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update log files for dipole and dreiding example inputs. add running some MD steps for dreiding

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This commit is contained in:
Axel Kohlmeyer
2018-11-28 16:07:12 -05:00
parent 3ce61c42d6
commit 37289f7476
7 changed files with 459 additions and 281 deletions
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35
examples/dipole/log.5Oct16.dipole.g++.1 → examples/dipole/log.27Nov18.dipole.g++.1
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@ -1,4 +1,5 @@
LAMMPS (5 Oct 2016)
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# Point dipoles in a 2d box
units lj
@ -13,6 +14,7 @@ Created orthogonal box = (0 0 -0.845154) to (16.9031 16.9031 0.845154)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 200 atoms
Time spent = 0.00140882 secs
# need both mass settings due to hybrid atom style
@ -46,13 +48,18 @@ thermo 500
run 10000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4 -> bins = 13 13 2
Memory usage per processor = 4.47689 Mbytes
binsize = 1.4, bins = 13 13 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut/dipole/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.049 | 5.049 | 5.049 Mbytes
Step Temp E_pair c_erot TotEng Press
0 0 -2.1909822 0 -2.1909822 -2.5750971
500 0.39335419 -2.7940623 0.20683255 -2.4026749 -0.24768899
@ -75,20 +82,20 @@ Step Temp E_pair c_erot TotEng Press
9000 0.42532413 -2.748856 0.21378021 -2.3256584 0.015079949
9500 0.42237159 -2.7266142 0.20255034 -2.3063545 -0.15538561
10000 0.40758268 -2.778401 0.2746675 -2.3728562 -0.20811978
Loop time of 1.05484 on 1 procs for 10000 steps with 200 atoms
Loop time of 0.851938 on 1 procs for 10000 steps with 200 atoms
Performance: 4095400.088 tau/day, 9480.093 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 5070791.481 tau/day, 11737.943 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 | 0.88325 | 0.88325 | 0.88325 | 0.0 | 83.73
Neigh | 0.038596 | 0.038596 | 0.038596 | 0.0 | 3.66
Comm | 0.034257 | 0.034257 | 0.034257 | 0.0 | 3.25
Output | 0.00013828 | 0.00013828 | 0.00013828 | 0.0 | 0.01
Modify | 0.083041 | 0.083041 | 0.083041 | 0.0 | 7.87
Other | | 0.01556 | | | 1.48
Pair | 0.64889 | 0.64889 | 0.64889 | 0.0 | 76.17
Neigh | 0.04038 | 0.04038 | 0.04038 | 0.0 | 4.74
Comm | 0.058003 | 0.058003 | 0.058003 | 0.0 | 6.81
Output | 0.00021219 | 0.00021219 | 0.00021219 | 0.0 | 0.02
Modify | 0.083454 | 0.083454 | 0.083454 | 0.0 | 9.80
Other | | 0.021 | | | 2.47
Nlocal: 200 ave 200 max 200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -101,4 +108,4 @@ Total # of neighbors = 1625
Ave neighs/atom = 8.125
Neighbor list builds = 673
Dangerous builds = 0
Total wall time: 0:00:01
Total wall time: 0:00:00

33
examples/dipole/log.5Oct16.dipole.g++.4 → examples/dipole/log.27Nov18.dipole.g++.4
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@ -1,4 +1,5 @@
LAMMPS (5 Oct 2016)
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# Point dipoles in a 2d box
units lj
@ -13,6 +14,7 @@ Created orthogonal box = (0 0 -0.845154) to (16.9031 16.9031 0.845154)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 200 atoms
Time spent = 0.00139761 secs
# need both mass settings due to hybrid atom style
@ -46,13 +48,18 @@ thermo 500
run 10000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4 -> bins = 13 13 2
Memory usage per processor = 4.47621 Mbytes
binsize = 1.4, bins = 13 13 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut/dipole/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.047 | 5.047 | 5.047 Mbytes
Step Temp E_pair c_erot TotEng Press
0 0 -2.1909822 0 -2.1909822 -2.5750971
500 0.39335419 -2.7940623 0.20683255 -2.4026749 -0.24768899
@ -75,20 +82,20 @@ Step Temp E_pair c_erot TotEng Press
9000 0.42318631 -2.7600929 0.25229644 -2.3390225 0.36820391
9500 0.42857449 -2.6958592 0.18686752 -2.2694276 0.15379721
10000 0.43323126 -2.71981 0.22185737 -2.2887449 0.038354509
Loop time of 0.406978 on 4 procs for 10000 steps with 200 atoms
Loop time of 0.396069 on 4 procs for 10000 steps with 200 atoms
