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 |
> |
return entry_plug->boxVol; |
155 |
> |
} |
156 |
> |
|
157 |
> |
double Thermo::getPressure() { |
158 |
> |
// returns the pressure in units of atm |
159 |
> |
// Relies on the calculation of the full molecular pressure tensor |
160 |
> |
|
161 |
> |
const double p_convert = 1.63882576e8; |
162 |
> |
double press[9]; |
163 |
> |
double pressure; |
164 |
> |
|
165 |
> |
this->getPressureTensor(press); |
166 |
> |
|
167 |
> |
pressure = p_convert * (press[0] + press[4] + press[8]) / 3.0; |
168 |
> |
|
169 |
> |
return pressure; |
170 |
> |
} |
171 |
> |
|
172 |
> |
|
173 |
> |
void Thermo::getPressureTensor(double press[9]){ |
174 |
> |
// returns pressure tensor in units amu*fs^-2*Ang^-1 |
175 |
|
// routine derived via viral theorem description in: |
176 |
|
// Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322 |
177 |
|
|
178 |
< |
const double convert = 4.184e-4; |
179 |
< |
double molmass; |
180 |
< |
double vcom[3]; |
181 |
< |
double p_local, p_sum, p_mol, virial; |
178 |
> |
const double e_convert = 4.184e-4; |
179 |
> |
|
180 |
> |
double molmass, volume; |
181 |
> |
double vcom[3]; |
182 |
> |
double p_local[9], p_global[9]; |
183 |
|
double theBox[3]; |
184 |
< |
double* tau; |
184 |
> |
//double* tau; |
185 |
|
int i, nMols; |
186 |
|
Molecule* molecules; |
187 |
|
|
188 |
|
nMols = entry_plug->n_mol; |
189 |
|
molecules = entry_plug->molecules; |
190 |
< |
tau = entry_plug->tau; |
190 |
> |
//tau = entry_plug->tau; |
191 |
|
|
192 |
|
// use velocities of molecular centers of mass and molecular masses: |
193 |
< |
p_local = 0.0; |
193 |
> |
for (i=0; i < 9; i++) { |
194 |
> |
p_local[i] = 0.0; |
195 |
> |
p_global[i] = 0.0; |
196 |
> |
} |
197 |
|
|
198 |
|
for (i=0; i < nMols; i++) { |
199 |
|
molmass = molecules[i].getCOMvel(vcom); |
200 |
< |
p_local += (vcom[0]*vcom[0] + vcom[1]*vcom[1] + vcom[2]*vcom[2]) * molmass; |
200 |
> |
|
201 |
> |
p_local[0] += molmass * (vcom[0] * vcom[0]); |
202 |
> |
p_local[1] += molmass * (vcom[0] * vcom[1]); |
203 |
> |
p_local[2] += molmass * (vcom[0] * vcom[2]); |
204 |
> |
p_local[3] += molmass * (vcom[1] * vcom[0]); |
205 |
> |
p_local[4] += molmass * (vcom[1] * vcom[1]); |
206 |
> |
p_local[5] += molmass * (vcom[1] * vcom[2]); |
207 |
> |
p_local[6] += molmass * (vcom[2] * vcom[0]); |
208 |
> |
p_local[7] += molmass * (vcom[2] * vcom[1]); |
209 |
> |
p_local[8] += molmass * (vcom[2] * vcom[2]); |
210 |
|
} |
211 |
|
|
212 |
|
// Get total for entire system from MPI. |
213 |
+ |
|
214 |
|
#ifdef IS_MPI |
215 |
< |
MPI_Allreduce(&p_local,&p_sum,1,MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
215 |
> |
MPI_Allreduce(p_local,p_global,9,MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
216 |
|
#else |
217 |
< |
p_sum = p_local; |
217 |
> |
for (i=0; i<9; i++) { |
218 |
> |
p_global[i] = p_local[i]; |
219 |
> |
} |
220 |
|
#endif // is_mpi |
221 |
|
|
222 |
< |
virial = tau[0] + tau[4] + tau[8]; |
171 |
< |
entry_plug->getBox(theBox); |
222 |
> |
volume = entry_plug->boxVol; |
223 |
|
|
224 |
< |
p_mol = (p_sum - virial*convert) / (3.0 * theBox[0] * theBox[1]* theBox[2]); |
225 |
< |
|
226 |
< |
return p_mol; |
224 |
> |
for(i=0; i<9; i++) { |
225 |
> |
press[i] = (p_global[i] - entry_plug->tau[i]*e_convert) / volume; |
226 |
> |
} |
227 |
|
} |
228 |
|
|
229 |
|
void Thermo::velocitize() { |