# Set up two problem regions, one for the cylinder
# and one for the fibres
$torso = 1;
$intestine = 2;

# Set up two problem classes - laplace for the cylinder
# and activation for the fibres 
$laplace = 1;
$active = 2;

fem define para;r;intestine
fem define coor;r;intestine
fem define regi;r;intestine

fem define nodes;r;fitted_new reg $intestine
fem de base;r;intestine_torso
fem define elements;r;fitted_new reg $intestine

# Group the intestine element to apply different grid schemes later
fem group elem 57,40,44,39,53,46,43,27,67,19,77,58,28,18 as grid10 reg $intestine
fem group elem 38,72,62,29,31,84,41,45,61,68,82,79,69,49,91,66,83,51,80,64,92,75,33,86,74,2,23,36,87 as grid15 reg $intestine
fem group elem 47,17,52,100,109,25,13,32,16,102,50,10,48,35,65,21,12,26,4,95,104,54,59,42,76 as grid20 reg $intestine
fem group elem 14,107,34,20,11,90,37,73,110,7,71,101,108,105,5,63,55,6,96,97,70,93,78 as grid25 reg $intestine
fem group elem 1,89,60,99,103,30,94,15,9,56,3 as grid30 reg $intestine
fem group elem 88,8,85,106,81,98 as grid35 reg $intestine
fem group elem 24,22 as grid40 reg $intestine

# Generate a finite different grid over the intestine
fem define grid;r;intestine reg $intestine
fem update grid geometry reg $intestine
fem update grid metric reg $intestine


# Define the activation in the intestine
fem define equ;r;ICCcmiss reg $intestine class $active
fem define cell;r;ICCcmiss reg $intestine class $active
fem define mate;r;ICCcmiss cell reg $intestine class $active
fem define mate;r;ICCcmiss reg $intestine class $active
fem update grid material reg $intestine class $active
fem define init;r;ICCcmiss reg $intestine class $active
fem define solv;r;ICCcmiss reg $intestine class $active


fem export node;intestine as intestine reg $intestine class $active
fem export ele;intestine reg $intestine class $active as intestine 
fem export ele;grid reg $intestine class $active as intestine grid_numbers
# Perform an initial solve
#fem solve reg $torso class $laplace
fem solve to 0 reg $intestine class $active
fem export ele;intestine_field0 reg $intestine class $active field as intestine; 
for $M ( 1..10) 
{
$time=$M
# Solve the grid problem
fem solve restart to $time reg $intestine class $active;
# Calculate the dipole sources
#fem define sour;c grid 
# Apply the sources to the laplace problem
#fem update sour reg $torso class $laplace
 # Solve the laplace problem
#fem solve reg $torso class $laplace
fem export ele;intestine_field$time reg $intestine class $active field as intestine; 
#fem write history time $time variables yqs binary;

}