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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 645 by tim, Tue Jul 22 19:54:52 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 > template<typename T> NVT<T>::NVT ( SimInfo *theInfo, ForceFields* the_ff):
15 >  T( 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() {
22 > template<typename T> void NVT<T>::moveA() {
23    
24 <  int i,j,k;
23 <  int atomIndex, aMatIndex;
24 >  int i, j;
25    DirectionalAtom* dAtom;
26 <  double Tb[3];
27 <  double ji[3];
26 >  double Tb[3], ji[3];
27 >  double A[3][3], I[3][3];
28 >  double angle, mass;
29 >  double vel[3], pos[3], frc[3];
30  
31 <  ke = tStats->getKinetic() * eConvert;
29 <  zeta += dt2 * ( (2.0 * ke  -  NkBT) / qmass );
31 >  double instTemp;
32  
33 +  instTemp = tStats->getTemperature();
34 +
35 +  // first evolve chi a half step
36 +  
37 +  chi += dt2 * ( instTemp / targetTemp - 1.0) / (tauThermostat*tauThermostat);
38 +
39    for( i=0; i<nAtoms; i++ ){
32 –    atomIndex = i * 3;
33 –    aMatIndex = i * 9;
34 –    
35 –    // velocity half step
36 –    for( j=atomIndex; j<(atomIndex+3); j++ )
37 –      vel[j] += dt2 * ((frc[j]/atoms[i]->getMass())*eConvert - vel[j]*zeta);
40  
41 <    // position whole step    
42 <    for( j=atomIndex; j<(atomIndex+3); j++ )
41 >    atoms[i]->getVel( vel );
42 >    atoms[i]->getPos( pos );
43 >    atoms[i]->getFrc( frc );
44 >
45 >    mass = atoms[i]->getMass();
46 >
47 >    for (j=0; j < 3; j++) {
48 >      // velocity half step
49 >      vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*chi);
50 >      // position whole step
51        pos[j] += dt * vel[j];
52 +    }
53  
54 +    atoms[i]->setVel( vel );
55 +    atoms[i]->setPos( pos );
56    
57      if( atoms[i]->isDirectional() ){
58  
# Line 47 | Line 60 | void NVT::moveA() {
60            
61        // get and convert the torque to body frame
62        
63 <      Tb[0] = dAtom->getTx();
51 <      Tb[1] = dAtom->getTy();
52 <      Tb[2] = dAtom->getTz();
53 <      
63 >      dAtom->getTrq( Tb );
64        dAtom->lab2Body( Tb );
65        
66        // get the angular momentum, and propagate a half step
67  
68 <      ji[0] = dAtom->getJx();
69 <      ji[1] = dAtom->getJy();
70 <      ji[2] = dAtom->getJz();
68 >      dAtom->getJ( ji );
69 >
70 >      for (j=0; j < 3; j++)
71 >        ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);
72        
62 –      ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*zeta);
63 –      ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*zeta);
64 –      ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*zeta);
65 –      
73        // use the angular velocities to propagate the rotation matrix a
74        // full time step
75 <      
75 >
76 >      dAtom->getA(A);
77 >      dAtom->getI(I);
78 >    
79        // rotate about the x-axis      
80 <      angle = dt2 * ji[0] / dAtom->getIxx();
81 <      this->rotate( 1, 2, angle, ji, &aMat[aMatIndex] );
82 <      
80 >      angle = dt2 * ji[0] / I[0][0];
81 >      this->rotate( 1, 2, angle, ji, A );
82 >
83        // rotate about the y-axis
84 <      angle = dt2 * ji[1] / dAtom->getIyy();
85 <      this->rotate( 2, 0, angle, ji, &aMat[aMatIndex] );
84 >      angle = dt2 * ji[1] / I[1][1];
85 >      this->rotate( 2, 0, angle, ji, A );
86        
87        // rotate about the z-axis
88 <      angle = dt * ji[2] / dAtom->getIzz();
89 <      this->rotate( 0, 1, angle, ji, &aMat[aMatIndex] );
88 >      angle = dt * ji[2] / I[2][2];
89 >      this->rotate( 0, 1, angle, ji, A);
90        
91        // rotate about the y-axis
92 <      angle = dt2 * ji[1] / dAtom->getIyy();
93 <      this->rotate( 2, 0, angle, ji, &aMat[aMatIndex] );
92 >      angle = dt2 * ji[1] / I[1][1];
93 >      this->rotate( 2, 0, angle, ji, A );
94        
95         // rotate about the x-axis
96 <      angle = dt2 * ji[0] / dAtom->getIxx();
97 <      this->rotate( 1, 2, angle, ji, &aMat[aMatIndex] );
96 >      angle = dt2 * ji[0] / I[0][0];
97 >      this->rotate( 1, 2, angle, ji, A );
98        
99 <      dAtom->setJx( ji[0] );
100 <      dAtom->setJy( ji[1] );
101 <      dAtom->setJz( ji[2] );
92 <    }
93 <    
99 >      dAtom->setJ( ji );
100 >      dAtom->setA( A  );    
101 >    }    
102    }
103   }
104  
105 < void Integrator::moveB( void ){
106 <  int i,j,k;
99 <  int atomIndex;
105 > template<typename T> void NVT<T>::moveB( void ){
106 >  int i, j;
107    DirectionalAtom* dAtom;
108 <  double Tb[3];
109 <  double ji[3];
108 >  double Tb[3], ji[3];
109 >  double vel[3], frc[3];
110 >  double mass;
111  
112 <  ke = tStats->getKinetic() * eConvert;
105 <  zeta += dt2 * ( (2.0 * ke  -  NkBT) / qmass );
112 >  double instTemp;
113    
114 +  instTemp = tStats->getTemperature();
115 +  chi += dt2 * ( instTemp / targetTemp - 1.0) / (tauThermostat*tauThermostat);
116 +  
117    for( i=0; i<nAtoms; i++ ){
118 <    atomIndex = i * 3;
119 <    
118 >
119 >    atoms[i]->getVel( vel );
120 >    atoms[i]->getFrc( frc );
121 >
122 >    mass = atoms[i]->getMass();
123 >
124      // velocity half step
125 <    for( j=atomIndex; j<(atomIndex+3); j++ )
126 <      vel[j] += dt2 * ((frc[j]/atoms[i]->getMass())*eConvert - vel[j]*zeta);
125 >    for (j=0; j < 3; j++)
126 >      vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*chi);
127      
128 +    atoms[i]->setVel( vel );
129 +
130      if( atoms[i]->isDirectional() ){
131 <      
131 >
132        dAtom = (DirectionalAtom *)atoms[i];
133 <      
134 <      // get and convert the torque to body frame
135 <      
136 <      Tb[0] = dAtom->getTx();
121 <      Tb[1] = dAtom->getTy();
122 <      Tb[2] = dAtom->getTz();
123 <      
133 >
134 >      // get and convert the torque to body frame      
135 >
136 >      dAtom->getTrq( Tb );
137        dAtom->lab2Body( Tb );
138 +
139 +      // get the angular momentum, and propagate a half step
140 +
141 +      dAtom->getJ( ji );
142 +
143 +      for (j=0; j < 3; j++)
144 +        ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);
145        
146 <      // get the angular momentum, and complete the angular momentum
147 <      // half step
128 <      
129 <      ji[0] = dAtom->getJx();
130 <      ji[1] = dAtom->getJy();
131 <      ji[2] = dAtom->getJz();
132 <      
133 <      ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*zeta);
134 <      ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*zeta);
135 <      ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*zeta);
136 <      
137 <      jx2 = ji[0] * ji[0];
138 <      jy2 = ji[1] * ji[1];
139 <      jz2 = ji[2] * ji[2];
140 <      
141 <      dAtom->setJx( ji[0] );
142 <      dAtom->setJy( ji[1] );
143 <      dAtom->setJz( ji[2] );
146 >
147 >      dAtom->setJ( ji );
148      }
149    }
150   }
151  
152 < int NVT::readyCheck() {
153 <  double NkBT;
150 <
152 > template<typename T> int NVT<T>::readyCheck() {
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   }
200 –
201 – #endif

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