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Make fixers work
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@yakutovicha
yakutovicha committed Dec 5, 2019
1 parent 1d22f02 commit 1c5babe
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Showing 7 changed files with 208 additions and 45 deletions.
21 changes: 11 additions & 10 deletions Dockerfile
View file
Expand Up @@ -7,30 +7,31 @@

FROM aiidateam/aiida-docker-stack

# Install cp2k
RUN apt-get update && apt-get install -y --no-install-recommends \
cp2k

# Set HOME variable:
# Set HOME and PATH variables:
ENV HOME="/home/aiida"
ENV PATH="${HOME}/.local/bin:${PATH}"

# Install cp2k
RUN apt-get update && apt-get install -y --no-install-recommends cp2k

# Install aiida-cp2k
# Copy local aiida-cp2k folder and change permissions
COPY . ${HOME}/code/aiida-cp2k
RUN chown -R aiida:aiida ${HOME}/code

# Install AiiDA
# Now do everything as the aiida user
USER aiida
ENV PATH="${HOME}/.local/bin:${PATH}"

# Install aiida-cp2k plugin and coveralls
# Set the plugin folder as the workdir
WORKDIR ${HOME}/code/aiida-cp2k

# Install aiida-cp2k plugin and coveralls
RUN pip install --user .[pre-commit,test]
RUN pip install --user coveralls

# Populate reentry cache for aiida user https://pypi.python.org/pypi/reentry/
RUN reentry scan

# Install the cp2k code
# Install the CP2K code to AiiDA
COPY .docker/opt/add-codes.sh /opt/
COPY .docker/my_init.d/add-codes.sh /etc/my_init.d/40_add-codes.sh

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41 changes: 34 additions & 7 deletions aiida_cp2k/fixers/geometry_optimization.py
View file
Expand Up @@ -7,7 +7,7 @@


@calcfunction
def add_restart_section(input_dict):
def add_restart_sections(input_dict):
"""Add restart section to the input dictionary."""
params = input_dict.get_dict()
restart_wfn_dict = {
Expand All @@ -27,23 +27,50 @@ def add_restart_section(input_dict):

def resubmit_unconverged_geometry(workchain, calc):
"""Resubmit a calculation it is not converged, but can be recovered."""

content_string = calc.outputs.retrieved.get_object_content(calc.get_attribute('output_filename'))

time_not_exceeded = "PROGRAM ENDED AT"
time_exceeded = "exceeded requested execution time"
one_step_done = "Max. gradient ="
workchain.ctx.inputs.parent_calc_folder = calc.outputs.remote_folder
params = workchain.ctx.inputs.parameters

# If the problem is recoverable then do restart
if (time_not_exceeded not in content_string or time_exceeded in content_string) and one_step_done in content_string:
workchain.ctx.inputs.parameters = add_restart_section(workchain.ctx.inputs.parameters)
workchain.ctx.inputs.parent_calc_folder = calc.outputs.remote_folder
workchain.report("Could fix the problem")
try:
# Firts check if all the restart keys are present in the input dictionary
wf_rest_fname_pointer = params['FORCE_EVAL']['DFT']['RESTART_FILE_NAME']
scf_guess_pointer = params['FORCE_EVAL']['DFT']['SCF']['SCF_GUESS']
restart_fname_pointer = params['EXT_RESTART']['RESTART_FILE_NAME']

# Also check if they all have the right value
if not (wf_rest_fname_pointer == './parent_calc/aiida-RESTART.wfn' and scf_guess_pointer == 'RESTART' and
restart_fname_pointer == './parent_calc/aiida-1.restart'):

# If some values are incorrect add them to the input dictionary
params = add_restart_sections(params)

# If not all the restart keys are present, adding them to the input dictionary
except KeyError:
params = add_restart_sections(params)

# Might be able to solve the problem
workchain.ctx.inputs.parameters = params # params (new or old ones) that for sure
# include the necessary restart key-value pairs
workchain.report(
"The CP2K calculation wasn't completed. The restart of the calculation might be able to fix the problem.")
return ErrorHandlerReport(True, True)

# If the problem is not recoverable
if (time_not_exceeded not in content_string or
time_exceeded in content_string) and one_step_done not in content_string:
workchain.report("Could NOT fix the problem")
return ErrorHandlerReport(False, True, ExitCode(555))

workchain.report("No problems!")
workchain.report("It seems that the restart of CP2K calculation wouldn't be able to fix the problem. "
"Sending a signal to stop the Base work chain.")

