Merge branch 'develop' of https://github.com/abinit/abipy into develop

README.rst

@@ -81,7 +81,7 @@ in the form of pre-compiled packages that can be easily installed with e.g.::
 
 Create a new conda_ environment (let's call it ``abienv``) with::
 
-    conda create --name abienv
+    conda create --name abienv python=3.11
 
 and activate it with::
 
@@ -106,7 +106,10 @@ in the `anaconda howto <http://abinit.github.io/abipy/installation#anaconda-howt
 Developmental version
 ---------------------
 
-Getting the developmental version of AbiPy is easy.
+To install the developmental version of AbiPy with pip, use::
+
+    pip install git+https://github.com/abinit/abipy.git@develop
+
 Clone the `github repository <https://github.com/abinit/abipy>`_ with::
 
     git clone https://github.com/abinit/abipy
@@ -118,7 +121,7 @@ For pip, use::
 
 If you are using conda_ (see `Installing conda`_ to install conda itself), create a new environment (``abienv``) with::
 
-    conda create -n abienv
+    conda create -n abienv python=3.11
     source activate abienv
 
 Add ``conda-forge``, and ``abinit`` to your channels with::
@@ -143,22 +146,6 @@ or alternately::
 to install the package in developmental mode.
 This is the recommended approach, especially if you are planning to implement new features.
 
-Note, however, that the developmental version of AbiPy is kept in sync with the
-developmental version of pymatgen thus ```python setup.py develop``` may
-try to download new versions from the PyPi portal and then fail with e.g. the error message::
-
-    ...
-    processing dependencies for abipy==0.6.0.dev0
-    error: scipy 1.0.0 is installed but scipy>=1.0.1 is required by {'pymatgen'}
-
-due to inconsistent dependencies.
-To solve the problem, use conda to update scipy to a version >= 1.0.1 with::
-
-    conda install "scipy>=1.0.1"
-
-then issue again python setup.py develop. If this fails, supposing you were upgrading abipy inside 
-an already existing conda environment, try to restart by creating from scratch a fresh conda environment, see above.
-
 Also note that the BLAS/Lapack libraries provided by conda have multithreading support activated by default.
 Each process will try to use all of the cores on your machine, which quickly overloads things
 if there are multiple processes running.

abipy/abio/factories.py

@@ -1692,6 +1692,7 @@ def minimal_scf_input(structure: Structure, pseudos) -> AbinitInput:
     inp["nband"] = 1
     inp["chkprim"] = 0
     inp["chksymbreak"] = 0
+    inp["maxnsym"] = 100000 # to be able to deal with supercells
     inp["charge"] = structure.num_valence_electrons(inp.pseudos) - 1
     inp["boxcutmin"] = 1.2
     return inp

abipy/abio/inputs.py

@@ -1229,7 +1229,7 @@ def set_autospinat(self, default=0.6) -> dict:
         for site in self.structure:
             if hasattr(site, 'magmom'):
                 spinat.append((0., 0., site.magmom))
-            elif hasattr(site.specie, 'spin'):
+            elif hasattr(site.specie, 'spin') and site.specie.spin:
                 spinat.append((0., 0., site.specie.spin))
             elif str(site.specie) in magmom_mp_conf:
                 spinat.append((0., 0., magmom_mp_conf.get(str(site.specie))))

abipy/abio/outputs.py

@@ -258,7 +258,13 @@ def pop_stack():
                 if dtidx is None:
                     vars_global[key] = value
                 else:
-                    vars_dataset[dtidx][key] = value
+                    try:
+                        vars_dataset[dtidx][key] = value
+                    except KeyError:
+                        if dtidx==0:
+                            vars_global[key] = value
+                        else:
+                            raise Exception("dataset index != 0 but still not found in vars_dataset")
 
         for line in lines:
             if not line: continue

abipy/abio/robots.py

@@ -817,36 +817,6 @@ def close(self) -> None:
                     print("Exception while closing: ", abifile.filepath)
                     print(exc)
 
-    #@classmethod
-    #def open(cls, obj, nids=None, **kwargs):
-    #    """
-    #    Flexible constructor. obj can be a :class:`Flow` or a string with the directory containing the Flow.
-    #    `nids` is an optional list of :class:`Node` identifiers used to filter the set of :class:`Task` in the Flow.
-    #    """
-    #    has_dirpath = False
-    #    if is_string(obj):
-    #        try:
-    #            from abipy.flowtk import Flow
-    #            obj = Flow.pickle_load(obj)
-    #        except:
-    #            has_dirpath = True
-
-    #    if not has_dirpath:
-    #        # We have a Flow. smeth is the name of the Task method used to open the file.
-    #        items = []
-    #        smeth = "open_" + cls.EXT.lower()
-    #        for task in obj.iflat_tasks(nids=nids): #, status=obj.S_OK):
-    #            open_method = getattr(task, smeth, None)
-    #            if open_method is None: continue
-    #            abifile = open_method()
-    #            if abifile is not None: items.append((task.pos_str, abifile))
-    #        return cls(*items)
-
-    #    else:
-    #        # directory --> search for files with the appropriate extension and open it with abiopen.
-    #        if nids is not None: raise ValueError("nids cannot be used when obj is a directory.")
-    #        return cls.from_dir(obj)
-
     #def get_attributes(self, attr_name, obj=None, retdict=False):
     #    od = OrderedDict()
     #    for label, abifile in self.items():
@@ -1241,10 +1211,14 @@ def get_baserobot_code_cells(self, title=None) -> list:
     @staticmethod
     def get_yvals_item_abifiles(item: Any, abifiles: list) -> np.ndarray:
         """Extract values for a list of Abinit files."""
+        def _float(obj):
+            if obj is None: return obj
+            return float(obj)
+
         if callable(item):
-            return np.array([float(item(a)) for a in abifiles])
+            return np.array([_float(item(a)) for a in abifiles])
         else:
-            return np.array([float(duck.getattrd(a, item)) for a in abifiles])
+            return np.array([_float(duck.getattrd(a, item)) for a in abifiles])
 
     @staticmethod
     def plot_xvals_or_xstr_ax(ax, xs, yvals, fontsize, **kwargs) -> list:

abipy/abio/tests/test_inputs.py

@@ -249,7 +249,7 @@ def test_helper_functions(self):
         assert inp["ndivsm"] == 3 and inp["iscf"] == -2 and len(inp["kptbounds"]) == 12
 
         inp.set_kpath(ndivsm=-20)
-        assert inp["nkpt"] == 156 and inp["iscf"] == -2
+        assert inp["nkpt"] in (156, 157) and inp["iscf"] == -2
 
         inp.set_qpath(ndivsm=3, qptbounds=None)
         assert len(inp["ph_qpath"]) == 12 and inp["ph_nqpath"] == 12 and inp["ph_ndivsm"] == 3
@@ -344,9 +344,9 @@ def test_new_with_structure_2(self):
                           abi_kwargs=abi_kwargs)
 
         n_val = inp.num_valence_electrons
-        n_cond = round(10)  
+        n_cond = round(10)
 
-        spin_up_gs = f"\n{int((n_val - 3) / 2)}*1 1 1   1 {n_cond}*0" 
+        spin_up_gs = f"\n{int((n_val - 3) / 2)}*1 1 1   1 {n_cond}*0"
         spin_dn_gs = f"\n{int((n_val - 3) / 2)}*1 1 0   0 {n_cond}*0"
 
         nsppol = 2
@@ -359,13 +359,13 @@ def test_new_with_structure_2(self):
 
         new_inp = inp.new_with_structure(new_structure=sc_stru,
                        scdims=[2,1,1],verbose=0)
-        assert new_inp["nband"] == '*276'  
-        #self.abivalidate_input(new_inp) 
+        assert new_inp["nband"] == '*276'
+        #self.abivalidate_input(new_inp)
         # Not valid now because occ should be rewritten as well
         # TODO
-        # go from 
+        # go from
         # occ='125*1 1 1 1 10*0'
-        # to 
+        # to
         # occ='125*1 1 1 1 125*1 1 1 1 10*0 10*0 '
         # if size is doubled.
 
@@ -573,7 +573,7 @@ def test_dfpt_methods(self):
         self.abivalidate_input(nscf_inp)
 
         # Test make_ebands_input with nband = "*91" (occopt 2)
-        gs_occopt2 = gs_inp.new_with_vars(nband="*91", occopt=2)
+        gs_occopt2 = gs_inp.new_with_vars(nband="*91", occopt=2, paral_kgb=0)
         nscf_inp = gs_occopt2.make_ebands_input(nb_extra=10)
         assert nscf_inp["nband"] == "*101"
         self.abivalidate_input(nscf_inp)

abipy/core/structure.py

@@ -358,6 +358,7 @@ def from_mpid(cls, material_id: str, final=True, api_key=None, endpoint=None) ->
         from abipy.core import restapi
         with restapi.get_mprester(api_key=api_key, endpoint=endpoint) as rest:
             new = rest.get_structure_by_material_id(material_id, final=final)
+            #new = rest.get_structure_by_material_id(material_id)
             return cls.as_structure(new)
 
     @classmethod
@@ -1801,7 +1802,10 @@ def convert(self, fmt: str = "cif", **kwargs) -> str:
             # Don't call super for poscar because we need more significant_figures to
             # avoid problems with abinit space group routines where the default numerical tolerance is tight.
             from pymatgen.io.vasp import Poscar
-            return Poscar(self).get_string(significant_figures=12)
+            try:
+                return Poscar(self).get_str(significant_figures=12)
+            except AttributeError:
+                return Poscar(self).get_string(significant_figures=12)
         else:
             return super().to(fmt=fmt, **kwargs)
 

abipy/core/testing.py

@@ -337,6 +337,11 @@ def skip_if_abinit_not_ge(self, version: str) -> None:
         if not self.has_abinit(version, op=op):
             raise unittest.SkipTest("This test requires Abinit version %s %s" % (op, version))
 
+    @staticmethod
+    def test_mprester():
+        """Skip MP rester tests."""
+        raise unittest.SkipTest("MPRester tests have been disabled")
+
     @staticmethod
     def has_matplotlib(version: Optional[str] = None, op: str = ">=") -> bool:
         return has_matplotlib(version=version, op=op)

abipy/core/tests/test_structure.py

@@ -205,16 +205,17 @@ def test_utils(self):
         self.assert_almost_equal(mgb2.lattice.angles, (90.0, 90.0, 120.00000000000001))
         self.assert_almost_equal(mgb2.lattice.volume * abu.Ang_Bohr ** 3, 196.07928976151663)
 
-        si = Structure.from_mpid("mp-149")
-        assert si.formula == "Si2"
-        with self.assertRaises(ValueError):
-            Structure.from_mpid("foobar")
-
-        # Test abiget_spginfo
-        d = si.abiget_spginfo(tolsym=None, pre="abi_")
-        assert d["abi_spg_symbol"] == "Fd-3m"
-        assert d["abi_spg_number"] == 227
-        assert d["abi_bravais"] == "Bravais cF (face-center cubic)"
+        if self.test_mprester():
+            si = Structure.from_mpid("mp-149")
+            assert si.formula == "Si2"
+            with self.assertRaises(ValueError):
+                Structure.from_mpid("foobar")
+
+            # Test abiget_spginfo
+            d = si.abiget_spginfo(tolsym=None, pre="abi_")
+            assert d["abi_spg_symbol"] == "Fd-3m"
+            assert d["abi_spg_number"] == 227
+            assert d["abi_bravais"] == "Bravais cF (face-center cubic)"
 
         llzo = Structure.from_file(abidata.cif_file("LLZO_oxi.cif"))
         assert llzo.is_ordered

abipy/data/lruj_data/lruj.out

@@ -0,0 +1,83 @@
+
+.Version 9.11.6 of LRUJ 
+.(MPI version, prepared for a x86_64_linux_intel18.0 computer) 
+
+.Copyright (C) 1998-2022 ABINIT group . 
+ LRUJ comes with ABSOLUTELY NO WARRANTY.
+ It is free software, and you are welcome to redistribute it
+ under certain conditions (GNU General Public License,
+ see ~abinit/COPYING or http://www.gnu.org/copyleft/gpl.txt).
+
+ ABINIT is a project of the Universite Catholique de Louvain,
+ Corning Inc. and other collaborators, see ~abinit/doc/developers/contributors.txt .
+ Please read https://docs.abinit.org/theory/acknowledgments for suggested
+ acknowledgments of the ABINIT effort.
+ For more information, see https://www.abinit.org .
+
+.Starting date : Wed 29 Nov 2023.
+- ( at 15h33 )
+
+ Number of perturbations detected:  6
+ Including unperturbed state, we have  7 data points.
+ Hunds J determination, implemented by L. MacEnulty August 2021
+ Maximum degree of polynomials analyzed:  5
+ NOTE: Unlike the ujdet utility, lruj treats the 
+ response functions as scalars, not matrices!
+ See lruj tutorial for more information.
+
+
+*************************************************************************************************
+**************************************  Linear Response J  **************************************
+
+ Total number of atoms:    4
+ Index of perturbed atom:    1
+ Value of macro_uj:     4
+ Value of dmatpuopt:     3
+ Mixing constant factored out of Chi0:   0.450
+ Percentage of AE orbital within the PAW sphere of perturbed subspace:     90.46723%
+
+  Perturbations         Magnetizations
+ --------------- -----------------------------
+    beta [eV]     Unscreened      Screened
+ --------------- -----------------------------
+  -0.1500000676   1.3322568566   1.3664401054
+  -0.1000000451   1.3250447778   1.3485578255
+  -0.0500000225   1.3176770671   1.3298301923
+   0.0000000000   1.3101482092   1.3101482092
+   0.0500000225   1.3024514902   1.2893790961
+   0.1000000451   1.2945812190   1.2673571836
+   0.1500000676   1.2865306151   1.2438737113
+                                                                       RMS Errors
+                                                         ---------------------------------------
+ Regression   Chi0 [eV^-1]   Chi [eV^-1]      J [eV]    | Chi0 [eV^-1]  Chi [eV^-1]     J [eV]
+--------------------------------------------------------|---------------------------------------
+ Linear:        -0.3386211    -0.4075366     0.4993858  |    0.0006971    0.0020836    0.1364740
+ Quadratic:     -0.3386211    -0.4075366     0.4993858  |    0.0000137    0.0001529    0.0322580
+ Cubic:         -0.3383005    -0.4039797     0.4805799  |    0.0000002    0.0000120    0.0086817
+ Degree 4 :     -0.3383005    -0.4039797     0.4805799  |    0.0000001    0.0000009    0.0025307
+ Degree 5 :     -0.3383000    -0.4040198     0.4808302  |    0.0000001    0.0000000    0.0011046
+*************************************************************************************************
+*************************************************************************************************
+
+Linear Response UJ (LRUJ) program complete. Live long and prosper. ~LMac
+
+
+--- !LRUJ_Abipy_Plots
+natom: 4
+ndata: 7
+pawujat: 1
+macro_uj: 4
+diem_token: diemixmag
+diem:   4.50000000E-01
+chi0_coefficients_degree1: [  1.30981289E+00,  -1.52379516E-01, ]
+chi_coefficients_degree1: [  1.30794090E+00,  -4.07536646E-01, ]
+chi0_coefficients_degree2: [  1.31014818E+00,  -1.52379516E-01,  -3.35292571E-02, ]
+chi_coefficients_degree2: [  1.31016241E+00,  -4.07536646E-01,  -2.22150364E-01, ]
+chi0_coefficients_degree3: [  1.31014818E+00,  -1.52235216E-01,  -3.35292571E-02,  -8.24572223E-03, ]
+chi_coefficients_degree3: [  1.31016241E+00,  -4.03979653E-01,  -2.22150364E-01,  -2.03256604E-01, ]
+chi0_coefficients_degree4: [  1.31014812E+00,  -1.52235216E-01,  -3.35038810E-02,  -8.24572223E-03,  -1.06049292E-03, ]
+chi_coefficients_degree4: [  1.31014819E+00,  -4.03979653E-01,  -2.16856067E-01,  -2.03256604E-01,  -2.21254002E-01, ]
+chi0_coefficients_degree5: [  1.31014812E+00,  -1.52234989E-01,  -3.35038810E-02,  -8.28815298E-03,  -1.06049292E-03,   1.45476754E-03, ]
+chi_coefficients_degree5: [  1.31014819E+00,  -4.04019800E-01,  -2.16856067E-01,  -1.95748183E-01,  -2.21254002E-01,  -2.57431330E-01, ]
+...
+