ChIMES Active Learning Driver Configuration File Options

Optional config.py Variables:

Assorted General Options

Input variable	Variable type	Required	Default	Value/Options/Notes
EMAIL_ADD       =	str	N	False	E-mail address for driver to send status updates to. If False or blank (“”), no emails are sent.
SEED            =	int	N	1	Only used for active learning strategies are selected. Seed for random number generator.
ATOM_TYPES      =	list of str	Y	None	List of atom types in system of interest, e.g. [“C”,”H”,”O”].
NO_CASES        =	int	Y	None	Number of different state points at which to conduct iterative learning.
STOP_AFTER      =	str	N	None	Stop without doing any iterative/active learning. Options: “SOLVE_AMAT” (stop once the first parameter file is generated) or “RUN_MD” (stop after the first MD simulation).
MOLANAL_SPECIES =	list of str	N	[“”]	List of species to track in molanal output, e.g. ["C1 O1 1(O-C)", "C1 O2 2(O-C)"].
USE_AL_STRS     =	int	N	-1	Cycle at which to start including stress tensors from ALC-generated configurations.
STRS_STYLE      =	str	N	“ALL”	How stress tensors should be included in the fit. Options are: “DIAG” or “ALL”.
THIS_SMEAR      =	int	N	None	Thermal smearing temperature in K; if "None", different values are used for each case, set in the ALL_BASE_FILES traj_list.dat.
DRIVER_DIR      =	str	Y	None	Location of the source directory for ALD
WORKING_DIR      =	str	Y	None	Location of the ALD job being ran

General HPC Options

Input variable	Variable type	Required	Default	Value/Options/Notes
HPC_PPN     =	int	Y	36	Number of processors per node on HPC platform.
HPC_ACCOUNT =	str	Y	None	Charge bank/account name on HPC platform.
HPC_SYSTEM  =	str	N	slurm	HPC platform type. Options: slurm, conda-slurm, TACC, UM-ARC, or torque.
HPC_PYTHON  =	str	N	“python3”	Full path to python3 executable on HPC platform.
HPC_EMAIL   =	bool	N	False	Controls whether driver status updates are e-mailed to user.

ChIMES LSQ Options

Input variable	Variable type	Required	Default	Value/Options/Notes
ALC0_FILES         =	str	N	WORKING_DIR + “ALL_BASE_FILES/ALC-0_BASEFILES/”	Path to LSQ base files required by the driver (e.g. traj_list.dat, fm_setup.in, etc.)-Note: In greatlakes, all paths provided must be absolute paths using the “realpath” command, not just the current working directory from “pwd”.
CHIMES_LSQ         =	str	Y	CHIMES_SRCDIR + “../build/chimes_lsq”	Absolute path to ChIMES_lsq executable.
CHIMES_LSQ_MODULES =	str	N	“”	System-specific modules needed to run ChIMES-LSQ jobs
CHIMES_SOLVER      =	str	N	CHIMES_SRCDIR + “../build/chimes_lsq.py”	Absolute path to chimes_lsq.py (formerly, lsq2.py).
CHIMES_POSTPRC     =	str	N	CHIMES_SRCDIR + “../build/post_proc_chimes_lsq.py”	Absolute path to post_proc_chimes_lsq.py.
CHIMES_SRCDIR      =	str	Y	“”	Path to directory containing the ChIMES_LSQ source code
CHIMES_BUILD_NODES =	int	Y	4	Number of nodes to use when running chimes_lsq.
CHIMES_BUILD_QUEUE =	str	Y	pbatch	Queue to submit chimes_lsq job to.
CHIMES_BUILD_TIME  =	str	Y	“04:00:00”	Walltime for chimes_lsq job.
CHIMES_SOLVE_NODES =	int	Y	8	Number of nodes to use when running dlasso
CHIMES_SOLVE_PPN   =	int	Y	HPC_PPN	Number of procs per node to use when running dlasso
CHIMES_SOLVE_QUEUE =	str	Y	pbatch	Queue to submit the dlasso job to
CHIMES_SOLVE_TIME  =	str	Y	“24:00:00”	Walltime for dlasso job
N_HYPER_SETS  =	int	N	1	Number of independent ChIMES layers to create. If N is 1, a standard (single-layer) ChIMES model will be generated. If N is greater than 1, a multilayer model is generated, and a separate fm_setup.in file is needed for each layer (e.g., 0.fm_setup.in, 1.fm_setup.in, …). For additional details on the multilayer ChIMES method and workflow, ; see Multilayer (TurboChIMES) Fitting Mode.
REGRESS_ALG        =	str	N	dlasso	Regression algorithm to use for fitting; only dlasso supported for now
REGRESS_VAR        =	float	N	1e-5	Regression regularization variable.
REGRESS_NRM        =	bool	N	True	Controls whether A-matrix is normalized prior to solution.
WEIGHTS_SET_ALC_0  =	bool	N	False	Should ALC-0 (or 1 if no clustering) weights be read directly from a user specified file?
WEIGHTS_ALC_0      =	str	N	None	Set if WEIGHTS_SET_ALC_0 is true; path to user specified ALC-0 (or ALC-1) weights.
WEIGHTS_FORCE      =	special	N	1.0	Weights to apply to full-frame forces - many options, see note below.
WEIGHTS_FGAS       =	special	N	5.0	Weights to apply to gas phase forces - many options, see note below.
WEIGHTS_ENER       =	special	N	0.1	Weights to apply to full-frame energies - many options, see note below.
WEIGHTS_EGAS       =	special	N	0.1	Weights to apply to gas phase energies - many options, see note below.
WEIGHTS_STRES      =	special	N	250.0	Weights to apply to full-frame stress tensor components - many options, see note below.

Note

There are numerous options available for weighting, and weights are applied separately to full-frame forces, gas phase forces, full-frame energies, gas phase energies, and full-frame stress.

If a WEIGHTS_* option is set to a single floating point value, that value is applied to all candidate data of that type, e.g., if WEIGHTS_FORCE = 1.0, all full-frame forces will be assigned a weight of 1.0.

Additional weighting styles can be selected by letter:

A w = a0

B w = a0*(this_cycle-1)^a1 # NOTE: treats this_cycle = 0 as this_cycle = 1

C w = a0*exp(a1*|X|/a2)

D w = a0*exp(a1[X-a2]/a3)

E w = n_atoms^a0

F w = a0*exp(a1[ X/n_atoms-a2]/a3)

G w = a0*exp(a1(|X|-a2)/a3)

where “X” is the value being weighted.

WEIGHTS_FORCE = [["B"],[1.0,-1.0]] would select weighting style B and apply a weight of 1.0 to each full-frame force component in the first ALD cycle; weighting would decrease by a factor (this_cycle)^(-1.0) each cycle.

Multiple weighting schemes can be combined as well. For example WEIGHTS_FORCE = [ ["A","B"], [[100.0  ],[1.0,-1.0]]] would add an additional multiplicative factor of 100 to the previous example.

