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Merge pull request #727 from lammps/fix-gcmc-examples

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new example scripts for fix gcmc
This commit is contained in:
Steve Plimpton
2017-12-07 08:19:56 -07:00
committed by GitHub
parent 83ec9815fe e4b14213b4
commit bc3a84b480
9 changed files with 323 additions and 234 deletions
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11
examples/gcmc/in.gcmc.co2
View File

@ -67,6 +67,15 @@ 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
# atom counts
variable carbon atom "type==1"
variable oxygen atom "type==2"
group carbon dynamic all var carbon
group oxygen dynamic all var oxygen
variable nC equal count(carbon)
variable nO equal count(oxygen)
# output
variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
@ -74,7 +83,7 @@ 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_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO
thermo 1000
# run

11
examples/gcmc/in.gcmc.h2o
View File

@ -72,6 +72,15 @@ 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
# atom counts
variable oxygen atom "type==1"
variable hydrogen atom "type==2"
group oxygen dynamic all var oxygen
group hydrogen dynamic all var hydrogen
variable nO equal count(oxygen)
variable nH equal count(hydrogen)
# output
variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
@ -79,7 +88,7 @@ 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_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nO v_nH
thermo 1000
# run

11
examples/gcmc/in.gcmc.lj
View File

@ -33,6 +33,12 @@ mass * 1.0
fix mygcmc all gcmc 1 100 100 1 29494 ${temp} ${mu} ${disp}
# atom count
variable type1 atom "type==1"
group type1 dynamic all var type1
variable n1 equal count(type1)
# averaging
variable rho equal density
@ -40,10 +46,11 @@ variable p equal press
variable nugget equal 1.0e-8
variable lambda equal 1.0
variable muex equal ${mu}-${temp}*ln(density*${lambda}+${nugget})
fix ave all ave/time 10 100 1000 v_rho v_p v_muex ave one file rho_vs_p.dat
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
@ -51,7 +58,7 @@ variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+${nugget})
variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+${nugget})
variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+${nugget})
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
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

82
examples/gcmc/log.6Jul17.gcmc.co2.g++.1 → examples/gcmc/log.23Oct17.gcmc.co2.g++.1
View File

@ -1,4 +1,4 @@
LAMMPS (6 Jul 2017)
LAMMPS (23 Oct 2017)
using 1 OpenMP thread(s) per MPI task
# GCMC for CO2 molecular fluid, rigid/small/nvt dynamics
# Rigid CO2 TraPPE model
@ -46,6 +46,7 @@ Read molecule co2mol:
0 impropers with 0 types
create_atoms 0 box mol co2mol 464563 units box
Created 24 atoms
Time spent = 0.00196958 secs
# rigid CO2 TraPPE model
@ -87,6 +88,17 @@ fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol
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)
@ -94,7 +106,7 @@ 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_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO
thermo 1000
# run
@ -124,45 +136,45 @@ Neighbor list info ...
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
0 364.27579 4238.8631 -9.6809388 13.391989 0.5846359 24 0 0 0 0
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 -9.6956123 15.456579 0.5846359 24 0.20879341 0.20713005 0 0
2000 302.29516 -547.83641 -22.017674 14.11699 0.73079488 30 0.1742478 0.1678018 0 0
3000 316.6934 -1080.2672 -8.2218891 10.069364 0.51155641 21 0.13544917 0.13720634 0 0
4000 246.81618 -679.83642 -14.577244 10.29997 0.65771539 27 0.1568939 0.15860229 0 0
5000 260.22849 -896.29914 -16.097593 10.859684 0.65771539 27 0.13138744 0.13547049 0 0
6000 291.70796 -1521.99 -22.303136 13.622574 0.73079488 30 0.12615476 0.12717694 0 0
7000 236.02638 -599.92186 -27.580831 13.367447 0.87695385 36 0.119703 0.12145398 0 0
8000 321.45341 688.10577 -10.09204 11.817696 0.5846359 24 0.10917411 0.11032646 0 0
9000 502.85382 -302.31056 -0.22330142 0.99927447 0.073079488 3 0.1254105 0.12905828 0 0
10000 249.98239 -510.0091 -32.815145 15.399767 0.95003334 39 0.1274504 0.12875623 0 0
11000 247.59424 -1129.0274 -25.320205 12.792544 0.80387436 33 0.11739076 0.11916784 0 0
12000 0 -20.39554 -0.14872889 -0 0 0 0.1254933 0.12920375 0 0
13000 1272.2738 -474.79484 -0.29450485 8.8489483 0.14615898 6 0.13767133 0.14112496 0 0
14000 516.54246 -36.296516 -5.0012009 11.291243 0.36539744 15 0.15632744 0.15955377 0 0
15000 307.09233 1951.9301 -14.820362 12.815375 0.65771539 27 0.15393544 0.15716192 0 0
16000 198.31989 -559.48443 -30.459487 11.231925 0.87695385 36 0.1482565 0.15025652 0 0
17000 246.99311 657.85683 -18.579206 11.53442 0.73079488 30 0.14143958 0.14375423 0 0
18000 467.13468 167.03738 -1.0945268 5.569759 0.21923846 9 0.13847359 0.14098533 0 0
19000 359.54027 -1413.5407 -12.156233 13.217895 0.5846359 24 0.15169146 0.15294205 0 0
20000 227.79597 -1204.5652 -23.24144 10.637925 0.73079488 30 0.14917199 0.15022946 0 0
Loop time of 20.153 on 1 procs for 20000 steps with 30 atoms
1000 420.43475 1722.4052 -9.6956123 15.456579 0.5846359 24 0.20879341 0.20713005 0 0 8 16
2000 302.29516 -547.83641 -22.017674 14.11699 0.73079488 30 0.1742478 0.1678018 0 0 10 20
3000 316.6934 -1080.2672 -8.2218891 10.069364 0.51155641 21 0.13544917 0.13720634 0 0 7 14
4000 246.81618 -679.83642 -14.577244 10.29997 0.65771539 27 0.1568939 0.15860229 0 0 9 18
5000 260.22849 -896.29914 -16.097593 10.859684 0.65771539 27 0.13138744 0.13547049 0 0 9 18
6000 291.70796 -1521.99 -22.303136 13.622574 0.73079488 30 0.12615476 0.12717694 0 0 10 20
7000 236.02638 -599.92186 -27.580831 13.367447 0.87695385 36 0.119703 0.12145398 0 0 12 24
8000 321.45341 688.10577 -10.09204 11.817696 0.5846359 24 0.10917411 0.11032646 0 0 8 16
9000 502.85382 -302.31056 -0.22330142 0.99927447 0.073079488 3 0.1254105 0.12905828 0 0 1 2
10000 249.98239 -510.0091 -32.815145 15.399767 0.95003334 39 0.1274504 0.12875623 0 0 13 26
11000 247.59424 -1129.0274 -25.320205 12.792544 0.80387436 33 0.11739076 0.11916784 0 0 11 22
12000 0 -20.39554 -0.14872889 -0 0 0 0.1254933 0.12920375 0 0 0 0
13000 1272.2738 -474.79484 -0.29450485 8.8489483 0.14615898 6 0.13767133 0.14112496 0 0 2 4
14000 516.54246 -36.296516 -5.0012009 11.291243 0.36539744 15 0.15632744 0.15955377 0 0 5 10
15000 307.09233 1951.9301 -14.820362 12.815375 0.65771539 27 0.15393544 0.15716192 0 0 9 18
16000 198.31989 -559.48443 -30.459487 11.231925 0.87695385 36 0.1482565 0.15025652 0 0 12 24
17000 246.99311 657.85683 -18.579206 11.53442 0.73079488 30 0.14143958 0.14375423 0 0 10 20
18000 467.13468 167.03738 -1.0945268 5.569759 0.21923846 9 0.13847359 0.14098533 0 0 3 6
19000 359.54027 -1413.5407 -12.156233 13.217895 0.5846359 24 0.15169146 0.15294205 0 0 8 16
20000 227.79597 -1204.5652 -23.24144 10.637925 0.73079488 30 0.14917199 0.15022946 0 0 10 20
Loop time of 20.6928 on 1 procs for 20000 steps with 30 atoms
Performance: 85.744 ns/day, 0.280 hours/ns, 992.408 timesteps/s
99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 83.507 ns/day, 0.287 hours/ns, 966.519 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 | 2.5352 | 2.5352 | 2.5352 | 0.0 | 12.58
Bond | 0.026112 | 0.026112 | 0.026112 | 0.0 | 0.13
Kspace | 0.25 | 0.25 | 0.25 | 0.0 | 1.24
Neigh | 0.10364 | 0.10364 | 0.10364 | 0.0 | 0.51
Comm | 0.22907 | 0.22907 | 0.22907 | 0.0 | 1.14
Output | 0.0013065 | 0.0013065 | 0.0013065 | 0.0 | 0.01
Modify | 16.957 | 16.957 | 16.957 | 0.0 | 84.14
Other | | 0.05061 | | | 0.25
Pair | 2.5462 | 2.5462 | 2.5462 | 0.0 | 12.30
Bond | 0.029783 | 0.029783 | 0.029783 | 0.0 | 0.14
Kspace | 0.26167 | 0.26167 | 0.26167 | 0.0 | 1.26
Neigh | 0.10705 | 0.10705 | 0.10705 | 0.0 | 0.52
Comm | 0.23409 | 0.23409 | 0.23409 | 0.0 | 1.13
Output | 0.0013416 | 0.0013416 | 0.0013416 | 0.0 | 0.01
Modify | 17.458 | 17.458 | 17.458 | 0.0 | 84.37
Other | | 0.05433 | | | 0.26
Nlocal: 30 ave 30 max 30 min
Histogram: 1 0 0 0 0 0 0 0 0 0

84
examples/gcmc/log.6Jul17.gcmc.co2.g++.4 → examples/gcmc/log.23Oct17.gcmc.co2.g++.4
View File

@ -1,4 +1,4 @@
LAMMPS (6 Jul 2017)
LAMMPS (23 Oct 2017)
using 1 OpenMP thread(s) per MPI task
# GCMC for CO2 molecular fluid, rigid/small/nvt dynamics
# Rigid CO2 TraPPE model
@ -46,6 +46,7 @@ Read molecule co2mol:
0 impropers with 0 types
create_atoms 0 box mol co2mol 464563 units box
Created 24 atoms
Time spent = 0.00261331 secs
# rigid CO2 TraPPE model
@ -87,6 +88,17 @@ fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol
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)
@ -94,7 +106,7 @@ 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_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO
thermo 1000
# run
@ -124,45 +136,45 @@ Neighbor list info ...
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
0 386.52184 23582.465 -3.2433417 14.209828 0.5846359 24 0 0 0 0
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
2000 459.73529 238.91592 -0.42937831 5.4815343 0.21923846 9 0.30392058 0.30105616 0 0
3000 255.47773 -479.67802 -36.850434 15.738299 0.95003334 39 0.22220744 0.2197582 0 0
4000 182.70803 -1059.2262 -43.044833 12.163134 1.0231128 42 0.16781689 0.16716177 0 0
5000 234.00907 -1821.0444 -46.04795 15.578317 1.0231128 42 0.13498091 0.13704201 0 0
6000 163.42759 -774.67294 -49.686261 11.691518 1.0961923 45 0.11401677 0.11296973 0 0
7000 171.64616 -355.23516 -49.323434 12.27947 1.0961923 45 0.098302308 0.098552065 0 0
8000 251.29791 -905.47863 -37.841209 15.480807 0.95003334 39 0.086856972 0.08638658 0 0
9000 143.69498 -849.95393 -49.073188 10.279858 1.0961923 45 0.078261061 0.077955243 0 0
10000 239.35727 -1158.1879 -43.562047 15.934355 1.0231128 42 0.070789792 0.070807529 0 0
11000 169.51213 -1574.7885 -51.125228 12.126803 1.0961923 45 0.065008734 0.06498871 0 0
12000 181.39739 160.11631 -46.850937 12.977068 1.0961923 45 0.059648717 0.059514803 0 0
13000 164.14601 -1107.7629 -50.726722 11.742914 1.0961923 45 0.055207333 0.055097701 0 0
14000 287.26285 418.51463 -41.664766 19.123497 1.0231128 42 0.051346789 0.051222285 0 0
15000 256.94593 -532.36615 -41.651618 17.105257 1.0231128 42 0.047870301 0.047861685 0 0
16000 166.92132 151.15933 -39.957018 11.11219 1.0231128 42 0.045205599 0.045042211 0 0
17000 163.22452 -1299.8119 -42.677558 10.866089 1.0231128 42 0.043122086 0.042993687 0 0
18000 158.01154 475.77329 -48.803162 11.304057 1.0961923 45 0.041016683 0.040647229 0 0
19000 138.49297 -1585.1508 -47.517099 9.9077098 1.0961923 45 0.038929287 0.038436764 0 0
20000 173.84439 -1362.6301 -53.002743 12.436731 1.0961923 45 0.036973919 0.036523816 0 0
Loop time of 31.8386 on 4 procs for 20000 steps with 45 atoms
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 -1059.2262 -43.044833 12.163134 1.0231128 42 0.16781689 0.16716177 0 0 14 28
5000 234.00907 -1821.0444 -46.04795 15.578317 1.0231128 42 0.13498091 0.13704201 0 0 14 28
6000 163.42759 -774.67294 -49.686261 11.691518 1.0961923 45 0.11401677 0.11296973 0 0 15 30
7000 171.64616 -355.23516 -49.323434 12.27947 1.0961923 45 0.098302308 0.098552065 0 0 15 30
8000 251.29791 -905.47863 -37.841209 15.480807 0.95003334 39 0.086856972 0.08638658 0 0 13 26
9000 143.69498 -849.95393 -49.073188 10.279858 1.0961923 45 0.078261061 0.077955243 0 0 15 30
10000 239.35727 -1158.1879 -43.562047 15.934355 1.0231128 42 0.070789792 0.070807529 0 0 14 28
11000 169.51213 -1574.7885 -51.125228 12.126803 1.0961923 45 0.065008734 0.06498871 0 0 15 30
12000 181.39739 160.11631 -46.850937 12.977068 1.0961923 45 0.059648717 0.059514803 0 0 15 30
13000 164.14601 -1107.7629 -50.726722 11.742914 1.0961923 45 0.055207333 0.055097701 0 0 15 30
14000 287.26285 418.51463 -41.664766 19.123497 1.0231128 42 0.051346789 0.051222285 0 0 14 28
15000 256.94593 -532.36615 -41.651618 17.105257 1.0231128 42 0.047870301 0.047861685 0 0 14 28
16000 166.92132 151.15933 -39.957018 11.11219 1.0231128 42 0.045205599 0.045042211 0 0 14 28
17000 163.22452 -1299.8119 -42.677558 10.866089 1.0231128 42 0.043122086 0.042993687 0 0 14 28
18000 158.01154 475.77329 -48.803162 11.304057 1.0961923 45 0.041016683 0.040647229 0 0 15 30
19000 138.49297 -1585.1508 -47.517099 9.9077098 1.0961923 45 0.038929287 0.038436764 0 0 15 30
20000 173.84439 -1362.6301 -53.002743 12.436731 1.0961923 45 0.036973919 0.036523816 0 0 15 30
Loop time of 32.4481 on 4 procs for 20000 steps with 45 atoms
Performance: 54.274 ns/day, 0.442 hours/ns, 628.168 timesteps/s
98.5% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 53.254 ns/day, 0.451 hours/ns, 616.369 timesteps/s
98.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.1546 | 1.6687 | 2.1338 | 29.5 | 5.24
Bond | 0.019769 | 0.020369 | 0.02132 | 0.4 | 0.06
Kspace | 0.53392 | 0.99911 | 1.5116 | 37.8 | 3.14
Neigh | 0.06737 | 0.067842 | 0.068412 | 0.2 | 0.21
Comm | 1.9408 | 1.9582 | 1.9733 | 1.1 | 6.15
Output | 0.0019503 | 0.0020472 | 0.0022476 | 0.3 | 0.01
Modify | 26.974 | 26.99 | 27.001 | 0.2 | 84.77
Other | | 0.1322 | | | 0.42
Pair | 1.1687 | 1.6702 | 2.1864 | 30.8 | 5.15
Bond | 0.018828 | 0.020035 | 0.020975 | 0.6 | 0.06
Kspace | 0.57506 | 1.0931 | 1.5898 | 37.7 | 3.37
Neigh | 0.068863 | 0.069524 | 0.070128 | 0.2 | 0.21
Comm | 2.0735 | 2.0865 | 2.0979 | 0.7 | 6.43
Output | 0.0025017 | 0.0025966 | 0.0027781 | 0.2 | 0.01
Modify | 27.335 | 27.344 | 27.363 | 0.2 | 84.27
Other | | 0.1621 | | | 0.50
Nlocal: 11.25 ave 14 max 8 min
Histogram: 1 0 0 0 0 1 1 0 0 1
@ -177,4 +189,4 @@ Ave special neighs/atom = 2
Neighbor list builds = 20394
Dangerous builds = 0
Total wall time: 0:00:31
Total wall time: 0:00:32

