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lammps/examples/gcmc/log.6Jul17.gcmc.h2o.g++.4
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log.6Jul17.gcmc.h2o.g++.4
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LAMMPS (6 Jul 2017)
using 1 OpenMP thread(s) per MPI task
# fix gcmc example with fix shake
# variables available on command line
variable mu index -8.1
variable disp index 0.5
variable temp index 338.0
variable lbox index 10.0
variable spacing index 5.0
# global model settings
units real
atom_style full
boundary p p p
pair_style lj/cut/coul/long 14
pair_modify mix arithmetic tail yes
kspace_style ewald 0.0001
bond_style harmonic
angle_style harmonic
# box, start molecules on simple cubic lattice
lattice sc ${spacing}
lattice sc 5.0
Lattice spacing in x,y,z = 5 5 5
region box block 0 ${lbox} 0 ${lbox} 0 ${lbox} units box
region box block 0 10.0 0 ${lbox} 0 ${lbox} units box
region box block 0 10.0 0 10.0 0 ${lbox} units box
region box block 0 10.0 0 10.0 0 10.0 units box
create_box 2 box bond/types 1 angle/types 1 extra/bond/per/atom 2 extra/angle/per/atom 1 extra/special/per/atom 2
Created orthogonal box = (0 0 0) to (10 10 10)
1 by 2 by 2 MPI processor grid
# we can load multiple molecule templates, but don't have to use them all
molecule co2mol CO2.txt
Read molecule co2mol:
3 atoms with 2 types
2 bonds with 1 types
1 angles with 1 types
0 dihedrals with 0 types
0 impropers with 0 types
molecule h2omol H2O.txt
Read molecule h2omol:
3 atoms with 2 types
2 bonds with 1 types
1 angles with 1 types
0 dihedrals with 0 types
0 impropers with 0 types
create_atoms 0 box mol h2omol 464563 units box
Created 24 atoms
# rigid SPC/E water model
pair_coeff 1 1 0.15535 3.166
pair_coeff * 2 0.0000 0.0000
bond_coeff 1 1000 1.0
angle_coeff 1 100 109.47
# masses
mass 1 15.9994
mass 2 1.0
# MD settings
group h2o type 1 2
24 atoms in group h2o
neighbor 2.0 bin
neigh_modify every 1 delay 1 check yes
velocity all create ${temp} 54654
velocity all create 338.0 54654
timestep 1.0
minimize 0.0 0.0 100 1000
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:168)
Ewald initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.170448
estimated absolute RMS force accuracy = 0.0332064
estimated relative force accuracy = 0.0001
KSpace vectors: actual max1d max3d = 16 2 62
kxmax kymax kzmax = 2 2 2
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 16
ghost atom cutoff = 16
binsize = 8, bins = 2 2 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 11.85 | 11.85 | 11.85 Mbytes
Step Temp E_pair E_mol TotEng Press
0 338 -4.9610706 9.2628112e-06 18.211756 730.90791
100 338 -15.742442 0.14954269 7.579918 -637.49568
Loop time of 0.0828406 on 4 procs for 100 steps with 24 atoms
98.7% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = max iterations
Energy initial, next-to-last, final =
-4.96106135393 -15.5388622715 -15.592899346
Force two-norm initial, final = 15.474 18.1478
Force max component initial, final = 5.80042 7.56514
Final line search alpha, max atom move = 0.00151131 0.0114333
Iterations, force evaluations = 100 328
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.012844 | 0.025471 | 0.047008 | 8.1 | 30.75
Bond | 0.00038934 | 0.00046468 | 0.00054336 | 0.0 | 0.56
Kspace | 0.0061138 | 0.027556 | 0.04014 | 7.8 | 33.26
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.023276 | 0.023636 | 0.023804 | 0.1 | 28.53
Output | 3.171e-05 | 3.3557e-05 | 3.8147e-05 | 0.0 | 0.04
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.00568 | | | 6.86
Nlocal: 6 ave 8 max 3 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Nghost: 1722 ave 1725 max 1720 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Neighs: 1256.75 ave 2101 max 667 min
Histogram: 1 0 1 0 1 0 0 0 0 1
Total # of neighbors = 5027
Ave neighs/atom = 209.458
Ave special neighs/atom = 2
Neighbor list builds = 0
Dangerous builds = 0
reset_timestep 0
# rigid constraints with thermostat
fix mynvt all nvt temp ${temp} ${temp} 100
fix mynvt all nvt temp 338.0 ${temp} 100
fix mynvt all nvt temp 338.0 338.0 100
fix wshake all shake 0.0001 50 0 b 1 a 1 mol h2omol
0 = # of size 2 clusters
0 = # of size 3 clusters
0 = # of size 4 clusters
8 = # of frozen angles
# gcmc
run 1000
Ewald initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.170448
estimated absolute RMS force accuracy = 0.0332064
estimated relative force accuracy = 0.0001
KSpace vectors: actual max1d max3d = 16 2 62
kxmax kymax kzmax = 2 2 2
Per MPI rank memory allocation (min/avg/max) = 11.6 | 11.6 | 11.6 Mbytes
Step Temp E_pair E_mol TotEng Press
0 518.26667 -15.742442 0 7.4303753 -613.0781
1000 369.81793 -54.202686 0 -37.667331 294.98823
Loop time of 0.199641 on 4 procs for 1000 steps with 24 atoms
Performance: 432.777 ns/day, 0.055 hours/ns, 5008.996 timesteps/s
98.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.017161 | 0.034988 | 0.05833 | 8.0 | 17.53
Bond | 0.00017357 | 0.00021374 | 0.00027347 | 0.0 | 0.11
