Moved some relevant examples to a better place

Added more consistent extras_component_raw() in a way that doesn't break
stuff (although it's not super-consistent with everything else)

examples/temp/pes/pswater/contract-extras/input.xml → examples/features/outputs/contract-extras/input.xml

@@ -6,6 +6,8 @@
     <trajectory filename='for' format='xyz' stride='2'> forces </trajectory>
     <trajectory filename='kin' format='xyz' stride='2'> kinetic_cv </trajectory>
     <trajectory filename='dip' stride='2' extra_type='dipole'> extras </trajectory>
+    <!-- these two output the extras for the contracted beads -->
+    <trajectory filename='dip_raw' stride='2' extra_type='dipole'> extras_component_raw(0) </trajectory>
     <checkpoint stride='100' filename='chk' overwrite='true'/>
     <checkpoint stride='2000' filename='restart' overwrite='false'/>
   </output>

ipi/engine/forces.py

@@ -1199,7 +1199,6 @@ def extras_component(self, index):
         Does not attempt to apply weights or interpolate, always returns raw stuff.
         """
 
-        print("accessing extras ", self.mforces[index].extras)
         return self.mforces[index].extras
 
     def forcesvirs_4th_order(self, index):

ipi/engine/outputs.py

@@ -345,7 +345,7 @@ def open_stream(self, mode):
             "velocities",
             "forces",
             "extras",
-            "extras_component_raw",
+            # "extras_component_raw", write out a single file as we don't know how to do contraction here
             "extras_bias",
             "forces_sc",
             "momenta",
@@ -368,7 +368,10 @@ def open_stream(self, mode):
                     self.out.append(None)
         else:
             # open one file
-            filename = self.filename + "." + self.format
+            filename = self.filename
+            # prepare format string for file name
+            if getkey(self.what)[:6] != "extras":
+                filename += "." + self.format
             self.out = open_backup(filename, mode)
 
     def close_stream(self):
@@ -479,13 +482,26 @@ def write_traj(
 
         key = getkey(what)
         if key in ["extras", "extras_component_raw", "extras_bias"]:
-            stream.write(
-                " #%s(%s)# Step:  %10d  Bead:  %5d  \n"
-                % (key.upper(), self.extra_type, self.system.simul.step + 1, b)
-            )
+            if key == "extras_component_raw":
+                stream.write(
+                    " #%s(%s)# Step:  %10d  Bead:  %5d  \n"
+                    % (key.upper(), self.extra_type, self.system.simul.step + 1, b)
+                )
+            else:
+                stream.write(
+                    " #%s(%s)# Step:  %10d \n"
+                    % (key.upper(), self.extra_type, self.system.simul.step + 1)
+                )
             if self.extra_type in data:
                 try:
-                    floatarray = np.asarray(data[self.extra_type][b], dtype=float)
+                    if key == "extras_component_raw":
+                        # don't partition into beads as there might be a different number when contracting
+                        floatarray = np.asarray(
+                            data[self.extra_type], dtype=float
+                        ).squeeze()
+                    else:
+                        # picks up the desired bead
+                        floatarray = np.asarray(data[self.extra_type][b], dtype=float)
                     if floatarray.ndim == 2:
                         stream.write(
                             "\n".join(

ipi/engine/properties.py

@@ -2872,8 +2872,10 @@ def __init__(self):
                 "help": """The additional data returned by the client code, printed verbatim or expanded 
                            as a dictionary. See "extras". 
                            Fetches the extras from a specific force component, indicated in parentheses 
-                           [extras_component_raw(idx)]. Never applies weighting or contraction""",
-                "func": (lambda idx: self.system.forces.extras_component(int(idx))),
+                           and a specific bead [extras_component_raw(idx; bead=0)]. 
+                           Never applies weighting or contraction, and does not automatically sum 
+                           over beads as we don't know if the extras are numeric""",
+                "func": (lambda idx: (self.system.forces.extras_component(int(idx)))),
             },
             "extras_bias": {
                 "help": """The additional data returned by the bias forcefield, printed verbatim or expanded as a dictionary. See "extras". """,