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#include <iostream> |
| 2 |
< |
#include <cstdlib> |
| 3 |
< |
#include <cmath> |
| 2 |
> |
#include <stdlib.h> |
| 3 |
> |
#include <math.h> |
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|
| 5 |
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#ifdef IS_MPI |
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#include "mpiSimulation.hpp" |
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#include <unistd.h> |
| 8 |
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#endif //is_mpi |
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|
| 10 |
+ |
#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" |
| 15 |
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#include "simError.h" |
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|
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|
| 18 |
< |
Integrator::Integrator( SimInfo *theInfo, ForceFields* the_ff ){ |
| 19 |
< |
|
| 18 |
> |
template<typename T> Integrator<T>::Integrator(SimInfo* theInfo, |
| 19 |
> |
ForceFields* the_ff){ |
| 20 |
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info = theInfo; |
| 21 |
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myFF = the_ff; |
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isFirst = 1; |
| 25 |
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nMols = info->n_mol; |
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|
| 27 |
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// give a little love back to the SimInfo object |
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|
| 25 |
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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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|
| 29 |
+ |
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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std::cerr << "integ nAtoms = " << nAtoms << "\n"; |
| 31 |
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|
| 35 |
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// check for constraints |
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< |
|
| 37 |
< |
constrainedA = NULL; |
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< |
constrainedB = NULL; |
| 36 |
> |
|
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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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oldPos = NULL; |
| 43 |
< |
|
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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(){ |
| 50 |
> |
if (nConstrained){ |
| 51 |
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delete[] constrainedA; |
| 52 |
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delete[] constrainedB; |
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delete[] constrainedDsqr; |
| 55 |
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delete[] moved; |
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delete[] oldPos; |
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} |
| 56 |
– |
|
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} |
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|
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< |
void Integrator::checkConstraints( void ){ |
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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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|
| 68 |
> |
|
| 69 |
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SRI** theArray; |
| 70 |
< |
for(int i = 0; i < nMols; i++){ |
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|
| 72 |
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theArray = (SRI**) molecules[i].getMyBonds(); |
| 73 |
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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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|
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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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std::cerr << "Is the folowing bond constrained \n"; |
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theArray[j]->printMe(); |
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|
| 79 |
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if(constrained){ |
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|
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std::cerr << "Yes\n"; |
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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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|
| 82 |
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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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|
| 90 |
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nConstrained++; |
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constrained = 0; |
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} |
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else std::cerr << "No.\n"; |
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nConstrained++; |
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> |
constrained = 0; |
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> |
} |
| 85 |
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} |
| 86 |
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|
| 87 |
< |
theArray = (SRI**) molecules[i].getMyBends(); |
| 88 |
< |
for(int j=0; j<molecules[i].getNBends(); j++){ |
| 98 |
< |
|
| 87 |
> |
theArray = (SRI * *) molecules[i].getMyBends(); |
| 88 |
> |
for (int j = 0; j < molecules[i].getNBends(); j++){ |
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constrained = theArray[j]->is_constrained(); |
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|
| 91 |
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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() ); |
| 95 |
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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() ); |
| 97 |
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|
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nConstrained++; |
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constrained = 0; |
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> |
|
| 91 |
> |
if (constrained){ |
| 92 |
> |
dummy_plug = theArray[j]->get_constraint(); |
| 93 |
> |
temp_con[nConstrained].set_a(dummy_plug->get_a()); |
| 94 |
> |
temp_con[nConstrained].set_b(dummy_plug->get_b()); |
| 95 |
> |
temp_con[nConstrained].set_dsqr(dummy_plug->get_dsqr()); |
| 96 |
> |
|
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> |
nConstrained++; |
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> |
constrained = 0; |
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} |
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} |
| 101 |
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|
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< |
theArray = (SRI**) molecules[i].getMyTorsions(); |
| 103 |
< |
for(int j=0; j<molecules[i].getNTorsions(); j++){ |
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< |
|
| 102 |
> |
theArray = (SRI * *) molecules[i].getMyTorsions(); |
| 103 |
> |
for (int j = 0; j < molecules[i].getNTorsions(); j++){ |
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constrained = theArray[j]->is_constrained(); |
| 105 |
< |
|
| 106 |
< |
if(constrained){ |
| 107 |
< |
|
| 108 |
< |
dummy_plug = theArray[j]->get_constraint(); |
| 109 |
< |
temp_con[nConstrained].set_a( dummy_plug->get_a() ); |
| 110 |
< |
temp_con[nConstrained].set_b( dummy_plug->get_b() ); |
| 111 |
< |
temp_con[nConstrained].set_dsqr( dummy_plug->get_dsqr() ); |
| 112 |
< |
|
| 113 |
< |
nConstrained++; |
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< |
constrained = 0; |
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> |
|
| 106 |
> |
if (constrained){ |
| 107 |
> |
dummy_plug = theArray[j]->get_constraint(); |
| 108 |
> |
temp_con[nConstrained].set_a(dummy_plug->get_a()); |
| 109 |
> |
temp_con[nConstrained].set_b(dummy_plug->get_b()); |
| 110 |
> |
temp_con[nConstrained].set_dsqr(dummy_plug->get_dsqr()); |
| 111 |
> |
|
| 112 |
> |
nConstrained++; |
| 113 |
> |
constrained = 0; |
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} |
| 115 |
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} |
| 116 |
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} |
| 117 |
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|
| 118 |
< |
if(nConstrained > 0){ |
| 119 |
< |
|
| 118 |
> |
|
| 119 |
> |
if (nConstrained > 0){ |
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isConstrained = 1; |
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|
| 122 |
< |
if(constrainedA != NULL ) delete[] constrainedA; |
| 123 |
< |
if(constrainedB != NULL ) delete[] constrainedB; |
| 124 |
< |
if(constrainedDsqr != NULL ) delete[] constrainedDsqr; |
| 122 |
> |
if (constrainedA != NULL) |
| 123 |
> |
delete[] constrainedA; |
| 124 |
> |
if (constrainedB != NULL) |
| 125 |
> |
delete[] constrainedB; |
| 126 |
> |
if (constrainedDsqr != NULL) |
| 127 |
> |
delete[] constrainedDsqr; |
| 128 |
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|
| 129 |
< |
constrainedA = new int[nConstrained]; |
| 130 |
< |
constrainedB = new int[nConstrained]; |
| 129 |
> |
constrainedA = new int[nConstrained]; |
| 130 |
> |
constrainedB = new int[nConstrained]; |
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constrainedDsqr = new double[nConstrained]; |
| 132 |
< |
|
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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. |
| 141 |
< |
|
| 139 |
> |
|
| 140 |
> |
// save oldAtoms to check for lode balancing later on. |
| 141 |
> |
|
| 142 |
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oldAtoms = nAtoms; |
| 143 |
< |
|
| 143 |
> |
|
| 144 |
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moving = new int[nAtoms]; |
| 145 |
< |
moved = new int[nAtoms]; |
| 145 |
> |
moved = new int[nAtoms]; |
| 146 |
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|
| 147 |
< |
oldPos = new double[nAtoms*3]; |
| 147 |
> |
oldPos = new double[nAtoms * 3]; |
| 148 |
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} |
| 149 |
< |
|
| 149 |
> |
|
| 150 |
|
delete[] temp_con; |
| 151 |
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} |
| 152 |
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|
