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)