yixiangd/coagulation_cascade

Multiscale simulation on the blood coagulation cascade with comparisons between normal and diabetic blood

coagulation_cascade's Issues

Error in running nrbc

when I am trying this command :
../../lmp_stam < chan.equil.run

I saw an error :
bash: ../../lmp_stam: No such file or directory

When I add this folder manually in the defined address, it cannot run chan.equil.run as well. Does it need any prerequisite prior to running the case?

Iteration time

Hi,
When I am going to run the system to equilibrium, without force, I cannot see any progress during the run on terminal or creating any log file. Do you know the reason?

Error regardin style_asphere.h

Hello,
I am trying to compile this code. However, in the first step, (make in src folder), I am receiving this error:
fatal error: style_asphere.h: No such file or directory

which is required to make following files:
g++: error: atom.o: No such file or directory
g++: error: input.o: No such file or directory
g++: error: update.o: No such file or directory
g++: error: modify.o: No such file or directory
g++: error: output.o: No such file or directory
g++: error: domain.o: No such file or directory
g++: error: force.o: No such file or directory

Can you please update this required file in this repo?

bounce-back boundary

I checked the script but I don‘t figure it out for the setting of boundary condition. I really appreciate it, if you would explain the meaning of each line in the .dat file for the boundary conditiion of rbc cell.😊

"bc_channel_rbc.dat"
24 1
1 4.000000 solvent
1.7 0.2 0.0 0.1 1 0 486000
0 1.0 1.0 4.0 2 400 400 0 solvent
0 1.0 1.0 6.0 2 500 500
1 100 1.58 100 1.58 -0.00 0 force_press_rbc.dat force_shear_t.dat force_shear_n.dat rbc
1 110.000000 20.000000 -15.000000 110.000000 20.000000 15.000000 60.000000 20.000000 -15.000000 3 -1 0 0.
0.000000 0.000000 0.000000
1 60.000000 20.000000 15.000000 60.000000 20.000000 -15.000000 110.000000 20.000000 15.000000 3 -1 0 0.
0.000000 0.000000 0.000000
1 30.000000 20.000000 -15.000000 30.000000 20.000000 15.000000 -10.000000 20.000000 -15.000000 3 -1 0 0.
0.000000 0.000000 0.000000
1 -10.000000 20.000000 15.000000 -10.000000 20.000000 -15.000000 30.000000 20.000000 15.000000 3 -1 0 0.
0.000000 0.000000 0.000000
1 -10.000000 0.000000 -15.000000 -10.000000 0.000000 15.000000 30.000000 0.000000 -15.000000 3 -1 0 0.
0.000000 0.000000 0.000000
1 30.000000 0.000000 15.000000 30.000000 0.000000 -15.000000 -10.000000 0.000000 15.000000 3 -1 0 0.
0.000000 0.000000 0.000000
1 60.000000 0.000000 -15.000000 60.000000 0.000000 15.000000 110.000000 0.000000 -15.000000 3 -1 0 0.
0.000000 0.000000 0.000000
1 110.000000 0.000000 15.000000 110.000000 0.000000 -15.000000 60.000000 0.000000 15.000000 3 -1 0 0.
0.000000 0.000000 0.000000
1 30.000000 20.000000 -15.000000 37.500000 20.000000 -15.000000 30.000000 20.000000 15.000000 3 -1 0 0.
0.000000 0.000000 0.000000
1 37.500000 20.000000 15.000000 30.000000 20.000000 15.000000 37.500000 20.000000 -15.000000 3 -1 0 0.
0.000000 0.000000 0.000000
1 37.500000 20.000000 -15.000000 45.000000 20.000000 -15.000000 37.500000 20.000000 15.000000 3 -1 0 0.
0.000000 0.000000 0.000000
1 45.000000 20.000000 15.000000 37.500000 20.000000 15.000000 45.000000 20.000000 -15.000000 3 -1 0 0.
0.000000 0.000000 0.000000
1 45.000000 20.000000 -15.000000 52.500000 20.000000 -15.000000 45.000000 20.000000 15.000000 3 -1 0 0.
0.000000 0.000000 0.000000
1 52.500000 20.000000 15.000000 45.000000 20.000000 15.000000 52.500000 20.000000 -15.000000 3 -1 0 0.
0.000000 0.000000 0.000000
1 52.500000 20.000000 -15.000000 60.000000 20.000000 -15.000000 52.500000 20.000000 15.000000 3 -1 0 0.
0.000000 0.000000 0.000000
1 60.000000 20.000000 15.000000 52.500000 20.000000 15.000000 60.000000 20.000000 -15.000000 3 -1 0 0.
0.000000 0.000000 0.000000
1 30.000000 0.000000 -15.000000 30.000000 0.000000 15.000000 37.500000 0.000000 -15.000000 3 -1 0 0.
0.000000 0.000000 0.000000
1 37.500000 0.000000 15.000000 37.500000 0.000000 -15.000000 30.000000 0.000000 15.000000 3 -1 0 0.
0.000000 0.000000 0.000000
1 37.500000 0.000000 -15.000000 37.500000 0.000000 15.000000 45.000000 0.000000 -15.000000 3 -1 0 0.
0.000000 0.000000 0.000000
1 45.000000 0.000000 15.000000 45.000000 0.000000 -15.000000 37.500000 0.000000 15.000000 3 -1 0 0.
0.000000 0.000000 0.000000
1 45.000000 0.000000 -15.000000 45.000000 0.000000 15.000000 52.500000 0.000000 -15.000000 3 -1 0 0.
0.000000 0.000000 0.000000
1 52.500000 0.000000 15.000000 52.500000 0.000000 -15.000000 45.000000 0.000000 15.000000 3 -1 0 0.
0.000000 0.000000 0.000000
1 52.500000 0.000000 -15.000000 52.500000 0.000000 15.000000 60.000000 0.000000 -15.000000 3 -1 0 0.
0.000000 0.000000 0.000000
1 60.000000 0.000000 15.000000 60.000000 0.000000 -15.000000 52.500000 0.000000 15.000000 3 -1 0 0.
0.000000 0.000000 0.000000