def run_dih_elem(self, m):
fnameb = m.name
coengine_name = "coengine_" + fnameb
f = open("../Data/Engine/" + coengine_name, 'w')
#f=open(coengine_name,'w')
if self._styp == "diha":
print >> f, "mode opt"
else:
print >> f, "mode single"
print >> f, "infile " + fnameb + "_inp.pcm"
print >> f, "outfile " + fnameb + "_out.pcm"
print >> f, "print 3"
if self._mm == "mm3":
print >> f, "forcefield mm3"
print >> f, "addpar add_MM3.prm"
elif self._mm == "mmff94":
print >> f, "forcefield mmff94"
print >> f, "addpar add_MMFF94.prm"
else:
print "Scan.run_scan: Wrong MM-name!"
f.close()
#
timeout = 1
while True:
status = run_engine_timeout(self.engine_path, coengine_name,
timeout)
if status:
break
else:
p, c, ol_templ, lines = read_add(self._mm, self._opt_lin,
self._np, self._nc, 1,
self._styp)
p[0] += 0.001
#pert_add_param("add_MM3.prm")
write_add(self.sdir, p, c, self._mm, ol_templ, lines, 1, None,
None)
#
comm = "rm ../Data/Engine/" + coengine_name
#comm="rm "+coengine_name
system(comm)
def run_dih_elem(self,m):
fnameb=m.name
coengine_name="coengine_"+fnameb
f=open("../Data/Engine/"+coengine_name,'w')
#f=open(coengine_name,'w')
if self._styp=="diha":
print >>f,"mode opt"
else:
print >>f,"mode single"
print >>f,"infile "+fnameb+"_inp.pcm"
print >>f,"outfile "+fnameb+"_out.pcm"
print >>f,"print 3"
if self._mm=="mm3":
print >>f,"forcefield mm3"
print >>f,"addpar add_MM3.prm"
elif self._mm=="mmff94":
print >>f,"forcefield mmff94"
print >>f,"addpar add_MMFF94.prm"
else:
print "Scan.run_scan: Wrong MM-name!"
f.close()
#
timeout=1
while True:
status=run_engine_timeout(self.engine_path,coengine_name,timeout)
if status:
break
else:
p,c,ol_templ,lines=read_add(self._mm,self._opt_lin,self._np,self._nc,1,self._styp)
p[0]+=0.001
#pert_add_param("add_MM3.prm")
write_add(self.sdir,p,c,self._mm,ol_templ,lines,1,None,None)
#
comm="rm ../Data/Engine/"+coengine_name
#comm="rm "+coengine_name
system(comm)
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_run(PF_if):
scan_type, gopt_type, gopt_s_fnameb, tup, bes, engine_path, mm, mode, alg, 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: 10.0 * 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: 10.0 * 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()
elif gopt_type[i] == "comp":
ds[i].read_gouts_data()
elif gopt_type[i] == "ginp":
ds[i].write_gamess_inputs()
quit()
else:
"Par_Fit: Wrong gopt_type!"
ds[i].write_engine_inputs()
def engine_rmse(p):
n = len(ds)
rmse = 0.0
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(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 = 0.0
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(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!"
#print ds.da_rt
#print ds.dt
#ds.read_gamess_outputs()
#ds.write_gouts_data()
#ds.read_gouts_data()
#ds.write_engine_inputs()
#engine_rmse(p)
default_input_fname="dih_scan_inp"
gopt_type,gopt_s_fnameb,t1234,bes,engine_path,mm,mode,alg,opt_lin,np,nc,step_int,csv=par_fit_inp(default_input_fname)
ds=DihScan(gopt_s_fnameb,engine_path,mm,opt_lin,np,nc,bes,t1234)
if not gopt_type=="ginp":
environ["ENGINE_DIR"]=engine_path+"engine_dir"
p,c,ol_templ,lines=read_add(mm,opt_lin,np,nc,1)
def engine_rmse(p):
print p
step=1
step_int=10
write_add(p,c,mm,ol_templ,lines,1,step,step_int)
ds.run_scan(p,c,mm,ol_templ,lines)
rmse=ds.calc_rmse(csv,step,step_int)
print rmse
return rmse
if gopt_type=="full":
ds.read_gamess_outputs()
elif gopt_type=="comp":
ds.read_gouts_data()
#print ds.dt
#ds.read_gamess_outputs()
#ds.write_gouts_data()
#ds.read_gouts_data()
#ds.write_engine_inputs()
#engine_rmse(p)
default_input_fname = "dih_scan_inp"
gopt_type, gopt_s_fnameb, t1234, bes, engine_path, mm, mode, ref_p, alg, opt_lin, np, nc, step_int, csv = par_fit_inp(
default_input_fname)
ds = DihScan(gopt_s_fnameb, engine_path, mm, opt_lin, np, nc, bes, t1234)
if not gopt_type == "ginp":
environ["ENGINE_DIR"] = engine_path + "engine_dir"
p, c, ol_templ, lines = read_add(mm, opt_lin, np, nc, 1)
def engine_rmse(p):
print p
step = 1
step_int = 10
write_add(p, c, mm, ol_templ, lines, 1, step, step_int)
ds.run_scan(p, c, mm, ol_templ, lines)
rmse = ds.calc_rmse(csv, step, step_int)
print rmse
return rmse
if gopt_type == "full":
ds.read_gamess_outputs()
elif gopt_type == "comp":
ds.read_gouts_data()