src/gromacs/mdtypes/inputrec.h

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  37 #ifndef GMX_MDTYPES_INPUTREC_H
  38 #define GMX_MDTYPES_INPUTREC_H
  39
  40 #include <cstdio>
  41
  42 #include <memory>
  43
  44 #include "gromacs/math/vectypes.h"
  45 #include "gromacs/mdtypes/md_enums.h"
  46 #include "gromacs/utility/basedefinitions.h"
  47 #include "gromacs/utility/real.h"
  48
  49 #define EGP_EXCL  (1<<0)
  50 #define EGP_TABLE (1<<1)
  51
  52 struct gmx_enfrot;
  53 struct gmx_enfrotgrp;
  54 struct pull_params_t;
  55 struct pull_t;
  56 struct t_gmx_IMD;
  57 typedef struct t_swap *gmx_swapcoords_t;
  58
  59 namespace gmx
  60 {
  61 class Awh;
  62 struct AwhParams;
  63 class KeyValueTreeObject;
  64 }
  65
  66 struct t_grpopts
  67 {
  68     //! Number of T-Coupl groups
  69     int    ngtc;
  70     //! Number of of Nose-Hoover chains per group
  71     int    nhchainlength;
  72     //! Number of Accelerate groups
  73     int    ngacc;
  74     //! Number of Freeze groups
  75     int    ngfrz;
  76     //! Number of Energy groups
  77     int    ngener;
  78     //! Number of degrees of freedom in a group
  79     real  *nrdf;
  80     //! Coupling temperature    per group
  81     real  *ref_t;
  82     //! No/simple/periodic simulated annealing for each group
  83     int   *annealing;
  84     //! Number of annealing time points per group
  85     int   *anneal_npoints;
  86     //! For each group: Time points
  87     real **anneal_time;
  88     //! For each group: Temperature at these times. Final temp after all intervals is ref_t
  89     real **anneal_temp;
  90     //! Tau coupling time
  91     real  *tau_t;
  92     //! Acceleration per group
  93     rvec  *acc;
  94     //! Whether the group will be frozen in each direction
  95     ivec  *nFreeze;
  96     //! Exclusions/tables of energy group pairs
  97     int   *egp_flags;
  98
  99     /* QMMM stuff */
 100     //! Number of QM groups
 101     int       ngQM;
 102     //! Level of theory in the QM calculation
 103     int      *QMmethod;
 104     //! Basisset in the QM calculation
 105     int      *QMbasis;
 106     //! Total charge in the QM region
 107     int      *QMcharge;
 108     //! Spin multiplicicty in the QM region
 109     int      *QMmult;
 110     //! Surface hopping (diabatic hop only)
 111     gmx_bool *bSH;
 112     //! Number of orbiatls in the active space
 113     int      *CASorbitals;
 114     //! Number of electrons in the active space
 115     int      *CASelectrons;
 116     //! At which gap (A.U.) the SA is switched on
 117     real     *SAon;
 118     //! At which gap (A.U.) the SA is switched off
 119     real     *SAoff;
 120     //! In how many steps SA goes from 1-1 to 0.5-0.5
 121     int      *SAsteps;
 122 };
 123
 124 struct t_simtemp
 125 {
 126     //! Simulated temperature scaling; linear or exponential
 127     int   eSimTempScale;
 128     //! The low temperature for simulated tempering
 129     real  simtemp_low;
 130     //! The high temperature for simulated tempering
 131     real  simtemp_high;
 132     //! The range of temperatures used for simulated tempering
 133     real *temperatures;
 134 };
 135
 136 struct t_lambda
 137 {
 138     //! The frequency for calculating dhdl
 139     int      nstdhdl;
 140     //! Fractional value of lambda (usually will use init_fep_state, this will only be for slow growth, and for legacy free energy code. Only has a valid value if positive)
 141     double   init_lambda;
 142     //! The initial number of the state
 143     int      init_fep_state;
 144     //! Change of lambda per time step (fraction of (0.1)
 145     double   delta_lambda;
 146     //! Print no, total or potential energies in dhdl
 147     int      edHdLPrintEnergy;
 148     //! The number of foreign lambda points
 149     int      n_lambda;
 150     //! The array of all lambda values
 151     double **all_lambda;
 152     //! The number of neighboring lambda states to calculate the energy for in up and down directions (-1 for all)
 153     int      lambda_neighbors;
 154     //! The first lambda to calculate energies for
 155     int      lambda_start_n;
 156     //! The last lambda +1 to calculate energies for
 157     int      lambda_stop_n;
 158     //! Free energy soft-core parameter
 159     real     sc_alpha;
 160     //! Lambda power for soft-core interactions
 161     int      sc_power;
 162     //! R power for soft-core interactions
 163     real     sc_r_power;
 164     //! Free energy soft-core sigma when c6 or c12=0
 165     real     sc_sigma;
 166     //! Free energy soft-core sigma for ?????
