134 |
|
return temperature; |
135 |
|
} |
136 |
|
|
137 |
< |
double Thermo::getPressure(){ |
138 |
< |
// returns pressure in units amu*fs^-2*Ang^-1 |
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 |
> |
|
171 |
> |
// Relies on the calculation of the full molecular pressure tensor |
172 |
> |
|
173 |
> |
const double p_convert = 1.63882576e8; |
174 |
> |
double press[9]; |
175 |
> |
double pressure; |
176 |
> |
|
177 |
> |
this->getPressureTensor(press); |
178 |
> |
|
179 |
> |
pressure = p_convert * (press[0] + press[4] + press[8]) / 3.0; |
180 |
> |
|
181 |
> |
return pressure; |
182 |
> |
} |
183 |
> |
|
184 |
> |
|
185 |
> |
void Thermo::getPressureTensor(double press[9]){ |
186 |
> |
// returns pressure tensor in units amu*fs^-2*Ang^-1 |
187 |
|
// routine derived via viral theorem description in: |
188 |
|
// Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322 |
189 |
|
|
190 |
< |
return 0.0; |
190 |
> |
const double e_convert = 4.184e-4; |
191 |
> |
|
192 |
> |
double molmass, volume; |
193 |
> |
double vcom[3]; |
194 |
> |
double p_local[9], p_global[9]; |
195 |
> |
double theBox[3]; |
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; |
203 |
> |
|
204 |
> |
// use velocities of molecular centers of mass and molecular masses: |
205 |
> |
for (i=0; i < 9; i++) { |
206 |
> |
p_local[i] = 0.0; |
207 |
> |
p_global[i] = 0.0; |
208 |
> |
} |
209 |
> |
|
210 |
> |
for (i=0; i < nMols; i++) { |
211 |
> |
molmass = molecules[i].getCOMvel(vcom); |
212 |
> |
|
213 |
> |
p_local[0] += molmass * (vcom[0] * vcom[0]); |
214 |
> |
p_local[1] += molmass * (vcom[0] * vcom[1]); |
215 |
> |
p_local[2] += molmass * (vcom[0] * vcom[2]); |
216 |
> |
p_local[3] += molmass * (vcom[1] * vcom[0]); |
217 |
> |
p_local[4] += molmass * (vcom[1] * vcom[1]); |
218 |
> |
p_local[5] += molmass * (vcom[1] * vcom[2]); |
219 |
> |
p_local[6] += molmass * (vcom[2] * vcom[0]); |
220 |
> |
p_local[7] += molmass * (vcom[2] * vcom[1]); |
221 |
> |
p_local[8] += molmass * (vcom[2] * vcom[2]); |
222 |
> |
} |
223 |
> |
|
224 |
> |
// Get total for entire system from MPI. |
225 |
> |
|
226 |
> |
#ifdef IS_MPI |
227 |
> |
MPI_Allreduce(p_local,p_global,9,MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
228 |
> |
#else |
229 |
> |
for (i=0; i<9; i++) { |
230 |
> |
p_global[i] = p_local[i]; |
231 |
> |
} |
232 |
> |
#endif // is_mpi |
233 |
> |
|
234 |
> |
volume = entry_plug->boxVol; |
235 |
> |
|
236 |
> |
for(i=0; i<9; i++) { |
237 |
> |
press[i] = (p_global[i] - entry_plug->tau[i]*e_convert) / volume; |
238 |
> |
} |
239 |
|
} |
240 |
|
|
241 |
|
void Thermo::velocitize() { |