def usage():
"""
Display the usage information for this script
"""
size = psize.Psize()
usage = "\n"
usage = usage + "Use this script to generate new APBS input files or split an existing\n"
usage = usage + "parallel input file into multiple async files.\n\n"
usage = usage + "Usage: inputgen.py [opts] <filename>\n"
usage = usage + "Optional Arguments:\n"
usage = usage + " --help : Display this text\n"
usage = usage + " --split : Split an existing parallel input file to multiple\n"
usage = usage + " async input files.\n"
usage = usage + " --potdx : Create an input to compute an electrostatic potential map.\n"
usage = usage + " --method=<value> : Force output file to write a specific APBS ELEC\n"
usage = usage + " method. Options are para (parallel), auto\n"
usage = usage + " (automatic), manual (manual), or async (asynchronous).\n"
usage = usage + " solve. async will result in multiple input files.\n"
usage = usage + " --cfac=<value> : Factor by which to expand molecular dimensions to\n"
usage = usage + " get coarse grid dimensions.\n"
usage = usage + " [default = %g]\n" % size.getConstant(
"cfac")
usage = usage + " --fadd=<value> : Amount to add to molecular dimensions to get fine\n"
usage = usage + " grid dimensions.\n"
usage = usage + " [default = %g]\n" % size.getConstant(
"fadd")
usage = usage + " --space=<value> : Desired fine mesh resolution\n"
usage = usage + " [default = %g]\n" % size.getConstant(
"space")
usage = usage + " --gmemfac=<value> : Number of bytes per grid point required\n"
usage = usage + " for sequential MG calculation\n"
usage = usage + " [default = %g]\n" % size.getConstant(
"gmemfac")
usage = usage + " --gmemceil=<value> : Max MB allowed for sequential MG\n"
usage = usage + " calculation. Adjust this to force the\n"
usage = usage + " script to perform faster calculations (which\n"
usage = usage + " require more parallelism).\n"
usage = usage + " [default = %g]\n" % size.getConstant(
"gmemceil")
usage = usage + " --ofrac=<value> : Overlap factor between mesh partitions\n"
usage = usage + " [default = %g]\n" % size.getConstant(
"ofrac")
usage = usage + " --redfac=<value> : The maximum factor by which a domain\n"
usage = usage + " dimension can be reduced during focusing\n"
usage = usage + " [default = %g]\n" % size.getConstant(
"redfac")
usage = usage + " --istrng=<value> : Ionic strength (M). Na+ anc Cl- ions will be used\n"
sys.stderr.write(usage)
sys.exit(2)
def usage():
"""
Display the usage information for this script
"""
size = psize.Psize()
usage = "\n"
usage = usage + "Use this script to generate new APBS input files or split an existing\n"
usage = usage + "parallel input file into multiple async files.\n\n"
usage = usage + "Usage: inputgen.py [opts] <filename>\n"
usage = usage + "Optional Arguments:\n"
usage = usage + " --help : Display this text\n"
usage = usage + " --split : Split an existing parallel input file to multiple\n"
usage = usage + " async input files.\n"
usage = usage + " --METHOD=<value> : Force output file to write a specific APBS ELEC\n"
usage = usage + " method. Options are para (parallel), auto\n"
usage = usage + " (automatic), manual (manual), or async (asynchronous).\n"
usage = usage + " solve. async will result in multiple input files.\n"
usage = usage + " --CFAC=<value> : Factor by which to expand molecular dimensions to\n"
usage = usage + " get coarse grid dimensions.\n"
usage = usage + " [default = %g]\n" % size.getConstant(
"CFAC")
usage = usage + " --FADD=<value> : Amount to add to molecular dimensions to get fine\n"
