PreparingAnSjobFile

The .sjob files are of the following format:

###################################################
######## example_mix_transferability.sjob #########
###################################################

### compute_dir
compute_dir="/home/dcarls0n/compute/"

### Transferability or parameterization run
runtype="transf" 				# "transf"/"param"
portion="full" 					# "full"/"EMD"/"parseEMD"

### hwtype: pascal/mpi-fsl/turing/ampere
hwtype="mpi-fsl"				# Hardware to run on

### compounds (space-seperated string list of compounds) -- 1 element for pure-component
compounds=(n-dodecane n-butylcyclohexane n-butylbenzene 2-2-4-4-6-8-8-heptamethylnonane)

### mixture mole fractions (space-seperated list of mole fractions)
mixmolefracs=(0.0666 0.0667 0.8000 0.0667)

### temperature, pressure
temp=333.15					# Kelvin
press=1.00					# atm

### system size preferences
N_NPT=800					# number of molecules in the NPT (density) portion
N_NPT_tol=50					# tolerance in number of molecules in the NPT (density) portion
N_NVT=150					# number of molecules in the NVT (viscosity/EMD) portion
N_NVT_tol=50					# tolerance in number of molecules in the NVT (viscosity/EMD) portion

### number of replicates
NPT_replicates=60				# number of simulation replicates for the NPT (density) portion
NVT_replicates=360				# number of simulation replicates for the NVT (viscosity/EMD) portion

### force field
ff="TLVMie"					# force field name
fftype="UA"					# force field type "UA" (united-atom) or "AA" (all-atom)
ffcharge="chargeless"				# force field charge considerations
# ff="TraPPEUA"
# fftype="UA"
# ffcharge="chargeless"
# ff="OPLSAA"
# fftype="AA"
# ffcharge="charged"

### Mie n-6 force field parameters to implement (only used for parameterization runs: runtype="param")
### units are determined from lammps "units real"
# atomID=3 					# atomID=3 corresponds to the CH2 group
# eps=0.121 					# kcal/mol
# sig=4.015 					# Angstroms
# n=16 						# Mie n-6 repulsive exponent (unitless)

###################################################
##### End of example_mix_transferability.sjob #####
###################################################

An explanation of each variable follows:

compute_dir - Defines the directory in which the folder structure of the simulation replicates will be built and subsequent simulations will be run. The results of these simulations will be output into the compute_dir/EMD/csvdata/ directory.
runtype - Defines the run type: transferability (used to make predictions using the existing TLVMie parameters) or parameterization (used to probe the predictive capability of different parameter values by changing the values of the nonbonded parameters of a specific atom pair at runtime). These parameters are discussed further below (atomID, eps, sig, and n)
portion - Specifies the portion to run. Should always be set to "full", unless a partial run already exists. If a successful NPT run exists, specify "EMD" to skip the NPT portion and run the EMD portion. If both the NPT and EMD(NVT) portions were completed, but the post-processing analysis remains incomplete, specify "parseEMD" to run only the post-processing steps on the completed simulation results.
hwtype - Specify the hardware to run on. mpi-fsl runs CPU-only mpi jobs on FSL (Fulton Supercomputing Lab @ BYU). pascal runs GPU-accelerated jobs on FSL's pascal architecture nodes (m9g). The turing or ampere flags should be set here when running on the poise supercomputing cluster, which has GPUs from both the NVIDIA turing and ampere architectures. It is recommended that a user running many simulations utilize both mpi-fsl and pascal jobs. There are much less GPU (pascal) nodes on FSL, but jobs run significantly faster with GPU-acceleration.
compounds - List the compounds to be simulated. A pure component simulation would only list one compound. Mixture simulations should list compounds in a "space-separated" list. Compound names must match exactly how they are listed in /resources/block_compounds/ and /resources/compound_lookup.csv
mixmolefracs - List the mole fractions of the mixture. A pure component simulation would contain only one entry: 1.00. Mixture simulations should list mole fractions in a "space-separated" list.
temp - Specify the system temperature in Kelvin
press - Specify the system pressure in atm
N_NPT - Specify the system size for the density (NPT) portion. The TLVMie methodology suggests 800 molecules or larger.
N_NVT - Specify the system size for the viscosity (NVT a.k.a. EMD) portion. The TLVMie methodology suggests 128 molecules or larger.
N_NPT_tol - Specify the tolerance in number of molecules on the value of N_NPT. This tolerance setting is only relevant for mixtures, where N_NPT will be selected within the range N_NPT-N_NPT_tol to N_NPT+N_NPT_tol such that the effective mole fraction simulated best replicates the mole fraction specified by the user above.
N_NVT_tol - Specify the tolerance in number of molecules on the value of N_NVT. This tolerance setting is only relevant for mixtures, where N_NVT will be selected within the range N_NVT-N_NVT_tol to N_NVT+N_NVT_tol such that the effective mole fraction simulated best replicates the mole fraction specified by the user above.
NPT_replicates - Determines the number of simulation replicates for the NPT portion from which a predicted density will be determined. Larger values will provide additional precision but require more simulation time. Currently supports values up to 999
NVT_replicates - Determines the number of simulation replicates for the NVT/EMD portion from which a predicted viscosity will be determined. Larger values will provide additional precision but require more simulation time. Currently supports values up to 999
ff - Specify the force field to be used. Note that for each force field and COMPOUND, a moltemplate COMPOUND_FORCEFIELD.lt file must be defined in resources/block_compounds/COMPOUND/moltemplate_files
fftype - Specify the force field type ("UA" or "AA"). TLVMie and TraPPEUA are united-atom "UA" approaches. OPLSAA is an all-atom "AA" approach.
ffcharge - Specify whether charges are considered. Should be set to "chargeless" for the TLVMie force field in its current state. The TLVMie force field is currently only parameterized for normal alkanes, branched alkanes, alkylbenzenes, and cycloalkanes. Due to the nature of the TLVMie force field being united-atom, none of these groups include charge considerations. The addition of hydrogen explicit functional groups to TLVMie will necessitate charge considerations (like for the individually defined O and H groups in alcohols). OPLSAA, being an all-atom approach, necessitates charge considerations, even for simple hydrocarbons, as there is a charge dipole across the C-H bonds.
atomID - Parameterization parameter. Atom ID of the atom pair to be investigated. The values of epsilon, sigma, and n below will be set for the atomID specified here at runtime. The atomID for each TLVMie group are listed in workspaceNNN/lammps_files/log.lammps when the TLVMie force field definition is loaded.
eps - Parameterization parameter. Specifies the value of epsilon in the Mie n-6 potential.
sig - Parameterization parameter. Specifies the value of sigma in the Mie n-6 potential.
n - Parameterization parameter. Specifies the value of the repulsive exponent, n, in the Mie n-6 potential.

An example .sjob file for a parameterization job the predictive capability of a different set of values for epsilon, sigma, and n for the alkyl CH2 group as applied to n-heptane at 333.15 K and 1 atm is shown below for reference:

###################################################
######## example_pc_parameterization.sjob #########
###################################################

### compute_dir
compute_dir="/home/dcarls0n/compute/"

### Transferability or parameterization run
runtype="param" 				# "transf"/"param"
portion="full" 					# "full"/"EMD"/"parseEMD"

### hwtype: pascal/mpi-fsl/turing/ampere
hwtype="mpi-fsl"				# Hardware to run on

### compounds (space-seperated string list of compounds) -- 1 element for pure-component
compounds=(n-heptane)

### mixture mole fractions (space-seperated list of mole fractions)
mixmolefracs=(1.000)

### temperature, pressure
temp=333.15					# Kelvin
press=1.00					# atm

### system size preferences
N_NPT=800					# number of molecules in the NPT (density) portion
N_NPT_tol=50					# tolerance in number of molecules in the NPT (density) portion
N_NVT=150					# number of molecules in the NVT (viscosity/EMD) portion
N_NVT_tol=50					# tolerance in number of molecules in the NVT (viscosity/EMD) portion

### number of replicates
NPT_replicates=60				# number of simulation replicates for the NPT (density) portion
NVT_replicates=360				# number of simulation replicates for the NVT (viscosity/EMD) portion

### force field
ff="TLVMie"					# force field name
fftype="UA"					# force field type "UA" (united-atom) or "AA" (all-atom)
ffcharge="chargeless"				# force field charge considerations
# ff="TraPPEUA"
# fftype="UA"
# ffcharge="chargeless"
# ff="OPLSAA"
# fftype="AA"
# ffcharge="charged"

### force field parameters to implement (only used for parameterization runs: runtype="param")
### units are determined from lammps "units real"
atomID=3 					# atomID=3 corresponds to the CH2 group
eps=0.100 					# kcal/mol
sig=3.750 					# Angstroms
n=16 						# Mie n-6 repulsive exponent (unitless)

###################################################
##### End of example_pc_parameterization.sjob #####
###################################################