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38 #ifndef GMX_MDTYPES_INPUTREC_H
39 #define GMX_MDTYPES_INPUTREC_H
46 #include "gromacs/math/vectypes.h"
47 #include "gromacs/mdtypes/md_enums.h"
48 #include "gromacs/utility/enumerationhelpers.h"
49 #include "gromacs/utility/real.h"
51 #define EGP_EXCL (1 << 0)
52 #define EGP_TABLE (1 << 1)
62 class KeyValueTreeObject;
68 //! Number of T-Coupl groups
70 //! Number of of Nose-Hoover chains per group
71 int nhchainlength = 0;
72 //! Number of Freeze groups
74 //! Number of Energy groups
76 //! Number of degrees of freedom in a group
78 //! Coupling temperature per group
79 real* ref_t = nullptr;
80 //! No/simple/periodic simulated annealing for each group
81 SimulatedAnnealing* annealing = nullptr;
82 //! Number of annealing time points per group
83 int* anneal_npoints = nullptr;
84 //! For each group: Time points
85 real** anneal_time = nullptr;
86 //! For each group: Temperature at these times. Final temp after all intervals is ref_t
87 real** anneal_temp = nullptr;
89 real* tau_t = nullptr;
90 //! Whether the group will be frozen in each direction
91 ivec* nFreeze = nullptr;
92 //! Exclusions/tables of energy group pairs
93 int* egp_flags = nullptr;
96 //! Number of QM groups
102 //! Simulated temperature scaling; linear or exponential
103 SimulatedTempering eSimTempScale = SimulatedTempering::Default;
104 //! The low temperature for simulated tempering
105 real simtemp_low = 0;
106 //! The high temperature for simulated tempering
107 real simtemp_high = 0;
108 //! The range of temperatures used for simulated tempering
109 std::vector<real> temperatures;
114 //! The frequency for calculating dhdl
116 //! 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)
117 double init_lambda = 0;
118 //! The initial number of the state
119 int init_fep_state = 0;
120 //! Change of lambda per time step (fraction of (0.1)
121 double delta_lambda = 0;
122 //! Print no, total or potential energies in dhdl
123 FreeEnergyPrintEnergy edHdLPrintEnergy = FreeEnergyPrintEnergy::Default;
124 //! The number of foreign lambda points
126 //! The array of all lambda values
127 gmx::EnumerationArray<FreeEnergyPerturbationCouplingType, std::vector<double>> all_lambda;
128 //! The number of neighboring lambda states to calculate the energy for in up and down directions (-1 for all)
129 int lambda_neighbors = 0;
130 //! The first lambda to calculate energies for
131 int lambda_start_n = 0;
132 //! The last lambda +1 to calculate energies for
133 int lambda_stop_n = 0;
134 //! Free energy soft-core parameter
136 //! Lambda power for soft-core interactions
138 //! R power for soft-core interactions
140 //! Free energy soft-core sigma when c6 or c12=0
142 //! Free energy soft-core sigma for ?????
143 real sc_sigma_min = 0;
144 //! Use softcore for the coulomb portion as well (default FALSE)
145 bool bScCoul = false;
146 //! The specific soft-core function to use
147 SoftcoreType softcoreFunction = SoftcoreType::Beutler;
148 //! scale for the linearization point for the vdw interaction with gapsys soft-core
149 real scGapsysScaleLinpointLJ = 0.85;
150 //! scale for the linearization point for the coulomb interaction with gapsys soft-core
151 real scGapsysScaleLinpointQ = 0.3;
152 //! lower bound for c12/c6 in gapsys soft-core
153 real scGapsysSigmaLJ = 0.3;
154 //! Whether to print the dvdl term associated with this term; if it is not specified as separate, it is lumped with the FEP term
155 gmx::EnumerationArray<FreeEnergyPerturbationCouplingType, bool> separate_dvdl;
156 //! Whether to write a separate dhdl.xvg file note: NOT a gmx_bool, but an enum
157 SeparateDhdlFile separate_dhdl_file = SeparateDhdlFile::Default;
158 //! Whether to calculate+write dhdl derivatives note: NOT a gmx_bool, but an enum
159 DhDlDerivativeCalculation dhdl_derivatives = DhDlDerivativeCalculation::Default;
160 //! The maximum table size for the dH histogram
161 int dh_hist_size = 0;
162 //! The spacing for the dH histogram
163 double dh_hist_spacing = 0;
168 //! The frequency of expanded ensemble state changes
170 //! Which type of move updating do we use for lambda monte carlo (or no for none)
171 LambdaWeightCalculation elamstats = LambdaWeightCalculation::Default;
172 //! What move set will be we using for state space moves
173 LambdaMoveCalculation elmcmove = LambdaMoveCalculation::Default;
174 //! The method we use to decide of we have equilibrated the weights
175 LambdaWeightWillReachEquilibrium elmceq = LambdaWeightWillReachEquilibrium::Default;
176 //! The minumum number of samples at each lambda for deciding whether we have reached a minimum
177 int equil_n_at_lam = 0;
178 //! Wang-Landau delta at which we stop equilibrating weights
179 real equil_wl_delta = 0;
180 //! Use the ratio of weights (ratio of minimum to maximum) to decide when to stop equilibrating
181 real equil_ratio = 0;
182 //! After equil_steps steps we stop equilibrating the weights
184 //! After equil_samples total samples (steps/nstfep), we stop equilibrating the weights
185 int equil_samples = 0;
186 //! Random number seed for lambda mc switches
188 //! Whether to use minumum variance weighting
190 //! The number of samples needed before kicking into minvar routine
192 //! The offset for the variance in MinVar
193 real minvar_const = 0;
194 //! Range of cvalues used for BAR
196 //! Whether to print symmetrized matrices
197 bool bSymmetrizedTMatrix = false;
198 //! How frequently to print the transition matrices
200 //! Number of repetitions in the MC lambda jumps MRS -- VERIFY THIS
202 //! Minimum number of samples for each state before free sampling MRS -- VERIFY THIS!
203 int lmc_forced_nstart = 0;
204 //! Distance in lambda space for the gibbs interval
205 int gibbsdeltalam = 0;
206 //! Scaling factor for Wang-Landau
208 //! Ratio between largest and smallest number for freezing the weights
210 //! Starting delta for Wang-Landau
211 real init_wl_delta = 0;
212 //! Use one over t convergence for Wang-Landau when the delta get sufficiently small
213 bool bWLoneovert = false;
214 //! Did we initialize the weights? TODO: REMOVE FOR 5.0, no longer needed with new logic
215 bool bInit_weights = false;
216 //! To override the main temperature, or define it if it's not defined
218 //! User-specified initial weights to start with
219 std::vector<real> init_lambda_weights;
224 //! Rotation type for this group
225 EnforcedRotationGroupType eType;
226 //! Use mass-weighed positions?
228 //! Number of atoms in the group
230 //! The global atoms numbers
232 //! The reference positions
234 //! The normalized rotation vector
236 //! Rate of rotation (degree/ps)
238 //! Force constant (kJ/(mol nm^2)
240 //! Pivot point of rotation axis (nm)
242 //! Type of fit to determine actual group angle
243 RotationGroupFitting eFittype;
244 //! Number of angles around the reference angle for which the rotation potential is also evaluated (for fit type 'potential' only)
246 //! Distance between two angles in degrees (for fit type 'potential' only)
248 //! Slab distance (nm)
250 //! Minimum value the gaussian must have so that the force is actually evaluated
252 //! Additive constant for radial motion2 and flexible2 potentials (nm^2)
258 //! Number of rotation groups
260 //! Output frequency for main rotation outfile
262 //! Output frequency for per-slab data
270 //! Number of interactive atoms
272 //! The global indices of the interactive atoms
278 //! Name of the swap group, e.g. NA, CL, SOL
280 //! Number of atoms in this group
282 //! The global ion group atoms numbers
284 //! Requested number of molecules of this type per compartment
285 gmx::EnumerationArray<Compartment, int> nmolReq;
290 //! Period between when a swap is attempted
292 //! Use mass-weighted positions in split group
294 /*! \brief Split cylinders defined by radius, upper and lower
295 * extension. The split cylinders define the channels and are
296 * each anchored in the center of the split group */
302 //! Coupling constant (number of swap attempt steps)
304 //! Ion counts may deviate from the requested values by +-threshold before a swap is done
306 //! Offset of the swap layer (='bulk') with respect to the compartment-defining layers
307 gmx::EnumerationArray<Compartment, real> bulkOffset;
308 //! Number of groups to be controlled
310 //! All swap groups, including split and solvent
314 struct t_inputrec // NOLINT (clang-analyzer-optin.performance.Padding)
317 explicit t_inputrec(const t_inputrec&) = delete;
318 t_inputrec& operator=(const t_inputrec&) = delete;
321 //! Integration method
322 IntegrationAlgorithm eI = IntegrationAlgorithm::Default;
323 //! Number of steps to be taken
325 //! Used in checkpointing to separate chunks
326 int simulation_part = 0;
327 //! Start at a stepcount >0 (used w. convert-tpr)
328 int64_t init_step = 0;
329 //! Frequency of energy calc. and T/P coupl. upd.
330 int nstcalcenergy = 0;
331 //! Group or verlet cutoffs
332 CutoffScheme cutoff_scheme = CutoffScheme::Default;
333 //! Number of steps before pairlist is generated
335 //! Number of steps after which center of mass motion is removed
337 //! Center of mass motion removal algorithm
338 ComRemovalAlgorithm comm_mode = ComRemovalAlgorithm::Default;
339 //! Number of steps after which print to logfile
341 //! Number of steps after which X is output
343 //! Number of steps after which V is output
345 //! Number of steps after which F is output
347 //! Number of steps after which energies printed
349 //! Number of steps after which compressed trj (.xtc,.tng) is output
350 int nstxout_compressed = 0;
351 //! Initial time (ps)
355 //! Whether we use multiple time stepping
357 //! The multiple time stepping levels
358 std::vector<gmx::MtsLevel> mtsLevels;
359 //! Precision of x in compressed trajectory file
360 real x_compression_precision = 0;
361 //! Requested fourier_spacing, when nk? not set
362 real fourier_spacing = 0;
363 //! Number of k vectors in x dimension for fourier methods for long range electrost.
365 //! Number of k vectors in y dimension for fourier methods for long range electrost.
367 //! Number of k vectors in z dimension for fourier methods for long range electrost.
369 //! Interpolation order for PME
371 //! Real space tolerance for Ewald, determines the real/reciprocal space relative weight
373 //! Real space tolerance for LJ-Ewald
374 real ewald_rtol_lj = 0;
375 //! Normal/3D ewald, or pseudo-2D LR corrections
376 EwaldGeometry ewald_geometry = EwaldGeometry::Default;
377 //! Epsilon for PME dipole correction
378 real epsilon_surface = 0;
379 //! Type of combination rule in LJ-PME
380 LongRangeVdW ljpme_combination_rule = LongRangeVdW::Default;
381 //! Type of periodic boundary conditions
382 PbcType pbcType = PbcType::Default;
383 //! Periodic molecules
384 bool bPeriodicMols = false;
385 //! Continuation run: starting state is correct (ie. constrained)
386 bool bContinuation = false;
387 //! Temperature coupling
388 TemperatureCoupling etc = TemperatureCoupling::Default;
389 //! Interval in steps for temperature coupling
391 //! Whether to print nose-hoover chains
392 bool bPrintNHChains = false;
393 //! Pressure coupling
394 PressureCoupling epc = PressureCoupling::Default;
395 //! Pressure coupling type
396 PressureCouplingType epct = PressureCouplingType::Default;
397 //! Interval in steps for pressure coupling
399 //! Pressure coupling time (ps)
401 //! Reference pressure (kJ/(mol nm^3))
402 tensor ref_p = { { 0 } };
403 //! Compressibility ((mol nm^3)/kJ)
404 tensor compress = { { 0 } };
405 //! How to scale absolute reference coordinates
406 RefCoordScaling refcoord_scaling = RefCoordScaling::Default;
407 //! The COM of the posres atoms
408 rvec posres_com = { 0, 0, 0 };
409 //! The B-state COM of the posres atoms
410 rvec posres_comB = { 0, 0, 0 };
411 //! Random seed for Andersen thermostat (obsolete)
412 int andersen_seed = 0;
413 //! Per atom pair energy drift tolerance (kJ/mol/ps/atom) for list buffer
414 real verletbuf_tol = 0;
415 //! Short range pairlist cut-off (nm)
417 //! Radius for test particle insertion
419 //! Type of electrostatics treatment
420 CoulombInteractionType coulombtype = CoulombInteractionType::Default;
421 //! Modify the Coulomb interaction
422 InteractionModifiers coulomb_modifier = InteractionModifiers::Default;
423 //! Coulomb switch range start (nm)
424 real rcoulomb_switch = 0;
425 //! Coulomb cutoff (nm)
427 //! Relative dielectric constant
429 //! Relative dielectric constant of the RF
431 //! Always false (no longer supported)
432 bool implicit_solvent = false;
433 //! Type of Van der Waals treatment
434 VanDerWaalsType vdwtype = VanDerWaalsType::Default;
435 //! Modify the Van der Waals interaction
436 InteractionModifiers vdw_modifier = InteractionModifiers::Default;
437 //! Van der Waals switch range start (nm)
438 real rvdw_switch = 0;
439 //! Van der Waals cutoff (nm)
441 //! Perform Long range dispersion corrections
442 DispersionCorrectionType eDispCorr = DispersionCorrectionType::Default;
443 //! Extension of the table beyond the cut-off, as well as the table length for 1-4 interac.
445 //! Tolerance for shake
447 //! Free energy calculations
448 FreeEnergyPerturbationType efep = FreeEnergyPerturbationType::Default;
449 //! Data for the FEP state
450 std::unique_ptr<t_lambda> fepvals;
451 //! Whether to do simulated tempering
452 bool bSimTemp = false;
453 //! Variables for simulated tempering
454 std::unique_ptr<t_simtemp> simtempvals;
455 //! Whether expanded ensembles are used
456 bool bExpanded = false;
457 //! Expanded ensemble parameters
458 std::unique_ptr<t_expanded> expandedvals;
459 //! Type of distance restraining
460 DistanceRestraintRefinement eDisre = DistanceRestraintRefinement::Default;
461 //! Force constant for time averaged distance restraints
463 //! Type of weighting of pairs in one restraints
464 DistanceRestraintWeighting eDisreWeighting = DistanceRestraintWeighting::Default;
465 //! Use combination of time averaged and instantaneous violations
466 bool bDisreMixed = false;
467 //! Frequency of writing pair distances to enx
469 //! Time constant for memory function in disres
471 //! Force constant for orientational restraints
473 //! Time constant for memory function in orires
475 //! Frequency of writing tr(SD) to energy output
477 //! The stepsize for updating
478 real em_stepsize = 0;
481 //! Number of iterations for convergence of steepest descent in relax_shells
483 //! Stepsize for directional minimization in relax_shells
484 real fc_stepsize = 0;
485 //! Number of steps after which a steepest descents step is done while doing cg
487 //! Number of corrections to the Hessian to keep
489 //! Type of constraint algorithm
490 ConstraintAlgorithm eConstrAlg = ConstraintAlgorithm::Default;
491 //! Order of the LINCS Projection Algorithm
493 //! Warn if any bond rotates more than this many degrees
494 real LincsWarnAngle = 0;
495 //! Number of iterations in the final LINCS step
497 //! Use successive overrelaxation for shake
498 bool bShakeSOR = false;
499 //! Friction coefficient for BD (amu/ps)
501 //! Random seed for SD and BD
503 //! The number of walls
505 //! The type of walls
506 WallType wall_type = WallType::Default;
507 //! The potentail is linear for r<=wall_r_linpot
508 real wall_r_linpot = 0;
509 //! The atom type for walls
510 int wall_atomtype[2] = { 0, 0 };
511 //! Number density for walls
512 real wall_density[2] = { 0, 0 };
513 //! Scaling factor for the box for Ewald
514 real wall_ewald_zfac = 0;
516 /* COM pulling data */
517 //! Do we do COM pulling?
519 //! The data for center of mass pulling
520 std::unique_ptr<pull_params_t> pull;
523 //! Whether to use AWH biasing for PMF calculations
525 //! AWH biasing parameters
526 std::unique_ptr<gmx::AwhParams> awhParams;
528 /* Enforced rotation data */
529 //! Whether to calculate enforced rotation potential(s)
531 //! The data for enforced rotation potentials
532 t_rot* rot = nullptr;
534 //! Whether to do ion/water position exchanges (CompEL)
535 SwapType eSwapCoords = SwapType::Default;
536 //! Swap data structure.
537 t_swapcoords* swap = nullptr;
539 //! Whether the tpr makes an interactive MD session possible.
541 //! Interactive molecular dynamics
542 t_IMD* imd = nullptr;
544 //! Acceleration for viscosity calculation
546 //! Triclinic deformation velocities (nm/ps)
547 tensor deform = { { 0 } };
548 /*! \brief User determined parameters */
561 //! QM/MM calculation
564 /* Fields for removed features go here (better caching) */
565 //! Whether AdResS is enabled - always false if a valid .tpr was read
566 bool bAdress = false;
567 //! Whether twin-range scheme is active - always false if a valid .tpr was read
568 bool useTwinRange = false;
569 //! Whether we have constant acceleration - removed in GROMACS 2022
570 bool useConstantAcceleration = false;
572 //! KVT object that contains input parameters converted to the new style.
573 gmx::KeyValueTreeObject* params = nullptr;
575 //! KVT for storing simulation parameters that are not part of the mdp file.
576 std::unique_ptr<gmx::KeyValueTreeObject> internalParameters;
579 int ir_optimal_nstcalcenergy(const t_inputrec* ir);
581 int tcouple_min_integration_steps(TemperatureCoupling etc);
583 int ir_optimal_nsttcouple(const t_inputrec* ir);
585 int pcouple_min_integration_steps(PressureCoupling epc);
587 int ir_optimal_nstpcouple(const t_inputrec* ir);
589 /* Returns if the Coulomb force or potential is switched to zero */
590 bool ir_coulomb_switched(const t_inputrec* ir);
592 /* Returns if the Coulomb interactions are zero beyond the rcoulomb.