| 153 |
|
|
| 154 |
< |
void Integrator::integrate( void ){ |
| 154 |
> |
template<typename T> void Integrator<T>::integrate(void){ |
| 155 |
|
|
| 156 |
< |
int i, j; // loop counters |
| 157 |
< |
|
| 158 |
< |
double runTime = info->run_time; |
| 171 |
< |
double sampleTime = info->sampleTime; |
| 172 |
< |
double statusTime = info->statusTime; |
| 156 |
> |
double runTime = info->run_time; |
| 157 |
> |
double sampleTime = info->sampleTime; |
| 158 |
> |
double statusTime = info->statusTime; |
| 159 |
|
double thermalTime = info->thermalTime; |
| 160 |
+ |
double resetTime = info->resetTime; |
| 161 |
|
|
| 162 |
+ |
|
| 163 |
|
double currSample; |
| 164 |
|
double currThermal; |
| 165 |
|
double currStatus; |
| 166 |
< |
double currTime; |
| 166 |
> |
double currReset; |
| 167 |
|
|
| 168 |
|
int calcPot, calcStress; |
| 181 |
– |
int isError; |
| 169 |
|
|
| 170 |
+ |
tStats = new Thermo(info); |
| 171 |
+ |
statOut = new StatWriter(info); |
| 172 |
+ |
dumpOut = new DumpWriter(info); |
| 173 |
|
|
| 184 |
– |
|
| 185 |
– |
tStats = new Thermo( info ); |
| 186 |
– |
statOut = new StatWriter( info ); |
| 187 |
– |
dumpOut = new DumpWriter( info ); |
| 188 |
– |
|
| 174 |
|
atoms = info->atoms; |
| 190 |
– |
DirectionalAtom* dAtom; |
| 175 |
|
|
| 176 |
|
dt = info->dt; |
| 177 |
|
dt2 = 0.5 * dt; |
| 178 |
|
|
| 179 |
+ |
readyCheck(); |
| 180 |
+ |
|
| 181 |
|
// initialize the forces before the first step |
| 182 |
|
|
| 183 |
< |
myFF->doForces(1,1); |
| 183 |
> |
calcForce(1, 1); |
| 184 |
> |
|
| 185 |
> |
//temp test |
| 186 |
> |
tStats->getPotential(); |
| 187 |
|
|
| 188 |
< |
if( info->setTemp ){ |
| 189 |
< |
|
| 190 |
< |
tStats->velocitize(); |
| 188 |
> |
if (nConstrained){ |
| 189 |
> |
preMove(); |
| 190 |
> |
constrainA(); |
| 191 |
> |
calcForce(1, 1); |
| 192 |
> |
constrainB(); |
| 193 |
|
} |
| 194 |
|
|
| 195 |
< |
dumpOut->writeDump( 0.0 ); |
| 196 |
< |
statOut->writeStat( 0.0 ); |
| 197 |
< |
|
| 195 |
> |
if (info->setTemp){ |
| 196 |
> |
thermalize(); |
| 197 |
> |
} |
| 198 |
> |
|
| 199 |
|
calcPot = 0; |
| 200 |
|
calcStress = 0; |
| 201 |
< |
currSample = sampleTime; |
| 202 |
< |
currThermal = thermalTime; |
| 203 |
< |
currStatus = statusTime; |
| 204 |
< |
currTime = 0.0;; |
| 201 |
> |
currSample = sampleTime + info->getTime(); |
| 202 |
> |
currThermal = thermalTime+ info->getTime(); |
| 203 |
> |
currStatus = statusTime + info->getTime(); |
| 204 |
> |
currReset = resetTime + info->getTime(); |
| 205 |
|
|
| 206 |
+ |
dumpOut->writeDump(info->getTime()); |
| 207 |
+ |
statOut->writeStat(info->getTime()); |
| 208 |
|
|
| 215 |
– |
readyCheck(); |
| 209 |
|
|
| 210 |
|
#ifdef IS_MPI |
| 211 |
< |
strcpy( checkPointMsg, |
| 219 |
< |
"The integrator is ready to go." ); |
| 211 |
> |
strcpy(checkPointMsg, "The integrator is ready to go."); |
| 212 |
|
MPIcheckPoint(); |
| 213 |
|
#endif // is_mpi |
| 214 |
|
|
| 215 |
< |
|
| 216 |
< |
pos = Atom::getPosArray(); |
| 225 |
< |
vel = Atom::getVelArray(); |
| 226 |
< |
frc = Atom::getFrcArray(); |
| 227 |
< |
|
| 228 |
< |
while( currTime < runTime ){ |
| 229 |
< |
|
| 230 |
< |
if( (currTime+dt) >= currStatus ){ |
| 215 |
> |
while (info->getTime() < runTime){ |
| 216 |
> |
if ((info->getTime() + dt) >= currStatus){ |
| 217 |
|
calcPot = 1; |
| 218 |
|
calcStress = 1; |
| 219 |
|
} |
| 220 |
|
|
| 221 |
< |
std::cerr << currTime << "\n"; |
| 221 |
> |
#ifdef PROFILE |
| 222 |
> |
startProfile( pro1 ); |
| 223 |
> |
#endif |
| 224 |
> |
|
| 225 |
> |
integrateStep(calcPot, calcStress); |
| 226 |
|
|
| 227 |
< |
integrateStep( calcPot, calcStress ); |
| 228 |
< |
|
| 239 |
< |
currTime += dt; |
| 227 |
> |
#ifdef PROFILE |
| 228 |
> |
endProfile( pro1 ); |
| 229 |
|
|
| 230 |
< |
if( info->setTemp ){ |
| 231 |
< |
if( currTime >= currThermal ){ |
| 232 |
< |
tStats->velocitize(); |
| 233 |
< |
currThermal += thermalTime; |
| 230 |
> |
startProfile( pro2 ); |
| 231 |
> |
#endif // profile |
| 232 |
> |
|
| 233 |
> |
info->incrTime(dt); |
| 234 |
> |
|
| 235 |
> |
if (info->setTemp){ |
| 236 |
> |
if (info->getTime() >= currThermal){ |
| 237 |
> |
thermalize(); |
| 238 |
> |
currThermal += thermalTime; |
| 239 |
|
} |
| 240 |
|
} |
| 241 |
|
|
| 242 |
< |
if( currTime >= currSample ){ |
| 243 |
< |
dumpOut->writeDump( currTime ); |
| 242 |
> |
if (info->getTime() >= currSample){ |
| 243 |
> |
dumpOut->writeDump(info->getTime()); |
| 244 |
|
currSample += sampleTime; |
| 245 |
|
} |
| 246 |
|
|
| 247 |
< |
if( currTime >= currStatus ){ |
| 248 |
< |
statOut->writeStat( currTime ); |
| 249 |
< |
calcPot = 0; |
| 247 |
> |
if (info->getTime() >= currStatus){ |
| 248 |
> |
statOut->writeStat(info->getTime()); |
| 249 |
> |
calcPot = 0; |
| 250 |
|
calcStress = 0; |
| 251 |
|
currStatus += statusTime; |
| 252 |
< |
} |
| 252 |
> |
} |
| 253 |
|
|
| 254 |
+ |
if (info->resetIntegrator){ |
| 255 |
+ |
if (info->getTime() >= currReset){ |
| 256 |
+ |
this->resetIntegrator(); |
| 257 |
+ |
currReset += resetTime; |
| 258 |
+ |
} |
| 259 |
+ |
} |
| 260 |
+ |
|
| 261 |
+ |
#ifdef PROFILE |
| 262 |
+ |
endProfile( pro2 ); |
| 263 |
+ |
#endif //profile |
| 264 |
+ |
|
| 265 |
|
#ifdef IS_MPI |
| 266 |
< |
strcpy( checkPointMsg, |
| 262 |
< |
"successfully took a time step." ); |
