Various fixes and modifs for atomate2 development (#283)

* Read SHG AR contrib

* test spinat

* modif set_autospinat

* modif for atomate2

* fix EventParser for RelaxConvergenceWarning + quick fix wrapper as_dict pmg_serialize

* remove VT

abipy/abio/inputs.py

@@ -1229,7 +1229,7 @@ def set_autospinat(self, default=0.6) -> dict:
         for site in self.structure:
             if hasattr(site, 'magmom'):
                 spinat.append((0., 0., site.magmom))
-            elif hasattr(site.specie, 'spin'):
+            elif hasattr(site.specie, 'spin') and site.specie.spin:
                 spinat.append((0., 0., site.specie.spin))
             elif str(site.specie) in magmom_mp_conf:
                 spinat.append((0., 0., magmom_mp_conf.get(str(site.specie))))

abipy/abio/outputs.py

@@ -258,7 +258,13 @@ def pop_stack():
                 if dtidx is None:
                     vars_global[key] = value
                 else:
-                    vars_dataset[dtidx][key] = value
+                    try:
+                        vars_dataset[dtidx][key] = value
+                    except KeyError:
+                        if dtidx==0:
+                            vars_global[key] = value
+                        else:
+                            raise Exception("dataset index != 0 but still not found in vars_dataset")
 
         for line in lines:
             if not line: continue

abipy/electrons/optic.py

@@ -28,7 +28,10 @@
         "longname": "Second Harmonic Generation",
         "rank": 3,
         "terms": ["shg_inter2w", "shg_inter1w", "shg_intra2w",
-                  "shg_intra1w", "shg_intra1wS", "shg_chi2tot"],
+                  "shg_intra1w", "shg_intra1wS", "shg_chi2tot",
+                  "shg_inter2w_AR", "shg_inter1w_AR", "shg_intra2w_AR",
+                  "shg_intra1w_AR", "shg_intra1wS_AR", "shg_chi2tot_AR",
+                  "shg_chi2full"],
         }
         #"latex": r"\chi(-2\omega, \omega, \omega)"
     ),

abipy/flowtk/events.py

@@ -433,6 +433,7 @@ def parse(self, filename: str, verbose: int = 0) -> EventReport:
                 if w.match(doc.tag):
                     #print("got doc.tag", doc.tag,"--")
                     try:
+                        doc.text  = doc.text.replace('\n    \n', '\n')
                         #print(doc.text)
                         event = yaml.load(doc.text)   # Can't use ruamel safe_load!
                         # FIXME: This new (recommend) API does not reproduce yaml.load behavior. bug in ruamel?

abipy/flowtk/qadapters.py

@@ -215,7 +215,7 @@ def __init__(self, **kwargs):
 
         # Convert memory to megabytes.
         m = str(kwargs.pop("mem_per_node"))
-        self.mem_per_node = int(Memory.from_str(m).to("Mb"))
+        self.mem_per_node = int(Memory.from_string(m).to("Mb"))
 
         if self.mem_per_node <= 0 or self.sockets_per_node <= 0 or self.cores_per_socket <= 0:
             raise ValueError("invalid parameters: %s" % kwargs)

abipy/tools/serialization.py

@@ -26,6 +26,8 @@ def pmg_serialize(method):
 
     @functools.wraps(method)
     def wrapper(*args, **kwargs):
+        if not args:
+            return None
         self = args[0]
         d = method(*args, **kwargs)
         # Add @module and @class