def pf_run(input_fname):
scan_type, gopt_s_fnameb, tup, bes = ginp_inp(input_fname)
if scan_type == "diha":
bes = map(int, bes)
ds = DihAScan(None, gopt_s_fnameb, None, "mm3", None, None, None, bes, tup)
ds.write_gamess_inputs()
elif scan_type == "bond":
bes = map(lambda x: 10.0 * x, bes)
bes = map(int, bes)
ds = BondScan(None, gopt_s_fnameb, None, "mm3", None, None, None, bes, tup)
ds.write_gamess_inputs()
elif scan_type == "angl":
bes = map(lambda x: 10.0 * x, bes)
bes = map(int, bes)
ds = AnglScan(None, gopt_s_fnameb, None, "mm3", None, None, None, bes, tup)
ds.write_gamess_inputs()
def pf_run(PF_if):
scan_type, gopt_type, gopt_s_fnameb, tup, bes, engine_path, mm, mode, alg, ref_p, opt_lin, np, nc, step_int, csv = par_fit_inp(
PF_if)
#scan_type=scan_type.strip()
if engine_path == "":
engine_path = "../Engine"
sdir = []
pref = "../Data/ParFit/" + PF_if
sdir.append(pref)
if os.path.exists(pref):
print
print 'Warning: The directory', pref, 'exists!'
print
sys.exit()
os.mkdir(pref)
for gsf in gopt_s_fnameb:
sd_gsf = pref + "/" + gsf
sdir.append(sd_gsf)
os.mkdir(sd_gsf)
n = len(gopt_type)
ds = []
if scan_type == "diha":
for i in range(n):
if not bes[i] == ():
bes[i] = map(int, bes[i])
sds = DihAScan(sdir, gopt_s_fnameb[i], engine_path, mm, opt_lin,
np, nc, bes[i], tup[i])
ds.append(sds)
elif scan_type == "bond":
for i in range(n):
if not bes[i] == ():
bes[i] = map(lambda x: 10. * x, bes[i])
bes[i] = map(int, bes[i])
sds = BondScan(sdir, gopt_s_fnameb[i], engine_path, mm, opt_lin,
np, nc, bes[i], tup[i])
ds.append(sds)
elif scan_type == "angl":
for i in range(n):
if not bes[i] == ():
bes[i] = map(lambda x: 10. * x, bes[i])
bes[i] = map(int, bes[i])
sds = AnglScan(sdir, gopt_s_fnameb[i], engine_path, mm, opt_lin,
np, nc, bes[i], tup[i])
ds.append(sds)
if not gopt_type[0] == "ginp":
os.environ["ENGINE_DIR"] = engine_path + "/engine_dir"
p, c, ol_templ, lines = read_add(mm, opt_lin, np, nc, 1, scan_type)
for i in range(n):
if gopt_type[i] == "full":
ds[i].read_gamess_outputs()
ds[i].find_min_ge_key()
elif gopt_type[i] == "comp":
ds[i].read_gouts_data()
ds[i].find_min_ge_key()
elif gopt_type[i] == "ginp":
ds[i].write_gamess_inputs()
ds[i].find_min_ge_key()
quit()
else:
"Par_Fit: Wrong gopt_type!"
ds[i].write_engine_inputs()
def engine_rmse(p):
n = len(ds)
rmse = 0.
for i in range(n):
write_add(sdir, p, c, mm, ol_templ, lines, 1, engine_rmse.step,
step_int)
ds[i].run_scan(p, c, mm, ol_templ)
rmse += ds[i].calc_rmse(ref_p, csv, i, engine_rmse.step, step_int)
print engine_rmse.step, round(rmse / n, 4), p
engine_rmse.step += 1
return round(rmse / n, 4)
engine_rmse.step = 1
def engine_rmse2(p):
n = len(ds)
rmse = 0.
