Deformation of the full prolate heart model
# CMISS (cm) command file for full ventricular mechanics. # # Prolate spheroidal coordinates are used to define the mesh consists # using 120 elements with tricubicHermite interpolation for lambda and # trilinear interpolation for mu, theta and the hydrostatic pressure. # Fibre and sheet angles are interpolated with bilinear-cubicHermite # and bicubicHermite-linear bases, resp. (imbrication angles are all # zero). Equations of finite deformation elasticity govern the # boundary value problem and the material response is described by the # pole-zero constitutive law, with prescribed residual strains from # Omens et al (??). Active fibre tension is modelled using the # Hunter-McCulloch-ter Keurs equations for active myocyte contraction # (n.b. zero for passive inflation). LV and RV cavities (endocardial # surfaces) are inflated to 1.0 and 0.2 kPa, resp., while lambda and # its in-wall-plane derivs are fixed for all epicardial nodes. # # Created: Martyn Nash October 2000 # set echo; #========================================================================================================== print "\033[0;30;42m ============================================================ \033[0m\n"; print "\033[0;30;42m Execution Flow \033[0m\n"; print "\033[0;30;42m ============================================================ \033[0m\n"; #========================================================================================================== set echo; # set num_threads 12; # fem define parameters;r;full_big; # $OUTPUT_DIR = "output/"; if( ! -d ${OUTPUT_DIR}) { mkdir ${OUTPUT_DIR}; } # $TRUE = 1; $FALSE = 0; # # Solve for or read in deformations # $MAX_PRESS = 10; $SOLVE_INFLATION = $TRUE; $SOLVE_ISOVOLUMIC_CONTRACTION = $TRUE; $SOLVE_EJECTION = $TRUE; $SOLVE_ISOVOLUMIC_RELAXATION = $FALSE; # if ( $SOLVE_ISOVOLUMIC_CONTRACTION || $SOLVE_EJECTION || $SOLVE_ISOVOLUMIC_RELAXATION ) { $COUPLED_PROBLEM = $TRUE; } else { $COUPLED_PROBLEM = $FALSE; } set echo; #========================================================================================================== print "\033[0;30;42m ============================================================ \033[0m\n"; print "\033[0;30;42m Regions & Classes \033[0m\n"; print "\033[0;30;42m ============================================================ \033[0m\n"; #========================================================================================================== set echo; # $WALL = 1; $LV_CAVITY = 2; $RV_CAVITY = 3; set echo; #========================================================================================================== print "\033[0;30;42m ============================================================ \033[0m\n"; print "\033[0;30;42m Geometry \033[0m\n"; print "\033[0;30;42m ============================================================ \033[0m\n"; #========================================================================================================== set echo; # fem define coord;r;fullheart_refmu region $WALL; fem define node;r region $WALL; fem define base;r;fullheart; fem define element;r;fullheart_refmu region $WALL; fem define fibre;r;fullheart_refmu region $WALL; fem define element;r;fullheart_refmu fibre region $WALL; # # # Define element groups # fem group elements 63..68 as base_lvfree_epi region $WALL; fem group elements 93..98 as base_lvfree_endo region $WALL; fem group elements 91,92,99,100 as base_septal region $WALL; fem group elements 61,62,69,70 as base_rv region $WALL; fem group elements base_lvfree_epi,base_lvfree_endo,base_septal,base_rv as base region $WALL; # fem group elements 3..8 as equatora_lvfree_epi region $WALL; fem group elements 33..38 as equatora_lvfree_endo region $WALL; fem group elements 31,32,39,40 as equatora_septal region $WALL; fem group elements 1,2,9,10 as equatora_rv region $WALL; fem group elements equatora_lvfree_epi,equatora_lvfree_endo,equatora_septal,equatora_rv as equatora region $WALL; # fem group elements 73..78 as equatorb_lvfree_epi region $WALL; fem group elements 103..108 as equatorb_lvfree_endo region $WALL; fem group elements 101,102,109,110 as equatorb_septal region $WALL; fem group elements 71,72,79,80 as equatorb_rv region $WALL; fem group elements equatorb_lvfree_epi,equatorb_lvfree_endo as equatorb_lvfree region $WALL; fem group elements equatorb_lvfree,equatorb_septal,equatorb_rv as equatorb region $WALL; # fem group elements 13..18 as equatorc_lvfree_epi region $WALL; fem group elements 43..48 as equatorc_lvfree_endo region $WALL; fem group elements 41,42,49,50 as equatorc_septal region $WALL; fem group elements 11,12,19,20 as equatorc_rv region $WALL; fem group elements equatorc_lvfree_epi,equatorc_lvfree_endo as equatorc_lvfree region $WALL; fem group elements equatorc_lvfree,equatorc_septal,equatorc_rv as equatorc region $WALL; # fem group elements equatora_lvfree_epi,equatorb_lvfree_epi,equatorc_lvfree_epi as equator_lvfree_epi region $WALL; fem group elements equatora_lvfree_endo,equatorb_lvfree_endo,equatorc_lvfree_endo as equator_lvfree_endo region $WALL; fem group elements equatora_septal,equatorb_septal,equatorc_septal as equator_septal region $WALL; fem group elements equatora_rv,equatorb_rv,equatorc_rv as equator_rv region $WALL; fem group elements equator_lvfree_epi,equator_lvfree_endo,equator_septal,equator_rv as equator region $WALL; # fem group elements 81..90 as apexa_epi region $WALL; fem group elements 111..120 as apexa_endo region $WALL; fem group elements apexa_epi,apexa_endo as apexa region $WALL; # fem group elements 21..30 as apexb_epi region $WALL; fem group elements 51..60 as apexb_endo region $WALL; fem group elements apexb_epi,apexb_endo as apexb region $WALL; # fem group elements apexa_epi,apexb_epi as apex_epi_elems region $WALL; fem group elements apexa_endo,apexb_endo as apex_endo_elems region $WALL; fem group elements apex_endo_elems,apex_epi_elems as apex_elems region $WALL; # fem group elements base_lvfree_endo,equator_lvfree_endo as lvfree_endo_elems region $WALL; fem group elements base_lvfree_epi,equator_lvfree_epi as lvfree_epi_elems region $WALL; fem group elements base_rv,equator_rv as rv_elems region $WALL; fem group elements base_septal,equator_septal as septal_elems region $WALL; # # # Define node groups # fem group nodes xi2=1 xi3=1 external elements base_lvfree_epi,base_rv as base_epi_nodes region $WALL; fem group nodes xi2=1 xi3=0 external elements base_lvfree_endo,base_septal as base_lv_endo_nodes region $WALL; fem group nodes xi2=1 xi3=0 external elements base_rv as base_rvfree_endo_nodes region $WALL; fem group nodes xi2=1 xi3=1 external elements base_septal as base_rvsept_endo_nodes region $WALL; fem group nodes base_lv_endo_nodes,base_rvfree_endo_nodes,base_rvsept_endo_nodes as base_endo_nodes region $WALL; fem group nodes xi2=1 external elements base as base_nodes region $WALL; # # LV endo node groups fem group nodes xi2=1 xi3=0 external elements equatora_lvfree_endo,equatora_septal as eqa_lv_endo_nodes region $WALL; fem group nodes xi2=1 xi3=0 external elements equatorb_lvfree_endo,equatorb_septal as eqb_lv_endo_nodes region $WALL; fem group nodes xi2=1 xi3=0 external elements equatorc_lvfree_endo,equatorc_septal as eqc_lv_endo_nodes region $WALL; fem group nodes xi2=1 xi3=0 external elements apexa_endo as apexa_lv_endo_nodes region $WALL; fem group nodes xi2=1 xi3=0 external elements apexb_endo as apexb_lv_endo_nodes region $WALL; fem group nodes eqa_lv_endo_nodes,eqb_lv_endo_nodes,eqc_lv_endo_nodes,apexa_lv_endo_nodes as equator_lv_endo_nodes region $WALL; # # Epi node groups fem group nodes xi2=1 xi3=1 external elements equatora_lvfree_epi,equatora_rv as eqa_epi_nodes region $WALL; fem group nodes xi2=1 xi3=1 external elements equatorb_lvfree_epi,equatorb_rv as eqb_epi_nodes region $WALL; fem group nodes xi2=1 xi3=1 external elements equatorc_lvfree_epi,equatorc_rv as eqc_epi_nodes region $WALL; fem group nodes xi2=1 xi3=1 external elements apexa_epi as apexa_epi_nodes region $WALL; fem group nodes xi2=1 xi3=1 external elements apexb_epi as apexb_epi_nodes region $WALL; fem group nodes eqa_epi_nodes,eqb_epi_nodes,eqc_epi_nodes,apexa_epi_nodes as equator_epi_nodes region $WALL; # fem group nodes xi3=0 external elements equator_rv as equator_rvfree_endo_nodes region $WALL; fem group nodes xi3=1 external elements equator_septal as equator_rvsept_endo_nodes region $WALL; fem group nodes equator_rvfree_endo_nodes,equator_rvsept_endo_nodes as equator_rv_endo_nodes region $WALL; fem group nodes xi3=1 elements equator_lvfree_endo,apex_endo_elems as equator_lv_mid_nodes region $WALL; fem group nodes xi3=1 external elements lvfree_epi_elems,rv_elems,apex_epi_elems as epi_nodes region $WALL; # fem group nodes xi2=0 elements apexb as apex_nodes region $WALL; fem group nodes xi2=0 xi3=0 external elements apexa_endo as near_apex_endo_nodes region $WALL; fem group nodes xi2=0 xi3=1 external elements apexa_epi as near_apex_epi_nodes region $WALL; fem group nodes equator_lv_mid_nodes,equator_rv_endo_nodes as equator_mid_nodes_temp region $WALL; fem group nodes equator_mid_nodes_temp,near_apex_endo_nodes,near_apex_epi_nodes as equator_mid_nodes region $WALL; # set echo; #========================================================================================================== print "\033[0;30;42m ============================================================ \033[0m\n"; print "\033[0;30;42m Dependent variable/material information \033[0m\n"; print "\033[0;30;42m ============================================================ \033[0m\n"; #========================================================================================================== set echo; # fem define equation;r;finelas_tch_incomp region $WALL lock; fem define material;r;orth_incomp_active_residstrain region $WALL; fem define active;r;active0_00 region $WALL; fem define initial;r;fullheart_inflate_pericard region $WALL; fem define solve;r;newton region $WALL; set echo; #========================================================================================================== print "\033[0;30;42m ============================================================ \033[0m\n"; print "\033[0;30;42m Inflation \033[0m\n"; print "\033[0;30;42m ============================================================ \033[0m\n"; #========================================================================================================== if ( $SOLVE_INFLATION ) { print "\033[0;30;43m Increase cavity pressures incrementally to simulate diastole \033[0m\n"; # set output;${OUTPUT_DIR}fullheart_inflate on; $NAME1 = "fullheart_def_00"; $NAME2 = "_active_0000"; $ITERS = 50; $ERROR_TOLERANCE = 0.001; # for $PRESS ( 0..$MAX_PRESS ) { print "\033[0;30;43m Pressure = $PRESS \033[0m\n"; $NUMZEROS=2-length($PRESS); $PRESSNUM=""; for $Z ( 1..$NUMZEROS ) { $PRESSNUM=$PRESSNUM."0"; } $PRESSNUM=$PRESSNUM.$PRESS; if( $PRESS == 0 ) { $INCREM = 0.0; } else { $INCREM = 0.1; } fem solve increment $INCREM iterate $ITERS error $ERROR_TOLERANCE; $FILENAME = ${NAME1}.${PRESSNUM}.${NAME2}; fem define initial;w;${OUTPUT_DIR}.${FILENAME} region $WALL; fem export nodes;${OUTPUT_DIR}.${FILENAME} as heart; fem export nodes;${OUTPUT_DIR}${FILENAME}_def field as heart; fem export elements;${OUTPUT_DIR}.${FILENAME} as wall; fem export elements;${OUTPUT_DIR}${FILENAME}_def field as wall; } set output off; } else { print "\033[0;30;43m Reading in end-diastolic state \033[0m\n"; # $FILENAME = "fullheart_def_00".${MAX_PRESS}."_active_0000"; fem define initial;r;${OUTPUT_DIR}.${FILENAME} region $WALL; fem define solve;r;newton region $WALL; fem export nodes;${OUTPUT_DIR}.${FILENAME} as heart; fem export nodes;${OUTPUT_DIR}${FILENAME}_def field as heart; fem export elements;${OUTPUT_DIR}.${FILENAME} as wall; fem export elements;${OUTPUT_DIR}${FILENAME}_def field as wall; } set echo; if ( $COUPLED_PROBLEM ) { # Set up coupled regions set echo; #========================================================================================================== print "\033[0;30;42m ============================================================ \033[0m\n"; print "\033[0;30;42m Set up Coupled Regions \033[0m\n"; print "\033[0;30;42m ============================================================ \033[0m\n"; #========================================================================================================== # # Save scale factors for the ventricular wall elements # fem define base;r;fullheart_readse; #redefine bases to read in scale factors fem def line;w;fullheart_refmu region $WALL; #write out scale factors for wall elements fem define base;r;fullheart; #redefine bases to calculate scale factors # # Define geometry and dependent variable information for LV and RV cavities # fem define region;r;coupled; fem define coord;r;lvcavity_refmu region $LV_CAVITY; fem define node;r region $LV_CAVITY; fem define coord;r;rvcavity_refmu region $RV_CAVITY; fem define node;r region $RV_CAVITY; fem define element;r;lvcavity_refmu region $LV_CAVITY; fem define element;r;rvcavity_refmu region $RV_CAVITY; fem group elem 121..180 as lv_cavity_elems region $LV_CAVITY; fem group elem 151..160 as lv_cavity_base_elems region $LV_CAVITY; fem group nodes xi2=1 xi3=1 elem lv_cavity_base_elems as lv_cavity_base_nodes region $LV_CAVITY; fem group elem 181..198 as rv_cavity_elems region $RV_CAVITY; fem define equation;r;coupled region $WALL,$LV_CAVITY,$RV_CAVITY lock; fem define material;r;cavity region $LV_CAVITY; fem define material;r;cavity region $RV_CAVITY; fem define initial;r;lvcavity_refmu region $LV_CAVITY; fem define initial;r;rvcavity_refmu region $RV_CAVITY; # # Define cavity/wall coupling and solution information # fem define coupling;r;coupled; fem define solve;r;coupled coupled region $WALL,$LV_CAVITY,$RV_CAVITY; fem update solution coupled source_region $WALL; $NHlambda = 1; fem update solution cavity_reference average 196 in $NHlambda node lv_cavity_base_nodes region $LV_CAVITY; fem update solution cavity_reference average 203 in $NHlambda node 14,18 region $RV_CAVITY; # # Read back in scale factors for the ventricular wall elements # fem define base;r;fullheart_readse; #redefine bases to read in scale factors fem def line;r;fullheart_refmu region $WALL; #read in scale factors for wall elements fem define base;r;fullheart; #redefine bases to calculate scale factors fem export nodes;${OUTPUT_DIR}heart as heart region all; fem export elements;${OUTPUT_DIR}lv_cavity as lv_cavity region $LV_CAVITY; fem export elements;${OUTPUT_DIR}rv_cavity as rv_cavity region $RV_CAVITY; fem export elements;${OUTPUT_DIR}wall as wall region $WALL; fem export nodes;${OUTPUT_DIR}heart_def field as heart region all; fem export elements;${OUTPUT_DIR}lv_cavity_def field as lv_cavity region $LV_CAVITY; fem export elements;${OUTPUT_DIR}rv_cavity_def field as rv_cavity region $RV_CAVITY; fem export elements;${OUTPUT_DIR}wall_def field as wall region $WALL; set echo; } if ( $SOLVE_ISOVOLUMIC_CONTRACTION ) { set echo; #========================================================================================================== print "\033[0;30;42m ============================================================ \033[0m\n"; print "\033[0;30;42m Solving Isovolumic Contraction \033[0m\n"; print "\033[0;30;42m ============================================================ \033[0m\n"; #========================================================================================================== set output;${OUTPUT_DIR}steps_contract_infl0_${MAX_PRESS} on; $NAME1 = "active0_"; $NAME2 = "fullheart_def_00".