Molecular Dynamics Options

Input variable	Variable type	Required	Default	Value/Options/Notes
MD_STYLE          =	str	Y	None	Iterative MD method. Options are “CHIMES” (ChIMES model development), “DFTB+” (ChIMES corrections to DFTB), or “LMP” (LAMMPS-driven MD).
CHIMES_MD_MPI     =	str	N	CHIMES_SRCDIR + “/../build/chimes_md-mpi”	Only used when MD_STYLE set to “CHIMES”. MPI-compatible ChIMES_md exectuable absolute path.
CHIMES_MD_SER     =	str	N	CHIMES_SRCDIR + “/../build/chimes_md-serial”	Used when MD_STYLE set to “CHIMES”. Serial ChIMES_md executable absolute path. (See note below)
MD_NODES          =	list of int	N	[4] * NO_CASES	Number of nodes to use for MD jobs at each case. Number can be different for each case (e.g., [2,2,4,8] for four cases).
MD_QUEUE          =	list of str	N	[“pbatch”] * NO_CASES	Queue type to use for MD jobs at each case. Can be different for each case.
MD_TIME           =	list of str	N	[“4:00:00”] * NO_CASES	Walltime to use for MD jobs at each case. Can be different for each case.
MD_FILES          =	str	N	WORKING_DIR + “ALL_BASE_FILES/CHIMESMD_BASEFILES/”	Absolute path to MD input files like case-0.indep-0.run_md.in (synonym: MDFILES)
MD_MPI            =	str	N	MD_SER	MPI-compatible MD executable absolute path (e.g., path to "lmp_mpi_chimes" or "chimes_md-mpi").
MD_SER            =	str	N	MD_MPI	Serial MD executable absolute path (LAMMPS, DFTB+, or chimes_md-serial, per MD_STYLE).
MD_OMPEXPORTS     =	str	N	None	Export statements prepended to MD job scripts (e.g., OpenMP settings for DFTB+ runs).
RUN_MOLANAL       =	bool	N	True	Controls whether molanal-based speciation analysis is run on MD trajectories.
CHIMES_MD_MODULES =	str	N	“”	System-specific modules needed to run ChIMES MD jobs.
CHIMES_PEN_PREFAC =	float	N	1.0E6	ChIMES penalty function prefactor.
CHIMES_PEN_DIST   =	float	N	0.02	ChIMES penalty function kick-in distance
MOLANAL           =	str	N	None	Absolute path to molanal executable.
LMP_FILES         =	str	N	QM_FILES	Path to input files if using it as a reference ("QM") method.
LMP_NODES         =	int	N	1	Number of nodes to use for LAMMPS jobs.
LMP_POSTPRC       =	str	N	DRIVER_DIR + “/src/lmp_to_xyz.py”	Path to lmp2xyz.py
LMP_PPN           =	int	N	1	Number of procs per node to use for LAMMPS jobs.
LMP_TIME          =	str	N	“00:30:00”	Walltime for LAMMPS calculations (HH:MM:SS).
LMP_QUEUE         =	str	N	“pdebug”	Queue to submit LAMMPS jobs to.
LMP_EXE           =	str	N	None	Absolute path to LAMMPS executable.
LMP_MODULES       =	str	N	None	System-specific modules needed to run LAMMPS.
LMP_MEM           =	str	N	“”	Memory requirements for running LAMMPS jobs.
LMP_UNITS         =	str	N	REAL	Units LAMMPS input/output is expected to be.

Correction Fitting Options

Input variable	Variable type	Required	Default	Value/Options/Notes
FIT_CORRECTION          =	bool	N	False	Is this ChIMES model being fit as a correction to another method?
CORRECTED_TYPE          =	str	N	None	Method type being corrected. Currently only “DFTB+” is supported
CORRECTED_TYPE_FILES    =	str	N	None	Path to directory containing files needed to run single points with the method to be corrected (e.g., <temperature>.dftb_in.hsd and .skf files)
CORRECTED_TYPE_EXE      =	str	N	None	Executable to use when subtracting existing forces/energies/stresses from method to be corrected
CORRECTED_TEMPS_BY_FILE =	bool	N	False	Should electron temperatures be set to values in traj_list.dat (false) or in specified file location, for correction calculation? Only needed if correction method is QM-based. See notes below.

Note

Note: If corrections are used, ChIMES_MD_{NODES,QUEUE,TIME} are all used to specify DFTB runs. These should be renamed to simulation_{...} for the generalized MD block (which should become SIM block).

Note: If CORRECTED_TEMPS_BY_FILE is set to be True , temperatures in traj_list.dat are ignored by correction FES subtraction. Instead, each training trajectory file in ALL_BASE_FILES/ALC-0_BASEFILES needs a corresponding .temps file that gives the temperature for each frame

Cluster-Based Active Learning Options

The following options control cluster-based active learning; see the Cluster AL page for a detailed description and a worked example. Aside from DO_CLUSTER, these options are only read when DO_CLUSTER = True.

Input variable	Variable type	Default	Value/Options/Notes
DO_CLUSTER =	bool	False	Should cluster extraction/selection be performed?
MAX_CLUATM =	int	None	Maximum number of atoms to consider in a cluster
TIGHT_CRIT =	str	None	Path to the file with tight (molecule) bond criteria
LOOSE_CRIT =	str	None	Path to the file with loose (nominal transition state) bond criteria; if set equal to TIGHT_CRIT, no “loose” clusters are generated
CLU_CODE =	str	None	Path to the cluster extraction code (e.g., utilities/new_ts_clu.cpp)
MEM_BINS =	int	40	Number of bins for cluster-selection energy histograms
MEM_CYCL =	int	MEM_BINS/10	Number of cycles for cluster selection
MEM_NSEL =	int	400	Number of clusters to select each ALC
MEM_ECUT =	float	100.0	Energy cutoff (kcal/mol/atom); clusters above this absolute energy are ignored
CALC_REPO_ENER_CENT_QUEUE =	str	“pdebug”	Queue for central-repository cluster energy calculations
CALC_REPO_ENER_CENT_TIME =	str	“00:10:00”	Walltime for central-repository cluster energy calculations
CALC_REPO_ENER_QUEUE =	str	“pbatch”	Queue for cluster energy calculations
CALC_REPO_ENER_TIME =	str	“04:00:00”	Walltime for cluster energy calculations

Hierarchical Fitting Options

Input variable	Variable type	Default	Value/Options/Notes
DO_HIERARCH          =	bool	False	Is this a hierarchical fit (i.e., building on existing parameters?”)
HIERARCH_PARAM_FILES =	list of str	None	List of parameter files to build on, which should be in ALL_BASE_FILES/HIERARCH_PARAMS
HIERARCH_METHOD      =	str	None	MD method to use for subtracting existing parameter contributions - current options are CHIMES or LMP
HIERARCH_EXE         =	str	None	Executable to use when subtracting existing parameter contributions

Multilayer (TurboChIMES) Fitting Options

Multilayer (TurboChIMES) fitting uses multiple ChIMES functional layers, typically a short-range layer and a long-range layer, trained simultaneously on the same reference database. The number of layers is controlled by N_HYPER_SETS and implemented through numbered fm_setup.in files (e.g. 0.fm_setup.in, 1.fm_setup.in). Where as, hierarchical fitting (table above) partitions work across element / cross-interaction tiles and optional pre-fit parameter files. Hence, Multilayer (TurboChIMES) does not use DO_HIERARCH or HIERARCH_PARAM_FILES.For workflow, mathematics, directory layout, and example files, see Multilayer (TurboChIMES) Fitting Mode.

Reference QM Method Options

Input variable	Variable type	Default	Value/Options/Notes
QM_FILES       =	str	WORKING_DIR + “ALL_BASE_FILES/QM_BASEFILES”	Absolute path to QM input files generic to all QM methods. Can specify separately if multiple methods are being used (see code-specific options below)
BULK_QM_METHOD =	str	VASP	Specifies which nominal QM code to use for bulk configurations; options are “VASP”, “DFTB+”, “CP2K”, or “LMP”
IGAS_QM_METHOD =	str	VASP	Specifies which nominal QM code to use for gas configurations; options are “VASP”, “DFTB+”, “CP2K”, “LMP”, or “Gaussian”

VASP-Specific Options

Input variable	Variable type	Default	Value/Options/Notes
VASP_NODES   =	list of int	[6] * NO_CASES	Number of nodes to use for VASP jobs
VASP_PPN     =	int	HPC_PPN	Number of processors to use per node for VASP jobs
VASP_TIME    =	str	“04:00:00”	Walltime for VASP calculations (HH:MM:SS)
VASP_QUEUE   =	str	“pbatch”	Queue to submit VASP jobs to
VASP_EXE     =	str	None	A path to a VASP executable must be specified if BULK_QM_METHOD or IGAS_QM_METHOD are set to “VASP”
VASP_MODULES =	str	“mkl”	Modules to load during VASP run
VASP_POSTPRC =	str	DRIVER_DIR + “/src/vasp2xyzf.py”	Absolute path to vasp2xyzf.py
VASP_MEM =	str	“”	Memory requirements for running VASP jobs

DFTB+ -Specific Options

Input variable	Variable type	Default	Value/Options/Notes
DFTB_FILES   =	str	QM_FILES	Absolute path to DFTB+ input files.
DFTB_NODES   =	int	1	Number of nodes to use for DFTB+ jobs
DFTB_PPN     =	int	1	Number of processors to use per node for DFTB+ jobs
DFTB_TIME    =	str	“04:00:00”	Walltime for DFTB+ calculations (HH:MM:SS)
DFTB_QUEUE   =	str	“pbatch”	Queue to submit DFTB+ jobs to
DFTB_EXE     =	str	None	A path to a DFTB+ executable must be specified if BULK_QM_METHOD or IGAS_QM_METHOD are set to “DFTB+”
DFTB_MODULES =	str	“mkl”	Modules to load during DFTB+ run
DFTB_MEM     =	str	“”	Memory requirements for running DFTB+ jobs
DFTB_POSTPRC =	str	CHIMES_SRCDIR + “/../contrib/dftbgen_to_xyz.py”	Absolute path to dftbgen_to_xyz.py

CP2K-Specific Options

Input variable	Variable type	Default	Value/Options/Notes
CP2K_NODES   =	list of int	[3] * NO_CASES	Number of nodes to use for CP2K jobs
CP2K_PPN     =	int	1	Number of processors to use per node for CP2K jobs
CP2K_TIME    =	str	“04:00:00”	Walltime for CP2K calculations (HH:MM:SS)
CP2K_QUEUE   =	str	“pbatch”	Queue to submit CP2K jobs to
CP2K_EXE     =	str	None	A path to a CP2K executable must be specified if BULK_QM_METHOD or IGAS_QM_METHOD are set to “CP2K”
CP2K_MODULES =	str	“mkl”	Modules to load during CP2K run
CP2K_POSTPRC =	str	DRIVER_DIR + “/src/cp2k_to_xyz.py”	Absolute path to cp2k_to_xyz.py
CP2K_MEM =	str	“”	Memory requirements for running CP2K jobs
CP2K_DATADIR =	str	None	Path to the directory containing potential and functional files for CP2K
CP2K_FILES =	str	QM_FILES	Absolute path to CP2K input files (inp and potentials)

Gaussian-Specific Options

Input variable	Variable type	Default	Value/Options/Notes
GAUS_NODES =	int	4	Number of nodes to use for Gaussian jobs
GAUS_PPN   =	int	HPC_PPN	Number of processors to use per node for Gaussian jobs
GAUS_TIME  =	str	“04:00:00”	Walltime for Gaussian calculations (HH:MM:SS)
GAUS_QUEUE =	str	“pbatch”	Queue to submit Gaussian jobs to
GAUS_EXE   =	str	None	A path to a Gaussian executable must be specified if IGAS_QM_METHOD is set to “Gaussian”
GAUS_SCR   =	str	None	Absolute path to Gaussian scratch directory
GAUS_REF   =	str	None	Name of file containing single atom energies from Gaussian and target planewave method
GAUS_MEM   =	str	“”	Memory requirements for running Gaussian jobs

Note

The file specified for GAUS_REF is structured like:

<chemical symbol> <Gaussian energy> <planewave code energy>
<chemical symbol> <Gaussian energy> <planewave code energy>
<chemical symbol> <Gaussian energy> <planewave code energy>
...
<chemical symbol> <Gaussian energy> <planewave code energy>

Energies are expected in kcal/mol and there should be an entry for each atom type of interest.