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	“”	E-mail address for driver to sent status updates to. If 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.
MOLANAL_SPECIES =	list of str	Y	[]	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	0	Cycle at which to start including stress tensors from ALC generated configrations.
STRS_STYLE      =	str	N	“ALL”	How stress tensors should be included in the fit. Options are: “DIAG” or “ALL”.
THIS_SMEAR      =	int	N	float	Thermal smearing temperature in K; if "None", different values are used for each case, set in the ALL_BASE_FILES traj_list.dat.

General HPC Options

Input variable	Variable type	Required	Default	Value/Options/Notes
HPC_PPN     =	int	N	36	Number of processors per node on HPC platform.
HPC_ACCOUNT =	str	N	pbronze	Charge bank/account name on HPC platform.
HPC_SYSTEM  =	str	N	slurm	HPC platform type (Only “slurm” supported currently).
HPC_PYTHON  =	str	N	/usr/tce/bin/python	Full path to python2.X exectuable on HPC platform.
HPC_EMAIL   =	bool	N	True	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 base files required by the driver (e.g. ChIMES input files, VASP, input files, etc.)
CHIMES_LSQ         =	str	N	CHIMES_SRCDIR + “chimes_lsq”	Absolute path to ChIMES_lsq executable.
CHIMES_SOLVER      =	str	N	CHIMES_SRCDIR + “lsq2.py”	Absolute path to ChIMES_lsq.py (formely, lsq2.py).
CHIMES_POSTPRC     =	str	N	CHIMES_SRCDIR + “post_proc_lsq2.py”	Absolute path to post_proc_lsq2.py.
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.
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.
CHIMES_BUILD_NODES =	int	N	4	Number of nodes to use when running chimes_lsq.
CHIMES_BUILD_QUEUE =	str	N	pbatch	Queue to submit chimes_lsq job to.
CHIMES_BUILD_TIME  =	str	N	“04:00:00”	Walltime for chimes_lsq job.
CHIMES_SOLVE_NODES =	int	N	8	Number of nodes to use when running dlasso
CHIMES_SOLVE_PPN   =	int	N	HPC_PPN	Number of procs per node to use when running dlasso
CHIMES_SOLVE_QUEUE =	str	N	pbatch	Queue to submit the dlasso job to
CHIMES_SOLVE_TIME  =	str	N	“04:00:00”	Walltime for dlasso job

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:

1. w = a0

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

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

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

5. w = n_atoms^a0

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” (used for ChIMES model development) or “DFTB” (used when generating ChIMES corrections to DFTB).
DFTB_MD_SER       =	str	N	None	Only used when MD_STYLE set to “DFTB”. DFTBplus executable absolute path.
CHIMES_MD_MPI     =	str	N	CHIMES_SRCDIR + “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 + “chimes_md-serial”	Used when MD_STYLE set to either “CHIMES” or “DFTB*”. Serial ChIMES_md executable absolute path.
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.
MDFILES           =	str	N	WORKING_DIR + “ALL_BASE_FILES/CHIMESMD_BASEFILES/”	Absolute path to MD input files like case-0.indep-0.run_md.in
CHIMES_PEN_PREFAC =	float	N	1.0E6	ChIMES penalty function prefactor.
CHIMES_PEN_DIST   =	float	N	0.02	ChIMES pentalty function kick-in distance
MOLANAL           =	str	N	None	Absolute path to molanal executable.

• CHIMES_MD_SER is used for old i/o based ChIMES/DFTB linking - update required, but needs bad_cfg printing in DFTB+ (requires change to interface)

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	?!?!?!?!IS THIS A PATH OR A FILENAME? Files needed to run simulations/single points with the method to be corrected
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	None	???!?!! String or path??? 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.

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). If FIT_CORRECTION is True, temperaturess in traj_list.dat are ignored by correction FES subtraction. Instead, searches for <filesnames>.temps where .temps replaces whatever last extension was, in CORRECTED_TYPE_FILES.

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_EXE         =	str	None	Executable to use when subtracting existing parameter contributions

Note

Consider the case of fitting 2+3+4-body C/N parameters on top of existing C- and N- parameter sets.

