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root/group/trunk/OOPSE/libmdtools/Symplectic.cpp
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Comparing trunk/OOPSE/libmdtools/Symplectic.cpp (file contents):
Revision 443 by mmeineke, Wed Apr 2 22:19:03 2003 UTC vs.
Revision 542 by mmeineke, Fri May 30 21:31:48 2003 UTC

# Line 1 | Line 1
1   #include <iostream>
2   #include <cstdlib>
3  
4 + #ifdef IS_MPI
5 + #include "mpiSimulation.hpp"
6 + #include <unistd.h>
7 + #endif //is_mpi
8 +
9   #include "Integrator.hpp"
5 – #include "Thermo.hpp"
6 – #include "ReadWrite.hpp"
7 – #include "ForceFields.hpp"
10   #include "simError.h"
11  
10 – extern "C"{
11 –  
12 –  void v_constrain_a_( double &dt, int &n_atoms, double* mass,
13 –                       double* Rx, double* Ry, double* Rz,
14 –                       double* Vx, double* Vy, double* Vz,
15 –                       double* Fx, double* Fy, double* Fz,
16 –                       int &n_constrained, double *constr_sqr,
17 –                       int* constr_i, int* constr_j,
18 –                       double &box_x, double &box_y, double &box_z );
12  
13 <  void v_constrain_b_( double &dt, int &n_atoms, double* mass,
14 <                       double* Rx, double* Ry, double* Rz,
15 <                       double* Vx, double* Vy, double* Vz,
23 <                       double* Fx, double* Fy, double* Fz,
24 <                       double &Kinetic,
25 <                       int &n_constrained, double *constr_sqr,
26 <                       int* constr_i, int* constr_j,
27 <                       double &box_x, double &box_y, double &box_z );
28 < }
29 <
30 <
31 <
32 <
33 < Symplectic::Symplectic( SimInfo* the_entry_plug, ForceFields* the_ff ){
34 <  entry_plug = the_entry_plug;
13 > Symplectic::Symplectic( SimInfo* theInfo, ForceFields* the_ff ){
14 >  
15 >  info = theInfo;
16    myFF = the_ff;
17    isFirst = 1;
18  
19 <  molecules = entry_plug->molecules;
20 <  nMols = entry_plug->n_mol;
19 >  molecules = info->molecules;
20 >  nMols = info->n_mol;
21  
22    // give a little love back to the SimInfo object
23    
24 <  if( entry_plug->the_integrator != NULL ) delete entry_plug->the_integrator;
25 <  entry_plug->the_integrator = this;
24 >  if( info->the_integrator != NULL ) delete info->the_integrator;
25 >  info->the_integrator = this;
26  
27 <  // grab the masses
27 >  // check for constraints
28 >  
29 >  constrainedI = NULL;
30 >  constrainedJ = NULL;
31 >  constrainedDsqr = NULL;
32 >  nConstrained = 0;
33  
34 <  mass = new double[entry_plug->n_atoms];
35 <  for(int i = 0; i < entry_plug->n_atoms; i++){
50 <    mass[i] = entry_plug->atoms[i]->getMass();
51 <  }
34 >  checkConstraints();
35 > }
36  
37 + Symplectic::~Symplectic() {
38    
39 <
40 <  // check for constraints
39 >  if( nConstrained ){
40 >    delete[] constrainedI;
41 >    delete[] constrainedJ;
42 >    delete[] constrainedDsqr;
43 >  }
44 >  
45 > }
46  
47 <  is_constrained = 0;
47 > void Symplectic::checkConstraints( void ){
48  
49 +
50 +  isConstrained = 0;
51 +
52    Constraint *temp_con;
53    Constraint *dummy_plug;
54 <  temp_con = new Constraint[entry_plug->n_SRI];
55 <  n_constrained = 0;
54 >  temp_con = new Constraint[info->n_SRI];
55 >  nConstrained = 0;
56    int constrained = 0;
57    
58    SRI** theArray;
# Line 73 | Line 66 | Symplectic::Symplectic( SimInfo* the_entry_plug, Force
66        if(constrained){
67          
68          dummy_plug = theArray[j]->get_constraint();
69 <        temp_con[n_constrained].set_a( dummy_plug->get_a() );
70 <        temp_con[n_constrained].set_b( dummy_plug->get_b() );
71 <        temp_con[n_constrained].set_dsqr( dummy_plug->get_dsqr() );
69 >        temp_con[nConstrained].set_a( dummy_plug->get_a() );
