Construct_arrays.c
/*
*~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*
*<LicenseText>
*
* CitcomS by Louis Moresi, Shijie Zhong, Lijie Han, Eh Tan,
* Clint Conrad, Michael Gurnis, and Eun-seo Choi.
* Copyright (C) 1994-2005, California Institute of Technology.
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 2 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*
*</LicenseText>
*
*~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
#include <math.h>
#include <sys/types.h>
#include "element_definitions.h"
#include "global_defs.h"
int layers_r(struct All_variables *,float );
int layers(struct All_variables *,int );
/*========================================================
Function to make the IEN array for a mesh of given
dimension. IEN is an externally defined structure array
NOTE: this is not really general enough for new elements:
it should be done through a pre-calculated lookup table.
======================================================== */
void construct_ien( struct All_variables *E )
{
int lev,p,q,r,rr,j;
int element,start,nel,nno;
int elz,elx,ely,nox,noy,noz;
const int dims=E->mesh.nsd;
const int ends=enodes[dims];
for (lev=E->mesh.levmax;lev>=E->mesh.levmin;lev--) {
elx = E->lmesh.ELX[lev];
elz = E->lmesh.ELZ[lev];
ely = E->lmesh.ELY[lev];
nox = E->lmesh.NOX[lev];
noz = E->lmesh.NOZ[lev];
noy = E->lmesh.NOY[lev];
nel=E->lmesh.NEL[lev];
nno=E->lmesh.NNO[lev];
for(r=1;r<=ely;r++)
for(q=1;q<=elx;q++)
for(p=1;p<=elz;p++) {
element = (r-1)*elx*elz + (q-1)*elz + p;
start = (r-1)*noz*nox + (q-1)*noz + p;
for(rr=1;rr<=ends;rr++)
E->IEN[lev][element].node[rr]= start
+ offset[rr].vector[0]
+ offset[rr].vector[1]*noz
+ offset[rr].vector[2]*noz*nox;
}
} /* end loop for lev */
}
/* determine surface things */
void construct_surface( struct All_variables *E)
{
int i, j, e, element;
e = 0;
for(element=1;element<=E->lmesh.nel;element++)
if ( element%E->lmesh.elz==0) { /* top */
e ++;
E->sien[e].node[1] = E->ien[element].node[5]/E->lmesh.noz;
E->sien[e].node[2] = E->ien[element].node[6]/E->lmesh.noz;
E->sien[e].node[3] = E->ien[element].node[7]/E->lmesh.noz;
E->sien[e].node[4] = E->ien[element].node[8]/E->lmesh.noz;
E->surf_element[e] = element;
}
E->lmesh.snel = e;
for (i=1;i<=E->lmesh.nsf;i++)
E->surf_node[i] = i*E->lmesh.noz;
if(E->control.verbose) {
for(e=1;e<=E->lmesh.snel;e++) {
fprintf(E->fp_out, "sien sel=%d node=%d %d %d %d\n",
e, E->sien[e].node[1], E->sien[e].node[2],
E->sien[e].node[3], E->sien[e].node[4]);
}
}
}
/*============================================
Function to make the ID array for above case
============================================ */
void construct_id( struct All_variables *E )
{
int i,j,k;
int eqn_count,node,nno;
int neq, gneq;
unsigned int type,doff;
int lev;
void get_bcs_id_for_residual();
const int dims=E->mesh.nsd,dofs=E->mesh.dof;
const int ends=enodes[dims];
for(lev=E->mesh.gridmax;lev>=E->mesh.gridmin;lev--) {
eqn_count = 0;
for(node=1;node<=E->lmesh.NNO[lev];node++)
for(doff=1;doff<=dims;doff++) {
E->ID[lev][node].doff[doff] = eqn_count;
eqn_count ++;
}
E->lmesh.NEQ[lev] = eqn_count;
i = 0;
for(node=1;node<=E->lmesh.NNO[lev];node++) {
if (E->NODE[lev][node] & SKIP)
for(doff=1;doff<=dims;doff++) {
i++;
E->parallel.Skip_id[lev][i] = E->ID[lev][node].doff[doff];
}
}
E->parallel.Skip_neq[lev] = i;
/* global # of unskipped eqn */
neq = E->lmesh.NEQ[lev] - E->parallel.Skip_neq[lev];
MPI_Allreduce(&neq, &gneq, 1, MPI_INT, MPI_SUM, E->parallel.world);
E->mesh.NEQ[lev] = gneq;
get_bcs_id_for_residual(E,lev);
} /* end for lev */
E->lmesh.neq = E->lmesh.NEQ[E->mesh.levmax];
E->mesh.neq = E->mesh.NEQ[E->mesh.levmax];
}
void get_bcs_id_for_residual(struct All_variables *E, int level)
{
int i,j;
const int nno=E->lmesh.NNO[level];
j = 0;
for(i=1;i<=nno;i++) {
if ( (E->NODE[level][i] & VBX) != 0 ) {
j++;
E->zero_resid[level][j] = E->ID[level][i].doff[1];
}
if ( (E->NODE[level][i] & VBY) != 0 ) {
j++;
E->zero_resid[level][j] = E->ID[level][i].doff[2];
}
if ( (E->NODE[level][i] & VBZ) != 0 ) {
j++;
E->zero_resid[level][j] = E->ID[level][i].doff[3];
}
}
E->num_zero_resid[level] = j;
}
/*==========================================================
Function to construct the LM array from the ID and IEN arrays
========================================================== */
void construct_lm(E)
struct All_variables *E;
{
int i,j,a,e;
int lev,eqn_no;
int nel, nel2;
const int dims=E->mesh.nsd,dofs=E->mesh.dof;
const int ends=enodes[dims];
return;
}
/* =====================================================
Function to build the local node matrix indexing maps
===================================================== */
void construct_node_maps( struct All_variables *E )
{
double time1,CPU_time0();
int ii,noz,noxz,m,n,nn,lev,i,j,k,jj,kk,ia,ja,is,ie,js,je,ks,ke,doff;
int neq,nno,dims2,matrix,nox,noy;
const int dims=E->mesh.nsd,dofs=E->mesh.dof;
const int ends=enodes[dims];
int max_eqn;
dims2 = dims-1;
for(lev=E->mesh.gridmax;lev>=E->mesh.gridmin;lev--) {
neq=E->lmesh.NEQ[lev];
nno=E->lmesh.NNO[lev];
noxz = E->lmesh.NOX[lev]*E->lmesh.NOZ[lev];
noz = E->lmesh.NOZ[lev];
noy = E->lmesh.NOY[lev];
nox = E->lmesh.NOX[lev];
max_eqn = 14*dims;
matrix = max_eqn*nno;
E->Node_map[lev]=(int *) malloc (matrix*sizeof(int));
for(i=0;i<matrix;i++)
E->Node_map[lev][i] = neq; /* neq indicates an invalid eqn # */
for (ii=1;ii<=noy;ii++)
for (jj=1;jj<=nox;jj++)
for (kk=1;kk<=noz;kk++) {
nn = kk + (jj-1)*noz+ (ii-1)*noxz;
for(doff=1;doff<=dims;doff++)
E->Node_map[lev][(nn-1)*max_eqn+doff-1] =
E->ID[lev][nn].doff[doff];
ia = 0;
is=1; ie=dims2;
js=1; je=dims;
ks=1; ke=dims;
if (kk==1 ) ks=2;
if (kk==noz) ke=2;
if (jj==1 ) js=2;
if (jj==nox) je=2;
if (ii==1 ) is=2;
if (ii==noy) ie=2;
for (i=is;i<=ie;i++)
for (j=js;j<=je;j++)
for (k=ks;k<=ke;k++) {
ja = nn-((2-i)*noxz + (2-j)*noz + 2-k);
if (ja<nn) {
ia++;
for (doff=1;doff<=dims;doff++)
E->Node_map[lev][(nn-1)*max_eqn+ia*dims+doff-1] =
E->ID[lev][ja].doff[doff];
}
}
}
E->Eqn_k1[lev] =
(higher_precision *)malloc(matrix*sizeof(higher_precision));
E->Eqn_k2[lev] =
(higher_precision *)malloc(matrix*sizeof(higher_precision));
E->Eqn_k3[lev] =
(higher_precision *)malloc(matrix*sizeof(higher_precision));
E->mesh.matrix_size[lev] = matrix;
if(E->control.verbose) {
fprintf(E->fp_out, "output Node_map lev=%d m=%d\n", lev, m);
fprintf(E->fp_out, "neq=%d nno=%d max_eqn=%d matrix=%d\n", neq, nno, max_eqn, matrix);
for(i=0;i<matrix;i++)
fprintf(E->fp_out, "%d %d\n", i, E->Node_map[lev][i]);
}
} /* end for level */
}
void construct_node_ks(struct All_variables *E)
{
int m,level,i,j,k,e;
int node,node1,eqn1,eqn2,eqn3,loc0,loc1,loc2,loc3,found,element,index,pp,qq;
int neq,nno,nel,max_eqn;
double elt_K[24*24];
double w1,w2,w3,ww1,ww2,ww3,zero;
higher_precision *B1,*B2,*B3;
void get_elt_k();
void get_aug_k();
void build_diagonal_of_K();
void parallel_process_termination();
const int dims=E->mesh.nsd,dofs=E->mesh.dof;
const int ends=enodes[dims];
const int lms=loc_mat_size[E->mesh.nsd];
zero = 0.0;
max_eqn = 14*dims;
for(level=E->mesh.gridmax;level>=E->mesh.gridmin;level--) {
neq=E->lmesh.NEQ[level];
nel=E->lmesh.NEL[level];
nno=E->lmesh.NNO[level];
for(i=0;i<neq;i++)
E->BI[level][i] = zero;
for(i=0;i<E->mesh.matrix_size[level];i++) {
E->Eqn_k1[level][i] = zero;
E->Eqn_k2[level][i] = zero;
E->Eqn_k3[level][i] = zero;
}
for(element=1;element<=nel;element++) {
get_elt_k(E,element,elt_K,level,0);
if (E->control.augmented_Lagr)
get_aug_k(E,element,elt_K,level);
build_diagonal_of_K(E,element,elt_K,level);
for(i=1;i<=ends;i++) { /* i, is the node we are storing to */
node=E->IEN[level][element].node[i];
pp=(i-1)*dims;
w1=w2=w3=1.0;
loc0=(node-1)*max_eqn;
if(E->NODE[level][node] & VBX) w1=0.0;
if(E->NODE[level][node] & VBZ) w3=0.0;
if(E->NODE[level][node] & VBY) w2=0.0;
for(j=1;j<=ends;j++) { /* j is the node we are receiving from */
node1=E->IEN[level][element].node[j];
/* only for half of the matrix ,because of the symmetry */
if (node1<=node) {
ww1=ww2=ww3=1.0;
qq=(j-1)*dims;
eqn1=E->ID[level][node1].doff[1];
eqn2=E->ID[level][node1].doff[2];
eqn3=E->ID[level][node1].doff[3];
if(E->NODE[level][node1] & VBX)
ww1=0.0;
if(E->NODE[level][node1] & VBZ)
ww3=0.0;
if(E->NODE[level][node1] & VBY)
ww2=0.0;
/* search for direction 1*/
found=0;
for(k=0;k<max_eqn;k++)
if(E->Node_map[level][loc0+k] == eqn1) {
/* found, index next equation */
index=k;
found++;
break;
}
assert(found /* direction 1 */);
E->Eqn_k1[level][loc0+index] += w1*ww1*elt_K[pp*lms+qq]; /* dir 1 */
E->Eqn_k2[level][loc0+index] += w2*ww1*elt_K[(pp+1)*lms+qq];/*dir 1*/
E->Eqn_k3[level][loc0+index] += w3*ww1*elt_K[(pp+2)*lms+qq];/*dir 1*/
/* search for direction 2*/
found=0;
for(k=0;k<max_eqn;k++)
if(E->Node_map[level][loc0+k] == eqn2) {
/* found, index next equation */
index=k;
found++;
break;
}
assert(found /* direction 2 */);
E->Eqn_k1[level][loc0+index] += w1*ww2*elt_K[pp*lms+qq+1];/*dir 1*/
E->Eqn_k2[level][loc0+index] += w2*ww2*elt_K[(pp+1)*lms+qq+1];/*dir2*/
E->Eqn_k3[level][loc0+index] += w3*ww2*elt_K[(pp+2)*lms+qq+1];/*dir3*/
/* search for direction 3*/
found=0;
for(k=0;k<max_eqn;k++)
if(E->Node_map[level][loc0+k] == eqn3) {
/* found, index next equation */
index=k;
found++;
break;
}
assert(found /* direction 3 */);
E->Eqn_k1[level][loc0+index] += w1*ww3*elt_K[pp*lms+qq+2];/*dir 1*/
E->Eqn_k2[level][loc0+index] += w2*ww3*elt_K[(pp+1)*lms+qq+2];/*dir2*/
E->Eqn_k3[level][loc0+index] += w3*ww3*elt_K[(pp+2)*lms+qq+2];/*dir3*/
} /* end for node1 <= node */
} /* end for j */
} /* end for i */
} /* end for element */
(E->solver.exchange_id_d)(E, E->BI[level], level);
neq=E->lmesh.NEQ[level];
for(j=0;j<neq;j++) {
if(E->BI[level][j] ==0.0)
fprintf(stderr,"me= %d level %d, equation %d/%d has zero diagonal term\n",E->parallel.me,level,j,neq);
assert( E->BI[level][j] != 0 ); /* diagonal of matrix = 0 */
E->BI[level][j] = (double) 1.0/E->BI[level][j];
}
} /* end for level */
}
void rebuild_BI_on_boundary(E)
struct All_variables *E;
{
int m,level,i,j;
int eqn1,eqn2,eqn3;
higher_precision *B1,*B2,*B3;
int *C;
const int dims=E->mesh.nsd,dofs=E->mesh.dof;
const int max_eqn = dims*14;
for(level=E->mesh.gridmax;level>=E->mesh.gridmin;level--) {
for(j=0;j<=E->lmesh.NEQ[level];j++)
E->temp[j]=0.0;
for(i=1;i<=E->lmesh.NNO[level];i++) {
eqn1=E->ID[level][i].doff[1];
eqn2=E->ID[level][i].doff[2];
eqn3=E->ID[level][i].doff[3];
C=E->Node_map[level] + (i-1)*max_eqn;
B1=E->Eqn_k1[level]+(i-1)*max_eqn;
B2=E->Eqn_k2[level]+(i-1)*max_eqn;
B3=E->Eqn_k3[level]+(i-1)*max_eqn;
for(j=3;j<max_eqn;j++) {
E->temp[eqn1] += fabs(B1[j]);
E->temp[eqn2] += fabs(B2[j]);
E->temp[eqn3] += fabs(B3[j]);
}
for(j=0;j<max_eqn;j++)
E->temp[C[j]] += fabs(B1[j]) + fabs(B2[j]) + fabs(B3[j]);
}
(E->solver.exchange_id_d)(E, E->temp, level);
for(i=0;i<E->lmesh.NEQ[level];i++) {
E->temp[i] = E->temp[i] - 1.0/E->BI[level][i];
}
for(i=1;i<=E->lmesh.NNO[level];i++)
if (E->NODE[level][i] & OFFSIDE) {
eqn1=E->ID[level][i].doff[1];
eqn2=E->ID[level][i].doff[2];
eqn3=E->ID[level][i].doff[3];
E->BI[level][eqn1] = (double) 1.0/E->temp[eqn1];
E->BI[level][eqn2] = (double) 1.0/E->temp[eqn2];
E->BI[level][eqn3] = (double) 1.0/E->temp[eqn3];
}
} /* end for level */
}
/* ============================================
Function to set up the boundary condition
masks and other indicators.
============================================ */
/* Add lid/edge masks/nodal weightings */
void construct_masks(struct All_variables *E)
{
int i,j,k,l,node,el,elt;
int lev,elx,elz,ely,nno,nox,noz,noy;
for(lev=E->mesh.gridmax;lev>=E->mesh.gridmin;lev--) {
elz = E->lmesh.ELZ[lev];
ely = E->lmesh.ELY[lev];
noy = E->lmesh.NOY[lev];
noz = E->lmesh.NOZ[lev];
nno = E->lmesh.NNO[lev];
if (E->parallel.me_loc[3]==0 )
for (i=1;i<=E->parallel.NUM_NNO[lev].bound[5];i++) {
node = E->parallel.NODE[lev][i].bound[5];
E->NODE[lev][node] = E->NODE[lev][node] | TZEDGE;
}
if ( E->parallel.me_loc[3]==E->parallel.nprocz-1 )
for (i=1;i<=E->parallel.NUM_NNO[lev].bound[6];i++) {
node = E->parallel.NODE[lev][i].bound[6];
E->NODE[lev][node] = E->NODE[lev][node] | TZEDGE;
}
}/* end for lev */
}
/* ==========================================
build the sub-element reference matrices
========================================== */
void construct_sub_element( struct All_variables *E )
{
int i,j,k,l,m;
int lev,nox,noy,noz,nnn,elx,elz,ely,elzu,elxu,elt,eltu;
for(lev=E->mesh.levmax-1;lev>=E->mesh.levmin;lev--) {
elx = E->lmesh.ELX[lev];
elz = E->lmesh.ELZ[lev];
ely = E->lmesh.ELY[lev];
nox = E->lmesh.NOX[lev];
noy = E->lmesh.NOY[lev];
noz = E->lmesh.NOZ[lev];
elz = E->lmesh.ELZ[lev];
ely = E->lmesh.ELY[lev];
elxu = 2 * elx;
elzu = 2 * elz;
if (!E->control.NMULTIGRID) {
elzu = 1;
if (lev == E->mesh.levmax-1)
elzu = E->lmesh.ELZ[E->mesh.levmax];
}
for(i=1;i<=elx;i++)
for(j=1;j<=elz;j++)
for(k=1;k<=ely;k++) {
elt = j + (i-1)*elz +(k-1)*elz*elx;
eltu = (j*2-1) + elzu *2*(i-1) + elxu*elzu*2*(k-1);
for(l=1;l<=enodes[E->mesh.nsd];l++) {
E->EL[lev][elt].sub[l] = eltu + offset[l].vector[0]
+ offset[l].vector[1] * elzu
+ offset[l].vector[2] * elzu * elxu;
}
}
}
}
void construct_elt_ks( struct All_variables *E )
{
int e,el,lev,j,k,ii;
void get_elt_k();
void get_aug_k();
void build_diagonal_of_K();
const int dims=E->mesh.nsd;
const int n=loc_mat_size[E->mesh.nsd];
for(lev=E->mesh.gridmin;lev<=E->mesh.gridmax;lev++) {
for(el=1;el<=E->lmesh.NEL[lev];el++) {
get_elt_k(E,el,E->elt_k[lev][el].k,lev,0);
if (E->control.augmented_Lagr)
get_aug_k(E,el,E->elt_k[lev][el].k,lev);
build_diagonal_of_K(E,el,E->elt_k[lev][el].k,lev);
}
(E->solver.exchange_id_d)(E, E->BI[lev], lev); /*correct BI */
for(j=0;j<E->lmesh.NEQ[lev];j++) {
if(E->BI[lev][j] == 0.0)
fprintf(stderr,"me= %d level %d, equation %d/%d has zero diagonal term\n",E->parallel.me,lev,j,E->lmesh.NEQ[lev]);
assert( E->BI[lev][j] != 0 ); /* diagonal of matrix = 0 */
E->BI[lev][j] = (double) 1.0/E->BI[lev][j];
}
} /* end for level */
}
void construct_elt_gs( struct All_variables *E )
{
int el,lev,a;
void get_elt_g();
for(lev=E->mesh.gridmin;lev<=E->mesh.gridmax;lev++)
for(el=1;el<=E->lmesh.NEL[lev];el++)
get_elt_g(E,el,E->elt_del[lev][el].g,lev);
}
/*==============================================
For compressible cases, construct c matrix,
where c = \frac{d rho_r}{dr} / rho_r * u_r
==============================================*/
void construct_elt_cs(struct All_variables *E)
{
int el, lev;
void get_elt_c();
for(lev=E->mesh.gridmin;lev<=E->mesh.gridmax;lev++)
for(el=1;el<=E->lmesh.NEL[lev];el++)
get_elt_c(E,el,E->elt_c[lev][el].c,lev);
}
/* ==============================================================
routine for constructing stiffness and node_maps
============================================================== */
void construct_stiffness_B_matrix( struct All_variables *E )
{
void build_diagonal_of_K();
void build_diagonal_of_Ahat();
void project_viscosity();
void construct_node_maps();
void construct_node_ks();
void construct_elt_ks();
void rebuild_BI_on_boundary();
if (E->control.NMULTIGRID)
project_viscosity(E);
if (E->control.NMULTIGRID || E->control.NASSEMBLE) {
construct_node_ks(E);
}
else {
construct_elt_ks(E);
}
build_diagonal_of_Ahat(E);
if (E->control.NMULTIGRID || (E->control.NASSEMBLE && !E->control.CONJ_GRAD))
rebuild_BI_on_boundary(E);
}
/* took this apart to allow call from other subroutines */
/*
determine viscosity layer number based on radial coordinate r
if E->viscosity.z... set to Earth values, and old, num_mat=4 style is
used then
1: lithosphere 2: 100-410 3: 410-660 and 4: lower mantle
if z_layer is used, the layer numbers will refer to those read in with
z_layer
*/
int layers_r(struct All_variables *E,float r)
{
int llayers, i;
float rl;
/*
the z-values, as read in, are non-dimensionalized depth convert to radii
*/
rl = r + E->sphere.ro;
llayers = 0;
for(i = 0;i < E->viscosity.num_mat;i++)
if(r > (E->sphere.ro - E->viscosity.zbase_layer[i])){
i++;
break;
}
llayers = i;
return (llayers);
}
/* determine layer number of node "node" of cap "m" */
int layers(struct All_variables *E,int node)
{
return(layers_r(E,E->sx[3][node]));
}
/* ==============================================================
construct array mat
============================================================== */
void construct_mat_group( struct All_variables *E )
{
int i,j,k,kk,el,lev,a,nodea,els,llayer;
void read_visc_layer_file(struct All_variables *E);
const int dims=E->mesh.nsd,dofs=E->mesh.dof;
const int ends=enodes[dims];
if(E->viscosity.layer_control) {
read_visc_layer_file(E);
/* assign the global nz to mat group */
for(el=1;el<=E->lmesh.nel;el++) {
int nz;
nz = ((el-1) % E->lmesh.elz) + 1;
E->mat[el] = E->mesh.elz - (nz + E->lmesh.ezs) + 1;
}
} else {
for(el=1;el<=E->lmesh.nel;el++) {
E->mat[el] = 1;
nodea = E->ien[el].node[2];
llayer = layers(E,nodea);
if (llayer){
E->mat[el] = llayer;
}
}
}
}