| 266 |
> |
strcpy(checkPointMsg, "successfully took a time step."); |
| 267 |
|
MPIcheckPoint(); |
| 268 |
|
#endif // is_mpi |
| 265 |
– |
|
| 269 |
|
} |
| 270 |
|
|
| 268 |
– |
dumpOut->writeFinal(currTime); |
| 269 |
– |
|
| 271 |
|
delete dumpOut; |
| 272 |
|
delete statOut; |
| 273 |
|
} |
| 274 |
|
|
| 275 |
< |
void Integrator::integrateStep( int calcPot, int calcStress ){ |
| 276 |
< |
|
| 276 |
< |
|
| 277 |
< |
|
| 275 |
> |
template<typename T> void Integrator<T>::integrateStep(int calcPot, |
| 276 |
> |
int calcStress){ |
| 277 |
|
// Position full step, and velocity half step |
| 278 |
|
|
| 279 |
+ |
#ifdef PROFILE |
| 280 |
+ |
startProfile(pro3); |
| 281 |
+ |
#endif //profile |
| 282 |
+ |
|
| 283 |
|
preMove(); |
| 284 |
+ |
|
| 285 |
+ |
#ifdef PROFILE |
| 286 |
+ |
endProfile(pro3); |
| 287 |
+ |
|
| 288 |
+ |
startProfile(pro4); |
| 289 |
+ |
#endif // profile |
| 290 |
+ |
|
| 291 |
|
moveA(); |
| 282 |
– |
//if( nConstrained ) constrainA(); |
| 292 |
|
|
| 293 |
+ |
#ifdef PROFILE |
| 294 |
+ |
endProfile(pro4); |
| 295 |
+ |
|
| 296 |
+ |
startProfile(pro5); |
| 297 |
+ |
#endif//profile |
| 298 |
+ |
|
| 299 |
+ |
|
| 300 |
+ |
#ifdef IS_MPI |
| 301 |
+ |
strcpy(checkPointMsg, "Succesful moveA\n"); |
| 302 |
+ |
MPIcheckPoint(); |
| 303 |
+ |
#endif // is_mpi |
| 304 |
+ |
|
| 305 |
+ |
|
| 306 |
|
// calc forces |
| 307 |
|
|
| 308 |
< |
myFF->doForces(calcPot,calcStress); |
| 308 |
> |
calcForce(calcPot, calcStress); |
| 309 |
|
|
| 310 |
+ |
#ifdef IS_MPI |
| 311 |
+ |
strcpy(checkPointMsg, "Succesful doForces\n"); |
| 312 |
+ |
MPIcheckPoint(); |
| 313 |
+ |
#endif // is_mpi |
| 314 |
+ |
|
| 315 |
+ |
#ifdef PROFILE |
| 316 |
+ |
endProfile( pro5 ); |
| 317 |
+ |
|
| 318 |
+ |
startProfile( pro6 ); |
| 319 |
+ |
#endif //profile |
| 320 |
+ |
|
| 321 |
|
// finish the velocity half step |
| 322 |
< |
|
| 322 |
> |
|
| 323 |
|
moveB(); |
| 324 |
< |
if( nConstrained ) constrainB(); |
| 325 |
< |
|
| 324 |
> |
|
| 325 |
> |
#ifdef PROFILE |
| 326 |
> |
endProfile(pro6); |
| 327 |
> |
#endif // profile |
| 328 |
> |
|
| 329 |
> |
#ifdef IS_MPI |
| 330 |
> |
strcpy(checkPointMsg, "Succesful moveB\n"); |
| 331 |
> |
MPIcheckPoint(); |
| 332 |
> |
#endif // is_mpi |
| 333 |
|
} |
| 334 |
|
|
| 335 |
|
|
| 336 |
< |
void Integrator::moveA( void ){ |
| 337 |
< |
|
| 298 |
< |
int i,j,k; |
| 299 |
< |
int atomIndex, aMatIndex; |
| 336 |
> |
template<typename T> void Integrator<T>::moveA(void){ |
| 337 |
> |
int i, j; |
| 338 |
|
DirectionalAtom* dAtom; |
| 339 |
< |
double Tb[3]; |
| 340 |
< |
double ji[3]; |
| 341 |
< |
double angle; |
| 304 |
< |
double A[3][3], At[3][3]; |
| 339 |
> |
double Tb[3], ji[3]; |
| 340 |
> |
double vel[3], pos[3], frc[3]; |
| 341 |
> |
double mass; |
| 342 |
|
|
| 343 |
+ |
for (i = 0; i < nAtoms; i++){ |
| 344 |
+ |
atoms[i]->getVel(vel); |
| 345 |
+ |
atoms[i]->getPos(pos); |
| 346 |
+ |
atoms[i]->getFrc(frc); |
| 347 |
|
|
| 348 |
< |
for( i=0; i<nAtoms; i++ ){ |
| 308 |
< |
atomIndex = i * 3; |
| 309 |
< |
aMatIndex = i * 9; |
| 348 |
> |
mass = atoms[i]->getMass(); |
| 349 |
|
|
| 350 |
< |
// velocity half step |
| 351 |
< |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
| 352 |
< |
vel[j] += ( dt2 * frc[j] / atoms[i]->getMass() ) * eConvert; |
| 350 |
> |
for (j = 0; j < 3; j++){ |
| 351 |
> |
// velocity half step |
| 352 |
> |
vel[j] += (dt2 * frc[j] / mass) * eConvert; |
| 353 |
> |
// position whole step |
| 354 |
> |
pos[j] += dt * vel[j]; |
| 355 |
> |
} |
| 356 |
|
|
| 357 |
+ |
atoms[i]->setVel(vel); |
| 358 |
+ |
atoms[i]->setPos(pos); |
| 359 |
|
|
| 360 |
< |
// position whole step |
| 361 |
< |
for( j=atomIndex; j<(atomIndex+3); j++ ) pos[j] += dt * vel[j]; |
| 318 |
< |
|
| 360 |
> |
if (atoms[i]->isDirectional()){ |
| 361 |
> |
dAtom = (DirectionalAtom *) atoms[i]; |
| 362 |
|
|
| 320 |
– |
if( atoms[i]->isDirectional() ){ |
| 321 |
– |
|
| 322 |
– |
dAtom = (DirectionalAtom *)atoms[i]; |
| 323 |
– |
|
| 363 |
|
// get and convert the torque to body frame |
| 325 |
– |
|
| 326 |
– |
Tb[0] = dAtom->getTx(); |
| 327 |
– |
Tb[1] = dAtom->getTy(); |
| 328 |
– |
Tb[2] = dAtom->getTz(); |
| 364 |
|
|
| 365 |
< |
dAtom->lab2Body( Tb ); |
| 365 |
> |
dAtom->getTrq(Tb); |
| 366 |
> |
dAtom->lab2Body(Tb); |
| 367 |
|
|
| 368 |
|
// get the angular momentum, and propagate a half step |
| 333 |
– |
|
| 334 |
– |
ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * eConvert; |
| 335 |
– |
ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * eConvert; |
| 336 |
– |
ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * eConvert; |
| 337 |
– |
|
| 338 |
– |
// use the angular velocities to propagate the rotation matrix a |
| 339 |
– |
// full time step |
| 340 |
– |
|
| 341 |
– |
// rotate about the x-axis |
| 342 |
– |
angle = dt2 * ji[0] / dAtom->getIxx(); |
| 343 |
– |
this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] ); |
| 369 |
|
|
| 370 |
< |
// rotate about the y-axis |
| 346 |
< |
angle = dt2 * ji[1] / dAtom->getIyy(); |
| 347 |
< |
this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] ); |
| 348 |
< |
|
| 349 |
< |
// rotate about the z-axis |
| 350 |
< |
angle = dt * ji[2] / dAtom->getIzz(); |
| 351 |
< |
this->rotate( 0, 1, angle, ji, &Amat[aMatIndex] ); |
| 352 |
