Merge branch 'master' of github.com:ekwan/cctk

README.md

@@ -67,6 +67,20 @@ $ conda env create -f env.yml
 Now, run `conda activate cctk` to enter the *cctk* Python environment (and `conda deactivate` to leave).
 (More complete guides to `conda` usage can be found elsewhere.)
 
+#### Upgrading *cctk*
+
+To get the latest release of *cctk*, navigate to the correct `conda` environment and run:
+
+```
+$ pip install --upgrade cctk
+```
+
+To install the development version (may be unstable!), run:
+
+```
+$ pip install --upgrade [email protected]:ekwan/cctk.git@master 
+```
+
 ## Contents: 
 
 - `cctk/` contains the Python modules for *cctk* and the accompanying static data files.  

cctk/parse_gaussian.py

@@ -292,7 +292,19 @@ def read_nmr_shifts(lines, num_atoms):
     Returns:
         list of isotropic NMR shifts (np.ndarray)
     """
-    return np.zeros(shape=num_atoms)
+    # assumes that lines only come from one Link1 section
+    shieldings = []
+    for line in lines:
+        if line[14:23] == "Isotropic":
+            fields = line.split()
+            assert len(fields) == 8, f"Expected 8 fields on an NMR shielding output line but found {len(fields)} instead!"
+            try:
+                shielding = float(fields[4])
+            except:
+                raise ValueError(f"Error parsing NMR shielding output line:\n{line}")
+            shieldings.append(shielding)
+    assert len(shieldings) == num_atoms, f"Expected {num_atoms} shieldings but found {len(shieldings)}!"
+    return np.asarray(shieldings)
 
 def split_link1(lines):
     """

test/test_nmr.py

@@ -1,12 +1,46 @@
 import unittest, sys, os, io, copy, math
 import numpy as np
 import cctk
+from cctk.gaussian_file import JobType
 
+# run from cctk root with
+# python -m unittest test.test_nmr.TestNMR
 class TestNMR(unittest.TestCase):
 
-    def test_link1(self):
-        molecule = cctk.GaussianFile.read_file("test/static/methane2.out")
+    def test_nmr1(self):
+        # this file has a single point NMR calculation on methane
+        gaussian_file = cctk.GaussianFile.read_file("test/static/methane.out")
+        ensemble = gaussian_file.molecules
+        molecule = ensemble[-1]
+        self.assertListEqual(list(molecule.nmr_isotropic), [198.2259, 32.6869, 32.6869, 32.6869, 32.6869])
 
+    def test_nmr2(self):
+        # this file contains opt freq followed by Link1 NMR on methane
+        gaussian_file = cctk.GaussianFile.read_file("test/static/methane2.out")
+        self.assertEqual(len(gaussian_file), 2)
+        first_link = gaussian_file[0]
+        self.assertListEqual(first_link.job_types, [JobType.OPT, JobType.FREQ])
+        second_link = gaussian_file[1]
+        ensemble = second_link.molecules
+        molecule = ensemble[-1]
+        self.assertListEqual(list(molecule.nmr_isotropic), [192.9242, 31.8851, 31.8851, 31.8851, 31.8851])
+
+    def test_nmr3(self):
+        # this file contains opt freq / Link1 NMR on ethane then Link1 single point NMR on methane
+        gaussian_file = cctk.GaussianFile.read_file("test/static/ethane.out")
+        self.assertEqual(len(gaussian_file), 3)
+        first_link = gaussian_file[0]
+        self.assertListEqual(first_link.job_types, [JobType.OPT, JobType.FREQ])
+        second_link = gaussian_file[1]
+        self.assertListEqual(second_link.job_types, [JobType.NMR])
+        ensemble = second_link.molecules
+        molecule = ensemble[-1]
+        self.assertListEqual(list(molecule.nmr_isotropic), [180.3673, 31.2068, 31.207, 31.2068, 180.3673, 31.2068, 31.207, 31.2068])
+        third_link = gaussian_file[2]
+        self.assertListEqual(third_link.job_types, [JobType.NMR])
+        ensemble = third_link.molecules
+        molecule = ensemble[-1]
+        self.assertListEqual(list(molecule.nmr_isotropic), [198.2259, 32.6869, 32.6869, 32.6869, 32.6869])
 
 '''
     def load_molecule(self, path="test/static/LSD_custom.out"):