70 >        temp_con[nConstrained].set_b( dummy_plug->get_b() );
71 >        temp_con[nConstrained].set_dsqr( dummy_plug->get_dsqr() );
72          
73 <        n_constrained++;
73 >        nConstrained++;
74          constrained = 0;
75        }
76      }
# Line 90 | Line 83 | Symplectic::Symplectic( SimInfo* the_entry_plug, Force
83        if(constrained){
84          
85          dummy_plug = theArray[j]->get_constraint();
86 <        temp_con[n_constrained].set_a( dummy_plug->get_a() );
87 <        temp_con[n_constrained].set_b( dummy_plug->get_b() );
88 <        temp_con[n_constrained].set_dsqr( dummy_plug->get_dsqr() );
86 >        temp_con[nConstrained].set_a( dummy_plug->get_a() );
87 >        temp_con[nConstrained].set_b( dummy_plug->get_b() );
88 >        temp_con[nConstrained].set_dsqr( dummy_plug->get_dsqr() );
89          
90 <        n_constrained++;
90 >        nConstrained++;
91          constrained = 0;
92        }
93      }
# Line 107 | Line 100 | Symplectic::Symplectic( SimInfo* the_entry_plug, Force
100        if(constrained){
101          
102          dummy_plug = theArray[j]->get_constraint();
103 <        temp_con[n_constrained].set_a( dummy_plug->get_a() );
104 <        temp_con[n_constrained].set_b( dummy_plug->get_b() );
105 <        temp_con[n_constrained].set_dsqr( dummy_plug->get_dsqr() );
103 >        temp_con[nConstrained].set_a( dummy_plug->get_a() );
104 >        temp_con[nConstrained].set_b( dummy_plug->get_b() );
105 >        temp_con[nConstrained].set_dsqr( dummy_plug->get_dsqr() );
106          
107 <        n_constrained++;
107 >        nConstrained++;
108          constrained = 0;
109        }
110      }
111    }
112  
113 <  if(n_constrained > 0){
113 >  if(nConstrained > 0){
114      
115 <    is_constrained = 1;
116 <    constrained_i = new int[n_constrained];
117 <    constrained_j = new int[n_constrained];
118 <    constrained_dsqr = new double[n_constrained];
115 >    isConstrained = 1;
116 >
117 >    if(constrainedI != NULL )    delete[] constrainedI;
118 >    if(constrainedJ != NULL )    delete[] constrainedJ;
119 >    if(constrainedDsqr != NULL ) delete[] constrainedDsqr;
120 >
121 >    constrainedI =    new int[nConstrained];
122 >    constrainedJ =    new int[nConstrained];
123 >    constrainedDsqr = new double[nConstrained];
124      
125 <    for( int i = 0; i < n_constrained; i++){
125 >    for( int i = 0; i < nConstrained; i++){
126        
127 <      /* add 1 to the index for the fortran arrays. */
128 <
129 <      constrained_i[i] = temp_con[i].get_a() + 1;
132 <      constrained_j[i] = temp_con[i].get_b() + 1;
133 <      constrained_dsqr[i] = temp_con[i].get_dsqr();
127 >      constrainedI[i] = temp_con[i].get_a();
128 >      constrainedJ[i] = temp_con[i].get_b();
129 >      constrainedDsqr[i] = temp_con[i].get_dsqr();
130      }
131    }
132    
133    delete[] temp_con;
134   }
135  
140 – Symplectic::~Symplectic() {
141 –  
142 –  if( n_constrained ){
143 –    delete[] constrained_i;
144 –    delete[] constrained_j;
145 –    delete[] constrained_dsqr;
146 –  }
147 –  
148 – }
136  
150 –
137   void Symplectic::integrate( void ){
138  
153 –  const double e_convert = 4.184e-4; // converts kcal/mol -> amu*A^2/fs^2
154 –
139    int i, j;                         // loop counters
140 <  int nAtoms = entry_plug->n_atoms; // the number of atoms
140 >  int nAtoms = info->n_atoms; // the number of atoms
141    double kE = 0.0;                  // the kinetic energy  
142    double rot_kE;
143    double trans_kE;
# Line 161 | Line 145 | void Symplectic::integrate( void ){
145    double dt2;                       // half the dt
146  
147    double vx, vy, vz;    // the velocities
148 < //  double vx2, vy2, vz2; // the square of the velocities
148 >  double vx2, vy2, vz2; // the square of the velocities
149    double rx, ry, rz;    // the postitions
150    
151    double ji[3];   // the body frame angular momentum
# Line 169 | Line 153 | void Symplectic::integrate( void ){
153    double Tb[3];   // torque in the body frame
154    double angle;   // the angle through which to rotate the rotation matrix
155    double A[3][3]; // the rotation matrix
156 +  double press[9];
157  
158    int time;
159  
160 <  double dt          = entry_plug->dt;
161 <  double runTime     = entry_plug->run_time;
162 <  double sampleTime  = entry_plug->sampleTime;
163 <  double statusTime  = entry_plug->statusTime;
164 <  double thermalTime = entry_plug->thermalTime;
160 >  double dt          = info->dt;
161 >  double runTime     = info->run_time;
162 >  double sampleTime  = info->sampleTime;
163 >  double statusTime  = info->statusTime;
164 >  double thermalTime = info->thermalTime;
165  
166    int n_loops  = (int)( runTime / dt );
167    int sample_n = (int)( sampleTime / dt );
168    int status_n = (int)( statusTime / dt );
169    int vel_n    = (int)( thermalTime / dt );
170  
171 <  int calcPot;
171 >  int calcPot, calcStress;
172 >  int isError;
173  
174 <   Thermo *tStats = new Thermo( entry_plug );
174 >  tStats   = new Thermo( info );
175 >  e_out    = new StatWriter( info );
176 >  dump_out = new DumpWriter( info );
177  
178 <  StatWriter*  e_out    = new StatWriter( entry_plug );
191 <  DumpWriter*  dump_out = new DumpWriter( entry_plug );
192 <
193 <  Atom** atoms = entry_plug->atoms;
178 >  Atom** atoms = info->atoms;
179    DirectionalAtom* dAtom;
180    dt2 = 0.5 * dt;
181  
182 <  // initialize the forces the before the first step
182 >  // initialize the forces before the first step
183  
184 <  myFF->doForces(1,0);
184 >  myFF->doForces(1,1);
185    
186 <  if( entry_plug->setTemp ){
186 >  if( info->setTemp ){
187      
188      tStats->velocitize();
189    }
# Line 208 | Line 193 | void Symplectic::integrate( void ){
193    
194    calcPot = 0;
195  
196 <  if( n_constrained ){
196 >  for( tl=0; tl<nLoops; tl++){
197  
198 <    double *Rx = new double[nAtoms];
199 <    double *Ry = new double[nAtoms];
200 <    double *Rz = new double[nAtoms];
198 >    integrateStep( calcPot, calcStress );
199 >      
200 >    time = tl + 1;
201      
202 <    double *Vx = new double[nAtoms];
203 <    double *Vy = new double[nAtoms];
204 <    double *Vz = new double[nAtoms];
205 <    
206 <    double *Fx = new double[nAtoms];
207 <    double *Fy = new double[nAtoms];
208 <    double *Fz = new double[nAtoms];
209 <    
202 >    if( info->setTemp ){
203 >      if( !(time % vel_n) ) tStats->velocitize();
204 >    }
205 >    if( !(time % sample_n) ) dump_out->writeDump( time * dt );
206 >    if( !((time+1) % status_n) ) {
207 >      calcPot = 1;
208 >      calcStress = 1;
209 >    }
210 >    if( !(time % status_n) ){
211 >      e_out->writeStat( time * dt );
212 >      calcPot = 0;
213 >      if (!strcasecmp(info->ensemble, "NPT")) calcStress = 1;
214 >      else calcStress = 0;
215 >    }    
216  
217 <    for( tl=0; tl < n_loops; tl++ ){
218 <      
228 <      for( j=0; j<nAtoms; j++ ){
217 >  
218 >  }
219  
220 <        Rx[j] = atoms[j]->getX();
231 <        Ry[j] = atoms[j]->getY();
232 <        Rz[j] = atoms[j]->getZ();
220 >  dump_out->writeFinal();
221  
222 <        Vx[j] = atoms[j]->get_vx();
223 <        Vy[j] = atoms[j]->get_vy();
224 <        Vz[j] = atoms[j]->get_vz();
222 >  delete dump_out;
223 >  delete e_out;
224 > }
225  
238 –        Fx[j] = atoms[j]->getFx();
239 –        Fy[j] = atoms[j]->getFy();
240 –        Fz[j] = atoms[j]->getFz();
226  
227 <      }
228 <        
229 <      v_constrain_a_( dt, nAtoms, mass, Rx, Ry, Rz, Vx, Vy, Vz,
230 <                      Fx, Fy, Fz,
