update to 2.3.0. Fix tests and MacOS numpy bug.

theochem · Dec 7, 2021 · 0980bc9 · 0980bc9
1 parent deee884
commit 0980bc9
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diff --git a/conda/meta.yaml b/conda/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "2.2.0" %}
+{% set version = "2.3.0" %}
 
 package:
   name: horton 
@@ -8,7 +8,7 @@ source:
   path: ..
 
 build:
-  number: 1
+  number: 3
   binary_relocation: true
 
 requirements:
@@ -20,7 +20,7 @@ requirements:
     - make
     - git
   host:
-    - python {{ python }}
+    - python 3.8
     - numpy
     - scipy
     - cython
@@ -38,8 +38,13 @@ requirements:
     - libint
     - cython
 test:
+  requires:
+    - nose
   imports:
     - horton
+  commands:
+    - nosetests -v horton
+
 
 about:
   summary: "Helpful Open-source Research TOol for N-fermion systems"

diff --git a/data/examples/hf_dft/rks_water_mgga.py b/data/examples/hf_dft/rks_water_mgga.py
@@ -89,18 +89,17 @@
 }
 # BEGIN AUTOGENERATED CODE. DO NOT CHANGE MANUALLY.
 rt_previous = {
-    'energy': -76.407936399996032,
+    'energy': -76.40793639999603,
+    'grid': -9.361522808603524,
+    'hartree': 46.863292284107445,
+    'kin': 76.04013863983127,
+    'ne': -199.10702002940846,
+    'nn': 9.157175036429987,
     'orb_alpha': np.array([
-        -18.88140274471057, -0.92689455671943777, -0.48003995365965246,
-        -0.3068412737938469, -0.23305348781949642, 0.055765650587591052,
-        0.13876252429050115, 0.78022341323374989, 0.82177783193535281,
-        0.86268998494640037, 0.89541154561880765, 1.0425268139841128, 1.3431492859747944,
-        1.7062096596569536, 1.7110987254283361, 1.7506809108152641, 2.2882571842385735,
-        2.5849159392493357
+        -18.88111781424959, -0.9268543449664615, -0.48002911517925373,
+        -0.30683434349364513, -0.2330605499821571, 0.0557054298179647,
+        0.13869017199033926, 0.7800372422845757, 0.8216102286054293, 0.8625906847694965,
+        0.8952633368928019, 1.042433280068831, 1.3430244064105015, 1.706049355089985,
+        1.7109366502306933, 1.7505342468014848, 2.2877661960982287, 2.5842347375036807
     ]),
-    'grid': -9.361522808603524,
-    'hartree': 46.86311076030199,
-    'kin': 76.04019446027614,
-    'ne': -199.10689384840063,
-    'nn': 9.1571750364299866,
 }
diff --git a/data/examples/hf_dft/uks_methyl_mgga.py b/data/examples/hf_dft/uks_methyl_mgga.py
@@ -96,25 +96,25 @@
 # BEGIN AUTOGENERATED CODE. DO NOT CHANGE MANUALLY.
 rt_previous = {
     'energy': -39.836677347925914,
+    'grid': -6.447581456959345,
+    'hartree': 28.092648155263227,
+    'kin': 39.36712413305364,
+    'ne': -109.92865317406965,
+    'nn': 9.079784942663636,
     'orb_alpha': np.array([
-        -10.019635076738147, -0.61357555665158736, -0.3628121339087883,
-        -0.36276528782852813, -0.19070293326772045, 0.071676580515679725,
-        0.1451627609382326, 0.14520445336541474, 0.51037249458810541, 0.55245497246844399,
-        0.55247011455993678, 0.66897270052023006, 0.84604700858521387,
-        0.84613026545140801, 0.89858158554272938, 1.6194517568114566, 1.6194677518472744,
-        1.9300340527577873, 2.0952910889031027, 2.0961171453114171
+        -10.01932345515595, -0.6135259960982921, -0.36276560205876457,
+        -0.3627187398579602, -0.19075935105245162, 0.07150035135891722,
+        0.14494635637871764, 0.14498775711923603, 0.510315601262867, 0.5521868550528035,
+        0.5522018808304408, 0.6683335215978065, 0.8453792117712211, 0.8454609326443266,
+        0.8983531847806548, 1.619269238542316, 1.6192862967691806, 1.9292046668075504,
+        2.093858169207324, 2.0946697177558007
     ]),
     'orb_beta': np.array([
-        -10.004003922798798, -0.5755426452796184, -0.35601452017897062,
-        -0.35588391063394165, -0.06548534259187741, 0.098337149121920125,
-        0.1595980803482438, 0.15986087404787613, 0.56917620502894739, 0.56946718254784001,
-        0.60089298391388379, 0.70441988947800527, 0.87990225342684414,
-        0.88198311255364803, 0.95807927778738833, 1.7277678928512459, 1.7299240596423406,
-        2.0576938854035931, 2.174113280602203, 2.1750154723644353
+        -10.003689426590137, -0.5754877487524174, -0.3559723619217707,
+        -0.35584153775415894, -0.06554258134740852, 0.09814780282274696,
+        0.1593816751966446, 0.15964525579884276, 0.5688913029872666, 0.5691828001315896,
+        0.6008399202646769, 0.7037253351266851, 0.8792123495562243, 0.8812997469246673,
+        0.957810069192318, 1.7275803186575, 1.729736365896011, 2.0569028489921184,
+        2.1726342557791885, 2.173521534951844
     ]),
-    'grid': -6.447610544950923,
-    'hartree': 28.092381575581616,
-    'kin': 39.36717793738765,
-    'ne': -109.9284112586079,
-    'nn': 9.0797849426636361,
 }
diff --git a/horton/__init__.py b/horton/__init__.py
@@ -21,7 +21,7 @@
 '''The main HORTON Package'''
 
 
-__version__ = '2.1.0'
+__version__ = '2.3.0'
 
 
 # Extensions are imported first to call fpufix as early as possible

diff --git a/horton/grid/poisson.py b/horton/grid/poisson.py
@@ -20,15 +20,13 @@
 # --
 '''Becke-style numerical Poisson solver'''
 
-
 import numpy as np
 
 from horton.log import timer, biblio
 from horton.grid.cext import CubicSpline, PotentialExtrapolation
 from horton.grid.ode2 import solve_ode2
 from horton.grid.radial import RadialGrid
 
-
 __all__ = ['solve_poisson_becke']
 
 
@@ -47,15 +45,16 @@ def solve_poisson_becke(density_decomposition):
        density).
     '''
     biblio.cite('becke1988_poisson', 'the numerical integration of the Poisson equation')
+    np.seterr(invalid="print")
 
     lmax = np.sqrt(len(density_decomposition)) - 1
     assert lmax == int(lmax)
     lmax = int(lmax)
 
     result = []
     counter = 0
-    for l in range(0, lmax+1):
-        for m in range(-l, l+1):
+    for l in range(0, lmax + 1):
+        for m in range(-l, l + 1):
             rho = density_decomposition[counter]
             rtf = rho.rtransform
             rgrid = RadialGrid(rtf)
@@ -64,21 +63,21 @@ def solve_poisson_becke(density_decomposition):
             # u = r*V in Eq. (21) in Becke's paper. After this transformation,
             # the boundary conditions can be implemented such that the output
             # is more accurate.
-            fy = -4*np.pi*rho.y
-            fd = -4*np.pi*rho.dx
+            fy = -4 * np.pi * rho.y
+            fd = -4 * np.pi * rho.dx
             f = CubicSpline(fy, fd, rtf)
-            b = CubicSpline(2/radii, -2/radii**2, rtf)
-            a = CubicSpline(-l*(l+1)*radii**-2, 2*l*(l+1)*radii**-3, rtf)
+            b = CubicSpline(2 / radii, -2 / radii ** 2, rtf)
+            a = CubicSpline(-l * (l + 1) * radii ** -2, 2 * l * (l + 1) * radii ** -3, rtf)
             # Derivation of boundary condition at rmax:
             # Multiply differential equation with r**l and integrate. Using
             # partial integration and the fact that V(r)=A/r**(l+1) for large
             # r, we find -(2l+1)A=-4pi*int_0^infty r**2 r**l rho(r) and so
             # V(rmax) = A/rmax**(l+1) = integrate(r**l rho(r))/(2l+1)/rmax**(l+1)
-            V_rmax = rgrid.integrate(rho.y*radii**l)/radii[-1]**(l+1)/(2*l+1)
+            V_rmax = rgrid.integrate(rho.y * radii ** l) / radii[-1] ** (l + 1) / (2 * l + 1)
             # Derivation of boundary condition at rmin:
             # Same as for rmax, but multiply differential equation with r**(-l-1)
             # and assume that V(r)=B*r**l for small r.
-            V_rmin = rgrid.integrate(rho.y*radii**(-l-1))*radii[0]**(l)/(2*l+1)
+            V_rmin = rgrid.integrate(rho.y * radii ** (-l - 1)) * radii[0] ** (l) / (2 * l + 1)
             bcs = (V_rmin, None, V_rmax, None)
             v = solve_ode2(b, a, f, bcs, PotentialExtrapolation(l))
             result.append(v)