593 * Note: always returns TRUE for the Verlet cut-off scheme.
595 bool ir_coulomb_is_zero_at_cutoff(const t_inputrec* ir);
597 /* As ir_coulomb_is_zero_at_cutoff, but also returns TRUE for user tabulated
598 * interactions, since these might be zero beyond rcoulomb.
600 bool ir_coulomb_might_be_zero_at_cutoff(const t_inputrec* ir);
602 /* Returns if the Van der Waals force or potential is switched to zero */
603 bool ir_vdw_switched(const t_inputrec* ir);
605 /* Returns if the Van der Waals interactions are zero beyond the rvdw.
606 * Note: always returns TRUE for the Verlet cut-off scheme.
608 bool ir_vdw_is_zero_at_cutoff(const t_inputrec* ir);
610 /* As ir_vdw_is_zero_at_cutoff, but also returns TRUE for user tabulated
611 * interactions, since these might be zero beyond rvdw.
613 bool ir_vdw_might_be_zero_at_cutoff(const t_inputrec* ir);
615 /*! \brief Free memory from input record.
617 * All arrays and pointers will be freed.
619 * \param[in] ir The data structure
621 void done_inputrec(t_inputrec* ir);
623 void pr_inputrec(FILE* fp, int indent, const char* title, const t_inputrec* ir, bool bMDPformat);
625 void cmp_inputrec(FILE* fp, const t_inputrec* ir1, const t_inputrec* ir2, real ftol, real abstol);
627 void comp_pull_AB(FILE* fp, const pull_params_t& pull, real ftol, real abstol);
630 bool inputrecDeform(const t_inputrec* ir);
632 bool inputrecDynamicBox(const t_inputrec* ir);
634 bool inputrecPreserveShape(const t_inputrec* ir);
636 bool inputrecNeedMutot(const t_inputrec* ir);
638 bool inputrecTwinRange(const t_inputrec* ir);
640 bool inputrecExclForces(const t_inputrec* ir);
642 bool inputrecNptTrotter(const t_inputrec* ir);
644 bool inputrecNvtTrotter(const t_inputrec* ir);
646 bool inputrecNphTrotter(const t_inputrec* ir);
648 /*! \brief Return true if the simulation is 2D periodic with two walls. */
649 bool inputrecPbcXY2Walls(const t_inputrec* ir);
651 //! \brief Return true if the simulation has frozen atoms (non-trivial freeze groups).
652 bool inputrecFrozenAtoms(const t_inputrec* ir);
654 /*! \brief Returns true for MD integator with T and/or P-coupling that supports
655 * calculating a conserved energy quantity.
657 * Note that dynamical integrators without T and P coupling (ie NVE)
658 * return false, i.e. the return value refers to whether there
659 * is a conserved quantity different than the total energy.
661 bool integratorHasConservedEnergyQuantity(const t_inputrec* ir);
663 /*! \brief Returns true when temperature is coupled or constant. */
664 bool integratorHasReferenceTemperature(const t_inputrec* ir);
666 /*! \brief Return the number of bounded dimensions
668 * \param[in] ir The input record with MD parameters
669 * \return the number of dimensions in which
670 * the coordinates of the particles are bounded, starting at X.
672 int inputrec2nboundeddim(const t_inputrec* ir);
674 /*! \brief Returns the number of degrees of freedom in center of mass motion
676 * \param[in] ir The inputrec structure
677 * \return the number of degrees of freedom of the center of mass
679 int ndof_com(const t_inputrec* ir);
681 /*! \brief Returns the maximum reference temperature over all coupled groups
683 * Returns 0 for energy minimization and normal mode computation.
684 * Returns -1 for MD without temperature coupling.
686 * \param[in] ir The inputrec structure
688 real maxReferenceTemperature(const t_inputrec& ir);
690 /*! \brief Returns whether there is an Ewald surface contribution
692 bool haveEwaldSurfaceContribution(const t_inputrec& ir);
694 /*! \brief Check if calculation of the specific FEP type was requested.
696 * \param[in] ir Input record.
697 * \param[in] fepType Free-energy perturbation type to check for.
699 * \returns If the \p fepType is perturbed in this run.
701 bool haveFreeEnergyType(const t_inputrec& ir, int fepType);
703 #endif /* GMX_MDTYPES_INPUTREC_H */