src/gromacs/fileio/tpxio.h

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
   5  * Copyright (c) 2001-2004, The GROMACS development team.
   6  * Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
   7  * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
   8  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   9  * and including many others, as listed in the AUTHORS file in the
  10  * top-level source directory and at http://www.gromacs.org.
  11  *
  12  * GROMACS is free software; you can redistribute it and/or
  13  * modify it under the terms of the GNU Lesser General Public License
  14  * as published by the Free Software Foundation; either version 2.1
  15  * of the License, or (at your option) any later version.
  16  *
  17  * GROMACS is distributed in the hope that it will be useful,
  18  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  19  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  20  * Lesser General Public License for more details.
  21  *
  22  * You should have received a copy of the GNU Lesser General Public
  23  * License along with GROMACS; if not, see
  24  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  25  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  26  *
  27  * If you want to redistribute modifications to GROMACS, please
  28  * consider that scientific software is very special. Version
  29  * control is crucial - bugs must be traceable. We will be happy to
  30  * consider code for inclusion in the official distribution, but
  31  * derived work must not be called official GROMACS. Details are found
  32  * in the README & COPYING files - if they are missing, get the
  33  * official version at http://www.gromacs.org.
  34  *
  35  * To help us fund GROMACS development, we humbly ask that you cite
  36  * the research papers on the package. Check out http://www.gromacs.org.
  37  */
  38 #ifndef GMX_FILEIO_TPXIO_H
  39 #define GMX_FILEIO_TPXIO_H
  40
  41 #include <cstdio>
  42
  43 #include <vector>
  44
  45 #include "gromacs/math/vectypes.h"
  46 #include "gromacs/pbcutil/pbc.h"
  47 #include "gromacs/utility/basedefinitions.h"
  48 #include "gromacs/utility/real.h"
  49
  50 struct gmx_mtop_t;
  51 struct t_atoms;
  52 struct t_block;
  53 struct t_inputrec;
  54 class t_state;
  55 struct t_topology;
  56
  57 namespace gmx
  58 {
  59 template<typename>
  60 class ArrayRef;
  61 }
  62 /*! \libinternal
  63  * \brief
  64  * First part of the TPR file structure containing information about
  65  * the general aspect of the system.
  66  */
  67 struct TpxFileHeader
  68 {
  69     //! Non zero if input_rec is present.
  70     bool bIr = false;
  71     //! Non zero if a box is present.
  72     bool bBox = false;
  73     //! Non zero if a topology is present.
  74     bool bTop = false;
  75     //! Non zero if coordinates are present.
  76     bool bX = false;
  77     //! Non zero if velocities are present.
  78     bool bV = false;
  79     //! Non zero if forces are present (no longer supported, but retained so old .tpr can be read)
  80     bool bF = false;
  81     //! The total number of atoms.
  82     int natoms = 0;
  83     //! The number of temperature coupling groups.
  84     int ngtc = 0;
  85     //! Current value of lambda.
  86     real lambda = 0;
  87     //! Current value of the alchemical state - not yet printed out.
  88     int fep_state = 0;
  89     /*a better decision will eventually (5.0 or later) need to be made
  90        on how to treat the alchemical state of the system, which can now
  91        vary through a simulation, and cannot be completely described
  92        though a single lambda variable, or even a single state
  93        index. Eventually, should probably be a vector. MRS*/
  94     //! Size of the TPR body in chars (equal to number of bytes) during I/O.
  95     int64_t sizeOfTprBody = 0;
  96     //! File version.
  97     int fileVersion = 0;
  98     //! File generation.
  99     int fileGeneration = 0;
 100     //! If the tpr file was written in double precision.
 101     bool isDouble = false;
 102 };
 103
 104 /*! \brief
 105  * Contains the partly deserialized contents of a TPR file.
 106  *
 107  * Convenience struct that holds a fully deserialized TPR file header,
 108  * and the body of the TPR file as char buffer that can be deserialized
 109  * independently from the header.
 110  */
 111 struct PartialDeserializedTprFile
 112 {
 113     //! The file header.
 114     TpxFileHeader header;
 115     //! The file body.
 116     std::vector<char> body;
 117     //! Flag for PBC needed by legacy implementation.
 118     PbcType pbcType = PbcType::Unset;
 119 };
 120
 121 /*
 122  * These routines handle reading and writing of preprocessed
 123  * topology files in any of the following formats:
 124  * TPR : topology in XDR format, portable accross platforms
 125  *
 126  * Files are written in the precision with which the source are compiled,
 127  * but double and single precision can be read by either.
 128  */
 129
 130 /*! \brief
 131  * Read the header from a tpx file and then close it again.
