Merge branch 'master' into master
This commit is contained in:
Stan Moore
@ -22,6 +22,17 @@ A - C - G - T - A - C - G - T
|
||||
| | | | | | | |
|
||||
T - G - C - A T - G - C - A
|
||||
|
||||
/examples/duplex3:
|
||||
This is basically the duplex1 run with sequence-dependent stacking
|
||||
and hydrogen-bonding strengths enabled and both nucleotide mass and
|
||||
moment of inertia set to the value of the standalone implementation
|
||||
of oxDNA (M = I = 1). To achieve this, the masses can be set directly
|
||||
in the input and data file, whereas the moment of inertia is set via
|
||||
the diameter of the ellipsoid in the data file and has a value of 3.16227766.
|
||||
The change of mass and moment of inertia allows direct comparision of
|
||||
e.g. trajectory data, energies or time-dependent observables on a per-timestep
|
||||
basis until numerical noise causes deviations at later simulation times.
|
||||
|
||||
/util:
|
||||
This directory contains a simple python setup tool which creates
|
||||
single straight or helical DNA strands, DNA duplexes or arrays of DNA
|
||||
|
||||
@ -32,7 +32,7 @@ Atoms
|
||||
9 3 4.860249842674775e-01 3.518234140414733e-01 3.897628551303121e-01 2 1 1
|
||||
10 4 5.999999999999996e-01 -1.332267629550188e-16 -1.110223024625157e-16 2 1 1
|
||||
|
||||
# Atom-ID, translational, rotational velocity
|
||||
# Atom-ID, translational velocity, angular momentum
|
||||
Velocities
|
||||
|
||||
1 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
|
||||
@ -1,6 +1,7 @@
|
||||
variable number equal 1
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
variable T equal 0.1
|
||||
|
||||
units lj
|
||||
|
||||
@ -30,7 +31,7 @@ bond_coeff * 2.0 0.25 0.7525
|
||||
# oxDNA pair interactions
|
||||
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
|
||||
pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna/stk seqav ${T} 1.3448 2.6568 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
@ -39,9 +40,9 @@ pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1
|
||||
|
||||
# NVE ensemble
|
||||
fix 1 all nve/dot
|
||||
#fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
#fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10
|
||||
#fix 1 all nve/asphere
|
||||
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10
|
||||
|
||||
timestep 1e-5
|
||||
|
||||
@ -72,6 +73,6 @@ fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${e
|
||||
#dump_modify out sort id
|
||||
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
run 10000
|
||||
run 1000000
|
||||
|
||||
#write_restart config.${number}.*
|
||||
|
||||
1165
examples/USER/cgdna/examples/oxDNA/duplex1/log.18Jun19.duplex1.g++.1
Normal file
1165
examples/USER/cgdna/examples/oxDNA/duplex1/log.18Jun19.duplex1.g++.1
Normal file
File diff suppressed because it is too large
Load Diff
1165
examples/USER/cgdna/examples/oxDNA/duplex1/log.18Jun19.duplex1.g++.4
Normal file
1165
examples/USER/cgdna/examples/oxDNA/duplex1/log.18Jun19.duplex1.g++.4
Normal file
File diff suppressed because it is too large
Load Diff
@ -1,172 +0,0 @@
|
||||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
variable number equal 1
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
|
||||
units lj
|
||||
|
||||
dimension 3
|
||||
|
||||
newton off
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid
|
||||
atom_modify sort 0 1.0
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
read_data data.duplex1
|
||||
orthogonal box = (-20 -20 -20) to (20 20 20)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
10 atoms
|
||||
reading velocities ...
|
||||
10 velocities
|
||||
10 ellipsoids
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
reading bonds ...
|
||||
8 bonds
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
2 = max # of 1-4 neighbors
|
||||
4 = max # of special neighbors
|
||||
|
||||
set atom * mass 3.1575
|
||||
10 settings made for mass
|
||||
|
||||
group all type 1 4
|
||||
10 atoms in group all
|
||||
|
||||
# oxDNA bond interactions - FENE backbone
|
||||
bond_style oxdna/fene
|
||||
bond_coeff * 2.0 0.25 0.7525
|
||||
|
||||
# oxDNA pair interactions
|
||||
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
|
||||
pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
|
||||
|
||||
# NVE ensemble
|
||||
fix 1 all nve/dot
|
||||
#fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
#fix 1 all nve/asphere
|
||||
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
|
||||
timestep 1e-5
|
||||
|
||||
#comm_style tiled
|
||||
#fix 3 all balance 10000 1.1 rcb
|
||||
|
||||
#compute mol all chunk/atom molecule
|
||||
#compute mychunk all vcm/chunk mol
|
||||
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
|
||||
|
||||
#dump pos all xyz ${ofreq} traj.${number}.xyz
|
||||
|
||||
#compute quat all property/atom quatw quati quatj quatk
|
||||
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
|
||||
#dump_modify quat sort id
|
||||
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
compute epot all pe
|
||||
variable erot equal c_erot
|
||||
variable ekin equal c_ekin
|
||||
variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
|
||||
#dump_modify out sort id
|
||||
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.92828
|
||||
ghost atom cutoff = 1.92828
|
||||
binsize = 0.964142, bins = 42 42 42
|
||||
5 neighbor lists, perpetual/occasional/extra = 5 0 0
|
||||
(1) pair oxdna/excv, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: half/bin/3d/newtoff
|
||||
bin: standard
|
||||
(2) pair oxdna/stk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) pair oxdna/hbond, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(4) pair oxdna/xstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(5) pair oxdna/coaxstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.859 | 2.859 | 2.859 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -1.4711818 0.0069384985 -1.4642433 -6.2745089e-05
|
||||
1000 ekin = 0.00113448721737003 | erot = 0.00413455947734281 | epot = -14.6477022915193 | etot = -14.6424332448246
|
||||
2000 ekin = 0.00449927223902336 | erot = 0.0164446434455805 | epot = -14.6633771605337 | etot = -14.6424332448491
|
||||
3000 ekin = 0.00997964450841065 | erot = 0.0366523356056461 | epot = -14.6890652250033 | etot = -14.6424332448892
|
||||
4000 ekin = 0.0173888111295073 | erot = 0.0643039804300221 | epot = -14.7241260365031 | etot = -14.6424332449436
|
||||
5000 ekin = 0.0264744514136619 | erot = 0.0987844033142066 | epot = -14.7676920997383 | etot = -14.6424332450104
|
||||
6000 ekin = 0.0369277948556079 | erot = 0.139336571052565 | epot = -14.8186976109956 | etot = -14.6424332450875
|
||||
7000 ekin = 0.04839505571915 | erot = 0.18508629569208 | epot = -14.8759145965832 | etot = -14.642433245172
|
||||
8000 ekin = 0.0604909336920643 | erot = 0.23507130752353 | epot = -14.9379954864767 | etot = -14.6424332452611
|
||||
9000 ekin = 0.0728137406440561 | erot = 0.288273694501537 | epot = -15.003520680497 | etot = -14.6424332453514
|
||||
10000 ekin = 0.0849615563085879 | erot = 0.343654369293472 | epot = -15.0710491710418 | etot = -14.6424332454398
|
||||
10000 0.0062934486 -1.5138305 0.0067255788 -1.4986088 -9.9021593e-05
|
||||
Loop time of 0.141929 on 1 procs for 10000 steps with 10 atoms
|
||||
|
||||
Performance: 60875.649 tau/day, 70457.927 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.11467 | 0.11467 | 0.11467 | 0.0 | 80.79
|
||||
Bond | 0.0050094 | 0.0050094 | 0.0050094 | 0.0 | 3.53
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0013616 | 0.0013616 | 0.0013616 | 0.0 | 0.96
|
||||
Output | 4.0531e-06 | 4.0531e-06 | 4.0531e-06 | 0.0 | 0.00
|
||||
Modify | 0.017901 | 0.017901 | 0.017901 | 0.0 | 12.61
|
||||
Other | | 0.002982 | | | 2.10
|
||||
|
||||
Nlocal: 10 ave 10 max 10 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 43 ave 43 max 43 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 43
|
||||
Ave neighs/atom = 4.3
|
||||
Ave special neighs/atom = 3.6
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
#write_restart config.${number}.*
|
||||
Total wall time: 0:00:00
|
||||
@ -1,172 +0,0 @@
|
||||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
variable number equal 1
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
|
||||
units lj
|
||||
|
||||
dimension 3
|
||||
|
||||
newton off
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid
|
||||
atom_modify sort 0 1.0
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
read_data data.duplex1
|
||||
orthogonal box = (-20 -20 -20) to (20 20 20)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
10 atoms
|
||||
reading velocities ...
|
||||
10 velocities
|
||||
10 ellipsoids
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
reading bonds ...
|
||||
8 bonds
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
2 = max # of 1-4 neighbors
|
||||
4 = max # of special neighbors
|
||||
|
||||
set atom * mass 3.1575
|
||||
10 settings made for mass
|
||||
|
||||
group all type 1 4
|
||||
10 atoms in group all
|
||||
|
||||
# oxDNA bond interactions - FENE backbone
|
||||
bond_style oxdna/fene
|
||||
bond_coeff * 2.0 0.25 0.7525
|
||||
|
||||
# oxDNA pair interactions
|
||||
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
|
||||
pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
|
||||
|
||||
# NVE ensemble
|
||||
fix 1 all nve/dot
|
||||
#fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
#fix 1 all nve/asphere
|
||||
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
|
||||
timestep 1e-5
|
||||
|
||||
#comm_style tiled
|
||||
#fix 3 all balance 10000 1.1 rcb
|
||||
|
||||
#compute mol all chunk/atom molecule
|
||||
#compute mychunk all vcm/chunk mol
|
||||
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
|
||||
|
||||
#dump pos all xyz ${ofreq} traj.${number}.xyz
|
||||
|
||||
#compute quat all property/atom quatw quati quatj quatk
|
||||
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
|
||||
#dump_modify quat sort id
|
||||
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
compute epot all pe
|
||||
variable erot equal c_erot
|
||||
variable ekin equal c_ekin
|
||||
variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
|
||||
#dump_modify out sort id
|
||||
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.92828
|
||||
ghost atom cutoff = 1.92828
|
||||
binsize = 0.964142, bins = 42 42 42
|
||||
5 neighbor lists, perpetual/occasional/extra = 5 0 0
|
||||
(1) pair oxdna/excv, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: half/bin/3d/newtoff
|
||||
bin: standard
|
||||
(2) pair oxdna/stk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) pair oxdna/hbond, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(4) pair oxdna/xstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(5) pair oxdna/coaxstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.341 | 7.523 | 7.705 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -1.4711818 0.0069384985 -1.4642433 -6.2745089e-05
|
||||
1000 ekin = 0.00113448721737009 | erot = 0.0041345594773427 | epot = -14.6477022915193 | etot = -14.6424332448246
|
||||
2000 ekin = 0.00449927223902292 | erot = 0.0164446434455803 | epot = -14.6633771605337 | etot = -14.6424332448491
|
||||
3000 ekin = 0.00997964450840756 | erot = 0.0366523356056465 | epot = -14.6890652250033 | etot = -14.6424332448892
|
||||
4000 ekin = 0.017388811129498 | erot = 0.0643039804300254 | epot = -14.7241260365031 | etot = -14.6424332449436
|
||||
5000 ekin = 0.0264744514136422 | erot = 0.098784403314214 | epot = -14.7676920997383 | etot = -14.6424332450104
|
||||
6000 ekin = 0.0369277948555727 | erot = 0.139336571052581 | epot = -14.8186976109956 | etot = -14.6424332450875
|
||||
7000 ekin = 0.0483950557190949 | erot = 0.185086295692111 | epot = -14.8759145965832 | etot = -14.642433245172
|
||||
8000 ekin = 0.0604909336919856 | erot = 0.235071307523583 | epot = -14.9379954864767 | etot = -14.6424332452611
|
||||
9000 ekin = 0.0728137406439517 | erot = 0.288273694501617 | epot = -15.003520680497 | etot = -14.6424332453514
|
||||
10000 ekin = 0.0849615563084573 | erot = 0.34365436929359 | epot = -15.0710491710418 | etot = -14.6424332454398
|
||||
10000 0.0062934486 -1.5138305 0.0067255788 -1.4986088 -0.00010196899
|
||||
Loop time of 0.134536 on 4 procs for 10000 steps with 10 atoms
|
||||
|
||||
Performance: 64220.659 tau/day, 74329.466 timesteps/s
|
||||
97.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0030077 | 0.052212 | 0.093066 | 17.4 | 38.81
|
||||
Bond | 0.00061846 | 0.00234 | 0.0039451 | 2.8 | 1.74
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.013431 | 0.014091 | 0.014596 | 0.4 | 10.47
|
||||
Output | 5.0783e-05 | 5.1141e-05 | 5.1498e-05 | 0.0 | 0.04
|
||||
Modify | 0.0011578 | 0.0059478 | 0.010331 | 4.8 | 4.42
|
||||
Other | | 0.05989 | | | 44.52
|
||||
|
||||
Nlocal: 2.5 ave 5 max 0 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||
Nghost: 7.5 ave 10 max 5 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||
Neighs: 17.5 ave 33 max 0 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 70
|
||||
Ave neighs/atom = 7
|
||||
Ave special neighs/atom = 3.6
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
#write_restart config.${number}.*
|
||||
Total wall time: 0:00:00
|
||||
@ -38,7 +38,7 @@ Atoms
|
||||
15 3 4.860249842674773e-01 3.518234140414733e-01 3.897628551303119e-01 2 1 1
|
||||
16 4 5.999999999999995e-01 -3.330669073875470e-17 -3.330669073875470e-16 2 1 1
|
||||
|
||||
# Atom-ID, translational, rotational velocity
|
||||
# Atom-ID, translational velocity, angular momentum
|
||||
Velocities
|
||||
|
||||
1 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
|
||||
@ -1,6 +1,7 @@
|
||||
variable number equal 2
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
variable T equal 0.1
|
||||
|
||||
units lj
|
||||
|
||||
@ -30,7 +31,7 @@ bond_coeff * 2.0 0.25 0.7525
|
||||
# oxDNA pair interactions
|
||||
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
|
||||
pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna/stk seqav ${T} 1.3448 2.6568 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
@ -39,9 +40,9 @@ pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1
|
||||
|
||||
# NVE ensemble
|
||||
#fix 1 all nve/dot
|
||||
fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10
|
||||
#fix 1 all nve/asphere
|
||||
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10
|
||||
|
||||
timestep 1e-5
|
||||
|
||||
@ -72,6 +73,6 @@ fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${e
|
||||
#dump_modify out sort id
|
||||
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
run 10000
|
||||
run 1000000
|
||||
|
||||
#write_restart config.${number}.*
|
||||
|
||||
1167
examples/USER/cgdna/examples/oxDNA/duplex2/log.18Jun19.duplex2.g++.1
Normal file
1167
examples/USER/cgdna/examples/oxDNA/duplex2/log.18Jun19.duplex2.g++.1
Normal file
File diff suppressed because it is too large
Load Diff
1167
examples/USER/cgdna/examples/oxDNA/duplex2/log.18Jun19.duplex2.g++.4
Normal file
1167
examples/USER/cgdna/examples/oxDNA/duplex2/log.18Jun19.duplex2.g++.4
Normal file
File diff suppressed because it is too large
Load Diff
@ -1,172 +0,0 @@
|
||||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
variable number equal 2
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
|
||||
units lj
|
||||
|
||||
dimension 3
|
||||
|
||||
newton off
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid
|
||||
atom_modify sort 0 1.0
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
read_data data.duplex2
|
||||
orthogonal box = (-20 -20 -20) to (20 20 20)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
16 atoms
|
||||
reading velocities ...
|
||||
16 velocities
|
||||
16 ellipsoids
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
reading bonds ...
|
||||
13 bonds
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
4 = max # of 1-4 neighbors
|
||||
6 = max # of special neighbors
|
||||
|
||||
set atom * mass 3.1575
|
||||
16 settings made for mass
|
||||
|
||||
group all type 1 4
|
||||
16 atoms in group all
|
||||
|
||||
# oxDNA bond interactions - FENE backbone
|
||||
bond_style oxdna/fene
|
||||
bond_coeff * 2.0 0.25 0.7525
|
||||
|
||||
# oxDNA pair interactions
|
||||
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
|
||||
pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
|
||||
|
||||
# NVE ensemble
|
||||
#fix 1 all nve/dot
|
||||
fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
#fix 1 all nve/asphere
|
||||
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
|
||||
timestep 1e-5
|
||||
|
||||
#comm_style tiled
|
||||
#fix 3 all balance 10000 1.1 rcb
|
||||
|
||||
#compute mol all chunk/atom molecule
|
||||
#compute mychunk all vcm/chunk mol
|
||||
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
|
||||
|
||||
#dump pos all xyz ${ofreq} traj.${number}.xyz
|
||||
|
||||
#compute quat all property/atom quatw quati quatj quatk
|
||||
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
|
||||
#dump_modify quat sort id
|
||||
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
compute epot all pe
|
||||
variable erot equal c_erot
|
||||
variable ekin equal c_ekin
|
||||
variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
|
||||
#dump_modify out sort id
|
||||
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.92828
|
||||
ghost atom cutoff = 1.92828
|
||||
binsize = 0.964142, bins = 42 42 42
|
||||
5 neighbor lists, perpetual/occasional/extra = 5 0 0
|
||||
(1) pair oxdna/excv, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: half/bin/3d/newtoff
|
||||
bin: standard
|
||||
(2) pair oxdna/stk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) pair oxdna/hbond, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(4) pair oxdna/xstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(5) pair oxdna/coaxstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.861 | 2.861 | 2.861 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -1.5402493 0.0070469125 -1.5332024 -8.5641987e-05
|
||||
1000 ekin = 1.54234964773389 | erot = 1.71563526070267 | epot = -24.5477045187653 | etot = -21.2897196103287
|
||||
2000 ekin = 1.85988866919215 | erot = 1.9424302796508 | epot = -24.4843044999595 | etot = -20.6819855511165
|
||||
3000 ekin = 2.68354339452998 | erot = 2.14216528317607 | epot = -24.4019350693561 | etot = -19.57622639165
|
||||
4000 ekin = 2.04461800191989 | erot = 1.49015219763162 | epot = -24.2959428773347 | etot = -20.7611726777832
|
||||
5000 ekin = 1.76794859210155 | erot = 2.54289684465818 | epot = -24.2337587736863 | etot = -19.9229133369266
|
||||
6000 ekin = 3.1106424806079 | erot = 2.04409805200892 | epot = -24.1585729744133 | etot = -19.0038324417964
|
||||
7000 ekin = 3.21360097519306 | erot = 2.71941303605722 | epot = -24.0566262531609 | etot = -18.1236122419107
|
||||
8000 ekin = 2.82489935901743 | erot = 2.66790555575696 | epot = -24.0194805097633 | etot = -18.526675594989
|
||||
9000 ekin = 2.69381302856378 | erot = 2.59107820129446 | epot = -23.9216126050554 | etot = -18.6367213751972
|
||||
10000 ekin = 2.65765007662471 | erot = 1.95562671446597 | epot = -23.7978334881241 | etot = -19.1845566970334
|
||||
10000 0.11811778 -1.4992295 0.011864944 -1.3212615 -0.00013416809
|
||||
Loop time of 0.295538 on 1 procs for 10000 steps with 16 atoms
|
||||
|
||||
Performance: 29234.801 tau/day, 33836.575 timesteps/s
|
||||
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.20959 | 0.20959 | 0.20959 | 0.0 | 70.92
|
||||
Bond | 0.0073669 | 0.0073669 | 0.0073669 | 0.0 | 2.49
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0016472 | 0.0016472 | 0.0016472 | 0.0 | 0.56
|
||||
Output | 5.0068e-06 | 5.0068e-06 | 5.0068e-06 | 0.0 | 0.00
|
||||
Modify | 0.073117 | 0.073117 | 0.073117 | 0.0 | 24.74
|
||||
Other | | 0.003813 | | | 1.29
|
||||
|
||||
Nlocal: 16 ave 16 max 16 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 88 ave 88 max 88 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 88
|
||||
Ave neighs/atom = 5.5
|
||||
Ave special neighs/atom = 3.75
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
#write_restart config.${number}.*
|
||||
Total wall time: 0:00:00
|
||||
@ -1,172 +0,0 @@
|
||||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
variable number equal 2
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
|
||||
units lj
|
||||
|
||||
dimension 3
|
||||
|
||||
newton off
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid
|
||||
atom_modify sort 0 1.0
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
read_data data.duplex2
|
||||
orthogonal box = (-20 -20 -20) to (20 20 20)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
16 atoms
|
||||
reading velocities ...
|
||||
16 velocities
|
||||
16 ellipsoids
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
reading bonds ...
|
||||
13 bonds
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
4 = max # of 1-4 neighbors
|
||||
6 = max # of special neighbors
|
||||
|
||||
set atom * mass 3.1575
|
||||
16 settings made for mass
|
||||
|
||||
group all type 1 4
|
||||
16 atoms in group all
|
||||
|
||||
# oxDNA bond interactions - FENE backbone
|
||||
bond_style oxdna/fene
|
||||
bond_coeff * 2.0 0.25 0.7525
|
||||
|
||||
# oxDNA pair interactions
|
||||
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
|
||||
pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
|
||||
|
||||
# NVE ensemble
|
||||
#fix 1 all nve/dot
|
||||
fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
#fix 1 all nve/asphere
|
||||
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
|
||||
timestep 1e-5
|
||||
|
||||
#comm_style tiled
|
||||
#fix 3 all balance 10000 1.1 rcb
|
||||
|
||||
#compute mol all chunk/atom molecule
|
||||
#compute mychunk all vcm/chunk mol
|
||||
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
|
||||
|
||||
#dump pos all xyz ${ofreq} traj.${number}.xyz
|
||||
|
||||
#compute quat all property/atom quatw quati quatj quatk
|
||||
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
|
||||
#dump_modify quat sort id
|
||||
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
compute epot all pe
|
||||
variable erot equal c_erot
|
||||
variable ekin equal c_ekin
|
||||
variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
|
||||
#dump_modify out sort id
|
||||
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.92828
|
||||
ghost atom cutoff = 1.92828
|
||||
binsize = 0.964142, bins = 42 42 42
|
||||
5 neighbor lists, perpetual/occasional/extra = 5 0 0
|
||||
(1) pair oxdna/excv, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: half/bin/3d/newtoff
|
||||
bin: standard
|
||||
(2) pair oxdna/stk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) pair oxdna/hbond, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(4) pair oxdna/xstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(5) pair oxdna/coaxstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.466 | 7.648 | 7.83 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -1.5402493 0.0070469125 -1.5332024 -8.5641987e-05
|
||||
1000 ekin = 1.34565986428024 | erot = 2.31051421234078 | epot = -24.5061991591502 | etot = -20.8500250825292
|
||||
2000 ekin = 2.15911766687235 | erot = 2.16031365874707 | epot = -24.4723177103698 | etot = -20.1528863847504
|
||||
3000 ekin = 3.26561948796015 | erot = 2.75651822936604 | epot = -24.412573068346 | etot = -18.3904353510198
|
||||
4000 ekin = 1.92438809241066 | erot = 2.12016940074985 | epot = -24.3496233970111 | etot = -20.3050659038506
|
||||
5000 ekin = 1.35986357015476 | erot = 1.99413493074226 | epot = -24.2789445616949 | etot = -20.9249460607979
|
||||
6000 ekin = 2.19432475124593 | erot = 1.74281260409078 | epot = -24.2128064295788 | etot = -20.2756690742421
|
||||
7000 ekin = 2.65619274477635 | erot = 1.74094257048458 | epot = -24.1673462333493 | etot = -19.7702109180883
|
||||
8000 ekin = 2.51333548501168 | erot = 2.34649854571051 | epot = -24.0812769481836 | etot = -19.2214429174614
|
||||
9000 ekin = 2.24506493169711 | erot = 2.0652555461504 | epot = -23.9906736063989 | etot = -19.6803531285514
|
||||
10000 ekin = 2.36632635249862 | erot = 1.7959247176153 | epot = -23.9002627850602 | etot = -19.7380117149463
|
||||
10000 0.10517006 -1.5057137 0.011947302 -1.345871 -9.5924016e-05
|
||||
Loop time of 0.251867 on 4 procs for 10000 steps with 16 atoms
|
||||
|
||||
Performance: 34303.820 tau/day, 39703.495 timesteps/s
|
||||
97.8% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0035377 | 0.092047 | 0.17435 | 26.0 | 36.55
|
||||
Bond | 0.00065637 | 0.0031857 | 0.0053554 | 3.8 | 1.26
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.013929 | 0.01497 | 0.015733 | 0.6 | 5.94
|
||||
Output | 5.0783e-05 | 5.2691e-05 | 5.3883e-05 | 0.0 | 0.02
|
||||
Modify | 0.0013576 | 0.020825 | 0.040231 | 11.8 | 8.27
|
||||
Other | | 0.1208 | | | 47.96
|
||||
|
||||
Nlocal: 4 ave 8 max 0 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 1 1
|
||||
Nghost: 9 ave 10 max 8 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
Neighs: 34.5 ave 67 max 0 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 138
|
||||
Ave neighs/atom = 8.625
|
||||
Ave special neighs/atom = 3.75
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
#write_restart config.${number}.*
|
||||
Total wall time: 0:00:00
|
||||
@ -32,7 +32,7 @@ Atoms
|
||||
9 3 4.860249842674775e-01 3.518234140414733e-01 3.897628551303121e-01 2 1 1
|
||||
10 4 5.999999999999996e-01 -1.332267629550188e-16 -1.110223024625157e-16 2 1 1
|
||||
|
||||
# Atom-ID, translational, rotational velocity
|
||||
# Atom-ID, translational velocity, angular momentum
|
||||
Velocities
|
||||
|
||||
1 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
|
||||
@ -1,6 +1,7 @@
|
||||
variable number equal 1
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
variable T equal 0.1
|
||||
|
||||
units lj
|
||||
|
||||
@ -30,19 +31,19 @@ bond_coeff * 2.0 0.25 0.7564
|
||||
# oxDNA pair interactions
|
||||
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
|
||||
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna2/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/stk seqav ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
|
||||
pair_coeff * * oxdna2/dh 0.1 1.0 0.815
|
||||
pair_coeff * * oxdna2/dh ${T} 1.0 0.815
|
||||
|
||||
# NVE ensemble
|
||||
fix 1 all nve/dot
|
||||
#fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
#fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10
|
||||
#fix 1 all nve/asphere
|
||||
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10
|
||||
|
||||
timestep 1e-5
|
||||
|
||||
@ -73,6 +74,6 @@ fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${e
|
||||
#dump_modify out sort id
|
||||
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
run 10000
|
||||
run 1000000
|
||||
|
||||
#write_restart config.${number}.*
|
||||
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
@ -1,178 +0,0 @@
|
||||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
variable number equal 1
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
|
||||
units lj
|
||||
|
||||
dimension 3
|
||||
|
||||
newton off
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid
|
||||
atom_modify sort 0 1.0
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
read_data data.duplex1
|
||||
orthogonal box = (-20 -20 -20) to (20 20 20)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
10 atoms
|
||||
reading velocities ...
|
||||
10 velocities
|
||||
10 ellipsoids
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
reading bonds ...
|
||||
8 bonds
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
2 = max # of 1-4 neighbors
|
||||
4 = max # of special neighbors
|
||||
|
||||
set atom * mass 3.1575
|
||||
10 settings made for mass
|
||||
|
||||
group all type 1 4
|
||||
10 atoms in group all
|
||||
|
||||
# oxDNA bond interactions - FENE backbone
|
||||
bond_style oxdna2/fene
|
||||
bond_coeff * 2.0 0.25 0.7564
|
||||
|
||||
# oxDNA pair interactions
|
||||
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
|
||||
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna2/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
|
||||
pair_coeff * * oxdna2/dh 0.1 1.0 0.815
|
||||
|
||||
# NVE ensemble
|
||||
fix 1 all nve/dot
|
||||
#fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
#fix 1 all nve/asphere
|
||||
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
|
||||
timestep 1e-5
|
||||
|
||||
#comm_style tiled
|
||||
#fix 3 all balance 10000 1.1 rcb
|
||||
|
||||
#compute mol all chunk/atom molecule
|
||||
#compute mychunk all vcm/chunk mol
|
||||
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
|
||||
|
||||
#dump pos all xyz ${ofreq} traj.${number}.xyz
|
||||
|
||||
#compute quat all property/atom quatw quati quatj quatk
|
||||
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
|
||||
#dump_modify quat sort id
|
||||
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
compute epot all pe
|
||||
variable erot equal c_erot
|
||||
variable ekin equal c_ekin
|
||||
variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
|
||||
#dump_modify out sort id
|
||||
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
run 10000
|
||||
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
|
||||
6 neighbor lists, perpetual/occasional/extra = 6 0 0
|
||||
(1) pair oxdna2/excv, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: half/bin/3d/newtoff
|
||||
bin: standard
|
||||
(2) pair oxdna2/stk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) pair oxdna2/hbond, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(4) pair oxdna2/xstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(5) pair oxdna2/coaxstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(6) pair oxdna2/dh, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.023 | 3.023 | 3.023 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -1.4712768 0.009525411 -1.4617514 -5.8922361e-05
|
||||
1000 ekin = 0.00113086229080528 | erot = 0.0043101016040658 | epot = -14.6229549982368 | etot = -14.617514034342
|
||||
2000 ekin = 0.0044853322434243 | erot = 0.0171407706505008 | epot = -14.6391401372615 | etot = -14.6175140343675
|
||||
3000 ekin = 0.00995035259649284 | erot = 0.0381961780846485 | epot = -14.6656605650904 | etot = -14.6175140344093
|
||||
4000 ekin = 0.0173418024862054 | erot = 0.0669935184860634 | epot = -14.7018493554381 | etot = -14.6175140344659
|
||||
5000 ekin = 0.0264109356286075 | erot = 0.102878288094517 | epot = -14.7468032582586 | etot = -14.6175140345355
|
||||
6000 ekin = 0.0368533113591442 | erot = 0.14504542056987 | epot = -14.7994127665447 | etot = -14.6175140346157
|
||||
7000 ekin = 0.0483200640564843 | erot = 0.19256586251551 | epot = -14.8583999612756 | etot = -14.6175140347036
|
||||
8000 ekin = 0.0604312317605998 | erot = 0.24441787013151 | epot = -14.9223631366883 | etot = -14.6175140347962
|
||||
9000 ekin = 0.0727907119671751 | erot = 0.299521949931843 | epot = -14.989826696789 | etot = -14.6175140348899
|
||||
10000 ekin = 0.0850022498875221 | erot = 0.356777997217908 | epot = -15.0592942820869 | etot = -14.6175140349815
|
||||
10000 0.006296463 -1.5144685 0.0085391004 -1.4974292 -0.00010794792
|
||||
Loop time of 0.149406 on 1 procs for 10000 steps with 10 atoms
|
||||
|
||||
Performance: 57828.835 tau/day, 66931.522 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.11971 | 0.11971 | 0.11971 | 0.0 | 80.12
|
||||
Bond | 0.0051196 | 0.0051196 | 0.0051196 | 0.0 | 3.43
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0013614 | 0.0013614 | 0.0013614 | 0.0 | 0.91
|
||||
Output | 5.0068e-06 | 5.0068e-06 | 5.0068e-06 | 0.0 | 0.00
|
||||
Modify | 0.018941 | 0.018941 | 0.018941 | 0.0 | 12.68
|
||||
Other | | 0.004268 | | | 2.86
|
||||
|
||||
Nlocal: 10 ave 10 max 10 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 45 ave 45 max 45 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 45
|
||||
Ave neighs/atom = 4.5
|
||||
Ave special neighs/atom = 3.6
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
#write_restart config.${number}.*
|
||||
Total wall time: 0:00:00
|
||||
@ -1,178 +0,0 @@
|
||||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
variable number equal 1
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
|
||||
units lj
|
||||
|
||||
dimension 3
|
||||
|
||||
newton off
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid
|
||||
atom_modify sort 0 1.0
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
read_data data.duplex1
|
||||
orthogonal box = (-20 -20 -20) to (20 20 20)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
10 atoms
|
||||
reading velocities ...
|
||||
10 velocities
|
||||
10 ellipsoids
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
reading bonds ...
|
||||
8 bonds
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
2 = max # of 1-4 neighbors
|
||||
4 = max # of special neighbors
|
||||
|
||||
set atom * mass 3.1575
|
||||
10 settings made for mass
|
||||
|
||||
group all type 1 4
|
||||
10 atoms in group all
|
||||
|
||||
# oxDNA bond interactions - FENE backbone
|
||||
bond_style oxdna2/fene
|
||||
bond_coeff * 2.0 0.25 0.7564
|
||||
|
||||
# oxDNA pair interactions
|
||||
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
|
||||
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna2/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
|
||||
pair_coeff * * oxdna2/dh 0.1 1.0 0.815
|
||||
|
||||
# NVE ensemble
|
||||
fix 1 all nve/dot
|
||||
#fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
#fix 1 all nve/asphere
|
||||
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
|
||||
timestep 1e-5
|
||||
|
||||
#comm_style tiled
|
||||
#fix 3 all balance 10000 1.1 rcb
|
||||
|
||||
#compute mol all chunk/atom molecule
|
||||
#compute mychunk all vcm/chunk mol
|
||||
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
|
||||
|
||||
#dump pos all xyz ${ofreq} traj.${number}.xyz
|
||||
|
||||
#compute quat all property/atom quatw quati quatj quatk
|
||||
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
|
||||
#dump_modify quat sort id
|
||||
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
compute epot all pe
|
||||
variable erot equal c_erot
|
||||
variable ekin equal c_ekin
|
||||
variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
|
||||
#dump_modify out sort id
|
||||
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
run 10000
|
||||
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
|
||||
6 neighbor lists, perpetual/occasional/extra = 6 0 0
|
||||
(1) pair oxdna2/excv, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: half/bin/3d/newtoff
|
||||
bin: standard
|
||||
(2) pair oxdna2/stk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) pair oxdna2/hbond, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(4) pair oxdna2/xstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(5) pair oxdna2/coaxstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(6) pair oxdna2/dh, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.652 | 7.834 | 8.016 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -1.4712768 0.009525411 -1.4617514 -5.8922361e-05
|
||||
1000 ekin = 0.00113086229080478 | erot = 0.00431010160406708 | epot = -14.6229549982368 | etot = -14.617514034342
|
||||
2000 ekin = 0.00448533224342286 | erot = 0.0171407706505013 | epot = -14.6391401372615 | etot = -14.6175140343675
|
||||
3000 ekin = 0.0099503525964896 | erot = 0.0381961780846438 | epot = -14.6656605650904 | etot = -14.6175140344093
|
||||
4000 ekin = 0.0173418024861991 | erot = 0.0669935184860479 | epot = -14.7018493554381 | etot = -14.6175140344659
|
||||
5000 ekin = 0.0264109356285965 | erot = 0.102878288094482 | epot = -14.7468032582586 | etot = -14.6175140345355
|
||||
6000 ekin = 0.0368533113591268 | erot = 0.145045420569809 | epot = -14.7994127665446 | etot = -14.6175140346156
|
||||
7000 ekin = 0.0483200640564584 | erot = 0.192565862515413 | epot = -14.8583999612755 | etot = -14.6175140347036
|
||||
8000 ekin = 0.0604312317605635 | erot = 0.24441787013137 | epot = -14.9223631366881 | etot = -14.6175140347962
|
||||
9000 ekin = 0.072790711967127 | erot = 0.299521949931654 | epot = -14.9898266967887 | etot = -14.6175140348899
|
||||
10000 ekin = 0.0850022498874609 | erot = 0.356777997217666 | epot = -15.0592942820866 | etot = -14.6175140349815
|
||||
10000 0.006296463 -1.5144685 0.0085391004 -1.4974292 -0.00010794792
|
||||
Loop time of 0.14583 on 4 procs for 10000 steps with 10 atoms
|
||||
|
||||
Performance: 59247.054 tau/day, 68572.979 timesteps/s
|
||||
97.5% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0034175 | 0.055587 | 0.10059 | 17.9 | 38.12
|
||||
Bond | 0.00064635 | 0.002131 | 0.0035357 | 2.5 | 1.46
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.014538 | 0.014932 | 0.015271 | 0.2 | 10.24
|
||||
Output | 5.7459e-05 | 5.7697e-05 | 5.7936e-05 | 0.0 | 0.04
|
||||
Modify | 0.0012829 | 0.0063873 | 0.011321 | 5.2 | 4.38
|
||||
Other | | 0.06674 | | | 45.76
|
||||
|
||||
Nlocal: 2.5 ave 5 max 0 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||
Nghost: 7.5 ave 10 max 5 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||
Neighs: 18.5 ave 35 max 0 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 74
|
||||
Ave neighs/atom = 7.4
|
||||
Ave special neighs/atom = 3.6
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
#write_restart config.${number}.*
|
||||
Total wall time: 0:00:00
|
||||
@ -38,7 +38,7 @@ Atoms
|
||||
15 3 4.860249842674773e-01 3.518234140414733e-01 3.897628551303119e-01 2 1 1
|
||||
16 4 5.999999999999995e-01 -3.330669073875470e-17 -3.330669073875470e-16 2 1 1
|
||||
|
||||
# Atom-ID, translational, rotational velocity
|
||||
# Atom-ID, translational velocity, angular momentum
|
||||
Velocities
|
||||
|
||||
1 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
variable number equal 2
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
|
||||
variable T equal 0.1
|
||||
units lj
|
||||
|
||||
dimension 3
|
||||
@ -30,19 +30,19 @@ bond_coeff * 2.0 0.25 0.7564
|
||||
# oxDNA pair interactions
|
||||
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
|
||||
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna2/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/stk seqav ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
|
||||
pair_coeff * * oxdna2/dh 0.1 1.0 0.815
|
||||
pair_coeff * * oxdna2/dh ${T} 1.0 0.815
|
||||
|
||||
# NVE ensemble
|
||||
#fix 1 all nve/dot
|
||||
fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10
|
||||
#fix 1 all nve/asphere
|
||||
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10
|
||||
|
||||
timestep 1e-5
|
||||
|
||||
@ -73,6 +73,6 @@ fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${e
|
||||
#dump_modify out sort id
|
||||
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
run 10000
|
||||
run 1000000
|
||||
|
||||
#write_restart config.${number}.*
|
||||
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
@ -1,178 +0,0 @@
|
||||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
variable number equal 2
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
|
||||
units lj
|
||||
|
||||
dimension 3
|
||||
|
||||
newton off
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid
|
||||
atom_modify sort 0 1.0
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
read_data data.duplex2
|
||||
orthogonal box = (-20 -20 -20) to (20 20 20)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
16 atoms
|
||||
reading velocities ...
|
||||
16 velocities
|
||||
16 ellipsoids
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
reading bonds ...
