/*
- *
- * 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.
+ * This file is part of the GROMACS molecular simulation package.
+ *
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team,
- * check out http://www.gromacs.org for more information.
-
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
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+ * in the README & COPYING files - if they are missing, get the
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+ *
* 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.
- *
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+ * the research papers on the package. Check out http://www.gromacs.org.
*/
-#include "ns.h"
-#include "genborn.h"
-#include "qmmmrec.h"
-#include "idef.h"
-#include "nb_verlet.h"
-#include "interaction_const.h"
-#include "hw_info.h"
+#ifndef GMX_LEGACYHEADERS_TYPES_FORCEREC_H
+#define GMX_LEGACYHEADERS_TYPES_FORCEREC_H
+
+#include "gromacs/legacyheaders/types/enums.h"
+#include "gromacs/legacyheaders/types/genborn.h"
+#include "gromacs/legacyheaders/types/hw_info.h"
+#include "gromacs/legacyheaders/types/interaction_const.h"
+#include "gromacs/legacyheaders/types/ns.h"
+#include "gromacs/legacyheaders/types/qmmmrec.h"
+#include "gromacs/topology/idef.h"
#ifdef __cplusplus
extern "C" {
/* Abstract type for PME that is defined only in the routine that use them. */
typedef struct gmx_pme *gmx_pme_t;
-
-
+struct nonbonded_verlet_t;
/* Structure describing the data in a single table */
typedef struct
enum gmx_table_interaction interaction; /* Types of interactions stored in this table */
enum gmx_table_format format; /* Interpolation type and data format */
- real r; /* range of the table */
- int n; /* n+1 is the number of table points */
- real scale; /* distance (nm) between two table points */
- real scale_exp; /* distance for exponential part of VdW table, not always used */
- real * data; /* the actual table data */
+ real r; /* range of the table */
+ int n; /* n+1 is the number of table points */
+ real scale; /* distance (nm) between two table points */
+ real scale_exp; /* distance for exponential part of VdW table, not always used */
+ real * data; /* the actual table data */
/* Some information about the table layout. This can also be derived from the interpolation
* type and the table interactions, but it is convenient to have here for sanity checks, and it makes it
t_nblist nlist_lr[eNL_NR];
} t_nblists;
-/* macros for the cginfo data in forcerec */
-/* The maximum cg size in cginfo is 63
+/* macros for the cginfo data in forcerec
+ *
+ * Since the tpx format support max 256 energy groups, we do the same here.
+ * Note that we thus have bits 8-14 still unused.
+ *
+ * The maximum cg size in cginfo is 63
* because we only have space for 6 bits in cginfo,
* this cg size entry is actually only read with domain decomposition.
* But there is a smaller limit due to the t_excl data structure
* which is defined in nblist.h.
*/
-#define SET_CGINFO_GID(cgi,gid) (cgi) = (((cgi) & ~65535) | (gid) )
-#define GET_CGINFO_GID(cgi) ( (cgi) & 65535)
+#define SET_CGINFO_GID(cgi, gid) (cgi) = (((cgi) & ~255) | (gid))
+#define GET_CGINFO_GID(cgi) ( (cgi) & 255)
+#define SET_CGINFO_FEP(cgi) (cgi) = ((cgi) | (1<<15))
+#define GET_CGINFO_FEP(cgi) ( (cgi) & (1<<15))
#define SET_CGINFO_EXCL_INTRA(cgi) (cgi) = ((cgi) | (1<<16))
#define GET_CGINFO_EXCL_INTRA(cgi) ( (cgi) & (1<<16))
#define SET_CGINFO_EXCL_INTER(cgi) (cgi) = ((cgi) | (1<<17))
#define GET_CGINFO_EXCL_INTER(cgi) ( (cgi) & (1<<17))
-#define SET_CGINFO_SOLOPT(cgi,opt) (cgi) = (((cgi) & ~(3<<18)) | ((opt)<<18))
+#define SET_CGINFO_SOLOPT(cgi, opt) (cgi) = (((cgi) & ~(3<<18)) | ((opt)<<18))
#define GET_CGINFO_SOLOPT(cgi) (((cgi)>>18) & 3)
#define SET_CGINFO_CONSTR(cgi) (cgi) = ((cgi) | (1<<20))
#define GET_CGINFO_CONSTR(cgi) ( (cgi) & (1<<20))
#define GET_CGINFO_HAS_VDW(cgi) ( (cgi) & (1<<23))
#define SET_CGINFO_HAS_Q(cgi) (cgi) = ((cgi) | (1<<24))
#define GET_CGINFO_HAS_Q(cgi) ( (cgi) & (1<<24))
-#define SET_CGINFO_NATOMS(cgi,opt) (cgi) = (((cgi) & ~(63<<25)) | ((opt)<<25))
+#define SET_CGINFO_NATOMS(cgi, opt) (cgi) = (((cgi) & ~(63<<25)) | ((opt)<<25))
#define GET_CGINFO_NATOMS(cgi) (((cgi)>>25) & 63)
#define GMX_CUTOFF_INF 1E+18
/* enums for the neighborlist type */
-enum { enbvdwNONE,enbvdwLJ,enbvdwBHAM,enbvdwTAB,enbvdwNR};
+enum {
+ enbvdwNONE, enbvdwLJ, enbvdwBHAM, enbvdwTAB, enbvdwNR
+};
/* OOR is "one over r" -- standard coul */
-enum { enbcoulNONE,enbcoulOOR,enbcoulRF,enbcoulTAB,enbcoulGB,enbcoulFEWALD,enbcoulNR};
+enum {
+ enbcoulNONE, enbcoulOOR, enbcoulRF, enbcoulTAB, enbcoulGB, enbcoulFEWALD, enbcoulNR
+};
-enum { egCOULSR, egLJSR, egBHAMSR, egCOULLR, egLJLR, egBHAMLR,
- egCOUL14, egLJ14, egGB, egNR };
+enum {
+ egCOULSR, egLJSR, egBHAMSR, egCOULLR, egLJLR, egBHAMLR,
+ egCOUL14, egLJ14, egGB, egNR
+};
typedef struct {
- int nener; /* The number of energy group pairs */
- real *ener[egNR]; /* Energy terms for each pair of groups */
+ int nener; /* The number of energy group pairs */
+ real *ener[egNR]; /* Energy terms for each pair of groups */
} gmx_grppairener_t;
typedef struct {
- real term[F_NRE]; /* The energies for all different interaction types */
- gmx_grppairener_t grpp;
- double dvdl_lin[efptNR]; /* Contributions to dvdl with linear lam-dependence */
- double dvdl_nonlin[efptNR]; /* Idem, but non-linear dependence */
- int n_lambda;
- int fep_state; /*current fep state -- just for printing */
- double *enerpart_lambda; /* Partial energy for lambda and flambda[] */
+ real term[F_NRE]; /* The energies for all different interaction types */
+ gmx_grppairener_t grpp;
+ double dvdl_lin[efptNR]; /* Contributions to dvdl with linear lam-dependence */
+ double dvdl_nonlin[efptNR]; /* Idem, but non-linear dependence */
+ int n_lambda;
+ int fep_state; /*current fep state -- just for printing */
+ double *enerpart_lambda; /* Partial energy for lambda and flambda[] */
+ real foreign_term[F_NRE]; /* alternate array for storing foreign lambda energies */
+ gmx_grppairener_t foreign_grpp; /* alternate array for storing foreign lambda energies */
} gmx_enerdata_t;
/* The idea is that dvdl terms with linear lambda dependence will be added
* automatically to enerpart_lambda. Terms with non-linear lambda dependence
*/
typedef struct {
- int cg_start;
- int cg_end;
- int cg_mod;
- int *cginfo;
+ int cg_start;
+ int cg_end;
+ int cg_mod;
+ int *cginfo;
} cginfo_mb_t;
/* ewald table type */
-typedef struct ewald_tab *ewald_tab_t;
+typedef struct ewald_tab *ewald_tab_t;
typedef struct {
- rvec *f;
- int f_nalloc;
- unsigned red_mask; /* Mask for marking which parts of f are filled */
- rvec *fshift;
- real ener[F_NRE];
+ rvec *f;
+ int f_nalloc;
+ unsigned red_mask; /* Mask for marking which parts of f are filled */
+ rvec *fshift;
+ real ener[F_NRE];
gmx_grppairener_t grpp;
- real Vcorr;
- real dvdl[efptNR];
- tensor vir;
+ real Vcorr_q;
+ real Vcorr_lj;
+ real dvdl[efptNR];
+ tensor vir_q;
+ tensor vir_lj;
} f_thread_t;
typedef struct {
- interaction_const_t *ic;
-
- /* Domain Decomposition */
- gmx_bool bDomDec;
-
- /* PBC stuff */
- int ePBC;
- gmx_bool bMolPBC;
- int rc_scaling;
- rvec posres_com;
- rvec posres_comB;
-
- gmx_hw_info_t *hwinfo;
- gmx_bool use_cpu_acceleration;
-
- /* Interaction for calculated in kernels. In many cases this is similar to
- * the electrostatics settings in the inputrecord, but the difference is that
- * these variables always specify the actual interaction in the kernel - if
- * we are tabulating reaction-field the inputrec will say reaction-field, but
- * the kernel interaction will say cubic-spline-table. To be safe we also
- * have a kernel-specific setting for the modifiers - if the interaction is
- * tabulated we already included the inputrec modification there, so the kernel
- * modification setting will say 'none' in that case.
