| 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 |
< |
NPTf::NPTf ( SimInfo *theInfo, ForceFields* the_ff): |
| 24 |
< |
Integrator( theInfo, the_ff ) |
| 23 |
> |
template<typename T> NPTf<T>::NPTf ( SimInfo *theInfo, ForceFields* the_ff): |
| 24 |
> |
T( theInfo, the_ff ) |
| 25 |
|
{ |
| 26 |
|
int i, j; |
| 27 |
|
chi = 0.0; |
| 36 |
|
have_target_pressure = 0; |
| 37 |
|
} |
| 38 |
|
|
| 39 |
< |
void NPTf::moveA() { |
| 39 |
> |
template<typename T> void NPTf<T>::moveA() { |
| 40 |
|
|
| 41 |
|
int i, j, k; |
| 42 |
|
DirectionalAtom* dAtom; |
| 51 |
|
double sc[3]; |
| 52 |
|
double eta2ij; |
| 53 |
|
double press[3][3], vScale[3][3], hm[3][3], hmnew[3][3], scaleMat[3][3]; |
| 54 |
+ |
double bigScale, smallScale, offDiagMax; |
| 55 |
|
|
| 56 |
|
tt2 = tauThermostat * tauThermostat; |
| 57 |
|
tb2 = tauBarostat * tauBarostat; |
| 110 |
|
|
| 111 |
|
for (j = 0; j < 3; j++ ) |
| 112 |
|
pos[j] += dt * (vel[j] + sc[j]); |
| 113 |
+ |
|
| 114 |
+ |
atoms[i]->setPos( pos ); |
| 115 |
|
|
| 116 |
|
if( atoms[i]->isDirectional() ){ |
| 117 |
|
|
| 165 |
|
// Use a taylor expansion for eta products: Hmat = Hmat . exp(dt * etaMat) |
| 166 |
|
// Hmat = Hmat . ( Ident + dt * etaMat + dt^2 * etaMat*etaMat / 2) |
| 167 |
|
|
| 168 |
+ |
bigScale = 1.0; |
| 169 |
+ |
smallScale = 1.0; |
| 170 |
+ |
offDiagMax = 0.0; |
| 171 |
|
|
| 172 |
|
for(i=0; i<3; i++){ |
| 173 |
|
for(j=0; j<3; j++){ |
| 185 |
|
if (i == j) scaleMat[i][j] = 1.0; |
| 186 |
|
// Taylor expansion for the exponential truncated at second order: |
| 187 |
|
scaleMat[i][j] += dt*eta[i][j] + 0.5*dt*dt*eta2ij; |
| 188 |
+ |
|
| 189 |
+ |
if (i != j) |
| 190 |
+ |
if (fabs(scaleMat[i][j]) > offDiagMax) |
| 191 |
+ |
offDiagMax = fabs(scaleMat[i][j]); |
| 192 |
|
|
| 193 |
|
} |
| 194 |
+ |
|
| 195 |
+ |
if (scaleMat[i][i] > bigScale) bigScale = scaleMat[i][i]; |
| 196 |
+ |
if (scaleMat[i][i] < smallScale) smallScale = scaleMat[i][i]; |
| 197 |
|
} |
| 198 |
|
|
| 199 |
< |
info->getBoxM(hm); |
| 200 |
< |
info->matMul3(hm, scaleMat, hmnew); |
| 201 |
< |
info->setBoxM(hmnew); |
| 199 |
> |
if ((bigScale > 1.1) || (smallScale < 0.9)) { |
| 200 |
> |
sprintf( painCave.errMsg, |
| 201 |
> |
"NPTf error: Attempting a Box scaling of more than 10 percent.\n" |
| 202 |
> |
" Check your tauBarostat, as it is probably too small!\n\n" |
| 203 |
> |
" scaleMat = [%lf\t%lf\t%lf]\n" |
| 204 |
> |
" [%lf\t%lf\t%lf]\n" |
| 205 |
> |
" [%lf\t%lf\t%lf]\n", |
| 206 |
> |
scaleMat[0][0],scaleMat[0][1],scaleMat[0][2], |
| 207 |
> |
scaleMat[1][0],scaleMat[1][1],scaleMat[1][2], |
| 208 |
> |
scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]); |
| 209 |
> |
painCave.isFatal = 1; |
| 210 |
> |
simError(); |
| 211 |
> |
} else if (offDiagMax > 0.1) { |
| 212 |
> |
sprintf( painCave.errMsg, |
| 213 |
> |
"NPTf error: Attempting an off-diagonal Box scaling of more than 10 percent.\n" |
| 214 |
> |
" Check your tauBarostat, as it is probably too small!\n\n" |
| 215 |
> |
" scaleMat = [%lf\t%lf\t%lf]\n" |
| 216 |
> |
" [%lf\t%lf\t%lf]\n" |
| 217 |
> |
" [%lf\t%lf\t%lf]\n", |
| 218 |
> |
scaleMat[0][0],scaleMat[0][1],scaleMat[0][2], |
| 219 |
> |
scaleMat[1][0],scaleMat[1][1],scaleMat[1][2], |
| 220 |
> |
scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]); |
| 221 |
> |
painCave.isFatal = 1; |
| 222 |
> |
simError(); |
| 223 |
> |
} else { |
| 224 |
> |
info->getBoxM(hm); |
| 225 |
> |
info->matMul3(hm, scaleMat, hmnew); |
| 226 |
> |
info->setBoxM(hmnew); |
| 227 |
> |
} |
| 228 |
|
|
| 229 |
|
} |
| 230 |
|
|
| 231 |
< |
void NPTf::moveB( void ){ |
| 231 |
> |
template<typename T> void NPTf<T>::moveB( void ){ |
| 232 |
|
|
| 233 |
|
int i, j; |
| 234 |
|
DirectionalAtom* dAtom; |
| 310 |
|
} |
| 311 |
|
} |
| 312 |
|
|
| 313 |
< |
int NPTf::readyCheck() { |
| 313 |
> |
template<typename T> int NPTf<T>::readyCheck() { |
| 314 |
> |
|
| 315 |
> |
//check parent's readyCheck() first |
| 316 |
> |
if (T::readyCheck() == -1) |
| 317 |
> |
return -1; |
| 318 |
|
|
| 319 |
|
// First check to see if we have a target temperature. |
| 320 |
|
// Not having one is fatal. |
