Merge pull request #4787 from jtkrogel/nx_spinor_workflow

Nexus: enable driving spinor workflows

nexus/lib/nexus.py

@@ -50,6 +50,7 @@
 
 from qmcpack_converters import Pw2qmcpack , Pw2qmcpackInput , Pw2qmcpackAnalyzer , generate_pw2qmcpack_input , generate_pw2qmcpack
 from qmcpack_converters import Convert4qmc, Convert4qmcInput, Convert4qmcAnalyzer, generate_convert4qmc_input, generate_convert4qmc
+from qmcpack_converters import Convertpw4qmc, Convertpw4qmcInput, Convertpw4qmcAnalyzer, generate_convertpw4qmc_input, generate_convertpw4qmc
 from qmcpack_converters import PyscfToAfqmc, PyscfToAfqmcInput, PyscfToAfqmcAnalyzer, generate_pyscf_to_afqmc_input, generate_pyscf_to_afqmc
 
 from pwscf_postprocessors import PP      , PPInput      , PPAnalyzer      , generate_pp_input      , generate_pp

nexus/lib/qmcpack.py

@@ -39,7 +39,7 @@
 from qmcpack_input import generate_opt,generate_opts
 from qmcpack_input import check_excitation_type
 from qmcpack_analyzer import QmcpackAnalyzer
-from qmcpack_converters import Pw2qmcpack,Convert4qmc,PyscfToAfqmc
+from qmcpack_converters import Pw2qmcpack,Convert4qmc,Convertpw4qmc,PyscfToAfqmc
 from debug import ci,ls,gs
 from developer import unavailable
 from nexus_base import nexus_core
@@ -174,7 +174,7 @@ def incorporate_result(self,result_name,result,sim):
         input = self.input
         system = self.system
         if result_name=='orbitals':
-            if isinstance(sim,Pw2qmcpack):
+            if isinstance(sim,Pw2qmcpack) or isinstance(sim,Convertpw4qmc):
 
                 h5file = result.h5file
 
@@ -283,6 +283,18 @@ def incorporate_result(self,result_name,result,sim):
                 opt = QmcpackInput(opt_file)
                 wavefunction = input.get('wavefunction')
                 optwf = opt.qmcsystem.wavefunction
+                # handle spinor case
+                spinor = input.get('spinor')
+                if spinor is not None and spinor:
+                    # remove u-d term from optmized jastrow
+                    J2 = optwf.get('J2')
+                    if J2 is not None:
+                        corr = J2.get('correlation')
+                        if 'ud' in corr:
+                            del corr.ud
+                        #end if
+                    #end if
+                #end if
                 def process_jastrow(wf):                
                     if 'jastrow' in wf:
                         js = [wf.jastrow]

nexus/lib/qmcpack_converters.py

@@ -746,7 +746,6 @@ def __init__(self,*args,**kwargs):
         self.input_code = None
     #end def __init__
 
-
     def set_app_name(self,app_name):
         self.app_name = app_name
         self.input.set_app_name(app_name)
@@ -927,6 +926,170 @@ def generate_convert4qmc(**kwargs):
 
 
 
+class Convertpw4qmcInput(SimulationInput):
+    def __init__(self,data_file=None):
+        self.data_file=data_file
+    #end def __init__
+
+    def read(self, filepath):
+        None
+    #end def read
+
+    def write(self, filepath):
+        None
+
+#end class Convertpw4qmcInput
+
+def generate_convertpw4qmc_input(**kwargs):
+    return Convertpw4qmcInput(**kwargs)
+#end def genreate_convertpw4qmc_input
+
+class Convertpw4qmcAnalyzer(SimulationAnalyzer):
+    def __init__(self,arg0):
+        if isinstance(arg0,Simulation):
+            self.infile = arg0.infile
+        else:
+            self.infile = arg0
+        #end if
+    #end def __init__
+
+    def analyze(self):
+        None
+    #end def analyze
+#end class Convertpw4qmcAnalyzer
+
+
+class Convertpw4qmc(Simulation):
+    input_type             = Convertpw4qmcInput
+    analyzer_type          = Convertpw4qmcAnalyzer
+    generic_identifier     = 'convertpw4qmc'
+    application            = 'convertpw4qmc'
+    application_properties = set(['serial'])
+    application_results    = set(['orbitals'])
+    renew_app_command      = True
+
+    def set_app_name(self,app_name):
+        self.app_name = app_name
+    #end def set_app_name
+
+    def propagate_identifier(self):
+        None
+    #end def propagate_identifier
+
+    def set_files(self):
+        # no input file
+        self.infile = None
+        if self.outfile is None:
+            self.outfile = self.identifier + self.outfile_extension
+        #end if
+        if self.errfile is None:
+            self.errfile = self.identifier + self.errfile_extension
+        #end if
+    #end def set_files
+
+    def check_result(self,result_name,sim):
+        return result_name=='orbitals'
+    #end def check_result
+
+    def get_result(self,result_name,sim):
+        result = obj()
+        input = self.input
+        if result_name=='orbitals':
+            wfn_file = 'eshdf.h5'
+            orbfile = os.path.join(self.locdir,wfn_file)
+            result.location = orbfile
+            result.h5file = orbfile
+        else:
+            self.error('ability to get result '+result_name+' has not been implemented')
+        #end if        
+        return result
+    #end def get_result
+
+    def get_output_files(self):
+        output_files = []
+        return output_files
+    #end def get_output_files
+
+    def app_command(self):
+        app_name  = self.app_name
+        data_file = self.input.data_file 
+        command = '{} {}'.format(app_name,data_file)
+        return command
+    #end def app_command
+
+    def incorporate_result(self,result_name,result,sim):
+        implemented = True
+        if result_name=='orbitals':
+            if isinstance(sim,Pwscf):
+                pwin = sim.input.control
+                pwprefix = 'pwscf'
+                p2prefix = 'pwscf'
+                pwoutdir = './'
+                p2outdir = './'
+                if 'prefix' in pwin:
+                    pwprefix = pwin.prefix
+                #end if
+                if 'outdir' in pwin:
+                    pwoutdir = pwin.outdir
+                #end if
+                if pwoutdir.startswith('./'):
+                    pwoutdir = pwoutdir[2:]
+                #end if
+                pwsdir = os.path.abspath(os.path.join(sim.locdir ,pwoutdir, pwprefix+'.save'))
+                charge_density_h5 = os.path.join(pwsdir, 'charge-density.hdf5')
+                data_file_schema  = os.path.join(pwsdir, 'data-file-schema.xml')
+                errors = False
+                if not os.path.exists(data_file_schema):
+                    self.error('to use orbitals, '+self.generic_identifier+' must have data-file-schema.xml file', exit=False)
+                    errors = True
+                #end if
+                if not os.path.exists(charge_density_h5):
+                    self.error('to use orbitals, '+self.generic_identifier+' must have charge-density.h5 file.\nNeed to rebuild QE with hdf5 support', exit=False)
+                    errors = True
+                #end if
+                if errors:
+                    self.error(self.generic_identifier+' cannot use orbitals from pwscf')
+                #end if
+                if self.input.data_file is None:
+                    self.input.data_file = data_file_schema
+            else:
+                implemented = False
+            #end if
+        else:
+            implemented = False
+        #end if
+        if not implemented:
+            self.error('ability to incorporate result "{0}" from {1} has not been implemented'.format(result_name,sim.__class__.__name__))
+        #end if                
+    #end def incorporate_result
+
+    def check_sim_status(self):
+        h5file   = os.path.join(self.locdir,'eshdf.h5')
+        must_exist = [h5file]
+
+        files_exist = True
+        for file in must_exist:
+            files_exist = files_exist and os.path.exists(file)
+        #end for
+        success = files_exist
+
+        self.finished = files_exist and self.job.finished
+    #end def check_sim_status
+#end class Convertpw4qmc
+
+
+
+def generate_convertpw4qmc(**kwargs):
+    sim_args,inp_args = Simulation.separate_inputs(kwargs)
+
+    if not 'input' in sim_args:
+        sim_args.input = generate_convertpw4qmc_input(**inp_args)
+    #end if
+    sim = Convertpw4qmc(**sim_args)
+
+    return sim
+#end def generate_convertpw4qmc
+
 
 
 class PyscfToAfqmcInput(SimulationInput):