- */
- int nbkernel_elec_interaction;
- int nbkernel_vdw_interaction;
- int nbkernel_elec_modifier;
- int nbkernel_vdw_modifier;
-
- /* Use special N*N kernels? */
- gmx_bool bAllvsAll;
- /* Private work data */
- void *AllvsAll_work;
- void *AllvsAll_workgb;
-
- /* Cut-Off stuff.
- * Infinite cut-off's will be GMX_CUTOFF_INF (unlike in t_inputrec: 0).
- */
- real rlist,rlistlong;
-
- /* Dielectric constant resp. multiplication factor for charges */
- real zsquare,temp;
- real epsilon_r,epsilon_rf,epsfac;
-
- /* Constants for reaction fields */
- real kappa,k_rf,c_rf;
-
- /* Charge sum and dipole for topology A/B ([0]/[1]) for Ewald corrections */
- double qsum[2];
- double q2sum[2];
- rvec mu_tot[2];
-
- /* Dispersion correction stuff */
- int eDispCorr;
-
- /* The shift of the shift or user potentials */
- real enershiftsix;
- real enershifttwelve;
- /* Integrated differces for energy and virial with cut-off functions */
- real enerdiffsix;
- real enerdifftwelve;
- real virdiffsix;
- real virdifftwelve;
- /* Constant for long range dispersion correction (average dispersion)
- * for topology A/B ([0]/[1]) */
- real avcsix[2];
- /* Constant for long range repulsion term. Relative difference of about
- * 0.1 percent with 0.8 nm cutoffs. But hey, it's cheap anyway...
- */
- real avctwelve[2];
-
- /* Fudge factors */
- real fudgeQQ;
-
- /* Table stuff */
- gmx_bool bcoultab;
- gmx_bool bvdwtab;
- /* The normal tables are in the nblists struct(s) below */
- t_forcetable tab14; /* for 1-4 interactions only */
-
- /* PPPM & Shifting stuff */
- int coulomb_modifier;
- real rcoulomb_switch,rcoulomb;
- real *phi;
-
- /* VdW stuff */
- int vdw_modifier;
- double reppow;
- real rvdw_switch,rvdw;
- real bham_b_max;
-
- /* Free energy */
- int efep;
- real sc_alphavdw;
- real sc_alphacoul;
- int sc_power;
- real sc_r_power;
- real sc_sigma6_def;
- real sc_sigma6_min;
- gmx_bool bSepDVDL;
-
- /* NS Stuff */
- int eeltype;
- int vdwtype;
- int cg0,hcg;
- /* solvent_opt contains the enum for the most common solvent
- * in the system, which will be optimized.
