Created paddedvector.h

[gromacs.git] / src / gromacs / applied-forces / electricfield.cpp

/*
 * This file is part of the GROMACS molecular simulation package.
 *
 * Copyright (c) 2015,2016, 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
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/*! \internal \file
 * \brief
 * Declares data structure and utilities for electric fields
 *
 * \author David van der Spoel <david.vanderspoel@icm.uu.se>
 * \ingroup module_applied_forces
 */
#include "gmxpre.h"

#include "electricfield.h"

#include <cmath>

#include "gromacs/commandline/filenm.h"
#include "gromacs/fileio/gmxfio.h"
#include "gromacs/fileio/gmxfio-xdr.h"
#include "gromacs/fileio/readinp.h"
#include "gromacs/fileio/warninp.h"
#include "gromacs/fileio/xvgr.h"
#include "gromacs/gmxlib/network.h"
#include "gromacs/math/units.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdtypes/commrec.h"
#include "gromacs/mdtypes/forcerec.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/mdatom.h"
#include "gromacs/options/basicoptions.h"
#include "gromacs/options/ioptionscontainerwithsections.h"
#include "gromacs/options/optionsection.h"
#include "gromacs/utility/compare.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/keyvaluetreebuilder.h"
#include "gromacs/utility/keyvaluetreetransform.h"
#include "gromacs/utility/pleasecite.h"
#include "gromacs/utility/strconvert.h"
#include "gromacs/utility/stringutil.h"
#include "gromacs/utility/txtdump.h"

namespace gmx
{

namespace
{

/*! \internal
 * \brief Declaration of storage unit for fields
 */
class ElectricFieldData
{
    public:
        ElectricFieldData() : a_(0), omega_(0), t0_(0), sigma_(0)
        {
        }

        /*! \brief
         * Adds an option section to specify parameters for this field component.
         */
        void initMdpOptions(IOptionsContainerWithSections *options, const char *sectionName)
        {
            auto section = options->addSection(OptionSection(sectionName));
            section.addOption(RealOption("E0").store(&a_));
            section.addOption(RealOption("omega").store(&omega_));
            section.addOption(RealOption("t0").store(&t0_));
            section.addOption(RealOption("sigma").store(&sigma_));
        }

        /*! \brief Evaluates this field component at given time.
         *
         * \param[in] t The time to evualate at
         * \return The electric field
         */
        real evaluate(real t) const
        {
            if (sigma_ > 0)
            {
                return a_ * (std::cos(omega_*(t-t0_))
                             * std::exp(-square(t-t0_)/(2.0*square(sigma_))));
            }
            else
            {
                return a_ * std::cos(omega_*t);
            }
        }

        /*! \brief Initiate the field values
         *
         * \param[in] a     Amplitude
         * \param[in] omega Frequency
         * \param[in] t0    Peak of the pulse
         * \param[in] sigma Width of the pulse
         */
        void setField(real a, real omega, real t0, real sigma)
        {
            a_     = a;
            omega_ = omega;
            t0_    = t0;
            sigma_ = sigma;
        }

        //! Return the amplitude
        real a()     const { return a_; }
        //! Return the frequency
        real omega() const { return omega_; }
        //! Return the time for the peak of the pulse
        real t0()    const { return t0_; }
        //! Return the width of the pulse (0 means inifinite)
        real sigma() const { return sigma_; }

    private:
        //! Coeffient (V / nm)
        real a_;
        //! Frequency (1/ps)
        real omega_;
        //! Central time point (ps) for pulse
        real t0_;
        //! Width of pulse (ps, if zero there is no pulse)
        real sigma_;
};

/*! \internal
 * \brief Describe time dependent electric field
 *
 * Class that implements a force to be evaluated in mdrun.
 * The electric field can be pulsed and oscillating, simply
 * oscillating, or static, in each of X,Y,Z directions.
 */
class ElectricField : public IInputRecExtension, public IForceProvider
{
    public:
        ElectricField() : fpField_(nullptr) {}

        // From IInputRecExtension
        virtual void doTpxIO(t_fileio *fio, bool bRead);
        virtual void initMdpTransform(IKeyValueTreeTransformRules *transform);
        virtual void initMdpOptions(IOptionsContainerWithSections *options);
        virtual void broadCast(const t_commrec *cr);
        virtual void compare(FILE                     *fp,
                             const IInputRecExtension *field2,
                             real                      reltol,
                             real                      abstol);
        virtual void printParameters(FILE *fp, int indent);
        virtual void initOutput(FILE *fplog, int nfile, const t_filenm fnm[],
                                bool bAppendFiles, const gmx_output_env_t *oenv);
        virtual void finishOutput();
        virtual void initForcerec(t_forcerec *fr);

        //! \copydoc gmx::IForceProvider::calculateForces
        virtual void calculateForces(const t_commrec  *cr,
                                     const t_mdatoms  *atoms,
                                     PaddedRVecVector *force,
                                     double            t);

    private:
        //! Return whether or not to apply a field
        bool isActive() const;

        /*! \brief Add a component to the electric field
         *
         * The electric field has three spatial dimensions that are
         * added to the data structure one at a time.
         * \param[in] dim   Dimension, XX, YY, ZZ (0, 1, 2)
         * \param[in] a     Amplitude of the field in V/nm
         * \param[in] omega Frequency (1/ps)
         * \param[in] t0    Time of pulse peak (ps)
         * \param[in] sigma Width of peak (ps)
         */
        void setFieldTerm(int dim, real a, real omega, real t0, real sigma);

        /*! \brief Return the field strength
         *
         * \param[in] dim The spatial direction
         * \param[in] t   The time (ps)
         * \return The field strength in V/nm units
         */
        real field(int dim, real t) const;

        /*! \brief Return amplitude of field
         *
         * \param[in] dim Direction of the field (XX, YY, ZZ)
         * \return Amplitude of the field
         */
        real a(int dim)     const { return efield_[dim].a(); }
        /*! \brief Return frequency of field (1/ps)
         *
         * \param[in] dim Direction of the field (XX, YY, ZZ)
         * \return Frequency of the field
         */
        real omega(int dim) const { return efield_[dim].omega(); }
        /*! \brief Return time of pulse peak
         *
         * \param[in] dim Direction of the field (XX, YY, ZZ)
         * \return Time of pulse peak
         */
        real t0(int dim) const { return efield_[dim].t0(); }
        /*! \brief Return width of the pulse
         *
         * \param[in] dim Direction of the field (XX, YY, ZZ)
         * \return Width of the pulse
         */
        real sigma(int dim) const { return efield_[dim].sigma(); }

        /*! \brief Print the field components to a file
         *
         * \param[in] t   The time
         * Will throw and exit with fatal error if file is not open.
         */
        void printComponents(double t) const;

        //! The field strength in each dimension
        ElectricFieldData efield_[DIM];
        //! File pointer for electric field
        FILE             *fpField_;
};

void ElectricField::doTpxIO(t_fileio *fio, bool bRead)
{
    // The content of the tpr file for this feature has
    // been the same since gromacs 4.0 that was used for
    // developing.
    for (int j = 0; (j < DIM); j++)
    {
        int n = 0, nt = 0;
        if (!bRead)
        {
            n = 1;
            if (omega(j) != 0 || sigma(j) != 0 || t0(j) != 0)
            {
                nt = 1;
            }
        }
        gmx_fio_do_int(fio, n);
        gmx_fio_do_int(fio, nt);
        std::vector<real> aa, phi, at, phit;
        if (!bRead)
        {
            aa.push_back(a(j));
            phi.push_back(t0(j));
            at.push_back(omega(j));
            phit.push_back(sigma(j));
        }
        else
        {
            aa.resize(n+1);
            phi.resize(nt+1);
            at.resize(nt+1);
            phit.resize(nt+1);
        }
        gmx_fio_ndo_real(fio, aa.data(),  n);
        gmx_fio_ndo_real(fio, phi.data(), n);
        gmx_fio_ndo_real(fio, at.data(),  nt);
        gmx_fio_ndo_real(fio, phit.data(), nt);
        if (bRead && n > 0)
        {
            setFieldTerm(j, aa[0], at[0], phi[0], phit[0]);
            if (n > 1 || nt > 1)
            {
                gmx_fatal(FARGS, "Can not handle tpr files with more than one electric field term per direction.");
            }
        }
    }
}

