From bec694b16ef12be4bf78b141b27b34614616ca34 Mon Sep 17 00:00:00 2001
From: Sylvain Tricot <sylvain.tricot@univ-rennes1.fr>
Date: Mon, 15 Jun 2020 16:39:44 +0200
Subject: [PATCH] Minor changes in sprkkr test example.

---
 src/msspec/utils.py       |  4 ++--
 tests/sprkkr/copper/Cu.py | 18 ++++++++++++++++++
 2 files changed, 20 insertions(+), 2 deletions(-)

diff --git a/src/msspec/utils.py b/src/msspec/utils.py
index 3097dd3..f2ee65d 100644
--- a/src/msspec/utils.py
+++ b/src/msspec/utils.py
@@ -115,7 +115,7 @@ class ForeignPotential(object):
 class SPRKKRPotential(ForeignPotential):
     def __init__(self, atoms, potfile, *exported_files):
         super().__init__()
-
+        """
         def read(content, pattern, types):
             # compile the pattern for regex matching
             pat = re.compile(pattern, re.MULTILINE)
@@ -152,7 +152,7 @@ class SPRKKRPotential(ForeignPotential):
                              (r'^\s*OCCUPATION\s*\n(\s*(?P<KEYS>IQ.*)\n'
                               r'(?P<DATA>(.*\n)+?))\*+'),
                              [int] * 5 + [float])
-
+        """
         for f in exported_files:
             # get the IT from the filename
             # m=re.match('SPRKKR-IT_(?P<IT>\d+)-PHAGEN.*', os.path.basename(f))
diff --git a/tests/sprkkr/copper/Cu.py b/tests/sprkkr/copper/Cu.py
index f7096f0..b1f1996 100644
--- a/tests/sprkkr/copper/Cu.py
+++ b/tests/sprkkr/copper/Cu.py
@@ -1,6 +1,7 @@
 #!/usr/bin/env python
 import glob
 import logging
+import os
 import sys
 from msspec.calculator import MSSPEC
 from msspec.utils import get_atom_index
@@ -36,6 +37,23 @@ if 'sprkkr' in sys.argv:
     # calc2.input.control_section.set(POTFIL="Fe.pot_new")
     # calc2.phagen()
 
+    #
+    # EXPORT POTENTIAL FOR PHAGEN
+    #
+    #change task and command
+    calc.set_command('PHAGEN')
+    # Change output file
+    calc.set_outfile('Cu_phagen.out')
+    #to change task we need to replace input file tempate
+    calc.set_inpfile("Cu_phagen.inp")
+    calc.input.control_section.set(DATASET="PHAGEN", ADSI="PHAGEN")
+    #set potetential file to converged potential
+    conv_potfile=os.path.join(calc.potfile+'_new')
+
+    calc.set_potfile(conv_potfile)
+    #run given task
+    calc.phagen()
+
 
 # ######### MsSpec part
 if 'msspec' in sys.argv: