| 1 |
#include <iostream> |
| 2 |
#include <stdlib.h> |
| 3 |
|
| 4 |
#include "Atom.hpp" |
| 5 |
#include "SRI.hpp" |
| 6 |
#include "Integrator.hpp" |
| 7 |
#include "SimInfo.hpp" |
| 8 |
#include "Thermo.hpp" |
| 9 |
#include "ReadWrite.hpp" |
| 10 |
#include "ExtendedSystem.hpp" |
| 11 |
|
| 12 |
#include "simError.h" |
| 13 |
|
| 14 |
extern "C"{ |
| 15 |
|
| 16 |
void v_constrain_a_( double &dt, int &n_atoms, double* mass, |
| 17 |
double* Rx, double* Ry, double* Rz, |
| 18 |
double* Vx, double* Vy, double* Vz, |
| 19 |
double* Fx, double* Fy, double* Fz, |
| 20 |
int &n_constrained, double *constr_sqr, |
| 21 |
int* constr_i, int* constr_j, |
| 22 |
double &box_x, double &box_y, double &box_z, |
| 23 |
int &isError ); |
| 24 |
|
| 25 |
void v_constrain_b_( double &dt, int &n_atoms, double* mass, |
| 26 |
double* Rx, double* Ry, double* Rz, |
| 27 |
double* Vx, double* Vy, double* Vz, |
| 28 |
double* Fx, double* Fy, double* Fz, |
| 29 |
double &Kinetic, |
| 30 |
int &n_constrained, double *constr_sqr, |
| 31 |
int* constr_i, int* constr_j, |
| 32 |
double &box_x, double &box_y, double &box_z, |
| 33 |
int &isError); |
| 34 |
} |
| 35 |
|
| 36 |
|
| 37 |
Verlet::Verlet( SimInfo &info, ForceFields* the_ff, ExtendedSystem* the_es ){ |
| 38 |
|
| 39 |
// get what information we need from the SimInfo object |
| 40 |
|
| 41 |
entry_plug = &info; |
| 42 |
myFF = the_ff; |
| 43 |
myES = the_es; |
| 44 |
|
| 45 |
c_natoms = info.n_atoms; |
| 46 |
c_atoms = info.atoms; |
| 47 |
nMols = info.n_mol; |
| 48 |
molecules = info.molecules; |
| 49 |
c_is_constrained = 0; |
| 50 |
c_box_x = info.box_x; |
| 51 |
c_box_y = info.box_y; |
| 52 |
c_box_z = info.box_z; |
| 53 |
|
| 54 |
// give a little love back to the SimInfo object |
| 55 |
|
| 56 |
if( info.the_integrator != NULL ) delete info.the_integrator; |
| 57 |
info.the_integrator = this; |
| 58 |
|
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// the rest are initialization issues |
| 60 |
|
| 61 |
is_first = 1; // let the integrate method know when the first call is |
| 62 |
|
| 63 |
// mass array setup |
| 64 |
|
| 65 |
c_mass = new double[c_natoms]; |
| 66 |
|
| 67 |
for(int i = 0; i < c_natoms; i++){ |
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c_mass[i] = c_atoms[i]->getMass(); |
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} |
| 70 |
|
| 71 |
// check for constraints |
| 72 |
|
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Constraint *temp_con; |
| 74 |
Constraint *dummy_plug; |
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temp_con = new Constraint[info.n_SRI]; |
| 76 |
|
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c_n_constrained = 0; |
| 78 |
int constrained = 0; |
| 79 |
SRI** theArray; |
| 80 |
for(int i = 0; i < nMols; i++){ |
| 81 |
|
| 82 |
theArray = (SRI**) molecules[i].getMyBonds(); |
| 83 |
for(int j=0; j<molecules[i].getNBonds(); j++){ |
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|
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constrained = theArray[j]->is_constrained(); |
| 86 |
|
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if(constrained){ |
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|
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dummy_plug = theArray[j]->get_constraint(); |
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temp_con[c_n_constrained].set_a( dummy_plug->get_a() ); |
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temp_con[c_n_constrained].set_b( dummy_plug->get_b() ); |
| 92 |
temp_con[c_n_constrained].set_dsqr( dummy_plug->get_dsqr() ); |
| 93 |
|
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c_n_constrained++; |
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constrained = 0; |
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} |
| 97 |
} |
| 98 |
|
| 99 |
theArray = (SRI**) molecules[i].getMyBends(); |
| 100 |
for(int j=0; j<molecules[i].getNBends(); j++){ |
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|
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constrained = theArray[j]->is_constrained(); |
| 103 |
|
| 104 |
if(constrained){ |
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|
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dummy_plug = theArray[j]->get_constraint(); |
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temp_con[c_n_constrained].set_a( dummy_plug->get_a() ); |
| 108 |
temp_con[c_n_constrained].set_b( dummy_plug->get_b() ); |
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temp_con[c_n_constrained].set_dsqr( dummy_plug->get_dsqr() ); |
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|
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c_n_constrained++; |
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constrained = 0; |
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} |
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} |
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|
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theArray = (SRI**) molecules[i].getMyTorsions(); |
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for(int j=0; j<molecules[i].getNTorsions(); j++){ |
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|
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constrained = theArray[j]->is_constrained(); |
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|
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if(constrained){ |
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|
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dummy_plug = theArray[j]->get_constraint(); |
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temp_con[c_n_constrained].set_a( dummy_plug->get_a() ); |
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temp_con[c_n_constrained].set_b( dummy_plug->get_b() ); |
| 126 |
temp_con[c_n_constrained].set_dsqr( dummy_plug->get_dsqr() ); |
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|
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c_n_constrained++; |
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constrained = 0; |
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} |
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} |
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|
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|
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} |
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|
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if(c_n_constrained > 0){ |
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|
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c_is_constrained = 1; |
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c_constrained_i = new int[c_n_constrained]; |
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c_constrained_j = new int[c_n_constrained]; |
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c_constrained_dsqr = new double[c_n_constrained]; |
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|
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for( int i = 0; i < c_n_constrained; i++){ |
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|
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/* add 1 to the index for the fortran arrays. */ |
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|
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c_constrained_i[i] = temp_con[i].get_a() + 1; |
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c_constrained_j[i] = temp_con[i].get_b() + 1; |
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c_constrained_dsqr[i] = temp_con[i].get_dsqr(); |
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} |
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} |
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|
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delete[] temp_con; |
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} |
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|
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|
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Verlet::~Verlet(){ |
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|
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if( c_is_constrained ){ |
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|
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delete[] c_constrained_i; |
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delete[] c_constrained_j; |
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delete[] c_constrained_dsqr; |
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} |
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|
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delete[] c_mass; |
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c_mass = 0; |
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} |
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|
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|
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void Verlet::integrate( void ){ |
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|
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int i, j; /* loop counters */ |
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int calcPot, calcStress; |
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|
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double kE; |
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|
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double *Rx = new double[c_natoms]; |
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double *Ry = new double[c_natoms]; |
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double *Rz = new double[c_natoms]; |
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|
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double *Vx = new double[c_natoms]; |
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double *Vy = new double[c_natoms]; |
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double *Vz = new double[c_natoms]; |
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|
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double *Fx = new double[c_natoms]; |
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double *Fy = new double[c_natoms]; |
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double *Fz = new double[c_natoms]; |
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|
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int time; |
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|
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double press[9]; |
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|
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double dt = entry_plug->dt; |
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double runTime = entry_plug->run_time; |
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double sampleTime = entry_plug->sampleTime; |
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double statusTime = entry_plug->statusTime; |
| 198 |
double thermalTime = entry_plug->thermalTime; |
| 199 |
|
| 200 |
int n_loops = (int)( runTime / dt ); |
| 201 |
int sample_n = (int)( sampleTime / dt ); |
| 202 |
int status_n = (int)( statusTime / dt ); |
| 203 |
int vel_n = (int)( thermalTime / dt ); |
| 204 |
|
| 205 |
int isError; |
| 206 |
|
| 207 |
Thermo *tStats = new Thermo( entry_plug ); |
| 208 |
|
| 209 |
StatWriter* e_out = new StatWriter( entry_plug ); |
| 210 |
DumpWriter* dump_out = new DumpWriter( entry_plug ); |
| 211 |
|
| 212 |
// the first time integrate is called, the forces need to be initialized |
| 213 |
|
| 214 |
myFF->doForces(1,1); |
| 215 |
|
| 216 |
if( entry_plug->setTemp ){ |
| 217 |
tStats->velocitize(); |
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} |
| 219 |
|
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dump_out->writeDump( 0.0 ); |
| 221 |
|
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e_out->writeStat( 0.0 ); |
| 223 |
|
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calcPot = 0; |
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|
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if (!strcasecmp( entry_plug->ensemble, "NPT")) { |
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calcStress = 1; |
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} else { |
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calcStress = 0; |
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} |
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|
| 232 |
if( c_is_constrained ){ |
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for(i = 0; i < n_loops; i++){ |
| 234 |
|
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|
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// fill R, V, and F arrays and RATTLE in fortran |
| 237 |
|
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for( j=0; j<c_natoms; j++ ){ |
| 239 |
|
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Rx[j] = c_atoms[j]->getX(); |
| 241 |
Ry[j] = c_atoms[j]->getY(); |
| 242 |
Rz[j] = c_atoms[j]->getZ(); |
| 243 |
|
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Vx[j] = c_atoms[j]->get_vx(); |
| 245 |
Vy[j] = c_atoms[j]->get_vy(); |
| 246 |
Vz[j] = c_atoms[j]->get_vz(); |
| 247 |
|
| 248 |
Fx[j] = c_atoms[j]->getFx(); |
| 249 |
Fy[j] = c_atoms[j]->getFy(); |
| 250 |
Fz[j] = c_atoms[j]->getFz(); |
| 251 |
|
| 252 |
} |
| 253 |
|
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isError = 0; |
| 255 |
v_constrain_a_( dt, c_natoms, c_mass, Rx, Ry, Rz, Vx, Vy, Vz, |
| 256 |
Fx, Fy, Fz, |
| 257 |
c_n_constrained, c_constrained_dsqr, |
| 258 |
c_constrained_i, c_constrained_j, |
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c_box_x, c_box_y, c_box_z, |
| 260 |
isError); |
| 261 |
|
| 262 |
if( isError ){ |
| 263 |
|
| 264 |
sprintf( painCave.errMsg, |
| 265 |
"Constraint Failure in Fortran move A\n" ); |
| 266 |
painCave.isFatal = 1; |
| 267 |
simError(); |
| 268 |
} |
| 269 |
|
| 270 |
#ifdef IS_MPI |
| 271 |
sprintf( checkPointMsg, |
| 272 |
"succesful return from move a.\n" ); |
| 273 |
MPIcheckPoint(); |
| 274 |
|
| 275 |
#endif //is_mpi |
| 276 |
|
| 277 |
for( j=0; j<c_natoms; j++ ){ |
| 278 |
|
| 279 |
c_atoms[j]->setX(Rx[j]); |
| 280 |
c_atoms[j]->setY(Ry[j]); |
| 281 |
c_atoms[j]->setZ(Rz[j]); |
| 282 |
|
| 283 |
c_atoms[j]->set_vx(Vx[j]); |
| 284 |
c_atoms[j]->set_vy(Vy[j]); |
| 285 |
c_atoms[j]->set_vz(Vz[j]); |
| 286 |
} |
| 287 |
|
| 288 |
if (!strcasecmp( entry_plug->ensemble, "NVT")) |
| 289 |
myES->NoseHooverNVT( dt / 2.0 , tStats->getKinetic() ); |
| 290 |
|
| 291 |
// calculate the forces |
| 292 |
|
| 293 |
myFF->doForces(calcPot,calcStress); |
| 294 |
|
| 295 |
// finish the constrain move ( same as above. ) |
| 296 |
|
| 297 |
for( j=0; j<c_natoms; j++ ){ |
| 298 |
|
| 299 |
Rx[j] = c_atoms[j]->getX(); |
| 300 |
Ry[j] = c_atoms[j]->getY(); |
| 301 |
Rz[j] = c_atoms[j]->getZ(); |
| 302 |
|
| 303 |
Vx[j] = c_atoms[j]->get_vx(); |
| 304 |
Vy[j] = c_atoms[j]->get_vy(); |
| 305 |
Vz[j] = c_atoms[j]->get_vz(); |
| 306 |
|
| 307 |
Fx[j] = c_atoms[j]->getFx(); |
| 308 |
Fy[j] = c_atoms[j]->getFy(); |
| 309 |
Fz[j] = c_atoms[j]->getFz(); |
| 310 |
} |
| 311 |
|
| 312 |
|
| 313 |
isError = 0; |
| 314 |
v_constrain_b_( dt, c_natoms, c_mass, Rx, Ry, Rz, Vx, Vy, Vz, |
| 315 |
Fx, Fy, Fz, |
| 316 |
kE, c_n_constrained, c_constrained_dsqr, |
| 317 |
c_constrained_i, c_constrained_j, |
| 318 |
c_box_x, c_box_y, c_box_z, isError ); |
| 319 |
|
| 320 |
if( isError ){ |
| 321 |
|
| 322 |
sprintf( painCave.errMsg, |
| 323 |
"Constraint Failure in Fortran move B\n" ); |
| 324 |
painCave.isFatal = 1; |
| 325 |
simError(); |
| 326 |
} |
| 327 |
|
| 328 |
#ifdef IS_MPI |
| 329 |
sprintf( checkPointMsg, |
| 330 |
"succesful return from move B.\n" ); |
| 331 |
MPIcheckPoint(); |
| 332 |
|
| 333 |
#endif //is_mpi |
| 334 |
|
| 335 |
|
| 336 |
for( j=0; j<c_natoms; j++ ){ |
| 337 |
|
| 338 |
c_atoms[j]->setX(Rx[j]); |
| 339 |
c_atoms[j]->setY(Ry[j]); |
| 340 |
c_atoms[j]->setZ(Rz[j]); |
| 341 |
|
| 342 |
c_atoms[j]->set_vx(Vx[j]); |
| 343 |
c_atoms[j]->set_vy(Vy[j]); |
| 344 |
c_atoms[j]->set_vz(Vz[j]); |
| 345 |
} |
| 346 |
|
| 347 |
if (!strcasecmp( entry_plug->ensemble, "NVT")) |
| 348 |
myES->NoseHooverNVT( dt / 2.0, tStats->getKinetic() ); |
| 349 |
|
| 350 |
if (!strcasecmp( entry_plug->ensemble, "NPT") ) { |
| 351 |
tStats->getPressureTensor(press); |
| 352 |
myES->NoseHooverAndersonNPT( dt, |
| 353 |
tStats->getKinetic(), |
| 354 |
press); |
| 355 |
} |
| 356 |
|
| 357 |
time = i + 1; |
| 358 |
|
| 359 |
if( entry_plug->setTemp ){ |
| 360 |
if( !(time % vel_n) ) tStats->velocitize(); |
| 361 |
} |
| 362 |
if( !(time % sample_n) ) dump_out->writeDump( time * dt ); |
| 363 |
|
| 364 |
if( !((time+1) % status_n) ) { |
| 365 |
calcPot = 1; |
| 366 |
calcStress = 1; |
| 367 |
} |
| 368 |
if( !(time % status_n) ){ |
| 369 |
e_out->writeStat( time * dt ); |
| 370 |
calcPot = 0; |
| 371 |
if (!strcasecmp(entry_plug->ensemble, "NPT")) calcStress = 1; |
| 372 |
else calcStress = 0; |
| 373 |
} |
| 374 |
} |
| 375 |
} |
| 376 |
else{ |
| 377 |
for(i = 0; i < n_loops; i++){ |
| 378 |
|
| 379 |
|
| 380 |
move_a( dt ); |
| 381 |
|
| 382 |
if (!strcasecmp( entry_plug->ensemble, "NVT")) |
| 383 |
myES->NoseHooverNVT( dt / 2.0, tStats->getKinetic() ); |
| 384 |
|
| 385 |
// calculate the forces |
| 386 |
|
| 387 |
myFF->doForces(calcPot,calcStress); |
| 388 |
|
| 389 |
// complete the verlet move |
| 390 |
|
| 391 |
move_b( dt ); |
| 392 |
|
| 393 |
if (!strcasecmp( entry_plug->ensemble, "NVT")) |
| 394 |
myES->NoseHooverNVT( dt / 2.0 , tStats->getKinetic() ); |
| 395 |
|
| 396 |
if (!strcasecmp( entry_plug->ensemble, "NPT") ) { |
| 397 |
tStats->getPressureTensor(press); |
| 398 |
myES->NoseHooverAndersonNPT( dt, |
| 399 |
tStats->getKinetic(), |
| 400 |
press); |
| 401 |
} |
| 402 |
|
| 403 |
time = i + 1; |
| 404 |
|
| 405 |
if( entry_plug->setTemp ){ |
| 406 |
if( !(time % vel_n) ) tStats->velocitize(); |
| 407 |
} |
| 408 |
if( !(time % sample_n) ) dump_out->writeDump( time * dt ); |
| 409 |
if( !((time+1) % status_n) ) { |
| 410 |
calcPot = 1; |
| 411 |
calcStress = 1; |
| 412 |
} |
| 413 |
if( !(time % status_n) ){ |
| 414 |
e_out->writeStat( time * dt ); |
| 415 |
calcPot = 0; |
| 416 |
if (!strcasecmp(entry_plug->ensemble, "NPT")) calcStress = 1; |
| 417 |
else calcStress = 0; |
| 418 |
} |
| 419 |
} |
| 420 |
} |
| 421 |
|
| 422 |
dump_out->writeFinal(); |
| 423 |
|
| 424 |
delete dump_out; |
| 425 |
delete e_out; |
| 426 |
|
| 427 |
} |
| 428 |
|
| 429 |
|
| 430 |
void Verlet::move_a(double dt){ |
| 431 |
|
| 432 |
const double e_convert = 4.184e-4; // converts kcal/mol -> amu*A^2/fs^2 |
| 433 |
|
| 434 |
double qx, qy, qz; |
| 435 |
double vx, vy, vz; |
| 436 |
int ma; |
| 437 |
double h_dt = 0.5 * dt; |
| 438 |
double h_dt2 = h_dt * dt; |
| 439 |
|
| 440 |
for( ma = 0; ma < c_natoms; ma++){ |
| 441 |
|
| 442 |
qx = c_atoms[ma]->getX() + dt * c_atoms[ma]->get_vx() + |
| 443 |
h_dt2 * c_atoms[ma]->getFx() * e_convert / c_atoms[ma]->getMass(); |
| 444 |
qy = c_atoms[ma]->getY() + dt * c_atoms[ma]->get_vy() + |
| 445 |
h_dt2 * c_atoms[ma]->getFy() * e_convert / c_atoms[ma]->getMass(); |
| 446 |
qz = c_atoms[ma]->getZ() + dt * c_atoms[ma]->get_vz() + |
| 447 |
h_dt2 * c_atoms[ma]->getFz() * e_convert / c_atoms[ma]->getMass(); |
| 448 |
|
| 449 |
vx = c_atoms[ma]->get_vx() + |
| 450 |
h_dt * c_atoms[ma]->getFx() * e_convert / c_atoms[ma]->getMass(); |
| 451 |
vy = c_atoms[ma]->get_vy() + |
| 452 |
h_dt * c_atoms[ma]->getFy() * e_convert / c_atoms[ma]->getMass(); |
| 453 |
vz = c_atoms[ma]->get_vz() + |
| 454 |
h_dt * c_atoms[ma]->getFz() * e_convert / c_atoms[ma]->getMass(); |
| 455 |
|
| 456 |
c_atoms[ma]->setX(qx); |
| 457 |
c_atoms[ma]->setY(qy); |
| 458 |
c_atoms[ma]->setZ(qz); |
| 459 |
|
| 460 |
c_atoms[ma]->set_vx(vx); |
| 461 |
c_atoms[ma]->set_vy(vy); |
| 462 |
c_atoms[ma]->set_vz(vz); |
| 463 |
} |
| 464 |
} |
| 465 |
|
| 466 |
void Verlet::move_b( double dt ){ |
| 467 |
|
| 468 |
const double e_convert = 4.184e-4; // converts kcal/mol -> amu*A^2/fs^2 |
| 469 |
|
| 470 |
double vx, vy, vz; |
| 471 |
int mb; |
| 472 |
double h_dt = 0.5 * dt; |
| 473 |
|
| 474 |
|
| 475 |
for( mb = 0; mb < c_natoms; mb++){ |
| 476 |
|
| 477 |
vx = c_atoms[mb]->get_vx() + |
| 478 |
h_dt * c_atoms[mb]->getFx() * e_convert / c_atoms[mb]->getMass(); |
| 479 |
vy = c_atoms[mb]->get_vy() + |
| 480 |
h_dt * c_atoms[mb]->getFy() * e_convert / c_atoms[mb]->getMass(); |
| 481 |
vz = c_atoms[mb]->get_vz() + |
| 482 |
h_dt * c_atoms[mb]->getFz() * e_convert / c_atoms[mb]->getMass(); |
| 483 |
|
| 484 |
c_atoms[mb]->set_vx(vx); |
| 485 |
c_atoms[mb]->set_vy(vy); |
| 486 |
c_atoms[mb]->set_vz(vz); |
| 487 |
} |
| 488 |
} |