- * It can be set to esolNO to disable all water optimization */
- int solvent_opt;
- int nWatMol;
- gmx_bool bGrid;
- gmx_bool bExcl_IntraCGAll_InterCGNone;
- cginfo_mb_t *cginfo_mb;
- int *cginfo;
- rvec *cg_cm;
- int cg_nalloc;
- rvec *shift_vec;
-
- /* The neighborlists including tables */
- int nnblists;
- int *gid2nblists;
- t_nblists *nblists;
-
- int cutoff_scheme; /* group- or Verlet-style cutoff */
- gmx_bool bNonbonded; /* true if nonbonded calculations are *not* turned off */
- nonbonded_verlet_t *nbv;
-
- /* The wall tables (if used) */
- int nwall;
- t_forcetable **wall_tab;
-
- /* The number of charge groups participating in do_force_lowlevel */
- int ncg_force;
- /* The number of atoms participating in do_force_lowlevel */
- int natoms_force;
- /* The number of atoms participating in force and constraints */
- int natoms_force_constr;
- /* The allocation size of vectors of size natoms_force */
- int nalloc_force;
-
- /* Twin Range stuff, f_twin has size natoms_force */
- gmx_bool bTwinRange;
- int nlr;
- rvec *f_twin;
-
- /* Forces that should not enter into the virial summation:
- * PPPM/PME/Ewald/posres
- */
- gmx_bool bF_NoVirSum;
- int f_novirsum_n;
- int f_novirsum_nalloc;
- rvec *f_novirsum_alloc;
- /* Pointer that points to f_novirsum_alloc when pressure is calcaluted,
- * points to the normal force vectors wen pressure is not requested.
- */
- rvec *f_novirsum;
-
- /* Long-range forces and virial for PPPM/PME/Ewald */
- gmx_pme_t pmedata;
- tensor vir_el_recip;
-
- /* PME/Ewald stuff */
- gmx_bool bEwald;
- real ewaldcoeff;
- ewald_tab_t ewald_table;
-
- /* Virial Stuff */
- rvec *fshift;
- rvec vir_diag_posres;
- dvec vir_wall_z;
-
- /* Non bonded Parameter lists */
- int ntype; /* Number of atom types */
- gmx_bool bBHAM;
- real *nbfp;
-
- /* Energy group pair flags */
- int *egp_flags;
-
- /* xmdrun flexible constraints */
- real fc_stepsize;
-
- /* Generalized born implicit solvent */
- gmx_bool bGB;
- /* Generalized born stuff */
- real gb_epsilon_solvent;
- /* Table data for GB */
- t_forcetable gbtab;
- /* VdW radius for each atomtype (dim is thus ntype) */
- real *atype_radius;
- /* Effective radius (derived from effective volume) for each type */
- real *atype_vol;
- /* Implicit solvent - surface tension for each atomtype */
- real *atype_surftens;
- /* Implicit solvent - radius for GB calculation */
- real *atype_gb_radius;
- /* Implicit solvent - overlap for HCT model */
- real *atype_S_hct;
- /* Generalized born interaction data */
- gmx_genborn_t *born;
-
- /* Table scale for GB */
- real gbtabscale;
- /* Table range for GB */
- real gbtabr;
- /* GB neighborlists (the sr list will contain for each atom all other atoms
- * (for use in the SA calculation) and the lr list will contain
- * for each atom all atoms 1-4 or greater (for use in the GB calculation)
- */
- t_nblist gblist_sr;
- t_nblist gblist_lr;
- t_nblist gblist;
-
- /* Inverse square root of the Born radii for implicit solvent */
- real *invsqrta;
- /* Derivatives of the potential with respect to the Born radii */
- real *dvda;
- /* Derivatives of the Born radii with respect to coordinates */
- real *dadx;
- real *dadx_rawptr;
- int nalloc_dadx; /* Allocated size of dadx */
-
- /* If > 0 signals Test Particle Insertion,
- * the value is the number of atoms of the molecule to insert
- * Only the energy difference due to the addition of the last molecule
- * should be calculated.
- */
- gmx_bool n_tpi;
-
- /* Neighbor searching stuff */
- gmx_ns_t ns;
-
- /* QMMM stuff */
- gmx_bool bQMMM;
- t_QMMMrec *qr;
-
- /* QM-MM neighborlists */
- t_nblist QMMMlist;
-
- /* Limit for printing large forces, negative is don't print */
- real print_force;
-
- /* coarse load balancing time measurement */
- double t_fnbf;
- double t_wait;
- int timesteps;
-
- /* parameter needed for AdResS simulation */
- int adress_type;
- gmx_bool badress_tf_full_box;
- real adress_const_wf;
- real adress_ex_width;
- real adress_hy_width;
- int adress_icor;
- int adress_site;
- rvec adress_refs;
- int n_adress_tf_grps;
- int * adress_tf_table_index;
- int *adress_group_explicit;
- t_forcetable * atf_tabs;
- real adress_ex_forcecap;
- gmx_bool adress_do_hybridpairs;
-
- /* User determined parameters, copied from the inputrec */
- int userint1;
- int userint2;
- int userint3;
- int userint4;
- real userreal1;
- real userreal2;
- real userreal3;
- real userreal4;
-
- /* Thread local force and energy data */
- /* FIXME move to bonded_thread_data_t */
- int nthreads;
- int red_ashift;
- int red_nblock;
- f_thread_t *f_t;
-
- /* Exclusion load distribution over the threads */
- int *excl_load;
+ interaction_const_t *ic;
+
+ /* Domain Decomposition */
+ gmx_bool bDomDec;
+
+ /* PBC stuff */
+ int ePBC;
+ gmx_bool bMolPBC;
+ int rc_scaling;
+ rvec posres_com;
+ rvec posres_comB;
+
+ const gmx_hw_info_t *hwinfo;
+ const gmx_gpu_opt_t *gpu_opt;
+ gmx_bool use_simd_kernels;
+
+ /* Interaction for calculated in kernels. In many cases this is similar to
+ * the electrostatics settings in the inputrecord, but the difference is that
+ * these variables always specify the actual interaction in the kernel - if
+ * we are tabulating reaction-field the inputrec will say reaction-field, but
+ * the kernel interaction will say cubic-spline-table. To be safe we also
+ * have a kernel-specific setting for the modifiers - if the interaction is
+ * tabulated we already included the inputrec modification there, so the kernel
+ * modification setting will say 'none' in that case.
+ */
+ int nbkernel_elec_interaction;
+ int nbkernel_vdw_interaction;
+ int nbkernel_elec_modifier;
+ int nbkernel_vdw_modifier;
+
+ /* Use special N*N kernels? */
+ gmx_bool bAllvsAll;
+ /* Private work data */
+ void *AllvsAll_work;
+ void *AllvsAll_workgb;
+
+ /* Cut-Off stuff.
+ * Infinite cut-off's will be GMX_CUTOFF_INF (unlike in t_inputrec: 0).
+ */
+ real rlist, rlistlong;
+
+ /* Dielectric constant resp. multiplication factor for charges */
+ real zsquare, temp;
+ real epsilon_r, epsilon_rf, epsfac;
+
+ /* Constants for reaction fields */
+ real kappa, k_rf, c_rf;
+
+ /* Charge sum and dipole for topology A/B ([0]/[1]) for Ewald corrections */
+ double qsum[2];
+ double q2sum[2];
+ double c6sum[2];
+ rvec mu_tot[2];
+
+ /* Dispersion correction stuff */
+ int eDispCorr;
+
+ /* The shift of the shift or user potentials */
+ real enershiftsix;
+ real enershifttwelve;
+ /* Integrated differces for energy and virial with cut-off functions */
+ real enerdiffsix;
+ real enerdifftwelve;
+ real virdiffsix;
+ real virdifftwelve;
+ /* Constant for long range dispersion correction (average dispersion)
+ * for topology A/B ([0]/[1]) */
+ real avcsix[2];
+ /* Constant for long range repulsion term. Relative difference of about
+ * 0.1 percent with 0.8 nm cutoffs. But hey, it's cheap anyway...