|
||||
13 bonds
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
4 = max # of 1-4 neighbors
|
||||
6 = max # of special neighbors
|
||||
|
||||
set atom * mass 3.1575
|
||||
16 settings made for mass
|
||||
|
||||
group all type 1 4
|
||||
16 atoms in group all
|
||||
|
||||
# oxDNA bond interactions - FENE backbone
|
||||
bond_style oxdna2/fene
|
||||
bond_coeff * 2.0 0.25 0.7564
|
||||
|
||||
# oxDNA pair interactions
|
||||
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
|
||||
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna2/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
|
||||
pair_coeff * * oxdna2/dh 0.1 1.0 0.815
|
||||
|
||||
# NVE ensemble
|
||||
#fix 1 all nve/dot
|
||||
fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
#fix 1 all nve/asphere
|
||||
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
|
||||
timestep 1e-5
|
||||
|
||||
#comm_style tiled
|
||||
#fix 3 all balance 10000 1.1 rcb
|
||||
|
||||
#compute mol all chunk/atom molecule
|
||||
#compute mychunk all vcm/chunk mol
|
||||
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
|
||||
|
||||
#dump pos all xyz ${ofreq} traj.${number}.xyz
|
||||
|
||||
#compute quat all property/atom quatw quati quatj quatk
|
||||
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
|
||||
#dump_modify quat sort id
|
||||
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
compute epot all pe
|
||||
variable erot equal c_erot
|
||||
variable ekin equal c_ekin
|
||||
variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
|
||||
#dump_modify out sort id
|
||||
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
run 10000
|
||||
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
|
||||
6 neighbor lists, perpetual/occasional/extra = 6 0 0
|
||||
(1) pair oxdna2/excv, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: half/bin/3d/newtoff
|
||||
bin: standard
|
||||
(2) pair oxdna2/stk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) pair oxdna2/hbond, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(4) pair oxdna2/xstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(5) pair oxdna2/coaxstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(6) pair oxdna2/dh, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.025 | 3.025 | 3.025 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -1.5358787 0.0096742456 -1.5262045 -7.9568629e-05
|
||||
1000 ekin = 1.54282272464468 | erot = 1.71757897250772 | epot = -24.4403527731341 | etot = -21.1799510759817
|
||||
2000 ekin = 1.86109566690716 | erot = 1.93804145796026 | epot = -24.3759816748265 | etot = -20.5768445499591
|
||||
3000 ekin = 2.68769182431188 | erot = 2.14559269500086 | epot = -24.2916556822451 | etot = -19.4583711629324
|
||||
4000 ekin = 2.04710303757243 | erot = 1.48774072590987 | epot = -24.190371461807 | etot = -20.6555276983247
|
||||
5000 ekin = 1.77654023802719 | erot = 2.534186505221 | epot = -24.1246365663843 | etot = -19.8139098231361
|
||||
6000 ekin = 3.12253137872527 | erot = 2.04028266818831 | epot = -24.0491248750916 | etot = -18.886310828178
|
||||
7000 ekin = 3.22418765752177 | erot = 2.72037570174023 | epot = -23.9458569915548 | etot = -18.0012936322928
|
||||
8000 ekin = 2.83204202112963 | erot = 2.67060276413777 | epot = -23.9211291529766 | etot = -18.4184843677092
|
||||
9000 ekin = 2.69585642754481 | erot = 2.59559820250212 | epot = -23.8340823338302 | etot = -18.5426277037833
|
||||
10000 ekin = 2.66058119525512 | erot = 1.95965933336077 | epot = -23.7132443170725 | etot = -19.0930037884566
|
||||
10000 0.11824805 -1.4953627 0.013284973 -1.3157914 -0.00012999454
|
||||
Loop time of 0.32781 on 1 procs for 10000 steps with 16 atoms
|
||||
|
||||
Performance: 26356.746 tau/day, 30505.493 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.24211 | 0.24211 | 0.24211 | 0.0 | 73.86
|
||||
Bond | 0.0075173 | 0.0075173 | 0.0075173 | 0.0 | 2.29
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0014515 | 0.0014515 | 0.0014515 | 0.0 | 0.44
|
||||
Output | 5.4836e-06 | 5.4836e-06 | 5.4836e-06 | 0.0 | 0.00
|
||||
Modify | 0.073331 | 0.073331 | 0.073331 | 0.0 | 22.37
|
||||
Other | | 0.003398 | | | 1.04
|
||||
|
||||
Nlocal: 16 ave 16 max 16 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 116 ave 116 max 116 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 116
|
||||
Ave neighs/atom = 7.25
|
||||
Ave special neighs/atom = 3.75
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
#write_restart config.${number}.*
|
||||
Total wall time: 0:00:00
|
||||
@ -1,178 +0,0 @@
|
||||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
variable number equal 2
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
|
||||
units lj
|
||||
|
||||
dimension 3
|
||||
|
||||
newton off
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid
|
||||
atom_modify sort 0 1.0
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
read_data data.duplex2
|
||||
orthogonal box = (-20 -20 -20) to (20 20 20)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
16 atoms
|
||||
reading velocities ...
|
||||
16 velocities
|
||||
16 ellipsoids
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
reading bonds ...
|
||||
13 bonds
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
4 = max # of 1-4 neighbors
|
||||
6 = max # of special neighbors
|
||||
|
||||
set atom * mass 3.1575
|
||||
16 settings made for mass
|
||||
|
||||
group all type 1 4
|
||||
16 atoms in group all
|
||||
|
||||
# oxDNA bond interactions - FENE backbone
|
||||
bond_style oxdna2/fene
|
||||
bond_coeff * 2.0 0.25 0.7564
|
||||
|
||||
# oxDNA pair interactions
|
||||
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
|
||||
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna2/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
|
||||
pair_coeff * * oxdna2/dh 0.1 1.0 0.815
|
||||
|
||||
# NVE ensemble
|
||||
#fix 1 all nve/dot
|
||||
fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
#fix 1 all nve/asphere
|
||||
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
|
||||
timestep 1e-5
|
||||
|
||||
#comm_style tiled
|
||||
#fix 3 all balance 10000 1.1 rcb
|
||||
|
||||
#compute mol all chunk/atom molecule
|
||||
#compute mychunk all vcm/chunk mol
|
||||
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
|
||||
|
||||
#dump pos all xyz ${ofreq} traj.${number}.xyz
|
||||
|
||||
#compute quat all property/atom quatw quati quatj quatk
|
||||
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
|
||||
#dump_modify quat sort id
|
||||
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
compute epot all pe
|
||||
variable erot equal c_erot
|
||||
variable ekin equal c_ekin
|
||||
variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
|
||||
#dump_modify out sort id
|
||||
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
run 10000
|
||||
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
|
||||
6 neighbor lists, perpetual/occasional/extra = 6 0 0
|
||||
(1) pair oxdna2/excv, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: half/bin/3d/newtoff
|
||||
bin: standard
|
||||
(2) pair oxdna2/stk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) pair oxdna2/hbond, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(4) pair oxdna2/xstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(5) pair oxdna2/coaxstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(6) pair oxdna2/dh, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.777 | 7.959 | 8.142 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -1.5358787 0.0096742456 -1.5262045 -7.9568629e-05
|
||||
1000 ekin = 1.34554291364716 | erot = 2.30525041754444 | epot = -24.3924150888896 | etot = -20.741621757698
|
||||
2000 ekin = 2.15972469811184 | erot = 2.1628675965276 | epot = -24.3548203354875 | etot = -20.0322280408481
|
||||
3000 ekin = 3.26433550542939 | erot = 2.76107866472085 | epot = -24.2947953202752 | etot = -18.269381150125
|
||||
4000 ekin = 1.9203212531997 | erot = 2.13339438425299 | epot = -24.234098584123 | etot = -20.1803829466703
|
||||
5000 ekin = 1.35481075814721 | erot = 2.00854026688447 | epot = -24.1768963201279 | etot = -20.8135452950963
|
||||
6000 ekin = 2.18974627635306 | erot = 1.73271671162435 | epot = -24.1096616118305 | etot = -20.1871986238531
|
||||
7000 ekin = 2.65472853187395 | erot = 1.73258720631296 | epot = -24.0561118130561 | etot = -19.6687960748691
|
||||
8000 ekin = 2.51192327964357 | erot = 2.34132844779952 | epot = -23.9708695663488 | etot = -19.1176178389058
|
||||
9000 ekin = 2.24554900802464 | erot = 2.0522939078286 | epot = -23.874757758319 | etot = -19.5769148424658
|
||||
10000 ekin = 2.36227360512089 | erot = 1.80185994066737 | epot = -23.7793375260418 | etot = -19.6152039802535
|
||||
10000 0.10498994 -1.5020657 0.015857071 -1.3385665 -8.8930899e-05
|
||||
Loop time of 0.291642 on 4 procs for 10000 steps with 16 atoms
|
||||
|
||||
Performance: 29625.313 tau/day, 34288.557 timesteps/s
|
||||
96.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0035026 | 0.1107 | 0.20674 | 28.3 | 37.96
|
||||
Bond | 0.00062203 | 0.0029532 | 0.0049176 | 3.6 | 1.01
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.016712 | 0.018041 | 0.01914 | 0.7 | 6.19
|
||||
Output | 5.0306e-05 | 5.424e-05 | 5.579e-05 | 0.0 | 0.02
|
||||
Modify | 0.0013862 | 0.020914 | 0.039594 | 11.7 | 7.17
|
||||
Other | | 0.139 | | | 47.65
|
||||
|
||||
Nlocal: 4 ave 8 max 0 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 1 1
|
||||
Nghost: 11 ave 14 max 8 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 1 1
|
||||
Neighs: 46 ave 89 max 0 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 184
|
||||
Ave neighs/atom = 11.5
|
||||
Ave special neighs/atom = 3.75
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
#write_restart config.${number}.*
|
||||
Total wall time: 0:00:00
|
||||
73
examples/USER/cgdna/examples/oxDNA2/duplex3/data.duplex3
Normal file
73
examples/USER/cgdna/examples/oxDNA2/duplex3/data.duplex3
Normal file
@ -0,0 +1,73 @@
|
||||
# LAMMPS data file
|
||||
10 atoms
|
||||
10 ellipsoids
|
||||
8 bonds
|
||||
|
||||
4 atom types
|
||||
1 bond types
|
||||
|
||||
# System size
|
||||
-20.000000 20.000000 xlo xhi
|
||||
-20.000000 20.000000 ylo yhi
|
||||
-20.000000 20.000000 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 1.0
|
||||
2 1.0
|
||||
3 1.0
|
||||
4 1.0
|
||||
|
||||
# Atom-ID, type, position, molecule-ID, ellipsoid flag, density
|
||||
Atoms
|
||||
|
||||
1 1 -6.000000000000001e-01 0.000000000000000e+00 0.000000000000000e+00 1 1 1
|
||||
2 2 -4.860249842674776e-01 -3.518234140414736e-01 3.897628551303122e-01 1 1 1
|
||||
3 3 -1.874009511073395e-01 -5.699832309147915e-01 7.795257102606244e-01 1 1 1
|
||||
4 4 1.824198365552941e-01 -5.715968887521518e-01 1.169288565390937e+00 1 1 1
|
||||
5 1 4.829362784135484e-01 -3.560513319622209e-01 1.559051420521249e+00 1 1 1
|
||||
6 4 -4.829362784135484e-01 3.560513319622209e-01 1.559051420521249e+00 2 1 1
|
||||
7 1 -1.824198365552941e-01 5.715968887521516e-01 1.169288565390937e+00 2 1 1
|
||||
8 2 1.874009511073395e-01 5.699832309147913e-01 7.795257102606243e-01 2 1 1
|
||||
9 3 4.860249842674775e-01 3.518234140414733e-01 3.897628551303121e-01 2 1 1
|
||||
10 4 5.999999999999996e-01 -1.332267629550188e-16 -1.110223024625157e-16 2 1 1
|
||||
|
||||
# Atom-ID, translational velocity, angular momentum
|
||||
Velocities
|
||||
|
||||
1 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
2 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
3 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
4 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
5 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
6 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
7 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
8 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
9 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
10 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
|
||||
# Atom-ID, shape, quaternion
|
||||
Ellipsoids
|
||||
|
||||
1 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
2 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 9.513258223252946e-01 0.000000000000000e+00 0.000000000000000e+00 3.081869234362515e-01
|
||||
3 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 8.100416404457962e-01 0.000000000000000e+00 0.000000000000000e+00 5.863723567357894e-01
|
||||
4 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 5.899012371043606e-01 0.000000000000000e+00 0.000000000000000e+00 8.074754054847398e-01
|
||||
5 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 3.123349185122326e-01 0.000000000000000e+00 0.000000000000000e+00 9.499720515246527e-01
|
||||
6 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 0.000000000000000e+00 9.499720515246527e-01 -3.123349185122326e-01 -0.000000000000000e+00
|
||||
7 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 0.000000000000000e+00 8.074754054847401e-01 -5.899012371043604e-01 0.000000000000000e+00
|
||||
8 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 0.000000000000000e+00 5.863723567357896e-01 -8.100416404457959e-01 0.000000000000000e+00
|
||||
9 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 -0.000000000000000e+00 -3.081869234362514e-01 9.513258223252947e-01 0.000000000000000e+00
|
||||
10 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 -0.000000000000000e+00 1.110223024625157e-16 1.000000000000000e+00 -0.000000000000000e+00
|
||||
|
||||
# Bond topology
|
||||
Bonds
|
||||
|
||||
1 1 1 2
|
||||
2 1 2 3
|
||||
3 1 3 4
|
||||
4 1 4 5
|
||||
5 1 6 7
|
||||
6 1 7 8
|
||||
7 1 8 9
|
||||
8 1 9 10
|
||||
79
examples/USER/cgdna/examples/oxDNA2/duplex3/in.duplex3
Normal file
79
examples/USER/cgdna/examples/oxDNA2/duplex3/in.duplex3
Normal file
@ -0,0 +1,79 @@
|
||||
variable number equal 1
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
variable T equal 0.1
|
||||
|
||||
units lj
|
||||
|
||||
dimension 3
|
||||
|
||||
newton off
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid
|
||||
atom_modify sort 0 1.0
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
read_data data.duplex3
|
||||
|
||||
set atom * mass 1.0
|
||||
|
||||
group all type 1 4
|
||||
|
||||
# oxDNA bond interactions - FENE backbone
|
||||
bond_style oxdna2/fene
|
||||
bond_coeff * 2.0 0.25 0.7564
|
||||
|
||||
# oxDNA pair interactions
|
||||
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
|
||||
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna2/stk seqdep ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/hbond seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
|
||||
pair_coeff * * oxdna2/dh ${T} 1.0 0.815
|
||||
|
||||
# NVE ensemble
|
||||
fix 1 all nve/dot
|
||||
#fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10
|
||||
#fix 1 all nve/asphere
|
||||
#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10
|
||||
|
||||
timestep 1e-5
|
||||
|
||||
#comm_style tiled
|
||||
#fix 3 all balance 10000 1.1 rcb
|
||||
|
||||
#compute mol all chunk/atom molecule
|
||||
#compute mychunk all vcm/chunk mol
|
||||
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
|
||||
|
||||
#dump pos all xyz ${ofreq} traj.${number}.xyz
|
||||
|
||||
#compute quat all property/atom quatw quati quatj quatk
|
||||
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
|
||||
#dump_modify quat sort id
|
||||
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
compute epot all pe
|
||||
variable erot equal c_erot
|
||||
variable ekin equal c_ekin
|
||||
variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
|
||||
#dump_modify out sort id
|
||||
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
run 1000000
|
||||
|
||||
#write_restart config.${number}.*
|
||||
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
@ -38,6 +38,8 @@ fix myrxns all bond/react stabilization yes statted_grp .03 &
|
||||
|
||||
fix 1 statted_grp_REACT nvt temp 300 300 100
|
||||
|
||||
# optionally, you can customize behavior of reacting atoms,
|
||||
# by using the internally-created 'bond_react_MASTER_group', like so:
|
||||
fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1
|
||||
|
||||
thermo_style custom step temp press density f_myrxns[1] f_myrxns[2]
|
||||
@ -0,0 +1,48 @@
|
||||
# two monomer nylon example
|
||||
# reaction produces a condensed water molecule
|
||||
|
||||
units real
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style full
|
||||
|
||||
kspace_style pppm 1.0e-4
|
||||
|
||||
pair_style lj/class2/coul/long 8.5
|
||||
|
||||
angle_style class2
|
||||
|
||||
bond_style class2
|
||||
|
||||
dihedral_style class2
|
||||
|
||||
improper_style class2
|
||||
|
||||
read_data tiny_nylon.data
|
||||
|
||||
velocity all create 300.0 4928459 dist gaussian
|
||||
|
||||
molecule mol1 rxn1_stp1_unreacted.data_template
|
||||
molecule mol2 rxn1_stp1_reacted.data_template
|
||||
molecule mol3 rxn1_stp2_unreacted.data_template
|
||||
molecule mol4 rxn1_stp2_reacted.data_template
|
||||
|
||||
thermo 50
|
||||
|
||||
# dump 1 all xyz 1 test_vis.xyz
|
||||
|
||||
fix myrxns all bond/react stabilization no &
|
||||
react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map &
|
||||
react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
|
||||
|
||||
fix 1 all nve/limit .03
|
||||
|
||||
thermo_style custom step temp press density f_myrxns[1] f_myrxns[2]
|
||||
|
||||
# restart 100 restart1 restart2
|
||||
|
||||
run 1000
|
||||
|
||||
# write_restart restart_longrun
|
||||
# write_data restart_longrun.data
|
||||
@ -1,370 +0,0 @@
|
||||
LAMMPS (20 Apr 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# two monomer nylon example
|
||||
# reaction produces a condensed water molecule
|
||||
|
||||
units real
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style full
|
||||
|
||||
kspace_style pppm 1.0e-4
|
||||
|
||||
pair_style lj/class2/coul/long 8.5
|
||||
|
||||
angle_style class2
|
||||
|
||||
bond_style class2
|
||||
|
||||
dihedral_style class2
|
||||
|
||||
improper_style class2
|
||||
|
||||
read_data tiny_nylon.data
|
||||
orthogonal box = (-25 -25 -25) to (25 25 25)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
44 atoms
|
||||
reading velocities ...
|
||||
44 velocities
|
||||
scanning bonds ...
|
||||
9 = max bonds/atom
|
||||
scanning angles ...
|
||||
21 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
29 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
29 = max impropers/atom
|
||||
reading bonds ...
|
||||
42 bonds
|
||||
reading angles ...
|
||||
74 angles
|
||||
reading dihedrals ...
|
||||
100 dihedrals
|
||||
reading impropers ...
|
||||
44 impropers
|
||||
4 = max # of 1-2 neighbors
|
||||
6 = max # of 1-3 neighbors
|
||||
12 = max # of 1-4 neighbors
|
||||
41 = max # of special neighbors
|
||||
|
||||
velocity all create 300.0 4928459 dist gaussian
|
||||
|
||||
molecule mol1 rxn1_stp1_unreacted.data_template
|
||||
Read molecule mol1:
|
||||
18 atoms with max type 8
|
||||
16 bonds with max type 14
|
||||
25 angles with max type 28
|
||||
23 dihedrals with max type 36
|
||||
14 impropers with max type 11
|
||||
molecule mol2 rxn1_stp1_reacted.data_template
|
||||
Read molecule mol2:
|
||||
18 atoms with max type 9
|
||||
17 bonds with max type 13
|
||||
31 angles with max type 27
|
||||
39 dihedrals with max type 33
|
||||
20 impropers with max type 1
|
||||
molecule mol3 rxn1_stp2_unreacted.data_template
|
||||
Read molecule mol3:
|
||||
15 atoms with max type 9
|
||||
14 bonds with max type 13
|
||||
25 angles with max type 27
|
||||
30 dihedrals with max type 33
|
||||
16 impropers with max type 1
|
||||
molecule mol4 rxn1_stp2_reacted.data_template
|
||||
Read molecule mol4:
|
||||
15 atoms with max type 11
|
||||
13 bonds with max type 15
|
||||
19 angles with max type 29
|
||||
16 dihedrals with max type 32
|
||||
10 impropers with max type 13
|
||||
|
||||
thermo 50
|
||||
|
||||
# dump 1 all xyz 1 test_vis.xyz
|
||||
|
||||
fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
|
||||
WARNING: An atom in 'react #1' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
|
||||
WARNING: An atom in 'react #2' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
|
||||
dynamic group bond_react_MASTER_group defined
|
||||
dynamic group statted_grp defined
|
||||
dynamic group bond_react_MASTER_group defined
|
||||
dynamic group statted_grp defined
|
||||
|
||||
fix 1 statted_grp nvt temp 300 300 100
|
||||
|
||||
fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1
|
||||
|
||||
thermo_style custom step temp press density f_myrxns[1] f_myrxns[2]
|
||||
|
||||
# restart 100 restart1 restart2
|
||||
|
||||
run 10000
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (../kspace.cpp:321)
|
||||
G vector (1/distance) = 0.0534597
|
||||
grid = 2 2 2
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0402256
|
||||
estimated relative force accuracy = 0.000121138
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 343 8
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 10.5
|
||||
ghost atom cutoff = 10.5
|
||||
binsize = 5.25, bins = 10 10 10
|
||||
2 neighbor lists, perpetual/occasional/extra = 1 1 0
|
||||
(1) pair lj/class2/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
(2) fix bond/react, occasional, copy from (1)
|
||||
attributes: half, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
WARNING: Inconsistent image flags (../domain.cpp:786)
|
||||
Per MPI rank memory allocation (min/avg/max) = 33.34 | 33.34 | 33.34 Mbytes
|
||||
Step Temp Press Density f_myrxns[1] f_myrxns[2]
|
||||
0 300 346.78165 0.0034851739 0 0
|
||||
50 296.70408 -51.30066 0.0034851739 1 0
|
||||
100 274.25324 46.715512 0.0034851739 1 1
|
||||
150 471.61579 31.321598 0.0034851739 1 1
|
||||
200 362.87766 42.061118 0.0034851739 1 1
|
||||
250 367.58058 65.303109 0.0034851739 1 1
|
||||
300 372.38236 -52.421725 0.0034851739 1 1
|
||||
350 297.69957 17.869945 0.0034851739 1 1
|
||||
400 258.30433 49.19156 0.0034851739 1 1
|
||||
450 253.34384 -5.8162637 0.0034851739 1 1
|
||||
500 269.96465 -43.337517 0.0034851739 1 1
|
||||
550 303.23718 10.180246 0.0034851739 1 1
|
||||
600 329.59579 -48.97461 0.0034851739 1 1
|
||||
650 350.42568 50.983183 0.0034851739 1 1
|
||||
700 342.03272 35.43465 0.0034851739 1 1
|
||||
750 269.23405 -41.873166 0.0034851739 1 1
|
||||
800 245.15025 13.953092 0.0034851739 1 1
|
||||
850 257.85421 -3.1492141 0.0034851739 1 1
|
||||
900 316.15644 7.7798301 0.0034851739 1 1
|
||||
950 299.9124 -15.77014 0.0034851739 1 1
|
||||
1000 302.89968 -17.049693 0.0034851739 1 1
|
||||
1050 308.91651 71.84632 0.0034851739 1 1
|
||||
1100 348.43932 -18.742012 0.0034851739 1 1
|
||||
1150 309.03036 50.536311 0.0034851739 1 1
|
||||
1200 318.9761 -16.905746 0.0034851739 1 1
|
||||
1250 320.42806 -0.057975092 0.0034851739 1 1
|
||||
1300 289.7824 18.200772 0.0034851739 1 1
|
||||
1350 284.79836 -9.1978427 0.0034851739 1 1
|
||||
1400 325.43292 42.082833 0.0034851739 1 1
|
||||
1450 261.5041 -37.823325 0.0034851739 1 1
|
||||
1500 298.88723 -5.1647385 0.0034851739 1 1
|
||||
1550 291.37403 -7.7764201 0.0034851739 1 1
|
||||
1600 293.83475 22.2458 0.0034851739 1 1
|
||||
1650 293.80611 24.202512 0.0034851739 1 1
|
||||
1700 291.70205 -23.397884 0.0034851739 1 1
|
||||
1750 292.32437 -10.671214 0.0034851739 1 1
|
||||
1800 302.01367 -11.671025 0.0034851739 1 1
|
||||
1850 322.1651 24.438331 0.0034851739 1 1
|
||||
1900 310.45076 45.343592 0.0034851739 1 1
|
||||
1950 325.91745 -19.847809 0.0034851739 1 1
|
||||
2000 276.89662 63.387098 0.0034851739 1 1
|
||||
2050 311.33783 -24.683247 0.0034851739 1 1
|
||||
2100 346.2336 -27.526891 0.0034851739 1 1
|
||||
2150 345.30604 -15.722411 0.0034851739 1 1
|
||||
2200 346.7718 -17.857633 0.0034851739 1 1
|
||||
2250 304.28676 -1.9965581 0.0034851739 1 1
|
||||
2300 322.56372 -31.786868 0.0034851739 1 1
|
||||
2350 282.64326 6.1982735 0.0034851739 1 1
|
||||
2400 286.65759 -63.207781 0.0034851739 1 1
|
||||
2450 257.05528 32.931491 0.0034851739 1 1
|
||||
2500 283.64386 26.912373 0.0034851739 1 1
|
||||
2550 299.54005 27.277039 0.0034851739 1 1
|
||||
2600 283.92503 14.660972 0.0034851739 1 1
|
||||
2650 321.93453 -18.977358 0.0034851739 1 1
|
||||
2700 376.7189 31.826935 0.0034851739 1 1
|
||||
2750 372.20075 -32.821697 0.0034851739 1 1
|
||||
2800 361.40604 83.035183 0.0034851739 1 1
|
||||
2850 332.27269 -23.927452 0.0034851739 1 1
|
||||
2900 331.14638 -0.12328446 0.0034851739 1 1
|
||||
2950 303.67489 -24.078857 0.0034851739 1 1
|
||||
3000 311.40462 21.563537 0.0034851739 1 1
|
||||
3050 284.72849 -23.849667 0.0034851739 1 1
|
||||
3100 303.48477 39.347763 0.0034851739 1 1
|
||||
3150 264.2739 -0.22299879 0.0034851739 1 1
|
||||
3200 300.03351 31.545323 0.0034851739 1 1
|
||||
3250 288.56663 5.7225228 0.0034851739 1 1
|
||||
3300 200.13238 -31.239655 0.0034851739 1 1
|
||||
3350 231.32512 16.631728 0.0034851739 1 1
|
||||
3400 260.57402 2.1717992 0.0034851739 1 1
|
||||
3450 301.47128 -42.210623 0.0034851739 1 1
|
||||
3500 321.77414 40.074365 0.0034851739 1 1
|
||||
3550 353.21858 28.387783 0.0034851739 1 1
|
||||
3600 331.45989 -57.800858 0.0034851739 1 1
|
||||
3650 303.88123 44.86596 0.0034851739 1 1
|
||||
3700 329.73833 -0.80615652 0.0034851739 1 1
|
||||
3750 297.55588 -0.49626039 0.0034851739 1 1
|
||||
3800 286.38794 -10.010003 0.0034851739 1 1
|
||||
3850 290.17417 -43.51187 0.0034851739 1 1
|
||||
3900 247.88933 51.23735 0.0034851739 1 1
|
||||
3950 332.31324 -18.194985 0.0034851739 1 1
|
||||
4000 325.56802 18.402825 0.0034851739 1 1
|
||||
4050 338.37593 36.430977 0.0034851739 1 1
|
||||
4100 370.95478 39.290285 0.0034851739 1 1
|
||||
4150 348.47859 -7.0779678 0.0034851739 1 1
|
||||
4200 241.30632 -33.371788 0.0034851739 1 1
|
||||
4250 242.17258 -9.986197 0.0034851739 1 1
|
||||
4300 300.85311 -7.9244294 0.0034851739 1 1
|
||||
4350 273.15684 -21.257283 0.0034851739 1 1
|
||||
4400 305.77463 -5.8720722 0.0034851739 1 1
|
||||
4450 314.97697 45.0373 0.0034851739 1 1
|
||||
4500 310.77723 16.958773 0.0034851739 1 1
|
||||
4550 302.1742 12.156862 0.0034851739 1 1
|
||||
4600 319.74799 6.84889 0.0034851739 1 1
|
||||
4650 270.86805 -13.767905 0.0034851739 1 1
|
||||
4700 249.81731 -31.197487 0.0034851739 1 1
|
||||
4750 285.86481 -9.8916364 0.0034851739 1 1
|
||||
4800 233.98321 7.1338571 0.0034851739 1 1
|
||||
4850 302.60551 49.262889 0.0034851739 1 1
|
||||
4900 316.55056 34.663247 0.0034851739 1 1
|
||||
4950 357.32741 11.583006 0.0034851739 1 1
|
||||
5000 400.21045 -8.1781061 0.0034851739 1 1
|
||||
5050 390.01845 -20.490275 0.0034851739 1 1
|
||||
5100 378.84247 -41.328757 0.0034851739 1 1
|
||||
5150 324.02038 -15.023862 0.0034851739 1 1
|
||||
5200 262.08429 10.937354 0.0034851739 1 1
|
||||
5250 255.75508 16.381455 0.0034851739 1 1
|
||||
5300 277.84989 40.68232 0.0034851739 1 1
|
||||
5350 302.92832 9.1989494 0.0034851739 1 1
|
||||
5400 283.7196 -1.6584671 0.0034851739 1 1
|
||||
5450 300.71266 -4.7030295 0.0034851739 1 1
|
||||
5500 343.5499 -0.30550044 0.0034851739 1 1
|
||||
5550 369.51271 21.691649 0.0034851739 1 1
|
||||
5600 372.69789 -38.67994 0.0034851739 1 1
|
||||
5650 327.41266 11.352137 0.0034851739 1 1
|
||||
5700 278.98614 -23.827304 0.0034851739 1 1
|
||||
5750 308.30054 -20.756187 0.0034851739 1 1
|
||||
5800 341.45594 28.058441 0.0034851739 1 1
|
||||
5850 322.97844 -10.731921 0.0034851739 1 1
|
||||
5900 304.53591 32.825279 0.0034851739 1 1
|
||||
5950 287.1752 -36.780091 0.0034851739 1 1
|
||||
6000 296.52681 18.781896 0.0034851739 1 1
|
||||
6050 314.25442 15.992829 0.0034851739 1 1
|
||||
6100 313.86576 3.4342714 0.0034851739 1 1
|
||||
6150 325.64196 32.392039 0.0034851739 1 1
|
||||
6200 367.42931 -27.160706 0.0034851739 1 1
|
||||
6250 369.30798 39.020934 0.0034851739 1 1
|
||||
6300 328.92285 -23.175157 0.0034851739 1 1
|
||||
6350 305.63077 4.9024453 0.0034851739 1 1
|
||||
6400 241.70341 -13.676629 0.0034851739 1 1
|
||||
6450 265.66717 2.40612 0.0034851739 1 1
|
||||
6500 249.36037 13.420255 0.0034851739 1 1
|
||||
6550 294.53814 10.853462 0.0034851739 1 1
|
||||
6600 308.2025 18.995308 0.0034851739 1 1
|
||||
6650 305.43797 -49.56785 0.0034851739 1 1
|
||||
6700 320.27344 11.336281 0.0034851739 1 1
|
||||
6750 321.78666 -23.463899 0.0034851739 1 1
|
||||
6800 303.40388 7.6224553 0.0034851739 1 1
|
||||
6850 297.18966 51.52256 0.0034851739 1 1
|
||||
6900 284.18909 -8.4947203 0.0034851739 1 1
|
||||
6950 331.03663 13.233655 0.0034851739 1 1
|
||||
7000 311.37928 -43.265479 0.0034851739 1 1
|
||||
7050 286.81661 -14.174683 0.0034851739 1 1
|
||||
7100 302.84119 12.048954 0.0034851739 1 1
|
||||
7150 297.19357 -43.111968 0.0034851739 1 1
|
||||
7200 332.47359 26.048249 0.0034851739 1 1
|
||||
7250 262.70677 41.176242 0.0034851739 1 1
|
||||
7300 250.61405 -23.413982 0.0034851739 1 1
|
||||
7350 296.91117 35.88133 0.0034851739 1 1
|
||||
7400 245.09229 -13.447194 0.0034851739 1 1
|
||||
7450 272.28131 -23.322585 0.0034851739 1 1
|
||||
7500 209.04985 13.871239 0.0034851739 1 1
|
||||
7550 255.00955 4.9325621 0.0034851739 1 1
|
||||
7600 312.30937 -37.368274 0.0034851739 1 1
|
||||
7650 305.65903 55.245496 0.0034851739 1 1
|
||||
7700 325.09504 -18.347711 0.0034851739 1 1
|
||||
7750 363.28282 -22.479686 0.0034851739 1 1
|
||||
7800 350.17429 26.849547 0.0034851739 1 1
|
||||
7850 271.70853 -17.764575 0.0034851739 1 1
|
||||
7900 272.66484 -11.701967 0.0034851739 1 1
|
||||
7950 298.60202 -12.765675 0.0034851739 1 1
|
||||
8000 274.58852 49.641532 0.0034851739 1 1
|
||||
8050 304.72347 -0.55414183 0.0034851739 1 1
|
||||
8100 328.30757 -39.861301 0.0034851739 1 1
|
||||
8150 406.67601 2.8999409 0.0034851739 1 1
|
||||
8200 332.20083 -51.217399 0.0034851739 1 1
|
||||
8250 354.50609 53.128769 0.0034851739 1 1
|
||||
8300 337.2758 20.68562 0.0034851739 1 1
|
||||
8350 361.89708 -54.185869 0.0034851739 1 1
|
||||
8400 305.63496 24.058529 0.0034851739 1 1
|
||||
8450 303.27461 4.304683 0.0034851739 1 1
|
||||
8500 253.53694 -10.909021 0.0034851739 1 1
|
||||
8550 277.03017 23.241479 0.0034851739 1 1
|
||||
8600 291.41844 -22.240665 0.0034851739 1 1
|
||||
8650 307.85368 31.919587 0.0034851739 1 1
|
||||
8700 309.19724 0.53529642 0.0034851739 1 1
|
||||
8750 354.6583 11.565515 0.0034851739 1 1
|
||||
8800 329.78598 19.5996 0.0034851739 1 1
|
||||
8850 240.79198 21.803515 0.0034851739 1 1
|
||||
8900 318.40749 -59.816923 0.0034851739 1 1
|
||||
8950 308.47211 -57.808635 0.0034851739 1 1
|
||||
9000 271.51207 50.943482 0.0034851739 1 1
|
||||
9050 249.4005 6.7529187 0.0034851739 1 1
|
||||
9100 221.8772 47.196092 0.0034851739 1 1
|
||||
9150 297.9351 4.0058184 0.0034851739 1 1
|
||||
9200 274.85051 -24.774393 0.0034851739 1 1
|
||||
9250 336.04757 5.3799028 0.0034851739 1 1
|
||||
9300 380.44956 -22.389381 0.0034851739 1 1
|
||||
9350 336.9824 23.050616 0.0034851739 1 1
|
||||
9400 304.46425 32.530218 0.0034851739 1 1
|
||||
9450 317.55591 -22.265425 0.0034851739 1 1
|
||||
9500 323.70901 -7.0159787 0.0034851739 1 1
|
||||
9550 316.07308 28.062131 0.0034851739 1 1
|
||||
9600 262.74608 -0.78519192 0.0034851739 1 1
|
||||
9650 271.55045 -21.430123 0.0034851739 1 1
|
||||
9700 239.6022 14.483637 0.0034851739 1 1
|
||||
9750 338.1437 -0.72765302 0.0034851739 1 1
|
||||
9800 334.50189 19.495144 0.0034851739 1 1
|
||||
9850 354.87554 19.272719 0.0034851739 1 1
|
||||
9900 334.02141 -22.393457 0.0034851739 1 1
|
||||
9950 293.63651 19.178873 0.0034851739 1 1
|
||||
10000 319.81736 21.904414 0.0034851739 1 1
|
||||
Loop time of 1.84987 on 1 procs for 10000 steps with 44 atoms
|
||||
|
||||
Performance: 467.059 ns/day, 0.051 hours/ns, 5405.774 timesteps/s
|
||||
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.26152 | 0.26152 | 0.26152 | 0.0 | 14.14
|
||||
Bond | 0.74069 | 0.74069 | 0.74069 | 0.0 | 40.04
|
||||
Kspace | 0.30505 | 0.30505 | 0.30505 | 0.0 | 16.49
|
||||
Neigh | 0.39991 | 0.39991 | 0.39991 | 0.0 | 21.62
|
||||
Comm | 0.02261 | 0.02261 | 0.02261 | 0.0 | 1.22
|
||||
Output | 0.0034585 | 0.0034585 | 0.0034585 | 0.0 | 0.19
|
||||
Modify | 0.099979 | 0.099979 | 0.099979 | 0.0 | 5.40
|
||||
Other | | 0.01666 | | | 0.90
|
||||
|
||||
Nlocal: 44 ave 44 max 44 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 44 ave 44 max 44 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 823 ave 823 max 823 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 823
|
||||
Ave neighs/atom = 18.7045
|
||||
Ave special neighs/atom = 9.77273
|
||||
Neighbor list builds = 10000
|
||||
Dangerous builds = 0
|
||||
|
||||
# write_restart restart_longrun
|
||||
# write_data restart_longrun.data
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:01
|
||||
@ -1,370 +0,0 @@
|
||||
LAMMPS (20 Apr 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# two monomer nylon example
|
||||
# reaction produces a condensed water molecule
|
||||
|
||||
units real
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style full
|
||||
|
||||
kspace_style pppm 1.0e-4
|
||||
|
||||
pair_style lj/class2/coul/long 8.5
|
||||
|
||||
angle_style class2
|
||||
|
||||
bond_style class2
|
||||
|
||||
dihedral_style class2
|
||||
|
||||
improper_style class2
|
||||
|
||||
read_data tiny_nylon.data
|
||||
orthogonal box = (-25 -25 -25) to (25 25 25)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
44 atoms
|
||||
reading velocities ...
|
||||
44 velocities
|
||||
scanning bonds ...
|
||||
9 = max bonds/atom
|
||||
scanning angles ...
|
||||
21 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
29 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
29 = max impropers/atom
|
||||
reading bonds ...
|
||||
42 bonds
|
||||
reading angles ...
|
||||
74 angles
|
||||
reading dihedrals ...
|
||||
100 dihedrals
|
||||
reading impropers ...
|
||||
44 impropers
|
||||
4 = max # of 1-2 neighbors
|
||||
6 = max # of 1-3 neighbors
|
||||
12 = max # of 1-4 neighbors
|
||||
41 = max # of special neighbors
|
||||
|
||||
velocity all create 300.0 4928459 dist gaussian
|
||||
|
||||
molecule mol1 rxn1_stp1_unreacted.data_template
|
||||
Read molecule mol1:
|
||||
18 atoms with max type 8
|
||||
16 bonds with max type 14
|
||||
25 angles with max type 28
|
||||
23 dihedrals with max type 36
|
||||
14 impropers with max type 11
|
||||
molecule mol2 rxn1_stp1_reacted.data_template
|
||||
Read molecule mol2:
|
||||
18 atoms with max type 9
|
||||
17 bonds with max type 13
|
||||
31 angles with max type 27
|
||||
39 dihedrals with max type 33
|
||||
20 impropers with max type 1
|
||||
molecule mol3 rxn1_stp2_unreacted.data_template
|
||||
Read molecule mol3:
|
||||
15 atoms with max type 9
|
||||
14 bonds with max type 13
|
||||
25 angles with max type 27
|
||||
30 dihedrals with max type 33
|
||||
16 impropers with max type 1
|
||||
molecule mol4 rxn1_stp2_reacted.data_template
|
||||
Read molecule mol4:
|
||||
15 atoms with max type 11
|
||||
13 bonds with max type 15
|
||||
19 angles with max type 29
|
||||
16 dihedrals with max type 32
|
||||
10 impropers with max type 13
|
||||
|
||||
thermo 50
|
||||
|
||||
# dump 1 all xyz 1 test_vis.xyz
|
||||
|
||||
fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
|
||||
WARNING: An atom in 'react #1' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
|
||||
WARNING: An atom in 'react #2' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
|
||||
dynamic group bond_react_MASTER_group defined
|
||||
dynamic group statted_grp defined
|
||||
dynamic group bond_react_MASTER_group defined
|
||||
dynamic group statted_grp defined
|
||||
|
||||
fix 1 statted_grp nvt temp 300 300 100
|
||||
|
||||
fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1
|
||||
|
||||
thermo_style custom step temp press density f_myrxns[1] f_myrxns[2]
|
||||
|
||||
# restart 100 restart1 restart2
|
||||
|
||||
run 10000
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (../kspace.cpp:321)
|
||||
G vector (1/distance) = 0.0534597
|
||||
grid = 2 2 2
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0402256
|
||||
estimated relative force accuracy = 0.000121138
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 252 2
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 10.5
|
||||
ghost atom cutoff = 10.5
|
||||
binsize = 5.25, bins = 10 10 10
|
||||
2 neighbor lists, perpetual/occasional/extra = 1 1 0
|
||||
(1) pair lj/class2/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
(2) fix bond/react, occasional, copy from (1)
|
||||
attributes: half, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
WARNING: Inconsistent image flags (../domain.cpp:786)
|
||||
Per MPI rank memory allocation (min/avg/max) = 33.34 | 33.69 | 34.37 Mbytes
|
||||
Step Temp Press Density f_myrxns[1] f_myrxns[2]
|
||||
0 300 346.78165 0.0034851739 0 0
|
||||
50 296.70408 -51.30066 0.0034851739 1 0
|
||||
100 274.25324 46.715512 0.0034851739 1 1
|
||||
150 471.61579 31.321598 0.0034851739 1 1
|
||||
200 362.87766 42.061118 0.0034851739 1 1
|
||||
250 367.58058 65.303109 0.0034851739 1 1
|
||||
300 372.38236 -52.421725 0.0034851739 1 1
|
||||
350 297.69957 17.869945 0.0034851739 1 1
|
||||
400 258.30433 49.19156 0.0034851739 1 1
|
||||
450 253.34384 -5.8162637 0.0034851739 1 1
|
||||
500 269.96465 -43.337517 0.0034851739 1 1
|
||||
550 303.23718 10.180246 0.0034851739 1 1
|
||||
600 329.59579 -48.97461 0.0034851739 1 1
|
||||
650 350.42568 50.983183 0.0034851739 1 1
|
||||
700 342.03272 35.43465 0.0034851739 1 1
|
||||
750 269.23405 -41.873166 0.0034851739 1 1
|
||||
800 245.15025 13.953092 0.0034851739 1 1
|
||||
850 257.85421 -3.1492141 0.0034851739 1 1
|
||||
900 316.15644 7.7798301 0.0034851739 1 1
|
||||
950 299.9124 -15.77014 0.0034851739 1 1
|
||||
1000 302.89968 -17.049693 0.0034851739 1 1
|
||||
1050 308.91651 71.84632 0.0034851739 1 1
|
||||
1100 348.43932 -18.742012 0.0034851739 1 1
|
||||
1150 309.03036 50.536311 0.0034851739 1 1
|
||||
1200 318.9761 -16.905746 0.0034851739 1 1
|
||||
1250 320.42806 -0.057975092 0.0034851739 1 1
|
||||
1300 289.7824 18.200772 0.0034851739 1 1
|
||||
1350 284.79836 -9.1978427 0.0034851739 1 1
|
||||
1400 325.43292 42.082833 0.0034851739 1 1
|
||||
1450 261.5041 -37.823325 0.0034851739 1 1
|
||||
1500 298.88723 -5.1647385 0.0034851739 1 1
|
||||
1550 291.37403 -7.7764201 0.0034851739 1 1
|
||||
1600 293.83475 22.2458 0.0034851739 1 1
|
||||
1650 293.80611 24.202512 0.0034851739 1 1
|
||||
1700 291.70205 -23.397884 0.0034851739 1 1
|
||||
1750 292.32437 -10.671214 0.0034851739 1 1
|
||||
1800 302.01367 -11.671025 0.0034851739 1 1
|
||||
1850 322.1651 24.438331 0.0034851739 1 1
|
||||
1900 310.45076 45.343592 0.0034851739 1 1
|
||||
1950 325.91745 -19.847809 0.0034851739 1 1
|
||||
2000 276.89662 63.387098 0.0034851739 1 1
|
||||
2050 311.33783 -24.683247 0.0034851739 1 1
|
||||
2100 346.2336 -27.526891 0.0034851739 1 1
|
||||
2150 345.30604 -15.722411 0.0034851739 1 1
|
||||
2200 346.7718 -17.857633 0.0034851739 1 1
|
||||
2250 304.28676 -1.9965581 0.0034851739 1 1
|
||||
2300 322.56372 -31.786868 0.0034851739 1 1
|
||||
2350 282.64326 6.1982735 0.0034851739 1 1
|
||||
2400 286.65759 -63.207781 0.0034851739 1 1
|
||||
2450 257.05528 32.931491 0.0034851739 1 1
|
||||
2500 283.64386 26.912373 0.0034851739 1 1
|
||||
2550 299.54005 27.277039 0.0034851739 1 1
|
||||
2600 283.92503 14.660972 0.0034851739 1 1
|
||||
2650 321.93453 -18.977358 0.0034851739 1 1
|
||||
2700 376.7189 31.826935 0.0034851739 1 1
|
||||
2750 372.20075 -32.821697 0.0034851739 1 1
|
||||
2800 361.40604 83.035183 0.0034851739 1 1
|
||||
2850 332.27269 -23.927452 0.0034851739 1 1
|
||||
2900 331.14638 -0.12328446 0.0034851739 1 1
|
||||
2950 303.67489 -24.078857 0.0034851739 1 1
|
||||
3000 311.40462 21.563537 0.0034851739 1 1
|
||||
3050 284.72849 -23.849667 0.0034851739 1 1
|
||||
3100 303.48477 39.347763 0.0034851739 1 1
|
||||
3150 264.2739 -0.22299878 0.0034851739 1 1
|
||||
3200 300.03351 31.545323 0.0034851739 1 1
|
||||
3250 288.56663 5.7225229 0.0034851739 1 1
|
||||
3300 200.13238 -31.239655 0.0034851739 1 1
|
||||
3350 231.32512 16.631728 0.0034851739 1 1
|
||||
3400 260.57402 2.1717992 0.0034851739 1 1
|
||||
3450 301.47128 -42.210623 0.0034851739 1 1
|
||||
3500 321.77414 40.074365 0.0034851739 1 1
|
||||
3550 353.21858 28.387783 0.0034851739 1 1
|
||||
3600 331.45989 -57.800858 0.0034851739 1 1
|
||||
3650 303.88123 44.86596 0.0034851739 1 1
|
||||
3700 329.73833 -0.8061567 0.0034851739 1 1
|
||||
3750 297.55588 -0.49626022 0.0034851739 1 1
|
||||
3800 286.38794 -10.010003 0.0034851739 1 1
|
||||
3850 290.17417 -43.51187 0.0034851739 1 1
|
||||
3900 247.88933 51.23735 0.0034851739 1 1
|
||||
3950 332.31324 -18.194985 0.0034851739 1 1
|
||||
4000 325.56802 18.402825 0.0034851739 1 1
|
||||
4050 338.37594 36.430977 0.0034851739 1 1
|
||||
4100 370.95478 39.290285 0.0034851739 1 1
|
||||
4150 348.47859 -7.0779683 0.0034851739 1 1
|
||||
4200 241.30632 -33.371789 0.0034851739 1 1
|
||||
4250 242.17258 -9.9861962 0.0034851739 1 1
|
||||
4300 300.85311 -7.924429 0.0034851739 1 1
|
||||
4350 273.15684 -21.257282 0.0034851739 1 1
|
||||
4400 305.77464 -5.8720712 0.0034851739 1 1
|
||||
4450 314.97697 45.037299 0.0034851739 1 1
|
||||
4500 310.77723 16.958771 0.0034851739 1 1
|
||||
4550 302.17421 12.156862 0.0034851739 1 1
|
||||
4600 319.74799 6.8488914 0.0034851739 1 1
|
||||
4650 270.86805 -13.767907 0.0034851739 1 1
|
||||
4700 249.81731 -31.197484 0.0034851739 1 1
|
||||
4750 285.86481 -9.8916332 0.0034851739 1 1
|
||||
4800 233.98321 7.1338518 0.0034851739 1 1
|
||||
4850 302.60551 49.262886 0.0034851739 1 1
|
||||
4900 316.55055 34.663238 0.0034851739 1 1
|
||||
4950 357.32741 11.583013 0.0034851739 1 1
|
||||
5000 400.21044 -8.1780861 0.0034851739 1 1
|
||||
5050 390.01845 -20.490268 0.0034851739 1 1
|
||||
5100 378.84249 -41.328772 0.0034851739 1 1
|
||||
5150 324.02039 -15.023852 0.0034851739 1 1
|
||||
5200 262.08427 10.937367 0.0034851739 1 1
|
||||
5250 255.75506 16.381495 0.0034851739 1 1
|
||||
5300 277.84991 40.682283 0.0034851739 1 1
|
||||
5350 302.92834 9.1989644 0.0034851739 1 1
|
||||
5400 283.71964 -1.6583895 0.0034851739 1 1
|
||||
5450 300.71261 -4.703054 0.0034851739 1 1
|
||||
5500 343.54987 -0.30546396 0.0034851739 1 1
|
||||
5550 369.51272 21.691639 0.0034851739 1 1
|
||||
5600 372.69786 -38.679919 0.0034851739 1 1
|
||||
5650 327.41256 11.352201 0.0034851739 1 1
|
||||
5700 278.9861 -23.82728 0.0034851739 1 1
|
||||
5750 308.30037 -20.756238 0.0034851739 1 1
|
||||
5800 341.4559 28.058314 0.0034851739 1 1
|
||||
5850 322.9786 -10.731862 0.0034851739 1 1
|
||||
5900 304.53598 32.825105 0.0034851739 1 1
|
||||
5950 287.17515 -36.780057 0.0034851739 1 1
|
||||
6000 296.52688 18.782156 0.0034851739 1 1
|
||||
6050 314.25411 15.99272 0.0034851739 1 1
|
||||
6100 313.86572 3.4344108 0.0034851739 1 1
|
||||
6150 325.64197 32.39212 0.0034851739 1 1
|
||||
6200 367.4298 -27.161154 0.0034851739 1 1
|
||||
6250 369.30937 39.020881 0.0034851739 1 1
|
||||
6300 328.92245 -23.175612 0.0034851739 1 1
|
||||
6350 305.6293 4.9011587 0.0034851739 1 1
|
||||
6400 241.70456 -13.675247 0.0034851739 1 1
|
||||
6450 265.66574 2.4049735 0.0034851739 1 1
|
||||
6500 249.3592 13.420453 0.0034851739 1 1
|
||||
6550 294.5367 10.856753 0.0034851739 1 1
|
||||
6600 308.20246 18.992923 0.0034851739 1 1
|
||||
6650 305.43756 -49.57151 0.0034851739 1 1
|
||||
6700 320.27395 11.339101 0.0034851739 1 1
|
||||
6750 321.7875 -23.463361 0.0034851739 1 1
|
||||
6800 303.40316 7.6256997 0.0034851739 1 1
|
||||
6850 297.18652 51.52186 0.0034851739 1 1
|
||||
6900 284.19084 -8.496294 0.0034851739 1 1
|
||||
6950 331.04173 13.227745 0.0034851739 1 1
|
||||
7000 311.38027 -43.26105 0.0034851739 1 1
|
||||
7050 286.82046 -14.171194 0.0034851739 1 1
|
||||
7100 302.81691 12.058085 0.0034851739 1 1
|
||||
7150 297.18018 -43.110658 0.0034851739 1 1
|
||||
7200 332.46131 26.051496 0.0034851739 1 1
|
||||
7250 262.72288 41.161451 0.0034851739 1 1
|
||||
7300 250.62739 -23.440907 0.0034851739 1 1
|
||||
7350 296.92141 35.869216 0.0034851739 1 1
|
||||
7400 245.06807 -13.467896 0.0034851739 1 1
|
||||
7450 272.2659 -23.292836 0.0034851739 1 1
|
||||
7500 209.05776 13.888665 0.0034851739 1 1
|
||||
7550 255.03716 4.9662624 0.0034851739 1 1
|
||||
7600 312.26011 -37.350427 0.0034851739 1 1
|
||||
7650 305.5823 55.208039 0.0034851739 1 1
|
||||
7700 325.13382 -18.370791 0.0034851739 1 1
|
||||
7750 363.24898 -22.473126 0.0034851739 1 1
|
||||
7800 350.19254 26.792307 0.0034851739 1 1
|
||||
7850 271.76418 -17.843445 0.0034851739 1 1
|
||||
7900 272.70301 -11.709349 0.0034851739 1 1
|
||||
7950 298.5993 -12.736235 0.0034851739 1 1
|
||||
8000 274.52611 49.657345 0.0034851739 1 1
|
||||
8050 304.73711 -0.52485689 0.0034851739 1 1
|
||||
8100 328.29239 -39.901891 0.0034851739 1 1
|
||||
8150 406.52096 2.8669076 0.0034851739 1 1
|
||||
8200 332.17309 -51.168754 0.0034851739 1 1
|
||||
8250 354.68419 53.003157 0.0034851739 1 1
|
||||
8300 337.28934 20.766408 0.0034851739 1 1
|
||||
8350 361.81133 -54.159227 0.0034851739 1 1
|
||||
8400 305.59597 24.011667 0.0034851739 1 1
|
||||
8450 303.25823 4.423341 0.0034851739 1 1
|
||||
8500 253.50747 -11.026949 0.0034851739 1 1
|
||||
8550 277.13504 23.204625 0.0034851739 1 1
|
||||
8600 291.40211 -22.253861 0.0034851739 1 1
|
||||
8650 307.93765 32.14162 0.0034851739 1 1
|
||||
8700 309.1529 0.36279434 0.0034851739 1 1
|
||||
8750 355.10326 11.677219 0.0034851739 1 1
|
||||
8800 330.21328 19.235269 0.0034851739 1 1
|
||||
8850 241.29109 21.707386 0.0034851739 1 1
|
||||
8900 319.15363 -60.010115 0.0034851739 1 1
|
||||
8950 308.88552 -57.637014 0.0034851739 1 1
|
||||
9000 272.22373 51.15837 0.0034851739 1 1
|
||||
9050 248.84947 7.3390565 0.0034851739 1 1
|
||||
9100 221.91564 48.387079 0.0034851739 1 1
|
||||
9150 298.03506 2.9058639 0.0034851739 1 1
|
||||
9200 274.25114 -24.597819 0.0034851739 1 1
|
||||
9250 334.08373 5.1079577 0.0034851739 1 1
|
||||
9300 383.07285 -23.274763 0.0034851739 1 1
|
||||
9350 335.00581 20.94212 0.0034851739 1 1
|
||||
9400 309.23862 34.074744 0.0034851739 1 1
|
||||
9450 312.62262 -28.468057 0.0034851739 1 1
|
||||
9500 324.54274 2.851136 0.0034851739 1 1
|
||||
9550 313.32781 22.468182 0.0034851739 1 1
|
||||
9600 269.04372 4.064934 0.0034851739 1 1
|
||||
9650 270.98476 -21.520127 0.0034851739 1 1
|
||||
9700 236.8736 16.250728 0.0034851739 1 1
|
||||
9750 333.94686 1.6864148 0.0034851739 1 1
|
||||
9800 330.91875 12.150018 0.0034851739 1 1
|
||||
9850 343.8603 25.338853 0.0034851739 1 1
|
||||
9900 330.93364 -28.292992 0.0034851739 1 1
|
||||
9950 291.25518 25.795948 0.0034851739 1 1
|
||||
10000 319.25565 25.323846 0.0034851739 1 1
|
||||
Loop time of 3.55353 on 4 procs for 10000 steps with 44 atoms
|
||||
|
||||
Performance: 243.139 ns/day, 0.099 hours/ns, 2814.105 timesteps/s
|
||||
93.4% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0030422 | 0.10454 | 0.35211 | 44.8 | 2.94
|
||||
Bond | 0.0063896 | 0.29222 | 0.94356 | 71.3 | 8.22
|
||||
Kspace | 0.88508 | 1.6486 | 1.979 | 35.1 | 46.39
|
||||
Neigh | 0.61154 | 0.62212 | 0.63307 | 1.0 | 17.51
|
||||
Comm | 0.18944 | 0.24549 | 0.29196 | 7.9 | 6.91
|
||||
Output | 0.0050066 | 0.011804 | 0.032134 | 10.8 | 0.33
|
||||
Modify | 0.52282 | 0.60522 | 0.69588 | 7.9 | 17.03
|
||||
Other | | 0.02359 | | | 0.66
|
||||
|
||||
Nlocal: 11 ave 44 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 33 ave 44 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 3
|
||||
Neighs: 205.75 ave 823 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 823
|
||||
Ave neighs/atom = 18.7045
|
||||
Ave special neighs/atom = 9.77273
|
||||
Neighbor list builds = 10000
|
||||
Dangerous builds = 0
|
||||
|
||||
# write_restart restart_longrun
|
||||
# write_data restart_longrun.data
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:03
|
||||
@ -0,0 +1,148 @@
|
||||
LAMMPS (5 Jun 2019)
|
||||
Reading data file ...
|
||||
orthogonal box = (-25 -25 -25) to (25 25 25)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
44 atoms
|
||||
reading velocities ...
|
||||
44 velocities
|
||||
scanning bonds ...
|
||||
9 = max bonds/atom
|
||||
scanning angles ...
|
||||
21 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
29 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
29 = max impropers/atom
|
||||
reading bonds ...
|
||||
42 bonds
|
||||
reading angles ...
|
||||
74 angles
|
||||
reading dihedrals ...
|
||||
100 dihedrals
|
||||
reading impropers ...
|
||||
44 impropers
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
4 = max # of 1-2 neighbors
|
||||
6 = max # of 1-3 neighbors
|
||||
12 = max # of 1-4 neighbors
|
||||
41 = max # of special neighbors
|
||||
special bonds CPU = 0.000181113 secs
|
||||
read_data CPU = 0.0251833 secs
|
||||
Read molecule mol1:
|
||||
18 atoms with max type 8
|
||||
16 bonds with max type 14
|
||||
25 angles with max type 28
|
||||
23 dihedrals with max type 36
|
||||
14 impropers with max type 11
|
||||
Read molecule mol2:
|
||||
18 atoms with max type 9
|
||||
17 bonds with max type 13
|
||||
31 angles with max type 27
|
||||
39 dihedrals with max type 33
|
||||
20 impropers with max type 1
|
||||
Read molecule mol3:
|
||||
15 atoms with max type 9
|
||||
14 bonds with max type 13
|
||||
25 angles with max type 27
|
||||
30 dihedrals with max type 33
|
||||
16 impropers with max type 1
|
||||
Read molecule mol4:
|
||||
15 atoms with max type 11
|
||||
13 bonds with max type 15
|
||||
19 angles with max type 29
|
||||
16 dihedrals with max type 32
|
||||
10 impropers with max type 13
|
||||
WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (../fix_bond_react.cpp:1785)
|
||||
WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (../fix_bond_react.cpp:1785)
|
||||
dynamic group bond_react_MASTER_group defined
|
||||
dynamic group statted_grp_REACT defined
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (../kspace.cpp:319)
|
||||
G vector (1/distance) = 0.0534597
|
||||
grid = 2 2 2
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0402256
|
||||
estimated relative force accuracy = 0.000121138
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 343 8
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 10.5
|
||||
ghost atom cutoff = 10.5
|
||||
binsize = 5.25, bins = 10 10 10
|
||||
2 neighbor lists, perpetual/occasional/extra = 1 1 0
|
||||
(1) pair lj/class2/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
(2) fix bond/react, occasional, copy from (1)
|
||||
attributes: half, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Setting up Verlet run ...
|
||||
Unit style : real
|
||||
Current step : 0
|
||||
Time step : 1
|
||||
WARNING: Inconsistent image flags (../domain.cpp:784)
|
||||
Per MPI rank memory allocation (min/avg/max) = 34.41 | 34.41 | 34.41 Mbytes
|
||||
Step Temp Press Density f_myrxns[1] f_myrxns[2]
|
||||
0 300 346.78165 0.0034851739 0 0
|
||||
50 293.70542 -52.547388 0.0034851739 1 0
|
||||
100 276.36755 54.81826 0.0034851739 1 1
|
||||
150 448.65869 16.874435 0.0034851739 1 1
|
||||
200 379.84257 11.578545 0.0034851739 1 1
|
||||
250 298.21983 90.656585 0.0034851739 1 1
|
||||
300 333.3111 -30.139607 0.0034851739 1 1
|
||||
350 266.57108 6.4505134 0.0034851739 1 1
|
||||
400 264.05476 10.513204 0.0034851739 1 1
|
||||
450 250.70418 -18.635379 0.0034851739 1 1
|
||||
500 261.21632 10.231013 0.0034851739 1 1
|
||||
550 309.89024 -8.8299506 0.0034851739 1 1
|
||||
600 373.45851 30.368993 0.0034851739 1 1
|
||||
650 338.26242 9.0362267 0.0034851739 1 1
|
||||
700 295.67794 -5.6007538 0.0034851739 1 1
|
||||
750 310.86563 -59.228181 0.0034851739 1 1
|
||||
800 286.22678 -9.9022407 0.0034851739 1 1
|
||||
850 218.42135 27.845352 0.0034851739 1 1
|
||||
900 259.62551 24.216336 0.0034851739 1 1
|
||||
950 250.21307 -14.560985 0.0034851739 1 1
|
||||
1000 274.29245 -0.38768626 0.0034851739 1 1
|
||||
Loop time of 0.341061 on 1 procs for 1000 steps with 44 atoms
|
||||
|
||||
Performance: 253.327 ns/day, 0.095 hours/ns, 2932.025 timesteps/s
|
||||
87.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.031135 | 0.031135 | 0.031135 | 0.0 | 9.13
|
||||
Bond | 0.12623 | 0.12623 | 0.12623 | 0.0 | 37.01
|
||||
Kspace | 0.036491 | 0.036491 | 0.036491 | 0.0 | 10.70
|
||||
Neigh | 0.046395 | 0.046395 | 0.046395 | 0.0 | 13.60
|
||||
Comm | 0.0025396 | 0.0025396 | 0.0025396 | 0.0 | 0.74
|
||||
Output | 0.07775 | 0.07775 | 0.07775 | 0.0 | 22.80
|
||||
Modify | 0.019219 | 0.019219 | 0.019219 | 0.0 | 5.64
|
||||
Other | | 0.001306 | | | 0.38
|
||||
|
||||
Nlocal: 44 ave 44 max 44 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 2 ave 2 max 2 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 740 ave 740 max 740 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 740
|
||||
Ave neighs/atom = 16.8182
|
||||
Ave special neighs/atom = 9.77273
|
||||
Neighbor list builds = 1000
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:00
|
||||
@ -0,0 +1,148 @@
|
||||
LAMMPS (5 Jun 2019)
|
||||
Reading data file ...
|
||||
orthogonal box = (-25 -25 -25) to (25 25 25)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
44 atoms
|
||||
reading velocities ...
|
||||
44 velocities
|
||||
scanning bonds ...
|
||||
9 = max bonds/atom
|
||||
scanning angles ...
|
||||
21 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
29 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
29 = max impropers/atom
|
||||
reading bonds ...
|
||||
42 bonds
|
||||
reading angles ...
|
||||
74 angles
|
||||
reading dihedrals ...
|
||||
100 dihedrals
|
||||
reading impropers ...
|
||||
44 impropers
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
4 = max # of 1-2 neighbors
|
||||
6 = max # of 1-3 neighbors
|
||||
12 = max # of 1-4 neighbors
|
||||
41 = max # of special neighbors
|
||||
special bonds CPU = 0.000178751 secs
|
||||
read_data CPU = 0.0385782 secs
|
||||
Read molecule mol1:
|
||||
18 atoms with max type 8
|
||||
16 bonds with max type 14
|
||||
25 angles with max type 28
|
||||
23 dihedrals with max type 36
|
||||
14 impropers with max type 11
|
||||
Read molecule mol2:
|
||||
18 atoms with max type 9
|
||||
17 bonds with max type 13
|
||||
31 angles with max type 27
|
||||
39 dihedrals with max type 33
|
||||
20 impropers with max type 1
|
||||
Read molecule mol3:
|
||||
15 atoms with max type 9
|
||||
14 bonds with max type 13
|
||||
25 angles with max type 27
|
||||
30 dihedrals with max type 33
|
||||
16 impropers with max type 1
|
||||
Read molecule mol4:
|
||||
15 atoms with max type 11
|
||||
13 bonds with max type 15
|
||||
19 angles with max type 29
|
||||
16 dihedrals with max type 32
|
||||
10 impropers with max type 13
|
||||
WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (../fix_bond_react.cpp:1785)
|
||||
WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (../fix_bond_react.cpp:1785)
|
||||
dynamic group bond_react_MASTER_group defined
|
||||
dynamic group statted_grp_REACT defined
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (../kspace.cpp:319)
|
||||
G vector (1/distance) = 0.0534597
|
||||
grid = 2 2 2
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0402256
|
||||
estimated relative force accuracy = 0.000121138
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 252 2
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 10.5
|
||||
ghost atom cutoff = 10.5
|
||||
binsize = 5.25, bins = 10 10 10
|
||||
2 neighbor lists, perpetual/occasional/extra = 1 1 0
|
||||
(1) pair lj/class2/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
(2) fix bond/react, occasional, copy from (1)
|
||||
attributes: half, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Setting up Verlet run ...
|
||||
Unit style : real
|
||||
Current step : 0
|
||||
Time step : 1
|
||||
WARNING: Inconsistent image flags (../domain.cpp:784)
|
||||
Per MPI rank memory allocation (min/avg/max) = 34.42 | 34.77 | 35.45 Mbytes
|
||||
Step Temp Press Density f_myrxns[1] f_myrxns[2]
|
||||
0 300 346.78165 0.0034851739 0 0
|
||||
50 293.70542 -52.547388 0.0034851739 1 0
|
||||
100 276.36755 54.81826 0.0034851739 1 1
|
||||
150 448.65869 16.874435 0.0034851739 1 1
|
||||
200 379.84257 11.578545 0.0034851739 1 1
|
||||
250 298.21983 90.656585 0.0034851739 1 1
|
||||
300 333.3111 -30.139607 0.0034851739 1 1
|
||||
350 266.57108 6.4505134 0.0034851739 1 1
|
||||
400 264.05476 10.513204 0.0034851739 1 1
|
||||
450 250.70418 -18.635379 0.0034851739 1 1
|
||||
500 261.21632 10.231013 0.0034851739 1 1
|
||||
550 309.89024 -8.8299506 0.0034851739 1 1
|
||||
600 373.45851 30.368993 0.0034851739 1 1
|
||||
650 338.26242 9.0362267 0.0034851739 1 1
|
||||
700 295.67794 -5.6007538 0.0034851739 1 1
|
||||
750 310.86563 -59.228181 0.0034851739 1 1
|
||||
800 286.22678 -9.9022407 0.0034851739 1 1
|
||||
850 218.42135 27.845352 0.0034851739 1 1
|
||||
900 259.62551 24.216336 0.0034851739 1 1
|
||||
950 250.21307 -14.560985 0.0034851739 1 1
|
||||
1000 274.29245 -0.38768626 0.0034851739 1 1
|
||||
Loop time of 0.271242 on 4 procs for 1000 steps with 44 atoms
|
||||
|
||||
Performance: 318.535 ns/day, 0.075 hours/ns, 3686.747 timesteps/s
|
||||
98.6% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.00023773 | 0.0077322 | 0.016042 | 8.4 | 2.85
|
||||
Bond | 0.00073385 | 0.032108 | 0.08446 | 19.4 | 11.84
|
||||
Kspace | 0.041659 | 0.098095 | 0.13373 | 12.3 | 36.16
|
||||
Neigh | 0.028894 | 0.029247 | 0.029558 | 0.1 | 10.78
|
||||
Comm | 0.012367 | 0.013642 | 0.01503 | 0.9 | 5.03
|
||||
Output | 0.032475 | 0.040504 | 0.061019 | 5.9 | 14.93
|
||||
Modify | 0.032934 | 0.049086 | 0.0577 | 4.3 | 18.10
|
||||
Other | | 0.0008281 | | | 0.31
|
||||
|
||||
Nlocal: 11 ave 21 max 0 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 0 2
|
||||
Nghost: 32.5 ave 43 max 23 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Neighs: 185 ave 376 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 740
|
||||
Ave neighs/atom = 16.8182
|
||||
Ave special neighs/atom = 9.77273
|
||||
Neighbor list builds = 1000
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:00
|
||||
@ -0,0 +1,147 @@
|
||||
LAMMPS (5 Jun 2019)
|
||||
Reading data file ...
|
||||
orthogonal box = (-25 -25 -25) to (25 25 25)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
44 atoms
|
||||
reading velocities ...
|
||||
44 velocities
|
||||
scanning bonds ...
|
||||
9 = max bonds/atom
|
||||
scanning angles ...
|
||||
21 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
29 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
29 = max impropers/atom
|
||||
reading bonds ...
|
||||
42 bonds
|
||||
reading angles ...
|
||||
74 angles
|
||||
reading dihedrals ...
|
||||
100 dihedrals
|
||||
reading impropers ...
|
||||
44 impropers
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
4 = max # of 1-2 neighbors
|
||||
6 = max # of 1-3 neighbors
|
||||
12 = max # of 1-4 neighbors
|
||||
41 = max # of special neighbors
|
||||
special bonds CPU = 0.000217102 secs
|
||||
read_data CPU = 0.00630778 secs
|
||||
Read molecule mol1:
|
||||
18 atoms with max type 8
|
||||
16 bonds with max type 14
|
||||
25 angles with max type 28
|
||||
23 dihedrals with max type 36
|
||||
14 impropers with max type 11
|
||||
Read molecule mol2:
|
||||
18 atoms with max type 9
|
||||
17 bonds with max type 13
|
||||
31 angles with max type 27
|
||||
39 dihedrals with max type 33
|
||||
20 impropers with max type 1
|
||||
Read molecule mol3:
|
||||
15 atoms with max type 9
|
||||
14 bonds with max type 13
|
||||
25 angles with max type 27
|
||||
30 dihedrals with max type 33
|
||||
16 impropers with max type 1
|
||||
Read molecule mol4:
|
||||
15 atoms with max type 11
|
||||
13 bonds with max type 15
|
||||
19 angles with max type 29
|
||||
16 dihedrals with max type 32
|
||||
10 impropers with max type 13
|
||||
WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (../fix_bond_react.cpp:1785)
|
||||
WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (../fix_bond_react.cpp:1785)
|
||||
dynamic group bond_react_MASTER_group defined
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (../kspace.cpp:319)
|
||||
G vector (1/distance) = 0.0534597
|
||||
grid = 2 2 2
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0402256
|
||||
estimated relative force accuracy = 0.000121138
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 343 8
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 10.5
|
||||
ghost atom cutoff = 10.5
|
||||
binsize = 5.25, bins = 10 10 10
|
||||
2 neighbor lists, perpetual/occasional/extra = 1 1 0
|
||||
(1) pair lj/class2/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
(2) fix bond/react, occasional, copy from (1)
|
||||
attributes: half, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Setting up Verlet run ...
|
||||
Unit style : real
|
||||
Current step : 0
|
||||
Time step : 1
|
||||
WARNING: Inconsistent image flags (../domain.cpp:784)
|
||||
Per MPI rank memory allocation (min/avg/max) = 34.35 | 34.35 | 34.35 Mbytes
|
||||
Step Temp Press Density f_myrxns[1] f_myrxns[2]
|
||||
0 300 346.78165 0.0034851739 0 0
|
||||
50 416.49412 -20.293038 0.0034851739 1 0
|
||||
100 746.49323 91.912227 0.0034851739 1 1
|
||||
150 515.15907 -1.4024709 0.0034851739 1 1
|
||||
200 441.14572 -19.333087 0.0034851739 1 1
|
||||
250 376.40996 30.717679 0.0034851739 1 1
|
||||
300 326.15127 -3.0433799 0.0034851739 1 1
|
||||
350 326.21116 6.235391 0.0034851739 1 1
|
||||
400 366.48556 3.9807338 0.0034851739 1 1
|
||||
450 313.79097 7.6674629 0.0034851739 1 1
|
||||
500 278.89836 14.102052 0.0034851739 1 1
|
||||
550 267.50214 18.241417 0.0034851739 1 1
|
||||
600 276.28064 7.4649611 0.0034851739 1 1
|
||||
650 255.26713 -8.5258573 0.0034851739 1 1
|
||||
700 258.59752 -5.3341215 0.0034851739 1 1
|
||||
750 263.71264 33.369869 0.0034851739 1 1
|
||||
800 246.22976 -15.349137 0.0034851739 1 1
|
||||
850 255.93887 16.331669 0.0034851739 1 1
|
||||
900 239.72525 -0.20075789 0.0034851739 1 1
|
||||
950 213.73064 12.17619 0.0034851739 1 1
|
||||
1000 218.25094 -9.0955642 0.0034851739 1 1
|
||||
Loop time of 0.348252 on 1 procs for 1000 steps with 44 atoms
|
||||
|
||||
Performance: 248.096 ns/day, 0.097 hours/ns, 2871.483 timesteps/s
|
||||
91.8% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.031941 | 0.031941 | 0.031941 | 0.0 | 9.17
|
||||
Bond | 0.13031 | 0.13031 | 0.13031 | 0.0 | 37.42
|
||||
Kspace | 0.037554 | 0.037554 | 0.037554 | 0.0 | 10.78
|
||||
Neigh | 0.047397 | 0.047397 | 0.047397 | 0.0 | 13.61
|
||||
Comm | 0.0025814 | 0.0025814 | 0.0025814 | 0.0 | 0.74
|
||||
Output | 0.083526 | 0.083526 | 0.083526 | 0.0 | 23.98
|
||||
Modify | 0.013602 | 0.013602 | 0.013602 | 0.0 | 3.91
|
||||
Other | | 0.001336 | | | 0.38
|
||||
|
||||
Nlocal: 44 ave 44 max 44 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 3 ave 3 max 3 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 818 ave 818 max 818 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 818
|
||||
Ave neighs/atom = 18.5909
|
||||
Ave special neighs/atom = 9.77273
|
||||
Neighbor list builds = 1000
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:00
|
||||
@ -0,0 +1,147 @@
|
||||
LAMMPS (5 Jun 2019)
|
||||
Reading data file ...
|
||||
orthogonal box = (-25 -25 -25) to (25 25 25)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
44 atoms
|
||||
reading velocities ...
|
||||
44 velocities
|
||||
scanning bonds ...
|
||||
9 = max bonds/atom
|
||||
scanning angles ...
|
||||
21 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
29 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
29 = max impropers/atom
|
||||
reading bonds ...
|
||||
42 bonds
|
||||
reading angles ...
|
||||
74 angles
|
||||
reading dihedrals ...
|
||||
100 dihedrals
|
||||
reading impropers ...
|
||||
44 impropers
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
4 = max # of 1-2 neighbors
|
||||
6 = max # of 1-3 neighbors
|
||||
12 = max # of 1-4 neighbors
|
||||
41 = max # of special neighbors
|
||||
special bonds CPU = 0.000163256 secs
|
||||
read_data CPU = 0.0244579 secs
|
||||
Read molecule mol1:
|
||||
18 atoms with max type 8
|
||||
16 bonds with max type 14
|
||||
25 angles with max type 28
|
||||
23 dihedrals with max type 36
|
||||
14 impropers with max type 11
|
||||
Read molecule mol2:
|
||||
18 atoms with max type 9
|
||||
17 bonds with max type 13
|
||||
31 angles with max type 27
|
||||
39 dihedrals with max type 33
|
||||
20 impropers with max type 1
|
||||
Read molecule mol3:
|
||||
15 atoms with max type 9
|
||||
14 bonds with max type 13
|
||||
25 angles with max type 27
|
||||
30 dihedrals with max type 33
|
||||
16 impropers with max type 1
|
||||
Read molecule mol4:
|
||||
15 atoms with max type 11
|
||||
13 bonds with max type 15
|
||||
19 angles with max type 29
|
||||
16 dihedrals with max type 32
|
||||
10 impropers with max type 13
|
||||
WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (../fix_bond_react.cpp:1785)
|
||||
WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (../fix_bond_react.cpp:1785)
|
||||
dynamic group bond_react_MASTER_group defined
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (../kspace.cpp:319)
|
||||
G vector (1/distance) = 0.0534597
|
||||
grid = 2 2 2
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0402256
|
||||
estimated relative force accuracy = 0.000121138
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 252 2
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 10.5
|
||||
ghost atom cutoff = 10.5
|
||||
binsize = 5.25, bins = 10 10 10
|
||||
2 neighbor lists, perpetual/occasional/extra = 1 1 0
|
||||
(1) pair lj/class2/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
(2) fix bond/react, occasional, copy from (1)
|
||||
attributes: half, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Setting up Verlet run ...
|
||||
Unit style : real
|
||||
Current step : 0
|
||||
Time step : 1
|
||||
WARNING: Inconsistent image flags (../domain.cpp:784)
|
||||
Per MPI rank memory allocation (min/avg/max) = 33.34 | 33.69 | 34.37 Mbytes
|
||||
Step Temp Press Density f_myrxns[1] f_myrxns[2]
|
||||
0 300 346.78165 0.0034851739 0 0
|
||||
50 416.49412 -20.293038 0.0034851739 1 0
|
||||
100 746.49323 91.912227 0.0034851739 1 1
|
||||
150 515.15907 -1.4024709 0.0034851739 1 1
|
||||
200 441.14572 -19.333087 0.0034851739 1 1
|
||||
250 376.40996 30.717679 0.0034851739 1 1
|
||||
300 326.15127 -3.0433799 0.0034851739 1 1
|
||||
350 326.21116 6.235391 0.0034851739 1 1
|
||||
400 366.48556 3.9807338 0.0034851739 1 1
|
||||
450 313.79097 7.6674629 0.0034851739 1 1
|
||||
500 278.89836 14.102052 0.0034851739 1 1
|
||||
550 267.50214 18.241417 0.0034851739 1 1
|
||||
600 276.28064 7.4649611 0.0034851739 1 1
|
||||
650 255.26713 -8.5258573 0.0034851739 1 1
|
||||
700 258.59752 -5.3341215 0.0034851739 1 1
|
||||
750 263.71264 33.369869 0.0034851739 1 1
|
||||
800 246.22976 -15.349137 0.0034851739 1 1
|
||||
850 255.93887 16.331669 0.0034851739 1 1
|
||||
900 239.72525 -0.20075789 0.0034851739 1 1
|
||||
950 213.73064 12.17619 0.0034851739 1 1
|
||||
1000 218.25094 -9.0955642 0.0034851739 1 1
|
||||
Loop time of 0.254903 on 4 procs for 1000 steps with 44 atoms
|
||||
|
||||
Performance: 338.952 ns/day, 0.071 hours/ns, 3923.053 timesteps/s
|
||||
99.8% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.00014252 | 0.0090715 | 0.021332 | 9.6 | 3.56
|
||||
Bond | 0.00047028 | 0.037261 | 0.10789 | 22.7 | 14.62
|
||||
Kspace | 0.051006 | 0.12756 | 0.1693 | 13.6 | 50.04
|
||||
Neigh | 0.035644 | 0.036088 | 0.036523 | 0.2 | 14.16
|
||||
Comm | 0.013984 | 0.016074 | 0.018676 | 1.6 | 6.31
|
||||
Output | 0.0002816 | 0.00033726 | 0.00044251 | 0.0 | 0.13
|
||||
Modify | 0.023697 | 0.027803 | 0.033552 | 2.5 | 10.91
|
||||
Other | | 0.0007123 | | | 0.28
|
||||
|
||||
Nlocal: 11 ave 29 max 0 min
|
||||
Histogram: 1 1 0 0 1 0 0 0 0 1
|
||||
Nghost: 25 ave 31 max 12 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 2 1
|
||||
Neighs: 204.5 ave 443 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 818
|
||||
Ave neighs/atom = 18.5909
|
||||
Ave special neighs/atom = 9.77273
|
||||
Neighbor list builds = 1000
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:00
|
||||
1372
examples/USER/misc/ilp_graphene_hbn/Bi_gr_AB_stack_2L_noH.data
Normal file
1372
examples/USER/misc/ilp_graphene_hbn/Bi_gr_AB_stack_2L_noH.data
Normal file
File diff suppressed because it is too large
Load Diff
@ -1 +0,0 @@
|
||||
../../../../../potentials/BNCH-old.ILP
|
||||
File diff suppressed because it is too large
Load Diff
@ -1 +0,0 @@
|
||||
../../../../../potentials/CH.airebo
|
||||
@ -1,61 +0,0 @@
|
||||
# Initialization
|
||||
units metal
|
||||
boundary p p p
|
||||
atom_style full
|
||||
processors * * 1 # domain decomposition over x and y
|
||||
|
||||
# System and atom definition
|
||||
# we use 2 atom types so that inter- and intra-layer
|
||||
# interactions can be specified separately
|
||||
# read lammps data file
|
||||
read_data Bi_gr_AB_stack_2L_noH_300K.data
|
||||
mass 1 12.0107 # carbon mass (g/mole) | membrane
|
||||
mass 2 12.0107 # carbon mass (g/mole) | adsorbate
|
||||
# Separate atom groups
|
||||
group membrane type 1
|
||||
group adsorbate type 2
|
||||
|
||||
######################## Potential defition ########################
|
||||
pair_style hybrid/overlay rebo ilp/graphene/hbn 16.0
|
||||
####################################################################
|
||||
pair_coeff * * rebo CH.airebo NULL C # chemical
|
||||
pair_coeff * * ilp/graphene/hbn BNCH-old.ILP C C # long range
|
||||
####################################################################
|
||||
# Neighbor update settings
|
||||
neighbor 2.0 bin
|
||||
neigh_modify every 1
|
||||
neigh_modify delay 0
|
||||
neigh_modify check yes
|
||||
|
||||
# calculate the COM
|
||||
variable adsxcom equal xcm(adsorbate,x)
|
||||
variable adsycom equal xcm(adsorbate,y)
|
||||
variable adszcom equal xcm(adsorbate,z)
|
||||
variable adsvxcom equal vcm(adsorbate,x)
|
||||
variable adsvycom equal vcm(adsorbate,y)
|
||||
variable adsvzcom equal vcm(adsorbate,z)
|
||||
|
||||
#### Simulation settings ####
|
||||
timestep 0.001
|
||||
#velocity adsorbate create 300.0 12345
|
||||
fix subf membrane setforce 0.0 0.0 0.0
|
||||
fix thermostat all nve
|
||||
|
||||
compute 0 all pair rebo
|
||||
compute 1 all pair ilp/graphene/hbn
|
||||
variable REBO equal c_0
|
||||
variable ILP equal c_1
|
||||
|
||||
############################
|
||||
|
||||
# Output
|
||||
thermo 100
|
||||
thermo_style custom step etotal pe ke v_REBO v_ILP temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
|
||||
thermo_modify line one format float %.10f
|
||||
thermo_modify flush yes norm no lost warn
|
||||
|
||||
#dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu
|
||||
#dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
|
||||
|
||||
###### Run molecular dynamics ######
|
||||
run 1000
|
||||
@ -1,137 +0,0 @@
|
||||
LAMMPS (8 Mar 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Initialization
|
||||
units metal
|
||||
boundary p p p
|
||||
atom_style full
|
||||
processors * * 1 # domain decomposition over x and y
|
||||
|
||||
# System and atom definition
|
||||
# we use 2 atom types so that inter- and intra-layer
|
||||
# interactions can be specified separately
|
||||
# read lammps data file
|
||||
read_data Bi_gr_AB_stack_2L_noH_300K.data
|
||||
orthogonal box = (0 0 0) to (42.6 41.8117 100)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
1360 atoms
|
||||
reading velocities ...
|
||||
1360 velocities
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
mass 1 12.0107 # carbon mass (g/mole) | membrane
|
||||
mass 2 12.0107 # carbon mass (g/mole) | adsorbate
|
||||
# Separate atom groups
|
||||
group membrane type 1
|
||||
680 atoms in group membrane
|
||||
group adsorbate type 2
|
||||
680 atoms in group adsorbate
|
||||
|
||||
######################## Potential defition ########################
|
||||
pair_style hybrid/overlay rebo ilp/graphene/hbn 16.0
|
||||
####################################################################
|
||||
pair_coeff * * rebo CH.airebo NULL C # chemical
|
||||
Reading potential file CH.airebo with DATE: 2011-10-25
|
||||
pair_coeff * * ilp/graphene/hbn BNCH-old.ILP C C # long range
|
||||
####################################################################
|
||||
# Neighbor update settings
|
||||
neighbor 2.0 bin
|
||||
neigh_modify every 1
|
||||
neigh_modify delay 0
|
||||
neigh_modify check yes
|
||||
|
||||
# calculate the COM
|
||||
variable adsxcom equal xcm(adsorbate,x)
|
||||
variable adsycom equal xcm(adsorbate,y)
|
||||
variable adszcom equal xcm(adsorbate,z)
|
||||
variable adsvxcom equal vcm(adsorbate,x)
|
||||
variable adsvycom equal vcm(adsorbate,y)
|
||||
variable adsvzcom equal vcm(adsorbate,z)
|
||||
|
||||
#### Simulation settings ####
|
||||
timestep 0.001
|
||||
#velocity adsorbate create 300.0 12345
|
||||
fix subf membrane setforce 0.0 0.0 0.0
|
||||
fix thermostat all nve
|
||||
|
||||
compute 0 all pair rebo
|
||||
compute 1 all pair ilp/graphene/hbn
|
||||
variable REBO equal c_0
|
||||
variable ILP equal c_1
|
||||
|
||||
############################
|
||||
|
||||
# Output
|
||||
thermo 100
|
||||
thermo_style custom step etotal pe ke v_REBO v_ILP temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
|
||||
thermo_modify line one format float %.10f
|
||||
thermo_modify flush yes norm no lost warn
|
||||
|
||||
#dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu
|
||||
#dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
|
||||
|
||||
###### Run molecular dynamics ######
|
||||
run 1000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 18
|
||||
ghost atom cutoff = 18
|
||||
binsize = 9, bins = 5 5 12
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair rebo, perpetual, skip from (2)
|
||||
attributes: full, newton on, ghost
|
||||
pair build: skip/ghost
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair ilp/graphene/hbn, 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) = 16.96 | 16.96 | 16.96 Mbytes
|
||||
Step TotEng PotEng KinEng v_REBO v_ILP Temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
|
||||
0 -5029.3801131277 -5044.0700799791 14.6899668514 -5011.2636297759 -32.8064502032 83.6251135127 22.0155657205 20.2812150219 3.4623630945 0.0282287195 0.0535565745 0.2193320108
|
||||
100 -5029.3895815657 -5045.3201249690 15.9305434033 -5012.4897058028 -32.8304191662 90.6873047362 22.0181751545 20.2867946176 3.4502536831 0.0239131349 0.0576557373 -0.4387830564
|
||||
200 -5029.3874064119 -5045.8119502228 16.4245438109 -5012.7276250747 -33.0843251481 93.4994853617 22.0202931358 20.2926890775 3.3883512918 0.0180268639 0.0596894423 -0.6964675465
|
||||
300 -5029.3851410393 -5044.9928147367 15.6076736974 -5012.1131531405 -32.8796615962 88.8493144891 22.0216852689 20.2985091183 3.3368274018 0.0093519893 0.0546775051 -0.2110676539
|
||||
400 -5029.3900102082 -5045.6706717598 16.2806615516 -5012.7330095297 -32.9376622301 92.6804113372 22.0220931529 20.3035219616 3.3560233852 -0.0015365116 0.0454268927 0.5478139709
|
||||
500 -5029.3985510533 -5046.0433160610 16.6447650078 -5013.0924334585 -32.9508826025 94.7531316612 22.0214795944 20.3074656871 3.4232399722 -0.0107212024 0.0332249366 0.6595923534
|
||||
600 -5029.3929936746 -5045.4367231195 16.0437294449 -5012.7046931021 -32.7320300174 91.3316353653 22.0200027176 20.3101652565 3.4651727438 -0.0178110391 0.0210056002 0.1144372537
|
||||
700 -5029.3934435811 -5045.6074608403 16.2140172592 -5012.7886962164 -32.8187646239 92.3010274644 22.0178838793 20.3116257077 3.4432436715 -0.0242636237 0.0078323424 -0.5162836955
|
||||
800 -5029.3892931255 -5046.2270462380 16.8377531124 -5013.2383770824 -32.9886691555 95.8517489911 22.0151485191 20.3116305041 3.3780520461 -0.0302821178 -0.0083184719 -0.6710801515
|
||||
900 -5029.3930414672 -5046.0272003818 16.6341589146 -5013.2317798384 -32.7954205434 94.6927546874 22.0119224940 20.3099187654 3.3350551183 -0.0341747588 -0.0256858066 -0.0799872839
|
||||
1000 -5029.3908907831 -5045.6437703691 16.2528795861 -5012.6800867885 -32.9636835807 92.5222578135 22.0084902521 20.3065746721 3.3658243730 -0.0336536245 -0.0406018547 0.6191660974
|
||||
Loop time of 137.46 on 1 procs for 1000 steps with 1360 atoms
|
||||
|
||||
Performance: 0.629 ns/day, 38.183 hours/ns, 7.275 timesteps/s
|
||||
95.1% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 137.33 | 137.33 | 137.33 | 0.0 | 99.90
|
||||
Bond | 0.00071788 | 0.00071788 | 0.00071788 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.067907 | 0.067907 | 0.067907 | 0.0 | 0.05
|
||||
Output | 0.0016029 | 0.0016029 | 0.0016029 | 0.0 | 0.00
|
||||
Modify | 0.036542 | 0.036542 | 0.036542 | 0.0 | 0.03
|
||||
Other | | 0.02574 | | | 0.02
|
||||
|
||||
Nlocal: 1360 ave 1360 max 1360 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 7964 ave 7964 max 7964 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: 265206 ave 265206 max 265206 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 265206
|
||||
Ave neighs/atom = 195.004
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:02:17
|
||||
@ -1,137 +0,0 @@
|
||||
LAMMPS (8 Mar 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Initialization
|
||||
units metal
|
||||
boundary p p p
|
||||
atom_style full
|
||||
processors * * 1 # domain decomposition over x and y
|
||||
|
||||
# System and atom definition
|
||||
# we use 2 atom types so that inter- and intra-layer
|
||||
# interactions can be specified separately
|
||||
# read lammps data file
|
||||
read_data Bi_gr_AB_stack_2L_noH_300K.data
|
||||
orthogonal box = (0 0 0) to (42.6 41.8117 100)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
1360 atoms
|
||||
reading velocities ...
|
||||
1360 velocities
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
mass 1 12.0107 # carbon mass (g/mole) | membrane
|
||||
mass 2 12.0107 # carbon mass (g/mole) | adsorbate
|
||||
# Separate atom groups
|
||||
group membrane type 1
|
||||
680 atoms in group membrane
|
||||
group adsorbate type 2
|
||||
680 atoms in group adsorbate
|
||||
|
||||
######################## Potential defition ########################
|
||||
pair_style hybrid/overlay rebo ilp/graphene/hbn 16.0
|
||||
####################################################################
|
||||
pair_coeff * * rebo CH.airebo NULL C # chemical
|
||||
Reading potential file CH.airebo with DATE: 2011-10-25
|
||||
pair_coeff * * ilp/graphene/hbn BNCH-old.ILP C C # long range
|
||||
####################################################################
|
||||
# Neighbor update settings
|
||||
neighbor 2.0 bin
|
||||
neigh_modify every 1
|
||||
neigh_modify delay 0
|
||||
neigh_modify check yes
|
||||
|
||||
# calculate the COM
|
||||
variable adsxcom equal xcm(adsorbate,x)
|
||||
variable adsycom equal xcm(adsorbate,y)
|
||||
variable adszcom equal xcm(adsorbate,z)
|
||||
variable adsvxcom equal vcm(adsorbate,x)
|
||||
variable adsvycom equal vcm(adsorbate,y)
|
||||
variable adsvzcom equal vcm(adsorbate,z)
|
||||
|
||||
#### Simulation settings ####
|
||||
timestep 0.001
|
||||
#velocity adsorbate create 300.0 12345
|
||||
fix subf membrane setforce 0.0 0.0 0.0
|
||||
fix thermostat all nve
|
||||
|
||||
compute 0 all pair rebo
|
||||
compute 1 all pair ilp/graphene/hbn
|
||||
variable REBO equal c_0
|
||||
variable ILP equal c_1
|
||||
|
||||
############################
|
||||
|
||||
# Output
|
||||
thermo 100
|
||||
thermo_style custom step etotal pe ke v_REBO v_ILP temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
|
||||
thermo_modify line one format float %.10f
|
||||
thermo_modify flush yes norm no lost warn
|
||||
|
||||
#dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu
|
||||
#dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
|
||||
|
||||
###### Run molecular dynamics ######
|
||||
run 1000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 18
|
||||
ghost atom cutoff = 18
|
||||
binsize = 9, bins = 5 5 12
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair rebo, perpetual, skip from (2)
|
||||
attributes: full, newton on, ghost
|
||||
pair build: skip/ghost
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair ilp/graphene/hbn, 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) = 11.13 | 11.13 | 11.13 Mbytes
|
||||
Step TotEng PotEng KinEng v_REBO v_ILP Temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
|
||||
0 -5029.3801131277 -5044.0700799791 14.6899668514 -5011.2636297759 -32.8064502032 83.6251135127 22.0155657205 20.2812150219 3.4623630945 0.0282287195 0.0535565745 0.2193320108
|
||||
100 -5029.3895815657 -5045.3201249690 15.9305434033 -5012.4897058028 -32.8304191662 90.6873047362 22.0181751545 20.2867946176 3.4502536831 0.0239131349 0.0576557373 -0.4387830564
|
||||
200 -5029.3874064119 -5045.8119502228 16.4245438109 -5012.7276250747 -33.0843251481 93.4994853617 22.0202931358 20.2926890775 3.3883512918 0.0180268639 0.0596894423 -0.6964675465
|
||||
300 -5029.3851410393 -5044.9928147367 15.6076736974 -5012.1131531405 -32.8796615962 88.8493144891 22.0216852689 20.2985091183 3.3368274018 0.0093519893 0.0546775051 -0.2110676539
|
||||
400 -5029.3900102082 -5045.6706717598 16.2806615516 -5012.7330095297 -32.9376622301 92.6804113371 22.0220931529 20.3035219616 3.3560233852 -0.0015365116 0.0454268927 0.5478139709
|
||||
500 -5029.3985510533 -5046.0433160611 16.6447650078 -5013.0924334585 -32.9508826025 94.7531316612 22.0214795944 20.3074656871 3.4232399722 -0.0107212024 0.0332249366 0.6595923534
|
||||
600 -5029.3929936746 -5045.4367231195 16.0437294449 -5012.7046931021 -32.7320300174 91.3316353653 22.0200027176 20.3101652565 3.4651727438 -0.0178110391 0.0210056002 0.1144372537
|
||||
700 -5029.3934435811 -5045.6074608403 16.2140172592 -5012.7886962164 -32.8187646239 92.3010274643 22.0178838793 20.3116257077 3.4432436715 -0.0242636237 0.0078323424 -0.5162836955
|
||||
800 -5029.3892931255 -5046.2270462380 16.8377531124 -5013.2383770824 -32.9886691555 95.8517489911 22.0151485191 20.3116305041 3.3780520461 -0.0302821178 -0.0083184719 -0.6710801515
|
||||
900 -5029.3930414671 -5046.0272003818 16.6341589146 -5013.2317798384 -32.7954205434 94.6927546874 22.0119224940 20.3099187654 3.3350551183 -0.0341747588 -0.0256858066 -0.0799872839
|
||||
1000 -5029.3908907831 -5045.6437703692 16.2528795861 -5012.6800867885 -32.9636835807 92.5222578135 22.0084902521 20.3065746721 3.3658243730 -0.0336536245 -0.0406018547 0.6191660974
|
||||
Loop time of 36.0917 on 4 procs for 1000 steps with 1360 atoms
|
||||
|
||||
Performance: 2.394 ns/day, 10.025 hours/ns, 27.707 timesteps/s
|
||||
97.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 33.204 | 34.289 | 35.893 | 17.3 | 95.01
|
||||
Bond | 0.00038719 | 0.00065947 | 0.00097609 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.1539 | 1.7595 | 2.8464 | 76.7 | 4.88
|
||||
Output | 0.0013447 | 0.0014529 | 0.0016887 | 0.4 | 0.00
|
||||
Modify | 0.010811 | 0.012037 | 0.013764 | 1.0 | 0.03
|
||||
Other | | 0.0287 | | | 0.08
|
||||
|
||||
Nlocal: 340 ave 344 max 334 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 1 1
|
||||
Nghost: 4628 ave 4634 max 4624 min
|
||||
Histogram: 1 0 1 0 1 0 0 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 66301.5 ave 67860 max 63963 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 1 1
|
||||
|
||||
Total # of neighbors = 265206
|
||||
Ave neighs/atom = 195.004
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:36
|
||||
@ -1 +0,0 @@
|
||||
../../../../../potentials/BNC.tersoff
|
||||
@ -1 +0,0 @@
|
||||
../../../../../potentials/BNCH-old.ILP
|
||||
@ -1 +0,0 @@
|
||||
../../../../../potentials/CH.airebo
|
||||
@ -1,71 +0,0 @@
|
||||
# Initialization
|
||||
units metal
|
||||
boundary p p p
|
||||
atom_style full
|
||||
processors * * 1 # domain decomposition over x and y
|
||||
|
||||
# System and atom definition
|
||||
# we use 2 atom types so that inter- and intra-layer
|
||||
# interactions can be specified separately
|
||||
read_data gr_hBN_Cstack_2L_noH.data
|
||||
mass 1 10.8110 # boron mass (g/mole) | membrane
|
||||
mass 2 14.0067 # nitrogen mass (g/mole) | membrane
|
||||
mass 3 12.0107 # carbon mass (g/mole) | adsorbate
|
||||
# Separate atom groups
|
||||
group membrane type 1 2
|
||||
group adsorbate type 3
|
||||
|
||||
######################## Potential defition ########################
|
||||
pair_style hybrid/overlay rebo tersoff ilp/graphene/hbn 16.0 coul/shield 16.0
|
||||
####################################################################
|
||||
pair_coeff * * rebo CH.airebo NULL NULL C # chemical
|
||||
pair_coeff * * tersoff BNC.tersoff B N NULL # chemical
|
||||
pair_coeff * * ilp/graphene/hbn BNCH-old.ILP B N C # long range
|
||||
pair_coeff 1 1 coul/shield 0.70
|
||||
pair_coeff 1 2 coul/shield 0.69498201415576216335
|
||||
pair_coeff 2 2 coul/shield 0.69
|
||||
####################################################################
|
||||
# Neighbor update settings
|
||||
neighbor 2.0 bin
|
||||
neigh_modify every 1
|
||||
neigh_modify delay 0
|
||||
neigh_modify check yes
|
||||
|
||||
# calculate the COM
|
||||
variable adsxcom equal xcm(adsorbate,x)
|
||||
variable adsycom equal xcm(adsorbate,y)
|
||||
variable adszcom equal xcm(adsorbate,z)
|
||||
variable adsvxcom equal vcm(adsorbate,x)
|
||||
variable adsvycom equal vcm(adsorbate,y)
|
||||
variable adsvzcom equal vcm(adsorbate,z)
|
||||
|
||||
#### Simulation settings ####
|
||||
timestep 0.001
|
||||
velocity all create 300.0 12345
|
||||
fix thermostat all nve
|
||||
|
||||
compute 0 all pair rebo
|
||||
compute 1 all pair tersoff
|
||||
compute 2 all pair ilp/graphene/hbn
|
||||
compute 3 all pair coul/shield
|
||||
variable REBO equal c_0
|
||||
variable Tersoff equal c_1
|
||||
variable EILP equal c_2
|
||||
variable Ecoul equal c_3
|
||||
|
||||
# Calculate the pair potential between the substrate and slider
|
||||
compute sldsub adsorbate group/group membrane
|
||||
variable Evdw equal c_sldsub
|
||||
|
||||
############################
|
||||
|
||||
# Output
|
||||
thermo 100
|
||||
thermo_style custom step etotal pe ke v_Evdw v_Tersoff v_REBO v_EILP v_Ecoul temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
|
||||
thermo_modify line one format float %.10f
|
||||
|
||||
#dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu
|
||||
#dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
|
||||
|
||||
###### Run molecular dynamics ######
|
||||
run 1000
|
||||
@ -1,171 +0,0 @@
|
||||
LAMMPS (8 Mar 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Initialization
|
||||
units metal
|
||||
boundary p p p
|
||||
atom_style full
|
||||
processors * * 1 # domain decomposition over x and y
|
||||
|
||||
# System and atom definition
|
||||
# we use 2 atom types so that inter- and intra-layer
|
||||
# interactions can be specified separately
|
||||
read_data gr_hBN_Cstack_2L_noH.data
|
||||
orthogonal box = (0 0 0) to (44.583 42.9 100)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
1440 atoms
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
mass 1 10.8110 # boron mass (g/mole) | membrane
|
||||
mass 2 14.0067 # nitrogen mass (g/mole) | membrane
|
||||
mass 3 12.0107 # carbon mass (g/mole) | adsorbate
|
||||
# Separate atom groups
|
||||
group membrane type 1 2
|
||||
720 atoms in group membrane
|
||||
group adsorbate type 3
|
||||
720 atoms in group adsorbate
|
||||
|
||||
######################## Potential defition ########################
|
||||
pair_style hybrid/overlay rebo tersoff ilp/graphene/hbn 16.0 coul/shield 16.0
|
||||
####################################################################
|
||||
pair_coeff * * rebo CH.airebo NULL NULL C # chemical
|
||||
Reading potential file CH.airebo with DATE: 2011-10-25
|
||||
pair_coeff * * tersoff BNC.tersoff B N NULL # chemical
|
||||
Reading potential file BNC.tersoff with DATE: 2013-03-21
|
||||
pair_coeff * * ilp/graphene/hbn BNCH-old.ILP B N C # long range
|
||||
pair_coeff 1 1 coul/shield 0.70
|
||||
pair_coeff 1 2 coul/shield 0.69498201415576216335
|
||||
pair_coeff 2 2 coul/shield 0.69
|
||||
####################################################################
|
||||
# Neighbor update settings
|
||||
neighbor 2.0 bin
|
||||
neigh_modify every 1
|
||||
neigh_modify delay 0
|
||||
neigh_modify check yes
|
||||
|
||||
# calculate the COM
|
||||
variable adsxcom equal xcm(adsorbate,x)
|
||||
variable adsycom equal xcm(adsorbate,y)
|
||||
variable adszcom equal xcm(adsorbate,z)
|
||||
variable adsvxcom equal vcm(adsorbate,x)
|
||||
variable adsvycom equal vcm(adsorbate,y)
|
||||
variable adsvzcom equal vcm(adsorbate,z)
|
||||
|
||||
#### Simulation settings ####
|
||||
timestep 0.001
|
||||
velocity all create 300.0 12345
|
||||
fix thermostat all nve
|
||||
|
||||
compute 0 all pair rebo
|
||||
compute 1 all pair tersoff
|
||||
compute 2 all pair ilp/graphene/hbn
|
||||
compute 3 all pair coul/shield
|
||||
variable REBO equal c_0
|
||||
variable Tersoff equal c_1
|
||||
variable EILP equal c_2
|
||||
variable Ecoul equal c_3
|
||||
|
||||
# Calculate the pair potential between the substrate and slider
|
||||
compute sldsub adsorbate group/group membrane
|
||||
variable Evdw equal c_sldsub
|
||||
|
||||
############################
|
||||
|
||||
# Output
|
||||
thermo 100
|
||||
thermo_style custom step etotal pe ke v_Evdw v_Tersoff v_REBO v_EILP v_Ecoul temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
|
||||
thermo_modify line one format float %.10f
|
||||
|
||||
#dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu
|
||||
#dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
|
||||
|
||||
###### Run molecular dynamics ######
|
||||
run 1000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 18
|
||||
ghost atom cutoff = 18
|
||||
binsize = 9, bins = 5 5 12
|
||||
7 neighbor lists, perpetual/occasional/extra = 6 1 0
|
||||
(1) pair rebo, perpetual, skip from (3)
|
||||
attributes: full, newton on, ghost
|
||||
pair build: skip/ghost
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair tersoff, perpetual, skip from (6)
|
||||
attributes: full, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) pair ilp/graphene/hbn, perpetual
|
||||
attributes: full, newton on, ghost
|
||||
pair build: full/bin/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(4) pair coul/shield, perpetual, half/full from (2)
|
||||
attributes: half, newton on
|
||||
pair build: halffull/newton/skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(5) compute group/group, occasional, copy from (7)
|
||||
attributes: half, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(6) neighbor class addition, perpetual, copy from (3)
|
||||
attributes: full, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(7) neighbor class addition, perpetual, half/full from (6)
|
||||
attributes: half, newton on
|
||||
pair build: halffull/newton
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 25.93 | 25.93 | 25.93 Mbytes
|
||||
Step TotEng PotEng KinEng v_Evdw v_Tersoff v_REBO v_EILP v_Ecoul Temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
|
||||
0 -10708.4531746010 -10764.2547791975 55.8016045965 -66.8250335416 -5401.7347845703 -5322.2780762734 -40.2419183538 0.0000000000 300.0000000000 21.6722857297 22.1650000000 3.3300000000 0.1682661410 -0.0842226772 0.1056563755
|
||||
100 -10708.2491256387 -10738.4532793285 30.2041536898 -68.8603937785 -5389.4304136167 -5309.6361134033 -39.3867523085 0.0000000000 162.3832535368 21.6879886706 22.1574778199 3.3223279482 0.1346509596 -0.0580689194 -0.1274433614
|
||||
200 -10708.1985754490 -10736.7142682477 28.5156927987 -70.0276479251 -5388.8677096501 -5308.3263464524 -39.5202121452 0.0000000000 153.3057678444 21.6968427596 22.1541506320 3.3143666142 0.0334706445 -0.0081639882 -0.0055006321
|
||||
300 -10708.1878214116 -10736.9033486636 28.7155272520 -68.2422175765 -5388.5952548022 -5308.9505338445 -39.3575600169 0.0000000000 154.3801157314 21.6939171741 22.1551483321 3.3251666346 -0.0896064591 0.0248921781 0.1717740196
|
||||
400 -10708.2036103906 -10738.2295882994 30.0259779088 -67.4993928655 -5389.4510311345 -5309.1985887571 -39.5799684078 0.0000000000 161.4253467759 21.6806789605 22.1589742804 3.3300374170 -0.1615300496 0.0532638209 -0.1185426799
|
||||
500 -10708.1853082161 -10736.0245173060 27.8392090900 -69.9737746636 -5387.9379921501 -5308.5551693329 -39.5313558230 0.0000000000 149.6688632411 21.6641276776 22.1655659011 3.3143210751 -0.1579504334 0.0766822604 -0.1154029266
|
||||
600 -10708.1781001285 -10736.4254568396 28.2473567110 -69.9368770273 -5388.3515507737 -5308.6700567475 -39.4038493184 0.0000000000 151.8631421907 21.6516789999 22.1733266592 3.3149997184 -0.0805825343 0.0684349609 0.1419617624
|
||||
700 -10708.1867253590 -10736.6143955088 28.4276701498 -67.1597096579 -5387.8570063253 -5309.0676141640 -39.6897750195 0.0000000000 152.8325414049 21.6489884054 22.1774523945 3.3315351816 0.0259900263 0.0094570835 0.0707953688
|
||||
800 -10708.1733385055 -10736.0277775931 27.8544390876 -68.6354557276 -5388.1933954711 -5308.5094712719 -39.3249108500 0.0000000000 149.7507425941 21.6565725156 22.1751617515 3.3227650180 0.1222442823 -0.0531420670 -0.1677749693
|
||||
900 -10708.1827888042 -10737.2646739167 29.0818851126 -70.2218493216 -5387.9824857335 -5309.6527953488 -39.6293928345 0.0000000000 156.3497250098 21.6716950833 22.1680989334 3.3131455846 0.1650154385 -0.0820901425 0.0072049300
|
||||
1000 -10708.1804322657 -10736.1966428009 28.0162105352 -68.3753745517 -5388.2611029662 -5308.4521913187 -39.4833485160 0.0000000000 150.6204565501 21.6865468141 22.1602434319 3.3246621699 0.1213363701 -0.0688593023 0.1701174943
|
||||
Loop time of 149.449 on 1 procs for 1000 steps with 1440 atoms
|
||||
|
||||
Performance: 0.578 ns/day, 41.514 hours/ns, 6.691 timesteps/s
|
||||
96.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 149.06 | 149.06 | 149.06 | 0.0 | 99.74
|
||||
Bond | 0.00082946 | 0.00082946 | 0.00082946 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.068351 | 0.068351 | 0.068351 | 0.0 | 0.05
|
||||
Output | 0.25935 | 0.25935 | 0.25935 | 0.0 | 0.17
|
||||
Modify | 0.030915 | 0.030915 | 0.030915 | 0.0 | 0.02
|
||||
Other | | 0.02702 | | | 0.02
|
||||
|
||||
Nlocal: 1440 ave 1440 max 1440 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 8180 ave 8180 max 8180 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 140400 ave 140400 max 140400 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 280800 ave 280800 max 280800 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 280800
|
||||
Ave neighs/atom = 195
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:02:29
|
||||
@ -1,171 +0,0 @@
|
||||
LAMMPS (8 Mar 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Initialization
|
||||
units metal
|
||||
boundary p p p
|
||||
atom_style full
|
||||
processors * * 1 # domain decomposition over x and y
|
||||
|
||||
# System and atom definition
|
||||
# we use 2 atom types so that inter- and intra-layer
|
||||
# interactions can be specified separately
|
||||
read_data gr_hBN_Cstack_2L_noH.data
|
||||
orthogonal box = (0 0 0) to (44.583 42.9 100)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
1440 atoms
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
mass 1 10.8110 # boron mass (g/mole) | membrane
|
||||
mass 2 14.0067 # nitrogen mass (g/mole) | membrane
|
||||
mass 3 12.0107 # carbon mass (g/mole) | adsorbate
|
||||
# Separate atom groups
|
||||
group membrane type 1 2
|
||||
720 atoms in group membrane
|
||||
group adsorbate type 3
|
||||
720 atoms in group adsorbate
|
||||
|
||||
######################## Potential defition ########################
|
||||
pair_style hybrid/overlay rebo tersoff ilp/graphene/hbn 16.0 coul/shield 16.0
|
||||
####################################################################
|
||||
pair_coeff * * rebo CH.airebo NULL NULL C # chemical
|
||||
Reading potential file CH.airebo with DATE: 2011-10-25
|
||||
pair_coeff * * tersoff BNC.tersoff B N NULL # chemical
|
||||
Reading potential file BNC.tersoff with DATE: 2013-03-21
|
||||
pair_coeff * * ilp/graphene/hbn BNCH-old.ILP B N C # long range
|
||||
pair_coeff 1 1 coul/shield 0.70
|
||||
pair_coeff 1 2 coul/shield 0.69498201415576216335
|
||||
pair_coeff 2 2 coul/shield 0.69
|
||||
####################################################################
|
||||
# Neighbor update settings
|
||||
neighbor 2.0 bin
|
||||
neigh_modify every 1
|
||||
neigh_modify delay 0
|
||||
neigh_modify check yes
|
||||
|
||||
# calculate the COM
|
||||
variable adsxcom equal xcm(adsorbate,x)
|
||||
variable adsycom equal xcm(adsorbate,y)
|
||||
variable adszcom equal xcm(adsorbate,z)
|
||||
variable adsvxcom equal vcm(adsorbate,x)
|
||||
variable adsvycom equal vcm(adsorbate,y)
|
||||
variable adsvzcom equal vcm(adsorbate,z)
|
||||
|
||||
#### Simulation settings ####
|
||||
timestep 0.001
|
||||
velocity all create 300.0 12345
|
||||
fix thermostat all nve
|
||||
|
||||
compute 0 all pair rebo
|
||||
compute 1 all pair tersoff
|
||||
compute 2 all pair ilp/graphene/hbn
|
||||
compute 3 all pair coul/shield
|
||||
variable REBO equal c_0
|
||||
variable Tersoff equal c_1
|
||||
variable EILP equal c_2
|
||||
variable Ecoul equal c_3
|
||||
|
||||
# Calculate the pair potential between the substrate and slider
|
||||
compute sldsub adsorbate group/group membrane
|
||||
variable Evdw equal c_sldsub
|
||||
|
||||
############################
|
||||
|
||||
# Output
|
||||
thermo 100
|
||||
thermo_style custom step etotal pe ke v_Evdw v_Tersoff v_REBO v_EILP v_Ecoul temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
|
||||
thermo_modify line one format float %.10f
|
||||
|
||||
#dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu
|
||||
#dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
|
||||
|
||||
###### Run molecular dynamics ######
|
||||
run 1000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 18
|
||||
ghost atom cutoff = 18
|
||||
binsize = 9, bins = 5 5 12
|
||||
7 neighbor lists, perpetual/occasional/extra = 6 1 0
|
||||
(1) pair rebo, perpetual, skip from (3)
|
||||
attributes: full, newton on, ghost
|
||||
pair build: skip/ghost
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair tersoff, perpetual, skip from (6)
|
||||
attributes: full, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) pair ilp/graphene/hbn, perpetual
|
||||
attributes: full, newton on, ghost
|
||||
pair build: full/bin/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(4) pair coul/shield, perpetual, half/full from (2)
|
||||
attributes: half, newton on
|
||||
pair build: halffull/newton/skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(5) compute group/group, occasional, copy from (7)
|
||||
attributes: half, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(6) neighbor class addition, perpetual, copy from (3)
|
||||
attributes: full, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(7) neighbor class addition, perpetual, half/full from (6)
|
||||
attributes: half, newton on
|
||||
pair build: halffull/newton
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 14.25 | 14.25 | 14.25 Mbytes
|
||||
Step TotEng PotEng KinEng v_Evdw v_Tersoff v_REBO v_EILP v_Ecoul Temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
|
||||
0 -10708.4531746011 -10764.2547791976 55.8016045965 -66.8250335415 -5401.7347845703 -5322.2780762735 -40.2419183538 0.0000000000 300.0000000000 21.6722857297 22.1650000000 3.3300000000 0.1682661410 -0.0842226772 0.1056563755
|
||||
100 -10708.2491256387 -10738.4532793285 30.2041536898 -68.8603937785 -5389.4304136167 -5309.6361134033 -39.3867523085 0.0000000000 162.3832535368 21.6879886706 22.1574778199 3.3223279482 0.1346509596 -0.0580689194 -0.1274433614
|
||||
200 -10708.1985754490 -10736.7142682477 28.5156927987 -70.0276479251 -5388.8677096501 -5308.3263464524 -39.5202121452 0.0000000000 153.3057678444 21.6968427596 22.1541506320 3.3143666142 0.0334706445 -0.0081639882 -0.0055006321
|
||||
300 -10708.1878214116 -10736.9033486636 28.7155272520 -68.2422175765 -5388.5952548022 -5308.9505338445 -39.3575600169 0.0000000000 154.3801157314 21.6939171741 22.1551483321 3.3251666346 -0.0896064591 0.0248921781 0.1717740196
|
||||
400 -10708.2036103906 -10738.2295882994 30.0259779088 -67.4993928655 -5389.4510311345 -5309.1985887571 -39.5799684078 0.0000000000 161.4253467759 21.6806789605 22.1589742804 3.3300374170 -0.1615300496 0.0532638209 -0.1185426799
|
||||
500 -10708.1853082161 -10736.0245173060 27.8392090900 -69.9737746636 -5387.9379921501 -5308.5551693329 -39.5313558230 0.0000000000 149.6688632411 21.6641276776 22.1655659011 3.3143210751 -0.1579504334 0.0766822604 -0.1154029266
|
||||
600 -10708.1781001285 -10736.4254568396 28.2473567110 -69.9368770273 -5388.3515507736 -5308.6700567475 -39.4038493184 0.0000000000 151.8631421907 21.6516789999 22.1733266592 3.3149997184 -0.0805825343 0.0684349609 0.1419617624
|
||||
700 -10708.1867253590 -10736.6143955089 28.4276701498 -67.1597096579 -5387.8570063253 -5309.0676141640 -39.6897750195 0.0000000000 152.8325414049 21.6489884054 22.1774523945 3.3315351816 0.0259900263 0.0094570835 0.0707953688
|
||||
800 -10708.1733385055 -10736.0277775930 27.8544390876 -68.6354557276 -5388.1933954711 -5308.5094712719 -39.3249108500 0.0000000000 149.7507425941 21.6565725156 22.1751617515 3.3227650180 0.1222442823 -0.0531420670 -0.1677749693
|
||||
900 -10708.1827888042 -10737.2646739167 29.0818851126 -70.2218493216 -5387.9824857335 -5309.6527953488 -39.6293928345 0.0000000000 156.3497250098 21.6716950833 22.1680989334 3.3131455846 0.1650154385 -0.0820901425 0.0072049300
|
||||
1000 -10708.1804322657 -10736.1966428009 28.0162105352 -68.3753745517 -5388.2611029662 -5308.4521913187 -39.4833485160 0.0000000000 150.6204565501 21.6865468141 22.1602434319 3.3246621699 0.1213363701 -0.0688593023 0.1701174943
|
||||
Loop time of 39.6206 on 4 procs for 1000 steps with 1440 atoms
|
||||
|
||||
Performance: 2.181 ns/day, 11.006 hours/ns, 25.239 timesteps/s
|
||||
98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 34.948 | 37.122 | 39.309 | 31.6 | 93.69
|
||||
Bond | 0.00046444 | 0.0005914 | 0.00089121 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.20131 | 2.3895 | 4.565 | 124.7 | 6.03
|
||||
Output | 0.069107 | 0.069157 | 0.069264 | 0.0 | 0.17
|
||||
Modify | 0.010056 | 0.010403 | 0.010688 | 0.3 | 0.03
|
||||
Other | | 0.02875 | | | 0.07
|
||||
|
||||
Nlocal: 360 ave 380 max 340 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Nghost: 4716 ave 4736 max 4696 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Neighs: 35100 ave 37050 max 33150 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
FullNghs: 70200 ave 74100 max 66300 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 280800
|
||||
Ave neighs/atom = 195
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:39
|
||||
1372
examples/USER/misc/ilp_graphene_hbn/hBN_AA_prime_stack_2L_noH.data
Normal file
1372
examples/USER/misc/ilp_graphene_hbn/hBN_AA_prime_stack_2L_noH.data
Normal file
File diff suppressed because it is too large
Load Diff
51
examples/USER/misc/ilp_graphene_hbn/in.bilayer-graphene
Normal file
51
examples/USER/misc/ilp_graphene_hbn/in.bilayer-graphene
Normal file
@ -0,0 +1,51 @@
|
||||
# Initialization
|
||||
units metal
|
||||
boundary p p p
|
||||
atom_style full
|
||||
processors * * 1 # domain decomposition over x and y
|
||||
|
||||
# System and atom definition
|
||||
# we use different molecule ids for each layer of hBN
|
||||
# so that inter- and intra-layer
|
||||
# interactions can be specified separately
|
||||
|
||||
read_data Bi_gr_AB_stack_2L_noH.data
|
||||
mass 1 12.0107 # carbon mass (g/mole) | membrane
|
||||
mass 2 12.0107 # carbon mass (g/mole) | adsorbate
|
||||
# Separate atom groups
|
||||
group layer1 molecule 1
|
||||
group layer2 molecule 2
|
||||
|
||||
######################## Potential defition ########################
|
||||
pair_style hybrid/overlay rebo ilp/graphene/hbn 16.0
|
||||
####################################################################
|
||||
pair_coeff * * rebo CH.rebo C C # chemical
|
||||
pair_coeff * * ilp/graphene/hbn BNCH.ILP C C # long range
|
||||
####################################################################
|
||||
# Neighbor update settings
|
||||
neighbor 2.0 bin
|
||||
neigh_modify every 1
|
||||
neigh_modify delay 0
|
||||
neigh_modify check yes
|
||||
|
||||
#### Simulation settings ####
|
||||
timestep 0.001
|
||||
velocity all create 300.0 12345
|
||||
|
||||
compute 0 all pair rebo
|
||||
compute 1 all pair ilp/graphene/hbn
|
||||
variable REBO equal c_0 # REBO energy
|
||||
variable ILP equal c_1 # total interlayer energy
|
||||
variable Evdw equal c_1[1] # attractive energy
|
||||
variable Erep equal c_1[2] # repulsive energy
|
||||
|
||||
############################
|
||||
|
||||
# Output
|
||||
thermo 100
|
||||
thermo_style custom step etotal pe ke v_REBO v_ILP v_Erep v_Evdw temp
|
||||
thermo_modify lost warn
|
||||
|
||||
###### Run molecular dynamics ######
|
||||
fix thermostat all nve
|
||||
run 1000
|
||||
56
examples/USER/misc/ilp_graphene_hbn/in.bilayer-hBN
Normal file
56
examples/USER/misc/ilp_graphene_hbn/in.bilayer-hBN
Normal file
@ -0,0 +1,56 @@
|
||||
# Initialization
|
||||
units metal
|
||||
boundary p p p
|
||||
atom_style full
|
||||
processors * * 1 # domain decomposition over x and y
|
||||
|
||||
# System and atom definition
|
||||
# we use different molecule ids for each layer of hBN
|
||||
# so that inter- and intra-layer
|
||||
# interactions can be specified separately
|
||||
read_data hBN_AA_prime_stack_2L_noH.data
|
||||
mass 1 10.8110 # boron mass (g/mole) | membrane
|
||||
mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate
|
||||
mass 3 10.8110 # boron mass (g/mole) | membrane
|
||||
mass 4 14.0067 # nitrogen mass (g/mole) | adsorbate
|
||||
# Separate atom groups
|
||||
group layer1 molecule 1
|
||||
group layer2 molecule 2
|
||||
|
||||
######################## Potential defition ########################
|
||||
pair_style hybrid/overlay tersoff ilp/graphene/hbn 16.0 coul/shield 16.0 1
|
||||
####################################################################
|
||||
pair_coeff * * tersoff BNC.tersoff B N B N # chemical
|
||||
pair_coeff * * ilp/graphene/hbn BNCH.ILP B N B N # long range
|
||||
pair_coeff 1 3 coul/shield 0.70
|
||||
pair_coeff 1 4 coul/shield 0.69498201415576216335
|
||||
pair_coeff 2 3 coul/shield 0.69498201415576216335
|
||||
pair_coeff 2 4 coul/shield 0.69
|
||||
####################################################################
|
||||
# Neighbor update settings
|
||||
neighbor 2.0 bin
|
||||
neigh_modify every 1
|
||||
neigh_modify delay 0
|
||||
neigh_modify check yes
|
||||
|
||||
#### Simulation settings ####
|
||||
timestep 0.001
|
||||
velocity all create 300.0 12345 dist gaussian mom yes rot yes
|
||||
fix thermostat all nve
|
||||
|
||||
compute 0 all pair tersoff
|
||||
compute 1 all pair coul/shield ecoul
|
||||
compute 2 all pair ilp/graphene/hbn
|
||||
variable Tersoff equal c_0 # Tersoff energy
|
||||
variable Ecoul equal c_1 # Coulomb energy
|
||||
variable EILP equal c_2 # total interlayer energy
|
||||
variable Evdw equal c_2[1] # attractive energy
|
||||
variable Erep equal c_2[2] # repulsive energy
|
||||
|
||||
############# Output ###############
|
||||
thermo 100
|
||||
thermo_style custom step etotal pe ke v_Evdw v_Tersoff v_EILP v_Erep v_Evdw v_Ecoul temp
|
||||
thermo_modify lost warn
|
||||
|
||||
###### Run molecular dynamics ######
|
||||
run 1000
|
||||
56
examples/USER/misc/ilp_graphene_hbn/in.grhBN
Normal file
56
examples/USER/misc/ilp_graphene_hbn/in.grhBN
Normal file
@ -0,0 +1,56 @@
|
||||
# Initialization
|
||||
units metal
|
||||
boundary p p p
|
||||
atom_style full
|
||||
processors * * 1 # domain decomposition over x and y
|
||||
|
||||
# System and atom definition
|
||||
# we use different molecule ids for each layer
|
||||
# so that inter- and intra-layer
|
||||
# interactions can be specified separately
|
||||
read_data gr_hBN_Cstack_2L_noH.data
|
||||
mass 1 10.8110 # boron mass (g/mole) | membrane
|
||||
mass 2 14.0067 # nitrogen mass (g/mole) | membrane
|
||||
mass 3 12.0107 # carbon mass (g/mole) | adsorbate
|
||||
# Separate atom groups
|
||||
group hBN molecule 1
|
||||
group gr molecule 2
|
||||
|
||||
######################## Potential defition ########################
|
||||
pair_style hybrid/overlay rebo tersoff ilp/graphene/hbn 16.0 coul/shield 16.0
|
||||
####################################################################
|
||||
pair_coeff * * rebo CH.rebo NULL NULL C # chemical
|
||||
pair_coeff * * tersoff BNC.tersoff B N NULL # chemical
|
||||
pair_coeff * * ilp/graphene/hbn BNCH.ILP B N C # long range
|
||||
pair_coeff 1 1 coul/shield 0.70
|
||||
pair_coeff 1 2 coul/shield 0.69498201415576216335
|
||||
pair_coeff 2 2 coul/shield 0.69
|
||||
####################################################################
|
||||
# Neighbor update settings
|
||||
neighbor 2.0 bin
|
||||
neigh_modify every 1
|
||||
neigh_modify delay 0
|
||||
neigh_modify check yes
|
||||
|
||||
#### Simulation settings ####
|
||||
timestep 0.001
|
||||
velocity all create 300.0 12345 dist gaussian mom yes rot yes
|
||||
fix thermostat all nve
|
||||
|
||||
compute 0 all pair rebo
|
||||
compute 1 all pair tersoff
|
||||
compute 2 all pair ilp/graphene/hbn
|
||||
compute 3 all pair coul/shield
|
||||
variable REBO equal c_0
|
||||
variable Tersoff equal c_1
|
||||
variable EILP equal c_2 # total interlayer energy
|
||||
variable Evdw equal c_2[1] # attractive energy
|
||||
variable Erep equal c_2[2] # repulsive energy
|
||||
variable Ecoul equal c_3
|
||||
|
||||
############# Output ##############
|
||||
thermo 100
|
||||
thermo_style custom step etotal pe ke v_Evdw v_Tersoff v_REBO v_EILP v_Erep v_Evdw v_Ecoul temp
|
||||
|
||||
###### Run molecular dynamics ######
|
||||
run 1000
|
||||
@ -32,14 +32,6 @@ neigh_modify every 1
|
||||
neigh_modify delay 0
|
||||
neigh_modify check yes
|
||||
|
||||
# calculate the COM
|
||||
variable adsxcom equal xcm(adsorbate,x)
|
||||
variable adsycom equal xcm(adsorbate,y)
|
||||
variable adszcom equal xcm(adsorbate,z)
|
||||
variable adsvxcom equal vcm(adsorbate,x)
|
||||
variable adsvycom equal vcm(adsorbate,y)
|
||||
variable adsvzcom equal vcm(adsorbate,z)
|
||||
|
||||
#### Simulation settings ####
|
||||
timestep 0.001
|
||||
#velocity adsorbate create 300.0 12345
|
||||
@ -51,19 +43,16 @@ compute 1 all pair coul/shield ecoul
|
||||
compute 2 all pair ilp/graphene/hbn
|
||||
variable Tersoff equal c_0
|
||||
variable Ecoul equal c_1
|
||||
variable EILP equal c_2
|
||||
|
||||
# Calculate the pair potential between the substrate and slider
|
||||
compute sldsub adsorbate group/group membrane
|
||||
variable Evdw equal c_sldsub
|
||||
variable ILP equal c_2
|
||||
variable Evdw equal c_2[1]
|
||||
variable Erep equal c_2[2]
|
||||
|
||||
############################
|
||||
|
||||
# Output
|
||||
thermo 100
|
||||
thermo_style custom step etotal pe ke v_Evdw v_Tersoff v_EILP v_Ecoul temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom f_subf[1] f_subf[2] f_subf[3]
|
||||
thermo_modify line one format float %.10f
|
||||
thermo_modify flush yes norm no lost warn #ignore
|
||||
thermo_style custom step etotal pe ke v_Tersoff v_ILP v_Ecoul v_Erep v_Evdw temp
|
||||
thermo_modify lost warn #ignore
|
||||
|
||||
#dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu
|
||||
#dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
|
||||
|
||||
@ -1,168 +0,0 @@
|
||||
LAMMPS (8 Mar 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Initialization
|
||||
units metal
|
||||
boundary p p p
|
||||
atom_style full
|
||||
processors * * 1 # domain decomposition over x and y
|
||||
|
||||
# System and atom definition
|
||||
# we use 2 atom types so that inter- and intra-layer
|
||||
# interactions can be specified separately
|
||||
read_data hBN_AB_stack_2L_noH_equi_300K.data
|
||||
orthogonal box = (0 0 0) to (43.38 42.5773 100)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
1360 atoms
|
||||
reading velocities ...
|
||||
1360 velocities
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
mass 1 10.8110 # boron mass (g/mole) | membrane
|
||||
mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate
|
||||
mass 3 10.8110 # boron mass (g/mole) | membrane
|
||||
mass 4 14.0067 # nitrogen mass (g/mole) | adsorbate
|
||||
# Separate atom groups
|
||||
group membrane type 1 2
|
||||
680 atoms in group membrane
|
||||
group adsorbate type 3 4
|
||||
680 atoms in group adsorbate
|
||||
|
||||
######################## Potential defition ########################
|
||||
pair_style hybrid/overlay tersoff ilp/graphene/hbn 16.0 coul/shield 16.0 1
|
||||
####################################################################
|
||||
pair_coeff * * tersoff BNC.tersoff NULL NULL B N # chemical
|
||||
Reading potential file BNC.tersoff with DATE: 2013-03-21
|
||||
pair_coeff * * ilp/graphene/hbn BNCH-old.ILP B N B N # long range
|
||||
pair_coeff 1 3 coul/shield 0.70
|
||||
pair_coeff 1 4 coul/shield 0.69498201415576216335
|
||||
pair_coeff 2 3 coul/shield 0.69498201415576216335
|
||||
pair_coeff 2 4 coul/shield 0.69
|
||||
####################################################################
|
||||
# Neighbor update settings
|
||||
neighbor 2.0 bin
|
||||
neigh_modify every 1
|
||||
neigh_modify delay 0
|
||||
neigh_modify check yes
|
||||
|
||||
# calculate the COM
|
||||
variable adsxcom equal xcm(adsorbate,x)
|
||||
variable adsycom equal xcm(adsorbate,y)
|
||||
variable adszcom equal xcm(adsorbate,z)
|
||||
variable adsvxcom equal vcm(adsorbate,x)
|
||||
variable adsvycom equal vcm(adsorbate,y)
|
||||
variable adsvzcom equal vcm(adsorbate,z)
|
||||
|
||||
#### Simulation settings ####
|
||||
timestep 0.001
|
||||
#velocity adsorbate create 300.0 12345
|
||||
fix subf membrane setforce 0.0 0.0 0.0
|
||||
fix thermostat all nve
|
||||
|
||||
compute 0 all pair tersoff
|
||||
compute 1 all pair coul/shield ecoul
|
||||
compute 2 all pair ilp/graphene/hbn
|
||||
variable Tersoff equal c_0
|
||||
variable Ecoul equal c_1
|
||||
variable EILP equal c_2
|
||||
|
||||
# Calculate the pair potential between the substrate and slider
|
||||
compute sldsub adsorbate group/group membrane
|
||||
variable Evdw equal c_sldsub
|
||||
|
||||
############################
|
||||
|
||||
# Output
|
||||
thermo 100
|
||||
thermo_style custom step etotal pe ke v_Evdw v_Tersoff v_EILP v_Ecoul temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom f_subf[1] f_subf[2] f_subf[3]
|
||||
thermo_modify line one format float %.10f
|
||||
thermo_modify flush yes norm no lost warn #ignore
|
||||
|
||||
#dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu
|
||||
#dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
|
||||
|
||||
###### Run molecular dynamics ######
|
||||
run 1000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 18
|
||||
ghost atom cutoff = 18
|
||||
binsize = 9, bins = 5 5 12
|
||||
6 neighbor lists, perpetual/occasional/extra = 5 1 0
|
||||
(1) pair tersoff, perpetual, skip from (5)
|
||||
attributes: full, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair ilp/graphene/hbn, perpetual
|
||||
attributes: full, newton on, ghost
|
||||
pair build: full/bin/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(3) pair coul/shield, perpetual, skip from (6)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(4) compute group/group, occasional, copy from (6)
|
||||
attributes: half, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(5) neighbor class addition, perpetual, copy from (2)
|
||||
attributes: full, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(6) neighbor class addition, perpetual, half/full from (5)
|
||||
attributes: half, newton on
|
||||
pair build: halffull/newton
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 57.85 | 57.85 | 57.85 Mbytes
|
||||
Step TotEng PotEng KinEng v_Evdw v_Tersoff v_EILP v_Ecoul Temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom f_subf[1] f_subf[2] f_subf[3]
|
||||
0 -5114.6628078598 -5127.8586355055 13.1958276458 -75.3652234209 -5091.4120857465 -36.0831137829 -0.3634359761 75.1194741238 20.9113202537 20.6582215878 3.2895976612 -0.0495147937 -0.0552233516 -0.0166592619 -0.1742790202 -0.0884665936 -0.8010816801
|
||||
100 -5114.6620580583 -5127.6958349342 13.0337768758 -75.2249487778 -5091.2407919311 -36.0927601416 -0.3622828614 74.1969727889 20.9076129631 20.6534162972 3.2908118318 -0.0234802196 -0.0397832410 0.0332404745 -0.2430042439 -0.1598109185 -0.5351246275
|
||||
200 -5114.6630637865 -5127.5945140906 12.9314503041 -74.6445167393 -5091.1507571912 -36.0866688941 -0.3570880053 73.6144615235 20.9067696105 20.6505240051 3.2976575241 0.0078967872 -0.0170385302 0.0850447973 -0.2934041648 -0.2405295165 0.2309200807
|
||||
300 -5114.6693830121 -5128.3286231421 13.6592401300 -74.2223518942 -5091.8645555419 -36.1107860098 -0.3532815904 77.7575278367 20.9090146500 20.6502445717 3.3024525026 0.0352437329 0.0112279015 -0.0021399216 -0.2166516175 -0.2410661267 0.9007458614
|
||||
400 -5114.6614035404 -5127.6423784754 12.9809749350 -74.6548295432 -5091.2348011465 -36.0496340516 -0.3579432773 73.8963888364 20.9136276183 20.6526810045 3.2977225951 0.0556629502 0.0358324354 -0.0738287296 -0.1431221016 -0.1626739623 0.0673046122
|
||||
500 -5114.6599876234 -5127.4097813122 12.7497936887 -75.2268687829 -5090.9284608504 -36.1195707042 -0.3617497575 72.5803506074 20.9197050770 20.6571510311 3.2909058903 0.0631939085 0.0530269602 -0.0516940297 -0.0112976844 -0.1217009147 -0.4713422319
|
||||
600 -5114.6672773464 -5128.0912983829 13.4240210364 -75.3848112535 -5091.6338883189 -36.0938401510 -0.3635699131 76.4185034811 20.9258252862 20.6628322031 3.2892805234 0.0573396226 0.0579085440 0.0291853982 0.1059950758 0.0102266125 -0.7683214794
|
||||
700 -5114.6609647250 -5127.7466720637 13.0857073388 -74.7981789470 -5091.2811095008 -36.1066385732 -0.3589239897 74.4925957063 20.9307092134 20.6683554324 3.2957959411 0.0396744013 0.0503347378 0.0818267711 0.1737903706 0.1258761156 0.1307185989
|
||||
800 -5114.6622627667 -5128.0130406264 13.3507778597 -74.2952448854 -5091.5693975625 -36.0897180314 -0.3539250325 76.0015543464 20.9334441079 20.6725125240 3.3019570181 0.0142277646 0.0313116646 0.0291673132 0.2457478793 0.1912082770 0.7239823553
|
||||
900 -5114.6675469561 -5128.1496933801 13.4821464240 -74.3644898573 -5091.6703861750 -36.1246785145 -0.3546286905 76.7493920516 20.9334403558 20.6744181494 3.3005582394 -0.0141399355 0.0063543986 -0.0561206619 0.2370151923 0.2115707560 0.7822017606
|
||||
1000 -5114.6683146144 -5128.3364609113 13.6681462969 -75.1091579020 -5091.9370210069 -36.0375964349 -0.3618434694 77.8082276935 20.9306643096 20.6737238853 3.2922181699 -0.0411219854 -0.0200694204 -0.0788193565 0.2225175431 0.2377413412 -0.5875288557
|
||||
Loop time of 202.063 on 1 procs for 1000 steps with 1360 atoms
|
||||
|
||||
Performance: 0.428 ns/day, 56.129 hours/ns, 4.949 timesteps/s
|
||||
91.0% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 201.4 | 201.4 | 201.4 | 0.0 | 99.67
|
||||
Bond | 0.00092697 | 0.00092697 | 0.00092697 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.086005 | 0.086005 | 0.086005 | 0.0 | 0.04
|
||||
Output | 0.50438 | 0.50438 | 0.50438 | 0.0 | 0.25
|
||||
Modify | 0.038846 | 0.038846 | 0.038846 | 0.0 | 0.02
|
||||
Other | | 0.03093 | | | 0.02
|
||||
|
||||
Nlocal: 1360 ave 1360 max 1360 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 7840 ave 7840 max 7840 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 249628 ave 249628 max 249628 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 253390 ave 253390 max 253390 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 253390
|
||||
Ave neighs/atom = 186.316
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:03:22
|
||||
@ -1,168 +0,0 @@
|
||||
LAMMPS (8 Mar 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Initialization
|
||||
units metal
|
||||
boundary p p p
|
||||
atom_style full
|
||||
processors * * 1 # domain decomposition over x and y
|
||||
|
||||
# System and atom definition
|
||||
# we use 2 atom types so that inter- and intra-layer
|
||||
# interactions can be specified separately
|
||||
read_data hBN_AB_stack_2L_noH_equi_300K.data
|
||||
orthogonal box = (0 0 0) to (43.38 42.5773 100)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
1360 atoms
|
||||
reading velocities ...
|
||||
1360 velocities
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
mass 1 10.8110 # boron mass (g/mole) | membrane
|
||||
mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate
|
||||
mass 3 10.8110 # boron mass (g/mole) | membrane
|
||||
mass 4 14.0067 # nitrogen mass (g/mole) | adsorbate
|
||||
# Separate atom groups
|
||||
group membrane type 1 2
|
||||
680 atoms in group membrane
|
||||
group adsorbate type 3 4
|
||||
680 atoms in group adsorbate
|
||||
|
||||
######################## Potential defition ########################
|
||||
pair_style hybrid/overlay tersoff ilp/graphene/hbn 16.0 coul/shield 16.0 1
|
||||
####################################################################
|
||||
pair_coeff * * tersoff BNC.tersoff NULL NULL B N # chemical
|
||||
Reading potential file BNC.tersoff with DATE: 2013-03-21
|
||||
pair_coeff * * ilp/graphene/hbn BNCH-old.ILP B N B N # long range
|
||||
pair_coeff 1 3 coul/shield 0.70
|
||||
pair_coeff 1 4 coul/shield 0.69498201415576216335
|
||||
pair_coeff 2 3 coul/shield 0.69498201415576216335
|
||||
pair_coeff 2 4 coul/shield 0.69
|
||||
####################################################################
|
||||
# Neighbor update settings
|
||||
neighbor 2.0 bin
|
||||
neigh_modify every 1
|
||||
neigh_modify delay 0
|
||||
neigh_modify check yes
|
||||
|
||||
# calculate the COM
|
||||
variable adsxcom equal xcm(adsorbate,x)
|
||||
variable adsycom equal xcm(adsorbate,y)
|
||||
variable adszcom equal xcm(adsorbate,z)
|
||||
variable adsvxcom equal vcm(adsorbate,x)
|
||||
variable adsvycom equal vcm(adsorbate,y)
|
||||
variable adsvzcom equal vcm(adsorbate,z)
|
||||
|
||||
#### Simulation settings ####
|
||||
timestep 0.001
|
||||
#velocity adsorbate create 300.0 12345
|
||||
fix subf membrane setforce 0.0 0.0 0.0
|
||||
fix thermostat all nve
|
||||
|
||||
compute 0 all pair tersoff
|
||||
compute 1 all pair coul/shield ecoul
|
||||
compute 2 all pair ilp/graphene/hbn
|
||||
variable Tersoff equal c_0
|
||||
variable Ecoul equal c_1
|
||||
variable EILP equal c_2
|
||||
|
||||
# Calculate the pair potential between the substrate and slider
|
||||
compute sldsub adsorbate group/group membrane
|
||||
variable Evdw equal c_sldsub
|
||||
|
||||
############################
|
||||
|
||||
# Output
|
||||
thermo 100
|
||||
thermo_style custom step etotal pe ke v_Evdw v_Tersoff v_EILP v_Ecoul temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom f_subf[1] f_subf[2] f_subf[3]
|
||||
thermo_modify line one format float %.10f
|
||||
thermo_modify flush yes norm no lost warn #ignore
|
||||
|
||||
#dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu
|
||||
#dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
|
||||
|
||||
###### Run molecular dynamics ######
|
||||
run 1000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 18
|
||||
ghost atom cutoff = 18
|
||||
binsize = 9, bins = 5 5 12
|
||||
6 neighbor lists, perpetual/occasional/extra = 5 1 0
|
||||
(1) pair tersoff, perpetual, skip from (5)
|
||||
attributes: full, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair ilp/graphene/hbn, perpetual
|
||||
attributes: full, newton on, ghost
|
||||
pair build: full/bin/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(3) pair coul/shield, perpetual, skip from (6)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(4) compute group/group, occasional, copy from (6)
|
||||
attributes: half, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(5) neighbor class addition, perpetual, copy from (2)
|
||||
attributes: full, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(6) neighbor class addition, perpetual, half/full from (5)
|
||||
attributes: half, newton on
|
||||
pair build: halffull/newton
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 30.63 | 30.63 | 30.64 Mbytes
|
||||
Step TotEng PotEng KinEng v_Evdw v_Tersoff v_EILP v_Ecoul Temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom f_subf[1] f_subf[2] f_subf[3]
|
||||
0 -5114.6628078598 -5127.8586355055 13.1958276458 -75.3652234209 -5091.4120857465 -36.0831137829 -0.3634359761 75.1194741238 20.9113202537 20.6582215878 3.2895976612 -0.0495147937 -0.0552233516 -0.0166592619 -0.1742790202 -0.0884665936 -0.8010816801
|
||||
100 -5114.6620580583 -5127.6958349342 13.0337768758 -75.2249487778 -5091.2407919311 -36.0927601416 -0.3622828614 74.1969727889 20.9076129631 20.6534162972 3.2908118318 -0.0234802196 -0.0397832410 0.0332404745 -0.2430042439 -0.1598109185 -0.5351246275
|
||||
200 -5114.6630637865 -5127.5945140906 12.9314503041 -74.6445167393 -5091.1507571912 -36.0866688941 -0.3570880053 73.6144615235 20.9067696105 20.6505240051 3.2976575241 0.0078967872 -0.0170385302 0.0850447973 -0.2934041648 -0.2405295165 0.2309200807
|
||||
300 -5114.6693830121 -5128.3286231421 13.6592401300 -74.2223518942 -5091.8645555419 -36.1107860098 -0.3532815904 77.7575278367 20.9090146500 20.6502445717 3.3024525026 0.0352437329 0.0112279015 -0.0021399216 -0.2166516175 -0.2410661267 0.9007458614
|
||||
400 -5114.6614035404 -5127.6423784754 12.9809749350 -74.6548295432 -5091.2348011465 -36.0496340516 -0.3579432773 73.8963888364 20.9136276183 20.6526810045 3.2977225951 0.0556629502 0.0358324354 -0.0738287296 -0.1431221016 -0.1626739623 0.0673046122
|
||||
500 -5114.6599876234 -5127.4097813122 12.7497936887 -75.2268687829 -5090.9284608504 -36.1195707042 -0.3617497575 72.5803506074 20.9197050770 20.6571510311 3.2909058903 0.0631939085 0.0530269602 -0.0516940297 -0.0112976844 -0.1217009147 -0.4713422319
|
||||
600 -5114.6672773464 -5128.0912983829 13.4240210364 -75.3848112535 -5091.6338883189 -36.0938401510 -0.3635699131 76.4185034811 20.9258252862 20.6628322031 3.2892805234 0.0573396226 0.0579085440 0.0291853982 0.1059950758 0.0102266125 -0.7683214794
|
||||
700 -5114.6609647250 -5127.7466720637 13.0857073388 -74.7981789470 -5091.2811095008 -36.1066385732 -0.3589239897 74.4925957063 20.9307092134 20.6683554324 3.2957959411 0.0396744013 0.0503347378 0.0818267711 0.1737903706 0.1258761156 0.1307185989
|
||||
800 -5114.6622627667 -5128.0130406264 13.3507778597 -74.2952448854 -5091.5693975625 -36.0897180314 -0.3539250325 76.0015543464 20.9334441079 20.6725125240 3.3019570181 0.0142277646 0.0313116646 0.0291673132 0.2457478793 0.1912082770 0.7239823553
|
||||
900 -5114.6675469561 -5128.1496933801 13.4821464240 -74.3644898573 -5091.6703861750 -36.1246785145 -0.3546286905 76.7493920516 20.9334403558 20.6744181494 3.3005582394 -0.0141399355 0.0063543986 -0.0561206619 0.2370151923 0.2115707560 0.7822017606
|
||||
1000 -5114.6683146144 -5128.3364609113 13.6681462969 -75.1091579020 -5091.9370210069 -36.0375964349 -0.3618434694 77.8082276935 20.9306643096 20.6737238853 3.2922181699 -0.0411219854 -0.0200694204 -0.0788193565 0.2225175431 0.2377413412 -0.5875288557
|
||||
Loop time of 53.3155 on 4 procs for 1000 steps with 1360 atoms
|
||||
|
||||
Performance: 1.621 ns/day, 14.810 hours/ns, 18.756 timesteps/s
|
||||
97.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 49.475 | 50.978 | 52.988 | 18.0 | 95.62
|
||||
Bond | 0.00045061 | 0.00066602 | 0.00086665 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.16491 | 2.1759 | 3.679 | 87.0 | 4.08
|
||||
Output | 0.11871 | 0.11882 | 0.11911 | 0.0 | 0.22
|
||||
Modify | 0.012956 | 0.013504 | 0.01387 | 0.3 | 0.03
|
||||
Other | | 0.02828 | | | 0.05
|
||||
|
||||
Nlocal: 340 ave 346 max 336 min
|
||||
Histogram: 1 0 1 0 1 0 0 0 0 1
|
||||
Nghost: 4537.5 ave 4540 max 4534 min
|
||||
Histogram: 1 0 0 0 0 0 2 0 0 1
|
||||
Neighs: 62407 ave 62413 max 62402 min
|
||||
Histogram: 1 0 0 1 1 0 0 0 0 1
|
||||
FullNghs: 63347.5 ave 65585 max 61866 min
|
||||
Histogram: 1 1 0 1 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 253926
|
||||
Ave neighs/atom = 186.71
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:53
|
||||
@ -0,0 +1,127 @@
|
||||
LAMMPS (31 Jul 2019)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Initialization
|
||||
units metal
|
||||
boundary p p p
|
||||
atom_style full
|
||||
processors * * 1 # domain decomposition over x and y
|
||||
|
||||
# System and atom definition
|
||||
# we use different molecule ids for each layer of hBN
|
||||
# so that inter- and intra-layer
|
||||
# interactions can be specified separately
|
||||
|
||||
read_data Bi_gr_AB_stack_2L_noH.data
|
||||
orthogonal box = (0 0 0) to (42.6 41.8117 100)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
1360 atoms
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
special bonds CPU = 0.000290871 secs
|
||||
read_data CPU = 0.00159073 secs
|
||||
mass 1 12.0107 # carbon mass (g/mole) | membrane
|
||||
mass 2 12.0107 # carbon mass (g/mole) | adsorbate
|
||||
# Separate atom groups
|
||||
group layer1 molecule 1
|
||||
680 atoms in group layer1
|
||||
group layer2 molecule 2
|
||||
680 atoms in group layer2
|
||||
|
||||
######################## Potential defition ########################
|
||||
pair_style hybrid/overlay rebo ilp/graphene/hbn 16.0
|
||||
####################################################################
|
||||
pair_coeff * * rebo CH.rebo C C # chemical
|
||||
Reading potential file CH.rebo with DATE: 2018-7-3
|
||||
pair_coeff * * ilp/graphene/hbn BNCH.ILP C C # long range
|
||||
####################################################################
|
||||
# Neighbor update settings
|
||||
neighbor 2.0 bin
|
||||
neigh_modify every 1
|
||||
neigh_modify delay 0
|
||||
neigh_modify check yes
|
||||
|
||||
#### Simulation settings ####
|
||||
timestep 0.001
|
||||
velocity all create 300.0 12345
|
||||
|
||||
compute 0 all pair rebo
|
||||
compute 1 all pair ilp/graphene/hbn
|
||||
variable REBO equal c_0 # REBO energy
|
||||
variable ILP equal c_1 # total interlayer energy
|
||||
variable Evdw equal c_1[1] # attractive energy
|
||||
variable Erep equal c_1[2] # repulsive energy
|
||||
|
||||
############################
|
||||
|
||||
# Output
|
||||
thermo 100
|
||||
thermo_style custom step etotal pe ke v_REBO v_ILP v_Erep v_Evdw temp
|
||||
thermo_modify lost warn
|
||||
|
||||
###### Run molecular dynamics ######
|
||||
fix thermostat all nve
|
||||
run 1000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 18
|
||||
ghost atom cutoff = 18
|
||||
binsize = 9, bins = 5 5 12
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair rebo, perpetual
|
||||
attributes: full, newton on, ghost
|
||||
pair build: full/bin/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) pair ilp/graphene/hbn, perpetual, copy from (1)
|
||||
attributes: full, newton on, ghost
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 17.21 | 17.21 | 17.21 Mbytes
|
||||
Step TotEng PotEng KinEng v_REBO v_ILP v_Erep v_Evdw Temp
|
||||
0 -10037.285 -10089.985 52.699361 -10057.189 -32.795185 43.640104 -76.435288 300
|
||||
100 -10037.034 -10064.765 27.73131 -10032.181 -32.58421 34.730868 -67.315078 157.86516
|
||||
200 -10036.963 -10061.144 24.18111 -10028.856 -32.288132 28.179936 -60.468068 137.65505
|
||||
300 -10037.003 -10063.5 26.496726 -10030.823 -32.677105 34.923849 -67.600954 150.83708
|
||||
400 -10037.032 -10064.389 27.356526 -10031.853 -32.535415 44.242347 -76.777762 155.73164
|
||||
500 -10037.023 -10064.114 27.090279 -10031.431 -32.682418 37.229232 -69.91165 154.21598
|
||||
600 -10037.003 -10063.657 26.653718 -10031.327 -32.329664 28.509073 -60.838737 151.73078
|
||||
700 -10037.004 -10063.35 26.345697 -10030.801 -32.549231 32.564686 -65.113917 149.97732
|
||||
800 -10037.025 -10064.219 27.194765 -10031.766 -32.453653 43.381557 -75.83521 154.81078
|
||||
900 -10037.028 -10064.668 27.639127 -10032.167 -32.500121 39.99345 -72.493571 157.34039
|
||||
1000 -10037.003 -10063.662 26.658825 -10031.337 -32.325053 29.573578 -61.898631 151.75986
|
||||
Loop time of 149.887 on 1 procs for 1000 steps with 1360 atoms
|
||||
|
||||
Performance: 0.576 ns/day, 41.635 hours/ns, 6.672 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 | 149.75 | 149.75 | 149.75 | 0.0 | 99.91
|
||||
Bond | 0.00024772 | 0.00024772 | 0.00024772 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.086328 | 0.086328 | 0.086328 | 0.0 | 0.06
|
||||
Output | 0.00036383 | 0.00036383 | 0.00036383 | 0.0 | 0.00
|
||||
Modify | 0.028636 | 0.028636 | 0.028636 | 0.0 | 0.02
|
||||
Other | | 0.01708 | | | 0.01
|
||||
|
||||
Nlocal: 1360 ave 1360 max 1360 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 7964 ave 7964 max 7964 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: 1.037e+06 ave 1.037e+06 max 1.037e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1037000
|
||||
Ave neighs/atom = 762.5
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:02:30
|
||||
@ -0,0 +1,127 @@
|
||||
LAMMPS (31 Jul 2019)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Initialization
|
||||
units metal
|
||||
boundary p p p
|
||||
atom_style full
|
||||
processors * * 1 # domain decomposition over x and y
|
||||
|
||||
# System and atom definition
|
||||
# we use different molecule ids for each layer of hBN
|
||||
# so that inter- and intra-layer
|
||||
# interactions can be specified separately
|
||||
|
||||
read_data Bi_gr_AB_stack_2L_noH.data
|
||||
orthogonal box = (0 0 0) to (42.6 41.8117 100)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
1360 atoms
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
special bonds CPU = 0.000157118 secs
|
||||
read_data CPU = 0.00145698 secs
|
||||
mass 1 12.0107 # carbon mass (g/mole) | membrane
|
||||
mass 2 12.0107 # carbon mass (g/mole) | adsorbate
|
||||
# Separate atom groups
|
||||
group layer1 molecule 1
|
||||
680 atoms in group layer1
|
||||
group layer2 molecule 2
|
||||
680 atoms in group layer2
|
||||
|
||||
######################## Potential defition ########################
|
||||
pair_style hybrid/overlay rebo ilp/graphene/hbn 16.0
|
||||
####################################################################
|
||||
pair_coeff * * rebo CH.rebo C C # chemical
|
||||
Reading potential file CH.rebo with DATE: 2018-7-3
|
||||
pair_coeff * * ilp/graphene/hbn BNCH.ILP C C # long range
|
||||
####################################################################
|
||||
# Neighbor update settings
|
||||
neighbor 2.0 bin
|
||||
neigh_modify every 1
|
||||
neigh_modify delay 0
|
||||
neigh_modify check yes
|
||||
|
||||
#### Simulation settings ####
|
||||
timestep 0.001
|
||||
velocity all create 300.0 12345
|
||||
|
||||
compute 0 all pair rebo
|
||||
compute 1 all pair ilp/graphene/hbn
|
||||
variable REBO equal c_0 # REBO energy
|
||||
variable ILP equal c_1 # total interlayer energy
|
||||
variable Evdw equal c_1[1] # attractive energy
|
||||
variable Erep equal c_1[2] # repulsive energy
|
||||
|
||||
############################
|
||||
|
||||
# Output
|
||||
thermo 100
|
||||
thermo_style custom step etotal pe ke v_REBO v_ILP v_Erep v_Evdw temp
|
||||
thermo_modify lost warn
|
||||
|
||||
###### Run molecular dynamics ######
|
||||
fix thermostat all nve
|
||||
run 1000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 18
|
||||
ghost atom cutoff = 18
|
||||
binsize = 9, bins = 5 5 12
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair rebo, perpetual
|
||||
attributes: full, newton on, ghost
|
||||
pair build: full/bin/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) pair ilp/graphene/hbn, perpetual, copy from (1)
|
||||
attributes: full, newton on, ghost
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 9.879 | 9.879 | 9.879 Mbytes
|
||||
Step TotEng PotEng KinEng v_REBO v_ILP v_Erep v_Evdw Temp
|
||||
0 -10037.285 -10089.985 52.699361 -10057.189 -32.795185 43.640104 -76.435288 300
|
||||
100 -10037.034 -10064.765 27.73131 -10032.181 -32.58421 34.730868 -67.315078 157.86516
|
||||
200 -10036.963 -10061.144 24.18111 -10028.856 -32.288132 28.179936 -60.468068 137.65505
|
||||
300 -10037.003 -10063.5 26.496726 -10030.823 -32.677105 34.923849 -67.600954 150.83708
|
||||
400 -10037.032 -10064.389 27.356526 -10031.853 -32.535415 44.242347 -76.777762 155.73164
|
||||
500 -10037.023 -10064.114 27.090279 -10031.431 -32.682418 37.229232 -69.91165 154.21598
|
||||
600 -10037.003 -10063.657 26.653718 -10031.327 -32.329664 28.509073 -60.838737 151.73078
|
||||
700 -10037.004 -10063.35 26.345697 -10030.801 -32.549231 32.564686 -65.113917 149.97732
|
||||
800 -10037.025 -10064.219 27.194765 -10031.766 -32.453653 43.381557 -75.83521 154.81078
|
||||
900 -10037.028 -10064.668 27.639127 -10032.167 -32.500121 39.99345 -72.493571 157.34039
|
||||
1000 -10037.003 -10063.662 26.658825 -10031.337 -32.325053 29.573578 -61.898631 151.75986
|
||||
Loop time of 44.6551 on 4 procs for 1000 steps with 1360 atoms
|
||||
|
||||
Performance: 1.935 ns/day, 12.404 hours/ns, 22.394 timesteps/s
|
||||
93.9% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 40.304 | 41.221 | 41.998 | 9.5 | 92.31
|
||||
Bond | 0.00027633 | 0.00029379 | 0.00031424 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 2.5678 | 3.3334 | 4.2403 | 32.9 | 7.46
|
||||
Output | 0.0051446 | 0.0054518 | 0.0059683 | 0.4 | 0.01
|
||||
Modify | 0.0088317 | 0.009002 | 0.0090654 | 0.1 | 0.02
|
||||
Other | | 0.08586 | | | 0.19
|
||||
|
||||
Nlocal: 340 ave 340 max 340 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 4628 ave 4628 max 4628 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 259250 ave 259250 max 259250 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1037000
|
||||
Ave neighs/atom = 762.5
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:44
|
||||
@ -0,0 +1,142 @@
|
||||
LAMMPS (31 Jul 2019)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Initialization
|
||||
units metal
|
||||
boundary p p p
|
||||
atom_style full
|
||||
processors * * 1 # domain decomposition over x and y
|
||||
|
||||
# System and atom definition
|
||||
# we use different molecule ids for each layer of hBN
|
||||
# so that inter- and intra-layer
|
||||
# interactions can be specified separately
|
||||
read_data hBN_AA_prime_stack_2L_noH.data
|
||||
orthogonal box = (0 0 0) to (43.38 42.5773 100)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
1360 atoms
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
special bonds CPU = 0.000375509 secs
|
||||
read_data CPU = 0.00181293 secs
|
||||
mass 1 10.8110 # boron mass (g/mole) | membrane
|
||||
mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate
|
||||
mass 3 10.8110 # boron mass (g/mole) | membrane
|
||||
mass 4 14.0067 # nitrogen mass (g/mole) | adsorbate
|
||||
# Separate atom groups
|
||||
group layer1 molecule 1
|
||||
680 atoms in group layer1
|
||||
group layer2 molecule 2
|
||||
680 atoms in group layer2
|
||||
|
||||
######################## Potential defition ########################
|
||||
pair_style hybrid/overlay tersoff ilp/graphene/hbn 16.0 coul/shield 16.0 1
|
||||
####################################################################
|
||||
pair_coeff * * tersoff BNC.tersoff B N B N # chemical
|
||||
Reading potential file BNC.tersoff with DATE: 2013-03-21
|
||||
pair_coeff * * ilp/graphene/hbn BNCH.ILP B N B N # long range
|
||||
pair_coeff 1 3 coul/shield 0.70
|
||||
pair_coeff 1 4 coul/shield 0.69498201415576216335
|
||||
pair_coeff 2 3 coul/shield 0.69498201415576216335
|
||||
pair_coeff 2 4 coul/shield 0.69
|
||||
####################################################################
|
||||
# Neighbor update settings
|
||||
neighbor 2.0 bin
|
||||
neigh_modify every 1
|
||||
neigh_modify delay 0
|
||||
neigh_modify check yes
|
||||
|
||||
#### Simulation settings ####
|
||||
timestep 0.001
|
||||
velocity all create 300.0 12345 dist gaussian mom yes rot yes
|
||||
fix thermostat all nve
|
||||
|
||||
compute 0 all pair tersoff
|
||||
compute 1 all pair coul/shield ecoul
|
||||
compute 2 all pair ilp/graphene/hbn
|
||||
variable Tersoff equal c_0 # Tersoff energy
|
||||
variable Ecoul equal c_1 # Coulomb energy
|
||||
variable EILP equal c_2 # total interlayer energy
|
||||
variable Evdw equal c_2[1] # attractive energy
|
||||
variable Erep equal c_2[2] # repulsive energy
|
||||
|
||||
############# Output ###############
|
||||
thermo 100
|
||||
thermo_style custom step etotal pe ke v_Evdw v_Tersoff v_EILP v_Erep v_Evdw v_Ecoul temp
|
||||
thermo_modify lost warn
|
||||
|
||||
###### Run molecular dynamics ######
|
||||
run 1000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 18
|
||||
ghost atom cutoff = 18
|
||||
binsize = 9, bins = 5 5 12
|
||||
4 neighbor lists, perpetual/occasional/extra = 4 0 0
|
||||
(1) pair tersoff, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
(2) pair ilp/graphene/hbn, perpetual
|
||||
attributes: full, newton on, ghost
|
||||
pair build: full/bin/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(3) pair coul/shield, perpetual, skip from (4)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(4) neighbor class addition, perpetual, half/full from (1)
|
||||
attributes: half, newton on
|
||||
pair build: halffull/newton
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 35.9 | 35.9 | 35.9 Mbytes
|
||||
Step TotEng PotEng KinEng v_Evdw v_Tersoff v_EILP v_Erep v_Evdw v_Ecoul Temp
|
||||
0 -10193.138 -10245.837 52.699361 -77.557069 -10208.73 -36.776483 40.780586 -77.557069 -0.33075117 300
|
||||
100 -10192.814 -10215.193 22.37957 -80.997619 -10177.878 -36.967736 44.029884 -80.997619 -0.34809915 127.39947
|
||||
200 -10192.922 -10221.807 28.884855 -86.370319 -10184.251 -37.168986 49.201334 -86.370319 -0.38644764 164.43191
|
||||
300 -10192.878 -10219.029 26.151464 -83.063924 -10182.349 -36.30412 46.759804 -83.063924 -0.37660157 148.87162
|
||||
400 -10192.892 -10218.834 25.942229 -78.394242 -10181.398 -37.110968 41.283274 -78.394242 -0.32494569 147.68051
|
||||
500 -10192.909 -10221.331 28.422213 -81.768531 -10184.03 -36.946226 44.822304 -81.768531 -0.35489965 161.79824
|
||||
600 -10192.886 -10219.371 26.48495 -86.278335 -10182.669 -36.29515 49.983185 -86.278335 -0.40636253 150.77004
|
||||
700 -10192.902 -10220.95 28.048108 -82.28873 -10183.208 -37.39374 44.89499 -82.28873 -0.34777958 159.66859
|
||||
800 -10192.88 -10218.51 25.630186 -78.011019 -10181.427 -36.754209 41.256811 -78.011019 -0.32904942 145.90415
|
||||
900 -10192.894 -10220.56 27.665437 -82.474379 -10183.801 -36.381157 46.093222 -82.474379 -0.37703328 157.49017
|
||||
1000 -10192.897 -10219.01 26.11313 -87.125683 -10181.252 -37.361898 49.763785 -87.125683 -0.39607952 148.65339
|
||||
Loop time of 211.527 on 1 procs for 1000 steps with 1360 atoms
|
||||
|
||||
Performance: 0.408 ns/day, 58.757 hours/ns, 4.728 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 211.4 | 211.4 | 211.4 | 0.0 | 99.94
|
||||
Bond | 0.00018859 | 0.00018859 | 0.00018859 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.082034 | 0.082034 | 0.082034 | 0.0 | 0.04
|
||||
Output | 0.00037289 | 0.00037289 | 0.00037289 | 0.0 | 0.00
|
||||
Modify | 0.027928 | 0.027928 | 0.027928 | 0.0 | 0.01
|
||||
Other | | 0.0159 | | | 0.01
|
||||
|
||||
Nlocal: 1360 ave 1360 max 1360 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 7836 ave 7836 max 7836 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 249560 ave 249560 max 249560 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 1.00504e+06 ave 1.00504e+06 max 1.00504e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1005040
|
||||
Ave neighs/atom = 739
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:03:31
|
||||
@ -0,0 +1,142 @@
|
||||
LAMMPS (31 Jul 2019)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Initialization
|
||||
units metal
|
||||
boundary p p p
|
||||
atom_style full
|
||||
processors * * 1 # domain decomposition over x and y
|
||||
|
||||
# System and atom definition
|
||||
# we use different molecule ids for each layer of hBN
|
||||
# so that inter- and intra-layer
|
||||
# interactions can be specified separately
|
||||
read_data hBN_AA_prime_stack_2L_noH.data
|
||||
orthogonal box = (0 0 0) to (43.38 42.5773 100)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
1360 atoms
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
special bonds CPU = 0.000224352 secs
|
||||
read_data CPU = 0.00160909 secs
|
||||
mass 1 10.8110 # boron mass (g/mole) | membrane
|
||||
mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate
|
||||
mass 3 10.8110 # boron mass (g/mole) | membrane
|
||||
mass 4 14.0067 # nitrogen mass (g/mole) | adsorbate
|
||||
# Separate atom groups
|
||||
group layer1 molecule 1
|
||||
680 atoms in group layer1
|
||||
group layer2 molecule 2
|
||||
680 atoms in group layer2
|
||||
|
||||
######################## Potential defition ########################
|
||||
pair_style hybrid/overlay tersoff ilp/graphene/hbn 16.0 coul/shield 16.0 1
|
||||
####################################################################
|
||||
pair_coeff * * tersoff BNC.tersoff B N B N # chemical
|
||||
Reading potential file BNC.tersoff with DATE: 2013-03-21
|
||||
pair_coeff * * ilp/graphene/hbn BNCH.ILP B N B N # long range
|
||||
pair_coeff 1 3 coul/shield 0.70
|
||||
pair_coeff 1 4 coul/shield 0.69498201415576216335
|
||||
pair_coeff 2 3 coul/shield 0.69498201415576216335
|
||||
pair_coeff 2 4 coul/shield 0.69
|
||||
####################################################################
|
||||
# Neighbor update settings
|
||||
neighbor 2.0 bin
|
||||
neigh_modify every 1
|
||||
neigh_modify delay 0
|
||||
neigh_modify check yes
|
||||
|
||||
#### Simulation settings ####
|
||||
timestep 0.001
|
||||
velocity all create 300.0 12345 dist gaussian mom yes rot yes
|
||||
fix thermostat all nve
|
||||
|
||||
compute 0 all pair tersoff
|
||||
compute 1 all pair coul/shield ecoul
|
||||
compute 2 all pair ilp/graphene/hbn
|
||||
variable Tersoff equal c_0 # Tersoff energy
|
||||
variable Ecoul equal c_1 # Coulomb energy
|
||||
variable EILP equal c_2 # total interlayer energy
|
||||
variable Evdw equal c_2[1] # attractive energy
|
||||
variable Erep equal c_2[2] # repulsive energy
|
||||
|
||||
############# Output ###############
|
||||
thermo 100
|
||||
thermo_style custom step etotal pe ke v_Evdw v_Tersoff v_EILP v_Erep v_Evdw v_Ecoul temp
|
||||
thermo_modify lost warn
|
||||
|
||||
###### Run molecular dynamics ######
|
||||
run 1000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 18
|
||||
ghost atom cutoff = 18
|
||||
binsize = 9, bins = 5 5 12
|
||||
4 neighbor lists, perpetual/occasional/extra = 4 0 0
|
||||
(1) pair tersoff, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
(2) pair ilp/graphene/hbn, perpetual
|
||||
attributes: full, newton on, ghost
|
||||
pair build: full/bin/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(3) pair coul/shield, perpetual, skip from (4)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(4) neighbor class addition, perpetual, half/full from (1)
|
||||
attributes: half, newton on
|
||||
pair build: halffull/newton
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 18.99 | 18.99 | 18.99 Mbytes
|
||||
Step TotEng PotEng KinEng v_Evdw v_Tersoff v_EILP v_Erep v_Evdw v_Ecoul Temp
|
||||
0 -10193.138 -10245.837 52.699361 -77.557069 -10208.73 -36.776483 40.780586 -77.557069 -0.33075117 300
|
||||
100 -10192.814 -10215.193 22.37957 -80.997619 -10177.878 -36.967736 44.029884 -80.997619 -0.34809915 127.39947
|
||||
200 -10192.922 -10221.807 28.884855 -86.370319 -10184.251 -37.168986 49.201334 -86.370319 -0.38644764 164.43191
|
||||
300 -10192.878 -10219.029 26.151464 -83.063924 -10182.349 -36.30412 46.759804 -83.063924 -0.37660157 148.87162
|
||||
400 -10192.892 -10218.834 25.942229 -78.394242 -10181.398 -37.110968 41.283274 -78.394242 -0.32494569 147.68051
|
||||
500 -10192.909 -10221.331 28.422213 -81.768531 -10184.03 -36.946226 44.822304 -81.768531 -0.35489965 161.79824
|
||||
600 -10192.886 -10219.371 26.48495 -86.278335 -10182.669 -36.29515 49.983185 -86.278335 -0.40636253 150.77004
|
||||
700 -10192.902 -10220.95 28.048108 -82.28873 -10183.208 -37.39374 44.89499 -82.28873 -0.34777958 159.66859
|
||||
800 -10192.88 -10218.51 25.630186 -78.011019 -10181.427 -36.754209 41.256811 -78.011019 -0.32904942 145.90415
|
||||
900 -10192.894 -10220.56 27.665437 -82.474379 -10183.801 -36.381157 46.093222 -82.474379 -0.37703328 157.49017
|
||||
1000 -10192.897 -10219.01 26.11313 -87.125683 -10181.252 -37.361898 49.763785 -87.125683 -0.39607952 148.65339
|
||||
Loop time of 68.3631 on 4 procs for 1000 steps with 1360 atoms
|
||||
|
||||
Performance: 1.264 ns/day, 18.990 hours/ns, 14.628 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 | 64.58 | 66.38 | 67.402 | 13.2 | 97.10
|
||||
Bond | 0.0001719 | 0.00021869 | 0.00024033 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.93767 | 1.9601 | 3.76 | 77.0 | 2.87
|
||||
Output | 0.00033593 | 0.00061601 | 0.0014501 | 0.0 | 0.00
|
||||
Modify | 0.0085733 | 0.0089303 | 0.0093236 | 0.4 | 0.01
|
||||
Other | | 0.01285 | | | 0.02
|
||||
|
||||
Nlocal: 340 ave 340 max 340 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 4536 ave 4536 max 4536 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 62390 ave 62390 max 62390 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 251260 ave 251260 max 251260 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1005040
|
||||
Ave neighs/atom = 739
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:01:08
|
||||
153
examples/USER/misc/ilp_graphene_hbn/log.31Jul19.grhBN.g++.1
Normal file
153
examples/USER/misc/ilp_graphene_hbn/log.31Jul19.grhBN.g++.1
Normal file
@ -0,0 +1,153 @@
|
||||
LAMMPS (31 Jul 2019)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Initialization
|
||||
units metal
|
||||
boundary p p p
|
||||
atom_style full
|
||||
processors * * 1 # domain decomposition over x and y
|
||||
|
||||
# System and atom definition
|
||||
# we use different molecule ids for each layer
|
||||
# so that inter- and intra-layer
|
||||
# interactions can be specified separately
|
||||
read_data gr_hBN_Cstack_2L_noH.data
|
||||
orthogonal box = (0 0 0) to (44.583 42.9 100)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
1440 atoms
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
special bonds CPU = 0.000282049 secs
|
||||
read_data CPU = 0.00159025 secs
|
||||
mass 1 10.8110 # boron mass (g/mole) | membrane
|
||||
mass 2 14.0067 # nitrogen mass (g/mole) | membrane
|
||||
mass 3 12.0107 # carbon mass (g/mole) | adsorbate
|
||||
# Separate atom groups
|
||||
group hBN molecule 1
|
||||
720 atoms in group hBN
|
||||
group gr molecule 2
|
||||
720 atoms in group gr
|
||||
|
||||
######################## Potential defition ########################
|
||||
pair_style hybrid/overlay rebo tersoff ilp/graphene/hbn 16.0 coul/shield 16.0
|
||||
####################################################################
|
||||
pair_coeff * * rebo CH.rebo NULL NULL C # chemical
|
||||
Reading potential file CH.rebo with DATE: 2018-7-3
|
||||
pair_coeff * * tersoff BNC.tersoff B N NULL # chemical
|
||||
Reading potential file BNC.tersoff with DATE: 2013-03-21
|
||||
pair_coeff * * ilp/graphene/hbn BNCH.ILP B N C # long range
|
||||
pair_coeff 1 1 coul/shield 0.70
|
||||
pair_coeff 1 2 coul/shield 0.69498201415576216335
|
||||
pair_coeff 2 2 coul/shield 0.69
|
||||
####################################################################
|
||||
# Neighbor update settings
|
||||
neighbor 2.0 bin
|
||||
neigh_modify every 1
|
||||
neigh_modify delay 0
|
||||
neigh_modify check yes
|
||||
|
||||
#### Simulation settings ####
|
||||
timestep 0.001
|
||||
velocity all create 300.0 12345 dist gaussian mom yes rot yes
|
||||
fix thermostat all nve
|
||||
|
||||
compute 0 all pair rebo
|
||||
compute 1 all pair tersoff
|
||||
compute 2 all pair ilp/graphene/hbn
|
||||
compute 3 all pair coul/shield
|
||||
variable REBO equal c_0
|
||||
variable Tersoff equal c_1
|
||||
variable EILP equal c_2 # total interlayer energy
|
||||
variable Evdw equal c_2[1] # attractive energy
|
||||
variable Erep equal c_2[2] # repulsive energy
|
||||
variable Ecoul equal c_3
|
||||
|
||||
############# Output ##############
|
||||
thermo 100
|
||||
thermo_style custom step etotal pe ke v_Evdw v_Tersoff v_REBO v_EILP v_Erep v_Evdw v_Ecoul temp
|
||||
|
||||
###### Run molecular dynamics ######
|
||||
run 1000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 18
|
||||
ghost atom cutoff = 18
|
||||
binsize = 9, bins = 5 5 12
|
||||
6 neighbor lists, perpetual/occasional/extra = 6 0 0
|
||||
(1) pair rebo, perpetual, skip from (3)
|
||||
attributes: full, newton on, ghost
|
||||
pair build: skip/ghost
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair tersoff, perpetual, skip from (5)
|
||||
attributes: full, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) pair ilp/graphene/hbn, perpetual
|
||||
attributes: full, newton on, ghost
|
||||
pair build: full/bin/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(4) pair coul/shield, perpetual, half/full from (2)
|
||||
attributes: half, newton on
|
||||
pair build: halffull/newton/skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(5) neighbor class addition, perpetual, copy from (3)
|
||||
attributes: full, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(6) neighbor class addition, perpetual, half/full from (5)
|
||||
attributes: half, newton on
|
||||
pair build: halffull/newton
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 22.52 | 22.52 | 22.52 Mbytes
|
||||
Step TotEng PotEng KinEng v_Evdw v_Tersoff v_REBO v_EILP v_Erep v_Evdw v_Ecoul Temp
|
||||
0 -10707.284 -10763.085 55.801605 -75.247726 -5401.7348 -5322.2781 -39.072409 36.175318 -75.247726 0 300
|
||||
100 -10707.074 -10737.127 30.05353 -73.217322 -5389.9568 -5309.2004 -37.970102 35.24722 -73.217322 0 161.57347
|
||||
200 -10707.016 -10734.932 27.91576 -71.603097 -5389.1294 -5307.7455 -38.056875 33.546222 -71.603097 0 150.08042
|
||||
300 -10707.013 -10734.987 27.973705 -75.082134 -5388.9196 -5308.1165 -37.950947 37.131186 -75.082134 0 150.39194
|
||||
400 -10707.012 -10735.498 28.486171 -76.339871 -5389.1657 -5308.153 -38.179442 38.160429 -76.339871 0 153.14706
|
||||
500 -10707.007 -10734.681 27.674101 -73.312354 -5388.7261 -5307.7384 -38.216944 35.09541 -73.312354 0 148.78121
|
||||
600 -10707.018 -10735.833 28.815132 -71.927763 -5389.0798 -5308.596 -38.157333 33.77043 -71.927763 0 154.91561
|
||||
700 -10707.02 -10735.656 28.635377 -74.679371 -5389.2971 -5308.1866 -38.172002 36.507368 -74.679371 0 153.94921
|
||||
800 -10707.004 -10734.352 27.347425 -76.371288 -5388.5923 -5307.7206 -38.038736 38.332552 -76.371288 0 147.02494
|
||||
900 -10707.014 -10735.832 28.817405 -73.699332 -5388.9674 -5308.7964 -38.068078 35.631254 -73.699332 0 154.92783
|
||||
1000 -10706.995 -10733.562 26.56615 -71.439868 -5388.0186 -5307.4414 -38.101452 33.338415 -71.439868 0 142.82466
|
||||
Loop time of 152.66 on 1 procs for 1000 steps with 1440 atoms
|
||||
|
||||
Performance: 0.566 ns/day, 42.406 hours/ns, 6.550 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 | 152.52 | 152.52 | 152.52 | 0.0 | 99.91
|
||||
Bond | 0.00023174 | 0.00023174 | 0.00023174 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.087147 | 0.087147 | 0.087147 | 0.0 | 0.06
|
||||
Output | 0.0004189 | 0.0004189 | 0.0004189 | 0.0 | 0.00
|
||||
Modify | 0.029972 | 0.029972 | 0.029972 | 0.0 | 0.02
|
||||
Other | | 0.02057 | | | 0.01
|
||||
|
||||
Nlocal: 1440 ave 1440 max 1440 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 8180 ave 8180 max 8180 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 140400 ave 140400 max 140400 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 280800 ave 280800 max 280800 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 280800
|
||||
Ave neighs/atom = 195
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:02:32
|
||||
153
examples/USER/misc/ilp_graphene_hbn/log.31Jul19.grhBN.g++.4
Normal file
153
examples/USER/misc/ilp_graphene_hbn/log.31Jul19.grhBN.g++.4
Normal file
@ -0,0 +1,153 @@
|
||||
LAMMPS (31 Jul 2019)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Initialization
|
||||
units metal
|
||||
boundary p p p
|
||||
atom_style full
|
||||
processors * * 1 # domain decomposition over x and y
|
||||
|
||||
# System and atom definition
|
||||
# we use different molecule ids for each layer
|
||||
# so that inter- and intra-layer
|
||||
# interactions can be specified separately
|
||||
read_data gr_hBN_Cstack_2L_noH.data
|
||||
orthogonal box = (0 0 0) to (44.583 42.9 100)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
1440 atoms
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
special bonds CPU = 0.00012207 secs
|
||||
read_data CPU = 0.00357461 secs
|
||||
mass 1 10.8110 # boron mass (g/mole) | membrane
|
||||
mass 2 14.0067 # nitrogen mass (g/mole) | membrane
|
||||
mass 3 12.0107 # carbon mass (g/mole) | adsorbate
|
||||
# Separate atom groups
|
||||
group hBN molecule 1
|
||||
720 atoms in group hBN
|
||||
group gr molecule 2
|
||||
720 atoms in group gr
|
||||
|
||||
######################## Potential defition ########################
|
||||
pair_style hybrid/overlay rebo tersoff ilp/graphene/hbn 16.0 coul/shield 16.0
|
||||
####################################################################
|
||||
pair_coeff * * rebo CH.rebo NULL NULL C # chemical
|
||||
Reading potential file CH.rebo with DATE: 2018-7-3
|
||||
pair_coeff * * tersoff BNC.tersoff B N NULL # chemical
|
||||
Reading potential file BNC.tersoff with DATE: 2013-03-21
|
||||
pair_coeff * * ilp/graphene/hbn BNCH.ILP B N C # long range
|
||||
pair_coeff 1 1 coul/shield 0.70
|
||||
pair_coeff 1 2 coul/shield 0.69498201415576216335
|
||||
pair_coeff 2 2 coul/shield 0.69
|
||||
####################################################################
|
||||
# Neighbor update settings
|
||||
neighbor 2.0 bin
|
||||
neigh_modify every 1
|
||||
neigh_modify delay 0
|
||||
neigh_modify check yes
|
||||
|
||||
#### Simulation settings ####
|
||||
timestep 0.001
|
||||
velocity all create 300.0 12345 dist gaussian mom yes rot yes
|
||||
fix thermostat all nve
|
||||
|
||||
compute 0 all pair rebo
|
||||
compute 1 all pair tersoff
|
||||
compute 2 all pair ilp/graphene/hbn
|
||||
compute 3 all pair coul/shield
|
||||
variable REBO equal c_0
|
||||
variable Tersoff equal c_1
|
||||
variable EILP equal c_2 # total interlayer energy
|
||||
variable Evdw equal c_2[1] # attractive energy
|
||||
variable Erep equal c_2[2] # repulsive energy
|
||||
variable Ecoul equal c_3
|
||||
|
||||
############# Output ##############
|
||||
thermo 100
|
||||
thermo_style custom step etotal pe ke v_Evdw v_Tersoff v_REBO v_EILP v_Erep v_Evdw v_Ecoul temp
|
||||
|
||||
###### Run molecular dynamics ######
|
||||
run 1000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 18
|
||||
ghost atom cutoff = 18
|
||||
binsize = 9, bins = 5 5 12
|
||||
6 neighbor lists, perpetual/occasional/extra = 6 0 0
|
||||
(1) pair rebo, perpetual, skip from (3)
|
||||
attributes: full, newton on, ghost
|
||||
pair build: skip/ghost
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair tersoff, perpetual, skip from (5)
|
||||
attributes: full, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) pair ilp/graphene/hbn, perpetual
|
||||
attributes: full, newton on, ghost
|
||||
pair build: full/bin/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(4) pair coul/shield, perpetual, half/full from (2)
|
||||
attributes: half, newton on
|
||||
pair build: halffull/newton/skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(5) neighbor class addition, perpetual, copy from (3)
|
||||
attributes: full, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(6) neighbor class addition, perpetual, half/full from (5)
|
||||
attributes: half, newton on
|
||||
pair build: halffull/newton
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 12.45 | 12.45 | 12.45 Mbytes
|
||||
Step TotEng PotEng KinEng v_Evdw v_Tersoff v_REBO v_EILP v_Erep v_Evdw v_Ecoul Temp
|
||||
0 -10707.284 -10763.085 55.801605 -75.247726 -5401.7348 -5322.2781 -39.072409 36.175318 -75.247726 0 300
|
||||
100 -10707.074 -10737.127 30.05353 -73.217322 -5389.9568 -5309.2004 -37.970102 35.24722 -73.217322 0 161.57347
|
||||
200 -10707.016 -10734.932 27.91576 -71.603097 -5389.1294 -5307.7455 -38.056875 33.546222 -71.603097 0 150.08042
|
||||
300 -10707.013 -10734.987 27.973705 -75.082134 -5388.9196 -5308.1165 -37.950947 37.131186 -75.082134 0 150.39194
|
||||
400 -10707.012 -10735.498 28.486171 -76.339871 -5389.1657 -5308.153 -38.179442 38.160429 -76.339871 0 153.14706
|
||||
500 -10707.007 -10734.681 27.674101 -73.312354 -5388.7261 -5307.7384 -38.216944 35.09541 -73.312354 0 148.78121
|
||||
600 -10707.018 -10735.833 28.815132 -71.927763 -5389.0798 -5308.596 -38.157333 33.77043 -71.927763 0 154.91561
|
||||
700 -10707.02 -10735.656 28.635377 -74.679371 -5389.2971 -5308.1866 -38.172002 36.507368 -74.679371 0 153.94921
|
||||
800 -10707.004 -10734.352 27.347425 -76.371288 -5388.5923 -5307.7206 -38.038736 38.332552 -76.371288 0 147.02494
|
||||
900 -10707.014 -10735.832 28.817405 -73.699332 -5388.9674 -5308.7964 -38.068078 35.631254 -73.699332 0 154.92783
|
||||
1000 -10706.995 -10733.562 26.56615 -71.439868 -5388.0186 -5307.4414 -38.101452 33.338415 -71.439868 0 142.82466
|
||||
Loop time of 54.095 on 4 procs for 1000 steps with 1440 atoms
|
||||
|
||||
Performance: 1.597 ns/day, 15.026 hours/ns, 18.486 timesteps/s
|
||||
84.8% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 42.138 | 45.531 | 49.106 | 42.0 | 84.17
|
||||
Bond | 0.0003159 | 0.00037384 | 0.000489 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 4.71 | 8.2803 | 11.682 | 98.3 | 15.31
|
||||
Output | 0.0021999 | 0.0055975 | 0.013382 | 6.0 | 0.01
|
||||
Modify | 0.0092845 | 0.010981 | 0.012538 | 1.3 | 0.02
|
||||
Other | | 0.2673 | | | 0.49
|
||||
|
||||
Nlocal: 360 ave 380 max 340 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Nghost: 4716 ave 4736 max 4696 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Neighs: 35100 ave 37050 max 33150 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
FullNghs: 70200 ave 74100 max 66300 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 280800
|
||||
Ave neighs/atom = 195
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:54
|
||||
@ -0,0 +1,154 @@
|
||||
LAMMPS (31 Jul 2019)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Initialization
|
||||
units metal
|
||||
boundary p p p
|
||||
atom_style full
|
||||
processors * * 1 # domain decomposition over x and y
|
||||
|
||||
# System and atom definition
|
||||
# we use 2 atom types so that inter- and intra-layer
|
||||
# interactions can be specified separately
|
||||
read_data hBN_AB_stack_2L_noH_equi_300K.data
|
||||
orthogonal box = (0 0 0) to (43.38 42.5773 100)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
1360 atoms
|
||||
reading velocities ...
|
||||
1360 velocities
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
special bonds CPU = 0.000251532 secs
|
||||
read_data CPU = 0.00451231 secs
|
||||
mass 1 10.8110 # boron mass (g/mole) | membrane
|
||||
mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate
|
||||
mass 3 10.8110 # boron mass (g/mole) | membrane
|
||||
mass 4 14.0067 # nitrogen mass (g/mole) | adsorbate
|
||||
# Separate atom groups
|
||||
group membrane type 1 2
|
||||
680 atoms in group membrane
|
||||
group adsorbate type 3 4
|
||||
680 atoms in group adsorbate
|
||||
|
||||
######################## Potential defition ########################
|
||||
pair_style hybrid/overlay tersoff ilp/graphene/hbn 16.0 coul/shield 16.0 1
|
||||
####################################################################
|
||||
pair_coeff * * tersoff BNC.tersoff NULL NULL B N # chemical
|
||||
Reading potential file BNC.tersoff with DATE: 2013-03-21
|
||||
pair_coeff * * ilp/graphene/hbn BNCH-old.ILP B N B N # long range
|
||||
pair_coeff 1 3 coul/shield 0.70
|
||||
pair_coeff 1 4 coul/shield 0.69498201415576216335
|
||||
pair_coeff 2 3 coul/shield 0.69498201415576216335
|
||||
pair_coeff 2 4 coul/shield 0.69
|
||||
####################################################################
|
||||
# Neighbor update settings
|
||||
neighbor 2.0 bin
|
||||
neigh_modify every 1
|
||||
neigh_modify delay 0
|
||||
neigh_modify check yes
|
||||
|
||||
#### Simulation settings ####
|
||||
timestep 0.001
|
||||
#velocity adsorbate create 300.0 12345
|
||||
fix subf membrane setforce 0.0 0.0 0.0
|
||||
fix thermostat all nve
|
||||
|
||||
compute 0 all pair tersoff
|
||||
compute 1 all pair coul/shield ecoul
|
||||
compute 2 all pair ilp/graphene/hbn
|
||||
variable Tersoff equal c_0
|
||||
variable Ecoul equal c_1
|
||||
variable ILP equal c_2
|
||||
variable Evdw equal c_2[1]
|
||||
variable Erep equal c_2[2]
|
||||
|
||||
############################
|
||||
|
||||
# Output
|
||||
thermo 100
|
||||
thermo_style custom step etotal pe ke v_Tersoff v_ILP v_Ecoul v_Erep v_Evdw temp
|
||||
thermo_modify lost warn #ignore
|
||||
|
||||
#dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu
|
||||
#dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
|
||||
|
||||
###### Run molecular dynamics ######
|
||||
run 1000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 18
|
||||
ghost atom cutoff = 18
|
||||
binsize = 9, bins = 5 5 12
|
||||
5 neighbor lists, perpetual/occasional/extra = 5 0 0
|
||||
(1) pair tersoff, perpetual, skip from (4)
|
||||
attributes: full, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair ilp/graphene/hbn, perpetual
|
||||
attributes: full, newton on, ghost
|
||||
pair build: full/bin/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(3) pair coul/shield, perpetual, skip from (5)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(4) neighbor class addition, perpetual, copy from (2)
|
||||
attributes: full, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(5) neighbor class addition, perpetual, half/full from (4)
|
||||
attributes: half, newton on
|
||||
pair build: halffull/newton
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 54.59 | 54.59 | 54.59 Mbytes
|
||||
Step TotEng PotEng KinEng v_Tersoff v_ILP v_Ecoul v_Erep v_Evdw Temp
|
||||
0 -5114.6628 -5127.8586 13.195828 -5091.4121 -36.083114 -0.36343598 38.918674 -75.001787 75.119474
|
||||
100 -5114.6621 -5127.6958 13.033777 -5091.2408 -36.09276 -0.36228286 38.769906 -74.862666 74.196973
|
||||
200 -5114.6631 -5127.5945 12.93145 -5091.1508 -36.086669 -0.35708801 38.20076 -74.287429 73.614462
|
||||
300 -5114.6694 -5128.3286 13.65924 -5091.8646 -36.110786 -0.35328159 37.758284 -73.86907 77.757528
|
||||
400 -5114.6614 -5127.6424 12.980975 -5091.2348 -36.049634 -0.35794328 38.247252 -74.296886 73.896389
|
||||
500 -5114.66 -5127.4098 12.749794 -5090.9285 -36.119571 -0.36174976 38.745548 -74.865119 72.580351
|
||||
600 -5114.6673 -5128.0913 13.424021 -5091.6339 -36.09384 -0.36356991 38.927401 -75.021241 76.418503
|
||||
700 -5114.661 -5127.7467 13.085707 -5091.2811 -36.106639 -0.35892399 38.332616 -74.439255 74.492596
|
||||
800 -5114.6623 -5128.013 13.350778 -5091.5694 -36.089718 -0.35392503 37.851602 -73.94132 76.001554
|
||||
900 -5114.6675 -5128.1497 13.482146 -5091.6704 -36.124679 -0.35462869 37.885183 -74.009861 76.749392
|
||||
1000 -5114.6683 -5128.3365 13.668146 -5091.937 -36.037596 -0.36184347 38.709718 -74.747314 77.808228
|
||||
Loop time of 207.028 on 1 procs for 1000 steps with 1360 atoms
|
||||
|
||||
Performance: 0.417 ns/day, 57.508 hours/ns, 4.830 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 206.9 | 206.9 | 206.9 | 0.0 | 99.94
|
||||
Bond | 0.00019169 | 0.00019169 | 0.00019169 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.081397 | 0.081397 | 0.081397 | 0.0 | 0.04
|
||||
Output | 0.00036597 | 0.00036597 | 0.00036597 | 0.0 | 0.00
|
||||
Modify | 0.033408 | 0.033408 | 0.033408 | 0.0 | 0.02
|
||||
Other | | 0.01615 | | | 0.01
|
||||
|
||||
Nlocal: 1360 ave 1360 max 1360 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 7840 ave 7840 max 7840 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 249628 ave 249628 max 249628 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 253390 ave 253390 max 253390 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 253390
|
||||
Ave neighs/atom = 186.316
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:03:27
|
||||
@ -0,0 +1,154 @@
|
||||
LAMMPS (31 Jul 2019)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Initialization
|
||||
units metal
|
||||
boundary p p p
|
||||
atom_style full
|
||||
processors * * 1 # domain decomposition over x and y
|
||||
|
||||
# System and atom definition
|
||||
# we use 2 atom types so that inter- and intra-layer
|
||||
# interactions can be specified separately
|
||||
read_data hBN_AB_stack_2L_noH_equi_300K.data
|
||||
orthogonal box = (0 0 0) to (43.38 42.5773 100)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
1360 atoms
|
||||
reading velocities ...
