Index: /issm/trunk-jpl/src/m/mech/basalstress.m
===================================================================
--- /issm/trunk-jpl/src/m/mech/basalstress.m	(revision 13140)
+++ /issm/trunk-jpl/src/m/mech/basalstress.m	(revision 13140)
@@ -0,0 +1,22 @@
+function [bx by b]=basalstress(md)
+%BASALSTRESS - compute basal stress from basal drag and geometric information. 
+%
+%   Usage:
+%      [bx by b]=basalstress(md);
+%
+%   See also: plot_basaldrag
+
+
+%compute exponents
+s=averaging(md,1./md.friction.p,0);
+r=averaging(md,md.friction.q./md.friction.p,0);
+
+%compute horizontal velocity
+ub=sqrt(md.initialization.vx.^2+md.initialization.vy.^2)/md.constants.yts;
+ubx=md.initialization.vx/md.constants.yts;
+uby=md.initialization.vy/md.constants.yts;
+
+%compute basal drag
+bx=(md.constants.g*(md.materials.rho_ice*md.geometry.thickness+md.materials.rho_water*md.geometry.bed)).^r.*(md.friction.coefficient).^2.*ubx.^s;
+by=(md.constants.g*(md.materials.rho_ice*md.geometry.thickness+md.materials.rho_water*md.geometry.bed)).^r.*(md.friction.coefficient).^2.*uby.^s;
+b=(md.constants.g*(md.materials.rho_ice*md.geometry.thickness+md.materials.rho_water*md.geometry.bed)).^r.*(md.friction.coefficient).^2.*ub.^s;
Index: /issm/trunk-jpl/src/m/mech/cfl_step.m
===================================================================
--- /issm/trunk-jpl/src/m/mech/cfl_step.m	(revision 13140)
+++ /issm/trunk-jpl/src/m/mech/cfl_step.m	(revision 13140)
@@ -0,0 +1,23 @@
+function maxtime=cfl_step(md,vx,vy);
+%CFL_STEP - return the maximum time step for the model in years
+%
+%   Dt < 0.5 / ( u/Dx +v/Dy )
+%
+%   Usage:
+%      maxtime=cfl_step(md,vx,vy);
+%
+%   Example:
+%      dt=cfl_step(md,md.results.DiagnosticSolution.Vx,md.results.DiagnosticSolution.Vy)
+
+%Check length of velocities 
+if size(vx,1)~=md.mesh.numberofvertices & size(vy,1)~=md.mesh.numberofvertices,
+	error('timestpes error message: size of velocity components must be the same as md.mesh.numberofvertices');
+end
+
+index=md.mesh.elements;
+edgex=max(md.mesh.x(index),[],2)-min(md.mesh.x(index),[],2);
+edgey=max(md.mesh.y(index),[],2)-min(md.mesh.y(index),[],2);
+vx=max(abs(vx(index)),[],2);
+vy=max(abs(vy(index)),[],2);
+
+maxtime=1/2*min(1./(vx./edgex+vy./edgey));
Index: /issm/trunk-jpl/src/m/mech/drivingstress.m
===================================================================
--- /issm/trunk-jpl/src/m/mech/drivingstress.m	(revision 13140)
+++ /issm/trunk-jpl/src/m/mech/drivingstress.m	(revision 13140)
@@ -0,0 +1,18 @@
+function [px,py,pmag]=drivingstress(md)
+%DRIVINGSTRESS -  evaluates the driving stress
+%
+%   The driving stress is computed according to the following formula: 
+%   driving stress= rho_ice*g*H*slope
+%
+%   Usage:
+%      [Fx,Fy,Fmag]=drivingstress(md)
+
+%Get slope
+[sx,sy,s]=slope(md);
+
+%Average thickness over elements
+thickness_bar=(md.geometry.thickness(md.mesh.elements(:,1))+md.geometry.thickness(md.mesh.elements(:,2))+md.geometry.thickness(md.mesh.elements(:,3)))/3;
+
+px=md.materials.rho_ice*md.constants.g*thickness_bar.*sx;
+py=md.materials.rho_ice*md.constants.g*thickness_bar.*sy;
+pmag=sqrt(px.^2+py.^2);
Index: /issm/trunk-jpl/src/m/mech/mechanicalproperties.m
===================================================================
--- /issm/trunk-jpl/src/m/mech/mechanicalproperties.m	(revision 13140)
+++ /issm/trunk-jpl/src/m/mech/mechanicalproperties.m	(revision 13140)
@@ -0,0 +1,118 @@
+function md=mechanicalproperties(md,vx,vy)
+%MECHANICALPROPERTIES - compute stress and strain rate for a goven velocity
+%
+%   this routine computes the components of the stress tensor
+%   strain rate tensor and their respective principal directions.
