Merge pull request #230 from jtkrogel/dev

fix for parallel pw2qmcpack workflow, other small updates

nexus/library/bundle.py

@@ -194,7 +194,7 @@ class SimulationBundle(Simulation):
 
 
     def progress(self,dependency_id=None):
-        if dependency_id!=None:
+        if dependency_id!=None and dependency_id in self.wait_ids:
             self.wait_ids.remove(dependency_id)
         #end if
         if len(self.wait_ids)==0 and not self.block and not self.failed:

nexus/library/developer.py

@@ -366,3 +366,13 @@ def unavailable(module,*items):
         return voids
     #end if
 #end def unavailable
+
+
+def available(*items):
+    for item in items:
+        if isinstance(item,Void):
+            return False
+        #end if
+    #end for
+    return True
+#end def available

nexus/library/generic.py

@@ -609,6 +609,16 @@ class obj(object_interface):
 
 
     # dict extensions
+    def random_key(self):
+        key = None
+        nkeys = len(self)
+        if nkeys>0:
+            key = self._keys()[randint(0,nkeys-1)]
+        #end if
+        return key
+    #end def random_key
+
+
     def set(self,*objs,**kwargs):
         for key,value in kwargs.iteritems():
             self[key]=value
@@ -858,6 +868,25 @@ class obj(object_interface):
         return new
     #end def inverse
 
+    def serial(self,s=None,path=None):
+        first = s is None
+        if first:
+            s = obj()
+            path = ''
+        #end if
+        for k,v in self._iteritems():
+            p = path+str(k)
+            if isinstance(v,obj):
+                v._serial(s,p+'/')
+            else:
+                s[p]=v
+            #end if
+        #end for
+        if first:
+            return s
+        #end if
+    #end def serial
+
 
 
     # access preserving functions
@@ -885,6 +914,8 @@ class obj(object_interface):
     def _select_random(self,*args,**kwargs):
         return obj.select_random(self,*args,**kwargs)
     #  dict extensions
+    def _random_key(self,*args,**kwargs):
+        obj.random_key(self,*args,**kwargs)
     def _set(self,*args,**kwargs):
         obj.set(self,*args,**kwargs)
     def _set_optional(self,*args,**kwargs):
@@ -923,6 +954,8 @@ class obj(object_interface):
         obj.shallow_copy(self,*args,**kwargs)
     def _inverse(self,*args,**kwargs):
         return obj.inverse(self,*args,**kwargs)
+    def _serial(self,*args,**kwargs):
+        return obj.serial(self,*args,**kwargs)
 
 #end class obj
 

nexus/library/nexus.py

@@ -386,6 +386,7 @@ def run_project(*args,**kwargs):
     pm = ProjectManager()
     pm.add_simulations(*args,**kwargs)
     pm.run_project()
+    return pm
 #end def run_project
 
 

nexus/library/project_manager.py

@@ -330,6 +330,22 @@ class ProjectManager(NexusCore):
     #end def write_cascade_status
 
 
+    def write_sim_dependencies(self,idkey=None):
+        for simid in sorted(self.simulations.keys()):
+            sim = self.simulations[simid]
+            if idkey is None or sim.identifier==idkey:
+                self.log('\n{0} {1} {2}'.format(sim.identifier,simid,sim.locdir))
+                for did in sorted(sim.dependencies.keys()):
+                    dep = sim.dependencies[did]
+                    dsim  = dep.sim
+                    names = dep.result_names
+                    self.log('  {0} {1} {2} {3}'.format(dsim.identifier,dsim.simid,names,dsim.locdir))
+                #end for
+            #end if
+        #end for
+    #end def write_sim_dependencies
+
+
     def write_cascade_dependents(self):
         self.log('cascade dependents',n=1)
         for cascade in self.cascades:
@@ -411,7 +427,7 @@ class ProjectManager(NexusCore):
             cascade.reset_wait_ids()
         #end for
         for cid,cascade in progressing_cascades.iteritems():
-            if not cascade.bundled:
+            if not cascade.bundled or cascade.bundler.finished:
                 cascade.progress()
             #end if
             cascade.check_subcascade()

nexus/library/pwscf.py

@@ -96,9 +96,9 @@ class Pwscf(Simulation):
         if result_name=='charge_density':
             calculating_result = True
         elif result_name=='orbitals':
-            calculating_result = 'wf_collect' in control and control.wf_collect
+            calculating_result = 'calculation' not in control or 'scf' in control.calculation.lower()
         elif result_name=='structure':
-            calculating_result = 'relax' in control.calculation.lower()
+            calculating_result = 'calculation' in control and 'relax' in control.calculation.lower()
         else:
             calculating_result = False
         #end if

nexus/library/pwscf_input.py

@@ -55,6 +55,7 @@ from generic import obj
 from structure import Structure,kmesh
 from physical_system import PhysicalSystem
 from developer import DevBase,warn
+from pseudopotential import pp_elem_label
 from simulation import SimulationInput
 from debug import *
 
@@ -1747,7 +1748,8 @@ def generate_any_pwscf_input(**kwargs):
     pseudopotentials = obj()
     atoms = []
     for ppname in pseudos:
-        element = ppname[0:2].strip('.')
+        #element = ppname[0:2].strip('.')
+        label,element = pp_elem_label(ppname,guard=True)
         atoms.append(element)
         pseudopotentials[element] = ppname
     #end for

nexus/library/qmcpack_input.py

@@ -1940,6 +1940,14 @@ class kspace_jastrow(QIxml):
     write_types = obj(optimize=yesno)
 #end class kspace_jastrow
 
+class rpa_jastrow(QIxml):
+    tag = 'jastrow'
+    attributes = ['type','name','source','function','kc']
+    parameters = ['longrange']
+    identifier = 'name'
+    write_types = obj(longrange=yesno)
+#end class rpa_jastrow
+
 class correlation(QIxml):
     attributes = ['elementtype','speciesa','speciesb','size','ispecies','especies',
                   'especies1','especies2','isize','esize','rcut','cusp','pairtype',
@@ -1977,7 +1985,7 @@ class distancetable(QIxml):
 
 jastrow = QIxmlFactory(
     name = 'jastrow',
-    types   = dict(one_body=jastrow1,two_body=jastrow2,jastrow1=jastrow1,jastrow2=jastrow2,eei=jastrow3,jastrow3=jastrow3,kspace=kspace_jastrow),
+    types   = dict(one_body=jastrow1,two_body=jastrow2,jastrow1=jastrow1,jastrow2=jastrow2,eei=jastrow3,jastrow3=jastrow3,kspace=kspace_jastrow,kspace_jastrow=kspace_jastrow,rpa=rpa_jastrow,rpa_jastrow=rpa_jastrow),
     typekey = 'type'
     )
 
@@ -2133,9 +2141,9 @@ class structurefactor(QIxml):
 class force(QIxml):
     tag = 'estimator'
     attributes = ['type','name','mode','source','species','target','addionion']
-    write_types= obj(addionion=yesno)
     parameters = ['rcut','nbasis','weightexp']
     identifier = 'name'
+    write_types= obj(addionion=yesno)
 #end class force
 
 class forwardwalking(QIxml):
@@ -2183,7 +2191,7 @@ class skall(QIxml):
     tag = 'estimator'
     attributes = ['name','type','hdf5','source','target','writeionion']
     identifier = 'name'
-    write_types = obj(hdf5=yesno)
+    write_types = obj(hdf5=yesno,writeionion=yesno)
 #end class skall
 
 class gofr(QIxml):
@@ -2449,7 +2457,7 @@ classes = [   #standard classes
     header,local,force,forwardwalking,observable,record,rmc,pressure,dmccorrection,
     nofk,mpc_est,flux,distancetable,cpp,element,spline,setparams,
     backflow,transformation,cubicgrid,molecular_orbital_builder,cmc,sk,skall,gofr,
-    host,date,user,
+    host,date,user,rpa_jastrow
     ]
 types = dict( #simple types and factories
     #host           = param,
@@ -2624,7 +2632,15 @@ density.defaults.set(
 spindensity.defaults.set(
     type='spindensity',name='SpinDensity'
     )
-
+skall.defaults.set(
+    type='skall',name='skall'
+    )
+force.defaults.set(
+    type='Force',name='force'
+    )
+pressure.defaults.set(
+    type='Pressure'
+    )
 
 
 linear.defaults.set(

nexus/library/qmcpack_workflows.py

@@ -1963,7 +1963,10 @@ def gen_vmc(simlabel,ch,depset,J,test=0,loc=''):
     else:
         qmcjob = wf.job
     #end if
-    if J=='J0':
+    other_inputs = obj(task.inputs)
+    if 'jastrows' in other_inputs:
+        jastrows = other_inputs.delete('jastrows')
+    elif J=='J0':
         jastrows = []
     elif J=='J2':
         jastrows = jastrow_factor(**task.J2_inputs)
@@ -1976,7 +1979,7 @@ def gen_vmc(simlabel,ch,depset,J,test=0,loc=''):
         jastrows     = jastrows,
         calculations = vmc_sections(test=test,J0=J=='J0',**task.sec_inputs),
         dependencies = deps,
-        **task.inputs
+        **other_inputs
         )
     sims[simlabel] = qmc
 #end def gen_vmc
@@ -2031,14 +2034,16 @@ def gen_dmc(simlabel,ch,depset,J,nlmove=None,test=0,loc=''):
     else:
         qmcjob = wf.job
     #end if
-    if J=='J0':
+    other_inputs = obj(task.inputs)
+    if 'jastrows' in other_inputs:
+        jastrows = other_inputs.delete('jastrows')    
+    elif J=='J0':
         jastrows = []
     elif J=='J2':
         jastrows = jastrow_factor(**task.J2_inputs)
     elif J=='J3':
         jastrows = jastrow_factor(**task.J3_inputs)
     #end if
-    other_inputs = obj(task.inputs)
     if 'calculations' not in other_inputs:
         other_inputs.calculations = dmc_sections(nlmove=nlmove,test=test,J0=J=='J0',**task.sec_inputs)
     #end if