Extra works

abipy/flowtk/finitediff_works.py

@@ -0,0 +1,101 @@
+# coding: utf-8
+"""Work subclasses related to GS calculations."""
+from __future__ import annotations
+
+import json
+
+from pymatgen.analysis.eos import EOS
+from abipy.core.structure import Structure
+from abipy.abio.inputs import AbinitInput
+from abipy.electrons.gsr import GsrRobot
+from .works import Work
+
+#class FiniteDiffStressWork(Work):
+#    """
+#    Work for the computation of the stress tensor with finite difference
+#    """
+#
+#    @classmethod
+#    def from_scf_input(cls, scf_input, delta=1e-4, ecutsm=0.5, manager=None):
+#        """
+#        Build a EosWork from an AbinitInput representing a SCF-GS calculation.
+#
+#        Args:
+#            scf_input: AbinitInput for SCF-GS used as template to generate the other inputs.
+#	    delta:
+#            ecutsm: Value of ecutsm input variable. If `scf_input` does not provide ecutsm, this
+#                value will be used else the vale in `scf_input`.
+#            manager: TaskManager instance. Use default if None.
+#
+#        Return: EosWork instance.
+#        """
+#	scf_input = scf_input.deepcopy()
+#
+#        if "ecutsm" not in scf_input:
+#            scf_input.set_vars(ecutsm=ecutsm)
+#            print("Input does not define ecutsm input variable.\n",
+#                  "A default value of %s will be added to all the EOS inputs" % ecutsm)
+#
+#        new_work = cls(manager=manager)
+#        self.unstrained_task = new_work.register_scf_task(scf_input)
+#
+#	voigt_inds = [(0, 0)]
+#
+#	self.delta = float(delta)
+#	self.tasks_voigt = {}
+#	for voigt in voigt_inds:
+#	    self.tasks_voigt[voigt] = defaultdict(list)
+#	    for isign in (-1, +1):
+#		# Apply strain to the lattice.
+#                strain = np.zeros((3, 3))
+#                strain[voigt] = float(isign) * delta
+#                new_structure = scf_input.structure.deepcopy()
+#                new_structure.apply_strain(strain)
+#                new_input = scf_input.new_with_structure(new_structure)
+#
+#                # Perform GS calculations with strained cell.
+#                task = new_work.register_scf_task(new_input)
+#                self.tasks_voigt[voigt].append(task)
+#
+#        return new_work
+#
+#    def compute_and_write_stress(self):
+#        """
+#        This method is called when all tasks reach S_OK.
+#	It reads the energies and the volumes from the GSR file, computes the EOS and produce a
+#        JSON file `eos_data.json` in outdata.
+#        """
+#	with self.unstrained_task.open_gsr() as gsr0:
+#	    e0, v0 = gsr0.energy, gsr0.structure.volume
+#	    cart_stress_tensor = gsr0.cart_stress_tensor
+#
+#	fd_tensor = np.empty((3, 3))
+#	for voigt in voigt_inds:
+#	    tasks = self.tasks_voigt[voigt]
+#	    energies_ev, volumes = np.empty(len(tasks), np.empty(len(tasks))
+#	    for i, task in enumerate(task):
+#                with task.open_gsr() as gsr:
+#                   energies_ev[i] = float(gsr.energy))
+#
+#	    d = (e_plus - e_minus) / (2 * self.delta * v0)
+#            fd_tensor[voigt] = d
+#            fd_tensor[voigt[1], voigt[0]] = d
+#
+#	data = {
+#             "dfpt_cart_stress_tensor": cart_stress_tensor,
+#             "finite_diff_cart_stress_tensor": fd_cart_stress_tensor,
+#        }
+#
+#        with open(self.outdir.path_in("stress.json"), "wt") as fh:
+#            json.dump(data, fh, indent=4, sort_keys=True)
+#
+#        return data
+#
+#    def on_all_ok(self):
+#        """
+#        This method is called when all tasks reach S_OK. It reads the energies
+#        and the volumes from the GSR file, computes the EOS and produce a
+#        JSON file `eos_data.json` in outdata.
+#        """
+#        self.compute_and_write_stress()
+#        return dict(returncode=0, message="EOS computed and file written")