from utility cimport * from math cimport * cdef extern from "gromacs/legacyheaders/types/energy.h": ctypedef struct t_energy: real e double eav double esum cdef extern from "gromacs/legacyheaders/types/inputrec.h": ctypedef struct t_simtemp: pass ctypedef struct t_lambda: pass ctypedef struct t_expanded: pass ctypedef struct t_rot: pass ctypedef struct t_IMD: pass ctypedef struct t_grpopts: int ngtc real *ref_t # Coupling temperature per group */ ctypedef struct t_cosines: pass ctypedef struct t_swapcoords: pass ctypedef struct t_inputrec: int eI # Integration method */ int nsteps # number of steps to be taken */ int simulation_part # Used in checkpointing to separate chunks */ int 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) */ double x_compression_precision # precision of x in compressed trajectory file */ double 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 */ double ewald_rtol # double space tolerance for Ewald, determines */ # the double/reciprocal space relative weight */ double ewald_rtol_lj # double space tolerance for LJ-Ewald */ int ewald_geometry # normal/3d ewald, or pseudo-2d LR corrections */ double 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 */ bint bContinuation # Continuation run: starting state is correct */ int etc # temperature coupling */ int nsttcouple # interval in steps for temperature coupling */ bint bPrintNHChains # whether to print nose-hoover chains */ int epc # pressure coupling */ int epct # pressure coupling type */ int nstpcouple # interval in steps for pressure coupling */ double 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) */ double verletbuf_tol # Per atom pair energy drift tolerance (kJ/mol/ps/atom) for list buffer */ double rlist # short range pairlist cut-off (nm) */ double rtpi # Radius for test particle insertion */ int coulombtype # Type of electrostatics treatment */ int coulomb_modifier # Modify the Coulomb interaction */ double rcoulomb_switch # Coulomb switch range start (nm) */ double rcoulomb # Coulomb cutoff (nm) */ double epsilon_r # relative dielectric constant */ double 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 */ double rgbradii # Cutoff for GB radii calculation */ double gb_saltconc # Salt concentration (M) for GBSA models */ double gb_epsilon_solvent # dielectric coeff. of implicit solvent */ double gb_obc_alpha # 1st scaling factor for Bashford-Case GB */ double gb_obc_beta # 2nd scaling factor for Bashford-Case GB */ double gb_obc_gamma # 3rd scaling factor for Bashford-Case GB */ double gb_dielectric_offset # Dielectric offset for Still/HCT/OBC */ int sa_algorithm # Algorithm for SA part of GBSA */ double 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 */ double rvdw_switch # Van der Waals switch range start (nm) */ double rvdw # Van der Waals cutoff (nm) */ int eDispCorr # Perform Long range dispersion corrections */ double tabext # Extension of the table beyond the cut-off, * # * as well as the table length for 1-4 interac. */ double shake_tol # tolerance for shake */ int efep # free energy calculations */ t_lambda *fepvals # Data for the FEP state */ bint bSimTemp # Whether to do simulated tempering */ t_simtemp *simtempvals # Variables for simulated tempering */ bint bExpanded # Whether expanded ensembles are used */ t_expanded *expandedvals # Expanded ensemble parameters */ int eDisre # Type of distance restraining */ double dr_fc # force constant for ta_disre */ int eDisreWeighting # type of weighting of pairs in one restraints */ bint bDisreMixed # Use comb of time averaged and instan. viol's */ int nstdisreout # frequency of writing pair distances to enx */ double dr_tau # time constant for memory function in disres */ double orires_fc # force constant for orientational restraints */ double orires_tau # time constant for memory function in orires */ int nstorireout # frequency of writing tr(SD) to enx */ double em_stepsize # The stepsize for updating */ double em_tol # The tolerance */ int niter # Number of iterations for convergence of */ # steepest descent in relax_shells */ double 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 */ double LincsWarnAngle # If bond rotates more than %g degrees, warn */ int nLincsIter # Number of iterations in the final Lincs step */ bint bShakeSOR # Use successive overrelaxation for shake */ double 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 */ double wall_r_linpot # The potentail is linear for r<=wall_r_linpot */ int wall_atomtype[2] # The atom type for walls */ double wall_density[2] # Number density for walls */ double wall_ewald_zfac # Scaling factor for the box for Ewald */ # COM pulling data */ bint bPull # Do we do COM pulling? */ #struct pull_params_t *pull # The data for center of mass pulling */ #struct pull_t *pull_work # The COM pull force calculation data structure TODO this pointer should live somewhere else */ # Enforced rotation data */ bint 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 bint bIMD # Allow interactive MD sessions for this .tpr? */ t_IMD *imd # Interactive molecular dynamics */ double cos_accel # Acceleration for viscosity calculation */ tensor deform # Triclinic deformation velocities (nm/ps) */ int userint1 # User determined parameters */ int userint2 int userint3 int userint4 double userdouble1 double userdouble2 double userdouble3 double userdouble4 t_grpopts opts # Group options */ t_cosines ex[0] # Electric field stuff (spatial part) */ t_cosines et[0] # Electric field stuff (time part) */ bint bQMMM # QM/MM calculation */ int QMconstraints # constraints on QM bonds */ int QMMMscheme # Scheme: ONIOM or normal */ double scalefactor # factor for scaling the MM charges in QM calc.*/ # Fields for removed features go here (better caching) */ bint bAdress # Whether AdResS is enabled - always false if a valid .tpr was read bint useTwinRange # Whether twin-range scheme is active - always false if a valid .tpr was read