Clean up Code
This commit is contained in:
Niels Mueller
@ -30,153 +30,164 @@ cdef extern from "gromacs/mdtypes/inputrec.h":
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pass
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ctypedef struct t_inputrec:
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int eI # Integration method */
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int nsteps # number of steps to be taken */
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int simulation_part # Used in checkpointing to separate chunks */
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int init_step # start at a stepcount >0 (used w. convert-tpr) */
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int nstcalcenergy # frequency of energy calc. and T/P coupl. upd. */
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int cutoff_scheme # group or verlet cutoffs */
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int ns_type # which ns method should we use? */
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int nstlist # number of steps before pairlist is generated */
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int ndelta # number of cells per rlong */
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int nstcomm # number of steps after which center of mass */
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# motion is removed */
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int comm_mode # Center of mass motion removal algorithm */
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int nstlog # number of steps after which print to logfile */
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int nstxout # number of steps after which X is output */
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int nstvout # id. for V */
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int nstfout # id. for F */
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int nstenergy # number of steps after which energies printed */
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int nstxout_compressed # id. for compressed trj (.xtc,.tng) */
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double init_t # initial time (ps) */
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double delta_t # time step (ps) */
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double x_compression_precision # precision of x in compressed trajectory file */
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double fourier_spacing # requested fourier_spacing, when nk? not set */
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int nkx, nky, nkz # number of k vectors in each spatial dimension*/
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# for fourier methods for long range electrost.*/
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int pme_order # interpolation order for PME */
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double ewald_rtol # double space tolerance for Ewald, determines */
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# the double/reciprocal space relative weight */
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double ewald_rtol_lj # double space tolerance for LJ-Ewald */
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int ewald_geometry # normal/3d ewald, or pseudo-2d LR corrections */
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double epsilon_surface # Epsilon for PME dipole correction */
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int ljpme_combination_rule # Type of combination rule in LJ-PME */
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int ePBC # Type of periodic boundary conditions */
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int bPeriodicMols # Periodic molecules */
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bint bContinuation # Continuation run: starting state is correct */
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int etc # temperature coupling */
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int nsttcouple # interval in steps for temperature coupling */
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bint bPrintNHChains # whether to print nose-hoover chains */
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int epc # pressure coupling */
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int epct # pressure coupling type */
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int nstpcouple # interval in steps for pressure coupling */
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double tau_p # pressure coupling time (ps) */
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tensor ref_p # reference pressure (kJ/(mol nm^3)) */
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tensor compress # compressability ((mol nm^3)/kJ) */
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int refcoord_scaling # How to scale absolute reference coordinates */
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rvec posres_com # The COM of the posres atoms */
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rvec posres_comB # The B-state COM of the posres atoms */
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int andersen_seed # Random seed for Andersen thermostat (obsolete) */
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double verletbuf_tol # Per atom pair energy drift tolerance (kJ/mol/ps/atom) for list buffer */
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double rlist # short range pairlist cut-off (nm) */
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double rtpi # Radius for test particle insertion */
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int coulombtype # Type of electrostatics treatment */
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int coulomb_modifier # Modify the Coulomb interaction */
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double rcoulomb_switch # Coulomb switch range start (nm) */
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double rcoulomb # Coulomb cutoff (nm) */
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double epsilon_r # relative dielectric constant */
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double epsilon_rf # relative dielectric constant of the RF */
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int implicit_solvent # No (=explicit water), or GBSA solvent models */
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int gb_algorithm # Algorithm to use for calculation Born radii */
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int nstgbradii # Frequency of updating Generalized Born radii */
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double rgbradii # Cutoff for GB radii calculation */
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double gb_saltconc # Salt concentration (M) for GBSA models */
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double gb_epsilon_solvent # dielectric coeff. of implicit solvent */
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double gb_obc_alpha # 1st scaling factor for Bashford-Case GB */
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double gb_obc_beta # 2nd scaling factor for Bashford-Case GB */
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double gb_obc_gamma # 3rd scaling factor for Bashford-Case GB */
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double gb_dielectric_offset # Dielectric offset for Still/HCT/OBC */
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int sa_algorithm # Algorithm for SA part of GBSA */
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double sa_surface_tension # Energy factor for SA part of GBSA */
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int vdwtype # Type of Van der Waals treatment */
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int vdw_modifier # Modify the VdW interaction */
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double rvdw_switch # Van der Waals switch range start (nm) */
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double rvdw # Van der Waals cutoff (nm) */
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int eDispCorr # Perform Long range dispersion corrections */
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double tabext # Extension of the table beyond the cut-off, *
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# * as well as the table length for 1-4 interac. */
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double shake_tol # tolerance for shake */
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int efep # free energy calculations */
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t_lambda *fepvals # Data for the FEP state */
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bint bSimTemp # Whether to do simulated tempering */
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t_simtemp *simtempvals # Variables for simulated tempering */
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bint bExpanded # Whether expanded ensembles are used */
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t_expanded *expandedvals # Expanded ensemble parameters */
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int eDisre # Type of distance restraining */
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double dr_fc # force constant for ta_disre */
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int eDisreWeighting # type of weighting of pairs in one restraints */
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bint bDisreMixed # Use comb of time averaged and instan. viol's */
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int nstdisreout # frequency of writing pair distances to enx */
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double dr_tau # time constant for memory function in disres */
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double orires_fc # force constant for orientational restraints */
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double orires_tau # time constant for memory function in orires */
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int nstorireout # frequency of writing tr(SD) to enx */
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double em_stepsize # The stepsize for updating */
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double em_tol # The tolerance */
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int niter # Number of iterations for convergence of */
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# steepest descent in relax_shells */
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double fc_stepsize # Stepsize for directional minimization */
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# in relax_shells */
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int nstcgsteep # number of steps after which a steepest */
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# descents step is done while doing cg */
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int nbfgscorr # Number of corrections to the hessian to keep */
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int eConstrAlg # Type of constraint algorithm */
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int nProjOrder # Order of the LINCS Projection Algorithm */
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double LincsWarnAngle # If bond rotates more than %g degrees, warn */
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int nLincsIter # Number of iterations in the final Lincs step */
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bint bShakeSOR # Use successive overrelaxation for shake */
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double bd_fric # Friction coefficient for BD (amu/ps) */
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int ld_seed # Random seed for SD and BD */
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int nwall # The number of walls */
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int wall_type # The type of walls */
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double wall_r_linpot # The potentail is linear for r<=wall_r_linpot */
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int wall_atomtype[2] # The atom type for walls */
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double wall_density[2] # Number density for walls */
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double wall_ewald_zfac # Scaling factor for the box for Ewald */
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# t_inputrec()
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# explicit t_inputrec(const t_inputrec &) = delete
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# t_inputrec &operator=(const t_inputrec &) = delete
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# ~t_inputrec()
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int eI # Integration method */
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gmx_int64_t nsteps # number of steps to be taken */
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int simulation_part # Used in checkpointing to separate chunks */
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gmx_int64_t init_step # start at a stepcount >0 (used w. convert-tpr) */
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int nstcalcenergy # frequency of energy calc. and T/P coupl. upd. */
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int cutoff_scheme # group or verlet cutoffs */
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int ns_type # which ns method should we use? */
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int nstlist # number of steps before pairlist is generated */
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int ndelta # number of cells per rlong */
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int nstcomm # number of steps after which center of mass */
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# motion is removed */
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int comm_mode # Center of mass motion removal algorithm */
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int nstlog # number of steps after which print to logfile */
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int nstxout # number of steps after which X is output */
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int nstvout # id. for V */
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int nstfout # id. for F */
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int nstenergy # number of steps after which energies printed */
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int nstxout_compressed # id. for compressed trj (.xtc,.tng) */
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double init_t # initial time (ps) */
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double delta_t # time step (ps) */
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real x_compression_precision # precision of x in compressed trajectory file */
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real fourier_spacing # requested fourier_spacing, when nk? not set */
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int nkx, nky, nkz # number of k vectors in each spatial dimension*/
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# for fourier methods for long range electrost.*/
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int pme_order # interpolation order for PME */
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real ewald_rtol # Real space tolerance for Ewald, determines */
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# the real/reciprocal space relative weight */
