def construct_conditions(args, fileformatter, inp_filebase, system_file):
bias_tags, windows = us_process.read_windows_file(args.windows_filename)
bias_functions = json.load(open(args.bias_functions_filename))
op_tags = us_process.get_op_tags_from_bias_functions(
bias_functions, bias_tags)
# Linear square well functions are all the same
for bias_function in bias_functions['origami']['bias_functions']:
if bias_function['type'] == 'LinearStepWell':
slope = bias_function['slope']
min_outside_bias = bias_function['min_bias']
grid_biases = []
for window in windows:
for rep in range(args.reps):
filebase = '{}_run-{}_rep-{}'.format(inp_filebase, args.run, rep)
grid_biases.append(biases.GridBias(op_tags, window,
min_outside_bias, slope, args.temp, filebase))
conditions_map = {'temp': [args.temp],
'staple_m': [args.staple_m],
'bias': grid_biases}
# either get rid of this too or make a list of filebases for creating sim collections
return conditions.AllSimConditions(conditions_map, fileformatter, system_file)
def construct_variable_temp_conditions(args, stack_mult, fileformatter, system_file):
stack_bias = biases.StackingBias(args.stack_ene, stack_mult)
conditions_map = {'temp': args.temps,
'staple_m': [args.staple_m],
'bias': [stack_bias]}
return conditions.AllSimConditions(conditions_map, fileformatter, system_file)
def construct_conditions(args, fileformatter):
conditions_map = {
'temp': args.temps,
'staple_m': [args.staple_m],
'bias': [biases.NoBias()]
}
return conditions.AllSimConditions(conditions_map, fileformatter)
def main():
args = parse_args()
conditions_map = construct_conditions_map(args)
fileformatter = construct_fileformatter()
all_conditions = conditions.AllSimConditions(conditions_map, fileformatter)
inp_filebase = create_input_filepathbase(args)
enums = outputs.EnumCollection(inp_filebase, all_conditions)
out_filebase = create_output_filepathbase(args)
enums.calc_all_1d_means(out_filebase)
def construct_conditions(args, fileformatter):
stack_biases = []
for stack_mult in args.stack_mults:
stack_bias = biases.StackingBias(args.stack_ene, stack_mult)
stack_biases.append(stack_bias)
conditions_map = {'temp': args.temps,
'staple_m': [args.staple_m],
'bias': stack_biases}
return conditions.AllSimConditions(conditions_map, fileformatter)
def main():
args = parse_args()
system_file = files.JSONStructInpFile(args.system_filename)
conditions_map = construct_conditions_map(args)
fileformatter = construct_fileformatter()
all_conditions = conditions.AllSimConditions(
conditions_map, fileformatter, system_file)
inp_filebase = create_input_filepathbase(args)
enums = outputs.EnumCollection(inp_filebase, all_conditions)
out_filebase = create_output_filepathbase(args)
enums.calc_all_1d_means(out_filebase)