124
examples/gcmc/log.6Jul17.gcmc.h2o.g++.1 → examples/gcmc/log.23Oct17.gcmc.h2o.g++.1
View File

@ -1,4 +1,4 @@
LAMMPS (6 Jul 2017)
LAMMPS (23 Oct 2017)
using 1 OpenMP thread(s) per MPI task
# fix gcmc example with fix shake
@ -51,6 +51,7 @@ Read molecule h2omol:
0 impropers with 0 types
create_atoms 0 box mol h2omol 464563 units box
Created 24 atoms
Time spent = 0.00201297 secs
# rigid SPC/E water model
@ -100,9 +101,9 @@ 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
Loop time of 0.0507543 on 1 procs for 100 steps with 24 atoms
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = max iterations
@ -116,14 +117,14 @@ Minimization stats:
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
Pair | 0.042597 | 0.042597 | 0.042597 | 0.0 | 83.93
Bond | 0.00047708 | 0.00047708 | 0.00047708 | 0.0 | 0.94
Kspace | 0.0031135 | 0.0031135 | 0.0031135 | 0.0 | 6.13
Neigh | 0.00045919 | 0.00045919 | 0.00045919 | 0.0 | 0.90
Comm | 0.0032997 | 0.0032997 | 0.0032997 | 0.0 | 6.50
Output | 1.359e-05 | 1.359e-05 | 1.359e-05 | 0.0 | 0.03
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.0008333 | | | 1.58
Other | | 0.0007946 | | | 1.57
Nlocal: 24 ave 24 max 24 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -164,22 +165,22 @@ 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
Loop time of 0.141449 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
Performance: 610.819 ns/day, 0.039 hours/ns, 7069.663 timesteps/s
99.7% 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
Pair | 0.10788 | 0.10788 | 0.10788 | 0.0 | 76.27
Bond | 0.00018954 | 0.00018954 | 0.00018954 | 0.0 | 0.13
Kspace | 0.011867 | 0.011867 | 0.011867 | 0.0 | 8.39
Neigh | 0.0045254 | 0.0045254 | 0.0045254 | 0.0 | 3.20
Comm | 0.011277 | 0.011277 | 0.011277 | 0.0 | 7.97
Output | 1.5497e-05 | 1.5497e-05 | 1.5497e-05 | 0.0 | 0.01
Modify | 0.00383 | 0.00383 | 0.00383 | 0.0 | 2.71
Other | | 0.001868 | | | 1.32
Nlocal: 24 ave 24 max 24 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -201,6 +202,17 @@ fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol
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)
@ -208,7 +220,7 @@ 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_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nO v_nH
thermo 1000
# run
@ -226,44 +238,44 @@ WARNING: Fix gcmc using full_energy option (../fix_gcmc.cpp:445)
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
Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc v_nO v_nH
1000 326.9865 -4.3509713 -62.258445 14.62027 0.23910963 24 0 0 0 0 8 16
2000 116.99793 -5344.1527 -286.61595 17.088682 0.74721761 75 0.048183096 0.013941446 0 0 25 50
3000 106.86746 -3920.4926 -361.60598 18.794545 0.89666113 90 0.035637919 0.012768883 0 0 30 60
4000 75.002668 540.46846 -414.8511 14.531966 0.98632724 99 0.025963651 0.0093451705 0 0 33 66
5000 79.924788 -2131.1173 -437.21216 15.962121 1.0162159 102 0.019879728 0.0070418993 0 0 34 68
6000 95.552773 -3647.0233 -438.24276 19.083253 1.0162159 102 0.015753613 0.0056885133 0 0 34 68
7000 79.501736 -2071.5369 -440.77351 15.877631 1.0162159 102 0.01326216 0.0046915318 0 0 34 68
8000 62.567091 -3102.9616 -442.21884 12.495541 1.0162159 102 0.011305503 0.0040437885 0 0 34 68
9000 68.324047 -3812.7866 -440.46835 13.645287 1.0162159 102 0.0099549538 0.0035157329 0 0 34 68
10000 83.857631 -2158.2659 -444.8183 16.747566 1.0162159 102 0.0088200922 0.0031354281 0 0 34 68
11000 68.350984 -2084.0789 -440.14081 13.650667 1.0162159 102 0.0081331455 0.0030247424 0 0 34 68
12000 76.867315 -1585.6723 -443.36199 15.3515 1.0162159 102 0.0073845932 0.0027532534 0 0 34 68
13000 59.74266 -2211.0211 -446.07791 11.931462 1.0162159 102 0.0067756276 0.0025213898 0 0 34 68
14000 81.154979 -907.0176 -441.53368 16.207808 1.0162159 102 0.0062527642 0.0023280719 0 0 34 68
15000 66.814346 -2804.5134 -455.80704 13.7421 1.0461046 105 0.0059590528 0.0021576214 0 0 35 70
16000 71.42983 -3930.4004 -458.43218 14.691394 1.0461046 105 0.0055547473 0.0020163729 0 0 35 70
17000 89.624855 -3569.8136 -455.18164 18.433672 1.0461046 105 0.0052173265 0.0018867687 0 0 35 70
18000 63.519962 -1882.8157 -456.58939 13.064525 1.0461046 105 0.0049082049 0.0017765986 0 0 35 70
19000 71.872698 -2243.5046 -454.93359 14.782481 1.0461046 105 0.0046439115 0.0016748361 0 0 35 70
20000 73.660765 -2285.3173 -476.35473 15.589381 1.0759934 108 0.0045124933 0.0015837653 0 0 36 72
21000 95.675868 987.92089 -475.46736 20.248603 1.0759934 108 0.004285814 0.0015049513 0 0 36 72
Loop time of 220.662 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
Performance: 7.831 ns/day, 3.065 hours/ns, 90.637 timesteps/s
99.6% 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
Pair | 37.459 | 37.459 | 37.459 | 0.0 | 16.98
Bond | 0.087067 | 0.087067 | 0.087067 | 0.0 | 0.04
Kspace | 0.90234 | 0.90234 | 0.90234 | 0.0 | 0.41
Neigh | 1.2299 | 1.2299 | 1.2299 | 0.0 | 0.56
Comm | 0.95437 | 0.95437 | 0.95437 | 0.0 | 0.43
Output | 0.0010636 | 0.0010636 | 0.0010636 | 0.0 | 0.00
Modify | 179.85 | 179.85 | 179.85 | 0.0 | 81.51
Other | | 0.1754 | | | 0.08
Nlocal: 108 ave 108 max 108 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -278,4 +290,4 @@ Ave special neighs/atom = 2
Neighbor list builds = 20439
Dangerous builds = 0
Total wall time: 0:03:46
Total wall time: 0:03:40

120
examples/gcmc/log.6Jul17.gcmc.h2o.g++.4 → examples/gcmc/log.23Oct17.gcmc.h2o.g++.4
View File

