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#include <iostream> |
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#include <cstdlib> |
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#include <stdlib.h> |
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#include <math.h> |
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|
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#ifdef IS_MPI |
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#include "mpiSimulation.hpp" |
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#include "simError.h" |
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|
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|
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Integrator::Integrator( SimInfo* theInfo, ForceFields* the_ff ){ |
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|
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template<typename T> Integrator<T>::Integrator(SimInfo* theInfo, |
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ForceFields* the_ff){ |
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info = theInfo; |
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myFF = the_ff; |
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isFirst = 1; |
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nMols = info->n_mol; |
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|
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// give a little love back to the SimInfo object |
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|
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if( info->the_integrator != NULL ) delete info->the_integrator; |
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info->the_integrator = this; |
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|
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if (info->the_integrator != NULL){ |
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delete info->the_integrator; |
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} |
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|
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nAtoms = info->n_atoms; |
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|
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// check for constraints |
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|
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constrainedA = NULL; |
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constrainedB = NULL; |
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|
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constrainedA = NULL; |
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constrainedB = NULL; |
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constrainedDsqr = NULL; |
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moving = NULL; |
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moved = NULL; |
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prePos = NULL; |
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|
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moving = NULL; |
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moved = NULL; |
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oldPos = NULL; |
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|
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nConstrained = 0; |
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|
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checkConstraints(); |
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} |
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|
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Integrator::~Integrator() { |
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|
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if( nConstrained ){ |
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template<typename T> Integrator<T>::~Integrator(){ |
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if (nConstrained){ |
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delete[] constrainedA; |
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delete[] constrainedB; |
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delete[] constrainedDsqr; |
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delete[] moving; |
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delete[] moved; |
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delete[] prePos; |
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k |
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delete[] oldPos; |
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} |
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|
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} |
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|
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void Integrator::checkConstraints( void ){ |
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|
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|
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template<typename T> void Integrator<T>::checkConstraints(void){ |
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isConstrained = 0; |
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|
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Constraint *temp_con; |
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Constraint *dummy_plug; |
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Constraint* temp_con; |
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Constraint* dummy_plug; |
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temp_con = new Constraint[info->n_SRI]; |
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nConstrained = 0; |
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int constrained = 0; |
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|
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|
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SRI** theArray; |
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for(int i = 0; i < nMols; i++){ |
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|
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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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|
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for (int i = 0; i < nMols; i++){ |
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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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|
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if(constrained){ |
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|
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dummy_plug = theArray[j]->get_constraint(); |
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temp_con[nConstrained].set_a( dummy_plug->get_a() ); |
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temp_con[nConstrained].set_b( dummy_plug->get_b() ); |
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temp_con[nConstrained].set_dsqr( dummy_plug->get_dsqr() ); |
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|
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nConstrained++; |
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constrained = 0; |
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|
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if (constrained){ |
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dummy_plug = theArray[j]->get_constraint(); |
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temp_con[nConstrained].set_a(dummy_plug->get_a()); |
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temp_con[nConstrained].set_b(dummy_plug->get_b()); |
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temp_con[nConstrained].set_dsqr(dummy_plug->get_dsqr()); |
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|
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nConstrained++; |
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constrained = 0; |
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} |
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} |
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|
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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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|
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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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|
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if(constrained){ |
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|
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dummy_plug = theArray[j]->get_constraint(); |
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temp_con[nConstrained].set_a( dummy_plug->get_a() ); |
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temp_con[nConstrained].set_b( dummy_plug->get_b() ); |
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temp_con[nConstrained].set_dsqr( dummy_plug->get_dsqr() ); |
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|
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nConstrained++; |
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constrained = 0; |
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|
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if (constrained){ |
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dummy_plug = theArray[j]->get_constraint(); |
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temp_con[nConstrained].set_a(dummy_plug->get_a()); |
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temp_con[nConstrained].set_b(dummy_plug->get_b()); |
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temp_con[nConstrained].set_dsqr(dummy_plug->get_dsqr()); |
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|
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nConstrained++; |
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constrained = 0; |
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} |
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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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|
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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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|
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if(constrained){ |
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|
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dummy_plug = theArray[j]->get_constraint(); |
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temp_con[nConstrained].set_a( dummy_plug->get_a() ); |
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temp_con[nConstrained].set_b( dummy_plug->get_b() ); |
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temp_con[nConstrained].set_dsqr( dummy_plug->get_dsqr() ); |
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|
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nConstrained++; |
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constrained = 0; |
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|
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if (constrained){ |
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dummy_plug = theArray[j]->get_constraint(); |
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temp_con[nConstrained].set_a(dummy_plug->get_a()); |
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temp_con[nConstrained].set_b(dummy_plug->get_b()); |
105 |
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temp_con[nConstrained].set_dsqr(dummy_plug->get_dsqr()); |
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|
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nConstrained++; |
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constrained = 0; |
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} |
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} |
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} |
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|
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if(nConstrained > 0){ |
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|
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if (nConstrained > 0){ |
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isConstrained = 1; |
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|
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if(constrainedA != NULL ) delete[] constrainedA; |
117 |
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if(constrainedB != NULL ) delete[] constrainedB; |
118 |
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if(constrainedDsqr != NULL ) delete[] constrainedDsqr; |
116 |
> |
if (constrainedA != NULL) |
117 |
> |
delete[] constrainedA; |
118 |
> |
if (constrainedB != NULL) |
119 |
> |
delete[] constrainedB; |
120 |
> |
if (constrainedDsqr != NULL) |
121 |
> |
delete[] constrainedDsqr; |
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|
123 |
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constrainedA = new int[nConstrained]; |
124 |
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constrainedB = new int[nConstrained]; |
123 |
> |
constrainedA = new int[nConstrained]; |
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> |
constrainedB = new int[nConstrained]; |
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constrainedDsqr = new double[nConstrained]; |
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|
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for( int i = 0; i < nConstrained; i++){ |
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|
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|
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for (int i = 0; i < nConstrained; i++){ |
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constrainedA[i] = temp_con[i].get_a(); |
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constrainedB[i] = temp_con[i].get_b(); |
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constrainedDsqr[i] = temp_con[i].get_dsqr(); |
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} |
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|
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|
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|
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// save oldAtoms to check for lode balanceing later on. |
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|
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|
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oldAtoms = nAtoms; |
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|
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|
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moving = new int[nAtoms]; |
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moved = new int[nAtoms]; |
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> |
moved = new int[nAtoms]; |
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|
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prePos = new double[nAtoms*3]; |
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> |
oldPos = new double[nAtoms * 3]; |
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} |
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|
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|
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delete[] temp_con; |
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} |
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|
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|
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< |
void Integrator::integrate( void ){ |
148 |
> |
template<typename T> void Integrator<T>::integrate(void){ |
149 |
|
|
150 |
< |
int i, j; // loop counters |
151 |
< |
double kE = 0.0; // the kinetic energy |
152 |
< |
double rot_kE; |
162 |
< |
double trans_kE; |
163 |
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int tl; // the time loop conter |
164 |
< |
double dt2; // half the dt |
165 |
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|
166 |
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double vx, vy, vz; // the velocities |
167 |
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double vx2, vy2, vz2; // the square of the velocities |
168 |
< |
double rx, ry, rz; // the postitions |
169 |
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|
170 |
< |
double ji[3]; // the body frame angular momentum |
171 |
< |
double jx2, jy2, jz2; // the square of the angular momentums |
172 |
< |
double Tb[3]; // torque in the body frame |
173 |
< |
double angle; // the angle through which to rotate the rotation matrix |
174 |
< |
double A[3][3]; // the rotation matrix |
175 |
< |
double press[9]; |
176 |
< |
|
177 |
< |
double dt = info->dt; |
178 |
< |
double runTime = info->run_time; |
179 |
< |
double sampleTime = info->sampleTime; |
180 |
< |
double statusTime = info->statusTime; |
150 |
> |
double runTime = info->run_time; |
151 |
> |
double sampleTime = info->sampleTime; |
152 |
> |
double statusTime = info->statusTime; |
153 |
|
double thermalTime = info->thermalTime; |
154 |
+ |
double resetTime = info->resetTime; |
155 |
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|
156 |
+ |
|
157 |
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double currSample; |
158 |
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double currThermal; |
159 |
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double currStatus; |
160 |
< |
double currTime; |
160 |
> |
double currReset; |
161 |
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|
162 |
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int calcPot, calcStress; |
189 |
– |
int isError; |
163 |
|
|
164 |
< |
tStats = new Thermo( info ); |
165 |
< |
e_out = new StatWriter( info ); |
166 |
< |
dump_out = new DumpWriter( info ); |
164 |
> |
tStats = new Thermo(info); |
165 |
> |
statOut = new StatWriter(info); |
166 |
> |
dumpOut = new DumpWriter(info); |
167 |
|
|
168 |
< |
Atom** atoms = info->atoms; |
169 |
< |
DirectionalAtom* dAtom; |
168 |
> |
atoms = info->atoms; |
169 |
> |
|
170 |
> |
dt = info->dt; |
171 |
|
dt2 = 0.5 * dt; |
172 |
|
|
173 |
+ |
readyCheck(); |
174 |
+ |
|
175 |
|
// initialize the forces before the first step |
176 |
|
|
177 |
< |
myFF->doForces(1,1); |
178 |
< |
|
179 |
< |
if( info->setTemp ){ |
180 |
< |
|
181 |
< |
tStats->velocitize(); |
177 |
> |
calcForce(1, 1); |
178 |
> |
|
179 |
> |
if (nConstrained){ |
180 |
> |
preMove(); |
181 |
> |
constrainA(); |
182 |
> |
calcForce(1, 1); |
183 |
> |
constrainB(); |
184 |
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} |
185 |
|
|
186 |
< |
dump_out->writeDump( 0.0 ); |
187 |
< |
e_out->writeStat( 0.0 ); |
188 |
< |
|
186 |
> |
if (info->setTemp){ |
187 |
> |
thermalize(); |
188 |
> |
} |
189 |
> |
|
190 |
|
calcPot = 0; |
191 |
|
calcStress = 0; |
192 |
< |
currSample = sampleTime; |
193 |
< |
currThermal = thermalTime; |
194 |
< |
currStatus = statusTime; |
195 |
< |
currTime = 0.0;; |
192 |
> |
currSample = sampleTime + info->getTime(); |
193 |
> |
currThermal = thermalTime+ info->getTime(); |
194 |
> |
currStatus = statusTime + info->getTime(); |
195 |
> |
currReset = resetTime + info->getTime(); |
196 |
|
|
197 |
< |
while( currTime < runTime ){ |
197 |
> |
dumpOut->writeDump(info->getTime()); |
198 |
> |
statOut->writeStat(info->getTime()); |
199 |
|
|
200 |
< |
if( (currTime+dt) >= currStatus ){ |
200 |
> |
|
201 |
> |
#ifdef IS_MPI |
202 |
> |
strcpy(checkPointMsg, "The integrator is ready to go."); |
203 |
> |
MPIcheckPoint(); |
204 |
> |
#endif // is_mpi |
205 |
> |
|
206 |
> |
while (info->getTime() < runTime){ |
207 |
> |
if ((info->getTime() + dt) >= currStatus){ |
208 |
|
calcPot = 1; |
209 |
|
calcStress = 1; |
210 |
|
} |
224 |
– |
|
225 |
– |
integrateStep( calcPot, calcStress ); |
226 |
– |
|
227 |
– |
currTime += dt; |
211 |
|
|
212 |
< |
if( info->setTemp ){ |
213 |
< |
if( currTime >= currThermal ){ |
214 |
< |
tStats->velocitize(); |
215 |
< |
currThermal += thermalTime; |
212 |
> |
integrateStep(calcPot, calcStress); |
213 |
> |
|
214 |
> |
info->incrTime(dt); |
215 |
> |
|
216 |
> |
if (info->setTemp){ |
217 |
> |
if (info->getTime() >= currThermal){ |
218 |
> |
thermalize(); |
219 |
> |
currThermal += thermalTime; |
220 |
|
} |
221 |
|
} |
222 |
|
|
223 |
< |
if( currTime >= currSample ){ |
224 |
< |
dump_out->writeDump( currTime ); |
223 |
> |
if (info->getTime() >= currSample){ |
224 |
> |
dumpOut->writeDump(info->getTime()); |
225 |
|
currSample += sampleTime; |
226 |
|
} |
227 |
|
|
228 |
< |
if( currTime >= currStatus ){ |
229 |
< |
e_out->writeStat( time * dt ); |
230 |
< |
calcPot = 0; |
228 |
> |
if (info->getTime() >= currStatus){ |
229 |
> |
statOut->writeStat(info->getTime()); |
230 |
> |
calcPot = 0; |
231 |
|
calcStress = 0; |
232 |
|
currStatus += statusTime; |
233 |
< |
} |
247 |
< |
} |
248 |
< |
|
249 |
< |
dump_out->writeFinal(); |
233 |
> |
} |
234 |
|
|
235 |
< |
delete dump_out; |
236 |
< |
delete e_out; |
237 |
< |
} |
235 |
> |
if (info->resetIntegrator){ |
236 |
> |
if (info->getTime() >= currReset){ |
237 |
> |
this->resetIntegrator(); |
238 |
> |
currReset += resetTime; |
239 |
> |
} |
240 |
> |
} |
241 |
|
|
242 |
< |
void Integrator::integrateStep( int calcPot, int calcStress ){ |
242 |
> |
#ifdef IS_MPI |
243 |
> |
strcpy(checkPointMsg, "successfully took a time step."); |
244 |
> |
MPIcheckPoint(); |
245 |
> |
#endif // is_mpi |
246 |
> |
} |
247 |
|
|
248 |
+ |
|
249 |
+ |
// write the last frame |
250 |
+ |
dumpOut->writeDump(info->getTime()); |
251 |
+ |
|
252 |
+ |
delete dumpOut; |
253 |
+ |
delete statOut; |
254 |
+ |
} |
255 |
+ |
|
256 |
+ |
template<typename T> void Integrator<T>::integrateStep(int calcPot, |
257 |
+ |
int calcStress){ |
258 |
|
// Position full step, and velocity half step |
259 |
+ |
preMove(); |
260 |
|
|
259 |
– |
//preMove(); |
261 |
|
moveA(); |
261 |
– |
if( nConstrained ) constrainA(); |
262 |
|
|
263 |
+ |
|
264 |
+ |
|
265 |
+ |
|
266 |
+ |
#ifdef IS_MPI |
267 |
+ |
strcpy(checkPointMsg, "Succesful moveA\n"); |
268 |
+ |
MPIcheckPoint(); |
269 |
+ |
#endif // is_mpi |
270 |
+ |
|
271 |
+ |
|
272 |
|
// calc forces |
273 |
|
|
274 |
< |
myFF->doForces(calcPot,calcStress); |
274 |
> |
calcForce(calcPot, calcStress); |
275 |
|
|
276 |
+ |
#ifdef IS_MPI |
277 |
+ |
strcpy(checkPointMsg, "Succesful doForces\n"); |
278 |
+ |
MPIcheckPoint(); |
279 |
+ |
#endif // is_mpi |
280 |
+ |
|
281 |
+ |
|
282 |
|
// finish the velocity half step |
283 |
< |
|
283 |
> |
|
284 |
|
moveB(); |
285 |
< |
if( nConstrained ) constrainB(); |
286 |
< |
|
285 |
> |
|
286 |
> |
|
287 |
> |
|
288 |
> |
#ifdef IS_MPI |
289 |
> |
strcpy(checkPointMsg, "Succesful moveB\n"); |
290 |
> |
MPIcheckPoint(); |
291 |
> |
#endif // is_mpi |
292 |
|
} |
293 |
|
|
294 |
|
|
295 |
< |
void Integrator::moveA( void ){ |
296 |
< |
|
277 |
< |
int i,j,k; |
278 |
< |
int atomIndex, aMatIndex; |
295 |
> |
template<typename T> void Integrator<T>::moveA(void){ |