 167     real     sc_sigma_min;
 168     //! Use softcore for the coulomb portion as well (default FALSE)
 169     gmx_bool bScCoul;
 170     //! Whether to print the dvdl term associated with this term; if it is not specified as separate, it is lumped with the FEP term
 171     gmx_bool separate_dvdl[efptNR];
 172     //! Whether to write a separate dhdl.xvg file note: NOT a gmx_bool, but an enum
 173     int      separate_dhdl_file;
 174     //! Whether to calculate+write dhdl derivatives note: NOT a gmx_bool, but an enum
 175     int      dhdl_derivatives;
 176     //! The maximum table size for the dH histogram
 177     int      dh_hist_size;
 178     //! The spacing for the dH histogram
 179     double   dh_hist_spacing;
 180 };
 181
 182 struct t_expanded {
 183     //! The frequency of expanded ensemble state changes
 184     int      nstexpanded;
 185     //! Which type of move updating do we use for lambda monte carlo (or no for none)
 186     int      elamstats;
 187     //! What move set will be we using for state space moves
 188     int      elmcmove;
 189     //! The method we use to decide of we have equilibrated the weights
 190     int      elmceq;
 191     //! The minumum number of samples at each lambda for deciding whether we have reached a minimum
 192     int      equil_n_at_lam;
 193     //! Wang-Landau delta at which we stop equilibrating weights
 194     real     equil_wl_delta;
 195     //! Use the ratio of weights (ratio of minimum to maximum) to decide when to stop equilibrating
 196     real     equil_ratio;
 197     //! After equil_steps steps we stop equilibrating the weights
 198     int      equil_steps;
 199     //! After equil_samples total samples (steps/nstfep), we stop equilibrating the weights
 200     int      equil_samples;
 201     //! Random number seed for lambda mc switches
 202     int      lmc_seed;
 203     //! Whether to use minumum variance weighting
 204     gmx_bool minvar;
 205     //! The number of samples needed before kicking into minvar routine
 206     int      minvarmin;
 207     //! The offset for the variance in MinVar
 208     real     minvar_const;
 209     //! Range of cvalues used for BAR
 210     int      c_range;
 211     //! Whether to print symmetrized matrices
 212     gmx_bool bSymmetrizedTMatrix;
 213     //! How frequently to print the transition matrices
 214     int      nstTij;
 215     //! Number of repetitions in the MC lambda jumps MRS -- VERIFY THIS
 216     int      lmc_repeats;
 217     //! Minimum number of samples for each state before free sampling MRS -- VERIFY THIS!
 218     int      lmc_forced_nstart;
 219     //! Distance in lambda space for the gibbs interval
 220     int      gibbsdeltalam;
 221     //! Scaling factor for Wang-Landau
 222     real     wl_scale;
 223     //! Ratio between largest and smallest number for freezing the weights
 224     real     wl_ratio;
 225     //! Starting delta for Wang-Landau
 226     real     init_wl_delta;
 227     //! Use one over t convergence for Wang-Landau when the delta get sufficiently small
 228     gmx_bool bWLoneovert;
 229     //! Did we initialize the weights? TODO: REMOVE FOR 5.0, no longer needed with new logic
 230     gmx_bool bInit_weights;
 231     //! To override the main temperature, or define it if it's not defined
 232     real     mc_temp;
 233     //! User-specified initial weights to start with
 234     real    *init_lambda_weights;
 235 };
 236
 237 struct t_rotgrp
 238 {
 239     //! Rotation type for this group
 240     int              eType;
 241     //! Use mass-weighed positions?
 242     int              bMassW;
 243     //! Number of atoms in the group
 244     int              nat;
 245     //! The global atoms numbers
 246     int             *ind;
 247     //! The reference positions
 248     rvec            *x_ref;
 249     //! The normalized rotation vector
 250     rvec             inputVec;
 251     //! Rate of rotation (degree/ps)
 252     real             rate;
 253     //! Force constant (kJ/(mol nm^2)
 254     real             k;
 255     //! Pivot point of rotation axis (nm)
 256     rvec             pivot;
 257     //! Type of fit to determine actual group angle
 258     int              eFittype;
 259     //! Number of angles around the reference angle for which the rotation potential is also evaluated (for fit type 'potential' only)
 260     int              PotAngle_nstep;
 261     //! Distance between two angles in degrees (for fit type 'potential' only)
 262     real             PotAngle_step;
 263     //! Slab distance (nm)
 264     real             slab_dist;
 265     //! Minimum value the gaussian must have so that the force is actually evaluated
 266     real             min_gaussian;
 267     //! Additive constant for radial motion2 and flexible2 potentials (nm^2)
 268     real             eps;
 269 };
 270
 271 struct t_rot
 272 {
 273     //! Number of rotation groups
 274     int                   ngrp;
 275     //! Output frequency for main rotation outfile
 276     int                   nstrout;
 277     //! Output frequency for per-slab data
 278     int                   nstsout;
 279     //! Groups to rotate
 280     t_rotgrp             *grp;
 281 };
 282
 283 struct t_IMD
 284 {
 285     //! Number of interactive atoms
 286     int              nat;
 287     //! The global indices of the interactive atoms
 288     int             *ind;
 289     //! Stores non-inputrec IMD data
 290     t_gmx_IMD       *setup;
 291 };
 292
 293 struct t_swapGroup
 294 {
 295     //! Name of the swap group, e.g. NA, CL, SOL
 296     char            *molname;
 297     //! Number of atoms in this group
 298     int              nat;
 299     //! The global ion group atoms numbers
 300     int             *ind;
 301     //! Requested number of molecules of this type per compartment
 302     int              nmolReq[eCompNR];
 303 };
 304
 305 struct t_swapcoords
 306 {
 307     //! Period between when a swap is attempted
 308     int      nstswap;
 309     //! Use mass-weighted positions in split group
 310     gmx_bool massw_split[2];
 311     /*! \brief Split cylinders defined by radius, upper and lower
 312      * extension. The split cylinders define the channels and are
 313      * each anchored in the center of the split group */
 314     /**@{*/
 315     real cyl0r, cyl1r;
 316     real cyl0u, cyl1u;
 317     real cyl0l, cyl1l;
 318     /**@}*/
 319     //! Coupling constant (number of swap attempt steps)
 320     int                      nAverage;
 321     //! Ion counts may deviate from the requested values by +-threshold before a swap is done
 322     real                     threshold;
 323     //! Offset of the swap layer (='bulk') with respect to the compartment-defining layers
 324     real                     bulkOffset[eCompNR];
 325     //! Number of groups to be controlled
 326     int                      ngrp;
 327     //! All swap groups, including split and solvent
 328     t_swapGroup             *grp;
 329     //! Swap private data accessible in swapcoords.cpp
 330     gmx_swapcoords_t         si_priv;
 331 };
 332
 333 struct t_inputrec
 334 {
 335     t_inputrec();
 336     explicit t_inputrec(const t_inputrec &) = delete;
 337     t_inputrec &operator=(const t_inputrec &) = delete;
 338     ~t_inputrec();
 339
 340     //! Integration method
 341     int                         eI;
 342     //! Number of steps to be taken
 343     int64_t                     nsteps;
 344     //! Used in checkpointing to separate chunks
 345     int                         simulation_part;
 346     //! Start at a stepcount >0 (used w. convert-tpr)
 347     int64_t                     init_step;
 348     //! Frequency of energy calc. and T/P coupl. upd.
 349     int                         nstcalcenergy;
 350     //! Group or verlet cutoffs
 351     int                         cutoff_scheme;
 352     //! Which neighbor search method should we use?
 353     int                         ns_type;
 354     //! Number of steps before pairlist is generated
 355     int                         nstlist;
 356     //! Number of cells per rlong
 357     int                         ndelta;
 358     //! Number of steps after which center of mass motion is removed
 359     int                         nstcomm;
 360     //! Center of mass motion removal algorithm
 361     int                         comm_mode;
 362     //! Number of steps after which print to logfile
 363     int                         nstlog;
 364     //! Number of steps after which X is output
 365     int                         nstxout;
 366     //! Number of steps after which V is output
 367     int                         nstvout;
 368     //! Number of steps after which F is output
 369     int                         nstfout;
 370     //! Number of steps after which energies printed
 371     int                         nstenergy;
 372     //! Number of steps after which compressed trj (.xtc,.tng) is output
 373     int                         nstxout_compressed;
 374     //! Initial time (ps)
 375     double                      init_t;
 376     //! Time step (ps)
 377     double                      delta_t;
 378     //! Precision of x in compressed trajectory file
 379     real                        x_compression_precision;
 380     //! Requested fourier_spacing, when nk? not set
 381     real                        fourier_spacing;
 382     //! Number of k vectors in x dimension for fourier methods for long range electrost.
 383     int                         nkx;
 384     //! Number of k vectors in y dimension for fourier methods for long range electrost.
 385     int                         nky;
 386     //! Number of k vectors in z dimension for fourier methods for long range electrost.
 387     int                         nkz;
 388     //! Interpolation order for PME
 389     int                         pme_order;
 390     //! Real space tolerance for Ewald, determines the real/reciprocal space relative weight
 391     real                        ewald_rtol;
 392     //! Real space tolerance for LJ-Ewald
 393     real                        ewald_rtol_lj;
 394     //! Normal/3D ewald, or pseudo-2D LR corrections
 395     int                         ewald_geometry;
 396     //! Epsilon for PME dipole correction
 397     real                        epsilon_surface;
 398     //! Type of combination rule in LJ-PME
 399     int                         ljpme_combination_rule;
 400     //! Type of periodic boundary conditions
 401     int                         ePBC;
 402     //! Periodic molecules
 403     int                         bPeriodicMols;
 404     //! Continuation run: starting state is correct (ie. constrained)
 405     gmx_bool                    bContinuation;
 406     //! Temperature coupling
 407     int                         etc;
 408     //! Interval in steps for temperature coupling
 409     int                         nsttcouple;
 410     //! Whether to print nose-hoover chains
 411     gmx_bool                    bPrintNHChains;
 412     //! Pressure coupling
 413     int                         epc;
 414     //! Pressure coupling type
 415     int                         epct;
 416     //! Interval in steps for pressure coupling
 417     int                         nstpcouple;
 418     //! Pressure coupling time (ps)
 419     real                        tau_p;
 420     //! Reference pressure (kJ/(mol nm^3))
 421     tensor                      ref_p;
 422     //! Compressibility ((mol nm^3)/kJ)
 423     tensor                      compress;
 424     //! How to scale absolute reference coordinates
 425     int                         refcoord_scaling;
 426     //! The COM of the posres atoms
 427     rvec                        posres_com;
 428     //! The B-state COM of the posres atoms
 429     rvec                        posres_comB;
 430     //! Random seed for Andersen thermostat (obsolete)
 431     int                         andersen_seed;
 432     //! Per atom pair energy drift tolerance (kJ/mol/ps/atom) for list buffer
 433     real                        verletbuf_tol;
 434     //! Short range pairlist cut-off (nm)
 435     real                        rlist;
 436     //! Radius for test particle insertion
 437     real                        rtpi;
 438     //! Type of electrostatics treatment
 439     int                         coulombtype;
 440     //! Modify the Coulomb interaction
 441     int                         coulomb_modifier;
 442     //! Coulomb switch range start (nm)
 443     real                        rcoulomb_switch;
 444     //! Coulomb cutoff (nm)
 445     real                        rcoulomb;
 446     //! Relative dielectric constant
 447     real                        epsilon_r;
 448     //! Relative dielectric constant of the RF
 449     real                        epsilon_rf;
 450     //! Always false (no longer supported)
 451     bool                        implicit_solvent;
 452     //! Type of Van der Waals treatment
 453     int                         vdwtype;
 454     //! Modify the Van der Waals interaction
 455     int                         vdw_modifier;
 456     //! Van der Waals switch range start (nm)
 457     real                        rvdw_switch;
 458     //! Van der Waals cutoff (nm)
 459     real                        rvdw;
 460     //! Perform Long range dispersion corrections
 461     int                         eDispCorr;
 462     //! Extension of the table beyond the cut-off, as well as the table length for 1-4 interac.
 463     real                        tabext;
 464     //! Tolerance for shake
 465     real                        shake_tol;
 466     //! Free energy calculations
 467     int                         efep;
 468     //! Data for the FEP state
 469     t_lambda                   *fepvals;
 470     //! Whether to do simulated tempering
 471     gmx_bool                    bSimTemp;
 472     //! Variables for simulated tempering
 473     t_simtemp                  *simtempvals;
 474     //! Whether expanded ensembles are used
 475     gmx_bool                    bExpanded;
 476     //! Expanded ensemble parameters
 477     t_expanded                 *expandedvals;
 478     //! Type of distance restraining
 479     int                         eDisre;
 480     //! Force constant for time averaged distance restraints
 481     real                        dr_fc;
 482     //! Type of weighting of pairs in one restraints
 483     int                         eDisreWeighting;
 484     //! Use combination of time averaged and instantaneous violations
 485     gmx_bool                    bDisreMixed;
 486     //! Frequency of writing pair distances to enx
 487     int                         nstdisreout;
 488     //! Time constant for memory function in disres
 489     real                        dr_tau;
 490     //! Force constant for orientational restraints
 491     real                        orires_fc;
 492     //! Time constant for memory function in orires
 493     real                        orires_tau;
 494     //! Frequency of writing tr(SD) to energy output
 495     int                         nstorireout;
 496     //! The stepsize for updating
 497     real                        em_stepsize;
 498     //! The tolerance
 499     real                        em_tol;
 500     //! Number of iterations for convergence of steepest descent in relax_shells
 501     int                         niter;
 502     //! Stepsize for directional minimization in relax_shells
 503     real                        fc_stepsize;
 504     //! Number of steps after which a steepest descents step is done while doing cg
 505     int                         nstcgsteep;
 506     //! Number of corrections to the Hessian to keep
 507     int                         nbfgscorr;
 508     //! Type of constraint algorithm
 509     int                         eConstrAlg;
 510     //! Order of the LINCS Projection Algorithm
 511     int                         nProjOrder;
 512     //! Warn if any bond rotates more than this many degrees
 513     real                        LincsWarnAngle;
 514     //! Number of iterations in the final LINCS step
 515     int                         nLincsIter;
 516     //! Use successive overrelaxation for shake
 517     gmx_bool                    bShakeSOR;
 518     //! Friction coefficient for BD (amu/ps)
 519     real                        bd_fric;
 520     //! Random seed for SD and BD
 521     int64_t                     ld_seed;
 522     //! The number of walls
 523     int                         nwall;
 524     //! The type of walls
 525     int                         wall_type;
 526     //! The potentail is linear for r<=wall_r_linpot
 527     real                        wall_r_linpot;
 528     //! The atom type for walls
 529     int                         wall_atomtype[2];
 530     //! Number density for walls
 531     real                        wall_density[2];
 532     //! Scaling factor for the box for Ewald
 533     real                        wall_ewald_zfac;
 534
 535     /* COM pulling data */
 536     //! Do we do COM pulling?
 537     gmx_bool       bPull;
 538     //! The data for center of mass pulling
 539     pull_params_t *pull;
 540     // TODO: Remove this by converting pull into a ForceProvider
 541     //! The COM pull force calculation data structure
 542     pull_t *pull_work;
 543
 544     /* AWH bias data */
 545     //! Whether to use AWH biasing for PMF calculations
 546     gmx_bool        bDoAwh;
 547     //! AWH biasing parameters
 548     gmx::AwhParams *awhParams;
 549
 550     /* Enforced rotation data */
 551     //! Whether to calculate enforced rotation potential(s)
 552     gmx_bool               bRot;
 553     //! The data for enforced rotation potentials
 554     t_rot                 *rot;
 555
 556     //! Whether to do ion/water position exchanges (CompEL)
 557     int                           eSwapCoords;
 558     //! Swap data structure.
 559     t_swapcoords                 *swap;
 560
 561     //! Whether to do an interactive MD session
 562     gmx_bool               bIMD;
 563     //! Interactive molecular dynamics
 564     t_IMD                 *imd;
 565
 566     //! Acceleration for viscosity calculation
 567     real   cos_accel;
 568     //! Triclinic deformation velocities (nm/ps)
 569     tensor deform;
 570     /*! \brief User determined parameters */
 571     /**@{*/
 572     int  userint1;
 573     int  userint2;
 574     int  userint3;
 575     int  userint4;
 576     real userreal1;
 577     real userreal2;
 578     real userreal3;
 579     real userreal4;
 580     /**@}*/
 581     //! Group options
 582     t_grpopts opts;
 583     //! QM/MM calculation
 584     gmx_bool  bQMMM;
 585     //! Constraints on QM bonds
 586     int       QMconstraints;
 587     //! Scheme: ONIOM or normal
 588     int       QMMMscheme;
 589     //! Factor for scaling the MM charges in QM calc.
 590     real      scalefactor;
 591
 592     /* Fields for removed features go here (better caching) */
 593     //! Whether AdResS is enabled - always false if a valid .tpr was read
 594     gmx_bool                 bAdress;
 595     //! Whether twin-range scheme is active - always false if a valid .tpr was read
 596     gmx_bool                 useTwinRange;
 597
 598     //! KVT object that contains input parameters converted to the new style.
 599     gmx::KeyValueTreeObject *params;
 600 };
 601
 602 int ir_optimal_nstcalcenergy(const t_inputrec *ir);
 603
 604 int tcouple_min_integration_steps(int etc);
 605
 606 int ir_optimal_nsttcouple(const t_inputrec *ir);
 607
 608 int pcouple_min_integration_steps(int epc);
 609
 610 int ir_optimal_nstpcouple(const t_inputrec *ir);
 611
 612 /* Returns if the Coulomb force or potential is switched to zero */
 613 gmx_bool ir_coulomb_switched(const t_inputrec *ir);
 614
 615 /* Returns if the Coulomb interactions are zero beyond the rcoulomb.
 616  * Note: always returns TRUE for the Verlet cut-off scheme.
 617  */
 618 gmx_bool ir_coulomb_is_zero_at_cutoff(const t_inputrec *ir);
 619
 620 /* As ir_coulomb_is_zero_at_cutoff, but also returns TRUE for user tabulated
 621  * interactions, since these might be zero beyond rcoulomb.
 622  */
 623 gmx_bool ir_coulomb_might_be_zero_at_cutoff(const t_inputrec *ir);
 624
 625 /* Returns if the Van der Waals force or potential is switched to zero */
 626 gmx_bool ir_vdw_switched(const t_inputrec *ir);
 627
 628 /* Returns if the Van der Waals interactions are zero beyond the rvdw.
 629  * Note: always returns TRUE for the Verlet cut-off scheme.
 630  */
 631 gmx_bool ir_vdw_is_zero_at_cutoff(const t_inputrec *ir);
 632
 633 /* As ir_vdw_is_zero_at_cutoff, but also returns TRUE for user tabulated
 634  * interactions, since these might be zero beyond rvdw.
 635  */
 636 gmx_bool ir_vdw_might_be_zero_at_cutoff(const t_inputrec *ir);
 637
 638 /*! \brief Free memory from input record.
 639  *
 640  * All arrays and pointers will be freed.
 641  *
 642  * \param[in] ir The data structure
 643  */
 644 void done_inputrec(t_inputrec *ir);
 645
 646 void pr_inputrec(FILE *fp, int indent, const char *title, const t_inputrec *ir,
 647                  gmx_bool bMDPformat);
 648
 649 void cmp_inputrec(FILE *fp, const t_inputrec *ir1, const t_inputrec *ir2, real ftol, real abstol);
 650
 651 void comp_pull_AB(FILE *fp, pull_params_t *pull, real ftol, real abstol);
 652
 653
 654 gmx_bool inputrecDeform(const t_inputrec *ir);
 655
 656 gmx_bool inputrecDynamicBox(const t_inputrec *ir);
 657
 658 gmx_bool inputrecPreserveShape(const t_inputrec *ir);
 659
 660 gmx_bool inputrecNeedMutot(const t_inputrec *ir);
 661
 662 gmx_bool inputrecTwinRange(const t_inputrec *ir);
 663
 664 gmx_bool inputrecExclForces(const t_inputrec *ir);
 665
 666 gmx_bool inputrecNptTrotter(const t_inputrec *ir);
 667
 668 gmx_bool inputrecNvtTrotter(const t_inputrec *ir);
 669
 670 gmx_bool inputrecNphTrotter(const t_inputrec *ir);
 671
 672 /*! \brief Return true if the simulation is 2D periodic with two walls. */
 673 bool     inputrecPbcXY2Walls(const t_inputrec *ir);
 674
 675 /*! \brief Returns true for MD integator with T and/or P-coupling that supports
 676  * calculating the conserved energy quantity.
 677  */
 678 bool integratorHasConservedEnergyQuantity(const t_inputrec *ir);
 679
 680 /*! \brief Returns true when temperature is coupled or constant. */
 681 bool integratorHasReferenceTemperature(const t_inputrec *ir);
 682
 683 /*! \brief Return the number of bounded dimensions
 684  *
 685  * \param[in] ir The input record with MD parameters
 686  * \return the number of dimensions in which
 687  * the coordinates of the particles are bounded, starting at X.
 688  */
 689 int inputrec2nboundeddim(const t_inputrec *ir);
 690
 691 /*! \brief Returns the number of degrees of freedom in center of mass motion
 692  *
 693  * \param[in] ir the inputrec structure
 694  * \return the number of degrees of freedom of the center of mass
 695  */
 696 int ndof_com(const t_inputrec *ir);
 697
 698 #endif /* GMX_MDTYPES_INPUTREC_H */