Composition_related.c
``````/*
*~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*
*
* 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
* 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
*
*
*~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

#include <math.h>
#include "global_defs.h"
#include "parsing.h"
#include "parallel_related.h"
#include "composition_related.h"

static void allocate_composition_memory(struct All_variables *E);
static void compute_elemental_composition_ratio_method(struct All_variables *E);
static void init_bulk_composition(struct All_variables *E);
static void check_initial_composition(struct All_variables *E);
static void fill_composition_from_neighbors(struct All_variables *E);

void composition_input(struct All_variables *E)
{
int i;
int m = E->parallel.me;

input_boolean("chemical_buoyancy",
&(E->composition.ichemical_buoyancy),
"1,0,nomax",m);

if (E->control.tracer && E->composition.ichemical_buoyancy) {

/* ibuoy_type=0 (absolute method) */
/* ibuoy_type=1 (ratio method) */

input_int("buoy_type",&(E->composition.ibuoy_type),"1,0,nomax",m);
if (E->composition.ibuoy_type!=1) {
fprintf(stderr,"Terror-Sorry, only ratio method allowed now\n");
fflush(stderr);
parallel_process_termination();
}

if (E->composition.ibuoy_type==0)
E->composition.ncomp = E->trace.nflavors;
else if (E->composition.ibuoy_type==1)
E->composition.ncomp = E->trace.nflavors - 1;

E->composition.buoyancy_ratio = (double*) malloc(E->composition.ncomp
*sizeof(double));

/* default values .... */
for (i=0; i<E->composition.ncomp; i++)
E->composition.buoyancy_ratio[i] = 1.0;

input_double_vector("buoyancy_ratio", E->composition.ncomp,
E->composition.buoyancy_ratio,m);

}

/* compositional rheology */

/* icompositional_rheology=0 (off) */
/* icompositional_rheology=1 (on) */
E->composition.icompositional_rheology = 0;
/*
input_int("compositional_rheology",
&(E->composition.icompositional_rheology),"1,0,nomax",m);

if (E->composition.icompositional_rheology==1) {
input_double("compositional_prefactor",
&(E->composition.compositional_rheology_prefactor),
"1.0",m);
}
*/

return;
}

void composition_setup(struct All_variables *E)
{
allocate_composition_memory(E);

return;
}

void write_composition_instructions(struct All_variables *E)
{
int k;

if (E->composition.ichemical_buoyancy ||
E->composition.icompositional_rheology)
E->composition.on = 1;

if (E->composition.on) {

if (E->trace.nflavors < 1) {
fprintf(E->trace.fpt, "Tracer flavors must be greater than 1 to track composition\n");
parallel_process_termination();
}

if (!E->composition.ichemical_buoyancy)
fprintf(E->trace.fpt,"Passive Tracers\n");
else
fprintf(E->trace.fpt,"Active Tracers\n");

if (E->composition.ibuoy_type==1)
fprintf(E->trace.fpt,"Ratio Method\n");
if (E->composition.ibuoy_type==0)
fprintf(E->trace.fpt,"Absolute Method\n");

for(k=0; k<E->composition.ncomp; k++) {
fprintf(E->trace.fpt,"Buoyancy Ratio: %f\n", E->composition.buoyancy_ratio[k]);
}

/*
if (E->composition.icompositional_rheology==0) {
fprintf(E->trace.fpt,"Compositional Rheology - OFF\n");
}
else if (E->composition.icompositional_rheology>0) {
fprintf(E->trace.fpt,"Compositional Rheology - ON\n");
fprintf(E->trace.fpt,"Compositional Prefactor: %f\n",
E->composition.compositional_rheology_prefactor);
}
*/

fflush(E->trace.fpt);
}

return;
}

/************ FILL COMPOSITION ************************/
void fill_composition(struct All_variables *E)
{

/* XXX: Currently, only the ratio method works here.           */
/* Will have to come back here to include the absolute method. */

/* ratio method */

if (E->composition.ibuoy_type==1) {
compute_elemental_composition_ratio_method(E);
}

/* absolute method */

if (E->composition.ibuoy_type!=1) {
fprintf(E->trace.fpt,"Error(compute...)-only ratio method now\n");
fflush(E->trace.fpt);
exit(10);
}

/* Map elemental composition to nodal points */

map_composition_to_nodes(E);

return;
}

static void allocate_composition_memory(struct All_variables *E)
{
int i, j;

for (i=0; i<E->composition.ncomp; i++) {
E->composition.bulk_composition = (double*) malloc(E->composition.ncomp*sizeof(double));
E->composition.initial_bulk_composition = (double*) malloc(E->composition.ncomp*sizeof(double));
E->composition.error_fraction = (double*) malloc(E->composition.ncomp*sizeof(double));
}

/* allocat memory for composition fields at the nodes and elements */

for (j=1;j<=E->sphere.caps_per_proc;j++) {
if ((E->composition.comp_el[j]=(double **)malloc((E->composition.ncomp)*sizeof(double*)))==NULL) {
fprintf(E->trace.fpt,"AKM(allocate_composition_memory)-no memory 8987y\n");
fflush(E->trace.fpt);
exit(10);
}
if ((E->composition.comp_node[j]=(double **)malloc((E->composition.ncomp)*sizeof(double*)))==NULL) {
fprintf(E->trace.fpt,"AKM(allocate_composition_memory)-no memory 8988y\n");
fflush(E->trace.fpt);
exit(10);
}

for (i=0; i<E->composition.ncomp; i++) {
if ((E->composition.comp_el[j][i]=(double *)malloc((E->lmesh.nel+1)*sizeof(double)))==NULL) {
fprintf(E->trace.fpt,"AKM(allocate_composition_memory)-no memory 8989y\n");
fflush(E->trace.fpt);
exit(10);
}

if ((E->composition.comp_node[j][i]=(double *)malloc((E->lmesh.nno+1)*sizeof(double)))==NULL) {
fprintf(E->trace.fpt,"AKM(allocate_composition_memory)-no memory 983rk\n");
fflush(E->trace.fpt);
exit(10);
}
}
}

return;
}

void init_composition(struct All_variables *E)
{
if (E->composition.ichemical_buoyancy &&
E->composition.ibuoy_type) {
fill_composition(E);
check_initial_composition(E);
init_bulk_composition(E);
}
return;
}

static void check_initial_composition(struct All_variables *E)
{
/* check empty element if using ratio method */
if (E->composition.ibuoy_type == 1) {
if (E->trace.istat_iempty) {
fprintf(E->trace.fpt,"WARNING(check_initial_composition)-number of tracers is REALLY LOW, %d elements contain no tracer\n", E->trace.istat_iempty);

/* if there are only a few empty elements, using neighboring */
/* elements to determine the initial composition.            */
if ((1e4*E->trace.istat_iempty) < E->lmesh.nel)
fill_composition_from_neighbors(E);
else if (E->trace.itracer_warnings) {
fflush(E->trace.fpt);
exit(10);
}
}
}

return;
}

/*********** COMPUTE ELEMENTAL COMPOSITION RATIO METHOD ***/
/*                                                        */
/* This function computes the composition per element.    */
/* The concentration of material i in an element is       */
/* defined as:                                            */
/*   (# of tracers of flavor i) / (# of all tracers)      */

static void compute_elemental_composition_ratio_method(struct All_variables *E)
{
int i, j, e, flavor, numtracers;
int iempty = 0;

for (j=1; j<=E->sphere.caps_per_proc; j++) {
for (e=1; e<=E->lmesh.nel; e++) {
numtracers = 0;
for (flavor=0; flavor<E->trace.nflavors; flavor++)
numtracers += E->trace.ntracer_flavor[j][flavor][e];

/* Check for empty entries and compute ratio.  */
/* If no tracers are in an element, skip this element, */
/* use previous composition. */
if (numtracers == 0) {
iempty++;
/* fprintf(E->trace.fpt, "No tracer in element %d!\n", e); */
continue;
}

for(i=0;i<E->composition.ncomp;i++) {
flavor = i + 1;
E->composition.comp_el[j][i][e] =
E->trace.ntracer_flavor[j][flavor][e] / (double)numtracers;
}
}

if (iempty) {

if ((1.0*iempty/E->lmesh.nel)>0.80) {
fprintf(E->trace.fpt,"WARNING(compute_elemental...)-number of tracers is REALLY LOW\n");
fflush(E->trace.fpt);
if (E->trace.itracer_warnings) exit(10);
}
}

} /* end j */

E->trace.istat_iempty += iempty;

return;
}

/********** MAP COMPOSITION TO NODES ****************/
/*                                                  */

void map_composition_to_nodes(struct All_variables *E)
{
double *tmp[NCS];
int i, n, kk;
int nelem, nodenum;
int j;

for (j=1;j<=E->sphere.caps_per_proc;j++) {

/* first, initialize node array */
for(i=0;i<E->composition.ncomp;i++) {
for (kk=1;kk<=E->lmesh.nno;kk++)
E->composition.comp_node[j][i][kk]=0.0;
}

/* Loop through all elements */
for (nelem=1;nelem<=E->lmesh.nel;nelem++) {

/* for each element, loop through element nodes */

/* weight composition */

for (nodenum=1;nodenum<=8;nodenum++) {
n = E->ien[j][nelem].node[nodenum];
for(i=0;i<E->composition.ncomp;i++) {

E->composition.comp_node[j][i][n] +=
E->composition.comp_el[j][i][nelem]*
E->TWW[E->mesh.levmax][j][nelem].node[nodenum];
}
}

} /* end nelem */
} /* end j */

for(i=0;i<E->composition.ncomp;i++) {
for (j=1;j<=E->sphere.caps_per_proc;j++)
tmp[j] = E->composition.comp_node[j][i];

(E->exchange_node_d)(E,tmp,E->mesh.levmax);
}

/* Divide by nodal volume */
for (j=1;j<=E->sphere.caps_per_proc;j++) {
for(i=0;i<E->composition.ncomp;i++)
for (kk=1;kk<=E->lmesh.nno;kk++)
E->composition.comp_node[j][i][kk] *= E->MASS[E->mesh.levmax][j][kk];

/* testing */
/**
for(i=0;i<E->composition.ncomp;i++)
for (kk=1;kk<=E->lmesh.nel;kk++) {
fprintf(E->trace.fpt,"%d %f\n",kk,E->composition.comp_el[j][i][kk]);
}

for(i=0;i<E->composition.ncomp;i++)
for (kk=1;kk<=E->lmesh.nno;kk++) {
fprintf(E->trace.fpt,"%d %f %f\n",kk,E->sx[j][3][kk],E->composition.comp_node[j][i][kk]);
}
fflush(E->trace.fpt);
/**/

} /* end j */

return;
}

/****************************************************************/

static void fill_composition_from_neighbors(struct All_variables *E)
{
int i, j, k, e, ee, n, flavor, numtracers, count;
double *sum;
const int n_nghbrs = 4;
int nghbrs[n_nghbrs];
int *is_empty;

fprintf(E->trace.fpt,"Using neighboring elements for initial composition...\n");

/* index shift for neighboring elements in horizontal direction */
nghbrs[0] = E->lmesh.elz;
nghbrs[1] = -E->lmesh.elz;
nghbrs[2] = E->lmesh.elz * E->lmesh.elx;
nghbrs[3] = -E->lmesh.elz * E->lmesh.elx;

is_empty = (int *)calloc(E->lmesh.nel+1, sizeof(int));
sum = (double *)malloc(E->composition.ncomp * sizeof(double));

for (j=1; j<=E->sphere.caps_per_proc; j++) {
/* which element is empty? */
for (e=1; e<=E->lmesh.nel; e++) {
numtracers = 0;
for (flavor=0; flavor<E->trace.nflavors; flavor++)
numtracers += E->trace.ntracer_flavor[j][flavor][e];

if (numtracers == 0)
is_empty[e] = 1;
}

/* using the average comp_el from neighboring elements */
for (e=1; e<=E->lmesh.nel; e++) {
if(is_empty[e]) {
count = 0;
for (i=0; i<E->composition.ncomp; i++)
sum[i] = 0.0;

for(n=0; n<n_nghbrs; n++) {
ee = e + nghbrs[n];
/* is ee a valid element number and the elemnt is not empty? */
if((ee>0) && (ee<=E->lmesh.nel) && (!is_empty[ee])) {
count++;
for (i=0; i<E->composition.ncomp; i++)
sum[i] += E->composition.comp_el[j][i][ee];
}
}

if(count == 0) {
fprintf(E->trace.fpt,"Error(fill_composition_from_neighbors)-all neighboring elements are empty\n");
fflush(E->trace.fpt);
exit(10);
}

for (i=0; i<E->composition.ncomp; i++)
E->composition.comp_el[j][i][e] = sum[i] / count;
}
}
}

free(is_empty);
free(sum);

fprintf(E->trace.fpt,"Done.\n");
fflush(E->trace.fpt);
return;
}

/*********** GET BULK COMPOSITION *******************************/

static void init_bulk_composition(struct All_variables *E)
{

double return_bulk_value_d();
double volume;
double *tmp[NCS];
int i, m;
const int ival=0;

for (i=0; i<E->composition.ncomp; i++) {

for (m=1;m<=E->sphere.caps_per_proc;m++)
tmp[m] = E->composition.comp_node[m][i];

/* ival=0 returns integral not average */
volume = return_bulk_value_d(E,tmp,ival);

E->composition.bulk_composition[i] = volume;
E->composition.initial_bulk_composition[i] = volume;
}

return;
}

void get_bulk_composition(struct All_variables *E)
{

double return_bulk_value_d();
double volume;
double *tmp[NCS];
int i, m;
const int ival = 0;

for (i=0; i<E->composition.ncomp; i++) {

for (m=1;m<=E->sphere.caps_per_proc;m++)
tmp[m] = E->composition.comp_node[m][i];

/* ival=0 returns integral not average */
volume = return_bulk_value_d(E,tmp,ival);

E->composition.bulk_composition[i] = volume;

E->composition.error_fraction[i] = (volume - E->composition.initial_bulk_composition[i]) / E->composition.initial_bulk_composition[i];
}

return;
}
``````