| Line | Branch | Exec | Source |
|---|---|---|---|
| 1 | #pragma once | ||
| 2 | |||
| 3 | #include <H5Cpp.h> | ||
| 4 | #include <cstddef> | ||
| 5 | #include <filesystem> | ||
| 6 | #include <fstream> | ||
| 7 | #include <string> | ||
| 8 | #include <thread> | ||
| 9 | #include <unordered_map> | ||
| 10 | #include <vector> | ||
| 11 | #include <yaml-cpp/yaml.h> | ||
| 12 | |||
| 13 | #include "trajectories.hpp" | ||
| 14 | #include "types.hpp" | ||
| 15 | |||
| 16 | class System; | ||
| 17 | struct Stage; | ||
| 18 | struct Particle; | ||
| 19 | class Integrator; | ||
| 20 | class Observables; | ||
| 21 | class Simulation; | ||
| 22 | class Timeseries; | ||
| 23 | |||
| 24 | class Teebuf : public std::streambuf { | ||
| 25 | std::streambuf *sbuf1; | ||
| 26 | std::streambuf *sbuf2; | ||
| 27 | |||
| 28 | public: | ||
| 29 | Teebuf(std::streambuf *sbuf1, std::streambuf *sbuf2); | ||
| 30 | int overflow(int c); | ||
| 31 | int sync(); | ||
| 32 | }; | ||
| 33 | |||
| 34 | class Output { | ||
| 35 | void writeStats(Simulation *simulation, const std::string &filename); | ||
| 36 | |||
| 37 | virtual void writeObservables(Observables *observables, int stage) = 0; | ||
| 38 | virtual void writeTimeseries(Timeseries *timeseries, int stage) = 0; | ||
| 39 | |||
| 40 | protected: | ||
| 41 | std::filesystem::path outputPath; | ||
| 42 | bool dryrun; | ||
| 43 | std::ofstream logFile; | ||
| 44 | Teebuf *tee; | ||
| 45 | std::streambuf *clogbuf; | ||
| 46 | |||
| 47 | public: | ||
| 48 | Output(const std::filesystem::path &outputPath, bool dryrun); | ||
| 49 | virtual ~Output(); | ||
| 50 | |||
| 51 | void emitConfig(const YAML::Node &config); | ||
| 52 | void writeParticles(const std::vector<Particle> &particles, const std::string &filename); | ||
| 53 | virtual void write(Simulation *simulation); | ||
| 54 | // If you want trajectories in the data files, call this method *every step*! | ||
| 55 | virtual void writeTrajectoryFrame(Trajectories *trajectories, System *system, int stage); | ||
| 56 | }; | ||
| 57 | |||
| 58 | class H5MDOutput : public Output { | ||
| 59 | H5::H5File file; | ||
| 60 | |||
| 61 | ✗ | struct TrajectoryQuantityProps { | |
| 62 | H5::PredType type; | ||
| 63 | size_t dim; | ||
| 64 | H5::DataSet dataset = H5::DataSet(); | ||
| 65 | void *data = nullptr; | ||
| 66 | }; | ||
| 67 | |||
| 68 | struct { | ||
| 69 | std::vector<Vec> r; | ||
| 70 | std::vector<ArrayI> box; | ||
| 71 | std::vector<Vec> v; | ||
| 72 | std::vector<Vec> F; | ||
| 73 | std::vector<Vec> Fext; | ||
| 74 | std::vector<Vec> Fint; | ||
| 75 | std::vector<Vec> rRand; | ||
| 76 | std::vector<double> m; | ||
| 77 | std::vector<int> species; | ||
| 78 | } trajectoryBuffers; | ||
| 79 | |||
| 80 | std::map<std::string, TrajectoryQuantityProps> trajectoryQuantities; | ||
| 81 | std::thread trajectoryWriter; | ||
| 82 | |||
| 83 | void initFile(const std::filesystem::path &path, const std::string &filename); | ||
| 84 | void writeMeta(); | ||
| 85 | void initParticlesGroup(Trajectories *trajectories, System *system); | ||
| 86 | |||
| 87 | void writeObservables(Observables *observables, int stage); | ||
| 88 | void writeTimeseries(Timeseries *timeseries, int stage); | ||
| 89 | |||
| 90 | public: | ||
| 91 | H5MDOutput(const std::filesystem::path &outputPath, bool dryrun); | ||
| 92 | ~H5MDOutput(); | ||
| 93 | |||
| 94 | void write(Simulation *simulation); | ||
| 95 | void writeTrajectoryFrame(Trajectories *trajectories, System *system, int stage); | ||
| 96 | }; | ||
| 97 | |||
| 98 | class ASCIIOutput : public Output { | ||
| 99 | void writeObservables(Observables *observables, int stage); | ||
| 100 | void writeTimeseries(Timeseries *timeseries, int stage); | ||
| 101 | |||
| 102 | public: | ||
| 103 | ASCIIOutput(const std::filesystem::path &outputPath, bool dryrun); | ||
| 104 | }; | ||
| 105 |