def testAnalytCylDifn(testDir, dirDict):
""" Analytical test for diffusion in a cylinder """
shutil.copy(osp.join(dirDict["baseConfig"], "params_system.cfg"), testDir)
shutil.copy(osp.join(dirDict["baseConfig"], "params_c.cfg"), testDir)
psys = osp.join(testDir, "params_system.cfg")
ptrode = osp.join(testDir, "params_c.cfg")
P_s = IO.get_config(psys)
P_s.set("Sim Params", "profileType", "CV")
P_s.set("Sim Params", "Vset", "0.10")
P_s.set("Sim Params", "tend", "1e+6")
P_s.set("Sim Params", "tsteps", "1800")
P_s.set("Sim Params", "relTol", "1e-7")
P_s.set("Sim Params", "tramp", "1e-6")
P_s.set("Particles", "mean_c", "100e-9")
P_s.set("Particles", "mean_c", "100e-9")
P_s.set("Particles", "cs0_c", "0.5")
IO.write_config_file(P_s, psys)
P = IO.get_config(ptrode)
P.set("Particles", "type", "diffn")
P.set("Particles", "discretization", "3e-10")
P.set("Particles", "shape", "cylinder")
P.set("Material", "muRfunc", "testIS_ss")
P.set("Material", "D", "1e-20")
P.set("Reactions", "rxnType", "BV_raw")
P.set("Reactions", "k0", "1e+1")
IO.write_config_file(P, ptrode)
main.main(psys, keepArchive=False)
shutil.move(dirDict["simOut"], testDir)
def test017(testDir, dirDict, pflag):
""" test CV continuation """
shutil.copy(osp.join(dirDict["baseConfig"], "params_system.cfg"), testDir)
shutil.copy(osp.join(dirDict["baseConfig"], "params_c.cfg"), testDir)
psys = osp.join(testDir, "params_system.cfg")
ptrode = osp.join(testDir, "params_c.cfg")
P_s = IO.get_config(psys)
P_s.set("Sim Params", "profileType", "CV")
P_s.set("Sim Params", "Vset", "3.45")
P_s.set("Sim Params", "tend", "3e3")
P_s.set("Sim Params", "Nvol_c", "3")
P_s.set("Sim Params", "Npart_c", "3")
test008dir = str(osp.join(testDir, "..", "test008", "sim_output"))
P_s.set("Sim Params", "prevDir", test008dir)
IO.write_config_file(P_s, psys)
P = IO.get_config(ptrode)
P.set("Particles", "type", "homog_sdn")
P.set("Material", "muRfunc", "LiFePO4")
IO.write_config_file(P, ptrode)
main.main(psys, keepArchive=False)
shutil.move(dirDict["simOut"], testDir)
if pflag:
corePlots(testDir, dirDict)
elytePlots(testDir, dirDict)
electrodePlots(testDir, dirDict, "c")
cmpr.bulkpf(testDir, dirDict, "c")
def test011(testDir, dirDict, pflag):
""" Graphite-2param CHR sphere """
shutil.copy(osp.join(dirDict["baseConfig"], "params_system.cfg"), testDir)
shutil.copy(osp.join(dirDict["baseConfig"], "params_c.cfg"), testDir)
psys = osp.join(testDir, "params_system.cfg")
ptrode = osp.join(testDir, "params_c.cfg")
P_s = IO.get_config(psys)
P_s.set("Sim Params", "Crate", "1e-2")
P_s.set("Sim Params", "relTol", "1e-7")
P_s.set("Sim Params", "absTol", "1e-7")
IO.write_config_file(P_s, psys)
P = IO.get_config(ptrode)
P.set("Particles", "type", "CHR2")
P.set("Particles", "discretization", "2e-9")
P.set("Particles", "shape", "sphere")
P.set("Material", "muRfunc", "LiC6")
P.set("Material", "Dfunc", "lattice")
P.set("Material", "B", "0.1e9")
P.set("Material", "kappa", "2.5e-10")
IO.write_config_file(P, ptrode)
main.main(psys, keepArchive=False)
shutil.move(dirDict["simOut"], testDir)
if pflag:
