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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 <unistd.h> |
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#endif //is_mpi |
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|
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#ifdef PROFILE |
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#include "mdProfile.hpp" |
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#endif // profile |
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|
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#include "Integrator.hpp" |
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#include "simError.h" |
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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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delete[] oldPos; |
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} |
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} |
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void Integrator::checkConstraints( void ){ |
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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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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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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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|
| 90 |
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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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< |
|
| 112 |
< |
nConstrained++; |
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< |
constrained = 0; |
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> |
|
| 105 |
> |
if (constrained){ |
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> |
dummy_plug = theArray[j]->get_constraint(); |
| 107 |
> |
temp_con[nConstrained].set_a(dummy_plug->get_a()); |
| 108 |
> |
temp_con[nConstrained].set_b(dummy_plug->get_b()); |
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> |
temp_con[nConstrained].set_dsqr(dummy_plug->get_dsqr()); |
| 110 |
> |
|
| 111 |
> |
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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< |
|
| 117 |
> |
if (nConstrained > 0){ |
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isConstrained = 1; |
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|
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< |
if(constrainedA != NULL ) delete[] constrainedA; |
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< |
if(constrainedB != NULL ) delete[] constrainedB; |
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< |
if(constrainedDsqr != NULL ) delete[] constrainedDsqr; |
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> |
if (constrainedA != NULL) |
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> |
delete[] constrainedA; |
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> |
if (constrainedB != NULL) |
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> |
delete[] constrainedB; |
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> |
if (constrainedDsqr != NULL) |
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> |
delete[] constrainedDsqr; |
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|
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< |
constrainedA = new int[nConstrained]; |
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< |
constrainedB = new int[nConstrained]; |
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> |
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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// save oldAtoms to check for lode balanceing later on. |
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> |
|
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oldAtoms = nAtoms; |
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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]; |
| 145 |
> |
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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< |
void Integrator::integrate( void ){ |
| 152 |
> |
template<typename T> void Integrator<T>::integrate(void){ |
| 153 |
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|
| 154 |
< |
int i, j; // loop counters |
| 155 |
< |
double kE = 0.0; // the kinetic energy |
| 156 |
< |
double rot_kE; |
| 161 |
< |
double trans_kE; |
| 162 |
< |
int tl; // the time loop conter |
| 163 |
< |
double dt2; // half the dt |
| 164 |
< |
|
| 165 |
< |
double vx, vy, vz; // the velocities |
| 166 |
< |
double vx2, vy2, vz2; // the square of the velocities |
| 167 |
< |
double rx, ry, rz; // the postitions |
| 168 |
< |
|
| 169 |
< |
double ji[3]; // the body frame angular momentum |
| 170 |
< |
double jx2, jy2, jz2; // the square of the angular momentums |
| 171 |
< |
double Tb[3]; // torque in the body frame |
| 172 |
< |
double angle; // the angle through which to rotate the rotation matrix |
| 173 |
< |
double A[3][3]; // the rotation matrix |
| 174 |
< |
double press[9]; |
| 175 |
< |
|
| 176 |
< |
double dt = info->dt; |
| 177 |
< |
double runTime = info->run_time; |
| 178 |
< |
double sampleTime = info->sampleTime; |
| 179 |
< |
double statusTime = info->statusTime; |
| 154 |
> |
double runTime = info->run_time; |
| 155 |
> |
double sampleTime = info->sampleTime; |
| 156 |
> |
double statusTime = info->statusTime; |
| 157 |
|
double thermalTime = info->thermalTime; |
| 158 |
+ |
double resetTime = info->resetTime; |
| 159 |
|
|
| 160 |
+ |
|
| 161 |
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double currSample; |
| 162 |
|
double currThermal; |
| 163 |
|
double currStatus; |
| 164 |
< |
double currTime; |
| 164 |
> |
double currReset; |
| 165 |
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|
| 166 |
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int calcPot, calcStress; |
| 188 |
– |
int isError; |
| 167 |
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|
| 168 |
< |
tStats = new Thermo( info ); |
| 169 |
< |
e_out = new StatWriter( info ); |
| 170 |
< |
dump_out = new DumpWriter( info ); |
| 168 |
> |
tStats = new Thermo(info); |
| 169 |
> |
statOut = new StatWriter(info); |
| 170 |
> |
dumpOut = new DumpWriter(info); |
| 171 |
|
|
| 172 |
< |
Atom** atoms = info->atoms; |
| 173 |
< |
DirectionalAtom* dAtom; |
| 172 |
> |
atoms = info->atoms; |
| 173 |
> |
|
| 174 |
> |
dt = info->dt; |
| 175 |
|
dt2 = 0.5 * dt; |
| 176 |
|
|
| 177 |
+ |
readyCheck(); |
| 178 |
+ |
|
| 179 |
|
// initialize the forces before the first step |
| 180 |
|
|
| 181 |
< |
myFF->doForces(1,1); |
| 182 |
< |
|
| 183 |
< |
if( info->setTemp ){ |
| 184 |
< |
|
| 185 |
< |
tStats->velocitize(); |
| 181 |
> |
calcForce(1, 1); |
| 182 |
> |
|
| 183 |
> |
if (nConstrained){ |
| 184 |
> |
preMove(); |
| 185 |
> |
constrainA(); |
| 186 |
> |
calcForce(1, 1); |
| 187 |
> |
constrainB(); |
| 188 |
|
} |
| 189 |
|
|
| 190 |
< |
dump_out->writeDump( 0.0 ); |
| 191 |
< |
e_out->writeStat( 0.0 ); |
| 192 |
< |
|
| 190 |
> |
if (info->setTemp){ |
| 191 |
> |
thermalize(); |
| 192 |
> |
} |
| 193 |
> |
|
| 194 |
|
calcPot = 0; |
| 195 |
|
calcStress = 0; |
| 196 |
< |
currSample = sampleTime; |
| 197 |
< |
currThermal = thermalTime; |
| 198 |
< |
currStatus = statusTime; |
| 199 |
< |
currTime = 0.0;; |
| 196 |
> |
currSample = sampleTime + info->getTime(); |
| 197 |
> |
currThermal = thermalTime+ info->getTime(); |
| 198 |
> |
currStatus = statusTime + info->getTime(); |
| 199 |
> |
currReset = resetTime + info->getTime(); |
| 200 |
|
|
| 201 |
+ |
dumpOut->writeDump(info->getTime()); |
| 202 |
+ |
statOut->writeStat(info->getTime()); |
| 203 |
|
|
| 218 |
– |
readyCheck(); |
| 204 |
|
|
| 205 |
|
#ifdef IS_MPI |
| 206 |
< |
strcpy( checkPointMsg, |
| 222 |
< |
"The integrator is ready to go." ); |
| 206 |
> |
strcpy(checkPointMsg, "The integrator is ready to go."); |
| 207 |
|
MPIcheckPoint(); |
| 208 |
|
#endif // is_mpi |
| 209 |
|
|
| 210 |
< |
while( currTime < runTime ){ |
| 211 |
< |
|
| 228 |
< |
if( (currTime+dt) >= currStatus ){ |
| 210 |
> |
while (info->getTime() < runTime){ |
| 211 |
> |
if ((info->getTime() + dt) >= currStatus){ |
| 212 |
|
calcPot = 1; |
| 213 |
|
calcStress = 1; |
| 214 |
|
} |
| 215 |
+ |
|
| 216 |
+ |
#ifdef PROFILE |
| 217 |
+ |
startProfile( pro1 ); |
| 218 |
+ |
#endif |
| 219 |
|
|
| 220 |
< |
integrateStep( calcPot, calcStress ); |
| 234 |
< |
|
| 235 |
< |
currTime += dt; |
| 220 |
> |
integrateStep(calcPot, calcStress); |
| 221 |
|
|
| 222 |
< |
if( info->setTemp ){ |
| 223 |
< |
if( currTime >= currThermal ){ |
| 224 |
< |
tStats->velocitize(); |
| 225 |
< |
currThermal += thermalTime; |
| 222 |
> |
#ifdef PROFILE |
| 223 |
> |
endProfile( pro1 ); |
| 224 |
> |
|
| 225 |
> |
startProfile( pro2 ); |
| 226 |
> |
#endif // profile |
| 227 |
> |
|
| 228 |
> |
info->incrTime(dt); |
| 229 |
> |
|
| 230 |
> |
if (info->setTemp){ |
| 231 |
> |
if (info->getTime() >= currThermal){ |
| 232 |
> |
thermalize(); |
| 233 |
> |
currThermal += thermalTime; |
| 234 |
|
} |
| 235 |
|
} |
| 236 |
|
|
| 237 |
< |
if( currTime >= currSample ){ |
| 238 |
< |
dump_out->writeDump( currTime ); |
| 237 |
> |
if (info->getTime() >= currSample){ |
| 238 |
> |
dumpOut->writeDump(info->getTime()); |
| 239 |
|
currSample += sampleTime; |
| 240 |
|
} |
| 241 |
|
|
| 242 |
< |
if( currTime >= currStatus ){ |
| 243 |
< |
e_out->writeStat( time * dt ); |
| 244 |
< |
calcPot = 0; |
| 242 |
> |
if (info->getTime() >= currStatus){ |
| 243 |
> |
statOut->writeStat(info->getTime()); |
| 244 |
> |
calcPot = 0; |
| 245 |
|
calcStress = 0; |
| 246 |
|
currStatus += statusTime; |
| 247 |
< |
} |
| 247 |
> |
} |
| 248 |
|
|
| 249 |
+ |
if (info->resetIntegrator){ |
| 250 |
+ |
if (info->getTime() >= currReset){ |
| 251 |
+ |
this->resetIntegrator(); |
| 252 |
+ |
currReset += resetTime; |
| 253 |
+ |
} |
| 254 |
+ |
} |
| 255 |
+ |
|
| 256 |
+ |
#ifdef PROFILE |
| 257 |
+ |
endProfile( pro2 ); |
| 258 |
+ |
#endif //profile |
| 259 |
+ |
|
| 260 |
|
#ifdef IS_MPI |
| 261 |
< |
strcpy( checkPointMsg, |
| 258 |
< |
"successfully took a time step." ); |
| 261 |
> |
strcpy(checkPointMsg, "successfully took a time step."); |
| 262 |
|
MPIcheckPoint(); |
| 263 |
|
#endif // is_mpi |
| 261 |
– |
|
| 264 |
|
} |
| 265 |
|
|
| 264 |
– |
dump_out->writeFinal(); |
| 266 |
|
|
| 267 |
< |
delete dump_out; |
| 268 |
< |
delete e_out; |
| 267 |
> |
// write the last frame |
| 268 |
> |
dumpOut->writeDump(info->getTime()); |
| 269 |
> |
|
| 270 |
> |
delete dumpOut; |
| 271 |
> |
delete statOut; |
| 272 |
|
} |
| 273 |
|
|
| 274 |
< |
void Integrator::integrateStep( int calcPot, int calcStress ){ |
| 275 |
< |
|
| 274 |
> |
template<typename T> void Integrator<T>::integrateStep(int calcPot, |
| 275 |
> |
int calcStress){ |
| 276 |
|
// Position full step, and velocity half step |
| 277 |
|
|
| 278 |
< |
//preMove(); |
| 278 |
> |
#ifdef PROFILE |
| 279 |
> |
startProfile(pro3); |
| 280 |
> |
#endif //profile |
| 281 |
> |
|
| 282 |
> |
preMove(); |
| 283 |
> |
|
| 284 |
> |
#ifdef PROFILE |
| 285 |
> |
endProfile(pro3); |
| 286 |
> |
|
| 287 |
> |
startProfile(pro4); |
| 288 |
> |
#endif // profile |
| 289 |
> |
|
| 290 |
|
moveA(); |
| 276 |
– |
if( nConstrained ) constrainA(); |
| 291 |
|
|
| 292 |
+ |
#ifdef PROFILE |
| 293 |
+ |
endProfile(pro4); |
| 294 |
+ |
|
| 295 |
+ |
startProfile(pro5); |
| 296 |
+ |
#endif//profile |
| 297 |
+ |
|
| 298 |
+ |
|
| 299 |
+ |
#ifdef IS_MPI |
| 300 |
+ |
strcpy(checkPointMsg, "Succesful moveA\n"); |
| 301 |
+ |
MPIcheckPoint(); |
| 302 |
+ |
#endif // is_mpi |
| 303 |
+ |
|
| 304 |
+ |
|
| 305 |
|
// calc forces |
| 306 |
|
|
| 307 |
< |
myFF->doForces(calcPot,calcStress); |
| 307 |
> |
calcForce(calcPot, calcStress); |
| 308 |
|
|
| 309 |
+ |
#ifdef IS_MPI |
| 310 |
+ |
strcpy(checkPointMsg, "Succesful doForces\n"); |
| 311 |
+ |
MPIcheckPoint(); |
| 312 |
+ |
#endif // is_mpi |
| 313 |
+ |
|
| 314 |
+ |
#ifdef PROFILE |
| 315 |
+ |
endProfile( pro5 ); |
| 316 |
+ |
|
| 317 |
+ |
startProfile( pro6 ); |
| 318 |
+ |
#endif //profile |
| 319 |
+ |
|
| 320 |
|
// finish the velocity half step |
| 321 |
< |
|
| 321 |
> |
|
| 322 |
|
moveB(); |
| 323 |
< |
if( nConstrained ) constrainB(); |
| 324 |
< |
|
| 323 |
> |
|
| 324 |
> |
#ifdef PROFILE |
| 325 |
> |
endProfile(pro6); |
| 326 |
> |
#endif // profile |
| 327 |
> |
|
| 328 |
> |
#ifdef IS_MPI |
| 329 |
> |
strcpy(checkPointMsg, "Succesful moveB\n"); |
| 330 |
> |
MPIcheckPoint(); |
| 331 |
> |
#endif // is_mpi |
| 332 |
|
} |
| 333 |
|
|
| 334 |
|
|
| 335 |
< |
void Integrator::moveA( void ){ |
| 336 |
< |
|
| 292 |
< |
int i,j,k; |
| 293 |
< |
int atomIndex, aMatIndex; |
| 335 |
> |
template<typename T> void Integrator<T>::moveA(void){ |
| 336 |
> |
int i, j; |
| 337 |
|
DirectionalAtom* dAtom; |
| 338 |
< |
double Tb[3]; |
| 339 |
< |
double ji[3]; |
| 338 |
> |
double Tb[3], ji[3]; |
| 339 |
> |
double vel[3], pos[3], frc[3]; |
| 340 |
> |
double mass; |
| 341 |
|
|
| 342 |
< |
for( i=0; i<nAtoms; i++ ){ |
| 343 |
< |
atomIndex = i * 3; |
| 344 |
< |
aMatIndex = i * 9; |
| 345 |
< |
|
| 302 |
< |
// velocity half step |
| 303 |
< |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
| 304 |
< |
vel[j] += ( dt2 * frc[j] / atoms[i]->getMass() ) * eConvert; |
| 342 |
> |
for (i = 0; i < nAtoms; i++){ |
| 343 |
> |
atoms[i]->getVel(vel); |
| 344 |
> |
atoms[i]->getPos(pos); |
| 345 |
> |
atoms[i]->getFrc(frc); |
| 346 |
|
|
| 347 |
< |
// position whole step |
| 348 |
< |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
| 347 |
> |
mass = atoms[i]->getMass(); |
| 348 |
> |
|
| 349 |
> |
for (j = 0; j < 3; j++){ |
| 350 |
> |
// velocity half step |
| 351 |
> |
vel[j] += (dt2 * frc[j] / mass) * eConvert; |
| 352 |
> |
// position whole step |
| 353 |
|
pos[j] += dt * vel[j]; |
| 354 |
+ |
} |
| 355 |
|
|
| 356 |
< |
|
| 357 |
< |
if( atoms[i]->isDirectional() ){ |
| 356 |
> |
atoms[i]->setVel(vel); |
| 357 |
> |
atoms[i]->setPos(pos); |
| 358 |
|
|
| 359 |
< |
