/* * File: GlobOpt.h * Author: flong * * Created on February 12, 2013, 3:44 PM */ #ifndef GLOBOPT_H #define GLOBOPT_H #ifndef KERNEL_H #include "../kernel/kernel.h" #endif #ifndef ATOM_H #include "../kernel/atom.h" #endif #ifndef BOND_H #include "../kernel/bond.h" #endif #ifndef ANGLE_H #include "../kernel/angle.h" #endif #ifndef TORSION_H #include "../kernel/torsion.h" #endif #ifndef RESIDUE_H #include "../kernel/residue.h" #endif #ifndef RING_H #include "../kernel/ring.h" #endif #ifndef PLANE_H #include "../kernel/plane.h" #endif #ifndef CHAIN_H #include "../kernel/chain.h" #endif #ifndef UTILITY_H #include "../kernel/utility.h" #endif #ifndef NEIGHBLIST_H #include "../kernel/neighbList.h" #endif #ifndef LINALG_H #include "LinAlg.h" #endif #ifndef ALLSYSTEM_H #include "../kernel/AllSystem.h" #endif #ifndef TRANSCOORD_H #include "../kernel/TransCoord.h" #endif namespace GO { class OptimSet { public : // Default constructor OptimSet(); // Default destructor ~OptimSet(); LIBMOL::REAL objValue; std::vector atoms; }; class FindGlobMin { public: // Default constructor FindGlobMin(); // Constructor using a AllSystem FindGlobMin(const LIBMOL::AllSystem & aSystem, std::string tFileNameeRoot, std::string tMonoRoot); FindGlobMin(const LIBMOL::AllSystem & aSystem); FindGlobMin(const LIBMOL::AllSystem & aSystem, int nOpt); // Default destructor ~FindGlobMin(); // Common routines void Driver(); void Driver(bool useCoords, int nOpt); bool SetDefinedInitPositions(); void SetRanDomInitPositions(); void UpdatePositionsWithRandomShifts(); void PreIdealization(); void ProIdealization(); void singleCompsIdealization(); /* !!!!!!!!! Different Global min schemes * * 1 Tunneling and local minimum scheme * * 2 Fast SA (Evolution + Flash-freezing) * 2.1 Using MC + CG * 2.2 Using MD + CG * * */ // 1 Tunneling and local minimum scheme void SetTAndRRatio(bool & i_err); void SetBalanceValue(int & idx_error, LIBMOL::REAL & bal_value); void SetBalanceValueAndDeriv(int & idx_error, LIBMOL::REAL & bal_value, LIBMOL::REAL ** bal_deriv); void SetBalanceValueAndDeriv_EXP(int & idx_error, LIBMOL::REAL coeffi_ad, LIBMOL::REAL & bal_value, LIBMOL::REAL ** bal_deriv, LIBMOL::REAL ** pos_m); void SetBalanceValueAndDeriv_LOG(int & idx_error, LIBMOL::REAL & o_diff, LIBMOL::REAL & bal_value, LIBMOL::REAL ** bal_deriv); void RootFinder_Broyden(); void RootFinder_Newton(); void RootFinder_Newton_GV(); void Tunnelling_Newton_EXP(); void Tunnelling_Newton_LOG(); void TunnellingAndMinDriver(); void TunnellingAndMinDriver(int nOpt); // A hybrid SA/CG/scheme void HybridSA_CGMinDriver(); void Fast_SA(); void FastAnnealing(int num_steps); void MD_Init(int idx_way, LIBMOL::REAL & obj_d, LIBMOL::REAL & b_value, LIBMOL::REAL ** b_deriv); void InitCartDisplaces(); void InitCartVeloAndAccels(int idx_way, LIBMOL::REAL & obj_d, LIBMOL::REAL & b_value, LIBMOL::REAL ** b_deriv); void HYBRID_MC(LIBMOL::REAL & obj_d, LIBMOL::REAL & b_value, LIBMOL::REAL ** b_deriv, int & steps_cur); void AcceptanceRules(bool & l_accept, LIBMOL::REAL e_diff, LIBMOL::REAL h_diff); LIBMOL::REAL GetHamilton (LIBMOL::REAL e_pot); // Detailed calculations of object