Repository files navigation 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 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 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 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. 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 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
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