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; |
37 |
|
|
38 |
|
void NPTf::moveA() { |
39 |
|
|
40 |
< |
int i,j,k; |
37 |
< |
int atomIndex, aMatIndex; |
40 |
> |
int i, j, k; |
41 |
|
DirectionalAtom* dAtom; |
42 |
< |
double Tb[3]; |
43 |
< |
double ji[3]; |
42 |
> |
double Tb[3], ji[3]; |
43 |
> |
double A[3][3], I[3][3]; |
44 |
> |
double angle, mass; |
45 |
> |
double vel[3], pos[3], frc[3]; |
46 |
> |
|
47 |
|
double rj[3]; |
42 |
– |
double ident[3][3], eta1[3][3], eta2[3][3], hmnew[3][3]; |
43 |
– |
double hm[9]; |
44 |
– |
double vx, vy, vz; |
45 |
– |
double scx, scy, scz; |
48 |
|
double instaTemp, instaPress, instaVol; |
49 |
|
double tt2, tb2; |
50 |
< |
double angle; |
51 |
< |
double press[9]; |
52 |
< |
const double p_convert = 1.63882576e8; |
50 |
> |
double sc[3]; |
51 |
> |
double eta2ij; |
52 |
> |
double press[3][3], vScale[3][3], hm[3][3], hmnew[3][3], scaleMat[3][3]; |
53 |
|
|
54 |
|
tt2 = tauThermostat * tauThermostat; |
55 |
|
tb2 = tauBarostat * tauBarostat; |
56 |
|
|
57 |
|
instaTemp = tStats->getTemperature(); |
58 |
|
tStats->getPressureTensor(press); |
57 |
– |
|
58 |
– |
for (i=0; i < 9; i++) press[i] *= p_convert; |
59 |
– |
|
59 |
|
instaVol = tStats->getVolume(); |
60 |
|
|
61 |
|
// first evolve chi a half step |
62 |
|
|
63 |
|
chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
64 |
< |
|
65 |
< |
eta[0] += dt2 * instaVol * (press[0] - targetPressure) / (NkBT*tb2); |
66 |
< |
eta[1] += dt2 * instaVol * press[1] / (NkBT*tb2); |
67 |
< |
eta[2] += dt2 * instaVol * press[2] / (NkBT*tb2); |
68 |
< |
eta[3] += dt2 * instaVol * press[3] / (NkBT*tb2); |
69 |
< |
eta[4] += dt2 * instaVol * (press[4] - targetPressure) / (NkBT*tb2); |
70 |
< |
eta[5] += dt2 * instaVol * press[5] / (NkBT*tb2); |
71 |
< |
eta[6] += dt2 * instaVol * press[6] / (NkBT*tb2); |
72 |
< |
eta[7] += dt2 * instaVol * press[7] / (NkBT*tb2); |
73 |
< |
eta[8] += dt2 * instaVol * (press[8] - targetPressure) / (NkBT*tb2); |
74 |
< |
|
64 |
> |
|
65 |
> |
for (i = 0; i < 3; i++ ) { |
66 |
> |
for (j = 0; j < 3; j++ ) { |
67 |
> |
if (i == j) { |
68 |
> |
|
69 |
> |
eta[i][j] += dt2 * instaVol * |
70 |
> |
(press[i][j] - targetPressure/p_convert) / (NkBT*tb2); |
71 |
> |
|
72 |
> |
vScale[i][j] = eta[i][j] + chi; |
73 |
> |
|
74 |
> |
} else { |
75 |
> |
|
76 |
> |
eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2); |
77 |
> |
|
78 |
> |
vScale[i][j] = eta[i][j]; |
79 |
> |
|
80 |
> |
} |
81 |
> |
} |
82 |
> |
} |
83 |
> |
|
84 |
|
for( i=0; i<nAtoms; i++ ){ |
85 |
< |
atomIndex = i * 3; |
86 |
< |
aMatIndex = i * 9; |
85 |
> |
|
86 |
> |
atoms[i]->getVel( vel ); |
87 |
> |
atoms[i]->getPos( pos ); |
88 |
> |
atoms[i]->getFrc( frc ); |
89 |
> |
|
90 |
> |
mass = atoms[i]->getMass(); |
91 |
|
|
92 |
|
// velocity half step |
93 |
+ |
|
94 |
+ |
info->matVecMul3( vScale, vel, sc ); |
95 |
|
|
96 |
< |
vx = vel[atomIndex]; |
97 |
< |
vy = vel[atomIndex+1]; |
98 |
< |
vz = vel[atomIndex+2]; |
99 |
< |
|
86 |
< |
scx = (chi + eta[0])*vx + eta[1]*vy + eta[2]*vz; |
87 |
< |
scy = eta[3]*vx + (chi + eta[4])*vy + eta[5]*vz; |
88 |
< |
scz = eta[6]*vx + eta[7]*vy + (chi + eta[8])*vz; |
89 |
< |
|
90 |
< |
vx += dt2 * ((frc[atomIndex] /atoms[i]->getMass())*eConvert - scx); |
91 |
< |
vy += dt2 * ((frc[atomIndex+1]/atoms[i]->getMass())*eConvert - scy); |
92 |
< |
vz += dt2 * ((frc[atomIndex+2]/atoms[i]->getMass())*eConvert - scz); |
96 |
> |
for (j = 0; j < 3; j++) { |
97 |
> |
vel[j] += dt2 * ((frc[j] / mass) * eConvert - sc[j]); |
98 |
> |
rj[j] = pos[j]; |
99 |
> |
} |
100 |
|
|
101 |
< |
vel[atomIndex] = vx; |
95 |
< |
vel[atomIndex+1] = vy; |
96 |
< |
vel[atomIndex+2] = vz; |
101 |
> |
atoms[i]->setVel( vel ); |
102 |
|
|
103 |
|
// position whole step |
104 |
|
|
100 |
– |
rj[0] = pos[atomIndex]; |
101 |
– |
rj[1] = pos[atomIndex+1]; |
102 |
– |
rj[2] = pos[atomIndex+2]; |
103 |
– |
|
105 |
|
info->wrapVector(rj); |
106 |
|
|
107 |
< |
scx = eta[0]*rj[0] + eta[1]*rj[1] + eta[2]*rj[2]; |
107 |
< |
scy = eta[3]*rj[0] + eta[4]*rj[1] + eta[5]*rj[2]; |
108 |
< |
scz = eta[6]*rj[0] + eta[7]*rj[1] + eta[8]*rj[2]; |
107 |
> |
info->matVecMul3( eta, rj, sc ); |
108 |
|
|
109 |
< |
pos[atomIndex] += dt * (vel[atomIndex] + scx); |
110 |
< |
pos[atomIndex+1] += dt * (vel[atomIndex+1] + scy); |
112 |
< |
pos[atomIndex+2] += dt * (vel[atomIndex+2] + scz); |
109 |
> |
for (j = 0; j < 3; j++ ) |
110 |
> |
pos[j] += dt * (vel[j] + sc[j]); |
111 |
|
|
112 |
|
if( atoms[i]->isDirectional() ){ |
113 |
|
|
115 |
|
|
116 |
|
// get and convert the torque to body frame |
117 |
|
|
118 |
< |
Tb[0] = dAtom->getTx(); |
121 |
< |
Tb[1] = dAtom->getTy(); |
122 |
< |
Tb[2] = dAtom->getTz(); |
123 |
< |
|
118 |
> |
dAtom->getTrq( Tb ); |
119 |
|
dAtom->lab2Body( Tb ); |
120 |
|
|
121 |
|
// get the angular momentum, and propagate a half step |
122 |
|
|
123 |
< |
ji[0] = dAtom->getJx(); |
124 |
< |
ji[1] = dAtom->getJy(); |
125 |
< |
ji[2] = dAtom->getJz(); |
123 |
> |
dAtom->getJ( ji ); |
124 |
> |
|
125 |
> |
for (j=0; j < 3; j++) |
126 |
> |
ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi); |
127 |
|
|
132 |
– |
ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*chi); |
133 |
– |
ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*chi); |
134 |
– |
ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*chi); |
135 |
– |
|
128 |
|
// use the angular velocities to propagate the rotation matrix a |
129 |
|
// full time step |
130 |
< |
|
130 |
> |
|
131 |
> |
dAtom->getA(A); |
132 |
> |
dAtom->getI(I); |
133 |
> |
|
134 |
|
// rotate about the x-axis |
135 |
< |
angle = dt2 * ji[0] / dAtom->getIxx(); |
136 |
< |
this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] ); |
137 |
< |
|
135 |
> |
angle = dt2 * ji[0] / I[0][0]; |
136 |
> |
this->rotate( 1, 2, angle, ji, A ); |
137 |
> |
|
138 |
|
// rotate about the y-axis |
139 |
< |
angle = dt2 * ji[1] / dAtom->getIyy(); |
140 |
< |
this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] ); |
139 |
> |
angle = dt2 * ji[1] / I[1][1]; |
140 |
> |
