Sa

.gitignore

@@ -33,3 +33,9 @@
 .project
 .cproject
 .settings/
+# Simulation outputs
+*.vtu
+*.vti
+*.vtr
+\Sucrose*
+*.csv

CADES_README.md

@@ -0,0 +1,40 @@
+# Instructions for NUFEB + phototroph on CADES CONDO
+
+
+# clone repo
+module load env/cades-cnms
+```shell
+cd $SCRATCH
+git clone https://github.com/Jsakkos/NUFEB --recursive
+git checkout add_phototroph
+git pull
+```
+# To build
+```shell
+. $SOFTWARECNMS/spack/share/spack/setup-env.sh
+spack load openmpi/qnfab5m
+spack load vtk%[email protected]
+
+./install_cades.sh --enable-vtk
+```
+# To test
+## interactively
+```shell
+salloc -A cnms -p high_mem --nodes=1 --mem=80G --exclusive -t 00:30:00
+srun --ntasks-per-node 32 -n 32 ../../lammps/src/lmp_mpi -in Inputscript.lammps
+```
+## batches
+```shell
+module load env/cades-cnms
+module load anaconda3
+cd $SCRATCH
+cd NUFEB/examples/cyanobacteria-sucrose
+python NUFEBatom --n 3 --r 3
+./slurmRun.sh
+```
+# To login remotely
+https://support.cades.ornl.gov/user-documentation/_book/external-access-ucams.html
+```shell
+ssh [email protected]
+ssh [email protected]
+```

Inputscript-template.txt

@@ -0,0 +1,116 @@
+# NUFEB simulation
+
+atom_style	bio
+atom_modify	map array sort 1000 5.0e-7
+boundary	ff ff ff
+newton		off
+processors  * * *
+
+
+# Amount of bacteria and Nutrients information
+# n_cyanos ${n_cyanos}
+# co2 ${co2}
+# light ${light}
+# SucRatio ${SucRatio}
+# Nsample ${Nsample}
+
+comm_modify	vel yes
+read_data_bio atom_${n_cyanos}_${co2}_${light}_${SucRatio}_${Nsample}.in
+
+
+###############Output directories##############################
+shell mkdir Run_${n_cyanos}_${co2}_${light}_${SucRatio}_${Nsample}
+shell cd Run_${n_cyanos}_${co2}_${light}_${SucRatio}_${Nsample}
+
+##############Define initial particle distribution##############
+
+lattice sc 1e-6 origin 0 0 0
+region reg block 0 1000 0 1000 0 100
+
+${CYANOGroup}
+${ECWGroup}
+
+neighbor	5e-7 bin
+neigh_modify	delay 0 one 5000
+
+##############Define DEM Variables&Commands##############
+
+pair_style  gran/hooke/history 1.e-4 NULL 1.e-5 NULL 0.0 1
+pair_coeff  * *
+
+#pair_style brownian 1.5 0 0 1e-6 1e-5 300 5878567
+#pair_coeff * *
+
+timestep 10
+
+fix 1 all nve/limit 1e-8
+fix fv all viscous 1e-5
+
+fix zw all wall/gran hooke/history 2000 NULL 500.0 NULL 1.5 0 zplane  0.0  ${Zheight}
+
+variable kanc equal 50
+
+#fix zwa all walladh v_kanc zplane  0.0  1e-04
+
+variable ke equal 5e+10
+#fix j1 all epsadh 1 v_ke 1
+
+##############Define IBm Variables##############
+
+#variables used in fix eps_extract
+variable EPSdens equal 30
+variable EPSratio equal 1.3
+
+#variables used in fix division
+variable divDia1 equal 1.96e-6
+variable divDia2 equal 1.04e-6
+
+#variables used in fix kinetics
+variable diffT equal 1e-4
+variable tol equal 1e-13
+variable etaHET equal 0.6
+variable layer equal -1
+
+#variables used in fix death
+#variable deadDia equal 9e-7
+
+
+##############Define IBm Commands##############
+
+fix k1 all kinetics 100 ${GridMesh} v_diffT v_layer niter 1000000
+fix kgm all kinetics/growth/monod sucexp $SucRatio
+fix g1 all kinetics/diffusion v_tol closedflag $Closed
+${CYANODiv}
+${ECWDiv}
+#fix d2 all death 1 v_deadDia demflag 0
+
+
+##############Define IBm Computes##############
+
+compute myNtypes all ntypes
+compute myMass all biomass
+compute myCon all avg_con
+
+##############Simulation exit condition##############
+variable co2 equal c_myCon[4]
+fix 10 all halt 1 v_co2 <= 1e-19
+
+variable light equal c_myCon[1]
+fix 11 all halt 1 v_light <= 1e-19
+
+
+##############Simulation Output##############
+
+#dump		id all custom 100 output.lammmps id type diameter x y z
+dump            traj all bio/hdf5 100 trajectory.h5 id type radius x y z con
+#${DumpOutput}
+#dump		du1 all vtk 100 atom_*.vtu id type diameter x y z
+#dump		du2 all grid 100 grid_%_*.vti con
+dump            du3 all bio 100 ntypes biomass avg_con
+thermo_style    custom step cpu atoms c_myNtypes[*] c_myMass[*] c_myCon[*]
+thermo		100
+thermo_modify	lost ignore
+
+run $Timesteps
+shell cd ..
+clear