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root/group/trunk/OOPSE/libmdtools/NVT.cpp
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Comparing trunk/OOPSE/libmdtools/NVT.cpp (file contents):
Revision 560 by gezelter, Fri Jun 20 16:49:33 2003 UTC vs.
Revision 565 by gezelter, Tue Jun 24 22:51:57 2003 UTC

# Line 6 | Line 6
6   #include "Thermo.hpp"
7   #include "ReadWrite.hpp"
8   #include "Integrator.hpp"
9 < #include "NVT.hpp"
10 <
9 > #include "simError.h"
10 >
11 >
12   // Basic thermostating via Hoover, Phys.Rev.A, 1985, Vol. 31 (5) 1695-1697
13  
14 < NVT::NVT() {
15 <  zeta = 0.0;
14 > NVT::NVT ( SimInfo *theInfo, ForceFields* the_ff):
15 >  Integrator( theInfo, the_ff )
16 > {
17 >  chi = 0.0;
18    have_tau_thermostat = 0;
19    have_target_temp = 0;
17 –  have_qmass = 0;
20   }
21  
22   void NVT::moveA() {
# Line 24 | Line 26 | void NVT::moveA() {
26    DirectionalAtom* dAtom;
27    double Tb[3];
28    double ji[3];
29 +  double instTemp;
30 +  double angle;
31  
32 <  ke = tStats->getKinetic() * eConvert;
29 <  zeta += dt2 * ( (2.0 * ke  -  NkBT) / qmass );
32 >  instTemp = tStats->getTemperature();
33  
34 +  // first evolve chi a half step
35 +  
36 +  chi += dt2 * ( instTemp / targetTemp - 1.0) / (tauThermostat*tauThermostat);
37 +
38    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]*zeta);
44 >      vel[j] += dt2 * ((frc[j]/atoms[i]->getMass())*eConvert - vel[j]*chi);
45  
46      // position whole step    
47      for( j=atomIndex; j<(atomIndex+3); j++ )
# Line 59 | Line 66 | void NVT::moveA() {
66        ji[1] = dAtom->getJy();
67        ji[2] = dAtom->getJz();
68        
69 <      ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*zeta);
70 <      ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*zeta);
71 <      ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*zeta);
69 >      ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*chi);
70 >      ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*chi);
71 >      ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*chi);
72        
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] );
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] );
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] );
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] );
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] );
94 >      this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] );
95        
96        dAtom->setJx( ji[0] );
97        dAtom->setJy( ji[1] );
# Line 94 | Line 101 | void Integrator::moveB( void ){
101    }
102   }
103  
104 < void Integrator::moveB( void ){
104 > void NVT::moveB( void ){
105    int i,j,k;
106    int atomIndex;
107    DirectionalAtom* dAtom;
108    double Tb[3];
109    double ji[3];
110 <
104 <  ke = tStats->getKinetic() * eConvert;
105 <  zeta += dt2 * ( (2.0 * ke  -  NkBT) / qmass );
110 >  double instTemp;
111    
112 +  instTemp = tStats->getTemperature();
113 +  chi += dt2 * ( instTemp / targetTemp - 1.0) / (tauThermostat*tauThermostat);
114 +  
115    for( i=0; i<nAtoms; i++ ){
116      atomIndex = i * 3;
117      
118      // velocity half step
119      for( j=atomIndex; j<(atomIndex+3); j++ )
120 <      vel[j] += dt2 * ((frc[j]/atoms[i]->getMass())*eConvert - vel[j]*zeta);
120 >      vel[j] += dt2 * ((frc[j]/atoms[i]->getMass())*eConvert - vel[j]*chi);
121      
122      if( atoms[i]->isDirectional() ){
123        
# Line 130 | Line 138 | void Integrator::moveB( void ){
138        ji[1] = dAtom->getJy();
139        ji[2] = dAtom->getJz();
140        
141 <      ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*zeta);
142 <      ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*zeta);
143 <      ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*zeta);
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        
137 –      jx2 = ji[0] * ji[0];
138 –      jy2 = ji[1] * ji[1];
139 –      jz2 = ji[2] * ji[2];
140 –      
145        dAtom->setJx( ji[0] );
146        dAtom->setJy( ji[1] );
147        dAtom->setJz( ji[2] );
# Line 146 | Line 150 | int NVT::readyCheck() {
150   }
151  
152   int NVT::readyCheck() {
153 <  double NkBT;
150 <
153 >
154    // First check to see if we have a target temperature.
155    // Not having one is fatal.
156    
# Line 159 | Line 162 | int NVT::readyCheck() {
162      simError();
163      return -1;
164    }
165 <    
166 <  // Next check to see that we have a reasonable number of degrees of freedom
167 <  // and then set NkBT if we do have it.   Unreasonable numbers of DOFs
168 <  // are also fatal.
166 <
167 <  if (entry_plug->ndf > 0) {
168 <    NkBT = (double)entry_plug->ndf * kB * targetTemp;
169 <  } else {
165 >  
166 >  // We must set tauThermostat.
167 >  
168 >  if (!have_tau_thermostat) {
169      sprintf( painCave.errMsg,
170 <             "NVT error: We got a silly number of degrees of freedom!\n"
171 <             );
170 >             "NVT error: If you use the constant temperature\n"
171 >             "   integrator, you must set tauThermostat.\n");
172      painCave.isFatal = 1;
173      simError();
174      return -1;
175 <  }
177 <    
178 <  // We have our choice on setting qmass or tauThermostat.  One of them
179 <  // must be set.
180 <
181 <  if (!have_qmass) {
182 <    if (have_tau_thermostat) {
183 <      sprintf( painCave.errMsg,
184 <               "NVT info: Setting qMass = %d\n", tauThermostat * NkBT);
185 <      this->setQmass(tauThermostat * NkBT);      
186 <      painCave.isFatal = 0;
187 <      simError();
188 <    } else {
189 <      sprintf( painCave.errMsg,
190 <               "NVT error: If you use the constant temperature\n"
191 <               "   integrator, you must set either tauThermostat or qMass.\n");
192 <      painCave.isFatal = 1;
193 <      simError();
194 <      return -1;
195 <    }
196 <  }
197 <  
175 >  }    
176    return 1;
177   }
178  
201 – #endif

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