Merge pull request #86 from hegdevinayi/bugfix/parse_cell_param

Bugfix: handle more verbose output from recent QE versions

Author: maxhutch

README.md

@@ -35,6 +35,12 @@ from dfttopif import directory_to_pif
 data = directory_to_pif('/path/to/calculation/')
 ```
 
+Currently supported DFT codes
+-----------------------------
+
+ - VASP (versions tested: 5.2.11, 5.3.2, 5.3.5)
+ - PWSCF (Quantum Espresso) (versions tested: 4.3.2, 5.0, 5.4.0, 6.0, 6.4.1)
+
 Development
 -----------
 

dfttopif/parsers/pwscf.py

@@ -279,10 +279,12 @@ def get_output_structure(self):
                     if "Begin final coordinates" in line:
                         if 'new unit-cell volume' in next(fp):
                             # unit cell allowed to change
-                            next(fp) # blank line
+                            cellheader = next(fp)
+                            # skip irrelevant lines (density/blank line/etc)
+                            while 'CELL_PARAMETER' not in cellheader:
+                                cellheader = next(fp)
                             # get the final unit cell
                             unit_cell = []
-                            cellheader = next(fp)
                             if 'bohr' in cellheader.lower():
                                 cell_conv_factor = bohr_to_angstrom
                             elif 'angstrom' in cellheader.lower():

examples/pwscf/FeO.vc-relax.tar.gz

@@ -5,5 +5,5 @@ flask
 flask-cors
 gunicorn
 pypif==2.0.1
-dftparse==0.3.0
+git+git://github.com/CitrineInformatics/dftparse@develop#egg=dftparse
 pypif-sdk==2.1.0

requirements.txt

@@ -5,6 +5,7 @@
 import os
 import shutil
 
+
 class TestPWSCFParser(unittest.TestCase):
 
     def get_parser(self,name):
@@ -33,6 +34,8 @@ def test_Au_nscf(self):
         self.assertAlmostEqual(fin_volume.scalars[0].value, 16.978781940985)
         self.assertEqual(fin_volume.units, 'Angstrom^3/cell')
 
+        delete_example('Au.nscf')
+
     def test_NaF(self):
         # Parse the results
         parser = self.get_parser('NaF.scf')
@@ -158,6 +161,19 @@ def test_TiO2(self):
 
         # Delete the data
         delete_example('TiO2.vcrelax')
+
+    def test_FeO(self):
+        # Parse the results
+        parser = self.get_parser('FeO.vc-relax')
+
+        strc = parser.get_output_structure()
+        self.assertAlmostEqual(strc.cell[0][0], 1.319092613)
+        self.assertAlmostEqual(strc.cell[2][1], -1.523156949)
+        self.assertEquals(['Fe', 'O'], strc.get_chemical_symbols())
+        self.assertEquals('FeO', parser.get_composition())
+
+        # Delete the data
+        delete_example('FeO.vc-relax')
 
     def test_VS2(self):
         # Parse the results