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Fix autodetect #254

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Merged
srmnitc merged 5 commits into from
Jun 23, 2026
Merged

Fix autodetect #254

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e426fc2
roll back automated ts and instead add RangeScan
srmnitc Jun 19, 2026
7333dfd
remove the phase trf detection from the actual ts run
srmnitc Jun 23, 2026
cb2eaae
update threshold for onset temperature
srmnitc Jun 23, 2026
1e7b076
turn off old checking
srmnitc Jun 23, 2026
ac26b0e
Bump version: 1.8.2 → 1.8.3
srmnitc Jun 23, 2026
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2 changes: 1 addition & 1 deletion .bumpversion.cfg
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
[bumpversion]
current_version = 1.8.2
current_version = 1.8.3
commit = True
tag = True

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2 changes: 1 addition & 1 deletion calphy/__init__.py
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Expand Up @@ -4,7 +4,7 @@
from calphy.alchemy import Alchemy
from calphy.routines import MeltingTemp

__version__ = "1.8.2"
__version__ = "1.8.3"

def addtest(a,b):
return a+b
3 changes: 0 additions & 3 deletions calphy/alchemy.py
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Expand Up @@ -117,9 +117,6 @@ def run_averaging(self):
else:
self.run_finite_pressure_equilibration(lmp)

# create the fluctuation monitor before the pressure-convergence cycle loop
self._create_monitor("solid")

# this is when the averaging routine starts
self.run_pressure_convergence(lmp)

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2 changes: 1 addition & 1 deletion calphy/errors.py
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Expand Up @@ -35,6 +35,6 @@ class SolidifiedError(CustomError):
pass

class PhaseTransitionError(CustomError):
"""Raised when the ts-sweep transition detector flags a phase transition."""
"""Raised when the pre-flight temperature-range scan flags a phase transition."""
pass

126 changes: 88 additions & 38 deletions calphy/input.py
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Expand Up @@ -49,7 +49,7 @@
from ase.io import read, write
import shutil

__version__ = "1.8.2"
__version__ = "1.8.3"


def _check_equal(val):
Expand Down Expand Up @@ -248,33 +248,41 @@ class Queue(BaseModel, title="Options for configuring queue"):
class Tolerance(BaseModel, title="Tolerance settings for convergence"):
lattice_constant: Annotated[float, Field(default=0.0002, ge=0)]
spring_constant: Annotated[float, Field(default=0.1, gt=0)]
solid_fraction: Annotated[float, Field(default=0.7, ge=0)]
liquid_fraction: Annotated[float, Field(default=0.05, ge=0)]
# Structural phase-stability checks during equilibration are OFF by
# default: solid_fraction=0 means the melt check (solid_fraction < this)
# never fires, and liquid_fraction=1.0 means the solidify check
# (solid_fraction > this) never fires. Set solid_fraction > 0 (e.g. 0.7)
# to re-enable melt detection for a solid run, or liquid_fraction < 1
# (e.g. 0.05) to re-enable solidification detection for a liquid run.
solid_fraction: Annotated[float, Field(default=0.0, ge=0)]
liquid_fraction: Annotated[float, Field(default=1.0, ge=0)]
pressure: Annotated[float, Field(default=10.0, ge=0)]


class PhaseTransitionDetection(BaseModel, title="Settings for fluctuation-based phase transition detection"):
class PhaseTransitionDetection(BaseModel, title="Settings for the pre-flight temperature-range scan"):
mode: Annotated[
Literal["none", "warn", "recover", "stop"],
Literal["none", "adapt", "warn", "stop"],
Field(
default="none",
description=(
"Controls what happens when a phase transition is detected "
"during a reversible-scaling sweep.\n"
" 'none' — detection is disabled; sweep always completes "
"(default).\n"
" 'warn' — detection runs and a warning is logged with the "
"estimated transition temperature and triggering signals; "
"response-function plots are generated; the sweep continues "
"to completion uninterrupted. Use this to observe detection "
"without changing the calculation outcome.\n"
" 'recover' — truncate the forward sweep at the last clean "
"block boundary, save a checkpoint, and continue with a "
"backward sweep over the reduced range [T0, T_k]. A valid "
"free-energy curve is produced for the single-phase region.\n"
" 'stop' — raise PhaseTransitionError and abort. Use "
"when you want to inspect the raw data before deciding how "
"to proceed."
"Controls the pre-flight temperature-range scan that runs "
"before a reversible-scaling (ts) sweep. The scan performs a "
"single fast real-thermostat temperature ramp (T0 -> Tf under "
"NPT) and watches the fluctuation response functions for the "
"onset of a phase transition.\n"
" 'none' — the scan is disabled; the ts sweep runs over the "
"requested [T0, Tf] range as-is (default).\n"
" 'adapt' — if the scan detects a transition, reduce the upper "
"temperature to the detected clean onset and run the ts sweep "
"over [T0, T_clean] (keeping the same number of switching "
"steps). If the scan is clean the range is unchanged.\n"
" 'warn' — run the scan and log the detected clean range, but "
"do NOT modify the calculation; the ts sweep runs over the full "
"requested range. Use this to observe detection without "
"changing the outcome.\n"
" 'stop' — if a transition is detected, raise "
"PhaseTransitionError reporting the clean range so you can "
"re-submit with a corrected temperature range."
),
),
]
Expand Down Expand Up @@ -312,29 +320,71 @@ class PhaseTransitionDetection(BaseModel, title="Settings for fluctuation-based
default=4.0,
gt=0,
description=(
"Walk-back threshold used to locate the onset temperature from a "
"detected peak. Applied to all signals: variance-based signals "
"(Cp, kappa_T, alpha_P) walk back to where the signal falls below "
"baseline_median + onset_sigma * MAD; slope-break signals "
"(H_break, V_break) walk back to where |z| falls below onset_sigma. "
"Lower values give earlier (more conservative) onsets and therefore "
"earlier recovery cuts; higher values place the onset closer to the "
"unambiguous part of the peak. Default 4.0."
"Walk-back threshold for the variance-based signals (Cp, "
"kappa_T, alpha_P), whose rolling-window peak sits AT the "
"transition. Their onset is walked back from the peak to where "
"the signal falls below baseline_median + onset_sigma * MAD. "
"The slope-break signals use onset_level instead. Default 4.0."
),
),
]
baseline_window: Annotated[int, Field(default=50, ge=5)]
recent_window: Annotated[int, Field(default=50, ge=5)]
min_samples_before_check: Annotated[int, Field(default=100, ge=10)]
temperature_window: Annotated[
onset_level: Annotated[
float,
Field(
default=50.0,
ge=0,
default=1.5,
gt=0,
description=(
"Low-sigma walk-back level for the slope-break signals (H_break, "
"V_break), used to place the clean boundary at the FOOT of the "
"transition — where the mean enthalpy/volume first starts leaving "
"the single-phase equation of state — rather than at its collapse. "
"This matters because a reversible-scaling sweep equilibrates the "
"system at the boundary temperature, so the boundary must sit "
"where the phase is still cleanly stable, not at the point where a "
"fast diagnostic ramp finally lost (super)stability. It is "
"phase-agnostic (melting, solid-solid, freezing). Lower values "
"place the cut earlier (more margin); higher values place it "
"closer to the collapse. Default 1.5."
),
),
]
onset_fraction: Annotated[
float,
Field(
default=0.85,
gt=0,
le=1.0,
description=(
"Fractional safety margin applied to the detected onset: the "
"adapted upper temperature is "
"T_clean = T0 + onset_fraction * (T_onset - T0). The detected "
"onset is the foot of the deviation in a *fast* diagnostic ramp, "
"but a reversible-scaling sweep then EQUILIBRATES at the boundary "
"for many steps and the metastable phase has more time to "
"nucleate the transition there — so its practical stability "
"limit is somewhat below the ramp onset, and the exact onset is "
"also noisy. Backing the boundary off by a fraction of the "
"super-heated/cooled span makes the adapted sweep robust to both "
"effects. 1.0 disables the margin (cut exactly at the onset); "
"lower values give more margin (and less usable range). "
"Default 0.85."
),
),
]
prescan_steps: Annotated[
int,
Field(
default=20000,
ge=1000,
description=(
"Split each TS sweep into blocks of this width (in Kelvin). "
"The transition detector is called at each block boundary. "
"Set to 0 to run a single sweep with post-hoc detection only."
"Number of MD steps for the pre-flight temperature ramp from "
"T0 to Tf. Typically a little shorter than the production "
"switching length. Note that a *faster* ramp superheats (or "
"supercools) the metastable phase further and yields noisier "
"response-function signals, pushing the detected onset closer "
"to the collapse; if the adapted ts sweep melts/freezes during "
"its equilibration, increase this (or lower onset_level). "
"Default 20000."
),
),
]
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3 changes: 0 additions & 3 deletions calphy/liquid.py
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Original file line number Diff line number Diff line change
Expand Up @@ -219,9 +219,6 @@ def run_averaging(self):
# now assign correct temperature and equilibrate
self.run_zero_pressure_equilibration(lmp)

# create the fluctuation monitor before the pressure-convergence cycle loop
self._create_monitor("liquid")

# converge pressure
self.run_pressure_convergence(lmp)
else:
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