| 1 |
+ |
#include <math.h> |
| 2 |
+ |
|
| 3 |
|
#include "Atom.hpp" |
| 4 |
|
#include "SRI.hpp" |
| 5 |
|
#include "AbstractClasses.hpp" |
| 8 |
|
#include "Thermo.hpp" |
| 9 |
|
#include "ReadWrite.hpp" |
| 10 |
|
#include "Integrator.hpp" |
| 11 |
< |
#include "simError.h" |
| 11 |
> |
#include "simError.h" |
| 12 |
|
|
| 13 |
|
|
| 14 |
|
// Basic thermostating via Hoover, Phys.Rev.A, 1985, Vol. 31 (5) 1695-1697 |
| 16 |
|
template<typename T> NVT<T>::NVT ( SimInfo *theInfo, ForceFields* the_ff): |
| 17 |
|
T( theInfo, the_ff ) |
| 18 |
|
{ |
| 19 |
+ |
GenericData* data; |
| 20 |
+ |
DoubleData * chiValue; |
| 21 |
+ |
DoubleData * integralOfChidtValue; |
| 22 |
+ |
|
| 23 |
+ |
chiValue = NULL; |
| 24 |
+ |
integralOfChidtValue = NULL; |
| 25 |
+ |
|
| 26 |
|
chi = 0.0; |
| 27 |
|
have_tau_thermostat = 0; |
| 28 |
|
have_target_temp = 0; |
| 29 |
|
have_chi_tolerance = 0; |
| 30 |
|
integralOfChidt = 0.0; |
| 31 |
|
|
| 32 |
+ |
// retrieve chi and integralOfChidt from simInfo |
| 33 |
+ |
data = info->getProperty(CHIVALUE_ID); |
| 34 |
+ |
if(data){ |
| 35 |
+ |
chiValue = dynamic_cast<DoubleData*>(data); |
| 36 |
+ |
} |
| 37 |
+ |
|
| 38 |
+ |
data = info->getProperty(INTEGRALOFCHIDT_ID); |
| 39 |
+ |
if(data){ |
| 40 |
+ |
integralOfChidtValue = dynamic_cast<DoubleData*>(data); |
| 41 |
+ |
} |
| 42 |
+ |
|
| 43 |
+ |
// chi and integralOfChidt should appear by pair |
| 44 |
+ |
if(chiValue && integralOfChidtValue){ |
| 45 |
+ |
chi = chiValue->getData(); |
| 46 |
+ |
integralOfChidt = integralOfChidtValue->getData(); |
| 47 |
+ |
} |
| 48 |
+ |
|
| 49 |
|
oldVel = new double[3*nAtoms]; |
| 50 |
|
oldJi = new double[3*nAtoms]; |
| 51 |
|
} |
| 56 |
|
} |
| 57 |
|
|
| 58 |
|
template<typename T> void NVT<T>::moveA() { |
| 59 |
< |
|
| 59 |
> |
|
| 60 |
|
int i, j; |
| 61 |
|
DirectionalAtom* dAtom; |
| 62 |
|
double Tb[3], ji[3]; |
| 63 |
< |
double A[3][3], I[3][3]; |
| 38 |
< |
double angle, mass; |
| 63 |
> |
double mass; |
| 64 |
|
double vel[3], pos[3], frc[3]; |
| 65 |
|
|
| 66 |
|
double instTemp; |
| 68 |
|
// We need the temperature at time = t for the chi update below: |
| 69 |
|
|
| 70 |
|
instTemp = tStats->getTemperature(); |
| 71 |
< |
|
| 71 |
> |
|
| 72 |
|
for( i=0; i<nAtoms; i++ ){ |
| 73 |
|
|
| 74 |
|
atoms[i]->getVel( vel ); |
| 86 |
|
|
| 87 |
|
atoms[i]->setVel( vel ); |
| 88 |
|
atoms[i]->setPos( pos ); |
| 89 |
< |
|
| 89 |
> |
|
| 90 |
|
if( atoms[i]->isDirectional() ){ |
| 91 |
|
|
| 92 |
|
dAtom = (DirectionalAtom *)atoms[i]; |
| 93 |
< |
|
| 93 |
> |
|
| 94 |
|
// get and convert the torque to body frame |
| 95 |
< |
|
| 95 |
> |
|
| 96 |
|
dAtom->getTrq( Tb ); |
| 97 |
|
dAtom->lab2Body( Tb ); |
| 98 |
< |
|
| 98 |
> |
|
| 99 |
|
// get the angular momentum, and propagate a half step |
| 100 |
|
|
| 101 |
|
dAtom->getJ( ji ); |
| 102 |
|
|
| 103 |
< |
for (j=0; j < 3; j++) |
| 103 |
> |
for (j=0; j < 3; j++) |
| 104 |
|
ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi); |
| 80 |
– |
|
| 81 |
– |
// use the angular velocities to propagate the rotation matrix a |
| 82 |
– |
// full time step |
| 105 |
|
|
| 106 |
< |
dAtom->getA(A); |
| 85 |
< |
dAtom->getI(I); |
| 86 |
< |
|
| 87 |
< |
// rotate about the x-axis |
| 88 |
< |
angle = dt2 * ji[0] / I[0][0]; |
| 89 |
< |
this->rotate( 1, 2, angle, ji, A ); |
| 106 |
> |
this->rotationPropagation( dAtom, ji ); |
| 107 |
|
|
| 91 |
– |
// rotate about the y-axis |
| 92 |
– |
angle = dt2 * ji[1] / I[1][1]; |
| 93 |
– |
this->rotate( 2, 0, angle, ji, A ); |
| 94 |
– |
|
| 95 |
– |
// rotate about the z-axis |
| 96 |
– |
angle = dt * ji[2] / I[2][2]; |
| 97 |
– |
this->rotate( 0, 1, angle, ji, A); |
| 98 |
– |
|
| 99 |
– |
// rotate about the y-axis |
| 100 |
– |
angle = dt2 * ji[1] / I[1][1]; |
| 101 |
– |
this->rotate( 2, 0, angle, ji, A ); |
| 102 |
– |
|
| 103 |
– |
// rotate about the x-axis |
| 104 |
– |
angle = dt2 * ji[0] / I[0][0]; |
| 105 |
– |
this->rotate( 1, 2, angle, ji, A ); |
| 106 |
– |
|
| 108 |
|
dAtom->setJ( ji ); |
| 109 |
< |
dAtom->setA( A ); |
| 109 |
< |
} |
| 109 |
> |
} |
| 110 |
|
} |
| 111 |
< |
|
| 111 |
> |
|
| 112 |
|
if (nConstrained){ |
| 113 |
|
constrainA(); |
| 114 |
|
} |
| 115 |
|
|
| 116 |
< |
// Finally, evolve chi a half step (just like a velocity) using |
| 116 |
> |
// Finally, evolve chi a half step (just like a velocity) using |
| 117 |
|
// temperature at time t, not time t+dt/2 |
| 118 |
|
|
| 119 |
|
chi += dt2 * ( instTemp / targetTemp - 1.0) / (tauThermostat*tauThermostat); |
| 156 |
|
// do the iteration: |
| 157 |
|
|
| 158 |
|
for (k=0; k < 4; k++) { |
| 159 |
< |
|
| 159 |
> |
|
| 160 |
|
instTemp = tStats->getTemperature(); |
| 161 |
|
|
| 162 |
|
// evolve chi another half step using the temperature at t + dt/2 |
| 163 |
|
|
| 164 |
|
prevChi = chi; |
| 165 |
< |
chi = oldChi + dt2 * ( instTemp / targetTemp - 1.0) / |
| 165 |
> |
chi = oldChi + dt2 * ( instTemp / targetTemp - 1.0) / |
| 166 |
|
(tauThermostat*tauThermostat); |
| 167 |
< |
|
| 167 |
> |
|
| 168 |
|
for( i=0; i<nAtoms; i++ ){ |
| 169 |
|
|
| 170 |
|
atoms[i]->getFrc( frc ); |
| 171 |
|
atoms[i]->getVel(vel); |
| 172 |
< |
|
| 172 |
> |
|
| 173 |
|
mass = atoms[i]->getMass(); |
| 174 |
< |
|
| 174 |
> |
|
| 175 |
|
// velocity half step |
| 176 |
< |
for (j=0; j < 3; j++) |
| 176 |
> |
for (j=0; j < 3; j++) |
| 177 |
|
vel[j] = oldVel[3*i+j] + dt2 * ((frc[j] / mass ) * eConvert - oldVel[3*i + j]*chi); |
| 178 |
< |
|
| 179 |
< |
atoms[i]->setVel( vel ); |
| 180 |
< |
|
| 178 |
> |
|
| 179 |
> |
atoms[i]->setVel( vel ); |
| 180 |
> |
|
| 181 |
|
if( atoms[i]->isDirectional() ){ |
| 182 |
< |
|
| 182 |
> |
|
| 183 |
|
dAtom = (DirectionalAtom *)atoms[i]; |
| 184 |
< |
|
| 185 |
< |
// get and convert the torque to body frame |
| 186 |
< |
|
| 184 |
> |
|
| 185 |
> |
// get and convert the torque to body frame |
| 186 |
> |
|
| 187 |
|
dAtom->getTrq( Tb ); |
| 188 |
< |
dAtom->lab2Body( Tb ); |
| 189 |
< |
|
| 190 |
< |
for (j=0; j < 3; j++) |
| 188 |
> |
dAtom->lab2Body( Tb ); |
| 189 |
> |
|
| 190 |
> |
for (j=0; j < 3; j++) |
| 191 |
|
ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * eConvert - oldJi[3*i+j]*chi); |
| 192 |
< |
|
| 192 |
> |
|
| 193 |
|
dAtom->setJ( ji ); |
| 194 |
|
} |
| 195 |
|
} |
| 200 |
|
|
| 201 |
|
if (fabs(prevChi - chi) <= chiTolerance) break; |
| 202 |
|
} |
| 203 |
< |
|
| 203 |
> |
|
| 204 |
|
