| 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, const int listsize, const std::vector< Vector > &positions, const double cell[3], double forcecutoff, const std::vector< int > &point, const std::vector< int > &list, std::vector< Vector > &forces, double &engconf) | PLMD::cltools::SimpleMD | inlineprivate |
| compute_list(const int natoms, const int listsize, const std::vector< Vector > &positions, const double cell[3], const double listcutoff, std::vector< int > &point, 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 &maxneighbours, int &ndim, int &idum) | 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_last_time_reopened | PLMD::cltools::SimpleMD | private |
| ~CLTool() | PLMD::CLTool | inlinevirtual |
1.8.17