diff --git a/.gitignore b/.gitignore
index 0df39c4..fb8c8e6 100644
--- a/.gitignore
+++ b/.gitignore
@@ -325,3 +325,4 @@ __pycache__/
/Examples/MCMC/Dextran/nsga3_mcmc_6_emcee12_new
/Examples/MCMC/Dextran/nsga3_mcmc_6_emcee6_new
/Examples/MCMC/NonBinding/fit_delay
+/Examples/MCMC/Linear/fit
diff --git a/CADETMatch.egg-info/PKG-INFO b/CADETMatch.egg-info/PKG-INFO
index 7f8d9af..c004e49 100644
--- a/CADETMatch.egg-info/PKG-INFO
+++ b/CADETMatch.egg-info/PKG-INFO
@@ -1,6 +1,6 @@
Metadata-Version: 2.1
Name: CADETMatch
-Version: 0.5.26
+Version: 0.5.27
Summary: CADETMatch is a parameter estimation and error modeling library for CADET
Home-page: https://github.com/modsim/CADET-Match
Author: William Heymann
diff --git a/CADETMatch.egg-info/SOURCES.txt b/CADETMatch.egg-info/SOURCES.txt
index 5c47fd0..cd2afaf 100644
--- a/CADETMatch.egg-info/SOURCES.txt
+++ b/CADETMatch.egg-info/SOURCES.txt
@@ -11,6 +11,7 @@ CADETMatch/de_snooker.py
CADETMatch/evo.py
CADETMatch/fitness.py
CADETMatch/ga_simple.py
+CADETMatch/generate_autocorr_graphs.py
CADETMatch/generate_corner_graphs.py
CADETMatch/generate_graphs.py
CADETMatch/grad.py
diff --git a/CADETMatch/CADETMatch.pyproj b/CADETMatch/CADETMatch.pyproj
index 5911bef..f665d86 100644
--- a/CADETMatch/CADETMatch.pyproj
+++ b/CADETMatch/CADETMatch.pyproj
@@ -4,7 +4,7 @@
2.0
0067cb6f-0de6-4dd6-8086-20ea899a691d
.
- generate_autocorr_graphs.py
+ match.py
..
@@ -14,7 +14,7 @@
False
CondaEnv|CondaEnv|CADETMatch
Standard Python launcher
- "C:\Users\kosh_000\Documents\Visual Studio 2017\Projects\CADETMatch\Examples\MCMC\Dextran\nsga3_mcmc_6_emcee12_new\mcmc_refine\MCMC_dextran_nsga3.json" 1
+ "C:\Users\kosh_000\Documents\Visual Studio 2017\Projects\CADETMatch\Examples\MCMC\Linear\fit\mcmc_refine\MCMC_linear.json" 6
False
diff --git a/CADETMatch/__main__.py b/CADETMatch/__main__.py
index 2f5793e..97b93e5 100644
--- a/CADETMatch/__main__.py
+++ b/CADETMatch/__main__.py
@@ -81,7 +81,7 @@ def run_command(module, json, number_of_jobs, additional=None):
if args.generate_corner:
sys.exit(run_command('CADETMatch.generate_corner_graphs', args.json, args.n))
if args.generate_graphs_autocorr:
- sys.exit(run_command('CADETMatch.generate_graphs_autocorr', args.json, args.n))
+ sys.exit(run_command('CADETMatch.generate_autocorr_graphs', args.json, args.n))
if args.generate_graphs:
sys.exit(run_command('CADETMatch.generate_graphs', args.json, args.n, ['1']))
if args.generate_graphs_all:
diff --git a/CADETMatch/generate_autocorr_graphs.py b/CADETMatch/generate_autocorr_graphs.py
index 259aa7b..bb9596f 100644
--- a/CADETMatch/generate_autocorr_graphs.py
+++ b/CADETMatch/generate_autocorr_graphs.py
@@ -80,7 +80,7 @@ def main(map_function):
graph_dir = cache.settings['resultsDirSpace'] / "mcmc"
- input_headers = cache.parameter_headers
+ input_headers = cache.parameter_headers_actual
for chain in ("full_chain", "train_full_chain", "bounds_full_chain"):
if chain in mcmc_store.root:
diff --git a/CADETMatch/search/mcmc.py b/CADETMatch/search/mcmc.py
index 6ef8f0c..276991b 100644
--- a/CADETMatch/search/mcmc.py
+++ b/CADETMatch/search/mcmc.py
@@ -279,7 +279,15 @@ def sampler_auto_bounds(cache, checkpoint, sampler, checkpointFile, mcmc_store):
parameters = len(cache.MIN_VALUE)
- new_parameters = len(cache.settings['parameters']) - len(cache.settings.get('parameters_mcmc', []))
+ if 'mcmc_h5' in cache.settings:
+ data = cadet.H5()
+ data.filename = cache.settings['mcmc_h5']
+ data.load(paths='/bounds_change/center_trans')
+ previous_parameters = data.root.bounds_change.center_trans.shape[1]
+ else:
+ previous_parameters = 0
+
+ new_parameters = parameters - previous_parameters
finished = False
@@ -324,6 +332,7 @@ def sampler_auto_bounds(cache, checkpoint, sampler, checkpointFile, mcmc_store):
converged, lb, ub = converged_bounds(bounds_chain[:,:,:new_parameters], 200, 1e-3)
if converged:
+ #sys.exit()
finished = True
new_min_value, center, new_max_value = rescale(cache, lb, ub, numpy.array(cache.MIN_VALUE), numpy.array(cache.MAX_VALUE), mcmc_store)
diff --git a/Examples/MCMC/Linear/MCMC_linear.json b/Examples/MCMC/Linear/MCMC_linear.json
index 6a04e01..ce6d55f 100644
--- a/Examples/MCMC/Linear/MCMC_linear.json
+++ b/Examples/MCMC/Linear/MCMC_linear.json
@@ -4,15 +4,37 @@
"resultsDir": "fit/",
"CSV": "linear_MCMC.csv",
"checkpointFile": "check",
- "searchMethod": "MCMC",
- "population": 100,
- "roundParameters": 6,
- "roundScores": 6,
+ "stopAverage": 1.1,
+ "stopBest": 1.1,
+ "gradCheck": 1.1,
+ "gradVector": 1,
+ "searchMethod": "NSGA3",
+ "mutationRate": 1.0,
+ "crossoverRate": 1.0,
+ "generations": 1000,
+ "population": 24,
"metaResultsOnly": 1,
"sobolGeneration":1,
- "scoreMCMC":"score",
- "graphSpearman": 0,
+ "stallGenerations": 50,
"normalizeOutput":1,
+ "graphMetaTime": 600,
+ "finalGradRefinement": 1,
+ "continueMCMC": 1,
+ "MCMCpopulationSet": 24,
+ "kde_synthetic": [
+ {
+ "file_path": "linear_pulse.h5",
+ "experimental_csv": "linear_pulse.csv",
+ "name": "main",
+ "units": [2],
+ "delay": [0.0, 2.0],
+ "flow": [1.0,0.007],
+ "load": [1.0,0.007],
+ "uv_noise": [0.0,1e-8],
+ "base": 100.0,
+ "count": 4000
+ }
+ ],
"parameters": [
{
"transform": "norm_keq",
@@ -30,19 +52,15 @@
],
"experiments": [
{
- "CSV": "F:/CADET_ParameterEstimation/adsorption/lrmp/linear/linear_pulse.csv",
+ "CSV": "linear_pulse.csv",
"isotherm": "/output/solution/unit_001/SOLUTION_OUTLET_COMP_000",
- "HDF5": "F:/CADET_ParameterEstimation/adsorption/lrmp/linear/linear_pulse.h5",
+ "HDF5": "linear_pulse.h5",
"name": "main",
"timeout": 3.785061836242676,
"features": [
{
"name": "Pulse",
- "type": "similarityHybrid2"
- },
- {
- "name": "Deriv",
- "type": "derivative_similarity_hybrid2"
+ "type": "ShapeDecay"
}
]
}