this->rotate( 2, 0, angle, ji, A ); |
141 |
|
|
142 |
|
// rotate about the z-axis |
143 |
< |
angle = dt * ji[2] / dAtom->getIzz(); |
144 |
< |
this->rotate( 0, 1, angle, ji, &Amat[aMatIndex] ); |
143 |
> |
angle = dt * ji[2] / I[2][2]; |
144 |
> |
this->rotate( 0, 1, angle, ji, A); |
145 |
|
|
146 |
|
// rotate about the y-axis |
147 |
< |
angle = dt2 * ji[1] / dAtom->getIyy(); |
148 |
< |
this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] ); |
147 |
> |
angle = dt2 * ji[1] / I[1][1]; |
148 |
> |
this->rotate( 2, 0, angle, ji, A ); |
149 |
|
|
150 |
|
// rotate about the x-axis |
151 |
< |
angle = dt2 * ji[0] / dAtom->getIxx(); |
152 |
< |
this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] ); |
151 |
> |
angle = dt2 * ji[0] / I[0][0]; |
152 |
> |
this->rotate( 1, 2, angle, ji, A ); |
153 |
|
|
154 |
< |
dAtom->setJx( ji[0] ); |
155 |
< |
dAtom->setJy( ji[1] ); |
156 |
< |
dAtom->setJz( ji[2] ); |
162 |
< |
} |
163 |
< |
|
154 |
> |
dAtom->setJ( ji ); |
155 |
> |
dAtom->setA( A ); |
156 |
> |
} |
157 |
|
} |
158 |
< |
|
158 |
> |
|
159 |
|
// Scale the box after all the positions have been moved: |
160 |
< |
|
160 |
> |
|
161 |
|
// Use a taylor expansion for eta products: Hmat = Hmat . exp(dt * etaMat) |
162 |
|
// Hmat = Hmat . ( Ident + dt * etaMat + dt^2 * etaMat*etaMat / 2) |
163 |
< |
|
164 |
< |
|
163 |
> |
|
164 |
> |
|
165 |
|
for(i=0; i<3; i++){ |
166 |
|
for(j=0; j<3; j++){ |
167 |
< |
ident[i][j] = 0.0; |
168 |
< |
eta1[i][j] = eta[3*i+j]; |
169 |
< |
eta2[i][j] = 0.0; |
167 |
> |
|
168 |
> |
// Calculate the matrix Product of the eta array (we only need |
169 |
> |
// the ij element right now): |
170 |
> |
|
171 |
> |
eta2ij = 0.0; |
172 |
|
for(k=0; k<3; k++){ |
173 |
< |
eta2[i][j] += eta[3*i+k] * eta[3*k+j]; |
173 |
> |
eta2ij += eta[i][k] * eta[k][j]; |
174 |
|
} |
175 |
< |
} |
176 |
< |
ident[i][i] = 1.0; |
177 |
< |
} |
178 |
< |
|
179 |
< |
|
180 |
< |
info->getBoxM(hm); |
181 |
< |
|
187 |
< |
for(i=0; i<3; i++){ |
188 |
< |
for(j=0; j<3; j++){ |
189 |
< |
hmnew[i][j] = 0.0; |
190 |
< |
for(k=0; k<3; k++){ |
191 |
< |
// remember that hmat has transpose ordering for Fortran compat: |
192 |
< |
hmnew[i][j] += hm[3*k+i] * (ident[k][j] |
193 |
< |
+ dt * eta1[k][j] |
194 |
< |
+ 0.5 * dt * dt * eta2[k][j]); |
195 |
< |
} |
175 |
> |
|
176 |
> |
scaleMat[i][j] = 0.0; |
177 |
> |
// identity matrix (see above): |
178 |
> |
if (i == j) scaleMat[i][j] = 1.0; |
179 |
> |
// Taylor expansion for the exponential truncated at second order: |
180 |
> |
scaleMat[i][j] += dt*eta[i][j] + 0.5*dt*dt*eta2ij; |
181 |
> |
|
182 |
|
} |
183 |
|
} |
184 |
|
|
185 |
< |
for (i = 0; i < 3; i++) { |
186 |
< |
for (j = 0; j < 3; j++) { |
187 |
< |
// remember that hmat has transpose ordering for Fortran compat: |
202 |
< |
hm[3*j + 1] = hmnew[i][j]; |
203 |
< |
} |
204 |
< |
} |
205 |
< |
|
206 |
< |
info->setBoxM(hm); |
185 |
> |
info->getBoxM(hm); |
186 |
> |
info->matMul3(hm, scaleMat, hmnew); |
187 |
> |
info->setBoxM(hmnew); |
188 |
|
|
189 |
|
} |
190 |
|
|
191 |
|
void NPTf::moveB( void ){ |
192 |
< |
int i,j,k; |
193 |
< |
int atomIndex; |
192 |
> |
|
193 |
> |
int i, j; |
194 |
|
DirectionalAtom* dAtom; |
195 |
< |
double Tb[3]; |
196 |
< |
double ji[3]; |
197 |
< |
double press[9]; |
198 |
< |
double instaTemp, instaVol; |
195 |
> |
double Tb[3], ji[3]; |
196 |
> |
double vel[3], frc[3]; |
197 |
> |
double mass; |
198 |
> |
|
199 |
> |
double instaTemp, instaPress, instaVol; |
200 |
|
double tt2, tb2; |
201 |
< |
double vx, vy, vz; |
202 |
< |
double scx, scy, scz; |
221 |
< |
const double p_convert = 1.63882576e8; |
201 |
> |
double sc[3]; |
202 |
> |
double press[3][3], vScale[3][3]; |
203 |
|
|
204 |
|
tt2 = tauThermostat * tauThermostat; |
205 |
|
tb2 = tauBarostat * tauBarostat; |
206 |
|
|
207 |
|
instaTemp = tStats->getTemperature(); |
208 |
|
tStats->getPressureTensor(press); |
228 |
– |
|
229 |
– |
for (i=0; i < 9; i++) press[i] *= p_convert; |
230 |
– |
|
209 |
|
instaVol = tStats->getVolume(); |
210 |
|
|
211 |
|
// first evolve chi a half step |
212 |
|
|
213 |
|
chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
214 |
|
|
215 |
< |
eta[0] += dt2 * instaVol * (press[0] - targetPressure) / (NkBT*tb2); |
216 |
< |
eta[1] += dt2 * instaVol * press[1] / (NkBT*tb2); |
217 |
< |
eta[2] += dt2 * instaVol * press[2] / (NkBT*tb2); |
240 |
< |
eta[3] += dt2 * instaVol * press[3] / (NkBT*tb2); |
241 |
< |
eta[4] += dt2 * instaVol * (press[4] - targetPressure) / (NkBT*tb2); |
242 |
< |
eta[5] += dt2 * instaVol * press[5] / (NkBT*tb2); |
243 |
< |
eta[6] += dt2 * instaVol * press[6] / (NkBT*tb2); |
244 |
< |
eta[7] += dt2 * instaVol * press[7] / (NkBT*tb2); |
245 |
< |
eta[8] += dt2 * instaVol * (press[8] - targetPressure) / (NkBT*tb2); |
215 |
> |
for (i = 0; i < 3; i++ ) { |
216 |
> |
for (j = 0; j < 3; j++ ) { |
217 |
> |
if (i == j) { |
218 |
|
|
219 |
+ |
eta[i][j] += dt2 * instaVol * |
220 |
+ |
(press[i][j] - targetPressure/p_convert) / (NkBT*tb2); |
221 |
+ |
|
222 |
+ |
vScale[i][j] = eta[i][j] + chi; |
223 |
+ |
|
224 |
+ |
} else { |
225 |
+ |
|
226 |
+ |
eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2); |
227 |
+ |
|
228 |
+ |
vScale[i][j] = eta[i][j]; |
229 |
+ |
|
230 |
+ |
} |
231 |
+ |
} |
232 |
+ |
} |
233 |
+ |
|
234 |
|
for( i=0; i<nAtoms; i++ ){ |
248 |
– |
atomIndex = i * 3; |
235 |
|
|
236 |
+ |
atoms[i]->getVel( vel ); |
237 |
+ |
atoms[i]->getFrc( frc ); |
238 |
+ |
|
239 |
+ |
mass = atoms[i]->getMass(); |
240 |
+ |
|
241 |
|
// velocity half step |
242 |
+ |
|
243 |
+ |
info->matVecMul3( vScale, vel, sc ); |
244 |
|
|
245 |
< |
vx = vel[atomIndex]; |
246 |
< |
vy = vel[atomIndex+1]; |
247 |
< |
vz = vel[atomIndex+2]; |
255 |
< |
|
256 |
< |
scx = (chi + eta[0])*vx + eta[1]*vy + eta[2]*vz; |
257 |
< |
scy = eta[3]*vx + (chi + eta[4])*vy + eta[5]*vz; |
258 |
< |
scz = eta[6]*vx + eta[7]*vy + (chi + eta[8])*vz; |
259 |
< |
|
260 |
< |
vx += dt2 * ((frc[atomIndex] /atoms[i]->getMass())*eConvert - scx); |
261 |
< |
vy += dt2 * ((frc[atomIndex+1]/atoms[i]->getMass())*eConvert - scy); |
262 |
< |
vz += dt2 * ((frc[atomIndex+2]/atoms[i]->getMass())*eConvert - scz); |
245 |
> |
for (j = 0; j < 3; j++) { |
246 |
> |
vel[j] += dt2 * ((frc[j] / mass) * eConvert - sc[j]); |
247 |
> |
} |
248 |
|
|
249 |
< |
vel[atomIndex] = vx; |
265 |
< |
vel[atomIndex+1] = vy; |
266 |
< |
vel[atomIndex+2] = vz; |
249 |
> |
atoms[i]->setVel( vel ); |
250 |
|
|
251 |
|
if( atoms[i]->isDirectional() ){ |
252 |
< |
|
252 |
> |
|
253 |
|
dAtom = (DirectionalAtom *)atoms[i]; |
254 |
< |
|
254 |
> |
|
255 |
|
// get and convert the torque to body frame |
256 |
|
|
257 |
< |
Tb[0] = dAtom->getTx(); |
275 |
< |
Tb[1] = dAtom->getTy(); |
276 |
< |
Tb[2] = dAtom->getTz(); |
277 |
< |
|
257 |
> |
dAtom->getTrq( Tb ); |
258 |
|
dAtom->lab2Body( Tb ); |
259 |
|
|
260 |
< |
// get the angular momentum, and complete the angular momentum |
281 |
< |
// half step |
260 |
> |
// get the angular momentum, and propagate a half step |
261 |
|
|
262 |
< |
ji[0] = dAtom->getJx(); |
284 |
< |
ji[1] = dAtom->getJy(); |
285 |
< |
ji[2] = dAtom->getJz(); |
262 |
> |
dAtom->getJ( ji ); |
263 |
|
|
264 |
< |
ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*chi); |
265 |
< |
ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*chi); |
289 |
< |
ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*chi); |
264 |
> |
for (j=0; j < 3; j++) |
265 |
> |
ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi); |
266 |
|
|
267 |
< |
dAtom->setJx( ji[0] ); |
268 |
< |
dAtom->setJy( ji[1] ); |
269 |
< |
dAtom->setJz( ji[2] ); |
294 |
< |
} |
267 |
> |
dAtom->setJ( ji ); |
268 |
> |
|
269 |
> |
} |
270 |
|
} |
271 |
|
} |
272 |
|
|
273 |
< |
int NPTi::readyCheck() { |
273 |
> |
int NPTf::readyCheck() { |
274 |
|
|
275 |
|
// First check to see if we have a target temperature. |
276 |
|
// Not having one is fatal. |
277 |
|
|
278 |
|
if (!have_target_temp) { |
279 |
|
sprintf( painCave.errMsg, |
280 |
< |
"NPTi error: You can't use the NPTi integrator\n" |
280 |
> |
"NPTf error: You can't use the NPTf integrator\n" |
281 |
|
" without a targetTemp!\n" |
282 |
|
); |
283 |
|
painCave.isFatal = 1; |
287 |
|
|
288 |
|
if (!have_target_pressure) { |
289 |
|
sprintf( painCave.errMsg, |
290 |
< |
"NPTi error: You can't use the NPTi integrator\n" |
290 |
> |
"NPTf error: You can't use the NPTf integrator\n" |
291 |
|
" without a targetPressure!\n" |
292 |
|
); |
293 |
|
painCave.isFatal = 1; |
299 |
|
|
300 |
|
if (!have_tau_thermostat) { |
301 |
|
sprintf( painCave.errMsg, |
302 |
< |
"NPTi error: If you use the NPTi\n" |
302 |
> |
"NPTf error: If you use the NPTf\n" |
303 |
|
" integrator, you must set tauThermostat.\n"); |
304 |
|
painCave.isFatal = 1; |
305 |
|
simError(); |
310 |
|
|
311 |
|
if (!have_tau_barostat) { |
312 |
|
sprintf( painCave.errMsg, |
313 |
< |
"NPTi error: If you use the NPTi\n" |
313 |
> |
"NPTf error: If you use the NPTf\n" |
314 |
|
" integrator, you must set tauBarostat.\n"); |
315 |
|
painCave.isFatal = 1; |
316 |
|
simError(); |