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Searched refs:nneigh (Results 1 – 25 of 60) sorted by relevance

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/dports/science/tinker/tinker/source/
H A Demetal1.f71 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
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H A Demetal.f34 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
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/dports/science/plumed/plumed2-2.7.2/src/adjmat/
H A DOutputCluster.cpp74 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()
H A DAdjacencyMatrixVessel.cpp102 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()
H A DDFSClustering.cpp77 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()
/dports/biology/iqtree/IQ-TREE-2.0.6/booster/
H A Dtree.c63 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()
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H A Dtest.c36 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()
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/dports/science/lammps/lammps-stable_29Sep2021/src/ML-IAP/
H A Dmliap_data.cpp223 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()
/dports/science/healpix/Healpix_3.50/src/idl/toolkit/
H A Dneighbours_ring.pro28 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
H A Dneighbours_nest.pro134 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
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/dports/science/clipper/clipper-2.1/clipper/contrib/
H A Dskeleton.cpp158 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()
/dports/science/PETSc/petsc-3.14.1/src/vec/is/is/tests/
H A Dex5.c10 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()
/dports/science/elmerfem/elmerfem-release-9.0/fem/src/
H A DFeti.F90192 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
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H A DSParIterSolver.F902349 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) )
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/dports/science/smoldyn/smoldyn-2.67/source/Smoldyn/
H A Dsmolboxes.c289 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()
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/dports/science/octopus/octopus-10.5/src/grid/
H A Dmesh_partition.F90702 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)
/dports/cad/calculix-ccx/CalculiX/ccx_2.18/src/
H A Dlinkdissimilar.f30 integer nneigh,j,nodef(8),nodei,nrcg(*),icount,
42 nneigh=10
45 & netri,ineigh,nneigh)
49 do j=1,nneigh
H A Dfindslavcfd.f32 & 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)
/dports/science/plumed/plumed2-2.7.2/src/gridtools/
H A DGridVessel.cpp298 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()
H A DHistogramOnGrid.cpp69 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()
/dports/astro/astrometry/astrometry.net-0.85/util/
H A Dget-healpix.c147 int nneigh; in main() local
148 nneigh = healpix_get_neighbours(healpix, neigh, Nside); in main()
150 for (i=0; i<nneigh; i++) in main()
/dports/science/plumed/plumed2-2.7.2/src/tools/
H A DGrid.cpp275 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
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/dports/math/R-cran-spdep/spdep/R/
H A Dnblag.R58 nneigh <- which(ncard == 0) functionVar
59 for (i in nneigh) lags[[i]] <- 0L
/dports/science/py-scipy/scipy-1.7.1/scipy/ndimage/src/
H A Dni_measure.c218 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()
/dports/biology/seaview/seaview/
H A Dtbe.cxx394 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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