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delete old log files. new log files are approved by @athomps

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Axel Kohlmeyer
2017-11-28 11:35:49 -05:00
parent adbc75cae6
commit e4b14213b4
6 changed files with 0 additions and 1248 deletions
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193
examples/gcmc/log.6Jul17.gcmc.co2.g++.1
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LAMMPS (22 Sep 2017)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# GCMC for CO2 molecular fluid, rigid/small/nvt dynamics
# Rigid CO2 TraPPE model
# [Potoff and J.I. Siepmann, Vapor-liquid equilibria of
# mixtures containing alkanes, carbon dioxide and
# nitrogen AIChE J., 47,1676-1682 (2001)].
# 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
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
create_atoms 0 box mol co2mol 464563 units box
Created 24 atoms
Time spent = 0.00136113 secs
# rigid CO2 TraPPE model
pair_coeff 1 1 0.053649 2.8
pair_coeff 2 2 0.156973 3.05
bond_coeff 1 0 1.16
angle_coeff 1 0 180
# masses
mass 1 12.0107
mass 2 15.9994
# MD settings
group co2 type 1 2
24 atoms in group co2
neighbor 2.0 bin
neigh_modify every 1 delay 10 check yes
velocity all create ${temp} 54654
velocity all create 338.0 54654
timestep 1.0
# rigid constraints with thermostat
fix myrigidnvt all rigid/nvt/small molecule temp ${temp} ${temp} 100 mol co2mol
fix myrigidnvt all rigid/nvt/small molecule temp 338.0 ${temp} 100 mol co2mol
fix myrigidnvt all rigid/nvt/small molecule temp 338.0 338.0 100 mol co2mol
8 rigid bodies with 24 atoms
1.16 = max distance from body owner to body atom
fix_modify myrigidnvt dynamic/dof no
# gcmc
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 co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
fix mygcmc all gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert 1.66666666666667 group co2 rigid myrigidnvt
# atom counts
variable carbon atom "type==1"
variable oxygen atom "type==2"
group carbon dynamic all var carbon
dynamic group carbon defined
group oxygen dynamic all var oxygen
dynamic group oxygen defined
variable nC equal count(carbon)
variable nO equal count(oxygen)
# 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 v_nC v_nO
thermo 1000
# run
run 20000
Ewald initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.164636
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:476)
Neighbor list info ...
update every 1 steps, delay 10 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) = 15.62 | 15.62 | 15.62 Mbytes
Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO
0 364.27579 4238.8631 -9.6809388 13.391989 0.5846359 24 0 0 0 0 8 16
WARNING: Using kspace solver on system with no charge (../kspace.cpp:289)
1000 420.43475 1722.4052 -9.6956122 15.456579 0.5846359 24 0.20879341 0.20713005 0 0 8 16
2000 302.29516 -547.83642 -22.017674 14.11699 0.73079488 30 0.1742478 0.1678018 0 0 10 20
3000 316.6934 -1080.2673 -8.2218902 10.069364 0.51155641 21 0.13544917 0.13720634 0 0 7 14
4000 246.81614 -679.83628 -14.57724 10.299968 0.65771539 27 0.1568939 0.15860229 0 0 9 18
5000 260.23291 -896.27949 -16.097524 10.859868 0.65771539 27 0.13138744 0.13547049 0 0 9 18
6000 291.64889 -1524.1007 -22.306243 13.619816 0.73079488 30 0.12615476 0.12717694 0 0 10 20
7000 235.90417 -565.40879 -27.600934 13.360525 0.87695385 36 0.119703 0.12145398 0 0 12 24
8000 483.381 2017.6258 -7.1315833 15.369247 0.51155641 21 0.10942279 0.11082908 0 0 7 14
9000 468.87446 -285.22545 -0.22330095 0.93175047 0.073079488 3 0.13029748 0.13349433 0 0 1 2
10000 245.34708 -254.65444 -16.192443 11.457551 0.73079488 30 0.15023549 0.15176828 0 0 10 20
11000 233.27704 523.81197 -24.29051 12.052812 0.80387436 33 0.1438083 0.14547187 0 0 11 22