Performance: 10614834.981 tau/day, 24571.377 timesteps/s
99.5% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 10907185.759 tau/day, 25248.115 timesteps/s
96.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.18518 | 0.23558 | 0.25487 | 6.0 | 57.88
Neigh | 0.0090437 | 0.011033 | 0.011971 | 1.1 | 2.71
Comm | 0.086857 | 0.10807 | 0.16262 | 9.6 | 26.56
Output | 0.00029182 | 0.00031263 | 0.00035739 | 0.1 | 0.08
Modify | 0.022396 | 0.025649 | 0.026865 | 1.2 | 6.30
Other | | 0.02633 | | | 6.47
Pair | 0.13746 | 0.17338 | 0.19067 | 5.1 | 43.77
Neigh | 0.0096052 | 0.011424 | 0.012275 | 1.0 | 2.88
Comm | 0.12394 | 0.14718 | 0.1914 | 7.1 | 37.16
Output | 0.00037861 | 0.00056618 | 0.0011225 | 0.0 | 0.14
Modify | 0.021838 | 0.024665 | 0.026625 | 1.1 | 6.23
Other | | 0.03886 | | | 9.81
Nlocal: 50 ave 53 max 41 min
Histogram: 1 0 0 0 0 0 0 0 0 3

40
examples/dreiding/in.dreiding
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@ -2,28 +2,28 @@ units real
atom_style full
boundary p p p
dielectric 1
special_bonds lj/coul 0.0 0.0 1.0
special_bonds lj/coul 0.0 0.0 1.0
pair_style hybrid/overlay hbond/dreiding/lj 2 6 6.5 90 lj/cut/coul/long 8.50000 11.5
bond_style harmonic
angle_style harmonic
bond_style harmonic
angle_style harmonic
dihedral_style harmonic
improper_style none
kspace_style pppm 0.001
kspace_style pppm 0.001
read_data data.dreiding
pair_coeff 1 1 lj/cut/coul/long 0.015200000256300 2.846421344984478
pair_coeff 1 2 lj/cut/coul/long 0.001232882795416 2.846421344984478
pair_coeff 1 3 lj/cut/coul/long 0.038019995160237 3.159705878878677
pair_coeff 1 4 lj/cut/coul/long 0.038139744011598 2.939787518071103
pair_coeff 2 2 lj/cut/coul/long 9.99999974737875e-05 2.846421344984478
pair_coeff 2 3 lj/cut/coul/long 0.003083828758188 3.159705878878677
pair_coeff 2 4 lj/cut/coul/long 0.003093541672406 2.939787518071103
pair_coeff 3 3 lj/cut/coul/long 0.095100000500679 3.472990412772877
pair_coeff 3 4 lj/cut/coul/long 0.095399530150179 3.253072051965302
pair_coeff 4 4 lj/cut/coul/long 0.095700003206730 3.033153691157727
pair_coeff 4 4 hbond/dreiding/lj 2 i 0.4000E+01 2.750000000000000 4
pair_coeff 1 1 lj/cut/coul/long 0.015200000256300 2.846421344984478
pair_coeff 1 2 lj/cut/coul/long 0.001232882795416 2.846421344984478
pair_coeff 1 3 lj/cut/coul/long 0.038019995160237 3.159705878878677
pair_coeff 1 4 lj/cut/coul/long 0.038139744011598 2.939787518071103
pair_coeff 2 2 lj/cut/coul/long 9.99999974737875e-05 2.846421344984478
pair_coeff 2 3 lj/cut/coul/long 0.003083828758188 3.159705878878677
pair_coeff 2 4 lj/cut/coul/long 0.003093541672406 2.939787518071103
pair_coeff 3 3 lj/cut/coul/long 0.095100000500679 3.472990412772877
pair_coeff 3 4 lj/cut/coul/long 0.095399530150179 3.253072051965302
pair_coeff 4 4 lj/cut/coul/long 0.095700003206730 3.033153691157727
pair_coeff 4 4 hbond/dreiding/lj 2 i 4.000 2.750000000000000 4
pair_modify mix arithmetic
neighbor 2.0 multi
neigh_modify every 2 delay 4 check yes
@ -33,7 +33,11 @@ variable sname index ch3oh.box.dreiding
compute hb all pair hbond/dreiding/lj
variable C_hbond equal c_hb[1] #number hbonds
variable E_hbond equal c_hb[2] #hbond energy
thermo_style custom etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong v_E_hbond v_C_hbond press vol
thermo_modify line multi format float %14.6f
thermo_style custom etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong v_E_hbond v_C_hbond press vol
thermo_modify line multi format float %14.6f
run 0
fix 1 all nve
thermo 10
run 100

198
examples/dreiding/log.27Nov18.dreiding.g++.1 Normal file
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@ -0,0 +1,198 @@
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
units real
atom_style full
boundary p p p
dielectric 1
special_bonds lj/coul 0.0 0.0 1.0
pair_style hybrid/overlay hbond/dreiding/lj 2 6 6.5 90 lj/cut/coul/long 8.50000 11.5
bond_style harmonic
angle_style harmonic
dihedral_style harmonic
improper_style none
kspace_style pppm 0.001
read_data data.dreiding
orthogonal box = (0 0 0) to (19.9969 19.1282 19.4697)
1 by 1 by 1 MPI processor grid
reading atoms ...
384 atoms
scanning bonds ...
4 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
3 = max dihedrals/atom
reading bonds ...
320 bonds
reading angles ...
448 angles
reading dihedrals ...
192 dihedrals
4 = max # of 1-2 neighbors
3 = max # of 1-3 neighbors
5 = max # of special neighbors
pair_coeff 1 1 lj/cut/coul/long 0.015200000256300 2.846421344984478
pair_coeff 1 2 lj/cut/coul/long 0.001232882795416 2.846421344984478
pair_coeff 1 3 lj/cut/coul/long 0.038019995160237 3.159705878878677
pair_coeff 1 4 lj/cut/coul/long 0.038139744011598 2.939787518071103
pair_coeff 2 2 lj/cut/coul/long 9.99999974737875e-05 2.846421344984478
pair_coeff 2 3 lj/cut/coul/long 0.003083828758188 3.159705878878677
pair_coeff 2 4 lj/cut/coul/long 0.003093541672406 2.939787518071103
pair_coeff 3 3 lj/cut/coul/long 0.095100000500679 3.472990412772877
pair_coeff 3 4 lj/cut/coul/long 0.095399530150179 3.253072051965302
pair_coeff 4 4 lj/cut/coul/long 0.095700003206730 3.033153691157727
pair_coeff 4 4 hbond/dreiding/lj 2 i 4.000 2.750000000000000 4
pair_modify mix arithmetic
neighbor 2.0 multi
neigh_modify every 2 delay 4 check yes
variable input index in.ch3oh.box.dreiding
variable sname index ch3oh.box.dreiding
compute hb all pair hbond/dreiding/lj
variable C_hbond equal c_hb[1] #number hbonds
variable E_hbond equal c_hb[2] #hbond energy
thermo_style custom etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong v_E_hbond v_C_hbond press vol
thermo_modify line multi format float %14.6f
fix 1 all nve
thermo 10
run 100
PPPM initialization ...
WARNING: System is not charge neutral, net charge = -0.00064 (src/kspace.cpp:302)
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
G vector (1/distance) = 0.142073
grid = 3 3 3
stencil order = 5
estimated absolute RMS force accuracy = 0.154715
estimated relative force accuracy = 0.00046592
using double precision FFTs
3d grid and FFT values/proc = 512 27
Neighbor list info ...
update every 2 steps, delay 4 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 13.5
ghost atom cutoff = 13.5
binsize = 6.75, bins = 3 3 3
3 neighbor lists, perpetual/occasional/extra = 3 0 0
(1) pair hbond/dreiding/lj, perpetual, skip from (3)
attributes: full, newton on
pair build: skip
stencil: none
bin: none
(2) pair lj/cut/coul/long, perpetual, half/full from (3)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
(3) neighbor class addition, perpetual
attributes: full, newton on
pair build: full/multi
stencil: full/multi/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 11.47 | 11.47 | 11.47 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = 113.723601 KinEng = 0.000000 Temp = 0.000000
PotEng = 113.723601 E_bond = 0.535673 E_angle = 1.281880
E_dihed = 1.232497 E_impro = 0.000000 E_vdwl = -125.381324
E_coul = 597.219740 E_long = -361.164864 v_E_hbond = -69.322152
v_C_hbond = 235.000000 Press = -328.847347 Volume = 7447.236335
---------------- Step 10 ----- CPU = 0.0306 (sec) ----------------
TotEng = 113.773202 KinEng = 1.537257 Temp = 1.346522
PotEng = 112.235945 E_bond = 0.530880 E_angle = 1.407481
E_dihed = 1.084172 E_impro = 0.000000 E_vdwl = -126.339883
E_coul = 596.742306 E_long = -361.189011 v_E_hbond = -69.944278
v_C_hbond = 240.000000 Press = -395.900496 Volume = 7447.236335
---------------- Step 20 ----- CPU = 0.0597 (sec) ----------------
TotEng = 113.879292 KinEng = 2.999580 Temp = 2.627407
PotEng = 110.879711 E_bond = 0.549156 E_angle = 1.323582
E_dihed = 1.357398 E_impro = 0.000000 E_vdwl = -127.482103
E_coul = 596.318729 E_long = -361.187051 v_E_hbond = -70.088343
v_C_hbond = 237.000000 Press = -487.150418 Volume = 7447.236335
---------------- Step 30 ----- CPU = 0.0889 (sec) ----------------
TotEng = 113.587474 KinEng = 4.369566 Temp = 3.827412
PotEng = 109.217908 E_bond = 0.416485 E_angle = 1.294630
E_dihed = 1.710254 E_impro = 0.000000 E_vdwl = -128.565697
E_coul = 595.560846 E_long = -361.198612 v_E_hbond = -69.848068
v_C_hbond = 238.000000 Press = -423.966898 Volume = 7447.236335
---------------- Step 40 ----- CPU = 0.1178 (sec) ----------------
TotEng = 113.915503 KinEng = 6.466349 Temp = 5.664037
