FPLOIO examples¶
Reading =.in files¶
This tutorial shows how to use INParser
and PObj
to read =.in
-files.
The tutorial files are in
FPLO.../DOC/pyfplo/Examples/fploio/fploio/readinfile
where FPLO...
stands for your version’s FPLO directory, e.g. FPLO21.00-61
. Here
are the files of this directory:
- readinfile.py
=.in
readinfile.py
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 | #! /usr/bin/env python
# ===================================================================
# file: bandplot.py
# author: k.koepernik@ifw-dresden.de
# date: 19 Apr 2017
from __future__ import print_function
import sys
import pyfplo.fploio as fploio
# ===================================================================
#
# ===================================================================
def work():
print( '\nThis example shows how to parse =.in files.\n')
p=fploio.INParser()
p.parseFile('=.in')
d=p()
print( 'sorts:',d('nsort').L)
print( 'lattice constants:',d('lattice_constants').listD)
print( 'or\nlattice constants:',d('lattice_constants').listS)
print( '\nWyckoff positions')
dw=d('wyckoff_positions')
for i in range(dw.size()):
dd=dw[i]
print( dd('element').S,dd('tau').listS)
print( '\nAlternative way of doing it')
for i in range(dw.size()):
dd=dw[i]
print( dd('element').S,dd('tau')[0].S,dd('tau')[1].S,dd('tau')[2].S)
print( '\nYet another way')
for i in range(dw.size()):
dd=dw[i]
print( dd('element').S,dd('tau[0]').S,dd('tau[1]').S,dd('tau[2]').S)
print( '\nsingle shot')
print( d('wyckoff_positions[0].element').S,
d('wyckoff_positions[0].tau').listS)
print( '\noptions')
do=d('options')
for i in range(do.size()):
print( do[i].S,)
if ((i+1)%4)==0: print()
print()
print( '\nsetting CALC_PLASMON_FREQ and CALC_DOS')
do['CALC_PLASMON_FREQ'].L=True
do['CALC_DOS'].L=True
print( '\nwhich now are',bool(do['CALC_PLASMON_FREQ'].L)
,'and',bool(do['CALC_DOS'].L))
print( '\nhave another look at options')
do=d('options')
for i in range(do.size()):
print( do[i].S,)
if (i%4)==0: print()
print()
return
# ===================================================================
#
# ===================================================================
if __name__ == '__main__':
work()
sys.exit(0)
|
=.files to json¶
This tutorial shows how to convert files with the =.in
syntax
into json
-files. It demonstrates the usage of PObj
.
The tutorial files are in
FPLO.../DOC/pyfplo/Examples/fploio/equaldot2json
where FPLO...
stands for your version’s FPLO directory, e.g. FPLO21.00-61
. Here
are the files of this directory:
- equaldot2json.py
=.in
equaldot2json.py
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 | #! /usr/bin/env python
# ===================================================================
# file: testscan.py
# author: k.koepernik@ifw-dresden.de
# date: 04 Okt 2018
from __future__ import print_function
import pyfplo.fploio as fploio
import argparse
import json
version = 20181002
parser = argparse.ArgumentParser(description='Translates `=.*` files \
(e.g., `=.in`, `=.xef`, `=.dens`) into \
a JSON file without calling pyfplo. \
Works with Python 2, but the order \
of entries is retained in Python 3, \
only.', conflict_handler='resolve',
epilog="Please report any bugs to \
Oleg Janson <olegjanson@gmail.com>.")
parser.add_argument('-i', '--input', default='=.in',
type=str,dest='input',
help='FPLO input file (default:%(default)s)')
parser.add_argument('-o', '--output', type=argparse.FileType('w'),
default='-', help='JSON output file')
parser.add_argument('-n', '--nice', dest='nice', action='store_true',
help='add indents (otherwise just a single line)')
parser.set_defaults(nice=False)
parser.add_argument('-v', '--version', action='version',\
help='print the version',\
version='%(prog)s version {:d}'.format(version))
args = parser.parse_args()
jsonprintoptions = ({}, {'indent':4})[args.nice]
# ===================================================================
#
# ===================================================================
def scanStruct(d,dictdata,ind=''):
n=d.first()
while True:
if n.isScalar():
if n.isInt():
dictdata[n.name()]=n.L
elif n.isReal():
dictdata[n.name()]=n.D
elif n.isLogical():
dictdata[n.name()]=bool(n.L)
elif n.isFlag():
dictdata[n.name()]=bool(n.L)
else:
dictdata[n.name()]=n.S
elif n.isArray():
dictdata[n.name()]=[]
scanArray(n,dictdata[n.name()],n.sizes(),len(n.sizes()))
elif n.isStruct():
dictdata[n.name()]={}
scanStruct(n,dictdata[n.name()],ind+' ')
elif n.isStructArray():
dictdata[n.name()]=[]
for i in range(n.size()):
dictdata[n.name()].append({})
scanStruct(n[i],dictdata[n.name()][-1],ind+' ')
if not n.hasNext(): break
n=n.next()
return
# ===================================================================
#
# ===================================================================
def scanArray(d,dictdata,sizes,dim,idx=[],ind=''):
if dim==len(sizes):
idx=[0]*dim
for i in range(sizes[dim-1]):
idx[dim-1]=i
if dim==1:
n=d[tuple(idx)]
if n.isInt():
dictdata.append(n.L)
elif n.isReal():
dictdata.append(n.D)
elif n.isLogical():
dictdata.append(bool(n.L))
elif n.isFlag():
dictdata.append({n.S[0:-3]:bool(n.L)})
else:
dictdata.append(n.S)
else:
dictdata.append([])
scanArray(d,dictdata[-1],sizes,dim-1,idx,ind='')
return
# ===================================================================
#
# ===================================================================
if __name__ == '__main__':
p=fploio.INParser()
p.parseFile(args.input)
dictdata={}
scanStruct(p(),dictdata)
with args.output as jsonfile:
json.dump(dictdata, jsonfile, **jsonprintoptions)
|
Reading cif-files¶
This tutorial demonstrates how to read cif
-files.
See structureFromCIFFile
.
The tutorial files are in
FPLO.../DOC/pyfplo/Examples/fploio/cif
where FPLO...
stands for your version’s FPLO directory, e.g. FPLO21.00-61
. Here
are the files of this directory:
- README
- fromcif.py
RuW.cif
README
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 | This demonstrates the reading of cif files and some of the possible options.
Execute:
python fromcif.py raw
which loads the cif as it is (which happens to have spacegroup 1).
Have a look at the output, especially the Wyckoff positions.
Next, execute:
python fromcif.py smoothed
and have a look at the output, especially the Wyckoff positions,
which are now fractionals.
Next, execute:
python fromcif.py raw detsym
and have a look at the output: we got space group 63 and
2 Ru positions, due to the approximate fractional 0.1666 and such.
Finally, execute:
python fromcif.py smoothed detsym
Now we have one Ru and W position with fractionals and spacegroup 194
|
fromcif.py
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 | #! /usr/bin/env python
# ===================================================================
# file: fromcif.py
# author: k.koepernik@ifw-dresden.de
# date: 22 Mar 2018
from __future__ import print_function
import sys
import pyfplo.fploio as fploio
import pyfplo.fedit as fedit
# ===================================================================
#
# ===================================================================
def work(mode='raw',detsym=False):
print( '\nThis example shows how to import cif files.')