${MAX_PRESS}."_active_00"; $INCREM = 0.0; $ITER = 20; $ERROR_TOLERANCE = 0.001; # # Isovolumically contract the ventricles by incrementally # increasing intracellular calcium concentration and solving. if ( $MAX_PRESS == 10 ) { $MAX_CA = 24; } elsif ( $MAX_PRESS == 30 ) { $MAX_CA = 30; } else { fem quit # required activation level unknown } for $CA ( 1..$MAX_CA ) { $NUMZEROS=2-length($CA); $CANUM=""; for $Z ( 1..$NUMZEROS ) { $CANUM=$CANUM."0"; } $CANUM=$CANUM.$CA print "\033[0;30;43m Calcium Level = ${CA} \033[0m\n"; $FILENAME=${NAME2}.${CANUM} fem define active;r;${NAME1}.${CANUM} region $WALL; fem solve increment $INCREM iter $ITER coupled error $ERROR_TOLERANCE; fem define initial;w;${OUTPUT_DIR}.${FILENAME} region $WALL,$LV_CAVITY,$RV_CAVITY; fem export nodes;${OUTPUT_DIR}.${FILENAME} as heart region all; fem export nodes;${OUTPUT_DIR}${FILENAME}_def field as heart region all; } set out off set echo; } if ( $SOLVE_EJECTION ) { set echo; #========================================================================================================== print "\033[0;30;42m ============================================================ \033[0m\n"; print "\033[0;30;42m Solving Ejection \033[0m\n"; print "\033[0;30;42m ============================================================ \033[0m\n"; #========================================================================================================== if ( !$SOLVE_ISOVOLUMIC_CONTRACTION ) { print "\033[0;30;43m Reading in state at the end of isovolumic contraction \033[0m\n"; $CA = 24; fem define active;r;"active0_".${CA} region $WALL; fem define initial;r;${OUTPUT_DIR}."fullheart_def_00".${MAX_PRESS}."_active_00".${CA} nofix region $WALL,$LV_CAVITY,$RV_CAVITY; } $CA = 24; set out;${OUTPUT_DIR}."steps_eject_infl0_".${MAX_PRESS}."_act0_".${CA} on; $NAME1 = "cavity_"; $NAME2 = "fullheart_def_00".${MAX_PRESS}."_active_00".${CA}."_cavk_"; $INCREM = 0.0; $ITERS = 20; $ERROR_TOLERANCE = 0.001; # # Simulate ventricular ejection by incrementally decreasing the # cavity impedances. $CAVITY_K =640; for $I ( 1..26 ) { $CAVITY_K2 = int($CAVITY_K*1000); $NUMZEROS=8-length($CAVITY_K2) $CAVITY_K_NUMBER=""; for $Z ( 1..$NUMZEROS ) { $CAVITY_K_NUMBER=$CAVITY_K_NUMBER."0"; } $CAVITY_K_NUMBER=$CAVITY_K_NUMBER.$CAVITY_K2; $FILENAME=${NAME2}.${CAVITY_K_NUMBER}; print "\033[0;30;43m Cavity Stiffness Number ${CAVITY_K_NUMBER} \033[0m\n"; fem define material;r;${NAME1}.${CAVITY_K_NUMBER} region $LV_CAVITY; fem define material;r;${NAME1}.${CAVITY_K_NUMBER} region $RV_CAVITY; fem solve increment $INCREM iterate $ITERS coupled error $ERROR_TOLERANCE; fem define initial;w;${OUTPUT_DIR}.${NAME2}.${CAVITY_K_NUMBER} region $WALL,$LV_CAVITY,$RV_CAVITY; fem export nodes;${OUTPUT_DIR}.${FILENAME} as heart region all; fem export nodes;${OUTPUT_DIR}${FILENAME}_def field as heart region all; if( $CAVITY_K > 10 ) { $CAVITY_K = $CAVITY_K / 2.0; } elsif( $CAVITY_K > 4 ) { $CAVITY_K = $CAVITY_K - 1.0; } else { $CAVITY_K = $CAVITY_K - 0.3; } } set out off; set echo; } if ( $SOLVE_ISOVOLUMIC_RELAXATION ) { set echo; #========================================================================================================== print "\033[0;30;42m ============================================================ \033[0m\n"; print "\033[0;30;42m Solving Isovolumic Relaxation \033[0m\n"; print "\033[0;30;42m ============================================================ \033[0m\n"; #========================================================================================================== set echo; }
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Name Modified Size
examples_8_81_811_8111.tar.gz 17-Aug-2010 10.0M
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