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public release 4.2.0 - see README.md and CHANGES.md for details

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muntwiler_m
2026-01-08 19:10:45 +01:00
parent ef781e2db4
commit b64beb694c
181 changed files with 39388 additions and 6527 deletions
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0
pmsco/calculators/phagen/__init__.py
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44
pmsco/calculators/phagen/makefile
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@@ -1,44 +0,0 @@
SHELL=/bin/sh
# makefile for PHAGEN program and module
#
# the PHAGEN source code is not included in the public distribution.
# please obtain the PHAGEN code from the original author,
# and copy it to this directory before compilation.
#
# see the top-level makefile for additional information.
.SUFFIXES:
.SUFFIXES: .c .cpp .cxx .exe .f .h .i .o .py .pyf .so
.PHONY: all clean phagen
FC?=gfortran
FCOPTS?=-std=legacy
F2PY?=f2py
F2PYOPTS?=--f77flags=-std=legacy --f90flags=-std=legacy
CC?=gcc
CCOPTS?=
SWIG?=swig
SWIGOPTS?=
PYTHON?=python
PYTHONOPTS?=
PYTHONINC?=
PYTHON_CONFIG = ${PYTHON}-config
PYTHON_CFLAGS ?= $(shell ${PYTHON_CONFIG} --cflags)
PYTHON_EXT_SUFFIX ?= $(shell ${PYTHON_CONFIG} --extension-suffix)
all: phagen
phagen: phagen.exe phagen$(PYTHON_EXT_SUFFIX)
phagen.exe: phagen_scf.f msxas3.inc msxasc3.inc
$(FC) $(FCOPTS) -o phagen.exe phagen_scf.f
phagen.pyf: | phagen_scf.f
$(F2PY) -h phagen.pyf -m phagen phagen_scf.f only: libmain
phagen$(PYTHON_EXT_SUFFIX): phagen_scf.f phagen.pyf msxas3.inc msxasc3.inc
$(F2PY) -c $(F2PYOPTS) -m phagen phagen.pyf phagen_scf.f
clean:
rm -f *.so *.o *.exe

102
pmsco/calculators/phagen/phagen_scf.f.patch
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@@ -1,102 +0,0 @@
--- phagen_scf.orig.f 2019-06-05 16:45:52.977855859 +0200
+++ phagen_scf.f 2019-05-09 16:32:35.790286429 +0200
@@ -174,6 +174,99 @@
1100 format(//,1x,' ** phagen terminated normally ** ',//)
end
+
+c-----------------------------------------------------------------------
+ subroutine libmain(infile,outfile,etcfile)
+c main calculation routine
+c entry point for external callers
+c
+c infile: name of parameter input file
+c
+c outfile: base name of output files
+c output files with endings .list, .clu, .pha, .tl, .rad
+c will be created
+c-----------------------------------------------------------------------
+ implicit real*8 (a-h,o-z)
+c
+ include 'msxas3.inc'
+ include 'msxasc3.inc'
+
+ character*60 infile,outfile,etcfile
+ character*70 listfile,clufile,tlfile,radfile,phafile
+
+c
+c.. constants
+ antoau = 0.52917715d0
+ pi = 3.141592653589793d0
+ ev = 13.6058d0
+ zero = 0.d0
+c.. threshold for linearity
+ thresh = 1.d-4
+c.. fortran io units
+ idat = 5
+ iwr = 6
+ iphas = 30
+ iedl0 = 31
+ iwf = 32
+ iof = 17
+
+ iii=LnBlnk(outfile)+1
+ listfile=outfile
+ listfile(iii:)='.list'
+ clufile=outfile
+ clufile(iii:)='.clu'
+ phafile=outfile
+ phafile(iii:)='.pha'
+ tlfile=outfile
+ tlfile(iii:)='.tl'
+ radfile=outfile
+ radfile(iii:)='.rad'
+
+ open(idat,file=infile,form='formatted',status='old')
+ open(iwr,file=listfile,form='formatted',status='unknown')
+ open(10,file=clufile,form='formatted',status='unknown')
+ open(35,file=tlfile,form='formatted',status='unknown')
+ open(55,file=radfile,form='formatted',status='unknown')
+ open(iphas,file=phafile,form='formatted',status='unknown')
+
+ open(iedl0,form='unformatted',status='scratch')
+ open(iof,form='unformatted',status='scratch')
+ open(unit=21,form='unformatted',status='scratch')
+ open(60,form='formatted',status='scratch')
+ open(50,form='formatted',status='scratch')
+ open(unit=13,form='formatted',status='scratch')
+ open(unit=14,form='formatted',status='scratch')
+ open(unit=11,status='scratch')
+ open(unit=iwf,status='scratch')
+ open(unit=33,status='scratch')
+ open(unit=66,status='scratch')
+
+ call inctrl
+ call intit(iof)
+ call incoor
+ call calphas
+
+ close(idat)
+ close(iwr)
+ close(10)
+ close(35)
+ close(55)
+ close(iphas)
+ close(iedl0)
+ close(iof)
+ close(60)
+ close(50)
+ close(13)
+ close(14)
+ close(11)
+ close(iwf)
+ close(33)
+ close(66)
+ close(21)
+
+ endsubroutine
+
+
subroutine inctrl
implicit real*8 (a-h,o-z)
include 'msxas3.inc'

82
pmsco/calculators/phagen/runner.py
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@@ -2,33 +2,41 @@
@package pmsco.calculators.phagen.runner
Natoli/Sebilleau PHAGEN interface
this module runs the PHAGEN program to calculate scattering factors and radial matrix element.
This module runs the PHAGEN program to calculate scattering factors and radial matrix elements.
Requires PHAGEN version 2.2 from https://git.ipr.univ-rennes.fr/epsi/msspec_python3.git (contained in subprojects).
@author Matthias Muntwiler
@copyright (c) 2015-19 by Paul Scherrer Institut @n
@copyright (c) 2015-23 by Paul Scherrer Institut @n
Licensed under the Apache License, Version 2.0 (the "License"); @n
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import logging
import os
import shutil
import tempfile
from pathlib import Path
import sys
from pmsco.calculators.calculator import AtomicCalculator
from pmsco.calculators.phagen.phagen import libmain
from pmsco.calculators.phagen.translator import Translator
import pmsco.cluster
from pmsco.helpers import stdout_redirected
import pmsco.project
logger = logging.getLogger(__name__)
try:
import phagen
except (ImportError, ModuleNotFoundError) as e:
phagen = None
logger.critical("Error importing the phagen package.", exc_info=e)
class PhagenCalculator(AtomicCalculator):
"""
@@ -37,7 +45,11 @@ class PhagenCalculator(AtomicCalculator):
this produces scatterer, radial matrix element and cluster files for EDAC.
"""
def run(self, params, cluster, scan, output_file):
def run(self,
params: pmsco.project.CalculatorParams,
cluster: pmsco.cluster.Cluster,
scan: pmsco.project.Scan,
output_file: str):
"""
create the input file, run PHAGEN, and translate the output to EDAC format.
@@ -85,19 +97,16 @@ class PhagenCalculator(AtomicCalculator):
phagen_cluster = pmsco.cluster.Cluster()
files = {}
prev_wd = os.getcwd()
prev_wd = Path.cwd()
try:
with tempfile.TemporaryDirectory() as temp_dir:
os.chdir(temp_dir)
os.mkdir("div")
os.mkdir("div/wf")
os.mkdir("plot")
os.mkdir("data")
# prepare input for phagen
infile = "phagen.in"
outfile = "phagen.out"
temp_path = Path(temp_dir)
in_path = temp_path / "input"
in_path.mkdir(exist_ok=True)
out_path = temp_path / "output"
out_path.mkdir(exist_ok=True)
infile = in_path / "input.ms"
try:
transl.write_input(infile)
report_infile = os.path.join(prev_wd, output_file + ".phagen.in")
@@ -106,12 +115,22 @@ class PhagenCalculator(AtomicCalculator):
except IOError:
logger.warning("error writing phagen input file {fi}.".format(fi=infile))
# call phagen
libmain(infile, outfile)
report_listfile = os.path.join(prev_wd, output_file + ".phagen.list")
files[report_listfile] = "log"
# call phagen, redirect stdout (unit 6)
os.chdir(out_path)
with open(report_listfile, "wb") as f:
with stdout_redirected(f):
phagen.phagen()
phafile = out_path / "div" / "phases.dat"
radfile = out_path / "fort.55"
# tlfile = out_path / "fort.35"
clufile = out_path / "clus" / "clus.out"
# collect results
try:
phafile = outfile + ".pha"
transl.parse_phagen_phase(phafile)
report_phafile = os.path.join(prev_wd, output_file + ".phagen.pha")
shutil.copy(phafile, report_phafile)
@@ -120,7 +139,6 @@ class PhagenCalculator(AtomicCalculator):
logger.error("error loading phagen phase file {fi}".format(fi=phafile))
try:
radfile = outfile + ".rad"
transl.parse_radial_file(radfile)
report_radfile = os.path.join(prev_wd, output_file + ".phagen.rad")
shutil.copy(radfile, report_radfile)
@@ -129,31 +147,23 @@ class PhagenCalculator(AtomicCalculator):
logger.error("error loading phagen radial file {fi}".format(fi=radfile))
try:
clufile = outfile + ".clu"
phagen_cluster.load_from_file(clufile, pmsco.cluster.FMT_PHAGEN_OUT)
except IOError:
logger.error("error loading phagen cluster file {fi}".format(fi=clufile))
try:
listfile = outfile + ".list"
report_listfile = os.path.join(prev_wd, output_file + ".phagen.list")
shutil.copy(listfile, report_listfile)
files[report_listfile] = "log"
except IOError:
logger.error("error loading phagen list file {fi}".format(fi=listfile))
finally:
os.chdir(prev_wd)
# write edac files
scatfile = output_file + "_{}.scat"
scatfiles = transl.write_edac_scattering(scatfile)
params.phase_files = {c: scatfiles[c] for c in scatfiles}
files.update({scatfiles[c]: "atomic" for c in scatfiles})
params.phase_files = scatfiles.copy()
files.update({f: "atomic" for f in params.phase_files.values()})
rmefile = output_file + ".rme"
transl.write_edac_emission(rmefile)
files[rmefile] = "atomic"
rmefile = output_file + "_{}.rme"
rmefiles = transl.write_edac_emission(rmefile)
params.rme_files = rmefiles.copy()
files.update({f: "atomic" for f in params.rme_files.values()})
cluster.update_atoms(phagen_cluster, {'c'})
clufile = output_file + ".pmsco.clu"

63
pmsco/calculators/phagen/translator.py
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@@ -13,14 +13,12 @@ Licensed under the Apache License, Version 2.0 (the "License"); @n
http://www.apache.org/licenses/LICENSE-2.0
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import logging
import numpy as np
from pmsco.cluster import Cluster
from pmsco.compat import open
logger = logging.getLogger(__name__)
## rydberg energy in electron volts
ERYDBERG = 13.6056923
@@ -59,7 +57,7 @@ class TranslationParams(object):
self.initial_state = "1s"
self.binding_energy = 0.
self.cluster = None
self.kinetic_energies = np.empty(0, dtype=np.float)
self.kinetic_energies = np.empty(0, dtype=float)
@property
def l_init(self):
@@ -287,7 +285,7 @@ class Translator(object):
self.write_cluster(f)
self.write_ionicity(f)
else:
with open(f, "w") as fi:
with open(f, "wt", encoding="latin1") as fi:
self.write_input(fi)
def parse_phagen_phase(self, f):
@@ -392,7 +390,7 @@ class Translator(object):
f.write(" 0 0")
f.write("\n")
else:
with open(f, "w") as fi:
with open(f, "wt", encoding="latin1") as fi:
self.write_edac_scattering_file(fi, scat)
def write_edac_phase_file(self, f, scat):
@@ -426,26 +424,36 @@ class Translator(object):
f.write(" 0")
f.write("\n")
else:
with open(f, "w") as fi:
with open(f, "wt", encoding="latin1") as fi:
self.write_edac_phase_file(fi, scat)
def parse_radial_file(self, f):
"""
parse the radial matrix element output file from phagen.
parse the radial matrix element output file from phagen version 2.2.
the file contains 7 header lines and one data line per requested energy.
the data line contains real and imaginary parts of the matrix elements.
the first four columns contain the electric dipole transitions Rd(li --> li - 1) and Rd(li --> li + 1),
followed by higher orders that we do not use here.
@param f: file or path (any file-like or path-like object that can be passed to numpy.genfromtxt).
@return: None
@raise ValueError if the file is in a wrong format.
"""
dt = [('ar', 'f8'), ('ai', 'f8'), ('br', 'f8'), ('bi', 'f8')]
data = np.atleast_1d(np.genfromtxt(f, dtype=dt))
data = np.atleast_2d(np.genfromtxt(f, skip_header=7))
if data.shape[0] != self.params.kinetic_energies.shape[0] or data.shape[1] < 4:
raise ValueError(f"Unexpected array size of Phagen radial matrix elements output: "
f"expected ({self.params.kinetic_energies.shape[0]}, >= 4), received {data.shape}")
self.emission = np.resize(self.emission, data.shape)
self.emission = np.resize(self.emission, data.shape[0:1])
emission = self.emission
emission['dw'] = data['ar'] + 1j * data['ai']
emission['up'] = data['br'] + 1j * data['bi']
emission['e'] = self.params.kinetic_energies
emission['dw'] = data[:, 0] + 1j * data[:, 1]
emission['up'] = data[:, 2] + 1j * data[:, 3]
def write_edac_emission(self, f):
def write_edac_emission_file(self, f):
"""
write the radial photoemission matrix element in EDAC format.
@@ -472,5 +480,24 @@ class Translator(object):
f.write(" {0:.6f} {1:.6f}".format(item['dw'].real, item['dw'].imag))
f.write("\n")
else:
with open(f, "w") as of:
self.write_edac_emission(of)
with open(f, "wt", encoding="latin1") as of:
self.write_edac_emission_file(of)
def write_edac_emission(self, filename_format):
"""
write the radial photoemission matrix element in EDAC format.
requires self.scattering, self.emission, self.params.kinetic_energies and self.params.initial_state.
@param filename_format: file name including, optionally, a placeholder {} for the atom class.
since phagen calculates only one emitter, the placeholder is not necessary.
@return: dictionary that maps atom classes to file names.
since phagen calculates only one emitter, this dictionary will contain just one entry.
"""
scat = self.scattering
atom = scat['a'][0]
f = filename_format.format(atom)
self.write_edac_emission_file(f)
files = {atom: f}
return files