138 |
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|
139 |
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const double e_convert = 4.184E-4; // convert kcal/mol -> (amu A^2)/fs^2 |
140 |
|
double u, p, v; |
141 |
< |
double press[9]; |
141 |
> |
double press[3][3]; |
142 |
|
|
143 |
|
u = this->getTotalE(); |
144 |
|
|
145 |
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this->getPressureTensor(press); |
146 |
< |
p = (press[0] + press[4] + press[8]) / 3.0; |
146 |
> |
p = (press[0][0] + press[1][1] + press[2][2]) / 3.0; |
147 |
|
|
148 |
|
v = this->getVolume(); |
149 |
|
|
160 |
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// Relies on the calculation of the full molecular pressure tensor |
161 |
|
|
162 |
|
const double p_convert = 1.63882576e8; |
163 |
< |
double press[9]; |
163 |
> |
double press[3][3]; |
164 |
|
double pressure; |
165 |
|
|
166 |
|
this->getPressureTensor(press); |
167 |
|
|
168 |
< |
pressure = p_convert * (press[0] + press[4] + press[8]) / 3.0; |
168 |
> |
pressure = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0; |
169 |
|
|
170 |
|
return pressure; |
171 |
|
} |
172 |
|
|
173 |
|
|
174 |
< |
void Thermo::getPressureTensor(double press[9]){ |
174 |
> |
void Thermo::getPressureTensor(double press[3][3]){ |
175 |
|
// returns pressure tensor in units amu*fs^-2*Ang^-1 |
176 |
|
// routine derived via viral theorem description in: |
177 |
|
// Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322 |
181 |
|
double molmass, volume; |
182 |
|
double vcom[3]; |
183 |
|
double p_local[9], p_global[9]; |
184 |
< |
double theBox[3]; |
185 |
< |
//double* tau; |
186 |
< |
int i, nMols; |
184 |
> |
int i, j, k, l, nMols; |
185 |
|
Molecule* molecules; |
186 |
|
|
187 |
|
nMols = entry_plug->n_mol; |
220 |
|
|
221 |
|
volume = entry_plug->boxVol; |
222 |
|
|
223 |
< |
for(i=0; i<9; i++) { |
224 |
< |
press[i] = (p_global[i] - entry_plug->tau[i]*e_convert) / volume; |
223 |
> |
for(i = 0; i < 3; i++) { |
224 |
> |
for (j = 0; j < 3; j++) { |
225 |
> |
k = 3*i + j; |
226 |
> |
l = 3*j + i; |
227 |
> |
press[i][j] = (p_global[k] - entry_plug->tau[l]*e_convert) / volume; |
228 |
> |
} |
229 |
|
} |
230 |
|
} |
231 |
|
|