//! Converts static parameters from mdp format to E0.
real convertStaticParameters(const std::string &value)
{
    // TODO: Better context for the exceptions here (possibly
    // also convert them to warning_errors or such).
    const std::vector<std::string> sx = splitString(value);
    if (sx.empty())
    {
        return 0.0;
    }
    const int n = fromString<int>(sx[0]);
    if (n <= 0)
    {
        return 0.0;
    }
    if (n != 1)
    {
        GMX_THROW(InvalidInputError("Only one electric field term supported for each dimension"));
    }
    if (sx.size() != 3)
    {
        GMX_THROW(InvalidInputError("Expected exactly one electric field amplitude value"));
    }
    return fromString<real>(sx[1]);
}

//! Converts dynamic parameters from mdp format to (omega, t0, sigma).
void convertDynamicParameters(gmx::KeyValueTreeObjectBuilder *builder,
                              const std::string              &value)
{
    const std::vector<std::string> sxt = splitString(value);
    if (sxt.empty())
    {
        return;
    }
    const int n = fromString<int>(sxt[0]);
    switch (n)
    {
        case 1:
            if (sxt.size() != 3)
            {
                GMX_THROW(InvalidInputError("Please specify 1 omega 0 for non-pulsed fields"));
            }
            builder->addValue<real>("omega", fromString<real>(sxt[1]));
            break;
        case 3:
            if (sxt.size() != 7)
            {
                GMX_THROW(InvalidInputError("Please specify 1 omega 0 t0 0 sigma 0 for pulsed fields"));
            }
            builder->addValue<real>("omega", fromString<real>(sxt[1]));
            builder->addValue<real>("t0", fromString<real>(sxt[3]));
            builder->addValue<real>("sigma", fromString<real>(sxt[5]));
            break;
        default:
            GMX_THROW(InvalidInputError("Incomprehensible input for electric field"));
    }
}

void ElectricField::initMdpTransform(IKeyValueTreeTransformRules *rules)
{
    rules->addRule().from<std::string>("/E-x").to<real>("/electric-field/x/E0")
        .transformWith(&convertStaticParameters);
    rules->addRule().from<std::string>("/E-xt").toObject("/electric-field/x")
        .transformWith(&convertDynamicParameters);
    rules->addRule().from<std::string>("/E-y").to<real>("/electric-field/y/E0")
        .transformWith(&convertStaticParameters);
    rules->addRule().from<std::string>("/E-yt").toObject("/electric-field/y")
        .transformWith(&convertDynamicParameters);
    rules->addRule().from<std::string>("/E-z").to<real>("/electric-field/z/E0")
        .transformWith(&convertStaticParameters);
    rules->addRule().from<std::string>("/E-zt").toObject("/electric-field/z")
        .transformWith(&convertDynamicParameters);
}

void ElectricField::initMdpOptions(IOptionsContainerWithSections *options)
{
    //CTYPE ("Format is E0 (V/nm), omega (1/ps), t0 (ps), sigma (ps) ");
    auto section = options->addSection(OptionSection("electric-field"));
    efield_[XX].initMdpOptions(&section, "x");
    efield_[YY].initMdpOptions(&section, "y");
    efield_[ZZ].initMdpOptions(&section, "z");
}

void ElectricField::broadCast(const t_commrec *cr)
{
    rvec a1, omega1, sigma1, t01;

    if (MASTER(cr))
    {
        // Load the parameters read from tpr into temp vectors
        for (int m = 0; m < DIM; m++)
        {
            a1[m]     = a(m);
            omega1[m] = omega(m);
            sigma1[m] = sigma(m);
            t01[m]    = t0(m);
        }
    }
    // Broadcasting the parameters
    gmx_bcast(DIM*sizeof(a1[0]), a1, cr);
    gmx_bcast(DIM*sizeof(omega1[0]), omega1, cr);
    gmx_bcast(DIM*sizeof(t01[0]), t01, cr);
    gmx_bcast(DIM*sizeof(sigma1[0]), sigma1, cr);

