Replace np.complex with complex from builtins

abipy/embedding/embedding_ifc.py

@@ -1,25 +1,25 @@
+from __future__ import annotations
 
-from phonopy import Phonopy
 import numpy as np
+import os, shutil
 
+from phonopy import Phonopy
 from pymatgen.io.phonopy import get_pmg_structure,get_phonopy_structure
 
 from abipy.core.abinit_units import eV_to_THz
+from abipy.core.structure import Structure
 from abipy.dfpt.converters import phonopy_to_abinit
-import os,shutil
 from abipy.embedding.utils_ifc import accoustic_sum,map_two_structures_coords,clean_structure
-from abipy.core.structure import Structure
 
 
 class Embedded_phonons(Phonopy):
     """
     Defines a Phonopy object implementing the Interatomic Force Constants embedding method defined in:
-    https://pubs.acs.org/doi/10.1021/acs.chemmater.3c00537    
-    https://iopscience.iop.org/article/10.1088/1367-2630/16/7/073026/meta
-    https://journals.aps.org/prmaterials/abstract/10.1103/PhysRevMaterials.5.084603
 
+        https://pubs.acs.org/doi/10.1021/acs.chemmater.3c00537    
+        https://iopscience.iop.org/article/10.1088/1367-2630/16/7/073026/meta
+        https://journals.aps.org/prmaterials/abstract/10.1103/PhysRevMaterials.5.084603
     """
-
     # Inherits from Phonopy class
     def __init__(self,stru_pristine,stru_defect,stru_emb,ifc_emb,nac_params) :
         """
@@ -38,8 +38,6 @@ def __init__(self,stru_pristine,stru_defect,stru_emb,ifc_emb,nac_params) :
         self.stru_defect=stru_defect
         self.stru_emb=stru_emb
 
-
-
     @classmethod
     def from_phonopy_instances(cls,
                                phonopy_pristine,
@@ -56,34 +54,31 @@ def from_phonopy_instances(cls,
                                verbose=0,
                                asr=True) -> Phonopy :
         """
-
         Args:
             phonopy_pristine: Phonopy object of the pristine structure
-            phonopy_defect  : Phonopy object of the defect structure
-            structure_defect_wo_relax : Supercell structure associated to the defect structure, but without relaxation. Needed for an easier mapping.
+            phonopy_defect: Phonopy object of the defect structure
+            structure_defect_wo_relax: Supercell structure associated to the defect structure, but without relaxation. Needed for an easier mapping.
                 Should corresponds to order of phonopy_defect structure!
-            main_defect_coords_in_pristine : Main coordinates of the defect in pristine structure, if defect complex, can be set to the
+            main_defect_coords_in_pristine: Main coordinates of the defect in pristine structure, if defect complex, can be set to the
                 center of mass of the complex
             main_defect_coords_in_defect : Main coordinates of the defect in defect structure, if defect complex, can be set to the
                 center of mass of the complex
-            substitutions_list : List of substitutions infos [index,specie], ex : [[0, "Eu"],[1,"N"]]
-            vacancies_list : List of indices where the vacancies are, ex: [13,14]
-            interstitial_list : List of interstitial infos [specie, cart_coord], ex [['Eu',[0,0,0]],['Ce','[0,0,3]']]
-            tol_mapping : Tolerance in angstrom for the mapping between structures
-            cut_off_mode : Cut off mode for the radii of the sphere centered around the defect (rc_2). if 'auto' : the code tries to find the largest sphere 
+            substitutions_list: List of substitutions infos [index,specie], ex : [[0, "Eu"],[1,"N"]]
+            vacancies_list: List of indices where the vacancies are, ex: [13,14]
+            interstitial_list: List of interstitial infos [specie, cart_coord], ex [['Eu',[0,0,0]],['Ce','[0,0,3]']]
+            tol_mapping: Tolerance in angstrom for the mapping between structures
+            cut_off_mode: Cut off mode for the radii of the sphere centered around the defect (rc_2). if 'auto' : the code tries to find the largest sphere 
                 inscribed in the defect supercell. If 'manual' :  rc_1 and rc_2 should be provided.
-            rc_1 : Radii of the sphere centered around the defect outside which the IFCs are set to zero, allows to get sparse matrix. 
-            rc_2 : Radii of the sphere centered around the defect where the IFCs of the defect computation are included 
-            factor_ifc : Multiply the IFCs inside the sphere of radii rc_2 by factor_ifc, usefull to introduce fictious high-frequency local mode 
+            rc_1: Radii of the sphere centered around the defect outside which the IFCs are set to zero, allows to get sparse matrix. 
+            rc_2: Radii of the sphere centered around the defect where the IFCs of the defect computation are included 
+            factor_ifc: Multiply the IFCs inside the sphere of radii rc_2 by factor_ifc, usefull to introduce fictious high-frequency local mode 
             verbose : Print explicitely all the IFCs replacements 
-            asr : If True, re-enforce acoustic sum rule after IFCs embedding, following eq. (S4) of https://pubs.acs.org/doi/10.1021/acs.chemmater.3c00537
+            asr: If True, re-enforce acoustic sum rule after IFCs embedding, following eq. (S4) of https://pubs.acs.org/doi/10.1021/acs.chemmater.3c00537
 
         Returns:
             A new phonopy object with the embedded structure and embedded IFCs.
-
         """
-
-
+
         ########################
         # Structures manipulations and mapping
         ########################
@@ -107,7 +102,6 @@ def from_phonopy_instances(cls,
 
         stru_emb=clean_structure(stru_emb,defect_coord=main_defect_coords_in_pristine)
         structure_defect_wo_relax=clean_structure(structure_defect_wo_relax,defect_coord=main_defect_coords_in_defect)
-
 
         mapping=map_two_structures_coords(structure_defect_wo_relax,stru_emb,tol=tol_mapping)
 
@@ -131,32 +125,29 @@ def from_phonopy_instances(cls,
 
                 ifc_pristine=np.append(ifc_pristine,np.zeros(shape=[len(ifc_pristine),1,3,3]),axis=1)
 
-
-
         ########################
         # Print infos
         ########################
 
         print(f"Number of atoms in the pristine supercell      : {len(stru_pristine)}")
         print(f"Number of atoms in the defective supercell     : {len(stru_defect)}")
 
-        print(f"Defect infos")
+        print("Defect infos")
         if substitutions_list is not None:
-            print(f"    Substitutions :")
+            print("    Substitutions:")
             for sub in substitutions_list:
                 print(f"       {sub[0]}, {stru_pristine[sub[0]].coords}, {stru_pristine[sub[0]].species} replaced by {sub[1]}")
 
         if vacancies_list is not None:
-            print(f"    Vacancies :" )
+            print("    Vacancies:" )
             for vac in vacancies_list:
                 print(f"       {vac}, {stru_pristine[vac].coords}, {stru_pristine[vac].species} removed")
 
         if interstitial_list is not None:
-            print(f"    Interstitials :" )
+            print("    Interstitials:")
             for inter in interstitial_list:
                 print(f"       {inter[0]}, {inter[1]} added")
 
-
         print(f"Mapping after structure manipulation           : {len(mapping)}/{len(stru_defect)}")
 
         ########################
@@ -220,7 +211,6 @@ def from_phonopy_instances(cls,
         ########################
 
         if phonopy_pristine.nac_params is not None:
-
             # Simply copy the nac params from the pristine
             nac_params_emb=phonopy_pristine.nac_params.copy()
 
@@ -231,10 +221,9 @@ def from_phonopy_instances(cls,
 
         ########################
 
-        print(f"\n Embedding procedure done")
+        print("\n Embedding procedure done")
 
         return cls(stru_pristine,stru_defect,stru_emb,ifc_emb,nac_params_emb)
-
 
     def get_gamma_freq_with_vec_abipy_fmt(self):
         """
@@ -252,7 +241,6 @@ def get_gamma_freq_with_vec_abipy_fmt(self):
 
         return ph_freq, ph_vec
 
-
     def to_ddb(self,embedded_ddb_path='out_DDB',workdir=None):
         """
         Call the converter to go from phonopy to a DDB
@@ -267,7 +255,3 @@ def to_ddb(self,embedded_ddb_path='out_DDB',workdir=None):
                                    tolsym=None,workdir=workdir,nsym=1)
 
         return ddb_sc
-
-
-
-

abipy/eph/gkq.py

@@ -148,7 +148,7 @@ def read_all_gkq(self, mode="phonon"):
         natom3 = natom * 3
         phfreqs_ha, phdispl_red = self.phfreqs_ha, self.phdispl_red
         gkq_nu = np.empty_like(gkq_atm)
-        cwork = np.empty((natom3, nb2), dtype=np.complex)
+        cwork = np.empty((natom3, nb2), dtype=complex)
         for spin in range(self.ebands.nsppol):
             for ik in range(self.ebands.nkpt):
                 g = np.reshape(gkq_atm[spin, ik], (-1, nb2))
@@ -177,7 +177,7 @@ def read_all_gkq(self, mode="phonon"):
     #           gkq_atm = gkq_atm[:, 0] + 1j * gkq_atm[:, 1]
     #
     #           # Transform the gkk matrix elements from (atom, red_direction) basis to phonon-mode basis.
-    #           gkq_nu = np.zeros(natom3), dtype=np.complex)
+    #           gkq_nu = np.zeros(natom3), dtype=complex)
     #           for nu in range(natom3):
     #               if self.phfreqs_ha[nu] < eph_wtol: continue
     #               gkq_nu[nu] = np.dot(self.phdispl_red[nu], gkq_atm) / np.sqrt(2.0 * self.phfreqs_ha[nu])
@@ -441,8 +441,8 @@ def plot_gkq2_qpath(self, band_kq, band_k, kpoint=0, with_glr=False, qdamp=None,
         natom3 = len(self.abifiles[0].structure) * 3
         nsppol = self.abifiles[0].nsppol
         nqpt = len(self.abifiles)
-        gkq_snuq = np.empty((nsppol, natom3, nqpt), dtype=np.complex)
-        if with_glr: gkq_lr = np.empty((nsppol, natom3, nqpt), dtype=np.complex)
+        gkq_snuq = np.empty((nsppol, natom3, nqpt), dtype=complex)
+        if with_glr: gkq_lr = np.empty((nsppol, natom3, nqpt), dtype=complex)
 
