Free topology in non-DD simulations

[gromacs.git] / src / testutils / simulationdatabase.cpp

/*
 * This file is part of the GROMACS molecular simulation package.
 *
 * Copyright (c) 2016,2018, by the GROMACS development team, led by
 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
 * and including many others, as listed in the AUTHORS file in the
 * top-level source directory and at http://www.gromacs.org.
 *
 * GROMACS is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public License
 * as published by the Free Software Foundation; either version 2.1
 * of the License, or (at your option) any later version.
 *
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/*! \internal \file
 * \brief
 * Implements declarations from in simulationdatabase.h
 *
 * \author Mark Abraham <mark.j.abraham@gmail.com>
 * \ingroup module_testutils
 */
#include "gmxpre.h"

#include "simulationdatabase.h"

#include <algorithm>
#include <map>
#include <string>

#include "gromacs/utility/stringutil.h"

#include "testutils/testasserts.h"

namespace gmx
{
namespace test
{

namespace
{

struct DatabaseEntry
{
    MdpFieldValues   mdpFieldValues;
    std::vector<int> validPpRankCounts;
};

//! Helper typedef
using MdpFileValues = std::map<std::string, DatabaseEntry>;

//! Database of .mdp strings that supports prepareDefaultMdpValues()
const MdpFileValues mdpFileValueDatabase_g
{
    // Simple system with 12 argon atoms, fairly widely separated
    {
        "argon12", { { {
                           "ref-t", "80"
                       },
                       {
                           "compressibility", "5e-10"
                       },
                       {
                           "tau-p", "1000"
                       } },
                     {
                         1, 2, 3, 4
                     } }
    },
    // Simple system with 5 water molecules, fairly widely separated
    {
        "spc5", { { {
                        "compressibility", "5e-10"
                    },
                    {
                        "tau-p", "1000"
                    } },
                  {
                      1, 2, 3, 4, 5, 6, 8, 9
                  } }
    },
    // Simple system with 5832 argon atoms, suitable for normal pressure coupling
    {
        "argon5832", { { {
                             "ref-t", "80"
                         } },
                       {
                           // TODO This test case is not currently used, so we
                           // have not tested which rank counts work.
                           1, 2, 3, 4, 5, 6, 7, 8, 9
                       } }
    },
    // Simple system with 216 water molecules, condensed phase
    {
        "spc216", { { },
                    {
                        // TODO This test case is not currently used, so we
                        // have not tested which rank counts work.
                        1, 2, 3, 4, 5, 6, 7, 8, 9 // TODO tpi test
                    } }
    },
    // Capped alanine peptide in vacuo with virtual sites
    {
        "alanine_vsite_vacuo", { { {
                                       "constraints", "all-bonds"
                                   },
                                   {
                                       "compressibility", "5e-10"
                                   },
                                   {
                                       "tau-p", "1000"
                                   } },
                                 {
                                     1, 2, 3, 4, 6, 9
                                 } }
    },
    // Capped alanine peptide in aqueous condensed phase, with virtual sites
    {
        "alanine_vsite_solvated", { { {
                                          "constraints", "all-bonds"
                                      },
                                      {
                                          "compressibility", "5e-10"
                                      },
                                      {
                                          "tau-p", "1000"
                                      } },
                                    {
                                        // TODO This test case is not currently used, so we
                                        // have not tested which rank counts work.
                                        1, 2, 3, 4, 5, 6, 7, 8, 9
                                    } }
    },
    // Zwitterionic glycine in vacuo
    {
        "glycine_vacuo", { { {
                                 "constraints", "h-bonds"
                             } },
                           {
                               1, 2, 3, 4, 5, 6, 7, 8, 9
                           } }
    },
    // Zwitterionic glycine in vacuo, without constraints
    {
        "glycine_no_constraints_vacuo", { { {
                                                "constraints", "none"
                                            } },
                                          {
                                              1, 2, 3, 4, 5, 6, 7, 8, 9
                                          } }
    },
    // Scaled water for NMA
    {
        "scaled-water", { { },
                          {
                              1, 2, 3, 4, 5, 6
                          } }
    },
    // Villin for NMA
    {
        "villin", { { },
                    {
                        1, 2, 3, 4, 5, 6
                    } }
    },
    // SPC-Dimer for NMA
    {
        "spc-dimer", { { },
                       {
                           1, 2, 3, 4, 5, 6
                       } }
    },
    // SW-Dimer for NMA
    {
        "sw-dimer", { { {
                            "nstcalcenergy", "1"
                        } },
                      {
                          1, 2, 3, 4, 5, 6
                      } }
    },
    // TIP5P for NMA
    {
        "one-tip5p", { { },
                       {
                           1, 2, 3, 4, 5, 6
                       } }
    },
    // ICE-Binding protein for NMA
    {
        "ice-binding", { { },
                         {
                             1, 2, 3, 4, 5, 6
                         } }
    },
    // Nonanol molecule in vacuo, topology suitable for testing FEP
    // on KE, angles, dihedral restraints, coulomb and vdw
    {
        "nonanol_vacuo", { { {
                                 "nsteps", "16"
                             },
                             {
                                 "compressibility", "5e-10"
                             },
                             {
                                 "tau-p", "1000"
                             },
                             {
                                 "constraints", "h-bonds"
                             },
                             {
                                 "other",
                                 R"(free-energy         = yes
                                  sc-alpha            = 0.5
                                  sc-r-power          = 6
                                  nstdhdl             = 4
                                  init-lambda-state   = 3
                                  mass-lambdas        = 0.0 0.5 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0
                                  bonded-lambdas      = 0.0 0.0 0.0 0.5 1.0 1.0 1.0 1.0 1.0 1.0 1.0
                                  restraint-lambdas   = 0.0 0.0 0.0 0.0 0.0 0.5 1.0 1.0 1.0 1.0 1.0
                                  vdw-lambdas         = 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.5 1.0 1.0 1.0
                                  coul-lambdas        = 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.5 1.0
                                  ;couple-moltype      = nonanol
                                  ;couple-lambda0      = none
                                  ;couple-lambda1      = vdw-q
                                  ;couple-intramol     = yes)"
                             } },
                           {
                               1, 2, 3, 4, 5, 6, 8, 9
                           } }
    }
};

