def main():
parser = argparse.ArgumentParser(
description=desc, formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument(
'--ndof',
help=
'Number of total degrees of freedom (e.g. 3*number of atoms). This is simply the length of a coordinates vector.',
type=int,
default=1)
# parser.add_argument('--Database','-d', help = 'Name of database to write into', type = str, default="optimdb.sqlite")
# parser.add_argument('--Mindata','-m', help = 'Name of min.data file', type = str, default="min.data")
# parser.add_argument('--Tsdata','-t', help = 'Name of ts.data file', type = str, default="ts.data")
# parser.add_argument('--Pointsmin','-p', help = 'Name of points.min file', type = str, default="points.min")
# parser.add_argument('--Pointsts','-q', help = 'Name of points.ts file', type = str, default="points.ts")
# parser.add_argument('--endianness', help = 'set the endianness of the binary data. Can be "<" for little-endian or ">" for big-endian', type = str, default="=")
args = parser.parse_args()
system = BaseSystem()
db = system.create_database()
converter = OptimDBConverter(db,
mindata="min.data",
tsdata="ts.data",
pointsmin="points.min",
pointsts="points.ts",
endianness="=",
assert_coords=False)
converter.convert_no_coords()
system.get_ndof = lambda: args.ndof
run_gui(system, db=db)
print(db.number_of_minima())
def setUp(self):
from pele.utils.optim_compatibility import OptimDBConverter
from pele.storage import Database
ndof = 10 # wrong, but who cares.
self.db = Database()
current_dir = os.path.dirname(__file__)
converter = OptimDBConverter(self.db, ndof=ndof, mindata=current_dir+"/collagen.min.data",
tsdata=current_dir+"/collagen.ts.data", assert_coords=False)
converter.convert_no_coords()
parser.add_argument("--Tmin", type=float, help="Minimum temperature for the calculation.", default=0.02)
parser.add_argument("--Tmax", type=float, help="Minimum temperature for the calculation.", default=1.0)
parser.add_argument("--Tcount", type=int, help="Number of temperature points for the calculation.", default=300)
parser.add_argument("--OPTIM", action="store_true", help="read data from a min.data file instead."
"fname should be the filename of the min.data file")
args = parser.parse_args()
print args.fname
print args
k = args.k
# get the list of minima
if args.OPTIM:
# fname is a min.data file
db = Database()
converter = OptimDBConverter(db, mindata=args.fname)
converter.convert_no_coords()
minima = db.minima()
else:
dbfname = args.fname
db = Database(dbfname, createdb=False)
minima = [m for m in db.minima() if m.fvib is not None and m.pgorder is not None]
if len(minima) == 0:
print "There are not minima with the necessary thermodynamic information in the database. Have you computed the normal mode"\
" frequencies and point group order for all the minima? See pele.thermodynamics "\
" for more information"
exit(1)
print "computing heat capacity from", len(minima), "minima"
Tmin = args.Tmin
Tmax = args.Tmax
nT = args.Tcount
def main():
if len(sys.argv) < 2:
usage()
exit(1)
kwargs = {}
outfile = None
OPTIM = False
opts, args = getopt.gnu_getopt(sys.argv[1:], "ho:",
["help", "nlevels=", "subgraph_size=", "OPTIM",
"order_by_basin_size", "order_by_energy",
"include_gmin",
"center_gmin",
"Emax=",
])
for o, a in opts:
if o == "-h" or o == "--help":
usage()
exit(1)
if o == "-o":
outfile = a
elif o == "--nlevels":
kwargs["nlevels"] = int(a)
elif o == "--Emax":
kwargs["Emax"] = float(a)
elif o == "--subgraph_size":
kwargs["subgraph_size"] = int(a)
elif o == "--order_by_basin_size":
kwargs["order_by_basin_size"] = True
elif o == "--order_by_energy":
kwargs["order_by_energy"] = True
elif o == "--includer_gmin":
kwargs["includer_gmin"] = True
elif o == "--center_gmin":
kwargs["center_gmin"] = True
elif o == "--OPTIM":
OPTIM = True
else:
print "don't understand", o, a
print ""
usage()
exit(1)
groups = None
if OPTIM:
#make database from min.data ts.data
db = Database()
converter = OptimDBConverter(db)
converter.convert_no_coords()
groups = read_AB(db)
else:
if len(args) == 0:
print "you must specify database file"
print ""
usage()
exit()
dbfile = args[0]
if not os.path.exists(dbfile):
print "database file doesn't exist", dbfile
exit()
db = Database(dbfile)
if outfile is None and use_gui:
app = QApplication(sys.argv)
kwargs["show_minima"] = False
md = DGraphDialog(db, params=kwargs)
md.rebuild_disconnectivity_graph()
if groups is not None:
md.dgraph_widget.dg.color_by_group(groups)
md.dgraph_widget.redraw_disconnectivity_graph()
md.show()
sys.exit(app.exec_())
# make graph from database
t0 = time.time()
if "Emax" in kwargs and use_gui:
graph = reduced_db2graph(db, kwargs['Emax'])
else:
graph = dg.database2graph(db)
t1 = time.time()
print "loading the data into a transition state graph took", t1-t0, "seconds"
# do the disconnectivity graph analysis
mydg = dg.DisconnectivityGraph(graph, **kwargs)
print "doing disconnectivity graph analysis"
sys.stdout.flush()
t1 = time.time()
mydg.calculate()
t2 = time.time()
print "d-graph analysis finished in", t2-t1, "seconds"
print "number of minima:", mydg.tree_graph.number_of_leaves()
print "plotting disconnectivigy graph"
sys.stdout.flush()
# make the figure and save it
mydg.plot()
if outfile is None:
plt.show()
else:
plt.savefig(outfile)
t3 = time.time()
print "plotting finished in", t3-t2, "seconds"