 132  *
 133  * By setting \p canReadTopologyOnly to true, it is possible to read future
 134  * versions too (we skip the changed inputrec), provided we havent
 135  * changed the topology description. If it is possible to read
 136  * the inputrec it will still be done even if canReadTopologyOnly is true.
 137  *
 138  * \param[in] fileName The name of the input file.
 139  * \param[in] canReadTopologyOnly If reading the inputrec can be skipped or not.
 140  * \returns An initialized and populated TPX File header object.
 141  */
 142 TpxFileHeader readTpxHeader(const char* fileName, bool canReadTopologyOnly);
 143
 144 void write_tpx_state(const char* fn, const t_inputrec* ir, const t_state* state, const gmx_mtop_t* mtop);
 145 /* Write a file, and close it again.
 146  */
 147
 148 /*! \brief
 149  * Complete deserialization of TPR file into the individual data structures.
 150  *
 151  * If \p state is nullptr, only populates ir and mtop.
 152  *
 153  * \param[in] partialDeserializedTpr Struct with header and char buffer needed to populate system.
 154  * \param[out] ir Input rec to populate.
 155  * \param[out] state System state variables to populate.
 156  * \param[out] x Separate vector for coordinates, deprecated.
 157  * \param[out] v Separate vector for velocities, deprecated.
 158  * \param[out] mtop Global topology to populate.
 159  *
 160  * \returns PBC flag.
 161  */
 162 PbcType completeTprDeserialization(PartialDeserializedTprFile* partialDeserializedTpr,
 163                                    t_inputrec*                 ir,
 164                                    t_state*                    state,
 165                                    rvec*                       x,
 166                                    rvec*                       v,
 167                                    gmx_mtop_t*                 mtop);
 168
 169 //! Overload for final TPR deserialization when not using state vectors.
 170 PbcType completeTprDeserialization(PartialDeserializedTprFile* partialDeserializedTpr,
 171                                    t_inputrec*                 ir,
 172                                    gmx_mtop_t*                 mtop);
 173
 174 /*! \brief
 175  * Read a file to set up a simulation and close it after reading.
 176  *
 177  * Main function used to initialize simulations. Reads the input \p fn
 178  * to populate the \p state, \p ir and \p mtop needed to run a simulations.
 179  *
 180  * This function returns the partial deserialized TPR file
 181  * that can then be communicated to set up non-master nodes to run simulations.
 182  *
 183  * \param[in] fn Input file name.
 184  * \param[out] ir Input parameters to be set, or nullptr.
 185  * \param[out] state State variables for the simulation.
 186  * \param[out] mtop Global simulation topolgy.
 187  * \returns Struct with header and body in char vector.
 188  */
 189 PartialDeserializedTprFile read_tpx_state(const char* fn, t_inputrec* ir, t_state* state, gmx_mtop_t* mtop);
 190
 191 /*! \brief
 192  * Read a file and close it again.
 193  *
 194  * Reads a topology input file and populates the fields if the passed
 195  * variables are valid. It is possible to pass \p ir, \p natoms,
 196  * \p x, \p v or \p mtop as nullptr to the function. In those cases,
 197  * the variables will not be populated from the input file. Passing both
 198  * \p x and \p v as nullptr is not supported. If both \p natoms and
 199  * \p mtop are passed as valid objects to the function, the total atom
 200  * number from \p mtop will be set in \p natoms. Otherwise \p natoms
 201  * will not be changed. If \p box is valid, the box will be set from
 202  * the information read in from the file.
 203  *
 204  * \param[in] fn Input file name.
 205  * \param[out] ir Input parameters to be set, or nullptr.
 206  * \param[out] box Box matrix.
 207  * \param[out] natoms Total atom numbers to be set, or nullptr.
 208  * \param[out] x Positions to be filled from file, or nullptr.
 209  * \param[out] v Velocities to be filled from file, or nullptr.
 210  * \param[out] mtop Topology to be populated, or nullptr.
 211  * \returns ir->pbcType if it was read from the file.
 212  */
 213 PbcType read_tpx(const char* fn, t_inputrec* ir, matrix box, int* natoms, rvec* x, rvec* v, gmx_mtop_t* mtop);
 214
 215 PbcType read_tpx_top(const char* fn, t_inputrec* ir, matrix box, int* natoms, rvec* x, rvec* v, t_topology* top);
 216 /* As read_tpx, but for the old t_topology struct */
 217
 218 gmx_bool fn2bTPX(const char* file);
 219 /* return if *file is one of the TPX file types */
 220
 221 void pr_tpxheader(FILE* fp, int indent, const char* title, const TpxFileHeader* sh);
 222
 223 #endif