PotEng = 107.449154 E_bond = 0.514530 E_angle = 1.342583
E_dihed = 1.536929 E_impro = 0.000000 E_vdwl = -129.858713
E_coul = 595.186400 E_long = -361.272576 v_E_hbond = -69.871393
v_C_hbond = 237.000000 Press = -498.152652 Volume = 7447.236335
---------------- Step 50 ----- CPU = 0.1467 (sec) ----------------
TotEng = 113.787839 KinEng = 8.050614 Temp = 7.051734
PotEng = 105.737226 E_bond = 0.652153 E_angle = 1.416041
E_dihed = 1.363560 E_impro = 0.000000 E_vdwl = -130.513518
E_coul = 594.139769 E_long = -361.320780 v_E_hbond = -69.593967
v_C_hbond = 233.000000 Press = -557.299799 Volume = 7447.236335
---------------- Step 60 ----- CPU = 0.1755 (sec) ----------------
TotEng = 114.120941 KinEng = 10.318793 Temp = 9.038489
PotEng = 103.802148 E_bond = 0.576578 E_angle = 1.285008
E_dihed = 1.123936 E_impro = 0.000000 E_vdwl = -131.268312
E_coul = 593.450009 E_long = -361.365070 v_E_hbond = -70.107165
v_C_hbond = 238.000000 Press = -571.907188 Volume = 7447.236335
---------------- Step 70 ----- CPU = 0.2044 (sec) ----------------
TotEng = 113.836161 KinEng = 11.873184 Temp = 10.400019
PotEng = 101.962977 E_bond = 0.633521 E_angle = 1.315999
E_dihed = 1.055318 E_impro = 0.000000 E_vdwl = -131.673572
E_coul = 592.039194 E_long = -361.407483 v_E_hbond = -70.518544
v_C_hbond = 240.000000 Press = -576.731444 Volume = 7447.236335
---------------- Step 80 ----- CPU = 0.2333 (sec) ----------------
TotEng = 113.589436 KinEng = 13.546467 Temp = 11.865689
PotEng = 100.042970 E_bond = 0.637759 E_angle = 1.439918
E_dihed = 1.020307 E_impro = 0.000000 E_vdwl = -131.980346
E_coul = 590.365879 E_long = -361.440548 v_E_hbond = -71.174370
v_C_hbond = 245.000000 Press = -735.254308 Volume = 7447.236335
---------------- Step 90 ----- CPU = 0.2622 (sec) ----------------
TotEng = 114.100567 KinEng = 15.870735 Temp = 13.901574
PotEng = 98.229832 E_bond = 0.724671 E_angle = 1.435914
E_dihed = 1.028167 E_impro = 0.000000 E_vdwl = -132.680267
E_coul = 589.225626 E_long = -361.504279 v_E_hbond = -72.653223
v_C_hbond = 245.000000 Press = -820.598954 Volume = 7447.236335
---------------- Step 100 ----- CPU = 0.2911 (sec) ----------------
TotEng = 113.670041 KinEng = 17.406803 Temp = 15.247054
PotEng = 96.263238 E_bond = 0.711253 E_angle = 1.338059
E_dihed = 1.474770 E_impro = 0.000000 E_vdwl = -132.917719
E_coul = 587.219020 E_long = -361.562145 v_E_hbond = -74.299795
v_C_hbond = 246.000000 Press = -786.245946 Volume = 7447.236335
Loop time of 0.291149 on 1 procs for 100 steps with 384 atoms
Performance: 29.676 ns/day, 0.809 hours/ns, 343.467 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 | 0.255 | 0.255 | 0.255 | 0.0 | 87.59
Bond | 0.0042725 | 0.0042725 | 0.0042725 | 0.0 | 1.47
Kspace | 0.027151 | 0.027151 | 0.027151 | 0.0 | 9.33
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0034399 | 0.0034399 | 0.0034399 | 0.0 | 1.18
Output | 0.00025988 | 0.00025988 | 0.00025988 | 0.0 | 0.09
Modify | 0.00059223 | 0.00059223 | 0.00059223 | 0.0 | 0.20
Other | | 0.0004294 | | | 0.15
Nlocal: 384 ave 384 max 384 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4637 ave 4637 max 4637 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 101854 ave 101854 max 101854 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 5624 ave 5624 max 5624 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 101854
Ave neighs/atom = 265.245
Ave special neighs/atom = 4
Neighbor list builds = 0
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:00

198
examples/dreiding/log.27Nov18.dreiding.g++.4 Normal file
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@ -0,0 +1,198 @@
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
units real
atom_style full
boundary p p p
dielectric 1
special_bonds lj/coul 0.0 0.0 1.0
pair_style hybrid/overlay hbond/dreiding/lj 2 6 6.5 90 lj/cut/coul/long 8.50000 11.5
bond_style harmonic
angle_style harmonic
dihedral_style harmonic
improper_style none
kspace_style pppm 0.001
read_data data.dreiding
orthogonal box = (0 0 0) to (19.9969 19.1282 19.4697)
2 by 1 by 2 MPI processor grid
reading atoms ...
