Add LogFile and AvgChunkFile readers

Implements changes proposed in #144

unittest/python/python-formats.py

@@ -0,0 +1,91 @@
+import os
+import unittest
+from lammps.formats import LogFile, AvgChunkFile
+
+EXAMPLES_DIR=os.path.abspath(os.path.join(__file__, '..', '..', '..', 'examples'))
+
+DEFAULT_STYLE_EXAMPLE_LOG="melt/log.27Nov18.melt.g++.1"
+MULTI_STYLE_EXAMPLE_LOG="USER/fep/CC-CO/fep10/log.lammps"
+AVG_CHUNK_FILE="VISCOSITY/profile.13Oct16.nemd.2d.g++.1"
+
+class Logfiles(unittest.TestCase):
+    def testLogFileNotFound(self):
+        with self.assertRaises(FileNotFoundError):
+            LogFile('test.log')
+
+    def testDefaultLogFile(self):
+        log = LogFile(os.path.join(EXAMPLES_DIR, DEFAULT_STYLE_EXAMPLE_LOG))
+        self.assertEqual(len(log.runs), 1)
+        run = log.runs[0]
+        self.assertEqual(len(run.keys()), 6)
+        self.assertIn("Step", run)
+        self.assertIn("Temp", run)
+        self.assertIn("E_pair", run)
+        self.assertIn("E_mol", run)
+        self.assertIn("TotEng", run)
+        self.assertIn("Press", run)
+        self.assertEqual(len(run["Step"]), 6)
+        self.assertEqual(len(run["Temp"]), 6)
+        self.assertEqual(len(run["E_pair"]), 6)
+        self.assertEqual(len(run["E_mol"]), 6)
+        self.assertEqual(len(run["TotEng"]), 6)
+        self.assertEqual(len(run["Press"]), 6)
+        self.assertEqual(log.runs[0]["Step"], [0, 50, 100, 150, 200, 250])
+
+    def testMultiLogFile(self):
+        log = LogFile(os.path.join(EXAMPLES_DIR, MULTI_STYLE_EXAMPLE_LOG))
+        self.assertEqual(len(log.runs), 2)
+        run0 = log.runs[0]
+        run1 = log.runs[1]
+
+        self.assertEqual(len(run0.keys()), 15)
+        self.assertIn("Step", run0)
+        self.assertIn("CPU", run0)
+        self.assertIn("TotEng", run0)
+        self.assertIn("KinEng", run0)
+        self.assertIn("Temp", run0)
+        self.assertIn("PotEng", run0)
+        self.assertIn("E_bond", run0)
+        self.assertIn("E_angle", run0)
+        self.assertIn("E_dihed", run0)
+        self.assertIn("E_impro", run0)
+        self.assertIn("E_vdwl", run0)
+        self.assertIn("E_coul", run0)
+        self.assertIn("E_long", run0)
+        self.assertIn("Press", run0)
+        self.assertIn("Volume", run0)
+
+        for k in run0:
+            self.assertEqual(len(run0[k]), 51)
+
+        self.assertEqual(run0["Step"], list(range(0,255000, 5000)))
+
+
+class AvgChunkFiles(unittest.TestCase):
+    def testAvgChunkFileNotFound(self):
+        with self.assertRaises(FileNotFoundError):
+            AvgChunkFile('test.log')
+
+    def testRead(self):
+        cfile = AvgChunkFile(os.path.join(EXAMPLES_DIR, AVG_CHUNK_FILE))
+        self.assertEqual(cfile.fix_name, "4")
+        self.assertEqual(cfile.group_name, "all")
+        self.assertEqual(cfile.timesteps, list(range(10000, 110000, 5000)))
+
+        ntimesteps = len(cfile.timesteps)
+        nchunks = len(cfile.chunks)
+        self.assertEqual(nchunks, 20)
+
+        for i in range(1, nchunks+1):
+            chunk  = cfile.chunks[i-1];
+            self.assertEqual(chunk['id'], i)
+            self.assertEqual(len(chunk['coord']), ntimesteps)
+            self.assertEqual(len(chunk['ncount']), ntimesteps)
+            self.assertIn("vx", chunk)
+            self.assertEqual(len(chunk['vx']), ntimesteps)
+
+        self.assertEqual(len(chunk['coord'][0]), 1)
+
+
+if __name__ == "__main__":
+    unittest.main()