api/include/gmxapi/gmxapicompat.h

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  35
  36 /*! \file
  37  * \brief Compatibility header for functionality differences in gmxapi releases.
  38  *
  39  * Also handle the transitioning installed headers from GROMACS 2019 moving forward.
  40  *
  41  * \todo Configure for gmxapi 0.0.7, 0.0.8, GROMACS 2019, GROMACS master...
  42  *
  43  * \defgroup gmxapi_compat
  44  * \author M. Eric Irrgang <ericirrgang@gmail.com>
  45  * \ingroup gmxapi_compat
  46  */
  47
  48 #ifndef GMXAPICOMPAT_H
  49 #define GMXAPICOMPAT_H
  50
  51 #include <map>
  52 #include <string>
  53
  54 #include "gmxapi/exceptions.h"
  55 #include "gmxapi/gmxapi.h"
  56 #include "gmxapi/gromacsfwd.h"
  57
  58 /*!
  59  * \brief Compatibility code for features that may not be in the gmxapi specification yet.
  60  *
  61  * \ingroup gmxapi_compat
  62  */
  63 namespace gmxapicompat
  64 {
  65
  66 /*!
  67  * \brief The key name provided for a key-value mapping is invalid.
  68  */
  69 class KeyError : public gmxapi::BasicException<KeyError>
  70 {
  71     using gmxapi::BasicException<KeyError>::BasicException;
  72 };
  73
  74 /*!
  75  * \brief The value provided for a key-value mapping is invalid.
  76  */
  77 class ValueError : public gmxapi::BasicException<ValueError>
  78 {
  79     using gmxapi::BasicException<ValueError>::BasicException;
  80 };
  81
  82 /*!
  83  * \brief Value provided for a key-value mapping is of an incompatible type.
  84  */
  85 class TypeError : public gmxapi::BasicException<TypeError>
  86 {
  87     using gmxapi::BasicException<TypeError>::BasicException;
  88 };
  89
  90 /*!
  91  * \brief Static map of GROMACS MDP user input to normalized "type".
  92  *
  93  * Note that only fields present in the TPR file are named. Additional names
  94  * may be accepted as mdp file entries, but we cannot discern which parameter
  95  * name was used from inspection of the TPR file and this is an interim solution
  96  * that does not need to support a complete MDP file converter.
  97  */
  98 std::map<std::string, gmxapi::GmxapiType> simulationParameterTypeMap();
  99
 100 std::map<std::string, bool t_inputrec::*>    boolParams();
 101 std::map<std::string, int t_inputrec::*>     int32Params();
 102 std::map<std::string, float t_inputrec::*>   float32Params();
 103 std::map<std::string, double t_inputrec::*>  float64Params();
 104 std::map<std::string, int64_t t_inputrec::*> int64Params();
 105
 106 /*!
 107  * \brief Static mapping of parameter names to gmxapi types for GROMACS.
 108  *
 109  * \param name MDP entry name.
 110  * \return enumeration value for known parameters.
 111  *
 112  * \throws gmxapi_compat::ValueError for parameters with no mapping.
 113  */
 114 gmxapi::GmxapiType mdParamToType(const std::string& name);
 115
 116 /*!
 117  * \brief Facade for objects that can provide atomic data for a configuration.
 118  */
 119 class StructureSource;
 120
 121 /*!
 122  * \brief Facade for objects that can provide molecular topology information for a structure.
 123  */
 124 class TopologySource;
 125
 126 /*!
 127  * \brief Proxy to simulation state data.
 128  */
 129 class SimulationState;
 130
 131 /*!
 132  * \brief Handle / manager for GROMACS molecular computation input parameters.
 133  *
 134  * Interface should be consistent with MDP file entries, but data maps to TPR
 135  * file interface. For type safety and simplicity, we don't have generic operator
 136  * accessors. Instead, we have templated accessors that throw exceptions when
 137  * there is trouble.
 138  *
 139  * When MDP input is entirely stored in a key-value tree, this class can be a
 140  * simple adapter or wrapper. Until then, we need a manually maintained mapping
 141  * of MDP entries to TPR data.
 142  *
 143  * Alternatively, we could update the infrastructure used by list_tpx to provide
 144  * more generic output, but our efforts may be better spent in updating the
 145  * infrastructure for the key-value tree input system.
 146  */
 147 class GmxMdParams;
 148
 149 /*!
 150  * \brief Handle for a TPR data resource.
 151  *
 152  * Can provide StructureSource, TopologySource, GmxMdParams, and SimulationState.
 153  *
 154  * This is the type of object we allow Python clients to hold references to, though
 155  * we don't expose any methods to Python. Python clients should acquire access
 156  * to TPR file contents with read_tpr().
 157  *
 158  * \todo gmxapi C++ API should provide mechanisms for subscribing to simulation
 159  *       input data from various sources.
 160  */
 161 class TprReadHandle;
 162
 163 /*!
 164  * \brief Open a TPR file and retrieve a handle.
 165  *
 166  * \param filename Path of file to read.
 167  * \return handle that may share ownership of TPR file resource.
 168  */
 169 std::unique_ptr<TprReadHandle> readTprFile(const std::string& filename);
 170
 171 /*!
 172  * \brief Write a new TPR file to the filesystem with the provided contents.
 173  *
 174  * \param filename output file path
 175  * \param params simulation parameters
 176  * \param structure system structure (atomic configuration)
 177  * \param state simulation state
 178  * \param topology molecular topology
 179  *
 180  * \throws ValueError for invalid or irreconcilable input.
 181  */
 182 void writeTprFile(const std::string&     filename,
 183                   const GmxMdParams&     params,
 184                   const StructureSource& structure,
 185                   const SimulationState& state,
 186                   const TopologySource&  topology);
 187
 188 /*!
 189  * \brief Get a topology source from the TPR contents collection.
 190  * \param handle
 191  * \return
 192  *
 193  * \todo replace with a helper template on T::topologySource() member function existence.
 194  */
 195
 196 std::unique_ptr<TopologySource> getTopologySource(const TprReadHandle& handle);
 197
 198 /*!
 199  * \brief Get a source of simulation state from the TPR contents collection.
 200  * \param handle
 201  * \return
 202  *
 203  * \todo template on T::simulationState() member function existence.
 204  */
 205 std::unique_ptr<SimulationState> getSimulationState(const TprReadHandle& handle);
 206
 207 /*!
 208  * \brief Get a source of atomic structure from the TPR contents collection.
 209  * \param handle
 210  * \return
 211  */
 212 std::unique_ptr<StructureSource> getStructureSource(const TprReadHandle& handle);
 213
 214 /*!
 215  * \brief Get an initialized parameters structure.
 216  * \param handle
 217  * \return
 218  */
 219 std::unique_ptr<GmxMdParams> getMdParams(const TprReadHandle& handle);
 220
 221 /*!
 222  * \brief A set of overloaded functions to fetch parameters of the indicated type, if possible.
 223  *
 224  * \param params Handle to a parameters structure from which to extract.
 225  * \param name Parameter name
 226  * \param (tag) type for dispatch
 227  *
 228  * Could be used for dispatch and/or some sort of templating in the future, but
 229  * invoked directly for now.
 230  */
 231 int     extractParam(const GmxMdParams& params, const std::string& name, int /*unused*/);
 232 int64_t extractParam(const GmxMdParams& params, const std::string& name, int64_t /*unused*/);
 233 float   extractParam(const GmxMdParams& params, const std::string& name, float /*unused*/);
 234 double  extractParam(const GmxMdParams& params, const std::string& name, double /*unused*/);
 235
 236 void setParam(GmxMdParams* params, const std::string& name, double value);
 237 void setParam(GmxMdParams* params, const std::string& name, int64_t value);
 238 // TODO: unsetParam
 239
 240 } // end namespace gmxapicompat
 241
 242 #endif // GMXAPICOMPAT_H