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refactor how properties computed by the fix are accessed

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lambda is no an (intensive) scalar property
and the vector property only has the potential energies.
pressure is accessed via compute pressure/alchemy.
This commit is contained in:
Axel Kohlmeyer
2023-02-25 12:47:49 -05:00
parent d691d1db78
commit 60129958c8
5 changed files with 52 additions and 42 deletions
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4
examples/PACKAGES/alchemy/in.twowater
View File

@ -86,8 +86,8 @@ fix_modify integrate press pressure
# "dump 1 all atom 100 ${name}.lammpstrj" &
# "dump_modify 1 sort id"
thermo_style custom step temp press etotal density pe ke f_transform[1] f_transform[4]
thermo_modify colname f_transform[1] lambda colname f_transform[4] EPot_mixed
thermo_style custom step temp press etotal density pe ke f_transform f_transform[3]
thermo_modify colname f_transform lambda colname f_transform[3] EPot_mixed
thermo_modify press pressure
thermo 100

22
examples/PACKAGES/alchemy/log.25Feb23.twowater.g++.4.0
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@ -167,8 +167,8 @@ fix_modify integrate press pressure
# only need to output a dump file from one partition
# if "${name} == twowater" then # "dump 1 all atom 100 ${name}.lammpstrj" # "dump_modify 1 sort id"
thermo_style custom step temp press etotal density pe ke f_transform[1] f_transform[4]
thermo_modify colname f_transform[1] lambda colname f_transform[4] EPot_mixed
thermo_style custom step temp press etotal density pe ke f_transform f_transform[3]
thermo_modify colname f_transform lambda colname f_transform[3] EPot_mixed
thermo_modify press pressure
thermo 100
@ -377,21 +377,21 @@ Per MPI rank memory allocation (min/avg/max) = 7.535 | 7.535 | 7.535 Mbytes
19800 295.68946 81474.342 2308.3249 1.0240743 2219.3041 89.020804 0.01 1910.5545
19900 306.4947 43488.052 2330.4958 1.0222707 2238.222 92.27385 0.005 1957.4368
20000 313.31679 -25133.284 -1161.6979 1.0163289 -1256.0256 94.327722 0 -1649.7551
Loop time of 11.8252 on 2 procs for 20000 steps with 102 atoms
Loop time of 11.7903 on 2 procs for 20000 steps with 102 atoms
Performance: 29.226 ns/day, 0.821 hours/ns, 1691.296 timesteps/s, 172.512 katom-step/s
Performance: 29.312 ns/day, 0.819 hours/ns, 1696.311 timesteps/s, 173.024 katom-step/s
99.3% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 6.8298 | 8.6298 | 10.43 | 61.3 | 72.98
Bond | 0.045072 | 0.045296 | 0.045519 | 0.1 | 0.38
Neigh | 0.10567 | 0.10572 | 0.10577 | 0.0 | 0.89
Comm | 0.73714 | 2.5381 | 4.3392 | 113.0 | 21.46
Output | 0.0032977 | 0.0035468 | 0.003796 | 0.4 | 0.03
Modify | 0.43872 | 0.44155 | 0.44438 | 0.4 | 3.73
Other | | 0.06121 | | | 0.52
Pair | 6.8605 | 8.6071 | 10.354 | 59.5 | 73.00
Bond | 0.044148 | 0.044761 | 0.045375 | 0.3 | 0.38
Neigh | 0.10568 | 0.10573 | 0.10578 | 0.0 | 0.90
Comm | 0.74919 | 2.4939 | 4.2386 | 110.5 | 21.15
Output | 0.0033838 | 0.0036358 | 0.0038879 | 0.4 | 0.03
Modify | 0.46825 | 0.47526 | 0.48227 | 1.0 | 4.03
Other | | 0.05993 | | | 0.51
Nlocal: 51 ave 51 max 51 min
Histogram: 2 0 0 0 0 0 0 0 0 0

24
examples/PACKAGES/alchemy/log.25Feb23.twowater.g++.4.1
View File

@ -45,7 +45,7 @@ Read molecule template water:
create_atoms 0 single -2.0 0.0 0.0 mol water 453624
Created 3 atoms
using lattice units in orthogonal box = (-5 -5 -5) to (5 5 5)
create_atoms CPU = 0.004 seconds
create_atoms CPU = 0.003 seconds
create_atoms 0 single 2.0 0.0 0.0 mol water 767353
Created 3 atoms
using lattice units in orthogonal box = (-5 -5 -5) to (5 5 5)
@ -191,8 +191,8 @@ fix_modify integrate press pressure
# only need to output a dump file from one partition
# if "${name} == twowater" then # "dump 1 all atom 100 ${name}.lammpstrj" # "dump_modify 1 sort id"
thermo_style custom step temp press etotal density pe ke f_transform[1] f_transform[4]
thermo_modify colname f_transform[1] lambda colname f_transform[4] EPot_mixed
thermo_style custom step temp press etotal density pe ke f_transform f_transform[3]
thermo_modify colname f_transform lambda colname f_transform[3] EPot_mixed
thermo_modify press pressure
thermo 100
@ -402,21 +402,21 @@ Per MPI rank memory allocation (min/avg/max) = 7.535 | 7.535 | 7.535 Mbytes
19800 295.68946 81474.342 1996.4567 1.0240743 1907.4359 89.020804 0.99 1910.5545
19900 306.4947 43488.052 2048.2997 1.0222707 1956.0258 92.27385 0.995 1957.4368
20000 313.31679 -25133.284 -1555.4274 1.0163289 -1649.7551 94.327722 1 -1649.7551
Loop time of 11.8253 on 2 procs for 20000 steps with 102 atoms
Loop time of 11.7903 on 2 procs for 20000 steps with 102 atoms
Performance: 29.226 ns/day, 0.821 hours/ns, 1691.295 timesteps/s, 172.512 katom-step/s
Performance: 29.312 ns/day, 0.819 hours/ns, 1696.310 timesteps/s, 173.024 katom-step/s
99.3% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 6.8508 | 8.6272 | 10.404 | 60.5 | 72.96
Bond | 0.045829 | 0.046542 | 0.047256 | 0.3 | 0.39
Neigh | 0.10781 | 0.10791 | 0.108 | 0.0 | 0.91
Comm | 0.75178 | 2.5281 | 4.3045 | 111.7 | 21.38
Output | 0.0032916 | 0.0035722 | 0.0038527 | 0.5 | 0.03
Modify | 0.44867 | 0.45212 | 0.45556 | 0.5 | 3.82
Other | | 0.05976 | | | 0.51
Pair | 6.8748 | 8.631 | 10.387 | 59.8 | 73.20
Bond | 0.04667 | 0.047105 | 0.04754 | 0.2 | 0.40
Neigh | 0.10858 | 0.10862 | 0.10866 | 0.0 | 0.92
Comm | 0.74367 | 2.4997 | 4.2558 | 111.1 | 21.20
Output | 0.0034405 | 0.0037033 | 0.003966 | 0.4 | 0.03
Modify | 0.4338 | 0.4388 | 0.4438 | 0.8 | 3.72
Other | | 0.06136 | | | 0.52
Nlocal: 51 ave 51 max 51 min
Histogram: 2 0 0 0 0 0 0 0 0 0