struct gmx_enfrot;
struct gmx_enfrotgrp;
struct pull_params_t;
-enum class ComRemovalAlgorithm : int;
namespace gmx
{
struct MtsLevel;
} // namespace gmx
-enum class PbcType;
-
struct t_grpopts
{
//! Number of T-Coupl groups
- int ngtc;
+ int ngtc = 0;
//! Number of of Nose-Hoover chains per group
- int nhchainlength;
+ int nhchainlength = 0;
//! Number of Freeze groups
- int ngfrz;
+ int ngfrz = 0;
//! Number of Energy groups
- int ngener;
+ int ngener = 0;
//! Number of degrees of freedom in a group
- real* nrdf;
+ real* nrdf = nullptr;
//! Coupling temperature per group
- real* ref_t;
+ real* ref_t = nullptr;
//! No/simple/periodic simulated annealing for each group
- SimulatedAnnealing* annealing;
+ SimulatedAnnealing* annealing = nullptr;
//! Number of annealing time points per group
- int* anneal_npoints;
+ int* anneal_npoints = nullptr;
//! For each group: Time points
- real** anneal_time;
+ real** anneal_time = nullptr;
//! For each group: Temperature at these times. Final temp after all intervals is ref_t
- real** anneal_temp;
+ real** anneal_temp = nullptr;
//! Tau coupling time
- real* tau_t;
+ real* tau_t = nullptr;
//! Whether the group will be frozen in each direction
- ivec* nFreeze;
+ ivec* nFreeze = nullptr;
//! Exclusions/tables of energy group pairs
- int* egp_flags;
+ int* egp_flags = nullptr;
/* QMMM stuff */
//! Number of QM groups
- int ngQM;
+ int ngQM = 0;
};
struct t_simtemp
{
//! Simulated temperature scaling; linear or exponential
- SimulatedTempering eSimTempScale;
+ SimulatedTempering eSimTempScale = SimulatedTempering::Default;
//! The low temperature for simulated tempering
- real simtemp_low;
+ real simtemp_low = 0;
//! The high temperature for simulated tempering
- real simtemp_high;
+ real simtemp_high = 0;
//! The range of temperatures used for simulated tempering
std::vector<real> temperatures;
};
struct t_lambda
{
//! The frequency for calculating dhdl
- int nstdhdl;
+ int nstdhdl = 0;
//! Fractional value of lambda (usually will use init_fep_state, this will only be for slow growth, and for legacy free energy code. Only has a valid value if positive)
- double init_lambda;
+ double init_lambda = 0;
//! The initial number of the state
- int init_fep_state;
+ int init_fep_state = 0;
//! Change of lambda per time step (fraction of (0.1)
- double delta_lambda;
+ double delta_lambda = 0;
//! Print no, total or potential energies in dhdl
- FreeEnergyPrintEnergy edHdLPrintEnergy;
+ FreeEnergyPrintEnergy edHdLPrintEnergy = FreeEnergyPrintEnergy::Default;
//! The number of foreign lambda points
- int n_lambda;
+ int n_lambda = 0;
//! The array of all lambda values
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;
+ int lambda_neighbors = 0;
//! The first lambda to calculate energies for
- int lambda_start_n;
+ int lambda_start_n = 0;
//! The last lambda +1 to calculate energies for
- int lambda_stop_n;
+ int lambda_stop_n = 0;
//! Free energy soft-core parameter
- real sc_alpha;
+ real sc_alpha = 0;
//! Lambda power for soft-core interactions
- int sc_power;
+ int sc_power = 0;
//! R power for soft-core interactions
- real sc_r_power;
+ real sc_r_power = 0;
//! Free energy soft-core sigma when c6 or c12=0
- real sc_sigma;
+ real sc_sigma = 0;
//! Free energy soft-core sigma for ?????
- real sc_sigma_min;
+ real sc_sigma_min = 0;
//! Use softcore for the coulomb portion as well (default FALSE)
- bool bScCoul;
+ bool bScCoul = false;
//! 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::EnumerationArray<FreeEnergyPerturbationCouplingType, bool> separate_dvdl;
//! Whether to write a separate dhdl.xvg file note: NOT a gmx_bool, but an enum
- SeparateDhdlFile separate_dhdl_file;
+ SeparateDhdlFile separate_dhdl_file = SeparateDhdlFile::Default;
//! Whether to calculate+write dhdl derivatives note: NOT a gmx_bool, but an enum
- DhDlDerivativeCalculation dhdl_derivatives;
+ DhDlDerivativeCalculation dhdl_derivatives = DhDlDerivativeCalculation::Default;
//! The maximum table size for the dH histogram
- int dh_hist_size;
+ int dh_hist_size = 0;
//! The spacing for the dH histogram
- double dh_hist_spacing;
+ double dh_hist_spacing = 0;
};
struct t_expanded
{
//! The frequency of expanded ensemble state changes
- int nstexpanded;
+ int nstexpanded = 0;
//! Which type of move updating do we use for lambda monte carlo (or no for none)
- LambdaWeightCalculation elamstats;
+ LambdaWeightCalculation elamstats = LambdaWeightCalculation::Default;
//! What move set will be we using for state space moves
- LambdaMoveCalculation elmcmove;
+ LambdaMoveCalculation elmcmove = LambdaMoveCalculation::Default;
//! The method we use to decide of we have equilibrated the weights
- LambdaWeightWillReachEquilibrium elmceq;
+ LambdaWeightWillReachEquilibrium elmceq = LambdaWeightWillReachEquilibrium::Default;
//! The minumum number of samples at each lambda for deciding whether we have reached a minimum
- int equil_n_at_lam;
+ int equil_n_at_lam = 0;
//! Wang-Landau delta at which we stop equilibrating weights
- real equil_wl_delta;
+ real equil_wl_delta = 0;
//! Use the ratio of weights (ratio of minimum to maximum) to decide when to stop equilibrating
- real equil_ratio;
+ real equil_ratio = 0;
//! After equil_steps steps we stop equilibrating the weights
- int equil_steps;
+ int equil_steps = 0;
//! After equil_samples total samples (steps/nstfep), we stop equilibrating the weights
- int equil_samples;
+ int equil_samples = 0;
//! Random number seed for lambda mc switches
- int lmc_seed;
+ int lmc_seed = 0;
//! Whether to use minumum variance weighting
- bool minvar;
+ bool minvar = false;
//! The number of samples needed before kicking into minvar routine
- int minvarmin;
+ int minvarmin = 0;
//! The offset for the variance in MinVar
- real minvar_const;
+ real minvar_const = 0;
//! Range of cvalues used for BAR
- int c_range;
+ int c_range = 0;
//! Whether to print symmetrized matrices
- bool bSymmetrizedTMatrix;
+ bool bSymmetrizedTMatrix = false;
//! How frequently to print the transition matrices
- int nstTij;
+ int nstTij = 0;
//! Number of repetitions in the MC lambda jumps MRS -- VERIFY THIS
- int lmc_repeats;
+ int lmc_repeats = 0;
//! Minimum number of samples for each state before free sampling MRS -- VERIFY THIS!
- int lmc_forced_nstart;
+ int lmc_forced_nstart = 0;
//! Distance in lambda space for the gibbs interval
- int gibbsdeltalam;
+ int gibbsdeltalam = 0;
//! Scaling factor for Wang-Landau
- real wl_scale;
+ real wl_scale = 0;
//! Ratio between largest and smallest number for freezing the weights
- real wl_ratio;
+ real wl_ratio = 0;
//! Starting delta for Wang-Landau
- real init_wl_delta;
+ real init_wl_delta = 0;
//! Use one over t convergence for Wang-Landau when the delta get sufficiently small
- bool bWLoneovert;
+ bool bWLoneovert = false;
//! Did we initialize the weights? TODO: REMOVE FOR 5.0, no longer needed with new logic
- bool bInit_weights;
+ bool bInit_weights = false;
//! To override the main temperature, or define it if it's not defined
- real mc_temp;
+ real mc_temp = 0;
//! User-specified initial weights to start with
std::vector<real> init_lambda_weights;
};
~t_inputrec();
//! Integration method
- IntegrationAlgorithm eI;
+ IntegrationAlgorithm eI = IntegrationAlgorithm::Default;
//! Number of steps to be taken
- int64_t nsteps;
+ int64_t nsteps = 0;
//! Used in checkpointing to separate chunks
- int simulation_part;
+ int simulation_part = 0;
//! Start at a stepcount >0 (used w. convert-tpr)
- int64_t init_step;
+ int64_t init_step = 0;
//! Frequency of energy calc. and T/P coupl. upd.