for i in range(n):
write_add(sdir, p, c, mm, ol_templ, lines, 1, engine_rmse2.step,
step_int)
ds[i].run_scan(p, c, mm, ol_templ)
rmse += ds[i].calc_rmse(ref_p, csv, i, engine_rmse2.step, step_int)
engine_rmse2.step += 1
return (round(rmse / n, 4), )
engine_rmse2.step = 1
if mode == "sense":
eps = 0.01
np = len(p)
ppM = numpy.zeros(np)
ppP = numpy.zeros(np)
p0 = engine_rmse(p)
for i in range(np):
for j in range(np):
ppM[j] = p[j]
ppP[j] = p[j]
ppM[i] -= eps
ppP[i] += eps
pM = engine_rmse(ppM)
pP = engine_rmse(ppP)
print i + 1, (pM - p0) / eps, (pP - p0) / eps
else:
np = len(p)
if alg == "ga":
print "Warning: The genetic algorithm printout will not start immediately!"
hof = run_ga(engine_rmse2, np, 40)
hof0 = numpy.array(hof[0])
write_add(sdir, hof0, c, mm, ol_templ, lines, 1, "ga", None)
elif alg == "fmin":
#print fmin_powell(engine_rmse,p)
print fmin(engine_rmse, p, ftol=0.2)
elif alg == "hybr":
print "Warning: The genetic algorithm printout will not start immediately!"
hof = run_ga(engine_rmse2, np, 40)
hof0 = numpy.array(hof[0])
write_add(sdir, hof0, c, mm, ol_templ, lines, 1, "ga", None)
fmin(engine_rmse, hof0, ftol=0.2)
else:
"'alg' is not a known algorithm!"
def pf_inp_run(input_fname):
prog_type, scan_type, gopt_s_fnameb, tup, bes = ginp_inp(input_fname)
if scan_type == "diha":
bes = map(int, bes)
ds = DihAScan(None, gopt_s_fnameb, None, "mm3", None, None, None, bes,
tup)
if prog_type == "nwchem":
ds.write_nwchem_inputs()
else:
ds.write_gamess_inputs()
elif scan_type == "bond":
bes = map(lambda x: 10. * x, bes)
bes = map(int, bes)
ds = BondScan(None, gopt_s_fnameb, None, "mm3", None, None, None, bes,
tup)
if prog_type == "nwchem":
ds.write_nwchem_inputs()
else:
ds.write_gamess_inputs()
elif scan_type == "angl":
bes = map(lambda x: 10. * x, bes)
bes = map(int, bes)
ds = AnglScan(None, gopt_s_fnameb, None, "mm3", None, None, None, bes,
tup)
if prog_type == "nwchem":
ds.write_nwchem_inputs()
else:
ds.write_gamess_inputs()
def pf_out_run(input_fname):
prog_type,scan_type,gopt_s_fnameb,tup,bes=ginp_inp(input_fname)
if scan_type=="diha":
bes=map(int,bes)
ds=DihAScan(None,gopt_s_fnameb,None,"mm3",None,None,None,bes,tup)
ds=DihAScan(None,gopt_s_fnameb,None,"mm3",None,None,None,bes,tup)
if prog_type=="nwchem":
ds.read_nwchem_outputs()
else:
ds.read_gamess_outputs()
ds.write_gouts_data()
elif scan_type=="bond":
bes=map(lambda x:10.*x,bes)
bes=map(int,bes)
ds=BondScan(None,gopt_s_fnameb,None,"mm3",None,None,None,bes,tup)
if prog_type=="nwchem":
ds.read_nwchem_outputs()
else:
ds.read_gamess_outputs()
ds.write_gouts_data()
elif scan_type=="angl":
bes=map(lambda x:10.*x,bes)
bes=map(int,bes)
ds=AnglScan(None,gopt_s_fnameb,None,"mm3",None,None,None,bes,tup)
if prog_type=="nwchem":
ds.read_nwchem_outputs()
else:
ds.read_gamess_outputs()
ds.write_gouts_data()
