Merge pull request #67 from tovrstra/fix_hartree_splines

Fix asymptotics of Poisson solver for small r (final)

.travis.yml

@@ -6,10 +6,12 @@ python:
 
 addons:
   apt:
+    sources:
+     - ubuntu-toolchain-r-test
     packages:
-     - gcc
-     - g++
-     - gfortran
+     - gcc-6
+     - g++-6
+     - gfortran-6
      - libatlas-base-dev
      - libhdf5-serial-dev
      # libtool is needed by libint
@@ -24,6 +26,9 @@ env:
      - PIP_WHEEL_DIR=$CACHED/wheels
      - PIP_FIND_LINKS=file://$CACHED/wheels
      - PIP_NO_CACHE_DIR=no
+     - CXX="g++-6"
+     - CC="gcc-6"
+     - FC="gfortran-6"
 
 cache:
   directories:

dependencies.txt

@@ -1,9 +1,9 @@
 [{
     "name": "gcc",
     "title": "GCC, G++ and GFortran",
-    "version_requirement": ">= 4.5",
+    "version_requirement": ">= 4.9",
     "homepage": "http://gcc.gnu.org",
-    "comment": "In principle the Intel compilers or any other of your favorite compilers should work. The GNU compilers are used for development and testing.",
+    "comment": "In principle the Intel compilers or any other combination of C++11 and Fortran compiler should work. The GNU compilers are used for development and testing.",
     "fedora_24_rpm": "gcc gcc-c++ gcc-gfortran redhat-rpm-config",
     "fedora_22_rpm": "gcc gcc-c++ gcc-gfortran redhat-rpm-config",
     "fedora_21_rpm": "gcc gcc-c++ gcc-gfortran",

doc/tech_dev_checklist.rst

@@ -986,17 +986,22 @@ CPPCheck
 
 See http://cppcheck.sourceforge.net/
 
-CPPCheck is executed with all checks enabled and with the C++11 flag. The only exception
-is ``missingIncludeSystem`` due to the large number of false positives. All other errors
-must be fixed.
+CPPCheck is executed with all checks enabled and with the C++11 flag. The following
+exceptions are added due to false positives:
+
+- ``missingIncludeSystem``
+- ``unusedFunction``
+
+All other errors must be fixed.
 
 
 CPPLint
 ~~~~~~~
 
 See https://github.com/google/styleguide/tree/gh-pages/cpplint
 
-CPPLint is executed with the default settings. All errors must be fixed.
+CPPLint is executed with the default settings, except that the maximum line length is set
+to 100. All errors must be fixed.
 
 
 Manual checks

horton/correlatedwfn/test/test_1dm_ap1rog.py

@@ -23,7 +23,8 @@
 import numpy as np
 from nose.plugins.attrib import attr
 
-from horton import *
+from horton import *  # pylint: disable=wildcard-import,unused-wildcard-import
+
 from horton.test.common import check_delta, numpy_seed
 
 

horton/correlatedwfn/test/test_geminals.py

@@ -23,7 +23,8 @@
 import numpy as np
 from nose.plugins.attrib import attr
 
-from horton import *
+from horton import *  # pylint: disable=wildcard-import,unused-wildcard-import
+
 from horton.test.common import tmpdir
 
 

horton/correlatedwfn/test/test_lagrange.py

@@ -24,7 +24,8 @@
 from nose.tools import assert_raises
 from nose.plugins.attrib import attr
 
-from horton import *
+from horton import *  # pylint: disable=wildcard-import,unused-wildcard-import
+
 from horton.test.common import numpy_seed
 
 

horton/espfit/test/test_cext.py

@@ -23,7 +23,8 @@
 import numpy as np
 from nose.plugins.attrib import attr
 
-from horton import *
+from horton import *  # pylint: disable=wildcard-import,unused-wildcard-import
+
 from horton.test.common import get_random_cell
 
 

horton/espfit/test/test_cost.py

@@ -23,7 +23,8 @@
 import numpy as np, h5py as h5
 from nose.plugins.attrib import attr
 
-from horton import *
+from horton import *  # pylint: disable=wildcard-import,unused-wildcard-import
+
 from horton.test.common import check_delta
 
 

horton/espfit/test/test_mask.py

@@ -21,7 +21,8 @@
 
 
 import numpy as np
-from horton import *
+
+from horton import *  # pylint: disable=wildcard-import,unused-wildcard-import
 
 
 def get_fake_system():

horton/gbasis/test/test_boys.py

@@ -22,7 +22,8 @@
 
 import numpy as np
 from nose.tools import assert_raises
-from horton import *
+
+from horton import *  # pylint: disable=wildcard-import,unused-wildcard-import
 
 
 def test_boys_functions():

horton/gbasis/test/test_cartpure.py

@@ -24,7 +24,7 @@
 from nose.tools import assert_raises
 from nose.plugins.attrib import attr
 
-from horton import *
+from horton import *  # pylint: disable=wildcard-import,unused-wildcard-import
 
 
 tfs = {

horton/gbasis/test/test_cholesky.py

@@ -22,7 +22,8 @@
 import numpy as np
 from nose.tools import assert_raises
 
-from horton import *
+from horton import *  # pylint: disable=wildcard-import,unused-wildcard-import
+
 
 def get_h2o_er(linalg_factory=DenseLinalgFactory):
     fn = context.get_fn('test/water.xyz')

horton/gbasis/test/test_common.py

@@ -20,7 +20,7 @@
 #--
 
 
-from horton import *
+from horton import *  # pylint: disable=wildcard-import,unused-wildcard-import
 
 
 def test_fac():

horton/gbasis/test/test_fns.py

@@ -24,7 +24,7 @@
 from nose.plugins.attrib import attr
 from nose.tools import assert_raises
 
-from horton import *
+from horton import *  # pylint: disable=wildcard-import,unused-wildcard-import
 
 
 def test_exceptions():

horton/gbasis/test/test_gbw.py

@@ -22,7 +22,8 @@
 import numpy as np
 from nose.tools import assert_raises
 
-from horton import *
+from horton import *  # pylint: disable=wildcard-import,unused-wildcard-import
+
 
 def get_h2o_er():
     fn = context.get_fn('test/water.xyz')

horton/gbasis/test/test_gobasis.py

@@ -24,7 +24,8 @@
 from nose.tools import assert_raises
 from nose.plugins.attrib import attr
 
-from horton import *
+from horton import *  # pylint: disable=wildcard-import,unused-wildcard-import
+
 from horton.test.common import compare_operators
 
 

horton/gbasis/test/test_ints.py

@@ -23,7 +23,7 @@
 import numpy as np
 from nose.tools import assert_raises
 
-from horton import *
+from horton import *  # pylint: disable=wildcard-import,unused-wildcard-import
 
 
 def test_gpt_coeff():

horton/gbasis/test/test_iobas.py

@@ -22,7 +22,7 @@
 
 import numpy as np
 
-from horton import *
+from horton import *  # pylint: disable=wildcard-import,unused-wildcard-import
 
 
 def test_str_to_shell_types_cart():

horton/gbasis/test/test_iter.py

@@ -23,7 +23,7 @@
 import numpy as np
 from nose.tools import assert_raises
 
-from horton import *
+from horton import *  # pylint: disable=wildcard-import,unused-wildcard-import
 
 
 def test_iter_pow1_inc_l0():

horton/grid/cext.pyx

@@ -52,7 +52,7 @@ __all__ = [
     'becke_helper_atom',
     # cubic_spline
     'Extrapolation', 'ZeroExtrapolation', 'CuspExtrapolation',
-    'PowerExtrapolation', 'tridiagsym_solve', 'CubicSpline',
+    'PowerExtrapolation', 'PotentialExtrapolation', 'tridiagsym_solve', 'CubicSpline',
     'compute_cubic_spline_int_weights',
     # evaluate
     'index_wrap', 'eval_spline_cube', 'eval_spline_grid',
@@ -246,6 +246,11 @@ cdef class Extrapolation(object):
                 raise ValueError('PowerExtrapolation takes one argument.')
             power = float(words[1])
             return PowerExtrapolation(power)
+        elif words[0] == 'PotentialExtrapolation':
+            if len(words) != 2:
+                raise ValueError('PotentialExtrapolation takes one argument.')
+            l = int(words[1])
+            return PotentialExtrapolation(l)
         else:
             raise NotImplementedError
 
@@ -268,14 +273,38 @@ cdef class PowerExtrapolation(Extrapolation):
         self._this = <cubic_spline.Extrapolation*>(new cubic_spline.PowerExtrapolation(power))
 
     property power:
-        '''The power parameters'''
+        '''The power parameter'''
         def __get__(self):
             return (<cubic_spline.PowerExtrapolation*>self._this).get_power()
 
     def to_string(self):
         return 'PowerExtrapolation %s' % repr(self.power)
 
 
+cdef class PotentialExtrapolation(Extrapolation):
+    """Zero at the right side, power law at the left side"""
+    def __cinit__(self, long l):
+        self._this = <cubic_spline.Extrapolation*>(new cubic_spline.PotentialExtrapolation(l))
+
+    property l:
+        """The angular momentum parameter"""
+        def __get__(self):
+            return (<cubic_spline.PotentialExtrapolation*>self._this).get_l()
+
+    property amp_left:
+        """The amplitude of the polynomial on the left side"""
+        def __get__(self):
+            return (<cubic_spline.PotentialExtrapolation*>self._this).get_amp_left()
+
+    property amp_right:
+        """The amplitude of the polynomial on the right side"""
+        def __get__(self):
+            return (<cubic_spline.PotentialExtrapolation*>self._this).get_amp_right()
+
+    def to_string(self):
+        return 'PotentialExtrapolation %s' % repr(self.l)
+
+
 cdef class CubicSpline(object):
     '''A cubic spline object