namespace
{
-//! Helper type
-using MdpField = MdpFieldValues::value_type;
-
/*! \brief Test fixture base for normal mode analysis
*
* This test ensures mdrun can run a normal mode analysis, reaching
mdpFieldValues["rlist"] = "5.6";
mdpFieldValues["rvdw"] = "5.6";
mdpFieldValues["constraints"] = "none";
- mdpFieldValues.insert(MdpField("coulombtype", "Cut-off"));
- mdpFieldValues.insert(MdpField("vdwtype", "Cut-off"));
+ mdpFieldValues["coulombtype"] = "Cut-off";
+ mdpFieldValues["vdwtype"] = "Cut-off";
// prepare the .tpr file
{
mdpFieldValues["nstfout"] = "4";
mdpFieldValues["constraints"] = "none";
mdpFieldValues["nstcalcenergy"] = "4";
- mdpFieldValues.insert(MdpField("coulombtype", "Cut-off"));
- mdpFieldValues.insert(MdpField("vdwtype", "Cut-off"));
+ mdpFieldValues["coulombtype"] = "Cut-off";
+ mdpFieldValues["vdwtype"] = "Cut-off";
// Prepare the .tpr file
{
* bit of a jungle until we transition to using IMdpOptions more.
*
* \throws std::bad_alloc if out of memory
- * std::out_of_range if \c simulationName is not in the database */
+ * std::out_of_range if \c simulationName is not in the database
+ *
+ * Note: Any mdp options that are not added here cannot be used
+ */
MdpFieldValues prepareDefaultMdpFieldValues(const std::string& simulationName)
{
using MdpField = MdpFieldValues::value_type;
mdpFieldValues.insert(MdpField("compressibility", "5e-5"));
mdpFieldValues.insert(MdpField("constraints", "none"));
mdpFieldValues.insert(MdpField("other", ""));
+ mdpFieldValues.insert(MdpField("coulombtype", "Cut-off"));
mdpFieldValues.insert(MdpField("rcoulomb", "0.7"));
+ mdpFieldValues.insert(MdpField("vdwtype", "Cut-off"));
mdpFieldValues.insert(MdpField("rvdw", "0.7"));
mdpFieldValues.insert(MdpField("nstcalcenergy", "100"));
* currently have a good way to compare forces at steps where
* energies were not computed with those from rerun on the same
* coordinates.
+ *
+ * Note: Any mdp options that are not printed here cannot be used
*/
return formatString(
- R"(rcoulomb = %s
+ R"(coulombtype = %s
+ rcoulomb = %s
+ vdwtype = %s
rvdw = %s
rlist = -1
bd-fric = 1000
comm-mode = %s
nstcomm = %s
%s)",
- mdpFieldValues.at("rcoulomb").c_str(), mdpFieldValues.at("rvdw").c_str(),
+ mdpFieldValues.at("coulombtype").c_str(), mdpFieldValues.at("rcoulomb").c_str(),
+ mdpFieldValues.at("vdwtype").c_str(), mdpFieldValues.at("rvdw").c_str(),
mdpFieldValues.at("nsteps").c_str(), mdpFieldValues.at("nstenergy").c_str(),
mdpFieldValues.at("nstxout").c_str(), mdpFieldValues.at("nstvout").c_str(),
mdpFieldValues.at("nstfout").c_str(), mdpFieldValues.at("nstxout-compressed").c_str(),