check_list(const int natoms, const std::vector< Vector > &positions, const std::vector< Vector > &positions0, const double listcutoff, const double forcecutoff, bool &recompute) | PLMD::cltools::SimpleMD | inlineprivate |
CLTool(const CLToolOptions &co) | PLMD::CLTool | explicit |
commandline enum value | PLMD::CLTool | |
compute_engkin(const int natoms, const std::vector< double > &masses, const std::vector< Vector > &velocities, double &engkin) | PLMD::cltools::SimpleMD | inlineprivate |
compute_forces(const int natoms, double epsilon, double sigma, const std::vector< Vector > &positions, const double cell[3], double forcecutoff, const std::vector< std::vector< int > > &list, std::vector< Vector > &forces, double &engconf) | PLMD::cltools::SimpleMD | inlineprivate |
compute_list(const int natoms, const std::vector< Vector > &positions, const double cell[3], const double listcutoff, std::vector< std::vector< int > > &list) | PLMD::cltools::SimpleMD | inlineprivate |
description() const override | PLMD::cltools::SimpleMD | inlineprivatevirtual |
error(const std::string &msg) | PLMD::CLTool | protected |
getInputData() | PLMD::CLTool | inline |
ifile enum value | PLMD::CLTool | |
inputData | PLMD::CLTool | private |
inputdata | PLMD::CLTool | |
keywords | PLMD::CLTool | private |
main(FILE *in, FILE *out, PLMD::Communicator &pc) override | PLMD::cltools::SimpleMD | inlineprivatevirtual |
name | PLMD::CLTool | private |
parse(const std::string &key, T &t) | PLMD::CLTool | protected |
parseFlag(const std::string &key, bool &t) | PLMD::CLTool | protected |
parseVector(const std::string &key, std::vector< T > &t) | PLMD::CLTool | protected |
pbc(const double cell[3], const Vector &vin, Vector &vout) | PLMD::cltools::SimpleMD | inlineprivate |
randomize_velocities(const int natoms, const int ndim, const double temperature, const std::vector< double > &masses, std::vector< Vector > &velocities, Random &random) | PLMD::cltools::SimpleMD | inlineprivate |
read_input(double &temperature, double &tstep, double &friction, double &forcecutoff, double &listcutoff, int &nstep, int &nconfig, int &nstat, bool &wrapatoms, std::string &inputfile, std::string &outputfile, std::string &trajfile, std::string &statfile, int &ndim, int &idum, double &epsilon, double &sigma) | PLMD::cltools::SimpleMD | inlineprivate |
read_natoms(const std::string &inputfile, int &natoms) | PLMD::cltools::SimpleMD | inlineprivate |
read_positions(const std::string &inputfile, int natoms, std::vector< Vector > &positions, double cell[3]) | PLMD::cltools::SimpleMD | inlineprivate |
readCommandLineArgs(int argc, char **argv, FILE *out) | PLMD::CLTool | private |
readInput(int argc, char **argv, FILE *in, FILE *out) | PLMD::CLTool | |
readInputFile(int argc, char **argv, FILE *in, FILE *out) | PLMD::CLTool | private |
registerKeywords(Keywords &keys) | PLMD::cltools::SimpleMD | inlinestatic |
setInputData(const std::map< std::string, std::string > &inputData) | PLMD::CLTool | inline |
setRemainingToDefault(FILE *out) | PLMD::CLTool | private |
SimpleMD(const CLToolOptions &co) | PLMD::cltools::SimpleMD | inlineexplicit |
thermostat(const int natoms, const int ndim, const std::vector< double > &masses, const double dt, const double friction, const double temperature, std::vector< Vector > &velocities, double &engint, Random &random) | PLMD::cltools::SimpleMD | inlineprivate |
unset enum value | PLMD::CLTool | |
write_final_positions(const std::string &outputfile, int natoms, const std::vector< Vector > &positions, const double cell[3], const bool wrapatoms) | PLMD::cltools::SimpleMD | inlineprivate |
write_positions(const std::string &trajfile, int natoms, const std::vector< Vector > &positions, const double cell[3], const bool wrapatoms) | PLMD::cltools::SimpleMD | inlineprivate |
write_positions_first | PLMD::cltools::SimpleMD | private |
write_statistics(const std::string &statfile, const int istep, const double tstep, const int natoms, const int ndim, const double engkin, const double engconf, const double engint) | PLMD::cltools::SimpleMD | inlineprivate |
write_statistics_first | PLMD::cltools::SimpleMD | private |
write_statistics_fp | PLMD::cltools::SimpleMD | private |
write_statistics_fp_deleter | PLMD::cltools::SimpleMD | private |
write_statistics_last_time_reopened | PLMD::cltools::SimpleMD | private |
~CLTool() | PLMD::CLTool | inlinevirtual |