|
||||
1360 velocities
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
special bonds CPU = 0.000332117 secs
|
||||
read_data CPU = 0.00270581 secs
|
||||
mass 1 10.8110 # boron mass (g/mole) | membrane
|
||||
mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate
|
||||
mass 3 10.8110 # boron mass (g/mole) | membrane
|
||||
mass 4 14.0067 # nitrogen mass (g/mole) | adsorbate
|
||||
# Separate atom groups
|
||||
group membrane type 1 2
|
||||
680 atoms in group membrane
|
||||
group adsorbate type 3 4
|
||||
680 atoms in group adsorbate
|
||||
|
||||
######################## Potential defition ########################
|
||||
pair_style hybrid/overlay tersoff ilp/graphene/hbn 16.0 coul/shield 16.0 1
|
||||
####################################################################
|
||||
pair_coeff * * tersoff BNC.tersoff NULL NULL B N # chemical
|
||||
Reading potential file BNC.tersoff with DATE: 2013-03-21
|
||||
pair_coeff * * ilp/graphene/hbn BNCH-old.ILP B N B N # long range
|
||||
pair_coeff 1 3 coul/shield 0.70
|
||||
pair_coeff 1 4 coul/shield 0.69498201415576216335
|
||||
pair_coeff 2 3 coul/shield 0.69498201415576216335
|
||||
pair_coeff 2 4 coul/shield 0.69
|
||||
####################################################################
|
||||
# Neighbor update settings
|
||||
neighbor 2.0 bin
|
||||
neigh_modify every 1
|
||||
neigh_modify delay 0
|
||||
neigh_modify check yes
|
||||
|
||||
#### Simulation settings ####
|
||||
timestep 0.001
|
||||
#velocity adsorbate create 300.0 12345
|
||||
fix subf membrane setforce 0.0 0.0 0.0
|
||||
fix thermostat all nve
|
||||
|
||||
compute 0 all pair tersoff
|
||||
compute 1 all pair coul/shield ecoul
|
||||
compute 2 all pair ilp/graphene/hbn
|
||||
variable Tersoff equal c_0
|
||||
variable Ecoul equal c_1
|
||||
variable ILP equal c_2
|
||||
variable Evdw equal c_2[1]
|
||||
variable Erep equal c_2[2]
|
||||
|
||||
############################
|
||||
|
||||
# Output
|
||||
thermo 100
|
||||
thermo_style custom step etotal pe ke v_Tersoff v_ILP v_Ecoul v_Erep v_Evdw temp
|
||||
thermo_modify lost warn #ignore
|
||||
|
||||
#dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu
|
||||
#dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
|
||||
|
||||
###### Run molecular dynamics ######
|
||||
run 1000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 18
|
||||
ghost atom cutoff = 18
|
||||
binsize = 9, bins = 5 5 12
|
||||
5 neighbor lists, perpetual/occasional/extra = 5 0 0
|
||||
(1) pair tersoff, perpetual, skip from (4)
|
||||
attributes: full, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair ilp/graphene/hbn, perpetual
|
||||
attributes: full, newton on, ghost
|
||||
pair build: full/bin/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(3) pair coul/shield, perpetual, skip from (5)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(4) neighbor class addition, perpetual, copy from (2)
|
||||
attributes: full, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(5) neighbor class addition, perpetual, half/full from (4)
|
||||
attributes: half, newton on
|
||||
pair build: halffull/newton
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 28.9 | 28.9 | 28.9 Mbytes
|
||||
Step TotEng PotEng KinEng v_Tersoff v_ILP v_Ecoul v_Erep v_Evdw Temp
|
||||
0 -5114.6628 -5127.8586 13.195828 -5091.4121 -36.083114 -0.36343598 38.918674 -75.001787 75.119474
|
||||
100 -5114.6621 -5127.6958 13.033777 -5091.2408 -36.09276 -0.36228286 38.769906 -74.862666 74.196973
|
||||
200 -5114.6631 -5127.5945 12.93145 -5091.1508 -36.086669 -0.35708801 38.20076 -74.287429 73.614462
|
||||
300 -5114.6694 -5128.3286 13.65924 -5091.8646 -36.110786 -0.35328159 37.758284 -73.86907 77.757528
|
||||
400 -5114.6614 -5127.6424 12.980975 -5091.2348 -36.049634 -0.35794328 38.247252 -74.296886 73.896389
|
||||
500 -5114.66 -5127.4098 12.749794 -5090.9285 -36.119571 -0.36174976 38.745548 -74.865119 72.580351
|
||||
600 -5114.6673 -5128.0913 13.424021 -5091.6339 -36.09384 -0.36356991 38.927401 -75.021241 76.418503
|
||||
700 -5114.661 -5127.7467 13.085707 -5091.2811 -36.106639 -0.35892399 38.332616 -74.439255 74.492596
|
||||
800 -5114.6623 -5128.013 13.350778 -5091.5694 -36.089718 -0.35392503 37.851602 -73.94132 76.001554
|
||||
900 -5114.6675 -5128.1497 13.482146 -5091.6704 -36.124679 -0.35462869 37.885183 -74.009861 76.749392
|
||||
1000 -5114.6683 -5128.3365 13.668146 -5091.937 -36.037596 -0.36184347 38.709718 -74.747314 77.808228
|
||||
Loop time of 65.9005 on 4 procs for 1000 steps with 1360 atoms
|
||||
|
||||
Performance: 1.311 ns/day, 18.306 hours/ns, 15.174 timesteps/s
|
||||
98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 63.244 | 64.208 | 65.281 | 10.1 | 97.43
|
||||
Bond | 0.00013971 | 0.00017679 | 0.00022101 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.58237 | 1.6612 | 2.6292 | 63.1 | 2.52
|
||||
Output | 0.0003171 | 0.00062358 | 0.0015192 | 0.0 | 0.00
|
||||
Modify | 0.010251 | 0.010509 | 0.01075 | 0.2 | 0.02
|
||||
Other | | 0.02025 | | | 0.03
|
||||
|
||||
Nlocal: 340 ave 346 max 336 min
|
||||
Histogram: 1 0 1 0 1 0 0 0 0 1
|
||||
Nghost: 4537.5 ave 4540 max 4534 min
|
||||
Histogram: 1 0 0 0 0 0 2 0 0 1
|
||||
Neighs: 62407 ave 62413 max 62402 min
|
||||
Histogram: 1 0 0 1 1 0 0 0 0 1
|
||||
FullNghs: 63347.5 ave 65585 max 61866 min
|
||||
Histogram: 1 1 0 1 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 253926
|
||||
Ave neighs/atom = 186.71
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:01:06
|
||||
1372
examples/USER/misc/kolmogorov_crespi_full/Bi_gr_AB_stack_2L_noH.data
Normal file
1372
examples/USER/misc/kolmogorov_crespi_full/Bi_gr_AB_stack_2L_noH.data
Normal file
File diff suppressed because it is too large
Load Diff
1
examples/USER/misc/kolmogorov_crespi_full/CH.KC
Symbolic link
1
examples/USER/misc/kolmogorov_crespi_full/CH.KC
Symbolic link
@ -0,0 +1 @@
|
||||
../../../../potentials/CH.KC
|
||||
1
examples/USER/misc/kolmogorov_crespi_full/CH_taper.KC
Symbolic link
1
examples/USER/misc/kolmogorov_crespi_full/CH_taper.KC
Symbolic link
@ -0,0 +1 @@
|
||||
../../../../potentials/CH_taper.KC
|
||||
@ -5,21 +5,22 @@ atom_style full
|
||||
processors * * 1 # domain decomposition over x and y
|
||||
|
||||
# System and atom definition
|
||||
# we use 2 atom types so that inter- and intra-layer
|
||||
# we use different molecule ids for each layer of hBN
|
||||
# so that inter- and intra-layer
|
||||
# interactions can be specified separately
|
||||
# read lammps data file
|
||||
read_data Bi_gr_AB_stack_2L_noH_300K.data
|
||||
|
||||
read_data Bi_gr_AB_stack_2L_noH.data
|
||||
mass 1 12.0107 # carbon mass (g/mole) | membrane
|
||||
mass 2 12.0107 # carbon mass (g/mole) | adsorbate
|
||||
# Separate atom groups
|
||||
group membrane type 1
|
||||
group adsorbate type 2
|
||||
group layer1 molecule 1
|
||||
group layer2 molecule 2
|
||||
|
||||
######################## Potential defition ########################
|
||||
pair_style hybrid/overlay rebo kolmogorov/crespi/full 16.0
|
||||
pair_style hybrid/overlay rebo kolmogorov/crespi/full 16.0 1
|
||||
####################################################################
|
||||
pair_coeff * * rebo CH.rebo NULL C # chemical
|
||||
pair_coeff * * kolmogorov/crespi/full CC.KC-full C C # long range
|
||||
pair_coeff * * rebo CH.rebo C C # chemical
|
||||
pair_coeff * * kolmogorov/crespi/full CH_taper.KC C C # long range
|
||||
####################################################################
|
||||
# Neighbor update settings
|
||||
neighbor 2.0 bin
|
||||
@ -27,34 +28,25 @@ neigh_modify every 1
|
||||
neigh_modify delay 0
|
||||
neigh_modify check yes
|
||||
|
||||
# calculate the COM
|
||||
variable adsxcom equal xcm(adsorbate,x)
|
||||
variable adsycom equal xcm(adsorbate,y)
|
||||
variable adszcom equal xcm(adsorbate,z)
|
||||
variable adsvxcom equal vcm(adsorbate,x)
|
||||
variable adsvycom equal vcm(adsorbate,y)
|
||||
variable adsvzcom equal vcm(adsorbate,z)
|
||||
|
||||
#### Simulation settings ####
|
||||
timestep 0.001
|
||||
fix subf membrane setforce 0.0 0.0 0.0
|
||||
fix thermostat all nve
|
||||
timestep 0.001
|
||||
velocity all create 300.0 12345
|
||||
|
||||
compute 0 all pair rebo
|
||||
compute 1 all pair kolmogorov/crespi/full
|
||||
variable REBO equal c_0
|
||||
variable KC equal c_1
|
||||
compute 0 all pair rebo
|
||||
compute 1 all pair kolmogorov/crespi/full
|
||||
variable REBO equal c_0 # REBO energy
|
||||
variable KC equal c_1 # total interlayer energy
|
||||
variable Evdw equal c_1[1] # attractive energy
|
||||
variable Erep equal c_1[2] # repulsive energy
|
||||
|
||||
############################
|
||||
|
||||
# Output
|
||||
thermo 100
|
||||
thermo_style custom step etotal pe ke v_REBO v_KC temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
|
||||
thermo_modify line one format float %.10f
|
||||
thermo_modify flush yes norm no lost warn #ignore
|
||||
|
||||
#dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu
|
||||
#dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
|
||||
thermo_style custom step cpu etotal pe ke v_REBO v_KC v_Erep v_Evdw temp
|
||||
thermo_modify line one format float %.16f
|
||||
thermo_modify flush yes norm no lost warn
|
||||
|
||||
###### Run molecular dynamics ######
|
||||
run 1000
|
||||
fix thermostat all nve
|
||||
run 1000
|
||||
|
||||
@ -0,0 +1,129 @@
|
||||
LAMMPS (5 Jun 2019)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:88)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Initialization
|
||||
units metal
|
||||
boundary p p p
|
||||
atom_style full
|
||||
processors * * 1 # domain decomposition over x and y
|
||||
|
||||
# System and atom definition
|
||||
# we use different molecule ids for each layer of hBN
|
||||
# so that inter- and intra-layer
|
||||
# interactions can be specified separately
|
||||
|
||||
read_data Bi_gr_AB_stack_2L_noH.data
|
||||
orthogonal box = (0 0 0) to (42.6 41.8117 100)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
1360 atoms
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
special bonds CPU = 0.000143357 secs
|
||||
read_data CPU = 0.00128686 secs
|
||||
mass 1 12.0107 # carbon mass (g/mole) | membrane
|
||||
mass 2 12.0107 # carbon mass (g/mole) | adsorbate
|
||||
# Separate atom groups
|
||||
group layer1 molecule 1
|
||||
680 atoms in group layer1
|
||||
group layer2 molecule 2
|
||||
680 atoms in group layer2
|
||||
|
||||
######################## Potential defition ########################
|
||||
pair_style hybrid/overlay rebo kolmogorov/crespi/full 16.0 1
|
||||
####################################################################
|
||||
pair_coeff * * rebo CH.rebo C C # chemical
|
||||
Reading potential file CH.rebo with DATE: 2018-7-3
|
||||
pair_coeff * * kolmogorov/crespi/full CH_taper.KC C C # long range
|
||||
####################################################################
|
||||
# Neighbor update settings
|
||||
neighbor 2.0 bin
|
||||
neigh_modify every 1
|
||||
neigh_modify delay 0
|
||||
neigh_modify check yes
|
||||
|
||||
#### Simulation settings ####
|
||||
timestep 0.001
|
||||
velocity all create 300.0 12345
|
||||
|
||||
compute 0 all pair rebo
|
||||
compute 1 all pair kolmogorov/crespi/full
|
||||
variable REBO equal c_0 # REBO energy
|
||||
variable KC equal c_1 # total interlayer energy
|
||||
variable Evdw equal c_1[1] # attractive energy
|
||||
variable Erep equal c_1[2] # repulsive energy
|
||||
|
||||
############################
|
||||
|
||||
# Output
|
||||
thermo 100
|
||||
thermo_style custom step cpu etotal pe ke v_REBO v_KC v_Erep v_Evdw temp
|
||||
thermo_modify line one format float %.16f
|
||||
thermo_modify flush yes norm no lost warn
|
||||
|
||||
###### Run molecular dynamics ######
|
||||
fix thermostat all nve
|
||||
run 1000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 18
|
||||
ghost atom cutoff = 18
|
||||
binsize = 9, bins = 5 5 12
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair rebo, perpetual
|
||||
attributes: full, newton on, ghost
|
||||
pair build: full/bin/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) pair kolmogorov/crespi/full, perpetual, copy from (1)
|
||||
attributes: full, newton on, ghost
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 17.21 | 17.21 | 17.21 Mbytes
|
||||
Step CPU TotEng PotEng KinEng v_REBO v_KC v_Erep v_Evdw Temp
|
||||
0 0.0000000000000000 -10037.7640583248121402 -10090.4634194413119985 52.6993611164999436 -10057.1894932863488066 -33.2739261549639664 35.9559834316876348 -69.2299095866357561 299.9999999999996589
|
||||
100 5.3877589240437374 -10037.5122858156355505 -10065.4637593850693520 27.9514735694345475 -10032.2132655062632693 -33.2504938788055995 25.2100699045900747 -58.4605637833913789 159.1184768311149185
|
||||
200 10.7755050340201706 -10037.4414086674350983 -10061.6271012692632212 24.1856926018286202 -10028.9093252939674130 -32.7177759752951403 18.5366534598604176 -51.2544294351563394 137.6811336385792970
|
||||
300 16.1665089030284435 -10037.4824653300311184 -10064.2845326005663082 26.8020672705344225 -10030.9195389405322203 -33.3649936600345924 26.3639208740001152 -59.7289145340284122 152.5752876469470891
|
||||
400 21.5454839280573651 -10037.5105626329259394 -10064.8769084956420556 27.3663458627154164 -10031.8478821022799821 -33.0290263933626349 36.6142885774199272 -69.6433149707719963 155.7875386888538571
|
||||
500 26.9370588400634006 -10037.5010433785082569 -10064.8363209936451312 27.3352776151367571 -10031.4417172103931080 -33.3946037832518243 26.2980262321670750 -59.6926300154142595 155.6106774503846850
|
||||
600 32.4204196080099791 -10037.4817772372425679 -10064.1925798287738871 26.7108025915316247 -10031.4376178099264507 -32.7549620188478201 18.5745873777024606 -51.3295493965519327 152.0557480714992380
|
||||
700 37.8001567909959704 -10037.4834430268438155 -10064.1291975032218033 26.6457544763788299 -10030.8722888097800023 -33.2569086934421492 25.2322818106646771 -58.4891905041015008 151.6854507067418467
|
||||
800 43.1622281169984490 -10037.5047888097760733 -10064.8671187128948077 27.3623299031188978 -10031.9815058608437539 -32.8856128520517217 36.5236695083771536 -69.4092823604148350 155.7646771616279011
|
||||
900 48.5261204120470211 -10037.5068323940176924 -10065.3998155271074211 27.8929831330889542 -10032.1734374829957233 -33.2263780441125931 27.7314849391008309 -60.9578629832065317 158.7855101588076820
|
||||
1000 53.8888844919856638 -10037.4811494880468672 -10064.0099109142265661 26.5287614261789670 -10031.3325267421259923 -32.6773841721003464 18.9005970229871600 -51.5779811950879434 151.0194480396057202
|
||||
Loop time of 53.8889 on 1 procs for 1000 steps with 1360 atoms
|
||||
|
||||
Performance: 1.603 ns/day, 14.969 hours/ns, 18.557 timesteps/s
|
||||
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 53.836 | 53.836 | 53.836 | 0.0 | 99.90
|
||||
Bond | 0.00043479 | 0.00043479 | 0.00043479 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.032452 | 0.032452 | 0.032452 | 0.0 | 0.06
|
||||
Output | 0.00058326 | 0.00058326 | 0.00058326 | 0.0 | 0.00
|
||||
Modify | 0.0094135 | 0.0094135 | 0.0094135 | 0.0 | 0.02
|
||||
Other | | 0.009815 | | | 0.02
|
||||
|
||||
Nlocal: 1360 ave 1360 max 1360 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 7964 ave 7964 max 7964 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: 1.037e+06 ave 1.037e+06 max 1.037e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1037000
|
||||
Ave neighs/atom = 762.5
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:54
|
||||
@ -0,0 +1,129 @@
|
||||
LAMMPS (5 Jun 2019)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:88)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Initialization
|
||||
units metal
|
||||
boundary p p p
|
||||
atom_style full
|
||||
processors * * 1 # domain decomposition over x and y
|
||||
|
||||
# System and atom definition
|
||||
# we use different molecule ids for each layer of hBN
|
||||
# so that inter- and intra-layer
|
||||
# interactions can be specified separately
|
||||
|
||||
read_data Bi_gr_AB_stack_2L_noH.data
|
||||
orthogonal box = (0 0 0) to (42.6 41.8117 100)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
1360 atoms
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
special bonds CPU = 0.000245051 secs
|
||||
read_data CPU = 0.00257704 secs
|
||||
mass 1 12.0107 # carbon mass (g/mole) | membrane
|
||||
mass 2 12.0107 # carbon mass (g/mole) | adsorbate
|
||||
# Separate atom groups
|
||||
group layer1 molecule 1
|
||||
680 atoms in group layer1
|
||||
group layer2 molecule 2
|
||||
680 atoms in group layer2
|
||||
|
||||
######################## Potential defition ########################
|
||||
pair_style hybrid/overlay rebo kolmogorov/crespi/full 16.0 1
|
||||
####################################################################
|
||||
pair_coeff * * rebo CH.rebo C C # chemical
|
||||
Reading potential file CH.rebo with DATE: 2018-7-3
|
||||
pair_coeff * * kolmogorov/crespi/full CH_taper.KC C C # long range
|
||||
####################################################################
|
||||
# Neighbor update settings
|
||||
neighbor 2.0 bin
|
||||
neigh_modify every 1
|
||||
neigh_modify delay 0
|
||||
neigh_modify check yes
|
||||
|
||||
#### Simulation settings ####
|
||||
timestep 0.001
|
||||
velocity all create 300.0 12345
|
||||
|
||||
compute 0 all pair rebo
|
||||
compute 1 all pair kolmogorov/crespi/full
|
||||
variable REBO equal c_0 # REBO energy
|
||||
variable KC equal c_1 # total interlayer energy
|
||||
variable Evdw equal c_1[1] # attractive energy
|
||||
variable Erep equal c_1[2] # repulsive energy
|
||||
|
||||
############################
|
||||
|
||||
# Output
|
||||
thermo 100
|
||||
thermo_style custom step cpu etotal pe ke v_REBO v_KC v_Erep v_Evdw temp
|
||||
thermo_modify line one format float %.16f
|
||||
thermo_modify flush yes norm no lost warn
|
||||
|
||||
###### Run molecular dynamics ######
|
||||
fix thermostat all nve
|
||||
run 1000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 18
|
||||
ghost atom cutoff = 18
|
||||
binsize = 9, bins = 5 5 12
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair rebo, perpetual
|
||||
attributes: full, newton on, ghost
|
||||
pair build: full/bin/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) pair kolmogorov/crespi/full, perpetual, copy from (1)
|
||||
attributes: full, newton on, ghost
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 9.878 | 9.878 | 9.878 Mbytes
|
||||
Step CPU TotEng PotEng KinEng v_REBO v_KC v_Erep v_Evdw Temp
|
||||
0 0.0000000000000000 -10037.7640583250176860 -10090.4634194415175443 52.6993611164999933 -10057.1894932866325689 -33.2739261548851388 35.9559834317043467 -69.2299095866038954 299.9999999999999432
|
||||
100 1.5180600649910048 -10037.5122858156355505 -10065.4637593850711710 27.9514735694348637 -10032.2132655062741833 -33.2504938787968172 25.2100699046001573 -58.4605637833912795 159.1184768311167090
|
||||
200 3.0089348420733586 -10037.4414086674296414 -10061.6271012692577642 24.1856926018279914 -10028.9093252939601371 -32.7177759752976272 18.5366534598677504 -51.2544294351567515 137.6811336385757158
|
||||
300 4.5315427089808509 -10037.4824653300020145 -10064.2845326005372044 26.8020672705348311 -10030.9195389405158494 -33.3649936600211205 26.3639208740115549 -59.7289145340278722 152.5752876469494197
|
||||
400 6.0353655620710924 -10037.5105626329095685 -10064.8769084956238657 27.3663458627148124 -10031.8478821022818011 -33.0290263933414394 36.6142885774347562 -69.6433149707726074 155.7875386888504181
|
||||
500 7.5396006110822782 -10037.5010433784900670 -10064.8363209936269413 27.3352776151361780 -10031.4417172103858320 -33.3946037832416351 26.2980262321774489 -59.6926300154146787 155.6106774503813881
|
||||
600 9.2617433650884777 -10037.4817772372534819 -10064.1925798287848011 26.7108025915320830 -10031.4376178099319077 -32.7549620188514226 18.5745873777100208 -51.3295493965524017 152.0557480715018528
|
||||
700 10.7484918619738892 -10037.4834430268347205 -10064.1291975032127084 26.6457544763787268 -10030.8722888097836403 -33.2569086934306739 25.2322818106757047 -58.4891905041008613 151.6854507067412499
|
||||
800 12.2509897360578179 -10037.5047888097869873 -10064.8671187129039026 27.3623299031166667 -10031.9815058608728577 -32.8856128520297801 36.5236695083899718 -69.4092823604150908 155.7646771616151966
|
||||
900 13.7584852169966325 -10037.5068323939758557 -10065.3998155270637653 27.8929831330881477 -10032.1734374829648004 -33.2263780440982259 27.7314849391120788 -60.9578629832060841 158.7855101588031062
|
||||
1000 15.2755981830414385 -10037.4811494880432292 -10064.0099109142211091 26.5287614261777058 -10031.3325267421205353 -32.6773841721017888 18.9005970229946634 -51.5779811950868776 151.0194480395985295
|
||||
Loop time of 15.2757 on 4 procs for 1000 steps with 1360 atoms
|
||||
|
||||
Performance: 5.656 ns/day, 4.243 hours/ns, 65.464 timesteps/s
|
||||
99.9% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 13.985 | 14.446 | 14.823 | 7.9 | 94.57
|
||||
Bond | 0.00040979 | 0.00042456 | 0.00046059 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.43692 | 0.81428 | 1.2749 | 33.2 | 5.33
|
||||
Output | 0.00028016 | 0.00037143 | 0.00063561 | 0.0 | 0.00
|
||||
Modify | 0.0045586 | 0.0046468 | 0.0047903 | 0.1 | 0.03
|
||||
Other | | 0.01041 | | | 0.07
|
||||
|
||||
Nlocal: 340 ave 340 max 340 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 4628 ave 4628 max 4628 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 259250 ave 259250 max 259250 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1037000
|
||||
Ave neighs/atom = 762.5
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:15
|
||||
65
examples/USER/misc/momentum/in.momentum
Normal file
65
examples/USER/misc/momentum/in.momentum
Normal file
@ -0,0 +1,65 @@
|
||||
# Test compute momentum with by comparing it's output with compute reduce
|
||||
|
||||
# Script will output the two computations of the total momentum as
|
||||
# thermo vars - they should be identical
|
||||
|
||||
# 3D LJ Poiseuille flow simulation
|
||||
dimension 3
|
||||
boundary p p p
|
||||
|
||||
atom_style atomic
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
# create geometry
|
||||
lattice hcp 0.5
|
||||
region box block 0 20 0 10 0 10
|
||||
create_box 3 box
|
||||
create_atoms 1 box
|
||||
|
||||
mass 1 1.0
|
||||
mass 2 1.0
|
||||
mass 3 1.0
|
||||
|
||||
# LJ potentials
|
||||
pair_style lj/cut 1.0
|
||||
pair_coeff * * 1.0 1.0 1.0
|
||||
|
||||
# define groups
|
||||
region 1 block INF INF INF 1.0 INF INF
|
||||
group lower region 1
|
||||
region 2 block INF INF 9.0 INF INF INF
|
||||
group upper region 2
|
||||
group boundary union lower upper
|
||||
group liquid subtract all boundary
|
||||
|
||||
set group lower type 2
|
||||
set group upper type 3
|
||||
|
||||
# temperature settings
|
||||
compute mobile liquid temp
|
||||
velocity liquid create 1.0 100 temp mobile
|
||||
fix 1 all nve
|
||||
fix 2 liquid temp/rescale 200 1.0 2.0 0.02 1.0
|
||||
fix_modify 2 temp mobile
|
||||
|
||||
velocity boundary set 0.0 0.0 0.0
|
||||
fix 4 lower setforce 0.0 0.0 0.0
|
||||
fix 5 upper setforce 0.0 0.0 0.0
|
||||
fix 6 liquid addforce 0.1 0.0 0.0
|
||||
|
||||
# Compute total momentum
|
||||
compute mom liquid momentum
|
||||
|
||||
# Comparison (momentum variables + compute reduce)
|
||||
variable mx atom mass*vx
|
||||
variable my atom mass*vy
|
||||
variable mz atom mass*vz
|
||||
compute mom_red liquid reduce sum v_mx v_my v_mz
|
||||
|
||||
# Run
|
||||
timestep 0.003
|
||||
thermo 1000
|
||||
thermo_style custom step c_mom_red[*] c_mom[*]
|
||||
|
||||
run 100000
|
||||
1
examples/kim/.gitignore
vendored
Normal file
1
examples/kim/.gitignore
vendored
Normal file
@ -0,0 +1 @@
|
||||
/kim.log
|
||||
@ -14,20 +14,14 @@ variable xx equal 20*$x
|
||||
variable yy equal 20*$y
|
||||
variable zz equal 20*$z
|
||||
|
||||
units metal
|
||||
atom_style atomic
|
||||
newton on
|
||||
kim_init LennardJones_Ar real
|
||||
|
||||
lattice fcc 4.4300
|
||||
region box block 0 ${xx} 0 ${yy} 0 ${zz}
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
|
||||
#pair_style lj/cut 8.1500
|
||||
#pair_coeff 1 1 0.0104 3.4000
|
||||
|
||||
pair_style kim LennardJones_Ar
|
||||
pair_coeff * * Ar
|
||||
kim_interactions Ar
|
||||
|
||||
mass 1 39.95
|
||||
velocity all create 200.0 232345 loop geom
|
||||
46
examples/kim/in.kim-pm-query.melt
Normal file
46
examples/kim/in.kim-pm-query.melt
Normal file
@ -0,0 +1,46 @@
|
||||
# 3d Lennard-Jones melt
|
||||
#
|
||||
# This example requires that the KIM Portable Model (PM)
|
||||
# SW_StillingerWeber_1985_Si__MO_405512056662_005
|
||||
# is installed. This can be done with the command
|
||||
# kim-api-collections-management install user SW_StillingerWeber_1985_Si__MO_405512056662_005
|
||||
# If this command does not work, you may need to setup your PATH to find the utility.
|
||||
# If you installed the kim-api using the LAMMPS CMake build, you can do the following
|
||||
# (where the current working directory is assumed to be the LAMMPS build directory)
|
||||
# source ./kim_build-prefix/bin/kim-api-activate
|
||||
# If you installed the kim-api using the LAMMPS Make build, you can do the following
|
||||
# (where the current working directory is assumed to be the LAMMPS src directory)
|
||||
# source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate
|
||||
# (where you should relplace X.Y.Z with the appropriate kim-api version number).
|
||||
#
|
||||
# Or, see https://openkim.org/doc/obtaining-models for alternative options.
|
||||
#
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable xx equal 20*$x
|
||||
variable yy equal 20*$y
|
||||
variable zz equal 20*$z
|
||||
|
||||
kim_init SW_StillingerWeber_1985_Si__MO_405512056662_005 real
|
||||
kim_query a0 get_lattice_constant_cubic crystal=["fcc"] species=["Si"] units=["angstrom"]
|
||||
|
||||
lattice fcc ${a0}
|
||||
region box block 0 ${xx} 0 ${yy} 0 ${zz}
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
|
||||
kim_interactions Si
|
||||
|
||||
mass 1 39.95
|
||||
velocity all create 200.0 232345 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
|
||||
|
||||
run 100
|
||||
45
examples/kim/in.kim-pm.melt
Normal file
45
examples/kim/in.kim-pm.melt
Normal file
@ -0,0 +1,45 @@
|
||||
# 3d Lennard-Jones melt
|
||||
#
|
||||
# This example requires that the KIM Portable Model (PM)
|
||||
# SW_StillingerWeber_1985_Si__MO_405512056662_005
|
||||
# is installed. This can be done with the command
|
||||
# kim-api-collections-management install user SW_StillingerWeber_1985_Si__MO_405512056662_005
|
||||
# If this command does not work, you may need to setup your PATH to find the utility.
|
||||
# If you installed the kim-api using the LAMMPS CMake build, you can do the following
|
||||
# (where the current working directory is assumed to be the LAMMPS build directory)
|
||||
# source ./kim_build-prefix/bin/kim-api-activate
|
||||
# If you installed the kim-api using the LAMMPS Make build, you can do the following
|
||||
# (where the current working directory is assumed to be the LAMMPS src directory)
|
||||
# source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate
|
||||
# (where you should relplace X.Y.Z with the appropriate kim-api version number).
|
||||
#
|
||||
# Or, see https://openkim.org/doc/obtaining-models for alternative options.
|
||||
#
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable xx equal 20*$x
|
||||
variable yy equal 20*$y
|
||||
variable zz equal 20*$z
|
||||
|
||||
kim_init SW_StillingerWeber_1985_Si__MO_405512056662_005 real
|
||||
|
||||
lattice fcc 4.4300
|
||||
region box block 0 ${xx} 0 ${yy} 0 ${zz}
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
|
||||
kim_interactions Si
|
||||
|
||||
mass 1 39.95
|
||||
velocity all create 200.0 232345 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
|
||||
|
||||
run 100
|
||||
45
examples/kim/in.kim-sm.melt
Normal file
45
examples/kim/in.kim-sm.melt
Normal file
@ -0,0 +1,45 @@
|
||||
# 3d Lennard-Jones melt
|
||||
#
|
||||
# This example requires that the KIM Simulator Model (PM)
|
||||
# Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000
|
||||
# is installed. This can be done with the command
|
||||
# kim-api-collections-management install user Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000
|
||||
# If this command does not work, you may need to setup your PATH to find the utility.
|
||||
# If you installed the kim-api using the LAMMPS CMake build, you can do the following
|
||||
# (where the current working directory is assumed to be the LAMMPS build directory)
|
||||
# source ./kim_build-prefix/bin/kim-api-activate
|
||||
# If you installed the kim-api using the LAMMPS Make build, you can do the following
|
||||
# (where the current working directory is assumed to be the LAMMPS src directory)
|
||||
# source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate
|
||||
# (where you should relplace X.Y.Z with the appropriate kim-api version number).
|
||||
#
|
||||
# See https://openkim.org/doc/obtaining-models for alternative options.
|
||||
#
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable xx equal 20*$x
|
||||
variable yy equal 20*$y
|
||||
variable zz equal 20*$z
|
||||
|
||||
kim_init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 real
|
||||
|
||||
lattice fcc 4.4300
|
||||
region box block 0 ${xx} 0 ${yy} 0 ${zz}
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
|
||||
kim_interactions O
|
||||
|
||||
mass 1 39.95
|
||||
velocity all create 200.0 232345 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
|
||||
|
||||
run 100
|
||||
@ -1,35 +0,0 @@
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable xx equal 20*$x
|
||||
variable yy equal 20*$y
|
||||
variable zz equal 20*$z
|
||||
|
||||
units metal
|
||||
atom_style atomic
|
||||
newton off
|
||||
|
||||
lattice fcc 4.4300
|
||||
region box block 0 ${xx} 0 ${yy} 0 ${zz}
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
|
||||
pair_style lj/cut 8.1500
|
||||
pair_coeff 1 1 0.0104 3.4000
|
||||
|
||||
#pair_style kim LennardJones_Ar
|
||||
#pair_coeff * * Ar
|
||||
|
||||
mass 1 39.95
|
||||
velocity all create 200.0 232345 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
|
||||
|
||||
run 100
|
||||
@ -1,41 +0,0 @@
|
||||
# 3d Lennard-Jones melt
|
||||
#
|
||||
# This example requires that the example models provided with
|
||||
# the kim-api package are installed. see the ./lib/kim/README or
|
||||
# ./lib/kim/Install.py files for details on how to install these
|
||||
# example models.
|
||||
#
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable xx equal 20*$x
|
||||
variable yy equal 20*$y
|
||||
variable zz equal 20*$z
|
||||
|
||||
units metal
|
||||
atom_style atomic
|
||||
newton off
|
||||
|
||||
lattice fcc 4.4300
|
||||
region box block 0 ${xx} 0 ${yy} 0 ${zz}
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
|
||||
#pair_style lj/cut 8.1500
|
||||
#pair_coeff 1 1 0.0104 3.4000
|
||||
|
||||
pair_style kim LennardJones_Ar
|
||||
pair_coeff * * Ar
|
||||
|
||||
mass 1 39.95
|
||||
velocity all create 200.0 232345 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
|
||||
|
||||
run 100
|
||||
@ -8,9 +8,7 @@ variable xx equal 20*$x
|
||||
variable yy equal 20*$y
|
||||
variable zz equal 20*$z
|
||||
|
||||
units metal
|
||||
atom_style atomic
|
||||
newton on
|
||||
units real
|
||||
|
||||
lattice fcc 4.4300
|
||||
region box block 0 ${xx} 0 ${yy} 0 ${zz}
|
||||
@ -1,11 +0,0 @@
|
||||
|
||||
# example for performing a query to the OpenKIM test database to retrieve
|
||||
# a parameter to be used in the input. here it requests the aluminium
|
||||
# lattice constant for a specific test used for a specific model and then
|
||||
# assigns it to the variable 'latconst'
|
||||
|
||||
units metal
|
||||
info variables out log
|
||||
kim_query latconst get_test_result test=TE_156715955670 species=["Al"] model=MO_800509458712 prop=structure-cubic-crystal-npt keys=["a"] units=["angstrom"]
|
||||
info variables out log
|
||||
lattice fcc ${latconst}
|
||||
@ -1,55 +0,0 @@
|
||||
LAMMPS (1 Feb 2019)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
Lattice spacing in x,y,z = 4.43 4.43 4.43
|
||||
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
Created 32000 atoms
|
||||
Time spent = 0.004499 secs
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 8.45
|
||||
ghost atom cutoff = 8.45
|
||||
binsize = 4.225, bins = 21 21 21
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: half/bin/3d/newtoff
|
||||
bin: standard
|
||||
Setting up Verlet run ...
|
||||
Unit style : metal
|
||||
Current step : 0
|
||||
Time step : 0.001
|
||||
Per MPI rank memory allocation (min/avg/max) = 20.37 | 20.37 | 20.37 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 200 6290.8194 0 7118.0584 129712.25
|
||||
100 95.179725 6718.814 0 7112.496 133346.59
|
||||
Loop time of 2.92885 on 1 procs for 100 steps with 32000 atoms
|
||||
|
||||
Performance: 2.950 ns/day, 8.136 hours/ns, 34.143 timesteps/s
|
||||
99.1% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.5638 | 2.5638 | 2.5638 | 0.0 | 87.54
|
||||
Neigh | 0.31935 | 0.31935 | 0.31935 | 0.0 | 10.90
|
||||
Comm | 0.006833 | 0.006833 | 0.006833 | 0.0 | 0.23
|
||||
Output | 0.000107 | 0.000107 | 0.000107 | 0.0 | 0.00
|
||||
Modify | 0.027806 | 0.027806 | 0.027806 | 0.0 | 0.95
|
||||
Other | | 0.01091 | | | 0.37
|
||||
|
||||
Nlocal: 32000 ave 32000 max 32000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 19911 ave 19911 max 19911 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 2.3705e+06 ave 2.3705e+06 max 2.3705e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 2370499
|
||||
Ave neighs/atom = 74.0781
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:03
|
||||
@ -1,55 +0,0 @@
|
||||
LAMMPS (1 Feb 2019)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
Lattice spacing in x,y,z = 4.43 4.43 4.43
|
||||
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
Created 32000 atoms
|
||||
Time spent = 0.001039 secs
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 8.45
|
||||
ghost atom cutoff = 8.45
|
||||
binsize = 4.225, bins = 21 21 21
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: half/bin/3d/newtoff
|
||||
bin: standard
|
||||
Setting up Verlet run ...
|
||||
Unit style : metal
|
||||
Current step : 0
|
||||
Time step : 0.001
|
||||
Per MPI rank memory allocation (min/avg/max) = 8.013 | 8.013 | 8.013 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 200 6290.8194 0 7118.0584 129712.25
|
||||
100 95.179725 6718.814 0 7112.496 133346.59
|
||||
Loop time of 0.778581 on 4 procs for 100 steps with 32000 atoms
|
||||
|
||||
Performance: 11.097 ns/day, 2.163 hours/ns, 128.439 timesteps/s
|
||||
99.8% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.65171 | 0.65891 | 0.67656 | 1.3 | 84.63
|
||||
Neigh | 0.07924 | 0.079548 | 0.07997 | 0.1 | 10.22
|
||||
Comm | 0.006755 | 0.0069015 | 0.007072 | 0.2 | 0.89
|
||||
Output | 4.6e-05 | 9.725e-05 | 0.000203 | 0.0 | 0.01
|
||||
Modify | 0.006841 | 0.006941 | 0.007015 | 0.1 | 0.89
|
||||
Other | | 0.02618 | | | 3.36
|
||||
|
||||
Nlocal: 8000 ave 8018 max 7967 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 0 2
|
||||
Nghost: 9131 ave 9164 max 9113 min
|
||||
Histogram: 2 0 0 1 0 0 0 0 0 1
|
||||
Neighs: 630904 ave 632094 max 628209 min
|
||||
Histogram: 1 0 0 0 0 0 0 1 0 2
|
||||
|
||||
Total # of neighbors = 2523614
|
||||
Ave neighs/atom = 78.8629
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
@ -1,55 +0,0 @@
|
||||
LAMMPS (1 Feb 2019)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
Lattice spacing in x,y,z = 4.43 4.43 4.43
|
||||
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
Created 32000 atoms
|
||||
Time spent = 0.003479 secs
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 8.45
|
||||
ghost atom cutoff = 8.45
|
||||
binsize = 4.225, bins = 21 21 21
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Setting up Verlet run ...
|
||||
Unit style : metal
|
||||
Current step : 0
|
||||
Time step : 0.001
|
||||
Per MPI rank memory allocation (min/avg/max) = 19.23 | 19.23 | 19.23 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 200 6290.8194 0 7118.0584 129712.25
|
||||
100 95.179725 6718.814 0 7112.496 133346.59
|
||||
Loop time of 2.17978 on 1 procs for 100 steps with 32000 atoms
|
||||
|
||||
Performance: 3.964 ns/day, 6.055 hours/ns, 45.876 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.9892 | 1.9892 | 1.9892 | 0.0 | 91.26
|
||||
Neigh | 0.14506 | 0.14506 | 0.14506 | 0.0 | 6.65
|
||||
Comm | 0.011049 | 0.011049 | 0.011049 | 0.0 | 0.51
|
||||
Output | 9.1e-05 | 9.1e-05 | 9.1e-05 | 0.0 | 0.00
|
||||
Modify | 0.02347 | 0.02347 | 0.02347 | 0.0 | 1.08
|
||||
Other | | 0.01094 | | | 0.50
|
||||
|
||||
Nlocal: 32000 ave 32000 max 32000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 19911 ave 19911 max 19911 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 2.12688e+06 ave 2.12688e+06 max 2.12688e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 2126875
|
||||
Ave neighs/atom = 66.4648
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:02
|
||||
@ -1,55 +0,0 @@
|
||||
LAMMPS (1 Feb 2019)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
Lattice spacing in x,y,z = 4.43 4.43 4.43
|
||||
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
Created 32000 atoms
|
||||
Time spent = 0.000919 secs
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 8.45
|
||||
ghost atom cutoff = 8.45
|
||||
binsize = 4.225, bins = 21 21 21
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Setting up Verlet run ...
|
||||
Unit style : metal
|
||||
Current step : 0
|
||||
Time step : 0.001
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.632 | 7.632 | 7.632 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 200 6290.8194 0 7118.0584 129712.25
|
||||
100 95.179725 6718.814 0 7112.496 133346.59
|
||||
Loop time of 0.63515 on 4 procs for 100 steps with 32000 atoms
|
||||
|
||||
Performance: 13.603 ns/day, 1.764 hours/ns, 157.443 timesteps/s
|
||||
99.8% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.55365 | 0.5566 | 0.55868 | 0.2 | 87.63
|
||||
Neigh | 0.041495 | 0.0418 | 0.04211 | 0.1 | 6.58
|
||||
Comm | 0.019086 | 0.021075 | 0.023898 | 1.2 | 3.32
|
||||
Output | 4.4e-05 | 5.025e-05 | 6e-05 | 0.0 | 0.01
|
||||
Modify | 0.009315 | 0.0093595 | 0.009422 | 0.0 | 1.47
|
||||
Other | | 0.006263 | | | 0.99
|
||||
|
||||
Nlocal: 8000 ave 8018 max 7967 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 0 2
|
||||
Nghost: 9131 ave 9164 max 9113 min
|
||||
Histogram: 2 0 0 1 0 0 0 0 0 1
|
||||
Neighs: 531719 ave 533273 max 529395 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 2126875
|
||||
Ave neighs/atom = 66.4648
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
@ -1,59 +0,0 @@
|
||||
LAMMPS (1 Feb 2019)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
Lattice spacing in x,y,z = 4.43 4.43 4.43
|
||||
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
Created 32000 atoms
|
||||
Time spent = 0.003446 secs
|
||||
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097)
|
||||
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 8.45
|
||||
ghost atom cutoff = 8.45
|
||||
binsize = 4.225, bins = 21 21 21
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair kim, perpetual
|
||||
attributes: full, newton off, cut 8.45
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Setting up Verlet run ...
|
||||
Unit style : metal
|
||||
Current step : 0
|
||||
Time step : 0.001
|
||||
Per MPI rank memory allocation (min/avg/max) = 28.51 | 28.51 | 28.51 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 200 6290.8194 0 7118.0584 129712.25
|
||||
100 95.179725 6718.814 0 7112.496 133346.59
|
||||
Loop time of 3.01669 on 1 procs for 100 steps with 32000 atoms
|
||||
|
||||
Performance: 2.864 ns/day, 8.380 hours/ns, 33.149 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.6562 | 2.6562 | 2.6562 | 0.0 | 88.05
|
||||
Neigh | 0.31903 | 0.31903 | 0.31903 | 0.0 | 10.58
|
||||
Comm | 0.00634 | 0.00634 | 0.00634 | 0.0 | 0.21
|
||||
Output | 9.1e-05 | 9.1e-05 | 9.1e-05 | 0.0 | 0.00
|
||||
Modify | 0.024723 | 0.024723 | 0.024723 | 0.0 | 0.82
|
||||
Other | | 0.01032 | | | 0.34
|
||||
|
||||
Nlocal: 32000 ave 32000 max 32000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 19911 ave 19911 max 19911 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: 4.25375e+06 ave 4.25375e+06 max 4.25375e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 4253750
|
||||
Ave neighs/atom = 132.93
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:03
|
||||
@ -1,65 +0,0 @@
|
||||
LAMMPS (1 Feb 2019)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
Lattice spacing in x,y,z = 4.43 4.43 4.43
|
||||
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
Created 32000 atoms
|
||||
Time spent = 0.000921 secs
|
||||
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097)
|
||||
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102)
|
||||
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097)
|
||||
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102)
|
||||
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097)
|
||||
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102)
|
||||
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097)
|
||||
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 8.45
|
||||
ghost atom cutoff = 8.45
|
||||
binsize = 4.225, bins = 21 21 21
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair kim, perpetual
|
||||
attributes: full, newton off, cut 8.45
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Setting up Verlet run ...