dAtom = (DirectionalAtom *)atoms[i]; |
| 360 |
< |
|
| 359 |
> |
if (atoms[i]->isDirectional()){ |
| 360 |
> |
dAtom = (DirectionalAtom *) atoms[i]; |
| 361 |
> |
|
| 362 |
|
// get and convert the torque to body frame |
| 363 |
< |
|
| 364 |
< |
Tb[0] = dAtom->getTx(); |
| 365 |
< |
Tb[1] = dAtom->getTy(); |
| 366 |
< |
Tb[2] = dAtom->getTz(); |
| 320 |
< |
|
| 321 |
< |
dAtom->lab2Body( Tb ); |
| 322 |
< |
|
| 363 |
> |
|
| 364 |
> |
dAtom->getTrq(Tb); |
| 365 |
> |
dAtom->lab2Body(Tb); |
| 366 |
> |
|
| 367 |
|
// get the angular momentum, and propagate a half step |
| 368 |
< |
|
| 369 |
< |
ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * eConvert; |
| 370 |
< |
ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * eConvert; |
| 371 |
< |
ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * eConvert; |
| 372 |
< |
|
| 373 |
< |
// use the angular velocities to propagate the rotation matrix a |
| 374 |
< |
// full time step |
| 375 |
< |
|
| 376 |
< |
// rotate about the x-axis |
| 333 |
< |
angle = dt2 * ji[0] / dAtom->getIxx(); |
| 334 |
< |
this->rotate( 1, 2, angle, ji, &aMat[aMatIndex] ); |
| 335 |
< |
|
| 336 |
< |
// rotate about the y-axis |
| 337 |
< |
angle = dt2 * ji[1] / dAtom->getIyy(); |
| 338 |
< |
this->rotate( 2, 0, angle, ji, &aMat[aMatIndex] ); |
| 339 |
< |
|
| 340 |
< |
// rotate about the z-axis |
| 341 |
< |
angle = dt * ji[2] / dAtom->getIzz(); |
| 342 |
< |
this->rotate( 0, 1, angle, ji, &aMat[aMatIndex] ); |
| 343 |
< |
|
| 344 |
< |
// rotate about the y-axis |
| 345 |
< |
angle = dt2 * ji[1] / dAtom->getIyy(); |
| 346 |
< |
this->rotate( 2, 0, angle, ji, &aMat[aMatIndex] ); |
| 347 |
< |
|
| 348 |
< |
// rotate about the x-axis |
| 349 |
< |
angle = dt2 * ji[0] / dAtom->getIxx(); |
| 350 |
< |
this->rotate( 1, 2, angle, ji, &aMat[aMatIndex] ); |
| 351 |
< |
|
| 352 |
< |
dAtom->setJx( ji[0] ); |
| 353 |
< |
dAtom->setJy( ji[1] ); |
| 354 |
< |
dAtom->setJz( ji[2] ); |
| 368 |
> |
|
| 369 |
> |
dAtom->getJ(ji); |
| 370 |
> |
|
| 371 |
> |
for (j = 0; j < 3; j++) |
| 372 |
> |
ji[j] += (dt2 * Tb[j]) * eConvert; |
| 373 |
> |
|
| 374 |
> |
this->rotationPropagation( dAtom, ji ); |
| 375 |
> |
|
| 376 |
> |
dAtom->setJ(ji); |
| 377 |
|
} |
| 356 |
– |
|
| 378 |
|
} |
| 379 |
+ |
|
| 380 |
+ |
if (nConstrained){ |
| 381 |
+ |
constrainA(); |
| 382 |
+ |
} |
| 383 |
|
} |
| 384 |
|
|
| 385 |
|
|
| 386 |
< |
void Integrator::moveB( void ){ |
| 387 |
< |
int i,j,k; |
| 363 |
< |
int atomIndex; |
| 386 |
> |
template<typename T> void Integrator<T>::moveB(void){ |
| 387 |
> |
int i, j; |
| 388 |
|
DirectionalAtom* dAtom; |
| 389 |
< |
double Tb[3]; |
| 390 |
< |
double ji[3]; |
| 389 |
> |
double Tb[3], ji[3]; |
| 390 |
> |
double vel[3], frc[3]; |
| 391 |
> |
double mass; |
| 392 |
|
|
| 393 |
< |
for( i=0; i<nAtoms; i++ ){ |
| 394 |
< |
atomIndex = i * 3; |
| 393 |
> |
for (i = 0; i < nAtoms; i++){ |
| 394 |
> |
atoms[i]->getVel(vel); |
| 395 |
> |
atoms[i]->getFrc(frc); |
| 396 |
|
|
| 397 |
+ |
mass = atoms[i]->getMass(); |
| 398 |
+ |
|
| 399 |
|
// velocity half step |
| 400 |
< |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
| 401 |
< |
vel[j] += ( dt2 * frc[j] / atoms[i]->getMass() ) * eConvert; |
| 400 |
> |
for (j = 0; j < 3; j++) |
| 401 |
> |
vel[j] += (dt2 * frc[j] / mass) * eConvert; |
| 402 |
|
|
| 403 |
< |
if( atoms[i]->isDirectional() ){ |
| 404 |
< |
|
| 405 |
< |
dAtom = (DirectionalAtom *)atoms[i]; |
| 406 |
< |
|
| 403 |
> |
atoms[i]->setVel(vel); |
| 404 |
> |
|
| 405 |
> |
if (atoms[i]->isDirectional()){ |
| 406 |
> |
dAtom = (DirectionalAtom *) atoms[i]; |
| 407 |
> |
|
| 408 |
|
// get and convert the torque to body frame |
| 409 |
< |
|
| 410 |
< |
Tb[0] = dAtom->getTx(); |
| 411 |
< |
Tb[1] = dAtom->getTy(); |
| 412 |
< |
Tb[2] = dAtom->getTz(); |
| 413 |
< |
|
| 414 |
< |
dAtom->lab2Body( Tb ); |
| 415 |
< |
|
| 416 |
< |
// get the angular momentum, and complete the angular momentum |
| 417 |
< |
// half step |
| 418 |
< |
|
| 419 |
< |
ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * eConvert; |
| 420 |
< |
ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * eConvert; |
| 421 |
< |
ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * eConvert; |
| 393 |
< |
|
| 394 |
< |
jx2 = ji[0] * ji[0]; |
| 395 |
< |
jy2 = ji[1] * ji[1]; |
| 396 |
< |
jz2 = ji[2] * ji[2]; |
| 397 |
< |
|
| 398 |
< |
dAtom->setJx( ji[0] ); |
| 399 |
< |
dAtom->setJy( ji[1] ); |
| 400 |
< |
dAtom->setJz( ji[2] ); |
| 409 |
> |
|
| 410 |
> |
dAtom->getTrq(Tb); |
| 411 |
> |
dAtom->lab2Body(Tb); |
| 412 |
> |
|
| 413 |
> |
// get the angular momentum, and propagate a half step |
| 414 |
> |
|
| 415 |
> |
dAtom->getJ(ji); |
| 416 |
> |
|
| 417 |
> |
