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root/OpenMD/trunk/src/nonbonded/Electrostatic.cpp
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Comparing trunk/src/nonbonded/Electrostatic.cpp (file contents):
Revision 1900 by gezelter, Fri Jul 12 17:38:06 2013 UTC vs.
Revision 1925 by gezelter, Wed Aug 7 15:24:16 2013 UTC

# Line 44 | Line 44
44   #include <string.h>
45  
46   #include <cmath>
47 + #include <numeric>
48   #include "nonbonded/Electrostatic.hpp"
49   #include "utils/simError.h"
50   #include "types/NonBondedInteractionType.hpp"
# Line 55 | Line 56
56   #include "utils/PhysicalConstants.hpp"
57   #include "math/erfc.hpp"
58   #include "math/SquareMatrix.hpp"
59 + #include "primitives/Molecule.hpp"
60 + #ifdef IS_MPI
61 + #include <mpi.h>
62 + #endif
63  
64   namespace OpenMD {
65    
# Line 191 | Line 196 | namespace OpenMD {
196        simError();
197      }
198            
199 <    if (screeningMethod_ == DAMPED) {      
199 >    if (screeningMethod_ == DAMPED || summationMethod_ == esm_EWALD_FULL) {
200        if (!simParams_->haveDampingAlpha()) {
201          // first set a cutoff dependent alpha value
202          // we assume alpha depends linearly with rcut from 0 to 20.5 ang
203          dampingAlpha_ = 0.425 - cutoffRadius_* 0.02;
204 <        if (dampingAlpha_ < 0.0) dampingAlpha_ = 0.0;
200 <        
204 >        if (dampingAlpha_ < 0.0) dampingAlpha_ = 0.0;        
205          // throw warning
206          sprintf( painCave.errMsg,
207                   "Electrostatic::initialize: dampingAlpha was not specified in the\n"
# Line 213 | Line 217 | namespace OpenMD {
217        haveDampingAlpha_ = true;
218      }
219  
220 +
221      Etypes.clear();
222      Etids.clear();
223      FQtypes.clear();
# Line 262 | Line 267 | namespace OpenMD {
267        b3c = (5.0 * b2c + pow(2.0*a2, 3) * expTerm * invArootPi) / r2;
268        b4c = (7.0 * b3c + pow(2.0*a2, 4) * expTerm * invArootPi) / r2;
269        b5c = (9.0 * b4c + pow(2.0*a2, 5) * expTerm * invArootPi) / r2;
265 –      //selfMult1_ = - 2.0 * a2 * invArootPi;
266 –      //selfMult2_ = - 4.0 * a2 * a2 * invArootPi / 3.0;
267 –      //selfMult4_ = - 8.0 * a2 * a2 * a2 * invArootPi / 5.0;
270        // Half the Smith self piece:
271        selfMult1_ = - a2 * invArootPi;
272        selfMult2_ = - 2.0 * a2 * a2 * invArootPi / 3.0;
# Line 288 | Line 290 | namespace OpenMD {
290      db0c_3 =          3.0*r*b2c  - r2*r*b3c;
291      db0c_4 =          3.0*b2c  - 6.0*r2*b3c     + r2*r2*b4c;
292      db0c_5 =                    -15.0*r*b3c + 10.0*r2*r*b4c - r2*r2*r*b5c;  
291 –    
292 –    selfMult1_ -= b0c;
293 –    selfMult2_ += (db0c_2 + 2.0*db0c_1*ric) /  3.0;
294 –    selfMult4_ -= (db0c_4 + 4.0*db0c_3*ric) / 15.0;
293  
294 +    if (summationMethod_ != esm_EWALD_FULL) {
295 +      selfMult1_ -= b0c;
296 +      selfMult2_ += (db0c_2 + 2.0*db0c_1*ric) /  3.0;
297 +      selfMult4_ -= (db0c_4 + 4.0*db0c_3*ric) / 15.0;
298 +    }
299 +
300      // working variables for the splines:
301      RealType ri, ri2;
302      RealType b0, b1, b2, b3, b4, b5;
# Line 327 | Line 331 | namespace OpenMD {
331      vector<RealType> v21v, v22v;
332      vector<RealType> v31v, v32v;
333      vector<RealType> v41v, v42v, v43v;
330 –
331 –    /*
332 –    vector<RealType> dv01v;
333 –    vector<RealType> dv11v;
334 –    vector<RealType> dv21v, dv22v;
335 –    vector<RealType> dv31v, dv32v;
336 –    vector<RealType> dv41v, dv42v, dv43v;
337 –    */
334  
335      for (int i = 1; i < np_ + 1; i++) {
336        r = RealType(i) * dx;
# Line 499 | Line 495 | namespace OpenMD {
495  
496        case esm_SWITCHING_FUNCTION:
497        case esm_HARD:
498 +      case esm_EWALD_FULL:
499  
500          v01 = f;
501          v11 = g;
# Line 557 | Line 554 | namespace OpenMD {
554  
555          break;
556                  
560 –      case esm_EWALD_FULL:
557        case esm_EWALD_PME:
558        case esm_EWALD_SPME:
559        default :
# Line 586 | Line 582 | namespace OpenMD {
582        v41v.push_back(v41);
583        v42v.push_back(v42);
584        v43v.push_back(v43);
589 –      /*
590 –      dv01v.push_back(dv01);
591 –      dv11v.push_back(dv11);
592 –      dv21v.push_back(dv21);
593 –      dv22v.push_back(dv22);
594 –      dv31v.push_back(dv31);
595 –      dv32v.push_back(dv32);      
596 –      dv41v.push_back(dv41);
597 –      dv42v.push_back(dv42);
598 –      dv43v.push_back(dv43);
599 –      */
585      }
586  
587      // construct the spline structures and fill them with the values we've
# Line 620 | Line 605 | namespace OpenMD {
605      v42s->addPoints(rv, v42v);
606      v43s = new CubicSpline();
607      v43s->addPoints(rv, v43v);
623 –
624 –    /*
625 –    dv01s = new CubicSpline();
626 –    dv01s->addPoints(rv, dv01v);
627 –    dv11s = new CubicSpline();
628 –    dv11s->addPoints(rv, dv11v);
629 –    dv21s = new CubicSpline();
630 –    dv21s->addPoints(rv, dv21v);
631 –    dv22s = new CubicSpline();
632 –    dv22s->addPoints(rv, dv22v);
633 –    dv31s = new CubicSpline();
634 –    dv31s->addPoints(rv, dv31v);
635 –    dv32s = new CubicSpline();
636 –    dv32s->addPoints(rv, dv32v);
637 –    dv41s = new CubicSpline();
638 –    dv41s->addPoints(rv, dv41v);
639 –    dv42s = new CubicSpline();
640 –    dv42s->addPoints(rv, dv42v);
641 –    dv43s = new CubicSpline();
642 –    dv43s->addPoints(rv, dv43v);
643 –    */
608  
609      haveElectroSplines_ = true;
610  
# Line 715 | Line 679 | namespace OpenMD {
679        FQtids[atid] = fqtid;
680        Jij[fqtid].resize(nFlucq_);
681  
682 <      // Now, iterate over all known fluctuating and add to the coulomb integral map:
682 >      // Now, iterate over all known fluctuating and add to the
683 >      // coulomb integral map:
684        
685        std::set<int>::iterator it;
686        for( it = FQtypes.begin(); it != FQtypes.end(); ++it) {    
# Line 1202 | Line 1167 | namespace OpenMD {
1167        
1168      case esm_SHIFTED_FORCE:
1169      case esm_SHIFTED_POTENTIAL:
1170 +    case esm_TAYLOR_SHIFTED:
1171 +    case esm_EWALD_FULL:
1172        if (i_is_Charge)
1173          self += selfMult1_ * pre11_ * C_a * (C_a + *(sdat.skippedCharge));      
1174        if (i_is_Dipole)
# Line 1227 | Line 1194 | namespace OpenMD {
1194      // cases.
1195      return 12.0;
1196    }
1197 +
1198 +
1199 +  void Electrostatic::ReciprocalSpaceSum(RealType& pot) {
1200 +    
1201 +    RealType kPot = 0.0;
1202 +    RealType kVir = 0.0;
1203 +    
1204 +    const RealType mPoleConverter = 0.20819434; // converts from the
1205 +                                                // internal units of
1206 +                                                // Debye (for dipoles)
1207 +                                                // or Debye-angstroms
1208 +                                                // (for quadrupoles) to
1209 +                                                // electron angstroms or
1210 +                                                // electron-angstroms^2
1211 +    
1212 +    const RealType eConverter = 332.0637778; // convert the
1213 +                                             // Charge-Charge
1214 +                                             // electrostatic
1215 +                                             // interactions into kcal /
1216 +                                             // mol assuming distances
1217 +                                             // are measured in
1218 +                                             // angstroms.
1219 +
1220 +    Mat3x3d hmat = info_->getSnapshotManager()->getCurrentSnapshot()->getHmat();
1221 +    Vector3d box = hmat.diagonals();
1222 +    RealType boxMax = box.max();
1223 +    
1224 +    //int kMax = int(2.0 * M_PI / (pow(dampingAlpha_,2)*cutoffRadius_ * boxMax) );
1225 +    int kMax = 7;
1226 +    int kSqMax = kMax*kMax + 2;
1227 +    
1228 +    int kLimit = kMax+1;
1229 +    int kLim2 = 2*kMax+1;
1230 +    int kSqLim = kSqMax;
1231 +    
1232 +    vector<RealType> AK(kSqLim+1, 0.0);
1233 +    RealType xcl = 2.0 * M_PI / box.x();
1234 +    RealType ycl = 2.0 * M_PI / box.y();
1235 +    RealType zcl = 2.0 * M_PI / box.z();
1236 +    RealType rcl = 2.0 * M_PI / boxMax;
1237 +    RealType rvol = 2.0 * M_PI /(box.x() * box.y() * box.z());
1238 +    
1239 +    if(dampingAlpha_ < 1.0e-12) return;
1240 +    
1241 +    RealType ralph = -0.25/pow(dampingAlpha_,2);
1242 +    
1243 +    // Calculate and store exponential factors  
1244 +    
1245 +    vector<vector<RealType> > elc;
1246 +    vector<vector<RealType> > emc;
1247 +    vector<vector<RealType> > enc;
1248 +    vector<vector<RealType> > els;
1249 +    vector<vector<RealType> > ems;
1250 +    vector<vector<RealType> > ens;
1251 +
1252 +    
1253 +    int nMax = info_->getNAtoms();
1254 +    
1255 +    elc.resize(kLimit+1);
1256 +    emc.resize(kLimit+1);
1257 +    enc.resize(kLimit+1);
1258 +    els.resize(kLimit+1);
1259 +    ems.resize(kLimit+1);
1260 +    ens.resize(kLimit+1);
1261 +
1262 +    for (int j = 0; j < kLimit+1; j++) {
1263 +      elc[j].resize(nMax);
1264 +      emc[j].resize(nMax);
1265 +      enc[j].resize(nMax);
1266 +      els[j].resize(nMax);
1267 +      ems[j].resize(nMax);
1268 +      ens[j].resize(nMax);
1269 +    }
1270 +    
1271 +    Vector3d t( 2.0 * M_PI );
1272 +    t.Vdiv(t, box);
1273 +
1274 +    
1275 +    SimInfo::MoleculeIterator mi;
1276 +    Molecule::AtomIterator ai;
1277 +    int i;
1278 +    Vector3d r;
1279 +    Vector3d tt;
1280 +    
1281 +    for (Molecule* mol = info_->beginMolecule(mi); mol != NULL;
1282 +         mol = info_->nextMolecule(mi)) {
1283 +      for(Atom* atom = mol->beginAtom(ai); atom != NULL;
1284 +          atom = mol->nextAtom(ai)) {  
1285 +        
1286 +        i = atom->getLocalIndex();
1287 +        r = atom->getPos();
1288 +        info_->getSnapshotManager()->getCurrentSnapshot()->wrapVector(r);
1289 +        
1290 +        tt.Vmul(t, r);
1291 +
1292 +        elc[1][i] = 1.0;
1293 +        emc[1][i] = 1.0;
1294 +        enc[1][i] = 1.0;
1295 +        els[1][i] = 0.0;
1296 +        ems[1][i] = 0.0;
1297 +        ens[1][i] = 0.0;
1298 +
1299 +        elc[2][i] = cos(tt.x());
1300 +        emc[2][i] = cos(tt.y());
1301 +        enc[2][i] = cos(tt.z());
1302 +        els[2][i] = sin(tt.x());
1303 +        ems[2][i] = sin(tt.y());
1304 +        ens[2][i] = sin(tt.z());
1305 +        
1306 +        for(int l = 3; l <= kLimit; l++) {
1307 +          elc[l][i]=elc[l-1][i]*elc[2][i]-els[l-1][i]*els[2][i];
1308 +          emc[l][i]=emc[l-1][i]*emc[2][i]-ems[l-1][i]*ems[2][i];
1309 +          enc[l][i]=enc[l-1][i]*enc[2][i]-ens[l-1][i]*ens[2][i];
1310 +          els[l][i]=els[l-1][i]*elc[2][i]+elc[l-1][i]*els[2][i];
1311 +          ems[l][i]=ems[l-1][i]*emc[2][i]+emc[l-1][i]*ems[2][i];
1312 +          ens[l][i]=ens[l-1][i]*enc[2][i]+enc[l-1][i]*ens[2][i];
1313 +        }
1314 +      }
1315 +    }
1316 +    
1317 +    // Calculate and store AK coefficients:
1318 +    
1319 +    RealType eksq = 1.0;
1320 +    RealType expf = 0.0;
1321 +    if (ralph < 0.0) expf = exp(ralph*rcl*rcl);
1322 +    for (i = 1; i <= kSqLim; i++) {
1323 +      RealType rksq = float(i)*rcl*rcl;
1324 +      eksq = expf*eksq;
1325 +      AK[i] = eConverter * eksq/rksq;
1326 +    }
1327 +    
1328 +    /*
1329 +     * Loop over all k vectors k = 2 pi (ll/Lx, mm/Ly, nn/Lz)
1330 +     * the values of ll, mm and nn are selected so that the symmetry of
1331 +     * reciprocal lattice is taken into account i.e. the following
1332 +     * rules apply.
1333 +     *
1334 +     * ll ranges over the values 0 to kMax only.
1335 +     *
1336 +     * mm ranges over 0 to kMax when ll=0 and over
1337 +     *            -kMax to kMax otherwise.
1338 +     * nn ranges over 1 to kMax when ll=mm=0 and over
1339 +     *            -kMax to kMax otherwise.
1340 +     *
1341 +     * Hence the result of the summation must be doubled at the end.    
1342 +     */
1343 +    
1344 +    std::vector<RealType> clm(nMax, 0.0);
1345 +    std::vector<RealType> slm(nMax, 0.0);
1346 +    std::vector<RealType> ckr(nMax, 0.0);
1347 +    std::vector<RealType> skr(nMax, 0.0);
1348 +    std::vector<RealType> ckc(nMax, 0.0);
1349 +    std::vector<RealType> cks(nMax, 0.0);
1350 +    std::vector<RealType> dkc(nMax, 0.0);
1351 +    std::vector<RealType> dks(nMax, 0.0);
1352 +    std::vector<RealType> qkc(nMax, 0.0);
1353 +    std::vector<RealType> qks(nMax, 0.0);
1354 +    std::vector<Vector3d> dxk(nMax, V3Zero);
1355 +    std::vector<Vector3d> qxk(nMax, V3Zero);
1356 +    RealType rl, rm, rn;
1357 +    Vector3d kVec;
1358 +    Vector3d Qk;
1359 +    Mat3x3d k2;
1360 +    RealType ckcs, ckss, dkcs, dkss, qkcs, qkss;
1361 +    int atid;
1362 +    ElectrostaticAtomData data;
1363 +    RealType C, dk, qk;
1364 +    Vector3d D;
1365 +    Mat3x3d  Q;
1366 +
1367 +    int mMin = kLimit;
1368 +    int nMin = kLimit + 1;
1369 +    for (int l = 1; l <= kLimit; l++) {
1370 +      int ll = l - 1;
1371 +      rl = xcl * float(ll);
1372 +      for (int mmm = mMin; mmm <= kLim2; mmm++) {
1373 +        int mm = mmm - kLimit;
1374 +        int m = abs(mm) + 1;
1375 +        rm = ycl * float(mm);
1376 +        // Set temporary products of exponential terms
1377 +        for (Molecule* mol = info_->beginMolecule(mi); mol != NULL;
1378 +             mol = info_->nextMolecule(mi)) {
1379 +          for(Atom* atom = mol->beginAtom(ai); atom != NULL;
1380 +              atom = mol->nextAtom(ai)) {
