def test_pw2qmcpack_incorporate_result():
from generic import NexusError,obj
from simulation import Simulation
from test_pwscf_simulation import pseudo_inputs,get_pwscf_sim
tpath = testing.setup_unit_test_output_directory('pwscf_simulation','test_check_result',**pseudo_inputs)
other = Simulation()
scf = get_pwscf_sim('scf')
sim = get_pw2qmcpack_sim(path='scf')
try:
sim.incorporate_result('unknown',None,other)
raise TestFailed
except NexusError:
None
except FailedTest:
failed()
except Exception as e:
failed(str(e))
#end try
sim.incorporate_result('orbitals',None,scf)
clear_all_sims()
restore_nexus()
def test_convert4qmc_get_result():
from generic import NexusError,obj
sim = get_convert4qmc_sim()
try:
sim.get_result('unknown',None)
raise FailedTest
except NexusError:
None
except FailedTest:
failed()
except Exception as e:
failed(str(e))
#end try
result = sim.get_result('orbitals',None)
result_ref = obj(
location = './runs/sample.wfj.xml',
)
assert(object_eq(result,result_ref))
result = sim.get_result('particles',None)
result_ref = obj(
location = './runs/sample.structure.xml',
)
assert(object_eq(result,result_ref))
clear_all_sims()
def test_pyscf_to_afqmc_get_result():
from generic import NexusError,obj
sim = get_pyscf_to_afqmc_sim()
sim.input.output = 'afqmc.h5'
try:
sim.get_result('unknown',None)
raise FailedTest
except NexusError:
None
except FailedTest:
failed()
except Exception as e:
failed(str(e))
#end try
result_ref = obj(
h5_file = './runs/afqmc.h5',
)
result = sim.get_result('wavefunction',None)
assert(object_eq(result,result_ref))
result = sim.get_result('hamiltonian',None)
assert(object_eq(result,result_ref))
clear_all_sims()
def test_pw2qmcpack_check_sim_status():
import os
from generic import NexusError, obj
from nexus_base import nexus_core
tpath = testing.setup_unit_test_output_directory(
'qmcpack_converter_simulations',
'test_pw2qmcpack_check_sim_status',
divert=True)
nexus_core.runs = ''
sim = get_pw2qmcpack_sim()
assert (sim.locdir.rstrip('/') == tpath.rstrip('/'))
assert (not sim.finished)
assert (not sim.failed)
try:
sim.check_sim_status()
raise FailedTest
except IOError:
None
except Exception as e:
failed(str(e))
#end try
sim.create_directories()
outfile = os.path.join(sim.locdir, sim.outfile)
outfile_text = 'JOB DONE'
out = open(outfile, 'w')
out.write(outfile_text)
out.close()
assert (outfile_text in open(outfile, 'r').read())
prefix = sim.input.inputpp.prefix
outdir = sim.input.inputpp.outdir
outdir_path = os.path.join(tpath, outdir)
if not os.path.exists(outdir_path):
os.makedirs(outdir_path)
#end if
filenames = [
prefix + '.pwscf.h5', prefix + '.ptcl.xml', prefix + '.wfs.xml'
]
for filename in filenames:
filepath = os.path.join(tpath, outdir, filename)
f = open(filepath, 'w')
f.write('')
f.close()
assert (os.path.exists(filepath))
#end for
sim.job.finished = True
sim.check_sim_status()
assert (sim.finished)
assert (not sim.failed)
clear_all_sims()
restore_nexus()
def test_pyscf_to_afqmc_incorporate_result():
import os
from generic import NexusError,obj
from simulation import Simulation
from test_pyscf_simulation import get_pyscf_sim
other = Simulation()
scf = get_pyscf_sim()
sim = get_pyscf_to_afqmc_sim()
try:
sim.incorporate_result('unknown',None,other)
raise TestFailed
except NexusError:
None
except FailedTest:
failed()
except Exception as e:
failed(str(e))
#end try
result = obj(
chkfile = os.path.join(scf.locdir,'scf.chk'),
)
assert(sim.input.input==None)
sim.incorporate_result('wavefunction',result,scf)
assert(sim.input.input=='scf.chk')
clear_all_sims()
def test_pw2qmcpack_check_result():
sim = get_pw2qmcpack_sim()
assert(not sim.check_result('unknown',None))
assert(sim.check_result('orbitals',None))
clear_all_sims()
def test_pw2qmcpack_get_result():
from generic import NexusError,obj
sim = get_pw2qmcpack_sim()
try:
sim.get_result('unknown',None)
raise FailedTest
except NexusError:
None
except FailedTest:
failed()
except Exception as e:
failed(str(e))
#end try
result = sim.get_result('orbitals',None)
result_ref = obj(
h5file = './runs/pwscf_output/pwscf.pwscf.h5',
ptcl_xml = './runs/pwscf_output/pwscf.ptcl.xml',
wfs_xml = './runs/pwscf_output/pwscf.wfs.xml',
)
assert(object_eq(result,result_ref))
clear_all_sims()
def test_check_sim_status():
import os
tpath = testing.setup_unit_test_output_directory('vasp_simulation',
'test_check_sim_status',
**pseudo_inputs)
sim = setup_vasp_sim(tpath)
assert (sim.locdir.strip('/') == tpath.strip('/'))
assert (not sim.finished)
assert (not sim.input.performing_neb())
sim.check_sim_status()
assert (not sim.finished)
outcar_file = os.path.join(tpath, 'OUTCAR')
outcar_text = 'General timing and accounting'
outcar = open(outcar_file, 'w')
outcar.write(outcar_text)
outcar.close()
assert (os.path.exists(outcar_file))
assert (outcar_text in open(outcar_file, 'r').read())
sim.check_sim_status()
assert (sim.finished)
assert (not sim.failed)
clear_all_sims()
restore_nexus()
def test_get_output_files():
import os
tpath = testing.setup_unit_test_output_directory('vasp_simulation',
'test_get_output_files',
**pseudo_inputs)
sim = setup_vasp_sim(tpath)
vfiles = 'INCAR KPOINTS POSCAR CONTCAR OUTCAR'.split()
for vfile in vfiles:
f = open(os.path.join(tpath, vfile), 'w')
f.write('')
f.close()
#end for
files = sim.get_output_files()
assert (value_eq(files, vfiles))
for vfile in vfiles:
assert (os.path.exists(
os.path.join(tpath, sim.identifier + '.' + vfile)))
#end for
clear_all_sims()
restore_nexus()
def test_convert4qmc_check_result():
sim = get_convert4qmc_sim()
assert(not sim.check_result('unknown',None))
assert(sim.check_result('orbitals',None))
assert(sim.check_result('particles',None))
clear_all_sims()
def test_minimal_init():
from machines import job
from vasp import Vasp, generate_vasp
sim = generate_vasp(job=job(machine='ws1', cores=1), )
assert (isinstance(sim, Vasp))
clear_all_sims()
def test_pyscf_to_afqmc_minimal_init():
from machines import job
from qmcpack_converters import PyscfToAfqmc, generate_pyscf_to_afqmc
sim = generate_pyscf_to_afqmc(job=job(machine='ws1', cores=1), )
assert (isinstance(sim, PyscfToAfqmc))
clear_all_sims()
def test_pw2qmcpack_minimal_init():
from machines import job
from qmcpack_converters import Pw2qmcpack, generate_pw2qmcpack
sim = generate_pw2qmcpack(job=job(machine='ws1', cores=1), )
assert (isinstance(sim, Pw2qmcpack))
clear_all_sims()
def test_minimal_init():
from machines import job
for cls,gen in get_class_generators():
sim = gen(job=job(machine='ws1',cores=1))
assert(isinstance(sim,cls))
#end for
clear_all_sims()
def test_minimal_init():
from machines import job
from pyscf_sim import Pyscf, generate_pyscf
sim = generate_pyscf(job=job(machine='ws1', cores=1), )
assert (isinstance(sim, Pyscf))
clear_all_sims()
def test_incorporate_result():
import os
import shutil
from numpy import array
from generic import obj
tpath = testing.setup_unit_test_output_directory(
'vasp_simulation', 'test_incorporate_result', **pseudo_inputs)
sim = setup_vasp_sim(tpath, identifier='diamond', files=True)
pcfile = os.path.join(tpath, 'diamond_POSCAR')
ccfile = os.path.join(tpath, sim.identifier + '.CONTCAR')
assert (sim.locdir.strip('/') == tpath.strip('/'))
shutil.copy2(pcfile, ccfile)
assert (os.path.exists(ccfile))
result = sim.get_result('structure', None)
sim2 = setup_vasp_sim(tpath)
pid = id(sim2.input.poscar)
sim2.incorporate_result('structure', result, None)
assert (id(sim2.input.poscar) != pid)
poscar_ref = obj(
axes=array([[3.57, 3.57, 0.], [0., 3.57, 3.57], [3.57, 0., 3.57]],
dtype=float),
coord='cartesian',
description=None,
dynamic=None,
elem=['C'],
elem_count=[16],
pos=array([[0., 0., 0.], [0.8925, 0.8925, 0.8925], [1.785, 1.785, 0.],
[2.6775, 2.6775, 0.8925], [0., 1.785, 1.785],
[0.8925, 2.6775, 2.6775], [1.785, 3.57, 1.785],
[2.6775, 4.4625, 2.6775], [1.785, 0., 1.785],
[2.6775, 0.8925, 2.6775], [3.57, 1.785, 1.785],
[4.4625, 2.6775, 2.6775], [1.785, 1.785, 3.57],
[2.6775, 2.6775, 4.4625], [3.57, 3.57, 3.57],
[4.4625, 4.4625, 4.4625]],
dtype=float),
scale=1.0,
vel=None,
vel_coord=None,
)
assert (object_eq(sim2.input.poscar.to_obj(), poscar_ref))
clear_all_sims()
restore_nexus()
def test_check_result():
from machines import job
for cls,gen in get_class_generators():
sim = gen(job=job(machine='ws1',cores=1))
assert(isinstance(sim,cls))
assert(not sim.check_result('anything',None))
#end for
clear_all_sims()
def test_minimal_init():
from machines import job
from rmg import Rmg,generate_rmg
sim = generate_rmg(
job = job(machine='ws1',cores=1),
)
assert(isinstance(sim,Rmg))
clear_all_sims()
def test_minimal_init():
from machines import job
from pwscf import Pwscf,generate_pwscf
sim = generate_pwscf(
job = job(machine='ws1',cores=1),
system = get_system(),
)
assert(isinstance(sim,Pwscf))
clear_all_sims()
def test_check_sim_status():
from machines import job
for cls,gen in get_class_generators():
sim = gen(job=job(machine='ws1',cores=1))
assert(isinstance(sim,cls))
sim.check_sim_status()
assert(sim.finished)
assert(not sim.failed)
#end for
clear_all_sims()
def test_check_result():
tpath = testing.setup_unit_test_output_directory('pwscf_simulation','test_check_result',**pseudo_inputs)
sim = get_pwscf_sim('scf')
assert(not sim.check_result('unknown',None))
assert(sim.check_result('charge_density',None))
assert(sim.check_result('restart',None))
assert(sim.check_result('orbitals',None))
assert(not sim.check_result('structure',None))
clear_all_sims()
restore_nexus()
def test_pyscf_to_afqmc_check_result():
sim = get_pyscf_to_afqmc_sim()
assert(not sim.check_result('unknown',None))
assert(not sim.check_result('wavefunction',None))
assert(not sim.check_result('hamiltonian',None))
sim.input.output = 'afqmc.h5'
assert(sim.check_result('wavefunction',None))
assert(sim.check_result('hamiltonian',None))
clear_all_sims()
def test_check_result():
tpath = testing.setup_unit_test_output_directory('vasp_simulation',
'test_check_result',
**pseudo_inputs)
sim = setup_vasp_sim(tpath)
assert (not sim.check_result('unknown', None))
assert (sim.check_result('structure', None))
clear_all_sims()
restore_nexus()
def test_pyscf_to_afqmc_check_sim_status():
import os
from generic import NexusError, obj
from nexus_base import nexus_core
tpath = testing.setup_unit_test_output_directory(
'qmcpack_converter_simulations',
'test_pyscf_to_afqmc_check_sim_status',
divert=True)
nexus_core.runs = ''
sim = get_pyscf_to_afqmc_sim()
assert (sim.locdir.rstrip('/') == tpath.rstrip('/'))
assert (not sim.finished)
assert (not sim.failed)
try:
sim.check_sim_status()
raise FailedTest
except IOError:
None
except Exception as e:
failed(str(e))
#end try
sim.input.output = 'afqmc.h5'
sim.create_directories()
outfile = os.path.join(sim.locdir, sim.outfile)
outfile_text = '# Finished.'
out = open(outfile, 'w')
out.write(outfile_text)
out.close()
assert (outfile_text in open(outfile, 'r').read())
output_file = os.path.join(sim.locdir, sim.input.output)
f = open(output_file, 'w')
f.write('')
f.close()
assert (os.path.exists(output_file))
sim.job.finished = True
sim.check_sim_status()
assert (sim.finished)
assert (not sim.failed)
clear_all_sims()
restore_nexus()
def test_get_result():
from generic import NexusError
tpath = testing.setup_unit_test_output_directory('pwscf_simulation','test_get_result',**pseudo_inputs)
sim = get_pwscf_sim('scf')
try:
sim.get_result('unknown',None)
raise FailedTest
except NexusError:
None
except FailedTest:
failed()
except Exception as e:
failed(str(e))
#end try
result = sim.get_result('charge_density',None)
result2 = sim.get_result('restart',None)
assert(object_eq(result,result2))
result_ref = dict(
locdir = 'scf',
outdir = 'scf/pwscf_output',
location = 'scf/pwscf_output/pwscf.save/charge-density.dat',
spin_location = 'scf/pwscf_output/pwscf.save/spin-polarization.dat',
)
assert(set(result.keys())==set(result_ref.keys()))
for k,path in result.items():
path = path.replace(tpath,'').lstrip('/')
assert(path==result_ref[k])
#end for
result = sim.get_result('orbitals',None)
result_ref = dict(
location = 'scf/pwscf_output/pwscf.wfc1',
)
assert(set(result.keys())==set(result_ref.keys()))
for k,path in result.items():
path = path.replace(tpath,'').lstrip('/')
assert(path==result_ref[k])
#end for
clear_all_sims()
restore_nexus()
def test_incorporate_result():
from generic import obj
tpath = testing.setup_unit_test_output_directory('pwscf_simulation','test_incorporate_result',**pseudo_inputs)
sim = get_pwscf_sim('scf')
sim_start = sim.to_obj().copy()
assert(object_eq(sim.to_obj(),sim_start))
# charge density
result = obj(
locdir = sim.locdir,
)
sim.incorporate_result('charge_density',result,None)
assert(object_eq(sim.to_obj(),sim_start))
# restart
sim.incorporate_result('restart',result,None)
c = sim.input.control
assert(c.restart_mode=='restart')
del c.restart_mode
assert(object_eq(sim.to_obj(),sim_start))
# structure
altered_structure = sim.system.structure.copy()
altered_structure.pos += 0.1
result = obj(
structure = altered_structure,
)
sim.incorporate_result('structure',result,None)
sim_ref = sim_start.copy()
pos_ref = sim_ref.system.structure.delete('pos')+0.1
sim_ref.input.atomic_positions.delete('positions')
pos = sim.system.structure.delete('pos')
apos = sim.input.atomic_positions.delete('positions')
assert(value_eq(pos,pos_ref))
assert(value_eq(apos,pos_ref))
assert(object_eq(sim.to_obj(),sim_ref))
clear_all_sims()
restore_nexus()
def test_check_sim_status():
import os
tpath = testing.setup_unit_test_output_directory('pwscf_simulation','test_check_sim_status',**pseudo_inputs)
sim = get_pwscf_sim('scf')
assert(sim.locdir.rstrip('/')==os.path.join(tpath,'scf').rstrip('/'))
if not os.path.exists(sim.locdir):
os.makedirs(sim.locdir)
#end if
assert(not sim.finished)
try:
sim.check_sim_status()
except IOError:
None
except Exception as e:
failed(str(e))
#end try
assert(not sim.finished)
out_path = os.path.join(tpath,'scf',sim.outfile)
out_text = ''
outfile = open(out_path,'w')
outfile.write(out_text)
outfile.close()
assert(os.path.exists(out_path))
sim.check_sim_status()
assert(not sim.finished)
out_text = 'JOB DONE'
outfile = open(out_path,'w')
outfile.write(out_text)
outfile.close()
assert(out_text in open(out_path,'r').read())
sim.check_sim_status()
assert(sim.finished)
assert(not sim.failed)
clear_all_sims()
restore_nexus()
def test_check_sim_status():
import os
from nexus_base import nexus_core
tpath = testing.setup_unit_test_output_directory('qmcpack_simulation',
'test_check_sim_status',
divert=True)
nexus_core.runs = ''
sim = get_qmcpack_sim(identifier='qmc')
assert (sim.locdir.rstrip('/') == tpath.rstrip('/'))
assert (not sim.finished)
assert (not sim.failed)
try:
sim.check_sim_status()
except IOError:
None
#end try
assert (not sim.finished)
assert (not sim.failed)
outfile = os.path.join(tpath, sim.outfile)
out_text = 'Total Execution'
out = open(outfile, 'w')
out.write(out_text)
out.close()
assert (os.path.exists(outfile))
assert (out_text in open(outfile, 'r').read())
errfile = os.path.join(tpath, sim.errfile)
err = open(errfile, 'w')
err.write('')
err.close()
assert (os.path.exists(errfile))
sim.check_sim_status()
assert (sim.finished)
assert (not sim.failed)
clear_all_sims()
restore_nexus()
def test_get_result():
import os
from generic import NexusError, obj
from nexus_base import nexus_core
tpath = testing.setup_unit_test_output_directory('pyscf_simulation',
'test_get_result',
divert=True)
nexus_core.runs = ''
template_file = 'scf_template.py'
template_text = 'template $chkfile'
template_filepath = os.path.join(tpath, template_file)
f = open(template_filepath, 'w')
f.write(template_text)
f.close()
sim = get_pyscf_sim(
prefix='scf',
checkpoint='scf.chk',
template=template_filepath,
)
try:
sim.get_result('unknown', None)
raise FailedTest
except NexusError:
None
except FailedTest:
failed()
except Exception as e:
failed(str(e))
#end try
result = sim.get_result('orbitals', None)
assert (result.h5_file.replace(tpath, '').lstrip('/') == 'scf.h5')
result = sim.get_result('wavefunction', None)
assert (result.chkfile.replace(tpath, '').lstrip('/') == 'scf.chk')
clear_all_sims()
restore_nexus()
def test_check_sim_status():
sim = get_pyscf_sim()
assert (not sim.failed)
assert (not sim.finished)
sim.check_sim_status()
assert (not sim.failed)
assert (not sim.finished)
sim.job.finished = True
sim.check_sim_status()
assert (not sim.failed)
assert (sim.finished)
clear_all_sims()