22 |
|
NPTf::NPTf ( SimInfo *theInfo, ForceFields* the_ff): |
23 |
|
Integrator( theInfo, the_ff ) |
24 |
|
{ |
25 |
< |
int i; |
25 |
> |
int i, j; |
26 |
|
chi = 0.0; |
27 |
< |
for(i = 0; i < 9; i++) eta[i] = 0.0; |
27 |
> |
|
28 |
> |
for(i = 0; i < 3; i++) |
29 |
> |
for (j = 0; j < 3; j_++) |
30 |
> |
eta[i][j] = 0.0; |
31 |
> |
|
32 |
|
have_tau_thermostat = 0; |
33 |
|
have_tau_barostat = 0; |
34 |
|
have_target_temp = 0; |
42 |
|
DirectionalAtom* dAtom; |
43 |
|
double Tb[3]; |
44 |
|
double ji[3]; |
45 |
< |
double rj[3]; |
46 |
< |
double ident[3][3], eta1[3][3], eta2[3][3], hmnew[3][3]; |
47 |
< |
double hm[9]; |
44 |
< |
double vx, vy, vz; |
45 |
< |
double scx, scy, scz; |
46 |
< |
double instaTemp, instaPress, instaVol; |
47 |
< |
double tt2, tb2; |
45 |
> |
double ri[3], vi[3], sc[3]; |
46 |
> |
double instaTemp, instaVol; |
47 |
> |
double tt2, tb2, eta2ij; |
48 |
|
double angle; |
49 |
< |
double press[9]; |
49 |
> |
double press[3][3], vScale[3][3], hm[3][3], hmnew[3][3], scaleMat[3][3]; |
50 |
|
|
51 |
|
tt2 = tauThermostat * tauThermostat; |
52 |
|
tb2 = tauBarostat * tauBarostat; |
58 |
|
// first evolve chi a half step |
59 |
|
|
60 |
|
chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
61 |
< |
|
62 |
< |
eta[0] += dt2 * instaVol * (press[0] - targetPressure/p_convert) / |
63 |
< |
(NkBT*tb2); |
64 |
< |
eta[1] += dt2 * instaVol * press[1] / (NkBT*tb2); |
65 |
< |
eta[2] += dt2 * instaVol * press[2] / (NkBT*tb2); |
66 |
< |
eta[3] += dt2 * instaVol * press[3] / (NkBT*tb2); |
67 |
< |
eta[4] += dt2 * instaVol * (press[4] - targetPressure/p_convert) / |
68 |
< |
(NkBT*tb2); |
69 |
< |
eta[5] += dt2 * instaVol * press[5] / (NkBT*tb2); |
70 |
< |
eta[6] += dt2 * instaVol * press[6] / (NkBT*tb2); |
71 |
< |
eta[7] += dt2 * instaVol * press[7] / (NkBT*tb2); |
72 |
< |
eta[8] += dt2 * instaVol * (press[8] - targetPressure/p_convert) / |
73 |
< |
(NkBT*tb2); |
74 |
< |
|
61 |
> |
|
62 |
> |
for (i = 0; i < 3; i++ ) { |
63 |
> |
for (j = 0; j < 3; j++ ) { |
64 |
> |
if (i == j) { |
65 |
> |
|
66 |
> |
eta[i][j] += dt2 * instaVol * |
67 |
> |
(press[i][j] - targetPressure/p_convert) / (NkBT*tb2); |
68 |
> |
|
69 |
> |
vScale[i][j] = eta[i][j] + chi; |
70 |
> |
|
71 |
> |
} else { |
72 |
> |
|
73 |
> |
eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2); |
74 |
> |
|
75 |
> |
vScale[i][j] = eta[i][j]; |
76 |
> |
|
77 |
> |
} |
78 |
> |
} |
79 |
> |
} |
80 |
> |
|
81 |
|
for( i=0; i<nAtoms; i++ ){ |
82 |
|
atomIndex = i * 3; |
83 |
|
aMatIndex = i * 9; |
84 |
|
|
85 |
|
// velocity half step |
86 |
|
|
87 |
< |
vx = vel[atomIndex]; |
88 |
< |
vy = vel[atomIndex+1]; |
89 |
< |
vz = vel[atomIndex+2]; |
87 |
> |
vi[0] = vel[atomIndex]; |
88 |
> |
vi[1] = vel[atomIndex+1]; |
89 |
> |
vi[2] = vel[atomIndex+2]; |
90 |
|
|
91 |
< |
scx = (chi + eta[0])*vx + eta[1]*vy + eta[2]*vz; |
86 |
< |
scy = eta[3]*vx + (chi + eta[4])*vy + eta[5]*vz; |
87 |
< |
scz = eta[6]*vx + eta[7]*vy + (chi + eta[8])*vz; |
91 |
> |
info->matVecMul3( vScale, vi, sc ); |
92 |
|
|
93 |
< |
vx += dt2 * ((frc[atomIndex] /atoms[i]->getMass())*eConvert - scx); |
94 |
< |
vy += dt2 * ((frc[atomIndex+1]/atoms[i]->getMass())*eConvert - scy); |
95 |
< |
vz += dt2 * ((frc[atomIndex+2]/atoms[i]->getMass())*eConvert - scz); |
93 |
> |
vi[0] += dt2 * ((frc[atomIndex] /atoms[i]->getMass())*eConvert - sc[0]); |
94 |
> |
vi[1] += dt2 * ((frc[atomIndex+1]/atoms[i]->getMass())*eConvert - sc[1]); |
95 |
> |
vi[2] += dt2 * ((frc[atomIndex+2]/atoms[i]->getMass())*eConvert - sc[2]); |
96 |
|
|
97 |
< |
vel[atomIndex] = vx; |
98 |
< |
vel[atomIndex+1] = vy; |
99 |
< |
vel[atomIndex+2] = vz; |
97 |
> |
vel[atomIndex] = vi[0] |
98 |
> |
vel[atomIndex+1] = vi[1]; |
99 |
> |
vel[atomIndex+2] = vi[2]; |
100 |
|
|
101 |
|
// position whole step |
102 |
|
|
103 |
< |
rj[0] = pos[atomIndex]; |
104 |
< |
rj[1] = pos[atomIndex+1]; |
105 |
< |
rj[2] = pos[atomIndex+2]; |
103 |
> |
ri[0] = pos[atomIndex]; |
104 |
> |
ri[1] = pos[atomIndex+1]; |
105 |
> |
ri[2] = pos[atomIndex+2]; |
106 |
|
|
107 |
< |
info->wrapVector(rj); |
107 |
> |
info->wrapVector(ri); |
108 |
|
|
109 |
< |
scx = eta[0]*rj[0] + eta[1]*rj[1] + eta[2]*rj[2]; |
106 |
< |
scy = eta[3]*rj[0] + eta[4]*rj[1] + eta[5]*rj[2]; |
107 |
< |
scz = eta[6]*rj[0] + eta[7]*rj[1] + eta[8]*rj[2]; |
109 |
> |
info->matVecMul3( eta, ri, sc ); |
110 |
|
|
111 |
< |
pos[atomIndex] += dt * (vel[atomIndex] + scx); |
112 |
< |
pos[atomIndex+1] += dt * (vel[atomIndex+1] + scy); |
113 |
< |
pos[atomIndex+2] += dt * (vel[atomIndex+2] + scz); |
111 |
> |
pos[atomIndex] += dt * (vel[atomIndex] + sc[0]); |
112 |
> |
pos[atomIndex+1] += dt * (vel[atomIndex+1] + sc[1]); |
113 |
> |
pos[atomIndex+2] += dt * (vel[atomIndex+2] + sc[2]); |
114 |
|
|
115 |
|
if( atoms[i]->isDirectional() ){ |
116 |
|
|
172 |
|
|
173 |
|
for(i=0; i<3; i++){ |
174 |
|
for(j=0; j<3; j++){ |
