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#include "Thermo.hpp" |
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#include "ReadWrite.hpp" |
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#include "ForceFields.hpp" |
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#include "ExtendedSystem.hpp" |
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#include "simError.h" |
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extern "C"{ |
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Symplectic::Symplectic( SimInfo* the_entry_plug, ForceFields* the_ff ){ |
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Symplectic::Symplectic( SimInfo* the_entry_plug, ForceFields* the_ff, |
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ExtendedSystem* the_es ){ |
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entry_plug = the_entry_plug; |
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myFF = the_ff; |
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myES = the_es; |
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isFirst = 1; |
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molecules = entry_plug->molecules; |
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nMols = entry_plug->n_mol; |
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srInteractions = entry_plug->sr_interactions; |
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nSRI = entry_plug->n_SRI; |
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// give a little love back to the SimInfo object |
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if( entry_plug->the_integrator != NULL ) delete entry_plug->the_integrator; |
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mass = new double[entry_plug->n_atoms]; |
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for(int i = 0; i < entry_plug->n_atoms; i++){ |
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mass[i] = entry_plug->atoms[i]->getMass(); |
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} |
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} |
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// check for constraints |
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Constraint *temp_con; |
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Constraint *dummy_plug; |
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temp_con = new Constraint[nSRI]; |
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temp_con = new Constraint[entry_plug->n_SRI]; |
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n_constrained = 0; |
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int constrained = 0; |
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for(int i = 0; i < nSRI; i++){ |
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SRI** theArray; |
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for(int i = 0; i < nMols; i++){ |
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constrained = srInteractions[i]->is_constrained(); |
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if(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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dummy_plug = srInteractions[i]->get_constraint(); |
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temp_con[n_constrained].set_a( dummy_plug->get_a() ); |
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temp_con[n_constrained].set_b( dummy_plug->get_b() ); |
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temp_con[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[n_constrained].set_a( dummy_plug->get_a() ); |
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temp_con[n_constrained].set_b( dummy_plug->get_b() ); |
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temp_con[n_constrained].set_dsqr( dummy_plug->get_dsqr() ); |
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n_constrained++; |
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constrained = 0; |
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} |
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} |
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n_constrained++; |
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constrained = 0; |
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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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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[n_constrained].set_a( dummy_plug->get_a() ); |
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temp_con[n_constrained].set_b( dummy_plug->get_b() ); |
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temp_con[n_constrained].set_dsqr( dummy_plug->get_dsqr() ); |
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n_constrained++; |
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constrained = 0; |
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} |
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} |
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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[n_constrained].set_a( dummy_plug->get_a() ); |
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temp_con[n_constrained].set_b( dummy_plug->get_b() ); |
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temp_con[n_constrained].set_dsqr( dummy_plug->get_dsqr() ); |
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n_constrained++; |
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constrained = 0; |
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} |
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} |
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} |
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for(i=0; i<3; i++){ |
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for(j=0; j<3; j++){ |
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tempA[i][j] = A[i][j]; |
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tempA[j][i] = A[i][j]; |
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} |
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} |
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for(j=0; j<3; j++){ |
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A[j][i] = 0.0; |
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for(k=0; k<3; k++){ |
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A[j][i] += tempA[k][i] * rot[j][k]; |
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A[j][i] += tempA[i][k] * rot[j][k]; |
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} |
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} |
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} |
