1 |
tim |
1695 |
#include <math.h>
|
2 |
|
|
|
3 |
|
|
#include "primitives/Atom.hpp"
|
4 |
|
|
#include "primitives/SRI.hpp"
|
5 |
|
|
#include "primitives/AbstractClasses.hpp"
|
6 |
|
|
#include "brains/SimInfo.hpp"
|
7 |
|
|
#include "UseTheForce/ForceFields.hpp"
|
8 |
|
|
#include "brains/Thermo.hpp"
|
9 |
|
|
#include "io/ReadWrite.hpp"
|
10 |
|
|
#include "integrators/Integrator.hpp"
|
11 |
|
|
#include "utils/simError.h"
|
12 |
|
|
|
13 |
|
|
|
14 |
|
|
// Basic thermostating via Hoover, Phys.Rev.A, 1985, Vol. 31 (5) 1695-1697
|
15 |
|
|
|
16 |
|
|
template<typename T> NVT<T>::NVT ( SimInfo *theInfo, ForceFields* the_ff):
|
17 |
|
|
T( theInfo, the_ff )
|
18 |
|
|
{
|
19 |
|
|
GenericData* data;
|
20 |
|
|
DoubleGenericData * chiValue;
|
21 |
|
|
DoubleGenericData * integralOfChidtValue;
|
22 |
|
|
|
23 |
|
|
chiValue = NULL;
|
24 |
|
|
integralOfChidtValue = NULL;
|
25 |
|
|
|
26 |
|
|
chi = 0.0;
|
27 |
|
|
have_tau_thermostat = 0;
|
28 |
|
|
have_target_temp = 0;
|
29 |
|
|
have_chi_tolerance = 0;
|
30 |
|
|
integralOfChidt = 0.0;
|
31 |
|
|
|
32 |
|
|
|
33 |
|
|
if( theInfo->useInitXSstate ){
|
34 |
|
|
|
35 |
|
|
// retrieve chi and integralOfChidt from simInfo
|
36 |
|
|
data = info->getProperty(CHIVALUE_ID);
|
37 |
|
|
if(data){
|
38 |
|
|
chiValue = dynamic_cast<DoubleGenericData*>(data);
|
39 |
|
|
}
|
40 |
|
|
|
41 |
|
|
data = info->getProperty(INTEGRALOFCHIDT_ID);
|
42 |
|
|
if(data){
|
43 |
|
|
integralOfChidtValue = dynamic_cast<DoubleGenericData*>(data);
|
44 |
|
|
}
|
45 |
|
|
|
46 |
|
|
// chi and integralOfChidt should appear by pair
|
47 |
|
|
if(chiValue && integralOfChidtValue){
|
48 |
|
|
chi = chiValue->getData();
|
49 |
|
|
integralOfChidt = integralOfChidtValue->getData();
|
50 |
|
|
}
|
51 |
|
|
}
|
52 |
|
|
|
53 |
|
|
oldVel = new double[3*integrableObjects.size()];
|
54 |
|
|
oldJi = new double[3*integrableObjects.size()];
|
55 |
|
|
}
|
56 |
|
|
|
57 |
|
|
template<typename T> NVT<T>::~NVT() {
|
58 |
|
|
delete[] oldVel;
|
59 |
|
|
delete[] oldJi;
|
60 |
|
|
}
|
61 |
|
|
|
62 |
|
|
template<typename T> void NVT<T>::moveA() {
|
63 |
|
|
|
64 |
|
|
int i, j;
|
65 |
|
|
DirectionalAtom* dAtom;
|
66 |
|
|
Vector3d Tb;
|
67 |
|
|
Vector3d ji;
|
68 |
|
|
double mass;
|
69 |
|
|
Vector3d vel;
|
70 |
|
|
Vector3d pos;
|
71 |
|
|
Vector3d frc;
|
72 |
|
|
|
73 |
|
|
double instTemp;
|
74 |
|
|
|
75 |
|
|
// We need the temperature at time = t for the chi update below:
|
76 |
|
|
|
77 |
|
|
instTemp = tStats->getTemperature();
|
78 |
|
|
|
79 |
|
|
for( i=0; i < integrableObjects.size(); i++ ){
|
80 |
|
|
|
81 |
|
|
vel = integrableObjects[i]->getVel();
|
82 |
|
|
pos = integrableObjects[i]->getPos();
|
83 |
|
|
integrableObjects[i]->getFrc( frc );
|
84 |
|
|
|
85 |
|
|
mass = integrableObjects[i]->getMass();
|
86 |
|
|
|
87 |
|
|
for (j=0; j < 3; j++) {
|
88 |
|
|
// velocity half step (use chi from previous step here):
|
89 |
|
|
vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*chi);
|
90 |
|
|
// position whole step
|
91 |
|
|
pos[j] += dt * vel[j];
|
92 |
|
|
}
|
93 |
|
|
|
94 |
|
|
integrableObjects[i]->setVel( vel );
|
95 |
|
|
integrableObjects[i]->setPos( pos );
|
96 |
|
|
|
97 |
|
|
if( integrableObjects[i]->isDirectional() ){
|
98 |
|
|
|
99 |
|
|
// get and convert the torque to body frame
|
100 |
|
|
|
101 |
|
|
Tb = integrableObjects[i]->getTrq();
|
102 |
|
|
integrableObjects[i]->lab2Body( Tb );
|
103 |
|
|
|
104 |
|
|
// get the angular momentum, and propagate a half step
|
105 |
|
|
|
106 |
|
|
ji = integrableObjects[i]->getJ();
|
107 |
|
|
|
108 |
|
|
for (j=0; j < 3; j++)
|
109 |
|
|
ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);
|
110 |
|
|
|
111 |
|
|
this->rotationPropagation( integrableObjects[i], ji );
|
112 |
|
|
|
113 |
|
|
integrableObjects[i]->setJ( ji );
|
114 |
|
|
}
|
115 |
|
|
}
|
116 |
|
|
|
117 |
|
|
if(nConstrained)
|
118 |
|
|
constrainA();
|
119 |
|
|
|
120 |
|
|
// Finally, evolve chi a half step (just like a velocity) using
|
121 |
|
|
// temperature at time t, not time t+dt/2
|
122 |
|
|
|
123 |
|
|
//std::cerr << "targetTemp = " << targetTemp << " instTemp = " << instTemp << " tauThermostat = " << tauThermostat << " integral of Chi = " << integralOfChidt << "\n";
|
124 |
|
|
|
125 |
|
|
chi += dt2 * ( instTemp / targetTemp - 1.0) / (tauThermostat*tauThermostat);
|
126 |
|
|
integralOfChidt += chi*dt2;
|
127 |
|
|
|
128 |
|
|
}
|
129 |
|
|
|
130 |
|
|
template<typename T> void NVT<T>::moveB( void ){
|
131 |
|
|
int i, j, k;
|
132 |
|
|
double Tb[3], ji[3];
|
133 |
|
|
double vel[3], frc[3];
|
134 |
|
|
double mass;
|
135 |
|
|
double instTemp;
|
136 |
|
|
double oldChi, prevChi;
|
137 |
|
|
|
138 |
|
|
// Set things up for the iteration:
|
139 |
|
|
|
140 |
|
|
oldChi = chi;
|
141 |
|
|
|
142 |
|
|
for( i=0; i < integrableObjects.size(); i++ ){
|
143 |
|
|
|
144 |
|
|
vel = integrableObjects[i]->getVel();
|
145 |
|
|
|
146 |
|
|
for (j=0; j < 3; j++)
|
147 |
|
|
oldVel[3*i + j] = vel[j];
|
148 |
|
|
|
149 |
|
|
if( integrableObjects[i]->isDirectional() ){
|
150 |
|
|
|
151 |
|
|
ji = integrableObjects[i]->getJ();
|
152 |
|
|
|
153 |
|
|
for (j=0; j < 3; j++)
|
154 |
|
|
oldJi[3*i + j] = ji[j];
|
155 |
|
|
|
156 |
|
|
}
|
157 |
|
|
}
|
158 |
|
|
|
159 |
|
|
// do the iteration:
|
160 |
|
|
|
161 |
|
|
for (k=0; k < 4; k++) {
|
162 |
|
|
|
163 |
|
|
instTemp = tStats->getTemperature();
|
164 |
|
|
|
165 |
|
|
// evolve chi another half step using the temperature at t + dt/2
|
166 |
|
|
|
167 |
|
|
prevChi = chi;
|
168 |
|
|
chi = oldChi + dt2 * ( instTemp / targetTemp - 1.0) /
|
169 |
|
|
(tauThermostat*tauThermostat);
|
170 |
|
|
|
171 |
|
|
for( i=0; i < integrableObjects.size(); i++ ){
|
172 |
|
|
|
173 |
|
|
integrableObjects[i]->getFrc( frc );
|
174 |
|
|
vel = integrableObjects[i]->getVel();
|
175 |
|
|
|
176 |
|
|
mass = integrableObjects[i]->getMass();
|
177 |
|
|
|
178 |
|
|
// velocity half step
|
179 |
|
|
for (j=0; j < 3; j++)
|
180 |
|
|
vel[j] = oldVel[3*i+j] + dt2 * ((frc[j] / mass ) * eConvert - oldVel[3*i + j]*chi);
|
181 |
|
|
|
182 |
|
|
integrableObjects[i]->setVel( vel );
|
183 |
|
|
|
184 |
|
|
if( integrableObjects[i]->isDirectional() ){
|
185 |
|
|
|
186 |
|
|
// get and convert the torque to body frame
|
187 |
|
|
|
188 |
|
|
Tb = integrableObjects[i]->getTrq();
|
189 |
|
|
integrableObjects[i]->lab2Body( Tb );
|
190 |
|
|
|
191 |
|
|
for (j=0; j < 3; j++)
|
192 |
|
|
ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * eConvert - oldJi[3*i+j]*chi);
|
193 |
|
|
|
194 |
|
|
integrableObjects[i]->setJ( ji );
|
195 |
|
|
}
|
196 |
|
|
}
|
197 |
|
|
|
198 |
|
|
if(nConstrained)
|
199 |
|
|
constrainB();
|
200 |
|
|
|
201 |
|
|
if (fabs(prevChi - chi) <= chiTolerance) break;
|
202 |
|
|
}
|
203 |
|
|
|
204 |
|
|
integralOfChidt += dt2*chi;
|
205 |
|
|
}
|
206 |
|
|
|
207 |
|
|
template<typename T> void NVT<T>::resetIntegrator( void ){
|
208 |
|
|
|
209 |
|
|
chi = 0.0;
|
210 |
|
|
integralOfChidt = 0.0;
|
211 |
|
|
}
|
212 |
|
|
|
213 |
|
|
template<typename T> int NVT<T>::readyCheck() {
|
214 |
|
|
|
215 |
|
|
//check parent's readyCheck() first
|
216 |
|
|
if (T::readyCheck() == -1)
|
217 |
|
|
return -1;
|
218 |
|
|
|
219 |
|
|
// First check to see if we have a target temperature.
|
220 |
|
|
// Not having one is fatal.
|
221 |
|
|
|
222 |
|
|
if (!have_target_temp) {
|
223 |
|
|
sprintf( painCave.errMsg,
|
224 |
|
|
"You can't use the NVT integrator without a targetTemp!\n"
|
225 |
|
|
);
|
226 |
|
|
painCave.isFatal = 1;
|
227 |
|
|
painCave.severity = OOPSE_ERROR;
|
228 |
|
|
simError();
|
229 |
|
|
return -1;
|
230 |
|
|
}
|
231 |
|
|
|
232 |
|
|
// We must set tauThermostat.
|
233 |
|
|
|
234 |
|
|
if (!have_tau_thermostat) {
|
235 |
|
|
sprintf( painCave.errMsg,
|
236 |
|
|
"If you use the constant temperature\n"
|
237 |
|
|
"\tintegrator, you must set tauThermostat.\n");
|
238 |
|
|
painCave.severity = OOPSE_ERROR;
|
239 |
|
|
painCave.isFatal = 1;
|
240 |
|
|
simError();
|
241 |
|
|
return -1;
|
242 |
|
|
}
|
243 |
|
|
|
244 |
|
|
if (!have_chi_tolerance) {
|
245 |
|
|
sprintf( painCave.errMsg,
|
246 |
|
|
"In NVT integrator: setting chi tolerance to 1e-6\n");
|
247 |
|
|
chiTolerance = 1e-6;
|
248 |
|
|
have_chi_tolerance = 1;
|
249 |
|
|
painCave.severity = OOPSE_INFO;
|
250 |
|
|
painCave.isFatal = 0;
|
251 |
|
|
simError();
|
252 |
|
|
}
|
253 |
|
|
|
254 |
|
|
return 1;
|
255 |
|
|
|
256 |
|
|
}
|
257 |
|
|
|
258 |
|
|
template<typename T> double NVT<T>::getConservedQuantity(void){
|
259 |
|
|
|
260 |
|
|
double conservedQuantity;
|
261 |
|
|
double fkBT;
|
262 |
|
|
double Energy;
|
263 |
|
|
double thermostat_kinetic;
|
264 |
|
|
double thermostat_potential;
|
265 |
|
|
|
266 |
|
|
fkBT = (double)(info->ndf) * kB * targetTemp;
|
267 |
|
|
|
268 |
|
|
Energy = tStats->getTotalE();
|
269 |
|
|
|
270 |
|
|
thermostat_kinetic = fkBT* tauThermostat * tauThermostat * chi * chi /
|
271 |
|
|
(2.0 * eConvert);
|
272 |
|
|
|
273 |
|
|
thermostat_potential = fkBT * integralOfChidt / eConvert;
|
274 |
|
|
|
275 |
|
|
conservedQuantity = Energy + thermostat_kinetic + thermostat_potential;
|
276 |
|
|
|
277 |
|
|
return conservedQuantity;
|
278 |
|
|
}
|
279 |
|
|
|
280 |
|
|
template<typename T> string NVT<T>::getAdditionalParameters(void){
|
281 |
|
|
string parameters;
|
282 |
|
|
const int BUFFERSIZE = 2000; // size of the read buffer
|
283 |
|
|
char buffer[BUFFERSIZE];
|
284 |
|
|
|
285 |
|
|
sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt);
|
286 |
|
|
parameters += buffer;
|
287 |
|
|
|
288 |
|
|
return parameters;
|
289 |
|
|
}
|