DiadFit 1.0.5__py3-none-any.whl → 1.0.8__py3-none-any.whl

DiadFit/relaxifi.py

@@ -162,7 +162,7 @@ class power_creep_law_constants:
         self.IgasR= 8.314  # Gas constant in J/(mol*K)
 
 # Helper function to calculate change in radius over time (dR/dt)
-def calculate_dR_dt(*,R_m, b_m, T_K,  Pinternal_MPa, Pexternal_MPa):
+def calculate_dR_dt(*, R_m, b_m, T_K, Pinternal_MPa, Pexternal_MPa):
     """
     Calculate the rate of change of inclusion radius (dR/dt) based on power law creep.
 
@@ -176,18 +176,29 @@ def calculate_dR_dt(*,R_m, b_m, T_K,  Pinternal_MPa, Pexternal_MPa):
     Returns:
     - dR_dt (float): Rate of change of inclusion radius in meters per second.
     """
-    
+
     pl_Cs = power_creep_law_constants()
-    if Pinternal_MPa<Pexternal_MPa==True:
-        S=-1
-    else:
-        S=1
+
+    # Ensure R_m is not zero to avoid division by zero in the final term
+    if R_m == 0:
+        raise ValueError("R_m cannot be zero")
+    
+    # Avoid division by zero or very small numbers in the term (b_m**(3 / pl_Cs.n)) - (R_m**(3 / pl_Cs.n))
+    denominator = (b_m**(3 / pl_Cs.n)) - (R_m**(3 / pl_Cs.n))
+    if abs(denominator) < 1e-8:  # Check if the value is too close to zero
+        raise ValueError("the distance to the defect (b_m) and the radii of the inclusion (R_m) are too close, causing division by zero. Please tweak these parameters!")
+    
+    # Set the sign based on internal and external pressure difference
+    S = -1 if Pinternal_MPa < Pexternal_MPa else 1
+
     try:
-        dR_dt = 2 * (S * pl_Cs.A * math.exp(-pl_Cs.Q / (pl_Cs.IgasR * T_K))) * (((R_m * b_m)**3) / (((b_m**(3 / pl_Cs.n)) - (R_m**(3 / pl_Cs.n))))**pl_Cs.n) * (((3 * abs(Pinternal_MPa - Pexternal_MPa)) / (2 * pl_Cs.n))**pl_Cs.n) / R_m**2
+        # Compute dR/dt with the necessary checks
+        dR_dt = 2 * (S * pl_Cs.A * math.exp(-pl_Cs.Q / (pl_Cs.IgasR * T_K))) * (((R_m * b_m)**3) / (denominator**pl_Cs.n)) * (((3 * abs(Pinternal_MPa - Pexternal_MPa)) / (2 * pl_Cs.n))**pl_Cs.n) / R_m**2
         return dR_dt
 
     except FloatingPointError:
         return np.nan
+
     
 # Helper function to numerically solve for R (uses Runge-Kutta method, orders 1-4)   
 def get_R(R_m,b_m,T_K,Pinternal_MPa,Pexternal_MPa,dt_s,method='RK1'):
@@ -405,6 +416,8 @@ def stretch_in_ascent(*, R_m, b_m, T_K, ascent_rate_ms, depth_path_ini_fin_step=
 
     CO2_dens_initial, CO2_mass_initial = get_initial_CO2(R_m=R_m, T_K=T_K, P_MPa=Pinternal_MPa, EOS=EOS)
 
+
+    # This is just to initiate the code, the input values dont matter. 
     
