src/programs/mdrun/tests/mdruncomparisonfixture.cpp

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   4  * Copyright (c) 2016, by the GROMACS development team, led by
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  35 /*! \internal \file
  36  * \brief
  37  * Implements classes in mdruncomparisonfixture.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 "mdruncomparisonfixture.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 MdrunComparisonFixture::~MdrunComparisonFixture()
  61 {
  62 }
  63
  64 namespace
  65 {
  66
  67 //! Helper typedef
  68 typedef std::map<std::string, MdrunComparisonFixture::MdpFieldValues> MdpFileValues;
  69
  70 //! Database of .mdp strings that supports MdrunComparisonFixture::prepareSimulation()
  71 MdpFileValues mdpFileValueDatabase_g
  72 {
  73     // Simple system with 12 argon atoms, fairly widely separated
  74     {
  75         "argon12", { {
  76                          "ref-t", "80"
  77                      },
  78                      {
  79                          "compressibility", "5e-10"
  80                      },
  81                      {
  82                          "tau-p", "1000"
  83                      } }
  84     },
  85     // Simple system with 5 water molecules, fairly widely separated
  86     {
  87         "spc5", { {
  88                       "compressibility", "5e-10"
  89                   },
  90                   {
  91                       "tau-p", "1000"
  92                   } }
  93     },
  94     // Simple system with 5832 argon atoms, suitable for normal pressure coupling
  95     {
  96         "argon5832", { {
  97                            "ref-t", "80"
  98                        } }
  99     },
 100     // Simple system with 216 water molecules, condensed phase
 101     {
 102         "spc216", { }
 103     },
 104     // Capped alanine peptide in vacuo with virtual sites
 105     {
 106         "alanine_vsite_vacuo", { {
 107                                      "constraints", "all-bonds"
 108                                  },
 109                                  {
 110                                      "compressibility", "5e-10"
 111                                  },
 112                                  {
 113                                      "tau-p", "1000"
 114                                  } }
 115     },
 116     // Capped alanine peptide in aqueous condensed phase, with virtual sites
 117     {
 118         "alanine_vsite_solvated", { {
 119                                         "constraints", "all-bonds"
 120                                     } }
 121     },
 122     // Nonanol molecule in vacuo, topology suitable for FEP testing
 123     {
 124         "nonanol_vacuo", { {
 125                                "nsteps", "16"
 126                            },
 127                            {
 128                                "compressibility", "5e-10"
 129                            },
 130                            {
 131                                "tau-p", "1000"
 132                            },
 133                            {
 134                                "constraints", "h-bonds"
 135                            },
 136                            {
 137                                "other",
 138                                "free-energy       = yes\n"
 139                                "sc-alpha          = 0.5\n"
 140                                "sc-r-power        = 6\n"
 141                                "nstdhdl           = 4\n"
 142                                "init-lambda-state = 3\n"
 143                                "fep_lambdas       = 0.00 0.50 1.00 1.00 1.00\n"
 144                                "vdw_lambdas       = 0.00 0.00 0.00 0.50 1.00\n"
 145                                "couple-moltype    = nonanol\n"
 146                                "couple-lambda0    = vdw-q\n"
 147                                "couple-lambda1    = none\n"
 148                                "couple-intramol   = yes\n"
 149                            } }
 150     }
 151 };
 152
 153 }       // namespace
 154
 155 MdrunComparisonFixture::MdpFieldValues MdrunComparisonFixture::prepareMdpFieldValues(const char *simulationName)
 156 {
 157     /* Insert suitable .mdp defaults, so that the database set up
 158      * above does not need to specify redundant values. This works
 159      * because std::map.insert() does not over-write elements that
 160      * already exist.
