/*
- *
+ *
* This source code is part of
- *
+ *
* G R O M A C S
- *
+ *
* GROningen MAchine for Chemical Simulations
- *
+ *
* VERSION 3.2.0
* Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
- *
+ *
* If you want to redistribute modifications, please consider that
* scientific software is very special. Version control is crucial -
* bugs must be traceable. We will be happy to consider code for
* inclusion in the official distribution, but derived work must not
* be called official GROMACS. Details are found in the README & COPYING
* files - if they are missing, get the official version at www.gromacs.org.
- *
+ *
* To help us fund GROMACS development, we humbly ask that you cite
* the papers on the package - you can find them in the top README file.
- *
+ *
* For more info, check our website at http://www.gromacs.org
- *
+ *
* And Hey:
* Gromacs Runs On Most of All Computer Systems
*/
extern "C" {
#endif
-static const char *sepdvdlformat=" %-30s V %12.5e dVdl %12.5e\n";
+static const char *sepdvdlformat = " %-30s V %12.5e dVdl %12.5e\n";
-void calc_vir(FILE *fplog,int nxf,rvec x[],rvec f[],tensor vir,
- gmx_bool bScrewPBC,matrix box);
+void calc_vir(FILE *fplog, int nxf, rvec x[], rvec f[], tensor vir,
+ gmx_bool bScrewPBC, matrix box);
/* Calculate virial for nxf atoms, and add it to vir */
-void f_calc_vir(FILE *fplog,int i0,int i1,rvec x[],rvec f[],tensor vir,
- t_graph *g,rvec shift_vec[]);
+void f_calc_vir(FILE *fplog, int i0, int i1, rvec x[], rvec f[], tensor vir,
+ t_graph *g, rvec shift_vec[]);
/* Calculate virial taking periodicity into account */
real RF_excl_correction(FILE *fplog,
- const t_forcerec *fr,t_graph *g,
- const t_mdatoms *mdatoms,const t_blocka *excl,
- rvec x[],rvec f[],rvec *fshift,const t_pbc *pbc,
- real lambda,real *dvdlambda);
+ const t_forcerec *fr, t_graph *g,
+ const t_mdatoms *mdatoms, const t_blocka *excl,
+ rvec x[], rvec f[], rvec *fshift, const t_pbc *pbc,
+ real lambda, real *dvdlambda);
/* Calculate the reaction-field energy correction for this node:
* epsfac q_i q_j (k_rf r_ij^2 - c_rf)
* and force correction for all excluded pairs, including self pairs.
*/
-void calc_rffac(FILE *fplog,int eel,real eps_r,real eps_rf,
- real Rc,real Temp,
- real zsq,matrix box,
- real *kappa,real *krf,real *crf);
+void calc_rffac(FILE *fplog, int eel, real eps_r, real eps_rf,
+ real Rc, real Temp,
+ real zsq, matrix box,
+ real *kappa, real *krf, real *crf);
/* Determine the reaction-field constants */
void init_generalized_rf(FILE *fplog,
- const gmx_mtop_t *mtop,const t_inputrec *ir,
- t_forcerec *fr);
+ const gmx_mtop_t *mtop, const t_inputrec *ir,
+ t_forcerec *fr);
/* Initialize the generalized reaction field parameters */
/* In wall.c */
-void make_wall_tables(FILE *fplog,const output_env_t oenv,
- const t_inputrec *ir,const char *tabfn,
- const gmx_groups_t *groups,
- t_forcerec *fr);
+void make_wall_tables(FILE *fplog, const output_env_t oenv,
+ const t_inputrec *ir, const char *tabfn,
+ const gmx_groups_t *groups,
+ t_forcerec *fr);
-real do_walls(t_inputrec *ir,t_forcerec *fr,matrix box,t_mdatoms *md,
- rvec x[],rvec f[],real lambda,real Vlj[],t_nrnb *nrnb);
+real do_walls(t_inputrec *ir, t_forcerec *fr, matrix box, t_mdatoms *md,
+ rvec x[], rvec f[], real lambda, real Vlj[], t_nrnb *nrnb);
t_forcerec *mk_forcerec(void);
#define GMX_MAKETABLES_FORCEUSER (1<<0)
#define GMX_MAKETABLES_14ONLY (1<<1)
-t_forcetable make_tables(FILE *fp,const output_env_t oenv,
- const t_forcerec *fr, gmx_bool bVerbose,
- const char *fn, real rtab,int flags);
+t_forcetable make_tables(FILE *fp, const output_env_t oenv,
+ const t_forcerec *fr, gmx_bool bVerbose,
+ const char *fn, real rtab, int flags);
/* Return tables for inner loops. When bVerbose the tables are printed
* to .xvg files
*/
-
-bondedtable_t make_bonded_table(FILE *fplog,char *fn,int angle);
+
+bondedtable_t make_bonded_table(FILE *fplog, char *fn, int angle);
/* Return a table for bonded interactions,
* angle should be: bonds 0, angles 1, dihedrals 2
*/
/* Return a table for GB calculations */
-t_forcetable make_gb_table(FILE *out,const output_env_t oenv,
- const t_forcerec *fr,
- const char *fn,
- real rtab);
+t_forcetable make_gb_table(FILE *out, const output_env_t oenv,
+ const t_forcerec *fr,
+ const char *fn,
+ real rtab);
/* Read a table for AdResS Thermo Force calculations */
-extern t_forcetable make_atf_table(FILE *out,const output_env_t oenv,
- const t_forcerec *fr,
- const char *fn,
- matrix box);
+extern t_forcetable make_atf_table(FILE *out, const output_env_t oenv,
+ const t_forcerec *fr,
+ const char *fn,
+ matrix box);
-void pr_forcerec(FILE *fplog,t_forcerec *fr,t_commrec *cr);
+void pr_forcerec(FILE *fplog, t_forcerec *fr, t_commrec *cr);
void
forcerec_set_ranges(t_forcerec *fr,
- int ncg_home,int ncg_force,
- int natoms_force,
- int natoms_force_constr,int natoms_f_novirsum);
+ int ncg_home, int ncg_force,
+ int natoms_force,
+ int natoms_force_constr, int natoms_f_novirsum);
/* Set the number of cg's and atoms for the force calculation */
gmx_bool can_use_allvsall(const t_inputrec *ir, const gmx_mtop_t *mtop,
- gmx_bool bPrintNote,t_commrec *cr,FILE *fp);
+ gmx_bool bPrintNote, t_commrec *cr, FILE *fp);
/* Returns if we can use all-vs-all loops.
* If bPrintNote==TRUE, prints a note, if necessary, to stderr
* and fp (if !=NULL) on the master node.
*/
-gmx_bool uses_simple_tables(int cutoff_scheme,
+gmx_bool uses_simple_tables(int cutoff_scheme,
nonbonded_verlet_t *nbv,
- int group);
+ int group);
/* Returns whether simple tables (i.e. not for use with GPUs) are used
* with the type of kernel indicated.
*/
-void init_interaction_const_tables(FILE *fp,
+void init_interaction_const_tables(FILE *fp,
interaction_const_t *ic,
- gmx_bool bSimpleTable,
- real rtab);
+ gmx_bool bSimpleTable,
+ real rtab);
/* Initializes the tables in the interaction constant data structure.
* Setting verlet_kernel_type to -1 always initializes tables for
* use with group kernels.
*/
-void init_interaction_const(FILE *fp,
+void init_interaction_const(FILE *fp,
interaction_const_t **interaction_const,
- const t_forcerec *fr,
- real rtab);
-/* Initializes the interaction constant data structure. Currently it
- * uses forcerec as input.
+ const t_forcerec *fr,
+ real rtab);
+/* Initializes the interaction constant data structure. Currently it
+ * uses forcerec as input.
*/
-void init_forcerec(FILE *fplog,
- const output_env_t oenv,
- t_forcerec *fr,
- t_fcdata *fcd,
- const t_inputrec *ir,
- const gmx_mtop_t *mtop,
- const t_commrec *cr,
- matrix box,
- gmx_bool bMolEpot,
- const char *tabfn,
- const char *tabafn,
- const char *tabpfn,
- const char *tabbfn,
- const char *nbpu_opt,
- gmx_bool bNoSolvOpt,
- real print_force);
-/* The Force rec struct must be created with mk_forcerec
+void init_forcerec(FILE *fplog,
+ const output_env_t oenv,
+ t_forcerec *fr,
+ t_fcdata *fcd,
+ const t_inputrec *ir,
+ const gmx_mtop_t *mtop,
+ const t_commrec *cr,
+ matrix box,
+ gmx_bool bMolEpot,
+ const char *tabfn,
+ const char *tabafn,
+ const char *tabpfn,
+ const char *tabbfn,
+ const char *nbpu_opt,
+ gmx_bool bNoSolvOpt,
+ real print_force);
+/* The Force rec struct must be created with mk_forcerec
* The gmx_booleans have the following meaning:
* bSetQ: Copy the charges [ only necessary when they change ]
* bMolEpot: Use the free energy stuff per molecule
*/
void forcerec_set_excl_load(t_forcerec *fr,
- const gmx_localtop_t *top,const t_commrec *cr);
- /* Set the exclusion load for the local exclusions and possibly threads */
+ const gmx_localtop_t *top, const t_commrec *cr);
+/* Set the exclusion load for the local exclusions and possibly threads */
-void init_enerdata(int ngener,int n_lambda,gmx_enerdata_t *enerd);
+void init_enerdata(int ngener, int n_lambda, gmx_enerdata_t *enerd);
/* Intializes the energy storage struct */
void destroy_enerdata(gmx_enerdata_t *enerd);
/* Resets only the foreign energy data */
void reset_enerdata(t_grpopts *opts,
- t_forcerec *fr,gmx_bool bNS,
- gmx_enerdata_t *enerd,
- gmx_bool bMaster);
+ t_forcerec *fr, gmx_bool bNS,
+ gmx_enerdata_t *enerd,
+ gmx_bool bMaster);
/* Resets the energy data, if bNS=TRUE also zeros the long-range part */
void sum_epot(t_grpopts *opts, gmx_grppairener_t *grpp, real *epot);
/* Locally sum the non-bonded potential energy terms */
-void sum_dhdl(gmx_enerdata_t *enerd,real *lambda,t_lambda *fepvals);
+void sum_dhdl(gmx_enerdata_t *enerd, real *lambda, t_lambda *fepvals);
/* Sum the free energy contributions */
-void update_forcerec(FILE *fplog,t_forcerec *fr,matrix box);
+void update_forcerec(FILE *fplog, t_forcerec *fr, matrix box);
/* Updates parameters in the forcerec that are time dependent */
/* Compute the average C6 and C12 params for LJ corrections */
-void set_avcsixtwelve(FILE *fplog,t_forcerec *fr,
- const gmx_mtop_t *mtop);
-
-extern void do_force(FILE *log,t_commrec *cr,
- t_inputrec *inputrec,
- gmx_large_int_t step,t_nrnb *nrnb,gmx_wallcycle_t wcycle,
- gmx_localtop_t *top,
- gmx_mtop_t *mtop,
- gmx_groups_t *groups,
- matrix box,rvec x[],history_t *hist,
- rvec f[],
- tensor vir_force,
- t_mdatoms *mdatoms,
- gmx_enerdata_t *enerd,t_fcdata *fcd,
- real *lambda,t_graph *graph,
- t_forcerec *fr,
- gmx_vsite_t *vsite,rvec mu_tot,
- double t,FILE *field,gmx_edsam_t ed,
- gmx_bool bBornRadii,
- int flags);
+void set_avcsixtwelve(FILE *fplog, t_forcerec *fr,
+ const gmx_mtop_t *mtop);
+
+extern void do_force(FILE *log, t_commrec *cr,
+ t_inputrec *inputrec,
+ gmx_large_int_t step, t_nrnb *nrnb, gmx_wallcycle_t wcycle,
+ gmx_localtop_t *top,
+ gmx_mtop_t *mtop,
+ gmx_groups_t *groups,
+ matrix box, rvec x[], history_t *hist,
+ rvec f[],
+ tensor vir_force,
+ t_mdatoms *mdatoms,
+ gmx_enerdata_t *enerd, t_fcdata *fcd,
+ real *lambda, t_graph *graph,
+ t_forcerec *fr,
+ gmx_vsite_t *vsite, rvec mu_tot,
+ double t, FILE *field, gmx_edsam_t ed,
+ gmx_bool bBornRadii,
+ int flags);
/* Communicate coordinates (if parallel).
* Do neighbor searching (if necessary).
* f is always required.
*/
-void ns(FILE *fplog,
- t_forcerec *fr,
- rvec x[],
- matrix box,
- gmx_groups_t *groups,
- t_grpopts *opts,
- gmx_localtop_t *top,
- t_mdatoms *md,
- t_commrec *cr,
- t_nrnb *nrnb,
- real *lambda,
- real *dvdlambda,
- gmx_grppairener_t *grppener,
- gmx_bool bFillGrid,
- gmx_bool bDoLongRangeNS);
+void ns(FILE *fplog,
+ t_forcerec *fr,
+ rvec x[],
+ matrix box,
+ gmx_groups_t *groups,
+ t_grpopts *opts,
+ gmx_localtop_t *top,
+ t_mdatoms *md,
+ t_commrec *cr,
+ t_nrnb *nrnb,
+ real *lambda,
+ real *dvdlambda,
+ gmx_grppairener_t *grppener,
+ gmx_bool bFillGrid,
+ gmx_bool bDoLongRangeNS);
/* Call the neighborsearcher */
-extern void do_force_lowlevel(FILE *fplog,
- gmx_large_int_t step,
- t_forcerec *fr,
- t_inputrec *ir,
- t_idef *idef,
- t_commrec *cr,
- t_nrnb *nrnb,
- gmx_wallcycle_t wcycle,
- t_mdatoms *md,
- t_grpopts *opts,
- rvec x[],
- history_t *hist,
- rvec f_shortrange[],
- rvec f_longrange[],
- gmx_enerdata_t *enerd,
- t_fcdata *fcd,
- gmx_mtop_t *mtop,
- gmx_localtop_t *top,
- gmx_genborn_t *born,
- t_atomtypes *atype,
- gmx_bool bBornRadii,
- matrix box,
- t_lambda *fepvals,
- real *lambda,
- t_graph *graph,
- t_blocka *excl,
- rvec mu_tot[2],
- int flags,
- float *cycles_pme);
+extern void do_force_lowlevel(FILE *fplog,
+ gmx_large_int_t step,
+ t_forcerec *fr,
+ t_inputrec *ir,
+ t_idef *idef,
+ t_commrec *cr,
+ t_nrnb *nrnb,
+ gmx_wallcycle_t wcycle,
+ t_mdatoms *md,
+ t_grpopts *opts,
+ rvec x[],
+ history_t *hist,
+ rvec f_shortrange[],
+ rvec f_longrange[],
+ gmx_enerdata_t *enerd,
+ t_fcdata *fcd,
+ gmx_mtop_t *mtop,
+ gmx_localtop_t *top,
+ gmx_genborn_t *born,
+ t_atomtypes *atype,
+ gmx_bool bBornRadii,
+ matrix box,
+ t_lambda *fepvals,
+ real *lambda,
+ t_graph *graph,
+ t_blocka *excl,
+ rvec mu_tot[2],
+ int flags,
+ float *cycles_pme);
/* Call all the force routines */
#ifdef __cplusplus
}
#endif
-#endif /* _force_h */
+#endif /* _force_h */
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff