def start_from_beginning(maindir,srclmp,lmp_execdir,destdir,\
data_fname,temp,polywtperc,rcut,blist,\
alist,k_phi,wlccheck,anglstyl,nchains,\
polydens,graftMW,initcom,nmonval,\
graftval,epsval,graftopt,geninp_list,\
begin_fresh,key_epsval,epsval_pg):
if begin_fresh == -1:
list_of_files = glob.glob('*')
if list_of_files != []:
for f in list_of_files:
if not os.path.isdir(f):
os.remove(f)
for fylcnt in range(len(geninp_list)):
cpy_main_files(maindir, destdir, geninp_list[fylcnt])
# Manipulate Files
os.chdir(destdir)
print("Manipulating input parameter file..")
launch_fyl = 'params_input.dat'
fr = open('params_input_var.dat', 'r')
fw = open(launch_fyl, 'w')
fid = fr.read().replace("py_inputname",str(data_fname)).\
replace("py_graftstyle",str(int(graftopt))).\
replace("py_nchains_bb",str(nchains)).\
replace("py_nmons_bb",str(nmonval)).\
replace("py_graftperc",str(graftval)).\
replace("py_polydens",str(polydens)).\
replace("py_graftmons",str(graftMW)).\
replace("py_comdist", str(initcom)).\
replace("py_polyperc",str(polywtperc))
fw.write(fid)
fw.close()
fr.close()
# Generate Required Files for LAMMPS
print("Running FORTRAN script for generating Datafile")
subprocess.call(["ifort","-r8","-qopenmp","-mkl",\
"ran_numbers.f90","lmp_params.f90",\
"lammps_inp2.f90","-o","lmpinp.o"])
subprocess.call(["./lmpinp.o", "params_input.dat"])
datafind = 1
if not os.path.exists(data_fname):
print(data_fname, "not found - check input code")
datafind = -1
if datafind == 1:
cpy_lammps_files(maindir,srclmp,lmp_execdir,destdir,graftopt,\
data_fname,nmonval,graftval,anglstyl)
create_infile(maindir,srclmp,destdir,nmonval,epsval,graftopt,\
temp,graftval,polywtperc,rcut,blist,alist,k_phi,\
wlccheck,anglstyl,graftval,key_epsval,epsval_pg)
generate_backup(maindir, srclmp, lmp_execdir, destdir)
if not os.path.isdir(workdir_subpdi):
print("ERROR: ", workdir_subpdi, " not found")
continue
os.chdir(workdir_subpdi)
destdir = os.getcwd()
print( "Starting analysis for case ", ncases_pdi[casenum], "in ",\
free_chains[ifree],dirstr)
#---Copying files------
print("Current Dir ", destdir)
print("Copying Files")
for fyllist in range(len(ana_files)):
cpy_main_files(maindir, destdir, ana_files[fyllist])
for fyllist in range(len(job_files)):
cpy_main_files(jobdir, destdir, job_files[fyllist])
dataname = find_datafyle(free_chains[ifree],fylstr,\
ncases_pdi[casenum],destdir)
if dataname == 'ERROR':
print("ERROR: No restart files found")
continue
#latest_traj = find_latest_trajfyle(traj_pref,destdir)
#if latest_traj == 'ERROR':
# print("ERROR: No trajectory files found")
# continue
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)
create_infile(maindir, srclmpdir, smd_workdir, nmons[bblen],
epsarr_pg[eps], graftopt, temp)
gen_launch_fyl(smd_workdir, 'jobsmd_var.sh', 'jobsmd.sh',
graftarr[glen], epsarr_pg[eps])
subprocess.call(['qsub', 'jobsmd.sh'])
cleanup_files(umbdir, "f90")
print("Archive files found: RESTARTING from archives")
if archive_flag == 0:
os.chdir(workdir_subpdi)
destdir = os.getcwd()
print( "Starting case", ncases_pdi[caselen], "for ",\
free_chains[ifree],dirstr)
#---Copying files------
print("Current Dir ", destdir)
print("Copying Files")
for fyllist in range(len(f90_files)):
cpy_main_files(maindir, destdir, f90_files[fyllist])
for fyllist in range(len(lmp_files)):
cpy_main_files(lmpdir, destdir, lmp_files[fyllist])
srcfyl = '/home/dorfmank/vsethura/mylammps/src/lmp_mesabi'
desfyl = destdir + '/lmp_mesabi'
shutil.copy2(srcfyl, desfyl)
#----Run PDI code------
print("Running PDI calculation file")
tot_chains = free_chains[ifree] + graft_chains
init_pdi_write(pdi_free,free_avg_mw,free_chains[ifree],\
pdi_graft,graft_avg_mw,graft_chains,destdir)
compile_and_run_pdi(destdir)
print( "EpsValue_polymer_graft: ", epsarr_pg[eps])
workdir3 = workdir1 + '/epsval_' + str(epsarr_pg[eps])
if not os.path.isdir(workdir3):
print(workdir3, " does not exist")
continue
#------All copying/manipulations-------------------------------------
os.chdir(workdir3)
destdir = os.getcwd()
print( "Copying Files..")
for fylcnt in range(len(fyl_list)):
cpy_main_files(maindir, destdir, fyl_list[fylcnt])
print("Creating/finding Datafile..")
if int(graftopt) == 3:
[datafyle,flag] = find_datafyl(destdir,
epsarr_ps[eps],epsarr_sg[eps],epsarr_pg[eps],wlccheck)
else:
[datafyle,flag] = find_datafyl_mc(destdir,
epsarr_pg[eps])
if flag == -1:
print("datafile not found in ", destdir)
continue
if allana == 0: #Only analyzing the latest trajectory
data_fname = "input_" + str(epsarr_pg[eps]) + ".dat"
print("EpsValue_polymer_graft: ", epsarr_pg[eps])
workdir3 = workdir1 + '/epsval_' + str(epsarr_pg[eps])
if not os.path.isdir(workdir3):
os.mkdir(workdir3)
os.chdir(workdir3)
destdir = os.getcwd()
if restart == 0:
for fylcnt in range(len(geninp_list)):
cpy_main_files(maindir, destdir, geninp_list[fylcnt])
# Manipulate Files
os.chdir(destdir)
print("Manipulating input parameter file..")
launch_fyl = 'params_input.dat'
fr = open('params_input_var.dat', 'r')
fw = open(launch_fyl, 'w')
fid = fr.read().replace("py_inputname",str(data_fname)).\
replace("py_graftstyle",str(int(graftopt))).\
replace("py_nchains_bb",str(nchains)).\
replace("py_nmons_bb",str(nmons[bblen])).\
replace("py_graftperc",str(graftarr[glen])).\
replace("py_polydens",str(polydens)).\
replace("py_graftmons",str(graftMW)).\