384 atoms
scanning bonds ...
4 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
3 = max dihedrals/atom
reading bonds ...
320 bonds
reading angles ...
448 angles
reading dihedrals ...
192 dihedrals
4 = max # of 1-2 neighbors
3 = max # of 1-3 neighbors
5 = max # of special neighbors
pair_coeff 1 1 lj/cut/coul/long 0.015200000256300 2.846421344984478
pair_coeff 1 2 lj/cut/coul/long 0.001232882795416 2.846421344984478
pair_coeff 1 3 lj/cut/coul/long 0.038019995160237 3.159705878878677
pair_coeff 1 4 lj/cut/coul/long 0.038139744011598 2.939787518071103
pair_coeff 2 2 lj/cut/coul/long 9.99999974737875e-05 2.846421344984478
pair_coeff 2 3 lj/cut/coul/long 0.003083828758188 3.159705878878677
pair_coeff 2 4 lj/cut/coul/long 0.003093541672406 2.939787518071103
pair_coeff 3 3 lj/cut/coul/long 0.095100000500679 3.472990412772877
pair_coeff 3 4 lj/cut/coul/long 0.095399530150179 3.253072051965302
pair_coeff 4 4 lj/cut/coul/long 0.095700003206730 3.033153691157727
pair_coeff 4 4 hbond/dreiding/lj 2 i 4.000 2.750000000000000 4
pair_modify mix arithmetic
neighbor 2.0 multi
neigh_modify every 2 delay 4 check yes
variable input index in.ch3oh.box.dreiding
variable sname index ch3oh.box.dreiding
compute hb all pair hbond/dreiding/lj
variable C_hbond equal c_hb[1] #number hbonds
variable E_hbond equal c_hb[2] #hbond energy
thermo_style custom etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong v_E_hbond v_C_hbond press vol
thermo_modify line multi format float %14.6f
fix 1 all nve
thermo 10
run 100
PPPM initialization ...
WARNING: System is not charge neutral, net charge = -0.00064 (src/kspace.cpp:302)
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
G vector (1/distance) = 0.142073
grid = 3 3 3
stencil order = 5
estimated absolute RMS force accuracy = 0.154715
estimated relative force accuracy = 0.00046592
using double precision FFTs
3d grid and FFT values/proc = 392 12
Neighbor list info ...
update every 2 steps, delay 4 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 13.5
ghost atom cutoff = 13.5
binsize = 6.75, bins = 3 3 3
3 neighbor lists, perpetual/occasional/extra = 3 0 0
(1) pair hbond/dreiding/lj, perpetual, skip from (3)
attributes: full, newton on
pair build: skip
stencil: none
bin: none
(2) pair lj/cut/coul/long, perpetual, half/full from (3)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
(3) neighbor class addition, perpetual
attributes: full, newton on
pair build: full/multi
stencil: full/multi/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 10.17 | 10.17 | 10.17 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = 113.723601 KinEng = 0.000000 Temp = 0.000000
PotEng = 113.723601 E_bond = 0.535673 E_angle = 1.281880
E_dihed = 1.232497 E_impro = 0.000000 E_vdwl = -125.381324
E_coul = 597.219740 E_long = -361.164864 v_E_hbond = -69.322152
v_C_hbond = 235.000000 Press = -328.847347 Volume = 7447.236335
---------------- Step 10 ----- CPU = 0.0112 (sec) ----------------
TotEng = 113.773202 KinEng = 1.537257 Temp = 1.346522
PotEng = 112.235945 E_bond = 0.530880 E_angle = 1.407481
E_dihed = 1.084172 E_impro = 0.000000 E_vdwl = -126.339883
E_coul = 596.742306 E_long = -361.189011 v_E_hbond = -69.944278
v_C_hbond = 240.000000 Press = -395.900496 Volume = 7447.236335
---------------- Step 20 ----- CPU = 0.0206 (sec) ----------------
TotEng = 113.879292 KinEng = 2.999580 Temp = 2.627407