/*! \brief Prepare default .mdp values
 *
 * Insert suitable .mdp defaults, so that \c mdpFileValueDatabase_g
 * does not need to specify repetitive values. This works because
 * std::map.insert() does not over-write elements that already exist.
 *
 * \todo ideally some of these default values should be the same as
 * grompp uses, and sourced from the same place, but that code is a
 * bit of a jungle until we transition to using IMdpOptions more.
 *
 * \throws  std::bad_alloc     if out of memory
 *          std::out_of_range  if \c simulationName is not in the database */
MdpFieldValues prepareDefaultMdpFieldValues(const char *simulationName)
{
    using MdpField = MdpFieldValues::value_type;

    auto mdpFieldValues = mdpFileValueDatabase_g.at(simulationName).mdpFieldValues;
    mdpFieldValues.insert(MdpField("nsteps", "16"));
    mdpFieldValues.insert(MdpField("ref-t", "298"));
    mdpFieldValues.insert(MdpField("tau-p", "1"));
    mdpFieldValues.insert(MdpField("compressibility", "5e-5"));
    mdpFieldValues.insert(MdpField("constraints", "none"));
    mdpFieldValues.insert(MdpField("other", ""));
    mdpFieldValues.insert(MdpField("rcoulomb", "0.7"));
    mdpFieldValues.insert(MdpField("rvdw", "0.7"));
    mdpFieldValues.insert(MdpField("nstcalcenergy", "100"));

