/*
*~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*
*
*
* 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
*
*
*
*~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
/* Set up the finite element problem to suit: returns with all memory */
/* allocated, temperature, viscosity, node locations and how to use */
/* them all established. 8.29.92 or 29.8.92 depending on your nationality*/
#include
#include
#include
#include
#include
#include
#include
#include
#include "element_definitions.h"
#include "global_defs.h"
#include "citcom_init.h"
#include "initial_temperature.h"
#include "lith_age.h"
#include "material_properties.h"
#include "output.h"
#include "output_h5.h"
#include "parallel_related.h"
#include "parsing.h"
#include "phase_change.h"
void parallel_process_termination();
void allocate_common_vars(struct All_variables*);
void allocate_velocity_vars(struct All_variables*);
void check_bc_consistency(struct All_variables*);
void construct_elt_gs(struct All_variables*);
void construct_elt_cs(struct All_variables*);
void construct_shape_function_derivatives(struct All_variables *E);
void construct_id(struct All_variables*);
void construct_ien(struct All_variables*);
void construct_lm(struct All_variables*);
void construct_masks(struct All_variables*);
void construct_shape_functions(struct All_variables*);
void construct_sub_element(struct All_variables*);
void construct_surf_det (struct All_variables*);
void construct_bdry_det (struct All_variables*);
void construct_surface (struct All_variables*);
void get_initial_elapsed_time(struct All_variables*);
void lith_age_init(struct All_variables *E);
void mass_matrix(struct All_variables*);
void output_init(struct All_variables*);
void set_elapsed_time(struct All_variables*);
void set_sphere_harmonics (struct All_variables*);
void set_starting_age(struct All_variables*);
void tracer_initial_settings(struct All_variables*);
void tracer_input(struct All_variables*);
void viscosity_input(struct All_variables*);
void vtk_output(struct All_variables*, int);
void get_vtk_filename(char *,int,struct All_variables *,int);
void myerror(struct All_variables *,char *);
void open_qfiles(struct All_variables *) ;
void read_rayleigh_from_file(struct All_variables *);
void read_initial_settings(struct All_variables *);
void check_settings_consistency(struct All_variables *);
void global_derived_values(struct All_variables *);
void initial_mesh_solver_setup(struct All_variables *E)
{
int chatty;
//chatty = ((E->parallel.me == 0)&&(E->control.verbose))?(1):(0);
chatty = E->parallel.me == 0;
E->monitor.cpu_time_at_last_cycle =
E->monitor.cpu_time_at_start = CPU_time0();
output_init(E);
(E->problem_derived_values)(E); /* call this before global_derived_ */
global_derived_values(E);
(E->solver.parallel_processor_setup)(E); /* get # of proc in x,y,z */
(E->solver.parallel_domain_decomp0)(E); /* get local nel, nno, elx, nox et al */
allocate_common_vars(E);
(E->problem_allocate_vars)(E);
(E->solver_allocate_vars)(E);
if(chatty)fprintf(stderr,"memory allocation done\n");
/* logical domain */
construct_ien(E);
construct_surface(E);
(E->solver.construct_boundary)(E);
(E->solver.parallel_domain_boundary_nodes)(E);
if(chatty)fprintf(stderr,"parallel setup done\n");
/* physical domain */
(E->solver.node_locations)(E);
if(chatty)fprintf(stderr,"node locations done\n");
allocate_velocity_vars(E);
if(chatty)fprintf(stderr,"velocity vars done\n");
get_initial_elapsed_time(E); /* Set elapsed time */
set_starting_age(E); /* set the starting age to elapsed time, if desired */
set_elapsed_time(E); /* reset to elapsed time to zero, if desired */
/* open the heatflow files here because we need to know about loc_me */
if(E->output.write_q_files)
open_qfiles(E);
else{
E->output.fpqt = E->output.fpqb = NULL;
}
if(E->control.lith_age)
lith_age_init(E);
(E->problem_boundary_conds)(E);
check_bc_consistency(E);
if(chatty)fprintf(stderr,"boundary conditions done\n");
construct_masks(E); /* order is important here */
construct_id(E);
construct_lm(E);
if(chatty)fprintf(stderr,"id/lm done\n");
(E->solver.parallel_communication_routs_v)(E);
if(chatty)fprintf(stderr,"v communications done\n");
if(E->control.use_cbf_topo){
(E->solver.parallel_communication_routs_s)(E);
if(chatty)fprintf(stderr,"s communications done\n");
}
reference_state(E);
construct_sub_element(E);
construct_shape_functions(E);
construct_shape_function_derivatives(E);
if(chatty)fprintf(stderr,"shape functions done\n");
construct_elt_gs(E);
if(E->control.inv_gruneisen != 0)
construct_elt_cs(E);
/* this matrix results from spherical geometry */
/* construct_c3x3matrix(E); */
mass_matrix(E);
construct_surf_det (E);
construct_bdry_det (E);
if(chatty)fprintf(stderr,"mass matrix, dets done\n");
set_sphere_harmonics (E);
if(E->control.tracer) {
tracer_initial_settings(E);
(E->problem_tracer_setup)(E);
if(chatty)fprintf(stderr,"tracer setup done\n");
}
#ifdef USE_GGRD
/* updating local rayleigh number (based on Netcdf grds, the
rayleigh number may be modified laterally in the surface
layers) */
if(E->control.ggrd.ray_control)
read_rayleigh_from_file(E);
#endif
if(chatty)fprintf(stderr,"initial_mesh_solver_setup done\n");
}
/* This function is replaced by CitcomS.*.setProperties() in Pyre. */
void read_instructions(struct All_variables *E, char *filename)
{
void read_initial_settings();
void setup_parser();
void shutdown_parser();
/* ==================================================
Initialize from the command line
from startup files. (See Parsing.c).
================================================== */
setup_parser(E,filename);
read_initial_settings(E);
shutdown_parser(E);
return;
}
/* This function is replaced by CitcomS.Solver.initial_setup() in Pyre. */
void initial_setup(struct All_variables *E)
{
initial_mesh_solver_setup(E);
general_stokes_solver_setup(E);
(E->next_buoyancy_field_init)(E);
}
void initialize_material(struct All_variables *E)
{
void construct_mat_group();
void read_mat_from_file();
if(E->control.mat_control)
read_mat_from_file(E);
else
construct_mat_group(E);
}
/* This function is replaced by CitcomS.Components.IC.launch()*/
void initial_conditions(struct All_variables *E)
{
void initialize_tracers();
void init_composition();
void common_initial_fields();
initialize_material(E);
if (E->control.tracer==1) {
initialize_tracers(E);
if (E->composition.on)
init_composition(E);
}
(E->problem_initial_fields)(E); /* temperature/chemistry/melting etc */
common_initial_fields(E); /* velocity/pressure/viscosity (viscosity must be done LAST) */
return;
}
void read_initial_settings(struct All_variables *E)
{
void set_convection_defaults();
void set_cg_defaults();
void set_mg_defaults();
float tmp;
double ell_tmp;
int m=E->parallel.me,i;
double levmax;
int tmp_int_in;
/* first the problem type (defines subsequent behaviour) */
input_string("Problem",E->control.PROBLEM_TYPE,"convection",m);
if ( strcmp(E->control.PROBLEM_TYPE,"convection") == 0)
set_convection_defaults(E);
else if ( strcmp(E->control.PROBLEM_TYPE,"convection-chemical") == 0)
set_convection_defaults(E);
else {
fprintf(E->fp,"Unable to determine problem type, assuming convection ... \n");
set_convection_defaults(E);
}
input_string("Geometry",E->control.GEOMETRY,"sphere",m);
if ( strcmp(E->control.GEOMETRY,"sphere") == 0)
(E->solver.set_3dsphere_defaults)(E);
else {
fprintf(E->fp,"Unable to determine geometry, assuming sphere 3d ... \n");
(E->solver.set_3dsphere_defaults)(E);
}
input_string("Solver",E->control.SOLVER_TYPE,"cgrad",m);
if ( strcmp(E->control.SOLVER_TYPE,"cgrad") == 0)
set_cg_defaults(E);
else if ( strcmp(E->control.SOLVER_TYPE,"multigrid") == 0)
set_mg_defaults(E);
else {
if (E->parallel.me==0) fprintf(stderr,"Unable to determine how to solve, specify Solver=VALID_OPTION \n");
parallel_process_termination();
}
/* Information on which files to print, which variables of the flow to calculate and print.
Default is no information recorded (apart from special things for given applications.
*/
input_string("datadir",E->control.data_dir,".",m);
input_string("datafile",E->control.data_prefix,"initialize",m);
input_string("datadir_old",E->control.data_dir_old,".",m);
input_string("datafile_old",E->control.data_prefix_old,"initialize",m);
input_int("nproc_surf",&(E->parallel.nprocxy),"1",m);
input_int("nprocx",&(E->parallel.nprocx),"1",m);
input_int("nprocy",&(E->parallel.nprocy),"1",m);
input_int("nprocz",&(E->parallel.nprocz),"1",m);
if (E->control.CONJ_GRAD) {
input_int("nodex",&(E->mesh.nox),"essential",m);
input_int("nodez",&(E->mesh.noz),"essential",m);
input_int("nodey",&(E->mesh.noy),"essential",m);
E->mesh.mgunitx = (E->mesh.nox - 1) / E->parallel.nprocx;
E->mesh.mgunity = (E->mesh.noy - 1) / E->parallel.nprocy;
E->mesh.mgunitz = (E->mesh.noz - 1) / E->parallel.nprocz;
E->mesh.levels = 1;
}
else {
input_int("mgunitx",&(E->mesh.mgunitx),"1",m);
input_int("mgunitz",&(E->mesh.mgunitz),"1",m);
input_int("mgunity",&(E->mesh.mgunity),"1",m);
input_int("levels",&(E->mesh.levels),"1",m);
levmax = E->mesh.levels - 1;
E->mesh.nox = E->mesh.mgunitx * (int) pow(2.0,levmax) * E->parallel.nprocx + 1;
E->mesh.noy = E->mesh.mgunity * (int) pow(2.0,levmax) * E->parallel.nprocy + 1;
E->mesh.noz = E->mesh.mgunitz * (int) pow(2.0,levmax) * E->parallel.nprocz + 1;
}
input_double("radius_outer",&(E->sphere.ro),"1",m);
input_double("radius_inner",&(E->sphere.ri),"0.55",m);
if(E->sphere.caps == 1) {
input_double("theta_min",&(E->control.theta_min),"essential",m);
input_double("theta_max",&(E->control.theta_max),"essential",m);
input_double("fi_min",&(E->control.fi_min),"essential",m);
input_double("fi_max",&(E->control.fi_max),"essential",m);
}
input_int("coor",&(E->control.coor),"0",m);
if(E->control.coor == 2){
/*
refinement in two layers
*/
/* number of refinement layers */
E->control.coor_refine[0] = 0.10; /* bottom 10% */
E->control.coor_refine[1] = 0.15; /* get 15% of the nodes */
E->control.coor_refine[2] = 0.10; /* top 10% */
E->control.coor_refine[3] = 0.20; /* get 20% of the nodes */
input_float_vector("coor_refine",4,E->control.coor_refine,m);
}else if(E->control.coor == 3){
/*
refinement CitcomCU style, by reading in layers, e.g.
r_grid_layers=3 # minus 1 is number of layers with uniform grid in r
rr=0.5,0.75,1.0 # starting and ending r coodinates
nr=1,37,97 # starting and ending node in r direction
*/
input_int("r_grid_layers", &(E->control.rlayers), "1",m);
if(E->control.rlayers > 20)
myerror(E,"number of rlayers out of bounds (20) for coor = 3");
/* layers radii */
input_float_vector("rr", E->control.rlayers, (E->control.rrlayer),m);
/* associated node numbers */
input_int_vector("nr", E->control.rlayers, (E->control.nrlayer),m);
}
input_string("coor_file",E->control.coor_file,"",m);
input_boolean("node_assemble",&(E->control.NASSEMBLE),"off",m);
/* general mesh structure */
input_boolean("verbose",&(E->control.verbose),"off",m);
input_boolean("see_convergence",&(E->control.print_convergence),"off",m);
input_boolean("stokes_flow_only",&(E->control.stokes),"off",m);
//input_boolean("remove_hor_buoy_avg",&(E->control.remove_hor_buoy_avg),"on",m);
/* restart from checkpoint file */
input_boolean("restart",&(E->control.restart),"off",m);
input_int("post_p",&(E->control.post_p),"0",m);
input_int("solution_cycles_init",&(E->monitor.solution_cycles_init),"0",m);
/* for layers */
input_int("num_mat",&(E->viscosity.num_mat),"1",m); /* number of layers, moved
from Viscosity_structures.c */
if(E->viscosity.num_mat > CITCOM_MAX_VISC_LAYER)
myerror(E,"too many viscosity layers as per num_mat, increase CITCOM_MAX_VISC_LAYER");
/* those are specific depth layers associated with phase
transitions, default values should be fixed */
input_float("z_cmb",&(E->viscosity.zcmb),"0.45",m); /* 0.45063569 */
input_float("z_lmantle",&(E->viscosity.zlm),"0.103594412180191",m); /*0.10359441 */
input_float("z_410",&(E->viscosity.z410),"0.0643541045361796",m); /* 0.06434, more like it */
input_float("z_lith",&(E->viscosity.zlith),"0.0156961230576048",m); /* 0.0157, more like it */
/* those are depth layers associated with viscosity or material
jumps, they may or may not be identical with the phase changes */
E->viscosity.zbase_layer[0] = E->viscosity.zbase_layer[1] = -999;
input_float_vector("z_layer",E->viscosity.num_mat,(E->viscosity.zbase_layer),m);
/* the start age and initial subduction history */
input_float("start_age",&(E->control.start_age),"0.0",m);
input_int("reset_startage",&(E->control.reset_startage),"0",m);
input_int("zero_elapsed_time",&(E->control.zero_elapsed_time),"0",m);
input_int("output_ll_max",&(E->output.llmax),"1",m);
input_int("topvbc",&(E->mesh.topvbc),"0",m);
input_int("botvbc",&(E->mesh.botvbc),"0",m);
/*
internal boundary conditions
*/
input_int("toplayerbc",&(E->mesh.toplayerbc),"0",m); /* > 0: apply surface boundary condition
throughout all nodes with r > toplayerbc_r
< 0: apply to single node layer noz+toplayerbc
*/
input_float("toplayerbc_r",&(E->mesh.toplayerbc_r),"0.984303876942",m); /* minimum r to apply BC to,
100 km depth */
input_float("topvbxval",&(E->control.VBXtopval),"0.0",m);
input_float("botvbxval",&(E->control.VBXbotval),"0.0",m);
input_float("topvbyval",&(E->control.VBYtopval),"0.0",m);
input_float("botvbyval",&(E->control.VBYbotval),"0.0",m);
input_float("T_interior_max_for_exit",&(E->monitor.T_interior_max_for_exit),"1.5",m);
input_int("pseudo_free_surf",&(E->control.pseudo_free_surf),"0",m);
input_int("toptbc",&(E->mesh.toptbc),"1",m);
input_int("bottbc",&(E->mesh.bottbc),"1",m);
input_float("toptbcval",&(E->control.TBCtopval),"0.0",m);
input_float("bottbcval",&(E->control.TBCbotval),"1.0",m);
input_boolean("side_sbcs",&(E->control.side_sbcs),"off",m);
input_int("file_vbcs",&(E->control.vbcs_file),"0",m);
input_string("vel_bound_file",E->control.velocity_boundary_file,"",m);
input_int("file_tbcs",&(E->control.tbcs_file),"0",m);
input_string("temp_bound_file",E->control.temperature_boundary_file,"",m);
input_int("reference_state",&(E->refstate.choice),"1",m);
if(E->refstate.choice == 0) {
input_string("refstate_file",E->refstate.filename,"refstate.dat",m);
}
input_int("mineral_physics_model",&(E->control.mineral_physics_model),"1",m);
input_int("mat_control",&(E->control.mat_control),"0",m);
input_string("mat_file",E->control.mat_file,"",m);
input_boolean("precise_strain_rate",&(E->control.precise_strain_rate),"off",m);
#ifdef USE_GGRD
/*
note that this part of the code might override mat_control, file_vbcs,
MATERIAL CONTROL
usage:
(a)
ggrd_mat_control=2
ggrd_mat_file="weak.grd"
read in time-constant prefactors from weak.grd netcdf file that apply to top two E->mat layers
i.e. ggrd_mat_control > 0 --> assign to layers with ilayer <= ggrd_mat_control
ggrd_mat_control < 0 --> assign to layers with ilayer == -ggrd_mat_control
(b)
ggrd_mat_control=2
ggrd_mat_file="mythist"
ggrd_time_hist_file="mythist/times.dat"
time-dependent, will look for n files named mythist/i/weak.grd
where i = 1...n and n is the number of times as specified in
