More about run DFTTK
To run DFTTK, the user should the following Linux command style:
dfttk 'module' [option]
where the available module
can be:
module |
function |
|
DFT job submission. Call VASP to perform 0 K E-V, phonon, elastic moduli, Born effective charge (dielectric tensor), etc |
|
Set basic dfttk run envirnment, such as path to pseudopotential, batch job prototype |
|
Remove certain data in MongoDB to save storage cost |
|
Download data from MongoDB database & postprocess them to get thermodynamic properties, elastic constant, etc |
|
Check the MongoDB database for DFT results followed by
calling the |
|
Find the metadata tags that have 0 K static calculaton finished. |
Examples
Check run results
To get a brief summary for data in the database, use
dfttk thfind -v 1
this will report the metadata, number of finished phonon calculations, number of finished static calculations, supercell size used for the phonon calculations, brief phase name; and the following command reports the location where the DFT calculations were submitted
dfttk thfind -v 1 -jobpath parentfolder
where parentfolder is the parent folder whose subfolders hold the individual DFT calculation job submission data.
Batch postprocessing results
dfttk thfind -get -py -td -50 -plot find_or_DFT -eq 4 -renew -ss 30 -w Pb-Ti-O
where -get
instruct thfind to call thelec
module to postprocess the data, -py
to use Yphon to recalculate the phonon density of states based on the force constants saved in the phonon
collection, -td -50
to use the self-adapted temperature mesh, -eq 4
to use Birch-Murnaghan fitting to get equilibrium volume, -ss 30
means only handle results with supercell size larger thatn 30, -w elist means only extract for compounds with all elements in the list of elist. Other enhanced screening conditions can be combinations of the follows
-all elist # compounds must contain all elements in the list of elist;
-any elist # compounds contain any elements in the list of elist;
-xall elist # compounds must not contain all elements in the list of elist;
-xany elist # compounds must not contain an y elements in the list of elist.
Batch run dfttk
Depend on the cases, dfttk postprocess may take longer time to finish. If it is the case, it is recommended to submit batch job. When submit batch, make sure compatibilities of non-ascii character by including the following in the job script:
export LC_ALL='en_US.utf8' #for bsh;
setenv LC_ALL en_US.utf8 #for csh
Usage of run module
dfttk run
: call VASP to perform 0 K E-V, phonon, elastic moduli, Born effective charge (dielectric tensor), etc
usage: dfttk run [-h] [-f STRUCTURE_FOLDER] [-mh MATCH_PATTERN] [-s SETTINGS]
[-r] [-wf WORKFLOW] [-ph] [-tag TAG] [-a] [-l] [-m [MAX_JOB]]
[-o]
optional arguments:
-h, --help show this help message and exit
-f STRUCTURE_FOLDER, --structure_folder STRUCTURE_FOLDER
The folder/file containing the structure, Default: '.'
-mh MATCH_PATTERN, --match_pattern MATCH_PATTERN
The match pattern for structure file, and it should be
place in quotes. e.g. '*POSCAR*'. Default: * --
everything except SETTING files, ref. -s
-s SETTINGS, --setting SETTINGS
Specify the name of SETTINGS files (yaml or json file)
Default: SETTINGS (case insensitive and without ext)
The following filename will be treat as SETTINGS file
SETTINGS (global settings in the folder) Start with
SETTINGS- (individual settings for struct) End with
-SETTINGS (individual settings)
-r, --recursive Recursive the path.
-wf WORKFLOW, --workflow WORKFLOW
Specify the workflow to run. Default: robust (run
get_wf_gibbs_robust workflow) (NOTE: currently, only
robust and born are supported.)
-ph, --phonon Run phonon. This is equivalent with set phonon=True in
SETTINGS file
-tag TAG, --tag TAG Specify the tag for continue mode
-a, --append Append calculation according to metadata, e.g.
appending volumes or phonon
-l, --launch Launch the wf to launchpad
-m [MAX_JOB], --max_job [MAX_JOB]
Run the job, only works when -l is specified. Default:
0 (Not submit to queue) 1: qlaunch singleshot (single
job) N(N>1): qlaunch rapidfire -m N
-o, --write_out_wf Write out the workflow
Usage of thelec module
thelec
Download data from MongoDB database & postprocess them to getthermodynamic properties, elastic constant, etc
try
dfttk thelec -h
for command available line options
dfttk thelec [-h] [-py] [-T0 [T0]] [-T1 [T1]] [-dT [TD]] [-xdn [XDN]]
[-xup [XUP]] [-dope [DOPE]] [-ne [NDOSMX]]
[-natom [NATOM]] [-e [EVERYT]] [-gauss [GAUSSIAN]]
[-i [DOSCAR]] [-o [OUTF]] [-noel] [-metatag [METATAG]]
[-qhamode [QHAMODE]] [-pn [PHASENAME]] [-eq [EQMODE]]
[-el [ELMODE]] [-s] [-plot] [-g] [-expt [EXPT]]
[-xlim [XLIM]]
optional arguments:
-h, --help show this help message and exit
-py, --pyphon use Yphon to recalculate vibrational properties.
Default: False
-T0 [T0], -t0 [T0] Low temperature limit. Default: 0
-T1 [T1], -t1 [T1] High temperature limit. Default: 1300
-dT [TD], -td [TD] Temperature increment. Default: 10
-xdn [XDN], --xdn [XDN]
Low band energy limit. Default: -100 (eV)
-xup [XUP], --xup [XUP]
High band energy limit. Default: 100
-dope [DOPE], --dope [DOPE]
dope level (electrons). Default: -1.e-8 for numerical
stability
-ne [NDOSMX], --ndosmx [NDOSMX]
new DOS mesh. Default: 10001
-natom [NATOM], --natom [NATOM]
number of atoms in the DOSCAR. Default: 1
-e [EVERYT], --everyT [EVERYT]
number of temperature points skipped from QHA
analysis. Default: 1
-gauss [GAUSSIAN], --gauss [GAUSSIAN]
densing number near the Fermi energy. Default: 1000
-i [DOSCAR], --doscar [DOSCAR]
DOSCAR filename. Default: DOSCAR
-o [OUTF], -outf [OUTF]
output filename for calculated thermoelectric
properties. Default: fvib_ele
-noel, -noel do not consider the thermal electron contribution.
Default: False
-metatag [METATAG], -metatag [METATAG]
metatag: MongoDB metadata tag field. Default: None
-qhamode [QHAMODE], -qhamode [QHAMODE]
quasiharmonic mode: debye, phonon, or yphon. Default:
debye
-pn [PHASENAME], -phasename [PHASENAME]
assigan phase name. Default: None
-eq [EQMODE], --eqmode [EQMODE]
Mode to calculate LTC. 0: Symmetrical Central
differential; 4: 4-parameter BM fitting. 5:
5-parameter BM fitting. Default: 0
-el [ELMODE], --elmode [ELMODE]
Mode to interpolate thermal electronic contribution:
0: interp1d; 1: UnivariateSpline. Default: 0
-s, -smooth smooth the LTC. Default: False
-plot, -plot plot the figure. Default: False
-g, --debug turn on debug mode by reducing the mesh. Default:
False
-expt [EXPT], -expt [EXPT]
json file path for experimental thermodynamic
properties for plot. Default: None
-xlim [XLIM], -xlim [XLIM]
Up temperature limit for plot. Default: None
Usage of thfind module
thfind
: Check the MongoDB database for DFT results followed by calling the ‘thelec’ module to get thermodynamic properties when the option ‘-get’ is given.
try
dfttk thfind -h
for command available line options
dfttk thfind [-h] [-q [QHAMODE]] [-w [WITHIN]] [-all [CONTAINALL]]
[-any [CONTAINANY]] [-v [NV]] [-ss [SUPERCELLN]] [-get]
[-py] [-T0 [T0]] [-T1 [T1]] [-dT [TD]] [-xdn [XDN]]
[-xup [XUP]] [-dope [DOPE]] [-ne [NDOSMX]]
[-natom [NATOM]] [-e [EVERYT]] [-gauss [GAUSSIAN]]
[-i [DOSCAR]] [-o [OUTF]] [-noel] [-metatag [METATAG]]
[-qhamode [QHAMODE]] [-eq [EQMODE]] [-el [ELMODE]] [-s]
[-plot] [-g] [-expt [EXPT]] [-xlim [XLIM]]
optional arguments:
-h, --help show this help message and exit
-q [QHAMODE], --qhamode [QHAMODE]
Collection. 'phonon', 'qha'. Default: 'phonon'
-w [WITHIN], --within [WITHIN]
find calculations within element list Default: None
-all [CONTAINALL], --containall [CONTAINALL]
find calculations must contain all elements in the
list Default: None
-any [CONTAINANY], --containany [CONTAINANY]
find calculations contain any elements in the list
Default: None
-v [NV], --nV [NV] Return phonon calculations finished for number of
volumes larger or equals to. Default: 6
-ss [SUPERCELLN], --supercellsize [SUPERCELLN]
only return phonon calculation with supercell size
larger than. Default: 0
-get, --get get the thermodyamic data for all found entries.
Default: False
-py, --pyphon use Yphon to recalculate vibrational properties.
Default: False
-T0 [T0], -t0 [T0] Low temperature limit. Default: 0
-T1 [T1], -t1 [T1] High temperature limit. Default: 1300
-dT [TD], -td [TD] Temperature increment. Default: 10
-xdn [XDN], --xdn [XDN]
Low band energy limit. Default: -100 (eV)
-xup [XUP], --xup [XUP]
High band energy limit. Default: 100
-dope [DOPE], --dope [DOPE]
dope level (electrons). Default: -1.e-8 for numerical
stability
-ne [NDOSMX], --ndosmx [NDOSMX]
new DOS mesh. Default: 10001
-natom [NATOM], --natom [NATOM]
number of atoms in the DOSCAR. Default: 1
-e [EVERYT], --everyT [EVERYT]
number of temperature points skipped from QHA
analysis. Default: 1
-gauss [GAUSSIAN], --gauss [GAUSSIAN]
densing number near the Fermi energy. Default: 1000
-i [DOSCAR], --doscar [DOSCAR]
DOSCAR filename. Default: DOSCAR
-o [OUTF], -outf [OUTF]
output filename for calculated thermoelectric
properties. Default: fvib_ele
-noel, -noel do not consider the thermal electron contribution.
Default: False
-metatag [METATAG], -metatag [METATAG]
metatag: MongoDB metadata tag field. Default: None
-qhamode [QHAMODE], -qhamode [QHAMODE]
quasiharmonic mode: debye, phonon, or yphon. Default:
debye
-eq [EQMODE], --eqmode [EQMODE]
Mode to calculate LTC. 0: Symmetrical Central
differential; 4: 4-parameter BM fitting. 5:
5-parameter BM fitting. Default: 0
-el [ELMODE], --elmode [ELMODE]
Mode to interpolate thermal electronic contribution:
0: interp1d; 1: UnivariateSpline. Default: 0
-s, -smooth smooth the LTC. Default: False
-plot, -plot plot the figure. Default: False
-g, --debug turn on debug mode by reducing the mesh. Default:
False
-expt [EXPT], -expt [EXPT]
json file path for experimental thermodynamic
properties for plot. Default: None
-xlim [XLIM], -xlim [XLIM]