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Commit 44fcdc40 authored by Axel Kohlmeyer's avatar Axel Kohlmeyer
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update reference examples with versions that do not vary by MPI rank count

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examples/USER/misc/mop/data.mop 0 → 100644
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examples/USER/misc/mop/in.compute_stress_mop
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variable T equal 0.8
variable p_solid equal 0.05
lattice fcc 1.0
region box block 0.0 6.0 0.0 6.0 -2.0 12.0
create_box 2 box
read_data data.mop
mass * 1.0
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0
pair_coeff 1 2 0.5 1.0
pair_coeff 2 2 0.0 0.0
neigh_modify delay 0
region solid_bottom block INF INF INF INF -1.1 0.1
region liquid block INF INF INF INF 1.1 8.9
region solid_up block INF INF INF INF 9.9 11.1
create_atoms 1 region liquid
delete_atoms porosity liquid 0.26 88765
group liquid region liquid
create_atoms 2 region solid_bottom
group solid_bottom region solid_bottom
create_atoms 2 region solid_up
group solid_up region solid_up
group solid union solid_bottom solid_up
group liquid type 1
group solid type 2
region bottom block INF INF INF INF INF 7.0
group bottom region bottom
group solid_bottom intersect solid bottom
group solid_up subtract solid solid_bottom
variable faSolid equal ${p_solid}*lx*ly/count(solid_up)
fix piston_up solid_up aveforce NULL NULL -${faSolid}
......@@ -35,28 +25,16 @@ compute Tliq liquid temp
fix nvtliq liquid nvt temp $T $T 0.5
fix_modify nvtliq temp Tliq
thermo 10000
thermo 1000
thermo_modify flush yes temp Tliq
dump 1 all atom 10000 dump.lammpstrj
fix fxbal all balance 1000 1.05 shift z 10 1.05
velocity liquid create $T 47298 dist gaussian rot yes
run 50000
undump 1
reset_timestep 0
compute bin_z liquid chunk/atom bin/1d z 0.0 0.1 units box
compute liquidStress_ke liquid stress/atom NULL ke
compute liquidStress_vir liquid stress/atom NULL virial
fix profile_z liquid ave/chunk 10 1000 10000 bin_z density/number temp c_liquidStress_ke[1] c_liquidStress_ke[2] c_liquidStress_ke[3] c_liquidStress_ke[4] c_liquidStress_ke[5] c_liquidStress_ke[6] c_liquidStress_vir[1] c_liquidStress_vir[2] c_liquidStress_vir[3] c_liquidStress_vir[4] c_liquidStress_vir[5] c_liquidStress_vir[6] ave running overwrite file profile.z
compute mopz0 all stress/mop z center kin conf
fix mopz0t all ave/time 10 1000 10000 c_mopz0[*] file mopz0.time
fix mopz0t all ave/time 1 1 1 c_mopz0[*] file mopz0.time
compute moppz liquid stress/mop/profile z 0.0 0.1 kin conf
fix moppzt all ave/time 100 100 10000 c_moppz[*] ave running overwrite file moppz.time mode vector
fix moppzt all ave/time 1 1 1 c_moppz[*] ave running overwrite file moppz.time mode vector
run 40000
run 0
examples/USER/misc/mop/log.5Sep18.compute_stress_mop.g++.1 0 → 100644
+ 111
− 0
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LAMMPS (5 Sep 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
variable T equal 0.8
variable p_solid equal 0.05
read_data data.mop
orthogonal box = (0 0 -2) to (9.52441 9.52441 16)
1 by 1 by 1 MPI processor grid
reading atoms ...
1224 atoms
reading velocities ...
1224 velocities
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0
pair_coeff 1 2 0.5 1.0
pair_coeff 2 2 0.0 0.0
neigh_modify delay 0
group liquid type 1
792 atoms in group liquid
group solid type 2
432 atoms in group solid
region bottom block INF INF INF INF INF 7.0
group bottom region bottom
630 atoms in group bottom
group solid_bottom intersect solid bottom
216 atoms in group solid_bottom
group solid_up subtract solid solid_bottom
216 atoms in group solid_up
variable faSolid equal ${p_solid}*lx*ly/count(solid_up)
variable faSolid equal 0.05*lx*ly/count(solid_up)
fix piston_up solid_up aveforce NULL NULL -${faSolid}
fix piston_up solid_up aveforce NULL NULL -0.0209986841649146
fix freeze_up solid_up setforce 0.0 0.0 NULL
fix freeze_bottom solid_bottom setforce 0.0 0.0 0.0
fix nvesol solid nve
compute Tliq liquid temp
fix nvtliq liquid nvt temp $T $T 0.5
fix nvtliq liquid nvt temp 0.8 $T 0.5
fix nvtliq liquid nvt temp 0.8 0.8 0.5
fix_modify nvtliq temp Tliq
WARNING: Temperature for fix modify is not for group all (src/fix_nh.cpp:1404)
thermo 1000
thermo_modify flush yes temp Tliq
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488)
fix fxbal all balance 1000 1.05 shift z 10 1.05
compute mopz0 all stress/mop z center kin conf
fix mopz0t all ave/time 1 1 1 c_mopz0[*] file mopz0.time
compute moppz liquid stress/mop/profile z 0.0 0.1 kin conf
fix moppzt all ave/time 1 1 1 c_moppz[*] ave running overwrite file moppz.time mode vector
run 0
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 7 7 13
3 neighbor lists, perpetual/occasional/extra = 1 2 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
(2) compute stress/mop, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
(3) compute stress/mop/profile, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 3.596 | 3.596 | 3.596 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0.82011245 -3.0642111 0 -2.2692246 0.16906107 1632.8577
Loop time of 1.19209e-06 on 1 procs for 0 steps with 1224 atoms
167.8% 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 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 1.192e-06 | | |100.00
Nlocal: 1224 ave 1224 max 1224 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2975 ave 2975 max 2975 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 40241 ave 40241 max 40241 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 40241
Ave neighs/atom = 32.8766
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00
examples/USER/misc/mop/log.5Sep18.compute_stress_mop.g++.4 0 → 100644
+ 111
− 0
View file @ 44fcdc40
LAMMPS (5 Sep 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
variable T equal 0.8
variable p_solid equal 0.05
read_data data.mop
orthogonal box = (0 0 -2) to (9.52441 9.52441 16)
1 by 2 by 2 MPI processor grid
reading atoms ...
1224 atoms
reading velocities ...
1224 velocities
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0
pair_coeff 1 2 0.5 1.0
pair_coeff 2 2 0.0 0.0
neigh_modify delay 0
group liquid type 1
792 atoms in group liquid
group solid type 2
432 atoms in group solid
region bottom block INF INF INF INF INF 7.0
group bottom region bottom
630 atoms in group bottom
group solid_bottom intersect solid bottom
216 atoms in group solid_bottom
group solid_up subtract solid solid_bottom
216 atoms in group solid_up
variable faSolid equal ${p_solid}*lx*ly/count(solid_up)
variable faSolid equal 0.05*lx*ly/count(solid_up)
fix piston_up solid_up aveforce NULL NULL -${faSolid}
fix piston_up solid_up aveforce NULL NULL -0.0209986841649146
fix freeze_up solid_up setforce 0.0 0.0 NULL
fix freeze_bottom solid_bottom setforce 0.0 0.0 0.0
fix nvesol solid nve
compute Tliq liquid temp
fix nvtliq liquid nvt temp $T $T 0.5
fix nvtliq liquid nvt temp 0.8 $T 0.5
fix nvtliq liquid nvt temp 0.8 0.8 0.5
fix_modify nvtliq temp Tliq
WARNING: Temperature for fix modify is not for group all (src/fix_nh.cpp:1404)
thermo 1000
thermo_modify flush yes temp Tliq
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488)
fix fxbal all balance 1000 1.05 shift z 10 1.05
compute mopz0 all stress/mop z center kin conf
fix mopz0t all ave/time 1 1 1 c_mopz0[*] file mopz0.time
compute moppz liquid stress/mop/profile z 0.0 0.1 kin conf
fix moppzt all ave/time 1 1 1 c_moppz[*] ave running overwrite file moppz.time mode vector
run 0
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 7 7 13
3 neighbor lists, perpetual/occasional/extra = 1 2 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
(2) compute stress/mop, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
(3) compute stress/mop/profile, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 3.509 | 3.51 | 3.511 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0.82011245 -3.0642111 0 -2.2692246 0.16906107 1632.8577
Loop time of 4.06504e-05 on 4 procs for 0 steps with 1224 atoms
65.2% 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 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 4.065e-05 | | |100.00
Nlocal: 306 ave 320 max 295 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Nghost: 1450.25 ave 1485 max 1422 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Neighs: 10060.2 ave 10866 max 9507 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Total # of neighbors = 40241
Ave neighs/atom = 32.8766
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00
examples/USER/misc/mop/moppz.time.reference
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examples/USER/misc/mop/mopz0.time.reference
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# Time-averaged data for fix mopz0t
# TimeStep c_mopz0[1] c_mopz0[2] c_mopz0[3] c_mopz0[4] c_mopz0[5] c_mopz0[6]
10000 -0.0267908 -0.0366912 0.634417 0.00702203 0.00200985 -0.552264
20000 0.0202912 -0.0217482 0.597513 -0.00157669 -0.00587006 -0.537147
30000 -0.00244239 -0.02829 0.616384 0.00640645 0.00932437 -0.561132
40000 0.00541112 -0.0764546 0.613812 -0.00450554 -0.0038376 -0.537305
0 1.62633 1.08234 0.844097 1.18575 -0.408792 -0.752394
examples/USER/misc/mop/profile.z.reference deleted 100644 → 0
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− 227
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