1 // 2 // PBSAM.h 3 // pbsam 4 /* 5 Copyright (c) 2015, Teresa Head-Gordon, Lisa Felberg, Enghui Yap, David Brookes 6 All rights reserved. 7 8 Redistribution and use in source and binary forms, with or without 9 modification, are permitted provided that the following conditions are met: 10 * Redistributions of source code must retain the above copyright 11 notice, this list of conditions and the following disclaimer. 12 * Redistributions in binary form must reproduce the above copyright 13 notice, this list of conditions and the following disclaimer in the 14 documentation and/or other materials provided with the distribution. 15 * Neither the name of UC Berkeley nor the 16 names of its contributors may be used to endorse or promote products 17 derived from this software without specific prior written permission. 18 19 THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 20 ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 21 WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 22 DISCLAIMED. IN NO EVENT SHALL COPYRIGHT HOLDERS BE LIABLE FOR ANY 23 DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 24 (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 25 LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 26 ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 27 (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 28 SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 29 */ 30 31 #ifndef PBSAM_H 32 #define PBSAM_H 33 34 #include <memory> 35 #include <time.h> 36 //#include "PBAMStruct.h" 37 #include "PBSAMStruct.h" 38 #include "ElectrostaticsSAM.h" 39 #include "BDSAM.h" 40 41 using namespace std; 42 43 class PBSAM : protected PBSAMInput 44 { 45 protected: 46 shared_ptr<Setup> _setp_; 47 shared_ptr<SystemSAM> _syst_; 48 shared_ptr<Constants> _consts_; 49 50 shared_ptr<BesselConstants> _bessl_consts_; 51 shared_ptr<BesselCalc> _bessl_calc_; 52 shared_ptr<SHCalcConstants> _sh_consts_; 53 shared_ptr<SHCalc> _sh_calc_; 54 shared_ptr<ExpansionConstants> _exp_consts_; 55 56 shared_ptr<Solver> solvr_; 57 58 vector<shared_ptr<IEMatrix > > imats_; 59 vector<shared_ptr<HMatrix > > h_spol_; 60 vector<shared_ptr<FMatrix > > f_spol_; 61 62 double force_[MOL_MAX][3]; 63 double torque_[MOL_MAX][3]; 64 double nrg_intera_[MOL_MAX]; 65 66 int poles_; 67 double solveTol_; 68 69 public: 70 71 // Constructors 72 PBSAM(); 73 PBSAM(string infile); 74 // For APBS 75 PBSAM(const PBAMInput& pbami, const PBSAMInput& pbsami, 76 vector<shared_ptr<BaseMolecule> > mls ); 77 78 friend PBSAMInput getPBSAMParams(); 79 friend PBAMInput getPBAMParams(); 80 81 // Copy constructors 82 PBSAM( const PBSAM& pbsam ) ; 83 PBSAM( const PBSAM* pbsam ) ; 84 85 void check_setup(); 86 void check_system(); 87 88 void init_write_system(); 89 void init_consts_calcs(); 90 void initialize_pbsam(); 91 92 int run(); 93 // for running the APBS version 94 PBAMOutput run_apbs( ); 95 96 void run_bodyapprox(); 97 void run_dynamics(); 98 void run_electrostatics(); 99 void run_energyforce(); 100 101 shared_ptr<SystemSAM> make_subsystem(vector<int> mol_idx); 102 }; 103 104 105 #endif 106