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Comparing:
trunk/OOPSE/libmdtools/NVT.cpp (file contents), Revision 565 by gezelter, Tue Jun 24 22:51:57 2003 UTC vs.
branches/new-templateless/OOPSE/libmdtools/NVT.cpp (file contents), Revision 850 by mmeineke, Mon Nov 3 22:07:17 2003 UTC

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

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