+%   the results are in the model md: md.results
+%
+%   Usage:
+%      md=mechanicalproperties(md,vx,vy)
+%
+%   Example:
+%      md=mechanicalproperties(md,md.initialization.vx,md.initialization.vy);
+%      md=mechanicalproperties(md,md.inversion.vx_obs,md.inversion.vy_obs);
+
+%some checks
+if length(vx)~=md.mesh.numberofvertices | length(vy)~=md.mesh.numberofvertices,
+	error(['the input velocity should be of size ' num2str(md.mesh.numberofvertices) '!'])
+end
+if ~(md.mesh.dimension==2)
+	error('only 2d model supported yet');
+end
+if any(md.flowequation.element_equation~=2),
+	disp('Warning: the model has some non macayeal elements. These will be treated like MacAyeal''s elements');
+end
+
+%initialization
+numberofelements=md.mesh.numberofelements;
+index=md.mesh.elements;
+summation=[1;1;1];
+directionsstress=zeros(numberofelements,4);
+directionsstrain=zeros(numberofelements,4);
+valuesstress=zeros(numberofelements,2);
+valuesstrain=zeros(numberofelements,2);
+
+%compute nodal functions coefficients N(x,y)=alpha x + beta y +gamma
+[alpha beta]=GetNodalFunctionsCoeff(index,md.mesh.x,md.mesh.y);
+
+%compute shear
+vxlist=vx(index)/md.constants.yts;
+vylist=vy(index)/md.constants.yts;
+ux=(vxlist.*alpha)*summation;
+uy=(vxlist.*beta)*summation;
+vx=(vylist.*alpha)*summation;
+vy=(vylist.*beta)*summation;						
+uyvx=(vx+uy)./2;
+clear vxlist vylist
+
+%compute viscosity
+nu=zeros(numberofelements,1);
+B_bar=md.materials.rheology_B(index)*summation/3;
+power=(md.materials.rheology_n-1)./(2*md.materials.rheology_n);
+second_inv=(ux.^2+vy.^2+((uy+vx).^2)/4+ux.*vy);
+%some corrections
+location=find(second_inv~=0);
+nu(location)=B_bar(location)./(second_inv(location).^power(location));
+location=find(second_inv==0 & power~=0);
+nu(location)=10^18; 	%arbitrary maximum viscosity to apply where there is no effective shear
+location=find(second_inv==0 & power==0);
+nu(location)=B_bar(location);
+clear B_bar location second_inv power
+
+%compute stress
+tau_xx=nu.*ux;
+tau_yy=nu.*vy;
+tau_xy=nu.*uyvx;
+
+%compute principal properties of stress
+for i=1:numberofelements,
+
+	%compute stress and strainrate matrices
+	stress=[tau_xx(i) tau_xy(i)
+	tau_xy(i)  tau_yy(i)];
+	strain=[ux(i) uyvx(i)
+	uyvx(i)  vy(i)];
+
+	%eigen values and vectors
+	[directions,value]=eig(stress);
+	valuesstress(i,:)=[value(1,1) value(2,2)];
+	directionsstress(i,:)=directions(:)';
+	[directions,value]=eig(strain);
+	valuesstrain(i,:)=[value(1,1) value(2,2)];
+	directionsstrain(i,:)=directions(:)';
+end
+
+%plug onto the model
+%NB: Matlab sorts the eigen value in increasing order, we want the reverse
+stress=struct('xx',[],'yy',[],'xy',[],'principalvalue1',[],'principalaxis1',[],'principalvalue2',[],'principalaxis2',[],'effectivevalue',[]);
+stress.xx=tau_xx;
+stress.yy=tau_yy;
+stress.xy=tau_xy;
+stress.principalvalue2=valuesstress(:,1);
+stress.principalaxis2=directionsstress(:,1:2);
+stress.principalvalue1=valuesstress(:,2);
+stress.principalaxis1=directionsstress(:,3:4);
+stress.effectivevalue=1/sqrt(2)*sqrt(stress.xx.^2+stress.yy.^2+2*stress.xy.^2);
+md.results.stress=stress;
+
+strainrate=struct('xx',[],'yy',[],'xy',[],'principalvalue1',[],'principalaxis1',[],'principalvalue2',[],'principalaxis2',[],'effectivevalue',[]);
+strainrate.xx=ux;
+strainrate.yy=vy;
+strainrate.xy=uyvx;
+strainrate.principalvalue2=valuesstrain(:,1)*(365.25*24*3600); %strain rate in 1/a instead of 1/s
+strainrate.principalaxis2=directionsstrain(:,1:2);
+strainrate.principalvalue1=valuesstrain(:,2)*(365.25*24*3600); %strain rate in 1/a instead of 1/s
+strainrate.principalaxis1=directionsstrain(:,3:4);
+strainrate.effectivevalue=1/sqrt(2)*sqrt(strainrate.xx.^2+strainrate.yy.^2+2*strainrate.xy.^2);
+md.results.strainrate=strainrate;
+
+deviatoricstress=struct('xx',[],'yy',[],'xy',[],'principalvalue1',[],'principalaxis1',[],'principalvalue2',[],'principalaxis2',[],'effectivevalue',[]);
+deviatoricstress.xx=tau_xx;
+deviatoricstress.yy=tau_yy;
+deviatoricstress.xy=tau_xy;
+deviatoricstress.principalvalue2=valuesstress(:,1);
+deviatoricstress.principalaxis2=directionsstress(:,1:2);
+deviatoricstress.principalvalue1=valuesstress(:,2);
+deviatoricstress.principalaxis1=directionsstress(:,3:4);
+deviatoricstress.effectivevalue=1/sqrt(2)*sqrt(stress.xx.^2+stress.yy.^2+2*stress.xy.^2);
+md.results.deviatoricstress=deviatoricstress;
Index: /issm/trunk-jpl/src/m/mech/shear2d.m
===================================================================
--- /issm/trunk-jpl/src/m/mech/shear2d.m	(revision 13140)
+++ /issm/trunk-jpl/src/m/mech/shear2d.m	(revision 13140)
@@ -0,0 +1,23 @@
+function [sx,sy,sxy,s]=shear2d(md)
+%SHEAR2D - computes 2d strain rate
+%
+%   This routine computes the strain rate of 2d models
+%
+%   Usage:
+%      [sx,sy,sxy,s]=shear2d(md);
+%      s=shear2d(md);
+
+[alpha beta]=GetNodalFunctionsCoeff(md.mesh.elements,md.mesh.x,md.mesh.y); 
+
+summation=[1;1;1];
+sx=(md.initialization.vx(md.mesh.elements).*alpha)*summation;
+uy=(md.initialization.vx(md.mesh.elements).*beta)*summation;
+vx=(md.initialization.vy(md.mesh.elements).*alpha)*summation;
+sy=(md.initialization.vy(md.mesh.elements).*beta)*summation;						
+sxy=(uy+vx)/2;
+s=sqrt(sx.^2+sy.^2+sxy.^2+sx.*sy);
+
+%if user requested only one output, it must be the norm
+if nargout==1,
+	sx=s;
+end