# Signaling to the base work chain that the problem could not be recovered.
return ErrorHandlerReport(False, True, ExitCode(1))

# If everything is alright
return None
2 changes: 1 addition & 1 deletion conftest.py
View file
Expand Up @@ -8,4 +8,4 @@

@pytest.fixture(scope='function')
def cp2k_code(aiida_local_code_factory): # pylint: disable=unused-argument
return aiida_local_code_factory("cp2k.popt", "cp2k")
return aiida_local_code_factory("cp2k", "cp2k.popt")
5 changes: 5 additions & 0 deletions examples/data/h2o.xyz
View file
@@ -0,0 +1,5 @@
3
Lattice="10.0 0.0 0.0 0.0 10.0 0.0 0.0 0.0 10.0" Properties=species:S:1:pos:R:3 pbc="F F F"
O 5.0 5.763239 5.596309
H 5.0 6.526478 5.000000
H 5.0 5.000000 5.000000
139 changes: 139 additions & 0 deletions examples/files/GTH_POTENTIALS
View file
Expand Up @@ -200,3 +200,142 @@ Ar GTH-PADE-q8 GTH-LDA-q8 GTH-PADE GTH-LDA
5.60251627
0.35161921 1 4.97880101
#
################################################################################
#
# PBE functional
#
################################################################################
#
H GTH-PBE-q1 GTH-PBE
1
0.20000000 2 -4.17890044 0.72446331
0
#
He GTH-PBE-q2 GTH-PBE
2
0.20000000 2 -9.12214383 1.70270770
0
#
Li GTH-PBE-q3 GTH-PBE
3
0.40000000 4 -14.08115455 9.62621962 -1.78361605 0.08515207
0
#
Be GTH-PBE-q4 GTH-PBE
4
0.32500000 4 -24.06746684 17.27902186 -3.33910629 0.16554912
0
#
B GTH-PBE-q3 GTH-PBE
2 1
0.41899145 2 -5.85946171 0.90375643
2
0.37132046 1 6.29728018
0.36456308 0
#
C GTH-PBE-q4 GTH-PBE
2 2
0.33847124 2 -8.80367398 1.33921085
2
0.30257575 1 9.62248665
0.29150694 0
#
N GTH-PBE-q5 GTH-PBE
2 3
0.28379051 2 -12.41522559 1.86809592
2
0.25540500 1 13.63026257
0.24549453 0
#
O GTH-PBE-q6 GTH-PBE
2 4
0.24455430 2 -16.66721480 2.48731132
2
0.22095592 1 18.33745811
0.21133247 0
#
F GTH-PBE-q7 GTH-PBE
2 5
0.21492959 2 -21.57302836 3.19977615
2
0.19468402 1 23.74354045
0.18615608 0
#
Ne GTH-PBE-q8 GTH-PBE
2 6
0.19000000 2 -27.12015973 4.36044962
2
0.17605938 2 28.17737082 0.83365601
-1.07624528
0.19547452 1 -0.23629360
#
Na GTH-PBE-q9 GTH-PBE
3 6
0.23652322 2 0.29510499 -0.91388488
2
0.14356046 1 34.60149228
0.12993224 1 -14.27746168
#
Mg GTH-PBE-q10 GTH-PBE
4 6
0.19275787 2 -20.57539077 3.04016732
2
0.14140682 1 41.04729209
0.10293187 1 -9.98562566
#
Mg GTH-PBE-q2
2
0.57696017 1 -2.69040744
2
0.59392350 2 3.50321099 -0.71677167
0.92534825
0.70715728 1 0.83115848
#
Al GTH-PBE-q3 GTH-PBE
2 1
0.45000000 1 -7.55476126
2
0.48743529 2 6.95993832 -1.88883584
2.43847659
0.56218949 1 1.86529857
#
Si GTH-PBE-q4 GTH-PBE
2 2
0.44000000 1 -6.26928833
2
0.43563383 2 8.95174150 -2.70627082
3.49378060
0.49794218 1 2.43127673
#
P GTH-PBE-q5 GTH-PBE
2 3
0.43000000 1 -5.87594327
2
0.39637742 2 11.00886207 -3.47035607
4.48021042
0.44829838 1 3.05606416
#
S GTH-PBE-q6 GTH-PBE
2 4
0.42000000 1 -5.98626038
2
0.36482035 2 13.14354448 -4.24183045
5.47617957
0.40948048 1 3.70089057
#
Cl GTH-PBE-q7 GTH-PBE
2 5
0.41000000 1 -6.39208181
2
0.33953864 2 15.21898983 -4.93452321
6.37044208
0.37847416 1 4.33877527
#
Ar GTH-PBE-q8 GTH-PBE
2 6
0.40000000 1 -7.10000000
2
0.31881468 2 17.25203807 -5.58548836
7.21083447
0.35337019 1 4.97421551
#
20 changes: 8 additions & 12 deletions examples/single_calculations/example_failure.py
View file
Expand Up @@ -15,11 +15,7 @@

from aiida.orm import (Code, Dict)
from aiida.common import NotExistent
from aiida.engine import run
from aiida.common.exceptions import OutputParsingError
from aiida.plugins import CalculationFactory

Cp2kCalculation = CalculationFactory('cp2k')
from aiida.engine import run_get_node


def example_failure(cp2k_code):
Expand All @@ -33,7 +29,7 @@ def example_failure(cp2k_code):
print("Submitted calculation...")

# Construct process builder
builder = Cp2kCalculation.get_builder()
builder = cp2k_code.get_builder()
builder.parameters = parameters
builder.code = cp2k_code
builder.metadata.options.resources = {
Expand All @@ -42,13 +38,13 @@ def example_failure(cp2k_code):
}
builder.metadata.options.max_wallclock_seconds = 1 * 2 * 60

try:
run(builder)
print("ERROR!")
print("CP2K failure was not recognized")
sys.exit(3)
except OutputParsingError:
_, calc = run_get_node(builder)
if not calc.is_finished_ok:
print("CP2K failure correctly recognized")
return

print("ERROR!\nCP2K failure was not recognized")
sys.exit(3)


@click.command('cli')
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25 changes: 10 additions & 15 deletions examples/workchains/example_base.py
View file
Expand Up @@ -13,9 +13,10 @@

import os
import sys
import ase.build
import click

import ase.io

from aiida.engine import run
from aiida.orm import (Code, Dict, SinglefileData, StructureData)
from aiida.common import NotExistent
Expand All @@ -27,27 +28,25 @@
def example_base(cp2k_code):
"""Run simple DFT calculation through a workchain"""

pwd = os.path.dirname(os.path.realpath(__file__))
thisdir = os.path.dirname(os.path.realpath(__file__))

print("Testing CP2K ENERGY on H2O (DFT) through a workchain...")

# basis set
basis_file = SinglefileData(file=os.path.join(pwd, "..", "files", "BASIS_MOLOPT"))
basis_file = SinglefileData(file=os.path.join(thisdir, "..", "files", "BASIS_MOLOPT"))

# pseudopotentials
pseudo_file = SinglefileData(file=os.path.join(pwd, "..", "files", "GTH_POTENTIALS"))
pseudo_file = SinglefileData(file=os.path.join(thisdir, "..", "files", "GTH_POTENTIALS"))

# structure
atoms = ase.build.molecule('H2O')
atoms.center(vacuum=5.0)
structure = StructureData(ase=atoms)
structure = StructureData(ase=ase.io.read(os.path.join(thisdir, '..', 'data', 'h2o.xyz')))

# parameters
parameters = Dict(
dict={
'GLOBAL': {
'RUN_TYPE': 'GEO_OPT',
'WALLTIME': '00:00:30', # too short
'WALLTIME': '00:30:30', # too short
},
'FORCE_EVAL': {
'METHOD': 'Quickstep',
Expand All @@ -66,25 +65,21 @@ def example_base(cp2k_code):
},
'XC': {
'XC_FUNCTIONAL': {
'_': 'LDA',
'_': 'PBE',
},
},
'POISSON': {
'PERIODIC': 'none',
'PSOLVER': 'MT',
},
},
'SUBSYS': {
'KIND': [
{
'_': 'O',
'BASIS_SET': 'DZVP-MOLOPT-SR-GTH',
'POTENTIAL': 'GTH-LDA-q6'
'POTENTIAL': 'GTH-PBE-q6'
},
{
'_': 'H',
'BASIS_SET': 'DZVP-MOLOPT-SR-GTH',
'POTENTIAL': 'GTH-LDA-q1'
'POTENTIAL': 'GTH-PBE-q1'
},
],
},
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