12000 230.75966 -2161.9134 -23.812352 11.922746 0.80387436 33 0.1338274 0.13534617 0 0 11 22
13000 216.09982 -930.72014 -23.138263 11.16531 0.80387436 33 0.12480714 0.12612138 0 0 11 22
14000 343.12403 -327.36241 -16.995149 16.023672 0.73079488 30 0.12006081 0.12108416 0 0 10 20
15000 369.60805 581.40471 -11.495738 13.588021 0.5846359 24 0.11372814 0.11534691 0 0 8 16
16000 221.23125 -918.58249 -30.702491 12.529519 0.87695385 36 0.11489536 0.11560548 0 0 12 24
17000 301.82269 -450.56586 -14.373996 12.595466 0.65771539 27 0.11226626 0.11350321 0 0 9 18
18000 1065.1385 474.31881 -0.45476519 7.4082761 0.14615898 6 0.11419593 0.11580815 0 0 2 4
19000 217.29422 -1111.0114 -12.048289 7.988458 0.5846359 24 0.12564213 0.1261457 0 0 8 16
20000 353.35515 465.29269 -6.8428553 9.4795613 0.43847693 18 0.12529827 0.12590018 0 0 6 12
Loop time of 14.604 on 1 procs for 20000 steps with 18 atoms
Performance: 118.323 ns/day, 0.203 hours/ns, 1369.484 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 | 1.8966 | 1.8966 | 1.8966 | 0.0 | 12.99
Bond | 0.019538 | 0.019538 | 0.019538 | 0.0 | 0.13
Kspace | 0.14784 | 0.14784 | 0.14784 | 0.0 | 1.01
Neigh | 0.070002 | 0.070002 | 0.070002 | 0.0 | 0.48
Comm | 0.15055 | 0.15055 | 0.15055 | 0.0 | 1.03
Output | 0.0017672 | 0.0017672 | 0.0017672 | 0.0 | 0.01
Modify | 12.287 | 12.287 | 12.287 | 0.0 | 84.13
Other | | 0.03089 | | | 0.21
Nlocal: 18 ave 18 max 18 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1335 ave 1335 max 1335 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2797 ave 2797 max 2797 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2797
Ave neighs/atom = 155.389
Ave special neighs/atom = 2
Neighbor list builds = 20401
Dangerous builds = 0
Total wall time: 0:00:14

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LAMMPS (22 Sep 2017)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# GCMC for CO2 molecular fluid, rigid/small/nvt dynamics
# Rigid CO2 TraPPE model
# [Potoff and J.I. Siepmann, Vapor-liquid equilibria of
# mixtures containing alkanes, carbon dioxide and
# nitrogen AIChE J., 47,1676-1682 (2001)].
# 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 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
create_atoms 0 box mol co2mol 464563 units box
Created 24 atoms
Time spent = 0.00223303 secs
# rigid CO2 TraPPE model
pair_coeff 1 1 0.053649 2.8
pair_coeff 2 2 0.156973 3.05
bond_coeff 1 0 1.16
angle_coeff 1 0 180
# masses
mass 1 12.0107
mass 2 15.9994
# MD settings
group co2 type 1 2
24 atoms in group co2
neighbor 2.0 bin
neigh_modify every 1 delay 10 check yes
velocity all create ${temp} 54654
velocity all create 338.0 54654
timestep 1.0
# rigid constraints with thermostat
fix myrigidnvt all rigid/nvt/small molecule temp ${temp} ${temp} 100 mol co2mol
fix myrigidnvt all rigid/nvt/small molecule temp 338.0 ${temp} 100 mol co2mol
fix myrigidnvt all rigid/nvt/small molecule temp 338.0 338.0 100 mol co2mol
8 rigid bodies with 24 atoms
1.16 = max distance from body owner to body atom
fix_modify myrigidnvt dynamic/dof no
# gcmc
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 co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
fix mygcmc all gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert 1.66666666666667 group co2 rigid myrigidnvt
# atom counts
variable carbon atom "type==1"
variable oxygen atom "type==2"
group carbon dynamic all var carbon
dynamic group carbon defined
group oxygen dynamic all var oxygen
dynamic group oxygen defined
variable nC equal count(carbon)
variable nO equal count(oxygen)
# 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 v_nC v_nO
thermo 1000
# run
run 20000
Ewald initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.164636
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:476)
Neighbor list info ...
update every 1 steps, delay 10 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) = 15.41 | 15.41 | 15.41 Mbytes
Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO
0 386.52184 23582.465 -3.2433417 14.209828 0.5846359 24 0 0 0 0 8 16
WARNING: Using kspace solver on system with no charge (../kspace.cpp:289)
1000 335.66829 -3.7743052 -4.6268612 7.3374649 0.36539744 15 0.20601899 0.20787963 0 0 5 10
2000 459.73529 238.91592 -0.42937831 5.4815343 0.21923846 9 0.30392058 0.30105616 0 0 3 6
3000 255.47773 -479.67802 -36.850434 15.738299 0.95003334 39 0.22220744 0.2197582 0 0 13 26
4000 182.70803 -1059.2265 -43.04484 12.163134 1.0231128 42 0.16781689 0.16716177 0 0 14 28
5000 234.00901 -1821.0459 -46.047939 15.578313 1.0231128 42 0.13498091 0.13704201 0 0 14 28
6000 163.42358 -774.64962 -49.686149 11.691232 1.0961923 45 0.11401677 0.11296973 0 0 15 30
7000 171.36765 -359.28792 -49.34022 12.259546 1.0961923 45 0.098302308 0.098552065 0 0 15 30
8000 215.2905 -905.73479 -38.206404 13.262629 0.95003334 39 0.086608098 0.086135456 0 0 13 26
9000 185.19905 -2320.8255 -52.964346 13.249037 1.0961923 45 0.077379246 0.077059206 0 0 15 30
10000 241.5783 -1410.8134 -51.37248 17.282377 1.0961923 45 0.069600048 0.069395413 0 0 15 30
11000 153.38332 -2647.9572 -53.967244 10.972957 1.0961923 45 0.063207938 0.06315287 0 0 15 30
12000 188.93059 -1639.9304 -52.218219 13.515989 1.0961923 45 0.05816163 0.058001715 0 0 15 30
13000 243.39974 -1127.2881 -44.54519 16.203468 1.0231128 42 0.053682268 0.053700858 0 0 14 28
14000 200.88474 -272.11992 -41.725507 13.373183 1.0231128 42 0.050212054 0.050071222 0 0 14 28
15000 204.6505 -1616.9057 -44.631997 13.623875 1.0231128 42 0.046944632 0.046920585 0 0 14 28
16000 169.22546 105.40991 -42.46103 11.26558 1.0231128 42 0.044460451 0.044287314 0 0 14 28
17000 163.55389 -783.34837 -36.841459 10.075477 0.95003334 39 0.042304052 0.042283048 0 0 13 26
18000 499.48334 -503.24838 -8.94456 15.881226 0.51155641 21 0.04035334 0.040870565 0 0 7 14
19000 658.81004 391.68747 -2.6979013 11.12813 0.29231795 12 0.055391781 0.056188676 0 0 4 8
20000 489.87356 -122.40743 -13.636951 18.00938 0.5846359 24 0.061378424 0.061821941 0 0 8 16
Loop time of 17.1274 on 4 procs for 20000 steps with 24 atoms
Performance: 100.891 ns/day, 0.238 hours/ns, 1167.718 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 | 0.81646 | 1.1504 | 1.4937 | 23.0 | 6.72
Bond | 0.011878 | 0.012255 | 0.013296 | 0.5 | 0.07
Kspace | 0.23802 | 0.58086 | 0.91304 | 32.3 | 3.39
Neigh | 0.04321 | 0.043291 | 0.043372 | 0.0 | 0.25
Comm | 0.90855 | 0.90959 | 0.91112 | 0.1 | 5.31
Output | 0.0011697 | 0.0012506 | 0.001482 | 0.4 | 0.01
Modify | 14.362 | 14.365 | 14.367 | 0.1 | 83.87
Other | | 0.06436 | | | 0.38
Nlocal: 6 ave 8 max 4 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Nghost: 1465.25 ave 1556 max 1376 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Neighs: 1243.5 ave 1726 max 748 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Total # of neighbors = 4974
Ave neighs/atom = 207.25
Ave special neighs/atom = 2
Neighbor list builds = 20375
Dangerous builds = 0
Total wall time: 0:00:17

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LAMMPS (22 Sep 2017)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
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
Time spent = 0.00136209 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 ...
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 -27.771871 0.61137788 -3.9876753 -2259.9107
Loop time of 0.0333829 on 1 procs for 100 steps with 24 atoms
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = max iterations
Energy initial, next-to-last, final =
-4.18904713252 -26.8589493819 -27.1604926722
Force two-norm initial, final = 18.0027 28.6823
Force max component initial, final = 5.8993 11.77
Final line search alpha, max atom move = 0.00301381 0.0354725
Iterations, force evaluations = 100 239
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.028252 | 0.028252 | 0.028252 | 0.0 | 84.63
Bond | 0.00025415 | 0.00025415 | 0.00025415 | 0.0 | 0.76
Kspace | 0.0017328 | 0.0017328 | 0.0017328 | 0.0 | 5.19
Neigh | 0.00038004 | 0.00038004 | 0.00038004 | 0.0 | 1.14
Comm | 0.0022359 | 0.0022359 | 0.0022359 | 0.0 | 6.70
Output | 2.1935e-05 | 2.1935e-05 | 2.1935e-05 | 0.0 | 0.07
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.0005062 | | | 1.52
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: 4939 ave 4939 max 4939 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 4939
Ave neighs/atom = 205.792
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 -27.771871 0 -4.5990532 3.1322213
1000 277.5448 -45.272615 0 -32.86299 -1575.2641
Loop time of 0.101694 on 1 procs for 1000 steps with 24 atoms
Performance: 849.609 ns/day, 0.028 hours/ns, 9833.435 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 | 0.078345 | 0.078345 | 0.078345 | 0.0 | 77.04
Bond | 0.00010109 | 0.00010109 | 0.00010109 | 0.0 | 0.10
Kspace | 0.0079424 | 0.0079424 | 0.0079424 | 0.0 | 7.81
Neigh | 0.003454 | 0.003454 | 0.003454 | 0.0 | 3.40
Comm | 0.0080469 | 0.0080469 | 0.0080469 | 0.0 | 7.91
Output | 1.9073e-05 | 1.9073e-05 | 1.9073e-05 | 0.0 | 0.02
Modify | 0.0026064 | 0.0026064 | 0.0026064 | 0.0 | 2.56
Other | | 0.001179 | | | 1.16
Nlocal: 24 ave 24 max 24 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1688 ave 1688 max 1688 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 4952 ave 4952 max 4952 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 4952
Ave neighs/atom = 206.333
Ave special neighs/atom = 2
Neighbor list builds = 26
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
# 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)
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 v_nO v_nH
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:476)
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 v_nO v_nH
1000 277.5448 -1575.1516 -45.272615 12.409625 0.23910963 24 0 0 0 0 8 16
2000 84.31104 -7419.6538 -330.36966 13.319705 0.80699501 81 0.048183096 0.0099581757 0 0 27 54
3000 79.654082 -7034.6542 -345.84563 13.058853 0.83688372 84 0.027492109 0.0068755525 0 0 28 56
4000 73.831702 -3905.1456 -380.27757 12.984619 0.89666113 90 0.020637774 0.0060076096 0 0 30 60
5000 95.397292 -3523.6886 -414.9618 18.483479 0.98632724 99 0.016897769 0.0045269353 0 0 33 66
6000 74.46018 -4913.3009 -425.33102 14.426857 0.98632724 99 0.013390571 0.0036569014 0 0 33 66
7000 59.601812 -3108.7781 -425.91441 11.548009 0.98632724 99 0.01160439 0.0033510941 0 0 33 66
8000 74.104787 -1710.7687 -444.03326 14.799784 1.0162159 102 0.010174953 0.0028884203 0 0 34 68
9000 92.497957 -1255.2193 -435.57266 18.473162 1.0162159 102 0.0089594585 0.0025112378 0 0 34 68
10000 71.075249 -3191.4633 -454.19438 14.618465 1.0461046 105 0.0081585853 0.0022395915 0 0 35 70
11000 60.402203 -2011.6602 -461.68383 12.423277 1.0461046 105 0.0073396679 0.0020164949 0 0 35 70
12000 92.903919 -3023.4452 -462.20701 19.108096 1.0461046 105 0.0066641451 0.0018355023 0 0 35 70
13000 51.285407 -1016.3672 -466.29402 10.548172 1.0461046 105 0.0061145907 0.0016809265 0 0 35 70
14000 72.733554 -3284.3632 -463.38578 14.959539 1.0461046 105 0.0056427384 0.0015520479 0 0 35 70
15000 76.324778 -1795.0839 -477.59722 16.153186 1.0759934 108 0.005391524 0.0014384143 0 0 36 72
16000 78.185379 345.92387 -481.1903 16.546959 1.0759934 108 0.0050257238 0.0013442486 0 0 36 72
17000 79.868226 -3095.839 -478.59141 16.903113 1.0759934 108 0.0047204383 0.0012578458 0 0 36 72
18000 69.578814 -1884.4164 -482.28013 14.725487 1.0759934 108 0.0044407568 0.0011843991 0 0 36 72
19000 73.973471 -1943.8906 -480.82986 15.655561 1.0759934 108 0.0042016342 0.0011165574 0 0 36 72
20000 59.614528 -2439.1076 -485.78451 12.616671 1.0759934 108 0.0040927265 0.0011614279 0 0 36 72
21000 89.393596 -728.94872 -484.62787 18.919038 1.0759934 108 0.0038871336 0.0011036309 0 0 36 72
Loop time of 148.361 on 1 procs for 20000 steps with 108 atoms
Performance: 11.647 ns/day, 2.061 hours/ns, 134.806 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 | 26.404 | 26.404 | 26.404 | 0.0 | 17.80
Bond | 0.058909 | 0.058909 | 0.058909 | 0.0 | 0.04
Kspace | 0.58222 | 0.58222 | 0.58222 | 0.0 | 0.39
Neigh | 0.81976 | 0.81976 | 0.81976 | 0.0 | 0.55
Comm | 0.60514 | 0.60514 | 0.60514 | 0.0 | 0.41
Output | 0.00070596 | 0.00070596 | 0.00070596 | 0.0 | 0.00
Modify | 119.77 | 119.77 | 119.77 | 0.0 | 80.73
Other | | 0.1157 | | | 0.08
Nlocal: 108 ave 108 max 108 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 7908 ave 7908 max 7908 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 99854 ave 99854 max 99854 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 99854
Ave neighs/atom = 924.574
Ave special neighs/atom = 2
Neighbor list builds = 20442
Dangerous builds = 0
Total wall time: 0:02:28

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LAMMPS (22 Sep 2017)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
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
Time spent = 0.00236797 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 ...
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 -15.815905 0.10936727 7.4662793 -278.75864
Loop time of 0.0389402 on 4 procs for 100 steps with 24 atoms
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = max iterations
Energy initial, next-to-last, final =
-4.96106135393 -15.696637101 -15.7065379926
Force two-norm initial, final = 15.474 4.38071
Force max component initial, final = 5.80042 2.01432
Final line search alpha, max atom move = 0.00468711 0.00944132
Iterations, force evaluations = 100 346
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0067904 | 0.012084 | 0.019882 | 4.5 | 31.03
Bond | 0.0001657 | 0.00019389 | 0.00022459 | 0.0 | 0.50
Kspace | 0.0032685 | 0.010629 | 0.015032 | 4.4 | 27.30
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.013826 | 0.014182 | 0.015051 | 0.4 | 36.42
Output | 2.0027e-05 | 2.2769e-05 | 3.0994e-05 | 0.0 | 0.06
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.001829 | | | 4.70
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 -15.815905 0 7.3569121 -385.7767
1000 240.84589 -44.723106 0 -33.954368 61.365522
Loop time of 0.0971818 on 4 procs for 1000 steps with 24 atoms
Performance: 889.055 ns/day, 0.027 hours/ns, 10289.993 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 | 0.010939 | 0.020819 | 0.033432 | 5.8 | 21.42
Bond | 9.5129e-05 | 0.00010997 | 0.0001266 | 0.0 | 0.11
Kspace | 0.0058987 | 0.017954 | 0.027383 | 5.9 | 18.47
Neigh | 0.0018289 | 0.001851 | 0.0018759 | 0.0 | 1.90
Comm | 0.033144 | 0.033717 | 0.034395 | 0.3 | 34.69
Output | 1.3113e-05 | 1.6809e-05 | 2.5988e-05 | 0.0 | 0.02
Modify | 0.020795 | 0.020843 | 0.020866 | 0.0 | 21.45
Other | | 0.001872 | | | 1.93
Nlocal: 6 ave 9 max 1 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Nghost: 1375.25 ave 1495 max 1251 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Neighs: 1263.25 ave 2045 max 122 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Total # of neighbors = 5053
Ave neighs/atom = 210.542
Ave special neighs/atom = 2
Neighbor list builds = 30
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
# 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)
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 v_nO v_nH
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:476)
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 v_nO v_nH
1000 240.84589 61.724018 -44.723106 10.768738 0.23910963 24 0 0 0 0 8 16
2000 90.409434 -6561.5238 -333.25624 14.822134 0.83688372 84 0.050190725 0.0099581757 0 0 28 56
3000 67.305679 -341.32154 -396.19372 12.238152 0.92654983 93 0.030546787 0.0068755525 0 0 31 62
4000 70.339514 -2575.9146 -419.94752 13.628467 0.98632724 99 0.021303508 0.0046725853 0 0 33 66
5000 85.676845 -3904.0268 -427.45932 17.110889 1.0162159 102 0.016400775 0.0035209497 0 0 34 68
6000 55.817537 -2067.5498 -448.02732 11.147559 1.0162159 102 0.012996731 0.0028442566 0 0 34 68
7000 87.59123 -3931.0089 -442.0299 17.493219 1.0162159 102 0.01160439 0.0030159847 0 0 34 68
8000 77.695862 -1684.9299 -461.16897 15.980166 1.0461046 105 0.010174953 0.0025995783 0 0 35 70
9000 70.375873 -6250.5951 -467.15813 14.474621 1.0461046 105 0.0089594585 0.002260114 0 0 35 70
10000 85.004974 -3406.0315 -464.23871 17.483474 1.0461046 105 0.007938083 0.0020156323 0 0 35 70
11000 55.459986 -3437.3858 -470.38117 11.406782 1.0461046 105 0.0071412985 0.0018148454 0 0 35 70
12000 80.59057 -2145.2149 -464.5658 16.575538 1.0461046 105 0.0064840331 0.0016519521 0 0 35 70
13000 52.183725 -3956.875 -470.42779 10.732934 1.0461046 105 0.0059493315 0.0015128339 0 0 35 70
14000 78.482417 -4895.8977 -465.0452 16.141941 1.0461046 105 0.005490232 0.0013968431 0 0 35 70
15000 61.802226 -6148.8506 -469.41496 12.711228 1.0461046 105 0.0051077595 0.0012945729 0 0 35 70
16000 69.59917 -5755.4737 -462.37636 14.314872 1.0461046 105 0.004761212 0.0012098238 0 0 35 70
17000 78.44382 -4103.8449 -461.5505 16.134003 1.0461046 105 0.0044719941 0.0011320612 0 0 35 70
18000 76.04971 -3994.5995 -464.26842 15.641592 1.0461046 105 0.0042070328 0.0010659592 0 0 35 70
19000 70.676514 -4558.507 -463.40477 14.536455 1.0461046 105 0.0039804956 0.0010049017 0 0 35 70
20000 79.682951 -3876.5977 -462.70391 16.388862 1.0461046 105 0.0037779014 0.00095025921 0 0 35 70
21000 56.755378 -4224.8128 -465.66199 11.673213 1.0461046 105 0.0035881233 0.00090297077 0 0 35 70
Loop time of 63.5274 on 4 procs for 20000 steps with 105 atoms
Performance: 27.201 ns/day, 0.882 hours/ns, 314.825 timesteps/s
99.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 6.7399 | 8.4644 | 10.565 | 49.0 | 13.32
Bond | 0.021824 | 0.024522 | 0.0278 | 1.4 | 0.04
Kspace | 0.47207 | 2.5646 | 4.286 | 88.8 | 4.04
Neigh | 0.25299 | 0.2535 | 0.25374 | 0.1 | 0.40
Comm | 2.011 | 2.0187 | 2.0311 | 0.5 | 3.18
Output | 0.00063848 | 0.00072688 | 0.00099015 | 0.0 | 0.00
Modify | 50.025 | 50.035 | 50.051 | 0.1 | 78.76
Other | | 0.166 | | | 0.26
Nlocal: 26.25 ave 30 max 24 min
Histogram: 1 1 0 1 0 0 0 0 0 1
Nghost: 5965 ave 6026 max 5911 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Neighs: 23614.8 ave 29343 max 16281 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Total # of neighbors = 94459
Ave neighs/atom = 899.61
Ave special neighs/atom = 2
Neighbor list builds = 20437
Dangerous builds = 0
Total wall time: 0:01:03

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LAMMPS (22 Sep 2017)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# GCMC for LJ simple fluid, no dynamics
# T = 2.0
# rho ~ 0.5
# p ~ 1.5
# mu_ex ~ 0.0
# comparable to Frenkel and Smit GCMC Case Study, Figure 5.8
# variables modifiable using -var command line switch
variable mu index -1.25
variable temp index 2.0
variable disp index 1.0
variable lbox index 5.0
# global model settings
units lj
atom_style atomic
pair_style lj/cut 3.0
pair_modify tail no # turn of to avoid triggering full_energy
# box
region box block 0 ${lbox} 0 ${lbox} 0 ${lbox}
region box block 0 5.0 0 ${lbox} 0 ${lbox}
region box block 0 5.0 0 5.0 0 ${lbox}
region box block 0 5.0 0 5.0 0 5.0
create_box 1 box
Created orthogonal box = (0 0 0) to (5 5 5)
1 by 1 by 1 MPI processor grid
# lj parameters
pair_coeff * * 1.0 1.0
mass * 1.0
# gcmc
fix mygcmc all gcmc 1 100 100 1 29494 ${temp} ${mu} ${disp}
fix mygcmc all gcmc 1 100 100 1 29494 2.0 ${mu} ${disp}
fix mygcmc all gcmc 1 100 100 1 29494 2.0 -1.25 ${disp}
fix mygcmc all gcmc 1 100 100 1 29494 2.0 -1.25 1.0
# atom count
variable type1 atom "type==1"
group type1 dynamic all var type1
dynamic group type1 defined
variable n1 equal count(type1)
# averaging
variable rho equal density
variable p equal press
variable nugget equal 1.0e-8
variable lambda equal 1.0
variable muex equal ${mu}-${temp}*ln(density*${lambda}+${nugget})
variable muex equal -1.25-${temp}*ln(density*${lambda}+${nugget})
variable muex equal -1.25-2.0*ln(density*${lambda}+${nugget})
variable muex equal -1.25-2.0*ln(density*1+${nugget})
variable muex equal -1.25-2.0*ln(density*1+1e-08)
fix ave all ave/time 10 100 1000 v_rho v_p v_muex v_n1 ave one file rho_vs_p.dat
variable rhoav equal f_ave[1]
variable pav equal f_ave[2]
variable muexav equal f_ave[3]
variable n1av equal f_ave[4]
# output
variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+${nugget})
variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+1e-08)
variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+${nugget})
variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+1e-08)
variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+${nugget})
variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+1e-08)
compute_modify thermo_temp dynamic yes
thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav v_n1av
thermo 1000
# run
run 10000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 3.3
ghost atom cutoff = 3.3
binsize = 1.65, bins = 4 4 4
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
Per MPI rank memory allocation (min/avg/max) = 0.433 | 0.433 | 0.433 Mbytes
Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav v_n1av
0 0 0 0 -0 0 0 0 0 0 0 0 0 0
1000 2.4038954 2.1735585 -2.7041368 3.5476844 0.496 62 0.064790036 0.06313096 0.1081294 0.54304 1.4513524 -0.025479219 64.98
2000 2.0461168 1.1913842 -2.9880181 3.0212194 0.512 64 0.067416408 0.066335853 0.11306166 0.52736 1.3274665 0.034690004 62.97
3000 1.7930436 1.3788681 -3.2212667 2.6505861 0.552 69 0.067733191 0.066877836 0.1133516 0.5344 1.3834744 0.0070582537 63.5
4000 1.981449 1.2541054 -2.8222868 2.9217977 0.472 59 0.068546991 0.067856412 0.11442807 0.52504 1.3815629 0.043309657 62.17
5000 2.0946818 1.0701629 -3.5213291 3.0977688 0.568 71 0.06813743 0.067567891 0.11342906 0.53824 1.4049567 -0.0054539777 64.15
6000 1.9793484 0.68224187 -3.410211 2.9247088 0.536 67 0.067797628 0.067420108 0.11295333 0.5384 1.401683 -0.0066894359 64.37
7000 2.1885798 1.6745012 -3.185499 3.2345922 0.544 68 0.068630201 0.068261832 0.11403705 0.5244 1.449239 0.045987399 62.33
8000 2.2175324 1.5897263 -3.078898 3.2759002 0.528 66 0.068180395 0.067899629 0.11332691 0.53928 1.5488388 -0.01075766 64.29
9000 1.8610779 1.0396231 -2.923262 2.7465908 0.496 62 0.068346453 0.068028117 0.1134132 0.52912 1.4352871 0.027082544 62.87
10000 2.1079271 1.1746643 -2.9112062 3.1091925 0.48 60 0.068352878 0.068054948 0.11335434 0.5316 1.4462327 0.018503094 63.2
Loop time of 13.1886 on 1 procs for 10000 steps with 60 atoms
Performance: 327555.715 tau/day, 758.231 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 | 0.37102 | 0.37102 | 0.37102 | 0.0 | 2.81
Neigh | 0.86986 | 0.86986 | 0.86986 | 0.0 | 6.60
Comm | 0.10394 | 0.10394 | 0.10394 | 0.0 | 0.79
Output | 0.00025702 | 0.00025702 | 0.00025702 | 0.0 | 0.00
Modify | 11.833 | 11.833 | 11.833 | 0.0 | 89.72
Other | | 0.01084 | | | 0.08
Nlocal: 60 ave 60 max 60 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 663 ave 663 max 663 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2133 ave 2133 max 2133 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2133
Ave neighs/atom = 35.55
Neighbor list builds = 10000
Dangerous builds = 0
Total wall time: 0:00:13

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examples/gcmc/log.6Jul17.gcmc.lj.g++.4
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LAMMPS (22 Sep 2017)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# GCMC for LJ simple fluid, no dynamics
# T = 2.0
# rho ~ 0.5
# p ~ 1.5
# mu_ex ~ 0.0
# comparable to Frenkel and Smit GCMC Case Study, Figure 5.8
# variables modifiable using -var command line switch
variable mu index -1.25
variable temp index 2.0
variable disp index 1.0
variable lbox index 5.0
# global model settings
units lj
atom_style atomic
pair_style lj/cut 3.0
pair_modify tail no # turn of to avoid triggering full_energy
# box
region box block 0 ${lbox} 0 ${lbox} 0 ${lbox}
region box block 0 5.0 0 ${lbox} 0 ${lbox}
region box block 0 5.0 0 5.0 0 ${lbox}
region box block 0 5.0 0 5.0 0 5.0
create_box 1 box
Created orthogonal box = (0 0 0) to (5 5 5)
1 by 2 by 2 MPI processor grid
# lj parameters
pair_coeff * * 1.0 1.0
mass * 1.0
# gcmc
fix mygcmc all gcmc 1 100 100 1 29494 ${temp} ${mu} ${disp}
fix mygcmc all gcmc 1 100 100 1 29494 2.0 ${mu} ${disp}
fix mygcmc all gcmc 1 100 100 1 29494 2.0 -1.25 ${disp}
