1 |
#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 |
DoubleData * chiValue; |
21 |
DoubleData * 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<DoubleData*>(data); |
39 |
} |
40 |
|
41 |
data = info->getProperty(INTEGRALOFCHIDT_ID); |
42 |
if(data){ |
43 |
integralOfChidtValue = dynamic_cast<DoubleData*>(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 |
double Tb[3], ji[3]; |
67 |
double mass; |
68 |
double vel[3], pos[3], frc[3]; |
69 |
|
70 |
double instTemp; |
71 |
|
72 |
// We need the temperature at time = t for the chi update below: |
73 |
|
74 |
instTemp = tStats->getTemperature(); |
75 |
|
76 |
for( i=0; i < integrableObjects.size(); i++ ){ |
77 |
|
78 |
integrableObjects[i]->getVel( vel ); |
79 |
integrableObjects[i]->getPos( pos ); |
80 |
integrableObjects[i]->getFrc( frc ); |
81 |
|
82 |
mass = integrableObjects[i]->getMass(); |
83 |
|
84 |
for (j=0; j < 3; j++) { |
85 |
// velocity half step (use chi from previous step here): |
86 |
vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*chi); |
87 |
// position whole step |
88 |
pos[j] += dt * vel[j]; |
89 |
} |
90 |
|
91 |
integrableObjects[i]->setVel( vel ); |
92 |
integrableObjects[i]->setPos( pos ); |
93 |
|
94 |
if( integrableObjects[i]->isDirectional() ){ |
95 |
|
96 |
// get and convert the torque to body frame |
97 |
|
98 |
integrableObjects[i]->getTrq( Tb ); |
99 |
integrableObjects[i]->lab2Body( Tb ); |
100 |
|
101 |
// get the angular momentum, and propagate a half step |
102 |
|
103 |
integrableObjects[i]->getJ( ji ); |
104 |
|
105 |
for (j=0; j < 3; j++) |
106 |
ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi); |
107 |
|
108 |
this->rotationPropagation( integrableObjects[i], ji ); |
109 |
|
110 |
integrableObjects[i]->setJ( ji ); |
111 |
} |
112 |
} |
113 |
|
114 |
if(nConstrained) |
115 |
constrainA(); |
116 |
|
117 |
// Finally, evolve chi a half step (just like a velocity) using |
118 |
// temperature at time t, not time t+dt/2 |
119 |
|
120 |
//std::cerr << "targetTemp = " << targetTemp << " instTemp = " << instTemp << " tauThermostat = " << tauThermostat << " integral of Chi = " << integralOfChidt << "\n"; |
121 |
|
122 |
chi += dt2 * ( instTemp / targetTemp - 1.0) / (tauThermostat*tauThermostat); |
123 |
integralOfChidt += chi*dt2; |
124 |
|
125 |
} |
126 |
|
127 |
template<typename T> void NVT<T>::moveB( void ){ |
128 |
int i, j, k; |
129 |
double Tb[3], ji[3]; |
130 |
double vel[3], frc[3]; |
131 |
double mass; |
132 |
double instTemp; |
133 |
double oldChi, prevChi; |
134 |
|
135 |
// Set things up for the iteration: |
136 |
|
137 |
oldChi = chi; |
138 |
|
139 |
for( i=0; i < integrableObjects.size(); i++ ){ |
140 |
|
141 |
integrableObjects[i]->getVel( vel ); |
142 |
|
143 |
for (j=0; j < 3; j++) |
144 |
oldVel[3*i + j] = vel[j]; |
145 |
|
146 |
if( integrableObjects[i]->isDirectional() ){ |
147 |
|
148 |
integrableObjects[i]->getJ( ji ); |
149 |
|
150 |
for (j=0; j < 3; j++) |
151 |
oldJi[3*i + j] = ji[j]; |
152 |
|
153 |
} |
154 |
} |
155 |
|
156 |
// do the iteration: |
157 |
|
158 |
for (k=0; k < 4; k++) { |
159 |
|
160 |
instTemp = tStats->getTemperature(); |
161 |
|
162 |
// evolve chi another half step using the temperature at t + dt/2 |
163 |
|
164 |
prevChi = chi; |
165 |
chi = oldChi + dt2 * ( instTemp / targetTemp - 1.0) / |
166 |
(tauThermostat*tauThermostat); |
167 |
|
168 |
for( i=0; i < integrableObjects.size(); i++ ){ |
169 |
|
170 |
integrableObjects[i]->getFrc( frc ); |
171 |
integrableObjects[i]->getVel(vel); |
172 |
|
173 |
mass = integrableObjects[i]->getMass(); |
174 |
|
175 |
// velocity half step |
176 |
for (j=0; j < 3; j++) |
177 |
vel[j] = oldVel[3*i+j] + dt2 * ((frc[j] / mass ) * eConvert - oldVel[3*i + j]*chi); |
178 |
|
179 |
integrableObjects[i]->setVel( vel ); |
180 |
|
181 |
if( integrableObjects[i]->isDirectional() ){ |
182 |
|
183 |
// get and convert the torque to body frame |
184 |
|
185 |
integrableObjects[i]->getTrq( Tb ); |
186 |
integrableObjects[i]->lab2Body( Tb ); |
187 |
|
188 |
for (j=0; j < 3; j++) |
189 |
ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * eConvert - oldJi[3*i+j]*chi); |
190 |
|
191 |
integrableObjects[i]->setJ( ji ); |
192 |
} |
193 |
} |
194 |
|
195 |
if(nConstrained) |
196 |
constrainB(); |
197 |
|
198 |
if (fabs(prevChi - chi) <= chiTolerance) break; |
199 |
} |
200 |
|
201 |
integralOfChidt += dt2*chi; |
202 |
} |
203 |
|
204 |
template<typename T> void NVT<T>::resetIntegrator( void ){ |
205 |
|
206 |
chi = 0.0; |
207 |
integralOfChidt = 0.0; |
208 |
} |
209 |
|
210 |
template<typename T> int NVT<T>::readyCheck() { |
211 |
|
212 |
//check parent's readyCheck() first |
213 |
if (T::readyCheck() == -1) |
214 |
return -1; |
215 |
|
216 |
// First check to see if we have a target temperature. |
217 |
// Not having one is fatal. |
218 |
|
219 |
if (!have_target_temp) { |
220 |
sprintf( painCave.errMsg, |
221 |
"You can't use the NVT integrator without a targetTemp!\n" |
222 |
); |
223 |
painCave.isFatal = 1; |
224 |
painCave.severity = OOPSE_ERROR; |
225 |
simError(); |
226 |
return -1; |
227 |
} |
228 |
|
229 |
// We must set tauThermostat. |
230 |
|
231 |
if (!have_tau_thermostat) { |
232 |
sprintf( painCave.errMsg, |
233 |
"If you use the constant temperature\n" |
234 |
"\tintegrator, you must set tauThermostat.\n"); |
235 |
painCave.severity = OOPSE_ERROR; |
236 |
painCave.isFatal = 1; |
237 |
simError(); |
238 |
return -1; |
239 |
} |
240 |
|
241 |
if (!have_chi_tolerance) { |
242 |
sprintf( painCave.errMsg, |
243 |
"In NVT integrator: setting chi tolerance to 1e-6\n"); |
244 |
chiTolerance = 1e-6; |
245 |
have_chi_tolerance = 1; |
246 |
painCave.severity = OOPSE_INFO; |
247 |
painCave.isFatal = 0; |
248 |
simError(); |
249 |
} |
250 |
|
251 |
return 1; |
252 |
|
253 |
} |
254 |
|
255 |
template<typename T> double NVT<T>::getConservedQuantity(void){ |
256 |
|
257 |
double conservedQuantity; |
258 |
double fkBT; |
259 |
double Energy; |
260 |
double thermostat_kinetic; |
261 |
double thermostat_potential; |
262 |
|
263 |
fkBT = (double)(info->ndf) * kB * targetTemp; |
264 |
|
265 |
Energy = tStats->getTotalE(); |
266 |
|
267 |
thermostat_kinetic = fkBT* tauThermostat * tauThermostat * chi * chi / |
268 |
(2.0 * eConvert); |
269 |
|
270 |
thermostat_potential = fkBT * integralOfChidt / eConvert; |
271 |
|
272 |
conservedQuantity = Energy + thermostat_kinetic + thermostat_potential; |
273 |
|
274 |
return conservedQuantity; |
275 |
} |
276 |
|
277 |
template<typename T> string NVT<T>::getAdditionalParameters(void){ |
278 |
string parameters; |
279 |
const int BUFFERSIZE = 2000; // size of the read buffer |
280 |
char buffer[BUFFERSIZE]; |
281 |
|
282 |
sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt); |
283 |
parameters += buffer; |
284 |
|
285 |
return parameters; |
286 |
} |