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41 #include "types/commrec.h"
49 econqCoord, /* Constrain coordinates (mass weighted) */
50 econqVeloc, /* Constrain velocities (mass weighted) */
51 econqDeriv, /* Constrain a derivative (mass weighted), *
52 * for instance velocity or acceleration, *
53 * constraint virial can not be calculated. */
54 econqDeriv_FlexCon, /* As econqDeriv, but only output flex. con. */
55 econqForce, /* Constrain forces (non mass-weighted) */
56 econqForceDispl /* Constrain forces (mass-weighted 1/0 for freeze) */
59 int n_flexible_constraints(struct gmx_constr *constr);
60 /* Returns the total number of flexible constraints in the system */
62 void too_many_constraint_warnings(int eConstrAlg, int warncount);
63 /* Generate a fatal error because of too many LINCS/SETTLE warnings */
65 gmx_shakedata_t shake_init();
66 /* Initializes and return the SHAKE data structure */
68 gmx_bool bshakef(FILE *log, /* Log file */
69 gmx_shakedata_t shaked, /* Total number of atoms */
70 real invmass[], /* Atomic masses */
71 int nblocks, /* The number of shake blocks */
72 int sblock[], /* The shake blocks */
73 t_idef *idef, /* The interaction def */
74 t_inputrec *ir, /* Input record */
75 rvec x_s[], /* Coords before update */
76 rvec prime[], /* Output coords */
77 t_nrnb *nrnb, /* Performance measure */
78 real *lagr, /* The Lagrange multipliers */
79 real lambda, /* FEP lambda */
80 real *dvdlambda, /* FEP force */
81 real invdt, /* 1/delta_t */
82 rvec *v, /* Also constrain v if v!=NULL */
83 gmx_bool bCalcVir, /* Calculate r x m delta_r */
84 tensor vir_r_m_dr, /* sum r x m delta_r */
85 gmx_bool bDumpOnError, /* Dump debugging stuff on error*/
86 int econq, /* which type of constrainint is occurring */
87 t_vetavars *vetavar); /* veta for pressure control */
88 /* Shake all the atoms blockwise. It is assumed that all the constraints
89 * in the idef->shakes field are sorted, to ascending block nr. The
90 * sblock array points into the idef->shakes.iatoms field, with block 0
92 * at sblock[0] and running to ( < ) sblock[1], block n running from
93 * sblock[n] to sblock[n+1]. Array sblock should be large enough.
94 * Return TRUE when OK, FALSE when shake-error
97 gmx_settledata_t settle_init(real mO, real mH, real invmO, real invmH,
99 /* Initializes and returns a structure with SETTLE parameters */
101 void csettle(gmx_settledata_t settled,
102 int nsettle, /* Number of settles */
103 t_iatom iatoms[], /* The settle iatom list */
104 const t_pbc *pbc, /* PBC data pointer, can be NULL */
105 real b4[], /* Old coordinates */
106 real after[], /* New coords, to be settled */
107 real invdt, /* 1/delta_t */
108 real *v, /* Also constrain v if v!=NULL */
109 int calcvir_atom_end, /* Calculate r x m delta_r up to this atom */
110 tensor vir_r_m_dr, /* sum r x m delta_r */
112 t_vetavars *vetavar /* variables for pressure control */
115 void settle_proj(gmx_settledata_t settled, int econq,
116 int nsettle, t_iatom iatoms[],
117 const t_pbc *pbc, /* PBC data pointer, can be NULL */
119 rvec *der, rvec *derp,
120 int CalcVirAtomEnd, tensor vir_r_m_dder,
121 t_vetavars *vetavar);
122 /* Analytical algorithm to subtract the components of derivatives
123 * of coordinates working on settle type constraint.
126 void cshake(atom_id iatom[], int ncon, int *nnit, int maxnit,
127 real dist2[], real xp[], real rij[], real m2[], real omega,
128 real invmass[], real tt[], real lagr[], int *nerror);
129 /* Regular iterative shake */
131 void crattle(atom_id iatom[], int ncon, int *nnit, int maxnit,
132 real dist2[], real vp[], real rij[], real m2[], real omega,
133 real invmass[], real tt[], real lagr[], int *nerror, real invdt, t_vetavars *vetavar);
135 gmx_bool constrain(FILE *log, gmx_bool bLog, gmx_bool bEner,
139 gmx_ekindata_t *ekind,
141 gmx_int64_t step, int delta_step,
143 rvec *x, rvec *xprime, rvec *min_proj,
144 gmx_bool bMolPBC, matrix box,
145 real lambda, real *dvdlambda,
146 rvec *v, tensor *vir,
147 t_nrnb *nrnb, int econq, gmx_bool bPscal, real veta, real vetanew);
149 * When econq=econqCoord constrains coordinates xprime using th
150 * directions in x, min_proj is not used.
152 * When econq=econqDeriv, calculates the components xprime in
153 * the constraint directions and subtracts these components from min_proj.
154 * So when min_proj=xprime, the constraint components are projected out.
156 * When econq=econqDeriv_FlexCon, the same is done as with econqDeriv,
157 * but only the components of the flexible constraints are stored.
159 * When bMolPBC=TRUE, assume that molecules might be broken: correct PBC.
161 * delta_step is used for determining the constraint reference lengths
162 * when lenA != lenB or will the pull code with a pulling rate.
163 * step + delta_step is the step at which the final configuration
164 * is meant to be; for update delta_step = 1.
166 * If v!=NULL also constrain v by adding the constraint corrections / dt.
168 * If vir!=NULL calculate the constraint virial.
170 * if veta != NULL, constraints are done assuming isotropic pressure control
171 * (i.e. constraining rdot.r = (v + veta*r).r = 0 instead of v
173 * Init_constraints must have be called once, before calling constrain.
175 * Return TRUE if OK, FALSE in case of shake error
179 gmx_constr_t init_constraints(FILE *log,
180 gmx_mtop_t *mtop, t_inputrec *ir,
181 gmx_edsam_t ed, t_state *state,
183 /* Initialize constraints stuff */
185 void set_constraints(gmx_constr_t constr,
190 /* Set up all the local constraints for the node */
192 /* The at2con t_blocka struct returned by the routines below
193 * contains a list of constraints per atom.
194 * The F_CONSTRNC constraints in this structure number consecutively
195 * after the F_CONSTR constraints.
198 t_blocka make_at2con(int start, int natoms,
199 t_ilist *ilist, t_iparams *iparams,
200 gmx_bool bDynamics, int *nflexiblecons);
201 /* Returns a block struct to go from atoms to constraints */
203 const t_blocka *atom2constraints_moltype(gmx_constr_t constr);
204 /* Returns the an array of atom to constraints lists for the moltypes */
206 const int **atom2settle_moltype(gmx_constr_t constr);
207 /* Returns the an array of atom to settle for the moltypes */
209 #define constr_iatomptr(nconstr, iatom_constr, iatom_constrnc, con) ((con) < (nconstr) ? (iatom_constr)+(con)*3 : (iatom_constrnc)+(con-nconstr)*3)
210 /* Macro for getting the constraint iatoms for a constraint number con
211 * which comes from a list where F_CONSTR and F_CONSTRNC constraints
215 gmx_bool inter_charge_group_constraints(const gmx_mtop_t *mtop);
216 /* Returns if there are inter charge group constraints */
218 gmx_bool inter_charge_group_settles(const gmx_mtop_t *mtop);
219 /* Returns if there are inter charge group settles */
221 real *constr_rmsd_data(gmx_constr_t constr);
222 /* Return the data for determining constraint RMS relative deviations.
223 * Returns NULL when LINCS is not used.
226 real constr_rmsd(gmx_constr_t constr, gmx_bool bSD2);
227 /* Return the RMSD of the constraint, bSD2 selects the second SD step */
229 real *lincs_rmsd_data(gmx_lincsdata_t lincsd);
230 /* Return the data for determining constraint RMS relative deviations */
232 real lincs_rmsd(gmx_lincsdata_t lincsd, gmx_bool bSD2);
233 /* Return the RMSD of the constraint, bSD2 selects the second SD step */
235 gmx_lincsdata_t init_lincs(FILE *fplog, gmx_mtop_t *mtop,
236 int nflexcon_global, t_blocka *at2con,
237 gmx_bool bPLINCS, int nIter, int nProjOrder);
238 /* Initializes and returns the lincs data struct */
240 void set_lincs(t_idef *idef, t_mdatoms *md,
241 gmx_bool bDynamics, t_commrec *cr,
243 /* Initialize lincs stuff */
245 void set_lincs_matrix(gmx_lincsdata_t li, real *invmass, real lambda);
246 /* Sets the elements of the LINCS constraint coupling matrix */
248 real constr_r_max(FILE *fplog, gmx_mtop_t *mtop, t_inputrec *ir);
249 /* Returns an estimate of the maximum distance between atoms
250 * required for LINCS.
254 constrain_lincs(FILE *log, gmx_bool bLog, gmx_bool bEner,
257 gmx_lincsdata_t lincsd, t_mdatoms *md,
259 rvec *x, rvec *xprime, rvec *min_proj,
260 matrix box, t_pbc *pbc,
261 real lambda, real *dvdlambda,
263 gmx_bool bCalcVir, tensor vir_r_m_dr,
266 int maxwarn, int *warncount);
267 /* Returns if the constraining succeeded */
270 /* helper functions for andersen temperature control, because the
271 * gmx_constr construct is only defined in constr.c. Return the list
272 * of blocks (get_sblock) and the number of blocks (get_nblocks). */
274 int *get_sblock(struct gmx_constr *constr);
276 int get_nblocks(struct gmx_constr *constr);