296 |
> |
int i, j; |
297 |
|
DirectionalAtom* dAtom; |
298 |
< |
double Tb[3]; |
299 |
< |
double ji[3]; |
298 |
> |
double Tb[3], ji[3]; |
299 |
> |
double vel[3], pos[3], frc[3]; |
300 |
> |
double mass; |
301 |
|
|
302 |
< |
for( i=0; i<nAtoms; i++ ){ |
303 |
< |
atomIndex = i * 3; |
304 |
< |
aMatIndex = i * 9; |
305 |
< |
|
287 |
< |
// velocity half step |
288 |
< |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
289 |
< |
vel[j] += ( dt2 * frc[j] / atoms[i]->getMass() ) * eConvert; |
302 |
> |
for (i = 0; i < nAtoms; i++){ |
303 |
> |
atoms[i]->getVel(vel); |
304 |
> |
atoms[i]->getPos(pos); |
305 |
> |
atoms[i]->getFrc(frc); |
306 |
|
|
307 |
< |
// position whole step |
308 |
< |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
307 |
> |
mass = atoms[i]->getMass(); |
308 |
> |
|
309 |
> |
for (j = 0; j < 3; j++){ |
310 |
> |
// velocity half step |
311 |
> |
vel[j] += (dt2 * frc[j] / mass) * eConvert; |
312 |
> |
// position whole step |
313 |
|
pos[j] += dt * vel[j]; |
314 |
+ |
} |
315 |
|
|
316 |
< |
|
317 |
< |
if( atoms[i]->isDirectional() ){ |
316 |
> |
atoms[i]->setVel(vel); |
317 |
> |
atoms[i]->setPos(pos); |
318 |
|
|
319 |
< |
dAtom = (DirectionalAtom *)atoms[i]; |
320 |
< |
|
319 |
> |
if (atoms[i]->isDirectional()){ |
320 |
> |
dAtom = (DirectionalAtom *) atoms[i]; |
321 |
> |
|
322 |
|
// get and convert the torque to body frame |
323 |
< |
|
324 |
< |
Tb[0] = dAtom->getTx(); |
325 |
< |
Tb[1] = dAtom->getTy(); |
326 |
< |
Tb[2] = dAtom->getTz(); |
305 |
< |
|
306 |
< |
dAtom->lab2Body( Tb ); |
307 |
< |
|
323 |
> |
|
324 |
> |
dAtom->getTrq(Tb); |
325 |
> |
dAtom->lab2Body(Tb); |
326 |
> |
|
327 |
|
// get the angular momentum, and propagate a half step |
328 |
< |
|
329 |
< |
ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * eConvert; |
330 |
< |
ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * eConvert; |
331 |
< |
ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * eConvert; |
332 |
< |
|
333 |
< |
// use the angular velocities to propagate the rotation matrix a |
334 |
< |
// full time step |
335 |
< |
|
336 |
< |
// rotate about the x-axis |
318 |
< |
angle = dt2 * ji[0] / dAtom->getIxx(); |
319 |
< |
this->rotate( 1, 2, angle, ji, &aMat[aMatIndex] ); |
320 |
< |
|
321 |
< |
// rotate about the y-axis |
322 |
< |
angle = dt2 * ji[1] / dAtom->getIyy(); |
323 |
< |
this->rotate( 2, 0, angle, ji, &aMat[aMatIndex] ); |
324 |
< |
|
325 |
< |
// rotate about the z-axis |
326 |
< |
angle = dt * ji[2] / dAtom->getIzz(); |
327 |
< |
this->rotate( 0, 1, angle, ji, &aMat[aMatIndex] ); |
328 |
< |
|
329 |
< |
// rotate about the y-axis |
330 |
< |
angle = dt2 * ji[1] / dAtom->getIyy(); |
331 |
< |
this->rotate( 2, 0, angle, ji, &aMat[aMatIndex] ); |
332 |
< |
|
333 |
< |
// rotate about the x-axis |
334 |
< |
angle = dt2 * ji[0] / dAtom->getIxx(); |
335 |
< |
this->rotate( 1, 2, angle, ji, &aMat[aMatIndex] ); |
336 |
< |
|
337 |
< |
dAtom->setJx( ji[0] ); |
338 |
< |
dAtom->setJy( ji[1] ); |
339 |
< |
dAtom->setJz( ji[2] ); |
328 |
> |
|
329 |
> |
dAtom->getJ(ji); |
330 |
> |
|
331 |
> |
for (j = 0; j < 3; j++) |
332 |
> |
ji[j] += (dt2 * Tb[j]) * eConvert; |
333 |
> |
|
334 |
> |
this->rotationPropagation( dAtom, ji ); |
335 |
> |
|
336 |
> |
dAtom->setJ(ji); |
337 |
|
} |
341 |
– |
|
338 |
|
} |
339 |
+ |
|
340 |
+ |
if (nConstrained){ |
341 |
+ |
constrainA(); |
342 |
+ |
} |
343 |
|
} |
344 |
|
|
345 |
|
|
346 |
< |
void Integrator::moveB( void ){ |
347 |
< |
int i,j,k; |
348 |
< |
int atomIndex; |
346 |
> |
template<typename T> void Integrator<T>::moveB(void){ |
347 |
> |
int i, j; |
348 |
|
DirectionalAtom* dAtom; |
349 |
< |
double Tb[3]; |
350 |
< |
double ji[3]; |
349 |
> |
double Tb[3], ji[3]; |
350 |
> |
double vel[3], frc[3]; |
351 |
> |
double mass; |
352 |
|
|
353 |
< |
for( i=0; i<nAtoms; i++ ){ |
354 |
< |
atomIndex = i * 3; |
353 |
> |
for (i = 0; i < nAtoms; i++){ |
354 |
> |
atoms[i]->getVel(vel); |
355 |
> |
atoms[i]->getFrc(frc); |
356 |
|
|
357 |
+ |
mass = atoms[i]->getMass(); |
358 |
+ |
|
359 |
|
// velocity half step |
360 |
< |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
361 |
< |
vel[j] += ( dt2 * frc[j] / atoms[i]->getMass() ) * eConvert; |
360 |
> |
for (j = 0; j < 3; j++) |
361 |
> |
vel[j] += (dt2 * frc[j] / mass) * eConvert; |
362 |
|
|
363 |
< |
if( atoms[i]->isDirectional() ){ |
364 |
< |
|
365 |
< |
dAtom = (DirectionalAtom *)atoms[i]; |
366 |
< |
|
363 |
> |
atoms[i]->setVel(vel); |
364 |
> |
|
365 |
> |
if (atoms[i]->isDirectional()){ |
366 |
> |
dAtom = (DirectionalAtom *) atoms[i]; |
367 |
> |
|
368 |
|
// get and convert the torque to body frame |
369 |
< |
|
370 |
< |
Tb[0] = dAtom->getTx(); |
371 |
< |
Tb[1] = dAtom->getTy(); |
372 |
< |
Tb[2] = dAtom->getTz(); |
373 |
< |
|
374 |
< |
dAtom->lab2Body( Tb ); |
375 |
< |
|
376 |
< |
// get the angular momentum, and complete the angular momentum |
377 |
< |
// half step |
378 |
< |
|
379 |
< |
ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * eConvert; |
380 |
< |
ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * eConvert; |
381 |
< |
ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * eConvert; |
378 |
< |
|
379 |
< |
jx2 = ji[0] * ji[0]; |
380 |
< |
jy2 = ji[1] * ji[1]; |
381 |
< |
jz2 = ji[2] * ji[2]; |
382 |
< |
|
383 |
< |
dAtom->setJx( ji[0] ); |
384 |
< |
dAtom->setJy( ji[1] ); |
385 |
< |
dAtom->setJz( ji[2] ); |
369 |
> |
|
370 |
> |
dAtom->getTrq(Tb); |
371 |
> |
dAtom->lab2Body(Tb); |
372 |
> |
|
373 |
> |
// get the angular momentum, and propagate a half step |
374 |
> |
|
375 |
> |
dAtom->getJ(ji); |
376 |
> |
|
377 |
> |
for (j = 0; j < 3; j++) |
378 |
> |
ji[j] += (dt2 * Tb[j]) * eConvert; |
379 |
> |
|
380 |
> |
|
381 |
> |
dAtom->setJ(ji); |
382 |
|
} |
383 |
|
} |
384 |
|
|
385 |
+ |
if (nConstrained){ |
