src/gromacs/mdlib/tests/constrtestdata.h

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
   5  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   6  * and including many others, as listed in the AUTHORS file in the
   7  * top-level source directory and at http://www.gromacs.org.
   8  *
   9  * GROMACS is free software; you can redistribute it and/or
  10  * modify it under the terms of the GNU Lesser General Public License
  11  * as published by the Free Software Foundation; either version 2.1
  12  * of the License, or (at your option) any later version.
  13  *
  14  * GROMACS is distributed in the hope that it will be useful,
  15  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  16  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  17  * Lesser General Public License for more details.
  18  *
  19  * You should have received a copy of the GNU Lesser General Public
  20  * License along with GROMACS; if not, see
  21  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  22  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  23  *
  24  * If you want to redistribute modifications to GROMACS, please
  25  * consider that scientific software is very special. Version
  26  * control is crucial - bugs must be traceable. We will be happy to
  27  * consider code for inclusion in the official distribution, but
  28  * derived work must not be called official GROMACS. Details are found
  29  * in the README & COPYING files - if they are missing, get the
  30  * official version at http://www.gromacs.org.
  31  *
  32  * To help us fund GROMACS development, we humbly ask that you cite
  33  * the research papers on the package. Check out http://www.gromacs.org.
  34  */
  35 /*! \internal \file
  36  * \brief SHAKE and LINCS tests header.
  37  *
  38  * Contains description and constructor for the test data accumulating object,
  39  * declares CPU- and GPU-based functions used to apply SHAKE or LINCS on the
  40  * test data.
  41  *
  42  * \author Artem Zhmurov <zhmurov@gmail.com>
  43  * \ingroup module_mdlib
  44  */
  45
  46 #ifndef GMX_MDLIB_TESTS_CONSTRTESTDATA_H
  47 #define GMX_MDLIB_TESTS_CONSTRTESTDATA_H
  48
  49 #include <memory>
  50 #include <vector>
  51
  52 #include "gromacs/gmxlib/nrnb.h"
  53 #include "gromacs/gpu_utils/gpu_testutils.h"
  54 #include "gromacs/math/paddedvector.h"
  55 #include "gromacs/math/vec.h"
  56 #include "gromacs/math/vectypes.h"
  57 #include "gromacs/mdlib/gmx_omp_nthreads.h"
  58 #include "gromacs/mdlib/lincs.h"
  59 #include "gromacs/mdlib/shake.h"
  60 #include "gromacs/mdtypes/inputrec.h"
  61 #include "gromacs/mdtypes/mdatom.h"
  62 #include "gromacs/pbcutil/pbc.h"
  63 #include "gromacs/topology/idef.h"
  64 #include "gromacs/topology/ifunc.h"
  65 #include "gromacs/topology/topology.h"
  66
  67 namespace gmx
  68 {
  69 namespace test
  70 {
  71
  72 /* \brief
  73  * Constraints test data structure.
  74  *
  75  * Structure to collect all the necessary data, including system coordinates and topology,
  76  * constraints information, etc. The structure can be reset and reused.
  77  */
  78 class ConstraintsTestData
  79 {
  80 public:
  81     //! Human-friendly name for a system
  82     std::string title_;
  83     //! Number of atoms
  84     int numAtoms_;
  85     //! Topology
  86     gmx_mtop_t mtop_;
  87     //! Masses
  88     std::vector<real> masses_;
  89     //! Inverse masses
  90     std::vector<real> invmass_;
  91     //! Input record (info that usually in .mdp file)
  92     t_inputrec ir_;
  93     //! Local topology
  94     std::unique_ptr<InteractionDefinitions> idef_;
  95     //! MD atoms
  96     t_mdatoms md_;
  97     //! Computational time array (normally used to benchmark performance)
  98     t_nrnb nrnb_;
  99
 100     //! Inverse timestep
 101     real invdt_;
 102     //! Number of flexible constraints
 103     int nflexcon_ = 0;
 104     //! Whether the virial should be computed
 105     bool computeVirial_;
 106     //! Scaled virial
 107     tensor virialScaled_;
 108     //! Scaled virial (reference values)
 109     tensor virialScaledRef_;
 110     //! If the free energy is computed
 111     bool compute_dHdLambda_;
 112     //! For free energy computation
 113     real dHdLambda_;
 114     //! For free energy computation (reference value)
 115     real dHdLambdaRef_;
 116
 117     //! Coordinates before the timestep
 118     PaddedVector<RVec> x_;
 119     //! Coordinates after timestep, output for the constraints
 120     PaddedVector<RVec> xPrime_;
 121     //! Backup for coordinates (for reset)
 122     PaddedVector<RVec> xPrime0_;
 123     //! Intermediate set of coordinates (normally used for projection correction)
 124     PaddedVector<RVec> xPrime2_;
 125     //! Velocities
 126     PaddedVector<RVec> v_;
 127     //! Backup for velocities (for reset)
 128     PaddedVector<RVec> v0_;
 129
 130     //! Constraints data (type1-i1-j1-type2-i2-j2-...)
