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Comparing trunk/OOPSE/libmdtools/NPTi.cpp (file contents):
Revision 611 by gezelter, Tue Jul 15 17:10:50 2003 UTC vs.
Revision 787 by mmeineke, Thu Sep 25 19:27:15 2003 UTC

# Line 9 | Line 9
9   #include "Integrator.hpp"
10   #include "simError.h"
11  
12 + #ifdef IS_MPI
13 + #include "mpiSimulation.hpp"
14 + #endif
15  
16   // Basic isotropic thermostating and barostating via the Melchionna
17   // modification of the Hoover algorithm:
# Line 20 | Line 23
23   //
24   //    Hoover, W. G., 1986, Phys. Rev. A, 34, 2499.
25  
26 < NPTi::NPTi ( SimInfo *theInfo, ForceFields* the_ff):
27 <  Integrator( theInfo, the_ff )
26 > template<typename T> NPTi<T>::NPTi ( SimInfo *theInfo, ForceFields* the_ff):
27 >  T( theInfo, the_ff )
28   {
26 –  chi = 0.0;
29    eta = 0.0;
30 <  have_tau_thermostat = 0;
29 <  have_tau_barostat = 0;
30 <  have_target_temp = 0;
31 <  have_target_pressure = 0;
30 >  oldEta = 0.0;
31   }
32  
33 < void NPTi::moveA() {
34 <  
35 <  int i, j;
37 <  DirectionalAtom* dAtom;
38 <  double Tb[3], ji[3];
39 <  double A[3][3], I[3][3];
40 <  double angle, mass;
41 <  double vel[3], pos[3], frc[3];
33 > template<typename T> NPTi<T>::~NPTi() {
34 >  //nothing for now
35 > }
36  
37 <  double rj[3];
38 <  double instaTemp, instaPress, instaVol;
39 <  double tt2, tb2, scaleFactor;
37 > template<typename T> void NPTi<T>::resetIntegrator() {
38 >  eta = 0.0;
39 >  T::resetIntegrator();
40 > }
41  
42 <  tt2 = tauThermostat * tauThermostat;
43 <  tb2 = tauBarostat * tauBarostat;
42 > template<typename T> void NPTi<T>::evolveEtaA() {
43 >  eta += dt2 * ( instaVol * (instaPress - targetPressure) /
44 >                 (p_convert*NkBT*tb2));
45 >  oldEta = eta;
46 > }
47  
48 <  instaTemp = tStats->getTemperature();
51 <  instaPress = tStats->getPressure();
52 <  instaVol = tStats->getVolume();
53 <  
54 <   // first evolve chi a half step
48 > template<typename T> void NPTi<T>::evolveEtaB() {
49    
50 <  chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
51 <  eta += dt2 * ( instaVol * (instaPress - targetPressure) /
50 >  prevEta = eta;
51 >  eta = oldEta + dt2 * ( instaVol * (instaPress - targetPressure) /
52                   (p_convert*NkBT*tb2));
53 + }
54  
55 <  for( i=0; i<nAtoms; i++ ){
56 <    atoms[i]->getVel( vel );
62 <    atoms[i]->getPos( pos );
63 <    atoms[i]->getFrc( frc );
55 > template<typename T> void NPTi<T>::getVelScaleA(double sc[3], double vel[3]) {
56 >  int i;
57  
58 <    mass = atoms[i]->getMass();
58 >  for(i=0; i<3; i++) sc[i] = vel[i] * ( chi + eta );
59 > }
60  
61 <    for (j=0; j < 3; j++) {
62 <      vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*(chi+eta));
69 <      rj[j] = pos[j];
70 <    }
61 > template<typename T> void NPTi<T>::getVelScaleB(double sc[3], int index ){
62 >  int i;
63  
64 <    atoms[i]->setVel( vel );
64 >  for(i=0; i<3; i++) sc[i] = oldVel[index*3 + i] * ( chi + eta );
65 > }
66  
74 –    info->wrapVector(rj);
67  
68 <    for (j = 0; j < 3; j++)
69 <      pos[j] += dt * (vel[j] + eta*rj[j]);
68 > template<typename T> void NPTi<T>::getPosScale(double pos[3], double COM[3],
69 >                                               int index, double sc[3]){
70 >  int j;
71  
72 +  for(j=0; j<3; j++)
73 +    sc[j] = ( oldPos[index*3+j] + pos[j]) / 2.0 - COM[j];
74  
75 <    atoms[i]->setPos( pos );
75 >  for(j=0; j<3; j++)
76 >    sc[j] *= eta;
77 > }
78  
79 + template<typename T> void NPTi<T>::scaleSimBox( void ){
80  
81 <    if( atoms[i]->isDirectional() ){
81 >  double scaleFactor;
82  
85 –      dAtom = (DirectionalAtom *)atoms[i];
86 –          
87 –      // get and convert the torque to body frame
88 –      
89 –      dAtom->getTrq( Tb );
90 –      dAtom->lab2Body( Tb );
91 –      
92 –      // get the angular momentum, and propagate a half step
93 –
94 –      dAtom->getJ( ji );
95 –
96 –      for (j=0; j < 3; j++)
97 –        ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);
98 –      
99 –      // use the angular velocities to propagate the rotation matrix a
100 –      // full time step
101 –
102 –      dAtom->getA(A);
103 –      dAtom->getI(I);
104 –    
105 –      // rotate about the x-axis      
106 –      angle = dt2 * ji[0] / I[0][0];
107 –      this->rotate( 1, 2, angle, ji, A );
108 –
109 –      // rotate about the y-axis
110 –      angle = dt2 * ji[1] / I[1][1];
111 –      this->rotate( 2, 0, angle, ji, A );
112 –      
113 –      // rotate about the z-axis
114 –      angle = dt * ji[2] / I[2][2];
115 –      this->rotate( 0, 1, angle, ji, A);
116 –      
117 –      // rotate about the y-axis
118 –      angle = dt2 * ji[1] / I[1][1];
119 –      this->rotate( 2, 0, angle, ji, A );
120 –      
121 –       // rotate about the x-axis
122 –      angle = dt2 * ji[0] / I[0][0];
123 –      this->rotate( 1, 2, angle, ji, A );
124 –      
125 –      dAtom->setJ( ji );
126 –      dAtom->setA( A  );    
127 –    }                
128 –
129 –  }
130 –
131 –  // Scale the box after all the positions have been moved:
132 –  
83    scaleFactor = exp(dt*eta);
84  
85 <  if (scaleFactor > 1.1 || scaleFactor < 0.9) {
85 >  if ((scaleFactor > 1.1) || (scaleFactor < 0.9)) {
86      sprintf( painCave.errMsg,
87               "NPTi error: Attempting a Box scaling of more than 10 percent"
88               " check your tauBarostat, as it is probably too small!\n"
# Line 141 | Line 91 | void NPTi::moveA() {
91      painCave.isFatal = 1;
92      simError();
93    } else {        
94 <    info->scaleBox(exp(dt*eta));      
95 <  }
94 >    info->scaleBox(scaleFactor);      
95 >  }  
96 >
97   }
98  
99 < void NPTi::moveB( void ){
99 > template<typename T> bool NPTi<T>::etaConverged() {
100  
101 <  int i, j;
102 <  DirectionalAtom* dAtom;
152 <  double Tb[3], ji[3];
153 <  double vel[3], frc[3];
154 <  double mass;
101 >  return ( fabs(prevEta - eta) <= etaTolerance );
102 > }
103  
104 <  double instaTemp, instaPress, instaVol;
157 <  double tt2, tb2;
158 <  
159 <  tt2 = tauThermostat * tauThermostat;
160 <  tb2 = tauBarostat * tauBarostat;
104 > template<typename T> double NPTi<T>::getConservedQuantity(void){
105  
106 <  instaTemp = tStats->getTemperature();
107 <  instaPress = tStats->getPressure();
108 <  instaVol = tStats->getVolume();
109 <
110 <  chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
111 <  eta += dt2 * ( instaVol * (instaPress - targetPressure) /
168 <                 (p_convert*NkBT*tb2));
106 >  double conservedQuantity;
107 >  double Energy;
108 >  double thermostat_kinetic;
109 >  double thermostat_potential;
110 >  double barostat_kinetic;
111 >  double barostat_potential;
112    
113 <  for( i=0; i<nAtoms; i++ ){
113 >  Energy = tStats->getTotalE();
114  
115 <    atoms[i]->getVel( vel );
116 <    atoms[i]->getFrc( frc );
115 >  thermostat_kinetic = fkBT* tt2 * chi * chi /
116 >    (2.0 * eConvert);
117  
118 <    mass = atoms[i]->getMass();
118 >  thermostat_potential = fkBT* integralOfChidt / eConvert;
119  
177 –    // velocity half step
178 –    for (j=0; j < 3; j++)
179 –      vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*(chi+eta));
180 –    
181 –    atoms[i]->setVel( vel );
120  
121 <    if( atoms[i]->isDirectional() ){
122 <
185 <      dAtom = (DirectionalAtom *)atoms[i];
186 <
187 <      // get and convert the torque to body frame      
188 <
189 <      dAtom->getTrq( Tb );
190 <      dAtom->lab2Body( Tb );
191 <
192 <      // get the angular momentum, and propagate a half step
193 <
194 <      dAtom->getJ( ji );
195 <
196 <      for (j=0; j < 3; j++)
197 <        ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);    
198 <
199 <      dAtom->setJ( ji );
200 <    }
201 <  }
202 < }
203 <
204 < int NPTi::readyCheck() {
205 <
206 <  // First check to see if we have a target temperature.
207 <  // Not having one is fatal.
121 >  barostat_kinetic = 3.0 * NkBT * tb2 * eta * eta /
122 >    (2.0 * eConvert);
123    
124 <  if (!have_target_temp) {
125 <    sprintf( painCave.errMsg,
211 <             "NPTi error: You can't use the NPTi integrator\n"
212 <             "   without a targetTemp!\n"
213 <             );
214 <    painCave.isFatal = 1;
215 <    simError();
216 <    return -1;
217 <  }
124 >  barostat_potential = (targetPressure * tStats->getVolume() / p_convert) /
125 >    eConvert;
126  
127 <  if (!have_target_pressure) {
128 <    sprintf( painCave.errMsg,
221 <             "NPTi error: You can't use the NPTi integrator\n"
222 <             "   without a targetPressure!\n"
223 <             );
224 <    painCave.isFatal = 1;
225 <    simError();
226 <    return -1;
227 <  }
127 >  conservedQuantity = Energy + thermostat_kinetic + thermostat_potential +
128 >    barostat_kinetic + barostat_potential;
129    
130 <  // We must set tauThermostat.
131 <  
231 <  if (!have_tau_thermostat) {
232 <    sprintf( painCave.errMsg,
233 <             "NPTi error: If you use the NPTi\n"
234 <             "   integrator, you must set tauThermostat.\n");
235 <    painCave.isFatal = 1;
236 <    simError();
237 <    return -1;
238 <  }    
130 > //   cout.width(8);
131 > //   cout.precision(8);
132  
133 <  // We must set tauBarostat.
134 <  
135 <  if (!have_tau_barostat) {
136 <    sprintf( painCave.errMsg,
244 <             "NPTi error: If you use the NPTi\n"
245 <             "   integrator, you must set tauBarostat.\n");
246 <    painCave.isFatal = 1;
247 <    simError();
248 <    return -1;
249 <  }    
250 <
251 <  // We need NkBT a lot, so just set it here:
252 <
253 <  NkBT = (double)info->ndf * kB * targetTemp;
254 <
255 <  return 1;
133 > //   cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic <<
134 > //       "\t" << thermostat_potential << "\t" << barostat_kinetic <<
135 > //       "\t" << barostat_potential << "\t" << conservedQuantity << endl;
136 >  return conservedQuantity;
137   }

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