def test_run_staged_ingredients(self):
topmetad = MASTFile("files/top_metadata_single")
topmetad.data.append("origin_dir = %s/files\n" % testdir) #give origin directory
topmetad.to_file("recipedir/metadata.txt")
#metad = MASTFile("files/metadata_single")
#metad.to_file("%s/metadata.txt" % ingdir)
rp = RecipePlan("recipedir")
rp.ingredients['ing1']="C"
rp.ingredients['ing2a'] = "W"
rp.ingredients['ing2b'] = "S"
rp.ingredients['ing3'] = "W"
kdict=dict()
kdict['mast_program']='vasp'
kdict['mast_xc']='pw91'
kdict['mast_kpoints']=[1,2,3,"G"]
rp.ingred_input_options['ing2b']=dict()
rp.ingred_input_options['ing2b']['name']="recipedir/ing2b"
rp.ingred_input_options['ing2b']['program_keys']=kdict
rp.ingred_input_options['ing2b']['structure']=pymatgen.io.vaspio.Poscar.from_file("files/perfect_structure").structure
rp.write_methods['ing2b']=[['write_singlerun']]
rp.write_ingredient('ing2b')
rp.ready_methods['ing2b']=[['ready_singlerun']]
rp.run_methods['ing2b']=[['run_singlerun']]
rp.complete_methods['ing2b']=[['complete_singlerun']]
rp.run_staged_ingredients()
mysubmit = MASTFile("test_control/submitlist")
self.assertEquals(mysubmit.data[0],"recipedir/ing2b\n")
self.assertEquals(rp.ingredients,{'ing1':'C','ing2a':'W','ing2b':'P','ing3':'W'})
def create_archive_files(self):
"""Save off archive files.
Returns:
creates archive_input_options.txt
creates archive_recipe_plan.txt
"""
inputsave = MASTFile()
inputsave.data = repr(self.input_options)
inputsave.to_file(
os.path.join(self.working_directory, 'archive_input_options.txt'))
recipesave = MASTFile()
recipesave.data = repr(self.recipe_plan)
recipesave.to_file(
os.path.join(self.working_directory, 'archive_recipe_plan.txt'))
#pickle_plan = os.path.join(self.working_directory, 'archive_recipe_plan.pickle')
#pm = PickleManager(pickle_plan)
#pm.save_variable(self.recipe_plan)
#pickle_options = os.path.join(self.working_directory, 'archive_input_options.pickle')
#pm = PickleManager(pickle_options)
#pm.save_variable(self.input_options)
#create the *.py input script
#ipc_obj = InputPythonCreator(input_options=self.input_options)
#ipc_filename = ipc_obj.write_script(self.working_directory, 'archive_input_options.py')
return
def test_give_phonon_single_forces_and_displacements(self):
ingdir = "%s/writedir/single_phonon_label1" % testdir
recipedir = "%s/writedir" % testdir
topmetad = MASTFile("files/top_metadata_single")
topmetad.data.append("origin_dir = %s/files\n" %
testdir) #give origin directory
topmetad.to_file("writedir/metadata.txt")
metad = MASTFile("files/metadata_single_phonon")
metad.to_file("%s/metadata.txt" % ingdir)
mypos = MASTFile("files/phonon_initial_POSCAR")
mypos.to_file("%s/POSCAR" % ingdir)
kdict = dict()
kdict['mast_program'] = 'vasp'
my_structure = pymatgen.io.vaspio.Poscar.from_file(
"files/perfect_structure").structure
myxdat = MASTFile("files/XDATCAR_compare")
myxdat.to_file("%s/XDATCAR" % ingdir)
mydynmat = MASTFile("files/DYNMAT_compare")
mydynmat.to_file("%s/DYNMAT" % ingdir)
myuci = ChopIngredient(name=ingdir,
program_keys=kdict,
structure=my_structure)
myuci.give_phonon_single_forces_and_displacements("next_ingred")
newpos = MASTFile("%s/writedir/next_ingred/POSCAR_prePHON" % testdir)
newdyn = MASTFile("%s/writedir/next_ingred/DYNMAT" % testdir)
newxdat = MASTFile("%s/writedir/next_ingred/XDATCAR" % testdir)
comparepos = MASTFile("files/phonon_initial_POSCAR")
comparedyn = MASTFile("files/DYNMAT_compare")
comparexdat = MASTFile("%s/XDATCAR" % ingdir)
self.assertEqual(newpos.data, comparepos.data)
self.assertEqual(newdyn.data, comparedyn.data)
self.assertEqual(newxdat.data, comparexdat.data)
def test_give_phonon_single_forces_and_displacements(self):
ingdir="%s/writedir/single_phonon_label1" % testdir
recipedir="%s/writedir" % testdir
topmetad = MASTFile("files/top_metadata_single")
topmetad.data.append("origin_dir = %s/files\n" % testdir) #give origin directory
topmetad.to_file("writedir/metadata.txt")
metad = MASTFile("files/metadata_single_phonon")
metad.to_file("%s/metadata.txt" % ingdir)
mypos = MASTFile("files/phonon_initial_POSCAR")
mypos.to_file("%s/POSCAR" % ingdir)
kdict=dict()
kdict['mast_program'] = 'vasp'
my_structure = pymatgen.io.vaspio.Poscar.from_file("files/perfect_structure").structure
myxdat = MASTFile("files/XDATCAR_compare")
myxdat.to_file("%s/XDATCAR" % ingdir)
mydynmat = MASTFile("files/DYNMAT_compare")
mydynmat.to_file("%s/DYNMAT" % ingdir)
myuci = ChopIngredient(name=ingdir,program_keys=kdict, structure=my_structure)
myuci.give_phonon_single_forces_and_displacements("next_ingred")
newpos = MASTFile("%s/writedir/next_ingred/POSCAR_prePHON" % testdir)
newdyn = MASTFile("%s/writedir/next_ingred/DYNMAT" % testdir)
newxdat = MASTFile("%s/writedir/next_ingred/XDATCAR" % testdir)
comparepos = MASTFile("files/phonon_initial_POSCAR")
comparedyn = MASTFile("files/DYNMAT_compare")
comparexdat = MASTFile("%s/XDATCAR" % ingdir)
self.assertEqual(newpos.data, comparepos.data)
self.assertEqual(newdyn.data, comparedyn.data)
self.assertEqual(newxdat.data, comparexdat.data)
def test_write_ingredient(self):
topmetad = MASTFile("files/top_metadata_single")
topmetad.data.append("origin_dir = %s/files\n" %
testdir) #give origin directory
topmetad.to_file("recipedir/metadata.txt")
#metad = MASTFile("files/metadata_single")
#metad.to_file("%s/metadata.txt" % ingdir)
rp = RecipePlan("recipedir")
rp.ingredients['ing2b'] = "I"
kdict = dict()
kdict['mast_program'] = 'vasp'
kdict['mast_xc'] = 'pw91'
kdict['mast_kpoints'] = [1, 2, 3, "G"]
rp.ingred_input_options['ing2b'] = dict()
rp.ingred_input_options['ing2b']['name'] = "recipedir/ing2b"
rp.ingred_input_options['ing2b']['program_keys'] = kdict
rp.ingred_input_options['ing2b'][
'structure'] = pymatgen.io.vaspio.Poscar.from_file(
"files/perfect_structure").structure
rp.write_methods['ing2b'] = [['write_singlerun']]
rp.write_ingredient('ing2b')
self.assertTrue(os.path.isfile('recipedir/ing2b/INCAR'))
self.assertTrue(os.path.isfile('recipedir/ing2b/POSCAR'))
self.assertTrue(os.path.isfile('recipedir/ing2b/POTCAR'))
self.assertTrue(os.path.isfile('recipedir/ing2b/KPOINTS'))
self.assertTrue(os.path.isfile('recipedir/ing2b/submit.sh'))
def test_run_subfolders(self):
#raise SkipTest
ingdir="%s/writedir/single_label1" % testdir
recipedir="%s/writedir" % testdir
topmetad = MASTFile("files/top_metadata_single")
topmetad.data.append("origin_dir = %s/files\n" % testdir) #give origin directory
topmetad.to_file("writedir/metadata.txt")
metad = MASTFile("files/metadata_single")
metad.to_file("%s/metadata.txt" % ingdir)
kdict=dict()
kdict['mast_program'] = 'vasp'
kdict['mast_kpoints'] = [2,2,2,"M"]
kdict['mast_xc'] = 'pw91'
my_structure = Poscar.from_file("files/perfect_structure").structure
for subfolder in ['sub1','sub2','sub3','sub4']:
subname = "%s/%s" % (ingdir, subfolder)
os.mkdir(subname)
shutil.copy("files/metadata_single","%s/metadata.txt" % subname)
mywr = ChopIngredient(name=subname, program_keys = kdict, structure=my_structure)
mywr.write_singlerun()
myri = ChopIngredient(name=ingdir,program_keys=kdict, structure=my_structure)
myri.run_subfolders()
self.assertFalse(myri.checker.is_ready_to_run())
for subfolder in ['sub1','sub2','sub3','sub4']:
subname = "%s/%s" % (ingdir, subfolder)
myri.checker.keywords['name'] = subname
self.assertTrue(myri.checker.is_ready_to_run())
mysubmit = MASTFile("%s/submitlist" % self.test_control)
self.assertEquals(mysubmit.data[0], "%s/sub1\n" % ingdir)
self.assertEquals(mysubmit.data[1], "%s/sub2\n" % ingdir)
self.assertEquals(mysubmit.data[2], "%s/sub3\n" % ingdir)
self.assertEquals(mysubmit.data[3], "%s/sub4\n" % ingdir)
def create_workflow_test_script(inputfile):
myvars = get_variables()
# set up testing directory tree
wtdir=myvars['workflow_test_directory']
mast_test_dir=os.path.join(wtdir,"no_directory_yet")
while not (os.path.isdir(mast_test_dir)):
timestamp=time.strftime("%Y%m%dT%H%M%S")
mast_test_dir = os.path.join(wtdir,"output_test_%s" % timestamp)
if not (os.path.isdir(mast_test_dir)):
shutil.copytree("%s/mini_mast_tree" % wtdir, mast_test_dir)
# set up output file and submission script
shortname = inputfile.split(".")[0]
output="%s/output_%s" % (wtdir, shortname)
submitscript="%s/submit_%s.sh" % (wtdir, shortname)
generic_script="%s/generic_mast_workflow.sh" % wtdir
bashcommand="bash %s %s %s %s %s %s >> %s" % (generic_script,
mast_test_dir,
myvars["workflow_examples_located"],
inputfile,
myvars["workflow_activate_command"],
myvars["workflow_testing_environment"],
output)
submitfile=MASTFile()
submitfile.data.append(bashcommand + "\n")
submitfile.to_file(submitscript)
return [mast_test_dir, submitscript, output]
def test_give_neb_structures_to_neb(self):
ingdir = "%s/writedir/neb_labelinit-labelfin" % testdir
recipedir = "%s/writedir" % testdir
topmetad = MASTFile("files/top_metadata_neb")
topmetad.data.append("origin_dir = %s/files\n" %
testdir) #give origin directory
topmetad.to_file("writedir/metadata.txt")
metad = MASTFile("files/metadata_neb")
metad.to_file("%s/metadata.txt" % ingdir)
kdict = dict()
kdict['mast_program'] = 'vasp_neb'
kdict['mast_neb_settings'] = dict()
kdict['mast_neb_settings']['images'] = 3
my_structure = pymatgen.io.vaspio.Poscar.from_file(
"files/perfect_structure").structure
myrelaxed = dict()
for subdir in ['00', '01', '02', '03', '04']:
os.mkdir("writedir/neb_labelinit-labelfin/%s" % subdir)
myrelaxed[subdir] = MASTFile("files/POSCAR_%s" % subdir)
myrelaxed[subdir].to_file(
"writedir/neb_labelinit-labelfin/%s/CONTCAR" % subdir)
myuci = ChopIngredient(name=ingdir,
program_keys=kdict,
structure=my_structure)
myuci.give_neb_structures_to_neb("next_ingred")
for subdir in ['01', '02', '03']:
givenstr = MASTFile(
"%s/writedir/next_ingred/parent_structure_labelinit-labelfin_%s"
% (testdir, subdir))
self.assertEqual(myrelaxed[subdir].data, givenstr.data)
def change_my_status(self, newstatus):
"""Change an ingredient status by writing the new status to
change_status.txt in the ingredient folder, to get picked
up by the recipe plan.
Args:
newstatus <str>: New status to which to change the ingredient.
"""
ingdir = self.keywords['name']
oneup = os.path.dirname(ingdir)
tryrecipe = os.path.basename(oneup)
statuspath = ""
if dirutil.dir_is_in_scratch(tryrecipe):
statuspath = "%s/change_status.txt" % ingdir
else:
twoup = os.path.dirname(oneup)
tryrecipe = os.path.basename(twoup)
if dirutil.dir_is_in_scratch(tryrecipe):
statuspath = "%s/change_status.txt" % oneup
else:
raise MASTError(
self.__class__.__name__,
"Cannot change status of ingredient %s as recipe %s or %s is not found in $MAST_SCRATCH."
% (self.keywords['name'], oneup, twoup))
if os.path.isfile(statuspath):
statusfile = MASTFile(statuspath)
else:
statusfile = MASTFile()
statusfile.data.append("%s:recommend:%s" % (newstatus, time.asctime()))
statusfile.to_file(statuspath)
self.logger.info("Recommending status change to %s" % newstatus)
def status_change_recommended(self, iname):
"""Check if a status change is recommended for the ingredient,
as listed in the ingredient folder/change_status.txt.
Args:
iname <str>: ingredient name
Returns:
True if a status change was recommended, and
changes the status of the ingredient in self.ingredients.
False otherwise
"""
statuspath = os.path.join(self.working_directory, iname, "change_status.txt")
if not os.path.isfile(statuspath):
return False
statusfile = MASTFile(statuspath)
newdata=list()
changed=False
for sline in statusfile.data: #status:recommend:timestamp
if not "status_changed" in sline:
newstatus = sline.split(":")[0]
self.ingredients[iname]=newstatus
newline = sline + ":status_changed:" + time.asctime() + "\n"
self.logger.info("Status of %s changed to %s" % (iname, newstatus))
changed=True
newdata.append(newline)
else:
newdata.append(sline)
statusfile.data=list(newdata)
statusfile.to_file(statuspath)
return changed
def test_give_saddle_structure(self):
ingdir="%s/writedir/neb_labelinit-labelfin" % testdir
recipedir="%s/writedir" % testdir
topmetad = MASTFile("files/top_metadata_neb")
topmetad.data.append("origin_dir = %s/files\n" % testdir) #give origin directory
topmetad.to_file("writedir/metadata.txt")
metad = MASTFile("files/metadata_neb")
metad.to_file("%s/metadata.txt" % ingdir)
kdict=dict()
kdict['mast_program'] = 'vasp_neb'
kdict['images'] = 3
my_structure = pymatgen.io.vaspio.Poscar.from_file("files/perfect_structure").structure
myrelaxed=dict()
myosz=dict()
mywav=dict()
mychg=dict()
for subdir in ['00','01','02','03','04']:
os.mkdir("writedir/neb_labelinit-labelfin/%s" % subdir)
myrelaxed[subdir] = MASTFile("files/POSCAR_%s" % subdir)
myrelaxed[subdir].to_file("writedir/neb_labelinit-labelfin/%s/CONTCAR" % subdir)
myosz[subdir] = MASTFile("files/OSZICAR_%s" % subdir)
myosz[subdir].to_file("writedir/neb_labelinit-labelfin/%s/OSZICAR" % subdir)
mychg[subdir] = MASTFile("files/CHGCAR")
mychg[subdir].to_file("writedir/neb_labelinit-labelfin/%s/CHGCAR" % subdir)
mywav[subdir] = MASTFile("files/WAVECAR")
mywav[subdir].to_file("writedir/neb_labelinit-labelfin/%s/WAVECAR" % subdir)
myuci = ChopIngredient(name=ingdir,program_keys=kdict, structure=my_structure)
myuci.give_saddle_structure("next_ingred") #should be OSZ3
saddle = MASTFile("%s/writedir/next_ingred/POSCAR" % testdir)
self.assertEqual(myrelaxed['03'].data, saddle.data)
saddledir = myuci.get_saddle_dir()
self.assertEqual(saddledir, "03")
def test_update_children(self):
topmetad = MASTFile("files/top_metadata_single")
topmetad.data.append("origin_dir = %s/files\n" % testdir) #give origin directory
topmetad.to_file("recipedir/metadata.txt")
#metad = MASTFile("files/metadata_single")
#metad.to_file("%s/metadata.txt" % ingdir)
rp = RecipePlan("%s/recipedir" % testdir)
rp.ingredients['ing1'] = "I"
kdict=dict()
kdict['mast_program']='vasp'
kdict['mast_xc']='pw91'
kdict['mast_kpoints']=[1,2,3,"G"]
rp.ingred_input_options['ing1']=dict()
rp.ingred_input_options['ing1']['name']="%s/ing1" % rp.working_directory
rp.ingred_input_options['ing1']['program_keys']=kdict
rp.ingred_input_options['ing1']['structure']=pymatgen.io.vaspio.Poscar.from_file("files/perfect_structure").structure
rp.update_methods['ing1']=dict()
rp.update_methods['ing1']['ing2a']=[['give_structure']]
rp.update_methods['ing1']['ing2b']=[['give_structure_and_restart_files']]
rp.update_children('ing1')
self.assertTrue(os.path.isfile("recipedir/ing2a/POSCAR"))
self.assertTrue(os.path.isfile("recipedir/ing2b/POSCAR"))
#CHGCAR softlink only sent to second child
self.assertFalse(os.path.exists("recipedir/ing2a/CHGCAR"))
self.assertTrue(os.path.exists("recipedir/ing2b/CHGCAR"))
def test_run_ingredient(self):
topmetad = MASTFile("files/top_metadata_single")
topmetad.data.append("origin_dir = %s/files\n" %
testdir) #give origin directory
topmetad.to_file("recipedir/metadata.txt")
#metad = MASTFile("files/metadata_single")
#metad.to_file("%s/metadata.txt" % ingdir)
rp = RecipePlan("recipedir")
rp.ingredients['ing2b'] = "I"
kdict = dict()
kdict['mast_program'] = 'vasp'
kdict['mast_xc'] = 'pw91'
kdict['mast_kpoints'] = [1, 2, 3, "G"]
rp.ingred_input_options['ing2b'] = dict()
rp.ingred_input_options['ing2b']['name'] = "recipedir/ing2b"
rp.ingred_input_options['ing2b']['program_keys'] = kdict
rp.ingred_input_options['ing2b'][
'structure'] = pymatgen.io.vaspio.Poscar.from_file(
"files/perfect_structure").structure
rp.write_methods['ing2b'] = [['write_singlerun']]
rp.write_ingredient('ing2b')
rp.run_methods['ing2b'] = [['run_singlerun']]
rp.run_ingredient('ing2b')
mysubmit = MASTFile("test_control/submitlist")
self.assertEquals(mysubmit.data[0], "recipedir/ing2b\n")
def create_workflow_test_script(inputfile):
myvars = get_variables()
# set up testing directory tree
wtdir = myvars['workflow_test_directory']
mast_test_dir = os.path.join(wtdir, "no_directory_yet")
while not (os.path.isdir(mast_test_dir)):
timestamp = time.strftime("%Y%m%dT%H%M%S")
mast_test_dir = os.path.join(wtdir, "output_test_%s" % timestamp)
if not (os.path.isdir(mast_test_dir)):
shutil.copytree("%s/mini_mast_tree" % wtdir, mast_test_dir)
# set up output file and submission script
shortname = inputfile.split(".")[0]
output = "%s/output_%s" % (wtdir, shortname)
submitscript = "%s/submit_%s.sh" % (wtdir, shortname)
generic_script = "%s/generic_mast_workflow.sh" % wtdir
bashcommand = "bash %s %s %s %s %s %s >> %s" % (
generic_script, mast_test_dir, myvars["workflow_examples_located"],
inputfile, myvars["workflow_activate_command"],
myvars["workflow_testing_environment"], output)
submitfile = MASTFile()
submitfile.data.append(bashcommand + "\n")
submitfile.to_file(submitscript)
return [mast_test_dir, submitscript, output]
def test_ready_neb_subfolders(self):
ingdir = "%s/writedir/single_label1" % testdir
recipedir = "%s/writedir" % testdir
topmetad = MASTFile("files/top_metadata_single")
topmetad.data.append("origin_dir = %s/files\n" %
testdir) #give origin directory
topmetad.to_file("writedir/metadata.txt")
metad = MASTFile("files/metadata_single")
metad.to_file("%s/metadata.txt" % ingdir)
kdict = dict()
kdict['mast_program'] = 'vasp'
kdict['mast_kpoints'] = [2, 2, 2, "M"]
kdict['mast_xc'] = 'pw91'
kdict['mast_neb_settings'] = dict()
kdict['mast_neb_settings']['images'] = 3
my_structure = pymatgen.io.vaspio.Poscar.from_file(
"files/perfect_structure").structure
mywr = ChopIngredient(name=ingdir,
program_keys=kdict,
structure=my_structure)
for subdir in ['00', '01', '02', '03', '04']:
subname = "%s/%s" % (ingdir, subdir)
os.mkdir(subname)
mywr.keywords['name'] = subname
mywr.checker.keywords['name'] = subname
if not subdir in ['00', '04']:
mywr.write_singlerun()
mywr.write_submit_script()
myrdi = ChopIngredient(name=ingdir,
program_keys=kdict,
structure=my_structure)
self.assertTrue(myrdi.ready_neb_subfolders())
os.remove("%s/01/POSCAR" % ingdir)
self.assertFalse(myrdi.ready_neb_subfolders())
def test_write_phonon_single(self):
ingdir = "writedir/single_phonon_label1"
topmetad = MASTFile("files/top_metadata_single_phonon")
topmetad.data.append("origin_dir = %s/files\n" %
testdir) #give origin directory
topmetad.to_file("writedir/metadata.txt")
metad = MASTFile("files/metadata_single_phonon")
metad.to_file("%s/metadata.txt" % ingdir)
kdict = dict()
kdict['mast_kpoints'] = [3, 3, 3, "G"]
kdict['mast_xc'] = 'pbe'
kdict['mast_program'] = 'vasp'
kdict['mast_phonon_settings'] = dict()
kdict['mast_phonon_settings']['phonon_center_site'] = "0.33 0.25 0.0"
kdict['mast_phonon_settings']['phonon_center_radius'] = "1"
kdict['mast_phonon_settings']['threshold'] = "0.075"
my_structure = pymatgen.io.vaspio.Poscar.from_file(
"files/perfect_structure").structure
mywi = ChopIngredient(name=ingdir,
program_keys=kdict,
structure=my_structure)
mywi.write_phonon_single()
self.assertTrue(mywi.checker.is_ready_to_run())
compare_phon_single = MASTFile("files/phon_single_POSCAR")
phon_singlepos = MASTFile("%s/POSCAR" % ingdir)
self.assertEqual(phon_singlepos.data, compare_phon_single.data)
def test_ready_neb_subfolders(self):
ingdir="%s/writedir/single_label1" % testdir
recipedir="%s/writedir" % testdir
topmetad = MASTFile("files/top_metadata_single")
topmetad.data.append("origin_dir = %s/files\n" % testdir) #give origin directory
topmetad.to_file("writedir/metadata.txt")
metad = MASTFile("files/metadata_single")
metad.to_file("%s/metadata.txt" % ingdir)
kdict=dict()
kdict['mast_program'] = 'vasp'
kdict['mast_kpoints'] = [2,2,2,"M"]
kdict['mast_xc'] = 'pw91'
kdict['mast_neb_settings']=dict()
kdict['mast_neb_settings']['images'] = 3
my_structure = pymatgen.io.vaspio.Poscar.from_file("files/perfect_structure").structure
mywr = ChopIngredient(name=ingdir, program_keys = kdict, structure=my_structure)
for subdir in ['00','01','02','03','04']:
subname = "%s/%s" % (ingdir, subdir)
os.mkdir(subname)
mywr.keywords['name'] = subname
mywr.checker.keywords['name'] = subname
if not subdir in ['00','04']:
mywr.write_singlerun()
mywr.write_submit_script()
myrdi = ChopIngredient(name=ingdir,program_keys=kdict, structure=my_structure)
self.assertTrue(myrdi.ready_neb_subfolders())
os.remove("%s/01/POSCAR" % ingdir)
self.assertFalse(myrdi.ready_neb_subfolders())
def change_my_status(self, newstatus):
"""Change an ingredient status by writing the new status to
change_status.txt in the ingredient folder, to get picked
up by the recipe plan.
Args:
newstatus <str>: New status to which to change the ingredient.
"""
ingdir = self.keywords['name']
oneup = os.path.dirname(ingdir)
tryrecipe = os.path.basename(oneup)
statuspath = ""
if dirutil.dir_is_in_scratch(tryrecipe):
statuspath = "%s/change_status.txt" % ingdir
else:
twoup = os.path.dirname(oneup)
tryrecipe = os.path.basename(twoup)
if dirutil.dir_is_in_scratch(tryrecipe):
statuspath = "%s/change_status.txt" % oneup
else:
raise MASTError(self.__class__.__name__, "Cannot change status of ingredient %s as recipe %s or %s is not found in $MAST_SCRATCH." % (self.keywords['name'],oneup, twoup))
if os.path.isfile(statuspath):
statusfile = MASTFile(statuspath)
else:
statusfile=MASTFile()
statusfile.data.append("%s:recommend:%s" % (newstatus, time.asctime()))
statusfile.to_file(statuspath)
self.logger.info("Recommending status change to %s" % newstatus)
def test_get_my_phonon_params(self):
ingdir = "writedir/single_phonon_label1"
topmetad = MASTFile("files/top_metadata_single_phonon")
topmetad.data.append("origin_dir = %s/files\n" %
testdir) #give origin directory
topmetad.to_file("writedir/metadata.txt")
metad = MASTFile("files/metadata_single_phonon")
metad.to_file("%s/metadata.txt" % ingdir)
kdict = dict()
kdict['mast_kpoints'] = [3, 3, 3, "G"]
kdict['mast_xc'] = 'pbe'
kdict['mast_program'] = 'vasp'
kdict['mast_phonon_settings'] = dict()
kdict['mast_phonon_settings']['phonon_center_site'] = "0.33 0.25 0.0"
kdict['mast_phonon_settings']['phonon_center_radius'] = "1"
kdict['mast_phonon_settings']['threshold'] = "0.075"
my_structure = pymatgen.io.vaspio.Poscar.from_file(
"files/perfect_structure").structure
mywi = ChopIngredient(name=ingdir,
program_keys=kdict,
structure=my_structure)
[mysite, myrad, mythresh] = mywi.get_my_phonon_params()
self.assertEqual(mysite, "0.33 0.25 0.0")
self.assertEqual(myrad, "1")
self.assertEqual(mythresh, "0.075")
def create_archive_files(self):
"""Save off archive files.
Returns:
creates archive_input_options.txt
creates archive_recipe_plan.txt
"""
inputsave = MASTFile()
inputsave.data = repr(self.input_options)
inputsave.to_file(os.path.join(self.working_directory, 'archive_input_options.txt'))
recipesave = MASTFile()
recipesave.data = repr(self.recipe_plan)
recipesave.to_file(os.path.join(self.working_directory, 'archive_recipe_plan.txt'))
#pickle_plan = os.path.join(self.working_directory, 'archive_recipe_plan.pickle')
#pm = PickleManager(pickle_plan)
#pm.save_variable(self.recipe_plan)
#pickle_options = os.path.join(self.working_directory, 'archive_input_options.pickle')
#pm = PickleManager(pickle_options)
#pm.save_variable(self.input_options)
#create the *.py input script
#ipc_obj = InputPythonCreator(input_options=self.input_options)
#ipc_filename = ipc_obj.write_script(self.working_directory, 'archive_input_options.py')
return
def test_update_children(self):
topmetad = MASTFile("files/top_metadata_single")
topmetad.data.append("origin_dir = %s/files\n" %
testdir) #give origin directory
topmetad.to_file("recipedir/metadata.txt")
#metad = MASTFile("files/metadata_single")
#metad.to_file("%s/metadata.txt" % ingdir)
rp = RecipePlan("%s/recipedir" % testdir)
rp.ingredients['ing1'] = "I"
kdict = dict()
kdict['mast_program'] = 'vasp'
kdict['mast_xc'] = 'pw91'
kdict['mast_kpoints'] = [1, 2, 3, "G"]
rp.ingred_input_options['ing1'] = dict()
rp.ingred_input_options['ing1'][
'name'] = "%s/ing1" % rp.working_directory
rp.ingred_input_options['ing1']['program_keys'] = kdict
rp.ingred_input_options['ing1'][
'structure'] = pymatgen.io.vaspio.Poscar.from_file(
"files/perfect_structure").structure
rp.update_methods['ing1'] = dict()
rp.update_methods['ing1']['ing2a'] = [['give_structure']]
rp.update_methods['ing1']['ing2b'] = [[
'give_structure_and_restart_files'
]]
rp.update_children('ing1')
self.assertTrue(os.path.isfile("recipedir/ing2a/POSCAR"))
self.assertTrue(os.path.isfile("recipedir/ing2b/POSCAR"))
#CHGCAR softlink only sent to second child
self.assertFalse(os.path.exists("recipedir/ing2a/CHGCAR"))
self.assertTrue(os.path.exists("recipedir/ing2b/CHGCAR"))
def evaluate_ga_vasp_and_update(self, childname=""):
"""Evaluate the Genetic Algorithm VASP ingredient.
"""
raise NotImplementedError
childpath = os.path.join(os.path.dirname(self.keywords['name']), childname)
from mastlib.amy_ga_code import fitness_evaluation
from MAST.ingredients.checker import VaspChecker
from MAST.utility import MASTFile
dircontents = os.listdir(self.keywords['name'])
subfolders = list()
for diritem in dircontents:
fulldir = os.path.join(self.keywords['name'],diritem)
if os.path.isdir(fulldir) and diritem.isdigit():
subfolders.append(fulldir)
energylist = list()
structurelist = list()
for subfolder in subfolders:
mychecker = VaspChecker(subfolder, self.keywords['program_keys'], self.keywords['structure'])
mystructure = mychecker.get_final_structure_from_directory()
structurelist.append(mystructure)
myenergy = mychecker.get_energy_from_energy_file()
energylist.append(myenergy)
[fitoutput, fitstructure] = fitness_evaluation.evaluate(structurelist, energylist)
#If output is a structure or xyz file, could just write it directly.
fitfile = MASTFile()
fitfile.data = fitoutput
import time
timestamp = time.strftime("%Y%m%d_%H%M%S")
outputname = "my_output_%s" % timestamp
outputstrname = "my_structure_%s" % timestamp
fitfile.to_file(os.path.join(childpath, outputname))
fitstructure.write_file(os.path.join(childpath, outputstrname))
return " %s and %s written in %s" % (outputname, outputstrname, childpath)
def test_ready_singlerun(self):
ingdir = "%s/writedir/single_label1" % testdir
recipedir = "%s/writedir" % testdir
topmetad = MASTFile("files/top_metadata_single")
topmetad.data.append("origin_dir = %s/files\n" %
testdir) #give origin directory
topmetad.to_file("writedir/metadata.txt")
metad = MASTFile("files/metadata_single")
metad.to_file("%s/metadata.txt" % ingdir)
kdict = dict()
kdict['mast_program'] = 'vasp'
kdict['mast_kpoints'] = [2, 2, 2, "M"]
kdict['mast_xc'] = 'pw91'
my_structure = pymatgen.io.vaspio.Poscar.from_file(
"files/perfect_structure").structure
mywr = ChopIngredient(name=ingdir,
program_keys=kdict,
structure=my_structure)
mywr.write_singlerun()
myrdi = ChopIngredient(name=ingdir,
program_keys=kdict,
structure=my_structure)
self.assertTrue(myrdi.ready_singlerun())
os.remove("%s/POSCAR" % ingdir)
self.assertFalse(myrdi.ready_singlerun())
def test_run_singlerun(self):
#raise SkipTest
ingdir = "%s/writedir/single_label1" % testdir
recipedir = "%s/writedir" % testdir
topmetad = MASTFile("files/top_metadata_single")
topmetad.data.append("origin_dir = %s/files\n" %
testdir) #give origin directory
topmetad.to_file("writedir/metadata.txt")
metad = MASTFile("files/metadata_single")
metad.to_file("%s/metadata.txt" % ingdir)
kdict = dict()
kdict['mast_program'] = 'vasp'
kdict['mast_kpoints'] = [2, 2, 2, "M"]
kdict['mast_xc'] = 'pw91'
my_structure = Poscar.from_file("files/perfect_structure").structure
mywr = ChopIngredient(name=ingdir,
program_keys=kdict,
structure=my_structure)
mywr.write_singlerun()
myri = ChopIngredient(name=ingdir,
program_keys=kdict,
structure=my_structure)
myri.run_singlerun()
self.assertTrue(myri.checker.is_ready_to_run())
mysubmit = MASTFile("%s/submitlist" % self.test_control)
self.assertEquals(mysubmit.data[0], "%s\n" % ingdir)
def test_parse(self):
#ipfile='small_workflow_with_scaling.inp'
ipfile = 'phonon_with_neb.inp'
workdir = os.path.join(testdir, 'workdir')
shutil.copy(os.path.join(testdir, ipfile), workdir)
input_file = os.path.join(workdir, ipfile)
parser_obj = InputParser(inputfile=input_file)
input_options = parser_obj.parse()
recipe_file_contents = input_options.get_item('recipe', 'recipe_file')
myrtp = RecipeTemplateParser(inputOptions=input_options,
working_directory=workdir,
templateFile=recipe_file_contents,
personalRecipe=input_file)
parsed_lines = myrtp.parse()
output_parsed = MASTFile()
output_parsed.data = list(parsed_lines)
output_parsed.to_file('workdir/personal_recipe_test_output.txt')
self.assertEquals(len(myrtp.chunks), 5)
#mypr = MASTFile(pr)
#for line in mypr.data:
# print line.rstrip()
compare_pr = MASTFile(
os.path.join(testdir, 'compare',
'personal_recipe_test_output.txt'))
self.assertEquals(parsed_lines, compare_pr.data)
def test_get_parent_image_structures(self):
kdict=dict()
kdict['mast_program'] = 'vasp_neb'
neblines = list()
neblines.append(["Cr","0.0 0.9 0.8","0.0 0.8 0.7"])
neblines.append(["Cr","0.4 0.2 0.1","0.3 0.3 0.2"])
neblines.append(["Cr","0.29 0.05 0.05","0.01 0.01 0.98"])
neblines.append(["Ni","0.61 0.99 0.98","0.25 0.01 0.97"])
kdict['mast_neb_settings']=dict()
kdict['mast_neb_settings']['images']=3
kdict['mast_neb_settings']['lines']=neblines
ingdir = "writedir/neb_labelinit-labelfin"
topmetad = MASTFile("files/top_metadata_neb")
topmetad.to_file("writedir/metadata.txt")
metad = MASTFile("files/metadata_neb")
metad.to_file("%s/metadata.txt" % ingdir)
unsorted_01 = MASTFile("unsorted/parent_structure_labelinit-labelfin_01")
unsorted_01.to_file("%s/parent_structure_labelinit-labelfin_01" % ingdir)
unsorted_02 = MASTFile("unsorted/parent_structure_labelinit-labelfin_02")
unsorted_02.to_file("%s/parent_structure_labelinit-labelfin_02" % ingdir)
unsorted_03 = MASTFile("unsorted/parent_structure_labelinit-labelfin_03")
unsorted_03.to_file("%s/parent_structure_labelinit-labelfin_03" % ingdir)
my_structure=pymatgen.io.vaspio.Poscar.from_file("files/perfect_structure").structure
mywi = ChopIngredient(name=ingdir,program_keys=kdict,structure=my_structure)
imstrs = mywi.get_parent_image_structures()
compare_01 = pymatgen.io.vaspio.Poscar.from_file("files/parent_structure_labelinit-labelfin_01").structure
compare_02 = pymatgen.io.vaspio.Poscar.from_file("files/parent_structure_labelinit-labelfin_02").structure
compare_03 = pymatgen.io.vaspio.Poscar.from_file("files/parent_structure_labelinit-labelfin_03").structure
self.assertEqual(imstrs[0].sites, compare_01.sites)
self.assertEqual(imstrs[0].lattice, compare_01.lattice)
self.assertEqual(imstrs[1].sites, compare_02.sites)
self.assertEqual(imstrs[1].lattice, compare_02.lattice)
self.assertEqual(imstrs[2].sites, compare_03.sites)
self.assertEqual(imstrs[2].lattice, compare_03.lattice)
def test_check_if_ready_to_proceed_are_complete(self):
metad = MASTFile("files/metadata_single")
metad.to_file("recipedir/ing1/metadata.txt")
metad = MASTFile("files/metadata_single")
metad.to_file("recipedir/ing2a/metadata.txt")
rp = RecipePlan("recipedir")
rp.ingredients['ing1'] = "P"
rp.ingredients['ing2a'] = "I"
rp.ingredients['ing2b'] = "I"
rp.ingredients['ing3'] = "I"
kdict=dict()
kdict['mast_program']='vasp'
kdict['mast_xc']='pw91'
kdict['mast_kpoints']=[1,2,3,"G"]
my_struc = pymatgen.io.vaspio.Poscar.from_file("files/perfect_structure").structure
rp.ingred_input_options['ing1']=dict()
rp.ingred_input_options['ing1']['name']="%s/recipedir/ing1" % testdir
rp.ingred_input_options['ing1']['program_keys']=kdict
rp.ingred_input_options['ing1']['structure']=my_struc
rp.complete_methods['ing1']=[['complete_singlerun']]
rp.update_methods['ing1']=dict()
rp.update_methods['ing1']['ing2a']=[['give_structure']]
rp.update_methods['ing1']['ing2b']=[['give_structure']]
rp.ingred_input_options['ing2a']=dict()
rp.ingred_input_options['ing2a']['name']="%s/recipedir/ing2a" % testdir
rp.ingred_input_options['ing2a']['program_keys']=kdict
rp.ingred_input_options['ing2a']['structure']=my_struc
rp.complete_methods['ing2a']=[['complete_singlerun']]
rp.ready_methods['ing2a']=[['ready_structure']]
rp.check_if_ready_to_proceed_are_complete()
self.assertTrue(rp.ready_ingredient('ing2a'))
self.assertEquals
self.assertEquals(rp.ingredients,{'ing1':'C','ing2a':'I','ing2b':'I','ing3':'I'})
def test_give_structure_and_charge_density_full_copy(self):
ingdir = "%s/writedir/single_label1" % testdir
recipedir = "%s/writedir" % testdir
topmetad = MASTFile("files/top_metadata_single")
topmetad.data.append("origin_dir = %s/files\n" %
testdir) #give origin directory
topmetad.to_file("writedir/metadata.txt")
metad = MASTFile("files/metadata_single")
metad.to_file("%s/metadata.txt" % ingdir)
kdict = dict()
kdict['mast_program'] = 'vasp'
my_structure = pymatgen.io.vaspio.Poscar.from_file(
"files/perfect_structure").structure
myrelaxed = MASTFile("files/relaxed_structure")
myrelaxed.to_file("%s/CONTCAR" % ingdir)
mychg = MASTFile("files/CHGCAR")
mychg.to_file("%s/CHGCAR" % ingdir)
mywave = MASTFile("files/WAVECAR")
mywave.to_file("%s/WAVECAR" % ingdir)
myuci = ChopIngredient(name=ingdir,
program_keys=kdict,
structure=my_structure)
myuci.give_structure_and_charge_density_full_copy("next_ingred")
givenstr = MASTFile("%s/writedir/next_ingred/POSCAR" % testdir)
self.assertEqual(myrelaxed.data, givenstr.data)
self.assertTrue(
os.path.exists("%s/writedir/next_ingred/CHGCAR" % testdir))
def test_fast_forward_check_complete(self):
topmetad = MASTFile("files/top_metadata_single")
topmetad.data.append("origin_dir = %s/files\n" % testdir) #give origin directory
topmetad.to_file("recipedir/metadata.txt")
metad = MASTFile("files/metadata_single")
metad.to_file("recipedir/ing1/metadata.txt")
metad = MASTFile("files/metadata_single")
metad.data.append("defect_label = labela\n")
metad.to_file("recipedir/ing2a/metadata.txt")
metad = MASTFile("files/metadata_single")
metad.data.append("defect_label = labelb\n")
metad.to_file("recipedir/ing2b/metadata.txt")
metad = MASTFile("files/metadata_single")
metad.to_file("recipedir/ing3/metadata.txt")
rp = RecipePlan("recipedir")
rp.ingredients['ing1'] = "I"
rp.ingredients['ing2a'] = "I"
rp.ingredients['ing2b'] = "I"
rp.ingredients['ing3'] = "I"
kdict=dict()
kdict['mast_program']='vasp'
kdict['mast_xc']='pw91'
kdict['mast_kpoints']=[1,2,3,"G"]
my_struc = pymatgen.io.vaspio.Poscar.from_file("files/perfect_structure").structure
rp.ingred_input_options['ing1']=dict()
rp.ingred_input_options['ing1']['name']="%s/recipedir/ing1" % testdir
rp.ingred_input_options['ing1']['program_keys']=kdict
rp.ingred_input_options['ing1']['structure']=my_struc
rp.complete_methods['ing1']=[['complete_singlerun']]
rp.update_methods['ing1']=dict()
rp.update_methods['ing1']['ing2a']=[['give_structure']]
rp.update_methods['ing1']['ing2b']=[['give_structure']]
rp.ingred_input_options['ing2a']=dict()
rp.ingred_input_options['ing2a']['name']="%s/recipedir/ing2a" % testdir
rp.ingred_input_options['ing2a']['program_keys']=kdict
rp.ingred_input_options['ing2a']['structure']=my_struc
rp.complete_methods['ing2a']=[['complete_singlerun']]
rp.ready_methods['ing2a']=[['ready_structure']]
rp.ingred_input_options['ing2b']=dict()
rp.ingred_input_options['ing2b']['name']="%s/recipedir/ing2b" % testdir
rp.ingred_input_options['ing2b']['program_keys']=kdict
rp.ingred_input_options['ing2b']['structure']=my_struc
rp.complete_methods['ing2b']=[['complete_singlerun']]
rp.ready_methods['ing2b']=[['ready_structure']]
rp.ingred_input_options['ing3']=dict()
rp.ingred_input_options['ing3']['name']="%s/recipedir/ing3" % testdir
rp.ingred_input_options['ing3']['program_keys']=kdict
rp.ingred_input_options['ing3']['structure']=my_struc
rp.complete_methods['ing3']=[['complete_singlerun']]
rp.ready_methods['ing3']=[['ready_structure']]
rp.fast_forward_check_complete()
#self.assertTrue(rp.complete_ingredient('ing1'))
self.assertEquals(rp.ingredients, {'ing1':'C','ing2a':'I','ing2b':'I','ing3':'I'})
self.assertTrue(rp.ready_ingredient('ing2a'))
self.assertTrue(rp.ready_ingredient('ing2b'))
def test_inputpythoncreator(self):
raise SkipTest
myip = InputParser(inputfile='mast.inp')
myoptions=myip.parse()
myipc = InputPythonCreator(input_options=myoptions)
mylines=myipc.print_input_options()
myfile = MASTFile()
myfile.data = mylines
myfile.to_file("./input_python_created")
#print mylines
self.assertTrue(filecmp.cmp("input_python_created","test_input_python_created"))
def test__fullpath_childname(self):
ingdir="%s/writedir/single_label1" % testdir
topmetad = MASTFile("files/top_metadata_single")
topmetad.data.append("origin_dir = %s/files\n" % testdir) #give origin directory
topmetad.to_file("writedir/metadata.txt")
metad = MASTFile("files/metadata_single")
metad.to_file("%s/metadata.txt" % ingdir)
kdict=dict()
kdict['mast_program'] = 'vasp'
my_structure = pymatgen.io.vaspio.Poscar.from_file("files/perfect_structure").structure
myuci = ChopIngredient(name=ingdir,program_keys=kdict,structure=my_structure)
fullpath = myuci._fullpath_childname("next_ingred")
self.assertEqual(fullpath, "%s/writedir/next_ingred" % testdir)
def test_complete_subfolders(self):
#raise SkipTest
ingdir="%s/writedir/single_label1" % testdir
recipedir="%s/writedir" % testdir
topmetad = MASTFile("files/top_metadata_single")
topmetad.data.append("origin_dir = %s/files\n" % testdir) #give origin directory
topmetad.to_file("writedir/metadata.txt")
metad = MASTFile("files/metadata_single")
metad.to_file("%s/metadata.txt" % ingdir)
kdict=dict()
kdict['mast_program'] = 'vasp'
kdict['mast_kpoints'] = [2,2,2,"M"]
kdict['mast_xc'] = 'pw91'
my_structure = pymatgen.io.vaspio.Poscar.from_file("files/perfect_structure").structure
mywr = ChopIngredient(name=ingdir, program_keys = kdict, structure=my_structure)
myoutcar = MASTFile("files/OUTCAR_completed")
myoszicar = MASTFile("files/OSZICAR_completed")
for subdir in ['00','01','02','03','04']:
subname = "%s/%s" % (ingdir, subdir)
os.mkdir(subname)
mywr.keywords['name'] = subname
mywr.checker.keywords['name'] = subname
mywr.write_singlerun()
mywr.write_submit_script()
myoutcar.to_file("%s/OUTCAR" % subname)
myoszicar.to_file("%s/OSZICAR" % subname)
myci = ChopIngredient(name=ingdir,program_keys=kdict, structure=my_structure)
self.assertTrue(myci.complete_subfolders())
os.remove("%s/04/OUTCAR" % ingdir)
self.assertFalse(myci.complete_subfolders())
def test_place_parent_energy_files(self):
ingdir = "writedir/neb_labelinit-labelfin"
topmetad = MASTFile("files/top_metadata_neb")
topmetad.data.append("origin_dir = %s/files\n" %
testdir) #give origin directory
topmetad.to_file("writedir/metadata.txt")
metad = MASTFile("files/metadata_neb")
metad.to_file("%s/metadata.txt" % ingdir)
peinit = MASTFile("files/parent_energy_labelinit")
peinit.to_file("%s/parent_energy_labelinit" % ingdir)
pefin = MASTFile("files/parent_energy_labelfin")
pefin.to_file("%s/parent_energy_labelfin" % ingdir)
kdict = dict()
kdict['mast_kpoints'] = [3, 3, 3, "G"]
kdict['mast_xc'] = 'pbe'
kdict['mast_program'] = 'vasp_neb'
kdict['mast_neb_settings'] = dict()
kdict['mast_neb_settings']['images'] = 3
my_structure = pymatgen.io.vaspio.Poscar.from_file(
"files/perfect_structure").structure
mywi = ChopIngredient(name=ingdir,
program_keys=kdict,
structure=my_structure)
os.mkdir(ingdir + '/00')
os.mkdir(ingdir + '/04')
mywi.place_parent_energy_files()
self.assertTrue(os.path.isfile(ingdir + '/00/OSZICAR'))
self.assertTrue(os.path.isfile(ingdir + '/04/OSZICAR'))
oszinit = MASTFile(ingdir + "/00/OSZICAR")
oszfinal = MASTFile(ingdir + "/04/OSZICAR")
self.assertEqual(oszinit.data, peinit.data)
self.assertEqual(oszfinal.data, pefin.data)
def test_get_parent_structures(self):
kdict=dict()
kdict['mast_program'] = 'vasp_neb'
neblines = list()
neblines.append(["Cr","0.0 0.9 0.8","0.0 0.8 0.7"])
neblines.append(["Cr","0.4 0.2 0.1","0.3 0.3 0.2"])
neblines.append(["Cr","0.29 0.05 0.05","0.01 0.01 0.98"])
neblines.append(["Ni","0.61 0.99 0.98","0.25 0.01 0.97"])
kdict['mast_neb_settings']=dict()
kdict['mast_neb_settings']['images']=3
kdict['mast_neb_settings']['lines']=neblines
ingdir = "writedir/neb_labelinit-labelfin"
topmetad = MASTFile("files/top_metadata_neb")
topmetad.to_file("writedir/metadata.txt")
metad = MASTFile("files/metadata_neb")
metad.to_file("%s/metadata.txt" % ingdir)
unsorted_init = MASTFile("unsorted/parent_structure_labelinit")
#unsorted_init = MASTFile("unsorted/parent_structure_labelinit_scrambled")
unsorted_init.to_file("%s/parent_structure_labelinit" % ingdir)
unsorted_fin = MASTFile("unsorted/parent_structure_labelfin")
unsorted_fin.to_file("%s/parent_structure_labelfin" % ingdir)
my_structure=pymatgen.io.vaspio.Poscar.from_file("files/perfect_structure").structure
mywi = ChopIngredient(name=ingdir,program_keys=kdict,structure=my_structure)
[sinit, sfin] = mywi.get_parent_structures()
init_compare = pymatgen.io.vaspio.Poscar.from_file("files/parent_structure_labelinit").structure
fin_compare = pymatgen.io.vaspio.Poscar.from_file("files/parent_structure_labelfin").structure
#print sinit
#print init_compare
#print sfin
#print fin_compare
self.assertEqual(sinit.sites, init_compare.sites)
self.assertEqual(sinit.lattice, init_compare.lattice)
self.assertEqual(sfin.sites, fin_compare.sites)
self.assertEqual(sfin.lattice, fin_compare.lattice)
def test_place_parent_energy_files(self):
ingdir="writedir/neb_labelinit-labelfin"
topmetad = MASTFile("files/top_metadata_neb")
topmetad.data.append("origin_dir = %s/files\n" % testdir) #give origin directory
topmetad.to_file("writedir/metadata.txt")
metad = MASTFile("files/metadata_neb")
metad.to_file("%s/metadata.txt" % ingdir)
peinit = MASTFile("files/parent_energy_labelinit")
peinit.to_file("%s/parent_energy_labelinit" % ingdir)
pefin = MASTFile("files/parent_energy_labelfin")
pefin.to_file("%s/parent_energy_labelfin" % ingdir)
kdict=dict()
kdict['mast_kpoints']=[3,3,3,"G"]
kdict['mast_xc']='pbe'
kdict['mast_program']='vasp_neb'
kdict['mast_neb_settings']=dict()
kdict['mast_neb_settings']['images']=3
my_structure=pymatgen.io.vaspio.Poscar.from_file("files/perfect_structure").structure
mywi = ChopIngredient(name=ingdir,program_keys=kdict,structure=my_structure)
os.mkdir(ingdir + '/00')
os.mkdir(ingdir + '/04')
mywi.place_parent_energy_files()
self.assertTrue(os.path.isfile(ingdir + '/00/OSZICAR'))
self.assertTrue(os.path.isfile(ingdir + '/04/OSZICAR'))
oszinit = MASTFile(ingdir + "/00/OSZICAR")
oszfinal = MASTFile(ingdir + "/04/OSZICAR")
self.assertEqual(oszinit.data, peinit.data)
self.assertEqual(oszfinal.data, pefin.data)
def test_give_structure_and_energy_to_neb(self):
ingdir = "%s/writedir/single_label1" % testdir
recipedir = "%s/writedir" % testdir
topmetad = MASTFile("files/top_metadata_single")
topmetad.data.append("origin_dir = %s/files\n" %
testdir) #give origin directory
topmetad.to_file("writedir/metadata.txt")
metad = MASTFile("files/metadata_single")
metad.data.append("defect_label = label1\n")
metad.to_file("%s/metadata.txt" % ingdir)
kdict = dict()
kdict['mast_program'] = 'vasp'
my_structure = pymatgen.io.vaspio.Poscar.from_file(
"files/perfect_structure").structure
myrelaxed = MASTFile("files/relaxed_structure")
myrelaxed.to_file("%s/CONTCAR" % ingdir)
myenergy = MASTFile("files/OSZICAR_relaxed")
myenergy.to_file("%s/OSZICAR" % ingdir)
myuci = ChopIngredient(name=ingdir,
program_keys=kdict,
structure=my_structure)
myuci.give_structure_and_energy_to_neb("next_ingred")
givenstr = MASTFile("%s/writedir/next_ingred/parent_structure_label1" %
testdir)
givenenergy = MASTFile("%s/writedir/next_ingred/parent_energy_label1" %
testdir)
self.assertEqual(myrelaxed.data, givenstr.data)
self.assertEqual(myenergy.data, givenenergy.data)
def test_get_statuses_from_file(self):
rp = RecipePlan("recipedir")
mystatus = MASTFile("files/status_random.txt")
self.assertRaises(MASTError, rp.get_statuses_from_file)
mystatus.to_file("recipedir/status.txt")
rp.ingredients['ing1']="I"
rp.ingredients['ing2a']="I"
rp.ingredients['ing2b']="I"
self.assertRaises(MASTError,rp.get_statuses_from_file)
rp.ingredients['ing3']="I"
rp.get_statuses_from_file()
statusdict=dict()
statusdict={'ing1':'alpha','ing2a':'beta','ing2b':'gamma','ing3':'delta'}
self.assertEquals(rp.ingredients, statusdict)
def test_write_singlerun(self):
ingdir="writedir/single_label1"
topmetad = MASTFile("files/top_metadata_single")
topmetad.data.append("origin_dir = %s/files\n" % testdir) #give origin directory
topmetad.to_file("writedir/metadata.txt")
metad = MASTFile("files/metadata_single")
metad.to_file("%s/metadata.txt" % ingdir)
kdict=dict()
kdict['mast_kpoints']=[3,3,3,"G"]
kdict['mast_xc']='pbe'
kdict['mast_program']='vasp'
my_structure=pymatgen.io.vaspio.Poscar.from_file("files/perfect_structure").structure
mywi = ChopIngredient(name=ingdir,program_keys=kdict,structure=my_structure)
mywi.write_singlerun()
self.assertTrue(mywi.checker.is_ready_to_run())
def create_archive_files(self):
"""Save off archive files.
Returns:
creates archive_input_options.txt
creates archive_recipe_plan.txt
"""
inputsave = MASTFile()
inputsave.data = repr(self.input_options)
inputsave.to_file(os.path.join(self.recdir, 'archive_input_options_%s.txt' % self.timestamp))
recipesave = MASTFile()
recipesave.data = repr(self.recipe_plan)
recipesave.to_file(os.path.join(self.recdir, 'archive_recipe_plan_%s.txt' % self.timestamp))
return
def print_table(self,scsize):
if not self.e_defects:
self._calculate_defect_formation_energies(scsize)
myfile = MASTFile()
for conditions, defects in self.e_defects.items():
myfile.data.append('\n\nDefect formation energies for %s conditions.\n' % conditions.upper())
myfile.data.append('%-20s | %10s\n' % ('Defect', 'DFE'))
myfile.data.append('---------------------------------\n')
for defect, energies in defects.items():
for energy in energies:
myfile.data.append('%-14s(q=%2i) | %8.4f\n' % (defect, energy[0], energy[1]))
myfile.data.append(str()) # Add a blank line here
myfile.data.append('---------------------------------\n')
myfile.to_file(os.path.join(os.getcwd(),"dfe.txt"))
for line in myfile.data:
print line.strip()
def test__fullpath_childname(self):
ingdir = "%s/writedir/single_label1" % testdir
topmetad = MASTFile("files/top_metadata_single")
topmetad.data.append("origin_dir = %s/files\n" %
testdir) #give origin directory
topmetad.to_file("writedir/metadata.txt")
metad = MASTFile("files/metadata_single")
metad.to_file("%s/metadata.txt" % ingdir)
kdict = dict()
kdict['mast_program'] = 'vasp'
my_structure = pymatgen.io.vaspio.Poscar.from_file(
"files/perfect_structure").structure
myuci = ChopIngredient(name=ingdir,
program_keys=kdict,
structure=my_structure)
fullpath = myuci._fullpath_childname("next_ingred")
self.assertEqual(fullpath, "%s/writedir/next_ingred" % testdir)
def test_vasp_kpoints_setup_from_metafile(self):
kdict = dict()
mymeta = MASTFile("childdir/metadata.txt")
mymeta.data.append("kpoints = 3x1x7 G 0.5 0.2 .1\n")
mymeta.to_file("childdir/metadata.txt")
mymeta2 = MASTFile("childdir/metadata.txt")
print mymeta2.data
myvc = VaspChecker(name="childdir", program_keys=kdict)
mykpt = myvc._vasp_kpoints_setup()
kpt_compare = pymatgen.io.vaspio.Kpoints.from_file("files/KPOINTS_317G")
self.assertEqual(kpt_compare.kpts[0][0], mykpt.kpts[0][0])
self.assertEqual(kpt_compare.kpts[0][1], mykpt.kpts[0][1])
self.assertEqual(kpt_compare.kpts[0][2], mykpt.kpts[0][2])
self.assertEqual(kpt_compare.num_kpts, mykpt.num_kpts)
self.assertEqual(kpt_compare.style, mykpt.style)
# self.assertEqual(kpt_compare.kpts_shift, mykpt.kpts_shift)
self.assertEqual((0.5, 0.2, 0.1), mykpt.kpts_shift)
def test_get_parent_image_structures(self):
kdict = dict()
kdict['mast_program'] = 'vasp_neb'
neblines = list()
neblines.append(["Cr", "0.0 0.9 0.8", "0.0 0.8 0.7"])
neblines.append(["Cr", "0.4 0.2 0.1", "0.3 0.3 0.2"])
neblines.append(["Cr", "0.29 0.05 0.05", "0.01 0.01 0.98"])
neblines.append(["Ni", "0.61 0.99 0.98", "0.25 0.01 0.97"])
kdict['mast_neb_settings'] = dict()
kdict['mast_neb_settings']['images'] = 3
kdict['mast_neb_settings']['lines'] = neblines
ingdir = "writedir/neb_labelinit-labelfin"
topmetad = MASTFile("files/top_metadata_neb")
topmetad.to_file("writedir/metadata.txt")
metad = MASTFile("files/metadata_neb")
metad.to_file("%s/metadata.txt" % ingdir)
unsorted_01 = MASTFile(
"unsorted/parent_structure_labelinit-labelfin_01")
unsorted_01.to_file("%s/parent_structure_labelinit-labelfin_01" %
ingdir)
unsorted_02 = MASTFile(
"unsorted/parent_structure_labelinit-labelfin_02")
unsorted_02.to_file("%s/parent_structure_labelinit-labelfin_02" %
ingdir)
unsorted_03 = MASTFile(
"unsorted/parent_structure_labelinit-labelfin_03")
unsorted_03.to_file("%s/parent_structure_labelinit-labelfin_03" %
ingdir)
my_structure = pymatgen.io.vaspio.Poscar.from_file(
"files/perfect_structure").structure
mywi = ChopIngredient(name=ingdir,
program_keys=kdict,
structure=my_structure)
imstrs = mywi.get_parent_image_structures()
compare_01 = pymatgen.io.vaspio.Poscar.from_file(
"files/parent_structure_labelinit-labelfin_01").structure
compare_02 = pymatgen.io.vaspio.Poscar.from_file(
"files/parent_structure_labelinit-labelfin_02").structure
compare_03 = pymatgen.io.vaspio.Poscar.from_file(
"files/parent_structure_labelinit-labelfin_03").structure
self.assertEqual(imstrs[0].sites, compare_01.sites)
self.assertEqual(imstrs[0].lattice, compare_01.lattice)
self.assertEqual(imstrs[1].sites, compare_02.sites)
self.assertEqual(imstrs[1].lattice, compare_02.lattice)
self.assertEqual(imstrs[2].sites, compare_03.sites)
self.assertEqual(imstrs[2].lattice, compare_03.lattice)
def test_vasp_kpoints_setup_from_metafile(self):
kdict = dict()
mymeta = MASTFile("childdir/metadata.txt")
mymeta.data.append("kpoints = 3x1x7 G 0.5 0.2 .1\n")
mymeta.to_file("childdir/metadata.txt")
mymeta2 = MASTFile("childdir/metadata.txt")
print mymeta2.data
myvc = VaspChecker(name="childdir", program_keys=kdict)
mykpt = myvc._vasp_kpoints_setup()
kpt_compare = pymatgen.io.vaspio.Kpoints.from_file(
"files/KPOINTS_317G")
self.assertEqual(kpt_compare.kpts[0][0], mykpt.kpts[0][0])
self.assertEqual(kpt_compare.kpts[0][1], mykpt.kpts[0][1])
self.assertEqual(kpt_compare.kpts[0][2], mykpt.kpts[0][2])
self.assertEqual(kpt_compare.num_kpts, mykpt.num_kpts)
self.assertEqual(kpt_compare.style, mykpt.style)
#self.assertEqual(kpt_compare.kpts_shift, mykpt.kpts_shift)
self.assertEqual((0.5, 0.2, 0.1), mykpt.kpts_shift)
def test_ready_structure(self):
ingdir="%s/writedir/single_label1" % testdir
recipedir="%s/writedir" % testdir
topmetad = MASTFile("files/top_metadata_single")
topmetad.data.append("origin_dir = %s/files\n" % testdir) #give origin directory
topmetad.to_file("writedir/metadata.txt")
metad = MASTFile("files/metadata_single")
metad.to_file("%s/metadata.txt" % ingdir)
kdict=dict()
kdict['mast_program'] = 'vasp'
kdict['mast_kpoints'] = [2,2,2,"M"]
kdict['mast_xc'] = 'pw91'
my_pos = pymatgen.io.vaspio.Poscar.from_file("files/perfect_structure")
my_pos.write_file("writedir/single_label1/POSCAR")
myrdi = ChopIngredient(name=ingdir,program_keys=kdict, structure=my_pos.structure)
self.assertTrue(myrdi.ready_structure())
os.remove("%s/POSCAR" % ingdir)
self.assertFalse(myrdi.ready_structure())
def test_complete_ingredient(self):
topmetad = MASTFile("files/top_metadata_single")
topmetad.data.append("origin_dir = %s/files\n" % testdir) #give origin directory
topmetad.to_file("recipedir/metadata.txt")
#metad = MASTFile("files/metadata_single")
#metad.to_file("%s/metadata.txt" % ingdir)
rp = RecipePlan("recipedir")
rp.ingredients['ing1'] = "I"
kdict=dict()
kdict['mast_program']='vasp'
kdict['mast_xc']='pw91'
kdict['mast_kpoints']=[1,2,3,"G"]
rp.ingred_input_options['ing1']=dict()
rp.ingred_input_options['ing1']['name']="%s/recipedir/ing1" % testdir
rp.ingred_input_options['ing1']['program_keys']=kdict
rp.ingred_input_options['ing1']['structure']=pymatgen.io.vaspio.Poscar.from_file("files/perfect_structure").structure
rp.complete_methods['ing1']=[['complete_singlerun']]
self.assertTrue(rp.complete_ingredient('ing1'))
def print_table(self, scsize):
if not self.e_defects:
self._calculate_defect_formation_energies(scsize)
myfile = MASTFile()
for conditions, defects in self.e_defects.items():
myfile.data.append(
'\n\nDefect formation energies for %s conditions.\n' %
conditions.upper())
myfile.data.append('%-20s | %10s\n' % ('Defect', 'DFE'))
myfile.data.append('---------------------------------\n')
for defect, energies in defects.items():
for energy in energies:
myfile.data.append('%-14s(q=%2i) | %8.4f\n' %
(defect, energy[0], energy[1]))
myfile.data.append(str()) # Add a blank line here
myfile.data.append('---------------------------------\n')
myfile.to_file(os.path.join(os.getcwd(), "dfe.txt"))
for line in myfile.data:
print line.strip()
def test_write_singlerun(self):
ingdir = "writedir/single_label1"
topmetad = MASTFile("files/top_metadata_single")
topmetad.data.append("origin_dir = %s/files\n" %
testdir) #give origin directory
topmetad.to_file("writedir/metadata.txt")
metad = MASTFile("files/metadata_single")
metad.to_file("%s/metadata.txt" % ingdir)
kdict = dict()
kdict['mast_kpoints'] = [3, 3, 3, "G"]
kdict['mast_xc'] = 'pbe'
kdict['mast_program'] = 'vasp'
my_structure = pymatgen.io.vaspio.Poscar.from_file(
"files/perfect_structure").structure
mywi = ChopIngredient(name=ingdir,
program_keys=kdict,
structure=my_structure)
mywi.write_singlerun()
self.assertTrue(mywi.checker.is_ready_to_run())
def test_get_statuses_from_file(self):
rp = RecipePlan("recipedir")
mystatus = MASTFile("files/status_random.txt")
self.assertRaises(MASTError, rp.get_statuses_from_file)
mystatus.to_file("recipedir/status.txt")
rp.ingredients['ing1'] = "I"
rp.ingredients['ing2a'] = "I"
rp.ingredients['ing2b'] = "I"
self.assertRaises(MASTError, rp.get_statuses_from_file)
rp.ingredients['ing3'] = "I"
rp.get_statuses_from_file()
statusdict = dict()
statusdict = {
'ing1': 'alpha',
'ing2a': 'beta',
'ing2b': 'gamma',
'ing3': 'delta'
}
self.assertEquals(rp.ingredients, statusdict)
def create_archive_files(self):
"""Save off archive files.
Returns:
creates archive_input_options.txt
creates archive_recipe_plan.txt
"""
inputsave = MASTFile()
inputsave.data = repr(self.input_options)
inputsave.to_file(
os.path.join(self.recdir,
'archive_input_options_%s.txt' % self.timestamp))
recipesave = MASTFile()
recipesave.data = repr(self.recipe_plan)
recipesave.to_file(
os.path.join(self.recdir,
'archive_recipe_plan_%s.txt' % self.timestamp))
return
def test_write_singlerun_automesh(self):
ingdir="writedir/single_label1"
topmetad = MASTFile("files/top_metadata_single")
topmetad.data.append("origin_dir = %s/files\n" % testdir) #give origin directory
topmetad.to_file("writedir/metadata.txt")
metad = MASTFile("files/metadata_single")
metad.to_file("%s/metadata.txt" % ingdir)
kdict=dict()
kdict['mast_kpoints']=[3,3,3,"G"]
kdict['mast_xc']='pbe'
kdict['mast_program']='vasp'
kdict['mast_kpoint_density']='1000'
mypos=pymatgen.io.vaspio.Poscar.from_file("files/perfect_structure")
mypos.write_file("writedir/single_label1/POSCAR")
mywi = ChopIngredient(name=ingdir,program_keys=kdict,structure=mypos.structure)
mywi.write_singlerun_automesh()
mykpts = pymatgen.io.vaspio.Kpoints.from_file("writedir/single_label1/KPOINTS")
self.assertEqual(mykpts.to_dict['kpoints'][0],[8,8,8])
#print mykpts
self.assertTrue(mywi.checker.is_ready_to_run())
def main():
recipe_name, script_head_dir = parse_arguments()
mast_scratch = dirutil.get_mast_scratch_path()
mymon = MASTMon()
my_recipe_plan = mymon.set_up_recipe_plan(os.path.join(mast_scratch, recipe_name), 1)
my_dag_contents=list()
for iname in my_recipe_plan.ingredients: #all JOB lines need to be at top
my_dag_contents.append("JOB %s submit.sh DIR %s\n" % (iname, iname))
for iname in my_recipe_plan.ingredients:
my_dag_contents.append("SCRIPT PRE %s %s/mast_do_setup.sh %s %s\n" % (iname, script_head_dir, recipe_name, iname))
my_dag_contents.append("SCRIPT POST %s %s/mast_check_is_complete.sh %s %s\n" % (iname, script_head_dir, recipe_name, iname))
my_dag_contents.append("RETRY %s 5\n" % iname)
ptc = list(my_recipe_plan.parents_to_check[iname])
for pname in ptc:
my_dag_contents.append("PARENT %s CHILD %s\n" % (pname, iname))
my_dag_file = MASTFile()
my_dag_file.data = my_dag_contents
my_dag_file.to_file(os.path.join(mast_scratch, recipe_name, "recipe.dag"))
#print_to_file(recipe_name, ing_name, "MAIN: is complete: %s" % is_complete)
return 0
def test_complete_ingredient(self):
topmetad = MASTFile("files/top_metadata_single")
topmetad.data.append("origin_dir = %s/files\n" %
testdir) #give origin directory
topmetad.to_file("recipedir/metadata.txt")
#metad = MASTFile("files/metadata_single")
#metad.to_file("%s/metadata.txt" % ingdir)
rp = RecipePlan("recipedir")
rp.ingredients['ing1'] = "I"
kdict = dict()
kdict['mast_program'] = 'vasp'
kdict['mast_xc'] = 'pw91'
kdict['mast_kpoints'] = [1, 2, 3, "G"]
rp.ingred_input_options['ing1'] = dict()
rp.ingred_input_options['ing1']['name'] = "%s/recipedir/ing1" % testdir
rp.ingred_input_options['ing1']['program_keys'] = kdict
rp.ingred_input_options['ing1'][
'structure'] = pymatgen.io.vaspio.Poscar.from_file(
"files/perfect_structure").structure
rp.complete_methods['ing1'] = [['complete_singlerun']]
self.assertTrue(rp.complete_ingredient('ing1'))
def test_get_my_phonon_params(self):
ingdir="writedir/single_phonon_label1"
topmetad = MASTFile("files/top_metadata_single_phonon")
topmetad.data.append("origin_dir = %s/files\n" % testdir) #give origin directory
topmetad.to_file("writedir/metadata.txt")
metad = MASTFile("files/metadata_single_phonon")
metad.to_file("%s/metadata.txt" % ingdir)
kdict=dict()
kdict['mast_kpoints']=[3,3,3,"G"]
kdict['mast_xc']='pbe'
kdict['mast_program']='vasp'
kdict['mast_phonon_settings']=dict()
kdict['mast_phonon_settings']['phonon_center_site']="0.33 0.25 0.0"
kdict['mast_phonon_settings']['phonon_center_radius']="1"
kdict['mast_phonon_settings']['threshold']="0.075"
my_structure=pymatgen.io.vaspio.Poscar.from_file("files/perfect_structure").structure
mywi = ChopIngredient(name=ingdir,program_keys=kdict,structure=my_structure)
[mysite, myrad, mythresh] = mywi.get_my_phonon_params()
self.assertEqual(mysite,"0.33 0.25 0.0")
self.assertEqual(myrad,"1")
self.assertEqual(mythresh,"0.075")
def test_run_singlerun(self):
#raise SkipTest
ingdir="%s/writedir/single_label1" % testdir
recipedir="%s/writedir" % testdir
topmetad = MASTFile("files/top_metadata_single")
topmetad.data.append("origin_dir = %s/files\n" % testdir) #give origin directory
topmetad.to_file("writedir/metadata.txt")
metad = MASTFile("files/metadata_single")
metad.to_file("%s/metadata.txt" % ingdir)
kdict=dict()
kdict['mast_program'] = 'vasp'
kdict['mast_kpoints'] = [2,2,2,"M"]
kdict['mast_xc'] = 'pw91'
my_structure = Poscar.from_file("files/perfect_structure").structure
mywr = ChopIngredient(name=ingdir, program_keys = kdict, structure=my_structure)
mywr.write_singlerun()
myri = ChopIngredient(name=ingdir,program_keys=kdict, structure=my_structure)
myri.run_singlerun()
self.assertTrue(myri.checker.is_ready_to_run())
mysubmit = MASTFile("%s/submitlist" % self.test_control)
self.assertEquals(mysubmit.data[0], "%s\n" % ingdir)
def test_run_scale(self):
#raise SkipTest
ingdir = "%s/writedir/single_label1" % testdir
recipedir = "%s/writedir" % testdir
topmetad = MASTFile("files/top_metadata_single")
topmetad.data.append("origin_dir = %s/files\n" %
testdir) #give origin directory
topmetad.to_file("writedir/metadata.txt")
metad = MASTFile("files/metadata_single")
metad.data.append("defect_label = label1\n")
metad.data.append("scaling_size = [2,2,2]\n")
metad.to_file("%s/metadata.txt" % ingdir)
kdict = dict()
kdict['mast_program'] = 'vasp'
my_structure = Poscar.from_file("files/POSCAR_perfect").structure
myperf = MASTFile("files/POSCAR_perfect")
myperf.to_file("%s/POSCAR" % ingdir)
myri = ChopIngredient(name=ingdir,
program_keys=kdict,
structure=my_structure)
myri.run_scale()
my_scaled = Poscar.from_file("%s/CONTCAR" %
ingdir).structure.get_sorted_structure()
scaled_compare = Poscar.from_file(
"files/POSCAR_scaled").structure.get_sorted_structure()
self.assertEquals(my_scaled, scaled_compare)
def test_check_if_ready_to_proceed_are_complete(self):
metad = MASTFile("files/metadata_single")
metad.to_file("recipedir/ing1/metadata.txt")
metad = MASTFile("files/metadata_single")
metad.to_file("recipedir/ing2a/metadata.txt")
rp = RecipePlan("recipedir")
rp.ingredients['ing1'] = "P"
rp.ingredients['ing2a'] = "I"
rp.ingredients['ing2b'] = "I"
rp.ingredients['ing3'] = "I"
kdict = dict()
kdict['mast_program'] = 'vasp'
kdict['mast_xc'] = 'pw91'
kdict['mast_kpoints'] = [1, 2, 3, "G"]
my_struc = pymatgen.io.vaspio.Poscar.from_file(
"files/perfect_structure").structure
rp.ingred_input_options['ing1'] = dict()
rp.ingred_input_options['ing1']['name'] = "%s/recipedir/ing1" % testdir
rp.ingred_input_options['ing1']['program_keys'] = kdict
rp.ingred_input_options['ing1']['structure'] = my_struc
rp.complete_methods['ing1'] = [['complete_singlerun']]
rp.update_methods['ing1'] = dict()
rp.update_methods['ing1']['ing2a'] = [['give_structure']]
rp.update_methods['ing1']['ing2b'] = [['give_structure']]
rp.ingred_input_options['ing2a'] = dict()
rp.ingred_input_options['ing2a'][
'name'] = "%s/recipedir/ing2a" % testdir
rp.ingred_input_options['ing2a']['program_keys'] = kdict
rp.ingred_input_options['ing2a']['structure'] = my_struc
rp.complete_methods['ing2a'] = [['complete_singlerun']]
rp.ready_methods['ing2a'] = [['ready_structure']]
rp.check_if_ready_to_proceed_are_complete()
self.assertTrue(rp.ready_ingredient('ing2a'))
self.assertEquals
self.assertEquals(rp.ingredients, {
'ing1': 'C',
'ing2a': 'I',
'ing2b': 'I',
'ing3': 'I'
})
def test_give_saddle_structure(self):
ingdir = "%s/writedir/neb_labelinit-labelfin" % testdir
recipedir = "%s/writedir" % testdir
topmetad = MASTFile("files/top_metadata_neb")
topmetad.data.append("origin_dir = %s/files\n" %
testdir) #give origin directory
topmetad.to_file("writedir/metadata.txt")
metad = MASTFile("files/metadata_neb")
metad.to_file("%s/metadata.txt" % ingdir)
kdict = dict()
kdict['mast_program'] = 'vasp_neb'
kdict['images'] = 3
my_structure = pymatgen.io.vaspio.Poscar.from_file(
"files/perfect_structure").structure
myrelaxed = dict()
myosz = dict()
mywav = dict()
mychg = dict()
for subdir in ['00', '01', '02', '03', '04']:
os.mkdir("writedir/neb_labelinit-labelfin/%s" % subdir)
myrelaxed[subdir] = MASTFile("files/POSCAR_%s" % subdir)
myrelaxed[subdir].to_file(
"writedir/neb_labelinit-labelfin/%s/CONTCAR" % subdir)
myosz[subdir] = MASTFile("files/OSZICAR_%s" % subdir)
myosz[subdir].to_file(
"writedir/neb_labelinit-labelfin/%s/OSZICAR" % subdir)
mychg[subdir] = MASTFile("files/CHGCAR")
mychg[subdir].to_file("writedir/neb_labelinit-labelfin/%s/CHGCAR" %
subdir)
mywav[subdir] = MASTFile("files/WAVECAR")
mywav[subdir].to_file(
"writedir/neb_labelinit-labelfin/%s/WAVECAR" % subdir)
myuci = ChopIngredient(name=ingdir,
program_keys=kdict,
structure=my_structure)
myuci.give_saddle_structure("next_ingred") #should be OSZ3
saddle = MASTFile("%s/writedir/next_ingred/POSCAR" % testdir)
self.assertEqual(myrelaxed['03'].data, saddle.data)
saddledir = myuci.get_saddle_dir()
self.assertEqual(saddledir, "03")