1381 +            
1382 +            i = atom->getLocalIndex();
1383 +            if(mm < 0) {
1384 +              clm[i]=elc[l][i]*emc[m][i]+els[l][i]*ems[m][i];
1385 +              slm[i]=els[l][i]*emc[m][i]-ems[m][i]*elc[l][i];
1386 +            } else {
1387 +              clm[i]=elc[l][i]*emc[m][i]-els[l][i]*ems[m][i];
1388 +              slm[i]=els[l][i]*emc[m][i]+ems[m][i]*elc[l][i];
1389 +            }
1390 +          }
1391 +        }
1392 +        for (int nnn = nMin; nnn <= kLim2; nnn++) {
1393 +          int nn = nnn - kLimit;          
1394 +          int n = abs(nn) + 1;
1395 +          rn = zcl * float(nn);
1396 +          // Test on magnitude of k vector:
1397 +          int kk=ll*ll + mm*mm + nn*nn;
1398 +          if(kk <= kSqLim) {
1399 +            kVec = Vector3d(rl, rm, rn);
1400 +            k2 = outProduct(kVec, kVec);
1401 +            // Calculate exp(ikr) terms
1402 +            for (Molecule* mol = info_->beginMolecule(mi); mol != NULL;
1403 +                 mol = info_->nextMolecule(mi)) {
1404 +              for(Atom* atom = mol->beginAtom(ai); atom != NULL;
1405 +                  atom = mol->nextAtom(ai)) {
1406 +                i = atom->getLocalIndex();
1407 +                
1408 +                if (nn < 0) {
1409 +                  ckr[i]=clm[i]*enc[n][i]+slm[i]*ens[n][i];
1410 +                  skr[i]=slm[i]*enc[n][i]-clm[i]*ens[n][i];
1411 +
1412 +                } else {
1413 +                  ckr[i]=clm[i]*enc[n][i]-slm[i]*ens[n][i];
1414 +                  skr[i]=slm[i]*enc[n][i]+clm[i]*ens[n][i];
1415 +                }
1416 +              }
1417 +            }
1418 +            
1419 +            // Calculate scalar and vector products for each site:
1420 +            
1421 +            for (Molecule* mol = info_->beginMolecule(mi); mol != NULL;
1422 +                 mol = info_->nextMolecule(mi)) {
1423 +              for(Atom* atom = mol->beginAtom(ai); atom != NULL;
1424 +                  atom = mol->nextAtom(ai)) {
1425 +                i = atom->getLocalIndex();
1426 +                int atid = atom->getAtomType()->getIdent();
1427 +                data = ElectrostaticMap[Etids[atid]];
1428 +                              
1429 +                if (data.is_Charge) {
1430 +                  C = data.fixedCharge;
1431 +                  if (atom->isFluctuatingCharge()) C += atom->getFlucQPos();
1432 +                  ckc[i] = C * ckr[i];
1433 +                  cks[i] = C * skr[i];
1434 +                }
1435 +                
1436 +                if (data.is_Dipole) {
1437 +                  D = atom->getDipole() * mPoleConverter;
1438 +                  dk = dot(D, kVec);
1439 +                  dxk[i] = cross(D, kVec);
1440 +                  dkc[i] = dk * ckr[i];
1441 +                  dks[i] = dk * skr[i];
1442 +                }
1443 +                if (data.is_Quadrupole) {
1444 +                  Q = atom->getQuadrupole();
1445 +                  Q *= mPoleConverter;
1446 +                  Qk = Q * kVec;
1447 +                  qk = dot(kVec, Qk);
1448 +                  qxk[i] = cross(kVec, Qk);
1449 +                  qkc[i] = qk * ckr[i];
1450 +                  qks[i] = qk * skr[i];
1451 +                }              
1452 +              }
1453 +            }
1454 +
1455 +            // calculate vector sums
1456 +            
1457 +            ckcs = std::accumulate(ckc.begin(),ckc.end(),0.0);
1458 +            ckss = std::accumulate(cks.begin(),cks.end(),0.0);
1459 +            dkcs = std::accumulate(dkc.begin(),dkc.end(),0.0);
1460 +            dkss = std::accumulate(dks.begin(),dks.end(),0.0);
1461 +            qkcs = std::accumulate(qkc.begin(),qkc.end(),0.0);
1462 +            qkss = std::accumulate(qks.begin(),qks.end(),0.0);
1463 +            
1464 + #ifdef IS_MPI
1465 +            MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &ckcs, 1, MPI::REALTYPE,
1466 +                                      MPI::SUM);
1467 +            MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &ckss, 1, MPI::REALTYPE,
1468 +                                      MPI::SUM);
1469 +            MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &dkcs, 1, MPI::REALTYPE,
1470 +                                      MPI::SUM);
1471 +            MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &dkss, 1, MPI::REALTYPE,
1472 +                                      MPI::SUM);
1473 +            MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &qkcs, 1, MPI::REALTYPE,
1474 +                                      MPI::SUM);
1475 +            MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &qkss, 1, MPI::REALTYPE,
1476 +                                      MPI::SUM);
1477 + #endif        
1478 +            
1479 +            // Accumulate potential energy and virial contribution:
1480 +
1481 +            kPot += 2.0 * rvol * AK[kk]*((ckss+dkcs-qkss)*(ckss+dkcs-qkss)
1482 +                                         + (ckcs-dkss-qkcs)*(ckcs-dkss-qkcs));
1483 +
1484 +            kVir += 2.0 * rvol  * AK[kk]*(ckcs*ckcs+ckss*ckss
1485 +                                          +4.0*(ckss*dkcs-ckcs*dkss)
1486 +                                          +3.0*(dkcs*dkcs+dkss*dkss)
1487 +                                          -6.0*(ckss*qkss+ckcs*qkcs)
1488 +                                          +8.0*(dkss*qkcs-dkcs*qkss)
1489 +                                          +5.0*(qkss*qkss+qkcs*qkcs));
1490 +            
1491 +            // Calculate force and torque for each site:
1492 +            
1493 +            for (Molecule* mol = info_->beginMolecule(mi); mol != NULL;
1494 +                 mol = info_->nextMolecule(mi)) {
1495 +              for(Atom* atom = mol->beginAtom(ai); atom != NULL;
1496 +                  atom = mol->nextAtom(ai)) {
1497 +                
1498 +                i = atom->getLocalIndex();
1499 +                atid = atom->getAtomType()->getIdent();
1500 +                data = ElectrostaticMap[Etids[atid]];
1501 +
1502 +                RealType qfrc = AK[kk]*((cks[i]+dkc[i]-qks[i])*(ckcs-dkss-qkcs)
1503 +                                     - (ckc[i]-dks[i]-qkc[i])*(ckss+dkcs-qkss));
1504 +                RealType qtrq1 = AK[kk]*(skr[i]*(ckcs-dkss-qkcs)
1505 +                                         -ckr[i]*(ckss+dkcs-qkss));
1506 +                RealType qtrq2 = 2.0*AK[kk]*(ckr[i]*(ckcs-dkss-qkcs)
1507 +                                             +skr[i]*(ckss+dkcs-qkss));
1508 +              
1509 +                atom->addFrc( 4.0 * rvol * qfrc * kVec );
1510 +                
1511 +                if (data.is_Dipole) {
1512 +                  atom->addTrq( 4.0 * rvol * qtrq1 * dxk[i] );
1513 +                }
1514 +                if (data.is_Quadrupole) {
1515 +                  atom->addTrq( 4.0 * rvol * qtrq2 * qxk[i] );
1516 +                }
1517 +              }
1518 +            }
1519 +          }
1520 +        }
1521 +        nMin = 1;
1522 +      }
1523 +      mMin = 1;
1524 +    }
1525 +    pot += kPot;  
1526 +  }
1527   }

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