< |
|
| 353 |
< |
// rotate about the y-axis |
| 354 |
< |
angle = dt2 * ji[1] / dAtom->getIyy(); |
| 355 |
< |
this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] ); |
| 356 |
< |
|
| 357 |
< |
// rotate about the x-axis |
| 358 |
< |
angle = dt2 * ji[0] / dAtom->getIxx(); |
| 359 |
< |
this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] ); |
| 360 |
< |
|
| 361 |
< |
dAtom->setJx( ji[0] ); |
| 362 |
< |
dAtom->setJy( ji[1] ); |
| 363 |
< |
dAtom->setJz( ji[2] ); |
| 370 |
> |
dAtom->getJ(ji); |
| 371 |
|
|
| 372 |
< |
std::cerr << "Amat[" << i << "]\n"; |
| 373 |
< |
info->printMat9( &Amat[aMatIndex] ); |
| 374 |
< |
|
| 375 |
< |
std::cerr << "ji[" << i << "]\t" |
| 376 |
< |
<< ji[0] << "\t" |
| 377 |
< |
<< ji[1] << "\t" |
| 371 |
< |
<< ji[2] << "\n"; |
| 372 |
< |
|
| 372 |
> |
for (j = 0; j < 3; j++) |
| 373 |
> |
ji[j] += (dt2 * Tb[j]) * eConvert; |
| 374 |
> |
|
| 375 |
> |
this->rotationPropagation( dAtom, ji ); |
| 376 |
> |
|
| 377 |
> |
dAtom->setJ(ji); |
| 378 |
|
} |
| 374 |
– |
|
| 379 |
|
} |
| 380 |
+ |
|
| 381 |
+ |
if (nConstrained){ |
| 382 |
+ |
constrainA(); |
| 383 |
+ |
} |
| 384 |
|
} |
| 385 |
|
|
| 386 |
|
|
| 387 |
< |
void Integrator::moveB( void ){ |
| 388 |
< |
int i,j,k; |
| 381 |
< |
int atomIndex, aMatIndex; |
| 387 |
> |
template<typename T> void Integrator<T>::moveB(void){ |
| 388 |
> |
int i, j; |
| 389 |
|
DirectionalAtom* dAtom; |
| 390 |
< |
double Tb[3]; |
| 391 |
< |
double ji[3]; |
| 390 |
> |
double Tb[3], ji[3]; |
| 391 |
> |
double vel[3], frc[3]; |
| 392 |
> |
double mass; |
| 393 |
|
|
| 394 |
< |
for( i=0; i<nAtoms; i++ ){ |
| 395 |
< |
atomIndex = i * 3; |
| 396 |
< |
aMatIndex = i * 9; |
| 394 |
> |
for (i = 0; i < nAtoms; i++){ |
| 395 |
> |
atoms[i]->getVel(vel); |
| 396 |
> |
atoms[i]->getFrc(frc); |
| 397 |
|
|
| 398 |
+ |
mass = atoms[i]->getMass(); |
| 399 |
+ |
|
| 400 |
|
// velocity half step |
| 401 |
< |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
| 402 |
< |
vel[j] += ( dt2 * frc[j] / atoms[i]->getMass() ) * eConvert; |
| 401 |
> |
for (j = 0; j < 3; j++) |
| 402 |
> |
vel[j] += (dt2 * frc[j] / mass) * eConvert; |
| 403 |
|
|
| 404 |
< |
|
| 405 |
< |
if( atoms[i]->isDirectional() ){ |
| 406 |
< |
|
| 407 |
< |
dAtom = (DirectionalAtom *)atoms[i]; |
| 408 |
< |
|
| 404 |
> |
atoms[i]->setVel(vel); |
| 405 |
> |
|
| 406 |
> |
if (atoms[i]->isDirectional()){ |
| 407 |
> |
dAtom = (DirectionalAtom *) atoms[i]; |
| 408 |
> |
|
| 409 |
|
// get and convert the torque to body frame |
| 400 |
– |
|
| 401 |
– |
Tb[0] = dAtom->getTx(); |
| 402 |
– |
Tb[1] = dAtom->getTy(); |
| 403 |
– |
Tb[2] = dAtom->getTz(); |
| 404 |
– |
|
| 405 |
– |
std::cerr << "TrqB[" << i << "]\t" |
| 406 |
– |
<< Tb[0] << "\t" |
| 407 |
– |
<< Tb[1] << "\t" |
| 408 |
– |
<< Tb[2] << "\n"; |
| 410 |
|
|
| 411 |
< |
dAtom->lab2Body( Tb ); |
| 412 |
< |
|
| 412 |
< |
// get the angular momentum, and complete the angular momentum |
| 413 |
< |
// half step |
| 414 |
< |
|
| 415 |
< |
ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * eConvert; |
| 416 |
< |
ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * eConvert; |
| 417 |
< |
ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * eConvert; |
| 418 |
< |
|
| 419 |
< |
dAtom->setJx( ji[0] ); |
| 420 |
< |
dAtom->setJy( ji[1] ); |
| 421 |
< |
dAtom->setJz( ji[2] ); |
| 411 |
> |
dAtom->getTrq(Tb); |
| 412 |
> |
dAtom->lab2Body(Tb); |
| 413 |
|
|
| 414 |
+ |
// get the angular momentum, and propagate a half step |
| 415 |
|
|
| 416 |
< |
std::cerr << "Amat[" << i << "]\n"; |
| 417 |
< |
info->printMat9( &Amat[aMatIndex] ); |
| 418 |
< |
|
| 419 |
< |
std::cerr << "ji[" << i << "]\t" |
| 420 |
< |
<< ji[0] << "\t" |
| 421 |
< |
<< ji[1] << "\t" |
| 422 |
< |
<< ji[2] << "\n"; |
| 416 |
> |
dAtom->getJ(ji); |
| 417 |
> |
|
| 418 |
> |
for (j = 0; j < 3; j++) |
| 419 |
> |
ji[j] += (dt2 * Tb[j]) * eConvert; |
| 420 |
> |
|
| 421 |
> |
|
| 422 |
> |
dAtom->setJ(ji); |
| 423 |
|
} |
| 424 |
|
} |
| 425 |
|
|
| 426 |
+ |
if (nConstrained){ |
| 427 |
+ |
constrainB(); |
| 428 |
+ |
} |
| 429 |
|
} |
| 430 |
|
|
| 431 |
< |
void Integrator::preMove( void ){ |
| 432 |
< |
int i; |
| 431 |
> |
template<typename T> void Integrator<T>::preMove(void){ |
| 432 |
> |
int i, j; |
| 433 |
> |
double pos[3]; |
| 434 |
|
|
| 435 |
< |
if( nConstrained ){ |
| 435 |
> |
if (nConstrained){ |
| 436 |
> |
for (i = 0; i < nAtoms; i++){ |
| 437 |
> |
atoms[i]->getPos(pos); |
| 438 |
|
|
| 439 |
< |
for(i=0; i<(nAtoms*3); i++) oldPos[i] = pos[i]; |
| 439 |
> |
for (j = 0; j < 3; j++){ |
| 440 |
> |
oldPos[3 * i + j] = pos[j]; |
| 441 |
> |
} |
| 442 |
> |
} |
| 443 |
|
} |
| 444 |
< |
} |
| 444 |
> |
} |
| 445 |
|
|
| 446 |
< |
void Integrator::constrainA(){ |
| 447 |
< |
|
| 447 |
< |
int i,j,k; |
| 446 |
> |
template<typename T> void Integrator<T>::constrainA(){ |
| 447 |
> |
int i, j; |
| 448 |
|
int done; |
| 449 |
+ |
double posA[3], posB[3]; |
| 450 |
+ |
double velA[3], velB[3]; |
| 451 |
|
double pab[3]; |
| 452 |
|
double rab[3]; |
| 453 |
|
int a, b, ax, ay, az, bx, by, bz; |
| 459 |
|
double gab; |
| 460 |
|
int iteration; |
| 461 |
|
|
| 462 |
< |
for( i=0; i<nAtoms; i++){ |
| 461 |
< |
|
| 462 |
> |
for (i = 0; i < nAtoms; i++){ |
| 463 |
|
moving[i] = 0; |
| 464 |
< |
moved[i] = 1; |
| 464 |
> |
moved[i] = 1; |
| 465 |
|
} |
| 466 |
|
|
| 467 |
|
iteration = 0; |
| 468 |
|
done = 0; |
| 469 |
< |
while( !done && (iteration < maxIteration )){ |
| 469 |
< |
|
| 469 |
> |
while (!done && (iteration < maxIteration)){ |
| 470 |
|
done = 1; |
| 471 |
< |
for(i=0; i<nConstrained; i++){ |
| 472 |
< |
|
| 471 |
> |
for (i = 0; i < nConstrained; i++){ |
| 472 |
|
a = constrainedA[i]; |
| 473 |
|
b = constrainedB[i]; |
| 475 |
– |
|
| 476 |
– |
ax = (a*3) + 0; |
| 477 |
– |
ay = (a*3) + 1; |
| 478 |
– |
az = (a*3) + 2; |
| 474 |
|
|
| 475 |
< |
bx = (b*3) + 0; |
| 476 |
< |
by = (b*3) + 1; |
| 477 |
< |
bz = (b*3) + 2; |
| 475 |
> |
ax = (a * 3) + 0; |
| 476 |
> |
ay = (a * 3) + 1; |
| 477 |
> |
az = (a * 3) + 2; |
| 478 |
|
|
| 479 |
< |
if( moved[a] || moved[b] ){ |
| 480 |
< |
|
| 481 |
< |
pab[0] = pos[ax] - pos[bx]; |
| 487 |
< |
pab[1] = pos[ay] - pos[by]; |
| 488 |
< |
pab[2] = pos[az] - pos[bz]; |
| 479 |
> |
bx = (b * 3) + 0; |
| 480 |
> |
by = (b * 3) + 1; |
| 481 |
> |
bz = (b * 3) + 2; |
| 482 |
|
|
| 483 |
< |
//periodic boundary condition |
| 483 |
> |
if (moved[a] || moved[b]){ |
| 484 |
> |
atoms[a]->getPos(posA); |
| 485 |
> |
atoms[b]->getPos(posB); |
| 486 |
|
|
| 487 |
< |
info->wrapVector( pab ); |
| 487 |
> |
for (j = 0; j < 3; j++) |
| 488 |
> |
pab[j] = posA[j] - posB[j]; |
| 489 |
|
|
| 490 |
< |
pabsq = pab[0] * pab[0] + pab[1] * pab[1] + pab[2] * pab[2]; |
| 490 |
> |
//periodic boundary condition |
| 491 |
|
|
| 492 |
< |
rabsq = constrainedDsqr[i]; |
| 497 |
< |
diffsq = rabsq - pabsq; |
| 492 |
> |
info->wrapVector(pab); |
| 493 |
|
|
| 494 |
< |
// the original rattle code from alan tidesley |
| 500 |
< |
if (fabs(diffsq) > (tol*rabsq*2)) { |
| 501 |
< |
rab[0] = oldPos[ax] - oldPos[bx]; |
| 502 |
< |
rab[1] = oldPos[ay] - oldPos[by]; |
| 503 |
< |
rab[2] = oldPos[az] - oldPos[bz]; |
| 494 |
> |
pabsq = pab[0] * pab[0] + pab[1] * pab[1] + pab[2] * pab[2]; |
| 495 |
|
|
| 496 |
< |
info->wrapVector( rab ); |
| 496 |
> |
rabsq = constrainedDsqr[i]; |
| 497 |
> |
diffsq = rabsq - pabsq; |
| 498 |
|
|
| 499 |
< |
rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2]; |
| 499 |
> |
// the original rattle code from alan tidesley |
| 500 |
> |
if (fabs(diffsq) > (tol * rabsq * 2)){ |
| 501 |
> |
rab[0] = oldPos[ax] - oldPos[bx]; |
| 502 |
> |
rab[1] = oldPos[ay] - oldPos[by]; |
| 503 |
> |
rab[2] = oldPos[az] - oldPos[bz]; |
| 504 |
|
|
| 505 |
< |
rpabsq = rpab * rpab; |
| 505 |
> |
info->wrapVector(rab); |
| 506 |
|
|
| 507 |
+ |
rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2]; |
| 508 |
|
|
| 509 |
< |
if (rpabsq < (rabsq * -diffsq)){ |
| 509 |
> |
rpabsq = rpab * rpab; |
| 510 |
|
|
| 511 |
+ |
|
| 512 |
+ |
if (rpabsq < (rabsq * -diffsq)){ |
| 513 |
|
#ifdef IS_MPI |
| 514 |
< |
a = atoms[a]->getGlobalIndex(); |
| 515 |
< |
b = atoms[b]->getGlobalIndex(); |
| 514 |
> |
a = atoms[a]->getGlobalIndex(); |
| 515 |
> |
b = atoms[b]->getGlobalIndex(); |
| 516 |
|
#endif //is_mpi |
| 517 |
< |
sprintf( painCave.errMsg, |
| 518 |
< |
"Constraint failure in constrainA at atom %d and %d.\n", |
| 519 |
< |
a, b ); |
| 520 |
< |
painCave.isFatal = 1; |
| 521 |
< |
simError(); |
| 522 |
< |
} |
| 517 |
> |
sprintf(painCave.errMsg, |
| 518 |
> |
"Constraint failure in constrainA at atom %d and %d.\n", a, |
| 519 |
> |
b); |
| 520 |
> |
painCave.isFatal = 1; |
| 521 |
> |
simError(); |
| 522 |
> |
} |
| 523 |
|
|
| 524 |
< |
rma = 1.0 / atoms[a]->getMass(); |
| 525 |
< |
rmb = 1.0 / atoms[b]->getMass(); |
| 524 |
> |
rma = 1.0 / atoms[a]->getMass(); |
| 525 |
> |
rmb = 1.0 / atoms[b]->getMass(); |
| 526 |
|
|
| 527 |
< |
gab = diffsq / ( 2.0 * ( rma + rmb ) * rpab ); |
| 527 |
> |
gab = diffsq / (2.0 * (rma + rmb) * rpab); |
| 528 |
|
|
| 529 |
|
dx = rab[0] * gab; |
| 530 |
|
dy = rab[1] * gab; |
| 531 |
|
dz = rab[2] * gab; |
| 532 |
|
|
| 533 |
< |
pos[ax] += rma * dx; |
| 534 |
< |
pos[ay] += rma * dy; |
| 535 |
< |
pos[az] += rma * dz; |
| 533 |
> |
posA[0] += rma * dx; |
| 534 |
> |
posA[1] += rma * dy; |
| 535 |
> |
posA[2] += rma * dz; |
| 536 |
|
|
| 537 |
< |
pos[bx] -= rmb * dx; |
| 539 |
< |
pos[by] -= rmb * dy; |
| 540 |
< |
pos[bz] -= rmb * dz; |
| 537 |
> |
atoms[a]->setPos(posA); |
| 538 |
|
|
| 539 |
+ |
posB[0] -= rmb * dx; |
| 540 |
+ |
posB[1] -= rmb * dy; |
| 541 |
+ |
posB[2] -= rmb * dz; |
| 542 |
+ |
|
| 543 |
+ |
atoms[b]->setPos(posB); |
| 544 |
+ |
|
| 545 |
|
dx = dx / dt; |
| 546 |
|
dy = dy / dt; |
| 547 |
|
dz = dz / dt; |
| 548 |
|
|
| 549 |
< |
vel[ax] += rma * dx; |
| 547 |
< |
vel[ay] += rma * dy; |
| 548 |
< |
vel[az] += rma * dz; |
| 549 |
> |
atoms[a]->getVel(velA); |
| 550 |
|
|
| 551 |
< |
vel[bx] -= rmb * dx; |
| 552 |
< |
vel[by] -= rmb * dy; |
| 553 |
< |
vel[bz] -= rmb * dz; |
| 551 |
> |
velA[0] += rma * dx; |
| 552 |
> |
velA[1] += rma * dy; |
| 553 |
> |
velA[2] += rma * dz; |
| 554 |
|
|
| 555 |
< |
moving[a] = 1; |
| 556 |
< |
moving[b] = 1; |
| 557 |
< |
done = 0; |
| 558 |
< |
} |
| 555 |
> |
atoms[a]->setVel(velA); |
| 556 |
> |
|
| 557 |
> |
atoms[b]->getVel(velB); |
| 558 |
> |
|
| 559 |
> |
velB[0] -= rmb * dx; |
| 560 |
> |
velB[1] -= rmb * dy; |
| 561 |
> |
velB[2] -= rmb * dz; |
| 562 |
> |
|
| 563 |
> |
atoms[b]->setVel(velB); |
| 564 |
> |
