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10 * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
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33 * GRoups of Organic Molecules in ACtion for Science
40 #include "../sysstuff.h"
48 int n; /* Number of terms */
49 real *a; /* Coeffients (V / nm ) */
50 real *phi; /* Phase angles */
54 real E0; /* Field strength (V/nm) */
55 real omega; /* Frequency (1/ps) */
56 real t0; /* Centre of the Gaussian pulse (ps) */
57 real sigma; /* Width of the Gaussian pulse (FWHM) (ps) */
60 #define EGP_EXCL (1<<0)
61 #define EGP_TABLE (1<<1)
64 int ngtc; /* # T-Coupl groups */
65 int nhchainlength; /* # of nose-hoover chains per group */
66 int ngacc; /* # Accelerate groups */
67 int ngfrz; /* # Freeze groups */
68 int ngener; /* # Ener groups */
69 real *nrdf; /* Nr of degrees of freedom in a group */
70 real *ref_t; /* Coupling temperature per group */
71 int *annealing; /* No/simple/periodic SA for each group */
72 int *anneal_npoints; /* Number of annealing time points per grp */
73 real **anneal_time; /* For ea. group: Time points */
74 real **anneal_temp; /* For ea. grp: Temperature at these times */
75 /* Final temp after all intervals is ref_t */
76 real *tau_t; /* Tau coupling time */
77 rvec *acc; /* Acceleration per group */
78 ivec *nFreeze; /* Freeze the group in each direction ? */
79 int *egp_flags; /* Exclusions/tables of energy group pairs */
82 int ngQM; /* nr of QM groups */
83 int *QMmethod; /* Level of theory in the QM calculation */
84 int *QMbasis; /* Basisset in the QM calculation */
85 int *QMcharge; /* Total charge in the QM region */
86 int *QMmult; /* Spin multiplicicty in the QM region */
87 gmx_bool *bSH; /* surface hopping (diabatic hop only) */
88 int *CASorbitals; /* number of orbiatls in the active space */
89 int *CASelectrons;/* number of electrons in the active space */
90 real *SAon; /* at which gap (A.U.) the SA is switched on */
92 int *SAsteps; /* in how many steps SA goes from 1-1 to 0.5-0.5*/
97 enum { epgrppbcNONE, epgrppbcREFAT, epgrppbcCOS };
100 int nat; /* Number of atoms in the pull group */
101 atom_id *ind; /* The global atoms numbers */
102 int nat_loc; /* Number of local pull atoms */
103 int nalloc_loc; /* Allocation size for ind_loc and weight_loc */
104 atom_id *ind_loc; /* Local pull indices */
105 int nweight; /* The number of weights (0 or nat) */
106 real *weight; /* Weights (use all 1 when weight==NULL) */
107 real *weight_loc; /* Weights for the local indices */
108 int epgrppbc; /* The type of pbc for this pull group, see enum above */
109 atom_id pbcatom; /* The reference atom for pbc (global number) */
110 rvec vec; /* The pull vector, direction or position */
111 rvec init; /* Initial reference displacement */
112 real rate; /* Rate of motion (nm/ps) */
113 real k; /* force constant */
114 real kB; /* force constant for state B */
115 real wscale; /* scaling factor for the weights: sum w m/sum w w m */
116 real invtm; /* inverse total mass of the group: 1/wscale sum w m */
117 dvec x; /* center of mass before update */
118 dvec xp; /* center of mass after update before constraining */
119 dvec dr; /* The distance from the reference group */
120 double f_scal; /* Scalar force for directional pulling */
121 dvec f; /* force due to the pulling/constraining */
125 int eSimTempScale; /* simulated temperature scaling; linear or exponential */
126 real simtemp_low; /* the low temperature for simulated tempering */
127 real simtemp_high; /* the high temperature for simulated tempering */
128 real *temperatures; /* the range of temperatures used for simulated tempering */
132 int nstdhdl; /* The frequency for calculating dhdl */
133 double init_lambda; /* fractional value of lambda (usually will use init_fep_state, this will only be for slow growth, and for legacy free energy code) */
134 int init_fep_state; /* the initial number of the state */
135 double delta_lambda; /* change of lambda per time step (fraction of (0.1) */
