using MdpFileValues = std::map<std::string, DatabaseEntry>;
//! Database of .mdp strings that supports prepareDefaultMdpValues()
-const MdpFileValues mdpFileValueDatabase_g
-{
+const MdpFileValues mdpFileValueDatabase_g{
// Simple system with 12 argon atoms, fairly widely separated
- {
- "argon12", { { {
- "ref-t", "80"
- },
- {
- "compressibility", "5e-10"
- },
- {
- "tau-p", "1000"
- } },
- {
- 1, 2, 3, 4
- } }
- },
+ { "argon12",
+ { { { "ref-t", "80" }, { "compressibility", "5e-10" }, { "tau-p", "1000" } }, { 1, 2, 3, 4 } } },
// Simple system with 5 water molecules, fairly widely separated
- {
- "tip3p5", { { {
- "compressibility", "5e-10"
- },
- {
- "tau-p", "1000"
- } },
- {
- 1, 2, 3, 4, 5, 6, 8, 9
- } }
- },
+ { "tip3p5", { { { "compressibility", "5e-10" }, { "tau-p", "1000" } }, { 1, 2, 3, 4, 5, 6, 8, 9 } } },
// Simple system with 5832 argon atoms, suitable for normal pressure coupling
- {
- "argon5832", { { {
- "ref-t", "80"
- } },
- {
- // TODO This test case is not currently used, so we
- // have not tested which rank counts work.
- 1, 2, 3, 4, 5, 6, 7, 8, 9
- } }
- },
+ { "argon5832",
+ { { { "ref-t", "80" } },
+ { // TODO This test case is not currently used, so we
+ // have not tested which rank counts work.
+ 1, 2, 3, 4, 5, 6, 7, 8, 9 } } },
// Simple system with 2 nearby water molecules
- {
- "spc2", { { },
- {
- // TODO This test case is not currently used, so we
- // have not tested which rank counts work.
- 1, 2, 3, 4, 5, 6, 7, 8, 9
- } }
- },
+ { "spc2",
+ { {},
+ { // TODO This test case is not currently used, so we
+ // have not tested which rank counts work.
+ 1, 2, 3, 4, 5, 6, 7, 8, 9 } } },
// Simple system with 216 water molecules, condensed phase
- {
- "spc216", { { },
- {
- // TODO This test case is not currently used, so we
- // have not tested which rank counts work.
- 1, 2, 3, 4, 5, 6, 7, 8, 9 // TODO tpi test
- } }
- },
+ { "spc216",
+ { {},
+ {
+ // TODO This test case is not currently used, so we
+ // have not tested which rank counts work.
+ 1, 2, 3, 4, 5, 6, 7, 8, 9 // TODO tpi test
+ } } },
// Capped alanine peptide in vacuo with virtual sites
- {
- "alanine_vsite_vacuo", { { {
- "constraints", "all-bonds"
- },
- {
- "compressibility", "5e-10"
- },
- {
- "tau-p", "1000"
- } },
- {
- 1, 2, 3, 4, 6, 9
- } }
- },
+ { "alanine_vsite_vacuo",
+ { { { "constraints", "all-bonds" }, { "compressibility", "5e-10" }, { "tau-p", "1000" } },
+ { 1, 2, 3, 4, 6, 9 } } },
// Capped alanine peptide in aqueous condensed phase, with virtual sites
- {
- "alanine_vsite_solvated", { { {
- "constraints", "all-bonds"
- },
- {
- "compressibility", "5e-10"
- },
- {
- "tau-p", "1000"
- } },
- {
- // TODO This test case is not currently used, so we
- // have not tested which rank counts work.
- 1, 2, 3, 4, 5, 6, 7, 8, 9
- } }
- },
+ { "alanine_vsite_solvated",
+ { { { "constraints", "all-bonds" }, { "compressibility", "5e-10" }, { "tau-p", "1000" } },
+ { // TODO This test case is not currently used, so we
+ // have not tested which rank counts work.
+ 1, 2, 3, 4, 5, 6, 7, 8, 9 } } },
// Zwitterionic glycine in vacuo
- {
- "glycine_vacuo", { { {
- "constraints", "h-bonds"
- } },
- {
- 1, 2, 3, 4, 5, 6, 7, 8, 9
- } }
- },
+ { "glycine_vacuo", { { { "constraints", "h-bonds" } }, { 1, 2, 3, 4, 5, 6, 7, 8, 9 } } },
// Zwitterionic glycine in vacuo, without constraints
- {
- "glycine_no_constraints_vacuo", { { {
- "constraints", "none"
- } },
- {
- 1, 2, 3, 4, 5, 6, 7, 8, 9
- } }
- },
+ { "glycine_no_constraints_vacuo", { { { "constraints", "none" } }, { 1, 2, 3, 4, 5, 6, 7, 8, 9 } } },
// Simple mdrun tests of energy
- {
- "angles1", { { },
- {
- 1, 2
- } }
- },
+ { "angles1", { {}, { 1, 2 } } },
// Scaled water for NMA
- {
- "scaled-water", { { },
- {
- 1, 2, 3, 4, 5, 6
- } }
- },
+ { "scaled-water", { {}, { 1, 2, 3, 4, 5, 6 } } },
// Villin for NMA
- {
- "villin", { { },
- {
- 1, 2, 3, 4, 5, 6
- } }
- },
+ { "villin", { {}, { 1, 2, 3, 4, 5, 6 } } },
// SPC-Dimer for NMA
- {
- "spc-dimer", { { },
- {
- 1, 2, 3, 4, 5, 6
- } }
- },
+ { "spc-dimer", { {}, { 1, 2, 3, 4, 5, 6 } } },
// SW-Dimer for NMA
- {
- "sw-dimer", { { {
- "nstcalcenergy", "1"
- } },
- {
- 1, 2, 3, 4, 5, 6
- } }
- },
+ { "sw-dimer", { { { "nstcalcenergy", "1" } }, { 1, 2, 3, 4, 5, 6 } } },
// TIP5P for NMA
- {
- "one-tip5p", { { },
- {
- 1, 2, 3, 4, 5, 6
- } }
- },
+ { "one-tip5p", { {}, { 1, 2, 3, 4, 5, 6 } } },
// ICE-Binding protein for NMA
- {
- "ice-binding", { { },
- {
- 1, 2, 3, 4, 5, 6
- } }
- },
+ { "ice-binding", { {}, { 1, 2, 3, 4, 5, 6 } } },
// Nonanol molecule in vacuo, topology suitable for testing FEP
// on KE, angles, dihedral restraints, coulomb and vdw
- {
- "nonanol_vacuo", { { {
- "nsteps", "16"
- },
- {
- "compressibility", "5e-10"
- },
- {
- "tau-p", "1000"
- },
- {
- "constraints", "h-bonds"
- },
- {
- "other",
- R"(free-energy = yes
+ { "nonanol_vacuo",
+ { { { "nsteps", "16" },
+ { "compressibility", "5e-10" },
+ { "tau-p", "1000" },
+ { "constraints", "h-bonds" },
+ { "other",
+ R"(free-energy = yes
sc-alpha = 0.5
sc-r-power = 6
mass-lambdas = 0.0 0.5 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0
;couple-moltype = nonanol
;couple-lambda0 = none
;couple-lambda1 = vdw-q
- ;couple-intramol = yes)"
- } },
- {
- 1, 2, 3, 4, 5, 6, 8, 9
- } }
- }
+ ;couple-intramol = yes)" } },
+ { 1, 2, 3, 4, 5, 6, 8, 9 } } }
};
/*! \brief Prepare default .mdp values
*
* \throws std::bad_alloc if out of memory
* std::out_of_range if \c simulationName is not in the database */
-MdpFieldValues prepareDefaultMdpFieldValues(const std::string &simulationName)
+MdpFieldValues prepareDefaultMdpFieldValues(const std::string& simulationName)
{
using MdpField = MdpFieldValues::value_type;
return mdpFieldValues;
}
-} // namespace
+} // namespace
-bool
-isNumberOfPpRanksSupported(const std::string &simulationName,
- int possibleNumberOfPpRanks)
+bool isNumberOfPpRanksSupported(const std::string& simulationName, int possibleNumberOfPpRanks)
{
- const auto &possibleNumbers = mdpFileValueDatabase_g.at(simulationName).validPpRankCounts;
- return (std::find(std::begin(possibleNumbers), std::end(possibleNumbers),
- possibleNumberOfPpRanks) != std::end(possibleNumbers));
+ const auto& possibleNumbers = mdpFileValueDatabase_g.at(simulationName).validPpRankCounts;
+ return (std::find(std::begin(possibleNumbers), std::end(possibleNumbers), possibleNumberOfPpRanks)
+ != std::end(possibleNumbers));
}
-std::string
-reportNumbersOfPpRanksSupported(const std::string &simulationName)
+std::string reportNumbersOfPpRanksSupported(const std::string& simulationName)
{
- const auto &possibleNumbers = mdpFileValueDatabase_g.at(simulationName).validPpRankCounts;
- return formatAndJoin(std::begin(possibleNumbers), std::end(possibleNumbers),
- ",", StringFormatter("%d"));
+ const auto& possibleNumbers = mdpFileValueDatabase_g.at(simulationName).validPpRankCounts;
+ return formatAndJoin(std::begin(possibleNumbers), std::end(possibleNumbers), ",",
+ StringFormatter("%d"));
}
-MdpFieldValues
-prepareMdpFieldValues(const std::string &simulationName,
- const std::string &integrator,
- const std::string &tcoupl,
- const std::string &pcoupl)
+MdpFieldValues prepareMdpFieldValues(const std::string& simulationName,
+ const std::string& integrator,
+ const std::string& tcoupl,
+ const std::string& pcoupl)
{
using MdpField = MdpFieldValues::value_type;
return mdpFieldValues;
}
-MdpFieldValues
-prepareMdpFieldValues(const char *simulationName,
- const char *integrator,
- const char *tcoupl,
- const char *pcoupl)
+MdpFieldValues prepareMdpFieldValues(const char* simulationName,
+ const char* integrator,
+ const char* tcoupl,
+ const char* pcoupl)
{
return prepareMdpFieldValues(std::string(simulationName), integrator, tcoupl, pcoupl);
}
-std::string
-prepareMdpFileContents(const MdpFieldValues &mdpFieldValues)
+std::string prepareMdpFileContents(const MdpFieldValues& mdpFieldValues)
{
/* Set up an .mdp file that permits a highly reproducible
* simulation. The format string needs to be configured with
* energies were not computed with those from rerun on the same
* coordinates.
*/
- return formatString(R"(rcoulomb = %s
+ return formatString(
+ R"(rcoulomb = %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("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(),
- mdpFieldValues.at("nstdhdl").c_str(),
- mdpFieldValues.at("integrator").c_str(),
- mdpFieldValues.at("tcoupl").c_str(),
- mdpFieldValues.at("nsttcouple").c_str(),
- mdpFieldValues.at("ref-t").c_str(),
- mdpFieldValues.at("pcoupl").c_str(),
- mdpFieldValues.at("nstpcouple").c_str(),
- mdpFieldValues.at("tau-p").c_str(),
- mdpFieldValues.at("compressibility").c_str(),
- mdpFieldValues.at("constraints").c_str(),
- mdpFieldValues.at("nstcalcenergy").c_str(),
- mdpFieldValues.at("comm-mode").c_str(),
- mdpFieldValues.at("nstcomm").c_str(),
- mdpFieldValues.at("other").c_str());
+ mdpFieldValues.at("rcoulomb").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(),
+ mdpFieldValues.at("nstdhdl").c_str(), mdpFieldValues.at("integrator").c_str(),
+ mdpFieldValues.at("tcoupl").c_str(), mdpFieldValues.at("nsttcouple").c_str(),
+ mdpFieldValues.at("ref-t").c_str(), mdpFieldValues.at("pcoupl").c_str(),
+ mdpFieldValues.at("nstpcouple").c_str(), mdpFieldValues.at("tau-p").c_str(),
+ mdpFieldValues.at("compressibility").c_str(), mdpFieldValues.at("constraints").c_str(),
+ mdpFieldValues.at("nstcalcenergy").c_str(), mdpFieldValues.at("comm-mode").c_str(),
+ mdpFieldValues.at("nstcomm").c_str(), mdpFieldValues.at("other").c_str());
}
} // namespace test
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff