/dports/science/tinker/tinker/source/ |
H A D | emetal1.f | 71 nneigh = 0 95 nneigh = nneigh + 1 110 rback(1,nneigh) = rback(1,nneigh) 112 rback(2,nneigh) = rback(2,nneigh) 114 rback(3,nneigh) = rback(3,nneigh) 121 rback2 = rback(1,nneigh)**2 + rback(2,nneigh)**2 129 dfacback(1,nneigh) = 2.0d0*(alpha*sqrt(r2)*rback(1,nneigh) 132 & -2.0d0*facback(nneigh)*rback(1,nneigh)/rback2 133 dfacback(2,nneigh) = 2.0d0*(alpha*sqrt(r2)*rback(2,nneigh) 136 & -2.0d0*facback(nneigh)*rback(2,nneigh)/rback2 [all …]
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H A D | emetal.f | 34 integer nneigh,ineigh,jneigh local 63 nneigh = 0 87 nneigh = nneigh + 1 102 rback(1,nneigh) = rback(1,nneigh) 104 rback(2,nneigh) = rback(2,nneigh) 106 rback(3,nneigh) = rback(3,nneigh) 113 rback2 = rback(1,nneigh)**2 + rback(2,nneigh)**2 122 do ineigh = 1, nneigh 132 do ineigh = 1, nneigh 135 do ineigh = 1, nneigh [all …]
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/dports/science/plumed/plumed2-2.7.2/src/adjmat/ |
H A D | OutputCluster.cpp | 74 std::vector<unsigned> nneigh; member in PLMD::adjmat::OutputCluster 146 nneigh.resize( myatoms.size(), 0 ); adj_list.resize( myatoms.size(), myatoms.size() ); in update() 149 …, atomsin[j] ).modulo2()<=rcut2 ) { adj_list(i,nneigh[i])=j; adj_list(j,nneigh[j])=i; nneigh[i]++;… in update() 169 nneigh.assign( nneigh.size(), 0 ); in update() 172 …ected( myatoms[i], myatoms[j] ) ) { adj_list(i,nneigh[i])=j; adj_list(j,nneigh[j])=i; nneigh[i]++;… in update() 182 for(unsigned k=0; k<nneigh[j]; ++k) { in update() 209 for(unsigned i=0; i<nneigh[index]; ++i) { in explore() 219 for(unsigned i=0; i<nneigh[index]; ++i) { in explore_dfs()
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H A D | AdjacencyMatrixVessel.cpp | 102 void AdjacencyMatrixVessel::retrieveAdjacencyLists( std::vector<unsigned>& nneigh, Matrix<unsigned>… in retrieveAdjacencyLists() argument 105 for(unsigned i=0; i<nneigh.size(); ++i) nneigh[i]=0; in retrieveAdjacencyLists() 116 …if( nneigh[j]>=adj_list.ncols() || nneigh[k]>=adj_list.ncols() ) error("adjacency lists are not la… in retrieveAdjacencyLists() 119 adj_list(k,nneigh[k])=j; nneigh[k]++; in retrieveAdjacencyLists() 120 adj_list(j,nneigh[j])=k; nneigh[j]++; in retrieveAdjacencyLists()
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H A D | DFSClustering.cpp | 77 std::vector<unsigned> nneigh; 113 nneigh.resize( getNumberOfNodes() ); color.resize(getNumberOfNodes()); in DFSClustering() 134 getAdjacencyVessel()->retrieveAdjacencyLists( nneigh, adj_list ); in performClustering() 148 for(unsigned i=0; i<nneigh[index]; ++i) { in explore()
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/dports/biology/iqtree/IQ-TREE-2.0.6/booster/ |
H A D | tree.c | 63 int i, n = a->nneigh; in dir_a_to_b() 244 nn->nneigh = degree; in new_node() 377 if(node_l->nneigh ==1){ in graft_new_node_on_branch() 445 int i, j, n1 = node1->nneigh, n2 = node2->nneigh; in collapse_branch() 451 new->nneigh = degree; in collapse_branch() 595 connect_node->nneigh--; in remove_taxon() 645 r_node->nneigh--; in remove_taxon() 1620 if (target->nneigh == 1) in update_node_depths_post_doer() 1707 int i, n = orig->nneigh; in update_hashtables_pre_doer() 1813 int i, n = root->nneigh; in update_all_i_c_post_order_ref_tree() [all …]
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H A D | test.c | 36 if(node->nneigh == 1){ in fill_all_taxa_ids() 40 for(i=0; i < node->nneigh; i++){ in fill_all_taxa_ids() 93 if(left->nneigh == 1 || right->nneigh==1){ in swap_branches() 101 int picked_left_index = rand_to(left->nneigh-1)+1; in swap_branches() 102 int picked_right_index = rand_to(right->nneigh-1)+1; in swap_branches() 267 int i, n = current->nneigh; in test_fill_hashtable_post_order() 306 if(e->right->nneigh>1 && in test_swap_branches() 307 e->left->nneigh>1 in test_swap_branches() 421 e->right->nneigh == 1 || in test_transfer_2() 422 e->left->nneigh == 1 ){ in test_transfer_2() [all …]
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/dports/science/lammps/lammps-stable_29Sep2021/src/ML-IAP/ |
H A D | mliap_data.cpp | 223 int nneigh = 0; in grow_neigharrays() local 248 nneigh += ninside; in grow_neigharrays() 251 if (nneigh_max < nneigh) { in grow_neigharrays() 252 memory->grow(jatoms,nneigh,"MLIAPData:jatoms"); in grow_neigharrays() 253 memory->grow(jelems,nneigh,"MLIAPData:jelems"); in grow_neigharrays() 254 memory->grow(rij,nneigh,3,"MLIAPData:rij"); in grow_neigharrays() 256 memory->grow(graddesc,nneigh,ndescriptors,3,"MLIAPData:graddesc"); in grow_neigharrays() 257 nneigh_max = nneigh; in grow_neigharrays()
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/dports/science/healpix/Healpix_3.50/src/idl/toolkit/ |
H A D | neighbours_ring.pro | 28 pro neighbours_ring, nside, ipix, list, nneigh 39 ; neighbours_ring, nside, ipix, list [, nneigh] 46 ; list: list of neighbours of size nneigh (see below) 57 ; nneigh: number of neighbours: usually 8, sometimes 7 (for 8 pixels) 83 nneigh = -1 101 neighbours_nest, nside, ipnest, listnest, nneigh
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H A D | neighbours_nest.pro | 134 pro neighbours_nest, nside, ipix, list, nneigh 145 ; neighbours_nest, nside, ipix, list [, nneigh] 192 nneigh = -1 210 nneigh = 6 337 nneigh=7 375 nneigh=7 456 nneigh=7 468 nneigh=7 549 nneigh=7 587 nneigh=7 [all …]
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/dports/science/clipper/clipper-2.1/clipper/contrib/ |
H A D | skeleton.cpp | 158 int nneigh = 0; in isInSkel() local 160 if ( cube[neigh[i]] > 0 ) nneigh++; in isInSkel() 161 if ( nneigh > 14 ) return false; in isInSkel() 162 if ( nneigh < 1 ) return false; in isInSkel() 300 int nneigh = 0; in isInSkel() local 305 if ( cube[dx][dy][dz] > 0 ) nneigh++; in isInSkel() 307 if ( nneigh > 14 ) return false; in isInSkel() 308 if ( nneigh < 1 ) return false; in isInSkel()
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/dports/science/PETSc/petsc-3.14.1/src/vec/is/is/tests/ |
H A D | ex5.c | 10 PetscInt nlocal,local[5],nneigh,*neigh,**ineigh,*numneigh; in main() local 26 ierr = ISLocalToGlobalMappingGetInfo(mapping,&nneigh,&neigh,&numneigh,&ineigh);CHKERRQ(ierr); in main() 27 ierr = ISLocalToGlobalMappingRestoreInfo(mapping,&nneigh,&neigh,&numneigh,&ineigh);CHKERRQ(ierr); in main()
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/dports/science/elmerfem/elmerfem-release-9.0/fem/src/ |
H A D | Feti.F90 | 192 nneigh=nneigh+1 217 DO i=1,nneigh 229 DO i=1,nneigh 294 DO i=1,nneigh 302 DO i=1,nneigh 307 DO i=1,nneigh 379 ALLOCATE(toSend(nneigh),toReceive(nneigh)) 406 DO i=1,nneigh 671 ALLOCATE(toSend(nneigh),toReceive(nneigh)) 698 DO i=1,nneigh [all …]
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H A D | SParIterSolver.F90 | 2349 INTEGER :: nneigh local 2368 ALLOCATE( neigh(nneigh) ) 2375 IF ( j==nneigh ) EXIT 2383 ALLOCATE( buffer(nneigh) ) 2384 DO i=1,nneigh 2388 ALLOCATE( requests(nneigh) ) 2474 INTEGER :: nneigh local 2501 ALLOCATE( neigh(nneigh) ) 2508 IF ( j==nneigh ) EXIT 2516 ALLOCATE( buffer(nneigh) ) [all …]
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/dports/science/smoldyn/smoldyn-2.67/source/Smoldyn/ |
H A D | smolboxes.c | 289 bptr->nneigh=0; in boxalloc() 478 for(b2=0;b2<bptr->nneigh;b2++) { in boxoutput() 716 int dim,d,nbox,b,b2,w,er,nneigh,nwall; in boxesupdatelists() local 775 if(nneigh==-1) return 1; in boxesupdatelists() 777 if(sim->accur>=6) for(b2=0;b2<nneigh;b2++) w+=wptemp[b2]; in boxesupdatelists() 779 if(nneigh && nneigh!=bptr->nneigh) { in boxesupdatelists() 783 bptr->neigh=(boxptr*) calloc(nneigh,sizeof(boxptr)); in boxesupdatelists() 786 bptr->wpneigh=allocZV(nneigh); in boxesupdatelists() 788 bptr->nneigh=nneigh; } in boxesupdatelists() 789 if(nneigh) in boxesupdatelists() [all …]
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/dports/science/octopus/octopus-10.5/src/grid/ |
H A D | mesh_partition.F90 | 702 integer, allocatable :: nghost(:), nbound(:), nlocal(:), nneigh(:) local 723 SAFE_ALLOCATE(nneigh(1:npart)) 733 nneigh = 0 770 nneigh(ipart) = count(is_a_neigh(1:npart)) 778 …call MPI_Allgather(MPI_IN_PLACE, 1, MPI_INTEGER, nneigh(1), 1, MPI_INTEGER, mesh%mpi_grp%comm, mpi… 809 ' Average : ', sum(nneigh)/npart, ' ', sum(nghost)/npart 811 ' Minimum : ', minval(nneigh), ' ', minval(nghost) 813 ' Maximum : ', maxval(nneigh), ' ', maxval(nghost) 821 ' Neighbours :', nneigh(ipart), & 835 SAFE_DEALLOCATE_A(nneigh)
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/dports/cad/calculix-ccx/CalculiX/ccx_2.18/src/ |
H A D | linkdissimilar.f | 30 integer nneigh,j,nodef(8),nodei,nrcg(*),icount, 42 nneigh=10 45 & netri,ineigh,nneigh) 49 do j=1,nneigh
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H A D | findslavcfd.f | 32 & nmast,inomat(*),nr(*),nz(*),noden(1),nneigh,ncs,kflag,node 96 nneigh=1 118 call near2d(rcs0,zcs0,rcs,zcs,nr,nz,rp,zp,ncs,noden,nneigh)
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/dports/science/plumed/plumed2-2.7.2/src/gridtools/ |