corePlots(testDir, dirDict)
electrodePlots(testDir, dirDict, "c")
def test015(testDir, dirDict, pflag):
""" testRS homog with CVsegments, bulkCond, partCond """
shutil.copy(osp.join(dirDict["baseConfig"], "params_system.cfg"), testDir)
shutil.copy(osp.join(dirDict["baseConfig"], "params_c.cfg"), testDir)
psys = osp.join(testDir, "params_system.cfg")
ptrode = osp.join(testDir, "params_c.cfg")
P_s = IO.get_config(psys)
P_s.set("Sim Params", "profileType", "CVsegments")
P_s.set("Sim Params", "Npart_c", "3")
P_s.set("Sim Params", "Nvol_c", "3")
P_s.set("Sim Params", "segments",
"[(-0.3, 25), (0., 10), (0.3, 30)]")
P_s.set("Sim Params", "tramp", "1e+0")
P_s.set("Sim Params", "absTol", "1e-5")
P_s.set("Conductivity", "simBulkCond_c", "true")
P_s.set("Conductivity", "sigma_s_c", "1e-2")
P_s.set("Conductivity", "simPartCond_c", "true")
P_s.set("Conductivity", "G_mean_c", "1e-14")
IO.write_config_file(P_s, psys)
P = IO.get_config(ptrode)
P.set("Particles", "type", "homog")
P.set("Material", "muRfunc", "testRS")
P.set("Reactions", "rxnType", "BV_raw")
IO.write_config_file(P, ptrode)
main.main(psys, keepArchive=False)
shutil.move(dirDict["simOut"], testDir)
if pflag:
corePlots(testDir, dirDict)
elytePlots(testDir, dirDict)
electrodePlots(testDir, dirDict, "c")
cmpr.bulkpf(testDir, dirDict, "c")
def test001(testDir, dirDict, pflag):
""" LFP ACR C3 """
shutil.copy(osp.join(dirDict["baseConfig"], "params_system.cfg"), testDir)
shutil.copy(osp.join(dirDict["baseConfig"], "params_c.cfg"), testDir)
psys = osp.join(testDir, "params_system.cfg")
ptrode = osp.join(testDir, "params_c.cfg")
P_s = IO.get_config(psys)
P_s.set("Sim Params", "Crate", "1e-2")
IO.write_config_file(P_s, psys)
P = IO.get_config(ptrode)
P.set("Particles", "type", "ACR")
P.set("Material", "muRfunc", "LiFePO4")
IO.write_config_file(P, ptrode)
main.main(psys, keepArchive=False)
shutil.move(dirDict["simOut"], testDir)
if pflag:
corePlots(testDir, dirDict)
electrodePlots(testDir, dirDict, "c")
def test019(testDir, dirDict, pflag):
""" SM electrolyte with LFP homog, sep + cathode, significant elyte polarization """
shutil.copy(osp.join(dirDict["baseConfig"], "params_system.cfg"), testDir)
shutil.copy(osp.join(dirDict["baseConfig"], "params_c.cfg"), testDir)
psys = osp.join(testDir, "params_system.cfg")
ptrode = osp.join(testDir, "params_c.cfg")
P_s = IO.get_config(psys)
P_s.set("Sim Params", "Nvol_c", "3")
P_s.set("Sim Params", "Nvol_s", "3")
P_s.set("Geometry", "L_c", "120e-6")
P_s.set("Geometry", "L_s", "90e-6")
P_s.set("Electrolyte", "elyteModelType", "SM")
IO.write_config_file(P_s, psys)
P = IO.get_config(ptrode)
P.set("Particles", "type", "homog")
P.set("Material", "muRfunc", "LiFePO4")
IO.write_config_file(P, ptrode)
main.main(psys, keepArchive=False)
shutil.move(dirDict["simOut"], testDir)
if pflag:
corePlots(testDir, dirDict)
elytePlots(testDir, dirDict)
electrodePlots(testDir, dirDict, "c")
def test014(testDir, dirDict, pflag):
""" LFP homog with CCsegments, MHC, Rser """
shutil.copy(osp.join(dirDict["baseConfig"], "params_system.cfg"), testDir)
shutil.copy(osp.join(dirDict["baseConfig"], "params_c.cfg"), testDir)
psys = osp.join(testDir, "params_system.cfg")
ptrode = osp.join(testDir, "params_c.cfg")
P_s = IO.get_config(psys)
P_s.set("Sim Params", "profileType", "CCsegments")
P_s.set("Sim Params", "segments",
"[(1., 25), (-2., 10), (0., 30)]")
P_s.set("Sim Params", "tramp", "1e+0")
P_s.set("Sim Params", "Rser", "1e-3")
IO.write_config_file(P_s, psys)
P = IO.get_config(ptrode)
P.set("Particles", "type", "homog")
P.set("Material", "muRfunc", "LiFePO4")
P.set("Reactions", "rxnType", "MHC")
IO.write_config_file(P, ptrode)
main.main(psys, keepArchive=False)
shutil.move(dirDict["simOut"], testDir)
if pflag:
corePlots(testDir, dirDict)
electrodePlots(testDir, dirDict, "c")
def test004(testDir, dirDict, pflag):
""" LFP CHR sphere with noise """
shutil.copy(osp.join(dirDict["baseConfig"], "params_system.cfg"), testDir)
shutil.copy(osp.join(dirDict["baseConfig"], "params_c.cfg"), testDir)
psys = osp.join(testDir, "params_system.cfg")
ptrode = osp.join(testDir, "params_c.cfg")
P_s = IO.get_config(psys)
P_s.set("Sim Params", "Crate", "1e-2")
IO.write_config_file(P_s, psys)
P = IO.get_config(ptrode)
P.set("Particles", "type", "CHR")
P.set("Particles", "discretization", "2e-9")
P.set("Particles", "shape", "sphere")
P.set("Material", "muRfunc", "LiFePO4")
P.set("Material", "noise", "true")
P.set("Material", "numnoise", "100")
P.set("Material", "Dfunc", "lattice")
P.set("Material", "dgammadc", "-2e-30")
IO.write_config_file(P, ptrode)
main.main(psys, keepArchive=False)
shutil.move(dirDict["simOut"], testDir)
if pflag:
corePlots(testDir, dirDict)
electrodePlots(testDir, dirDict, "c")
def test008(testDir, dirDict, pflag):
""" LFP homog_sdn """
shutil.copy(osp.join(dirDict["baseConfig"], "params_system.cfg"), testDir)
shutil.copy(osp.join(dirDict["baseConfig"], "params_c.cfg"), testDir)
psys = osp.join(testDir, "params_system.cfg")
ptrode = osp.join(testDir, "params_c.cfg")
P_s = IO.get_config(psys)
P_s.set("Sim Params", "Crate", "1e-2")
P_s.set("Sim Params", "Nvol_c", "3")
P_s.set("Sim Params", "Npart_c", "3")
P_s.set("Particles", "stddev_c", "25e-9")
P_s.set("Sim Params", "capFrac", "0.6")
IO.write_config_file(P_s, psys)
P = IO.get_config(ptrode)
P.set("Particles", "type", "homog_sdn")
P.set("Material", "muRfunc", "LiFePO4")
IO.write_config_file(P, ptrode)
main.main(psys, keepArchive=False)
shutil.move(dirDict["simOut"], testDir)
if pflag:
corePlots(testDir, dirDict)
elytePlots(testDir, dirDict)
electrodePlots(testDir, dirDict, "c")
cmpr.bulkpf(testDir, dirDict, "c")
def test013(testDir, dirDict, pflag):
""" Solid solution, diffn cylinder, homog, testIS_ss, LiMn2O4_ss2
Marcus, BV_raw
cathode + separator + anode
"""
shutil.copy(osp.join(dirDict["baseConfig"], "params_system.cfg"), testDir)
shutil.copy(osp.join(dirDict["baseConfig"], "params_c.cfg"), testDir)
shutil.copy(osp.join(dirDict["baseConfig"], "params_a.cfg"), testDir)
psys = osp.join(testDir, "params_system.cfg")
ptrodec = osp.join(testDir, "params_c.cfg")
ptrodea = osp.join(testDir, "params_a.cfg")
P_s = IO.get_config(psys)
P_s.set("Sim Params", "profileType", "CV")
P_s.set("Sim Params", "Vset", "3.8")
P_s.set("Sim Params", "tsteps", "25")
P_s.set("Sim Params", "Nvol_c", "2")
P_s.set("Sim Params", "Nvol_s", "2")
P_s.set("Sim Params", "Nvol_a", "2")
P_s.set("Particles", "cs0_c", "0.2")
P_s.set("Particles", "cs0_a", "0.95")
P_s.set("Electrolyte", "elyteModelType", "dilute")
IO.write_config_file(P_s, psys)
P = IO.get_config(ptrodec)
P.set("Particles", "type", "homog")
P.set("Particles", "shape", "sphere")
P.set("Material", "muRfunc", "LiMn2O4_ss2")
P.set("Reactions", "rxnType", "Marcus")
IO.write_config_file(P, ptrodec)
P = IO.get_config(ptrodea)
P.set("Particles", "discretization", "2.5e-9")
P.set("Particles", "shape", "cylinder")
P.set("Material", "muRfunc", "testIS_ss")
P.set("Reactions", "rxnType", "BV_raw")
IO.write_config_file(P, ptrodea)
main.main(psys, keepArchive=False)
shutil.move(dirDict["simOut"], testDir)
if pflag:
corePlots(testDir, dirDict)
elytePlots(testDir, dirDict)
electrodePlots(testDir, dirDict, "c")
cmpr.bulkpf(testDir, dirDict, "c")
electrodePlots(testDir, dirDict, "a")
cmpr.bulkpf(testDir, dirDict, "a")
def test012(testDir, dirDict, pflag):
""" Solid solution, diffn sphere, homog, LiC6_coke_ss2, LiMn2O4_ss2
BV_mod01, BV_mod02
cathode + anode
"""
shutil.copy(osp.join(dirDict["baseConfig"], "params_system.cfg"), testDir)
shutil.copy(osp.join(dirDict["baseConfig"], "params_c.cfg"), testDir)
shutil.copy(osp.join(dirDict["baseConfig"], "params_a.cfg"), testDir)
psys = osp.join(testDir, "params_system.cfg")
ptrodec = osp.join(testDir, "params_c.cfg")
ptrodea = osp.join(testDir, "params_a.cfg")
P_s = IO.get_config(psys)
P_s.set("Sim Params", "Crate", "1e-2")
P_s.set("Sim Params", "capFrac", "0.67")
P_s.set("Sim Params", "tsteps", "25")
P_s.set("Sim Params", "Nvol_c", "2")
P_s.set("Sim Params", "Nvol_a", "2")
P_s.set("Sim Params", "Vmin", "2e0")
P_s.set("Particles", "cs0_c", "0.2")
P_s.set("Particles", "cs0_a", "0.495")
P_s.set("Electrolyte", "elyteModelType", "SM")
IO.write_config_file(P_s, psys)
P = IO.get_config(ptrodec)
P.set("Particles", "type", "homog")
P.set("Particles", "shape", "cylinder")
P.set("Material", "muRfunc", "LiMn2O4_ss2")
P.set("Reactions", "rxnType", "BV_mod01")
IO.write_config_file(P, ptrodec)
P = IO.get_config(ptrodea)
P.set("Particles", "discretization", "2.5e-9")
P.set("Particles", "shape", "sphere")
P.set("Material", "muRfunc", "LiC6_coke_ss2")
P.set("Reactions", "rxnType", "BV_mod02")
IO.write_config_file(P, ptrodea)
main.main(psys, keepArchive=False)
shutil.move(dirDict["simOut"], testDir)
if pflag:
corePlots(testDir, dirDict)
elytePlots(testDir, dirDict)
electrodePlots(testDir, dirDict, "c")
cmpr.bulkpf(testDir, dirDict, "c")
electrodePlots(testDir, dirDict, "a")
cmpr.bulkpf(testDir, dirDict, "a")
def main(paramfile, keepArchive=True):
timeStart = time.time()
# Get the parameters dictionary (and the config instance) from the
# parameter file
P_s, P_e = IO.get_configs(paramfile)
dD_s, ndD_s, dD_e, ndD_e = IO.get_dicts_from_configs(P_s, P_e)
# Directories we'll store output in.
outdir_name = time.strftime("%Y%m%d_%H%M%S", time.localtime())
outdir_path = os.path.join(os.getcwd(), "history")
outdir = os.path.join(outdir_path, outdir_name)
# Make sure there's a place to store the output
try:
os.makedirs(outdir)
except OSError as exception:
if exception.errno == errno.EEXIST:
print("The output directory, {dirname}, exists. Aborting.".format(dirname=outdir))
sys.exit()
else:
raise
paramFileName = "input_params_system.cfg"
paramFile = os.path.join(outdir, paramFileName)
IO.write_config_file(P_s, filename=paramFile)
dictFile = os.path.join(outdir, "input_dict_system")
IO.write_dicts(dD_s, ndD_s, filenamebase=dictFile)
for trode in ndD_s["trodes"]:
paramFileName = "input_params_{t}.cfg".format(t=trode)
paramFile = os.path.join(outdir, paramFileName)
IO.write_config_file(P_e[trode], filename=paramFile)
dictFile = os.path.join(outdir, "input_dict_{t}".format(t=trode))
IO.write_dicts(dD_e[trode], ndD_e[trode], filenamebase=dictFile)
# Store info about this script
# mpet.py script directory
localDir = os.path.dirname(os.path.abspath(__file__))
commit_hash = ""
try:
# Git option, if it works -- commit info and current diff
branch_name, commit_hash, commit_diff = utils.get_git_info(localDir, shell=False)
except FileNotFoundError:
try:
branch_name, commit_hash, commit_diff = utils.get_git_info(localDir, shell=True)
except subp.CalledProcessError:
pass
except subp.CalledProcessError:
pass
fo=open(os.path.join(outdir, 'run_info.txt'), 'w')
#Print mpet version
print("mpet version:", file=fo)
print(mpet.__version__+"\n", file=fo)
#Print git commit info if it exists
if commit_hash != "":
# Store commit info to file, as well as how to patch if
# there's a diff
print("branch name:", file=fo)
print(branch_name, file=fo)
print("commit hash:", file=fo)
print(commit_hash, file=fo)
print("to run, from the root repo directory, copy relevant files there,", file=fo)
print("edit input_params_system.cfg to point to correct material", file=fo)
print("params files, and:", file=fo)
print("$ git checkout [commit hash]", file=fo)
print("$ patch -p1 < commit.diff:", file=fo)
print("$ python[3] mpetrun.py input_params_system.cfg", file=fo)
with open(os.path.join(outdir, 'commit.diff'), 'w') as fo:
print(commit_diff, file=fo)
else:
# At least keep a copy of the python files in this directory
# with the output
snapshotDir = os.path.join(outdir, "simSnapshot")
os.makedirs(snapshotDir)
pyFiles = glob.glob(os.path.join(localDir, "*.py"))
for pyFile in pyFiles:
shutil.copy(pyFile, snapshotDir)
fo.close()
# External functions are not supported by the Compute Stack approach.
# Activate the Evaluation Tree approach if noise, logPad, CCsegments,
# or CVsegments are used
cfg = dae.daeGetConfig()
noise=ndD_e['c']['noise']
logPad=ndD_e['c']['logPad']
segments = ndD_s["profileType"] in ["CCsegments","CVsegments"]
if (noise or logPad or (segments and ndD_s["tramp"]>0)) and cfg.has_key('daetools.core.equations.evaluationMode'):
cfg.SetString('daetools.core.equations.evaluationMode', 'evaluationTree_OpenMP')
with open(os.path.join(outdir, "daetools_config_options.txt"), 'w') as fo:
print(cfg, file=fo)
#Disable printStats
cfg.SetString('daetools.activity.printStats','false')
# Carry out the simulation
run_simulation(ndD_s, ndD_e, dD_s["td"], outdir)
# Final output for user
print("\n\nUsed parameter file ""{fname}""\n\n".format(fname=paramfile))
timeEnd = time.time()
tTot = timeEnd - timeStart
print("Total time:", tTot, "s")
try:
with open(os.path.join(outdir, 'run_info.txt'), 'a') as fo:
print("\nTotal run time:", tTot, "s", file=fo)
except Exception:
pass
# Copy simulation output to current directory
tmpDir_name = "sim_output"
tmpDir = os.path.join(os.getcwd(), tmpDir_name)
try:
os.makedirs(tmpDir)
except OSError as exception:
if exception.errno != errno.EEXIST:
raise
for fname in os.listdir(outdir):
tocopy = os.path.join(outdir, fname)
if os.path.isfile(tocopy):
shutil.copy(tocopy, tmpDir)
if not keepArchive:
shutil.rmtree(outdir)
