def run_dih_elem(self,m):
fnameb=m.name
coengine_name="coengine_"+fnameb
f=open("../Data/Engine/"+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
system(comm)
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.*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()
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.
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.
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]=ppM[i]-eps
ppP[i]=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()
