nexus: enable cis and fci workflows for quantum package

nexus/library/machines.py

@@ -641,6 +641,13 @@ def total_days(self):
     #end def total_days
 
 
+    def clone(self):
+        job = self.copy()
+        job.set_id()
+        return job
+    #end def clone
+
+
     def split_nodes(self,n):
         run_options = self.run_options
         if not isinstance(n,int):
@@ -652,10 +659,8 @@ def split_nodes(self,n):
         if m.app_launcher=='srun':
             self.error('splitting jobs by nodes is not currently supported on machine "{0}" (SLURM)'.format(m.name))
         #end if
-        job1 = self.copy()
-        job2 = self.copy()
-        job1.set_id()
-        job2.set_id()
+        job1 = self.clone()
+        job2 = self.clone()
         job1.nodes = n
         job2.nodes = self.nodes - n
         m.process_job(job1)
@@ -2257,10 +2262,11 @@ def process_job_extra(self,job):
         #    self.error('threads must be 1,2,3,4,6, or 12 on Cooley\nyou provided: {0}'.format(job.threads))
         ##end if
 
-        job.run_options.add(
+        #job.run_options.add(
             #f   = '-f $COBALT_NODEFILE',
             #ppn = '-ppn {0}'.format(job.processes_per_node),
-            )
+            #)
+        return
     #end def process_job_extra
 
     def write_job_header(self,job):

nexus/library/quantum_package.py

@@ -35,6 +35,8 @@ class QuantumPackage(Simulation):
     application_properties = set(['serial','mpi'])
     application_results    = set([]) 
 
+    allow_overlapping_files = True
+
     qprc = None
 
     slave_partners = obj(
@@ -60,6 +62,11 @@ def restore_default_settings():
         QuantumPackage.qprc = None
     #end def restore_default_settings
 
+    def pre_init(self):
+        prefix = self.input.run_control.prefix
+        self.infile = prefix + self.infile_extension
+    #end def pre_init
+
 
     def post_init(self):
         qprc = QuantumPackage.qprc
@@ -70,6 +77,20 @@ def post_init(self):
     #end def post_init
 
 
+    def write_prep(self):
+        # write an ascii represenation of the input changes
+        infile = self.identifier+'.in'
+        infile = os.path.join(self.locdir,infile)
+        f = open(infile,'w')
+        s = self.input.delete_optional('structure',None)
+        f.write(str(self.input))
+        if s is not None:
+            self.input.structure = s
+        #end if
+        f.close()
+    #end def write_prep
+
+
     def check_result(self,result_name,sim):
         return False
     #end def check_result
@@ -111,9 +132,58 @@ def get_slave(self):
 
 
     def app_command(self):
-        run_type = self.input.run_control.run_type
+
+        # get run controls
+        input = self.input
+        rc = input.run_control
+
+        # make the basic app command, no splitting etc
+        run_type = rc.run_type
         app_command = self.app_name+' '+run_type+' '+self.infile
+
+        # prepare local vars in case splitting or other tricks are needed
+        fc = ''
         job = self.job
+
+        # add cis-loop runs if requested
+        if 'cis_loop' in rc:
+            nloop = 0
+            if isinstance(rc.cis_loop,bool) and rc.cis_loop:
+                nloop = 2
+            else:
+                nloop = rc.cis_loop
+            #end for
+            if nloop>0:
+                jloop = job.clone()
+                fc+='\n'
+                for n in range(nloop):
+                    jloop.app_command = self.app_name+' cis '+self.infile
+                    fc += jloop.run_command()+' >{0}_{1}.out 2>{0}_{1}.err\n'.format(self.identifier,n)
+                    jloop.app_command = self.app_name+' save_natorb '+self.infile
+                    fc += jloop.run_command()+'\n'
+                #end for
+                fc+='\n'
+                integrals = [
+                    'integrals_monoelec/disk_access_ao_one_integrals',
+                    'integrals_monoelec/disk_access_mo_one_integrals',
+                    'integrals_bielec/disk_access_ao_integrals',
+                    'integrals_bielec/disk_access_mo_integrals',
+                    ]
+                cl = ''
+                for integral in integrals:
+                    isec,ivar = integral.split('/')
+                    if input.present(ivar):
+                        val = input.delete(ivar)
+                        cl += 'echo "{0}" > {1}/{2}\n'.format(val,self.infile,integral)
+                    #end if
+                #end for
+                if len(cl)>0:
+                    fc+=cl+'\n'
+                #end if
+            #end if
+        #end if
+
+        # perform master-slave job splitting if necessary
         slave = self.get_slave()
         split_nodes  = job.nodes>1 and job.full_command is None
         split_nodes &= slave is not None
@@ -130,11 +200,21 @@ def app_command(self):
             job1,job2 = job.split_nodes(1)
             job1.app_command = app_command
             job2.app_command = slave_command
-            s  = ''
-            s += job1.run_command()+' >{0} 2>{1}&\n'.format(outfile,errfile)
-            s += 'sleep {0}\n'.format(self.input.run_control.sleep)
-            s += job2.run_command()+' >{0} 2>{1}\n'.format(slave_outfile,slave_errfile)
-            job.full_command = s
+            fc += job1.run_command()+' >{0} 2>{1}&\n'.format(outfile,errfile)
+            fc += 'sleep {0}\n'.format(self.input.run_control.sleep)
+            fc += job2.run_command()+' >{0} 2>{1}\n'.format(slave_outfile,slave_errfile)
+
+            if 'davidson' in slave and not input.present('distributed_davidson'):
+                input.set(distributed_davidson=True)
+            #end if
+        elif len(fc)>0:
+            job.divert_out_err()
+            job.app_command = app_command
+            fc += job.run_command()+' >{0} 2>{1}\n'.format(self.outfile,self.errfile)
+        #end if
+
+        if len(fc)>0:
+            job.full_command = fc
         #end if
 
         return app_command

nexus/library/quantum_package_input.py

@@ -356,6 +356,12 @@ class QuantumPackageInput(SimulationInput):
         fci_zmq
         '''.split())
 
+    integral_write_allowed = set('''
+        SCF
+        cis
+        fci_zmq
+        '''.split())
+
 
     def __init__(self,filepath=None):
         self.structure   = None
@@ -366,6 +372,55 @@ def __init__(self,filepath=None):
     #end def __init__
 
 
+    def present(self,name):
+        if name not in known_variables:
+            self.error('attempted to check presence of unknown variable "{0}"valid options are: {1}'.format(name,sorted(known_variables)))
+        #end if
+        secname = variable_section[name]
+        return secname in self and name in self[secname]
+    #end def present
+
+
+    def set(self,**kwargs):
+        for name,value in kwargs.iteritems():
+            if name not in known_variables:
+                self.error('cannot set variable\nattempted to set unknown variable "{0}"\nwith value: {1}\nvalid options are: {2}'.format(name,value,sorted(known_variables)))
+            #end if
+            secname = variable_section[name]
+            if secname not in self:
+                self[secname] = Section()
+            #end if
+            self[secname][name] = value
+        #end for
+    #end def set
+
+
+    def get(self,name):
+        if name not in known_variables:
+            self.error('cannot get variable\nattempted to get unknown variable "{0}"\nvalid options are: {1}'.format(name,sorted(known_variables)))
+        #end if
+        value = None
+        secname = variable_section[name]
+        if secname in self and name in self[secname]:
+            value = self[secname][name]
+        #end if
+        return value
+    #end def get
+
+
+    def delete(self,name):
+        if name not in known_variables:
+            self.error('cannot get variable\nattempted to get unknown variable "{0}"\nvalid options are: {1}'.format(name,sorted(known_variables)))
+        #end if
+        value = None
+        secname = variable_section[name]
+        if secname in self and name in self[secname]:
+            value = self[secname].delete(name)
+        #end if
+        return value
+    #end def delete
+
+
     def extract_added_keys(self):
         extra = obj()
         extra.move_from(self,QuantumPackageInput.added_keys)
@@ -410,7 +465,11 @@ def write(self,filepath=None):
         if filepath is None:
             return str(self)
         #end if
+
+        # get the ezfio path
         epath = filepath.rstrip('/')
+
+        # check that write can occur
         if not epath.endswith('.ezfio'):
             self.error('cannot write input\nprovided path does not end in an ezfio directory\ndirectory must end with .ezfio\npath provided:  {0}'.format(epath))
         #end if
@@ -421,6 +480,8 @@ def write(self,filepath=None):
         if not os.path.exists(path):
             self.error('cannot write input\nattempted to write ezfio directory "{0}" at non-existent destination path\ndestination path: {1}'.format(edir,path))
         #end if
+
+        # if there is no ezfio directory, initialize one
         if not os.path.exists(epath):
             if self.structure is None:
                 self.error('cannot write input\nstructure is missing\ninput path provided: {0}'.format(epath))
@@ -444,6 +505,8 @@ def write(self,filepath=None):
             execute('qp_edit -c '+edir)
             os.chdir(cwd)
         #end if
+
+        # write inputs into the ezfio directory/file tree
         extra = self.extract_added_keys()
         for secname,sec in self.iteritems():
             secpath = os.path.join(epath,secname)
@@ -456,6 +519,18 @@ def write(self,filepath=None):
             #end for
         #end for
         self.restore_added_keys(extra)
+
+        # take other steps that modify the input, as requested
+        if 'run_control' in self:
+            rc = self.run_control
+            if 'frozen_core' in rc and rc.frozen_core:
+                cwd = os.getcwd()
+                os.chdir(path)
+                execute('qp_set_frozen_core.py '+edir)
+                os.chdir(cwd)
+            #end if
+        #end if
+
         return ''
     #end def write
 
@@ -540,7 +615,10 @@ def is_valid(self):
 
 
 run_inputs = set('''
+    prefix
     run_type
+    frozen_core
+    cis_loop
     sleep
     slave
     postprocess
@@ -554,7 +632,10 @@ def is_valid(self):
 added_inputs = run_inputs | gen_inputs
 added_types = obj(
     # run inputs
+    prefix         = str,
     run_type       = str,
+    frozen_core    = bool,
+    cis_loop       = (bool,int),
     sleep          = (int,float),
     slave          = str,
     postprocess    = (tuple,list),
@@ -566,6 +647,7 @@ def is_valid(self):
     )
 added_required = set('''
     system
+    prefix
     sleep
     '''.split())
 qp_defaults_version = 'v1'
@@ -610,9 +692,6 @@ def generate_quantum_package_input(**kwargs):
         QuantumPackageInput.class_error('cannot generate input\nrequested invalid default set\ndefault set requested: {0}\nvalid options are: {1}'.format(kw.defaults,sorted(qp_defaults.keys())))
     #end if
     kw.set_optional(**qp_defaults[kw.defaults])
-    if kw.save_integrals:
-        kw.set_optional(**save_ints_defaults)
-    #end if
 
     # check for required variables
     req_missing = kw.check_required(added_required,exit=False)
@@ -640,6 +719,10 @@ def generate_quantum_package_input(**kwargs):
     # separate generation inputs from input file variables
     gen_kw = kw.extract_optional(gen_inputs)
 
+    if gen_kw.save_integrals and run_kw.run_type in QuantumPackageInput.integral_write_allowed:
+        kw.set_optional(**save_ints_defaults)
+    #end if
+
     # partition inputs into sections and variables
     sections = obj()
     variables = obj()

nexus/library/simulation.py

@@ -412,6 +412,7 @@ def __init__(self,**kwargs):
                              # accessed by dependents when calling get_dependencies
 
         self.set(**kwargs)
+        self.pre_init()
         self.set_directories()
         self.set_files()
         self.propagate_identifier()
@@ -610,6 +611,10 @@ def propagate_identifier(self):
         None
     #end def propagate_identifier
 
+    def pre_init(self):
+        None
+    #end def pre_init
+
     def post_init(self):
         None
     #end def post_init
@@ -947,7 +952,7 @@ def write_inputs(self,save_image=True):
         self.enter(self.locdir,False,self.simid)
         self.log('writing input files'+self.idstr(),n=3)
         self.write_prep()
-        if self.infile!=None:
+        if self.infile is not None:
             infile = os.path.join(self.locdir,self.infile)
             self.input.write(infile)
         #end if