Nexus: First step to ridding us of Particles

nexus/nexus/gamess.py

@@ -154,7 +154,7 @@ def incorporate_result(self,result_name,result,sim):
                     self.block()
                 #end if
                 guess_inputs = obj()
-                ecounts = self.system.particles.electron_counts()
+                ecounts = self.system.n_up, self.system.n_down
                 orbs = result.orbitals
                 order_map = obj(up='iorder',down='jorder')
                 nelec_map = obj(up=ecounts[0],down=ecounts[1])

nexus/nexus/physical_system.py

@@ -634,6 +634,56 @@ def kf_rpa(self):
       kfs = [(3*nelec*kvol1/(4*np.pi))**(1./3) for nelec in nelecs]
       return np.array(kfs)
     #end def kf_rpa
+
+
+    @property
+    def n_elec(self):
+        ions = self.structure.elem.tolist()
+        tot_charge = 0
+        for ion in ions:
+            if hasattr(self, "valency"):
+                if ion in self.valency:
+                    tot_charge += self.valency[ion]
+                else:
+                    _, element = Elements.is_element(ion, return_element=True)
+                    tot_charge += element.atomic_number
+            else:
+                _, element = Elements.is_element(ion, return_element=True)
+                tot_charge += element.atomic_number
+
+        return tot_charge - self.net_charge
+
+    @property
+    def n_up(self):
+        return (self.n_elec + self.net_spin) // 2
+
+    @property
+    def n_down(self):
+        return (self.n_elec - self.net_spin) // 2
+
+    @property
+    def n_species(self):
+        return len(set(self.structure.elem))
+
+    @property
+    def n_ions(self):
+        return len(self.structure.elem)
+
+    @property
+    def ion_labels(self):
+        return set(self.structure.elem)
+
+    @property
+    def Zeff(self):
+        if hasattr(self, "valency"):
+            return self.valency
+
+        Zeff = {}
+        for ion in self.ion_labels:
+            _, element = Elements.is_element(ion, return_element=True)
+            Zeff[ion] = element.atomic_number
+
+        return Zeff
 #end class PhysicalSystem
 
 

nexus/nexus/pwscf_input.py

@@ -1675,17 +1675,17 @@ def incorporate_system(self,system,elem_order=None):
         system.check_folded_system()
         system.update_particles()
         system.change_units('B')
-        p  = system.particles
         s  = system.structure
         nc = system.net_charge
         ns = system.net_spin
 
-        nup = p.up_electron.count
-        ndn = p.down_electron.count
+        nup = system.n_up
+        ndn = system.n_down
 
         self.system.ibrav        = 0
 #        self.system['celldm(1)'] = 1.0e0
-        nions,nspecies = p.count_ions(species=True)
+        nions = system.n_ions
+        nspecies = system.n_species
         self.system.nat          = nions
         self.system.ntyp         = nspecies
         self.system.tot_charge   = nc
@@ -1717,19 +1717,19 @@ def incorporate_system(self,system,elem_order=None):
             #end if
         #end if
 
-        atoms = p.get_ions()
         if 'masses' not in self.atomic_species:
             self.atomic_species.masses = obj()
         #end if
-        for name,a in atoms.items():
-            self.atomic_species.masses[name] = convert(a.mass,'me','amu')
+        for name in system.ion_labels:
+            is_elem, element = Elements.is_element(name, return_element=True)
+            self.atomic_species.masses[name] = element.atomic_weight
         #end for
         if elem_order is None:
-            self.atomic_species.atoms = list(sorted(atoms.keys()))
+            self.atomic_species.atoms = list(sorted(system.ion_labels))
         else:
-            if set(elem_order)!=set(atoms.keys()):
-                self.error('elem_order is missing some atomic species\natomic species present: {0}\nelem_order: {1}'.format(sorted(atoms.keys()),elem_order))
-            elif len(elem_order)!=len(atoms):
+            if set(elem_order)!=set(system.ion_labels):
+                self.error('elem_order is missing some atomic species\natomic species present: {0}\nelem_order: {1}'.format(sorted(system.ion_labels),elem_order))
+            elif len(elem_order)!=system.n_ions:
                 self.error('elem_order has repeated elements\nelem_order: {0}'.format(elem_order))
             #end if
             self.atomic_species.atoms = list(elem_order)
@@ -1739,7 +1739,8 @@ def incorporate_system(self,system,elem_order=None):
         pp = self.atomic_species.pseudopotentials
         for atom in self.atomic_species.atoms:
             if atom not in pp:
-                iselem,symbol = p.is_element(atom,symbol=True)
+                iselem,element = Elements.is_element(atom,return_element=True)
+                symbol = element.symbol
                 if iselem and symbol in pp:
                     pp[atom] = str(pp[symbol])
                 #end if
@@ -1770,17 +1771,17 @@ def incorporate_system_old(self,system,spin_polarized=None):
         system.check_folded_system()
         system.update_particles()
         system.change_units('B')
-        p  = system.particles
         s  = system.structure
         nc = system.net_charge
         ns = system.net_spin
 
-        nup = p.up_electron.count
-        ndn = p.down_electron.count
+        nup = system.n_up
+        ndn = system.n_down
 
         self.system.ibrav        = 0
 #        self.system['celldm(1)'] = 1.0e0
-        nions,nspecies = p.count_ions(species=True)
+        nions = system.n_ions
+        nspecies = system.n_species
         self.system.nat          = nions
         self.system.ntyp         = nspecies
         #self.system.nelec        = nup+ndn
@@ -1819,18 +1820,19 @@ def incorporate_system_old(self,system,spin_polarized=None):
             #end if
         #end if
 
-        atoms = p.get_ions()
         masses = obj()
-        for name,a in atoms.items():
-            masses[name] = convert(a.mass,'me','amu')
+        for name in system.ion_labels:
+            is_elem, element = Elements.is_element(name, return_element=True)
+            masses[name] = element.atomic_weight
         #end for
-        self.atomic_species.atoms  = list(sorted(atoms.keys()))
+        self.atomic_species.atoms  = list(sorted(system.ion_labels))
         self.atomic_species.masses = masses
         # set pseudopotentials for renamed atoms (e.g. Cu3 is same as Cu)
         pp = self.atomic_species.pseudopotentials
         for atom in self.atomic_species.atoms:
             if atom not in pp:
-                iselem,symbol = p.is_element(atom,symbol=True)
+                iselem,element = Elements.is_element(atom,return_element=True)
+                symbol = element.symbol
                 if iselem and symbol in pp:
                     pp[atom] = str(pp[symbol])
                 #end if
@@ -2265,7 +2267,7 @@ def generate_any_pwscf_input(**kwargs):
 
     # set nbnd using bandfac, if provided
     if nbnd is None and bandfac is not None:
-        nocc = max(system.particles.electron_counts())
+        nocc = max(system.n_up, system.n_down)
         pw.system.nbnd = int(np.ceil(nocc*bandfac))
     #end if
 

nexus/nexus/qmcpack.py

@@ -188,11 +188,11 @@ def unfolded_nelecs(self):
         Returns the number of electrons in the primitive cell
         '''
         if self.system.folded_system is None:
-            n_up = self.system.particles.up_electron.count
-            n_dn = self.system.particles.down_electron.count
+            n_up = self.system.n_up
+            n_dn = self.system.n_down
         else:
-            n_up = self.system.folded_system.particles.up_electron.count
-            n_dn = self.system.folded_system.particles.down_electron.count
+            n_up = self.system.folded_system.n_up
+            n_dn = self.system.folded_system.n_down
         #end if
         nelecs = n_up + n_dn
         return nelecs
@@ -463,8 +463,8 @@ def sum_charge_twists(self):
         '''
         Returns the net charge of a system with multiple twists (not averaged)
         '''
-        n_up = self.system.particles.up_electron.count
-        n_dn = self.system.particles.down_electron.count
+        n_up = self.system.n_up
+        n_dn = self.system.n_down
         n_total = n_up + n_dn
         nelecs_at_twist = self.nelecs_at_twist
         kweights = np.array(self.system.structure.kweights)
@@ -536,8 +536,8 @@ def write_gcta_report(self, locdir, fermi_level, scf_magnet = None):
             spin_sum_twists = self.sum_spin_twists()
             qmc_magnet = spin_sum_twists / nosym_kpoints
         #end if
-        n_up = self.system.particles.up_electron.count
-        n_dn = self.system.particles.down_electron.count
+        n_up = self.system.n_up
+        n_dn = self.system.n_down
         n_total = n_up + n_dn
         nelecs_at_twist = self.nelecs_at_twist
         fermi_level = np.array(fermi_level)