Merge branch 'master' of github.com:bbusemeyer/autogenv2

Author: bbusemeyer

TODO.md

@@ -1,8 +1,11 @@
-- [ ] Manage path setup with setup script.
-  - crystal, properties, pyscf, and qwalk executible names and locations.
+- [ ] Model fitting example.
+- [ ] How to handle qwfiles better? Interaction between manager and trialfunc is currently not too flexible. For example it depends on kpoints being a list.
+  - Possible to move the `export_qwalk` into `trialfunc`?
 - [ ] Bad use case: accidentally putting the same writer for multiple managers
       will screw up the process because the first time the writer writes, it delares itself 'done'
 - [ ] Comparable defaults between PySCF and Crystal are not the same.
 - [ ] Cannot yet do different paths with QMC and crystal because the basis and the orb file needs to be in the same place.
   - May need to have the crystal manager export the results to the same directory (this means there are redundant files then).
 - [ ] PySCF Si run in `simple_test` doesn't make any sense.
+- [x] Manage path setup with setup script.
+  - crystal, properties, pyscf, and qwalk executible names and locations.

autorunner.py

@@ -35,6 +35,14 @@ def add_task(self,exestr):
     else:
       self.exelines.append("mpirun -n {tnp} {exe}".format(tnp=self.nn*self.np,exe=exestr))
 
+  #-------------------------------------
+  def add_command(self,cmdstr):
+    ''' Accumulate commands that don't get an MPI command.
+    Args: 
+      cmdstr (str): executible statement. Will be prepended with appropriate mpirun. 
+    '''
+    self.exelines.append(cmdstr)
+
   #-------------------------------------
   def script(self,scriptfile):
     ''' Dump accumulated commands into a script for another job to run.
@@ -250,9 +258,10 @@ def script(self,scriptfile):
     return True
 
   #-------------------------------------
-  def submit(self,jobname=None):
+  def submit(self,jobname=None,ppath=None):
     ''' Submit series of commands.
     Note: jobname is not used because it doesn't submit anything.'''
+    sys.path=ppath+sys.path
 
     if len(self.exelines)==0:
       #print(self.__class__.__name__,": All tasks completed or queued.")

dmc.py

@@ -111,7 +111,7 @@ def check_complete(self):
       print("DMC incomplete: Run completed %d blocks, but requires %d."%\
           (self.output['total blocks']-self.output['warmup blocks'],self.minblocks))
       completed=False
-    return complete
+    return completed
 
   #------------------------------------------------
   def collect(self,outfile):

manager.py

@@ -168,8 +168,8 @@ def __init__(self,writer,runner,creader=None,name='crystal_run',path=None,
     else: self.runner=runner
 
     # Internal.
-    self.crysinpfn=self.name+'.in'
-    self.propinpfn=self.name+'.prop.in'
+    self.crysinpfn=self.name
+    self.propinpfn=self.name+'.prop'
     self.crysoutfn=self.crysinpfn+'.o'
     self.propoutfn=self.propinpfn+'.o'
     self.restarts=0
@@ -617,7 +617,7 @@ def __init__(self,writer,reader,runner=None,trialfunc=None,
     self.completed=False
     self.scriptfile=None
     self.bundle_ready=False
-    self.infile="%s.%s"%(name,writer.qmc_abr)
+    self.infile=name
     self.outfile="%s.o"%self.infile
     # Note: qwfiles stores file names of results, used for exporting trial wave functions.
     self.qwfiles={