     results = pd.DataFrame([{'Time(s)': 0,
                             'Step':0,
@@ -459,8 +472,28 @@ def stretch_in_ascent(*, R_m, b_m, T_K, ascent_rate_ms, depth_path_ini_fin_step=
 
     return results
 
+
+def calculate_exponential_time_steps(totaltime_s, steps):
+    """
+    Generate exponentially spaced time steps with smaller steps at the beginning and larger steps towards the end.
+
+    Parameters:
+    - totaltime_s (float): The total time for the simulation.
+    - steps (int): The number of steps in the simulation.
+
+    Returns:
+    - dt_s_array (np.ndarray): Array of time intervals (dt_s) with smaller steps at the beginning.
+    """
+    linear_space = np.linspace(0, 1, steps)  # Linear space from 0 to 1
+    non_uniform_space = np.exp(5 * (linear_space - 1))  # Exponential distribution with smaller steps at the beginning
+    non_uniform_space = non_uniform_space / non_uniform_space.sum()  # Normalize so the sum equals 1
+    dt_s_array = non_uniform_space * totaltime_s  # Scale to the total time
+
+    return dt_s_array
+    
+    
 # This function is to model stretching at fixed External Pressure (e.g., during stalling or upon eruption)
-def stretch_at_constant_Pext(*,R_m,b_m,T_K,EOS='SW96',Pinternal_MPa,Pexternal_MPa,totaltime_s,steps,method='RK4',report_results='fullpath',plotfig=False,update_b=False):
+def stretch_at_constant_Pext(*,R_m,b_m,T_K,EOS='SW96',Pinternal_MPa,Pexternal_MPa,totaltime_s,steps,method='RK4',report_results='fullpath',plotfig=False,update_b=False, step_type='linear', max_perc_change=5):
     """
     Simulate the stretching of a CO2 fluid inclusion (FI) under constant external pressure (e.g., quenching or storage).
 
@@ -489,13 +522,23 @@ def stretch_at_constant_Pext(*,R_m,b_m,T_K,EOS='SW96',Pinternal_MPa,Pexternal_MP
     """
 
     CO2_dens_initial,CO2_mass_initial=get_initial_CO2(R_m=R_m,T_K=T_K,P_MPa=Pinternal_MPa,EOS=EOS)
+    
+    # Check that you arent getting imaginary numbers. 
+    dR_dt = calculate_dR_dt(R_m=R_m, b_m=b_m, Pinternal_MPa=Pinternal_MPa, Pexternal_MPa=Pexternal_MPa, T_K=T_K)
+    
+    # Check if the result is complex
+    if isinstance(dR_dt, complex):
+        raise ValueError(f"The calculation returned a complex number due to invalid inputs. Most likely the inclusion radius, {1000000*R_m} (um),  is too close, or even bigger than the defect distance, {1000000*b_m} um")
+
+
 
     results = pd.DataFrame([{'Time(s)': 0,
                              'Step':0,
                              'dt(s)':0,
                             'Pexternal(MPa)': float(Pexternal_MPa),
                             'Pinternal(MPa)': float(Pinternal_MPa),
-                            'dR/dt(m/s)': float(calculate_dR_dt(R_m=R_m, b_m=b_m, Pinternal_MPa=Pinternal_MPa, Pexternal_MPa=Pexternal_MPa, T_K=T_K)),
+                            'deltaP (internal-external, MPa)':float(Pinternal_MPa)- float(Pexternal_MPa),
+                            'dR/dt(m/s)': float(calculate_dR_dt(R_m=R_m, b_m=b_m, Pinternal_MPa=Pinternal_MPa, Pexternal_MPa=Pexternal_MPa, T_K=T_K)), # ditched function due to issue with imaginary numbers
                             'Fi_radius(μm)': float(R_m*10**6),
                             'b (distance to xtal rim -μm)':float(b_m*10**6),
                             '\u0394R/R0 (fractional change in radius)':0,
@@ -507,6 +550,7 @@ def stretch_at_constant_Pext(*,R_m,b_m,T_K,EOS='SW96',Pinternal_MPa,Pexternal_MP
         'dt(s)': 'float64',
         'Pexternal(MPa)': 'float64',
         'Pinternal(MPa)': 'float64',
+        'deltaP (internal-external, MPa)': 'float64',
         'dR/dt(m/s)': 'float64',
         'Fi_radius(μm)': 'float64',
         'b (distance to xtal rim -μm)': 'float64',
@@ -515,24 +559,105 @@ def stretch_at_constant_Pext(*,R_m,b_m,T_K,EOS='SW96',Pinternal_MPa,Pexternal_MP
     })
 
 
-    dt_s=totaltime_s/steps
-    
-    for step in range(1,steps):
+    if step_type== 'linear':
 
-        R_new,dR_dt = get_R(R_m=R_m,b_m=b_m,T_K=T_K,Pinternal_MPa=Pinternal_MPa,Pexternal_MPa=Pexternal_MPa,dt_s=dt_s,method=method)
-
-        CO2_dens_new,P_new = get_CO2dens_P(R_m=R_new,T_K=T_K,CO2_mass=CO2_mass_initial,EOS=EOS)
-
-        Pinternal_MPa = P_new
-        R_m=R_new
-
-        if update_b==True:
-            b_m=1000*R_m
+        dt_s=totaltime_s/steps
         
-        results.loc[step] = [float(step * dt_s), int(step), float(dt_s), float(Pexternal_MPa), float(Pinternal_MPa), 
-                     float(dR_dt), float(R_m * 10 ** 6), float(b_m * 10 ** 6), 
-                     float((R_m * 10 ** 6 - results.loc[0, 'Fi_radius(μm)']) / results.loc[0, 'Fi_radius(μm)']),
-                     float(CO2_dens_new)]
+        for step in range(1,steps):
+    
+            R_new,dR_dt = get_R(R_m=R_m,b_m=b_m,T_K=T_K,Pinternal_MPa=Pinternal_MPa,Pexternal_MPa=Pexternal_MPa,dt_s=dt_s,method=method)
+    
+            CO2_dens_new,P_new = get_CO2dens_P(R_m=R_new,T_K=T_K,CO2_mass=CO2_mass_initial,EOS=EOS)
+    
+            Pinternal_MPa = P_new
+            R_m=R_new
+    
+            if update_b==True:
+                b_m=1000*R_m
+
+            
+            results.loc[step] = [float(step * dt_s), int(step), float(dt_s), float(Pexternal_MPa), float(Pinternal_MPa), float(Pinternal_MPa-Pexternal_MPa),
+                        float(dR_dt), float(R_m * 10 ** 6), float(b_m * 10 ** 6), 
+                        float((R_m * 10 ** 6 - results.loc[0, 'Fi_radius(μm)']) / results.loc[0, 'Fi_radius(μm)']),
+                        float(CO2_dens_new)]
+                        
+    elif step_type == 'exponential':
+        total_time = 0
+        dt_s_array = calculate_exponential_time_steps(totaltime_s, steps)
+        local_step = 0  # Track position in the new dt_s_array
+    
+        # Loop over steps
+        for step in range(steps):  # Use global step index
+            
+    
+            if local_step >= len(dt_s_array):  # Ensure no out-of-bounds access in the recalculated array
+                print(local_step)
+                print(dt_s_array)
+                print(f"Local step {local_step} exceeds the length of dt_s_array {len(dt_s_array)}, skipping.")
+                break  # Avoid out-of-bounds access
+            
+            dt_s = dt_s_array[local_step]  # Use the local step to access dt_s_array
+            prev_Pinternal = Pinternal_MPa
+    
+            # Accumulate the total time up to the current step
+            total_time += dt_s
+    
+            # Update radius and pressure based on the current step
+            R_new, dR_dt = get_R(R_m=R_m, b_m=b_m, T_K=T_K, Pinternal_MPa=Pinternal_MPa, Pexternal_MPa=Pexternal_MPa, dt_s=dt_s, method=method)
+            CO2_dens_new, P_new = get_CO2dens_P(R_m=R_new, T_K=T_K, CO2_mass=CO2_mass_initial, EOS=EOS)
+    
+            # Calculate the percentage change in internal pressure
+            perc_change = abs((P_new - prev_Pinternal) / prev_Pinternal) * 100
+    
+    
+            # Check if the pressure change exceeds the maximum allowed percentage change
+            while perc_change > max_perc_change:
+                print(f'Reducing step size, as pressure change was more than {max_perc_change}%.')
+    
+                dt_s /= 2  # Reduce the step size
+                total_time -= dt_s  # Remove the original dt_s from total_time
+                total_time += dt_s  # Add the smaller dt_s
+    
+                # Recalculate with the smaller dt_s
+                R_new, dR_dt = get_R(R_m=R_m, b_m=b_m, T_K=T_K, Pinternal_MPa=Pinternal_MPa, Pexternal_MPa=Pexternal_MPa, dt_s=dt_s, method=method)
+                CO2_dens_new, P_new = get_CO2dens_P(R_m=R_new, T_K=T_K, CO2_mass=CO2_mass_initial, EOS=EOS)
+    
+                # Recalculate the percentage change
+                perc_change = abs((P_new - prev_Pinternal) / prev_Pinternal) * 100
+    
+                # Recalculate dt_s_array to adjust future time steps based on the new dt_s
+                remaining_time = totaltime_s - total_time  # Remaining time after this step
+                remaining_steps = steps - step  # Remaining steps
+    
+                if remaining_steps > 0:
+                    dt_s_array = calculate_exponential_time_steps(remaining_time, remaining_steps)
+                    local_step = 0  # Reset local step to start from the new dt_s_array's first value
+
+            # Increment local_step for the next iteration
+            local_step += 1
+
+            
+            # Update the current internal pressure and radius
+            Pinternal_MPa = P_new
+            R_m = R_new
+            
+            # Optionally update b_m if update_b is True
+            if update_b:
+                b_m = 1000 * R_m
+            
+            # Store results for this step, using the accumulated total time
+            results.loc[step] = [float(total_time),    # Accumulated total time
+                                int(step),            # Current step number
+                                float(dt_s),          # Time step for the current iteration
+                                float(Pexternal_MPa), 
+                                float(Pinternal_MPa), 
+                                float(Pinternal_MPa-Pexternal_MPa),
+                                float(dR_dt), 
+                                float(R_m * 10 ** 6), 
+                                float(b_m * 10 ** 6), 
+                                float((R_m * 10 ** 6 - results.loc[0, 'Fi_radius(μm)']) / results.loc[0, 'Fi_radius(μm)']),
+                                float(CO2_dens_new)]
+
 
     if report_results == 'startendonly':
         results.drop(index=list(range(1, results.shape[0] - 1)), inplace=True)  # Drop all rows except first and last
@@ -577,7 +702,7 @@ def stretch_at_constant_Pext(*,R_m,b_m,T_K,EOS='SW96',Pinternal_MPa,Pexternal_MP
 # This function can loop through different R and b value sets using stretch at constant Pext
 
 def loop_R_b_constant_Pext(*,R_m_values, b_m_values, T_K, EOS, Pinternal_MPa, Pexternal_MPa, totaltime_s, steps, T4endcalc_PD, method='RK4',
-                            plotfig=False, crustal_model_config=config_crustalmodel(crust_dens_kgm3=2750)):
+                            plotfig=False, crustal_model_config=config_crustalmodel(crust_dens_kgm3=2750), step_type='linear', max_perc_change=5):
 
     """
     Perform multiple simulations under constant external pressure with various R and b values.
@@ -614,7 +739,7 @@ def loop_R_b_constant_Pext(*,R_m_values, b_m_values, T_K, EOS, Pinternal_MPa, Pe
             b_key = f'b{idx_b}'  # Use 'b' followed by the index
             results = stretch_at_constant_Pext(R_m=R, b_m=b, T_K=T_K, Pinternal_MPa=Pinternal_MPa, Pexternal_MPa=Pexternal_MPa,
                                               totaltime_s=totaltime_s, steps=steps, EOS=EOS, method=method,
-                                              plotfig=plotfig)
+                                              plotfig=plotfig, step_type=step_type, max_perc_change=max_perc_change)
             results['Calculated depths (km)_StorageT'] = convert_pressure_to_depth(
                 P_kbar=results['Pinternal(MPa)'] / 100,
                 crust_dens_kgm3=crustal_model_config.crust_dens_kgm3, g=9.81,
@@ -633,4 +758,4 @@ def loop_R_b_constant_Pext(*,R_m_values, b_m_values, T_K, EOS, Pinternal_MPa, Pe
 
             results_dict[R_key][b_key] = results
 
-    return results_dict
+    return results_dict

{DiadFit-1.0.5.dist-info → DiadFit-1.0.8.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: DiadFit
-Version: 1.0.5
+Version: 1.0.8
 Summary: DiadFit
 Home-page: https://github.com/PennyWieser/DiadFit
 Author: Penny Wieser

{DiadFit-1.0.5.dist-info → DiadFit-1.0.8.dist-info}/RECORD

@@ -1,4 +1,4 @@
-DiadFit/CO2_EOS.py,sha256=H2_th8DP5m9oJ-IZCg9XncuOogQy_AE8ihiT-4zlIOo,74170
+DiadFit/CO2_EOS.py,sha256=BFrmPxaMAdbLt_K0vTUnEyJZmyyWUyp_hVRScu9t7TI,74165
 DiadFit/CO2_in_bubble_error.py,sha256=Nq5YEf2oa2rWRreEPXl2lEA86NXOGvll0Gca2AOu_RE,21224
 DiadFit/H2O_fitting.py,sha256=XLNNgqmiIyj-ysRQeQFnk08Dlr6tFHFySY3Z-wEadxs,44914
 DiadFit/Highrho_polyfit_data.pkl,sha256=7t6uXxI-HdfsvreAWORzMa9dXxUsnXqKBSo1O3EgiBw,1213
@@ -29,21 +29,22 @@ DiadFit/Mediumrho_polyfit_data_CCMR.pkl,sha256=U6ODSdurqS0-lynm1MG1zktg8NuhYRbrY
 DiadFit/Mediumrho_polyfit_data_CMASS.pkl,sha256=SBy1pIdqCAF9UtB9FLNTuD0-tFyD7swwJppdE2U_FsY,1557
 DiadFit/Psensor.py,sha256=C2xSlgxhUJIKIBDvUp02QaYRs5QsIqjGGRMP25ZLRZ0,10435
 DiadFit/__init__.py,sha256=F-HjhCYKL_U8PfiH8tZ9DUCkxPvo6lAslJS4fyvxkbY,1148
-DiadFit/_version.py,sha256=599vLXXrjZtWlaxUrZujLY2-Ub1qzeOKj5Sk5VZAYKo,295
+DiadFit/_version.py,sha256=nKWaPgClU1xtZYZ6_YcxZaeEJaW2vSv3ADjLG6ofSoo,295
 DiadFit/argon_lines.py,sha256=vtzsuDdEgrAmEF9xwpejpFqKV9hKPS1JUYhIl4AfXZ0,7675
 DiadFit/cosmicray_filter.py,sha256=a45x2_nmpi9Qcjc_L39UA9JOd1NMorIjtTRGnCdG3MU,23634
 DiadFit/densimeter_fitting.py,sha256=zEyCwq1zDV3z6-MIu-eZqgp3YQPUGqwZiKczN3-22LQ,8247
 DiadFit/densimeters.py,sha256=pSD8s9_9949bjWTbXU6SwoNgvsVBKGfQVf-JYMMtjrs,55282
-DiadFit/density_depth_crustal_profiles.py,sha256=b072IJaoGDydKpqWWKoJHeXKIkcIXxKf82whpvLAPpw,17761
-DiadFit/diads.py,sha256=ELG6wgEaGCYFj0IeA2F9QasYNmMVmFOi0rOl0oXv1pU,180906
-DiadFit/error_propagation.py,sha256=ipYI-Nwjv4f0sBdUiGeYV4wLcLGUXzKRrquNnc72d3c,50620
