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Merge pull request #865 from athomps/fix_gcmc_temperature 

Made ndof dynamic for temperature fixes and computes
This commit is contained in:
Steve Plimpton 2018-04-13 08:44:41 -06:00 committed by GitHub
parent 1b965d4d3a 4fa95de91c
commit 7f9400eadc
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GPG Key ID: 4AEE18F83AFDEB23
11 changed files with 616 additions and 706 deletions
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7
examples/gcmc/in.gcmc.co2
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@ -59,7 +59,9 @@ timestep 1.0
# rigid constraints with thermostat
fix myrigidnvt co2 rigid/nvt/small molecule temp ${temp} ${temp} 100 mol co2mol
fix_modify myrigidnvt dynamic/dof no
# dynamically update fix rigid/nvt/small temperature ndof
fix_modify myrigidnvt dynamic/dof yes
# gcmc
@ -82,7 +84,10 @@ 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)
# dynamically update default temperature ndof
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

17
examples/gcmc/in.gcmc.h2o
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@ -30,8 +30,6 @@ create_box 2 box &
extra/angle/per/atom 1 &
extra/special/per/atom 2
# we can load multiple molecule templates, but don't have to use them all
molecule co2mol CO2.txt
molecule h2omol H2O.txt
create_atoms 0 box mol h2omol 464563 units box
@ -58,18 +56,24 @@ timestep 1.0
minimize 0.0 0.0 100 1000
reset_timestep 0
# rigid constraints with thermostat
fix mynvt all nvt temp ${temp} ${temp} 100
fix wshake all shake 0.0001 50 0 b 1 a 1 mol h2omol
# gcmc
fix mynvt h2o nvt temp ${temp} ${temp} 100
fix wshake h2o shake 0.0001 50 0 b 1 a 1 mol h2omol
# important to make temperature dofs dynamic
compute_modify thermo_temp dynamic/dof yes
compute_modify mynvt_temp dynamic/dof yes
run 1000
reset_timestep 0
# 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 &
fix mygcmc h2o gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol &
h2omol tfac_insert ${tfac} group h2o shake wshake
# atom counts
@ -87,7 +91,6 @@ 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

192
examples/gcmc/log.23Oct17.gcmc.co2.g++.4
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@ -1,192 +0,0 @@
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
# [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 = 0.00261331 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:472)
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 -1059.2262 -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: 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 | 1.1687 | 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
Nghost: 2639.75 ave 2656 max 2617 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Neighs: 4320 ave 5824 max 2201 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Total # of neighbors = 17280
Ave neighs/atom = 384
Ave special neighs/atom = 2
Neighbor list builds = 20394
Dangerous builds = 0
Total wall time: 0:00:32

293
examples/gcmc/log.23Oct17.gcmc.h2o.g++.4
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@ -1,293 +0,0 @@
LAMMPS (23 Oct 2017)
using 1 OpenMP thread(s) per MPI task
# fix gcmc example with fix shake
# variables available on command line
variable mu index -8.1
variable disp index 0.5
variable temp index 338.0
variable lbox index 10.0
variable spacing index 5.0
# global model settings
units real
atom_style full
boundary p p p
pair_style lj/cut/coul/long 14
pair_modify mix arithmetic tail yes
kspace_style ewald 0.0001
bond_style harmonic
angle_style harmonic
# box, start molecules on simple cubic lattice
lattice sc ${spacing}
lattice sc 5.0
Lattice spacing in x,y,z = 5 5 5
region box block 0 ${lbox} 0 ${lbox} 0 ${lbox} units box
region box block 0 10.0 0 ${lbox} 0 ${lbox} units box
region box block 0 10.0 0 10.0 0 ${lbox} units box
region box block 0 10.0 0 10.0 0 10.0 units box
create_box 2 box bond/types 1 angle/types 1 extra/bond/per/atom 2 extra/angle/per/atom 1 extra/special/per/atom 2
Created orthogonal box = (0 0 0) to (10 10 10)
1 by 2 by 2 MPI processor grid
# we can load multiple molecule templates, but don't have to use them all
molecule co2mol CO2.txt
Read molecule co2mol:
3 atoms with 2 types
2 bonds with 1 types
1 angles with 1 types
0 dihedrals with 0 types
0 impropers with 0 types
molecule h2omol H2O.txt
Read molecule h2omol:
3 atoms with 2 types
2 bonds with 1 types
1 angles with 1 types
0 dihedrals with 0 types
0 impropers with 0 types
create_atoms 0 box mol h2omol 464563 units box
Created 24 atoms
Time spent = 0.00174451 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 -15.742442 0.14954269 7.579918 -637.49568
Loop time of 0.0566185 on 4 procs for 100 steps with 24 atoms
98.8% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = max iterations
Energy initial, next-to-last, final =
-4.96106135393 -15.5388622715 -15.592899346
Force two-norm initial, final = 15.474 18.1478
Force max component initial, final = 5.80042 7.56514
Final line search alpha, max atom move = 0.00151131 0.0114333
Iterations, force evaluations = 100 328
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0085177 | 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 | 0.018515 | 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 | | 0.005213 | | | 9.21
Nlocal: 6 ave 8 max 3 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Nghost: 1722 ave 1725 max 1720 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Neighs: 1256.75 ave 2101 max 667 min
Histogram: 1 0 1 0 1 0 0 0 0 1
Total # of neighbors = 5027
Ave neighs/atom = 209.458
Ave special neighs/atom = 2
Neighbor list builds = 0
Dangerous builds = 0
reset_timestep 0
# rigid constraints with thermostat
fix mynvt all nvt temp ${temp} ${temp} 100
fix mynvt all nvt temp 338.0 ${temp} 100
fix mynvt all nvt temp 338.0 338.0 100
fix wshake all shake 0.0001 50 0 b 1 a 1 mol h2omol
0 = # of size 2 clusters
0 = # of size 3 clusters
0 = # of size 4 clusters
8 = # of frozen angles
# gcmc
run 1000
Ewald initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.170448
estimated absolute RMS force accuracy = 0.0332064
estimated relative force accuracy = 0.0001
KSpace vectors: actual max1d max3d = 16 2 62
kxmax kymax kzmax = 2 2 2
Per MPI rank memory allocation (min/avg/max) = 11.6 | 11.6 | 11.6 Mbytes
Step Temp E_pair E_mol TotEng Press
0 518.26667 -15.742442 0 7.4303753 -613.0781
1000 369.81793 -54.202686 0 -37.667331 294.98823
Loop time of 0.154891 on 4 procs for 1000 steps with 24 atoms
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 | 0.0154 | 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
Nghost: 1331.5 ave 1369 max 1290 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Neighs: 1259.75 ave 1642 max 428 min
Histogram: 1 0 0 0 0 0 0 1 0 2
Total # of neighbors = 5039
Ave neighs/atom = 209.958
Ave special neighs/atom = 2
Neighbor list builds = 27
Dangerous builds = 0
variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans)
fix mygcmc all gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake
fix mygcmc all gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake
fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake
fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol h2omol tfac_insert ${tfac} group h2o shake wshake
fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol h2omol tfac_insert 1.66666666666667 group h2o shake wshake
# 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: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 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: 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 | 6.3571 | 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
Nghost: 6049.25 ave 6133 max 5962 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Neighs: 23613 ave 35083 max 14025 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Total # of neighbors = 94452
Ave neighs/atom = 899.543
Ave special neighs/atom = 2
Neighbor list builds = 20428
Dangerous builds = 0
Total wall time: 0:01:24

