PetThermoTools 0.2.37__tar.gz → 0.2.39__tar.gz

{PetThermoTools-0.2.37/src/PetThermoTools.egg-info → PetThermoTools-0.2.39}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: PetThermoTools
-Version: 0.2.37
+Version: 0.2.39
 Summary: PetThermoTools
 Home-page: https://github.com/gleesonm1/PetThermoTools
 Author: Matthew Gleeson

{PetThermoTools-0.2.37 → PetThermoTools-0.2.39}/src/PetThermoTools/GenFuncs.py

@@ -46,6 +46,31 @@ Names_MM = {'liq1': '_Liq',
             'spn1': '_Sp',
             'spn2': '_Sp2'}
 
+def label_results(Result,label):
+    Results = Result.copy()
+    new_out = {}
+    if  label == "CO2":
+        for r in Results:
+            new_out['CO2 = ' + str(Results[r]['Input']['comp']['CO2_Liq']) + ' wt%'] = Results[r].copy()
+        new_out = dict(sorted(new_out.items(), key=lambda x: float(x[0].split('=')[1].split(' ')[1])))
+    elif label == "pressure" or label == "P" or label == "P_bar":
+        for r in Results:
+            new_out['P = ' + str(Results[r]['Input']['P_bar']) + ' bars'] = Results[r].copy()
+        new_out = dict(sorted(new_out.items(), key=lambda x: float(x[0].split('=')[1].split(' ')[1])))
+    elif label == "fO2":
+        for r in Results:
+            new_out['fO2 = ' + Results[r]['Input']['fO2_buffer'] + ' ' + str(round(Results[r]['Input']['fO2_offset'],2))] = Results[r].copy()
+        new_out = dict(sorted(new_out.items(), key=lambda x: float(x[0].split('=')[1].split(' ')[2])))
+    elif label == 'H2O':
+        for r in Results:
+            new_out['H2O = ' + str(Results[r]['Input']['comp']['H2O_Liq']) + ' wt%'] = Results[r].copy()
+        new_out = dict(sorted(new_out.items(), key=lambda x: float(x[0].split('=')[1].split(' ')[1])))
+    
+    if len(new_out) == 0:
+        new_out = Results.copy()
+    
+    return new_out
+
 def supCalc(Model = "MELTSv1.0.2", bulk = None, phase = None, T_C = None, P_bar = None,
              Fe3Fet_Liq = None, H2O_Liq = None, CO2_Liq = None, fO2_buffer = None, fO2_offset = None, 
              melts = None):

{PetThermoTools-0.2.37 → PetThermoTools-0.2.39}/src/PetThermoTools/Melting.py

@@ -49,14 +49,15 @@ def AdiabaticDecompressionMelting(cores = multiprocessing.cpu_count(),
                                   P_path_bar = None, Frac = False, prop = None, 
                                   fO2_buffer = None, fO2_offset = None, Fe3Fet = None, MELTS_filter = True):
     
-    try:
-        import pyMelt as m
-        Lithologies = {'KLB-1': m.lithologies.matthews.klb1(),
-                    'KG1': m.lithologies.matthews.kg1(),
-                    'G2': m.lithologies.matthews.eclogite(),
-                    'hz': m.lithologies.shorttle.harzburgite()}
-    except ImportError:
-        raise RuntimeError('You havent installed pyMelt or there is an error when importing pyMelt. pyMelt is currently required to estimate the starting point for the melting calculations.')
+    if Tp_Method == "pyMelt":
+        try:
+            import pyMelt as m
+            Lithologies = {'KLB-1': m.lithologies.matthews.klb1(),
+                        'KG1': m.lithologies.matthews.kg1(),
+                        'G2': m.lithologies.matthews.eclogite(),
+                        'hz': m.lithologies.shorttle.harzburgite()}
+        except ImportError:
+            raise RuntimeError('You havent installed pyMelt or there is an error when importing pyMelt. pyMelt is currently required to estimate the starting point for the melting calculations.')
 
