Merge remote-tracking branch 'origin/develop' into cudatoolkit

nexus/lib/pwscf_analyzer.py

@@ -924,14 +924,14 @@ def plot_bandstructure(self, filename=None, filepath=None, max_min_e = None, sho
                 #end if              
             #end for
             for ln, li in enumerate(labels):
-                if li is not '':
+                if li != '':
                     axvline(x[ln], ymin=-100, ymax=100, linewidth=3, color='k')
                     if li == 'GAMMA':
                         labels[ln] = r'$\Gamma$'
-                    elif li is not '':
+                    elif li != '':
                         labels[ln] = '${0}$'.format(li)
                     #end if
-                    if labels[ln-1] is not '' and ln > 0:
+                    if labels[ln-1] != '' and ln > 0:
                         labels[ln] = labels[ln-1]+'|'+labels[ln]
                         labels[ln-1] = ''
                     #end if

nexus/lib/qmcpack_converters.py

@@ -799,10 +799,8 @@ def get_result(self,result_name,sim):
         wfn_file,ptcl_file = self.list_output_files()
         if result_name=='orbitals':
             result.location = os.path.join(self.locdir,wfn_file)
-            if self.input.hdf5==True:
-                orbfile = self.get_prefix()+'.orbs.h5'
-                result.orbfile = os.path.join(self.locdir,orbfile)
-            #end if
+            orbfile = self.get_prefix()+'.orbs.h5'
+            result.orbfile = os.path.join(self.locdir,orbfile)
         elif result_name=='particles':
             result.location = os.path.join(self.locdir,ptcl_file)
         else:
@@ -841,15 +839,15 @@ def incorporate_result(self,result_name,result,sim):
             self.input_code = 'pyscf'
             if result_name=='orbitals':
                 orbpath = os.path.relpath(result.h5_file,self.locdir)
-                input.pyscf = orbpath
+                input.orbitals = orbpath
             else:
                 implemented = False
             #end if
         elif isinstance(sim,QuantumPackage):
             self.input_code = 'qp'
             if result_name=='orbitals':
                 orbpath = os.path.relpath(result.outfile,self.locdir)
-                input.qp = orbpath
+                input.orbitals = orbpath
             else:
                 implemented = False
             #end if

nexus/lib/qmcpack_input.py

@@ -5377,7 +5377,7 @@ def generate_jastrow1(function='bspline',size=8,rcut=None,coeff=None,cusp=0.,ena
     corrs = []
     for i in range(len(elements)):
         element = elements[i]
-        if cusp is 'Z':
+        if cusp == 'Z':
             QmcpackInput.class_error('need to implement Z cusp','generate_jastrow1')
         else:
             lcusp  = cusp

nexus/lib/structure.py

@@ -5562,7 +5562,7 @@ def _getseekpath(
         structure = structure.folded_structure
     #end if
     structure = structure.copy()
-    if structure.units is not 'A':
+    if structure.units != 'A':
         structure.change_units('A')
     #end if
     axes       = structure.axes
@@ -6783,10 +6783,12 @@ def __init__(self,
         pos  = []
         if basis_vectors is None:
             basis_vectors = axes
-        elif basis_vectors is 'primitive':
-            basis_vectors = axes_prim
-        elif basis_vectors is 'conventional':
-            basis_vectors = axes_conv
+        elif isinstance(basis_vectors,str):
+            if basis_vectors=='primitive':
+                basis_vectors = axes_prim
+            elif basis_vectors=='conventional':
+                basis_vectors = axes_conv
+            #end if
         #end if
         nbasis = len(atoms)
         for point in points:

nexus/tests/unit/test_qmcpack_converter_simulations.py

@@ -251,6 +251,7 @@ def test_convert4qmc_get_result():
 
     result_ref = obj(
         location = './runs/sample.wfj.xml',
+        orbfile  = './runs/sample.orbs.h5',
         )
 
     assert(object_eq(result,result_ref))
@@ -338,7 +339,7 @@ def test_convert4qmc_incorporate_result():
     sim.incorporate_result('orbitals',pscf_result,pscf)
 
     assert(sim.input_code=='pyscf')
-    assert(sim.input.pyscf=='../scf.h5')
+    assert(sim.input.orbitals=='../scf.h5')
 
     # incorporate orbitals from quantum package
     sim = sim_start.copy()
@@ -349,7 +350,8 @@ def test_convert4qmc_incorporate_result():
     sim.incorporate_result('orbitals',qp_result,qp)
 
     assert(sim.input_code=='qp')
-    assert(sim.input.qp=='../qp_savewf.out')
+    #assert(sim.input.qp=='../qp_savewf.out')
+    assert(sim.input.orbitals=='../qp_savewf.out')
 
     clear_all_sims()
 #end def test_convert4qmc_incorporate_result

nexus/tests/unit/test_qmcpack_simulation.py

@@ -272,7 +272,8 @@ def test_incorporate_result():
 
     result = c4q_orb.get_result('orbitals',None)
 
-    wfn_file = os.path.join(tpath,'c4q_orbitals.wfj.xml')
+    wfn_file  = os.path.join(tpath,'c4q_orbitals.wfj.xml')
+    wfn_file2 = os.path.join(tpath,'c4q_orbitals.orbs.h5')
     input = sim.input.copy()
     dset = input.get('determinantset')
     dset.href = 'orbs.h5'
@@ -281,6 +282,8 @@ def test_incorporate_result():
     input.qmcsystem = qs
     input.write(wfn_file)
     assert(os.path.exists(wfn_file))
+    open(wfn_file2,'w').write('fake')
+    assert(os.path.exists(wfn_file2))
 
     from qmcpack_input import QmcpackInput
     inp = QmcpackInput(wfn_file)
@@ -291,7 +294,7 @@ def test_incorporate_result():
     sim.incorporate_result('orbitals',result,c4q_orb)
 
     dset = sim.input.get('determinantset')
-    assert(dset.href=='orbs.h5')
+    assert(dset.href=='c4q_orbitals.orbs.h5')
 
 
     # incorporate qmcpack jastrow