Increase fmax to 0.03 if NEB + fix problem with get_Stress with voigt

abipy/flowtk/qutils.py

@@ -15,6 +15,7 @@
 from pymatgen.core.units import Time, Memory
 from abipy.tools.typing import PathLike
 from abipy.tools import duck
+from abipy.tools.text import rm_multiple_spaces
 
 
 def slurm_parse_timestr(s: str) -> Time:
@@ -196,11 +197,11 @@ class SlurmJobArray:
 queue_id = job_array.sbatch("job.sh")
     """
 
-    def __init__(self, header, command, arr_options):
-        self.command = str(command)
-        self.header = str(header)
+    def __init__(self, header: str, command: str, arr_options: list[str]):
+        self.command = command
+        if not self.command.endswith(" "): self.command += " "
+        self.header = header
         self.arr_options = arr_options
-        from abipy.tools.text import rm_multiple_spaces
         self.arr_options_str = rm_multiple_spaces("\n".join(arr_options))
 
     def __str__(self):

abipy/ml/aseml.py

@@ -239,9 +239,15 @@ def from_atoms(cls, atoms: Atoms, calc=None) -> AseResults:
         """Build the object from an atoms instance with a calculator."""
         if calc is not None:
             atoms.calc = calc
+
+        from ase.stress import voigt_6_to_full_3x3_strain
+        stress_voigt = atoms.get_stress()
+        print(stress_voigt)
+        stress = voigt_6_to_full_3x3_strain(stress_voigt)
+
         results = cls(atoms=atoms.copy(),
                       ene=float(atoms.get_potential_energy()),
-                      stress=atoms.get_stress(voigt=False),
+                      stress=stress,
                       forces=atoms.get_forces())
         if calc is not None:
             atoms.calc = None

abipy/scripts/abiml.py

@@ -66,7 +66,7 @@ def wrapper(*args, **kw):
             print("Command line options:")
             print(json.dumps(kw, indent=4), end="\n")
 
-        # Set OMP_NUM_THREADS to 1 if env var is not defined.
+        # IMPORTANT: Set OMP_NUM_THREADS to 1 if env variable is not defined.
         num_threads = cli.fix_omp_num_threads()
 
         t_start = time()
@@ -118,7 +118,7 @@ def add_neb_opts(f):
     f = click.option("--relax-mode", "-r", default="ions", show_default=True, type=click.Choice(["no", "ions", "cell"]),
             help="Relax initial and final structure. Use `cell` to relax ions and cell, " +
                  "`ions` to relax atomic positions only, `no` to disable relaxation")(f)
-    f = click.option("--fmax", default=0.01, type=float, show_default=True, help='Stopping criterion.')(f)
+    f = click.option("--fmax", default=0.03, type=float, show_default=True, help='Stopping criterion.')(f)
     f = click.option("--pressure", default=0.0, type=float, show_default=True, help='Scalar pressure')(f)
     f = click.option("--optimizer", "-o", default="BFGS", show_default=True, type=click.Choice(ASE_OPTIMIZERS),
                      help="ASE optimizer class.")(f)