Complete Examples¶
Note
Disclaimer: Please note that the examples given here do not generally qualify as production calculations because the supercell size, optimization process, DMC timestep and other key parameters may not be converged. Pseudopotentials are provided “as is” and should not be trusted without explicit validation.
Complete examples of calculations performed with Nexus are provided in the following sections. These examples are intended to highlight basic features of Nexus and act as templates for future calculations. If there is an example you would like to contribute, or if you feel an example on a particular topic is needed, please contact the developer at krogeljt@ornl.gov to discuss the possibilities.
To perform the example calculations yourself, consult the examples
directory in your Nexus installation:
The examples assume that you have working versions of pw.x,
pw2qmcpack.x, qmcpack (real version), and qmcpack_complex
(complex version) installed and in your PATH. A brief description of
each example is given below.
- Bulk Diamond VMC
- A representative bulk calculation. A simple workflow consisting of orbital generation with PWSCF, orbital conversion with pw2qmcpack, and a short VMC calculation with QMCPACK is performed.
- Graphene Sheet DMC
- A representative slab calculation. The total DMC energy of a graphene “sheet” consisting of 8 atoms is computed. DFT is performed with PWSCF on the primitive cell followed by Jastrow optimization by QMCPACK and finally a supercell VMC+DMC calculation by QMCPACK.
- C 20 Molecule DMC
- A representative molecular calculation. The total DMC energy of an ideal C 20 molecule is computed. DFT is performed with PWSCF on a periodic cell with some vacuum surrounding the molecule. QMCPACK optimization and VMC+DMC follow on the system with open boundary conditions.
(Note that without the crystal field splitting afforded by the initial artificial periodicity, the Kohn-Sham HOMO would be degenerate, and so a production calculation would likely require more care in appropriately setting up the wavefunction.)
- Oxygen Dimer DMC
- An example demonstrating automation of a simple parameter scan, in this case the interparticle spacing in an oxygen dimer. The reader will gain some experience modifying Nexus user scripts to produce automated workflows.
- Bulk Diamond Excited States VMC
- A representative bulk excited states calculation. A simple workflow consisting of orbital generation with PWSCF, orbital conversion with pw2qmcpack, and a short VMC calculation with QMCPACK is performed.
Example 1: Bulk Diamond VMC¶
The files for this example are found in:
/your_download_path/nexus/examples/qmcpack/diamond
By following the instructions contained in this section the reader can execute a simple workflow with Nexus. The workflow presented here is intended to illustrate basic Nexus usage. The example workflow has three stages: (1) orbital generation in a primitive (2 atom) cell of diamond with PWSCF, (2) conversion of the orbitals from the native PWSCF format to the ESHDF format that QMCPACK reads, and (3) a minimal variational Monte Carlo (VMC) run of a 16 atom supercell of diamond with QMCPACK. The Nexus input script corresponding to this workflow is shown below.
The script is similar to the one discussed in Nexus imports, differing mainly in the name-by-name imports and
the description of the physical system. Instead of reading an external
VASP POSCAR file, the structure is specified in a format native to
Nexus. The physical system is specified by providing the unit system
(Angstrom in this case), the three vectors comprising the axes of the
simulation cell, and the names and positions (Cartesian coordinates) of
the atoms involved. The use of “tiling=(2,2,2)” communicates the
request that a \(2\times2\times2\) supercell be constructed out of
the specified 2 atom primitive cell. The k-point grid applies to the
supercell and is comprised of a single k-point. The eight corresponding
primitive cell images of this k-point are determined automatically by
Nexus. The text “C = 4” specifies the number of valence electrons
for the carbon pseudopotential. The pseudopotential files used in this
example (C.BFD.*) have been adapted from an open access
pseudopotential database (see
http://www.burkatzki.com/pseudos/index.2.html) for use in PWSCF and
QMCPACK. Since the PhysicalSystem object, “dia16”, contains both
the supercell and its equivalent folded/primitive version, the PWSCF DFT
calculation will be performed in the primitive cell to save memory for
the subsequent VMC calculation of the full supercell performed with
QMCPACK.
#! /usr/bin/env python3
# nexus imports
from nexus import settings,Job,run_project
from nexus import generate_physical_system
from nexus import generate_pwscf
from nexus import generate_pw2qmcpack
from nexus import generate_qmcpack,vmc
# general settings for nexus
settings(
pseudo_dir = '../pseudopotentials',# directory with all pseudopotentials
status_only = 0, # only show status of runs
generate_only = 0, # only make input files
sleep = 3, # check on runs every 3 seconds
machine = 'ws16' # local machine is 16 core workstation
)
# generate diamond structure
dia16 = generate_physical_system(
units = 'A', # Angstrom units
axes = [[1.785,1.785,0. ], # cell axes
[0. ,1.785,1.785],
[1.785,0. ,1.785]],
elem = ['C','C'], # 2 C atoms
pos = [[0. ,0. ,0. ], # atomic positions
[0.8925,0.8925,0.8925]],
tiling = (2,2,2), # tile to 16 atom cell
kgrid = (1,1,1), # single supercell k-point
kshift = (0,0,0), # at gamma
C = 4 # pseudo-C (4 val. elec.)
)
# scf run produces orbitals
scf = generate_pwscf(
identifier = 'scf', # identifier/file prefix
path = 'diamond/scf', # directory for scf run
job = Job(cores=16,app='pw.x'),
input_type = 'generic',
calculation = 'scf', # perform scf calculation
input_dft = 'lda', # dft functional
ecutwfc = 200, # planewave energy cutoff
conv_thr = 1e-8, # scf convergence threshold
nosym = True, # don't use symmetry
wf_collect = True, # write orbitals
system = dia16, # run diamond system
pseudos = ['C.BFD.upf'], # pwscf PP for C
)
# convert orbitals for qmcpack
conv = generate_pw2qmcpack(
identifier = 'conv', # identifier/file prefix
path = 'diamond/scf', # directory for conv job
job = Job(cores=1,app='pw2qmcpack.x'),
write_psir = False, # output in k-space
dependencies = (scf,'orbitals') # get orbitals from scf
)
# vmc run
qmc = generate_qmcpack(
identifier = 'vmc', # identifier/file prefix
path = 'diamond/vmc', # directory for vmc run
job = Job(cores=16,threads=4,app='qmcpack'),
input_type = 'basic',
system = dia16, # run diamond system
pseudos = ['C.BFD.xml'], # qmcpack PP for C
jastrows = [], # no jastrows, test run
calculations = [
vmc( # vmc inputs
walkers = 1, # one walker per core
warmupsteps = 20, # 20 steps before measurement
blocks = 200, # 200 blocks
steps = 10, # of 10 MC steps each
substeps = 2, # 2 substeps w/o measurement
timestep = .4 # 0.4/Ha timestep
)
],
dependencies = (conv,'orbitals')# get orbitals from conv job
)
# nexus monitors all runs
run_project(scf,conv,qmc)
To fully execute the usage example provided here, copies of PWSCF,
QMCPACK, and the orbital converter pw2qmcpack will need to be installed
on the local machine. The example assumes that the executables are in
the user’s PATH and are named pw.x, qmcpack, and
pw2qmcpack.x. See Helpful Links for Installing Electronic Structure Codes for download and
installation instructions for these codes. A test of Nexus including the
generation of input files, but without actual job submission, can be
performed without installing these codes. However, Python itself and
NumPy are required to run Nexus (see Helpful Links for Installing Python Modules. The
example also assumes the local machine is a workstation with 16
available cores (“ws16”). If fewer than 16 cores are available,
e.g. 4, change the example files to reflect this:
ws16\(\rightarrow\)ws4,
Job(cores=16,\ldots)\(\rightarrow\)Job(cores=4,\ldots).
In this example, we will run Nexus in three different modes:
status mode: print the status of each simulation and then exit (
status_only=1).generate mode: generate input files but do not execute workflows (
generate_only=1).execute mode: execute workflows by submitting jobs and monitoring simulation progress (
status_only=0, generate_only=0).
Only the last mode requires executables for PWSCF and QMCPACK.
First, run Nexus in status mode. Enter the examples/qmcpack/diamond
directory, open diamond.py with a text editor and set
“status_only=1”. Run the script by typing “./diamond.py” at
the command line and inspect the output. The output should be similar to
the text below (without the comments):
Pseudopotentials
reading pp: ../pseudopotentials/C.BFD.upf # dft PP found
reading pp: ../pseudopotentials/C.BFD.xml # qmc PP found
Project starting
checking for file collisions # files do not overlap
loading cascade images # load saved workflow state
cascade 0 checking in # only one workflow/cascade
checking cascade dependencies # match producers/consumers
all simulation dependencies satisfied
cascade status
setup, sent_files, submitted, finished, got_output, analyzed
000000 scf ./runs/diamond/scf # no work has been done yet
000000 conv ./runs/diamond/scf # for any of the
000000 vmc ./runs/diamond/vmc # three simulations
setup, sent_files, submitted, finished, got_output, analyzed
The binary string “000000” indicates that none of the six stages of
simulation progression have been completed. These stages correpond to
the following actions/states: writing input files (“setup”), copying
pseudopotential files (“sent_files”), submitting simulation jobs for
execution (“submitted”), the completion of a simulation job
(“finished”), collecting output files (“got_output”), and
preprocessing output files for later analysis (“analyzed”) . In a
production setting, this mode is useful for checking the status of
current workflows/cascades prior to adding new ones. It is also useful
in general for detecting any problems with the Nexus input script
itself.
Next, run the example in generate mode. Set “status_only =0” and
“generate_only =1”, then run the example script again. Instead of
showing workflow status, Nexus will now perform a dry run of the
workflows by generating all of the run directories and input files. The
output should contain text similar to what is shown below:
starting runs: # start submitting jobs
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
poll 0 memory 60.45 MB # first poll cycle
Entering ./runs/diamond/scf 0 # scf job
writing input files 0 scf # input file written
Entering ./runs/diamond/scf 0
sending required files 0 scf # PP files copied
submitting job 0 scf # job is in virtual queue
Entering ./runs/diamond/scf 0
Would have executed: # shows submission command
export OMP_NUM_THREADS=1 # does not execute
mpirun -np 16 pw.x -input scf.in
poll 1 memory 60.72 MB
Entering ./runs/diamond/scf 0
copying results 0 scf # output file copying stage
Entering ./runs/diamond/scf 0
analyzing 0 scf # output analysis stage
poll 2 memory 60.73 MB # third poll cycle
Entering ./runs/diamond/scf 1 # similar for conv job
writing input files 1 conv
Entering ./runs/diamond/scf 1
sending required files 1 conv
submitting job 1 conv
Entering ./runs/diamond/scf 1
Would have executed:
export OMP_NUM_THREADS=1
mpirun -np 1 pw2qmcpack.x<conv.in
poll 3 memory 60.73 MB
Entering ./runs/diamond/scf 1
copying results 1 conv
Entering ./runs/diamond/scf 1
analyzing 1 conv
poll 4 memory 60.73 MB # fifth poll cycle
Entering ./runs/diamond/vmc 2 # similar for vmc job
writing input files 2 vmc
Entering ./runs/diamond/vmc 2
sending required files 2 vmc
submitting job 2 vmc
Entering ./runs/diamond/vmc 2
Would have executed:
export OMP_NUM_THREADS=4
mpirun -np 4 qmcpack vmc.in.xml
poll 5 memory 60.78 MB
Entering ./runs/diamond/vmc 2
copying results 2 vmc
Entering ./runs/diamond/vmc 2
analyzing 2 vmc
Project finished # jobs finished
The output describes the progress of each simulation. The run submission
commands are also clearly shown as well as the amount of memory used by
Nexus. There should now be a “runs” directory containing the
generated input files with the following structure:
runs/
\-- diamond # main diamond directory
|-- scf # scf directory
|-- |-- C.BFD.upf # pwscf PP file
|-- |-- conv.in # conv job input file
|-- |-- pwscf_output # pwscf output directory
|-- |-- scf.in # scf job input file
|-- |-- sim_conv # nexus directory for conv
|-- |-- |-- input.p # stored input object
|-- |-- \-- sim.p # simulation status file
|-- \-- sim_scf # nexus directory for scf
|-- |-- input.p # stored input object
|-- \-- sim.p # simulation status file
\-- vmc # vmc directory
|-- C.BFD.xml # qmcpack PP file
|-- sim_vmc # nexus directory for vmc
|-- |-- input.p # stored input object
|-- \-- sim.p # simulation status file
\-- vmc.in.xml # vmc job input file
The “sim.p” files record the state of each simulation. Inspect the
input files generated by Nexus (scf.in, conv.in, and
vmc.in.xml). Compare the files with the input provided to Nexus in
diamond.py.
Finally, run the example in execute mode. Remove the “runs” and
“results” directories, set “status_only =0” and
“generate_only =0”, and rerun the script. The output shown should
be similar to what was seen for generate mode, only now there may be
multiple workflow polls while a particular simulation is running. The
“sleep” keyword controls how often the polls occur (every 3 seconds
in this example). Note that the Nexus host process sleeps in between
polls so that a minimum of computational resources are occupied. Once
“Project finished” is displayed, all the simulation runs should be
complete. Confirm the success of the runs by checking the output files.
The text “JOB DONE.” should appear near the end of the PWSCF output
file scf.out. QMCPACK has completed successfully if
“Total Execution time” appears near the end of the output in
vmc.out.
Example 2: Graphene Sheet DMC¶
The files for this example are found in:
/your_download_path/nexus/examples/qmcpack/graphene
Take a moment to study the “input file” script (graphene.py) and the
attendant comments (prefixed with #).
#! /usr/bin/env python3
from nexus import settings,Job,run_project
from nexus import generate_physical_system
from nexus import generate_pwscf
from nexus import generate_pw2qmcpack
from nexus import generate_qmcpack
from nexus import loop,linear,vmc,dmc
# general settings for nexus
settings(
pseudo_dir = '../pseudopotentials',# directory with all pseudopotentials
sleep = 3, # check on runs every 'sleep' seconds
generate_only = 0, # only make input files
status_only = 0, # only show status of runs
machine = 'ws16', # local machine is 16 core workstation
)
# generate the graphene physical system
graphene = generate_physical_system(
lattice = 'hexagonal', # hexagonal cell shape
cell = 'primitive', # primitive cell
centering = 'P', # primitive basis centering
constants = (2.462,10.0), # a,c constants
units = 'A', # in Angstrom
atoms = ('C','C'), # C primitive atoms
basis = [[ 0 , 0 , 0], # basis vectors
[2./3,1./3, 0]],
tiling = (2,2,1), # tiling of primitive cell
kgrid = (1,1,1), # Monkhorst-Pack grid
kshift = (.5,.5,.5), # and shift
C = 4 # C has 4 valence electrons
)
# list of simulations in workflow
sims = []
# scf run produces charge density
scf = generate_pwscf(
# nexus inputs
identifier = 'scf', # identifier/file prefix
path = 'graphene/scf', # directory for scf run
job = Job(cores=16), # run on 16 cores
pseudos = ['C.BFD.upf'], # pwscf PP file
system = graphene, # run graphene
# input format selector
input_type = 'scf', # scf, nscf, relax, or generic
# pwscf input parameters
input_dft = 'lda', # dft functional
ecut = 150 , # planewave energy cutoff (Ry)
conv_thr = 1e-6, # scf convergence threshold (Ry)
mixing_beta = .7, # charge mixing factor
kgrid = (8,8,8), # MP grid of primitive cell
kshift = (1,1,1), # to converge charge density
wf_collect = False, # don't collect orbitals
use_folded = True # use primitive rep of graphene
)
sims.append(scf)
# nscf run to produce orbitals for jastrow optimization
nscf_opt = generate_pwscf(
# nexus inputs
identifier = 'nscf', # identifier/file prefix
path = 'graphene/nscf_opt', # directory for nscf run
job = Job(cores=16), # run on 16 cores
pseudos = ['C.BFD.upf'], # pwscf PP file
system = graphene, # run graphene
# input format selector
input_type = 'nscf', # scf, nscf, relax, or generic
# pwscf input parameters
input_dft = 'lda', # dft functional
ecut = 150 , # planewave energy cutoff (Ry)
conv_thr = 1e-6, # scf convergence threshold (Ry)
mixing_beta = .7, # charge mixing factor
nosym = True, # don't symmetrize k-points
use_folded = True, # use primitive rep of graphene
wf_collect = True, # write out orbitals
kgrid = (1,1,1), # single k-point for opt
kshift = (0,0,0), # gamma point
# workflow dependencies
dependencies = (scf,'charge_density')
)
sims.append(nscf_opt)
# orbital conversion job for jastrow optimization
p2q_opt = generate_pw2qmcpack(
# nexus inputs
identifier = 'p2q',
path = 'graphene/nscf_opt',
job = Job(cores=1),
# pw2qmcpack input parameters
write_psir = False,
# workflow dependencies
dependencies = (nscf_opt,'orbitals')
)
sims.append(p2q_opt)
# Jastrow optimization
opt = generate_qmcpack(
# nexus inputs
identifier = 'opt', # identifier/file prefix
path = 'graphene/opt', # directory for opt run
job = Job(cores=16,app='qmcpack'),
pseudos = ['C.BFD.xml'], # qmcpack PP file
system = graphene, # run graphene
# input format selector
input_type = 'basic',
# qmcpack input parameters
corrections = [],
jastrows = [('J1','bspline',8), # 1 body bspline jastrow
('J2','bspline',8)], # 2 body bspline jastrow
calculations = [
loop(max = 6, # No. of loop iterations
qmc = linear( # linearized optimization method
energy = 0.0, # cost function
unreweightedvariance = 1.0, # is all unreweighted variance
reweightedvariance = 0.0, # no energy or r.w. var.
timestep = 0.5, # vmc timestep (1/Ha)
warmupsteps = 100, # MC steps before data collected
samples = 16000,# samples used for cost function
stepsbetweensamples = 10, # steps between uncorr. samples
blocks = 10, # ignore this
minwalkers = 0.1,# and this
bigchange = 15.0,# and this
alloweddifference = 1e-4 # and this, for now
)
)
],
# workflow dependencies
dependencies = (p2q_opt,'orbitals')
)
sims.append(opt)
# nscf run to produce orbitals for final dmc
nscf = generate_pwscf(
# nexus inputs
identifier = 'nscf', # identifier/file prefix
path = 'graphene/nscf', # directory for nscf run
job = Job(cores=16), # run on 16 cores
pseudos = ['C.BFD.upf'], # pwscf PP file
system = graphene, # run graphene
# input format selector
input_type = 'nscf', # scf, nscf, relax, or generic
# pwscf input parameters
input_dft = 'lda', # dft functional
ecut = 150 , # planewave energy cutoff (Ry)
conv_thr = 1e-6, # scf convergence threshold (Ry)
mixing_beta = .7, # charge mixing factor
nosym = True, # don't symmetrize k-points
use_folded = True, # use primitive rep of graphene
wf_collect = True, # write out orbitals
# workflow dependencies
dependencies = (scf,'charge_density')
)
sims.append(nscf)
# orbital conversion job for final dmc
p2q = generate_pw2qmcpack(
# nexus inputs
identifier = 'p2q',
path = 'graphene/nscf',
job = Job(cores=1),
# pw2qmcpack input parameters
write_psir = False,
# workflow dependencies
dependencies = (nscf,'orbitals')
)
sims.append(p2q)
# final dmc run
qmc = generate_qmcpack(
# nexus inputs
identifier = 'qmc', # identifier/file prefix
path = 'graphene/qmc', # directory for dmc run
job = Job(cores=16,app='qmcpack'),
pseudos = ['C.BFD.xml'], # qmcpack PP file
system = graphene, # run graphene
# input format selector
input_type = 'basic',
# qmcpack input parameters
corrections = [], # no finite size corrections
jastrows = [], # overwritten from opt
calculations = [ # qmcpack input parameters for qmc
vmc( # vmc parameters
timestep = 0.5, # vmc timestep (1/Ha)
warmupsteps = 100, # No. of MC steps before data is collected
blocks = 200, # No. of data blocks recorded in scalar.dat
steps = 10, # No. of steps per block
substeps = 3, # MC steps taken w/o computing E_local
samplesperthread = 40 # No. of dmc walkers per thread
),
dmc( # dmc parameters
timestep = 0.01, # dmc timestep (1/Ha)
warmupsteps = 50, # No. of MC steps before data is collected
blocks = 400, # No. of data blocks recorded in scalar.dat
steps = 5, # No. of steps per block
nonlocalmoves = True # use Casula's T-moves
), # (retains variational principle for NLPP's)
],
# workflow dependencies
dependencies = [(p2q,'orbitals'),
(opt,'jastrow')]
)
# nexus monitors all runs
run_project(sims)
# print out the total energy
performed_runs = not settings.generate_only and not settings.status_only
if performed_runs:
# get the qmcpack analyzer object
# it contains all of the statistically analyzed data from the run
qa = qmc.load_analyzer_image()
# get the local energy from dmc.dat
le = qa.dmc[1].dmc.LocalEnergy # dmc series 1, dmc.dat, local energy
# print the total energy for the 8 atom system
print 'The DMC ground state energy for graphene is:'
print ' {0} +/- {1} Ha'.format(le.mean,le.error)
#end if
To run the example, navigate to the example directory and type
./graphene.py
or, alternatively,
python ./graphene.py
You should see output like this (without the added # comments):
Pseudopotentials # reading pseudopotential files
reading pp: ../pseudopotentials/C.BFD.upf
reading pp: ../pseudopotentials/C.BFD.xml
Project starting
checking for file collisions # ensure created files don't overlap
loading cascade images # load previous simulation state
cascade 0 checking in
checking cascade dependencies # ensure sim.'s have needed dep.'s
all simulation dependencies satisfied
starting runs: # start submitting jobs
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
poll 0 memory 56.28 MB
Entering ./runs/graphene/scf 0 # scf job
writing input files 0 scf # input file written
Entering ./runs/graphene/scf 0
sending required files 0 scf # PP files copied
submitting job 0 scf # job is in virtual queue
Entering ./runs/graphene/scf 0
Executing: # job executed on workstation
export OMP_NUM_THREADS=1
mpirun -np 16 pw.x -input scf.in
poll 1 memory 56.30 MB # waiting for job to finish
poll 2 memory 56.30 MB
poll 3 memory 56.30 MB
poll 4 memory 56.30 MB
Entering ./runs/graphene/scf 0
copying results 0 scf # job is finished, copy results
Entering ./runs/graphene/scf 0
analyzing 0 scf # analyze output data
# now do the same for
# nscf job for Jastrow opt
# single k-point
# nscf job for VMC/DMC
# multiple k-points
poll 5 memory 56.31 MB
Entering ./runs/graphene/nscf 1 # nscf dmc
writing input files 1 nscf
...
Entering ./runs/graphene/nscfopt 4 # nscf opt
writing input files 4 nscf
...
# now convert KS orbitals
# to eshdf format
# with pw2qmcpack.x
# for nscf opt & nscf dmc
poll 7 memory 56.32 MB
Entering ./runs/graphene/nscf 2 # convert dmc orbitals
sending required files 2 p2q
...
Entering ./runs/graphene/nscfopt 4 # convert opt orbitals
copying results 4 nscf
...
poll 10 memory 56.32 MB
Entering ./runs/graphene/opt 6 # submit jastrow opt
writing input files 6 opt # write input file
Entering ./runs/graphene/opt 6
sending required files 6 opt # copy PP files
submitting job 6 opt # job is in virtual queue
Entering ./runs/graphene/opt 6
Executing: # run qmcpack
export OMP_NUM_THREADS=1 # w/ complex arithmetic
mpirun -np 16 qmcpack_complex opt.in.xml
poll 11 memory 56.32 MB
poll 12 memory 56.32 MB
poll 13 memory 56.32 MB
...
...
...
poll 793 memory 56.32 MB # qmcpack opt finishes
poll 794 memory 56.32 MB # nearly an hour later
poll 795 memory 56.32 MB
Entering ./runs/graphene/opt 6
copying results 6 opt # copy output files
Entering ./runs/graphene/opt 6
analyzing 6 opt # analyze the results
poll 796 memory 56.41 MB
Entering ./runs/graphene/qmc 3 # submit dmc
writing input files 3 qmc # write input file
Entering ./runs/graphene/qmc 3
sending required files 3 qmc # copy PP files
submitting job 3 qmc # job is in virtual queue
Entering ./runs/graphene/qmc 3
Executing: # run qmcpack
export OMP_NUM_THREADS=1
mpirun -np 16 qmcpack_complex qmc.in.xml
poll 797 memory 57.31 MB
poll 798 memory 57.31 MB
poll 799 memory 57.31 MB
...
...
...
poll 1041 memory 57.31 MB # qmcpack dmc finishes
poll 1042 memory 57.31 MB # about 15 minutes later
poll 1043 memory 57.31 MB
Entering ./runs/graphene/qmc 3
copying results 3 qmc # copy output files
Entering ./runs/graphene/qmc 3
analyzing 3 qmc # analyze the results
Project finished # all jobs are finished
The DMC ground state energy for graphene is:
-45.824960552 +/- 0.00498990689364 Ha # one value from
# qmcpack analyzer
If successful, you have just performed a start-to-finish DMC calculation. The total energy quoted above probably will not match the one you produce due to different compilation environments and the probabilistic nature of DMC. They should not, however differ by three sigma.
Take some time to inspect the input files generated by Nexus and the
output files from PWSCF and QMCPACK. The runs were performed in
sub-directories of the runs directory. The order of execution of the
simulations is roughly scf, nscf, nscfopt, opt, then
qmc.
runs
└── graphene_test
├── nscf
│ ├── nscf.in
│ └── nscf.out
├── nscfopt
│ ├── nscf.in
│ └── nscf.out
├── opt
│ ├── opt.in.xml
│ └── opt.out
├── qmc
│ ├── qmc.in.xml
│ └── qmc.out
└── scf
├── scf.in
└── scf.out
The directories above contain all the files generated by the
simulations. Often one only wants to save the files with the most
important data, which are generally small. These are copied to the
results directory which mirrors the structure of runs.
results
└── runs
└── graphene_test
├── nscf
│ ├── nscf.in
│ └── nscf.out
├── nscfopt
│ ├── nscf.in
│ └── nscf.out
├── opt
│ ├── opt.in.xml
│ └── opt.out
├── qmc
│ ├── qmc.in.xml
│ └── qmc.out
└── scf
├── scf.in
└── scf.out
Although this QMC run was performed at a single k-point, a
twist-averaged run could be performed simply by changing kgrid in
generate_physical_system from (1,1,1) to (4,4,1), or
similar.
Example 3: C 20 Molecule DMC¶
The files for this example are found in:
/your_download_path/nexus/examples/qmcpack/c20
Take a moment to study the “input file” script (c20_example.py) and
the attendant comments (prefixed with #). The relevant differences from
the graphene example mostly involve how the structure is procured (it is
read from an XYZ file rather than being generated), the boundary
conditions (open BC’s, see bconds in the QMCPACK input parameters),
and the workflow involved.
#! /usr/bin/env python3
from nexus import settings,Job,run_project
from nexus import Structure,PhysicalSystem
from nexus import generate_pwscf
from nexus import generate_pw2qmcpack
from nexus import generate_qmcpack
from nexus import loop,linear,vmc,dmc
# general settings for nexus
settings(
pseudo_dir = '../pseudopotentials',# directory with all pseudopotentials
sleep = 3, # check on runs every 'sleep' seconds
generate_only = 0, # only make input files
status_only = 0, # only show status of runs
machine = 'ws16', # local machine is 16 core workstation
)
#generate the C20 physical system
# specify the xyz file
structure_file = 'c20.cage.xyz'
# make an empty structure object
structure = Structure()
# read in the xyz file
structure.read_xyz(structure_file)
# place a bounding box around the structure
structure.bounding_box(
box = 'cubic', # cube shaped cell
scale = 1.5 # 50% extra space
)
# make it a gamma point cell
structure.add_kmesh(
kgrid = (1,1,1), # Monkhorst-Pack grid
kshift = (0,0,0) # and shift
)
# add electronic information
c20 = PhysicalSystem(
structure = structure, # C20 structure
net_charge = 0, # net charge in units of e
net_spin = 0, # net spin in units of e-spin
C = 4 # C has 4 valence electrons
)
# list of simulations in workflow
sims = []
# scf run produces charge density
scf = generate_pwscf(
# nexus inputs
identifier = 'scf', # identifier/file prefix
path = 'c20/scf', # directory for scf run
job = Job(cores=16), # run on 16 cores
pseudos = ['C.BFD.upf'], # pwscf PP file
system = c20, # run c20
# input format selector
input_type = 'scf', # scf, nscf, relax, or generic
# pwscf input parameters
input_dft = 'lda', # dft functional
ecut = 150 , # planewave energy cutoff (Ry)
conv_thr = 1e-6, # scf convergence threshold (Ry)
mixing_beta = .7, # charge mixing factor
nosym = True, # don't use symmetry
wf_collect = True, # write out orbitals
)
sims.append(scf)
# orbital conversion job for opt and dmc
p2q = generate_pw2qmcpack(
# nexus inputs
identifier = 'p2q',
path = 'c20/nscf',
job = Job(cores=1),
# pw2qmcpack input parameters
write_psir = False,
# workflow dependencies
dependencies = (scf,'orbitals')
)
sims.append(p2q)
# Jastrow optimization
opt = generate_qmcpack(
# nexus inputs
identifier = 'opt', # identifier/file prefix
path = 'c20/opt', # directory for opt run
job = Job(cores=16,app='qmcpack'),
pseudos = ['C.BFD.xml'], # qmcpack PP file
system = c20, # run c20
# input format selector
input_type = 'basic',
# qmcpack input parameters
corrections = [],
jastrows = [('J1','bspline',8,6), # 1 body bspline jastrow
('J2','bspline',8,8)], # 2 body bspline jastrow
calculations = [
loop(max = 6, # No. of loop iterations
qmc = linear( # linearized optimization method
energy = 0.0, # cost function
unreweightedvariance = 1.0, # is all unreweighted variance
reweightedvariance = 0.0, # no energy or r.w. var.
timestep = 0.5, # vmc timestep (1/Ha)
warmupsteps = 100, # MC steps before data collected
samples = 16000,# samples used for cost function
stepsbetweensamples = 10, # steps between uncorr. samples
blocks = 10, # ignore this
minwalkers = 0.1,# and this
bigchange = 15.0,# and this
alloweddifference = 1e-4 # and this, for now
)
)
],
# workflow dependencies
dependencies = (p2q,'orbitals')
)
sims.append(opt)
# final dmc run
qmc = generate_qmcpack(
# nexus inputs
identifier = 'qmc', # identifier/file prefix
path = 'c20/qmc', # directory for dmc run
job = Job(cores=16,app='qmcpack'),
pseudos = ['C.BFD.xml'], # qmcpack PP file
system = c20, # run c20
# input format selector
input_type = 'basic',
# qmcpack input parameters
corrections = [], # no finite size corrections
jastrows = [], # overwritten from opt
calculations = [ # qmcpack input parameters for qmc
vmc( # vmc parameters
timestep = 0.5, # vmc timestep (1/Ha)
warmupsteps = 100, # No. of MC steps before data is collected
blocks = 200, # No. of data blocks recorded in scalar.dat
steps = 10, # No. of steps per block
substeps = 3, # MC steps taken w/o computing E_local
samplesperthread = 40 # No. of dmc walkers per thread
),
dmc( # dmc parameters
timestep = 0.01, # dmc timestep (1/Ha)
warmupsteps = 50, # No. of MC steps before data is collected
blocks = 400, # No. of data blocks recorded in scalar.dat
steps = 5, # No. of steps per block
nonlocalmoves = True # use Casula's T-moves
), # (retains variational principle for NLPP's)
],
# workflow dependencies
dependencies = [(p2q,'orbitals'),
(opt,'jastrow')]
)
# nexus monitors all runs
run_project(sims)
# print out the total energy
performed_runs = not settings.generate_only and not settings.status_only
if performed_runs:
# get the qmcpack analyzer object
# it contains all of the statistically analyzed data from the run
qa = qmc.load_analyzer_image()
# get the local energy from dmc.dat
le = qa.dmc[1].dmc.LocalEnergy # dmc series 1, dmc.dat, local energy
# print the total energy for the 20 atom system
print 'The DMC ground state energy for C20 is:'
print ' {0} +/- {1} Ha'.format(le.mean,le.error)
#end if
To run the example, navigate to the example directory and type
./c20.py
or, alternatively,
python ./c20.py
You should see output like this (without the added # comments):
Pseudopotentials # reading pseudopotential files
reading pp: ../pseudopotentials/C.BFD.upf
reading pp: ../pseudopotentials/C.BFD.xml
Project starting
checking for file collisions # ensure created files don't overlap
loading cascade images # load previous simulation state
cascade 0 checking in
checking cascade dependencies # ensure sim.'s have needed dep.'s
all simulation dependencies satisfied
starting runs: # start submitting jobs
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
poll 0 memory 56.21 MB
Entering ./runs/c20/scf 0 # scf job
writing input files 0 scf # input file written
Entering ./runs/c20/scf 0
sending required files 0 scf # PP files copied
submitting job 0 scf # job is in the virtual queue
Entering ./runs/c20/scf 0
Executing: # job executed on workstation
export OMP_NUM_THREADS=1
mpirun -np 16 pw.x -input scf.in
poll 1 memory 56.23 MB # waiting for job to finish
poll 2 memory 56.23 MB
poll 3 memory 56.23 MB
poll 4 memory 56.23 MB
poll 5 memory 56.23 MB
poll 6 memory 56.23 MB
poll 7 memory 56.23 MB
poll 8 memory 56.23 MB
Entering ./runs/c20/scf 0
copying results 0 scf # job is finished, copy results
Entering ./runs/c20/scf 0
analyzing 0 scf # analyze output data
poll 9 memory 56.23 MB # now convert KS orbitals
Entering ./runs/c20/scf 1 # to eshdf format
writing input files 1 p2q # with pw2qmcpack.x
...
poll 12 memory 56.23 MB
Entering ./runs/c20/opt 3 # submit jastrow opt
writing input files 3 opt # write input file
Entering ./runs/c20/opt 3
sending required files 3 opt # copy PP files
submitting job 3 opt # job is in virtual queue
Entering ./runs/c20/opt 3
Executing: # run qmcpack
export OMP_NUM_THREADS=1 # w/ real arithmetic
mpirun -np 16 qmcpack opt.in.xml
poll 13 memory 56.24 MB
poll 14 memory 56.24 MB
poll 15 memory 56.24 MB
...
...
...
poll 204 memory 56.24 MB # qmcpack opt finishes
poll 205 memory 56.24 MB # about 10 minutes later
poll 206 memory 56.24 MB
Entering ./runs/c20/opt 3
copying results 3 opt # copy output files
Entering ./runs/c20/opt 3
analyzing 3 opt # analyze the results
poll 207 memory 56.27 MB
Entering ./runs/c20/qmc 2 # submit dmc
writing input files 2 qmc # write input file
Entering ./runs/c20/qmc 2
sending required files 2 qmc # copy PP files
submitting job 2 qmc # job is in virtual queue
Entering ./runs/c20/qmc 2
Executing: # run qmcpack
export OMP_NUM_THREADS=1
mpirun -np 16 qmcpack qmc.in.xml
poll 208 memory 56.49 MB
poll 209 memory 56.49 MB
poll 210 memory 56.49 MB
...
...
...
poll 598 memory 56.49 MB # qmcpack dmc finishes
poll 599 memory 56.49 MB # about 20 minutes later
poll 600 memory 56.49 MB
Entering ./runs/c20/qmc 2
copying results 2 qmc # copy output files
Entering ./runs/c20/qmc 2
analyzing 2 qmc # analyze the results
Project finished # all jobs are finished
The DMC ground state energy for C20 is:
-112.890695404 +/- 0.0151688786226 Ha # one value from
# qmcpack analyzer
Again, the total energy quoted above probably will not match the one you produce due to different compilation environments and the probabilistic nature of QMC. The results should still be statistically comparable.
The directory trees generated by Nexus for C 20 have a similar structure
to the graphene example. Note the absence of the nscf runs. The
order of execution of the simulations is scf, opt, then qmc.
runs
└── c20_test
├── opt
│ ├── opt.in.xml
│ └── opt.out
├── qmc
│ ├── qmc.in.xml
│ └── qmc.out
└── scf
├── scf.in
└── scf.out
results
└── runs
└── c20_test
├── opt
│ ├── opt.in.xml
│ └── opt.out
├── qmc
│ ├── qmc.in.xml
│ └── qmc.out
└── scf
├── scf.in
└── scf.out
Example 4 Automated oxygen dimer binding curve¶
The files for this example are found in:
/your_download_path/nexus/examples/qmcpack/oxygen_dimer
Enter the examples/qmcpack/oxygen_dimer directory. Open
oxygen_dimer.py with a text editor. The overall format is similar to
the example file shown in the prior sections. The header material,
including Nexus imports, settings, and the job parameters for QMC are
nearly identical.
Following the job parameters, inputs for the optimization method are given. The keywords are identical to the parameters of QMCPACK’s XML input file.
linopt1 = linear(
energy = 0.0,
unreweightedvariance = 1.0,
reweightedvariance = 0.0,
timestep = 0.4,
samples = 5000,
warmupsteps = 50,
blocks = 200,
substeps = 1,
nonlocalpp = True,
usebuffer = True,
walkers = 1,
minwalkers = 0.5,
maxweight = 1e9,
usedrift = True,
minmethod = 'quartic',
beta = 0.025,
exp0 = -16,
bigchange = 15.0,
alloweddifference = 1e-4,
stepsize = 0.2,
stabilizerscale = 1.0,
nstabilizers = 3
)
Requesting multiple loop’s with different numbers of samples is more compact than in the native XML input file:
linopt1 = ...
linopt2 = linopt1.copy()
linopt2.samples = 20000 # opt w/ 20000 samples
linopt3 = linopt1.copy()
linopt3.samples = 40000 # opt w/ 40000 samples
opt_calcs = [loop(max=8,qmc=linopt1), # loops over opt's
loop(max=6,qmc=linopt2),
loop(max=4,qmc=linopt3)]
The VMC/DMC method inputs also mirror the XML:
qmc_calcs = [
vmc(
walkers = 1,
warmupsteps = 30,
blocks = 20,
steps = 10,
substeps = 2,
timestep = .4,
samples = 2048
),
dmc(
warmupsteps = 100,
blocks = 400,
steps = 32,
timestep = 0.01,
nonlocalmoves = True
)
]
As in the prior examples, the oxygen dimer is generated with the generate_physical_system function:
dimer = generate_physical_system(
type = 'dimer',
dimer = ('O','O'),
separation = 1.2074*scale,
Lbox = 15.0,
units = 'A',
net_spin = 2,
O = 6
)
Similar syntax can be used to generate crystal structures or to specify systems with arbitrary atomic configurations and simulation cells. Notice that a “scale” variable has been introduced to stretch or compress the dimer.
Next, objects representing DFT calculations and orbital conversions are
constructed with the generate_pwscf and generate_pw2qmcpack
functions.
scf = generate_pwscf(
identifier = 'scf',
...
)
sims.append(scf)
p2q = generate_pw2qmcpack(
identifier = 'p2q',
...
dependencies = (scf,'orbitals')
)
sims.append(p2q)
Finally, objects representing QMCPACK simulations are constructed with the generate_qmcpack function:
Finally, objects representing QMCPACK simulations are constructed with
the generate_qmcpack function:
opt = generate_qmcpack(
identifier = 'opt',
...
jastrows = [('J1','bspline',8,4.5),
('J2','pade',0.5,0.5)],
calculations = opt_calcs,
dependencies = (p2q,'orbitals')
)
sims.append(opt)
qmc = generate_qmcpack(
identifier = 'qmc',
...
jastrows = [],
calculations = qmc_calcs,
dependencies = [(p2q,'orbitals'),
(opt,'jastrow')]
)
sims.append(qmc)
Shared details such as the run directory, job, pseudopotentials, and
orbital file have been omitted (...). The “opt” run will
optimize a 1-body B-spline Jastrow with 8 knots having a cutoff of 4.5
Bohr and a 2-body Padé Jastrow with up-up and up-down “B” parameters
set to 0.5 1/Bohr. The Jastrow list for the DMC run is empty and a new
keyword is present: dependencies. The usage of dependencies
above indicates that the DMC run depends on the optimization run for the
Jastrow factor. Nexus will submit the “opt” run first and upon
completion it will scan the output, select the optimal set of
parameters, pass the Jastrow information to the “qmc” run and then
submit the DMC job. Independent job workflows are submitted in parallel
when permitted. No input files are written or job submissions made until
the “run_project” function is reached.
As written, oxygen_dimer.py will only perform calculations at the
equilibrium separation distance of 1.2074 Angstrom. Modify the file now
to perform DMC calculations across a range of separation distances with
each DMC run using the Jastrow factor optimized at the equilibrium
separation distance. The necessary Python for loop syntax should
look something like this:
sims = []
for scale in [1.00,0.90,0.95,1.05,1.10]:
...
dimer = ...
if scale==1.00:
opt = ...
...
#end if
qmc = ...
...
#end for
run_project(sims)
Note that the text inside the for loop and the if block must be
indented by precisely four spaces. If you use Emacs, changes in
indentation can be performed easily with Cntrl-C > and Cntrl-C <
after highlighting a block of text (other editors should have similar
functionality).
Change the “status_only” parameter in the “settings” function to
1 and type “./oxygen_dimer.py” at the command line. This will print
the status of all simulations:
Project starting
checking for file collisions
loading cascade images
cascade 0 checking in
checking cascade dependencies
all simulation dependencies satisfied
cascade status
setup, sent_files, submitted, finished, got_output, analyzed
000000 scf ./scale_1.0
000000 scf ./scale_0.9
000000 scf ./scale_0.95
000000 scf ./scale_1.05
000000 scf ./scale_1.1
000000 p2q ./scale_1.0
000000 p2q ./scale_0.9
000000 p2q ./scale_0.95
000000 p2q ./scale_1.05
000000 p2q ./scale_1.1
000000 opt ./scale_1.0
000000 qmc ./scale_1.0
000000 qmc ./scale_0.9
000000 qmc ./scale_0.95
000000 qmc ./scale_1.05
000000 qmc ./scale_1.1
setup, sent_files, submitted, finished, got_output, analyzed
In this case, a single independent simulation “cascade” (workflow) has
been identified, containing one “opt” and five dependent “qmc”
runs. The six status flags (setup, sent_files, submitted,
finished, got_output, analyzed) each show 0, indicating
that no work has been done yet.
Now change “status_only” back to 0, set “generate_only” to
1, and run oxygen_dimer.py again. This will perform a dry-run of
all simulations. The dry-run should finish in about 20 seconds:
Project starting
checking for file collisions
loading cascade images
cascade 0 checking in
checking cascade dependencies
all simulation dependencies satisfied
starting runs:
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
poll 0 memory 88.54 MB
Entering ./scale_1.0 0
writing input files 0 opt
Entering ./scale_1.0 0
sending required files 0 opt
submitting job 0 opt
Entering ./scale_1.0 1
Would have executed: qsub --mode script --env BG_SHAREDMEMSIZE=32 opt.qsub.in
poll 1 memory 88.54 MB
Entering ./scale_1.0 0
copying results 0 opt
Entering ./scale_1.0 0
analyzing 0 opt
poll 2 memory 88.87 MB
Entering ./scale_1.0 1
writing input files 1 qmc
Entering ./scale_1.0 1
sending required files 1 qmc
submitting job 1 qmc
...
Entering ./scale_1.0 2
Would have executed: qsub --mode script --env BG_SHAREDMEMSIZE=32 qmc.qsub.in
...
Project finished
Nexus polls the simulation status every 3 seconds and sleeps in between.
The scale_ directories should now contain several files:
scale_1.0
├── O2.pwscf.h5
├── O.BFD.xml
├── opt.in.xml
├── opt.qsub.in
├── qmc.in.xml
├── qmc.qsub.in
├── sim_opt
│ ├── analyzer.p
│ ├── input.p
│ └── sim.p
└── sim_qmc
├── analyzer.p
├── input.p
└── sim.p
Take a minute to inspect the generated input (opt.in.xml,
qmc.in.xml) and submission (opt.qsub.in, qmc.qsub.in) files.
The pseudopotential file O.BFD.xml has been copied into each local
directory. Two additional directories have been created: sim_opt and
sim_qmc. The sim.p files in each directory contain the current
status of each simulation. If you run oxygen_dimer.py again, it
should not attempt to rerun any of the simulations:
Project starting
checking for file collisions
loading cascade images
cascade 0 checking in
cascade 8 checking in
cascade 2 checking in
cascade 4 checking in
cascade 6 checking in
checking cascade dependencies
all simulation dependencies satisfied
starting runs:
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
poll 0 memory 60.10 MB
Project finished
This way one can continue to add to the oxygen_dimer.py file (e.g.
adding more separation distances) without worrying about duplicate job
submissions.
Now actually submit the optimization and DMC jobs. Reset the state of
the simulations by removing the sim.p files
(“rm ./scale*/sim*/sim.p”), set “generate_only” to 0, and
rerun oxygen_dimer.py. It should take about 15 minutes for all the
jobs to complete. You may wish to open another terminal to monitor the
progress of the individual jobs while the current terminal runs
oxygen_dimer.py in the foreground.
After completion, try expanding to the full set of “scale”
values:[0.90,0.925,0.95,0.975,1.00,1.025,1.05,1.075,1.10]. Nexus
should only run the workflows that correspond to new values. In this
way, Nexus scripts can be expanded over time to include new aspects of
growing projects.
Example 5: Bulk Diamond Excited States VMC¶
The files for this example are found in:
/your_download_path/nexus/examples/qmcpack/rsqmc_misc/excited
Please study Lab 5 in QMCPACK manual for an in-depth discussion of the excited states calculations. The primitive cell for a structure is not unique, therefore it must be standardized to generate reproducible Brillouin zones (BZ). For this end, we use “SeeK-Path” python libraries to generate standardized primitive cells and generate band structure paths. Therefore, SeeK-Path libraries must be installed using “pip install seekpath”, prior to running scripts in this example. In this example, input file script “vmc.py” is identical to “optical.py” in Lab5 of the QMCPACK manual.
We use neutral primitive cells at the wavefunction generation. However,
creation / annihilation operations are applied at VMC level to simulate
optical excitations. Compared to the ground state bulk calculations, a
tiling matrix that is commensurate with the wavevectors involved in the
excitation must be chosen. This process has been automatized in Nexus
using the “get_band_tiling” function. There are two VMC scripts in this
lab that generate the tiling matrix in different ways: vmc.py script
uses a non-optimal tiling matrix from Lab 5 in QMCPACK, whereas
vmc-opt-tiling.py uses the “get_band_tiling” function. In this
example, we will use vmc-opt-tiling.py. Note, there is also an
additional VMC script included vmc_excitation_alternatives.py which
does not use a tiling matrix but includes a variety of ways that
excitations can be specified with Nexus.
In Lab 5 of the QMCPACK manual we found that VBM is located at \(\Gamma\) and the CBM is located at \(\Delta\) ([0.377, 0., 0.377]), hence C-diamond is an indirect band gap material. However, studying this transition at the given exact points would involve a very large simulation cell. Therefore, we try to round \(\Delta\) to the nearest fraction with integer denominator. Tolerance of this rounding procedure is controlled by “max_volfac” keyword in the “get_band_tiling” function. “max_volfac” basically controls the maximum volume factor of the supercell being searched, which inherently controls the highest k-point grid density in one dimension.
vmc_excitation_alternatives.py
for examples using the various excitation types.
Examples are also provided in Lab 5 of the QMCPACK manual.#! /usr/bin/env python3
from nexus import settings,job,run_project
from nexus import generate_physical_system
from nexus import generate_pwscf
from nexus import generate_pw2qmcpack
from nexus import generate_qmcpack,vmc
from structure import *
settings(
pseudo_dir = '../pseudopotentials',
status_only = 0,
generate_only = 0,
sleep = 3,
machine = 'ws16'
)
#Input structure
dia = generate_physical_system(
units = 'A',
axes = [[ 1.785, 1.785, 0. ],
[ 0. , 1.785, 1.785],
[ 1.785, 0. , 1.785]],
elem = ['C','C'],
pos = [[ 0. , 0. , 0. ],
[ 0.8925, 0.8925, 0.8925]],
C = 4
)
# Standardized Primitive cell -- run rest of the calculations on this cell
dia2_structure = get_primitive_cell(structure=dia.structure)['structure']
# get_band_tiling and get_primitiev_cell require "SeeK-path" python libraries
# Returns commensurate optimum tiling matrix for the kpoints_rel wavevectors
# max_volfac is default to 20
tiling = get_band_tiling(structure = dia2_structure,
kpoints_rel = [[0.000, 0.000, 0.000],
[0.3768116, 0., 0.3768116]])
# Numerical value for the second wavevector can be different in different computers,
# adjust accordingly
# All wavevectors must be on the iBZ k_path! (get_kpath output in band.py)
# K-points can also be defined using their labels
# (for high symmetry k-points only). For example:
# tiling = get_band_tiling(structure = dia2_structure,
# kpoints_label = ['GAMMA', 'X'])
dia2 = generate_physical_system(
structure = dia2_structure,
kgrid = (1,1,1),
kshift = (0,0,0), # Assumes we study transitions from Gamma.
#For non-gamma tilings, use kshift appropriately
tiling = tiling,
C = 4,
)
scf = generate_pwscf(
identifier = 'scf',
path = 'diamond/scf',
job = job(nodes=1, app='pw.x',hours=1),
input_type = 'generic',
calculation = 'scf',
nspin = 2,
input_dft = 'lda',
ecutwfc = 200,
conv_thr = 1e-8,
nosym = True,
wf_collect = True,
system = dia2,
tot_magnetization = 0,
pseudos = ['C.BFD.upf'],
)
nscf = generate_pwscf(
identifier = 'nscf',
path ='diamond/nscf_opt_tiling',
job = job(nodes=1, app='pw.x',hours=1),
input_type = 'generic',
calculation = 'nscf',
input_dft = 'lda',
ecutwfc = 200,
nspin = 2,
conv_thr = 1e-8,
nosym = True,
wf_collect = True,
system = dia2,
nbnd = 8, #a sensible nbnd value can be given
verbosity = 'high', #verbosity must be set to high
pseudos = ['C.BFD.upf'],
dependencies = (scf, 'charge_density'),
)
conv = generate_pw2qmcpack(
identifier = 'conv',
path = 'diamond/nscf_opt_tiling',
job = job(cores=1,app='pw2qmcpack.x',hours=1),
write_psir = False,
dependencies = (nscf,'orbitals'),
)
qmc = generate_qmcpack(
det_format = 'old',
identifier = 'vmc',
path = 'diamond/vmc_opt_tiling',
job = job(cores=16,threads=16,app='qmcpack',hours = 1),
input_type = 'basic',
spin_polarized = True,
system = dia2,
pseudos = ['C.BFD.xml'],
jastrows = [],
calculations = [
vmc(
walkers = 16,
warmupsteps = 20,
blocks = 1000,
steps = 10,
substeps = 2,
timestep = .4
)
],
dependencies = (conv,'orbitals'),
)
qmc_optical = generate_qmcpack(
det_format = 'old',
identifier = 'vmc',
path = 'diamond/vmc_opt_tiling_optical',
job = job(cores=16,threads=16,app='qmcpack',hours = 1),
input_type = 'basic',
spin_polarized = True,
system = dia2,
excitation = ['up', '0 3 1 4'], #
pseudos = ['C.BFD.xml'],
jastrows = [],
calculations = [
vmc(
walkers = 16,
warmupsteps = 20,
blocks = 1000,
steps = 10,
substeps = 2,
timestep = .4
)
],
dependencies = (conv,'orbitals'),
)
run_project(scf,nscf,conv,qmc)