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/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.
+   DTArray& dd = *temp3;
+
    Range all = Range::all();
 
 //   fprintf(stderr,"Matrix multiply\n");
@@ -943,6 +982,17 @@ void Cheb_2dmg::matrix_multiply(ubox * & lhs, fbox * & rhs) {
    grad_2d->get_dx(&dx);
    grad_2d->get_dz(&dz);
 
+    DTArray& helmCoef1 = *c1;
+    DTArray& helmCoef2 = *c2;
+    DTArray& helmCoef3 = *c3;
+    DTArray& helmCoef4 = *c4;
+
+   // Derek: add first derivative terms to RHS
+   *rhs->gridbox = helmCoef1*dx + helmCoef3*dz;
+   //*rhs->gridbox = (*c1)*dx - (*c3)*dz; //Derek: Need minus if not
+                                          //doing setjac(-1,...) on
+                                          // z-coordinate.
+
 //   fprintf(stderr,"Dx\n");
 //   fprintf(stderr,"Dz\n");
 
@@ -953,8 +1003,11 @@ void Cheb_2dmg::matrix_multiply(ubox * & lhs, fbox * & rhs) {
       grad_2d->setup_array(&dx,SINE,NONE,CHEBY);
    else
       grad_2d->setup_array(&dx,type_x,NONE,CHEBY);
-      
-   grad_2d->get_dx(rhs->gridbox);
+
+   // Derek:
+   grad_2d->get_dx(&dd);
+   *rhs->gridbox = *rhs->gridbox + helmCoef2*dd;
+
    // lhs_zz
    if (type_x == SINE)
       grad_2d->setup_array(&dz,COSINE,NONE,CHEBY);
@@ -962,7 +1015,10 @@ void Cheb_2dmg::matrix_multiply(ubox * & lhs, fbox * & rhs) {
       grad_2d->setup_array(&dz,SINE,NONE,CHEBY);
    else
       grad_2d->setup_array(&dz,type_x,NONE,CHEBY);
-   grad_2d->get_dz(rhs->gridbox,true);
+
+   // Derek:
+   grad_2d->get_dz(&dd);
+   *rhs->gridbox = *rhs->gridbox + helmCoef4*dd;
 
    // apply helmholtz
 

src/gmres_2d_solver_impl.hpp

@@ -81,6 +81,10 @@ class Cheb_2dmg : public GMRES_Interface < fbox * , ubox *> {
       // used
       DTArray * temp1, * temp2, * temp3;
 
+      //Derek: variable coefficients for more general problem
+      // c1 u_x + c2 u_xx + c3 u_z + c4 u_zz - u = f
+      DTArray * c1, * c2, * c3, * c4;
+
       // C-ordered arrays for interfacing with the multigrid preconditioner
       Array<double,2> * r2d, * s2d;
 
@@ -137,6 +141,9 @@ class Cheb_2dmg : public GMRES_Interface < fbox * , ubox *> {
 
       bool noisy() const;
 
+      // Derek: method for setting variable coefficients
+      void set_ci(DTArray * cin, int i); 
+
    private:
       // Allocation data
       vector<fbox *> r_free;