|
| 565 |
> |
moving[a] = 1; |
| 566 |
> |
moving[b] = 1; |
| 567 |
> |
done = 0; |
| 568 |
> |
} |
| 569 |
|
} |
| 570 |
|
} |
| 571 |
< |
|
| 572 |
< |
for(i=0; i<nAtoms; i++){ |
| 562 |
< |
|
| 571 |
> |
|
| 572 |
> |
for (i = 0; i < nAtoms; i++){ |
| 573 |
|
moved[i] = moving[i]; |
| 574 |
|
moving[i] = 0; |
| 575 |
|
} |
| 577 |
|
iteration++; |
| 578 |
|
} |
| 579 |
|
|
| 580 |
< |
if( !done ){ |
| 581 |
< |
|
| 582 |
< |
sprintf( painCave.errMsg, |
| 583 |
< |
"Constraint failure in constrainA, too many iterations: %d\n", |
| 574 |
< |
iteration ); |
| 580 |
> |
if (!done){ |
| 581 |
> |
sprintf(painCave.errMsg, |
| 582 |
> |
"Constraint failure in constrainA, too many iterations: %d\n", |
| 583 |
> |
iteration); |
| 584 |
|
painCave.isFatal = 1; |
| 585 |
|
simError(); |
| 586 |
|
} |
| 587 |
|
|
| 588 |
|
} |
| 589 |
|
|
| 590 |
< |
void Integrator::constrainB( void ){ |
| 591 |
< |
|
| 583 |
< |
int i,j,k; |
| 590 |
> |
template<typename T> void Integrator<T>::constrainB(void){ |
| 591 |
> |
int i, j; |
| 592 |
|
int done; |
| 593 |
+ |
double posA[3], posB[3]; |
| 594 |
+ |
double velA[3], velB[3]; |
| 595 |
|
double vxab, vyab, vzab; |
| 596 |
|
double rab[3]; |
| 597 |
|
int a, b, ax, ay, az, bx, by, bz; |
| 598 |
|
double rma, rmb; |
| 599 |
|
double dx, dy, dz; |
| 600 |
< |
double rabsq, pabsq, rvab; |
| 591 |
< |
double diffsq; |
| 600 |
> |
double rvab; |
| 601 |
|
double gab; |
| 602 |
|
int iteration; |
| 603 |
|
|
| 604 |
< |
for(i=0; i<nAtoms; i++){ |
| 604 |
> |
for (i = 0; i < nAtoms; i++){ |
| 605 |
|
moving[i] = 0; |
| 606 |
|
moved[i] = 1; |
| 607 |
|
} |
| 608 |
|
|
| 609 |
|
done = 0; |
| 610 |
|
iteration = 0; |
| 611 |
< |
while( !done && (iteration < maxIteration ) ){ |
| 603 |
< |
|
| 611 |
> |
while (!done && (iteration < maxIteration)){ |
| 612 |
|
done = 1; |
| 613 |
|
|
| 614 |
< |
for(i=0; i<nConstrained; i++){ |
| 607 |
< |
|
| 614 |
> |
for (i = 0; i < nConstrained; i++){ |
| 615 |
|
a = constrainedA[i]; |
| 616 |
|
b = constrainedB[i]; |
| 617 |
|
|
| 618 |
< |
ax = (a*3) + 0; |
| 619 |
< |
ay = (a*3) + 1; |
| 620 |
< |
az = (a*3) + 2; |
| 618 |
> |
ax = (a * 3) + 0; |
| 619 |
> |
ay = (a * 3) + 1; |
| 620 |
> |
az = (a * 3) + 2; |
| 621 |
|
|
| 622 |
< |
bx = (b*3) + 0; |
| 623 |
< |
by = (b*3) + 1; |
| 624 |
< |
bz = (b*3) + 2; |
| 622 |
> |
bx = (b * 3) + 0; |
| 623 |
> |
by = (b * 3) + 1; |
| 624 |
> |
bz = (b * 3) + 2; |
| 625 |
|
|
| 626 |
< |
if( moved[a] || moved[b] ){ |
| 627 |
< |
|
| 628 |
< |
vxab = vel[ax] - vel[bx]; |
| 622 |
< |
vyab = vel[ay] - vel[by]; |
| 623 |
< |
vzab = vel[az] - vel[bz]; |
| 626 |
> |
if (moved[a] || moved[b]){ |
| 627 |
> |
atoms[a]->getVel(velA); |
| 628 |
> |
atoms[b]->getVel(velB); |
| 629 |
|
|
| 630 |
< |
rab[0] = pos[ax] - pos[bx]; |
| 631 |
< |
rab[1] = pos[ay] - pos[by]; |
| 632 |
< |
rab[2] = pos[az] - pos[bz]; |
| 628 |
< |
|
| 629 |
< |
info->wrapVector( rab ); |
| 630 |
< |
|
| 631 |
< |
rma = 1.0 / atoms[a]->getMass(); |
| 632 |
< |
rmb = 1.0 / atoms[b]->getMass(); |
| 630 |
> |
vxab = velA[0] - velB[0]; |
| 631 |
> |
vyab = velA[1] - velB[1]; |
| 632 |
> |
vzab = velA[2] - velB[2]; |
| 633 |
|
|
| 634 |
< |
rvab = rab[0] * vxab + rab[1] * vyab + rab[2] * vzab; |
| 635 |
< |
|
| 636 |
< |
gab = -rvab / ( ( rma + rmb ) * constrainedDsqr[i] ); |
| 634 |
> |
atoms[a]->getPos(posA); |
| 635 |
> |
atoms[b]->getPos(posB); |
| 636 |
|
|
| 637 |
< |
if (fabs(gab) > tol) { |
| 638 |
< |
|
| 640 |
< |
dx = rab[0] * gab; |
| 641 |
< |
dy = rab[1] * gab; |
| 642 |
< |
dz = rab[2] * gab; |
| 643 |
< |
|
| 644 |
< |
vel[ax] += rma * dx; |
| 645 |
< |
vel[ay] += rma * dy; |
| 646 |
< |
vel[az] += rma * dz; |
| 637 |
> |
for (j = 0; j < 3; j++) |
| 638 |
> |
rab[j] = posA[j] - posB[j]; |
| 639 |
|
|
| 640 |
< |
vel[bx] -= rmb * dx; |
| 641 |
< |
vel[by] -= rmb * dy; |
| 642 |
< |
vel[bz] -= rmb * dz; |
| 643 |
< |
|
| 644 |
< |
moving[a] = 1; |
| 645 |
< |
moving[b] = 1; |
| 646 |
< |
done = 0; |
| 647 |
< |
} |
| 640 |
> |
info->wrapVector(rab); |
| 641 |
> |
|
| 642 |
> |
rma = 1.0 / atoms[a]->getMass(); |
| 643 |
> |
rmb = 1.0 / atoms[b]->getMass(); |
| 644 |
> |
|
| 645 |
> |
rvab = rab[0] * vxab + rab[1] * vyab + rab[2] * vzab; |
| 646 |
> |
|
| 647 |
> |
gab = -rvab / ((rma + rmb) * constrainedDsqr[i]); |
| 648 |
> |
|
| 649 |
> |
if (fabs(gab) > tol){ |
| 650 |
> |
dx = rab[0] * gab; |
| 651 |
> |
dy = rab[1] * gab; |
| 652 |
> |
dz = rab[2] * gab; |
| 653 |
> |
|
| 654 |
> |
velA[0] += rma * dx; |
| 655 |
> |
velA[1] += rma * dy; |
| 656 |
> |
velA[2] += rma * dz; |
| 657 |
> |
|
| 658 |
> |
atoms[a]->setVel(velA); |
| 659 |
> |
|
| 660 |
> |
velB[0] -= rmb * dx; |
| 661 |
> |
velB[1] -= rmb * dy; |
| 662 |
> |
velB[2] -= rmb * dz; |
| 663 |
> |
|
| 664 |
> |
atoms[b]->setVel(velB); |
| 665 |
> |
|
| 666 |
> |
moving[a] = 1; |
| 667 |
> |
moving[b] = 1; |
| 668 |
> |
done = 0; |
| 669 |
> |
} |
| 670 |
|
} |
| 671 |
|
} |
| 672 |
|
|
| 673 |
< |
for(i=0; i<nAtoms; i++){ |
| 673 |
> |
for (i = 0; i < nAtoms; i++){ |
| 674 |
|
moved[i] = moving[i]; |
| 675 |
|
moving[i] = 0; |
| 676 |
|
} |
| 677 |
< |
|
| 677 |
> |
|
| 678 |
|
iteration++; |
| 679 |
|
} |
| 680 |
|
|
| 681 |
< |
if( !done ){ |
| 682 |
< |
|
| 683 |
< |
|
| 684 |
< |
sprintf( painCave.errMsg, |
| 671 |
< |
"Constraint failure in constrainB, too many iterations: %d\n", |
| 672 |
< |
iteration ); |
| 681 |
> |
if (!done){ |
| 682 |
> |
sprintf(painCave.errMsg, |
| 683 |
> |
"Constraint failure in constrainB, too many iterations: %d\n", |
| 684 |
> |
iteration); |
| 685 |
|
painCave.isFatal = 1; |
| 686 |
|
simError(); |
| 687 |
< |
} |
| 676 |
< |
|
| 687 |
> |
} |
| 688 |
|
} |
| 689 |
|
|
| 690 |
+ |
template<typename T> void Integrator<T>::rotationPropagation |
| 691 |
+ |
( DirectionalAtom* dAtom, double ji[3] ){ |
| 692 |
|
|
| 693 |
+ |
double angle; |
| 694 |
+ |
double A[3][3], I[3][3]; |
| 695 |
|
|
| 696 |
+ |
// use the angular velocities to propagate the rotation matrix a |
| 697 |
+ |
// full time step |
| 698 |
|
|
| 699 |
+ |
dAtom->getA(A); |
| 700 |
+ |
dAtom->getI(I); |
| 701 |
|
|
| 702 |
+ |
// rotate about the x-axis |
| 703 |
+ |
angle = dt2 * ji[0] / I[0][0]; |
| 704 |
+ |
this->rotate( 1, 2, angle, ji, A ); |
| 705 |
|
|
| 706 |
+ |
// rotate about the y-axis |
| 707 |
+ |
angle = dt2 * ji[1] / I[1][1]; |
| 708 |
+ |
this->rotate( 2, 0, angle, ji, A ); |
| 709 |
|
|
| 710 |
< |
void Integrator::rotate( int axes1, int axes2, double angle, double ji[3], |
| 711 |
< |
double A[9] ){ |
| 710 |
> |
// rotate about the z-axis |
| 711 |
> |
angle = dt * ji[2] / I[2][2]; |
| 712 |
> |
this->rotate( 0, 1, angle, ji, A); |
| 713 |
|
|
| 714 |
< |
int i,j,k; |
| 714 |
> |
// rotate about the y-axis |
| 715 |
> |
angle = dt2 * ji[1] / I[1][1]; |
| 716 |
> |
this->rotate( 2, 0, angle, ji, A ); |
| 717 |
> |
|
| 718 |
> |
// rotate about the x-axis |
| 719 |
> |
angle = dt2 * ji[0] / I[0][0]; |
| 720 |
> |
this->rotate( 1, 2, angle, ji, A ); |
| 721 |
> |
|
| 722 |
> |
dAtom->setA( A ); |
| 723 |
> |
} |
| 724 |
> |
|
| 725 |
> |
template<typename T> void Integrator<T>::rotate(int axes1, int axes2, |
| 726 |
> |
double angle, double ji[3], |
| 727 |
> |
double A[3][3]){ |
| 728 |
> |
int i, j, k; |
| 729 |
|
double sinAngle; |
| 730 |
|
double cosAngle; |
| 731 |
|
double angleSqr; |
| 735 |
|
double tempA[3][3]; |
| 736 |
|
double tempJ[3]; |
| 737 |
|
|
| 698 |
– |
|
| 738 |
|
// initialize the tempA |
| 739 |
|
|
| 740 |
< |
for(i=0; i<3; i++){ |
| 741 |
< |
for(j=0; j<3; j++){ |
| 742 |
< |
tempA[j][i] = A[3*i+j]; |
| 740 |
> |
for (i = 0; i < 3; i++){ |
| 741 |
> |
for (j = 0; j < 3; j++){ |
| 742 |
> |
tempA[j][i] = A[i][j]; |
| 743 |
|
} |
| 744 |
|
} |
| 745 |
|
|
| 746 |
|
// initialize the tempJ |
| 747 |
|
|
| 748 |
< |
for( i=0; i<3; i++) tempJ[i] = ji[i]; |
| 749 |
< |
|
| 748 |
> |
for (i = 0; i < 3; i++) |
| 749 |
> |
tempJ[i] = ji[i]; |
| 750 |
> |
|
| 751 |
|
// initalize rot as a unit matrix |
| 752 |
|
|
| 753 |
|
rot[0][0] = 1.0; |
| 757 |
|
rot[1][0] = 0.0; |
| 758 |
|
rot[1][1] = 1.0; |
| 759 |
|
rot[1][2] = 0.0; |
| 760 |
< |
|
| 760 |
> |
|
| 761 |
|
rot[2][0] = 0.0; |
| 762 |
|
rot[2][1] = 0.0; |
| 763 |
|
rot[2][2] = 1.0; |
| 764 |
< |
|
| 764 |
> |
|
| 765 |
|
// use a small angle aproximation for sin and cosine |
| 766 |
|
|
| 767 |
< |
angleSqr = angle * angle; |
| 767 |
> |
angleSqr = angle * angle; |
| 768 |
|
angleSqrOver4 = angleSqr / 4.0; |
| 769 |
|
top = 1.0 - angleSqrOver4; |
| 770 |
|
bottom = 1.0 + angleSqrOver4; |
| 777 |
|
|
| 778 |
|
rot[axes1][axes2] = sinAngle; |
| 779 |
|
rot[axes2][axes1] = -sinAngle; |
| 780 |
< |
|
| 780 |
> |
|
| 781 |
|
// rotate the momentum acoording to: ji[] = rot[][] * ji[] |
| 782 |
< |
|
| 783 |
< |
for(i=0; i<3; i++){ |
| 782 |
> |
|
| 783 |
> |
for (i = 0; i < 3; i++){ |
| 784 |
|
ji[i] = 0.0; |
| 785 |
< |
for(k=0; k<3; k++){ |
| 785 |
> |
for (k = 0; k < 3; k++){ |
| 786 |
|
ji[i] += rot[i][k] * tempJ[k]; |
| 787 |
|
} |
| 788 |
|
} |
| 789 |
|
|
| 790 |
< |
// rotate the Rotation matrix acording to: |
| 790 |
> |
// rotate the Rotation matrix acording to: |
| 791 |
|
// A[][] = A[][] * transpose(rot[][]) |
| 792 |
|
|
| 793 |
|
|
| 795 |
|
// calculation as: |
| 796 |
|
// transpose(A[][]) = transpose(A[][]) * transpose(rot[][]) |
| 797 |
|
|
| 798 |
< |
for(i=0; i<3; i++){ |
| 799 |
< |
for(j=0; j<3; j++){ |
| 800 |
< |
A[3*j+i] = 0.0; |
| 801 |
< |
for(k=0; k<3; k++){ |
| 802 |
< |
A[3*j+i] += tempA[i][k] * rot[j][k]; |
| 798 |
> |
for (i = 0; i < 3; i++){ |
| 799 |
> |
for (j = 0; j < 3; j++){ |
| 800 |
> |
A[j][i] = 0.0; |
| 801 |
> |
for (k = 0; k < 3; k++){ |
| 802 |
> |
A[j][i] += tempA[i][k] * rot[j][k]; |
| 803 |
|
} |
| 804 |
|
} |
| 805 |
|
} |
| 806 |
|
} |
| 807 |
+ |
|
| 808 |
+ |
template<typename T> void Integrator<T>::calcForce(int calcPot, int calcStress){ |
| 809 |
+ |
myFF->doForces(calcPot, calcStress); |
| 810 |
+ |
} |
| 811 |
+ |
|
| 812 |
+ |
template<typename T> void Integrator<T>::thermalize(){ |
| 813 |
+ |
tStats->velocitize(); |
| 814 |
+ |
} |
| 815 |
+ |
|
| 816 |
+ |
template<typename T> double Integrator<T>::getConservedQuantity(void){ |
| 817 |
+ |
return tStats->getTotalE(); |
| 818 |
+ |
} |
| 819 |
+ |
template<typename T> string Integrator<T>::getAdditionalParameters(void){ |
| 820 |
+ |
//By default, return a null string |
| 821 |
+ |
//The reason we use string instead of char* is that if we use char*, we will |
| 822 |
+ |
//return a pointer point to local variable which might cause problem |
| 823 |
+ |
return string(); |
| 824 |
+ |
} |