+ */
+ real avctwelve[2];
+
+ /* Fudge factors */
+ real fudgeQQ;
+
+ /* Table stuff */
+ gmx_bool bcoultab;
+ gmx_bool bvdwtab;
+ /* The normal tables are in the nblists struct(s) below */
+ t_forcetable tab14; /* for 1-4 interactions only */
+
+ /* PPPM & Shifting stuff */
+ int coulomb_modifier;
+ real rcoulomb_switch, rcoulomb;
+ real *phi;
+
+ /* VdW stuff */
+ int vdw_modifier;
+ double reppow;
+ real rvdw_switch, rvdw;
+ real bham_b_max;
+
+ /* Free energy */
+ int efep;
+ real sc_alphavdw;
+ real sc_alphacoul;
+ int sc_power;
+ real sc_r_power;
+ real sc_sigma6_def;
+ real sc_sigma6_min;
+
+ /* NS Stuff */
+ int eeltype;
+ int vdwtype;
+ int cg0, hcg;
+ /* solvent_opt contains the enum for the most common solvent
+ * in the system, which will be optimized.
+ * It can be set to esolNO to disable all water optimization */
+ int solvent_opt;
+ int nWatMol;
+ gmx_bool bGrid;
+ gmx_bool bExcl_IntraCGAll_InterCGNone;
+ cginfo_mb_t *cginfo_mb;
+ int *cginfo;
+ rvec *cg_cm;
+ int cg_nalloc;
+ rvec *shift_vec;
+
+ /* The neighborlists including tables */
+ int nnblists;
+ int *gid2nblists;
+ t_nblists *nblists;
+
+ int cutoff_scheme; /* group- or Verlet-style cutoff */
+ gmx_bool bNonbonded; /* true if nonbonded calculations are *not* turned off */
+ struct nonbonded_verlet_t *nbv;
+
+ /* The wall tables (if used) */
+ int nwall;
+ t_forcetable **wall_tab;
+
+ /* The number of charge groups participating in do_force_lowlevel */
+ int ncg_force;
+ /* The number of atoms participating in do_force_lowlevel */
+ int natoms_force;
+ /* The number of atoms participating in force and constraints */
+ int natoms_force_constr;
+ /* The allocation size of vectors of size natoms_force */
+ int nalloc_force;
+
+ /* Twin Range stuff, f_twin has size natoms_force */
+ gmx_bool bTwinRange;
+ int nlr;
+ rvec *f_twin;
+ /* Constraint virial correction for multiple time stepping */
+ tensor vir_twin_constr;
+
+ /* Forces that should not enter into the virial summation:
+ * PPPM/PME/Ewald/posres
+ */
+ gmx_bool bF_NoVirSum;
+ int f_novirsum_n;
+ int f_novirsum_nalloc;
+ rvec *f_novirsum_alloc;
+ /* Pointer that points to f_novirsum_alloc when pressure is calcaluted,
+ * points to the normal force vectors wen pressure is not requested.
+ */
+ rvec *f_novirsum;
+
+ /* Long-range forces and virial for PPPM/PME/Ewald */
+ gmx_pme_t pmedata;
+ int ljpme_combination_rule;
+ tensor vir_el_recip;
+ tensor vir_lj_recip;
+
+ /* PME/Ewald stuff */
+ gmx_bool bEwald;
+ real ewaldcoeff_q;
+ real ewaldcoeff_lj;
+ ewald_tab_t ewald_table;
+
+ /* Virial Stuff */
+ rvec *fshift;
+ rvec vir_diag_posres;
+ dvec vir_wall_z;
+
+ /* Non bonded Parameter lists */
+ int ntype; /* Number of atom types */
+ gmx_bool bBHAM;
+ real *nbfp;
+ real *ljpme_c6grid; /* C6-values used on grid in LJPME */
+
+ /* Energy group pair flags */
+ int *egp_flags;
+
+ /* Shell molecular dynamics flexible constraints */
+ real fc_stepsize;
+
+ /* Generalized born implicit solvent */
+ gmx_bool bGB;
+ /* Generalized born stuff */
+ real gb_epsilon_solvent;
+ /* Table data for GB */
+ t_forcetable gbtab;
+ /* VdW radius for each atomtype (dim is thus ntype) */
+ real *atype_radius;
+ /* Effective radius (derived from effective volume) for each type */
+ real *atype_vol;
+ /* Implicit solvent - surface tension for each atomtype */
+ real *atype_surftens;
+ /* Implicit solvent - radius for GB calculation */
+ real *atype_gb_radius;
+ /* Implicit solvent - overlap for HCT model */
+ real *atype_S_hct;
+ /* Generalized born interaction data */
+ gmx_genborn_t *born;
+
+ /* Table scale for GB */
+ real gbtabscale;
+ /* Table range for GB */
+ real gbtabr;
+ /* GB neighborlists (the sr list will contain for each atom all other atoms
+ * (for use in the SA calculation) and the lr list will contain
+ * for each atom all atoms 1-4 or greater (for use in the GB calculation)
+ */
+ t_nblist gblist_sr;
+ t_nblist gblist_lr;
+ t_nblist gblist;
+
+ /* Inverse square root of the Born radii for implicit solvent */
+ real *invsqrta;
+ /* Derivatives of the potential with respect to the Born radii */
+ real *dvda;
+ /* Derivatives of the Born radii with respect to coordinates */
+ real *dadx;
+ real *dadx_rawptr;
+ int nalloc_dadx; /* Allocated size of dadx */
+
+ /* If > 0 signals Test Particle Insertion,
+ * the value is the number of atoms of the molecule to insert
+ * Only the energy difference due to the addition of the last molecule
+ * should be calculated.
+ */
+ gmx_bool n_tpi;
+
+ /* Neighbor searching stuff */
+ gmx_ns_t ns;
+
+ /* QMMM stuff */
+ gmx_bool bQMMM;
+ t_QMMMrec *qr;
+
+ /* QM-MM neighborlists */
+ t_nblist QMMMlist;
+
+ /* Limit for printing large forces, negative is don't print */
+ real print_force;
+
+ /* coarse load balancing time measurement */
+ double t_fnbf;
+ double t_wait;
+ int timesteps;
+
+ /* parameter needed for AdResS simulation */
+ int adress_type;
+ gmx_bool badress_tf_full_box;
+ real adress_const_wf;
+ real adress_ex_width;
+ real adress_hy_width;
+ int adress_icor;
+ int adress_site;
+ rvec adress_refs;
+ int n_adress_tf_grps;
+ int * adress_tf_table_index;
+ int *adress_group_explicit;
+ t_forcetable * atf_tabs;
+ real adress_ex_forcecap;
+ gmx_bool adress_do_hybridpairs;
+
+ /* User determined parameters, copied from the inputrec */
+ int userint1;
+ int userint2;
+ int userint3;
+ int userint4;
+ real userreal1;
+ real userreal2;
+ real userreal3;
+ real userreal4;
+
+ /* Thread local force and energy data */
+ /* FIXME move to bonded_thread_data_t */
+ int nthreads;
+ int red_ashift;
+ int red_nblock;
+ f_thread_t *f_t;
+
+ /* Exclusion load distribution over the threads */
+ int *excl_load;
} t_forcerec;
/* Important: Starting with Gromacs-4.6, the values of c6 and c12 in the nbfp array have
* been scaled by 6.0 or 12.0 to save flops in the kernels. We have corrected this everywhere
* in the code, but beware if you are using these macros externally.
*/
-#define C6(nbfp,ntp,ai,aj) (nbfp)[2*((ntp)*(ai)+(aj))]
-#define C12(nbfp,ntp,ai,aj) (nbfp)[2*((ntp)*(ai)+(aj))+1]
-#define BHAMC(nbfp,ntp,ai,aj) (nbfp)[3*((ntp)*(ai)+(aj))]
-#define BHAMA(nbfp,ntp,ai,aj) (nbfp)[3*((ntp)*(ai)+(aj))+1]
-#define BHAMB(nbfp,ntp,ai,aj) (nbfp)[3*((ntp)*(ai)+(aj))+2]
+#define C6(nbfp, ntp, ai, aj) (nbfp)[2*((ntp)*(ai)+(aj))]
+#define C12(nbfp, ntp, ai, aj) (nbfp)[2*((ntp)*(ai)+(aj))+1]
+#define BHAMC(nbfp, ntp, ai, aj) (nbfp)[3*((ntp)*(ai)+(aj))]
+#define BHAMA(nbfp, ntp, ai, aj) (nbfp)[3*((ntp)*(ai)+(aj))+1]
+#define BHAMB(nbfp, ntp, ai, aj) (nbfp)[3*((ntp)*(ai)+(aj))+2]
#ifdef __cplusplus
}
#endif
-
+#endif
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff