| 1 |
gezelter |
578 |
#include <cmath> |
| 2 |
gezelter |
574 |
#include "Atom.hpp" |
| 3 |
|
|
#include "SRI.hpp" |
| 4 |
|
|
#include "AbstractClasses.hpp" |
| 5 |
|
|
#include "SimInfo.hpp" |
| 6 |
|
|
#include "ForceFields.hpp" |
| 7 |
|
|
#include "Thermo.hpp" |
| 8 |
|
|
#include "ReadWrite.hpp" |
| 9 |
|
|
#include "Integrator.hpp" |
| 10 |
|
|
#include "simError.h" |
| 11 |
|
|
|
| 12 |
|
|
|
| 13 |
|
|
// Basic isotropic thermostating and barostating via the Melchionna |
| 14 |
|
|
// modification of the Hoover algorithm: |
| 15 |
|
|
// |
| 16 |
|
|
// Melchionna, S., Ciccotti, G., and Holian, B. L., 1993, |
| 17 |
|
|
// Molec. Phys., 78, 533. |
| 18 |
|
|
// |
| 19 |
|
|
// and |
| 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 ) |
| 25 |
|
|
{ |
| 26 |
|
|
chi = 0.0; |
| 27 |
|
|
eta = 0.0; |
| 28 |
|
|
have_tau_thermostat = 0; |
| 29 |
|
|
have_tau_barostat = 0; |
| 30 |
|
|
have_target_temp = 0; |
| 31 |
|
|
have_target_pressure = 0; |
| 32 |
|
|
} |
| 33 |
|
|
|
| 34 |
|
|
void NPTi::moveA() { |
| 35 |
|
|
|
| 36 |
|
|
int i,j,k; |
| 37 |
|
|
int atomIndex, aMatIndex; |
| 38 |
|
|
DirectionalAtom* dAtom; |
| 39 |
|
|
double Tb[3]; |
| 40 |
|
|
double ji[3]; |
| 41 |
|
|
double rj[3]; |
| 42 |
|
|
double instaTemp, instaPress, instaVol; |
| 43 |
|
|
double tt2, tb2; |
| 44 |
|
|
double angle; |
| 45 |
|
|
|
| 46 |
|
|
tt2 = tauThermostat * tauThermostat; |
| 47 |
|
|
tb2 = tauBarostat * tauBarostat; |
| 48 |
|
|
|
| 49 |
|
|
instaTemp = tStats->getTemperature(); |
| 50 |
|
|
instaPress = tStats->getPressure(); |
| 51 |
|
|
instaVol = tStats->getVolume(); |
| 52 |
|
|
|
| 53 |
|
|
// first evolve chi a half step |
| 54 |
|
|
|
| 55 |
|
|
chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
| 56 |
|
|
eta += dt2 * ( instaVol * (instaPress - targetPressure) / (NkBT*tb2)); |
| 57 |
|
|
|
| 58 |
|
|
for( i=0; i<nAtoms; i++ ){ |
| 59 |
|
|
atomIndex = i * 3; |
| 60 |
|
|
aMatIndex = i * 9; |
| 61 |
|
|
|
| 62 |
|
|
// velocity half step |
| 63 |
|
|
for( j=atomIndex; j<(atomIndex+3); j++ ) |
| 64 |
|
|
vel[j] += dt2 * ((frc[j]/atoms[i]->getMass())*eConvert |
| 65 |
|
|
- vel[j]*(chi+eta)); |
| 66 |
|
|
|
| 67 |
|
|
// position whole step |
| 68 |
|
|
|
| 69 |
gezelter |
577 |
rj[0] = pos[atomIndex]; |
| 70 |
|
|
rj[1] = pos[atomIndex+1]; |
| 71 |
|
|
rj[2] = pos[atomIndex+2]; |
| 72 |
|
|
|
| 73 |
|
|
info->wrapVector(rj); |
| 74 |
gezelter |
574 |
|
| 75 |
gezelter |
577 |
pos[atomIndex] += dt * (vel[atomIndex] + eta*rj[0]); |
| 76 |
|
|
pos[atomIndex+1] += dt * (vel[atomIndex+1] + eta*rj[1]); |
| 77 |
|
|
pos[atomIndex+2] += dt * (vel[atomIndex+2] + eta*rj[2]); |
| 78 |
gezelter |
574 |
|
| 79 |
|
|
if( atoms[i]->isDirectional() ){ |
| 80 |
|
|
|
| 81 |
|
|
dAtom = (DirectionalAtom *)atoms[i]; |
| 82 |
|
|
|
| 83 |
|
|
// get and convert the torque to body frame |
| 84 |
|
|
|
| 85 |
|
|
Tb[0] = dAtom->getTx(); |
| 86 |
|
|
Tb[1] = dAtom->getTy(); |
| 87 |
|
|
Tb[2] = dAtom->getTz(); |
| 88 |
|
|
|
| 89 |
|
|
dAtom->lab2Body( Tb ); |
| 90 |
|
|
|
| 91 |
|
|
// get the angular momentum, and propagate a half step |
| 92 |
|
|
|
| 93 |
|
|
ji[0] = dAtom->getJx(); |
| 94 |
|
|
ji[1] = dAtom->getJy(); |
| 95 |
|
|
ji[2] = dAtom->getJz(); |
| 96 |
|
|
|
| 97 |
|
|
ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*chi); |
| 98 |
|
|
ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*chi); |
| 99 |
|
|
ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*chi); |
| 100 |
|
|
|
| 101 |
|
|
// use the angular velocities to propagate the rotation matrix a |
| 102 |
|
|
// full time step |
| 103 |
|
|
|
| 104 |
|
|
// rotate about the x-axis |
| 105 |
|
|
angle = dt2 * ji[0] / dAtom->getIxx(); |
| 106 |
|
|
this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] ); |
| 107 |
|
|
|
| 108 |
|
|
// rotate about the y-axis |
| 109 |
|
|
angle = dt2 * ji[1] / dAtom->getIyy(); |
| 110 |
|
|
this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] ); |
| 111 |
|
|
|
| 112 |
|
|
// rotate about the z-axis |
| 113 |
|
|
angle = dt * ji[2] / dAtom->getIzz(); |
| 114 |
|
|
this->rotate( 0, 1, angle, ji, &Amat[aMatIndex] ); |
| 115 |
|
|
|
| 116 |
|
|
// rotate about the y-axis |
| 117 |
|
|
angle = dt2 * ji[1] / dAtom->getIyy(); |
| 118 |
|
|
this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] ); |
| 119 |
|
|
|
| 120 |
|
|
// rotate about the x-axis |
| 121 |
|
|
angle = dt2 * ji[0] / dAtom->getIxx(); |
| 122 |
|
|
this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] ); |
| 123 |
|
|
|
| 124 |
|
|
dAtom->setJx( ji[0] ); |
| 125 |
|
|
dAtom->setJy( ji[1] ); |
| 126 |
|
|
dAtom->setJz( ji[2] ); |
| 127 |
|
|
} |
| 128 |
|
|
|
| 129 |
|
|
} |
| 130 |
gezelter |
577 |
// Scale the box after all the positions have been moved: |
| 131 |
|
|
|
| 132 |
|
|
info->scaleBox(exp(dt*eta)); |
| 133 |
|
|
|
| 134 |
gezelter |
574 |
} |
| 135 |
|
|
|
| 136 |
|
|
void NPTi::moveB( void ){ |
| 137 |
|
|
int i,j,k; |
| 138 |
|
|
int atomIndex; |
| 139 |
|
|
DirectionalAtom* dAtom; |
| 140 |
|
|
double Tb[3]; |
| 141 |
|
|
double ji[3]; |
| 142 |
|
|
double instaTemp, instaPress, instaVol; |
| 143 |
|
|
double tt2, tb2; |
| 144 |
|
|
|
| 145 |
|
|
tt2 = tauThermostat * tauThermostat; |
| 146 |
|
|
tb2 = tauBarostat * tauBarostat; |
| 147 |
|
|
|
| 148 |
|
|
instaTemp = tStats->getTemperature(); |
| 149 |
|
|
instaPress = tStats->getPressure(); |
| 150 |
|
|
instaVol = tStats->getVolume(); |
| 151 |
|
|
|
| 152 |
|
|
chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
| 153 |
|
|
eta += dt2 * ( instaVol * (instaPress - targetPressure) / (NkBT*tb2)); |
| 154 |
|
|
|
| 155 |
|
|
for( i=0; i<nAtoms; i++ ){ |
| 156 |
|
|
atomIndex = i * 3; |
| 157 |
|
|
|
| 158 |
|
|
// velocity half step |
| 159 |
|
|
for( j=atomIndex; j<(atomIndex+3); j++ ) |
| 160 |
|
|
for( j=atomIndex; j<(atomIndex+3); j++ ) |
| 161 |
|
|
vel[j] += dt2 * ((frc[j]/atoms[i]->getMass())*eConvert |
| 162 |
|
|
- vel[j]*(chi+eta)); |
| 163 |
|
|
|
| 164 |
|
|
if( atoms[i]->isDirectional() ){ |
| 165 |
|
|
|
| 166 |
|
|
dAtom = (DirectionalAtom *)atoms[i]; |
| 167 |
|
|
|
| 168 |
|
|
// get and convert the torque to body frame |
| 169 |
|
|
|
| 170 |
|
|
Tb[0] = dAtom->getTx(); |
| 171 |
|
|
Tb[1] = dAtom->getTy(); |
| 172 |
|
|
Tb[2] = dAtom->getTz(); |
| 173 |
|
|
|
| 174 |
|
|
dAtom->lab2Body( Tb ); |
| 175 |
|
|
|
| 176 |
|
|
// get the angular momentum, and complete the angular momentum |
| 177 |
|
|
// half step |
| 178 |
|
|
|
| 179 |
|
|
ji[0] = dAtom->getJx(); |
| 180 |
|
|
ji[1] = dAtom->getJy(); |
| 181 |
|
|
ji[2] = dAtom->getJz(); |
| 182 |
|
|
|
| 183 |
|
|
ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*chi); |
| 184 |
|
|
ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*chi); |
| 185 |
|
|
ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*chi); |
| 186 |
|
|
|
| 187 |
|
|
dAtom->setJx( ji[0] ); |
| 188 |
|
|
dAtom->setJy( ji[1] ); |
| 189 |
|
|
dAtom->setJz( ji[2] ); |
| 190 |
|
|
} |
| 191 |
|
|
} |
| 192 |
|
|
} |
| 193 |
|
|
|
| 194 |
|
|
int NPTi::readyCheck() { |
| 195 |
|
|
|
| 196 |
|
|
// First check to see if we have a target temperature. |
| 197 |
|
|
// Not having one is fatal. |
| 198 |
|
|
|
| 199 |
|
|
if (!have_target_temp) { |
| 200 |
|
|
sprintf( painCave.errMsg, |
| 201 |
|
|
"NPTi error: You can't use the NPTi integrator\n" |
| 202 |
|
|
" without a targetTemp!\n" |
| 203 |
|
|
); |
| 204 |
|
|
painCave.isFatal = 1; |
| 205 |
|
|
simError(); |
| 206 |
|
|
return -1; |
| 207 |
|
|
} |
| 208 |
|
|
|
| 209 |
|
|
if (!have_target_pressure) { |
| 210 |
|
|
sprintf( painCave.errMsg, |
| 211 |
|
|
"NPTi error: You can't use the NPTi integrator\n" |
| 212 |
|
|
" without a targetPressure!\n" |
| 213 |
|
|
); |
| 214 |
|
|
painCave.isFatal = 1; |
| 215 |
|
|
simError(); |
| 216 |
|
|
return -1; |
| 217 |
|
|
} |
| 218 |
|
|
|
| 219 |
|
|
// We must set tauThermostat. |
| 220 |
|
|
|
| 221 |
|
|
if (!have_tau_thermostat) { |
| 222 |
|
|
sprintf( painCave.errMsg, |
| 223 |
|
|
"NPTi error: If you use the NPTi\n" |
| 224 |
|
|
" integrator, you must set tauThermostat.\n"); |
| 225 |
|
|
painCave.isFatal = 1; |
| 226 |
|
|
simError(); |
| 227 |
|
|
return -1; |
| 228 |
|
|
} |
| 229 |
|
|
|
| 230 |
|
|
// We must set tauBarostat. |
| 231 |
|
|
|
| 232 |
|
|
if (!have_tau_barostat) { |
| 233 |
|
|
sprintf( painCave.errMsg, |
| 234 |
|
|
"NPTi error: If you use the NPTi\n" |
| 235 |
|
|
" integrator, you must set tauBarostat.\n"); |
| 236 |
|
|
painCave.isFatal = 1; |
| 237 |
|
|
simError(); |
| 238 |
|
|
return -1; |
| 239 |
|
|
} |
| 240 |
|
|
|
| 241 |
|
|
// We need NkBT a lot, so just set it here: |
| 242 |
|
|
|
| 243 |
|
|
NkBT = (double)info->ndf * kB * targetTemp; |
| 244 |
|
|
|
| 245 |
|
|
return 1; |
| 246 |
|
|
} |
