feat: added calculate_tr and caculate_rdf

Author: CPrescher

changelog.md

@@ -1,10 +1,15 @@
+## 2.2.2 (upcoming)
+
+### New features
+
+- added calculate_rdf and calculate_tr functions to the transform module
+
 ## 2.2.1 (2025/07/21)
 
 ### Bugfixes
 
 - when optimizing the density, the lorch modififcation function is applied in accordance with the calculation configuration. This means, that it is applied before the chi-square calculation.
 
-
 ## 2.2.0 (2025/07/21)
 
 ### New features

glassure/transform.py

@@ -217,3 +217,35 @@ def calculate_gr(fr_pattern: Pattern, atomic_density: float) -> Pattern:
     r_safe = np.where(r == 0, 1e-10, r)
     g_r = 1 + f_r / (4.0 * np.pi * r_safe * atomic_density)
     return Pattern(r, g_r)
+
+
+def calculate_rdf(gr_pattern: Pattern, atomic_density: float) -> Pattern:
+    """
+    Calculates a RDF pattern from a given g(r) pattern and the atomic density
+
+    RDF = 4 * pi * r^2 * g(r) * rho
+
+    :param gr_pattern:     g(r) pattern
+    :param atomic_density:  atomic density in atoms/A^3
+
+    :return: RDF pattern
+    """
+    r, g_r = gr_pattern.data
+    rdf = 4 * np.pi * r**2 * g_r * atomic_density
+    return Pattern(r, rdf)
+
+
+def calculate_tr(gr_pattern: Pattern, atomic_density: float) -> Pattern:
+    """
+    Calculates a transfer function from a given g(r) pattern and the atomic density
+
+    T(r) = 4 * pi * r * g(r) * rho = RDF/r
+
+    :param gr_pattern:     g(r) pattern
+    :param atomic_density:  atomic density in atoms/A^3
+
+    :return: transfer function
+    """
+    r, g_r = gr_pattern.data
+    tr = 4 * np.pi * r * g_r * atomic_density
+    return Pattern(r, tr)

tests/test_transform.py

@@ -16,7 +16,10 @@
     calculate_sq,
     calculate_fr,
     calculate_gr,
+    calculate_rdf,
     calculate_sq_from_fr,
+    calculate_rdf,
+    calculate_tr,
 )
 
 from . import unittest_data_path
@@ -186,3 +189,20 @@ def test_calculate_fr_then_sq_and_fr(sq):
     sq_from_fr = calculate_sq_from_fr(fr, sq.x, method="fft")
     fr_from_sq = calculate_fr(sq_from_fr)
     assert np.allclose(fr.y, fr_from_sq.y, atol=0.2)
+
+
+def test_calculate_rdf(sq, atomic_density):
+    fr = calculate_fr(sq)
+    gr = calculate_gr(fr, atomic_density)
+
+    rdf = calculate_rdf(gr, atomic_density)
+
+    assert np.allclose(rdf.y, 4 * np.pi * gr.x**2 * atomic_density * gr.y, atol=0.2)
+
+
+def test_calculate_tr(sq, atomic_density):
+    fr = calculate_fr(sq)
+    gr = calculate_gr(fr, atomic_density)
+    rdf = calculate_rdf(gr, atomic_density)
+    tr = calculate_tr(gr, atomic_density)
+    assert np.allclose(tr.y, rdf.y / gr.x, atol=0.2)