print("EpsValue_polymer_graft: ", epsarr_pg[eps])
if ana_flag == 'smd':
print("Generating SMD initial conditions ..")
#------Create SMD work directory-----------------------
traj_workdir = workdir3
smd_workdir = traj_workdir + '/smd_main'
if not os.path.isdir(smd_workdir):
os.mkdir(smd_workdir)
#------All copying/manipulations-----------------------
print("Finding latest archived restart file..")
refyle = find_recent_file(traj_workdir, res_prefix)
if refyle == "nil":
print("no restart file found in ", traj_workdir)
continue
else:
os.chdir(smd_workdir)
print("Creating datafile..")
cpy_main_files(traj_workdir, smd_workdir, refyle)
lmp_execfile = lmp_execdir + '/' + lmp_fylename
create_datafyle(lmp_execfile, refyle, smd_fylename)
for fylcnt in range(len(fyls_main)):
cpy_main_files(srclmpdir, smd_workdir, fyls_main[fylcnt])
cpy_main_files(lmp_execdir, smd_workdir, lmp_fylename)
else:
print("%s\t %g\t %d\t %s\t %d\t" %
("Restarting simulation for pdi/nfree/arch/casenum",
pdi_free, free_chains[ifree], fylstr,
ncases_pdi[caselen]))
if not os.path.isdir(workdir_subpdi):
print(workdir_subpdi, "not found")
continue
os.chdir(workdir_subpdi)
destdir = os.getcwd()
os.chdir(workdir_subpdi)
print("Current path: ", workdir_subpdi)
latest_restfyl = find_recent_file(destdir, archive_file_style)
delimited_vals = re.split("\W+|_", latest_restfyl)
timeval = delimited_vals[len(delimited_vals) - 2]
print("timeval", timeval)
if int(timeval) > maxtime:
print('Max time reached: ', timeval, maxtime)
continue
elif int(timeval) > equiltime:
print('Running production cycle..')
for fyllist in range(len(lmp_long)):
cpy_main_files(lmpdir, destdir, lmp_long[fyllist])
fylename = destdir + '/lmp_mesabi'
if list_of_files == []:
begin_fresh = 1 #No files here to start with
print("No files found in: ", destdir)
print("Beginning new simulation")
start_from_beginning(maindir,srclmp,lmp_execdir,destdir,\
data_fname,temp,polywtperc,rcut,blist,\
alist,k_phi,wlccheck,anglstyl,nchains,\
polydens,graftMW,initcom,nmons[bblen],\
graftarr[glen],epsarr_gg[eps],graftopt,\
geninp_list,begin_fresh,key_eps_pg,\
epsval_pg)
else:
latest_restfyl = find_recent_file(destdir,restname)
#restart file should be of type archive_*
# check whether archive files are present
if latest_restfyl == "nil":
restflag = -1
print("ERROR: Could not find restart files")
continue
else:
delimited_vals = re.split("\W+|_",latest_restfyl)
timeval = delimited_vals[len(delimited_vals)-1]
if int(timeval) < min_equilsteps:
print("ERROR: Timestep<",min_equilsteps)
continue
else:
os.chdir(workdir3)
destdir = os.getcwd()
print("Currently in: ", destdir)
list_of_files = glob.glob('*')
if list_of_files == []:
print("No files here: Check path")
continue
else:
trajflag = 1 #trajectory found=1
flagstr = -1 #is a string = 1
latest_trajfyl = find_recent_file(destdir, dumpname)
#dumpfile should be of type dump_stage_*
if latest_trajfyl == "nil":
trajflag = -1
else:
delimited_vals = re.split("\W+|_", latest_trajfyl)
timeval = delimited_vals[len(delimited_vals) - 2]
#check whether the dumpfile is dump_stage1.*
flagstr = check_integer(timeval)
if flagstr == 1:
print("Did not find matching dumpfile, restarting")
trajflag = -1
elif int(timeval) < 1000000:
print("Timestep less than 1000000, restarting")
trajflag = -1
else: