1 |
|
#include <math.h> |
2 |
+ |
|
3 |
|
#include "Atom.hpp" |
4 |
|
#include "SRI.hpp" |
5 |
|
#include "AbstractClasses.hpp" |
40 |
|
} |
41 |
|
} |
42 |
|
|
43 |
+ |
|
44 |
+ |
if( theInfo->useInitXSstate ){ |
45 |
|
// retrieve eta array from simInfo if it exists |
46 |
|
data = info->getProperty(ETAVALUE_ID); |
47 |
|
if(data){ |
48 |
|
etaValue = dynamic_cast<DoubleArrayData*>(data); |
49 |
< |
|
49 |
> |
|
50 |
|
if(etaValue){ |
51 |
< |
etaArray = etaValue->getData(); |
52 |
< |
|
53 |
< |
for(i = 0; i < 3; i++){ |
54 |
< |
for (j = 0; j < 3; j++){ |
55 |
< |
eta[i][j] = etaArray[3*i+j]; |
56 |
< |
oldEta[i][j] = eta[i][j]; |
57 |
< |
} |
58 |
< |
} |
56 |
< |
|
51 |
> |
etaArray = etaValue->getData(); |
52 |
> |
|
53 |
> |
for(i = 0; i < 3; i++){ |
54 |
> |
for (j = 0; j < 3; j++){ |
55 |
> |
eta[i][j] = etaArray[3*i+j]; |
56 |
> |
oldEta[i][j] = eta[i][j]; |
57 |
> |
} |
58 |
> |
} |
59 |
|
} |
60 |
|
} |
61 |
+ |
} |
62 |
|
|
63 |
|
} |
64 |
|
|
117 |
|
} |
118 |
|
} |
119 |
|
|
120 |
< |
template<typename T> void NPTf<T>::getVelScaleA(double sc[3], double vel[3]) { |
120 |
> |
template<typename T> void NPTf<T>::calcVelScale(void){ |
121 |
|
int i,j; |
119 |
– |
double vScale[3][3]; |
122 |
|
|
123 |
|
for (i = 0; i < 3; i++ ) { |
124 |
|
for (j = 0; j < 3; j++ ) { |
129 |
|
} |
130 |
|
} |
131 |
|
} |
132 |
+ |
} |
133 |
|
|
134 |
+ |
template<typename T> void NPTf<T>::getVelScaleA(double sc[3], double vel[3]) { |
135 |
+ |
|
136 |
|
info->matVecMul3( vScale, vel, sc ); |
137 |
|
} |
138 |
|
|
139 |
|
template<typename T> void NPTf<T>::getVelScaleB(double sc[3], int index ){ |
140 |
< |
int i,j; |
140 |
> |
int j; |
141 |
|
double myVel[3]; |
142 |
|
double vScale[3][3]; |
138 |
– |
|
139 |
– |
for (i = 0; i < 3; i++ ) { |
140 |
– |
for (j = 0; j < 3; j++ ) { |
141 |
– |
vScale[i][j] = eta[i][j]; |
143 |
|
|
143 |
– |
if (i == j) { |
144 |
– |
vScale[i][j] += chi; |
145 |
– |
} |
146 |
– |
} |
147 |
– |
} |
148 |
– |
|
144 |
|
for (j = 0; j < 3; j++) |
145 |
|
myVel[j] = oldVel[3*index + j]; |
146 |
|
|
203 |
|
if (scaleMat[i][i] < smallScale) smallScale = scaleMat[i][i]; |
204 |
|
} |
205 |
|
|
206 |
< |
if ((bigScale > 1.1) || (smallScale < 0.9)) { |
206 |
> |
if ((bigScale > 1.01) || (smallScale < 0.99)) { |
207 |
|
sprintf( painCave.errMsg, |
208 |
< |
"NPTf error: Attempting a Box scaling of more than 10 percent.\n" |
208 |
> |
"NPTf error: Attempting a Box scaling of more than 1 percent.\n" |
209 |
|
" Check your tauBarostat, as it is probably too small!\n\n" |
210 |
|
" scaleMat = [%lf\t%lf\t%lf]\n" |
211 |
|
" [%lf\t%lf\t%lf]\n" |
215 |
|
scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]); |
216 |
|
painCave.isFatal = 1; |
217 |
|
simError(); |
218 |
< |
} else if (offDiagMax > 0.1) { |
218 |
> |
} else if (offDiagMax > 0.01) { |
219 |
|
sprintf( painCave.errMsg, |
220 |
< |
"NPTf error: Attempting an off-diagonal Box scaling of more than 10 percent.\n" |
220 |
> |
"NPTf error: Attempting an off-diagonal Box scaling of more than 1 percent.\n" |
221 |
|
" Check your tauBarostat, as it is probably too small!\n\n" |
222 |
|
" scaleMat = [%lf\t%lf\t%lf]\n" |
223 |
|
" [%lf\t%lf\t%lf]\n" |
278 |
|
conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential + |
279 |
|
barostat_kinetic + barostat_potential; |
280 |
|
|
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 |
– |
|
281 |
|
return conservedQuantity; |
282 |
|
|
283 |
|
} |
287 |
|
const int BUFFERSIZE = 2000; // size of the read buffer |
288 |
|
char buffer[BUFFERSIZE]; |
289 |
|
|
290 |
< |
sprintf(buffer,"\t%f\t%f;", chi, integralOfChidt); |
290 |
> |
sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt); |
291 |
|
parameters += buffer; |
292 |
|
|
293 |
|
for(int i = 0; i < 3; i++){ |
294 |
< |
sprintf(buffer,"\t%g\t%g\t%g;", eta[3*i], eta[3*i+1], eta[3*i+2]); |
294 |
> |
sprintf(buffer,"\t%G\t%G\t%G;", eta[i][0], eta[i][1], eta[i][2]); |
295 |
|
parameters += buffer; |
296 |
|
} |
297 |
|
|