| 5 |
|
#include "Thermo.hpp" |
| 6 |
|
#include "ReadWrite.hpp" |
| 7 |
|
#include "ForceFields.hpp" |
| 8 |
+ |
#include "ExtendedSystem.hpp" |
| 9 |
|
#include "simError.h" |
| 10 |
|
|
| 11 |
|
extern "C"{ |
| 31 |
|
|
| 32 |
|
|
| 33 |
|
|
| 34 |
< |
Symplectic::Symplectic( SimInfo* the_entry_plug, ForceFields* the_ff ){ |
| 34 |
> |
Symplectic::Symplectic( SimInfo* the_entry_plug, ForceFields* the_ff, |
| 35 |
> |
ExtendedSystem* the_es ){ |
| 36 |
|
entry_plug = the_entry_plug; |
| 37 |
|
myFF = the_ff; |
| 38 |
+ |
myES = the_es; |
| 39 |
|
isFirst = 1; |
| 40 |
|
|
| 41 |
|
molecules = entry_plug->molecules; |
| 51 |
|
mass = new double[entry_plug->n_atoms]; |
| 52 |
|
for(int i = 0; i < entry_plug->n_atoms; i++){ |
| 53 |
|
mass[i] = entry_plug->atoms[i]->getMass(); |
| 54 |
< |
} |
| 52 |
< |
|
| 53 |
< |
|
| 54 |
> |
} |
| 55 |
|
|
| 56 |
|
// check for constraints |
| 57 |
|
|
| 582 |
|
|
| 583 |
|
for(i=0; i<3; i++){ |
| 584 |
|
for(j=0; j<3; j++){ |
| 585 |
< |
tempA[i][j] = A[i][j]; |
| 585 |
> |
tempA[j][i] = A[i][j]; |
| 586 |
|
} |
| 587 |
|
} |
| 588 |
|
|
| 641 |
|
for(j=0; j<3; j++){ |
| 642 |
|
A[j][i] = 0.0; |
| 643 |
|
for(k=0; k<3; k++){ |
| 644 |
< |
A[j][i] += tempA[k][i] * rot[j][k]; |
| 644 |
> |
A[j][i] += tempA[i][k] * rot[j][k]; |
| 645 |
|
} |
| 646 |
|
} |
| 647 |
|
} |
