| 1 |
#include <iostream> |
| 2 |
|
| 3 |
using namespace std; |
| 4 |
|
| 5 |
|
| 6 |
#include <stdlib.h> |
| 7 |
|
| 8 |
#ifdef IS_MPI |
| 9 |
#include <mpi.h> |
| 10 |
#endif // is_mpi |
| 11 |
|
| 12 |
|
| 13 |
#ifdef PROFILE |
| 14 |
#include "mdProfile.hpp" |
| 15 |
#endif |
| 16 |
|
| 17 |
#include "simError.h" |
| 18 |
#include "ForceFields.hpp" |
| 19 |
#include "Atom.hpp" |
| 20 |
#include "fortranWrappers.hpp" |
| 21 |
|
| 22 |
|
| 23 |
void ForceFields::calcRcut( void ){ |
| 24 |
|
| 25 |
#ifdef IS_MPI |
| 26 |
double tempBig = bigSigma; |
| 27 |
MPI_Allreduce( &tempBig, &bigSigma, 1, MPI_DOUBLE, MPI_MAX, |
| 28 |
MPI_COMM_WORLD); |
| 29 |
#endif //is_mpi |
| 30 |
|
| 31 |
//calc rCut and rList |
| 32 |
|
| 33 |
entry_plug->setDefaultRcut( 2.5 * bigSigma ); |
| 34 |
|
| 35 |
} |
| 36 |
|
| 37 |
void ForceFields::setRcut( double LJrcut ) { |
| 38 |
|
| 39 |
#ifdef IS_MPI |
| 40 |
double tempBig = bigSigma; |
| 41 |
MPI_Allreduce( &tempBig, &bigSigma, 1, MPI_DOUBLE, MPI_MAX, |
| 42 |
MPI_COMM_WORLD); |
| 43 |
#endif //is_mpi |
| 44 |
|
| 45 |
if (LJrcut < 2.5 * bigSigma) { |
| 46 |
sprintf( painCave.errMsg, |
| 47 |
"Setting Lennard-Jones cutoff radius to %lf.\n" |
| 48 |
"\tThis value is smaller than %lf, which is\n" |
| 49 |
"\t2.5 * bigSigma, where bigSigma is the largest\n" |
| 50 |
"\tvalue of sigma present in the simulation.\n" |
| 51 |
"\tThis is potentially a problem since the LJ potential may\n" |
| 52 |
"\tbe appreciable at this distance. If you don't want the\n" |
| 53 |
"\tsmaller cutoff, change the LJrcut variable.\n", |
| 54 |
LJrcut, 2.5*bigSigma); |
| 55 |
painCave.isFatal = 0; |
| 56 |
simError(); |
| 57 |
} else { |
| 58 |
sprintf( painCave.errMsg, |
| 59 |
"Setting Lennard-Jones cutoff radius to %lf.\n" |
| 60 |
"\tThis value is larger than %lf, which is\n" |
| 61 |
"\t2.5 * bigSigma, where bigSigma is the largest\n" |
| 62 |
"\tvalue of sigma present in the simulation. This should\n" |
| 63 |
"\tnot be a problem, but could adversely effect performance.\n", |
| 64 |
LJrcut, 2.5*bigSigma); |
| 65 |
painCave.isFatal = 0; |
| 66 |
simError(); |
| 67 |
} |
| 68 |
|
| 69 |
//calc rCut and rList |
| 70 |
|
| 71 |
entry_plug->setDefaultRcut( LJrcut ); |
| 72 |
} |
| 73 |
|
| 74 |
void ForceFields::doForces( int calcPot, int calcStress ){ |
| 75 |
|
| 76 |
int i, j, isError; |
| 77 |
double* frc; |
| 78 |
double* pos; |
| 79 |
double* trq; |
| 80 |
double* A; |
| 81 |
double* u_l; |
| 82 |
double* rc; |
| 83 |
double* massRatio; |
| 84 |
double factor; |
| 85 |
SimState* config; |
| 86 |
|
| 87 |
Molecule* myMols; |
| 88 |
Atom** myAtoms; |
| 89 |
int numAtom; |
| 90 |
int curIndex; |
| 91 |
double mtot; |
| 92 |
int numMol; |
| 93 |
int numCutoffGroups; |
| 94 |
CutoffGroup* myCutoffGroup; |
| 95 |
vector<CutoffGroup*>::iterator iterCutoff; |
| 96 |
double com[3]; |
| 97 |
vector<double> rcGroup; |
| 98 |
|
| 99 |
short int passedCalcPot = (short int)calcPot; |
| 100 |
short int passedCalcStress = (short int)calcStress; |
| 101 |
|
| 102 |
// forces are zeroed here, before any are accumulated. |
| 103 |
// NOTE: do not rezero the forces in Fortran. |
| 104 |
|
| 105 |
for(i=0; i<entry_plug->n_atoms; i++){ |
| 106 |
entry_plug->atoms[i]->zeroForces(); |
| 107 |
} |
| 108 |
|
| 109 |
#ifdef PROFILE |
| 110 |
startProfile(pro7); |
| 111 |
#endif |
| 112 |
|
| 113 |
for(i=0; i<entry_plug->n_mol; i++ ){ |
| 114 |
// CalcForces in molecules takes care of mapping rigid body coordinates |
| 115 |
// into atomic coordinates |
| 116 |
entry_plug->molecules[i].calcForces(); |
| 117 |
} |
| 118 |
|
| 119 |
#ifdef PROFILE |
| 120 |
endProfile( pro7 ); |
| 121 |
#endif |
| 122 |
|
| 123 |
config = entry_plug->getConfiguration(); |
| 124 |
|
| 125 |
frc = config->getFrcArray(); |
| 126 |
pos = config->getPosArray(); |
| 127 |
trq = config->getTrqArray(); |
| 128 |
A = config->getAmatArray(); |
| 129 |
u_l = config->getUlArray(); |
| 130 |
|
| 131 |
if(entry_plug->haveCutoffGroups){ |
| 132 |
myMols = entry_plug->molecules; |
| 133 |
numMol = entry_plug->n_mol; |
| 134 |
for(int i = 0; i < numMol; i++){ |
| 135 |
|
| 136 |
numCutoffGroups = myMols[i].getNCutoffGroups(); |
| 137 |
for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff); myCutoffGroup != NULL; |
| 138 |
myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){ |
| 139 |
//get center of mass of the cutoff group |
| 140 |
myCutoffGroup->getCOM(com); |
| 141 |
|
| 142 |
rcGroup.push_back(com[0]); |
| 143 |
rcGroup.push_back(com[1]); |
| 144 |
rcGroup.push_back(com[2]); |
| 145 |
|
| 146 |
}// end for(myCutoffGroup) |
| 147 |
|
| 148 |
}//end for(int i = 0) |
| 149 |
|
| 150 |
rc = &rcGroup[0]; |
| 151 |
} |
| 152 |
else{ |
| 153 |
// center of mass of the group is the same as position of the atom if cutoff group does not exist |
| 154 |
rc = pos; |
| 155 |
} |
| 156 |
|
| 157 |
|
| 158 |
|
| 159 |
isError = 0; |
| 160 |
entry_plug->lrPot = 0.0; |
| 161 |
|
| 162 |
for (i=0; i<9; i++) { |
| 163 |
entry_plug->tau[i] = 0.0; |
| 164 |
} |
| 165 |
|
| 166 |
|
| 167 |
#ifdef PROFILE |
| 168 |
startProfile(pro8); |
| 169 |
#endif |
| 170 |
|
| 171 |
fortranForceLoop( pos, |
| 172 |
rc, |
| 173 |
A, |
| 174 |
u_l, |
| 175 |
frc, |
| 176 |
trq, |
| 177 |
entry_plug->tau, |
| 178 |
&(entry_plug->lrPot), |
| 179 |
&passedCalcPot, |
| 180 |
&passedCalcStress, |
| 181 |
&isError ); |
| 182 |
|
| 183 |
|
| 184 |
#ifdef PROFILE |
| 185 |
endProfile(pro8); |
| 186 |
#endif |
| 187 |
|
| 188 |
|
| 189 |
if( isError ){ |
| 190 |
