def main(commands, args):
cout("Atomistic module")
if len(commands) == 0:
commands = ['help']
############## HELP ####################
if commands[0] == "help":
cout(atomistic_help_text)
elif len(commands)==2 and commands[0] == "visualize" and commands[1] == "help":
cout(visualize_help_text)
############## VISUALIZE ##############
elif commands[0] == "visualize":
import httk.atomistic.vis
from httk.atomistic import Structure
for command in commands[1:]:
struct = httk.load(command)
struct.vis.show()
#######################################
else:
cerr("Unknown command in atomistic module:", commands[0])
exit(1)
def test_read_all_spacegroups(self):
compdir = 'structreading_data'
topdir = '../Tutorial/tutorial_data'
reldir = 'all_spacegroups/cifs/'
def print_num_matrix(l):
outstr = ""
for i in l:
if isinstance(i, list):
outstr += print_num_matrix(i)
outstr += "\n"
else:
outstr += str(i) + "\n"
return outstr
structdir = os.path.join(topdir, reldir)
for subdir, dirs, files in os.walk(structdir):
for f in files:
if f.endswith('.cif'):
print("TESTING:", f)
reldir = os.path.relpath(subdir, topdir)
ff = os.path.join(subdir, f)
relf = os.path.join(reldir, f + '.check')
struct = httk.load(ff)
#if not os.path.exists(reldir):
# os.makedirs(reldir)
if struct.assignments.ratios != [1] * len(
struct.assignments.ratios):
print("Disordered structure, skipping")
continue
if f in ['70.cif', '26.cif', '190.cif']:
print(
"Skipping structure incorrectly read by cif2cell")
continue
#if f == '184.cif' or f == '119.cif' or f == '217.cif' or f == '200.cif':
# # For some reason cif2cell has a different orientation here
# continue
of = open('structreading.tmp', "w")
#of.write(" ".join(struct.uc_formula_symbols)+"\n")
#of.write(" ".join([str(x) for x in struct.pc.uc_counts])+"\n")
#of.write(print_num_matrix(struct.pc.uc_cell.basis.to_floats()))
#of.write(print_num_matrix(struct.pc.uc_reduced_coords.to_floats()))
of.write(" ".join(struct.uc_formula_symbols) + "\n\n\n")
of.write(" ".join([str(x)
for x in struct.uc_counts]) + "\n\n\n")
of.write(print_num_matrix(
struct.uc_cell.basis.to_floats()))
of.write("\n")
of.write(
print_num_matrix(struct.uc_reduced_coords.to_floats()))
of.close()
compf = os.path.join(compdir, relf)
f = open(compf)
s1 = f.read()
f.close()
f = open('structreading.tmp')
s2 = f.read()
f.close()
self.assert_numeric_data(s1, s2)
def main():
parser = argparse.ArgumentParser(description="Creates the tutorial sqlite database file")
parser.add_argument('-debug', action='store_true')
parser.add_argument('file', metavar='run', nargs='*', help='filenames or directories to import')
args = parser.parse_args()
debug = args.debug
#debug = True
process_with_isotropy = True
process_with_tidy = True
if process_with_isotropy:
import httk.external.isotropy_ext
try:
os.remove('tutorial.sqlite')
except OSError as e:
if e.errno != errno.ENOENT:
raise
backend = httk.db.backend.Sqlite('tutorial.sqlite')
store = httk.db.store.SqlStore(backend)
# This is good practice if you are going to add several things to the database, nothing is written to the database until 'commit' is called.
# (Special case: if the database is completely newly created, some database engines commit data)
store.delay_commit()
codeobj = httk.Code.create("create_tutorial_database", '1.0', refs=[httk.citation.httk_reference_main])
store.save(codeobj)
print("==== Name of this code:", codeobj.name)
today = datetime.datetime.today().isoformat()
print("==== Db import program started: "+today)
if len(args.file) == 0:
files = [os.path.join(httk.httk_root, 'Tutorial/tutorial_data')]
else:
files = args.file
argcount = len(files)
seen = {}
for filek in range(argcount):
f = files[filek]
if not os.path.exists(f):
print("File or dir "+f+" not found.")
continue
if os.path.isdir(f):
filelist = []
dirname = os.path.dirname(f)
for root, dirs, files in os.walk(f):
for file in files:
if file.endswith(".cif") or file.endswith(".vasp"):
filelist += [os.path.join(root, file)]
# Make sure we always generate the same manifest
filelist = sorted(filelist)
else:
dirname = os.path.dirname(f)
filelist = [f]
for i in range(len(filelist)):
filename = filelist[i]
print("Filename:"+filename)
# Uncomment for better control in how to load structures
#if filename.endswith(".cif"):
# struct = httk.httkio.cif_to_struct(filename,backends=['cif2cell_reduce'])
#elif filename.endswith(".vasp"):
# struct = httk.iface.vasp_if.poscar_to_structure(filename)
struct = httk.load(filename).clean()
print("The formula is:", struct.formula+" ("+struct.anonymous_formula+")")
print("Volume", float(struct.uc_volume))
print("Tags:", [str(struct.get_tag(x)) for x in struct.get_tags()])
print("Refs:", [str(x) for x in struct.get_refs()])
if process_with_isotropy:
try:
newstruct = httk.external.isotropy_ext.struct_process_with_isotropy(struct).clean()
newstruct.add_tag("isotropy/findsym", "done")
struct = newstruct
except Exception as e:
print("Isotropy failed with:"+str(e))
struct.add_tag("isotropy", "failed")
if debug:
raise
if process_with_tidy:
try:
newstruct = struct.tidy()
newstruct.add_tag("structure_tidy", "done")
struct = newstruct
except Exception as e:
print("Structure tidy failed with:"+str(e))
struct.add_tag("structure_tidy", "failed")
if debug:
raise
store.save(struct)
compound = Compound.create(base_on_structure=struct)
store.save(compound)
cs = CompoundStructure.create(compound, struct)
store.save(cs)
store.commit()
print("==== Committing changes to database.")
store.commit()
print("==== Commit complete.")
#!/usr/bin/env python
#
# Simplest possible httk program. Loads a structure and prints out some information on the console.
from __future__ import print_function
import httk
struct = httk.load("example.cif")
print("Formula:", struct.formula)
print("Primitive cell info:")
print("Volume:", float(struct.pc.uc_volume))
print("Assignments", struct.assignments.symbols)
print("Counts:", struct.pc.uc_counts)
print("Coords", struct.pc.uc_reduced_coords.to_floats())
print()
print("Conventional cell info:")
print("Volume:", float(struct.cc.uc_volume))
print("Assignments", struct.assignments.symbols)
print("Counts:", struct.cc.uc_counts)
print("Coords", struct.cc.uc_reduced_coords.to_floats())
httk.save(struct, 'test.vasp')
class TotalEnergyResult(httk.Result):
@httk.httk_typed_init({
'computation': httk.Computation,
'structure': Structure,
'total_energy': float
})
def __init__(self, computation, structure, total_energy):
self.computation = computation
self.structure = structure
self.total_energy = total_energy
backend = httk.db.backend.Sqlite('example.sqlite')
store = httk.db.store.SqlStore(backend)
reader = httk.task.reader('./', 'Runs/', 'Normal VASP total energy run')
print(
"Storing results (please note that first store call will take some time, since the database is created)"
)
for rundir, computation in reader:
struct = httk.load(os.path.join(rundir, "CONTCAR"))
print("Reading outcar:", struct.formula)
outcar = httk.iface.vasp_if.read_outcar(
os.path.join(rundir, "OUTCAR.cleaned.relax-final"))
total_energy_result = TotalEnergyResult(computation, struct,
float(outcar.final_energy))
store.save(total_energy_result)
store.commit()
#!/usr/bin/env python
from __future__ import print_function
import httk, httk.db
from httk.atomistic import Structure
backend = httk.db.backend.Sqlite('example.sqlite')
store = httk.db.store.SqlStore(backend)
tablesalt = httk.load('../../Tutorial/Step7/NaCl.cif')
tablesalt.add_tag('common name', 'salt')
arsenic = httk.load('../../Tutorial/Step7/As.cif')
store.save(tablesalt)
store.save(arsenic)
# Search for anything with Na (cf. the search for a material system in tutorial step6, where all symbols must be in a set, 'add' vs. 'add_all'.)
search = store.searcher()
search_struct = search.variable(Structure)
search.add(search_struct.formula_symbols.is_in('Na'))
search.output(search_struct, 'structure')
for match, header in list(search):
struct = match[0]
print("Found structure", struct.formula,
[str(struct.get_tags()[x]) for x in struct.get_tags()])
#!/usr/bin/env python
import httk, httk.db
from httk.atomistic import Structure
class StructureIsEdible(httk.HttkObject):
@httk.httk_typed_init({'structure': Structure, 'is_edible': bool})
def __init__(self, structure, is_edible):
self.structure = structure
self.is_edible = is_edible
backend = httk.db.backend.Sqlite('example.sqlite')
store = httk.db.store.SqlStore(backend)
tablesalt = httk.load('NaCl.cif')
arsenic = httk.load('As.cif')
edible = StructureIsEdible(tablesalt, True)
store.save(edible)
edible = StructureIsEdible(arsenic, False)
store.save(edible)