ggrd_time_hist_file which has time in Ma for n stages like so
-->age is positive, and forward marching in time decreases the age<--
0 15
15 30
30 60
in the example above, the input grid is a layer. if it's a 3D model, provide
ggrd_mat_depth_file, akin to temperature input
*/
ggrd_init_master(&E->control.ggrd);
/* this is controlling velocities, material, and age */
/* time history file, if not specified, will use constant VBCs and material grids */
input_string("ggrd_time_hist_file",
E->control.ggrd.time_hist.file,"",m);
/* if > 0, will use top E->control.ggrd.mat_control layers and assign a prefactor for the viscosity */
/* if < 0, will assign only to layer == -ggrd_mat_control */
input_int("ggrd_mat_control",&(E->control.ggrd.mat_control),"0",m);
input_boolean("ggrd_mat_limit_prefactor",&(E->control.ggrd_mat_limit_prefactor),"on",m); /* limit prefactor to with 1e+/-5 */
input_int("ggrd_mat_is_code",&(E->control.ggrd_mat_is_code),"0",m); /* the viscosity grids are
actually codes for
different types of
rheologies, from 1 .... cmax
*/
if(E->control.ggrd_mat_is_code){
/* we need code assignments */
E->control.ggrd_mat_code_viscosities = (float *)malloc(sizeof(float)*E->control.ggrd_mat_is_code);
for(i=0;i < E->control.ggrd_mat_is_code;i++)
E->control.ggrd_mat_code_viscosities[i] = 1;
input_float_vector("ggrd_mat_code_viscosities",
E->control.ggrd_mat_is_code,(E->control.ggrd_mat_code_viscosities),m);
}
input_string("ggrd_mat_file",E->control.ggrd.mat_file,"",m); /* file to read prefactors from */
input_string("ggrd_mat_depth_file",
E->control.ggrd_mat_depth_file,"_i_do_not_exist_",m);
if(E->control.ggrd.mat_control != 0) /* this will override mat_control setting */
E->control.mat_control = 1;
/*
Surface layer Rayleigh number control, similar to above
*/
input_int("ggrd_rayleigh_control",
&(E->control.ggrd.ray_control),"0",m);
input_string("ggrd_rayleigh_file",
E->control.ggrd.ray_file,"",m); /* file to read prefactors from */
/*
surface velocity control, similar to material control above
if time-dependent, will look for ggrd_vtop_file/i/v?.grd
if constant, will look for ggrd_vtop_file/v?.grd
where vp/vt.grd are Netcdf GRD files with East and South velocities in cm/yr
*/
input_int("ggrd_vtop_control",&(E->control.ggrd.vtop_control),"0",m);
input_string("ggrd_vtop_dir",E->control.ggrd.vtop_dir,"",m); /* file to read prefactors from */
/*
if ggrd_vtop_euler is set, will read
wx wy wz
from E->control.ggrd.vtop_dir/rotvec.dat
and location codes from E->control.ggrd.vtop_dir/code.grd
assigning euler vector velocities in cm/yr assuming wx/wy/wz are in deg/Myr
codes go between 1....N where N is the number of entries in rotvec.dat
*/
input_boolean("ggrd_vtop_euler",&(E->control.ggrd_vtop_euler),"off",m);
if(E->control.ggrd_vtop_euler)
E->control.ggrd.vtop_control = 1;
if(E->control.ggrd.vtop_control) /* this will override mat_control setting */
E->control.vbcs_file = 1;
/* if set, will check the theta velocities from grid input for
scaled (internal non dim) values of > 1e9. if found, those nodes will
be set to free slip
*/
input_boolean("allow_mixed_vbcs",&(E->control.ggrd_allow_mixed_vbcs),"off",m);
/* when assigning composition from grid file, allow values between 0 and 1 ?
default will ronud up/down to 0 or 1
*/
input_boolean("ggrd_comp_smooth",&(E->control.ggrd_comp_smooth),"off",m);
#endif
input_boolean("aug_lagr",&(E->control.augmented_Lagr),"off",m);
input_double("aug_number",&(E->control.augmented),"0.0",m);
input_boolean("remove_rigid_rotation",&(E->control.remove_rigid_rotation),"on",m);
input_boolean("inner_remove_rigid_rotation",&(E->control.inner_remove_rigid_rotation),"off",m);
input_boolean("remove_angular_momentum",&(E->control.remove_angular_momentum),"on",m);
input_boolean("self_gravitation",&(E->control.self_gravitation),"off",m);
input_boolean("use_cbf_topo",&(E->control.use_cbf_topo),"off",m); /* make default on later XXX TWB */
input_int("storage_spacing",&(E->control.record_every),"10",m);
input_int("checkpointFrequency",&(E->control.checkpoint_frequency),"100",m);
input_int("cpu_limits_in_seconds",&(E->control.record_all_until),"5",m);
input_int("write_q_files",&(E->output.write_q_files),"0",m);/* write additional
heat flux files? */
if(E->output.write_q_files){ /* make sure those get written at
least as often as velocities */
E->output.write_q_files = min(E->output.write_q_files,E->control.record_every);
}
input_boolean("precond",&(E->control.precondition),"off",m);
input_int("mg_cycle",&(E->control.mg_cycle),"2,0,nomax",m);
input_int("down_heavy",&(E->control.down_heavy),"1,0,nomax",m);
input_int("up_heavy",&(E->control.up_heavy),"1,0,nomax",m);
input_double("accuracy",&(E->control.accuracy),"1.0e-4,0.0,1.0",m);
input_double("inner_accuracy_scale",&(E->control.inner_accuracy_scale),"1.0,0.000001,1.0",m);
input_boolean("force_iteration",&(E->control.force_iteration),"off",m);
input_boolean("check_continuity_convergence",&(E->control.check_continuity_convergence),"on",m);
input_boolean("check_pressure_convergence",&(E->control.check_pressure_convergence),"on",m);
/* for backward compatibility, override */
input_boolean("only_check_vel_convergence",&tmp_int_in,"off",m);
if(tmp_int_in){
E->control.check_continuity_convergence = 0;
E->control.check_pressure_convergence = 0;
}
input_int("vhighstep",&(E->control.v_steps_high),"1,0,nomax",m);
input_int("vlowstep",&(E->control.v_steps_low),"250,0,nomax",m);
input_int("max_mg_cycles",&(E->control.max_mg_cycles),"50,0,nomax",m);
input_int("piterations",&(E->control.p_iterations),"100,0,nomax",m);
input_float("rayleigh",&(E->control.Atemp),"essential",m);
input_float("dissipation_number",&(E->control.disptn_number),"0.0",m);
input_float("gruneisen",&(tmp),"0.0",m);
/* special case: if tmp==0, set gruneisen as inf */
if(tmp != 0)
E->control.inv_gruneisen = 1/tmp;
else
E->control.inv_gruneisen = 0;
if(E->control.inv_gruneisen != 0) {
/* which compressible solver to use: "cg" or "bicg" */
input_string("uzawa",E->control.uzawa,"cg",m);
if(strcmp(E->control.uzawa, "cg") == 0) {
/* more convergence parameters for "cg" */
input_int("compress_iter_maxstep",&(E->control.compress_iter_maxstep),"100",m);
}
else if(strcmp(E->control.uzawa, "bicg") == 0) {
}
else
myerror(E, "Error: unknown Uzawa iteration\n");
}
input_float("surfaceT",&(E->control.surface_temp),"0.1",m);
/*input_float("adiabaticT0",&(E->control.adiabaticT0),"0.4",m);*/
input_float("Q0",&(E->control.Q0),"0.0",m);
/* Q0_enriched gets read in Tracer_setup.c */
/* data section */
input_float("gravacc",&(E->data.grav_acc),"9.81",m);
input_float("thermexp",&(E->data.therm_exp),"3.0e-5",m);
input_float("cp",&(E->data.Cp),"1200.0",m);
input_float("thermdiff",&(E->data.therm_diff),"1.0e-6",m);
input_float("density",&(E->data.density),"3340.0",m);
input_float("density_above",&(E->data.density_above),"1030.0",m);
input_float("density_below",&(E->data.density_below),"6600.0",m);
input_float("refvisc",&(E->data.ref_viscosity),"1.0e21",m);
input_double("ellipticity",&ell_tmp,"0.0",m);
#ifdef ALLOW_ELLIPTICAL
/*
ellipticity and rotation settings
*/
/* f = (a-c)/a, where c is the short, a=b the long axis
1/298.257 = 0.00335281317789691 for Earth at present day
*/
E->data.ellipticity = ell_tmp;
if(fabs(E->data.ellipticity) > 5e-7){
/* define ra and rc such that R=1 is the volume equivalanet */
E->data.ra = pow((1.-E->data.ellipticity),-1./3.); /* non dim long axis */
E->data.rc = 1./(E->data.ra * E->data.ra); /* non dim short axis */
E->data.efac = (1.-E->data.ellipticity)*(1.-E->data.ellipticity);
if(E->parallel.me == 0){
fprintf(stderr,"WARNING: EXPERIMENTAL: ellipticity: %.5e equivalent radii: r_a: %g r_b: %g\n",
E->data.ellipticity,E->data.ra,E->data.rc);
}
E->data.use_ellipse = 1;
}else{
E->data.ra = E->data.rc = E->data.efac=1.0;
E->data.use_ellipse = 0;
}
/*
centrifugal ratio between \omega^2 a^3/GM, 3.46775e-3 for the
Earth at present day
*/
input_double("rotation_m",&E->data.rotm,"0.0",m);
if(fabs(E->data.rotm) > 5e-7){
/* J2 from flattening */
E->data.j2 = 2./3.*E->data.ellipticity*(1.-E->data.ellipticity/2.)-
E->data.rotm/3.*(1.-3./2.*E->data.rotm-2./7.*E->data.ellipticity);
/* normalized gravity at the equator */
E->data.ge = 1/(E->data.ra*E->data.ra)*(1+3./2.*E->data.j2-E->data.rotm);
if(E->parallel.me==0)
fprintf(stderr,"WARNING: rotational fraction m: %.5e J2: %.5e g_e: %g\n",
E->data.rotm,E->data.j2,E->data.ge);
E->data.use_rotation_g = 1;
}else{
E->data.use_rotation_g = 0;
}
#else
if(fabs(ell_tmp) > 5e-7){
myerror(E,"ellipticity not zero, but not compiled with ALLOW_ELLIPTICAL");
}
#endif
input_float("radius",&tmp,"6371e3.0",m);
E->data.radius_km = tmp / 1e3;
E->data.therm_cond = E->data.therm_diff * E->data.density * E->data.Cp;
E->data.ref_temperature = E->control.Atemp * E->data.therm_diff
* E->data.ref_viscosity
/ (E->data.density * E->data.grav_acc * E->data.therm_exp)
/ (E->data.radius_km * E->data.radius_km * E->data.radius_km * 1e9);
output_common_input(E);
h5input_params(E);
phase_change_input(E);
lith_age_input(E);
tic_input(E);
tracer_input(E);
viscosity_input(E); /* moved the viscosity input behind
the tracer input */
(E->problem_settings)(E);
#ifdef USE_PETSC
/* PETSc related flags */
input_boolean("use_petsc",&E->control.use_petsc,"off",m);
input_boolean("petsc_linear",&E->control.petsc_linear,"on",m);
input_boolean("petsc_nonlinear",&E->control.petsc_nonlinear,"off",m);
input_boolean("petsc_schur",&E->control.petsc_schur,"off",m);
input_float("petsc_uzawa_tol", &E->control.petsc_uzawa_tol, "1e-6", m);
#endif
check_settings_consistency(E);
return;
}
/* Checking the consistency of input parameters */
void check_settings_consistency(struct All_variables *E)
{
if (E->control.CONJ_GRAD) {
/* conjugate gradient has only one level */
if(E->mesh.levels != 1)
myerror(E, "Conjugate gradient solver is used. 'levels' must be 1.\n");
}
else {
/* multigrid solver needs two or more levels */
if(E->mesh.levels < 2)
myerror(E, "number of multigrid levels < 2\n");
if(E->mesh.levels > MAX_LEVELS)
myerror(E, "number of multigrid levels out of bound\n");
}
/* remove angular momentum/rigid rotation should only be done in free
convection of global models. */
if(E->sphere.caps == 12 &&
(E->control.remove_angular_momentum || E->control.remove_rigid_rotation) &&
(E->mesh.topvbc || E->mesh.botvbc || E->control.side_sbcs)) {
if(E->parallel.me == 0)
fprintf(stderr,"\nWARNING: The input parameters impose boundary velocity, but also remove angular momentum/rigid rotation!\n\n");
}
/* no z_layer input found */
if((fabs(E->viscosity.zbase_layer[0]+999) < 1e-5) &&
(fabs(E->viscosity.zbase_layer[1]+999) < 1e-5)) {
if(E->viscosity.num_mat != 4)
myerror(E,"error: either use z_layer for non dim layer depths, or set num_mat to four");
E->viscosity.zbase_layer[0] = E->viscosity.zlith;
E->viscosity.zbase_layer[1] = E->viscosity.z410;
E->viscosity.zbase_layer[2] = E->viscosity.zlm;
E->viscosity.zbase_layer[3] = E->viscosity.zcmb; /* the lowest layers is never checked, really
if x3 < zlm, then the last layers gets assigned
i left this in for backward compatibility
*/
}
if (strcmp(E->output.vtk_format, "binary") == 0) {
#ifndef USE_GZDIR
/* zlib is required for vtk binary output */
if(E->parallel.me == 0) {
fputs("VTK binary output requires zlib, but couldn't find it at 'configure' time. Please either use VTK ascii output or re-run 'configure' with suitable flags.\n", stderr);
}
parallel_process_termination();
#endif
}
return;
}
/* Setup global mesh parameters */
void global_derived_values(struct All_variables *E)
{
int d,i,nox,noz,noy;
E->mesh.levmax = E->mesh.levels-1;
E->mesh.gridmax = E->mesh.levmax;
E->mesh.elx = E->mesh.nox-1;
E->mesh.ely = E->mesh.noy-1;
E->mesh.elz = E->mesh.noz-1;
if(E->sphere.caps == 1) {
/* number of nodes, excluding overlaping nodes between processors */
E->mesh.nno = E->sphere.caps * E->mesh.nox * E->mesh.noy * E->mesh.noz;
}
else {
/* number of nodes, excluding overlaping nodes between processors */
/* each cap has one row of nox and one row of noy overlapped, exclude these nodes.
* nodes at north/south poles are exclued by all caps, include them by 2*noz*/
E->mesh.nno = E->sphere.caps * (E->mesh.nox-1) * (E->mesh.noy-1) * E->mesh.noz
+ 2*E->mesh.noz;
}
E->mesh.nel = E->sphere.caps*E->mesh.elx*E->mesh.elz*E->mesh.ely;
E->mesh.nnov = E->mesh.nno;
/* this is a rough estimate for global neq, a more accurate neq will
be computed later. */
E->mesh.neq = E->mesh.nnov*E->mesh.nsd;
E->mesh.npno = E->mesh.nel;
E->mesh.nsf = E->mesh.nox*E->mesh.noy;
for(i=E->mesh.levmax;i>=E->mesh.levmin;i--) {
nox = E->mesh.mgunitx * (int) pow(2.0,(double)i)*E->parallel.nprocx + 1;
noy = E->mesh.mgunity * (int) pow(2.0,(double)i)*E->parallel.nprocy + 1;
noz = E->mesh.mgunitz * (int) pow(2.0,(double)i)*E->parallel.nprocz + 1;
E->mesh.ELX[i] = nox-1;
E->mesh.ELY[i] = noy-1;
E->mesh.ELZ[i] = noz-1;
if(E->sphere.caps == 1) {
E->mesh.NNO[i] = nox * noz * noy;
}
else {
E->mesh.NNO[i] = E->sphere.caps * (nox-1) * (noy-1) * noz + 2 * noz;
}
E->mesh.NEL[i] = E->sphere.caps * (nox-1) * (noz-1) * (noy-1);
E->mesh.NPNO[i] = E->mesh.NEL[i] ;
E->mesh.NOX[i] = nox;
E->mesh.NOZ[i] = noz;
E->mesh.NOY[i] = noy;
E->mesh.NNOV[i] = E->mesh.NNO[i];
E->mesh.NEQ[i] = E->mesh.nsd * E->mesh.NNOV[i] ;
}
/* Scaling from dimensionless units to Millions of years for input velocity
and time, timdir is the direction of time for advection. CPC 6/25/00 */
/* Myr */
E->data.scalet = (E->data.radius_km*1e3*E->data.radius_km*1e3/E->data.therm_diff)/(1.e6*365.25*24*3600);
/* cm/yr */
E->data.scalev = (E->data.radius_km*1e3/E->data.therm_diff)/(100*365.25*24*3600);
E->data.timedir = E->control.Atemp / fabs(E->control.Atemp);
if(E->control.print_convergence && E->parallel.me==0) {
fprintf(stderr,"Problem has %i x %i x %i nodes per cap, %i nodes and %i elements in total\n",
E->mesh.nox, E->mesh.noz, E->mesh.noy, E->mesh.nno, E->mesh.nel);
fprintf(E->fp,"Problem has %i x %i x %i nodes per cap, %i nodes and %i elements in total\n",
E->mesh.nox, E->mesh.noz, E->mesh.noy, E->mesh.nno, E->mesh.nel);
}
return;
}
/* ===================================
Functions which set up details
common to all problems follow ...
=================================== */
void allocate_common_vars(E)
struct All_variables *E;
{
void set_up_nonmg_aliases();
int m,n,snel,nsf,elx,ely,nox,noy,noz,nno,nel,npno,lim;
int k,i,j,d,l,nno_l,npno_l,nozl,nnov_l,nxyz;
m=0;
n=1;
npno = E->lmesh.npno;
nel = E->lmesh.nel;
nno = E->lmesh.nno;
nsf = E->lmesh.nsf;
noz = E->lmesh.noz;
nox = E->lmesh.nox;
noy = E->lmesh.noy;
elx = E->lmesh.elx;
ely = E->lmesh.ely;
E->P = (double *) malloc(npno*sizeof(double));
E->T = (double *) malloc((nno+1)*sizeof(double));
E->NP = (float *) malloc((nno+1)*sizeof(float));
E->buoyancy[CPPR] = (double *) malloc((nno+1)*sizeof(double));
E->gstress = (float *) malloc((6*nno+1)*sizeof(float));
// TWB do we need this anymore XXX
//E->stress[j] = (float *) malloc((12*nsf+1)*sizeof(float));
for(i=1;i<=E->mesh.nsd;i++)
E->sphere.cap[CPPR].TB[i] = (float *) malloc((nno+1)*sizeof(float));
E->slice.tpg = (float *)malloc((nsf+2)*sizeof(float));
E->slice.tpgb = (float *)malloc((nsf+2)*sizeof(float));
E->slice.divg = (float *)malloc((nsf+2)*sizeof(float));
E->slice.vort = (float *)malloc((nsf+2)*sizeof(float));
E->slice.shflux = (float *)malloc((nsf+2)*sizeof(float));
E->slice.bhflux = (float *)malloc((nsf+2)*sizeof(float));
/* if(E->mesh.topvbc==2 && E->control.pseudo_free_surf) */
E->slice.freesurf = (float *)malloc((nsf+2)*sizeof(float));
E->mat = (int *) malloc((nel+2)*sizeof(int));
E->VIP = (float *) malloc((nel+2)*sizeof(float));
E->heating_adi = (double *) malloc((nel+1)*sizeof(double));
E->heating_visc = (double *) malloc((nel+1)*sizeof(double));
E->heating_latent = (double *) malloc((nel+1)*sizeof(double));
/* lump mass matrix for the energy eqn */
E->TMass = (double *) malloc((nno+1)*sizeof(double));
/* nodal mass */
E->NMass = (double *) malloc((nno+1)*sizeof(double));
nxyz = max(nox*noz,nox*noy);
nxyz = 2*max(nxyz,noz*noy);
E->sien = (struct SIEN *) malloc((nxyz+2)*sizeof(struct SIEN));
E->surf_element = (int *) malloc((nxyz+2)*sizeof(int));
E->surf_node = (int *) malloc((nsf+2)*sizeof(int));
/* density field */
E->rho = (double *) malloc((nno+1)*sizeof(double));
/* horizontal average */
E->Have.T = (float *)malloc((E->lmesh.noz+2)*sizeof(float));
E->Have.V[1] = (float *)malloc((E->lmesh.noz+2)*sizeof(float));
E->Have.V[2] = (float *)malloc((E->lmesh.noz+2)*sizeof(float));
E->sphere.gr = (double *)malloc((E->mesh.noz+1)*sizeof(double));
for(i=E->mesh.levmin;i<=E->mesh.levmax;i++) {
E->sphere.R[i] = (double *) malloc((E->lmesh.NOZ[i]+1)*sizeof(double));
nno = E->lmesh.NNO[i];
npno = E->lmesh.NPNO[i];
nel = E->lmesh.NEL[i];
nox = E->lmesh.NOX[i];
noz = E->lmesh.NOZ[i];
noy = E->lmesh.NOY[i];
elx = E->lmesh.ELX[i];
ely = E->lmesh.ELY[i];
snel=E->lmesh.SNEL[i];
for(d=1;d<=E->mesh.nsd;d++) {
E->X[i][d] = (double *) malloc((nno+1)*sizeof(double));
E->SX[i][d] = (double *) malloc((nno+1)*sizeof(double));
}
for(d=0;d<=3;d++)
E->SinCos[i][d] = (double *) malloc((nno+1)*sizeof(double));
E->IEN[i] = (struct IEN *) malloc((nel+2)*sizeof(struct IEN));
E->EL[i] = (struct SUBEL *) malloc((nel+2)*sizeof(struct SUBEL));
E->sphere.area1[i][CPPR] = (double *) malloc((snel+1)*sizeof(double));
for (k=1;k<=4;k++)
E->sphere.angle1[i][CPPR][k] = (double *) malloc((snel+1)*sizeof(double));
E->GNX[i] = (struct Shape_function_dx *)malloc((nel+1)*sizeof(struct Shape_function_dx));
E->GDA[i] = (struct Shape_function_dA *)malloc((nel+1)*sizeof(struct Shape_function_dA));
E->MASS[i]= (double *) malloc((nno+1)*sizeof(double));
E->ECO[i] = (struct COORD *) malloc((nno+2)*sizeof(struct COORD));
E->TWW[i] = (struct FNODE *) malloc((nel+2)*sizeof(struct FNODE));
for(d=1;d<=E->mesh.nsd;d++)
for(l=1;l<=E->lmesh.NNO[i];l++) {
E->SX[i][d][l] = 0.0;
E->X[i][d][l] = 0.0;
}
}
for(i=0;i<=E->output.llmax;i++)
E->sphere.hindex[i] = (int *) malloc((E->output.llmax+3)
*sizeof(int));
for(i=E->mesh.gridmin;i<=E->mesh.gridmax;i++) {
nno = E->lmesh.NNO[i];
npno = E->lmesh.NPNO[i];
nel = E->lmesh.NEL[i];
nox = E->lmesh.NOX[i];
noz = E->lmesh.NOZ[i];
noy = E->lmesh.NOY[i];
elx = E->lmesh.ELX[i];
ely = E->lmesh.ELY[i];
nxyz = elx*ely;
E->CC[i] =(struct CC *) malloc((1)*sizeof(struct CC));
E->CCX[i]=(struct CCX *) malloc((1)*sizeof(struct CCX));
E->elt_del[i] = (struct EG *) malloc((nel+1)*sizeof(struct EG));
if(E->control.inv_gruneisen != 0)
E->elt_c[i] = (struct EC *) malloc((nel+1)*sizeof(struct EC));
E->EVI[i] = (float *) malloc((nel+1)*vpoints[E->mesh.nsd]*sizeof(float));
E->BPI[i] = (double *) malloc((npno+1)*sizeof(double));
E->ID[i] = (struct ID *) malloc((nno+1)*sizeof(struct ID));
E->VI[i] = (float *) malloc((nno+1)*sizeof(float));
E->NODE[i] = (unsigned int *)malloc((nno+1)*sizeof(unsigned int));
nxyz = max(nox*noz,nox*noy);
nxyz = 2*max(nxyz,noz*noy);
nozl = max(noy,nox*2);
E->parallel.EXCHANGE_sNODE[i] = (struct PASS *) malloc((nozl+2)*sizeof(struct PASS));
E->parallel.NODE[i] = (struct BOUND *) malloc((nxyz+2)*sizeof(struct BOUND));
E->parallel.EXCHANGE_NODE[i]= (struct PASS *) malloc((nxyz+2)*sizeof(struct PASS));
E->parallel.EXCHANGE_ID[i] = (struct PASS *) malloc((nxyz*E->mesh.nsd+3)*sizeof(struct PASS));
for(l=1;l<=E->lmesh.NNO[i];l++) {
E->NODE[i][l] = (INTX | INTY | INTZ); /* and any others ... */
E->VI[i][l] = 1.0;
}
} /* end for cap and i & j */
#ifdef CITCOM_ALLOW_ANISOTROPIC_VISC
if(E->viscosity.allow_anisotropic_viscosity){ /* any anisotropic
viscosity */
for(i=E->mesh.gridmin;i<=E->mesh.gridmax;i++) {
nel = E->lmesh.NEL[i];
nno = E->lmesh.NNO[i];
E->EVI2[i][CPPR] = (float *) malloc((nel+1)*vpoints[E->mesh.nsd]*sizeof(float));
E->avmode[i][CPPR] = (unsigned char *) malloc((nel+1)*vpoints[E->mesh.nsd]*sizeof(unsigned char));
E->EVIn1[i][CPPR] = (float *) malloc((nel+1)*vpoints[E->mesh.nsd]*sizeof(float));
E->EVIn2[i][CPPR] = (float *) malloc((nel+1)*vpoints[E->mesh.nsd]*sizeof(float));
E->EVIn3[i][CPPR] = (float *) malloc((nel+1)*vpoints[E->mesh.nsd]*sizeof(float));
E->VI2[i][CPPR] = (float *) malloc((nno+1)*sizeof(float));
E->VIn1[i][CPPR] = (float *) malloc((nno+1)*sizeof(float));
E->VIn2[i][CPPR] = (float *) malloc((nno+1)*sizeof(float));
E->VIn3[i][CPPR] = (float *) malloc((nno+1)*sizeof(float));
if((!(E->EVI2[i][CPPR]))||(!(E->VI2[i][CPPR]))||
(!(E->EVIn1[i][CPPR]))||(!(E->EVIn2[i][CPPR]))||(!(E->EVIn3[i][CPPR]))||
(!(E->VIn1[i][CPPR]))||(!(E->VIn2[i][CPPR]))||(!(E->VIn3[i][CPPR]))){
fprintf(stderr, "Error: Cannot allocate anisotropic visc memory, rank=%i\n",
E->parallel.me);
parallel_process_termination();
}
}
E->viscosity.anisotropic_viscosity_init = FALSE;
}
#endif
for(k=1;k<=E->mesh.nsd;k++)
for(i=1;i<=E->lmesh.nno;i++)
E->sphere.cap[CPPR].TB[k][i] = 0.0;
for(i=1;i<=E->lmesh.nno;i++)
E->T[i] = 0.0;
for(i=1;i<=E->lmesh.nel;i++) {
E->mat[i]=1;
E->VIP[i]=1.0;
E->heating_adi[i] = 0;
E->heating_visc[i] = 0;
E->heating_latent[i] = 1.0;
}
for(i=0;ilmesh.npno;i++)
E->P[i] = 0.0;
mat_prop_allocate(E);
phase_change_allocate(E);
set_up_nonmg_aliases(E);
if (strcmp(E->output.format, "hdf5") == 0)
h5output_allocate_memory(E);
}
/* ========================================================= */
void allocate_velocity_vars(E)
struct All_variables *E;
{
int m,n,i,j,k,l;
E->monitor.incompressibility = 0;
E->monitor.fdotf = 0;
E->monitor.vdotv = 0;
E->monitor.pdotp = 0;
m=0;
n=1;
E->lmesh.nnov = E->lmesh.nno;
E->lmesh.neq = E->lmesh.nnov * E->mesh.nsd;
E->temp = (double *) malloc((E->lmesh.neq+1)*sizeof(double));
E->temp1 = (double *) malloc(E->lmesh.neq*sizeof(double));
E->F = (double *) malloc(E->lmesh.neq*sizeof(double));
E->U = (double *) malloc(E->lmesh.neq*sizeof(double));
E->u1 = (double *) malloc(E->lmesh.neq*sizeof(double));
for(i=1;i<=E->mesh.nsd;i++) {
E->sphere.cap[CPPR].V[i] = (float *) malloc((E->lmesh.nnov+1)*sizeof(float));
E->sphere.cap[CPPR].VB[i] = (float *)malloc((E->lmesh.nnov+1)*sizeof(float));
E->sphere.cap[CPPR].Vprev[i] = (float *) malloc((E->lmesh.nnov+1)*sizeof(float));
}
for(i=0;ilmesh.neq;i++)
E->U[i] = E->temp[i] = E->temp1[i] = 0.0;
for(k=1;k<=E->mesh.nsd;k++)
for(i=1;i<=E->lmesh.nnov;i++)
E->sphere.cap[CPPR].VB[k][i] = 0.0;
for(l=E->mesh.gridmin;l<=E->mesh.gridmax;l++) {
E->lmesh.NEQ[l] = E->lmesh.NNOV[l] * E->mesh.nsd;
E->BI[l] = (double *) malloc((E->lmesh.NEQ[l])*sizeof(double));
k = (E->lmesh.NOX[l]*E->lmesh.NOZ[l]+E->lmesh.NOX[l]*E->lmesh.NOY[l]+
E->lmesh.NOY[l]*E->lmesh.NOZ[l])*6;
E->zero_resid[l] = (int *) malloc((k+2)*sizeof(int));
E->parallel.Skip_id[l] = (int *) malloc((k+2)*sizeof(int));
for(i=0;ilmesh.NEQ[l];i++) {
E->BI[l][i]=0.0;
}
} /* end for j & l */
}
/* ========================================================= */
void global_default_values(E)
struct All_variables *E;
{
/* FIRST: values which are not changed routinely by the user */
E->control.v_steps_low = 10;
E->control.v_steps_upper = 1;
E->control.accuracy = 1.0e-4;
E->control.verbose=0; /* debugging/profiles */
/* SECOND: values for which an obvious default setting is useful */
E->control.stokes=0;
E->control.restart=0;
E->control.CONVECTION = 0;
E->control.CART2D = 0;
E->control.CART3D = 0;
E->control.CART2pt5D = 0;
E->control.AXI = 0;
E->control.CONJ_GRAD = 0;
E->control.NMULTIGRID = 0;
E->control.augmented_Lagr = 0;
E->control.augmented = 0.0;
E->trace.fpt = NULL;
E->control.tracer = 0;
E->composition.on = 0;
E->parallel.nprocx=1; E->parallel.nprocz=1; E->parallel.nprocy=1;
E->mesh.levmax=0;
E->mesh.levmin=0;
E->mesh.gridmax=0;
E->mesh.gridmin=0;
E->mesh.noz = 1; E->mesh.nzs = 1; E->lmesh.noz = 1; E->lmesh.nzs = 1;
E->mesh.noy = 1; E->mesh.nys = 1; E->lmesh.noy = 1; E->lmesh.nys = 1;
E->mesh.nox = 1; E->mesh.nxs = 1; E->lmesh.nox = 1; E->lmesh.nxs = 1;
E->sphere.ro = 1.0;
E->sphere.ri = 0.5;
E->control.precondition = 0; /* for larger visc contrasts turn this back on */
E->mesh.toptbc = 1; /* fixed t */
E->mesh.bottbc = 1;
E->mesh.topvbc = 0; /* stress */
E->mesh.botvbc = 0;
E->control.VBXtopval=0.0;
E->control.VBYtopval=0.0;
E->control.VBXbotval=0.0;
E->control.VBYbotval=0.0;
E->data.radius_km = 6370.0; /* Earth, whole mantle defaults */
E->data.grav_acc = 9.81;
E->data.therm_diff = 1.0e-6;
E->data.therm_exp = 3.e-5;
E->data.density = 3300.0;
E->data.ref_viscosity=1.e21;
E->data.density_above = 1000.0; /* sea water */
E->data.density_below = 6600.0; /* sea water */
E->data.Cp = 1200.0;
E->data.therm_cond = 3.168;
E->data.res_density = 3300.0; /* density when X = ... */
E->data.res_density_X = 0.3;
E->data.melt_density = 2800.0;
E->data.permeability = 3.0e-10;
E->data.gas_const = 8.3;
E->data.surf_heat_flux = 4.4e-2;
E->data.grav_const = 6.6742e-11;
E->data.youngs_mod = 1.0e11;
E->data.Te = 0.0;
E->data.T_sol0 = 1373.0; /* Dave's values 1991 (for the earth) */
E->data.Tsurf = 273.0;
E->data.dTsol_dz = 3.4e-3 ;
E->data.dTsol_dF = 440.0;
E->data.dT_dz = 0.48e-3;
E->data.delta_S = 250.0;
E->data.ref_temperature = 2 * 1350.0; /* fixed temperature ... delta T */
/* THIRD: you forgot and then went home, let's see if we can help out */
sprintf(E->control.data_prefix,"citcom.tmp.%d",getpid());
E->control.NASSEMBLE = 0;
E->monitor.elapsed_time=0.0;
E->control.record_all_until = 10000000;
return;
}
/* =============================================================
============================================================= */
void check_bc_consistency(E)
struct All_variables *E;
{
int i,j,lev;
for(i=1;i<=E->lmesh.nno;i++) {
if ((E->node[i] & VBX) && (E->node[i] & SBX))
printf("Inconsistent x velocity bc at %d\n",i);
if ((E->node[i] & VBZ) && (E->node[i] & SBZ))
printf("Inconsistent z velocity bc at %d\n",i);
if ((E->node[i] & VBY) && (E->node[i] & SBY))
printf("Inconsistent y velocity bc at %d\n",i);
if ((E->node[i] & TBX) && (E->node[i] & FBX))
printf("Inconsistent x temperature bc at %d\n",i);
if ((E->node[i] & TBZ) && (E->node[i] & FBZ))
printf("Inconsistent z temperature bc at %d\n",i);
if ((E->node[i] & TBY) && (E->node[i] & FBY))
printf("Inconsistent y temperature bc at %d\n",i);
}
for(lev=E->mesh.gridmin;lev<=E->mesh.gridmax;lev++) {
for(i=1;i<=E->lmesh.NNO[lev];i++) {
if ((E->NODE[lev][i] & VBX) && (E->NODE[lev][i] & SBX))
printf("Inconsistent x velocity bc at %d,%d\n",lev,i);
if ((E->NODE[lev][i] & VBZ) && (E->NODE[lev][i] & SBZ))
printf("Inconsistent z velocity bc at %d,%d\n",lev,i);
if ((E->NODE[lev][i] & VBY) && (E->NODE[lev][i] & SBY))
printf("Inconsistent y velocity bc at %d,%d\n",lev,i);
/* Tbc's not applicable below top level */
}
} /* end for j and lev */
}
void set_up_nonmg_aliases(struct All_variables *E)
{ /* Aliases for functions only interested in the highest mg level */
int i;
E->eco = E->ECO[E->mesh.levmax];
E->ien = E->IEN[E->mesh.levmax];
E->id = E->ID[E->mesh.levmax];
E->Vi = E->VI[E->mesh.levmax];
E->EVi = E->EVI[E->mesh.levmax];
E->node = E->NODE[E->mesh.levmax];
E->cc = E->CC[E->mesh.levmax];
E->ccx = E->CCX[E->mesh.levmax];
E->Mass = E->MASS[E->mesh.levmax];
E->gDA = E->GDA[E->mesh.levmax];
E->gNX = E->GNX[E->mesh.levmax];
for (i=1;i<=E->mesh.nsd;i++) {
E->x[i] = E->X[E->mesh.levmax][i];
E->sx[i] = E->SX[E->mesh.levmax][i];
}
}
void report(E,string)
struct All_variables *E;
char * string;
{ if(E->control.verbose && E->parallel.me==0)
{ fprintf(stderr,"%s\n",string);
fflush(stderr);
}
}
void record(E,string)
struct All_variables *E;
char * string;
{ if(E->control.verbose && E->fp)
{ fprintf(E->fp,"%s\n",string);
fflush(E->fp);
}
return;
}
/* =============================================================
Initialize values which are not problem dependent.
NOTE: viscosity may be a function of all previous
input fields (temperature, pressure, velocity, chemistry) and
so is always to be done last.
============================================================= */
/* This function is replaced by CitcomS.Components.IC.launch()*/
void common_initial_fields(E)
struct All_variables *E;
{
void initial_pressure();
void initial_velocity();
void initial_viscosity();
initial_pressure(E);
initial_velocity(E);
initial_viscosity(E);
return;
}
/* ========================================== */
void initial_pressure(E)
struct All_variables *E;
{
int i,m;
report(E,"Initialize pressure field");
for(i=0;ilmesh.npno;i++)
E->P[i]=0.0;
}
void initial_velocity(E)
struct All_variables *E;
{
int i,m;
report(E,"Initialize velocity field");
for(i=1;i<=E->lmesh.nnov;i++) {
E->sphere.cap[CPPR].V[1][i]=0.0;
E->sphere.cap[CPPR].V[2][i]=0.0;
E->sphere.cap[CPPR].V[3][i]=0.0;
}
}
static void open_log(struct All_variables *E)
{
char logfile[255];
E->fp = NULL;
if (strcmp(E->output.format, "ascii-gz") == 0)
sprintf(logfile,"%s/log", E->control.data_dir);
else
sprintf(logfile,"%s.log", E->control.data_file);
if (E->control.restart || E->control.post_p)
/* append the log file if restart */
E->fp = output_open(logfile, "a");
else
E->fp = output_open(logfile, "w");
return;
}
static void open_time(struct All_variables *E)
{
char timeoutput[255];
E->fptime = NULL;
if (E->parallel.me == 0) {
if (strcmp(E->output.format, "ascii-gz") == 0)
sprintf(timeoutput,"%s/time", E->control.data_dir);
else
sprintf(timeoutput,"%s.time", E->control.data_file);
if (E->control.restart || E->control.post_p)
/* append the time file if restart */
E->fptime = output_open(timeoutput, "a");
else
E->fptime = output_open(timeoutput, "w");
}
return;
}
static void open_info(struct All_variables *E)
{
char output_file[255];
E->fp_out = NULL;
if (E->control.verbose) {
if (strcmp(E->output.format, "ascii-gz") == 0)
sprintf(output_file,"%s/info.%d", E->control.data_dir, E->parallel.me);
else
sprintf(output_file,"%s.info.%d", E->control.data_file, E->parallel.me);
E->fp_out = output_open(output_file, "w");
}
return;
}
void open_qfiles(struct All_variables *E) /* additional heat
flux output */
{
char output_file[255];
/* only one CPU will write to those */
if((E->parallel.me_loc[3] == E->parallel.nprocz-1) &&
(E->parallel.me==E->parallel.nprocz-1)){
/* top heat flux and other stat quantities */
if (strcmp(E->output.format, "ascii-gz") == 0)
sprintf(output_file,"%s/qt.dat", E->control.data_dir);
else
sprintf(output_file,"%s.qt.dat", E->control.data_file);
if(E->control.restart)
E->output.fpqt = output_open(output_file, "a"); /* append for restart */
else
E->output.fpqt = output_open(output_file, "w");
}else{
E->output.fpqt = NULL;
}
if (E->parallel.me_loc[3] == 0) {
/* bottom heat flux and other stat quantities */
if (strcmp(E->output.format, "ascii-gz") == 0)
sprintf(output_file,"%s/qb.dat", E->control.data_dir);
else
sprintf(output_file,"%s.qb.dat", E->control.data_file);
if(E->control.restart)
E->output.fpqb = output_open(output_file, "a"); /* append */
else
E->output.fpqb = output_open(output_file, "w");
}else{
E->output.fpqb = NULL;
}
return;
}
static void output_parse_optional(struct All_variables *E)
{
char* strip(char*);
int pos, len;
char *prev, *next;
len = strlen(E->output.optional);
/* fprintf(stderr, "### length of optional is %d\n", len); */
pos = 0;
next = E->output.optional;
E->output.connectivity = 0;
E->output.stress = 0;
E->output.pressure = 0;
E->output.surf = 0;
E->output.botm = 0;
E->output.geoid = 0;
E->output.horiz_avg = 0;
E->output.seismic = 0;
E->output.coord_bin = 0;
E->output.tracer = 0;
E->output.comp_el = 0;
E->output.comp_nd = 0;
E->output.heating = 0;
while(1) {
/* get next field */
prev = strsep(&next, ",");
/* break if no more field */
if(prev == NULL) break;
/* skip if empty */
if(prev[0] == '\0') continue;
/* strip off leading and trailing whitespaces */
prev = strip(prev);
/* skip empty field */
if (strlen(prev) == 0) continue;
/* fprintf(stderr, "### %s: %s\n", prev, next); */
if(strcmp(prev, "connectivity")==0)
E->output.connectivity = 1;
else if(strcmp(prev, "stress")==0)
E->output.stress = 1;
else if(strcmp(prev, "pressure")==0)
E->output.pressure = 1;
else if(strcmp(prev, "surf")==0)
E->output.surf = 1;
else if(strcmp(prev, "botm")==0)
E->output.botm = 1;
else if(strcmp(prev, "geoid")==0)
if (E->parallel.nprocxy != 12) {
fprintf(stderr, "Warning: geoid calculation only works in full version. Disabled\n");
