src/programs/mdrun/tests/mdruncomparison.cpp

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 2016,2018, 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.
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   9  * GROMACS is free software; you can redistribute it and/or
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  35 /*! \internal \file
  36  * \brief
  37  * Implements declarations from in mdruncomparison.h.
  38  *
  39  * \author Mark Abraham <mark.j.abraham@gmail.com>
  40  * \ingroup module_mdrun_integration_tests
  41  */
  42 #include "gmxpre.h"
  43
  44 #include "mdruncomparison.h"
  45
  46 #include <map>
  47 #include <string>
  48 #include <utility>
  49 #include <vector>
  50
  51 #include "gromacs/utility/stringutil.h"
  52
  53 #include "testutils/testasserts.h"
  54
  55 namespace gmx
  56 {
  57 namespace test
  58 {
  59
  60 namespace
  61 {
  62
  63 //! Helper typedef
  64 using MdpFileValues = std::map<std::string, MdpFieldValues>;
  65
  66 //! Database of .mdp strings that supports prepareDefaultMdpValues()
  67 MdpFileValues mdpFileValueDatabase_g
  68 {
  69     // Simple system with 12 argon atoms, fairly widely separated
  70     {
  71         "argon12", { {
  72                          "ref-t", "80"
  73                      },
  74                      {
  75                          "compressibility", "5e-10"
  76                      },
  77                      {
  78                          "tau-p", "1000"
  79                      } }
  80     },
  81     // Simple system with 5 water molecules, fairly widely separated
  82     {
  83         "spc5", { {
  84                       "compressibility", "5e-10"
  85                   },
  86                   {
  87                       "tau-p", "1000"
  88                   } }
  89     },
  90     // Simple system with 5832 argon atoms, suitable for normal pressure coupling
  91     {
  92         "argon5832", { {
  93                            "ref-t", "80"
  94                        } }
  95     },
  96     // Simple system with 216 water molecules, condensed phase
  97     {
  98         "spc216", { }
  99     },
 100     // Capped alanine peptide in vacuo with virtual sites
 101     {
 102         "alanine_vsite_vacuo", { {
 103                                      "constraints", "all-bonds"
 104                                  },
 105                                  {
 106                                      "compressibility", "5e-10"
 107                                  },
 108                                  {
 109                                      "tau-p", "1000"
 110                                  } }
 111     },
 112     // Capped alanine peptide in aqueous condensed phase, with virtual sites
 113     {
 114         "alanine_vsite_solvated", { {
 115                                         "constraints", "all-bonds"
 116                                     } }
 117     },
 118     // Nonanol molecule in vacuo, topology suitable for testing FEP
 119     // on KE, angles, dihedral restraints, coulomb and vdw
 120     {
 121         "nonanol_vacuo", { {
 122                                "nsteps", "16"
 123                            },
 124                            {
 125                                "compressibility", "5e-10"
 126                            },
 127                            {
 128                                "tau-p", "1000"
 129                            },
 130                            {
 131                                "constraints", "h-bonds"
 132                            },
 133                            {
 134                                "other",
 135                                R"(free-energy         = yes
 136                                   sc-alpha            = 0.5
 137                                   sc-r-power          = 6
 138                                   nstdhdl             = 4
 139                                   init-lambda-state   = 3
 140                                   mass-lambdas        = 0.0 0.5 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0
 141                                   bonded-lambdas      = 0.0 0.0 0.0 0.5 1.0 1.0 1.0 1.0 1.0 1.0 1.0
 142                                   restraint-lambdas   = 0.0 0.0 0.0 0.0 0.0 0.5 1.0 1.0 1.0 1.0 1.0
 143                                   vdw-lambdas         = 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.5 1.0 1.0 1.0
 144                                   coul-lambdas        = 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.5 1.0
 145                                   ;couple-moltype      = nonanol
 146                                   ;couple-lambda0      = none
 147                                   ;couple-lambda1      = vdw-q
 148                                   ;couple-intramol     = yes)"
 149                            } }
 150     }
 151 };
 152
 153 /*! \brief Prepare default .mdp values
 154  *
 155  * Insert suitable .mdp defaults, so that \c mdpFileValueDatabase_g
 156  * does not need to specify repetitive values. This works because
 157  * std::map.insert() does not over-write elements that already exist.
 158  *
 159  * \todo ideally some of these default values should be the same as
 160  * grompp uses, and sourced from the same place, but that code is a
 161  * bit of a jungle until we transition to using IMdpOptions more.
