96 |
|
p_mol = p_int; |
97 |
|
|
98 |
|
entry_plug->getBox(oldBox); |
99 |
– |
|
99 |
|
volume = oldBox[0]*oldBox[1]*oldBox[2]; |
100 |
|
|
101 |
|
ke_temp = ke * e_convert; |
107 |
|
(tauRelax*tauRelax * kB * targetTemp) ); |
108 |
|
|
109 |
|
|
110 |
< |
std::cerr << "p_mol = " << p_mol << " p_ext = " << p_ext << " volume = " << volume << " tauRelax = " << tauRelax << "\n"; |
110 |
> |
std::cerr << "dt = " << dt << " tauRelax = " << tauRelax << " kB = " << kB << "targetTemp = " << targetTemp << "\n"; |
111 |
|
|
113 |
– |
|
112 |
|
// determine the change in cell volume |
113 |
|
scale = pow( (1.0 + dt * 3.0 * epsilonDot), (1.0 / 3.0)); |
114 |
|
|
115 |
+ |
std::cerr << "p_mol = " << p_mol << " p_ext = " << p_ext << " scale = " << scale << "\n"; |
116 |
+ |
|
117 |
+ |
|
118 |
|
newBox[0] = oldBox[0] * scale; |
119 |
|
newBox[1] = oldBox[1] * scale; |
120 |
|
newBox[2] = oldBox[2] * scale; |
181 |
|
percentScale[1] = (newBox[1] - oldBox[1]) / oldBox[1]; |
182 |
|
percentScale[2] = (newBox[2] - oldBox[2]) / oldBox[2]; |
183 |
|
|
184 |
+ |
std::cerr << "ps = " << percentScale[0] <<" " << percentScale[1] << " " << percentScale[2] << "\n"; |
185 |
+ |
|
186 |
+ |
|
187 |
|
for (i=0; i < entry_plug->n_mol; i++) { |
188 |
|
|
189 |
|
molecules[i].getCOM(r); |
190 |
< |
|
190 |
> |
|
191 |
|
// find the minimum image coordinates of the molecular centers of mass: |
192 |
|
|
193 |
|
boxNum[0] = oldBox[0] * copysign(1.0,r[0]) * |
199 |
|
boxNum[2] = oldBox[2] * copysign(1.0,r[2]) * |
200 |
|
(double)(int)(fabs(r[2]/oldBox[2]) + 0.5); |
201 |
|
|
202 |
+ |
|
203 |
+ |
std::cerr << "boxNum = " << boxNum[0] << " " << boxNum[1] << " " << boxNum[2] << "\n"; |
204 |
+ |
|
205 |
|
rxi = r[0] - boxNum[0]; |
206 |
|
ryi = r[1] - boxNum[1]; |
207 |
|
rzi = r[2] - boxNum[2]; |