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Updated iterative_fitter.py

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pull/1/head
titusquah 5 years ago
parent fabec1e7ed
commit e275b50e2c
5 changed files with 159 additions and 129 deletions
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68
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data/xmls/PC88A_HCL_NdPrCeLaDySmY_w_pitzer.xml
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</binarySaltParameters>
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<binarySaltParameters anion="Cl-" cation="Sm+++">
<beta0 updated="Updated at 22:29 7-15-2020"> 0.5977991609880217, 0.0, 0.0, 0.0, 0.0 </beta0>
<beta1 updated="Updated at 22:29 7-15-2020"> 5.278978873123928, 0.0, 0.0, 0.0, 0.0 </beta1>
<beta0 updated="Updated at 2:48 7-16-2020"> 0.6989806503460452, 0.0, 0.0, 0.0, 0.0 </beta0>
<beta1 updated="Updated at 1:25 7-16-2020"> 6.8744371885601625, 0.0, 0.0, 0.0, 0.0 </beta1>
<beta2> 0.0, 0.0, 0.0, 0.0, 0.0 </beta2>
<Cphi updated="Updated at 22:11 7-15-2020"> -0.019920000110321332, 0.0, 0.0, 0.0, 0.0 </Cphi>
<Cphi updated="Updated at 23:0 7-15-2020"> -0.019920000110321332, 0.0, 0.0, 0.0, 0.0 </Cphi>
<Alpha1> 2 </Alpha1>
<Alpha2> 0 </Alpha2>
<source>

25
docs/Examples/iterative_fitter.py
Unescape View File

@ -91,7 +91,8 @@ ignore_list = []
optimizer = 'scipy_minimize'
output_dict = {'iter': [0],
'best_obj': [1e20],
'rel_diff': [1e20]}
'rel_diff': [1e20],
'ext_h0': [1e20]}
for species in species_list:
output_dict['{0}_slope'.format(species)] = [1e20]
output_dict['{0}_intercept'.format(species)] = [1e20]
@ -103,6 +104,7 @@ while rel_diff > 1e-4:
i += 1
print(i)
best_obj = 1e20
best_ext_h0 = 0
output_dict['iter'].append(i)
for species in species_list:
print(species)
@ -156,15 +158,27 @@ while rel_diff > 1e-4:
optimizer_kwargs=optimizer_kwargs)
if obj_value < best_obj:
best_obj = obj_value
keys = list(opt_dict.keys())
best_ext_h0 = opt_dict['(HA)2(org)_h0']['input_value']
for lin_param in lin_param_list:
if '{0}_{1}'.format(species, lin_param) not in ignore_list:
mini_dict = opt_dict['{0}_{1}'.format(species, lin_param)]
value = mini_dict['input_value']
output_dict['{0}_{1}'.format(species, lin_param)].append(value)
else:
value = output_dict['{0}_{1}'.format(species, lin_param)][-1]
output_dict['{0}_{1}'.format(species, lin_param)].append(value)
for pitzer_param in pitzer_param_list:
if '{0}_{1}'.format(species, pitzer_param) not in ignore_list:
mini_dict = opt_dict['{0}_{1}'.format(species, pitzer_param)]
value = mini_dict['input_value']
output_dict['{0}_{1}'.format(species, pitzer_param)].append(value)
output_dict['{0}_{1}'.format(
species, pitzer_param)].append(value)
else:
value = output_dict['{0}_{1}'.format(
species, pitzer_param)][-1]
output_dict['{0}_{1}'.format(
species, pitzer_param)].append(value)
estimator.update_custom_objects_dict(info_dict)
estimator.update_xml(opt_dict)
pitzer_guess_dict = {'species': [],
@ -204,11 +218,12 @@ while rel_diff > 1e-4:
pitzer_guess_df = pd.DataFrame(pitzer_guess_dict)
lin_guess_df = pd.DataFrame(lin_guess_dict)
output_dict['best_ext_h0'].append(best_ext_h0)
output_dict['best_obj'].append(best_obj)
output_dict['rel_diff'].append(100)
output_df = pd.DataFrame(output_dict)
old_row = output_df.iloc[-2, :].values[3:]
new_row = output_df.iloc[-1, :].values[3:]
old_row = output_df.iloc[-2, :].values[4:]
new_row = output_df.iloc[-1, :].values[4:]
rel_diff = np.sum(np.abs(new_row - old_row) / np.abs(old_row))
del(output_dict['rel_diff'][-1])
output_dict['rel_diff'].append(rel_diff)

31
docs/Examples/iterative_fitter_monitor.py
Unescape View File

@ -2,13 +2,13 @@ import matplotlib.pyplot as plt
import pandas as pd
go = 'y'
parameters = 'slope,intercept,beta0,beta1,Cphi'.split(',')
while go == 'y':
go = input('continue? ')
if go != 'y':
break
plt.close('all')
df = pd.read_csv('outputs/iterative_fitter_output_df.csv')
parameters = 'slope,intercept,beta0,beta1'.split(',')
# while go == 'y':
# go = input('continue? ')
# if go != 'y':
# break
# plt.close('all')
df = pd.read_csv('outputs/iterative_fitter_output.csv')
info_cols = {parameter: [] for parameter in parameters}
for col in df.columns:
for parameter in parameters:
@ -19,8 +19,8 @@ while go == 'y':
fig, ax = plt.subplots()
ax.set_title(parameter)
for col in info_cols[parameter]:
ax.plot(df['iters'].values,
df[col].values,
ax.plot(df['iter'].values[1:],
df[col].values[1:],
label=col,
linestyle='-',
marker='o')
@ -30,8 +30,17 @@ while go == 'y':
plt.show()
fig, ax = plt.subplots()
ax.set_title('best_obj_value')
ax.plot(df['iters'].values,
df['best_obj'].values,
ax.plot(df['iter'].values[1:],
df['best_obj'].values[1:],
linestyle='-',
marker='o')
ax.set_xlabel('iteration')
ax.set_ylabel('Value')
plt.show()
fig, ax = plt.subplots()
ax.set_title('rel_diff')
ax.plot(df['iter'].values[1:],
df['rel_diff'].values[1:],
linestyle='-',
marker='o')
ax.set_xlabel('iteration')

