| 6 |
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* redistribute this software in source and binary code form, provided |
| 7 |
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* that the following conditions are met: |
| 8 |
|
* |
| 9 |
< |
* 1. Acknowledgement of the program authors must be made in any |
| 10 |
< |
* publication of scientific results based in part on use of the |
| 11 |
< |
* program. An acceptable form of acknowledgement is citation of |
| 12 |
< |
* the article in which the program was described (Matthew |
| 13 |
< |
* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
| 14 |
< |
* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
| 15 |
< |
* Parallel Simulation Engine for Molecular Dynamics," |
| 16 |
< |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
| 17 |
< |
* |
| 18 |
< |
* 2. Redistributions of source code must retain the above copyright |
| 9 |
> |
* 1. Redistributions of source code must retain the above copyright |
| 10 |
|
* notice, this list of conditions and the following disclaimer. |
| 11 |
|
* |
| 12 |
< |
* 3. Redistributions in binary form must reproduce the above copyright |
| 12 |
> |
* 2. Redistributions in binary form must reproduce the above copyright |
| 13 |
|
* notice, this list of conditions and the following disclaimer in the |
| 14 |
|
* documentation and/or other materials provided with the |
| 15 |
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* distribution. |
| 28 |
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* arising out of the use of or inability to use software, even if the |
| 29 |
|
* University of Notre Dame has been advised of the possibility of |
| 30 |
|
* such damages. |
| 31 |
+ |
* |
| 32 |
+ |
* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
| 33 |
+ |
* research, please cite the appropriate papers when you publish your |
| 34 |
+ |
* work. Good starting points are: |
| 35 |
+ |
* |
| 36 |
+ |
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 37 |
+ |
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 38 |
+ |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). |
| 39 |
+ |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
+ |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
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*/ |
| 42 |
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|
| 43 |
|
#include "brains/SimInfo.hpp" |
| 45 |
|
#include "integrators/IntegratorCreator.hpp" |
| 46 |
|
#include "integrators/NPAT.hpp" |
| 47 |
|
#include "primitives/Molecule.hpp" |
| 48 |
< |
#include "utils/OOPSEConstant.hpp" |
| 48 |
> |
#include "utils/PhysicalConstants.hpp" |
| 49 |
|
#include "utils/simError.h" |
| 50 |
|
|
| 51 |
< |
namespace oopse { |
| 51 |
> |
namespace OpenMD { |
| 52 |
|
|
| 53 |
|
void NPAT::evolveEtaA() { |
| 54 |
|
|
| 55 |
< |
eta(2,2) += dt2 * instaVol * (press(2, 2) - targetPressure/OOPSEConstant::pressureConvert) / (NkBT*tb2); |
| 55 |
> |
eta(2,2) += dt2 * instaVol * (press(2, 2) - targetPressure/PhysicalConstants::pressureConvert) / (NkBT*tb2); |
| 56 |
|
oldEta = eta; |
| 57 |
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} |
| 58 |
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|
| 60 |
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|
| 61 |
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prevEta = eta; |
| 62 |
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eta(2,2) = oldEta(2, 2) + dt2 * instaVol * |
| 63 |
< |
(press(2, 2) - targetPressure/OOPSEConstant::pressureConvert) / (NkBT*tb2); |
| 63 |
> |
(press(2, 2) - targetPressure/PhysicalConstants::pressureConvert) / (NkBT*tb2); |
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} |
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|
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|
void NPAT::calcVelScale(){ |