- int nstcalcenergy;
+ int nstcalcenergy = 0;
//! Group or verlet cutoffs
- CutoffScheme cutoff_scheme;
+ CutoffScheme cutoff_scheme = CutoffScheme::Default;
//! Number of steps before pairlist is generated
- int nstlist;
+ int nstlist = 0;
//! Number of steps after which center of mass motion is removed
- int nstcomm;
+ int nstcomm = 0;
//! Center of mass motion removal algorithm
- ComRemovalAlgorithm comm_mode;
+ ComRemovalAlgorithm comm_mode = ComRemovalAlgorithm::Default;
//! Number of steps after which print to logfile
- int nstlog;
+ int nstlog = 0;
//! Number of steps after which X is output
- int nstxout;
+ int nstxout = 0;
//! Number of steps after which V is output
- int nstvout;
+ int nstvout = 0;
//! Number of steps after which F is output
- int nstfout;
+ int nstfout = 0;
//! Number of steps after which energies printed
- int nstenergy;
+ int nstenergy = 0;
//! Number of steps after which compressed trj (.xtc,.tng) is output
- int nstxout_compressed;
+ int nstxout_compressed = 0;
//! Initial time (ps)
- double init_t;
+ double init_t = 0;
//! Time step (ps)
- double delta_t;
+ double delta_t = 0;
//! Whether we use multiple time stepping
- bool useMts;
+ bool useMts = false;
//! The multiple time stepping levels
std::vector<gmx::MtsLevel> mtsLevels;
//! Precision of x in compressed trajectory file
- real x_compression_precision;
+ real x_compression_precision = 0;
//! Requested fourier_spacing, when nk? not set
- real fourier_spacing;
+ real fourier_spacing = 0;
//! Number of k vectors in x dimension for fourier methods for long range electrost.
- int nkx;
+ int nkx = 0;
//! Number of k vectors in y dimension for fourier methods for long range electrost.
- int nky;
+ int nky = 0;
//! Number of k vectors in z dimension for fourier methods for long range electrost.
- int nkz;
+ int nkz = 0;
//! Interpolation order for PME
- int pme_order;
+ int pme_order = 0;
//! Real space tolerance for Ewald, determines the real/reciprocal space relative weight
- real ewald_rtol;
+ real ewald_rtol = 0;
//! Real space tolerance for LJ-Ewald
- real ewald_rtol_lj;
+ real ewald_rtol_lj = 0;
//! Normal/3D ewald, or pseudo-2D LR corrections
- EwaldGeometry ewald_geometry;
+ EwaldGeometry ewald_geometry = EwaldGeometry::Default;
//! Epsilon for PME dipole correction
- real epsilon_surface;
+ real epsilon_surface = 0;
//! Type of combination rule in LJ-PME
- LongRangeVdW ljpme_combination_rule;
+ LongRangeVdW ljpme_combination_rule = LongRangeVdW::Default;
//! Type of periodic boundary conditions
- PbcType pbcType;
+ PbcType pbcType = PbcType::Default;
//! Periodic molecules
- bool bPeriodicMols;
+ bool bPeriodicMols = false;
//! Continuation run: starting state is correct (ie. constrained)
- bool bContinuation;
+ bool bContinuation = false;
//! Temperature coupling
- TemperatureCoupling etc;
+ TemperatureCoupling etc = TemperatureCoupling::Default;
//! Interval in steps for temperature coupling
- int nsttcouple;
+ int nsttcouple = 0;
//! Whether to print nose-hoover chains
- bool bPrintNHChains;
+ bool bPrintNHChains = false;
//! Pressure coupling
- PressureCoupling epc;
+ PressureCoupling epc = PressureCoupling::Default;
//! Pressure coupling type
- PressureCouplingType epct;
+ PressureCouplingType epct = PressureCouplingType::Default;
//! Interval in steps for pressure coupling
- int nstpcouple;
+ int nstpcouple = 0;
//! Pressure coupling time (ps)
- real tau_p;
+ real tau_p = 0;
//! Reference pressure (kJ/(mol nm^3))
- tensor ref_p;
+ tensor ref_p = { { 0 } };
//! Compressibility ((mol nm^3)/kJ)
- tensor compress;
+ tensor compress = { { 0 } };
//! How to scale absolute reference coordinates
- RefCoordScaling refcoord_scaling;
+ RefCoordScaling refcoord_scaling = RefCoordScaling::Default;
//! The COM of the posres atoms
- rvec posres_com;
+ rvec posres_com = { 0, 0, 0 };
//! The B-state COM of the posres atoms
- rvec posres_comB;
+ rvec posres_comB = { 0, 0, 0 };
//! Random seed for Andersen thermostat (obsolete)
- int andersen_seed;
+ int andersen_seed = 0;
//! Per atom pair energy drift tolerance (kJ/mol/ps/atom) for list buffer
- real verletbuf_tol;
+ real verletbuf_tol = 0;
//! Short range pairlist cut-off (nm)
- real rlist;
+ real rlist = 0;
//! Radius for test particle insertion
- real rtpi;
+ real rtpi = 0;
//! Type of electrostatics treatment
- CoulombInteractionType coulombtype;
+ CoulombInteractionType coulombtype = CoulombInteractionType::Default;
//! Modify the Coulomb interaction
- InteractionModifiers coulomb_modifier;
+ InteractionModifiers coulomb_modifier = InteractionModifiers::Default;
//! Coulomb switch range start (nm)
- real rcoulomb_switch;
+ real rcoulomb_switch = 0;
//! Coulomb cutoff (nm)
- real rcoulomb;
+ real rcoulomb = 0;
//! Relative dielectric constant
- real epsilon_r;
+ real epsilon_r = 0;
//! Relative dielectric constant of the RF
- real epsilon_rf;
+ real epsilon_rf = 0;
//! Always false (no longer supported)
- bool implicit_solvent;
+ bool implicit_solvent = false;
//! Type of Van der Waals treatment
- VanDerWaalsType vdwtype;
+ VanDerWaalsType vdwtype = VanDerWaalsType::Default;
//! Modify the Van der Waals interaction
- InteractionModifiers vdw_modifier;
+ InteractionModifiers vdw_modifier = InteractionModifiers::Default;
//! Van der Waals switch range start (nm)
- real rvdw_switch;
+ real rvdw_switch = 0;
//! Van der Waals cutoff (nm)
- real rvdw;
+ real rvdw = 0;
//! Perform Long range dispersion corrections
- DispersionCorrectionType eDispCorr;
+ DispersionCorrectionType eDispCorr = DispersionCorrectionType::Default;
//! Extension of the table beyond the cut-off, as well as the table length for 1-4 interac.
- real tabext;
+ real tabext = 0;
//! Tolerance for shake
- real shake_tol;
+ real shake_tol = 0;
//! Free energy calculations
- FreeEnergyPerturbationType efep;
+ FreeEnergyPerturbationType efep = FreeEnergyPerturbationType::Default;
//! Data for the FEP state
std::unique_ptr<t_lambda> fepvals;
//! Whether to do simulated tempering
- bool bSimTemp;
+ bool bSimTemp = false;
//! Variables for simulated tempering
std::unique_ptr<t_simtemp> simtempvals;
//! Whether expanded ensembles are used
- bool bExpanded;
+ bool bExpanded = false;
//! Expanded ensemble parameters
std::unique_ptr<t_expanded> expandedvals;
//! Type of distance restraining
- DistanceRestraintRefinement eDisre;
+ DistanceRestraintRefinement eDisre = DistanceRestraintRefinement::Default;
//! Force constant for time averaged distance restraints
- real dr_fc;
+ real dr_fc = 0;
//! Type of weighting of pairs in one restraints
- DistanceRestraintWeighting eDisreWeighting;
+ DistanceRestraintWeighting eDisreWeighting = DistanceRestraintWeighting::Default;
//! Use combination of time averaged and instantaneous violations
- bool bDisreMixed;
+ bool bDisreMixed = false;
//! Frequency of writing pair distances to enx
- int nstdisreout;
+ int nstdisreout = 0;
//! Time constant for memory function in disres
- real dr_tau;
+ real dr_tau = 0;
//! Force constant for orientational restraints
- real orires_fc;
+ real orires_fc = 0;
//! Time constant for memory function in orires
- real orires_tau;
+ real orires_tau = 0;
//! Frequency of writing tr(SD) to energy output
- int nstorireout;
+ int nstorireout = 0;
//! The stepsize for updating
- real em_stepsize;
+ real em_stepsize = 0;
//! The tolerance
- real em_tol;
+ real em_tol = 0;
//! Number of iterations for convergence of steepest descent in relax_shells
- int niter;
+ int niter = 0;
//! Stepsize for directional minimization in relax_shells
- real fc_stepsize;
+ real fc_stepsize = 0;
//! Number of steps after which a steepest descents step is done while doing cg
- int nstcgsteep;
+ int nstcgsteep = 0;
//! Number of corrections to the Hessian to keep
- int nbfgscorr;
+ int nbfgscorr = 0;
//! Type of constraint algorithm
- ConstraintAlgorithm eConstrAlg;
+ ConstraintAlgorithm eConstrAlg = ConstraintAlgorithm::Default;
//! Order of the LINCS Projection Algorithm
- int nProjOrder;
+ int nProjOrder = 0;
//! Warn if any bond rotates more than this many degrees
- real LincsWarnAngle;
+ real LincsWarnAngle = 0;
//! Number of iterations in the final LINCS step
- int nLincsIter;
+ int nLincsIter = 0;
//! Use successive overrelaxation for shake
- bool bShakeSOR;
+ bool bShakeSOR = false;
//! Friction coefficient for BD (amu/ps)
- real bd_fric;
+ real bd_fric = 0;
//! Random seed for SD and BD
- int64_t ld_seed;
+ int64_t ld_seed = 0;
//! The number of walls
- int nwall;
+ int nwall = 0;
//! The type of walls
- WallType wall_type;
+ WallType wall_type = WallType::Default;
//! The potentail is linear for r<=wall_r_linpot
- real wall_r_linpot;
+ real wall_r_linpot = 0;
//! The atom type for walls
- int wall_atomtype[2];
+ int wall_atomtype[2] = { 0, 0 };
//! Number density for walls
- real wall_density[2];
+ real wall_density[2] = { 0, 0 };
//! Scaling factor for the box for Ewald
- real wall_ewald_zfac;
+ real wall_ewald_zfac = 0;
/* COM pulling data */
//! Do we do COM pulling?
- bool bPull;
+ bool bPull = false;
//! The data for center of mass pulling
std::unique_ptr<pull_params_t> pull;
/* AWH bias data */
//! Whether to use AWH biasing for PMF calculations
- bool bDoAwh;
+ bool bDoAwh = false;
//! AWH biasing parameters
std::unique_ptr<gmx::AwhParams> awhParams;
/* Enforced rotation data */
//! Whether to calculate enforced rotation potential(s)
- bool bRot;
+ bool bRot = false;
//! The data for enforced rotation potentials
- t_rot* rot;
+ t_rot* rot = nullptr;
//! Whether to do ion/water position exchanges (CompEL)
- SwapType eSwapCoords;
+ SwapType eSwapCoords = SwapType::Default;
//! Swap data structure.
- t_swapcoords* swap;
+ t_swapcoords* swap = nullptr;
//! Whether the tpr makes an interactive MD session possible.
- bool bIMD;
+ bool bIMD = false;
//! Interactive molecular dynamics
- t_IMD* imd;
+ t_IMD* imd = nullptr;
//! Acceleration for viscosity calculation
- real cos_accel;
+ real cos_accel = 0;
//! Triclinic deformation velocities (nm/ps)
- tensor deform;
+ tensor deform = { { 0 } };
/*! \brief User determined parameters */
/**@{*/
- int userint1;
- int userint2;
- int userint3;
- int userint4;
- real userreal1;
- real userreal2;
- real userreal3;
- real userreal4;
+ int userint1 = 0;
+ int userint2 = 0;
+ int userint3 = 0;
+ int userint4 = 0;
+ real userreal1 = 0;
+ real userreal2 = 0;
+ real userreal3 = 0;
+ real userreal4 = 0;
/**@}*/
//! Group options
t_grpopts opts;
//! QM/MM calculation
- bool bQMMM;
+ bool bQMMM = false;
/* Fields for removed features go here (better caching) */
//! Whether AdResS is enabled - always false if a valid .tpr was read
- bool bAdress;
+ bool bAdress = false;
//! Whether twin-range scheme is active - always false if a valid .tpr was read
- bool useTwinRange;
+ bool useTwinRange = false;
//! Whether we have constant acceleration - removed in GROMACS 2022
- bool useConstantAcceleration;
+ bool useConstantAcceleration = false;
//! KVT object that contains input parameters converted to the new style.
- gmx::KeyValueTreeObject* params;
+ gmx::KeyValueTreeObject* params = nullptr;
//! KVT for storing simulation parameters that are not part of the mdp file.
std::unique_ptr<gmx::KeyValueTreeObject> internalParameters;
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff