#include "simple.h"
+#include "enums.h"
#include "../sysstuff.h"
#ifdef __cplusplus
} t_adress;
typedef struct {
- 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. tpbconv) */
- 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 */
+ 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. tpbconv) */
+ 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 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 */
- 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 */
- gmx_bool bOptFFT; /* optimize the fft plan at start */
- 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 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 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 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 */
+ gmx_bool bOptFFT; /* optimize the fft plan at start */
+ 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 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;
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff