def make_nmers(weights,corr,waters,n):
for i,j in corr.items():
j.weight=weights[len(j.sn)-1]
for comb in combinations(range(0,6),n):
key=""
for i in comb:
key=key+str(i)+" "
corr[key]=psr.NMerInfo()
corr[key].nmer=psr.System(waters[0].nmer,False)
for i in comb:
corr[key].nmer.union_assign(waters[i].nmer)
for i in range(6):
if i in comb: continue
for ai in waters[i].nmer:
corr[key].nmer.insert(psr.make_ghost_atom(ai))
corr[key].weight=1.0
corr[key].sn=set(comb)
def make_nmers(corr,waters,n):
for real in combinations(range(0,6),n): #all frags in this m-mer
for i in range(0,n):
for ghost in combinations(real,i):#with above is powerset of real
sn=[]
for j in real:
if j in ghost:sn.append(j+6)
else: sn.append(j)
sn.sort()
key=""
for j in sn:key=key+str(j)+" "
corr[key]=psr.NMerInfo()
corr[key].nmer=psr.System(waters[0].nmer,False)
for j in real:
if j in ghost:
for ai in waters[j].nmer:
corr[key].nmer.insert(psr.make_ghost_atom(ai))
else: corr[key].nmer.union_assign(waters[j].nmer)
corr[key].weight=1.0 if i%2==0 else -1.0
corr[key].sn=set(sn)
def run_test():
tester = psr.PyTester("Testing the Atom class")
H, H2 = psr.create_atom([0.0, 0.0, 0.0], 1), psr.create_atom([0.0, 0.0, 0.0], 1, 1)
tester.test_return("create_atom works", True, True, H.__eq__, H2)
tester.test_equal("correct Z", 1, H.Z)
tester.test_equal("correct isotope", 1, H.isotope)
tester.test_equal("correct mass", 1.007975, H.mass)
tester.test_equal("correct isotope mass", 1.0078250322, H.isotope_mass)
tester.test_equal("correct charge", 0, H.charge)
tester.test_equal("correct multiplicity", 2, H.multiplicity)
tester.test_equal("correct nelectrons", 1, H.nelectrons)
tester.test_equal("correct covalent radius", 0.5858150988919267, H.cov_radius)
tester.test_equal("correct vDW radius", 2.267671350549394, H.vdw_radius)
H3 = psr.Atom(H2)
tester.test_return("copy constructor works", True, True, H.__eq__, H3)
D = psr.create_atom([0.0, 0.0, 0.0], 1, 2)
tester.test_equal("Isotopes work", 2, D.isotope)
tester.test_return("Isotopes are different", True, True, D.__ne__, H)
tester.test_return("hash works", True, H.my_hash(), H2.my_hash)
tester.test_return("hash works 1", True, H.my_hash(), H3.my_hash)
GH = psr.make_ghost_atom(H2)
tester.test_return("ghost works", True, True, psr.is_ghost_atom, GH)
q = psr.make_point_charge(H2, 3.3)
q2 = psr.make_point_charge(H2.get_coords(), 3.3)
tester.test_return("point charges work", True, True, psr.is_point_charge, q)
tester.test_return("point charges work 2", True, True, psr.is_point_charge, q2)
tester.test_return("is same point charge", True, True, q.__eq__, q2)
Dm = psr.make_dummy_atom(H)
Dm2 = psr.make_dummy_atom(H.get_coords())
tester.test_return("is dummy atom", True, True, psr.is_dummy_atom, Dm)
tester.test_return("is dummy atom 2", True, True, psr.is_dummy_atom, Dm2)
tester.test_return("is same dummy atom", True, True, Dm.__eq__, Dm2)
tester.print_results()
return tester.nfailed()
def run(mm):
tester = psr.PyTester("Testing CPGhoster")
water6=psr.make_system("""
0 1
O -2.0449536949999998 -1.6898322539999999 0.0354707364500000
H -2.3427132454308994 -2.1474611062791298 0.8216939386571565
H -1.1344686596866658 -1.9649570182333860 -0.0720244010028244
O 2.4859145229999999 -0.9260656876000000 0.0354704040100000
H 2.2689370278862486 -0.0000001286725659 -0.0720246525395077
H 3.0311125996609807 -0.9551186438629339 0.8216935421441762
O -2.4859145329999999 0.9260657306000000 -0.0354704090300000
H -3.0311126049484312 0.9551186852913661 -0.8216935504901171
H -2.2689370387823162 0.0000001718485472 0.0720246508442851
O 2.0449536849999999 1.6898322980000000 -0.0354707319800000
H 1.1344686495378762 1.9649570616208789 0.0720244057802314
H 2.3427132361387448 2.1474611537792310 -0.8216939318818128
O -0.4409608357000000 2.6158980070000002 0.0354706148100000
H -0.6883991903307550 3.1025798186648132 0.8216938113975091
H -1.1344683993833504 1.9649572116176803 -0.0720244084283669
O 0.4409608257000000 -2.6158979640000002 -0.0354706097500000
H 0.6883991785965635 -3.1025797787366964 -0.8216938049817561
H 1.1344683896564345 -1.9649571682424622 0.0720244094544075
""")
#This makes the six waters and ghosts them
waters=[psr.NMerInfo() for x in range(0,6)]
asu=water6.as_universe()
for i in water6:asu.insert(psr.make_ghost_atom(i))
ghost_water6=psr.System(asu,False)
for i,wateri in enumerate(waters):
wateri.nmer=psr.System(ghost_water6,False)
wateri.weight=1.0
wateri.sn={i}
for i,atomi in enumerate(water6):
waters[int((i-i%3)/3)].nmer.insert(atomi)
mm.load_supermodule("pulsar_modules")
mm.change_option("PSR_CP_FRAG","SYSTEM_FRAGMENTER_KEY","PSR_NMER_FRAG")
mm.change_option("PSR_NMER_FRAG","TRUNCATION_ORDER",0)
my_mod=mm.get_module("PSR_CP_FRAG",0)
corr={}
key=mm.generate_unique_key()
mm.duplicate_key("PSR_NMER_FRAG",key)
mm.change_option(key,"TRUNCATION_ORDER",1)
my_mod.options().change("SYSTEM_FRAGMENTER_KEY",key)
corr={str(i)+" ":psr.NMerInfo(waters[i]) for i in range(0,6)}
for i in range(6):
for j in range(6):
if i==j: continue
for ai in waters[j].nmer:
corr[str(i)+" "].nmer.insert(psr.make_ghost_atom(ai))
tester.test_return("Resulting fragments are correct n=1",True,corr,
my_mod.fragmentize,water6)
#Weights for n=2 to 6 respectively
cs=[[-4.0],[6.0,-3.0],[-4.0,3.0,-2.0],[1.0,-1.0,1.0,-1.0],
[0.0 for i in range(5)]]
for n,c in enumerate(cs):
make_nmers(c,corr,waters,n+2)
key=mm.generate_unique_key()
mm.duplicate_key("PSR_NMER_FRAG",key)
mm.change_option(key,"TRUNCATION_ORDER",n+2)
my_mod.options().change("SYSTEM_FRAGMENTER_KEY",key)
tester.test_return("Resulting fragments are correct n="+str(n+2),True,
corr,my_mod.fragmentize,water6)
tester.print_results()
return tester.nfailed()
def run_test():
tester=psr.PyTester("Testing Make System Python Function")
carts=[
-2.0449536949999998, -1.6898322539999999, 0.0354707364500000,
-2.3427132454308994, -2.1474611062791298, 0.8216939386571565,
-1.1344686596866658, -1.9649570182333860, -0.0720244010028244,
2.4859145229999999, -0.9260656876000000, 0.0354704040100000,
2.2689370278862486, -0.0000001286725659, -0.0720246525395077,
3.0311125996609807, -0.9551186438629339, 0.8216935421441762
]
ToAu=1/0.52917721067
all_atoms=[
psr.create_atom([carts[i]*ToAu for i in range(0,3)],8),
psr.create_atom([carts[i]*ToAu for i in range(3,6)],1),
psr.create_atom([carts[i]*ToAu for i in range(6,9)],1),
psr.create_atom([carts[i]*ToAu for i in range(9,12)],8),
psr.create_atom([carts[i]*ToAu for i in range(12,15)],1),
psr.create_atom([carts[i]*ToAu for i in range(15,18)],1)
]
unv=psr.AtomSetUniverse(all_atoms)
for i in all_atoms:
unv.insert(psr.make_ghost_atom(i))
corr_mol1=psr.System(unv,False)
corr_mol2=psr.System(corr_mol1)
for i in all_atoms:
corr_mol2.insert(i)
corr_mol3=psr.System(corr_mol1)
for i in all_atoms[0:3]:
corr_mol3.insert(psr.make_ghost_atom(i))
for i in all_atoms[3:6]:
corr_mol3.insert(i)
mol1="""
#0 1
#O -2.0449536949999998 -1.6898322539999999 0.0354707364500000
#H -2.3427132454308994 -2.1474611062791298 0.8216939386571565
#H -1.1344686596866658 -1.9649570182333860 -0.0720244010028244
#O 2.4859145229999999 -0.9260656876000000 0.0354704040100000
#H 2.2689370278862486 -0.0000001286725659 -0.0720246525395077
#H 3.0311125996609807 -0.9551186438629339 0.8216935421441762
"""
tester.test_return("Comments work",True,corr_mol1,psr.make_system,mol1)
mol2="""
0 1
O -2.0449536949999998 -1.6898322539999999 0.0354707364500000
H -2.3427132454308994 -2.1474611062791298 0.8216939386571565
H -1.1344686596866658 -1.9649570182333860 -0.0720244010028244
O 2.4859145229999999 -0.9260656876000000 0.0354704040100000
H 2.2689370278862486 -0.0000001286725659 -0.0720246525395077
H 3.0311125996609807 -0.9551186438629339 0.8216935421441762
"""
tester.test_return("Normal molecule works",True,corr_mol2,psr.make_system,mol2)
mol3="""
0 1
@O -2.0449536949999998 -1.6898322539999999 0.0354707364500000
@H -2.3427132454308994 -2.1474611062791298 0.8216939386571565
@H -1.1344686596866658 -1.9649570182333860 -0.0720244010028244
O 2.4859145229999999 -0.9260656876000000 0.0354704040100000
H 2.2689370278862486 -0.0000001286725659 -0.0720246525395077
H 3.0311125996609807 -0.9551186438629339 0.8216935421441762
"""
#tester.test_return("@ for ghost works",True,corr_mol3,psr.make_system,mol3)
mol4="""
0 1
Gh(O) -2.0449536949999998 -1.6898322539999999 0.0354707364500000
Gh(H) -2.3427132454308994 -2.1474611062791298 0.8216939386571565
Gh(H) -1.1344686596866658 -1.9649570182333860 -0.0720244010028244
O 2.4859145229999999 -0.9260656876000000 0.0354704040100000
H 2.2689370278862486 -0.0000001286725659 -0.0720246525395077
H 3.0311125996609807 -0.9551186438629339 0.8216935421441762
"""
#tester.test_return("Gh(X) for ghosts works",True,corr_mol3,psr.make_system,mol4)
tester.print_results()
return tester.nfailed()