diff --git a/include/faunus/energy.h b/include/faunus/energy.h index 22f0399e8..2ce86f241 100644 --- 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 SASAEnergy : public Energybase { @@ -3031,8 +3043,8 @@ class SASAEnergy : public Energybase { 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 index cf795e38b..926df19a8 100644 --- 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 index de30bd9f4..5c9f688b0 100644 --- 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 ()