finish off refinement self-test

Author: briantoby

GSASII/GSASII.py

@@ -14,7 +14,6 @@
 
 if pkginfo is None:  # fixup path if GSASII not installed into Python
     os.environ["GSASII_YOLO_PATH"] = "True"
-    #print('GSAS-II not installed in Python: Hacking sys.path')
     sys.path.insert(0,os.path.dirname(os.path.dirname(__file__)))
 
 from GSASII.GSASIIGUI import main

GSASII/GSASIIctrlGUI.py

@@ -49,7 +49,6 @@
 from . import GSASIImath as G2mth
 from . import GSASIIstrMain as G2stMn
 from . import GSASIImiscGUI as G2IO
-from . import config_example
 from .tutorialIndex import tutorialIndex
 if sys.version_info[0] >= 3:
     unicode = str

docs/source/GSASIIscriptable.rst

@@ -631,8 +631,9 @@ Sample Parameters                           Should be provided as a **list** of
                                             Available for powder histograms only.
 \                     Absorption
 \                     Contrast
-\                     DisplaceX             Sample displacement along the X direction
-\                     DisplaceY             Sample displacement along the Y direction
+\                     DisplaceX             Sample displacement along the X direction (Debye-Scherrer)
+\                     DisplaceY             Sample displacement along the Y direction (Debye-Scherrer)
+\                     Shift                 Bragg-Brentano sample displacement 
 \                     Scale                 Histogram Scale factor
 
 Background                                  Sample background. Value will be a dict or 

tests/test_scripting.py

@@ -4,34 +4,68 @@
 import os
 import sys
 import tempfile
+import numpy.testing as npt
 home = os.path.dirname(__file__)
 work = tempfile.gettempdir()
+work='/tmp/'
 
 import importlib  # fixup path if GSASII not installed into Python
 if importlib.util.find_spec('GSASII') is None:
-    print('Path hacking!')
+    print('GSAS-II not installed in Python: Hacking sys.path')
     os.environ["GSASII_YOLO_PATH"] = "True"
     sys.path.append(os.path.dirname(home))
 
 import GSASII.GSASIIscriptable as G2sc
 
-dataloc = lambda fil: os.path.join(home,'testinp',fil)
-workloc = lambda fil: os.path.join(work,fil)
-gpx = G2sc.G2Project(newgpx=workloc('test_scripting.gpx'))
-# setup step 1: add two histograms to the project
-hist1 = gpx.add_powder_histogram(dataloc("PBSO4.XRA"),dataloc("INST_XRY.PRM"),
-                                     fmthint='GSAS powder')
-hist2 = gpx.add_powder_histogram(dataloc("PBSO4.CWN"),dataloc("inst_d1a.prm"),
-                                     fmthint='GSAS powder')
-# setup step 2: add a phase and link it to the previous histograms
-phase0 = gpx.add_phase(dataloc("PbSO4-Wyckoff.cif"),
-                      phasename="PbSO4", histograms=[hist1,hist2])
-gpx.set_Controls('cycles', 0)
-gpx.refine()
-print(hist1.residuals['wR'])
-print(hist2.residuals['wR'])
-gpx.set_Controls('cycles', 8)
-refdict0 = {"set": {"Background": { "no. coeffs": 3, "refine": True }}}
-gpx.do_refinements([refdict0])
-print(hist1.residuals['wR'])
-print(hist2.residuals['wR'])
+def test_refine():
+    def testR(msg,w1,w2):
+        print(f"*** {msg}: Rwp(h1)={h1.residuals['wR']:.5f}, Rwp(h2)={h2.residuals['wR']:.5f}")
+        npt.assert_allclose([h1.residuals['wR'],h2.residuals['wR']],
+                            [w1,w2], rtol=0.0001)
+
+    print('test_refine(): test a small refinement')
+    dataloc = lambda fil: os.path.join(home,'testinp',fil)
+    workloc = lambda fil: os.path.join(work,fil)
+    gpx = G2sc.G2Project(newgpx=workloc('test_scripting.gpx'))
+    # setup step 1: add two histograms to the project
+    h1 = gpx.add_powder_histogram(dataloc("PBSO4.XRA"),dataloc("INST_XRY.PRM"),
+                                         fmthint='GSAS powder')
+    h2 = gpx.add_powder_histogram(dataloc("PBSO4.CWN"),dataloc("inst_d1a.prm"),
+                                         fmthint='GSAS powder')
+    # setup step 2: add a phase and link it to the previous histograms
+    phase0 = gpx.add_phase(dataloc("PbSO4-Wyckoff.cif"),
+                               phasename="PbSO4", histograms=[h1,h2])
+    gpx.set_Controls('cycles', 0)
+    gpx.refine()
+    testR('Before fitting',96.681098,99.748994)
+    # 
+    h1.set_refinements({'Limits': [16.,158.4]})
+    h2.set_refinements({'Limits': [19.,153.]})
+    gpx.set_Controls('cycles', 8)
+    h1.set_refinements({"Background": { "no. coeffs": 6, "refine": True }})
+    h2.set_refinements({"Background": { "no. coeffs": 3, "refine": True }})
+    gpx.refine()
+    testR('Fit scale & bkg',40.64193551740201,18.6189841945785)
+    #
+    phase0.set_refinements({'Cell':True})
+    phase0.set_HAP_refinements({'HStrain':True},[h2])
+    gpx.refine()
+    testR('Fit cells',30.072804646662338,15.014744642359773)
+    #
+    phase0.set_HAP_refinements({'Mustrain':{'refine':True}},[h1])
+    #phase0.set_HAP_refinements({'Size':{'refine':True}},[h1])
+    h1.set_refinements({"Sample Parameters": {"Shift": True}})
+    h2.set_refinements({"Sample Parameters":["DisplaceX","DisplaceY"]})
+    phase0.set_refinements({"Atoms":{"all":"XU"}})
+    gpx.refine()
+    testR('add Mustrain, Shift, Displace[XY], atomic X & Uiso',
+              12.66845815113383,6.695761603085025)
+    #
+    h1.set_refinements({'Instrument Parameters': ['U', 'V', 'W']})
+    h2.set_refinements({'Instrument Parameters': ['U', 'V', 'W']})
+    gpx.refine()
+    testR('add UVW',10.518485346229324,4.495180030877684)
+    print('OK')
+    
+if __name__ == '__main__':
+    test_refine()