| 1 |
+ |
#include <cmath> |
| 2 |
|
#include "Atom.hpp" |
| 3 |
|
#include "SRI.hpp" |
| 4 |
|
#include "AbstractClasses.hpp" |
| 20 |
|
// |
| 21 |
|
// Hoover, W. G., 1986, Phys. Rev. A, 34, 2499. |
| 22 |
|
|
| 23 |
< |
NPTi::NPTi ( SimInfo *theInfo, ForceFields* the_ff): |
| 24 |
< |
Integrator( theInfo, the_ff ) |
| 23 |
> |
template<typename T> NPTi<T>::NPTi ( SimInfo *theInfo, ForceFields* the_ff): |
| 24 |
> |
T( theInfo, the_ff ) |
| 25 |
|
{ |
| 26 |
|
chi = 0.0; |
| 27 |
|
eta = 0.0; |
| 31 |
|
have_target_pressure = 0; |
| 32 |
|
} |
| 33 |
|
|
| 34 |
< |
void NPTi::moveA() { |
| 34 |
> |
template<typename T> void NPTi<T>::moveA() { |
| 35 |
|
|
| 36 |
< |
int i,j,k; |
| 36 |
< |
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; |
| 43 |
< |
double angle; |
| 45 |
> |
double tt2, tb2, scaleFactor; |
| 46 |
|
|
| 47 |
|
tt2 = tauThermostat * tauThermostat; |
| 48 |
|
tb2 = tauBarostat * tauBarostat; |
| 51 |
|
instaPress = tStats->getPressure(); |
| 52 |
|
instaVol = tStats->getVolume(); |
| 53 |
|
|
| 54 |
< |
// first evolve chi a half step |
| 54 |
> |
// first evolve chi a half step |
| 55 |
|
|
| 56 |
|
chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
| 57 |
< |
eta += dt2 * ( instaVol * (instaPress - targetPressure) / (NkBT*tb2)); |
| 57 |
> |
eta += dt2 * ( instaVol * (instaPress - targetPressure) / |
| 58 |
> |
(p_convert*NkBT*tb2)); |
| 59 |
|
|
| 60 |
|
for( i=0; i<nAtoms; i++ ){ |
| 61 |
< |
atomIndex = i * 3; |
| 62 |
< |
aMatIndex = i * 9; |
| 63 |
< |
|
| 61 |
< |
// velocity half step |
| 62 |
< |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
| 63 |
< |
vel[j] += dt2 * ((frc[j]/atoms[i]->getMass())*eConvert |
| 64 |
< |
- 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 |
> |
atoms[i]->setPos( pos ); |
| 80 |
> |
|
| 81 |
|
if( atoms[i]->isDirectional() ){ |
| 82 |
|
|
| 83 |
|
dAtom = (DirectionalAtom *)atoms[i]; |
| 84 |
|
|
| 85 |
|
// get and convert the torque to body frame |
| 86 |
|
|
| 87 |
< |
Tb[0] = dAtom->getTx(); |
| 85 |
< |
Tb[1] = dAtom->getTy(); |
| 86 |
< |
Tb[2] = dAtom->getTz(); |
| 87 |
< |
|
| 87 |
> |
dAtom->getTrq( Tb ); |
| 88 |
|
dAtom->lab2Body( Tb ); |
| 89 |
|
|
| 90 |
|
// get the angular momentum, and propagate a half step |
| 91 |
|
|
| 92 |
< |
ji[0] = dAtom->getJx(); |
| 93 |
< |
ji[1] = dAtom->getJy(); |
| 94 |
< |
ji[2] = dAtom->getJz(); |
| 92 |
> |
dAtom->getJ( ji ); |
| 93 |
> |
|
| 94 |
> |
for (j=0; j < 3; j++) |
| 95 |
> |
ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi); |
| 96 |
|
|
| 96 |
– |
ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*chi); |
| 97 |
– |
ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*chi); |
| 98 |
– |
ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*chi); |
| 99 |
– |
|
| 97 |
|
// use the angular velocities to propagate the rotation matrix a |
| 98 |
|
// full time step |
| 99 |
< |
|
| 99 |
> |
|
| 100 |
> |
dAtom->getA(A); |
| 101 |
> |
dAtom->getI(I); |
| 102 |
> |
|
| 103 |
|
// rotate about the x-axis |
| 104 |
< |
angle = dt2 * ji[0] / dAtom->getIxx(); |
| 105 |
< |
this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] ); |
| 106 |
< |
|
| 104 |
> |
angle = dt2 * ji[0] / I[0][0]; |
| 105 |
> |
this->rotate( 1, 2, angle, ji, A ); |
| 106 |
> |
|
| 107 |
|
// rotate about the y-axis |
| 108 |
< |
angle = dt2 * ji[1] / dAtom->getIyy(); |
| 109 |
< |
this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] ); |
| 108 |
> |
angle = dt2 * ji[1] / I[1][1]; |
| 109 |
> |
this->rotate( 2, 0, angle, ji, A ); |
| 110 |
|
|
| 111 |
|
// rotate about the z-axis |
| 112 |
< |
angle = dt * ji[2] / dAtom->getIzz(); |
| 113 |
< |
this->rotate( 0, 1, angle, ji, &Amat[aMatIndex] ); |
| 112 |
> |
angle = dt * ji[2] / I[2][2]; |
| 113 |
> |
this->rotate( 0, 1, angle, ji, A); |
| 114 |
|
|
| 115 |
|
// rotate about the y-axis |
| 116 |
< |
angle = dt2 * ji[1] / dAtom->getIyy(); |
| 117 |
< |
this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] ); |
| 116 |
> |
angle = dt2 * ji[1] / I[1][1]; |
| 117 |
> |
this->rotate( 2, 0, angle, ji, A ); |
| 118 |
|
|
| 119 |
|
// rotate about the x-axis |
| 120 |
< |
angle = dt2 * ji[0] / dAtom->getIxx(); |
| 121 |
< |
this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] ); |
| 120 |
> |
angle = dt2 * ji[0] / I[0][0]; |
| 121 |
> |
this->rotate( 1, 2, angle, ji, A ); |
| 122 |
|
|
| 123 |
< |
dAtom->setJx( ji[0] ); |
| 124 |
< |
dAtom->setJy( ji[1] ); |
| 125 |
< |
dAtom->setJz( ji[2] ); |
| 126 |
< |
} |
| 127 |
< |
|
| 123 |
> |
dAtom->setJ( ji ); |
| 124 |
> |
dAtom->setA( A ); |
| 125 |
> |
} |
| 126 |
> |
|
| 127 |
|
} |
| 128 |
+ |
|
| 129 |
|
// Scale the box after all the positions have been moved: |
| 130 |
+ |
|
| 131 |
+ |
scaleFactor = exp(dt*eta); |
| 132 |
|
|
| 133 |
< |
info->scaleBox(exp(dt*eta)); |
| 133 |
> |
if ((scaleFactor > 1.1) || (scaleFactor < 0.9)) { |
| 134 |
> |
sprintf( painCave.errMsg, |
| 135 |
> |
"NPTi error: Attempting a Box scaling of more than 10 percent" |
| 136 |
> |
" check your tauBarostat, as it is probably too small!\n" |
| 137 |
> |
" eta = %lf, scaleFactor = %lf\n", eta, scaleFactor |
| 138 |
> |
); |
| 139 |
> |
painCave.isFatal = 1; |
| 140 |
> |
simError(); |
| 141 |
> |
} else { |
| 142 |
> |
info->scaleBox(exp(dt*eta)); |
| 143 |
> |
} |
| 144 |
|
|
| 145 |
|
} |
| 146 |
|
|
| 147 |
< |
void NPTi::moveB( void ){ |
| 148 |
< |
int i,j,k; |
| 149 |
< |
int atomIndex; |
| 147 |
> |
template<typename T> void NPTi<T>::moveB( void ){ |
| 148 |
> |
|
| 149 |
> |
int i, j; |
| 150 |
|
DirectionalAtom* dAtom; |
| 151 |
< |
double Tb[3]; |
| 152 |
< |
double ji[3]; |
| 151 |
> |
double Tb[3], ji[3]; |
| 152 |
> |
double vel[3], frc[3]; |
| 153 |
> |
double mass; |
| 154 |
> |
|
| 155 |
|
double instaTemp, instaPress, instaVol; |
| 156 |
|
double tt2, tb2; |
| 157 |
|
|
| 163 |
|
instaVol = tStats->getVolume(); |
| 164 |
|
|
| 165 |
|
chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
| 166 |
< |
eta += dt2 * ( instaVol * (instaPress - targetPressure) / (NkBT*tb2)); |
| 166 |
> |
eta += dt2 * ( instaVol * (instaPress - targetPressure) / |
| 167 |
> |
(p_convert*NkBT*tb2)); |
| 168 |
|
|
| 169 |
|
for( i=0; i<nAtoms; i++ ){ |
| 170 |
< |
atomIndex = i * 3; |
| 171 |
< |
|
| 170 |
> |
|
| 171 |
> |
atoms[i]->getVel( vel ); |
| 172 |
> |
atoms[i]->getFrc( frc ); |
| 173 |
> |
|
| 174 |
> |
mass = atoms[i]->getMass(); |
| 175 |
> |
|
| 176 |
|
// velocity half step |
| 177 |
< |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
| 178 |
< |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
| 160 |
< |
vel[j] += dt2 * ((frc[j]/atoms[i]->getMass())*eConvert |
| 161 |
< |
- vel[j]*(chi+eta)); |
| 177 |
> |
for (j=0; j < 3; j++) |
| 178 |
> |
vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*(chi+eta)); |
| 179 |
|
|
| 180 |
+ |
atoms[i]->setVel( vel ); |
| 181 |
+ |
|
| 182 |
|
if( atoms[i]->isDirectional() ){ |
| 183 |
< |
|
| 183 |
> |
|
| 184 |
|
dAtom = (DirectionalAtom *)atoms[i]; |
| 185 |
< |
|
| 186 |
< |
// get and convert the torque to body frame |
| 187 |
< |
|
| 188 |
< |
Tb[0] = dAtom->getTx(); |
| 170 |
< |
Tb[1] = dAtom->getTy(); |
| 171 |
< |
Tb[2] = dAtom->getTz(); |
| 172 |
< |
|
| 185 |
> |
|
| 186 |
> |
// get and convert the torque to body frame |
| 187 |
> |
|
| 188 |
> |
dAtom->getTrq( Tb ); |
| 189 |
|
dAtom->lab2Body( Tb ); |
| 190 |
< |
|
| 191 |
< |
// get the angular momentum, and complete the angular momentum |
| 192 |
< |
// half step |
| 193 |
< |
|
| 194 |
< |
ji[0] = dAtom->getJx(); |
| 195 |
< |
ji[1] = dAtom->getJy(); |
| 196 |
< |
ji[2] = dAtom->getJz(); |
| 197 |
< |
|
| 198 |
< |
ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*chi); |
| 183 |
< |
ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*chi); |
| 184 |
< |
ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*chi); |
| 185 |
< |
|
| 186 |
< |
dAtom->setJx( ji[0] ); |
| 187 |
< |
dAtom->setJy( ji[1] ); |
| 188 |
< |
dAtom->setJz( ji[2] ); |
| 190 |
> |
|
| 191 |
> |
// get the angular momentum, and propagate a half step |
| 192 |
> |
|
| 193 |
> |
dAtom->getJ( ji ); |
| 194 |
> |
|
| 195 |
> |
for (j=0; j < 3; j++) |
| 196 |
> |
ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi); |
| 197 |
> |
|
| 198 |
> |
dAtom->setJ( ji ); |
| 199 |
|
} |
| 200 |
|
} |
| 201 |
|
} |
| 202 |
|
|
| 203 |
< |
int NPTi::readyCheck() { |
| 203 |
> |
template<typename T> int NPTi<T>::readyCheck() { |
| 204 |
> |
|
| 205 |
> |
//check parent's readyCheck() first |
| 206 |
> |
if (T::readyCheck() == -1) |
| 207 |
> |
return -1; |
| 208 |
|
|
| 209 |
|
// First check to see if we have a target temperature. |
| 210 |
|
// Not having one is fatal. |
