mirror of https://gitlab.com/QEF/q-e.git
Added a tool to convert ibrav/celldm to lattice vectors (not so useful) and another to convert the lattice vectors (in bohr or angstrom) to ibrav/celldm
Added documentation, sort of, for all the tools (README) Does anybody know if bs.awk and mv.awk are used for anything, or can understand what they do? git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@13419 c92efa57-630b-4861-b058-cf58834340f0
This commit is contained in:
paulatto
parent
0c6aa7ed23
commit
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@ -13,13 +13,18 @@ TLDEPS= bindir mods libs pw libfft libla
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LIBOBJS = ../../clib/clib.a ../../iotk/src/libiotk.a
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all : tldeps dist.x ev.x kpoints.x pwi2xsf.x
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all : tldeps dist.x ev.x kpoints.x pwi2xsf.x ibrav2cell.x
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dist.x : dist.o $(PWOBJS) $(QEMODS) $(LIBOBJS)
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$(LD) $(LDFLAGS) -o $@ \
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dist.o $(PWOBJS) $(QEMODS) $(LIBOBJS) $(LIBS)
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- ( cd ../../bin ; ln -fs ../PW/tools/$@ . )
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ibrav2cell.x : ibrav2cell.o $(PWOBJS) $(QEMODS) $(LIBOBJS)
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$(LD) $(LDFLAGS) -o $@ \
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ibrav2cell.o $(PWOBJS) $(QEMODS) $(LIBOBJS) $(LIBS)
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- ( cd ../../bin ; ln -fs ../PW/tools/$@ . )
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ev.x : ev.o ev_xml.o $(PWOBJS) $(QEMODS) $(LIBOBJS)
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$(LD) $(LDFLAGS) -o $@ \
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ev.o ev_xml.o $(PWOBJS) $(QEMODS) $(LIBOBJS) $(LIBS)
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@ -0,0 +1,36 @@
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A collection of simple tools for specific tasks:
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ev.x :
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Run interatively. It reads a file containing 2 columns: lattice parameter and
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corresponding total energy, it gives in output optimized lattice parameter,
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bulk modulus and more.
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Contributions by Eyvaz Isaev
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dist.x :
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Same input as pw.x, find distances, nearest neighbors, angles
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taking into account periodicity
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ibrav2cell.x :
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read a &system namelist containing only ibrav and celldm(1..6) (same meaning as in pw.x and cp.x)
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prints on standard output the unit cell in Bohr
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cell2ibrav.py :
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python script that takes a unit cell in Bohr or Angstrom units and find the value
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of ibrav and celldm(1..6) that generate it. Run 'cell2ibrav.py -h' for help.
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(it works in the stupidest way possible, by checking all of them, it uses ibrav2cell.x)
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pwi2xsf.sh, pwo2xsf.sh :
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convert a pw.x input or output to the xcrysden format
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qeout2axsf.sh :
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convert pw.x output to aniimated xcrysden file
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cif2qe.sh :
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generate a pw.x format from the crystal structure in a cif file
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castep2qe.sh :
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convert a CASTEP input to pw.x
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md_analyzer.sh :
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it reads the pw.x output of an md run and prints, for each step, total, kinetic and potential energies, and temperature
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@ -0,0 +1,177 @@
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#!/usr/bin/python
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from os.path import realpath
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from sys import argv
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binary=realpath(__file__)
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#myself=argv[0].replace("./","")
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binary = binary.replace("cell2ibrav.py","ibrav2cell.x")
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#print binary
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binary = "/home/paulatto/espresso/bin/ibrav2cell.x"
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def main() :
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from numpy import array
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from argparse import ArgumentParser
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parser = ArgumentParser()
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#parser.add_argument('-t', type=str, default="pbtex", dest="type_cal")
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#parser.add_argument('-n', type=int, default=1, dest="n_random")
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#parser.add_argument('-d', type=str, default="./", dest="data_dir")
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#parser.add_argument('-p', type=int, default=1, dest="population")
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#parser.add_argument('-f', type=str, default="2x2_dynq", dest="fildyn_prefix_harmonic")
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##parser.add_argument('--e0', type=float, default=0., dest="e0")
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#parser.add_argument('--nq', type=int, default=[3, 2, 2, 2], nargs=4, dest="nq",
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#metavar=("NQ_irr","NQ_x","NQ_y","NQ_z"))
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#parser.add_argument('--const', action='append', type=str, metavar="par=value", default=[])
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#parser.add_argument(metavar='par', type=str, nargs='*', default=["p3", "p4"], dest="parameters",
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#help="name of the parameters to minimize." )
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parser.add_argument('-i', action='append', type=int, metavar="ibrav", dest="ibrav_list", default=[],
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help="ibrav value to explore, can be repeated (default: all)")
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parser.add_argument('-c', type=float, default=[0, 0, 0, 0, 0, 0, 0, 0, 0], nargs=9, dest="at",
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metavar=("a1x","a1y","a1z","a2x","a2y","a2z", "a3x", "a3y", "a3z"),
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help="cell parameters (default: read from standard input)")
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parser.add_argument('-A', default=False, action="store_true", dest="angst", help="cell is entered in Agstrom units (default: bohr")
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parser.add_argument('--celldm', type=float, default=[1, 1, 1, 0.5, 0.5, 0.5], nargs=6, dest="celldm",
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metavar=("1","2","3","4","5","6"), help="initial values of celldm(1..6), you have to specify all 6 (default: '1 0 0 0 0 0')")
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parser.add_argument('-t', type=float, default=1.e-3, dest="mthr", help="match threshold", metavar="THR")
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parser.add_argument('-k', type=float, default=1.e-15, dest="kthr", help="convergence threshold", metavar="THR")
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parser.add_argument('-x', type=str, dest="binary", help="full path to the ibrav2cell.x tool from PW/tools/ (default: look in the same directory as this program)", metavar="/path/to/ibrav2cell.x")
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args = parser.parse_args()
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ibrav_list = [1,2,3,4,5,-5,6,7,8,9,-9,10,11,12,-12,13,14]
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if args.ibrav_list == []:
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args.ibrav_list = ibrav_list
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#print args
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if args.binary:
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global binary
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binary = args.binary
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# cell = [ 3.900896593574796, -2.252183691403927, 18.043044401344225,
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# 0.000000000000000, 4.504367382807855, 18.043044401344225,
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# -3.900896593574796, -2.252183691403927, 18.043044401344225]
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# cell = [ 1.200000000000000E+01, 0.000000000000000E+00, 0.000000000000000E+00,
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# 1.224000000000000E+01, 7.585670702053973E+00, 0.000000000000000E+00,
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# 7.979999999999999E+00, 1.474991525399383E+00, 2.168870673876157E+00]
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cell = args.at
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if all(array(cell) == 0) :
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cell = cell_stdin()
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if args.angst:
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cell = array(cell)*1.889725989
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bnds = ((0,None), (0,None), (0,None), (-1,1), (-1,1), (-1,1))
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for ibrav in args.ibrav_list:
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p=args.celldm #[1,1,1,0.5,0.5,0.5]
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options = { "ibrav" : ibrav,
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"cell" : cell
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}
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from scipy.optimize import minimize
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from scipy.optimize import basinhopping
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#r = basinhopping(recompute, p, minimizer_kwargs={"args":tuple([options])}, niter=10, bounds=bnds)
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r = minimize(recompute, p, args=tuple([options]), method="L-BFGS-B", tol=args.kthr, bounds=bnds)
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if r["fun"] < args.mthr:
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print "match found: ibrav =", ibrav
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check_zero(r["x"], ibrav)
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#print make_namelist(ibrav,r["x"])
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def run_command(executable_file, input_data):
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import subprocess
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proc = subprocess.Popen(executable_file,
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stdin=subprocess.PIPE,
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stdout=subprocess.PIPE,
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stderr=subprocess.STDOUT,
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)
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output, error = proc.communicate(input_data)
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return (output, error)
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def make_namelist(ibrav,p):
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replacements = { "ibrav" : ibrav,
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"celldm1" : p[0],
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"celldm2" : p[1],
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"celldm3" : p[2],
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"celldm4" : p[3],
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"celldm5" : p[4],
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"celldm6" : p[5]
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}
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systemnl = """
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&system
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ibrav = {ibrav},
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celldm(1) ={celldm1},
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celldm(2) ={celldm2},
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celldm(3) ={celldm3},
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celldm(4) ={celldm4},
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celldm(5) ={celldm5},
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celldm(6) ={celldm6}
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/
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"""
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return systemnl.format(**replacements)
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def constraint(p):
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result = all(p[0:3]>=0)
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result = result and all(abs(p[4:7])<=1)
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if result:
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return 0
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else:
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return 1
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def cell_stdin():
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import fileinput
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from sys import argv
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print "Type '{} -h' for help".format(argv[0])
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print
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print "Please enter cell parameters: "
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at = []
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for line in fileinput.input():
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for w in map(float, line.split()):
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at.append(w)
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if(len(at)>=9) :
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print " ------------------------ok"
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return at
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def compute_cell(namelist):
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from numpy import isnan
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output,error = run_command(binary,namelist)
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try:
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at = map(float, output.split())
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except ValueError:
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at = [0,0,0, 0,0,0, 0,0,0]
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if any(isnan(at)):
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at = [0,0,0, 0,0,0, 0,0,0]
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return at
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def check_zero(p, ibrav):
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from numpy import array
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from numpy.linalg import norm
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namelist = make_namelist(ibrav,p)
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at0 = array(compute_cell(namelist))
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p_out=list(p)
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for i in range(len(p)):
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q = list(p)
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q[i] = 0
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namelist = make_namelist(ibrav,q)
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at1 = array(compute_cell(namelist))
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if norm(at0-at1)==0:
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p_out[i] = 0
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else:
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print " celldm({:d}) = {:.6f}".format(i+1, p[i])
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return array(p_out)
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def recompute(p, options):
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from numpy import array
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from numpy.linalg import norm
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namelist = make_namelist(options["ibrav"],p)
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at = compute_cell(namelist)
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at1 = array(at)
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at0 = array(options["cell"])
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return norm(at1-at0)
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main()
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@ -0,0 +1,32 @@
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!
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! Copyright (C) 2014 Quantum ESPRESSO group
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! This file is ibrav2cellributed under the terms of the
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! GNU General Public License. See the file `License'
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! in the root directory of the present ibrav2cellribution,
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! or http://www.gnu.org/copyleft/gpl.txt .
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!
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!----------------------------------------------------------------------
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PROGRAM ibrav2cell
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!----------------------------------------------------------------------
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!
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USE Kinds, ONLY : DP
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!
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IMPLICIT NONE
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INTEGER :: ibrav
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REAL(DP) :: celldm(6)
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!
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REAL(DP) :: at(3,3), omega, alat
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!
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NAMELIST /system/ ibrav, celldm
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READ(*,system)
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CALL latgen( ibrav, celldm, at(:,1), at(:,2), at(:,3), omega )
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! at=at/celldm(1)
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! CALL recips(at(:,1), at(:,2), at(:,3), bg(:,1), bg(:,2), bg(:,3))
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!WRITE(*,'(a)') "Unit cell (bohr):"
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WRITE(*,'(3es24.15)') at(:,1)
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WRITE(*,'(3es24.15)') at(:,2)
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WRITE(*,'(3es24.15)') at(:,3)
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!WRITE(*,'(a,es24.15)') "Volume (bohr^3):", omega
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!
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END PROGRAM ibrav2cell
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!----------------------------------------------------------------------
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