Now abiml.py relax Prints the initial and final structure

README.rst

@@ -74,12 +74,8 @@ The installation process is greatly simplified if you install the required
 python packages through `Anaconda <https://continuum.io/downloads>`_ (or conda).
 See `Installing conda`_ to install conda itself.
 We routinely use conda_ to test new developments with multiple Python versions and multiple virtual environments.
-The anaconda distribution already provides the most critical dependencies (matplotlib_, scipy_, numpy_, netcdf4-python_)
-in the form of pre-compiled packages that can be easily installed with e.g.::
 
-    conda install numpy scipy netcdf4
-
-Create a new conda_ environment (let's call it ``abienv``) with::
+Create a new conda_ environment based on python 3.11 (let's call it ``abienv``) with::
 
     conda create --name abienv python=3.11
 
@@ -89,15 +85,11 @@ and activate it with::
 
 You should see the name of the conda environment in the shell prompt.
 
-Now add ``conda-forge`` to your conda channels with::
-
-    conda config --add channels conda-forge
-
-This is the channel from which we will download pymatgen, abipy and abinit.
-
 Finally, install AbiPy with::
 
-    conda install abipy
+    conda install abipy -c conda-forge
+
+Please note that, at present, conda-forge does not provide executables 
 
 Additional information on the steps required to install AbiPy with anaconda are available
 in the `anaconda howto <http://abinit.github.io/abipy/installation#anaconda-howto>`_.
@@ -199,7 +191,6 @@ Otherwise, follow the usual abinit installation instructions, and make sure abin
 
     abinit --version
 
-
 Configuration files for Abipy
 =============================
 
@@ -379,6 +370,7 @@ The following scripts can be invoked directly from the terminal:
 * ``abirun.py``     Execute AbiPy flow from terminal.
 * ``abidoc.py``     Document Abinit input variables and Abipy configuration files.
 * ``abinp.py``      Build input files (simplified interface for the AbiPy factory functions).
+* ``abipsp.py``     Download pseudopotential tables from the PseudoDojo.
 
 Use ``SCRIPT --help`` to get the list of supported commands and
 ``SCRIPT COMMAND --help`` to get the documentation for ``COMMAND``.

abipy/abio/robots.py

@@ -1266,7 +1266,7 @@ def plot_abs_conv(ax1, ax2, xs, yvals, abs_conv, xlabel, fontsize, hatch, **kwar
         """
         y_xmax = yvals[-1]
         span_style = dict(alpha=0.2, color="green", hatch=hatch)
-        ax1.axhspan(y_xmax - abs_conv, y_xmax + abs_conv, label=r"$|y-y(x_{max})}| \leq %s$" % abs_conv, **span_style)
+        ax1.axhspan(y_xmax - abs_conv, y_xmax + abs_conv, label=r"$|y-y(x_{max})| \leq %s$" % abs_conv, **span_style)
 
         # Plot |y - y_xmax| in log scale on ax2.
         ax2.plot(xs, np.abs(yvals - y_xmax), **kwargs)

abipy/ml/aseml.py

@@ -1011,8 +1011,24 @@ def traj(self):
             raise RuntimeError("Cannot read ASE traj as traj_path is None")
         return read(self.traj_path, index=":")
 
-    #def __str__(self):
-    #def to_string(self, verbose=0)
+    def __str__(self) -> str:
+        return to_string()
+
+    def to_string(self, verbose: int = 0) -> str:
+        """
+        String representation with verbosity level verbose
+        """
+        lines = []
+        app = lines.append
+        app("Initial structure:")
+        s0 = Structure.as_structure(self.r0.atoms)
+        app(str(s0))
+        app("")
+        app("Relaxed structure:")
+        s1 = Structure.as_structure(self.r1.atoms)
+        app(str(s1))
+
+        return "\n".join(lines)
 
     def summarize(self, tags=None, mode="smart", stream=sys.stdout):
         """"""
@@ -2042,6 +2058,8 @@ def run(self):
         relax = relax_atoms(self.atoms, **relax_kws)
         relax.summarize(tags=["unrelaxed", "relaxed"])
 
+        print(relax.to_string(verbose=self.verbose))
+
         # Write files with final structure and dynamics.
         formats = ["poscar",]
         outpath_fmt = write_atoms(self.atoms, workdir, self.verbose, formats=formats)

abipy/scripts/abicomp.py

@@ -592,6 +592,25 @@ def abicomp_abiwan(options):
     return _invoke_robot(options)
 
 
+def abicomp_abiwan_ebands(options):
+    """
+    Compare Wannier-interpolated band structure with ab-initio results.
+    """
+    if len(options.paths) != 2:
+        raise ValueError("Two arguments with ABIWAN.nc and nc file with ElectronBands are required.")
+    from abipy.wannier90 import AbiwanFile
+    abiwan_path, ebands_path = options.paths[0], options.paths[1]
+    if not abiwan_path.endswith("ABIWAN.nc"):
+        abiwan_path, ebands_path = ebands_path, abiwan_path
+
+    abiwan = AbiwanFile(abiwan_path)
+    print(abiwan)
+    abiwan.hwan.plot()
+    abiwan.plot_with_ebands(ebands_path)
+
+    return 0
+
+
 def abicomp_pseudos(options):
     """"Compare multiple pseudos and print table to terminal."""
     # Make sure entries in index are unique.
@@ -841,6 +860,7 @@ def get_epilog():
   abicomp.py edos *_WFK.nc -nb                  => Compare electron DOS in the jupyter notebook.
   abicomp.py optic DIR -nb                      => Compare optic results in the jupyter notebook.
   abicomp.py abiwan *_ABIWAN.nc --expose        => Compare ABIWAN results, produce matplotlib figures.
+  abicomp.py abiwan_ebands out_ABIWAN.nc out_GSR.nc --expose  => Compare Wannier-interpolated band structure with ab-initio results.
 
 #########
 # Phonons
@@ -995,7 +1015,6 @@ def get_parser(with_epilog=False):
 
     # Parent parser for commands supporting expose
     expose_parser = argparse.ArgumentParser(add_help=False)
-
     expose_parser.add_argument("-e", '--expose', default=False, action="store_true",
             help='Execute robot.expose to produce a pre-defined list of (matplotlib|plotly) figures.')
     expose_parser.add_argument("-s", "--slide-mode", default=False, action="store_true",
@@ -1148,6 +1167,9 @@ def get_parser(with_epilog=False):
     p_abiwan = subparsers.add_parser('abiwan', parents=robot_parents, help=abicomp_abiwan.__doc__)
     p_gwr = subparsers.add_parser('gwr', parents=robot_parents, help=abicomp_gwr.__doc__)
 
+    # Subparser for abiwan_ebands command.
+    p_abiwan_ebands = subparsers.add_parser('abiwan_ebands', parents=[copts_parser], help=abicomp_abiwan_ebands.__doc__)
+
     # Subparser for pseudos command.
     p_pseudos = subparsers.add_parser('pseudos', parents=[copts_parser], help=abicomp_pseudos.__doc__)
     p_pspsp = subparsers.add_parser('psps', parents=robot_parents, help=abicomp_psps.__doc__)

abipy/wannier90/abiwan.py

@@ -351,6 +351,16 @@ def interpolate_ebands(self, vertices_names=None, line_density=20,
                              occfacts, self.ebands.nelect, self.nspinor, self.nspden,
                              smearing=self.ebands.smearing)
 
+    @add_fig_kwargs
+    def plot_with_ebands(self, ebands, **kwargs):
+        """
+        Receiven an ab-initio electronic strucuture, interpolate the energies on the same list of k-points
+        and compare the two.
+        """
+        plotter = self.get_plotter_from_ebands(ebands)
+        linestyle_dict = {"Interpolated": dict(linewidth=0, color="red", marker="o")}
+        return plotter.combiplot(linestyle_dict=linestyle_dict, **kwargs)
+
     def get_plotter_from_ebands(self, ebands: ElectronBands) -> ElectronBandsPlotter:
         """
         Interpolate energies using the k-points given in input |ElectronBands| ebands.
@@ -608,7 +618,7 @@ def get_interpolated_ebands_plotter(self, vertices_names=None, knames=None, line
         diff_str = self.has_different_structures()
         if diff_str: cprint(diff_str, "yellow")
 
-        # Need KpointList object (assume same structures in Robot)
+        # Need KpointList object (assuming same structures in the Robot)
         nc0 = self.abifiles[0]
         if kpoints is None:
             if ngkpt is not None:
@@ -658,6 +668,6 @@ def write_notebook(self, nbpath=None) -> str:
 
         # Mixins
         #nb.cells.extend(self.get_baserobot_code_cells())
-        #nb.cells.extend(self.get_ebands_code_cells())
+        #nb.cells.extend(self.get_ebands_code_cells())wannier90.wout
 
         return self._write_nb_nbpath(nb, nbpath)

abipy/wannier90/win.py

@@ -11,8 +11,10 @@
 from abipy.abio.inputs import AbstractInput
 #from abipy.tools.typing import Figure
 
+import abipy.core.abinit_units as abu
 
-def structure2wannier90(structure) -> str:
+
+def structure2wannier90(structure, units="Bohr") -> str:
     """
     Return string with stucture in wannier90 format.
     """
@@ -27,8 +29,17 @@ def structure2wannier90(structure) -> str:
     # Write lattice vectors.
     # Set small values to zero. This usually happens when the CIF file
     # does not give structure parameters with enough digits.
-    app("begin unit_cell_cart\nAng")
+    if units == "Bohr":
+        fact = abu.Ang_Bohr
+        app("begin unit_cell_cart\nBohr")
+    elif units == "Ang":
+        fact = 1.0
+        app("begin unit_cell_cart\nAng")
+    else:
+        raise ValueError(f"Invalid {units =}")
+
     for r in np.where(np.abs(structure.lattice.matrix) > 1e-8, structure.lattice.matrix, 0.0):
+        r = r * fact
         app("    %.10f %.10f %.10f" % (r[0], r[1], r[2]))
     app("end unit_cell_cart\n")
     app("begin atoms_frac")

abipy/wannier90/wout.py

@@ -46,7 +46,7 @@ def __init__(self, filepath):
     def close(self) -> None:
         """Close file. Required by abc protocol."""
 
-    def __str__(self) ->str:
+    def __str__(self) -> str:
         return self.to_string()
 
     def to_string(self, verbose=0) -> str:
@@ -337,7 +337,7 @@ def plot(self, fontsize=8, **kwargs) -> Figure:
     def plot_centers_spread(self, fontsize=8, **kwargs) -> Figure:
         """
         Plot the convergence of the Wannier centers and spread
-        as function of iteration number
+        as a function of the iteration number
 
         Args:
             fontsize: legend and label fontsize.