-DiadFit/importing_data_files.py,sha256=0Cx_CKJZR8efssMzQit0aPRh_rsjQFGXgLtI285FW_k,41961
+DiadFit/density_depth_crustal_profiles.py,sha256=Vvtw3-_xuWIYEuhuDzXstkprluXyBkUcdm9iP7qBwyQ,19754
+DiadFit/diads.py,sha256=lv6u9m71850_UnPqAOdFFeITMx5b0Dhn21i8tpDWj_Q,180939
+DiadFit/error_propagation.py,sha256=ZN9EspONh_vUGxBHxxWNkYskKqFMRvJMNr2h2RXv-54,50624
+DiadFit/importing_data_files.py,sha256=j7cSEPZ6iKmYnSqYEIcCl7YNdqqkCD56W-4V9T2oWOE,52010
 DiadFit/lookup_table.csv,sha256=Hs1tmSQ9ArTUDv3ymEXbvnLlPBxYUP0P51dz7xAKk-Q,2946857
 DiadFit/lookup_table_noneg.csv,sha256=HelvewKbBy4cqT2GAqsMo-1ps1lBYqZ-8hCJZWPGfhI,3330249
-DiadFit/molar_gas_proportions.py,sha256=_oEZn_vndHGDaXAjZ6UU8ycujBx_qB2KGCGqZSzotQU,3389
-DiadFit/ne_lines.py,sha256=in27yyvtlONf80KA2SREJ8xEemHvYTiWmd2-LOeJ7Tk,63955
-DiadFit/relaxifi.py,sha256=ZJ1LPWU1qKM8kU1ym4Ltp8skI_lMlhbCVhW6C1UhLb8,32109
-DiadFit-1.0.5.dist-info/METADATA,sha256=rz8zJHYmknOrLusf8A65vAdHe3-T3JeTriprj6FT4RI,1171
-DiadFit-1.0.5.dist-info/WHEEL,sha256=eOLhNAGa2EW3wWl_TU484h7q1UNgy0JXjjoqKoxAAQc,92
-DiadFit-1.0.5.dist-info/top_level.txt,sha256=yZC6OFLVznaFA5kcPlFPkvhKotcVd-YO4bKxZZw3LQE,8
-DiadFit-1.0.5.dist-info/RECORD,,
+DiadFit/molar_gas_proportions.py,sha256=mEcseIBFim5K7--9F0QwMT0QHin8Ubnm9U9iMSp7bI8,7337
+DiadFit/ne_lines.py,sha256=KR1s33pZB_O8e3irtDLdBpepGwUjxWudjJNyHyXqfbg,63980
+DiadFit/relaxfi_PW.py,sha256=vXXW9JjEBRf0UR9p-DJLx8j4Z2ePpUDweoAok-2nMJ0,32119
+DiadFit/relaxifi.py,sha256=DSHAUP0tnkiMrHQgQPBK-9P3cWYmegURKzYOUgdAlos,38569
+DiadFit-1.0.8.dist-info/METADATA,sha256=reLyXTzuAFqhm7f93wEwig0vQpWQxqgAK0w62Ehq3gQ,1171
+DiadFit-1.0.8.dist-info/WHEEL,sha256=tZoeGjtWxWRfdplE7E3d45VPlLNQnvbKiYnx7gwAy8A,92
+DiadFit-1.0.8.dist-info/top_level.txt,sha256=yZC6OFLVznaFA5kcPlFPkvhKotcVd-YO4bKxZZw3LQE,8
+DiadFit-1.0.8.dist-info/RECORD,,

{DiadFit-1.0.5.dist-info → DiadFit-1.0.8.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.44.0)
+Generator: bdist_wheel (0.45.1)
 Root-Is-Purelib: true
 Tag: py3-none-any