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index c6e1713d15ff013aa9d125cf10c9d1406b64c8c0..9a91fb22f3e6eea8aa986cb960fbe2f91d80a1e9 100644 GIT binary patch delta 129 zcmbO-mu1yl7M2EFG^A%j3LxCXa{!W9sAvMTyDgvPzR* z$S6(jkCfUhCp(3aQGT)=kA$#}!lQ;|v6@p_r!-EfouZM!+M_-BfxGzR4|3cPb2k5y d<9^6LwT+Jf3^Lebr(}puzWCo{s|TYG9{>^ND6;?n delta 104 zcmZ2Amu1Ra7M2ER^a z*{mr$g^^KevK@~EU##Yo)+vosYNu#qu=c2eRBRTM=X%JW!5%v$Lv(5b9|IU{)naVm F0|1dH9`gVI diff --git a/docs/_build/html/.buildinfo b/docs/_build/html/.buildinfo index d86ed8e..9679eeb 100644 --- a/docs/_build/html/.buildinfo +++ b/docs/_build/html/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. -config: 94676c5802e9cc7945d72deedc90526c +config: 274f61b94c8f9344114b86ece68c44b9 tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/docs/_build/html/_modules/index.html b/docs/_build/html/_modules/index.html index 45b7324..0a29df9 100644 --- a/docs/_build/html/_modules/index.html +++ b/docs/_build/html/_modules/index.html @@ -4,7 +4,7 @@ - Overview: module code — olm 0.35 documentation + Overview: module code — olm 0.36 documentation @@ -26,7 +26,7 @@

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    • diff --git a/docs/_build/html/_modules/olm/calcite.html b/docs/_build/html/_modules/olm/calcite.html index e8d8854..e9a4c0e 100644 --- a/docs/_build/html/_modules/olm/calcite.html +++ b/docs/_build/html/_modules/olm/calcite.html @@ -4,7 +4,7 @@ - olm.calcite — olm 0.35 documentation + olm.calcite — olm 0.36 documentation @@ -26,7 +26,7 @@

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    • @@ -331,7 +331,7 @@

    Source code for olm.calcite

     
 #Calculate H+ concentration given Ca and PCO2, makes no relaxed charge
 #balance assumption
-
    [docs]def solutionFromCaPCO2(Ca, PCO2, T_C = 25., per_tol = 0.001):
+
    [docs]def solutionFromCaPCO2(Ca, PCO2, T_C = 25., per_tol = 0.001, max_iter=1000):
     """
     Creates a solution object from a given concentration of calcium and PCO2.
 
@@ -345,7 +345,8 @@ 
    Source code for olm.calcite
            temperature of solution in degrees Celsius (default = 25 C)
     per_tol : float
        the fractional change in H concentration between iterations upon which the iteration is terminated
-
+    max_iter : int
+       the number of iterations allowed in the solution. Returns None if solution does not converge in max_iter.
 
     Returns
     -------
@@ -366,6 +367,7 @@ 
    Source code for olm.calcite
             K_2 = calc_K_2(T_K)
         K_6 = K_1*(1.+1./K_0)
         found=False
+        niter = 0
         while not(found):
             #estimate activity coefficients
             gamma_H = gamma('H', I_guess, T_C=T_C_in)
@@ -387,6 +389,9 @@ 
    Source code for olm.calcite
                     H_guess = H_new
                 I_guess = I_new
             #calculate non-charge ions
+            niter += 1
+            if niter > max_iter:
+                return None
         CO2 = K_H*PCO2_in
         H2CO3 = (K_H/K_0)*PCO2_in
         H2CO3s = H2CO3 + CO2
@@ -1377,7 +1382,7 @@ 
    Source code for olm.calcite
             return calc_rate(sol, PCO2, rho)
    
 
 
-
    [docs]def dissRateFromCaPCO2(Ca, PCO2, T_C, rho=2.6, method=None, impure=True, per_tol=0.001, error=False, error_num=100, Ca_err=None, PCO2_err=None, molL=False):
+
    [docs]def dissRateFromCaPCO2(Ca, PCO2, T_C, rho=2.6, method=None, impure=True, per_tol=0.001, error=False, error_num=100, Ca_err=None, PCO2_err=None, molL=False, confidence=0., return_samples = False):
     """
     Calculates the calcite/limestone dissolution rate from given calcium concentration and PCO2. Optionally uses Monte Carlo error propagation to calculate uncertainty in rates.
 
@@ -1407,6 +1412,10 @@ 
    Source code for olm.calcite
            Percent error in PCO2 values (1=100%)
     molL : boolean
        Are Ca units in mol/L. If so, set to true. Otherwise, units assumed are mg/L. (default=False, i.e. mg/L)
+    confidence : float
+       If non-zero then confidence intervals will be used in error estimation (e.g. 90 = 90% confidence). Default is 0.
+    return_samples : boolean
+       If true (default is false), then return entire random samples within error arrays.
 
     Returns
     -------
@@ -1417,7 +1426,7 @@ 
    Source code for olm.calcite
     
     """
     #Function for Monte Carlo error estimation
-    def err_est(Ca,PCO2,T_C):
+    def err_est(Ca,PCO2,T_C,Ca_err,PCO2_err):
         rate_sample = np.zeros(error_num)
         Ca_factor = 1. + Ca_err*np.random.randn(error_num)
         Ca_sample = Ca*Ca_factor
@@ -1426,7 +1435,16 @@ 
    Source code for olm.calcite
             for j in np.arange(error_num):
         #    print j, Ca_sample[j], PCO2_sample[j]
             #Create solution object
-            rand_sol = solutionFromCaPCO2(Ca_sample[j], PCO2_sample[j], T_C=T_C, per_tol=per_tol)
+            found = False
+            while not found:
+                rand_sol = solutionFromCaPCO2(Ca_sample[j], PCO2_sample[j], T_C=T_C, per_tol=per_tol)
+                if type(rand_sol) != type(None):
+                    found=True
+                else:
+                    new_Ca_factor = 1. + Ca_err*np.random.randn(1)
+                    Ca_sample[j] = Ca*new_Ca_factor
+                    print('Solution did not converge for this error calculation.')
+                    print('Ca_sample=',Ca_sample[j], '   PCO2_sample=',PCO2_sample[j])
             #Calculate dissolution rate
             if method=='PWP':
                 rate_sample[j] = pwp_to_mm_yr(pwpFromSolution(rand_sol, PCO2=PCO2_sample[j]), rho=rho)
@@ -1435,9 +1453,16 @@ 
    Source code for olm.calcite
                 else:
                 print( "Invalid method keyword!")
                 return None
-        #Estimated error is standard deviation from random sample
-        return np.std(rate_sample)
-
+        if return_samples:
+            return rate_sample
+        if confidence==0:
+            #Estimated error is standard deviation from random sample
+            return np.std(rate_sample)
+        else:
+            #Error estimated using confidence intervals
+            lower = np.percentile(rate_sample, 100.-confidence)
+            upper = np.percentile(rate_sample, confidence)
+            return [upper, lower]
 
 
     if not molL:
@@ -1445,12 +1470,18 @@ 
    Source code for olm.calcite
             Ca = mgL_to_molL(Ca, 'Ca')
     is_series = (type(Ca)==pandas.core.series.Series)
     if (type(Ca)==np.ndarray) or is_series:
-        rate_arr = np.empty(np.size(Ca), dtype=object)
+        rate_arr = np.empty(np.size(Ca), dtype=float)
         if error:
-            err_arr = np.empty(np.size(Ca), dtype=object)
+            if return_samples:
+                err_arr = np.empty((np.size(Ca),error_num), dtype=float)
+            elif confidence == 0:
+                err_arr = np.empty(np.size(Ca), dtype=float)
+            else:
+                err_arr = np.empty((np.size(Ca),2), dtype=float)
         for i, this_Ca in enumerate(Ca):
             if (i % 100)==0:
                 print( "Solution number "+str(i))
+                #print( "Ca = ", this_Ca, "  CO2 = ", PCO2[i], '  Ca_err = ', Ca_err[i], ' CO2_err = ', PCO2_err)
             #Create solution object
             if np.size(T_C)==1:
                 sol = solutionFromCaPCO2(this_Ca, PCO2[i], T_C=T_C, per_tol=per_tol)
@@ -1467,14 +1498,34 @@ 
    Source code for olm.calcite
                 #Monte Carlo error estimate on rate
             if error:
                 if np.size(T_C)==1:
-                    err_arr[i] = err_est(this_Ca, PCO2[i], T_C)
+                    if confidence == 0 and not return_samples:
+                        err_arr[i] = err_est(this_Ca, PCO2[i], T_C, Ca_err, PCO2_err)
+                    else:
+                        err_arr[i,:] = err_est(this_Ca, PCO2[i], T_C, Ca_err, PCO2_err)
                 else:
-                    err_arr[i] = err_est(this_Ca, PCO2[i], T_C[i])
+                    if np.size(Ca_err)==1:
+                        this_Ca_err = Ca_err
+                    else:
+                        this_Ca_err = Ca_err[i]
+                    if np.size(PCO2_err)==1:
+                        this_PCO2_err = PCO2_err
+                    else:
+                        this_PCO2_err = PCO2_err[i]
+                    if confidence == 0 and not return_samples:
+                        err_arr[i] = err_est(this_Ca, PCO2[i], T_C[i], this_Ca_err, this_PCO2_err)
+                    else:
+                        err_arr[i,:] = err_est(this_Ca, PCO2[i], T_C[i], this_Ca_err, this_PCO2_err)
 
