int KimNeighborNEIGHPUREH::GetNeighbors(int n, int *neighbors, Vec *diffs, double *diffs2, int& size, double r /* = -1.0 */ ) const { int currentAtom; int number; int *rawneighbors; double *Rij; // Not used in this KIM neighborlist mode. int ier = KIM_API_get_neigh((void*)pkim, nbmode, check_iterator(n), ¤tAtom, &number, &rawneighbors, &Rij); if (KIM_STATUS_OK != ier) throw AsapError("KIM_API_get_neigh failed ") << __FILE__ << ":" << __LINE__; assert(currentAtom == n); // Now construct the list of distance vectors const Vec *pos = atoms->GetPositions(); const Vec *thispos = pos + n; int numnb = 0; double rcut2 = this->rcut2; if (r > 0) rcut2 = r*r; for (int i = 0; i < number; i++) { const Vec *otherpos = pos + rawneighbors[i]; diffs[numnb] = *otherpos - *thispos; diffs2[numnb] = diffs[numnb] * diffs[numnb]; if (diffs2[numnb] <= rcut2) { neighbors[numnb] = rawneighbors[i]; numnb++; } } assert(numnb <= size); size -= numnb; return numnb; }
/* compute function */ static int compute(void* km) { /* local variables */ intptr_t* pkim = *((intptr_t**) km); double R; double Rsqij; double phi; double dphi; double dEidr = 0.0; double Rij[DIM]; int ier; int i; int j; int jj; int k; int numOfPartNeigh; int currentPart; int comp_energy; int comp_force; int comp_particleEnergy; int comp_virial; int IterOrLoca; int HalfOrFull; int NBC; const char* NBCstr; int numberContrib; int* nParts; int* particleSpecies; double* Rij_list; double* coords; double* energy; double* force; double* particleEnergy; double* virial; int* neighListOfCurrentPart; double* boxSideLengths; int* numContrib; /* Determine neighbor list boundary condition (NBC) */ /* and half versus full mode: */ /***************************** * HalfOrFull = 1 -- Half * = 2 -- Full *****************************/ ier = KIM_API_get_NBC_method(pkim, &NBCstr); if (KIM_STATUS_OK > ier) { KIM_API_report_error(__LINE__, __FILE__, "KIM_API_get_NBC_method", ier); return ier; } if (!strcmp("NEIGH_RVEC_H",NBCstr)) { NBC = 0; HalfOrFull = 1; } else if (!strcmp("NEIGH_PURE_H",NBCstr)) { NBC = 1; HalfOrFull = 1; } else if (!strcmp("NEIGH_RVEC_F",NBCstr)) { NBC = 0; HalfOrFull = 2; } else if (!strcmp("NEIGH_PURE_F",NBCstr)) { NBC = 1; HalfOrFull = 2; } else if (!strcmp("MI_OPBC_H",NBCstr)) { NBC = 2; HalfOrFull = 1; } else if (!strcmp("MI_OPBC_F",NBCstr)) { NBC = 2; HalfOrFull = 2; } else if (!strcmp("CLUSTER",NBCstr)) { NBC = 3; HalfOrFull = 1; } else { ier = KIM_STATUS_FAIL; KIM_API_report_error(__LINE__, __FILE__, "Unknown NBC method", ier); return ier; } /* determine neighbor list handling mode */ if (NBC != 3) { /***************************** * IterOrLoca = 1 -- Iterator * = 2 -- Locator *****************************/ IterOrLoca = KIM_API_get_neigh_mode(pkim, &ier); if (KIM_STATUS_OK > ier) { KIM_API_report_error(__LINE__, __FILE__, "KIM_API_get_neigh_mode", ier); return ier; } if ((IterOrLoca != 1) && (IterOrLoca != 2)) { printf("* ERROR: Unsupported IterOrLoca mode = %i\n", IterOrLoca); return KIM_STATUS_FAIL; } } else { IterOrLoca = 2; /* for CLUSTER NBC */ } /* check to see if we have been asked to compute the forces, particleEnergy, energy and virial */ KIM_API_getm_compute(pkim, &ier, 4*3, "energy", &comp_energy, 1, "forces", &comp_force, 1, "particleEnergy", &comp_particleEnergy, 1, "virial", &comp_virial, 1); if (KIM_STATUS_OK > ier) { KIM_API_report_error(__LINE__, __FILE__, "KIM_API_getm_compute", ier); return ier; } /* unpack data from KIM object */ KIM_API_getm_data(pkim, &ier, 9*3, "numberOfParticles", &nParts, 1, "particleSpecies", &particleSpecies,1, "coordinates", &coords, 1, "numberContributingParticles", &numContrib, (HalfOrFull==1), "boxSideLengths", &boxSideLengths, (NBC==2), "energy", &energy, (comp_energy==1), "forces", &force, (comp_force==1), "particleEnergy", &particleEnergy, (comp_particleEnergy==1), "virial", &virial, (comp_virial==1)); if (KIM_STATUS_OK > ier) { KIM_API_report_error(__LINE__, __FILE__, "KIM_API_getm_data", ier); return ier; } if (HalfOrFull == 1) { if (3 != NBC) /* non-CLUSTER cases */ { numberContrib = *numContrib; } else { numberContrib = *nParts; } } else { /* provide initialization even if not used */ numberContrib = *nParts; } /* Check to be sure that the species are correct */ /**/ ier = KIM_STATUS_FAIL; /* assume an error */ for (i = 0; i < *nParts; ++i) { if ( SPECCODE != particleSpecies[i]) { KIM_API_report_error(__LINE__, __FILE__, "Unexpected species detected", ier); return ier; } } ier = KIM_STATUS_OK; /* everything is ok */ /* initialize potential energies, forces, and virial term */ if (comp_particleEnergy) { for (i = 0; i < *nParts; ++i) { particleEnergy[i] = 0.0; } } if (comp_energy) { *energy = 0.0; } if (comp_force) { for (i = 0; i < *nParts; ++i) { for (k = 0; k < DIM; ++k) { force[i*DIM + k] = 0.0; } } } if (comp_virial) { for (i = 0; i < 6; ++i) { virial[i] = 0.0; } } /* Initialize neighbor handling for CLUSTER NBC */ if (3 == NBC) /* CLUSTER */ { neighListOfCurrentPart = (int *) malloc((*nParts)*sizeof(int)); } /* Initialize neighbor handling for Iterator mode */ if (1 == IterOrLoca) { ier = KIM_API_get_neigh(pkim, 0, 0, ¤tPart, &numOfPartNeigh, &neighListOfCurrentPart, &Rij_list); /* check for successful initialization */ if (KIM_STATUS_NEIGH_ITER_INIT_OK != ier) { KIM_API_report_error(__LINE__, __FILE__, "KIM_API_get_neigh", ier); ier = KIM_STATUS_FAIL; return ier; } } /* Compute energy and forces */ /* loop over particles and compute enregy and forces */ i = -1; while( 1 ) { /* Set up neighbor list for next particle for all NBC methods */ if (1 == IterOrLoca) /* ITERATOR mode */ { ier = KIM_API_get_neigh(pkim, 0, 1, ¤tPart, &numOfPartNeigh, &neighListOfCurrentPart, &Rij_list); if (KIM_STATUS_NEIGH_ITER_PAST_END == ier) /* the end of the list, terminate loop */ { break; } if (KIM_STATUS_OK > ier) /* some sort of problem, return */ { KIM_API_report_error(__LINE__, __FILE__, "KIM_API_get_neigh", ier); return ier; } i = currentPart; } else { i++; if (*nParts <= i) /* incremented past end of list, terminate loop */ { break; } if (3 == NBC) /* CLUSTER NBC method */ { numOfPartNeigh = *nParts - (i + 1); for (k = 0; k < numOfPartNeigh; ++k) { neighListOfCurrentPart[k] = i + k + 1; } ier = KIM_STATUS_OK; } else /* All other NBCs */ { ier = KIM_API_get_neigh(pkim, 1, i, ¤tPart, &numOfPartNeigh, &neighListOfCurrentPart, &Rij_list); if (KIM_STATUS_OK != ier) /* some sort of problem, return */ { KIM_API_report_error(__LINE__, __FILE__, "KIM_API_get_neigh", ier); ier = KIM_STATUS_FAIL; return ier; } } } /* loop over the neighbors of particle i */ for (jj = 0; jj < numOfPartNeigh; ++ jj) { j = neighListOfCurrentPart[jj]; /* get neighbor ID */ /* compute relative position vector and squared distance */ Rsqij = 0.0; for (k = 0; k < DIM; ++k) { if (0 != NBC) /* all methods except NEIGH_RVEC */ { Rij[k] = coords[j*DIM + k] - coords[i*DIM + k]; } else /* NEIGH_RVEC_F method */ { Rij[k] = Rij_list[jj*DIM + k]; } /* apply periodic boundary conditions if required */ if (2 == NBC) { if (abs(Rij[k]) > 0.5*boxSideLengths[k]) { Rij[k] -= (Rij[k]/fabs(Rij[k]))*boxSideLengths[k]; } } /* compute squared distance */ Rsqij += Rij[k]*Rij[k]; } /* compute energy and force */ if (Rsqij < MODEL_CUTSQ) /* particles are interacting ? */ { R = sqrt(Rsqij); if (comp_force || comp_virial) { /* compute pair potential and its derivative */ calc_phi_dphi(R, &phi, &dphi); /* compute dEidr */ if ((1 == HalfOrFull) && (j < numberContrib)) { /* HALF mode -- double contribution */ dEidr = dphi; } else { /* FULL mode -- regular contribution */ dEidr = 0.5*dphi; } } else { /* compute just pair potential */ calc_phi(R, &phi); } /* contribution to energy */ if (comp_particleEnergy) { particleEnergy[i] += 0.5*phi; /* if half list add energy for the other particle in the pair */ if ((1 == HalfOrFull) && (j < numberContrib)) particleEnergy[j] += 0.5*phi; } if (comp_energy) { if ((1 == HalfOrFull) && (j < numberContrib)) { /* Half mode -- add v to total energy */ *energy += phi; } else { /* Full mode -- add half v to total energy */ *energy += 0.5*phi; } } /* contribution to virial tensor */ if (comp_virial) { /* virial(i,j) = r(i)*r(j)*(dV/dr)/r */ virial[0] += Rij[0]*Rij[0]*dEidr/R; virial[1] += Rij[1]*Rij[1]*dEidr/R; virial[2] += Rij[2]*Rij[2]*dEidr/R; virial[3] += Rij[1]*Rij[2]*dEidr/R; virial[4] += Rij[0]*Rij[2]*dEidr/R; virial[5] += Rij[0]*Rij[1]*dEidr/R; } /* contribution to forces */ if (comp_force) { for (k = 0; k < DIM; ++k) { force[i*DIM + k] += dEidr*Rij[k]/R; /* accumulate force on particle i */ force[j*DIM + k] -= dEidr*Rij[k]/R; /* accumulate force on particle j */ } } } } /* loop on jj */ } /* infinite while loop (terminated by break statements above */ /* Free temporary storage */ if (3 == NBC) { free(neighListOfCurrentPart); } /* everything is great */ ier = KIM_STATUS_OK; return ier; }