Merge pull request #30 from rjkoch/fix_qbroad_bug

modified JeongPeakWidth to include new Q_broad term

Author: sbillinge

.travis.yml

@@ -147,3 +147,7 @@ after_success:
   - cd $TRAVIS_BUILD_DIR
   - pip install $MYPIPFLAGS codecov
   - codecov
+  -
+deploy:
+  - provider: releases
+  - draft: true

src/diffpy/srreal/JeongPeakWidth.cpp

@@ -30,14 +30,16 @@ using namespace std;
 // Constructors --------------------------------------------------------------
 
 JeongPeakWidth::JeongPeakWidth() :
-    mdelta1(0.0), mdelta2(0.0), mqbroad(0.0)
+    mdelta1(0.0), mdelta2(0.0), mqbroad(0.0), mqbroad_seperable(0.0)
 {
     this->registerDoubleAttribute("delta1",
             this, &JeongPeakWidth::getDelta1, &JeongPeakWidth::setDelta1);
     this->registerDoubleAttribute("delta2",
             this, &JeongPeakWidth::getDelta2, &JeongPeakWidth::setDelta2);
     this->registerDoubleAttribute("qbroad",
             this, &JeongPeakWidth::getQbroad, &JeongPeakWidth::setQbroad);
+    this->registerDoubleAttribute("qbroad_seperable",
+            this, &JeongPeakWidth::getQbroad_seperable, &JeongPeakWidth::setQbroad_seperable);
 }
 
 
@@ -69,7 +71,8 @@ double JeongPeakWidth::calculate(const BaseBondGenerator& bnds) const
     double corr = this->msdSharpeningRatio(r);
     // avoid calculating square root of negative value
     double fwhm = (corr <= 0) ? 0.0 :
-        (sqrt(corr) * this->DebyeWallerPeakWidth::calculate(bnds));
+        (sqrt(corr) * this->DebyeWallerPeakWidth::calculate(bnds) +
+        pow(this->getQbroad_seperable()*r, 2));
     return fwhm;
 }
 
@@ -82,7 +85,7 @@ double JeongPeakWidth::maxWidth(StructureAdapterPtr stru,
             this->msdSharpeningRatio(rmin),
             this->msdSharpeningRatio(rmax));
     // if the sharpening factor is larger than 1 adjust the maximum width
-    double rv = maxwidth0 * sqrt(max(1.0, maxmsdsharp));
+    double rv = maxwidth0 * sqrt(max(1.0, maxmsdsharp))+ pow(this->getQbroad_seperable()*rmax, 2);
     return rv;
 }
 
@@ -118,6 +121,19 @@ const double& JeongPeakWidth::getQbroad() const
 }
 
 
+const double& JeongPeakWidth::getQbroad_seperable() const
+{
+    return mqbroad_seperable;
+}
+
+
+void JeongPeakWidth::setQbroad_seperable(double qbroad_seperable)
+{
+    if (mqbroad_seperable != qbroad_seperable)  mticker.click();
+    mqbroad_seperable = qbroad_seperable;
+}
+
+
 void JeongPeakWidth::setQbroad(double qbroad)
 {
     if (mqbroad != qbroad)  mticker.click();

src/diffpy/srreal/JeongPeakWidth.hpp

@@ -49,13 +49,16 @@ class JeongPeakWidth : public DebyeWallerPeakWidth
         void setDelta2(double);
         const double& getQbroad() const;
         void setQbroad(double);
+        const double& getQbroad_seperable() const;
+        void setQbroad_seperable(double);
 
     private:
 
         // data
         double mdelta1;
         double mdelta2;
         double mqbroad;
+        double mqbroad_seperable;
 
         // methods
         double msdSharpeningRatio(const double& r) const;
@@ -71,6 +74,7 @@ class JeongPeakWidth : public DebyeWallerPeakWidth
             ar & mdelta1;
             ar & mdelta2;
             ar & mqbroad;
+            ar & mqbroad_seperable;
         }
 
 };

src/tests/TestPDFCalculator.hpp

@@ -55,15 +55,18 @@ class TestPDFCalculator : public CxxTest::TestSuite
             TS_ASSERT_EQUALS(0.0, jpw0->getDoubleAttr("delta1"));
             TS_ASSERT_EQUALS(0.0, jpw0->getDoubleAttr("delta2"));
             TS_ASSERT_EQUALS(0.0, jpw0->getDoubleAttr("qbroad"));
+            TS_ASSERT_EQUALS(0.0, jpw0->getDoubleAttr("qbroad_seperable"));
             JeongPeakWidth jpw;
             jpw.setDelta1(1.0);
             jpw.setDelta2(2.0);
             jpw.setQbroad(3.0);
+            jpw.setQbroad_seperable(4.0);
             mpdfc->setPeakWidthModel(jpw.clone());
             const PeakWidthModelPtr& jpw1 = mpdfc->getPeakWidthModel();
             TS_ASSERT_EQUALS(1.0, jpw1->getDoubleAttr("delta1"));
             TS_ASSERT_EQUALS(2.0, jpw1->getDoubleAttr("delta2"));
             TS_ASSERT_EQUALS(3.0, jpw1->getDoubleAttr("qbroad"));
+            TS_ASSERT_EQUALS(4.0, jpw1->getDoubleAttr("qbroad_seperable"));
         }
 
 

src/tests/TestPeakWidthModel.hpp

@@ -84,13 +84,15 @@ class TestPeakWidthModel : public CxxTest::TestSuite
         void test_attributes()
         {
             TS_ASSERT_EQUALS(0, mdwpw->namesOfDoubleAttributes().size());
-            TS_ASSERT_EQUALS(3, mjepw->namesOfDoubleAttributes().size());
+            TS_ASSERT_EQUALS(4, mjepw->namesOfDoubleAttributes().size());
             mcjepw->setDelta1(0.1);
             mcjepw->setDelta2(0.2);
             mcjepw->setQbroad(0.3);
+            mcjepw->setQbroad_seperable(0.4);
             TS_ASSERT_EQUALS(0.1, mjepw->getDoubleAttr("delta1"));
             TS_ASSERT_EQUALS(0.2, mjepw->getDoubleAttr("delta2"));
             TS_ASSERT_EQUALS(0.3, mjepw->getDoubleAttr("qbroad"));
+            TS_ASSERT_EQUALS(0.4, mjepw->getDoubleAttr("qbroad_seperable"));
         }
 
 
@@ -108,6 +110,7 @@ class TestPeakWidthModel : public CxxTest::TestSuite
             TS_ASSERT_DELTA(0.5 * w, mjepw->calculate(*bnds), meps);
             mcjepw->setDelta2(0);
             mcjepw->setQbroad(sqrt(3));
+            mcjepw->setQbroad_seperable(0);
             TS_ASSERT_DELTA(2 * w, mjepw->calculate(*bnds), meps);
         }
 
@@ -121,12 +124,14 @@ class TestPeakWidthModel : public CxxTest::TestSuite
             mcjepw->setDelta1(1.1);
             mcjepw->setDoubleAttr("delta2", 2.2);
             mcjepw->setDoubleAttr("qbroad", 0.03);
+            mcjepw->setDoubleAttr("qbroad_seperable", 0.003);
             PeakWidthModelPtr pwm2 = dumpandload(mjepw);
             JeongPeakWidth* cpwm2 = dynamic_cast<JeongPeakWidth*>(pwm2.get());
             TS_ASSERT(cpwm2);
             TS_ASSERT_EQUALS(1.1, pwm2->getDoubleAttr("delta1"));
             TS_ASSERT_EQUALS(2.2, pwm2->getDoubleAttr("delta2"));
             TS_ASSERT_EQUALS(0.03, pwm2->getDoubleAttr("qbroad"));
+            TS_ASSERT_EQUALS(0.003, pwm2->getDoubleAttr("qbroad_seperable"));
         }