3 * This source code is part of
7 * GROningen MAchine for Chemical Simulations
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
47 /* check kernel/toppush.c when you change these numbers */
49 #define MAXFORCEPARAM 12
53 typedef atom_id t_iatom;
55 /* this MUST correspond to the
56 t_interaction_function[F_NRE] in gmxlib/ifunc.c */
144 F_DVDL_TEMPERATURE, /* not calculated for now, but should just be the energy (NVT) or enthalpy (NPT), or 0 (NVE) */
145 F_NRE /* This number is for the total number of energies */
148 #define IS_RESTRAINT_TYPE(ifunc) (((ifunc==F_POSRES) || (ifunc==F_DISRES) || (ifunc==F_RESTRBONDS) || (ifunc==F_DISRESVIOL) || (ifunc==F_ORIRES) || (ifunc==F_ORIRESDEV) || (ifunc==F_ANGRES) || (ifunc == F_ANGRESZ) || (ifunc==F_DIHRES)))
150 /* A macro for checking if ftype is an explicit pair-listed LJ or COULOMB
152 * bonded LJ (usually 1-4), or special listed non-bonded for FEP.
154 #define IS_LISTED_LJ_C(ftype) ((ftype) >= F_LJ14 && (ftype) <= F_LJC_PAIRS_NB)
158 /* Some parameters have A and B values for free energy calculations.
159 * The B values are not used for regular simulations of course.
160 * Free Energy for nonbondeds can be computed by changing the atom type.
161 * The harmonic type is used for all harmonic potentials:
162 * bonds, angles and improper dihedrals
164 struct {real a,b,c; } bham;
165 struct {real rA,krA,rB,krB; } harmonic;
166 struct {real klinA,aA,klinB,aB; } linangle;
167 struct {real lowA,up1A,up2A,kA,lowB,up1B,up2B,kB; } restraint;
168 /* No free energy supported for cubic bonds, FENE, WPOL or cross terms */
169 struct {real b0,kb,kcub; } cubic;
170 struct {real bm,kb; } fene;
171 struct {real r1e,r2e,krr; } cross_bb;
172 struct {real r1e,r2e,r3e,krt; } cross_ba;
173 struct {real thetaA,kthetaA,r13A,kUBA,thetaB,kthetaB,r13B,kUBB;} u_b;
174 struct {real theta,c[5]; } qangle;
175 struct {real alpha; } polarize;
176 struct {real alpha,drcut,khyp; } anharm_polarize;
177 struct {real al_x,al_y,al_z,rOH,rHH,rOD; } wpol;
178 struct {real a,alpha1,alpha2,rfac; } thole;
179 struct {real c6,c12; } lj;
180 struct {real c6A,c12A,c6B,c12B; } lj14;
181 struct {real fqq,qi,qj,c6,c12; } ljc14;
182 struct {real qi,qj,c6,c12; } ljcnb;
183 /* Proper dihedrals can not have different multiplicity when
184 * doing free energy calculations, because the potential would not
185 * be periodic anymore.
187 struct {real phiA,cpA;int mult;real phiB,cpB; } pdihs;
188 struct {real dA,dB; } constr;
189 /* Settle can not be used for Free energy calculations of water bond geometry.
190 * Use shake (or lincs) instead if you have to change the water bonds.
192 struct {real doh,dhh; } settle;
193 struct {real b0A,cbA,betaA,b0B,cbB,betaB; } morse;
194 struct {real pos0A[DIM],fcA[DIM],pos0B[DIM],fcB[DIM]; } posres;
195 struct {real pos0[DIM],r,k; int geom; } fbposres;
196 struct {real rbcA[NR_RBDIHS], rbcB[NR_RBDIHS]; } rbdihs;
197 struct {real a,b,c,d,e,f; } vsite;
198 struct {int n; real a; } vsiten;
199 /* NOTE: npair is only set after reading the tpx file */
200 struct {real low,up1,up2,kfac;int type,label,npair; } disres;
201 struct {real phiA,dphiA,kfacA,phiB,dphiB,kfacB; } dihres;
202 struct {int ex,power,label; real c,obs,kfac; } orires;
203 struct {int table;real kA;real kB; } tab;
204 struct {real sar,st,pi,gbr,bmlt; } gb;
205 struct {int cmapA,cmapB; } cmap;
206 struct {real buf[MAXFORCEPARAM]; } generic; /* Conversion */
209 typedef int t_functype;
212 * The nonperturbed/perturbed interactions are now separated (sorted) in the
213 * ilist, such that the first 0..(nr_nonperturbed-1) ones are exactly that, and
214 * the remaining ones from nr_nonperturbed..(nr-1) are perturbed bonded
226 * The struct t_ilist defines a list of atoms with their interactions.
227 * General field description:
229 * the size (nr elements) of the interactions array (iatoms[]).
231 * specifies which atoms are involved in an interaction of a certain
232 * type. The layout of this array is as follows:
234 * +-----+---+---+---+-----+---+---+-----+---+---+---+-----+---+---+...
235 * |type1|at1|at2|at3|type2|at1|at2|type1|at1|at2|at3|type3|at1|at2|
236 * +-----+---+---+---+-----+---+---+-----+---+---+---+-----+---+---+...
238 * So for interaction type type1 3 atoms are needed, and for type2 and
239 * type3 only 2. The type identifier is used to select the function to
240 * calculate the interaction and its actual parameters. This type
241 * identifier is an index in a params[] and functype[] array.
246 real *cmap; /* Has length 4*grid_spacing*grid_spacing, */
247 /* there are 4 entries for each cmap type (V,dVdx,dVdy,d2dVdxdy) */
252 int ngrid; /* Number of allocated cmap (cmapdata_t ) grids */
253 int grid_spacing; /* Grid spacing */
254 cmapdata_t *cmapdata; /* Pointer to grid with actual, pre-interpolated data */
262 t_functype *functype;
264 double reppow; /* The repulsion power for VdW: C12*r^-reppow */
265 real fudgeQQ; /* The scaling factor for Coulomb 1-4: f*q1*q2 */
266 gmx_cmap_t cmap_grid; /* The dihedral correction maps */
270 ilsortUNKNOWN, ilsortNO_FE, ilsortFE_UNSORTED, ilsortFE_SORTED
277 t_functype *functype;
280 gmx_cmap_t cmap_grid;
281 t_iparams *iparams_posres,*iparams_fbposres;
282 int iparams_posres_nalloc,iparams_fbposres_nalloc;
289 * The struct t_idef defines all the interactions for the complete
290 * simulation. The structure is setup in such a way that the multinode
291 * version of the program can use it as easy as the single node version.
292 * General field description:
294 * defines the number of elements in functype[] and param[].
296 * the node id (if parallel machines)
298 * the number of atomtypes
299 * t_functype *functype
300 * array of length ntypes, defines for every force type what type of
301 * function to use. Every "bond" with the same function but different
302 * force parameters is a different force type. The type identifier in the
303 * forceatoms[] array is an index in this array.
305 * array of length ntypes, defines the parameters for every interaction
306 * type. The type identifier in the actual interaction list
307 * (ilist[ftype].iatoms[]) is an index in this array.
308 * gmx_cmap_t cmap_grid
309 * the grid for the dihedral pair correction maps.
310 * t_iparams *iparams_posres, *iparams_fbposres
311 * defines the parameters for position restraints only.
312 * Position restraints are the only interactions that have different
313 * parameters (reference positions) for different molecules
314 * of the same type. ilist[F_POSRES].iatoms[] is an index in this array.
316 * The list of interactions for each type. Note that some,
317 * such as LJ and COUL will have 0 entries.
321 int n; /* n+1 is the number of points */
322 real scale; /* distance between two points */
323 real *tab; /* the actual tables, per point there are 4 numbers */