From ab22ad423e20c207074d5c5e274f8f7fd7247c6c Mon Sep 17 00:00:00 2001
From: James Graham <J.A.Graham@soton.ac.uk>
Date: Fri, 16 Dec 2016 11:28:36 +0000
Subject: [PATCH] Remove empirical_scale and factor_2 from options They were
 useful during testing, but are now unnecessary

---
 doc/tutorial_files/md.mdp |  1 -
 pycgtool.py               |  2 --
 pycgtool/bondset.py       | 19 ++-----------------
 test/test_pycgtool.py     |  2 +-
 4 files changed, 3 insertions(+), 21 deletions(-)

diff --git a/doc/tutorial_files/md.mdp b/doc/tutorial_files/md.mdp
index 04fc9ef..4d82b1f 100644
--- a/doc/tutorial_files/md.mdp
+++ b/doc/tutorial_files/md.mdp
@@ -29,7 +29,6 @@ nstxout-compressed       = 1000
 compressed-x-precision   = 100
 compressed-x-grps        = System
 energygrps               = System
-imd-group                = Other
 
 ; NEIGHBOURLIST and MARTINI 
 ; To achieve faster simulations in combination with the Verlet-neighborlist
diff --git a/pycgtool.py b/pycgtool.py
index 4de6f40..6082e27 100755
--- a/pycgtool.py
+++ b/pycgtool.py
@@ -39,8 +39,6 @@ if __name__ == "__main__":
         ("default_fc", False),
         ("generate_angles", True),
         ("generate_dihedrals", False),
-        ("empirical_corr", False),
-        ("factor_two", 1),
         ("length_form", "harmonic"),
         ("angle_form", "cosharmonic"),
         ("dihedral_form", "harmonic")
diff --git a/pycgtool/bondset.py b/pycgtool/bondset.py
index 9dce2ac..def598f 100644
--- a/pycgtool/bondset.py
+++ b/pycgtool/bondset.py
@@ -105,14 +105,6 @@ class BondSet:
 
         self._fconst_constr_threshold = options.constr_threshold
 
-        self._empirical_correction_factor = 1.
-        try:
-            self._empirical_correction = options.empirical_corr
-            if self._empirical_correction:
-                self._empirical_correction_factor = 1.05
-        except AttributeError:
-            self._empirical_correction = False
-
         try:
             self._temperature = options.temperature
         except AttributeError:
@@ -123,11 +115,6 @@ class BondSet:
         except AttributeError:
             self._default_fc = False
 
-        try:
-            self._factor_two = options.factor_two
-        except AttributeError:
-            self._factor_two = 1
-
         functional_forms = FunctionalForms()
         self._functional_forms = {}
         try:
@@ -290,12 +277,10 @@ class BondSet:
                 print("\n[ {0:s} ]".format(section_header), file=itp)
             for bond in bonds:
                 # Factor is usually 1, unless doing correction
-                eqm = bond.eqm * self._empirical_correction_factor
-                fconst = bond.fconst * self._empirical_correction_factor
                 line = " ".join(["{0:4d}".format(atnum + 1) for atnum in bond.atom_numbers])
-                line += " {0:4d} {1:12.5f}".format(1, eqm)
+                line += " {0:4d} {1:12.5f}".format(1, bond.eqm)
                 if print_fconst:
-                    line += " {0:12.5f}".format(fconst)
+                    line += " {0:12.5f}".format(bond.fconst)
                 if multiplicity is not None:
                     line += " {0:4d}".format(multiplicity)
                 print(line, file=itp)
diff --git a/test/test_pycgtool.py b/test/test_pycgtool.py
index 9667425..ab03b97 100644
--- a/test/test_pycgtool.py
+++ b/test/test_pycgtool.py
@@ -37,7 +37,7 @@ class PycgtoolTest(unittest.TestCase):
                       ("map_center", "geom"),
                       ("constr_threshold", 100000),
                       ("dump_measurements", False),
-                      ("dump_n_values", 100000),
+                      ("dump_n_values", 10000),
                       ("output_forcefield", False),
                       ("temperature", 310),
                       ("default_fc", False),
-- 
GitLab