Users must create a new folder, HIERARCH_PARAMS in their ALL_BASE_FILES directory and place in it the pure-C and pure-N parameter files, i.e.:

$: ls -l <my_fit>/ALL_BASE_FILES/HIERARCH_PARAMS
-rw------- 1 rlindsey rlindsey 169630 May  1 10:55 C.params.txt.reduced
-rw------- 1 rlindsey rlindsey 160015 May  1 10:55 N.params.txt.reduced

Hierarchical fitting also requires special options in ALL_BASE_FILES/ALC-0_BASEFILES/fm_setup.in to ensure base the parameter types (e.g., in {C,N}.params.txt.reduced) are properly excluded from the fit. First, one must ensure that requested polynomial orders are greater or equal to those in the reference ALL_BASE_FILES/HIERARCH_PARAMS parameter files. Next, add the highlighted lines to fm_setup.in:

    # Snippet from ALL_BASE_FILES/ALC-0_BASEFILES/fm_setup.in

    # PAIRTYP #
            CHEBYSHEV 25 10 4 -1 1
    # CHBTYPE #
            MORSE
    # SPLITFI #
            false
    # HIERARC #
            true

Users must also specify which interactions to exclude from the fit (i.e., interactions fully described by the ALL_BASE_FILES/HIERARCH_PARAMS files. For the present C/N fitting example, those lines would look like:

####### TOPOLOGY VARIABLES #######

EXCLUDE 1B INTERACTION: 2
C
N

EXCLUDE 2B INTERACTION: 2
C C
N N

EXCLUDE 3B INTERACTION: 2
C C C
N N N

EXCLUDE 4B INTERACTION: 2
C C C C
N N N N

Users must also ensure that the fm_setup.in topolgy contents are consistent with those in the ALL_BASE_FILES/HIERARCH_PARAMS files. For the present C/N fitting example, those would be the highlighted lines below:

# NATMTYP #
        2

# TYPEIDX #     # ATM_TYP #     # ATMCHRG #     # ATMMASS #
1               C               0.0             12.0107
2               N               0.0             14.0067

# PAIRIDX #     # ATM_TY1 #     # ATM_TY1 #     # S_MINIM #     # S_MAXIM #     # S_DELTA #     # MORSE_LAMBDA #        # USEOVRP #     # NIJBINS #     # NIKBINS #     # NJKBINS #
1               C               C               0.98            5.0             0.01            1.4                     false           0               0               0
2               N               N               0.86            8.0             0.01            1.09                    false           0               0               0
3               C               N               1.0             5.0             0.01            1.34                    false           0               0               0

Users must explicitly define how many (and which) many-body interactions will be fit, and the corresponding outer cutoffs to use. Note that the option ALL cannot be used when performing hierarchical fits.

SPECIAL 3B S_MAXIM: SPECIFIC 2
CCCNCN   CC CN CN 5.0 5.0 5.0
CNCNNN   CN CN NN 5.0 5.0 5.0

SPECIAL 4B S_MAXIM: SPECIFIC 3
CCCCCNCCCNCN    CC CC CN CC CN CN 4.5 4.5 4.5 4.5 4.5 4.5
CCCNCNCNCNNN    CC CN CN CN CN NN 4.5 4.5 4.5 4.5 4.5 4.5
CNCNCNNNNNNN    CN CN CN NN NN NN 4.5 4.5 4.5 4.5 4.5 4.5

Note

Each training trajectory file in ALL_BASE_FILES/ALC-0_BASEFILES needs a corresponding .temps file that gives the temperature for each frame WHY?!?!?.

TO DO ADD VASP MODULES TO CODE

Reference QM Method Options

Input variable	Variable type	Default	Value/Options/Notes
QM_FILES       =	str	WORKING_DIR + “ALL_BASE_FILES/VASP_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” or “DFTB+”
IGAS_QM_METHOD =	int	VASP	Specifies which nominal QM code to use for gas configurations; options are “VASP”, “DFTB+”, and “Gaussian”

VASP-Specific Options

Input variable	Variable type	Default	Value/Options/Notes
VASP_FILES   =	str	QM_FILES	Absolute path to VASP input filess.
VASP_NODES   =	int	6	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

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 VASP jobs
DFTB_PPN     =	int	1	Number of processors to use per node for VASP jobs
DFTB_TIME    =	str	“04:00:00”	Walltime for VASP calculations (HH:MM:SS)
DFTB_QUEUE   =	str	“pbatch”	ueue to submit VASP jobs to
DFTB_EXE     =	str	None	A path to a VASP executable must be specified if BULK_QM_METHOD or IGAS_QM_METHOD are set to “DFTB+”
DFTB_MODULES =	str	“mkl”	Modules to load during VASP run

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”	ueue 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

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.