integralOfChidt += dt2*chi; |
| 205 |
|
} |
| 206 |
|
|
| 207 |
|
template<typename T> void NVT<T>::resetIntegrator( void ){ |
| 208 |
< |
|
| 208 |
> |
|
| 209 |
|
chi = 0.0; |
| 210 |
|
integralOfChidt = 0.0; |
| 211 |
|
} |
| 215 |
|
//check parent's readyCheck() first |
| 216 |
|
if (T::readyCheck() == -1) |
| 217 |
|
return -1; |
| 218 |
< |
|
| 219 |
< |
// First check to see if we have a target temperature. |
| 220 |
< |
// Not having one is fatal. |
| 221 |
< |
|
| 218 |
> |
|
| 219 |
> |
// First check to see if we have a target temperature. |
| 220 |
> |
// Not having one is fatal. |
| 221 |
> |
|
| 222 |
|
if (!have_target_temp) { |
| 223 |
|
sprintf( painCave.errMsg, |
| 224 |
|
"NVT error: You can't use the NVT integrator without a targetTemp!\n" |
| 227 |
|
simError(); |
| 228 |
|
return -1; |
| 229 |
|
} |
| 230 |
< |
|
| 230 |
> |
|
| 231 |
|
// We must set tauThermostat. |
| 232 |
< |
|
| 232 |
> |
|
| 233 |
|
if (!have_tau_thermostat) { |
| 234 |
|
sprintf( painCave.errMsg, |
| 235 |
|
"NVT error: If you use the constant temperature\n" |
| 237 |
|
painCave.isFatal = 1; |
| 238 |
|
simError(); |
| 239 |
|
return -1; |
| 240 |
< |
} |
| 240 |
> |
} |
| 241 |
|
|
| 242 |
|
if (!have_chi_tolerance) { |
| 243 |
|
sprintf( painCave.errMsg, |
| 246 |
|
have_chi_tolerance = 1; |
| 247 |
|
painCave.isFatal = 0; |
| 248 |
|
simError(); |
| 249 |
< |
} |
| 249 |
> |
} |
| 250 |
|
|
| 251 |
< |
return 1; |
| 251 |
> |
return 1; |
| 252 |
|
|
| 253 |
|
} |
| 254 |
|
|
| 255 |
|
template<typename T> double NVT<T>::getConservedQuantity(void){ |
| 256 |
|
|
| 257 |
|
double conservedQuantity; |
| 258 |
< |
double E_NVT; |
| 258 |
> |
double fkBT; |
| 259 |
> |
double Energy; |
| 260 |
> |
double thermostat_kinetic; |
| 261 |
> |
double thermostat_potential; |
| 262 |
|
|
| 263 |
< |
//HNVE |
| 261 |
< |
conservedQuantity = tStats->getTotalE(); |
| 262 |
< |
//HNVE |
| 263 |
< |
|
| 264 |
< |
E_NVT = (info->getNDF() * kB * targetTemp * |
| 265 |
< |
(integralOfChidt + tauThermostat * tauThermostat * chi * chi / 2.0 )) / eConvert; |
| 263 |
> |
fkBT = (double)(info->getNDF() ) * kB * targetTemp; |
| 264 |
|
|
| 265 |
< |
conservedQuantity += E_NVT; |
| 265 |
> |
Energy = tStats->getTotalE(); |
| 266 |
|
|
| 267 |
< |
//cerr << info->getTime() << "\t" << chi << "\t" << integralOfChidt << "\t" << E_NVT << endl; |
| 267 |
> |
thermostat_kinetic = fkBT* tauThermostat * tauThermostat * chi * chi / |
| 268 |
> |
(2.0 * eConvert); |
| 269 |
|
|
| 270 |
< |
return conservedQuantity; |
| 270 |
> |
thermostat_potential = fkBT * integralOfChidt / eConvert; |
| 271 |
> |
|
| 272 |
> |
conservedQuantity = Energy + thermostat_kinetic + thermostat_potential; |
| 273 |
> |
|
| 274 |
> |
return conservedQuantity; |
| 275 |
|
} |
| 276 |
+ |
|
| 277 |
+ |
template<typename T> string NVT<T>::getAdditionalParameters(void){ |
| 278 |
+ |
string parameters; |
| 279 |
+ |
const int BUFFERSIZE = 2000; // size of the read buffer |
| 280 |
+ |
char buffer[BUFFERSIZE]; |
| 281 |
+ |
|
| 282 |
+ |
sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt); |
| 283 |
+ |
parameters += buffer; |
| 284 |
+ |
|
| 285 |
+ |
return parameters; |
| 286 |
+ |
} |
