Comments (3)
jotelha
commented on July 16, 2024
Looking at the two chained commands' stderr in CI now, there are a) warnings about the numpy & scipy version, and b) an error on reading from stdout in the second chained command. This looks like stdout is polluted by some plain text again, as had been the case in #211.
______________ ElectrochemistryCliTest.test_pnp_c2d_pipeline_mode ______________
self = <test_electrochemistry_cli.ElectrochemistryCliTest testMethod=test_pnp_c2d_pipeline_mode>
def test_pnp_c2d_pipeline_mode(self):
"""poisson-nernst-planck -c 0.1 0.1 -u 0.05 -l 1.0e-7 -bc cell | continuous2discrete > NaCl.xyz"""
print(" RUN test_pnp_c2d_pipeline_mode")
with tempfile.TemporaryDirectory() as tmpdir:
pnp = subprocess.Popen(
['pnp', '-c', '0.1', '0.1', '-z', '1', '-1',
'-u', '0.05', '-l', '1.0e-7', '-bc', 'cell'],
stdout=subprocess.PIPE, stderr=subprocess.PIPE,
cwd=tmpdir, encoding='utf-8', env=self.myenv)
c2d = subprocess.Popen(['c2d'],
stdin=pnp.stdout, stdout=subprocess.PIPE, stderr=subprocess.PIPE,
cwd=tmpdir, encoding='utf-8', env=self.myenv)
pnp.stdout.close() # Allow pnp to receive a SIGPIPE if p2 exits.
print(" poisson-nernst-planck stderr")
print(pnp.stderr.read())
print(" poisson-nernst-planck stderr")
print(c2d.stderr.read())
> self.assertEqual(c2d.wait(),0)
test_electrochemistry_cli.py:195:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
matscipytest.py:91: in assertEqual
self.fail('%s != %s' % (a,b))
E AssertionError: 1 != 0
----------------------------- Captured stdout call -----------------------------
RUN test_pnp_c2d_pipeline_mode
poisson-nernst-planck stderr
/usr/lib/python3/dist-packages/scipy/__init__.py:146: UserWarning: A NumPy version >=1.17.3 and <1.25.0 is required for this version of SciPy (detected version 1.26.3
warnings.warn(f"A NumPy version >={np_minversion} and <{np_maxversion}"
poisson-nernst-planck stderr
/usr/lib/python3/dist-packages/scipy/__init__.py:146: UserWarning: A NumPy version >=1.17.3 and <1.25.0 is required for this version of SciPy (detected version 1.26.3
warnings.warn(f"A NumPy version >={np_minversion} and <{np_maxversion}"
ValueError: could not convert string to float: 'Calling'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/tmp/tmpty526hk4/c2d", line 312, in <module>
main()
File "/tmp/tmpty526hk4/c2d", line 208, in main
data = np.loadtxt(infile, unpack=True)
File "/usr/local/lib/python3.10/dist-packages/numpy/lib/npyio.py", line 1373, in loadtxt
arr = _read(fname, dtype=dtype, comment=comment, delimiter=delimiter,
File "/usr/local/lib/python3.10/dist-packages/numpy/lib/npyio.py", line 1016, in _read
arr = _load_from_filelike(
ValueError: could not convert string 'Calling' to float64 at row 0, column 1.
WIll inspect content of stdout next.
from matscipy.
jotelha
commented on July 16, 2024
The culprit are again fenics messages being printed to stdout, now have to figure out why that still happens in CI,
https://github.com/libAtoms/matscipy/actions/runs/7519293192/job/20467663371#step:6:951
______________ ElectrochemistryCliTest.test_pnp_c2d_pipeline_mode ______________
self = <test_electrochemistry_cli.ElectrochemistryCliTest testMethod=test_pnp_c2d_pipeline_mode>
def test_pnp_c2d_pipeline_mode(self):
"""poisson-nernst-planck -c 0.1 0.1 -u 0.05 -l 1.0e-7 -bc cell | continuous2discrete > NaCl.xyz"""
print(" RUN test_pnp_c2d_pipeline_mode")
with tempfile.TemporaryDirectory() as tmpdir:
pnp = subprocess.Popen(
['pnp', '-c', '0.1', '0.1', '-z', '1', '-1',
'-u', '0.05', '-l', '1.0e-7', '-bc', 'cell'],
stdout=subprocess.PIPE, stderr=subprocess.PIPE,
cwd=tmpdir, encoding='utf-8', env=self.myenv)
# detour via python string
pnp_output, pnp_error = pnp.communicate()
c2d = subprocess.Popen(['c2d'],
stdin=subprocess.PIPE, stdout=subprocess.PIPE, stderr=subprocess.PIPE,
cwd=tmpdir, encoding='utf-8', env=self.myenv)
# pnp.stdout.close() # Allow pnp to receive a SIGPIPE if p2 exits.
c2d_output, c2d_error = c2d.communicate(input=pnp_output)
print(" poisson-nernst-planck stdout")
print(pnp_output)
print(" poisson-nernst-planck stderr")
print(pnp_error)
print(" continuous2discrete output")
print(c2d_output)
print(" continuous2discrete stderr")
print(c2d_error)
> self.assertEqual(c2d.wait(),0)
test_electrochemistry_cli.py:205:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
matscipytest.py:91: in assertEqual
self.fail('%s != %s' % (a,b))
E AssertionError: 1 != 0
----------------------------- Captured stdout call -----------------------------
RUN test_pnp_c2d_pipeline_mode
poisson-nernst-planck stdout
Calling FFC just-in-time (JIT) compiler, this may take some time.
Calling FFC just-in-time (JIT) compiler, this may take some time.
Calling FFC just-in-time (JIT) compiler, this may take some time.
Calling FFC just-in-time (JIT) compiler, this may take some time.
Calling FFC just-in-time (JIT) compiler, this may take some time.
Calling FFC just-in-time (JIT) compiler, this may take some time.
Calling FFC just-in-time (JIT) compiler, this may take some time.
Calling FFC just-in-time (JIT) compiler, this may take some time.
Calling FFC just-in-time (JIT) compiler, this may take some time.
# Poisson-Nernst-Planck system, generated on fv-az695-896, 2024-01-14 13:14:05
# All quantities in SI units.
# grid x (m), potential u (V), concentration c (mM)
# x u c00 c01
0.000000000000000e+00 2.500000000000000e-02 3.361699383958267e-02 2.353606298450038e-01
5.000000000000000e-10 2.456698205542749e-02 3.418836980166941e-02 2.314271458267463e-01
1.000000000000000e-09 2.414076617627088e-02 3.476025330092748e-02 2.276196544149400e-01
1.500000000000000e-09 2.372120132620931e-02 3.533255522990080e-02 2.239327666027845e-01
2.000000000000000e-09 2.330814061426506e-02 3.590518905246078e-02 2.203613754058880e-01
2.500000000000000e-09 2.290144112162466e-02 3.647807082208459e-02 2.169006382607436e-01
3.000000000000000e-09 2.250096373749287e-02 3.705111919817845e-02 2.135459606908529e-01
3.500000000000000e-09 2.210657300341518e-02 3.762425546050122e-02 2.102929811372246e-01
4.000000000000000e-09 2.171813696554525e-02 3.819740352174557e-02 2.071375568593481e-01
4.500000000000000e-09 2.133552703437018e-02 3.877048993833473e-02 2.040757508211749e-01
5.000000000000001e-09 2.095861785144087e-02 3.934344391949386e-02 2.011038194842408e-01
5.500000000000000e-09 2.058728716268605e-02 3.991619733465646e-02 1.982182014369213e-01
6.000000000000000e-09 2.022141569791732e-02 4.048868471926654e-02 1.954155067950029e-01
6.500000000000000e-09 1.986088705615933e-02 4.106084327903828e-02 1.926925073143549e-01
7.000000000000001e-09 1.950558759646397e-02 4.163261289273545e-02 1.900461271615480e-01
7.499999999999999e-09 1.915540633388987e-02 4.220393611353353e-02 1.874734342928608e-01
8.000000000000000e-09 1.881023484034987e-02 4.277475816902727e-02 1.849716323962712e-01
8.500000000000000e-09 1.846996715004838e-02 4.334502695994780e-02 1.825380533548103e-01
9.000000000000000e-09 1.813449966924880e-02 4.391469305765255e-02 1.801701501930849e-01
9.499999999999999e-09 1.780373109012753e-02 4.448370970045194e-02 1.778654904718952e-01
1.000000000000000e-08 1.747756230848704e-02 4.505203278883679e-02 1.756217500987125e-01
1.050000000000000e-08 1.715589634511455e-02 4.561962087967032e-02 1.734367075243687e-01
1.100000000000000e-08 1.683863827058618e-02 4.618643517940831e-02 1.713082382986646e-01
1.150000000000000e-08 1.652569513332930e-02 4.675243953641139e-02 1.692343099597595e-01
1.200000000000000e-08 1.621697589076671e-02 4.731760043241223e-02 1.672129772341627e-01
1.250000000000000e-08 1.591239134337755e-02 4.788188697320131e-02 1.652423775259481e-01
1.300000000000000e-08 1.561185407151962e-02 4.844527087859334e-02 1.633207266754531e-01
1.350000000000000e-08 1.531527837486709e-02 4.900772647173724e-02 1.614463149692253e-01
1.400000000000000e-08 1.502258021432637e-02 4.956923066783086e-02 1.596175033843604e-01
1.450000000000000e-08 1.473367715630098e-02 5.012976296230229e-02 1.578327200516320e-01
1.500000000000000e-08 1.444848831918378e-02 5.068930541851820e-02 1.560904569229802e-01
1.550000000000000e-08 1.416693432196204e-02 5.124784265507988e-02 1.543892666299813e-01
1.600000000000000e-08 1.388893723482745e-02 5.180536183276595e-02 1.527277595209037e-01
1.650000000000000e-08 1.361442053168925e-02 5.236185264118143e-02 1.511046008648508e-01
1.700000000000000e-08 1.334330904449453e-02 5.291730728517109e-02 1.495185082123208e-01
1.750000000000000e-08 1.307552891926519e-02 5.347172047105506e-02 1.479682489022716e-01
1.800000000000000e-08 1.281100757376584e-02 5.402508939274360e-02 1.464526377064834e-01
1.850000000000000e-08 1.254967365672211e-02 5.457741371778740e-02 1.449705346026564e-01
1.900000000000000e-08 1.229145700851281e-02 5.512869557341933e-02 1.435208426682789e-01
1.950000000000000e-08 1.203628862326401e-02 5.567893953264202e-02 1.421025060878502e-01
2.000000000000000e-08 1.178410061227650e-02 5.622815260041659e-02 1.407145082665546e-01
2.050000000000000e-08 1.153482616872223e-02 5.677634420000507e-02 1.393558700439495e-01
2.100000000000000e-08 1.128839953354863e-02 5.732352615952033e-02 1.380256480016684e-01
2.150000000000000e-08 1.104475596253263e-02 5.786971269873538e-02 1.367229328595420e-01
2.200000000000000e-08 1.080383169442985e-02 5.841492041620399e-02 1.354468479549113e-01
2.250000000000000e-08 1.056556392016667e-02 5.895916827674337e-02 1.341965478002552e-01
2.300000000000000e-08 1.032989075302607e-02 5.950247759932989e-02 1.329712167145732e-01
2.350000000000000e-08 1.009675119978024e-02 6.004487204545725e-02 1.317700675242618e-01
2.400000000000000e-08 9.866085132725766e-03 6.058637760800684e-02 1.305923403294988e-01
2.450000000000000e-08 9.637833262579087e-03 6.112702260067892e-02 1.294373013324064e-01
2.500000000000000e-08 9.411937112192150e-03 6.166683764803337e-02 1.283042417235012e-01
2.550000000000000e-08 9.188338991050331e-03 6.220585567618742e-02 1.271924766231610e-01
2.600000000000000e-08 8.966981970516293e-03 6.274411190421876e-02 1.261013440750441e-01
2.650000000000000e-08 8.747809859785419e-03 6.328164383632048e-02 1.250302040885877e-01
2.700000000000000e-08 8.530767182520079e-03 6.381849125475535e-02 1.239784377278923e-01
2.750000000000000e-08 8.315799154131491e-03 6.435469621365593e-02 1.229454462444624e-01
2.800000000000000e-08 8.102851659679543e-03 6.489030303371719e-02 1.219306502514308e-01
2.850000000000000e-08 7.891871232362216e-03 6.542535829782788e-02 1.209334889370378e-01
2.900000000000000e-08 7.682805032567656e-03 6.595991084768697e-02 1.199534193152710e-01
2.950000000000000e-08 7.475600827463202e-03 6.649401178145170e-02 1.189899155116966e-01
3.000000000000000e-08 7.270206971096714e-03 6.702771445246332e-02 1.180424680826331e-01
3.050000000000000e-08 7.066572384986891e-03 6.756107446909727e-02 1.171105833659249e-01
3.100000000000000e-08 6.864646539180095e-03 6.809414969578405e-02 1.161937828616773e-01
3.150000000000000e-08 6.664379433752324e-03 6.862700025524836e-02 1.152916026414125e-01
3.200000000000000e-08 6.465721580735872e-03 6.915968853201317e-02 1.144035927841903e-01
3.250000000000000e-08 6.268623986451110e-03 6.969227917721654e-02 1.135293168383290e-01
3.300000000000000e-08 6.073038134224648e-03 7.022483911478984e-02 1.126683513074329e-01
3.350000000000000e-08 5.878915967475947e-03 7.075743754904533e-02 1.118202851595133e-01
3.400000000000000e-08 5.686209873155166e-03 7.129014597372343e-02 1.109847193580530e-01
3.450000000000000e-08 5.494872665515800e-03 7.182303818254908e-02 1.101612664139346e-01
3.500000000000000e-08 5.304857570206247e-03 7.235619028134878e-02 1.093495499572095e-01
3.550000000000000e-08 5.116118208665122e-03 7.288968070178033e-02 1.085492043277430e-01
3.600000000000000e-08 4.928608582805771e-03 7.342359021672797e-02 1.077598741838255e-01
3.650000000000000e-08 4.742283059975877e-03 7.395800195741757e-02 1.069812141278891e-01
3.700000000000000e-08 4.557096358178748e-03 7.449300143230728e-02 1.062128883485147e-01
3.750000000000000e-08 4.373003531543189e-03 7.502867654781073e-02 1.054545702779619e-01
3.800000000000000e-08 4.189959956029533e-03 7.556511763091078e-02 1.047059422644943e-01
3.850000000000000e-08 4.007921315359663e-03 7.610241745372467e-02 1.039666952588117e-01
3.900000000000000e-08 3.826843587159425e-03 7.664067126008174e-02 1.032365285139383e-01
3.950000000000000e-08 3.646683029302109e-03 7.717997679417796e-02 1.025151492979497e-01
4.000000000000001e-08 3.467396166442170e-03 7.772043433137284e-02 1.018022726189576e-01
4.050000000000000e-08 3.288939776728568e-03 7.826214671119711e-02 1.010976209617961e-01
4.100000000000000e-08 3.111270878687549e-03 7.880521937264109e-02 1.004009240358886e-01
4.150000000000000e-08 2.934346718264964e-03 7.934976039179700e-02 9.971191853379702e-02
4.200000000000000e-08 2.758124756018458e-03 7.989588052193052e-02 9.903034789998452e-02
4.250000000000000e-08 2.582562654450210e-03 8.044369323606035e-02 9.835596210934433e-02
4.300000000000000e-08 2.407618265471100e-03 8.099331477212689e-02 9.768851745507198e-02
4.349999999999999e-08 2.233249617987428e-03 8.154486418083473e-02 9.702777634547938e-02
4.400000000000000e-08 2.059414905601513e-03 8.209846337625756e-02 9.637350710936947e-02
4.450000000000000e-08 1.886072474417785e-03 8.265423718929614e-02 9.572548380961053e-02
4.500000000000000e-08 1.713180810945974e-03 8.321231342408623e-02 9.508348606456535e-02
4.550000000000000e-08 1.540698530093412e-03 8.377282291745491e-02 9.444729887705032e-02
4.600000000000000e-08 1.368584363238412e-03 8.433589960153018e-02 9.381671247051346e-02
4.650000000000001e-08 1.196797146376974e-03 8.490168056961167e-02 9.319152213213780e-02
4.700000000000000e-08 1.025295808335103e-03 8.547030614541629e-02 9.257152806258939e-02
4.750000000000000e-08 8.540393590391493e-04 8.604191995581699e-02 9.195653523214393e-02
4.800000000000000e-08 6.829868778367766e-04 8.661666900719855e-02 9.134635324293924e-02
4.850000000000000e-08 5.120975018610807e-04 8.719470376556024e-02 9.074079619711183e-02
4.900000000000000e-08 3.413304144305969e-04 8.777617824050044e-02 9.013968257058949e-02
4.950000000000001e-08 1.706448334779643e-04 8.836125007322586e-02 8.954283509232067e-02
5.000000000000000e-08 -4.538986873934043e-18 8.895008062873327e-02 8.895008062873339e-02
5.050000000000000e-08 -1.706448334779687e-04 8.954283509232054e-02 8.836125007322598e-02
5.100000000000000e-08 -3.413304144306010e-04 9.013968257058935e-02 8.777617824050059e-02
5.150000000000000e-08 -5.120975018610846e-04 9.074079619711169e-02 8.719470376556036e-02
5.200000000000000e-08 -6.829868778367807e-04 9.134635324293910e-02 8.661666900719869e-02
5.250000000000000e-08 -8.540393590391531e-04 9.195653523214382e-02 8.604191995581713e-02
5.300000000000000e-08 -1.025295808335107e-03 9.257152806258928e-02 8.547030614541641e-02
5.350000000000000e-08 -1.196797146376978e-03 9.319152213213767e-02 8.490168056961181e-02
5.400000000000000e-08 -1.368584363238416e-03 9.381671247051332e-02 8.433589960153032e-02
5.450000000000000e-08 -1.540698530093417e-03 9.444729887705021e-02 8.377282291745503e-02
5.500000000000000e-08 -1.713180810945979e-03 9.508348606456524e-02 8.321231342408636e-02
5.550000000000000e-08 -1.886072474417789e-03 9.572548380961039e-02 8.265423718929626e-02
5.600000000000001e-08 -2.059414905601518e-03 9.637350710936936e-02 8.209846337625766e-02
5.650000000000000e-08 -2.233249617987429e-03 9.702777634547927e-02 8.154486418083483e-02
5.700000000000000e-08 -2.407618265471104e-03 9.768851745507189e-02 8.099331477212697e-02
5.750000000000000e-08 -2.582562654450215e-03 9.835596210934421e-02 8.044369323606043e-02
5.800000000000000e-08 -2.758124756018462e-03 9.903034789998438e-02 7.989588052193061e-02
5.850000000000000e-08 -2.934346718264967e-03 9.971191853379686e-02 7.934976039179710e-02
5.900000000000000e-08 -3.111270878687551e-03 1.004009240358885e-01 7.880521937264121e-02
5.950000000000000e-08 -3.288939776728571e-03 1.010976209617960e-01 7.826214671119719e-02
5.999999999999999e-08 -3.467396166442174e-03 1.018022726189574e-01 7.772043433137293e-02
6.050000000000001e-08 -3.646683029302113e-03 1.025151492979495e-01 7.717997679417804e-02
6.100000000000000e-08 -3.826843587159427e-03 1.032365285139381e-01 7.664067126008185e-02
6.150000000000000e-08 -4.007921315359667e-03 1.039666952588116e-01 7.610241745372480e-02
6.200000000000000e-08 -4.189959956029538e-03 1.047059422644942e-01 7.556511763091089e-02
6.250000000000001e-08 -4.373003531543195e-03 1.054545702779618e-01 7.502867654781081e-02
6.300000000000001e-08 -4.557096358178754e-03 1.062128883485146e-01 7.449300143230737e-02
6.349999999999999e-08 -4.742283059975881e-03 1.069812141278891e-01 7.395800195741765e-02
6.400000000000000e-08 -4.928608582805772e-03 1.077598741838254e-01 7.342359021672808e-02
6.450000000000000e-08 -5.116118208665124e-03 1.085492043277429e-01 7.288968070178044e-02
6.500000000000000e-08 -5.304857570206242e-03 1.093495499572095e-01 7.235619028134890e-02
6.550000000000000e-08 -5.494872665515795e-03 1.101612664139346e-01 7.182303818254916e-02
6.600000000000000e-08 -5.686209873155159e-03 1.109847193580529e-01 7.129014597372353e-02
6.649999999999999e-08 -5.878915967475935e-03 1.118202851595132e-01 7.075743754904547e-02
6.699999999999999e-08 -6.073038134224638e-03 1.126683513074329e-01 7.022483911478997e-02
6.750000000000000e-08 -6.268623986451099e-03 1.135293168383289e-01 6.969227917721668e-02
6.800000000000000e-08 -6.465721580735864e-03 1.144035927841903e-01 6.915968853201328e-02
6.850000000000000e-08 -6.664379433752315e-03 1.152916026414125e-01 6.862700025524850e-02
6.900000000000001e-08 -6.864646539180085e-03 1.161937828616773e-01 6.809414969578419e-02
6.950000000000001e-08 -7.066572384986883e-03 1.171105833659248e-01 6.756107446909741e-02
7.000000000000000e-08 -7.270206971096700e-03 1.180424680826330e-01 6.702771445246350e-02
7.050000000000000e-08 -7.475600827463190e-03 1.189899155116965e-01 6.649401178145187e-02
7.100000000000000e-08 -7.682805032567647e-03 1.199534193152709e-01 6.595991084768713e-02
7.150000000000000e-08 -7.891871232362197e-03 1.209334889370378e-01 6.542535829782804e-02
7.200000000000000e-08 -8.102851659679524e-03 1.219306502514307e-01 6.489030303371734e-02
7.250000000000001e-08 -8.315799154131472e-03 1.229454462444624e-01 6.435469621365607e-02
7.300000000000001e-08 -8.530767182520054e-03 1.239784377278923e-01 6.381849125475550e-02
7.349999999999999e-08 -8.747809859785391e-03 1.250302040885877e-01 6.328164383632066e-02
7.400000000000000e-08 -8.966981970516265e-03 1.261013440750441e-01 6.274411190421897e-02
7.450000000000000e-08 -9.188338991050302e-03 1.271924766231611e-01 6.220585567618763e-02
7.500000000000001e-08 -9.411937112192121e-03 1.283042417235012e-01 6.166683764803358e-02
7.550000000000001e-08 -9.637833262579056e-03 1.294373013324064e-01 6.112702260067914e-02
7.599999999999999e-08 -9.866085132725732e-03 1.305923403294988e-01 6.058637760800705e-02
7.650000000000000e-08 -1.009675119978020e-02 1.317700675242618e-01 6.004487204545747e-02
7.700000000000000e-08 -1.032989075302603e-02 1.329712167145733e-01 5.950247759933011e-02
7.750000000000001e-08 -1.056556392016663e-02 1.341965478002553e-01 5.895916827674359e-02
7.800000000000000e-08 -1.080383169442980e-02 1.354468479549114e-01 5.841492041620423e-02
7.850000000000001e-08 -1.104475596253259e-02 1.367229328595421e-01 5.786971269873564e-02
7.900000000000001e-08 -1.128839953354859e-02 1.380256480016685e-01 5.732352615952059e-02
7.949999999999999e-08 -1.153482616872219e-02 1.393558700439496e-01 5.677634420000535e-02
8.000000000000001e-08 -1.178410061227646e-02 1.407145082665548e-01 5.622815260041685e-02
8.050000000000000e-08 -1.203628862326397e-02 1.421025060878504e-01 5.567893953264230e-02
8.100000000000000e-08 -1.229145700851277e-02 1.435208426682791e-01 5.512869557341959e-02
8.150000000000001e-08 -1.254967365672207e-02 1.449705346026567e-01 5.457741371778770e-02
8.199999999999999e-08 -1.281100757376580e-02 1.464526377064836e-01 5.402508939274389e-02
8.250000000000000e-08 -1.307552891926516e-02 1.479682489022719e-01 5.347172047105534e-02
8.300000000000000e-08 -1.334330904449450e-02 1.495185082123211e-01 5.291730728517137e-02
8.350000000000000e-08 -1.361442053168921e-02 1.511046008648511e-01 5.236185264118171e-02
8.400000000000000e-08 -1.388893723482741e-02 1.527277595209039e-01 5.180536183276627e-02
8.450000000000001e-08 -1.416693432196201e-02 1.543892666299816e-01 5.124784265508017e-02
8.499999999999999e-08 -1.444848831918374e-02 1.560904569229805e-01 5.068930541851849e-02
8.549999999999999e-08 -1.473367715630093e-02 1.578327200516322e-01 5.012976296230257e-02
8.600000000000000e-08 -1.502258021432633e-02 1.596175033843607e-01 4.956923066783116e-02
8.650000000000000e-08 -1.531527837486705e-02 1.614463149692257e-01 4.900772647173756e-02
8.699999999999998e-08 -1.561185407151957e-02 1.633207266754533e-01 4.844527087859365e-02
8.750000000000000e-08 -1.591239134337750e-02 1.652423775259484e-01 4.788188697320159e-02
8.799999999999999e-08 -1.621697589076666e-02 1.672129772341630e-01 4.731760043241252e-02
8.850000000000000e-08 -1.652569513332925e-02 1.692343099597600e-01 4.675243953641165e-02
8.900000000000000e-08 -1.683863827058613e-02 1.713082382986650e-01 4.618643517940858e-02
8.950000000000000e-08 -1.715589634511450e-02 1.734367075243691e-01 4.561962087967058e-02
9.000000000000000e-08 -1.747756230848701e-02 1.756217500987131e-01 4.505203278883707e-02
9.050000000000001e-08 -1.780373109012749e-02 1.778654904718957e-01 4.448370970045223e-02
9.099999999999999e-08 -1.813449966924875e-02 1.801701501930853e-01 4.391469305765284e-02
9.150000000000001e-08 -1.846996715004834e-02 1.825380533548108e-01 4.334502695994810e-02
9.200000000000000e-08 -1.881023484034983e-02 1.849716323962717e-01 4.277475816902754e-02
9.249999999999999e-08 -1.915540633388983e-02 1.874734342928613e-01 4.220393611353384e-02
9.300000000000001e-08 -1.950558759646394e-02 1.900461271615486e-01 4.163261289273575e-02
9.350000000000000e-08 -1.986088705615930e-02 1.926925073143554e-01 4.106084327903858e-02
9.399999999999999e-08 -2.022141569791728e-02 1.954155067950034e-01 4.048868471926686e-02
9.450000000000001e-08 -2.058728716268602e-02 1.982182014369218e-01 3.991619733465676e-02
9.499999999999999e-08 -2.095861785144083e-02 2.011038194842412e-01 3.934344391949416e-02
9.550000000000000e-08 -2.133552703437016e-02 2.040757508211753e-01 3.877048993833503e-02
9.600000000000000e-08 -2.171813696554524e-02 2.071375568593485e-01 3.819740352174587e-02
9.650000000000001e-08 -2.210657300341517e-02 2.102929811372251e-01 3.762425546050149e-02
9.700000000000000e-08 -2.250096373749285e-02 2.135459606908533e-01 3.705111919817873e-02
9.749999999999999e-08 -2.290144112162465e-02 2.169006382607440e-01 3.647807082208487e-02
9.800000000000000e-08 -2.330814061426505e-02 2.203613754058883e-01 3.590518905246105e-02
9.849999999999999e-08 -2.372120132620929e-02 2.239327666027848e-01 3.533255522990110e-02
9.900000000000001e-08 -2.414076617627088e-02 2.276196544149405e-01 3.476025330092776e-02
9.950000000000000e-08 -2.456698205542748e-02 2.314271458267466e-01 3.418836980166970e-02
1.000000000000000e-07 -2.500000000000000e-02 2.353606298450042e-01 3.361699383958291e-02
poisson-nernst-planck stderr
/usr/lib/python3/dist-packages/scipy/__init__.py:146: UserWarning: A NumPy version >=1.17.3 and <1.25.0 is required for this version of SciPy (detected version 1.26.3
warnings.warn(f"A NumPy version >={np_minversion} and <{np_maxversion}"
continuous2discrete output
continuous2discrete stderr
/usr/lib/python3/dist-packages/scipy/__init__.py:146: UserWarning: A NumPy version >=1.17.3 and <1.25.0 is required for this version of SciPy (detected version 1.26.3
warnings.warn(f"A NumPy version >={np_minversion} and <{np_maxversion}"
ValueError: could not convert string to float: 'Calling'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/tmp/tmpnp7o5v6o/c2d", line 312, in <module>
main()
File "/tmp/tmpnp7o5v6o/c2d", line 208, in main
data = np.loadtxt(infile, unpack=True)
File "/usr/local/lib/python3.10/dist-packages/numpy/lib/npyio.py", line 1373, in loadtxt
arr = _read(fname, dtype=dtype, comment=comment, delimiter=delimiter,
File "/usr/local/lib/python3.10/dist-packages/numpy/lib/npyio.py", line 1016, in _read
arr = _load_from_filelike(
ValueError: could not convert string 'Calling' to float64 at row 0, column 1.
from matscipy.
jotelha
commented on July 16, 2024
Resolved with #218
from matscipy.
Related Issues (20)
- [JOSS Review] Paper and statement of need HOT 2
- [JOSS Review] Reproducibility and functionality HOT 1
- [JOSS Review] Tests HOT 2
- [JOSS Review] Documentation HOT 2
- JOSS Review: Examples and Tutorials HOT 1
- Editable install won't run HOT 1
- Documentation appearance HOT 3
- Generalise surface reconstruction code
- Conda-forge build not working for version 0.8.0 HOT 5
- Some fenics log messages are written to stdout instead of stderr HOT 1
- Autogenerate documentation previews on pull requests in CI
- v0.8.1 and v0.9.0 releases HOT 4
- Part of the electrochemistry module does not follow coding style HOT 2
- Building documentation requires Fenics HOT 4
- Interactive visualisation of atomic structures in documentation is broken HOT 12
- Clean up extra files created by running docs + tests HOT 7
- Improve performance of unittests
- Switch arm64 from Cirrus to GHA HOT 1
- Pair potential for the real part of the Ewald sum HOT 2
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from matscipy.