Merge pull request #169 from cadenmyers13/recipeorg-dep2

deprecate: deprecate the rest of the methods in `recipeorganizer.py`

Author: sbillinge

docs/examples/coreshellnp.py

@@ -91,14 +91,14 @@ def makeRecipe(stru1, stru2, datname):
     # diameter to twice the shell radius.
     recipe.add_variable(contribution.radius, 15)
     recipe.add_variable(contribution.thickness, 11)
-    recipe.constrain(contribution.psize, "2 * radius")
+    recipe.add_constraint(contribution.psize, "2 * radius")
 
     # Configure the fit variables
     # Start by configuring the scale factor and resolution factors.
     # We want the sum of the phase scale factors to be 1.
     recipe.create_new_variable("scale_CdS", 0.7)
-    recipe.constrain(generator_cds.scale, "scale_CdS")
-    recipe.constrain(generator_zns.scale, "1 - scale_CdS")
+    recipe.add_constraint(generator_cds.scale, "scale_CdS")
+    recipe.add_constraint(generator_zns.scale, "1 - scale_CdS")
     # We also want the resolution factor to be the same on each.
 
     # Vary the global scale as well.
@@ -117,7 +117,7 @@ def makeRecipe(stru1, stru2, datname):
     )
     # Since we know these have stacking disorder, constrain the B33 adps for
     # each atom type.
-    recipe.constrain("B33_1_cds", "B33_0_cds")
+    recipe.add_constraint("B33_1_cds", "B33_0_cds")
     recipe.add_variable(generator_cds.delta2, name="delta2_cds", value=5)
 
     phase_zns = generator_zns.phase
@@ -128,7 +128,7 @@ def makeRecipe(stru1, stru2, datname):
     recipe.add_variable(
         phase_zns.sgpars.xyzpars.z_1, name="z_1_zns", tag="xyz"
     )
-    recipe.constrain("B33_1_zns", "B33_0_zns")
+    recipe.add_constraint("B33_1_zns", "B33_0_zns")
     recipe.add_variable(generator_zns.delta2, name="delta2_zns", value=2.5)
 
     # Give the recipe away so it can be used!

docs/examples/crystalpdfall.py

@@ -113,24 +113,24 @@ def makeRecipe(
     for par in phase_ni.sgpars:
         recipe.add_variable(par, name=par.name + "_ni")
     delta2_ni = recipe.create_new_variable("delta2_ni", 2.5)
-    recipe.constrain(xgenerator_ni.delta2, delta2_ni)
-    recipe.constrain(ngenerator_ni.delta2, delta2_ni)
-    recipe.constrain(xgenerator_sini_ni.delta2, delta2_ni)
+    recipe.add_constraint(xgenerator_ni.delta2, delta2_ni)
+    recipe.add_constraint(ngenerator_ni.delta2, delta2_ni)
+    recipe.add_constraint(xgenerator_sini_ni.delta2, delta2_ni)
 
     for par in phase_si.sgpars:
         recipe.add_variable(par, name=par.name + "_si")
     delta2_si = recipe.create_new_variable("delta2_si", 2.5)
-    recipe.constrain(xgenerator_si.delta2, delta2_si)
-    recipe.constrain(xgenerator_sini_si.delta2, delta2_si)
+    recipe.add_constraint(xgenerator_si.delta2, delta2_si)
+    recipe.add_constraint(xgenerator_sini_si.delta2, delta2_si)
 
     # Now the experimental parameters
     recipe.add_variable(xgenerator_ni.scale, name="xscale_ni")
     recipe.add_variable(xgenerator_si.scale, name="xscale_si")
     recipe.add_variable(ngenerator_ni.scale, name="nscale_ni")
     recipe.add_variable(xcontribution_sini.scale, 1.0, "xscale_sini")
     recipe.create_new_variable("pscale_sini_ni", 0.8)
-    recipe.constrain(xgenerator_sini_ni.scale, "pscale_sini_ni")
-    recipe.constrain(xgenerator_sini_si.scale, "1 - pscale_sini_ni")
+    recipe.add_constraint(xgenerator_sini_ni.scale, "pscale_sini_ni")
+    recipe.add_constraint(xgenerator_sini_si.scale, "1 - pscale_sini_ni")
 