fix mygcmc all gcmc 1 100 100 1 29494 2.0 -1.25 1.0
# atom count
variable type1 atom "type==1"
group type1 dynamic all var type1
dynamic group type1 defined
variable n1 equal count(type1)
# averaging
variable rho equal density
variable p equal press
variable nugget equal 1.0e-8
variable lambda equal 1.0
variable muex equal ${mu}-${temp}*ln(density*${lambda}+${nugget})
variable muex equal -1.25-${temp}*ln(density*${lambda}+${nugget})
variable muex equal -1.25-2.0*ln(density*${lambda}+${nugget})
variable muex equal -1.25-2.0*ln(density*1+${nugget})
variable muex equal -1.25-2.0*ln(density*1+1e-08)
fix ave all ave/time 10 100 1000 v_rho v_p v_muex v_n1 ave one file rho_vs_p.dat
variable rhoav equal f_ave[1]
variable pav equal f_ave[2]
variable muexav equal f_ave[3]
variable n1av equal f_ave[4]
# output
variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+${nugget})
variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+1e-08)
variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+${nugget})
variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+1e-08)
variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+${nugget})
variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+1e-08)
compute_modify thermo_temp dynamic yes
thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav v_n1av
thermo 1000
# run
run 10000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 3.3
ghost atom cutoff = 3.3
binsize = 1.65, bins = 4 4 4
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
Per MPI rank memory allocation (min/avg/max) = 0.4477 | 0.4477 | 0.4477 Mbytes
Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav v_n1av
0 0 0 0 -0 0 0 0 0 0 0 0 0 0
1000 1.956397 1.7699101 -2.7889468 2.8864874 0.488 61 0.068894746 0.067229075 0.1141726 0.53288 1.3832798 0.013392866 63.44
2000 2.040943 0.56060899 -2.8001647 3.0077055 0.456 57 0.069858594 0.068831934 0.11629114 0.5232 1.3587174 0.049995794 62.19
3000 2.0004866 1.5736515 -3.3098044 2.9572411 0.552 69 0.069594029 0.068727791 0.11592543 0.53096 1.4129434 0.020022578 63.23
4000 2.1127942 2.642809 -2.8865084 3.1211733 0.528 66 0.070268697 0.069533235 0.11693806 0.52424 1.3444615 0.046884078 62.57
5000 2.3663648 1.354269 -3.1917346 3.4957662 0.528 66 0.070519633 0.069960064 0.11710321 0.52688 1.3595814 0.036270867 62.56
6000 1.9224136 0.82756699 -3.1965 2.839257 0.52 65 0.06985018 0.069474645 0.11628632 0.536 1.47062 0.00141549 63.76
7000 2.0266192 1.5593811 -2.9972341 2.9931606 0.52 65 0.070244693 0.069880791 0.11666541 0.52528 1.3246332 0.040754793 62.2
8000 1.7790467 1.8680568 -2.8028819 2.6275151 0.52 65 0.070454494 0.070172368 0.11736806 0.524 1.4213649 0.047985191 62.03
9000 1.7968847 1.3195587 -3.261001 2.6550983 0.536 67 0.069952011 0.069618327 0.11650087 0.53904 1.4624201 -0.01069837 64.36
10000 2.1566109 1.1015729 -3.4999837 3.1880335 0.552 69 0.069603309 0.069284134 0.11625548 0.53128 1.3587249 0.02075238 63.24
Loop time of 13.089 on 4 procs for 10000 steps with 69 atoms
Performance: 330047.561 tau/day, 763.999 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 | 0.088209 | 0.093632 | 0.098849 | 1.4 | 0.72
Neigh | 0.25982 | 0.26669 | 0.27885 | 1.5 | 2.04
Comm | 0.27092 | 0.28815 | 0.29998 | 2.1 | 2.20
Output | 0.00030112 | 0.00035518 | 0.00037479 | 0.0 | 0.00
Modify | 12.432 | 12.433 | 12.433 | 0.0 | 94.98
Other | | 0.007692 | | | 0.06
Nlocal: 17.25 ave 23 max 10 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Nghost: 506.5 ave 519 max 490 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Neighs: 705.75 ave 998 max 369 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Total # of neighbors = 2823
Ave neighs/atom = 40.913
Neighbor list builds = 10000
Dangerous builds = 0
Total wall time: 0:00:13