Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Update equilibria in desc.examples #1406

Merged
merged 31 commits into from
Dec 11, 2024
Merged
Show file tree
Hide file tree
Changes from 24 commits
Commits
Show all changes
31 commits
Select commit Hold shift + click to select a range
89a22d1
Update regenerate example script to allow saving to new dir
f0uriest Nov 12, 2024
58e05bf
Don't check for nestedness when initializing continuation
f0uriest Nov 20, 2024
2045ee1
Ensure correct z modes used when parsing axis
f0uriest Nov 20, 2024
3e8a5dc
Don't give axis guess when using continuiation method
f0uriest Nov 20, 2024
4147249
Use 2 steps for heliotron shaping
f0uriest Nov 20, 2024
976d647
Use automatic continuation for w7x
f0uriest Nov 20, 2024
ad05116
Re-run example equilibria
f0uriest Nov 21, 2024
b3eac3f
Add action to remind us to update examples and notebooks
f0uriest Nov 21, 2024
db1ab5d
Merge branch 'master' into rc/examples
dpanici Nov 21, 2024
c66a34b
Merge branch 'master' into rc/examples
dpanici Nov 25, 2024
bcfe01c
Merge branch 'rc/stopping_criteria' into rc/examples
f0uriest Dec 3, 2024
7e2b297
Update ncsx tols
f0uriest Dec 3, 2024
53a64f3
Rerun with rescaled termination criteria
f0uriest Dec 3, 2024
d44f467
Merge branch 'rc/stopping_criteria' into rc/examples
f0uriest Dec 4, 2024
cecc2f0
Merge branch 'master' into rc/examples
f0uriest Dec 4, 2024
4b6b0d6
Update baseline images
f0uriest Dec 5, 2024
4a7f7db
Update test tolerances
f0uriest Dec 5, 2024
40ce938
Update test tolerances 2
f0uriest Dec 5, 2024
bf4f277
Merge branch 'master' into rc/examples
dpanici Dec 6, 2024
ee4423c
Merge branch 'master' into rc/examples
f0uriest Dec 9, 2024
5596cae
Update master compute data
f0uriest Dec 10, 2024
ed1aa51
Adjust test tolerances
f0uriest Dec 10, 2024
b8ffcc1
Update baseline image
f0uriest Dec 10, 2024
aad22aa
Merge branch 'master' into rc/examples
f0uriest Dec 10, 2024
70431da
Merge branch 'master' into rc/examples
f0uriest Dec 10, 2024
8674583
Merge branch 'master' into rc/examples
f0uriest Dec 11, 2024
c4cb55e
Merge branch 'master' into rc/examples
f0uriest Dec 11, 2024
04714ed
Reduce radial resolution of heliotron and atf examples
f0uriest Dec 11, 2024
18f1f5e
Revert "Reduce radial resolution of heliotron and atf examples"
f0uriest Dec 11, 2024
36a11ae
Merge branch 'master' into rc/examples
f0uriest Dec 11, 2024
0e91df9
Merge branch 'master' into rc/examples
f0uriest Dec 11, 2024
File filter

Filter by extension

Filter by extension


Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
75 changes: 75 additions & 0 deletions .github/workflows/update_notebook_examples.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,75 @@
name: Update Notebooks and Examples
on:
schedule:
# runs on the first of every month at noon
- cron: '00 12 1 * *'

jobs:
create_issue:
name: Create issues to update notebooks and examples
runs-on: ubuntu-latest
permissions:
issues: write
steps:
- name: Create issue to update notebooks
run: |
if [[ $CLOSE_PREVIOUS == true ]]; then
previous_issue_number=$(gh issue list \
--label "$LABELS" \
--json number \
--jq '.[0].number')
if [[ -n $previous_issue_number ]]; then
gh issue close "$previous_issue_number"
gh issue unpin "$previous_issue_number"
fi
fi
new_issue_url=$(gh issue create \
--title "$TITLE" \
--assignee "$ASSIGNEES" \
--label "$LABELS" \
--body "$BODY")
if [[ $PINNED == true ]]; then
gh issue pin "$new_issue_url"
fi
env:
GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
GH_REPO: ${{ github.repository }}
TITLE: Update Notebooks
ASSIGNEES: f0uriest, dpanici, ddudt, rahulgaur104, kianorr, YigitElma
LABELS: monthly_update_notebooks
BODY: |
Reminder to check that notebooks evaluate correctly, and to update
if necessary.
PINNED: false
CLOSE_PREVIOUS: true
- name: Create issue to update notebooks
run: |
if [[ $CLOSE_PREVIOUS == true ]]; then
previous_issue_number=$(gh issue list \
--label "$LABELS" \
--json number \
--jq '.[0].number')
if [[ -n $previous_issue_number ]]; then
gh issue close "$previous_issue_number"
gh issue unpin "$previous_issue_number"
fi
fi
new_issue_url=$(gh issue create \
--title "$TITLE" \
--assignee "$ASSIGNEES" \
--label "$LABELS" \
--body "$BODY")
if [[ $PINNED == true ]]; then
gh issue pin "$new_issue_url"
fi
env:
GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
GH_REPO: ${{ github.repository }}
TITLE: Update Examples
ASSIGNEES: f0uriest, dpanici, ddudt, rahulgaur104, kianorr, YigitElma
LABELS: monthly_update_examples
BODY: |
Reminder to check that examples run correctly, and to update
if necessary.
PINNED: false
CLOSE_PREVIOUS: true
2 changes: 1 addition & 1 deletion desc/__main__.py
Original file line number Diff line number Diff line change
Expand Up @@ -37,7 +37,7 @@
and (inputs[-1]["pres_ratio"] is None)
and (inputs[-1]["bdry_ratio"] is None)
):
eq = Equilibrium(**inputs[-1], check_kwargs=False)
eq = Equilibrium(**inputs[-1], check_kwargs=False, ensure_nested=False)

Check warning on line 40 in desc/__main__.py

View check run for this annotation

Codecov / codecov/patch

desc/__main__.py#L40

Added line #L40 was not covered by tests
equil_fam = EquilibriaFamily.solve_continuation_automatic(
eq,
objective=inputs[-1]["objective"],
Expand Down
1 change: 1 addition & 0 deletions desc/equilibrium/utils.py
Original file line number Diff line number Diff line change
Expand Up @@ -141,6 +141,7 @@ def parse_axis(axis, NFP=1, sym=True, surface=None):
axis[:, 1],
axis[:, 2],
axis[:, 0].astype(int),
axis[:, 0].astype(int),
Copy link
Collaborator

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

what is this doing? seems to be passing in the same modes for Rn as Zn?

Copy link
Collaborator

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

That seems off? or do we ensure before this that we have the full mode spectrum in n and just set the non-symmetric modes to zero if it is stell symmetric?

NFP=NFP,
sym=sym,
name="axis",
Expand Down
Binary file modified desc/examples/ARIES-CS_output.h5
Binary file not shown.
4 changes: 0 additions & 4 deletions desc/examples/ATF
YigitElma marked this conversation as resolved.
Show resolved Hide resolved
Original file line number Diff line number Diff line change
Expand Up @@ -34,10 +34,6 @@ l: 0 p = 5.00000000E+05 i = -3.50000000E-01
l: 2 p = -1.00000000E+06 i = -6.50000000E-01
l: 4 p = 5.00000000E+05 i = 0.00000000E+00

# magnetic axis initial guess
n: 0 R0 = 2.10000000E+00 Z0 = 0.00000000E+00
n: 1 R0 = 0.10000000E+00 Z0 = 0.10000000E+00

# fixed-boundary surface shape
m: -2 n: -1 R1 = -2.50000000E-02 Z1 = 0.00000000E+00
m: -2 n: 0 R1 = 0.00000000E+00 Z1 = -6.75000000E-03
Expand Down
Binary file modified desc/examples/ATF_output.h5
Binary file not shown.
Binary file modified desc/examples/DSHAPE_CURRENT_output.h5
Binary file not shown.
Binary file modified desc/examples/DSHAPE_output.h5
Binary file not shown.
Binary file modified desc/examples/ESTELL_output.h5
Binary file not shown.
4 changes: 2 additions & 2 deletions desc/examples/HELIOTRON
Original file line number Diff line number Diff line change
Expand Up @@ -14,15 +14,15 @@ M_grid = 12, 18
N_grid = 0, 0, 6

# continuation parameters
bdry_ratio = 0, 0, 1
bdry_ratio = 0, 0, 0.5, 1
pres_ratio = 0, 1, 1
pert_order = 2

# solver tolerances
ftol = 1e-2
xtol = 1e-6
gtol = 1e-6
maxiter = 100
maxiter = 50

# solver methods
optimizer = lsq-exact
Expand Down
Binary file modified desc/examples/HELIOTRON_output.h5
Binary file not shown.
Binary file modified desc/examples/HSX_output.h5
Binary file not shown.
2 changes: 1 addition & 1 deletion desc/examples/NCSX
Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@ pert_order = 2.0
# solver tolerances
ftol = 1e-2
xtol = 1e-6
gtol = 1e-2
gtol = 1e-8
maxiter = 50

# solver methods
Expand Down
Binary file modified desc/examples/NCSX_output.h5
Binary file not shown.
Binary file modified desc/examples/SOLOVEV_output.h5
Binary file not shown.
14 changes: 4 additions & 10 deletions desc/examples/W7-X
Original file line number Diff line number Diff line change
Expand Up @@ -6,25 +6,19 @@ NFP = 5
Psi = -2.13300000E+00

# spectral resolution
L_rad = 12,16,24
L_rad = 12
M_pol = 12
N_tor = 12
M_grid = 16
N_grid = 16
N_tor = 12
M_grid = 16
N_grid = 16

# continuation parameters
# because we specify these and a sequence for L_rad, it will not use the automatic continuation
bdry_ratio=1.0
pert_order = 2


# solver methods
optimizer = lsq-exact
objective = force
spectral_indexing = fringe
ftol=1e-4
xtol= 1e-6
maxiter=150

# pressure and rotational transform profiles
l: 0 p = 1.85596929e+05 i = -8.56047021e-01
Expand Down
Binary file modified desc/examples/W7-X_output.h5
Binary file not shown.
Binary file modified desc/examples/WISTELL-A_output.h5
Binary file not shown.
Binary file modified desc/examples/precise_QA_output.h5
Binary file not shown.
Binary file modified desc/examples/precise_QH_output.h5
Binary file not shown.
88 changes: 56 additions & 32 deletions desc/examples/regenerate_all_equilibria.py
Original file line number Diff line number Diff line change
Expand Up @@ -4,43 +4,67 @@

python3 regenerate_all_equilibria.py

Copy the two lines below to the main code to run it on a GPU
from desc import set_device
set_device("gpu")
"""
import argparse
import glob
import os
import subprocess as spr
import sys
from pathlib import Path

from desc.__main__ import main
from desc.io import load
from desc.vmec import VMECIO
parser = argparse.ArgumentParser(
prog="regenerate_all_equilibria",
)
parser.add_argument(
"-o",
"--output",
metavar="output_dir",
help="Path to output files. If not specified, defaults to input dir",
)
parser.add_argument(
"--gpu",
"-g",
action="store_true",
help="Use GPU if available. If more than one are available, selects the "
+ "GPU with most available memory. ",
)
parser.add_argument(
"--noprecise",
action="store_true",
help="Don't regenerate precise QS equilibria.",
)


args = parser.parse_args(sys.argv[1:])

pwd = os.getcwd()
if args.output:
output_path = os.path.abspath(args.output)
else:
output_path = pwd

Path(output_path).mkdir(parents=True, exist_ok=True)

files = sorted(glob.glob(pwd + "/*.h5"))
print("Regenerating files:")
for f in files:
print(f)
print("saving to: ", output_path)
names = [f.split("/")[-1].split(".")[0].replace("_output", "") for f in files]
names = [f for f in names if "precise" not in f]

for fname in names:
print(f"Running the input file {fname} \n")
cargs = [
"desc",
fname,
"-vv",
f"-o {os.path.join(output_path, fname + '_output.h5')}",
]
if args.gpu:
cargs += ["-g"]
spr.run(cargs)

for fname in glob.glob(pwd + "/*.h5"):
if (
fname.split(".")[-1] == "h5"
and os.path.isfile(fname.split(".")[-1] + ".nc") is True
and fname.split(".")[0].split("/")[-1].split("_")[0] != "precise"
):
finputname = fname.split(".")[0].split("/")[-1].split("_")[0]
print(f"Running the input file {finputname} \n")
main(cl_args=[str(f"{finputname}"), "-vv"])
# save wout file
eq = load(f"{pwd}/{finputname}")[-1]
VMECIO.save(eq, "wout_" + fname + ".nc", surfs=256)
elif (
fname.split(".")[-1] == "h5"
and os.path.isfile(fname + ".nc") is False
and fname.split(".")[0].split("/")[-1].split("_")[0] != "precise"
):
finputname = fname.split(".")[0].split("/")[-1].split("_")[0]
print(f"Running the input file {finputname} \n")
main(cl_args=[str(f"{finputname}"), "-vv"])
else:
continue

main(cl_args=["DSHAPE_CURRENT", "-vv"])
spr.call(["python3 -u precise_QA.py"], shell=True)
spr.call(["python3 -u precise_QH.py"], shell=True)
if not args.noprecise:
spr.run(["python3", "-u", "precise_QA.py"])
spr.run(["python3", "-u", "precise_QH.py"])
Binary file modified tests/baseline/test_1d_elongation.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file modified tests/baseline/test_2d_g_tz.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file modified tests/baseline/test_2d_logF.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file modified tests/baseline/test_effective_ripple.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file modified tests/baseline/test_fsa_F_normalized.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file modified tests/baseline/test_plot_b_mag.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file modified tests/baseline/test_plot_boozer_modes_breaking_only.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file modified tests/baseline/test_plot_boozer_modes_no_norm.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file modified tests/baseline/test_plot_boozer_surface.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file modified tests/baseline/test_plot_coefficients.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file modified tests/baseline/test_plot_normF_2d.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file modified tests/baseline/test_plot_normF_section.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file modified tests/baseline/test_plot_poincare.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file modified tests/baseline/test_section_F.png
YigitElma marked this conversation as resolved.
Show resolved Hide resolved
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file modified tests/baseline/test_section_logF.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file modified tests/inputs/master_compute_data_rpz.pkl
Binary file not shown.
3 changes: 2 additions & 1 deletion tests/test_axis_limits.py
Original file line number Diff line number Diff line change
Expand Up @@ -293,9 +293,10 @@ def test_limit_continuity(self):
"iota_num_rr": {"atol": 5e-5},
"grad(B)": {"rtol": 1e-4},
"alpha_r (secular)": {"atol": 1e-4},
"grad(alpha) (secular)": {"atol": 1e-4},
"grad(alpha) (secular)": {"atol": 2e-4},
"gbdrift (secular)": {"atol": 1e-4},
"gbdrift (secular)/phi": {"atol": 1e-4},
"(psi_r/sqrt(g))_rr": {"rtol": 2e-5},
}
zero_map = dict.fromkeys(zero_limits, {"desired_at_axis": 0})
kwargs = weaker_tolerance | zero_map
Expand Down
11 changes: 5 additions & 6 deletions tests/test_bootstrap.py
Original file line number Diff line number Diff line change
Expand Up @@ -1589,13 +1589,12 @@ def test_bootstrap_optimization_comparison_qa():
objective=objective,
constraints=constraints,
optimizer="proximal-lsq-exact",
maxiter=5,
gtol=1e-16,
maxiter=10,
verbose=3,
)

# method 2
niters = 3
niters = 4
for k in range(niters):
eq2 = eq2.copy()
data = eq2.compute("current Redl", grid)
Expand All @@ -1616,11 +1615,11 @@ def test_bootstrap_optimization_comparison_qa():
data2 = eq2.compute(["<J*B> Redl", "<J*B>"], grid)

np.testing.assert_allclose(
grid.compress(data1["<J*B>"]), grid.compress(data1["<J*B> Redl"]), rtol=2.1e-2
grid.compress(data1["<J*B>"]), grid.compress(data1["<J*B> Redl"]), rtol=2e-2
)
np.testing.assert_allclose(
grid.compress(data2["<J*B>"]), grid.compress(data2["<J*B> Redl"]), rtol=1.8e-2
grid.compress(data2["<J*B>"]), grid.compress(data2["<J*B> Redl"]), rtol=2e-2
)
np.testing.assert_allclose(
grid.compress(data1["<J*B>"]), grid.compress(data2["<J*B>"]), rtol=1.9e-2
grid.compress(data1["<J*B>"]), grid.compress(data2["<J*B>"]), rtol=2e-2
)
2 changes: 1 addition & 1 deletion tests/test_neoclassical.py
Original file line number Diff line number Diff line change
Expand Up @@ -46,7 +46,7 @@ def test_fieldline_average():
np.testing.assert_allclose(
data["fieldline length"] / data["fieldline length/volume"],
data["V_r(r)"] / (4 * np.pi**2),
rtol=1e-3,
rtol=2e-3,
)
assert np.all(data["fieldline length"] > 0)
assert np.all(data["fieldline length/volume"] > 0)
Expand Down
4 changes: 2 additions & 2 deletions tests/test_objective_funs.py
Original file line number Diff line number Diff line change
Expand Up @@ -373,7 +373,7 @@ def test_qh_boozer(self):
# check that the objective returns the lowest amplitudes
# 120 ~ smallest amplitudes BEFORE QH modes show up so that sorting both arrays
# should have the same values up until then
np.testing.assert_allclose(f[idx_f][:120], B_mn[idx_B][:120])
np.testing.assert_allclose(f[idx_f][:120], B_mn[idx_B][:120], rtol=1e-6)

@pytest.mark.unit
def test_qh_boozer_multiple_surfaces(self):
Expand Down Expand Up @@ -2862,7 +2862,7 @@ def test_compute_scalar_resolution_others(self, objective):
)
obj.build(verbose=0)
f[i] = obj.compute_scalar(obj.x())
np.testing.assert_allclose(f, f[-1], rtol=5e-2)
np.testing.assert_allclose(f, f[-1], rtol=6e-2)

@pytest.mark.regression
@pytest.mark.parametrize(
Expand Down
4 changes: 2 additions & 2 deletions tests/test_optimizer.py
Original file line number Diff line number Diff line change
Expand Up @@ -1416,6 +1416,6 @@ def test_optimize_coil_currents(DummyCoilSet):
)
# check that optimized coil currents changed by more than 15% from initial values
np.testing.assert_array_less(
np.asarray(coils.current) * 0.15,
np.abs(np.asarray(coils_opt.current) - np.asarray(coils.current)),
np.asarray(coils.current).mean() * 0.15,
np.abs(np.asarray(coils_opt.current) - np.asarray(coils.current)).mean(),
)
6 changes: 3 additions & 3 deletions tests/test_stability_funs.py
Original file line number Diff line number Diff line change
Expand Up @@ -160,7 +160,7 @@ def test(eq, vmec, rho_range=DEFAULT_RANGE, rtol=DEFAULT_RTOL, atol=DEFAULT_ATOL
test(
desc.examples.get("HELIOTRON"),
".//tests//inputs//wout_HELIOTRON.nc",
(0.01, 0.45),
(0.07, 0.45),
rtol=1.75e-1,
)
test(
Expand Down Expand Up @@ -512,11 +512,11 @@ def test_ballooning_geometry(tmpdir_factory):
)
cvdrift_alt = -sign_psi * data["cvdrift"] * 2 * Bref * Lref**2 * np.sqrt(psi)

np.testing.assert_allclose(gds2, gds2_alt, rtol=4e-3)
np.testing.assert_allclose(gds2, gds2_alt, rtol=6e-3)
np.testing.assert_allclose(gds22, gds22_alt)
# gds21 is a zero crossing quantity, rtol won't work,
# shifting the grid slightly can change rtol requirement significantly
np.testing.assert_allclose(gds21, gds21_alt, atol=1e-3)
np.testing.assert_allclose(gds21, gds21_alt, atol=2e-3)
np.testing.assert_allclose(gbdrift, gbdrift_alt)
# cvdrift is a zero crossing quantity, rtol won't work,
# shifting the grid slightly can change rtol requirement significantly
Expand Down
Loading