 131     std::vector<int> constraints_;
 132     //! Target lengths for all constraint types
 133     std::vector<real> constraintsR0_;
 134
 135     /*! \brief
 136      * Constructor for the object with all parameters and variables needed by constraints algorithms.
 137      *
 138      * This constructor assembles stubs for all the data structures, required to initialize
 139      * and apply LINCS and SHAKE constraints. The coordinates and velocities before constraining
 140      * are saved to allow for reset. The constraints data are stored for testing after constraints
 141      * were applied.
 142      *
 143      * \param[in]  title                Human-friendly name of the system.
 144      * \param[in]  numAtoms             Number of atoms in the system.
 145      * \param[in]  masses               Atom masses. Size of this vector should be equal to numAtoms.
 146      * \param[in]  constraints          List of constraints, organized in triples of integers.
 147      *                                  First integer is the index of type for a constraint, second
 148      *                                  and third are the indices of constrained atoms. The types
 149      *                                  of constraints should be sequential but not necessarily
 150      *                                  start from zero (which is the way they normally are in
 151      *                                  GROMACS).
 152      * \param[in]  constraintsR0        Target values for bond lengths for bonds of each type. The
 153      *                                  size of this vector should be equal to the total number of
 154      *                                  unique types in constraints vector.
 155      * \param[in]  computeVirial        Whether the virial should be computed.
 156      * \param[in]  virialScaledRef      Reference values for scaled virial tensor.
 157      * \param[in]  compute_dHdLambda    Whether free energy should be computed.
 158      * \param[in]  dHdLambdaRef         Reference value for dHdLambda.
 159      * \param[in]  initialTime          Initial time.
 160      * \param[in]  timestep             Timestep.
 161      * \param[in]  x                    Coordinates before integration step.
 162      * \param[in]  xPrime               Coordinates after integration step, but before constraining.
 163      * \param[in]  v                    Velocities before constraining.
 164      * \param[in]  shakeTolerance       Target tolerance for SHAKE.
 165      * \param[in]  shakeUseSOR          Use successive over-relaxation method for SHAKE iterations.
 166      *                                  The general formula is:
 167      *                                     x_n+1 = (1-omega)*x_n + omega*f(x_n),
 168      *                                  where omega = 1 if SOR is off and may be < 1 if SOR is on.
 169      * \param[in]  lincsNumIterations   Number of iterations used to compute the inverse matrix.
 170      * \param[in]  lincsExpansionOrder  The order for algorithm that adjusts the direction of the
 171      *                                  bond after constraints are applied.
 172      * \param[in]  lincsWarnAngle       The threshold value for the change in bond angle. When
 173      *                                  exceeded the program will issue a warning.
 174      *
 175      */
 176     ConstraintsTestData(const std::string&       title,
 177                         int                      numAtoms,
 178                         std::vector<real>        masses,
 179                         std::vector<int>         constraints,
 180                         std::vector<real>        constraintsR0,
 181                         bool                     computeVirial,
 182                         tensor                   virialScaledRef,
 183                         bool                     compute_dHdLambda,
 184                         float                    dHdLambdaRef,
 185                         real                     initialTime,
 186                         real                     timestep,
 187                         const std::vector<RVec>& x,
 188                         const std::vector<RVec>& xPrime,
 189                         const std::vector<RVec>& v,
 190                         real                     shakeTolerance,
 191                         gmx_bool                 shakeUseSOR,
 192                         int                      lincsNumIterations,
 193                         int                      lincsExpansionOrder,
 194                         real                     lincsWarnAngle);
 195
 196     /*! \brief
 197      * Reset the data structure so it can be reused.
 198      *
 199      * Set the coordinates and velocities back to their values before
 200      * constraining. The scaled virial tensor and dHdLambda are zeroed.
 201      *
 202      */
 203     void reset();
 204 };
 205
 206 } // namespace test
 207 } // namespace gmx
 208
 209 #endif // GMX_MDLIB_TESTS_CONSTRTESTDATA_H