From e05db94f7302ae13b57a6c6e03edf6de3009aa28 Mon Sep 17 00:00:00 2001 From: Riccardo Bertossa Date: Tue, 12 Nov 2024 15:40:09 +0000 Subject: [PATCH 1/2] the parser works when using many thermo_style before the parser was adding all the data in the same array, and parsing the numbers with the last headers found messing up if many headers and data columns were present in the output file. Now, if many header are present, the old data is forgotten as soon as a new Step ... header is found, and only the last one will be parsed in the output. This allows to parse output from LammpsRawCalculation with different thermo_style without errors, as the one found in https://docs.lammps.org/compute_heat_flux.html#example-input-file added test --- .../parsers/parse_raw/lammps_output.py | 2 + .../fixtures/raw/thermo_style/lammps.out | 147 ++++++++++++++++++ tests/parsers/test_raw.py | 14 ++ .../test_raw/test_double_thermo_style.yml | 17 ++ 4 files changed, 180 insertions(+) create mode 100644 tests/parsers/fixtures/raw/thermo_style/lammps.out create mode 100644 tests/parsers/test_raw/test_double_thermo_style.yml diff --git a/src/aiida_lammps/parsers/parse_raw/lammps_output.py b/src/aiida_lammps/parsers/parse_raw/lammps_output.py index 1c47eb6..d58463d 100644 --- a/src/aiida_lammps/parsers/parse_raw/lammps_output.py +++ b/src/aiida_lammps/parsers/parse_raw/lammps_output.py @@ -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() diff --git a/tests/parsers/fixtures/raw/thermo_style/lammps.out b/tests/parsers/fixtures/raw/thermo_style/lammps.out new file mode 100644 index 0000000..354681f --- /dev/null +++ b/tests/parsers/fixtures/raw/thermo_style/lammps.out @@ -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 diff --git a/tests/parsers/test_raw.py b/tests/parsers/test_raw.py index 97887b4..a0aecbd 100644 --- a/tests/parsers/test_raw.py +++ b/tests/parsers/test_raw.py @@ -18,6 +18,20 @@ def test_default(generate_calc_job_node, data_regression, fixture_localhost): assert calcfunction.is_finished_ok, calcfunction.exit_message 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.""" diff --git a/tests/parsers/test_raw/test_double_thermo_style.yml b/tests/parsers/test_raw/test_double_thermo_style.yml new file mode 100644 index 0000000..1e17f22 --- /dev/null +++ b/tests/parsers/test_raw/test_double_thermo_style.yml @@ -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: [] From 19f90952739c5b43babe6b0cfc1373adca3fd9ae Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Thu, 14 Nov 2024 18:19:10 +0000 Subject: [PATCH 2/2] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- .../fixtures/raw/thermo_style/lammps.out | 116 +++++++++--------- tests/parsers/test_raw.py | 5 +- 2 files changed, 62 insertions(+), 59 deletions(-) diff --git a/tests/parsers/fixtures/raw/thermo_style/lammps.out b/tests/parsers/fixtures/raw/thermo_style/lammps.out index 354681f..5bb22a6 100644 --- a/tests/parsers/fixtures/raw/thermo_style/lammps.out +++ b/tests/parsers/fixtures/raw/thermo_style/lammps.out @@ -25,12 +25,12 @@ Setting up Verlet run ... 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 + 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 @@ -63,58 +63,58 @@ Setting up Verlet run ... 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 + 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 diff --git a/tests/parsers/test_raw.py b/tests/parsers/test_raw.py index a0aecbd..a4d6883 100644 --- a/tests/parsers/test_raw.py +++ b/tests/parsers/test_raw.py @@ -18,7 +18,10 @@ def test_default(generate_calc_job_node, data_regression, fixture_localhost): assert calcfunction.is_finished_ok, calcfunction.exit_message data_regression.check({"results": results["results"].get_dict()}) -def test_double_thermo_style(generate_calc_job_node, data_regression, fixture_localhost): + +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,