#include "gromacs/math/vectypes.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/enumerationhelpers.h"
#include "gromacs/utility/real.h"
#define EGP_EXCL (1 << 0)
//! Coupling temperature per group
real* ref_t;
//! No/simple/periodic simulated annealing for each group
- int* annealing;
+ SimulatedAnnealing* annealing;
//! Number of annealing time points per group
int* anneal_npoints;
//! For each group: Time points
struct t_simtemp
{
//! Simulated temperature scaling; linear or exponential
- int eSimTempScale;
+ SimulatedTempering eSimTempScale;
//! The low temperature for simulated tempering
real simtemp_low;
//! The high temperature for simulated tempering
//! Change of lambda per time step (fraction of (0.1)
double delta_lambda;
//! Print no, total or potential energies in dhdl
- int edHdLPrintEnergy;
+ FreeEnergyPrintEnergy edHdLPrintEnergy;
//! The number of foreign lambda points
int n_lambda;
//! The array of all lambda values
- double** all_lambda;
+ gmx::EnumerationArray<FreeEnergyPerturbationCouplingType, std::vector<double>> all_lambda;
//! The number of neighboring lambda states to calculate the energy for in up and down directions (-1 for all)
int lambda_neighbors;
//! The first lambda to calculate energies for
//! Use softcore for the coulomb portion as well (default FALSE)
gmx_bool bScCoul;
//! Whether to print the dvdl term associated with this term; if it is not specified as separate, it is lumped with the FEP term
- gmx_bool separate_dvdl[efptNR];
+ gmx::EnumerationArray<FreeEnergyPerturbationCouplingType, bool> separate_dvdl;
//! Whether to write a separate dhdl.xvg file note: NOT a gmx_bool, but an enum
- int separate_dhdl_file;
+ SeparateDhdlFile separate_dhdl_file;
//! Whether to calculate+write dhdl derivatives note: NOT a gmx_bool, but an enum
- int dhdl_derivatives;
+ DhDlDerivativeCalculation dhdl_derivatives;
//! The maximum table size for the dH histogram
int dh_hist_size;
//! The spacing for the dH histogram
//! The frequency of expanded ensemble state changes
int nstexpanded;
//! Which type of move updating do we use for lambda monte carlo (or no for none)
- int elamstats;
+ LambdaWeightCalculation elamstats;
//! What move set will be we using for state space moves
- int elmcmove;
+ LambdaMoveCalculation elmcmove;
//! The method we use to decide of we have equilibrated the weights
- int elmceq;
+ LambdaWeightWillReachEquilibrium elmceq;
//! The minumum number of samples at each lambda for deciding whether we have reached a minimum
int equil_n_at_lam;
//! Wang-Landau delta at which we stop equilibrating weights
//! To override the main temperature, or define it if it's not defined
real mc_temp;
//! User-specified initial weights to start with
- real* init_lambda_weights;
+ std::vector<real> init_lambda_weights;
};
struct t_rotgrp
{
//! Rotation type for this group
- int eType;
+ EnforcedRotationGroupType eType;
//! Use mass-weighed positions?
- int bMassW;
+ bool bMassW;
//! Number of atoms in the group
int nat;
//! The global atoms numbers
//! Pivot point of rotation axis (nm)
rvec pivot;
//! Type of fit to determine actual group angle
- int eFittype;
+ RotationGroupFitting eFittype;
//! Number of angles around the reference angle for which the rotation potential is also evaluated (for fit type 'potential' only)
int PotAngle_nstep;
//! Distance between two angles in degrees (for fit type 'potential' only)
~t_inputrec();
//! Integration method
- int eI;
+ IntegrationAlgorithm eI;
//! Number of steps to be taken
int64_t nsteps;
//! Used in checkpointing to separate chunks
//! Frequency of energy calc. and T/P coupl. upd.
