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48 econqCoord, /* Constrain coordinates (mass weighted) */
49 econqVeloc, /* Constrain velocities (mass weighted) */
50 econqDeriv, /* Constrain a derivative (mass weighted), *
51 * for instance velocity or acceleration, *
52 * constraint virial can not be calculated. */
53 econqDeriv_FlexCon, /* As econqDeriv, but only output flex. con. */
54 econqForce, /* Constrain forces (non mass-weighted) */
55 econqForceDispl /* Constrain forces (mass-weighted 1/0 for freeze) */
58 int n_flexible_constraints(struct gmx_constr *constr);
59 /* Returns the total number of flexible constraints in the system */
61 void too_many_constraint_warnings(int eConstrAlg, int warncount);
62 /* Generate a fatal error because of too many LINCS/SETTLE warnings */
64 gmx_shakedata_t shake_init();
65 /* Initializes and return the SHAKE data structure */
67 gmx_bool bshakef(FILE *log, /* Log file */
68 gmx_shakedata_t shaked, /* Total number of atoms */
69 real invmass[], /* Atomic masses */
70 int nblocks, /* The number of shake blocks */
71 int sblock[], /* The shake blocks */
72 t_idef *idef, /* The interaction def */
73 t_inputrec *ir, /* Input record */
74 rvec x_s[], /* Coords before update */
75 rvec prime[], /* Output coords */
76 t_nrnb *nrnb, /* Performance measure */
77 real *lagr, /* The Lagrange multipliers */
78 real lambda, /* FEP lambda */
79 real *dvdlambda, /* FEP force */
80 real invdt, /* 1/delta_t */
81 rvec *v, /* Also constrain v if v!=NULL */
82 gmx_bool bCalcVir, /* Calculate r x m delta_r */
83 tensor vir_r_m_dr, /* sum r x m delta_r */
84 gmx_bool bDumpOnError, /* Dump debugging stuff on error*/
85 int econq, /* which type of constrainint is occurring */
86 t_vetavars *vetavar); /* veta for pressure control */
87 /* Shake all the atoms blockwise. It is assumed that all the constraints
88 * in the idef->shakes field are sorted, to ascending block nr. The
89 * sblock array points into the idef->shakes.iatoms field, with block 0
91 * at sblock[0] and running to ( < ) sblock[1], block n running from
92 * sblock[n] to sblock[n+1]. Array sblock should be large enough.
93 * Return TRUE when OK, FALSE when shake-error
96 gmx_settledata_t settle_init(real mO, real mH, real invmO, real invmH,
98 /* Initializes and returns a structure with SETTLE parameters */
100 void csettle(gmx_settledata_t settled,
101 int nsettle, /* Number of settles */
102 t_iatom iatoms[], /* The settle iatom list */
103 const t_pbc *pbc, /* PBC data pointer, can be NULL */
104 real b4[], /* Old coordinates */
105 real after[], /* New coords, to be settled */
106 real invdt, /* 1/delta_t */
107 real *v, /* Also constrain v if v!=NULL */
108 int calcvir_atom_end, /* Calculate r x m delta_r up to this atom */
109 tensor vir_r_m_dr, /* sum r x m delta_r */
111 t_vetavars *vetavar /* variables for pressure control */
114 void settle_proj(gmx_settledata_t settled, int econq,
115 int nsettle, t_iatom iatoms[],
116 const t_pbc *pbc, /* PBC data pointer, can be NULL */
118 rvec *der, rvec *derp,
119 int CalcVirAtomEnd, tensor vir_r_m_dder,
120 t_vetavars *vetavar);
121 /* Analytical algorithm to subtract the components of derivatives
122 * of coordinates working on settle type constraint.
125 void cshake(atom_id iatom[], int ncon, int *nnit, int maxnit,
126 real dist2[], real xp[], real rij[], real m2[], real omega,
127 real invmass[], real tt[], real lagr[], int *nerror);
128 /* Regular iterative shake */
130 void crattle(atom_id iatom[], int ncon, int *nnit, int maxnit,
131 real dist2[], real vp[], real rij[], real m2[], real omega,
132 real invmass[], real tt[], real lagr[], int *nerror, real invdt, t_vetavars *vetavar);
134 gmx_bool constrain(FILE *log, gmx_bool bLog, gmx_bool bEner,
138 gmx_ekindata_t *ekind,
140 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 * step_scaling can be used to update coordinates based on the time
167 * step multiplied by this factor. Thus, normally 1.0 is passed. The
168 * SD1 integrator uses 0.5 in one of its calls, to correct positions
169 * for half a step of changed velocities.
