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#include "SimInfo.hpp" |
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#include "Thermo.hpp" |
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#include "ReadWrite.hpp" |
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#include "ExtendedSystem.hpp" |
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extern "C"{ |
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} |
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Verlet::Verlet( SimInfo &info, ForceFields* the_ff ){ |
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Verlet::Verlet( SimInfo &info, ForceFields* the_ff, ExtendedSystem* the_es ){ |
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// get what information we need from the SimInfo object |
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entry_plug = &info; |
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myFF = the_ff; |
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myES = the_es; |
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c_natoms = info.n_atoms; |
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c_atoms = info.atoms; |
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c_sr_interactions = info.sr_interactions; |
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c_n_SRI = info.n_SRI; |
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nMols = info.n_mol; |
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molecules = info.molecules; |
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c_is_constrained = 0; |
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c_box_x = info.box_x; |
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c_box_y = info.box_y; |
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Constraint *temp_con; |
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Constraint *dummy_plug; |
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temp_con = new Constraint[c_n_SRI]; |
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temp_con = new Constraint[info.n_SRI]; |
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c_n_constrained = 0; |
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int constrained = 0; |
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for(int i = 0; i < c_n_SRI; i++){ |
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SRI** theArray; |
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for(int i = 0; i < nMols; i++){ |
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constrained = c_sr_interactions[i]->is_constrained(); |
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theArray = (SRI**) molecules[i].getMyBonds(); |
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for(int j=0; j<molecules[i].getNBonds(); j++){ |
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constrained = theArray[j]->is_constrained(); |
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if(constrained){ |
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dummy_plug = theArray[j]->get_constraint(); |
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temp_con[c_n_constrained].set_a( dummy_plug->get_a() ); |
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temp_con[c_n_constrained].set_b( dummy_plug->get_b() ); |
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temp_con[c_n_constrained].set_dsqr( dummy_plug->get_dsqr() ); |
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c_n_constrained++; |
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constrained = 0; |
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} |
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} |
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if(constrained){ |
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theArray = (SRI**) molecules[i].getMyBends(); |
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for(int j=0; j<molecules[i].getNBends(); j++){ |
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dummy_plug = c_sr_interactions[i]->get_constraint(); |
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temp_con[c_n_constrained].set_a( dummy_plug->get_a() ); |
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temp_con[c_n_constrained].set_b( dummy_plug->get_b() ); |
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temp_con[c_n_constrained].set_dsqr( dummy_plug->get_dsqr() ); |
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constrained = theArray[j]->is_constrained(); |
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if(constrained){ |
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dummy_plug = theArray[j]->get_constraint(); |
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temp_con[c_n_constrained].set_a( dummy_plug->get_a() ); |
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temp_con[c_n_constrained].set_b( dummy_plug->get_b() ); |
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temp_con[c_n_constrained].set_dsqr( dummy_plug->get_dsqr() ); |
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c_n_constrained++; |
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constrained = 0; |
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} |
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} |
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c_n_constrained++; |
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constrained = 0; |
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theArray = (SRI**) molecules[i].getMyTorsions(); |
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for(int j=0; j<molecules[i].getNTorsions(); j++){ |
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constrained = theArray[j]->is_constrained(); |
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if(constrained){ |
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dummy_plug = theArray[j]->get_constraint(); |
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temp_con[c_n_constrained].set_a( dummy_plug->get_a() ); |
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temp_con[c_n_constrained].set_b( dummy_plug->get_b() ); |
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temp_con[c_n_constrained].set_dsqr( dummy_plug->get_dsqr() ); |
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c_n_constrained++; |
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constrained = 0; |
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} |
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} |
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} |
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if(c_n_constrained > 0){ |
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c_constrained_i = new int[c_n_constrained]; |
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c_constrained_j = new int[c_n_constrained]; |
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c_constrained_dsqr = new double[c_n_constrained]; |
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for( int i = 0; i < c_n_constrained; i++){ |
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/* add 1 to the index for the fortran arrays. */ |
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c_constrained_i[i] = temp_con[i].get_a() + 1; |
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c_constrained_j[i] = temp_con[i].get_b() + 1; |
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c_constrained_dsqr[i] = temp_con[i].get_dsqr(); |
