Add customized ipython shell (scripts.abilab)

README.rst

@@ -58,16 +58,30 @@ Otherwise, these packages should be available on `PyPI <http://pypi.python.org>`
 
 6. netCDF4
 
+7. pyyaml 3.1.0+
+
 Optional dependencies
 ---------------------
 
 Optional libraries that are required if you need certain features:
 
-1. nose - For complete unittesting.
+1. wxPython - For the GUI 
 
-2. wxPython - For the GUI 
+2. wxmplot
+
+3. nose - For complete unittesting.
+
+Installing wxPython
+-------------------
+
+Mac users can download the
+
+Linux users:
+    TODO
+
+The directory `abipy.gui.demos` contains demos that can be used to test the installation 
+(run the script `runall.py` to have an overview of the different graphical interfaces).
 
-3. wxmplot
 
 Using abipy
 ===========

abipy/__init__.py

@@ -72,7 +72,7 @@ def abifile_subclass_from_filename(filename):
 
 def abiopen(filepath):
     """
-    Factory function that returns the appropriate object
+    Factory function that opens any file supported by abipy.
 
     Args:
         filepath:

abipy/abilab.py

@@ -3,6 +3,7 @@ from pymatgen.io.abinitio.task import TaskManager
 from pymatgen.io.abinitio import qadapters as qadapters
 
 import abipy.core.constants as constants
+from abipy import abiopen
 from abipy.core.structure import Structure, StructureModifier
 from abipy.htc.input import AbiInput
 from abipy.htc.workflows import Workflow

abipy/core/structure.py

@@ -1,4 +1,4 @@
-"""This module defines the structure object that store information on the crystalline structure and its symmetries."""
+"""This module defines basic objects representing the crystalline structure."""
 from __future__ import division, print_function
 
 import collections
@@ -10,7 +10,6 @@ from .symmetries import SpaceGroup
 from abipy.iotools import as_etsfreader, Visualizer
 from abipy.iotools import xsf
 
-
 __all__ = [
     "Lattice",
     "Structure",
@@ -19,15 +18,14 @@ __all__ = [
 
 class Lattice(pymatgen.Lattice):
     """
-    Extends the pymatgen Lattice with methods that allows one to construct
+    Extends pymatgen.Lattice with methods that allows one 
-    the object from ABINIT variables or to produce the set of input variables
+    to construct a Lattice object from ABINIT variables.
-    from a structure
     """
     @classmethod
     def from_abivars(cls, d):
         """
-        Returns a new instance from a dictionary with the ABINIT variable that 
+        Returns a new instance from a dictionary with the variables 
-        define the unit cell.
+        used in ABINIT to define the unit cell.
         """
         rprim = d.get("rprim", None)
         angdeg = d.get("angdeg", None)
@@ -61,12 +59,12 @@ class Structure(pymatgen.Structure):
     @classmethod
     def from_file(cls, filepath):
         """
-        Return a new instance from a NetCDF file containing 
+        Return a new Structure instance from a NetCDF file 
-        crystallographic data in the ETSF-IO format.
 
         Args:
-            ncdata:
+            filename:
-                filename or NetcdfReader instance.
+                netcdf file with crystallographic data in the ETSF-IO format.
+                or any other file format supported by `pymatgen.io.smartio`.
         """
         if filepath.endswith(".nc"):
             file, closeit = as_etsfreader(filepath)
@@ -102,7 +100,7 @@ class Structure(pymatgen.Structure):
 
     @property
     def has_spacegroup(self):
-        """True is self contains info on the spacegroup."""
+        """True is the structure contains info on the spacegroup."""
         return self.spacegroup is not None
 
     @property
@@ -161,7 +159,7 @@ class Structure(pymatgen.Structure):
     @property
     def hsym_stars(self):
         """
-        List of `Star` objects. Each start is associated to one of the special k-points 
+        List of `Star` objects. Each star is associated to one of the special k-points 
         present in the pymatgen database.
         """
         try:
@@ -274,6 +272,7 @@ class Structure(pymatgen.Structure):
 
     @classmethod
     def from_abivars(cls, d):
+        """Build a `Structure` object from a dictionary containing ABINIT variables."""
         lattice = Lattice.from_abivars(d)
 
         coords, coords_are_cartesian = d.get("xred", None), False
@@ -309,8 +308,13 @@ class Structure(pymatgen.Structure):
 
     def write_structure(self, filename):
         """See `pymatgen.io.smartio.write_structure`"""
-        from pymatgen.io.smartio import write_structure
+
-        write_structure(self, filename)
+        if filepath.endswith(".nc"):
+            raise NotImplementedError("Cannot write a structure to a netcdfile file yet")
+
+        else:
+            from pymatgen.io.smartio import write_structure
+            write_structure(self, filename)
 
     def displace(self, displ, eta, frac_coords=True):
         """

abipy/data/runs/README.rst

@@ -12,5 +12,20 @@ advantages:
 In order to facilitate the automatic execution and validation, the python scripts 
 must satisfy some basic rules and conventions.
 
-1) The name of the script must match the regular expression:
+#. The name of the script must match the regular expression run_[*].py so that 
-  run_[*].py
+   we can run all the tests easily with run_all.py
+
+#. The execution of the test should be managed by a `Tester` object
+   The `Tester` is responsible for the definition of the working directory (constructed
+   from the name of the script by just removing the prefix `run_`), the submission
+   of the calculation (tester.set_work_and_run) and the analysis of the final results
+   (tester.finalize).
+
+#. The script should remove all the output files produced by the run that are not needed 
+   for the automatic tests and/or the tutorials. Each file should have a unique (meanigfull) name 
+   so that we can easily access it with the syntax:
+
+        import abipy.data as data
+        path_to_reference_file = data.ref_file("basename_of_the_file")
+
+    An exception is raised if this rule is not respected.

abipy/data/runs/run_raman.py

@@ -106,6 +106,8 @@ def raman_workflow(workdir, structure, pseudos, shiftk):
     )
 
     # Initialize the workflow.
+    policy=dict(autoparal=1, max_ncpus=2)
+
     manager = abilab.TaskManager(qtype="slurm",
        qparams=dict(
            ntasks=2,
@@ -123,10 +125,10 @@ def raman_workflow(workdir, structure, pseudos, shiftk):
          LD_LIBRARY_PATH="/home/naps/ygillet/NAPS/intel13/lib:$LD_LIBRARY_PATH",
        ),
        mpi_runner="mpirun",
-       policy=dict(autoparal=1, max_ncpus=2),
+       policy=policy
     )
 
-    #manager = abilab.TaskManager.simple_mpi(mpi_ncpus=1)
+    manager = abilab.TaskManager.simple_mpi(mpi_ncpus=1, policy=policy)
 
     work = abilab.Workflow(workdir, manager)
 

abipy/electrons/ebands.py

@@ -62,6 +62,7 @@ class KSState(collections.namedtuple("KSState", "spin kpoint band eig occ")):
         return tuple(fields)
 
     def asdict(self):
+        """Convert self into a dict.""" 
         return super(KSState, self)._asdict()
 
     def to_strdict(self, fmt=None):
@@ -242,10 +243,13 @@ class ElectronBands(object):
             assert new.__class__ == cls
             return new
 
-    def __str__(self):
+    def __repr__(self):
-        return self.tostring()
+        return self.to_string()
 
-    def tostring(self, prtvol=0):
+    def __str__(self):
+        return self.to_string()
+
+    def to_string(self, prtvol=0):
         """String representation."""
         lines = []
         app = lines.append
@@ -419,7 +423,6 @@ class ElectronBands(object):
 
     def enemin(self, spin=None, band=None):
         """Compute the minimum of the eigenvalues."""
-
         spin_range = self.spins
         if spin is not None:
             assert isinstance(spin, int)
@@ -1231,35 +1234,6 @@ class ElectronBands(object):
         return 1.0/ders2
 
 
-#class NestingFactor(object):
-#
-#    def __init__(self, bands):
-#
-#        self.bands = bands
-#
-#        # Check whether k-points form a homogeneous sampling.
-#        if not self.bands.has_bzmesh:
-#            msg = "The computation of the nesting factor requires a homogeneous k-point sampling"
-#            raise ValueError(msg)
-#
-#    @classmethod
-#    def from_file(cls, filepath):
-#        """
-#        Initialize the object from a netcdf file containing an electronic band structure.
-#        """
-#        return cls(ElectronBands.from_file(filepath))
-#
-#    def compute_nesting(self, qpath):
-#        mesh, values = None, None
-#        return Function1D(mesh, values)
-#
-#    def plot(self, qpath):
-#        nesting = self.compute_nesting(qpath)
-#        nesting.plot()
-
-#########################################################################################
-
-
 class ElectronBandsPlotter(object):
     """
     Class for plotting electronic bands structure and DOSes.
@@ -1592,3 +1566,32 @@ class ElectronsReader(ETSF_Reader, KpointsReaderMixin):
     #def read_xc_parameters(self):
     #   """Returns a dictionary with info on the XC functional."""
     #    return XC_Parameters.from_ixc(self.read_value("ixc"))
+
+
+#class NestingFactor(object):
+#
+#    def __init__(self, bands):
+#
+#        self.bands = bands
+#
+#        # Check whether k-points form a homogeneous sampling.
+#        if not self.bands.has_bzmesh:
+#            msg = "The computation of the nesting factor requires a homogeneous k-point sampling"
+#            raise ValueError(msg)
+#
+#    @classmethod
+#    def from_file(cls, filepath):
+#        """
+#        Initialize the object from a netcdf file containing an electronic band structure.
+#        """
+#        return cls(ElectronBands.from_file(filepath))
+#
+#    def compute_nesting(self, qpath):
+#        mesh, values = None, None
+#        return Function1D(mesh, values)
+#
+#    def plot(self, qpath):
+#        nesting = self.compute_nesting(qpath)
+#        nesting.plot()
+
+#########################################################################################

abipy/scripts/abilab

@@ -0,0 +1,55 @@
+#!/usr/bin/env python
+from IPython.config.loader import Config
+
+try:
+    get_ipython
+
+except NameError:
+    nested = 0
+    cfg = Config()
+    prompt_config = cfg.PromptManager
+    prompt_config.in_template = 'In [\\#]: '
+    prompt_config.in2_template = '   .\\D.: '
+    prompt_config.out_template = 'Out[\\#]: '
+
+else:
+    print("Running nested copies of IPython.")
+    print("The prompts for the nested copy have been modified")
+    cfg = Config()
+    nested = 1
+
+# First import the embeddable shell class
+from IPython.frontend.terminal.embed import InteractiveShellEmbed
+
+# Now create an instance of the embeddable shell. The first argument is a
+# string with options exactly as you would type them if you were starting
+# IPython at the system command line. Any parameters you want to define for
+# configuration can thus be specified here.
+import pymatgen as pymatgen
+import abipy.abilab as abilab
+
+#from pymatgen import *
+from abipy.abilab import *
+
+abi_builtins = [n for n in dir(abilab) if not n.startswith("_")]
+               #[n for n in dir(pymatgen) if not n.startswith("_")] + \
+del abilab #, pymatgen
+
+abi_builtins = sorted(set(abi_builtins))
+
+import textwrap
+banner = textwrap.fill(str(abi_builtins), width=70)
+del textwrap
+
+banner = ("Custom ipython environment for abipy. Useful aliases such as:\n" + 
+          banner + "\n" + 
+          "have been loaded.\n" + 
+          "Type abi_builtins to get the complete list."
+          )
+
+ipshell = InteractiveShellEmbed(
+    config=cfg,
+    banner1=banner,
+    exit_msg='Leaving abipy interpreter, back to program.')
+
+ipshell()