231 <                      n_constrained, constrained_dsqr,
232 <                      constrained_i, constrained_j,
233 <                      entry_plug->box_x,
249 <                      entry_plug->box_y,
250 <                      entry_plug->box_z );
251 <      
252 <      for( j=0; j<nAtoms; j++ ){
227 > void Symplectic::moveA( void ){
228 >  
229 >  int i,j,k;
230 >  int atomIndex, aMatIndex;
231 >  DirectionalAtom* dAtom;
232 >  double Tb[3];
233 >  double ji[3];
234  
235 <        atoms[j]->setX(Rx[j]);
236 <        atoms[j]->setY(Ry[j]);
237 <        atoms[j]->setZ(Rz[j]);
238 <        
239 <        atoms[j]->set_vx(Vx[j]);
240 <        atoms[j]->set_vy(Vy[j]);
241 <        atoms[j]->set_vz(Vz[j]);
261 <      }
235 >  for( i=0; i<nAtoms; i++ ){
236 >    atomIndex = i * 3;
237 >    aMatIndex = i * 9;
238 >    
239 >    // velocity half step
240 >    for( j=atomIndex; j<(atomIndex+3); j++ )
241 >      vel[j] += ( dt2 * frc[j] / atoms[i]->getMass() ) * eConvert;
242  
243 +    // position whole step    
244 +    for( j=atomIndex; j<(atomIndex+3); j++ )
245 +      pos[j] += dt * vel[j];
246  
247 <      for( i=0; i<nAtoms; i++ ){
248 <        if( atoms[i]->isDirectional() ){
249 <                  
250 <          dAtom = (DirectionalAtom *)atoms[i];
247 >  
248 >    if( atoms[i]->isDirectional() ){
249 >
250 >      dAtom = (DirectionalAtom *)atoms[i];
251            
252 <          // get and convert the torque to body frame
270 <          
271 <          Tb[0] = dAtom->getTx();
272 <          Tb[1] = dAtom->getTy();
273 <          Tb[2] = dAtom->getTz();
274 <          
275 <          dAtom->lab2Body( Tb );
276 <          
277 <          // get the angular momentum, and propagate a half step
278 <          
279 <          ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * e_convert;
280 <          ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * e_convert;
281 <          ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * e_convert;
282 <          
283 <          // get the atom's rotation matrix
284 <          
285 <          A[0][0] = dAtom->getAxx();
286 <          A[0][1] = dAtom->getAxy();
287 <          A[0][2] = dAtom->getAxz();
288 <          
289 <          A[1][0] = dAtom->getAyx();
290 <          A[1][1] = dAtom->getAyy();
291 <          A[1][2] = dAtom->getAyz();
292 <          
293 <          A[2][0] = dAtom->getAzx();
294 <          A[2][1] = dAtom->getAzy();
295 <          A[2][2] = dAtom->getAzz();
296 <          
297 <          
298 <          // use the angular velocities to propagate the rotation matrix a
299 <          // full time step
300 <          
301 <          
302 <          angle = dt2 * ji[0] / dAtom->getIxx();
303 <          this->rotate( 1, 2, angle, ji, A ); // rotate about the x-axis
304 <          
305 <          angle = dt2 * ji[1] / dAtom->getIyy();
306 <          this->rotate( 2, 0, angle, ji, A ); // rotate about the y-axis
307 <          
308 <          angle = dt * ji[2] / dAtom->getIzz();
309 <          this->rotate( 0, 1, angle, ji, A ); // rotate about the z-axis
310 <          
311 <          angle = dt2 * ji[1] / dAtom->getIyy();
312 <          this->rotate( 2, 0, angle, ji, A ); // rotate about the y-axis
313 <          
314 <          angle = dt2 * ji[0] / dAtom->getIxx();
315 <          this->rotate( 1, 2, angle, ji, A ); // rotate about the x-axis
316 <          
317 <          
318 <          dAtom->setA( A );
319 <          dAtom->setJx( ji[0] );
320 <          dAtom->setJy( ji[1] );
321 <          dAtom->setJz( ji[2] );
322 <        }
323 <      }
252 >      // get and convert the torque to body frame
253        
254 <      // calculate the forces
255 <      
256 <      myFF->doForces(calcPot, 0);
328 <      
329 <      // move b
