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root/group/trunk/OOPSE/libmdtools/NPT.cpp
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Comparing trunk/OOPSE/libmdtools/NPT.cpp (file contents):
Revision 837 by tim, Wed Oct 29 00:19:10 2003 UTC vs.
Revision 1234 by tim, Fri Jun 4 03:15:31 2004 UTC

# Line 1 | Line 1
1   #include <math.h>
2 +
3   #include "Atom.hpp"
4   #include "SRI.hpp"
5   #include "AbstractClasses.hpp"
# Line 61 | Line 62 | template<typename T> NPT<T>::NPT ( SimInfo *theInfo, F
62      integralOfChidt = integralOfChidtValue->getData();
63    }
64  
65 <  oldPos = new double[3*nAtoms];
66 <  oldVel = new double[3*nAtoms];
67 <  oldJi = new double[3*nAtoms];
67 < #ifdef IS_MPI
68 <  Nparticles = mpiSim->getTotAtoms();
69 < #else
70 <  Nparticles = theInfo->n_atoms;
71 < #endif
65 >  oldPos = new double[3*integrableObjects.size()];
66 >  oldVel = new double[3*integrableObjects.size()];
67 >  oldJi = new double[3*integrableObjects.size()];
68  
69   }
70  
# Line 82 | Line 78 | template<typename T> void NPT<T>::moveA() {
78  
79    //new version of NPT
80    int i, j, k;
85 –  DirectionalAtom* dAtom;
81    double Tb[3], ji[3];
82    double mass;
83    double vel[3], pos[3], frc[3];
# Line 97 | Line 92 | template<typename T> void NPT<T>::moveA() {
92    tStats->getCOM(COM);
93  
94    //evolve velocity half step
100 –  for( i=0; i<nAtoms; i++ ){
95  
96 <    atoms[i]->getVel( vel );
97 <    atoms[i]->getFrc( frc );
96 >  calcVelScale();
97 >  
98 >  for( i=0; i<integrableObjects.size(); i++ ){
99  
100 <    mass = atoms[i]->getMass();
100 >    integrableObjects[i]->getVel( vel );
101 >    integrableObjects[i]->getFrc( frc );
102  
103 +    mass = integrableObjects[i]->getMass();
104 +
105      getVelScaleA( sc, vel );
106  
107      for (j=0; j < 3; j++) {
# Line 113 | Line 111 | template<typename T> void NPT<T>::moveA() {
111  
112      }
113  
114 <    atoms[i]->setVel( vel );
114 >    integrableObjects[i]->setVel( vel );
115  
116 <    if( atoms[i]->isDirectional() ){
116 >    if( integrableObjects[i]->isDirectional() ){
117  
120 –      dAtom = (DirectionalAtom *)atoms[i];
121 –
118        // get and convert the torque to body frame
119  
120 <      dAtom->getTrq( Tb );
121 <      dAtom->lab2Body( Tb );
120 >      integrableObjects[i]->getTrq( Tb );
121 >      integrableObjects[i]->lab2Body( Tb );
122  
123        // get the angular momentum, and propagate a half step
124  
125 <      dAtom->getJ( ji );
125 >      integrableObjects[i]->getJ( ji );
126  
127        for (j=0; j < 3; j++)
128          ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);
129  
130 <      this->rotationPropagation( dAtom, ji );
130 >      this->rotationPropagation( integrableObjects[i], ji );
131  
132 <      dAtom->setJ( ji );
132 >      integrableObjects[i]->setJ( ji );
133      }
134    }
135  
# Line 146 | Line 142 | template<typename T> void NPT<T>::moveA() {
142    integralOfChidt += dt2*chi;
143  
144    //save the old positions
145 <  for(i = 0; i < nAtoms; i++){
146 <    atoms[i]->getPos(pos);
145 >  for(i = 0; i < integrableObjects.size(); i++){
146 >    integrableObjects[i]->getPos(pos);
147      for(j = 0; j < 3; j++)
148        oldPos[i*3 + j] = pos[j];
149    }
# Line 156 | Line 152 | template<typename T> void NPT<T>::moveA() {
152  
153    for(k = 0; k < 5; k ++){
154  
155 <    for(i =0 ; i < nAtoms; i++){
155 >    for(i =0 ; i < integrableObjects.size(); i++){
156  
157 <      atoms[i]->getVel(vel);
158 <      atoms[i]->getPos(pos);
157 >      integrableObjects[i]->getVel(vel);
158 >      integrableObjects[i]->getPos(pos);
159  
160        this->getPosScale( pos, COM, i, sc );
161  
162        for(j = 0; j < 3; j++)
163          pos[j] = oldPos[i*3 + j] + dt*(vel[j] + sc[j]);
164  
