add flags for ianalyze and neighborlist #511 and #508

Signed-off-by: felipez <tifonzafel@gmail.com>

CHANGELOG.rst

@@ -50,6 +50,7 @@ Version 1.7-dev
 -  added verbose option for rootfinder (#503)
 -  fix orca pointcharges (#504)
 -  remove constant cutoff from neighborlist (#508)
+-  fix default and flags properties issue (#511)
 
 Version 1.6.1 (released 21.06.20)
 =================================

share/xtp/xml/ianalyze.xml

@@ -4,5 +4,8 @@
     <resolution_logJ2 help="Bin size of histogram log(J2)" default="0.5" choices="float+"/>
     <resolution_space help="Bin size for r in log(J2(r))" unit="nm" default="0.05" choices="float+"/>
     <states help="states to analyze" default="e, h, s, t" choices="[e,h,s,t]"/>
+    <do_pairtype default="false" choices="bool"/>
+    <pairtype help="method to compute the pairtype" choices="Hopping,Excitoncl"/>
+    <do_resolution_spatial default="false" choices="bool"/>
   </ianalyze>
 </options>

share/xtp/xml/neighborlist.xml

@@ -1,5 +1,11 @@
 <?xml version="1.0"?>
 <options>
   <neighborlist help="Determines neighbouring pairs for exciton transport" section="sec:neighborlist">
+  <type help="segments names if the segmentname method is used"/>
+  <cutoff help="cutoff value if the segmentname method is used" unit="nm"/>
+  <cutoff_type help="method to define the cutoff" default="constant" choices="constant,segmentname"/>
+  <constant help="cutoff for all other types of pairs if the constant method is used" unit="nm" default="1.5" choices="float+"/>
+  <use_exciton_cutoff help="Use exciton cutoff" default="false" choices="bool"/>
+  <exciton_cutoff help="value" units="nm">
   </neighborlist>
 </options>

src/libxtp/calculators/ianalyze.cc

@@ -45,7 +45,7 @@ void IAnalyze::Initialize(const tools::Property &user_options) {
   }
 
   _resolution_logJ2 = options.get(".resolution_logJ2").as<double>();
-  if (options.exists(".pairtype")) {
+  if (options.get(".pairtype").as<bool>()) {
     _do_pairtype = true;
     std::string _store_stdstring = options.get(".pairtype").as<std::string>();
     if (_store_stdstring.find("Hopping") != std::string::npos) {
@@ -59,7 +59,7 @@ void IAnalyze::Initialize(const tools::Property &user_options) {
       _do_pairtype = false;
     }
   }
-  if (options.exists(".resolution_spatial")) {
+  if (options.get(".do_resolution_spatial").as<bool>()) {
     _resolution_spatial = options.get(".resolution_spatial").as<double>();
     if (_resolution_spatial != 0.0) {
       _do_IRdependence = true;

src/libxtp/calculators/neighborlist.cc

@@ -57,14 +57,15 @@ void Neighborlist::Initialize(const tools::Property& user_options) {
     }
   }
 
-  if (options.exists(".constant")) {
+  const std::string& cutoff_type = options.get("cutoff_type").as<std::string>();
+  if (cutoff_type == "constant") {
     _useConstantCutoff = true;
     _constantCutoff =
         options.get(".constant").as<double>() * tools::conv::nm2bohr;
   } else {
     _useConstantCutoff = false;
   }
-  if (options.exists(".exciton_cutoff")) {
+  if (options.get(".use_exciton_cutoff").as<bool>()) {
     _useExcitonCutoff = true;
     _excitonqmCutoff =
         options.get(".exciton_cutoff").as<double>() * tools::conv::nm2bohr;