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#include <iostream> |
2 |
#include <cstdlib> |
3 |
|
4 |
#include "Integrator.hpp" |
5 |
#include "Thermo.hpp" |
6 |
#include "ReadWrite.hpp" |
7 |
|
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|
9 |
extern "C"{ |
10 |
|
11 |
void v_constrain_a_( double &dt, int &n_atoms, double* mass, |
12 |
double* Rx, double* Ry, double* Rz, |
13 |
double* Vx, double* Vy, double* Vz, |
14 |
double* Fx, double* Fy, double* Fz, |
15 |
int &n_constrained, double *constr_sqr, |
16 |
int* constr_i, int* constr_j, |
17 |
double &box_x, double &box_y, double &box_z ); |
18 |
|
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void v_constrain_b_( double &dt, int &n_atoms, double* mass, |
20 |
double* Rx, double* Ry, double* Rz, |
21 |
double* Vx, double* Vy, double* Vz, |
22 |
double* Fx, double* Fy, double* Fz, |
23 |
double &Kinetic, |
24 |
int &n_constrained, double *constr_sqr, |
25 |
int* constr_i, int* constr_j, |
26 |
double &box_x, double &box_y, double &box_z ); |
27 |
} |
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|
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|
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|
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|
32 |
Symplectic::Symplectic( SimInfo* the_entry_plug ){ |
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entry_plug = the_entry_plug; |
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isFirst = 1; |
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|
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srInteractions = entry_plug->sr_interactions; |
37 |
longRange = entry_plug->longRange; |
38 |
nSRI = entry_plug->n_SRI; |
39 |
|
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// give a little love back to the SimInfo object |
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|
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if( entry_plug->the_integrator != NULL ) delete entry_plug->the_integrator; |
43 |
entry_plug->the_integrator = this; |
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|
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// grab the masses |
46 |
|
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mass = new double[entry_plug->n_atoms]; |
48 |
for(int i = 0; i < entry_plug->n_atoms; i++){ |
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mass[i] = entry_plug->atoms[i]->getMass(); |
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} |
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|
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|
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// check for constraints |
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|
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is_constrained = 0; |
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|
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Constraint *temp_con; |
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Constraint *dummy_plug; |
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temp_con = new Constraint[nSRI]; |
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n_constrained = 0; |
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int constrained = 0; |
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|
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for(int i = 0; i < nSRI; i++){ |
64 |
|
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constrained = srInteractions[i]->is_constrained(); |
66 |
|
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if(constrained){ |
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|
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dummy_plug = srInteractions[i]->get_constraint(); |
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temp_con[n_constrained].set_a( dummy_plug->get_a() ); |
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temp_con[n_constrained].set_b( dummy_plug->get_b() ); |
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temp_con[n_constrained].set_dsqr( dummy_plug->get_dsqr() ); |
73 |
|
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n_constrained++; |
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constrained = 0; |
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} |
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} |
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|
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if(n_constrained > 0){ |
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|
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is_constrained = 1; |
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constrained_i = new int[n_constrained]; |
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constrained_j = new int[n_constrained]; |
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constrained_dsqr = new double[n_constrained]; |
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|
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for( int i = 0; i < n_constrained; i++){ |
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|
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/* add 1 to the index for the fortran arrays. */ |
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|
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constrained_i[i] = temp_con[i].get_a() + 1; |
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constrained_j[i] = temp_con[i].get_b() + 1; |
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constrained_dsqr[i] = temp_con[i].get_dsqr(); |
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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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Symplectic::~Symplectic() { |
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|
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if( n_constrained ){ |
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delete[] constrained_i; |
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delete[] constrained_j; |
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delete[] constrained_dsqr; |
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} |
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|
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} |
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|
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|
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void Symplectic::integrate( void ){ |
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|
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const double e_convert = 4.184e-4; // converts kcal/mol -> amu*A^2/fs^2 |
113 |
|
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int i, j; // loop counters |
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int nAtoms = entry_plug->n_atoms; // the number of atoms |
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double kE = 0.0; // the kinetic energy |
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double rot_kE; |
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double trans_kE; |
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int tl; // the time loop conter |
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double dt2; // half the dt |
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|
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double vx, vy, vz; // the velocities |
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double vx2, vy2, vz2; // the square of the velocities |
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double rx, ry, rz; // the postitions |
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|
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double ji[3]; // the body frame angular momentum |
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double jx2, jy2, jz2; // the square of the angular momentums |
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double Tb[3]; // torque in the body frame |
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double angle; // the angle through which to rotate the rotation matrix |
130 |
double A[3][3]; // the rotation matrix |
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|
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|
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double dt = entry_plug->dt; |
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double runTime = entry_plug->run_time; |
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double sampleTime = entry_plug->sampleTime; |
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double statusTime = entry_plug->statusTime; |
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double thermalTime = entry_plug->thermalTime; |
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|
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int n_loops = (int)( runTime / dt ); |
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int sample_n = (int)( sampleTime / dt ); |
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int status_n = (int)( statusTime / dt ); |
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int vel_n = (int)( thermalTime / dt ); |
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|
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Thermo *tStats = new Thermo( entry_plug ); |
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|
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StatWriter* e_out = new StatWriter( entry_plug ); |
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DumpWriter* dump_out = new DumpWriter( entry_plug ); |
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|
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|
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Atom** atoms = entry_plug->atoms; |
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DirectionalAtom* dAtom; |
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dt2 = 0.5 * dt; |
153 |
|
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// initialize the forces the before the first step |
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|
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|
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for(i = 0; i < nAtoms; i++){ |
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atoms[i]->zeroForces(); |
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} |
160 |
|
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for(i = 0; i < nSRI; i++){ |
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|
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srInteractions[i]->calc_forces(); |
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} |
165 |
|
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longRange->calc_forces(); |
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|
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if( entry_plug->setTemp ){ |
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|
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tStats->velocitize(); |
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} |
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|
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if( n_constrained ){ |
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|
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double *Rx = new double[nAtoms]; |
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double *Ry = new double[nAtoms]; |
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double *Rz = new double[nAtoms]; |
178 |
|
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double *Vx = new double[nAtoms]; |
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double *Vy = new double[nAtoms]; |
181 |
double *Vz = new double[nAtoms]; |
182 |
|
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double *Fx = new double[nAtoms]; |
184 |
double *Fy = new double[nAtoms]; |
185 |
double *Fz = new double[nAtoms]; |
186 |
|
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|
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for( tl=0; tl < n_loops; tl++ ){ |
189 |
|
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for( j=0; j<nAtoms; j++ ){ |
191 |
|
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Rx[j] = atoms[j]->getX(); |
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Ry[j] = atoms[j]->getY(); |
194 |
Rz[j] = atoms[j]->getZ(); |
195 |
|
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Vx[j] = atoms[j]->get_vx(); |
197 |
Vy[j] = atoms[j]->get_vy(); |
198 |
Vz[j] = atoms[j]->get_vz(); |
199 |
|
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Fx[j] = atoms[j]->getFx(); |
201 |
Fy[j] = atoms[j]->getFy(); |
202 |
Fz[j] = atoms[j]->getFz(); |
203 |
|
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} |
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|
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v_constrain_a_( dt, nAtoms, mass, Rx, Ry, Rz, Vx, Vy, Vz, |
207 |
Fx, Fy, Fz, |
208 |
n_constrained, constrained_dsqr, |
209 |
constrained_i, constrained_j, |
210 |
entry_plug->box_x, |
211 |
entry_plug->box_y, |
212 |
entry_plug->box_z ); |
213 |
|
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for( j=0; j<nAtoms; j++ ){ |
215 |
|
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atoms[j]->setX(Rx[j]); |
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atoms[j]->setY(Ry[j]); |
218 |
atoms[j]->setZ(Rz[j]); |
219 |
|
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atoms[j]->set_vx(Vx[j]); |
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atoms[j]->set_vy(Vy[j]); |
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atoms[j]->set_vz(Vz[j]); |
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} |
224 |
|
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|
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for( i=0; i<nAtoms; i++ ){ |
227 |
if( atoms[i]->isDirectional() ){ |
228 |
|
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dAtom = (DirectionalAtom *)atoms[i]; |
230 |
|
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// get and convert the torque to body frame |
232 |
|
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Tb[0] = dAtom->getTx(); |
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Tb[1] = dAtom->getTy(); |
235 |
Tb[2] = dAtom->getTz(); |
236 |
|
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dAtom->lab2Body( Tb ); |
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|
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// get the angular momentum, and propagate a half step |
240 |
|
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ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * e_convert; |
242 |
ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * e_convert; |
243 |
ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * e_convert; |
244 |
|
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// get the atom's rotation matrix |
246 |
|
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A[0][0] = dAtom->getAxx(); |
248 |
A[0][1] = dAtom->getAxy(); |
249 |
A[0][2] = dAtom->getAxz(); |
250 |
|
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A[1][0] = dAtom->getAyx(); |
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A[1][1] = dAtom->getAyy(); |
253 |
A[1][2] = dAtom->getAyz(); |
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|
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A[2][0] = dAtom->getAzx(); |
256 |
A[2][1] = dAtom->getAzy(); |
257 |
A[2][2] = dAtom->getAzz(); |
258 |
|
259 |
|
260 |
// use the angular velocities to propagate the rotation matrix a |
261 |
// full time step |
262 |
|
263 |
|
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angle = dt2 * ji[0] / dAtom->getIxx(); |
265 |
this->rotate( 1, 2, angle, ji, A ); // rotate about the x-axis |
266 |
|
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angle = dt2 * ji[1] / dAtom->getIyy(); |
268 |
this->rotate( 2, 0, angle, ji, A ); // rotate about the y-axis |
269 |
|
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angle = dt * ji[2] / dAtom->getIzz(); |
271 |
this->rotate( 0, 1, angle, ji, A ); // rotate about the z-axis |
272 |
|
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angle = dt2 * ji[1] / dAtom->getIyy(); |
274 |
this->rotate( 2, 0, angle, ji, A ); // rotate about the y-axis |
275 |
|
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angle = dt2 * ji[0] / dAtom->getIxx(); |
277 |
this->rotate( 1, 2, angle, ji, A ); // rotate about the x-axis |
278 |
|
279 |
|
280 |
dAtom->setA( A ); |
281 |
dAtom->setJx( ji[0] ); |
282 |
dAtom->setJy( ji[1] ); |
283 |
dAtom->setJz( ji[2] ); |
284 |
} |
285 |
} |
286 |
|
287 |
// calculate the forces |
288 |
|
289 |
for(j = 0; j < nAtoms; j++){ |
290 |
atoms[j]->zeroForces(); |
291 |
} |
292 |
|
293 |
for(j = 0; j < nSRI; j++){ |
294 |
srInteractions[j]->calc_forces(); |
295 |
} |
296 |
|
297 |
longRange->calc_forces(); |
298 |
|
299 |
// move b |
300 |
|
301 |
for( j=0; j<nAtoms; j++ ){ |
302 |
|
303 |
Rx[j] = atoms[j]->getX(); |
304 |
Ry[j] = atoms[j]->getY(); |
305 |
Rz[j] = atoms[j]->getZ(); |
306 |
|
307 |
Vx[j] = atoms[j]->get_vx(); |
308 |
Vy[j] = atoms[j]->get_vy(); |
309 |
Vz[j] = atoms[j]->get_vz(); |
310 |
|
311 |
Fx[j] = atoms[j]->getFx(); |
312 |
Fy[j] = atoms[j]->getFy(); |
313 |
Fz[j] = atoms[j]->getFz(); |
314 |
} |
315 |
|
316 |
v_constrain_b_( dt, nAtoms, mass, Rx, Ry, Rz, Vx, Vy, Vz, |
317 |
Fx, Fy, Fz, |
318 |
kE, n_constrained, constrained_dsqr, |
319 |
constrained_i, constrained_j, |
320 |
entry_plug->box_x, |
321 |
entry_plug->box_y, |
322 |
entry_plug->box_z ); |
323 |
|
324 |
for( j=0; j<nAtoms; j++ ){ |
325 |
|
326 |
atoms[j]->setX(Rx[j]); |
327 |
atoms[j]->setY(Ry[j]); |
328 |
atoms[j]->setZ(Rz[j]); |
329 |
|
330 |
atoms[j]->set_vx(Vx[j]); |
331 |
atoms[j]->set_vy(Vy[j]); |
332 |
atoms[j]->set_vz(Vz[j]); |
333 |
} |
334 |
|
335 |
for( i=0; i< nAtoms; i++ ){ |
336 |
|
337 |
if( atoms[i]->isDirectional() ){ |
338 |
|
339 |
dAtom = (DirectionalAtom *)atoms[i]; |
340 |
|
341 |
// get and convert the torque to body frame |
342 |
|
343 |
Tb[0] = dAtom->getTx(); |
344 |
Tb[1] = dAtom->getTy(); |
345 |
Tb[2] = dAtom->getTz(); |
346 |
|
347 |
dAtom->lab2Body( Tb ); |
348 |
|
349 |
// get the angular momentum, and complete the angular momentum |
350 |
// half step |
351 |
|
352 |
ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * e_convert; |
353 |
ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * e_convert; |
354 |
ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * e_convert; |
355 |
|
356 |
dAtom->setJx( ji[0] ); |
357 |
dAtom->setJy( ji[1] ); |
358 |
dAtom->setJz( ji[2] ); |
359 |
} |
360 |
} |
361 |
|
362 |
if( entry_plug->setTemp ){ |
363 |
if( !(tl % vel_n) ) tStats->velocitize(); |
364 |
} |
365 |
if( !(tl % sample_n) ) dump_out->writeDump( tl * dt ); |
366 |
if( !(tl % status_n) ) e_out->writeStat( tl * dt ); |
367 |
} |
368 |
} |
369 |
else{ |
370 |
|
371 |
for( tl=0; tl<n_loops; tl++ ){ |
372 |
|
373 |
kE = 0.0; |
374 |
rot_kE= 0.0; |
375 |
trans_kE = 0.0; |
376 |
|
377 |
for( i=0; i<nAtoms; i++ ){ |
378 |
|
379 |
// velocity half step |
380 |
|
381 |
vx = atoms[i]->get_vx() + |
382 |
( dt2 * atoms[i]->getFx() / atoms[i]->getMass() ) * e_convert; |
383 |
vy = atoms[i]->get_vy() + |
384 |
( dt2 * atoms[i]->getFy() / atoms[i]->getMass() ) * e_convert; |
385 |
vz = atoms[i]->get_vz() + |
386 |
( dt2 * atoms[i]->getFz() / atoms[i]->getMass() ) * e_convert; |
387 |
|
388 |
// position whole step |
389 |
|
390 |
rx = atoms[i]->getX() + dt * vx; |
391 |
ry = atoms[i]->getY() + dt * vy; |
392 |
rz = atoms[i]->getZ() + dt * vz; |
393 |
|
394 |
atoms[i]->setX( rx ); |
395 |
atoms[i]->setY( ry ); |
396 |
atoms[i]->setZ( rz ); |
397 |
|
398 |
atoms[i]->set_vx( vx ); |
399 |
atoms[i]->set_vy( vy ); |
400 |
atoms[i]->set_vz( vz ); |
401 |
|
402 |
if( atoms[i]->isDirectional() ){ |
403 |
|
404 |
dAtom = (DirectionalAtom *)atoms[i]; |
405 |
|
406 |
// get and convert the torque to body frame |
407 |
|
408 |
Tb[0] = dAtom->getTx(); |
409 |
Tb[1] = dAtom->getTy(); |
410 |
Tb[2] = dAtom->getTz(); |
411 |
|
412 |
dAtom->lab2Body( Tb ); |
413 |
|
414 |
// get the angular momentum, and propagate a half step |
415 |
|
416 |
ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * e_convert; |
417 |
ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * e_convert; |
418 |
ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * e_convert; |
419 |
|
420 |
// get the atom's rotation matrix |
421 |
|
422 |
A[0][0] = dAtom->getAxx(); |
423 |
A[0][1] = dAtom->getAxy(); |
424 |
A[0][2] = dAtom->getAxz(); |
425 |
|
426 |
A[1][0] = dAtom->getAyx(); |
427 |
A[1][1] = dAtom->getAyy(); |
428 |
A[1][2] = dAtom->getAyz(); |
429 |
|
430 |
A[2][0] = dAtom->getAzx(); |
431 |
A[2][1] = dAtom->getAzy(); |
432 |
A[2][2] = dAtom->getAzz(); |
433 |
|
434 |
|
435 |
// use the angular velocities to propagate the rotation matrix a |
436 |
// full time step |
437 |
|
438 |
|
439 |
angle = dt2 * ji[0] / dAtom->getIxx(); |
440 |
this->rotate( 1, 2, angle, ji, A ); // rotate about the x-axis |
441 |
|
442 |
angle = dt2 * ji[1] / dAtom->getIyy(); |
443 |
this->rotate( 2, 0, angle, ji, A ); // rotate about the y-axis |
444 |
|
445 |
angle = dt * ji[2] / dAtom->getIzz(); |
446 |
this->rotate( 0, 1, angle, ji, A ); // rotate about the z-axis |
447 |
|
448 |
angle = dt2 * ji[1] / dAtom->getIyy(); |
449 |
this->rotate( 2, 0, angle, ji, A ); // rotate about the y-axis |
450 |
|
451 |
angle = dt2 * ji[0] / dAtom->getIxx(); |
452 |
this->rotate( 1, 2, angle, ji, A ); // rotate about the x-axis |
453 |
|
454 |
|
455 |
dAtom->setA( A ); |
456 |
dAtom->setJx( ji[0] ); |
457 |
dAtom->setJy( ji[1] ); |
458 |
dAtom->setJz( ji[2] ); |
459 |
} |
460 |
} |
461 |
|
462 |
// calculate the forces |
463 |
|
464 |
for(j = 0; j < nAtoms; j++){ |
465 |
atoms[j]->zeroForces(); |
466 |
} |
467 |
|
468 |
for(j = 0; j < nSRI; j++){ |
469 |
srInteractions[j]->calc_forces(); |
470 |
} |
471 |
|
472 |
longRange->calc_forces(); |
473 |
|
474 |
for( i=0; i< nAtoms; i++ ){ |
475 |
|
476 |
// complete the velocity half step |
477 |
|
478 |
vx = atoms[i]->get_vx() + |
479 |
( dt2 * atoms[i]->getFx() / atoms[i]->getMass() ) * e_convert; |
480 |
vy = atoms[i]->get_vy() + |
481 |
( dt2 * atoms[i]->getFy() / atoms[i]->getMass() ) * e_convert; |
482 |
vz = atoms[i]->get_vz() + |
483 |
( dt2 * atoms[i]->getFz() / atoms[i]->getMass() ) * e_convert; |
484 |
|
485 |
atoms[i]->set_vx( vx ); |
486 |
atoms[i]->set_vy( vy ); |
487 |
atoms[i]->set_vz( vz ); |
488 |
|
489 |
vx2 = vx * vx; |
490 |
vy2 = vy * vy; |
491 |
vz2 = vz * vz; |
492 |
|
493 |
if( atoms[i]->isDirectional() ){ |
494 |
|
495 |
dAtom = (DirectionalAtom *)atoms[i]; |
496 |
|
497 |
// get and convert the torque to body frame |
498 |
|
499 |
Tb[0] = dAtom->getTx(); |
500 |
Tb[1] = dAtom->getTy(); |
501 |
Tb[2] = dAtom->getTz(); |
502 |
|
503 |
dAtom->lab2Body( Tb ); |
504 |
|
505 |
// get the angular momentum, and complete the angular momentum |
506 |
// half step |
507 |
|
508 |
ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * e_convert; |
509 |
ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * e_convert; |
510 |
ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * e_convert; |
511 |
|
512 |
jx2 = ji[0] * ji[0]; |
513 |
jy2 = ji[1] * ji[1]; |
514 |
jz2 = ji[2] * ji[2]; |
515 |
|
516 |
rot_kE += (jx2 / dAtom->getIxx()) + (jy2 / dAtom->getIyy()) |
517 |
+ (jz2 / dAtom->getIzz()); |
518 |
|
519 |
dAtom->setJx( ji[0] ); |
520 |
dAtom->setJy( ji[1] ); |
521 |
dAtom->setJz( ji[2] ); |
522 |
} |
523 |
} |
524 |
|
525 |
if( entry_plug->setTemp ){ |
526 |
if( !(tl % vel_n) ) tStats->velocitize(); |
527 |
} |
528 |
if( !(tl % sample_n) ) dump_out->writeDump( tl * dt ); |
529 |
if( !(tl % status_n) ) e_out->writeStat( tl * dt ); |
530 |
} |
531 |
} |
532 |
|
533 |
dump_out->writeFinal(); |
534 |
|
535 |
delete dump_out; |
536 |
delete e_out; |
537 |
} |
538 |
|
539 |
void Symplectic::rotate( int axes1, int axes2, double angle, double ji[3], |
540 |
double A[3][3] ){ |
541 |
|
542 |
int i,j,k; |
543 |
double sinAngle; |
544 |
double cosAngle; |
545 |
double angleSqr; |
546 |
double angleSqrOver4; |
547 |
double top, bottom; |
548 |
double rot[3][3]; |
549 |
double tempA[3][3]; |
550 |
double tempJ[3]; |
551 |
|
552 |
// initialize the tempA |
553 |
|
554 |
for(i=0; i<3; i++){ |
555 |
for(j=0; j<3; j++){ |
556 |
tempA[i][j] = A[i][j]; |
557 |
} |
558 |
} |
559 |
|
560 |
// initialize the tempJ |
561 |
|
562 |
for( i=0; i<3; i++) tempJ[i] = ji[i]; |
563 |
|
564 |
// initalize rot as a unit matrix |
565 |
|
566 |
rot[0][0] = 1.0; |
567 |
rot[0][1] = 0.0; |
568 |
rot[0][2] = 0.0; |
569 |
|
570 |
rot[1][0] = 0.0; |
571 |
rot[1][1] = 1.0; |
572 |
rot[1][2] = 0.0; |
573 |
|
574 |
rot[2][0] = 0.0; |
575 |
rot[2][1] = 0.0; |
576 |
rot[2][2] = 1.0; |
577 |
|
578 |
// use a small angle aproximation for sin and cosine |
579 |
|
580 |
angleSqr = angle * angle; |
581 |
angleSqrOver4 = angleSqr / 4.0; |
582 |
top = 1.0 - angleSqrOver4; |
583 |
bottom = 1.0 + angleSqrOver4; |
584 |
|
585 |
cosAngle = top / bottom; |
586 |
sinAngle = angle / bottom; |
587 |
|
588 |
rot[axes1][axes1] = cosAngle; |
589 |
rot[axes2][axes2] = cosAngle; |
590 |
|
591 |
rot[axes1][axes2] = sinAngle; |
592 |
rot[axes2][axes1] = -sinAngle; |
593 |
|
594 |
// rotate the momentum acoording to: ji[] = rot[][] * ji[] |
595 |
|
596 |
for(i=0; i<3; i++){ |
597 |
ji[i] = 0.0; |
598 |
for(k=0; k<3; k++){ |
599 |
ji[i] += rot[i][k] * tempJ[k]; |
600 |
} |
601 |
} |
602 |
|
603 |
// rotate the Rotation matrix acording to: |
604 |
// A[][] = A[][] * transpose(rot[][]) |
605 |
|
606 |
|
607 |
// NOte for as yet unknown reason, we are setting the performing the |
608 |
// calculation as: |
609 |
// transpose(A[][]) = transpose(A[][]) * transpose(rot[][]) |
610 |
|
611 |
for(i=0; i<3; i++){ |
612 |
for(j=0; j<3; j++){ |
613 |
A[j][i] = 0.0; |
614 |
for(k=0; k<3; k++){ |
615 |
A[j][i] += tempA[k][i] * rot[j][k]; |
616 |
} |
617 |
} |
618 |
} |
619 |
} |