| 1 |
< |
#include <math.h> |
| 2 |
< |
#include "math/MatVec3.h" |
| 3 |
< |
#include "primitives/Atom.hpp" |
| 4 |
< |
#include "primitives/SRI.hpp" |
| 5 |
< |
#include "primitives/AbstractClasses.hpp" |
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> |
/* |
| 2 |
> |
* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
| 3 |
> |
* |
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> |
* The University of Notre Dame grants you ("Licensee") a |
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> |
* non-exclusive, royalty free, license to use, modify and |
| 6 |
> |
* redistribute this software in source and binary code form, provided |
| 7 |
> |
* that the following conditions are met: |
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> |
* |
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> |
* 1. Acknowledgement of the program authors must be made in any |
| 10 |
> |
* publication of scientific results based in part on use of the |
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> |
* program. An acceptable form of acknowledgement is citation of |
| 12 |
> |
* the article in which the program was described (Matthew |
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> |
* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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> |
* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
| 15 |
> |
* Parallel Simulation Engine for Molecular Dynamics," |
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> |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
| 17 |
> |
* |
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> |
* 2. Redistributions of source code must retain the above copyright |
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> |
* notice, this list of conditions and the following disclaimer. |
| 20 |
> |
* |
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> |
* 3. Redistributions in binary form must reproduce the above copyright |
| 22 |
> |
* notice, this list of conditions and the following disclaimer in the |
| 23 |
> |
* documentation and/or other materials provided with the |
| 24 |
> |
* distribution. |
| 25 |
> |
* |
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> |
* This software is provided "AS IS," without a warranty of any |
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> |
* kind. All express or implied conditions, representations and |
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> |
* warranties, including any implied warranty of merchantability, |
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> |
* fitness for a particular purpose or non-infringement, are hereby |
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> |
* excluded. The University of Notre Dame and its licensors shall not |
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> |
* be liable for any damages suffered by licensee as a result of |
| 32 |
> |
* using, modifying or distributing the software or its |
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> |
* derivatives. In no event will the University of Notre Dame or its |
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> |
* licensors be liable for any lost revenue, profit or data, or for |
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> |
* direct, indirect, special, consequential, incidental or punitive |
| 36 |
> |
* damages, however caused and regardless of the theory of liability, |
| 37 |
> |
* arising out of the use of or inability to use software, even if the |
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> |
* University of Notre Dame has been advised of the possibility of |
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> |
* such damages. |
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> |
*/ |
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> |
|
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|
#include "brains/SimInfo.hpp" |
| 7 |
– |
#include "UseTheForce/ForceFields.hpp" |
| 43 |
|
#include "brains/Thermo.hpp" |
| 44 |
< |
#include "io/ReadWrite.hpp" |
| 45 |
< |
#include "integrators/Integrator.hpp" |
| 44 |
> |
#include "integrators/IntegratorCreator.hpp" |
| 45 |
> |
#include "integrators/NPTxyz.hpp" |
| 46 |
> |
#include "primitives/Molecule.hpp" |
| 47 |
> |
#include "utils/OOPSEConstant.hpp" |
| 48 |
|
#include "utils/simError.h" |
| 49 |
|
|
| 13 |
– |
#ifdef IS_MPI |
| 14 |
– |
#include "brains/mpiSimulation.hpp" |
| 15 |
– |
#endif |
| 16 |
– |
|
| 50 |
|
// Basic non-isotropic thermostating and barostating via the Melchionna |
| 51 |
|
// modification of the Hoover algorithm: |
| 52 |
|
// |
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// |
| 58 |
|
// Hoover, W. G., 1986, Phys. Rev. A, 34, 2499. |
| 59 |
|
|
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< |
template<typename T> NPTxyz<T>::NPTxyz ( SimInfo *theInfo, ForceFields* the_ff): |
| 28 |
< |
T( theInfo, the_ff ) |
| 29 |
< |
{ |
| 30 |
< |
GenericData* data; |
| 31 |
< |
DoubleArrayData * etaValue; |
| 32 |
< |
vector<double> etaArray; |
| 33 |
< |
int i,j; |
| 60 |
> |
namespace oopse { |
| 61 |
|
|
| 62 |
< |
for(i = 0; i < 3; i++){ |
| 63 |
< |
for (j = 0; j < 3; j++){ |
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> |
|
| 63 |
> |
double NPTxyz::calcConservedQuantity(){ |
| 64 |
|
|
| 65 |
< |
eta[i][j] = 0.0; |
| 66 |
< |
oldEta[i][j] = 0.0; |
| 67 |
< |
} |
| 68 |
< |
} |
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> |
// We need NkBT a lot, so just set it here: This is the RAW number |
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> |
// of integrableObjects, so no subtraction or addition of constraints or |
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> |
// orientational degrees of freedom: |
| 68 |
> |
NkBT = info_->getNGlobalIntegrableObjects()*OOPSEConstant::kB *targetTemp; |
| 69 |
|
|
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+ |
// fkBT is used because the thermostat operates on more degrees of freedom |
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+ |
// than the barostat (when there are particles with orientational degrees |
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+ |
// of freedom). |
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+ |
fkBT = info_->getNdf()*OOPSEConstant::kB *targetTemp; |
| 74 |
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|
| 75 |
< |
if( theInfo->useInitXSstate ){ |
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> |
double conservedQuantity; |
| 76 |
> |
double totalEnergy; |
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> |
double thermostat_kinetic; |
| 78 |
> |
double thermostat_potential; |
| 79 |
> |
double barostat_kinetic; |
| 80 |
> |
double barostat_potential; |
| 81 |
> |
double trEta; |
| 82 |
|
|
| 83 |
< |
// retrieve eta array from simInfo if it exists |
| 47 |
< |
data = info->getProperty(ETAVALUE_ID); |
| 48 |
< |
if(data){ |
| 49 |
< |
etaValue = dynamic_cast<DoubleArrayData*>(data); |
| 50 |
< |
|
| 51 |
< |
if(etaValue){ |
| 52 |
< |
etaArray = etaValue->getData(); |
| 53 |
< |
|
| 54 |
< |
for(i = 0; i < 3; i++){ |
| 55 |
< |
for (j = 0; j < 3; j++){ |
| 56 |
< |
eta[i][j] = etaArray[3*i+j]; |
| 57 |
< |
oldEta[i][j] = eta[i][j]; |
| 58 |
< |
} |
| 59 |
< |
} |
| 60 |
< |
} |
| 61 |
< |
} |
| 62 |
< |
} |
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< |
} |
| 83 |
> |
totalEnergy = thermo.getTotalE(); |
| 84 |
|
|
| 85 |
< |
template<typename T> NPTxyz<T>::~NPTxyz() { |
| 85 |
> |
thermostat_kinetic = fkBT * tt2 * chi * chi /(2.0 * OOPSEConstant::energyConvert); |
| 86 |
|
|
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< |
// empty for now |
| 68 |
< |
} |
| 87 |
> |
thermostat_potential = fkBT* integralOfChidt / OOPSEConstant::energyConvert; |
| 88 |
|
|
| 89 |
< |
template<typename T> void NPTxyz<T>::resetIntegrator() { |
| 89 |
> |
SquareMatrix<double, 3> tmp = eta.transpose() * eta; |
| 90 |
> |
trEta = tmp.trace(); |
| 91 |
|
|
| 92 |
< |
int i, j; |
| 92 |
> |
barostat_kinetic = NkBT * tb2 * trEta /(2.0 * OOPSEConstant::energyConvert); |
| 93 |
|
|
| 94 |
< |
for(i = 0; i < 3; i++) |
| 75 |
< |
for (j = 0; j < 3; j++) |
| 76 |
< |
eta[i][j] = 0.0; |
| 94 |
> |
barostat_potential = (targetPressure * thermo.getVolume() / OOPSEConstant::pressureConvert) /OOPSEConstant::energyConvert; |
| 95 |
|
|
| 96 |
< |
T::resetIntegrator(); |
| 97 |
< |
} |
| 96 |
> |
conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential + |
| 97 |
> |
barostat_kinetic + barostat_potential; |
| 98 |
|
|
| 81 |
– |
template<typename T> void NPTxyz<T>::evolveEtaA() { |
| 99 |
|
|
| 100 |
< |
int i, j; |
| 100 |
> |
return conservedQuantity; |
| 101 |
|
|
| 85 |
– |
for(i = 0; i < 3; i ++){ |
| 86 |
– |
for(j = 0; j < 3; j++){ |
| 87 |
– |
if( i == j) |
| 88 |
– |
eta[i][j] += dt2 * instaVol * |
| 89 |
– |
(press[i][j] - targetPressure/p_convert) / (NkBT*tb2); |
| 90 |
– |
else |
| 91 |
– |
eta[i][j] = 0.0; |
| 92 |
– |
} |
| 102 |
|
} |
| 103 |
|
|
| 104 |
< |
for(i = 0; i < 3; i++) |
| 105 |
< |
for (j = 0; j < 3; j++) |
| 97 |
< |
oldEta[i][j] = eta[i][j]; |
| 98 |
< |
} |
| 104 |
> |
|
| 105 |
> |
void NPTxyz::scaleSimBox(){ |
| 106 |
|
|
| 107 |
< |
template<typename T> void NPTxyz<T>::evolveEtaB() { |
| 107 |
> |
int i,j,k; |
| 108 |
> |
Mat3x3d scaleMat; |
| 109 |
> |
double eta2ij, scaleFactor; |
| 110 |
> |
double bigScale, smallScale, offDiagMax; |
| 111 |
> |
Mat3x3d hm; |
| 112 |
> |
Mat3x3d hmnew; |
| 113 |
|
|
| 102 |
– |
int i,j; |
| 114 |
|
|
| 104 |
– |
for(i = 0; i < 3; i++) |
| 105 |
– |
for (j = 0; j < 3; j++) |
| 106 |
– |
prevEta[i][j] = eta[i][j]; |
| 115 |
|
|
| 116 |
< |
for(i = 0; i < 3; i ++){ |
| 109 |
< |
for(j = 0; j < 3; j++){ |
| 110 |
< |
if( i == j) { |
| 111 |
< |
eta[i][j] = oldEta[i][j] + dt2 * instaVol * |
| 112 |
< |
(press[i][j] - targetPressure/p_convert) / (NkBT*tb2); |
| 113 |
< |
} else { |
| 114 |
< |
eta[i][j] = 0.0; |
| 115 |
< |
} |
| 116 |
< |
} |
| 117 |
< |
} |
| 118 |
< |
} |
| 116 |
> |
// Scale the box after all the positions have been moved: |
| 117 |
|
|
| 118 |
< |
template<typename T> void NPTxyz<T>::calcVelScale(void) { |
| 119 |
< |
int i,j; |
| 118 |
> |
// Use a taylor expansion for eta products: Hmat = Hmat . exp(dt * etaMat) |
| 119 |
> |
// Hmat = Hmat . ( Ident + dt * etaMat + dt^2 * etaMat*etaMat / 2) |
| 120 |
|
|
| 121 |
< |
for (i = 0; i < 3; i++ ) { |
| 122 |
< |
for (j = 0; j < 3; j++ ) { |
| 123 |
< |
vScale[i][j] = eta[i][j]; |
| 121 |
> |
bigScale = 1.0; |
| 122 |
> |
smallScale = 1.0; |
| 123 |
> |
offDiagMax = 0.0; |
| 124 |
|
|
| 125 |
< |
if (i == j) { |
| 126 |
< |
vScale[i][j] += chi; |
| 125 |
> |
for(i=0; i<3; i++){ |
| 126 |
> |
for(j=0; j<3; j++){ |
| 127 |
> |
scaleMat(i, j) = 0.0; |
| 128 |
> |
if(i==j) { |
| 129 |
> |
scaleMat(i, j) = 1.0; |
| 130 |
> |
} |
| 131 |
|
} |
| 132 |
|
} |
| 131 |
– |
} |
| 132 |
– |
} |
| 133 |
|
|
| 134 |
< |
template<typename T> void NPTxyz<T>::getVelScaleA(double sc[3], double vel[3]) { |
| 135 |
< |
matVecMul3( vScale, vel, sc ); |
| 136 |
< |
} |
| 134 |
> |
for(i=0;i<3;i++){ |
| 135 |
|
|
| 136 |
< |
template<typename T> void NPTxyz<T>::getVelScaleB(double sc[3], int index ){ |
| 139 |
< |
int j; |
| 140 |
< |
double myVel[3]; |
| 136 |
> |
// calculate the scaleFactors |
| 137 |
|
|
| 138 |
< |
for (j = 0; j < 3; j++) |
| 143 |
< |
myVel[j] = oldVel[3*index + j]; |
| 138 |
> |
scaleFactor = exp(dt*eta(i, i)); |
| 139 |
|
|
| 140 |
< |
matVecMul3( vScale, myVel, sc ); |
| 146 |
< |
} |
| 140 |
> |
scaleMat(i, i) = scaleFactor; |
| 141 |
|
|
| 142 |
< |
template<typename T> void NPTxyz<T>::getPosScale(double pos[3], double COM[3], |
| 143 |
< |
int index, double sc[3]){ |
| 144 |
< |
int j; |
| 145 |
< |
double rj[3]; |
| 142 |
> |
if (scaleMat(i, i) > bigScale) { |
| 143 |
> |
bigScale = scaleMat(i, i); |
| 144 |
> |
} |
| 145 |
> |
|
| 146 |
> |
if (scaleMat(i, i) < smallScale) { |
| 147 |
> |
smallScale = scaleMat(i, i); |
| 148 |
> |
} |
| 149 |
> |
} |
| 150 |
|
|
| 151 |
< |
for(j=0; j<3; j++) |
| 152 |
< |
rj[j] = ( oldPos[index*3+j] + pos[j]) / 2.0 - COM[j]; |
| 151 |
> |
if ((bigScale > 1.1) || (smallScale < 0.9)) { |
| 152 |
> |
sprintf( painCave.errMsg, |
| 153 |
> |
"NPTxyz error: Attempting a Box scaling of more than 10 percent.\n" |
| 154 |
> |
" Check your tauBarostat, as it is probably too small!\n\n" |
| 155 |
> |
" scaleMat = [%lf\t%lf\t%lf]\n" |
| 156 |
> |
" [%lf\t%lf\t%lf]\n" |
| 157 |
> |
" [%lf\t%lf\t%lf]\n", |
| 158 |
> |
scaleMat(0, 0),scaleMat(0, 1),scaleMat(0, 2), |
| 159 |
> |
scaleMat(1, 0),scaleMat(1, 1),scaleMat(1, 2), |
| 160 |
> |
scaleMat(2, 0),scaleMat(2, 1),scaleMat(2, 2)); |
| 161 |
> |
painCave.isFatal = 1; |
| 162 |
> |
simError(); |
| 163 |
> |
} else { |
| 164 |
|
|
| 165 |
< |
matVecMul3( eta, rj, sc ); |
| 166 |
< |
} |
| 167 |
< |
|
| 159 |
< |
template<typename T> void NPTxyz<T>::scaleSimBox( void ){ |
| 160 |
< |
|
| 161 |
< |
int i,j,k; |
| 162 |
< |
double scaleMat[3][3]; |
| 163 |
< |
double eta2ij, scaleFactor; |
| 164 |
< |
double bigScale, smallScale, offDiagMax; |
| 165 |
< |
double hm[3][3], hmnew[3][3]; |
| 166 |
< |
|
| 167 |
< |
|
| 168 |
< |
|
| 169 |
< |
// Scale the box after all the positions have been moved: |
| 170 |
< |
|
| 171 |
< |
// Use a taylor expansion for eta products: Hmat = Hmat . exp(dt * etaMat) |
| 172 |
< |
// Hmat = Hmat . ( Ident + dt * etaMat + dt^2 * etaMat*etaMat / 2) |
| 173 |
< |
|
| 174 |
< |
bigScale = 1.0; |
| 175 |
< |
smallScale = 1.0; |
| 176 |
< |
offDiagMax = 0.0; |
| 177 |
< |
|
| 178 |
< |
for(i=0; i<3; i++){ |
| 179 |
< |
for(j=0; j<3; j++){ |
| 180 |
< |
scaleMat[i][j] = 0.0; |
| 181 |
< |
if(i==j) scaleMat[i][j] = 1.0; |
| 165 |
> |
Mat3x3d hmat = currentSnapshot_->getHmat(); |
| 166 |
> |
hmat = hmat *scaleMat; |
| 167 |
> |
currentSnapshot_->setHmat(hmat); |
| 168 |
|
} |
| 169 |
|
} |
| 170 |
|
|
| 171 |
< |
for(i=0;i<3;i++){ |
| 172 |
< |
|
| 187 |
< |
// calculate the scaleFactors |
| 188 |
< |
|
| 189 |
< |
scaleFactor = exp(dt*eta[i][i]); |
| 190 |
< |
|
| 191 |
< |
scaleMat[i][i] = scaleFactor; |
| 192 |
< |
|
| 193 |
< |
if (scaleMat[i][i] > bigScale) bigScale = scaleMat[i][i]; |
| 194 |
< |
if (scaleMat[i][i] < smallScale) smallScale = scaleMat[i][i]; |
| 171 |
> |
void NPTxyz::loadEta() { |
| 172 |
> |
eta= currentSnapshot_->getEta(); |
| 173 |
|
} |
| 174 |
|
|
| 197 |
– |
// for(i=0; i<3; i++){ |
| 198 |
– |
// for(j=0; j<3; j++){ |
| 199 |
– |
|
| 200 |
– |
// // Calculate the matrix Product of the eta array (we only need |
| 201 |
– |
// // the ij element right now): |
| 202 |
– |
|
| 203 |
– |
// eta2ij = 0.0; |
| 204 |
– |
// for(k=0; k<3; k++){ |
| 205 |
– |
// eta2ij += eta[i][k] * eta[k][j]; |
| 206 |
– |
// } |
| 207 |
– |
|
| 208 |
– |
// scaleMat[i][j] = 0.0; |
| 209 |
– |
// // identity matrix (see above): |
| 210 |
– |
// if (i == j) scaleMat[i][j] = 1.0; |
| 211 |
– |
// // Taylor expansion for the exponential truncated at second order: |
| 212 |
– |
// scaleMat[i][j] += dt*eta[i][j] + 0.5*dt*dt*eta2ij; |
| 213 |
– |
|
| 214 |
– |
// if (i != j) |
| 215 |
– |
// if (fabs(scaleMat[i][j]) > offDiagMax) |
| 216 |
– |
// offDiagMax = fabs(scaleMat[i][j]); |
| 217 |
– |
// } |
| 218 |
– |
|
| 219 |
– |
// if (scaleMat[i][i] > bigScale) bigScale = scaleMat[i][i]; |
| 220 |
– |
// if (scaleMat[i][i] < smallScale) smallScale = scaleMat[i][i]; |
| 221 |
– |
// } |
| 222 |
– |
|
| 223 |
– |
if ((bigScale > 1.1) || (smallScale < 0.9)) { |
| 224 |
– |
sprintf( painCave.errMsg, |
| 225 |
– |
"NPTxyz error: Attempting a Box scaling of more than 10 percent.\n" |
| 226 |
– |
" Check your tauBarostat, as it is probably too small!\n\n" |
| 227 |
– |
" scaleMat = [%lf\t%lf\t%lf]\n" |
| 228 |
– |
" [%lf\t%lf\t%lf]\n" |
| 229 |
– |
" [%lf\t%lf\t%lf]\n", |
| 230 |
– |
scaleMat[0][0],scaleMat[0][1],scaleMat[0][2], |
| 231 |
– |
scaleMat[1][0],scaleMat[1][1],scaleMat[1][2], |
| 232 |
– |
scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]); |
| 233 |
– |
painCave.isFatal = 1; |
| 234 |
– |
simError(); |
| 235 |
– |
} else { |
| 236 |
– |
info->getBoxM(hm); |
| 237 |
– |
matMul3(hm, scaleMat, hmnew); |
| 238 |
– |
info->setBoxM(hmnew); |
| 239 |
– |
} |
| 175 |
|
} |
| 241 |
– |
|
| 242 |
– |
template<typename T> bool NPTxyz<T>::etaConverged() { |
| 243 |
– |
int i; |
| 244 |
– |
double diffEta, sumEta; |
| 245 |
– |
|
| 246 |
– |
sumEta = 0; |
| 247 |
– |
for(i = 0; i < 3; i++) |
| 248 |
– |
sumEta += pow(prevEta[i][i] - eta[i][i], 2); |
| 249 |
– |
|
| 250 |
– |
diffEta = sqrt( sumEta / 3.0 ); |
| 251 |
– |
|
| 252 |
– |
return ( diffEta <= etaTolerance ); |
| 253 |
– |
} |
| 254 |
– |
|
| 255 |
– |
template<typename T> double NPTxyz<T>::getConservedQuantity(void){ |
| 256 |
– |
|
| 257 |
– |
double conservedQuantity; |
| 258 |
– |
double totalEnergy; |
| 259 |
– |
double thermostat_kinetic; |
| 260 |
– |
double thermostat_potential; |
| 261 |
– |
double barostat_kinetic; |
| 262 |
– |
double barostat_potential; |
| 263 |
– |
double trEta; |
| 264 |
– |
double a[3][3], b[3][3]; |
| 265 |
– |
|
| 266 |
– |
totalEnergy = tStats->getTotalE(); |
| 267 |
– |
|
| 268 |
– |
thermostat_kinetic = fkBT * tt2 * chi * chi / |
| 269 |
– |
(2.0 * eConvert); |
| 270 |
– |
|
| 271 |
– |
thermostat_potential = fkBT* integralOfChidt / eConvert; |
| 272 |
– |
|
| 273 |
– |
transposeMat3(eta, a); |
| 274 |
– |
matMul3(a, eta, b); |
| 275 |
– |
trEta = matTrace3(b); |
| 276 |
– |
|
| 277 |
– |
barostat_kinetic = NkBT * tb2 * trEta / |
| 278 |
– |
(2.0 * eConvert); |
| 279 |
– |
|
| 280 |
– |
barostat_potential = (targetPressure * tStats->getVolume() / p_convert) / |
| 281 |
– |
eConvert; |
| 282 |
– |
|
| 283 |
– |
conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential + |
| 284 |
– |
barostat_kinetic + barostat_potential; |
| 285 |
– |
|
| 286 |
– |
// cout.width(8); |
| 287 |
– |
// cout.precision(8); |
| 288 |
– |
|
| 289 |
– |
// cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic << |
| 290 |
– |
// "\t" << thermostat_potential << "\t" << barostat_kinetic << |
| 291 |
– |
// "\t" << barostat_potential << "\t" << conservedQuantity << endl; |
| 292 |
– |
|
| 293 |
– |
return conservedQuantity; |
| 294 |
– |
|
| 295 |
– |
} |
| 296 |
– |
|
| 297 |
– |
template<typename T> string NPTxyz<T>::getAdditionalParameters(void){ |
| 298 |
– |
string parameters; |
| 299 |
– |
const int BUFFERSIZE = 2000; // size of the read buffer |
| 300 |
– |
char buffer[BUFFERSIZE]; |
| 301 |
– |
|
| 302 |
– |
sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt); |
| 303 |
– |
parameters += buffer; |
| 304 |
– |
|
| 305 |
– |
for(int i = 0; i < 3; i++){ |
| 306 |
– |
sprintf(buffer,"\t%G\t%G\t%G;", eta[i][0], eta[i][1], eta[i][2]); |
| 307 |
– |
parameters += buffer; |
| 308 |
– |
} |
| 309 |
– |
|
| 310 |
– |
return parameters; |
| 311 |
– |
|
| 312 |
– |
} |
