125 |
|
return total; |
126 |
|
} |
127 |
|
|
128 |
< |
int Thermo::getNDF(){ |
129 |
< |
int ndf_local, ndf; |
128 |
> |
double Thermo::getTemperature(){ |
129 |
> |
|
130 |
> |
const double kb = 1.9872179E-3; // boltzman's constant in kcal/(mol K) |
131 |
> |
double temperature; |
132 |
|
|
133 |
< |
ndf_local = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented |
134 |
< |
- entry_plug->n_constraints; |
133 |
> |
temperature = ( 2.0 * this->getKinetic() ) / ((double)entry_plug->ndf * kb ); |
134 |
> |
return temperature; |
135 |
> |
} |
136 |
|
|
137 |
< |
#ifdef IS_MPI |
135 |
< |
MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
136 |
< |
#else |
137 |
< |
ndf = ndf_local; |
138 |
< |
#endif |
137 |
> |
double Thermo::getEnthalpy() { |
138 |
|
|
139 |
< |
ndf = ndf - 3; |
139 |
> |
const double e_convert = 4.184E-4; // convert kcal/mol -> (amu A^2)/fs^2 |
140 |
> |
double u, p, v; |
141 |
> |
double press[3][3]; |
142 |
|
|
143 |
< |
return ndf; |
143 |
< |
} |
143 |
> |
u = this->getTotalE(); |
144 |
|
|
145 |
< |
int Thermo::getNDFraw() { |
146 |
< |
int ndfRaw_local, ndfRaw; |
145 |
> |
this->getPressureTensor(press); |
146 |
> |
p = (press[0][0] + press[1][1] + press[2][2]) / 3.0; |
147 |
|
|
148 |
< |
// Raw degrees of freedom that we have to set |
149 |
< |
ndfRaw_local = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented; |
150 |
< |
|
151 |
< |
#ifdef IS_MPI |
152 |
< |
MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
153 |
< |
#else |
154 |
< |
ndfRaw = ndfRaw_local; |
155 |
< |
#endif |
148 |
> |
v = this->getVolume(); |
149 |
|
|
150 |
< |
return ndfRaw; |
150 |
> |
return (u + (p*v)/e_convert); |
151 |
|
} |
152 |
|
|
153 |
+ |
double Thermo::getVolume() { |
154 |
|
|
155 |
< |
double Thermo::getTemperature(){ |
155 |
> |
return entry_plug->boxVol; |
156 |
> |
} |
157 |
|
|
158 |
< |
const double kb = 1.9872179E-3; // boltzman's constant in kcal/(mol K) |
159 |
< |
double temperature; |
158 |
> |
double Thermo::getPressure() { |
159 |
> |
|
160 |
> |
// Relies on the calculation of the full molecular pressure tensor |
161 |
|
|
162 |
< |
temperature = ( 2.0 * this->getKinetic() ) / ( (double)this->getNDF() * kb ); |
163 |
< |
return temperature; |
162 |
> |
const double p_convert = 1.63882576e8; |
163 |
> |
double press[3][3]; |
164 |
> |
double pressure; |
165 |
> |
|
166 |
> |
this->getPressureTensor(press); |
167 |
> |
|
168 |
> |
pressure = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0; |
169 |
> |
|
170 |
> |
return pressure; |
171 |
|
} |
172 |
|
|
173 |
< |
double Thermo::getPressure(){ |
174 |
< |
// returns pressure in units amu*fs^-2*Ang^-1 |
173 |
> |
|
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 |
178 |
|
|
179 |
< |
return 0.0; |
179 |
> |
const double e_convert = 4.184e-4; |
180 |
> |
|
181 |
> |
double molmass, volume; |
182 |
> |
double vcom[3]; |
183 |
> |
double p_local[9], p_global[9]; |
184 |
> |
int i, j, k, l, nMols; |
185 |
> |
Molecule* molecules; |
186 |
> |
|
187 |
> |
nMols = entry_plug->n_mol; |
188 |
> |
molecules = entry_plug->molecules; |
189 |
> |
//tau = entry_plug->tau; |
190 |
> |
|
191 |
> |
// use velocities of molecular centers of mass and molecular masses: |
192 |
> |
for (i=0; i < 9; i++) { |
193 |
> |
p_local[i] = 0.0; |
194 |
> |
p_global[i] = 0.0; |
195 |
> |
} |
196 |
> |
|
197 |
> |
for (i=0; i < nMols; i++) { |
198 |
> |
molmass = molecules[i].getCOMvel(vcom); |
199 |
> |
|
200 |
> |
p_local[0] += molmass * (vcom[0] * vcom[0]); |
201 |
> |
p_local[1] += molmass * (vcom[0] * vcom[1]); |
202 |
> |
p_local[2] += molmass * (vcom[0] * vcom[2]); |
203 |
> |
p_local[3] += molmass * (vcom[1] * vcom[0]); |
204 |
> |
p_local[4] += molmass * (vcom[1] * vcom[1]); |
205 |
> |
p_local[5] += molmass * (vcom[1] * vcom[2]); |
206 |
> |
p_local[6] += molmass * (vcom[2] * vcom[0]); |
207 |
> |
p_local[7] += molmass * (vcom[2] * vcom[1]); |
208 |
> |
p_local[8] += molmass * (vcom[2] * vcom[2]); |
209 |
> |
} |
210 |
> |
|
211 |
> |
// Get total for entire system from MPI. |
212 |
> |
|
213 |
> |
#ifdef IS_MPI |
214 |
> |
MPI_Allreduce(p_local,p_global,9,MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
215 |
> |
#else |
216 |
> |
for (i=0; i<9; i++) { |
217 |
> |
p_global[i] = p_local[i]; |
218 |
> |
} |
219 |
> |
#endif // is_mpi |
220 |
> |
|
221 |
> |
volume = entry_plug->boxVol; |
222 |
> |
|
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 |
|
|
232 |
|
void Thermo::velocitize() { |
240 |
|
const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc. |
241 |
|
double av2; |
242 |
|
double kebar; |
189 |
– |
int ndf, ndf_local; // number of degrees of freedom |
190 |
– |
int ndfRaw, ndfRaw_local; // the raw number of degrees of freedom |
243 |
|
int n_atoms; |
244 |
|
Atom** atoms; |
245 |
|
DirectionalAtom* dAtom; |
253 |
|
n_oriented = entry_plug->n_oriented; |
254 |
|
n_constraints = entry_plug->n_constraints; |
255 |
|
|
256 |
< |
kebar = kb * temperature * (double)this->getNDF() / |
257 |
< |
( 2.0 * (double)this->getNDFraw() ); |
256 |
> |
kebar = kb * temperature * (double)entry_plug->ndf / |
257 |
> |
( 2.0 * (double)entry_plug->ndfRaw ); |
258 |
|
|
259 |
|
for(vr = 0; vr < n_atoms; vr++){ |
260 |
|
|