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42 #include "gromacs/legacyheaders/types/enums.h"
43 #include "gromacs/legacyheaders/types/simple.h"
44 #include "gromacs/swap/enums.h"
52 int n; /* Number of terms */
53 real *a; /* Coeffients (V / nm ) */
54 real *phi; /* Phase angles */
58 real E0; /* Field strength (V/nm) */
59 real omega; /* Frequency (1/ps) */
60 real t0; /* Centre of the Gaussian pulse (ps) */
61 real sigma; /* Width of the Gaussian pulse (FWHM) (ps) */
64 #define EGP_EXCL (1<<0)
65 #define EGP_TABLE (1<<1)
68 int ngtc; /* # T-Coupl groups */
69 int nhchainlength; /* # of nose-hoover chains per group */
70 int ngacc; /* # Accelerate groups */
71 int ngfrz; /* # Freeze groups */
72 int ngener; /* # Ener groups */
73 real *nrdf; /* Nr of degrees of freedom in a group */
74 real *ref_t; /* Coupling temperature per group */
75 int *annealing; /* No/simple/periodic SA for each group */
76 int *anneal_npoints; /* Number of annealing time points per grp */
77 real **anneal_time; /* For ea. group: Time points */
78 real **anneal_temp; /* For ea. grp: Temperature at these times */
79 /* Final temp after all intervals is ref_t */
80 real *tau_t; /* Tau coupling time */
81 rvec *acc; /* Acceleration per group */
82 ivec *nFreeze; /* Freeze the group in each direction ? */
83 int *egp_flags; /* Exclusions/tables of energy group pairs */
86 int ngQM; /* nr of QM groups */
87 int *QMmethod; /* Level of theory in the QM calculation */
88 int *QMbasis; /* Basisset in the QM calculation */
89 int *QMcharge; /* Total charge in the QM region */
90 int *QMmult; /* Spin multiplicicty in the QM region */
91 gmx_bool *bSH; /* surface hopping (diabatic hop only) */
92 int *CASorbitals; /* number of orbiatls in the active space */
93 int *CASelectrons; /* number of electrons in the active space */
94 real *SAon; /* at which gap (A.U.) the SA is switched on */
96 int *SAsteps; /* in how many steps SA goes from 1-1 to 0.5-0.5*/
102 int nat; /* Number of atoms in the pull group */
103 atom_id *ind; /* The global atoms numbers */
104 int nweight; /* The number of weights (0 or nat) */
105 real *weight; /* Weights (use all 1 when weight==NULL) */
106 atom_id pbcatom; /* The reference atom for pbc (global number) */
110 int group[4]; /* The pull groups, index in group in t_pull */
111 int eType; /* The pull type: umbrella, constraint, ... */
112 int eGeom; /* The pull geometry */
113 ivec dim; /* Used to select components for constraint */
114 rvec origin; /* The origin for the absolute reference */
115 rvec vec; /* The pull vector, direction or position */
116 gmx_bool bStart; /* Set init based on the initial structure */
117 real init; /* Initial reference displacement */
118 real rate; /* Rate of motion (nm/ps) */
119 real k; /* force constant */
120 real kB; /* force constant for state B */
124 int eSimTempScale; /* simulated temperature scaling; linear or exponential */
125 real simtemp_low; /* the low temperature for simulated tempering */
126 real simtemp_high; /* the high temperature for simulated tempering */
127 real *temperatures; /* the range of temperatures used for simulated tempering */
131 int nstdhdl; /* The frequency for calculating dhdl */
132 double init_lambda; /* fractional value of lambda (usually will use
133 init_fep_state, this will only be for slow growth,
134 and for legacy free energy code. Only has a
135 valid value if positive) */
136 int init_fep_state; /* the initial number of the state */
137 double delta_lambda; /* change of lambda per time step (fraction of (0.1) */
138 int edHdLPrintEnergy; /* print no, total or potential energies in dhdl */
139 int n_lambda; /* The number of foreign lambda points */
140 double **all_lambda; /* The array of all lambda values */
141 int lambda_neighbors; /* The number of neighboring lambda states to
142 calculate the energy for in up and down directions
144 int lambda_start_n; /* The first lambda to calculate energies for */
145 int lambda_stop_n; /* The last lambda +1 to calculate energies for */
146 real sc_alpha; /* free energy soft-core parameter */
147 int sc_power; /* lambda power for soft-core interactions */
148 real sc_r_power; /* r power for soft-core interactions */
149 real sc_sigma; /* free energy soft-core sigma when c6 or c12=0 */
150 real sc_sigma_min; /* free energy soft-core sigma for ????? */
151 gmx_bool bScCoul; /* use softcore for the coulomb portion as well (default FALSE) */
152 gmx_bool separate_dvdl[efptNR]; /* whether to print the dvdl term associated with
153 this term; if it is not specified as separate,
154 it is lumped with the FEP term */
155 int separate_dhdl_file; /* whether to write a separate dhdl.xvg file
156 note: NOT a gmx_bool, but an enum */
157 int dhdl_derivatives; /* whether to calculate+write dhdl derivatives
158 note: NOT a gmx_bool, but an enum */
159 int dh_hist_size; /* The maximum table size for the dH histogram */
160 double dh_hist_spacing; /* The spacing for the dH histogram */
164 int nstexpanded; /* The frequency of expanded ensemble state changes */
165 int elamstats; /* which type of move updating do we use for lambda monte carlo (or no for none) */
166 int elmcmove; /* what move set will be we using for state space moves */
167 int elmceq; /* the method we use to decide of we have equilibrated the weights */
168 int equil_n_at_lam; /* the minumum number of samples at each lambda for deciding whether we have reached a minimum */
169 real equil_wl_delta; /* WL delta at which we stop equilibrating weights */
170 real equil_ratio; /* use the ratio of weights (ratio of minimum to maximum) to decide when to stop equilibrating */
171 int equil_steps; /* after equil_steps steps we stop equilibrating the weights */
172 int equil_samples; /* after equil_samples total samples (steps/nstfep), we stop equilibrating the weights */
173 int lmc_seed; /* random number seed for lambda mc switches */
174 gmx_bool minvar; /* whether to use minumum variance weighting */
175 int minvarmin; /* the number of samples needed before kicking into minvar routine */
176 real minvar_const; /* the offset for the variance in MinVar */
177 int c_range; /* range of cvalues used for BAR */
178 gmx_bool bSymmetrizedTMatrix; /* whether to print symmetrized matrices */
179 int nstTij; /* How frequently to print the transition matrices */
180 int lmc_repeats; /* number of repetitions in the MC lambda jumps */ /*MRS -- VERIFY THIS */
181 int lmc_forced_nstart; /* minimum number of samples for each state before free sampling */ /* MRS -- VERIFY THIS! */
182 int gibbsdeltalam; /* distance in lambda space for the gibbs interval */
183 real wl_scale; /* scaling factor for wang-landau */
184 real wl_ratio; /* ratio between largest and smallest number for freezing the weights */
185 real init_wl_delta; /* starting delta for wang-landau */
186 gmx_bool bWLoneovert; /* use one over t convergece for wang-landau when the delta get sufficiently small */
187 gmx_bool bInit_weights; /* did we initialize the weights? TODO: REMOVE FOR 5.0, no longer needed with new logic */
188 real mc_temp; /* To override the main temperature, or define it if it's not defined */
189 real *init_lambda_weights; /* user-specified initial weights to start with */
193 int ngroup; /* number of pull groups */
194 int ncoord; /* number of pull coordinates */
195 real cylinder_r; /* radius of cylinder for dynamic COM */
196 real constr_tol; /* absolute tolerance for constraints in (nm) */
197 gmx_bool bPrintCOM1; /* Print coordinates of COM 1 for each coord */
198 gmx_bool bPrintCOM2; /* Print coordinates of COM 2 for each coord */
199 gmx_bool bPrintRefValue; /* Print the reference value for each coord */
200 gmx_bool bPrintComp; /* Print cartesian components for each coord with geometry=distance */
201 int nstxout; /* Output frequency for pull x */
202 int nstfout; /* Output frequency for pull f */
204 t_pull_group *group; /* groups to pull/restrain/etc/ */
205 t_pull_coord *coord; /* the pull coordinates */
208 /* Abstract type for COM pull caclulations only defined in the pull module */
212 /* Abstract types for enforced rotation only defined in pull_rotation.c */
213 typedef struct gmx_enfrot *gmx_enfrot_t;
214 typedef struct gmx_enfrotgrp *gmx_enfrotgrp_t;
217 int eType; /* Rotation type for this group */
218 int bMassW; /* Use mass-weighed positions? */
219 int nat; /* Number of atoms in the group */
220 atom_id *ind; /* The global atoms numbers */
221 rvec *x_ref; /* The reference positions */
222 rvec vec; /* The normalized rotation vector */
223 real rate; /* Rate of rotation (degree/ps) */
224 real k; /* Force constant (kJ/(mol nm^2) */
225 rvec pivot; /* Pivot point of rotation axis (nm) */
226 int eFittype; /* Type of fit to determine actual group angle */
227 int PotAngle_nstep; /* Number of angles around the reference angle
228 for which the rotation potential is also
229 evaluated (for fit type 'potential' only) */
230 real PotAngle_step; /* Distance between two angles in degrees (for
231 fit type 'potential' only) */
232 real slab_dist; /* Slab distance (nm) */
233 real min_gaussian; /* Minimum value the gaussian must have so that
234 the force is actually evaluated */
235 real eps; /* Additive constant for radial motion2 and
236 flexible2 potentials (nm^2) */
237 gmx_enfrotgrp_t enfrotgrp; /* Stores non-inputrec rotation data per group */
241 int ngrp; /* Number of rotation groups */
242 int nstrout; /* Output frequency for main rotation outfile */
243 int nstsout; /* Output frequency for per-slab data */
244 t_rotgrp *grp; /* Groups to rotate */
245 gmx_enfrot_t enfrot; /* Stores non-inputrec enforced rotation data */
248 /* Abstract type for IMD only defined in IMD.c */
249 typedef struct gmx_IMD *t_gmx_IMD;
252 int nat; /* Number of interactive atoms */
253 atom_id *ind; /* The global indices of the interactive atoms */
254 t_gmx_IMD setup; /* Stores non-inputrec IMD data */
257 /* Abstract types for position swapping only defined in swapcoords.c */
258 typedef struct t_swap *gmx_swapcoords_t;
261 int nstswap; /* Every how many steps a swap is attempted? */
262 int nat; /* Number of atoms in the ion group */
263 int nat_split[2]; /* Number of atoms in the split group */
264 int nat_sol; /* Number of atoms in the solvent group */
265 atom_id *ind; /* The global ion group atoms numbers */
266 atom_id *ind_split[2]; /* Split groups for compartment partitioning */
267 atom_id *ind_sol; /* The global solvent group atom numbers */
268 gmx_bool massw_split[2]; /* Use mass-weighted positions in split group? */
269 real cyl0r, cyl1r; /* Split cylinders defined by radius, upper and */
270 real cyl0u, cyl1u; /* ... lower extension. The split cylinders de- */
271 real cyl0l, cyl1l; /* ... fine the channels and are each anchored */
272 /* ... in the center of the split group */
273 int nanions[eCompNR]; /* Requested number of anions and */
274 int nAverage; /* Coupling constant (nr of swap attempt steps) */
275 real threshold; /* Ion counts may deviate from the requested
276 values by +-threshold before a swap is done */
277 int ncations[eCompNR]; /* ... cations for both compartments */
278 gmx_swapcoords_t si_priv; /* swap private data accessible in
284 int type; /* type of AdResS simulation */
285 gmx_bool bnew_wf; /* enable new AdResS weighting function */
286 gmx_bool bchempot_dx; /*true:interaction table format input is F=-dmu/dx false: dmu_dwp */
287 gmx_bool btf_full_box; /* true: appy therm force everywhere in the box according to table false: only in hybrid region */
288 real const_wf; /* value of weighting function for eAdressConst */
289 real ex_width; /* center of the explicit zone */
290 real hy_width; /* width of the hybrid zone */
291 int icor; /* type of interface correction */
292 int site; /* AdResS CG site location */
293 rvec refs; /* Coordinates for AdResS reference */
294 real ex_forcecap; /* in the hybrid zone, cap forces large then this to adress_ex_forcecap */
295 gmx_bool do_hybridpairs; /* If true pair interaction forces are also scaled in an adress way*/
297 int * tf_table_index; /* contains mapping of energy group index -> i-th adress tf table*/
304 int eI; /* Integration method */
305 gmx_int64_t nsteps; /* number of steps to be taken */
306 int simulation_part; /* Used in checkpointing to separate chunks */
307 gmx_int64_t init_step; /* start at a stepcount >0 (used w. convert-tpr) */
308 int nstcalcenergy; /* frequency of energy calc. and T/P coupl. upd. */
309 int cutoff_scheme; /* group or verlet cutoffs */
310 int ns_type; /* which ns method should we use? */
311 int nstlist; /* number of steps before pairlist is generated */
312 int ndelta; /* number of cells per rlong */
313 int nstcomm; /* number of steps after which center of mass */
314 /* motion is removed */
315 int comm_mode; /* Center of mass motion removal algorithm */
316 int nstlog; /* number of steps after which print to logfile */
317 int nstxout; /* number of steps after which X is output */
318 int nstvout; /* id. for V */
319 int nstfout; /* id. for F */
320 int nstenergy; /* number of steps after which energies printed */
321 int nstxout_compressed; /* id. for compressed trj (.xtc,.tng) */
322 double init_t; /* initial time (ps) */
323 double delta_t; /* time step (ps) */
324 real x_compression_precision; /* precision of x in compressed trajectory file */
325 real fourier_spacing; /* requested fourier_spacing, when nk? not set */
326 int nkx, nky, nkz; /* number of k vectors in each spatial dimension*/
327 /* for fourier methods for long range electrost.*/
328 int pme_order; /* interpolation order for PME */
329 real ewald_rtol; /* Real space tolerance for Ewald, determines */
330 /* the real/reciprocal space relative weight */
331 real ewald_rtol_lj; /* Real space tolerance for LJ-Ewald */
332 int ewald_geometry; /* normal/3d ewald, or pseudo-2d LR corrections */
333 real epsilon_surface; /* Epsilon for PME dipole correction */
334 int ljpme_combination_rule; /* Type of combination rule in LJ-PME */
335 int ePBC; /* Type of periodic boundary conditions */
336 int bPeriodicMols; /* Periodic molecules */
337 gmx_bool bContinuation; /* Continuation run: starting state is correct */
338 int etc; /* temperature coupling */
339 int nsttcouple; /* interval in steps for temperature coupling */
340 gmx_bool bPrintNHChains; /* whether to print nose-hoover chains */
341 int epc; /* pressure coupling */
342 int epct; /* pressure coupling type */
343 int nstpcouple; /* interval in steps for pressure coupling */
344 real tau_p; /* pressure coupling time (ps) */
345 tensor ref_p; /* reference pressure (kJ/(mol nm^3)) */
346 tensor compress; /* compressability ((mol nm^3)/kJ) */
347 int refcoord_scaling; /* How to scale absolute reference coordinates */
348 rvec posres_com; /* The COM of the posres atoms */
349 rvec posres_comB; /* The B-state COM of the posres atoms */
350 int andersen_seed; /* Random seed for Andersen thermostat (obsolete) */
351 real verletbuf_tol; /* Per atom pair energy drift tolerance (kJ/mol/ps/atom) for list buffer */
352 real rlist; /* short range pairlist cut-off (nm) */
353 real rlistlong; /* long range pairlist cut-off (nm) */
354 int nstcalclr; /* Frequency of evaluating direct space long-range interactions */
355 real rtpi; /* Radius for test particle insertion */
356 int coulombtype; /* Type of electrostatics treatment */
357 int coulomb_modifier; /* Modify the Coulomb interaction */
358 real rcoulomb_switch; /* Coulomb switch range start (nm) */
359 real rcoulomb; /* Coulomb cutoff (nm) */
360 real epsilon_r; /* relative dielectric constant */
361 real epsilon_rf; /* relative dielectric constant of the RF */
362 int implicit_solvent; /* No (=explicit water), or GBSA solvent models */
363 int gb_algorithm; /* Algorithm to use for calculation Born radii */
364 int nstgbradii; /* Frequency of updating Generalized Born radii */
365 real rgbradii; /* Cutoff for GB radii calculation */
366 real gb_saltconc; /* Salt concentration (M) for GBSA models */
367 real gb_epsilon_solvent; /* dielectric coeff. of implicit solvent */
368 real gb_obc_alpha; /* 1st scaling factor for Bashford-Case GB */
369 real gb_obc_beta; /* 2nd scaling factor for Bashford-Case GB */
370 real gb_obc_gamma; /* 3rd scaling factor for Bashford-Case GB */
371 real gb_dielectric_offset; /* Dielectric offset for Still/HCT/OBC */
372 int sa_algorithm; /* Algorithm for SA part of GBSA */
373 real sa_surface_tension; /* Energy factor for SA part of GBSA */
374 int vdwtype; /* Type of Van der Waals treatment */
375 int vdw_modifier; /* Modify the VdW interaction */
376 real rvdw_switch; /* Van der Waals switch range start (nm) */
377 real rvdw; /* Van der Waals cutoff (nm) */
378 int eDispCorr; /* Perform Long range dispersion corrections */
379 real tabext; /* Extension of the table beyond the cut-off, *
380 * as well as the table length for 1-4 interac. */
381 real shake_tol; /* tolerance for shake */
382 int efep; /* free energy calculations */
383 t_lambda *fepvals; /* Data for the FEP state */
384 gmx_bool bSimTemp; /* Whether to do simulated tempering */
385 t_simtemp *simtempvals; /* Variables for simulated tempering */
386 gmx_bool bExpanded; /* Whether expanded ensembles are used */
387 t_expanded *expandedvals; /* Expanded ensemble parameters */
388 int eDisre; /* Type of distance restraining */
389 real dr_fc; /* force constant for ta_disre */
390 int eDisreWeighting; /* type of weighting of pairs in one restraints */
391 gmx_bool bDisreMixed; /* Use comb of time averaged and instan. viol's */
392 int nstdisreout; /* frequency of writing pair distances to enx */
393 real dr_tau; /* time constant for memory function in disres */
394 real orires_fc; /* force constant for orientational restraints */
395 real orires_tau; /* time constant for memory function in orires */
396 int nstorireout; /* frequency of writing tr(SD) to enx */
397 real em_stepsize; /* The stepsize for updating */
398 real em_tol; /* The tolerance */
399 int niter; /* Number of iterations for convergence of */
400 /* steepest descent in relax_shells */
401 real fc_stepsize; /* Stepsize for directional minimization */
402 /* in relax_shells */
403 int nstcgsteep; /* number of steps after which a steepest */
404 /* descents step is done while doing cg */
405 int nbfgscorr; /* Number of corrections to the hessian to keep */
406 int eConstrAlg; /* Type of constraint algorithm */
407 int nProjOrder; /* Order of the LINCS Projection Algorithm */
408 real LincsWarnAngle; /* If bond rotates more than %g degrees, warn */
409 int nLincsIter; /* Number of iterations in the final Lincs step */
410 gmx_bool bShakeSOR; /* Use successive overrelaxation for shake */
411 real bd_fric; /* Friction coefficient for BD (amu/ps) */
412 gmx_int64_t ld_seed; /* Random seed for SD and BD */
413 int nwall; /* The number of walls */
414 int wall_type; /* The type of walls */
415 real wall_r_linpot; /* The potentail is linear for r<=wall_r_linpot */
416 int wall_atomtype[2]; /* The atom type for walls */
417 real wall_density[2]; /* Number density for walls */
418 real wall_ewald_zfac; /* Scaling factor for the box for Ewald */
419 gmx_bool bPull; /* Do we do COM pulling? */
420 pull_params_t *pull; /* The data for center of mass pulling */
421 struct pull_t *pull_work; /* The COM pull force calculation data structure; TODO this pointer should live somewhere else */
423 gmx_bool bRot; /* Calculate enforced rotation potential(s)? */
424 t_rot *rot; /* The data for enforced rotation potentials */
425 int eSwapCoords; /* Do ion/water position exchanges (CompEL)? */
427 gmx_bool bIMD; /* Allow interactive MD sessions for this .tpr? */
428 t_IMD *imd; /* Interactive molecular dynamics */
429 real cos_accel; /* Acceleration for viscosity calculation */
430 tensor deform; /* Triclinic deformation velocities (nm/ps) */
431 int userint1; /* User determined parameters */
439 t_grpopts opts; /* Group options */
440 t_cosines ex[DIM]; /* Electric field stuff (spatial part) */
441 t_cosines et[DIM]; /* Electric field stuff (time part) */
442 gmx_bool bQMMM; /* QM/MM calculation */
443 int QMconstraints; /* constraints on QM bonds */
444 int QMMMscheme; /* Scheme: ONIOM or normal */
445 real scalefactor; /* factor for scaling the MM charges in QM calc.*/
446 /* parameter needed for AdResS simulation */
447 gmx_bool bAdress; /* Is AdResS enabled ? */
448 t_adress *adress; /* The data for adress simulations */
451 #define DEFORM(ir) ((ir).deform[XX][XX] != 0 || (ir).deform[YY][YY] != 0 || (ir).deform[ZZ][ZZ] != 0 || (ir).deform[YY][XX] != 0 || (ir).deform[ZZ][XX] != 0 || (ir).deform[ZZ][YY] != 0)
453 #define DYNAMIC_BOX(ir) ((ir).epc != epcNO || (ir).eI == eiTPI || DEFORM(ir))
455 #define PRESERVE_SHAPE(ir) ((ir).epc != epcNO && (ir).deform[XX][XX] == 0 && ((ir).epct == epctISOTROPIC || (ir).epct == epctSEMIISOTROPIC))
457 #define NEED_MUTOT(ir) (((ir).coulombtype == eelEWALD || EEL_PME((ir).coulombtype)) && ((ir).ewald_geometry == eewg3DC || (ir).epsilon_surface != 0))
459 #define IR_TWINRANGE(ir) ((ir).rlist > 0 && ((ir).rlistlong == 0 || (ir).rlistlong > (ir).rlist))
461 #define IR_ELEC_FIELD(ir) ((ir).ex[XX].n > 0 || (ir).ex[YY].n > 0 || (ir).ex[ZZ].n > 0)
463 #define IR_EXCL_FORCES(ir) (EEL_FULL((ir).coulombtype) || (EEL_RF((ir).coulombtype) && (ir).coulombtype != eelRF_NEC) || (ir).implicit_solvent != eisNO)
464 /* use pointer definitions of ir here, since that's what's usually used in the code */
465 #define IR_NPT_TROTTER(ir) ((((ir)->eI == eiVV) || ((ir)->eI == eiVVAK)) && (((ir)->epc == epcMTTK) && ((ir)->etc == etcNOSEHOOVER)))
467 #define IR_NVT_TROTTER(ir) ((((ir)->eI == eiVV) || ((ir)->eI == eiVVAK)) && ((!((ir)->epc == epcMTTK)) && ((ir)->etc == etcNOSEHOOVER)))
469 #define IR_NPH_TROTTER(ir) ((((ir)->eI == eiVV) || ((ir)->eI == eiVVAK)) && (((ir)->epc == epcMTTK) && (!(((ir)->etc == etcNOSEHOOVER)))))