@ -1,4 +1,4 @@
LAMMPS (6 Jul 2017)
LAMMPS (23 Oct 2017)
using 1 OpenMP thread(s) per MPI task
# fix gcmc example with fix shake
@ -51,6 +51,7 @@ Read molecule h2omol:
0 impropers with 0 types
create_atoms 0 box mol h2omol 464563 units box
Created 24 atoms
Time spent = 0.00174451 secs
# rigid SPC/E water model
@ -100,9 +101,9 @@ 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
Loop time of 0.0566185 on 4 procs for 100 steps with 24 atoms
98.7% CPU use with 4 MPI tasks x 1 OpenMP threads
98.8% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = max iterations
@ -116,14 +117,14 @@ Minimization stats:
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
Pair | 0.0085177 | 0.016083 | 0.026787 | 5.3 | 28.41
Bond | 0.00022459 | 0.00031394 | 0.00037575 | 0.0 | 0.55
Kspace | 0.0049062 | 0.014122 | 0.02044 | 5.0 | 24.94
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
Comm | 0.018515 | 0.02086 | 0.023246 | 1.2 | 36.84
Output | 2.4796e-05 | 2.6047e-05 | 2.9802e-05 | 0.0 | 0.05
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.00568 | | | 6.86
Other | | 0.005213 | | | 9.21
Nlocal: 6 ave 8 max 3 min
Histogram: 1 0 0 0 1 0 0 0 0 2
@ -164,22 +165,22 @@ 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
Loop time of 0.154891 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
Performance: 557.810 ns/day, 0.043 hours/ns, 6456.135 timesteps/s
98.3% 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
Pair | 0.0154 | 0.028993 | 0.040525 | 5.5 | 18.72
Bond | 0.00016999 | 0.0001902 | 0.00023293 | 0.0 | 0.12
Kspace | 0.019093 | 0.028112 | 0.038976 | 4.3 | 18.15
Neigh | 0.0020263 | 0.0022184 | 0.002408 | 0.4 | 1.43
Comm | 0.04947 | 0.053627 | 0.058009 | 1.4 | 34.62
Output | 2.5749e-05 | 2.7537e-05 | 3.2187e-05 | 0.0 | 0.02
Modify | 0.035275 | 0.036815 | 0.038425 | 0.7 | 23.77
Other | | 0.004909 | | | 3.17
Nlocal: 6 ave 8 max 3 min
Histogram: 1 0 0 0 0 0 1 0 1 1
@ -201,6 +202,17 @@ fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol
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)
@ -208,7 +220,7 @@ 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_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nO v_nH
thermo 1000
# run
@ -226,44 +238,44 @@ WARNING: Fix gcmc using full_energy option (../fix_gcmc.cpp:445)
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
Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc v_nO v_nH
1000 369.81793 295.32434 -54.202686 16.535355 0.23910963 24 0 0 0 0 8 16
2000 84.544466 -2810.9047 -344.81664 14.364627 0.86677242 87 0.052198354 0.0099581757 0 0 29 58
3000 75.188527 -3688.256 -425.02228 14.567977 0.98632724 99 0.030546787 0.0049111089 0 0 33 66
4000 75.019396 -5669.3063 -427.69454 14.535207 0.98632724 99 0.019972039 0.0033375609 0 0 33 66
5000 90.415371 -2141.7596 -434.65925 17.518218 0.98632724 99 0.014909796 0.002514964 0 0 33 66
6000 78.212628 -943.75125 -428.80584 15.153904 0.98632724 99 0.01181521 0.0020316119 0 0 33 66
7000 71.754139 -2028.5122 -435.2139 13.902555 0.98632724 99 0.0099466198 0.0016755471 0 0 33 66
8000 84.446231 -1969.1657 -428.27313 16.361681 0.98632724 99 0.0084791272 0.0014442102 0 0 33 66
9000 70.952348 -2476.9812 -446.33824 14.170197 1.0162159 102 0.0077150892 0.0012556189 0 0 34 68
10000 71.418543 -1875.7083 -443.7214 14.263302 1.0162159 102 0.0068355714 0.0011197957 0 0 34 68
11000 86.094994 -4508.7581 -444.82687 17.194399 1.0162159 102 0.0061494515 0.0010082475 0 0 34 68
12000 81.906091 -1547.8105 -442.36719 16.357815 1.0162159 102 0.0055834729 0.00091775114 0 0 34 68
13000 57.221548 -4607.6222 -448.30939 11.42796 1.0162159 102 0.0051230355 0.00084046326 0 0 34 68
14000 61.288344 -2518.1779 -445.70636 12.240157 1.0162159 102 0.0047276997 0.00077602396 0 0 34 68
15000 85.787669 -2407.7111 -443.3834 17.133022 1.0162159 102 0.0043983485 0.00071920715 0 0 34 68
16000 74.845939 -3288.3403 -445.8247 14.947802 1.0162159 102 0.0042321884 0.00080654918 0 0 34 68
17000 73.835431 -1926.9566 -445.67476 14.745989 1.0162159 102 0.0039751059 0.00075470749 0 0 34 68
18000 72.634985 -3997.552 -447.2351 14.506243 1.0162159 102 0.0037395847 0.00071063946 0 0 34 68
19000 96.776472 -714.44132 -453.65552 19.904587 1.0461046 105 0.0036487876 0.00066993446 0 0 35 70
20000 75.470786 183.16972 -464.04688 15.522521 1.0461046 105 0.0034630763 0.00063350614 0 0 35 70
21000 65.658309 -773.41266 -466.27068 13.504331 1.0461046 105 0.003289113 0.00060198052 0 0 35 70
Loop time of 84.4085 on 4 procs for 20000 steps with 105 atoms
Performance: 18.405 ns/day, 1.304 hours/ns, 213.024 timesteps/s
Performance: 20.472 ns/day, 1.172 hours/ns, 236.943 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
Pair | 6.3571 | 9.7574 | 13.984 | 90.7 | 11.56
Bond | 0.026374 | 0.031321 | 0.035482 | 2.1 | 0.04
Kspace | 0.57402 | 4.7894 | 8.1754 | 129.0 | 5.67
Neigh | 0.34952 | 0.34987 | 0.35021 | 0.1 | 0.41
Comm | 2.4028 | 2.4228 | 2.4372 | 0.9 | 2.87
Output | 0.0012269 | 0.0012826 | 0.0014355 | 0.2 | 0.00
Modify | 66.819 | 66.828 | 66.837 | 0.1 | 79.17
Other | | 0.2281 | | | 0.27
Nlocal: 26.25 ave 31 max 22 min
Histogram: 1 0 1 0 0 0 1 0 0 1
@ -278,4 +290,4 @@ Ave special neighs/atom = 2
Neighbor list builds = 20428
Dangerous builds = 0
Total wall time: 0:01:34
Total wall time: 0:01:24

56
examples/gcmc/log.6Jul17.gcmc.lj.g++.1 → examples/gcmc/log.23Oct17.gcmc.lj.g++.1
View File

@ -1,4 +1,4 @@
LAMMPS (6 Jul 2017)
LAMMPS (23 Oct 2017)
using 1 OpenMP thread(s) per MPI task
# GCMC for LJ simple fluid, no dynamics
# T = 2.0
@ -43,6 +43,13 @@ 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 ${disp}
fix mygcmc all gcmc 1 100 100 1 29494 2.0 -1.25 1.0
# atom count
variable type1 atom "type==1"
group type1 dynamic all var type1
dynamic group type1 defined
variable n1 equal count(type1)
# averaging
variable rho equal density
@ -54,10 +61,11 @@ variable muex equal -1.25-${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+${nugget})
variable muex equal -1.25-2.0*ln(density*1+1e-08)
fix ave all ave/time 10 100 1000 v_rho v_p v_muex ave one file rho_vs_p.dat
fix ave all ave/time 10 100 1000 v_rho v_p v_muex v_n1 ave one file rho_vs_p.dat
variable rhoav equal f_ave[1]
variable pav equal f_ave[2]
variable muexav equal f_ave[3]
variable n1av equal f_ave[4]
# output
@ -68,7 +76,7 @@ variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+1e-08)
variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+${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
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
@ -87,32 +95,32 @@ Neighbor list info ...
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
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
2000 2.0461168 1.1913842 -2.9880181 3.0212194 0.512 64 0.067416408 0.066335853 0.11306166 0.52736 1.3274665 0.034690004
3000 1.7930436 1.3788681 -3.2212667 2.6505861 0.552 69 0.067733191 0.066877836 0.1133516 0.5344 1.3834744 0.0070582537
4000 1.981449 1.2541054 -2.8222868 2.9217977 0.472 59 0.068546991 0.067856412 0.11442807 0.52504 1.3815629 0.043309657
5000 2.0946818 1.0701629 -3.5213291 3.0977688 0.568 71 0.06813743 0.067567891 0.11342906 0.53824 1.4049567 -0.0054539777
6000 1.9793484 0.68224187 -3.410211 2.9247088 0.536 67 0.067797628 0.067420108 0.11295333 0.5384 1.401683 -0.0066894359
7000 2.1885798 1.6745012 -3.185499 3.2345922 0.544 68 0.068630201 0.068261832 0.11403705 0.5244 1.449239 0.045987399
8000 2.2175324 1.5897263 -3.078898 3.2759002 0.528 66 0.068180395 0.067899629 0.11332691 0.53928 1.5488388 -0.01075766
9000 1.8610779 1.0396231 -2.923262 2.7465908 0.496 62 0.068346453 0.068028117 0.1134132 0.52912 1.4352871 0.027082544
10000 2.1079271 1.1746643 -2.9112062 3.1091925 0.48 60 0.068352878 0.068054948 0.11335434 0.5316 1.4462327 0.018503094
Loop time of 20.6892 on 1 procs for 10000 steps with 60 atoms
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 20.4081 on 1 procs for 10000 steps with 60 atoms
Performance: 208804.611 tau/day, 483.344 timesteps/s
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 211680.375 tau/day, 490.001 timesteps/s
98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.47227 | 0.47227 | 0.47227 | 0.0 | 2.28
Neigh | 1.1729 | 1.1729 | 1.1729 | 0.0 | 5.67
Comm | 0.17133 | 0.17133 | 0.17133 | 0.0 | 0.83
Output | 0.00028253 | 0.00028253 | 0.00028253 | 0.0 | 0.00
Modify | 18.852 | 18.852 | 18.852 | 0.0 | 91.12
Other | | 0.02063 | | | 0.10
Pair | 0.46484 | 0.46484 | 0.46484 | 0.0 | 2.28
Neigh | 1.1447 | 1.1447 | 1.1447 | 0.0 | 5.61
Comm | 0.1696 | 0.1696 | 0.1696 | 0.0 | 0.83
Output | 0.000319 | 0.000319 | 0.000319 | 0.0 | 0.00
Modify | 18.607 | 18.607 | 18.607 | 0.0 | 91.17
Other | | 0.02194 | | | 0.11
Nlocal: 60 ave 60 max 60 min
Histogram: 1 0 0 0 0 0 0 0 0 0

