From f436222852d3f7bb2e34e7f98ee9b123ea3dd77f Mon Sep 17 00:00:00 2001 From: Wirawan Purwanto Date: Thu, 28 May 2015 17:23:13 -0400 Subject: [PATCH] * Added testsuite for stochastic fitting (one testcase). --- TESTS/test_stochastic_fitting.py | 119 +++++++++++++++++++++++++++++++ 1 file changed, 119 insertions(+) create mode 100644 TESTS/test_stochastic_fitting.py diff --git a/TESTS/test_stochastic_fitting.py b/TESTS/test_stochastic_fitting.py new file mode 100644 index 0000000..7d9fd82 --- /dev/null +++ b/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()