    return mdpFieldValues;
}

}       // namespace

bool
isNumberOfPpRanksSupported(const std::string &simulationName,
                           int                possibleNumberOfPpRanks)
{
    const auto &possibleNumbers = mdpFileValueDatabase_g.at(simulationName).validPpRankCounts;
    return (std::find(std::begin(possibleNumbers), std::end(possibleNumbers),
                      possibleNumberOfPpRanks) != std::end(possibleNumbers));
}

std::string
reportNumbersOfPpRanksSupported(const std::string &simulationName)
{
    const auto &possibleNumbers = mdpFileValueDatabase_g.at(simulationName).validPpRankCounts;
    return formatAndJoin(std::begin(possibleNumbers), std::end(possibleNumbers),
                         ",", StringFormatter("%d"));
}

MdpFieldValues
prepareMdpFieldValues(const char *simulationName,
                      const char *integrator,
                      const char *tcoupl,
                      const char *pcoupl)
{
    using MdpField = MdpFieldValues::value_type;

    auto mdpFieldValues = prepareDefaultMdpFieldValues(simulationName);
    mdpFieldValues.insert(MdpField("integrator", integrator));
    mdpFieldValues.insert(MdpField("tcoupl", tcoupl));
    mdpFieldValues.insert(MdpField("pcoupl", pcoupl));
    return mdpFieldValues;
}

std::string
prepareMdpFileContents(const MdpFieldValues &mdpFieldValues)
{
    /* Set up an .mdp file that permits a highly reproducible
     * simulation. The format string needs to be configured with
     * values for various .mdp fields to suit the kind of system
     * used and testing needed. It also
     * - writes frames from different kinds of steps: starting, ending, intermediate NS, intermediate non-NS
     * - has other steps between frame-writing steps
     * - has enough buffer that e.g. a rerun will compute the same potential energy even though it does NS every frame
     * - has very slow pressure coupling and weak compressibility (since otherwise the box will shrink too fast)
     * - can have arbitrary chunks of .mdp content appended to it (but it is up to grompp how it deals with duplicate fields)
     * - sets random seeds to known values
     * - uses cutoffs that fit inside boxes even after GPU mdrun scales rlist
     *
     * Note that forces computed in the absence of energy computations
     * generally follow a different code path from those computed with
     * energies. However a rerun always computes energies, so we don't
     * currently have a good way to compare forces at steps where
     * energies were not computed with those from rerun on the same
     * coordinates.
     */
    return formatString(R"(rcoulomb                = %s
                           rvdw                    = %s
                           rlist                   = -1
                           bd-fric                 = 1000
                           verlet-buffer-tolerance = 0.000001
                           nsteps                  = %s
                           nstenergy               = 4
                           nstlist                 = 8
                           nstxout                 = 4
                           nstvout                 = 4
                           nstfout                 = 4
                           integrator              = %s
                           ld-seed                 = 234262
                           tcoupl                  = %s
                           ref-t                   = %s
                           tau-t                   = 1
                           tc-grps                 = System
                           pcoupl                  = %s
                           pcoupltype              = isotropic
                           ref-p                   = 1
                           tau-p                   = %s
                           compressibility         = %s
                           constraints             = %s
                           constraint-algorithm    = lincs
                           lincs-order             = 2
                           lincs-iter              = 5
                           nstcalcenergy           = %s
                           %s)",
                        mdpFieldValues.at("rcoulomb").c_str(),
                        mdpFieldValues.at("rvdw").c_str(),
                        mdpFieldValues.at("nsteps").c_str(),
                        mdpFieldValues.at("integrator").c_str(),
                        mdpFieldValues.at("tcoupl").c_str(),
                        mdpFieldValues.at("ref-t").c_str(),
                        mdpFieldValues.at("pcoupl").c_str(),
                        mdpFieldValues.at("tau-p").c_str(),
                        mdpFieldValues.at("compressibility").c_str(),
                        mdpFieldValues.at("constraints").c_str(),
                        mdpFieldValues.at("nstcalcenergy").c_str(),
                        mdpFieldValues.at("other").c_str());
}

} // namespace test
} // namespace gmx