| 1 |
+ |
#include <cmath> |
| 2 |
|
#include "Atom.hpp" |
| 3 |
|
#include "Molecule.hpp" |
| 4 |
|
#include "SRI.hpp" |
| 23 |
|
// The NPTfm variant scales the molecular center-of-mass coordinates |
| 24 |
|
// instead of the atomic coordinates |
| 25 |
|
|
| 26 |
< |
NPTfm::NPTfm ( SimInfo *theInfo, ForceFields* the_ff): |
| 27 |
< |
Integrator( theInfo, the_ff ) |
| 26 |
> |
template<typename T> NPTfm<T>::NPTfm ( SimInfo *theInfo, ForceFields* the_ff): |
| 27 |
> |
T( theInfo, the_ff ) |
| 28 |
|
{ |
| 29 |
|
int i, j; |
| 30 |
|
chi = 0.0; |
| 39 |
|
have_target_pressure = 0; |
| 40 |
|
} |
| 41 |
|
|
| 42 |
< |
void NPTfm::moveA() { |
| 42 |
> |
template<typename T> void NPTfm<T>::moveA() { |
| 43 |
|
|
| 44 |
|
int i, j, k; |
| 45 |
|
DirectionalAtom* dAtom; |
| 52 |
|
double instaTemp, instaPress, instaVol; |
| 53 |
|
double tt2, tb2; |
| 54 |
|
double sc[3]; |
| 55 |
< |
double eta2ij; |
| 55 |
> |
double eta2ij, smallScale, bigScale, offDiagMax; |
| 56 |
|
double press[3][3], vScale[3][3], hm[3][3], hmnew[3][3], scaleMat[3][3]; |
| 57 |
|
|
| 58 |
|
int nInMol; |
| 128 |
|
|
| 129 |
|
for (k = 0; k < 3; k++ ) |
| 130 |
|
pos[k] += dt * (vel[k] + sc[k]); |
| 131 |
+ |
|
| 132 |
+ |
myAtoms[j]->setPos( pos ); |
| 133 |
|
|
| 134 |
|
if( myAtoms[j]->isDirectional() ){ |
| 135 |
|
|
| 186 |
|
// Hmat = Hmat . ( Ident + dt * etaMat + dt^2 * etaMat*etaMat / 2) |
| 187 |
|
|
| 188 |
|
|
| 189 |
+ |
bigScale = 1.0; |
| 190 |
+ |
smallScale = 1.0; |
| 191 |
+ |
offDiagMax = 0.0; |
| 192 |
+ |
|
| 193 |
|
for(i=0; i<3; i++){ |
| 194 |
|
for(j=0; j<3; j++){ |
| 195 |
|
|
| 206 |
|
if (i == j) scaleMat[i][j] = 1.0; |
| 207 |
|
// Taylor expansion for the exponential truncated at second order: |
| 208 |
|
scaleMat[i][j] += dt*eta[i][j] + 0.5*dt*dt*eta2ij; |
| 209 |
< |
|
| 209 |
> |
|
| 210 |
> |
if (i != j) |
| 211 |
> |
if (fabs(scaleMat[i][j]) > offDiagMax) |
| 212 |
> |
offDiagMax = fabs(scaleMat[i][j]); |
| 213 |
|
} |
| 214 |
+ |
if (scaleMat[i][i] > bigScale) bigScale = scaleMat[i][i]; |
| 215 |
+ |
if (scaleMat[i][i] < smallScale) smallScale = scaleMat[i][i]; |
| 216 |
|
} |
| 217 |
|
|
| 218 |
< |
info->getBoxM(hm); |
| 219 |
< |
info->matMul3(hm, scaleMat, hmnew); |
| 220 |
< |
info->setBoxM(hmnew); |
| 221 |
< |
|
| 218 |
> |
if ((bigScale > 1.1) || (smallScale < 0.9)) { |
| 219 |
> |
sprintf( painCave.errMsg, |
| 220 |
> |
"NPTf error: Attempting a Box scaling of more than 10 percent.\n" |
| 221 |
> |
" Check your tauBarostat, as it is probably too small!\n\n" |
| 222 |
> |
" scaleMat = [%lf\t%lf\t%lf]\n" |
| 223 |
> |
" [%lf\t%lf\t%lf]\n" |
| 224 |
> |
" [%lf\t%lf\t%lf]\n", |
| 225 |
> |
scaleMat[0][0],scaleMat[0][1],scaleMat[0][2], |
| 226 |
> |
scaleMat[1][0],scaleMat[1][1],scaleMat[1][2], |
| 227 |
> |
scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]); |
| 228 |
> |
painCave.isFatal = 1; |
| 229 |
> |
simError(); |
| 230 |
> |
} else if (offDiagMax > 0.1) { |
| 231 |
> |
sprintf( painCave.errMsg, |
| 232 |
> |
"NPTf error: Attempting an off-diagonal Box scaling of more than 10 percent.\n" |
| 233 |
> |
" Check your tauBarostat, as it is probably too small!\n\n" |
| 234 |
> |
" scaleMat = [%lf\t%lf\t%lf]\n" |
| 235 |
> |
" [%lf\t%lf\t%lf]\n" |
| 236 |
> |
" [%lf\t%lf\t%lf]\n", |
| 237 |
> |
scaleMat[0][0],scaleMat[0][1],scaleMat[0][2], |
| 238 |
> |
scaleMat[1][0],scaleMat[1][1],scaleMat[1][2], |
| 239 |
> |
scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]); |
| 240 |
> |
painCave.isFatal = 1; |
| 241 |
> |
simError(); |
| 242 |
> |
} else { |
| 243 |
> |
info->getBoxM(hm); |
| 244 |
> |
info->matMul3(hm, scaleMat, hmnew); |
| 245 |
> |
info->setBoxM(hmnew); |
| 246 |
> |
} |
| 247 |
|
} |
| 248 |
|
|
| 249 |
< |
void NPTfm::moveB( void ){ |
| 249 |
> |
template<typename T> void NPTfm<T>::moveB( void ){ |
| 250 |
|
|
| 251 |
|
int i, j; |
| 252 |
|
DirectionalAtom* dAtom; |
| 328 |
|
} |
| 329 |
|
} |
| 330 |
|
|
| 331 |
< |
int NPTfm::readyCheck() { |
| 331 |
> |
template<typename T> int NPTfm<T>::readyCheck() { |
| 332 |
|
|
| 333 |
|
// First check to see if we have a target temperature. |
| 334 |
|
// Not having one is fatal. |