330 <
331 <      for( j=0; j<nAtoms; j++ ){
332 <
333 <        Rx[j] = atoms[j]->getX();
334 <        Ry[j] = atoms[j]->getY();
335 <        Rz[j] = atoms[j]->getZ();
336 <
337 <        Vx[j] = atoms[j]->get_vx();
338 <        Vy[j] = atoms[j]->get_vy();
339 <        Vz[j] = atoms[j]->get_vz();
340 <
341 <        Fx[j] = atoms[j]->getFx();
342 <        Fy[j] = atoms[j]->getFy();
343 <        Fz[j] = atoms[j]->getFz();
344 <      }
345 <        
346 <      v_constrain_b_( dt, nAtoms, mass, Rx, Ry, Rz, Vx, Vy, Vz,
347 <                      Fx, Fy, Fz,
348 <                      kE, n_constrained, constrained_dsqr,
349 <                      constrained_i, constrained_j,
350 <                      entry_plug->box_x,
351 <                      entry_plug->box_y,
352 <                      entry_plug->box_z );
254 >      Tb[0] = dAtom->getTx();
255 >      Tb[1] = dAtom->getTy();
256 >      Tb[2] = dAtom->getTz();
257        
258 <      for( j=0; j<nAtoms; j++ ){
355 <
356 <        atoms[j]->setX(Rx[j]);
357 <        atoms[j]->setY(Ry[j]);
358 <        atoms[j]->setZ(Rz[j]);
359 <
360 <        atoms[j]->set_vx(Vx[j]);
361 <        atoms[j]->set_vy(Vy[j]);
362 <        atoms[j]->set_vz(Vz[j]);
363 <      }
258 >      dAtom->lab2Body( Tb );
259        
260 <      for( i=0; i< nAtoms; i++ ){
366 <
367 <        if( atoms[i]->isDirectional() ){
368 <
369 <          dAtom = (DirectionalAtom *)atoms[i];
370 <          
371 <          // get and convert the torque to body frame
372 <          
373 <          Tb[0] = dAtom->getTx();
374 <          Tb[1] = dAtom->getTy();
375 <          Tb[2] = dAtom->getTz();
376 <          
377 <          dAtom->lab2Body( Tb );
378 <          
379 <          // get the angular momentum, and complete the angular momentum
380 <          // half step
381 <          
382 <          ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * e_convert;
383 <          ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * e_convert;
384 <          ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * e_convert;
385 <          
386 <          dAtom->setJx( ji[0] );
387 <          dAtom->setJy( ji[1] );
388 <          dAtom->setJz( ji[2] );
389 <        }
390 <      }
391 <    
392 <      time = tl + 1;
260 >      // get the angular momentum, and propagate a half step
261        
262 <      if( entry_plug->setTemp ){
263 <        if( !(time % vel_n) ) tStats->velocitize();
264 <      }
265 <      if( !(time % sample_n) ) dump_out->writeDump( time * dt );
266 <      if( !((time+1) % status_n) ) calcPot = 1;
267 <      if( !(time % status_n) ){ e_out->writeStat( time * dt ); calcPot = 0; }
262 >      ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * eConvert;
263 >      ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * eConvert;
264 >      ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * eConvert;
265 >      
266 >      // use the angular velocities to propagate the rotation matrix a
267 >      // full time step
268 >      
269 >      // rotate about the x-axis      
270 >      angle = dt2 * ji[0] / dAtom->getIxx();
271 >      this->rotate( 1, 2, angle, ji, &aMat[aMatIndex] );
272 >      
273 >      // rotate about the y-axis
274 >      angle = dt2 * ji[1] / dAtom->getIyy();
275 >      this->rotate( 2, 0, angle, ji, &aMat[aMatIndex] );
276 >      
277 >      // rotate about the z-axis
278 >      angle = dt * ji[2] / dAtom->getIzz();
279 >      this->rotate( 0, 1, angle, ji, &aMat[aMatIndex] );
280 >      
281 >      // rotate about the y-axis
282 >      angle = dt2 * ji[1] / dAtom->getIyy();
283 >      this->rotate( 2, 0, angle, ji, &aMat[aMatIndex] );
284 >      
285 >       // rotate about the x-axis
286 >      angle = dt2 * ji[0] / dAtom->getIxx();
287 >      this->rotate( 1, 2, angle, ji, &aMat[aMatIndex] );
288 >      
289 >      dAtom->setJx( ji[0] );
290 >      dAtom->setJy( ji[1] );
291 >      dAtom->setJz( ji[2] );
292      }
293 +    
294    }
295 <  else{
295 > }
296  
297 <    for( tl=0; tl<n_loops; tl++ ){
297 >
298 > void Integrator::moveB( void ){
299 >  int i,j,k;
300 >  int atomIndex;
301 >  DirectionalAtom* dAtom;
302 >  double Tb[3];
303 >  double ji[3];
304 >
305 >  for( i=0; i<nAtoms; i++ ){
306 >    atomIndex = i * 3;
307 >
308 >    // velocity half step
309 >    for( j=atomIndex; j<(atomIndex+3); j++ )
310 >      vel[j] += ( dt2 * frc[j] / atoms[i]->getMass() ) * eConvert;
311 >
312 >    if( atoms[i]->isDirectional() ){
313        
314 <      kE = 0.0;
407 <      rot_kE= 0.0;
408 <      trans_kE = 0.0;
314 >      dAtom = (DirectionalAtom *)atoms[i];
315        
316 <      for( i=0; i<nAtoms; i++ ){
411 <        
412 <        // velocity half step
413 <        
414 <        vx = atoms[i]->get_vx() +
415 <          ( dt2 * atoms[i]->getFx() / atoms[i]->getMass() ) * e_convert;
416 <        vy = atoms[i]->get_vy() +
417 <          ( dt2 * atoms[i]->getFy() / atoms[i]->getMass() ) * e_convert;
418 <        vz = atoms[i]->get_vz() +
419 <          ( dt2 * atoms[i]->getFz() / atoms[i]->getMass() ) * e_convert;
420 <        
421 <        // position whole step
422 <        
423 <        rx = atoms[i]->getX() + dt * vx;
424 <        ry = atoms[i]->getY() + dt * vy;
425 <        rz = atoms[i]->getZ() + dt * vz;
426 <        
427 <        atoms[i]->setX( rx );
428 <        atoms[i]->setY( ry );
429 <        atoms[i]->setZ( rz );
430 <        
431 <        atoms[i]->set_vx( vx );
432 <        atoms[i]->set_vy( vy );
433 <        atoms[i]->set_vz( vz );
434 <        
435 <        if( atoms[i]->isDirectional() ){
436 <
437 <          dAtom = (DirectionalAtom *)atoms[i];
438 <          
439 <          // get and convert the torque to body frame
440 <          
441 <          Tb[0] = dAtom->getTx();
442 <          Tb[1] = dAtom->getTy();
443 <          Tb[2] = dAtom->getTz();
444 <          
445 <          dAtom->lab2Body( Tb );
446 <          
447 <          // get the angular momentum, and propagate a half step
448 <          
449 <          ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * e_convert;
450 <          ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * e_convert;
451 <          ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * e_convert;
452 <          
453 <          // get the atom's rotation matrix
454 <          
455 <          A[0][0] = dAtom->getAxx();
456 <          A[0][1] = dAtom->getAxy();
457 <          A[0][2] = dAtom->getAxz();
458 <          
459 <          A[1][0] = dAtom->getAyx();
460 <          A[1][1] = dAtom->getAyy();
461 <          A[1][2] = dAtom->getAyz();
462 <          
463 <          A[2][0] = dAtom->getAzx();
464 <          A[2][1] = dAtom->getAzy();
465 <          A[2][2] = dAtom->getAzz();
466 <          
467 <          
468 <          // use the angular velocities to propagate the rotation matrix a
469 <          // full time step
470 <          
471 <          
472 <          angle = dt2 * ji[0] / dAtom->getIxx();
473 <          this->rotate( 1, 2, angle, ji, A ); // rotate about the x-axis
474 <          
475 <          angle = dt2 * ji[1] / dAtom->getIyy();
476 <          this->rotate( 2, 0, angle, ji, A ); // rotate about the y-axis
477 <          
478 <          angle = dt * ji[2] / dAtom->getIzz();
479 <          this->rotate( 0, 1, angle, ji, A ); // rotate about the z-axis
480 <          
481 <          angle = dt2 * ji[1] / dAtom->getIyy();
482 <          this->rotate( 2, 0, angle, ji, A ); // rotate about the y-axis
483 <          
484 <          angle = dt2 * ji[0] / dAtom->getIxx();
485 <          this->rotate( 1, 2, angle, ji, A ); // rotate about the x-axis
486 <          
487 <          
488 <          dAtom->setA( A );
489 <          dAtom->setJx( ji[0] );
490 <          dAtom->setJy( ji[1] );
491 <          dAtom->setJz( ji[2] );
492 <        }
493 <      }
316 >      // get and convert the torque to body frame
317        
318 <      // calculate the forces
318 >      Tb[0] = dAtom->getTx();
319 >      Tb[1] = dAtom->getTy();
320 >      Tb[2] = dAtom->getTz();
321        
322 <      myFF->doForces(calcPot,0);
322 >      dAtom->lab2Body( Tb );
323        
324 <      for( i=0; i< nAtoms; i++ ){
325 <        
501 <        // complete the velocity half step
502 <        
503 <        vx = atoms[i]->get_vx() +
504 <          ( dt2 * atoms[i]->getFx() / atoms[i]->getMass() ) * e_convert;
505 <        vy = atoms[i]->get_vy() +
506 <          ( dt2 * atoms[i]->getFy() / atoms[i]->getMass() ) * e_convert;
507 <        vz = atoms[i]->get_vz() +
508 <          ( dt2 * atoms[i]->getFz() / atoms[i]->getMass() ) * e_convert;
509 <        
510 <        atoms[i]->set_vx( vx );
511 <        atoms[i]->set_vy( vy );
512 <        atoms[i]->set_vz( vz );
513 <        
514 < //      vx2 = vx * vx;
515 < //      vy2 = vy * vy;
516 < //      vz2 = vz * vz;
517 <        
518 <        if( atoms[i]->isDirectional() ){
519 <
520 <          dAtom = (DirectionalAtom *)atoms[i];
521 <          
522 <          // get and convert the torque to body frame
523 <          
524 <          Tb[0] = dAtom->getTx();
525 <          Tb[1] = dAtom->getTy();
526 <          Tb[2] = dAtom->getTz();
527 <          
528 <          dAtom->lab2Body( Tb );
529 <          
530 <          // get the angular momentum, and complete the angular momentum
531 <          // half step
532 <          
533 <          ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * e_convert;
534 <          ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * e_convert;
535 <          ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * e_convert;
536 <          
537 <          jx2 = ji[0] * ji[0];
538 <          jy2 = ji[1] * ji[1];
539 <          jz2 = ji[2] * ji[2];
540 <          
541 <          rot_kE += (jx2 / dAtom->getIxx()) + (jy2 / dAtom->getIyy())
542 <            + (jz2 / dAtom->getIzz());
543 <          
544 <          dAtom->setJx( ji[0] );
545 <          dAtom->setJy( ji[1] );
546 <          dAtom->setJz( ji[2] );
547 <        }
548 <      }
324 >      // get the angular momentum, and complete the angular momentum
325 >      // half step
326        
327 <      time = tl + 1;
327 >      ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * eConvert;
328 >      ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * eConvert;
329 >      ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * eConvert;
330        
331 <      if( entry_plug->setTemp ){
332 <        if( !(time % vel_n) ) tStats->velocitize();
333 <      }
334 <      if( !(time % sample_n) ) dump_out->writeDump( time * dt );
335 <      if( !((time+1) % status_n) ) calcPot = 1;
336 <      if( !(time % status_n) ){ e_out->writeStat( time * dt ); calcPot = 0; }
331 >      jx2 = ji[0] * ji[0];
332 >      jy2 = ji[1] * ji[1];
333 >      jz2 = ji[2] * ji[2];
334 >      
335 >      dAtom->setJx( ji[0] );
336 >      dAtom->setJy( ji[1] );
337 >      dAtom->setJz( ji[2] );
338      }
339    }
340  
341 <  dump_out->writeFinal();
341 > }
342  
343 <  delete dump_out;
344 <  delete e_out;
343 >
344 > void Integrator::constrainA(){
345 >
346 >  
347 >
348 >
349   }
350  
351 +
352 +
353 +
354 +
355 +
356 +
357 +
358 +
359   void Symplectic::rotate( int axes1, int axes2, double angle, double ji[3],
360                           double A[3][3] ){
361  

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