Changeset d9e1d1

Timestamp:

Apr 23, 2021, 8:34:11 PM (5 years ago)

Author:

Frederik Heber <frederik.heber@…>

Branches:

Candidate_v1.7.0, stable

Children:

ef0f8f

Parents:

addb51

git-author:

Frederik Heber <frederik.heber@…> (10/03/20 21:20:26)

git-committer:

Frederik Heber <frederik.heber@…> (04/23/21 20:34:11)

Message:

Extending PairCorrelation to correlate element and set of atoms.

• one may also correlate an element with a selected set of atoms.
• TEST: Added regression test case.

Files:

• doc/userguide/userguide.xml (modified) (1 diff)
• src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) (1 diff)
• src/Actions/AnalysisAction/PairCorrelationAction.def (modified) (2 diffs)
• tests/regression/Analysis/PairCorrelation/testsuite-analysis-pair-correlation.at (modified) (1 diff)

doc/userguide/userguide.xml

@@ -1743 +1743 @@
           of a hydrogen and an oxygen atom can be found within its distance
           interval. These data files can be used for plotting the distribution right away in order to check on the correlation between the elements.</para>
+          <para>The action may also be called with just a single element in the
+          option <emphasis>elements</emphasis>. This will then trigger a pair
+          correlation between all atoms of this element and the set of 
+          currently selected atoms.</para>
         </section>
         <section xml:id="analysis.dipole-correlation">

src/Actions/AnalysisAction/PairCorrelationAction.cpp

@@ -68 +68 @@
   binoutput.open(params.binoutputname.get().string().c_str());
   PairCorrelationMap *correlationmap = NULL;
-  ASSERT(params.elements.get().size() == 2,
-      "AnalysisPairCorrelationAction::performCall() - Exactly two elements are required for pair correlation.");
-  std::vector<const element *>::const_iterator elemiter = params.elements.get().begin();
-  const World::ConstAtomComposite atoms_first =
-      const_cast<const World &>(World::getInstance()).getAllAtoms(AtomByType(*(elemiter++)));
-  const World::ConstAtomComposite atoms_second =
-      const_cast<const World &>(World::getInstance()).getAllAtoms(AtomByType(*(elemiter++)));
-  ASSERT(elemiter == params.elements.get().end(),
-      "AnalysisPairCorrelationAction::performCall() - Exactly two elements are required for pair correlation.");
+  World::ConstAtomComposite atoms_first;
+  World::ConstAtomComposite atoms_second;
+  if (params.elements.get().size() == 2) {
+    std::vector<const element *>::const_iterator elemiter = params.elements.get().begin();
+    atoms_first = World::getConstInstance().getAllAtoms(AtomByType(*(elemiter++)));
+    if (elemiter != params.elements.get().end()) {
+      atoms_second = World::getConstInstance().getAllAtoms(AtomByType(*(elemiter++)));
+    } else {
+      atoms_second = World::getConstInstance().getSelectedAtoms();
+    }
+  } else if (params.elements.get().size() == 1) {
+    std::vector<const element *>::const_iterator elemiter = params.elements.get().begin();
+    atoms_first = World::getConstInstance().getSelectedAtoms();
+    atoms_second = World::getConstInstance().getAllAtoms(AtomByType(*(elemiter++)));
+  } else {
+    STATUS("Either one or two elements must be given.");
+    return Action::failure;
+  }
   double max_distance = params.BinEnd.get();
   if (params.BinEnd.get() <= 0.) {

src/Actions/AnalysisAction/PairCorrelationAction.def

@@ -29 +29 @@
 #define paramdefaults (NOPARAM_DEFAULT)(NOPARAM_DEFAULT)(PARAM_DEFAULT(0.5))(NOPARAM_DEFAULT)(NOPARAM_DEFAULT)(NOPARAM_DEFAULT)(PARAM_DEFAULT(false))
 #define paramvalids \
-(STLVectorValidator< std::vector<const element *> >(2,2, ElementValidator())) \
+(STLVectorValidator< std::vector<const element *> >(1,2, ElementValidator())) \
 (BoxLengthValidator()) \
 (BoxLengthValidator()) \
@@ -45 +45 @@
 
 // finally the information stored in the ActionTrait specialization
-#define DESCRIPTION "pair correlation analysis between two elements"
+#define DESCRIPTION "pair correlation analysis between all atoms of two given elements, or between the selected atoms and the atoms of the single given element"
 #define SHORTFORM "C"

tests/regression/Analysis/PairCorrelation/testsuite-analysis-pair-correlation.at

@@ -35 +35 @@
 AT_CLEANUP
 
+
+AT_SETUP([Analysis - pair correlation against element])
+AT_KEYWORDS([analysis correlation pair-correlation element])
+
+# here, we correlate all atoms against all of a single element
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Analysis/PairCorrelation/pre/test.conf .], 0)
+AT_CHECK([../../molecuilder -i test.conf  -v 3 --set-boundary-conditions Wrap Wrap Wrap --pair-correlation --elements 8 --output-file output.csv --bin-output-file bin_output.csv --bin-start 0 --bin-end 20], 0, [stdout], [stderr])
+AT_CHECK([fgrep "Begin of PairCorrelation" stdout], 0, [ignore], [ignore])
+#AT_CHECK([file=output.csv; diff $file ${abs_top_srcdir}/tests/regression/Analysis/PairCorrelation/post/output.csv], 0, [ignore], [ignore])
+AT_CHECK([file=bin_output.csv; diff $file ${abs_top_srcdir}/tests/regression/Analysis/PairCorrelation/post/bin_output.csv], 0, [ignore], [ignore])
+sum=0;
+for num in `tail -n 41 bin_output.csv | awk -F" " {'print $4'}`; do
+        let sum=$sum+$num;
+done;
+# 31 oxygens on 62 hydrogens yields 1922 values
+AT_CHECK([test $sum -eq 1922], 0, [ignore], [ignore])
+
+AT_CLEANUP
+
+