lammps/examples/gcmc/log.30Mar18.gcmc.h2o.g++.4

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LAMMPS (30 Mar 2018)
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
molecule h2omol H2O.txt
Read molecule h2omol:
3 atoms with max type 2
2 bonds with max type 1
1 angles with max type 1
0 dihedrals with max type 0
0 impropers with max type 0
create_atoms 0 box mol h2omol 464563 units box
Created 24 atoms
Time spent = 0.00285625 secs
# 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 ...
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 0.0695416 on 4 procs for 100 steps with 24 atoms
94.4% 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 | 0.0093951 | 0.017625 | 0.028943 | 5.3 | 25.34
Bond | 0.00035357 | 0.00042325 | 0.00055075 | 0.0 | 0.61
Kspace | 0.00664 | 0.019695 | 0.029924 | 6.1 | 28.32
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.022505 | 0.02509 | 0.027851 | 1.3 | 36.08
Output | 3.3855e-05 | 3.5942e-05 | 4.1485e-05 | 0.0 | 0.05
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.006672 | | | 9.59
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 h2o nvt temp ${temp} ${temp} 100
fix mynvt h2o nvt temp 338.0 ${temp} 100
fix mynvt h2o nvt temp 338.0 338.0 100
fix wshake h2o 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
# important to make temperature dofs dynamic
compute_modify thermo_temp dynamic/dof yes
compute_modify mynvt_temp dynamic/dof yes
run 1000
Ewald initialization ...
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 -54.202682 0 -37.667327 294.98832
Loop time of 0.191619 on 4 procs for 1000 steps with 24 atoms
Performance: 450.894 ns/day, 0.053 hours/ns, 5218.680 timesteps/s
96.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.015873 | 0.028989 | 0.040172 | 5.3 | 15.13
Bond | 0.00024271 | 0.00027657 | 0.00034404 | 0.0 | 0.14
Kspace | 0.022896 | 0.034492 | 0.047924 | 5.1 | 18.00
Neigh | 0.0025764 | 0.0025961 | 0.0026152 | 0.0 | 1.35
Comm | 0.068467 | 0.070095 | 0.071535 | 0.4 | 36.58
Output | 4.8161e-05 | 5.0783e-05 | 5.7936e-05 | 0.0 | 0.03
Modify | 0.049141 | 0.049894 | 0.05072 | 0.3 | 26.04
Other | | 0.005226 | | | 2.73
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
reset_timestep 0
# gcmc
variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans)
fix mygcmc h2o gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake
fix mygcmc h2o gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake
fix mygcmc h2o gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake
fix mygcmc h2o gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol h2omol tfac_insert ${tfac} group h2o shake wshake
fix mygcmc h2o gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol h2omol tfac_insert 1.66666666666667 group h2o shake wshake
# atom counts
variable oxygen atom "type==1"
variable hydrogen atom "type==2"
group oxygen dynamic all var oxygen
dynamic group oxygen defined
group hydrogen dynamic all var hydrogen
dynamic group hydrogen defined
variable nO equal count(oxygen)
variable nH equal count(hydrogen)
# 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)
thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nO v_nH
thermo 1000
# run
run 20000
Ewald initialization ...
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:485)
0 atoms in group FixGCMC:gcmc_exclusion_group:mygcmc
0 atoms in group FixGCMC:rotation_gas_atoms:mygcmc
ERROR: fix gcmc does currently not support full_energy option with molecules on more than 1 MPI process. (../fix_gcmc.cpp:721)
Last command: run 20000