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lammps/examples/gcmc/log.6Jul17.gcmc.h2o.g++.1
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log.6Jul17.gcmc.h2o.g++.1
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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 1 by 1 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) = 11.88 | 11.88 | 11.88 Mbytes
Step Temp E_pair E_mol TotEng Press
0 338 -4.1890564 9.2628112e-06 18.98377 739.06991
100 338 -30.182886 0.85607237 -6.1539961 -2535.3207
Loop time of 0.0525794 on 1 procs for 100 steps with 24 atoms
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = max iterations
Energy initial, next-to-last, final =
-4.18904713252 -28.9258064504 -29.3268133965
Force two-norm initial, final = 18.0027 42.4511
Force max component initial, final = 5.8993 16.0523
Final line search alpha, max atom move = 0.00353207 0.056698
Iterations, force evaluations = 100 238
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.044199 | 0.044199 | 0.044199 | 0.0 | 84.06
Bond | 0.00049019 | 0.00049019 | 0.00049019 | 0.0 | 0.93
Kspace | 0.0031631 | 0.0031631 | 0.0031631 | 0.0 | 6.02
Neigh | 0.00046444 | 0.00046444 | 0.00046444 | 0.0 | 0.88
Comm | 0.0034101 | 0.0034101 | 0.0034101 | 0.0 | 6.49
Output | 1.9073e-05 | 1.9073e-05 | 1.9073e-05 | 0.0 | 0.04
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.0008333 | | | 1.58
Nlocal: 24 ave 24 max 24 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2047 ave 2047 max 2047 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 4936 ave 4936 max 4936 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 4936
Ave neighs/atom = 205.667
Ave special neighs/atom = 2
Neighbor list builds = 2
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) = 11.63 | 11.63 | 11.63 Mbytes
Step Temp E_pair E_mol TotEng Press
0 518.26667 -30.182886 0 -7.0100684 993.1985
1000 326.9865 -62.258445 0 -47.638175 -5.3440813
Loop time of 0.14263 on 1 procs for 1000 steps with 24 atoms
Performance: 605.764 ns/day, 0.040 hours/ns, 7011.155 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 | 0.10849 | 0.10849 | 0.10849 | 0.0 | 76.07
Bond | 0.00015426 | 0.00015426 | 0.00015426 | 0.0 | 0.11
Kspace | 0.01205 | 0.01205 | 0.01205 | 0.0 | 8.45
Neigh | 0.0046577 | 0.0046577 | 0.0046577 | 0.0 | 3.27
Comm | 0.011531 | 0.011531 | 0.011531 | 0.0 | 8.08
Output | 1.6212e-05 | 1.6212e-05 | 1.6212e-05 | 0.0 | 0.01
Modify | 0.0037699 | 0.0037699 | 0.0037699 | 0.0 | 2.64
Other | | 0.001957 | | | 1.37
Nlocal: 24 ave 24 max 24 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1660 ave 1660 max 1660 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 5112 ave 5112 max 5112 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 5112
Ave neighs/atom = 213
Ave special neighs/atom = 2
Neighbor list builds = 25
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) = 11.63 | 11.63 | 11.63 Mbytes
Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc
1000 326.9865 -4.3509713 -62.258445 14.62027 0.23910963 24 0 0 0 0
2000 116.99793 -5344.1527 -286.61595 17.088682 0.74721761 75 0.048183096 0.013941446 0 0
3000 106.86746 -3920.4926 -361.60598 18.794545 0.89666113 90 0.035637919 0.012768883 0 0
4000 75.002668 540.46846 -414.8511 14.531966 0.98632724 99 0.025963651 0.0093451705 0 0
5000 79.924788 -2131.1173 -437.21216 15.962121 1.0162159 102 0.019879728 0.0070418993 0 0
6000 95.552773 -3647.0233 -438.24276 19.083253 1.0162159 102 0.015753613 0.0056885133 0 0
7000 79.501736 -2071.5369 -440.77351 15.877631 1.0162159 102 0.01326216 0.0046915318 0 0
8000 62.567091 -3102.9616 -442.21884 12.495541 1.0162159 102 0.011305503 0.0040437885 0 0
9000 68.324047 -3812.7866 -440.46835 13.645287 1.0162159 102 0.0099549538 0.0035157329 0 0
10000 83.857631 -2158.2659 -444.8183 16.747566 1.0162159 102 0.0088200922 0.0031354281 0 0
11000 68.350984 -2084.0789 -440.14081 13.650667 1.0162159 102 0.0081331455 0.0030247424 0 0
12000 76.867315 -1585.6723 -443.36199 15.3515 1.0162159 102 0.0073845932 0.0027532534 0 0
13000 59.74266 -2211.0211 -446.07791 11.931462 1.0162159 102 0.0067756276 0.0025213898 0 0
14000 81.154979 -907.0176 -441.53368 16.207808 1.0162159 102 0.0062527642 0.0023280719 0 0
15000 66.814346 -2804.5134 -455.80704 13.7421 1.0461046 105 0.0059590528 0.0021576214 0 0
16000 71.42983 -3930.4004 -458.43218 14.691394 1.0461046 105 0.0055547473 0.0020163729 0 0
17000 89.624855 -3569.8136 -455.18164 18.433672 1.0461046 105 0.0052173265 0.0018867687 0 0
18000 63.519962 -1882.8157 -456.58939 13.064525 1.0461046 105 0.0049082049 0.0017765986 0 0
19000 71.872698 -2243.5046 -454.93359 14.782481 1.0461046 105 0.0046439115 0.0016748361 0 0
20000 73.660765 -2285.3173 -476.35473 15.589381 1.0759934 108 0.0045124933 0.0015837653 0 0
21000 95.675868 987.92089 -475.46736 20.248603 1.0759934 108 0.004285814 0.0015049513 0 0
Loop time of 226.155 on 1 procs for 20000 steps with 108 atoms
Performance: 7.641 ns/day, 3.141 hours/ns, 88.435 timesteps/s
99.2% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 38.053 | 38.053 | 38.053 | 0.0 | 16.83
Bond | 0.089673 | 0.089673 | 0.089673 | 0.0 | 0.04
Kspace | 0.92778 | 0.92778 | 0.92778 | 0.0 | 0.41
Neigh | 1.2619 | 1.2619 | 1.2619 | 0.0 | 0.56
Comm | 0.97483 | 0.97483 | 0.97483 | 0.0 | 0.43
Output | 0.0013306 | 0.0013306 | 0.0013306 | 0.0 | 0.00
Modify | 184.68 | 184.68 | 184.68 | 0.0 | 81.66
Other | | 0.171 | | | 0.08
Nlocal: 108 ave 108 max 108 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 7850 ave 7850 max 7850 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 99828 ave 99828 max 99828 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 99828
Ave neighs/atom = 924.333
Ave special neighs/atom = 2
Neighbor list builds = 20439
Dangerous builds = 0
Total wall time: 0:03:46
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