 162  *
 163  * \throws  std::bad_alloc     if out of memory
 164  *          std::out_of_range  if \c simulationName is not in the database */
 165 MdpFieldValues prepareDefaultMdpFieldValues(const char *simulationName)
 166 {
 167     using MdpField = MdpFieldValues::value_type;
 168
 169     auto &mdpFieldValues = mdpFileValueDatabase_g.at(simulationName);
 170     mdpFieldValues.insert(MdpField("nsteps", "16"));
 171     mdpFieldValues.insert(MdpField("ref-t", "298"));
 172     mdpFieldValues.insert(MdpField("tau-p", "1"));
 173     mdpFieldValues.insert(MdpField("compressibility", "5e-5"));
 174     mdpFieldValues.insert(MdpField("constraints", "none"));
 175     mdpFieldValues.insert(MdpField("other", ""));
 176
 177     return mdpFieldValues;
 178 }
 179
 180 }       // namespace
 181
 182 MdpFieldValues
 183 prepareMdpFieldValues(const char *simulationName,
 184                       const char *integrator,
 185                       const char *tcoupl,
 186                       const char *pcoupl)
 187 {
 188     using MdpField = MdpFieldValues::value_type;
 189
 190     auto mdpFieldValues = prepareDefaultMdpFieldValues(simulationName);
 191     mdpFieldValues.insert(MdpField("integrator", integrator));
 192     mdpFieldValues.insert(MdpField("tcoupl", tcoupl));
 193     mdpFieldValues.insert(MdpField("pcoupl", pcoupl));
 194     return mdpFieldValues;
 195 }
 196
 197 std::string
 198 prepareMdpFileContents(const MdpFieldValues &mdpFieldValues)
 199 {
 200     /* Set up an .mdp file that permits a highly reproducible
 201      * simulation. The format string needs to be configured with
 202      * values for various .mdp fields to suit the kind of system
 203      * used and testing needed. It also
 204      * - writes frames from different kinds of steps: starting, ending, intermediate NS, intermediate non-NS
 205      * - has other steps between frame-writing steps
 206      * - has enough buffer that e.g. a rerun will compute the same potential energy even though it does NS every frame
 207      * - has very slow pressure coupling and weak compressibility (since otherwise the box will shrink too fast)
 208      * - can have arbitrary chunks of .mdp content appended to it (but it is up to grompp how it deals with duplicate fields)
 209      * - sets random seeds to known values
 210      * - uses cutoffs that fit inside boxes even after GPU mdrun scales rlist
 211      *
 212      * Note that forces computed in the absence of energy computations
 213      * generally follow a different code path from those computed with
 214      * energies. However a rerun always computes energies, so we don't
 215      * currently have a good way to compare forces at steps where
 216      * energies were not computed with those from rerun on the same
 217      * coordinates.
 218      */
 219     return formatString(R"(rcoulomb                = 0.7
 220                            rvdw                    = 0.7
 221                            rlist                   = -1
 222                            bd-fric                 = 1000
 223                            verlet-buffer-tolerance = 0.000001
 224                            nsteps                  = %s
 225                            nstenergy               = 4
 226                            nstlist                 = 8
 227                            nstxout                 = 4
 228                            nstvout                 = 4
 229                            nstfout                 = 4
 230                            integrator              = %s
 231                            ld-seed                 = 234262
 232                            tcoupl                  = %s
 233                            ref-t                   = %s
 234                            tau-t                   = 1
 235                            tc-grps                 = System
 236                            pcoupl                  = %s
 237                            pcoupltype              = isotropic
 238                            ref-p                   = 1
 239                            tau-p                   = %s
 240                            compressibility         = %s
 241                            constraints             = %s
 242                            constraint-algorithm    = lincs
 243                            lincs-order             = 2
 244                            lincs-iter              = 5
 245                            %s)",
 246                         mdpFieldValues.at("nsteps").c_str(),
 247                         mdpFieldValues.at("integrator").c_str(),
 248                         mdpFieldValues.at("tcoupl").c_str(),
 249                         mdpFieldValues.at("ref-t").c_str(),
 250                         mdpFieldValues.at("pcoupl").c_str(),
 251                         mdpFieldValues.at("tau-p").c_str(),
 252                         mdpFieldValues.at("compressibility").c_str(),
 253                         mdpFieldValues.at("constraints").c_str(),
 254                         mdpFieldValues.at("other").c_str());
 255 }
 256
 257 } // namespace test
 258 } // namespace gmx