/*
- *
+ *
* 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:
* Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
*/
/* This file contains XMDRUN datatypes and function prototypes, grouped
* neatly according to parts of the functionalisty
*/
-
+
/* GENERAL COUPLING THEORY (GCT) STUFF */
-enum { eoPres, eoEpot, eoVir, eoDist, eoMu, eoForce, eoFx, eoFy, eoFz,
- eoPx, eoPy, eoPz,
- eoPolarizability, eoDipole, eoObsNR,
- eoMemory=eoObsNR, eoInter, eoUseVirial, eoCombRule, eoNR };
+enum {
+ eoPres, eoEpot, eoVir, eoDist, eoMu, eoForce, eoFx, eoFy, eoFz,
+ eoPx, eoPy, eoPz,
+ eoPolarizability, eoDipole, eoObsNR,
+ eoMemory = eoObsNR, eoInter, eoUseVirial, eoCombRule, eoNR
+};
extern const char *eoNames[eoNR];
typedef struct {
- int at_i,at_j; /* Atom type # for i and j */
- int eObs; /* Observable to couple to */
- gmx_bool bPrint; /* Does this struct have to be printed */
- real c6,c12; /* Actual value of params */
- real xi_6,xi_12; /* Constants for coupling C6 and C12 */
+ int at_i, at_j; /* Atom type # for i and j */
+ int eObs; /* Observable to couple to */
+ gmx_bool bPrint; /* Does this struct have to be printed */
+ real c6, c12; /* Actual value of params */
+ real xi_6, xi_12; /* Constants for coupling C6 and C12 */
} t_coupl_LJ;
typedef struct {
- int at_i,at_j; /* Atom type # for i and j */
- int eObs; /* Observable to couple to */
- gmx_bool bPrint; /* Does this struct have to be printed */
- real a,b,c; /* Actual value of params */
- real xi_a,xi_b,xi_c; /* Constants for coupling A, B and C */
+ int at_i, at_j; /* Atom type # for i and j */
+ int eObs; /* Observable to couple to */
+ gmx_bool bPrint; /* Does this struct have to be printed */
+ real a, b, c; /* Actual value of params */
+ real xi_a, xi_b, xi_c; /* Constants for coupling A, B and C */
} t_coupl_BU;
typedef struct {
- int at_i; /* Atom type */
- int eObs; /* Observable to couple to */
- gmx_bool bPrint; /* Does this struct have to be printed */
- real Q; /* Actual value of charge */
- real xi_Q; /* Constant for coupling Q */
+ int at_i; /* Atom type */
+ int eObs; /* Observable to couple to */
+ gmx_bool bPrint; /* Does this struct have to be printed */
+ real Q; /* Actual value of charge */
+ real xi_Q; /* Constant for coupling Q */
} t_coupl_Q;
typedef struct {
- int type; /* Type number in the iparams struct */
- int eObs; /* Observable to couple to */
- t_iparams xi; /* Parameters that need to be changed */
- t_iparams iprint;
+ int type; /* Type number in the iparams struct */
+ int eObs; /* Observable to couple to */
+ t_iparams xi; /* Parameters that need to be changed */
+ t_iparams iprint;
} t_coupl_iparams;
typedef struct {
- real act_value[eoObsNR];
- real av_value [eoObsNR];
- real ref_value[eoObsNR];
- gmx_bool bObsUsed[eoObsNR];
- int nLJ,nBU,nQ,nIP;
- t_coupl_LJ *tcLJ;
- t_coupl_BU *tcBU;
- t_coupl_Q *tcQ;
- t_coupl_iparams *tIP;
- int nmemory;
- gmx_bool bInter;
- gmx_bool bVirial;
- int combrule;
+ real act_value[eoObsNR];
+ real av_value [eoObsNR];
+ real ref_value[eoObsNR];
+ gmx_bool bObsUsed[eoObsNR];
+ int nLJ, nBU, nQ, nIP;
+ t_coupl_LJ *tcLJ;
+ t_coupl_BU *tcBU;
+ t_coupl_Q *tcQ;
+ t_coupl_iparams *tIP;
+ int nmemory;
+ gmx_bool bInter;
+ gmx_bool bVirial;
+ int combrule;
} t_coupl_rec;
-extern void write_gct(const char *fn,t_coupl_rec *tcr,t_idef *idef);
+extern void write_gct(const char *fn, t_coupl_rec *tcr, t_idef *idef);
+
+extern void read_gct(const char *fn, t_coupl_rec *tcr);
-extern void read_gct(const char *fn,t_coupl_rec *tcr);
+extern void comm_tcr(FILE *log, t_commrec *cr, t_coupl_rec **tcr);
-extern void comm_tcr(FILE *log,t_commrec *cr,t_coupl_rec **tcr);
+extern void copy_ff(t_coupl_rec *tcr, t_forcerec *fr, t_mdatoms *md,
+ t_idef *idef);
-extern void copy_ff(t_coupl_rec *tcr,t_forcerec *fr,t_mdatoms *md,
- t_idef *idef);
+extern t_coupl_rec *init_coupling(FILE *log, int nfile, const t_filenm fnm[],
+ t_commrec *cr, t_forcerec *fr, t_mdatoms *md,
+ t_idef *idef);
-extern t_coupl_rec *init_coupling(FILE *log,int nfile, const t_filenm fnm[],
- t_commrec *cr,t_forcerec *fr,t_mdatoms *md,
- t_idef *idef);
-
-extern void calc_force(int natom,rvec f[],rvec fff[]);
+extern void calc_force(int natom, rvec f[], rvec fff[]);
-extern void calc_f_dev(int natoms,real charge[],rvec x[],rvec f[],
- t_idef *idef,real *xiH,real *xiS);
+extern void calc_f_dev(int natoms, real charge[], rvec x[], rvec f[],
+ t_idef *idef, real *xiH, real *xiS);
-extern void do_coupling(FILE *log,const output_env_t oenv,int nfile,
+extern void do_coupling(FILE *log, const output_env_t oenv, int nfile,
const t_filenm fnm[],
- t_coupl_rec *tcr,real t,int step,real ener[],
- t_forcerec *fr,t_inputrec *ir,gmx_bool bMaster,
- t_mdatoms *md,t_idef *idef,real mu_aver,int nmols,
- t_commrec *cr,matrix box,tensor virial,
- tensor pres,rvec mu_tot,
- rvec x[],rvec f[],gmx_bool bDoIt);
+ t_coupl_rec *tcr, real t, int step, real ener[],
+ t_forcerec *fr, t_inputrec *ir, gmx_bool bMaster,
+ t_mdatoms *md, t_idef *idef, real mu_aver, int nmols,
+ t_commrec *cr, matrix box, tensor virial,
+ tensor pres, rvec mu_tot,
+ rvec x[], rvec f[], gmx_bool bDoIt);
/* CODE TO ADD SPECIAL 2-DIMENSIONAL LENNARD-JONES CORRECTION TO FORCES AND ENERGY */
-extern void do_glas(FILE *log,int start,int homenr,rvec x[],rvec f[],
- t_forcerec *fr,t_mdatoms *md,int atnr,t_inputrec *ir,
- real ener[]);
+extern void do_glas(FILE *log, int start, int homenr, rvec x[], rvec f[],
+ t_forcerec *fr, t_mdatoms *md, int atnr, t_inputrec *ir,
+ real ener[]);
-extern real mol_dipole(int k0,int k1,rvec x[],real q[]);
+extern real mol_dipole(int k0, int k1, rvec x[], real q[]);
/* Calculate total dipole for group of atoms */
-extern real calc_mu_aver(t_commrec *cr,rvec x[],real q[],rvec mu,
- t_block *mols,t_mdatoms *md,int gnx,atom_id grpindex[]);
+extern real calc_mu_aver(t_commrec *cr, rvec x[], real q[], rvec mu,
+ t_block *mols, t_mdatoms *md, int gnx, atom_id grpindex[]);
/* Compute average dipole */
/********************************************************************/
/* Force field scanning stuff */
typedef struct {
- real tol,f_max,npow,epot,fac_epot,fac_pres,fac_msf,pres;
- int molsize,nmol;
- gmx_bool bComb,bVerbose,bLogEps;
+ real tol, f_max, npow, epot, fac_epot, fac_pres, fac_msf, pres;
+ int molsize, nmol;
+ gmx_bool bComb, bVerbose, bLogEps;
} t_ffscan;
extern gmx_bool update_forcefield(FILE *fplog,
- int nfile,const t_filenm fnm[],t_forcerec *fr,
- int natoms,rvec x[],matrix box);
+ int nfile, const t_filenm fnm[], t_forcerec *fr,
+ int natoms, rvec x[], matrix box);
/* Modify the parameters. Return TRUE when the scan is finished. */
-extern gmx_bool print_forcefield(FILE *fp,real ener[],int natoms,rvec f[],
- rvec fshake[],rvec x[],t_block *mols,real mass[],
- tensor pres);
+extern gmx_bool print_forcefield(FILE *fp, real ener[], int natoms, rvec f[],
+ rvec fshake[], rvec x[], t_block *mols, real mass[],
+ tensor pres);
/* Print results. Return TRUE when the scan is finished. */
extern void set_ffvars(t_ffscan *ff);
/* Set variables for force scanning */
-#endif /* _xmdrun_h */
+#endif /* _xmdrun_h */
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff