| 33 |
|
|
| 34 |
|
void NPTi::moveA() { |
| 35 |
|
|
| 36 |
< |
int i,j,k; |
| 37 |
< |
int atomIndex, aMatIndex; |
| 36 |
> |
int i, j; |
| 37 |
|
DirectionalAtom* dAtom; |
| 38 |
< |
double Tb[3]; |
| 39 |
< |
double ji[3]; |
| 38 |
> |
double Tb[3], ji[3]; |
| 39 |
> |
double A[3][3], I[3][3]; |
| 40 |
> |
double angle, mass; |
| 41 |
> |
double vel[3], pos[3], frc[3]; |
| 42 |
> |
|
| 43 |
|
double rj[3]; |
| 44 |
|
double instaTemp, instaPress, instaVol; |
| 45 |
|
double tt2, tb2; |
| 44 |
– |
double angle; |
| 46 |
|
|
| 46 |
– |
|
| 47 |
|
tt2 = tauThermostat * tauThermostat; |
| 48 |
|
tb2 = tauBarostat * tauBarostat; |
| 49 |
|
|
| 58 |
|
(p_convert*NkBT*tb2)); |
| 59 |
|
|
| 60 |
|
for( i=0; i<nAtoms; i++ ){ |
| 61 |
< |
atomIndex = i * 3; |
| 62 |
< |
aMatIndex = i * 9; |
| 63 |
< |
|
| 64 |
< |
// velocity half step |
| 65 |
< |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
| 66 |
< |
vel[j] += dt2 * ((frc[j]/atoms[i]->getMass())*eConvert |
| 67 |
< |
- vel[j]*(chi+eta)); |
| 61 |
> |
atoms[i]->getVel( vel ); |
| 62 |
> |
atoms[i]->getPos( pos ); |
| 63 |
> |
atoms[i]->getFrc( frc ); |
| 64 |
|
|
| 65 |
< |
// position whole step |
| 65 |
> |
mass = atoms[i]->getMass(); |
| 66 |
|
|
| 67 |
< |
rj[0] = pos[atomIndex]; |
| 68 |
< |
rj[1] = pos[atomIndex+1]; |
| 69 |
< |
rj[2] = pos[atomIndex+2]; |
| 70 |
< |
|
| 67 |
> |
for (j=0; j < 3; j++) { |
| 68 |
> |
vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*(chi+eta)); |
| 69 |
> |
rj[j] = pos[j]; |
| 70 |
> |
} |
| 71 |
> |
|
| 72 |
> |
atoms[i]->setVel( vel ); |
| 73 |
> |
|
| 74 |
|
info->wrapVector(rj); |
| 75 |
|
|
| 76 |
< |
pos[atomIndex] += dt * (vel[atomIndex] + eta*rj[0]); |
| 77 |
< |
pos[atomIndex+1] += dt * (vel[atomIndex+1] + eta*rj[1]); |
| 78 |
< |
pos[atomIndex+2] += dt * (vel[atomIndex+2] + eta*rj[2]); |
| 79 |
< |
|
| 76 |
> |
for (j = 0; j < 3; j++) |
| 77 |
> |
pos[j] += dt * (vel[j] + eta*rj[j]); |
| 78 |
> |
|
| 79 |
> |
|
| 80 |
> |
atoms[i]->setPos( pos ); |
| 81 |
> |
|
| 82 |
> |
|
| 83 |
|
if( atoms[i]->isDirectional() ){ |
| 84 |
|
|
| 85 |
|
dAtom = (DirectionalAtom *)atoms[i]; |
| 86 |
|
|
| 87 |
|
// get and convert the torque to body frame |
| 88 |
|
|
| 89 |
< |
Tb[0] = dAtom->getTx(); |
| 88 |
< |
Tb[1] = dAtom->getTy(); |
| 89 |
< |
Tb[2] = dAtom->getTz(); |
| 90 |
< |
|
| 89 |
> |
dAtom->getTrq( Tb ); |
| 90 |
|
dAtom->lab2Body( Tb ); |
| 91 |
|
|
| 92 |
|
// get the angular momentum, and propagate a half step |
| 93 |
|
|
| 94 |
< |
ji[0] = dAtom->getJx(); |
| 95 |
< |
ji[1] = dAtom->getJy(); |
| 96 |
< |
ji[2] = dAtom->getJz(); |
| 94 |
> |
dAtom->getJ( ji ); |
| 95 |
> |
|
| 96 |
> |
for (j=0; j < 3; j++) |
| 97 |
> |
ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi); |
| 98 |
|
|
| 99 |
– |
ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*chi); |
| 100 |
– |
ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*chi); |
| 101 |
– |
ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*chi); |
| 102 |
– |
|
| 99 |
|
// use the angular velocities to propagate the rotation matrix a |
| 100 |
|
// full time step |
| 101 |
< |
|
| 101 |
> |
|
| 102 |
> |
dAtom->getA(A); |
| 103 |
> |
dAtom->getI(I); |
| 104 |
> |
|
| 105 |
|
// rotate about the x-axis |
| 106 |
< |
angle = dt2 * ji[0] / dAtom->getIxx(); |
| 107 |
< |
this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] ); |
| 108 |
< |
|
| 106 |
> |
angle = dt2 * ji[0] / I[0][0]; |
| 107 |
> |
this->rotate( 1, 2, angle, ji, A ); |
| 108 |
> |
|
| 109 |
|
// rotate about the y-axis |
| 110 |
< |
angle = dt2 * ji[1] / dAtom->getIyy(); |
| 111 |
< |
this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] ); |
| 110 |
> |
angle = dt2 * ji[1] / I[1][1]; |
| 111 |
> |
this->rotate( 2, 0, angle, ji, A ); |
| 112 |
|
|
| 113 |
|
// rotate about the z-axis |
| 114 |
< |
angle = dt * ji[2] / dAtom->getIzz(); |
| 115 |
< |
this->rotate( 0, 1, angle, ji, &Amat[aMatIndex] ); |
| 114 |
> |
angle = dt * ji[2] / I[2][2]; |
| 115 |
> |
this->rotate( 0, 1, angle, ji, A); |
| 116 |
|
|
| 117 |
|
// rotate about the y-axis |
| 118 |
< |
angle = dt2 * ji[1] / dAtom->getIyy(); |
| 119 |
< |
this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] ); |
| 118 |
> |
angle = dt2 * ji[1] / I[1][1]; |
| 119 |
> |
this->rotate( 2, 0, angle, ji, A ); |
| 120 |
|
|
| 121 |
|
// rotate about the x-axis |
| 122 |
< |
angle = dt2 * ji[0] / dAtom->getIxx(); |
| 123 |
< |
this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] ); |
| 122 |
> |
angle = dt2 * ji[0] / I[0][0]; |
| 123 |
> |
this->rotate( 1, 2, angle, ji, A ); |
| 124 |
|
|
| 125 |
< |
dAtom->setJx( ji[0] ); |
| 126 |
< |
dAtom->setJy( ji[1] ); |
| 127 |
< |
dAtom->setJz( ji[2] ); |
| 128 |
< |
} |
| 130 |
< |
|
| 125 |
> |
dAtom->setJ( ji ); |
| 126 |
> |
dAtom->setA( A ); |
| 127 |
> |
} |
| 128 |
> |
|
| 129 |
|
} |
| 130 |
|
// Scale the box after all the positions have been moved: |
| 131 |
< |
|
| 131 |
> |
|
| 132 |
|
cerr << "eta = " << eta |
| 133 |
|
<< "; exp(dt*eta) = " << exp(eta*dt) << "\n"; |
| 134 |
< |
|
| 135 |
< |
info->scaleBox(exp(dt*eta)); |
| 138 |
< |
|
| 134 |
> |
|
| 135 |
> |
info->scaleBox(exp(dt*eta)); |
| 136 |
|
} |
| 137 |
|
|
| 138 |
|
void NPTi::moveB( void ){ |
| 139 |
< |
int i,j,k; |
| 140 |
< |
int atomIndex; |
| 139 |
> |
|
| 140 |
> |
int i, j; |
| 141 |
|
DirectionalAtom* dAtom; |
| 142 |
< |
double Tb[3]; |
| 143 |
< |
double ji[3]; |
| 142 |
> |
double Tb[3], ji[3]; |
| 143 |
> |
double vel[3], frc[3]; |
| 144 |
> |
double mass; |
| 145 |
> |
|
| 146 |
|
double instaTemp, instaPress, instaVol; |
| 147 |
|
double tt2, tb2; |
| 148 |
|
|
| 158 |
|
(p_convert*NkBT*tb2)); |
| 159 |
|
|
| 160 |
|
for( i=0; i<nAtoms; i++ ){ |
| 161 |
< |
atomIndex = i * 3; |
| 162 |
< |
|
| 161 |
> |
|
| 162 |
> |
atoms[i]->getVel( vel ); |
| 163 |
> |
atoms[i]->getFrc( frc ); |
| 164 |
> |
|
| 165 |
> |
mass = atoms[i]->getMass(); |
| 166 |
> |
|
| 167 |
|
// velocity half step |
| 168 |
< |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
| 169 |
< |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
| 167 |
< |
vel[j] += dt2 * ((frc[j]/atoms[i]->getMass())*eConvert |
| 168 |
< |
- vel[j]*(chi+eta)); |
| 168 |
> |
for (j=0; j < 3; j++) |
| 169 |
> |
vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*(chi+eta)); |
| 170 |
|
|
| 171 |
+ |
atoms[i]->setVel( vel ); |
| 172 |
+ |
|
| 173 |
|
if( atoms[i]->isDirectional() ){ |
| 174 |
< |
|
| 174 |
> |
|
| 175 |
|
dAtom = (DirectionalAtom *)atoms[i]; |
| 176 |
< |
|
| 177 |
< |
// get and convert the torque to body frame |
| 178 |
< |
|
| 179 |
< |
Tb[0] = dAtom->getTx(); |
| 177 |
< |
Tb[1] = dAtom->getTy(); |
| 178 |
< |
Tb[2] = dAtom->getTz(); |
| 179 |
< |
|
| 176 |
> |
|
| 177 |
> |
// get and convert the torque to body frame |
| 178 |
> |
|
| 179 |
> |
dAtom->getTrq( Tb ); |
| 180 |
|
dAtom->lab2Body( Tb ); |
| 181 |
< |
|
| 182 |
< |
// get the angular momentum, and complete the angular momentum |
| 183 |
< |
// half step |
| 184 |
< |
|
| 185 |
< |
ji[0] = dAtom->getJx(); |
| 186 |
< |
ji[1] = dAtom->getJy(); |
| 187 |
< |
ji[2] = dAtom->getJz(); |
| 188 |
< |
|
| 189 |
< |
ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*chi); |
| 190 |
< |
ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*chi); |
| 191 |
< |
ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*chi); |
| 192 |
< |
|
| 193 |
< |
dAtom->setJx( ji[0] ); |
| 194 |
< |
dAtom->setJy( ji[1] ); |
| 195 |
< |
dAtom->setJz( ji[2] ); |
| 181 |
> |
|
| 182 |
> |
// get the angular momentum, and propagate a half step |
| 183 |
> |
|
| 184 |
> |
dAtom->getJ( ji ); |
| 185 |
> |
|
| 186 |
> |
for (j=0; j < 3; j++) |
| 187 |
> |
ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi); |
| 188 |
> |
|
| 189 |
> |
dAtom->setJ( ji ); |
| 190 |
|
} |
| 191 |
|
} |
| 192 |
|
} |