175 |
< |
ident[i][j] = 0.0; |
176 |
< |
eta1[i][j] = eta[3*i+j]; |
177 |
< |
eta2[i][j] = 0.0; |
178 |
< |
for(k=0; k<3; k++){ |
179 |
< |
eta2[i][j] += eta[3*i+k] * eta[3*k+j]; |
175 |
> |
|
176 |
> |
// Calculate the matrix Product of the eta array (we only need |
177 |
> |
// the ij element right now): |
178 |
> |
|
179 |
> |
eta2ij = 0.0; |
180 |
> |
for(k=0; k<3; k++){ |
181 |
> |
eta2ij += eta[i][k] * eta[k][j]; |
182 |
|
} |
183 |
+ |
|
184 |
+ |
scaleMat[i][j] = 0.0; |
185 |
+ |
// identity matrix (see above): |
186 |
+ |
if (i == j) scaleMat[i][j] = 1.0; |
187 |
+ |
// Taylor expansion for the exponential truncated at second order: |
188 |
+ |
scaleMat[i][j] += dt*eta[i][j] + 0.5*dt*dt*eta2ij; |
189 |
+ |
|
190 |
|
} |
180 |
– |
ident[i][i] = 1.0; |
191 |
|
} |
182 |
– |
|
192 |
|
|
193 |
|
info->getBoxM(hm); |
194 |
< |
|
195 |
< |
for(i=0; i<3; i++){ |
187 |
< |
for(j=0; j<3; j++){ |
188 |
< |
hmnew[i][j] = 0.0; |
189 |
< |
for(k=0; k<3; k++){ |
190 |
< |
// remember that hmat has transpose ordering for Fortran compat: |
191 |
< |
hmnew[i][j] += hm[3*k+i] * (ident[k][j] |
192 |
< |
+ dt * eta1[k][j] |
193 |
< |
+ 0.5 * dt * dt * eta2[k][j]); |
194 |
< |
} |
195 |
< |
} |
196 |
< |
} |
194 |
> |
info->matMul3(hm, scaleMat, hmnew); |
195 |
> |
info->setBoxM(hmnew); |
196 |
|
|
198 |
– |
for (i = 0; i < 3; i++) { |
199 |
– |
for (j = 0; j < 3; j++) { |
200 |
– |
// remember that hmat has transpose ordering for Fortran compat: |
201 |
– |
hm[3*j + i] = hmnew[i][j]; |
202 |
– |
} |
203 |
– |
} |
204 |
– |
|
205 |
– |
info->setBoxM(hm); |
206 |
– |
|
197 |
|
} |
198 |
|
|
199 |
|
void NPTf::moveB( void ){ |
200 |
< |
int i,j,k; |
200 |
> |
int i,j, k; |
201 |
|
int atomIndex; |
202 |
|
DirectionalAtom* dAtom; |
203 |
|
double Tb[3]; |
204 |
|
double ji[3]; |
205 |
< |
double press[9]; |
205 |
> |
double vi[3], sc[3]; |
206 |
|
double instaTemp, instaVol; |
207 |
|
double tt2, tb2; |
208 |
< |
double vx, vy, vz; |
219 |
< |
double scx, scy, scz; |
220 |
< |
const double p_convert = 1.63882576e8; |
208 |
> |
double press[3][3], vScale[3][3]; |
209 |
|
|
210 |
|
tt2 = tauThermostat * tauThermostat; |
211 |
|
tb2 = tauBarostat * tauBarostat; |
218 |
|
|
219 |
|
chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
220 |
|
|
221 |
< |
eta[0] += dt2 * instaVol * (press[0] - targetPressure/p_convert) / |
222 |
< |
(NkBT*tb2); |
223 |
< |
eta[1] += dt2 * instaVol * press[1] / (NkBT*tb2); |
236 |
< |
eta[2] += dt2 * instaVol * press[2] / (NkBT*tb2); |
237 |
< |
eta[3] += dt2 * instaVol * press[3] / (NkBT*tb2); |
238 |
< |
eta[4] += dt2 * instaVol * (press[4] - targetPressure/p_convert) / |
239 |
< |
(NkBT*tb2); |
240 |
< |
eta[5] += dt2 * instaVol * press[5] / (NkBT*tb2); |
241 |
< |
eta[6] += dt2 * instaVol * press[6] / (NkBT*tb2); |
242 |
< |
eta[7] += dt2 * instaVol * press[7] / (NkBT*tb2); |
243 |
< |
eta[8] += dt2 * instaVol * (press[8] - targetPressure/p_convert) / |
244 |
< |
(NkBT*tb2); |
221 |
> |
for (i = 0; i < 3; i++ ) { |
222 |
> |
for (j = 0; j < 3; j++ ) { |
223 |
> |
if (i == j) { |
224 |
|
|
225 |
+ |
eta[i][j] += dt2 * instaVol * |
226 |
+ |
(press[i][j] - targetPressure/p_convert) / (NkBT*tb2); |
227 |
+ |
|
228 |
+ |
vScale[i][j] = eta[i][j] + chi; |
229 |
+ |
|
230 |
+ |
} else { |
231 |
+ |
|
232 |
+ |
eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2); |
233 |
+ |
|
234 |
+ |
vScale[i][j] = eta[i][j]; |
235 |
+ |
|
236 |
+ |
} |
237 |
+ |
} |
238 |
+ |
} |
239 |
+ |
|
240 |
|
for( i=0; i<nAtoms; i++ ){ |
241 |
|
atomIndex = i * 3; |
242 |
|
|
243 |
|
// velocity half step |
244 |
|
|
245 |
< |
vx = vel[atomIndex]; |
246 |
< |
vy = vel[atomIndex+1]; |
247 |
< |
vz = vel[atomIndex+2]; |
245 |
> |
vi[0] = vel[atomIndex]; |
246 |
> |
vi[1] = vel[atomIndex+1]; |
247 |
> |
vi[2] = vel[atomIndex+2]; |
248 |
|
|
249 |
< |
scx = (chi + eta[0])*vx + eta[1]*vy + eta[2]*vz; |
256 |
< |
scy = eta[3]*vx + (chi + eta[4])*vy + eta[5]*vz; |
257 |
< |
scz = eta[6]*vx + eta[7]*vy + (chi + eta[8])*vz; |
249 |
> |
info->matVecMul3( vScale, vi, sc ); |
250 |
|
|
251 |
< |
vx += dt2 * ((frc[atomIndex] /atoms[i]->getMass())*eConvert - scx); |
252 |
< |
vy += dt2 * ((frc[atomIndex+1]/atoms[i]->getMass())*eConvert - scy); |
253 |
< |
vz += dt2 * ((frc[atomIndex+2]/atoms[i]->getMass())*eConvert - scz); |
251 |
> |
vi[0] += dt2 * ((frc[atomIndex] /atoms[i]->getMass())*eConvert - sc[0]); |
252 |
> |
vi[1] += dt2 * ((frc[atomIndex+1]/atoms[i]->getMass())*eConvert - sc[1]); |
253 |
> |
vi[2] += dt2 * ((frc[atomIndex+2]/atoms[i]->getMass())*eConvert - sc[2]); |
254 |
|
|
255 |
< |
vel[atomIndex] = vx; |
256 |
< |
vel[atomIndex+1] = vy; |
257 |
< |
vel[atomIndex+2] = vz; |
255 |
> |
vel[atomIndex] = vi[0] |
256 |
> |
vel[atomIndex+1] = vi[1]; |
257 |
> |
vel[atomIndex+2] = vi[2]; |
258 |
|
|
259 |
|
if( atoms[i]->isDirectional() ){ |
260 |
|
|