58
examples/gcmc/log.6Jul17.gcmc.lj.g++.4 → examples/gcmc/log.23Oct17.gcmc.lj.g++.4
View File

@ -1,4 +1,4 @@
LAMMPS (6 Jul 2017)
LAMMPS (23 Oct 2017)
using 1 OpenMP thread(s) per MPI task
# GCMC for LJ simple fluid, no dynamics
# T = 2.0
@ -43,6 +43,13 @@ 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 ${disp}
fix mygcmc all gcmc 1 100 100 1 29494 2.0 -1.25 1.0
# atom count
variable type1 atom "type==1"
group type1 dynamic all var type1
dynamic group type1 defined
variable n1 equal count(type1)
# averaging
variable rho equal density
@ -54,10 +61,11 @@ variable muex equal -1.25-${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+${nugget})
variable muex equal -1.25-2.0*ln(density*1+1e-08)
fix ave all ave/time 10 100 1000 v_rho v_p v_muex ave one file rho_vs_p.dat
fix ave all ave/time 10 100 1000 v_rho v_p v_muex v_n1 ave one file rho_vs_p.dat
variable rhoav equal f_ave[1]
variable pav equal f_ave[2]
variable muexav equal f_ave[3]
variable n1av equal f_ave[4]
# output
@ -68,7 +76,7 @@ variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+1e-08)
variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+${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
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
@ -87,32 +95,32 @@ Neighbor list info ...
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
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
2000 2.040943 0.56060899 -2.8001647 3.0077055 0.456 57 0.069858594 0.068831934 0.11629114 0.5232 1.3587174 0.049995794
3000 2.0004866 1.5736515 -3.3098044 2.9572411 0.552 69 0.069594029 0.068727791 0.11592543 0.53096 1.4129434 0.020022578
4000 2.1127942 2.642809 -2.8865084 3.1211733 0.528 66 0.070268697 0.069533235 0.11693806 0.52424 1.3444615 0.046884078
5000 2.3663648 1.354269 -3.1917346 3.4957662 0.528 66 0.070519633 0.069960064 0.11710321 0.52688 1.3595814 0.036270867
6000 1.9224136 0.82756699 -3.1965 2.839257 0.52 65 0.06985018 0.069474645 0.11628632 0.536 1.47062 0.00141549
7000 2.0266192 1.5593811 -2.9972341 2.9931606 0.52 65 0.070244693 0.069880791 0.11666541 0.52528 1.3246332 0.040754793
8000 1.7790467 1.8680568 -2.8028819 2.6275151 0.52 65 0.070454494 0.070172368 0.11736806 0.524 1.4213649 0.047985191
9000 1.7968847 1.3195587 -3.261001 2.6550983 0.536 67 0.069952011 0.069618327 0.11650087 0.53904 1.4624201 -0.01069837
10000 2.1566109 1.1015729 -3.4999837 3.1880335 0.552 69 0.069603309 0.069284134 0.11625548 0.53128 1.3587249 0.02075238
Loop time of 24.9916 on 4 procs for 10000 steps with 69 atoms
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 23.8213 on 4 procs for 10000 steps with 69 atoms
Performance: 172857.936 tau/day, 400.134 timesteps/s
98.2% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 181350.388 tau/day, 419.793 timesteps/s
97.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.11696 | 0.12516 | 0.1321 | 1.7 | 0.50
Neigh | 0.34874 | 0.35644 | 0.36545 | 1.2 | 1.43
Comm | 0.48531 | 0.51366 | 0.54755 | 3.8 | 2.06
Output | 0.0005362 | 0.00069767 | 0.00076008 | 0.0 | 0.00
Modify | 23.956 | 23.972 | 23.988 | 0.3 | 95.92
Other | | 0.02376 | | | 0.10
Pair | 0.10935 | 0.11844 | 0.12741 | 2.1 | 0.50
Neigh | 0.33 | 0.33945 | 0.35091 | 1.6 | 1.42
Comm | 0.49249 | 0.51745 | 0.53856 | 2.7 | 2.17
Output | 0.00053334 | 0.0007208 | 0.0007906 | 0.0 | 0.00
Modify | 22.82 | 22.822 | 22.825 | 0.0 | 95.81
Other | | 0.02289 | | | 0.10
Nlocal: 17.25 ave 23 max 10 min
Histogram: 1 0 0 0 0 0 2 0 0 1
@ -125,4 +133,4 @@ Total # of neighbors = 2823
Ave neighs/atom = 40.913
Neighbor list builds = 10000
Dangerous builds = 0
Total wall time: 0:00:24
Total wall time: 0:00:23