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real ewald_rtol_lj # Real space tolerance for LJ-Ewald */
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int ewald_geometry # normal/3d ewald, or pseudo-2d LR corrections */
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real epsilon_surface # Epsilon for PME dipole correction */
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int ljpme_combination_rule # Type of combination rule in LJ-PME */
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int ePBC # Type of periodic boundary conditions */
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int bPeriodicMols # Periodic molecules */
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gmx_bool bContinuation # Continuation run: starting state is correct */
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int etc # temperature coupling */
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int nsttcouple # interval in steps for temperature coupling */
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gmx_bool bPrintNHChains # whether to print nose-hoover chains */
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int epc # pressure coupling */
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int epct # pressure coupling type */
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int nstpcouple # interval in steps for pressure coupling */
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real tau_p # pressure coupling time (ps) */
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tensor ref_p # reference pressure (kJ/(mol nm^3)) */
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tensor compress # compressability ((mol nm^3)/kJ) */
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int refcoord_scaling # How to scale absolute reference coordinates */
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rvec posres_com # The COM of the posres atoms */
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rvec posres_comB # The B-state COM of the posres atoms */
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int andersen_seed # Random seed for Andersen thermostat (obsolete) */
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real verletbuf_tol # Per atom pair energy drift tolerance (kJ/mol/ps/atom) for list buffer */
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real rlist # short range pairlist cut-off (nm) */
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real rtpi # Radius for test particle insertion */
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int coulombtype # Type of electrostatics treatment */
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int coulomb_modifier # Modify the Coulomb interaction */
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real rcoulomb_switch # Coulomb switch range start (nm) */
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real rcoulomb # Coulomb cutoff (nm) */
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real epsilon_r # relative dielectric constant */
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real epsilon_rf # relative dielectric constant of the RF */
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int implicit_solvent # No (=explicit water), or GBSA solvent models */
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int gb_algorithm # Algorithm to use for calculation Born radii */
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int nstgbradii # Frequency of updating Generalized Born radii */
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real rgbradii # Cutoff for GB radii calculation */
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real gb_saltconc # Salt concentration (M) for GBSA models */
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real gb_epsilon_solvent # dielectric coeff. of implicit solvent */
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real gb_obc_alpha # 1st scaling factor for Bashford-Case GB */
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real gb_obc_beta # 2nd scaling factor for Bashford-Case GB */
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real gb_obc_gamma # 3rd scaling factor for Bashford-Case GB */
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real gb_dielectric_offset # Dielectric offset for Still/HCT/OBC */
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int sa_algorithm # Algorithm for SA part of GBSA */
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real sa_surface_tension # Energy factor for SA part of GBSA */
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int vdwtype # Type of Van der Waals treatment */
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int vdw_modifier # Modify the VdW interaction */
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real rvdw_switch # Van der Waals switch range start (nm) */
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real rvdw # Van der Waals cutoff (nm) */
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int eDispCorr # Perform Long range dispersion corrections */
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real tabext # Extension of the table beyond the cut-off, *
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# * as well as the table length for 1-4 interac. */
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real shake_tol # tolerance for shake */
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int efep # free energy calculations */
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t_lambda *fepvals # Data for the FEP state */
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gmx_bool bSimTemp # Whether to do simulated tempering */
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t_simtemp *simtempvals # Variables for simulated tempering */
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gmx_bool bExpanded # Whether expanded ensembles are used */
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t_expanded *expandedvals # Expanded ensemble parameters */
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int eDisre # Type of distance restraining */
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real dr_fc # force constant for ta_disre */
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int eDisreWeighting # type of weighting of pairs in one restraints */
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gmx_bool bDisreMixed # Use comb of time averaged and instan. viol's */
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int nstdisreout # frequency of writing pair distances to enx */
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real dr_tau # time constant for memory function in disres */
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real orires_fc # force constant for orientational restraints */
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real orires_tau # time constant for memory function in orires */
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int nstorireout # frequency of writing tr(SD) to enx */
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real em_stepsize # The stepsize for updating */
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real em_tol # The tolerance */
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int niter # Number of iterations for convergence of */
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# steepest descent in relax_shells */
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real fc_stepsize # Stepsize for directional minimization */
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# in relax_shells */
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int nstcgsteep # number of steps after which a steepest */
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# descents step is done while doing cg */
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int nbfgscorr # Number of corrections to the hessian to keep */
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int eConstrAlg # Type of constraint algorithm */
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int nProjOrder # Order of the LINCS Projection Algorithm */
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real LincsWarnAngle # If bond rotates more than %g degrees, warn */
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int nLincsIter # Number of iterations in the final Lincs step */
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gmx_bool bShakeSOR # Use successive overrelaxation for shake */
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real bd_fric # Friction coefficient for BD (amu/ps) */
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gmx_int64_t ld_seed # Random seed for SD and BD */
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int nwall # The number of walls */
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int wall_type # The type of walls */
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real wall_r_linpot # The potentail is linear for r<=wall_r_linpot */
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int wall_atomtype[2] # The atom type for walls */
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real wall_density[2] # Number density for walls */
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real wall_ewald_zfac # Scaling factor for the box for Ewald */
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# COM pulling data */
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bint bPull # Do we do COM pulling? */
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#struct pull_params_t *pull # The data for center of mass pulling */
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#struct pull_t *pull_work # The COM pull force calculation data structure TODO this pointer should live somewhere else */
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# gmx_bool bPull # Do we do COM pulling? */
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# struct pull_params_t *pull # The data for center of mass pulling */
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# TODO: Remove this by converting pull into a ForceProvider
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# struct pull_t *pull_work # The COM pull force calculation data structure */
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# AWH bias data */
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gmx_bool bDoAwh # Use awh biasing for PMF calculations? */
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# gmx::AwhParams *awhParams # AWH biasing parameters */
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# TODO: Remove this by converting AWH into a ForceProvider
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# gmx::Awh *awh # AWH work object */
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# Enforced rotation data */
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bint bRot # Calculate enforced rotation potential(s)? */
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t_rot *rot # The data for enforced rotation potentials */
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gmx_bool bRot # Calculate enforced rotation potential(s)? */
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t_rot *rot # The data for enforced rotation potentials */
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int eSwapCoords # Do ion/water position exchanges (CompEL)? */
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t_swapcoords *swap
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int eSwapCoords # Do ion/water position exchanges (CompEL)? */
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t_swapcoords *swap
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bint bIMD # Allow interactive MD sessions for this .tpr? */
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t_IMD *imd # Interactive molecular dynamics */
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gmx_bool bIMD # Allow interactive MD sessions for this .tpr? */
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t_IMD *imd # Interactive molecular dynamics */
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double cos_accel # Acceleration for viscosity calculation */
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tensor deform # Triclinic deformation velocities (nm/ps) */
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int userint1 # User determined parameters */
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int userint2
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int userint3
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int userint4
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double userdouble1
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double userdouble2
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double userdouble3
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double userdouble4
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t_grpopts opts # Group options */
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t_cosines ex[0] # Electric field stuff (spatial part) */
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t_cosines et[0] # Electric field stuff (time part) */
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bint bQMMM # QM/MM calculation */
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int QMconstraints # constraints on QM bonds */
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int QMMMscheme # Scheme: ONIOM or normal */
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double scalefactor # factor for scaling the MM charges in QM calc.*/
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real cos_accel # Acceleration for viscosity calculation */
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tensor deform # Triclinic deformation velocities (nm/ps) */
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int userint1 # User determined parameters */
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int userint2
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int userint3
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int userint4
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real userreal1
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real userreal2
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real userreal3
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real userreal4
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t_grpopts opts # Group options */
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gmx_bool bQMMM # QM/MM calculation */
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int QMconstraints # constraints on QM bonds */
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int QMMMscheme # Scheme: ONIOM or normal */
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real scalefactor # factor for scaling the MM charges in QM calc.*/
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# Fields for removed features go here (better caching) */
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bint bAdress # Whether AdResS is enabled - always false if a valid .tpr was read
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bint useTwinRange # Whether twin-range scheme is active - always false if a valid .tpr was read
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gmx_bool bAdress # Whether AdResS is enabled - always false if a valid .tpr was read
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gmx_bool useTwinRange # Whether twin-range scheme is active - always false if a valid .tpr was read
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# gmx::KeyValueTreeObject *params
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