58
docs/Examples/outputs/temp.xml
Unescape View File

@ -33,7 +33,7 @@
<thermo>
<const_cp Tmax="300.0" Tmin="298.0">
<t0 units="K">298.14999999999998</t0>
<h0 units="J/mol" updated="Updated at 22:31 7-15-2020">-1376877.765519179</h0>
<h0 units="J/mol" updated="Updated at 2:49 7-16-2020">-1376877.154483614</h0>
<s0 units="J/mol/K"> 558.9824 </s0>
<cp0 units="J/mol/K"> 0.0</cp0>
</const_cp>
@ -50,7 +50,7 @@
<const_cp Tmax="300.0" Tmin="298.0">
<t0 units="K">298.14999999999998</t0>
<h0 units="J/mol" updated="Updated at 22:11 7-15-2020">-4926549.797810851</h0>
<h0 units="J/mol" updated="Updated at 2:49 7-16-2020">-4933435.73807457</h0>
<s0 units="J/mol/K"> 1117.965 </s0>
<cp0 units="J/mol/K">0.0</cp0>
</const_cp>
@ -67,7 +67,7 @@
<const_cp Tmax="300.0" Tmin="298.0">
<t0 units="K">298.14999999999998</t0>
<h0 units="J/mol" updated="Updated at 22:11 7-15-2020">-4935519.640701385</h0>
<h0 units="J/mol" updated="Updated at 2:49 7-16-2020">-4936620.461887979</h0>
<s0 units="J/mol/K"> 1117.965 </s0>
<cp0 units="J/mol/K">0.0</cp0>
</const_cp>
@ -85,7 +85,7 @@
<const_cp Tmax="300.0" Tmin="298.0">
<t0 units="K">298.14999999999998</t0>
<h0 units="J/mol" updated="Updated at 22:11 7-15-2020">-4928317.781440989</h0>
<h0 units="J/mol" updated="Updated at 2:49 7-16-2020">-4932173.388635787</h0>
<s0 units="J/mol/K"> 1117.965 </s0>
<cp0 units="J/mol/K">0.0</cp0>
</const_cp>
@ -103,7 +103,7 @@
<const_cp Tmax="300.0" Tmin="298.0">
<t0 units="K">298.14999999999998</t0>
<h0 units="J/mol" updated="Updated at 22:11 7-15-2020">-4927428.65973482</h0>
<h0 units="J/mol" updated="Updated at 2:49 7-16-2020">-4991281.90783811</h0>
<s0 units="J/mol/K"> 1117.965 </s0>
<cp0 units="J/mol/K">0.0</cp0>
</const_cp>
@ -120,7 +120,7 @@
<const_cp Tmax="300.0" Tmin="298.0">
<t0 units="K">298.14999999999998</t0>
<h0 units="J/mol" updated="Updated at 22:11 7-15-2020">-4935155.356789877</h0>
<h0 units="J/mol" updated="Updated at 2:49 7-16-2020">-4935739.024047113</h0>
<s0 units="J/mol/K"> 1117.965 </s0>
<cp0 units="J/mol/K">0.0</cp0>
</const_cp>
@ -138,7 +138,7 @@
<const_cp Tmax="300.0" Tmin="298.0">
<t0 units="K">298.14999999999998</t0>
<h0 units="J/mol" updated="Updated at 22:11 7-15-2020">-4944228.17930387</h0>
<h0 units="J/mol" updated="Updated at 2:49 7-16-2020">-4944084.986155681</h0>
<s0 units="J/mol/K"> 1117.965 </s0>
<cp0 units="J/mol/K">0.0</cp0>
</const_cp>
@ -157,7 +157,7 @@
<const_cp Tmax="300.0" Tmin="298.0">
<t0 units="K">298.14999999999998</t0>
<h0 units="J/mol" updated="Updated at 22:11 7-15-2020">-4925606.187988869</h0>
<h0 units="J/mol" updated="Updated at 2:49 7-16-2020">-4924682.918862937</h0>
<s0 units="J/mol/K"> 1117.965 </s0>
<cp0 units="J/mol/K">0.0</cp0>
</const_cp>
@ -245,10 +245,10 @@
</binarySaltParameters>
<binarySaltParameters anion="Cl-" cation="Pr+++">
<beta0 updated="Updated at 22:21 7-15-2020"> 0.58791088654164, 0.0, 0.0, 0.0, 0.0 </beta0>
<beta1 updated="Updated at 22:21 7-15-2020"> 5.4483244544866825, 0.0, 0.0, 0.0, 0.0 </beta1>
<beta0 updated="Updated at 1:53 7-16-2020"> 0.9335616000781043, 0.0, 0.0, 0.0, 0.0 </beta0>
<beta1 updated="Updated at 1:53 7-16-2020"> 10.555396864028587, 0.0, 0.0, 0.0, 0.0 </beta1>
<beta2> 0.0, 0.0, 0.0, 0.0, 0.0 </beta2>
<Cphi updated="Updated at 22:11 7-15-2020"> -0.02066999867229882, 0.0, 0.0, 0.0, 0.0 </Cphi>
<Cphi updated="Updated at 23:0 7-15-2020"> -0.02066999867229882, 0.0, 0.0, 0.0, 0.0 </Cphi>
<Alpha1> 2 </Alpha1>
<Alpha2> 0 </Alpha2>
<source>
@ -261,10 +261,10 @@
</binarySaltParameters>
<binarySaltParameters anion="Cl-" cation="Nd+++">
<beta0 updated="Updated at 22:19 7-15-2020"> 0.8967941630491562, 0.0, 0.0, 0.0, 0.0 </beta0>
<beta1 updated="Updated at 22:19 7-15-2020"> 9.427003409136933, 0.0, 0.0, 0.0, 0.0 </beta1>
<beta0 updated="Updated at 1:36 7-16-2020"> 0.951206693355039, 0.0, 0.0, 0.0, 0.0 </beta0>
<beta1 updated="Updated at 1:36 7-16-2020"> 9.262520235612426, 0.0, 0.0, 0.0, 0.0 </beta1>
<beta2> 0.0, 0.0, 0.0, 0.0, 0.0 </beta2>