 161      *
 162      * TODO ideally some of these default values should be the same as
 163      * grompp uses, and sourced from the same place, but that code is
 164      * a bit of a jungle. */
 165
 166     typedef MdpFieldValues::value_type MdpField;
 167
 168     auto &mdpFieldValues = mdpFileValueDatabase_g.at(simulationName);
 169     mdpFieldValues.insert(MdpField("nsteps", "16"));
 170     mdpFieldValues.insert(MdpField("ref-t", "298"));
 171     mdpFieldValues.insert(MdpField("tau-p", "1"));
 172     mdpFieldValues.insert(MdpField("compressibility", "5e-5"));
 173     mdpFieldValues.insert(MdpField("constraints", "none"));
 174     mdpFieldValues.insert(MdpField("other", ""));
 175
 176     return mdpFieldValues;
 177 }
 178
 179 void MdrunComparisonFixture::prepareMdpFile(const MdpFieldValues &mdpFieldValues,
 180                                             const char           *integrator,
 181                                             const char           *tcoupl,
 182                                             const char           *pcoupl)
 183 {
 184     /* Set up an .mdp file that permits a highly reproducible
 185      * simulation. The format string needs to be configured with
 186      * values for various .mdp fields to suit the kind of system
 187      * used and testing needed. It also
 188      * - writes frames from different kinds of steps: starting, ending, intermediate NS, intermediate non-NS
 189      * - has other steps between frame-writing steps
 190      * - has enough buffer that e.g. a rerun will compute the same potential energy even though it does NS every frame
 191      * - has very slow pressure coupling and weak compressibility (since otherwise the box will shrink too fast)
 192      * - can have arbitrary chunks of .mdp content appended to it (but it is up to grompp how it deals with duplicate fields)
 193      * - sets random seeds to known values
 194      * - uses cutoffs that fit inside boxes even after GPU mdrun scales rlist
 195      *
 196      * Note that forces computed in the absence of energy computations
 197      * generally follow a different code path from those computed with
 198      * energies. However a rerun always computes energies, so we don't
 199      * currently have a good way to compare forces at steps where
 200      * energies were not computed with those from rerun on the same
 201      * coordinates.
 202      */
 203     runner_.useStringAsMdpFile(formatString("rcoulomb                = 0.7\n"
 204                                             "rvdw                    = 0.7\n"
 205                                             "rlist                   = -1\n"
 206                                             "bd-fric                 = 1000\n"
 207                                             "verlet-buffer-tolerance = 0.000001\n"
 208                                             "nsteps                  = %s\n"
 209                                             "nstenergy               = 4\n"
 210                                             "nstlist                 = 8\n"
 211                                             "nstxout                 = 4\n"
 212                                             "nstvout                 = 4\n"
 213                                             "nstfout                 = 4\n"
 214                                             "integrator              = %s\n"
 215                                             "ld-seed                 = 234262\n"
 216                                             "tcoupl                  = %s\n"
 217                                             "ref-t                   = %s\n"
 218                                             "tau-t                   = 1\n"
 219                                             "tc-grps                 = System\n"
 220                                             "pcoupl                  = %s\n"
 221                                             "pcoupltype              = isotropic\n"
 222                                             "ref-p                   = 1\n"
 223                                             "tau-p                   = %s\n"
 224                                             "compressibility         = %s\n"
 225                                             "constraints             = %s\n"
 226                                             "constraint-algorithm    = lincs\n"
 227                                             "lincs-order             = 2\n"
 228                                             "lincs-iter              = 5\n"
 229                                             "%s",
 230                                             mdpFieldValues.at("nsteps").c_str(),
 231                                             integrator, tcoupl,
 232                                             mdpFieldValues.at("ref-t").c_str(),
 233                                             pcoupl,
 234                                             mdpFieldValues.at("tau-p").c_str(),
 235                                             mdpFieldValues.at("compressibility").c_str(),
 236                                             mdpFieldValues.at("constraints").c_str(),
 237                                             mdpFieldValues.at("other").c_str()));
 238 }
 239
 240 void MdrunComparisonFixture::runTest(const char            *simulationName,
 241                                      const char            *integrator,
 242                                      const char            *tcoupl,
 243                                      const char            *pcoupl,
 244                                      FloatingPointTolerance tolerance)
 245 {
 246     CommandLine caller;
 247     caller.append("grompp");
 248     runTest(caller, simulationName, integrator, tcoupl, pcoupl, tolerance);
 249 }
 250
 251 } // namespace test
 252 } // namespace gmx