Index: /issm/trunk/src/m/classes/@modellist/get.m =================================================================== --- /issm/trunk/src/m/classes/@modellist/get.m (revision 8297) +++ /issm/trunk/src/m/classes/@modellist/get.m (revision 8298) @@ -8,6 +8,6 @@ case 'numberofelements' val = a.numberofelements; -case 'numberofgrids' - val = a.numberofgrids; +case 'numberofnodes' + val = a.numberofnodes; case 'elements' val = a.elements; Index: /issm/trunk/src/m/classes/model.m =================================================================== --- /issm/trunk/src/m/classes/model.m (revision 8297) +++ /issm/trunk/src/m/classes/model.m (revision 8298) @@ -27,5 +27,5 @@ dim=0; numberofelements=0; - numberofgrids=0; + numberofnodes=0; elements=NaN; elements_type=NaN; @@ -47,5 +47,5 @@ %Initial 2d mesh numberofelements2d=0; - numberofgrids2d=0; + numberofnodes2d=0; elements2d=NaN; elements_type2d=NaN; @@ -72,8 +72,8 @@ %Nodes - gridonhutter=NaN; - gridonmacayeal=NaN; - gridonpattyn=NaN; - gridonstokes=NaN; + nodeonhutter=NaN; + nodeonmacayeal=NaN; + nodeonpattyn=NaN; + nodeonstokes=NaN; borderstokes=NaN; @@ -95,8 +95,8 @@ %Projections - uppergrids=NaN; + uppernodes=NaN; upperelements=NaN; lowerelements=NaN; - lowergrids=NaN; + lowernodes=NaN; %Extrusion @@ -105,11 +105,11 @@ elementonbed=NaN; elementonsurface=NaN; - gridonbed=NaN; - gridonsurface=NaN; + nodeonbed=NaN; + nodeonsurface=NaN; minh=0; firn_layer=NaN; %Extraction - extractedgrids=NaN; + extractednodes=NaN; extractedelements=NaN; @@ -146,8 +146,8 @@ elementonwater=NaN; elementonnuna=NaN; - gridoniceshelf=NaN; - gridonicesheet=NaN; - gridonwater=NaN; - gridonnuna=NaN; + nodeoniceshelf=NaN; + nodeonicesheet=NaN; + nodeonwater=NaN; + nodeonnuna=NaN; surface=NaN; thickness=NaN; @@ -158,5 +158,5 @@ %Boundary conditions - gridonboundary=NaN; + nodeonboundary=NaN; pressureload=NaN; spcvelocity=NaN; Index: /issm/trunk/src/m/kml/README.txt =================================================================== --- /issm/trunk/src/m/kml/README.txt (revision 8297) +++ /issm/trunk/src/m/kml/README.txt (revision 8298) @@ -61,5 +61,5 @@ There are some other utilities that are used in the construction of topological tables for the kml writing. -nodeconnectivity.m - create a node connectivity table (ngrids x mxepg+1) +nodeconnectivity.m - create a node connectivity table (nnodes x mxepg+1) edgeadjacency.m - create an edge adjacency array (elems x edges) edgeperimeter.m - create an edge perimeter (edgeper x 2) and element perimeter (edgeper x 1) list Index: /issm/trunk/src/m/kml/kml_mesh_elem.m =================================================================== --- /issm/trunk/src/m/kml/kml_mesh_elem.m (revision 8297) +++ /issm/trunk/src/m/kml/kml_mesh_elem.m (revision 8298) @@ -76,5 +76,5 @@ if (numel(data)==md.numberofelements) edata=data; - elseif (numel(data)==md.numberofgrids) + elseif (numel(data)==md.numberofnodes) ndata=data; display('Averaging nodal data to element data.'); @@ -123,6 +123,6 @@ end kfold.visibility=1; -kfold.descript =sprintf('Elements=%d, Grids=%d',... - md.numberofelements,md.numberofgrids); +kfold.descript =sprintf('Elements=%d, Nodes=%d',... + md.numberofelements,md.numberofnodes); % see matlab_oop, "initializing a handle object array" %kfold.feature ={repmat(kml_placemark(),1,size(md.elements,1))}; Index: /issm/trunk/src/m/kml/kml_mesh_write.m =================================================================== --- /issm/trunk/src/m/kml/kml_mesh_write.m (revision 8297) +++ /issm/trunk/src/m/kml/kml_mesh_write.m (revision 8298) @@ -82,5 +82,5 @@ if (numel(data)==md.numberofelements) edata=data; - elseif (numel(data)==md.numberofgrids) + elseif (numel(data)==md.numberofnodes) ndata=data; display('Averaging nodal data to element data.'); Index: /issm/trunk/src/m/kml/kml_part_edges.m =================================================================== --- /issm/trunk/src/m/kml/kml_part_edges.m (revision 8297) +++ /issm/trunk/src/m/kml/kml_part_edges.m (revision 8298) @@ -77,5 +77,5 @@ if (numel(data)==md.numberofelements) edata=data; - elseif (numel(data)==md.numberofgrids) + elseif (numel(data)==md.numberofnodes) ndata=data; display('Averaging nodal data to element data.'); @@ -123,5 +123,5 @@ kfold.visibility=1; kfold.descript =sprintf('Partitions=%d, Nodes=%d',... - md.npart,md.numberofgrids); + md.npart,md.numberofnodes); kfold.feature ={repmat(kml_placemark(),1,md.npart)}; @@ -150,5 +150,5 @@ elemp=md.elements(irow,:); epartp=epart(irow,:); - nodeconp=nodeconnectivity(elemp,md.numberofgrids); + nodeconp=nodeconnectivity(elemp,md.numberofnodes); [edgeadjp]=edgeadjacency(elemp,nodeconp); [edgeper,elemper,iloop]=edgeperimeter(elemp,nodeconp,edgeadjp); Index: /issm/trunk/src/m/kml/kml_part_elems.m =================================================================== --- /issm/trunk/src/m/kml/kml_part_elems.m (revision 8297) +++ /issm/trunk/src/m/kml/kml_part_elems.m (revision 8298) @@ -77,5 +77,5 @@ if (numel(data)==md.numberofelements) edata=data; - elseif (numel(data)==md.numberofgrids) + elseif (numel(data)==md.numberofnodes) ndata=data; display('Averaging nodal data to element data.'); @@ -123,5 +123,5 @@ kfold.visibility=1; kfold.descript =sprintf('Partitions=%d, Nodes=%d\n',... - md.npart,md.numberofgrids); + md.npart,md.numberofnodes); kfold.feature ={repmat(kml_placemark(),1,md.npart)}; Index: /issm/trunk/src/m/kml/kml_partitions.m =================================================================== --- /issm/trunk/src/m/kml/kml_partitions.m (revision 8297) +++ /issm/trunk/src/m/kml/kml_partitions.m (revision 8298) @@ -78,5 +78,5 @@ if (numel(data)==md.numberofelements) edata=data; - elseif (numel(data)==md.numberofgrids) + elseif (numel(data)==md.numberofnodes) ndata=data; display('Averaging nodal data to element data.'); @@ -124,5 +124,5 @@ kfold.visibility=1; kfold.descript =sprintf('Partitions=%d, Nodes=%d',... - md.npart,md.numberofgrids); + md.npart,md.numberofnodes); kfold.feature ={repmat(kml_placemark(),1,md.npart)}; @@ -151,5 +151,5 @@ elemp=md.elements(irow,:); epartp=epart(irow,:); - nodeconp=nodeconnectivity(elemp,md.numberofgrids); + nodeconp=nodeconnectivity(elemp,md.numberofnodes); [edgeadjp]=edgeadjacency(elemp,nodeconp); [edgeper,elemper,iloop]=edgeperimeter(elemp,nodeconp,edgeadjp); Index: /issm/trunk/src/m/kml/nodeconnectivity.m =================================================================== --- /issm/trunk/src/m/kml/nodeconnectivity.m (revision 8297) +++ /issm/trunk/src/m/kml/nodeconnectivity.m (revision 8298) @@ -2,5 +2,5 @@ % create a node connectivity table for the elements in the model. % -% [nodecon]=edgeadjacency(elem,ngrids,mxepg) +% [nodecon]=edgeadjacency(elem,nnodes,mxepg) % % where the required input is: @@ -8,11 +8,11 @@ % % and the required output is: -% nodecon (numeric, node connectivity array (ngrids x mxepg+1)) +% nodecon (numeric, node connectivity array (nnodes x mxepg+1)) % % the optional input is: -% ngrids (numeric, number of grids) -% mxepg (numeric, max elements per grid) +% nnodes (numeric, number of nodes) +% mxepg (numeric, max elements per node) % -function [nodecon]=nodeconnectivity(elem,ngrids,mxepg) +function [nodecon]=nodeconnectivity(elem,nnodes,mxepg) if ~nargin @@ -21,6 +21,6 @@ end -if ~exist('ngrids','var') || isempty(ngrids) - ngrids=max(max(elem)); +if ~exist('nnodes','var') || isempty(nnodes) + nnodes=max(max(elem)); end if ~exist('mxepg','var') || isempty(mxepg) @@ -30,5 +30,5 @@ %% create the node connectivity array -nodecon=zeros(ngrids,mxepg+1); +nodecon=zeros(nnodes,mxepg+1); % loop over the elements Index: /issm/trunk/src/m/model/BasinConstrain.m =================================================================== --- /issm/trunk/src/m/model/BasinConstrain.m (revision 8297) +++ /issm/trunk/src/m/model/BasinConstrain.m (revision 8298) @@ -14,13 +14,13 @@ % md=BasinConstrain(md,'~Iceshelves.exp'); -%now, flag grids and elements outside the domain outline. +%now, flag nodes and elements outside the domain outline. if ischar(domain), if isempty(domain), elementondomain=zeros(md.numberofelements,1); - gridondomain=zeros(md.numberofgrids,1); + nodeondomain=zeros(md.numberofnodes,1); invert=0; elseif strcmpi(domain,'all') elementondomain=ones(md.numberofelements,1); - gridondomain=ones(md.numberofgrids,1); + nodeondomain=ones(md.numberofnodes,1); invert=0; else @@ -33,8 +33,8 @@ end %ok, flag elements and nodes - [gridondomain elementondomain]=ContourToMesh(md.elements(:,1:3),md.x,md.y,domain,'element and node',2); + [nodeondomain elementondomain]=ContourToMesh(md.elements(:,1:3),md.x,md.y,domain,'element and node',2); end if invert, - gridondomain=~gridondomain; + nodeondomain=~nodeondomain; elementondomain=~elementondomain; end @@ -44,20 +44,20 @@ %list of elements and nodes not on domain -gridnotondomain=find(~gridondomain); +nodenotondomain=find(~nodeondomain); elementnotondomain=find(~elementondomain); -%all elements outside the constraint domain are equivalent to water. all grids outside are spc'd. -md.spcvelocity(gridnotondomain,1:2)=1; -md.spcvelocity(gridnotondomain,4)=md.vx_obs(gridnotondomain); -md.spcvelocity(gridnotondomain,5)=md.vy_obs(gridnotondomain); +%all elements outside the constraint domain are equivalent to water. all nodes outside are spc'd. +md.spcvelocity(nodenotondomain,1:2)=1; +md.spcvelocity(nodenotondomain,4)=md.vx_obs(nodenotondomain); +md.spcvelocity(nodenotondomain,5)=md.vy_obs(nodenotondomain); md.elementonwater(elementnotondomain)=1; -%now, make sure all elements on water have grids that are spc'd, otherwise, we'll get a singular problem. +%now, make sure all elements on water have nodes that are spc'd, otherwise, we'll get a singular problem. pos=find(~md.elementonwater); numpos=unique(md.elements(pos,:)); -grids=setdiff(1:1:md.numberofgrids,numpos); -md.spcvelocity(grids,1:2)=1; -md.spcvelocity(grids,4)=md.vx_obs(grids); -md.spcvelocity(grids,5)=md.vy_obs(grids); +nodes=setdiff(1:1:md.numberofnodes,numpos); +md.spcvelocity(nodes,1:2)=1; +md.spcvelocity(nodes,4)=md.vx_obs(nodes); +md.spcvelocity(nodes,5)=md.vy_obs(nodes); %make sure icefronts that are completely spc'd are taken out: Index: /issm/trunk/src/m/model/BasinConstrain2.m =================================================================== --- /issm/trunk/src/m/model/BasinConstrain2.m (revision 8297) +++ /issm/trunk/src/m/model/BasinConstrain2.m (revision 8298) @@ -14,13 +14,13 @@ % md=BasinConstrain(md,'~Iceshelves.exp'); -%now, flag grids and elements outside the domain outline. +%now, flag nodes and elements outside the domain outline. if ischar(domain), if isempty(domain), elementondomain=zeros(md.numberofelements,1); - gridondomain=zeros(md.numberofgrids,1); + nodeondomain=zeros(md.numberofnodes,1); invert=0; elseif strcmpi(domain,'all') elementondomain=ones(md.numberofelements,1); - gridondomain=ones(md.numberofgrids,1); + nodeondomain=ones(md.numberofnodes,1); invert=0; else @@ -33,8 +33,8 @@ end %ok, flag elements and nodes - [gridondomain elementondomain]=ContourToMesh(md.elements(:,1:3),md.x,md.y,domain,'element and node',2); + [nodeondomain elementondomain]=ContourToMesh(md.elements(:,1:3),md.x,md.y,domain,'element and node',2); end if invert, - gridondomain=~gridondomain; + nodeondomain=~nodeondomain; elementondomain=~elementondomain; end @@ -44,20 +44,20 @@ %list of elements and nodes not on domain -gridnotondomain=find(~gridondomain); +nodenotondomain=find(~nodeondomain); elementnotondomain=find(~elementondomain); -%all elements outside the constraint domain are equivalent to water. all grids outside are spc'd. -md.spcvelocity(gridnotondomain,1:2)=1; -md.spcvelocity(gridnotondomain,4)=md.vx_obs(gridnotondomain); -md.spcvelocity(gridnotondomain,5)=md.vy_obs(gridnotondomain); +%all elements outside the constraint domain are equivalent to water. all nodes outside are spc'd. +md.spcvelocity(nodenotondomain,1:2)=1; +md.spcvelocity(nodenotondomain,4)=md.vx_obs(nodenotondomain); +md.spcvelocity(nodenotondomain,5)=md.vy_obs(nodenotondomain); md.elementonwater(elementnotondomain)=1; -%now, make sure all elements on water have grids that are spc'd, otherwise, we'll get a singular problem. +%now, make sure all elements on water have nodes that are spc'd, otherwise, we'll get a singular problem. pos=find(~md.elementonwater); numpos=unique(md.elements(pos,:)); -grids=setdiff(1:1:md.numberofgrids,numpos); -md.spcvelocity(grids,1:2)=1; -md.spcvelocity(grids,4)=md.vx_obs(grids); -md.spcvelocity(grids,5)=md.vy_obs(grids); +nodes=setdiff(1:1:md.numberofnodes,numpos); +md.spcvelocity(nodes,1:2)=1; +md.spcvelocity(nodes,4)=md.vx_obs(nodes); +md.spcvelocity(nodes,5)=md.vy_obs(nodes); Index: /issm/trunk/src/m/model/BasinConstrainShelf.m =================================================================== --- /issm/trunk/src/m/model/BasinConstrainShelf.m (revision 8297) +++ /issm/trunk/src/m/model/BasinConstrainShelf.m (revision 8298) @@ -14,13 +14,13 @@ % md=BasinConstrain(md,'~Iceshelves.exp'); -%now, flag grids and elements outside the domain outline. +%now, flag nodes and elements outside the domain outline. if ischar(domain), if isempty(domain), elementondomain=zeros(md.numberofelements,1); - gridondomain=zeros(md.numberofgrids,1); + nodeondomain=zeros(md.numberofnodes,1); invert=0; elseif strcmpi(domain,'all') elementondomain=ones(md.numberofelements,1); - gridondomain=ones(md.numberofgrids,1); + nodeondomain=ones(md.numberofnodes,1); invert=0; else @@ -33,8 +33,8 @@ end %ok, flag elements and nodes - [gridondomain elementondomain]=ContourToMesh(md.elements(:,1:3),md.x,md.y,domain,'element and node',2); + [nodeondomain elementondomain]=ContourToMesh(md.elements(:,1:3),md.x,md.y,domain,'element and node',2); end if invert, - gridondomain=~gridondomain; + nodeondomain=~nodeondomain; elementondomain=~elementondomain; end @@ -44,23 +44,23 @@ %list of elements and nodes not on domain -gridnotondomain=find(~gridondomain); +nodenotondomain=find(~nodeondomain); elementnotondomain=find(~elementondomain); -%all elements outside the constraint domain are equivalent to water. all grids outside are spc'd. -md.spcvelocity(gridnotondomain,1:2)=1; -md.spcvelocity(gridnotondomain,4)=md.vx_obs(gridnotondomain); -md.spcvelocity(gridnotondomain,5)=md.vy_obs(gridnotondomain); +%all elements outside the constraint domain are equivalent to water. all nodes outside are spc'd. +md.spcvelocity(nodenotondomain,1:2)=1; +md.spcvelocity(nodenotondomain,4)=md.vx_obs(nodenotondomain); +md.spcvelocity(nodenotondomain,5)=md.vy_obs(nodenotondomain); md.elementonwater(elementnotondomain)=1; -%now, make sure all elements on water have grids that are spc'd, otherwise, we'll get a singular problem. +%now, make sure all elements on water have nodes that are spc'd, otherwise, we'll get a singular problem. pos=find(~md.elementonwater); numpos=unique(md.elements(pos,:)); -grids=setdiff(1:1:md.numberofgrids,numpos); -md.spcvelocity(grids,1:2)=1; -md.spcvelocity(grids,4)=md.vx_obs(grids); -md.spcvelocity(grids,5)=md.vy_obs(grids); +nodes=setdiff(1:1:md.numberofnodes,numpos); +md.spcvelocity(nodes,1:2)=1; +md.spcvelocity(nodes,4)=md.vx_obs(nodes); +md.spcvelocity(nodes,5)=md.vy_obs(nodes); -%make sure any grid with NaN velocity is spc'd: +%make sure any node with NaN velocity is spc'd: pos=find(isnan(md.vel_obs_raw)); md.spcvelocity(pos,1:2)=1; @@ -69,6 +69,6 @@ md.spcvelocity(pos,5)=md.vy_obs(pos); -%iceshelves: any grid on icesheet is spc'd -pos=find(md.gridonicesheet); +%iceshelves: any node on icesheet is spc'd +pos=find(md.nodeonicesheet); md.spcvelocity(pos,1:2)=1; md.spcvelocity(pos,4)=md.vx_obs(pos); Index: /issm/trunk/src/m/model/DepthAverage.m =================================================================== --- /issm/trunk/src/m/model/DepthAverage.m (revision 8297) +++ /issm/trunk/src/m/model/DepthAverage.m (revision 8298) @@ -14,6 +14,6 @@ %nods data -if (length(vector)==md.numberofgrids), - vector_average=zeros(md.numberofgrids2d,1); +if (length(vector)==md.numberofnodes), + vector_average=zeros(md.numberofnodes2d,1); for i=1:md.numlayers-1, vector_average=vector_average+(project2d(md,vector,i)+project2d(md,vector,i+1))/2.*(project2d(md,md.z,i+1)-project2d(md,md.z,i)); Index: /issm/trunk/src/m/model/MeltingGroundingLines.m =================================================================== --- /issm/trunk/src/m/model/MeltingGroundingLines.m (revision 8297) +++ /issm/trunk/src/m/model/MeltingGroundingLines.m (revision 8298) @@ -7,5 +7,5 @@ %get nodes on ice sheet and on ice shelf -pos_shelf=find(~md.gridonicesheet); +pos_shelf=find(~md.nodeonicesheet); pos_GL=intersect(unique(md.elements(find(md.elementonicesheet),:)),unique(md.elements(find(md.elementoniceshelf),:))); @@ -16,5 +16,5 @@ end - %search the grid on ice sheet the closest to i + %search the node on ice sheet the closest to i [d posd]=min(sqrt((md.x(pos_shelf(i))-md.x(pos_GL)).^2+(md.y(pos_shelf(i))-md.y(pos_GL)).^2)); Index: /issm/trunk/src/m/model/SectionValues.m =================================================================== --- /issm/trunk/src/m/model/SectionValues.m (revision 8297) +++ /issm/trunk/src/m/model/SectionValues.m (revision 8298) @@ -72,9 +72,9 @@ Y(end+1)=y(nods); -%Number of grids: -numberofgrids=size(X,1); +%Number of nodes: +numberofnodes=size(X,1); %Compute Z -Z=zeros(numberofgrids,1); +Z=zeros(numberofnodes,1); %New mesh and Data interpolation @@ -86,5 +86,5 @@ %Compute index - index=[1:1:(numberofgrids-1);2:1:numberofgrids]'; + index=[1:1:(numberofnodes-1);2:1:numberofnodes]'; else @@ -99,11 +99,11 @@ %Some useful parameters layers=ceil(mean(md.thickness)/res_v); - gridsperlayer=numberofgrids; - gridstot=gridsperlayer*layers; - elementsperlayer=gridsperlayer-1; - elementstot=(gridsperlayer-1)*(layers-1); + nodesperlayer=numberofnodes; + nodestot=nodesperlayer*layers; + elementsperlayer=nodesperlayer-1; + elementstot=(nodesperlayer-1)*(layers-1); %initialization - X3=zeros(gridsperlayer*layers,1); Y3=zeros(gridsperlayer*layers,1); Z3=zeros(gridsperlayer*layers,1); S3=zeros(gridsperlayer*layers,1); index3=zeros(elementstot,4); + X3=zeros(nodesperlayer*layers,1); Y3=zeros(nodesperlayer*layers,1); Z3=zeros(nodesperlayer*layers,1); S3=zeros(nodesperlayer*layers,1); index3=zeros(elementstot,4); %Get new coordinates in 3d @@ -115,5 +115,5 @@ if i50000); @@ -47,5 +47,5 @@ end - %search the grid on ice sheet the closest to i + %search the node on ice sheet the closest to i [d posd]=min(sqrt((md.x(pos_shelf(i))-md.x(pos_GL)).^2+(md.y(pos_shelf(i))-md.y(pos_GL)).^2)); Index: /issm/trunk/src/m/model/averageconnectivity.m =================================================================== --- /issm/trunk/src/m/model/averageconnectivity.m (revision 8297) +++ /issm/trunk/src/m/model/averageconnectivity.m (revision 8298) @@ -6,6 +6,6 @@ nnz=0; -for i=1:md.numberofgrids, +for i=1:md.numberofnodes, nnz=nnz+length(find(md.elements==i)); end -conn=nnz/md.numberofgrids; +conn=nnz/md.numberofnodes; Index: /issm/trunk/src/m/model/averaging.m =================================================================== --- /issm/trunk/src/m/model/averaging.m (revision 8297) +++ /issm/trunk/src/m/model/averaging.m (revision 8298) @@ -2,9 +2,9 @@ %AVERAGING - smooths the input over the mesh % -% This routine takes a list over the elements or the grids in input -% and return a list over the grids. +% This routine takes a list over the elements or the nodes in input +% and return a list over the nodes. % For each iterations it computes the average over each element (average -% of the vertices values) and then computes the average over each grid -% by taking the average of the element around a grid weighted by the +% of the vertices values) and then computes the average over each node +% by taking the average of the element around a node weighted by the % elements volume % @@ -16,15 +16,15 @@ % pressure=averaging(md,md.pressure,0); -if length(data)~=md.numberofelements & length(data)~=md.numberofgrids +if length(data)~=md.numberofelements & length(data)~=md.numberofnodes error('averaging error message: data not supported yet'); end %initialization -weights=zeros(md.numberofgrids,1); +weights=zeros(md.numberofnodes,1); data=data(:); %load some variables (it is much faster if the variab;es are loaded from md once for all) index=md.elements; -numberofgrids=md.numberofgrids; +numberofnodes=md.numberofnodes; numberofelements=md.numberofelements; @@ -41,22 +41,22 @@ linesize=rep*numberofelements; -%update weights that holds the volume of all the element holding the grid i -weights=sparse(line,ones(linesize,1),repmat(areas,rep,1),numberofgrids,1); +%update weights that holds the volume of all the element holding the node i +weights=sparse(line,ones(linesize,1),repmat(areas,rep,1),numberofnodes,1); %initialization if length(data)==numberofelements - average_grid=sparse(line,ones(linesize,1),repmat(areas.*data,rep,1),numberofgrids,1); - average_grid=average_grid./weights; + average_node=sparse(line,ones(linesize,1),repmat(areas.*data,rep,1),numberofnodes,1); + average_node=average_node./weights; else - average_grid=data; + average_node=data; end %loop over iteration for i=1:iterations - average_el=average_grid(index)*summation; - average_grid=sparse(line,ones(linesize,1),repmat(areas.*average_el,rep,1),numberofgrids,1); - average_grid=average_grid./weights; + average_el=average_node(index)*summation; + average_node=sparse(line,ones(linesize,1),repmat(areas.*average_el,rep,1),numberofnodes,1); + average_node=average_node./weights; end %return output as a full matrix (C code do not like sparse matrices) -average=full(average_grid); +average=full(average_node); Index: /issm/trunk/src/m/model/bamg.m =================================================================== --- /issm/trunk/src/m/model/bamg.m (revision 8297) +++ /issm/trunk/src/m/model/bamg.m (revision 8298) @@ -25,5 +25,5 @@ % - maxnbv : maximum number of vertices used to allocate memory (default is 10^6) % - maxsubdiv : maximum subdivision of exisiting elements (default is 10) -% - metric : matrix (numberofgrids x 3) used as a metric +% - metric : matrix (numberofnodes x 3) used as a metric % - Metrictype : 1 -> absolute error c/(err coeff^2) * Abs(H) (default) % 2 -> relative error c/(err coeff^2) * Abs(H)/max(s,cutoff*max(s)) @@ -265,10 +265,10 @@ % Bamg Mesh parameters {{{1 -if (~exist(options,'domain') & md.numberofgrids~=0 & md.dim==2), +if (~exist(options,'domain') & md.numberofnodes~=0 & md.dim==2), if isstruct(md.bamg), bamg_mesh=bamgmesh(md.bamg.mesh); else - bamg_mesh.Vertices=[md.x md.y ones(md.numberofgrids,1)]; + bamg_mesh.Vertices=[md.x md.y ones(md.numberofnodes,1)]; bamg_mesh.Triangles=[md.elements ones(md.numberofelements,1)]; end @@ -327,12 +327,12 @@ md.dim=2; md.numberofelements=size(md.elements,1); -md.numberofgrids=length(md.x); -md.z=zeros(md.numberofgrids,1); -md.gridonbed=ones(md.numberofgrids,1); -md.gridonwater=zeros(md.numberofgrids,1); -md.gridonsurface=ones(md.numberofgrids,1); +md.numberofnodes=length(md.x); +md.z=zeros(md.numberofnodes,1); +md.nodeonbed=ones(md.numberofnodes,1); +md.nodeonwater=zeros(md.numberofnodes,1); +md.nodeonsurface=ones(md.numberofnodes,1); md.elementonbed=ones(md.numberofelements,1); md.elementonsurface=ones(md.numberofelements,1); -md.gridonboundary=zeros(md.numberofgrids,1); md.gridonboundary(md.segments(:,1:2))=1; +md.nodeonboundary=zeros(md.numberofnodes,1); md.nodeonboundary(md.segments(:,1:2))=1; md.counter=1; md.elementconnectivity=md.bamg.mesh.ElementConnectivity; @@ -340,5 +340,5 @@ %Check for orphan -if any(~ismember(1:md.numberofgrids,sort(unique(md.elements(:))))) +if any(~ismember(1:md.numberofnodes,sort(unique(md.elements(:))))) error('Output mesh has orphans. Decrease MaxCornerAngle to prevent outside points (ex: 0.01)'); end Index: /issm/trunk/src/m/model/bedslope.m =================================================================== --- /issm/trunk/src/m/model/bedslope.m (revision 8297) +++ /issm/trunk/src/m/model/bedslope.m (revision 8298) @@ -8,10 +8,10 @@ if (md.dim==2), numberofelements=md.numberofelements; - numberofgrids=md.numberofgrids; + numberofnodes=md.numberofnodes; index=md.elements; x=md.x; y=md.y; z=md.z; else numberofelements=md.numberofelements2d; - numberofgrids=md.numberofgrids2d; + numberofnodes=md.numberofnodes2d; index=md.elements2d; x=md.x2d; y=md.y2d; z=md.z2d; Index: /issm/trunk/src/m/model/collapse.m =================================================================== --- /issm/trunk/src/m/model/collapse.m (revision 8297) +++ /issm/trunk/src/m/model/collapse.m (revision 8298) @@ -18,5 +18,5 @@ %Start with changing alle the fields from the 3d mesh -%drag is limited to grids that are on the bedrock. +%drag is limited to nodes that are on the bedrock. md.drag_coefficient=project2d(md,md.drag_coefficient,1); @@ -46,6 +46,6 @@ md.elementonbed=ones(md.numberofelements2d,1); md.elementonsurface=ones(md.numberofelements2d,1); -md.gridonbed=ones(md.numberofgrids2d,1); -md.gridonsurface=ones(md.numberofgrids2d,1); +md.nodeonbed=ones(md.numberofnodes2d,1); +md.nodeonsurface=ones(md.numberofnodes2d,1); %elementstype @@ -55,8 +55,8 @@ md.elements_type=project2d(md,md.elements_type,1); end -md.gridonhutter=project2d(md,md.gridonhutter,1); -md.gridonmacayeal=project2d(md,md.gridonmacayeal,1); -md.gridonpattyn=project2d(md,md.gridonpattyn,1); -md.gridonstokes=project2d(md,md.gridonstokes,1); +md.nodeonhutter=project2d(md,md.nodeonhutter,1); +md.nodeonmacayeal=project2d(md,md.nodeonmacayeal,1); +md.nodeonpattyn=project2d(md,md.nodeonpattyn,1); +md.nodeonstokes=project2d(md,md.nodeonstokes,1); %boundary conditions @@ -84,5 +84,5 @@ %Collapse the mesh -grids2d=md.numberofgrids2d; +nodes2d=md.numberofnodes2d; elements2d=md.numberofelements2d; @@ -91,9 +91,9 @@ md.thickness=project2d(md,md.thickness,1); md.bed=project2d(md,md.bed,1); -md.gridonboundary=project2d(md,md.gridonboundary,1); +md.nodeonboundary=project2d(md,md.nodeonboundary,1); md.elementoniceshelf=project2d(md,md.elementoniceshelf,1); -md.gridoniceshelf=project2d(md,md.gridoniceshelf,1); +md.nodeoniceshelf=project2d(md,md.nodeoniceshelf,1); md.elementonicesheet=project2d(md,md.elementonicesheet,1); -md.gridonicesheet=project2d(md,md.gridonicesheet,1); +md.nodeonicesheet=project2d(md,md.nodeonicesheet,1); %Initialize with the 2d mesh @@ -101,11 +101,11 @@ md.y=md.y2d; md.z=md.z2d; -md.numberofgrids=md.numberofgrids2d; +md.numberofnodes=md.numberofnodes2d; md.numberofelements=md.numberofelements2d; md.elements=md.elements2d; -%Keep a trace of lower and upper grids -md.lowergrids=NaN; -md.uppergrids=NaN; +%Keep a trace of lower and upper nodes +md.lowernodes=NaN; +md.uppernodes=NaN; %Remove old mesh @@ -116,5 +116,5 @@ md.elements_type2d=md.elements_type; md.numberofelements2d=md.numberofelements; -md.numberofgrids2d=md.numberofgrids; +md.numberofnodes2d=md.numberofnodes; md.numlayers=0; Index: /issm/trunk/src/m/model/contourenvelope.m =================================================================== --- /issm/trunk/src/m/model/contourenvelope.m (revision 8297) +++ /issm/trunk/src/m/model/contourenvelope.m (revision 8298) @@ -23,6 +23,6 @@ %Now, build the connectivity tables for this mesh. %Computing connectivity -if size(md.nodeconnectivity,1)~=md.numberofgrids, - md.nodeconnectivity=NodeConnectivity(md.elements,md.numberofgrids); +if size(md.nodeconnectivity,1)~=md.numberofnodes, + md.nodeconnectivity=NodeConnectivity(md.elements,md.numberofnodes); end if size(md.elementconnectivity,1)~=md.numberofelements, @@ -68,5 +68,5 @@ ord2=find(nods1(2)==md.elements(el1,:)); - %swap segment grids if necessary + %swap segment nodes if necessary if ( (ord1==1 & ord2==2) | (ord1==2 & ord2==3) | (ord1==3 & ord2==1) ), temp=segments(count,1); Index: /issm/trunk/src/m/model/contourmassbalance.m =================================================================== --- /issm/trunk/src/m/model/contourmassbalance.m (revision 8297) +++ /issm/trunk/src/m/model/contourmassbalance.m (revision 8298) @@ -10,6 +10,6 @@ error('contourmassbalance error message: bad usage'); end -if ((length(md.vx)~=md.numberofgrids)|(length(md.vy)~=md.numberofgrids)) - error(['thicknessevolution error message: vx and vy should have a length of ' num2str(md.numberofgrids)]) +if ((length(md.vx)~=md.numberofnodes)|(length(md.vy)~=md.numberofnodes)) + error(['thicknessevolution error message: vx and vy should have a length of ' num2str(md.numberofnodes)]) end if ~exist(file), Index: /issm/trunk/src/m/model/display/displaybc.m =================================================================== --- /issm/trunk/src/m/model/display/displaybc.m (revision 8297) +++ /issm/trunk/src/m/model/display/displaybc.m (revision 8298) @@ -12,9 +12,9 @@ disp(sprintf('\n geography:')); -fielddisplay(md,'gridonboundary','grid on boundary flags list'); +fielddisplay(md,'nodeonboundary','node on boundary flags list'); fielddisplay(md,'elementoniceshelf','element on ice shelf flags list'); -fielddisplay(md,'gridoniceshelf','grid on ice shelf flags list'); +fielddisplay(md,'nodeoniceshelf','node on ice shelf flags list'); fielddisplay(md,'elementonicesheet','element on ice sheet flags list'); -fielddisplay(md,'gridonicesheet','grid on ice sheet flags list'); +fielddisplay(md,'nodeonicesheet','node on ice sheet flags list'); disp(sprintf('\n diagnostic:')); Index: /issm/trunk/src/m/model/display/displaymesh.m =================================================================== --- /issm/trunk/src/m/model/display/displaymesh.m (revision 8297) +++ /issm/trunk/src/m/model/display/displaymesh.m (revision 8298) @@ -15,6 +15,6 @@ disp(sprintf('\n Elements and nodes of the original 2d mesh:')); fielddisplay(md,'numberofelements2d','number of elements'); - fielddisplay(md,'numberofgrids2d','number of nodes'); - fielddisplay(md,'elements2d','index into (x,y,z), coordinates of the grids'); + fielddisplay(md,'numberofnodes2d','number of nodes'); + fielddisplay(md,'elements2d','index into (x,y,z), coordinates of the nodes'); fielddisplay(md,'elements_type2d','element types'); fielddisplay(md,'x2d','nodes x coordinate'); @@ -27,6 +27,6 @@ end fielddisplay(md,'numberofelements','number of elements'); -fielddisplay(md,'numberofgrids','number of nodes'); -fielddisplay(md,'elements','index into (x,y,z), coordinates of the grids'); +fielddisplay(md,'numberofnodes','number of nodes'); +fielddisplay(md,'elements','index into (x,y,z), coordinates of the nodes'); fielddisplay(md,'elements_type','element types'); fielddisplay(md,'x','nodes x coordinate'); @@ -41,6 +41,6 @@ fielddisplay(md,'bamg','Geometry and 2d mesh properties (if generated by Bamg)'); fielddisplay(md,'penalties','penalties list'); -fielddisplay(md,'gridonbed','lower nodes flags list'); +fielddisplay(md,'nodeonbed','lower nodes flags list'); fielddisplay(md,'elementonbed','lower elements flags list'); -fielddisplay(md,'gridonsurface','upper nodes flags list'); +fielddisplay(md,'nodeonsurface','upper nodes flags list'); fielddisplay(md,'elementonsurface','upper elements flags list'); Index: /issm/trunk/src/m/model/display/displayparameters.m =================================================================== --- /issm/trunk/src/m/model/display/displayparameters.m (revision 8297) +++ /issm/trunk/src/m/model/display/displayparameters.m (revision 8298) @@ -19,6 +19,6 @@ fielddisplay(md,'elementonbed','element on bed flags list'); fielddisplay(md,'elementonsurface','element on surface flags list'); -fielddisplay(md,'gridonbed','grid on bed flags list'); -fielddisplay(md,'gridonsurface','grid on surface flags list'); +fielddisplay(md,'nodeonbed','node on bed flags list'); +fielddisplay(md,'nodeonsurface','node on surface flags list'); disp(sprintf('\n physical parameters:')); Index: /issm/trunk/src/m/model/divergence.m =================================================================== --- /issm/trunk/src/m/model/divergence.m (revision 8297) +++ /issm/trunk/src/m/model/divergence.m (revision 8298) @@ -7,10 +7,10 @@ if (md.dim==2), numberofelements=md.numberofelements; - numberofgrids=md.numberofgrids; + numberofnodes=md.numberofnodes; index=md.elements; x=md.x; y=md.y; z=md.z; else numberofelements=md.numberofelements2d; - numberofgrids=md.numberofgrids2d; + numberofnodes=md.numberofnodes2d; index=md.elements2d; x=md.x2d; y=md.y2d; z=md.z2d; Index: /issm/trunk/src/m/model/extrude.m =================================================================== --- /issm/trunk/src/m/model/extrude.m (revision 8297) +++ /issm/trunk/src/m/model/extrude.m (revision 8298) @@ -75,6 +75,6 @@ x3d=[]; y3d=[]; -z3d=[]; %the lower grid is on the bed -thickness3d=md.thickness; %thickness and bed for these grids +z3d=[]; %the lower node is on the bed +thickness3d=md.thickness; %thickness and bed for these nodes bed3d=md.bed; @@ -83,23 +83,23 @@ x3d=[x3d; md.x]; y3d=[y3d; md.y]; - %grids are distributed between bed and surface accordingly to the given exponent + %nodes are distributed between bed and surface accordingly to the given exponent z3d=[z3d; bed3d+thickness3d*extrusionlist(i)]; end -number_grids3d=size(x3d,1); %number of 3d grids for the non extruded part of the mesh +number_nodes3d=size(x3d,1); %number of 3d nodes for the non extruded part of the mesh %Extrude elements elements3d=[]; for i=1:numlayers-1, - elements3d=[elements3d;[md.elements+(i-1)*md.numberofgrids md.elements+i*md.numberofgrids]]; %Create the elements of the 3d mesh for the non extruded part -end -number_el3d=size(elements3d,1); %number of 3d grids for the non extruded part of the mesh - -%Keep a trace of lower and upper grids -lowergrids=NaN*ones(number_grids3d,1); -uppergrids=NaN*ones(number_grids3d,1); -lowergrids(md.numberofgrids+1:end)=1:(numlayers-1)*md.numberofgrids; -uppergrids(1:(numlayers-1)*md.numberofgrids)=md.numberofgrids+1:number_grids3d; -md.lowergrids=lowergrids; -md.uppergrids=uppergrids; + elements3d=[elements3d;[md.elements+(i-1)*md.numberofnodes md.elements+i*md.numberofnodes]]; %Create the elements of the 3d mesh for the non extruded part +end +number_el3d=size(elements3d,1); %number of 3d nodes for the non extruded part of the mesh + +%Keep a trace of lower and upper nodes +lowernodes=NaN*ones(number_nodes3d,1); +uppernodes=NaN*ones(number_nodes3d,1); +lowernodes(md.numberofnodes+1:end)=1:(numlayers-1)*md.numberofnodes; +uppernodes(1:(numlayers-1)*md.numberofnodes)=md.numberofnodes+1:number_nodes3d; +md.lowernodes=lowernodes; +md.uppernodes=uppernodes; %same for lower and upper elements @@ -119,5 +119,5 @@ md.vertices_type2d=md.vertices_type; md.numberofelements2d=md.numberofelements; -md.numberofgrids2d=md.numberofgrids; +md.numberofnodes2d=md.numberofnodes; %Update mesh type @@ -130,10 +130,10 @@ md.z=z3d; md.numberofelements=number_el3d; -md.numberofgrids=number_grids3d; +md.numberofnodes=number_nodes3d; md.numlayers=numlayers; %Ok, now deal with the other fields from the 2d mesh: -%drag_coefficient is limited to grids that are on the bedrock. +%drag_coefficient is limited to nodes that are on the bedrock. md.drag_coefficient=project3d(md,md.drag_coefficient,'node',1); @@ -168,6 +168,6 @@ md.elementonbed=project3d(md,ones(md.numberofelements2d,1),'element',1); md.elementonsurface=project3d(md,ones(md.numberofelements2d,1),'element',md.numlayers-1); -md.gridonbed=project3d(md,ones(md.numberofgrids2d,1),'node',1); -md.gridonsurface=project3d(md,ones(md.numberofgrids2d,1),'node',md.numlayers); +md.nodeonbed=project3d(md,ones(md.numberofnodes2d,1),'node',1); +md.nodeonsurface=project3d(md,ones(md.numberofnodes2d,1),'node',md.numlayers); %elementstype @@ -176,8 +176,8 @@ md.elements_type=zeros(number_el3d,1); md.elements_type=project3d(md,oldelements_type,'element'); - md.gridonhutter=project3d(md,md.gridonhutter,'node'); - md.gridonmacayeal=project3d(md,md.gridonmacayeal,'node'); - md.gridonpattyn=project3d(md,md.gridonpattyn,'node'); - md.gridonstokes=project3d(md,md.gridonstokes,'node'); + md.nodeonhutter=project3d(md,md.nodeonhutter,'node'); + md.nodeonmacayeal=project3d(md,md.nodeonmacayeal,'node'); + md.nodeonpattyn=project3d(md,md.nodeonpattyn,'node'); + md.nodeonstokes=project3d(md,md.nodeonstokes,'node'); end @@ -185,5 +185,5 @@ if ~isnan(md.vertices_type) oldvertices_type=md.vertices_type2d; - md.vertices_type=zeros(number_grids3d,1); + md.vertices_type=zeros(number_nodes3d,1); md.vertices_type=project3d(md,oldvertices_type,'node'); end @@ -195,9 +195,9 @@ md.diagnostic_ref=project3d(md,md.diagnostic_ref,'node'); -%in 3d, pressureload: [grid1 grid2 grid3 grid4 element] -pressureload_layer1=[md.pressureload(:,1:2) md.pressureload(:,2)+md.numberofgrids2d md.pressureload(:,1)+md.numberofgrids2d md.pressureload(:,3:4)]; %Add two columns on the first layer +%in 3d, pressureload: [node1 node2 node3 node4 element] +pressureload_layer1=[md.pressureload(:,1:2) md.pressureload(:,2)+md.numberofnodes2d md.pressureload(:,1)+md.numberofnodes2d md.pressureload(:,3:4)]; %Add two columns on the first layer pressureload=[]; for i=1:numlayers-1, - pressureload=[pressureload ;pressureload_layer1(:,1:4)+(i-1)*md.numberofgrids2d pressureload_layer1(:,5)+(i-1)*md.numberofelements2d pressureload_layer1(:,6)]; + pressureload=[pressureload ;pressureload_layer1(:,1:4)+(i-1)*md.numberofnodes2d pressureload_layer1(:,5)+(i-1)*md.numberofelements2d pressureload_layer1(:,6)]; end md.pressureload=pressureload; @@ -220,11 +220,11 @@ md.thickness=project3d(md,md.thickness,'node'); md.bed=project3d(md,md.bed,'node'); -md.gridonboundary=project3d(md,md.gridonboundary,'node'); +md.nodeonboundary=project3d(md,md.nodeonboundary,'node'); md.elementoniceshelf=project3d(md,md.elementoniceshelf,'element'); -md.gridoniceshelf=project3d(md,md.gridoniceshelf,'node'); +md.nodeoniceshelf=project3d(md,md.nodeoniceshelf,'node'); md.elementonicesheet=project3d(md,md.elementonicesheet,'element'); -md.gridonicesheet=project3d(md,md.gridonicesheet,'node'); +md.nodeonicesheet=project3d(md,md.nodeonicesheet,'node'); md.elementonwater=project3d(md,md.elementonwater,'element'); -md.gridonwater=project3d(md,md.gridonwater,'node'); +md.nodeonwater=project3d(md,md.nodeonwater,'node'); if ~isnan(md.weights),md.weights=project3d(md,md.weights,'node');end; Index: /issm/trunk/src/m/model/geography.m =================================================================== --- /issm/trunk/src/m/model/geography.m (revision 8297) +++ /issm/trunk/src/m/model/geography.m (revision 8298) @@ -2,6 +2,6 @@ %GEOGRAPHY - establish boundaries between grounded and floating ice. % -% By default, ice is considered grounded. The contour iceshelfname defines grids -% for which ice is floating. The contour icesheetname defines grids inside an iceshelf, +% By default, ice is considered grounded. The contour iceshelfname defines nodes +% for which ice is floating. The contour icesheetname defines nodes inside an iceshelf, % that are grounded (ie: ice rises, islands, etc ...) % All input files are in the Argus format (extension .exp). @@ -32,18 +32,18 @@ elements=md.elements; -%Assign elementoniceshelf, elementonicesheet, gridonicesheet and gridoniceshelf. Only change at your own peril! This is synchronized heavily with the GroundingLineMigration module. {{{1 +%Assign elementoniceshelf, elementonicesheet, nodeonicesheet and nodeoniceshelf. Only change at your own peril! This is synchronized heavily with the GroundingLineMigration module. {{{1 elementoniceshelf=FlagElements(md,iceshelfname); elementonicesheet=FlagElements(md,icesheetname); -%Because icesheet grids and elements can be included into an iceshelf, we need to update. Remember, all the previous +%Because icesheet nodes and elements can be included into an iceshelf, we need to update. Remember, all the previous %arrays come from domain outlines that can intersect one another: elementoniceshelf=double((elementoniceshelf & ~elementonicesheet)); elementonicesheet=double(~elementoniceshelf); -%the order here is important. we choose gridonicesheet as default on the grounding line. -gridoniceshelf=zeros(md.numberofgrids,1); -gridonicesheet=zeros(md.numberofgrids,1); -gridonicesheet(md.elements(find(elementonicesheet),:))=1; -gridoniceshelf(find(~gridonicesheet))=1; +%the order here is important. we choose nodeonicesheet as default on the grounding line. +nodeoniceshelf=zeros(md.numberofnodes,1); +nodeonicesheet=zeros(md.numberofnodes,1); +nodeonicesheet(md.elements(find(elementonicesheet),:))=1; +nodeoniceshelf(find(~nodeonicesheet))=1; %}}} @@ -52,10 +52,10 @@ md.elementoniceshelf=elementoniceshelf; -md.gridoniceshelf=gridoniceshelf; +md.nodeoniceshelf=nodeoniceshelf; md.elementonicesheet=elementonicesheet; -md.gridonicesheet=gridonicesheet; +md.nodeonicesheet=nodeonicesheet; -md.gridonwater=zeros(md.numberofgrids,1); +md.nodeonwater=zeros(md.numberofnodes,1); md.elementonwater=zeros(md.numberofelements,1); Index: /issm/trunk/src/m/model/geography2.m =================================================================== --- /issm/trunk/src/m/model/geography2.m (revision 8297) +++ /issm/trunk/src/m/model/geography2.m (revision 8298) @@ -13,7 +13,7 @@ elements=md.elements; -%recover elements and grids on land. +%recover elements and nodes on land. if ischar(landname), - [gridonland,elementonland]=ContourToMesh(elements,x,y,landname,'element and node',2); + [nodeonland,elementonland]=ContourToMesh(elements,x,y,landname,'element and node',2); elseif isfloat(landname), if size(landname,1)~=md.numberofelements, @@ -21,6 +21,6 @@ end elementonland=landname; - gridonland=zeros(md.numberofgrids,1); - gridonland(md.elements(find(elementonland),:))=1; + nodeonland=zeros(md.numberofnodes,1); + nodeonland(md.elements(find(elementonland),:))=1; else error('Invalid area option option'); @@ -28,6 +28,6 @@ %Now, build the connectivity tables for this mesh. -if size(md.nodeconnectivity,1)~=md.numberofgrids, - md.nodeconnectivity=NodeConnectivity(md.elements,md.numberofgrids); +if size(md.nodeconnectivity,1)~=md.numberofnodes, + md.nodeconnectivity=NodeConnectivity(md.elements,md.numberofnodes); end if size(md.elementconnectivity,1)~=md.numberofelements, @@ -35,7 +35,7 @@ end -%any element with 3 grids on land should be on land: +%any element with 3 nodes on land should be on land: elementsonwater=find(~elementonland); -wrongelements=elementsonwater(find(( gridonland(md.elements(elementsonwater,1)) + gridonland(md.elements(elementsonwater,2)) + gridonland(md.elements(elementsonwater,3)) ... +wrongelements=elementsonwater(find(( nodeonland(md.elements(elementsonwater,1)) + nodeonland(md.elements(elementsonwater,2)) + nodeonland(md.elements(elementsonwater,3)) ... )==3)); elementonland(wrongelements)=1; @@ -69,16 +69,16 @@ elementonland(landelements)=1; -%recover arrays of ice shelf grids and elements, and ice sheet grids and elements. +%recover arrays of ice shelf nodes and elements, and ice sheet nodes and elements. elementoniceshelf=FlagElements(md,iceshelfname); elementonicesheet=FlagElements(md,icesheetname); -%Because icesheet grids and elements can be included into an iceshelf, we need to update. Remember, all the previous +%Because icesheet nodes and elements can be included into an iceshelf, we need to update. Remember, all the previous %arrays come from domain outlines that can intersect one another: -gridoniceshelf=zeros(md.numberofgrids,1); -gridonicesheet=zeros(md.numberofgrids,1); +nodeoniceshelf=zeros(md.numberofnodes,1); +nodeonicesheet=zeros(md.numberofnodes,1); elementoniceshelf=double((elementoniceshelf & ~elementonicesheet)); elementonicesheet=double(~elementoniceshelf); -gridoniceshelf(md.elements(find(elementoniceshelf),:))=1; -gridonicesheet(md.elements(find(elementonicesheet),:))=1; +nodeoniceshelf(md.elements(find(elementoniceshelf),:))=1; +nodeonicesheet(md.elements(find(elementonicesheet),:))=1; %now correct, so that none of the iceshelf and icesheet elements and nodes are in the water. @@ -87,18 +87,18 @@ elementonicesheet(pos)=0; -pos=find(~gridonland); -gridoniceshelf(pos)=0; -gridonicesheet(pos)=0; +pos=find(~nodeonland); +nodeoniceshelf(pos)=0; +nodeonicesheet(pos)=0; -%create gridonwater and elementonwater: -gridonwater=double(~gridonland); +%create nodeonwater and elementonwater: +nodeonwater=double(~nodeonland); elementonwater=double(~elementonland); %correct for islands: -gridoniceshelf=double(gridoniceshelf & ~gridonicesheet); +nodeoniceshelf=double(nodeoniceshelf & ~nodeonicesheet); elementoniceshelf=double(elementoniceshelf & ~elementonicesheet); %now, icesheets are everything except iceshelves and water -gridonicesheet=double(~gridoniceshelf & ~gridonwater); +nodeonicesheet=double(~nodeoniceshelf & ~nodeonwater); elementonicesheet=double(~elementoniceshelf & ~elementonwater); @@ -123,27 +123,27 @@ %some final checks: -%check that no grid thinks it's on an ice shelf or ice sheet, and lies actually in the middle of the water. -gridsgrounded=find(~gridonwater); +%check that no node thinks it's on an ice shelf or ice sheet, and lies actually in the middle of the water. +nodesgrounded=find(~nodeonwater); lengthconnectivity=size(md.nodeconnectivity,2); -groundedcounters=md.nodeconnectivity(gridsgrounded,lengthconnectivity); -groundedconnectivity=md.nodeconnectivity(gridsgrounded,1:lengthconnectivity-1); +groundedcounters=md.nodeconnectivity(nodesgrounded,lengthconnectivity); +groundedconnectivity=md.nodeconnectivity(nodesgrounded,1:lengthconnectivity-1); pos=find(groundedconnectivity); groundedconnectivity(pos)=elementonwater(groundedconnectivity(pos)); groundedsum=sum(groundedconnectivity,2); errorflags=find(groundedsum==groundedcounters); -errorgrids=gridsgrounded(errorflags); +errornodes=nodesgrounded(errorflags); -gridonwater(errorgrids)=1; -gridonicesheet(errorgrids)=0; -gridoniceshelf(errorgrids)=0; +nodeonwater(errornodes)=1; +nodeonicesheet(errornodes)=0; +nodeoniceshelf(errornodes)=0; %Return: -md.gridoniceshelf=gridoniceshelf; +md.nodeoniceshelf=nodeoniceshelf; md.elementoniceshelf=elementoniceshelf; -md.gridonwater=gridonwater; +md.nodeonwater=nodeonwater; md.elementonwater=elementonwater; -md.gridonicesheet=gridonicesheet; +md.nodeonicesheet=nodeonicesheet; md.elementonicesheet=elementonicesheet; Index: /issm/trunk/src/m/model/ismodelselfconsistent.m =================================================================== --- /issm/trunk/src/m/model/ismodelselfconsistent.m (revision 8297) +++ /issm/trunk/src/m/model/ismodelselfconsistent.m (revision 8298) @@ -42,5 +42,5 @@ checksize(md,fields,[md.numberofelements 6]); end -if any(~ismember(1:md.numberofgrids,sort(unique(md.elements(:))))); +if any(~ismember(1:md.numberofnodes,sort(unique(md.elements(:))))); error('orphan nodes have been found. Check the mesh'); end @@ -70,17 +70,17 @@ %}}} %NO NAN {{{1 -fields={'numberofelements','numberofgrids','x','y','z','drag_coefficient','drag_type','drag_p','drag_q',... +fields={'numberofelements','numberofnodes','x','y','z','drag_coefficient','drag_type','drag_p','drag_q',... 'rho_ice','rho_water','rheology_B','elementoniceshelf','surface','thickness','bed','g','lowmem','sparsity','nsteps','maxiter',... - 'tolx','eps_res','max_nonlinear_iterations','rheology_n','gridonbed','gridonsurface','elementonbed','elementonsurface','deltaH','DeltaH','timeacc','timedec','elementconnectivity'}; + 'tolx','eps_res','max_nonlinear_iterations','rheology_n','nodeonbed','nodeonsurface','elementonbed','elementonsurface','deltaH','DeltaH','timeacc','timedec','elementconnectivity'}; checknan(md,fields); %}}}} %FIELDS >= 0 {{{1 -fields={'numberofelements','numberofgrids','elements','drag_coefficient','drag_type','drag_p','drag_q',... +fields={'numberofelements','numberofnodes','elements','drag_coefficient','drag_type','drag_p','drag_q',... 'rho_ice','rho_water','rheology_B','elementoniceshelf','thickness','g','eps_res','max_nonlinear_iterations','eps_rel','eps_abs','nsteps','maxiter','tolx',... - 'sparsity','lowmem','rheology_n','gridonbed','gridonsurface','elementonbed','elementonsurface','deltaH','DeltaH','timeacc','timedec'}; + 'sparsity','lowmem','rheology_n','nodeonbed','nodeonsurface','elementonbed','elementonsurface','deltaH','DeltaH','timeacc','timedec'}; checkgreater(md,fields,0); %}}} %FIELDS > 0 {{{1 -fields={'numberofelements','numberofgrids','elements','drag_type','drag_p',... +fields={'numberofelements','numberofnodes','elements','drag_type','drag_p',... 'rho_ice','rho_water','rheology_B','thickness','g','max_nonlinear_iterations','eps_res','eps_rel','eps_abs','maxiter','tolx',... 'sparsity','deltaH','DeltaH','timeacc','timedec'}; @@ -92,10 +92,10 @@ %}}} %SIZE NUMBEROFGRIDS {{{1 -fields={'x','y','z','rheology_B','drag_coefficient','melting_rate','accumulation_rate','surface','thickness','bed','gridonbed','gridonsurface'}; -checksize(md,fields,[md.numberofgrids 1]); +fields={'x','y','z','rheology_B','drag_coefficient','melting_rate','accumulation_rate','surface','thickness','bed','nodeonbed','nodeonsurface'}; +checksize(md,fields,[md.numberofnodes 1]); %}}} %OTHER SIZES {{{1 fields={'spcvelocity','diagnostic_ref'}; -checksize(md,fields,[md.numberofgrids 6]); +checksize(md,fields,[md.numberofnodes 6]); %}}} %THICKNESS = SURFACE - BED {{{1 @@ -188,5 +188,5 @@ checksize(md,fields,[md.nsteps num_controls]); fields={'cm_min','cm_max'}; - checksize(md,fields,[md.numberofgrids num_controls]); + checksize(md,fields,[md.numberofnodes num_controls]); %RESPONSES @@ -195,5 +195,5 @@ %WEIGHTS fields={'weights'}; - checksize(md,fields,[md.numberofgrids 1]); + checksize(md,fields,[md.numberofnodes 1]); checkgreater(md,fields,0); @@ -201,9 +201,9 @@ if md.solution_type==BalancethicknessSolutionEnum fields={'thickness_obs'}; - checksize(md,fields,[md.numberofgrids 1]); + checksize(md,fields,[md.numberofnodes 1]); checknan(md,fields); else fields={'vx_obs','vy_obs'}; - checksize(md,fields,[md.numberofgrids 1]); + checksize(md,fields,[md.numberofnodes 1]); checknan(md,fields); end @@ -213,5 +213,5 @@ pos=find(md.thickness<=0); if any(find(md.spcthickness(pos,1)==0)), - error(['model not consistent: model ' md.name ' has some grids with 0 thickness']); + error(['model not consistent: model ' md.name ' has some nodes with 0 thickness']); end end @@ -228,8 +228,8 @@ end if ~isempty(md.part), - if numel(md.part)~=md.numberofgrids, - error(['model not consistent: user supplied partition for qmu analysis should have size md.numberofgrids x 1 ']); - end - if find(md.part)>=md.numberofgrids, + if numel(md.part)~=md.numberofnodes, + error(['model not consistent: user supplied partition for qmu analysis should have size md.numberofnodes x 1 ']); + end + if find(md.part)>=md.numberofnodes, error(['model not consistent: user supplied partition should be indexed from 0 (c-convention)']); end @@ -237,6 +237,6 @@ error(['model not consistent: partition vector not indexed from 0 on']); end - if max(md.part)>=md.numberofgrids, - error(['model not consistent: partition vector cannot have maximum index larger than number of grids']); + if max(md.part)>=md.numberofnodes, + error(['model not consistent: partition vector cannot have maximum index larger than number of nodes']); end if ~isempty(find(md.part<0)), @@ -319,6 +319,6 @@ end % probably going to need some checks on fm_flightreqs here - if (numel(md.fm_criterion) ~= md.numberofgrids) && (numel(md.fm_criterion) ~= md.numberofelements) - error(['model not consistent: fm_criterion vector must have number of nodes (' int2str(md.numberofgrids) ') or elements (' int2str(md.numberofelements) ') values, not ' int2str(numel(md.fm_criterion)) ' values.']); + if (numel(md.fm_criterion) ~= md.numberofnodes) && (numel(md.fm_criterion) ~= md.numberofelements) + error(['model not consistent: fm_criterion vector must have number of nodes (' int2str(md.numberofnodes) ') or elements (' int2str(md.numberofelements) ') values, not ' int2str(numel(md.fm_criterion)) ' values.']); end end @@ -343,5 +343,5 @@ %SINGULAR if ~any(sum(md.spcvelocity(:,1:2),2)==2), - error(['model not consistent: model ' md.name ' is not well posed (singular). You need at least one grid with fixed velocity!']) + error(['model not consistent: model ' md.name ' is not well posed (singular). You need at least one node with fixed velocity!']) end @@ -350,5 +350,5 @@ pos=find(md.thickness<=0); if any(find(md.spcthickness(pos,1)==0)), - error(['model not consistent: model ' md.name ' has some grids with 0 thickness']); + error(['model not consistent: model ' md.name ' has some nodes with 0 thickness']); end end @@ -369,8 +369,8 @@ end %CHECK THAT ROTATION IS IN THE (X,Y) PLANE FOR 2D MODELS - if any(md.gridonmacayeal), - pos=find(sum(isnan(md.diagnostic_ref),2)==0 & md.gridonmacayeal); + if any(md.nodeonmacayeal), + pos=find(sum(isnan(md.diagnostic_ref),2)==0 & md.nodeonmacayeal); if any(md.diagnostic_ref(pos,3:5)~=0); - error(['model not consistent: model ' md.name ' has problem with rotated spc. The rotation should be in the (x,y) plane for 2D diagnostic models (gridonmacayeal)']); + error(['model not consistent: model ' md.name ' has problem with rotated spc. The rotation should be in the (x,y) plane for 2D diagnostic models (nodeonmacayeal)']); end end @@ -380,5 +380,5 @@ fields={'vx','vy'}; checknan(md,fields); - checksize(md,fields,[md.numberofgrids 1]); + checksize(md,fields,[md.numberofnodes 1]); end @@ -400,5 +400,5 @@ %Check the size of verticess_type fields={'vertices_type'}; - checksize(md,fields,[md.numberofgrids 1]); + checksize(md,fields,[md.numberofnodes 1]); %Check the values of vertices_type checkvalues(md,{'vertices_type'},[MacAyealApproximationEnum() HutterApproximationEnum() PattynApproximationEnum()... @@ -436,5 +436,5 @@ %INITIAL VELOCITIES fields={'vx','vy'}; - checksize(md,fields,[md.numberofgrids 1]); + checksize(md,fields,[md.numberofnodes 1]); checknan(md,fields); @@ -460,5 +460,5 @@ %VELOCITIES AND PRESSURE fields={'vx','vy','vz','pressure','geothermalflux'}; - checksize(md,fields,[md.numberofgrids 1]); + checksize(md,fields,[md.numberofnodes 1]); checknan(md,fields); @@ -472,5 +472,5 @@ %INITIAL TEMPERATURE, MELTING AND ACCUMULATION fields={'temperature','accumulation_rate','melting_rate'}; - checksize(md,fields,[md.numberofgrids 1]); + checksize(md,fields,[md.numberofnodes 1]); checknan(md,fields); @@ -488,10 +488,10 @@ %VELOCITIES MELTING AND ACCUMULATION fields={'vx','vy','accumulation_rate','melting_rate','dhdt'}; - checksize(md,fields,[md.numberofgrids 1]); + checksize(md,fields,[md.numberofnodes 1]); checknan(md,fields); %SPC % if ~md.prognostic_DG, - % if any(md.spcthickness(find(md.gridonboundary))~=1), + % if any(md.spcthickness(find(md.nodeonboundary))~=1), % error(['model not consistent: model ' md.name ' should have all the nodes on boundary constrained in field spcthickness']); % end @@ -507,9 +507,9 @@ %VELOCITIES MELTING AND ACCUMULATION fields={'vx','vy','accumulation_rate','melting_rate'}; - checksize(md,fields,[md.numberofgrids 1]); + checksize(md,fields,[md.numberofnodes 1]); checknan(md,fields); %SPC - if any(md.spcvelocity(find(md.gridonboundary),[1:2])~=1), + if any(md.spcvelocity(find(md.nodeonboundary),[1:2])~=1), error(['model not consistent: model ' md.name ' should have all the nodes on boundary constrained in field spcvelocity']); end @@ -557,7 +557,7 @@ if strcmp(fields{i},'cm_min'), disp('!!! '); - disp('!!! WARNING: cm_min must now be of size [md.numberofgrids x 1]. Update your parameter file as follows:'); + disp('!!! WARNING: cm_min must now be of size [md.numberofnodes x 1]. Update your parameter file as follows:'); disp('!!! '); - disp('!!! md.cm_min=md.cm_min*ones(md.numberofgrids,1);'); + disp('!!! md.cm_min=md.cm_min*ones(md.numberofnodes,1);'); disp('!!! '); end @@ -565,7 +565,7 @@ if strcmp(fields{i},'cm_max'), disp('!!! '); - disp('!!! WARNING: cm_max must now be of size [md.numberofgrids x 1]. Update your parameter file as follows:'); + disp('!!! WARNING: cm_max must now be of size [md.numberofnodes x 1]. Update your parameter file as follows:'); disp('!!! '); - disp('!!! md.cm_max=md.cm_max*ones(md.numberofgrids,1);'); + disp('!!! md.cm_max=md.cm_max*ones(md.numberofnodes,1);'); disp('!!! '); end Index: /issm/trunk/src/m/model/isresultconsistent.m =================================================================== --- /issm/trunk/src/m/model/isresultconsistent.m (revision 8297) +++ /issm/trunk/src/m/model/isresultconsistent.m (revision 8298) @@ -37,5 +37,5 @@ %check size - if ~testsize(md,fields1,md.numberofgrids), + if ~testsize(md,fields1,md.numberofnodes), bool=0; return end @@ -66,5 +66,5 @@ %check size - if ~testsize(md,fields1,md.numberofgrids), + if ~testsize(md,fields1,md.numberofnodes), bool=0; return end @@ -101,5 +101,5 @@ fields={'results.DiagnosticAnalysis.gradient'}; %check size - if ~testsize(md,fields,md.numberofgrids), + if ~testsize(md,fields,md.numberofnodes), bool=0; return end @@ -126,25 +126,25 @@ %check size - if ~testsize(md,fields1,md.numberofgrids), - bool=0; return - end - - %no NAN - if ~testnan(md,fields1,md.numberofgrids), - bool=0; return - end - - %check value is real - if ~testreal(md,fields1,md.numberofgrids), + if ~testsize(md,fields1,md.numberofnodes), + bool=0; return + end + + %no NAN + if ~testnan(md,fields1,md.numberofnodes), + bool=0; return + end + + %check value is real + if ~testreal(md,fields1,md.numberofnodes), bool=0; return end %check value>=0 - if ~testpositive(md,fields2,md.numberofgrids), + if ~testpositive(md,fields2,md.numberofnodes), bool=0; return end %check melting (<=0 via penalties) - if any(abs(md.results.ThermalAnalysis(iter).melting(md.numberofgrids2d+1:end))>tolerance) + if any(abs(md.results.ThermalAnalysis(iter).melting(md.numberofnodes2d+1:end))>tolerance) disp(['''thermal'' result not consistent: increase penalty_melting (negative melting)']); bool=0; return; @@ -175,20 +175,20 @@ %check size - if ~testsize(md,fields1,md.numberofgrids), - bool=0; return - end - - %no NAN - if ~testnan(md,fields1,md.numberofgrids), - bool=0; return - end - - %check value is real - if ~testreal(md,fields1,md.numberofgrids), + if ~testsize(md,fields1,md.numberofnodes), + bool=0; return + end + + %no NAN + if ~testnan(md,fields1,md.numberofnodes), + bool=0; return + end + + %check value is real + if ~testreal(md,fields1,md.numberofnodes), bool=0; return end %check value>=0 - if ~testpositive(md,fields2,md.numberofgrids), + if ~testpositive(md,fields2,md.numberofnodes), bool=0; return end @@ -196,5 +196,5 @@ %check melting (<=0 via penalties) if (md.dim==3), - if any(abs(md.results.TransientAnalysis(iter).melting(md.numberofgrids2d+1:end))>tolerance) + if any(abs(md.results.TransientAnalysis(iter).melting(md.numberofnodes2d+1:end))>tolerance) disp(['''thermal'' result not consistent: increase penalty_melting (negative melting)']); bool=0; return; @@ -210,5 +210,5 @@ for i=1:length(fields), if length(eval(['md.' fields{i}]))~=fieldsize - disp(['results not consistent: field ' fields{i} ' size should be ' num2str(md.numberofgrids)]); + disp(['results not consistent: field ' fields{i} ' size should be ' num2str(md.numberofnodes)]); bool=0; return; end Index: /issm/trunk/src/m/model/marshall.m =================================================================== --- /issm/trunk/src/m/model/marshall.m (revision 8297) +++ /issm/trunk/src/m/model/marshall.m (revision 8298) @@ -23,5 +23,5 @@ WriteData(fid,md.dim,'Integer','dim'); -WriteData(fid,md.numberofgrids,'Integer','numberofgrids'); +WriteData(fid,md.numberofnodes,'Integer','numberofnodes'); WriteData(fid,md.numberofelements,'Integer','numberofelements'); WriteData(fid,md.x,'Mat','x'); @@ -32,13 +32,13 @@ WriteData(fid,md.elements_type,'Mat','elements_type'); WriteData(fid,md.vertices_type,'Mat','vertices_type'); -WriteData(fid,md.gridonhutter,'Mat','gridonhutter'); -WriteData(fid,md.gridonmacayeal,'Mat','gridonmacayeal'); +WriteData(fid,md.nodeonhutter,'Mat','nodeonhutter'); +WriteData(fid,md.nodeonmacayeal,'Mat','nodeonmacayeal'); if md.dim==3, WriteData(fid,md.numberofelements2d,'Integer','numberofelements2d'); - WriteData(fid,md.numberofgrids2d,'Integer','numberofgrids2d'); + WriteData(fid,md.numberofnodes2d,'Integer','numberofnodes2d'); WriteData(fid,md.elements2d,'Mat','elements2d'); WriteData(fid,md.numlayers,'Integer','numlayers'); - WriteData(fid,md.gridonpattyn,'Mat','gridonpattyn'); + WriteData(fid,md.nodeonpattyn,'Mat','nodeonpattyn'); end WriteData(fid,md.upperelements,'Mat','upperelements'); @@ -46,7 +46,7 @@ WriteData(fid,md.elementonbed,'Mat','elementonbed'); WriteData(fid,md.elementonsurface,'Mat','elementonsurface'); -WriteData(fid,md.gridonbed,'Mat','gridonbed'); -WriteData(fid,md.gridonsurface,'Mat','gridonsurface'); -WriteData(fid,md.gridonstokes,'Mat','gridonstokes'); +WriteData(fid,md.nodeonbed,'Mat','nodeonbed'); +WriteData(fid,md.nodeonsurface,'Mat','nodeonsurface'); +WriteData(fid,md.nodeonstokes,'Mat','nodeonstokes'); WriteData(fid,md.borderstokes,'Mat','borderstokes'); @@ -75,7 +75,7 @@ WriteData(fid,md.elementoniceshelf,'Mat','elementoniceshelf'); WriteData(fid,md.elementonwater,'Mat','elementonwater'); -WriteData(fid,md.gridonicesheet,'Mat','gridonicesheet'); -WriteData(fid,md.gridoniceshelf,'Mat','gridoniceshelf'); -WriteData(fid,md.gridonwater,'Mat','gridonwater'); +WriteData(fid,md.nodeonicesheet,'Mat','nodeonicesheet'); +WriteData(fid,md.nodeoniceshelf,'Mat','nodeoniceshelf'); +WriteData(fid,md.nodeonwater,'Mat','nodeonwater'); WriteData(fid,md.spcvelocity,'Mat','spcvelocity'); Index: /issm/trunk/src/m/model/mechanicalproperties.m =================================================================== --- /issm/trunk/src/m/model/mechanicalproperties.m (revision 8297) +++ /issm/trunk/src/m/model/mechanicalproperties.m (revision 8298) @@ -14,6 +14,6 @@ %some checks -if length(vx)~=md.numberofgrids | length(vy)~=md.numberofgrids, - error(['the input velocity should be of size ' num2str(md.numberofgrids) '!']) +if length(vx)~=md.numberofnodes | length(vy)~=md.numberofnodes, + error(['the input velocity should be of size ' num2str(md.numberofnodes) '!']) end if ~(md.dim==2) Index: /issm/trunk/src/m/model/mesh/findsegments.m =================================================================== --- /issm/trunk/src/m/model/mesh/findsegments.m (revision 8297) +++ /issm/trunk/src/m/model/mesh/findsegments.m (revision 8298) @@ -52,5 +52,5 @@ segments(count,:)=[nods1 el1]; - %swap segment grids if necessary + %swap segment nodes if necessary ord1=find(nods1(1)==md.elements(el1,:)); ord2=find(nods1(2)==md.elements(el1,:)); @@ -77,5 +77,5 @@ segments(count,:)=[nods el1]; - %swap segment grids if necessary + %swap segment nodes if necessary ord1=find(nods(1)==md.elements(el1,:)); ord2=find(nods(2)==md.elements(el1,:)); Index: /issm/trunk/src/m/model/mesh/mesh.m =================================================================== --- /issm/trunk/src/m/model/mesh/mesh.m (revision 8297) +++ /issm/trunk/src/m/model/mesh/mesh.m (revision 8298) @@ -15,5 +15,5 @@ % md=mesh(md,'DomainOutline.exp','Rifts.exp',1500); -%Figure out a characteristic area. Resolution is a grid oriented concept (ex a 1000m resolution grid would +%Figure out a characteristic area. Resolution is a node oriented concept (ex a 1000m resolution node would %be made of 1000*1000 area squares). if (nargin==3), @@ -43,8 +43,8 @@ [elements,x,y,segments,segmentmarkers]=TriMesh(domainname,riftname,area,'yes'); - %check that all the created grids belong to at least one element + %check that all the created nodes belong to at least one element orphan=find(~ismember([1:length(x)],sort(unique(elements(:))))); for i=1:length(orphan), - %get rid of the orphan grid i + %get rid of the orphan node i %update x and y x=[x(1:orphan(i)-(i-1)-1); x(orphan(i)-(i-1)+1:end)]; @@ -70,14 +70,14 @@ %Fill in rest of fields: md.numberofelements=length(md.elements); -md.numberofgrids=length(md.x); -md.z=zeros(md.numberofgrids,1); -md.gridonboundary=zeros(md.numberofgrids,1); md.gridonboundary(md.segments(:,1:2))=1; -md.gridonbed=ones(md.numberofgrids,1); -md.gridonsurface=ones(md.numberofgrids,1); +md.numberofnodes=length(md.x); +md.z=zeros(md.numberofnodes,1); +md.nodeonboundary=zeros(md.numberofnodes,1); md.nodeonboundary(md.segments(:,1:2))=1; +md.nodeonbed=ones(md.numberofnodes,1); +md.nodeonsurface=ones(md.numberofnodes,1); md.elementonbed=ones(md.numberofelements,1); md.elementonsurface=ones(md.numberofelements,1); %Now, build the connectivity tables for this mesh. -md.nodeconnectivity=NodeConnectivity(md.elements,md.numberofgrids); +md.nodeconnectivity=NodeConnectivity(md.elements,md.numberofnodes); md.elementconnectivity=ElementConnectivity(md.elements,md.nodeconnectivity); Index: /issm/trunk/src/m/model/mesh/meshadaptation.m =================================================================== --- /issm/trunk/src/m/model/mesh/meshadaptation.m (revision 8297) +++ /issm/trunk/src/m/model/mesh/meshadaptation.m (revision 8298) @@ -17,6 +17,6 @@ error('meshadaptation error message: adaptation for 3d meshes not implemented yet') end -if length(field)~=md.numberofgrids - error('meshadaptation error message: input field length shoud be numberofgrids') +if length(field)~=md.numberofnodes + error('meshadaptation error message: input field length shoud be numberofnodes') end @@ -25,8 +25,8 @@ %initialization index=md.elements; -numberofgrids=md.numberofgrids; +numberofnodes=md.numberofnodes; numberofelements=md.numberofelements; -gradx=zeros(numberofgrids,1); -grady=zeros(numberofgrids,1); +gradx=zeros(numberofnodes,1); +grady=zeros(numberofnodes,1); metric=zeros(numberofelements,1); @@ -48,10 +48,10 @@ grad_ely=sum(field(index).*beta,2); -%update weights that holds the volume of all the element holding the grid i -weights=sparse(line,ones(linesize,1),repmat(areas,3,1),numberofgrids,1); +%update weights that holds the volume of all the element holding the node i +weights=sparse(line,ones(linesize,1),repmat(areas,3,1),numberofnodes,1); -%Compute gradient for each grid (average of the elements around) -gradx=sparse(line,ones(linesize,1),repmat(areas.*grad_elx,3,1),numberofgrids,1); -grady=sparse(line,ones(linesize,1),repmat(areas.*grad_ely,3,1),numberofgrids,1); +%Compute gradient for each node (average of the elements around) +gradx=sparse(line,ones(linesize,1),repmat(areas.*grad_elx,3,1),numberofnodes,1); +grady=sparse(line,ones(linesize,1),repmat(areas.*grad_ely,3,1),numberofnodes,1); gradx=gradx./weights; grady=grady./weights; Index: /issm/trunk/src/m/model/mesh/meshbamg.m =================================================================== --- /issm/trunk/src/m/model/mesh/meshbamg.m (revision 8297) +++ /issm/trunk/src/m/model/mesh/meshbamg.m (revision 8298) @@ -76,5 +76,5 @@ %interpolate velocities onto mesh disp(' interpolating velocities...'); - if strcmpi(NamesV.interp,'grid'), + if strcmpi(NamesV.interp,'node'), vx_obs=InterpFromGridToMesh(Vel.(NamesV.xname),Vel.(NamesV.yname),Vel.(NamesV.vxname),md.x,md.y,0); vy_obs=InterpFromGridToMesh(Vel.(NamesV.xname),Vel.(NamesV.yname),Vel.(NamesV.vyname),md.x,md.y,0); @@ -87,5 +87,5 @@ if thicknesspresent, disp(' interpolating thickness...'); - if strcmpi(NamesH.interp,'grid'), + if strcmpi(NamesH.interp,'node'), h=InterpFromGridToMesh(Thi.(NamesH.xname),Thi.(NamesH.yname),Thi.(NamesH.dataname),md.x,md.y,0); else @@ -95,11 +95,11 @@ end - %set gridonwater field + %set nodeonwater field if ~strcmp(groundeddomain,'N/A'), - gridground=ContourToMesh(md.elements,md.x,md.y,groundeddomain,'node',2); - md.gridonwater=ones(md.numberofgrids,1); - md.gridonwater(find(gridground))=0; + nodeground=ContourToMesh(md.elements,md.x,md.y,groundeddomain,'node',2); + md.nodeonwater=ones(md.numberofnodes,1); + md.nodeonwater(find(nodeground))=0; else - md.gridonwater=zeros(md.numberofgrids,1); + md.nodeonwater=zeros(md.numberofnodes,1); end Index: /issm/trunk/src/m/model/mesh/meshconvert.m =================================================================== --- /issm/trunk/src/m/model/mesh/meshconvert.m (revision 8297) +++ /issm/trunk/src/m/model/mesh/meshconvert.m (revision 8298) @@ -38,11 +38,11 @@ md.dim=2; md.numberofelements=size(md.elements,1); -md.numberofgrids=length(md.x); -md.z=zeros(md.numberofgrids,1); -md.gridonbed=ones(md.numberofgrids,1); -md.gridonwater=zeros(md.numberofgrids,1); -md.gridonsurface=ones(md.numberofgrids,1); +md.numberofnodes=length(md.x); +md.z=zeros(md.numberofnodes,1); +md.nodeonbed=ones(md.numberofnodes,1); +md.nodeonwater=zeros(md.numberofnodes,1); +md.nodeonsurface=ones(md.numberofnodes,1); md.elementonbed=ones(md.numberofelements,1); md.elementonsurface=ones(md.numberofelements,1); -md.gridonboundary=zeros(md.numberofgrids,1); md.gridonboundary(md.segments(:,1:2))=1; +md.nodeonboundary=zeros(md.numberofnodes,1); md.nodeonboundary(md.segments(:,1:2))=1; md.counter=1; Index: /issm/trunk/src/m/model/mesh/meshnodensity.m =================================================================== --- /issm/trunk/src/m/model/mesh/meshnodensity.m (revision 8297) +++ /issm/trunk/src/m/model/mesh/meshnodensity.m (revision 8298) @@ -29,8 +29,8 @@ [elements,x,y,segments,segmentmarkers]=TriMeshNoDensity(domainname,riftname); - %check that all the created grids belong to at least one element + %check that all the created nodes belong to at least one element orphan=find(~ismember([1:length(x)],sort(unique(elements(:))))); for i=1:length(orphan), - %get rid of the orphan grid i + %get rid of the orphan node i %update x and y x=[x(1:orphan(i)-(i-1)-1); x(orphan(i)-(i-1)+1:end)]; @@ -56,14 +56,14 @@ %Fill in rest of fields: md.numberofelements=length(md.elements); -md.numberofgrids=length(md.x); -md.z=zeros(md.numberofgrids,1); -md.gridonboundary=zeros(md.numberofgrids,1); md.gridonboundary(md.segments(:,1:2))=1; -md.gridonbed=ones(md.numberofgrids,1); -md.gridonsurface=ones(md.numberofgrids,1); +md.numberofnodes=length(md.x); +md.z=zeros(md.numberofnodes,1); +md.nodeonboundary=zeros(md.numberofnodes,1); md.nodeonboundary(md.segments(:,1:2))=1; +md.nodeonbed=ones(md.numberofnodes,1); +md.nodeonsurface=ones(md.numberofnodes,1); md.elementonbed=ones(md.numberofelements,1); md.elementonsurface=ones(md.numberofelements,1); %Now, build the connectivity tables for this mesh. -md.nodeconnectivity=NodeConnectivity(md.elements,md.numberofgrids); +md.nodeconnectivity=NodeConnectivity(md.elements,md.numberofnodes); md.elementconnectivity=ElementConnectivity(md.elements,md.nodeconnectivity); Index: /issm/trunk/src/m/model/mesh/meshrefine.m =================================================================== --- /issm/trunk/src/m/model/mesh/meshrefine.m (revision 8297) +++ /issm/trunk/src/m/model/mesh/meshrefine.m (revision 8298) @@ -21,14 +21,14 @@ %Fill in rest of fields: md.numberofelements=length(md.elements); -md.numberofgrids=length(md.x); -md.z=zeros(md.numberofgrids,1); -md.gridonboundary=zeros(md.numberofgrids,1); md.gridonboundary(md.segments(:,1:2))=1; -md.gridonbed=ones(md.numberofgrids,1); -md.gridonsurface=ones(md.numberofgrids,1); +md.numberofnodes=length(md.x); +md.z=zeros(md.numberofnodes,1); +md.nodeonboundary=zeros(md.numberofnodes,1); md.nodeonboundary(md.segments(:,1:2))=1; +md.nodeonbed=ones(md.numberofnodes,1); +md.nodeonsurface=ones(md.numberofnodes,1); md.elementonbed=ones(md.numberofelements,1); md.elementonsurface=ones(md.numberofelements,1); %Now, build the connectivity tables for this mesh. -md.nodeconnectivity=NodeConnectivity(md.elements,md.numberofgrids); +md.nodeconnectivity=NodeConnectivity(md.elements,md.numberofnodes); md.elementconnectivity=ElementConnectivity(md.elements,md.nodeconnectivity); Index: /issm/trunk/src/m/model/mesh/meshyams.m =================================================================== --- /issm/trunk/src/m/model/mesh/meshyams.m (revision 8297) +++ /issm/trunk/src/m/model/mesh/meshyams.m (revision 8298) @@ -70,5 +70,5 @@ %interpolate velocities onto mesh disp(' interpolating velocities...'); - if strcmpi(Names.interp,'grid'), + if strcmpi(Names.interp,'node'), vx_obs=InterpFromGridToMesh(Vel.(Names.xname),Vel.(Names.yname),Vel.(Names.vxname),md.x,md.y,0); vy_obs=InterpFromGridToMesh(Vel.(Names.xname),Vel.(Names.yname),Vel.(Names.vyname),md.x,md.y,0); @@ -79,11 +79,11 @@ field=sqrt(vx_obs.^2+vy_obs.^2); - %set gridonwater field + %set nodeonwater field if ~strcmp(groundeddomain,'N/A'), - gridground=ContourToMesh(md.elements,md.x,md.y,groundeddomain,'node',2); - md.gridonwater=ones(md.numberofgrids,1); - md.gridonwater(find(gridground))=0; + nodeground=ContourToMesh(md.elements,md.x,md.y,groundeddomain,'node',2); + md.nodeonwater=ones(md.numberofnodes,1); + md.nodeonwater(find(nodeground))=0; else - md.gridonwater=zeros(md.numberofgrids,1); + md.nodeonwater=zeros(md.numberofnodes,1); end @@ -95,5 +95,5 @@ %rifts, because the segments are used in YamsCall to freeze the rifts elements during refinement. if md.numrifts, - md.nodeconnectivity=NodeConnectivity(md.elements,md.numberofgrids); + md.nodeconnectivity=NodeConnectivity(md.elements,md.numberofnodes); md.elementconnectivity=ElementConnectivity(md.elements,md.nodeconnectivity); md.segments=findsegments(md); @@ -106,25 +106,25 @@ %Now, build the connectivity tables for this mesh. -md.nodeconnectivity=NodeConnectivity(md.elements,md.numberofgrids); +md.nodeconnectivity=NodeConnectivity(md.elements,md.numberofnodes); md.elementconnectivity=ElementConnectivity(md.elements,md.nodeconnectivity); %recreate segments md.segments=findsegments(md); -md.gridonboundary=zeros(md.numberofgrids,1); md.gridonboundary(md.segments(:,1:2))=1; +md.nodeonboundary=zeros(md.numberofnodes,1); md.nodeonboundary(md.segments(:,1:2))=1; %Fill in rest of fields: -md.z=zeros(md.numberofgrids,1); -md.gridonbed=ones(md.numberofgrids,1); -md.gridonsurface=ones(md.numberofgrids,1); +md.z=zeros(md.numberofnodes,1); +md.nodeonbed=ones(md.numberofnodes,1); +md.nodeonsurface=ones(md.numberofnodes,1); md.elementonbed=ones(md.numberofelements,1); md.elementonsurface=ones(md.numberofelements,1); if ~strcmp(groundeddomain,'N/A'), - gridground=ContourToMesh(md.elements,md.x,md.y,groundeddomain,'node',2); - md.gridonwater=ones(md.numberofgrids,1); - md.gridonwater(find(gridground))=0; + nodeground=ContourToMesh(md.elements,md.x,md.y,groundeddomain,'node',2); + md.nodeonwater=ones(md.numberofnodes,1); + md.nodeonwater(find(nodeground))=0; else - md.gridonwater=zeros(md.numberofgrids,1); + md.nodeonwater=zeros(md.numberofnodes,1); end -if strcmpi(Names.interp,'grid'), +if strcmpi(Names.interp,'node'), md.vx_obs=InterpFromGridToMesh(Vel.(Names.xname),Vel.(Names.yname),Vel.(Names.vxname),md.x,md.y,0); md.vy_obs=InterpFromGridToMesh(Vel.(Names.xname),Vel.(Names.yname),Vel.(Names.vyname),md.x,md.y,0); Index: /issm/trunk/src/m/model/mesh/reorder.m =================================================================== --- /issm/trunk/src/m/model/mesh/reorder.m (revision 8297) +++ /issm/trunk/src/m/model/mesh/reorder.m (revision 8298) @@ -19,12 +19,12 @@ %reorder nodes -newgrids=randperm(md.numberofgrids)'; -tnewgrids=zeros(md.numberofgrids,1);tnewgrids(newgrids)=[1:md.numberofgrids]'; +newnodes=randperm(md.numberofnodes)'; +tnewnodes=zeros(md.numberofnodes,1);tnewnodes(newnodes)=[1:md.numberofnodes]'; %update all fields -md.elements=tnewgrids(md.elements(newelements,:)); -md.segments=[tnewgrids(md.segments(:,1)) tnewgrids(md.segments(:,2)) tnewelements(md.segments(:,3))]; -md.x=md.x(newgrids); -md.y=md.y(newgrids); -md.z=md.z(newgrids); -md.gridonboundary=zeros(md.numberofgrids,1); md.gridonboundary(md.segments(:,1:2))=1; +md.elements=tnewnodes(md.elements(newelements,:)); +md.segments=[tnewnodes(md.segments(:,1)) tnewnodes(md.segments(:,2)) tnewelements(md.segments(:,3))]; +md.x=md.x(newnodes); +md.y=md.y(newnodes); +md.z=md.z(newnodes); +md.nodeonboundary=zeros(md.numberofnodes,1); md.nodeonboundary(md.segments(:,1:2))=1; Index: /issm/trunk/src/m/model/mesh/rifts/meshaddrifts.m =================================================================== --- /issm/trunk/src/m/model/mesh/rifts/meshaddrifts.m (revision 8297) +++ /issm/trunk/src/m/model/mesh/rifts/meshaddrifts.m (revision 8298) @@ -56,6 +56,6 @@ %plug md2 mesh into md mesh: - [md.elements,md.x,md.y,md.z,md.numberofelements,md.numberofgrids,elconv,nodeconv,elconv2,nodeconv2]=meshplug(md.elements,md.x,md.y,md.z,... - md2.elements,md2.x,md2.y,md2.z,md2.extractedgrids,md2.extractedelements,domain_index); + [md.elements,md.x,md.y,md.z,md.numberofelements,md.numberofnodes,elconv,nodeconv,elconv2,nodeconv2]=meshplug(md.elements,md.x,md.y,md.z,... + md2.elements,md2.x,md2.y,md2.z,md2.extractednodes,md2.extractedelements,domain_index); %update md2 rifts using elconv and nodeconv, and plug them into md: @@ -80,12 +80,12 @@ %finish up "a la" mesh.h -md.gridonboundary=zeros(md.numberofgrids,1); md.gridonboundary(md.segments(:,1:2))=1; -md.gridonbed=ones(md.numberofgrids,1); -md.gridonsurface=ones(md.numberofgrids,1); +md.nodeonboundary=zeros(md.numberofnodes,1); md.nodeonboundary(md.segments(:,1:2))=1; +md.nodeonbed=ones(md.numberofnodes,1); +md.nodeonsurface=ones(md.numberofnodes,1); md.elementonbed=ones(md.numberofelements,1); md.elementonsurface=ones(md.numberofelements,1); %Now, build the connectivity tables for this mesh. -md.nodeconnectivity=NodeConnectivity(md.elements,md.numberofgrids); +md.nodeconnectivity=NodeConnectivity(md.elements,md.numberofnodes); md.elementconnectivity=ElementConnectivity(md.elements,md.nodeconnectivity); Index: /issm/trunk/src/m/model/mesh/rifts/meshplug.m =================================================================== --- /issm/trunk/src/m/model/mesh/rifts/meshplug.m (revision 8297) +++ /issm/trunk/src/m/model/mesh/rifts/meshplug.m (revision 8298) @@ -1,3 +1,3 @@ -function [elements,x,y,z,numberofelements,numberofgrids,elconv,nodeconv,elconv2,nodeconv2]=meshplug(elements,x,y,z,elements2,x2,y2,z2,extractedgrids,extractedelements,domain); +function [elements,x,y,z,numberofelements,numberofnodes,elconv,nodeconv,elconv2,nodeconv2]=meshplug(elements,x,y,z,elements2,x2,y2,z2,extractednodes,extractedelements,domain); %MESHPLUG - embed mesh into another one % See also meshaddrifts @@ -22,9 +22,9 @@ nodeconv2=(size(x,1)+1):(size(x,1)+size(x2,1)); nodeconv2=nodeconv2'; -extractedgrids_minusborder=extractedgrids; -extractedgrids_minusborder(domain)=[]; +extractednodes_minusborder=extractednodes; +extractednodes_minusborder(domain)=[]; -x(extractedgrids_minusborder)=NaN; -y(extractedgrids_minusborder)=NaN; +x(extractednodes_minusborder)=NaN; +y(extractednodes_minusborder)=NaN; %now, plug md2 mesh: @@ -33,17 +33,17 @@ elements2=elements2+length(x); -%NaN border grids in second mesh +%NaN border nodes in second mesh x2(1:length(domain))=NaN; y2(1:length(domain))=NaN; -%redirect border grids in elements2 to elements +%redirect border nodes in elements2 to elements for i=1:length(domain), pos=find(elements2==(i+length(x))); - elements2(pos)=extractedgrids(domain(i)); + elements2(pos)=extractednodes(domain(i)); end %same deal for nodeconv2: for i=1:length(domain), - nodeconv2(i)=extractedgrids(domain(i)); + nodeconv2(i)=extractednodes(domain(i)); end @@ -53,5 +53,5 @@ -%now, increase number of grids +%now, increase number of nodes x=[x; x2]; y=[y; y2]; @@ -62,28 +62,28 @@ pos=find(isnan(x)); - grid=pos(1); + node=pos(1); - %collapse grid - x(grid)=[]; - y(grid)=[]; - z(grid)=[]; + %collapse node + x(node)=[]; + y(node)=[]; + z(node)=[]; - %renumber all grids > grid in elements - pos=find(elements>grid); + %renumber all nodes > node in elements + pos=find(elements>node); elements(pos)=elements(pos)-1; %same deal for nodeconv2: - pos=find(nodeconv2>grid); + pos=find(nodeconv2>node); nodeconv2(pos)=nodeconv2(pos)-1; end -numberofgrids=length(x); +numberofnodes=length(x); numberofelements=length(elements); %finish nodeconv: -temp_nodeconv=nodeconv; temp_nodeconv(extractedgrids_minusborder)=[]; +temp_nodeconv=nodeconv; temp_nodeconv(extractednodes_minusborder)=[]; temp_nodeconvnum=1:length(temp_nodeconv); nodeconv(temp_nodeconv)=temp_nodeconvnum; -nodeconv(extractedgrids_minusborder)=NaN; +nodeconv(extractednodes_minusborder)=NaN; Index: /issm/trunk/src/m/model/mesh/rifts/meshprocessoutsiderifts.m =================================================================== --- /issm/trunk/src/m/model/mesh/rifts/meshprocessoutsiderifts.m (revision 8297) +++ /issm/trunk/src/m/model/mesh/rifts/meshprocessoutsiderifts.m (revision 8298) @@ -23,12 +23,12 @@ tip=outsidetips(j); %find tip in the segments, take first segment (there should be 2) that holds tip, - %and grid_connected_to_tip is the other node on this segment: + %and node_connected_to_tip is the other node on this segment: tipindex=find(rift.segments(:,1)==tip); if length(tipindex), tipindex=tipindex(1); - grid_connected_to_tip=rift.segments(tipindex,2); + node_connected_to_tip=rift.segments(tipindex,2); else tipindex=find(rift.segments(:,2)==tip); tipindex=tipindex(1); - grid_connected_to_tip=rift.segments(tipindex,1); + node_connected_to_tip=rift.segments(tipindex,1); end @@ -37,5 +37,5 @@ %side of the rift. A=tip; - B=grid_connected_to_tip; + B=node_connected_to_tip; elements=[]; @@ -58,5 +58,5 @@ md.x=[md.x;md.x(tip)]; md.y=[md.y;md.y(tip)]; - md.numberofgrids=num; + md.numberofnodes=num; %replace tip in elements @@ -84,11 +84,11 @@ %Fill in rest of fields: md.numberofelements=length(md.elements); -md.numberofgrids=length(md.x); -md.z=zeros(md.numberofgrids,1); -md.gridonboundary=zeros(length(md.x),1); md.gridonboundary(md.segments(:,1:2))=1; +md.numberofnodes=length(md.x); +md.z=zeros(md.numberofnodes,1); +md.nodeonboundary=zeros(length(md.x),1); md.nodeonboundary(md.segments(:,1:2))=1; md.numrifts=length(md.rifts); md.elements_type=3*ones(md.numberofelements,1); -md.gridonbed=ones(md.numberofgrids,1); -md.gridonsurface=ones(md.numberofgrids,1); +md.nodeonbed=ones(md.numberofnodes,1); +md.nodeonsurface=ones(md.numberofnodes,1); md.elementonbed=ones(md.numberofelements,1); md.elementonsurface=ones(md.numberofelements,1); Index: /issm/trunk/src/m/model/mesh/rifts/meshprocessrifts.m =================================================================== --- /issm/trunk/src/m/model/mesh/rifts/meshprocessrifts.m (revision 8297) +++ /issm/trunk/src/m/model/mesh/rifts/meshprocessrifts.m (revision 8298) @@ -29,11 +29,11 @@ %Fill in rest of fields: md.numberofelements=length(md.elements); -md.numberofgrids=length(md.x); -md.z=zeros(md.numberofgrids,1); -md.gridonboundary=zeros(length(md.x),1); md.gridonboundary(md.segments(:,1:2))=1; +md.numberofnodes=length(md.x); +md.z=zeros(md.numberofnodes,1); +md.nodeonboundary=zeros(length(md.x),1); md.nodeonboundary(md.segments(:,1:2))=1; md.numrifts=length(md.rifts); md.elements_type=3*ones(md.numberofelements,1); -md.gridonbed=ones(md.numberofgrids,1); -md.gridonsurface=ones(md.numberofgrids,1); +md.nodeonbed=ones(md.numberofnodes,1); +md.nodeonsurface=ones(md.numberofnodes,1); md.elementonbed=ones(md.numberofelements,1); md.elementonsurface=ones(md.numberofelements,1); Index: /issm/trunk/src/m/model/mesh/rifts/rifttipsrefine.m =================================================================== --- /issm/trunk/src/m/model/mesh/rifts/rifttipsrefine.m (revision 8297) +++ /issm/trunk/src/m/model/mesh/rifts/rifttipsrefine.m (revision 8298) @@ -5,5 +5,5 @@ % md=rifttipsrefine(md,filename,resolution,circleradius); -numberofgrids=50; +numberofnodes=50; %take rifts, and create refinement circles around tips @@ -15,6 +15,6 @@ tip2=[rifts(i).x(end) rifts(i).y(end)]; %create circle around tip - expcreatecircle('Circle1.exp',tip1(1),tip1(2),circleradius,numberofgrids); - expcreatecircle('Circle2.exp',tip2(1),tip2(2),circleradius,numberofgrids); + expcreatecircle('Circle1.exp',tip1(1),tip1(2),circleradius,numberofnodes); + expcreatecircle('Circle2.exp',tip2(1),tip2(2),circleradius,numberofnodes); !cat Circles.exp Circle1.exp Circle2.exp > Circles2.exp !mv Circles2.exp Circles.exp Index: /issm/trunk/src/m/model/modeldefault/defaultparams.m =================================================================== --- /issm/trunk/src/m/model/modeldefault/defaultparams.m (revision 8297) +++ /issm/trunk/src/m/model/modeldefault/defaultparams.m (revision 8298) @@ -47,5 +47,5 @@ %drag md.drag or stress md.drag_type=2; %0 none 1 plastic 2 viscous - md.drag_coefficient=300*ones(md.numberofgrids,1); %q=1. + md.drag_coefficient=300*ones(md.numberofnodes,1); %q=1. %zones of high md.drag @@ -89,10 +89,10 @@ disp(' creating accumulation rates'); - md.accumulation_rate=ones(md.numberofgrids,1); %1m/a + md.accumulation_rate=ones(md.numberofnodes,1); %1m/a %Deal with boundary conditions: disp(' thermal model'); - md.melting_rate=zeros(md.numberofgrids,1); + md.melting_rate=zeros(md.numberofnodes,1); md.observed_temperature=md.temperature; Index: /issm/trunk/src/m/model/modelextract.m =================================================================== --- /issm/trunk/src/m/model/modelextract.m (revision 8297) +++ /issm/trunk/src/m/model/modelextract.m (revision 8298) @@ -38,7 +38,7 @@ %kick out all elements with 3 dirichlets spc_elem=find(~flag_elem); -spc_grid=sort(unique(md1.elements(spc_elem,:))); -flag=ones(md1.numberofgrids,1); -flag(spc_grid)=0; +spc_node=sort(unique(md1.elements(spc_elem,:))); +flag=ones(md1.numberofnodes,1); +flag(spc_node)=0; pos=find(sum(flag(md1.elements),2)==0); flag_elem(pos)=0; @@ -46,30 +46,30 @@ %extracted elements and nodes lists pos_elem=find(flag_elem); -pos_grid=sort(unique(md1.elements(pos_elem,:))); +pos_node=sort(unique(md1.elements(pos_elem,:))); %keep track of some fields -numberofgrids1=md1.numberofgrids; +numberofnodes1=md1.numberofnodes; numberofelements1=md1.numberofelements; -numberofgrids2=length(pos_grid); +numberofnodes2=length(pos_node); numberofelements2=length(pos_elem); -flag_grid=zeros(numberofgrids1,1); -flag_grid(pos_grid)=1; - -%Create Pelem and Pgrid (transform old grids in new grids and same thing for the elements) +flag_node=zeros(numberofnodes1,1); +flag_node(pos_node)=1; + +%Create Pelem and Pnode (transform old nodes in new nodes and same thing for the elements) Pelem=zeros(numberofelements1,1); Pelem(pos_elem)=[1:numberofelements2]'; -Pgrid=zeros(numberofgrids1,1); -Pgrid(pos_grid)=[1:numberofgrids2]'; - -%renumber the elements (some grid won't exist anymore) +Pnode=zeros(numberofnodes1,1); +Pnode(pos_node)=[1:numberofnodes2]'; + +%renumber the elements (some node won't exist anymore) elements_1=md1.elements; elements_2=elements_1(pos_elem,:); -elements_2(:,1)=Pgrid(elements_2(:,1)); -elements_2(:,2)=Pgrid(elements_2(:,2)); -elements_2(:,3)=Pgrid(elements_2(:,3)); +elements_2(:,1)=Pnode(elements_2(:,1)); +elements_2(:,2)=Pnode(elements_2(:,2)); +elements_2(:,3)=Pnode(elements_2(:,3)); if md1.dim==3, - elements_2(:,4)=Pgrid(elements_2(:,4)); - elements_2(:,5)=Pgrid(elements_2(:,5)); - elements_2(:,6)=Pgrid(elements_2(:,6)); + elements_2(:,4)=Pnode(elements_2(:,4)); + elements_2(:,5)=Pnode(elements_2(:,5)); + elements_2(:,6)=Pnode(elements_2(:,6)); end @@ -89,7 +89,7 @@ fieldsize=size(field); - %size = number of grids * n - if fieldsize(1)==numberofgrids1 - md2.(model_fields(i))=field(pos_grid,:); + %size = number of nodes * n + if fieldsize(1)==numberofnodes1 + md2.(model_fields(i))=field(pos_node,:); %size = number of elements * n @@ -103,16 +103,16 @@ %Mesh md2.numberofelements=numberofelements2; - md2.numberofgrids=numberofgrids2; + md2.numberofnodes=numberofnodes2; md2.elements=elements_2; %uppernodes lowernodes if md1.dim==3 - md2.uppergrids=md1.uppergrids(pos_grid); - pos=find(~isnan(md2.uppergrids)); - md2.uppergrids(pos)=Pgrid(md2.uppergrids(pos)); - - md2.lowergrids=md1.lowergrids(pos_grid); - pos=find(~isnan(md2.lowergrids)); - md2.lowergrids(pos)=Pgrid(md2.lowergrids(pos)); + md2.uppernodes=md1.uppernodes(pos_node); + pos=find(~isnan(md2.uppernodes)); + md2.uppernodes(pos)=Pnode(md2.uppernodes(pos)); + + md2.lowernodes=md1.lowernodes(pos_node); + pos=find(~isnan(md2.lowernodes)); + md2.lowernodes(pos)=Pnode(md2.lowernodes(pos)); md2.upperelements=md1.upperelements(pos_elem); @@ -129,18 +129,18 @@ flag_elem_2d=flag_elem(1:md1.numberofelements2d); pos_elem_2d=find(flag_elem_2d); - flag_grid_2d=flag_grid(1:md1.numberofgrids2d); - pos_grid_2d=find(flag_grid_2d); + flag_node_2d=flag_node(1:md1.numberofnodes2d); + pos_node_2d=find(flag_node_2d); md2.numberofelements2d=length(pos_elem_2d); - md2.numberofgrids2d=length(pos_grid_2d); + md2.numberofnodes2d=length(pos_node_2d); md2.elements2d=md1.elements2d(pos_elem_2d,:); - md2.elements2d(:,1)=Pgrid(md2.elements2d(:,1)); - md2.elements2d(:,2)=Pgrid(md2.elements2d(:,2)); - md2.elements2d(:,3)=Pgrid(md2.elements2d(:,3)); + md2.elements2d(:,1)=Pnode(md2.elements2d(:,1)); + md2.elements2d(:,2)=Pnode(md2.elements2d(:,2)); + md2.elements2d(:,3)=Pnode(md2.elements2d(:,3)); if ~isnan(md2.elements_type2d), md2.elements_type2d=md1.elements_type2d(pos_elem_2d); end; - md2.x2d=md1.x(pos_grid_2d); - md2.y2d=md1.y(pos_grid_2d); - md2.z2d=md1.z(pos_grid_2d); + md2.x2d=md1.x(pos_node_2d); + md2.y2d=md1.y(pos_node_2d); + md2.z2d=md1.z(pos_node_2d); end @@ -149,6 +149,6 @@ %renumber first two columns pos=find(~isnan(md2.edges(:,4))); - md2.edges(: ,1)=Pgrid(md2.edges(:,1)); - md2.edges(: ,2)=Pgrid(md2.edges(:,2)); + md2.edges(: ,1)=Pnode(md2.edges(:,1)); + md2.edges(: ,2)=Pnode(md2.edges(:,2)); md2.edges(: ,3)=Pelem(md2.edges(:,3)); md2.edges(pos,4)=Pelem(md2.edges(pos,4)); @@ -175,5 +175,5 @@ if ~isnan(md2.penalties), for i=1:size(md1.penalties,1); - md2.penalties(i,:)=Pgrid(md1.penalties(i,:)); + md2.penalties(i,:)=Pnode(md1.penalties(i,:)); end md2.penalties=md2.penalties(find(md2.penalties(:,1)),:); @@ -182,8 +182,8 @@ %recreate segments if md1.dim==2 - md2.nodeconnectivity=NodeConnectivity(md2.elements,md2.numberofgrids); + md2.nodeconnectivity=NodeConnectivity(md2.elements,md2.numberofnodes); md2.elementconnectivity=ElementConnectivity(md2.elements,md2.nodeconnectivity); md2.segments=contourenvelope(md2); - md2.gridonboundary=zeros(numberofgrids2,1); md2.gridonboundary(md2.segments(:,1:2))=1; + md2.nodeonboundary=zeros(numberofnodes2,1); md2.nodeonboundary(md2.segments(:,1:2))=1; end @@ -191,15 +191,15 @@ %Catch the elements that have not been extracted orphans_elem=find(~flag_elem); - orphans_grid=unique(md1.elements(orphans_elem,:))'; - %Figure out which grid are on the boundary between md2 and md1 - gridstoflag1=intersect(orphans_grid,pos_grid); - gridstoflag2=Pgrid(gridstoflag1); + orphans_node=unique(md1.elements(orphans_elem,:))'; + %Figure out which node are on the boundary between md2 and md1 + nodestoflag1=intersect(orphans_node,pos_node); + nodestoflag2=Pnode(nodestoflag1); if ~isnan(md1.spcvelocity), - md2.spcvelocity(gridstoflag2,1:3)=1; + md2.spcvelocity(nodestoflag2,1:3)=1; if ~isnan(md1.vx_obs) & ~isnan(md1.vy_obs) - md2.spcvelocity(gridstoflag2,4)=md2.vx_obs(gridstoflag2); - md2.spcvelocity(gridstoflag2,5)=md2.vy_obs(gridstoflag2); + md2.spcvelocity(nodestoflag2,4)=md2.vx_obs(nodestoflag2); + md2.spcvelocity(nodestoflag2,5)=md2.vy_obs(nodestoflag2); else - md2.spcvelocity(gridstoflag2,4:5)=zeros(length(gridstoflag2),2); + md2.spcvelocity(nodestoflag2,4:5)=zeros(length(nodestoflag2),2); disp(' ') disp('!! modelextract warning: spc values should be checked !!') @@ -208,9 +208,9 @@ end if ~isnan(md1.spctemperature), - md2.spctemperature(gridstoflag2,1)=1; + md2.spctemperature(nodestoflag2,1)=1; if ~isnan(md1.observed_temperature) - md2.spctemperature(gridstoflag2,2)=md2.observed_temperature(gridstoflag2); + md2.spctemperature(nodestoflag2,2)=md2.observed_temperature(nodestoflag2); else - md2.spctemperature(gridstoflag2,2)=zeros(length(gridstoflag2),2); + md2.spctemperature(nodestoflag2,2)=zeros(length(nodestoflag2),2); disp(' ') disp('!! modelextract warning: spc values should be checked !!') @@ -221,10 +221,10 @@ %Diagnostic if ~isnan(md2.pressureload) - md2.pressureload(:,1)=Pgrid(md1.pressureload(:,1)); - md2.pressureload(:,2)=Pgrid(md1.pressureload(:,2)); + md2.pressureload(:,1)=Pnode(md1.pressureload(:,1)); + md2.pressureload(:,2)=Pnode(md1.pressureload(:,2)); md2.pressureload(:,end-1)=Pelem(md1.pressureload(:,end-1)); if md1.dim==3 - md2.pressureload(:,3)=Pgrid(md1.pressureload(:,3)); - md2.pressureload(:,4)=Pgrid(md1.pressureload(:,4)); + md2.pressureload(:,3)=Pnode(md1.pressureload(:,3)); + md2.pressureload(:,4)=Pnode(md1.pressureload(:,4)); end md2.pressureload=md2.pressureload(find(md2.pressureload(:,1) & md2.pressureload(:,2) & md2.pressureload(:,end)),:); @@ -240,6 +240,6 @@ for j=1:length(solutionsubfields), field=md1.results.(solutionfields(i)).(solutionsubfields(j)); - if length(field)==numberofgrids1, - md2.results.(solutionfields(i)).(solutionsubfields(j))=field(pos_grid); + if length(field)==numberofnodes1, + md2.results.(solutionfields(i)).(solutionsubfields(j))=field(pos_node); elseif length(field)==numberofelements1, md2.results.(solutionfields(i)).(solutionsubfields(j))=field(pos_elem); @@ -260,5 +260,5 @@ md2.strainrate=NaN; -%Keep track of pos_grid and pos_elem -md2.extractedgrids=pos_grid; +%Keep track of pos_node and pos_elem +md2.extractednodes=pos_node; md2.extractedelements=pos_elem; Index: /issm/trunk/src/m/model/outflow.m =================================================================== --- /issm/trunk/src/m/model/outflow.m (revision 8297) +++ /issm/trunk/src/m/model/outflow.m (revision 8298) @@ -11,4 +11,4 @@ VdotN=Vx.*Nx+Vy.*Ny; -flag=zeros(md.numberofgrids,1); +flag=zeros(md.numberofnodes,1); flag(A(find(VdotN>0)))=1; Index: /issm/trunk/src/m/model/parametercontroloptimization.m =================================================================== --- /issm/trunk/src/m/model/parametercontroloptimization.m (revision 8297) +++ /issm/trunk/src/m/model/parametercontroloptimization.m (revision 8298) @@ -35,5 +35,5 @@ md2.cm_jump=0.99*ones(md2.nsteps,1); md2.control_analysis=1; -md2.weights=ones(md2.numberofgrids,1); +md2.weights=ones(md2.numberofnodes,1); %loop over the set of parameters Index: /issm/trunk/src/m/model/parameterization/parametercontrolB.m =================================================================== --- /issm/trunk/src/m/model/parameterization/parametercontrolB.m (revision 8297) +++ /issm/trunk/src/m/model/parameterization/parametercontrolB.m (revision 8298) @@ -24,7 +24,7 @@ %weights -weights=getfieldvalue(options,'weights',ones(md.numberofgrids,1)); -if (length(weights)~=md.numberofgrids) - md.weights=ones(md.numberofgrids,1); +weights=getfieldvalue(options,'weights',ones(md.numberofnodes,1)); +if (length(weights)~=md.numberofnodes) + md.weights=ones(md.numberofnodes,1); else md.weights=weights; Index: /issm/trunk/src/m/model/parameterization/parametercontroldrag.m =================================================================== --- /issm/trunk/src/m/model/parameterization/parametercontroldrag.m (revision 8297) +++ /issm/trunk/src/m/model/parameterization/parametercontroldrag.m (revision 8298) @@ -24,7 +24,7 @@ %weights -weights=getfieldvalue(options,'weights',ones(md.numberofgrids,1)); -if (length(weights)~=md.numberofgrids) - md.weights=ones(md.numberofgrids,1); +weights=getfieldvalue(options,'weights',ones(md.numberofnodes,1)); +if (length(weights)~=md.numberofnodes) + md.weights=ones(md.numberofnodes,1); else md.weights=weights; @@ -40,8 +40,8 @@ %cm_min -cm_min=getfieldvalue(options,'cm_min',1*ones(md.numberofgrids,1)); +cm_min=getfieldvalue(options,'cm_min',1*ones(md.numberofnodes,1)); if (length(cm_min)==1) - md.cm_min=cm_min*ones(md.numberofgrids,1); -elseif (length(cm_min)==md.numberofgrids) + md.cm_min=cm_min*ones(md.numberofnodes,1); +elseif (length(cm_min)==md.numberofnodes) md.cm_min=cm_min; else @@ -50,8 +50,8 @@ %cm_max -cm_max=getfieldvalue(options,'cm_max',250*ones(md.numberofgrids,1)); +cm_max=getfieldvalue(options,'cm_max',250*ones(md.numberofnodes,1)); if (length(cm_max)==1) - md.cm_max=cm_max*ones(md.numberofgrids,1); -elseif (length(cm_max)==md.numberofgrids) + md.cm_max=cm_max*ones(md.numberofnodes,1); +elseif (length(cm_max)==md.numberofnodes) md.cm_max=cm_max; else Index: /issm/trunk/src/m/model/partition/adjacency.m =================================================================== --- /issm/trunk/src/m/model/partition/adjacency.m (revision 8297) +++ /issm/trunk/src/m/model/partition/adjacency.m (revision 8298) @@ -14,5 +14,5 @@ values=1; -md.adjacency=sparse(indi,indj,values,md.numberofgrids,md.numberofgrids); +md.adjacency=sparse(indi,indj,values,md.numberofnodes,md.numberofnodes); md.adjacency=double([md.adjacency | md.adjacency']); @@ -21,5 +21,5 @@ %get node connectivity -md.nodeconnectivity=NodeConnectivity(md.elements,md.numberofgrids); +md.nodeconnectivity=NodeConnectivity(md.elements,md.numberofnodes); connectivity=md.nodeconnectivity(:,1:end-1); Index: /issm/trunk/src/m/model/partition/partitioner.m =================================================================== --- /issm/trunk/src/m/model/partition/partitioner.m (revision 8297) +++ /issm/trunk/src/m/model/partition/partitioner.m (revision 8298) @@ -75,5 +75,5 @@ elseif strcmpi(package,'linear'), - part=1:1:md.numberofgrids; + part=1:1:md.numberofnodes; elseif strcmpi(package,'metis'), Index: /issm/trunk/src/m/model/plot/plot_contour.m =================================================================== --- /issm/trunk/src/m/model/plot/plot_contour.m (revision 8297) +++ /issm/trunk/src/m/model/plot/plot_contour.m (revision 8298) @@ -16,5 +16,5 @@ end -%first, process data: must be on grids +%first, process data: must be on nodes if datatype==1, %elements -> take average @@ -67,5 +67,5 @@ edges_tria=[vec(elementslist), vec(elementslist+numberofelements), vec(elementslist+2*numberofelements)]; -%segments [grids1 gruids2] +%segments [nodes1 nodes2] Seg1=index(:,[1 2]); Seg2=index(:,[2 3]); Index: /issm/trunk/src/m/model/plot/plot_gridnumbering.m =================================================================== --- /issm/trunk/src/m/model/plot/plot_gridnumbering.m (revision 8297) +++ /issm/trunk/src/m/model/plot/plot_gridnumbering.m (revision 8298) @@ -1,7 +1,7 @@ -function plot_gridnumbering(md,options,width,i); -%PLOT_GRIDNUMBERING - plot grid numbering +function plot_nodenumbering(md,options,width,i); +%PLOT_GRIDNUMBERING - plot node numbering % % Usage: -% plot_gridnumbering(md,options,width,i); +% plot_nodenumbering(md,options,width,i); % % See also: PLOTMODEL @@ -9,5 +9,5 @@ %process data and model [x y z elements is2d]=processmesh(md,[],options); -[gridnumbers datatype]=processdata(md,[1:md.numberofgrids]',options); +[nodenumbers datatype]=processdata(md,[1:md.numberofnodes]',options); %plot @@ -47,5 +47,5 @@ %apply options -options=addfielddefault(options,'title','Grid numbering'); +options=addfielddefault(options,'title','Node numbering'); options=addfielddefault(options,'colorbar',0); applyoptions(md,[],options); Index: /issm/trunk/src/m/model/plot/plot_highlightgrids.m =================================================================== --- /issm/trunk/src/m/model/plot/plot_highlightgrids.m (revision 8297) +++ /issm/trunk/src/m/model/plot/plot_highlightgrids.m (revision 8298) @@ -1,7 +1,7 @@ -function plot_highlightgrids(md,options,width,i); -%PLOT_HIGHLIGHTGRIDS - plot selected grids +function plot_highlightnodes(md,options,width,i); +%PLOT_HIGHLIGHTGRIDS - plot selected nodes % % Usage: -% plot_highlightgrids(md,options,width,i); +% plot_highlightnodes(md,options,width,i); % % See also: PLOTMODEL @@ -9,5 +9,5 @@ %process data and model [x y z elements is2d]=processmesh(md,[],options); -[gridnumbers datatype]=processdata(md,[1:md.numberofgrids]',options); +[nodenumbers datatype]=processdata(md,[1:md.numberofnodes]',options); %plot @@ -40,7 +40,7 @@ %apply options if ~exist(options,'highlight') - disp('highlightgrids warning : highlight option empty, not grid highlighted'); + disp('highlightnodes warning : highlight option empty, not node highlighted'); end -options=addfielddefault(options,'title','Highlighted Grids'); +options=addfielddefault(options,'title','Highlighted Nodes'); options=addfielddefault(options,'colorbar',0); applyoptions(md,[],options); Index: /issm/trunk/src/m/model/plot/plot_importancefactors.m =================================================================== --- /issm/trunk/src/m/model/plot/plot_importancefactors.m (revision 8297) +++ /issm/trunk/src/m/model/plot/plot_importancefactors.m (revision 8298) @@ -61,5 +61,5 @@ %distribute importance factor -gridimportance=importancefactors(npart); +nodeimportance=importancefactors(npart); %process data and model @@ -72,8 +72,8 @@ subplot(width,width,ii); -%ok, plot gridimportance now. +%ok, plot nodeimportance now. if is2d, A=elements(:,1); B=elements(:,2); C=elements(:,3); - patch( 'Faces', [A B C], 'Vertices', [x y z],'FaceVertexCData', gridimportance,'FaceColor','interp','EdgeColor',edgecolor); + patch( 'Faces', [A B C], 'Vertices', [x y z],'FaceVertexCData', nodeimportance,'FaceColor','interp','EdgeColor',edgecolor); else error('plot_importancefactors error message: 3d meshes not supported yet'); Index: /issm/trunk/src/m/model/plot/plot_manager.m =================================================================== --- /issm/trunk/src/m/model/plot/plot_manager.m (revision 8297) +++ /issm/trunk/src/m/model/plot/plot_manager.m (revision 8298) @@ -62,10 +62,10 @@ plot_elementstype(md,options,subplotwidth,i); return; - case 'gridnumbering', - plot_gridnumbering(md,options,subplotwidth,i); - return; - - case 'highlightgrids', - plot_highlightgrids(md,options,subplotwidth,i); + case 'nodenumbering', + plot_nodenumbering(md,options,subplotwidth,i); + return; + + case 'highlightnodes', + plot_highlightnodes(md,options,subplotwidth,i); return; case {'basal_drag','basal_dragx','basal_dragy'}, Index: /issm/trunk/src/m/model/plot/plot_overlay.m =================================================================== --- /issm/trunk/src/m/model/plot/plot_overlay.m (revision 8297) +++ /issm/trunk/src/m/model/plot/plot_overlay.m (revision 8298) @@ -11,5 +11,5 @@ if strcmpi(data,'none'), radaronly=1; - data=NaN*ones(md.numberofgrids,1); + data=NaN*ones(md.numberofnodes,1); datatype=1; else Index: /issm/trunk/src/m/model/plot/plot_penalties.m =================================================================== --- /issm/trunk/src/m/model/plot/plot_penalties.m (revision 8297) +++ /issm/trunk/src/m/model/plot/plot_penalties.m (revision 8298) @@ -40,5 +40,5 @@ P2=plot3(x(md.penalties(i,:)),y(md.penalties(i,:)),z(md.penalties(i,:)),'bo-','LineWidth',2,'MarkerSize',8,'MarkerFaceColor','b'); end - legend([P1 P2],'MacAyeal''s penalized grids','Pattyn''s penalized grids'); + legend([P1 P2],'MacAyeal''s penalized nodes','Pattyn''s penalized nodes'); end Index: /issm/trunk/src/m/model/plot/plot_qmumean.m =================================================================== --- /issm/trunk/src/m/model/plot/plot_qmumean.m (revision 8297) +++ /issm/trunk/src/m/model/plot/plot_qmumean.m (revision 8298) @@ -48,9 +48,9 @@ %now, project onto vertices -responses_on_grid=responses(md.part+1); +responses_on_node=responses(md.part+1); %plot A=elements(:,1); B=elements(:,2); C=elements(:,3); -patch( 'Faces', [A B C], 'Vertices', [x y z],'FaceVertexCData', responses_on_grid,'FaceColor','interp','EdgeColor',edgecolor); +patch( 'Faces', [A B C], 'Vertices', [x y z],'FaceVertexCData', responses_on_node,'FaceColor','interp','EdgeColor',edgecolor); %apply options Index: /issm/trunk/src/m/model/plot/plot_qmustddev.m =================================================================== --- /issm/trunk/src/m/model/plot/plot_qmustddev.m (revision 8297) +++ /issm/trunk/src/m/model/plot/plot_qmustddev.m (revision 8298) @@ -49,9 +49,9 @@ %now, project onto vertices -responses_on_grid=responses(md.part+1); +responses_on_node=responses(md.part+1); %plot A=elements(:,1); B=elements(:,2); C=elements(:,3); -patch( 'Faces', [A B C], 'Vertices', [x y z],'FaceVertexCData', responses_on_grid,'FaceColor','interp','EdgeColor',edgecolor); +patch( 'Faces', [A B C], 'Vertices', [x y z],'FaceVertexCData', responses_on_node,'FaceColor','interp','EdgeColor',edgecolor); %apply options Index: /issm/trunk/src/m/model/plot/plot_riftfraction.m =================================================================== --- /issm/trunk/src/m/model/plot/plot_riftfraction.m (revision 8297) +++ /issm/trunk/src/m/model/plot/plot_riftfraction.m (revision 8298) @@ -23,6 +23,6 @@ end -%first, build a vector of fractions, over all grids. -fractions=zeros(md.numberofgrids,1); +%first, build a vector of fractions, over all nodes. +fractions=zeros(md.numberofnodes,1); %plug riftproperties fractions: Index: /issm/trunk/src/m/model/plot/plot_riftnumbering.m =================================================================== --- /issm/trunk/src/m/model/plot/plot_riftnumbering.m (revision 8297) +++ /issm/trunk/src/m/model/plot/plot_riftnumbering.m (revision 8298) @@ -82,6 +82,6 @@ for j=1:size(penaltypairs,1), - grid=penaltypairs(j,1); - t=text(x(grid),y(grid),[num2str(i) '.' num2str(j)]); + node=penaltypairs(j,1); + t=text(x(node),y(node),[num2str(i) '.' num2str(j)]); set(t,'FontSize',fontsize); end Index: /issm/trunk/src/m/model/plot/plot_riftrelvel.m =================================================================== --- /issm/trunk/src/m/model/plot/plot_riftrelvel.m (revision 8297) +++ /issm/trunk/src/m/model/plot/plot_riftrelvel.m (revision 8298) @@ -8,5 +8,5 @@ %some checks -if (length(md.vx)~=md.numberofgrids | length(md.vy)~=md.numberofgrids), +if (length(md.vx)~=md.numberofnodes | length(md.vy)~=md.numberofnodes), error('plot_riftvel error message: vx and vy do not have the right size'), end @@ -21,6 +21,6 @@ %set as NaN all velocities not on rifts -u=NaN*ones(md.numberofgrids,1); -v=NaN*ones(md.numberofgrids,1); +u=NaN*ones(md.numberofnodes,1); +v=NaN*ones(md.numberofnodes,1); for i=1:md.numrifts, penaltypairs=md.rifts(i).penaltypairs(:,[1 2]); @@ -64,5 +64,5 @@ for i=1:md.numrifts, - %get grids on rift + %get nodes on rift penaltypairs=md.rifts(i).penaltypairs; Index: /issm/trunk/src/m/model/plot/plot_riftvel.m =================================================================== --- /issm/trunk/src/m/model/plot/plot_riftvel.m (revision 8297) +++ /issm/trunk/src/m/model/plot/plot_riftvel.m (revision 8298) @@ -8,5 +8,5 @@ %some checks -if (length(md.vx)~=md.numberofgrids | length(md.vy)~=md.numberofgrids), +if (length(md.vx)~=md.numberofnodes | length(md.vy)~=md.numberofnodes), error('plot_riftvel error message: vx and vy do not have the right size'), end @@ -17,6 +17,6 @@ %set as NaN all velocities not on rifts -u=NaN*ones(md.numberofgrids,1); -v=NaN*ones(md.numberofgrids,1); +u=NaN*ones(md.numberofnodes,1); +v=NaN*ones(md.numberofnodes,1); for i=1:md.numrifts, penaltypairs=md.rifts(i).penaltypairs(:,[1 2]); @@ -58,5 +58,5 @@ for i=1:size(md.rifts,1), - %get grids on rift + %get nodes on rift penaltypairs=md.rifts(i).penaltypairs; Index: /issm/trunk/src/m/model/plot/plot_tensor_principalaxis.m =================================================================== --- /issm/trunk/src/m/model/plot/plot_tensor_principalaxis.m (revision 8297) +++ /issm/trunk/src/m/model/plot/plot_tensor_principalaxis.m (revision 8298) @@ -27,5 +27,5 @@ end -%take the center of each element if ~isongrid +%take the center of each element if ~isonnode if datatype==1, x=mean(md.x(md.elements'))'; y=mean(md.y(md.elements'))'; z=mean(md.z(md.elements'))'; Index: /issm/trunk/src/m/model/plot/plotanalyse.m =================================================================== --- /issm/trunk/src/m/model/plot/plotanalyse.m (revision 8297) +++ /issm/trunk/src/m/model/plot/plotanalyse.m (revision 8298) @@ -7,5 +7,5 @@ %Do a series of plots that will help the user analyse what is going on. plot(md,'data','segmentonneumann_diag','title','dynamic boundary conditions',... - 'data','gridondirichlet_diag','title','fixed velocity grids',... + 'data','nodeondirichlet_diag','title','fixed velocity nodes',... 'data','vx_obs','title','vx observation (m/s)',... 'data','vy_obs','title','vy observation (m/s)',... @@ -19,5 +19,5 @@ plot(md,'data','elementoniceshelf','title','elements on iceshelf',... - 'data','gridoniceshelf','title','nodes on iceshelf',... + 'data','nodeoniceshelf','title','nodes on iceshelf',... 'data','elementonicesheet','title','elements on icesheet',... - 'data','gridonicesheet','title','nodes on icesheet','colorbar#all','on','figure',4); + 'data','nodeonicesheet','title','nodes on icesheet','colorbar#all','on','figure',4); Index: /issm/trunk/src/m/model/plot/plotdoc.m =================================================================== --- /issm/trunk/src/m/model/plot/plotdoc.m (revision 8297) +++ /issm/trunk/src/m/model/plot/plotdoc.m (revision 8298) @@ -22,7 +22,7 @@ disp(' - ''elements_type'': model used for each element'); disp(' - ''elementnumbering'': numbering of elements'); -disp(' - ''gridnumbering'': numbering of grids'); +disp(' - ''nodenumbering'': numbering of nodes'); disp(' - ''highlightelements'': to highlight elements to highlight the element list'); -disp(' - ''highlightgrids'': to highlight grids (use highlight option to enter the grid list'); +disp(' - ''highlightnodes'': to highlight nodes (use highlight option to enter the node list'); disp(' - ''mesh'': draw mesh using trisurf'); disp(' - ''riftvel'': velocities along rifts'); @@ -86,5 +86,5 @@ disp(' ''fontweight'': same as standard matlab option (normal: ''n'',bold: ''b'',light: ''l'',demi: ''d'')'); disp(' ''fontcolor'': same as standard matlab option'); -disp(' ''highlight'': highlights certain grids or elements when using ''gridnumbering'' or ''elementnumbering'' or ''highlightgrids '' or ''highlightelements'' option'); +disp(' ''highlight'': highlights certain nodes or elements when using ''nodenumbering'' or ''elementnumbering'' or ''highlightnodes '' or ''highlightelements'' option'); disp(' ''resolution'': resolution used by section value (array of type [horizontal_resolution vertical_resolution])'); disp(' horizontal_resolution must be in meter, and vertical_resolution a number of layers'); @@ -119,5 +119,5 @@ disp(' ''textcolor'': same as standard ''color'' matlab option applied to text, use a cell of strings if more than one'); disp(' ''textrotation'': same as standard ''Rotation'' matlab option applied to text, use a cell of strings if more than one'); -disp(' ''mask'': list of flags of size numberofgrids or numberofelements. Only ''true'' values are plotted '); +disp(' ''mask'': list of flags of size numberofnodes or numberofelements. Only ''true'' values are plotted '); disp(' ''partitionedges'': ''off'' by default. overlay plot of partition edges'); disp(' ''log'': value of log'); Index: /issm/trunk/src/m/model/plot/processdata.m =================================================================== --- /issm/trunk/src/m/model/plot/processdata.m (revision 8297) +++ /issm/trunk/src/m/model/plot/processdata.m (revision 8298) @@ -58,5 +58,5 @@ %check length - if datasize(1)~=md.numberofgrids & datasize(1)~=md.numberofelements & datasize(1)~=md.numberofgrids*6 & (md.dim==3 & ~(datasize(1)==md.numberofelements2d | datasize(1)==md.numberofgrids2d)) + if datasize(1)~=md.numberofnodes & datasize(1)~=md.numberofelements & datasize(1)~=md.numberofnodes*6 & (md.dim==3 & ~(datasize(1)==md.numberofelements2d | datasize(1)==md.numberofnodes2d)) error('plotmodel error message: data not supported yet'); end @@ -78,26 +78,26 @@ end - %treat the case datasize(1)=6*grids - if datasize(1)==6*md.numberofgrids + %treat the case datasize(1)=6*nodes + if datasize(1)==6*md.numberofnodes %keep the only norm of data - data1=data(1:6:md.numberofgrids*6,:); - data2=data(2:6:md.numberofgrids*6,:); + data1=data(1:6:md.numberofnodes*6,:); + data2=data(2:6:md.numberofnodes*6,:); data=sqrt(data1.^2+data2.^2); - datasize(1)=md.numberofgrids; - %---> go to grid data + datasize(1)=md.numberofnodes; + %---> go to node data end - %treat the case datasize(1)=grids2d - if (md.dim==3 & datasize(1)==md.numberofgrids2d), + %treat the case datasize(1)=nodes2d + if (md.dim==3 & datasize(1)==md.numberofnodes2d), data=project3d(md,data,'node'); - datasize(1)=md.numberofgrids; - %---> go to grid data + datasize(1)=md.numberofnodes; + %---> go to node data end - %treat the case datasize(1)=grids2d + %treat the case datasize(1)=nodes2d if (md.dim==3 & datasize(1)==md.numberofelements2d), data=project3d(md,data,'element'); datasize(1)=md.numberofelements; - %---> go to grid data + %---> go to node data end @@ -105,6 +105,6 @@ if exist(options,'smooth') data=averaging(md,data,getfieldvalue(options,'smooth')); - datasize(1)=md.numberofgrids; - %---> go to grid data + datasize(1)=md.numberofnodes; + %---> go to node data end end @@ -122,5 +122,5 @@ flags=getfieldvalue(options,'mask'); pos=find(~flags); - if length(flags)==md.numberofgrids, + if length(flags)==md.numberofnodes, [pos2 dummy]=find(ismember(md.elements,pos)); data(pos2,:)=NaN; @@ -128,5 +128,5 @@ data(pos,:)=NaN; else - disp('plotmodel warning: mask length not supported yet (supported length are md.numberofgrids and md.numberofelements'); + disp('plotmodel warning: mask length not supported yet (supported length are md.numberofnodes and md.numberofelements'); end end @@ -144,6 +144,6 @@ end -%grid data -if (datasize(1)==md.numberofgrids & datasize(2)==1), +%node data +if (datasize(1)==md.numberofnodes & datasize(2)==1), datatype=2; @@ -152,10 +152,10 @@ flags=getfieldvalue(options,'mask'); pos=find(~flags); - if length(flags)==md.numberofgrids, + if length(flags)==md.numberofnodes, data(pos,:)=NaN; elseif length(flags)==md.numberofelements data(md.elements(pos,:),:)=NaN; else - disp('plotmodel warning: mask length not supported yet (supported length are md.numberofgrids and md.numberofelements'); + disp('plotmodel warning: mask length not supported yet (supported length are md.numberofnodes and md.numberofelements'); end end Index: /issm/trunk/src/m/model/plot/processmesh.m =================================================================== --- /issm/trunk/src/m/model/plot/processmesh.m (revision 8297) +++ /issm/trunk/src/m/model/plot/processmesh.m (revision 8298) @@ -8,6 +8,6 @@ %some checks -if md.numberofgrids==md.numberofelements - error('plot error message: the number of elements is the same as the number of grids! cannot plot anything with model/plot, use matlab/plot instead') +if md.numberofnodes==md.numberofelements + error('plot error message: the number of elements is the same as the number of nodes! cannot plot anything with model/plot, use matlab/plot instead') end Index: /issm/trunk/src/m/model/plug.m =================================================================== --- /issm/trunk/src/m/model/plug.m (revision 8297) +++ /issm/trunk/src/m/model/plug.m (revision 8298) @@ -28,5 +28,5 @@ distance=sqrt( (md.x(index)-md.x).^2 + (md.y(index)-md.y).^2 ); - distance(holevalues)=10^10; %be sure we are not picking up the nan grids! + distance(holevalues)=10^10; %be sure we are not picking up the nan nodes! index2=find(distance==min(distance));index2=index2(1); Index: /issm/trunk/src/m/model/presolve.m =================================================================== --- /issm/trunk/src/m/model/presolve.m (revision 8297) +++ /issm/trunk/src/m/model/presolve.m (revision 8298) @@ -31,5 +31,5 @@ end -md.riftinfo=zeros(numpairs,12); % 2 for grids + 2 for elements+ 2 for normals + 1 for length + 1 for fill + 1 for friction + 1 for fraction + 1 for fractionincrement + 1 for state. +md.riftinfo=zeros(numpairs,12); % 2 for nodes + 2 for elements+ 2 for normals + 1 for length + 1 for fill + 1 for friction + 1 for fraction + 1 for fractionincrement + 1 for state. count=1; Index: /issm/trunk/src/m/model/project2d.m =================================================================== --- /issm/trunk/src/m/model/project2d.m (revision 8297) +++ /issm/trunk/src/m/model/project2d.m (revision 8298) @@ -32,6 +32,6 @@ end -if size(value,1)==md3d.numberofgrids, - projection_value=value((layer-1)*md3d.numberofgrids2d+1:layer*md3d.numberofgrids2d,:); +if size(value,1)==md3d.numberofnodes, + projection_value=value((layer-1)*md3d.numberofnodes2d+1:layer*md3d.numberofnodes2d,:); else projection_value=value((layer-1)*md3d.numberofelements2d+1:layer*md3d.numberofelements2d,:); Index: /issm/trunk/src/m/model/project3d.m =================================================================== --- /issm/trunk/src/m/model/project3d.m (revision 8297) +++ /issm/trunk/src/m/model/project3d.m (revision 8298) @@ -3,5 +3,5 @@ % % vertically project a vector from 2d mesh (split in noncoll and coll areas) into a 3d mesh. -% This vector can be a grid vector of size (md3d.numberofgrids2d,N/A) or an +% This vector can be a node vector of size (md3d.numberofnodes2d,N/A) or an % element vector of size (md3d.numberofelements2d,N/A). % type is 'element' or 'node'. layer an optional layer number where vector @@ -23,12 +23,12 @@ if strcmpi(type,'node'), - projected_vector=zeros(md3d.numberofgrids,size(vector2d,2)); + projected_vector=zeros(md3d.numberofnodes,size(vector2d,2)); if layer==0, for i=1:md3d.numlayers, - projected_vector(((i-1)*md3d.numberofgrids2d+1):(i*md3d.numberofgrids2d),:)=vector2d; + projected_vector(((i-1)*md3d.numberofnodes2d+1):(i*md3d.numberofnodes2d),:)=vector2d; end else - projected_vector(((layer-1)*md3d.numberofgrids2d+1):(layer*md3d.numberofgrids2d),:)=vector2d; + projected_vector(((layer-1)*md3d.numberofnodes2d+1):(layer*md3d.numberofnodes2d),:)=vector2d; end else Index: /issm/trunk/src/m/model/removeholes.m =================================================================== --- /issm/trunk/src/m/model/removeholes.m (revision 8297) +++ /issm/trunk/src/m/model/removeholes.m (revision 8298) @@ -3,5 +3,5 @@ % % as its name indicates, this routine takes a model, a field (value of some -% physical quantity evaluated at the mesh grids) of the model, and interpolates this field +% physical quantity evaluated at the mesh nodes) of the model, and interpolates this field % on the model mesh, without any hole. % Index: /issm/trunk/src/m/model/setelementstype.m =================================================================== --- /issm/trunk/src/m/model/setelementstype.m (revision 8297) +++ /issm/trunk/src/m/model/setelementstype.m (revision 8298) @@ -75,19 +75,19 @@ %1: Hutter elements -gridonhutter=zeros(md.numberofgrids,1); -gridonhutter(md.elements(find(hutterflag),:))=1; -md.gridonhutter=gridonhutter; +nodeonhutter=zeros(md.numberofnodes,1); +nodeonhutter(md.elements(find(hutterflag),:))=1; +md.nodeonhutter=nodeonhutter; md.elements_type(find(hutterflag))=HutterApproximationEnum(); %2: MacAyeal elements -gridonmacayeal=zeros(md.numberofgrids,1); -gridonmacayeal(md.elements(find(macayealflag),:))=1; -md.gridonmacayeal=gridonmacayeal; +nodeonmacayeal=zeros(md.numberofnodes,1); +nodeonmacayeal(md.elements(find(macayealflag),:))=1; +md.nodeonmacayeal=nodeonmacayeal; md.elements_type(find(macayealflag))=MacAyealApproximationEnum(); %3: Pattyn elements -gridonpattyn=zeros(md.numberofgrids,1); -gridonpattyn(md.elements(find(pattynflag),:))=1; -md.gridonpattyn=gridonpattyn; +nodeonpattyn=zeros(md.numberofnodes,1); +nodeonpattyn(md.elements(find(pattynflag),:))=1; +md.nodeonpattyn=nodeonpattyn; md.elements_type(find(pattynflag))=PattynApproximationEnum(); @@ -95,13 +95,13 @@ %First modify stokesflag to get rid of elements contrained everywhere (spc + border with pattyn or macayeal) if any(stokesflag), - gridonstokes=zeros(md.numberofgrids,1); - gridonstokes(md.elements(find(stokesflag),:))=1; - fullspcnodes=double(sum(md.spcvelocity(:,1:3),2)==3 | (gridonpattyn & gridonstokes)); %find all the grids on the boundary of the domain without icefront - fullspcelems=double(sum(fullspcnodes(md.elements),2)==6); %find all the grids on the boundary of the domain without icefront + nodeonstokes=zeros(md.numberofnodes,1); + nodeonstokes(md.elements(find(stokesflag),:))=1; + fullspcnodes=double(sum(md.spcvelocity(:,1:3),2)==3 | (nodeonpattyn & nodeonstokes)); %find all the nodes on the boundary of the domain without icefront + fullspcelems=double(sum(fullspcnodes(md.elements),2)==6); %find all the nodes on the boundary of the domain without icefront stokesflag(find(fullspcelems))=0; end -gridonstokes=zeros(md.numberofgrids,1); -gridonstokes(md.elements(find(stokesflag),:))=1; -md.gridonstokes=gridonstokes; +nodeonstokes=zeros(md.numberofnodes,1); +nodeonstokes(md.elements(find(stokesflag),:))=1; +md.nodeonstokes=nodeonstokes; md.elements_type(find(stokesflag))=StokesApproximationEnum(); @@ -110,11 +110,11 @@ if any(pattynflag), %fill with pattyn pattynflag(~stokesflag)=1; - gridonpattyn(md.elements(find(pattynflag),:))=1; - md.gridonpattyn=gridonpattyn; + nodeonpattyn(md.elements(find(pattynflag),:))=1; + md.nodeonpattyn=nodeonpattyn; md.elements_type(find(~stokesflag))=PattynApproximationEnum(); elseif any(macayealflag), %fill with macayeal macayealflag(~stokesflag)=1; - gridonmacayeal(md.elements(find(macayealflag),:))=1; - md.gridonmacayeal=gridonmacayeal; + nodeonmacayeal(md.elements(find(macayealflag),:))=1; + md.nodeonmacayeal=nodeonmacayeal; md.elements_type(find(~stokesflag))=MacAyealApproximationEnum(); else %fill with none @@ -126,18 +126,18 @@ %Now take care of the coupling between MacAyeal and Pattyn md.penalties=[]; -gridonmacayealpattyn=zeros(md.numberofgrids,1); -gridonpattynstokes=zeros(md.numberofgrids,1); -gridonmacayealstokes=zeros(md.numberofgrids,1); +nodeonmacayealpattyn=zeros(md.numberofnodes,1); +nodeonpattynstokes=zeros(md.numberofnodes,1); +nodeonmacayealstokes=zeros(md.numberofnodes,1); if strcmpi(coupling_method,'penalties'), - %Create the border grids between Pattyn and MacAyeal and extrude them - numgrids2d=md.numberofgrids2d; + %Create the border nodes between Pattyn and MacAyeal and extrude them + numnodes2d=md.numberofnodes2d; numlayers=md.numlayers; - bordergrids2d=find(gridonpattyn(1:numgrids2d) & gridonmacayeal(1:numgrids2d)); %Grids connected to two different types of elements + bordernodes2d=find(nodeonpattyn(1:numnodes2d) & nodeonmacayeal(1:numnodes2d)); %Nodes connected to two different types of elements %initialize and fill in penalties structure - if ~isnan(bordergrids2d), + if ~isnan(bordernodes2d), penalties=[]; for i=1:numlayers-1, - penalties=[penalties; [bordergrids2d bordergrids2d+md.numberofgrids2d*(i)]]; + penalties=[penalties; [bordernodes2d bordernodes2d+md.numberofnodes2d*(i)]]; end md.penalties=penalties; @@ -145,8 +145,8 @@ elseif strcmpi(coupling_method,'tiling'), if any(macayealflag) & any(pattynflag), %coupling macayeal pattyn - %Find grid at the border - gridonmacayealpattyn(find(gridonmacayeal & gridonpattyn))=1; + %Find node at the border + nodeonmacayealpattyn(find(nodeonmacayeal & nodeonpattyn))=1; %Macayeal elements in contact with this layer become MacAyealPattyn elements - matrixelements=ismember(md.elements,find(gridonmacayealpattyn)); + matrixelements=ismember(md.elements,find(nodeonmacayealpattyn)); commonelements=sum(matrixelements,2)~=0; commonelements(find(pattynflag))=0; %only one layer: the elements previously in macayeal @@ -154,18 +154,18 @@ macayealpattynflag=zeros(md.numberofelements,1); macayealpattynflag(find(commonelements))=1; - gridonmacayeal=zeros(md.numberofgrids,1); - gridonmacayeal(md.elements(find(macayealflag),:))=1; - md.gridonmacayeal=gridonmacayeal; + nodeonmacayeal=zeros(md.numberofnodes,1); + nodeonmacayeal(md.elements(find(macayealflag),:))=1; + md.nodeonmacayeal=nodeonmacayeal; %Create MacaAyealPattynApproximation where needed md.elements_type(find(macayealpattynflag))=MacAyealPattynApproximationEnum(); - %Now recreate gridonmacayeal and gridonmacayealpattyn - gridonmacayealpattyn(md.elements(find(macayealpattynflag),:))=1; + %Now recreate nodeonmacayeal and nodeonmacayealpattyn + nodeonmacayealpattyn(md.elements(find(macayealpattynflag),:))=1; elseif any(pattynflag) & any(stokesflag), %coupling pattyn stokes - %Find grid at the border - gridonpattynstokes(find(gridonpattyn & gridonstokes))=1; + %Find node at the border + nodeonpattynstokes(find(nodeonpattyn & nodeonstokes))=1; %Stokes elements in contact with this layer become PattynStokes elements - matrixelements=ismember(md.elements,find(gridonpattynstokes)); + matrixelements=ismember(md.elements,find(nodeonpattynstokes)); commonelements=sum(matrixelements,2)~=0; commonelements(find(pattynflag))=0; %only one layer: the elements previously in macayeal @@ -173,19 +173,19 @@ pattynstokesflag=zeros(md.numberofelements,1); pattynstokesflag(find(commonelements))=1; - gridonstokes=zeros(md.numberofgrids,1); - gridonstokes(md.elements(find(stokesflag),:))=1; - md.gridonstokes=gridonstokes; + nodeonstokes=zeros(md.numberofnodes,1); + nodeonstokes(md.elements(find(stokesflag),:))=1; + md.nodeonstokes=nodeonstokes; %Create MacaAyealPattynApproximation where needed md.elements_type(find(pattynstokesflag))=PattynStokesApproximationEnum(); - %Now recreate gridonpattynstokes - gridonpattynstokes=zeros(md.numberofgrids,1); - gridonpattynstokes(md.elements(find(pattynstokesflag),:))=1; + %Now recreate nodeonpattynstokes + nodeonpattynstokes=zeros(md.numberofnodes,1); + nodeonpattynstokes(md.elements(find(pattynstokesflag),:))=1; elseif any(stokesflag) & any(macayealflag), - %Find grid at the border - gridonmacayealstokes(find(gridonmacayeal & gridonstokes))=1; + %Find node at the border + nodeonmacayealstokes(find(nodeonmacayeal & nodeonstokes))=1; %Stokes elements in contact with this layer become MacAyealStokes elements - matrixelements=ismember(md.elements,find(gridonmacayealstokes)); + matrixelements=ismember(md.elements,find(nodeonmacayealstokes)); commonelements=sum(matrixelements,2)~=0; commonelements(find(macayealflag))=0; %only one layer: the elements previously in macayeal @@ -193,14 +193,14 @@ macayealstokesflag=zeros(md.numberofelements,1); macayealstokesflag(find(commonelements))=1; - gridonstokes=zeros(md.numberofgrids,1); - gridonstokes(md.elements(find(stokesflag),:))=1; - md.gridonstokes=gridonstokes; + nodeonstokes=zeros(md.numberofnodes,1); + nodeonstokes(md.elements(find(stokesflag),:))=1; + md.nodeonstokes=nodeonstokes; %Create MacaAyealMacAyealApproximation where needed md.elements_type(find(macayealstokesflag))=MacAyealStokesApproximationEnum(); - %Now recreate gridonmacayealstokes - gridonmacayealstokes=zeros(md.numberofgrids,1); - gridonmacayealstokes(md.elements(find(macayealstokesflag),:))=1; + %Now recreate nodeonmacayealstokes + nodeonmacayealstokes=zeros(md.numberofnodes,1); + nodeonmacayealstokes(md.elements(find(macayealstokesflag),:))=1; elseif any(stokesflag) & any(hutterflag), error('type of coupling not supported yet'); @@ -209,28 +209,28 @@ %Create vertices_type -md.vertices_type=zeros(md.numberofgrids,1); -pos=find(gridonhutter); +md.vertices_type=zeros(md.numberofnodes,1); +pos=find(nodeonhutter); md.vertices_type(pos)=HutterApproximationEnum(); -pos=find(gridonmacayeal); +pos=find(nodeonmacayeal); md.vertices_type(pos)=MacAyealApproximationEnum(); -pos=find(gridonpattyn); +pos=find(nodeonpattyn); md.vertices_type(pos)=PattynApproximationEnum(); -pos=find(gridonhutter); +pos=find(nodeonhutter); md.vertices_type(pos)=HutterApproximationEnum(); -pos=find(gridonpattyn & gridonmacayeal); +pos=find(nodeonpattyn & nodeonmacayeal); md.vertices_type(pos)=PattynApproximationEnum(); -pos=find(gridonmacayealpattyn); +pos=find(nodeonmacayealpattyn); md.vertices_type(pos)=MacAyealPattynApproximationEnum(); -pos=find(gridonstokes); +pos=find(nodeonstokes); md.vertices_type(pos)=StokesApproximationEnum(); if any(stokesflag), - pos=find(~gridonstokes); + pos=find(~nodeonstokes); if(~any(pattynflag) & ~any(macayealflag)), md.vertices_type(pos)=NoneApproximationEnum(); end end -pos=find(gridonpattynstokes); +pos=find(nodeonpattynstokes); md.vertices_type(pos)=PattynStokesApproximationEnum(); -pos=find(gridonmacayealstokes); +pos=find(nodeonmacayealstokes); md.vertices_type(pos)=MacAyealStokesApproximationEnum(); Index: /issm/trunk/src/m/model/slope.m =================================================================== --- /issm/trunk/src/m/model/slope.m (revision 8297) +++ /issm/trunk/src/m/model/slope.m (revision 8298) @@ -8,10 +8,10 @@ if (md.dim==2), numberofelements=md.numberofelements; - numberofgrids=md.numberofgrids; + numberofnodes=md.numberofnodes; index=md.elements; x=md.x; y=md.y; z=md.z; else numberofelements=md.numberofelements2d; - numberofgrids=md.numberofgrids2d; + numberofnodes=md.numberofnodes2d; index=md.elements2d; x=md.x2d; y=md.y2d; z=md.z2d; Index: /issm/trunk/src/m/model/thicknessevolution.m =================================================================== --- /issm/trunk/src/m/model/thicknessevolution.m (revision 8297) +++ /issm/trunk/src/m/model/thicknessevolution.m (revision 8298) @@ -9,6 +9,6 @@ % dhdt=thicknessevolution(md) -if (length(md.vx)~=md.numberofgrids)|(length(md.vy)~=md.numberofgrids) - error(['thicknessevolution error message: vx and vy should have a length of ' num2str(md.numberofgrids)]) +if (length(md.vx)~=md.numberofnodes)|(length(md.vy)~=md.numberofnodes) + error(['thicknessevolution error message: vx and vy should have a length of ' num2str(md.numberofnodes)]) end Index: /issm/trunk/src/m/model/tres.m =================================================================== --- /issm/trunk/src/m/model/tres.m (revision 8297) +++ /issm/trunk/src/m/model/tres.m (revision 8298) @@ -26,5 +26,5 @@ md.vz=PatchToVec(md.results.DiagnosticSolution.Vz); else - md.vz=zeros(md.numberofgrids,1); + md.vz=zeros(md.numberofnodes,1); end end Index: /issm/trunk/src/m/qmu/importancefactors.m =================================================================== --- /issm/trunk/src/m/qmu/importancefactors.m (revision 8297) +++ /issm/trunk/src/m/qmu/importancefactors.m (revision 8298) @@ -51,10 +51,10 @@ %weight importancefactors by area -%if numel(factors)==md.numberofgrids, +%if numel(factors)==md.numberofnodes, % %get areas for each vertex. % aire=GetAreas(md.elements,md.x,md.y); % num_elements_by_node=md.nodeconnectivity(:,end); -% grid_aire=zeros(md.numberofgrids,1); -% for i=1:md.numberofgrids, +% grid_aire=zeros(md.numberofnodes,1); +% for i=1:md.numberofnodes, % for j=1:num_elements_by_node(i), % grid_aire(i)=grid_aire(i)+aire(md.nodeconnectivity(i,j)); Index: /issm/trunk/src/m/utils/Analysis/resetspcs.m =================================================================== --- /issm/trunk/src/m/utils/Analysis/resetspcs.m (revision 8297) +++ /issm/trunk/src/m/utils/Analysis/resetspcs.m (revision 8298) @@ -3,5 +3,5 @@ resolution=20000; x_ellsworth=-1.24*10^6; y_ellsworth=1*10^5; pos=find((md.x>(x_ellsworth-resolution)) & (md.x<(x_ellsworth+resolution)) & (md.y>(y_ellsworth-resolution)) & (md.y<(y_ellsworth+resolution))); - md.spcvelocity=zeros(md.numberofgrids,6); + md.spcvelocity=zeros(md.numberofnodes,6); md.spcvelocity(pos,1:3)=1; Index: /issm/trunk/src/m/utils/BC/SetIceSheetBC.m =================================================================== --- /issm/trunk/src/m/utils/BC/SetIceSheetBC.m (revision 8297) +++ /issm/trunk/src/m/utils/BC/SetIceSheetBC.m (revision 8298) @@ -7,12 +7,12 @@ % See also: SETICESHELFBC, SETMARINEICESHEETBC -%grid on Dirichlet -pos=find(md.gridonboundary); -md.spcvelocity=zeros(md.numberofgrids,6); +%node on Dirichlet +pos=find(md.nodeonboundary); +md.spcvelocity=zeros(md.numberofnodes,6); md.spcvelocity(pos,1:3)=1; -md.diagnostic_ref=NaN*ones(md.numberofgrids,6); +md.diagnostic_ref=NaN*ones(md.numberofnodes,6); %Dirichlet Values -if (length(md.vx_obs)==md.numberofgrids & length(md.vy_obs)==md.numberofgrids) +if (length(md.vx_obs)==md.numberofnodes & length(md.vy_obs)==md.numberofnodes) disp(' boundary conditions for diagnostic model: spc set as observed velocities'); md.spcvelocity(:,4:5)=[md.vx_obs md.vy_obs]; %vz is zero @@ -30,22 +30,22 @@ %Create zeros melting_rate and accumulation_rate if not specified if isnan(md.accumulation_rate), - md.accumulation_rate=zeros(md.numberofgrids,1); + md.accumulation_rate=zeros(md.numberofnodes,1); disp(' no accumulation_rate specified: values set as zero'); end if isnan(md.melting_rate), - md.melting_rate=zeros(md.numberofgrids,1); + md.melting_rate=zeros(md.numberofnodes,1); disp(' no melting_rate specified: values set as zero'); end if isnan(md.dhdt), - md.dhdt=zeros(md.numberofgrids,1); + md.dhdt=zeros(md.numberofnodes,1); disp(' no dhdt specified: values set as zero'); end -md.spcthickness=zeros(md.numberofgrids,2); +md.spcthickness=zeros(md.numberofnodes,2); -if (length(md.observed_temperature)==md.numberofgrids), - md.spctemperature=[md.gridonsurface md.observed_temperature]; %impose observed temperature on surface - if (length(md.geothermalflux)~=md.numberofgrids), - md.geothermalflux=50*10^-3*ones(md.numberofgrids,1); %50 mW/m^2 +if (length(md.observed_temperature)==md.numberofnodes), + md.spctemperature=[md.nodeonsurface md.observed_temperature]; %impose observed temperature on surface + if (length(md.geothermalflux)~=md.numberofnodes), + md.geothermalflux=50*10^-3*ones(md.numberofnodes,1); %50 mW/m^2 end else Index: /issm/trunk/src/m/utils/BC/SetIceShelfBC.m =================================================================== --- /issm/trunk/src/m/utils/BC/SetIceShelfBC.m (revision 8297) +++ /issm/trunk/src/m/utils/BC/SetIceShelfBC.m (revision 8298) @@ -15,23 +15,23 @@ % See also: SETICESHEETBC, SETMARINEICESHEETBC -%grid on Dirichlet (boundary and ~icefront) +%node on Dirichlet (boundary and ~icefront) if nargin==2, icefrontfile=varargin{1}; if ~exist(icefrontfile), error(['SetIceShelfBC error message: ice front file ' icefrontfile ' not found']); end - gridinsideicefront=ContourToMesh(md.elements,md.x,md.y,icefrontfile,'node',2); - gridonicefront=double(md.gridonboundary & gridinsideicefront); + nodeinsideicefront=ContourToMesh(md.elements,md.x,md.y,icefrontfile,'node',2); + nodeonicefront=double(md.nodeonboundary & nodeinsideicefront); elseif nargin==1, - gridonicefront=zeros(md.numberofgrids,1); + nodeonicefront=zeros(md.numberofnodes,1); else help SetIceShelfBC error('bad usage'); end -pos=find(md.gridonboundary & ~gridonicefront); -md.spcvelocity=zeros(md.numberofgrids,6); +pos=find(md.nodeonboundary & ~nodeonicefront); +md.spcvelocity=zeros(md.numberofnodes,6); md.spcvelocity(pos,1:3)=1; -md.diagnostic_ref=NaN*ones(md.numberofgrids,6); +md.diagnostic_ref=NaN*ones(md.numberofnodes,6); %Dirichlet Values -if (length(md.vx_obs)==md.numberofgrids & length(md.vy_obs)==md.numberofgrids) +if (length(md.vx_obs)==md.numberofnodes & length(md.vy_obs)==md.numberofnodes) disp(' boundary conditions for diagnostic model: spc set as observed velocities'); md.spcvelocity(pos,4:5)=[md.vx_obs(pos) md.vy_obs(pos)]; %zeros for vz @@ -42,12 +42,12 @@ %segment on Ice Front %segment on Neumann (Ice Front) -pos=find(gridonicefront(md.segments(:,1)) | gridonicefront(md.segments(:,2))); +pos=find(nodeonicefront(md.segments(:,1)) | nodeonicefront(md.segments(:,2))); if (md.dim==2) pressureload=md.segments(pos,:); elseif md.dim==3 - pressureload_layer1=[md.segments(pos,1:2) md.segments(pos,2)+md.numberofgrids2d md.segments(pos,1)+md.numberofgrids2d md.segments(pos,3)]; + pressureload_layer1=[md.segments(pos,1:2) md.segments(pos,2)+md.numberofnodes2d md.segments(pos,1)+md.numberofnodes2d md.segments(pos,3)]; pressureload=[]; for i=1:md.numlayers-1, - pressureload=[pressureload ;pressureload_layer1(:,1:4)+(i-1)*md.numberofgrids2d pressureload_layer1(:,5)+(i-1)*md.numberofelements2d ]; + pressureload=[pressureload ;pressureload_layer1(:,1:4)+(i-1)*md.numberofnodes2d pressureload_layer1(:,5)+(i-1)*md.numberofelements2d ]; end end @@ -61,22 +61,22 @@ %Create zeros melting_rate and accumulation_rate if not specified if isnan(md.accumulation_rate), - md.accumulation_rate=zeros(md.numberofgrids,1); + md.accumulation_rate=zeros(md.numberofnodes,1); disp(' no accumulation_rate specified: values set as zero'); end if isnan(md.melting_rate), - md.melting_rate=zeros(md.numberofgrids,1); + md.melting_rate=zeros(md.numberofnodes,1); disp(' no melting_rate specified: values set as zero'); end if isnan(md.dhdt), - md.dhdt=zeros(md.numberofgrids,1); + md.dhdt=zeros(md.numberofnodes,1); disp(' no dhdt specified: values set as zero'); end -md.spcthickness=zeros(md.numberofgrids,2); +md.spcthickness=zeros(md.numberofnodes,2); -if (length(md.observed_temperature)==md.numberofgrids), - md.spctemperature=[md.gridonsurface md.observed_temperature]; %impose observed temperature on surface - if (length(md.geothermalflux)~=md.numberofgrids), - md.geothermalflux=zeros(md.numberofgrids,1); +if (length(md.observed_temperature)==md.numberofnodes), + md.spctemperature=[md.nodeonsurface md.observed_temperature]; %impose observed temperature on surface + if (length(md.geothermalflux)~=md.numberofnodes), + md.geothermalflux=zeros(md.numberofnodes,1); end else Index: /issm/trunk/src/m/utils/BC/SetMarineIceSheetBC.m =================================================================== --- /issm/trunk/src/m/utils/BC/SetMarineIceSheetBC.m (revision 8297) +++ /issm/trunk/src/m/utils/BC/SetMarineIceSheetBC.m (revision 8298) @@ -16,5 +16,5 @@ % See also: SETICESHELFBC, SETMARINEICESHEETBC -%grid on Dirichlet (boundary and ~icefront) +%node on Dirichlet (boundary and ~icefront) if nargin==2, %User provided Front.exp, use it @@ -23,22 +23,22 @@ error(['SetMarineIceSheetBC error message: ice front file ' icefrontfile ' not found']); end - gridinsideicefront=ContourToMesh(md.elements,md.x,md.y,icefrontfile,'node',2); - gridonicefront=double(md.gridonboundary & gridinsideicefront); + nodeinsideicefront=ContourToMesh(md.elements,md.x,md.y,icefrontfile,'node',2); + nodeonicefront=double(md.nodeonboundary & nodeinsideicefront); else %Guess where the ice front is - gridoniceshelf=zeros(md.numberofgrids,1); - gridoniceshelf(md.elements(find(md.elementoniceshelf),:))=1; - gridonicefront=double(md.gridonboundary & gridoniceshelf); + nodeoniceshelf=zeros(md.numberofnodes,1); + nodeoniceshelf(md.elements(find(md.elementoniceshelf),:))=1; + nodeonicefront=double(md.nodeonboundary & nodeoniceshelf); end -pos=find(md.gridonboundary & ~gridonicefront); +pos=find(md.nodeonboundary & ~nodeonicefront); if isempty(pos), warning('SetMarineIceSheetBC warning: ice front all around the glacier, no dirichlet found. Dirichlet must be added manually') end -md.spcvelocity=zeros(md.numberofgrids,6); +md.spcvelocity=zeros(md.numberofnodes,6); md.spcvelocity(pos,1:3)=1; -md.diagnostic_ref=NaN*ones(md.numberofgrids,6); +md.diagnostic_ref=NaN*ones(md.numberofnodes,6); %Dirichlet Values -if (length(md.vx_obs)==md.numberofgrids & length(md.vy_obs)==md.numberofgrids) +if (length(md.vx_obs)==md.numberofnodes & length(md.vy_obs)==md.numberofnodes) disp(' boundary conditions for diagnostic model: spc set as observed velocities'); md.spcvelocity(pos,4:5)=[md.vx_obs(pos) md.vy_obs(pos)]; %zeros for vz @@ -47,17 +47,17 @@ end -md.spcwatercolumn=zeros(md.numberofgrids,2); -pos=find(md.gridonboundary); +md.spcwatercolumn=zeros(md.numberofnodes,2); +pos=find(md.nodeonboundary); md.spcwatercolumn(pos,1)=1; %segment on Neumann (Ice Front) -pos=find(gridonicefront(md.segments(:,1)) | gridonicefront(md.segments(:,2))); +pos=find(nodeonicefront(md.segments(:,1)) | nodeonicefront(md.segments(:,2))); if (md.dim==2) pressureload=md.segments(pos,:); elseif md.dim==3 - pressureload_layer1=[md.segments(pos,1:2) md.segments(pos,2)+md.numberofgrids2d md.segments(pos,1)+md.numberofgrids2d md.segments(pos,3)]; + pressureload_layer1=[md.segments(pos,1:2) md.segments(pos,2)+md.numberofnodes2d md.segments(pos,1)+md.numberofnodes2d md.segments(pos,3)]; pressureload=[]; for i=1:md.numlayers-1, - pressureload=[pressureload ;pressureload_layer1(:,1:4)+(i-1)*md.numberofgrids2d pressureload_layer1(:,5)+(i-1)*md.numberofelements2d ]; + pressureload=[pressureload ;pressureload_layer1(:,1:4)+(i-1)*md.numberofnodes2d pressureload_layer1(:,5)+(i-1)*md.numberofelements2d ]; end end @@ -71,23 +71,23 @@ %Create zeros melting_rate and accumulation_rate if not specified if isnan(md.accumulation_rate), - md.accumulation_rate=zeros(md.numberofgrids,1); + md.accumulation_rate=zeros(md.numberofnodes,1); disp(' no accumulation_rate specified: values set as zero'); end if isnan(md.melting_rate), - md.melting_rate=zeros(md.numberofgrids,1); + md.melting_rate=zeros(md.numberofnodes,1); disp(' no melting_rate specified: values set as zero'); end if isnan(md.dhdt), - md.dhdt=zeros(md.numberofgrids,1); + md.dhdt=zeros(md.numberofnodes,1); disp(' no dhdt specified: values set as zero'); end -md.spcthickness=zeros(md.numberofgrids,2); +md.spcthickness=zeros(md.numberofnodes,2); -if (length(md.observed_temperature)==md.numberofgrids), - md.spctemperature=[md.gridonsurface md.observed_temperature]; %impose observed temperature on surface - if (length(md.geothermalflux)~=md.numberofgrids), - md.geothermalflux=zeros(md.numberofgrids,1); - md.geothermalflux(find(md.gridonicesheet))=50*10^-3; %50mW/m2 +if (length(md.observed_temperature)==md.numberofnodes), + md.spctemperature=[md.nodeonsurface md.observed_temperature]; %impose observed temperature on surface + if (length(md.geothermalflux)~=md.numberofnodes), + md.geothermalflux=zeros(md.numberofnodes,1); + md.geothermalflux(find(md.nodeonicesheet))=50*10^-3; %50mW/m2 end else Index: /issm/trunk/src/m/utils/DataProcessing/TracksToMatrix.m =================================================================== --- /issm/trunk/src/m/utils/DataProcessing/TracksToMatrix.m (revision 8297) +++ /issm/trunk/src/m/utils/DataProcessing/TracksToMatrix.m (revision 8298) @@ -72,5 +72,5 @@ %Create design site(points where we are looking for the data) -Points=gridsamp([x_f(1)+posting/2,y_f(1)+posting/2;x_f(end)-posting/2,y_f(end)-posting/2],[length(x_f)-1;length(y_f)-1]); +Points=nodesamp([x_f(1)+posting/2,y_f(1)+posting/2;x_f(end)-posting/2,y_f(end)-posting/2],[length(x_f)-1;length(y_f)-1]); %Compute data on these points Index: /issm/trunk/src/m/utils/Ecco3/ecco32issm.m =================================================================== --- /issm/trunk/src/m/utils/Ecco3/ecco32issm.m (revision 8297) +++ /issm/trunk/src/m/utils/Ecco3/ecco32issm.m (revision 8298) @@ -1,8 +1,8 @@ -function gridfield=ecco32issm(field,transition,xecco3,yecco3) +function nodefield=ecco32issm(field,transition,xecco3,yecco3) xecco3linear=xecco3(:); yecco3linear=yecco3(:); %linearize - gridfieldlinear=zeros(length(xecco3linear),1); - gridfieldlinear(transition(:,1))=field(transition(:,2)); - gridfield=xecco3; - gridfield(:)=gridfieldlinear; - %gridfield=gridfield'; %not sure we need that + nodefieldlinear=zeros(length(xecco3linear),1); + nodefieldlinear(transition(:,1))=field(transition(:,2)); + nodefield=xecco3; + nodefield(:)=nodefieldlinear; + %nodefield=nodefield'; %not sure we need that Index: /issm/trunk/src/m/utils/Ecco3/issm2ecco3.m =================================================================== --- /issm/trunk/src/m/utils/Ecco3/issm2ecco3.m (revision 8297) +++ /issm/trunk/src/m/utils/Ecco3/issm2ecco3.m (revision 8298) @@ -1,8 +1,8 @@ -function gridfield=issm2ecco3(field,transition,xecco3,yecco3) +function nodefield=issm2ecco3(field,transition,xecco3,yecco3) xecco3linear=xecco3(:); yecco3linear=yecco3(:); %linearize - gridfieldlinear=zeros(length(xecco3linear),1); - gridfieldlinear(transition(:,1))=field(transition(:,2)); - gridfield=xecco3; - gridfield(:)=gridfieldlinear; - %gridfield=gridfield'; %not sure we need that + nodefieldlinear=zeros(length(xecco3linear),1); + nodefieldlinear(transition(:,1))=field(transition(:,2)); + nodefield=xecco3; + nodefield(:)=nodefieldlinear; + %nodefield=nodefield'; %not sure we need that Index: /issm/trunk/src/m/utils/Exp/expcontract.m =================================================================== --- /issm/trunk/src/m/utils/Exp/expcontract.m (revision 8297) +++ /issm/trunk/src/m/utils/Exp/expcontract.m (revision 8298) @@ -1,3 +1,3 @@ -function normal_grid=expcontract(newfile,oldfile,distance) +function normal_node=expcontract(newfile,oldfile,distance) %EXPCONTRACT - contract or expand a profile, according to the normal. % @@ -12,5 +12,5 @@ normal=zeros(num-1,2); -normal_grid=zeros(num-1,2); +normal_node=zeros(num-1,2); for i=1:num-1, @@ -19,13 +19,13 @@ end -normal_grid(2:end,:)=[normal(1:end-1,:)+normal(2:end,:)]; -normal_grid(1,:)=normal(1,:)+normal(end,:); +normal_node(2:end,:)=[normal(1:end-1,:)+normal(2:end,:)]; +normal_node(1,:)=normal(1,:)+normal(end,:); -normal_grid_norm=sqrt(normal_grid(:,1).