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* summit configure * add spock scripts to FOM * get new models to build with hip * add hip slipping bc * testing communication on spock * update spock build based on olcf docs * update configure & test scripts for spock * Fixing potential bugs with communication * Adding simple test of GPU aware MPI * some changes to configure for spock * Modifying GPU aware MPI test to send multiple messages * playing with spock Gpu test * added gpu wrapper test * Cleaning up some compiler warnings * add barrier between pack / MPI send * Updating build to support HIP as a language * fixing gpu mpi sync * Adding script * local spock changes * add membrane class * update membrane structure * membrane communications * working on new comm data structures * add membrane unit test * membrane compiles * membrane test * Updating hip port to match cuda * update summit config * update summit config * add configure script for crusher * update membrane test * update membrane test * convention for inside / outside membrane link direction * working on membrane comm * try to fix time conversion factor for Poisson solver; to be built and tested * fix dumb typo * update summit config * tune launch for crusher * tune launch for mrt on crusher * update color * summit script with specific module versions * update crusher config * add crusher examples * add dense case for crusher * Fixing some quick annoying compile warnings * fix binding in example * working on fix * Adding simple crusher test * Adding new crusher MPI test * disable MPI thread multiple for crusher * updates to crusher configure * cpu test for crusher * Working on standalone reproducer for MPI bug * More work on creating standalone test * More work on creating standalone test * More work on creating standalone test * Reverting TestCrusher2, standalone version passes (TestCrusher3.cpp), need to figure out why * Working on standalone MPI test on crusher * Working on standalone MPI test on crusher * Getting closer to stand alone test * Still trying to create standalone reproducer * hang fix / workaround * Created standalone MPI failure test * Removing TestCrusher tests, the bug deals with the StackTrace which we disable the multistack trace for now. Moving the test out of LBPM * fix sendcount / recvcount * Testing persistent communication * Updating calculation of bandwidth * crusher hackathon final version * working on membrane communication structures * add cell simulator * added cell simulator * make sure halo is filled when measuring object * add membrane transport function for d3q7 * add membrane unpack function * poking at MF issue * update crusher build * membrane data structures compiling * update to membrane capability * update comments in ion model * fix dumb print bug * clean up relabel * adding membrane functions * move membrane to common folder * membrane structure in IonModel * membrane structure in IonModel * try at membrane simulator * add python script to generate bubble * add python script to generate bubble * cell simulator runs * read input files * add single cell example * refining cell example * start on cuda function * werkin * start on cuda function * start on hip function * updates and fix for user input reader * update cell example * add sigmoid to ion equilibrium dist * cuda build succeeds * update crusher script * getting ready to merge gpu * refactor compact AA routines for testing * add testing functions to ScaLBL * testing membrane ion transport * membrane transport test passing * membrane starts working ok... * original wang poisson solver (broken) * rex d3q19 (broken) * tau from wang paper * still broken wang * d319 poisson works good * Poisson working pretty good now * initialize nernst-planck simulator; to be built subject to debugging * fix a few syntax bugs and build passed * Poisson solver; enable specifying initial values * update cell example * add GPU functions for d3q19 poisson * fix dumb bugs * fix bugs in initializing electric potential; the Psi on solid was accidentally overwritten before. * small change * fix bugs in importing ion model's dummy velocity * add membrane concentration init * remove bad warnings * remove print staetements * add barriers to poisson solver * update print * print membrane input concentration * read Membrane ion concentration list * fix bad ref to D3Q7 * update error analysis for Poisson solver * fix typo * update hip poisson solver * deprecate old error methods * a bunch of summit debug things to roll back later * fix poisson typo * update hip * debug crusher * debug charge density problems on crusher * fix charge density (i think) * remove Stokes solver from cell simulator; need to test build * update cpu ion valence * added membrane properties to input db * update cell db * update executable list and NP_cell simulator * correct use_membrane functionality * add functionality for user to choose either D3Q7 or D3Q19 lattice for Poisson;to be built and tested * build passed * make further corrections * correct D3Q7 Poisson LB algorithm * correct ion LB collison * udpate output precision * add more tweaks for cell simulator * update print-out * this makes mpi hang error explicit;to be debugged * cleanup with help from valgrind * update to cell vis routine * add hip for ion update * fix missing bracket * add new ion code for cuda * add barrier to membrane transport * debug gpu launch issue for ion * debug gpu * add functions to copy send / recv list from ScaLBL * updating membrane communication structure * membrane test works with new comm * communication seems to work * add sample files for plane membrane * update gpu routines first try * update hip * multiple nvidia gpu working with membrane * added membrane analysis capability * added support for swc file * support for SWC input format * swc reader works with MPI * shift swc data * SWC reader update * SWC reader update 2 * add offset to Domain for swc * add input files for simple bacteria * add performance counters to ion / poisson solvers * fix bug with SWC * add BC to poisson solver * fix compiler warnings * fix memory leaks * fix zlib download path * Fixing memory leak * Fixing memory leaks * restart for Poisson model * fix bug in ion model restart * trying to fix yaml * fix workflow indentation * porosity factor in effperm * porosity factor in effperm * porosity factor in effperm * porosity factor in effperm Co-authored-by: James E McClure <mcclurej@vt.edu> Co-authored-by: Mark Berrill <berrillma@ornl.gov> Co-authored-by: Zhe Rex Li <zhe.rex.li@gmail.com> Co-authored-by: Zhe Li <zzl109@gadi-login-01.gadi.nci.org.au> Co-authored-by: Zhe Li <zzl109@gadi-login-04.gadi.nci.org.au> Co-authored-by: Zhe Li <zzl109@gadi-login-02.gadi.nci.org.au> Co-authored-by: Zhe Li <zzl109@gadi-login-06.gadi.nci.org.au> Co-authored-by: Zhe Li <zzl109@gadi-login-05.gadi.nci.org.au>
91 lines
2.8 KiB
Python
Executable File
91 lines
2.8 KiB
Python
Executable File
import numpy as np
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import math
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import matplotlib.pyplot as plt
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#physical constant
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k_B_const = 1.380649e-23 #[J/K]
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N_A_const = 6.02214076e23 #[1/mol]
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e_const = 1.602176634e-19 #[C]
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epsilon0_const = 8.85418782e-12 #[C/V/m]
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#other material property parameters
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epsilonr_water = 80.4
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T=310.15 #[K]
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#input ion concentration
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C_Na_in = 15e-3 #[mol/m^3]
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C_Na_out = 145e-3 #[mol/m^3]
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C_K_in = 150e-3 #[mol/m^3]
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C_K_out = 4e-3 #[mol/m^3]
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C_Cl_in = 10e-3 #[mol/m^3]
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C_Cl_out = 110e-3 #[mol/m^3]
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#calculating Debye length
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#For the definition of Debye lenght in electrolyte solution, see:
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#DOI:10.1016/j.cnsns.2014.03.005
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#Eq(42) in Yoshida etal., Coupled LB method for simulator electrokinetic flows
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prefactor= math.sqrt(epsilonr_water*epsilon0_const*k_B_const*T/2.0/N_A_const/e_const**2)
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debye_length_in = prefactor*np.sqrt(np.array([1.0/C_Na_in,1.0/C_K_in,1.0/C_Cl_in]))
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debye_length_out = prefactor*np.sqrt(np.array([1.0/C_Na_out,1.0/C_K_out,1.0/C_Cl_out]))
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print("Debye length inside membrane in [m]")
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print(debye_length_in)
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print("Debye length outside membrane in [m]")
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print(debye_length_out)
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#setup domain
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cube_length_z = 192
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cube_length_xy = 64
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#set LBPM domain resoluiton
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h=0.01 #[um]
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print("Image resolution = %.6g [um] (= %.6g [m])"%(h,h*1e-6))
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domain=2*np.ones((cube_length_z,cube_length_xy,cube_length_xy),dtype=np.int8)
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zgrid,ygrid,xgrid=np.meshgrid(np.arange(cube_length_z),np.arange(cube_length_xy),np.arange(cube_length_xy),indexing='ij')
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domain_centre=cube_length_xy/2
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make_bubble = np.logical_and(zgrid>=cube_length_z/4,zgrid<=cube_length_z*0.75)
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domain[make_bubble]=1
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##save domain
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file_name= "Pseudo3D_double_plane_membrane_z192_xy64_InsideLabel1_OutsideLabel2.raw"
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domain.tofile(file_name)
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print("save file: "+file_name)
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#debug plot
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#plt.figure(1)
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#plt.pcolormesh(domain[:,int(domain_centre),:])
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#plt.colorbar()
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#plt.axis("equal")
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#plt.show()
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##generate initial ion concentration - 3D
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#domain_Na = C_Na_out*np.ones_like(domain,dtype=np.float64)
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#domain_Na[make_bubble] = C_Na_in
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#domain_K = C_K_out*np.ones_like(domain,dtype=np.float64)
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#domain_K[make_bubble] = C_K_in
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#domain_Cl = C_Cl_out*np.ones_like(domain,dtype=np.float64)
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#domain_Cl[make_bubble] = C_Cl_in
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#
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#domain_Na.tofile("Pseudo3D_plane_membrane_concentration_Na_z192_xy64.raw")
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#domain_K.tofile("Pseudo3D_plane_membrane_concentration_K_z192_xy64.raw")
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#domain_Cl.tofile("Pseudo3D_plane_membrane_concentration_Cl_z192_xy64.raw")
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##debug plot
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#plt.figure(2)
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#plt.subplot(1,3,1)
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#plt.title("Na concentration")
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#plt.pcolormesh(domain_Na[:,int(bubble_centre),:])
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#plt.colorbar()
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#plt.axis("equal")
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#plt.subplot(1,3,2)
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#plt.title("K concentration")
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#plt.pcolormesh(domain_K[:,int(bubble_centre),:])
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#plt.colorbar()
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#plt.axis("equal")
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#plt.subplot(1,3,3)
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#plt.title("Cl concentration")
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#plt.pcolormesh(domain_Cl[:,int(bubble_centre),:])
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#plt.colorbar()
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#plt.axis("equal")
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#plt.show()
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