Restored SASA energy term and expanded its documentation

mlund · Oct 31, 2017 · cbdb480 · cbdb480
1 parent 52f5461
commit cbdb480
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Showing 3 changed files with 18 additions and 5 deletions.
diff --git a/include/faunus/energy.h b/include/faunus/energy.h
@@ -2980,7 +2980,19 @@ namespace Faunus
 /**
  * @brief SASA energy from transfer free energies
  *
- * Detailed description here...
+ * This energy term calculates the change in solvent accessible
+ * surface area (SASA) for each atom and use transfer free energies
+ * to estimate the free energy change. This can be used to capture
+ * salting-out effects caused by co-solutes.
+ * Transfer free energies are defined on a per atom basis via the `tfe`
+ * keyword in `AtomData`.
+ *
+ *  Keyword       | Description
+ *  :------------ | :------------------------------------------------
+ *  `proberadius` | Radius of probe (default: 1.4 angstrom)
+ *  `molarity`    | Molar concentration of co-solute
+ *
+ * For more information see: http://dx.doi.org/10.1002/jcc.21844
  */
 template<class Tspace>
 class SASAEnergy : public Energybase<Tspace> {
@@ -3031,8 +3043,8 @@ class SASAEnergy : public Energybase<Tspace> {
         SASAEnergy(Tmjson &j, const string &dir="sasaenergy") : base(dir) {
             base::name = "SASA Energy";
             auto _j = j["energy"][dir];
-            probe = _j["proberadius"] | 1.4; // angstrom
-            conc = _j["conc"] | 0.0;         // co-solute concentratil (mol/l);
+            probe = _j.value( "proberadius", 1.4 ); // angstrom
+            conc = _j.at("molarity");         // co-solute concentratil (mol/l);
         }
 
         auto tuple() -> decltype(std::make_tuple(this)) {

diff --git a/include/faunus/species.h b/include/faunus/species.h
@@ -215,7 +215,7 @@ namespace Faunus
    * `q`           | Valency / partial charge number [e]
    * `r`           | Radius = `sigma/2` [angstrom]
    * `sigma`       | `2*r` [angstrom] (overrides radius)
-   * `tfe`         | Transfer free energy [J/mol/angstrom^2/M] (default: 0)
+   * `tfe`         | Transfer free energy [J/mol/angstrom^2/M] (default: 0.0)
    * `alphax`      | Excess polarizability in units of [angstrom^3]
    */
 

diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
@@ -67,12 +67,13 @@ endif ()
 
 # ----------------------------
 #  Fetch 3rd-party sasa class
+#  doi:10.1002/jcc.21844
 # ----------------------------
 if (ENABLE_POWERSASA)
     foreach (powf array.hpp power_diagram.h power_sasa.h LICENSE)
         if (NOT EXISTS "${CMAKE_SOURCE_DIR}/include/faunus/sasa/${powf}")
             file(DOWNLOAD
-                    "http://sourceforge.net/p/pteros/code/ci/master/tree/src/core/sasa/${powf}?format=raw"
+                    "https://raw.githubusercontent.com/yesint/pteros/49ab75b/thirdparty/sasa/${powf}"
                     "${CMAKE_SOURCE_DIR}/include/faunus/sasa/${powf}" STATUS status)
         endif ()
     endforeach ()