         if is_series:
             rate_arr = pandas.Series(rate_arr, index=Ca.index)
             if error:
-                err_arr = pandas.Series(err_arr, index=Ca.index)
+                if confidence==0 and not return_samples:
+                    err_arr = pandas.Series(err_arr, index=Ca.index, dtype=float)
+                else:
+                    if return_samples:
+                        err_arr = pandas.DataFrame(err_arr, index=Ca.index, dtype=float)
+                    else:
+                        err_arr = pandas.DataFrame(err_arr, index=Ca.index, columns=['lower','upper'], dtype=float)
         if error:
             return rate_arr, err_arr
         else:
@@ -1491,7 +1542,7 @@ 
    Source code for olm.calcite
                 print("Invalid method keyword!")
             return None
         if error:
-            err = err_est(Ca, PCO2, T_C)
+            err = err_est(Ca, PCO2, T_C, Ca_err, PCO2_err)
             return R, err
         return R
    
 
    
@@ -1524,7 +1575,7 @@ 
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diff --git a/docs/_build/html/_modules/olm/general.html b/docs/_build/html/_modules/olm/general.html
index 1839d06..44dee9c 100644
--- a/docs/_build/html/_modules/olm/general.html
+++ b/docs/_build/html/_modules/olm/general.html
@@ -4,7 +4,7 @@
 
   
     
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+    olm.general — olm 0.36 documentation
     
     
     
@@ -26,7 +26,7 @@ 
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@@ -677,7 +677,7 @@ 
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diff --git a/docs/_build/html/_modules/olm/loggers/CampbellToolkit.html b/docs/_build/html/_modules/olm/loggers/CampbellToolkit.html
index 7186da5..a584cbb 100644
--- a/docs/_build/html/_modules/olm/loggers/CampbellToolkit.html
+++ b/docs/_build/html/_modules/olm/loggers/CampbellToolkit.html
@@ -4,7 +4,7 @@
 
   
     
-    olm.loggers.CampbellToolkit — olm 0.35 documentation
+    olm.loggers.CampbellToolkit — olm 0.36 documentation
     
     
     
@@ -26,7 +26,7 @@ 
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@@ -88,7 +88,7 @@ 
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diff --git a/docs/_build/html/_modules/olm/loggers/CyclopsToolkit.html b/docs/_build/html/_modules/olm/loggers/CyclopsToolkit.html
index dbe1977..0ad19ba 100644
--- a/docs/_build/html/_modules/olm/loggers/CyclopsToolkit.html
+++ b/docs/_build/html/_modules/olm/loggers/CyclopsToolkit.html
@@ -4,7 +4,7 @@
 
   
     
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@@ -26,7 +26,7 @@ 
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@@ -109,7 +109,7 @@ 
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diff --git a/docs/_build/html/_modules/olm/loggers/HoboToolkit.html b/docs/_build/html/_modules/olm/loggers/HoboToolkit.html
index 0653156..4d182d1 100644
--- a/docs/_build/html/_modules/olm/loggers/HoboToolkit.html
+++ b/docs/_build/html/_modules/olm/loggers/HoboToolkit.html
@@ -4,7 +4,7 @@
 
   
     
-    olm.loggers.HoboToolkit — olm 0.35 documentation
+    olm.loggers.HoboToolkit — olm 0.36 documentation
     
     
     
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diff --git a/docs/_build/html/_modules/olm/loggers/SchlumbergerCTDToolkit.html b/docs/_build/html/_modules/olm/loggers/SchlumbergerCTDToolkit.html
index 6f1aaf9..5bc42e5 100644
--- a/docs/_build/html/_modules/olm/loggers/SchlumbergerCTDToolkit.html
+++ b/docs/_build/html/_modules/olm/loggers/SchlumbergerCTDToolkit.html
@@ -4,7 +4,7 @@
 
   
     
-    olm.loggers.SchlumbergerCTDToolkit — olm 0.35 documentation
+    olm.loggers.SchlumbergerCTDToolkit — olm 0.36 documentation
     
     
     
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    Source code for olm.loggers.SchlumbergerCTDToolkit
    index_col = 0
     names = ['Pressure', 'Temperature', 'Conductivity']
     parse_dates = True
-    skip_footer = 1
-    df = read_csv(csvfile, sep=sep, names=names, skiprows=skiprows, index_col=index_col, parse_dates=parse_dates, skip_footer=skip_footer)
+    skipfooter = 1
+    df = read_csv(csvfile, sep=sep, names=names, skiprows=skiprows, index_col=index_col, parse_dates=parse_dates, skipfooter=skipfooter)
     return df
    
 
 #read in the CSV file from a CTD diver and return a pandas DataFrame
@@ -99,8 +99,8 @@ 
    Source code for olm.loggers.SchlumbergerCTDToolkit
    index_col = 0
     names = ['Pressure', 'Temperature']
     parse_dates = True
-    skip_footer = 1
-    df = read_csv(csvfile, sep=sep, names=names, skiprows=skiprows, index_col=index_col, parse_dates=parse_dates, skip_footer=skip_footer)
+    skipfooter = 1
+    df = read_csv(csvfile, sep=sep, names=names, skiprows=skiprows, index_col=index_col, parse_dates=parse_dates, skipfooter=skipfooter)
     return df
    
 
 
@@ -199,7 +199,7 @@ 
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diff --git a/docs/_build/html/_modules/olm/loggers/TruBluToolkit.html b/docs/_build/html/_modules/olm/loggers/TruBluToolkit.html
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--- a/docs/_build/html/_modules/olm/loggers/TruBluToolkit.html
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@@ -4,7 +4,7 @@
 
   
     
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    • diff --git a/docs/_build/html/olm.calcite.dissRateFromCaPCO2.html b/docs/_build/html/olm.calcite.dissRateFromCaPCO2.html index caaa556..6dd0651 100644 --- a/docs/_build/html/olm.calcite.dissRateFromCaPCO2.html +++ b/docs/_build/html/olm.calcite.dissRateFromCaPCO2.html @@ -4,7 +4,7 @@ - olm.calcite.dissRateFromCaPCO2 — olm 0.35 documentation + olm.calcite.dissRateFromCaPCO2 — olm 0.36 documentation @@ -34,7 +34,7 @@

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    olm.calcite.dissRateFromCaPCO2

    -olm.calcite.dissRateFromCaPCO2(Ca, PCO2, T_C, rho=2.6, method=None, impure=True, per_tol=0.001, error=False, error_num=100, Ca_err=None, PCO2_err=None, molL=False)[source]
    +olm.calcite.dissRateFromCaPCO2(Ca, PCO2, T_C, rho=2.6, method=None, impure=True, per_tol=0.001, error=False, error_num=100, Ca_err=None, PCO2_err=None, molL=False, confidence=0.0, return_samples=False)[source]

    Calculates the calcite/limestone dissolution rate from given calcium concentration and PCO2. Optionally uses Monte Carlo error propagation to calculate uncertainty in rates.

    Parameters
    @@ -77,6 +77,10 @@

    olm.calcite.dissRateFromCaPCO2boolean

    Are Ca units in mol/L. If so, set to true. Otherwise, units assumed are mg/L. (default=False, i.e. mg/L)

    +
    confidencefloat

    If non-zero then confidence intervals will be used in error estimation (e.g. 90 = 90% confidence). Default is 0.

    +
    +
    return_samplesboolean

    If true (default is false), then return entire random samples within error arrays.

    +

    Returns
    @@ -140,7 +144,7 @@

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    • diff --git a/docs/_build/html/olm.calcite.solutionFromCaPCO2.html b/docs/_build/html/olm.calcite.solutionFromCaPCO2.html index de97c5b..828731b 100644 --- a/docs/_build/html/olm.calcite.solutionFromCaPCO2.html +++ b/docs/_build/html/olm.calcite.solutionFromCaPCO2.html @@ -4,7 +4,7 @@ - olm.calcite.solutionFromCaPCO2 — olm 0.35 documentation + olm.calcite.solutionFromCaPCO2 — olm 0.36 documentation @@ -34,7 +34,7 @@

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    olm.calcite.solutionFromCaPCO2

    -olm.calcite.solutionFromCaPCO2(Ca, PCO2, T_C=25.0, per_tol=0.001)[source]
    +olm.calcite.solutionFromCaPCO2(Ca, PCO2, T_C=25.0, per_tol=0.001, max_iter=1000)[source]

    Creates a solution object from a given concentration of calcium and PCO2.

    Parameters
    @@ -61,6 +61,8 @@

    olm.calcite.solutionFromCaPCO2float

    the fractional change in H concentration between iterations upon which the iteration is terminated

    +
    max_iterint

    the number of iterations allowed in the solution. Returns None if solution does not converge in max_iter.

    +

    Returns
    @@ -123,7 +125,7 @@

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    solutionFromCaPCO2(Ca, PCO2[, T_C, per_tol])

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    solutionFromCaPCO2(Ca, PCO2[, T_C, per_tol, …])

    Creates a solution object from a given concentration of calcium and PCO2.

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