Merge branch 'ds/NHSW' into 'master'

Ds/nhsw

See merge request !1

src/Makefile

@@ -73,12 +73,21 @@ BASECASE_OBJS := $(addprefix BaseCase/,$(notdir $(BASECASE_CPPS:.cpp=.o)))
 SCIENCE_CPPS := $(wildcard Science/*.cpp)
 SCIENCE_OBJS := $(addprefix Science/,$(notdir $(SCIENCE_CPPS:.cpp=.o)))
 
+# Non-hydrostatic shallow water deps
+NH_BASE := TArray.o Parformer.o T_util.o gmres.o gmres_2d_solver.o gmres_1d_solver.o Splits.o Par_util.o gmres.o grad.o multigrid.o chebmat.o
+
 ##
 ## Recipes
 ##
 
 NSIntegrator.o: NSIntegrator.cpp NSIntegrator_impl.cc
 
+NHchannel_x: NHchannel.o $(NH_BASE)
+	$(LD) $(LDFLAGS) -o $@ $^ $(LDLIBS)
+
+NHdonut2d_x: NHdonut2d.o $(NH_BASE)
+	$(LD) $(LDFLAGS) -o $@ $^ $(LDLIBS)
+
 tests/test%.o: tests/test%.cpp
 	$(MPICXX) $(CFLAGS) -o $@ -c $<
 

src/NHdonut2d.cpp

+
+#include <blitz/array.h>
+#include <mpi.h>
+#include "T_util.hpp"
+#include "Par_util.hpp"
+#include "TArray.hpp"
+#include <stdio.h>
+#include <math.h>
+#include <iostream>
+#include <vector>
+#include "Splits.hpp"
+#include <random/normal.h>
+#include <fstream>
+#include "Parformer.hpp"
+#include <stdlib.h>
+#include <stdio.h>
+#include "gmres.hpp"
+#include "gmres_2d_solver.hpp"
+#include "gmres_2d_solver_impl.hpp"
+#include "grad.hpp"
+#include "chebmat.hpp"
+#include "lserk4.hpp"
+
+using namespace TArrayn;
+using namespace Transformer;
+
+using blitz::Array;
+using blitz::TinyVector;
+using blitz::GeneralArrayStorage;
+using blitz::Range;
+
+using ranlib::Normal;
+
+using namespace std;
+
+// Grid size
+
+#define N_R 32
+#define N_THETA 128
+
+// Grid lengths
+
+#define R_OUTER 8000.0
+#define R_INNER 1000.0
+
+#define L_R (R_OUTER - R_INNER)
+
+// Defines for physical parameters
+#define G (0.03*9.81)
+#define EARTH_OMEGA (2*M_PI/(24*3600))
+#define EARTH_RADIUS (6371e3)
+#define LATITUDE (M_PI/2)
+#define ROT_F (7.8828e-5)
+//#define ROT_F (2*EARTH_OMEGA*sin(LATITUDE))
+#define ROT_B (0*2*EARTH_OMEGA*cos(LATITUDE)/EARTH_RADIUS)
+#define H0 (12.8) 
+#define H_DEPTH (H0) //const for now.
+
+// Timestep parameters
+#define FINAL_T 1200.0
+//#define FINAL_T (3600.0*24.0*3.0)
+#define INITIAL_T 0.0
+#define SAFETY_FACTOR 0.25
+
+#define NUMOUTS 200.0
+
+// Filtering parameters
+#define FILTER_ON true
+#define F_CUTOFF 0.4  //0.4 usually
+#define F_ORDER 4
+#define F_STREN (-0.33) 
+
+// GMRES parameters
+#define MAXIT 30
+#define TOL 1.0e-8
+#define RESTARTS 1
+#define NOISYGMRES true
+
+// do we want to output at all?
+#define OUTFLAG true
+#define NHOUTFLAG true //output auxiliary variable, z?
+
+// Blitz index placeholders
+
+blitz::firstIndex ii;
+blitz::secondIndex jj;
+blitz::thirdIndex kk;
+
+int main(int argc, char ** argv) {
+   // Initialize MPI
+   MPI_Init(&argc, &argv);
+
+   // make grids
+   Array<double,1> theta(N_THETA), r(N_R);
+   // matrices for dealing with imposing Neuman bc's on eta
+   Array<double,2> Dr(N_R,N_R);
+   Array<double,2> neumatinv(2,2);
+
+   double dtheta = 2*M_PI/N_THETA;
+   theta = (ii+0.5)*dtheta;
+   r = -cos(M_PI*ii/(N_R-1));
+
+   // get cheb matrix on [-1,1]
+   Dr = chebmat(N_R);
+
+   //adjust from standard grids to physical grids
+   r = L_R*((r(ii)+1.0)/2.0) + R_INNER;
+
+   //apply Jacobian to get cheb matrix on physical grid.
+   Dr = (-2.0/L_R)*Dr; 
+   // put entries into 2x2 Neuman-imposing matrix
+   double neudet = Dr(0,0)*Dr(N_R-1,N_R-1)-Dr(0,N_R-1)*Dr(N_R-1,0);
+   neumatinv(0,0) = Dr(N_R-1,N_R-1);
+   neumatinv(0,1) = -Dr(0,N_R-1);
+   neumatinv(1,0) = -Dr(N_R-1,0);
+   neumatinv(1,1) = Dr(0,0);
+   neumatinv = (1/neudet)*neumatinv;
+
+   // Get parameters for local array storage
+   TinyVector<int,3> local_lbound, local_extent;
+   GeneralArrayStorage<3> local_storage;
+
+   local_lbound = alloc_lbound(N_THETA,1,N_R);
+   local_extent = alloc_extent(N_THETA,1,N_R);
+   local_storage = alloc_storage(N_THETA,1,N_R);
+
+   // Necessary FFT transformers (for filtering)
+   TransWrapper XY_xform(N_THETA,1,N_R,FOURIER,NONE,CHEBY);
+   
+
+   // Allocate space for flow variables
+   DTArray utheta(local_lbound,local_extent,local_storage);
+   DTArray ur(local_lbound,local_extent,local_storage);
+   DTArray eta(local_lbound,local_extent,local_storage);
+
+   // Runge-Kutta residual storage.
+   DTArray res_utheta(local_lbound,local_extent,local_storage);
+   DTArray res_ur(local_lbound,local_extent,local_storage);
+   DTArray res_eta(local_lbound,local_extent,local_storage);
+
+   
+   // Allocate array for depth profile  
+   DTArray H(local_lbound,local_extent,local_storage);
+
+   // Common geometric factor (1/r)
+   DTArray rinv(local_lbound,local_extent,local_storage), r2d(local_lbound,local_extent,local_storage);
+   rinv = 1/r(kk);
+   r2d = r(kk);
+
+   // set equal to expression defined in pre-processing
+   H = H_DEPTH;
+   double Hmax = max(H);
+
+
+   // set initial conditions
+   //etaq = (H0/4)*exp(-.1*((y(kk)/1e2)*(y(kk)/1e2))
+     //                           -1*((x(ii)-0.5*Lx)/3e2)*((x(ii)-0.5*Lx)/3e2));
+   eta = (H0/4.0)*(r2d/R_OUTER)*(cos(theta(ii)) + 0*kk);
+   ur = 0.0;
+   utheta = 0.0;
+
+   int tstep = 0;  //time-step counter
+   // Compute time-stepping details
+
+   double etamax = psmax(max(abs(eta)));
+   double c0max = sqrt(G*(Hmax + etamax));
+   double dr = fabs(r(1)-r(0));
+   double dt = SAFETY_FACTOR*fmin(dr,R_INNER*dtheta)/c0max;
+   // this assumes uniform spacing in Cheby (y-)direction, should fix.
+   double t = INITIAL_T;
+   double numsteps = (FINAL_T - INITIAL_T)/dt;
+   int outputinterval = (int) floor(numsteps/NUMOUTS);
+   // don't allow zero.
+   outputinterval = max(outputinterval,1);
+   if (master()) printf("Using timestep of %gs, with final time of %gs\n",dt,FINAL_T);
+   if (master()) printf("Reference: C_0_max = %g m/s, dr = %g m, d(arc) = %g m\n",c0max,L_R/N_R,R_INNER*dtheta);
+
+   // initialize output stream for times file, and write out initial time.
+   ofstream timefile;
+   if (master()) {
+       timefile.open("times", ios::out | ios::trunc);
+       timefile << t << "\n";
+       timefile.close();
+   }
+
+   // Allocate space for auxiliary elliptic variable
+   DTArray z(local_lbound,local_extent,local_storage);
+
+   if (OUTFLAG == true)  {
+       write_reader(eta, "eta", true);
+       write_reader(ur, "ur", true);
+       write_reader(utheta, "utheta", true);
+       write_reader(H, "H");
+
+       write_array(eta,"eta",tstep/outputinterval); 
+       write_array(ur,"ur",tstep/outputinterval);
+       write_array(utheta,"utheta",tstep/outputinterval);
+       write_array(H,"H");
+
+       if (NHOUTFLAG == true) 
+           write_reader(z,"z",true);
+   }
+   
+   // Allocate space for some temporaries
+   DTArray temp1(local_lbound,local_extent,local_storage),
+           temp2(local_lbound,local_extent,local_storage),
+           temp3(local_lbound,local_extent,local_storage),
+           temp4(local_lbound,local_extent,local_storage),
+           temp5(local_lbound,local_extent,local_storage);
+
+   // Allocate space for forcing vector
+   DTArray Fx(local_lbound,local_extent,local_storage),
+           Fy(local_lbound,local_extent,local_storage);
+
+   // Allocate space for elliptic problem variable coefficients.
+   DTArray cx(local_lbound,local_extent,local_storage),
+           cxx(local_lbound,local_extent,local_storage),
+           cy(local_lbound,local_extent,local_storage),
+           cyy(local_lbound,local_extent,local_storage);
+
+   // write grids to file
+   temp1 = theta(ii) + 0.0*kk;
+   write_array(temp1,"thetagrid");
+   write_reader(temp1,"thetagrid");
+ 
+   write_array(r2d,"rgrid");
+   write_reader(r2d,"rgrid");
+  
+   // Build gradient operator, calling seq: szx,szy,szz, s_exp in x,y,z
+   Grad mygrad(N_THETA,1,N_R,FOURIER,NONE,CHEBY);
+   
+   // set (constant) jacobian based on our rectangular grid. 
+   mygrad.set_jac(firstDim,firstDim,2*M_PI);
+   mygrad.set_jac(secondDim,secondDim,1.0);
+   mygrad.set_jac(thirdDim,thirdDim,-2/L_R); //Cheby grids need the '-'.
+   
+   // set coefficients of elliptic problem
+   cyy = (H*H)/6;  //coeff of z_rr
+   cxx = (rinv*rinv)*cyy;  //coeff of z_{\theta\theta}
+
+   //cx & cy (coefs of z_\theta and z_r) are calculated numerically.
+   mygrad.setup_array(&cxx, FOURIER,NONE,CHEBY);
+   mygrad.get_dx(&cx);  //get theta derivative, store in cx. This is d(H2o6/r^2)/d\theta
+
+   temp1 = r2d*cyy;
+   mygrad.setup_array(&temp1, FOURIER,NONE,CHEBY);
+   mygrad.get_dz(&temp2); //get r derivative, store in temp2. This is d(r*H2o6)/dr
+   cy = rinv*temp2;       // needs to be divided by r to complete the Christoffel symbol
+
+   
+   // create gmres-2d solver interface
+   Cheb_2dmg a(N_THETA, N_R);
+  
+   int itercount; //gmres iteration count  
+   double dbc=0.0;
+   double nbc=1.0;
+
+   // set variable coefs (must do before set_grad)
+   a.set_ci(&cx,1);
+   a.set_ci(&cxx,2);
+   a.set_ci(&cy,3);
+   a.set_ci(&cyy,4);
+
+   a.set_grad(&mygrad); // need to do this before set_bc 
+
+   // set_bc, calling sequence is helm, dir., neu., S_EXP ('x' series expans)
+   a.set_bc(-1.0,dbc,nbc,FOURIER,dbc,nbc);
+
+   // Initialize structures that are used by gmres object
+   fbox * init_r = a.alloc_resid();
+   ubox * final_u = a.alloc_basis();
+   
+   //Build the solver object with template class
+   GMRES_Solver<Cheb_2dmg> mysolver(&a);
+
+   // set forcing
+   Fx = 0;
+   Fy = 0;
+
+   double starttime = MPI_Wtime();
+
+   // Runge-Kutta steps
+   if (master()) printf("Entering main loop... \n");
+   while (t < FINAL_T) {
+      //make nice references for arrays used
+       DTArray &temp = temp1, &rhs=temp2, &a1 = temp3, &a2 = temp4, &dump = temp5;
+
+       //update forcing:
+       Fx = 0.0; Fy = 0.0;
+
+       // Initialize with zero RK residual.
+       res_utheta = 0.0; res_ur = 0.0; res_eta = 0.0;
+       for (int i=0; i < LSERK4::numStages; i++) {
+
+            //step eta:
+            //eta_p = eta_m - dt*((eta_n u)_x + (eta_n v)_y)
+            temp = -r2d*((H+eta)*ur);
+            mygrad.setup_array(&temp,FOURIER,NONE,CHEBY);
+            mygrad.get_dz(&rhs, false);  //get r derivative, store in rhs
+            rhs = rinv*rhs;                // (1/r)*d(r*F_r)/dr where F_r = (H+eta)u_r
+
+            temp = -rinv*(H+eta)*utheta;  //  d((1/r)*(H+eta)*utheta)/dtheta
+            mygrad.setup_array(&temp,FOURIER,NONE,CHEBY);
+            mygrad.get_dx(&rhs, true);  //get theta derivative. This time, we sum with old result (cumulative = true).
+
+            res_eta = LSERK4::rk4a[i]*res_eta + dt*rhs;
+            eta += LSERK4::rk4b[i]*res_eta;
+
+            // filter free surface
+            if (FILTER_ON == true)
+                filter3(eta,XY_xform,FOURIER,NONE,CHEBY,F_CUTOFF,F_ORDER,F_STREN);
+
+            //impose explicit Neuman conditions on eta.
+            double neurhs1 = 0.0;
+            double neurhs2 = 0.0;
+            for (int j=local_lbound(1); j<(local_lbound(1)+local_extent(1)); j++) {
+                neurhs1 = sum(-Dr(0,Range(1,N_R-2))*eta(j,0,Range(1,N_R-2)));
+                neurhs2 = sum(-Dr(N_R-1,Range(1,N_R-2))*eta(j,0,Range(1,N_R-2)));
+
+                // perform 2x2 matrix product at each point 
+                eta(j,0,0) = neumatinv(0,0)*neurhs1 + neumatinv(0,1)*neurhs2;
+                eta(j,0,N_R-1) = neumatinv(1,0)*neurhs1+ neumatinv(1,1)*neurhs2;
+            }
+
+            //form a1 and a2:
+            //nonlinear advection
+            mygrad.setup_array(&ur,FOURIER,NONE,CHEBY);
+            mygrad.get_dz(&temp,false); //d(ur)/dr
+            a1  = -ur*temp;             // ur * d(ur)/dr
+            mygrad.get_dx(&temp,false); //d(ur)/d\theta
+            a1 -= rinv*utheta*temp;     // (1/r)*utheta  * d(ur)/dtheta
+            a1 += rinv*utheta*utheta;   // Geometric term.
+
+                // a2
+            mygrad.setup_array(&utheta,FOURIER,NONE,CHEBY);
+            mygrad.get_dz(&temp,false); //d(utheta)/dr
+            a2  = -ur*temp;             // ur * d(utheta)/dr
+            mygrad.get_dx(&temp,false); //d(utheta)/d\theta
+            a2 -= rinv*utheta*temp;     // (1/r)(utheta) * d(utheta)/dtheta
+            a2 -= rinv*utheta*ur;       // Geometric term.
+
+            // pressure gradient
+            mygrad.setup_array(&eta,FOURIER,NONE,CHEBY);
+            mygrad.get_dz(&temp,false); // d(eta)/dr
+            a1 -= G*temp;
+            mygrad.get_dx(&temp,false); // (1/r)*d(eta)_/dtheta
+            a2 -= G*rinv*temp;
+
+            // Coriolis and forcing
+            a1 += (ROT_F+ROT_B*r(kk)*sin(theta(ii)))*utheta + Fx;
+            a2 -= (ROT_F+ROT_B*r(kk)*sin(theta(ii)))*ur     + Fy;
+            //done forming a1 & a2
+
+            // Perform Runge-Kutta incremental step..
+            res_ur     = LSERK4::rk4a[i]*res_ur + dt*a1;
+            res_utheta = LSERK4::rk4a[i]*res_utheta + dt*a2;
+
+            ur     += LSERK4::rk4b[i]*res_ur;
+            utheta += LSERK4::rk4b[i]*res_utheta;
+       } // RK-stages loop.
+
+
+       //compute - divergence of \vec{a}, store in rhs for helmholtz problem
+       dump = r2d*a1;
+       mygrad.setup_array(&dump,FOURIER,NONE,CHEBY);
+       mygrad.get_dz(&temp,false); 
+       temp = rinv*temp; // (1/r)*d(r*a1)/dr
+       rhs = -temp;
+       mygrad.setup_array(&a2,FOURIER,NONE,CHEBY);
+       mygrad.get_dx(&temp,false); 
+       rhs -= rinv*temp; // (1/r)*d(a2)/dtheta
+
+
+       //set bc's on RHS 
+       rhs(Range::all(),0,0)     = -a1(Range::all(),0,0)     / cyy(Range::all(),0,0);
+       rhs(Range::all(),0,N_R-1) = -a1(Range::all(),0,N_R-1) / cyy(Range::all(),0,N_R-1); 
+
+	   	// check for blow-up
+   	    double sanity = pvmax(rhs);
+	    if (master()) {
+			if (isnan(sanity) || isinf(sanity) || sanity > 1.e10) {
+                cout << "sanity: " << sanity << endl;
+				cout << "Numerical blow-up has occurred, gg." << endl;
+				return 1;
+			}
+	    }
+
+       //solve for z (non-hydrostatic pressure) with gmres
+       *init_r->gridbox = rhs;
+
+       itercount = mysolver.Solve(final_u,init_r,TOL,MAXIT,RESTARTS);
+
+		if (master() && itercount < 0) {
+			cout << "GMRES did not converged, with status: " << itercount << endl;
+			cout << "Terminating..." << endl;
+			return 1;
+		}
+
+       if (master() && NOISYGMRES == true)
+       		cout << "GMRES converged after " << itercount << " iterations." << endl;
+	
+       z = *final_u->gridbox;
+
+       //compute gradient of NH pressure, then time-step it & velocities
+       mygrad.setup_array(&z,FOURIER,NONE,CHEBY);
+       mygrad.get_dz(&temp,false); // dz/dr
+       ur += dt*(a1 + cyy*temp); //cyy = H2o6
+       mygrad.get_dx(&temp,false); // (1/r)dz/d\theta
+       utheta += dt*(a2 + cyy*rinv*temp); //cyy = H2o6
+
+       //filter velocity
+       if (FILTER_ON == true) {
+         filter3(ur,     XY_xform,FOURIER,NONE,CHEBY,F_CUTOFF,F_ORDER,F_STREN);
+         filter3(utheta, XY_xform,FOURIER,NONE,CHEBY,F_CUTOFF,F_ORDER,F_STREN);
+       }
+       //Impose BCs on v at r=R_INNER,R_OUTER (Dirichlet -> no normal flow)
+       ur(Range::all(),     0, 0) = 0;
+       ur(Range::all(), 0, N_R-1) = 0;
+
+       //increment time.
+       tstep++;
+       t+=dt;
+
+       // Check if it's time to output
+       if(!(tstep % outputinterval) && OUTFLAG == true){
+          if (master())
+               cout << "outputting at t=" << t << "\n";
+
+           write_array(ur    ,"ur",     tstep/outputinterval);
+           write_array(utheta,"utheta", tstep/outputinterval);
+           write_array(eta   ,"eta",    tstep/outputinterval);
+
+           if (NHOUTFLAG == true) 
+               write_array(z,"z",tstep/outputinterval);
+          
+           //append current time to times file
+           if (master()) {
+               timefile.open ("times", ios::out | ios::app);
+               timefile << t << "\n";
+               timefile.close();
+           }
+       } 
+
+       //generic log-style text output to screen
+       if(!(tstep % 100) || tstep < 20) {
+           if (master()) 
+              printf("Completed time %g (tstep %d)\n",t,tstep);
+           double mur = psmax(max(abs(ur))), mutheta = psmax(max(abs(utheta))), meta = psmax(max(abs(eta)));
+           if (master()) 
+             printf("Max ur %g, utheta %g, eta %g\n",mur,mutheta,meta);
+       }
+
+   } //end time-stepping loop
+   
+   double endtime = MPI_Wtime();
+   double runtime = endtime-starttime;
+   if (master()) {
+        printf("Finished run. Run-time = %g s \n", runtime);
+        timefile.open ("runtime", ios::out | ios::trunc);
+        timefile << runtime << "\n";
+        timefile.close();
+   }
+   
+   // free memory of residual and basis of gmres solver 
+   a.free_resid(init_r);
+   a.free_basis(final_u);
+    
+   MPI_Finalize();
+   return 0;
+}
\ No newline at end of file

src/chebmat.cpp

+#include "chebmat.hpp"
+
+using blitz::Array;
+using blitz::TinyVector;
+using blitz::GeneralArrayStorage;
+using blitz::Range;
+using blitz::firstDim;
+using blitz::secondDim;
+
+// Blitz index placeholders
+
+//blitz::firstIndex ii;
+//blitz::secondIndex jj;
+//blitz::thirdIndex kk;
+
+Array<double,2> chebmat(int Nx) {
+
+    blitz::firstIndex ii;
+    blitz::secondIndex jj;
+    
+    Array<double,1> x(Nx);
+    x = cos(M_PI*ii/(Nx-1));
+    
+   Array<double,2> myI(Nx,Nx);
+   Array<double,2> Dx(Nx,Nx);
+   Array<double,2> myX(Nx,Nx);
+   Array<double,1> myc(Nx);
+   Array<double,2> mydX(Nx,Nx);
+   Array<double,2> mysum(Nx,Nx);
+
+   // build identity matrix (any way to clean this up?)
+   for (int j=0; j<Nx; j++)
+       myI(j,j) = 1.0;
+
+   myc(0) = 2.0;
+   myc(Range(1,Nx-2)) = 1.0;
+   myc(Nx-1) = 2.0;
+   myc = myc*pow(-1.0,ii);
+
+   // like the "repmat" step - clean this up with blitz functionality?
+   for (int j=0; j<Nx; j++)
+        myX(Range::all(),j) = x;
+
+   mydX = myX-myX.transpose(secondDim,firstDim);
+   Dx = myc(ii)*(1/myc(jj));  //outer product
+   Dx = Dx/(mydX + myI);
+
+   // build diagonal matrix of row-sums
+   // perhaps try: sum(Dx(i,Range::all()))
+   double rowsum;
+   for (int i=0; i<Nx; i++) {
+       rowsum = 0.0;
+       for (int j=0; j<Nx; j++) {
+           rowsum+= Dx(i,j);
+       }
+       mysum(i,i) = rowsum;
+   }
+
+   Dx = Dx - mysum;
+
+   return Dx;
+}
\ No newline at end of file

