Merge main and drop .DS_Store

Author: lfierce3

DISCLAIMER

@@ -0,0 +1,10 @@
+Disclaimer
+
+This material was prepared as an account of work sponsored by an agency of the United States Government.  Neither the United States Government nor the United States Department of Energy, nor the Contractor, nor any or their employees, nor any jurisdiction or organization that has cooperated in the development of these materials, makes any warranty, express or implied, or assumes any legal liability or responsibility for the accuracy, completeness, or usefulness or any information, apparatus, product, software, or process disclosed, or represents that its use would not infringe privately owned rights.
+Reference herein to any specific commercial product, process, or service by trade name, trademark, manufacturer, or otherwise does not necessarily constitute or imply its endorsement, recommendation, or favoring by the United States Government or any agency thereof, or Battelle Memorial Institute. The views and opinions of authors expressed herein do not necessarily state or reflect those of the United States Government or any agency thereof.
+PACIFIC NORTHWEST NATIONAL LABORATORY
+operated by
+BATTELLE
+for the
+UNITED STATES DEPARTMENT OF ENERGY
+under Contract DE-AC05-76RL01830

src/part2pop.egg-info/SOURCES.txt

@@ -143,8 +143,6 @@ src/part2pop/analysis/population/factory/s_grid.py
 src/part2pop/analysis/population/factory/spec_mass_conc.py
 src/part2pop/analysis/population/factory/wvl_grid.py
 src/part2pop/data/__init__.py
-src/part2pop/data/__pycache__/__init__.cpython-311.pyc
-src/part2pop/data/__pycache__/__init__.cpython-312.pyc
 src/part2pop/data/species_data/aero_data.dat
 src/part2pop/data/species_data/freezing_data.dat
 src/part2pop/data/species_data/ri_water.csv

src/part2pop/aerosol_particle.py

@@ -49,7 +49,7 @@ def _equilibrate_h2o(
             RH=maxRH
 
         Ddry = self.get_Ddry()
-        Dwet = compute_Dwet(Ddry, self.get_tkappa(), RH, T, 
+        Dwet = compute_Dwet(Ddry, self.get_tkappa(), RH, T,
                      sigma_h2o=sigma_h2o, rho_h2o=rho_h2o, MW_h2o=MW_h2o)
         mass_h2o = compute_mass_h2o(Ddry,Dwet,rho_h2o=1000.)
         self.masses[self.idx_h2o()] = mass_h2o
@@ -65,14 +65,20 @@ def get_variable(self, varname, *kwargs):
         *kwargs : tuple
             Additional arguments forwarded to the underlying method.
         """
-        if varname == 'wet_diameter':
+        if varname == 'wet_diameter' or varname == 'Dwet':
             return self.get_Dwet(*kwargs)
-        elif varname == 'dry_diameter':
+        elif varname == 'dry_diameter' or varname == 'Ddry':
             return self.get_Ddry()
         elif varname == 'tkappa':
             return self.get_tkappa()
         elif varname == 'critical_supersaturation' or varname == 's_c':
             return self.get_critical_supersaturation(T, return_D_crit=False, sigma_h2o=0.072)
+        elif varname == 'vol_tot':
+            return self.get_vol_tot()
+        elif varname == 'vol_dry':
+            return self.get_vol_dry()
+        elif varname == 'concentrations':
+            return self.get_species_concs()
 
     def idx_h2o(self):
         return np.where([
@@ -81,13 +87,11 @@ def idx_h2o(self):
     def idx_dry(self):
         idx_all = np.arange(len(self.species))        
         idx_h2o = self.idx_h2o()
-        
+        spec_densities = self.get_spec_rhos()
         if idx_h2o == -1:
-            idx_not_h2o = idx_all[:-1]
-        elif idx_h2o >= 0:
-            idx_not_h2o = np.hstack([idx for idx in idx_all if idx != idx_h2o])
-        else:    
-            idx_not_h2o = np.hstack([idx_all[:idx_h2o],idx_all[idx_h2o:][1:]])
+            idx_not_h2o = np.hstack([idx for idx in idx_all[:-1] if idx != idx_h2o and spec_densities[idx]>0])
+        else:
+            idx_not_h2o = np.hstack([idx for idx in idx_all if idx != idx_h2o and spec_densities[idx]>0])
         return idx_not_h2o
 
     def idx_core(self,core_specs=['BC']):
@@ -177,14 +181,14 @@ def get_vks(self):
 
     def get_vol_tot(self):
         vks = self.get_vks()
-        vol_tot = np.sum(vks)
+        vol_tot = np.nansum(vks[self.idx_dry()]) + vks[self.idx_h2o()]
         return vol_tot
 
     def get_vol_dry(self):
         vks = self.get_vks()
         vol_dry = np.sum(vks[self.idx_dry()])
         return vol_dry
-
+        
     def get_vol_core(self):
         vks = self.get_vks()
         vol_core = np.sum(vks[self.idx_core()])
@@ -243,8 +247,7 @@ def get_tkappa(self):
         # compute effective kappa
         vks = self.get_vks()
         spec_kappas = self.get_spec_kappas()
-        idx_not_h2o, = np.where([one_spec.name.upper()!='H2O' for one_spec in self.species])
-        tkappa = np.sum(vks[idx_not_h2o]*spec_kappas[idx_not_h2o])/np.sum(vks[idx_not_h2o])
+        tkappa = np.sum(vks[self.idx_dry()]*spec_kappas[self.idx_dry()])/np.sum(vks[self.idx_dry()])
         return tkappa
 
     def get_shell_tkappa(self):
@@ -301,6 +304,12 @@ def get_critical_supersaturation(self, T, return_D_crit=False):
             return s_critical,D_critical
         else:
             return s_critical
+            
+    def get_species_concs(self):
+        water_volume = np.repeat(self.get_vol_tot() - self.get_vol_dry(), len(self.masses))
+        molec_masses = np.array([species.molar_mass for species in self.species])
+        concs = (self.masses/molec_masses)/water_volume
+        return concs
 
 
 # def make_particle(

src/part2pop/population/base.py

@@ -64,9 +64,11 @@ def add_particle(self, particle, part_id, num_conc):
             self.ids.append(part_id)
 
     def get_species_idx(self, spec_name):
-        idx, = np.where([
-            spec.name in spec_name for spec in self.species])
-        return idx[0]
+        names = [spec.name for spec in self.species]
+        try:
+            return np.where(np.array(names) == spec_name)[0][0]
+        except:
+            return None
 
     def _equilibrate_h2o(self,S,T,rho_h2o=1000., MW_h2o=18e-3):
         for (part_id,num_conc) in zip(self.ids,self.num_concs):
@@ -145,4 +147,11 @@ def reduce_mixing_state(self, mixing_state='part_res',
             mass_h2o = vol_h2o*rho_h2o
             particle.spec_masses[particle.idx_h2o()] = mass_h2o
             num_conc =self.num_conc[ii]
-            self.set_particle(particle, part_id, num_conc, suppress_warning=False)
+            self.set_particle(particle, part_id, num_conc, suppress_warning=False)
+            
+    def clone_detached(self):
+        """Return a copy that shares immutable data but has detached numeric arrays."""
+        return ParticlePopulation(
+            species=self.species, spec_masses=self.spec_masses.copy(),
+            num_concs=self.num_concs.copy(), ids=self.ids
+        )