120
examples/gcmc/log.23Oct17.gcmc.co2.g++.1 → examples/gcmc/log.30Mar18.gcmc.co2.g++.1
View File

@ -1,4 +1,4 @@
LAMMPS (23 Oct 2017)
LAMMPS (30 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# GCMC for CO2 molecular fluid, rigid/small/nvt dynamics
# Rigid CO2 TraPPE model
@ -39,14 +39,14 @@ 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
3 atoms with max type 2
2 bonds with max type 1
1 angles with max type 1
0 dihedrals with max type 0
0 impropers with max type 0
create_atoms 0 box mol co2mol 464563 units box
Created 24 atoms
Time spent = 0.00196958 secs
Time spent = 0.00241756 secs
# rigid CO2 TraPPE model
@ -72,29 +72,31 @@ 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
fix myrigidnvt co2 rigid/nvt/small molecule temp ${temp} ${temp} 100 mol co2mol
fix myrigidnvt co2 rigid/nvt/small molecule temp 338.0 ${temp} 100 mol co2mol
fix myrigidnvt co2 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
# dynamically update fix rigid/nvt/small temperature ndof
fix_modify myrigidnvt dynamic/dof yes
# 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
fix mygcmc co2 gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
fix mygcmc co2 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
group carbon dynamic co2 var carbon
dynamic group carbon defined
group oxygen dynamic all var oxygen
group oxygen dynamic co2 var oxygen
dynamic group oxygen defined
variable nC equal count(carbon)
variable nO equal count(oxygen)
@ -105,7 +107,10 @@ 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)
# dynamically update default temperature ndof
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
@ -113,13 +118,13 @@ thermo 1000
run 20000
Ewald initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
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)
WARNING: Fix gcmc using full_energy option (../fix_gcmc.cpp:485)
0 atoms in group FixGCMC:gcmc_exclusion_group:mygcmc
0 atoms in group FixGCMC:rotation_gas_atoms:mygcmc
WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (../neighbor.cpp:472)
@ -138,55 +143,54 @@ Neighbor list info ...
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 -9.6956123 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
1000 330.05964 -376.0111 -13.936335 13.773831 0.65771539 27 0.21142067 0.21453147 0 0 9 18
2000 293.79769 -321.3209 -19.049256 13.720163 0.73079488 30 0.25170944 0.25426294 0 0 10 20
3000 348.9085 259.04079 -0.23347965 2.4267366 0.14615898 6 0.22016906 0.23200597 0 0 2 4
4000 360.54577 -329.12072 -16.584234 15.046059 0.65771539 27 0.19173099 0.19785362 0 0 9 18
5000 275.58628 -58.283006 -12.520856 11.500585 0.65771539 27 0.16490585 0.17329884 0 0 9 18
6000 338.59574 364.93514 -19.866569 17.494353 0.80387436 33 0.17971759 0.18331589 0 0 11 22
7000 286.11586 -1252.5069 -19.588667 13.361427 0.73079488 30 0.15729895 0.16220459 0 0 10 20
8000 454.86786 -642.89382 -20.818357 21.242037 0.73079488 30 0.15500235 0.15802382 0 0 10 20
9000 326.36695 -364.71382 -31.376162 18.48392 0.87695385 36 0.14203985 0.14510714 0 0 12 24
10000 348.46961 -387.75245 -21.068466 18.00451 0.80387436 33 0.14000907 0.14343389 0 0 11 22
11000 409.74257 -15.843895 -20.648252 21.170323 0.80387436 33 0.14689306 0.15117074 0 0 11 22
12000 523.93502 1003.0729 -6.0563102 14.055757 0.43847693 18 0.15337575 0.1580166 0 0 6 12
13000 278.14441 -717.1097 -2.3488496 4.6982087 0.29231795 12 0.15952356 0.16422306 0 0 4 8
14000 367.89375 1239.0841 -11.203323 13.524997 0.5846359 24 0.17002439 0.17460294 0 0 8 16
15000 197.05319 -471.14343 -9.3890758 6.2653668 0.51155641 21 0.17702612 0.18155802 0 0 7 14
16000 138.17147 -935.93437 -2.3846783 2.3338898 0.29231795 12 0.17884346 0.18268758 0 0 4 8
17000 245.61833 -166.1694 -5.0970057 5.3690384 0.36539744 15 0.18909252 0.19317817 0 0 5 10
18000 232.0142 -175.732 -14.320198 9.6822635 0.65771539 27 0.18977089 0.19280537 0 0 9 18
19000 362.01189 864.87258 -6.4515321 9.7117982 0.43847693 18 0.19207244 0.19488984 0 0 6 12
20000 441.19548 186.19779 -18.147268 20.603546 0.73079488 30 0.19713351 0.199073 0 0 10 20
Loop time of 16.4949 on 1 procs for 20000 steps with 30 atoms
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
Performance: 104.760 ns/day, 0.229 hours/ns, 1212.498 timesteps/s
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.5462 | 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
Pair | 1.8955 | 1.8955 | 1.8955 | 0.0 | 11.49
Bond | 0.026564 | 0.026564 | 0.026564 | 0.0 | 0.16
Kspace | 0.21215 | 0.21215 | 0.21215 | 0.0 | 1.29
Neigh | 0.088336 | 0.088336 | 0.088336 | 0.0 | 0.54
Comm | 0.19828 | 0.19828 | 0.19828 | 0.0 | 1.20
Output | 0.001025 | 0.001025 | 0.001025 | 0.0 | 0.01
Modify | 14.024 | 14.024 | 14.024 | 0.0 | 85.02
Other | | 0.0491 | | | 0.30
Nlocal: 30 ave 30 max 30 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2310 ave 2310 max 2310 min
Nghost: 2094 ave 2094 max 2094 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 7736 ave 7736 max 7736 min
Neighs: 7664 ave 7664 max 7664 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 7736
Ave neighs/atom = 257.867
Total # of neighbors = 7664
Ave neighs/atom = 255.467
Ave special neighs/atom = 2
Neighbor list builds = 20349
Neighbor list builds = 20076
Dangerous builds = 0
Total wall time: 0:00:20
Total wall time: 0:00:16

131
examples/gcmc/log.30Mar18.gcmc.co2.g++.4 Normal file
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@ -0,0 +1,131 @@
LAMMPS (30 Mar 2018)
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 max type 2
2 bonds with max type 1
1 angles with max type 1
0 dihedrals with max type 0
0 impropers with max type 0
create_atoms 0 box mol co2mol 464563 units box
Created 24 atoms
Time spent = 0.00257635 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 co2 rigid/nvt/small molecule temp ${temp} ${temp} 100 mol co2mol
fix myrigidnvt co2 rigid/nvt/small molecule temp 338.0 ${temp} 100 mol co2mol
fix myrigidnvt co2 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
# dynamically update fix rigid/nvt/small temperature ndof
fix_modify myrigidnvt dynamic/dof yes
# gcmc
variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans)
fix mygcmc co2 gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
fix mygcmc co2 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 co2 var carbon
dynamic group carbon defined
group oxygen dynamic co2 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)
# dynamically update default temperature ndof
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 ...
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:485)
0 atoms in group FixGCMC:gcmc_exclusion_group:mygcmc
0 atoms in group FixGCMC:rotation_gas_atoms:mygcmc
ERROR: fix gcmc does currently not support full_energy option with molecules on more than 1 MPI process. (../fix_gcmc.cpp:721)
Last command: run 20000

175
examples/gcmc/log.23Oct17.gcmc.h2o.g++.1 → examples/gcmc/log.30Mar18.gcmc.h2o.g++.1
View File

@ -1,4 +1,4 @@
LAMMPS (23 Oct 2017)
LAMMPS (30 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# fix gcmc example with fix shake
@ -34,24 +34,16 @@ create_box 2 box bond/types 1
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
3 atoms with max type 2
2 bonds with max type 1
1 angles with max type 1
0 dihedrals with max type 0
0 impropers with max type 0
create_atoms 0 box mol h2omol 464563 units box
Created 24 atoms
Time spent = 0.00201297 secs
Time spent = 0.00204968 secs
# rigid SPC/E water model
@ -79,7 +71,7 @@ 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)
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
@ -101,9 +93,9 @@ 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 0.0507543 on 1 procs for 100 steps with 24 atoms
Loop time of 0.0512006 on 1 procs for 100 steps with 24 atoms
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = max iterations
@ -117,14 +109,14 @@ Minimization stats:
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
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
Pair | 0.04303 | 0.04303 | 0.04303 | 0.0 | 84.04
Bond | 0.00047088 | 0.00047088 | 0.00047088 | 0.0 | 0.92
Kspace | 0.0029728 | 0.0029728 | 0.0029728 | 0.0 | 5.81
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
Comm | 0.003406 | 0.003406 | 0.003406 | 0.0 | 6.65
Output | 2.265e-05 | 2.265e-05 | 2.265e-05 | 0.0 | 0.04
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.0007946 | | | 1.57
Other | | 0.0008392 | | | 1.64
Nlocal: 24 ave 24 max 24 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -139,23 +131,26 @@ 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
fix mynvt h2o nvt temp ${temp} ${temp} 100
fix mynvt h2o nvt temp 338.0 ${temp} 100
fix mynvt h2o nvt temp 338.0 338.0 100
fix wshake h2o shake 0.0001 50 0 b 1 a 1 mol h2omol
0 = # of size 2 clusters
0 = # of size 3 clusters
0 = # of size 4 clusters
8 = # of frozen angles
# gcmc
# important to make temperature dofs dynamic
compute_modify thermo_temp dynamic/dof yes
compute_modify mynvt_temp dynamic/dof yes
run 1000
Ewald initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
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
@ -164,23 +159,23 @@ WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
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 0.141449 on 1 procs for 1000 steps with 24 atoms
1000 326.9865 -62.258443 0 -47.638173 -5.3439918
Loop time of 0.139436 on 1 procs for 1000 steps with 24 atoms
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
Performance: 619.641 ns/day, 0.039 hours/ns, 7171.773 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 | 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
Pair | 0.10588 | 0.10588 | 0.10588 | 0.0 | 75.94
Bond | 0.00015759 | 0.00015759 | 0.00015759 | 0.0 | 0.11
Kspace | 0.011144 | 0.011144 | 0.011144 | 0.0 | 7.99
Neigh | 0.00459 | 0.00459 | 0.00459 | 0.0 | 3.29
Comm | 0.011396 | 0.011396 | 0.011396 | 0.0 | 8.17
Output | 1.7166e-05 | 1.7166e-05 | 1.7166e-05 | 0.0 | 0.01
Modify | 0.0043328 | 0.0043328 | 0.0043328 | 0.0 | 3.11
Other | | 0.001914 | | | 1.37
Nlocal: 24 ave 24 max 24 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -194,13 +189,16 @@ Ave neighs/atom = 213
Ave special neighs/atom = 2
Neighbor list builds = 25
Dangerous builds = 0
reset_timestep 0
# 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 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
fix mygcmc h2o gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake
fix mygcmc h2o gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake
fix mygcmc h2o gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake
fix mygcmc h2o gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol h2omol tfac_insert ${tfac} group h2o shake wshake
fix mygcmc h2o gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol h2omol tfac_insert 1.66666666666667 group h2o shake wshake
# atom counts
@ -219,7 +217,6 @@ 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
@ -227,67 +224,67 @@ thermo 1000
run 20000
Ewald initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
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)
WARNING: Fix gcmc using full_energy option (../fix_gcmc.cpp:485)
0 atoms in group FixGCMC:gcmc_exclusion_group:mygcmc
0 atoms in group FixGCMC:rotation_gas_atoms:mygcmc
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 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
0 326.9865 -4.3508819 -62.258443 14.62027 0.23910963 24 0 0 0 0 8 16
1000 354.423 -3760.1354 -235.34169 51.766914 0.74721761 75 0.046175467 0.011949811 0 0 25 50
2000 335.19661 -3018.659 -270.44089 52.955344 0.80699501 81 0.026473882 0.0068755525 0 0 27 54
3000 333.47175 2657.2052 -336.48359 64.611037 0.98632724 99 0.022634978 0.0060076096 0 0 33 66
4000 321.48504 2055.4786 -345.06113 62.288579 0.98632724 99 0.016897769 0.0045269353 0 0 33 66
5000 333.45735 1918.5375 -368.5463 66.596193 1.0162159 102 0.013784412 0.0036569014 0 0 34 68
6000 301.90666 -698.74074 -371.32122 60.295069 1.0162159 102 0.01160439 0.0030159847 0 0 34 68
7000 336.42505 1537.9483 -378.51731 69.194524 1.0461046 105 0.010174953 0.0025995783 0 0 35 70
8000 338.95331 -1032.1084 -390.7067 69.714524 1.0461046 105 0.0089594585 0.002260114 0 0 35 70
9000 311.44605 -1494.7788 -383.9272 64.056945 1.0461046 105 0.007938083 0.0020156323 0 0 35 70
10000 330.70877 2082.4597 -366.57249 68.018822 1.0461046 105 0.0071412985 0.0018148454 0 0 35 70
11000 286.34718 2238.3752 -370.91119 60.601806 1.0759934 108 0.0066641451 0.0016519521 0 0 36 72
12000 371.02522 3048.7157 -398.51333 78.522854 1.0759934 108 0.0061145907 0.0015128339 0 0 36 72
13000 392.87611 4486.1134 -387.07077 83.147323 1.0759934 108 0.0056427384 0.0013968431 0 0 36 72
14000 332.80747 3586.2698 -406.12151 70.434545 1.0759934 108 0.0052496417 0.0012945729 0 0 36 72
15000 325.61844 4198.3864 -387.5733 68.913077 1.0759934 108 0.0048934679 0.0012098238 0 0 36 72
16000 254.10285 1560.976 -409.98615 55.292559 1.1058821 111 0.0047204383 0.0011320612 0 0 37 74
17000 367.46414 2750.8283 -412.22037 79.959878 1.1058821 111 0.0044407568 0.0010659592 0 0 37 74
18000 407.74215 2308.5027 -408.73046 88.724338 1.1058821 111 0.0042016342 0.0010049017 0 0 37 74
19000 341.53799 5777.9814 -407.00637 74.31837 1.1058821 111 0.0039877848 0.00095025921 0 0 37 74
20000 395.75303 3159.4677 -403.82798 86.115516 1.1058821 111 0.0037874635 0.00090297077 0 0 37 74
Loop time of 231.351 on 1 procs for 20000 steps with 111 atoms
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
Performance: 7.469 ns/day, 3.213 hours/ns, 86.449 timesteps/s
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
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
Pair | 39.09 | 39.09 | 39.09 | 0.0 | 16.90
Bond | 0.092728 | 0.092728 | 0.092728 | 0.0 | 0.04
Kspace | 0.87751 | 0.87751 | 0.87751 | 0.0 | 0.38
Neigh | 3.9658 | 3.9658 | 3.9658 | 0.0 | 1.71
Comm | 1.0608 | 1.0608 | 1.0608 | 0.0 | 0.46
Output | 0.00096035 | 0.00096035 | 0.00096035 | 0.0 | 0.00
Modify | 186.07 | 186.07 | 186.07 | 0.0 | 80.43
Other | | 0.1892 | | | 0.08
Nlocal: 108 ave 108 max 108 min
Nlocal: 111 ave 111 max 111 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 7850 ave 7850 max 7850 min
Nghost: 8070 ave 8070 max 8070 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 99828 ave 99828 max 99828 min
Neighs: 105469 ave 105469 max 105469 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 99828
Ave neighs/atom = 924.333
Total # of neighbors = 105469
Ave neighs/atom = 950.171
Ave special neighs/atom = 2
Neighbor list builds = 20439
Neighbor list builds = 20910
Dangerous builds = 0
Total wall time: 0:03:40
Total wall time: 0:03:51

237
examples/gcmc/log.30Mar18.gcmc.h2o.g++.4 Normal file
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@ -0,0 +1,237 @@
LAMMPS (30 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# fix gcmc example with fix shake
# variables available on command line
variable mu index -8.1
variable disp index 0.5
variable temp index 338.0
variable lbox index 10.0
variable spacing index 5.0
# global model settings
units real
atom_style full
boundary p p p
pair_style lj/cut/coul/long 14
pair_modify mix arithmetic tail yes
kspace_style ewald 0.0001
bond_style harmonic
angle_style harmonic
# box, start molecules on simple cubic lattice
lattice sc ${spacing}
lattice sc 5.0
Lattice spacing in x,y,z = 5 5 5
region box block 0 ${lbox} 0 ${lbox} 0 ${lbox} units box
region box block 0 10.0 0 ${lbox} 0 ${lbox} units box
region box block 0 10.0 0 10.0 0 ${lbox} units box
region box block 0 10.0 0 10.0 0 10.0 units box
create_box 2 box bond/types 1 angle/types 1 extra/bond/per/atom 2 extra/angle/per/atom 1 extra/special/per/atom 2
Created orthogonal box = (0 0 0) to (10 10 10)
1 by 2 by 2 MPI processor grid
molecule h2omol H2O.txt
Read molecule h2omol:
3 atoms with max type 2
2 bonds with max type 1
1 angles with max type 1
0 dihedrals with max type 0
0 impropers with max type 0
create_atoms 0 box mol h2omol 464563 units box
Created 24 atoms
Time spent = 0.00285625 secs
# rigid SPC/E water model
pair_coeff 1 1 0.15535 3.166
pair_coeff * 2 0.0000 0.0000
bond_coeff 1 1000 1.0
angle_coeff 1 100 109.47
# masses
mass 1 15.9994
mass 2 1.0
# MD settings
group h2o type 1 2
24 atoms in group h2o
neighbor 2.0 bin
neigh_modify every 1 delay 1 check yes
velocity all create ${temp} 54654
velocity all create 338.0 54654
timestep 1.0
minimize 0.0 0.0 100 1000
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:168)
Ewald initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.170448
estimated absolute RMS force accuracy = 0.0332064
estimated relative force accuracy = 0.0001
KSpace vectors: actual max1d max3d = 16 2 62
kxmax kymax kzmax = 2 2 2
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 16
ghost atom cutoff = 16
binsize = 8, bins = 2 2 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 11.85 | 11.85 | 11.85 Mbytes
Step Temp E_pair E_mol TotEng Press
0 338 -4.9610706 9.2628112e-06 18.211756 730.90791
100 338 -15.742442 0.14954269 7.579918 -637.49568
Loop time of 0.0695416 on 4 procs for 100 steps with 24 atoms
94.4% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = max iterations
Energy initial, next-to-last, final =
-4.96106135393 -15.5388622715 -15.592899346
Force two-norm initial, final = 15.474 18.1478
Force max component initial, final = 5.80042 7.56514
Final line search alpha, max atom move = 0.00151131 0.0114333
Iterations, force evaluations = 100 328
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0093951 | 0.017625 | 0.028943 | 5.3 | 25.34
Bond | 0.00035357 | 0.00042325 | 0.00055075 | 0.0 | 0.61
Kspace | 0.00664 | 0.019695 | 0.029924 | 6.1 | 28.32
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.022505 | 0.02509 | 0.027851 | 1.3 | 36.08
Output | 3.3855e-05 | 3.5942e-05 | 4.1485e-05 | 0.0 | 0.05
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.006672 | | | 9.59
Nlocal: 6 ave 8 max 3 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Nghost: 1722 ave 1725 max 1720 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Neighs: 1256.75 ave 2101 max 667 min
Histogram: 1 0 1 0 1 0 0 0 0 1
Total # of neighbors = 5027
Ave neighs/atom = 209.458
Ave special neighs/atom = 2
Neighbor list builds = 0
Dangerous builds = 0
reset_timestep 0
# rigid constraints with thermostat
fix mynvt h2o nvt temp ${temp} ${temp} 100
fix mynvt h2o nvt temp 338.0 ${temp} 100
fix mynvt h2o nvt temp 338.0 338.0 100
fix wshake h2o shake 0.0001 50 0 b 1 a 1 mol h2omol
0 = # of size 2 clusters
0 = # of size 3 clusters
0 = # of size 4 clusters
8 = # of frozen angles
# important to make temperature dofs dynamic
compute_modify thermo_temp dynamic/dof yes
compute_modify mynvt_temp dynamic/dof yes
run 1000
Ewald initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.170448
estimated absolute RMS force accuracy = 0.0332064
estimated relative force accuracy = 0.0001
KSpace vectors: actual max1d max3d = 16 2 62
kxmax kymax kzmax = 2 2 2
Per MPI rank memory allocation (min/avg/max) = 11.6 | 11.6 | 11.6 Mbytes
Step Temp E_pair E_mol TotEng Press
0 518.26667 -15.742442 0 7.4303753 -613.0781
1000 369.81793 -54.202682 0 -37.667327 294.98832
Loop time of 0.191619 on 4 procs for 1000 steps with 24 atoms
Performance: 450.894 ns/day, 0.053 hours/ns, 5218.680 timesteps/s
96.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.015873 | 0.028989 | 0.040172 | 5.3 | 15.13
Bond | 0.00024271 | 0.00027657 | 0.00034404 | 0.0 | 0.14
Kspace | 0.022896 | 0.034492 | 0.047924 | 5.1 | 18.00
Neigh | 0.0025764 | 0.0025961 | 0.0026152 | 0.0 | 1.35
Comm | 0.068467 | 0.070095 | 0.071535 | 0.4 | 36.58
Output | 4.8161e-05 | 5.0783e-05 | 5.7936e-05 | 0.0 | 0.03
Modify | 0.049141 | 0.049894 | 0.05072 | 0.3 | 26.04
Other | | 0.005226 | | | 2.73
Nlocal: 6 ave 8 max 3 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Nghost: 1331.5 ave 1369 max 1290 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Neighs: 1259.75 ave 1642 max 428 min
Histogram: 1 0 0 0 0 0 0 1 0 2
Total # of neighbors = 5039
Ave neighs/atom = 209.958
Ave special neighs/atom = 2
Neighbor list builds = 27
Dangerous builds = 0
reset_timestep 0
# gcmc
variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans)
fix mygcmc h2o gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake
fix mygcmc h2o gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake
fix mygcmc h2o gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake
fix mygcmc h2o gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol h2omol tfac_insert ${tfac} group h2o shake wshake
fix mygcmc h2o gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol h2omol tfac_insert 1.66666666666667 group h2o shake wshake
# atom counts
variable oxygen atom "type==1"
variable hydrogen atom "type==2"
group oxygen dynamic all var oxygen
dynamic group oxygen defined
group hydrogen dynamic all var hydrogen
dynamic group hydrogen defined
variable nO equal count(oxygen)
variable nH equal count(hydrogen)
# output
variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)
variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)
variable racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1)
thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nO v_nH
thermo 1000
# run
run 20000
Ewald initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.170448
estimated absolute RMS force accuracy = 0.0332064
estimated relative force accuracy = 0.0001
KSpace vectors: actual max1d max3d = 16 2 62
kxmax kymax kzmax = 2 2 2
WARNING: Fix gcmc using full_energy option (../fix_gcmc.cpp:485)
0 atoms in group FixGCMC:gcmc_exclusion_group:mygcmc
0 atoms in group FixGCMC:rotation_gas_atoms:mygcmc
ERROR: fix gcmc does currently not support full_energy option with molecules on more than 1 MPI process. (../fix_gcmc.cpp:721)
Last command: run 20000

67
examples/gcmc/log.23Oct17.gcmc.lj.g++.1 → examples/gcmc/log.30Mar18.gcmc.lj.g++.1
View File

@ -1,4 +1,4 @@
LAMMPS (23 Oct 2017)
LAMMPS (30 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# GCMC for LJ simple fluid, no dynamics
# T = 2.0
@ -36,17 +36,22 @@ Created orthogonal box = (0 0 0) to (5 5 5)
pair_coeff * * 1.0 1.0
mass * 1.0
# we recommend setting up a dedicated group for gcmc
group gcmcgroup type 1
0 atoms in group gcmcgroup
# 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
fix mygcmc gcmcgroup gcmc 1 100 100 1 29494 ${temp} ${mu} ${disp}
fix mygcmc gcmcgroup gcmc 1 100 100 1 29494 2.0 ${mu} ${disp}
fix mygcmc gcmcgroup gcmc 1 100 100 1 29494 2.0 -1.25 ${disp}
fix mygcmc gcmcgroup 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
group type1 dynamic gcmcgroup var type1
dynamic group type1 defined
variable n1 equal count(type1)
@ -97,40 +102,40 @@ Neighbor list info ...
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 20.4081 on 1 procs for 10000 steps with 60 atoms
1000 2.0603874 2.9024736 -3.2576986 3.0482443 0.584 73 0.069266074 0.066959582 0.11158434 0.53624 1.3978532 0.0014407586 64.19
2000 2.1586837 1.5581387 -2.8420766 3.1857993 0.496 62 0.068487803 0.067570935 0.1126652 0.53128 1.3713694 0.020274019 63.41
3000 2.4664064 0.65471138 -3.3428236 3.6435549 0.528 66 0.068182273 0.067547792 0.11226502 0.53472 1.3892234 0.0070204504 63.68
4000 1.8880496 1.4802782 -2.7846019 2.785647 0.488 61 0.068250075 0.067843541 0.11299989 0.52744 1.299496 0.033918563 63.1
5000 2.0578649 1.3204331 -3.5571862 3.0433213 0.568 71 0.067858571 0.067732262 0.11271981 0.5364 1.4237505 0.00065741209 64
6000 2.3627973 0.97064566 -3.1107668 3.4879388 0.504 63 0.067846204 0.06757018 0.11272207 0.5332 1.3945131 0.014216594 63.7
7000 1.6629817 0.98138972 -2.7780297 2.4514644 0.464 58 0.067451389 0.067269791 0.11263692 0.53688 1.4207486 -0.0012887793 63.82
8000 2.2135488 2.0878792 -3.0471089 3.2707661 0.536 67 0.067926473 0.067738312 0.1135594 0.52736 1.4348314 0.034380623 62.43
9000 1.8904287 0.52639383 -3.3548657 2.7920177 0.52 65 0.06818197 0.068003094 0.11356319 0.53072 1.4528143 0.021683615 63.23
10000 2.2353281 0.73275312 -3.2197702 3.3006016 0.512 64 0.068465059 0.068208485 0.11414748 0.52712 1.4143492 0.03497858 62.44
Loop time of 21.2409 on 1 procs for 10000 steps with 64 atoms
Performance: 211680.375 tau/day, 490.001 timesteps/s
98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 203381.368 tau/day, 470.790 timesteps/s
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.46484 | 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
Pair | 0.45931 | 0.45931 | 0.45931 | 0.0 | 2.16
Neigh | 1.1637 | 1.1637 | 1.1637 | 0.0 | 5.48
Comm | 0.17294 | 0.17294 | 0.17294 | 0.0 | 0.81
Output | 0.00027394 | 0.00027394 | 0.00027394 | 0.0 | 0.00
Modify | 19.416 | 19.416 | 19.416 | 0.0 | 91.41
Other | | 0.02919 | | | 0.14
Nlocal: 60 ave 60 max 60 min
Nlocal: 64 ave 64 max 64 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 663 ave 663 max 663 min
Nghost: 714 ave 714 max 714 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2133 ave 2133 max 2133 min
Neighs: 2423 ave 2423 max 2423 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2133
Ave neighs/atom = 35.55
Total # of neighbors = 2423
Ave neighs/atom = 37.8594
Neighbor list builds = 10000
Dangerous builds = 0
Total wall time: 0:00:20
Total wall time: 0:00:21