src/chebmat.hpp

+#pragma once
+#include <blitz/array.h>
+#include <math.h>
+
+blitz::Array <double,2> chebmat(int Nx);
\ No newline at end of file

src/gmres_2d_solver.cpp

@@ -249,6 +249,11 @@ void Cheb_2dmg::build_precond() {
    // Now, get the Jacobian from grad_3d, carve off a relevant 2D slice, and
    // assign it to the 2d gradient's jacobian.
    double c_jac; // entry for constant jacobian
+
+   double myJ11=0.0, myJ22=0.0; //Derek: placeholders for constant jacobians.
+                     // We assume these two are consts, and 
+                     // J12=J21= 0
+
    // xx
    grad_3d->get_jac(firstDim,firstDim,c_jac,v_jac);
    if (!v_jac) {// constant
@@ -358,6 +363,7 @@ void Cheb_2dmg::build_precond() {
    /* J11 */
    grad_2d->get_jac(firstDim,firstDim,c_jac,v_jac);
    if (!v_jac) { // constant
+      myJ11 = c_jac; //Derek
       t1 = c_jac;
       t4 = 0;
    } else {
@@ -368,6 +374,7 @@ void Cheb_2dmg::build_precond() {
    // J22
    grad_2d->get_jac(thirdDim,thirdDim,c_jac,v_jac);
    if (!v_jac) { // constant
+      myJ22 = c_jac; //Derek
       t2 = c_jac;
       t5 = 0;
    } else {
@@ -403,6 +410,18 @@ void Cheb_2dmg::build_precond() {
       t2 = t2*t2 + (*v_jac)*(*v_jac);
    }
 
+    //Derek: try generalizing it for any box-domain:
+    DTArray& helmCoef1 = *c1;
+    DTArray& helmCoef2 = *c2;
+    DTArray& helmCoef3 = *c3;
+    DTArray& helmCoef4 = *c4;
+
+    
+    t1 = myJ11*myJ11*helmCoef2;
+    t2 = myJ22*myJ22*helmCoef4;
+    t4 = myJ11*helmCoef1;
+    t5 = myJ22*helmCoef3;   
+
    // Now, t1->t5 are set properly, so assign them to the MG operator
 //   fprintf(stderr,"PROBLEM SETUP\n");
 //   cerr << t1_2d << t2_2d << t3_2d << t4_2d << t5_2d;
@@ -820,6 +839,23 @@ void Cheb_2dmg::set_bc(double h, double zdir, double zneum, S_EXP sym_type, doub
    mg_precond->bc_setup(secondDim,dir_z,db_bot,da_bot,
                                  dir_z,db_top,da_top);
 }
+
+// Derek method for setting the object's variable coefs. (all pointers)
+void Cheb_2dmg::set_ci(DTArray * cin, int i) {
+
+    if (i==1)
+        c1 = cin;
+    else if (i==2)
+        c2 = cin;
+    else if (i==3)
+        c3 = cin;
+    else if (i==4)
+        c4 = cin;
+    else
+        fprintf(stderr,"set_ci\n");
+
+    return;
+}
    
 
 void Cheb_2dmg::precondition(fbox * & rhs, ubox * & soln) {
@@ -930,6 +966,9 @@ void Cheb_2dmg::matrix_multiply(ubox * & lhs, fbox * & rhs) {
 //   return;
    DTArray & dx = *temp1, & dz = *temp2;
 
+   //Derek:  temporary for 2nd derivative.