|
||||
Unit style : metal
|
||||
Current step : 0
|
||||
Time step : 0.001
|
||||
Per MPI rank memory allocation (min/avg/max) = 10.05 | 10.05 | 10.05 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 200 6290.8194 0 7118.0584 129712.25
|
||||
100 95.179725 6718.814 0 7112.496 133346.59
|
||||
Loop time of 0.890192 on 4 procs for 100 steps with 32000 atoms
|
||||
|
||||
Performance: 9.706 ns/day, 2.473 hours/ns, 112.335 timesteps/s
|
||||
99.7% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.77867 | 0.77906 | 0.7794 | 0.0 | 87.52
|
||||
Neigh | 0.087831 | 0.088176 | 0.088805 | 0.1 | 9.91
|
||||
Comm | 0.006358 | 0.0065898 | 0.006815 | 0.3 | 0.74
|
||||
Output | 4.9e-05 | 5.975e-05 | 6.8e-05 | 0.0 | 0.01
|
||||
Modify | 0.010265 | 0.010429 | 0.010678 | 0.2 | 1.17
|
||||
Other | | 0.005874 | | | 0.66
|
||||
|
||||
Nlocal: 8000 ave 8018 max 7967 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 0 2
|
||||
Nghost: 9131 ave 9164 max 9113 min
|
||||
Histogram: 2 0 0 1 0 0 0 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 1.06344e+06 ave 1.06594e+06 max 1.05881e+06 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 0 2
|
||||
|
||||
Total # of neighbors = 4253750
|
||||
Ave neighs/atom = 132.93
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
@ -1,59 +0,0 @@
|
||||
LAMMPS (1 Feb 2019)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
Lattice spacing in x,y,z = 4.43 4.43 4.43
|
||||
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
Created 32000 atoms
|
||||
Time spent = 0.003089 secs
|
||||
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097)
|
||||
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 8.45
|
||||
ghost atom cutoff = 8.45
|
||||
binsize = 4.225, bins = 21 21 21
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair kim, perpetual
|
||||
attributes: full, newton off, cut 8.45
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Setting up Verlet run ...
|
||||
Unit style : metal
|
||||
Current step : 0
|
||||
Time step : 0.001
|
||||
Per MPI rank memory allocation (min/avg/max) = 28.12 | 28.12 | 28.12 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 200 6290.8194 0 7118.0584 129712.25
|
||||
100 95.179725 6718.814 0 7112.496 133346.59
|
||||
Loop time of 3.05849 on 1 procs for 100 steps with 32000 atoms
|
||||
|
||||
Performance: 2.825 ns/day, 8.496 hours/ns, 32.696 timesteps/s
|
||||
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.6786 | 2.6786 | 2.6786 | 0.0 | 87.58
|
||||
Neigh | 0.33105 | 0.33105 | 0.33105 | 0.0 | 10.82
|
||||
Comm | 0.012602 | 0.012602 | 0.012602 | 0.0 | 0.41
|
||||
Output | 9.5e-05 | 9.5e-05 | 9.5e-05 | 0.0 | 0.00
|
||||
Modify | 0.024858 | 0.024858 | 0.024858 | 0.0 | 0.81
|
||||
Other | | 0.01132 | | | 0.37
|
||||
|
||||
Nlocal: 32000 ave 32000 max 32000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 19911 ave 19911 max 19911 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: 4.25375e+06 ave 4.25375e+06 max 4.25375e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 4253750
|
||||
Ave neighs/atom = 132.93
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:03
|
||||
@ -1,65 +0,0 @@
|
||||
LAMMPS (1 Feb 2019)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
Lattice spacing in x,y,z = 4.43 4.43 4.43
|
||||
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
Created 32000 atoms
|
||||
Time spent = 0.000893 secs
|
||||
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097)
|
||||
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102)
|
||||
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097)
|
||||
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102)
|
||||
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097)
|
||||
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102)
|
||||
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097)
|
||||
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 8.45
|
||||
ghost atom cutoff = 8.45
|
||||
binsize = 4.225, bins = 21 21 21
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair kim, perpetual
|
||||
attributes: full, newton off, cut 8.45
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Setting up Verlet run ...
|
||||
Unit style : metal
|
||||
Current step : 0
|
||||
Time step : 0.001
|
||||
Per MPI rank memory allocation (min/avg/max) = 9.789 | 9.789 | 9.789 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 200 6290.8194 0 7118.0584 129712.25
|
||||
100 95.179725 6718.814 0 7112.496 133346.59
|
||||
Loop time of 0.903182 on 4 procs for 100 steps with 32000 atoms
|
||||
|
||||
Performance: 9.566 ns/day, 2.509 hours/ns, 110.720 timesteps/s
|
||||
99.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.76173 | 0.76349 | 0.76597 | 0.2 | 84.53
|
||||
Neigh | 0.088773 | 0.088938 | 0.089074 | 0.0 | 9.85
|
||||
Comm | 0.032018 | 0.03452 | 0.03638 | 0.9 | 3.82
|
||||
Output | 4e-05 | 4.425e-05 | 5.2e-05 | 0.0 | 0.00
|
||||
Modify | 0.009278 | 0.0093917 | 0.009528 | 0.1 | 1.04
|
||||
Other | | 0.006797 | | | 0.75
|
||||
|
||||
Nlocal: 8000 ave 8018 max 7967 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 0 2
|
||||
Nghost: 9131 ave 9164 max 9113 min
|
||||
Histogram: 2 0 0 1 0 0 0 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 1.06344e+06 ave 1.06594e+06 max 1.05881e+06 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 0 2
|
||||
|
||||
Total # of neighbors = 4253750
|
||||
Ave neighs/atom = 132.93
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
@ -1,34 +0,0 @@
|
||||
LAMMPS (28 Feb 2019)
|
||||
|
||||
# example for performing a query to the OpenKIM test database to retrieve
|
||||
# a parameter to be used in the input. here it requests the aluminium
|
||||
# lattice constant for a specific test used for a specific model and then
|
||||
# assigns it to the variable 'latconst'
|
||||
|
||||
units metal
|
||||
info variables out log
|
||||
|
||||
Info-Info-Info-Info-Info-Info-Info-Info-Info-Info-Info
|
||||
Printed on Fri Mar 22 20:00:56 2019
|
||||
|
||||
|
||||
Variable information:
|
||||
|
||||
Info-Info-Info-Info-Info-Info-Info-Info-Info-Info-Info
|
||||
|
||||
kim_query latconst get_test_result test=TE_156715955670 species=["Al"] model=MO_800509458712 prop=structure-cubic-crystal-npt keys=["a"] units=["angstrom"]
|
||||
info variables out log
|
||||
|
||||
Info-Info-Info-Info-Info-Info-Info-Info-Info-Info-Info
|
||||
Printed on Fri Mar 22 20:00:57 2019
|
||||
|
||||
|
||||
Variable information:
|
||||
Variable[ 0]: latconst , style = string , def = 4.03208274841
|
||||
|
||||
Info-Info-Info-Info-Info-Info-Info-Info-Info-Info-Info
|
||||
|
||||
lattice fcc ${latconst}
|
||||
lattice fcc 4.03208274841
|
||||
Lattice spacing in x,y,z = 4.03208 4.03208 4.03208
|
||||
Total wall time: 0:00:00
|
||||
107
examples/kim/log.7Aug19.in.kim-ex.melt.clang.1
Normal file
107
examples/kim/log.7Aug19.in.kim-ex.melt.clang.1
Normal file
@ -0,0 +1,107 @@
|
||||
LAMMPS (7 Aug 2019)
|
||||
# 3d Lennard-Jones melt
|
||||
#
|
||||
# This example requires that the example models provided with
|
||||
# the kim-api package are installed. see the ./lib/kim/README or
|
||||
# ./lib/kim/Install.py files for details on how to install these
|
||||
# example models.
|
||||
#
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable xx equal 20*$x
|
||||
variable xx equal 20*1
|
||||
variable yy equal 20*$y
|
||||
variable yy equal 20*1
|
||||
variable zz equal 20*$z
|
||||
variable zz equal 20*1
|
||||
|
||||
kim_init LennardJones_Ar real
|
||||
#=== BEGIN kim-init ==========================================
|
||||
units real
|
||||
#=== END kim-init ============================================
|
||||
|
||||
|
||||
lattice fcc 4.4300
|
||||
Lattice spacing in x,y,z = 4.43 4.43 4.43
|
||||
region box block 0 ${xx} 0 ${yy} 0 ${zz}
|
||||
region box block 0 20 0 ${yy} 0 ${zz}
|
||||
region box block 0 20 0 20 0 ${zz}
|
||||
region box block 0 20 0 20 0 20
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 32000 atoms
|
||||
create_atoms CPU = 0.004321 secs
|
||||
|
||||
kim_interactions Ar
|
||||
#=== BEGIN kim_interactions ==================================
|
||||
pair_style kim LennardJones_Ar
|
||||
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (../pair_kim.cpp:974)
|
||||
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (../pair_kim.cpp:979)
|
||||
pair_coeff * * Ar
|
||||
#=== END kim_interactions ====================================
|
||||
|
||||
|
||||
mass 1 39.95
|
||||
velocity all create 200.0 232345 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
|
||||
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 8.45
|
||||
ghost atom cutoff = 8.45
|
||||
binsize = 4.225, bins = 21 21 21
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair kim, perpetual
|
||||
attributes: full, newton off, cut 8.45
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Setting up Verlet run ...
|
||||
Unit style : real
|
||||
Current step : 0
|
||||
Time step : 1
|
||||
Per MPI rank memory allocation (min/avg/max) = 28.12 | 28.12 | 28.12 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 200 145069.63 0 164146.22 128015.94
|
||||
100 95.179703 154939.42 0 164017.94 131602.75
|
||||
Loop time of 3.48256 on 1 procs for 100 steps with 32000 atoms
|
||||
|
||||
Performance: 2.481 ns/day, 9.674 hours/ns, 28.715 timesteps/s
|
||||
98.3% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 3.0502 | 3.0502 | 3.0502 | 0.0 | 87.59
|
||||
Neigh | 0.3646 | 0.3646 | 0.3646 | 0.0 | 10.47
|
||||
Comm | 0.01783 | 0.01783 | 0.01783 | 0.0 | 0.51
|
||||
Output | 6.8e-05 | 6.8e-05 | 6.8e-05 | 0.0 | 0.00
|
||||
Modify | 0.034349 | 0.034349 | 0.034349 | 0.0 | 0.99
|
||||
Other | | 0.01547 | | | 0.44
|
||||
|
||||
Nlocal: 32000 ave 32000 max 32000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 19911 ave 19911 max 19911 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: 4.25375e+06 ave 4.25375e+06 max 4.25375e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 4253750
|
||||
Ave neighs/atom = 132.93
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:03
|
||||
113
examples/kim/log.7Aug19.in.kim-ex.melt.clang.4
Normal file
113
examples/kim/log.7Aug19.in.kim-ex.melt.clang.4
Normal file
@ -0,0 +1,113 @@
|
||||
LAMMPS (7 Aug 2019)
|
||||
# 3d Lennard-Jones melt
|
||||
#
|
||||
# This example requires that the example models provided with
|
||||
# the kim-api package are installed. see the ./lib/kim/README or
|
||||
# ./lib/kim/Install.py files for details on how to install these
|
||||
# example models.
|
||||
#
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable xx equal 20*$x
|
||||
variable xx equal 20*1
|
||||
variable yy equal 20*$y
|
||||
variable yy equal 20*1
|
||||
variable zz equal 20*$z
|
||||
variable zz equal 20*1
|
||||
|
||||
kim_init LennardJones_Ar real
|
||||
#=== BEGIN kim-init ==========================================
|
||||
units real
|
||||
#=== END kim-init ============================================
|
||||
|
||||
|
||||
lattice fcc 4.4300
|
||||
Lattice spacing in x,y,z = 4.43 4.43 4.43
|
||||
region box block 0 ${xx} 0 ${yy} 0 ${zz}
|
||||
region box block 0 20 0 ${yy} 0 ${zz}
|
||||
region box block 0 20 0 20 0 ${zz}
|
||||
region box block 0 20 0 20 0 20
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 32000 atoms
|
||||
create_atoms CPU = 0.000989 secs
|
||||
|
||||
kim_interactions Ar
|
||||
#=== BEGIN kim_interactions ==================================
|
||||
pair_style kim LennardJones_Ar
|
||||
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (../pair_kim.cpp:974)
|
||||
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (../pair_kim.cpp:979)
|
||||
pair_coeff * * Ar
|
||||
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (../pair_kim.cpp:974)
|
||||
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (../pair_kim.cpp:979)
|
||||
#=== END kim_interactions ====================================
|
||||
|
||||
|
||||
mass 1 39.95
|
||||
velocity all create 200.0 232345 loop geom
|
||||
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (../pair_kim.cpp:974)
|
||||
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (../pair_kim.cpp:979)
|
||||
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (../pair_kim.cpp:974)
|
||||
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (../pair_kim.cpp:979)
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
|
||||
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 8.45
|
||||
ghost atom cutoff = 8.45
|
||||
binsize = 4.225, bins = 21 21 21
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair kim, perpetual
|
||||
attributes: full, newton off, cut 8.45
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Setting up Verlet run ...
|
||||
Unit style : real
|
||||
Current step : 0
|
||||
Time step : 1
|
||||
Per MPI rank memory allocation (min/avg/max) = 9.791 | 9.791 | 9.791 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 200 145069.63 0 164146.22 128015.94
|
||||
100 95.179703 154939.42 0 164017.94 131602.75
|
||||
Loop time of 0.924494 on 4 procs for 100 steps with 32000 atoms
|
||||
|
||||
Performance: 9.346 ns/day, 2.568 hours/ns, 108.167 timesteps/s
|
||||
99.6% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.76434 | 0.76847 | 0.77207 | 0.3 | 83.12
|
||||
Neigh | 0.09089 | 0.094446 | 0.099911 | 1.1 | 10.22
|
||||
Comm | 0.038599 | 0.044759 | 0.051381 | 2.1 | 4.84
|
||||
Output | 3.5e-05 | 4e-05 | 4.9e-05 | 0.0 | 0.00
|
||||
Modify | 0.009396 | 0.009685 | 0.009941 | 0.2 | 1.05
|
||||
Other | | 0.00709 | | | 0.77
|
||||
|
||||
Nlocal: 8000 ave 8018 max 7967 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 0 2
|
||||
Nghost: 9131 ave 9164 max 9113 min
|
||||
Histogram: 2 0 0 1 0 0 0 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 1.06344e+06 ave 1.06594e+06 max 1.05881e+06 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 0 2
|
||||
|
||||
Total # of neighbors = 4253750
|
||||
Ave neighs/atom = 132.93
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
124
examples/kim/log.7Aug19.in.kim-pm-query.melt.clang.1
Normal file
124
examples/kim/log.7Aug19.in.kim-pm-query.melt.clang.1
Normal file
@ -0,0 +1,124 @@
|
||||
LAMMPS (7 Aug 2019)
|
||||
# 3d Lennard-Jones melt
|
||||
#
|
||||
# This example requires that the KIM Portable Model (PM)
|
||||
# SW_StillingerWeber_1985_Si__MO_405512056662_005
|
||||
# is installed. This can be done with the command
|
||||
# kim-api-collections-management install user SW_StillingerWeber_1985_Si__MO_405512056662_005
|
||||
# If this command does not work, you may need to setup your PATH to find the utility.
|
||||
# If you installed the kim-api using the LAMMPS CMake build, you can do the following
|
||||
# (where the current working directory is assumed to be the LAMMPS build directory)
|
||||
# source ./kim_build-prefix/bin/kim-api-activate
|
||||
# If you installed the kim-api using the LAMMPS Make build, you can do the following
|
||||
# (where the current working directory is assumed to be the LAMMPS src directory)
|
||||
# source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate
|
||||
# (where you should relplace X.Y.Z with the appropriate kim-api version number).
|
||||
#
|
||||
# Or, see https://openkim.org/doc/obtaining-models for alternative options.
|
||||
#
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable xx equal 20*$x
|
||||
variable xx equal 20*1
|
||||
variable yy equal 20*$y
|
||||
variable yy equal 20*1
|
||||
variable zz equal 20*$z
|
||||
variable zz equal 20*1
|
||||
|
||||
kim_init SW_StillingerWeber_1985_Si__MO_405512056662_005 real
|
||||
#=== BEGIN kim-init ==========================================
|
||||
units real
|
||||
#=== END kim-init ============================================
|
||||
|
||||
kim_query a0 get_lattice_constant_cubic crystal=["fcc"] species=["Si"] units=["angstrom"]
|
||||
#=== BEGIN kim-query =========================================
|
||||
variable a0 string 4.146581932902336
|
||||
#=== END kim-query ===========================================
|
||||
|
||||
|
||||
lattice fcc ${a0}
|
||||
lattice fcc 4.146581932902336
|
||||
Lattice spacing in x,y,z = 4.14658 4.14658 4.14658
|
||||
region box block 0 ${xx} 0 ${yy} 0 ${zz}
|
||||
region box block 0 20 0 ${yy} 0 ${zz}
|
||||
region box block 0 20 0 20 0 ${zz}
|
||||
region box block 0 20 0 20 0 20
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (82.9316 82.9316 82.9316)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 32000 atoms
|
||||
create_atoms CPU = 0.005415 secs
|
||||
|
||||
kim_interactions Si
|
||||
#=== BEGIN kim_interactions ==================================
|
||||
pair_style kim SW_StillingerWeber_1985_Si__MO_405512056662_005
|
||||
pair_coeff * * Si
|
||||
#=== END kim_interactions ====================================
|
||||
|
||||
|
||||
mass 1 39.95
|
||||
velocity all create 200.0 232345 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
|
||||
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.07118
|
||||
ghost atom cutoff = 4.07118
|
||||
binsize = 2.03559, bins = 41 41 41
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair kim, perpetual
|
||||
attributes: full, newton off, cut 4.07118
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Setting up Verlet run ...
|
||||
Unit style : real
|
||||
Current step : 0
|
||||
Time step : 1
|
||||
Per MPI rank memory allocation (min/avg/max) = 10.36 | 10.36 | 10.36 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 200 -126084.25 0 -107007.66 1528.8768
|
||||
100 94.450495 -116016.03 0 -107007.07 2282.2685
|
||||
Loop time of 74.6055 on 1 procs for 100 steps with 32000 atoms
|
||||
|
||||
Performance: 0.116 ns/day, 207.238 hours/ns, 1.340 timesteps/s
|
||||
98.6% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 74.446 | 74.446 | 74.446 | 0.0 | 99.79
|
||||
Neigh | 0.096611 | 0.096611 | 0.096611 | 0.0 | 0.13
|
||||
Comm | 0.014594 | 0.014594 | 0.014594 | 0.0 | 0.02
|
||||
Output | 7.9e-05 | 7.9e-05 | 7.9e-05 | 0.0 | 0.00
|
||||
Modify | 0.03454 | 0.03454 | 0.03454 | 0.0 | 0.05
|
||||
Other | | 0.01396 | | | 0.02
|
||||
|
||||
Nlocal: 32000 ave 32000 max 32000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 9667 ave 9667 max 9667 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: 450192 ave 450192 max 450192 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 450192
|
||||
Ave neighs/atom = 14.0685
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:01:16
|
||||
124
examples/kim/log.7Aug19.in.kim-pm-query.melt.clang.4
Normal file
124
examples/kim/log.7Aug19.in.kim-pm-query.melt.clang.4
Normal file
@ -0,0 +1,124 @@
|
||||
LAMMPS (7 Aug 2019)
|
||||
# 3d Lennard-Jones melt
|
||||
#
|
||||
# This example requires that the KIM Portable Model (PM)
|
||||
# SW_StillingerWeber_1985_Si__MO_405512056662_005
|
||||
# is installed. This can be done with the command
|
||||
# kim-api-collections-management install user SW_StillingerWeber_1985_Si__MO_405512056662_005
|
||||
# If this command does not work, you may need to setup your PATH to find the utility.
|
||||
# If you installed the kim-api using the LAMMPS CMake build, you can do the following
|
||||
# (where the current working directory is assumed to be the LAMMPS build directory)
|
||||
# source ./kim_build-prefix/bin/kim-api-activate
|
||||
# If you installed the kim-api using the LAMMPS Make build, you can do the following
|
||||
# (where the current working directory is assumed to be the LAMMPS src directory)
|
||||
# source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate
|
||||
# (where you should relplace X.Y.Z with the appropriate kim-api version number).
|
||||
#
|
||||
# Or, see https://openkim.org/doc/obtaining-models for alternative options.
|
||||
#
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable xx equal 20*$x
|
||||
variable xx equal 20*1
|
||||
variable yy equal 20*$y
|
||||
variable yy equal 20*1
|
||||
variable zz equal 20*$z
|
||||
variable zz equal 20*1
|
||||
|
||||
kim_init SW_StillingerWeber_1985_Si__MO_405512056662_005 real
|
||||
#=== BEGIN kim-init ==========================================
|
||||
units real
|
||||
#=== END kim-init ============================================
|
||||
|
||||
kim_query a0 get_lattice_constant_cubic crystal=["fcc"] species=["Si"] units=["angstrom"]
|
||||
#=== BEGIN kim-query =========================================
|
||||
variable a0 string 4.146581932902336
|
||||
#=== END kim-query ===========================================
|
||||
|
||||
|
||||
lattice fcc ${a0}
|
||||
lattice fcc 4.146581932902336
|
||||
Lattice spacing in x,y,z = 4.14658 4.14658 4.14658
|
||||
region box block 0 ${xx} 0 ${yy} 0 ${zz}
|
||||
region box block 0 20 0 ${yy} 0 ${zz}
|
||||
region box block 0 20 0 20 0 ${zz}
|
||||
region box block 0 20 0 20 0 20
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (82.9316 82.9316 82.9316)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 32000 atoms
|
||||
create_atoms CPU = 0.000946 secs
|
||||
|
||||
kim_interactions Si
|
||||
#=== BEGIN kim_interactions ==================================
|
||||
pair_style kim SW_StillingerWeber_1985_Si__MO_405512056662_005
|
||||
pair_coeff * * Si
|
||||
#=== END kim_interactions ====================================
|
||||
|
||||
|
||||
mass 1 39.95
|
||||
velocity all create 200.0 232345 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
|
||||
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.07118
|
||||
ghost atom cutoff = 4.07118
|
||||
binsize = 2.03559, bins = 41 41 41
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair kim, perpetual
|
||||
attributes: full, newton off, cut 4.07118
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Setting up Verlet run ...
|
||||
Unit style : real
|
||||
Current step : 0
|
||||
Time step : 1
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.489 | 3.489 | 3.489 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 200 -126084.25 0 -107007.66 1528.8768
|
||||
100 94.450495 -116016.03 0 -107007.07 2282.2685
|
||||
Loop time of 19.0792 on 4 procs for 100 steps with 32000 atoms
|
||||
|
||||
Performance: 0.453 ns/day, 52.998 hours/ns, 5.241 timesteps/s
|
||||
99.4% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 18.78 | 18.855 | 18.937 | 1.5 | 98.83
|
||||
Neigh | 0.026047 | 0.026274 | 0.0266 | 0.1 | 0.14
|
||||
Comm | 0.09039 | 0.17196 | 0.24675 | 15.9 | 0.90
|
||||
Output | 3.9e-05 | 4.975e-05 | 6.1e-05 | 0.0 | 0.00
|
||||
Modify | 0.015667 | 0.015819 | 0.016008 | 0.1 | 0.08
|
||||
Other | | 0.01008 | | | 0.05
|
||||
|
||||
Nlocal: 8000 ave 8029 max 7968 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 0 2
|
||||
Nghost: 4259 ave 4303 max 4202 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: 112548 ave 113091 max 111995 min
|
||||
Histogram: 1 0 0 1 0 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 450192
|
||||
Ave neighs/atom = 14.0685
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:20
|
||||
118
examples/kim/log.7Aug19.in.kim-pm.melt.clang.1
Normal file
118
examples/kim/log.7Aug19.in.kim-pm.melt.clang.1
Normal file
@ -0,0 +1,118 @@
|
||||
LAMMPS (7 Aug 2019)
|
||||
# 3d Lennard-Jones melt
|
||||
#
|
||||
# This example requires that the KIM Portable Model (PM)
|
||||
# SW_StillingerWeber_1985_Si__MO_405512056662_005
|
||||
# is installed. This can be done with the command
|
||||
# kim-api-collections-management install user SW_StillingerWeber_1985_Si__MO_405512056662_005
|
||||
# If this command does not work, you may need to setup your PATH to find the utility.
|
||||
# If you installed the kim-api using the LAMMPS CMake build, you can do the following
|
||||
# (where the current working directory is assumed to be the LAMMPS build directory)
|
||||
# source ./kim_build-prefix/bin/kim-api-activate
|
||||
# If you installed the kim-api using the LAMMPS Make build, you can do the following
|
||||
# (where the current working directory is assumed to be the LAMMPS src directory)
|
||||
# source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate
|
||||
# (where you should relplace X.Y.Z with the appropriate kim-api version number).
|
||||
#
|
||||
# Or, see https://openkim.org/doc/obtaining-models for alternative options.
|
||||
#
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable xx equal 20*$x
|
||||
variable xx equal 20*1
|
||||
variable yy equal 20*$y
|
||||
variable yy equal 20*1
|
||||
variable zz equal 20*$z
|
||||
variable zz equal 20*1
|
||||
|
||||
kim_init SW_StillingerWeber_1985_Si__MO_405512056662_005 real
|
||||
#=== BEGIN kim-init ==========================================
|
||||
units real
|
||||
#=== END kim-init ============================================
|
||||
|
||||
|
||||
lattice fcc 4.4300
|
||||
Lattice spacing in x,y,z = 4.43 4.43 4.43
|
||||
region box block 0 ${xx} 0 ${yy} 0 ${zz}
|
||||
region box block 0 20 0 ${yy} 0 ${zz}
|
||||
region box block 0 20 0 20 0 ${zz}
|
||||
region box block 0 20 0 20 0 20
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 32000 atoms
|
||||
create_atoms CPU = 0.003591 secs
|
||||
|
||||
kim_interactions Si
|
||||
#=== BEGIN kim_interactions ==================================
|
||||
pair_style kim SW_StillingerWeber_1985_Si__MO_405512056662_005
|
||||
pair_coeff * * Si
|
||||
#=== END kim_interactions ====================================
|
||||
|
||||
|
||||
mass 1 39.95
|
||||
velocity all create 200.0 232345 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
|
||||
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.07118
|
||||
ghost atom cutoff = 4.07118
|
||||
binsize = 2.03559, bins = 44 44 44
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair kim, perpetual
|
||||
attributes: full, newton off, cut 4.07118
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Setting up Verlet run ...
|
||||
Unit style : real
|
||||
Current step : 0
|
||||
Time step : 1
|
||||
Per MPI rank memory allocation (min/avg/max) = 10.44 | 10.44 | 10.44 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 200 -85249.847 0 -66173.259 -33302.387
|
||||
100 253.43357 -90346.68 0 -66173.441 -14888.698
|
||||
Loop time of 74.248 on 1 procs for 100 steps with 32000 atoms
|
||||
|
||||
Performance: 0.116 ns/day, 206.244 hours/ns, 1.347 timesteps/s
|
||||
98.8% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 74.118 | 74.118 | 74.118 | 0.0 | 99.83
|
||||
Neigh | 0.069623 | 0.069623 | 0.069623 | 0.0 | 0.09
|
||||
Comm | 0.0137 | 0.0137 | 0.0137 | 0.0 | 0.02
|
||||
Output | 7.6e-05 | 7.6e-05 | 7.6e-05 | 0.0 | 0.00
|
||||
Modify | 0.031883 | 0.031883 | 0.031883 | 0.0 | 0.04
|
||||
Other | | 0.01433 | | | 0.02
|
||||
|
||||
Nlocal: 32000 ave 32000 max 32000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 7760 ave 7760 max 7760 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: 402352 ave 402352 max 402352 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 402352
|
||||
Ave neighs/atom = 12.5735
|
||||
Neighbor list builds = 4
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:01:14
|
||||
118
examples/kim/log.7Aug19.in.kim-pm.melt.clang.4
Normal file
118
examples/kim/log.7Aug19.in.kim-pm.melt.clang.4
Normal file
@ -0,0 +1,118 @@
|
||||
LAMMPS (7 Aug 2019)
|
||||
# 3d Lennard-Jones melt
|
||||
#
|
||||
# This example requires that the KIM Portable Model (PM)
|
||||
# SW_StillingerWeber_1985_Si__MO_405512056662_005
|
||||
# is installed. This can be done with the command
|
||||
# kim-api-collections-management install user SW_StillingerWeber_1985_Si__MO_405512056662_005
|
||||
# If this command does not work, you may need to setup your PATH to find the utility.
|
||||
# If you installed the kim-api using the LAMMPS CMake build, you can do the following
|
||||
# (where the current working directory is assumed to be the LAMMPS build directory)
|
||||
# source ./kim_build-prefix/bin/kim-api-activate
|
||||
# If you installed the kim-api using the LAMMPS Make build, you can do the following
|
||||
# (where the current working directory is assumed to be the LAMMPS src directory)
|
||||
# source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate
|
||||
# (where you should relplace X.Y.Z with the appropriate kim-api version number).
|
||||
#
|
||||
# Or, see https://openkim.org/doc/obtaining-models for alternative options.
|
||||
#
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable xx equal 20*$x
|
||||
variable xx equal 20*1
|
||||
variable yy equal 20*$y
|
||||
variable yy equal 20*1
|
||||
variable zz equal 20*$z
|
||||
variable zz equal 20*1
|
||||
|
||||
kim_init SW_StillingerWeber_1985_Si__MO_405512056662_005 real
|
||||
#=== BEGIN kim-init ==========================================
|
||||
units real
|
||||
#=== END kim-init ============================================
|
||||
|
||||
|
||||
lattice fcc 4.4300
|
||||
Lattice spacing in x,y,z = 4.43 4.43 4.43
|
||||
region box block 0 ${xx} 0 ${yy} 0 ${zz}
|
||||
region box block 0 20 0 ${yy} 0 ${zz}
|
||||
region box block 0 20 0 20 0 ${zz}
|
||||
region box block 0 20 0 20 0 20
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 32000 atoms
|
||||
create_atoms CPU = 0.000997 secs
|
||||
|
||||
kim_interactions Si
|
||||
#=== BEGIN kim_interactions ==================================
|
||||
pair_style kim SW_StillingerWeber_1985_Si__MO_405512056662_005
|
||||
pair_coeff * * Si
|
||||
#=== END kim_interactions ====================================
|
||||
|
||||
|
||||
mass 1 39.95
|
||||
velocity all create 200.0 232345 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
|
||||
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.07118
|
||||
ghost atom cutoff = 4.07118
|
||||
binsize = 2.03559, bins = 44 44 44
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair kim, perpetual
|
||||
attributes: full, newton off, cut 4.07118
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Setting up Verlet run ...
|
||||
Unit style : real
|
||||
Current step : 0
|
||||
Time step : 1
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.517 | 3.517 | 3.517 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 200 -85249.847 0 -66173.259 -33302.387
|
||||
100 253.43357 -90346.68 0 -66173.441 -14888.698
|
||||
Loop time of 19.0287 on 4 procs for 100 steps with 32000 atoms
|
||||
|
||||
Performance: 0.454 ns/day, 52.857 hours/ns, 5.255 timesteps/s
|
||||
99.1% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 18.81 | 18.838 | 18.883 | 0.6 | 99.00
|
||||
Neigh | 0.018598 | 0.01914 | 0.020732 | 0.7 | 0.10
|
||||
Comm | 0.10341 | 0.1475 | 0.17393 | 7.1 | 0.78
|
||||
Output | 6e-05 | 6.225e-05 | 6.7e-05 | 0.0 | 0.00
|
||||
Modify | 0.014839 | 0.014925 | 0.015047 | 0.1 | 0.08
|
||||
Other | | 0.008997 | | | 0.05
|
||||
|
||||
Nlocal: 8000 ave 8014 max 7988 min
|
||||
Histogram: 1 1 0 0 0 0 1 0 0 1
|
||||
Nghost: 3374.75 ave 3389 max 3361 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 100588 ave 100856 max 100392 min
|
||||
Histogram: 1 0 1 0 1 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 402352
|
||||
Ave neighs/atom = 12.5735
|
||||
Neighbor list builds = 4
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:19
|
||||
71
examples/kim/log.7Aug19.in.kim-sm.melt.clang.1
Normal file
71
examples/kim/log.7Aug19.in.kim-sm.melt.clang.1
Normal file
@ -0,0 +1,71 @@
|
||||
LAMMPS (7 Aug 2019)
|
||||
# 3d Lennard-Jones melt
|
||||
#
|
||||
# This example requires that the KIM Simulator Model (PM)
|
||||
# Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000
|
||||
# is installed. This can be done with the command
|
||||
# kim-api-collections-management install user Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000
|
||||
# If this command does not work, you may need to setup your PATH to find the utility.
|
||||
# If you installed the kim-api using the LAMMPS CMake build, you can do the following
|
||||
# (where the current working directory is assumed to be the LAMMPS build directory)
|
||||
# source ./kim_build-prefix/bin/kim-api-activate
|
||||
# If you installed the kim-api using the LAMMPS Make build, you can do the following
|
||||
# (where the current working directory is assumed to be the LAMMPS src directory)
|
||||
# source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate
|
||||
# (where you should relplace X.Y.Z with the appropriate kim-api version number).
|
||||
#
|
||||
# See https://openkim.org/doc/obtaining-models for alternative options.
|
||||
#
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable xx equal 20*$x
|
||||
variable xx equal 20*1
|
||||
variable yy equal 20*$y
|
||||
variable yy equal 20*1
|
||||
variable zz equal 20*$z
|
||||
variable zz equal 20*1
|
||||
|
||||
kim_init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 real
|
||||
#=== BEGIN kim-init ==========================================
|
||||
# Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000
|
||||
# For Simulator : LAMMPS 28 Feb 2019
|
||||
# Running on : LAMMPS 7 Aug 2019
|
||||
#
|
||||
units real
|
||||
atom_style charge
|
||||
neigh_modify one 4000
|
||||
#=== END kim-init ============================================
|
||||
|
||||
|
||||
lattice fcc 4.4300
|
||||
Lattice spacing in x,y,z = 4.43 4.43 4.43
|
||||
region box block 0 ${xx} 0 ${yy} 0 ${zz}
|
||||
region box block 0 20 0 ${yy} 0 ${zz}
|
||||
region box block 0 20 0 20 0 ${zz}
|
||||
region box block 0 20 0 20 0 20
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 32000 atoms
|
||||
create_atoms CPU = 0.003447 secs
|
||||
|
||||
kim_interactions O
|
||||
#=== BEGIN kim_interactions ==================================
|
||||
pair_style reax/c /var/tmp/kim-simulator-model-parameter-file-directory-6Acs1QDbXgBx/lmp_control safezone 2.0 mincap 100
|
||||
ERROR: Unrecognized pair style 'reax/c' is part of the USER-REAXC package which is not enabled in this LAMMPS binary. (../force.cpp:262)
|
||||
Last command: pair_style reax/c /var/tmp/kim-simulator-model-parameter-file-directory-6Acs1QDbXgBx/lmp_control safezone 2.0 mincap 100
|
||||
--------------------------------------------------------------------------
|
||||
Primary job terminated normally, but 1 process returned
|
||||
a non-zero exit code. Per user-direction, the job has been aborted.
|
||||
--------------------------------------------------------------------------
|
||||
--------------------------------------------------------------------------
|
||||
mpirun detected that one or more processes exited with non-zero status, thus causing
|
||||
the job to be terminated. The first process to do so was:
|
||||
|
||||
Process name: [[33054,1],0]
|
||||
Exit code: 1
|
||||
--------------------------------------------------------------------------
|
||||
60
examples/kim/log.7Aug19.in.kim-sm.melt.clang.4
Normal file
60
examples/kim/log.7Aug19.in.kim-sm.melt.clang.4
Normal file
@ -0,0 +1,60 @@
|
||||
LAMMPS (7 Aug 2019)
|
||||
# 3d Lennard-Jones melt
|
||||
#
|
||||
# This example requires that the KIM Simulator Model (PM)
|
||||
# Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000
|
||||
# is installed. This can be done with the command
|
||||
# kim-api-collections-management install user Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000
|
||||
# If this command does not work, you may need to setup your PATH to find the utility.
|
||||
# If you installed the kim-api using the LAMMPS CMake build, you can do the following
|
||||
# (where the current working directory is assumed to be the LAMMPS build directory)
|
||||
# source ./kim_build-prefix/bin/kim-api-activate
|
||||
# If you installed the kim-api using the LAMMPS Make build, you can do the following
|
||||
# (where the current working directory is assumed to be the LAMMPS src directory)
|
||||
# source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate
|
||||
# (where you should relplace X.Y.Z with the appropriate kim-api version number).
|
||||
#
|
||||
# See https://openkim.org/doc/obtaining-models for alternative options.
|
||||
#
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable xx equal 20*$x
|
||||
variable xx equal 20*1
|
||||
variable yy equal 20*$y
|
||||
variable yy equal 20*1
|
||||
variable zz equal 20*$z
|
||||
variable zz equal 20*1
|
||||
|
||||
kim_init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 real
|
||||
#=== BEGIN kim-init ==========================================
|
||||
# Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000
|
||||
# For Simulator : LAMMPS 28 Feb 2019
|
||||
# Running on : LAMMPS 7 Aug 2019
|
||||
#
|
||||
units real
|
||||
atom_style charge
|
||||
neigh_modify one 4000
|
||||
#=== END kim-init ============================================
|
||||
|
||||
|
||||
lattice fcc 4.4300
|
||||
Lattice spacing in x,y,z = 4.43 4.43 4.43
|
||||
region box block 0 ${xx} 0 ${yy} 0 ${zz}
|
||||
region box block 0 20 0 ${yy} 0 ${zz}
|
||||
region box block 0 20 0 20 0 ${zz}
|
||||
region box block 0 20 0 20 0 20
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 32000 atoms
|
||||
create_atoms CPU = 0.001307 secs
|
||||
|
||||
kim_interactions O
|
||||
#=== BEGIN kim_interactions ==================================
|
||||
pair_style reax/c /var/tmp/kim-simulator-model-parameter-file-directory-6tmKtZEXzhgv/lmp_control safezone 2.0 mincap 100
|
||||
ERROR: Unrecognized pair style 'reax/c' is part of the USER-REAXC package which is not enabled in this LAMMPS binary. (../force.cpp:262)
|
||||
Last command: pair_style reax/c /var/tmp/kim-simulator-model-parameter-file-directory-6tmKtZEXzhgv/lmp_control safezone 2.0 mincap 100
|
||||
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user