^2+normal_grid(:,2).^2); -normal_grid(:,1)=normal_grid(:,1)./normal_grid_norm; -normal_grid(:,2)=normal_grid(:,2)./normal_grid_norm; +normal_node_norm=sqrt(normal_node(:,1).^2+normal_node(:,2).^2); +normal_node(:,1)=normal_node(:,1)./normal_node_norm; +normal_node(:,2)=normal_node(:,2)./normal_node_norm; -contour.x(1:end-1)=contour.x(1:end-1)+distance*normal_grid(:,1); -contour.y(1:end-1)=contour.y(1:end-1)+distance*normal_grid(:,2); +contour.x(1:end-1)=contour.x(1:end-1)+distance*normal_node(:,1); +contour.y(1:end-1)=contour.y(1:end-1)+distance*normal_node(:,2); contour.x(end)=contour.x(1); Index: /issm/trunk/src/m/utils/Exp/expcreatecircle.m =================================================================== --- /issm/trunk/src/m/utils/Exp/expcreatecircle.m (revision 8297) +++ /issm/trunk/src/m/utils/Exp/expcreatecircle.m (revision 8298) @@ -1,18 +1,18 @@ -function expcreatecircle(filename,x0,y0,radius,numberofgrids) +function expcreatecircle(filename,x0,y0,radius,numberofnodes) %EXPCREATECIRCLE - create a circular contour corresponding to given parameters % % Creates a closed argus contour centered on x,y of radius size. -% The contour is made of numberofgrids +% The contour is made of numberofnodes % % Usage: -% expcreatecircle(filename,x0,y0,radius,numberofgrids) +% expcreatecircle(filename,x0,y0,radius,numberofnodes) % % See also EXPMASTER, EXPDOC %Calculate the cartesians coordinates of the points -x_list=ones(numberofgrids+1,1); -y_list=ones(numberofgrids+1,1); +x_list=ones(numberofnodes+1,1); +y_list=ones(numberofnodes+1,1); -theta=(0:2*pi/numberofgrids:2*pi*(1-1/numberofgrids))'; +theta=(0:2*pi/numberofnodes:2*pi*(1-1/numberofnodes))'; theta=[theta;0]; Index: /issm/trunk/src/m/utils/Interp/FieldFindVarNames.m =================================================================== --- /issm/trunk/src/m/utils/Interp/FieldFindVarNames.m (revision 8297) +++ /issm/trunk/src/m/utils/Interp/FieldFindVarNames.m (revision 8298) @@ -29,5 +29,5 @@ xenum=NaN; yenum=NaN; dataenum=NaN; indexenum=NaN; if length(A)==3, - isgrid=1; + isnode=1; for i=1:3 if strcmpi(A(i).name(1),'x'); @@ -42,5 +42,5 @@ end elseif length(A)==4, - isgrid=0; + isnode=0; for i=1:4 if strcmpi(A(i).name(1),'x'); @@ -57,9 +57,9 @@ end else - error(['FieldFindVarNames error message: file ' filename ' not supported yet (it should hold 3 variables x,y and data (for grids) OR 4 variables x,y,index and data (for mesh))']); + error(['FieldFindVarNames error message: file ' filename ' not supported yet (it should hold 3 variables x,y and data (for nodes) OR 4 variables x,y,index and data (for mesh))']); end %2: if only one item is missing, find it by elimination -if ~isgrid, +if ~isnode, pos=find(isnan([xenum yenum indexenum dataenum])); if length(pos)==1, @@ -95,5 +95,5 @@ %find index -if (~isgrid & isnan(indexenum)), +if (~isnode & isnan(indexenum)), for i=1:4 lengthi=min(A(i).size); @@ -108,5 +108,5 @@ %4: last chance -if ~isgrid, +if ~isnode, pos=find(isnan([xenum yenum indexenum dataenum])); if length(pos)==1, @@ -146,8 +146,8 @@ Names.yname=A(yenum).name; Names.dataname=A(dataenum).name; -if ~isgrid, +if ~isnode, Names.indexname=A(indexenum).name; Names.interp='mesh'; else - Names.interp='grid'; + Names.interp='node'; end Index: /issm/trunk/src/m/utils/Interp/FillHole.m =================================================================== --- /issm/trunk/src/m/utils/Interp/FillHole.m (revision 8297) +++ /issm/trunk/src/m/utils/Interp/FillHole.m (revision 8298) @@ -34,5 +34,5 @@ end - %search the grid on the closest to i, that is not in a hole either + %search the node on the closest to i, that is not in a hole either [d posd]=min(sqrt((x(pos_hole(i))-x_noholes).^2+(y(pos_hole(i))-y_noholes).^2)); field(pos_hole(i))=field_noholes(posd); Index: /issm/trunk/src/m/utils/Interp/InterpFromFile.m =================================================================== --- /issm/trunk/src/m/utils/Interp/InterpFromFile.m (revision 8297) +++ /issm/trunk/src/m/utils/Interp/InterpFromFile.m (revision 8298) @@ -38,5 +38,5 @@ Names=FieldFindVarNames(filename); Data=load(filename); -if strcmpi(Names.interp,'grid'), +if strcmpi(Names.interp,'node'), data_out=InterpFromGridToMesh(Data.(Names.xname),Data.(Names.yname),Data.(Names.dataname),x,y,default_value); else Index: /issm/trunk/src/m/utils/Interp/VelFindVarNames.m =================================================================== --- /issm/trunk/src/m/utils/Interp/VelFindVarNames.m (revision 8297) +++ /issm/trunk/src/m/utils/Interp/VelFindVarNames.m (revision 8298) @@ -29,5 +29,5 @@ xenum=NaN; yenum=NaN; vxenum=NaN; vyenum=NaN; indexenum=NaN; if length(A)==4, - isgrid=1; + isnode=1; for i=1:4 if strcmpi(A(i).name(1),'x'); @@ -44,5 +44,5 @@ end elseif length(A)==5, - isgrid=0; + isnode=0; for i=1:5 if strcmpi(A(i).name(1),'x'); @@ -61,5 +61,5 @@ end else - error(['VelFindVarNames error message: file ' filename ' not supported yet (it should hold 4 variables x,y,vx and vy (for grids) OR 5 variables x,y,index,vx and vy (for mesh))']); + error(['VelFindVarNames error message: file ' filename ' not supported yet (it should hold 4 variables x,y,vx and vy (for nodes) OR 5 variables x,y,index,vx and vy (for mesh))']); end @@ -70,5 +70,5 @@ %find index -if (~isgrid & isnan(indexenum)), +if (~isnode & isnan(indexenum)), for i=1:5 lengthi=min(A(i).size); @@ -115,8 +115,8 @@ Names.vxname=A(vxenum).name; Names.vyname=A(vyenum).name; -if ~isgrid, +if ~isnode, Names.indexname=A(indexenum).name; Names.interp='mesh'; else - Names.interp='grid'; + Names.interp='node'; end Index: /issm/trunk/src/m/utils/Interp/plugvelocities.m =================================================================== --- /issm/trunk/src/m/utils/Interp/plugvelocities.m (revision 8297) +++ /issm/trunk/src/m/utils/Interp/plugvelocities.m (revision 8298) @@ -28,5 +28,5 @@ %Interpolation -if strcmpi(Names.interp,'grid'), +if strcmpi(Names.interp,'node'), md.vx_obs=InterpFromGridToMesh(Vel.(Names.xname),Vel.(Names.yname),Vel.(Names.vxname),md.x,md.y,default_value); md.vy_obs=InterpFromGridToMesh(Vel.(Names.xname),Vel.(Names.yname),Vel.(Names.vyname),md.x,md.y,default_value); Index: /issm/trunk/src/m/utils/Mesh/BamgCall.m =================================================================== --- /issm/trunk/src/m/utils/Mesh/BamgCall.m (revision 8297) +++ /issm/trunk/src/m/utils/Mesh/BamgCall.m (revision 8298) @@ -25,6 +25,6 @@ %Compute metric t1=clock; fprintf('%s',' computing metric...'); -if length(md.gridonwater)==md.numberofgrids, - pos=find(md.gridonwater); +if length(md.nodeonwater)==md.numberofnodes, + pos=find(md.nodeonwater); else pos=[]; @@ -36,5 +36,5 @@ t1=clock; fprintf('%s',' writing initial mesh files...'); fid=fopen('carre0.met','w'); -fprintf(fid,'%i %i\n',md.numberofgrids,3); +fprintf(fid,'%i %i\n',md.numberofnodes,3); fprintf(fid,'%i %i %i\n',metric'); fclose(fid); @@ -49,6 +49,6 @@ %Vertices -fprintf(fid,'\n%s\n%i\n\n','Vertices',md.numberofgrids); -fprintf(fid,'%8g %8g %i\n',[md.x md.y ones(md.numberofgrids,1)]'); +fprintf(fid,'\n%s\n%i\n\n','Vertices',md.numberofnodes); +fprintf(fid,'%8g %8g %i\n',[md.x md.y ones(md.numberofnodes,1)]'); %Triangles @@ -72,5 +72,5 @@ md.z=zeros(A.nods,1); md.elements=A.index; -md.numberofgrids=A.nods; +md.numberofnodes=A.nods; md.numberofelements=A.nels; numberofelements2=md.numberofelements; Index: /issm/trunk/src/m/utils/Mesh/BamgCallFromMetric.m =================================================================== --- /issm/trunk/src/m/utils/Mesh/BamgCallFromMetric.m (revision 8297) +++ /issm/trunk/src/m/utils/Mesh/BamgCallFromMetric.m (revision 8298) @@ -17,5 +17,5 @@ t1=clock; fprintf('%s',' writing initial mesh files...'); fid=fopen('carre0.met','w'); -fprintf(fid,'%i %i\n',md.numberofgrids,3); +fprintf(fid,'%i %i\n',md.numberofnodes,3); fprintf(fid,'%i %i %i\n',metric'); fclose(fid); @@ -30,6 +30,6 @@ %Vertices -fprintf(fid,'\n%s\n%i\n\n','Vertices',md.numberofgrids); -fprintf(fid,'%8g %8g %i\n',[md.x md.y ones(md.numberofgrids,1)]'); +fprintf(fid,'\n%s\n%i\n\n','Vertices',md.numberofnodes); +fprintf(fid,'%8g %8g %i\n',[md.x md.y ones(md.numberofnodes,1)]'); %Triangles @@ -53,5 +53,5 @@ md.z=zeros(A.nods,1); md.elements=A.index; -md.numberofgrids=A.nods; +md.numberofnodes=A.nods; md.numberofelements=A.nels; numberofelements2=md.numberofelements; Index: /issm/trunk/src/m/utils/Mesh/ComputeHessian.m =================================================================== --- /issm/trunk/src/m/utils/Mesh/ComputeHessian.m (revision 8297) +++ /issm/trunk/src/m/utils/Mesh/ComputeHessian.m (revision 8298) @@ -13,9 +13,9 @@ %some variables -numberofgrids=length(x); +numberofnodes=length(x); numberofelements=size(index,1); %some checks -if length(field)~=numberofgrids & length(field)~=numberofelements, +if length(field)~=numberofnodes & length(field)~=numberofelements, error('ComputeHessian error message: the given field size not supported yet'); end @@ -32,10 +32,10 @@ areas=GetAreas(index,x,y); -%comput weights that holds the volume of all the element holding the grid i -weights=sparse(line,ones(linesize,1),repmat(areas,3,1),numberofgrids,1); +%comput weights that holds the volume of all the element holding the node i +weights=sparse(line,ones(linesize,1),repmat(areas,3,1),numberofnodes,1); %compute field on nodes if on elements if length(field)==numberofelements, - field=sparse(line,ones(linesize,1),repmat(areas.*field,3,1),numberofgrids,1)./weights ; + field=sparse(line,ones(linesize,1),repmat(areas.*field,3,1),numberofnodes,1)./weights ; end @@ -44,7 +44,7 @@ grad_ely=sum(field(index).*beta,2); -%Compute gradient for each grid (average of the elements around) -gradx=sparse(line,ones(linesize,1),repmat(areas.*grad_elx,3,1),numberofgrids,1); -grady=sparse(line,ones(linesize,1),repmat(areas.*grad_ely,3,1),numberofgrids,1); +%Compute gradient for each node (average of the elements around) +gradx=sparse(line,ones(linesize,1),repmat(areas.*grad_elx,3,1),numberofnodes,1); +grady=sparse(line,ones(linesize,1),repmat(areas.*grad_ely,3,1),numberofnodes,1); gradx=gradx./weights; grady=grady./weights; @@ -55,6 +55,6 @@ if strcmpi(type,'node') %Compute Hessian on the nodes (average of the elements around) - hessian=[sparse(line,ones(linesize,1),repmat(areas.*hessian(:,1),3,1),numberofgrids,1)./weights ... - sparse(line,ones(linesize,1),repmat(areas.*hessian(:,2),3,1),numberofgrids,1)./weights ... - sparse(line,ones(linesize,1),repmat(areas.*hessian(:,3),3,1),numberofgrids,1)./weights ]; + hessian=[sparse(line,ones(linesize,1),repmat(areas.*hessian(:,1),3,1),numberofnodes,1)./weights ... + sparse(line,ones(linesize,1),repmat(areas.*hessian(:,2),3,1),numberofnodes,1)./weights ... + sparse(line,ones(linesize,1),repmat(areas.*hessian(:,3),3,1),numberofnodes,1)./weights ]; end Index: /issm/trunk/src/m/utils/Mesh/ComputeMetric.m =================================================================== --- /issm/trunk/src/m/utils/Mesh/ComputeMetric.m (revision 8297) +++ /issm/trunk/src/m/utils/Mesh/ComputeMetric.m (revision 8298) @@ -7,5 +7,5 @@ % % Example: -% metric=ComputeMetric(hessian,2/9,10^-1,100,10^5,find(md.gridonwater) +% metric=ComputeMetric(hessian,2/9,10^-1,100,10^5,find(md.nodeonwater) %first, find the eigen values of eah line of H=[hessian(i,1) hessian(i,2); hessian(i,2) hessian(i,3)] Index: /issm/trunk/src/m/utils/Mesh/MeshQuality.m =================================================================== --- /issm/trunk/src/m/utils/Mesh/MeshQuality.m (revision 8297) +++ /issm/trunk/src/m/utils/Mesh/MeshQuality.m (revision 8298) @@ -17,6 +17,6 @@ %Compute metric -if length(md.gridonwater)==md.numberofgrids, - pos=find(md.gridonwater); +if length(md.nodeonwater)==md.numberofnodes, + pos=find(md.nodeonwater); else pos=[]; @@ -35,5 +35,5 @@ e3y=[y(index(:,1))-y(index(:,3))]; -%metric of each the 3 grids for each element +%metric of each the 3 nodes for each element M1=metric(index(:,1),:); M2=metric(index(:,2),:); @@ -60,6 +60,6 @@ lambda1=min(max(abs(lambda1)*scale/epsilon,1/hmax^2),1/hmin^2); lambda2=min(max(abs(lambda2)*scale/epsilon,1/hmax^2),1/hmin^2); -if length(md.gridonwater)==md.numberofgrids; - pos=find(md.gridonwater); +if length(md.nodeonwater)==md.numberofnodes; + pos=find(md.nodeonwater); lambda1(pos)=0; lambda2(pos)=0; Index: /issm/trunk/src/m/utils/Mesh/YamsCall.m =================================================================== --- /issm/trunk/src/m/utils/Mesh/YamsCall.m (revision 8297) +++ /issm/trunk/src/m/utils/Mesh/YamsCall.m (revision 8298) @@ -25,6 +25,6 @@ %Compute metric t1=clock; fprintf('%s',' computing metric...'); -if length(md.gridonwater)==md.numberofgrids, - pos=find(md.gridonwater); +if length(md.nodeonwater)==md.numberofnodes, + pos=find(md.nodeonwater); else pos=[]; @@ -46,6 +46,6 @@ %Vertices -fprintf(fid,'\n%s\n%i\n\n','Vertices',md.numberofgrids); -fprintf(fid,'%8g %8g %i\n',[md.x md.y zeros(md.numberofgrids,1)]'); +fprintf(fid,'\n%s\n%i\n\n','Vertices',md.numberofnodes); +fprintf(fid,'%8g %8g %i\n',[md.x md.y zeros(md.numberofnodes,1)]'); %Triangles @@ -92,5 +92,5 @@ md.z=zeros(size(Coor,1),1); md.elements=Tria; -md.numberofgrids=size(Coor,1); +md.numberofnodes=size(Coor,1); md.numberofelements=size(Tria,1); numberofelements2=md.numberofelements; Index: /issm/trunk/src/m/utils/Mesh/argusmesh.m =================================================================== --- /issm/trunk/src/m/utils/Mesh/argusmesh.m (revision 8297) +++ /issm/trunk/src/m/utils/Mesh/argusmesh.m (revision 8298) @@ -29,5 +29,5 @@ end -%Read first line of the argus mesh: grid and element parameters +%Read first line of the argus mesh: node and element parameters [buffer,bytecount]=fscanf(fileid,'%i %i %i %i',[1 4]); if bytecount~=4, @@ -37,8 +37,8 @@ nods=buffer(2); num_element_parameters=buffer(3); -num_grid_parameters=buffer(4); -disp([' argus model ''' root ''' contains ' num2str(nel) ' elements and ' num2str(nods) ' grids.']); +num_node_parameters=buffer(4); +disp([' argus model ''' root ''' contains ' num2str(nel) ' elements and ' num2str(nods) ' nodes.']); -%initialize elements and grids +%initialize elements and nodes elements=zeros(nel,3); element_parameters=zeros(nel,num_element_parameters); @@ -46,17 +46,17 @@ y=zeros(nods,1); z=zeros(nods,1); -grid_parameters=zeros(nods,num_grid_parameters); +node_parameters=zeros(nods,num_node_parameters); -%read grids: +%read nodes: format_string='%s %i %f %f '; -for n=1:num_grid_parameters, +for n=1:num_node_parameters, format_string=[format_string ' %i ']; end for n=1:nods, - [buffer,bytecount]=fscanf(fileid,format_string,[1,num_grid_parameters+4]); + [buffer,bytecount]=fscanf(fileid,format_string,[1,num_node_parameters+4]); x(n)=buffer(3); y(n)=buffer(4); - grid_parameters(n,:)=buffer(5:length(buffer)); + node_parameters(n,:)=buffer(5:length(buffer)); end @@ -81,8 +81,8 @@ md.y=y; md.z=z; -md.numberofgrids=size(md.x,1); +md.numberofnodes=size(md.x,1); md.numberofelements=size(md.elements,1); -md.gridonbed=ones(md.numberofgrids,1); -md.gridonsurface=ones(md.numberofgrids,1); +md.nodeonbed=ones(md.numberofnodes,1); +md.nodeonsurface=ones(md.numberofnodes,1); md.elementonbed=ones(md.numberofelements,1); md.elementonsurface=ones(md.numberofelements,1); @@ -93,7 +93,7 @@ md=addnote(md,notes); -%Add segments and grids on boundary +%Add segments and nodes on boundary md.segments=findsegments(md); -md.gridonboundary=zeros(md.numberofgrids,1); -md.gridonboundary(md.segments(:,1))=1; -md.gridonboundary(md.segments(:,2))=1; +md.nodeonboundary=zeros(md.numberofnodes,1); +md.nodeonboundary(md.segments(:,1))=1; +md.nodeonboundary(md.segments(:,2))=1; Index: /issm/trunk/src/m/utils/Mesh/squaremesh.m =================================================================== --- /issm/trunk/src/m/utils/Mesh/squaremesh.m (revision 8297) +++ /issm/trunk/src/m/utils/Mesh/squaremesh.m (revision 8298) @@ -56,12 +56,12 @@ segments(2*(ny-1)+(nx-1)+1:2*(nx-1)+2*(ny-1),:)=[[1:ny:(nx-2)*ny+1]' [ny+1:ny:ny*(nx-1)+1]' [1:2*(ny-1):2*(nx-2)*(ny-1)+1]']; -%plug coordinates and grids +%plug coordinates and nodes md.x=x; md.y=y; md.z=zeros(nods,1); -md.numberofgrids=nods; -md.gridonboundary=zeros(nods,1);md.gridonboundary(segments(:,1:2))=1; -md.gridonbed=ones(nods,1); -md.gridonsurface=ones(nods,1); +md.numberofnodes=nods; +md.nodeonboundary=zeros(nods,1);md.nodeonboundary(segments(:,1:2))=1; +md.nodeonbed=ones(nods,1); +md.nodeonsurface=ones(nods,1); %plug elements @@ -73,5 +73,5 @@ %Now, build the connectivity tables for this mesh. -md.nodeconnectivity=NodeConnectivity(md.elements,md.numberofgrids); +md.nodeconnectivity=NodeConnectivity(md.elements,md.numberofnodes); md.elementconnectivity=ElementConnectivity(md.elements,md.nodeconnectivity); Index: /issm/trunk/src/m/utils/Mesh/zerothickness_icesheetfront.m =================================================================== --- /issm/trunk/src/m/utils/Mesh/zerothickness_icesheetfront.m (revision 8297) +++ /issm/trunk/src/m/utils/Mesh/zerothickness_icesheetfront.m (revision 8298) @@ -18,9 +18,9 @@ segments_icesheet=segments(pos,:); -%retrieve grids on ice sheet front -grid_icesheetfront=intersect(segments_icesheet(:,1),segments_icesheet(:,2)); +%retrieve nodes on ice sheet front +node_icesheetfront=intersect(segments_icesheet(:,1),segments_icesheet(:,2)); %modify thickness, surface and bed to be a default value -thickness(grid_icesheetfront)=default_value; -bed(grid_icesheetfront)=surface(grid_icesheetfront)-thickness(grid_icesheetfront); +thickness(node_icesheetfront)=default_value; +bed(node_icesheetfront)=surface(node_icesheetfront)-thickness(node_icesheetfront); Index: /issm/trunk/src/m/utils/Numerics/cfl_step.m =================================================================== --- /issm/trunk/src/m/utils/Numerics/cfl_step.m (revision 8297) +++ /issm/trunk/src/m/utils/Numerics/cfl_step.m (revision 8298) @@ -11,6 +11,6 @@ %Check length of velocities -if size(vx,1)~=md.numberofgrids & size(vy,1)~=md.numberofgrids, - error('timestpes error message: size of velocity components must be the same as md.numberofgrids'); +if size(vx,1)~=md.numberofnodes & size(vy,1)~=md.numberofnodes, + error('timestpes error message: size of velocity components must be the same as md.numberofnodes'); end