I think that all you need to do is import nwchem inside the external module and then reference e.g. rtdb_get as nwchem.rtdb_get (or maybe do 'from nwchem import *', but I prefer the explicit naming).
Here's a module I was toying around with last summer. I called it nwhelp.py. You can import it while running NWChem and call the various functions.
import nwchem
class Helper(object):
def __init__(self):
pass
def rtdb_keys(self, prefix=""):
"""Get keys currently in the rtdb.
@param prefix: if non-empty, only include keys that start with it
@type prefix : str
@return: keys
@rtype : list
"""
#initialize/rewind to first rtdb key
keys = [nwchem.rtdb_first()]
while True:
try:
keys.append(nwchem.rtdb_next())
except nwchem.NWChemError:
break
filtered = [k for k in keys if k.startswith(prefix)]
return filtered
def rtdb_data(self, prefix=""):
"""Get a dict containing rtdb data keyed by name."""
d = {}
for key in self.rtdb_keys(prefix=prefix):
data = nwchem.rtdb_get(key)
meta = nwchem.rtdb_get_info(key)
d[key] = (data, meta)
return d
def geom_get_coords(self, name):
"""Get named geometry in atomic units."""
try:
actualname = nwchem.rtdb_get(name)
except nwchem.NWChemError:
actualname = name
coords = nwchem.rtdb_get('geometry:' + actualname + ':coords')
units = nwchem.rtdb_get('geometry:' + actualname + ':user units')
if (units == 'a.u.'):
factor = 1.0
elif (units == 'angstroms'):
prop = 'geometry:{0}:angstrom_to_au'.format(actualname)
factor = nwchem.rtdb_get(prop)
else:
raise nwchem.NWChemError('unknown units {0}'.format(repr(units)))
for k in range(len(coords)):
coords[k] /= factor
return coords
Here's a demonstration NWChem deck that calls it. If you have ipdb installed you get an interactive environment running inside Python inside NWChem. Not tested with parallel execution.
echo
start testpy
# test some basic python wrappers.
# if it did not abort, it worked.
print none
basis
h library 3-21g
end
python
import nwhelp
H = nwhelp.Helper()
import ipdb
print "value check:"
print "INT = ", INT
print "DBL = ", DBL
print "CHAR = ", CHAR
print "LOGICAL = ", LOGICAL
rtdb_put("test_int2", 22)
print ' Done 1'
rtdb_put("test_int", [22, 10, 3], INT)
print ' Done 2'
rtdb_put("test_dbl", [22.9, 12.4, 23.908], DBL)
print ' Done 3'
rtdb_put("test_str", "hello", CHAR)
print ' Done 4'
rtdb_put("test_logic", [0,1,0,1,0,1], LOGICAL)
print ' Done 5'
rtdb_put("test_logic2", 0, LOGICAL)
print ' Done 6'
rtdb_print(1)
print "test_str = ", rtdb_get("test_str")
print "test_int = ", rtdb_get("test_int")
print "test_in2 = ", rtdb_get("test_int2")
print "test_dbl = ", rtdb_get("test_dbl")
print "test_logic = ", rtdb_get("test_logic")
print "test_logic2 = ", rtdb_get("test_logic2")
def energy(r):
input_parse('''
geometry noprint noautoz
h 0 0 0
h 0 0 %f
end
''' % r)
return task_energy('scf')
for r in (0.4, 0.5, 0.6):
print r, energy(r)
print task_optimize('scf')
keys = H.rtdb_keys()
import pprint
pprint.pprint(keys)
ipdb.set_trace()
end
task python
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