Skip to content

Commit cdab60d

Browse files
zhichen3zhichen3
authored
Merge branch 'development' into update-python-actions
2 parents 94f7315 + c940047 commit cdab60d

File tree

12 files changed

+183
-117
lines changed

12 files changed

+183
-117
lines changed

‎CHANGES.md‎

Lines changed: 28 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -1,3 +1,31 @@
1+
# 26.02
2+
3+
* update CI due to Microphysics optimizations (#3189, #3203)
4+
5+
* `Detonation` : fix plotting script for mass fractions (#3200)
6+
7+
* fix make flags in ``job_info`` (#3195)
8+
9+
* fix radiation compilation due to ``Array4`` changes (#3198)
10+
11+
* ``xrb_spherical`` : fix ash field in plot output
12+
13+
* cppcheck fixes
14+
15+
* update to C++20 (#3097)
16+
17+
* optimization and cleaning of ``check_for_negative_density`` (#3191)
18+
19+
* diffusion optimization and modernization (#3192)
20+
21+
* optimize a divide in SDC react (#3194)
22+
23+
* optimize the transverse flux correction in CTU hydro (#3181)
24+
25+
* ``massive_star`` : add another 3D visualization script
26+
27+
* optimize ``ambient_fill` (#3190)
28+
129
# 26.01
230

331
* `massive_star` : add volume-rendering scripts (#3186)

‎Docs/source/_static/theme_overrides.css‎

Lines changed: 23 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -34,7 +34,7 @@ div#example-notebook div.highlight-default div.highlight {
3434

3535
.wy-side-nav-search>div.branch{
3636
font-weight:normal;
37-
color:rgba(255,255,255,0.3);
37+
color:rgba(255,255,255);
3838
font-size:100%;
3939
display:inline-block;
4040
padding:4px 6px;
@@ -47,4 +47,25 @@ div#example-notebook div.highlight-default div.highlight {
4747
margin-bottom:.809em; */
4848
color:#fcfcfc;
4949
font-weight:bold;
50-
}
50+
}
51+
52+
/* Underline links everywhere */
53+
.wy-nav-content a {
54+
text-decoration: underline;
55+
text-decoration-style: dotted;
56+
text-underline-offset: 0.15em;
57+
}
58+
59+
/* Left sidebar navigation links */
60+
.wy-menu a {
61+
text-decoration-line: underline;
62+
text-decoration-style: dotted;
63+
text-underline-offset: 0.15em;
64+
}
65+
66+
.wy-side-nav-search a {
67+
text-decoration-line: underline;
68+
text-decoration-style: dotted;
69+
text-underline-offset: 0.15em;
70+
}
71+

‎Docs/source/conf.py‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -60,6 +60,7 @@ def get_version():
6060
'sphinx_copybutton',
6161
'sphinx_prompt',
6262
'breathe',
63+
'sphinx_rtd_theme_ext_color_contrast',
6364
'IPython.sphinxext.ipython_console_highlighting']
6465

6566
# bibtex

‎Exec/Make.auto_source‎

Lines changed: 3 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -150,6 +150,9 @@ ifeq ($(USE_CUDA), TRUE)
150150
endif
151151

152152
clean_flags := $(filter-out --jobserver%,$(MAKEFLAGS))
153+
ifeq ($(strip $(clean_flags)),)
154+
clean_flags = $(MAKEOVERRIDES)
155+
endif
153156

154157
$(objEXETempDir)/AMReX_buildInfo.o: .FORCE
155158
@if [ ! -d $(objEXETempDir) ]; then mkdir -p $(objEXETempDir); fi

‎Exec/science/Detonation/analysis/profiles.py‎

Lines changed: 32 additions & 24 deletions
Original file line numberDiff line numberDiff line change
@@ -156,7 +156,7 @@ def plot_nuc_frac(prefix, nums, skip, limitlabels, xmin, xmax):
156156
f = plt.figure()
157157
f.set_size_inches(32.0, 20.0)
158158

159-
# Get set of colors to use and apply to plot
159+
# color setup
160160
numplots = int(len(nums) / skip)
161161
cm = plt.get_cmap('nipy_spectral')
162162
clist = [cm(0.95*i/numplots) for i in range(numplots + 1)]
@@ -165,45 +165,53 @@ def plot_nuc_frac(prefix, nums, skip, limitlabels, xmin, xmax):
165165
if limitlabels > 1:
166166
skiplabels = int(numplots / limitlabels)
167167
elif limitlabels < 0:
168-
print("Illegal value for limitlabels: %.0f" % limitlabels)
169-
sys.exit()
168+
raise ValueError("Illegal value for limitlabels")
170169
else:
171170
skiplabels = 1
172171

173-
pfile = f"{prefix}{nums[1]}"
174-
ds = yt.load(pfile, hint="castro")
172+
# load a dataset to discover species
173+
ds = yt.load(f"{prefix}{nums[0]}", hint="castro")
175174

176-
nuc_list = [f[1] for f in ds.field_list if f[1][0] == "X"]
175+
nuc_list = [f[1] for f in ds.field_list if f[1].startswith("X")]
177176
nuc_list.sort(key=nuc_list_filter)
178-
N = len(nuc_list)
177+
N_SPECIES = len(nuc_list)
179178

180-
nrows = math.ceil(math.sqrt(N))
181-
ncols = math.ceil(math.sqrt(N))
179+
nrows = math.ceil(math.sqrt(N_SPECIES))
180+
ncols = math.ceil(math.sqrt(N_SPECIES))
182181

183-
for i in range(N):
184-
ax = f.add_subplot(nrows, ncols, i+1)
182+
# create axes
183+
axes = []
184+
for i in range(N_SPECIES):
185+
ax = f.add_subplot(nrows, ncols, i + 1)
185186
ax.set_prop_cycle(cycler('color', hexclist))
187+
ax.set_ylabel(nuc_list[i])
188+
ax.set_yscale("log")
189+
if xmax > 0:
190+
ax.set_xlim(xmin, xmax)
191+
axes.append(ax)
186192

187-
index = 0
188-
for n in range(0, len(nums), skip):
193+
# Loop over different plot files
194+
index = 0
195+
for n in range(0, len(nums), skip):
189196

190-
pfile = f"{prefix}{nums[n]}"
197+
pfile = f"{prefix}{nums[n]}"
198+
time, x, nuc_prof = get_nuc_profile(pfile)
191199

192-
time, x, nuc_prof = get_nuc_profile(pfile)
200+
label = None
201+
if index % skiplabels == 0:
202+
label = f"t = {time:6.4g} s"
193203

194-
if i == 0 and index % skiplabels == 0:
195-
ax.plot(x, nuc_prof[i], label=f"t = {time:6.4g} s")
204+
# For each plot file, loop over axes to
205+
# plot the species
206+
for i, ax in enumerate(axes):
207+
if label is not None and i == 0:
208+
ax.plot(x, nuc_prof[i], label=label)
196209
else:
197210
ax.plot(x, nuc_prof[i])
198211

199-
index = index + 1
200-
201-
ax.legend(frameon=False)
202-
ax.set_ylabel(nuc_list[i])
203-
ax.set_yscale("log")
212+
index += 1
204213

205-
if xmax > 0:
206-
ax.set_xlim(xmin, xmax)
214+
axes[0].legend(frameon=False)
207215

208216
f.tight_layout()
209217
f.savefig("det_nuc.png")

‎Exec/science/Detonation/ci-benchmarks/sdc_det_plt00040_extrema.out‎

Lines changed: 66 additions & 66 deletions
Original file line numberDiff line numberDiff line change
@@ -1,80 +1,80 @@
11
plotfile = det_x_plt00040
22
time = 5.1558159140336702e-06
33
variables minimum value maximum value
4-
density 185258192.85 216602408.23
5-
xmom -46504100132 2.9545170078e+16
4+
density 185285191.99 217993251.92
5+
xmom -39453339128 3.013512724e+16
66
ymom 0 0
77
zmom 0 0
8-
rho_E 1.3062473821e+26 2.7894570581e+26
9-
rho_e 1.3062473821e+26 2.7751890329e+26
10-
Temp 50000000.026 7845892023.3
11-
rho_H1 2.1201744635e-22 0.020000093825
12-
rho_He3 0.0017224320228 0.021020120012
13-
rho_He4 94358680.307 200001380.3
14-
rho_C12 0.020000000216 21130190.363
15-
rho_N14 1.9999997568e-22 0.020000138814
16-
rho_O16 0.02 19208.971235
17-
rho_Ne20 0.02 3345.900962
18-
rho_Mg24 0.02 23316.810422
19-
rho_Si28 0.02 2014906.8671
20-
rho_S32 0.02 1655900.9204
21-
rho_Ar36 0.02 821645.4629
22-
rho_Ca40 0.02 725101.08718
23-
rho_Ti44 0.02 34164.565105
24-
rho_Cr48 0.02 78159.887474
25-
rho_Fe52 0.02 278026.13131
26-
rho_Fe54 0.02 94990636.169
27-
rho_Ni56 0.02 2241021.534
28-
rho_n 2.1201744635e-22 234640.70453
29-
rho_p 0.019999995438 3609229.1563
8+
rho_E 1.3062473821e+26 2.8257528514e+26
9+
rho_e 1.3062473821e+26 2.804299639e+26
10+
Temp 50000000.026 7845855177.6
11+
rho_H1 2.1180676269e-22 0.020000061488
12+
rho_He3 0.0017224693618 0.021003891605
13+
rho_He4 94608854.914 200001056.53
14+
rho_C12 0.020000000216 20374547.097
15+
rho_N14 2.1180676269e-22 0.02000010615
16+
rho_O16 0.02 19209.494677
17+
rho_Ne20 0.02 2796.9090803
18+
rho_Mg24 0.02 23368.959786
19+
rho_Si28 0.02 2014567.4523
20+
rho_S32 0.02 1654613.5881
21+
rho_Ar36 0.02 820655.39591
22+
rho_Ca40 0.02 721486.83199
23+
rho_Ti44 0.02 34116.330345
24+
rho_Cr48 0.02 77158.095076
25+
rho_Fe52 0.02 258970.48822
26+
rho_Fe54 0.02 94949961.02
27+
rho_Ni56 0.02 1897563.3361
28+
rho_n 2.1180676269e-22 234580.46736
29+
rho_p 0.019999995438 3605706.2276
3030
Shock 0 0
31-
rho_enuc -4.7045878771e+29 3.5763112794e+32
32-
pressure 5.5236728651e+25 1.1610601906e+26
33-
kineng 0 2.0499232063e+24
34-
soundspeed 612864631.21 895228359.43
35-
Gamma_1 1.3599756444 1.3819594037
36-
MachNumber 0 0.1612010102
37-
uplusc 612864631.21 999831635.41
38-
uminusc -895228575.82 -612861139.09
39-
entropy 98214767.758 336273404.4
31+
rho_enuc -4.7789220073e+29 3.5711190587e+32
32+
pressure 5.5236728651e+25 1.1736955217e+26
33+
kineng 0 2.145321245e+24
34+
soundspeed 612864631.21 895226135.3
35+
Gamma_1 1.3599756682 1.3816259238
36+
MachNumber 0 0.16289154049
37+
uplusc 612864631.21 1016459268.8
38+
uminusc -895226285.43 -612861958.03
39+
entropy 98214767.758 336272705
4040
magvort 0 0
41-
divu -97843.447695 33859.293026
42-
eint_E 6.5312369103e+17 1.3804411077e+18
43-
eint_e 6.5312369103e+17 1.3804411077e+18
44-
logden 8.2677774233 8.3356632809
45-
StateErr_0 185258192.85 216602408.23
46-
StateErr_1 50000000.026 7845892023.3
41+
divu -102954.46788 32714.660901
42+
eint_E 6.5312369103e+17 1.3804345617e+18
43+
eint_e 6.5312369103e+17 1.3804345617e+18
44+
logden 8.2678407118 8.33844305
45+
StateErr_0 185285191.99 217993251.92
46+
StateErr_1 50000000.026 7845855177.6
4747
StateErr_2 1e-30 9.9999779324e-11
4848
X(H1) 1e-30 9.9999779324e-11
49-
X(He3) 8.9858859563e-12 9.9999601254e-11
50-
X(He4) 0.48401882032 0.9999999982
51-
X(C12) 1.0000000108e-10 0.099662507624
52-
X(N14) 1e-30 1.0000000373e-10
53-
X(O16) 1e-10 9.6044829786e-05
54-
X(Ne20) 1e-10 1.5781253004e-05
55-
X(Mg24) 1e-10 0.00011114942576
56-
X(Si28) 1e-10 0.010056996916
57-
X(S32) 1e-10 0.0083479592032
58-
X(Ar36) 1e-10 0.0041660812823
59-
X(Ca40) 1e-10 0.0037108409454
60-
X(Ti44) 1e-10 0.00017303110403
61-
X(Cr48) 1e-10 0.00040092608765
62-
X(Fe52) 1e-10 0.0013387591067
63-
X(Fe54) 1e-10 0.46490849282
64-
X(Ni56) 1e-10 0.010346244773
65-
X(n) 1e-30 0.0011732032003
66-
X(p) 9.9999977003e-11 0.017598814998
67-
abar 4.000000001 6.7314528761
68-
Ye 0.49998613725 0.50001572797
69-
x_velocity -232.52047511 138765368.48
49+
X(He3) 8.9860480972e-12 9.9999601254e-11
50+
X(He4) 0.48553904736 0.9999999982
51+
X(C12) 1.0000000108e-10 0.096194034778
52+
X(N14) 1e-30 1.0000000231e-10
53+
X(O16) 1e-10 9.6047412581e-05
54+
X(Ne20) 1e-10 1.3205003678e-05
55+
X(Mg24) 1e-10 0.00011107878964
56+
X(Si28) 1e-10 0.01001879459
57+
X(S32) 1e-10 0.0083074942358
58+
X(Ar36) 1e-10 0.0041417862462
59+
X(Ca40) 1e-10 0.0036809080925
60+
X(Ti44) 1e-10 0.00017125524006
61+
X(Cr48) 1e-10 0.00039450513234
62+
X(Fe52) 1e-10 0.0013091948027
63+
X(Fe54) 1e-10 0.46430019283
64+
X(Ni56) 1e-10 0.0087046884221
65+
X(n) 1e-30 0.0011729015943
66+
X(p) 9.9999977007e-11 0.017490570549
67+
abar 4.000000001 6.7254968416
68+
Ye 0.49755750199 0.50000799285
69+
x_velocity -197.26667245 142380101.99
7070
y_velocity 0 0
7171
z_velocity 0 0
72-
t_sound_t_enuc 3.4412406685e-13 0.97449833131
73-
enuc -2.5013290295e+21 1.6510948833e+24
74-
magvel 0 138765368.48
75-
radvel -232.52047511 138765368.48
76-
circvel 0 1.4142135624
77-
magmom 0 2.9545170078e+16
72+
t_sound_t_enuc 3.4412116194e-13 0.96073439115
73+
enuc -2.5402909306e+21 1.6381787176e+24
74+
magvel 0 142380101.99
75+
radvel -197.26667245 142380101.99
76+
circvel 0 2
77+
magmom 0 3.013512724e+16
7878
angular_momentum_x 0 0
7979
angular_momentum_y 0 0
8080
angular_momentum_z 0 0

‎Exec/science/Detonation/inputs-det-x.nse_net‎

Lines changed: 3 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -106,10 +106,11 @@ integrator.atol_spec = 1.e-8
106106
integrator.rtol_enuc = 1.e-8
107107
integrator.atol_enuc = 1.e-8
108108

109-
integrator.jacobian = 2
109+
integrator.jacobian = 1
110110
integrator.ode_max_steps = 1500000
111111

112112
nse.nse_molar_independent = 0
113113
nse.nse_dx_independent = 0
114114
nse.ase_tol = 0.1
115-
nse.nse_skip_molar = 0
115+
nse.nse_skip_molar = 0
116+
nse.solve_nse_e_mode = 2

‎Exec/science/flame_wave/ci-benchmarks/job_info_params.txt‎

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -239,7 +239,8 @@
239239
integrator.retry_rtol_enuc = -1
240240
integrator.retry_atol_spec = -1
241241
integrator.retry_atol_enuc = -1
242-
integrator.do_species_clip = 1
242+
integrator.do_species_clip = 0
243+
integrator.do_corrector_validation = 1
243244
integrator.use_number_densities = 0
244245
integrator.scale_system = 0
245246
integrator.nse_deriv_dt_factor = 0.05

‎Exec/science/wdmerger/ci-benchmarks/wdmerger_collision_2D.out‎

Lines changed: 20 additions & 20 deletions
Original file line numberDiff line numberDiff line change
@@ -1,30 +1,30 @@
11
plotfile = plt00086
22
time = 1.25
33
variables minimum value maximum value
4-
density 8.6940338039e-05 19441641.365
4+
density 8.6940338039e-05 19441641.471
55
xmom -5.4953770559e+14 1.3594264808e+14
6-
ymom -2.4933244206e+15 2.4933251729e+15
6+
ymom -2.4933244205e+15 2.4933251728e+15
77
zmom 0 0
8-
rho_E 7.4973602186e+11 5.0768248404e+24
9-
rho_e 7.1068648972e+11 5.0744783698e+24
10-
Temp 242282.60874 1404450632.8
11-
rho_He4 8.6940338039e-17 3.3981073638
12-
rho_C12 3.4776135215e-05 7775850.9298
13-
rho_O16 5.2164202823e-05 11664450.004
14-
rho_Ne20 8.6940338039e-17 172485.53519
15-
rho_Mg24 8.6940338039e-17 1043.0542752
16-
rho_Si28 8.6940338039e-17 5.9869392078
17-
rho_S32 8.6940338039e-17 0.00016459247689
18-
rho_Ar36 8.6940338039e-17 1.9441643659e-05
19-
rho_Ca40 8.6940338039e-17 1.9441641388e-05
20-
rho_Ti44 8.6940338039e-17 1.9441641375e-05
21-
rho_Cr48 8.6940338039e-17 1.9441641374e-05
22-
rho_Fe52 8.6940338039e-17 1.9441641374e-05
23-
rho_Ni56 8.6940338039e-17 1.9441641374e-05
8+
rho_E 7.4973602186e+11 5.0768248027e+24
9+
rho_e 7.1068648972e+11 5.0744783325e+24
10+
Temp 242282.60874 1404450624.3
11+
rho_He4 8.6940338039e-17 3.3981070237
12+
rho_C12 3.4776135215e-05 7775851.0551
13+
rho_O16 5.2164202823e-05 11664451.023
14+
rho_Ne20 8.6940338039e-17 172485.47435
15+
rho_Mg24 8.6940338039e-17 1043.053977
16+
rho_Si28 8.6940338039e-17 5.9869383088
17+
rho_S32 8.6940338039e-17 0.00016459243184
18+
rho_Ar36 8.6940338039e-17 1.9441643971e-05
19+
rho_Ca40 8.6940338039e-17 1.9441641667e-05
20+
rho_Ti44 8.6940338039e-17 1.9441641535e-05
21+
rho_Cr48 8.6940338039e-17 1.9441641532e-05
22+
rho_Fe52 8.6940338039e-17 1.9441641533e-05
23+
rho_Ni56 8.6940338039e-17 1.9441641533e-05
2424
Shock 0 1
2525
phiGrav -5.8707431189e+17 -2.337549858e+16
2626
grav_x -685044085.35 -51428.268861
27-
grav_y -739591083.89 739591039.38
27+
grav_y -739591083.9 739591039.38
2828
grav_z 0 0
29-
rho_enuc 0 7.1503781707e+23
29+
rho_enuc 0 7.1503783769e+23
3030

‎external/Microphysics‎

Submodule Microphysics updated 567 files

0 commit comments

Comments
 (0)