 OpenMP thread(s) per MPI task

# AIREBO polyethelene benchmark



units		    metal

atom_style	    atomic



read_data	    data.airebo

  orthogonal box = (-2.1 -2.1 0) to (2.1 2.1 25.579)

  1 by 1 by 4 MPI processor grid

  reading atoms ...

  60 atoms



replicate	    17 16 2

  orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158)

  2 by 2 by 1 MPI processor grid

  32640 atoms

  Time spent = 0.000609159 secs



neighbor	    0.5 bin

neigh_modify	    delay 5 every 1



pair_style	    airebo 3.0 0 0

pair_coeff	    * * ../../potentials/CH.airebo C H

Reading potential file ../../potentials/CH.airebo with DATE: 2011-10-25



velocity	    all create 300.0 761341



fix		    1 all nve

timestep	    0.0005



thermo		    10

run		    100

Neighbor list info ...

  update every 1 steps, delay 5 steps, check yes

  max neighbors/atom: 2000, page size: 100000

  master list distance cutoff = 6.5

  ghost atom cutoff = 6.5

  binsize = 3.25, bins = 22 21 16

  1 neighbor lists, perpetual/occasional/extra = 1 0 0

  (1) pair airebo, perpetual

      attributes: full, newton on, ghost

      pair build: full/bin/ghost

      stencil: full/ghost/bin/3d

      bin: standard

Per MPI rank memory allocation (min/avg/max) = 11.75 | 11.94 | 12.13 Mbytes

Step Temp E_pair E_mol TotEng Press 

       0          300   -138442.83            0   -137177.16    2463.0756 

      10    179.38448   -137931.29            0   -137174.48    15656.689 

      20    206.89283   -138047.05            0   -137174.19   -24047.407 

      30    150.81289   -137807.48            0   -137171.21   -16524.191 

      40    173.24289   -137902.32            0   -137171.42   -5721.7187 

      50    151.80722   -137812.37            0   -137171.91    3489.8954 

      60    199.06038    -138013.7            0   -137173.88    17887.024 

      70    217.84848   -138093.82            0   -137174.73    -12266.16 

      80    202.34667   -138029.28            0   -137175.59   -7623.6635 

      90    194.92367   -137997.12            0   -137174.75   -32277.173 

     100     185.2078   -137954.64            0   -137173.26   -6888.5104 

Loop time of 1.50369 on 4 procs for 100 steps with 32640 atoms



Performance: 2.873 ns/day, 8.354 hours/ns, 66.503 timesteps/s

98.5% CPU use with 4 MPI tasks x 1 OpenMP threads



MPI task timing breakdown:

Section |  min time  |  avg time  |  max time  |%varavg| %total

---------------------------------------------------------------

Pair    | 0.92943    | 0.95749    | 0.97327    |   1.8 | 63.68

Neigh   | 0.456      | 0.46115    | 0.46657    |   0.7 | 30.67

Comm    | 0.048775   | 0.068415   | 0.10077    |   8.2 |  4.55

Output  | 0.00044918 | 0.00073665 | 0.0015814  |   0.0 |  0.05

Modify  | 0.0087936  | 0.0089477  | 0.0091038  |   0.1 |  0.60

Other   |            | 0.006951   |            |       |  0.46



Nlocal:    8160 ave 8163 max 8157 min

Histogram: 1 1 0 0 0 0 0 0 1 1

Nghost:    11605.8 ave 11615 max 11593 min

Histogram: 1 0 0 0 0 0 2 0 0 1

Neighs:    0 ave 0 max 0 min

Histogram: 4 0 0 0 0 0 0 0 0 0

FullNghs:  1.22553e+06 ave 1.22734e+06 max 1.22455e+06 min

Histogram: 2 0 0 1 0 0 0 0 0 1



Total # of neighbors = 4902134

Ave neighs/atom = 150.188

Neighbor list builds = 9

Dangerous builds = 0

Total wall time: 0:00:01

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