165 <      atoms[i]->setPos( pos );
165 >      integrableObjects[i]->setPos( pos );
166      }
167  
168 <    if (nConstrained){
173 <      constrainA();
174 <    }
168 >    rattle->doRattleA();
169    }
170  
171  
# Line 184 | Line 178 | template<typename T> void NPT<T>::moveB( void ){
178  
179    //new version of NPT
180    int i, j, k;
187 –  DirectionalAtom* dAtom;
181    double Tb[3], ji[3], sc[3];
182    double vel[3], frc[3];
183    double mass;
184  
185    // Set things up for the iteration:
186  
187 <  for( i=0; i<nAtoms; i++ ){
187 >  for( i=0; i<integrableObjects.size(); i++ ){
188  
189 <    atoms[i]->getVel( vel );
189 >    integrableObjects[i]->getVel( vel );
190  
191      for (j=0; j < 3; j++)
192        oldVel[3*i + j]  = vel[j];
193  
194 <    if( atoms[i]->isDirectional() ){
194 >    if( integrableObjects[i]->isDirectional() ){
195  
196 <      dAtom = (DirectionalAtom *)atoms[i];
196 >      integrableObjects[i]->getJ( ji );
197  
205 –      dAtom->getJ( ji );
206 –
198        for (j=0; j < 3; j++)
199          oldJi[3*i + j] = ji[j];
200  
# Line 223 | Line 214 | template<typename T> void NPT<T>::moveB( void ){
214  
215      this->evolveChiB();
216      this->evolveEtaB();
217 +    this->calcVelScale();
218  
219 <    for( i=0; i<nAtoms; i++ ){
219 >    for( i=0; i<integrableObjects.size(); i++ ){
220  
221 <      atoms[i]->getFrc( frc );
222 <      atoms[i]->getVel(vel);
221 >      integrableObjects[i]->getFrc( frc );
222 >      integrableObjects[i]->getVel(vel);
223  
224 <      mass = atoms[i]->getMass();
224 >      mass = integrableObjects[i]->getMass();
225  
226        getVelScaleB( sc, i );
227  
# Line 237 | Line 229 | template<typename T> void NPT<T>::moveB( void ){
229        for (j=0; j < 3; j++)
230          vel[j] = oldVel[3*i+j] + dt2 * ((frc[j] / mass ) * eConvert - sc[j]);
231  
232 <      atoms[i]->setVel( vel );
232 >      integrableObjects[i]->setVel( vel );
233  
234 <      if( atoms[i]->isDirectional() ){
234 >      if( integrableObjects[i]->isDirectional() ){
235  
244 –        dAtom = (DirectionalAtom *)atoms[i];
245 –
236          // get and convert the torque to body frame
237  
238 <        dAtom->getTrq( Tb );
239 <        dAtom->lab2Body( Tb );
238 >        integrableObjects[i]->getTrq( Tb );
239 >        integrableObjects[i]->lab2Body( Tb );
240  
241          for (j=0; j < 3; j++)
242            ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * eConvert - oldJi[3*i+j]*chi);
243  
244 <          dAtom->setJ( ji );
244 >          integrableObjects[i]->setJ( ji );
245        }
246      }
247  
248 <    if (nConstrained){
259 <      constrainB();
260 <    }
248 >    rattle->doRattleB();
249  
250      if ( this->chiConverged() && this->etaConverged() ) break;
251    }
# Line 359 | Line 347 | template<typename T> int NPT<T>::readyCheck() {
347    }
348  
349    // We need NkBT a lot, so just set it here: This is the RAW number
350 <  // of particles, so no subtraction or addition of constraints or
350 >  // of integrableObjects, so no subtraction or addition of constraints or
351    // orientational degrees of freedom:
352  
353 <  NkBT = (double)Nparticles * kB * targetTemp;
353 >  NkBT = (double)(info->getTotIntegrableObjects()) * kB * targetTemp;
354  
355    // fkBT is used because the thermostat operates on more degrees of freedom
356    // than the barostat (when there are particles with orientational degrees
357 <  // of freedom).  ndf = 3 * (n_atoms + n_oriented -1) - n_constraint - nZcons
357 >  // of freedom).  
358  
359 <  fkBT = (double)info->ndf * kB * targetTemp;
359 >  fkBT = (double)(info->getNDF()) * kB * targetTemp;
360  
361    tt2 = tauThermostat * tauThermostat;
362    tb2 = tauBarostat * tauBarostat;

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