sprintf( painCave.errMsg, |
| 191 |
"Error returned from the fortran force calculation.\n" ); |
| 192 |
painCave.isFatal = 1; |
| 193 |
simError(); |
| 194 |
} |
| 195 |
|
| 196 |
// scale forces if thermodynamic integration is used |
| 197 |
if (entry_plug->useSolidThermInt || entry_plug->useLiquidThermInt) { |
| 198 |
factor = pow(entry_plug->thermIntLambda, entry_plug->thermIntK); |
| 199 |
for (i=0; i < entry_plug->n_atoms; i++) { |
| 200 |
for (j=0; j< 3; j++) |
| 201 |
frc[3*i + j] *= factor; |
| 202 |
if (entry_plug->atoms[i]->isDirectional()) { |
| 203 |
for (j=0; j< 3; j++) |
| 204 |
trq[3*i + j] *= factor; |
| 205 |
} |
| 206 |
} |
| 207 |
entry_plug->vRaw = entry_plug->lrPot; |
| 208 |
entry_plug->lrPot *= factor; |
| 209 |
} |
| 210 |
|
| 211 |
// collect the atomic forces onto rigid bodies |
| 212 |
for(i=0; i<entry_plug->n_mol; i++ ){ |
| 213 |
entry_plug->molecules[i].atoms2rigidBodies(); |
| 214 |
} |
| 215 |
|
| 216 |
// do crystal restraint forces for thermodynamic integration |
| 217 |
if (entry_plug->useSolidThermInt){ |
| 218 |
entry_plug->lrPot += entry_plug->restraint->Calc_Restraint_Forces(entry_plug->integrableObjects); |
| 219 |
entry_plug->vHarm = entry_plug->restraint->getVharm(); |
| 220 |
} |
| 221 |
|
| 222 |
|
| 223 |
#ifdef IS_MPI |
| 224 |
sprintf( checkPointMsg, |
| 225 |
"returned from the force calculation.\n" ); |
| 226 |
MPIcheckPoint(); |
| 227 |
#endif // is_mpi |
| 228 |
|
| 229 |
|
| 230 |
} |
| 231 |
|
| 232 |
|
| 233 |
void ForceFields::initFortran(int ljMixPolicy, int useReactionField ){ |
| 234 |
|
| 235 |
int isError; |
| 236 |
|
| 237 |
isError = 0; |
| 238 |
initFortranFF( &ljMixPolicy, &useReactionField, &isError ); |
| 239 |
|
| 240 |
if(isError){ |
| 241 |
sprintf( painCave.errMsg, |
| 242 |
"ForceField error: There was an error initializing the forceField in fortran.\n" ); |
| 243 |
painCave.isFatal = 1; |
| 244 |
simError(); |
| 245 |
} |
| 246 |
|
| 247 |
|
| 248 |
#ifdef IS_MPI |
| 249 |
sprintf( checkPointMsg, "ForceField successfully initialized the fortran component list.\n" ); |
| 250 |
MPIcheckPoint(); |
| 251 |
#endif // is_mpi |
| 252 |
|
| 253 |
} |
| 254 |
|
| 255 |
|
| 256 |
void ForceFields::initRestraints(){ |
| 257 |
int i; |
| 258 |
// store the initial info. |
| 259 |
// set the omega values to zero |
| 260 |
for (i=0; i<entry_plug->integrableObjects.size(); i++) |
| 261 |
entry_plug->integrableObjects[i]->setZangle( 0.0 ); |
| 262 |
|
| 263 |
entry_plug->restraint->Store_Init_Info(entry_plug->integrableObjects); |
| 264 |
|
| 265 |
} |
| 266 |
|
| 267 |
void ForceFields::dumpzAngle(){ |
| 268 |
|
| 269 |
// store the initial info. |
| 270 |
entry_plug->restraint->Write_zAngle_File(entry_plug->integrableObjects); |
| 271 |
|
| 272 |
} |