386 |
+ |
constrainB(); |
387 |
+ |
} |
388 |
|
} |
389 |
|
|
390 |
< |
void Integrator::preMove( void ){ |
391 |
< |
int i; |
390 |
> |
template<typename T> void Integrator<T>::preMove(void){ |
391 |
> |
int i, j; |
392 |
> |
double pos[3]; |
393 |
|
|
394 |
< |
if( nConstrained ){ |
395 |
< |
if( oldAtoms != nAtoms ){ |
396 |
< |
|
397 |
< |
// save oldAtoms to check for lode balanceing later on. |
398 |
< |
|
399 |
< |
oldAtoms = nAtoms; |
400 |
< |
|
401 |
< |
delete[] moving; |
402 |
< |
delete[] moved; |
403 |
< |
delete[] oldPos; |
404 |
< |
|
405 |
< |
moving = new int[nAtoms]; |
406 |
< |
moved = new int[nAtoms]; |
407 |
< |
|
408 |
< |
oldPos = new double[nAtoms*3]; |
394 |
> |
if (nConstrained){ |
395 |
> |
for (i = 0; i < nAtoms; i++){ |
396 |
> |
atoms[i]->getPos(pos); |
397 |
> |
|
398 |
> |
for (j = 0; j < 3; j++){ |
399 |
> |
oldPos[3 * i + j] = pos[j]; |
400 |
> |
} |
401 |
|
} |
410 |
– |
|
411 |
– |
for(i=0; i<(nAtoms*3); i++) oldPos[i] = pos[i]; |
402 |
|
} |
403 |
< |
} |
403 |
> |
} |
404 |
|
|
405 |
< |
void Integrator::constrainA(){ |
406 |
< |
|
417 |
< |
int i,j,k; |
405 |
> |
template<typename T> void Integrator<T>::constrainA(){ |
406 |
> |
int i, j; |
407 |
|
int done; |
408 |
< |
double pxab, pyab, pzab; |
409 |
< |
double rxab, ryab, rzab; |
410 |
< |
int a, b; |
408 |
> |
double posA[3], posB[3]; |
409 |
> |
double velA[3], velB[3]; |
410 |
> |
double pab[3]; |
411 |
> |
double rab[3]; |
412 |
> |
int a, b, ax, ay, az, bx, by, bz; |
413 |
|
double rma, rmb; |
414 |
|
double dx, dy, dz; |
415 |
+ |
double rpab; |
416 |
|
double rabsq, pabsq, rpabsq; |
417 |
|
double diffsq; |
418 |
|
double gab; |
419 |
|
int iteration; |
420 |
|
|
421 |
< |
|
430 |
< |
|
431 |
< |
for( i=0; i<nAtoms; i++){ |
432 |
< |
|
421 |
> |
for (i = 0; i < nAtoms; i++){ |
422 |
|
moving[i] = 0; |
423 |
< |
moved[i] = 1; |
423 |
> |
moved[i] = 1; |
424 |
|
} |
425 |
< |
|
437 |
< |
|
425 |
> |
|
426 |
|
iteration = 0; |
427 |
|
done = 0; |
428 |
< |
while( !done && (iteration < maxIteration )){ |
441 |
< |
|
428 |
> |
while (!done && (iteration < maxIteration)){ |
429 |
|
done = 1; |
430 |
< |
for(i=0; i<nConstrained; i++){ |
444 |
< |
|
430 |
> |
for (i = 0; i < nConstrained; i++){ |
431 |
|
a = constrainedA[i]; |
432 |
|
b = constrainedB[i]; |
447 |
– |
|
448 |
– |
if( moved[a] || moved[b] ){ |
449 |
– |
|
450 |
– |
pxab = pos[3*a+0] - pos[3*b+0]; |
451 |
– |
pyab = pos[3*a+1] - pos[3*b+1]; |
452 |
– |
pzab = pos[3*a+2] - pos[3*b+2]; |
433 |
|
|
434 |
< |
//periodic boundary condition |
435 |
< |
pxab = pxab - info->box_x * copysign(1, pxab) |
436 |
< |
* int(pxab / info->box_x + 0.5); |
457 |
< |
pyab = pyab - info->box_y * copysign(1, pyab) |
458 |
< |
* int(pyab / info->box_y + 0.5); |
459 |
< |
pzab = pzab - info->box_z * copysign(1, pzab) |
460 |
< |
* int(pzab / info->box_z + 0.5); |
461 |
< |
|
462 |
< |
pabsq = pxab * pxab + pyab * pyab + pzab * pzab; |
463 |
< |
rabsq = constraintedDsqr[i]; |
464 |
< |
diffsq = pabsq - rabsq; |
434 |
> |
ax = (a * 3) + 0; |
435 |
> |
ay = (a * 3) + 1; |
436 |
> |
az = (a * 3) + 2; |
437 |
|
|
438 |
< |
// the original rattle code from alan tidesley |
439 |
< |
if (fabs(diffsq) > tol*rabsq*2) { |
440 |
< |
rxab = oldPos[3*a+0] - oldPos[3*b+0]; |
469 |
< |
ryab = oldPos[3*a+1] - oldPos[3*b+1]; |
470 |
< |
rzab = oldPos[3*a+2] - oldPos[3*b+2]; |
471 |
< |
|
472 |
< |
rxab = rxab - info->box_x * copysign(1, rxab) |
473 |
< |
* int(rxab / info->box_x + 0.5); |
474 |
< |
ryab = ryab - info->box_y * copysign(1, ryab) |
475 |
< |
* int(ryab / info->box_y + 0.5); |
476 |
< |
rzab = rzab - info->box_z * copysign(1, rzab) |
477 |
< |
* int(rzab / info->box_z + 0.5); |
438 |
> |
bx = (b * 3) + 0; |
439 |
> |
by = (b * 3) + 1; |
440 |
> |
bz = (b * 3) + 2; |
441 |
|
|
442 |
< |
rpab = rxab * pxab + ryab * pyab + rzab * pzab; |
443 |
< |
rpabsq = rpab * rpab; |
442 |
> |
if (moved[a] || moved[b]){ |
443 |
> |
atoms[a]->getPos(posA); |
444 |
> |
atoms[b]->getPos(posB); |
445 |
|
|
446 |
+ |
for (j = 0; j < 3; j++) |
447 |
+ |
pab[j] = posA[j] - posB[j]; |
448 |
|
|
449 |
< |
if (rpabsq < (rabsq * -diffsq)){ |
449 |
> |
//periodic boundary condition |
450 |
> |
|
451 |
> |
info->wrapVector(pab); |
452 |
> |
|
453 |
> |
pabsq = pab[0] * pab[0] + pab[1] * pab[1] + pab[2] * pab[2]; |
454 |
> |
|
455 |
> |
rabsq = constrainedDsqr[i]; |
456 |
> |
diffsq = rabsq - pabsq; |
457 |
> |
|
458 |
> |
// the original rattle code from alan tidesley |
459 |
> |
if (fabs(diffsq) > (tol * rabsq * 2)){ |
460 |
> |
rab[0] = oldPos[ax] - oldPos[bx]; |
461 |
> |
rab[1] = oldPos[ay] - oldPos[by]; |
462 |
> |
rab[2] = oldPos[az] - oldPos[bz]; |
463 |
> |
|
464 |
> |
info->wrapVector(rab); |
465 |
> |
|
466 |
> |
rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2]; |
467 |
> |
|
468 |
> |
rpabsq = rpab * rpab; |
469 |
> |
|
470 |
> |
|
471 |
> |
if (rpabsq < (rabsq * -diffsq)){ |
472 |
|
#ifdef IS_MPI |
473 |
< |
a = atoms[a]->getGlobalIndex(); |
474 |
< |
b = atoms[b]->getGlobalIndex(); |
473 |
> |
a = atoms[a]->getGlobalIndex(); |
474 |
> |
b = atoms[b]->getGlobalIndex(); |
475 |
|
#endif //is_mpi |
476 |
< |
sprintf( painCave.errMsg, |
477 |
< |
"Constraint failure in constrainA at atom %d and %d\n.", |
478 |
< |
a, b ); |
479 |
< |
painCave.isFatal = 1; |
480 |
< |
simError(); |
481 |
< |
} |
476 |
> |
sprintf(painCave.errMsg, |
477 |
> |
"Constraint failure in constrainA at atom %d and %d.\n", a, |
478 |
> |
b); |
479 |
> |
painCave.isFatal = 1; |
480 |
> |
simError(); |
481 |
> |
} |
482 |
|
|
483 |
< |
rma = 1.0 / atoms[a]->getMass(); |
484 |
< |
rmb = 1.0 / atoms[b]->getMass(); |
497 |
< |
|
498 |
< |
gab = diffsq / ( 2.0 * ( rma + rmb ) * rpab ); |
499 |
< |
dx = rxab * gab; |
500 |
< |
dy = ryab * gab; |
501 |
< |
dz = rzab * gab; |
483 |
> |
rma = 1.0 / atoms[a]->getMass(); |
484 |
> |
rmb = 1.0 / atoms[b]->getMass(); |
485 |
|
|
486 |
< |
pos[3*a+0] += rma * dx; |
504 |
< |
pos[3*a+1] += rma * dy; |
505 |
< |
pos[3*a+2] += rma * dz; |
486 |
> |
gab = diffsq / (2.0 * (rma + rmb) * rpab); |
487 |
|
|
488 |
< |
pos[3*b+0] -= rmb * dx; |
489 |
< |
pos[3*b+1] -= rmb * dy; |
490 |
< |
pos[3*b+2] -= rmb * dz; |
488 |
> |
dx = rab[0] * gab; |
489 |
> |
dy = rab[1] * gab; |
490 |
> |
dz = rab[2] * gab; |
491 |
|
|
492 |
+ |
posA[0] += rma * dx; |
493 |
+ |
posA[1] += rma * dy; |
494 |
+ |
posA[2] += rma * dz; |
495 |
+ |
|
496 |
+ |
atoms[a]->setPos(posA); |
497 |
+ |
|
498 |
+ |
posB[0] -= rmb * dx; |
499 |
+ |
posB[1] -= rmb * dy; |
500 |
+ |
posB[2] -= rmb * dz; |
501 |
+ |
|
502 |
+ |
atoms[b]->setPos(posB); |
503 |
+ |
|
504 |
|
dx = dx / dt; |
505 |
|
dy = dy / dt; |
506 |
|
dz = dz / dt; |
507 |
|
|
508 |
< |
vel[3*a+0] += rma * dx; |
516 |
< |
vel[3*a+1] += rma * dy; |
517 |
< |
vel[3*a+2] += rma * dz; |
508 |
> |
atoms[a]->getVel(velA); |
509 |
|
|
510 |
< |
vel[3*b+0] -= rmb * dx; |
511 |
< |
vel[3*b+1] -= rmb * dy; |
512 |
< |
vel[3*b+2] -= rmb * dz; |
510 |
> |
velA[0] += rma * dx; |
511 |
> |
velA[1] += rma * dy; |
512 |
> |
velA[2] += rma * dz; |
513 |
|
|
514 |
< |
moving[a] = 1; |
515 |
< |
moving[b] = 1; |
516 |
< |
done = 0; |
517 |
< |
} |
514 |
> |
atoms[a]->setVel(velA); |
515 |
> |
|
516 |
> |
atoms[b]->getVel(velB); |
517 |
> |
|
518 |
> |
velB[0] -= rmb * dx; |
519 |
> |
velB[1] -= rmb * dy; |
520 |
> |
velB[2] -= rmb * dz; |
521 |
> |
|
522 |
> |
atoms[b]->setVel(velB); |
523 |
> |
|
524 |
> |
moving[a] = 1; |
525 |
> |
moving[b] = 1; |
526 |
> |
done = 0; |
527 |
> |
} |
528 |
|
} |
529 |
|
} |
530 |
< |
|
531 |
< |
for(i=0; i<nAtoms; i++){ |
531 |
< |
|
530 |
> |
|
531 |
> |
for (i = 0; i < nAtoms; i++){ |
532 |
|
moved[i] = moving[i]; |
533 |
|
moving[i] = 0; |
534 |
|
} |
536 |
|
iteration++; |
537 |
|
} |
538 |
|
|
539 |
< |
if( !done ){ |
540 |
< |
|
541 |
< |
sprintf( painCae.errMsg, |
542 |
< |
"Constraint failure in constrainA, too many iterations: %d\n", |
543 |
< |
iterations ); |
539 |
> |
if (!done){ |
540 |
> |
sprintf(painCave.errMsg, |
541 |
> |
"Constraint failure in constrainA, too many iterations: %d\n", |
542 |
> |
iteration); |
543 |
|
painCave.isFatal = 1; |
544 |
|
simError(); |
545 |
|
} |
546 |
|
|
547 |
|
} |
548 |
|
|
549 |
< |
void Integrator::constrainB( void ){ |
550 |
< |
|
552 |
< |
int i,j,k; |
549 |
> |
template<typename T> void Integrator<T>::constrainB(void){ |
550 |
> |
int i, j; |
551 |
|
int done; |
552 |
+ |
double posA[3], posB[3]; |
553 |
+ |
double velA[3], velB[3]; |
554 |
|
double vxab, vyab, vzab; |
555 |
< |
double rxab, ryab, rzab; |
556 |
< |
int a, b; |
555 |
> |
double rab[3]; |
556 |
> |
int a, b, ax, ay, az, bx, by, bz; |
557 |
|
double rma, rmb; |
558 |
|
double dx, dy, dz; |
559 |
< |
double rabsq, pabsq, rvab; |
560 |
< |
double diffsq; |
559 |
> |
double rvab; |
560 |
|
double gab; |
561 |
|
int iteration; |
562 |
|
|
563 |
< |
for(i=0; i<nAtom; i++){ |
563 |
> |
for (i = 0; i < nAtoms; i++){ |
564 |
|
moving[i] = 0; |
565 |
|
moved[i] = 1; |
566 |
|
} |
567 |
|
|
568 |
|
done = 0; |
569 |
< |
while( !done && (iteration < maxIteration ) ){ |
569 |
> |
iteration = 0; |
570 |
> |
while (!done && (iteration < maxIteration)){ |
571 |
> |
done = 1; |
572 |
|
|
573 |
< |
for(i=0; i<nConstrained; i++){ |
573 |
< |
|
573 |
> |
for (i = 0; i < nConstrained; i++){ |
574 |
|
a = constrainedA[i]; |
575 |
|
b = constrainedB[i]; |
576 |
|
|
577 |
< |
if( moved[a] || moved[b] ){ |
578 |
< |
|
579 |
< |
vxab = vel[3*a+0] - vel[3*b+0]; |
580 |
< |
vyab = vel[3*a+1] - vel[3*b+1]; |
581 |
< |
vzab = vel[3*a+2] - vel[3*b+2]; |
577 |
> |
ax = (a * 3) + 0; |
578 |
> |
ay = (a * 3) + 1; |
579 |
> |
az = (a * 3) + 2; |
580 |
|
|
581 |
< |
rxab = pos[3*a+0] - pos[3*b+0];q |
582 |
< |
ryab = pos[3*a+1] - pos[3*b+1]; |
583 |
< |
rzab = pos[3*a+2] - pos[3*b+2]; |
586 |
< |
|
587 |
< |
rxab = rxab - info->box_x * copysign(1, rxab) |
588 |
< |
* int(rxab / info->box_x + 0.5); |
589 |
< |
ryab = ryab - info->box_y * copysign(1, ryab) |
590 |
< |
* int(ryab / info->box_y + 0.5); |
591 |
< |
rzab = rzab - info->box_z * copysign(1, rzab) |
592 |
< |
* int(rzab / info->box_z + 0.5); |
581 |
> |
bx = (b * 3) + 0; |
582 |
> |
by = (b * 3) + 1; |
583 |
> |
bz = (b * 3) + 2; |
584 |
|
|
585 |
< |
rma = 1.0 / atoms[a]->getMass(); |
586 |
< |
rmb = 1.0 / atoms[b]->getMass(); |
585 |
> |
if (moved[a] || moved[b]){ |
586 |
> |
atoms[a]->getVel(velA); |
587 |
> |
atoms[b]->getVel(velB); |
588 |
|
|
589 |
< |
rvab = rxab * vxab + ryab * vyab + rzab * vzab; |
590 |
< |
|
591 |
< |
gab = -rvab / ( ( rma + rmb ) * constraintsDsqr[i] ); |
589 |
> |
vxab = velA[0] - velB[0]; |
590 |
> |
vyab = velA[1] - velB[1]; |
591 |
> |
vzab = velA[2] - velB[2]; |
592 |
|
|
593 |
< |
if (fabs(gab) > tol) { |
594 |
< |
|
603 |
< |
dx = rxab * gab; |
604 |
< |
dy = ryab * gab; |
605 |
< |
dz = rzab * gab; |
606 |
< |
|
607 |
< |
vel[3*a+0] += rma * dx; |
608 |
< |
vel[3*a+1] += rma * dy; |
609 |
< |
vel[3*a+2] += rma * dz; |
593 |
> |
atoms[a]->getPos(posA); |
594 |
> |
atoms[b]->getPos(posB); |
595 |
|
|
596 |
< |
vel[3*b+0] -= rmb * dx; |
597 |
< |
vel[3*b+1] -= rmb * dy; |
598 |
< |
vel[3*b+2] -= rmb * dz; |
599 |
< |
|
600 |
< |
moving[a] = 1; |
601 |
< |
moving[b] = 1; |
602 |
< |
done = 0; |
603 |
< |
} |
596 |
> |
for (j = 0; j < 3; j++) |
597 |
> |
rab[j] = posA[j] - posB[j]; |
598 |
> |
|
599 |
> |
info->wrapVector(rab); |
600 |
> |
|
601 |
> |
rma = 1.0 / atoms[a]->getMass(); |
602 |
> |
rmb = 1.0 / atoms[b]->getMass(); |
603 |
> |
|
604 |
> |
rvab = rab[0] * vxab + rab[1] * vyab + rab[2] * vzab; |
605 |
> |
|
606 |
> |
gab = -rvab / ((rma + rmb) * constrainedDsqr[i]); |
607 |
> |
|
608 |
> |
if (fabs(gab) > tol){ |
609 |
> |
dx = rab[0] * gab; |
610 |
> |
dy = rab[1] * gab; |
611 |
> |
dz = rab[2] * gab; |
612 |
> |
|
613 |
> |
velA[0] += rma * dx; |
614 |
> |
velA[1] += rma * dy; |
615 |
> |
velA[2] += rma * dz; |
616 |
> |
|
617 |
> |
atoms[a]->setVel(velA); |
618 |
> |
|
619 |
> |
velB[0] -= rmb * dx; |
620 |
> |
velB[1] -= rmb * dy; |
621 |
> |
velB[2] -= rmb * dz; |
622 |
> |
|
623 |
> |
atoms[b]->setVel(velB); |
624 |
> |
|
625 |
> |
moving[a] = 1; |
626 |
> |
moving[b] = 1; |
627 |
> |
done = 0; |
628 |
> |
} |
629 |
|
} |
630 |
|
} |
631 |
|
|
632 |
< |
for(i=0; i<nAtoms; i++){ |
632 |
> |
for (i = 0; i < nAtoms; i++){ |
633 |
|
moved[i] = moving[i]; |
634 |
|
moving[i] = 0; |
635 |
|
} |
636 |
< |
|
636 |
> |
|
637 |
|
iteration++; |
638 |
|
} |
639 |
|
|
640 |
< |
if( !done ){ |
641 |
< |
|
642 |
< |
|
643 |
< |
sprintf( painCae.errMsg, |
634 |
< |
"Constraint failure in constrainB, too many iterations: %d\n", |
635 |
< |
iterations ); |
640 |
> |
if (!done){ |
641 |
> |
sprintf(painCave.errMsg, |
642 |
> |
"Constraint failure in constrainB, too many iterations: %d\n", |
643 |
> |
iteration); |
644 |
|
painCave.isFatal = 1; |
645 |
|
simError(); |
646 |
< |
} |
639 |
< |
|
646 |
> |
} |
647 |
|
} |
648 |
|
|
649 |
+ |
template<typename T> void Integrator<T>::rotationPropagation |
650 |
+ |
( DirectionalAtom* dAtom, double ji[3] ){ |
651 |
|
|
652 |
+ |
double angle; |
653 |
+ |
double A[3][3], I[3][3]; |
654 |
|
|
655 |
+ |
// use the angular velocities to propagate the rotation matrix a |
656 |
+ |
// full time step |
657 |
|
|
658 |
+ |
dAtom->getA(A); |
659 |
+ |
dAtom->getI(I); |
660 |
|
|
661 |
+ |
// rotate about the x-axis |
662 |
+ |
angle = dt2 * ji[0] / I[0][0]; |
663 |
+ |
this->rotate( 1, 2, angle, ji, A ); |
664 |
|
|
665 |
+ |
// rotate about the y-axis |
666 |
+ |
angle = dt2 * ji[1] / I[1][1]; |
667 |
+ |
this->rotate( 2, 0, angle, ji, A ); |
668 |
|
|
669 |
< |
void Integrator::rotate( int axes1, int axes2, double angle, double ji[3], |
670 |
< |
double A[3][3] ){ |
669 |
> |
// rotate about the z-axis |
670 |
> |
angle = dt * ji[2] / I[2][2]; |
671 |
> |
this->rotate( 0, 1, angle, ji, A); |
672 |
|
|
673 |
< |
int i,j,k; |
673 |
> |
// rotate about the y-axis |
674 |
> |
angle = dt2 * ji[1] / I[1][1]; |
675 |
> |
this->rotate( 2, 0, angle, ji, A ); |
676 |
> |
|
677 |
> |
// rotate about the x-axis |
678 |
> |
angle = dt2 * ji[0] / I[0][0]; |
679 |
> |
this->rotate( 1, 2, angle, ji, A ); |
680 |
> |
|
681 |
> |
dAtom->setA( A ); |
682 |
> |
} |
683 |
> |
|
684 |
> |
template<typename T> void Integrator<T>::rotate(int axes1, int axes2, |
685 |
> |
double angle, double ji[3], |
686 |
> |
double A[3][3]){ |
687 |
> |
int i, j, k; |
688 |
|
double sinAngle; |
689 |
|
double cosAngle; |
690 |
|
double angleSqr; |
696 |
|
|
697 |
|
// initialize the tempA |
698 |
|
|
699 |
< |
for(i=0; i<3; i++){ |
700 |
< |
for(j=0; j<3; j++){ |
699 |
> |
for (i = 0; i < 3; i++){ |
700 |
> |
for (j = 0; j < 3; j++){ |
701 |
|
tempA[j][i] = A[i][j]; |
702 |
|
} |
703 |
|
} |
704 |
|
|
705 |
|
// initialize the tempJ |
706 |
|
|
707 |
< |
for( i=0; i<3; i++) tempJ[i] = ji[i]; |
708 |
< |
|
707 |
> |
for (i = 0; i < 3; i++) |
708 |
> |
tempJ[i] = ji[i]; |
709 |
> |
|
710 |
|
// initalize rot as a unit matrix |
711 |
|
|
712 |
|
rot[0][0] = 1.0; |
716 |
|
rot[1][0] = 0.0; |
717 |
|
rot[1][1] = 1.0; |
718 |
|
rot[1][2] = 0.0; |
719 |
< |
|
719 |
> |
|
720 |
|
rot[2][0] = 0.0; |
721 |
|
rot[2][1] = 0.0; |
722 |
|
rot[2][2] = 1.0; |
723 |
< |
|
723 |
> |
|
724 |
|
// use a small angle aproximation for sin and cosine |
725 |
|
|
726 |
< |
angleSqr = angle * angle; |
726 |
> |
angleSqr = angle * angle; |
727 |
|
angleSqrOver4 = angleSqr / 4.0; |
728 |
|
top = 1.0 - angleSqrOver4; |
729 |
|
bottom = 1.0 + angleSqrOver4; |
736 |
|
|
737 |
|
rot[axes1][axes2] = sinAngle; |
738 |
|
rot[axes2][axes1] = -sinAngle; |
739 |
< |
|
739 |
> |
|
740 |
|
// rotate the momentum acoording to: ji[] = rot[][] * ji[] |
741 |
< |
|
742 |
< |
for(i=0; i<3; i++){ |
741 |
> |
|
742 |
> |
for (i = 0; i < 3; i++){ |
743 |
|
ji[i] = 0.0; |
744 |
< |
for(k=0; k<3; k++){ |
744 |
> |
for (k = 0; k < 3; k++){ |
745 |
|
ji[i] += rot[i][k] * tempJ[k]; |
746 |
|
} |
747 |
|
} |
748 |
|
|
749 |
< |
// rotate the Rotation matrix acording to: |
749 |
> |
// rotate the Rotation matrix acording to: |
750 |
|
// A[][] = A[][] * transpose(rot[][]) |
751 |
|
|
752 |
|
|
753 |
< |
// NOte for as yet unknown reason, we are setting the performing the |
753 |
> |
// NOte for as yet unknown reason, we are performing the |
754 |
|
// calculation as: |
755 |
|
// transpose(A[][]) = transpose(A[][]) * transpose(rot[][]) |
756 |
|
|
757 |
< |
for(i=0; i<3; i++){ |
758 |
< |
for(j=0; j<3; j++){ |
757 |
> |
for (i = 0; i < 3; i++){ |
758 |
> |
for (j = 0; j < 3; j++){ |
759 |
|
A[j][i] = 0.0; |
760 |
< |
for(k=0; k<3; k++){ |
761 |
< |
A[j][i] += tempA[i][k] * rot[j][k]; |
760 |
> |
for (k = 0; k < 3; k++){ |
761 |
> |
A[j][i] += tempA[i][k] * rot[j][k]; |
762 |
|
} |
763 |
|
} |
764 |
|
} |
765 |
|
} |
766 |
+ |
|
767 |
+ |
template<typename T> void Integrator<T>::calcForce(int calcPot, int calcStress){ |
768 |
+ |
myFF->doForces(calcPot, calcStress); |
769 |
+ |
} |
770 |
+ |
|
771 |
+ |
template<typename T> void Integrator<T>::thermalize(){ |
772 |
+ |
tStats->velocitize(); |
773 |
+ |
} |
774 |
+ |
|
775 |
+ |
template<typename T> double Integrator<T>::getConservedQuantity(void){ |
776 |
+ |
return tStats->getTotalE(); |
777 |
+ |
} |
778 |
+ |
template<typename T> string Integrator<T>::getAdditionalParameters(void){ |
779 |
+ |
//By default, return a null string |
780 |
+ |
//The reason we use string instead of char* is that if we use char*, we will |
781 |
+ |
//return a pointer point to local variable which might cause problem |
782 |
+ |
return string(); |
783 |
+ |
} |