for (j = 0; j < 3; j++) |
| 418 |
> |
ji[j] += (dt2 * Tb[j]) * eConvert; |
| 419 |
> |
|
| 420 |
> |
|
| 421 |
> |
dAtom->setJ(ji); |
| 422 |
|
} |
| 423 |
|
} |
| 424 |
|
|
| 425 |
+ |
if (nConstrained){ |
| 426 |
+ |
constrainB(); |
| 427 |
+ |
} |
| 428 |
|
} |
| 429 |
|
|
| 430 |
< |
void Integrator::preMove( void ){ |
| 431 |
< |
int i; |
| 430 |
> |
template<typename T> void Integrator<T>::preMove(void){ |
| 431 |
> |
int i, j; |
| 432 |
> |
double pos[3]; |
| 433 |
|
|
| 434 |
< |
if( nConstrained ){ |
| 435 |
< |
if( oldAtoms != nAtoms ){ |
| 436 |
< |
|
| 437 |
< |
// save oldAtoms to check for lode balanceing later on. |
| 438 |
< |
|
| 439 |
< |
oldAtoms = nAtoms; |
| 440 |
< |
|
| 416 |
< |
delete[] moving; |
| 417 |
< |
delete[] moved; |
| 418 |
< |
delete[] oldPos; |
| 419 |
< |
|
| 420 |
< |
moving = new int[nAtoms]; |
| 421 |
< |
moved = new int[nAtoms]; |
| 422 |
< |
|
| 423 |
< |
oldPos = new double[nAtoms*3]; |
| 434 |
> |
if (nConstrained){ |
| 435 |
> |
for (i = 0; i < nAtoms; i++){ |
| 436 |
> |
atoms[i]->getPos(pos); |
| 437 |
> |
|
| 438 |
> |
for (j = 0; j < 3; j++){ |
| 439 |
> |
oldPos[3 * i + j] = pos[j]; |
| 440 |
> |
} |
| 441 |
|
} |
| 425 |
– |
|
| 426 |
– |
for(i=0; i<(nAtoms*3); i++) oldPos[i] = pos[i]; |
| 442 |
|
} |
| 443 |
< |
} |
| 443 |
> |
} |
| 444 |
|
|
| 445 |
< |
void Integrator::constrainA(){ |
| 446 |
< |
|
| 432 |
< |
int i,j,k; |
| 445 |
> |
template<typename T> void Integrator<T>::constrainA(){ |
| 446 |
> |
int i, j; |
| 447 |
|
int done; |
| 448 |
< |
double pxab, pyab, pzab; |
| 449 |
< |
double rxab, ryab, rzab; |
| 450 |
< |
int a, b; |
| 448 |
> |
double posA[3], posB[3]; |
| 449 |
> |
double velA[3], velB[3]; |
| 450 |
> |
double pab[3]; |
| 451 |
> |
double rab[3]; |
| 452 |
> |
int a, b, ax, ay, az, bx, by, bz; |
| 453 |
|
double rma, rmb; |
| 454 |
|
double dx, dy, dz; |
| 455 |
+ |
double rpab; |
| 456 |
|
double rabsq, pabsq, rpabsq; |
| 457 |
|
double diffsq; |
| 458 |
|
double gab; |
| 459 |
|
int iteration; |
| 460 |
|
|
| 461 |
< |
|
| 445 |
< |
|
| 446 |
< |
for( i=0; i<nAtoms; i++){ |
| 447 |
< |
|
| 461 |
> |
for (i = 0; i < nAtoms; i++){ |
| 462 |
|
moving[i] = 0; |
| 463 |
< |
moved[i] = 1; |
| 463 |
> |
moved[i] = 1; |
| 464 |
|
} |
| 465 |
< |
|
| 452 |
< |
|
| 465 |
> |
|
| 466 |
|
iteration = 0; |
| 467 |
|
done = 0; |
| 468 |
< |
while( !done && (iteration < maxIteration )){ |
| 456 |
< |
|
| 468 |
> |
while (!done && (iteration < maxIteration)){ |
| 469 |
|
done = 1; |
| 470 |
< |
for(i=0; i<nConstrained; i++){ |
| 459 |
< |
|
| 470 |
> |
for (i = 0; i < nConstrained; i++){ |
| 471 |
|
a = constrainedA[i]; |
| 472 |
|
b = constrainedB[i]; |
| 462 |
– |
|
| 463 |
– |
if( moved[a] || moved[b] ){ |
| 464 |
– |
|
| 465 |
– |
pxab = pos[3*a+0] - pos[3*b+0]; |
| 466 |
– |
pyab = pos[3*a+1] - pos[3*b+1]; |
| 467 |
– |
pzab = pos[3*a+2] - pos[3*b+2]; |
| 473 |
|
|
| 474 |
< |
//periodic boundary condition |
| 475 |
< |
pxab = pxab - info->box_x * copysign(1, pxab) |
| 476 |
< |
* int(pxab / info->box_x + 0.5); |
| 472 |
< |
pyab = pyab - info->box_y * copysign(1, pyab) |
| 473 |
< |
* int(pyab / info->box_y + 0.5); |
| 474 |
< |
pzab = pzab - info->box_z * copysign(1, pzab) |
| 475 |
< |
* int(pzab / info->box_z + 0.5); |
| 476 |
< |
|
| 477 |
< |
pabsq = pxab * pxab + pyab * pyab + pzab * pzab; |
| 478 |
< |
rabsq = constraintedDsqr[i]; |
| 479 |
< |
diffsq = pabsq - rabsq; |
| 474 |
> |
ax = (a * 3) + 0; |
| 475 |
> |
ay = (a * 3) + 1; |
| 476 |
> |
az = (a * 3) + 2; |
| 477 |
|
|
| 478 |
< |
// the original rattle code from alan tidesley |
| 479 |
< |
if (fabs(diffsq) > tol*rabsq*2) { |
| 480 |
< |
rxab = oldPos[3*a+0] - oldPos[3*b+0]; |
| 484 |
< |
ryab = oldPos[3*a+1] - oldPos[3*b+1]; |
| 485 |
< |
rzab = oldPos[3*a+2] - oldPos[3*b+2]; |
| 486 |
< |
|
| 487 |
< |
rxab = rxab - info->box_x * copysign(1, rxab) |
| 488 |
< |
* int(rxab / info->box_x + 0.5); |
| 489 |
< |
ryab = ryab - info->box_y * copysign(1, ryab) |
| 490 |
< |
* int(ryab / info->box_y + 0.5); |
| 491 |
< |
rzab = rzab - info->box_z * copysign(1, rzab) |
| 492 |
< |
* int(rzab / info->box_z + 0.5); |
| 478 |
> |
bx = (b * 3) + 0; |
| 479 |
> |
by = (b * 3) + 1; |
| 480 |
> |
bz = (b * 3) + 2; |
| 481 |
|
|
| 482 |
< |
rpab = rxab * pxab + ryab * pyab + rzab * pzab; |
| 483 |
< |
rpabsq = rpab * rpab; |
| 482 |
> |
if (moved[a] || moved[b]){ |
| 483 |
> |
atoms[a]->getPos(posA); |
| 484 |
> |
atoms[b]->getPos(posB); |
| 485 |
|
|
| 486 |
+ |
for (j = 0; j < 3; j++) |
| 487 |
+ |
pab[j] = posA[j] - posB[j]; |
| 488 |
|
|
| 489 |
< |
if (rpabsq < (rabsq * -diffsq)){ |
| 489 |
> |
//periodic boundary condition |
| 490 |
> |
|
| 491 |
> |
info->wrapVector(pab); |
| 492 |
> |
|
| 493 |
> |
pabsq = pab[0] * pab[0] + pab[1] * pab[1] + pab[2] * pab[2]; |
| 494 |
> |
|
| 495 |
> |
rabsq = constrainedDsqr[i]; |
| 496 |
> |
diffsq = rabsq - pabsq; |
| 497 |
> |
|
| 498 |
> |
// the original rattle code from alan tidesley |
| 499 |
> |
if (fabs(diffsq) > (tol * rabsq * 2)){ |
| 500 |
> |
rab[0] = oldPos[ax] - oldPos[bx]; |
| 501 |
> |
rab[1] = oldPos[ay] - oldPos[by]; |
| 502 |
> |
rab[2] = oldPos[az] - oldPos[bz]; |
| 503 |
> |
|
| 504 |
> |
info->wrapVector(rab); |
| 505 |
> |
|
| 506 |
> |
rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2]; |
| 507 |
> |
|
| 508 |
> |
rpabsq = rpab * rpab; |
| 509 |
> |
|
| 510 |
> |
|
| 511 |
> |
if (rpabsq < (rabsq * -diffsq)){ |
| 512 |
|
#ifdef IS_MPI |
| 513 |
< |
a = atoms[a]->getGlobalIndex(); |
| 514 |
< |
b = atoms[b]->getGlobalIndex(); |
| 513 |
> |
a = atoms[a]->getGlobalIndex(); |
| 514 |
> |
b = atoms[b]->getGlobalIndex(); |
| 515 |
|
#endif //is_mpi |
| 516 |
< |
sprintf( painCave.errMsg, |
| 517 |
< |
"Constraint failure in constrainA at atom %d and %d\n.", |
| 518 |
< |
a, b ); |
| 519 |
< |
painCave.isFatal = 1; |
| 520 |
< |
simError(); |
| 521 |
< |
} |
| 516 |
> |
sprintf(painCave.errMsg, |
| 517 |
> |
"Constraint failure in constrainA at atom %d and %d.\n", a, |
| 518 |
> |
b); |
| 519 |
> |
painCave.isFatal = 1; |
| 520 |
> |
simError(); |
| 521 |
> |
} |
| 522 |
|
|
| 523 |
< |
rma = 1.0 / atoms[a]->getMass(); |
| 524 |
< |
rmb = 1.0 / atoms[b]->getMass(); |
| 512 |
< |
|
| 513 |
< |
gab = diffsq / ( 2.0 * ( rma + rmb ) * rpab ); |
| 514 |
< |
dx = rxab * gab; |
| 515 |
< |
dy = ryab * gab; |
| 516 |
< |
dz = rzab * gab; |
| 523 |
> |
rma = 1.0 / atoms[a]->getMass(); |
| 524 |
> |
rmb = 1.0 / atoms[b]->getMass(); |
| 525 |
|
|
| 526 |
< |
pos[3*a+0] += rma * dx; |
| 519 |
< |
pos[3*a+1] += rma * dy; |
| 520 |
< |
pos[3*a+2] += rma * dz; |
| 526 |
> |
gab = diffsq / (2.0 * (rma + rmb) * rpab); |
| 527 |
|
|
| 528 |
< |
pos[3*b+0] -= rmb * dx; |
| 529 |
< |
pos[3*b+1] -= rmb * dy; |
| 530 |
< |
pos[3*b+2] -= rmb * dz; |
| 528 |
> |
dx = rab[0] * gab; |
| 529 |
> |
dy = rab[1] * gab; |
| 530 |
> |
dz = rab[2] * gab; |
| 531 |
|
|
| 532 |
+ |
posA[0] += rma * dx; |
| 533 |
+ |
posA[1] += rma * dy; |
| 534 |
+ |
posA[2] += rma * dz; |
| 535 |
+ |
|
| 536 |
+ |
atoms[a]->setPos(posA); |
| 537 |
+ |
|
| 538 |
+ |
posB[0] -= rmb * dx; |
| 539 |
+ |
posB[1] -= rmb * dy; |
| 540 |
+ |
posB[2] -= rmb * dz; |
| 541 |
+ |
|
| 542 |
+ |
atoms[b]->setPos(posB); |
| 543 |
+ |
|
| 544 |
|
dx = dx / dt; |
| 545 |
|
dy = dy / dt; |
| 546 |
|
dz = dz / dt; |
| 547 |
|
|
| 548 |
< |
vel[3*a+0] += rma * dx; |
| 531 |
< |
vel[3*a+1] += rma * dy; |
| 532 |
< |
vel[3*a+2] += rma * dz; |
| 548 |
> |
atoms[a]->getVel(velA); |
| 549 |
|
|
| 550 |
< |
vel[3*b+0] -= rmb * dx; |
| 551 |
< |
vel[3*b+1] -= rmb * dy; |
| 552 |
< |
vel[3*b+2] -= rmb * dz; |
| 550 |
> |
velA[0] += rma * dx; |
| 551 |
> |
velA[1] += rma * dy; |
| 552 |
> |
velA[2] += rma * dz; |
| 553 |
|
|
| 554 |
< |
moving[a] = 1; |
| 555 |
< |
moving[b] = 1; |
| 556 |
< |
done = 0; |
| 557 |
< |
} |
| 554 |
> |
atoms[a]->setVel(velA); |
| 555 |
> |
|
| 556 |
> |
atoms[b]->getVel(velB); |
| 557 |
> |
|
| 558 |
> |
velB[0] -= rmb * dx; |
| 559 |
> |
velB[1] -= rmb * dy; |
| 560 |
> |
velB[2] -= rmb * dz; |
| 561 |
> |
|
| 562 |
> |
atoms[b]->setVel(velB); |
| 563 |
> |
|
| 564 |
> |
moving[a] = 1; |
| 565 |
> |
moving[b] = 1; |
| 566 |
> |
done = 0; |
| 567 |
> |
} |
| 568 |
|
} |
| 569 |
|
} |
| 570 |
< |
|
| 571 |
< |
for(i=0; i<nAtoms; i++){ |
| 546 |
< |
|
| 570 |
> |
|
| 571 |
> |
for (i = 0; i < nAtoms; i++){ |
| 572 |
|
moved[i] = moving[i]; |
| 573 |
|
moving[i] = 0; |
| 574 |
|
} |
| 576 |
|
iteration++; |
| 577 |
|
} |
| 578 |
|
|
| 579 |
< |
if( !done ){ |
| 580 |
< |
|
| 581 |
< |
sprintf( painCae.errMsg, |
| 582 |
< |
"Constraint failure in constrainA, too many iterations: %d\n", |
| 558 |
< |
iterations ); |
| 579 |
> |
if (!done){ |
| 580 |
> |
sprintf(painCave.errMsg, |
| 581 |
> |
"Constraint failure in constrainA, too many iterations: %d\n", |
| 582 |
> |
iteration); |
| 583 |
|
painCave.isFatal = 1; |
| 584 |
|
simError(); |
| 585 |
|
} |
| 586 |
|
|
| 587 |
|
} |
| 588 |
|
|
| 589 |
< |
void Integrator::constrainB( void ){ |
| 590 |
< |
|
| 567 |
< |
int i,j,k; |
| 589 |
> |
template<typename T> void Integrator<T>::constrainB(void){ |
| 590 |
> |
int i, j; |
| 591 |
|
int done; |
| 592 |
+ |
double posA[3], posB[3]; |
| 593 |
+ |
double velA[3], velB[3]; |
| 594 |
|
double vxab, vyab, vzab; |
| 595 |
< |
double rxab, ryab, rzab; |
| 596 |
< |
int a, b; |
| 595 |
> |
double rab[3]; |
| 596 |
> |
int a, b, ax, ay, az, bx, by, bz; |
| 597 |
|
double rma, rmb; |
| 598 |
|
double dx, dy, dz; |
| 599 |
< |
double rabsq, pabsq, rvab; |
| 575 |
< |
double diffsq; |
| 599 |
> |
double rvab; |
| 600 |
|
double gab; |
| 601 |
|
int iteration; |
| 602 |
|
|
| 603 |
< |
for(i=0; i<nAtom; i++){ |
| 603 |
> |
for (i = 0; i < nAtoms; i++){ |
| 604 |
|
moving[i] = 0; |
| 605 |
|
moved[i] = 1; |
| 606 |
|
} |
| 607 |
|
|
| 608 |
|
done = 0; |
| 609 |
< |
while( !done && (iteration < maxIteration ) ){ |
| 609 |
> |
iteration = 0; |
| 610 |
> |
while (!done && (iteration < maxIteration)){ |
| 611 |
> |
done = 1; |
| 612 |
|
|
| 613 |
< |
for(i=0; i<nConstrained; i++){ |
| 588 |
< |
|
| 613 |
> |
for (i = 0; i < nConstrained; i++){ |
| 614 |
|
a = constrainedA[i]; |
| 615 |
|
b = constrainedB[i]; |
| 616 |
|
|
| 617 |
< |
if( moved[a] || moved[b] ){ |
| 618 |
< |
|
| 619 |
< |
vxab = vel[3*a+0] - vel[3*b+0]; |
| 595 |
< |
vyab = vel[3*a+1] - vel[3*b+1]; |
| 596 |
< |
vzab = vel[3*a+2] - vel[3*b+2]; |
| 617 |
> |
ax = (a * 3) + 0; |
| 618 |
> |
ay = (a * 3) + 1; |
| 619 |
> |
az = (a * 3) + 2; |
| 620 |
|
|
| 621 |
< |
rxab = pos[3*a+0] - pos[3*b+0];q |
| 622 |
< |
ryab = pos[3*a+1] - pos[3*b+1]; |
| 623 |
< |
rzab = pos[3*a+2] - pos[3*b+2]; |
| 601 |
< |
|
| 602 |
< |
rxab = rxab - info->box_x * copysign(1, rxab) |
| 603 |
< |
* int(rxab / info->box_x + 0.5); |
| 604 |
< |
ryab = ryab - info->box_y * copysign(1, ryab) |
| 605 |
< |
* int(ryab / info->box_y + 0.5); |
| 606 |
< |
rzab = rzab - info->box_z * copysign(1, rzab) |
| 607 |
< |
* int(rzab / info->box_z + 0.5); |
| 621 |
> |
bx = (b * 3) + 0; |
| 622 |
> |
by = (b * 3) + 1; |
| 623 |
> |
bz = (b * 3) + 2; |
| 624 |
|
|
| 625 |
< |
rma = 1.0 / atoms[a]->getMass(); |
| 626 |
< |
rmb = 1.0 / atoms[b]->getMass(); |
| 625 |
> |
if (moved[a] || moved[b]){ |
| 626 |
> |
atoms[a]->getVel(velA); |
| 627 |
> |
atoms[b]->getVel(velB); |
| 628 |
|
|
| 629 |
< |
rvab = rxab * vxab + ryab * vyab + rzab * vzab; |
| 630 |
< |
|
| 631 |
< |
gab = -rvab / ( ( rma + rmb ) * constraintsDsqr[i] ); |
| 629 |
> |
vxab = velA[0] - velB[0]; |
| 630 |
> |
vyab = velA[1] - velB[1]; |
| 631 |
> |
vzab = velA[2] - velB[2]; |
| 632 |
|
|
| 633 |
< |
if (fabs(gab) > tol) { |
| 634 |
< |
|
| 618 |
< |
dx = rxab * gab; |
| 619 |
< |
dy = ryab * gab; |
| 620 |
< |
dz = rzab * gab; |
| 621 |
< |
|
| 622 |
< |
vel[3*a+0] += rma * dx; |
| 623 |
< |
vel[3*a+1] += rma * dy; |
| 624 |
< |
vel[3*a+2] += rma * dz; |
| 633 |
> |
atoms[a]->getPos(posA); |
| 634 |
> |
atoms[b]->getPos(posB); |
| 635 |
|
|
| 636 |
< |
vel[3*b+0] -= rmb * dx; |
| 637 |
< |
vel[3*b+1] -= rmb * dy; |
| 638 |
< |
vel[3*b+2] -= rmb * dz; |
| 639 |
< |
|
| 640 |
< |
moving[a] = 1; |
| 641 |
< |
moving[b] = 1; |
| 642 |
< |
done = 0; |
| 643 |
< |
} |
| 636 |
> |
for (j = 0; j < 3; j++) |
| 637 |
> |
rab[j] = posA[j] - posB[j]; |
| 638 |
> |
|
| 639 |
> |
info->wrapVector(rab); |
| 640 |
> |
|
| 641 |
> |
rma = 1.0 / atoms[a]->getMass(); |
| 642 |
> |
rmb = 1.0 / atoms[b]->getMass(); |
| 643 |
> |
|
| 644 |
> |
rvab = rab[0] * vxab + rab[1] * vyab + rab[2] * vzab; |
| 645 |
> |
|
| 646 |
> |
gab = -rvab / ((rma + rmb) * constrainedDsqr[i]); |
| 647 |
> |
|
| 648 |
> |
if (fabs(gab) > tol){ |
| 649 |
> |
dx = rab[0] * gab; |
| 650 |
> |
dy = rab[1] * gab; |
| 651 |
> |
dz = rab[2] * gab; |
| 652 |
> |
|
| 653 |
> |
velA[0] += rma * dx; |
| 654 |
> |
velA[1] += rma * dy; |
| 655 |
> |
velA[2] += rma * dz; |
| 656 |
> |
|
| 657 |
> |
atoms[a]->setVel(velA); |
| 658 |
> |
|
| 659 |
> |
velB[0] -= rmb * dx; |
| 660 |
> |
velB[1] -= rmb * dy; |
| 661 |
> |
velB[2] -= rmb * dz; |
| 662 |
> |
|
| 663 |
> |
atoms[b]->setVel(velB); |
| 664 |
> |
|
| 665 |
> |
moving[a] = 1; |
| 666 |
> |
moving[b] = 1; |
| 667 |
> |
done = 0; |
| 668 |
> |
} |
| 669 |
|
} |
| 670 |
|
} |
| 671 |
|
|
| 672 |
< |
for(i=0; i<nAtoms; i++){ |
| 672 |
> |
for (i = 0; i < nAtoms; i++){ |
| 673 |
|
moved[i] = moving[i]; |
| 674 |
|
moving[i] = 0; |
| 675 |
|
} |
| 676 |
< |
|
| 676 |
> |
|
| 677 |
|
iteration++; |
| 678 |
|
} |
| 679 |
|
|
| 680 |
< |
if( !done ){ |
| 681 |
< |
|
| 682 |
< |
|
| 683 |
< |
sprintf( painCae.errMsg, |
| 649 |
< |
"Constraint failure in constrainB, too many iterations: %d\n", |
| 650 |
< |
iterations ); |
| 680 |
> |
if (!done){ |
| 681 |
> |
sprintf(painCave.errMsg, |
| 682 |
> |
"Constraint failure in constrainB, too many iterations: %d\n", |
| 683 |
> |
iteration); |
| 684 |
|
painCave.isFatal = 1; |
| 685 |
|
simError(); |
| 686 |
< |
} |
| 654 |
< |
|
| 686 |
> |
} |
| 687 |
|
} |
| 688 |
|
|
| 689 |
+ |
template<typename T> void Integrator<T>::rotationPropagation |
| 690 |
+ |
( DirectionalAtom* dAtom, double ji[3] ){ |
| 691 |
|
|
| 692 |
+ |
double angle; |
| 693 |
+ |
double A[3][3], I[3][3]; |
| 694 |
|
|
| 695 |
+ |
// use the angular velocities to propagate the rotation matrix a |
| 696 |
+ |
// full time step |
| 697 |
|
|
| 698 |
+ |
dAtom->getA(A); |
| 699 |
+ |
dAtom->getI(I); |
| 700 |
|
|
| 701 |
+ |
// rotate about the x-axis |
| 702 |
+ |
angle = dt2 * ji[0] / I[0][0]; |
| 703 |
+ |
this->rotate( 1, 2, angle, ji, A ); |
| 704 |
|
|
| 705 |
+ |
// rotate about the y-axis |
| 706 |
+ |
angle = dt2 * ji[1] / I[1][1]; |
| 707 |
+ |
this->rotate( 2, 0, angle, ji, A ); |
| 708 |
|
|
| 709 |
< |
void Integrator::rotate( int axes1, int axes2, double angle, double ji[3], |
| 710 |
< |
double A[3][3] ){ |
| 709 |
> |
// rotate about the z-axis |
| 710 |
> |
angle = dt * ji[2] / I[2][2]; |
| 711 |
> |
this->rotate( 0, 1, angle, ji, A); |
| 712 |
|
|
| 713 |
< |
int i,j,k; |
| 713 |
> |
// rotate about the y-axis |
| 714 |
> |
angle = dt2 * ji[1] / I[1][1]; |
| 715 |
> |
this->rotate( 2, 0, angle, ji, A ); |
| 716 |
> |
|
| 717 |
> |
// rotate about the x-axis |
| 718 |
> |
angle = dt2 * ji[0] / I[0][0]; |
| 719 |
> |
this->rotate( 1, 2, angle, ji, A ); |
| 720 |
> |
|
| 721 |
> |
dAtom->setA( A ); |
| 722 |
> |
} |
| 723 |
> |
|
| 724 |
> |
template<typename T> void Integrator<T>::rotate(int axes1, int axes2, |
| 725 |
> |
double angle, double ji[3], |
| 726 |
> |
double A[3][3]){ |
| 727 |
> |
int i, j, k; |
| 728 |
|
double sinAngle; |
| 729 |
|
double cosAngle; |
| 730 |
|
double angleSqr; |
| 736 |
|
|
| 737 |
|
// initialize the tempA |
| 738 |
|
|
| 739 |
< |
for(i=0; i<3; i++){ |
| 740 |
< |
for(j=0; j<3; j++){ |
| 739 |
> |
for (i = 0; i < 3; i++){ |
| 740 |
> |
for (j = 0; j < 3; j++){ |
| 741 |
|
tempA[j][i] = A[i][j]; |
| 742 |
|
} |
| 743 |
|
} |
| 744 |
|
|
| 745 |
|
// initialize the tempJ |
| 746 |
|
|
| 747 |
< |
for( i=0; i<3; i++) tempJ[i] = ji[i]; |
| 748 |
< |
|
| 747 |
> |
for (i = 0; i < 3; i++) |
| 748 |
> |
tempJ[i] = ji[i]; |
| 749 |
> |
|
| 750 |
|
// initalize rot as a unit matrix |
| 751 |
|
|
| 752 |
|
rot[0][0] = 1.0; |
| 756 |
|
rot[1][0] = 0.0; |
| 757 |
|
rot[1][1] = 1.0; |
| 758 |
|
rot[1][2] = 0.0; |
| 759 |
< |
|
| 759 |
> |
|
| 760 |
|
rot[2][0] = 0.0; |
| 761 |
|
rot[2][1] = 0.0; |
| 762 |
|
rot[2][2] = 1.0; |
| 763 |
< |
|
| 763 |
> |
|
| 764 |
|
// use a small angle aproximation for sin and cosine |
| 765 |
|
|
| 766 |
< |
angleSqr = angle * angle; |
| 766 |
> |
angleSqr = angle * angle; |
| 767 |
|
angleSqrOver4 = angleSqr / 4.0; |
| 768 |
|
top = 1.0 - angleSqrOver4; |
| 769 |
|
bottom = 1.0 + angleSqrOver4; |
| 776 |
|
|
| 777 |
|
rot[axes1][axes2] = sinAngle; |
| 778 |
|
rot[axes2][axes1] = -sinAngle; |
| 779 |
< |
|
| 779 |
> |
|
| 780 |
|
// rotate the momentum acoording to: ji[] = rot[][] * ji[] |
| 781 |
< |
|
| 782 |
< |
for(i=0; i<3; i++){ |
| 781 |
> |
|
| 782 |
> |
for (i = 0; i < 3; i++){ |
| 783 |
|
ji[i] = 0.0; |
| 784 |
< |
for(k=0; k<3; k++){ |
| 784 |
> |
for (k = 0; k < 3; k++){ |
| 785 |
|
ji[i] += rot[i][k] * tempJ[k]; |
| 786 |
|
} |
| 787 |
|
} |
| 788 |
|
|
| 789 |
< |
// rotate the Rotation matrix acording to: |
| 789 |
> |
// rotate the Rotation matrix acording to: |
| 790 |
|
// A[][] = A[][] * transpose(rot[][]) |
| 791 |
|
|
| 792 |
|
|
| 793 |
< |
// NOte for as yet unknown reason, we are setting the performing the |
| 793 |
> |
// NOte for as yet unknown reason, we are performing the |
| 794 |
|
// calculation as: |
| 795 |
|
// transpose(A[][]) = transpose(A[][]) * transpose(rot[][]) |
| 796 |
|
|
| 797 |
< |
for(i=0; i<3; i++){ |
| 798 |
< |
for(j=0; j<3; j++){ |
| 797 |
> |
for (i = 0; i < 3; i++){ |
| 798 |
> |
for (j = 0; j < 3; j++){ |
| 799 |
|
A[j][i] = 0.0; |
| 800 |
< |
for(k=0; k<3; k++){ |
| 801 |
< |
A[j][i] += tempA[i][k] * rot[j][k]; |
| 800 |
> |
for (k = 0; k < 3; k++){ |
| 801 |
> |
A[j][i] += tempA[i][k] * rot[j][k]; |
| 802 |
|
} |
| 803 |
|
} |
| 804 |
|
} |
| 805 |
|
} |
| 806 |
+ |
|
| 807 |
+ |
template<typename T> void Integrator<T>::calcForce(int calcPot, int calcStress){ |
| 808 |
+ |
myFF->doForces(calcPot, calcStress); |
| 809 |
+ |
} |
| 810 |
+ |
|
| 811 |
+ |
template<typename T> void Integrator<T>::thermalize(){ |
| 812 |
+ |
tStats->velocitize(); |
| 813 |
+ |
} |
| 814 |
+ |
|
| 815 |
+ |
template<typename T> double Integrator<T>::getConservedQuantity(void){ |
| 816 |
+ |
return tStats->getTotalE(); |
| 817 |
+ |
} |
| 818 |
+ |
template<typename T> string Integrator<T>::getAdditionalParameters(void){ |
| 819 |
+ |
//By default, return a null string |
| 820 |
+ |
//The reason we use string instead of char* is that if we use char*, we will |
| 821 |
+ |
//return a pointer point to local variable which might cause problem |
| 822 |
+ |
return string(); |
| 823 |
+ |
} |
