Bug fix to 0.2.x branch. Fix to the plot functions. Previously all x-…

…axis values were being set to the `lowx` value given to the function.

CHANGES.md

@@ -1,5 +1,10 @@
 #Change Log
 
+##0.2.1 (2018-05-19)
+### Bug-Fixes
+
+* Fix to the plot functions. Previously all x-axis values were being set to the `lowx` value given to the function.
+
 ##0.2.0 (2018-05-01)
 ### New Features
 

atsim/potentials/__init__.py

@@ -82,7 +82,7 @@ def plotToFile(fileobj,lowx, highx, func, steps=10000):
   :param highx: X-axis upper value
   :param func: Function to be plotted
   :param steps: Number of data points to be plotted"""
-  step = int((highx - lowx) // steps)
+  step = (highx - lowx) / float(steps)
 
   for i in range(steps):
     v = lowx + float(i)*step

docs/conf.py

@@ -48,7 +48,7 @@
 
 # General information about the project.
 project = u'atsim.potentials'
-copyright = u'2014, M.J.D. Rushton'
+copyright = u'2018, M.J.D. Rushton'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the

docs/potentials/zbl_spline.py

@@ -4,7 +4,6 @@
 import atsim.potentials
 
 def main():
-
     bks_buck = potentialforms.buck(18003.7572, 1.0/4.87318, 133.5381)
     bks_coul = potentialforms.coul(2.4, -1.2)
 

setup.py

@@ -6,9 +6,9 @@
   namespace_packages = ["atsim"],
   test_suite = "tests",
   setup_requires = ["setuptools"],
-  install_requires = [],
+  install_requires = ["future"],
 
-  version = '0.2.0',
+  version = '0.2.1',
 
   # Meta-data for PyPI
   description = "atsim.potentials provides tools for working with pair and embedded atom method potential models including tabulation routines for DL_POLY and LAMMPS",

tests/_rundlpoly.py

@@ -1,5 +1,5 @@
-from future import standard_library
-standard_library.install_aliases()
+# from future import standard_library
+# standard_library.install_aliases()
 from builtins import next
 import unittest
 
@@ -11,11 +11,10 @@
 
 def runDLPoly():
   import subprocess
-  subprocess.getoutput('DLPOLY.Z')
+  subprocess.check_output('DLPOLY.Z', shell = True)
 
 def extractDLPOLYEnergy():
   with open('STATIS') as infile:
-    # import pdb;pdb.set_trace()
     next(infile)
     next(infile)
     next(infile)

tests/_runlammps.py

@@ -1,5 +1,5 @@
-from future import standard_library
-standard_library.install_aliases()
+# from future import standard_library
+# standard_library.install_aliases()
 import unittest
 
 import distutils
@@ -18,5 +18,5 @@ def extractLAMMPSEnergy():
 
 def runLAMMPS():
   import subprocess
-  output = subprocess.getoutput("lammps -in calc_energy.lmpin -log out.lmpout -echo none")
+  output = subprocess.check_output("lammps -in calc_energy.lmpin -log out.lmpout -echo none", shell = True)
 

tests/test_documentation_examples.py

@@ -7,6 +7,7 @@
 
 import os
 import unittest
+import pytest
 import imp
 import shutil
 
@@ -29,7 +30,6 @@ def _getLAMMPSResourceDirectory():
 def _getDLPolyResourceDirectory():
   return os.path.join(os.path.dirname(__file__), 'dl_poly_resources')
 
-
 def _loadModule(scriptname):
   name = os.path.basename(scriptname)
   name = os.path.splitext(name)[0]
@@ -145,8 +145,6 @@ def testLAMMPSExample(self):
     finally:
       os.chdir(oldpwd)
 
-
-
 #eam_tabulate_example1.py
 class eam_tabulate_example1TestCase(TempfileTestCase):
   """Test docs/potentials/eam_tabulate_example1.py"""
@@ -177,7 +175,6 @@ def testExample(self):
     finally:
       os.chdir(oldpwd)
 
-
 class eam_tabulate_example2TestCase(TempfileTestCase):
   """Test docs/potentials/eam_tabulate_example2a.py and docs/potentials/eam_tabulate_example2b.py"""
   test_nameA = os.path.join(_getDocsDirectory(), "eam_tabulate_example2a.py")
@@ -437,8 +434,6 @@ def testCrossCheckLAMMPS_DLPOLY(self):
     finally:
       os.chdir(oldpwd)
 
-
-
 #eam_tabulate_example3a.py
 class eam_tabulate_example3TestCase(TempfileTestCase):
   """Test docs/potentials/eam_tabulate_example3a.py and eam_tabulate_example3b.py"""
@@ -514,7 +509,6 @@ def testCrossCheckLAMMPS_DLPOLY(self):
 except ImportError:
   NUMPY_AVAILABLE = False
 
-
 #zbl_spline.py
 class zbl_splineTestCase(TempfileTestCase):
   """Test docs/potentials/zbl_spline.py"""
@@ -528,6 +522,21 @@ def testExample(self):
     os.chdir(self.tempdir)
     try:
       exampleModule.main()
+
+      output_path = os.path.join(self.tempdir, "bks_buck.dat")
+      assert os.path.exists(output_path)
+
+      with open(output_path) as infile:
+        line = next(infile)
+        tokens = line.split()
+        r = float(tokens[0])
+        assert pytest.approx(0.1) == r
+
+        line = next(infile)
+        tokens = line.split()
+        r = float(tokens[0])
+        assert pytest.approx(0.1 + (10.0-0.1)/5000.0) == r
+
     finally:
       os.chdir(oldpwd)