     # The qdamp parameters are too correlated to vary so we fix them based on
     # previous measurements.

docs/examples/crystalpdftwodata.py

@@ -121,8 +121,8 @@ def makeRecipe(ciffile, xdatname, ndatname):
     # delta2 is a non-structual material property. Thus, we constrain together
     # delta2 Parameter from each PDFGenerator.
     delta2 = recipe.create_new_variable("delta2", 2)
-    recipe.constrain(xgenerator.delta2, delta2)
-    recipe.constrain(ngenerator.delta2, delta2)
+    recipe.add_constraint(xgenerator.delta2, delta2)
+    recipe.add_constraint(ngenerator.delta2, delta2)
 
     # We only need to constrain phase properties once since there is a single
     # ObjCrystCrystalParSet for the Crystal.

docs/examples/crystalpdftwophase.py

@@ -90,12 +90,12 @@ def makeRecipe(niciffile, siciffile, datname):
     # Start by configuring the scale factor and resolution factors.
     # We want the sum of the phase scale factors to be 1.
     recipe.create_new_variable("scale_ni", 0.1)
-    recipe.constrain(generator_ni.scale, "scale_ni")
-    recipe.constrain(generator_si.scale, "1 - scale_ni")
+    recipe.add_constraint(generator_ni.scale, "scale_ni")
+    recipe.add_constraint(generator_si.scale, "1 - scale_ni")
     # We also want the resolution factor to be the same on each.
     recipe.create_new_variable("qdamp", 0.03)
-    recipe.constrain(generator_ni.qdamp, "qdamp")
-    recipe.constrain(generator_si.qdamp, "qdamp")
+    recipe.add_constraint(generator_ni.qdamp, "qdamp")
+    recipe.add_constraint(generator_si.qdamp, "qdamp")
 
     # Vary the global scale as well.
     recipe.add_variable(contribution.scale, 1)
@@ -123,18 +123,30 @@ def makeRecipe(niciffile, siciffile, datname):
     # derived has no uncertainty. Thus, we will tell the recipe to scale the
     # residual, which means that it will be weighted as much as the average
     # data point during the fit.
-    recipe.restrain("a_ni", lb=3.527, ub=3.527, scaled=True)
+    recipe.add_soft_bounds(
+        "a_ni", lower_bound=3.527, upper_bound=3.527, scaled=True
+    )
     # Now we do the same with the delta2 and Biso parameters (remember that
     # Biso = 8*pi**2*Uiso)
-    recipe.restrain("delta2_ni", lb=2.22, ub=2.22, scaled=True)
-    recipe.restrain("Biso_0_ni", lb=0.454, ub=0.454, scaled=True)
+    recipe.add_soft_bounds(
+        "delta2_ni", lower_bound=2.22, upper_bound=2.22, scaled=True
+    )
+    recipe.add_soft_bounds(
+        "Biso_0_ni", lower_bound=0.454, upper_bound=0.454, scaled=True
+    )
     #
     # We can do the same with the silicon values. We haven't done a thorough
     # job of measuring the uncertainties in the results, so we'll scale these
     # as well.
-    recipe.restrain("a_si", lb=5.430, ub=5.430, scaled=True)
-    recipe.restrain("delta2_si", lb=3.54, ub=3.54, scaled=True)
-    recipe.restrain("Biso_0_si", lb=0.645, ub=0.645, scaled=True)
+    recipe.add_soft_bounds(
+        "a_si", lower_bound=5.430, upper_bound=5.430, scaled=True
+    )
+    recipe.add_soft_bounds(
+        "delta2_si", lower_bound=3.54, upper_bound=3.54, scaled=True
+    )
+    recipe.add_soft_bounds(
+        "Biso_0_si", lower_bound=0.645, upper_bound=0.645, scaled=True
+    )
 
     # Give the recipe away so it can be used!
     return recipe

docs/examples/debyemodel.py

@@ -152,7 +152,7 @@ def makeRecipe():
     # breaking the restraint by the point-average chi^2 value so that the
     # restraint is roughly as significant as any other data point throughout
     # the fit.
-    recipe.restrain(recipe.offset, lb=0, scaled=True)
+    recipe.add_soft_bounds(recipe.offset, lower_bound=0, scaled=True)
 
     # We're done setting up the recipe. We can now do other things with it.
     return recipe

docs/examples/debyemodelII.py

@@ -89,8 +89,8 @@ def makeRecipeII():
     # We create a new Variable and use the recipe's "constrain" method to
     # associate the Debye temperature parameters with that variable.
     recipe.create_new_variable("thetaD", 100)
-    recipe.constrain(recipe.lowT.thetaD, "thetaD")
-    recipe.constrain(recipe.highT.thetaD, "thetaD")
+    recipe.add_constraint(recipe.lowT.thetaD, "thetaD")
+    recipe.add_constraint(recipe.highT.thetaD, "thetaD")
     return recipe
 
 

docs/examples/npintensity.py

@@ -290,15 +290,15 @@ def gaussian(q, q0, width):
     lattice = phase.getLattice()
     a = lattice.a
     recipe.add_variable(a)
-    recipe.constrain(lattice.b, a)
-    recipe.constrain(lattice.c, a)
+    recipe.add_constraint(lattice.b, a)
+    recipe.add_constraint(lattice.c, a)
     # We want to refine the thermal parameters as well. We will add a new
     # Variable that we call "Uiso" and constrain the atomic Uiso values to
     # this. Note that we don't give Uiso an initial value. The initial value
     # will be inferred from the following constraints.
     Uiso = recipe.create_new_variable("Uiso")
     for atom in phase.getScatterers():
-        recipe.constrain(atom.Uiso, Uiso)
+        recipe.add_constraint(atom.Uiso, Uiso)
 
     # Give the recipe away so it can be used!
     return recipe

docs/examples/npintensityII.py

@@ -173,15 +173,15 @@ def gaussian(q, q0, width):
     a = recipe.add_variable(lattice.a)
     # We want to allow for isotropic expansion, so we'll make constraints for
     # that.
-    recipe.constrain(lattice.b, a)
-    recipe.constrain(lattice.c, a)
+    recipe.add_constraint(lattice.b, a)
+    recipe.add_constraint(lattice.c, a)
     # We want to refine the thermal parameters as well. We will add a new
     # variable that we call "Uiso" and constrain the atomic Uiso values to
     # this. Note that we don't give Uiso an initial value. The initial value
     # will be inferred from the subsequent constraints.
     Uiso = recipe.create_new_variable("Uiso")
     for atom in phase.getScatterers():
-        recipe.constrain(atom.Uiso, Uiso)
+        recipe.add_constraint(atom.Uiso, Uiso)
 
     # Give the recipe away so it can be used!
     return recipe

docs/examples/nppdfobjcryst.py

@@ -73,7 +73,7 @@ def makeRecipe(molecule, datname):
         # has no scattering power. It is only used as a reference point for
         # our bond length. We don't want to constrain it.
         if not atom.isDummy():
-            recipe.constrain(atom.Biso, Biso)
+            recipe.add_constraint(atom.Biso, Biso)
 
     # We need to let the molecule expand. If we were modeling it as a crystal,
     # we could let the unit cell expand. For instruction purposes, we use a
@@ -97,7 +97,7 @@ def makeRecipe(molecule, datname):
         # This creates a Parameter that moves the second atom according to the
         # bond length. Note that each Parameter needs a unique name.
         par = c60.addBondLengthParameter("rad%i" % i, center, atom)
-        recipe.constrain(par, radius)
+        recipe.add_constraint(par, radius)
 
     # Add the correlation term, scale. The scale is too short to effectively
     # determine qdamp.

docs/examples/nppdfsas.py

@@ -113,8 +113,8 @@ def makeRecipe(ciffile, grdata, iqdata):
     # Even though the cfcalculator and sasgenerator depend on the same sas
     # model, we must still constrain the cfcalculator Parameters so that it is
     # informed of changes in the refined parameters.
-    recipe.constrain(cfcalculator.radius_a, "radius_a")
-    recipe.constrain(cfcalculator.radius_b, "radius_b")
+    recipe.add_constraint(cfcalculator.radius_a, "radius_a")
+    recipe.add_constraint(cfcalculator.radius_b, "radius_b")
 
     return recipe
 
@@ -126,9 +126,9 @@ def fitRecipe(recipe):
     recipe.set_weight(recipe.pdf, 0)
     recipe.fix("all")
     recipe.free("radius_a", "radius_b", iqscale=1e8)
-    recipe.constrain("radius_b", "radius_a")
+    recipe.add_constraint("radius_b", "radius_a")
     scipyOptimize(recipe)
-    recipe.unconstrain("radius_b")
+    recipe.remove_constraint("radius_b")
 
     # Tune PDF
     recipe.set_weight(recipe.pdf, 1)