Bugfix: update pypif behavior

dfttopif/parsers/base.py

@@ -1,12 +1,12 @@
 import os
 from collections import Counter
-from pypif.obj.common import Value, Property
+from pypif.obj.common import Value, Property, Scalar
 
 
 def Value_if_true(func):
     '''Returns:
         Value if x is True, else None'''
-    return lambda x: Value() if func(x) == True else None
+    return lambda x: Value(scalars=[Scalar(value=True)]) if func(x) == True else Value(scalars=[Scalar(value=False)])
 
 
 class DFTParser(object):
@@ -212,7 +212,7 @@ def is_converged(self):
         # Check for cached result
         if self._converged is None:
             self._converged = self._is_converged()
-        return Property(scalars=self._converged)
+        return Property(scalars=[Scalar(value=self._converged)])
 
     def get_pp_name(self):
         '''Read output to get the pseudopotentials names used for each elements

dfttopif/parsers/pwscf.py

@@ -1,4 +1,4 @@
-from pypif.obj.common.property import Property
+from pypif.obj.common import Property, Scalar
 
 from .base import DFTParser, Value_if_true
 import os
@@ -69,12 +69,12 @@ def get_xc_functional(self):
             if xcstring[word][0] == '(':
                 xcstring = xcstring[:word]
                 break
-        return Value(scalars=" ".join(xcstring))
+        return Value(scalars=[Scalar(value=" ".join(xcstring))])
 
     def get_cutoff_energy(self):
         '''Determine the cutoff energy from the output'''
         cutoff = self._get_line('kinetic-energy cutoff', self.outputf).split()[3:]
-        return Value(scalars=float(cutoff[0]), units=cutoff[1])
+        return Value(scalars=[Scalar(value=float(cutoff[0]))], units=cutoff[1])
 
     def get_total_energy(self):
         '''Determine the total energy from the output'''
@@ -83,23 +83,24 @@ def get_total_energy(self):
             for line in reversed(fp.readlines()):
                 if "!" in line and "total energy" in line:
                     energy = line.split()[4:]
-                    return Property(scalars=float(energy[0]), units=energy[1])
+                    return Property(scalars=[Scalar(value=float(energy[0]))], units=energy[1])
             raise Exception('%s not found in %s'%('! & total energy',os.path.join(self._directory, self.outputf)))
 
-    @Value_if_true
     def is_relaxed(self):
         '''Determine if relaxation run from the output'''
-        return self._get_line('Geometry Optimization', self.outputf, return_string=False)
+        result = self._get_line('Geometry Optimization', self.outputf, return_string=False)
+        return Property(scalars=[Scalar(value=result)])
 
     def _is_converged(self):
         '''Determine if calculation converged; for a relaxation (static) run
         we look for ionic (electronic) convergence in the output'''
-        if self.is_relaxed():
+        if self.is_relaxed().scalars[0].value:
             # relaxation run case
-            return self._get_line(['End of', 'Geometry Optimization'], self.outputf, return_string=False)
+            result = self._get_line(['End of', 'Geometry Optimization'], self.outputf, return_string=False)
         else:
             # static run case
-            return self._get_line('convergence has been achieved', self.outputf, return_string=False)
+            result = self._get_line('convergence has been achieved', self.outputf, return_string=False)
+        return result
 
     def get_KPPRA(self):
         '''Determine the no. of k-points in the BZ (from the input) times the
@@ -143,10 +144,10 @@ def get_KPPRA(self):
         fp.close()
         raise Exception('%s not found in %s'%('KPOINTS',os.path.join(self._directory, self.inputf)))
 
-    @Value_if_true
     def uses_SOC(self):
         '''Looks for line with "with spin-orbit" in the output'''
-        return self._get_line('with spin-orbit', self.outputf, return_string=False)
+        result = self._get_line('with spin-orbit', self.outputf, return_string=False)
+        return Property(scalars=[Scalar(value=result)])
 
     def get_pp_name(self):
         '''Determine the pseudopotential names from the output'''
@@ -262,7 +263,7 @@ def get_output_structure(self):
                     break
             if len(coords) == 0: raise Exception('Cannot find the initial atomic coordinates')
 
-        if type(self.is_relaxed()) == type(None):
+        if not self.is_relaxed().scalars[0].value:
             # static run: create, populate, and return the initial structure
             structure = Atoms(symbols=atom_symbols, cell=unit_cell, pbc=True)
             structure.set_positions(coords)
@@ -339,7 +340,7 @@ def get_dos(self):
             ls = line.split()
             energy.append(float(ls[0])-efermi)
             dos.append(sum([float(i) for i in ls[1:1+ndoscol]]))
-        return Property(scalars=dos, units='number of states per unit cell', conditions=Value(name='energy', scalars=energy, units='eV'))
+        return Property(scalars=[Scalar(value=x) for x in dos], units='number of states per unit cell', conditions=Value(name='energy', scalars=[Scalar(value=x) for x in energy], units='eV'))
 
     def get_forces(self):
         return None

dfttopif/parsers/vasp.py

@@ -1,4 +1,4 @@
-from pypif.obj.common.property import Property
+from pypif.obj.common import Property, Scalar
 
 from .base import DFTParser, Value_if_true
 import os
@@ -53,7 +53,7 @@ def get_cutoff_energy(self):
             for line in fp:
                 if "ENCUT" in line:
                     words = line.split()
-                    return Value(scalars=float(words[2]), units=words[3])
+                    return Value(scalars=[Scalar(value=float(words[2]))], units=words[3])
 
         # Error handling: ENCUT not found
         raise Exception('ENCUT not found')
@@ -149,7 +149,7 @@ def _is_converged(self):
         return self._call_ase(Vasp().read_convergence)
 
     def get_total_energy(self):
-        return Property(scalars=self._call_ase(Vasp().read_energy)[0], units='eV')
+        return Property(scalars=[Scalar(value=self._call_ase(Vasp().read_energy)[0])], units='eV')
 
     def get_version_number(self):
         # Open up the OUTCAR

requirements.txt

@@ -5,4 +5,4 @@ requests
 flask
 flask-cors
 gunicorn
-pypif==1.1.6
+pypif==1.2.0

setup.py

@@ -7,7 +7,7 @@
     url='https://github.com/CitrineInformatics/pif-dft',
     install_requires=[
         'ase',
-        'pypif==1.1.6',
+        'pypif>=1.2.0,<1.3.0',
     ],
     extras_require={
         'report': ["requests"],

tests/parsers/test_pwscf.py

@@ -34,8 +34,8 @@ def test_NaF(self):
         self.assertEquals(-143.96084355, energy.scalars[0].value)
         self.assertEquals('Ry', energy.units)
 
-        self.assertEquals(None, parser.uses_SOC())
-        self.assertEquals(None, parser.is_relaxed())
+        self.assertEquals(False, parser.uses_SOC().scalars[0].value)
+        self.assertEquals(False, parser.is_relaxed().scalars[0].value)
         self.assertEquals('SLA PW PBE PBE', parser.get_xc_functional().scalars[0].value)
         self.assertEquals(['f_pbe_v1.4.uspp.F.UPF','Na_pbe_v1.uspp.F.UPF'], list(map(lambda x: x.value, parser.get_pp_name().scalars)))
         self.assertEquals(3456, parser.get_KPPRA().scalars[0].value)