Fix script

Signed-off-by: Nicolas Bock <[email protected]>

examples/gpmd/test-energy.py

@@ -1,4 +1,7 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
+
+import argparse
+
 
 def compare_MD(reference, current, reltol):
     """Compare MD energies.
@@ -8,29 +11,24 @@ def compare_MD(reference, current, reltol):
 
     """
 
-    import sys
-    #energy = re.compile("MD_data\s+([0-9eE.+-]+)\s+([0-9eE.+-]+)")
-
-    fd = open(reference)
-    reference_energies = []
-    for line in fd:
-        result = line.split()
-        reference_energies.append(float(result[0]))
-    fd.close()
-
-    fd = open(current)
-    current_energies = []
-    for line in fd:
-        result = line.split()
-        current_energies.append(float(result[0]))
-    fd.close()
-
-
+    with open(reference, encoding="utf-8") as fd:
+        reference_energies = []
+        for line in fd:
+            result = line.split()
+            reference_energies.append(float(result[0]))
+
+    with open(current, encoding="utf-8") as fd:
+        current_energies = []
+        for line in fd:
+            result = line.split()
+            current_energies.append(float(result[0]))
+
     if len(reference_energies) != len(current_energies):
-        raise Exception("[error] different number of MD steps\n"
-                        + ("  reference ran for %4d steps\n" % (len(reference_energies)))
-                        + ("  current ran for   %4d steps\n" % (len(current_energies)))
-                        + "  can not compare")
+        raise Exception(
+            "[error] different number of MD steps\n"
+            + ("  reference ran for %4d steps\n" % (len(reference_energies)))
+            + ("  current ran for   %4d steps\n" % (len(current_energies)))
+            + "  can not compare")
 
     result = True
     for i in range(len(reference_energies)):
@@ -41,29 +39,34 @@ def compare_MD(reference, current, reltol):
             print("failure in MD step %d" % (i+1))
             result = False
     if not result:
-        raise Exception(("[error] when comparing '%s' with '%s'" % (reference, current))
-                        + "energies do not agree")
+        raise Exception(
+            ("[error] when comparing '%s' with '%s'" % (reference, current))
+            + "energies do not agree")
+
+    print("Energy test passed without failure ...")
 
-    print("Energy test passed without failure ...")  
 
 def main():
     """The main function.
     """
 
-    import argparse, os, sys
-
-    parser = argparse.ArgumentParser(description="""Script to compare MD results by using the total energy""")
-    parser.add_argument("--reference",
-                        help="The reference output")
-    parser.add_argument("--current",
-                        help="The current output")
-    parser.add_argument("--reltol",
-                        help="Relative tolerance when comparing, default is %(default)s",
-                        type=float,
-                        default=1e-10)
+    parser = argparse.ArgumentParser(description="""Script to compare
+                                     MD results by using the total energy""")
+    parser.add_argument(
+        "--reference",
+        help="The reference output")
+    parser.add_argument(
+        "--current",
+        help="The current output")
+    parser.add_argument(
+        "--reltol",
+        help="Relative tolerance when comparing, default is %(default)s",
+        type=float,
+        default=1e-10)
     options = parser.parse_args()
 
     compare_MD(options.reference, options.current, options.reltol)
 
+
 if __name__ == "__main__":
     main()