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40 #include "types/commrec.h"
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, /* SHAKE data */
69 int natoms, /* 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(FILE *fp,
116 gmx_settledata_t settled, int econq,
117 int nsettle, t_iatom iatoms[],
118 const t_pbc *pbc, /* PBC data pointer, can be NULL */
120 rvec *der, rvec *derp,
121 int CalcVirAtomEnd, tensor vir_r_m_dder,
122 t_vetavars *vetavar);
123 /* Analytical algorithm to subtract the components of derivatives
124 * of coordinates working on settle type constraint.
127 void cshake(atom_id iatom[], int ncon, int *nnit, int maxnit,
128 real dist2[], real xp[], real rij[], real m2[], real omega,
129 real invmass[], real tt[], real lagr[], int *nerror);
130 /* Regular iterative shake */
132 void crattle(atom_id iatom[], int ncon, int *nnit, int maxnit,
133 real dist2[], real vp[], real rij[], real m2[], real omega,
134 real invmass[], real tt[], real lagr[], int *nerror, real invdt, t_vetavars *vetavar);
136 gmx_bool constrain(FILE *log, gmx_bool bLog, gmx_bool bEner,
140 gmx_ekindata_t *ekind,
142 gmx_large_int_t step, int delta_step,
144 rvec *x, rvec *xprime, rvec *min_proj,
145 gmx_bool bMolPBC, matrix box,
146 real lambda, real *dvdlambda,
147 rvec *v, tensor *vir,
148 t_nrnb *nrnb, int econq, gmx_bool bPscal, real veta, real vetanew);
150 * When econq=econqCoord constrains coordinates xprime using th
151 * directions in x, min_proj is not used.
153 * When econq=econqDeriv, calculates the components xprime in
154 * the constraint directions and subtracts these components from min_proj.
155 * So when min_proj=xprime, the constraint components are projected out.
157 * When econq=econqDeriv_FlexCon, the same is done as with econqDeriv,
158 * but only the components of the flexible constraints are stored.
160 * When bMolPBC=TRUE, assume that molecules might be broken: correct PBC.
162 * delta_step is used for determining the constraint reference lengths
163 * when lenA != lenB or will the pull code with a pulling rate.
164 * step + delta_step is the step at which the final configuration
165 * is meant to be; for update delta_step = 1.
167 * If v!=NULL also constrain v by adding the constraint corrections / dt.
169 * If vir!=NULL calculate the constraint virial.
171 * if veta != NULL, constraints are done assuming isotropic pressure control
172 * (i.e. constraining rdot.r = (v + veta*r).r = 0 instead of v
174 * Init_constraints must have be called once, before calling constrain.
176 * Return TRUE if OK, FALSE in case of shake error
180 gmx_constr_t init_constraints(FILE *log,
181 gmx_mtop_t *mtop, t_inputrec *ir,
182 gmx_edsam_t ed, t_state *state,
184 /* Initialize constraints stuff */
186 void set_constraints(gmx_constr_t constr,
191 /* Set up all the local constraints for the node */
193 /* The at2con t_blocka struct returned by the routines below
194 * contains a list of constraints per atom.
195 * The F_CONSTRNC constraints in this structure number consecutively
196 * after the F_CONSTR constraints.
199 t_blocka make_at2con(int start, int natoms,
200 t_ilist *ilist, t_iparams *iparams,
201 gmx_bool bDynamics, int *nflexiblecons);
202 /* Returns a block struct to go from atoms to constraints */
204 const t_blocka *atom2constraints_moltype(gmx_constr_t constr);
205 /* Returns the an array of atom to constraints lists for the moltypes */
207 const int **atom2settle_moltype(gmx_constr_t constr);
208 /* Returns the an array of atom to settle for the moltypes */
210 #define constr_iatomptr(nconstr, iatom_constr, iatom_constrnc, con) ((con) < (nconstr) ? (iatom_constr)+(con)*3 : (iatom_constrnc)+(con-nconstr)*3)
211 /* Macro for getting the constraint iatoms for a constraint number con
212 * which comes from a list where F_CONSTR and F_CONSTRNC constraints
216 gmx_bool inter_charge_group_constraints(const gmx_mtop_t *mtop);
217 /* Returns if there are inter charge group constraints */
219 gmx_bool inter_charge_group_settles(const gmx_mtop_t *mtop);
220 /* Returns if there are inter charge group settles */
222 real *constr_rmsd_data(gmx_constr_t constr);
223 /* Return the data for determining constraint RMS relative deviations.
224 * Returns NULL when LINCS is not used.
227 real constr_rmsd(gmx_constr_t constr, gmx_bool bSD2);
228 /* Return the RMSD of the constraint, bSD2 selects the second SD step */
230 real *lincs_rmsd_data(gmx_lincsdata_t lincsd);
231 /* Return the data for determining constraint RMS relative deviations */
233 real lincs_rmsd(gmx_lincsdata_t lincsd, gmx_bool bSD2);
234 /* Return the RMSD of the constraint, bSD2 selects the second SD step */
236 gmx_lincsdata_t init_lincs(FILE *fplog, gmx_mtop_t *mtop,
237 int nflexcon_global, t_blocka *at2con,
238 gmx_bool bPLINCS, int nIter, int nProjOrder);
239 /* Initializes and returns the lincs data struct */
241 void set_lincs(t_idef *idef, t_mdatoms *md,
242 gmx_bool bDynamics, t_commrec *cr,
244 /* Initialize lincs stuff */
246 void set_lincs_matrix(gmx_lincsdata_t li, real *invmass, real lambda);
247 /* Sets the elements of the LINCS constraint coupling matrix */
249 real constr_r_max(FILE *fplog, gmx_mtop_t *mtop, t_inputrec *ir);
250 /* Returns an estimate of the maximum distance between atoms
251 * required for LINCS.
255 constrain_lincs(FILE *log, gmx_bool bLog, gmx_bool bEner,
257 gmx_large_int_t step,
258 gmx_lincsdata_t lincsd, t_mdatoms *md,
260 rvec *x, rvec *xprime, rvec *min_proj,
261 matrix box, t_pbc *pbc,
262 real lambda, real *dvdlambda,
264 gmx_bool bCalcVir, tensor vir_r_m_dr,
267 int maxwarn, int *warncount);
268 /* Returns if the constraining succeeded */
271 /* helper functions for andersen temperature control, because the
272 * gmx_constr construct is only defined in constr.c. Return the list
273 * of blocks (get_sblock) and the number of blocks (get_nblocks). */
275 int *get_sblock(struct gmx_constr *constr);
277 int get_nblocks(struct gmx_constr *constr);