Added fetch_input.py

Pytools/fetch_input.py

+#!/usr/bin/python3
+
+from __future__ import print_function
+import sys
+from os import path, remove
+import yaml
+import json
+
+rytoev = 13.6056980659
+
+#########################
+# STATIC DEFAULT VALUES #
+#########################
+
+default = {}
+# input_west
+default["input_west"] = {}
+default["input_west"]["qe_prefix"] = "pwscf"
+default["input_west"]["west_prefix"] = "west"
+default["input_west"]["outdir"] = "./"
+# wstat_control
+default["wstat_control"] = {}
+default["wstat_control"]["wstat_calculation"] = "S"
+default["wstat_control"]["n_pdep_eigen"] = 1 # dynamically set to the number of electrons 
+default["wstat_control"]["n_pdep_times"] = 4
+default["wstat_control"]["n_pdep_maxiter"] = 100
+default["wstat_control"]["n_dfpt_maxiter"] = 250
+default["wstat_control"]["n_pdep_read_from_file"] = 0
+default["wstat_control"]["trev_pdep"] = 1.e-3
+default["wstat_control"]["trev_pdep_rel"] = 1.e-1
+default["wstat_control"]["tr2_dfpt"] = 1.e-12
+default["wstat_control"]["l_kinetic_only"] = False
+default["wstat_control"]["l_minimize_exx_if_active"] = False
+default["wstat_control"]["l_use_ecutrho"] = False
+default["wstat_control"]["qlist"] = [ 1 ] # dynamically set to the actual number of q 
+# wfreq_control
+default["wfreq_control"] = {}
+default["wfreq_control"]["wfreq_calculation"] = "XWGQ"
+default["wfreq_control"]["n_pdep_eigen_to_use"] = 1 # dynamically set to the number of electrons
+default["wfreq_control"]["qp_bandrange"] = [1,2]
+default["wfreq_control"]["macropol_calculation"] = 'N'
+default["wfreq_control"]["n_lanczos"] = 30
+default["wfreq_control"]["n_imfreq"] = 128 
+default["wfreq_control"]["n_refreq"] = 272 # dynamically set so that ecut_refreq / n_refreq = 0.1 eV 
+default["wfreq_control"]["ecut_imfreq"] = 25. # dynamically set to ecutrho
+default["wfreq_control"]["ecut_refreq"] = 2. # dynamically set to contain eks + 0.5 Ry padding 
+default["wfreq_control"]["wfreq_eta"] = 0.05 / rytoev
+default["wfreq_control"]["n_secant_maxiter"] = 21
+default["wfreq_control"]["trev_secant"] = 0.05 / rytoev
+default["wfreq_control"]["l_enable_lanczos"] = True
+default["wfreq_control"]["o_restart_time"] = 0.
+default["wfreq_control"]["ecut_spectralf"] = [-2.,1.] 
+default["wfreq_control"]["n_spectralf"] = 204
+# westpp_control
+default["westpp_control"] = {}
+default["westpp_control"]["westpp_calculation"] = "r"
+default["westpp_control"]["westpp_range"] = [1,2]
+default["westpp_control"]["westpp_format"] = "C"
+default["westpp_control"]["westpp_sign"] = False
+default["westpp_control"]["westpp_n_pdep_eigen_to_use"] = 1
+default["westpp_control"]["westpp_r0"] = [0.,0.,0.]
+default["westpp_control"]["westpp_nr"] = 100
+default["westpp_control"]["westpp_rmax"] = 1.
+default["westpp_control"]["westpp_epsinfty"] = 1.
+
+############################
+# DYNAMICAL DEFAULT VALUES #
+############################
+
+def update_default_values(key,kwargs) :
+    assert key in default.keys()
+    #
+    if key == "wstat_control" :
+       #
+       assert("nq") in kwargs.keys()
+       nq = kwargs["nq"] 
+       default[key]["qlist"] = [ i+1 for i in range(nq) ]
+       #
+       assert("nelec") in kwargs.keys()
+       nelec = kwargs["nelec"] 
+       default[key]["n_pdep_eigen"] = nelec
+    #
+    if key == "wfreq_control" :
+       #
+       assert("nelec") in kwargs.keys()
+       nelec = kwargs["nelec"] 
+       default[key]["n_pdep_eigen_to_use"] = nelec
+       #
+       assert("ecutrho") in kwargs.keys()
+       ecutrho = kwargs["ecutrho"] 
+       default[key]["ecut_imfreq"] = ecutrho
+       #
+       assert("eksmax") in kwargs.keys()
+       eksmax = kwargs["eksmax"] 
+       default[key]["ecut_refreq"] = eksmax + 0.5
+       default[key]["n_refreq"] = int( default[key]["ecut_refreq"] * rytoev / 0.1 ) 
+
+################
+# OPEN & PARSE #
+################
+
+def open_and_parse_file(fileName="west.in") :
+    """Opens a file and parses it using the YAML sintax 
+
+    :param fileName: name of the file
+    :type fileName: ``string``
+    :return: parsed data
+    :rtype: ``dict``
+
+    """
+    data = {}
+    try : 
+       with open(fileName, 'r') as stream:
+           try:
+              data = yaml.load(stream,Loader=yaml.SafeLoader)
+           except:
+              print("Cannot parse file")
+    except : 
+       print("Cannot open file : ",fileName)
+    #
+    return data
+
+##############
+# CHECK DICT #
+##############
+
+def check_dict(parsed_data={}, default_data={}) : 
+    """Check data: returns a dictionary with the same keys of default_data. If keys are matching, values of default_data are replaced with those of parsed_data. 
+
+    :param parsed_data: parsed data 
+    :type parsed_data: ``dict``
+    :param default_data: default data 
+    :type default_data: ``dict``
+    :return: checked data
+    :rtype: ``dict``
+
+    """
+    #
+    data = {}
+    #
+    for key in default_data.keys() : 
+        if key in parsed_data.keys() : 
+           data[key] = parsed_data[key]
+        else : 
+           data[key] = default_data[key]
+    #
+    return data
+
+###########
+# SUPPORT #
+###########
+
+def print_bar(prefix="",nmarks=92) : 
+    """Prints bar.
+
+    :param prefix: prefix
+    :type prefix: ``string``
+    :param nmarks: number of marks
+    :type nmarks: ``int``
+    """
+    #
+    s = prefix
+    for i in range(nmarks) : 
+       s+="-"
+    print(s)
+
+#########
+# PRINT #
+#########
+
+def print_dict(title="input_west", data={}) : 
+    """Prints data.  
+
+    :param title: title
+    :type title: ``string``
+    :param data: data to print
+    :type default_data: ``dict``
+
+    """
+    #
+    nmarks = 92
+    nspaces = 5 
+    s = ""
+    for i in range(nspaces) : 
+       s+=" "
+    #
+    print_bar(s,nmarks)
+    print(s+"I/O Summary : "+str(title))
+    print_bar(s,nmarks)
+    for key in data.keys() :
+       print(s+key,"=",data[key])
+    print_bar(s,nmarks)
+    sys.stdout.flush()
+
+#############
+# INTERFACE #
+#############
+
+def read_keyword_from_file(*args, **kwargs):
+    """Read keyword from file  
+
+    :return: read data
+    :rtype: ``dict``
+
+    """
+    #
+    fileName = args[0]
+    keyword = args[1] 
+    #
+    # Assign static & dynamical defaults 
+    # 
+    default_data = default[keyword]
+    update_default_values(keyword,kwargs) 
+    #
+    # Read input file  
+    #
+    input_data = open_and_parse_file(fileName)
+    if keyword in input_data.keys() :
+       parsed_data = input_data[keyword]
+    else : 
+       parsed_data = {}
+    #
+    # Compare defaults and input variables 
+    #
+    data = check_dict( parsed_data, default_data )
+    #
+    # Print
+    #
+    print_dict(keyword, data)
+    #
+    return data
+
+########
+# TEST #
+########
+
+def test() :
+    #
+    fileName = "west.in"
+    #
+    with open(fileName, "w") as file :
+       file.write("""
+input_west : 
+   qe_prefix : molecule
+   west_prefix : molecule
+   outdir : "./"
+wstat_control : 
+   wstat_calculation : R # this is a comment
+   unknown_key : value # this line will be read but not passed 
+""")
+    #
+    read_keyword_from_file(fileName,"input_west")
+    read_keyword_from_file(fileName,"wstat_control",nq=20,nelec=10)
+    read_keyword_from_file(fileName,"wfreq_control",nelec=10,ecutrho=30.,eksmax=2.)
+    read_keyword_from_file(fileName,"westpp_control")
+    #
+    remove(fileName)
+
+if __name__ == "__main__":
+    # execute only if run as a script
+    test()
+