10 |
|
// get what information we need from the SimInfo object |
11 |
|
|
12 |
|
entry_plug = the_entry_plug; |
13 |
– |
nAtoms = entry_plug->n_atoms; |
14 |
– |
atoms = entry_plug->atoms; |
15 |
– |
nMols = entry_plug->n_mol; |
16 |
– |
molecules = entry_plug->molecules; |
17 |
– |
nOriented = entry_plug->n_oriented; |
18 |
– |
ndf = entry_plug->ndf; |
13 |
|
zeta = 0.0; |
14 |
|
epsilonDot = 0.0; |
21 |
– |
|
15 |
|
} |
16 |
|
|
17 |
|
void ExtendedSystem::NoseHooverNVT( double dt, double ke ){ |
25 |
|
const double e_convert = 4.184e-4; // to convert ke from kcal/mol to |
26 |
|
// amu*Ang^2*fs^-2/K |
27 |
|
DirectionalAtom* dAtom; |
28 |
+ |
atoms = entry_plug->atoms; |
29 |
|
|
30 |
|
ke_temp = ke * e_convert; |
31 |
< |
NkBT = (double)ndf * kB * targetTemp; |
31 |
> |
NkBT = (double)entry_plug->ndf * kB * targetTemp; |
32 |
|
|
33 |
|
// advance the zeta term to zeta(t + dt) - zeta is 0.0d0 on config. readin |
34 |
|
// qmass is set in the parameter file |
35 |
|
|
36 |
|
zeta += dt * ( (ke_temp*2.0 - NkBT) / qmass ); |
43 |
– |
std::cerr << "ke_temp = " << ke_temp << "\n"; |
37 |
|
|
38 |
|
zetaScale = zeta * dt; |
39 |
|
|
40 |
+ |
std::cerr << "zetaScale = " << zetaScale << "\n"; |
41 |
|
|
48 |
– |
|
42 |
|
// perform thermostat scaling on linear velocities and angular momentum |
43 |
< |
for(i = 0; i < nAtoms; i++){ |
43 |
> |
for(i = 0; i < entry_plug->n_atoms; i++){ |
44 |
|
|
45 |
|
vx = atoms[i]->get_vx(); |
46 |
|
vy = atoms[i]->get_vy(); |
47 |
|
vz = atoms[i]->get_vz(); |
48 |
< |
|
48 |
> |
|
49 |
|
atoms[i]->set_vx(vx * (1.0 - zetaScale)); |
50 |
|
atoms[i]->set_vy(vy * (1.0 - zetaScale)); |
51 |
|
atoms[i]->set_vz(vz * (1.0 - zetaScale)); |
52 |
|
} |
53 |
< |
if( nOriented ){ |
53 |
> |
if( entry_plug->n_oriented ){ |
54 |
|
|
55 |
< |
for( i=0; i < nAtoms; i++ ){ |
55 |
> |
for( i=0; i < entry_plug->n_atoms; i++ ){ |
56 |
|
|
57 |
|
if( atoms[i]->isDirectional() ){ |
58 |
|
|
85 |
|
const double e_convert = 4.184e-4; // to convert ke from kcal/mol to |
86 |
|
// amu*Ang^2*fs^-2/K |
87 |
|
|
88 |
+ |
int i; |
89 |
|
double p_ext, zetaScale, epsilonScale, scale, NkBT, ke_temp; |
90 |
|
double volume, p_mol; |
91 |
|
double vx, vy, vz, jx, jy, jz; |
92 |
|
DirectionalAtom* dAtom; |
93 |
< |
int i; |
93 |
> |
atoms = entry_plug->atoms; |
94 |
|
|
95 |
|
p_ext = targetPressure * p_units; |
96 |
|
p_mol = p_int * p_units; |
97 |
|
|
98 |
|
entry_plug->getBox(oldBox); |
105 |
– |
|
99 |
|
volume = oldBox[0]*oldBox[1]*oldBox[2]; |
100 |
|
|
101 |
|
ke_temp = ke * e_convert; |
102 |
< |
NkBT = (double)ndf * kB * targetTemp; |
102 |
> |
NkBT = (double)entry_plug->ndf * kB * targetTemp; |
103 |
|
|
104 |
|
// propogate the strain rate |
105 |
|
|
126 |
|
|
127 |
|
zeta += dt * ( (ke_temp*2.0 - NkBT) / qmass ); |
128 |
|
zetaScale = zeta * dt; |
129 |
+ |
|
130 |
+ |
std::cerr << "zetaScale = " << zetaScale << " epsilonScale = " << epsilonScale << "\n"; |
131 |
|
|
132 |
|
// apply barostating and thermostating to velocities and angular momenta |
133 |
< |
for(i = 0; i < nAtoms; i++){ |
133 |
> |
for(i = 0; i < entry_plug->n_atoms; i++){ |
134 |
|
|
135 |
|
vx = atoms[i]->get_vx(); |
136 |
|
vy = atoms[i]->get_vy(); |
140 |
|
atoms[i]->set_vy(vy * (1.0 - zetaScale - epsilonScale)); |
141 |
|
atoms[i]->set_vz(vz * (1.0 - zetaScale - epsilonScale)); |
142 |
|
} |
143 |
< |
if( nOriented ){ |
143 |
> |
if( entry_plug->n_oriented ){ |
144 |
|
|
145 |
< |
for( i=0; i < nAtoms; i++ ){ |
145 |
> |
for( i=0; i < entry_plug->n_atoms; i++ ){ |
146 |
|
|
147 |
|
if( atoms[i]->isDirectional() ){ |
148 |
|
|
166 |
|
double r[3]; |
167 |
|
double boxNum[3]; |
168 |
|
double percentScale[3]; |
169 |
+ |
double delta[3]; |
170 |
|
double rxi, ryi, rzi; |
171 |
+ |
|
172 |
+ |
molecules = entry_plug->molecules; |
173 |
|
|
174 |
|
// first determine the scaling factor from the box size change |
175 |
|
percentScale[0] = (newBox[0] - oldBox[0]) / oldBox[0]; |
176 |
|
percentScale[1] = (newBox[1] - oldBox[1]) / oldBox[1]; |
177 |
|
percentScale[2] = (newBox[2] - oldBox[2]) / oldBox[2]; |
178 |
|
|
179 |
< |
for (i=0; i < nMols; i++) { |
179 |
> |
for (i=0; i < entry_plug->n_mol; i++) { |
180 |
|
|
181 |
|
molecules[i].getCOM(r); |
182 |
< |
|
182 |
> |
|
183 |
|
// find the minimum image coordinates of the molecular centers of mass: |
184 |
|
|
185 |
|
boxNum[0] = oldBox[0] * copysign(1.0,r[0]) * |
200 |
|
ryi += ryi*percentScale[1]; |
201 |
|
rzi += rzi*percentScale[2]; |
202 |
|
|
203 |
< |
r[0] = rxi + boxNum[0]; |
204 |
< |
r[1] = ryi + boxNum[1]; |
205 |
< |
r[2] = rzi + boxNum[2]; |
203 |
> |
delta[0] = r[0] - (rxi + boxNum[0]); |
204 |
> |
delta[1] = r[1] - (ryi + boxNum[1]); |
205 |
> |
delta[2] = r[2] - (rzi + boxNum[2]); |
206 |
|
|
207 |
< |
molecules[i].moveCOM(r); |
207 |
> |
molecules[i].moveCOM(delta); |
208 |
|
} |
209 |
|
} |