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/*
*
* 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.
* 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
* 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:
* GRoups of Organic Molecules in ACtion for Science
*/
#ifndef _inputrec_h_
#define _inputrec_h_
#include "simple.h"
#include "../sysstuff.h"
#ifdef __cplusplus
extern "C" {
#endif
typedef struct {
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) */
} 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;
} t_grpopts;
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) */
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;
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 */
} t_pull;
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; /* fequency of energy calc. and T/P coupl. upd. */
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 */
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 */
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. */
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 */
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 */
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 interpolation no/yes */
double init_lambda; /* initial value for perturbation variable */
double delta_lambda; /* change of lambda per time step (1/dt) */
int n_flambda; /* The number of foreign lambda points */
double *flambda; /* The foreign lambda values */
real sc_alpha; /* free energy soft-core parameter */
int sc_power; /* lambda power for soft-core interactions */
real sc_sigma; /* free energy soft-core sigma when c6 or c12=0 */
real sc_sigma_min; /* minimum FE sc sigma (default: =sg_sigma) */
int nstdhdl; /* The frequency for writing to dhdl.xvg */
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 size for the dH histogram */
double dh_hist_spacing; /* The spacing for the dH histogram */
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 */
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 */
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.*/
} 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 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 IR_TWINRANGE(ir) ((ir).rlist > 0 && ((ir).rlistlong == 0 || (ir).rlistlong > (ir).rlist))
#define IR_ELEC_FIELD(ir) ((ir).ex[XX].n > 0 || (ir).ex[YY].n > 0 || (ir).ex[ZZ].n > 0)
#define IR_EXCL_FORCES(ir) (EEL_FULL((ir).coulombtype) || (EEL_RF((ir).coulombtype) && (ir).coulombtype != eelRF_NEC) || (ir).implicit_solvent != eisNO)
/* use pointer definitions of ir here, since that's what's usually used in the code */
#define IR_NVT_TROTTER(ir) ((((ir)->eI == eiVV) || ((ir)->eI == eiVVAK)) && ((ir)->etc == etcNOSEHOOVER))
#define IR_NPT_TROTTER(ir) ((((ir)->eI == eiVV) || ((ir)->eI == eiVVAK)) && ((ir)->epc == epcMTTK))
#ifdef __cplusplus
}
#endif
#endif
|