     if bulk is not None and comp_lith_1 is None:
         comp_lith_1 = bulk
@@ -155,7 +156,9 @@ def AdiabaticDecompressionMelting(cores = multiprocessing.cpu_count(),
 
     return Results
 
-def AdiabaticMelt(q, index, *, Model = None, comp_1 = None, comp_2 = None, comp_3 = None, Tp_C = None, P_start_bar = None, P_end_bar = None, dp_bar = None, P_path_bar = None, Frac = None, fO2_buffer = None, fO2_offset = None, prop = None):
+def AdiabaticMelt(q, index, *, Model = None, comp_1 = None, comp_2 = None, comp_3 = None, 
+                  Tp_C = None, P_start_bar = None, P_end_bar = None, dp_bar = None, P_path_bar = None, 
+                  Frac = None, fO2_buffer = None, fO2_offset = None, prop = None):
     '''
     Melting calculations to be performed in parallel.
 
@@ -163,21 +166,16 @@ def AdiabaticMelt(q, index, *, Model = None, comp_1 = None, comp_2 = None, comp_
     Results = {}
     if "MELTS" in Model:
         try:
-            Results = AdiabaticDecompressionMelting_MELTS(Model = Model, comp = comp_1, Tp_C = Tp_C, P_path_bar = P_path_bar, P_start_bar = P_start_bar, P_end_bar = P_end_bar, dp_bar = dp_bar, fO2_buffer = fO2_buffer, fO2_offset = fO2_offset)
+            Results = AdiabaticDecompressionMelting_MELTS(Model = Model, comp = comp_1, Tp_C = Tp_C, 
+                                                          P_path_bar = P_path_bar, P_start_bar = P_start_bar, P_end_bar = P_end_bar, dp_bar = dp_bar, 
+                                                          fO2_buffer = fO2_buffer, fO2_offset = fO2_offset)
             q.put([Results, index])
         except:
             q.put([])
 
         return
-
-    if Model == "Holland":
-        # import pyMAGEMINcalc as MM
-        # Results = MM.AdiabaticDecompressionMelting(comp = comp_1, T_p_C = Tp_C, P_start_kbar = P_start_bar/1000, P_end_kbar = P_end_bar/1000, dp_kbar = dp_bar/1000, Frac = 0)
-        print('Note that the ability to use MAGEMin to performed adiabatic decompression melting in PetThermoTools has been temporarily disabled. The underlying issue will be fixed soon and this funciton will once again become available.')
-        q.put([Results, index])
-        return
     
-    if Model == "pyMelt":
+    elif Model == "pyMelt":
         try:
             import pyMelt as m
             Lithologies = {'KLB-1': m.lithologies.matthews.klb1(),
@@ -239,5 +237,44 @@ def AdiabaticMelt(q, index, *, Model = None, comp_1 = None, comp_2 = None, comp_
         
