/*
- *
- * 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,
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+ * 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.
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* To help us fund GROMACS development, we humbly ask that you cite
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*/
#ifndef _inputrec_h_
#define _inputrec_h_
+#include <stdio.h>
-#include "simple.h"
-#include "../sysstuff.h"
+#include "gromacs/legacyheaders/types/enums.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/swap/enums.h"
#ifdef __cplusplus
extern "C" {
typedef struct {
- int n; /* Number of terms */
- real *a; /* Coeffients (V / nm ) */
- real *phi; /* Phase angles */
+ int n; /* Number of terms */
+ real *a; /* Coeffients (V / nm ) */
+ real *phi; /* Phase angles */
} t_cosines;
typedef struct {
- real E0; /* Field strength (V/nm) */
- real omega; /* Frequency (1/ps) */
- real t0; /* Centre of the Gaussian pulse (ps) */
- real sigma; /* Width of the Gaussian pulse (FWHM) (ps) */
+ real E0; /* Field strength (V/nm) */
+ real omega; /* Frequency (1/ps) */
+ real t0; /* Centre of the Gaussian pulse (ps) */
+ real sigma; /* Width of the Gaussian pulse (FWHM) (ps) */
} t_efield;
#define EGP_EXCL (1<<0)
#define EGP_TABLE (1<<1)
typedef struct {
- int ngtc; /* # T-Coupl groups */
- int nhchainlength; /* # of nose-hoover chains per group */
- int ngacc; /* # Accelerate groups */
- int ngfrz; /* # Freeze groups */
- int ngener; /* # Ener groups */
- real *nrdf; /* Nr of degrees of freedom in a group */
- real *ref_t; /* Coupling temperature per group */
- int *annealing; /* No/simple/periodic SA for each group */
- int *anneal_npoints; /* Number of annealing time points per grp */
- real **anneal_time; /* For ea. group: Time points */
- real **anneal_temp; /* For ea. grp: Temperature at these times */
- /* Final temp after all intervals is ref_t */
- real *tau_t; /* Tau coupling time */
- rvec *acc; /* Acceleration per group */
- ivec *nFreeze; /* Freeze the group in each direction ? */
- int *egp_flags; /* Exclusions/tables of energy group pairs */
-
- /* QMMM stuff */
- int ngQM; /* nr of QM groups */
- int *QMmethod; /* Level of theory in the QM calculation */
- int *QMbasis; /* Basisset in the QM calculation */
- int *QMcharge; /* Total charge in the QM region */
- int *QMmult; /* Spin multiplicicty in the QM region */
- gmx_bool *bSH; /* surface hopping (diabatic hop only) */
- int *CASorbitals; /* number of orbiatls in the active space */
- int *CASelectrons;/* number of electrons in the active space */
- real *SAon; /* at which gap (A.U.) the SA is switched on */
- real *SAoff;
- int *SAsteps; /* in how many steps SA goes from 1-1 to 0.5-0.5*/
- gmx_bool *bOPT;
- gmx_bool *bTS;
+ int ngtc; /* # T-Coupl groups */
+ int nhchainlength; /* # of nose-hoover chains per group */
+ int ngacc; /* # Accelerate groups */
+ int ngfrz; /* # Freeze groups */
+ int ngener; /* # Ener groups */
+ real *nrdf; /* Nr of degrees of freedom in a group */
+ real *ref_t; /* Coupling temperature per group */
+ int *annealing; /* No/simple/periodic SA for each group */
+ int *anneal_npoints; /* Number of annealing time points per grp */
+ real **anneal_time; /* For ea. group: Time points */
+ real **anneal_temp; /* For ea. grp: Temperature at these times */
+ /* Final temp after all intervals is ref_t */
+ real *tau_t; /* Tau coupling time */
+ rvec *acc; /* Acceleration per group */
+ ivec *nFreeze; /* Freeze the group in each direction ? */
+ int *egp_flags; /* Exclusions/tables of energy group pairs */
+
+ /* QMMM stuff */
+ int ngQM; /* nr of QM groups */
+ int *QMmethod; /* Level of theory in the QM calculation */
+ int *QMbasis; /* Basisset in the QM calculation */
+ int *QMcharge; /* Total charge in the QM region */
+ int *QMmult; /* Spin multiplicicty in the QM region */
+ gmx_bool *bSH; /* surface hopping (diabatic hop only) */
+ int *CASorbitals; /* number of orbiatls in the active space */
+ int *CASelectrons; /* number of electrons in the active space */
+ real *SAon; /* at which gap (A.U.) the SA is switched on */
+ real *SAoff;
+ int *SAsteps; /* in how many steps SA goes from 1-1 to 0.5-0.5*/
+ gmx_bool *bOPT;
+ gmx_bool *bTS;
} t_grpopts;
-enum { epgrppbcNONE, epgrppbcREFAT, epgrppbcCOS };
+enum {
+ epgrppbcNONE, epgrppbcREFAT, epgrppbcCOS
+};
+
+typedef struct {
+ int nat; /* Number of atoms in the pull group */
+ atom_id *ind; /* The global atoms numbers */
+ int nat_loc; /* Number of local pull atoms */
+ int nalloc_loc; /* Allocation size for ind_loc and weight_loc */
+ atom_id *ind_loc; /* Local pull indices */
+ int nweight; /* The number of weights (0 or nat) */
+ real *weight; /* Weights (use all 1 when weight==NULL) */
+ real *weight_loc; /* Weights for the local indices */
+ int epgrppbc; /* The type of pbc for this pull group, see enum above */
+ atom_id pbcatom; /* The reference atom for pbc (global number) */
+
+ /* Variables not present in mdp, but used at run time */
+ real wscale; /* scaling factor for the weights: sum w m/sum w w m */
+ real invtm; /* inverse total mass of the group: 1/wscale sum w m */
+ dvec x; /* center of mass before update */
+ dvec xp; /* center of mass after update before constraining */
+} t_pull_group;
typedef struct {
- int nat; /* Number of atoms in the pull group */
- atom_id *ind; /* The global atoms numbers */
- int nat_loc; /* Number of local pull atoms */
- int nalloc_loc; /* Allocation size for ind_loc and weight_loc */
- atom_id *ind_loc; /* Local pull indices */
- int nweight; /* The number of weights (0 or nat) */
- real *weight; /* Weights (use all 1 when weight==NULL) */
- real *weight_loc; /* Weights for the local indices */
- int epgrppbc; /* The type of pbc for this pull group, see enum above */
- atom_id pbcatom; /* The reference atom for pbc (global number) */
- rvec vec; /* The pull vector, direction or position */
- rvec init; /* Initial reference displacement */
- real rate; /* Rate of motion (nm/ps) */
- real k; /* force constant */
- real kB; /* force constant for state B */
- real wscale; /* scaling factor for the weights: sum w m/sum w w m */
- real invtm; /* inverse total mass of the group: 1/wscale sum w m */
- dvec x; /* center of mass before update */
- dvec xp; /* center of mass after update before constraining */
- dvec dr; /* The distance from the reference group */
- double f_scal; /* Scalar force for directional pulling */
- dvec f; /* force due to the pulling/constraining */
-} t_pullgrp;
+ int group[2]; /* The pull groups, index in group in t_pull */
+ rvec origin; /* The origin for the absolute reference */
+ rvec vec; /* The pull vector, direction or position */
+ real init; /* Initial reference displacement */
+ real rate; /* Rate of motion (nm/ps) */
+ real k; /* force constant */
+ real kB; /* force constant for state B */
+
+ /* Variables not present in mdp, but used at run time */
+ dvec dr; /* The distance from the reference group */
+ double f_scal; /* Scalar force for directional pulling */
+ dvec f; /* force due to the pulling/constraining */
+} t_pull_coord;
typedef struct {
- int eSimTempScale; /* simulated temperature scaling; linear or exponential */
- real simtemp_low; /* the low temperature for simulated tempering */
- real simtemp_high; /* the high temperature for simulated tempering */
- real *temperatures; /* the range of temperatures used for simulated tempering */
+ int eSimTempScale; /* simulated temperature scaling; linear or exponential */
+ real simtemp_low; /* the low temperature for simulated tempering */
+ real simtemp_high; /* the high temperature for simulated tempering */
+ real *temperatures; /* the range of temperatures used for simulated tempering */
} t_simtemp;
typedef struct {
- int nstdhdl; /* The frequency for calculating dhdl */
- double init_lambda; /* fractional value of lambda (usually will use init_fep_state, this will only be for slow growth, and for legacy free energy code) */
- int init_fep_state; /* the initial number of the state */
- double delta_lambda; /* change of lambda per time step (fraction of (0.1) */
- gmx_bool bPrintEnergy; /* Whether to print the energy in the dhdl */
- int n_lambda; /* The number of foreign lambda points */
- double **all_lambda; /* The array of all lambda values */
- real sc_alpha; /* free energy soft-core parameter */
- int sc_power; /* lambda power for soft-core interactions */
- real sc_r_power; /* r power for soft-core interactions */
- real sc_sigma; /* free energy soft-core sigma when c6 or c12=0 */
- real sc_sigma_min; /* free energy soft-core sigma for ????? */
- gmx_bool bScCoul; /* use softcore for the coulomb portion as well (default FALSE) */
- gmx_bool separate_dvdl[efptNR]; /* whether to print the dvdl term associated with
- this term; if it is not specified as separate,
- it is lumped with the FEP term */
- int separate_dhdl_file; /* whether to write a separate dhdl.xvg file
- note: NOT a gmx_bool, but an enum */
- int dhdl_derivatives; /* whether to calculate+write dhdl derivatives
- note: NOT a gmx_bool, but an enum */
- int dh_hist_size; /* The maximum table size for the dH histogram */
- double dh_hist_spacing; /* The spacing for the dH histogram */
+ int nstdhdl; /* The frequency for calculating dhdl */
+ double init_lambda; /* fractional value of lambda (usually will use
+ init_fep_state, this will only be for slow growth,
+ and for legacy free energy code. Only has a
+ valid value if positive) */
+ int init_fep_state; /* the initial number of the state */
+ double delta_lambda; /* change of lambda per time step (fraction of (0.1) */
+ int edHdLPrintEnergy; /* print no, total or potential energies in dhdl */
+ int n_lambda; /* The number of foreign lambda points */
+ double **all_lambda; /* The array of all lambda values */
+ int lambda_neighbors; /* The number of neighboring lambda states to
+ calculate the energy for in up and down directions
+ (-1 for all) */
+ int lambda_start_n; /* The first lambda to calculate energies for */
+ int lambda_stop_n; /* The last lambda +1 to calculate energies for */
+ real sc_alpha; /* free energy soft-core parameter */
+ int sc_power; /* lambda power for soft-core interactions */
+ real sc_r_power; /* r power for soft-core interactions */
