8476080312

Committed 29 Mar 2024 01:46AM UTC coverage: 55.461% (-7.2%) from 62.648%

Build # 8476080312

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Pull #126

github

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d-cogswell

Commit Message

Adds a benchmark section to docs.

Pull Request Pull Request #126: v1.0.0

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0.0

/mpet/plot/outmat2txt.py

"""This can be called to convert the default simulation output (.mat file) to csv files."""
import os

import numpy as np
import h5py

import mpet.plot.plot_data as plot_data
import mpet.utils as utils
from mpet.config import constants

# Strings to be used
RowsStr = "Rows correspond to time points (see generalData.txt).\n"
CCStr = "Columns correspond to cell center positions (see discData.txt)."
FCStr = "Columns correspond to face positions (see discData.txt)."
genDataHdr = ("Time [s], Filling fraction of anode, "
              + "Filling fraction of cathode, "
              + "Voltage [V], Current [C-rate], Current [A/m^2], "
              + "Power [W/m^2]")

zeroStr = "Zero is at the anode current collector."
dccpStr = "discretization cell center positions [m]. "
discCCbattery = ("Battery " + dccpStr + zeroStr)
discCCanode = ("Anode " + dccpStr + zeroStr)
discCCsep = ("Separator " + dccpStr + zeroStr)
discCCcathode = ("Cathode " + dccpStr + zeroStr)
discFC = ("Battery discretization face positions [m]. " + zeroStr)
particleIndxExpl = """
Particle output files are indexed such that Vol 0 is closest to the
anode current collector for both electrodes.  Indexing within volumes
is such that Part 0 is closest to the "carbon backbone" if simPartCond
was set to true for that electrode. Otherwise it is in arbitrary
order.
"""
particleDiscExpl = """
Particle discretization info follows.  Lengths and number of
discretization points are provided for each simulated particle.
Meshes are made as a linear space between zero and particle length
with the given number of points.  Rows correspond to different
simulation volumes with the first row being closest to the anode
current collector and the last closest to the cathode current
collector.  Columns represent individual particles within each
simulated volume in no particular order.
"""

elytecHdr = ("Electrolyte Concentrations [M]\n" + RowsStr + CCStr)
elytepHdr = ("Electrolyte Electric Potential [V]\n" + RowsStr + CCStr)
elyteiHdr = ("Electrolyte Current Density [A/m^2]\n" + RowsStr + FCStr)
elytediviHdr = ("Electrolyte Divergence of Current Density [A/m^3]\n"
                + RowsStr + CCStr)

seeDiscStr = "See discData.txt for particle indexing information."
partStr = "partTrode{l}vol{j}part{i}_"
solffStr = "Solid Filling Fractions"
solTail = ("\n" + RowsStr + CCStr + "\n" + seeDiscStr)
solHdr = (solffStr + solTail)
opStr = ", order parameter "
sol1Hdr = (solffStr + opStr + "1" + solTail)
sol2Hdr = (solffStr + opStr + "2" + solTail)
fnameSolL = "sld{l}Vol{j:03d}Part{i:03d}Conc"
fnameSolR = "Data.txt"
fnameSolBase = (fnameSolL + fnameSolR)
fnameSol1Base = (fnameSolL + "1" + fnameSolR)
fnameSol2Base = (fnameSolL + "2" + fnameSolR)

cbarHdrP1 = ("Average particle filling fractions.\n" + RowsStr)
cbarHdrP2 = """Columns correspond to particles specified by simulated
volume index / particle index within volume.
"""
cbarHdrBase = cbarHdrP1 + cbarHdrP2 + seeDiscStr + "\n"

bulkpHdrP2 = """Columns correspond to this electrode's cell center
positions (see discData.txt).
"""
bulkpHdr = ("Bulk electrode electric potential [V]\n" + RowsStr + bulkpHdrP2)
fnameBulkpBase = "bulkPot{l}Data.txt"

RowStrHdr1 = "First column corresponds to the cycle number.\n"
RowStrHdr2 = """Second, third and fourth columns respond to gravimetric charge capacity of limiting
electrode in mAh/g, gravimetric discharge capacity of limiting electrode in mAh/g, cycle
capacity fraction relative to original capacity, and cycle efficiency (discharge
capacity/charge capacity).\n"""
cyclerHdr = ("Cycling Data\n" + RowStrHdr1 + RowStrHdr2)
fnameCycleBase = "cycleData.txt"

RowStrHdr1Q = """Each (2*i,2*i+1) row represents the (V(t), Q(t)) in cycle i in units of
(V, Ah/m^2).\n"""
vQCyclerHdr = ("Voltage/Capacity Cycling Data\n" + RowStrHdr1Q)

RowStrHdr2Q = """Each (2*i,2*i+1) row represents the (V(t), dQ(t)dV) in cycle i in units of
(V, Ah/m^2).\n"""
vdQCyclerHdr = ("Voltage/dQ Cycling Data\n" + RowStrHdr2Q)


def main(indir, genData=True, discData=True, elyteData=True,
         csldData=True, cbarData=True, bulkpData=True):
    config = plot_data.show_data(
        indir, plot_type="params", print_flag=False, save_flag=False,
        data_only=True, color_changes=None, smooth_type=None)
    trodes = config["trodes"]
    CrateCurr = config["1C_current_density"]  # A/m^2
    psd_len_c = config["psd_len"]["c"]
    totalCycle = config["totalCycle"]
    Nv_c, Np_c = psd_len_c.shape
    dlm = ","

    def get_trode_str(tr):
        return ("Anode" if tr == "a" else "Cathode")
    if "a" in trodes:
        psd_len_a = config["psd_len"]["a"]
        Nv_a, Np_a = psd_len_a.shape
    tVec, vVec = plot_data.show_data(
        indir, plot_type="vt", print_flag=False, save_flag=False,
        data_only=True, color_changes=None, smooth_type=None)
    ntimes = len(tVec)

    if genData:
        ffVec_c = plot_data.show_data(
            indir, plot_type="soc_c", print_flag=False,
            save_flag=False, data_only=True, color_changes=None, smooth_type=None)[1]
        if "a" in trodes:
            ffVec_a = plot_data.show_data(
                indir, plot_type="soc_a", print_flag=False,
                save_flag=False, data_only=True, color_changes=None, smooth_type=None)[1]
        else:
            ffVec_a = np.ones(len(tVec))
        currVec = plot_data.show_data(
            indir, plot_type="curr", print_flag=False,
            save_flag=False, data_only=True, color_changes=None, smooth_type=None)[1]
        powerVec = plot_data.show_data(
            indir, plot_type="power", print_flag=False,
            save_flag=False, data_only=True, color_changes=None, smooth_type=None)[1]
        genMat = np.zeros((ntimes, 7))
        genMat[:,0] = tVec
        genMat[:,1] = ffVec_a
        genMat[:,2] = ffVec_c
        genMat[:,3] = vVec
        genMat[:,4] = currVec
        genMat[:,5] = currVec * CrateCurr
        genMat[:,6] = powerVec
        np.savetxt(os.path.join(indir, "generalData.txt"),
                   genMat, delimiter=dlm, header=genDataHdr)

    if discData:
        cellCentersVec, facesVec = plot_data.show_data(
            indir, plot_type="discData", print_flag=False,
            save_flag=False, data_only=True, color_changes=None, smooth_type=None)
        with open(os.path.join(indir, "discData.txt"), "w") as fo:
            print(discCCbattery, file=fo)
            print(",".join(map(str, cellCentersVec)), file=fo)
            offset = 0
            if "a" in trodes:
                print(file=fo)
                print(discCCanode, file=fo)
                print(",".join(map(str, cellCentersVec[:Nv_a])), file=fo)
                offset = Nv_a
            print(file=fo)
            print(discCCsep, file=fo)
            print(",".join(map(str, cellCentersVec[offset:-Nv_c])), file=fo)
            print(file=fo)
            print(discCCcathode, file=fo)
            print(",".join(map(str, cellCentersVec[-Nv_c:])), file=fo)
            print(file=fo)
            print(discFC, file=fo)
            print(",".join(map(str, facesVec)), file=fo)
            print(file=fo)
            print(particleIndxExpl, file=fo)
            print(particleDiscExpl, file=fo)
            for tr in trodes:
                print(file=fo)
                Trode = get_trode_str(tr)
                print((Trode + " particle sizes [m]"), file=fo)
                for vind in range(config["Nvol"][tr]):
                    print(",".join(map(str, config["psd_len"][tr][vind,:])), file=fo)
                print("\n" + Trode + " particle number of discr. points", file=fo)
                for vind in range(config["Nvol"][tr]):
                    print(",".join(map(str, config["psd_num"][tr][vind,:])), file=fo)

    if elyteData:
        valid_current = True
        # If there wasn't an electrolyte, then a ghost point variable wouldn't have been created,
        # so we'll get a KeyError in attempting to "plot" the electrolyte current density.
        try:
            plot_data.show_data(
                indir, plot_type="elytei", print_flag=False, save_flag=False, data_only=True,
                color_changes=None, smooth_type=None)
        except KeyError:
            valid_current = False
        elytecMat = plot_data.show_data(
            indir, plot_type="elytec", print_flag=False,
            save_flag=False, data_only=True, color_changes=None, smooth_type=None)[1]
        elytepMat = plot_data.show_data(
            indir, plot_type="elytep", print_flag=False,
            save_flag=False, data_only=True, color_changes=None, smooth_type=None)[1]
        np.savetxt(os.path.join(indir, "elyteConcData.txt"),
                   elytecMat, delimiter=dlm, header=elytecHdr)
        np.savetxt(os.path.join(indir, "elytePotData.txt"),
                   elytepMat, delimiter=dlm, header=elytepHdr)
        if valid_current:
            elyteiMat = plot_data.show_data(
                indir, plot_type="elytei", print_flag=False,
                save_flag=False, data_only=True, color_changes=None, smooth_type=None)[1]
            elytediviMat = plot_data.show_data(
                indir, plot_type="elytedivi", print_flag=False,
                save_flag=False, data_only=True, color_changes=None, smooth_type=None)[1]
            np.savetxt(os.path.join(indir, "elyteCurrDensData.txt"),
                       elyteiMat, delimiter=dlm, header=elyteiHdr)
            np.savetxt(os.path.join(indir, "elyteDivCurrDensData.txt"),
                       elytediviMat, delimiter=dlm, header=elytediviHdr)

    if csldData:
        dataFileName = "output_data"
        dataFile = os.path.join(indir, dataFileName)
        data = utils.open_data_file(dataFile)
        for tr in trodes:
            Trode = get_trode_str(tr)
            type2c = False
            if config[tr, "type"] in constants.one_var_types:
                str_base = partStr + "c"
            elif config[tr, "type"] in constants.two_var_types:
                type2c = True
                str1_base = partStr + "c1"
                str2_base = partStr + "c2"
            for i in range(config["Npart"][tr]):
                for j in range(config["Nvol"][tr]):
                    if type2c:
                        sol1 = str1_base.format(l=tr, i=i, j=j)
                        sol2 = str2_base.format(l=tr, i=i, j=j)
                        datay1 = utils.get_dict_key(data, sol1)
                        datay2 = utils.get_dict_key(data, sol2)
                        filename1 = fnameSol1Base.format(l=Trode, i=i, j=j)
                        filename2 = fnameSol2Base.format(l=Trode, i=i, j=j)
                        np.savetxt(os.path.join(indir, filename1), datay1,
                                   delimiter=dlm, header=sol1Hdr)
                        np.savetxt(os.path.join(indir, filename2), datay2,
                                   delimiter=dlm, header=sol2Hdr)
                    else:
                        sol = str_base.format(l=tr, i=i, j=j)
                        datay = utils.get_dict_key(data, sol)
                        filename = fnameSolBase.format(l=Trode, i=i, j=j)
                        np.savetxt(os.path.join(indir, filename), datay,
                                   delimiter=dlm, header=solHdr)

        # close file if it is a h5py file
        if isinstance(data, h5py._hl.files.File):
            data.close()

    if cbarData:
        cbarDict = plot_data.show_data(
            indir, plot_type="cbar_full", print_flag=False,
            save_flag=False, data_only=True, color_changes='discrete', smooth_type=None)
        for tr in trodes:
            Trode = get_trode_str(tr)
            fname = "cbar{l}Data.txt".format(l=Trode)
            Nv, Np = config["Nvol"][tr], config["Npart"][tr]
            NpartTot = Nv*Np
            cbarMat = np.zeros((ntimes, NpartTot))
            cbarHdr = cbarHdrBase
            partInd = 0
            for i in range(Nv):
                for j in range(Np):
                    cbarHdr += "{i}/{j},".format(j=j, i=i)
                    cbarMat[:,partInd] = cbarDict[tr][:,i,j]
                    partInd += 1
            np.savetxt(os.path.join(indir, fname), cbarMat,
                       delimiter=dlm, header=cbarHdr.rstrip(','))

    if bulkpData:
        if "a" in trodes:
            bulkp_aData = plot_data.show_data(
                indir, plot_type="bulkp_a", print_flag=False,
                save_flag=False, data_only=True, color_changes=None, smooth_type=None)[1]
            fname = fnameBulkpBase.format(l="Anode")
            np.savetxt(os.path.join(indir, fname), bulkp_aData,
                       delimiter=dlm, header=bulkpHdr)
        bulkp_cData = plot_data.show_data(
            indir, plot_type="bulkp_c", print_flag=False,
            save_flag=False, data_only=True, color_changes=None, smooth_type=None)[1]
        fname = fnameBulkpBase.format(l="Cathode")
        np.savetxt(os.path.join(indir, fname), bulkp_cData,
                   delimiter=dlm, header=bulkpHdr)

    if totalCycle > 1:
        # save general cycle data
        cycNum, cycleCapacityCh, cycleCapacityDisch = plot_data.show_data(
            indir, plot_type="cycle_capacity", print_flag=False, save_flag=False,
            data_only=True)
        cycleCapFrac = plot_data.show_data(
            indir, plot_type="cycle_cap_frac", print_flag=False,
            save_flag=False, data_only=True)[1]
        cycleEfficiency = plot_data.show_data(
            indir, plot_type="cycle_efficiency", print_flag=False,
            save_flag=False, data_only=True)[1]
        genMat = np.zeros((len(cycNum), 5))
        genMat[:,0] = cycNum
        genMat[:,1] = cycleCapacityCh
        genMat[:,2] = cycleCapacityDisch
        genMat[:,3] = cycleCapFrac
        genMat[:,4] = cycleEfficiency
        np.savetxt(os.path.join(indir, fnameCycleBase), genMat, delimiter=dlm,
                   header=cyclerHdr)

        # save QV and dQdV data
        voltCycle, capCycle = plot_data.show_data(
            indir, plot_type="cycle_Q_V", print_flag=False, save_flag=False,
            data_only=True)
        fname = "QVCycle.txt"
        genMat = np.zeros((voltCycle.shape[0]*2, voltCycle.shape[1]))
        genMat[:voltCycle.shape[0],:] = voltCycle
        genMat[voltCycle.shape[0]:voltCycle.shape[0]*2,:] = capCycle
        np.savetxt(os.path.join(indir, fname), genMat, delimiter=dlm,
                   header=vQCyclerHdr)

        voltCycle, dQdVCycle = plot_data.show_data(
            indir, plot_type="cycle_dQ_dV", print_flag=False, save_flag=False,
            data_only=True)
        fname = "dQdVCycle.txt"
        genMat = np.zeros((voltCycle.shape[0]*2, voltCycle.shape[1]))
        genMat[:voltCycle.shape[0],:] = voltCycle
        genMat[voltCycle.shape[0]:voltCycle.shape[0]*2,:] = dQdVCycle
        np.savetxt(os.path.join(indir, fname), genMat, delimiter=dlm,
                   header=vdQCyclerHdr)

        # close file if it is a h5py file
        if isinstance(data, h5py._hl.files.File):
            data.close()

    return

1	"""This can be called to convert the default simulation output (.mat file) to csv files."""
2	import os	×
3
4	import numpy as np	×
5	import h5py	×
6
7	import mpet.plot.plot_data as plot_data	×
8	import mpet.utils as utils	×
9	from mpet.config import constants	×
10
11	# Strings to be used
12	RowsStr = "Rows correspond to time points (see generalData.txt).\n"	×
13	CCStr = "Columns correspond to cell center positions (see discData.txt)."	×
14	FCStr = "Columns correspond to face positions (see discData.txt)."	×
15	genDataHdr = ("Time [s], Filling fraction of anode, "	×
16	+ "Filling fraction of cathode, "
17	+ "Voltage [V], Current [C-rate], Current [A/m^2], "
18	+ "Power [W/m^2]")
19
20	zeroStr = "Zero is at the anode current collector."	×
21	dccpStr = "discretization cell center positions [m]. "	×
22	discCCbattery = ("Battery " + dccpStr + zeroStr)	×
23	discCCanode = ("Anode " + dccpStr + zeroStr)	×
24	discCCsep = ("Separator " + dccpStr + zeroStr)	×
25	discCCcathode = ("Cathode " + dccpStr + zeroStr)	×
26	discFC = ("Battery discretization face positions [m]. " + zeroStr)	×
27	particleIndxExpl = """	×
28	Particle output files are indexed such that Vol 0 is closest to the
29	anode current collector for both electrodes. Indexing within volumes
30	is such that Part 0 is closest to the "carbon backbone" if simPartCond
31	was set to true for that electrode. Otherwise it is in arbitrary
32	order.
33	"""
34	particleDiscExpl = """	×
35	Particle discretization info follows. Lengths and number of
36	discretization points are provided for each simulated particle.
37	Meshes are made as a linear space between zero and particle length
38	with the given number of points. Rows correspond to different
39	simulation volumes with the first row being closest to the anode
40	current collector and the last closest to the cathode current
41	collector. Columns represent individual particles within each
42	simulated volume in no particular order.
43	"""
44
45	elytecHdr = ("Electrolyte Concentrations [M]\n" + RowsStr + CCStr)	×
46	elytepHdr = ("Electrolyte Electric Potential [V]\n" + RowsStr + CCStr)	×
47	elyteiHdr = ("Electrolyte Current Density [A/m^2]\n" + RowsStr + FCStr)	×
48	elytediviHdr = ("Electrolyte Divergence of Current Density [A/m^3]\n"	×
49	+ RowsStr + CCStr)
50
51	seeDiscStr = "See discData.txt for particle indexing information."	×
52	partStr = "partTrode{l}vol{j}part{i}_"	×
53	solffStr = "Solid Filling Fractions"	×
54	solTail = ("\n" + RowsStr + CCStr + "\n" + seeDiscStr)	×
55	solHdr = (solffStr + solTail)	×
56	opStr = ", order parameter "	×
57	sol1Hdr = (solffStr + opStr + "1" + solTail)	×
58	sol2Hdr = (solffStr + opStr + "2" + solTail)	×
59	fnameSolL = "sld{l}Vol{j:03d}Part{i:03d}Conc"	×
60	fnameSolR = "Data.txt"	×
61	fnameSolBase = (fnameSolL + fnameSolR)	×
62	fnameSol1Base = (fnameSolL + "1" + fnameSolR)	×
63	fnameSol2Base = (fnameSolL + "2" + fnameSolR)	×
64
65	cbarHdrP1 = ("Average particle filling fractions.\n" + RowsStr)	×
66	cbarHdrP2 = """Columns correspond to particles specified by simulated	×
67	volume index / particle index within volume.
68	"""
69	cbarHdrBase = cbarHdrP1 + cbarHdrP2 + seeDiscStr + "\n"	×
70
71	bulkpHdrP2 = """Columns correspond to this electrode's cell center	×
72	positions (see discData.txt).
73	"""
74	bulkpHdr = ("Bulk electrode electric potential [V]\n" + RowsStr + bulkpHdrP2)	×
75	fnameBulkpBase = "bulkPot{l}Data.txt"	×
76
77	RowStrHdr1 = "First column corresponds to the cycle number.\n"	×
78	RowStrHdr2 = """Second, third and fourth columns respond to gravimetric charge capacity of limiting	×
79	electrode in mAh/g, gravimetric discharge capacity of limiting electrode in mAh/g, cycle
80	capacity fraction relative to original capacity, and cycle efficiency (discharge
81	capacity/charge capacity).\n"""
82	cyclerHdr = ("Cycling Data\n" + RowStrHdr1 + RowStrHdr2)	×
83	fnameCycleBase = "cycleData.txt"	×
84
85	RowStrHdr1Q = """Each (2i,2i+1) row represents the (V(t), Q(t)) in cycle i in units of	×
86	(V, Ah/m^2).\n"""
87	vQCyclerHdr = ("Voltage/Capacity Cycling Data\n" + RowStrHdr1Q)	×
88
89	RowStrHdr2Q = """Each (2i,2i+1) row represents the (V(t), dQ(t)dV) in cycle i in units of	×
90	(V, Ah/m^2).\n"""
91	vdQCyclerHdr = ("Voltage/dQ Cycling Data\n" + RowStrHdr2Q)	×
92
93
94	def main(indir, genData=True, discData=True, elyteData=True,	×
95	csldData=True, cbarData=True, bulkpData=True):
96	config = plot_data.show_data(	×
97	indir, plot_type="params", print_flag=False, save_flag=False,
98	data_only=True, color_changes=None, smooth_type=None)
99	trodes = config["trodes"]	×
100	CrateCurr = config["1C_current_density"] # A/m^2	×
101	psd_len_c = config["psd_len"]["c"]	×
102	totalCycle = config["totalCycle"]	×
103	Nv_c, Np_c = psd_len_c.shape	×
104	dlm = ","	×
105
106	def get_trode_str(tr):	×
107	return ("Anode" if tr == "a" else "Cathode")	×
108	if "a" in trodes:	×
109	psd_len_a = config["psd_len"]["a"]	×
110	Nv_a, Np_a = psd_len_a.shape	×
111	tVec, vVec = plot_data.show_data(	×
112	indir, plot_type="vt", print_flag=False, save_flag=False,
113	data_only=True, color_changes=None, smooth_type=None)
114	ntimes = len(tVec)	×
115
116	if genData:	×
117	ffVec_c = plot_data.show_data(	×
118	indir, plot_type="soc_c", print_flag=False,
119	save_flag=False, data_only=True, color_changes=None, smooth_type=None)[1]
120	if "a" in trodes:	×
121	ffVec_a = plot_data.show_data(	×
122	indir, plot_type="soc_a", print_flag=False,
123	save_flag=False, data_only=True, color_changes=None, smooth_type=None)[1]
124	else:
125	ffVec_a = np.ones(len(tVec))	×
126	currVec = plot_data.show_data(	×
127	indir, plot_type="curr", print_flag=False,
128	save_flag=False, data_only=True, color_changes=None, smooth_type=None)[1]
129	powerVec = plot_data.show_data(	×
130	indir, plot_type="power", print_flag=False,
131	save_flag=False, data_only=True, color_changes=None, smooth_type=None)[1]
132	genMat = np.zeros((ntimes, 7))	×
133	genMat[:,0] = tVec	×
134	genMat[:,1] = ffVec_a	×
135	genMat[:,2] = ffVec_c	×
136	genMat[:,3] = vVec	×
137	genMat[:,4] = currVec	×
138	genMat[:,5] = currVec * CrateCurr	×
139	genMat[:,6] = powerVec	×
140	np.savetxt(os.path.join(indir, "generalData.txt"),	×
141	genMat, delimiter=dlm, header=genDataHdr)
142
143	if discData:	×
144	cellCentersVec, facesVec = plot_data.show_data(	×
145	indir, plot_type="discData", print_flag=False,
146	save_flag=False, data_only=True, color_changes=None, smooth_type=None)
147	with open(os.path.join(indir, "discData.txt"), "w") as fo:	×
148	print(discCCbattery, file=fo)	×
149	print(",".join(map(str, cellCentersVec)), file=fo)	×
150	offset = 0	×
151	if "a" in trodes:	×
152	print(file=fo)	×
153	print(discCCanode, file=fo)	×
154	print(",".join(map(str, cellCentersVec[:Nv_a])), file=fo)	×
155	offset = Nv_a	×
156	print(file=fo)	×
157	print(discCCsep, file=fo)	×
158	print(",".join(map(str, cellCentersVec[offset:-Nv_c])), file=fo)	×
159	print(file=fo)	×
160	print(discCCcathode, file=fo)	×
161	print(",".join(map(str, cellCentersVec[-Nv_c:])), file=fo)	×
162	print(file=fo)	×
163	print(discFC, file=fo)	×
164	print(",".join(map(str, facesVec)), file=fo)	×
165	print(file=fo)	×
166	print(particleIndxExpl, file=fo)	×
167	print(particleDiscExpl, file=fo)	×
168	for tr in trodes:	×
169	print(file=fo)	×
170	Trode = get_trode_str(tr)	×
171	print((Trode + " particle sizes [m]"), file=fo)	×
172	for vind in range(config["Nvol"][tr]):	×
173	print(",".join(map(str, config["psd_len"][tr][vind,:])), file=fo)	×
174	print("\n" + Trode + " particle number of discr. points", file=fo)	×
175	for vind in range(config["Nvol"][tr]):	×
176	print(",".join(map(str, config["psd_num"][tr][vind,:])), file=fo)	×
177
178	if elyteData:	×
179	valid_current = True	×
180	# If there wasn't an electrolyte, then a ghost point variable wouldn't have been created,
181	# so we'll get a KeyError in attempting to "plot" the electrolyte current density.
182	try:	×
183	plot_data.show_data(	×
184	indir, plot_type="elytei", print_flag=False, save_flag=False, data_only=True,
185	color_changes=None, smooth_type=None)
186	except KeyError:	×
187	valid_current = False	×
188	elytecMat = plot_data.show_data(	×
189	indir, plot_type="elytec", print_flag=False,
190	save_flag=False, data_only=True, color_changes=None, smooth_type=None)[1]
191	elytepMat = plot_data.show_data(	×
192	indir, plot_type="elytep", print_flag=False,
193	save_flag=False, data_only=True, color_changes=None, smooth_type=None)[1]
194	np.savetxt(os.path.join(indir, "elyteConcData.txt"),	×
195	elytecMat, delimiter=dlm, header=elytecHdr)
196	np.savetxt(os.path.join(indir, "elytePotData.txt"),	×
197	elytepMat, delimiter=dlm, header=elytepHdr)
198	if valid_current:	×
199	elyteiMat = plot_data.show_data(	×
200	indir, plot_type="elytei", print_flag=False,
201	save_flag=False, data_only=True, color_changes=None, smooth_type=None)[1]
202	elytediviMat = plot_data.show_data(	×
203	indir, plot_type="elytedivi", print_flag=False,
204	save_flag=False, data_only=True, color_changes=None, smooth_type=None)[1]
205	np.savetxt(os.path.join(indir, "elyteCurrDensData.txt"),	×
206	elyteiMat, delimiter=dlm, header=elyteiHdr)
207	np.savetxt(os.path.join(indir, "elyteDivCurrDensData.txt"),	×
208	elytediviMat, delimiter=dlm, header=elytediviHdr)
209
210	if csldData:	×
211	dataFileName = "output_data"	×
212	dataFile = os.path.join(indir, dataFileName)	×
213	data = utils.open_data_file(dataFile)	×
214	for tr in trodes:	×
215	Trode = get_trode_str(tr)	×
216	type2c = False	×
217	if config[tr, "type"] in constants.one_var_types:	×
218	str_base = partStr + "c"	×
219	elif config[tr, "type"] in constants.two_var_types:	×
220	type2c = True	×
221	str1_base = partStr + "c1"	×
222	str2_base = partStr + "c2"	×
223	for i in range(config["Npart"][tr]):	×
224	for j in range(config["Nvol"][tr]):	×
225	if type2c:	×
226	sol1 = str1_base.format(l=tr, i=i, j=j)	×
227	sol2 = str2_base.format(l=tr, i=i, j=j)	×
228	datay1 = utils.get_dict_key(data, sol1)	×
229	datay2 = utils.get_dict_key(data, sol2)	×
230	filename1 = fnameSol1Base.format(l=Trode, i=i, j=j)	×
231	filename2 = fnameSol2Base.format(l=Trode, i=i, j=j)	×
232	np.savetxt(os.path.join(indir, filename1), datay1,	×
233	delimiter=dlm, header=sol1Hdr)
234	np.savetxt(os.path.join(indir, filename2), datay2,	×
235	delimiter=dlm, header=sol2Hdr)
236	else:
237	sol = str_base.format(l=tr, i=i, j=j)	×
238	datay = utils.get_dict_key(data, sol)	×
239	filename = fnameSolBase.format(l=Trode, i=i, j=j)	×
240	np.savetxt(os.path.join(indir, filename), datay,	×
241	delimiter=dlm, header=solHdr)
242
243	# close file if it is a h5py file
244	if isinstance(data, h5py._hl.files.File):	×
245	data.close()	×
246
247	if cbarData:	×
248	cbarDict = plot_data.show_data(	×
249	indir, plot_type="cbar_full", print_flag=False,
250	save_flag=False, data_only=True, color_changes='discrete', smooth_type=None)
251	for tr in trodes:	×
252	Trode = get_trode_str(tr)	×
253	fname = "cbar{l}Data.txt".format(l=Trode)	×
254	Nv, Np = config["Nvol"][tr], config["Npart"][tr]	×
255	NpartTot = Nv*Np	×
256	cbarMat = np.zeros((ntimes, NpartTot))	×
257	cbarHdr = cbarHdrBase	×
258	partInd = 0	×
259	for i in range(Nv):	×
260	for j in range(Np):	×
261	cbarHdr += "{i}/{j},".format(j=j, i=i)	×
262	cbarMat[:,partInd] = cbarDict[tr][:,i,j]	×
263	partInd += 1	×
264	np.savetxt(os.path.join(indir, fname), cbarMat,	×
265	delimiter=dlm, header=cbarHdr.rstrip(','))
266
267	if bulkpData:	×
268	if "a" in trodes:	×
269	bulkp_aData = plot_data.show_data(	×
270	indir, plot_type="bulkp_a", print_flag=False,
271	save_flag=False, data_only=True, color_changes=None, smooth_type=None)[1]
272	fname = fnameBulkpBase.format(l="Anode")	×
273	np.savetxt(os.path.join(indir, fname), bulkp_aData,	×
274	delimiter=dlm, header=bulkpHdr)
275	bulkp_cData = plot_data.show_data(	×
276	indir, plot_type="bulkp_c", print_flag=False,
277	save_flag=False, data_only=True, color_changes=None, smooth_type=None)[1]
278	fname = fnameBulkpBase.format(l="Cathode")	×
279	np.savetxt(os.path.join(indir, fname), bulkp_cData,	×
280	delimiter=dlm, header=bulkpHdr)
281
282	if totalCycle > 1:	×
283	# save general cycle data
284	cycNum, cycleCapacityCh, cycleCapacityDisch = plot_data.show_data(	×
285	indir, plot_type="cycle_capacity", print_flag=False, save_flag=False,
286	data_only=True)
287	cycleCapFrac = plot_data.show_data(	×
288	indir, plot_type="cycle_cap_frac", print_flag=False,
289	save_flag=False, data_only=True)[1]
290	cycleEfficiency = plot_data.show_data(	×
291	indir, plot_type="cycle_efficiency", print_flag=False,
292	save_flag=False, data_only=True)[1]
293	genMat = np.zeros((len(cycNum), 5))	×
294	genMat[:,0] = cycNum	×
295	genMat[:,1] = cycleCapacityCh	×
296	genMat[:,2] = cycleCapacityDisch	×
297	genMat[:,3] = cycleCapFrac	×
298	genMat[:,4] = cycleEfficiency	×
299	np.savetxt(os.path.join(indir, fnameCycleBase), genMat, delimiter=dlm,	×
300	header=cyclerHdr)
301
302	# save QV and dQdV data
303	voltCycle, capCycle = plot_data.show_data(	×
304	indir, plot_type="cycle_Q_V", print_flag=False, save_flag=False,
305	data_only=True)
306	fname = "QVCycle.txt"	×
307	genMat = np.zeros((voltCycle.shape[0]*2, voltCycle.shape[1]))	×
308	genMat[:voltCycle.shape[0],:] = voltCycle	×
309	genMat[voltCycle.shape[0]:voltCycle.shape[0]*2,:] = capCycle	×
310	np.savetxt(os.path.join(indir, fname), genMat, delimiter=dlm,	×
311	header=vQCyclerHdr)
312
313	voltCycle, dQdVCycle = plot_data.show_data(	×
314	indir, plot_type="cycle_dQ_dV", print_flag=False, save_flag=False,
315	data_only=True)
316	fname = "dQdVCycle.txt"	×
317	genMat = np.zeros((voltCycle.shape[0]*2, voltCycle.shape[1]))	×
318	genMat[:voltCycle.shape[0],:] = voltCycle	×
319	genMat[voltCycle.shape[0]:voltCycle.shape[0]*2,:] = dQdVCycle	×
320	np.savetxt(os.path.join(indir, fname), genMat, delimiter=dlm,	×
321	header=vdQCyclerHdr)
322
323	# close file if it is a h5py file
324	if isinstance(data, h5py._hl.files.File):	×
325	data.close()	×
326
327	return	×

TRI-AMDD / mpet / 8476080312

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