One of the reasons we use vasp.py is to make it easy to run a lot of calculations conveniently. vasp.py automatically submits jobs to the queue for us, and provides some job control features to make it wait until they are finished.
Sometimes things go wrong though, e.g. you realize you used the wrong parameter and suddenly you have a lot of jobs in the queue to stop. Not to worry, vasp.py can help you out. Each calculator stores a jobid on it, and vasp.py provides some support to interact with the queue system (assuming you use Torque or something compatible with it)!
Here is an example where we setup and run 10 calculations. The first time we run this, 10 jobs get submitted.
from vasp import Vasp from ase import Atom, Atoms import matplotlib.pyplot as plt import numpy as np bond_lengths = np.linspace(1.05, 1.3, 10) calcs = [Vasp('molecules/co-n{0:02d}'.format(i), # output dir xc='PBE', nbands=6, encut=520, ismear=1, sigma=0.2, atoms=Atoms([Atom('C', [0, 0, 0]), Atom('O', [d, 0, 0])], cell=(6, 6, 6))) for i, d in enumerate(bond_lengths)] energies = [calc.potential_energy for calc in calcs] # Here are the jobids print([(c.jobid(), c.in_queue()) for c in calcs]) # Stop here until all calculations are done. Vasp.stop_if(None in energies) print(energies)
/home-research/jkitchin/dft-book/blog/source/org/molecules/co-n00 submitted: 1397279.gilgamesh.cheme.cmu.edu /home-research/jkitchin/dft-book/blog/source/org/molecules/co-n01 submitted: 1397280.gilgamesh.cheme.cmu.edu /home-research/jkitchin/dft-book/blog/source/org/molecules/co-n02 submitted: 1397281.gilgamesh.cheme.cmu.edu /home-research/jkitchin/dft-book/blog/source/org/molecules/co-n03 submitted: 1397282.gilgamesh.cheme.cmu.edu /home-research/jkitchin/dft-book/blog/source/org/molecules/co-n04 submitted: 1397283.gilgamesh.cheme.cmu.edu /home-research/jkitchin/dft-book/blog/source/org/molecules/co-n05 submitted: 1397284.gilgamesh.cheme.cmu.edu /home-research/jkitchin/dft-book/blog/source/org/molecules/co-n06 submitted: 1397285.gilgamesh.cheme.cmu.edu /home-research/jkitchin/dft-book/blog/source/org/molecules/co-n07 submitted: 1397286.gilgamesh.cheme.cmu.edu /home-research/jkitchin/dft-book/blog/source/org/molecules/co-n08 submitted: 1397287.gilgamesh.cheme.cmu.edu /home-research/jkitchin/dft-book/blog/source/org/molecules/co-n09 submitted: 1397288.gilgamesh.cheme.cmu.edu [(u'1397279.gilgamesh.cheme.cmu.edu', True), (u'1397280.gilgamesh.cheme.cmu.edu', True), (u'1397281.gilgamesh.cheme.cmu.edu', True), (u'1397282.gilgamesh.cheme.cmu.edu', True), (u'1397283.gilgamesh.cheme.cmu.edu', True), (u'1397284.gilgamesh.cheme.cmu.edu', True), (u'1397285.gilgamesh.cheme.cmu.edu', True), (u'1397286.gilgamesh.cheme.cmu.edu', True), (u'1397287.gilgamesh.cheme.cmu.edu', True), (u'1397288.gilgamesh.cheme.cmu.edu', True)]
Say we just realize we wanted to delete these jobs, and change a parameter. We just get the calculators, and call qdel on each one like this:
from vasp import Vasp import numpy as np bond_lengths = np.linspace(1.05, 1.3, 10) calcs = [Vasp('molecules/co-n{0:02d}'.format(i)) for i, d in enumerate(bond_lengths)] print([calc.qdel() for calc in calcs])
[(0, ''), (0, ''), (0, ''), (0, ''), (0, ''), (0, ''), (0, ''), (0, ''), (0, ''), (0, '')]
All those 0's just means the job deletion succeeded. Now, we just have to adjust the original parameter set, and rerun the original script! That will resubmit the new jobs for us.
Here is the output from one of those calculations. Note the path is an org-link, so you can just click on it to open the directory if you run this in Emacs.
from vasp import Vasp print(Vasp('molecules/co-n00'))
*************** VASP CALCULATION SUMMARY ***************
Vasp calculation directory:
---------------------------
[[/home-research/jkitchin/dft-book/blog/source/org/molecules/co-n00]]
Unit cell:
----------
x y z |v|
v0 6.000 0.000 0.000 6.000 Ang
v1 0.000 6.000 0.000 6.000 Ang
v2 0.000 0.000 6.000 6.000 Ang
a,b,c,alpha,beta,gamma (deg): 6.000 6.000 6.000 90.0 90.0 90.0
Total volume: 216.000 Ang^3
Stress: xx yy zz yz xz xy
-0.071 0.001 0.001 -0.000 -0.000 -0.000 GPa
ID tag sym x y z rmsF (eV/A)constraints (F=Frozen)
0 0 C 0.000 0.000 0.000 14.97 T T T
1 0 O 1.050 0.000 0.000 14.97 T T T
Potential energy: -14.1779 eV
INPUT Parameters:
-----------------
lcharg : False
pp : PBE
nbands : 6
xc : pbe
ismear : 1
lwave : False
sigma : 0.2
kpts : [1, 1, 1]
encut : 520
Pseudopotentials used:
----------------------
C: potpaw_PBE/C/POTCAR (git-hash: ee4d8576584f8e9f32e90853a0cbf9d4a9297330)
O: potpaw_PBE/O/POTCAR (git-hash: 592f34096943a6f30db8749d13efca516d75ec55)
Here is a summary of the job control functions and queue commands built in to vasp.py.
Runs all stored calculators on the Vasp class.
from vasp import Vasp help(Vasp.run)
Help on method run in module vasp.vasp_core:
run(cls, wait=False) method of __builtin__.type instance
Convenience function to run calculators.
The default behavior is to exit after doing this. If wait is
True, iy will cause it to wait with the default args to
Vasp.wait.
If wait is a dictionary, it will be passed as kwargs to
Vasp.wait.
Runs the instance calculator.
Returns whether all calculators are ready, e.g. with results.
from vasp import Vasp help(Vasp.all)
Help on method all in module vasp.vasp_core:
all(cls) method of __builtin__.type instance
Returns if all calculators in the class are ready.
Aborts the script if condition is not truthy
from vasp import Vasp help(Vasp.stop_if)
Help on method stop_if in module vasp.vasp_core:
stop_if(cls, condition) method of __builtin__.type instance
Stops the program if condition is truthy.
Aborts the script.
from vasp import Vasp help(Vasp.abort)
Help on method abort in module vasp.vasp_core:
abort(cls) method of __builtin__.type instance
Abort and exit the program the calculator is running in.
Allows a real time-elapsed wait for jobs to finish. This blocks the script.
from vasp import Vasp help(Vasp.wait)
Help on method wait in module vasp.vasp_core:
wait(cls, poll_interval=5, timeout=None, abort=False) method of __builtin__.type instance
Control function to wait until all calculators are ready.
if abort is truthy, stop the program.
Otherwise check the calculators every poll_interval seconds,
up to timeout seconds later. If timeout is None, poll forever.
Gets information about the job.
from vasp import Vasp import numpy as np calc = Vasp('molecules/co-n09') calc.qstat()
Job id Name User Time Use S Queue ------------------------- ---------------- --------------- -------- - ----- 1397268.gilgamesh .../co-n09 jkitchin 0 R short
Allows you to alter the queue parameters for a job.
from vasp import Vasp import numpy as np calc = Vasp('molecules/co-n09') calc.qalter('-l', 'walltime=20:00:00')
Allows you to delete the job
This will pop up an xterm window in the directory of the calculation. There you can run commands and see what is going on.
from vasp import Vasp import numpy as np calc = Vasp('molecules/co-n00') calc.xterm()
Returns contents of the queue output file if it exists. May be useful to debug.
from vasp import Vasp import numpy as np calc = Vasp('molecules/co-n00') print(calc.qoutput())
xmodmap: unable to open display ''
vasp.5.3.5 31Mar14 (build Aug 04 2015 12:48:45) complex
POSCAR found : 2 types and 2 ions
LDA part: xc-table for Pade appr. of Perdew
POSCAR found : 2 types and 2 ions
POSCAR, INCAR and KPOINTS ok, starting setup
WARNING: small aliasing (wrap around) errors must be expected
FFT: planning ...
WAVECAR not read
WARNING: random wavefunctions but no delay for mixing, default for NELMDL
entering main loop
N E dE d eps ncg rms rms(c)
DAV: 1 0.693510492725E+02 0.69351E+02 -0.29305E+03 12 0.855E+02
DAV: 2 -0.556930203939E+01 -0.74920E+02 -0.74931E+02 18 0.248E+02
DAV: 3 -0.151153850754E+02 -0.95461E+01 -0.95461E+01 12 0.964E+01
DAV: 4 -0.153607093341E+02 -0.24532E+00 -0.24532E+00 12 0.138E+01
DAV: 5 -0.153763439194E+02 -0.15635E-01 -0.15635E-01 24 0.343E+00 0.816E+00
DAV: 6 -0.144168400550E+02 0.95950E+00 -0.26887E+00 12 0.196E+01 0.429E+00
DAV: 7 -0.142207761391E+02 0.19606E+00 -0.48211E-01 18 0.795E+00 0.186E+00
DAV: 8 -0.142021024270E+02 0.18674E-01 -0.81621E-02 18 0.376E+00 0.582E-01
DAV: 9 -0.142016090043E+02 0.49342E-03 -0.11924E-02 12 0.136E+00 0.870E-02
DAV: 10 -0.142024449557E+02 -0.83595E-03 -0.55763E-04 12 0.268E-01 0.420E-02
DAV: 11 -0.142040155105E+02 -0.15706E-02 -0.43005E-04 18 0.201E-01 0.267E-02
DAV: 12 -0.142041222436E+02 -0.10673E-03 -0.11191E-04 6 0.106E-01 0.989E-03
DAV: 13 -0.142042422801E+02 -0.12004E-03 -0.26082E-05 6 0.587E-02 0.352E-03
DAV: 14 -0.142042518369E+02 -0.95569E-05 -0.35661E-06 6 0.202E-02
1 F= -.14204252E+02 E0= -.14208117E+02 d E =0.115958E-01
This command prints out an org-mode table with clickable links
from vasp import Vasp import numpy as np bond_lengths = np.linspace(1.05, 1.3, 10) calcs = [Vasp('molecules/co-n{0:02d}'.format(i)) for i, d in enumerate(bond_lengths)] print(Vasp.torque())