         q.put([Results, index])
         return
+
+    else:
+        # import pyMAGEMINcalc as MM
+        # Results = MM.AdiabaticDecompressionMelting(comp = comp_1, T_p_C = Tp_C, P_start_kbar = P_start_bar/1000, P_end_kbar = P_end_bar/1000, dp_kbar = dp_bar/1000, Frac = 0)
+        # print('Note that the ability to use MAGEMin to performed adiabatic decompression melting in PetThermoTools has been temporarily disabled. The underlying issue will be fixed soon and this funciton will once again become available.')
+        
+        try:
+            import pyMelt as m
+            Lithologies = {'KLB-1': m.lithologies.matthews.klb1(),
+                        'KG1': m.lithologies.matthews.kg1(),
+                        'G2': m.lithologies.matthews.eclogite(),
+                        'hz': m.lithologies.shorttle.harzburgite()}
+        except ImportError:
+            raise RuntimeError('You havent installed pyMelt or there is an error when importing pyMelt. pyMelt is currently required to estimate the starting point for the melting calculations.')
+
+        lz = m.lithologies.matthews.klb1()
+        mantle = m.mantle([lz], [1], ['Lz'])
+        T_start_C = mantle.adiabat(P_start_bar/10000.0, Tp_C)
+        
+        from juliacall import Main as jl, convert as jlconvert
+
+        jl.seval("using MAGEMinCalc")
+
+        comp_1['O'] = comp_1['Fe3Fet_Liq']*(((159.59/2)/71.844)*comp_1['FeOt_Liq'] - comp_1['FeOt_Liq'])
+
+        if type(comp_1) == dict:
+            comp_julia = jl.seval("Dict")(comp_1) 
+        else:
+            comp_new = comp_1.loc[i].to_dict()
+            comp_julia = jl.seval("Dict")(comp_new)
+
+        Output_jl = jl.MAGEMinCalc.AdiabaticDecompressionMelting(comp = comp_julia, P_start_kbar = P_start_bar/1000.0, 
+                                                              P_end_kbar = P_end_bar/1000.0, dp_kbar = dp_bar/1000.0,
+                                                              T_start_C = T_start_C, fo2_buffer = fO2_buffer, fo2_offset = fO2_offset, Model = Model)
+        Results = dict(Output_jl)
+        # Results = stich(Results, Model = Model)
+        
+        q.put([Results, index])
+        return
         
 

{PetThermoTools-0.2.37 → PetThermoTools-0.2.39}/src/PetThermoTools/Path.py

@@ -117,10 +117,8 @@ def multi_path(cores = None, Model = None, bulk = None, comp = None, Frac_solid
         Dictionary where each entry represents the results of a single calculation. Within the dictionary each single calculation is reported as a series of pandas DataFrames, displaying the composition and thermodynamic properties of each phase.
 
     '''
-    try:
-        from meltsdynamic import MELTSdynamic
-    except:
-        Warning('alphaMELTS for Python files are not on the python path. \n Please add these files to the path running \n import sys \n sys.path.append(r"insert_your_path_to_melts_here") \n You are looking for the location of the meltsdynamic.py file')
+    if timeout is None:
+        timeout = 180
 
     timeout_main = timeout
 
@@ -137,6 +135,12 @@ def multi_path(cores = None, Model = None, bulk = None, comp = None, Frac_solid
     if Model is None:
         Model == "MELTSv1.0.2"
 
+    if "MELTS" in Model:
+        try:
+            from meltsdynamic import MELTSdynamic
+        except:
+            Warning('alphaMELTS for Python files are not on the python path. \n Please add these files to the path running \n import sys \n sys.path.append(r"insert_your_path_to_melts_here") \n You are looking for the location of the meltsdynamic.py file')
+
     # if comp is entered as a pandas series, it must first be converted to a dict
     if type(comp) == pd.core.series.Series:
         comp = comp.to_dict()
@@ -357,89 +361,6 @@ def multi_path(cores = None, Model = None, bulk = None, comp = None, Frac_solid
         results = combined_results
 
         Results = stich(Res=results, multi=True, Model=Model, Frac_fluid = Frac_fluid, Frac_solid = Frac_solid)
-
-        # for j in tqdm(range(len(Group))):
-        #     ps = []
-
-        #     if Print_suppress is None:
-        #         print("Running " + Model + " calculations " + str(int(cores*j)) + " to " + str(int(cores*j) + Group[j] - 1) + " ...", end = "", flush = True)
-        #         s = time.time()
-
-        #     for i in range(int(cores*j), int(cores*j + Group[j])):
-        #         if type(comp) == dict:
-        #             p = Process(target = path, args = (q, i),
-        #                         kwargs = {'Model': Model, 'comp': comp, 'Frac_solid': Frac_solid, 'Frac_fluid': Frac_fluid,
-        #                                 'T_C': T_C[i], 'T_path_C': T_path_C[i], 'T_start_C': T_start_C[i], 'T_end_C': T_end_C[i], 'dt_C': dt_C[i],
-        #                                 'P_bar': P_bar[i], 'P_path_bar': P_path_bar[i], 'P_start_bar': P_start_bar[i], 'P_end_bar': P_end_bar[i], 'dp_bar': dp_bar[i],
-        #                                 'isenthalpic': isenthalpic, 'isentropic': isentropic, 'isochoric': isochoric, 'find_liquidus': find_liquidus,
-        #                                 'fO2_buffer': fO2_buffer, 'fO2_offset': fO2_offset[i], 'fluid_sat': fluid_sat, 'Crystallinity_limit': Crystallinity_limit,
-        #                                 'Suppress': Suppress, 'Suppress_except': Suppress_except})
-        #         else:
-        #             p = Process(target = path, args = (q, i),
-        #                         kwargs = {'Model': Model, 'comp': comp.loc[i].to_dict(), 'Frac_solid': Frac_solid, 'Frac_fluid': Frac_fluid,
-        #                                 'T_C': T_C[i], 'T_path_C': T_path_C[i], 'T_start_C': T_start_C[i], 'T_end_C': T_end_C[i], 'dt_C': dt_C[i],
-        #                                 'P_bar': P_bar[i], 'P_path_bar': P_path_bar[i], 'P_start_bar': P_start_bar[i], 'P_end_bar': P_end_bar[i], 'dp_bar': dp_bar[i],
-        #                                 'isenthalpic': isenthalpic, 'isentropic': isentropic, 'isochoric': isochoric, 'find_liquidus': find_liquidus,
-        #                                 'fO2_buffer': fO2_buffer, 'fO2_offset': fO2_offset[i], 'fluid_sat': fluid_sat, 'Crystallinity_limit': Crystallinity_limit,
-        #                                 'Suppress': Suppress, 'Suppress_except': Suppress_except})
-
-        #         ps.append(p)
-        #         p.start()
-
-        #     if timeout is None:
-        #         TIMEOUT = 240
-        #     else:
-        #         TIMEOUT = timeout
-
-        #     start = time.time()
-        #     first = True
-        #     for p in ps:
-        #         if time.time() - start < TIMEOUT - 10:
-        #             try:
-        #                 ret = q.get(timeout = TIMEOUT - (time.time()-start) + 10)
-        #             except:
-        #                 ret = []
-        #         else:
-        #             if first == True:
-        #                 print('Timeout Reached - this likely indicates the calculation failed. \n You can try increasing the timeout limit using the "timeout" kwarg.')
-        #                 first = False
-        #             try:
-        #                 ret = q.get(timeout = 10)
-        #             except:
-        #                 ret = []
-
-        #         qs.append(ret)
-
-        #     TIMEOUT = 5
-        #     start = time.time()
-        #     for p in ps:
-        #         if p.is_alive():
-        #             while time.time() - start <= TIMEOUT:
-        #                 if not p.is_alive():
-        #                     p.join()
-        #                     p.terminate()
-        #                     break
-        #                 time.sleep(.1)
-        #             else:
-        #                 p.terminate()
-        #                 p.join(5)
-        #         else:
-        #             p.join()
-        #             p.terminate()
-
-        #     if Print_suppress is None:
-        #         print(" Complete (time taken = " + str(round(time.time() - s,2)) + " seconds)", end = "\n", flush = True)
-
-
-        # Results = {}
-        # Out = {}
-        # for i in range(len(qs)):
-        #     if len(qs[i]) > 0:
-        #         Res, index = qs[i]
-        #         Results['index = ' + str(index)] = Res
-
-        #if "MELTS" in Model:
-        # Results = stich(Results, multi = True, Model = Model, Frac_fluid = Frac_fluid, Frac_solid = Frac_solid)
         
         for r in Results:
             i = int(r.split('=')[1].strip())
@@ -464,31 +385,6 @@ def multi_path(cores = None, Model = None, bulk = None, comp = None, Frac_solid
         else:
             return Results
 
-def label_results(Result,label):
-    Results = Result.copy()
-    new_out = {}
-    if  label == "CO2":
-        for r in Results:
-            new_out['CO2 = ' + str(Results[r]['Input']['comp']['CO2_Liq']) + ' wt%'] = Results[r].copy()
-        new_out = dict(sorted(new_out.items(), key=lambda x: float(x[0].split('=')[1].split(' ')[1])))
-    elif label == "pressure" or label == "P" or label == "P_bar":
-        for r in Results:
-            new_out['P = ' + str(Results[r]['Input']['P_bar']) + ' bars'] = Results[r].copy()
-        new_out = dict(sorted(new_out.items(), key=lambda x: float(x[0].split('=')[1].split(' ')[1])))
-    elif label == "fO2":
-        for r in Results:
-            new_out['fO2 = ' + Results[r]['Input']['fO2_buffer'] + ' ' + str(round(Results[r]['Input']['fO2_offset'],2))] = Results[r].copy()
-        new_out = dict(sorted(new_out.items(), key=lambda x: float(x[0].split('=')[1].split(' ')[2])))
-    elif label == 'H2O':
-        for r in Results:
-            new_out['H2O = ' + str(Results[r]['Input']['comp']['H2O_Liq']) + ' wt%'] = Results[r].copy()
-        new_out = dict(sorted(new_out.items(), key=lambda x: float(x[0].split('=')[1].split(' ')[1])))
-    
-    if len(new_out) == 0:
-        new_out = Results.copy()
-    
-    return new_out
-
 def path_multi(q, index, *, Model = None, comp = None, Frac_solid = None, Frac_fluid = None,
             T_C = None, T_path_C = None, T_start_C = None, T_end_C = None, dt_C = None,
             P_bar = None, P_path_bar = None, P_start_bar = None, P_end_bar = None, dp_bar = None,

{PetThermoTools-0.2.37 → PetThermoTools-0.2.39}/src/PetThermoTools/Plotting.py

@@ -359,7 +359,7 @@ def residualT_plot(Results = None, P_bar = None, phases = None, H2O_Liq = None,
                         a[i][j].set_zlim([0,50])
 
 def phase_plot(Results = None, y_axis = None, x_axis = None, 
-               phases = ['Liq','Ol', 'Opx', 'Cpx', 'Sp', 'Grt'], cmap = "Reds",
+               phases = ['Liq', 'Ol', 'Opx', 'Cpx', 'Sp', 'Grt'], cmap = "Reds",
                title = None, figsize = None):
     
     if type(Results) != list:
@@ -373,10 +373,11 @@ def phase_plot(Results = None, y_axis = None, x_axis = None,
 
         Stop = np.zeros(len(Results['All']['P_bar']))
         for idx, p in enumerate(phases):
-            a.fill_betweenx(Results['All']['P_bar'], Stop, 
-                            x2= Stop + Results['All']['Mass_' + p], alpha = 0.75, color = PhaseList[p], lw = 0)
+            if 'mass_' + p in Results['All'].keys():
+                a.fill_betweenx(Results['All']['P_bar'], Stop, 
+                                x2= Stop + Results['All']['mass_' + p], alpha = 0.75, color = PhaseList[p], lw = 0)
 
-            Stop = Stop + Results['All']['Mass_'+p]
+                Stop = Stop + Results['All']['mass_' + p]
 
         a.set_ylabel('Pressure (bars)')
         a.set_xlabel('Mass (g)')

{PetThermoTools-0.2.37 → PetThermoTools-0.2.39}/src/PetThermoTools/_version.py

@@ -5,4 +5,4 @@
 # 1) we don't load dependencies by storing it in __init__.py
 # 2) we can import it in setup.py for the same reason
 # 3) we can import it into your module
-__version__ = '0.2.37'
+__version__ = '0.2.39'

{PetThermoTools-0.2.37 → PetThermoTools-0.2.39/src/PetThermoTools.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: PetThermoTools
-Version: 0.2.37
+Version: 0.2.39
 Summary: PetThermoTools
 Home-page: https://github.com/gleesonm1/PetThermoTools
 Author: Matthew Gleeson