+ real sc_sigma; /* free energy soft-core sigma when c6 or c12=0 */
+ real sc_sigma_min; /* free energy soft-core sigma for ????? */
+ gmx_bool bScCoul; /* use softcore for the coulomb portion as well (default FALSE) */
+ gmx_bool separate_dvdl[efptNR]; /* whether to print the dvdl term associated with
+ this term; if it is not specified as separate,
+ it is lumped with the FEP term */
+ int separate_dhdl_file; /* whether to write a separate dhdl.xvg file
+ note: NOT a gmx_bool, but an enum */
+ int dhdl_derivatives; /* whether to calculate+write dhdl derivatives
+ note: NOT a gmx_bool, but an enum */
+ int dh_hist_size; /* The maximum table size for the dH histogram */
+ double dh_hist_spacing; /* The spacing for the dH histogram */
} t_lambda;
typedef struct {
- int nstexpanded; /* The frequency of expanded ensemble state changes */
- int elamstats; /* which type of move updating do we use for lambda monte carlo (or no for none) */
- int elmcmove; /* what move set will be we using for state space moves */
- int elmceq; /* the method we use to decide of we have equilibrated the weights */
- int equil_n_at_lam; /* the minumum number of samples at each lambda for deciding whether we have reached a minimum */
- real equil_wl_delta; /* WL delta at which we stop equilibrating weights */
- real equil_ratio; /* use the ratio of weights (ratio of minimum to maximum) to decide when to stop equilibrating */
- int equil_steps; /* after equil_steps steps we stop equilibrating the weights */
- int equil_samples; /* after equil_samples total samples (steps/nstfep), we stop equilibrating the weights */
- int lmc_seed; /* random number seed for lambda mc switches */
- gmx_bool minvar; /* whether to use minumum variance weighting */
- int minvarmin; /* the number of samples needed before kicking into minvar routine */
- real minvar_const; /* the offset for the variance in MinVar */
- int c_range; /* range of cvalues used for BAR */
- gmx_bool bSymmetrizedTMatrix; /* whether to print symmetrized matrices */
- int nstTij; /* How frequently to print the transition matrices */
- int lmc_repeats; /* number of repetitions in the MC lambda jumps */ /*MRS -- VERIFY THIS */
- int lmc_forced_nstart; /* minimum number of samples for each state before free sampling */ /* MRS -- VERIFY THIS! */
- int gibbsdeltalam; /* distance in lambda space for the gibbs interval */
- real wl_scale; /* scaling factor for wang-landau */
- real wl_ratio; /* ratio between largest and smallest number for freezing the weights */
- real init_wl_delta; /* starting delta for wang-landau */
- gmx_bool bWLoneovert; /* use one over t convergece for wang-landau when the delta get sufficiently small */
- gmx_bool bInit_weights; /* did we initialize the weights? */
- real mc_temp; /* To override the main temperature, or define it if it's not defined */
- real *init_lambda_weights; /* user-specified initial weights to start with */
+ int nstexpanded; /* The frequency of expanded ensemble state changes */
+ int elamstats; /* which type of move updating do we use for lambda monte carlo (or no for none) */
+ int elmcmove; /* what move set will be we using for state space moves */
+ int elmceq; /* the method we use to decide of we have equilibrated the weights */
+ int equil_n_at_lam; /* the minumum number of samples at each lambda for deciding whether we have reached a minimum */
+ real equil_wl_delta; /* WL delta at which we stop equilibrating weights */
+ real equil_ratio; /* use the ratio of weights (ratio of minimum to maximum) to decide when to stop equilibrating */
+ int equil_steps; /* after equil_steps steps we stop equilibrating the weights */
+ int equil_samples; /* after equil_samples total samples (steps/nstfep), we stop equilibrating the weights */
+ int lmc_seed; /* random number seed for lambda mc switches */
+ gmx_bool minvar; /* whether to use minumum variance weighting */
+ int minvarmin; /* the number of samples needed before kicking into minvar routine */
+ real minvar_const; /* the offset for the variance in MinVar */
+ int c_range; /* range of cvalues used for BAR */
+ gmx_bool bSymmetrizedTMatrix; /* whether to print symmetrized matrices */
+ int nstTij; /* How frequently to print the transition matrices */
+ int lmc_repeats; /* number of repetitions in the MC lambda jumps */ /*MRS -- VERIFY THIS */
+ int lmc_forced_nstart; /* minimum number of samples for each state before free sampling */ /* MRS -- VERIFY THIS! */
+ int gibbsdeltalam; /* distance in lambda space for the gibbs interval */
+ real wl_scale; /* scaling factor for wang-landau */
+ real wl_ratio; /* ratio between largest and smallest number for freezing the weights */
+ real init_wl_delta; /* starting delta for wang-landau */
+ gmx_bool bWLoneovert; /* use one over t convergece for wang-landau when the delta get sufficiently small */
+ gmx_bool bInit_weights; /* did we initialize the weights? TODO: REMOVE FOR 5.0, no longer needed with new logic */
+ real mc_temp; /* To override the main temperature, or define it if it's not defined */
+ real *init_lambda_weights; /* user-specified initial weights to start with */
} t_expanded;
typedef struct {
- int ngrp; /* number of groups */
- int eGeom; /* pull geometry */
- ivec dim; /* used to select components for constraint */
- real cyl_r1; /* radius of cylinder for dynamic COM */
- real cyl_r0; /* radius of cylinder including switch length */
- real constr_tol; /* absolute tolerance for constraints in (nm) */
- int nstxout; /* Output frequency for pull x */
- int nstfout; /* Output frequency for pull f */
- int ePBC; /* the boundary conditions */
- int npbcdim; /* do pbc in dims 0 <= dim < npbcdim */
- gmx_bool bRefAt; /* do we need reference atoms for a group COM ? */
- int cosdim; /* dimension for cosine weighting, -1 if none */
- gmx_bool bVirial; /* do we need to add the pull virial? */
- t_pullgrp *grp; /* groups to pull/restrain/etc/ */
- t_pullgrp *dyna; /* dynamic groups for use with local constraints */
- rvec *rbuf; /* COM calculation buffer */
- dvec *dbuf; /* COM calculation buffer */
- double *dbuf_cyl; /* cylinder ref. groups COM calculation buffer */
-
- FILE *out_x; /* output file for pull data */
- FILE *out_f; /* output file for pull data */
+ int ngroup; /* number of pull groups */
+ int ncoord; /* number of pull coordinates */
+ int eGeom; /* pull geometry */
+ ivec dim; /* used to select components for constraint */
+ real cyl_r1; /* radius of cylinder for dynamic COM */
+ real cyl_r0; /* radius of cylinder including switch length */
+ real constr_tol; /* absolute tolerance for constraints in (nm) */
+ gmx_bool bPrintRef; /* Print coordinates of the first group in each coord */
+ int nstxout; /* Output frequency for pull x */
+ int nstfout; /* Output frequency for pull f */
+ int ePBC; /* the boundary conditions */
+ int npbcdim; /* do pbc in dims 0 <= dim < npbcdim */
+ gmx_bool bRefAt; /* do we need reference atoms for a group COM ? */
+ int cosdim; /* dimension for cosine weighting, -1 if none */
+ gmx_bool bVirial; /* do we need to add the pull virial? */
+ t_pull_group *group; /* groups to pull/restrain/etc/ */
+ t_pull_coord *coord; /* the pull coordinates */
+
+ /* Variables not present in mdp, but used at run time */
+ t_pull_group *dyna; /* dynamic groups for use with local constraints */
+ gmx_bool bSetPBCatoms; /* Do we need to set x_pbc for the groups? */
+
+ rvec *rbuf; /* COM calculation buffer */
+ dvec *dbuf; /* COM calculation buffer */
+ double *dbuf_cyl; /* cylinder ref. groups COM calculation buffer */
+
+ FILE *out_x; /* output file for pull data */
+ FILE *out_f; /* output file for pull data */
} t_pull;
typedef struct gmx_enfrotgrp *gmx_enfrotgrp_t;
typedef struct {
- int eType; /* Rotation type for this group */
- int bMassW; /* Use mass-weighed positions? */
- int nat; /* Number of atoms in the group */
- atom_id *ind; /* The global atoms numbers */
- rvec *x_ref; /* The reference positions */
- rvec vec; /* The normalized rotation vector */
- real rate; /* Rate of rotation (degree/ps) */
- real k; /* Force constant (kJ/(mol nm^2) */
- rvec pivot; /* Pivot point of rotation axis (nm) */
- int eFittype; /* Type of fit to determine actual group angle */
- int PotAngle_nstep; /* Number of angles around the reference angle
- for which the rotation potential is also
- evaluated (for fit type 'potential' only) */
- real PotAngle_step; /* Distance between two angles in degrees (for
- fit type 'potential' only) */
- real slab_dist; /* Slab distance (nm) */
- real min_gaussian; /* Minimum value the gaussian must have so that
- the force is actually evaluated */
- real eps; /* Additive constant for radial motion2 and
- flexible2 potentials (nm^2) */
- gmx_enfrotgrp_t enfrotgrp; /* Stores non-inputrec rotation data per group */
+ int eType; /* Rotation type for this group */
+ int bMassW; /* Use mass-weighed positions? */
+ int nat; /* Number of atoms in the group */
+ atom_id *ind; /* The global atoms numbers */
+ rvec *x_ref; /* The reference positions */
+ rvec vec; /* The normalized rotation vector */
+ real rate; /* Rate of rotation (degree/ps) */
+ real k; /* Force constant (kJ/(mol nm^2) */
+ rvec pivot; /* Pivot point of rotation axis (nm) */
+ int eFittype; /* Type of fit to determine actual group angle */
+ int PotAngle_nstep; /* Number of angles around the reference angle
+ for which the rotation potential is also
+ evaluated (for fit type 'potential' only) */
+ real PotAngle_step; /* Distance between two angles in degrees (for
+ fit type 'potential' only) */
+ real slab_dist; /* Slab distance (nm) */
+ real min_gaussian; /* Minimum value the gaussian must have so that
+ the force is actually evaluated */
+ real eps; /* Additive constant for radial motion2 and
+ flexible2 potentials (nm^2) */
+ gmx_enfrotgrp_t enfrotgrp; /* Stores non-inputrec rotation data per group */
} t_rotgrp;
typedef struct {
- int ngrp; /* Number of rotation groups */
- int nstrout; /* Output frequency for main rotation outfile */
- int nstsout; /* Output frequency for per-slab data */
- t_rotgrp *grp; /* Groups to rotate */
- gmx_enfrot_t enfrot; /* Stores non-inputrec enforced rotation data */
+ int ngrp; /* Number of rotation groups */
+ int nstrout; /* Output frequency for main rotation outfile */
+ int nstsout; /* Output frequency for per-slab data */
+ t_rotgrp *grp; /* Groups to rotate */
+ gmx_enfrot_t enfrot; /* Stores non-inputrec enforced rotation data */
} t_rot;
+/* Abstract type for IMD only defined in IMD.c */
+typedef struct gmx_IMD *t_gmx_IMD;
+
+typedef struct {
+ int nat; /* Number of interactive atoms */
+ atom_id *ind; /* The global indices of the interactive atoms */
+ t_gmx_IMD setup; /* Stores non-inputrec IMD data */
+} t_IMD;
+
+/* Abstract types for position swapping only defined in swapcoords.c */
+typedef struct swap *gmx_swapcoords_t;
+
+typedef struct {
+ int nstswap; /* Every how many steps a swap is attempted? */
+ int nat; /* Number of atoms in the ion group */
+ int nat_split[2]; /* Number of atoms in the split group */
+ int nat_sol; /* Number of atoms in the solvent group */
+ atom_id *ind; /* The global ion group atoms numbers */
+ atom_id *ind_split[2]; /* Split groups for compartment partitioning */
+ atom_id *ind_sol; /* The global solvent group atom numbers */
+ gmx_bool massw_split[2]; /* Use mass-weighted positions in split group? */
+ real cyl0r, cyl1r; /* Split cylinders defined by radius, upper and */
+ real cyl0u, cyl1u; /* ... lower extension. The split cylinders de- */
+ real cyl0l, cyl1l; /* ... fine the channels and are each anchored */
+ /* ... in the center of the split group */
+ int nanions[eCompNR]; /* Requested number of anions and */
+ int nAverage; /* Coupling constant (nr of swap attempt steps) */
+ real threshold; /* Ion counts may deviate from the requested
+ values by +-threshold before a swap is done */
+ int ncations[eCompNR]; /* ... cations for both compartments */
+ gmx_swapcoords_t si_priv; /* swap private data accessible in
+ * swapcoords.c */
+} t_swapcoords;
+
typedef struct {
- int type; /* type of AdResS simulation */
- gmx_bool bnew_wf; /* enable new AdResS weighting function */
- gmx_bool bchempot_dx; /*true:interaction table format input is F=-dmu/dx false: dmu_dwp */
- gmx_bool btf_full_box; /* true: appy therm force everywhere in the box according to table false: only in hybrid region */
- real const_wf; /* value of weighting function for eAdressConst */
- real ex_width; /* center of the explicit zone */
- real hy_width; /* width of the hybrid zone */
- int icor; /* type of interface correction */
- int site; /* AdResS CG site location */
- rvec refs; /* Coordinates for AdResS reference */
- real ex_forcecap; /* in the hybrid zone, cap forces large then this to adress_ex_forcecap */
- gmx_bool do_hybridpairs; /* If true pair interaction forces are also scaled in an adress way*/
-
- int * tf_table_index; /* contains mapping of energy group index -> i-th adress tf table*/
- int n_tf_grps;
- int *group_explicit;
- int n_energy_grps;
+ int type; /* type of AdResS simulation */
+ gmx_bool bnew_wf; /* enable new AdResS weighting function */
+ gmx_bool bchempot_dx; /*true:interaction table format input is F=-dmu/dx false: dmu_dwp */
+ gmx_bool btf_full_box; /* true: appy therm force everywhere in the box according to table false: only in hybrid region */
+ real const_wf; /* value of weighting function for eAdressConst */
+ real ex_width; /* center of the explicit zone */
+ real hy_width; /* width of the hybrid zone */
+ int icor; /* type of interface correction */
+ int site; /* AdResS CG site location */
+ rvec refs; /* Coordinates for AdResS reference */
+ real ex_forcecap; /* in the hybrid zone, cap forces large then this to adress_ex_forcecap */
+ gmx_bool do_hybridpairs; /* If true pair interaction forces are also scaled in an adress way*/
+
+ int * tf_table_index; /* contains mapping of energy group index -> i-th adress tf table*/
+ int n_tf_grps;
+ int *group_explicit;
+ int n_energy_grps;
} t_adress;
typedef struct {
- int eI; /* Integration method */
- gmx_large_int_t nsteps; /* number of steps to be taken */
- int simulation_part; /* Used in checkpointing to separate chunks */
- gmx_large_int_t init_step; /* start at a stepcount >0 (used w. tpbconv) */
- int nstcalcenergy; /* frequency of energy calc. and T/P coupl. upd. */
- int cutoff_scheme; /* cut-off scheme: group or verlet */
- int ns_type; /* which ns method should we use? */
- int nstlist; /* number of steps before pairlist is generated */
- int ndelta; /* number of cells per rlong */
- int nstcomm; /* number of steps after which center of mass */
- /* motion is removed */
- int comm_mode; /* Center of mass motion removal algorithm */
- int nstcheckpoint; /* checkpointing frequency */
- int nstlog; /* number of steps after which print to logfile */
- int nstxout; /* number of steps after which X is output */
- int nstvout; /* id. for V */
- int nstfout; /* id. for F */
- int nstenergy; /* number of steps after which energies printed */
- int nstxtcout; /* id. for compressed trj (.xtc) */
- double init_t; /* initial time (ps) */
- double delta_t; /* time step (ps) */
- real xtcprec; /* precision of xtc file */
- real fourier_spacing; /* requested fourier_spacing, when nk? not set */
- int nkx,nky,nkz; /* number of k vectors in each spatial dimension*/
- /* for fourier methods for long range electrost.*/
- int pme_order; /* interpolation order for PME */
- real ewald_rtol; /* Real space tolerance for Ewald, determines */
- /* the real/reciprocal space relative weight */
- int ewald_geometry; /* normal/3d ewald, or pseudo-2d LR corrections */
- real epsilon_surface; /* Epsilon for PME dipole correction */
- gmx_bool bOptFFT; /* optimize the fft plan at start */
- int ePBC; /* Type of periodic boundary conditions */
- int bPeriodicMols; /* Periodic molecules */
- gmx_bool bContinuation; /* Continuation run: starting state is correct */
- int etc; /* temperature coupling */
- int nsttcouple; /* interval in steps for temperature coupling */
- gmx_bool bPrintNHChains; /* whether to print nose-hoover chains */
- int epc; /* pressure coupling */
- int epct; /* pressure coupling type */
- int nstpcouple; /* interval in steps for pressure coupling */
- real tau_p; /* pressure coupling time (ps) */
- tensor ref_p; /* reference pressure (kJ/(mol nm^3)) */
- tensor compress; /* compressability ((mol nm^3)/kJ) */
- int refcoord_scaling;/* How to scale absolute reference coordinates */
- rvec posres_com; /* The COM of the posres atoms */
- rvec posres_comB; /* The B-state COM of the posres atoms */
- int andersen_seed; /* Random seed for Andersen thermostat (obsolete) */
- real verletbuf_drift; /* Max. drift (kJ/mol/ps/atom) for list buffer */
- real rlist; /* short range pairlist cut-off (nm) */
- real rlistlong; /* long range pairlist cut-off (nm) */
- real rtpi; /* Radius for test particle insertion */
- int coulombtype; /* Type of electrostatics treatment */
- int coulomb_modifier; /* Modify the Coulomb interaction */
- real rcoulomb_switch; /* Coulomb switch range start (nm) */
- real rcoulomb; /* Coulomb cutoff (nm) */
- real epsilon_r; /* relative dielectric constant */
- real epsilon_rf; /* relative dielectric constant of the RF */
- int implicit_solvent;/* No (=explicit water), or GBSA solvent models */
- int gb_algorithm; /* Algorithm to use for calculation Born radii */
- int nstgbradii; /* Frequency of updating Generalized Born radii */
- real rgbradii; /* Cutoff for GB radii calculation */
- real gb_saltconc; /* Salt concentration (M) for GBSA models */
- real gb_epsilon_solvent; /* dielectric coeff. of implicit solvent */
- real gb_obc_alpha; /* 1st scaling factor for Bashford-Case GB */
- real gb_obc_beta; /* 2nd scaling factor for Bashford-Case GB */
- real gb_obc_gamma; /* 3rd scaling factor for Bashford-Case GB */
- real gb_dielectric_offset; /* Dielectric offset for Still/HCT/OBC */
- int sa_algorithm; /* Algorithm for SA part of GBSA */
- real sa_surface_tension; /* Energy factor for SA part of GBSA */
- int vdwtype; /* Type of Van der Waals treatment */
- int vdw_modifier; /* Modify the VdW interaction */
- real rvdw_switch; /* Van der Waals switch range start (nm) */
- real rvdw; /* Van der Waals cutoff (nm) */
- int eDispCorr; /* Perform Long range dispersion corrections */
- real tabext; /* Extension of the table beyond the cut-off, *
- * as well as the table length for 1-4 interac. */
- real shake_tol; /* tolerance for shake */
- int efep; /* free energy calculations */
- t_lambda *fepvals; /* Data for the FEP state */
- gmx_bool bSimTemp; /* Whether to do simulated tempering */
- t_simtemp *simtempvals;/* Variables for simulated tempering */
- gmx_bool bExpanded; /* Whether expanded ensembles are used */
- t_expanded *expandedvals; /* Expanded ensemble parameters */
- int eDisre; /* Type of distance restraining */
- real dr_fc; /* force constant for ta_disre */
- int eDisreWeighting; /* type of weighting of pairs in one restraints */
- gmx_bool bDisreMixed; /* Use comb of time averaged and instan. viol's */
- int nstdisreout; /* frequency of writing pair distances to enx */
- real dr_tau; /* time constant for memory function in disres */
- real orires_fc; /* force constant for orientational restraints */
- real orires_tau; /* time constant for memory function in orires */
- int nstorireout; /* frequency of writing tr(SD) to enx */
- real dihre_fc; /* force constant for dihedral restraints (obsolete) */
- real em_stepsize; /* The stepsize for updating */
- real em_tol; /* The tolerance */
- int niter; /* Number of iterations for convergence of */
- /* steepest descent in relax_shells */
- real fc_stepsize; /* Stepsize for directional minimization */
- /* in relax_shells */
- int nstcgsteep; /* number of steps after which a steepest */
- /* descents step is done while doing cg */
- int nbfgscorr; /* Number of corrections to the hessian to keep */
- int eConstrAlg; /* Type of constraint algorithm */
- int nProjOrder; /* Order of the LINCS Projection Algorithm */
- real LincsWarnAngle; /* If bond rotates more than %g degrees, warn */
- int nLincsIter; /* Number of iterations in the final Lincs step */
- gmx_bool bShakeSOR; /* Use successive overrelaxation for shake */
- real bd_fric; /* Friction coefficient for BD (amu/ps) */
- int ld_seed; /* Random seed for SD and BD */
- int nwall; /* The number of walls */
- int wall_type; /* The type of walls */
- real wall_r_linpot; /* The potentail is linear for r<=wall_r_linpot */
- int wall_atomtype[2];/* The atom type for walls */
- real wall_density[2]; /* Number density for walls */
- real wall_ewald_zfac; /* Scaling factor for the box for Ewald */
- int ePull; /* Type of pulling: no, umbrella or constraint */
- t_pull *pull; /* The data for center of mass pulling */
- gmx_bool bRot; /* Calculate enforced rotation potential(s)? */
- t_rot *rot; /* The data for enforced rotation potentials */
- real cos_accel; /* Acceleration for viscosity calculation */
- tensor deform; /* Triclinic deformation velocities (nm/ps) */
- int userint1; /* User determined parameters */
- int userint2;
- int userint3;
- int userint4;
- real userreal1;
- real userreal2;
- real userreal3;
- real userreal4;
- t_grpopts opts; /* Group options */
- t_cosines ex[DIM]; /* Electric field stuff (spatial part) */
- t_cosines et[DIM]; /* Electric field stuff (time part) */
- gmx_bool bQMMM; /* QM/MM calculation */
- int QMconstraints; /* constraints on QM bonds */
- int QMMMscheme; /* Scheme: ONIOM or normal */
- real scalefactor; /* factor for scaling the MM charges in QM calc.*/
- /* parameter needed for AdResS simulation */
- gmx_bool bAdress; /* Is AdResS enabled ? */
- t_adress *adress; /* The data for adress simulations */
+ int eI; /* Integration method */
+ gmx_int64_t nsteps; /* number of steps to be taken */
+ int simulation_part; /* Used in checkpointing to separate chunks */
+ gmx_int64_t init_step; /* start at a stepcount >0 (used w. convert-tpr) */
+ int nstcalcenergy; /* frequency of energy calc. and T/P coupl. upd. */
+ int cutoff_scheme; /* group or verlet cutoffs */
+ int ns_type; /* which ns method should we use? */
+ int nstlist; /* number of steps before pairlist is generated */
+ int ndelta; /* number of cells per rlong */
+ int nstcomm; /* number of steps after which center of mass */
+ /* motion is removed */
+ int comm_mode; /* Center of mass motion removal algorithm */
+ int nstlog; /* number of steps after which print to logfile */
+ int nstxout; /* number of steps after which X is output */
+ int nstvout; /* id. for V */
+ int nstfout; /* id. for F */
+ int nstenergy; /* number of steps after which energies printed */
+ int nstxout_compressed; /* id. for compressed trj (.xtc,.tng) */
+ double init_t; /* initial time (ps) */
+ double delta_t; /* time step (ps) */
+ real x_compression_precision; /* precision of x in compressed trajectory file */
+ real fourier_spacing; /* requested fourier_spacing, when nk? not set */
+ int nkx, nky, nkz; /* number of k vectors in each spatial dimension*/
+ /* for fourier methods for long range electrost.*/
+ int pme_order; /* interpolation order for PME */
+ real ewald_rtol; /* Real space tolerance for Ewald, determines */
+ /* the real/reciprocal space relative weight */
+ real ewald_rtol_lj; /* Real space tolerance for LJ-Ewald */
+ int ewald_geometry; /* normal/3d ewald, or pseudo-2d LR corrections */
+ real epsilon_surface; /* Epsilon for PME dipole correction */
+ int ljpme_combination_rule; /* Type of combination rule in LJ-PME */
+ int ePBC; /* Type of periodic boundary conditions */
+ int bPeriodicMols; /* Periodic molecules */
+ gmx_bool bContinuation; /* Continuation run: starting state is correct */
+ int etc; /* temperature coupling */
+ int nsttcouple; /* interval in steps for temperature coupling */
+ gmx_bool bPrintNHChains; /* whether to print nose-hoover chains */
+ int epc; /* pressure coupling */
+ int epct; /* pressure coupling type */
+ int nstpcouple; /* interval in steps for pressure coupling */
+ real tau_p; /* pressure coupling time (ps) */
+ tensor ref_p; /* reference pressure (kJ/(mol nm^3)) */
+ tensor compress; /* compressability ((mol nm^3)/kJ) */
+ int refcoord_scaling; /* How to scale absolute reference coordinates */
+ rvec posres_com; /* The COM of the posres atoms */
+ rvec posres_comB; /* The B-state COM of the posres atoms */
+ int andersen_seed; /* Random seed for Andersen thermostat (obsolete) */
+ real verletbuf_tol; /* Per atom pair energy drift tolerance (kJ/mol/ps/atom) for list buffer */
+ real rlist; /* short range pairlist cut-off (nm) */
+ real rlistlong; /* long range pairlist cut-off (nm) */
+ int nstcalclr; /* Frequency of evaluating direct space long-range interactions */
+ real rtpi; /* Radius for test particle insertion */
+ int coulombtype; /* Type of electrostatics treatment */
+ int coulomb_modifier; /* Modify the Coulomb interaction */
+ real rcoulomb_switch; /* Coulomb switch range start (nm) */
+ real rcoulomb; /* Coulomb cutoff (nm) */
+ real epsilon_r; /* relative dielectric constant */
+ real epsilon_rf; /* relative dielectric constant of the RF */
+ int implicit_solvent; /* No (=explicit water), or GBSA solvent models */
+ int gb_algorithm; /* Algorithm to use for calculation Born radii */
+ int nstgbradii; /* Frequency of updating Generalized Born radii */
+ real rgbradii; /* Cutoff for GB radii calculation */
+ real gb_saltconc; /* Salt concentration (M) for GBSA models */
+ real gb_epsilon_solvent; /* dielectric coeff. of implicit solvent */
+ real gb_obc_alpha; /* 1st scaling factor for Bashford-Case GB */
+ real gb_obc_beta; /* 2nd scaling factor for Bashford-Case GB */
+ real gb_obc_gamma; /* 3rd scaling factor for Bashford-Case GB */
+ real gb_dielectric_offset; /* Dielectric offset for Still/HCT/OBC */
+ int sa_algorithm; /* Algorithm for SA part of GBSA */
+ real sa_surface_tension; /* Energy factor for SA part of GBSA */
+ int vdwtype; /* Type of Van der Waals treatment */
+ int vdw_modifier; /* Modify the VdW interaction */
+ real rvdw_switch; /* Van der Waals switch range start (nm) */
+ real rvdw; /* Van der Waals cutoff (nm) */
+ int eDispCorr; /* Perform Long range dispersion corrections */
+ real tabext; /* Extension of the table beyond the cut-off, *
+ * as well as the table length for 1-4 interac. */
+ real shake_tol; /* tolerance for shake */
+ int efep; /* free energy calculations */
+ t_lambda *fepvals; /* Data for the FEP state */
+ gmx_bool bSimTemp; /* Whether to do simulated tempering */
+ t_simtemp *simtempvals; /* Variables for simulated tempering */
+ gmx_bool bExpanded; /* Whether expanded ensembles are used */
+ t_expanded *expandedvals; /* Expanded ensemble parameters */
+ int eDisre; /* Type of distance restraining */
+ real dr_fc; /* force constant for ta_disre */
+ int eDisreWeighting; /* type of weighting of pairs in one restraints */
+ gmx_bool bDisreMixed; /* Use comb of time averaged and instan. viol's */
+ int nstdisreout; /* frequency of writing pair distances to enx */
+ real dr_tau; /* time constant for memory function in disres */
+ real orires_fc; /* force constant for orientational restraints */
+ real orires_tau; /* time constant for memory function in orires */
+ int nstorireout; /* frequency of writing tr(SD) to enx */
+ real em_stepsize; /* The stepsize for updating */
+ real em_tol; /* The tolerance */
+ int niter; /* Number of iterations for convergence of */
+ /* steepest descent in relax_shells */
+ real fc_stepsize; /* Stepsize for directional minimization */
+ /* in relax_shells */
+ int nstcgsteep; /* number of steps after which a steepest */
+ /* descents step is done while doing cg */
+ int nbfgscorr; /* Number of corrections to the hessian to keep */
+ int eConstrAlg; /* Type of constraint algorithm */
+ int nProjOrder; /* Order of the LINCS Projection Algorithm */
+ real LincsWarnAngle; /* If bond rotates more than %g degrees, warn */
+ int nLincsIter; /* Number of iterations in the final Lincs step */
+ gmx_bool bShakeSOR; /* Use successive overrelaxation for shake */
+ real bd_fric; /* Friction coefficient for BD (amu/ps) */
+ gmx_int64_t ld_seed; /* Random seed for SD and BD */
+ int nwall; /* The number of walls */
+ int wall_type; /* The type of walls */
+ real wall_r_linpot; /* The potentail is linear for r<=wall_r_linpot */
+ int wall_atomtype[2]; /* The atom type for walls */
+ real wall_density[2]; /* Number density for walls */
+ real wall_ewald_zfac; /* Scaling factor for the box for Ewald */
+ int ePull; /* Type of pulling: no, umbrella or constraint */
+ t_pull *pull; /* The data for center of mass pulling */
+ gmx_bool bRot; /* Calculate enforced rotation potential(s)? */
+ t_rot *rot; /* The data for enforced rotation potentials */
+ int eSwapCoords; /* Do ion/water position exchanges (CompEL)? */
+ t_swapcoords *swap;
+ gmx_bool bIMD; /* Allow interactive MD sessions for this .tpr? */
+ t_IMD *imd; /* Interactive molecular dynamics */
+ real cos_accel; /* Acceleration for viscosity calculation */
+ tensor deform; /* Triclinic deformation velocities (nm/ps) */
+ int userint1; /* User determined parameters */
+ int userint2;
+ int userint3;
+ int userint4;
+ real userreal1;
+ real userreal2;
+ real userreal3;
+ real userreal4;
+ t_grpopts opts; /* Group options */
+ t_cosines ex[DIM]; /* Electric field stuff (spatial part) */
+ t_cosines et[DIM]; /* Electric field stuff (time part) */
+ gmx_bool bQMMM; /* QM/MM calculation */
+ int QMconstraints; /* constraints on QM bonds */
+ int QMMMscheme; /* Scheme: ONIOM or normal */
+ real scalefactor; /* factor for scaling the MM charges in QM calc.*/
+ /* parameter needed for AdResS simulation */
+ gmx_bool bAdress; /* Is AdResS enabled ? */
+ t_adress *adress; /* The data for adress simulations */
} t_inputrec;
-#define DEFORM(ir) ((ir).deform[XX][XX]!=0 || (ir).deform[YY][YY]!=0 || (ir).deform[ZZ][ZZ]!=0 || (ir).deform[YY][XX]!=0 || (ir).deform[ZZ][XX]!=0 || (ir).deform[ZZ][YY]!=0)
+#define DEFORM(ir) ((ir).deform[XX][XX] != 0 || (ir).deform[YY][YY] != 0 || (ir).deform[ZZ][ZZ] != 0 || (ir).deform[YY][XX] != 0 || (ir).deform[ZZ][XX] != 0 || (ir).deform[ZZ][YY] != 0)
-#define DYNAMIC_BOX(ir) ((ir).epc!=epcNO || (ir).eI==eiTPI || DEFORM(ir))
+#define DYNAMIC_BOX(ir) ((ir).epc != epcNO || (ir).eI == eiTPI || DEFORM(ir))
#define PRESERVE_SHAPE(ir) ((ir).epc != epcNO && (ir).deform[XX][XX] == 0 && ((ir).epct == epctISOTROPIC || (ir).epct == epctSEMIISOTROPIC))
-#define NEED_MUTOT(ir) (((ir).coulombtype==eelEWALD || EEL_PME((ir).coulombtype)) && ((ir).ewald_geometry==eewg3DC || (ir).epsilon_surface!=0))
+#define NEED_MUTOT(ir) (((ir).coulombtype == eelEWALD || EEL_PME((ir).coulombtype)) && ((ir).ewald_geometry == eewg3DC || (ir).epsilon_surface != 0))
#define IR_TWINRANGE(ir) ((ir).rlist > 0 && ((ir).rlistlong == 0 || (ir).rlistlong > (ir).rlist))
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff