np-electrostatics-lab

Install instructions on BigRed2

• First, git clone the project git clone https://github.com/softmaterialslab/np-electrostatics-lab.git
• Then, load the required modules using following command: module swap PrgEnv-cray PrgEnv-gnu && module load boost/1.65.0 && module load gsl
• Next, go to the root directory: cd np-electrostatics-lab
• Then, install the project: make install
• Fianlly, submit the job: make cluster-submit
• All outputs from the simulation will be stored in the data folder when the simulation is completed.

Necessary Modules for local run

• Load the necessary modules: module load gsl && module load openmpi/3.0.1 && module load boost/1_67_0
• Make sure to export BOOST_LIBDIR environment variable with location to the lib directory: export BOOST_LIBDIR=/opt/boost/gnu/openmpi_ib/lib/
• Also make sure to export OMP_NUM_THREADS environment variable with maximum threads available in your CPU: export OMP_NUM_THREADS=16

Local Install instructions

• First, git clone the project git clone https://github.com/softmaterialslab/np-electrostatics-lab.git
• Go to np-electrostatics-lab directory: cd np-electrostatics-lab
• You should provide the following make command to make the project. This will create the executable and Install the executable (np_electrostatics_lab) into bin directory (That is np-electrostatics-lab/bin) make local-install
• Next, go to the bin directory: cd bin
• Now you are ready to run the executable with aprun command using the following method:
  • Spehre: time mpirun -np 2 -N 16 ./np_electrostatics_lab -a 2.6775 -b 14.28 -e 2 -E 78.5 -V -60 -v 1 -g 1082 -m 6 -t 0.001 -s 10000 -p 100 -f 10 -M 6 -T 0.001 -k 0.0025 -q 0.001 -L 5 -l 5 -S 10000000 -P 100000 -F 100 -X 10000 -U 1000 -Y 500000 -W 1000000 -B 0.025
  • Disk: time mpirun -np 2 -N 16 ./np_electrostatics_lab -a 2.6775 -b 14.28 -e 2 -E 78.5 -V -60 -v 1 -g 1082 -m 6 -t 0.001 -s 10000 -p 100 -f 10 -M 6 -T 0.001 -k 0.0025 -q 0.001 -L 5 -l 5 -S 10000000 -P 100000 -F 100 -X 10000 -U 1000 -Y 500000 -W 1000000 -R 0.1 -B 0.4 -G "Disk"

NanoHUB app page:

• https://nanohub.org/tools/nselectrostatic/