Kspace | 0.018025 | 0.044624 | 0.065613 | 8.4 | 22.35
Neigh | 0.0029755 | 0.0033154 | 0.0036366 | 0.6 | 1.66
Comm | 0.059933 | 0.06537 | 0.070709 | 1.5 | 32.74
Output | 3.4571e-05 | 3.6657e-05 | 4.22e-05 | 0.0 | 0.02
Modify | 0.043458 | 0.045628 | 0.04767 | 0.9 | 22.86
Other | | 0.005465 | | | 2.74
Nlocal: 6 ave 8 max 3 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Nghost: 1331.5 ave 1369 max 1290 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Neighs: 1259.75 ave 1642 max 428 min
Histogram: 1 0 0 0 0 0 0 1 0 2
Total # of neighbors = 5039
Ave neighs/atom = 209.958
Ave special neighs/atom = 2
Neighbor list builds = 27
Dangerous builds = 0
variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans)
fix mygcmc all gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake
fix mygcmc all gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake
fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake
fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol h2omol tfac_insert ${tfac} group h2o shake wshake
fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol h2omol tfac_insert 1.66666666666667 group h2o shake wshake
# output
variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)
variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)
variable racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1)
compute_modify thermo_temp dynamic/dof yes
thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc
thermo 1000
# run
run 20000
Ewald initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.170448
estimated absolute RMS force accuracy = 0.0332064
estimated relative force accuracy = 0.0001
KSpace vectors: actual max1d max3d = 16 2 62
kxmax kymax kzmax = 2 2 2
WARNING: Fix gcmc using full_energy option (../fix_gcmc.cpp:445)
0 atoms in group FixGCMC:gcmc_exclusion_group:mygcmc
0 atoms in group FixGCMC:rotation_gas_atoms:mygcmc
WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (../neighbor.cpp:472)
Per MPI rank memory allocation (min/avg/max) = 11.6 | 11.6 | 11.6 Mbytes
Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc
1000 369.81793 295.32434 -54.202686 16.535355 0.23910963 24 0 0 0 0
2000 84.544466 -2810.9047 -344.81664 14.364627 0.86677242 87 0.052198354 0.0099581757 0 0
3000 75.188527 -3688.256 -425.02228 14.567977 0.98632724 99 0.030546787 0.0049111089 0 0
4000 75.019396 -5669.3063 -427.69454 14.535207 0.98632724 99 0.019972039 0.0033375609 0 0
5000 90.415371 -2141.7596 -434.65925 17.518218 0.98632724 99 0.014909796 0.002514964 0 0
6000 78.212628 -943.75125 -428.80584 15.153904 0.98632724 99 0.01181521 0.0020316119 0 0
7000 71.754139 -2028.5122 -435.2139 13.902555 0.98632724 99 0.0099466198 0.0016755471 0 0
8000 84.446231 -1969.1657 -428.27313 16.361681 0.98632724 99 0.0084791272 0.0014442102 0 0
9000 70.952348 -2476.9812 -446.33824 14.170197 1.0162159 102 0.0077150892 0.0012556189 0 0
10000 71.418543 -1875.7083 -443.7214 14.263302 1.0162159 102 0.0068355714 0.0011197957 0 0
11000 86.094994 -4508.7581 -444.82687 17.194399 1.0162159 102 0.0061494515 0.0010082475 0 0
12000 81.906091 -1547.8105 -442.36719 16.357815 1.0162159 102 0.0055834729 0.00091775114 0 0
13000 57.221548 -4607.6222 -448.30939 11.42796 1.0162159 102 0.0051230355 0.00084046326 0 0
14000 61.288344 -2518.1779 -445.70636 12.240157 1.0162159 102 0.0047276997 0.00077602396 0 0
15000 85.787669 -2407.7111 -443.3834 17.133022 1.0162159 102 0.0043983485 0.00071920715 0 0
16000 74.845939 -3288.3403 -445.8247 14.947802 1.0162159 102 0.0042321884 0.00080654918 0 0
17000 73.835431 -1926.9566 -445.67476 14.745989 1.0162159 102 0.0039751059 0.00075470749 0 0
18000 72.634985 -3997.552 -447.2351 14.506243 1.0162159 102 0.0037395847 0.00071063946 0 0
19000 96.776472 -714.44132 -453.65552 19.904587 1.0461046 105 0.0036487876 0.00066993446 0 0
20000 75.470786 183.16972 -464.04688 15.522521 1.0461046 105 0.0034630763 0.00063350614 0 0
21000 65.658309 -773.41266 -466.27068 13.504331 1.0461046 105 0.003289113 0.00060198052 0 0
Loop time of 93.8859 on 4 procs for 20000 steps with 105 atoms
Performance: 18.405 ns/day, 1.304 hours/ns, 213.024 timesteps/s
98.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 6.7882 | 10.264 | 14.758 | 93.2 | 10.93
Bond | 0.028286 | 0.034218 | 0.039038 | 2.5 | 0.04
Kspace | 0.57255 | 5.2227 | 8.8493 | 133.8 | 5.56
Neigh | 0.3635 | 0.36915 | 0.37473 | 0.9 | 0.39
Comm | 2.9961 | 3.2542 | 3.509 | 11.4 | 3.47
Output | 0.0011675 | 0.0012342 | 0.001375 | 0.2 | 0.00
Modify | 74.428 | 74.499 | 74.571 | 0.7 | 79.35
Other | | 0.2411 | | | 0.26
Nlocal: 26.25 ave 31 max 22 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Nghost: 6049.25 ave 6133 max 5962 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Neighs: 23613 ave 35083 max 14025 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Total # of neighbors = 94452
Ave neighs/atom = 899.543
Ave special neighs/atom = 2
Neighbor list builds = 20428
Dangerous builds = 0
Total wall time: 0:01:34
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