PotEng = 110.879711 E_bond = 0.549156 E_angle = 1.323582
E_dihed = 1.357398 E_impro = 0.000000 E_vdwl = -127.482103
E_coul = 596.318729 E_long = -361.187051 v_E_hbond = -70.088343
v_C_hbond = 237.000000 Press = -487.150418 Volume = 7447.236335
---------------- Step 30 ----- CPU = 0.0299 (sec) ----------------
TotEng = 113.587474 KinEng = 4.369566 Temp = 3.827412
PotEng = 109.217908 E_bond = 0.416485 E_angle = 1.294630
E_dihed = 1.710254 E_impro = 0.000000 E_vdwl = -128.565697
E_coul = 595.560846 E_long = -361.198612 v_E_hbond = -69.848068
v_C_hbond = 238.000000 Press = -423.966898 Volume = 7447.236335
---------------- Step 40 ----- CPU = 0.0403 (sec) ----------------
TotEng = 113.915503 KinEng = 6.466349 Temp = 5.664037
PotEng = 107.449154 E_bond = 0.514530 E_angle = 1.342583
E_dihed = 1.536929 E_impro = 0.000000 E_vdwl = -129.858713
E_coul = 595.186400 E_long = -361.272576 v_E_hbond = -69.871393
v_C_hbond = 237.000000 Press = -498.152652 Volume = 7447.236335
---------------- Step 50 ----- CPU = 0.0494 (sec) ----------------
TotEng = 113.787839 KinEng = 8.050614 Temp = 7.051734
PotEng = 105.737226 E_bond = 0.652153 E_angle = 1.416041
E_dihed = 1.363560 E_impro = 0.000000 E_vdwl = -130.513518
E_coul = 594.139769 E_long = -361.320780 v_E_hbond = -69.593967
v_C_hbond = 233.000000 Press = -557.299799 Volume = 7447.236335
---------------- Step 60 ----- CPU = 0.0588 (sec) ----------------
TotEng = 114.120941 KinEng = 10.318793 Temp = 9.038489
PotEng = 103.802148 E_bond = 0.576578 E_angle = 1.285008
E_dihed = 1.123936 E_impro = 0.000000 E_vdwl = -131.268312
E_coul = 593.450009 E_long = -361.365070 v_E_hbond = -70.107165
v_C_hbond = 238.000000 Press = -571.907188 Volume = 7447.236335
---------------- Step 70 ----- CPU = 0.0680 (sec) ----------------
TotEng = 113.836161 KinEng = 11.873184 Temp = 10.400019
PotEng = 101.962977 E_bond = 0.633521 E_angle = 1.315999
E_dihed = 1.055318 E_impro = 0.000000 E_vdwl = -131.673572
E_coul = 592.039194 E_long = -361.407483 v_E_hbond = -70.518544
v_C_hbond = 240.000000 Press = -576.731444 Volume = 7447.236335
---------------- Step 80 ----- CPU = 0.0790 (sec) ----------------
TotEng = 113.589436 KinEng = 13.546467 Temp = 11.865689
PotEng = 100.042970 E_bond = 0.637759 E_angle = 1.439918
E_dihed = 1.020307 E_impro = 0.000000 E_vdwl = -131.980346
E_coul = 590.365879 E_long = -361.440548 v_E_hbond = -71.174370
v_C_hbond = 245.000000 Press = -735.254308 Volume = 7447.236335
---------------- Step 90 ----- CPU = 0.0883 (sec) ----------------
TotEng = 114.100567 KinEng = 15.870735 Temp = 13.901574
PotEng = 98.229832 E_bond = 0.724671 E_angle = 1.435914
E_dihed = 1.028167 E_impro = 0.000000 E_vdwl = -132.680267
E_coul = 589.225626 E_long = -361.504279 v_E_hbond = -72.653223
v_C_hbond = 245.000000 Press = -820.598954 Volume = 7447.236335
---------------- Step 100 ----- CPU = 0.0976 (sec) ----------------
TotEng = 113.670041 KinEng = 17.406803 Temp = 15.247054
PotEng = 96.263238 E_bond = 0.711253 E_angle = 1.338059
E_dihed = 1.474770 E_impro = 0.000000 E_vdwl = -132.917719
E_coul = 587.219020 E_long = -361.562145 v_E_hbond = -74.299795
v_C_hbond = 246.000000 Press = -786.245946 Volume = 7447.236335
Loop time of 0.0976357 on 4 procs for 100 steps with 384 atoms
Performance: 88.492 ns/day, 0.271 hours/ns, 1024.215 timesteps/s
96.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.055383 | 0.065178 | 0.07438 | 2.7 | 66.76