         # TODO: Should take into account possible degeneracies in k and kq...
         xticks, xlabels = [], []

abipy/flowtk/abiphonopy.py

@@ -5,13 +5,9 @@
 import os
 import numpy as np
 
-try:
-    from phonopy import Phonopy, file_IO
-    from phonopy.interface.vasp import read_vasp_from_strings
-    from phonopy.interface.abinit import parse_set_of_forces
-except ImportError:
-    import warnings
-    warnings.warn("phonopy is required by abiphonopy. Install it with conda or pip install phonopy")
+from phonopy import Phonopy, file_IO
+from phonopy.interface.vasp import read_vasp_from_strings
+from phonopy.interface.abinit import parse_set_of_forces
 
 from abipy.core.structure import Structure
 from abipy.flowtk.works import Work

abipy/flowtk/effmass_works.py

@@ -80,8 +80,8 @@ def from_scf_input(cls, scf_input: AbinitInput,
         new.register_nscf_task(nscf_input, deps={scf_task: "DEN"})
 
         if ndivsm != 0:
-           ebands_inp = scf_input.make_ebands_input(ndivsm=ndivsm)
-           new.register_nscf_task(ebands_inp, deps={scf_task: "DEN"})
+            ebands_inp = scf_input.make_ebands_input(ndivsm=ndivsm)
+            new.register_nscf_task(ebands_inp, deps={scf_task: "DEN"})
 
         return new
 

abipy/flowtk/flows.py

@@ -2612,7 +2612,7 @@ def polish_doc(doc: str, node_type) -> str:
                 app(make_banner(s, mark="="))
                 app(polish_doc(task_cls.__doc__, "task"))
                 app("Tasks belonging to this class (%s):" % len(tasks))
-                for task  in tasks:
+                for task in tasks:
                     app(4 * " " + str(task) + ", status: " + task.status.colored)
 
         return "\n".join(lines)

abipy/flowtk/gw_works.py

@@ -5,7 +5,7 @@
 from __future__ import annotations
 
 import os
-import numpy as np
+#import numpy as np
 
 from . import wrappers
 from .nodes import Node

abipy/flowtk/lumi_works.py

@@ -6,6 +6,7 @@
 from abipy.abilab import abiopen
 from abipy.lumi.deltaSCF import DeltaSCF
 
+
 class LumiWork(Work):
     """
     This Work implements Fig 1 of https://arxiv.org/abs/2010.00423.
@@ -18,7 +19,7 @@ class LumiWork(Work):
     """
 
     @classmethod
-    def from_scf_inputs(cls, gs_scf_inp, ex_scf_inp, relax_kwargs_gs, relax_kwargs_ex, ndivsm=0, nb_extra=10, 
+    def from_scf_inputs(cls, gs_scf_inp, ex_scf_inp, relax_kwargs_gs, relax_kwargs_ex, ndivsm=0, nb_extra=10,
                         tolwfr=1e-12, four_points=True, meta=None, manager=None) -> LumiWork:
         """
         Args:
@@ -82,7 +83,7 @@ def on_all_ok(self):
         #with self.gs_relax_task.open_gsr() as gsr:
            # ag_relaxed_structure = gsr.structure
         with abiopen(self.gs_relax_task.output_file.path) as relax_gs_abo:
-           ag_relaxed_structure = relax_gs_abo.final_structure
+            ag_relaxed_structure = relax_gs_abo.final_structure
 
         if self.iteration_step == 0:
             print("in iteration step 0")
@@ -131,7 +132,6 @@ def on_all_ok(self):
             ae_scf_inp = self.gs_scf_inp.new_with_structure(aestar_relaxed_structure)
             self.ae_scf_task = self.register_scf_task((ae_scf_inp),deps={self.ex_relax_task: "DEN"})
 
-
             if self.ndivsm != 0:
                 # Compute band structure for Ag configuration.
                 self.ag_scf_task.add_ebands_task_to_work(self, ndivsm=self.ndivsm,
@@ -165,7 +165,6 @@ def on_all_ok(self):
             #with self.ex_relax_task.open_gsr() as gsr:
             self.json_data["ex_relax_filepath"]=self.ex_relax_task.gsr_path
 
-
             if self.four_points == True:
                 # Get Ag total energy.
                 #with self.ag_scf_task.open_gsr() as gsr:
@@ -200,6 +199,7 @@ def on_all_ok(self):
 
             return super().on_all_ok()
 
+
 class LumiWork_relaxations(Work):
     """
     This Work implements the ground and excited state relaxations only.
@@ -236,7 +236,6 @@ def from_scf_inputs(cls, gs_scf_inp, ex_scf_inp, relax_kwargs_gs, relax_kwargs_e
         new.gs_relax_task = new.register_relax_task(gs_scf_inp.new_with_vars(relax_kwargs_gs))
         new.ex_relax_task = new.register_relax_task(ex_scf_inp.new_with_vars(relax_kwargs_ex))
 
-
         new.json_data = {}
 
         return new
@@ -260,8 +259,6 @@ def on_all_ok(self):
         return super().on_all_ok()
 
 
-
-
 class LumiWorkFromRelax(Work):
     """
     Same as LumiWork, without the relaxations. Typically used after a LumiWork_relaxations work.
@@ -321,7 +318,6 @@ def from_scf_inputs(cls, gs_scf_inp, ex_scf_inp, gs_structure, ex_structure, ndi
         aestar_scf_inp = new.ex_scf_inp.new_with_structure(ex_structure)
         new.aestar_scf_task = new.register_scf_task(aestar_scf_inp)
 
-
         # Build GS SCF input for the Ag* configuration:
         # use same structure as Ag but with excited occupation factors.
         ae_scf_inp = new.gs_scf_inp.new_with_structure(ex_structure)
@@ -347,7 +343,6 @@ def on_all_ok(self):
 
         self.json_data["meta"] = self.meta
 
-
         # Get Ag total energy.
         # with self.ag_scf_task.open_gsr() as gsr:
         self.json_data["Ag_gsr_filepath"] = self.ag_scf_task.gsr_path
@@ -378,5 +373,4 @@ def on_all_ok(self):
         # save d in json format.
         self.write_json_in_outdir("Delta_SCF.json", d)
 
-        return super().on_all_ok()
-
+        return super().on_all_ok()

abipy/flowtk/qutils.py

@@ -9,7 +9,6 @@
 from __future__ import annotations
 
 import os
-#import json
 
 from subprocess import Popen, PIPE, run
 from monty.string import is_string
@@ -315,7 +314,7 @@ def get_sacct_info():
     try:
 
         result = run(['sacct', '--format=JobID,JobName,Partition,Account,AllocCPUS,State,ExitCode', '--noheader'],
-                      stdout=subprocess.PIPE, stderr=subprocess.PIPE, text=True)
+                      stdout=PIPE, stderr=PIPE, text=True)
 
         # Check if the command was successful
         if result.returncode != 0:
@@ -324,23 +323,24 @@ def get_sacct_info():
 
         # Process the output
         jobs_info = result.stdout.strip().split('\n')
-        jobs = [dict(zip(['JobID', 'JobName', 'Partition', 'Account', 'AllocCPUS', 'State', 'ExitCode'], job.split())) for job in jobs_info]
+        jobs = [dict(zip(['JobID', 'JobName', 'Partition', 'Account', 'AllocCPUS', 'State', 'ExitCode'], job.split())) 
+                for job in jobs_info]
         return jobs
 
     except Exception as e:
         print(f"An error occurred: {e}")
         return None
 
 
-def get_completed_job_info(job_id):
+def get_completed_job_info(job_id: int | str):
     try:
         # Define the fields we want to retrieve
         fields = "JobID,JobName,Partition,Account,AllocCPUS,State,ExitCode,Start,End,Elapsed,TotalCPU,MaxRSS"
 
         # Run the sacct command with the specified fields for the given job ID
         result = run(
-            ['sacct', '--jobs', job_id, '--format', fields, '--noheader', '--parsable2'],
-            stdout=subprocess.PIPE, stderr=subprocess.PIPE, text=True
+            ['sacct', '--jobs', str(job_id), '--format', fields, '--noheader', '--parsable2'],
+            stdout=PIPE, stderr=PIPE, text=True
         )
 
         # Check if the command was successful
@@ -451,4 +451,4 @@ def get_custodian_template() -> str:
 
 # Run the Custodian job
 c.run()
-"""
+"""