171 * If v!=NULL also constrain v by adding the constraint corrections / dt.
173 * If vir!=NULL calculate the constraint virial.
175 * if veta != NULL, constraints are done assuming isotropic pressure control
176 * (i.e. constraining rdot.r = (v + veta*r).r = 0 instead of v
178 * Init_constraints must have be called once, before calling constrain.
180 * Return TRUE if OK, FALSE in case of shake error
184 gmx_constr_t init_constraints(FILE *log,
185 gmx_mtop_t *mtop, t_inputrec *ir,
186 gmx_edsam_t ed, t_state *state,
188 /* Initialize constraints stuff */
190 void set_constraints(gmx_constr_t constr,
195 /* Set up all the local constraints for the node */
197 /* The at2con t_blocka struct returned by the routines below
198 * contains a list of constraints per atom.
199 * The F_CONSTRNC constraints in this structure number consecutively
200 * after the F_CONSTR constraints.
203 t_blocka make_at2con(int start, int natoms,
204 t_ilist *ilist, t_iparams *iparams,
205 gmx_bool bDynamics, int *nflexiblecons);
206 /* Returns a block struct to go from atoms to constraints */
208 const t_blocka *atom2constraints_moltype(gmx_constr_t constr);
209 /* Returns the an array of atom to constraints lists for the moltypes */
211 const int **atom2settle_moltype(gmx_constr_t constr);
212 /* Returns the an array of atom to settle for the moltypes */
214 #define constr_iatomptr(nconstr, iatom_constr, iatom_constrnc, con) ((con) < (nconstr) ? (iatom_constr)+(con)*3 : (iatom_constrnc)+(con-nconstr)*3)
215 /* Macro for getting the constraint iatoms for a constraint number con
216 * which comes from a list where F_CONSTR and F_CONSTRNC constraints
220 gmx_bool inter_charge_group_constraints(const gmx_mtop_t *mtop);
221 /* Returns if there are inter charge group constraints */
223 gmx_bool inter_charge_group_settles(const gmx_mtop_t *mtop);
224 /* Returns if there are inter charge group settles */
226 real *constr_rmsd_data(gmx_constr_t constr);
227 /* Return the data for determining constraint RMS relative deviations.
228 * Returns NULL when LINCS is not used.
231 real constr_rmsd(gmx_constr_t constr, gmx_bool bSD2);
232 /* Return the RMSD of the constraint, bSD2 selects the second SD step */
234 real *lincs_rmsd_data(gmx_lincsdata_t lincsd);
235 /* Return the data for determining constraint RMS relative deviations */
237 real lincs_rmsd(gmx_lincsdata_t lincsd, gmx_bool bSD2);
238 /* Return the RMSD of the constraint, bSD2 selects the second SD step */
240 gmx_lincsdata_t init_lincs(FILE *fplog, gmx_mtop_t *mtop,
241 int nflexcon_global, t_blocka *at2con,
242 gmx_bool bPLINCS, int nIter, int nProjOrder);
243 /* Initializes and returns the lincs data struct */
245 void set_lincs(t_idef *idef, t_mdatoms *md,
246 gmx_bool bDynamics, t_commrec *cr,
248 /* Initialize lincs stuff */
250 void set_lincs_matrix(gmx_lincsdata_t li, real *invmass, real lambda);
251 /* Sets the elements of the LINCS constraint coupling matrix */
253 real constr_r_max(FILE *fplog, gmx_mtop_t *mtop, t_inputrec *ir);
254 /* Returns an estimate of the maximum distance between atoms
255 * required for LINCS.
259 constrain_lincs(FILE *log, gmx_bool bLog, gmx_bool bEner,
262 gmx_lincsdata_t lincsd, t_mdatoms *md,
264 rvec *x, rvec *xprime, rvec *min_proj,
265 matrix box, t_pbc *pbc,
266 real lambda, real *dvdlambda,
268 gmx_bool bCalcVir, tensor vir_r_m_dr,
271 int maxwarn, int *warncount);
272 /* Returns if the constraining succeeded */
275 /* helper functions for andersen temperature control, because the
276 * gmx_constr construct is only defined in constr.c. Return the list
277 * of blocks (get_sblock) and the number of blocks (get_nblocks). */
279 int *get_sblock(struct gmx_constr *constr);
281 int get_nblocks(struct gmx_constr *constr);