Bond | 0.00099874 | 0.0011503 | 0.001229 | 0.3 | 1.18
Kspace | 0.013823 | 0.022918 | 0.032308 | 4.4 | 23.47
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0064669 | 0.0072899 | 0.0078194 | 0.6 | 7.47
Output | 0.00039268 | 0.00043893 | 0.00056481 | 0.0 | 0.45
Modify | 0.000175 | 0.00019002 | 0.00020623 | 0.0 | 0.19
Other | | 0.0004706 | | | 0.48
Nlocal: 96 ave 104 max 87 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Nghost: 3063.25 ave 3108 max 3024 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Neighs: 25463.5 ave 28799 max 22471 min
Histogram: 1 0 0 1 0 1 0 0 0 1
FullNghs: 1406 ave 1664 max 1237 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Total # of neighbors = 101854
Ave neighs/atom = 265.245
Ave special neighs/atom = 4
Neighbor list builds = 0
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:00

118
examples/dreiding/log.5Oct16.dreiding.g++.1
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@ -1,118 +0,0 @@
LAMMPS (5 Oct 2016)
units real
atom_style full
boundary p p p
dielectric 1
special_bonds lj/coul 0.0 0.0 1.0
pair_style hybrid/overlay hbond/dreiding/lj 2 6 6.5 90 lj/cut/coul/long 8.50000 11.5
bond_style harmonic
angle_style harmonic
dihedral_style harmonic
improper_style none
kspace_style pppm 0.001
read_data data.dreiding
orthogonal box = (0 0 0) to (19.9969 19.1282 19.4697)
1 by 1 by 1 MPI processor grid
reading atoms ...
384 atoms
scanning bonds ...
4 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
3 = max dihedrals/atom
reading bonds ...
320 bonds
reading angles ...
448 angles
reading dihedrals ...
192 dihedrals
4 = max # of 1-2 neighbors
3 = max # of 1-3 neighbors
5 = max # of special neighbors
pair_coeff 1 1 lj/cut/coul/long 0.015200000256300 2.846421344984478
pair_coeff 1 2 lj/cut/coul/long 0.001232882795416 2.846421344984478
pair_coeff 1 3 lj/cut/coul/long 0.038019995160237 3.159705878878677
pair_coeff 1 4 lj/cut/coul/long 0.038139744011598 2.939787518071103
pair_coeff 2 2 lj/cut/coul/long 9.99999974737875e-05 2.846421344984478
pair_coeff 2 3 lj/cut/coul/long 0.003083828758188 3.159705878878677
pair_coeff 2 4 lj/cut/coul/long 0.003093541672406 2.939787518071103
pair_coeff 3 3 lj/cut/coul/long 0.095100000500679 3.472990412772877
pair_coeff 3 4 lj/cut/coul/long 0.095399530150179 3.253072051965302
pair_coeff 4 4 lj/cut/coul/long 0.095700003206730 3.033153691157727
pair_coeff 4 4 hbond/dreiding/lj 2 i 0.4000E+01 2.750000000000000 4
pair_modify mix arithmetic
neighbor 2.0 multi
neigh_modify every 2 delay 4 check yes
variable input index in.ch3oh.box.dreiding
variable sname index ch3oh.box.dreiding
compute hb all pair hbond/dreiding/lj
variable C_hbond equal c_hb[1] #number hbonds
variable E_hbond equal c_hb[2] #hbond energy
thermo_style custom etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong v_E_hbond v_C_hbond press vol
thermo_modify line multi format float %14.6f
run 0
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
PPPM initialization ...
WARNING: System is not charge neutral, net charge = -0.00064 (../kspace.cpp:297)
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316)
G vector (1/distance) = 0.142073
grid = 3 3 3
stencil order = 5
estimated absolute RMS force accuracy = 0.154715
estimated relative force accuracy = 0.00046592
using double precision FFTs
3d grid and FFT values/proc = 512 27
Neighbor list info ...
