Installing and running ambient sample on BigRed3

• First, git clone the project: git clone https://github.com/softmaterialslab/nonadecane.git
• Then, load the required modules using following command: module swap PrgEnv-intel PrgEnv-gnu && module load lammps/gnu
• Next, go to the root directory: cd nonadecane

Phase 01

• Then, submit the job:
  • For squalane: make DIR_PATH=AMB_P1 METHOD=submit M=S CLUSTER=bigred3
  • For star molecule: make DIR_PATH=AMB_P1 METHOD=submit M=T CLUSTER=bigred3
• If you want to clean the project: make clean DIR_PATH=AMB_P1

Phase 02

• You must have restart file from phase1 to run the phase2
• Then, submit the job:
  • For squalane: make DIR_PATH=AMB_P2 METHOD=submit M=S CLUSTER=bigred3
  • For star molecule: make DIR_PATH=AMB_P2 METHOD=submit M=T CLUSTER=bigred3
• If you want to clean the project: make clean DIR_PATH=AMB_P2

High pressure sample generation

• You must have restart file from 0.1MPa-phase2 to run the 100MPa
• Then, submit the job:
  • For squalane 100MPa: make DIR_PATH=HP METHOD=submit CLUSTER=bigred3 M=S T=sql P=100 E=0.1 R=0.81843211 O=0.867
  • For squalane 300MPa: make DIR_PATH=HP METHOD=submit CLUSTER=bigred3 M=S T=sql P=300 E=100 R=0.86715711 O=0.923
• If you want to clean the project: make clean DIR_PATH=HP

Shearing

• You must have restart file from phase2 to start the shearing process
• Select F and S to change below to what is needed. Then, submit the job:
  • For squalane: make DIR_PATH=SHEAR METHOD=submit M=S P =0.1 S=1e10 F=1000 CLUSTER=bigred3
  • For star molecule: make DIR_PATH=SHEAR METHOD=submit M=T P =0.1 S=1e10 F=1000 CLUSTER=bigred3
• If you want to clean the project: make clean DIR_PATH=SHEAR

Installing and running ambient sample on local computer

• For running different phases of the program: please check bigred3 commands and change local make commands accordingly.
• First, git clone the project: git clone https://github.com/softmaterialslab/nonadecane.git
• Then, makesure you have either parellel LAMMPS or sequatial LAMMPS available in your environment.
• Next, findout what is your mpirun exe and lammps exe and use it appropriately in the following instructions.

Running parallel lammps

• Then, run using following commands: Here my mpi exe was mpirun and LAMMPS exe was lmp_daily
  • For squalane: make DIR_PATH=AMB_P1 METHOD=local-run-parallel M=S NODESIZE=4 MPI_EXE=mpirun LAMMPS_EXE=lmp_daily
  • For star molecule: make DIR_PATH=AMB_P1 METHOD=local-run-parallel M=T NODESIZE=4 MPI_EXE=mpirun LAMMPS_EXE=lmp_daily

Running serial lammps

• Then, run using following commands: Here my mpi exe was mpirun and LAMMPS exe was lmp_daily
  • For squalane: make DIR_PATH=AMB_P1 METHOD=local-run-serial M=S LAMMPS_EXE=lmp_daily
  • For star molecule: make DIR_PATH=AMB_P1 METHOD=local-run-serial M=T LAMMPS_EXE=lmp_daily
• If you want to clean the project: make clean DIR_PATH=AMB_P1