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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/basedefinitions.h"
49 #include "gromacs/utility/real.h"
51 #define EGP_EXCL (1 << 0)
52 #define EGP_TABLE (1 << 1)
62 class KeyValueTreeObject;
70 //! Number of T-Coupl groups
72 //! Number of of Nose-Hoover chains per group
74 //! Number of Accelerate groups
76 //! Number of Freeze groups
78 //! Number of Energy groups
80 //! Number of degrees of freedom in a group
82 //! Coupling temperature per group
84 //! No/simple/periodic simulated annealing for each group
86 //! Number of annealing time points per group
88 //! For each group: Time points
90 //! For each group: Temperature at these times. Final temp after all intervals is ref_t
94 //! Acceleration per group
96 //! Whether the group will be frozen in each direction
98 //! Exclusions/tables of energy group pairs
102 //! Number of QM groups
108 //! Simulated temperature scaling; linear or exponential
110 //! The low temperature for simulated tempering
112 //! The high temperature for simulated tempering
114 //! The range of temperatures used for simulated tempering
120 //! The frequency for calculating dhdl
122 //! 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)
124 //! The initial number of the state
126 //! Change of lambda per time step (fraction of (0.1)
128 //! Print no, total or potential energies in dhdl
129 int edHdLPrintEnergy;
130 //! The number of foreign lambda points
132 //! The array of all lambda values
134 //! The number of neighboring lambda states to calculate the energy for in up and down directions (-1 for all)
135 int lambda_neighbors;
136 //! The first lambda to calculate energies for
138 //! The last lambda +1 to calculate energies for
140 //! Free energy soft-core parameter
142 //! Lambda power for soft-core interactions
144 //! R power for soft-core interactions
146 //! Free energy soft-core sigma when c6 or c12=0
148 //! Free energy soft-core sigma for ?????
150 //! Use softcore for the coulomb portion as well (default FALSE)
152 //! Whether to print the dvdl term associated with this term; if it is not specified as separate, it is lumped with the FEP term
153 gmx_bool separate_dvdl[efptNR];
154 //! Whether to write a separate dhdl.xvg file note: NOT a gmx_bool, but an enum
155 int separate_dhdl_file;
156 //! Whether to calculate+write dhdl derivatives note: NOT a gmx_bool, but an enum
157 int dhdl_derivatives;
158 //! The maximum table size for the dH histogram
160 //! The spacing for the dH histogram
161 double dh_hist_spacing;
166 //! The frequency of expanded ensemble state changes
168 //! Which type of move updating do we use for lambda monte carlo (or no for none)
170 //! What move set will be we using for state space moves
172 //! The method we use to decide of we have equilibrated the weights
174 //! The minumum number of samples at each lambda for deciding whether we have reached a minimum
176 //! Wang-Landau delta at which we stop equilibrating weights
178 //! Use the ratio of weights (ratio of minimum to maximum) to decide when to stop equilibrating
180 //! After equil_steps steps we stop equilibrating the weights
182 //! After equil_samples total samples (steps/nstfep), we stop equilibrating the weights
184 //! Random number seed for lambda mc switches
186 //! Whether to use minumum variance weighting
188 //! The number of samples needed before kicking into minvar routine
190 //! The offset for the variance in MinVar
192 //! Range of cvalues used for BAR
194 //! Whether to print symmetrized matrices
195 gmx_bool bSymmetrizedTMatrix;
196 //! How frequently to print the transition matrices
198 //! Number of repetitions in the MC lambda jumps MRS -- VERIFY THIS
200 //! Minimum number of samples for each state before free sampling MRS -- VERIFY THIS!
201 int lmc_forced_nstart;
202 //! Distance in lambda space for the gibbs interval
204 //! Scaling factor for Wang-Landau
206 //! Ratio between largest and smallest number for freezing the weights
208 //! Starting delta for Wang-Landau
210 //! Use one over t convergence for Wang-Landau when the delta get sufficiently small
211 gmx_bool bWLoneovert;
212 //! Did we initialize the weights? TODO: REMOVE FOR 5.0, no longer needed with new logic
213 gmx_bool bInit_weights;
214 //! To override the main temperature, or define it if it's not defined
216 //! User-specified initial weights to start with
217 real* init_lambda_weights;
222 //! Rotation type for this group
224 //! Use mass-weighed positions?
226 //! Number of atoms in the group
228 //! The global atoms numbers
230 //! The reference positions
232 //! The normalized rotation vector
234 //! Rate of rotation (degree/ps)
236 //! Force constant (kJ/(mol nm^2)
238 //! Pivot point of rotation axis (nm)
240 //! Type of fit to determine actual group angle
242 //! Number of angles around the reference angle for which the rotation potential is also evaluated (for fit type 'potential' only)
244 //! Distance between two angles in degrees (for fit type 'potential' only)
246 //! Slab distance (nm)
248 //! Minimum value the gaussian must have so that the force is actually evaluated
250 //! Additive constant for radial motion2 and flexible2 potentials (nm^2)
256 //! Number of rotation groups
258 //! Output frequency for main rotation outfile
260 //! Output frequency for per-slab data
268 //! Number of interactive atoms
270 //! The global indices of the interactive atoms
276 //! Name of the swap group, e.g. NA, CL, SOL
278 //! Number of atoms in this group
280 //! The global ion group atoms numbers
282 //! Requested number of molecules of this type per compartment
283 int nmolReq[eCompNR];
288 //! Period between when a swap is attempted
290 //! Use mass-weighted positions in split group
291 gmx_bool massw_split[2];
292 /*! \brief Split cylinders defined by radius, upper and lower
293 * extension. The split cylinders define the channels and are
294 * each anchored in the center of the split group */
300 //! Coupling constant (number of swap attempt steps)
302 //! Ion counts may deviate from the requested values by +-threshold before a swap is done
304 //! Offset of the swap layer (='bulk') with respect to the compartment-defining layers
305 real bulkOffset[eCompNR];
306 //! Number of groups to be controlled
308 //! All swap groups, including split and solvent
312 struct t_inputrec // NOLINT (clang-analyzer-optin.performance.Padding)
315 explicit t_inputrec(const t_inputrec&) = delete;
316 t_inputrec& operator=(const t_inputrec&) = delete;
319 //! Integration method
321 //! Number of steps to be taken
323 //! Used in checkpointing to separate chunks
325 //! Start at a stepcount >0 (used w. convert-tpr)
327 //! Frequency of energy calc. and T/P coupl. upd.
329 //! Group or verlet cutoffs
331 //! Number of steps before pairlist is generated
333 //! Number of steps after which center of mass motion is removed
335 //! Center of mass motion removal algorithm
337 //! Number of steps after which print to logfile
339 //! Number of steps after which X is output
341 //! Number of steps after which V is output
343 //! Number of steps after which F is output
345 //! Number of steps after which energies printed
347 //! Number of steps after which compressed trj (.xtc,.tng) is output
348 int nstxout_compressed;
349 //! Initial time (ps)
353 //! Whether we use multiple time stepping
355 //! The multiple time stepping levels
356 std::vector<gmx::MtsLevel> mtsLevels;
357 //! Precision of x in compressed trajectory file
358 real x_compression_precision;
359 //! Requested fourier_spacing, when nk? not set
360 real fourier_spacing;
361 //! Number of k vectors in x dimension for fourier methods for long range electrost.
363 //! Number of k vectors in y dimension for fourier methods for long range electrost.
365 //! Number of k vectors in z dimension for fourier methods for long range electrost.
367 //! Interpolation order for PME
369 //! Real space tolerance for Ewald, determines the real/reciprocal space relative weight
371 //! Real space tolerance for LJ-Ewald
373 //! Normal/3D ewald, or pseudo-2D LR corrections
375 //! Epsilon for PME dipole correction
376 real epsilon_surface;
377 //! Type of combination rule in LJ-PME
378 int ljpme_combination_rule;
379 //! Type of periodic boundary conditions
381 //! Periodic molecules
383 //! Continuation run: starting state is correct (ie. constrained)
384 gmx_bool bContinuation;
385 //! Temperature coupling
387 //! Interval in steps for temperature coupling
389 //! Whether to print nose-hoover chains
390 gmx_bool bPrintNHChains;
391 //! Pressure coupling
393 //! Pressure coupling type
395 //! Interval in steps for pressure coupling
397 //! Pressure coupling time (ps)
399 //! Reference pressure (kJ/(mol nm^3))
401 //! Compressibility ((mol nm^3)/kJ)
403 //! How to scale absolute reference coordinates
404 int refcoord_scaling;
405 //! The COM of the posres atoms
407 //! The B-state COM of the posres atoms
409 //! Random seed for Andersen thermostat (obsolete)
411 //! Per atom pair energy drift tolerance (kJ/mol/ps/atom) for list buffer
413 //! Short range pairlist cut-off (nm)
415 //! Radius for test particle insertion
417 //! Type of electrostatics treatment
419 //! Modify the Coulomb interaction
420 int coulomb_modifier;
421 //! Coulomb switch range start (nm)
422 real rcoulomb_switch;
423 //! Coulomb cutoff (nm)
425 //! Relative dielectric constant
427 //! Relative dielectric constant of the RF
429 //! Always false (no longer supported)
430 bool implicit_solvent;
431 //! Type of Van der Waals treatment
433 //! Modify the Van der Waals interaction
435 //! Van der Waals switch range start (nm)
437 //! Van der Waals cutoff (nm)
439 //! Perform Long range dispersion corrections
441 //! Extension of the table beyond the cut-off, as well as the table length for 1-4 interac.
443 //! Tolerance for shake
445 //! Free energy calculations
447 //! Data for the FEP state
449 //! Whether to do simulated tempering
451 //! Variables for simulated tempering
452 t_simtemp* simtempvals;
453 //! Whether expanded ensembles are used
455 //! Expanded ensemble parameters
456 t_expanded* expandedvals;
457 //! Type of distance restraining
459 //! Force constant for time averaged distance restraints
461 //! Type of weighting of pairs in one restraints
463 //! Use combination of time averaged and instantaneous violations
464 gmx_bool bDisreMixed;
465 //! Frequency of writing pair distances to enx
467 //! Time constant for memory function in disres
469 //! Force constant for orientational restraints
471 //! Time constant for memory function in orires
473 //! Frequency of writing tr(SD) to energy output
475 //! The stepsize for updating
479 //! Number of iterations for convergence of steepest descent in relax_shells
481 //! Stepsize for directional minimization in relax_shells
483 //! Number of steps after which a steepest descents step is done while doing cg
485 //! Number of corrections to the Hessian to keep
487 //! Type of constraint algorithm
489 //! Order of the LINCS Projection Algorithm
491 //! Warn if any bond rotates more than this many degrees
493 //! Number of iterations in the final LINCS step
495 //! Use successive overrelaxation for shake
497 //! Friction coefficient for BD (amu/ps)
499 //! Random seed for SD and BD
501 //! The number of walls
503 //! The type of walls
505 //! The potentail is linear for r<=wall_r_linpot
507 //! The atom type for walls
508 int wall_atomtype[2];
509 //! Number density for walls
510 real wall_density[2];
511 //! Scaling factor for the box for Ewald
512 real wall_ewald_zfac;
514 /* COM pulling data */
515 //! Do we do COM pulling?
517 //! The data for center of mass pulling
521 //! Whether to use AWH biasing for PMF calculations
523 //! AWH biasing parameters
524 gmx::AwhParams* awhParams;
526 /* Enforced rotation data */
527 //! Whether to calculate enforced rotation potential(s)
529 //! The data for enforced rotation potentials
532 //! Whether to do ion/water position exchanges (CompEL)
534 //! Swap data structure.
537 //! Whether the tpr makes an interactive MD session possible.
539 //! Interactive molecular dynamics
542 //! Acceleration for viscosity calculation
544 //! Triclinic deformation velocities (nm/ps)
546 /*! \brief User determined parameters */
559 //! QM/MM calculation
562 /* Fields for removed features go here (better caching) */
563 //! Whether AdResS is enabled - always false if a valid .tpr was read
565 //! Whether twin-range scheme is active - always false if a valid .tpr was read
566 gmx_bool useTwinRange;
568 //! KVT object that contains input parameters converted to the new style.
569 gmx::KeyValueTreeObject* params;
571 //! KVT for storing simulation parameters that are not part of the mdp file.
572 std::unique_ptr<gmx::KeyValueTreeObject> internalParameters;
575 int ir_optimal_nstcalcenergy(const t_inputrec* ir);
577 int tcouple_min_integration_steps(int etc);
579 int ir_optimal_nsttcouple(const t_inputrec* ir);
581 int pcouple_min_integration_steps(int epc);
583 int ir_optimal_nstpcouple(const t_inputrec* ir);
585 /* Returns if the Coulomb force or potential is switched to zero */
586 gmx_bool ir_coulomb_switched(const t_inputrec* ir);
588 /* Returns if the Coulomb interactions are zero beyond the rcoulomb.
589 * Note: always returns TRUE for the Verlet cut-off scheme.
591 gmx_bool ir_coulomb_is_zero_at_cutoff(const t_inputrec* ir);
593 /* As ir_coulomb_is_zero_at_cutoff, but also returns TRUE for user tabulated
594 * interactions, since these might be zero beyond rcoulomb.
596 gmx_bool ir_coulomb_might_be_zero_at_cutoff(const t_inputrec* ir);
598 /* Returns if the Van der Waals force or potential is switched to zero */
599 gmx_bool ir_vdw_switched(const t_inputrec* ir);
601 /* Returns if the Van der Waals interactions are zero beyond the rvdw.
602 * Note: always returns TRUE for the Verlet cut-off scheme.
604 gmx_bool ir_vdw_is_zero_at_cutoff(const t_inputrec* ir);
606 /* As ir_vdw_is_zero_at_cutoff, but also returns TRUE for user tabulated
607 * interactions, since these might be zero beyond rvdw.
609 gmx_bool ir_vdw_might_be_zero_at_cutoff(const t_inputrec* ir);
611 /*! \brief Free memory from input record.
613 * All arrays and pointers will be freed.
615 * \param[in] ir The data structure
617 void done_inputrec(t_inputrec* ir);
619 void pr_inputrec(FILE* fp, int indent, const char* title, const t_inputrec* ir, gmx_bool bMDPformat);
621 void cmp_inputrec(FILE* fp, const t_inputrec* ir1, const t_inputrec* ir2, real ftol, real abstol);
623 void comp_pull_AB(FILE* fp, pull_params_t* pull, real ftol, real abstol);
626 gmx_bool inputrecDeform(const t_inputrec* ir);
628 gmx_bool inputrecDynamicBox(const t_inputrec* ir);
630 gmx_bool inputrecPreserveShape(const t_inputrec* ir);
632 gmx_bool inputrecNeedMutot(const t_inputrec* ir);
634 gmx_bool inputrecTwinRange(const t_inputrec* ir);
636 gmx_bool inputrecExclForces(const t_inputrec* ir);
638 gmx_bool inputrecNptTrotter(const t_inputrec* ir);
640 gmx_bool inputrecNvtTrotter(const t_inputrec* ir);
642 gmx_bool inputrecNphTrotter(const t_inputrec* ir);
644 /*! \brief Return true if the simulation is 2D periodic with two walls. */
645 bool inputrecPbcXY2Walls(const t_inputrec* ir);
647 /*! \brief Returns true for MD integator with T and/or P-coupling that supports
648 * calculating a conserved energy quantity.
650 * Note that dynamical integrators without T and P coupling (ie NVE)
651 * return false, i.e. the return value refers to whether there
652 * is a conserved quantity different than the total energy.
654 bool integratorHasConservedEnergyQuantity(const t_inputrec* ir);
656 /*! \brief Returns true when temperature is coupled or constant. */
657 bool integratorHasReferenceTemperature(const t_inputrec* ir);
659 /*! \brief Return the number of bounded dimensions
661 * \param[in] ir The input record with MD parameters
662 * \return the number of dimensions in which
663 * the coordinates of the particles are bounded, starting at X.
665 int inputrec2nboundeddim(const t_inputrec* ir);
667 /*! \brief Returns the number of degrees of freedom in center of mass motion
669 * \param[in] ir The inputrec structure
670 * \return the number of degrees of freedom of the center of mass
672 int ndof_com(const t_inputrec* ir);
674 /*! \brief Returns the maximum reference temperature over all coupled groups
676 * Returns 0 for energy minimization and normal mode computation.
677 * Returns -1 for MD without temperature coupling.
679 * \param[in] ir The inputrec structure
681 real maxReferenceTemperature(const t_inputrec& ir);
683 /*! \brief Returns whether there is an Ewald surface contribution
685 bool haveEwaldSurfaceContribution(const t_inputrec& ir);
687 /*! \brief Check if calculation of the specific FEP type was requested.
689 * \param[in] ir Input record.
690 * \param[in] fepType Free-energy perturbation type to check for.
692 * \returns If the \p fepType is perturbed in this run.
694 bool haveFreeEnergyType(const t_inputrec& ir, int fepType);
696 #endif /* GMX_MDTYPES_INPUTREC_H */