<Cphi updated="Updated at 22:11 7-15-2020"> -0.01963615126026457, 0.0, 0.0, 0.0, 0.0 </Cphi>
<Cphi updated="Updated at 23:0 7-15-2020"> -0.01963615126026457, 0.0, 0.0, 0.0, 0.0 </Cphi>
<Alpha1> 2 </Alpha1>
<Alpha2> 0 </Alpha2>
<source>
@ -277,10 +277,10 @@
</binarySaltParameters>
<binarySaltParameters anion="Cl-" cation="La+++">
<beta0 updated="Updated at 22:25 7-15-2020"> 0.5930012906158572, 0.0, 0.0, 0.0, 0.0 </beta0>
<beta1 updated="Updated at 22:25 7-15-2020"> 5.277035446184885, 0.0, 0.0, 0.0, 0.0 </beta1>
<beta0 updated="Updated at 2:48 7-16-2020"> 0.5362669407654791, 0.0, 0.0, 0.0, 0.0 </beta0>
<beta1 updated="Updated at 2:48 7-16-2020"> 19.878544145607385, 0.0, 0.0, 0.0, 0.0 </beta1>
<beta2> 0.0, 0.0, 0.0, 0.0, 0.0 </beta2>
<Cphi updated="Updated at 22:11 7-15-2020"> -0.024339999997603376, 0.0, 0.0, 0.0, 0.0 </Cphi>
<Cphi updated="Updated at 23:0 7-15-2020"> -0.024339999997603376, 0.0, 0.0, 0.0, 0.0 </Cphi>
<Alpha1> 2 </Alpha1>
<Alpha2> 0 </Alpha2>
<source>
@ -293,10 +293,10 @@
</binarySaltParameters>
<binarySaltParameters anion="Cl-" cation="Dy+++">
<beta0 updated="Updated at 22:27 7-15-2020"> 0.6129503793974099, 0.0, 0.0, 0.0, 0.0 </beta0>
<beta1 updated="Updated at 22:27 7-15-2020"> 5.359935242327716, 0.0, 0.0, 0.0, 0.0 </beta1>
<beta0 updated="Updated at 2:48 7-16-2020"> 0.6129504699810289, 0.0, 0.0, 0.0, 0.0 </beta0>
<beta1 updated="Updated at 2:48 7-16-2020"> 5.359936728131316, 0.0, 0.0, 0.0, 0.0 </beta1>
<beta2> 0.0, 0.0, 0.0, 0.0, 0.0 </beta2>
<Cphi updated="Updated at 22:11 7-15-2020"> -0.019699989216349984, 0.0, 0.0, 0.0, 0.0 </Cphi>
<Cphi updated="Updated at 23:0 7-15-2020"> -0.019699989216349984, 0.0, 0.0, 0.0, 0.0 </Cphi>
<Alpha1> 2 </Alpha1>
<Alpha2> 0 </Alpha2>
<source>
@ -309,10 +309,10 @@
</binarySaltParameters>
<binarySaltParameters anion="Cl-" cation="Ce+++">
<beta0 updated="Updated at 22:23 7-15-2020"> 0.6005000281456716, 0.0, 0.0, 0.0, 0.0 </beta0>
<beta1 updated="Updated at 22:23 7-15-2020"> 4.9100000484364354, 0.0, 0.0, 0.0, 0.0 </beta1>
<beta0 updated="Updated at 2:2 7-16-2020"> 0.3803360903827252, 0.0, 0.0, 0.0, 0.0 </beta0>
<beta1 updated="Updated at 2:2 7-16-2020"> 0.4715334506120701, 0.0, 0.0, 0.0, 0.0 </beta1>
<beta2> 0.0, 0.0, 0.0, 0.0, 0.0 </beta2>
<Cphi updated="Updated at 22:11 7-15-2020"> -0.02618999999473301, 0.0, 0.0, 0.0, 0.0 </Cphi>
<Cphi updated="Updated at 23:0 7-15-2020"> -0.02618999999473301, 0.0, 0.0, 0.0, 0.0 </Cphi>
<Alpha1> 2 </Alpha1>
<Alpha2> 0 </Alpha2>
<source>
@ -325,10 +325,10 @@
</binarySaltParameters>
<binarySaltParameters anion="Cl-" cation="Y+++">
<beta0 updated="Updated at 22:31 7-15-2020"> 0.96563586407358, 0.0, 0.0, 0.0, 0.0 </beta0>
<beta1 updated="Updated at 22:31 7-15-2020"> 8.514189357968196, 0.0, 0.0, 0.0, 0.0 </beta1>
<beta0 updated="Updated at 1:26 7-16-2020"> 0.8864576562457522, 0.0, 0.0, 0.0, 0.0 </beta0>
<beta1 updated="Updated at 1:26 7-16-2020"> 9.87156845120858, 0.0, 0.0, 0.0, 0.0 </beta1>
<beta2> 0.0, 0.0, 0.0, 0.0, 0.0 </beta2>
<Cphi updated="Updated at 22:11 7-15-2020"> -0.015467323909969704, 0.0, 0.0, 0.0, 0.0 </Cphi>
<Cphi updated="Updated at 23:0 7-15-2020"> -0.015467323909969704, 0.0, 0.0, 0.0, 0.0 </Cphi>
<Alpha1> 2 </Alpha1>
<Alpha2> 0 </Alpha2>
<source>
@ -341,10 +341,10 @@
</binarySaltParameters>
<binarySaltParameters anion="Cl-" cation="Sm+++">
<beta0 updated="Updated at 22:29 7-15-2020"> 0.5977991609880217, 0.0, 0.0, 0.0, 0.0 </beta0>
<beta1 updated="Updated at 22:29 7-15-2020"> 5.278978873123928, 0.0, 0.0, 0.0, 0.0 </beta1>
<beta0 updated="Updated at 2:49 7-16-2020"> 0.6989806463779159, 0.0, 0.0, 0.0, 0.0 </beta0>
<beta1 updated="Updated at 1:25 7-16-2020"> 6.8744371885601625, 0.0, 0.0, 0.0, 0.0 </beta1>
<beta2> 0.0, 0.0, 0.0, 0.0, 0.0 </beta2>
<Cphi updated="Updated at 22:11 7-15-2020"> -0.019920000110321332, 0.0, 0.0, 0.0, 0.0 </Cphi>
<Cphi updated="Updated at 23:0 7-15-2020"> -0.019920000110321332, 0.0, 0.0, 0.0, 0.0 </Cphi>
<Alpha1> 2 </Alpha1>
<Alpha2> 0 </Alpha2>
<source>

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