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the parser works when using many thermo_style #166

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Nov 18, 2024
Merged

the parser works when using many thermo_style #166

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e05db94
the parser works when using many thermo_style
rikigigi Nov 12, 2024
19f9095
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Nov 14, 2024
7b198cf
Merge branch 'master' into fix-parser-step-many
JPchico Nov 17, 2024
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2 changes: 2 additions & 0 deletions src/aiida_lammps/parsers/parse_raw/lammps_output.py
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Original file line number Diff line number Diff line change
Expand Up @@ -106,6 +106,8 @@ def parse_outputfile(
)

if line.startswith("Step"):
_data = []
end_found = False
header_line_position = index
header_line = [
re.sub("[^a-zA-Z0-9_]", "__", entry) for entry in line.split()
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147 changes: 147 additions & 0 deletions tests/parsers/fixtures/raw/thermo_style/lammps.out
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Original file line number Diff line number Diff line change
@@ -0,0 +1,147 @@
LAMMPS (29 Aug 2024 - Update 1)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
Lattice spacing in x,y,z = 5.376 5.376 5.376
Created orthogonal box = (0 0 0) to (21.504 21.504 21.504)
1 by 1 by 1 MPI processor grid
Created 256 atoms
using lattice units in orthogonal box = (0 0 0) to (21.504 21.504 21.504)
create_atoms CPU = 0.000 seconds
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 15
ghost atom cutoff = 15
binsize = 7.5, bins = 3 3 3
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Setting up Verlet run ...
Unit style : real
Current step : 0
Time step : 4
Per MPI rank memory allocation (min/avg/max) = 3.219 | 3.219 | 3.219 Mbytes
Step Temp E_pair E_mol TotEng Press
0 70 -505.75228 0 -452.54482 -1289.8945
2000 74.682256 -457.63699 0 -400.87052 547.1463
4000 73.36116 -460.69876 0 -404.93646 431.33436
6000 67.978895 -453.88308 0 -402.21187 653.83993
8000 64.247137 -462.836 0 -414.00133 329.70822
Loop time of 3.65187 on 1 procs for 8000 steps with 256 atoms

Performance: 757.092 ns/day, 0.032 hours/ns, 2190.659 timesteps/s, 560.809 katom-step/s
98.0% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.36 | 3.36 | 3.36 | 0.0 | 92.01
Neigh | 0.1196 | 0.1196 | 0.1196 | 0.0 | 3.27
Comm | 0.091569 | 0.091569 | 0.091569 | 0.0 | 2.51
Output | 0.00010239 | 0.00010239 | 0.00010239 | 0.0 | 0.00
Modify | 0.043827 | 0.043827 | 0.043827 | 0.0 | 1.20
Other | | 0.03682 | | | 1.01

Nlocal: 256 ave 256 max 256 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3173 ave 3173 max 3173 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 46468 ave 46468 max 46468 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 46468
Ave neighs/atom = 181.51562
Neighbor list builds = 116
Dangerous builds = 0
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Setting up Verlet run ...
Unit style : real
Current step : 0
Time step : 4
Per MPI rank memory allocation (min/avg/max) = 5.096 | 5.096 | 5.096 Mbytes
Step Temp v_Jx v_Jy v_Jz v_k11 v_k22 v_k33
0 64.247137 -1.8079942e-06 -8.7890766e-07 -8.457266e-07 0.0046430011 0.0010972136 0.0010159321
2000 61.525894 -2.1598221e-06 1.0240044e-06 1.9775571e-06 0.085351069 0.57508192 0.17631439
4000 63.72472 2.2409554e-06 -1.6104003e-06 6.5006041e-08 0.058053309 0.17470542 0.2134226
6000 64.544354 3.9665371e-06 2.7743094e-07 -1.3962294e-06 0.48489461 0.12364319 0.10073154
8000 65.8238 1.3884442e-07 -2.2290428e-06 6.1578573e-06 0.57368765 0.30293599 0.094771849
10000 61.90025 2.0628691e-08 -3.8429267e-06 -1.3669631e-07 0.44428628 0.28608541 0.065179307
12000 64.617723 1.7775555e-06 -7.5167728e-06 1.5244731e-06 0.40535052 0.42200227 0.094071588
14000 62.062981 5.8507965e-06 -8.2314658e-07 1.9386634e-07 0.40465712 0.60088211 0.16315905
16000 63.974837 -1.0745593e-06 -2.848019e-06 -7.2257276e-07 0.38002527 0.50959436 0.14997039
18000 62.366711 1.6218743e-06 -1.7189792e-06 2.6231651e-06 0.37335212 0.44943645 0.1818345
20000 63.35814 -1.8347676e-07 6.2252326e-07 1.1084105e-06 0.34894157 0.40034091 0.15528223
22000 69.342878 1.423516e-06 -2.2446676e-06 3.6250541e-06 0.34858894 0.3773924 0.17947248
24000 58.501486 -2.5080979e-06 -8.3621623e-07 -1.4212996e-06 0.31032444 0.37896275 0.17537428
26000 62.763231 1.9173142e-07 1.7557205e-06 -3.3271006e-07 0.31493569 0.35130261 0.12796826
28000 63.43571 -2.306012e-06 -9.1269595e-07 4.041346e-07 0.29342946 0.32234586 0.14031226
30000 64.672878 3.9564769e-06 3.1243623e-06 -8.7420521e-07 0.2723538 0.33779975 0.19755617
32000 66.158501 1.880267e-06 -2.0937431e-06 -6.1682203e-07 0.25070333 0.32797017 0.19945131
34000 67.46263 -1.0614188e-06 8.222906e-08 2.9876766e-06 0.27905678 0.31010677 0.17831269
36000 62.10909 -2.8469855e-06 -4.6502305e-06 1.1223538e-06 0.27268614 0.30170783 0.16163906
38000 68.223927 -4.5540226e-06 1.548782e-07 1.4079104e-06 0.25342992 0.28814925 0.1572844
40000 60.71867 -1.8838187e-06 -9.5928082e-07 3.2171931e-06 0.23445129 0.2797954 0.18269736
42000 63.322401 -3.7530825e-07 2.4923075e-06 -2.938255e-06 0.2223093 0.26328744 0.21723599
44000 61.983322 1.3970281e-06 -4.5642174e-08 2.3503367e-07 0.21461737 0.25278444 0.23425212
46000 62.867579 -4.5015621e-06 -2.7157351e-06 2.2098371e-06 0.20562955 0.24675866 0.30204928
48000 67.355454 -2.4491652e-06 1.2453223e-06 -2.1320399e-07 0.22129212 0.23828696 0.30327962
50000 60.895587 2.1804066e-06 3.2693656e-07 1.23064e-06 0.21765599 0.23327483 0.27418783
52000 63.87045 1.3170449e-06 2.3010037e-06 1.5758504e-06 0.26890127 0.25011837 0.26157802
54000 63.642782 1.3862033e-07 1.8111635e-06 6.4693025e-07 0.26838091 0.29179343 0.25716217
56000 62.000213 5.6818896e-07 -5.4689229e-07 1.3046324e-06 0.27030927 0.29637661 0.25795301
58000 66.633073 3.0132965e-06 7.1862822e-07 -7.9702673e-08 0.2619932 0.28474913 0.24514888
60000 61.932864 6.7789186e-06 -1.7228147e-06 2.9651378e-06 0.25476542 0.27105789 0.24344415
62000 67.730639 -4.8479584e-07 -2.6325008e-06 -2.0428717e-06 0.24458967 0.26203962 0.23648301
64000 61.144379 -1.1273114e-06 -9.9286044e-07 1.8248023e-06 0.23367492 0.29444383 0.24852866
66000 62.210646 -2.1319529e-06 -2.2198766e-06 -1.5480782e-06 0.22485215 0.29804936 0.24678006
68000 62.381233 -2.8568977e-06 -1.7579616e-06 2.8269342e-06 0.2163173 0.29064131 0.23681681
70000 63.061911 -5.9148019e-07 5.6632907e-07 2.5460687e-06 0.21130195 0.2872965 0.24396951
72000 65.799805 -2.5912563e-07 3.2049528e-06 -6.0646022e-07 0.21059792 0.27197304 0.23379899
74000 66.314917 3.0989796e-06 2.5407123e-06 9.1727192e-07 0.22099481 0.26486809 0.25857014
76000 59.378433 -3.5453259e-06 -3.0209319e-06 3.1232621e-06 0.21583578 0.26188808 0.26488965
78000 61.604179 6.2627304e-08 2.9554163e-06 5.5230142e-06 0.22471699 0.2488775 0.25364298
80000 58.837728 -4.1814589e-06 -2.0533193e-06 1.8953793e-06 0.24829924 0.24093423 0.24998458
82000 62.15903 -1.9418324e-06 2.4310144e-06 2.6541324e-06 0.26576646 0.23570854 0.24046833
84000 64.714896 -6.2887387e-06 -5.8555453e-07 3.6509298e-06 0.26615445 0.23668873 0.23401392
86000 61.031618 -2.0497528e-07 3.0562669e-06 2.7240488e-06 0.27110318 0.23271246 0.2290402
88000 63.341113 1.9386269e-06 -5.0463508e-07 7.0518402e-07 0.27944331 0.23766011 0.27765394
90000 62.853688 2.8472732e-06 2.1997331e-06 -1.2000712e-06 0.27096182 0.25218938 0.27813078
92000 62.883809 3.5212323e-07 -3.0337211e-06 -1.3839795e-06 0.26153682 0.25692921 0.30104626
94000 61.765562 -2.7175472e-06 1.5353385e-06 1.4675356e-06 0.26512315 0.25522882 0.28668193
96000 61.747073 9.6732172e-07 1.5750852e-07 -8.672387e-07 0.26879919 0.25234201 0.28455876
98000 61.103977 -1.6708854e-06 5.1839447e-06 1.5492511e-09 0.27614829 0.25507382 0.2838748
100000 65.563661 3.4048861e-06 -4.7928087e-08 -1.4188391e-06 0.26142703 0.24653363 0.28040529
Loop time of 50.5402 on 1 procs for 100000 steps with 256 atoms

Performance: 683.813 ns/day, 0.035 hours/ns, 1978.624 timesteps/s, 506.528 katom-step/s
97.8% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 46.569 | 46.569 | 46.569 | 0.0 | 92.14
Neigh | 1.3368 | 1.3368 | 1.3368 | 0.0 | 2.65
Comm | 1.1412 | 1.1412 | 1.1412 | 0.0 | 2.26
Output | 0.1926 | 0.1926 | 0.1926 | 0.0 | 0.38
Modify | 0.82607 | 0.82607 | 0.82607 | 0.0 | 1.63
Other | | 0.4748 | | | 0.94

Nlocal: 256 ave 256 max 256 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3173 ave 3173 max 3173 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 46456 ave 46456 max 46456 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 46456
Ave neighs/atom = 181.46875
Neighbor list builds = 1302
Dangerous builds = 0
average conductivity: 0.262788650407571[W/mK] @ 70 K, 0.0257443666020476 /A\^3
System init for write_data ...
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Total wall time: 0:00:54
17 changes: 17 additions & 0 deletions tests/parsers/test_raw.py
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Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,23 @@ def test_default(generate_calc_job_node, data_regression, fixture_localhost):
data_regression.check({"results": results["results"].get_dict()})


def test_double_thermo_style(
generate_calc_job_node, data_regression, fixture_localhost
):
"""Test parsing a double thermo_style output case."""
node = generate_calc_job_node(
computer=fixture_localhost,
entry_point_name="lammps.raw",
test_name="parsers/fixtures/raw/thermo_style",
)
parser = ParserFactory("lammps.raw")
results, calcfunction = parser.parse_from_node(node, store_provenance=False)

assert calcfunction.is_finished, calcfunction.exception
assert calcfunction.is_finished_ok, calcfunction.exit_message
data_regression.check({"results": results["results"].get_dict()})


def test_alt_timing_info(generate_calc_job_node, data_regression, fixture_localhost):
"""Test parsing an alt output case."""
node = generate_calc_job_node(
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17 changes: 17 additions & 0 deletions tests/parsers/test_raw/test_double_thermo_style.yml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,17 @@
results:
compute_variables:
bin: standard
bins:
- 3
- 3
- 3
binsize: 7.5
errors: []
ghost_atom_cutoff: 15
master_list_distance_cutoff: 15
max_neighbors_atom: 2000
steps_per_second: 2190.659
total_wall_time: 0:00:54
total_wall_time_seconds: 54
units_style: real
warnings: []