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vScale(i, j) = eta(i, j); |
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|
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if (i == j) { |
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< |
vScale(i, j) += chi; |
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> |
vScale(i, j) += thermostat.first; |
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|
} |
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} |
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} |
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|
void NPAT::getPosScale(const Vector3d& pos, const Vector3d& COM, int index, Vector3d& sc) { |
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|
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/**@todo */ |
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< |
Vector3d rj = (oldPos[index] + pos)/2.0 -COM; |
| 90 |
> |
Vector3d rj = (oldPos[index] + pos)/(RealType)2.0 -COM; |
| 91 |
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sc = eta * rj; |
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|
} |
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|
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void NPAT::scaleSimBox(){ |
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– |
|
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– |
int i; |
| 96 |
– |
int j; |
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– |
int k; |
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|
Mat3x3d scaleMat; |
| 99 |
– |
double eta2ij; |
| 100 |
– |
double bigScale, smallScale, offDiagMax; |
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– |
Mat3x3d hm; |
| 102 |
– |
Mat3x3d hmnew; |
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|
|
| 97 |
< |
|
| 98 |
< |
|
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< |
// Scale the box after all the positions have been moved: |
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< |
|
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< |
// Use a taylor expansion for eta products: Hmat = Hmat . exp(dt * etaMat) |
| 102 |
< |
// Hmat = Hmat . ( Ident + dt * etaMat + dt^2 * etaMat*etaMat / 2) |
| 110 |
< |
|
| 111 |
< |
bigScale = 1.0; |
| 112 |
< |
smallScale = 1.0; |
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< |
offDiagMax = 0.0; |
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< |
|
| 115 |
< |
for(i=0; i<3; i++){ |
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< |
for(j=0; j<3; j++){ |
| 117 |
< |
|
| 118 |
< |
// Calculate the matrix Product of the eta array (we only need |
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< |
// the ij element right now): |
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< |
|
| 121 |
< |
eta2ij = 0.0; |
| 122 |
< |
for(k=0; k<3; k++){ |
| 123 |
< |
eta2ij += eta(i, k) * eta(k, j); |
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< |
} |
| 125 |
< |
|
| 126 |
< |
scaleMat(i, j) = 0.0; |
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< |
// identity matrix (see above): |
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< |
if (i == j) scaleMat(i, j) = 1.0; |
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< |
// Taylor expansion for the exponential truncated at second order: |
| 130 |
< |
scaleMat(i, j) += dt*eta(i, j) + 0.5*dt*dt*eta2ij; |
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< |
|
| 132 |
< |
|
| 133 |
< |
if (i != j) |
| 134 |
< |
if (fabs(scaleMat(i, j)) > offDiagMax) |
| 135 |
< |
offDiagMax = fabs(scaleMat(i, j)); |
| 97 |
> |
for(int i=0; i<3; i++){ |
| 98 |
> |
for(int j=0; j<3; j++){ |
| 99 |
> |
scaleMat(i, j) = 0.0; |
| 100 |
> |
if(i==j) { |
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> |
scaleMat(i, j) = 1.0; |
| 102 |
> |
} |
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|
} |
| 137 |
– |
|
| 138 |
– |
if (scaleMat(i, i) > bigScale) bigScale = scaleMat(i, i); |
| 139 |
– |
if (scaleMat(i, i) < smallScale) smallScale = scaleMat(i, i); |
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} |
| 105 |
< |
|
| 106 |
< |
if ((bigScale > 1.01) || (smallScale < 0.99)) { |
| 107 |
< |
sprintf( painCave.errMsg, |
| 108 |
< |
"NPAT error: Attempting a Box scaling of more than 1 percent.\n" |
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< |
" 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 |
< |
} |
| 105 |
> |
|
| 106 |
> |
scaleMat(2, 2) = exp(dt*eta(2, 2)); |
| 107 |
> |
Mat3x3d hmat = snap->getHmat(); |
| 108 |
> |
hmat = hmat *scaleMat; |
| 109 |
> |
snap->setHmat(hmat); |
| 110 |
|
} |
| 111 |
|
|
| 112 |
|
bool NPAT::etaConverged() { |
| 113 |
|
int i; |
| 114 |
< |
double diffEta, sumEta; |
| 114 |
> |
RealType diffEta, sumEta; |
| 115 |
|
|
| 116 |
|
sumEta = 0; |
| 117 |
|
for(i = 0; i < 3; i++) { |
| 123 |
|
return ( diffEta <= etaTolerance ); |
| 124 |
|
} |
| 125 |
|
|
| 126 |
< |
double NPAT::calcConservedQuantity(){ |
| 126 |
> |
RealType NPAT::calcConservedQuantity(){ |
| 127 |
|
|
| 128 |
< |
chi= currentSnapshot_->getChi(); |
| 204 |
< |
integralOfChidt = currentSnapshot_->getIntegralOfChiDt(); |
| 128 |
> |
thermostat = snap->getThermostat(); |
| 129 |
|
loadEta(); |
| 130 |
|
|
| 131 |
|
// We need NkBT a lot, so just set it here: This is the RAW number |
| 132 |
|
// of integrableObjects, so no subtraction or addition of constraints or |
| 133 |
|
// orientational degrees of freedom: |
| 134 |
< |
NkBT = info_->getNGlobalIntegrableObjects()*OOPSEConstant::kB *targetTemp; |
| 134 |
> |
NkBT = info_->getNGlobalIntegrableObjects()*PhysicalConstants::kB *targetTemp; |
| 135 |
|
|
| 136 |
|
// fkBT is used because the thermostat operates on more degrees of freedom |
| 137 |
|
// than the barostat (when there are particles with orientational degrees |
| 138 |
|
// of freedom). |
| 139 |
< |
fkBT = info_->getNdf()*OOPSEConstant::kB *targetTemp; |
| 139 |
> |
fkBT = info_->getNdf()*PhysicalConstants::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(); |
| 149 |
> |
totalEnergy = thermo.getTotalEnergy(); |
| 150 |
|
|
| 151 |
< |
thermostat_kinetic = fkBT * tt2 * chi * chi /(2.0 * OOPSEConstant::energyConvert); |
| 151 |
> |
thermostat_kinetic = fkBT * tt2 * thermostat.first * |
| 152 |
> |
thermostat.first /(2.0 * PhysicalConstants::energyConvert); |
| 153 |
|
|
| 154 |
< |
thermostat_potential = fkBT* integralOfChidt / OOPSEConstant::energyConvert; |
| 154 |
> |
thermostat_potential = fkBT* thermostat.second / PhysicalConstants::energyConvert; |
| 155 |
|
|
| 156 |
< |
SquareMatrix<double, 3> tmp = eta.transpose() * eta; |
| 156 |
> |
SquareMatrix<RealType, 3> tmp = eta.transpose() * eta; |
| 157 |
|
trEta = tmp.trace(); |
| 158 |
|
|
| 159 |
< |
barostat_kinetic = NkBT * tb2 * trEta /(2.0 * OOPSEConstant::energyConvert); |
| 159 |
> |
barostat_kinetic = NkBT * tb2 * trEta /(2.0 * PhysicalConstants::energyConvert); |
| 160 |
|
|
| 161 |
< |
barostat_potential = (targetPressure * thermo.getVolume() / OOPSEConstant::pressureConvert) /OOPSEConstant::energyConvert; |
| 161 |
> |
barostat_potential = (targetPressure * thermo.getVolume() / PhysicalConstants::pressureConvert) /PhysicalConstants::energyConvert; |
| 162 |
|
|
| 163 |
|
conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential + |
| 164 |
|
barostat_kinetic + barostat_potential; |
| 168 |
|
} |
| 169 |
|
|
| 170 |
|
void NPAT::loadEta() { |
| 171 |
< |
eta= currentSnapshot_->getEta(); |
| 171 |
> |
eta= snap->getBarostat(); |
| 172 |
|
|
| 173 |
|
//if (!eta.isDiagonal()) { |
| 174 |
|
// sprintf( painCave.errMsg, |
| 179 |
|
} |
| 180 |
|
|
| 181 |
|
void NPAT::saveEta() { |
| 182 |
< |
currentSnapshot_->setEta(eta); |
| 182 |
> |
snap->setBarostat(eta); |
| 183 |
|
} |
| 184 |
|
|
| 185 |
|
} |
