* Added testsuite for stochastic fitting (one testcase).

TESTS/test_stochastic_fitting.py

@@ -0,0 +1,119 @@
+# Created: 20150528
+# Test module for stochastic fitting
+
+import numpy
+from wpylib.params import struct
+from wpylib.math.fitting.stochastic import StochasticFitting
+
+def setup_MC_TZ():
+  """
+  Internal identifier: Cr2_TZ_data_20140728uhf
+  Binding energy of Cr2, phaseless QMC/UHF, cc-pwCVTZ-DK, dt=0.01
+  """
+  global Cr2_TZ_data_20140728uhf
+  from numpy import asarray, matrix
+  Cr2_TZ_data_20140728uhf = asarray(matrix("""
+       1.550   -1.613    0.025  ;
+       1.600   -1.897    0.036  ;
+       1.6788  -2.141    0.016  ;
+       1.720   -2.143    0.025  ;
+       1.800   -2.190    0.022  ;
+       1.900   -2.064    0.020  ;
+       2.000   -2.038    0.023  ;
+       2.400   -1.611    0.019  ;
+       3.000   -1.037    0.018
+  """))
+
+
+
+def test_fit_PEC_MC_TZ(show_samples=True, save_fig=False):
+  """20150528
+  PEC fitting, using `morse2` functional form.
+
+  Options:
+  - show_samples : prints the sample data (recommended)
+  - save_fig : dumps the fit result for each stochastic snapshot
+    (not recommended unless you are debugging/diagnosing)
+
+  Modeled after do_morse2_sfit routine in Cr2 analysis script.
+
+  Example output:
+
+      test_MC_TZ_PEC_fit::
+      ansatz=morse2_fit_func
+      Raw data: (x, y, dy)
+             1.550   -1.613    0.025
+             1.600   -1.897    0.036
+             1.679   -2.141    0.016
+             1.720   -2.143    0.025
+             1.800   -2.190    0.022
+             1.900   -2.064    0.020
+             2.000   -2.038    0.023
+             2.400   -1.611    0.019
+             3.000   -1.037    0.018
+      Using guess param from NLF:  [-2.18625505  9.82497657  1.80455072  1.86192922]
+      Final parameters          : -2.187(10)  9.85(61)  1.8044(66)  1.864(83)
+      Total execution time = 0.55 secs
+      All testings passed.
+  """
+  from numpy import array
+  from wpylib.text_tools import matrix_str, str_indent
+  from wpylib.timer import block_timer as Timer
+  from wpylib.math.fitting.funcs_pec import morse2_fit_func
+  from wpylib.py import function_name
+
+  global MC_TZ_PEC_fit
+  global Cr2_TZ_data_20140728uhf
+
+  print("test_MC_TZ_PEC_fit::")
+  setup_MC_TZ()
+
+  # parameters etc
+  ansatz = morse2_fit_func()
+  rng = dict(seed=378711, rng_class=numpy.random.RandomState)
+  rawdata = Cr2_TZ_data_20140728uhf
+  sfit = MC_TZ_PEC_fit = StochasticFitting()
+
+  print("ansatz=%s" \
+        % (function_name(ansatz),))
+
+  # This corresponds to fit_variant==1 in the subroutine
+  ansatz.fit_method = "leastsq"
+  ansatz.fit_opts['leastsq'] = dict(xtol=1e-8, epsfcn=1e-6)
+
+  sfit.init_func(ansatz)
+  sfit.init_samples(x=rawdata[:,0], y=rawdata[:,1], dy=rawdata[:,2])
+  sfit.init_rng(**rng)
+  if show_samples:
+    print("Raw data: (x, y, dy)")
+    print(str_indent(matrix_str(rawdata, fmt="%8.3f")))
+
+  with Timer() as tmr:
+    sfit.mcfit_loop_begin_()
+    sfit.mcfit_loop1_(num_iter=200, save_fig=save_fig)
+    sfit.mcfit_loop_end_()
+    sfit.mcfit_analysis_()
+    sfit.mcfit_report_final_params()
+
+  nlf_fit_result = sfit.nlf_rec['xopt']
+
+  # Verify the results:
+  # * deterministic fit (only precise to these digits; more digits are discarded)
+  nlf_fit_ref = numpy.array([-2.18625505,  9.82497657,  1.80455072,  1.86192922])
+
+  assert numpy.allclose(nlf_fit_result, nlf_fit_ref, atol=0.6e-8, rtol=0)
+
+  def match_mc_param(name, val_ref, err_ref, atol):
+    vv = sfit.final_mc_params[name]
+    assert numpy.allclose(vv.value(), val_ref, atol=atol, rtol=0)
+    assert numpy.allclose(vv.error(), err_ref, atol=atol, rtol=0)
+
+  match_mc_param('E0', -2.187,  0.010,  0.6e-3)
+  match_mc_param('k',   9.85,   0.61,   0.6e-2)
+  match_mc_param('r0',  1.8044, 0.0066, 0.6e-4)
+  match_mc_param('a',   1.864,  0.083,  0.6e-3)
+  print("All testings passed.")
+
+
+if __name__ == '__main__':
+  test_fit_PEC_MC_TZ()