usage = usage + " grid dimensions.\n"
usage = usage + " [default = %g]\n" % size.getConstant(
"FADD")
usage = usage + " --SPACE=<value> : Desired fine mesh resolution\n"
usage = usage + " [default = %g]\n" % size.getConstant(
"SPACE")
usage = usage + " --GMEMFAC=<value> : Number of bytes per grid point required\n"
usage = usage + " for sequential MG calculation\n"
usage = usage + " [default = %g]\n" % size.getConstant(
"GMEMFAC")
usage = usage + " --GMEMCEIL=<value> : Max MB allowed for sequential MG\n"
usage = usage + " calculation. Adjust this to force the\n"
usage = usage + " script to perform faster calculations (which\n"
usage = usage + " require more parallelism).\n"
usage = usage + " [default = %g]\n" % size.getConstant(
"GMEMCEIL")
usage = usage + " --OFAC=<value> : Overlap factor between mesh partitions\n"
usage = usage + " [default = %g]\n" % size.getConstant(
"OFAC")
usage = usage + " --REDFAC=<value> : The maximum factor by which a domain\n"
usage = usage + " dimension can be reduced during focusing\n"
usage = usage + " [default = %g]\n" % size.getConstant(
"REDFAC")
sys.stderr.write(usage)
sys.exit(2)
]
try:
opts, args = getopt.getopt(sys.argv[1:], shortOptList, longOptList)
except getopt.GetoptError, details:
sys.stderr.write("Option error (%s)!\n" % details)
usage()
if len(args) != 1:
sys.stderr.write("Invalid argument list!\n")
usage()
else:
filename = args[0]
method = ""
size = psize.Psize()
async = 0
split = 0
for o, a in opts:
if o == "--help":
usage()
if o == "--split": split = 1
if o == "--method":
if a == "para":
sys.stdout.write("Forcing a parallel calculation\n")
method = "mg-para"
elif a == "auto":
sys.stdout.write("Forcing a sequential calculation\n")
method = "mg-auto"
elif a == "async":
def main():
"""
Main
"""
import getopt
filename = ""
short_opt_list = ""
long_opt_list = [
"help", "split", "potdx", "method=", "cfac=", "space=", "gmemceil=",
"gmemfac=", "ofrac=", "redfac=", "istrng=", "fadd="
]
try:
opts, args = getopt.getopt(sys.argv[1:], short_opt_list, long_opt_list)
except getopt.GetoptError as err:
sys.stderr.write("Option error (%s)!\n" % err)
usage()
if len(args) != 1:
sys.stderr.write("Invalid argument list!\n")
usage()
else:
filename = args[0]
method = ""
size = psize.Psize()
async_val = 0
split = 0
istrng = 0
potdx = 0
for opt, arg in opts:
if opt == "--help":
usage()
if opt == "--split":
split = 1
if opt == "--potdx":
potdx = 1
if opt == "--method":
if arg == "para":
sys.stdout.write("Forcing a parallel calculation\n")
method = "mg-para"
elif arg == "auto":
sys.stdout.write("Forcing a sequential calculation\n")
method = "mg-auto"
elif arg == "async":
sys.stdout.write("Forcing an asynchronous calculation\n")
method = "mg-para"
async_val = 1
elif arg == "manual":
sys.stdout.write("Forcing a manual calculation\n")
method = "mg-manual"
else:
sys.stdout.write("Incorrect method argument: %s\n" % arg)
sys.stdout.write("Defaulting to memory dependent result\n")
if opt == "--cfac":
size.setConstant("cfac", float(arg))
if opt == "--space":
size.setConstant("space", float(arg))
if opt == "--gmemfac":
size.setConstant("gmemfac", int(arg))
if opt == "--gmemceil":
size.setConstant("gmemceil", int(arg))
if opt == "--ofrac":
size.setConstant("ofrac", float(arg))
if opt == "--redfac":
size.setConstant("redfac", float(arg))
if opt == "--fadd":
size.setConstant("fadd", int(arg))
if opt == "--istrng":
istrng = float(arg)
if split == 1:
split_input(filename)
else:
size.runPsize(filename)
data = Input(filename, size, method, async_val, istrng, potdx)
data.print_input_files()