1 |
gezelter |
576 |
#include "Atom.hpp" |
2 |
|
|
#include "SRI.hpp" |
3 |
|
|
#include "AbstractClasses.hpp" |
4 |
|
|
#include "SimInfo.hpp" |
5 |
|
|
#include "ForceFields.hpp" |
6 |
|
|
#include "Thermo.hpp" |
7 |
|
|
#include "ReadWrite.hpp" |
8 |
|
|
#include "Integrator.hpp" |
9 |
|
|
#include "simError.h" |
10 |
|
|
|
11 |
|
|
|
12 |
|
|
// Basic isotropic thermostating and barostating via the Melchionna |
13 |
|
|
// modification of the Hoover algorithm: |
14 |
|
|
// |
15 |
|
|
// Melchionna, S., Ciccotti, G., and Holian, B. L., 1993, |
16 |
|
|
// Molec. Phys., 78, 533. |
17 |
|
|
// |
18 |
|
|
// and |
19 |
|
|
// |
20 |
|
|
// Hoover, W. G., 1986, Phys. Rev. A, 34, 2499. |
21 |
|
|
|
22 |
gezelter |
577 |
NPTf::NPTf ( SimInfo *theInfo, ForceFields* the_ff): |
23 |
gezelter |
576 |
Integrator( theInfo, the_ff ) |
24 |
|
|
{ |
25 |
|
|
int i; |
26 |
|
|
chi = 0.0; |
27 |
|
|
for(i = 0; i < 9; i++) eta[i] = 0.0; |
28 |
|
|
have_tau_thermostat = 0; |
29 |
|
|
have_tau_barostat = 0; |
30 |
|
|
have_target_temp = 0; |
31 |
|
|
have_target_pressure = 0; |
32 |
|
|
} |
33 |
|
|
|
34 |
gezelter |
577 |
void NPTf::moveA() { |
35 |
gezelter |
576 |
|
36 |
|
|
int i,j,k; |
37 |
|
|
int atomIndex, aMatIndex; |
38 |
|
|
DirectionalAtom* dAtom; |
39 |
|
|
double Tb[3]; |
40 |
|
|
double ji[3]; |
41 |
|
|
double rj[3]; |
42 |
|
|
double instaTemp, instaPress, instaVol; |
43 |
|
|
double tt2, tb2; |
44 |
|
|
double angle; |
45 |
gezelter |
577 |
double press[9]; |
46 |
|
|
const double p_convert = 1.63882576e8; |
47 |
gezelter |
576 |
|
48 |
|
|
tt2 = tauThermostat * tauThermostat; |
49 |
|
|
tb2 = tauBarostat * tauBarostat; |
50 |
|
|
|
51 |
|
|
instaTemp = tStats->getTemperature(); |
52 |
gezelter |
577 |
tStats->getPressureTensor(press); |
53 |
|
|
|
54 |
|
|
for (i=0; i < 9; i++) press[i] *= p_convert; |
55 |
|
|
|
56 |
gezelter |
576 |
instaVol = tStats->getVolume(); |
57 |
|
|
|
58 |
|
|
// first evolve chi a half step |
59 |
|
|
|
60 |
|
|
chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
61 |
|
|
|
62 |
gezelter |
577 |
eta[0] += dt2 * instaVol * (press[0] - targetPressure) / (NkBT*tb2); |
63 |
|
|
eta[1] += dt2 * instaVol * press[1] / (NkBT*tb2); |
64 |
|
|
eta[2] += dt2 * instaVol * press[2] / (NkBT*tb2); |
65 |
|
|
eta[3] += dt2 * instaVol * press[3] / (NkBT*tb2); |
66 |
|
|
eta[4] += dt2 * instaVol * (press[4] - targetPressure) / (NkBT*tb2); |
67 |
|
|
eta[5] += dt2 * instaVol * press[5] / (NkBT*tb2); |
68 |
|
|
eta[6] += dt2 * instaVol * press[6] / (NkBT*tb2); |
69 |
|
|
eta[7] += dt2 * instaVol * press[7] / (NkBT*tb2); |
70 |
|
|
eta[8] += dt2 * instaVol * (press[8] - targetPressure) / (NkBT*tb2); |
71 |
|
|
|
72 |
gezelter |
576 |
for( i=0; i<nAtoms; i++ ){ |
73 |
|
|
atomIndex = i * 3; |
74 |
|
|
aMatIndex = i * 9; |
75 |
|
|
|
76 |
|
|
// velocity half step |
77 |
gezelter |
577 |
|
78 |
|
|
vx = vel[atomIndex]; |
79 |
|
|
vy = vel[atomIndex+1]; |
80 |
|
|
vz = vel[atomIndex+2]; |
81 |
|
|
|
82 |
|
|
scx = (chi + eta[0])*vx + eta[1]*vy + eta[2]*vz; |
83 |
|
|
scy = eta[3]*vx + (chi + eta[4])*vy + eta[5]*vz; |
84 |
|
|
scz = eta[6]*vx + eta[7]*vy + (chi + eta[8])*vz; |
85 |
|
|
|
86 |
|
|
vx += dt2 * ((frc[atomIndex] /atoms[i]->getMass())*eConvert - scx); |
87 |
|
|
vy += dt2 * ((frc[atomIndex+1]/atoms[i]->getMass())*eConvert - scy); |
88 |
|
|
vz += dt2 * ((frc[atomIndex+2]/atoms[i]->getMass())*eConvert - scz); |
89 |
gezelter |
576 |
|
90 |
gezelter |
577 |
vel[atomIndex] = vx; |
91 |
|
|
vel[atomIndex+1] = vy; |
92 |
|
|
vel[atomIndex+2] = vz; |
93 |
|
|
|
94 |
gezelter |
576 |
// position whole step |
95 |
|
|
|
96 |
gezelter |
577 |
rj[0] = pos[atomIndex]; |
97 |
|
|
rj[1] = pos[atomIndex+1]; |
98 |
|
|
rj[2] = pos[atomIndex+2]; |
99 |
gezelter |
576 |
|
100 |
gezelter |
577 |
info->wrapVector(rj); |
101 |
gezelter |
576 |
|
102 |
gezelter |
577 |
scx = eta[0]*rj[0] + eta[1]*rj[1] + eta[2]*rj[2]; |
103 |
|
|
scy = eta[3]*rj[0] + eta[4]*rj[1] + eta[5]*rj[2]; |
104 |
|
|
scz = eta[6]*rj[0] + eta[7]*rj[1] + eta[8]*rj[2]; |
105 |
gezelter |
576 |
|
106 |
gezelter |
577 |
pos[atomIndex] += dt * (vel[atomIndex] + scx); |
107 |
|
|
pos[atomIndex+1] += dt * (vel[atomIndex+1] + scy); |
108 |
|
|
pos[atomIndex+2] += dt * (vel[atomIndex+2] + scz); |
109 |
gezelter |
576 |
|
110 |
|
|
if( atoms[i]->isDirectional() ){ |
111 |
|
|
|
112 |
|
|
dAtom = (DirectionalAtom *)atoms[i]; |
113 |
|
|
|
114 |
|
|
// get and convert the torque to body frame |
115 |
|
|
|
116 |
|
|
Tb[0] = dAtom->getTx(); |
117 |
|
|
Tb[1] = dAtom->getTy(); |
118 |
|
|
Tb[2] = dAtom->getTz(); |
119 |
|
|
|
120 |
|
|
dAtom->lab2Body( Tb ); |
121 |
|
|
|
122 |
|
|
// get the angular momentum, and propagate a half step |
123 |
|
|
|
124 |
|
|
ji[0] = dAtom->getJx(); |
125 |
|
|
ji[1] = dAtom->getJy(); |
126 |
|
|
ji[2] = dAtom->getJz(); |
127 |
|
|
|
128 |
|
|
ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*chi); |
129 |
|
|
ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*chi); |
130 |
|
|
ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*chi); |
131 |
|
|
|
132 |
|
|
// use the angular velocities to propagate the rotation matrix a |
133 |
|
|
// full time step |
134 |
|
|
|
135 |
|
|
// rotate about the x-axis |
136 |
|
|
angle = dt2 * ji[0] / dAtom->getIxx(); |
137 |
|
|
this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] ); |
138 |
|
|
|
139 |
|
|
// rotate about the y-axis |
140 |
|
|
angle = dt2 * ji[1] / dAtom->getIyy(); |
141 |
|
|
this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] ); |
142 |
|
|
|
143 |
|
|
// rotate about the z-axis |
144 |
|
|
angle = dt * ji[2] / dAtom->getIzz(); |
145 |
|
|
this->rotate( 0, 1, angle, ji, &Amat[aMatIndex] ); |
146 |
|
|
|
147 |
|
|
// rotate about the y-axis |
148 |
|
|
angle = dt2 * ji[1] / dAtom->getIyy(); |
149 |
|
|
this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] ); |
150 |
|
|
|
151 |
|
|
// rotate about the x-axis |
152 |
|
|
angle = dt2 * ji[0] / dAtom->getIxx(); |
153 |
|
|
this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] ); |
154 |
|
|
|
155 |
|
|
dAtom->setJx( ji[0] ); |
156 |
|
|
dAtom->setJy( ji[1] ); |
157 |
|
|
dAtom->setJz( ji[2] ); |
158 |
|
|
} |
159 |
|
|
|
160 |
|
|
} |
161 |
gezelter |
577 |
|
162 |
|
|
// Scale the box after all the positions have been moved: |
163 |
|
|
|
164 |
|
|
|
165 |
|
|
|
166 |
|
|
// Use a taylor expansion for eta products |
167 |
|
|
|
168 |
|
|
info->getBoxM(hm); |
169 |
|
|
|
170 |
|
|
|
171 |
|
|
|
172 |
|
|
|
173 |
|
|
|
174 |
|
|
|
175 |
|
|
info->scaleBox(exp(dt*eta)); |
176 |
|
|
|
177 |
|
|
|
178 |
gezelter |
576 |
} |
179 |
|
|
|
180 |
|
|
void NPTi::moveB( void ){ |
181 |
|
|
int i,j,k; |
182 |
|
|
int atomIndex; |
183 |
|
|
DirectionalAtom* dAtom; |
184 |
|
|
double Tb[3]; |
185 |
|
|
double ji[3]; |
186 |
|
|
double instaTemp, instaPress, instaVol; |
187 |
|
|
double tt2, tb2; |
188 |
|
|
|
189 |
|
|
tt2 = tauThermostat * tauThermostat; |
190 |
|
|
tb2 = tauBarostat * tauBarostat; |
191 |
|
|
|
192 |
|
|
instaTemp = tStats->getTemperature(); |
193 |
|
|
instaPress = tStats->getPressure(); |
194 |
|
|
instaVol = tStats->getVolume(); |
195 |
|
|
|
196 |
|
|
chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
197 |
|
|
eta += dt2 * ( instaVol * (instaPress - targetPressure) / (NkBT*tb2)); |
198 |
|
|
|
199 |
|
|
for( i=0; i<nAtoms; i++ ){ |
200 |
|
|
atomIndex = i * 3; |
201 |
|
|
|
202 |
|
|
// velocity half step |
203 |
|
|
for( j=atomIndex; j<(atomIndex+3); j++ ) |
204 |
|
|
for( j=atomIndex; j<(atomIndex+3); j++ ) |
205 |
|
|
vel[j] += dt2 * ((frc[j]/atoms[i]->getMass())*eConvert |
206 |
|
|
- vel[j]*(chi+eta)); |
207 |
|
|
|
208 |
|
|
if( atoms[i]->isDirectional() ){ |
209 |
|
|
|
210 |
|
|
dAtom = (DirectionalAtom *)atoms[i]; |
211 |
|
|
|
212 |
|
|
// get and convert the torque to body frame |
213 |
|
|
|
214 |
|
|
Tb[0] = dAtom->getTx(); |
215 |
|
|
Tb[1] = dAtom->getTy(); |
216 |
|
|
Tb[2] = dAtom->getTz(); |
217 |
|
|
|
218 |
|
|
dAtom->lab2Body( Tb ); |
219 |
|
|
|
220 |
|
|
// get the angular momentum, and complete the angular momentum |
221 |
|
|
// half step |
222 |
|
|
|
223 |
|
|
ji[0] = dAtom->getJx(); |
224 |
|
|
ji[1] = dAtom->getJy(); |
225 |
|
|
ji[2] = dAtom->getJz(); |
226 |
|
|
|
227 |
|
|
ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*chi); |
228 |
|
|
ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*chi); |
229 |
|
|
ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*chi); |
230 |
|
|
|
231 |
|
|
dAtom->setJx( ji[0] ); |
232 |
|
|
dAtom->setJy( ji[1] ); |
233 |
|
|
dAtom->setJz( ji[2] ); |
234 |
|
|
} |
235 |
|
|
} |
236 |
|
|
} |
237 |
|
|
|
238 |
|
|
int NPTi::readyCheck() { |
239 |
|
|
|
240 |
|
|
// First check to see if we have a target temperature. |
241 |
|
|
// Not having one is fatal. |
242 |
|
|
|
243 |
|
|
if (!have_target_temp) { |
244 |
|
|
sprintf( painCave.errMsg, |
245 |
|
|
"NPTi error: You can't use the NPTi integrator\n" |
246 |
|
|
" without a targetTemp!\n" |
247 |
|
|
); |
248 |
|
|
painCave.isFatal = 1; |
249 |
|
|
simError(); |
250 |
|
|
return -1; |
251 |
|
|
} |
252 |
|
|
|
253 |
|
|
if (!have_target_pressure) { |
254 |
|
|
sprintf( painCave.errMsg, |
255 |
|
|
"NPTi error: You can't use the NPTi integrator\n" |
256 |
|
|
" without a targetPressure!\n" |
257 |
|
|
); |
258 |
|
|
painCave.isFatal = 1; |
259 |
|
|
simError(); |
260 |
|
|
return -1; |
261 |
|
|
} |
262 |
|
|
|
263 |
|
|
// We must set tauThermostat. |
264 |
|
|
|
265 |
|
|
if (!have_tau_thermostat) { |
266 |
|
|
sprintf( painCave.errMsg, |
267 |
|
|
"NPTi error: If you use the NPTi\n" |
268 |
|
|
" integrator, you must set tauThermostat.\n"); |
269 |
|
|
painCave.isFatal = 1; |
270 |
|
|
simError(); |
271 |
|
|
return -1; |
272 |
|
|
} |
273 |
|
|
|
274 |
|
|
// We must set tauBarostat. |
275 |
|
|
|
276 |
|
|
if (!have_tau_barostat) { |
277 |
|
|
sprintf( painCave.errMsg, |
278 |
|
|
"NPTi error: If you use the NPTi\n" |
279 |
|
|
" integrator, you must set tauBarostat.\n"); |
280 |
|
|
painCave.isFatal = 1; |
281 |
|
|
simError(); |
282 |
|
|
return -1; |
283 |
|
|
} |
284 |
|
|
|
285 |
|
|
// We need NkBT a lot, so just set it here: |
286 |
|
|
|
287 |
|
|
NkBT = (double)info->ndf * kB * targetTemp; |
288 |
|
|
|
289 |
|
|
return 1; |
290 |
|
|
} |