}
else {
/* geoid calculation requires surface and CMB topo */
/* make sure the topos are available! */
E->output.geoid = 1;
}
else if(strcmp(prev, "horiz_avg")==0)
E->output.horiz_avg = 1;
else if(strcmp(prev, "seismic")==0) {
E->output.seismic = E->output.coord_bin = 1;
/* Total temperature contrast is important when computing seismic velocity,
* but it is derived from several parameters. Output it clearly. */
if(E->parallel.me==0) {
fprintf(stderr, "Total temperature contrast = %f K\n", E->data.ref_temperature);
fprintf(E->fp, "Total temperature contrast = %f K\n", E->data.ref_temperature);
}
}
else if(strcmp(prev, "tracer")==0)
E->output.tracer = 1;
else if(strcmp(prev, "comp_el")==0)
E->output.comp_el = 1;
else if(strcmp(prev, "comp_nd")==0)
E->output.comp_nd = 1;
else if(strcmp(prev, "heating")==0)
E->output.heating = 1;
else
if(E->parallel.me == 0)
fprintf(stderr, "Warning: unknown field for output_optional: %s\n", prev);
}
return;
}
/* check whether E->control.data_file contains a path seperator */
static void chk_prefix(struct All_variables *E)
{
char *found;
found = strchr(E->control.data_prefix, '/');
if (found) {
fprintf(stderr, "error in input parameter: datafile='%s' contains '/'\n", E->control.data_file);
parallel_process_termination();
}
if (E->control.restart || E->control.post_p ||
(E->convection.tic_method == -1) ||
(E->control.tracer && (E->trace.ic_method == 2))) {
found = strchr(E->control.data_prefix_old, '/');
if (found) {
fprintf(stderr, "error in input parameter: datafile_old='%s' contains '/'\n", E->control.data_file);
parallel_process_termination();
}
}
}
/* search src and substitue the 1st occurance of target by value */
static void expand_str(char *src, size_t max_size,
const char *target, const char *value)
{
char *pos, *end, *new_end;
size_t end_len, value_len;
/* is target a substring of src? */
pos = strstr(src, target);
if (pos != NULL) {
value_len = strlen(value);
/* the end part of the original string... */
end = pos + strlen(target);
/* ...and where it is going */
new_end = pos + value_len;
end_len = strlen(end);
if (new_end + end_len >= src + max_size) {
/* too long */
return;
}
/* move the end part of the original string */
memmove(new_end, end, end_len + 1); /* incl. null byte */
/* insert the value */
memcpy(pos, value, value_len);
}
}
static void expand_datadir(struct All_variables *E, char *datadir)
{
char *found, *err;
char tmp[150];
int diff;
FILE *pipe;
const char str1[] = "%HOSTNAME";
const char str2[] = "%RANK";
const char str3[] = "%DATADIR";
const char str3_prog[] = "citcoms_datadir";
/* expand str1 by machine's hostname */
found = strstr(datadir, str1);
if (found) {
gethostname(tmp, 100);
expand_str(datadir, 150, str1, tmp);
}
/* expand str2 by MPI rank */
found = strstr(datadir, str2);
if (found) {
sprintf(tmp, "%d", E->parallel.me);
expand_str(datadir, 150, str2, tmp);
}
/* expand str3 by the result of the external program */
diff = strcmp(datadir, str3);
if (!diff) {
pipe = popen(str3_prog, "r");
err = fgets(tmp, 150, pipe);
pclose(stdout);
if (err != NULL)
sscanf(tmp, " %s", datadir);
else {
fprintf(stderr, "Cannot get datadir from command '%s'\n", str3_prog);
parallel_process_termination();
}
}
}
void mkdatadir(const char *dir)
{
int err;
err = mkdir(dir, 0755);
if (err && errno != EEXIST) {
/* if error occured and the directory is not exisitng */
fprintf(stderr, "Cannot make new directory '%s'\n", dir);
parallel_process_termination();
}
}
void output_init(struct All_variables *E)
{
chk_prefix(E);
expand_datadir(E, E->control.data_dir);
mkdatadir(E->control.data_dir);
snprintf(E->control.data_file, 200, "%s/%s", E->control.data_dir,
E->control.data_prefix);
if (E->control.restart || E->control.post_p ||
(E->convection.tic_method == -1) ||
(E->control.tracer && (E->trace.ic_method == 2))) {
expand_datadir(E, E->control.data_dir_old);
snprintf(E->control.old_P_file, 200, "%s/%s", E->control.data_dir_old,
E->control.data_prefix_old);
}
open_log(E);
open_time(E);
open_info(E);
if (strcmp(E->output.format, "ascii") == 0) {
E->problem_output = output;
}
else if (strcmp(E->output.format, "hdf5") == 0)
E->problem_output = h5output;
else if (strcmp(E->output.format, "vtk") == 0)
E->problem_output = vtk_output;
#ifdef USE_GZDIR
else if (strcmp(E->output.format, "ascii-gz") == 0)
E->problem_output = gzdir_output;
else {
/* indicate error here */
if (E->parallel.me == 0) {
fprintf(stderr, "wrong output_format, must be 'ascii', 'hdf5', 'ascii-gz' or 'vtk'\n");
fprintf(E->fp, "wrong output_format, must be 'ascii', 'hdf5' 'ascii-gz', or 'vtk'\n");
}
parallel_process_termination();
}
#else
else {
/* indicate error here */
if (E->parallel.me == 0) {
fprintf(stderr, "wrong output_format, must be 'ascii', 'hdf5', or 'vtk' (USE_GZDIR undefined)\n");
fprintf(E->fp, "wrong output_format, must be 'ascii', 'hdf5', or 'vtk' (USE_GZDIR undefined)\n");
}
parallel_process_termination();
}
#endif
output_parse_optional(E);
}
void output_finalize(struct All_variables *E)
{
char message[255],files[255];
if (E->fp)
fclose(E->fp);
if (E->fptime)
fclose(E->fptime);
if (E->fp_out)
fclose(E->fp_out);
if (E->trace.fpt)
fclose(E->trace.fpt);
if(E->output.fpqt)
fclose(E->output.fpqt);
if(E->output.fpqb)
fclose(E->output.fpqb);
#ifdef USE_GZDIR
/*
remove VTK geo file in case we used that for IO
*/
if((E->output.gzdir.vtk_io != 0) &&
(strcmp(E->output.format, "ascii-gz") == 0)){
if((E->output.gzdir.vtk_io == 3)||(E->parallel.me == 0)){
/* delete the geo files */
get_vtk_filename(files,1,E,0);
remove(files);
if(E->parallel.me == 0){
/* close the log */
if(E->output.gzdir.vtk_fp)
fclose(E->output.gzdir.vtk_fp);
}
}
}
#endif
}
char* strip(char *input)
{
int end;
char *str;
end = strlen(input) - 1;
str = input;
/* trim trailing whitespace */
while (isspace(str[end]))
end--;
str[++end] = 0;
/* trim leading whitespace */
while(isspace(*str))
str++;
return str;
}