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Add eddiag error handling and fix AMIN error handling in VaspErrorHandler #302

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merged 12 commits into from
Nov 14, 2023
Merged

Add eddiag error handling and fix AMIN error handling in VaspErrorHandler #302

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b089f33
Added AMIN handler and unit test to VaspErrorHander logic, corrected …
Sep 8, 2023
95c2639
Added eddiag error handling and unit test
Sep 8, 2023
1325c0d
Tuning zheev/eddiag to remove OOM issues
Sep 8, 2023
233b894
Merge branch 'materialsproject:master' into master
esoteric-ephemera Oct 24, 2023
7e2fb03
Merge branch 'materialsproject:master' into master
esoteric-ephemera Nov 3, 2023
5bd9b4c
Merge branch 'materialsproject:master' into master
esoteric-ephemera Nov 6, 2023
e1cf431
pre-commit auto-fixes
pre-commit-ci[bot] Nov 6, 2023
d2e7b9b
pre-commit fix
Nov 6, 2023
fd374a9
Fix tests, ensure that custodian does not induce algo_tet errors
Nov 6, 2023
fe042b8
Merge branch 'materialsproject:master' into master
esoteric-ephemera Nov 14, 2023
3ec4eb2
simplify custodian/vasp/tests/test_validators.py
janosh Nov 14, 2023
5d33c92
Remove error files with too few bands.
janosh Nov 14, 2023
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21 changes: 14 additions & 7 deletions custodian/vasp/handlers.py
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Original file line number Diff line number Diff line change
Expand Up @@ -99,6 +99,7 @@ class VaspErrorHandler(ErrorHandler):
"grad_not_orth": ["EDWAV: internal error, the gradient is not orthogonal"],
"nicht_konv": ["ERROR: SBESSELITER : nicht konvergent"],
"zheev": ["ERROR EDDIAG: Call to routine ZHEEV failed!"],
"eddiag": ["ERROR in EDDIAG: call to ZHEEV/ZHEEVX/DSYEV/DSYEVX failed"],
"elf_kpar": ["ELF: KPAR>1 not implemented"],
"elf_ncl": ["WARNING: ELF not implemented for non collinear case"],
"rhosyg": ["RHOSYG"],
Expand Down Expand Up @@ -207,6 +208,11 @@ def correct(self):
actions.append({"dict": "INCAR", "action": {"_set": {"ISMEAR": 0, "SIGMA": 0.05}}})
self.error_count[err_type] += 1

# Missing AMIN error handler:
# previously, custodian would kill the job without letting it run if AMIN was flagged
if "amin" in self.errors and vi["INCAR"].get("AMIN", 0.1) > 0.01:
actions.append({"dict": "INCAR", "action": {"_set": {"AMIN": 0.01}}})

if "inv_rot_mat" in self.errors and vi["INCAR"].get("SYMPREC", 1e-5) > 1e-8:
actions.append({"dict": "INCAR", "action": {"_set": {"SYMPREC": 1e-8}}})

Expand Down Expand Up @@ -536,16 +542,18 @@ def correct(self):
UserWarning,
)

if "zheev" in self.errors:
if self.errors.intersection({"zheev", "eddiag"}):
# Copy CONTCAR to POSCAR if CONTCAR has already been populated.
try:
is_contcar = Poscar.from_file("CONTCAR")
except Exception:
is_contcar = False
if is_contcar:
actions.append({"file": "CONTCAR", "action": {"_file_copy": {"dest": "POSCAR"}}})
if vi["INCAR"].get("ALGO", "Normal").lower() != "exact":
actions.append({"dict": "INCAR", "action": {"_set": {"ALGO": "Exact"}}})
if vi["INCAR"].get("ALGO", "Normal").lower() == "fast":
actions.append({"dict": "INCAR", "action": {"_set": {"ALGO": "Normal"}}})
elif vi["INCAR"].get("ALGO", "Normal").lower() == "normal":
actions.append({"dict": "INCAR", "action": {"_set": {"ALGO": "exact"}}})

if "elf_kpar" in self.errors and vi["INCAR"].get("KPAR", 1) != 1:
actions.append({"dict": "INCAR", "action": {"_set": {"KPAR": 1}}})
Expand Down Expand Up @@ -645,7 +653,7 @@ def correct(self):
# This time try the recovery below.
actions.append({"dict": "INCAR", "action": {"_set": {"ALGO": "Fast"}}})
#
# We will only hit the 2nd algo_teet error if the ALGO was changed back from Fast to All/Damped
# We will only hit the 2nd algo_tet error if the ALGO was changed back from Fast to All/Damped
# by e.g. NonConvergingErrorHandler
# NOTE this relies on self.errors being reset on empty set on every .check call
if self.error_count["algo_tet"] > 0:
Expand Down Expand Up @@ -1052,9 +1060,8 @@ def correct(self):

if (
v.incar.get("ISMEAR", -1) >= 0
or not 50 <= v.incar.get("IALGO", 38) <= 59
and v.incar.get("METAGGA", "--") != "--"
and algo != "all"
and (algo != "all" or (not 50 <= v.incar.get("IALGO", 38) <= 59))
):
# If meta-GGA, go straight to Algo = All only if ISMEAR is greater or equal 0.
# Algo = All is recommended in the VASP manual and some meta-GGAs explicitly
Expand Down Expand Up @@ -1083,7 +1090,7 @@ def correct(self):
actions.append({"dict": "INCAR", "action": {"_set": {"ALGO": "Fast"}}})
elif algo == "fast":
actions.append({"dict": "INCAR", "action": {"_set": {"ALGO": "Normal"}}})
elif algo == "normal" and (v.incar.get("ISMEAR", -1) >= 0 or not 50 <= v.incar.get("IALGO", 38) <= 59):
elif (algo == "normal" or not 50 <= v.incar.get("IALGO", 38) <= 59) and v.incar.get("ISMEAR", -1) >= 0:
actions.append({"dict": "INCAR", "action": {"_set": {"ALGO": "All"}}})
else:
# Try mixing as last resort
Expand Down
31 changes: 31 additions & 0 deletions custodian/vasp/tests/test_handlers.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -548,6 +548,37 @@ def test_read_error(self):
assert dct["errors"] == ["read_error"]
assert dct["actions"] is None

def test_amin(self):
# Cell with at least one dimension >= 50 A, but AMIN > 0.01, and calculation not yet complete
shutil.copy("INCAR.amin", "INCAR")
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This overwrites the existing INCAR that was copied to tmp_path by setUP which might cause the downstream test failure.

h = VaspErrorHandler("vasp.amin")
h.check()
d = h.correct()
assert d["errors"] == ["amin"]
assert d["actions"] == [{"action": {"_set": {"AMIN": 0.01}}, "dict": "INCAR"}]

def test_eddiag(self):
# subspace rotation error
os.remove("CONTCAR")
h = VaspErrorHandler("vasp.eddiag")
h.check()
d = h.correct()
assert d["errors"] == ["eddiag"]
# first check that no CONTCAR exists, only action should be updating INCAR
assert d["actions"] == [{"action": {"_set": {"ALGO": "Normal"}}, "dict": "INCAR"}]

# now copy CONTCAR and check that both CONTCAR->POSCAR and INCAR updates are included
shutil.copy("CONTCAR.eddiag", "CONTCAR")
shutil.copy("INCAR.orig", "INCAR")
h = VaspErrorHandler("vasp.eddiag")
h.check()
d = h.correct()
print(d["actions"])
assert d["actions"] == [
{"file": "CONTCAR", "action": {"_file_copy": {"dest": "POSCAR"}}},
{"action": {"_set": {"ALGO": "Normal"}}, "dict": "INCAR"},
]


class AliasingErrorHandlerTest(PymatgenTest):
def setUp(self):
Expand Down
99 changes: 85 additions & 14 deletions test_files/CONTCAR
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Original file line number Diff line number Diff line change
@@ -1,16 +1,87 @@
Na2 Fe1 Ni1 O4
Cs6 U6 As12 O55
1.0
-2.816100 0.000000 0.000000
-0.000000 -4.877628 0.000000
-1.408050 0.812938 4.684533
Na Fe Ni O
2 1 1 4
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0.7401923066829772 9.5890356602029918 2.1332187291702365
0.0000000000000000 0.0000000000000000 20.5988000000000007
Cs U As O
6 6 12 55
direct
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0.359265 0.880245 0.271470 O
0.640735 0.119755 0.708530 O
0.140735 0.619755 0.708530 O
0.4957000000000000 0.3319500000000000 0.9441000000000001 Cs+
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0.0867000000000000 0.1105000000000000 0.6551800000000000 Cs+
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87 changes: 87 additions & 0 deletions test_files/CONTCAR.eddiag
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Original file line number Diff line number Diff line change
@@ -0,0 +1,87 @@
Cs6 U6 As12 O55
1.0
6.7346923911508014 0.0000000000000000 0.9285262282647135
0.7401923066829772 9.5890356602029918 2.1332187291702365
0.0000000000000000 0.0000000000000000 20.5988000000000007
Cs U As O
6 6 12 55
direct
0.4957000000000000 0.3319500000000000 0.9441000000000001 Cs+
0.9702000000000000 0.6994000000000000 0.6221800000000000 Cs+
0.0867000000000000 0.1105000000000000 0.6551800000000000 Cs+
0.7371000000000000 0.0299000000000000 0.2812500000000000 Cs+
0.3684000000000000 0.7777800000000000 0.9883999999999999 Cs+
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0.3278000000000000 0.0356500000000000 0.1334400000000000 U6+
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26 changes: 26 additions & 0 deletions test_files/INCAR.amin
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Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,26 @@
ADDGRID = False
ALGO = Fast
AMIN = 0.1
EDIFF = 1e-06
ENAUG = 1360
ENCUT = 680
ISMEAR = -5
ISPIN = 2
KPAR = 4
KSPACING = 0.22
LAECHG = False
LASPH = False
LCHARG = False
LELF = False
LMAXMIX = 6
LORBIT = 11
LREAL = Auto
LVTOT = False
LWAVE = False
MAGMOM = 99*0.6
NCORE = 1
NELM = 100
NSIM = 8
NSW = 0
PREC = Accurate
SIGMA = 0.05
6 changes: 2 additions & 4 deletions test_files/aliasing/INCAR
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@ ALGO = Fast
EDIFF = 0.0004
ENCUT = 520
IBRION = 2
ICHARG = 1
ICHARG = 10
ISIF = 3
ISMEAR = -5
ISPIN = 2
Expand All @@ -15,12 +15,10 @@ LMAXMIX = 4
LORBIT = 11
LREAL = Auto
LWAVE = False
MAGMOM = 2*0.6 1*5 5*0.6
MAGMOM = 2*0.6 1*5.0 5*0.6
NELM = 100
NELMIN = 6
NPAR = 1
NSW = 99
NGY = 1
NGZ = 1
PREC = Accurate
SIGMA = 0.05
26 changes: 26 additions & 0 deletions test_files/aliasing/INCAR (Aaron Kaplan's conflicted copy 2023-09-08)
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This looks like an accidental addition?

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Yes it's Dropbox's way of resolving internet failures

Original file line number Diff line number Diff line change
@@ -0,0 +1,26 @@
ALGO = Fast
EDIFF = 0.0004
ENCUT = 520
IBRION = 2
ICHARG = 1
ISIF = 3
ISMEAR = -5
ISPIN = 2
LDAU = True
LDAUJ = 0 0 0 0
LDAUL = 0 2 2 0
LDAUTYPE = 2
LDAUU = 0 4.0 6 0
LMAXMIX = 4
LORBIT = 11
LREAL = Auto
LWAVE = False
MAGMOM = 2*0.6 1*5 5*0.6
NELM = 100
NELMIN = 6
NPAR = 1
NSW = 99
NGY = 1
NGZ = 1
PREC = Accurate
SIGMA = 0.05
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