gamess update for mcscf workflows

git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@6410 e5b18d87-469d-4833-9cc0-8cdfa06e9491

nexus/library/convert4qmc.py

@@ -146,7 +146,13 @@ class Convert4qmc(Simulation):
 
     def incorporate_result(self,result_name,result,sim):
         if result_name=='orbitals':
-            self.input.gamess_ascii = os.path.relpath(result.location,self.locdir)
+            orbpath = os.path.relpath(result.location,self.locdir)
+            if result.scftyp=='mcscf':
+                self.input.gamess_ascii = orbpath
+                self.input.ci           = orbpath
+            else:
+                self.input.gamess_ascii = orbpath
+            #end if
             self.job.app_command = self.input.app_command()
         else:
             self.error('ability to incorporate result '+result_name+' has not been implemented')
@@ -184,6 +190,9 @@ class Convert4qmc(Simulation):
 
 def generate_convert4qmc(**kwargs):
     sim_args,inp_args = Simulation.separate_inputs(kwargs)
+    if 'identifier' in sim_args and not 'prefix' in inp_args:
+        inp_args.prefix = sim_args.identifier
+    #end if
 
     if not 'input' in sim_args:
         sim_args.input = generate_convert4qmc_input(**inp_args)

nexus/library/gamess.py

@@ -50,7 +50,7 @@ class Gamess(Simulation):
     def check_result(self,result_name,sim):
         input = self.input 
         if result_name=='orbitals':
-            calculating_result = 'contrl' in input and 'scftyp' in input.contrl and input.contrl.scftyp in ('rhf','rohf','uhf')
+            calculating_result = 'contrl' in input and 'scftyp' in input.contrl and input.contrl.scftyp.lower() in ('rhf','rohf','uhf','mcscf')
         else:
             calculating_result = False
         #end if
@@ -60,11 +60,13 @@ class Gamess(Simulation):
 
     def get_result(self,result_name,sim):
         result = obj()
+        input    = self.input
         analyzer = self.load_analyzer_image()
         if result_name=='orbitals':
             result.location  = os.path.join(self.locdir,self.outfile)
             result.vec       = None
             result.norbitals = 0
+            result.scftyp    = input.contrl.scftyp.lower()
             if 'punch' in analyzer and 'vec' in analyzer.punch:
                 result.norbitals = analyzer.punch.norbitals
                 result.vec       = analyzer.punch.vec
@@ -85,9 +87,11 @@ class Gamess(Simulation):
             if not 'guess' in input:
                 input.guess = GuessGroup()
             #end if
+            input.guess.clear()
             input.guess.set(
                 guess = 'moread',
-                norb  = result.norbitals
+                norb  = result.norbitals,
+                prtmo = True
                 )
             input.vec = FormattedGroup(result.vec)
         else:

nexus/library/gamess_input.py

@@ -608,6 +608,31 @@ class CidrtGroup(KeywordSpecGroup):
  
 
 
+class DetGroup(KeywordSpecGroup):
+    keywords = set([
+            'ncore' ,'nact'  ,'nels'  ,'sz'    ,'group' ,'stsym' ,'irreps',
+            'nstate','prttol','analys','itermx','cvgtol','nhgss' ,'nstgss',
+            'mxxpan','clobbr','pures' ,'iroot' ,'nflgdm','saflg' ,'wstate',
+            'idwref','dwparm'
+            ])
+
+    integers = set(['ncore','nact','nels','nstate','itermx','nhgss','nstgss',
+                    'mxxpan','iroot','idwref'])
+    reals    = set(['sz','prttol','cvgtol','dwparm'])
+    bools    = set(['analys','clobbr','pures','saflg'])
+    strings  = set(['group','stsym'])
+    arrays   = set(['irreps','nflgdm','wstate'])
+
+    allowed_values = obj(
+        group = set(['c1','c2','ci','cs','c2v','c2h','d2','d2h','c4v','d4','d4h']),
+        stsym = set(['a','ag','au','ap','app','a','b','a1','a2','b1','b2','ag',
+                     'bu','bg','au','a','b1','b2','b3','ag','b1g','b2g','b3g',
+                     'au','b1u','b2u','b3u']),
+        )
+#end class DetGroup
+
+
+
 #class XGroup(KeywordSpecGroup):
 #    keywords = set([''])
 #    integers = set([''])
@@ -655,7 +680,7 @@ class GamessInput(SimulationInput,GIbase):
     all_groups = set(group_order)
 
     key_groups  = set(['contrl','system','guess','scf','mcscf','dft',
-                       'gugdia','drt','cidrt'])
+                       'gugdia','drt','cidrt','det'])
 
     card_groups = set()
     #card_groups = set(['ecp','data','mcp','gcilst','points','stone','efrag',
@@ -674,7 +699,8 @@ class GamessInput(SimulationInput,GIbase):
         dft    = DftGroup,
         gugdia = GugdiaGroup,
         drt    = DrtGroup,
-        cidrt  = CidrtGroup
+        cidrt  = CidrtGroup,
+        det    = DetGroup
         )
     keyspec_group_order = []
     for gname in group_order:
@@ -951,7 +977,6 @@ def generate_any_gamess_input(**kwargs):
 
     invalid_names = kwset-GamessInput.all_name_aliases
     if len(invalid_names)>0:
-        obj.class_error('this\nthat\nother')
         GamessInput.class_error('invalid group names or keywords encountered\n  invalid names/keywords provided: {0}\n  please check if these group names or keywords are actually valid GAMESS inputs\n  if so, unsupported groups can be generated by providing the keywords as a single argument:\n    generate_gamess_input(\n      ...,\n      group_name = obj(assign keywords),\n      ...,\n      )'.format(sorted(invalid_names)),'generate_gamess_input')
     #end if
 
@@ -1016,7 +1041,7 @@ def generate_any_gamess_input(**kwargs):
     # handle nexus specific input generation keywords
     #  ecp 287
     #  data 37
-    if pskw.system!=None:
+    if pskw.system!=None and not 'data' in gi:
         system = pskw.system
         if not 'contrl' in gi:
             gi.contrl = ContrlGroup()

nexus/library/qmcpack.py

@@ -206,10 +206,9 @@ class Qmcpack(Simulation):
             elif isinstance(sim,Convert4qmc):
 
                 res = QmcpackInput(result.location)
-                wfn = res.qmcsystem.wavefunction
                 qs  = input.simulation.qmcsystem
                 oldwfn = qs.wavefunction
-                newwfn = wfn.copy()
+                newwfn = res.qmcsystem.wavefunction
                 if 'jastrows' in newwfn:
                     del newwfn.jastrows
                 #end if

nexus/library/qmcpack_input.py

@@ -140,7 +140,8 @@ class collection(hidden):
         #self.add(value)
     #end def __setitem__
 
-    def add(self,element,strict=True):
+    def add(self,element,strict=True,key=None):
+        if key is None:
             identifier = element.identifier
             public = self.public()
             missing_identifier = False
@@ -171,6 +172,10 @@ class collection(hidden):
                 #    return False
                 ##end if
             #end if
+        #end if
+        if key in public:
+            self.error('attempted to add duplicate key to collection: {0}\n keys present: {1}'.format(key,sorted(public.keys())))
+        #end if
         public[key] = element
         self.hidden().order.append(key)
         return True
@@ -196,6 +201,14 @@ class collection(hidden):
         #end for
         return lst
     #end def list
+
+    def pairlist(self):
+        pairs = []
+        for key in self.hidden().order:
+            pairs.append((key,self[key]))
+        #end for
+        return pairs
+    #end def pairlist
 #end class collection
 
 
@@ -1359,7 +1372,7 @@ param = Param()
 
 
 class simulation(QIxml):
-    elements   = ['project','random','qmcsystem','particleset','wavefunction','hamiltonian','init','traces','qmc','loop']
+    elements   = ['project','random','include','qmcsystem','particleset','wavefunction','hamiltonian','init','traces','qmc','loop']
     write_types = obj(random=yesno)
 #end class simulation
 
@@ -1373,12 +1386,15 @@ class application(QIxml):
     attributes = ['name','role','class','version']
 #end class application
 
-
 class random(QIxml):
     attributes = ['seed','parallel']
     write_types= obj(parallel=truefalse)
 #end class random
 
+class include(QIxml):
+    attributes = ['href']
+#end def include
+
 
 class qmcsystem(QIxml):
     elements = ['simulationcell','particleset','wavefunction','hamiltonian']
@@ -1729,7 +1745,7 @@ class traces(QIxml):
     write_types = obj(write_=yesno,verbose=yesno,scalar=yesno,array=yesno,
                       scalar_defaults=yesno,array_defaults=yesno,
                       particle=yesno,particle_defaults=yesno)
-#end class
+#end class traces
 
 
 class loop(QIxml):
@@ -1822,7 +1838,7 @@ classes = [   #standard classes
     atomicbasisset,basisgroup,init,var,traces,scalar_traces,particle_traces,array_traces,
     reference_points,nearestneighbors,neighbor_trace,dm1b,
     coefficient,radfunc,spindensity,structurefactor,
-    sposet,bspline_builder,composite_builder,heg_builder
+    sposet,bspline_builder,composite_builder,heg_builder,include
     ]
 types = dict( #simple types and factories
     host           = param,
@@ -1854,7 +1870,8 @@ plurals = obj(
     neighbor_traces = 'neighbor_trace',
     sposet_builders = 'sposet_builder',
     sposets         = 'sposet',
-    radfuncs        = 'radfunc'
+    radfuncs        = 'radfunc',
+    qmcsystems      = 'qmcsystem'
     )
 plurals_inv = plurals.inverse()
 plural_names = set(plurals.keys())
@@ -2400,6 +2417,146 @@ class QmcpackInput(SimulationInput,Names):
         Param.metadata = None
     #end def include_xml
 
+    # This include functionality is currently not being used
+    # The rationale is essentially this:
+    #   -Having includes explicitly represented in the input file object
+    #    makes it very difficult to search for various components
+    #    i.e. where is the particleset? the wavefunction? a particular determinant?
+    #   -Difficulty in locating components makes it difficult to modify them
+    #   -Includes necessarily introduce greater variability in input file structure
+    #    and it is difficult to ensure every possible form is preserved each and 
+    #    every time a modification is made
+    #   -The only time it is undesirable to incorporate the contents of an
+    #    include directly into the input file object is if the data is large
+    #    e.g. for an xml wavefunction or pseudopotential.
+    #    In these cases, an external file should be provided that contains
+    #    only the large object in question (pseudo or wavefunction).
+    #    This is already done for pseudopotentials and should be done for 
+    #    wavefunctions, e.g. multideterminants.
+    #    Until that time, wavefunctions will be explicitly read into the full
+    #    input file.
+    def add_include(self,element_type,href,placement='on'):
+        # check the element type
+        elems = ['cell','ptcl','wfs','ham']
+        emap  = obj(
+            simulationcell = 'cell',
+            particleset    = 'ptcl',
+            wavefunction   = 'wfs',
+            hamiltonian    = 'ham'
+            )
+        if not element_type in elems:
+            self.error('cannot add include for element of type {0}\n  valid element types are {1}'.format(element_type,elems))
+        #end if
+        # check the requested placement
+        placements = ('before','on','after')
+        if not placement in placements:
+            self.error('cannot add include for element with placement {0}\n  valid placements are {1}'.format(placement,list(placements)))
+        #end if
+        # check that the base element is a simulation
+        base = self.get_base()
+        if not isinstance(base,simulation):
+            self.error('an include can only be added to simulation\n  attempted to add to {0}'.format(base.__class__.__name__))
+        #end if
+        # gather a list of current qmcsystems
+        if 'qmcsystem' in base:
+            qslist = [(0,base.qmcsystem)]
+            del base.qmcsystem
+        elif 'qmcsystems' in base:
+            qslist = base.qmcsystems.pairlist()
+            del base.qmcsystems
+        else:
+            qslist = []
+        #end if
+        # organize the elements of the qmcsystems
+        cur_elems = obj()
+        for elem in elems:
+            for place in placements:
+                cur_elems[elem,place] = None
+            #end for
+        #end for
+        for qskey,qs in qslist:
+            if isinstance(qs,include):
+                inc = qs
+                ekey = qskey.split('_')[1]
+                if not ekey in elems:
+                    self.error('encountered invalid element key: {0}\n  valid keys are: {1}'.format(ekey,elems))
+                #end if
+                if cur_elems[ekey,'on'] is None:
+                    cur_elems[ekey,'before'] = ekey,inc
+                else:
+                    cur_elems[ekey,'after' ] = ekey,inc
+                #end if
+            elif not isinstance(qs,qmcsystem):
+                self.error('expected qmcsystem element, got {0}'.format(qs.__class__.__name__))
+            else:
+                for elem in qmcsystem.elements:
+                    elem_plural = elem+'s'
+                    name  = None
+                    if elem in qs:
+                        name = elem
+                    elif elem_plural in qs:
+                        name = elem_plural
+                    #end if
+                    if name!=None:
+                        cur_elems[emap[elem],'on'] = name,qs[name]
+                        del qs[name]
+                    #end if
+                #end for
+                residue = qs.keys()
+                if len(residue)>0:
+                    self.error('extra keys found in qmcsystem: {0}'.format(sorted(residue)))
+                #end if
+            #end if
+        #end for
+        for elem in elems:
+            pbef = cur_elems[elem,'before']
+            pon  = cur_elems[elem,'on'    ]
+            paft = cur_elems[elem,'after' ] 
+            if pon is None:
+                if not pbef is None and paft is None:
+                    cur_elems[elem,'on'    ] = pbef
+                    cur_elems[elem,'before'] = None
+                elif not paft is None and pbef is None:
+                    cur_elems[elem,'on'    ] = paft
+                    cur_elems[elem,'after' ] = None
+                #end if
+            #end if
+        #end for
+        # insert the new include
+        inc_name  = 'include_'+element_type
+        inc_value = include(href=href)
+        cur_elems[element_type,placement] = inc_name,inc_value
+        # create a collection of qmcsystems
+        qmcsystems = collection()
+        qskey = ''
+        qs    = qmcsystem()
+        for elem in elems:
+            for place in placements:
+                cur_elem = cur_elems[elem,place]
+                if cur_elem!=None:
+                    name,value = cur_elem
+                    if isinstance(value,include):
+                        if len(qskey)>0:
+                            qmcsystems.add(qs,key=qskey)
+                            qskey = ''
+                            qs    = qmcsystem()
+                        #end if
+                        qmcsystems.add(value,key=name)
+                    else:
+                        qskey += elem[0]
+                        qs[name] = value
+                    #end if
+                #end if
+            #end for
+        #end for
+        if len(qskey)>0:
+            qmcsystems.add(qs,key=qskey)
+        #end if
+        # attach the collection to the input file
+        base.qmcsystems = qmcsystems
+    #end def add_include
+
+
     def get_output_info(self,*requests):
         project = self.simulation.project
         prefix = project.id