125 |
|
return total; |
126 |
|
} |
127 |
|
|
128 |
– |
int Thermo::getNDF(){ |
129 |
– |
int ndf_local, ndf; |
130 |
– |
|
131 |
– |
ndf_local = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented |
132 |
– |
- entry_plug->n_constraints; |
133 |
– |
|
134 |
– |
#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 |
139 |
– |
|
140 |
– |
ndf = ndf - 3; |
141 |
– |
|
142 |
– |
return ndf; |
143 |
– |
} |
144 |
– |
|
145 |
– |
int Thermo::getNDFraw() { |
146 |
– |
int ndfRaw_local, ndfRaw; |
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 |
156 |
– |
|
157 |
– |
return ndfRaw; |
158 |
– |
} |
159 |
– |
|
160 |
– |
|
128 |
|
double Thermo::getTemperature(){ |
129 |
|
|
130 |
|
const double kb = 1.9872179E-3; // boltzman's constant in kcal/(mol K) |
131 |
|
double temperature; |
132 |
|
|
133 |
< |
temperature = ( 2.0 * this->getKinetic() ) / ( (double)this->getNDF() * kb ); |
133 |
> |
temperature = ( 2.0 * this->getKinetic() ) / ((double)entry_plug->ndf * kb ); |
134 |
|
return temperature; |
135 |
|
} |
136 |
|
|
139 |
|
// routine derived via viral theorem description in: |
140 |
|
// Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322 |
141 |
|
|
142 |
< |
return 0.0; |
142 |
> |
const double e_convert = 4.184e-4; |
143 |
> |
const double p_convert = 1.63882576e8; |
144 |
> |
double molmass; |
145 |
> |
double vcom[3]; |
146 |
> |
double p_local, p_sum, p_mol, virial; |
147 |
> |
double theBox[3]; |
148 |
> |
double* tau; |
149 |
> |
int i, nMols; |
150 |
> |
Molecule* molecules; |
151 |
> |
|
152 |
> |
nMols = entry_plug->n_mol; |
153 |
> |
molecules = entry_plug->molecules; |
154 |
> |
tau = entry_plug->tau; |
155 |
> |
|
156 |
> |
// use velocities of molecular centers of mass and molecular masses: |
157 |
> |
p_local = 0.0; |
158 |
> |
|
159 |
> |
for (i=0; i < nMols; i++) { |
160 |
> |
molmass = molecules[i].getCOMvel(vcom); |
161 |
> |
p_local += (vcom[0]*vcom[0] + vcom[1]*vcom[1] + vcom[2]*vcom[2]) * molmass; |
162 |
> |
} |
163 |
> |
|
164 |
> |
// Get total for entire system from MPI. |
165 |
> |
#ifdef IS_MPI |
166 |
> |
MPI_Allreduce(&p_local,&p_sum,1,MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
167 |
> |
#else |
168 |
> |
p_sum = p_local; |
169 |
> |
#endif // is_mpi |
170 |
> |
|
171 |
> |
virial = tau[0] + tau[4] + tau[8]; |
172 |
> |
entry_plug->getBox(theBox); |
173 |
> |
|
174 |
> |
p_mol = p_convert * (p_sum - virial*e_convert) / |
175 |
> |
(3.0 * theBox[0] * theBox[1]* theBox[2]); |
176 |
> |
|
177 |
> |
return p_mol; |
178 |
|
} |
179 |
|
|
180 |
|
void Thermo::velocitize() { |
188 |
|
const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc. |
189 |
|
double av2; |
190 |
|
double kebar; |
189 |
– |
int ndf, ndf_local; // number of degrees of freedom |
190 |
– |
int ndfRaw, ndfRaw_local; // the raw number of degrees of freedom |
191 |
|
int n_atoms; |
192 |
|
Atom** atoms; |
193 |
|
DirectionalAtom* dAtom; |
201 |
|
n_oriented = entry_plug->n_oriented; |
202 |
|
n_constraints = entry_plug->n_constraints; |
203 |
|
|
204 |
< |
kebar = kb * temperature * (double)this->getNDF() / |
205 |
< |
( 2.0 * (double)this->getNDFraw() ); |
204 |
> |
kebar = kb * temperature * (double)entry_plug->ndf / |
205 |
> |
( 2.0 * (double)entry_plug->ndfRaw ); |
206 |
|
|
207 |
|
for(vr = 0; vr < n_atoms; vr++){ |
208 |
|
|