whtol=1e-4 if mode=='smoothed' else 1e-6
# Create FPLOInput object and read =.in or create new parser
# content if =.in does not exist.
fio=fploio.FPLOInput('=.in')
# read cif file into parser
fio.structureFromCIFFile('RuW.cif',wyckofftolerance=whtol,
determinesymmetry=detsym)
# write =.in
fio.writeFile("=.in")
# here we have =.in with the structure from the cif file
# use fedit to set further input
fed=fedit.Fedit()
fed.iteration(n=100)
fed.bzintegration(nxyz=[12,12,6])
fed.pipeFedit()
print ('\n\nNow we have read the raw cif content as is,'+
' which results in \n'+
'the following symmetry settings:\n\n')
printsettings()
return
# ===================================================================
#
# ===================================================================
def printsettings():
fio=fploio.FPLOInput('=.in')
par=fio.parser()
d=par()
print( 'spacegroup number : ',d('spacegroup.number').S)
print( 'spacegroup setting: ',d('spacegroup.setting').S)
print( 'lattice constants : ',d('lattice_constants').listS)
print( 'axis angle : ',d('axis_angles').listS)
dw=d('wyckoff_positions')
print( 'Wyckoff positions: ',dw.size())
for i in range(dw.size()):
taus=dw[i]('tau').listS
print( '{0:>2s} {1:>20s} {2:>20s} {3:>20s}'
.format(dw[i]('element').S,taus[0],taus[1],taus[2]))
# ===================================================================
#
# ===================================================================
def usage():
print( 'usage: ',sys.argv[0],' ( raw | smoothed) [detsym]')
# ===================================================================
#
# ===================================================================
if __name__ == '__main__':
if len(sys.argv)<2:
usage()
sys.exit(0)
mode=sys.argv[1]
mode=mode.replace('-','')
if not (mode=='raw' or mode=='smoothed'):
usage()
sys.exit(0)
detsym=False
if len(sys.argv)>=3:
detsym=True
work(mode,detsym)
sys.exit(0)
|
Write =.in with low level routines¶
This tutorial shows how to use INParser
and PObj
to modify =.in
-files. This should not be done for symmetry input!
The tutorial files are in
FPLO.../DOC/pyfplo/Examples/fploio/fploio/writinfilelowlevel
where FPLO...
stands for your version’s FPLO directory, e.g. FPLO21.00-61
. Here
are the files of this directory:
writinfilelowlevel.py
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 | #! /usr/bin/env python
# ===================================================================
# file: bandplot.py
# author: k.koepernik@ifw-dresden.de
# date: 19 Apr 2017
from __future__ import print_function
import sys
import pyfplo.fploio as fploio
# ===================================================================
#
# ===================================================================
def work():
print( '\nThis example shows simple low level =.in writing.')
print( 'DO NOT DO THIS UNLESS YOU ARE CONFIDENT YOUR DOING THE '+
'RIGHT THING.\n')
p=fploio.INParser()
p.parseFile('=.in')
d=p()
d('bzone_integration.nkxyz').listL=[16,16,16]
d('spin.mspin').L=2
d('relativistic.type').L=3
# This illustrates one of the problems with the low level.
# In order to keep =.in consistent for human readers
# we should set the descriptions too.
# It is better to use pyfplo.fedit instead.
d('relativistic.description').S='full relativistic'
p.writeFile('=.in')
print( 'done')
return
# ===================================================================
#
# ===================================================================
if __name__ == '__main__':
work()
sys.exit(0)
|
Write =.in with mid level routines¶
This tutorial shows how to use FPLOInput
to modify =.in
-files. This should not be done for symmetry input!
The tutorial files are in
FPLO.../DOC/pyfplo/Examples/fploio/fploio/writinfilemidlevel
where FPLO...
stands for your version’s FPLO directory, e.g. FPLO21.00-61
. Here
are the files of this directory:
writinfilemidlevel.py
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 | #! /usr/bin/env python
# ===================================================================
# file: bandplot.py
# author: k.koepernik@ifw-dresden.de
# date: 19 Apr 2017
from __future__ import print_function
import sys,os
import pyfplo.fploio as fploio
# ===================================================================
#
# ===================================================================
def work():
print( '\nThis fictitious example shows simple mid level =.in writing.')
print( 'DO NOT DO THIS UNLESS YOU ARE CONFIDENT YOUR DOING THE '+
'RIGHT THING.\n')
fio=fploio.FPLOInput()
if os.path.exists('=.in'):
fio.parseInFile(True)
else:
fio.createNewFileContent()
p=fio.parser()
d=p() # the root of the data tree
# set length units
d("lengthunit.type").L=2
# not really needed but good for human readers of =.in
d("lengthunit.description").S='angstroem'
# set wyckoff positions
d("nsort").L=3
# yes, we need to do this too.
dw=d("wyckoff_positions")
dw.resize(3)
i=0 ;
di=dw[i]
di('element').S='Fe'
di('tau').listD=[0,0,0]
i+=1 ; di=dw[i]
di('element').S='Al'
di('tau').listS=['1/2','1/2','1/2']
i+=1 ; di=dw[i]
di('element').S='Mn'
di('tau').listS=['1/4','1/4','1/4']
d('lattice_constants').listD=[5.4,5.4,5.4]
#or
d('lattice_constants').listS=['5.4','5.4','5.4']
# symmetry update required
msg=fio.symmetryUpdate();
print( msg)
# reset all other input, to get a default file
fio.resetNonSymmetrySections()
# here we can set other things
d('spin.mspin').L=2
fio.writeFile("=.in")
print( 'done')
return
# ===================================================================
#
# ===================================================================
if __name__ == '__main__':
work()
sys.exit(0)
|
Extract default basis into =.basdef¶
This example extracts the default basis.
The tutorial files are in
FPLO.../DOC/pyfplo/Examples/fploio/basis/extract_default_basdef
where FPLO...
stands for your version’s FPLO directory, e.g. FPLO21.00-61
. Here
are the files of this directory:
README
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | Read the script to understand what it is doing.
It demonstrates how to extract the default basis from an existing =.in
into =.basdef
for manual basis manipulation, which could be done by a script (demonstrated elsewhere).
run extractdefaultbasis.py as
extractdefaultbasis.py
then have a look at =.basdef.
If pyfplo path needs to be set use wrapp.sh. First edit pyfplopath
in wrapp.sh and then just put it in front as in any of the following.
wrapp.sh extractdefaultbasis.py
|
A wrapper to setup paths wrapp.sh
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | #! /usr/bin/env sh
#
# Example wrapper script for path setting.
#
########################################################################
# set your path here
pyfplopath=$HOME/FPLO/FPLO22.00-62/PYTHON/
export PYTHONPATH=$pyfplopath:$PYTHONPATH
$*
|
The python script extractdefaultbasis.py
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 | #! /usr/bin/env python
# ===================================================================
# file: basis.py
# author: k.koepernik@ifw-dresden.de
# date: 06 Jun 2017
from __future__ import print_function
import sys
import os
import pyfplo.fedit as fedit
import pyfplo.fploio as fploio
print( '\npyfplo version=: {0}\nfrom: {1}\n'.format(fedit.version,fedit.__file__))
# protect against wrong version
#if fedit.version!='22.00': raise RuntimeError('pyfplo version is incorrect.')
# ===================================================================
#
# ===================================================================
def work_short_version(prot=True):
if not os.path.exists('=.in'):
print('ERROR: this script assumes the existence of an =.in-file.')
sys.exit(1)
p=fploio.INParser()
p.parseFile('=.in')
d=p()('wyckoff_positions')
elements=[d[i]('element').S for i in range(d.size())]
bastype=p()('basis.version.type').L
b=fploio.Basis(bastype,elements)
b.writeFile()
os.system('ls -ltr ; echo ; cat =.basdef')
return
# ===================================================================
#
# ===================================================================
def work_long_version(prot=True):
if not os.path.exists('=.in'):
print('ERROR: this script assumes the existence of an =.in-file.')
sys.exit(1)
# 1: Get info for hand-made basis creation
# Read =.in to get basisversion (optional) and
# element (optionally: atomic number) list
p=fploio.INParser()
p.parseFile('=.in')
d=p()('wyckoff_positions')
elements=[d[i]('element').S for i in range(d.size())]
atomicnumbers=list(map(lambda x: fploio.c_elements.index(x),elements))
if prot:
print(('\n=.in contains Wyckoff positions with\n\telements '
+'{}\n\tatomic numbers {}\n')
.format(elements,atomicnumbers))
basversion=(p()('basis.version.type').L,p()('basis.version.description').S)
print('basis version in =.in: key={0[0]} name="{0[1]}"\n'.format(basversion))
print('available versions:\n',fploio.Basis.versions,'\n')
# 2: Get default basis, compatible with =.in-content.
# We could use basversion[0], or basversion[1] as argument
# to fploio.Basis or (in later fplo versions) another basis ID.
b=fploio.Basis('default FPLO9 basis',elements)
# eqiuvalent:
# b=fploio.Basis(1,elements)
# or like this:
# b=fploio.Basis('default FPLO9 basis',atomicnumbers)
# 3: write basdeffile (=.basdef):
b.writeFile()
#or
#b.writeFile('=.basdef')
# Now we have the default basis in '=.basdef' which would be used by fplo
# on running. We could modify it by hand too.
os.system('ls -ltr ; echo ; cat =.basdef')
return
# ===================================================================
#
# ===================================================================
if __name__ == '__main__':
print('-'*72,'\nlong version\n','-'*72)
work_long_version()
print('-'*72,'\nshort version\n','-'*72)
work_short_version()
sys.exit(0)
|
User defined basis (in =.basdef)¶
This example extracts the default basis, modifies it and creates =.basdef.
The tutorial files are in
FPLO.../DOC/pyfplo/Examples/fploio/basis/modify_basdef
where FPLO...
stands for your version’s FPLO directory, e.g. FPLO21.00-61
. Here
are the files of this directory:
README
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 | Read the script to understand what it is doing.
It demonstrates how to extract the default basis into =.basdef and how to
modify it to achieve non-standard basis settings.
In fact it mostly replicates the fedit basis modification options using
low-level manipulation. This serves as a starting point for user-made
basis modifications.
run basis.py as
basis.py
If pyfplo path needs to be set use wrapp.sh. First edit pyfplopath
in wrapp.sh and then just put it in front as in any of the following.
wrapp.sh basis.py
|
A wrapper to setup paths wrapp.sh
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | #! /usr/bin/env sh
#
# Example wrapper script for path setting.
#
########################################################################
# set your path here
pyfplopath=$HOME/FPLO/FPLO22.00-62/PYTHON/
export PYTHONPATH=$pyfplopath:$PYTHONPATH
$*
|
The python script basis.py
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 | #! /usr/bin/env python
# ===================================================================
# file: basis.py
# author: k.koepernik@ifw-dresden.de
# date: 06 Jun 2017
from __future__ import print_function
import sys
import os
import pyfplo.fedit as fedit
import pyfplo.fploio as fploio
print( '\npyfplo version=: {0}\nfrom: {1}\n'.format(fedit.version,fedit.__file__))
# protect against wrong version
#if fedit.version!='22.00': raise RuntimeError('pyfplo version is incorrect.')
FPLO=fploio.fploExecutable()
# ===================================================================
#
# ===================================================================
def makeINFile(extensionlevel=1,core4f=None,core4fNoValenceF=None,
addf=False,add3d=False,multicore=None,):
''' make a (hypothetical compound) =.in-file '''
fed=fedit.Fedit(recreate=True)
fed.symmetry(spacegroup=123,latcon=[8,8,8],atoms=
[
['fe',[0,0,0]],
['eu',['1/2','1/2','1/2']],
['H',['1/2','0','0']],
])
fed.basis(extensionlevel=extensionlevel,core4f=core4f,
core4fNoValenceF=core4fNoValenceF,addf=addf,add3d=add3d,
multicore=multicore)
# write input file
fed.pipeFedit()
return
# ===================================================================
#
# ===================================================================
def getBasisIngredient(prot=False):
'''
Read =.in to get basisversion (optional) and
element (optinal: atomic number) list
'''
p=fploio.INParser()
p.parseFile('=.in')
d=p()('wyckoff_positions')
elements=[d[i]('element').S for i in range(d.size())]
atomicnumbers=list(map(lambda x: fploio.c_elements.index(x),elements))
if prot:
print(('\n=.in contains Wyckoff positions with\n\telements '
+'{}\n\tatomic numbers {}\n')
.format(elements,atomicnumbers))
basversion=(p()('basis.version.type').L,p()('basis.version.description').S)
return (basversion,elements,atomicnumbers)
# ===================================================================
#
# ===================================================================
def writeBasdef(basdeffile='=.basdef',extensionlevel=1,core4f=[],
core4fNoValenceF=[],addf=False,add3d=False,
multicore=None,
makesingle=False,doubleSemiCoreS=False):
(basversion,elements,atomicnumbers)=getBasisIngredient()
b=fploio.Basis('default FPLO9 basis',elements)
# modify
for bd in b:
for l in range(1,extensionlevel):
for o in bd.valence:
mu=o.multiplicity
o.append(Q=o.Q(mu-1)+2,P=max(min(o.P(mu-1),1.),0.85))
if add3d:
for bd in b:
haved=any([o.name[1]=='d' for o in bd.core])
haved=haved or any([o.name[1]=='d' for o in bd.semicore])
haved=haved or any([o.name[1]=='d' for o in bd.valence])
if not haved:
bd.valence.append('3d',Q=[5],P=[1])
# add S*f (D*f if uncommented)
if addf:
for bd in b:
nmain=3
for o in bd.core:
if o.name[1]=='f':
nmain=max(nmain,int(o.name[0]))
for o in bd.semicore:
if o.name[1]=='f':
nmain=max(nmain,int(o.name[0]))
for o in bd.valence:
if o.name[1]=='f':
nmain=max(nmain,int(o.name[0])+o.multiplicity-1)
if nmain<4:
bd.valence.append('{nm}f'.format(nm=nmain+1),Q=[5],P=[1])
#bd.valence.append('{nm}f'.format(nm=nmain+1),Q=[5,7],P=[1,1])
# move 4f to core, leave remaining f-valence
for c in core4f:
if isinstance(c,int):
isort=c
else:
isort=elements.index(c.capitalize())+1
bd=b[isort-1] # isort is one-based as in FPLO
for o in bd.valence:
if o.name=='4f':
o.removeFirst()
bd.core.append('4f')
# move 4f to core, no f-valence
for c in core4fNoValenceF:
if isinstance(c,int):
isort=c
else:
isort=elements.index(c.capitalize())+1
bd=b[isort-1] # isort is one-based as in FPLO
for i,o in enumerate(bd.valence):
if o.name=='4f':
bd.valence.remove(i)
bd.core.append('4f')
break
# make all valence MultiOrbitals single orbitals
# This option does not exist in fedit.
if makesingle:
for bd in b:
for o in bd.valence:
while o.multiplicity>1: o.removeLast()
# make only semicore s-orbitals double
# This option does not exist in fedit.
if doubleSemiCoreS:
for bd in b:
for o in bd.semicore:
mu=o.multiplicity
if o.name[1]=='s':
o.append(Q=0,S=5,P=max(min(o.P(mu-1),1.),0.85))
#o.set(0,Q=0,S=-5)
# make double core
if (multicore is not None) and len(multicore)>0:
for bd in b:
for o in bd.core:
o.set(0,Q=multicore[0][0],S=multicore[0][1])
for m in range(1,len(multicore)):
o.append(Q=multicore[m][0],S=multicore[m][1])
b.writeFile(basdeffile)
return
# ===================================================================
#
# ===================================================================
def extractBasDefFromOut(outfile='out',basdeffile='=.basdef'):
with open(outfile,'r') as fh:
lines=fh.readlines()
with open(basdeffile,'w') as fh:
start=False
for line in lines:
if line.startswith('Start: content of =.basdef'):
start=True
continue
if line.startswith('End : content of =.basdef'):
break
if start:
if line.startswith('---'): continue
fh.write(line)
return
# ===================================================================
#
# ===================================================================
def work():
# ---------------------------------------------------------------
# With basis level2 (from fedit):
makeINFile(extensionlevel=2,addf=True,add3d=True,
core4fNoValenceF=[2], # sort of Eu
multicore=[[0,0],[0,10]])
# Here we are all set ... including level2 basis defined in =.in.
# ---------------------------------------------------------------
# ---------------------------------------------------------------
# For later diff-checking, run fplo to extract the basis as defined
# in =.in from the outfile section :
# Start: content of =.basdef
# ...
# End : content of =.basdef
#
fed=fedit.Fedit(recreate=False)
fed.iteration(n=1) # single step, since we run for =.basdef extraction
fed.pipeFedit()
# we want =.in to determine the basis, so delete =.basdef
os.system('rm -f =.basdef')
print('running fplo to extract which basis was used, wait a few secs...')
os.system('{} > out'.format(FPLO))
extractBasDefFromOut('out',basdeffile='=.basdef_as_defined_by_in_file')
# ---------------------------------------------------------------
# ---------------------------------------------------------------
# Extract default =.basdef and modify it
writeBasdef(basdeffile='=.basdef',extensionlevel=2,
addf=True,add3d=True,core4fNoValenceF=[2],
multicore=[[0,0],[0,10]],
makesingle=False,doubleSemiCoreS=False)
# which now should have the same basis modifications as defined in =.in.
# Compare the two
print('Executing: diff =.basdef =.basdef_as_defined_by_in_file ":"') # same
os.system('diff =.basdef =.basdef_as_defined_by_in_file') # same
print('Nothing should be shown from the diff!')
# ---------------------------------------------------------------
return
# ===================================================================
#
# ===================================================================
if __name__ == '__main__':
work()
sys.exit(0)
|
Extract =.basdef from output file¶
This example extracts =.basdef
from an fplo output file.
The tutorial files are in
FPLO.../DOC/pyfplo/Examples/fploio/basis/extract_basdef_from_outfile
where FPLO...
stands for your version’s FPLO directory, e.g. FPLO21.00-61
. Here
are the files of this directory:
README
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 | Read the script to understand what it is doing.
It extracts =.basdef from an FPLO output file. This =.basdef
will contain the basis actually used during the calculation
(as opposed to the defualt =.basdef). Once extracted, it
will be used henceforth during calculations (and can be modified).
run extractbasdeffromout.py as
extractbasdeffromout.py
then have a look at =.basdef.
If pyfplo path needs to be set use wrapp.sh. First edit pyfplopath
in wrapp.sh and then just put it in front as in any of the following.
wrapp.sh extractbasdeffromout.py
|
A wrapper to setup paths wrapp.sh
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | #! /usr/bin/env sh
#
# Example wrapper script for path setting.
#
########################################################################
# set your path here
pyfplopath=$HOME/FPLO/FPLO22.00-62/PYTHON/
export PYTHONPATH=$pyfplopath:$PYTHONPATH
$*
|
The python script extractbasdeffromout.py
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 | #! /usr/bin/env python3
# ===================================================================
# file: extractbasdeffromout.py
# author: k.koepernik@ifw-dresden.de
# date: 24 Jun 2022
from __future__ import print_function
import sys
import numpy as np
# ===================================================================
#
# ===================================================================
def extractBasDefFromOut(outfile='out',basdeffile='=.basdef'):
with open(outfile,'r') as fh:
lines=fh.readlines()
with open(basdeffile,'w') as fh:
start=False
for line in lines:
if line.startswith('Start: content of =.basdef'):
start=True
continue
if line.startswith('End : content of =.basdef'):
break
if start:
if line.startswith('---'): continue
fh.write(line)
return
# ===================================================================
#
# ===================================================================
if __name__ == '__main__':
extractBasDefFromOut(outfile='out',basdeffile='=.basdef')
sys.exit(0)
|
Grep results¶
These examples extract all (or the latest) occurances via OutGrep
of some results in the outfile.
The tutorial files are in
FPLO.../DOC/pyfplo/Examples/fploio/grep/
where FPLO...
stands for your version’s FPLO directory, e.g. FPLO21.00-61
. Here
are the files of this directory:
README
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 | Demonstration of how to grep from FPLO output from within python scripts.
Read the scripts to understand what they are doing.
run scripts as
grepintodict.py
or
grepEtot.py
or
grepiterationprogress.py
If pyfplo path needs to be set use wrapp.sh. First edit pyfplopath
in wrapp.sh and then just put it in front as in any of the following.
wrapp.sh grepintodict.py
wrapp.sh grepEtot.py
wrapp.sh grepiterationprogress.py
|
A wrapper to setup paths wrapp.sh
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | #! /usr/bin/env sh
#
# Example wrapper script for path setting.
#
########################################################################
# set your path here
pyfplopath=$HOME/FPLO/FPLO22.00-62/PYTHON/
export PYTHONPATH=$pyfplopath:$PYTHONPATH
$*
|
The python script grepintodict.py
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 | #! /usr/bin/env python3
# ===================================================================
# file: g.py
# author: k.koepernik@ifw-dresden.de
# date: 22 Jun 2022
from __future__ import print_function
import sys
import numpy as np
import pyfplo.fploio as fploio
print( '\npyfplo version=: {0}\nfrom: {1}\n'.format(fploio.version,fploio.__file__))
# protect against wrong version
#if fploio.version!='22.00': raise RuntimeError('pyfplo version is incorrect.')
# ===================================================================
#
# ===================================================================
def work(printmodes=True):
if printmodes: # print grep modes
for k in fploio.OutGrep.modes.keys():
print('mode: {0:15s} : {1}'.format(k,fploio.OutGrep.modes[k]))
print('-'*72,'\n')
# this will read the file
og=fploio.OutGrep('out')
si=og.sites()
# grep some results from last appearance in file (last iteration)
results={}
results['etot'] = float(og.grep('EE')[-1])
results['total spin']= float(og.grep('SS')[-1])
for i,s in enumerate(si):
site=i+1
results['spin {0}{1:<3d}'.format(s.element,site)]\
=float(og.grep('SSat',site)[-1])
for k in results.keys():
print('{0:<20s} {1:>20.10f}'.format(k,results[k]))
if printmodes: print('\n','-'*72)
return
# ===================================================================
#
# ===================================================================
if __name__ == '__main__':
work()
sys.exit(0)
|
The python script grepEtot.py
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | #! /usr/bin/env python3
# ===================================================================
# file: g.py
# author: k.koepernik@ifw-dresden.de
# date: 22 Jun 2022
from __future__ import print_function
import pyfplo.fploio as fploio
print( '\npyfplo version=: {0}\nfrom: {1}\n'.format(fploio.version,fploio.__file__))
# protect against wrong version
#if fploio.version!='22.00': raise RuntimeError('pyfplo version is incorrect.')
og=fploio.OutGrep('out')
print('etot=',og.grep('EE')[-1],', gap=',og.grep('gap')[-1])
|
The python script grepiterationprogress.py
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 | #! /usr/bin/env python3
# ===================================================================
# file: g.py
# author: k.koepernik@ifw-dresden.de
# date: 22 Jun 2022
from __future__ import print_function
import os
import pyfplo.fploio as fploio
print( '\npyfplo version=: {0}\nfrom: {1}\n'.format(fploio.version,fploio.__file__))
# protect against wrong version
#if fploio.version!='22.00': raise RuntimeError('pyfplo version is incorrect.')
og=fploio.OutGrep('out')
si=og.sites()
with open('res','w') as fh:
res=og.grep('it')
fh.write('# step last_dev\n')
for i,r in enumerate(res):
fh.write('{} {}\n'.format(i,r))
fh.write('\n')
res=og.grep('EE')
fh.write('# step Etot\n')
for i,r in enumerate(res):
fh.write('{} {}\n'.format(i,r))
fh.write('\n')
res=og.grep('gap')
E0=float(res[0])
fh.write('# step gap\n')
for i,r in enumerate(res):
fh.write('{} {}\n'.format(i,r))
fh.write('\n')
with open('resspins','w') as fh:
for i,s in enumerate(si):
site=i+1
res=og.grep('SSat',site)
fh.write('# step \'atom spin {}{}\'\n'.format(s.element,site))
for it,r in enumerate(res):
fh.write('{} {}\n'.format(it,r))
fh.write('\n')
os.system('xfbp grepiterationprogress.xpy')
|