| 1 |
+ |
#include <stdlib.h> |
| 2 |
|
#include <math.h> |
| 3 |
+ |
#include <string.h> |
| 4 |
+ |
|
| 5 |
|
#include "Atom.hpp" |
| 6 |
|
#include "SRI.hpp" |
| 7 |
|
#include "AbstractClasses.hpp" |
| 27 |
|
// Hoover, W. G., 1986, Phys. Rev. A, 34, 2499. |
| 28 |
|
|
| 29 |
|
NPTf::NPTf ( SimInfo *theInfo, ForceFields* the_ff): |
| 30 |
< |
Integrator( theInfo, the_ff ) |
| 30 |
> |
NPT( theInfo, the_ff ) |
| 31 |
|
{ |
| 32 |
|
GenericData* data; |
| 33 |
< |
DoubleArrayData * etaValue; |
| 31 |
< |
vector<double> etaArray; |
| 33 |
> |
double *etaArray; |
| 34 |
|
int i,j; |
| 35 |
|
|
| 36 |
|
for(i = 0; i < 3; i++){ |
| 41 |
|
} |
| 42 |
|
} |
| 43 |
|
|
| 44 |
< |
// retrieve eta array from simInfo if it exists |
| 45 |
< |
data = info->getProperty(ETAVALUE_ID); |
| 46 |
< |
if(data){ |
| 47 |
< |
etaValue = dynamic_cast<DoubleArrayData*>(data); |
| 48 |
< |
|
| 49 |
< |
if(etaValue){ |
| 50 |
< |
etaArray = etaValue->getData(); |
| 51 |
< |
|
| 52 |
< |
for(i = 0; i < 3; i++){ |
| 53 |
< |
for (j = 0; j < 3; j++){ |
| 54 |
< |
eta[i][j] = etaArray[3*i+j]; |
| 55 |
< |
oldEta[i][j] = eta[i][j]; |
| 56 |
< |
} |
| 57 |
< |
} |
| 58 |
< |
|
| 57 |
< |
} |
| 44 |
> |
// retrieve eta array from simInfo if it exists |
| 45 |
> |
data = info->getProperty(ETAVALUE_ID); |
| 46 |
> |
if(data != NULL){ |
| 47 |
> |
|
| 48 |
> |
int test = data->getDarray(etaArray); |
| 49 |
> |
|
| 50 |
> |
if( test == 9 ){ |
| 51 |
> |
|
| 52 |
> |
for(i = 0; i < 3; i++){ |
| 53 |
> |
for (j = 0; j < 3; j++){ |
| 54 |
> |
eta[i][j] = etaArray[3*i+j]; |
| 55 |
> |
oldEta[i][j] = eta[i][j]; |
| 56 |
> |
} |
| 57 |
> |
} |
| 58 |
> |
delete[] etaArray; |
| 59 |
|
} |
| 60 |
< |
|
| 60 |
> |
else |
| 61 |
> |
std::cerr << "NPTf error: etaArray is not length 9 (actual = " << test |
| 62 |
> |
<< ").\n" |
| 63 |
> |
<< " Simulation wil proceed with eta = 0;\n"; |
| 64 |
> |
} |
| 65 |
|
} |
| 66 |
|
|
| 67 |
|
NPTf::~NPTf() { |
| 77 |
|
for (j = 0; j < 3; j++) |
| 78 |
|
eta[i][j] = 0.0; |
| 79 |
|
|
| 80 |
< |
Integrator::resetIntegrator(); |
| 80 |
> |
NPT::resetIntegrator(); |
| 81 |
|
} |
| 82 |
|
|
| 83 |
|
void NPTf::evolveEtaA() { |
| 141 |
|
double myVel[3]; |
| 142 |
|
double vScale[3][3]; |
| 143 |
|
|
| 144 |
+ |
// std::cerr << "velScaleB chi = " << chi << "\n"; |
| 145 |
+ |
|
| 146 |
|
for (i = 0; i < 3; i++ ) { |
| 147 |
|
for (j = 0; j < 3; j++ ) { |
| 148 |
|
vScale[i][j] = eta[i][j]; |
| 156 |
|
for (j = 0; j < 3; j++) |
| 157 |
|
myVel[j] = oldVel[3*index + j]; |
| 158 |
|
|
| 159 |
+ |
// std::cerr << "velScaleB = \n" |
| 160 |
+ |
// << "[ " << vScale[0][0] << " , " << vScale[0][1] << " , " << vScale[0][2] << "]\n" |
| 161 |
+ |
// << "[ " << vScale[1][0] << " , " << vScale[1][1] << " , " << vScale[1][2] << "]\n" |
| 162 |
+ |
// << "[ " << vScale[2][0] << " , " << vScale[2][1] << " , " << vScale[2][2] << "]\n\n"; |
| 163 |
+ |
|
| 164 |
+ |
|
| 165 |
+ |
// std::cerr << "myVel " << index << " in => " |
| 166 |
+ |
// << myVel[0] << ", " << myVel[1] << ", " << myVel[2] << "\n"; |
| 167 |
+ |
|
| 168 |
|
info->matVecMul3( vScale, myVel, sc ); |
| 169 |
+ |
|
| 170 |
+ |
// std::cerr << "sc " << index << " out => " |
| 171 |
+ |
// << sc[0] << ", " << sc[1] << ", " << sc[2] << "\n"; |
| 172 |
|
} |
| 173 |
|
|
| 174 |
|
void NPTf::getPosScale(double pos[3], double COM[3], |
| 313 |
|
|
| 314 |
|
} |
| 315 |
|
|
| 316 |
< |
string NPTf::getAdditionalParameters(void){ |
| 298 |
< |
string parameters; |
| 299 |
< |
const int BUFFERSIZE = 2000; // size of the read buffer |
| 300 |
< |
char buffer[BUFFERSIZE]; |
| 316 |
> |
char* NPTf::getAdditionalParameters(void){ |
| 317 |
|
|
| 318 |
< |
sprintf(buffer,"\t%lf\t%lf;", chi, integralOfChidt); |
| 319 |
< |
parameters += buffer; |
| 318 |
> |
sprintf(addParamBuffer, |
| 319 |
> |
"\t%G\t%G;" |
| 320 |
> |
"\t%G\t%G\t%G;" |
| 321 |
> |
"\t%G\t%G\t%G;" |
| 322 |
> |
"\t%G\t%G\t%G;", |
| 323 |
> |
chi, integralOfChidt, |
| 324 |
> |
eta[0][0], eta[0][1], eta[0][2], |
| 325 |
> |
eta[1][0], eta[1][1], eta[1][2], |
| 326 |
> |
eta[2][0], eta[2][1], eta[2][2] |
| 327 |
> |
); |
| 328 |
|
|
| 329 |
< |
for(int i = 0; i < 3; i++){ |
| 306 |
< |
sprintf(buffer,"\t%lf\t%lf\t%lf;", eta[3*i], eta[3*i+1], eta[3*i+2]); |
| 307 |
< |
parameters += buffer; |
| 308 |
< |
} |
| 309 |
< |
|
| 310 |
< |
return parameters; |
| 311 |
< |
|
| 329 |
> |
return addParamBuffer; |
| 330 |
|
} |