136 gmx_bool bPrintEnergy; /* Whether to print the energy in the dhdl */
137 int n_lambda; /* The number of foreign lambda points */
138 double **all_lambda; /* The array of all lambda values */
139 real sc_alpha; /* free energy soft-core parameter */
140 int sc_power; /* lambda power for soft-core interactions */
141 real sc_r_power; /* r power for soft-core interactions */
142 real sc_sigma; /* free energy soft-core sigma when c6 or c12=0 */
143 real sc_sigma_min; /* free energy soft-core sigma for ????? */
144 gmx_bool bScCoul; /* use softcore for the coulomb portion as well (default FALSE) */
145 gmx_bool separate_dvdl[efptNR]; /* whether to print the dvdl term associated with
146 this term; if it is not specified as separate,
147 it is lumped with the FEP term */
148 int separate_dhdl_file; /* whether to write a separate dhdl.xvg file
149 note: NOT a gmx_bool, but an enum */
150 int dhdl_derivatives; /* whether to calculate+write dhdl derivatives
151 note: NOT a gmx_bool, but an enum */
152 int dh_hist_size; /* The maximum table size for the dH histogram */
153 double dh_hist_spacing; /* The spacing for the dH histogram */
157 int nstexpanded; /* The frequency of expanded ensemble state changes */
158 int elamstats; /* which type of move updating do we use for lambda monte carlo (or no for none) */
159 int elmcmove; /* what move set will be we using for state space moves */
160 int elmceq; /* the method we use to decide of we have equilibrated the weights */
161 int equil_n_at_lam; /* the minumum number of samples at each lambda for deciding whether we have reached a minimum */
162 real equil_wl_delta; /* WL delta at which we stop equilibrating weights */
163 real equil_ratio; /* use the ratio of weights (ratio of minimum to maximum) to decide when to stop equilibrating */
164 int equil_steps; /* after equil_steps steps we stop equilibrating the weights */
165 int equil_samples; /* after equil_samples total samples (steps/nstfep), we stop equilibrating the weights */
166 int lmc_seed; /* random number seed for lambda mc switches */
167 gmx_bool minvar; /* whether to use minumum variance weighting */
168 int minvarmin; /* the number of samples needed before kicking into minvar routine */
169 real minvar_const; /* the offset for the variance in MinVar */
170 int c_range; /* range of cvalues used for BAR */
171 gmx_bool bSymmetrizedTMatrix; /* whether to print symmetrized matrices */
172 int nstTij; /* How frequently to print the transition matrices */
173 int lmc_repeats; /* number of repetitions in the MC lambda jumps */ /*MRS -- VERIFY THIS */
174 int lmc_forced_nstart; /* minimum number of samples for each state before free sampling */ /* MRS -- VERIFY THIS! */
175 int gibbsdeltalam; /* distance in lambda space for the gibbs interval */
176 real wl_scale; /* scaling factor for wang-landau */
177 real wl_ratio; /* ratio between largest and smallest number for freezing the weights */
178 real init_wl_delta; /* starting delta for wang-landau */
179 gmx_bool bWLoneovert; /* use one over t convergece for wang-landau when the delta get sufficiently small */
180 gmx_bool bInit_weights; /* did we initialize the weights? */
181 real mc_temp; /* To override the main temperature, or define it if it's not defined */
182 real *init_lambda_weights; /* user-specified initial weights to start with */
186 int ngrp; /* number of groups */
187 int eGeom; /* pull geometry */
188 ivec dim; /* used to select components for constraint */
189 real cyl_r1; /* radius of cylinder for dynamic COM */
190 real cyl_r0; /* radius of cylinder including switch length */
191 real constr_tol; /* absolute tolerance for constraints in (nm) */
192 int nstxout; /* Output frequency for pull x */
193 int nstfout; /* Output frequency for pull f */
194 int ePBC; /* the boundary conditions */
195 int npbcdim; /* do pbc in dims 0 <= dim < npbcdim */
196 gmx_bool bRefAt; /* do we need reference atoms for a group COM ? */
197 int cosdim; /* dimension for cosine weighting, -1 if none */
198 gmx_bool bVirial; /* do we need to add the pull virial? */
199 t_pullgrp *grp; /* groups to pull/restrain/etc/ */
200 t_pullgrp *dyna; /* dynamic groups for use with local constraints */
201 rvec *rbuf; /* COM calculation buffer */
202 dvec *dbuf; /* COM calculation buffer */
203 double *dbuf_cyl; /* cylinder ref. groups COM calculation buffer */
205 FILE *out_x; /* output file for pull data */
206 FILE *out_f; /* output file for pull data */
210 /* Abstract types for enforced rotation only defined in pull_rotation.c */
211 typedef struct gmx_enfrot *gmx_enfrot_t;
212 typedef struct gmx_enfrotgrp *gmx_enfrotgrp_t;
215 int eType; /* Rotation type for this group */
216 int bMassW; /* Use mass-weighed positions? */
217 int nat; /* Number of atoms in the group */
218 atom_id *ind; /* The global atoms numbers */
219 rvec *x_ref; /* The reference positions */
220 rvec vec; /* The normalized rotation vector */
221 real rate; /* Rate of rotation (degree/ps) */
222 real k; /* Force constant (kJ/(mol nm^2) */
223 rvec pivot; /* Pivot point of rotation axis (nm) */
224 int eFittype; /* Type of fit to determine actual group angle */
225 int PotAngle_nstep; /* Number of angles around the reference angle
226 for which the rotation potential is also
227 evaluated (for fit type 'potential' only) */
228 real PotAngle_step; /* Distance between two angles in degrees (for
229 fit type 'potential' only) */
230 real slab_dist; /* Slab distance (nm) */
231 real min_gaussian; /* Minimum value the gaussian must have so that
232 the force is actually evaluated */
233 real eps; /* Additive constant for radial motion2 and
234 flexible2 potentials (nm^2) */
235 gmx_enfrotgrp_t enfrotgrp; /* Stores non-inputrec rotation data per group */
239 int ngrp; /* Number of rotation groups */
240 int nstrout; /* Output frequency for main rotation outfile */
241 int nstsout; /* Output frequency for per-slab data */
242 t_rotgrp *grp; /* Groups to rotate */
243 gmx_enfrot_t enfrot; /* Stores non-inputrec enforced rotation data */
248 int type; /* type of AdResS simulation */
249 gmx_bool bnew_wf; /* enable new AdResS weighting function */
250 gmx_bool bchempot_dx; /*true:interaction table format input is F=-dmu/dx false: dmu_dwp */
251 gmx_bool btf_full_box; /* true: appy therm force everywhere in the box according to table false: only in hybrid region */
252 real const_wf; /* value of weighting function for eAdressConst */
253 real ex_width; /* center of the explicit zone */
254 real hy_width; /* width of the hybrid zone */
255 int icor; /* type of interface correction */
256 int site; /* AdResS CG site location */
257 rvec refs; /* Coordinates for AdResS reference */
258 real ex_forcecap; /* in the hybrid zone, cap forces large then this to adress_ex_forcecap */
259 gmx_bool do_hybridpairs; /* If true pair interaction forces are also scaled in an adress way*/
261 int * tf_table_index; /* contains mapping of energy group index -> i-th adress tf table*/
268 int eI; /* Integration method */
269 gmx_large_int_t nsteps; /* number of steps to be taken */
270 int simulation_part; /* Used in checkpointing to separate chunks */
271 gmx_large_int_t init_step; /* start at a stepcount >0 (used w. tpbconv) */
272 int nstcalcenergy; /* fequency of energy calc. and T/P coupl. upd. */
273 int ns_type; /* which ns method should we use? */
274 int nstlist; /* number of steps before pairlist is generated */
275 int ndelta; /* number of cells per rlong */
276 int nstcomm; /* number of steps after which center of mass */
277 /* motion is removed */
278 int comm_mode; /* Center of mass motion removal algorithm */
279 int nstcheckpoint; /* checkpointing frequency */
280 int nstlog; /* number of steps after which print to logfile */
281 int nstxout; /* number of steps after which X is output */
282 int nstvout; /* id. for V */
283 int nstfout; /* id. for F */
284 int nstenergy; /* number of steps after which energies printed */
285 int nstxtcout; /* id. for compressed trj (.xtc) */
286 double init_t; /* initial time (ps) */
287 double delta_t; /* time step (ps) */
288 real xtcprec; /* precision of xtc file */
289 int nkx,nky,nkz; /* number of k vectors in each spatial dimension*/
290 /* for fourier methods for long range electrost.*/
291 int pme_order; /* interpolation order for PME */
292 real ewald_rtol; /* Real space tolerance for Ewald, determines */
293 /* the real/reciprocal space relative weight */
294 int ewald_geometry; /* normal/3d ewald, or pseudo-2d LR corrections */
295 real epsilon_surface; /* Epsilon for PME dipole correction */
296 gmx_bool bOptFFT; /* optimize the fft plan at start */
297 int ePBC; /* Type of periodic boundary conditions */
298 int bPeriodicMols; /* Periodic molecules */
299 gmx_bool bContinuation; /* Continuation run: starting state is correct */
300 int etc; /* temperature coupling */
301 int nsttcouple; /* interval in steps for temperature coupling */
302 gmx_bool bPrintNHChains; /* whether to print nose-hoover chains */
303 int epc; /* pressure coupling */
304 int epct; /* pressure coupling type */
305 int nstpcouple; /* interval in steps for pressure coupling */
306 real tau_p; /* pressure coupling time (ps) */
307 tensor ref_p; /* reference pressure (kJ/(mol nm^3)) */
308 tensor compress; /* compressability ((mol nm^3)/kJ) */
309 int refcoord_scaling;/* How to scale absolute reference coordinates */
310 rvec posres_com; /* The COM of the posres atoms */
311 rvec posres_comB; /* The B-state COM of the posres atoms */
312 int andersen_seed; /* Random seed for Andersen thermostat (obsolete) */
313 real rlist; /* short range pairlist cut-off (nm) */
314 real rlistlong; /* long range pairlist cut-off (nm) */
315 real rtpi; /* Radius for test particle insertion */
316 int coulombtype; /* Type of electrostatics treatment */
317 real rcoulomb_switch; /* Coulomb switch range start (nm) */
318 real rcoulomb; /* Coulomb cutoff (nm) */
319 real epsilon_r; /* relative dielectric constant */
320 real epsilon_rf; /* relative dielectric constant of the RF */
321 int implicit_solvent;/* No (=explicit water), or GBSA solvent models */
322 int gb_algorithm; /* Algorithm to use for calculation Born radii */
323 int nstgbradii; /* Frequency of updating Generalized Born radii */
324 real rgbradii; /* Cutoff for GB radii calculation */
325 real gb_saltconc; /* Salt concentration (M) for GBSA models */
326 real gb_epsilon_solvent; /* dielectric coeff. of implicit solvent */
327 real gb_obc_alpha; /* 1st scaling factor for Bashford-Case GB */
328 real gb_obc_beta; /* 2nd scaling factor for Bashford-Case GB */
329 real gb_obc_gamma; /* 3rd scaling factor for Bashford-Case GB */
330 real gb_dielectric_offset; /* Dielectric offset for Still/HCT/OBC */
331 int sa_algorithm; /* Algorithm for SA part of GBSA */
332 real sa_surface_tension; /* Energy factor for SA part of GBSA */
333 int vdwtype; /* Type of Van der Waals treatment */
334 real rvdw_switch; /* Van der Waals switch range start (nm) */
335 real rvdw; /* Van der Waals cutoff (nm) */
336 int eDispCorr; /* Perform Long range dispersion corrections */
337 real tabext; /* Extension of the table beyond the cut-off, *
338 * as well as the table length for 1-4 interac. */
339 real shake_tol; /* tolerance for shake */
340 int efep; /* free energy calculations */
341 t_lambda *fepvals; /* Data for the FEP state */
342 gmx_bool bSimTemp; /* Whether to do simulated tempering */
343 t_simtemp *simtempvals;/* Variables for simulated tempering */
344 gmx_bool bExpanded; /* Whether expanded ensembles are used */
345 t_expanded *expandedvals; /* Expanded ensemble parameters */
346 int eDisre; /* Type of distance restraining */
347 real dr_fc; /* force constant for ta_disre */
348 int eDisreWeighting; /* type of weighting of pairs in one restraints */
349 gmx_bool bDisreMixed; /* Use comb of time averaged and instan. viol's */
350 int nstdisreout; /* frequency of writing pair distances to enx */
351 real dr_tau; /* time constant for memory function in disres */
352 real orires_fc; /* force constant for orientational restraints */
353 real orires_tau; /* time constant for memory function in orires */
354 int nstorireout; /* frequency of writing tr(SD) to enx */
355 real dihre_fc; /* force constant for dihedral restraints (obsolete) */
356 real em_stepsize; /* The stepsize for updating */
357 real em_tol; /* The tolerance */
358 int niter; /* Number of iterations for convergence of */
359 /* steepest descent in relax_shells */
360 real fc_stepsize; /* Stepsize for directional minimization */
361 /* in relax_shells */
362 int nstcgsteep; /* number of steps after which a steepest */
363 /* descents step is done while doing cg */
364 int nbfgscorr; /* Number of corrections to the hessian to keep */
365 int eConstrAlg; /* Type of constraint algorithm */
366 int nProjOrder; /* Order of the LINCS Projection Algorithm */
367 real LincsWarnAngle; /* If bond rotates more than %g degrees, warn */
368 int nLincsIter; /* Number of iterations in the final Lincs step */
369 gmx_bool bShakeSOR; /* Use successive overrelaxation for shake */
370 real bd_fric; /* Friction coefficient for BD (amu/ps) */
371 int ld_seed; /* Random seed for SD and BD */
372 int nwall; /* The number of walls */
373 int wall_type; /* The type of walls */
374 real wall_r_linpot; /* The potentail is linear for r<=wall_r_linpot */
375 int wall_atomtype[2];/* The atom type for walls */
376 real wall_density[2]; /* Number density for walls */
377 real wall_ewald_zfac; /* Scaling factor for the box for Ewald */
378 int ePull; /* Type of pulling: no, umbrella or constraint */
379 t_pull *pull; /* The data for center of mass pulling */
380 gmx_bool bRot; /* Calculate enforced rotation potential(s)? */
381 t_rot *rot; /* The data for enforced rotation potentials */
382 real cos_accel; /* Acceleration for viscosity calculation */
383 tensor deform; /* Triclinic deformation velocities (nm/ps) */
384 int userint1; /* User determined parameters */
392 t_grpopts opts; /* Group options */
393 t_cosines ex[DIM]; /* Electric field stuff (spatial part) */
394 t_cosines et[DIM]; /* Electric field stuff (time part) */
395 gmx_bool bQMMM; /* QM/MM calculation */
396 int QMconstraints; /* constraints on QM bonds */
397 int QMMMscheme; /* Scheme: ONIOM or normal */
398 real scalefactor; /* factor for scaling the MM charges in QM calc.*/
399 /* parameter needed for AdResS simulation */
400 gmx_bool bAdress; /* Is AdResS enabled ? */
401 t_adress *adress; /* The data for adress simulations */
404 #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)
406 #define DYNAMIC_BOX(ir) ((ir).epc!=epcNO || (ir).eI==eiTPI || DEFORM(ir))
408 #define PRESERVE_SHAPE(ir) ((ir).epc != epcNO && (ir).deform[XX][XX] == 0 && ((ir).epct == epctISOTROPIC || (ir).epct == epctSEMIISOTROPIC))
410 #define NEED_MUTOT(ir) (((ir).coulombtype==eelEWALD || EEL_PME((ir).coulombtype)) && ((ir).ewald_geometry==eewg3DC || (ir).epsilon_surface!=0))
412 #define IR_TWINRANGE(ir) ((ir).rlist > 0 && ((ir).rlistlong == 0 || (ir).rlistlong > (ir).rlist))
414 #define IR_ELEC_FIELD(ir) ((ir).ex[XX].n > 0 || (ir).ex[YY].n > 0 || (ir).ex[ZZ].n > 0)
416 #define IR_EXCL_FORCES(ir) (EEL_FULL((ir).coulombtype) || (EEL_RF((ir).coulombtype) && (ir).coulombtype != eelRF_NEC) || (ir).implicit_solvent != eisNO)
417 /* use pointer definitions of ir here, since that's what's usually used in the code */
418 #define IR_NPT_TROTTER(ir) ((((ir)->eI == eiVV) || ((ir)->eI == eiVVAK)) && (((ir)->epc == epcMTTK) && ((ir)->etc == etcNOSEHOOVER)))
420 #define IR_NVT_TROTTER(ir) ((((ir)->eI == eiVV) || ((ir)->eI == eiVVAK)) && ((!((ir)->epc == epcMTTK)) && ((ir)->etc == etcNOSEHOOVER)))
422 #define IR_NPH_TROTTER(ir) ((((ir)->eI == eiVV) || ((ir)->eI == eiVVAK)) && (((ir)->epc == epcMTTK) && (!(((ir)->etc == etcNOSEHOOVER)))))