73
examples/gcmc/log.23Oct17.gcmc.lj.g++.4 → examples/gcmc/log.30Mar18.gcmc.lj.g++.4
View File

@ -1,4 +1,4 @@
LAMMPS (23 Oct 2017)
LAMMPS (30 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# GCMC for LJ simple fluid, no dynamics
# T = 2.0
@ -36,17 +36,22 @@ Created orthogonal box = (0 0 0) to (5 5 5)
pair_coeff * * 1.0 1.0
mass * 1.0
# we recommend setting up a dedicated group for gcmc
group gcmcgroup type 1
0 atoms in group gcmcgroup
# 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
fix mygcmc gcmcgroup gcmc 1 100 100 1 29494 ${temp} ${mu} ${disp}
fix mygcmc gcmcgroup gcmc 1 100 100 1 29494 2.0 ${mu} ${disp}
fix mygcmc gcmcgroup gcmc 1 100 100 1 29494 2.0 -1.25 ${disp}
fix mygcmc gcmcgroup 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
group type1 dynamic gcmcgroup var type1
dynamic group type1 defined
variable n1 equal count(type1)
@ -97,40 +102,40 @@ Neighbor list info ...
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 23.8213 on 4 procs for 10000 steps with 69 atoms
1000 2.4378552 1.9014939 -3.23439 3.6030066 0.544 68 0.073050445 0.070796636 0.11934255 0.52552 1.3006333 0.04152087 62.56
2000 1.9339159 1.0360287 -3.5001391 2.8594327 0.56 70 0.069588893 0.068587488 0.11319584 0.542 1.4012888 -0.020696665 64.56
3000 1.8891807 2.2857708 -3.3755633 2.7954769 0.592 74 0.068329031 0.067640916 0.11187803 0.53536 1.3380926 0.0062359288 64.21
4000 2.0436517 1.7600211 -3.4067452 3.0229014 0.576 72 0.067464211 0.067003868 0.11060324 0.54144 1.4484907 -0.016246603 64.75
5000 2.1512268 1.0811095 -3.2418366 3.1786785 0.536 67 0.066830654 0.066717982 0.1094094 0.54368 1.4962073 -0.025791643 65.04
6000 2.128931 1.5444487 -3.1904474 3.1450116 0.528 66 0.067479197 0.067193531 0.1104464 0.53112 1.4247377 0.019908014 63.01
7000 1.8194311 0.72981963 -3.6601329 2.6912418 0.576 72 0.068131849 0.067910074 0.11182024 0.51968 1.4517098 0.063444774 61.72
8000 1.947817 0.74570466 -3.0935809 2.8753489 0.504 63 0.068034071 0.067855883 0.11217045 0.53304 1.4924302 0.012298733 63.45
9000 1.8942389 1.3367401 -2.8925016 2.7962574 0.504 63 0.068117479 0.067943081 0.11236152 0.536 1.4091106 0.0011494886 63.73
10000 2.2092799 0.95517153 -2.9117781 3.2586879 0.48 60 0.068264792 0.068016591 0.11310789 0.52272 1.4774174 0.051284873 62.04
Loop time of 29.2417 on 4 procs for 10000 steps with 60 atoms
Performance: 181350.388 tau/day, 419.793 timesteps/s
97.6% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 147733.999 tau/day, 341.977 timesteps/s
96.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.10935 | 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
Pair | 0.11648 | 0.1221 | 0.13001 | 1.5 | 0.42
Neigh | 0.34452 | 0.35618 | 0.36328 | 1.2 | 1.22
Comm | 0.63561 | 0.65617 | 0.67542 | 1.8 | 2.24
Output | 0.00056601 | 0.00069755 | 0.00074744 | 0.0 | 0.00
Modify | 28.069 | 28.076 | 28.082 | 0.1 | 96.01
Other | | 0.03094 | | | 0.11
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
Nlocal: 15 ave 16 max 14 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 437 ave 446 max 431 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Neighs: 529 ave 595 max 437 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Total # of neighbors = 2823
Ave neighs/atom = 40.913
Total # of neighbors = 2116
Ave neighs/atom = 35.2667
Neighbor list builds = 10000
Dangerous builds = 0
Total wall time: 0:00:23
Total wall time: 0:00:29

10
src/MC/fix_gcmc.cpp
View File

@ -686,7 +686,7 @@ void FixGCMC::init()
// warning if group id is "all"
if (groupbit & 1)
if ((comm->me == 0) && (groupbit & 1))
error->warning(FLERR, "Fix gcmc is being applied "
"to the default group all");
@ -1253,6 +1253,10 @@ void FixGCMC::attempt_molecule_deletion()
if (ngas == 0) return;
// work-around to avoid n=0 problem with fix rigid/nvt/small
if (ngas == natoms_per_molecule) return;
tagint deletion_molecule = pick_random_gas_molecule();
if (deletion_molecule == -1) return;
@ -1910,6 +1914,10 @@ void FixGCMC::attempt_molecule_deletion_full()
if (ngas == 0) return;
// work-around to avoid n=0 problem with fix rigid/nvt/small
if (ngas == natoms_per_molecule) return;
tagint deletion_molecule = pick_random_gas_molecule();
if (deletion_molecule == -1) return;