H A D | GridVessel.cpp | 298 plumed_dbg_assert( gtype==flat ); unsigned nneigh=unsigned(pow(2.0,int(dimension))); in getSplineNeighbors() local 299 if( mysneigh.size()!=nneigh ) mysneigh.resize(nneigh); in getSplineNeighbors() 305 for(unsigned i=0; i<nneigh; ++i) { in getSplineNeighbors() 377 void GridVessel::getNeighbors( const std::vector<double>& pp, const std::vector<unsigned>& nneigh, in getNeighbors() argument 382 plumed_dbg_assert( nneigh.size()==dimension ); in getNeighbors() 385 getNeighbors( indices, nneigh, num_neighbors, neighbors ); in getNeighbors() 396 …ridVessel::getNeighbors( const std::vector<unsigned>& indices, const std::vector<unsigned>& nneigh, in getNeighbors() argument 398 plumed_dbg_assert( gtype==flat && bounds_set && nneigh.size()==dimension ); in getNeighbors() 402 small_bin[i]=(2*nneigh[i]+1); in getNeighbors() 413 int i0=s_indices[i]-nneigh[i]+indices[i]; in getNeighbors()
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H A D | HistogramOnGrid.cpp | 69 nneigh=kernel.getSupport( dx ); std::vector<double> support( kernel.getContinuousSupport() ); in setBounds() 72 neigh_tot *= (2*nneigh[i]+1); in setBounds() 87 …kernel->normalize( Tools::unique2raw(values) ); getNeighbors( kernel->getCenter(), nneigh, num_nei… in getKernelAndNeighbors() 90 getNeighbors( point, nneigh, num_neigh, neighbors ); in getKernelAndNeighbors()
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/dports/astro/astrometry/astrometry.net-0.85/util/ |
H A D | get-healpix.c | 147 int nneigh; in main() local 148 nneigh = healpix_get_neighbours(healpix, neigh, Nside); in main() 150 for (i=0; i<nneigh; i++) in main()
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/dports/science/plumed/plumed2-2.7.2/src/tools/ |
H A D | Grid.cpp | 275 small_bin[j]=(2*nneigh[j]+1); in getNeighbors() 294 int i0=small_indices[i]-nneigh[i]+indices[i]; in getNeighbors() 309 (const vector<double> & x,const vector<unsigned> & nneigh)const { in getNeighbors() 311 return getNeighbors(getIndices(x),nneigh); in getNeighbors() 315 (index_t index,const vector<unsigned> & nneigh)const { in getNeighbors() 317 return getNeighbors(getIndices(index),nneigh); in getNeighbors() 322 unsigned nneigh=unsigned(pow(2.0,int(dimension_))); in getSplineNeighbors() local 323 if (neighbors.size()!=nneigh) neighbors.resize(nneigh); in getSplineNeighbors() 327 for(unsigned int i=0; i<nneigh; ++i) { in getSplineNeighbors() 432 vector<index_t> neigh; unsigned nneigh; getSplineNeighbors(indices, neigh, nneigh); in getValueAndDerivatives() local [all …]
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/dports/math/R-cran-spdep/spdep/R/ |
H A D | nblag.R | 58 nneigh <- which(ncard == 0) functionVar 59 for (i in nneigh) lags[[i]] <- 0L
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/dports/science/py-scipy/scipy-1.7.1/scipy/ndimage/src/ |
H A D | ni_measure.c | 218 npy_intp *nstrides = NULL, nneigh, ssize; in NI_WatershedIFT() local 365 nneigh = 0; in NI_WatershedIFT() 368 ++nneigh; in NI_WatershedIFT() 369 nstrides = malloc(nneigh * sizeof(npy_intp)); in NI_WatershedIFT() 382 for(kk = 0; kk < nneigh; kk++) in NI_WatershedIFT() 416 for(hh = 0; hh < nneigh; hh++) { in NI_WatershedIFT()
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/dports/biology/seaview/seaview/ |
H A D | tbe.cxx | 394 int nneigh = 0; in TBE_Is_Taxon() local 395 nneigh+=(n->v1!=NULL); in TBE_Is_Taxon() 396 nneigh+=(n->v2!=NULL); in TBE_Is_Taxon() 397 nneigh+=(n->v3!=NULL); in TBE_Is_Taxon() 398 return nneigh==1; in TBE_Is_Taxon()
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