132 |
|
|
133 |
|
temperature = ( 2.0 * this->getKinetic() ) / ((double)entry_plug->ndf * kb ); |
134 |
|
return temperature; |
135 |
+ |
} |
136 |
+ |
|
137 |
+ |
double Thermo::getEnthalpy() { |
138 |
+ |
|
139 |
+ |
const double e_convert = 4.184E-4; // convert kcal/mol -> (amu A^2)/fs^2 |
140 |
+ |
double u, p, v; |
141 |
+ |
double press[9]; |
142 |
+ |
|
143 |
+ |
u = this->getTotalE(); |
144 |
+ |
|
145 |
+ |
this->getPressureTensor(press); |
146 |
+ |
p = (press[0] + press[4] + press[8]) / 3.0; |
147 |
+ |
|
148 |
+ |
v = this->getVolume(); |
149 |
+ |
|
150 |
+ |
return (u + (p*v)/e_convert); |
151 |
+ |
} |
152 |
+ |
|
153 |
+ |
double Thermo::getVolume() { |
154 |
+ |
|
155 |
+ |
double volume; |
156 |
+ |
double Hmat[9]; |
157 |
+ |
|
158 |
+ |
entry_plug->getBoxM(Hmat); |
159 |
+ |
|
160 |
+ |
// volume = h1 (dot) h2 (cross) h3 |
161 |
+ |
|
162 |
+ |
volume = Hmat[0] * ( (Hmat[4]*Hmat[8]) - (Hmat[7]*Hmat[5]) ) |
163 |
+ |
+ Hmat[1] * ( (Hmat[5]*Hmat[6]) - (Hmat[8]*Hmat[3]) ) |
164 |
+ |
+ Hmat[2] * ( (Hmat[3]*Hmat[7]) - (Hmat[6]*Hmat[4]) ); |
165 |
+ |
|
166 |
+ |
return volume; |
167 |
|
} |
168 |
|
|
169 |
|
double Thermo::getPressure() { |
170 |
< |
// returns the pressure in units of atm |
170 |
> |
|
171 |
|
// Relies on the calculation of the full molecular pressure tensor |
172 |
|
|
173 |
|
const double p_convert = 1.63882576e8; |
193 |
|
double vcom[3]; |
194 |
|
double p_local[9], p_global[9]; |
195 |
|
double theBox[3]; |
196 |
< |
double* tau; |
196 |
> |
//double* tau; |
197 |
|
int i, nMols; |
198 |
|
Molecule* molecules; |
199 |
|
|
200 |
|
nMols = entry_plug->n_mol; |
201 |
|
molecules = entry_plug->molecules; |
202 |
< |
tau = entry_plug->tau; |
202 |
> |
//tau = entry_plug->tau; |
203 |
|
|
204 |
|
// use velocities of molecular centers of mass and molecular masses: |
205 |
|
for (i=0; i < 9; i++) { |
231 |
|
} |
232 |
|
#endif // is_mpi |
233 |
|
|
234 |
< |
entry_plug->getBox(theBox); |
234 |
> |
volume = entry_plug->boxVol; |
235 |
|
|
204 |
– |
volume = theBox[0] * theBox[1] * theBox[2]; |
205 |
– |
|
236 |
|
for(i=0; i<9; i++) { |
237 |
< |
press[i] = (p_global[i] - tau[i]*e_convert) / volume; |
237 |
> |
press[i] = (p_global[i] - entry_plug->tau[i]*e_convert) / volume; |
238 |
|
} |
239 |
|
} |
240 |
|
|