| 86 |
|
void NPAT::getPosScale(const Vector3d& pos, const Vector3d& COM, int index, Vector3d& sc) { |
| 87 |
|
|
| 88 |
|
/**@todo */ |
| 89 |
< |
Vector3d rj = (oldPos[index] + pos)/2.0 -COM; |
| 89 |
> |
Vector3d rj = (oldPos[index] + pos)/(RealType)2.0 -COM; |
| 90 |
|
sc = eta * rj; |
| 91 |
|
} |
| 92 |
|
|
| 93 |
|
void NPAT::scaleSimBox(){ |
| 94 |
– |
|
| 95 |
– |
int i; |
| 96 |
– |
int j; |
| 97 |
– |
int k; |
| 94 |
|
Mat3x3d scaleMat; |
| 99 |
– |
double eta2ij; |
| 100 |
– |
double bigScale, smallScale, offDiagMax; |
| 101 |
– |
Mat3x3d hm; |
| 102 |
– |
Mat3x3d hmnew; |
| 95 |
|
|
| 96 |
< |
|
| 97 |
< |
|
| 98 |
< |
// Scale the box after all the positions have been moved: |
| 99 |
< |
|
| 100 |
< |
// Use a taylor expansion for eta products: Hmat = Hmat . exp(dt * etaMat) |
| 101 |
< |
// Hmat = Hmat . ( Ident + dt * etaMat + dt^2 * etaMat*etaMat / 2) |
| 110 |
< |
|
| 111 |
< |
bigScale = 1.0; |
| 112 |
< |
smallScale = 1.0; |
| 113 |
< |
offDiagMax = 0.0; |
| 114 |
< |
|
| 115 |
< |
for(i=0; i<3; i++){ |
| 116 |
< |
for(j=0; j<3; j++){ |
| 117 |
< |
|
| 118 |
< |
// Calculate the matrix Product of the eta array (we only need |
| 119 |
< |
// the ij element right now): |
| 120 |
< |
|
| 121 |
< |
eta2ij = 0.0; |
| 122 |
< |
for(k=0; k<3; k++){ |
| 123 |
< |
eta2ij += eta(i, k) * eta(k, j); |
| 124 |
< |
} |
| 125 |
< |
|
| 126 |
< |
scaleMat(i, j) = 0.0; |
| 127 |
< |
// identity matrix (see above): |
| 128 |
< |
if (i == j) scaleMat(i, j) = 1.0; |
| 129 |
< |
// Taylor expansion for the exponential truncated at second order: |
| 130 |
< |
scaleMat(i, j) += dt*eta(i, j) + 0.5*dt*dt*eta2ij; |
| 131 |
< |
|
| 132 |
< |
|
| 133 |
< |
if (i != j) |
| 134 |
< |
if (fabs(scaleMat(i, j)) > offDiagMax) |
| 135 |
< |
offDiagMax = fabs(scaleMat(i, j)); |
| 96 |
> |
for(int i=0; i<3; i++){ |
| 97 |
> |
for(int j=0; j<3; j++){ |
| 98 |
> |
scaleMat(i, j) = 0.0; |
| 99 |
> |
if(i==j) { |
| 100 |
> |
scaleMat(i, j) = 1.0; |
| 101 |
> |
} |
| 102 |
|
} |
| 137 |
– |
|
| 138 |
– |
if (scaleMat(i, i) > bigScale) bigScale = scaleMat(i, i); |
| 139 |
– |
if (scaleMat(i, i) < smallScale) smallScale = scaleMat(i, i); |
| 103 |
|
} |
| 104 |
< |
|
| 105 |
< |
if ((bigScale > 1.01) || (smallScale < 0.99)) { |
| 106 |
< |
sprintf( painCave.errMsg, |
| 107 |
< |
"NPAT error: Attempting a Box scaling of more than 1 percent.\n" |
| 108 |
< |
" Check your tauBarostat, as it is probably too small!\n\n" |
| 146 |
< |
" scaleMat = [%lf\t%lf\t%lf]\n" |
| 147 |
< |
" [%lf\t%lf\t%lf]\n" |
| 148 |
< |
" [%lf\t%lf\t%lf]\n" |
| 149 |
< |
" eta = [%lf\t%lf\t%lf]\n" |
| 150 |
< |
" [%lf\t%lf\t%lf]\n" |
| 151 |
< |
" [%lf\t%lf\t%lf]\n", |
| 152 |
< |
scaleMat(0, 0),scaleMat(0, 1),scaleMat(0, 2), |
| 153 |
< |
scaleMat(1, 0),scaleMat(1, 1),scaleMat(1, 2), |
| 154 |
< |
scaleMat(2, 0),scaleMat(2, 1),scaleMat(2, 2), |
| 155 |
< |
eta(0, 0),eta(0, 1),eta(0, 2), |
| 156 |
< |
eta(1, 0),eta(1, 1),eta(1, 2), |
| 157 |
< |
eta(2, 0),eta(2, 1),eta(2, 2)); |
| 158 |
< |
painCave.isFatal = 1; |
| 159 |
< |
simError(); |
| 160 |
< |
} else if (offDiagMax > 0.01) { |
| 161 |
< |
sprintf( painCave.errMsg, |
| 162 |
< |
"NPAT error: Attempting an off-diagonal Box scaling of more than 1 percent.\n" |
| 163 |
< |
" Check your tauBarostat, as it is probably too small!\n\n" |
| 164 |
< |
" scaleMat = [%lf\t%lf\t%lf]\n" |
| 165 |
< |
" [%lf\t%lf\t%lf]\n" |
| 166 |
< |
" [%lf\t%lf\t%lf]\n" |
| 167 |
< |
" eta = [%lf\t%lf\t%lf]\n" |
| 168 |
< |
" [%lf\t%lf\t%lf]\n" |
| 169 |
< |
" [%lf\t%lf\t%lf]\n", |
| 170 |
< |
scaleMat(0, 0),scaleMat(0, 1),scaleMat(0, 2), |
| 171 |
< |
scaleMat(1, 0),scaleMat(1, 1),scaleMat(1, 2), |
| 172 |
< |
scaleMat(2, 0),scaleMat(2, 1),scaleMat(2, 2), |
| 173 |
< |
eta(0, 0),eta(0, 1),eta(0, 2), |
| 174 |
< |
eta(1, 0),eta(1, 1),eta(1, 2), |
| 175 |
< |
eta(2, 0),eta(2, 1),eta(2, 2)); |
| 176 |
< |
painCave.isFatal = 1; |
| 177 |
< |
simError(); |
| 178 |
< |
} else { |
| 179 |
< |
|
| 180 |
< |
Mat3x3d hmat = currentSnapshot_->getHmat(); |
| 181 |
< |
hmat = hmat *scaleMat; |
| 182 |
< |
currentSnapshot_->setHmat(hmat); |
| 183 |
< |
|
| 184 |
< |
} |
| 104 |
> |
|
| 105 |
> |
scaleMat(2, 2) = exp(dt*eta(2, 2)); |
| 106 |
> |
Mat3x3d hmat = currentSnapshot_->getHmat(); |
| 107 |
> |
hmat = hmat *scaleMat; |
| 108 |
> |
currentSnapshot_->setHmat(hmat); |
| 109 |
|
} |
| 110 |
|
|
| 111 |
|
bool NPAT::etaConverged() { |
| 112 |
|
int i; |
| 113 |
< |
double diffEta, sumEta; |
| 113 |
> |
RealType diffEta, sumEta; |
| 114 |
|
|
| 115 |
|
sumEta = 0; |
| 116 |
|
for(i = 0; i < 3; i++) { |
| 122 |
|
return ( diffEta <= etaTolerance ); |
| 123 |
|
} |
| 124 |
|
|
| 125 |
< |
double NPAT::calcConservedQuantity(){ |
| 125 |
> |
RealType NPAT::calcConservedQuantity(){ |
| 126 |
|
|
| 127 |
|
chi= currentSnapshot_->getChi(); |
| 128 |
|
integralOfChidt = currentSnapshot_->getIntegralOfChiDt(); |
| 138 |
|
// of freedom). |
| 139 |
|
fkBT = info_->getNdf()*OOPSEConstant::kB *targetTemp; |
| 140 |
|
|
| 141 |
< |
double conservedQuantity; |
| 142 |
< |
double totalEnergy; |
| 143 |
< |
double thermostat_kinetic; |
| 144 |
< |
double thermostat_potential; |
| 145 |
< |
double barostat_kinetic; |
| 146 |
< |
double barostat_potential; |
| 147 |
< |
double trEta; |
| 141 |
> |
RealType conservedQuantity; |
| 142 |
> |
RealType totalEnergy; |
| 143 |
> |
RealType thermostat_kinetic; |
| 144 |
> |
RealType thermostat_potential; |
| 145 |
> |
RealType barostat_kinetic; |
| 146 |
> |
RealType barostat_potential; |
| 147 |
> |
RealType trEta; |
| 148 |
|
|
| 149 |
|
totalEnergy = thermo.getTotalE(); |
| 150 |
|
|
| 152 |
|
|
| 153 |
|
thermostat_potential = fkBT* integralOfChidt / OOPSEConstant::energyConvert; |
| 154 |
|
|
| 155 |
< |
SquareMatrix<double, 3> tmp = eta.transpose() * eta; |
| 155 |
> |
SquareMatrix<RealType, 3> tmp = eta.transpose() * eta; |
| 156 |
|
trEta = tmp.trace(); |
| 157 |
|
|
| 158 |
|
barostat_kinetic = NkBT * tb2 * trEta /(2.0 * OOPSEConstant::energyConvert); |