functions and their derivatives // Methods related to transfer from the Cartesian description // to the angular(internal) description void CoordCartToAng(); void SetDThetaDx(LIBMOL::REAL ** dtheta_dx); void GetDvDq(int idx_atom, int idx_torsion); void TorsAngDri(int idx_torsion, LIBMOL::REAL * dPsidXi, LIBMOL::REAL ** dPsidXidXj); void VeloCartToAng (); // The objective function. LIBMOL::REAL GetObjValue(); LIBMOL::REAL GetObjValue(LIBMOL::REAL * vars); LIBMOL::REAL GetObjOneBond(std::vector::iterator tBo); LIBMOL::REAL GetObjOneAngle(std::vector::iterator tAn); LIBMOL::REAL GetObjOneTorsion(std::vector::iterator tTo); LIBMOL::REAL GetObjOnePlane(std::vector::iterator tPl); LIBMOL::REAL GetObjOneChiral(std::vector::iterator tCh); LIBMOL::REAL GetObjOneAtomVdw(std::vector::iterator tAt); void SetObjCart(); void SetObjTors(); void SetObjandForceCart(); // The force (only in Cartisan space) and // accelerate (in both Cartesian and internal space) void SetInForces(); void GetForBondOrder(int i_bond); void GetForBondAngs(int i_bondAngs); void GetForTorsionAngs(int i_atom, LIBMOL::REAL ** dPsi_dxdx); //-------- vdw and hydrogen bonding ---- // values of objective function LIBMOL::REAL GetObjVWRepuls(int i_atom, int j_atom); void CheckHYD(int i_atom, int j_atom, bool & l_hy); LIBMOL::REAL GetObjHdrBonding_qu(LIBMOL::REAL d_contact, LIBMOL::REAL r_distance, LIBMOL::REAL & obj_hyd); LIBMOL::REAL GetObjHdrBonding_inv(LIBMOL::REAL d_contact, LIBMOL::REAL r_distance, LIBMOL::REAL & obj_hyd); void CheckAndCalcHYDObj(int i_atom1, int i_atom2, LIBMOL::REAL d_contact, LIBMOL::REAL r_distance, LIBMOL::REAL & obj_hyd, bool & l_hyd_vdw); void CalcObjHYD_qu(LIBMOL::REAL d_contact, LIBMOL::REAL d_cutoff, LIBMOL::REAL r_distance, LIBMOL::REAL & obj_v); void CalcObjHYD_inv(LIBMOL::REAL d_contact, LIBMOL::REAL r_distance, LIBMOL::REAL & obj_v); void CalcObjVDW_qu(LIBMOL::REAL d_contact, LIBMOL::REAL d_cutoff, LIBMOL::REAL r_distance, LIBMOL::REAL & obj_v); // force void GetForVWRepuls(int i_atom); void CalcHBForce_qu(int i_atom1, int i_nbatom, LIBMOL::REAL d_contact, LIBMOL::REAL d_cutoff, LIBMOL::REAL r_distance, LIBMOL::REAL * r_comp); void CalcHBForce_inv(int i_atom1, int i_nbatom, LIBMOL::REAL d_contact, LIBMOL::REAL r_distance, LIBMOL::REAL * r_comp); void CalcVDWForce_qu(int i_atom1, int i_nbatom, LIBMOL::REAL d_contact, LIBMOL::REAL d_cutoff, LIBMOL::REAL r_distance, LIBMOL::REAL * r_comp); void CalcForce(int i_atom1, LIBMOL::REAL d_contact, LIBMOL::REAL d_cutoff, LIBMOL::REAL r_distance, LIBMOL::REAL * r_comp, bool l_hy_vdw, bool & l_next); // mixed calculation LIBMOL::REAL GetObjAndtForce(); LIBMOL::REAL GetBondLengthContrib( int idx_bond, int & idx_error); LIBMOL::REAL GetBondAngContrib(int idx__ang, int & idx_error); LIBMOL::REAL GetPlaneContrib(int idx__pl, int & idx_error); LIBMOL::REAL GetChiralityContrib(int idx__chira, int & idx_error); LIBMOL::REAL GetVWRandHBContrib(int idx_atom, int & idx_error); // derivatives void CheckAndCalcHYDFD(int i_atom1, int i_atom2, LIBMOL::REAL d_contact, LIBMOL::REAL r_distance, LIBMOL::REAL & d2f_dr2, bool & l_flag); void CalcHYDFD(LIBMOL::REAL d_contact, LIBMOL::REAL r_distance, LIBMOL::REAL & d2f_dr2, bool & l_hy_vdw); // normal matrix void VDWToNormalMatrixSparse(int atom1, int atom2, int vdw, LIBMOL::REAL ** f_ij); void HYDToNormalMatrixSparse(int i_atom1, int i_atom2, int i_hyd, bool & l_hyd_calc, LIBMOL::REAL ** fij); void SetFirstDerivVDW(int idx_atom, int idx_neighb, LIBMOL::REAL * dfdx_vdw); void SetFirstDerivHYD(int idx_atom, int idx_neighb, bool & l_hyd_calc, LIBMOL::REAL * dfdx_hyd); void SetVDWandHBConst(); void SetVDWContact (int i_atom1, int i_atom2, LIBMOL::REAL & d_cutoff); void SetHYDContact(int i_atom1, int i_atom2, LIBMOL::REAL & d_contact, LIBMOL::REAL & d_cutoff); void SetHBCoeffs(LIBMOL::REAL d_0, LIBMOL::REAL & A_ij, LIBMOL::REAL & B_ij); void CheckHYDFlag(int i_atom1, int i_atom2, int i_atom3, bool & l_flag); void CheckHYDFlag(int i_atom1, int i_atom2, bool & l_flag); void CheckHYD_DA_Flag(int i_atom1, int i_atom2, bool & l_flag); void CheckHYD_HA_Flag(int i_atom1, int i_atom2, bool & l_flag); // ----------------------------------------------------- void GetForPlanes(int i_plans); void GetForChiras(int i_chiras); void AccelCartesian(); void AccelCartesian(LIBMOL::REAL ** potential_deriv); void AccelTorsAng(); // Methods related to numeric integrations // a: Numerov algorithm void IntegEuler(LIBMOL::REAL & vaule_pre, LIBMOL::REAL & value, LIBMOL::REAL & velo_pre, LIBMOL::REAL & velo, LIBMOL::REAL & accel_pre, LIBMOL::REAL & accel, LIBMOL::REAL d_time); void IntegPred(LIBMOL::REAL & value_t, LIBMOL::REAL & value_pre, LIBMOL::REAL & value, LIBMOL::REAL & accel, LIBMOL::REAL d_time); void IntegCorr_1(LIBMOL::REAL & value_t, LIBMOL::REAL & value_pre, LIBMOL::REAL & value, LIBMOL::REAL & accel_pre, LIBMOL::REAL & accel_t, LIBMOL::REAL & accel, LIBMOL::REAL d_time); void IntegCorr_2(LIBMOL::REAL & value_pre, LIBMOL::REAL & value, LIBMOL::REAL & d_value_pre, LIBMOL::REAL & d_value_t, LIBMOL::REAL & d_value, LIBMOL::REAL d_time); void NumerovInt(); void NumerovInt(int i_iterations, LIBMOL::REAL & o_diff, LIBMOL::REAL & b_diff, LIBMOL::REAL ** b_deriv); // b: Velocity Verlet algorithm void VeloVerletInt(); // c: Conventional Verlet algorithm void VerletInt(); // A template methods that pick up the backbone torsion angles // out of all existing torsion angles in the tree // (Change will be made when the data structures are set void UpdatTors_t(); // Metheds that control MD process // Intialization needed by MD LIBMOL::REAL GetRand(); void InitCartVelo(int idx_way); void InitTorsVelo(int idx_way); void MD_Init(); void Dynamics(); void Evolution(); // put here temporarily // Methods linked to the kinetics (in MD) void CheckTotalE(); void TempScale(); void Quenching_V(); // Method related to debugging void StrucTransTest(); void VeloTransTest(); // Methods related to static minimizations(flash Freezing) // 1. process control void FlashingFreezing(); void SwitchSMIN(); void CheckShift(LIBMOL::REAL *d_x, int n_vars); // 2. The first and second derivatives in the Cartesian space void SetFirstDrivs(); void SetNormalMatrix(); void SetNormalMatrixSparse(int & num_block); void SetNormalMatrixSparseTors(int & num_block); void BondToNormalMatrix(); void BondToNormalMatrix(LIBMOL::REAL *** secdrivcart, LIBMOL::REAL * col_ind, LIBMOL::REAL * row_blk); void BondToNormalMatrixSparse(int atom1, int atom2, int bond, LIBMOL::REAL ** f_ij); void BondAngToNormalMatrix(); void BondAngToNormalMatrix(LIBMOL::REAL *** secdrivcart, LIBMOL::REAL * col_ind, LIBMOL::REAL * row_blk); void BondAngToNormalMatrixSparse(int atom1, int atom2, int ang, LIBMOL::REAL * dth_dx, LIBMOL::REAL ** f_ij); void TorsAngToNormalMatrix(); void TorsAngToNormalMatrix(LIBMOL::REAL *** secdrivcart, LIBMOL::REAL * col_ind, LIBMOL::REAL * row_blk); void TorsAngToNormalMatrixSparse(int atom1, int atom2, int tors, LIBMOL::REAL ** f_ij); void PlaneToNormalMatrix(); void PlaneToNormalMatrix(LIBMOL::REAL *** secdrivcart, LIBMOL::REAL * col_ind, LIBMOL::REAL * row_blk); void PlaneToNormalMatrixSparse(int atom1, int atom2, int plan, LIBMOL::REAL ** df_dx_p, LIBMOL::REAL ** f_ij); void ChiraToNormalMatrix(); void ChiraToNormalMatrix(LIBMOL::REAL *** secdrivcart, LIBMOL::REAL * col_ind, LIBMOL::REAL * row_blk); void ChiraToNormalMatrixSparse(int atom1, int atom2, int chir, LIBMOL::REAL * df_dx_c, LIBMOL::REAL ** f_ij); void VDWToNormalMatrix(); void VDWToNormalMatrix(LIBMOL::REAL *** secdrivcart, LIBMOL::REAL * col_ind, LIBMOL::REAL * row_blk); void SetFirstDerivBondOrder(int idx_bonds, LIBMOL::REAL * dfdx_b); void SetFirstDerivPlane(int idx_planes, LIBMOL::REAL ** df_dx_p); void SetFirstDerivChira(int idx_chira, LIBMOL::REAL *df_dx_c); void SetChiraAndFirstDeriv(int idx_chira, LIBMOL::REAL volume, LIBMOL::REAL *df_dx_c); // 3.The first and second derivatives in the Torsion angle space void SetTorsNormalUnit(); void SetTorsAcu(); void SetDobjDtorsFirst(); LIBMOL::REAL GetDobjDphi_i(int idx_tors); void SetDobjDtorsSecond(); void SetTorsDerivs(); void SetDerivTorsSpace(); // Find a minimum along a line // Put liner minimizer here because it involves many objective function // calculations void LinMin(LIBMOL::REAL * delta_x); void Bracket(int num_vars, LIBMOL::REAL * delta_x, LIBMOL::REAL * x_a, LIBMOL::REAL * x_b, LIBMOL::REAL * x_c, LIBMOL::REAL & obj_a, LIBMOL::REAL & obj_b, LIBMOL::REAL & obj_c); void Bracket(LIBMOL::REAL * x_a, LIBMOL::REAL * x_b); void GSection(LIBMOL::REAL * x_a, LIBMOL::REAL * x_b, LIBMOL::REAL * x_c, LIBMOL::REAL & obj_a, LIBMOL::REAL & obj_b, LIBMOL::REAL & obj_c); void checkConvergence(int idx_it, LIBMOL::REAL * tol_t); // 3. distance matrix void DistMatrixMin(); void LocalMin(); void AddToOptim(); void SelectBestOpt(); std::vector allAtoms; std::vector allHAtomIdx; //repeated ones std::vector allHydroAtoms; std::vector allBonds; std::vector allAngles; std::vector allTorsions; std::vector allChirals; std::vector allPlanes; std::map > allRings; std::vector allRingsV; std::vector allOptimSets; bool lGlob; int gWorkMode; int lWorkMode; int workSpace; int lComp; LIBMOL::REAL curObjValue; LIBMOL::REAL preObjValue; int numOptimSets; private: bool hasIniCoords; std::string itsFileNameRoot; std::string itsMonoRoot; }; class GetObjValue { }; extern bool sortOptSetByValues(const OptimSet & tSetA, const OptimSet & tSetB); } #endif /* GLOBOPT_H */