Nexus: update PWscf analyzer

docs/lab_excited.rst

@@ -238,8 +238,8 @@ following lines to get the exact location of VBM and CBM using
 .. code-block:: python
 
   p = band.load_analyzer_image()
-  print("VBM:\n{0}".format(p.bands.vbm))
-  print("CBM:\n{0}".format(p.bands.cbm))
+  print("VBM:\n{0}".format(p.results_out.bands.vbm))
+  print("CBM:\n{0}".format(p.results_out.bands.cbm))
 
 Output must be the following:
 
@@ -303,8 +303,8 @@ lines to get the exact location of VBM and CBM using
 .. code-block:: python
 
   p = band.load_analyzer_image()
-  print("VBM:\n{0}".format(p.bands.vbm))
-  print("CBM:\n{0}".format(p.bands.cbm))
+  print("VBM:\n{0}".format(p.results_out.bands.vbm))
+  print("CBM:\n{0}".format(p.results_out.bands.cbm))
 
 Output must be the following:
 
@@ -384,14 +384,14 @@ eigenvalues using their index numbers:
 
 .. code-block:: python
 
-  >>> print p.bands.up[51] ## CBM, $\Delta$ ##
+  >>> print p.results_out.bands.up[51] ## CBM, $\Delta$ ##
     eigs            = [-3.2076  4.9221  7.5433  7.5433 17.1545 19.7598 28.3242 28.3242]
     index           = 51
     kpoint_2pi_alat = [0.        0.1095605 0.       ]
     kpoint_rel      = [0.3695652 0.        0.3695652]
     occs            = [1. 1. 1. 1. 0. 0. 0. 0.]
     pol             = up
-  >>> print p.bands.up[46] ## $\Delta'$ ##
+  >>> print p.results_out.bands.up[46] ## $\Delta'$ ##
     eigs            = [-4.0953  6.1376  7.9247  7.9247 17.1972 20.6393 27.3653 27.3653]
     index           = 46
     kpoint_2pi_alat = [0.        0.0988193 0.       ]
@@ -458,11 +458,11 @@ Alternatively, we can also read the band and twist indexes using PwscfAnalyzer a
 
   p = nscf.load_analyzer_image()
   print('band information')
-  print(p.bands.up)
-  print('twist 0 k-point:',p.bands.up[0].kpoint_rel)
-  print('twist 4 k-point:',p.bands.up[4].kpoint_rel)
-  print('twist 0 band 3 eigenvalue:',p.bands.up[0].eigs[3])
-  print('twist 4 band 4 eigenvalue:',p.bands.up[4].eigs[4])
+  print(p.results_out.bands.up)
+  print('twist 0 k-point:',p.results_out.bands.up[0].kpoint_rel)
+  print('twist 4 k-point:',p.results_out.bands.up[4].kpoint_rel)
+  print('twist 0 band 3 eigenvalue:',p.results_out.bands.up[0].eigs[3])
+  print('twist 4 band 4 eigenvalue:',p.results_out.bands.up[4].eigs[4])
 
 Giving output:
 

labs/lab5_excited_states/band.py

@@ -72,10 +72,10 @@
 
 p = band.load_analyzer_image()
 p.plot_bandstructure()
-print("VBM:\n{0}".format(p.bands.vbm)) 
-print("CBM:\n{0}".format(p.bands.cbm))
+print("VBM:\n{0}".format(p.results_out.bands.vbm))
+print("CBM:\n{0}".format(p.results_out.bands.cbm))
 
 #print("CBM, Delta")
-#print(p.bands.up[51])
+#print(p.results_out.bands.up[51])
 #print("Delta prime")
-#print(p.bands.up[46])
+#print(p.results_out.bands.up[46])

labs/lab5_excited_states/optical.py

@@ -77,11 +77,11 @@
 try:
     p = nscf.load_analyzer_image()
     print('band information')
-    print(p.bands.up)
-    print('twist 0 k-point:',p.bands.up[0].kpoint_rel)
-    print('twist 4 k-point:',p.bands.up[4].kpoint_rel)
-    print('twist 0 band 3 eigenvalue:',p.bands.up[0].eigs[3])
-    print('twist 4 band 4 eigenvalue:',p.bands.up[4].eigs[4])
+    print(p.results_out.bands.up)
+    print('twist 0 k-point:',p.results_out.bands.up[0].kpoint_rel)
+    print('twist 4 k-point:',p.results_out.bands.up[4].kpoint_rel)
+    print('twist 0 band 3 eigenvalue:',p.results_out.bands.up[0].eigs[3])
+    print('twist 4 band 4 eigenvalue:',p.results_out.bands.up[4].eigs[4])
 except:
     print('band information not found')
 

nexus/nexus/examples/qmcpack/rsqmc_misc/excited/band.py

@@ -1,10 +1,7 @@
 #! /usr/bin/env python3
 
-from nexus import settings,job,run_project
-from nexus import generate_physical_system
-from nexus import generate_pwscf
-
-from nexus.structure import get_primitive_cell, get_kpath
+from nexus import generate_physical_system, generate_pwscf, job, run_project, settings
+from nexus.structure import get_kpath, get_primitive_cell
 
 settings(
     pseudo_dir    = '../../pseudopotentials',
@@ -83,11 +80,11 @@
 
 run_project()
 
-if band.finished:
+performed_runs = not settings.generate_only and not settings.status_only
+if performed_runs and band.finished:
     from nexus.pwscf_analyzer import PwscfAnalyzer
     p = PwscfAnalyzer(band)
     p.analyze()
-    p.plot_bandstructure()
-    print(f"VBM: {p.bands.vbm}")
-    print(f"CBM: {p.bands.cbm}")
+    print(f"VBM: {p.Evbm()}")
+    print(f"CBM: {p.Ecbm()}")
 #end if

nexus/nexus/examples/quantum_espresso/relax_Ge_T_vs_kpoints/relax_vs_kpoints_example.py

@@ -1,10 +1,6 @@
 #! /usr/bin/env python3
 
-from nexus import settings
-from nexus import generate_physical_system
-from nexus import generate_pwscf,job
-from nexus import run_project
-
+from nexus import generate_physical_system, generate_pwscf, job, run_project, settings
 
 # set global parameters of nexus
 settings(
@@ -39,7 +35,7 @@
     relax = generate_pwscf(             # make each relax simulation
         identifier = 'relax',               # file prefix
                                             # run directory
-        path       = 'relax/kgrid_{0}{1}{2}'.format(*kgrid),
+        path       = f'relax/kgrid_{kgrid[0]}{kgrid[1]}{kgrid[2]}',
         job        = job(cores=16),         # will run with mpirun -np 16
         input_type = 'relax',               # this is a relax calculation
         input_dft  = 'pbe',                 # PBE functional
@@ -74,16 +70,17 @@
         kgrid = supercell_kgrids[ik]
         relax = relaxations[ik]
         pa = relax.load_analyzer_image()
-        start_force = pa.tot_forces[0]
-        max_force   = pa.tot_forces.max()
-        ncycles     = len(pa.tot_forces)
-        print(f'  {kgrid:10}  {start_force:10}     {max_force:10}  {ncycles:8}')
+        forces      = pa.forces('Ry/B')
+        total_force = (forces**2).sum(axis=(1,2))**0.5
+        start_force = total_force[0]
+        max_force   = total_force.max()
+        ncycles     = len(total_force)
+        kgrid_text  = str(kgrid)
+        print(f'  {kgrid_text:10}  {start_force:10}     {max_force:10}  {ncycles:8}')
     #end for
     print()
     print()
     print('The final structure is:')
     print()
-    print(list(pa.structures.values())[-1].positions)
+    print(pa.relaxed_structure('B').pos)
 #end if
-
-

nexus/nexus/pwscf.py

@@ -215,7 +215,7 @@ def get_result(self,result_name,sim):
             result.location = os.path.join(self.locdir,outdir,prefix+'.wfc1')
         elif result_name=='structure':
             pa = self.load_analyzer_image()
-            structs = pa.structures
+            structs = pa.results_out.relax_structures
             struct  = structs[len(structs)-1]
             pos   = struct.positions
             atoms = struct.atoms
@@ -434,7 +434,7 @@ def fill_products(self):
         analyzer = self.load_analyzer_image()
         input    = analyzer.input
         if 'energy' in self.produces:
-            self.products.energy = analyzer.E
+            self.products.energy = analyzer.results_out.E
         if 'charge_density' in self.produces:
             outdir = input.control.outdir
             path   = os.path.join(self.locdir,outdir)
@@ -445,7 +445,7 @@ def fill_products(self):
             self.products.orbitals = path
         if 'structure' in self.produces:
             pa = analyzer
-            structs = pa.structures
+            structs = pa.results_out.relax_structures
             struct  = deepcopy(structs[len(structs)-1])
             pos     = struct.positions
             atoms   = struct.atoms