| 1 |
< |
#include <math.h> |
| 2 |
< |
#include "primitives/Atom.hpp" |
| 3 |
< |
#include "primitives/SRI.hpp" |
| 4 |
< |
#include "primitives/AbstractClasses.hpp" |
| 1 |
> |
/* |
| 2 |
> |
* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
| 3 |
> |
* |
| 4 |
> |
* The University of Notre Dame grants you ("Licensee") a |
| 5 |
> |
* 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: |
| 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 |
| 19 |
> |
* notice, this list of conditions and the following disclaimer. |
| 20 |
> |
* |
| 21 |
> |
* 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 |
> |
* |
| 26 |
> |
* This software is provided "AS IS," without a warranty of any |
| 27 |
> |
* kind. All express or implied conditions, representations and |
| 28 |
> |
* warranties, including any implied warranty of merchantability, |
| 29 |
> |
* fitness for a particular purpose or non-infringement, are hereby |
| 30 |
> |
* excluded. The University of Notre Dame and its licensors shall not |
| 31 |
> |
* be liable for any damages suffered by licensee as a result of |
| 32 |
> |
* using, modifying or distributing the software or its |
| 33 |
> |
* derivatives. In no event will the University of Notre Dame or its |
| 34 |
> |
* licensors be liable for any lost revenue, profit or data, or for |
| 35 |
> |
* 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 |
| 38 |
> |
* University of Notre Dame has been advised of the possibility of |
| 39 |
> |
* such damages. |
| 40 |
> |
*/ |
| 41 |
> |
|
| 42 |
> |
#include "NPTi.hpp" |
| 43 |
|
#include "brains/SimInfo.hpp" |
| 6 |
– |
#include "UseTheForce/ForceFields.hpp" |
| 44 |
|
#include "brains/Thermo.hpp" |
| 45 |
< |
#include "io/ReadWrite.hpp" |
| 46 |
< |
#include "integrators/Integrator.hpp" |
| 45 |
> |
#include "integrators/NPT.hpp" |
| 46 |
> |
#include "primitives/Molecule.hpp" |
| 47 |
> |
#include "utils/OOPSEConstant.hpp" |
| 48 |
|
#include "utils/simError.h" |
| 49 |
|
|
| 50 |
< |
#ifdef IS_MPI |
| 13 |
< |
#include "brains/mpiSimulation.hpp" |
| 14 |
< |
#endif |
| 50 |
> |
namespace oopse { |
| 51 |
|
|
| 52 |
< |
// Basic isotropic thermostating and barostating via the Melchionna |
| 53 |
< |
// modification of the Hoover algorithm: |
| 54 |
< |
// |
| 55 |
< |
// Melchionna, S., Ciccotti, G., and Holian, B. L., 1993, |
| 56 |
< |
// Molec. Phys., 78, 533. |
| 57 |
< |
// |
| 58 |
< |
// and |
| 59 |
< |
// |
| 60 |
< |
// Hoover, W. G., 1986, Phys. Rev. A, 34, 2499. |
| 52 |
> |
// Basic isotropic thermostating and barostating via the Melchionna |
| 53 |
> |
// modification of the Hoover algorithm: |
| 54 |
> |
// |
| 55 |
> |
// Melchionna, S., Ciccotti, G., and Holian, B. L., 1993, |
| 56 |
> |
// Molec. Phys., 78, 533. |
| 57 |
> |
// |
| 58 |
> |
// and |
| 59 |
> |
// |
| 60 |
> |
// Hoover, W. G., 1986, Phys. Rev. A, 34, 2499. |
| 61 |
|
|
| 62 |
< |
template<typename T> NPTi<T>::NPTi ( SimInfo *theInfo, ForceFields* the_ff): |
| 27 |
< |
T( theInfo, the_ff ) |
| 28 |
< |
{ |
| 29 |
< |
GenericData* data; |
| 30 |
< |
DoubleArrayData * etaValue; |
| 31 |
< |
vector<double> etaArray; |
| 62 |
> |
NPTi::NPTi ( SimInfo *info) : NPT(info){ |
| 63 |
|
|
| 64 |
< |
eta = 0.0; |
| 34 |
< |
oldEta = 0.0; |
| 64 |
> |
} |
| 65 |
|
|
| 66 |
< |
if( theInfo->useInitXSstate ){ |
| 67 |
< |
// retrieve eta from simInfo if |
| 68 |
< |
data = info->getProperty(ETAVALUE_ID); |
| 69 |
< |
if(data){ |
| 40 |
< |
etaValue = dynamic_cast<DoubleArrayData*>(data); |
| 41 |
< |
|
| 42 |
< |
if(etaValue){ |
| 43 |
< |
etaArray = etaValue->getData(); |
| 44 |
< |
eta = etaArray[0]; |
| 45 |
< |
oldEta = eta; |
| 46 |
< |
} |
| 47 |
< |
} |
| 66 |
> |
void NPTi::evolveEtaA() { |
| 67 |
> |
eta += dt2 * ( instaVol * (instaPress - targetPressure) / |
| 68 |
> |
(OOPSEConstant::pressureConvert*NkBT*tb2)); |
| 69 |
> |
oldEta = eta; |
| 70 |
|
} |
| 49 |
– |
} |
| 71 |
|
|
| 72 |
< |
template<typename T> NPTi<T>::~NPTi() { |
| 52 |
< |
//nothing for now |
| 53 |
< |
} |
| 72 |
> |
void NPTi::evolveEtaB() { |
| 73 |
|
|
| 74 |
< |
template<typename T> void NPTi<T>::resetIntegrator() { |
| 75 |
< |
eta = 0.0; |
| 76 |
< |
T::resetIntegrator(); |
| 77 |
< |
} |
| 74 |
> |
prevEta = eta; |
| 75 |
> |
eta = oldEta + dt2 * ( instaVol * (instaPress - targetPressure) / |
| 76 |
> |
(OOPSEConstant::pressureConvert*NkBT*tb2)); |
| 77 |
> |
} |
| 78 |
|
|
| 79 |
< |
template<typename T> void NPTi<T>::evolveEtaA() { |
| 80 |
< |
eta += dt2 * ( instaVol * (instaPress - targetPressure) / |
| 81 |
< |
(p_convert*NkBT*tb2)); |
| 63 |
< |
oldEta = eta; |
| 64 |
< |
} |
| 79 |
> |
void NPTi::calcVelScale() { |
| 80 |
> |
vScale = chi + eta; |
| 81 |
> |
} |
| 82 |
|
|
| 83 |
< |
template<typename T> void NPTi<T>::evolveEtaB() { |
| 83 |
> |
void NPTi::getVelScaleA(Vector3d& sc, const Vector3d& vel) { |
| 84 |
> |
sc = vel * vScale; |
| 85 |
> |
} |
| 86 |
|
|
| 87 |
< |
prevEta = eta; |
| 88 |
< |
eta = oldEta + dt2 * ( instaVol * (instaPress - targetPressure) / |
| 89 |
< |
(p_convert*NkBT*tb2)); |
| 71 |
< |
} |
| 87 |
> |
void NPTi::getVelScaleB(Vector3d& sc, int index ){ |
| 88 |
> |
sc = oldVel[index] * vScale; |
| 89 |
> |
} |
| 90 |
|
|
| 73 |
– |
template<typename T> void NPTi<T>::calcVelScale(void) { |
| 74 |
– |
vScale = chi + eta; |
| 75 |
– |
} |
| 91 |
|
|
| 92 |
< |
template<typename T> void NPTi<T>::getVelScaleA(double sc[3], double vel[3]) { |
| 93 |
< |
int i; |
| 92 |
> |
void NPTi::getPosScale(const Vector3d& pos, const Vector3d& COM, |
| 93 |
> |
int index, Vector3d& sc){ |
| 94 |
> |
/**@todo*/ |
| 95 |
> |
sc = (oldPos[index] + pos)/(RealType)2.0 -COM; |
| 96 |
> |
sc *= eta; |
| 97 |
> |
} |
| 98 |
|
|
| 99 |
< |
for(i=0; i<3; i++) sc[i] = vel[i] * vScale; |
| 81 |
< |
} |
| 99 |
> |
void NPTi::scaleSimBox(){ |
| 100 |
|
|
| 101 |
< |
template<typename T> void NPTi<T>::getVelScaleB(double sc[3], int index ){ |
| 84 |
< |
int i; |
| 101 |
> |
RealType scaleFactor; |
| 102 |
|
|
| 103 |
< |
for(i=0; i<3; i++) sc[i] = oldVel[index*3 + i] * vScale; |
| 87 |
< |
} |
| 103 |
> |
scaleFactor = exp(dt*eta); |
| 104 |
|
|
| 105 |
+ |
if ((scaleFactor > 1.1) || (scaleFactor < 0.9)) { |
| 106 |
+ |
sprintf( painCave.errMsg, |
| 107 |
+ |
"NPTi error: Attempting a Box scaling of more than 10 percent" |
| 108 |
+ |
" check your tauBarostat, as it is probably too small!\n" |
| 109 |
+ |
" eta = %lf, scaleFactor = %lf\n", eta, scaleFactor |
| 110 |
+ |
); |
| 111 |
+ |
painCave.isFatal = 1; |
| 112 |
+ |
simError(); |
| 113 |
+ |
} else { |
| 114 |
+ |
Mat3x3d hmat = currentSnapshot_->getHmat(); |
| 115 |
+ |
hmat *= scaleFactor; |
| 116 |
+ |
currentSnapshot_->setHmat(hmat); |
| 117 |
+ |
} |
| 118 |
|
|
| 119 |
< |
template<typename T> void NPTi<T>::getPosScale(double pos[3], double COM[3], |
| 91 |
< |
int index, double sc[3]){ |
| 92 |
< |
int j; |
| 119 |
> |
} |
| 120 |
|
|
| 121 |
< |
for(j=0; j<3; j++) |
| 95 |
< |
sc[j] = ( oldPos[index*3+j] + pos[j]) / 2.0 - COM[j]; |
| 121 |
> |
bool NPTi::etaConverged() { |
| 122 |
|
|
| 123 |
< |
for(j=0; j<3; j++) |
| 98 |
< |
sc[j] *= eta; |
| 99 |
< |
} |
| 100 |
< |
|
| 101 |
< |
template<typename T> void NPTi<T>::scaleSimBox( void ){ |
| 102 |
< |
|
| 103 |
< |
double scaleFactor; |
| 104 |
< |
|
| 105 |
< |
scaleFactor = exp(dt*eta); |
| 106 |
< |
|
| 107 |
< |
if ((scaleFactor > 1.1) || (scaleFactor < 0.9)) { |
| 108 |
< |
sprintf( painCave.errMsg, |
| 109 |
< |
"NPTi error: Attempting a Box scaling of more than 10 percent" |
| 110 |
< |
" check your tauBarostat, as it is probably too small!\n" |
| 111 |
< |
" eta = %lf, scaleFactor = %lf\n", eta, scaleFactor |
| 112 |
< |
); |
| 113 |
< |
painCave.isFatal = 1; |
| 114 |
< |
simError(); |
| 115 |
< |
} else { |
| 116 |
< |
info->scaleBox(scaleFactor); |
| 123 |
> |
return ( fabs(prevEta - eta) <= etaTolerance ); |
| 124 |
|
} |
| 125 |
|
|
| 126 |
< |
} |
| 126 |
> |
RealType NPTi::calcConservedQuantity(){ |
| 127 |
|
|
| 128 |
< |
template<typename T> bool NPTi<T>::etaConverged() { |
| 128 |
> |
chi= currentSnapshot_->getChi(); |
| 129 |
> |
integralOfChidt = currentSnapshot_->getIntegralOfChiDt(); |
| 130 |
> |
loadEta(); |
| 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; |
| 135 |
|
|
| 136 |
< |
return ( fabs(prevEta - eta) <= etaTolerance ); |
| 137 |
< |
} |
| 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; |
| 140 |
> |
|
| 141 |
> |
RealType conservedQuantity; |
| 142 |
> |
RealType Energy; |
| 143 |
> |
RealType thermostat_kinetic; |
| 144 |
> |
RealType thermostat_potential; |
| 145 |
> |
RealType barostat_kinetic; |
| 146 |
> |
RealType barostat_potential; |
| 147 |
|
|
| 148 |
< |
template<typename T> double NPTi<T>::getConservedQuantity(void){ |
| 148 |
> |
Energy =thermo.getTotalE(); |
| 149 |
|
|
| 150 |
< |
double conservedQuantity; |
| 129 |
< |
double Energy; |
| 130 |
< |
double thermostat_kinetic; |
| 131 |
< |
double thermostat_potential; |
| 132 |
< |
double barostat_kinetic; |
| 133 |
< |
double barostat_potential; |
| 150 |
> |
thermostat_kinetic = fkBT* tt2 * chi * chi / (2.0 * OOPSEConstant::energyConvert); |
| 151 |
|
|
| 152 |
< |
Energy = tStats->getTotalE(); |
| 152 |
> |
thermostat_potential = fkBT* integralOfChidt / OOPSEConstant::energyConvert; |
| 153 |
|
|
| 137 |
– |
thermostat_kinetic = fkBT* tt2 * chi * chi / |
| 138 |
– |
(2.0 * eConvert); |
| 154 |
|
|
| 155 |
< |
thermostat_potential = fkBT* integralOfChidt / eConvert; |
| 155 |
> |
barostat_kinetic = 3.0 * NkBT * tb2 * eta * eta /(2.0 * OOPSEConstant::energyConvert); |
| 156 |
|
|
| 157 |
+ |
barostat_potential = (targetPressure * thermo.getVolume() / OOPSEConstant::pressureConvert) / |
| 158 |
+ |
OOPSEConstant::energyConvert; |
| 159 |
|
|
| 160 |
< |
barostat_kinetic = 3.0 * NkBT * tb2 * eta * eta / |
| 161 |
< |
(2.0 * eConvert); |
| 160 |
> |
conservedQuantity = Energy + thermostat_kinetic + thermostat_potential + |
| 161 |
> |
barostat_kinetic + barostat_potential; |
| 162 |
> |
|
| 163 |
> |
return conservedQuantity; |
| 164 |
> |
} |
| 165 |
|
|
| 166 |
< |
barostat_potential = (targetPressure * tStats->getVolume() / p_convert) / |
| 167 |
< |
eConvert; |
| 166 |
> |
void NPTi::loadEta() { |
| 167 |
> |
Mat3x3d etaMat = currentSnapshot_->getEta(); |
| 168 |
> |
eta = etaMat(0,0); |
| 169 |
> |
//if (fabs(etaMat(1,1) - eta) >= oopse::epsilon || fabs(etaMat(1,1) - eta) >= oopse::epsilon || !etaMat.isDiagonal()) { |
| 170 |
> |
// sprintf( painCave.errMsg, |
| 171 |
> |
// "NPTi error: the diagonal elements of eta matrix are not the same or etaMat is not a diagonal matrix"); |
| 172 |
> |
// painCave.isFatal = 1; |
| 173 |
> |
// simError(); |
| 174 |
> |
//} |
| 175 |
> |
} |
| 176 |
|
|
| 177 |
< |
conservedQuantity = Energy + thermostat_kinetic + thermostat_potential + |
| 178 |
< |
barostat_kinetic + barostat_potential; |
| 179 |
< |
|
| 180 |
< |
// cout.width(8); |
| 181 |
< |
// cout.precision(8); |
| 182 |
< |
|
| 183 |
< |
// cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic << |
| 156 |
< |
// "\t" << thermostat_potential << "\t" << barostat_kinetic << |
| 157 |
< |
// "\t" << barostat_potential << "\t" << conservedQuantity << endl; |
| 158 |
< |
return conservedQuantity; |
| 177 |
> |
void NPTi::saveEta() { |
| 178 |
> |
Mat3x3d etaMat(0.0); |
| 179 |
> |
etaMat(0, 0) = eta; |
| 180 |
> |
etaMat(1, 1) = eta; |
| 181 |
> |
etaMat(2, 2) = eta; |
| 182 |
> |
currentSnapshot_->setEta(etaMat); |
| 183 |
> |
} |
| 184 |
|
} |
| 160 |
– |
|
| 161 |
– |
template<typename T> string NPTi<T>::getAdditionalParameters(void){ |
| 162 |
– |
string parameters; |
| 163 |
– |
const int BUFFERSIZE = 2000; // size of the read buffer |
| 164 |
– |
char buffer[BUFFERSIZE]; |
| 165 |
– |
|
| 166 |
– |
sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt); |
| 167 |
– |
parameters += buffer; |
| 168 |
– |
|
| 169 |
– |
sprintf(buffer,"\t%G\t0\t0;", eta); |
| 170 |
– |
parameters += buffer; |
| 171 |
– |
|
| 172 |
– |
sprintf(buffer,"\t0\t%G\t0;", eta); |
| 173 |
– |
parameters += buffer; |
| 174 |
– |
|
| 175 |
– |
sprintf(buffer,"\t0\t0\t%G;", eta); |
| 176 |
– |
parameters += buffer; |
| 177 |
– |
|
| 178 |
– |
return parameters; |
| 179 |
– |
|
| 180 |
– |
} |