3 neighbor list requests
update every 2 steps, delay 4 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 13.5
ghost atom cutoff = 13.5
binsize = 6.75 -> bins = 3 3 3
Memory usage per processor = 9.19186 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = 113.723601 KinEng = 0.000000 Temp = 0.000000
PotEng = 113.723601 E_bond = 0.535673 E_angle = 1.281880
E_dihed = 1.232497 E_impro = 0.000000 E_vdwl = -125.381324
E_coul = 597.219740 E_long = -361.164864 v_E_hbond = -69.322152
v_C_hbond = 235.000000 Press = -328.847347 Volume = 7447.236335
Loop time of 9.53674e-07 on 1 procs for 0 steps with 384 atoms
0.0% 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 | 0 | 0 | 0.0 | 0.00
Bond | 0 | 0 | 0 | 0.0 | 0.00
Kspace | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 9.537e-07 | | |100.00
Nlocal: 384 ave 384 max 384 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4637 ave 4637 max 4637 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 101854 ave 101854 max 101854 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 203708 ave 203708 max 203708 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 203708
Ave neighs/atom = 530.49
Ave special neighs/atom = 4
Neighbor list builds = 0
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:00

118
examples/dreiding/log.5Oct16.dreiding.g++.4
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@ -1,118 +0,0 @@
LAMMPS (5 Oct 2016)
units real
atom_style full
boundary p p p
dielectric 1
special_bonds lj/coul 0.0 0.0 1.0
pair_style hybrid/overlay hbond/dreiding/lj 2 6 6.5 90 lj/cut/coul/long 8.50000 11.5
bond_style harmonic
angle_style harmonic
dihedral_style harmonic
improper_style none
kspace_style pppm 0.001
read_data data.dreiding
orthogonal box = (0 0 0) to (19.9969 19.1282 19.4697)
2 by 1 by 2 MPI processor grid
reading atoms ...
384 atoms
scanning bonds ...
4 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
3 = max dihedrals/atom
reading bonds ...
320 bonds
reading angles ...
448 angles
reading dihedrals ...
192 dihedrals
4 = max # of 1-2 neighbors
3 = max # of 1-3 neighbors
5 = max # of special neighbors
pair_coeff 1 1 lj/cut/coul/long 0.015200000256300 2.846421344984478
pair_coeff 1 2 lj/cut/coul/long 0.001232882795416 2.846421344984478
pair_coeff 1 3 lj/cut/coul/long 0.038019995160237 3.159705878878677
pair_coeff 1 4 lj/cut/coul/long 0.038139744011598 2.939787518071103
pair_coeff 2 2 lj/cut/coul/long 9.99999974737875e-05 2.846421344984478
pair_coeff 2 3 lj/cut/coul/long 0.003083828758188 3.159705878878677
pair_coeff 2 4 lj/cut/coul/long 0.003093541672406 2.939787518071103
pair_coeff 3 3 lj/cut/coul/long 0.095100000500679 3.472990412772877
pair_coeff 3 4 lj/cut/coul/long 0.095399530150179 3.253072051965302
pair_coeff 4 4 lj/cut/coul/long 0.095700003206730 3.033153691157727
pair_coeff 4 4 hbond/dreiding/lj 2 i 0.4000E+01 2.750000000000000 4
pair_modify mix arithmetic
neighbor 2.0 multi
neigh_modify every 2 delay 4 check yes
variable input index in.ch3oh.box.dreiding
variable sname index ch3oh.box.dreiding
compute hb all pair hbond/dreiding/lj
variable C_hbond equal c_hb[1] #number hbonds
variable E_hbond equal c_hb[2] #hbond energy
thermo_style custom etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong v_E_hbond v_C_hbond press vol
thermo_modify line multi format float %14.6f
run 0
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
PPPM initialization ...
WARNING: System is not charge neutral, net charge = -0.00064 (../kspace.cpp:297)
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316)
G vector (1/distance) = 0.142073
grid = 3 3 3
stencil order = 5
estimated absolute RMS force accuracy = 0.154715
estimated relative force accuracy = 0.00046592
using double precision FFTs
3d grid and FFT values/proc = 392 12
Neighbor list info ...
3 neighbor list requests
update every 2 steps, delay 4 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 13.5
ghost atom cutoff = 13.5
binsize = 6.75 -> bins = 3 3 3
Memory usage per processor = 9.05502 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = 113.723601 KinEng = 0.000000 Temp = 0.000000
PotEng = 113.723601 E_bond = 0.535673 E_angle = 1.281880
E_dihed = 1.232497 E_impro = 0.000000 E_vdwl = -125.381324
E_coul = 597.219740 E_long = -361.164864 v_E_hbond = -69.322152
v_C_hbond = 235.000000 Press = -328.847347 Volume = 7447.236335
Loop time of 4.52995e-06 on 4 procs for 0 steps with 384 atoms
0.0% 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 | 0 | 0 | 0.0 | 0.00
Bond | 0 | 0 | 0 | 0.0 | 0.00
Kspace | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 4.53e-06 | | |100.00
Nlocal: 96 ave 104 max 87 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Nghost: 3063.25 ave 3108 max 3024 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Neighs: 25463.5 ave 28799 max 22471 min
Histogram: 1 0 0 1 0 1 0 0 0 1
FullNghs: 50927 ave 55516 max 46073 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Total # of neighbors = 203708
Ave neighs/atom = 530.49
Ave special neighs/atom = 4
Neighbor list builds = 0
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:00