    // And storing them locally
    if (!MASTER(cr))
    {
        for (int m = 0; m < DIM; m++)
        {
            setFieldTerm(m, a1[m], omega1[m], t01[m], sigma1[m]);
        }
    }
}

void ElectricField::initOutput(FILE *fplog, int nfile, const t_filenm fnm[],
                               bool bAppendFiles, const gmx_output_env_t *oenv)
{
    if (isActive())
    {
        please_cite(fplog, "Caleman2008a");

        // Optional outpuf file showing the field, see manual.
        if (opt2bSet("-field", nfile, fnm))
        {
            if (bAppendFiles)
            {
                fpField_ = gmx_fio_fopen(opt2fn("-field", nfile, fnm), "a+");
            }
            else
            {
                fpField_ = xvgropen(opt2fn("-field", nfile, fnm),
                                    "Applied electric field", "Time (ps)",
                                    "E (V/nm)", oenv);
            }
        }
    }
}

void ElectricField::finishOutput()
{
    if (fpField_ != nullptr)
    {
        // This is opened sometimes with xvgropen, sometimes with
        // gmx_fio_fopen, so we use the least common denominator for closing.
        gmx_fio_fclose(fpField_);
        fpField_ = nullptr;
    }
}

void ElectricField::initForcerec(t_forcerec *fr)
{
    if (isActive())
    {
        fr->bF_NoVirSum = TRUE;
        fr->efield      = this;
    }
}

void ElectricField::printParameters(FILE *fp, int indent)
{
    const char *const dimension[DIM] = { "X", "Y", "Z" };
    indent = pr_title(fp, indent, "ElectricField");
    for (int m = 0; m < DIM; m++)
    {
        pr_indent(fp, indent);
        fprintf(fp, "-%s E0 = %g omega = %g t0 = %g sigma = %g\n",
                dimension[m], a(m), omega(m), t0(m), sigma(m));
    }
}

void ElectricField::setFieldTerm(int dim, real a, real omega, real t0, real sigma)
{
    range_check(dim, 0, DIM);
    efield_[dim].setField(a, omega, t0, sigma);
}

real ElectricField::field(int dim, real t) const
{
    return efield_[dim].evaluate(t);
}

bool ElectricField::isActive() const
{
    return (efield_[XX].a() != 0 ||
            efield_[YY].a() != 0 ||
            efield_[ZZ].a() != 0);
}

void ElectricField::compare(FILE                     *fp,
                            const IInputRecExtension *other,
                            real                      reltol,
                            real                      abstol)
{
    GMX_ASSERT(dynamic_cast<const ElectricField *>(other) != nullptr,
               "Invalid other type");
    const ElectricField *f2 = static_cast<const ElectricField *>(other);
    for (int m = 0; (m < DIM); m++)
    {
        char buf[256];

        sprintf(buf, "inputrec->field[%d]", m);
        cmp_real(fp, buf, -1, a(m), f2->a(m), reltol, abstol);
        cmp_real(fp, buf, -1, omega(m), f2->omega(m), reltol, abstol);
        cmp_real(fp, buf, -1, t0(m), f2->t0(m), reltol, abstol);
        cmp_real(fp, buf, -1, sigma(m), f2->sigma(m), reltol, abstol);
    }
}

void ElectricField::printComponents(double t) const
{
    fprintf(fpField_, "%10g  %10g  %10g  %10g\n", t,
            field(XX, t), field(YY, t), field(ZZ, t));
}

void ElectricField::calculateForces(const t_commrec  *cr,
                                    const t_mdatoms  *mdatoms,
                                    PaddedRVecVector *force,
                                    double            t)
{
    if (isActive())
    {
        rvec *f = as_rvec_array(force->data());

        for (int m = 0; (m < DIM); m++)
        {
            real Ext = FIELDFAC*field(m, t);

            if (Ext != 0)
            {
                // TODO: Check parallellism
                for (int i = 0; i < mdatoms->homenr; ++i)
                {
                    // NOTE: Not correct with perturbed charges
                    f[i][m] += mdatoms->chargeA[i]*Ext;
                }
            }
        }
        if (MASTER(cr) && fpField_ != nullptr)
        {
            printComponents(t);
        }
    }
}

}   // namespace

std::unique_ptr<IInputRecExtension> createElectricFieldModule()
{
    return std::unique_ptr<IInputRecExtension>(new ElectricField());
}

} // namespace gmx