int nstcalcenergy;
//! Group or verlet cutoffs
- int cutoff_scheme;
+ CutoffScheme cutoff_scheme;
//! Number of steps before pairlist is generated
int nstlist;
//! Number of steps after which center of mass motion is removed
int nstcomm;
//! Center of mass motion removal algorithm
- int comm_mode;
+ ComRemovalAlgorithm comm_mode;
//! Number of steps after which print to logfile
int nstlog;
//! Number of steps after which X is output
//! Real space tolerance for LJ-Ewald
real ewald_rtol_lj;
//! Normal/3D ewald, or pseudo-2D LR corrections
- int ewald_geometry;
+ EwaldGeometry ewald_geometry;
//! Epsilon for PME dipole correction
real epsilon_surface;
//! Type of combination rule in LJ-PME
- int ljpme_combination_rule;
+ LongRangeVdW ljpme_combination_rule;
//! Type of periodic boundary conditions
PbcType pbcType;
//! Periodic molecules
//! Pressure coupling
PressureCoupling epc;
//! Pressure coupling type
- int epct;
+ PressureCouplingType epct;
//! Interval in steps for pressure coupling
int nstpcouple;
//! Pressure coupling time (ps)
//! Compressibility ((mol nm^3)/kJ)
tensor compress;
//! How to scale absolute reference coordinates
- int refcoord_scaling;
+ RefCoordScaling refcoord_scaling;
//! The COM of the posres atoms
rvec posres_com;
//! The B-state COM of the posres atoms
//! Radius for test particle insertion
real rtpi;
//! Type of electrostatics treatment
- int coulombtype;
+ CoulombInteractionType coulombtype;
//! Modify the Coulomb interaction
- int coulomb_modifier;
+ InteractionModifiers coulomb_modifier;
//! Coulomb switch range start (nm)
real rcoulomb_switch;
//! Coulomb cutoff (nm)
//! Always false (no longer supported)
bool implicit_solvent;
//! Type of Van der Waals treatment
- int vdwtype;
+ VanDerWaalsType vdwtype;
//! Modify the Van der Waals interaction
- int vdw_modifier;
+ InteractionModifiers vdw_modifier;
//! Van der Waals switch range start (nm)
real rvdw_switch;
//! Van der Waals cutoff (nm)
real rvdw;
//! Perform Long range dispersion corrections
- int eDispCorr;
+ DispersionCorrectionType eDispCorr;
//! Extension of the table beyond the cut-off, as well as the table length for 1-4 interac.
real tabext;
//! Tolerance for shake
real shake_tol;
//! Free energy calculations
- int efep;
+ FreeEnergyPerturbationType efep;
//! Data for the FEP state
- t_lambda* fepvals;
+ std::unique_ptr<t_lambda> fepvals;
//! Whether to do simulated tempering
gmx_bool bSimTemp;
//! Variables for simulated tempering
- t_simtemp* simtempvals;
+ std::unique_ptr<t_simtemp> simtempvals;
//! Whether expanded ensembles are used
gmx_bool bExpanded;
//! Expanded ensemble parameters
- t_expanded* expandedvals;
+ std::unique_ptr<t_expanded> expandedvals;
//! Type of distance restraining
- int eDisre;
+ DistanceRestraintRefinement eDisre;
//! Force constant for time averaged distance restraints
real dr_fc;
//! Type of weighting of pairs in one restraints
- int eDisreWeighting;
+ DistanceRestraintWeighting eDisreWeighting;
//! Use combination of time averaged and instantaneous violations
gmx_bool bDisreMixed;
//! Frequency of writing pair distances to enx
//! Number of corrections to the Hessian to keep
int nbfgscorr;
//! Type of constraint algorithm
- int eConstrAlg;
+ ConstraintAlgorithm eConstrAlg;
//! Order of the LINCS Projection Algorithm
int nProjOrder;
//! Warn if any bond rotates more than this many degrees
//! The number of walls
int nwall;
//! The type of walls
- int wall_type;
+ WallType wall_type;
//! The potentail is linear for r<=wall_r_linpot
real wall_r_linpot;
//! The atom type for walls
t_rot* rot;
//! Whether to do ion/water position exchanges (CompEL)
- int eSwapCoords;
+ SwapType eSwapCoords;
//! Swap data structure.
t_swapcoords* swap;
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff