Use FrechetCellFilter

abipy/dynamics/tests/test_analyzer.py

@@ -0,0 +1,34 @@
+""""Tests for analyzer module."""
+import abipy.data as abidata
+
+from abipy.core.testing import AbipyTest
+from abipy.dynamics.analyzer import MdAnalyzer, MultiMdAnalyzer, ArrheniusPlotter
+
+
+class AnalyzerTest(AbipyTest):
+    pass
+
+    #def test_md_analyzer(self):
+    #def test_multi_md_analyzer(self):
+
+    #def test_arrhenius_plotter(self):
+    #    key_path = {
+    #        "matgl-MD":  "diffusion_cLLZO-matgl.csv",
+    #        "m3gnet-MD": "diffusion_cLLZO-m3gnet.csv",
+    #    }
+
+    #    mpl_style_key = {
+    #        "matgl-MD" : dict(c='blue'),
+    #        "m3gnet-MD": dict(c='purple'),
+    #    }
+
+    #    plotter = ArrheniusPlotter()
+    #    for key, path in key_path.items():
+    #        plotter.add_entry_from_file(path, key, mpl_style=mpl_style_key[key])
+
+    #    # temperature grid refined
+    #    thinvt_arange = (0.6, 2.5, 0.01)
+    #    xlims, ylims = (0.5, 2.0), (-7, -4)
+
+    #    plotter.plot(thinvt_arange=thinvt_arange,
+    #                 xlims=xlims, ylims=ylims, text='LLZO cubic', savefig=None)

abipy/ml/aseml.py

@@ -34,13 +34,14 @@
 from ase.io import read
 from ase.optimize.optimize import Optimizer
 from ase.calculators.calculator import Calculator
-from ase.filters import ExpCellFilter
+from ase.filters import FrechetCellFilter # ExpCellFilter,
 from ase.io.vasp import write_vasp_xdatcar, write_vasp
-from ase.neb import NEB
+from ase.mep import NEB
+#from ase.neb import NEB
 from ase.md.npt import NPT
 from ase.md.nptberendsen import NPTBerendsen, Inhomogeneous_NPTBerendsen
 from ase.md.nvtberendsen import NVTBerendsen
-from ase.md.velocitydistribution import (MaxwellBoltzmannDistribution, Stationary, ZeroRotation)
+from ase.md.velocitydistribution import MaxwellBoltzmannDistribution, Stationary, ZeroRotation
 from ase.stress import voigt_6_to_full_3x3_stress, full_3x3_to_voigt_6_stress
 from ase.calculators.calculator import PropertyNotImplementedError
 from abipy.core import Structure
@@ -49,9 +50,9 @@
 from abipy.tools.printing import print_dataframe
 from abipy.tools.serialization import HasPickleIO, mjson_write
 from abipy.tools.context_managers import Timer
-from abipy.tools.parallel import get_max_nprocs # , pool_nprocs_pmode
+from abipy.tools.parallel import get_max_nprocs #, pool_nprocs_pmode
 from abipy.abio.enums import StrEnum, EnumMixin
-from abipy.core.mixins import TextFile # , NotebookWriter
+from abipy.core.mixins import TextFile #, NotebookWriter
 from abipy.tools.plotting import (set_axlims, add_fig_kwargs, get_ax_fig_plt, get_axarray_fig_plt, set_grid_legend,
     set_ax_xylabels, linear_fit_ax)
 from abipy.ml.tools import get_energy_step
@@ -1153,7 +1154,7 @@ def pf(*args, **kwargs):
 
         r0 = AseResults.from_atoms(atoms)
 
-        dyn = opt_class(ExpCellFilter(atoms, scalar_pressure=pressure), **opt_kwargs) if relax_mode == RX_MODE.cell else \
+        dyn = opt_class(FrechetCellFilter(atoms, scalar_pressure=pressure), **opt_kwargs) if relax_mode == RX_MODE.cell else \
               opt_class(atoms, **opt_kwargs)
 
         t_start = time.time()
@@ -2509,7 +2510,8 @@ def postprocess_images(self, images):
         post-process ASE NEB calculation.
         See <https://wiki.fysik.dtu.dk/ase/tutorials/neb/diffusion.html>
         """
-        from ase.neb import NEBTools
+        #from ase.neb import NEBTools
+        from ase.mep import NEBTools
         nebtools = NEBTools(images)
 
         # get the actual maximum force at this point in the simulation.
@@ -3551,7 +3553,7 @@ def run(self):
 
             relax_mode = RX_MODE.ions
             print(f"Relaxing initial atoms at fixed volume with {relax_mode=}.")
-            new_ucf = ExpCellFilter(new_atoms, constant_volume=True)
+            new_ucf = FrechetCellFilter(new_atoms, constant_volume=True)
             relax_kws = dict(optimizer=self.optimizer,
                              relax_mode=relax_mode,
                              fmax=self.fmax,