src/gromacs/applied-forces/electricfield.cpp

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  35 /*! \internal \file
  36  * \brief
  37  * Declares data structure and utilities for electric fields
  38  *
  39  * \author David van der Spoel <david.vanderspoel@icm.uu.se>
  40  * \ingroup module_applied_forces
  41  */
  42 #include "gmxpre.h"
  43
  44 #include "electricfield.h"
  45
  46 #include <cmath>
  47
  48 #include "gromacs/commandline/filenm.h"
  49 #include "gromacs/fileio/gmxfio.h"
  50 #include "gromacs/fileio/xvgr.h"
  51 #include "gromacs/math/units.h"
  52 #include "gromacs/math/vec.h"
  53 #include "gromacs/mdtypes/commrec.h"
  54 #include "gromacs/mdtypes/forcerec.h"
  55 #include "gromacs/mdtypes/iforceprovider.h"
  56 #include "gromacs/mdtypes/imdmodule.h"
  57 #include "gromacs/mdtypes/imdoutputprovider.h"
  58 #include "gromacs/mdtypes/imdpoptionprovider.h"
  59 #include "gromacs/mdtypes/mdatom.h"
  60 #include "gromacs/options/basicoptions.h"
  61 #include "gromacs/options/ioptionscontainerwithsections.h"
  62 #include "gromacs/options/optionsection.h"
  63 #include "gromacs/utility/exceptions.h"
  64 #include "gromacs/utility/keyvaluetreebuilder.h"
  65 #include "gromacs/utility/keyvaluetreetransform.h"
  66 #include "gromacs/utility/pleasecite.h"
  67 #include "gromacs/utility/strconvert.h"
  68 #include "gromacs/utility/stringutil.h"
  69
  70 namespace gmx
  71 {
  72
  73 namespace
  74 {
  75
  76 /*! \internal
  77  * \brief Declaration of storage unit for fields
  78  */
  79 class ElectricFieldData
  80 {
  81     public:
  82         ElectricFieldData() : a_(0), omega_(0), t0_(0), sigma_(0)
  83         {
  84         }
  85
  86         /*! \brief
  87          * Adds an option section to specify parameters for this field component.
  88          */
  89         void initMdpOptions(IOptionsContainerWithSections *options, const char *sectionName)
  90         {
  91             auto section = options->addSection(OptionSection(sectionName));
  92             section.addOption(RealOption("E0").store(&a_));
  93             section.addOption(RealOption("omega").store(&omega_));
  94             section.addOption(RealOption("t0").store(&t0_));
  95             section.addOption(RealOption("sigma").store(&sigma_));
  96         }
  97
  98         /*! \brief Evaluates this field component at given time.
  99          *
 100          * \param[in] t The time to evualate at
 101          * \return The electric field
 102          */
 103         real evaluate(real t) const
 104         {
 105             if (sigma_ > 0)
 106             {
 107                 return a_ * (std::cos(omega_*(t-t0_))
 108                              * std::exp(-square(t-t0_)/(2.0*square(sigma_))));
 109             }
 110             else
 111             {
 112                 return a_ * std::cos(omega_*t);
 113             }
 114         }
 115
 116         /*! \brief Initiate the field values
 117          *
 118          * \param[in] a     Amplitude
 119          * \param[in] omega Frequency
 120          * \param[in] t0    Peak of the pulse
 121          * \param[in] sigma Width of the pulse
 122          */
 123         void setField(real a, real omega, real t0, real sigma)
 124         {
 125             a_     = a;
 126             omega_ = omega;
 127             t0_    = t0;
 128             sigma_ = sigma;
 129         }
 130
 131         //! Return the amplitude
 132         real a()     const { return a_; }
 133         //! Return the frequency
 134         real omega() const { return omega_; }
 135         //! Return the time for the peak of the pulse
 136         real t0()    const { return t0_; }
 137         //! Return the width of the pulse (0 means inifinite)
 138         real sigma() const { return sigma_; }
 139
 140     private:
 141         //! Coeffient (V / nm)
 142         real a_;
 143         //! Frequency (1/ps)
 144         real omega_;
 145         //! Central time point (ps) for pulse
 146         real t0_;
 147         //! Width of pulse (ps, if zero there is no pulse)
 148         real sigma_;
 149 };
 150
 151 /*! \internal
 152  * \brief Describe time dependent electric field
 153  *
 154  * Class that implements a force to be evaluated in mdrun.
 155  * The electric field can be pulsed and oscillating, simply
 156  * oscillating, or static, in each of X,Y,Z directions.
 157  */
 158 class ElectricField : public IMDModule,
 159                       public IMdpOptionProvider, public IMDOutputProvider,
 160                       public IForceProvider
 161 {
 162     public:
 163         ElectricField() : fpField_(nullptr) {}
 164
 165         // From IMDModule
 166         virtual IMdpOptionProvider *mdpOptionProvider() { return this; }
 167         virtual IMDOutputProvider *outputProvider() { return this; }
 168         virtual IForceProvider *forceProvider() { return this; }
 169
 170         // From IMdpOptionProvider
 171         virtual void initMdpTransform(IKeyValueTreeTransformRules *transform);
 172         virtual void initMdpOptions(IOptionsContainerWithSections *options);
 173
 174         // From IMDOutputProvider
 175         virtual void initOutput(FILE *fplog, int nfile, const t_filenm fnm[],
 176                                 bool bAppendFiles, const gmx_output_env_t *oenv);
 177         virtual void finishOutput();
 178
 179         // From IForceProvider
 180         virtual void initForcerec(t_forcerec *fr);
 181         //! \copydoc IForceProvider::calculateForces()
 182         virtual void calculateForces(const t_commrec  *cr,
 183                                      const t_mdatoms  *mdatoms,
 184                                      PaddedRVecVector *force,
 185                                      double            t);
 186
 187     private:
 188         //! Return whether or not to apply a field
 189         bool isActive() const;
 190
 191         /*! \brief Return the field strength
 192          *
 193          * \param[in] dim The spatial direction
 194          * \param[in] t   The time (ps)
 195          * \return The field strength in V/nm units
 196          */
 197         real field(int dim, real t) const;
 198
 199         /*! \brief Return amplitude of field
 200          *
 201          * \param[in] dim Direction of the field (XX, YY, ZZ)
 202          * \return Amplitude of the field
 203          */
 204         real a(int dim)     const { return efield_[dim].a(); }
 205         /*! \brief Return frequency of field (1/ps)
 206          *
 207          * \param[in] dim Direction of the field (XX, YY, ZZ)
 208          * \return Frequency of the field
 209          */
 210         real omega(int dim) const { return efield_[dim].omega(); }
 211         /*! \brief Return time of pulse peak
 212          *
 213          * \param[in] dim Direction of the field (XX, YY, ZZ)
 214          * \return Time of pulse peak
 215          */
 216         real t0(int dim) const { return efield_[dim].t0(); }
 217         /*! \brief Return width of the pulse
 218          *
 219          * \param[in] dim Direction of the field (XX, YY, ZZ)
 220          * \return Width of the pulse
 221          */
 222         real sigma(int dim) const { return efield_[dim].sigma(); }
 223
 224         /*! \brief Print the field components to a file
 225          *
 226          * \param[in] t   The time
 227          * Will throw and exit with fatal error if file is not open.
 228          */
 229         void printComponents(double t) const;
 230
 231         //! The field strength in each dimension
 232         ElectricFieldData efield_[DIM];
 233         //! File pointer for electric field
 234         FILE             *fpField_;
 235 };
 236
 237 //! Converts static parameters from mdp format to E0.
 238 real convertStaticParameters(const std::string &value)
 239 {
 240     // TODO: Better context for the exceptions here (possibly
 241     // also convert them to warning_errors or such).
 242     const std::vector<std::string> sx = splitString(value);
 243     if (sx.empty())
 244     {
 245         return 0.0;
 246     }
 247     const int n = fromString<int>(sx[0]);
 248     if (n <= 0)
 249     {
 250         return 0.0;
 251     }
 252     if (n != 1)
 253     {
 254         GMX_THROW(InvalidInputError("Only one electric field term supported for each dimension"));
 255     }
 256     if (sx.size() != 3)
 257     {
 258         GMX_THROW(InvalidInputError("Expected exactly one electric field amplitude value"));
 259     }
 260     return fromString<real>(sx[1]);
 261 }
 262
 263 //! Converts dynamic parameters from mdp format to (omega, t0, sigma).
 264 void convertDynamicParameters(gmx::KeyValueTreeObjectBuilder *builder,
 265                               const std::string              &value)
 266 {
 267     const std::vector<std::string> sxt = splitString(value);
 268     if (sxt.empty())
 269     {
 270         return;
 271     }
 272     const int n = fromString<int>(sxt[0]);
 273     switch (n)
 274     {
 275         case 1:
 276             if (sxt.size() != 3)
 277             {
 278                 GMX_THROW(InvalidInputError("Please specify 1 omega 0 for non-pulsed fields"));
 279             }
 280             builder->addValue<real>("omega", fromString<real>(sxt[1]));
 281             break;
 282         case 3:
 283             if (sxt.size() != 7)
 284             {
 285                 GMX_THROW(InvalidInputError("Please specify 1 omega 0 t0 0 sigma 0 for pulsed fields"));
 286             }
 287             builder->addValue<real>("omega", fromString<real>(sxt[1]));
 288             builder->addValue<real>("t0", fromString<real>(sxt[3]));
 289             builder->addValue<real>("sigma", fromString<real>(sxt[5]));
 290             break;
 291         default:
 292             GMX_THROW(InvalidInputError("Incomprehensible input for electric field"));
 293     }
 294 }
 295
 296 void ElectricField::initMdpTransform(IKeyValueTreeTransformRules *rules)
 297 {
 298     // TODO This responsibility should be handled by the caller,
 299     // e.g. embedded in the rules, somehow.
 300     std::string prefix = "/applied-forces/";
 301
 302     rules->addRule().from<std::string>("/E-x").to<real>(prefix + "electric-field/x/E0")
 303         .transformWith(&convertStaticParameters);
 304     rules->addRule().from<std::string>("/E-xt").toObject(prefix + "electric-field/x")
 305         .transformWith(&convertDynamicParameters);
 306     rules->addRule().from<std::string>("/E-y").to<real>(prefix + "electric-field/y/E0")
 307         .transformWith(&convertStaticParameters);
 308     rules->addRule().from<std::string>("/E-yt").toObject(prefix + "electric-field/y")
 309         .transformWith(&convertDynamicParameters);
 310     rules->addRule().from<std::string>("/E-z").to<real>(prefix + "electric-field/z/E0")
 311         .transformWith(&convertStaticParameters);
 312     rules->addRule().from<std::string>("/E-zt").toObject(prefix + "electric-field/z")
 313         .transformWith(&convertDynamicParameters);
 314 }
 315
 316 void ElectricField::initMdpOptions(IOptionsContainerWithSections *options)
 317 {
 318     //CTYPE ("Format is E0 (V/nm), omega (1/ps), t0 (ps), sigma (ps) ");
 319     auto section = options->addSection(OptionSection("electric-field"));
 320     efield_[XX].initMdpOptions(&section, "x");
 321     efield_[YY].initMdpOptions(&section, "y");
 322     efield_[ZZ].initMdpOptions(&section, "z");
 323 }
 324
 325 void ElectricField::initOutput(FILE *fplog, int nfile, const t_filenm fnm[],
 326                                bool bAppendFiles, const gmx_output_env_t *oenv)
 327 {
 328     if (isActive())
 329     {
 330         please_cite(fplog, "Caleman2008a");
 331
 332         // Optional outpuf file showing the field, see manual.
 333         if (opt2bSet("-field", nfile, fnm))
 334         {
 335             if (bAppendFiles)
 336             {
 337                 fpField_ = gmx_fio_fopen(opt2fn("-field", nfile, fnm), "a+");
 338             }
 339             else
 340             {
 341                 fpField_ = xvgropen(opt2fn("-field", nfile, fnm),
 342                                     "Applied electric field", "Time (ps)",
 343                                     "E (V/nm)", oenv);
 344             }
 345         }
 346     }
 347 }
 348
 349 void ElectricField::finishOutput()
 350 {
 351     if (fpField_ != nullptr)
 352     {
 353         // This is opened sometimes with xvgropen, sometimes with
 354         // gmx_fio_fopen, so we use the least common denominator for closing.
 355         gmx_fio_fclose(fpField_);
 356         fpField_ = nullptr;
 357     }
 358 }
 359
 360 void ElectricField::initForcerec(t_forcerec *fr)
 361 {
 362     if (isActive())
 363     {
 364         fr->bF_NoVirSum = TRUE;
 365         fr->efield      = this;
 366     }
 367 }
 368
 369 real ElectricField::field(int dim, real t) const
 370 {
 371     return efield_[dim].evaluate(t);
 372 }
 373
 374 bool ElectricField::isActive() const
 375 {
 376     return (efield_[XX].a() != 0 ||
 377             efield_[YY].a() != 0 ||
 378             efield_[ZZ].a() != 0);
 379 }
 380
 381 void ElectricField::printComponents(double t) const
 382 {
 383     fprintf(fpField_, "%10g  %10g  %10g  %10g\n", t,
 384             field(XX, t), field(YY, t), field(ZZ, t));
 385 }
 386
 387 void ElectricField::calculateForces(const t_commrec  *cr,
 388                                     const t_mdatoms  *mdatoms,
 389                                     PaddedRVecVector *force,
 390                                     double            t)
 391 {
 392     if (isActive())
 393     {
 394         rvec *f = as_rvec_array(force->data());
 395
 396         for (int m = 0; (m < DIM); m++)
 397         {
 398             real Ext = FIELDFAC*field(m, t);
 399
 400             if (Ext != 0)
 401             {
 402                 // TODO: Check parallellism
 403                 for (int i = 0; i < mdatoms->homenr; ++i)
 404                 {
 405                     // NOTE: Not correct with perturbed charges
 406                     f[i][m] += mdatoms->chargeA[i]*Ext;
 407                 }
 408             }
 409         }
 410         if (MASTER(cr) && fpField_ != nullptr)
 411         {
 412             printComponents(t);
 413         }
 414     }
 415 }
 416
 417 }   // namespace
 418
 419 std::unique_ptr<IMDModule> createElectricFieldModule()
 420 {
 421     return std::unique_ptr<IMDModule>(new ElectricField());
 422 }
 423
 424 } // namespace gmx